Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 3 of 125
Found at i:363679 original size:14 final size:15
Alignment explanation
Indices: 363604--363679 Score: 68
Period size: 14 Copynumber: 5.2 Consensus size: 15
363594 TAAAACTCTT
** *
363604 AAACCCTAAACCTCT
1 AAACCCTAAAATTCA
363619 AAACCCTAAAATT-A
1 AAACCCTAAAATTCA
* * *
363633 AATCCCTAAAACATCC
1 AAACCCTAAAA-TTCA
363649 AAACCCTAAAATT-A
1 AAACCCTAAAATTCA
363663 AAACCCT-AAATTCA
1 AAACCCTAAAATTCA
363677 AAA
1 AAA
363680 ACCAAAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
13 5 0.10
14 21 0.43
15 13 0.27
16 10 0.20
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (15 bp):
AAACCCTAAAATTCA
Found at i:363865 original size:21 final size:22
Alignment explanation
Indices: 363832--363874 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
363822 AAACACGAAT
* *
363832 CCCTACAATTCAAAATCCTAAA
1 CCCTACAAATCAAAAACCTAAA
363854 CCCTA-AAATCAAAAACCTAAA
1 CCCTACAAATCAAAAACCTAAA
363875 AATCCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (22 bp):
CCCTACAAATCAAAAACCTAAA
Found at i:363911 original size:7 final size:7
Alignment explanation
Indices: 363899--363945 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
363889 AAAAACCCAT
363899 AAAATCC
1 AAAATCC
363906 AAAATCCC
1 AAAAT-CC
*
363914 AAACTCC
1 AAAATCC
363921 AAAATCC
1 AAAATCC
*
363928 AAAATCTA
1 AAAATC-C
363936 AAAATCC
1 AAAATCC
363943 AAA
1 AAA
363946 GGTAAAGACC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 22 0.65
8 12 0.35
ACGTcount: A:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATCC
Found at i:363916 original size:25 final size:25
Alignment explanation
Indices: 363863--363916 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
363853 ACCCTAAAAT
* * *
363863 CAAAAACCTAAAAATCCAAATTTCT
1 CAAAAACCCAAAAATCCAAATATCC
363888 CAAAAACCCATAAAATCCAAA-ATCC
1 CAAAAACCCA-AAAATCCAAATATCC
363913 CAAA
1 CAAA
363917 CTCCAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (25 bp):
CAAAAACCCAAAAATCCAAATATCC
Found at i:363939 original size:15 final size:15
Alignment explanation
Indices: 363858--363945 Score: 54
Period size: 15 Copynumber: 5.7 Consensus size: 15
363848 CCTAAACCCT
* *
363858 AAAATCAAAAACCTA
1 AAAATCCAAAATCTA
*
363873 AAAATCCAAATTTCTCA
1 AAAATCCAAA-ATCT-A
* *
363890 AAAACCCATAAAATC-C
1 AAAATCC--AAAATCTA
* *
363906 AAAATCCCAAA-CTCC
1 AAAATCCAAAATCT-A
363921 AAAATCCAAAATCTA
1 AAAATCCAAAATCTA
363936 AAAATCCAAA
1 AAAATCCAAA
363946 GGTAAAGACC
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
13 1 0.02
14 3 0.05
15 30 0.54
16 10 0.18
17 7 0.12
18 2 0.04
19 3 0.05
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATCCAAAATCTA
Found at i:363943 original size:22 final size:22
Alignment explanation
Indices: 363899--363945 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
363889 AAAAACCCAT
* *
363899 AAAATCCAAAATCCCAAACTCC
1 AAAATCCAAAATCCAAAAATCC
*
363921 AAAATCCAAAATCTAAAAATCC
1 AAAATCCAAAATCCAAAAATCC
363943 AAA
1 AAA
363946 GGTAAAGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAATCCAAAATCCAAAAATCC
Found at i:365599 original size:4 final size:4
Alignment explanation
Indices: 365577--365615 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
365567 TATATTATAC
*
365577 TTAT TT-T TTAT TTAC TTAT TTAT TTAT TTATT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTA
365616 CATTATTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.77
5 4 0.13
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:365599 original size:25 final size:26
Alignment explanation
Indices: 365582--365632 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
365572 TATACTTATT
365582 TTTTATTTAC-TTATTTATTTATTTA
1 TTTTATTTACATTATTTATTTATTTA
* *
365607 TTTTATTTACATTATTGATTTGTTTA
1 TTTTATTTACATTATTTATTTATTTA
365633 ATTCTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTATTTACATTATTTATTTATTTA
Found at i:365600 original size:12 final size:12
Alignment explanation
Indices: 365583--365627 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
365573 ATACTTATTT
365583 TTTATTTACTTA
1 TTTATTTACTTA
*
365595 TTTATTTATTTA
1 TTTATTTACTTA
365607 TTTTATTTACATTA
1 -TTTATTTAC-TTA
*
365621 TTGATTT
1 TTTATTT
365628 GTTTAATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.39
13 14 0.50
14 3 0.11
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTATTTACTTA
Found at i:365602 original size:16 final size:15
Alignment explanation
Indices: 365569--365606 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
365559 TTATGTCATA
365569 TATTATACTTATTTTT
1 TATT-TACTTATTTTT
365585 TATTTACTTATTTATT
1 TATTTACTTATTT-TT
365601 TATTTA
1 TATTTA
365607 TTTTATTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTACTTATTTTT
Found at i:375351 original size:12 final size:12
Alignment explanation
Indices: 375334--375361 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
375324 TATTTTACTT
375334 AAAAAAAAGAGA
1 AAAAAAAAGAGA
375346 AAAAAAAAGAGA
1 AAAAAAAAGAGA
375358 AAAA
1 AAAA
375362 GTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:376917 original size:100 final size:99
Alignment explanation
Indices: 376802--377137 Score: 395
Period size: 100 Copynumber: 3.3 Consensus size: 99
376792 GATAGTTGCT
* * *
376802 ATTCTCTGACTTGCGATTTAATCCTGATCTCTTTATTTTCTTAACTTACGGTTCAATCATGATCT
1 ATTCTCTGACTTGCGATTTAAT-CTGATCTCTTTATTTTCTTAACTCACGATTCAATCCTGATCT
* * *
376867 TTTTACTTTTGAGTCGCGATTTAATCCTGATCCTC
65 TTTTACTTCTAAGTCACGATTTAATCCTGATCCTC
* * * * * * *
376902 ATTCTTTGACTTGCGATTTAATTTTAGTTTCTTTATTTTTCTTGACTCGCGATTCAATCCCGATC
1 ATTCTCTGACTTGCGATTTAATCTGA-TCTCTTTA-TTTTCTTAACTCACGATTCAATCCTGATC
* *
376967 TCTTTACTTCTAAGTCACGATTTTATCCTGATCCTC
64 TTTTTACTTCTAAGTCACGATTTAATCCTGATCCTC
* * * *
377003 ATTCTCTGACTTACGATTTAATCTTGATCTTTTTATTTTTTTAACTCACGATTCAATCCTAATCT
1 ATTCTCTGACTTGCGATTTAATC-TGATCTCTTTATTTTCTTAACTCACGATTCAATCCTGATCT
* * * *
377068 TTTTAATTCTAAGTCACGGTTTAATCCCGATCATC
65 TTTTACTTCTAAGTCACGATTTAATCCTGATCCTC
*
377103 ATTCTCTGACTTGC-AGTTCAATCTCGATCTCTTTA
1 ATTCTCTGACTTGCGA-TTTAATCT-GATCTCTTTA
377138 CTTCTAAGTC
Statistics
Matches: 196, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
99 4 0.02
100 110 0.56
101 80 0.41
102 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.46
Consensus pattern (99 bp):
ATTCTCTGACTTGCGATTTAATCTGATCTCTTTATTTTCTTAACTCACGATTCAATCCTGATCTT
TTTACTTCTAAGTCACGATTTAATCCTGATCCTC
Found at i:376988 original size:101 final size:101
Alignment explanation
Indices: 376753--377116 Score: 394
Period size: 100 Copynumber: 3.6 Consensus size: 101
376743 ATTATGGTTT
* * ** **
376753 AATCCTAATCTCTTTAATTCTAAATCGTGATTTAATCCTGATAGTTGCTATTCTCTGACTTGCGA
1 AATCCTGATCTCTTTAATTCTAAGTCACGATTTAATCCTGAT-CCT-C-ATTCTCTGACTTGCGA
* * * *
376818 TTTAATCCTGATCTCTTTA-TTTTCTTAACTTACGGTTC
63 TTTAATCTTGATTTCTTTATTTTTCTTAACTCACGATTC
* * * * * * *
376856 AATCATGATCTTTTTACTTTTGAGTCGCGATTTAATCCTGATCCTCATTCTTTGACTTGCGATTT
1 AATCCTGATCTCTTTAATTCTAAGTCACGATTTAATCCTGATCCTCATTCTCTGACTTGCGATTT
* * *
376921 AAT-TTTAGTTTCTTTATTTTTCTTGACTCGCGATTC
66 AATCTTGA-TTTCTTTATTTTTCTTAACTCACGATTC
* * * *
376957 AATCCCGATCTCTTTACTTCTAAGTCACGATTTTATCCTGATCCTCATTCTCTGACTTACGATTT
1 AATCCTGATCTCTTTAATTCTAAGTCACGATTTAATCCTGATCCTCATTCTCTGACTTGCGATTT
377022 AATCTTGATCTT-TTTATTTTT-TTAACTCACGATTC
66 AATCTTGAT-TTCTTTATTTTTCTTAACTCACGATTC
* * * * *
377057 AATCCTAATCTTTTTAATTCTAAGTCACGGTTTAATCCCGATCATCATTCTCTGACTTGC
1 AATCCTGATCTCTTTAATTCTAAGTCACGATTTAATCCTGATCCTCATTCTCTGACTTGC
377117 AGTTCAATCT
Statistics
Matches: 218, Mismatches: 39, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
99 2 0.01
100 91 0.42
101 85 0.39
102 6 0.03
103 34 0.16
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (101 bp):
AATCCTGATCTCTTTAATTCTAAGTCACGATTTAATCCTGATCCTCATTCTCTGACTTGCGATTT
AATCTTGATTTCTTTATTTTTCTTAACTCACGATTC
Found at i:377125 original size:65 final size:65
Alignment explanation
Indices: 377054--377202 Score: 183
Period size: 65 Copynumber: 2.3 Consensus size: 65
377044 TAACTCACGA
* * * *
377054 TTCAATCCTAATCTTTTTAATTCTAAGTCACGGTTTAATCCCGATCATCATTCTCTGACTTGCAG
1 TTCAATCCTGATCTTTTTAATTCTAAGTCACGATTTAATCCCAATCATCATTCTCTGACTTACAG
* * * * * *
377119 TTCAAT-CTCGATCTCTTTACTTCTAAGTCATGATTTTATCCCAATCCTCATTCTTTGACTTACA
1 TTCAATCCT-GATCTTTTTAATTCTAAGTCACGATTTAATCCCAATCATCATTCTCTGACTTACA
377183 G
65 G
*
377184 TTTAATCCTGATCTTTTTA
1 TTCAATCCTGATCTTTTTA
377203 TTTTCTTAAC
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
64 2 0.03
65 66 0.94
66 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (65 bp):
TTCAATCCTGATCTTTTTAATTCTAAGTCACGATTTAATCCCAATCATCATTCTCTGACTTACAG
Found at i:377137 original size:165 final size:168
Alignment explanation
Indices: 376940--377306 Score: 516
Period size: 165 Copynumber: 2.2 Consensus size: 168
376930 TTCTTTATTT
* * **
376940 TTCT-TGACTCGC-GATTCAATCCCGATCTCTTTACTTCTAAGTCACGATTTTATCCTGATCCTC
1 TTCTCTGACTTGCAGATTCAATCTCGATCTCTTTACTTCTAAGTCACGATTTTATCCCAATCCTC
* *
377003 ATTCTCTGACTTAC-GATTTAATCTTGATCTTTTTATTTTTTTAACTCACGATTCAATCCTAATC
66 ATTCTCTGACTTACAG-TTTAATCCTGATCTTTTTATTTTCTTAACTCACGATTCAATCCTAATC
*
377067 TTTTTAATTCTAAGTCACGGTTTAATCCCGA-TCA-TCA
130 TTTTTAATTCTAAGTCACGGTCTAATCCCGATTCATTCA
*
377104 TTCTCTGACTTGCAG-TTCAATCTCGATCTCTTTACTTCTAAGTCATGATTTTATCCCAATCCTC
1 TTCTCTGACTTGCAGATTCAATCTCGATCTCTTTACTTCTAAGTCACGATTTTATCCCAATCCTC
* * * * *
377168 ATTCTTTGACTTACAGTTTAATCCTGATCTTTTTATTTTCTTAACTCTCGGTTCAATCTTGATCT
66 ATTCTCTGACTTACAGTTTAATCCTGATCTTTTTATTTTCTTAACTCACGATTCAATCCTAATCT
*
377233 TTTTAATTCTAAGTCACGGTCTAATCCCGATCTTCATTCT
131 TTTTAATTCTAAGTCACGGTCTAATCCCGA--TTCATTCA
377273 TTCTCTGACTTGCAGATT-AATCTC-AGTCTCTTTA
1 TTCTCTGACTTGCAGATTCAATCTCGA-TCTCTTTA
377307 TTTTCTTAAC
Statistics
Matches: 180, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
164 4 0.02
165 137 0.76
166 2 0.01
168 4 0.02
169 31 0.17
170 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (168 bp):
TTCTCTGACTTGCAGATTCAATCTCGATCTCTTTACTTCTAAGTCACGATTTTATCCCAATCCTC
ATTCTCTGACTTACAGTTTAATCCTGATCTTTTTATTTTCTTAACTCACGATTCAATCCTAATCT
TTTTAATTCTAAGTCACGGTCTAATCCCGATTCATTCA
Found at i:377225 original size:100 final size:99
Alignment explanation
Indices: 377118--377984 Score: 684
Period size: 100 Copynumber: 8.6 Consensus size: 99
377108 CTGACTTGCA
* * *
377118 GTTCAATCTCGATCTCTTTACTTCTAAGTCATGATTTTATCCCAATCCTCATTCTTTGACTTACA
1 GTTCAATC-CGATCTCTTTACTTCTAAGTCATGATTTAATCCCGATCCTCATTCTTTGACTTGCA
*
377183 GTTTAATCCTGATCTTTTTATTTTCTTAACTCTCG
65 GTTTAATCCTGATCTCTTTATTTTCTTAACTCTCG
* * * * * * *
377218 GTTCAATCTTGATCTTTTTAATTCTAAGTCACGGTCTAATCCCGATCTTCATTCTTTCTCTGACT
1 GTTCAATC-CGATCTCTTTACTTCTAAGTCATGATTTAATCCCGATCCTCATTC--T-T-TGACT
* * * *
377283 TGCAGATTAAT-CTCAGTCTCTTTATTTTCTTAACTCGCA
61 TGCAGTTTAATCCTGA-TCTCTTTATTTTCTTAACTCTCG
* * *
377322 GTTCAATCCTGATCTCTTTACTTTTAAGTCACGATTTTATCCCGATCCTCATT-TTCTGACTTGC
1 GTTCAATCC-GATCTCTTTACTTCTAAGTCATGATTTAATCCCGATCCTCATTCTT-TGACTTGC
* * * *
377386 AATTTAATCCTGATCTCTTTATTTTATTAACTCGCA
64 AGTTTAATCCTGATCTCTTTATTTTCTTAACTCTCG
* * * * * * * **
377422 GTTCAATCTCGATCTTTTTAATTCTAAGTTACGGTTTAATCCCGATCATCATTCTCTGACTTGTG
1 GTTCAATC-CGATCTCTTTACTTCTAAGTCATGATTTAATCCCGATCCTCATTCTTTGACTTGCA
* * *
377487 GTTTAAT-CTCGATCTTTTTATTTTTCTTGACTCACG
65 GTTTAATCCT-GATCTCTTTA-TTTTCTTAACTCTCG
* * * * *
377523 GTTCAATCCTGATCTCTTTACTTCTAAGTCACGATTTTATCTCGATCCTTATTCTTTGACTTGTA
1 GTTCAATCC-GATCTCTTTACTTCTAAGTCATGATTTAATCCCGATCCTCATTCTTTGACTTGCA
* * * *
377588 GTTTAATCCCGGTATCTTTATTTTCTTAACTCGT-A
65 GTTTAATCCTGATCTCTTTATTTTCTTAACTC-TCG
* * * * * * *
377623 GTTCAATCCCAATCTTTTTAATTCTAAGTC-TCGATTTAATCCCGATCCTTATTCTCTAACTTAC
1 GTTCAAT-CCGATCTCTTTACTTCTAAGTCAT-GATTTAATCCCGATCCTCATTCTTTGACTTGC
*
377687 -GATTTAATCCTGATCTCTTTATTTTTCTTGACT-TGCG
64 AG-TTTAATCCTGATCTCTTTA-TTTTCTTAACTCT-CG
* * * * **
377724 ATTCAATCCCGATCTCTTTACTTCTAAGTCGTGATTTTATCCCGATCCTCATTCTCTGACTTGTG
1 GTTCAAT-CCGATCTCTTTACTTCTAAGTCATGATTTAATCCCGATCCTCATTCTTTGACTTGCA
* *
377789 GTTTAATCTTGATCTCTTTATTTTTTTTTAACTCAT-G
65 GTTTAATCCTGATCTCTTTA--TTTTCTTAACTC-TCG
* * **
377826 GTTCAATCCTGATAT-TTTAATTCTAAGTCAT-AGTTTAATTTCGATCCTCATTATTTCTTTGAC
1 GTTCAATCC-GATCTCTTTACTTCTAAGTCATGA-TTTAATCCCGATCCTC---A-TTCTTTGAC
* * * * *
377889 TTACGGTTTAATCC-CAGTCTCTTTATTTT-TCTGACT-TAG
60 TTGCAGTTTAATCCTGA-TCTCTTTATTTTCT-TAACTCTCG
* **
377928 GTTCAATCCTAATCTCTTTACTTCTAAGT--TGCAGTTTAATCCTAATCCTCATTCTTT
1 GTTCAATCC-GATCTCTTTACTTCTAAGTCATG-A-TTTAATCCCGATCCTCATTCTTT
377985 CTCTAACTCG
Statistics
Matches: 623, Mismatches: 107, Indels: 75
0.77 0.13 0.09
Matches are distributed among these distances:
99 10 0.02
100 229 0.37
101 198 0.32
102 40 0.06
103 38 0.06
104 81 0.13
105 27 0.04
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (99 bp):
GTTCAATCCGATCTCTTTACTTCTAAGTCATGATTTAATCCCGATCCTCATTCTTTGACTTGCAG
TTTAATCCTGATCTCTTTATTTTCTTAACTCTCG
Found at i:377338 original size:35 final size:35
Alignment explanation
Indices: 377181--377429 Score: 108
Period size: 35 Copynumber: 7.3 Consensus size: 35
377171 CTTTGACTTA
* * *
377181 CAGTTTAATCCTGATCTTTTTATTTTCTTAACTCT
1 CAGTTCAATCCTGATCTCTTTATTTTCTTAACTCG
* * * * * *
377216 CGGTTCAATCTTGATCTTTTTA-ATTC-TAAGTCA
1 CAGTTCAATCCTGATCTCTTTATTTTCTTAACTCG
* * * * * *
377249 C-GGTCTAATCCCGATCTTCATT-CTTTCTCTGACTTG
1 CAGTTC-AATCCTGATC-TCTTTATTTTCT-TAACTCG
*
377285 CAGATT-AAT-CTCAGTCTCTTTATTTTCTTAACTCG
1 CAG-TTCAATCCTGA-TCTCTTTATTTTCTTAACTCG
* * *
377320 CAGTTCAATCCTGATCTCTTTA-CTT-TTAAGTCA
1 CAGTTCAATCCTGATCTCTTTATTTTCTTAACTCG
** * * * *
377353 C-GATTTTATCCCGATC-C-TCATTTTC-TGACTTG
1 CAG-TTCAATCCTGATCTCTTTATTTTCTTAACTCG
* * *
377385 CAATTTAATCCTGATCTCTTTATTTTATTAACTCG
1 CAGTTCAATCCTGATCTCTTTATTTTCTTAACTCG
377420 CAGTTCAATC
1 CAGTTCAATC
377430 TCGATCTTTT
Statistics
Matches: 151, Mismatches: 45, Indels: 36
0.65 0.19 0.16
Matches are distributed among these distances:
31 2 0.01
32 22 0.15
33 32 0.21
34 19 0.13
35 57 0.38
36 17 0.11
37 1 0.01
38 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (35 bp):
CAGTTCAATCCTGATCTCTTTATTTTCTTAACTCG
Found at i:377371 original size:369 final size:366
Alignment explanation
Indices: 376818--377506 Score: 985
Period size: 369 Copynumber: 1.9 Consensus size: 366
376808 TGACTTGCGA
* * * *
376818 TTTAATCCTGATCTCTTTATTTTCTTAACTTACGGTTCAATCATGATCTTTTTACTTTTGAGTCG
1 TTTAATCCTGATCTCTTTATTTTCTTAACTTACGGTTCAATCATGATCTTTTTAATTCTAAGTCA
* * * * * *
376883 CGATTTAATCCTGATCCTCATTCTTTGACTTGCGATTTAATTTTAGTTTCTTTATTTTTCTTGAC
66 CGATCTAATCCCGATCCTCATTCTTTGACTTGCGATTTAATCTCAGTCTCTTTATTTTTCTTAAC
*
376948 TCGCGATTCAATCCCGATCTCTTTACTTCTAAGTCACGATTTTATCCTGATCCTCATTCTCTGAC
131 TCGCGATTCAATCCCGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATTCTCTGAC
* * * *
377013 TTACGATTTAATCTTGATCTTTTTATTTTTTTAACTCAC-GATTCAATC-CTAATCTTTTTAATT
196 TTACAATTTAATCCTGATCTCTTTATTTTATTAACTCACAG-TTCAATCTC-AATCTTTTTAATT
377076 CTAAGTCACGGTTTAATCCCGATCATCATTCTCTGACTTGCAGTTCAATCTCGATCTCTTTACTT
259 CTAAGTCACGGTTTAATCCCGATCATCATTCTCTGACTTGCAGTTCAATCTCGATCTCTTTACTT
377141 CTAAGTCATGATTTTATCCCAATCCTCATTCTTTGACTTACAG
324 CTAAGTCATGATTTTATCCCAATCCTCATTCTTTGACTTACAG
* *
377184 TTTAATCCTGATCTTTTTATTTTCTTAACTCT-CGGTTCAATCTTGATCTTTTTAATTCTAAGTC
1 TTTAATCCTGATCTCTTTATTTTCTTAACT-TACGGTTCAATCATGATCTTTTTAATTCTAAGTC
* *
377248 ACGGTCTAATCCCGATCTTCATTCTTTCTCTGACTTGCAGA-TTAATCTCAGTCTCTTTA-TTTT
65 ACGATCTAATCCCGATCCTCATTC--T-T-TGACTTGC-GATTTAATCTCAGTCTCTTTATTTTT
* *
377311 CTTAACTCGC-AGTTCAATCCTGATCTCTTTACTTTTAAGTCACGATTTTATCCCGATCCTCATT
125 CTTAACTCGCGA-TTCAATCCCGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATT
* * * *
377375 TTCTGACTTGCAATTTAATCCTGATCTCTTTATTTTATTAACTCGCAGTTCAATCTCGATCTTTT
189 CTCTGACTTACAATTTAATCCTGATCTCTTTATTTTATTAACTCACAGTTCAATCTCAATCTTTT
* ** * *
377440 TAATTCTAAGTTACGGTTTAATCCCGATCATCATTCTCTGACTTGTGGTTTAATCTCGATCTTTT
254 TAATTCTAAGTCACGGTTTAATCCCGATCATCATTCTCTGACTTGCAGTTCAATCTCGATCTCTT
377505 TA
319 TA
377507 TTTTTCTTGA
Statistics
Matches: 284, Mismatches: 30, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
366 76 0.27
367 1 0.00
368 2 0.01
369 178 0.63
370 25 0.09
371 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (366 bp):
TTTAATCCTGATCTCTTTATTTTCTTAACTTACGGTTCAATCATGATCTTTTTAATTCTAAGTCA
CGATCTAATCCCGATCCTCATTCTTTGACTTGCGATTTAATCTCAGTCTCTTTATTTTTCTTAAC
TCGCGATTCAATCCCGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATTCTCTGAC
TTACAATTTAATCCTGATCTCTTTATTTTATTAACTCACAGTTCAATCTCAATCTTTTTAATTCT
AAGTCACGGTTTAATCCCGATCATCATTCTCTGACTTGCAGTTCAATCTCGATCTCTTTACTTCT
AAGTCATGATTTTATCCCAATCCTCATTCTTTGACTTACAG
Found at i:377608 original size:201 final size:202
Alignment explanation
Indices: 377118--377956 Score: 919
Period size: 201 Copynumber: 4.1 Consensus size: 202
377108 CTGACTTGCA
* * *
377118 GTTCAAT-CTCGATCTCTTTACTTCTAAGTCATGATTTTATCCCAATCCTCATTCTTTGACTTAC
1 GTTCAATCCT-GATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATTCTTTGACTTGC
* * * *
377182 AGTTTAATCCTGATCTTTTTATTTTCTTAACTCTCGGTTCAATCTTGATCTTTTTAATTCTAAGT
65 AGTTTAATCCTGATCTCTTTATTTTCTTAACTCGCAGTTCAATCTCGATCTTTTTAATTCTAAGT
* * * * *
377247 CACGGTCTAATCCCGATCTTCATTCTTTCTCTGACTTGCAGATTAATCTC-AGTCTCTTTA-TTT
130 CACGGTTTAATCCCGA-C-TCA-TCATTCTCTGACTTACGGTTTAATC-CGAGTCTCTTTATTTT
* * *
377310 TCTTAACTCGCA
191 TCTTGACTCACG
*
377322 GTTCAATCCTGATCTCTTTACTTTTAAGTCACGATTTTATCCCGATCCTCATT-TTCTGACTTGC
1 GTTCAATCCTGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATTCTT-TGACTTGC
* *
377386 AATTTAATCCTGATCTCTTTATTTTATTAACTCGCAGTTCAATCTCGATCTTTTTAATTCTAAGT
65 AGTTTAATCCTGATCTCTTTATTTTCTTAACTCGCAGTTCAATCTCGATCTTTTTAATTCTAAGT
* ** *
377451 TACGGTTTAATCCCGA-TCATCATTCTCTGACTTGTGGTTTAATCTCGA-TCTTTTTATTTTTCT
130 CACGGTTTAATCCCGACTCATCATTCTCTGACTTACGGTTTAATC-CGAGTCTCTTTATTTTTCT
377514 TGACTCACG
194 TGACTCACG
* * *
377523 GTTCAATCCTGATCTCTTTACTTCTAAGTCACGATTTTATCTCGATCCTTATTCTTTGACTTGTA
1 GTTCAATCCTGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATTCTTTGACTTGCA
* * * * * *
377588 GTTTAATCCCGGTATCTTTATTTTCTTAACTCGTAGTTCAATCCCAATCTTTTTAATTCTAAGTC
66 GTTTAATCCTGATCTCTTTATTTTCTTAACTCGCAGTTCAATCTCGATCTTTTTAATTCTAAGTC
* * * * * *
377653 TCGATTTAATCCCGA-TCCTTATTCTCTAACTTACGATTTAATCCTGA-TCTCTTTATTTTTCTT
131 ACGGTTTAATCCCGACTCATCATTCTCTGACTTACGGTTTAATCC-GAGTCTCTTTATTTTTCTT
**
377716 GACTTGCG
195 GACTCACG
* * ** * **
377724 ATTCAATCCCGATCTCTTTACTTCTAAGTCGTGATTTTATCCCGATCCTCATTCTCTGACTTGTG
1 GTTCAATCCTGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATTCTTTGACTTGCA
* * *** *
377789 GTTTAATCTTGATCTCTTTATTTTTTTTTAACTCATGGTTCAATC-CTGAT-ATTTTAATTCTAA
66 GTTTAATCCTGATCTCTTTA--TTTTCTTAACTCGCAGTTCAATCTC-GATCTTTTTAATTCTAA
** ** * * *
377852 GTCATAGTTTAATTTCGATCCTCATTATTTCTTTGACTTACGGTTTAATCCCAGTCTCTTTATTT
128 GTCACGGTTTAATCCCGA--CTCATCA-TTCTCTGACTTACGGTTTAATCCGAGTCTCTTTATTT
*
377917 TTC-TGACTTA-G
190 TTCTTGACTCACG
*
377928 GTTCAATCCTAATCTCTTTACTTCTAAGT
1 GTTCAATCCTGATCTCTTTACTTCTAAGT
377957 TGCAGTTTAA
Statistics
Matches: 545, Mismatches: 76, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
200 31 0.06
201 261 0.48
202 27 0.05
203 24 0.04
204 154 0.28
205 14 0.03
206 34 0.06
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (202 bp):
GTTCAATCCTGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATTCTTTGACTTGCA
GTTTAATCCTGATCTCTTTATTTTCTTAACTCGCAGTTCAATCTCGATCTTTTTAATTCTAAGTC
ACGGTTTAATCCCGACTCATCATTCTCTGACTTACGGTTTAATCCGAGTCTCTTTATTTTTCTTG
ACTCACG
Found at i:377690 original size:32 final size:36
Alignment explanation
Indices: 377654--377748 Score: 108
Period size: 36 Copynumber: 2.8 Consensus size: 36
377644 TTCTAAGTCT
377654 CGATTTAATCCCGATC-C-TTA-TTCTC-TAACTTA
1 CGATTTAATCCCGATCTCTTTATTTCTCTTAACTTA
* * * *
377686 CGATTTAATCCTGATCTCTTTATTTTTCTTGACTTG
1 CGATTTAATCCCGATCTCTTTATTTCTCTTAACTTA
* *
377722 CGATTCAATCCCGATCTCTTTACTTCT
1 CGATTTAATCCCGATCTCTTTATTTCT
377749 AAGTCGTGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 15 0.29
33 1 0.02
34 3 0.06
35 4 0.08
36 28 0.55
ACGTcount: A:0.20, C:0.26, G:0.08, T:0.45
Consensus pattern (36 bp):
CGATTTAATCCCGATCTCTTTATTTCTCTTAACTTA
Found at i:377933 original size:405 final size:404
Alignment explanation
Indices: 377118--377984 Score: 1008
Period size: 405 Copynumber: 2.1 Consensus size: 404
377108 CTGACTTGCA
*
377118 GTTCAAT-CTCGATCTCTTTACTTCTAAGTCATGATTTTATCCCAATCCTCATTCTTTGACTTAC
1 GTTCAATCCT-GATCTCTTTACTTCTAAGTCACGATTTTATCCCAATCCTCATTCTTTGACTTAC
* * * * ***
377182 AGTTTAATCCTGATCTTTTTATTTTCTTAACTCTCGGTTCAATCTTGATCTTTTTAATTCTAAGT
65 AGTTTAATCCCGATATCTTTATTTTCTTAACTCTCAGTTCAATCCCAATCTTTTTAATTCTAAGT
* * * *
377247 CACGGTCTAATCCCGATCTTCATTCTTTCTCTGACTTGCAGATTAATCTCAGTCTCTTTATTTTC
130 CACGATCTAATCCCGATC-TCATTCATTCTCTAACTTACAGATTAATCTCAGTCTCTTTATTTTC
* * *
377312 TTAACTCGCAGTTCAATCCTGATCTCTTTACTTTTAAGTCACGATTTTATCCCGATCCTCATTTT
194 TTAACTCGCAGTTCAATCCCGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATTCT
* *
377377 CTGACTTGCAATTTAATCCTGATCTCTTTATTTTATTAACTCGCAGTTCAATCTCGATCTTTTTA
259 CTGACTTGCAATTTAATCCTGATCTCTTTATTTTATTAACTCACAGTTCAATCTCGATCATTTTA
* * ** * *
377442 ATTCTAAGTTACGGTTTAATCCCGATCATCATTCTCTGACTTGTGGTTTAATCTCGATCTTTTTA
324 ATTCTAAGTCACAGTTTAATCCCGATCATCATTCTCTGACTTACGGTTTAATCCCGATCTCTTTA
377507 TTTTTCTTGACTCACG
389 TTTTTCTTGACTCACG
* * * **
377523 GTTCAATCCTGATCTCTTTACTTCTAAGTCACGATTTTATCTCGATCCTTATTCTTTGACTTGTA
1 GTTCAATCCTGATCTCTTTACTTCTAAGTCACGATTTTATCCCAATCCTCATTCTTTGACTTACA
*
377588 GTTTAATCCCGGTATCTTTATTTTCTTAACTCGT-AGTTCAATCCCAATCTTTTTAATTCTAAGT
66 GTTTAATCCCGATATCTTTATTTTCTTAACTC-TCAGTTCAATCCCAATCTTTTTAATTCTAAGT
* * *
377652 CTCGATTTAATCCCGATC-C-TT-ATTCTCTAACTTAC-GATTTAATC-CTGATCTCTTTATTTT
130 CACGATCTAATCCCGATCTCATTCATTCTCTAACTTACAGA-TTAATCTCAG-TCTCTTTA-TTT
* * **
377712 TCTTGACTTGC-GATTCAATCCCGATCTCTTTACTTCTAAGTCGTGATTTTATCCCGATCCTCAT
192 TCTTAACTCGCAG-TTCAATCCCGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCAT
*** * * **
377776 TCTCTGACTTGTGGTTTAATCTTGATCTCTTTATTTTTTTTTAACTCATGGTTCAATC-CTGAT-
256 TCTCTGACTTGCAATTTAATCCTGATCTCTTTA--TTTTATTAACTCACAGTTCAATCTC-GATC
* ** * *
377839 ATTTTAATTCTAAGTCATAGTTTAATTTCGATCCTCATTATTTCTTTGACTTACGGTTTAATCCC
318 ATTTTAATTCTAAGTCACAGTTTAATCCCGA---TCATCA-TTCTCTGACTTACGGTTTAATCCC
*
377904 -AGTCTCTTTATTTTTC-TGACTTA-G
379 GA-TCTCTTTATTTTTCTTGACTCACG
* * *
377928 GTTCAATCCTAATCTCTTTACTTCTAAGTTGCA-G-TTTAATCCTAATCCTCATTCTTT
1 GTTCAATCCTGATCTCTTTACTTCTAAG-T-CACGATTTTATCCCAATCCTCATTCTTT
377985 CTCTAACTCG
Statistics
Matches: 391, Mismatches: 55, Indels: 32
0.82 0.12 0.07
Matches are distributed among these distances:
400 4 0.01
401 26 0.07
402 89 0.23
403 27 0.07
404 22 0.06
405 171 0.44
406 17 0.04
407 35 0.09
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (404 bp):
GTTCAATCCTGATCTCTTTACTTCTAAGTCACGATTTTATCCCAATCCTCATTCTTTGACTTACA
GTTTAATCCCGATATCTTTATTTTCTTAACTCTCAGTTCAATCCCAATCTTTTTAATTCTAAGTC
ACGATCTAATCCCGATCTCATTCATTCTCTAACTTACAGATTAATCTCAGTCTCTTTATTTTCTT
AACTCGCAGTTCAATCCCGATCTCTTTACTTCTAAGTCACGATTTTATCCCGATCCTCATTCTCT
GACTTGCAATTTAATCCTGATCTCTTTATTTTATTAACTCACAGTTCAATCTCGATCATTTTAAT
TCTAAGTCACAGTTTAATCCCGATCATCATTCTCTGACTTACGGTTTAATCCCGATCTCTTTATT
TTTCTTGACTCACG
Found at i:377944 original size:34 final size:35
Alignment explanation
Indices: 377876--377952 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 35
377866 TCGATCCTCA
* *
377876 TTATTTCTTTGACTTACGGTTTAATCCCAGTCTCT
1 TTATTTCTTTGACTTACGGTTCAATCCCAATCTCT
*
377911 TTATTT-TTCTGACTTA-GGTTCAATCCTAATCTCT
1 TTATTTCTT-TGACTTACGGTTCAATCCCAATCTCT
*
377945 TTACTTCT
1 TTATTTCT
377953 AAGTTGCAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 22 0.61
35 14 0.39
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.51
Consensus pattern (35 bp):
TTATTTCTTTGACTTACGGTTCAATCCCAATCTCT
Found at i:378394 original size:28 final size:28
Alignment explanation
Indices: 378362--378441 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 28
378352 CGATTCCAAT
*
378362 TCAACTGGGCTTTAAGCCCAATTTTGGC
1 TCAACTGGGCTTTAAGCCCAATTTTGAC
* ** * *
378390 TCAACTGAGCTTCGAGCTCGATTTTGAC
1 TCAACTGGGCTTTAAGCCCAATTTTGAC
* *
378418 TCAATTGGGCTTTAGGCCCAATTT
1 TCAACTGGGCTTTAAGCCCAATTT
378442 GATCCAACTA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (28 bp):
TCAACTGGGCTTTAAGCCCAATTTTGAC
Found at i:380102 original size:14 final size:13
Alignment explanation
Indices: 380080--380136 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 13
380070 CCAAACCTCT
380080 AAACCCTAAAATC
1 AAACCCTAAAATC
380093 AAATCCCTAAAACATCC
1 AAA-CCCT-AAA-AT-C
*
380110 AAACCCTAAATTC
1 AAACCCTAAAATC
*
380123 AAAACCCAAAAATC
1 -AAACCCTAAAATC
380137 CAAAATCTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.11
14 16 0.44
15 6 0.17
16 6 0.17
17 4 0.11
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.16
Consensus pattern (13 bp):
AAACCCTAAAATC
Found at i:380227 original size:30 final size:30
Alignment explanation
Indices: 380191--380333 Score: 191
Period size: 30 Copynumber: 4.8 Consensus size: 30
380181 CTAAATTAAG
380191 CCCTAAACCCTCTTAACCCTAAAAACGAAA
1 CCCTAAACCCTCTTAACCCTAAAAACGAAA
* *
380221 CCCTAAACCCTCTTGACCTTAAAAACGAAA
1 CCCTAAACCCTCTTAACCCTAAAAACGAAA
*
380251 CCCTAAACCCTCTTAACCTTAAAAACGAAA
1 CCCTAAACCCTCTTAACCCTAAAAACGAAA
* ** *
380281 CCTTAAACCCTCCAAACCCTAAAATC-AAA
1 CCCTAAACCCTCTTAACCCTAAAAACGAAA
*
380310 CCCTAAATCCT-TTAAACCCTAAAA
1 CCCTAAACCCTCTT-AACCCTAAAA
380334 CTAAAATCTC
Statistics
Matches: 100, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.22
30 78 0.78
ACGTcount: A:0.43, C:0.35, G:0.03, T:0.20
Consensus pattern (30 bp):
CCCTAAACCCTCTTAACCCTAAAAACGAAA
Found at i:380316 original size:29 final size:30
Alignment explanation
Indices: 380065--380333 Score: 170
Period size: 30 Copynumber: 8.9 Consensus size: 30
380055 TTAAACTCTT
*
380065 AAACCCCAAA-CCTCTAAACCCTAAAATC-
1 AAACCCTAAACCCTCTAAACCCTAAAATCG
* * * * *
380093 AAATCCCTAAAACATCCAAACCCTAAATTCA
1 AAA-CCCTAAACCCTCTAAACCCTAAAATCG
* * * *
380124 AAACCCAAAAATCCAAAATCTCAAACCCTAAATTCC
1 AAACCC-TAAA-CC---CTCT-AAACCCTAAAATCG
** * * * *
380160 AGTCTCTAAACACTCTAAACACT-AAAT-T
1 AAACCCTAAACCCTCTAAACCCTAAAATCG
* * *
380188 AAGCCCTAAACCCTCTTAACCCTAAAAACG
1 AAACCCTAAACCCTCTAAACCCTAAAATCG
** * *
380218 AAACCCTAAACCCTCTTGACCTTAAAAACG
1 AAACCCTAAACCCTCTAAACCCTAAAATCG
* * *
380248 AAACCCTAAACCCTCTTAACCTTAAAAACG
1 AAACCCTAAACCCTCTAAACCCTAAAATCG
* *
380278 AAACCTTAAACCCTCCAAACCCTAAAATC-
1 AAACCCTAAACCCTCTAAACCCTAAAATCG
* *
380307 AAACCCTAAATCCTTTAAACCCTAAAA
1 AAACCCTAAACCCTCTAAACCCTAAAA
380334 CTAAAATCTC
Statistics
Matches: 192, Mismatches: 38, Indels: 21
0.76 0.15 0.08
Matches are distributed among these distances:
28 20 0.10
29 35 0.18
30 104 0.54
31 9 0.05
32 1 0.01
34 1 0.01
35 6 0.03
36 16 0.08
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.19
Consensus pattern (30 bp):
AAACCCTAAACCCTCTAAACCCTAAAATCG
Found at i:380408 original size:14 final size:15
Alignment explanation
Indices: 380379--380411 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
380369 CCTAAAATTC
*
380379 AAAATCGCAAACCCT
1 AAAATCGCAAAACCT
380394 AAAATC-CAAAACCT
1 AAAATCGCAAAACCT
380408 AAAA
1 AAAA
380412 ATTCAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.58, C:0.27, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAATCGCAAAACCT
Found at i:384602 original size:44 final size:44
Alignment explanation
Indices: 384549--384640 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
384539 GTTTAACATA
* * *
384549 TTAATATGAATTATGATATAATAATTTTTATATTTTATATGTAT
1 TTAACATGAACTATGATATAATAATTTTTATATTTTATATATAT
384593 TTAACATGAACTATGATATAATAATTTTTATATTTTATATATAT
1 TTAACATGAACTATGATATAATAATTTTTATATTTTATATATAT
384637 TTAA
1 TTAA
384641 TACAAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (44 bp):
TTAACATGAACTATGATATAATAATTTTTATATTTTATATATAT
Found at i:385376 original size:22 final size:22
Alignment explanation
Indices: 385351--385394 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
385341 TATATATTTA
* *
385351 TATTTGTATCTCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
385373 TATTTATATCCCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
385395 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTATATCCCTAGAATTAAG
Found at i:389274 original size:22 final size:22
Alignment explanation
Indices: 389249--389292 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
389239 TGTATATTTA
* *
389249 TATTTGTATCTCTAAAATTAAG
1 TATTTATATCCCTAAAATTAAG
389271 TATTTATATCCCTAAAATTAAG
1 TATTTATATCCCTAAAATTAAG
389293 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
TATTTATATCCCTAAAATTAAG
Found at i:393926 original size:12 final size:12
Alignment explanation
Indices: 393911--393939 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
393901 GCTTGGCCAC
393911 TAAATATGAAAT
1 TAAATATGAAAT
393923 TAAATATGAAAT
1 TAAATATGAAAT
393935 TAAAT
1 TAAAT
393940 CCATTTAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (12 bp):
TAAATATGAAAT
Found at i:394463 original size:13 final size:13
Alignment explanation
Indices: 394445--394479 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
394435 TCTTATTAAT
394445 ATTTAAAATAAAA
1 ATTTAAAATAAAA
* *
394458 ATTTAAAATGACA
1 ATTTAAAATAAAA
394471 ATTTAAAAT
1 ATTTAAAAT
394480 TATGCAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (13 bp):
ATTTAAAATAAAA
Found at i:394555 original size:17 final size:19
Alignment explanation
Indices: 394511--394560 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
394501 TTTTATCTAT
*
394511 TTGTAAATATAATTATATA
1 TTGTATATATAATTATATA
*
394530 TTGTATATATAGTTATATA
1 TTGTATATATAATTATATA
* *
394549 TTTTATAAATAA
1 TTGTATATATAA
394561 CTAAAACTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
TTGTATATATAATTATATA
Found at i:394998 original size:22 final size:21
Alignment explanation
Indices: 394956--394998 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
394946 GATAAAAAGC
* **
394956 AATTGAATTATTTTGTTTTTA
1 AATTGAATCATTTTGAGTTTA
394977 AATTGAAATCATTTTGAGTTTA
1 AATTG-AATCATTTTGAGTTTA
394999 TATAAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (21 bp):
AATTGAATCATTTTGAGTTTA
Found at i:399546 original size:12 final size:13
Alignment explanation
Indices: 399517--399552 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
399507 ATTTAATTAA
*
399517 AAATATATTTACT
1 AAATATATATACT
399530 AAATATATATA-T
1 AAATATATATACT
399542 AAATATATATA
1 AAATATATATA
399553 AGGTACAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATATATATACT
Found at i:405939 original size:30 final size:29
Alignment explanation
Indices: 405905--406000 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 29
405895 AATTGTAACC
*
405905 AAATAAGTTTTTAACTTTTAATTTGTACTT
1 AAATAAGTCTTTAACTTTTAATTTGTA-TT
* * *
405935 AAATAAATCATTATCTTTTAATTTGTATAT
1 AAATAAGTCTTTAACTTTTAATTTGTAT-T
* *
405965 AAATAAGCCTTTAACTTTTGATTTGTAATT
1 AAATAAGTCTTTAACTTTTAATTTGT-ATT
405995 AAATAA
1 AAATAA
406001 ACTATTAACA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 1 0.02
30 52 0.95
31 2 0.04
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (29 bp):
AAATAAGTCTTTAACTTTTAATTTGTATT
Found at i:411371 original size:24 final size:24
Alignment explanation
Indices: 411344--411391 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
411334 AATAATTTAG
411344 TAATTAAGTTTGAAAATATGCATT
1 TAATTAAGTTTGAAAATATGCATT
*
411368 TAATTGAGTTTGAAAATATGCATT
1 TAATTAAGTTTGAAAATATGCATT
411392 CGAAACATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.42
Consensus pattern (24 bp):
TAATTAAGTTTGAAAATATGCATT
Found at i:412324 original size:7 final size:7
Alignment explanation
Indices: 412314--412369 Score: 84
Period size: 7 Copynumber: 8.6 Consensus size: 7
412304 TGTTAAGTGC
412314 AATATCA
1 AATATCA
412321 AATATCA
1 AATATCA
412328 AATA--A
1 AATATCA
412333 AATATCA
1 AATATCA
412340 AATATCA
1 AATATCA
412347 AATA--A
1 AATATCA
412352 AATATCA
1 AATATCA
412359 AATATCA
1 AATATCA
412366 AATA
1 AATA
412370 ATTTTTCATG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.22
7 35 0.78
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (7 bp):
AATATCA
Found at i:412337 original size:12 final size:13
Alignment explanation
Indices: 412314--412369 Score: 64
Period size: 12 Copynumber: 4.3 Consensus size: 13
412304 TGTTAAGTGC
412314 AATATCAAATATCA
1 AATA-CAAATATCA
412328 AATA-AAATATCA
1 AATACAAATATCA
412340 AATATCAAATA--A
1 AATA-CAAATATCA
412352 AATATCAAATATCA
1 AATA-CAAATATCA
412366 AATA
1 AATA
412370 ATTTTTCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
12 24 0.63
14 14 0.37
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (13 bp):
AATACAAATATCA
Found at i:412338 original size:19 final size:19
Alignment explanation
Indices: 412314--412370 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
412304 TGTTAAGTGC
412314 AATATCAAATATCAAATAA
1 AATATCAAATATCAAATAA
412333 AATATCAAATATCAAATAA
1 AATATCAAATATCAAATAA
412352 AATATCAAATATCAAATAA
1 AATATCAAATATCAAATAA
412371 TTTTTCATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (19 bp):
AATATCAAATATCAAATAA
Found at i:413656 original size:7 final size:7
Alignment explanation
Indices: 413644--413688 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
413634 TCCTTTGATC
413644 CTTTTGA
1 CTTTTGA
413651 CTTTTGA
1 CTTTTGA
413658 CTTTTGA
1 CTTTTGA
*
413665 CCTTTGA
1 CTTTTGA
*
413672 CATTTGA
1 CTTTTGA
413679 -TTTTGA
1 CTTTTGA
413685 CTTT
1 CTTT
413689 AACCTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (7 bp):
CTTTTGA
Found at i:413672 original size:21 final size:21
Alignment explanation
Indices: 413637--413685 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
413627 GTTACACTCC
*
413637 TTTGATCCTTTTGACTTTTGACT
1 TTTGA-CCTTTTGACATTTGA-T
413660 TTTGACC-TTTGACATTTGAT
1 TTTGACCTTTTGACATTTGAT
413680 TTTGAC
1 TTTGAC
413686 TTTAACCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 7 0.28
21 11 0.44
22 2 0.08
23 5 0.20
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.53
Consensus pattern (21 bp):
TTTGACCTTTTGACATTTGAT
Found at i:421486 original size:24 final size:24
Alignment explanation
Indices: 421428--421496 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 24
421418 AAAAATTGTG
* *
421428 TTTTC-TATTTTAGAAACATCATTT
1 TTTTCATATTTTA-AAAAATAATTT
*
421452 TTGTT-AAATTTTAAAAAATAATTT
1 TT-TTCATATTTTAAAAAATAATTT
421476 TTTTCATATTTTTAATAAAAT
1 TTTTCATA-TTTTAA-AAAAT
421497 CCATATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
23 2 0.06
24 15 0.42
25 14 0.39
26 5 0.14
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (24 bp):
TTTTCATATTTTAAAAAATAATTT
Found at i:422177 original size:1 final size:1
Alignment explanation
Indices: 422171--422218 Score: 96
Period size: 1 Copynumber: 48.0 Consensus size: 1
422161 TCTCTTCTAT
422171 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
422219 CACTAAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:423059 original size:9 final size:9
Alignment explanation
Indices: 423011--423068 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
423001 TAATTAATAT
423011 AATTATTAA
1 AATTATTAA
423020 AA-TATTAAA
1 AATTATT-AA
*
423029 AATATATTGA
1 AAT-TATTAA
423039 AATTATT--
1 AATTATTAA
*
423046 TATTATTAA
1 AATTATTAA
423055 AATTATTAA
1 AATTATTAA
*
423064 TATTA
1 AATTA
423069 CAAATAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
7 6 0.15
8 4 0.10
9 22 0.55
10 4 0.10
11 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (9 bp):
AATTATTAA
Found at i:423073 original size:16 final size:15
Alignment explanation
Indices: 423032--423112 Score: 56
Period size: 16 Copynumber: 5.0 Consensus size: 15
423022 TATTAAAAAT
*
423032 ATATTGAAATTATTTA
1 ATATTAAAATTA-TTA
*
423048 TTATTAAAATTATTA
1 ATATTAAAATTATTA
*
423063 ATATTACAAATAATTA
1 ATATTA-AAATTATTA
*
423079 TATTTTAATAATAATATGTA
1 -ATATTAA-AAT--TAT-TA
423099 ATATTAAAA-TATTA
1 ATATTAAAATTATTA
423113 TGTTAATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.04
15 11 0.21
16 19 0.37
17 8 0.15
18 2 0.04
19 8 0.15
20 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (15 bp):
ATATTAAAATTATTA
Found at i:423081 original size:15 final size:15
Alignment explanation
Indices: 423049--423138 Score: 51
Period size: 15 Copynumber: 5.7 Consensus size: 15
423039 AATTATTTAT
*
423049 TATTAAAATTATTAA
1 TATTAAAATAATTAA
423064 TATTACAAATAATTATA
1 TATTA-AAATAATTA-A
*
423081 TTTTAATAATAATATGTAA
1 TATTAA-AAT-A-AT-TAA
423100 TATTAAAAT-ATT-A
1 TATTAAAATAATTAA
* * *
423113 TGTTAATATAA-AAA
1 TATTAAAATAATTAA
423127 TACTTAAAATAA
1 TA-TTAAAATAA
423139 AACTATTTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
13 8 0.14
14 4 0.07
15 15 0.26
16 9 0.16
17 8 0.14
18 4 0.07
19 8 0.14
20 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
TATTAAAATAATTAA
Found at i:423119 original size:19 final size:18
Alignment explanation
Indices: 423049--423128 Score: 62
Period size: 19 Copynumber: 4.6 Consensus size: 18
423039 AATTATTTAT
423049 TATTAAAAT--TAT-TAA
1 TATTAAAATAATATGTAA
*
423064 TATTACAAATAAT-TAT-A
1 TATTA-AAATAATATGTAA
*
423081 TTTTAATAATAATATGTAA
1 TATTAA-AATAATATGTAA
*
423100 TATTAAAATATTATGTTAA
1 TATTAAAATAATATG-TAA
*
423119 TATAAAAATA
1 TATTAAAATA
423129 CTTAAAATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
15 5 0.10
16 5 0.10
17 12 0.23
18 12 0.23
19 18 0.35
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (18 bp):
TATTAAAATAATATGTAA
Found at i:423174 original size:15 final size:15
Alignment explanation
Indices: 423156--423557 Score: 213
Period size: 13 Copynumber: 27.5 Consensus size: 15
423146 TATTATTCTT
423156 TATATTATTTATT-A
1 TATATTATTTATTAA
423170 -ATA-TA-TTA-TAA
1 TATATTATTTATTAA
423181 --TATTATTTATTAA
1 TATATTATTTATTAA
423194 TA-A-TATTTATTAA
1 TATATTATTTATTAA
423207 TATATTA--TATTAA
1 TATATTATTTATTAA
423220 TAGTATGCTATTTATTAATAA
1 TA-TAT--TATTTA-T--TAA
423241 TATATTATTTATTAA
1 TATATTATTTATTAA
423256 TATATTA-TTA-TAA
1 TATATTATTTATTAA
*
423269 TAT-TTATTAATTAAA
1 TATATTATTTATT-AA
* *
423284 TTAATAATATTTATTAT
1 -T-ATATTATTTATTAA
*
423301 TATGTTATTTATTAATA
1 TATATTATTTATT-A-A
423318 TAATATACTATTTATTAA
1 T-ATAT--TATTTATTAA
* *
423336 TATATTATATTAATAG
1 TATATTAT-TTATTAA
423352 TATATTATTTATTAGTAA
1 TATATTATTTA-T--TAA
423370 TATATTATTTATTAA
1 TATATTATTTATTAA
* * *
423385 CATATTA--TAATAT
1 TATATTATTTATTAA
*
423398 TAT-TTA-TTAATAA
1 TATATTATTTATTAA
**
423411 TATGCTATTTATT-A
1 TATATTATTTATTAA
423425 -ATA-TA-TTA-T-A
1 TATATTATTTATTAA
423435 -ATATTATTTATTAA
1 TATATTATTTATTAA
* *
423449 TATAATATTAATT-A
1 TATATTATTTATTAA
* *
423463 TTTATTA-ATATTAA
1 TATATTATTTATTAA
*
423477 TAAATTA-TTA-TAA
1 TATATTATTTATTAA
423490 TAT-TTATTT-TATAA
1 TATATTATTTAT-TAA
*
423504 TA-A-TATGTATTAA
1 TATATTATTTATTAA
423517 TATATTATTTATTAATA
1 TATATTATTTATT-A-A
423534 TAATATTATTTATTAA
1 T-ATATTATTTATTAA
423550 TATATTAT
1 TATATTAT
423558 AATATAATAT
Statistics
Matches: 306, Mismatches: 32, Indels: 99
0.70 0.07 0.23
Matches are distributed among these distances:
10 8 0.03
11 11 0.04
12 19 0.06
13 70 0.23
14 34 0.11
15 67 0.22
16 21 0.07
17 13 0.04
18 45 0.15
19 2 0.01
20 11 0.04
21 5 0.02
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (15 bp):
TATATTATTTATTAA
Found at i:423237 original size:18 final size:18
Alignment explanation
Indices: 423156--423551 Score: 129
Period size: 18 Copynumber: 21.9 Consensus size: 18
423146 TATTATTCTT
*
423156 TATATTATTTATTAATATA
1 TATACTATTTATTAATA-A
* *
423175 TTATAATA-TTATTTATTAA
1 -TATACTATTTA-TTAATAA
423194 TA-A-TATTTATTAAT-A
1 TATACTATTTATTAATAA
*
423209 TAT--TA--TATTAATAG
1 TATACTATTTATTAATAA
*
423223 TATGCTATTTATTAATAA
1 TATACTATTTATTAATAA
*
423241 TATATTATTTATTAATATATTA
1 TATACTATTTATT-A-ATA--A
*
423263 TTATAATATTTATTAATTAAA
1 -TATACTATTTATTAA-T-AA
*
423284 TTAATAATATTTATT-AT--
1 -T-ATACTATTTATTAATAA
**
423301 TATGTTATTTATTAATATAA
1 TATACTATTTATT-A-ATAA
423321 TATACTATTTATTAAT-A
1 TATACTATTTATTAATAA
*
423338 TAT--TA--TATTAATAG
1 TATACTATTTATTAATAA
* *
423352 TATATTATTTATTAGTAA
1 TATACTATTTATTAATAA
*
423370 TATATTATTTATTAACATATTA
1 TATACTATTTATT-A-ATA--A
*
423392 TAATATTATTTATTAATAA
1 T-ATACTATTTATTAATAA
*
423411 TATGCTATTTATTAATATA
1 TATACTATTTATTAATA-A
* *
423430 TTATAATA-TTATTTATTAA
1 -TATACTATTTA-TTAATAA
* * * *
423449 TATAATATTAATTATTTA
1 TATACTATTTATTAATAA
* * * *
423467 T-TAATATTAATAAATTAT
1 TATACTATTTATTAA-TAA
* *
423485 TATAATATTTATTTTATAA
1 TATACTATTTA-TTAATAA
*
423504 TA-A-TATGTATTAAT-A
1 TATACTATTTATTAATAA
423519 TAT--TATTTATTAAT-A
1 TATACTATTTATTAATAA
*
423534 TAATATTATTTATTAATA
1 T-ATACTATTTATTAATA
423552 TATTATAATA
Statistics
Matches: 299, Mismatches: 34, Indels: 87
0.71 0.08 0.21
Matches are distributed among these distances:
13 14 0.05
14 6 0.02
15 32 0.11
16 17 0.06
17 24 0.08
18 87 0.29
19 28 0.09
20 40 0.13
21 8 0.03
22 18 0.06
23 25 0.08
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (18 bp):
TATACTATTTATTAATAA
Found at i:423346 original size:129 final size:134
Alignment explanation
Indices: 423197--423473 Score: 386
Period size: 129 Copynumber: 2.1 Consensus size: 134
423187 TTATTAATAA
* *
423197 TATTTATTAATATATTATATTAATAGTATGCTATTTATTAATAATATATTATTTATTAATATATT
1 TATTTATTAATATATTATATTAATAGTATACTATTTATTAATAATATATTATTTATTAACATATT
* * * *
423262 ATTATAATATTTATTAATTAA-AT-TA-ATAAT-ATTTATTATTATGTTATTTATTAATATAATA
66 ATAATAATATTTATTAA-TAATATCTATATAATAATATATTATAATATTATTTATTAATATAATA
423323 -T-AC
130 TTAAC
* *
423326 TATTTATTAATATATTATATTAATAGTATATTATTTATTAGTAATATATTATTTATTAACATATT
1 TATTTATTAATATATTATATTAATAGTATACTATTTATTAATAATATATTATTTATTAACATATT
* * *
423391 ATAATATTATTTATTAATAATATGCTATTTATTAATATATTATAATATTATTTATTAATATAATA
66 ATAATAATATTTATTAATAATAT-CTATATAATAATATATTATAATATTATTTATTAATATAATA
*
423456 TTAAT
130 TTAAC
423461 TATTTATTAATAT
1 TATTTATTAATAT
423474 TAATAAATTA
Statistics
Matches: 129, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
128 3 0.02
129 78 0.60
131 2 0.02
132 3 0.02
133 28 0.22
134 1 0.01
135 14 0.11
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (134 bp):
TATTTATTAATATATTATATTAATAGTATACTATTTATTAATAATATATTATTTATTAACATATT
ATAATAATATTTATTAATAATATCTATATAATAATATATTATAATATTATTTATTAATATAATAT
TAAC
Found at i:423398 original size:41 final size:41
Alignment explanation
Indices: 423156--423576 Score: 346
Period size: 41 Copynumber: 10.0 Consensus size: 41
423146 TATTATTCTT
423156 TATATTATTTATTAATATATTATAATATTATTTATTAATAA
1 TATATTATTTATTAATATATTATAATATTATTTATTAATAA
* * *
423197 TAT-TTATTAATATATTATATTAATAGTATGCTATTTATTAATAA
1 TATATTATTTAT-TAATATATT-ATAATAT--TATTTATTAATAA
* *
423241 TATATTATTTATTAATATATTATTATAATATTTATTAATTAAA
1 TATATTATTTATTAATATATTATAATATTATTTATTAA-T-AA
* * * * *
423284 TTAATAATATTTATTATTATGTTAT-TTATTA-ATA-TAAT-A
1 -T-ATATTATTTATTAATATATTATAATATTATTTATTAATAA
* * *
423323 TACTATTTATTAATATATTATATTAATAGTATATTATTTATTAGTAA
1 TA-TA-TTATTTAT-TAATATATT-ATA--ATATTATTTATTAATAA
*
423370 TATATTATTTATTAACATATTATAATATTATTTATTAATAA
1 TATATTATTTATTAATATATTATAATATTATTTATTAATAA
**
423411 TATGCTATTTATTAATATATTATAATATTATTTATTAATATAA
1 TATATTATTTATTAATATATTATAATATTATTTATT-A-ATAA
*
423454 TATTAATTATTTATTAATAT-TAATAA-ATTA-TTA-TAAT-A
1 TA-T-ATTATTTATTAATATATTATAATATTATTTATTAATAA
* *
423492 TTTATT-TTATAATAATATGTATTA-ATATATTATTTATTAAT-A
1 TATATTATT-TATTAATA--TATTATA-ATATTATTTATTAATAA
* *
423534 TAATATTATTTATTAATATATTATAATATAATATTATTTATAA
1 T-ATATTATTTATTAATATATTATAATATTAT-TTATTAATAA
423577 GAAAAATTAC
Statistics
Matches: 307, Mismatches: 37, Indels: 70
0.74 0.09 0.17
Matches are distributed among these distances:
35 2 0.01
36 10 0.03
37 2 0.01
38 7 0.02
39 12 0.04
40 20 0.07
41 88 0.29
42 28 0.09
43 33 0.11
44 49 0.16
45 48 0.16
46 5 0.02
47 3 0.01
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (41 bp):
TATATTATTTATTAATATATTATAATATTATTTATTAATAA
Found at i:424309 original size:21 final size:19
Alignment explanation
Indices: 424265--424311 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
424255 AATTCCTTTT
424265 ACTT-TTTGAAAAAATCAA
1 ACTTATTTGAAAAAATCAA
* *
424283 ATTTATTTGATAAAAATTAA
1 ACTTATTTGA-AAAAATCAA
424303 ACCTTATTT
1 A-CTTATTT
424312 AGGAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.13
19 5 0.22
20 9 0.39
21 6 0.26
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (19 bp):
ACTTATTTGAAAAAATCAA
Found at i:425161 original size:13 final size:11
Alignment explanation
Indices: 425132--425176 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
425122 TTAGGTTAGG
*
425132 TTTAGGGTATT
1 TTTAGGGTTTT
425143 TTTAGGGTTTT
1 TTTAGGGTTTT
425154 GATTTAGGGTTTT
1 --TTTAGGGTTTT
425167 TTTAGGGTTT
1 TTTAGGGTTT
425177 CCACGATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 20 0.65
13 11 0.35
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (11 bp):
TTTAGGGTTTT
Found at i:426914 original size:34 final size:34
Alignment explanation
Indices: 426871--426938 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
426861 AATCTTAAAC
426871 AAGTTTTACTAAGTTGACTTATAGATCGACCTTT
1 AAGTTTTACTAAGTTGACTTATAGATCGACCTTT
426905 AAGTTTTACTAAGTTGACTTATAGATCGACCTTT
1 AAGTTTTACTAAGTTGACTTATAGATCGACCTTT
426939 GACTATTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (34 bp):
AAGTTTTACTAAGTTGACTTATAGATCGACCTTT
Found at i:428569 original size:20 final size:20
Alignment explanation
Indices: 428533--428582 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
428523 TATTTTTTTG
*
428533 TTTTTA-AAATTATATTTAA
1 TTTTTATAAATTAGATTTAA
*
428552 TTTTTATAATTTAGATTTAA
1 TTTTTATAAATTAGATTTAA
428572 TATTTTATAAA
1 T-TTTTATAAA
428583 ATATATGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 6 0.23
20 12 0.46
21 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTTATAAATTAGATTTAA
Found at i:428925 original size:20 final size:20
Alignment explanation
Indices: 428902--428952 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
428892 ATAATTATTT
428902 TATATATAAATCTAT-TTAAA
1 TATATATAAAT-TATATTAAA
*
428922 TATATTAAAAATTATATTAAA
1 TATA-TATAAATTATATTAAA
428943 -ATGATATAAA
1 TAT-ATATAAA
428953 AATTAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TATATATAAATTATATTAAA
Found at i:428944 original size:22 final size:22
Alignment explanation
Indices: 428914--428957 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
428904 TATATAAATC
*
428914 TATTTAAAT-ATATTAAAAATTA
1 TATTAAAATGATA-TAAAAATTA
428936 TATTAAAATGATATAAAAATTA
1 TATTAAAATGATATAAAAATTA
428958 AAAAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TATTAAAATGATATAAAAATTA
Found at i:429589 original size:71 final size:69
Alignment explanation
Indices: 429489--429743 Score: 246
Period size: 72 Copynumber: 3.6 Consensus size: 69
429479 ATTTTTGTTA
* * * * *
429489 TTTATAATTTTAACAAGTATTACGTTTTTAATATAAAAAAAGTAATGAATGATT-AAATTATATT
1 TTTAGAATTTTAACAA-AAATACATTTTTAAGATAAAAAAAGTAATG-ATG-TTAAAATT-TATT
429553 TTCAAAAT
62 TTCAAAAT
* * * *
429561 TTTAAAATTTTAATAAAAATACATTTTTAAGATAAAAGAA-TAGTGGATGTTAAAATTTATTTTC
1 TTTAGAATTTTAACAAAAATACATTTTTAAGATAAAAAAAGTAAT-GATGTTAAAATTTATTTTC
429625 AAAAT
65 AAAAT
* * * * * *
429630 TTTGGAATTTTAGCAAAATCTTCA-TTTTAAGATAAAAAAACATAATCGATGTTGAAATCTTATT
1 TTTAGAATTTTAACAAAA-ATACATTTTTAAGATAAAAAAA-GTAAT-GATGTTAAAAT-TTATT
429694 TTCAAAAT
62 TTCAAAAT
* *
429702 TTTAGAATTTTAACAAAAACTATATTTTTATGATAAAAAAAG
1 TTTAGAATTTTAACAAAAA-TACATTTTTAAGATAAAAAAAG
429744 ACCATAATTT
Statistics
Matches: 150, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
69 43 0.29
70 14 0.09
71 33 0.22
72 45 0.30
73 15 0.10
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (69 bp):
TTTAGAATTTTAACAAAAATACATTTTTAAGATAAAAAAAGTAATGATGTTAAAATTTATTTTCA
AAAT
Found at i:429710 original size:72 final size:70
Alignment explanation
Indices: 429513--429742 Score: 236
Period size: 69 Copynumber: 3.2 Consensus size: 70
429503 AAGTATTACG
* * * *
429513 TTTTTAATATAAAAAAAGTAAT-GAATGATT-AAATTATATTTTCAAAATTTTAAAATTTTAATA
1 TTTTTAAGATAAAAAAAATAATCG-ATG-TTAAAATT-TATTTTCAAAATTTTAGAATTTTAACA
* *
429576 AAAATACA
63 AAACTTCA
* * * * *
429584 TTTTTAAGAT-AAAAGAATAGTGGATGTTAAAATTTATTTTCAAAATTTTGGAATTTTAGCAAAA
1 TTTTTAAGATAAAAAAAATAATCGATGTTAAAATTTATTTTCAAAATTTTAGAATTTTAACAAAA
429648 TCTTCA
66 -CTTCA
*
429654 -TTTTAAGATAAAAAAACATAATCGATGTTGAAATCTTATTTTCAAAATTTTAGAATTTTAACAA
1 TTTTTAAGATAAAAAAA-ATAATCGATGTTAAAAT-TTATTTTCAAAATTTTAGAATTTTAAC-A
429718 AAACTAT-A
63 AAACT-TCA
*
429726 TTTTTATGATAAAAAAA
1 TTTTTAAGATAAAAAAA
429743 GACCATAATT
Statistics
Matches: 133, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
69 37 0.28
70 24 0.18
71 24 0.18
72 28 0.21
73 20 0.15
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (70 bp):
TTTTTAAGATAAAAAAAATAATCGATGTTAAAATTTATTTTCAAAATTTTAGAATTTTAACAAAA
CTTCA
Found at i:429774 original size:23 final size:24
Alignment explanation
Indices: 429727--429774 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
429717 AAAACTATAT
* *
429727 TTTTATGATAAAAAAAGACCATAA
1 TTTTAAGATAAAAAAAGAACATAA
*
429751 TTTTAAGATAAAAAAA-AACGTAA
1 TTTTAAGATAAAAAAAGAACATAA
429774 T
1 T
429775 GGATGTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (24 bp):
TTTTAAGATAAAAAAAGAACATAA
Found at i:429930 original size:43 final size:43
Alignment explanation
Indices: 429880--429967 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
429870 TGAAATTCTA
* *
429880 AAATTTTAACGAAAATTATATTTTTAAA-ATAAGAAATGTAATG
1 AAATTTTAACAAAAATGA-ATTTTTAAAGATAAGAAATGTAATG
* *
429923 AAATTTTAACAAAAATGACTTTTTAAAGATAAGAAATGTCATG
1 AAATTTTAACAAAAATGAATTTTTAAAGATAAGAAATGTAATG
429966 AA
1 AA
429968 TGTTACTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 8 0.20
43 32 0.80
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (43 bp):
AAATTTTAACAAAAATGAATTTTTAAAGATAAGAAATGTAATG
Found at i:430044 original size:37 final size:37
Alignment explanation
Indices: 430003--430073 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
429993 ATAATACATA
*
430003 AAATATCTTTATTTAATATTATTACATATAAAATCTT
1 AAATATATTTATTTAATATTATTACATATAAAATCTT
* *
430040 AAATATATTTATTTAATGTTATTACTTATAAAAT
1 AAATATATTTATTTAATATTATTACATATAAAAT
430074 TTATTCCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (37 bp):
AAATATATTTATTTAATATTATTACATATAAAATCTT
Found at i:436823 original size:41 final size:37
Alignment explanation
Indices: 436745--436823 Score: 88
Period size: 41 Copynumber: 2.0 Consensus size: 37
436735 AATTGTGAAA
*
436745 TAAAATTTAATAAAAAAAATTATTAAAGATATTATAT
1 TAAAATTTAATAAAAAAAATTATTAAAGATATGATAT
*
436782 TAAAATTTGAATAAAATACAAAATT-TTAAATTATATGATAT
1 TAAAATTT-AAT-AAA-A-AAAATTATTAAA-GATATGATAT
436823 T
1 T
436824 TATGAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
37 8 0.23
38 3 0.09
39 3 0.09
40 6 0.17
41 15 0.43
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (37 bp):
TAAAATTTAATAAAAAAAATTATTAAAGATATGATAT
Found at i:440772 original size:1 final size:1
Alignment explanation
Indices: 440730--440764 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
440720 TACTTAGTTG
*
440730 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
440765 CATTTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:440969 original size:21 final size:22
Alignment explanation
Indices: 440943--440987 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
440933 CAACGGGGGT
440943 TCAAGAT-CAACAACTGAATAG
1 TCAAGATACAACAACTGAATAG
440964 TCAAGATGAACAACAACTGAATAG
1 TCAAGAT--ACAACAACTGAATAG
440988 GAGCATACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
24 14 0.67
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (22 bp):
TCAAGATACAACAACTGAATAG
Found at i:443586 original size:21 final size:21
Alignment explanation
Indices: 443560--443655 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
443550 TTCACATCTT
* *
443560 AAAGATTCTCTTTTGAAATTC
1 AAAGATTCTCATTTAAAATTC
*
443581 AAAGATTCTCATTTAAAATTT
1 AAAGATTCTCATTTAAAATTC
* *
443602 AAATATTCTCATTTGAAATATC
1 AAAGATTCTCATTTAAAAT-TC
*
443624 AAAGATTCTCATCTAAAATTC
1 AAAGATTCTCATTTAAAATTC
*
443645 AAATATTCTCA
1 AAAGATTCTCA
443656 AAGATTCTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 47 0.73
22 17 0.27
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAGATTCTCATTTAAAATTC
Found at i:443641 original size:43 final size:42
Alignment explanation
Indices: 443558--443655 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 42
443548 GTTTCACATC
* * *
443558 TTAAAGATTCTCTTTTGAAATTCAAAGATTCTCATTTAAAAT
1 TTAAATATTCTCATTTGAAATTCAAAGATTCTCATCTAAAAT
443600 TTAAATATTCTCATTTGAAATATCAAAGATTCTCATCTAAAAT
1 TTAAATATTCTCATTTGAAAT-TCAAAGATTCTCATCTAAAAT
*
443643 TCAAATATTCTCA
1 TTAAATATTCTCA
443656 AAGATTCTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 19 0.37
43 32 0.63
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (42 bp):
TTAAATATTCTCATTTGAAATTCAAAGATTCTCATCTAAAAT
Found at i:443658 original size:31 final size:31
Alignment explanation
Indices: 443622--443686 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
443612 ATTTGAAATA
* *
443622 TCAAAGATTCTCATCTAAAATTCAAATATTC
1 TCAAAGATTCTCATCTAAAACTCAAAGATTC
* * *
443653 TCAAAGATTCTTATTTAAGACTCAAAGATTC
1 TCAAAGATTCTCATCTAAAACTCAAAGATTC
443684 TCA
1 TCA
443687 TTTAAAGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.35
Consensus pattern (31 bp):
TCAAAGATTCTCATCTAAAACTCAAAGATTC
Found at i:443676 original size:21 final size:21
Alignment explanation
Indices: 443652--443691 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
443642 TTCAAATATT
*
443652 CTCAAAGATTCTTATTTAAGA
1 CTCAAAGATTCTCATTTAAGA
443673 CTCAAAGATTCTCATTTAA
1 CTCAAAGATTCTCATTTAA
443692 AGATCCACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTAAGA
Found at i:444138 original size:63 final size:63
Alignment explanation
Indices: 444048--444208 Score: 162
Period size: 63 Copynumber: 2.6 Consensus size: 63
444038 TTCACCATTT
* * * * * ** *
444048 TAAGCTTCTTAGCATTAG-TCATCTCAGAATAAATTCTGTCTTCTATCACTTGATTATCGTTTA
1 TAAGCTTCTTAGCACTAGCT-ATTTCAGAATAAATTCTATCTTCCATCACTTGATTACCACTCA
* * * *
444111 TAAGCTTCTTAACACTAGCTATTTCAGAATAAATTTTATCTTCCATCATTTGGTTACCACTCA
1 TAAGCTTCTTAGCACTAGCTATTTCAGAATAAATTCTATCTTCCATCACTTGATTACCACTCA
* * * *
444174 TAGGTTTCTCAGCACTAGCCATTTCAGAATAAATT
1 TAAGCTTCTTAGCACTAGCTATTTCAGAATAAATT
444209 TCATATTCCA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 79 0.99
64 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (63 bp):
TAAGCTTCTTAGCACTAGCTATTTCAGAATAAATTCTATCTTCCATCACTTGATTACCACTCA
Found at i:449423 original size:167 final size:167
Alignment explanation
Indices: 449209--449532 Score: 476
Period size: 167 Copynumber: 1.9 Consensus size: 167
449199 AAACAATATG
* * * * *
449209 ACAATTATTTTTAATTGAAATTTCATTTTAATTCTTCCACCATTTGAGACAAATTTA-AAAAAAT
1 ACAATTATTTTTAATTAAAATTTCATCTAAATTATTCCACAATTTGAGACAAATTTAGAAAAAAT
*
449273 TTCTCACCTAGAA-ATTTCTTAGAAAATTTACAATTTGAAATTTTTTAAAATCTCATCATTAGAT
66 TT-TCACCTA-AAGATTTCTTAGAAAATTTACAATTTGAAATTTTTAAAAATCTCATCATTAGAT
449337 AATTATCAAATATTTTCAA-TCAGAAATTTAGAAAAGAAT
129 AATTATCAAATATTTTCAACT-AGAAATTTAGAAAAGAAT
*
449376 ACAATTACTTTTT-ATTAAAATTTCATCTAAATTATTTCACAATTTGAGACAAATTTAGAAAAAA
1 ACAATTA-TTTTTAATTAAAATTTCATCTAAATTATTCCACAATTTGAGACAAATTTAGAAAAAA
* * * * *
449440 TTTTCACCTAAAGATTTTTTAGAAAATTTACTATTTGAAATTTTTAAAAATCTTATTATTGGATA
65 TTTTCACCTAAAGATTTCTTAGAAAATTTACAATTTGAAATTTTTAAAAATCTCATCATTAGATA
449505 ATTATCAAATATTTTCAACTAGAAATTT
130 ATTATCAAATATTTTCAACTAGAAATTT
449533 TTATTTTTTC
Statistics
Matches: 141, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
166 2 0.01
167 124 0.88
168 15 0.11
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (167 bp):
ACAATTATTTTTAATTAAAATTTCATCTAAATTATTCCACAATTTGAGACAAATTTAGAAAAAAT
TTTCACCTAAAGATTTCTTAGAAAATTTACAATTTGAAATTTTTAAAAATCTCATCATTAGATAA
TTATCAAATATTTTCAACTAGAAATTTAGAAAAGAAT
Found at i:449822 original size:29 final size:28
Alignment explanation
Indices: 449767--449828 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
449757 TTAATCATGC
* *
449767 AAAAATACTAAAAAAAACACATAAAAAAT
1 AAAAATACCAAAAAAAACACA-AAAAAAA
* *
449796 AAAAATACCAAAAAAAATA-AAAGAAAA
1 AAAAATACCAAAAAAAACACAAAAAAAA
449823 AAAAAT
1 AAAAAT
449829 GAAACGGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 11 0.38
28 1 0.03
29 17 0.59
ACGTcount: A:0.79, C:0.08, G:0.02, T:0.11
Consensus pattern (28 bp):
AAAAATACCAAAAAAAACACAAAAAAAA
Found at i:456427 original size:7 final size:7
Alignment explanation
Indices: 456415--456448 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
456405 GAAAATTTTT
456415 TTTGTTG
1 TTTGTTG
456422 TTTGTTG
1 TTTGTTG
456429 TTTGTTG
1 TTTGTTG
*
456436 TTT-TTT
1 TTTGTTG
456442 TTTGTTG
1 TTTGTTG
456449 GATAATGCTA
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:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (7 bp):
TTTGTTG
Found at i:460427 original size:304 final size:305
Alignment explanation
Indices: 459835--460448 Score: 865
Period size: 304 Copynumber: 2.0 Consensus size: 305
459825 TTCTGGTTGA
*
459835 AAGGCTGGGGACTTGATTTTGGTTTTCTGTGGTCTCAGGGGTAAGGGCGCTTGGTGTAAGGGCAG
1 AAGGCTGGGGACTTGATTTTGGTTTTCTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAAGGGCAG
* ** * * *
459900 TTACATAGGTGAGGAGGGCTATGGTGCGCTGGTATAGTGGTTTGTATGAGGGATTGACTGGTGGC
66 TTACACAGGTGAAAAGGGCTATGGTGCGCTGGTAGAGTGGTTGGGATGAGGGATTGACTGGTGGC
* * * *
459965 TTCTATTTGGGTTGGTGGAACTGGTTGAAGAGGGGATCAATGATAGGAATGGGATGGTTCAATGG
131 TTCTAGTTGGGCTAGTGGAACTGGTTGAAAAGGGGATCAATGATAGGAATGGGATGGTTCAATGG
* * * * *
460030 AGTTTTTTGTGTGTTCCTTTTTCTCATGGGTGCTGGTTCGGATGCTGGTGAATGGTTGGGAATGT
196 AGCTTTTTGTGTGTTCCTCTTTCTCATAGGTGCTGGTTCGGACGCTGGTGAATGGTTGGGAACGT
* *
460095 TTGGTGCTTGGGGCCCTAAAAAGCGTAGGTGCACGGTCAAAGCAG
261 TTGGTGCCTGAGGCCCTAAAAAGCGTAGGTGCACGGTCAAAGCAG
* * *
460140 AAGGCTGGGGACTTGATTTTGGTTTTTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAGGGGCTG
1 AAGGCTGGGGACTTGATTTTGGTTTTCTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAAGGGCAG
* * *
460205 TTACACAGGTGAAAAGGGTTATGTTGCGGTGGTAGAGTGGTTGGGATGAGGGATTGACTGGTGGC
66 TTACACAGGTGAAAAGGGCTATGGTGCGCTGGTAGAGTGGTTGGGATGAGGGATTGACTGGTGGC
*
460270 TTCT-GTTGGGCTAGTGGAACTGGTTGAAAAAGGGG-TCGATGATA-GAAGTGGGATGGTTCAAT
131 TTCTAGTTGGGCTAGTGGAACTGGTTG-AAAAGGGGATCAATGATAGGAA-TGGGATGGTTCAAT
* * * *
460332 GGAGCTTTTTGTGTGTTCCTCTTTCTCTTAGGTGCTGTTTCGGACGTTGGTGAATGGTTTGGAAC
194 GGAGCTTTTTGTGTGTTCCTCTTTCTCATAGGTGCTGGTTCGGACGCTGGTGAATGGTTGGGAAC
* *** * * *
460397 GTTTGGTGCCTGAGGCTCTGGGATGCGTAGGTGTAGGGTCAAAGCAG
259 GTTTGGTGCCTGAGGCCCTAAAAAGCGTAGGTGCACGGTCAAAGCAG
460444 AAGGC
1 AAGGC
460449 CTCGGTGCTT
Statistics
Matches: 271, Mismatches: 36, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
303 3 0.01
304 140 0.52
305 128 0.47
ACGTcount: A:0.18, C:0.11, G:0.39, T:0.32
Consensus pattern (305 bp):
AAGGCTGGGGACTTGATTTTGGTTTTCTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAAGGGCAG
TTACACAGGTGAAAAGGGCTATGGTGCGCTGGTAGAGTGGTTGGGATGAGGGATTGACTGGTGGC
TTCTAGTTGGGCTAGTGGAACTGGTTGAAAAGGGGATCAATGATAGGAATGGGATGGTTCAATGG
AGCTTTTTGTGTGTTCCTCTTTCTCATAGGTGCTGGTTCGGACGCTGGTGAATGGTTGGGAACGT
TTGGTGCCTGAGGCCCTAAAAAGCGTAGGTGCACGGTCAAAGCAG
Found at i:460772 original size:19 final size:18
Alignment explanation
Indices: 460725--460772 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
460715 ACTATTGGCC
* *
460725 ATTCTTTTTTTGTTATTT
1 ATTCTTTTTTTATAATTT
* *
460743 TTTCTCTTTTTCATAATTT
1 ATTCT-TTTTTTATAATTT
460762 ATTCTTTTTTT
1 ATTCTTTTTTT
460773 TGTAAATTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.75
Consensus pattern (18 bp):
ATTCTTTTTTTATAATTT
Found at i:462310 original size:3 final size:3
Alignment explanation
Indices: 462257--462294 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
462247 GTCCACCTCT
462257 ATA A-A ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
462295 CAACATCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:462543 original size:68 final size:70
Alignment explanation
Indices: 462468--462603 Score: 240
Period size: 70 Copynumber: 2.0 Consensus size: 70
462458 AATTATTACT
*
462468 AATATTATATTTTGGAATATT-ATTTACTTTTTTAAAA-TTATAATAAAAAATTATTTGAAACAT
1 AATATTATATTTTGGAATATTGATTTACTTTTTTAAAATTTATAACAAAAAATTATTTGAAACAT
462531 TGACA
66 TGACA
*
462536 AATATTATATTTTGGAATATTGATTTACTTTTTTAAAATTTTTAACAAAAAATTATTTGAAACAT
1 AATATTATATTTTGGAATATTGATTTACTTTTTTAAAATTTATAACAAAAAATTATTTGAAACAT
462601 TGA
66 TGA
462604 AAGATAATAT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 21 0.33
69 16 0.25
70 27 0.42
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (70 bp):
AATATTATATTTTGGAATATTGATTTACTTTTTTAAAATTTATAACAAAAAATTATTTGAAACAT
TGACA
Found at i:462693 original size:6 final size:7
Alignment explanation
Indices: 462678--462704 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
462668 AAATGTTAAA
462678 TTTTATT
1 TTTTATT
462685 TTTTATT
1 TTTTATT
462692 TTTTATT
1 TTTTATT
462699 TTTTAT
1 TTTTAT
462705 AAGTTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:466975 original size:22 final size:22
Alignment explanation
Indices: 466945--466990 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
466935 GTTATAAAAC
466945 TCTCATTATAACTTCGTATAAG
1 TCTCATTATAACTTCGTATAAG
*
466967 TCTCGTTATAACTTCGTATAAG
1 TCTCATTATAACTTCGTATAAG
466989 TC
1 TC
466991 ATGAGGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (22 bp):
TCTCATTATAACTTCGTATAAG
Found at i:470045 original size:166 final size:166
Alignment explanation
Indices: 469855--470176 Score: 497
Period size: 166 Copynumber: 1.9 Consensus size: 166
469845 AAACAATATG
* * * * *
469855 ACAATTATTTTTATTGAAATTTCATTTAAATTCTTCCACCATTTGAGACAAATTTA-AAGAAATT
1 ACAATTATTTTTATTAAAATTTCATCTAAATTATTCCACAATTTGAGACAAATTTAGAAAAAATT
*
469919 TCTCACATAGAGATTTCTTATAAAATTTACAATTTGAAATTTTTAAAAATCTCAT-ATTAGATAA
66 T-TCACATAAAGATTTCTTATAAAATTTACAATTTGAAATTTTTAAAAATCTCATCATTAGATAA
469983 TTATCAAATATTTTCAA-TCAGAAATTTAGAAAAGAAT
130 TTATCAAATATTTTCAACT-AGAAATTTAGAAAAGAAT
*
470020 ACAATTACTTTTTATTAAAATTTCATCTAAATTATTTCACAATTTGAGACAAATTTAGAAAAAAT
1 ACAATTA-TTTTTATTAAAATTTCATCTAAATTATTCCACAATTTGAGACAAATTTAGAAAAAAT
* * * *
470085 TTTTACCTAAAGATTTCTTATAAAATTTACTATTTGAAATTTTTAAAAATCTCATCATTGGATAA
65 TTTCACATAAAGATTTCTTATAAAATTTACAATTTGAAATTTTTAAAAATCTCATCATTAGATAA
470150 TTATCAAATATTTTCAACTAGAAATTT
130 TTATCAAATATTTTCAACTAGAAATTT
470177 TTGTTTTTTC
Statistics
Matches: 142, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
165 7 0.05
166 93 0.65
167 41 0.29
168 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (166 bp):
ACAATTATTTTTATTAAAATTTCATCTAAATTATTCCACAATTTGAGACAAATTTAGAAAAAATT
TTCACATAAAGATTTCTTATAAAATTTACAATTTGAAATTTTTAAAAATCTCATCATTAGATAAT
TATCAAATATTTTCAACTAGAAATTTAGAAAAGAAT
Found at i:470466 original size:29 final size:29
Alignment explanation
Indices: 470412--470468 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
470402 TTAATCATGC
* * *
470412 AAAAATACTAAAAAAAACACATAAAAAAT
1 AAAAATACCAAAAAAAACAAAAAAAAAAT
*
470441 AAAAATACCAAAAAAAATAAAAAAAAAA
1 AAAAATACCAAAAAAAACAAAAAAAAAA
470469 ACAAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.11
Consensus pattern (29 bp):
AAAAATACCAAAAAAAACAAAAAAAAAAT
Found at i:470474 original size:18 final size:18
Alignment explanation
Indices: 470434--470475 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
470424 AAAAACACAT
**
470434 AAAAAATAAAAATACCAA
1 AAAAAATAAAAATAAAAA
470452 AAAAAATAAAAA-AAAAA
1 AAAAAATAAAAATAAAAA
470469 ACAAAAA
1 A-AAAAA
470476 AATGAAACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (18 bp):
AAAAAATAAAAATAAAAA
Found at i:470474 original size:29 final size:29
Alignment explanation
Indices: 470412--470475 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
470402 TTAATCATGC
* * *
470412 AAAAATACTAAAAAAAACACATAAAAAAT
1 AAAAATACCAAAAAAAACACAAAAAAAAA
* *
470441 AAAAATACCAAAAAAAATAAAAAAAAAAA
1 AAAAATACCAAAAAAAACACAAAAAAAAA
470470 CAAAAA
1 -AAAAA
470476 AATGAAACGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.09
Consensus pattern (29 bp):
AAAAATACCAAAAAAAACACAAAAAAAAA
Found at i:471224 original size:10 final size:10
Alignment explanation
Indices: 471209--471281 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 10
471199 CACCCATTCA
471209 TTTCTTTTTT
1 TTTCTTTTTT
*
471219 TTTCTTATTT
1 TTTCTTTTTT
* **
471229 TAT-TTTTCC
1 TTTCTTTTTT
**
471238 TTTCTTTTCC
1 TTTCTTTTTT
*
471248 TTTCATTTTT
1 TTTCTTTTTT
*
471258 TTTCTTCTTT
1 TTTCTTTTTT
471268 TTTCTTTATTT
1 TTTCTTT-TTT
471279 TTT
1 TTT
471282 GTCTTCTTTC
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
9 5 0.10
10 38 0.78
11 6 0.12
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:471265 original size:23 final size:22
Alignment explanation
Indices: 471239--471290 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
471229 TATTTTTCCT
*
471239 TTCTTTTCCTTTCATTTTTTTTC
1 TTCTTTTCCTTT-ATTTTTTGTC
*
471262 TTCTTTTTTCTTTATTTTTTGTC
1 TTC-TTTTCCTTTATTTTTTGTC
471285 TTCTTT
1 TTCTTT
471291 CACTGAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 3 0.12
23 15 0.58
24 8 0.31
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (22 bp):
TTCTTTTCCTTTATTTTTTGTC
Found at i:481130 original size:304 final size:303
Alignment explanation
Indices: 480517--481726 Score: 1412
Period size: 304 Copynumber: 3.9 Consensus size: 303
480507 TTCTGGTTGA
* *
480517 AAGGCTGGGGACTTGATTTTGGTTTTCTGTGGTCTCAGGGGTAAGGGCGCTTGGTGTAAGGGCAG
1 AAGGCTGGGGACTTGATTTTGGTTTTTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAAGGGCAG
* * * *
480582 TTACATAGGTGAGGAGGGCTATGGTGCGCTGGTATAGTGGTTTGTATGAGGGATTGACTGGTGGC
66 TTACACAGGTGAAGAGGGCTATGGTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGGC
* * * *
480647 TTCTATTTGGGTTGGTGGAACTGGTTGAAGAGGGGATCAATGATAGGAATGGGATGGTTCAATAG
131 TTCTAGTTGGGCTAGTGGAACTGGTTGAAAAGGGGATCAATGATAGGAATGGGATGGTTCAATAG
* * * *
480712 AGTTTTTTGTGTGTTCCTTTTTCTCATGGGTGCTGGTTCGGATGCTGGTGAATGGTCGGGAATGT
196 AGCTTTTTGTGTGTTCCTCTTTCTCATAGGTGCTGGTTCGGATGCTGGTGAATGGTCGGGAACGT
*
480777 TTGGTGCTTGGGGCTCTAAAAAGCGTAGGTGCACGGTCAAAGCAG
261 TTGGTGCTTGAGGCTCTAAAAA--GTAGGTGCACGGTCAAAGCAG
* *
480822 AAGGCTGGGGACTTGATTTTGGTTTTTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAGGGGCTG
1 AAGGCTGGGGACTTGATTTTGGTTTTTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAAGGGCAG
* *
480887 TTACACAGGTGAA-AGGGGTTATGTTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGG
66 TTACACAGGTGAAGA-GGGCTATGGTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGG
* *
480951 CTTCT-GTTGGGCTAGTGGAACTGGTTGAAAAAGGGG-TCGATGATAGGAGTGGGATGGTTCAAT
130 CTTCTAGTTGGGCTAGTGGAACTGGTTG-AAAAGGGGATCAATGATAGGAATGGGATGGTTCAAT
* * * * * **
481014 GGAGCTTTTTGTGTGTTCCTCTTTCTCTTAGGTGCTGTTTCGGAAGTTGGTGAATGGTTTGGAAC
194 AGAGCTTTTTGTGTGTTCCTCTTTCTCATAGGTGCTGGTTCGGATGCTGGTGAATGGTCGGGAAC
* *
481079 GTTTGGTGCTTGAGGCTCTGGGAAAAA-TAGGTGTAGGGTCAAAGCAG
259 GTTTGGTGCTTGAGGCTCT---AAAAAGTAGGTGCACGGTCAAAGCAG
* ** * * * * * **
481126 AAGGCCTCGGTG-CTTGGTGGAGACTGGGACTTCTTGTGGGAAAAGGCCCCAGATGGAAAAATAG
1 AAGG-CT-GGGGAC-T--T-GA-TTTTGG--TT-TT-T-TG---TGGTCTCAG--GG--GTA-AG
* * * * *
481190 TTGCGCTTGGTGTAAGGGCAGTTACATAGGTGAGGAGGGCTATGGTGCGCTGGTATAGTGGTTTG
46 -GGCACTTGGTGTAAGGGCAGTTACACAGGTGAAGAGGGCTATGGTGCGCTGGTAGAGTGGTTTG
* * * *
481255 TATGAGGGATTGACTGGTGGCTTCTATTTGGG-TTGATGGAACTGGTTGAAGAGGGGATCAATGA
110 GATGAGGGATTGACTGGTGGCTTCTAGTTGGGCTAG-TGGAACTGGTTGAAAAGGGGATCAATGA
* * * *
481319 TAAGAATGGGATGGTTCAATAGAGTTTTTTGTGTGTTCCTTTTTCTCATGGGTGCTGGTTCGGAT
174 TAGGAATGGGATGGTTCAATAGAGCTTTTTGTGTGTTCCTCTTTCTCATAGGTGCTGGTTCGGAT
* * *
481384 GCTGGTGAATGGTCGGGAATGTTAGGTGCTTGGGGCTCTAAAAAGCGTAGGTGCACGGTCAAAGC
239 GCTGGTGAATGGTCGGGAACGTTTGGTGCTTGAGGCTCTAAAAA--GTAGGTGCACGGTCAAAGC
481449 AG
302 AG
* * * *
481451 AAGGCTGGGGACTTGATTTTGGTTTGTTGTGGTCTTAGGGGTAAGGGCACTTGGTGTAGGGGCTG
1 AAGGCTGGGGACTTGATTTTGGTTTTTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAAGGGCAG
* *
481516 TTACACAGGTGAA-AGGGGTTATGTTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGG
66 TTACACAGGTGAAGA-GGGCTATGGTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGG
* * *
481580 CTT-TTGTTGGGCTAGTGGAACTGGTTGAAAAAGGGG-TCGATGATAGGAGTGGGATGGTTCAAT
130 CTTCTAGTTGGGCTAGTGGAACTGGTTG-AAAAGGGGATCAATGATAGGAATGGGATGGTTCAAT
* * * * * **
481643 GGAGCTTTTTGTGTGTTCCTCTTTCTCTTAGGTGCTGTTTCGGACGTTGGTGAATGGTTTGGAAC
194 AGAGCTTTTTGTGTGTTCCTCTTTCTCATAGGTGCTGGTTCGGATGCTGGTGAATGGTCGGGAAC
481708 GTTTGGTGCTTGAGGCTCT
259 GTTTGGTGCTTGAGGCTCT
481727 GGGATGCGCA
Statistics
Matches: 755, Mismatches: 113, Indels: 75
0.80 0.12 0.08
Matches are distributed among these distances:
304 253 0.34
305 216 0.29
306 6 0.01
307 6 0.01
308 1 0.00
309 4 0.01
310 3 0.00
311 5 0.01
312 2 0.00
313 2 0.00
314 2 0.00
315 2 0.00
316 1 0.00
317 2 0.00
318 6 0.01
319 3 0.00
320 4 0.01
321 1 0.00
322 6 0.01
323 6 0.01
324 89 0.12
325 135 0.18
ACGTcount: A:0.19, C:0.11, G:0.38, T:0.32
Consensus pattern (303 bp):
AAGGCTGGGGACTTGATTTTGGTTTTTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAAGGGCAG
TTACACAGGTGAAGAGGGCTATGGTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGGC
TTCTAGTTGGGCTAGTGGAACTGGTTGAAAAGGGGATCAATGATAGGAATGGGATGGTTCAATAG
AGCTTTTTGTGTGTTCCTCTTTCTCATAGGTGCTGGTTCGGATGCTGGTGAATGGTCGGGAACGT
TTGGTGCTTGAGGCTCTAAAAAGTAGGTGCACGGTCAAAGCAG
Found at i:481760 original size:629 final size:629
Alignment explanation
Indices: 480563--481818 Score: 2359
Period size: 629 Copynumber: 2.0 Consensus size: 629
480553 AGGGGTAAGG
480563 GCGCTTGGTGTAAGGGCAGTTACATAGGTGAGGAGGGCTATGGTGCGCTGGTATAGTGGTTTGTA
1 GCGCTTGGTGTAAGGGCAGTTACATAGGTGAGGAGGGCTATGGTGCGCTGGTATAGTGGTTTGTA
* *
480628 TGAGGGATTGACTGGTGGCTTCTATTTGGGTTGGTGGAACTGGTTGAAGAGGGGATCAATGATAG
66 TGAGGGATTGACTGGTGGCTTCTATTTGGGTTGATGGAACTGGTTGAAGAGGGGATCAATGATAA
480693 GAATGGGATGGTTCAATAGAGTTTTTTGTGTGTTCCTTTTTCTCATGGGTGCTGGTTCGGATGCT
131 GAATGGGATGGTTCAATAGAGTTTTTTGTGTGTTCCTTTTTCTCATGGGTGCTGGTTCGGATGCT
*
480758 GGTGAATGGTCGGGAATGTTTGGTGCTTGGGGCTCTAAAAAGCGTAGGTGCACGGTCAAAGCAGA
196 GGTGAATGGTCGGGAATGTTAGGTGCTTGGGGCTCTAAAAAGCGTAGGTGCACGGTCAAAGCAGA
*
480823 AGGCTGGGGACTTGATTTTGGTTTTTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAGGGGCTGT
261 AGGCTGGGGACTTGATTTTGGTTTGTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAGGGGCTGT
480888 TACACAGGTGAAAGGGGTTATGTTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGGCT
326 TACACAGGTGAAAGGGGTTATGTTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGGCT
480953 TCTGTTGGGCTAGTGGAACTGGTTGAAAAAGGGGTCGATGATAGGAGTGGGATGGTTCAATGGAG
391 TCTGTTGGGCTAGTGGAACTGGTTGAAAAAGGGGTCGATGATAGGAGTGGGATGGTTCAATGGAG
481018 CTTTTTGTGTGTTCCTCTTTCTCTTAGGTGCTGTTTCGGAAGTTGGTGAATGGTTTGGAACGTTT
456 CTTTTTGTGTGTTCCTCTTTCTCTTAGGTGCTGTTTCGGAAGTTGGTGAATGGTTTGGAACGTTT
*
481083 GGTGCTTGAGGCTCTGGGAAAAATAGGTGTAGGGTCAAAGCAGAAGGCCTCGGTGCTTGGTGGAG
521 GGTGCTTGAGGCTCTGGGAAAAACAGGTGTAGGGTCAAAGCAGAAGGCCTCGGTGCTTGGTGGAG
* *
481148 ACTGGGACTTCTTGTGGGAAAAGGCCCCAGATGGAAAAATAGTT
586 ACTCGGACTTCTCGTGGGAAAAGGCCCCAGATGGAAAAATAGTT
481192 GCGCTTGGTGTAAGGGCAGTTACATAGGTGAGGAGGGCTATGGTGCGCTGGTATAGTGGTTTGTA
1 GCGCTTGGTGTAAGGGCAGTTACATAGGTGAGGAGGGCTATGGTGCGCTGGTATAGTGGTTTGTA
481257 TGAGGGATTGACTGGTGGCTTCTATTTGGGTTGATGGAACTGGTTGAAGAGGGGATCAATGATAA
66 TGAGGGATTGACTGGTGGCTTCTATTTGGGTTGATGGAACTGGTTGAAGAGGGGATCAATGATAA
481322 GAATGGGATGGTTCAATAGAGTTTTTTGTGTGTTCCTTTTTCTCATGGGTGCTGGTTCGGATGCT
131 GAATGGGATGGTTCAATAGAGTTTTTTGTGTGTTCCTTTTTCTCATGGGTGCTGGTTCGGATGCT
481387 GGTGAATGGTCGGGAATGTTAGGTGCTTGGGGCTCTAAAAAGCGTAGGTGCACGGTCAAAGCAGA
196 GGTGAATGGTCGGGAATGTTAGGTGCTTGGGGCTCTAAAAAGCGTAGGTGCACGGTCAAAGCAGA
*
481452 AGGCTGGGGACTTGATTTTGGTTTGTTGTGGTCTTAGGGGTAAGGGCACTTGGTGTAGGGGCTGT
261 AGGCTGGGGACTTGATTTTGGTTTGTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAGGGGCTGT
481517 TACACAGGTGAAAGGGGTTATGTTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGGCT
326 TACACAGGTGAAAGGGGTTATGTTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGGCT
*
481582 TTTGTTGGGCTAGTGGAACTGGTTGAAAAAGGGGTCGATGATAGGAGTGGGATGGTTCAATGGAG
391 TCTGTTGGGCTAGTGGAACTGGTTGAAAAAGGGGTCGATGATAGGAGTGGGATGGTTCAATGGAG
*
481647 CTTTTTGTGTGTTCCTCTTTCTCTTAGGTGCTGTTTCGGACGTTGGTGAATGGTTTGGAACGTTT
456 CTTTTTGTGTGTTCCTCTTTCTCTTAGGTGCTGTTTCGGAAGTTGGTGAATGGTTTGGAACGTTT
**** *
481712 GGTGCTTGAGGCTCTGGGATGCGCAGGTGTAGGGTCAGAGCAGAAGGCCTCGGTGCTTGGTGGAG
521 GGTGCTTGAGGCTCTGGGAAAAACAGGTGTAGGGTCAAAGCAGAAGGCCTCGGTGCTTGGTGGAG
* *
481777 ACTCGGACTTCTCGTGGGAAAAGGCTCTAGATGGAAAAATAG
586 ACTCGGACTTCTCGTGGGAAAAGGCCCCAGATGGAAAAATAG
481819 GTGCTTCCCC
Statistics
Matches: 610, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
629 610 1.00
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.31
Consensus pattern (629 bp):
GCGCTTGGTGTAAGGGCAGTTACATAGGTGAGGAGGGCTATGGTGCGCTGGTATAGTGGTTTGTA
TGAGGGATTGACTGGTGGCTTCTATTTGGGTTGATGGAACTGGTTGAAGAGGGGATCAATGATAA
GAATGGGATGGTTCAATAGAGTTTTTTGTGTGTTCCTTTTTCTCATGGGTGCTGGTTCGGATGCT
GGTGAATGGTCGGGAATGTTAGGTGCTTGGGGCTCTAAAAAGCGTAGGTGCACGGTCAAAGCAGA
AGGCTGGGGACTTGATTTTGGTTTGTTGTGGTCTCAGGGGTAAGGGCACTTGGTGTAGGGGCTGT
TACACAGGTGAAAGGGGTTATGTTGCGCTGGTAGAGTGGTTTGGATGAGGGATTGACTGGTGGCT
TCTGTTGGGCTAGTGGAACTGGTTGAAAAAGGGGTCGATGATAGGAGTGGGATGGTTCAATGGAG
CTTTTTGTGTGTTCCTCTTTCTCTTAGGTGCTGTTTCGGAAGTTGGTGAATGGTTTGGAACGTTT
GGTGCTTGAGGCTCTGGGAAAAACAGGTGTAGGGTCAAAGCAGAAGGCCTCGGTGCTTGGTGGAG
ACTCGGACTTCTCGTGGGAAAAGGCCCCAGATGGAAAAATAGTT
Found at i:482365 original size:20 final size:21
Alignment explanation
Indices: 482328--482371 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
482318 AAAAAATTAC
*
482328 TTAAATCAATTTGAAT-AAAT
1 TTAAATCAATTCGAATAAAAT
* *
482348 TTAAATTAATTCGGATAAAAT
1 TTAAATCAATTCGAATAAAAT
482369 TTA
1 TTA
482372 GTCTTTACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (21 bp):
TTAAATCAATTCGAATAAAAT
Found at i:483860 original size:69 final size:70
Alignment explanation
Indices: 483787--483921 Score: 220
Period size: 70 Copynumber: 1.9 Consensus size: 70
483777 TAATTATTAT
* *
483787 TAATATTATATTTTGGAATATT-ATTTACTTTTTT-AAATTTTATAATAAAAAATTATTTGATAC
1 TAATATTATATTTTGGAATATTGATTTACTTTTTTAAAATTTT-TAACAAAAAATTATTTGAAAC
483850 ATAGAC
65 ATAGAC
*
483856 TAATATTTTATTTTGGAATATTGATTTACTTTTTTAAAATTTTTAACAAAAAATTATTTGAAACA
1 TAATATTATATTTTGGAATATTGATTTACTTTTTTAAAATTTTTAACAAAAAATTATTTGAAACA
483921 T
66 T
483922 TGAAAGATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
69 21 0.34
70 33 0.54
71 7 0.11
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (70 bp):
TAATATTATATTTTGGAATATTGATTTACTTTTTTAAAATTTTTAACAAAAAATTATTTGAAACA
TAGAC
Found at i:485754 original size:56 final size:56
Alignment explanation
Indices: 485668--485813 Score: 256
Period size: 56 Copynumber: 2.6 Consensus size: 56
485658 TATCGTCATT
485668 ATATTGTTATTGCTATGGTATAAAAGTATATTAGGTACTCTTTCCTTTTCTTTGTG
1 ATATTGTTATTGCTATGGTATAAAAGTATATTAGGTACTCTTTCCTTTTCTTTGTG
*
485724 ATATTGTTATTGCTATGGTATAAAAGTATATTAGGTACTCTTTCTTTTTCTTTGTG
1 ATATTGTTATTGCTATGGTATAAAAGTATATTAGGTACTCTTTCCTTTTCTTTGTG
* * *
485780 ATATTGTTATTGCTATGGAAAAAAAGTATCTTAG
1 ATATTGTTATTGCTATGGTATAAAAGTATATTAG
485814 TTTTTAATTT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 86 1.00
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (56 bp):
ATATTGTTATTGCTATGGTATAAAAGTATATTAGGTACTCTTTCCTTTTCTTTGTG
Found at i:488253 original size:67 final size:69
Alignment explanation
Indices: 488040--488242 Score: 315
Period size: 67 Copynumber: 3.0 Consensus size: 69
488030 ATGAATAACA
*
488040 AATATTTATATAGATAAAA-AACCAATTTTTTTCTAATTTATACATTTAAT-GTATTTATACATA
1 AATATTTATATAGATAAAAGAA-CAATTTTTTTCTAATTTATACATTT-ATCGTATTTATATATA
488103 AATAGT
64 AATAGT
* *
488109 AATATTTATATAGATAAAAG-ACCA-TTTTTTCTAATTTATACATTTAACGTATTTATATATAAA
1 AATATTTATATAGATAAAAGAACAATTTTTTTCTAATTTATACATTTATCGTATTTATATATAAA
488172 TAGT
66 TAGT
* *
488176 AATATTTATATAGATAAAAGAACAATTTTTTTCTGATTTATACATTTATCGTATTTATATGTAAA
1 AATATTTATATAGATAAAAGAACAATTTTTTTCTAATTTATACATTTATCGTATTTATATATAAA
488241 TA
66 TA
488243 ATATGGTATA
Statistics
Matches: 123, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
66 1 0.01
67 59 0.48
68 5 0.04
69 58 0.47
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (69 bp):
AATATTTATATAGATAAAAGAACAATTTTTTTCTAATTTATACATTTATCGTATTTATATATAAA
TAGT
Found at i:493526 original size:14 final size:14
Alignment explanation
Indices: 493507--493542 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
493497 AATTTACAAT
*
493507 TATTAAATTCTCAC
1 TATTAAACTCTCAC
493521 TATTAAAACTCTCAC
1 TATT-AAACTCTCAC
493536 TATTAAA
1 TATTAAA
493543 ACTTACATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (14 bp):
TATTAAACTCTCAC
Found at i:493533 original size:15 final size:15
Alignment explanation
Indices: 493515--493545 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
493505 ATTATTAAAT
493515 TCTCACTATTAAAAC
1 TCTCACTATTAAAAC
493530 TCTCACTATTAAAAC
1 TCTCACTATTAAAAC
493545 T
1 T
493546 TACATCATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (15 bp):
TCTCACTATTAAAAC
Found at i:497615 original size:20 final size:22
Alignment explanation
Indices: 497590--497635 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
497580 AGTACTTTGT
497590 ATATCTGAGC-A-AACTTATAA
1 ATATCTGAGCTATAACTTATAA
*
497610 ATATCTGATCTATAACTTATAA
1 ATATCTGAGCTATAACTTATAA
497632 ATAT
1 ATAT
497636 GATCTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.39
21 1 0.04
22 13 0.57
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (22 bp):
ATATCTGAGCTATAACTTATAA
Found at i:497640 original size:20 final size:22
Alignment explanation
Indices: 497601--497645 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
497591 TATCTGAGCA
497601 AACTTATAAATATCTGATCT-AT
1 AACTTATAAATA-CTGATCTCAT
497623 AACTTATAAATA-TGATCTCAT
1 AACTTATAAATACTGATCTCAT
497644 AA
1 AA
497646 ATAAGTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
22 12 0.55
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (22 bp):
AACTTATAAATACTGATCTCAT
Found at i:503745 original size:13 final size:13
Alignment explanation
Indices: 503727--503778 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
503717 TTTATTAAAC
503727 TTAATTTTTATTT
1 TTAATTTTTATTT
*
503740 TTAATTTTTACATAT
1 TTAATTTTT--ATTT
*
503755 ATAATTTTTATTT
1 TTAATTTTTATTT
503768 TTAATTTTTAT
1 TTAATTTTTAT
503779 ATATATGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 22 0.67
15 11 0.33
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
TTAATTTTTATTT
Found at i:503746 original size:7 final size:7
Alignment explanation
Indices: 503727--503777 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
503717 TTTATTAAAC
503727 TTAATTT
1 TTAATTT
503734 TT-ATTT
1 TTAATTT
503740 TTAATTT
1 TTAATTT
*
503747 TTACATAT
1 TTA-ATTT
*
503755 ATAATTT
1 TTAATTT
503762 TT-ATTT
1 TTAATTT
503768 TTAATTT
1 TTAATTT
503775 TTA
1 TTA
503778 TATATATGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 12 0.32
7 20 0.54
8 5 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (7 bp):
TTAATTT
Found at i:503746 original size:28 final size:29
Alignment explanation
Indices: 503728--503784 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
503718 TTATTAAACT
503728 TAATTTTTATTTTTAA-TTTTTACATATA
1 TAATTTTTATTTTTAATTTTTTACATATA
*
503756 TAATTTTTATTTTTAA-TTTTTATATATA
1 TAATTTTTATTTTTAATTTTTTACATATA
503784 T
1 T
503785 GTGAATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (29 bp):
TAATTTTTATTTTTAATTTTTTACATATA
Found at i:507569 original size:15 final size:16
Alignment explanation
Indices: 507539--507573 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
507529 AATTTGATAT
507539 ATAAAATTATAATAAA
1 ATAAAATTATAATAAA
507555 ATAAAATTA-AATAAA
1 ATAAAATTATAATAAA
507570 ATAA
1 ATAA
507574 GATAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAATTATAATAAA
Found at i:508658 original size:22 final size:21
Alignment explanation
Indices: 508633--508687 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
508623 AAAAAAATCA
508633 TAAAAAATAATTTTAAATTGTT
1 TAAAAAATAATTTTAAA-TGTT
508655 T-AAAAATAAATGTTTAAATGTT
1 TAAAAAAT-AAT-TTTAAATGTT
508677 TAAAAAA-AATT
1 TAAAAAATAATT
508688 GAAACATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 1 0.03
21 9 0.30
22 9 0.30
23 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TAAAAAATAATTTTAAATGTT
Found at i:508660 original size:23 final size:22
Alignment explanation
Indices: 508633--508685 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
508623 AAAAAAATCA
*
508633 TAAAAAATAAT-TTTAAATTGTT
1 TAAAAAAAAATGTTTAAA-TGTT
*
508655 TAAAAATAAATGTTTAAATGTT
1 TAAAAAAAAATGTTTAAATGTT
508677 TAAAAAAAA
1 TAAAAAAAA
508686 TTGAAACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (22 bp):
TAAAAAAAAATGTTTAAATGTT
Found at i:513275 original size:130 final size:128
Alignment explanation
Indices: 513064--513310 Score: 325
Period size: 130 Copynumber: 1.9 Consensus size: 128
513054 GCCAAATCAT
* * * * * * *
513064 CAATCAATATTATATAAAATTAATATCATCCAATTAATACATAATTATAGAAATAAACTTCTAAC
1 CAATAAATATTAGAAAAAATTAATATCATCAAAATAATAAATAATTATAGAAATAAACTTCTAAA
*
513129 AATAATAAATAAAATAAAAA-AATTATGCAAAACCTCACATAAATATACCAAAAAAATTAAAGGT
66 AATAATAAATAAAATAAAAATAA--ATGCAAAACCTCACATAAATACA-CAAAAAAATTAAAGGT
513193 C
128 C
* * * *
513194 CAATAAATATTAGAAAAAATTAATATCATTAAAATAATAAATGATTATAGAAATAAGCTTGTAAA
1 CAATAAATATTAGAAAAAATTAATATCATCAAAATAATAAATAATTATAGAAATAAACTTCTAAA
* **
513259 AATAATAAATAGAATAAAAATAAATGCAAAATTTCACATAAATACACAAAAA
66 AATAATAAATAAAATAAAAATAAATGCAAAACCTCACATAAATACACAAAAA
513311 TATAAATATT
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
128 6 0.06
129 20 0.20
130 73 0.72
131 2 0.02
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.27
Consensus pattern (128 bp):
CAATAAATATTAGAAAAAATTAATATCATCAAAATAATAAATAATTATAGAAATAAACTTCTAAA
AATAATAAATAAAATAAAAATAAATGCAAAACCTCACATAAATACACAAAAAAATTAAAGGTC
Found at i:517235 original size:14 final size:14
Alignment explanation
Indices: 517218--517248 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
517208 CAATCAATTT
*
517218 TTTCAAGTTTTCAA
1 TTTCAAGATTTCAA
517232 TTTCAAGATTTCAA
1 TTTCAAGATTTCAA
517246 TTT
1 TTT
517249 GGCTTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TTTCAAGATTTCAA
Found at i:518304 original size:13 final size:13
Alignment explanation
Indices: 518286--518311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
518276 CATTTTTTAG
518286 TTATTATTTACTT
1 TTATTATTTACTT
518299 TTATTATTTACTT
1 TTATTATTTACTT
518312 ATTAGAACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTATTTACTT
Found at i:519238 original size:20 final size:20
Alignment explanation
Indices: 519213--519254 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
519203 CTCTATCTTT
*
519213 ACACTCCCTTTCTCTCTCTA
1 ACACTCCCTTTCCCTCTCTA
**
519233 ACACTCTTTTTCCCTCTCTA
1 ACACTCCCTTTCCCTCTCTA
519253 AC
1 AC
519255 CAGACATTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (20 bp):
ACACTCCCTTTCCCTCTCTA
Found at i:521221 original size:140 final size:137
Alignment explanation
Indices: 520952--521222 Score: 296
Period size: 139 Copynumber: 2.0 Consensus size: 137
520942 ACCATGCCTA
* * *
520952 ATTTTGAAAGAGTCCTCTAACTAAAGGCTTTTAACTTTAAAAACTCATCTAACCAGAGGCTAGAC
1 ATTTTGAAAGAGTCATCTAACTAAAGGCTCTTAAATTTAAAAACTCATCTAACCAGAGGCTAGAC
** * ** *
521017 ACTTTAAATACTTAAAAAAAGGTACCTAAAGGTTTTAAAAATATGCTTAGAGGTCTTCAAAATCA
66 ACTTTAAATACTTAAAAAAAGAAACATAAAGGTTTTAAAAATATGCCCAAAGGTCTTCAAAATCA
521082 TTGCATT
131 TTGCATT
* * * *
521089 ATTTTGAAAAGAGTTATCTAACTAGAA-GCTCTTAAATTTAAAAAGCTCTTTTAACCAGAGGTTA
1 ATTTTG-AAAGAGTCATCTAACTA-AAGGCTCTTAAATTTAAAAA-CTCATCTAACCAGAGGCTA
** * * **
521153 TGACGTTTTAAATAAC-T-AAAAAAGAAACATAGAGGTTTTAAAGATCATGCCCAAAGGTCTTTG
63 -GACACTTTAAAT-ACTTAAAAAAAGAAACATAAAGGTTTTAAAAAT-ATGCCCAAAGGTCTTCA
521216 AAATCAT
125 AAATCAT
521223 GCTGAAAGAC
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
137 6 0.06
138 30 0.28
139 41 0.38
140 30 0.28
141 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (137 bp):
ATTTTGAAAGAGTCATCTAACTAAAGGCTCTTAAATTTAAAAACTCATCTAACCAGAGGCTAGAC
ACTTTAAATACTTAAAAAAAGAAACATAAAGGTTTTAAAAATATGCCCAAAGGTCTTCAAAATCA
TTGCATT
Found at i:521417 original size:44 final size:43
Alignment explanation
Indices: 521264--521440 Score: 131
Period size: 44 Copynumber: 4.0 Consensus size: 43
521254 CTTTGCAATT
* **
521264 ATGCCTGGAGGGTTTTATGATTATGATTGGAGGACTTTGAGATA
1 ATGCCTGGAGGTTTTTATGATTATG-CCGGAGGACTTTGAGATA
** * * * * **
521308 ATGTTTGGAAGTCTTTGTGATTATGCTCGGAGAACTTCAAGATA
1 ATGCCTGGAGGTTTTTATGATTATGC-CGGAGGACTTTGAGATA
* * *
521352 ATGCCCGAAGGTTTTCT-TGATTATGCCGAGAGGATTTTGAGATA
1 ATGCCTGGAGGTTTT-TATGATTATGCCG-GAGGACTTTGAGATA
* * * **
521396 AGGCCTGGAGGTTTTTATGATTTTGCTAGGAAAACTTTGAGATA
1 ATGCCTGGAGGTTTTTATGATTATGC-CGGAGGACTTTGAGATA
521440 A
1 A
521441 CGCATGAAGG
Statistics
Matches: 99, Mismatches: 29, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
43 3 0.03
44 94 0.95
45 2 0.02
ACGTcount: A:0.27, C:0.10, G:0.28, T:0.36
Consensus pattern (43 bp):
ATGCCTGGAGGTTTTTATGATTATGCCGGAGGACTTTGAGATA
Found at i:522651 original size:12 final size:13
Alignment explanation
Indices: 522632--522666 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
522622 AAACAAACAC
*
522632 ATAAATAAAATAC
1 ATAAATAAAATAA
522645 A-AAATAAAATAA
1 ATAAATAAAATAA
522657 ATAAATAAAA
1 ATAAATAAAA
522667 CCAAAAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAATAAAATAA
Found at i:523106 original size:31 final size:31
Alignment explanation
Indices: 523043--523107 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
523033 TGTTCATCGT
*
523043 AAAATTCAACTGGCATAAAAAAAGTGAACAA
1 AAAATTCAACTGGCATAAAAAAAGTCAACAA
* * * *
523074 AAAATTCAATTGGTATAAAAAAATTCACCAA
1 AAAATTCAACTGGCATAAAAAAAGTCAACAA
523105 AAA
1 AAA
523108 CTGAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.20
Consensus pattern (31 bp):
AAAATTCAACTGGCATAAAAAAAGTCAACAA
Found at i:523467 original size:7 final size:7
Alignment explanation
Indices: 523447--523546 Score: 55
Period size: 7 Copynumber: 14.3 Consensus size: 7
523437 AAGATAAATC
523447 AAATAAAA
1 AAAT-AAA
523455 AAATAAA
1 AAATAAA
*
523462 AGATAAA
1 AAATAAA
* *
523469 CAAT-CA
1 AAATAAA
523475 AAATAATA
1 AAATAA-A
*
523483 AAATAAT
1 AAATAAA
523490 AAATAAA
1 AAATAAA
**
523497 ACTTAAA
1 AAATAAA
523504 AAAGT--A
1 AAA-TAAA
523510 AAAT-AA
1 AAATAAA
523516 AAATAAA
1 AAATAAA
*
523523 TAAATGAA
1 -AAATAAA
*
523531 AAATGAA
1 AAATAAA
*
523538 AAACAAA
1 AAATAAA
523545 AA
1 AA
523547 TATATACTTG
Statistics
Matches: 71, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
5 1 0.01
6 13 0.18
7 39 0.55
8 18 0.25
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:523482 original size:23 final size:24
Alignment explanation
Indices: 523437--523526 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 24
523427 AGAAAACTTG
523437 AAGATAAATCAAATAAAAAAATAA
1 AAGATAAATCAAATAAAAAAATAA
*
523461 AAGATAAA-C-AATCAAAATAATAA
1 AAGATAAATCAAAT-AAAAAAATAA
* * *
523484 AATAATAAATAAAACTTAAAAAAGTAA
1 AA-GATAAATCAAA--TAAAAAAATAA
* *
523511 AATAAAAAT-AAATAAA
1 AAGATAAATCAAATAAA
523527 TGAAAAATGA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
22 3 0.06
23 16 0.30
24 13 0.25
25 3 0.06
26 7 0.13
27 10 0.19
28 1 0.02
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.19
Consensus pattern (24 bp):
AAGATAAATCAAATAAAAAAATAA
Found at i:523875 original size:41 final size:41
Alignment explanation
Indices: 523799--524136 Score: 328
Period size: 41 Copynumber: 8.2 Consensus size: 41
523789 TTTGAAAAAT
* * * *
523799 AAATAAA-GCTCCCCTAATCAGAGG-TACAACGACTTTTGGA
1 AAATAAAGGCTCCTCTAATCAGAGGCT-CAACAACTTTAGAA
* *
523839 AAATAAAGGCTCCTCTAAACAAAGGCTCAACAACTTT-GAA
1 AAATAAAGGCTCCTCTAATCAGAGGCTCAACAACTTTAGAA
*
523879 AAATAAAGGCTCCTCTAATCAGAGGCTCAACAACTTCAGAA
1 AAATAAAGGCTCCTCTAATCAGAGGCTCAACAACTTTAGAA
* *
523920 AAATAAAGGCTTCTCTAAGT-AGAGGTTCAACAACTTTAGAA
1 AAATAAAGGCTCCTCTAA-TCAGAGGCTCAACAACTTTAGAA
** *
523961 AAATAAAAGG-TTATCTAATCAGAGGCTCAACAGCTTTAGAA
1 AAAT-AAAGGCTCCTCTAATCAGAGGCTCAACAACTTTAGAA
* * * *
524002 AAATAAAAACGGCTCCTCTAATCAAAAGTTCAACAACTTTATAA
1 AAAT--AAA-GGCTCCTCTAATCAGAGGCTCAACAACTTTAGAA
** * * * *
524046 AACCAAAGGCTCCTCTAATTAGAGACTCAACAACTTCAAAA
1 AAATAAAGGCTCCTCTAATCAGAGGCTCAACAACTTTAGAA
* * *
524087 AAATAAATATGGCACCTCTAATCAGAGGCTCTATAACTTTAG-A
1 AAAT-AA-A-GGCTCCTCTAATCAGAGGCTCAACAACTTTAGAA
524130 AAATAAA
1 AAATAAA
524137 TAATATTCCT
Statistics
Matches: 247, Mismatches: 39, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
40 44 0.18
41 126 0.51
42 18 0.07
43 8 0.03
44 51 0.21
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (41 bp):
AAATAAAGGCTCCTCTAATCAGAGGCTCAACAACTTTAGAA
Found at i:523900 original size:81 final size:80
Alignment explanation
Indices: 523799--524093 Score: 292
Period size: 81 Copynumber: 3.6 Consensus size: 80
523789 TTTGAAAAAT
* * *
523799 AAATAAA-GCTCCCCTAATCAGAGG-TACAACGACTTTTGGAAAATAAAGGCTCCTCTAAACAAA
1 AAATAAAGGCTCCTCTAATCAGAGGCT-CAAC-ACTTTAGAAAAATAAAGGCTCCTCTAAACAAA
*
523862 GGCTCAACAACTTTGAA
64 GGTTCAACAACTTTGAA
* * ** *
523879 AAATAAAGGCTCCTCTAATCAGAGGCTCAACAACTTCAGAAAAATAAAGGCTTCTCTAAGTAGAG
1 AAATAAAGGCTCCTCTAATCAGAGGCTCAAC-ACTTTAGAAAAATAAAGGCTCCTCTAAACAAAG
523944 GTTCAACAACTTTAGAA
65 GTTCAACAACTTT-GAA
** *
523961 AAATAAAAGG-TTATCTAATCAGAGGCTCAACAGCTTTAGAAAAATAAAAACGGCTCCTCTAATC
1 AAAT-AAAGGCTCCTCTAATCAGAGGCTCAACA-CTTTAGAAAAAT--AAA-GGCTCCTCTAAAC
*
524025 AAAAGTTCAACAACTTT-ATA
61 AAAGGTTCAACAACTTTGA-A
* * * * *
524045 AAACCAAAGGCTCCTCTAATTAGAGACTCAACAACTTCAAAAAAATAAA
1 AAA-TAAAGGCTCCTCTAATCAGAGGCTCAAC-ACTTTAGAAAAATAAA
524094 TATGGCACCT
Statistics
Matches: 178, Mismatches: 25, Indels: 21
0.79 0.11 0.09
Matches are distributed among these distances:
80 7 0.04
81 59 0.33
82 38 0.21
83 9 0.05
84 12 0.07
85 52 0.29
86 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.22
Consensus pattern (80 bp):
AAATAAAGGCTCCTCTAATCAGAGGCTCAACACTTTAGAAAAATAAAGGCTCCTCTAAACAAAGG
TTCAACAACTTTGAA
Found at i:524062 original size:126 final size:127
Alignment explanation
Indices: 523851--524136 Score: 325
Period size: 126 Copynumber: 2.3 Consensus size: 127
523841 ATAAAGGCTC
* * * *
523851 CTCTAAACAAAGGCTCAACAACTTT-GAAAAAT--AAAGGCTCCTCTAATCAGAGGCTCAACAAC
1 CTCTAATCAGAGGCTCAACAACTTTAGAAAAATAAAAAGGCTCCTCTAATCAAAAGCTCAACAAC
* * ** * * *
523913 TTCAGAAAAATAAAGGCTTCTCTAAGTAGAGGTTCAACAACTTTAGAAAAATAAA-A-GGTTA
66 TTCAGAAAAACAAAGGCTCCTCTAAGTAGAGACTCAACAACTTCAAAAAAATAAATATGG-CA
* *
523974 -TCTAATCAGAGGCTCAACAGCTTTAGAAAAATAAAAACGGCTCCTCTAATCAAAAGTTCAACAA
1 CTCTAATCAGAGGCTCAACAACTTTAGAAAAATAAAAA-GGCTCCTCTAATCAAAAGCTCAACAA
* * * *
524038 CTTTATAAAACCAAAGGCTCCTCTAATTAGAGACTCAACAACTTCAAAAAAATAAATATGGCA
65 CTTCAGAAAAACAAAGGCTCCTCTAAGTAGAGACTCAACAACTTCAAAAAAATAAATATGGCA
* *
524101 CCTCTAATCAGAGGCTCTATAACTTTAG-AAAATAAA
1 -CTCTAATCAGAGGCTCAACAACTTTAGAAAAATAAA
524137 TAATATTCCT
Statistics
Matches: 135, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
122 21 0.16
123 7 0.05
125 3 0.02
126 69 0.51
127 2 0.01
128 10 0.07
129 23 0.17
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (127 bp):
CTCTAATCAGAGGCTCAACAACTTTAGAAAAATAAAAAGGCTCCTCTAATCAAAAGCTCAACAAC
TTCAGAAAAACAAAGGCTCCTCTAAGTAGAGACTCAACAACTTCAAAAAAATAAATATGGCA
Found at i:524125 original size:85 final size:83
Alignment explanation
Indices: 523806--524132 Score: 297
Period size: 85 Copynumber: 3.9 Consensus size: 83
523796 AATAAATAAA
* * ** * * * *
523806 GCTCCCCTAATCAGAGG-TACAACGACTTTTGGAAAAT-AAAGGCTCCTCTAAACAAAGGCTCAA
1 GCTCCTCTAATCAGAGGCT-CAACAACTTCAGAAAAATAAAAGGCTCCTCTAATCAGAGGTTCAA
* *
523869 CAACTTTGAAAAA-TAAAG
65 CAACTTTAAAAAACAAAAG
*
523887 GCTCCTCTAATCAGAGGCTCAACAACTTCAGAAAAAT-AAAGGCTTCTCTAAGT-AGAGGTTCAA
1 GCTCCTCTAATCAGAGGCTCAACAACTTCAGAAAAATAAAAGGCTCCTCTAA-TCAGAGGTTCAA
*
523950 CAACTTTAGAAAAATAAAAG
65 CAACTTTA-AAAAACAAAAG
** * * * *
523970 G-TTATCTAATCAGAGGCTCAACAGCTTTAGAAAAATAAAAACGGCTCCTCTAATCAAAAGTTCA
1 GCTCCTCTAATCAGAGGCTCAACAACTTCAGAAAAAT-AAAA-GGCTCCTCTAATCAGAGGTTCA
* *
524034 ACAACTTTATAAAACCAAAG
64 ACAACTTTAAAAAACAAAAG
* * * * * *
524054 GCTCCTCTAATTAGAGACTCAACAACTTCAAAAAAATAAATATGGCACCTCTAATCAGAGGCTCT
1 GCTCCTCTAATCAGAGGCTCAACAACTTCAGAAAAATAAA-A-GGCTCCTCTAATCAGAGGTTCA
* *
524119 ATAACTTTAGAAAA
64 ACAACTTTAAAAAA
524133 TAAATAATAT
Statistics
Matches: 200, Mismatches: 36, Indels: 16
0.79 0.14 0.06
Matches are distributed among these distances:
81 58 0.29
82 37 0.19
83 5 0.03
84 16 0.08
85 84 0.42
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (83 bp):
GCTCCTCTAATCAGAGGCTCAACAACTTCAGAAAAATAAAAGGCTCCTCTAATCAGAGGTTCAAC
AACTTTAAAAAACAAAAG
Found at i:524391 original size:23 final size:23
Alignment explanation
Indices: 524360--524428 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
524350 TTCAGATATA
*
524360 CAAGAATTCATATTTGTAAGATTT
1 CAAG-ATTCACATTTGTAAGATTT
* *
524384 CAATATTCGCATTTGTAAGATTT
1 CAAGATTCACATTTGTAAGATTT
524407 CAAGATTCACATTTGTAAGATT
1 CAAGATTCACATTTGTAAGATT
524429 CTCATCCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 37 0.93
24 3 0.08
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (23 bp):
CAAGATTCACATTTGTAAGATTT
Found at i:524472 original size:21 final size:19
Alignment explanation
Indices: 524444--524497 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 19
524434 CCAAAGTTTT
*
524444 AATTTAAGGATTCACATGCA
1 AATTTAA-GATTCACATCCA
*
524464 AATTGTAAGACTCACATCCA
1 AATT-TAAGATTCACATCCA
524484 ATATTTAAAGATTC
1 A-ATTT-AAGATTC
524498 TCATTCGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (19 bp):
AATTTAAGATTCACATCCA
Found at i:524579 original size:21 final size:21
Alignment explanation
Indices: 524553--524626 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
524543 CATCTTAAAG
*
524553 ATTCTCATTTAAAATTCAAAT
1 ATTCTCATTTAAAATTCAAAA
524574 ATTCTCATTTAAAATTCAAAA
1 ATTCTCATTTAAAATTCAAAA
* * *
524595 ACTCTCATTTGAGAACTCAAAA
1 ATTCTCATTT-AAAATTCAAAA
524617 ATTCTCATTT
1 ATTCTCATTT
524627 GAGGATTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 29 0.62
22 18 0.38
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.39
Consensus pattern (21 bp):
ATTCTCATTTAAAATTCAAAA
Found at i:524617 original size:22 final size:22
Alignment explanation
Indices: 524576--524629 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
524566 ATTCAAATAT
* *
524576 TCTCATTT-AAAATTCAAAAAC
1 TCTCATTTGAGAACTCAAAAAC
*
524597 TCTCATTTGAGAACTCAAAAAT
1 TCTCATTTGAGAACTCAAAAAC
524619 TCTCATTTGAG
1 TCTCATTTGAG
524630 GATTAACAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (22 bp):
TCTCATTTGAGAACTCAAAAAC
Done.