Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 24
Found at i:165901 original size:197 final size:197
Alignment explanation
Indices: 165566--165987 Score: 709
Period size: 197 Copynumber: 2.1 Consensus size: 197
165556 TAAGTAATTA
* * *
165566 ACCTATTTTATTATATAAGAGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTGT
* * * *
165631 TTGATAATGTTTCCAGTAATTAACATATTTTATTATATAAGTGTTACCTATTACATTATATAAGT
66 TTAATAATGTTTCCAGCAATTAACATATTTTATTATATAAGTGCTACCTATTACATTATATAAGC
* * *
165696 GGTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGCG
131 GGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCG
165761 CT
196 CT
*
165763 ACCTATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTGT
*
165828 TTAATAATGTTTCCAGCAATTAACCTATTTTATTATATAAGTGCTACCTATTACATTATATAAGC
66 TTAATAATGTTTCCAGCAATTAACATATTTTATTATATAAGTGCTACCTATTACATTATATAAGC
165893 GGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCG
131 GGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCG
165958 CT
196 CT
** *
165960 ACCTATTACATTATATAAGCGGTACCTA
1 ACCTATTTTATTATATAAGCGCTACCTA
165988 ATATGTTATT
Statistics
Matches: 210, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
197 210 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (197 bp):
ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTGT
TTAATAATGTTTCCAGCAATTAACATATTTTATTATATAAGTGCTACCTATTACATTATATAAGC
GGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCG
CT
Found at i:165972 original size:23 final size:23
Alignment explanation
Indices: 165937--165987 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
165927 CCAGTAATTA
**
165937 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
165960 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
165983 ACCTA
1 ACCTA
165988 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:166597 original size:31 final size:31
Alignment explanation
Indices: 166559--166635 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
166549 AAACAACGCA
166559 TCTAGTACCTAAACTATCAGTTTTAATCCGT
1 TCTAGTACCTAAACTATCAGTTTTAATCCGT
*
166590 TCTAGTACCTAAACTATCAGTTTTGATCCGT
1 TCTAGTACCTAAACTATCAGTTTTAATCCGT
166621 TCTAGTACCTAAACT
1 TCTAGTACCTAAACT
166636 TTCAAAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (31 bp):
TCTAGTACCTAAACTATCAGTTTTAATCCGT
Found at i:173582 original size:25 final size:25
Alignment explanation
Indices: 173551--173598 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
173541 CTAAAAAGTT
173551 TATAAATTAATTTTATAACATATCC
1 TATAAATTAATTTTATAACATATCC
173576 TATAAATTAATTTTATAACATAT
1 TATAAATTAATTTTATAACATAT
173599 ATATCCACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAAATTAATTTTATAACATATCC
Found at i:180307 original size:60 final size:60
Alignment explanation
Indices: 180148--180307 Score: 205
Period size: 60 Copynumber: 2.7 Consensus size: 60
180138 TATAGGGTAC
* * * * *
180148 TGATTTATTAAGTCAC-TCGATTATTAAAAGTTATAAAATAATCATATGATTATACAATGT
1 TGATTTGTTAAGTC-CTTCGACTATTAAAAGTTATAAAATGATCATATGACTATAAAATGT
* * * *
180208 TGATTTGTTAAGTCATTCAACCATTAAAAGTTATAAAATGATCATTTGACTATAAAATGT
1 TGATTTGTTAAGTCCTTCGACTATTAAAAGTTATAAAATGATCATATGACTATAAAATGT
* *
180268 TGCTTTGTTAAGTCCTTCGACTATTAAACGTTATAAAATG
1 TGATTTGTTAAGTCCTTCGACTATTAAAAGTTATAAAATG
180308 GTCACCCGAC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 85 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (60 bp):
TGATTTGTTAAGTCCTTCGACTATTAAAAGTTATAAAATGATCATATGACTATAAAATGT
Found at i:191738 original size:67 final size:67
Alignment explanation
Indices: 191616--191749 Score: 162
Period size: 67 Copynumber: 2.0 Consensus size: 67
191606 AATTTGTGTT
* * * *
191616 GTGACAGCTATAGATGGTTTATCCTTTTGATTTGGACAGAGAAAAACAGTTAGTGATTGTATAAA
1 GTGACAGCTATAGATGATTTATCCTTTTAATTTGGACAGAGAAAAACAGTAAGTGATTATATAAA
191681 GA
66 GA
* **** *
191683 GTGACAGCTATAGGTGATTTAT-CTTTTAAATTTGGACAGAGAGTCGCGGTAAGTGATTATATAA
1 GTGACAGCTATAGATGATTTATCCTTTT-AATTTGGACAGAGAAAAACAGTAAGTGATTATATAA
191747 AGA
65 AGA
191750 ATGGCAAACT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 5 0.09
67 51 0.91
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.33
Consensus pattern (67 bp):
GTGACAGCTATAGATGATTTATCCTTTTAATTTGGACAGAGAAAAACAGTAAGTGATTATATAAA
GA
Found at i:202886 original size:31 final size:31
Alignment explanation
Indices: 202848--202909 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
202838 CAGATGGCCC
202848 AACTCTTCATTTCAAGAAATCAGGACTGGAT
1 AACTCTTCATTTCAAGAAATCAGGACTGGAT
202879 AACTCTTCATTTCAAGAAATCAGGACTGGAT
1 AACTCTTCATTTCAAGAAATCAGGACTGGAT
202910 CTGGGAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (31 bp):
AACTCTTCATTTCAAGAAATCAGGACTGGAT
Found at i:203251 original size:48 final size:48
Alignment explanation
Indices: 203180--203276 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
203170 GGATATTACG
* *
203180 ATTTGTTTGTTGGATTCCAATCCTTGAATGATTTTCAAGCTAAATGGT
1 ATTTGGTTGTTAGATTCCAATCCTTGAATGATTTTCAAGCTAAATGGT
203228 ATTTGGTTGTTAGATTCCAATCCTTGAATGATTTTCAAGCTAAATGGT
1 ATTTGGTTGTTAGATTCCAATCCTTGAATGATTTTCAAGCTAAATGGT
203276 A
1 A
203277 CATGGATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (48 bp):
ATTTGGTTGTTAGATTCCAATCCTTGAATGATTTTCAAGCTAAATGGT
Found at i:207516 original size:104 final size:104
Alignment explanation
Indices: 207250--207550 Score: 340
Period size: 104 Copynumber: 2.9 Consensus size: 104
207240 ACTGAGGAGA
** * * * * *
207250 CATAGCTCCAGTGGACAAACAACCAATCCGAACGGTGGACCACGAGAGAATGACGAGTCAACCAA
1 CATAGCTCCAGTGGACGGACAACCAATCTGAACGATAGACTACGAGAGAATGACGAGTCGACCAA
* * *
207315 TATAGTCCAGTTTCAGGCCCGTCGGAC-AACTGATAGGC
66 TATAGTTCAGTTTCAGGCCCATCGGACGAACTAATAGGC
* * *
207353 CATAGCTCCAATGGA-GGAACAACCAAT-TCGAACGATAGACTAAGATAGAATGACGAGTCGACC
1 CATAGCTCCAGTGGACGG-ACAACCAATCT-GAACGATAGACTACGAGAGAATGACGAGTCGACC
* * * *
207416 AGTATAGTTCAATTTCAGGCCTATCGGACGAGCTAATGAGG-
64 AATATAGTTCAGTTTCAGGCCCATCGGACGAACTAAT-AGGC
* * * *
207457 CATAACTCCAGTGGACGGACAACCAATCTGAACGATAAACTACGAGAGAATGACAAGTCGATCAA
1 CATAGCTCCAGTGGACGGACAACCAATCTGAACGATAGACTACGAGAGAATGACGAGTCGACCAA
* *
207522 TATAGTTCAGTTTTAGGCCCATCAGACGA
66 TATAGTTCAGTTTCAGGCCCATCGGACGA
207551 TTGACAACGA
Statistics
Matches: 163, Mismatches: 29, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
103 75 0.46
104 82 0.50
105 6 0.04
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (104 bp):
CATAGCTCCAGTGGACGGACAACCAATCTGAACGATAGACTACGAGAGAATGACGAGTCGACCAA
TATAGTTCAGTTTCAGGCCCATCGGACGAACTAATAGGC
Found at i:211281 original size:273 final size:265
Alignment explanation
Indices: 210920--211442 Score: 638
Period size: 273 Copynumber: 1.9 Consensus size: 265
210910 ATTTAATACT
* ** * *
210920 TAAACTATCAATTTTTGTTTGTTTAAATACCTAAATTTTTAATTTTTTTCAAAATCATATATAAA
1 TAAACTATCAATTTTGGTTAATTTAAATACCTAAAATTTTAATTTTTTTCAAAATCATATACAAA
* * *
210985 ATTTAGTTTTTATTTCATTTTAGTATGTCACTGTTAAAAACTTAACG-AGTTTAGTATC-AAACT
66 ATTTAATTTTTATTTCATTTTAGTACGTCACTGTTAAAAACTTAACGCA-TTTAGTACCTAAACT
* * * * * * * *
211048 AAAAAATTTGATCCGTTTTAATACTTAGACTTTCAGGGT-TTTTTCTTCTTCAAAAATTAACGTT
130 AAAAAATTTGATACATTTTAATACCTAAAATTTC---CTATTTTT-TTC-T-AAAAATGAACATT
* * * *
211112 AAATTTTGAACAATTTTATTAAAATGAAACAAAAAAAACTAAGATTTAAGTATGATTTAAAAAAA
189 AAATTCTGAACAATTATATTAAAATGAAAC---AAAAACTAA-ATTTAAATATAATTTAAAAAAA
211177 TAAAAGTTTAGGTGCC
250 TAAAAGTTTAGGTGCC
* * * * *
211193 TAAACTATCAGTTTTGGTTAATTTCAATACCTAAAATTTTATTTTTTTTCAAAATCATATCCAAC
1 TAAACTATCAATTTTGGTTAATTTAAATACCTAAAATTTTAATTTTTTTCAAAATCATATACAAA
* *
211258 GTTTAATTTTTGTTTCATTTTAGTACGTCACTGTTAAAAACTTAACGCATTTAGTACCTAAACTA
66 ATTTAATTTTTATTTCATTTTAGTACGTCACTGTTAAAAACTTAACGCATTTAGTACCTAAACTA
** ** *
211323 TCAGTTTTGATATATTTTAATACCTAAAATTTCCTATTTTTTTCTAAAAATGAACATTAAATTCT
131 AAAAATTTGATACATTTTAATACCTAAAATTTCCTATTTTTTTCTAAAAATGAACATTAAATTCT
211388 GAACAATTATATTAAAATGAAACAAAAACTAAATTTAAATATAATTTAAAAAAAT
196 GAACAATTATATTAAAATGAAACAAAAACTAAATTTAAATATAATTTAAAAAAAT
211443 TAGGTAGTAA
Statistics
Matches: 215, Mismatches: 32, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
265 21 0.10
266 9 0.04
269 39 0.18
270 1 0.00
271 4 0.02
272 5 0.02
273 106 0.49
274 30 0.14
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (265 bp):
TAAACTATCAATTTTGGTTAATTTAAATACCTAAAATTTTAATTTTTTTCAAAATCATATACAAA
ATTTAATTTTTATTTCATTTTAGTACGTCACTGTTAAAAACTTAACGCATTTAGTACCTAAACTA
AAAAATTTGATACATTTTAATACCTAAAATTTCCTATTTTTTTCTAAAAATGAACATTAAATTCT
GAACAATTATATTAAAATGAAACAAAAACTAAATTTAAATATAATTTAAAAAAATAAAAGTTTAG
GTGCC
Found at i:214592 original size:42 final size:42
Alignment explanation
Indices: 214533--214652 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
214523 TTTCCCCGAA
*
214533 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
214575 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGGAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
214617 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
214653 TGTAATTCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:214885 original size:53 final size:53
Alignment explanation
Indices: 214826--214944 Score: 127
Period size: 55 Copynumber: 2.2 Consensus size: 53
214816 TTTTCATCAA
* **
214826 AATATTA-ATTATTAA-AATATTTAAAATATATTTATTAATATT-TATAATAATAT
1 AATATTATATTATTAATAATATATAAAATA-ATCAATT-ATATTATA-AATAATAT
* *
214879 AATATTATATTTTTAATATTATATAAAATAATCAATTATATTATAAATAATAT
1 AATATTATATTATTAATAATATATAAAATAATCAATTATATTATAAATAATAT
214932 AAGATATTATATT
1 -A-ATATTATATT
214945 TTTATTTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
53 20 0.36
54 15 0.27
55 21 0.38
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (53 bp):
AATATTATATTATTAATAATATATAAAATAATCAATTATATTATAAATAATAT
Found at i:214886 original size:26 final size:24
Alignment explanation
Indices: 214824--214886 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
214814 CATTTTCATC
214824 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
214848 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
214871 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
214887 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:214888 original size:22 final size:23
Alignment explanation
Indices: 214841--214901 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
214831 TAATTATTAA
* *
214841 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
214862 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
214885 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
214902 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:214957 original size:24 final size:24
Alignment explanation
Indices: 214930--214977 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
214920 TATAAATAAT
*
214930 ATAAGATATTAT-ATTTTTATTTTA
1 ATAAGATATAATAATTTTT-TTTTA
*
214954 ATAATATATAATAATTTTTTTTTA
1 ATAAGATATAATAATTTTTTTTTA
214978 TATATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
ATAAGATATAATAATTTTTTTTTA
Found at i:214975 original size:29 final size:30
Alignment explanation
Indices: 214924--215021 Score: 80
Period size: 29 Copynumber: 3.3 Consensus size: 30
214914 TTATATTATA
*
214924 AATAATATA-AGATA-TTATATTTTTATTTT
1 AATAATATATA-ATATTTATTTTTTTATTTT
214953 AATAATATATAATAATTT-TTTTTTATATATTT
1 AATAATATATAAT-ATTTATTTTTT-TAT-TTT
* * *
214985 AATAATGA-ATAATA-TTATTTATATATTTC
1 AATAAT-ATATAATATTTATTTTTTTATTTT
215014 AATAATAT
1 AATAATAT
215022 TTTAGTAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
28 1 0.02
29 19 0.33
30 12 0.21
31 10 0.18
32 14 0.25
33 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (30 bp):
AATAATATATAATATTTATTTTTTTATTTT
Found at i:214982 original size:22 final size:25
Alignment explanation
Indices: 214942--214990 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 25
214932 AAGATATTAT
214942 ATTTTTATTTTAATAATATATAATA
1 ATTTTTATTTTAATAATATATAATA
*
214967 ATTTTT-TTTT-AT-ATATTTAATA
1 ATTTTTATTTTAATAATATATAATA
214989 AT
1 AT
214991 GAATAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 2 0.09
24 4 0.17
25 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTTTATTTTAATAATATATAATA
Found at i:215265 original size:20 final size:20
Alignment explanation
Indices: 215187--215256 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
215177 TTTCCAGATG
215187 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
215207 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
215227 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
215247 TTTTCCAGAA
1 TTTTCCAGAA
215257 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:215265 original size:40 final size:40
Alignment explanation
Indices: 215187--215265 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
215177 TTTCCAGATG
* **
215187 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
215227 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
215266 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:215275 original size:15 final size:15
Alignment explanation
Indices: 215239--215320 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
215229 TTACAGAAAT
**
215239 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
215254 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
215268 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
215283 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
215298 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
215313 GTAATTCA
1 GTAATTCA
215321 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:215291 original size:30 final size:30
Alignment explanation
Indices: 215239--215320 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
215229 TTACAGAAAT
215239 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
215268 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
215298 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
215321 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:215313 original size:45 final size:44
Alignment explanation
Indices: 215239--215325 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
215229 TTACAGAAAT
**
215239 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
215283 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
215326 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:216689 original size:126 final size:126
Alignment explanation
Indices: 216521--216748 Score: 298
Period size: 126 Copynumber: 1.8 Consensus size: 126
216511 TGACCCTTCT
* * * * * *
216521 ATAACTTATAGTAGTCAAGGGGTTAAACAAAGCAATATTCTA-TATTCAAATGATTATTTTGTGA
1 ATAACTTATAATAGTCAAGGGGCTAAACAAAACAATAATCTATTATTCAAA-GATTATTTTATAA
* *
216585 TTTTTAATAATCGAATGACTTAATAAAATAATACTCTACGGTCGGGGAACTGTTTGTGTACC
65 CTTTTAATAATCGAAGGACTTAATAAAATAATACTCTACGGTCGGGGAACTGTTTGTGTACC
* * *
216647 ATAACTTATAATAGTCGAA-GGGCTCAACAAAACAATAATCTATTGTTGAAAGATTATTTTATAA
1 ATAACTTATAATAGTC-AAGGGGCTAAACAAAACAATAATCTATTATTCAAAGATTATTTTATAA
* * *
216711 CTTTTAATAGTCGAAGGACTTAGTAAAGTAATACTCTA
65 CTTTTAATAATCGAAGGACTTAATAAAATAATACTCTA
216749 TAGCTGGGAT
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
126 78 0.91
127 8 0.09
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (126 bp):
ATAACTTATAATAGTCAAGGGGCTAAACAAAACAATAATCTATTATTCAAAGATTATTTTATAAC
TTTTAATAATCGAAGGACTTAATAAAATAATACTCTACGGTCGGGGAACTGTTTGTGTACC
Found at i:219064 original size:15 final size:15
Alignment explanation
Indices: 219044--219078 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
219034 AATTTTTATT
219044 TTATTTTAATATTTA
1 TTATTTTAATATTTA
*
219059 TTATTTTAGTATTTA
1 TTATTTTAATATTTA
219074 TTATT
1 TTATT
219079 AAAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATTTTAATATTTA
Found at i:231107 original size:26 final size:26
Alignment explanation
Indices: 231078--231132 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
231068 TGAACTTATA
*
231078 AAAAAAAATTAGAGGATGATAAATAT
1 AAAAAAAATTAGAGGATGATAAAAAT
** *
231104 AAAAAATTTTAGAGGATGGTAAAAAT
1 AAAAAAAATTAGAGGATGATAAAAAT
231130 AAA
1 AAA
231133 TTATCAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (26 bp):
AAAAAAAATTAGAGGATGATAAAAAT
Found at i:232284 original size:23 final size:24
Alignment explanation
Indices: 232258--232302 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
232248 ACATAATTAA
*
232258 TAATATATTCTTTTA-ATATTCGT
1 TAATATATTCGTTTATATATTCGT
*
232281 TAATATTTTCGTTTATATATTC
1 TAATATATTCGTTTATATATTC
232303 AGAAAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.58
Consensus pattern (24 bp):
TAATATATTCGTTTATATATTCGT
Found at i:243841 original size:10 final size:10
Alignment explanation
Indices: 243817--243853 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
243807 ATAAAAGTAG
*
243817 AATAGAATAAA
1 AATA-AATAAT
243828 AATAAATAAT
1 AATAAATAAT
243838 AATAAATAAT
1 AATAAATAAT
243848 AATAAA
1 AATAAA
243854 AGGATTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 21 0.84
11 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
AATAAATAAT
Found at i:243848 original size:13 final size:13
Alignment explanation
Indices: 243822--243854 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
243812 AGTAGAATAG
243822 AATAAAAATAAAT
1 AATAAAAATAAAT
243835 AATAATAAAT-AAT
1 AATAA-AAATAAAT
243848 AATAAAA
1 AATAAAA
243855 GGATTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 13 0.68
14 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAAAATAAAT
Found at i:247714 original size:16 final size:17
Alignment explanation
Indices: 247693--247727 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
247683 AAATAAGTTC
*
247693 ATTTTTCT-TTAATTTT
1 ATTTTTCTGTAAATTTT
247709 ATTTTTCTGTAAATTTT
1 ATTTTTCTGTAAATTTT
247726 AT
1 AT
247728 CATGCCGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (17 bp):
ATTTTTCTGTAAATTTT
Found at i:250253 original size:59 final size:59
Alignment explanation
Indices: 250093--250256 Score: 206
Period size: 59 Copynumber: 2.8 Consensus size: 59
250083 CAAATGGCAC
* * *
250093 TATATGTGTTAAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCAT
1 TATATGTGCT-AAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGAAT
* * *
250153 TA-AGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGG-GAAT
1 TATA-TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATAT-GGAGAAT
* * *
250212 TATATGTGCTAAAACGGTAAGGGAATCATACTGAGTGTATGGATT
1 TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATT
250257 CTCAGATAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
59 79 0.89
60 10 0.11
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (59 bp):
TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGAAT
Found at i:250325 original size:118 final size:118
Alignment explanation
Indices: 250158--250374 Score: 278
Period size: 118 Copynumber: 1.8 Consensus size: 118
250148 AGCATTAAGT
* * * *
250158 GTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGGGAATTAT-ATGTGCT
1 GTGCTAAAAGGATAAGGAAATCATACTGAATATATGGATTTCCACATAGGGAATT-TCATATGCT
* * *
250222 AAAACGGTAAGGGAATCATACTGA-GTGTATGGATTCTCAGATAAATCACTAAAG
65 AAAACGGTAAAGAAATCATACTAATG-GTATGGATTCTCAGATAAATCACTAAAG
* * * *
250276 GTGCTACAAGGATAAGGAAATCATACT-AATGGTATGGATTTTCACATAGGGCATTTCATATGCT
1 GTGCTAAAAGGATAAGGAAATCATACTGAAT-ATATGGATTTCCACATAGGGAATTTCATATGCT
*
250340 AAAATGGTAAAGAAATCATACTAATGGTATGGATT
65 AAAACGGTAAAGAAATCATACTAATGGTATGGATT
250375 TTTGAATAGG
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
117 4 0.05
118 79 0.94
119 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (118 bp):
GTGCTAAAAGGATAAGGAAATCATACTGAATATATGGATTTCCACATAGGGAATTTCATATGCTA
AAACGGTAAAGAAATCATACTAATGGTATGGATTCTCAGATAAATCACTAAAG
Found at i:250399 original size:59 final size:58
Alignment explanation
Indices: 250289--250422 Score: 164
Period size: 59 Copynumber: 2.3 Consensus size: 58
250279 CTACAAGGAT
* * *
250289 AAGGAAATCATACTAATGGTATGGATTTTCACATAGGGCATTTCATATGCTAAAATGGTA
1 AAGGAAATCATACTAATGGTATGGATTTTCACATAGGACACTTCATATGCT-AAAT-GAA
* * *
250349 AA-GAAATCATACTAATGGTATGGATTTTTGA-ATAGGACACTTCGTGTGCTAAATGAA
1 AAGGAAATCATACTAATGGTATGGA-TTTTCACATAGGACACTTCATATGCTAAATGAA
*
250406 AAGGAAATCATATTAAT
1 AAGGAAATCATACTAAT
250423 TATATAATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
57 4 0.06
58 17 0.26
59 37 0.57
60 7 0.11
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31
Consensus pattern (58 bp):
AAGGAAATCATACTAATGGTATGGATTTTCACATAGGACACTTCATATGCTAAATGAA
Found at i:253119 original size:20 final size:19
Alignment explanation
Indices: 253094--253133 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
253084 TCAAGATAGA
253094 GGTCTTTAAAAAAAGTCAAC
1 GGTCTTT-AAAAAAGTCAAC
*
253114 GGTCTTTGAAAAAGTCAAC
1 GGTCTTTAAAAAAGTCAAC
253133 G
1 G
253134 ATCAAAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (19 bp):
GGTCTTTAAAAAAGTCAAC
Found at i:258536 original size:22 final size:23
Alignment explanation
Indices: 258499--258541 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
258489 ACGATTTTAA
*
258499 AAAATATAAATTTAAA-AAATAC
1 AAAATATAAATATAAACAAATAC
*
258521 AAAATATAAGTATAAACAAAT
1 AAAATATAAATATAAACAAAT
258542 TCCGTCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (23 bp):
AAAATATAAATATAAACAAATAC
Found at i:262276 original size:13 final size:13
Alignment explanation
Indices: 262260--262290 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
262250 TACTCACTGA
262260 ATTTTACAAATTG
1 ATTTTACAAATTG
262273 ATTTTACAAATTG
1 ATTTTACAAATTG
262286 ATTTT
1 ATTTT
262291 TTTTGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (13 bp):
ATTTTACAAATTG
Found at i:263986 original size:5 final size:5
Alignment explanation
Indices: 263976--264014 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
263966 AACTCTATAA
263976 CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAAT
1 CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAAT
264015 ATAATTGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (5 bp):
CAATG
Found at i:270837 original size:24 final size:23
Alignment explanation
Indices: 270794--270838 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
270784 CTCATGAAAA
270794 TTTAAAATTATCATATATTTTGG
1 TTTAAAATTATCATATATTTTGG
*
270817 TTTAAAATATATGATATATTTT
1 TTTAAAAT-TATCATATATTTT
270839 AAATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (23 bp):
TTTAAAATTATCATATATTTTGG
Found at i:282444 original size:15 final size:16
Alignment explanation
Indices: 282426--282458 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
282416 TAAAATTTGC
282426 TTTTTTTT-AAT-GTT
1 TTTTTTTTGAATAGTT
282440 TTTTTTTTGAATAGTT
1 TTTTTTTTGAATAGTT
282456 TTT
1 TTT
282459 ATGTTAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTTTTTGAATAGTT
Found at i:283660 original size:35 final size:36
Alignment explanation
Indices: 283620--283691 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
283610 AAGAAACGGC
283620 AAAACATGA-AAA-AATGCAAGTAACAGCAAACGGAA
1 AAAACATGATAAACAA-GCAAGTAACAGCAAACGGAA
* *
283655 AAAACATTATAAACAAGCAAGTAACAGCAAGCGGAA
1 AAAACATGATAAACAAGCAAGTAACAGCAAACGGAA
283691 A
1 A
283692 CACAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 8 0.24
36 23 0.70
37 2 0.06
ACGTcount: A:0.58, C:0.15, G:0.17, T:0.10
Consensus pattern (36 bp):
AAAACATGATAAACAAGCAAGTAACAGCAAACGGAA
Found at i:294911 original size:29 final size:29
Alignment explanation
Indices: 294842--294916 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
294832 TGAAAACCGA
*
294842 ATTAAACGGGAACGGAGAAAAACCGTTTAT
1 ATTAAACGGGGACGG-GAAAAACCGTTTAT
** *
294872 GCTAAATGGGGACGGGAAAAACCGTTTAT
1 ATTAAACGGGGACGGGAAAAACCGTTTAT
*
294901 ATTAGACGGGGACGGG
1 ATTAAACGGGGACGGG
294917 TTTAGTAATC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 26 0.70
30 11 0.30
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (29 bp):
ATTAAACGGGGACGGGAAAAACCGTTTAT
Found at i:295514 original size:31 final size:31
Alignment explanation
Indices: 295417--295515 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 31
295407 TGTATCATAT
* *
295417 GTCCCTAAATTATGATTCTCATTTTAAATTA
1 GTCCTTAAATTATGATTCTCATTATAAATTA
* * ** *
295448 GTCCTTAAGCTT-TTA-AAT-ATTATAATTTA
1 GTCCTTAA-ATTATGATTCTCATTATAAATTA
295477 -TCCTTAAATTATGATTCTCATTATAAATTA
1 GTCCTTAAATTATGATTCTCATTATAAATTA
295507 GTCCTTAAA
1 GTCCTTAAA
295516 CTTTTGAACA
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
27 2 0.04
28 9 0.18
29 10 0.20
30 11 0.22
31 17 0.33
32 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.45
Consensus pattern (31 bp):
GTCCTTAAATTATGATTCTCATTATAAATTA
Found at i:296448 original size:31 final size:32
Alignment explanation
Indices: 296404--296464 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
296394 TGATTTTGAA
*
296404 AAAAATAAAAGTTTAGGTACTAAA-ACATATC
1 AAAAATAAAAGTTTAAGTACTAAATACATATC
* *
296435 AAAATTAATAGTTTAAGTACTAAATACATA
1 AAAAATAAAAGTTTAAGTACTAAATACATA
296465 GTTTAGCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (32 bp):
AAAAATAAAAGTTTAAGTACTAAATACATATC
Found at i:299871 original size:6 final size:7
Alignment explanation
Indices: 299855--299879 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
299845 GAGCTGTATT
299855 AAAAAGA
1 AAAAAGA
299862 AAAAAGA
1 AAAAAGA
299869 AAAAAGA
1 AAAAAGA
299876 AAAA
1 AAAA
299880 TAAACCGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:301038 original size:30 final size:30
Alignment explanation
Indices: 300976--301058 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
300966 CCCTATGTTT
* * * *
300976 TTTTTGTCCAATTCGGTACTTAAAATTTTCA
1 TTTTT-TCCAATTTGGTACCTGAAATTGTCA
*
301007 TTTTTTCCAATTTGGTACCTGAACTTGTCA
1 TTTTTTCCAATTTGGTACCTGAAATTGTCA
* * *
301037 TTTTGTTCTAATGTGGTGCCTG
1 TTTT-TTCCAATTTGGTACCTG
301059 TCGTGATGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 24 0.56
31 19 0.44
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (30 bp):
TTTTTTCCAATTTGGTACCTGAAATTGTCA
Found at i:305583 original size:46 final size:46
Alignment explanation
Indices: 305530--305623 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
305520 GGGTTCTTGC
*
305530 AAGTAATTTATGCTAAAAACATGTTCT-GTTACATGTTTTGTTTAAA
1 AAGTAATTTATGCTAAAAACATGTT-TAGTTACATCTTTTGTTTAAA
*
305576 AAGTAATTTATGCTAAAAACATGTTTAGTTACGTCTTTTGTTTAAA
1 AAGTAATTTATGCTAAAAACATGTTTAGTTACATCTTTTGTTTAAA
305622 AA
1 AA
305624 CTAGTTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 1 0.02
46 44 0.98
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (46 bp):
AAGTAATTTATGCTAAAAACATGTTTAGTTACATCTTTTGTTTAAA
Found at i:310095 original size:105 final size:105
Alignment explanation
Indices: 309834--310283 Score: 323
Period size: 105 Copynumber: 4.3 Consensus size: 105
309824 TGTATGTGAT
* * * * * *
309834 AACATCAAGCTCAATGCGTTGTTTTCTCATTGAGTC-AGCAATATATTCAGCTTCACAAACCATC
1 AACATCAGGCTCAATGCCTTGCTTTCTCATTGTGTCGA-CAATATCTTCAGCTTCAGAAACCATC
* * * * * *
309898 CCCTTCTTGCAA-AGTGCATCGATCAATATATTGTACGTC-AC
65 CCCTCCTTGCAATA-AGCATCAACCAATATATTATATG-CGAC
* * *** * * * * * *
309939 AACATCAGGCTCAACGCCTTGCTTTCTCATTGTGAT-AATGGTACCTACAGCTTTAGAGATCTTC
1 AACATCAGGCTCAATGCCTTGCTTTCTCATTGTG-TCGACAATATCTTCAGCTTCAGAAACCATC
*
310003 CCCTCCTTGCAATAAGCATCAAGCAATATATTATATGCGAC
65 CCCTCCTTGCAATAAGCATCAACCAATATATTATATGCGAC
* * * * *
310044 AACGTCAGGCTCAATGCCTTGTTTTCTCATTTTGTCGACAATATCTTCAGCTGCAGACACCATCC
1 AACATCAGGCTCAATGCCTTGCTTTCTCATTGTGTCGACAATATCTTCAGCTTCAGAAACCATCC
* * ** * * *
310109 CCACCTTGGAATGCGCATCAACCAATATACTATATGTGAA
66 CCTCCTTGCAATAAGCATCAACCAATATATTATATGCGAC
* * * * * ** * ** **
310149 AACATCGGGCTCAATGCCATGCTTTCTCATTGTGTCAACAGTACCTAAAGATTCAGAAATTAGGC
1 AACATCAGGCTCAATGCCTTGCTTTCTCATTGTGTCGACAATATCTTCAGCTTCAGAAACCATCC
* * ** * * *
310214 CTTCCTTGCATTGCGCAGCAACCAATATATTATACGTGAC
66 CCTCCTTGCAATAAGCATCAACCAATATATTATATGCGAC
* *
310254 AAGATCAGGCTCAAGGCCTTGCTTTCTCAT
1 AACATCAGGCTCAATGCCTTGCTTTCTCAT
310284 CGTATCAATG
Statistics
Matches: 266, Mismatches: 74, Indels: 10
0.76 0.21 0.03
Matches are distributed among these distances:
104 2 0.01
105 261 0.98
106 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (105 bp):
AACATCAGGCTCAATGCCTTGCTTTCTCATTGTGTCGACAATATCTTCAGCTTCAGAAACCATCC
CCTCCTTGCAATAAGCATCAACCAATATATTATATGCGAC
Found at i:310222 original size:210 final size:210
Alignment explanation
Indices: 309837--310283 Score: 461
Period size: 210 Copynumber: 2.1 Consensus size: 210
309827 ATGTGATAAC
* * * *
309837 ATCAAGCTCAATGCGTTGTTTTCTCATTGAGTCAGCAATATATTCAGCTTCACAAACCATCCCCT
1 ATCAGGCTCAATGCCTTGTTTTCTCATTGAGTCAGCAATATATTCAGCTGCACAAACCATCCCCA
* * * * * * * *
309902 TCTTGCAAAGTGCATCGATCAATATATTGTACGTCACAACATCAGGCTCAACGCCTTGCTTTCTC
66 CCTTGCAAAGCGCATCAACCAATATACTATACGTCAAAACATCAGGCTCAACGCCATGCTTTCTC
** * * * * * * *
309967 ATTGTGATAATGGTACCTACAGCTTTAGAGATCTTCCCCTCCTTGCAATAAGCATCAAGCAATAT
131 ATTGTGATAACAGTACCTAAAGATTCAGAAATCTGCCCCTCCTTGCAATAAGCAGCAACCAATAT
*
310032 ATTATATGCGACAACG
196 ATTATACGCGACAA-G
** * * *
310048 -TCAGGCTCAATGCCTTGTTTTCTCATTTTGTC-GACAATATCTTCAGCTGCAGACACCATCCCC
1 ATCAGGCTCAATGCCTTGTTTTCTCATTGAGTCAG-CAATATATTCAGCTGCACAAACCATCCCC
* * * * * *
310111 ACCTTGGAATGCGCATCAACCAATATACTATATGTGAAAACATCGGGCTCAATGCCATGCTTTCT
65 ACCTTGCAAAGCGCATCAACCAATATACTATACGTCAAAACATCAGGCTCAACGCCATGCTTTCT
* * * **
310176 CATTGTG-TCAACAGTACCTAAAGATTCAGAAAT-TAGGCCTTCCTTGCATTGCGCAGCAACCAA
130 CATTGTGAT-AACAGTACCTAAAGATTCAGAAATCT-GCCCCTCCTTGCAATAAGCAGCAACCAA
*
310239 TATATTATACGTGACAAG
193 TATATTATACGCGACAAG
* *
310257 ATCAGGCTCAAGGCCTTGCTTTCTCAT
1 ATCAGGCTCAATGCCTTGTTTTCTCAT
310284 CGTATCAATG
Statistics
Matches: 191, Mismatches: 41, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
209 4 0.02
210 187 0.98
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (210 bp):
ATCAGGCTCAATGCCTTGTTTTCTCATTGAGTCAGCAATATATTCAGCTGCACAAACCATCCCCA
CCTTGCAAAGCGCATCAACCAATATACTATACGTCAAAACATCAGGCTCAACGCCATGCTTTCTC
ATTGTGATAACAGTACCTAAAGATTCAGAAATCTGCCCCTCCTTGCAATAAGCAGCAACCAATAT
ATTATACGCGACAAG
Found at i:310312 original size:105 final size:104
Alignment explanation
Indices: 310112--310365 Score: 253
Period size: 105 Copynumber: 2.4 Consensus size: 104
310102 ACCATCCCCA
* * * * * *
310112 CCTTGGAATGCGCATCAACCAATATACTATATGTGAAAACATCGGGCTCAATGCCATGCTTTCTC
1 CCTTGCAATGCGCAGCAACCAATATATTATACGTGAAAACATCAGGCTCAAGGCCATGCTTTCTC
* * *
310177 ATTGTGTCAACAGTACCTAAAGATTCAGAAAT-TAGGCCTT
66 ATCGTATCAACAGTACCTAAAGATTCAGAAATCT--GCCAT
* * * *
310217 CCTTGCATTGCGCAGCAACCAATATATTATACGTGACAAGATCAGGCTCAAGGCCTTGCTTTCTC
1 CCTTGCAATGCGCAGCAACCAATATATTATACGTGAAAACATCAGGCTCAAGGCCATGCTTTCTC
** * ** * * *
310282 ATCGTATCAATGGTATCTTTAGCTTTAGAAATCTTCCAT
66 ATCGTATCAACAGTACCTAAAGATTCAGAAATCTGCCAT
* *
310321 CCTTGCAATGTGCATG--ACCAATATATTATACGTGAAAATATCAGG
1 CCTTGCAATGCGCA-GCAACCAATATATTATACGTGAAAACATCAGG
310366 TGAAATATTG
Statistics
Matches: 122, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
103 27 0.22
104 15 0.12
105 79 0.65
106 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (104 bp):
CCTTGCAATGCGCAGCAACCAATATATTATACGTGAAAACATCAGGCTCAAGGCCATGCTTTCTC
ATCGTATCAACAGTACCTAAAGATTCAGAAATCTGCCAT
Found at i:311439 original size:20 final size:20
Alignment explanation
Indices: 311414--311480 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
311404 ATTATAAATA
311414 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* ** **
311434 TGCGATAGTTGAAAATCGCGT
1 TGCGAT-TTTCCATTTCGCGT
*
311455 TGCGATTTTCCATTTCGCAT
1 TGCGATTTTCCATTTCGCGT
311475 TGCGAT
1 TGCGAT
311481 AGTCTACATG
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (20 bp):
TGCGATTTTCCATTTCGCGT
Found at i:311525 original size:19 final size:20
Alignment explanation
Indices: 311474--311589 Score: 76
Period size: 22 Copynumber: 5.8 Consensus size: 20
311464 CCATTTCGCA
*
311474 TTGCGATAGTCTACATGTCG
1 TTGCGATAGTCTAAATGTCG
* **
311494 TTACGATTTTCTAAAT-TCG
1 TTGCGATAGTCTAAATGTCG
* *
311513 TTGCGATAGTCTACAGTTGTTG
1 TTGCGATAGTCTA-A-ATGTCG
* *
311535 TTGCGAAAGTCTACAGTTGTCG
1 TTGCGATAGTCTA-A-ATGTCG
** *
311557 TTGCGATTTTCCAAAT-TCG
1 TTGCGATAGTCTAAATGTCG
311576 TTGCGATAGT-TAAA
1 TTGCGATAGTCTAAA
311590 AAAAAAGATT
Statistics
Matches: 74, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
18 3 0.04
19 24 0.32
20 14 0.19
21 2 0.03
22 31 0.42
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCTAAATGTCG
Found at i:311540 original size:22 final size:22
Alignment explanation
Indices: 311474--311563 Score: 91
Period size: 22 Copynumber: 4.3 Consensus size: 22
311464 CCATTTCGCA
311474 TTGCGATAGTCTACA--TGTCG
1 TTGCGATAGTCTACAGTTGTCG
* ** *
311494 TTACGATTTTCTA-A-AT-TCG
1 TTGCGATAGTCTACAGTTGTCG
*
311513 TTGCGATAGTCTACAGTTGTTG
1 TTGCGATAGTCTACAGTTGTCG
*
311535 TTGCGAAAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
311557 TTGCGAT
1 TTGCGAT
311564 TTTCCAAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
19 14 0.25
20 12 0.22
21 1 0.02
22 28 0.51
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (22 bp):
TTGCGATAGTCTACAGTTGTCG
Found at i:312181 original size:6 final size:6
Alignment explanation
Indices: 312165--312196 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
312155 CCGTCCGTCC
312165 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
312197 AATGGTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:312202 original size:6 final size:6
Alignment explanation
Indices: 312193--312232 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
312183 GTCGTGGTCG
312193 TGGTAA TGGT-A TGGTAA TGGTAA TGGTAA TGGTAA TGGTA
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTA
312233 TACGTGTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:312202 original size:12 final size:12
Alignment explanation
Indices: 312187--312232 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
312177 GTCGTGGTCG
*
312187 TGGTCGTGGTAA
1 TGGTCATGGTAA
312199 TGGT-ATGGTAA
1 TGGTCATGGTAA
*
312210 TGGTAATGGTAA
1 TGGTCATGGTAA
*
312222 TGGTAATGGTA
1 TGGTCATGGTA
312233 TACGTGTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 10 0.31
12 22 0.69
ACGTcount: A:0.26, C:0.02, G:0.37, T:0.35
Consensus pattern (12 bp):
TGGTCATGGTAA
Found at i:312533 original size:19 final size:19
Alignment explanation
Indices: 312509--312577 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
312499 CAACGAATTT
312509 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
312528 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
312550 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
312569 TCGCAACGA
1 TCGCAACGA
312578 CAACTGTAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 22 0.56
20 2 0.05
21 2 0.05
22 13 0.33
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:312554 original size:41 final size:41
Alignment explanation
Indices: 312509--312618 Score: 186
Period size: 41 Copynumber: 2.7 Consensus size: 41
312499 CAACGAATTT
312509 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
312550 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
*
312591 TCGCAACGCGAA-ATGGAAAATCGCAACG
1 TCGCAA--CGAATTTGGAAAATCGCAACG
312619 TGAACTGGAA
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 47 0.71
42 15 0.23
43 4 0.06
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:312555 original size:22 final size:22
Alignment explanation
Indices: 312527--312598 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
312517 AATTTGGAAA
312527 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
312549 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
312568 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
312590 ATCGCAACG
1 ATCGCAACG
312599 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:312615 original size:20 final size:20
Alignment explanation
Indices: 312590--312651 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
312580 ACTGTAGACT
312590 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* *
312610 ATCGCAACGTGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
312630 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
312650 AT
1 AT
312652 TTTCAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:312645 original size:40 final size:41
Alignment explanation
Indices: 312521--312651 Score: 151
Period size: 41 Copynumber: 3.2 Consensus size: 41
312511 GCAACGAATT
** *
312521 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATT
1 TGGAAAATCGCAACGACAACTG-AGAAAATCGCAACGCGAA-A
**
312562 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTG-AGAAAATCGCAACGCGAAA
**
312604 TGGAAAATCGCAACGTGAACTG-GAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGAGAAAATCGCAACGCGAAA
312644 TGGAAAAT
1 TGGAAAAT
312652 TTTCAATTAT
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
40 24 0.29
41 35 0.42
42 20 0.24
43 4 0.05
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (41 bp):
TGGAAAATCGCAACGACAACTGAGAAAATCGCAACGCGAAA
Found at i:313267 original size:16 final size:17
Alignment explanation
Indices: 313232--313268 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
313222 ATGGGATGAA
313232 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
313249 AAAAAT-GTGATTATT-T
1 AAAAATAGT-ATTATTGT
313265 AAAA
1 AAAA
313269 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:313983 original size:10 final size:8
Alignment explanation
Indices: 313950--313976 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
313940 GTTGATCTAT
313950 TCTCCCTC
1 TCTCCCTC
313958 TCTCCCTC
1 TCTCCCTC
313966 TCTCCCTC
1 TCTCCCTC
313974 TCT
1 TCT
313977 TCTCCTCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (8 bp):
TCTCCCTC
Found at i:315101 original size:33 final size:33
Alignment explanation
Indices: 315056--315181 Score: 189
Period size: 33 Copynumber: 3.8 Consensus size: 33
315046 GCTCATCATG
* *
315056 TTCATCCTCATGCCTGGGTTCATGCCCATATTA
1 TTCATCCCCATGCCTGGATTCATGCCCATATTA
* * *
315089 TTCATCCCCATGCCTGGATACAAGCCCATGTTA
1 TTCATCCCCATGCCTGGATTCATGCCCATATTA
* *
315122 TTCATCCCAATGCCTGGATTCATACCCATATTA
1 TTCATCCCCATGCCTGGATTCATGCCCATATTA
315155 TTCATCCCCATGCCTGGATTCATGCCC
1 TTCATCCCCATGCCTGGATTCATGCCC
315182 GTTGGTTGTT
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 81 1.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.32
Consensus pattern (33 bp):
TTCATCCCCATGCCTGGATTCATGCCCATATTA
Found at i:315144 original size:18 final size:18
Alignment explanation
Indices: 315121--315177 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
315111 AGCCCATGTT
315121 ATTCATCCCAATGCCTGG
1 ATTCATCCCAATGCCTGG
315139 ATTCATACCCATAT---T--
1 ATTCAT-CCCA-ATGCCTGG
*
315154 ATTCATCCCCATGCCTGG
1 ATTCATCCCAATGCCTGG
315172 ATTCAT
1 ATTCAT
315178 GCCCGTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 14
0.67 0.02 0.30
Matches are distributed among these distances:
13 2 0.06
14 3 0.10
15 6 0.19
16 1 0.03
17 1 0.03
18 12 0.39
19 4 0.13
20 2 0.06
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.33
Consensus pattern (18 bp):
ATTCATCCCAATGCCTGG
Found at i:316335 original size:98 final size:98
Alignment explanation
Indices: 316083--316367 Score: 254
Period size: 98 Copynumber: 2.9 Consensus size: 98
316073 CTGGCTGTAC
* * * * * * * *
316083 GGATTAGCATTT-GACTGAGCAGGC-TGGCCATATGGAATAGCATTTGGCTGAGCAGGCAGGTCG
1 GGATTAACATTTCG-CTGAGCAGGCATGCCCA-ATGGATTAACATTTAGCGGAGCAGGCAGGACA
* * * **
316146 TAAGGATTAACATTCGGCTGTGCAGGCTGGCTGTAA
64 TACGGATTAACATTTGGCTGTGCA-GCTGCCCATAA
* * * * * * * *
316182 GGATTAGCATTTGGCTGAGCAGGCATGCCTAATGGATTACCATTTGGCTGAGCAGGCTGGCCATA
1 GGATTAACATTTCGCTGAGCAGGCATGCCCAATGGATTAACATTTAGCGGAGCAGGCAGGACATA
* * *
316247 GGGATTAACATTTGGCTGAGCAGCTGCCCATAG
66 CGGATTAACATTTGGCTGTGCAGCTGCCCATAA
*
316280 GGATTAACATTTCGCTGAGCAGGC-TGACCGCAAT-GATTAACATTTAGCGGTGCAGGCAGGACA
1 GGATTAACATTTCGCTGAGCAGGCATG-CC-CAATGGATTAACATTTAGCGGAGCAGGCAGGACA
* *
316343 TACGGATTAGCATCTGGCTGTGCAG
64 TACGGATTAACATTTGGCTGTGCAG
316368 GTTGGCCATA
Statistics
Matches: 155, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
97 2 0.01
98 75 0.48
99 73 0.47
100 5 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (98 bp):
GGATTAACATTTCGCTGAGCAGGCATGCCCAATGGATTAACATTTAGCGGAGCAGGCAGGACATA
CGGATTAACATTTGGCTGTGCAGCTGCCCATAA
Found at i:316385 original size:33 final size:33
Alignment explanation
Indices: 316012--316385 Score: 274
Period size: 33 Copynumber: 11.4 Consensus size: 33
316002 GTGGGCTGAG
* * *
316012 CATATGGATTAGCACTTAGCTGTA-CAGGCTGGT
1 CATATGGATTAGCATTTGGCTG-AGCAGGCTGGC
* ** * * * *
316045 CGTATATATTAGCACTGGGCTGTGTAGGCTGGC
1 CATATGGATTAGCATTTGGCTGAGCAGGCTGGC
** * *
316078 TGTACGGATTAGCATTTGACTGAGCAGGCTGGC
1 CATATGGATTAGCATTTGGCTGAGCAGGCTGGC
* * *
316111 CATATGGAATAGCATTTGGCTGAGCAGGCAGGT
1 CATATGGATTAGCATTTGGCTGAGCAGGCTGGC
* * * * *
316144 CGTAAGGATTAACATTCGGCTGTGCAGGCTGGC
1 CATATGGATTAGCATTTGGCTGAGCAGGCTGGC
** *
316177 TGTAAGGATTAGCATTTGGCTGAGCAGGCAT-GC
1 CATATGGATTAGCATTTGGCTGAGCAGGC-TGGC
*
316210 C-TAATGGATTACCATTTGGCTGAGCAGGCTGGC
1 CAT-ATGGATTAGCATTTGGCTGAGCAGGCTGGC
* * *
316243 CATAGGGATTAACATTTGGCTGAGCA-GCTGCC
1 CATATGGATTAGCATTTGGCTGAGCAGGCTGGC
* * * *
316275 CATAGGGATTAACATTTCGCTGAGCAGGCTGACC
1 CATATGGATTAGCATTTGGCTGAGCAGGCTG-GC
* * * * * *
316309 GCA-AT-GATTAACATTTAGCGGTGCAGGCAGGA
1 -CATATGGATTAGCATTTGGCTGAGCAGGCTGGC
* * * *
316341 CATACGGATTAGCATCTGGCTGTGCAGGTTGGC
1 CATATGGATTAGCATTTGGCTGAGCAGGCTGGC
316374 CATATGGATTAG
1 CATATGGATTAG
316386 TACTTGACTG
Statistics
Matches: 272, Mismatches: 59, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
31 2 0.01
32 33 0.12
33 230 0.85
34 5 0.02
35 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (33 bp):
CATATGGATTAGCATTTGGCTGAGCAGGCTGGC
Found at i:323326 original size:18 final size:18
Alignment explanation
Indices: 323303--323339 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
323293 CGGCAATTTC
323303 TTTTTTT-CTTTTTTCTTT
1 TTTTTTTCCTTTTTT-TTT
323321 TTTTTTTCCTTTTTTTTT
1 TTTTTTTCCTTTTTTTTT
323339 T
1 T
323340 ATTTGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTTTCCTTTTTTTTT
Found at i:323327 original size:11 final size:12
Alignment explanation
Indices: 323305--323339 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
323295 GCAATTTCTT
*
323305 TTTTTCTTTTTTC
1 TTTTT-TTTTTCC
323318 TTTTTTTTTTCC
1 TTTTTTTTTTCC
323330 TTTTTTTTTT
1 TTTTTTTTTT
323340 ATTTGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTCC
Found at i:330455 original size:29 final size:29
Alignment explanation
Indices: 330403--330489 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
330393 GATCTAGTGG
* *
330403 TATAATTGAAACAAAAATCAAAGTTTAGTAC
1 TATAATTG-AA-AAAATTAAAAGTTTAGTAC
* * * * **
330434 TATAATTGAGAAAATTGAAAGTTCAATGT
1 TATAATTGAAAAAATTAAAAGTTTAGTAC
*
330463 TGTAATTGAAAAAATTAAAAGTTTAGT
1 TATAATTGAAAAAATTAAAAGTTTAGT
330490 GATATAAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 35 0.80
30 1 0.02
31 8 0.18
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (29 bp):
TATAATTGAAAAAATTAAAAGTTTAGTAC
Found at i:339541 original size:25 final size:26
Alignment explanation
Indices: 339486--339543 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
339476 GGTAATTTTA
*
339486 AAAAATATTATTTAAATCAAAAACAT
1 AAAAATATTATTTAAATAAAAAACAT
339512 AAAAATATTA-TTAAATTAAAAAAC-T
1 AAAAATATTATTTAAA-TAAAAAACAT
*
339537 CAAAATA
1 AAAAATA
339544 AATTTTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAATATTATTTAAATAAAAAACAT
Found at i:340189 original size:20 final size:21
Alignment explanation
Indices: 340164--340215 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
340154 TTTTCCCAAT
*
340164 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
340184 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
340205 TCGCAATGCGA
1 TCGCAATGCGA
340216 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:340229 original size:20 final size:20
Alignment explanation
Indices: 340204--340317 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
340194 AATTGGGAAA
340204 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
340224 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
340244 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
340264 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
340285 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
340305 TTCGCAACGCGAT
1 ATCGCAATGCGAT
340318 TTACATAGCG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 65 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:340885 original size:19 final size:19
Alignment explanation
Indices: 340833--340879 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
340823 TTCGAGAATG
*
340833 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAACA
*
340852 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACA
340871 AAAATCGCA
1 AAAATCGCA
340880 TTGCGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.51, C:0.26, G:0.15, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:340926 original size:33 final size:33
Alignment explanation
Indices: 340889--340976 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
340879 ATTGCGATTT
* * *
340889 TCATTTCGCATTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
340922 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
340955 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
340977 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:340978 original size:20 final size:20
Alignment explanation
Indices: 340944--341001 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
340934 GCGATTCTCT
**
340944 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
340964 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
340984 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
341002 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:343063 original size:42 final size:42
Alignment explanation
Indices: 343003--343125 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
342993 GCCCGACTCG
* * *
343003 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
343045 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
343087 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
343126 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:343083 original size:21 final size:21
Alignment explanation
Indices: 343059--343125 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
343049 TCATTCCTCG
343059 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
343080 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
343101 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
343122 AGAG
1 AGAG
343126 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:344503 original size:14 final size:14
Alignment explanation
Indices: 344484--344519 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
344474 ATTGTTTAAT
344484 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
344498 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
344512 TGATTTGT
1 TGATTTGT
344520 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:344724 original size:33 final size:32
Alignment explanation
Indices: 344682--344808 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
344672 ATTAAATTCG
344682 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
344715 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
344748 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
344781 CGTTGCGATTTTCATTTCGTATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
344809 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:344765 original size:66 final size:66
Alignment explanation
Indices: 344675--344807 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
344665 ACGCGAAATT
*
344675 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
344740 G
66 G
* *
344741 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGTATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
344806 G
66 G
344807 A
1 A
344808 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:344807 original size:19 final size:18
Alignment explanation
Indices: 344684--344808 Score: 76
Period size: 19 Copynumber: 7.4 Consensus size: 18
344674 TAAATTCGCG
344684 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
**
344703 TTGCGA--TTC-CCTCG-
1 TTGCGATTTTCATTTCGA
344717 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
** *
344736 TTGCGAAATT-A--GCG-
1 TTGCGATTTTCATTTCGA
344750 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
*
344769 TTGCGA--TTC-TCTCG-
1 TTGCGATTTTCATTTCGA
344783 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCG-A
344802 TTGCGAT
1 TTGCGAT
344809 AGTAATTTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 30
0.65 0.10 0.25
Matches are distributed among these distances:
14 20 0.25
15 1 0.01
16 15 0.19
17 15 0.19
18 1 0.01
19 27 0.34
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGA
Found at i:345729 original size:75 final size:72
Alignment explanation
Indices: 345639--345882 Score: 219
Period size: 75 Copynumber: 3.3 Consensus size: 72
345629 ATATATACAC
* *
345639 ATATATATATTATATAGTTTGCAAATTGTTTTTGAAAATACATATATAATATATAGTTTAAAACA
1 ATATATATAATATATAGTTTG-AAAATGTTTTTGAAAAT--ATATATAATATATAGTTTAAAACA
345704 TTTTTTGAAA
63 TTTTTTGAAA
* * * *
345714 ATATGTATATTATATAGTTTTTAAAATATTTTTGAAAAT-TATATAATATATAGTTTTTGAAAAC
1 ATATATATAATATATAG-TTTGAAAATGTTTTTGAAAATATATATAATATATAG--TTT-AAAAC
*
345778 -GTTTTT-AAA
62 ATTTTTTGAAA
* * * * *
345787 ATATATATAATATATACTTTTGAAAACG-TTATGAAAACATTTATATAATATATAATTTTTAAAA
1 ATATATATAATATATA-GTTTGAAAATGTTTTTG-AAA-ATATATATAATATAT-A-GTTTAAAA
*
345851 -ACTATTTTGAAA
61 CA-TTTTTTGAAA
345863 ATATATATAATATATAGTTT
1 ATATATATAATATATAGTTT
345883 TTTTTTAAAC
Statistics
Matches: 140, Mismatches: 16, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
72 18 0.13
73 27 0.19
74 14 0.10
75 58 0.41
76 23 0.16
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (72 bp):
ATATATATAATATATAGTTTGAAAATGTTTTTGAAAATATATATAATATATAGTTTAAAACATTT
TTTGAAA
Found at i:345764 original size:36 final size:36
Alignment explanation
Indices: 345639--345884 Score: 221
Period size: 38 Copynumber: 6.6 Consensus size: 36
345629 ATATATACAC
* ** **
345639 ATATATATATTATATAGTTTGCAAATTGTTTTTGAAA
1 ATATATATAATATATAGTTTTTAAA-AATTTTTGAAA
345676 ATACATATATAATATATAG--TTTAAAACATTTTTTGAAA
1 AT--ATATATAATATATAGTTTTTAAAA-A-TTTTTGAAA
* *
345714 ATATGTATATTATATAGTTTTTAAAATATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAA-ATTTTTGAAA
*
345751 AT-TATATAATATATAGTTTTTGAAAACGTTTTT-AAA
1 ATATATATAATATATAGTTTTT-AAAA-ATTTTTGAAA
* * ** *
345787 ATATATATAATATATACTTTTGAAAACGTTATGAAAA
1 ATATATATAATATATAGTTTTTAAAAATTTTTG-AAA
* *
345824 CATTTATATAATATATAATTTTTAAAAACTATTTTGAAA
1 -ATATATATAATATATAGTTTTTAAAAA-T-TTTTGAAA
345863 ATATATATAATATATAGTTTTT
1 ATATATATAATATATAGTTTTT
345885 TTTTAAACAT
Statistics
Matches: 171, Mismatches: 25, Indels: 25
0.77 0.11 0.11
Matches are distributed among these distances:
35 3 0.02
36 39 0.23
37 46 0.27
38 62 0.36
39 17 0.10
40 4 0.02
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAAATTTTTGAAA
Found at i:345884 original size:38 final size:38
Alignment explanation
Indices: 345668--345928 Score: 231
Period size: 36 Copynumber: 6.9 Consensus size: 38
345658 TGCAAATTGT
*
345668 TTTTGAAAATACATATATAATATATAG--TTT-AAAACATT
1 TTTTGAAAAT--ATATATAATATATAGTTTTTGAAAAC-TA
* *
345706 TTTTGAAAATATGTATATTATATAGTTTTT-AAAA-TA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACTA
345742 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAACGT-
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAAC-TA
* *
345780 TTTT-AAAATATATATAATATATA-CTTTTGAAAAC-G
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACTA
* * * *
345815 TTATGAAAACATTTATATAATATATAATTTTTAAAAACTA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACTA
**
345855 TTTTGAAAATATATATAATATATAGTTTTTTTTTAAAC-A
1 TTTTGAAAATATATATAATATATAG--TTTTTGAAAACTA
* * *
345894 TTTTAAAAATTTATATATTATAT-GTTTTTGAAAAC
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAAC
345929 GTTTATATAT
Statistics
Matches: 187, Mismatches: 21, Indels: 32
0.78 0.09 0.13
Matches are distributed among these distances:
35 3 0.02
36 55 0.29
37 34 0.18
38 48 0.26
39 34 0.18
40 13 0.07
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (38 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACTA
Found at i:345966 original size:16 final size:17
Alignment explanation
Indices: 345947--345979 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
345937 ATATATAATA
345947 TTATTATT-ATTTATTT
1 TTATTATTAATTTATTT
*
345963 TTATTTTTAATTTATTT
1 TTATTATTAATTTATTT
345980 ATTTCTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTATTAATTTATTT
Found at i:347109 original size:10 final size:9
Alignment explanation
Indices: 347057--347101 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
347047 ATGTTTTCTG
347057 TATTTTTAT
1 TATTTTTAT
*
347066 TATTATTATT
1 TATTTTTA-T
*
347076 TATTCTCTAT
1 TATT-TTTAT
347086 TATTTTTAT
1 TATTTTTAT
347095 TATTTTT
1 TATTTTT
347102 CCTTATTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 18 0.60
10 10 0.33
11 2 0.07
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTTTAT
Found at i:349080 original size:12 final size:12
Alignment explanation
Indices: 349063--349087 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
349053 TCTTCGGGGA
349063 CTTTTTCTTCTT
1 CTTTTTCTTCTT
349075 CTTTTTCTTCTT
1 CTTTTTCTTCTT
349087 C
1 C
349088 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:350400 original size:20 final size:20
Alignment explanation
Indices: 350375--350492 Score: 200
Period size: 20 Copynumber: 5.9 Consensus size: 20
350365 ATTCATTTGA
350375 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
350395 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
350415 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
350435 TTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
350455 TTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
350475 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
350493 CGCAATGCGA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 96 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:350520 original size:19 final size:19
Alignment explanation
Indices: 350492--350621 Score: 242
Period size: 19 Copynumber: 6.8 Consensus size: 19
350482 AACGAGAAAA
*
350492 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
350511 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
350530 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
350549 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
350568 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
350587 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
350606 TCGCATTGTGATTTTC
1 TCGCATTGCGATTTTC
350622 TCGTTGCGAT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 109 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:350665 original size:20 final size:19
Alignment explanation
Indices: 350618--350689 Score: 99
Period size: 20 Copynumber: 3.7 Consensus size: 19
350608 GCATTGTGAT
*
350618 TTTCTCGTTGCGATAGCCA
1 TTTCGCGTTGCGATAGCCA
350637 TTTCGCGTTGCGATAGCCA
1 TTTCGCGTTGCGATAGCCA
*
350656 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATAGCCA
*
350676 TTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
350690 AAGTAAACTA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 21 0.44
20 24 0.50
21 3 0.06
ACGTcount: A:0.14, C:0.24, G:0.25, T:0.38
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGCCA
Found at i:351191 original size:18 final size:18
Alignment explanation
Indices: 351165--351209 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
351155 GTCGATCAGA
**
351165 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCAAGG
*
351183 TGATAGCTCTGGGCAAGG
1 TGATGGCTCTGGGCAAGG
351201 TGATGGCTC
1 TGATGGCTC
351210 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCAAGG
Found at i:352553 original size:20 final size:20
Alignment explanation
Indices: 352528--352565 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
352518 GAATAGTTCT
352528 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
352548 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
352566 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:352856 original size:22 final size:22
Alignment explanation
Indices: 352829--352872 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
352819 GATGGAGATA
352829 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
352851 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
352873 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:353131 original size:21 final size:21
Alignment explanation
Indices: 353098--353198 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
353088 TGCGAAAGTA
* * *
353098 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
353119 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
353139 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
353161 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
353182 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
353199 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:353154 original size:20 final size:20
Alignment explanation
Indices: 353060--353154 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
353050 AATTATGTAT
*
353060 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
353080 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
353100 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
353121 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
353141 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
353155 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:353173 original size:41 final size:41
Alignment explanation
Indices: 353082--353216 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
353072 AAAGTCAGTA
* * * ** *
353082 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
353122 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
353164 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
353205 TCGCGTTGCGAT
1 TCGCGTTGCGAT
353217 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:353208 original size:21 final size:20
Alignment explanation
Indices: 353143--353235 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
353133 ATAGTCAGTA
*
353143 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
353164 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
353184 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
353205 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
353225 TCGCATTGCGA
1 TCGCATTGCGA
353236 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:353217 original size:41 final size:41
Alignment explanation
Indices: 353143--353235 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
353133 ATAGTCAGTA
353143 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
353184 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
353225 TCGCATTGCGA
1 TCGCATTGCGA
353236 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:354532 original size:15 final size:15
Alignment explanation
Indices: 354497--354535 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
354487 CTTGATGCAA
*
354497 AAAATGCATTTGGGT
1 AAAATGCATTTGGAT
**
354512 GCAATGCATTTGGAT
1 AAAATGCATTTGGAT
354527 AAAATGCAT
1 AAAATGCAT
354536 GATTTAATGT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (15 bp):
AAAATGCATTTGGAT
Found at i:357919 original size:3 final size:3
Alignment explanation
Indices: 357907--357958 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
357897 TCTCATTTTT
357907 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
357954 ATA AT
1 ATA AT
357959 CTGGTTTTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:368752 original size:50 final size:50
Alignment explanation
Indices: 368677--368777 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
368667 TATTTTTTTC
368677 TCTCAGTTCTAAACCCTAGACACTTGTCTCATCGAACTCAATTGGAGTAG
1 TCTCAGTTCTAAACCCTAGACACTTGTCTCATCGAACTCAATTGGAGTAG
*
368727 TCTCAGTTCTAAACCCTAGACACTTGTCTCGTCGAACTCAATTGGAGTAG
1 TCTCAGTTCTAAACCCTAGACACTTGTCTCATCGAACTCAATTGGAGTAG
368777 T
1 T
368778 TAGGGTTTAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (50 bp):
TCTCAGTTCTAAACCCTAGACACTTGTCTCATCGAACTCAATTGGAGTAG
Found at i:371325 original size:26 final size:26
Alignment explanation
Indices: 371289--371340 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
371279 GTCCGGGAGA
371289 TAGAGAACAATACACTGATCTTCTTG
1 TAGAGAACAATACACTGATCTTCTTG
*
371315 TAGAGAACAATATACTGATCTTCTTG
1 TAGAGAACAATACACTGATCTTCTTG
371341 ATGGATTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (26 bp):
TAGAGAACAATACACTGATCTTCTTG
Found at i:376083 original size:2 final size:2
Alignment explanation
Indices: 376076--376111 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
376066 AAGTTGCAGG
* *
376076 TC TC TC TC TC TC TC TC TC TC TC TC AC TC AC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
376112 AGAGTAGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.06, C:0.50, G:0.00, T:0.44
Consensus pattern (2 bp):
TC
Found at i:377218 original size:37 final size:37
Alignment explanation
Indices: 377168--377252 Score: 170
Period size: 37 Copynumber: 2.3 Consensus size: 37
377158 TTCCGGGTAC
377168 TCCTTTTCTATCTGTTTCTTGTTCTTCCTCATCCTCT
1 TCCTTTTCTATCTGTTTCTTGTTCTTCCTCATCCTCT
377205 TCCTTTTCTATCTGTTTCTTGTTCTTCCTCATCCTCT
1 TCCTTTTCTATCTGTTTCTTGTTCTTCCTCATCCTCT
377242 TCCTTTTCTAT
1 TCCTTTTCTAT
377253 TCACATGTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.06, C:0.32, G:0.05, T:0.58
Consensus pattern (37 bp):
TCCTTTTCTATCTGTTTCTTGTTCTTCCTCATCCTCT
Found at i:379356 original size:18 final size:19
Alignment explanation
Indices: 379329--379366 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
379319 ATTTATCATC
*
379329 TTAATAAAAA-AATTAATT
1 TTAATAAAAATAATAAATT
*
379347 TTAATTAAAATAATAAATT
1 TTAATAAAAATAATAAATT
379366 T
1 T
379367 ACGATATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAATAAAAATAATAAATT
Found at i:384328 original size:53 final size:53
Alignment explanation
Indices: 384243--384348 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
384233 ATAATTCTAC
384243 TGCATGTTATTAGTGTTATAAATAGGTGGATTATCCTCG-AGGCTCCAACAAAT
1 TGCATGTTATTAGTGTTATAAATAGGTGGATTATCCTCGAAGGCTCCAA-AAAT
* *
384296 TGCATGTTATTAGTGTTATAGATAGGTTGATTATCCTCGAAGGCTCCAAAAAT
1 TGCATGTTATTAGTGTTATAAATAGGTGGATTATCCTCGAAGGCTCCAAAAAT
384349 GTGTAAAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 41 0.82
54 9 0.18
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (53 bp):
TGCATGTTATTAGTGTTATAAATAGGTGGATTATCCTCGAAGGCTCCAAAAAT
Found at i:386392 original size:15 final size:15
Alignment explanation
Indices: 386356--386386 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
386346 CCATGTTAGT
386356 GACTTAAACAAAAGG
1 GACTTAAACAAAAGG
386371 GACTTAAACAAAAGG
1 GACTTAAACAAAAGG
386386 G
1 G
386387 GTTTAATAAA
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:0.52, C:0.13, G:0.23, T:0.13
Consensus pattern (15 bp):
GACTTAAACAAAAGG
Found at i:392489 original size:502 final size:504
Alignment explanation
Indices: 391522--392525 Score: 1836
Period size: 502 Copynumber: 2.0 Consensus size: 504
391512 TGTAGTTAAG
* * *
391522 TGACACGTGTCATTTTTTTATTTATTTTTTTTAAAATAAAATATTTTAAAAAAATCTGGATGTTA
1 TGACACATGTCA-TTTTTTATTTATTTTTTTTAAAATAAAAAATTTTAAAAAAATCTGGACGTTA
*
391587 CACATGTCACGTAGCGTTTTTTAACGGTGGACACCTAAAAGTGTAATAGAAAAAACATTAGACAC
65 CACATGTCACGTAGCGTTTTTTAACGGTGGACACCTAAAAGTATAATAGAAAAAACATTAGACAC
391652 CTAAATTTTTTTGACTACTTTCTTTTATTGTATTTCTTTCGAATTTTATCTGTAAGTTATATTTT
130 CTAAATTTTTTTGACTACTTTCTTTTATTGTATTTCTTTCGAATTTTATCTGTAAGTTATATTTT
391717 TGTTAATCACTTTTTTATCTGTTGAAGTTTTTGGAGTTCTTGAAGGGCTAAAGTTTTATATCTTC
195 TGTTAATCACTTTTTTATCTGTTGAAGTTTTTGGAGTTCTTGAAGGGCTAAAGTTTTATATCTTC
391782 TAACTAAATACAAATATTTTAACACAATTATTGGCACATCCACGTAATCTATCATACTCAAATAT
260 TAACTAAATACAAATATTTTAACACAATTATTGGCACATCCACGTAATCTATCATACTCAAATAT
391847 GTTATTTTACAATTGTATCTATTTACCATGCTAGTTTTAAAAAGAATTTAAGGGTCATTTCTGTC
325 GTTATTTTACAATTGTATCTATTTACCATGCTAGTTTTAAAAAGAATTTAAGGGTCATTTCTGTC
391912 CTTATAGTTGACCCGACTTATCCTTTTCGCCCTGACCATATTTTTGTAGCAATTTAGAGATTGGG
390 CTTATAGTTGACCCGACTTATCCTTTTCGCCCTGACCATATTTTTGTAGCAATTTAGAGATTGGG
* *
391977 ATAGGAATATT-AAAAAAAGTTTAAAGGTCATTTCTTCCCTCAAAATAAT
455 ATAGGAATATTAAAAAAAAGTTTAAAGGTCATCTCTACCCTCAAAATAAT
392026 TGACACATGTCA-TTTTT-TTTA-TTTTTTTAAAATAAAAAATTTTAAAAAAATCTGGACGTTAC
1 TGACACATGTCATTTTTTATTTATTTTTTTTAAAATAAAAAATTTTAAAAAAATCTGGACGTTAC
*
392088 ACATGTCACGTAGCGTTTTTTAACGGTGGACACCTAAAAGTATAATAGAAAAAATATTAGACACC
66 ACATGTCACGTAGCGTTTTTTAACGGTGGACACCTAAAAGTATAATAGAAAAAACATTAGACACC
*
392153 TAAATTTTTTTGACTACTTTCTTTTTTTGTATTTCTTTCGAATTTTATCTGTAAGTTATATTTTT
131 TAAATTTTTTTGACTACTTTCTTTTATTGTATTTCTTTCGAATTTTATCTGTAAGTTATATTTTT
392218 GTTAATCACTTTTTTATCTGTTGAAGTTTTTGGAGTTCTTGAAGGGCTCTAAAGTTTTATATCTT
196 GTTAATCACTTTTTTATCTGTTGAAGTTTTTGGAGTTCTTGAAGGG--CTAAAGTTTTATATCTT
*
392283 CTAACTAAATACAAATATTTTAACATAATTATTGGCACATCCACGTAATCTATCATACTCAAATA
259 CTAACTAAATACAAATATTTTAACACAATTATTGGCACATCCACGTAATCTATCATACTCAAATA
*
392348 TGTTATTTTACAATTGTATCTATTTATCATGCTAGTTTTAAAAAGAATTTAAGGGTCATTTCTGT
324 TGTTATTTTACAATTGTATCTATTTACCATGCTAGTTTTAAAAAGAATTTAAGGGTCATTTCTGT
* * *
392413 CCTTATAGTTGACCTGACTTATCCTTTTCGTCCTGATCATATTTTTGTAGCAATTTAGAGATTGG
389 CCTTATAGTTGACCCGACTTATCCTTTTCGCCCTGACCATATTTTTGTAGCAATTTAGAGATTGG
392478 GATAGGAATATTAAAAAAAAGTTTAAAGGTCATCTCTACCCTCAAAAT
454 GATAGGAATATTAAAAAAAAGTTTAAAGGTCATCTCTACCCTCAAAAT
392526 TGTTTAATTG
Statistics
Matches: 484, Mismatches: 13, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
500 212 0.44
501 4 0.01
502 224 0.46
503 33 0.07
504 11 0.02
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.42
Consensus pattern (504 bp):
TGACACATGTCATTTTTTATTTATTTTTTTTAAAATAAAAAATTTTAAAAAAATCTGGACGTTAC
ACATGTCACGTAGCGTTTTTTAACGGTGGACACCTAAAAGTATAATAGAAAAAACATTAGACACC
TAAATTTTTTTGACTACTTTCTTTTATTGTATTTCTTTCGAATTTTATCTGTAAGTTATATTTTT
GTTAATCACTTTTTTATCTGTTGAAGTTTTTGGAGTTCTTGAAGGGCTAAAGTTTTATATCTTCT
AACTAAATACAAATATTTTAACACAATTATTGGCACATCCACGTAATCTATCATACTCAAATATG
TTATTTTACAATTGTATCTATTTACCATGCTAGTTTTAAAAAGAATTTAAGGGTCATTTCTGTCC
TTATAGTTGACCCGACTTATCCTTTTCGCCCTGACCATATTTTTGTAGCAATTTAGAGATTGGGA
TAGGAATATTAAAAAAAAGTTTAAAGGTCATCTCTACCCTCAAAATAAT
Found at i:394769 original size:2 final size:2
Alignment explanation
Indices: 394764--394788 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
394754 TCATAAATCC
394764 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
394789 AGCCCTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:397677 original size:60 final size:59
Alignment explanation
Indices: 397605--397759 Score: 134
Period size: 59 Copynumber: 2.6 Consensus size: 59
397595 TAATAAGGTT
* ** * *
397605 AAAG-TATAAAAATGATCCCTCAACTATAGGATGTTACTTTGTTGAATCCCTCGATTATTA
1 AAAGTTAT-AAAAT-ATCCCTCAACTATAGGATATTACTTTGTTGAATCAATAGACTATTA
* * * * *
397665 AAAGTTATAAAATAGTCCCT-GACTATAAGTTATTATTTTGTTGAGTCAATAGACTATTA
1 AAAGTTATAAAATA-TCCCTCAACTATAGGATATTACTTTGTTGAATCAATAGACTATTA
* * * *
397724 AAAGTTAGAAAACAATCCCTCAATTATAGGACATTA
1 AAAGTTATAAAA-TATCCCTCAACTATAGGATATTA
397760 TTTTTTTGTG
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
59 46 0.62
60 25 0.34
61 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (59 bp):
AAAGTTATAAAATATCCCTCAACTATAGGATATTACTTTGTTGAATCAATAGACTATTA
Found at i:400341 original size:60 final size:60
Alignment explanation
Indices: 400270--400382 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
400260 AGTTGAATGT
*
400270 TCATTTTATAACTTTT-GATAGTCGAAT-GACTCAACAAAATAATATATTATAATAAGAGAA
1 TCATTATATAACTTTTAG-TAGTCG-ATGGACTCAACAAAATAATATATTATAATAAGAGAA
* * *
400330 TCATTATATAACTTTTAGTAGTCGATGGACTCAATAAAATAATGTTTTATAAT
1 TCATTATATAACTTTTAGTAGTCGATGGACTCAACAAAATAATATATTATAAT
400383 CGGTGTACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 44 0.94
61 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.38
Consensus pattern (60 bp):
TCATTATATAACTTTTAGTAGTCGATGGACTCAACAAAATAATATATTATAATAAGAGAA
Found at i:404032 original size:20 final size:20
Alignment explanation
Indices: 404007--404045 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
403997 CTTCACCATC
404007 TTTCC-TCTTCTATTATTTGG
1 TTTCCTTCTTC-ATTATTTGG
*
404027 TTTCCTTGTTCATTATTTG
1 TTTCCTTCTTCATTATTTG
404046 CTTTAGCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.10, C:0.18, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTCCTTCTTCATTATTTGG
Found at i:405308 original size:19 final size:19
Alignment explanation
Indices: 405284--405324 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
405274 ATGTGGTAAT
*
405284 TTTAAAAATATATTTAAAA
1 TTTAAAAATATAATTAAAA
* *
405303 TTTAAAATTATAATTATAA
1 TTTAAAAATATAATTAAAA
405322 TTT
1 TTT
405325 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAAATATAATTAAAA
Found at i:409336 original size:22 final size:22
Alignment explanation
Indices: 409311--409352 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
409301 TTCTTGTAAT
*
409311 TTGCTTT-CAAAGTTTCTCCTTG
1 TTGCTTTGC-AAGCTTCTCCTTG
409333 TTGCTTTGCAAGCTTCTCCT
1 TTGCTTTGCAAGCTTCTCCT
409353 CCTTCTCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (22 bp):
TTGCTTTGCAAGCTTCTCCTTG
Found at i:413636 original size:60 final size:59
Alignment explanation
Indices: 413552--413663 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
413542 GAACATATGA
*
413552 ATAGTCGTGTGATCAATTTTTAACTTTCAATAGTCGAGGGACTCAACAAAACATCAGCAT
1 ATAGTCGTGTGATCAATTTTTAACTTTCAATAATC-AGGGACTCAACAAAACATCAGCAT
* * *
413612 ATAGTCGATG-GATC-ATTTTATAACTTTTAATAATCAGTGACTCAATAAAACA
1 ATAGTCG-TGTGATCAATTTT-TAACTTTCAATAATCAGGGACTCAACAAAACA
413664 ACATCCTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 20 0.43
60 24 0.52
61 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (59 bp):
ATAGTCGTGTGATCAATTTTTAACTTTCAATAATCAGGGACTCAACAAAACATCAGCAT
Found at i:414905 original size:26 final size:26
Alignment explanation
Indices: 414866--414918 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
414856 GTTGGGTCGT
*
414866 AATCGGATGGAGGATATATATTTTAC
1 AATCGGATGAAGGATATATATTTTAC
414892 AATCGGATGAAGGATATATATTTTAC
1 AATCGGATGAAGGATATATATTTTAC
414918 A
1 A
414919 GGTCAGATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (26 bp):
AATCGGATGAAGGATATATATTTTAC
Found at i:415269 original size:60 final size:61
Alignment explanation
Indices: 415199--415332 Score: 175
Period size: 60 Copynumber: 2.2 Consensus size: 61
415189 GAATCATCTA
* * * **
415199 ATCAGACTATGACTC-TCATTTCAAATTTGTCCTTAAATTTTTAAACATTTTAATTTCA-T
1 ATCAAACTATGACTCGTCATTTCAAATTGGTCCTTAAACTTTTAAACATTCCAATTTCATT
*
415258 ACTCAAACTATGAC-CGTCGTTTCAAATTGGTCCTTAAACTTTTAAACATTCCAATTTCATT
1 A-TCAAACTATGACTCGTCATTTCAAATTGGTCCTTAAACTTTTAAACATTCCAATTTCATT
*
415319 ATCAAATTATGACT
1 ATCAAACTATGACT
415333 TTTATTCTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 2 0.03
60 60 0.94
61 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (61 bp):
ATCAAACTATGACTCGTCATTTCAAATTGGTCCTTAAACTTTTAAACATTCCAATTTCATT
Found at i:415907 original size:2 final size:2
Alignment explanation
Indices: 415902--415938 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
415892 AAATACTTTA
415902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
415939 ATTTTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:416272 original size:23 final size:23
Alignment explanation
Indices: 416239--416293 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
416229 TTGAATAAAT
416239 ATATTAAAATAAA-ACAAAAGTTAA
1 ATATT-AAATAAATA-AAAAGTTAA
* *
416263 ATTTTAAATAAATAAAAATTTAA
1 ATATTAAATAAATAAAAAGTTAA
416286 ATATTAAA
1 ATATTAAA
416294 AGAGATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
ATATTAAATAAATAAAAAGTTAA
Found at i:416295 original size:37 final size:36
Alignment explanation
Indices: 416203--416295 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 36
416193 TAAACTTTCA
* * *
416203 AAAAATTTAAAATTTAATGTTAAATTTTGAATAAAT
1 AAAAATTTAAAATTAAAAGTTAAATTTTAAATAAAT
* *
416239 ATATTAAA-ATAAAA-CAAAAGTTAAATTTTAAATAAAT
1 A-A--AAATTTAAAATTAAAAGTTAAATTTTAAATAAAT
416276 AAAAATTTAAATATTAAAAG
1 AAAAATTTAAA-ATTAAAAG
416296 AGATTAAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
34 3 0.07
35 4 0.09
36 3 0.07
37 26 0.59
38 5 0.11
39 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (36 bp):
AAAAATTTAAAATTAAAAGTTAAATTTTAAATAAAT
Found at i:417181 original size:3 final size:3
Alignment explanation
Indices: 417173--417202 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
417163 TACAGAAATT
417173 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
417203 TATCCAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Done.