Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 64
Found at i:2403678 original size:14 final size:15
Alignment explanation
Indices: 2403661--2403689 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2403651 TATCTTTTTT
2403661 AAAATAA-TTTAAAA
1 AAAATAATTTTAAAA
2403675 AAAATAATTTTAAAA
1 AAAATAATTTTAAAA
2403690 GATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATAATTTTAAAA
Found at i:2405852 original size:82 final size:82
Alignment explanation
Indices: 2405698--2405898 Score: 280
Period size: 82 Copynumber: 2.5 Consensus size: 82
2405688 TGATGGGAGA
* * * **
2405698 TCTGCTCCACTCATGT-TTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTTTGGGTAGTCAGA
1 TCTGCTCCACT-ATTTATTCAGGGAAGATCAGACTTGATCTATGCCTCTTTTTCAGGTAGTCAGA
2405762 TCAATTTTGGAAGATGTG
65 TCAATTTTGGAAGATGTG
*
2405780 TCTGCTCCACTATTTATTCAGGGAAGATCAGACTTGATCTATGCCT-TTTTTCAGGTAGTTAGAT
1 TCTGCTCCACTATTTATTCAGGGAAGATCAGACTTGATCTATGCCTCTTTTTCAGGTAGTCAGAT
2405844 CAATTTTTGGAAGATGTG
66 CAA-TTTTGGAAGATGTG
* * * *
2405862 TCTACTCCACTATTCATTTATGGAAGATCAGACTTGA
1 TCTGCTCCACTATTTATTCAGGGAAGATCAGACTTGA
2405899 GAAATCTTTA
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
81 21 0.20
82 86 0.80
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (82 bp):
TCTGCTCCACTATTTATTCAGGGAAGATCAGACTTGATCTATGCCTCTTTTTCAGGTAGTCAGAT
CAATTTTGGAAGATGTG
Found at i:2406045 original size:47 final size:47
Alignment explanation
Indices: 2405913--2406045 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 47
2405903 TCTTTATAAA
* * * * *
2405913 ACGAATATTCTCCATTCTTGCTTT-AGGAAGATAA-AATCTAAGGGAAG
1 ACGAATATGCTCTACTCTTG-TTTCAGGGAGATAAGACTC-AAGGGAAG
* *
2405960 ACGAATTTGCTCTACTCTTGTTTTAGGGAGATAAGACTCAAGGGAAG
1 ACGAATATGCTCTACTCTTGTTTCAGGGAGATAAGACTCAAGGGAAG
* *
2406007 ATGAATATGCTCTACTCTTGTTTCAGGGAGATATGACTC
1 ACGAATATGCTCTACTCTTGTTTCAGGGAGATAAGACTC
2406046 GAGATATCTT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 3 0.04
47 68 0.92
48 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (47 bp):
ACGAATATGCTCTACTCTTGTTTCAGGGAGATAAGACTCAAGGGAAG
Found at i:2406327 original size:137 final size:137
Alignment explanation
Indices: 2406070--2406489 Score: 488
Period size: 137 Copynumber: 3.1 Consensus size: 137
2406060 TAACCCTAAT
* ** * * *
2406070 TTTAGGGATAATAGAGATAACATTATTCCTACGCAATGAGGAAGTCTGGCTATCTAAGGATGACG
1 TTTAGGGATAATGGAGATAACACAATTCCTAAGCAATGAGGAATTCTAGCTATCTAAGGATGACG
* * * * * * * *
2406135 CGGCTCATACGTGATGAGTAGATCTGATCGGTAGATGGCATTGTTTCTTCCTGATGAGAACGTCT
66 CGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGAACATCT
**
2406200 GGTCATC
131 GACCATC
*** ** * *
2406207 TTTTTTGATAATGGAGATAACACGGTTCCTAAGCGATGAGGAATTCTAGCTATCTAAGGATGATG
1 TTTAGGGATAATGGAGATAACACAATTCCTAAGCAATGAGGAATTCTAGCTATCTAAGGATGACG
* **
2406272 TGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGGGCATCT
66 CGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGAACATCT
2406337 GACCATC
131 GACCATC
* * * *
2406344 TTTAGGGATAATGGAGATAAAACAATTCCTACA-CTATGAGGAATTCTAGCTATATAAAGATGAC
1 TTTAGGGATAATGGAGATAACACAATTCCTA-AGCAATGAGGAATTCTAGCTATCTAAGGATGAC
* * ** *
2406408 GCGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATTATTCCTT--TG-TGAGGATGTT
65 GCGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGAACATC
2406470 TGACCATC
130 TGACCATC
2406478 TTTAGGGATAAT
1 TTTAGGGATAAT
2406490 TTGTTTCCTA
Statistics
Matches: 241, Mismatches: 41, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
134 26 0.11
135 2 0.01
137 212 0.88
138 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (137 bp):
TTTAGGGATAATGGAGATAACACAATTCCTAAGCAATGAGGAATTCTAGCTATCTAAGGATGACG
CGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGAACATCT
GACCATC
Found at i:2406711 original size:57 final size:57
Alignment explanation
Indices: 2406649--2406756 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
2406639 GAGTTCAACA
* *
2406649 AACATGACCGATTTACCCTGGCTGAACATCTTGATCCCATACTCTTTGATCGTAACT
1 AACATGACCGATTTACCCTAGCTGAACACCTTGATCCCATACTCTTTGATCGTAACT
* * * *
2406706 AACATGATCGATTTACCCTAGCTGAAGACCTTGATTCCATACTTTTTGATC
1 AACATGACCGATTTACCCTAGCTGAACACCTTGATCCCATACTCTTTGATC
2406757 AGATACGATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
AACATGACCGATTTACCCTAGCTGAACACCTTGATCCCATACTCTTTGATCGTAACT
Found at i:2411105 original size:25 final size:24
Alignment explanation
Indices: 2411065--2411112 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2411055 AGTTGTTACG
2411065 AATTAATAAATAAAATAT-TATTT
1 AATTAATAAATAAAATATATATTT
*
2411088 AATTAATTCAAATTAAATATATATT
1 AATTAA-T-AAATAAAATATATATT
2411113 AAAGACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 1 0.05
25 10 0.48
26 4 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTAATAAATAAAATATATATTT
Found at i:2421766 original size:4 final size:4
Alignment explanation
Indices: 2421757--2421781 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2421747 ATCAAGCAAA
2421757 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2421782 CACCAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2422308 original size:10 final size:10
Alignment explanation
Indices: 2422293--2422342 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
2422283 AACGTGAGAC
2422293 TAAATTAAAA
1 TAAATTAAAA
2422303 TAAATTAAAA
1 TAAATTAAAA
**
2422313 TTGCA-T-AAA
1 -TAAATTAAAA
*
2422322 CAAATTAAAA
1 TAAATTAAAA
2422332 TAAATTAAAA
1 TAAATTAAAA
2422342 T
1 T
2422343 TGAAAGGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
8 1 0.03
9 4 0.13
10 24 0.77
11 2 0.06
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:2422326 original size:29 final size:28
Alignment explanation
Indices: 2422294--2422370 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 28
2422284 ACGTGAGACT
*
2422294 AAATTAAAATAAATTAAAATTGCATAA-AC
1 AAATTAAAATAAATTAAAATTG-A-AAGAA
2422323 AAATTAAAATAAATTAAAATTGAAAGGAA
1 AAATTAAAATAAATTAAAATTGAAA-GAA
*
2422352 AAATTAAAATAAATAAAAA
1 AAATTAAAATAAATTAAAA
2422371 ACAGATTTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.05
28 1 0.02
29 41 0.93
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (28 bp):
AAATTAAAATAAATTAAAATTGAAAGAA
Found at i:2426306 original size:2 final size:2
Alignment explanation
Indices: 2426255--2426290 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2426245 AAAACAAAAG
2426255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2426291 AACAAACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2429090 original size:52 final size:52
Alignment explanation
Indices: 2429007--2429266 Score: 324
Period size: 52 Copynumber: 5.0 Consensus size: 52
2428997 GCATTTAACA
* * * *
2429007 TTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAATACATAGTTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCC
* * * * * * *
2429059 TTTCATCTAACTTTCCTTATTGGCACATTTCTGCCAATTGAACAATTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCC
* *
2429111 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATTGCACAGTTAGACC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCC
* * * * *
2429163 CTTCATTTAACTTACATTATTAACACATTTCTGCCAATATGCACAG-TAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAA-ATGCACAGTTAGGCC
*
2429215 TTTCATCTAACTTGCATTATTAACACCTTTCTGCCAATATGCACAGTTAGGC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAA-ATGCACAGTTAGGC
2429267 ATTTAACTTT
Statistics
Matches: 179, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
52 167 0.93
53 12 0.07
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (52 bp):
TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCC
Found at i:2429126 original size:104 final size:104
Alignment explanation
Indices: 2429007--2429266 Score: 360
Period size: 104 Copynumber: 2.5 Consensus size: 104
2428997 GCATTTAACA
* * * * *
2429007 TTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAATACATAGTTAGGCCTTTCATCTAACTT
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCCTTCATCTAACTT
* * ** *
2429072 TCCTTATTGGCACATTTCTGCCAAT-TGAACAATTAGGCC
66 ACATTATTAACACATTTCTGCCAATATGAAC-AGTAGGCC
* * *
2429111 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATTGCACAGTTAGACCCTTCATTTAACTT
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCCTTCATCTAACTT
*
2429176 ACATTATTAACACATTTCTGCCAATATGCACAGTAGGCC
66 ACATTATTAACACATTTCTGCCAATATGAACAGTAGGCC
*
2429215 TTTCATCTAACTTGCATTATTAACACCTTTCTGCCAATATGCACAGTTAGGC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAA-ATGCACAGTTAGGC
2429267 ATTTAACTTT
Statistics
Matches: 137, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
104 121 0.88
105 16 0.12
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (104 bp):
TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCCTTCATCTAACTT
ACATTATTAACACATTTCTGCCAATATGAACAGTAGGCC
Found at i:2429257 original size:27 final size:27
Alignment explanation
Indices: 2429177--2429257 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 27
2429167 ATTTAACTTA
*
2429177 CATTATTAACACATTTCTGCCAATATG
1 CATTATTAACACCTTTCTGCCAATATG
* * ** *
2429204 CA-CAGT-AGGCCTTTCAT-CTAACT-TG
1 CATTATTAACACCTTTC-TGCCAA-TATG
2429229 CATTATTAACACCTTTCTGCCAATATG
1 CATTATTAACACCTTTCTGCCAATATG
2429256 CA
1 CA
2429258 CAGTTAGGCA
Statistics
Matches: 37, Mismatches: 11, Indels: 12
0.62 0.18 0.20
Matches are distributed among these distances:
25 13 0.35
26 8 0.22
27 16 0.43
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.35
Consensus pattern (27 bp):
CATTATTAACACCTTTCTGCCAATATG
Found at i:2435965 original size:26 final size:26
Alignment explanation
Indices: 2435935--2436175 Score: 96
Period size: 26 Copynumber: 9.2 Consensus size: 26
2435925 TTCATCTAAC
2435935 TTGCATTATTGGCACCTTTCTGCCAA
1 TTGCATTATTGGCACCTTTCTGCCAA
* ** * *
2435961 ATGCACAATTAG-ACCTTTCAT-CTAA
1 TTGCATTATTGGCACCTTTC-TGCCAA
*
2435986 CTTGCATTATTGACACCTTTCTGCCAA
1 -TTGCATTATTGGCACCTTTCTGCCAA
*
2436013 TTGCA-TAGTTAGG--CCTTTCAT-CTAA
1 TTGCATTA-TT-GGCACCTTTC-TGCCAA
* * *
2436038 CTTGCATTATTGACACCTTTATGTCAA
1 -TTGCATTATTGGCACCTTTCTGCCAA
*
2436065 TTGCA-TAGTTAGG--CCTTTCAT-CTAA
1 TTGCATTA-TT-GGCACCTTTC-TGCCAA
* *
2436090 CTTACATTATTGACACCTTTCTGCCAA
1 -TTGCATTATTGGCACCTTTCTGCCAA
*
2436117 TATGCA-TAGTTAGG--CCTTTCAT-CTAA
1 T-TGCATTA-TT-GGCACCTTTC-TGCCAA
* *
2436143 CTTGCATTATTGACACCTTTCTACCAA
1 -TTGCATTATTGGCACCTTTCTGCCAA
2436170 TATGCA
1 T-TGCA
2436176 CAGTTATACA
Statistics
Matches: 156, Mismatches: 29, Indels: 59
0.64 0.12 0.24
Matches are distributed among these distances:
25 33 0.21
26 68 0.44
27 54 0.35
28 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (26 bp):
TTGCATTATTGGCACCTTTCTGCCAA
Found at i:2436144 original size:53 final size:53
Alignment explanation
Indices: 2435924--2436181 Score: 414
Period size: 52 Copynumber: 4.9 Consensus size: 53
2435914 GCATTTAACA
* * * *
2435924 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAA-ATGCACAATTAGACC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCATAGTTAGGCC
2435976 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAT-TGCATAGTTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCATAGTTAGGCC
* *
2436028 TTTCATCTAACTTGCATTATTGACACCTTTATGTCAAT-TGCATAGTTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCATAGTTAGGCC
*
2436080 TTTCATCTAACTTACATTATTGACACCTTTCTGCCAATATGCATAGTTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCATAGTTAGGCC
* *
2436133 TTTCATCTAACTTGCATTATTGACACCTTTCTACCAATATGCACAGTTA
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCATAGTTA
2436182 TACATTTAAC
Statistics
Matches: 192, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
52 132 0.69
53 60 0.31
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (53 bp):
TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCATAGTTAGGCC
Found at i:2436175 original size:27 final size:27
Alignment explanation
Indices: 2436094--2436175 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
2436084 ATCTAACTTA
*
2436094 CATTATTGACACCTTTCTGCCAATATG
1 CATTATTGACACCTTTCTACCAATATG
** *
2436121 CA-TAGTT-AGGCCTTTC-ATCTAACT-TG
1 CATTA-TTGACACCTTTCTA-CCAA-TATG
2436147 CATTATTGACACCTTTCTACCAATATG
1 CATTATTGACACCTTTCTACCAATATG
2436174 CA
1 CA
2436176 CAGTTATACA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
26 19 0.46
27 21 0.51
28 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.37
Consensus pattern (27 bp):
CATTATTGACACCTTTCTACCAATATG
Found at i:2436582 original size:16 final size:17
Alignment explanation
Indices: 2436563--2436595 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2436553 TTTTCAATTT
2436563 CTAT-TACAATTTTAGC
1 CTATATACAATTTTAGC
2436579 CTATCATACAATTTTAG
1 CTAT-ATACAATTTTAG
2436596 GCTCAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (17 bp):
CTATATACAATTTTAGC
Found at i:2441640 original size:24 final size:24
Alignment explanation
Indices: 2441592--2441670 Score: 108
Period size: 24 Copynumber: 3.4 Consensus size: 24
2441582 AACCAAAAAG
*
2441592 GTAGTATCGGTACCA-T-CACTAA
1 GTAGTATCGGTACTACTACACTAA
*
2441614 GTAGTATCGGTATTACTACACTAA
1 GTAGTATCGGTACTACTACACTAA
* *
2441638 GTAGTATCGATACTACTAAACTAA
1 GTAGTATCGGTACTACTACACTAA
2441662 GTAGTATCG
1 GTAGTATCG
2441671 ATATCGTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 13 0.26
23 1 0.02
24 36 0.72
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (24 bp):
GTAGTATCGGTACTACTACACTAA
Found at i:2441850 original size:24 final size:24
Alignment explanation
Indices: 2441802--2441865 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
2441792 AACCAAAAAG
*
2441802 GTAGTATCGGTACCA-T-CACTAA
1 GTAGTATCGGTACTACTACACTAA
*
2441824 GTAGTATCGGTATTACTACACTAA
1 GTAGTATCGGTACTACTACACTAA
*
2441848 GTAGTATCGATACTACTA
1 GTAGTATCGGTACTACTA
2441866 TCGATAGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.36
23 1 0.03
24 22 0.61
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (24 bp):
GTAGTATCGGTACTACTACACTAA
Found at i:2441924 original size:180 final size:185
Alignment explanation
Indices: 2441614--2441948 Score: 554
Period size: 180 Copynumber: 1.8 Consensus size: 185
2441604 CCATCACTAA
**
2441614 GTAGTATCGGTATTACTACACTAAGTAGTATCGATACTACTAAACTAAGTAGTATCGATATCGTA
1 GTAGTATCGGTACCACTACACTAAGTAGTATCGATACTACTAAACTAAGTAGTATCGATATC--A
*
2441679 TATGGTATCGATAGCATTTTAGCATTCTATTTTGACAATATCCGTACTGCCTCATCAGTATCGGT
64 TA-GCTATCGATAGCATTTTAGCATTCTATTTTGACAATATCCGTACTGCCTCATCAGTATCGGT
2441744 ACTACTTCATTGTTTTGGGCTTCAAATACTAGAATTTGACATACTCAAAACCAAAAAG
128 ACTACTTCATTGTTTTGGGCTTCAAATACTAGAATTTGACATACTCAAAACCAAAAAG
* * *
2441802 GTAGTATCGGTACCA-T-CACTAAGTAGTATCGGTATTACTACACTAAGTAGTATCGATA-C-TA
1 GTAGTATCGGTACCACTACACTAAGTAGTATCGATACTACTAAACTAAGTAGTATCGATATCATA
2441863 -CTATCGATAGCATTTTAGCATTCTATTTTGACAATATCCGTACTGCCTCATCAGTATCGGTACT
66 GCTATCGATAGCATTTTAGCATTCTATTTTGACAATATCCGTACTGCCTCATCAGTATCGGTACT
2441927 ACTTCATTGTTTTGGGCTTCAA
131 ACTTCATTGTTTTGGGCTTCAA
2441949 CATCGATATC
Statistics
Matches: 141, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
180 85 0.60
182 2 0.01
185 1 0.01
186 39 0.28
187 1 0.01
188 13 0.09
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (185 bp):
GTAGTATCGGTACCACTACACTAAGTAGTATCGATACTACTAAACTAAGTAGTATCGATATCATA
GCTATCGATAGCATTTTAGCATTCTATTTTGACAATATCCGTACTGCCTCATCAGTATCGGTACT
ACTTCATTGTTTTGGGCTTCAAATACTAGAATTTGACATACTCAAAACCAAAAAG
Found at i:2443150 original size:136 final size:132
Alignment explanation
Indices: 2442906--2443291 Score: 450
Period size: 136 Copynumber: 2.9 Consensus size: 132
2442896 TGTTCCATGG
** * * * *
2442906 TTACTCAGAGAATATCAAATCTTGAAAGAGAATGATTTGTTTCGCTTATTCTTTAGGGAAAATTA
1 TTACTCAG-GAATATCAAATCTTGAAAGAGAGGGATATGTTTCACTTTTTCTTGAGGGAAAATTA
* * * * *
2442971 GATATGGGGACGTTGATTCATTCCACTATTCCTCAAGGAAGATTGAATTGAGGCAGACTTGTTGG
65 GATCT-GGGATGTTGATTCATTCCACTGTTACTCAAGGAAGATTGAATCGAGGCAGACTTGTT--
2443036 ACACTA
127 ACACTA
* * * * * *
2443042 TTACTCAAGGAATATCAAGTATTGAAAGATAGGGATCTGTTTCACTTTTTCTTGAGGGGAAATCA
1 TTACTC-AGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCACTTTTTCTTGAGGGAAAATTA
* * * *
2443107 GATCTGGTGATGTTGATTCATCCCGCTGTTACTCAAGGAAGATTGAATCGAGGTAGACTTGTTCC
65 GATCTGG-GATGTTGATTCATTCCACTGTTACTCAAGGAAGATTGAATCGAGGCAGACTTGTTAC
*
2443172 ACTG
129 ACTA
* *
2443176 TTACTCTAGGAATATCAAATCTTGAAAGAGAGGGATATATTTCA-TTTCTTCTTGAGAGAAAATT
1 TTACTC-AGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCACTTT-TTCTTGAGGGAAAATT
* *
2443240 AGATCTTGGAATGTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGA
64 AGATC-TGGGATGTTGATTCATTCCACTGTTACTCAAGGAAGATTGAATCGA
2443292 ATTCGATTTT
Statistics
Matches: 212, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
133 3 0.01
134 99 0.47
135 5 0.02
136 103 0.49
137 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (132 bp):
TTACTCAGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCACTTTTTCTTGAGGGAAAATTAG
ATCTGGGATGTTGATTCATTCCACTGTTACTCAAGGAAGATTGAATCGAGGCAGACTTGTTACAC
TA
Found at i:2443228 original size:134 final size:131
Alignment explanation
Indices: 2442892--2443291 Score: 451
Period size: 134 Copynumber: 3.0 Consensus size: 131
2442882 TTGCCTGGTT
** * * *
2442892 GACTTGTTCCA-TGGTTACTCAGAGAATATCAAATCTTGAAAGAGAATGATTTGTTTCGCTTATT
1 GACTTGTTCCACT-GTTACTCAG-GAATATCAAATCTTGAAAGAGAGGGATATGTTTC-ATTTTT
* * * * * *
2442956 CTTTAGGGAAAATTAGATATGGGGACGTTGATTCATTCCACTATTCCTCAAGGAAGATTGAATTG
63 CTTGAGGGAAAATTAGATCT-GGGATGTTGATTCATTCCACTGTTACTCAAGGAAGATTGAATCG
2443021 AGGCA
127 AGGCA
* * * * * *
2443026 GACTTGTTGGACACTATTACTCAAGGAATATCAAGTATTGAAAGATAGGGATCTGTTTCACTTTT
1 GACTTGTT--CCACTGTTACTC-AGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCA-TTTT
* * * *
2443091 TCTTGAGGGGAAATCAGATCTGGTGATGTTGATTCATCCCGCTGTTACTCAAGGAAGATTGAATC
62 TCTTGAGGGAAAATTAGATCTGG-GATGTTGATTCATTCCACTGTTACTCAAGGAAGATTGAATC
*
2443156 GAGGTA
126 GAGGCA
*
2443162 GACTTGTTCCACTGTTACTCTAGGAATATCAAATCTTGAAAGAGAGGGATATATTTCATTTCTTC
1 GACTTGTTCCACTGTTACTC-AGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCATTT-TTC
* * *
2443227 TTGAGAGAAAATTAGATCTTGGAATGTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGA
64 TTGAGGGAAAATTAGATC-TGGGATGTTGATTCATTCCACTGTTACTCAAGGAAGATTGAATCGA
2443292 ATTCGATTTT
Statistics
Matches: 222, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
133 3 0.01
134 107 0.48
135 5 0.02
136 104 0.47
137 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (131 bp):
GACTTGTTCCACTGTTACTCAGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCATTTTTCTT
GAGGGAAAATTAGATCTGGGATGTTGATTCATTCCACTGTTACTCAAGGAAGATTGAATCGAGGC
A
Found at i:2443642 original size:42 final size:42
Alignment explanation
Indices: 2443595--2443674 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
2443585 CAAACGACTT
* *
2443595 ATCATCTTACTCAAAAGGCTTA-TAGATGACCCGAAGGATTTA
1 ATCATCATACTCAAAAGACTTACT-GATGACCCGAAGGATTTA
* * *
2443637 ATCATCATGCTCAGAAGACTTACTGATGGCCCGAAGGA
1 ATCATCATACTCAAAAGACTTACTGATGACCCGAAGGA
2443675 CTTACCAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 31 0.97
43 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (42 bp):
ATCATCATACTCAAAAGACTTACTGATGACCCGAAGGATTTA
Found at i:2446586 original size:6 final size:6
Alignment explanation
Indices: 2446577--2446754 Score: 176
Period size: 6 Copynumber: 29.8 Consensus size: 6
2446567 TTTATTTTAT
* * *
2446577 TTTTTC TTTTTTC TTTTTTC TTTTT- TTCTTC TTCTT- TTTTTC TTTTTT
1 TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
2446625 TTTTTC TTTTT- TTTTTC --TTT- TTTTTC TTTTTC TTTTTC TTTCTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TT-TTTC
*
2446671 TTTTTTC TTTTCTC TTTTTC TTTTTC TTTTTC TTTTTTC TTTTTTT TTTTTC
1 -TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC -TTTTTC -TTTTTC TTTTTC
*
2446723 TTTTT- TTTTT- TCTTT- TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
2446755 TATTTTGTCT
Statistics
Matches: 152, Mismatches: 8, Indels: 23
0.83 0.04 0.13
Matches are distributed among these distances:
4 3 0.02
5 29 0.19
6 76 0.50
7 37 0.24
8 7 0.05
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:2446600 original size:20 final size:20
Alignment explanation
Indices: 2446577--2446760 Score: 211
Period size: 20 Copynumber: 9.2 Consensus size: 20
2446567 TTTATTTTAT
2446577 TTTTTCTTTTTTCTTTTTTC
1 TTTTTCTTTTTTCTTTTTTC
2446597 TTTTT-TTCTTCTTCTTTTTTTC
1 TTTTTCTT-TT-TTC-TTTTTTC
2446619 TTTTT-TTTTTTC-TTTTT-
1 TTTTTCTTTTTTCTTTTTTC
*
2446636 TTTTTCTTTTTTTTCTTTTTC
1 TTTTTCTTTTTTCT-TTTTTC
2446657 TTTTTCTTTCTTTCTTTTTTC
1 TTTTTCTTT-TTTCTTTTTTC
2446678 -TTTTCTCTTTTTC-TTTTTC
1 TTTTTCT-TTTTTCTTTTTTC
*
2446697 TTTTTCTTTTTTCTTTTTTT
1 TTTTTCTTTTTTCTTTTTTC
* *
2446717 TTTTTCTTTTTTTTTTTCTTT
1 TTTTTCTTTTTTCTTTT-TTC
*
2446738 TTTTTC-TTTTTCTTTTTTA
1 TTTTTCTTTTTTCTTTTTTC
2446757 TTTT
1 TTTT
2446761 GTCTCTCTAT
Statistics
Matches: 146, Mismatches: 6, Indels: 25
0.82 0.03 0.14
Matches are distributed among these distances:
17 5 0.03
18 11 0.08
19 20 0.14
20 61 0.42
21 31 0.21
22 18 0.12
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTCTTTTTTCTTTTTTC
Found at i:2446655 original size:52 final size:51
Alignment explanation
Indices: 2446578--2446755 Score: 229
Period size: 52 Copynumber: 3.5 Consensus size: 51
2446568 TTATTTTATT
2446578 TTTTCTTTTTTCTTTTTTCTTTTTTTCTTCTTCTTTTTTTCTTTTTTTTTTTC
1 TTTT-TTTTTTCTTTTTT-TTTTTTTCTTCTTCTTTTTTTCTTTTTTTTTTTC
* *
2446631 TTTTTTTTTTCTTTTTTTTCTTTTTCTTTTTCTTTCTTTCTTTTTTCTTTTCTC
1 TTTTTTTTTTCTTTTTTTT-TTTTTCTTCTTCTTTTTTTCTTTTTT-TTTT-TC
* *
2446685 TTTTTCTTTTTC-TTTTTCTTTTTTCTT-TTTTTTTTTTCTTTTTTTTTTTC
1 TTTTT-TTTTTCTTTTTTTTTTTTTCTTCTTCTTTTTTTCTTTTTTTTTTTC
*
2446735 --TTTTTTTTCTTTTTCTTTTTT
1 TTTTTTTTTTCTTTTTTTTTTTT
2446756 ATTTTGTCTC
Statistics
Matches: 113, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
47 6 0.05
48 12 0.11
50 2 0.02
51 6 0.05
52 52 0.46
53 16 0.14
54 13 0.12
55 6 0.05
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (51 bp):
TTTTTTTTTTCTTTTTTTTTTTTTCTTCTTCTTTTTTTCTTTTTTTTTTTC
Found at i:2446774 original size:1 final size:1
Alignment explanation
Indices: 2446571--2446760 Score: 137
Period size: 1 Copynumber: 190.0 Consensus size: 1
2446561 ACTTGATTTA
* * * * * * * * *
2446571 TTTTATTTTTTCTTTTTTCTTTTTTCTTTTTTTCTTCTTCTTTTTTTCTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * *
2446636 TTTTTCTTTTTTTTCTTTTTCTTTTTCTTTCTTTCTTTTTTCTTTTCTCTTTTTCTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
2446701 TCTTTTTTCTTTTTTTTTTTTCTTTTTTTTTTTCTTTTTTTTCTTTTTCTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2446761 GTCTCTCTAT
Statistics
Matches: 135, Mismatches: 54, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 135 1.00
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:2446788 original size:40 final size:38
Alignment explanation
Indices: 2446577--2446789 Score: 216
Period size: 40 Copynumber: 5.3 Consensus size: 38
2446567 TTTATTTTAT
*
2446577 TTTTTCTTTTTTCTTTTTTCTTTTTTTCTTCTTCTTTTTTTC
1 TTTTTCTTTTTTC--TTTT-TTTTTTTC-TCTTTTTTTTTTC
*
2446619 TTTTT-TTTTTTC-TTTTTTTTTTCTTTTTTTTCTTTTTC
1 TTTTTCTTTTTTCTTTTTTTTTTTC-TCTTTTT-TTTTTC
*
2446657 TTTTTCTTTCTTTCTTTTTTCTTTTCTCTTTTTCTTTTTC
1 TTTTTCTTT-TTTCTTTTTTTTTTTCTCTTTTT-TTTTTC
2446697 TTTTTCTTTTTTCTTTTTTTTTTT-TCTTTTTTTTTTTC
1 TTTTTCTTTTTTCTTTTTTTTTTTCTC-TTTTTTTTTTC
* * *
2446735 TTTTTTTTCTTTTTCTTTTTTATTTTGTCTCTCTATTTTTTC
1 -TTTTTCT-TTTTTCTTTTTT-TTTT-TCTCTTTTTTTTTTC
*
2446777 ATTTTCATTTTTT
1 TTTTTC-TTTTTT
2446790 AATTTTTTCT
Statistics
Matches: 150, Mismatches: 10, Indels: 23
0.82 0.05 0.13
Matches are distributed among these distances:
37 14 0.09
38 22 0.15
39 28 0.19
40 38 0.25
41 30 0.20
42 16 0.11
43 2 0.01
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (38 bp):
TTTTTCTTTTTTCTTTTTTTTTTTCTCTTTTTTTTTTC
Found at i:2450416 original size:26 final size:26
Alignment explanation
Indices: 2450380--2450469 Score: 126
Period size: 26 Copynumber: 3.5 Consensus size: 26
2450370 TAGGAGTCTA
**
2450380 TGATCAACTTTGATATCTTCTCTCGT
1 TGATCAACTTTGAGCTCTTCTCTCGT
*
2450406 TGATTAACTTTGAGCTCTTCTCTCGT
1 TGATCAACTTTGAGCTCTTCTCTCGT
*
2450432 CGATCAACTTTGAGCTCTTCTCTCGT
1 TGATCAACTTTGAGCTCTTCTCTCGT
* *
2450458 CGATCAATTTTG
1 TGATCAACTTTG
2450470 TTTGTAAGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 58 1.00
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.43
Consensus pattern (26 bp):
TGATCAACTTTGAGCTCTTCTCTCGT
Found at i:2456285 original size:20 final size:20
Alignment explanation
Indices: 2456260--2456297 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2456250 GCAAAACCTG
*
2456260 ATGGGGGTATTAGTACCCTC
1 ATGGGGGTATCAGTACCCTC
2456280 ATGGGGGTATCAGTACCC
1 ATGGGGGTATCAGTACCC
2456298 ATTCAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (20 bp):
ATGGGGGTATCAGTACCCTC
Found at i:2456311 original size:23 final size:20
Alignment explanation
Indices: 2456262--2456313 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2456252 AAAACCTGAT
* *
2456262 GGGGGTATTAGTACCCTCAT
1 GGGGGTATCAGTACCCTCAA
2456282 GGGGGTATCAGTACCCATTCAAA
1 GGGGGTATCAGTACCC--TC-AA
2456305 GGGGGTATC
1 GGGGGTATC
2456314 GATACCTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 15 0.56
22 2 0.07
23 10 0.37
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGTATCAGTACCCTCAA
Found at i:2462491 original size:82 final size:82
Alignment explanation
Indices: 2462336--2462491 Score: 181
Period size: 82 Copynumber: 1.9 Consensus size: 82
2462326 CTGATCTTCA
* * *
2462336 TCTAACTTGTATTAGTGGCATCTTTCAGCCAAAATGCACCGTTAGGCAATAGTCTTTTATTCTAA
1 TCTAACTTGCATTAGTGGCACCTTTCAGCCAAAATGCACAGTTAGGCAATAGTCTTTTATTCTAA
**
2462401 AGGTATTTAACCTTTCT
66 AGCAATTTAACCTTTCT
* * * * * *
2462418 TCTAACTTGCATTATTGGGACCTTTTCTGCC-AAATGCATAGTTAGGCATTAGTCTTTTATTTTA
1 TCTAACTTGCATTAGTGGCACC-TTTCAGCCAAAATGCACAGTTAGGCAATAGTCTTTTATTCTA
2462482 GAA-CAATTTA
65 -AAGCAATTTA
2462492 TACTCTAATA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
82 52 0.85
83 9 0.15
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (82 bp):
TCTAACTTGCATTAGTGGCACCTTTCAGCCAAAATGCACAGTTAGGCAATAGTCTTTTATTCTAA
AGCAATTTAACCTTTCT
Found at i:2462687 original size:55 final size:54
Alignment explanation
Indices: 2462628--2462819 Score: 296
Period size: 55 Copynumber: 3.5 Consensus size: 54
2462618 TACCACTACT
2462628 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCAATAAA
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCC-ATAAA
* * *
2462683 GAAATTCATAAACTTATTATGAATTTCTTAATTTTGCACACAAAGTTTCCATACTA
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAG-TGCCATA-AA
*
2462739 -AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCATACAAAGTGCCCATAAA
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTG-CCATAAA
*
2462793 GAATTTCATAAACTTATTATGAATTTC
1 GAAATTCATAAACTTATTATGAATTTC
2462820 GTGGCTTGCA
Statistics
Matches: 125, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
54 2 0.02
55 119 0.95
56 4 0.03
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (54 bp):
GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCATAAA
Found at i:2462932 original size:54 final size:54
Alignment explanation
Indices: 2462797--2463105 Score: 379
Period size: 54 Copynumber: 5.7 Consensus size: 54
2462787 CATAAAGAAT
* * * * * * *
2462797 TTCATAAACTTATTATGAATTTCGTGGCTTGCACACATAGTGCCGAAACGGTTG
1 TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAGTGCCAAAATGGTTG
* * * *
2462851 TTTAT-AACATATGATGAATTATGTGGGTTGCACACATACTTCCAAAATGGTTG
1 TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAGTGCCAAAATGGTTG
*** * *
2462904 TTCATCAACATATGATGAATTCCATGGGTTGCAGACATAGT-CTCAAAACGGTTG
1 TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAGTGC-CAAAATGGTTG
* * * *
2462958 TTCATCAACATATGATGAATTCTGTGAGTTCCACACATAGTGCCGAAATGGTTG
1 TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAGTGCCAAAATGGTTG
* * *
2463012 TTCATCAACATATGATGAATTTTGTGAGTTGTACATATAGTGCCAAAATGGTTG
1 TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAGTGCCAAAATGGTTG
*
2463066 TTCATCAACATATGATGAATTTTGTGGGTTGTACACATAG
1 TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAG
2463106 CGTCGAAATG
Statistics
Matches: 221, Mismatches: 31, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
53 44 0.20
54 176 0.80
55 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTTTGTGGGTTGCACACATAGTGCCAAAATGGTTG
Found at i:2463014 original size:108 final size:109
Alignment explanation
Indices: 2462797--2464495 Score: 1443
Period size: 108 Copynumber: 15.9 Consensus size: 109
2462787 CATAAAGAAT
* * * * * *
2462797 TTCATAAACTTATTATGAATTTCGTGGCTTGCACACATAGTGC-CGAAACGGTTGTTTAT-AACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* * * * *
2462860 TATGATGAATTATGTGGGTTGCACACATACTTCCAAAATGGTTG
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
* * *
2462904 TTCATCAACATATGATGAATTCCATGGGTTGCAGACATAGT-CTCAAAACGGTTGTTCATCAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
*
2462968 TATGATGAATTCTGTGAGTTCCACACATAGTGCCGAAATGGTTG
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
** * * * * *
2463012 TTCATCAACATATGATGAATTTTGTGAGTTGTACATATAGTGC-CAAAATGGTTGTTCATCAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* * * * *
2463076 TATGATGAATTTTGTGGGTTGTACACATAGCGTCGAAATGGTATG
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGT-TG
2463121 ---AT----A-A--AT---TT-CGTGGGTTGCACACATAGTG-TCGAAACGGTTGTTCATCAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
*
2463171 TATGATGAATTCTGTGAGTTACACACATAGTGCCGAAATGGTT-
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
* * * * *
2463214 TTCATCAACATATGATGAATTCCGTGAGTTGCACACATA-T-CATTGAAATGATTGTTAATCAAC
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGC-TCGAAACGGTTGTTCATCAAC
* * *
2463277 ATATGATGAATTCCGTGAGTTGCACACATAGTGCTGAAACGGTTG
65 ATATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
* ** * * *
2463322 TTCATCAACATATGATTAATTCCGTGACTTGCACACATAGTGCT-AAAATGGATGTTCATCAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* * * ** *
2463386 TATGATGAATTCCGTGAGTTGCACACATATTACAAAAACGGTTG
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
* * * * *
2463430 TTCATCAACATTTGATTAATTCCTTGGGTTGCACACATATTGCT-AAAACGGTTGTTCATCAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* * * * ** *
2463494 TTTGATGAATTCCT-TGGGTTCCACACATAGT-AC-ATTTGG-TA
66 TATGATGAATT-CTGTGAGTTGCACACATAGTGCCGAAATGGTTG
* * * * * * * * * *** *
2463535 ATCATCATACTTATTAT-AATTTACGTGGGTTGCACACCTACTAC-C-ACTACTGAAATTCATAA
1 TTCATCA-ACATATGATGAA-TTCCGTGGGTTGCACACATAGTGCTCGA-AACGGTTGTTCATCA
* * * * * ***
2463597 ACTTATTATGAATTTCT-T-AGTTTTACACACAAAGTGGCC-ATAA-AGAAA
63 ACATATGATGAA-TTCTGTGAG--TTGCACACATAGT-GCCGA-AATGGTTG
* * * * * ** * * * * *** *
2463645 TTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGC-CCATACTGAAATTCATAAAC
1 TTCATCAACATATGATGAATTCCGT-GGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAAC
* * * * * * * ***
2463709 TTATTATGAATTTCT-T-AGTTTTGCATACAAAGTACCCATATGGAAA
65 ATATGATGAA-TTCTGTGAG--TTGCACACATAGTGCCGAAATGGTTG
* * * * *
2463755 TTCATAAACTTATTATGAATTTCGTGGCTTGCACACATAGTGC-CGAAACGGTTGTTCAT-AACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* *
2463818 TATGATGAATTCTGTGGGTTGTACACATAGTGCCGAAATGGTTG
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
* * ** *
2463862 TTCATCAACATATGATGAATTTCATGGGTTGCACACATAGTG-TCGAAATAGTTGTTCATTAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* * *
2463926 TATGATGAATTCCGTGAGTTACACACATAGTGCCAAAATGGTTG
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
* * * * *
2463970 TTCATCAACATATGATGAATTCCTTGAGTTGCACACATAGTG-TAGAAATGGTAGTTCATCAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* *
2464034 TATGATGAATT-TCGTGGGTTGCACACATAGCGCCGAAATGGTTG
66 TATGATGAATTCT-GTGAGTTGCACACATAGTGCCGAAATGGTTG
* * *
2464078 TTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGCGC-CGAAATGGTTGTTCATCAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* * *
2464142 TATGATGAATTTTGTGAGTTGCACACATAGTGCCGAAAAGGTTA
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
* ** * *
2464186 TTCATCAACATATGATGAATTCCGTGAGTTTTACACATAGTG-TCAAAACGATTGTTCATCAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* * *
2464250 TATGATGAATTCTGTGGGTTGCACACATAGTGCCAAAACGGTTG
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
* * * * *
2464294 TTCATCAACAAATGATGAATTGCGTTGGTTGCACACATAGTG-TCGAAATGGTTGTTCATCAATA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* ** *
2464358 TATGATGAA---T-TGACTTGCACACATAGTGCTTAAACT-GATG
66 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAA-TGGTTG
** *
2464398 TTCATCAACATATGATGAATTCCGTGATTTGCACACATAGTGCT-GAAACGGTTGTTTATCAACA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
* * * *
2464462 TTTAATGAATTCCT-TGGGTTCCACACATAGTGCC
66 TATGATGAATT-CTGTGAGTTGCACACATAGTGCC
2464496 ATTTGGTAAT
Statistics
Matches: 1319, Mismatches: 218, Indels: 109
0.80 0.13 0.07
Matches are distributed among these distances:
94 1 0.00
95 71 0.05
96 4 0.00
99 2 0.00
100 1 0.00
101 2 0.00
102 1 0.00
103 2 0.00
104 84 0.06
105 13 0.01
106 55 0.04
107 206 0.16
108 725 0.55
109 52 0.04
110 99 0.08
111 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (109 bp):
TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCTCGAAACGGTTGTTCATCAACA
TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTG
Found at i:2463032 original size:162 final size:162
Alignment explanation
Indices: 2462825--2464496 Score: 1394
Period size: 162 Copynumber: 10.4 Consensus size: 162
2462815 ATTTCGTGGC
* * *
2462825 TTGCACACATAGTGCCGAAACGGTTGTTTAT-AACATATGATGAATTATGTGGGTTGCACACATA
1 TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGTTGCACACATA
* * * *
2462889 CTTCCAAAATGGTTGTTCATCAACATATGATGAATTCCATGGGTTGCAGACATAGTCTCAAAACG
66 GTGCCAAAATGGTTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTCTCAAAACG
2462954 GTTGTTCATCAACATATGATGAATTCTGTGAG
131 GTTGTTCATCAACATATGATGAATTCTGTGAG
* * * * *
2462986 TTCCACACATAGTGCCGAAATGGTTGTTCATCAACATATGATGAATTTTGTGAGTTGTACATATA
1 TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGTTGCACACATA
** * * *
2463051 GTGCCAAAATGGTTGTTCATCAACATATGATGAATTTTGTGGGTTGTACACATAG-CGTCGAAAT
66 GTGCCAAAATGGTTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTC-TCAAAAC
*
2463115 GGTATG---AT----A-A--AT---TTC-GTGGG
130 GGT-TGTTCATCAACATATGATGAATTCTGTGAG
* *
2463135 TTGCACACATAGTGTCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGTTACACACATA
1 TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGTTGCACACATA
* * ** *
2463200 GTGCCGAAATGGTT-TTCATCAACATATGATGAATTCCGTGAGTTGCACACATA-TCATTGAAAT
66 GTGCCAAAATGGTTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTC-TCAAAAC
* * *
2463263 GATTGTTAATCAACATATGATGAATTCCGTGAG
130 GGTTGTTCATCAACATATGATGAATTCTGTGAG
* * * *
2463296 TTGCACACATAGTGCTGAAACGGTTGTTCATCAACATATGATTAATTCCGTGACTTGCACACATA
1 TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGTTGCACACATA
* * *
2463361 GTGCTAAAATGGATGTTCATCAACATATGATGAATTCCGTGAGTTGCACACATA-T-TACAAAAA
66 GTGCCAAAATGGTTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTCT-C-AAAA
* * *
2463424 CGGTTGTTCATCAACATTTGATTAATTCCT-TGGG
129 CGGTTGTTCATCAACATATGATGAATT-CTGTGAG
* ** * * *
2463458 TTGCACACATATTGCTAAAACGGTTGTTCATCAACATTTGATGAATTCCT-TGGGTTCCACACAT
1 TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATT-CTGTGAGTTGCACACAT
* ** ** * * * * * *
2463522 AGT-AC-ATTTGG-TAATCATCATACTTATTAT-AATTTACGTGGGTTGCACACCTACTAC-CAC
65 AGTGCCAAAATGGTTGTTCATCA-ACATATGATGAA-TTCCGTGGGTTGCACACATAGT-CTCAA
* * *** * * *
2463582 TACTGAAATTCATAAACTTATTATGAATTTCT-T-AG
127 AACGGTTGTTCATCAACATATGATGAA-TTCTGTGAG
* * * *** * * *
2463617 TTTTACACACAAAGTGGCC-ATAA-AGAAATTCATAAACTTATTATGAATTTCT-T-AGTTTTGC
1 --TTGCACACATAGT-GCCGA-AACGGTTGTTCATCAACATATGATGAA-TTCTGTGAG--TTGC
* * * *** * * * * * ** * *
2463678 ACACAAAGTGCCCATACT-GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCATACAAAGT
59 ACACATAGTG-CCAAAATGGTTGTTCATCAACATATGATGAATTCCGT-GGGTTGCACACATAGT
* * * *** * * *
2463742 AC-CCATATGGAAATTCATAAACTTATTATGAATT-TCGTG-G
122 -CTCAAAACGGTTGTTCATCAACATATGATGAATTCT-GTGAG
* *
2463782 CTTGCACACATAGTGCCGAAACGGTTGTTCAT-AACATATGATGAATTCTGTGGGTTGTACACAT
1 -TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGTTGCACACAT
* * * * * *
2463846 AGTGCCGAAATGGTTGTTCATCAACATATGATGAATTTCATGGGTTGCACACATAGTGTCGAAAT
65 AGTGCCAAAATGGTTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTCTCAAAAC
* * *
2463911 AGTTGTTCATTAACATATGATGAATTCCGTGAG
130 GGTTGTTCATCAACATATGATGAATTCTGTGAG
* * *
2463944 TTACACACATAGTGCCAAAATGGTTGTTCATCAACATATGATGAATTCCT-TGAGTTGCACACAT
1 TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATT-CTGTGAGTTGCACACAT
* * * * *
2464008 AGTG-TAGAAATGGTAGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAG-CGCCGAA
65 AGTGCCA-AAATGGTTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTC-TCAAA
* *
2464071 ATGGTTGTTCATCAACATATGATGAATT-TCGTGGG
128 ACGGTTGTTCATCAACATATGATGAATTCT-GTGAG
* * *
2464106 TTGCACACATAGCGCCGAAATGGTTGTTCATCAACATATGATGAATTTTGTGAGTTGCACACATA
1 TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGTTGCACACATA
* * ** *
2464171 GTGCCGAAAA-GGTTATTCATCAACATATGATGAATTCCGTGAGTTTTACACATAGTGTCAAAAC
66 GTGCC-AAAATGGTTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTCTCAAAAC
* *
2464235 GATTGTTCATCAACATATGATGAATTCTGTGGG
130 GGTTGTTCATCAACATATGATGAATTCTGTGAG
* *
2464268 TTGCACACATAGTGCCAAAACGGTTGTTCATCAACAAATGATGAATTGC-GTTG-GTTGCACACA
1 TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATT-CTG-TGAGTTGCACACA
* * * ** *
2464331 TAGTGTCGAAATGGTTGTTCATCAATATATGATGAA-T---TGACTTGCACACATAGTGCT-TAA
64 TAGTGCCAAAATGGTTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGT-CTCAAA
* * * *
2464391 ACTGATGTTCATCAACATATGATGAATTCCGTGAT
128 ACGGTTGTTCATCAACATATGATGAATTCTGTGAG
* * * * * *
2464426 TTGCACACATAGTGCTGAAACGGTTGTTTATCAACATTTAATGAATTCCT-TGGGTTCCACACAT
1 TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATT-CTGTGAGTTGCACACAT
2464490 AGTGCCA
65 AGTGCCA
2464497 TTTGGTAATC
Statistics
Matches: 1228, Mismatches: 214, Indels: 141
0.78 0.14 0.09
Matches are distributed among these distances:
147 2 0.00
148 44 0.04
149 75 0.06
150 5 0.00
153 2 0.00
154 1 0.00
155 2 0.00
156 1 0.00
157 4 0.00
158 102 0.08
159 11 0.01
160 56 0.05
161 212 0.17
162 595 0.48
163 30 0.02
164 37 0.03
165 49 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (162 bp):
TTGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGTTGCACACATA
GTGCCAAAATGGTTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTCTCAAAACG
GTTGTTCATCAACATATGATGAATTCTGTGAG
Found at i:2463134 original size:41 final size:41
Alignment explanation
Indices: 2463076--2463154 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
2463066 TTCATCAACA
* * *
2463076 TATGATGAATTTTGTGGGTTGTACACATAGCGTCGAAATGG
1 TATGATAAATTTCGTGGGTTGCACACATAGCGTCGAAATGG
*
2463117 TATGATAAATTTCGTGGGTTGCACACATAGTGTCGAAA
1 TATGATAAATTTCGTGGGTTGCACACATAGCGTCGAAA
2463155 CGGTTGTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33
Consensus pattern (41 bp):
TATGATAAATTTCGTGGGTTGCACACATAGCGTCGAAATGG
Found at i:2463197 original size:95 final size:95
Alignment explanation
Indices: 2463022--2463212 Score: 256
Period size: 95 Copynumber: 2.0 Consensus size: 95
2463012 TTCATCAACA
* * * * *
2463022 TATGATGAATTTTGTGAGTTGTACATATAGTGCCAAAATGGTTGTTCATCAACATATGATGAATT
1 TATGATAAATTTCGTGAGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATT
* * ** *
2463087 TTGTGGGTTGTACACATAGCGTCGAAATGG
66 CTGTGAGTTACACACATAGCGCCGAAATGG
* * *
2463117 TATGATAAATTTCGTGGGTTGCACACATAGTGTCGAAACGGTTGTTCATCAACATATGATGAATT
1 TATGATAAATTTCGTGAGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATT
*
2463182 CTGTGAGTTACACACATAGTGCCGAAATGG
66 CTGTGAGTTACACACATAGCGCCGAAATGG
2463212 T
1 T
2463213 TTTCATCAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.34
Consensus pattern (95 bp):
TATGATAAATTTCGTGAGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATT
CTGTGAGTTACACACATAGCGCCGAAATGG
Found at i:2463199 original size:54 final size:54
Alignment explanation
Indices: 2463117--2464495 Score: 1061
Period size: 54 Copynumber: 25.6 Consensus size: 54
2463107 GTCGAAATGG
* * * *
2463117 TATGATAAATT-TCGTGGGTTGCACACATAGTGTCGAAACGGTTGTTCATCAACA
1 TATGATGAATTCT-GTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
*
2463171 TATGATGAATTCTGTGAGTTACACACATAGTGCCGAAATGGTT-TTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * * *
2463224 TATGATGAATTCCGTGAGTTGCACACATA-T-CATTGAAATGATTGTTAATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGC--CGAAATGGTTGTTCATCAACA
* * *
2463278 TATGATGAATTCCGTGAGTTGCACACATAGTGCTGAAACGGTTGTTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * * ** *
2463332 TATGATTAATTCCGTGACTTGCACACATAGTGCTAAAATGGATGTTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * * ** *
2463386 TATGATGAATTCCGTGAGTTGCACACATATTACAAAAACGGTTGTTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * * * ** *
2463440 TTTGATTAATTCCT-TGGGTTGCACACATATTGCTAAAACGGTTGTTCATCAACA
1 TATGATGAATT-CTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * * * ** ** *
2463494 TTTGATGAATTCCT-TGGGTTCCACACATAGT-AC-ATTTGG-TAATCATCATACT
1 TATGATGAATT-CTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCA-ACA
* * * * * * *** * *
2463546 TATTAT-AATT-TACGTGGGTTGCACACCTACTACC-ACTACT-GAAATTCATAAACT
1 TATGATGAATTCT--GTGAGTTGCACACATAGTGCCGA--AATGGTTGTTCATCAACA
* * * * *** * *
2463600 TATTATGAATTTCT-T-AGTTTTACACACAAAGTGGCC-ATAA-AGAAATTCATAAACT
1 TATGATGAA-TTCTGTGAG--TTGCACACATAGT-GCCGA-AATGGTTGTTCATCAACA
* * * * *** * *
2463655 TATTATGAATTTCT-T-AGTTTTGCACACAAAGTGCCCATACT-GAAATTCATAAACT
1 TATGATGAA-TTCTGTGAG--TTGCACACATAGTGCCGA-AATGGTTGTTCATCAACA
* * * * * * *** * *
2463710 TATTATGAATTTCT-T-AGTTTTGCATACAAAGTACCCATATGGAAATTCATAAACT
1 TATGATGAA-TTCTGTGAG--TTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* *
2463765 TATTATGAATT-TCGTG-GCTTGCACACATAGTGCCGAAACGGTTGTTCAT-AACA
1 TATGATGAATTCT-GTGAG-TTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* *
2463818 TATGATGAATTCTGTGGGTTGTACACATAGTGCCGAAATGGTTGTTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * *
2463872 TATGATGAATTTCATG-G-GTTGCACACATAGTGTCGAAATAGTTGTTCATTAACA
1 TATGATGAA-TTC-TGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * *
2463926 TATGATGAATTCCGTGAGTTACACACATAGTGCCAAAATGGTTGTTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
** *
2463980 TATGATGAATTCCT-TGAGTTGCACACATAGTGTAGAAATGGTAGTTCATCAACA
1 TATGATGAATT-CTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* *
2464034 TATGATGAATT-TCGTGGGTTGCACACATAGCGCCGAAATGGTTGTTCATCAACA
1 TATGATGAATTCT-GTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* *
2464088 TATGATGAATT-TCGTGGGTTGCACACATAGCGCCGAAATGGTTGTTCATCAACA
1 TATGATGAATTCT-GTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * *
2464142 TATGATGAATTTTGTGAGTTGCACACATAGTGCCGAAAAGGTTATTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* ** * * * *
2464196 TATGATGAATTCCGTGAGTTTTACACATAGTGTCAAAACGATTGTTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * *
2464250 TATGATGAATTCTGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * *
2464304 AATGATGAATTGC-GTTG-GTTGCACACATAGTGTCGAAATGGTTGTTCATCAATA
1 TATGATGAATT-CTG-TGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* ** *
2464358 TATGATGAA---T-TGACTTGCACACATAGTGCTTAAACT-GATGTTCATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAA-TGGTTGTTCATCAACA
* * * * *
2464408 TATGATGAATTCCGTGATTTGCACACATAGTGCTGAAACGGTTGTTTATCAACA
1 TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
* * * *
2464462 TTTAATGAATTCCT-TGGGTTCCACACATAGTGCC
1 TATGATGAATT-CTGTGAGTTGCACACATAGTGCC
2464496 ATTTGGTAAT
Statistics
Matches: 1130, Mismatches: 145, Indels: 100
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.00
50 38 0.03
51 13 0.01
52 26 0.02
53 98 0.09
54 788 0.70
55 155 0.14
56 8 0.01
57 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (54 bp):
TATGATGAATTCTGTGAGTTGCACACATAGTGCCGAAATGGTTGTTCATCAACA
Found at i:2463626 original size:55 final size:55
Alignment explanation
Indices: 2463582--2463777 Score: 313
Period size: 55 Copynumber: 3.6 Consensus size: 55
2463572 CTACTACCAC
* **
2463582 TACTGAAATTCATAAACTTATTATGAATTTCTTAGTTTTACACACAAAGTGGCCA
1 TACTGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTACCCA
** *
2463637 TAAAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
1 TACTGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTACCCA
*
2463692 TACTGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCATACAAAGTACCCA
1 TACTGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTACCCA
2463747 TA-TGGAAATTCATAAACTTATTATGAATTTC
1 TACT-GAAATTCATAAACTTATTATGAATTTC
2463778 GTGGCTTGCA
Statistics
Matches: 132, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
54 1 0.01
55 131 0.99
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (55 bp):
TACTGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTACCCA
Found at i:2464061 original size:27 final size:27
Alignment explanation
Indices: 2464031--2464116 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
2464021 TAGTTCATCA
2464031 ACATATGATGAATTTCGTGGGTTGCAC
1 ACATATGATGAATTTCGTGGGTTGCAC
* ** * * *
2464058 ACATAGCGCCGAA-ATGGT-TGTT-CATC
1 ACATA-TGATGAATTTCGTGGGTTGCA-C
2464084 AACATATGATGAATTTCGTGGGTTGCAC
1 -ACATATGATGAATTTCGTGGGTTGCAC
2464112 ACATA
1 ACATA
2464117 GCGCCGAAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
25 2 0.05
26 8 0.20
27 21 0.51
28 8 0.20
29 2 0.05
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (27 bp):
ACATATGATGAATTTCGTGGGTTGCAC
Found at i:2464142 original size:27 final size:27
Alignment explanation
Indices: 2464058--2464143 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
2464048 TGGGTTGCAC
2464058 ACATAGCGCCGAAATGGTTGTTCATCA
1 ACATAGCGCCGAAATGGTTGTTCATCA
* ** * * *
2464085 ACATA-TGATGAATTTCGTGGGTTGCA-C-
1 ACATAGCGCCGAA-ATGGT-TGTT-CATCA
2464112 ACATAGCGCCGAAATGGTTGTTCATCA
1 ACATAGCGCCGAAATGGTTGTTCATCA
2464139 ACATA
1 ACATA
2464144 TGATGAATTT
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
25 2 0.05
26 8 0.20
27 21 0.51
28 8 0.20
29 2 0.05
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (27 bp):
ACATAGCGCCGAAATGGTTGTTCATCA
Found at i:2464858 original size:22 final size:22
Alignment explanation
Indices: 2464812--2464934 Score: 151
Period size: 22 Copynumber: 5.7 Consensus size: 22
2464802 GTTCTAGGCT
* *
2464812 CCATAGTATCGATAC-TC-CTA
1 CCATGGTATCGATACTTCTATA
2464832 CCATGGTATCGATACTTCTATA
1 CCATGGTATCGATACTTCTATA
2464854 CCATGGTATCGATACTTCTATA
1 CCATGGTATCGATACTTCTATA
*
2464876 CCATGGAATCGATACTTCTATA
1 CCATGGTATCGATACTTCTATA
* * * *
2464898 CTATGGAATCGATACTACTACA
1 CCATGGTATCGATACTTCTATA
* *
2464920 CTATGGTACCGATAC
1 CCATGGTATCGATAC
2464935 CATTTTGGCA
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 14 0.15
21 2 0.02
22 77 0.83
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (22 bp):
CCATGGTATCGATACTTCTATA
Found at i:2468704 original size:36 final size:36
Alignment explanation
Indices: 2468663--2468732 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
2468653 AAATCTCTAC
* *
2468663 AGGTTCAACTCTGATCAAGCTGGTAATTCCTTATAT
1 AGGTTCAACACTGATCAAGCTGATAATTCCTTATAT
* * *
2468699 AGGTTCAGCACTGATCAAGTTGATAGTTCCTTAT
1 AGGTTCAACACTGATCAAGCTGATAATTCCTTAT
2468733 TGACCTAAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (36 bp):
AGGTTCAACACTGATCAAGCTGATAATTCCTTATAT
Found at i:2470003 original size:20 final size:21
Alignment explanation
Indices: 2469949--2470005 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
2469939 TCTTTGATAA
2469949 AAAATAAATAATATTAAAATGAT
1 AAAATAAAT--TATTAAAATGAT
* *
2469972 AAAATAATTTATTAAAAT-TT
1 AAAATAAATTATTAAAATGAT
*
2469992 AATATAAATTATTA
1 AAAATAAATTATTA
2470006 TTGATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 13 0.43
21 9 0.30
23 8 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAATAAATTATTAAAATGAT
Found at i:2471446 original size:24 final size:26
Alignment explanation
Indices: 2471416--2471473 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
2471406 TTTGGGCCTG
2471416 TAATAATA-T-TTATTAATAATAAAA
1 TAATAATATTATTATTAATAATAAAA
* * *
2471440 TAATAATTATTATTATTATTATTATAA
1 TAATAA-TATTATTATTAATAATAAAA
2471467 TAATAAT
1 TAATAAT
2471474 GATAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.21
25 2 0.07
26 2 0.07
27 18 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATAATATTATTATTAATAATAAAA
Found at i:2472064 original size:112 final size:112
Alignment explanation
Indices: 2471838--2472252 Score: 558
Period size: 113 Copynumber: 3.7 Consensus size: 112
2471828 ATAGAATTAT
** *
2471838 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA--CTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
2471900 TTATAAACTTTCTCTGAAAAAGCTGATCCATTAAGTGATGGATTTGA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAA
*
2471947 GCAAAAGGTTAAACAAATTCTTCTCATTATGAA-T-TTCTT-CTTCTTCAGATGACGAGTTCTTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * * * *
2472009 TCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAA
63 TCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAA
*
2472059 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2472124 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAA
65 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAA
*
2472172 GCAAAAAGG-TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCT
2472236 CATTATGAACTTTCTCT
64 CATTATGAACTTTCTCT
2472253 AAAAATGTTG
Statistics
Matches: 270, Mismatches: 25, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
109 45 0.17
112 78 0.29
113 124 0.46
114 7 0.03
115 5 0.02
116 11 0.04
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAA
Found at i:2472148 original size:225 final size:221
Alignment explanation
Indices: 2471839--2472246 Score: 617
Period size: 225 Copynumber: 1.8 Consensus size: 221
2471829 TAGAATTATG
* *
2471839 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * *
2471904 AAACTTTCTCTGAAAAAGCTGATCCATTAAGTGATGGATTTGAGC-AAAAGGTTAAACAAATTCT
66 AAACTTTCTCTGAAAAAGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGG-TAAACAAATTCT
2471968 TCTCATTATGAA-T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGC
130 TCTCATTATGAACTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTACCTGGC
2472030 AATGTTGATCCATCAAATGATGAATTCAAA
192 AATGTTGATCCATCAAATGATGAATTCAAA
*
2472060 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCA
* * * *
2472125 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGGTGAACAAGT
62 TTATAAACTTTCTCTGAAAAAGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGGTAAACAAAT
2472190 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
127 TCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
2472247 TTCTCTAAAA
Statistics
Matches: 168, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
221 29 0.17
224 6 0.04
225 89 0.53
226 27 0.16
227 1 0.01
228 5 0.03
229 11 0.07
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (221 bp):
CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
AAACTTTCTCTGAAAAAGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGGTAAACAAATTCTT
CTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
TTGATCCATCAAATGATGAATTCAAA
Found at i:2473178 original size:114 final size:114
Alignment explanation
Indices: 2472973--2473309 Score: 584
Period size: 114 Copynumber: 3.0 Consensus size: 114
2472963 AATCATGATG
* * * ** *
2472973 TTCATCTTTCAATTCTAATGATTGGTTTTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
*
2473038 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
2473087 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAAATAACTCAAAGA
1 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
2473152 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
2473201 TTCATCTTTCAAGTCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
*
2473266 ACACTTCCAGAAGATGTTATTGGGTCTCCTTATTTCTACTATGA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGA
2473310 TAACGTGGCA
Statistics
Matches: 212, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 212 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:2484546 original size:15 final size:14
Alignment explanation
Indices: 2484513--2484551 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
2484503 CTCTGACAGA
2484513 AAAAT-AAATAATG
1 AAAATAAAATAATG
2484526 -AAATAAAATACATG
1 AAAATAAAATA-ATG
2484540 AAAATAAAATAA
1 AAAATAAAATAA
2484552 AATATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.17
13 5 0.22
14 4 0.17
15 10 0.43
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (14 bp):
AAAATAAAATAATG
Found at i:2484573 original size:17 final size:17
Alignment explanation
Indices: 2484513--2484576 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
2484503 CTCTGACAGA
*
2484513 AAAATA-AATAATGAAAT
1 AAAATATAA-AATAAAAT
2484530 AAAATACATGAAAATAAAAT
1 AAAAT--AT-AAAATAAAAT
2484550 AAAATATAAAA-AAAAT
1 AAAATATAAAATAAAAT
*
2484566 ATACATATAAA
1 A-AAATATAAA
2484577 TATTACGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 6 0.15
17 17 0.43
18 2 0.05
19 1 0.03
20 12 0.30
21 2 0.05
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAATATAAAATAAAAT
Found at i:2485222 original size:11 final size:12
Alignment explanation
Indices: 2485201--2485233 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2485191 AATAAATATT
2485201 ATAATAATTTAA
1 ATAATAATTTAA
2485213 ATAA-AATTTAA
1 ATAATAATTTAA
*
2485224 ATTATAATTT
1 ATAATAATTT
2485234 TTTTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAATAATTTAA
Found at i:2486750 original size:3 final size:3
Alignment explanation
Indices: 2486744--2486801 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
2486734 TAATATTTAT
* *
2486744 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2486791 T-A TAAA TAA TA
1 TAA T-AA TAA TA
2486802 TTTAAATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 42 0.88
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2487353 original size:37 final size:37
Alignment explanation
Indices: 2487311--2487382 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
2487301 AGAAATCTGT
*
2487311 GACGCATTATTTGGCATGGCTCCTCTCAAATCTCCAG
1 GACGCATTATTTGACATGGCTCCTCTCAAATCTCCAG
2487348 GACGCATTATTTGACATGGCTCCTCTCAAATCTCC
1 GACGCATTATTTGACATGGCTCCTCTCAAATCTCC
2487383 GGGAATTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (37 bp):
GACGCATTATTTGACATGGCTCCTCTCAAATCTCCAG
Found at i:2492798 original size:2 final size:2
Alignment explanation
Indices: 2492791--2492824 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2492781 ATCCTATCTT
2492791 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2492825 AGTAATTGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2493049 original size:13 final size:13
Alignment explanation
Indices: 2493019--2493047 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2493009 AATAGACATC
2493019 AAAATTTTATAAG
1 AAAATTTTATAAG
2493032 AAAATTTTA-AAG
1 AAAATTTTATAAG
2493044 AAAA
1 AAAA
2493048 ATCACGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
AAAATTTTATAAG
Found at i:2496878 original size:35 final size:35
Alignment explanation
Indices: 2496784--2496911 Score: 159
Period size: 35 Copynumber: 3.6 Consensus size: 35
2496774 GTTTAGCTCT
*
2496784 GATCAAGCTGGTAATTCCTTATATAGGTTCAAC-TC
1 GATC-AGCTAGTAATTCCTTATATAGGTTCAACATC
* *
2496819 TGATCAAGCTAGCAATTCTTTATATAGGTTCAACATC
1 -GATC-AGCTAGTAATTCCTTATATAGGTTCAACATC
* * * *
2496856 GATCGGTTAGTAATTCCTTATATAGGTTCAGCACC
1 GATCAGCTAGTAATTCCTTATATAGGTTCAACATC
2496891 GATCAGCTAGTAATTCCTTAT
1 GATCAGCTAGTAATTCCTTAT
2496912 GGATCTAAGG
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
35 44 0.55
36 34 0.43
37 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (35 bp):
GATCAGCTAGTAATTCCTTATATAGGTTCAACATC
Found at i:2499043 original size:2 final size:2
Alignment explanation
Indices: 2499036--2499068 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2499026 AATACACTAA
2499036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2499069 CAACACCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2499383 original size:17 final size:18
Alignment explanation
Indices: 2499361--2499401 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2499351 TACCCAAAAG
*
2499361 ATTTAATA-TAAAAGCTA
1 ATTTAATACTAAAACCTA
2499378 ATTTAA-ACTAAAACCTA
1 ATTTAATACTAAAACCTA
*
2499395 ATCTAAT
1 ATTTAAT
2499402 TGTAAACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (18 bp):
ATTTAATACTAAAACCTA
Found at i:2502006 original size:329 final size:328
Alignment explanation
Indices: 2501343--2502304 Score: 1335
Period size: 329 Copynumber: 2.9 Consensus size: 328
2501333 AAACATGTGT
* * * * **
2501343 GCTCCCT-ATTCTTTCAGAGAGTGTAGCACTCG-ATCAATCTTCGATC-AACGGGTTTGCTCCC-
1 GCTCCCTCTTTCTTTCAGA-AGTATAGAACTCGAAT-AATCTTCTA-CAAACGGGTTCACTCCCT
* * * * *
2501404 CATT-TTTCAGGGAGTATAGAACTCGAACATTTTCTTCAAACGGGTTCACTCCCTCTTTCTCTAG
63 CTTTCTTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCATCTTTCTCTAG
2501468 GGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAA
128 GGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAA
*
2501533 CTCGAACATCTTCTTCTTACGAGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATC
193 CTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATC
* * * *
2501598 TTCTGCAAACGGGTTCGCTCCCTCTTTCATTAGGAAGTATAGAACTCGAATAATCTTCTGCAAAC
258 TTCTGCAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCAAATAATCTTCTGCAAAC
2501663 GGGTTC
323 GGGTTC
2501669 GCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTACAAACGGGTTCACTCCCTCT
1 GCTCCCTCTTTCTTTCA-GAAGTATAGAACTCGAATAATCTTCTACAAACGGGTTCACTCCCTCT
*
2501734 TTCTTTCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCATCTTTCTCTAGGG
65 TTCTTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCATCTTTCTCTAGGG
*
2501799 AGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGCATGGAACT
130 AGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACT
* * *
2501864 GGAACATCTTCTTCTTACGGGTTCGTTCCCTCTTTCTCTAGGGAGTATAGAACTCAAATAATCTT
195 CGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTT
*
2501929 CTGCAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCAAATAATCTTCTGCAAATGG
260 CTGCAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCAAATAATCTTCTGCAAACGG
2501994 GTTC
325 GTTC
*
2501998 GCTCCCTCTTTCTTTCAGAAGTATAGAACTCGAATAATCTTCTGCAAACGGGTTCACTCCCTCTT
1 GCTCCCTCTTTCTTTCAGAAGTATAGAACTCGAATAATCTTCTACAAACGGGTTCACTCCCTCTT
* * * * * *
2502063 TCTTTCAGGAAGTATAGAACTCGAATAATCTTATGCAAATGGGTTCGCTCCTTCTTTCTTTCAGG
66 TCTTTCAGGAAGTATAGAACTCGAA-CATCTTCTTCAAACGGGTTCGCTCCATCTTTCTCT-AGG
* * ** * * * *
2502128 AAGTATAGAACTCAAATAATCTTCTGCAAACGGGTTCTCTCCCTCTTTCTTTCA-GGAGTATGGA
129 GAGTATGGAACTCGGA-CATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* * * * * *
2502192 ACTTGAATAATCTTCATCTTACGGGTTCACTCCCTCTTTCTCTAGGGAGTATAGAACTTGAA-CA
192 ACTCGAA-CATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAA
* ** * ** * *
2502256 TCTTCTTCTTATGGGTTTTCTCCCTCTTTCTCTAGGGAGTATGGAACTC
256 TCTTCTGCAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTC
2502305 GAACATCTTC
Statistics
Matches: 570, Mismatches: 55, Indels: 17
0.89 0.09 0.03
Matches are distributed among these distances:
326 8 0.01
327 40 0.07
328 78 0.14
329 292 0.51
330 15 0.03
331 88 0.15
332 49 0.09
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (328 bp):
GCTCCCTCTTTCTTTCAGAAGTATAGAACTCGAATAATCTTCTACAAACGGGTTCACTCCCTCTT
TCTTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCATCTTTCTCTAGGGA
GTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTC
TGCAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCAAATAATCTTCTGCAAACGGG
TTC
Found at i:2502319 original size:54 final size:55
Alignment explanation
Indices: 2501389--2502317 Score: 1038
Period size: 55 Copynumber: 17.0 Consensus size: 55
2501379 ATCTTCGATC
* * * *
2501389 AACGGGTTTGCTCCC-CATTTTTC-AGGGAGTATAGAACTCGAA-CATTTTCTTCA
1 AACGGGTTCGCTCCCTC-TTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * *
2501442 AACGGGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCGGA-CATCTTCTTCA
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* * *
2501496 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAA-CATCTTCTTCT
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* * *
2501550 TACGAGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTGCA
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* *
2501605 AACGGGTTCGCTCCCTCTTTCAT-TAGGAAGTATAGAACTCGAATAATCTTCTGCA
1 AACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* * *
2501660 AACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTACA
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * * *
2501716 AACGGGTTCACTCCCTCTTTCTTTCAGGAAGTATAGAACTCGGA-CATCTTCTTCA
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * *
2501771 AACGGGTTCGCTCCATCTTTCTCTAGGGAGTATGGAACTCGGA-CATCTTCTTCA
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * * *
2501825 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGCATGGAACTGGAA-CATCTTCTTCT
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * *
2501879 TACGGGTTCGTTCCCTCTTTCTCTAGGGAGTATAGAACTCAAATAATCTTCTGCA
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * *
2501934 AACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCAAATAATCTTCTGCA
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * *
2501989 AATGGGTTCGCTCCCTCTTTCTTTCA-GAAGTATAGAACTCGAATAATCTTCTGCA
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * * *
2502044 AACGGGTTCACTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTATGCA
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * * * *
2502100 AATGGGTTCGCTCCTTCTTTCTTTCAGGAAGTATAGAACTCAAATAATCTTCTGCA
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * * * *
2502156 AACGGGTTCTCTCCCTCTTTCTTTCA-GGAGTATGGAACTTGAATAATCTTCATCT
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAATAATCTTCTTCA
* * * * *
2502211 TACGGGTTCACTCCCTCTTTCTCTAGGGAGTATAGAACTTGAA-CATCTTCTTCT
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
* * ** * *
2502265 TATGGGTTTTCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAA-CATCTTCTTC
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTC
2502318 TTCTTCACTA
Statistics
Matches: 787, Mismatches: 79, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
53 18 0.02
54 292 0.37
55 301 0.38
56 176 0.22
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (55 bp):
AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCTTCTTCA
Found at i:2502516 original size:31 final size:31
Alignment explanation
Indices: 2502481--2502543 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
2502471 TACTCTTCGG
2502481 TGAAGGCTTAAGATAGATTTGCTTCACTACT
1 TGAAGGCTTAAGATAGATTTGCTTCACTACT
*
2502512 TGAAGGCTTAAGATGGATTTGCTTCACTACT
1 TGAAGGCTTAAGATAGATTTGCTTCACTACT
2502543 T
1 T
2502544 TTTAGTGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (31 bp):
TGAAGGCTTAAGATAGATTTGCTTCACTACT
Found at i:2502562 original size:37 final size:37
Alignment explanation
Indices: 2502320--2502684 Score: 238
Period size: 36 Copynumber: 10.0 Consensus size: 37
2502310 TCTTCTTCTT
* * * * *
2502320 CTTCACTATTTCTTCGGTGAATGCTTAAGATAG-TTTA
1 CTTCACTA-CTCTTCAGTGAAGGCTTAAGATGGATTTG
* * * * *
2502357 CTTCACTATTCTCCAATAAAGGCTTAAAATGG-TTTG
1 CTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTG
* * *
2502393 CTTCACTACTCTCCGGTGAAGGCTTAAGATGGA-TTA
1 CTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTG
* * * *
2502429 CCTCACTACTCTT-AGGTGAAGGCTTAGGATAGA-TCG
1 CTTCACTACTCTTCA-GTGAAGGCTTAAGATGGATTTG
* *
2502465 CTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTG
1 CTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTG
2502502 CTTCACTA--C-T---TGAAGGCTTAAGATGGATTTG
1 CTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTG
* * * **
2502533 CTTCACTACTTTTTAGTGAAGGCTTAAGATGTCCCAAATG
1 CTTCACTACTCTTCAGTGAAGGCTTAAGATG---GATTTG
* * *
2502573 ACTT-A--A-TCATCATTGTCGGAAGGCTTACTGATGAATTTG
1 -CTTCACTACTCTTCA--GT--GAAGGCTTA-AGATGGATTTG
* * *
2502612 CTTCACTACTCTTCAGTGAAAGCTTAATATTGATTTG
1 CTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTG
* *
2502649 CTTCGCTACTCTTCAGTGAAGGCTTAAGATTGATTT
1 CTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTT
2502685 TCTCCAGTTT
Statistics
Matches: 259, Mismatches: 46, Indels: 46
0.74 0.13 0.13
Matches are distributed among these distances:
31 28 0.11
34 2 0.01
35 1 0.00
36 106 0.41
37 76 0.29
38 12 0.05
39 6 0.02
40 6 0.02
41 13 0.05
42 9 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (37 bp):
CTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTTG
Found at i:2503532 original size:16 final size:18
Alignment explanation
Indices: 2503505--2503539 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2503495 ACCTCCACTG
2503505 TCACTGCTTCAT-CATTT
1 TCACTGCTTCATACATTT
2503522 TCACT-CTTCATACATTT
1 TCACTGCTTCATACATTT
2503539 T
1 T
2503540 TATCCCATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.20, C:0.29, G:0.03, T:0.49
Consensus pattern (18 bp):
TCACTGCTTCATACATTT
Found at i:2504753 original size:40 final size:39
Alignment explanation
Indices: 2504684--2504759 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
2504674 TATTTAGATA
*
2504684 AACTTTATTTAATTTGCCATTTTCTGGCTAGCTGAAATT
1 AACTTTATTTAATTTGCCATTTTCGGGCTAGCTGAAATT
*
2504723 AACTTTATTGTAATTTTCC-TTTATCGGGCTAGCTGAA
1 AACTTTATT-TAATTTGCCATTT-TCGGGCTAGCTGAA
2504760 GAGTTCATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 12 0.36
40 21 0.64
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (39 bp):
AACTTTATTTAATTTGCCATTTTCGGGCTAGCTGAAATT
Found at i:2504944 original size:2 final size:2
Alignment explanation
Indices: 2504928--2504981 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
2504918 ATCTTTATTG
*
2504928 TA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2504969 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
2504982 TGTTGGGTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2509675 original size:2 final size:2
Alignment explanation
Indices: 2509668--2509696 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2509658 AATACACTAA
2509668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2509697 CAACACCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2510011 original size:17 final size:18
Alignment explanation
Indices: 2509989--2510029 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2509979 TACCCAAAAG
*
2509989 ATTTAATA-TAAAAGCTA
1 ATTTAATACTAAAACCTA
2510006 ATTTAA-ACTAAAACCTA
1 ATTTAATACTAAAACCTA
*
2510023 ATCTAAT
1 ATTTAAT
2510030 TGTAAACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (18 bp):
ATTTAATACTAAAACCTA
Found at i:2514287 original size:43 final size:43
Alignment explanation
Indices: 2514234--2514431 Score: 236
Period size: 43 Copynumber: 4.6 Consensus size: 43
2514224 AGGGAAATGG
* *
2514234 TAAGGTCTTACCCTTGTACATAGCAAAGGAGCCTGGGGAAACTA
1 TAAGG-CTTACCCTTGCACATAGCAAAGGAACCTGGGGAAACTA
* * * * *
2514278 TAAGGCTTACTCTTGCACACAGCAAAAGAACATGGGGAAACTG
1 TAAGGCTTACCCTTGCACATAGCAAAGGAACCTGGGGAAACTA
*
2514321 TAAGGCTTACCCTTGCACATAGAAAAGGAACCTGGGGAAACTA
1 TAAGGCTTACCCTTGCACATAGCAAAGGAACCTGGGGAAACTA
* * ** * *
2514364 TAAGGCTTACCCTTACACACAGCAAAGGAACCTACGGTAA-TGG
1 TAAGGCTTACCCTTGCACATAGCAAAGGAACCTGGGGAAACT-A
2514407 TAAGGACTTACCCTTGCACATAGCA
1 TAAGG-CTTACCCTTGCACATAGCA
2514432 GAGCAGCCTG
Statistics
Matches: 130, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.01
43 107 0.82
44 22 0.17
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACATAGCAAAGGAACCTGGGGAAACTA
Found at i:2514355 original size:86 final size:87
Alignment explanation
Indices: 2514224--2514429 Score: 290
Period size: 86 Copynumber: 2.4 Consensus size: 87
2514214 CAAATGAGAC
* * * * *
2514224 AGGGAAATGGTAAGGTCTTACCCTTGTACATAGCAAAGGAGCCTGGGGAAACTATAAGGCTTACT
1 AGGGAAATGGTAAGGACTTACCCTTGCACATAGAAAAGGAACCTGGGGAAACTATAAGGCTTACC
*
2514289 CTTGCACACAGCAAAAGAACAT
66 CTTACACACAGCAAAAGAACAT
*
2514311 GGGGAAACT-GTAAGG-CTTACCCTTGCACATAGAAAAGGAACCTGGGGAAACTATAAGGCTTAC
1 AGGGAAA-TGGTAAGGACTTACCCTTGCACATAGAAAAGGAACCTGGGGAAACTATAAGGCTTAC
* *
2514374 CCTTACACACAGCAAAGGAACCT
65 CCTTACACACAGCAAAAGAACAT
* *
2514397 ACGGTAATGGTAAGGACTTACCCTTGCACATAG
1 AGGGAAATGGTAAGGACTTACCCTTGCACATAG
2514430 CAGAGCAGCC
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
85 1 0.01
86 74 0.70
87 29 0.28
88 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (87 bp):
AGGGAAATGGTAAGGACTTACCCTTGCACATAGAAAAGGAACCTGGGGAAACTATAAGGCTTACC
CTTACACACAGCAAAAGAACAT
Found at i:2515834 original size:27 final size:27
Alignment explanation
Indices: 2515804--2515868 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
2515794 TTTAGGCAAA
2515804 TTTACACTTTACAAACATTTTGGTCAT
1 TTTACACTTTACAAACATTTTGGTCAT
* *****
2515831 TTTACAATTTAGGGGTATTTTGGTCAT
1 TTTACACTTTACAAACATTTTGGTCAT
2515858 TTTACACTTTA
1 TTTACACTTTA
2515869 GGGTATTTCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (27 bp):
TTTACACTTTACAAACATTTTGGTCAT
Found at i:2515869 original size:27 final size:26
Alignment explanation
Indices: 2515820--2515876 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 26
2515810 CTTTACAAAC
2515820 ATTTTGGTCATTTTACAATTTAGGGGT
1 ATTTTGGTCATTTTACAATTTA-GGGT
*
2515847 ATTTTGGTCATTTTACACTTTAGGGT
1 ATTTTGGTCATTTTACAATTTAGGGT
2515873 ATTT
1 ATTT
2515877 CTATAATTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (26 bp):
ATTTTGGTCATTTTACAATTTAGGGT
Found at i:2515985 original size:17 final size:17
Alignment explanation
Indices: 2515948--2515985 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2515938 GTATAAGTTC
*
2515948 TCATGTCATCTCTATTA
1 TCATGTCATCTATATTA
2515965 TCATAGTCATCTATATT-
1 TCAT-GTCATCTATATTA
2515982 TCAT
1 TCAT
2515986 TTTACTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (17 bp):
TCATGTCATCTATATTA
Found at i:2519463 original size:7 final size:7
Alignment explanation
Indices: 2519451--2519484 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2519441 GTTCGAACTG
2519451 AATTTTT
1 AATTTTT
2519458 AATTTTT
1 AATTTTT
*
2519465 AA-TTTA
1 AATTTTT
2519471 AATTTTT
1 AATTTTT
2519478 AATTTTT
1 AATTTTT
2519485 GCATTTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:2519476 original size:13 final size:13
Alignment explanation
Indices: 2519458--2519482 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2519448 CTGAATTTTT
2519458 AATTTTTAATTTA
1 AATTTTTAATTTA
2519471 AATTTTTAATTT
1 AATTTTTAATTT
2519483 TTGCATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTTTAATTTA
Found at i:2522497 original size:43 final size:43
Alignment explanation
Indices: 2522436--2522519 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
2522426 TGAAGGGGTC
*
2522436 ATCCACGATTTCAACTCCACGACAGAGGATATCGTTCCCACGG
1 ATCCACGATTTCAACTCCACAACAGAGGATATCGTTCCCACGG
*
2522479 ATCCACGATTTCAACTCCACAACGGAGGATATCGTTCCCAC
1 ATCCACGATTTCAACTCCACAACAGAGGATATCGTTCCCAC
2522520 ACAACCATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACAACAGAGGATATCGTTCCCACGG
Found at i:2522536 original size:43 final size:43
Alignment explanation
Indices: 2522438--2522556 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 43
2522428 AAGGGGTCAT
* * * ** *
2522438 CCACGATTTCAACTCCACGACAGAGGATATCGTTCCCACGGAT
1 CCACGATCTCAACTCCACAACGGAGGATATCGTTCCCACACAA
*
2522481 CCACGATTTCAACTCCACAACGGAGGATATCGTTCCCACACAA
1 CCACGATCTCAACTCCACAACGGAGGATATCGTTCCCACACAA
* * * *
2522524 CCATGATCTCAACTTCACAACGAAGTATATCGT
1 CCACGATCTCAACTCCACAACGGAGGATATCGT
2522557 GCCAACTCTA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.31, C:0.32, G:0.15, T:0.22
Consensus pattern (43 bp):
CCACGATCTCAACTCCACAACGGAGGATATCGTTCCCACACAA
Found at i:2522937 original size:124 final size:124
Alignment explanation
Indices: 2522699--2522941 Score: 301
Period size: 124 Copynumber: 2.0 Consensus size: 124
2522689 CAGTACAAGC
* * * * *
2522699 TTGGATTTTAACTTCCCGACGAAGGATATTCAAGTCAAGGCTCAACTTAACGACAAATGGTCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTAACAACAAATGGGCCAT
* * ** *
2522764 CCACGGTTTCAACTTCACGACGAAGGGAATTGTGTACACGAACAGCATTCATCTCTAGA
66 CCACGGATTCAACTTCACGACGAAGGGAATCGTACACACGAACAACATTCATCTCTAGA
* * *
2522823 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTAACAACAAATGGGCCAT
* * * *
2522888 CCATGGATTCAACTTCATGACG-AGCGGAATCGTACCCATC-AGCAACATTCATCT
66 CCACGGATTCAACTTCACGACGAAG-GGAATCGTACACA-CGAACAACATTCATCT
2522942 TCAAGAACAA
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
123 2 0.02
124 97 0.97
125 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTAACAACAAATGGGCCAT
CCACGGATTCAACTTCACGACGAAGGGAATCGTACACACGAACAACATTCATCTCTAGA
Found at i:2523092 original size:36 final size:36
Alignment explanation
Indices: 2523041--2523140 Score: 139
Period size: 36 Copynumber: 2.8 Consensus size: 36
2523031 AGTTTTGTAT
* *
2523041 CTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCA
1 CTCTTGGGACAGTTTCCCTTGAAACAAATTTTATCA
* * *
2523077 CTCTTGGGACTGTTTCCCTTGAAACAAATTTTGTCT
1 CTCTTGGGACAGTTTCCCTTGAAACAAATTTTATCA
2523113 CTC-TGGAGACAGTTTCCCTTGAAACAAA
1 CTCTTGG-GACAGTTTCCCTTGAAACAAA
2523141 ATCTTTGAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 3 0.05
36 54 0.95
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (36 bp):
CTCTTGGGACAGTTTCCCTTGAAACAAATTTTATCA
Found at i:2523163 original size:65 final size:65
Alignment explanation
Indices: 2523033--2523193 Score: 180
Period size: 65 Copynumber: 2.4 Consensus size: 65
2523023 CAAAACATAG
* * * *
2523033 TTTTGTATCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCACTCTTGGGA-CTGTTTCCCTT
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA----AT--CT-TT-GAATCTGTTTTCCTT
2523097 GAAACAAA
58 GAAACAAA
*
2523105 TTTTGTCTCTCTGGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAA
* *
2523170 TTTTGTCTCCCTTAAGACAGTTTC
1 TTTTGTCTCTCTTGAGACAGTTTC
2523194 TTTTGGAACT
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
64 2 0.03
65 41 0.51
66 2 0.03
68 2 0.03
72 33 0.41
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.40
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAA
Found at i:2523258 original size:99 final size:100
Alignment explanation
Indices: 2523053--2523404 Score: 467
Period size: 99 Copynumber: 3.5 Consensus size: 100
2523043 CTTGAGACAG
* * * * * ** * *
2523053 TTTCTCTTGAAACAAATTTTATCACTCTTGGGACTGTTTCCCTTGAAAC-AAATTTTGTCTCTCT
1 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
*
2523117 GGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
65 -GAGACAG-TTCCCTTGAAACAAAATCTTTGAAGCTGT
*
2523155 TTTCCTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCAT
1 TTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC-T
2523220 GAGACAG-TCCCTTGAAAC-AAATCTTTGAAGCTGT
65 GAGACAGTTCCCTTGAAACAAAATCTTTGAAGCTGT
*
2523254 TTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTATGTTTTGTCTCTCTT
1 TTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC-T
*
2523319 GAGACAGTTTCCCTTGAAACAAAATCTTTGAAGCTAT
65 GAGACAG-TTCCCTTGAAACAAAATCTTTGAAGCTGT
* * * *
2523356 TTTCCTTTAAAAAAAATTTGTCTCCCTTGAGACAATTTTCTTTTGGAAC
1 TTTCCTTGAAACAAATTTTGTCTCCCTTGAGAC-AGTTTCTTTTGGAAC
2523405 AAAAATCTTT
Statistics
Matches: 225, Mismatches: 19, Indels: 11
0.88 0.07 0.04
Matches are distributed among these distances:
99 84 0.37
100 11 0.05
101 46 0.20
102 69 0.31
103 15 0.07
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (100 bp):
TTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTG
AGACAGTTCCCTTGAAACAAAATCTTTGAAGCTGT
Found at i:2523423 original size:67 final size:65
Alignment explanation
Indices: 2523307--2523535 Score: 262
Period size: 65 Copynumber: 3.5 Consensus size: 65
2523297 GGAACTATGT
*
2523307 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAGCTATTTTCCTTTAAAAAAAA
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTATTTTCCTTTAAAAAAAA
* * ** * * * *
2523372 TTTGTCTCCCTTGAGACAATTTTCTTTTGGAACAAAAATCTTTGAATCTATTTCCCTTGAAACAA
1 TTTGTCTCTCTTGAGAC-AGTTTCCCTTGAAAC-AAAATCTTTGAATCTATTTTCCTTTAAAAAA
*
2523437 AT
64 AA
* * * *
2523439 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCATT-AAACAAA
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTATTTTCCTTTAAAAAAAA
* * * *
2523503 TTCCGTCTCACTCGAGACAGTTTCTCTTGAAAC
1 TT-TGTCTCTCTTGAGACAGTTTCCCTTGAAAC
2523536 GCAAAAAAAA
Statistics
Matches: 134, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
64 6 0.04
65 62 0.46
66 22 0.16
67 44 0.33
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (65 bp):
TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTATTTTCCTTTAAAAAAAA
Found at i:2525033 original size:7 final size:7
Alignment explanation
Indices: 2525021--2525053 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2525011 GTTCGAACCG
2525021 AATTTTT
1 AATTTTT
2525028 AATTTTT
1 AATTTTT
2525035 AA-TTTT
1 AATTTTT
2525041 AA-TTTT
1 AATTTTT
2525047 AATTTTT
1 AATTTTT
2525054 GCATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
AATTTTT
Found at i:2529780 original size:24 final size:24
Alignment explanation
Indices: 2529752--2529806 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
2529742 TTCTTAATAG
*
2529752 ATGTGTTTACATGAATGATATAAT
1 ATGTGTTTACATGAATGAGATAAT
2529776 ATGTGTTTACATGAATGAGATAAT
1 ATGTGTTTACATGAATGAGATAAT
2529800 ATGTGTT
1 ATGTGTT
2529807 AAGTATCTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.42
Consensus pattern (24 bp):
ATGTGTTTACATGAATGAGATAAT
Found at i:2529898 original size:15 final size:14
Alignment explanation
Indices: 2529880--2529946 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 14
2529870 GTGTTTAGTA
2529880 TATATGTTTACTGAT
1 TATATGTTT-CTGAT
*
2529895 TATATATGTTCTGAT
1 TATATGT-TTCTGAT
2529910 TAGATATG-TTCTGAT
1 T--ATATGTTTCTGAT
*
2529925 AATATGTTTACTGAT
1 TATATGTTT-CTGAT
*
2529940 TGTATGT
1 TATATGT
2529947 GTTTAGTCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
13 5 0.12
14 2 0.05
15 29 0.69
16 2 0.05
17 4 0.10
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (14 bp):
TATATGTTTCTGAT
Found at i:2529931 original size:13 final size:15
Alignment explanation
Indices: 2529890--2529932 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
2529880 TATATGTTTA
*
2529890 CTGATTATATATGTT
1 CTGATTAGATATGTT
2529905 CTGATTAGATATGTT
1 CTGATTAGATATGTT
2529920 CTGA-TA-ATATGTT
1 CTGATTAGATATGTT
2529933 TACTGATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 7 0.26
14 2 0.07
15 18 0.67
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (15 bp):
CTGATTAGATATGTT
Found at i:2536207 original size:43 final size:43
Alignment explanation
Indices: 2536160--2536264 Score: 165
Period size: 43 Copynumber: 2.4 Consensus size: 43
2536150 AATAGGTCAC
* * * *
2536160 GAGATTTAGCGGCGTTTTTCCCACAAATGTCGTAATAGGTGTT
1 GAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGATGTT
2536203 GAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGATGTT
1 GAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGATGTT
*
2536246 GAGATTTAGCGGCATTTTT
1 GAGATTTAGCGGCGTTTTT
2536265 GGATACAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (43 bp):
GAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGATGTT
Found at i:2536305 original size:86 final size:85
Alignment explanation
Indices: 2536209--2536450 Score: 281
Period size: 86 Copynumber: 2.8 Consensus size: 85
2536199 TGTTGAGATT
*
2536209 TAGCGGCGTTTTTCCCACAAACGCCGCAATAGATGTTGAGAT-T-TAGCGGCATTTTTGGATACA
1 TAGCGACGTTTTTCCCACAAACGCCGCAA-A-ATGTT-AGATCTATAGCGGCATTTTTGGATACA
*
2536272 AATGCCGCAAAAGGTCAGATCTA
63 AACGCCGCAAAAGGTCAGATCTA
* *** * * *
2536295 TTGCGACGTTTTTGTATATAAATGCCGCAAAAGGTTAGATCTATAGCGGCATTTTTGGATACAAA
1 TAGCGACGTTTTT-CCCACAAACGCCGCAAAATGTTAGATCTATAGCGGCATTTTTGGATACAAA
* *
2536360 CGCCACAAAAGGTTAGATCTA
65 CGCCGCAAAAGGTCAGATCTA
* * * * * *
2536381 TAGTGGCGTTTTTCCCTCAAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTAGATACAAAC
1 TAGCGACGTTTTTCCCACAAACGCCGCAAAATGTTAGATCTATAGCGGCATTTTTGGATACAAAC
2536446 GCCGC
66 GCCGC
2536451 TAATTACCAT
Statistics
Matches: 128, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
84 4 0.03
85 51 0.40
86 62 0.48
87 11 0.09
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (85 bp):
TAGCGACGTTTTTCCCACAAACGCCGCAAAATGTTAGATCTATAGCGGCATTTTTGGATACAAAC
GCCGCAAAAGGTCAGATCTA
Found at i:2536318 original size:43 final size:43
Alignment explanation
Indices: 2536252--2536450 Score: 238
Period size: 43 Copynumber: 4.7 Consensus size: 43
2536242 TGTTGAGATT
* *
2536252 TAGCGGCATTTTTGGATACAAATGCCGCAAAAGGTCAGATCTA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
* * * * * *
2536295 TTGCGACGTTTTTGTATATAAATGCCGCAAAAGGTTAGATCTA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
* * *
2536338 TAGCGGCATTTTTGGATACAAACGCCACAAAAGGTTAGATCTA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
* *** *
2536381 TAGTGGCGTTTTTCCCT-CAAACGCCGCAAAATGTCAGATCTA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
*
2536423 TAGCGGCGTTTTTAGATACAAACGCCGC
1 TAGCGGCGTTTTTGGATACAAACGCCGC
2536451 TAATTACCAT
Statistics
Matches: 130, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 35 0.27
43 95 0.73
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTA
Found at i:2536420 original size:42 final size:43
Alignment explanation
Indices: 2536209--2536450 Score: 222
Period size: 43 Copynumber: 5.7 Consensus size: 43
2536199 TGTTGAGATT
* *
2536209 TAGCGGCGTTTTTCC-CACAAACGCCGCAATAGATGTTGAGAT-T-
1 TAGCGGCGTTTTTCCATACAAACGCCGCAA-A-AGGTT-AGATCTA
* ** * *
2536252 TAGCGGCATTTTTGGATACAAATGCCGCAAAAGGTCAGATCTA
1 TAGCGGCGTTTTTCCATACAAACGCCGCAAAAGGTTAGATCTA
* * ** * *
2536295 TTGCGACGTTTTTGTATATAAATGCCGCAAAAGGTTAGATCTA
1 TAGCGGCGTTTTTCCATACAAACGCCGCAAAAGGTTAGATCTA
* ** *
2536338 TAGCGGCATTTTTGGATACAAACGCCACAAAAGGTTAGATCTA
1 TAGCGGCGTTTTTCCATACAAACGCCGCAAAAGGTTAGATCTA
* * * *
2536381 TAGTGGCGTTTTTCCCT-CAAACGCCGCAAAATGTCAGATCTA
1 TAGCGGCGTTTTTCCATACAAACGCCGCAAAAGGTTAGATCTA
**
2536423 TAGCGGCGTTTTTAGATACAAACGCCGC
1 TAGCGGCGTTTTTCCATACAAACGCCGC
2536451 TAATTACCAT
Statistics
Matches: 163, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
41 4 0.02
42 39 0.24
43 108 0.66
44 12 0.07
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTTTCCATACAAACGCCGCAAAAGGTTAGATCTA
Found at i:2539510 original size:41 final size:40
Alignment explanation
Indices: 2539447--2539983 Score: 336
Period size: 41 Copynumber: 13.3 Consensus size: 40
2539437 CGGCGTTTGT
* **
2539447 GCCACTAAAGTACTAGTCTATAGCGGCGTAAGTATATAAAC
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGTATATAAAC
* * * *
2539488 GCCACTAAAGTACAAGCGTATAGTGACGTTTGTATAAAAAT
1 GCCACTAAAGTACAAGC-TATAGCGGCGTTTGTATATAAAC
* * * *
2539529 GCCACTAAAGTATAAGTGTATAACGACGTTTGTATATAAAC
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGTATATAAAC
* * * * * *
2539570 GCCACTAAAGTACGAGTCTTTAGTGGCGTTTCTAAACACAAAC
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGT--ATATAAAC
*
2539613 GCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATA-AAA-
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGTATATAAAC
*
2539652 GCGGACTTTAAAATTGTA-AA-CT-T-GCGGCGTTTG----T----
1 GC-CAC--T-AAA--GTACAAGCTATAGCGGCGTTTGTATATAAAC
* **
2539686 GCCACTAAAGTACTAGTCTATAGCGGCGTAAGTATATAAAC
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGTATATAAAC
* * *
2539727 GCCACTAAAGTACAAGCGTATAGTGACGTTTGTATA-AAAT
1 GCCACTAAAGTACAAGC-TATAGCGGCGTTTGTATATAAAC
* * * *
2539767 GCCACTAAAGTATAAGTGTATAACGACGTTTGTATATAAAC
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGTATATAAAC
* * * * * *
2539808 GCCACTAAAGTACGAGTCTTTAGTGGCGTTTCTAAACACAAAC
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGT--ATATAAAC
* *
2539851 GCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAAAC
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGTATATAAAC
* * * ** *
2539892 GCAACTAAAGTACTAGTCTTTAGCTTCGTTTGTATAAAAAC
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGTATATAAAC
** *
2539933 GCCACTAAAGTACGTGTCTTTAGCGGCG-TTGTATA-AAAC
1 GCCACTAAAGTACAAG-CTATAGCGGCGTTTGTATATAAAC
2539972 GCCACT-AAGTAC
1 GCCACTAAAGTAC
2539984 GAACTTTGCG
Statistics
Matches: 393, Mismatches: 74, Indels: 61
0.74 0.14 0.12
Matches are distributed among these distances:
28 3 0.01
29 1 0.00
30 3 0.01
31 3 0.01
32 1 0.00
33 10 0.03
34 2 0.01
37 1 0.00
38 6 0.02
39 12 0.03
40 58 0.15
41 215 0.55
42 2 0.01
43 71 0.18
44 2 0.01
45 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (40 bp):
GCCACTAAAGTACAAGCTATAGCGGCGTTTGTATATAAAC
Found at i:2539873 original size:238 final size:239
Alignment explanation
Indices: 2539415--2539889 Score: 943
Period size: 238 Copynumber: 2.0 Consensus size: 239
2539405 AAACTGCGCG
2539415 GGACTTTAAAATTGTAAACTTGCGGCGTTTGTGCCACTAAAGTACTAGTCTATAGCGGCGTAAGT
1 GGACTTTAAAATTGTAAACTTGCGGCGTTTGTGCCACTAAAGTACTAGTCTATAGCGGCGTAAGT
2539480 ATATAAACGCCACTAAAGTACAAGCGTATAGTGACGTTTGTATAAAAATGCCACTAAAGTATAAG
66 ATATAAACGCCACTAAAGTACAAGCGTATAGTGACGTTTGTATAAAAATGCCACTAAAGTATAAG
2539545 TGTATAACGACGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGTGGCGTTTCTAAACACA
131 TGTATAACGACGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGTGGCGTTTCTAAACACA
2539610 AACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAAGC
196 AACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAAGC
2539654 GGACTTTAAAATTGTAAACTTGCGGCGTTTGTGCCACTAAAGTACTAGTCTATAGCGGCGTAAGT
1 GGACTTTAAAATTGTAAACTTGCGGCGTTTGTGCCACTAAAGTACTAGTCTATAGCGGCGTAAGT
2539719 ATATAAACGCCACTAAAGTACAAGCGTATAGTGACGTTTGTAT-AAAATGCCACTAAAGTATAAG
66 ATATAAACGCCACTAAAGTACAAGCGTATAGTGACGTTTGTATAAAAATGCCACTAAAGTATAAG
2539783 TGTATAACGACGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGTGGCGTTTCTAAACACA
131 TGTATAACGACGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGTGGCGTTTCTAAACACA
2539848 AACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAA
196 AACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAA
2539890 ACGCAACTAA
Statistics
Matches: 236, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
238 128 0.54
239 108 0.46
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (239 bp):
GGACTTTAAAATTGTAAACTTGCGGCGTTTGTGCCACTAAAGTACTAGTCTATAGCGGCGTAAGT
ATATAAACGCCACTAAAGTACAAGCGTATAGTGACGTTTGTATAAAAATGCCACTAAAGTATAAG
TGTATAACGACGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGTGGCGTTTCTAAACACA
AACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAAGC
Found at i:2539952 original size:125 final size:124
Alignment explanation
Indices: 2539484--2539962 Score: 484
Period size: 125 Copynumber: 3.9 Consensus size: 124
2539474 GTAAGTATAT
* * * *
2539484 AAACGCCACTAAAGTACAAGCGTATAGTGACGTTTGTATAAAAATGCCACTAAAGTATAAGTGTA
1 AAACGCCACTAAAGTACAAGCGTATAGCGACGTTTGTAT-AAAACGCAACTAAAGTATAAGTCTA
* *
2539549 TAACGACGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGTGGCGTTTCTAAACAC
65 TAACGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTCTAAACAC
* * * * * *
2539609 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAA-GCGGACTTTAAAATTGTAA-A
1 AAACGCCACTAAAGTACAAGCGTATAGCGACGTTTGTATAAAACGC-AAC--T-AAAGTATAAGT
* * * * *** * *
2539672 CT-T-GCGGCGTTTG--T------GCCACTAAAGTACTAGTCTATAGCGGCGTAAGT--ATAT
62 CTATAACGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTCTAAACAC
* * * *
2539723 AAACGCCACTAAAGTACAAGCGTATAGTGACGTTTGTATAAAATGCCACTAAAGTATAAGTGTAT
1 AAACGCCACTAAAGTACAAGCGTATAGCGACGTTTGTATAAAACGCAACTAAAGTATAAGTCTAT
* *
2539788 AACGACGTTTGTATATAAACGCCACTAAAGTACGAGTCTTTAGTGGCGTTTCTAAACAC
66 AACGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTCTAAACAC
* *
2539847 AAACGCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAAACGCAACTAAAGTACT-AGTCT
1 AAACGCCACTAAAGTACAAGCGTATAGCGACGTTTGTAT-AAAACGCAACTAAAGTA-TAAGTCT
* * ** *
2539911 TTAGCTTCGTTTGTATAAAAACGCCACTAAAGTACGTGTCTTTAGCGGCGTT
64 ATAACGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTT
2539963 GTATAAAACG
Statistics
Matches: 285, Mismatches: 49, Indels: 40
0.76 0.13 0.11
Matches are distributed among these distances:
111 7 0.02
112 2 0.01
113 1 0.00
114 52 0.18
115 2 0.01
116 28 0.10
122 28 0.10
123 2 0.01
124 52 0.18
125 101 0.35
126 3 0.01
127 7 0.02
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (124 bp):
AAACGCCACTAAAGTACAAGCGTATAGCGACGTTTGTATAAAACGCAACTAAAGTATAAGTCTAT
AACGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTCTAAACAC
Found at i:2539967 original size:165 final size:163
Alignment explanation
Indices: 2539686--2539985 Score: 381
Period size: 165 Copynumber: 1.8 Consensus size: 163
2539676 CGGCGTTTGT
* * *
2539686 GCCACTAAAGTACTAGTCTATAGCGGCGTAAGTATATAAACGCCACTAAAGTACAAGCGTATAGT
1 GCCACTAAAGTACAAGTCTATAGCGGCGTAAGTATAAAAACGCAACTAAAGTACAAGCGTATAGT
* * *
2539751 GACGTTTGTATAAAATGCCACTAAAGTATAAGTGTATAACGACGTTTGTATATAAACGCCACTAA
66 GACGTTTGTATAAAACGCCACTAAAGTACAAGTCTATAACGACGTTTGTATA-AAACGCCACT-A
2539816 AGTACGAGTCTTTAGTGGCGTTTCTAAACACAAAC
129 AGTACGAGTCTTTAGTGGCGTTTCTAAACACAAAC
* ** * *
2539851 GCCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAAACGCAACTAAAGTACTAGTC-TTTAG
1 GCCACTAAAGTACAAGTCTATAGCGGCGTAAGTATAAAAACGCAACTAAAGTACAAG-CGTATAG
* ** * * *
2539915 CT-TCGTTTGTATAAAAACGCCACTAAAGTACGTGTCTTTAGCGGCG-TTGTATAAAACGCCACT
65 -TGACGTTTGTAT-AAAACGCCACTAAAGTACAAGTCTATAACGACGTTTGTATAAAACGCCACT
2539978 AAGTACGA
128 AAGTACGA
2539986 ACTTTGCGGT
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
163 8 0.07
164 10 0.09
165 70 0.61
166 27 0.23
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (163 bp):
GCCACTAAAGTACAAGTCTATAGCGGCGTAAGTATAAAAACGCAACTAAAGTACAAGCGTATAGT
GACGTTTGTATAAAACGCCACTAAAGTACAAGTCTATAACGACGTTTGTATAAAACGCCACTAAG
TACGAGTCTTTAGTGGCGTTTCTAAACACAAAC
Found at i:2544587 original size:139 final size:139
Alignment explanation
Indices: 2544171--2544590 Score: 535
Period size: 139 Copynumber: 3.0 Consensus size: 139
2544161 TAACCTATTC
* * **
2544171 AATTTTAATCAATTATTT-ACTCGAATAATTAAAATGGAACCTCGAGAAAAAG-TGAGAACCAAA
1 AATTTTAATCAATTATTTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGCAAAG-ACCAAA
* * * * * *
2544234 TTAAAAGATTCTCCTAAATTTAAAGAATAAGTATGAAATTAAGCATAAAATGGAGGCTCTAATAT
65 TTAAGA-ATTCACCTAAATTTAAGGACTAAATATGAAATTAAGCCTAAAATGGAGGCTCTAATAT
*
2544299 TAGTCCTAATC
129 TAGTCCTAATT
* * * *
2544310 AATTTTAACCAATTATTTGATTCGAATGATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAAT
1 AATTTTAATCAATTATTTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGCAAAGACCAAAT
* * *
2544375 TAAGAATTCCCCTAAATTTAAGGACTAGGAGTA--AAAGTAAGCCTAAAATGGAGGCTCTAATAT
66 TAAGAATTCACCTAAATTTAAGGACTA--AATATGAAATTAAGCCTAAAATGGAGGCTCTAATAT
2544438 TAGTCCTAATT
129 TAGTCCTAATT
* *
2544449 AATTTGAATCAATTATTTGATTCAAATAATTAAAATGGAACCTCGAGCAAAAGCAAAGACCAAAT
1 AATTTTAATCAATTATTTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGCAAAGACCAAAT
* * *
2544514 TAAGAATTCACCTAAATTTAAGGACTAAATTTGAAATT-AGACCTAAAGTGAAGGCTCTAATATT
66 TAAGAATTCACCTAAATTTAAGGACTAAATATGAAATTAAG-CCTAAAATGGAGGCTCTAATATT
**
2544578 AGTTTTAATT
130 AGTCCTAATT
2544588 AAT
1 AAT
2544591 ATTGCAATTC
Statistics
Matches: 246, Mismatches: 28, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
137 2 0.01
138 2 0.01
139 195 0.79
140 42 0.17
141 5 0.02
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (139 bp):
AATTTTAATCAATTATTTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGCAAAGACCAAAT
TAAGAATTCACCTAAATTTAAGGACTAAATATGAAATTAAGCCTAAAATGGAGGCTCTAATATTA
GTCCTAATT
Found at i:2545005 original size:14 final size:14
Alignment explanation
Indices: 2544956--2545008 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
2544946 CTAATTTAAG
*
2544956 ACAAAAATTAAAGTC
1 ACAAAAATTAAA-TA
*
2544971 A-AAAAATTAAATG
1 ACAAAAATTAAATA
* *
2544984 GCACAAATTAAATA
1 ACAAAAATTAAATA
2544998 ACAAAAATTAA
1 ACAAAAATTAA
2545009 GGCAATCGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.21
Consensus pattern (14 bp):
ACAAAAATTAAATA
Found at i:2546413 original size:3 final size:3
Alignment explanation
Indices: 2546405--2546499 Score: 95
Period size: 3 Copynumber: 31.0 Consensus size: 3
2546395 TTTTAAAACT
* * *
2546405 ATA ATA ATA ATAA ATA ATA ATA GTA ATA ATAA ATA ATA ATA ACA ATG
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* *
2546452 GTA A-A A-A ATGA ATA ATA ATA ATA ATA ATA ATAA ATA ATG ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
2546497 ATA
1 ATA
2546500 TTAAAAAAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
2 4 0.05
3 61 0.79
4 12 0.16
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2546504 original size:19 final size:19
Alignment explanation
Indices: 2546405--2546499 Score: 104
Period size: 19 Copynumber: 5.0 Consensus size: 19
2546395 TTTTAAAACT
2546405 ATAATAATAATAAATAATA
1 ATAATAATAATAAATAATA
*
2546424 ATAGTAATAATAAATAATA
1 ATAATAATAATAAATAATA
* ** *
2546443 ATAACAATGGTAAAAAATGA
1 ATAATAATAATAAATAAT-A
2546463 ATAATAATAAT-AATAATA
1 ATAATAATAATAAATAATA
*
2546481 ATAAATAATGAT-AATAATA
1 AT-AATAATAATAAATAATA
2546500 TTAAAAAAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 3 0.05
19 51 0.81
20 9 0.14
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAATAATAAATAATA
Found at i:2547188 original size:123 final size:123
Alignment explanation
Indices: 2546715--2547193 Score: 612
Period size: 123 Copynumber: 3.9 Consensus size: 123
2546705 GGTTTTGAGC
*
2546715 AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGACGAGTTCTTCTCATT
1 AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATT
* * * * * * * * *
2546780 ATGAACCCTTCCATTGGAAACGTTGAACCACTTCTTTCTTTGATAG-ATTTTGAGC--
66 ATGAACCCTTCCATTGGAAATGTCGATCCACCTCCTTCTGTGATGGTTTTTTAAGCAA
* * * * *
2546835 AAAAGGTCGAATAATTTCTTCTCATTATGAAATTCTTCCCCCTTTTTGGATGAG---TTCTCATT
1 AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATT
* * *
2546897 ATGAACCCTTCCATTGAAAATGTTGATCCACCTCCTTCTATGATGGTTTTTTAAGCAA
66 ATGAACCCTTCCATTGGAAATGTCGATCCACCTCCTTCTGTGATGGTTTTTTAAGCAA
* * * *
2546955 AAAATGTCGAACAAGTTCTTGTCATTATGAACTTATTCTCCCTCTTCGGATGAGTTCTTCTCATT
1 AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATT
* * ** *
2547020 ATGAACTCTTCCATTGGAAATGTCGATCTACCTTATTCTGCGATGGTTTTTTAAGCAA
66 ATGAACCCTTCCATTGGAAATGTCGATCCACCTCCTTCTGTGATGGTTTTTTAAGCAA
* * * *
2547078 AAAAGATCGAATAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGAAGAGTTCTTCTCATT
1 AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATT
*
2547143 ATGAACCCTTCCATTGGAAATGTCGATCCACCTCC-TCTTGTGATGGATTTT
66 ATGAACCCTTCCATTGGAAATGTCGATCCACCTCCTTC-TGTGATGGTTTTT
2547194 GAGTCTATAA
Statistics
Matches: 306, Mismatches: 46, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
117 47 0.15
118 7 0.02
120 93 0.30
122 2 0.01
123 157 0.51
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (123 bp):
AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATT
ATGAACCCTTCCATTGGAAATGTCGATCCACCTCCTTCTGTGATGGTTTTTTAAGCAA
Found at i:2548345 original size:11 final size:11
Alignment explanation
Indices: 2548327--2548384 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
2548317 TTCTGTCAAT
2548327 TTTTCTTTTT-
1 TTTTCTTTTTC
2548337 TTCTTCTTTTTC
1 TT-TTCTTTTTC
*
2548349 TATTTCTCTATT-
1 T-TTTCT-TTTTC
2548361 TTTTCTTTTTC
1 TTTTCTTTTTC
2548372 TTTTCTTTTTC
1 TTTTCTTTTTC
2548383 TT
1 TT
2548385 ATTTTTACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 5 0.12
11 26 0.63
12 6 0.15
13 4 0.10
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:2548348 original size:17 final size:17
Alignment explanation
Indices: 2548326--2548390 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
2548316 CTTCTGTCAA
2548326 TTTTTCTTTTTTTCTTC
1 TTTTTCTTTTTTTCTTC
* *
2548343 TTTTTCTATTTCTCTAT-
1 TTTTTCTTTTTTTCT-TC
2548360 TTTTTCTTTTTCTT-TTC
1 TTTTTCTTTTT-TTCTTC
2548377 TTTTTCTTATTTTT
1 TTTTTCTT-TTTTT
2548391 ACTTTTTAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.03
17 34 0.85
18 5 0.12
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTTTTCTTC
Found at i:2548349 original size:6 final size:6
Alignment explanation
Indices: 2548326--2548384 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
2548316 CTTCTGTCAA
* * * *
2548326 TTTTTC TTTTT- TTCTTC TTTTTC TATTTC TCTAT- TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
2548372 -TTTTC TTTTTC TT
1 TTTTTC TTTTTC TT
2548385 ATTTTTACTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
5 12 0.28
6 31 0.72
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:2548375 original size:28 final size:27
Alignment explanation
Indices: 2548344--2548397 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2548334 TTTTTCTTCT
*
2548344 TTTTCTATTTCTCTATTTTTTCTTTTTC
1 TTTTCTATTTCT-TATTTTTACTTTTTC
*
2548372 TTTTCTTTTTCTTATTTTTACTTTTT
1 TTTTCTATTTCTTATTTTTACTTTTT
2548398 AAGTGTAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTCTATTTCTTATTTTTACTTTTTC
Found at i:2550746 original size:12 final size:12
Alignment explanation
Indices: 2550729--2550760 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2550719 TTTATCAGTT
2550729 AATTGAGAAATG
1 AATTGAGAAATG
2550741 AATTGAGAAATG
1 AATTGAGAAATG
2550753 AATTGAGA
1 AATTGAGA
2550761 TATATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (12 bp):
AATTGAGAAATG
Found at i:2564238 original size:138 final size:139
Alignment explanation
Indices: 2564013--2564386 Score: 436
Period size: 139 Copynumber: 2.7 Consensus size: 139
2564003 CTCGAGCATT
* ** * *
2564013 AGAACCAAATCAAAAATTCTCCTAGGTTAAAGGACT-AGTTATGAAATTAATCCTAAAAATGGAG
1 AGAACCAAATTAAAAATTCTCCTAAATTTAAGGACTAAG-TATGAAATTAAGCCT-AAAATGGAG
* * * * *
2564077 TCTCTAAATATTA-ACCTATTCAATTTTAATTGA-TTATTTACTCT-AA-TATTAAAATAGAACC
64 GCTCT-AATATTAGTCCTAATCAATTTTAATTAATTTATTTA-TCTGAATTATCAAAATAGAACC
*
2564138 TCGAG-AAAAAGCG
127 TCAAGCAAAAA-CG
* *
2564151 AGAACCAAATTAAAAAATTATCCTAAATTTAAGGACTAAGTATGAAACTAAGCCTAAAATGGAGG
1 AGAACCAAATT-AAAAATTCTCCTAAATTTAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGG
** * *
2564216 CTCTAATATTAGTCCTAATCAATTTTAACCAATTTTTTTATTTGAATTATCAAAATAGAACCTCA
65 CTCTAATATTAGTCCTAATCAATTTTAATTAATTTATTTATCTGAATTATCAAAATAGAACCTCA
2564281 AGCAAAAACG
130 AGCAAAAACG
* * * * * *
2564291 AGGACCATATTAAGAATTCCCCTAAATTTAAGGACTAAGTATGAAATTAAGCGTAAAATGGAGGA
1 AGAACCAAATTAAAAATTCTCCTAAATTTAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGC
*
2564356 TCTAATATTAGTCCTAATTAATTTTAATTAA
66 TCTAATATTAGTCCTAATCAATTTTAATTAA
2564387 GCCTAAAATG
Statistics
Matches: 201, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
137 7 0.03
138 40 0.20
139 118 0.59
140 31 0.15
141 5 0.02
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (139 bp):
AGAACCAAATTAAAAATTCTCCTAAATTTAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGC
TCTAATATTAGTCCTAATCAATTTTAATTAATTTATTTATCTGAATTATCAAAATAGAACCTCAA
GCAAAAACG
Found at i:2564402 original size:46 final size:46
Alignment explanation
Indices: 2564335--2564429 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
2564325 CTAAGTATGA
* *
2564335 AATTAAGCGTAAAATGGAGGATCTAATATTAGTCCTAATTAATTTT
1 AATTAAGCCTAAAATGGAGGATCTAATAATAGTCCTAATTAATTTT
2564381 AATTAAGCCTAAAATGGAGGATCTAATAATAGTCCTAATTAATTTT
1 AATTAAGCCTAAAATGGAGGATCTAATAATAGTCCTAATTAATTTT
2564427 AAT
1 AAT
2564430 CAATTATTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (46 bp):
AATTAAGCCTAAAATGGAGGATCTAATAATAGTCCTAATTAATTTT
Found at i:2564511 original size:185 final size:185
Alignment explanation
Indices: 2564199--2564571 Score: 541
Period size: 185 Copynumber: 2.0 Consensus size: 185
2564189 AGTATGAAAC
* * * * * *
2564199 TAAGCCTAAAATGGAGGCTCTAATATTAGTCCTAATCAATTTTAACCAATTTTTTTATTTGAATT
1 TAAGCCTAAAATGGAGGATCTAATAATAGTCCTAATCAATTTTAACCAATTATTTGATTCGAATA
* * *
2564264 ATCAAAATAGAACCTCAAGCAAAAACGAGGACCATATTAAGAATTCCCCTAAATTTAAGGACTAA
66 ATCAAAATAGAACCTCAAGCAAAAACAAGGACCAAATTAAGAATTCACCTAAATTTAAGGACTAA
* * * *
2564329 GTATGAAATTAAGCGTAAAATGGAGGATCTAATATTAGTCCTAATTAATTTTAAT
131 ATATAAAATTAAGCCTAAAATGGAGGATCTAATATTAATCCTAATTAATTTTAAT
* *
2564384 TAAGCCTAAAATGGAGGATCTAATAATAGTCCTAATTAATTTTAATCAATTATTTGATTCGAATA
1 TAAGCCTAAAATGGAGGATCTAATAATAGTCCTAATCAATTTTAACCAATTATTTGATTCGAATA
* *
2564449 ATTAAAATAGAACCTCAAGCAAAAGCAAAGG-CCAAATTAAGAATTCACCTAAATTTAAGGACTA
66 ATCAAAATAGAACCTCAAGCAAAAAC-AAGGACCAAATTAAGAATTCACCTAAATTTAAGGACTA
* * * *
2564513 AATTTAAAATTAGGCCTAAAGTGGAGGCTCTAATATTAATCCTAATTAATTTTAAT
130 AATATAAAATTAAGCCTAAAATGGAGGATCTAATATTAATCCTAATTAATTTTAAT
2564569 TAA
1 TAA
2564572 TATTGCAATT
Statistics
Matches: 166, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
185 163 0.98
186 3 0.02
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (185 bp):
TAAGCCTAAAATGGAGGATCTAATAATAGTCCTAATCAATTTTAACCAATTATTTGATTCGAATA
ATCAAAATAGAACCTCAAGCAAAAACAAGGACCAAATTAAGAATTCACCTAAATTTAAGGACTAA
ATATAAAATTAAGCCTAAAATGGAGGATCTAATATTAATCCTAATTAATTTTAAT
Found at i:2564954 original size:15 final size:14
Alignment explanation
Indices: 2564934--2564988 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
2564924 GTAATTTAAG
2564934 ACAAAAATTAAAGTA
1 ACAAAAATTAAA-TA
*
2564949 ACAAAAATTTAAATG
1 ACAAAAA-TTAAATA
* *
2564964 GCACAAATTAAATA
1 ACAAAAATTAAATA
*
2564978 AGAAAAATTAA
1 ACAAAAATTAA
2564989 GGCAATCGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 14 0.44
15 13 0.41
16 5 0.16
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (14 bp):
ACAAAAATTAAATA
Found at i:2565853 original size:46 final size:41
Alignment explanation
Indices: 2565786--2565898 Score: 127
Period size: 41 Copynumber: 2.6 Consensus size: 41
2565776 GTTTCCAGAT
* * **
2565786 TCGCAACGCGATTTTGACTATCGCAATCTCAATGTGAATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAAT-GCAA--T-AATACAT-AA
*
2565832 TCGCAACGCGATTCTGACTATCGCAATGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAATGCAATAATACATAA
*
2565873 TCGCAACACGATTCTGACTATCGCAA
1 TCGCAACGCGATTCTGACTATCGCAA
2565899 CGCGATTCTG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
41 27 0.44
42 5 0.08
43 1 0.02
45 2 0.03
46 26 0.43
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAATGCAATAATACATAA
Found at i:2565856 original size:20 final size:20
Alignment explanation
Indices: 2565831--2565941 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
2565821 GAATATGTAA
2565831 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
2565851 ATCGCAATGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
*
2565871 AATCGCAACACGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
2565892 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
2565912 ATCGCAACGCGATTTTGATT
1 ATCGCAACGCGATTCTGACT
*
2565932 GTCGCAACGC
1 ATCGCAACGC
2565942 TGAATTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2565875 original size:41 final size:41
Alignment explanation
Indices: 2565830--2565941 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 41
2565820 TGAATATGTA
*
2565830 AATCGCAACGCGATTCTGACTATCGCAATGCGATAAT-ACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATGAC-T
* **
2565871 AATCGCAACACGATTCTGACTATCGCAACGCGATTCTGACT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATGACT
* * *
2565912 -ATCGCAACGCGATTTTGATTGTCGCAACGC
1 AATCGCAACGCGATTCTGACTATCGCAACGC
2565942 TGAATTTCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 26 0.42
41 34 0.55
42 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (41 bp):
AATCGCAACGCGATTCTGACTATCGCAACGCGATAATGACT
Found at i:2566782 original size:24 final size:24
Alignment explanation
Indices: 2566750--2566803 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2566740 GTATTCGAAA
2566750 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2566774 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2566798 TTTGAT
1 TTTGAT
2566804 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2569089 original size:18 final size:18
Alignment explanation
Indices: 2569066--2569100 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2569056 AGAAAAAGGC
*
2569066 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
2569084 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
2569101 CAACTGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2569413 original size:140 final size:140
Alignment explanation
Indices: 2569158--2569440 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
2569148 GCAAACGTTG
*
2569158 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGATT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGT
* *
2569223 TTGAACATTGCTATGATCTTTTCAGTTGTTATCACTTATTACACAATCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACAATCATTTGAATATCGCAACG
2569288 CGAATTTGAC
131 CGAATTTGAC
*
2569298 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGT
*
2569363 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACAATCATTTGAATATCGCAACG
2569428 CGAATTTGAC
131 CGAATTTGAC
2569438 TAT
1 TAT
2569441 CGCAACTCAA
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACAATCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:2569436 original size:20 final size:20
Alignment explanation
Indices: 2569411--2569595 Score: 169
Period size: 20 Copynumber: 9.8 Consensus size: 20
2569401 TTACACATTC
*
2569411 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2569431 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* * *
2569450 A----A-AATCGCAACACAA
1 ATTTGACTATCGCAACGCGA
2569465 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
2569484 A----A-GATCGCAACGCCA
1 ATTTGACTATCGCAACGCGA
* *
2569499 ATTTGACTATTGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
2569519 ATTTTACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2569539 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
2569559 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
2569579 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
2569596 AGAAAATTGC
Statistics
Matches: 134, Mismatches: 19, Indels: 24
0.76 0.11 0.14
Matches are distributed among these distances:
14 19 0.14
15 6 0.04
19 6 0.04
20 103 0.77
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2569468 original size:34 final size:34
Alignment explanation
Indices: 2569419--2569515 Score: 140
Period size: 34 Copynumber: 2.9 Consensus size: 34
2569409 TCATTTGAAT
* *
2569419 ATCGCAACGCGAATTTGACTATCGCAACTCAAAA
1 ATCGCAACGCAAATTTGACTATCGCAACGCAAAA
* *
2569453 ATCGCAACACAAATTTGACTATCGCAACGCAAAG
1 ATCGCAACGCAAATTTGACTATCGCAACGCAAAA
* *
2569487 ATCGCAACGCCAATTTGACTATTGCAACG
1 ATCGCAACGCAAATTTGACTATCGCAACG
2569516 TGAATTTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCAAATTTGACTATCGCAACGCAAAA
Found at i:2569643 original size:20 final size:20
Alignment explanation
Indices: 2569614--2569731 Score: 166
Period size: 20 Copynumber: 5.9 Consensus size: 20
2569604 GCAAAGTGTA
*
2569614 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
2569634 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
*
2569654 TTGACTTTCGCATTACGATT
1 TTGACTTTCGCATTGCGATT
2569674 TTGACTTAT-GCATTGCGATT
1 TTGACTT-TCGCATTGCGATT
2569694 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
2569714 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
2569732 AAGTGTACCT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 1 0.01
20 86 0.98
21 1 0.01
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:2569870 original size:14 final size:14
Alignment explanation
Indices: 2569851--2569887 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2569841 CATCAATTAA
2569851 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2569865 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2569879 ACAAATCAA
1 ACAAATCAA
2569888 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2569903 original size:77 final size:78
Alignment explanation
Indices: 2569786--2569950 Score: 287
Period size: 77 Copynumber: 2.1 Consensus size: 78
2569776 TGAAATCAAT
*
2569786 AAATCAACTTTTACATTTTAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAATTAA
1 AAATCAACTTTTACA---TAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAA
2569851 ACAAATCAACTTTTAC
63 ACAAATCAACTTTTAC
2569867 AAATCAACTTTTACA-AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACA
1 AAATCAACTTTTACATAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACA
2569931 AATCAACTTTTAC
66 AATCAACTTTTAC
2569944 AAATCAA
1 AAATCAA
2569951 TTAAACAAGC
Statistics
Matches: 83, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
77 68 0.82
81 15 0.18
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.30
Consensus pattern (78 bp):
AAATCAACTTTTACATAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACA
AATCAACTTTTAC
Found at i:2569929 original size:36 final size:36
Alignment explanation
Indices: 2569806--2569931 Score: 128
Period size: 36 Copynumber: 3.4 Consensus size: 36
2569796 TTACATTTTA
*
2569806 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
* *** * *
2569842 ATCAATTAAACAAATCAACTTTTACA-AATCAACTTTTACAA
1 ATCAATTAAAC-AAGC-ACAAATA-AGAAT-TA--TTTACAC
2569883 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
2569919 ATCAATTAAACAA
1 ATCAATTAAACAA
2569932 ATCAACTTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
36 29 0.41
37 3 0.04
38 9 0.13
39 9 0.13
40 3 0.04
41 17 0.24
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (36 bp):
ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
Done.