Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold765
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: 464481
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 3 of 3
Found at i:327994 original size:21 final size:21
Alignment explanation
Indices: 327970--328047 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
327960 AAATTTATCC
327970 AAATGTATCGATACATTTGTA
1 AAATGTATCGATACATTTGTA
*
327991 AAATGTATCGATACATTTGTG
1 AAATGTATCGATACATTTGTA
* *
328012 GAATGTATCGATACA-TTCTA
1 AAATGTATCGATACATTTGTA
328032 CAAATGTATCGATACA
1 -AAATGTATCGATACA
328048 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (21 bp):
AAATGTATCGATACATTTGTA
Found at i:328107 original size:19 final size:19
Alignment explanation
Indices: 328083--328137 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
328073 AATTCAACAA
328083 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
328102 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
328121 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
328138 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:328195 original size:13 final size:13
Alignment explanation
Indices: 328177--328202 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
328167 CATTTTTCTG
328177 TGTATCGATACAT
1 TGTATCGATACAT
328190 TGTATCGATACAT
1 TGTATCGATACAT
328203 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:328199 original size:33 final size:33
Alignment explanation
Indices: 328157--328223 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
328147 GCCAAGGAAA
***
328157 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
328190 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
328223 T
1 T
328224 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:330705 original size:27 final size:28
Alignment explanation
Indices: 330675--330750 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
330665 TTTCTTCACA
330675 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
330702 ATCGAGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
330730 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
330751 GTTTTATTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:330818 original size:52 final size:52
Alignment explanation
Indices: 330733--330955 Score: 224
Period size: 52 Copynumber: 4.3 Consensus size: 52
330723 TTATTTCTGA
* * * *
330733 GGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTT-TTCACAATC
1 GGGGATACTCCAACCCTGGTTTTATTTTCAAAAACACCAATTTTCTT--CAATC
* *
330785 GGGGATACTCCAACCCTGGTTTTATTTTC-AAAACGCCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCTGGTTTTATTTTCAAAAACACCAATTTT-CTTCAATC
* *
330837 GGGGATACTCCAACCCTGGTTTTATTTTC-AAAACGCCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCTGGTTTTATTTTCAAAAACACCAATTTT-CTTCAATC
* * * * *
330889 AGGGATACTCCAACTCC-GATTTTATTTCCAAAAATACCAATCTTTC-ACAATC
1 GGGGATACTCCAAC-CCTGGTTTTATTTTCAAAAACACCAAT-TTTCTTCAATC
*
330941 GAGGATACTCCAACC
1 GGGGATACTCCAACC
330956 TCGTTATTTC
Statistics
Matches: 151, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
51 1 0.01
52 130 0.86
53 15 0.10
54 5 0.03
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCTGGTTTTATTTTCAAAAACACCAATTTTCTTCAATC
Found at i:332942 original size:2 final size:2
Alignment explanation
Indices: 332929--332965 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
332919 TTATTTTATT
* *
332929 TA TA TG TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
332966 TTTAAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:339049 original size:36 final size:35
Alignment explanation
Indices: 338970--339049 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 35
338960 TCAAAATGAC
*
338970 AAAA-AAAAAGTCAAAAGCAAAAGCACAAAAAATG
1 AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
* *
339004 AAAAGAAAAAGTGCAAAAGCAAAA-TA-AAAAAAGGG
1 AAAACAAAAAGT-CAAAAGCAAAAGCACAAAAAA-GG
339039 AACAACAAAAA
1 AA-AACAAAAA
339050 TAAAAAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
34 10 0.26
35 11 0.28
36 18 0.46
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.05
Consensus pattern (35 bp):
AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
Found at i:339323 original size:13 final size:13
Alignment explanation
Indices: 339305--339330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
339295 ATCCTAAAAA
339305 AAAAAAAAAACCT
1 AAAAAAAAAACCT
339318 AAAAAAAAAACCT
1 AAAAAAAAAACCT
339331 TTTCACCCTA
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:0.77, C:0.15, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAACCT
Found at i:345533 original size:21 final size:21
Alignment explanation
Indices: 345507--345548 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
345497 ACACTTTATG
345507 GGAAAAAT-ACTATAAAATTTT
1 GGAAAAATCA-TATAAAATTTT
*
345528 GGAAAAATCATCTAAAATTTT
1 GGAAAAATCATATAAAATTTT
345549 AAGATGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
GGAAAAATCATATAAAATTTT
Found at i:349577 original size:11 final size:11
Alignment explanation
Indices: 349563--349587 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
349553 CAATTTGGTT
349563 TTTATTTTTTG
1 TTTATTTTTTG
349574 TTTATTTTTTG
1 TTTATTTTTTG
349585 TTT
1 TTT
349588 TTGACTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTATTTTTTG
Found at i:351291 original size:142 final size:142
Alignment explanation
Indices: 351021--351302 Score: 388
Period size: 142 Copynumber: 2.0 Consensus size: 142
351011 AAAATTTTTT
*
351021 CTAAGTTAAATTTATTATTCCATTTAAGAAAATTAGGTTTTTAACATTTTTCAAATTCAAAATAT
1 CTAAGTTAAATTTATTATTCCATTTAAGAAAATTAGGTTTTTAACATTTTTCAAAATCAAAATAT
* * *
351086 CGTTCGTACCCCATCAAATGAAGTCAAAGAAATATAAAATTTTACTTCATGAAATTTGGAAATC-
66 CATTAGTACCCCATCAAATGAAGTCAAAGAAATACAAAATTTTACTTCATGAAATTTGGAAATCT
351150 CTGATTTTATTTC
131 C-GATTTTATTTC
* * * * *
351163 CTAAGTTAAATTTATTATTGCATTTGAGAAAATTAGGTTTTTAATATTTTT-AAAATCTAAATGT
1 CTAAGTTAAATTTATTATTCCATTTAAGAAAATTAGGTTTTTAACATTTTTCAAAATCAAAATAT
* * ** * * *
351227 CATTAGTTCCCCATCGAATGAAGTTGAAGAAATACGAAGTTTTACTTTATGAAATTTGGAAAATC
66 CATTAGTACCCCATCAAATGAAGTCAAAGAAATACAAAATTTTACTTCATGAAATTTGG-AAATC
351292 TCGATTTTATT
130 TCGATTTTATT
351303 CTTTTTAAGA
Statistics
Matches: 122, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
141 59 0.48
142 62 0.51
143 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (142 bp):
CTAAGTTAAATTTATTATTCCATTTAAGAAAATTAGGTTTTTAACATTTTTCAAAATCAAAATAT
CATTAGTACCCCATCAAATGAAGTCAAAGAAATACAAAATTTTACTTCATGAAATTTGGAAATCT
CGATTTTATTTC
Found at i:355077 original size:632 final size:630
Alignment explanation
Indices: 353283--355162 Score: 3663
Period size: 629 Copynumber: 3.0 Consensus size: 630
353273 TAACTTCTAA
353283 TTTGATTAAATATATCTCTACACATAAATGATAAAATTTGACTATTAATTCTATGTTTAAATTTC
1 TTTGATTAAATATATCTCTACACATAAATGATAAAATTTGACTATTAATTCTATGTTTAAATTTC
353348 AATAGAAAAATGATTAATTAAAAATATTCACATAATTAAAGTAAATGACAATCAAATTAGGAGAA
66 AATAGAAAAATGATTAATTAAAAATATTCACATAATTAAAGTAAATGACAATCAAATTAGGAGAA
353413 CCTTATGGAAATTCTAAAAGGATTAAATGAAATTTTTATGTGAGAAAAAAAAAGAGAAAATTCCA
131 CCTTATGGAAATTCTAAAAGGATTAAATGAAATTTTTATGTGAGAAAAAAAAAGAGAAAATTCCA
*
353478 ATTACAAAACTTCATTTAAAAAAGGTGATAAAAAATATATTGATGGAATCCTAGTTAAAATTCAT
196 ATTACAAAACTTCATTTAAAAAAGGTGATAAAAAATATATTCATGGAATCCTAGTTAAAATTCAT
*
353543 ATGTATTAAATATTTAAATAAAAAATTACGTATGCAAGTCCCTAATTAAAAAATCTCATGAAAAA
261 ATGTATTAAATATTTAAATAAAAAATTACGTATGCAAGTCCCTAATTGAAAAATCTCATGAAAAA
353608 TTTTATTTAAAAAGACTAAAGTCTAAAAAATGAAAGTTCAATTAAAAACAAAATACACAAGTAGG
326 TTTTATTTAAAAAGACTAAAGTCTAAAAAATGAAAGTTCAATTAAAAACAAAATACACAAGTAGG
* *
353673 CAATTAAAATTGTATATGTTATAAAATTCAATTAAGAATTTAATCATGTAAAATTCTAGTCACAG
391 CAATTAAAATTGTATATGTTATAAAATTCAATTAAGAATTTAATCATGTAAAATTCTAATTACAG
353738 GACTATAAGGAGAAATTAAATTGAAAAAATTAATATGCAATAGGCTTTAATTAAAAATCAAATGG
456 GACTATAAGGAGAAATTAAATTGAAAAAATTAATATGCAATAGGCTTTAATTAAAAATCAAATGG
353803 GAAAAATTAGGTTGGAAGGACTAAAGTGTAAAAGAAAAAAATTGATTGAAATGAATTAAAATCCT
521 GAAAAATTAGGTTGGAAGGACTAAAGTGTAAAAGAAAAAAATTGATTGAAATGAATTAAAATCCT
*
353868 ACATATAGTAAACTCAATTAAGAGTTTAATCCAACATGATTAGAC
586 ACATATAGTAAACTCAATTAAGAGTTTAATCCAACATGATTAAAC
*
353913 TTTGATTAAATATATCTCTACACATAAATGATAAAATTTGACTATTAATTCTATTTTTAAATTTC
1 TTTGATTAAATATATCTCTACACATAAATGATAAAATTTGACTATTAATTCTATGTTTAAATTTC
353978 AATAGAAAAATGATTAATTAAAAATATTCACATAATTAAAGTAAATGACAATCAAATTAGGAGAA
66 AATAGAAAAATGATTAATTAAAAATATTCACATAATTAAAGTAAATGACAATCAAATTAGGAGAA
*
354043 CCTTATGGAAATTCTAAAAGGAGTAAATGAAATTTTTATGTGAG-AAAAAAAAGAGAAAATTCCA
131 CCTTATGGAAATTCTAAAAGGATTAAATGAAATTTTTATGTGAGAAAAAAAAAGAGAAAATTCCA
354107 ATTACAAAACTTCATTTAAAAAAGGTGATAAAAAATATATTCATGGAATCCTAGTTAAAATTCAT
196 ATTACAAAACTTCATTTAAAAAAGGTGATAAAAAATATATTCATGGAATCCTAGTTAAAATTCAT
354172 ATGTATTAAATATTTAAATAAAAAATTACGTATGCAAGTCCCTAATTGAAAAATCTCATGAAAAA
261 ATGTATTAAATATTTAAATAAAAAATTACGTATGCAAGTCCCTAATTGAAAAATCTCATGAAAAA
354237 TTTTATTTAAAAAGACTAAAGTCTAAAAAATGAAAGTTCAATTAAAAACAAAATACACAAGTAGG
326 TTTTATTTAAAAAGACTAAAGTCTAAAAAATGAAAGTTCAATTAAAAACAAAATACACAAGTAGG
354302 CAATTAAAATTGTATATGTTATAAAATTCAATTAAGAATTTAATCATGTAAAATTCTAATTACAG
391 CAATTAAAATTGTATATGTTATAAAATTCAATTAAGAATTTAATCATGTAAAATTCTAATTACAG
354367 GACTATAAGGAGAAATTAAATTGAAAAAATTAATATGCAATAGGCTTTAATTAAAAATCAAATGG
456 GACTATAAGGAGAAATTAAATTGAAAAAATTAATATGCAATAGGCTTTAATTAAAAATCAAATGG
354432 GAAAAATTAGGTTGGAAGGACTAAAGTGTAAAAGAAAAAAATTGATTGAAATGAATTAAAATCCT
521 GAAAAATTAGGTTGGAAGGACTAAAGTGTAAAAGAAAAAAATTGATTGAAATGAATTAAAATCCT
354497 ACATATAGTAAACTCAATTAAGAGTTTAATCCAACATGATTAAAC
586 ACATATAGTAAACTCAATTAAGAGTTTAATCCAACATGATTAAAC
354542 TTTGATTAAATATATCTCTACACATAAATGATAAAATTTGACTATTAATTCTATGTTTAAATTTC
1 TTTGATTAAATATATCTCTACACATAAATGATAAAATTTGACTATTAATTCTATGTTTAAATTTC
354607 AATAGAAAAATGATTAATTAAAAATATTCACATAATTAAAGTAAATGACAATCAAATTAGGAGAA
66 AATAGAAAAATGATTAATTAAAAATATTCACATAATTAAAGTAAATGACAATCAAATTAGGAGAA
354672 CCTTATGGAAATTCTAAAAGGATTAAATGAAATTTTTATGTGAGAAAAAAAAAAAGAGAAAATTC
131 CCTTATGGAAATTCTAAAAGGATTAAATGAAATTTTTATGTGAG--AAAAAAAAAGAGAAAATTC
354737 CAATTACAAAACTTCATTTAAAAAAGGTGATAAAAAATATATTCATGGAATCCTAGTTAAAATTC
194 CAATTACAAAACTTCATTTAAAAAAGGTGATAAAAAATATATTCATGGAATCCTAGTTAAAATTC
354802 ATATGTATTAAATATTTAAATAAAAAATTACGTATGCAAGTCCCTAATTGAAAAATCTCATGAAA
259 ATATGTATTAAATATTTAAATAAAAAATTACGTATGCAAGTCCCTAATTGAAAAATCTCATGAAA
354867 AATTTTATTTAAAAAGACTAAAGTCTAAAAAATGAAAGTTCAATTAAAAACAAAATACACAAGTA
324 AATTTTATTTAAAAAGACTAAAGTCTAAAAAATGAAAGTTCAATTAAAAACAAAATACACAAGTA
354932 GGCAATTAAAATTGTATATGTTATAAAATTCAATTAAGAATTTAATCATGTAAAATTCTAATTAC
389 GGCAATTAAAATTGTATATGTTATAAAATTCAATTAAGAATTTAATCATGTAAAATTCTAATTAC
*
354997 AGGACTATAAGGAGAAATTAAATTGAAAAAATTAATATACAATAGGCTTTAATTAAAAATCAAAT
454 AGGACTATAAGGAGAAATTAAATTGAAAAAATTAATATGCAATAGGCTTTAATTAAAAATCAAAT
355062 GGGAAAAATTAGGTTGGAAGGACTAAAGTGTAAAAGAAAAAAATTGATTGAAATGAATTAAAATC
519 GGGAAAAATTAGGTTGGAAGGACTAAAGTGTAAAAGAAAAAAATTGATTGAAATGAATTAAAATC
355127 CTACATATAGTAAACTCAATTAAGAGTTTAATCCAA
584 CTACATATAGTAAACTCAATTAAGAGTTTAATCCAA
355163 AAAATTTGGG
Statistics
Matches: 1237, Mismatches: 10, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
629 622 0.50
630 172 0.14
632 443 0.36
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (630 bp):
TTTGATTAAATATATCTCTACACATAAATGATAAAATTTGACTATTAATTCTATGTTTAAATTTC
AATAGAAAAATGATTAATTAAAAATATTCACATAATTAAAGTAAATGACAATCAAATTAGGAGAA
CCTTATGGAAATTCTAAAAGGATTAAATGAAATTTTTATGTGAGAAAAAAAAAGAGAAAATTCCA
ATTACAAAACTTCATTTAAAAAAGGTGATAAAAAATATATTCATGGAATCCTAGTTAAAATTCAT
ATGTATTAAATATTTAAATAAAAAATTACGTATGCAAGTCCCTAATTGAAAAATCTCATGAAAAA
TTTTATTTAAAAAGACTAAAGTCTAAAAAATGAAAGTTCAATTAAAAACAAAATACACAAGTAGG
CAATTAAAATTGTATATGTTATAAAATTCAATTAAGAATTTAATCATGTAAAATTCTAATTACAG
GACTATAAGGAGAAATTAAATTGAAAAAATTAATATGCAATAGGCTTTAATTAAAAATCAAATGG
GAAAAATTAGGTTGGAAGGACTAAAGTGTAAAAGAAAAAAATTGATTGAAATGAATTAAAATCCT
ACATATAGTAAACTCAATTAAGAGTTTAATCCAACATGATTAAAC
Found at i:355712 original size:30 final size:30
Alignment explanation
Indices: 355676--355737 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
355666 CAAGTTCAAG
355676 TTTTAAAAAATCAAACTGAGCTCAACGTAT
1 TTTTAAAAAATCAAACTGAGCTCAACGTAT
355706 TTTTAAAAAATCAAACTGAGCTCAACGTAT
1 TTTTAAAAAATCAAACTGAGCTCAACGTAT
355736 TT
1 TT
355738 ATCTAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (30 bp):
TTTTAAAAAATCAAACTGAGCTCAACGTAT
Found at i:356280 original size:2 final size:2
Alignment explanation
Indices: 356273--356303 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
356263 ATTAAGTTTC
*
356273 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
356304 CAAGCTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:356395 original size:15 final size:15
Alignment explanation
Indices: 356359--356401 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
356349 ATAAAAATTA
356359 TAAATAATATTAATAC
1 TAAAT-ATATTAATAC
356375 --AATATATTAATAC
1 TAAATATATTAATAC
*
356388 TAAATATATAAATA
1 TAAATATATTAATA
356402 AAATTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.42
14 3 0.12
15 11 0.46
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATTAATAC
Found at i:363182 original size:13 final size:13
Alignment explanation
Indices: 363164--363202 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
363154 ACAAAATTCT
* *
363164 TTGTATTGATATA
1 TTGTATCGATACA
363177 TTGTATCGATACA
1 TTGTATCGATACA
363190 TTGTATCGATACA
1 TTGTATCGATACA
363203 AGGGTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:363349 original size:22 final size:21
Alignment explanation
Indices: 363311--363351 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
363301 ATCAAATCTT
* *
363311 CTTCAAATTTCTTATTTTTCA
1 CTTCAAAATACTTATTTTTCA
363332 CTTCAAAATACTTCATTTTT
1 CTTCAAAATACTT-ATTTTT
363352 TTATCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.54
Consensus pattern (21 bp):
CTTCAAAATACTTATTTTTCA
Found at i:365616 original size:13 final size:13
Alignment explanation
Indices: 365598--365622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
365588 GATTATGCTT
365598 TGTATCGATACAA
1 TGTATCGATACAA
365611 TGTATCGATACA
1 TGTATCGATACA
365623 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:365635 original size:19 final size:21
Alignment explanation
Indices: 365607--365663 Score: 77
Period size: 19 Copynumber: 2.9 Consensus size: 21
365597 TTGTATCGAT
365607 ACAA-TGTATCGATACATGT-
1 ACAATTGTATCGATACATGTG
*
365626 TC-ATTGTATCGATACAT-TG
1 ACAATTGTATCGATACATGTG
365645 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
365664 AAACTGACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 15 0.47
20 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (21 bp):
ACAATTGTATCGATACATGTG
Found at i:365653 original size:20 final size:21
Alignment explanation
Indices: 365606--365662 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
365596 TTTGTATCGA
365606 TACAA-TGTATCGATACA-TG
1 TACAATTGTATCGATACATTG
*
365625 TTC-ATTGTATCGATACATTG
1 TACAATTGTATCGATACATTG
365645 -ACAATTGTATCGATACAT
1 TACAATTGTATCGATACAT
365663 GAAACTGACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.45
20 17 0.52
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
TACAATTGTATCGATACATTG
Found at i:365727 original size:13 final size:13
Alignment explanation
Indices: 365709--365738 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
365699 GATACATGGC
365709 ACATTGTATCGAT
1 ACATTGTATCGAT
365722 ACATTGTATCGAT
1 ACATTGTATCGAT
365735 ACAT
1 ACAT
365739 GATGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:365734 original size:33 final size:32
Alignment explanation
Indices: 365692--365760 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
365682 CTACCACTGT
365692 TTGTATCGATACATG-GCACATTGTATCGATACA
1 TTGTATCGATACATGAG-A-ATTGTATCGATACA
*
365725 TTGTATCGATACATGATGAATTGTGTCGATACA
1 TTGTATCGATACATGA-GAATTGTATCGATACA
365758 TTG
1 TTG
365761 CTTCTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACATGAGAATTGTATCGATACA
Found at i:366518 original size:13 final size:13
Alignment explanation
Indices: 366500--366556 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
366490 CATAAAGTGT
366500 TGTATCGATACAA
1 TGTATCGATACAA
366513 TGTATCGATACATAA
1 TGTATCGATAC--AA
366528 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
366545 TGTATCGATACA
1 TGTATCGATACA
366557 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:366535 original size:32 final size:32
Alignment explanation
Indices: 366480--366577 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
366470 TTCAACGATT
366480 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
366513 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
366545 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
366577 T
1 T
366578 TTAAGCTATT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:366537 original size:19 final size:18
Alignment explanation
Indices: 366478--366575 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
366468 ATTTCAACGA
366478 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
366497 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
366513 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
366529 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
366545 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
366561 TTTTGTATCGATACA
1 -TTTGTATCGATACA
366576 ATTTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:366636 original size:13 final size:13
Alignment explanation
Indices: 366618--366642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
366608 ATTACTCAAA
366618 TGTATCGATACAT
1 TGTATCGATACAT
366631 TGTATCGATACA
1 TGTATCGATACA
366643 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:366692 original size:32 final size:33
Alignment explanation
Indices: 366651--366727 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
366641 CACTGATCTT
366651 TGTATCGATACA-TGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATTGCAGGCAAATTTGCCCAGA
*
366683 TGTATCGATACATTGCAGGCAAATTTGGCCAGA
1 TGTATCGATACATTGCAGGCAAATTTGCCCAGA
366716 TGTATCGATACA
1 TGTATCGATACA
366728 CTATTAAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 12 0.28
33 31 0.72
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (33 bp):
TGTATCGATACATTGCAGGCAAATTTGCCCAGA
Found at i:370287 original size:17 final size:17
Alignment explanation
Indices: 370248--370289 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
370238 AATATTTGAG
*
370248 CCAAAAT-AATCTAAAT
1 CCAAAATAAATCTAAAC
**
370264 CTGAAATAAATCTAAAC
1 CCAAAATAAATCTAAAC
370281 CCAAAATAA
1 CCAAAATAA
370290 CCAAAATCCA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.21
Consensus pattern (17 bp):
CCAAAATAAATCTAAAC
Found at i:373393 original size:2 final size:2
Alignment explanation
Indices: 373386--373416 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
373376 ATTCTACTTT
*
373386 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
373417 TAGAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:375908 original size:18 final size:17
Alignment explanation
Indices: 375880--375920 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
375870 GTATTGAACT
*
375880 ATTTTTTATTTTTTAAA
1 ATTTTTTATTTGTTAAA
375897 ATTTTCTTATTTGTTAAA
1 ATTTT-TTATTTGTTAAA
*
375915 CTTTTT
1 ATTTTT
375921 AATCAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (17 bp):
ATTTTTTATTTGTTAAA
Found at i:378156 original size:8 final size:8
Alignment explanation
Indices: 378145--378180 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
378135 ATTTGTGTTT
378145 TATTTATA
1 TATTTATA
378153 TATTTATA
1 TATTTATA
378161 TATTTATA
1 TATTTATA
378169 TTTATTTATA
1 --TATTTATA
378179 TA
1 TA
378181 ATTTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 18 0.69
10 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTATA
Found at i:378188 original size:16 final size:16
Alignment explanation
Indices: 378153--378203 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
378143 TTTATTTATA
*
378153 TATTTATATATTTATATT
1 TATTTATATAATT-T-TT
378171 TATTTATATAATTTTT
1 TATTTATATAATTTTT
378187 TA-TTATAATATATTTTT
1 TATTTAT-ATA-ATTTTT
378204 ATCATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.13
16 7 0.23
17 7 0.23
18 12 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTATATAATTTTT
Found at i:378193 original size:13 final size:14
Alignment explanation
Indices: 378143--378205 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 14
378133 TAATTTGTGT
378143 TTTATTTA-TAT-A
1 TTTATTTATTATAA
*
378155 TTTATATATT-TATA
1 TTTATTTATTATA-A
378169 TTTATTTA-TATAA
1 TTTATTTATTATAA
378182 TTT-TTTATTATAA
1 TTTATTTATTATAA
*
378195 TATATTT-TTAT
1 TTTATTTATTAT
378206 CATATTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 12 0.29
13 17 0.40
14 13 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTATTATAA
Found at i:380441 original size:15 final size:14
Alignment explanation
Indices: 380419--380459 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
380409 GTAATTATAT
380419 AATAAATAAAATAC
1 AATAAATAAAATAC
*
380433 AATTAAATAAAATAT
1 AA-TAAATAAAATAC
*
380448 AATGAATAAAAT
1 AATAAATAAAAT
380460 TGTATATCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (14 bp):
AATAAATAAAATAC
Found at i:380979 original size:21 final size:21
Alignment explanation
Indices: 380923--380981 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
380913 TATTAAAAAT
* * **
380923 TGCATTTTTTCATCTAAAAAA
1 TGCATTCTTTCATCCAACTAA
*
380944 TGCATTCTTTTATCCAACTAA
1 TGCATTCTTTCATCCAACTAA
380965 TGCA-TCATTTCATCCAA
1 TGCATTC-TTTCATCCAA
380982 AGATACATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
TGCATTCTTTCATCCAACTAA
Found at i:383832 original size:21 final size:22
Alignment explanation
Indices: 383786--383830 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
383776 TTGCAAGATG
383786 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
383808 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
383828 AAA
1 AAA
383831 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:385653 original size:15 final size:15
Alignment explanation
Indices: 385633--385663 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
385623 TAAAAATGTC
*
385633 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
385648 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
385663 C
1 C
385664 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:387761 original size:13 final size:13
Alignment explanation
Indices: 387743--387768 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
387733 ACATTTTTCT
387743 TTGTATCGATACA
1 TTGTATCGATACA
387756 TTGTATCGATACA
1 TTGTATCGATACA
387769 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:390336 original size:13 final size:13
Alignment explanation
Indices: 390318--390343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
390308 TACACCAAGT
390318 ATGTATCGATACA
1 ATGTATCGATACA
390331 ATGTATCGATACA
1 ATGTATCGATACA
390344 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:390341 original size:32 final size:33
Alignment explanation
Indices: 390300--390363 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
390290 TAGCCAAACT
* **
390300 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
390332 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
390364 TTGGATTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:396686 original size:35 final size:34
Alignment explanation
Indices: 396638--396711 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
396628 CCATAATAGC
* *
396638 AATAAAGAAAAATTCATTTATTTAA-ATGCATATTA
1 AATAAAGAAAAATT-AATTATTTAATATGAATA-TA
**
396673 AATAAAGGTAAATTAATTATTTAATATGAATATA
1 AATAAAGAAAAATTAATTATTTAATATGAATATA
396707 AATAA
1 AATAA
396712 TTATTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 16 0.47
35 18 0.53
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (34 bp):
AATAAAGAAAAATTAATTATTTAATATGAATATA
Found at i:396750 original size:25 final size:24
Alignment explanation
Indices: 396720--396782 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
396710 AATTATTTAT
* *
396720 TTAAAAGACAAATACGTAAATAAA
1 TTAAAAGATAAATACATAAATAAA
*
396744 GTTAAAAGATAAATACATATATAAA
1 -TTAAAAGATAAATACATAAATAAA
396769 TATAAAAGATAAAT
1 T-TAAAAGATAAAT
396783 TTATTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 1 0.03
25 33 0.97
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (24 bp):
TTAAAAGATAAATACATAAATAAA
Found at i:396842 original size:20 final size:20
Alignment explanation
Indices: 396806--396844 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
396796 AATTAATTAA
*
396806 TTAATTAATTATTTAAAAGT
1 TTAATTAATTAATTAAAAGT
*
396826 TTAATTATTTAATTAAAAG
1 TTAATTAATTAATTAAAAG
396845 ATGAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAATTAATTAATTAAAAGT
Found at i:396855 original size:20 final size:20
Alignment explanation
Indices: 396818--396857 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
396808 AATTAATTAT
* * *
396818 TTAAAAGTTTAATTATTTAA
1 TTAAAAGATGAATAATTTAA
396838 TTAAAAGATGAATAATTTAA
1 TTAAAAGATGAATAATTTAA
396858 ATATTCTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
TTAAAAGATGAATAATTTAA
Found at i:404528 original size:9 final size:9
Alignment explanation
Indices: 404514--404539 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
404504 GTAGTTTTAG
404514 GATGATTTT
1 GATGATTTT
404523 GATGATTTT
1 GATGATTTT
404532 GATGATTT
1 GATGATTT
404540 AAAGTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (9 bp):
GATGATTTT
Found at i:409314 original size:151 final size:149
Alignment explanation
Indices: 409087--409388 Score: 457
Period size: 151 Copynumber: 2.0 Consensus size: 149
409077 AAGGATTGAA
*
409087 TGATAGCTCAAGCTTGTCGTTTATTAGACAAAGTATACCTACATCCTTTAACTCACATACTATAT
1 TGATAGCTCAAGCTTGTCATTTATTAGACAAAGTATACCTACATCCTTTAACTCACATACTATAT
* *
409152 CTAGCATTTACCTTACATGCCATCTTGTTTTGTGACTTGGGTGTTTCTTGTAAGTGTTC-AACTT
66 CTAGCATTTACCTTACATGCCACCTTGTATTGTGACTTGGGTGTTTCTTGTAAGTG-TCAAACTT
*
409216 GATAGTGAATTGCTTAAGTT
130 GATAGTGAATTGCCTAAGTT
* * *
409236 TGATAGCTCAAGCTTTTCATTTATTCGACAAAGTATGACC-AGCATCCTTTTAACTCACTTACTA
1 TGATAGCTCAAGCTTGTCATTTATTAGACAAAGTAT-ACCTA-CATCC-TTTAACTCACATACTA
* *
409300 TAT-TTGACATTTACCTTACATGCCGCCTTGTATTGTGACTTGGGTGTTTCTTGTAAGTGTCAAA
63 TATCTAG-CATTTACCTTACATGCCACCTTGTATTGTGACTTGGGTGTTTCTTGTAAGTGTCAAA
409364 CTTGATAGTGAATTGCCTAAGTT
127 CTTGATAGTGAATTGCCTAAGTT
409387 TG
1 TG
409389 GTAACCGATG
Statistics
Matches: 139, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
149 34 0.24
150 12 0.09
151 93 0.67
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (149 bp):
TGATAGCTCAAGCTTGTCATTTATTAGACAAAGTATACCTACATCCTTTAACTCACATACTATAT
CTAGCATTTACCTTACATGCCACCTTGTATTGTGACTTGGGTGTTTCTTGTAAGTGTCAAACTTG
ATAGTGAATTGCCTAAGTT
Found at i:410304 original size:61 final size:61
Alignment explanation
Indices: 410209--410329 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
410199 CCATGAAATA
410209 CTTAAAATTTGTGATTTCCTTTACGAATTGTTAGGCTAATAAAAAAGGCTACAATTCCCCC
1 CTTAAAATTTGTGATTTCCTTTACGAATTGTTAGGCTAATAAAAAAGGCTACAATTCCCCC
*
410270 CTTAAAATTTGTGATTTCCTTTACGAATTGTTAGGCTGATAAAAAAGGCTACAATTCCCC
1 CTTAAAATTTGTGATTTCCTTTACGAATTGTTAGGCTAATAAAAAAGGCTACAATTCCCC
410330 TTGCTCTATC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (61 bp):
CTTAAAATTTGTGATTTCCTTTACGAATTGTTAGGCTAATAAAAAAGGCTACAATTCCCCC
Found at i:414115 original size:20 final size:20
Alignment explanation
Indices: 414090--414141 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
414080 TACAAGCCAA
** *
414090 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
414110 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
414129 TGTATCGATACAA
1 TGTATCGATACAA
414142 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:414147 original size:19 final size:18
Alignment explanation
Indices: 414090--414147 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
414080 TACAAGCCAA
*
414090 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
*
414110 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
414129 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
414148 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:416226 original size:20 final size:21
Alignment explanation
Indices: 416187--416229 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
416177 GGCTAGTGTG
*
416187 GGGACTGCCTGGTTGCGACCT
1 GGGACTGCCTGGTCGCGACCT
*
416208 GGGAGTGCC-GGTCGCGACCT
1 GGGACTGCCTGGTCGCGACCT
416228 GG
1 GG
416230 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (21 bp):
GGGACTGCCTGGTCGCGACCT
Found at i:416708 original size:13 final size:13
Alignment explanation
Indices: 416670--416708 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
416660 ATAATCCCCC
*
416670 TGTATCGATACAC
1 TGTATCGATACAA
416683 TGTATCGATACAA
1 TGTATCGATACAA
416696 TGTATCGATACAA
1 TGTATCGATACAA
416709 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:422913 original size:13 final size:13
Alignment explanation
Indices: 422895--422920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
422885 CAATTTTTTG
422895 TGTATCGATACAT
1 TGTATCGATACAT
422908 TGTATCGATACAT
1 TGTATCGATACAT
422921 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:422935 original size:32 final size:33
Alignment explanation
Indices: 422875--422938 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
422865 TACAAGCCAA
** *
422875 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
422908 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
422939 AGTTTCGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:424667 original size:16 final size:17
Alignment explanation
Indices: 424646--424689 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
424636 AAAAGTTATG
424646 AAAAAATA-AAAAAATA
1 AAAAAATACAAAAAATA
*
424662 AAAAAA-ACAAAAGATA
1 AAAAAATACAAAAAATA
424678 AAAACAATACAA
1 AAAA-AATACAA
424690 CTTTCAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 2 0.08
18 4 0.17
ACGTcount: A:0.82, C:0.07, G:0.02, T:0.09
Consensus pattern (17 bp):
AAAAAATACAAAAAATA
Found at i:424864 original size:30 final size:30
Alignment explanation
Indices: 424799--424862 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
424789 TTTTTTTTGG
* *
424799 AAAAACAAAAAAAAAGTTGTTAAAAAAAGA
1 AAAAAGAAAAAAAAAGTTGTGAAAAAAAGA
*
424829 AAAAAGAACAAAAAAGTTGTG-AAAAAAGA
1 AAAAAGAAAAAAAAAGTTGTGAAAAAAAGA
424858 AAAAA
1 AAAAA
424863 AGGGATGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.11
Consensus pattern (30 bp):
AAAAAGAAAAAAAAAGTTGTGAAAAAAAGA
Found at i:439435 original size:65 final size:62
Alignment explanation
Indices: 439277--440652 Score: 1432
Period size: 62 Copynumber: 21.9 Consensus size: 62
439267 GAGCATGACG
* * * *
439277 TTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAAGATGCC
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
** * *
439339 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTGTTCAAG-CCTCAAAGAGCAAGACGCATT
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTC-AGTCCTCAAAGAGCAGGATGC--T
* *
439403 TTTCTTCTTTTAAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGGCAT-CT
1 TTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCA-GG-ATGC-
439467 T
62 T
* * *
439468 TTTCTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAAAGCAGGATGCT
1 TTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* *
439531 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCCGTCCTCAAAGAGCAAGATGCCTT
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATG-C-T
* * * * * *
439595 TTTTTCTTTTAAAGCCCACACAAGTTGGTAGCACCCGTTCAGTCCTTAAAGAGCATGACGCC
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* * *
439657 TTTTT-TTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGTAGGACGC-
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* * ** * *
439717 -ATTT-TTTAAAAGCCCACACAAGTTGGTGGCACCTGTTTAGTTCTCAAAGAGCAGGATG-T
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* ** * * * *
439776 TTTTT-TTTAAAAAAAAAAACCATACAAGTTGGTTGCACCCATTCAGTCCTCAAAGGGCCGGATG
1 TTTTTCTTT-----TAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATG
439840 CCT
61 -CT
* * * * *
439843 TTTTTCTTTGAAAACCCACACAAGTTGGTGGCACCCATTCAGTCCTTAAAGAGTAGGATGCC
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* * ** *
439905 TTTTTCTTTAAAAGCTCACACAAGTTGGTGGCACCTGTTCAAG-CCTCAAAGAGCAAGATGCATT
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTC-AGTCCTCAAAGAGCAGGATGC--T
* * * **
439969 TTTCTTCTTTTAAAGCCCATACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGGGCGTCTT
1 TTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATG-C-T
* * * * * *
440034 TTTCTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTTAAAAAGTAGGACGCT
1 TTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* *
440097 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCCA-TCCTCAAAGAGCATGATGCATT
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATT-CAGTCCTCAAAGAGCAGGATGC--T
* * * *
440161 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCATGACGCC
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* * * *
440223 TTTTTCTTTTAAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGTAGGA--CG
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* * * * * *
440283 TATTT-TTTAAAAGCCCACACAAGTTGGTGGCACCTATTTAGTTCTCAAAGAGCAAGATG-T
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* * * * * * **
440343 TTTTTTTTTTAAAAAAAAAG-CCATACAAGTTGGTTGCACCCATTCAATCTTCAAAGGGTTGGAT
1 TTTTTCTTTT------AAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGAT
440407 GCCT
60 G-CT
* * * * * *
440411 TTTTTCTTTGAAAACCCACAAAAGTTGGTGGCACCCATTAAGTCCTTAAAGAGCAGGATGCC
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* * * * * * *
440473 TTTTTCTTTAAAAGCCCACACAAGTTGGTGGCACTCGTTCAGTCCTAAAAGAGCAAGACGCC
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* * *
440535 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGTAGGACGCC
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
* * * *
440597 TTTTTCTTTAAAAGCCCACACAAGTTGGTGGCACTCGTTCAGTCCTCAAAAAGCAG
1 TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAG
440653 AACGCCATTT
Statistics
Matches: 1119, Mismatches: 153, Indels: 84
0.83 0.11 0.06
Matches are distributed among these distances:
59 97 0.09
60 15 0.01
61 52 0.05
62 428 0.38
63 97 0.09
64 127 0.11
65 243 0.22
66 37 0.03
67 11 0.01
68 12 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (62 bp):
TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGCAGGATGCT
Found at i:440349 original size:566 final size:566
Alignment explanation
Indices: 439277--440657 Score: 2267
Period size: 566 Copynumber: 2.4 Consensus size: 566
439267 GAGCATGACG
* * * *
439277 TTTTTCTCTT-AAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAAGATGCCTT
1 TTTTTCT-TTGAAAACCCACACAAGTTGGTGGCACCCATTCAGTCCTTAAAGAGCAGGATGCCTT
*
439341 TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTGTTCAAGCCTCAAAGAGCAAGACGCATTTTT
65 TTTCTTTAAAAGCCCACACAAGTTGGTGGCACCTGTTCAAGCCTCAAAGAGCAAGACGCATTTTT
*
439406 CTTCTTTTAAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGGCATCTTTTT
130 CTTCTTTTAAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGGCGTCTTTTT
*
439471 CTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAAAGCAGGATGCTTTTTT
195 CTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAAAGCAGGACGCTTTTTT
* *
439536 CTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCCGTCCTCAAAGAGCAAGATGCCTTTTTTTC
260 CTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCCATCCTCAAAGAGCAAGATGCATTTTTTTC
*
439601 TTTTAAAGCCCACACAAGTTGGTAGCACCCGTTCAGTCCTTAAAGAGCATGACGCCTTTTTTTTT
325 TTTTAAAGCCCACACAAGTTGGTAGCACCCGTTCAGTCCTCAAAGAGCATGACGCCTTTTTTTTT
439666 AAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGTAGGACGCATTTTTTAAAAGCC
390 AAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGTAGGACGCATTTTTTAAAAGCC
* *
439731 CACACAAGTTGGTGGCACCTGTTTAGTTCTCAAAGAGCAGGATGTTTTTTTTTAAAAAAAAAAAC
455 CACACAAGTTGGTGGCACCTATTTAGTTCTCAAAGAGCAAGATGTTTTTTTTTAAAAAAAAAAAC
*
439796 CATACAAGTTGGTTGCACCCATTCAGTCCTCAAAGGGCCGGATGCCT
520 CATACAAGTTGGTTGCACCCATTCAATCCTCAAAGGGCCGGATGCCT
*
439843 TTTTTCTTTGAAAACCCACACAAGTTGGTGGCACCCATTCAGTCCTTAAAGAGTAGGATGCCTTT
1 TTTTTCTTTGAAAACCCACACAAGTTGGTGGCACCCATTCAGTCCTTAAAGAGCAGGATGCCTTT
* *
439908 TTCTTTAAAAGCTCACACAAGTTGGTGGCACCTGTTCAAGCCTCAAAGAGCAAGATGCATTTTTC
66 TTCTTTAAAAGCCCACACAAGTTGGTGGCACCTGTTCAAGCCTCAAAGAGCAAGACGCATTTTTC
*
439973 TTCTTTTAAAGCCCATACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGGGCGTCTTTTTC
131 TTCTTTTAAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGGCGTCTTTTTC
* *
440038 TTTTTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTTAAAAAGTAGGACGCTTTTTTC
196 TTTTTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAAAGCAGGACGCTTTTTTC
* *
440103 TTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCCATCCTCAAAGAGCATGATGCATTTTTTTCT
261 TTTTAAAGCCCACACAAGTTGGTGGCACCCATTCCATCCTCAAAGAGCAAGATGCATTTTTTTCT
*
440168 TTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCATGACGCCTTTTTCTTTT
326 TTTAAAGCCCACACAAGTTGGTAGCACCCGTTCAGTCCTCAAAGAGCATGACGCCTTTTT-TTTT
* *
440233 AAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGTAGGACGTATTTTTTAAAAGCC
390 AAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGTAGGACGCATTTTTTAAAAGCC
* *
440298 CACACAAGTTGGTGGCACCTATTTAGTTCTCAAAGAGCAAGATGTTTTTTTTTTTAAAAAAAAAG
455 CACACAAGTTGGTGGCACCTATTTAGTTCTCAAAGAGCAAGATG-TTTTTTTTTAAAAAAAAAAA
* **
440363 CCATACAAGTTGGTTGCACCCATTCAATCTTCAAAGGGTTGGATGCCT
519 CCATACAAGTTGGTTGCACCCATTCAATCCTCAAAGGGCCGGATGCCT
* *
440411 TTTTTCTTTGAAAACCCACAAAAGTTGGTGGCACCCATTAAGTCCTTAAAGAGCAGGATGCCTTT
1 TTTTTCTTTGAAAACCCACACAAGTTGGTGGCACCCATTCAGTCCTTAAAGAGCAGGATGCCTTT
* *
440476 TTCTTTAAAAGCCCACACAAGTTGGTGGCA-CTCGTTC-AGTCCTAAAAGAGCAAGACGC--CTT
66 TTCTTTAAAAGCCCACACAAGTTGGTGGCACCT-GTTCAAG-CCTCAAAGAGCAAGACGCATTTT
* * * * *
440537 T-TTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGTAGGACGCCTTTT
129 TCTTCTTTTAAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGGCGTCTTTT
* * * * *
440601 TC---TTTAAAAGCCCACACAAGTTGGTGGCACTCGTTCAGTCCTCAAAAAGCAGAACGC
194 TCTTTTTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAAAGCAGGACGC
440658 CATTTTCTCA
Statistics
Matches: 761, Mismatches: 49, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
562 48 0.06
565 61 0.08
566 366 0.48
567 113 0.15
568 173 0.23
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (566 bp):
TTTTTCTTTGAAAACCCACACAAGTTGGTGGCACCCATTCAGTCCTTAAAGAGCAGGATGCCTTT
TTCTTTAAAAGCCCACACAAGTTGGTGGCACCTGTTCAAGCCTCAAAGAGCAAGACGCATTTTTC
TTCTTTTAAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGCAGGGCGTCTTTTTC
TTTTTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAAAGCAGGACGCTTTTTTC
TTTTAAAGCCCACACAAGTTGGTGGCACCCATTCCATCCTCAAAGAGCAAGATGCATTTTTTTCT
TTTAAAGCCCACACAAGTTGGTAGCACCCGTTCAGTCCTCAAAGAGCATGACGCCTTTTTTTTTA
AAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGTAGGACGCATTTTTTAAAAGCCC
ACACAAGTTGGTGGCACCTATTTAGTTCTCAAAGAGCAAGATGTTTTTTTTTAAAAAAAAAAACC
ATACAAGTTGGTTGCACCCATTCAATCCTCAAAGGGCCGGATGCCT
Found at i:440441 original size:129 final size:126
Alignment explanation
Indices: 439287--440646 Score: 639
Period size: 127 Copynumber: 10.8 Consensus size: 126
439277 TTTTTCTCTT
* * *
439287 AAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCAAGATGCCTTTTTCTTT----
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTAAAA
* * ** * * * *
439348 -TAAAGCCCACACAAGTTGGTGGCACCTGTTCAAGCCTCAAAGAGCAAGACGCATTTTTCTTCTT
66 AAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGACG----TAT-TT-TT
*
439412 TT
125 TA
* * * *
439414 AAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGC-AG-GGCATCTTTTTCTTT--
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGC--CTTTTTCTTTAA
**** * * * * * * *
439475 TTTTAAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAAAGCAGGATGCTTTTTTCTTT
64 AAAAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGA--CGTATTT-TTT
*
439540 T
126 A
* **
439541 AAAGCCCACACAAGTTGGTGGCACCCATTCCGTCCTCAAAGAGCAAGATGCCTTTTTTTCTTT--
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCC--TTTTTCTTTAA
* * * * * * * * * *
439604 ---TAAAGCCCACACAAGTTGGTAGCACCCGTTCAGTCCTTAAAGAGCATGACGCCTTTTTTTTT
64 AAAAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGACG--TATTTTTTA
* * * * * *
439666 AAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGTAGGACG-C-ATTT-TTT----
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTAAAA
* ** * * * * * *
439724 -AAAAGCCCACACAAGTTGGTGGCACCTGTTTAGTTCTCAAAGAGCAGGATGTTTTTTTTTAAAA
66 AAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGACG-TATTTTTT----
439788 AA
126 -A
** * * * * * **
439790 AAAAACCATACAAGTTGGTTGCACCCATTCAGTCCTCAAAGGGCCGGATGCCTTTTTTCTTT---
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCC-TTTTTCTTTAAA
* * * * * *
439852 -GAAAA-CCCACACAAGTTGGTGGCACCCATTCAGTCCTTAAAGAGTAGGATGCCTTTTTCTTTA
65 AAAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGA--CGTATTT-TTTA
* * ** *
439915 AAAGCTCACACAAGTTGGTGGCACCTGTTCAAG-CCTCAAAGAGCAAGATGCATTTTTCTTCT--
1 AAAGCCCACAAAAGTTGGTGGCACCCATT-AAGTCCTCAAAGAGCAAGATGCCTTTTTCTT-TAA
*** * * * * * *
439977 -TTTAAAGCCCATACAAGTTGGTGGCACCCGTTTAGTCCTCAAAGAGCAGGGCGTCTTTTTCTTT
64 AAAAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGACG------TATTT
*
440041 TTTT
123 TTTA
* * * * * * * *
440045 AAAGCCCACACAAGTTGGTGGCACCCATTTAGTCCTTAAAAAGTAGGACGCTTTTTTCTTT----
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTAAAA
* * * * * ** *
440106 -TAAAGCCCACACAAGTTGGTGGCACCCGTTCCATCCTCAAAGAGCATGATGCATTTTTTTCTTT
66 AAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAG--T-A-GGACGTATTT-TTT
*
440170 T
126 A
* * * * *
440171 AAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCTCAAAGAGCATGACGCCTTTTTCTTT----
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTAAAA
* * *
440232 -TAAAGCCCATACAAGTTGGTGGCACCCATTTAGTCCTCAAAGAGTAGGACGTATTTTTTA
66 AAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGACGTATTTTTTA
* * * * ** *
440292 AAAGCCCACACAAGTTGGTGGCACCTATTTAGTTCTCAAAGAGCAAGATGTTTTTTTTTTTAAAA
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTAAAA
* * * * * *
440357 AAAAAG-CCATACAAGTTGGTTGCACCCATTCAATCTTCAAAGGGTTGGATGCCTTTTTTCTTTG
66 AAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGA---CGTATTT-TTT-
440421 A
126 A
* *
440422 AAA-CCCACAAAAGTTGGTGGCACCCATTAAGTCCTTAAAGAGCAGGATGCCTTTTTCTTT----
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTAAAA
* * * * * * * * *
440482 -AAAAGCCCACACAAGTTGGTGGCACTCGTTCAGTCCTAAAAGAGCAAGACGCCTTTTTCTTTT
66 AAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGACG--TATTT-TTTA
* * * * *
440545 AAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTCAAAGAGTAGGACGCCTTTTTCTTT----
1 AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTAAAA
* * * *
440606 -AAAAGCCCACACAAGTTGGTGGCACTCGTTCAGTCCTCAAA
66 AAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAA
440647 AAGCAGAACG
Statistics
Matches: 1014, Mismatches: 163, Indels: 115
0.78 0.13 0.09
Matches are distributed among these distances:
119 8 0.01
120 46 0.05
121 58 0.06
122 7 0.01
123 4 0.00
124 158 0.16
125 165 0.16
126 156 0.15
127 181 0.18
128 51 0.05
129 74 0.07
130 100 0.10
131 5 0.00
132 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (126 bp):
AAAGCCCACAAAAGTTGGTGGCACCCATTAAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTAAAA
AAAAAGCCCATACAAGTTGGTGGCACCCATTCAATCCTCAAAGAGTAGGACGTATTTTTTA
Found at i:440759 original size:48 final size:48
Alignment explanation
Indices: 440617--440762 Score: 202
Period size: 49 Copynumber: 3.0 Consensus size: 48
440607 AAAGCCCACA
* *
440617 CAAGTTGGTGGCACTCGTTCAGTCCTCAAAAAGCAGAACGCCATTTTCT
1 CAAGTTGGTGGCAC-CGTTCAGTCCTCAAAGAGCAGAACGCCTTTTTCT
* * *
440666 CAAGTTGGTGGCACCTTTTTAGTCCTCAAAGAGCAAAACGCCTTTTTCT
1 CAAGTTGGTGGCACC-GTTCAGTCCTCAAAGAGCAGAACGCCTTTTTCT
* * *
440715 CAAGTTGGTGGTACCGTTCAGTCCTCAAAGAGCTGAACGTCTTTTTCT
1 CAAGTTGGTGGCACCGTTCAGTCCTCAAAGAGCAGAACGCCTTTTTCT
440763 TTAAAAACCC
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
48 29 0.34
49 56 0.66
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (48 bp):
CAAGTTGGTGGCACCGTTCAGTCCTCAAAGAGCAGAACGCCTTTTTCT
Found at i:440811 original size:33 final size:31
Alignment explanation
Indices: 440773--440844 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 31
440763 TTAAAAACCC
440773 ACACAAGTCAGTGGCACCTCTTTTCAAAAGCCT
1 ACACAAGTCAGTGGCACCT-TTTTC-AAAGCCT
** * *
440806 ACACAAGTTGGTGGCATCTTTTTCAAAGCGT
1 ACACAAGTCAGTGGCACCTTTTTCAAAGCCT
440837 ACACAAGT
1 ACACAAGT
440845 TGGTGGCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 14 0.40
32 5 0.14
33 16 0.46
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (31 bp):
ACACAAGTCAGTGGCACCTTTTTCAAAGCCT
Found at i:440834 original size:31 final size:33
Alignment explanation
Indices: 440773--440852 Score: 110
Period size: 31 Copynumber: 2.5 Consensus size: 33
440763 TTAAAAACCC
**
440773 ACACAAGTCAGTGGCACCTCTTTTCAAAAGCCT
1 ACACAAGTTGGTGGCACCTCTTTTCAAAAGCCT
* *
440806 ACACAAGTTGGTGGCATCT-TTTTC-AAAGCGT
1 ACACAAGTTGGTGGCACCTCTTTTCAAAAGCCT
440837 ACACAAGTTGGTGGCA
1 ACACAAGTTGGTGGCA
440853 ACCCTCTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 22 0.51
32 5 0.12
33 16 0.37
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (33 bp):
ACACAAGTTGGTGGCACCTCTTTTCAAAAGCCT
Found at i:441677 original size:31 final size:31
Alignment explanation
Indices: 441594--441677 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
441584 ATTTTTTTGG
* **
441594 AAAAACAAAAAAATAAAAAAAAAGTTGTTAA
1 AAAAAGAAAAAAGGAAAAAAAAAGTTGTTAA
*
441625 AAAAAGAAAAAAGGAACAAAAAAAGTTG-TGA
1 AAAAAGAAAAAAGGAA-AAAAAAAGTTGTTAA
* *
441656 AAAAAGAAAAATGGAGAAAAAA
1 AAAAAGAAAAAAGGAAAAAAAA
441678 GGGGTGGAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.13
31 29 0.63
32 11 0.24
ACGTcount: A:0.73, C:0.02, G:0.14, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAAAAGGAAAAAAAAAGTTGTTAA
Found at i:444919 original size:52 final size:52
Alignment explanation
Indices: 444841--444943 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
444831 TTACTTCTAA
444841 TTTCTTGGCACATTCAGTCCTCCATAACATGTTTTTCTTCTACAACTTTTAG
1 TTTCTTGGCACATTCAGTCCTCCATAACATGTTTTTCTTCTACAACTTTTAG
* *
444893 TTTCTTGGTATATTCAGTCCTCCATAACATGTTTTTCTTCTACAACTTTTA
1 TTTCTTGGCACATTCAGTCCTCCATAACATGTTTTTCTTCTACAACTTTTA
444944 ACGTAGCCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (52 bp):
TTTCTTGGCACATTCAGTCCTCCATAACATGTTTTTCTTCTACAACTTTTAG
Found at i:448467 original size:155 final size:155
Alignment explanation
Indices: 448269--448569 Score: 363
Period size: 155 Copynumber: 1.9 Consensus size: 155
448259 TAAAATATTG
* * * * * * *
448269 AAAAATTTTGCTCCAAGGACAAAGGTGATTGGTCGAATATTTCTTGTTAATTTTGGATGTGATTT
1 AAAAATTTTGCTCCAAGGACAAAAGTGATTAGCCGAATATTTCTTATGAATTGTGGATGTAATTT
* * * * * *
448334 TTGTCTTGGTTTTGATATATTTGATGCTTAATCTTATGTTTTAATGATGTA-AAATCCAATTTGC
66 TTGTATTGATTTTAATATATTTAATGCTTAATCTTATATTTTAATGATGTAGAAA-CCAATTTAC
*
448398 AAATTTA-AAGAGTTTATTTGTACTT
130 AAATTTAGAAAAGTTTATTTGTACTT
* * * * *
448423 AAAATATTTTGTTCCAAGGCCAAAAGTGATTAGCCGAATCTTTCTTATGACTTGTGTATGTAATT
1 AAAA-ATTTTGCTCCAAGGACAAAAGTGATTAGCCGAATATTTCTTATGAATTGTGGATGTAATT
* * * *
448488 TTTGTATTGATTTTAATATATTTAATGCTTAATTTTGTATTTTAATTATGTAGGAACCAATTTAC
65 TTTGTATTGATTTTAATATATTTAATGCTTAATCTTATATTTTAATGATGTAGAAACCAATTTAC
448553 AAATTTAGAAAAGTTTA
130 AAATTTAGAAAAGTTTA
448570 GGAACCATAA
Statistics
Matches: 121, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
154 4 0.03
155 107 0.88
156 10 0.08
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.45
Consensus pattern (155 bp):
AAAAATTTTGCTCCAAGGACAAAAGTGATTAGCCGAATATTTCTTATGAATTGTGGATGTAATTT
TTGTATTGATTTTAATATATTTAATGCTTAATCTTATATTTTAATGATGTAGAAACCAATTTACA
AATTTAGAAAAGTTTATTTGTACTT
Found at i:449598 original size:13 final size:15
Alignment explanation
Indices: 449570--449601 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
449560 CAAGGGAATT
449570 ATAATTAAATACTGA
1 ATAATTAAATACTGA
449585 ATAA-TAAA-ACTGA
1 ATAATTAAATACTGA
449598 ATAA
1 ATAA
449602 AAATCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (15 bp):
ATAATTAAATACTGA
Found at i:451938 original size:22 final size:23
Alignment explanation
Indices: 451913--451966 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
451903 GAGCATGTTC
*
451913 AATTTA-TTTAT-ATTCATGAAAA
1 AATTTAGTTTATGAATCAT-AAAA
451935 AA-TTAGTTTATGAATCATAAAA
1 AATTTAGTTTATGAATCATAAAA
451957 AA-TTAGTTTA
1 AATTTAGTTTA
451967 ATAGATCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 3 0.10
22 21 0.72
23 5 0.17
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (23 bp):
AATTTAGTTTATGAATCATAAAA
Found at i:452332 original size:30 final size:30
Alignment explanation
Indices: 452292--452350 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
452282 AACAATTTCA
* * *
452292 TTAATTTAAATGAA-TGAATTCAAACACAT
1 TTAATTTAAATAAATTAAACTCAAACACAT
452321 TTAATTTTAAATAAATTAAACTCAAACACA
1 TTAA-TTTAAATAAATTAAACTCAAACACA
452351 ATGTTACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 9 0.36
31 12 0.48
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (30 bp):
TTAATTTAAATAAATTAAACTCAAACACAT
Found at i:455923 original size:36 final size:34
Alignment explanation
Indices: 455881--455950 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 34
455871 AAATAATTAA
* *
455881 AAATTATATTTATGTTGAATAATAATTAAAATTATT
1 AAATTATATTTATATTGAAAAAT-ATT-AAATTATT
* *
455917 AAATTATGTTTATATTTAAAAATATTAAATTATT
1 AAATTATATTTATATTGAAAAATATTAAATTATT
455951 TTATATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 8 0.27
35 3 0.10
36 19 0.63
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (34 bp):
AAATTATATTTATATTGAAAAATATTAAATTATT
Found at i:455935 original size:26 final size:25
Alignment explanation
Indices: 455906--455957 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
455896 TGAATAATAA
*
455906 TTAAAATTATTAAATTATGTTTATAT
1 TTAAAAATATTAAATTAT-TTTATAT
455932 TTAAAAATATTAAATTATTTTATAT
1 TTAAAAATATTAAATTATTTTATAT
455957 T
1 T
455958 AAATAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAAAATATTAAATTATTTTATAT
Found at i:463620 original size:23 final size:25
Alignment explanation
Indices: 463594--463682 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 25
463584 TTTGATTCTT
*
463594 TGAAACAG-AAAAAAA-TTGAAAAA
1 TGAAAAAGAAAAAAAATTTGAAAAA
463617 TGAAAAAGAAAAAAAATTTGAAAAAA
1 TGAAAAAGAAAAAAAATTTG-AAAAA
* *
463643 TAGAAAAA-AAGAAAAA--TAAAAAA
1 T-GAAAAAGAAAAAAAATTTGAAAAA
463666 T-AAAAA-AATAAAAAATT
1 TGAAAAAGAA-AAAAAATT
463683 ATTTAAGCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
21 7 0.13
22 5 0.09
23 13 0.24
24 8 0.15
25 3 0.05
26 13 0.24
27 6 0.11
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.15
Consensus pattern (25 bp):
TGAAAAAGAAAAAAAATTTGAAAAA
Found at i:463649 original size:7 final size:8
Alignment explanation
Indices: 463638--463681 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
463628 AAAAATTTGA
463638 AAAAATAG
1 AAAAATAG
*
463646 AAAAAAAG
1 AAAAATAG
463654 AAAAATA-
1 AAAAATAG
*
463661 AAAAATAA
1 AAAAATAG
463669 AAAAATA-
1 AAAAATAG
463676 AAAAAT
1 AAAAAT
463682 TATTTAAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 13 0.39
8 20 0.61
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (8 bp):
AAAAATAG
Found at i:463664 original size:15 final size:15
Alignment explanation
Indices: 463637--463681 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
463627 AAAAAATTTG
463637 AAAAAATAGAAAAA-A
1 AAAAAATA-AAAAATA
463652 AGAAAAATAAAAAATA
1 A-AAAAATAAAAAATA
463668 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
463682 TATTTAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.11
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Done.