Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 4 of 25
Found at i:451930 original size:13 final size:13
Alignment explanation
Indices: 451912--451937 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
451902 CAATTTTTTG
451912 TGTATCGATACAT
1 TGTATCGATACAT
451925 TGTATCGATACAT
1 TGTATCGATACAT
451938 ACTTTGGTGT
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:458001 original size:15 final size:15
Alignment explanation
Indices: 457981--458011 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
457971 TAAAAATGTC
*
457981 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
457996 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
458011 C
1 C
458012 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:460110 original size:13 final size:13
Alignment explanation
Indices: 460092--460129 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
460082 CATTTTTCTT
460092 TGTATCGATACAA
1 TGTATCGATACAA
*
460105 TGTATCGATACAC
1 TGTATCGATACAA
460118 TGTATCGATACA
1 TGTATCGATACA
460130 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:469076 original size:951 final size:951
Alignment explanation
Indices: 467228--469131 Score: 3495
Period size: 951 Copynumber: 2.0 Consensus size: 951
467218 GTTGCTCATG
* *
467228 TAATGCTGCTTTATGCACATTAGTGCCTTAGTACCACCATTTAGATTACTCTCAGGATTGGCCGG
1 TAATGCCGCTTTATGCACATTAGTGCCTTAGTACCACCATTTAGATTACTCTCAAGATTGGCCGG
*
467293 TCCTTTTCTAGTATCAATAGTGCTTGTTTGCCCTTTGTTTTTCAAGGTTTCGGATAATAGCTTGG
66 TCCTTTTCTAGTATCAATAGTGCTTGTTTACCCTTTGTTTTTCAAGGTTTCGGATAATAGCTTGG
* * *
467358 TTAACTCTATGACTTGAGCTTGAAGTTTTTCACTTTTTCAGGGTGCCTATTCTTGGGATTCCCTG
131 TTAACTCTATCACTTGAGCTTGAAGTTTTTCACTTTTTCAAGCTGCCTATTCTTGGGATTCCCTG
* *
467423 TACATGAGCTCCAATCGCTCAATGGGAGCCTGATGATCGTTTTCCATAGCTCTACGATGAGTTTG
196 TACATGAGCTCCAATAGCTCAATGGGAGCCTGATGATCGTTTTCCATAGCTCTACGATGAGTTCG
467488 AGTATTGTATGAGTTTCTAAACATGAAGTCCATGTTTTTGGGACACGTTCATTTCAAATTATTAC
261 AGTATTGTATGAGTTTCTAAACATGAAGTCCATGTTTTTGGGACACGTTCATTTCAAATTATTAC
*
467553 TGTATTAGGCTTTTATGATATGCTTATGTACATGCTCTATGTAGCGAAAGTGATTATGCAATGAT
326 TGTATTAGGCTTTTATGATATACTTATGTACATGCTCTATGTAGCGAAAGTGATTATGCAATGAT
*
467618 GAATGAAACACATGAGAAAATTGGGTTAGTCATGCAAATGCAAAAGAAAGGTCAATTGGGTAAAT
391 GAATGAAACACATGAGAAAATTGGGTTAGTCATGCAAATGCAAAAGAAAGGTCAATTGGGTAAAA
*
467683 GGGGCAGCTCCACAAATAACACCTTTCATTGAAGCAATAACATGTCTTGGTTACACATGATTACA
456 GGGGCAGCTCCACAAATAACACCTTTCATTGAAGCAATAACATGTCCTGGTTACACATGATTACA
467748 TTTGAAAATGCCTGACACGATTACACTACTTGATTATATAATCCAGGAAATACAACAAGTTTTGT
521 TTTGAAAATGCCTGACACGATTACACTACTTGATTATATAATCCAGGAAATACAACAAGTTTTGT
*
467813 TCATAGACTCGAATAGGCAAGATATTACACGCTAGGGAACGAGCTGCATCCATCATATTTTCAAC
586 TCATAGACTCGAATAGGCAAGATATTACACGCTAGGGAACGAGCTACATCCATCATATTTTCAAC
467878 CTCCAATTAGGCTGCTTGGACCTGCTCGGTGAGATGGCAGCGATGATCTTGATAGTCCTAGTGTG
651 CTCCAATTAGGCTGCTTGGACCTGCTCGGTGAGATGGCAGCGATGATCTTGATAGTCCTAGTGTG
467943 CAAGGTCAACTGTTTATAGCCATTCTTATTTTCATTGCTGGAAGTCTCTCCTTAGTTCATCAATT
716 CAAGGTCAACTGTTTATAGCCATTCTTATTTTCATTGCTGGAAGTCTCTCCTTAGTTCATCAATT
468008 TAGTTTTGACAACCTTGTAGGGAGTGCTCTAAGGTTTGAATTCTGAGGGTTAGAGTCTCATTCTC
781 TAGTTTTGACAACCTTGTAGGGAGTGCTCTAAGGTTTGAATTCTGAGGGTTAGAGTCTCATTCTC
* * *
468073 AACTTGAATCCCCCTTAAACCTTGAATTCGATCTTCTTACCATCGATTCTGCCTTTGATAAGTTG
846 AACTTGAATCCCCCTTAAACCTTGAATTCGAGCTTCTTACCATCGATTCTGCCTTCGATAAGTTA
*
468138 AAACAAGAACTTGGGTTTGACAAGTTTTTCCTTATTGCCCT
911 AAACAAGAACCTGGGTTTGACAAGTTTTTCCTTATTGCCCT
* *
468179 TAATGCCGTTTTATGCACATTAGTGCCTTAGTACCACCGTTTAGATTACTCTCAAGATTGGCCGG
1 TAATGCCGCTTTATGCACATTAGTGCCTTAGTACCACCATTTAGATTACTCTCAAGATTGGCCGG
*
468244 TCCTTTTCTAGTATCAATAGTGCTTGTTTACCTTTTGTTTTTCAAGGTTTCGGATAATAGCTTGG
66 TCCTTTTCTAGTATCAATAGTGCTTGTTTACCCTTTGTTTTTCAAGGTTTCGGATAATAGCTTGG
*
468309 TTAACTCTGTCACTTGAGCTTGAAGTTTTTCACTTTTTCAAGCTGCCTATTCTTGGGATTCCCTG
131 TTAACTCTATCACTTGAGCTTGAAGTTTTTCACTTTTTCAAGCTGCCTATTCTTGGGATTCCCTG
468374 TACATGAGCTCCAATAGCTCAATGGGAGCCTGATGATCGTTTTCCATAGCTCTACGATGAGTTCG
196 TACATGAGCTCCAATAGCTCAATGGGAGCCTGATGATCGTTTTCCATAGCTCTACGATGAGTTCG
468439 AGTATTGTATGAGTTTCTAAACATGAAGTCCATGTTTTTGGGACAC-TGTCATTTCAAATTATTA
261 AGTATTGTATGAGTTTCTAAACATGAAGTCCATGTTTTTGGGACACGT-TCATTTCAAATTATTA
468503 CTGTATTAGGCTTTTATGATATACTTATGTACATGCTCTATGTAGCGAAAGTGATTATGCAATGA
325 CTGTATTAGGCTTTTATGATATACTTATGTACATGCTCTATGTAGCGAAAGTGATTATGCAATGA
*
468568 TGAATGAAACACATGAGAAAATTGGGTTAGTCATGCAAATGCAAAAGGAAGGTCAATTGGGTAAA
390 TGAATGAAACACATGAGAAAATTGGGTTAGTCATGCAAATGCAAAAGAAAGGTCAATTGGGTAAA
*
468633 AGGGGCAGCTCCACAAATAACACCTTTCATTGAGGCAATAACATGTCCTGGTTACACATGATTAC
455 AGGGGCAGCTCCACAAATAACACCTTTCATTGAAGCAATAACATGTCCTGGTTACACATGATTAC
* * *
468698 ATTTGAAAATGCCTGACATGGTTACACTGCTTGATTATATAATCCAGGAAATACAACAAGTTTTG
520 ATTTGAAAATGCCTGACACGATTACACTACTTGATTATATAATCCAGGAAATACAACAAGTTTTG
* * *
468763 TTCATAGACTCGAATAGGTAAGATATTACACGTTAGGGAACGAGCTACATCCATCATATTTTCGA
585 TTCATAGACTCGAATAGGCAAGATATTACACGCTAGGGAACGAGCTACATCCATCATATTTTCAA
468828 CCTCCAATTAGGCTGCTTGGACCTGCTCGGTGAGATGGCAGCGATGATCTTGATAGTCCTAGTGT
650 CCTCCAATTAGGCTGCTTGGACCTGCTCGGTGAGATGGCAGCGATGATCTTGATAGTCCTAGTGT
* *
468893 GCAAGGTCAACTGTTTGTAGCCATTCTTATTTTCGTTGCTGGAAGTCTCTCCTTAGTTCATCAAT
715 GCAAGGTCAACTGTTTATAGCCATTCTTATTTTCATTGCTGGAAGTCTCTCCTTAGTTCATCAAT
*
468958 TTAGTTTTGACAACCTTGTAGGGAGTGCTCTAAGTTTTGAATTCTGAGGGTTAGAGTCTCATTCT
780 TTAGTTTTGACAACCTTGTAGGGAGTGCTCTAAGGTTTGAATTCTGAGGGTTAGAGTCTCATTCT
*
469023 CAACTTGAATCCCCCTTAAACCTTGAATTCGAGCTTCTTACCATCGATTCTGCCTTCGATGAGTT
845 CAACTTGAATCCCCCTTAAACCTTGAATTCGAGCTTCTTACCATCGATTCTGCCTTCGATAAGTT
*
469088 AAAACAAGAGCCTGGGTTTGACAAGTTTTTCCTTATTGCCCT
910 AAAACAAGAACCTGGGTTTGACAAGTTTTTCCTTATTGCCCT
469130 TA
1 TA
469132 GCTTCTTTTT
Statistics
Matches: 919, Mismatches: 33, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
950 1 0.00
951 918 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (951 bp):
TAATGCCGCTTTATGCACATTAGTGCCTTAGTACCACCATTTAGATTACTCTCAAGATTGGCCGG
TCCTTTTCTAGTATCAATAGTGCTTGTTTACCCTTTGTTTTTCAAGGTTTCGGATAATAGCTTGG
TTAACTCTATCACTTGAGCTTGAAGTTTTTCACTTTTTCAAGCTGCCTATTCTTGGGATTCCCTG
TACATGAGCTCCAATAGCTCAATGGGAGCCTGATGATCGTTTTCCATAGCTCTACGATGAGTTCG
AGTATTGTATGAGTTTCTAAACATGAAGTCCATGTTTTTGGGACACGTTCATTTCAAATTATTAC
TGTATTAGGCTTTTATGATATACTTATGTACATGCTCTATGTAGCGAAAGTGATTATGCAATGAT
GAATGAAACACATGAGAAAATTGGGTTAGTCATGCAAATGCAAAAGAAAGGTCAATTGGGTAAAA
GGGGCAGCTCCACAAATAACACCTTTCATTGAAGCAATAACATGTCCTGGTTACACATGATTACA
TTTGAAAATGCCTGACACGATTACACTACTTGATTATATAATCCAGGAAATACAACAAGTTTTGT
TCATAGACTCGAATAGGCAAGATATTACACGCTAGGGAACGAGCTACATCCATCATATTTTCAAC
CTCCAATTAGGCTGCTTGGACCTGCTCGGTGAGATGGCAGCGATGATCTTGATAGTCCTAGTGTG
CAAGGTCAACTGTTTATAGCCATTCTTATTTTCATTGCTGGAAGTCTCTCCTTAGTTCATCAATT
TAGTTTTGACAACCTTGTAGGGAGTGCTCTAAGGTTTGAATTCTGAGGGTTAGAGTCTCATTCTC
AACTTGAATCCCCCTTAAACCTTGAATTCGAGCTTCTTACCATCGATTCTGCCTTCGATAAGTTA
AAACAAGAACCTGGGTTTGACAAGTTTTTCCTTATTGCCCT
Found at i:472431 original size:13 final size:13
Alignment explanation
Indices: 472383--472435 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
472373 ACATAAGTTT
*
472383 TGTATCAATACAA
1 TGTATCGATACAA
472396 TGTATCGATACAA
1 TGTATCGATACAA
472409 ---A--GAT-CAA
1 TGTATCGATACAA
472416 TGTATCGATACAA
1 TGTATCGATACAA
472429 TGTATCG
1 TGTATCG
472436 CTACGAAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 3 0.09
8 3 0.09
10 2 0.06
12 3 0.09
13 22 0.67
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:472499 original size:13 final size:13
Alignment explanation
Indices: 472481--472506 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
472471 TTATTCAAAA
472481 TATCGATACATTG
1 TATCGATACATTG
472494 TATCGATACATTG
1 TATCGATACATTG
472507 ATCTTTGTAT
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):
TATCGATACATTG
Found at i:472516 original size:20 final size:20
Alignment explanation
Indices: 472491--472541 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
472481 TATCGATACA
472491 TTGTATCGATACATTGATCT
1 TTGTATCGATACATTGATCT
472511 TTGTATCGATACATTGATCT
1 TTGTATCGATACATTGATCT
472531 TTGTATCGATA
1 TTGTATCGATA
472542 TATCTAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTGATCT
Found at i:477212 original size:28 final size:27
Alignment explanation
Indices: 477179--477249 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
477169 ATAAAGCCAA
*
477179 GGTTGGAGTATCCCC-TCGAAAATAACGG
1 GGTTGGAGTATCCCCAT-G-AAATAACAG
*
477207 GGTTGGAGTATCCCCAATGAAATAATAG
1 GGTTGGAGTATCCCC-ATGAAATAACAG
477235 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
477250 GATTGTGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 37 0.95
29 1 0.03
30 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (27 bp):
GGTTGGAGTATCCCCATGAAATAACAG
Found at i:477221 original size:79 final size:79
Alignment explanation
Indices: 476897--477221 Score: 311
Period size: 79 Copynumber: 4.1 Consensus size: 79
476887 ACGGGGCTGA
* * * * * *
476897 AGTATCCCATGATTATGAAAAATTGGTGTTCTAGAAATAAAATCGAGGTTGGAGTATCCCCTC-A
1 AGTATCCC-CGATTATGAGAAATTGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGA
* *
476961 GAAATAACAAGGTTGG
65 -AAATAACGAGGTTAG
* * * ** *
476977 AGCATCCCTGATTAT-AGAAAATCGGCATTTT-GAGAATAAAATCGAGGTTGGAGTATCCCCTCG
1 AGTATCCCCGATTATGAG-AAATTGATATTTTAGA-AATAAAACCGAGGTTGGAGTATCCCCTCG
*
477040 AAAATAACG-GGATTAA
64 AAAATAACGAGG-TTAG
* ** * * *
477056 AGTATCCCCGATTATGAAAAATTGAT-TCTTTAG-AATAAGGCCGGGGTTGGAGTATCCTCGCGA
1 AGTATCCCCGATTATGAGAAATTGATAT-TTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGA
477119 AAATAACGAGGTTAG
65 AAATAACGAGGTTAG
* * * *
477134 AGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAAAGCCAAGGTTGGAGTATCCCCTCGAA
1 AGTATCCCCGATTATGAGAAATTGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAA
* *
477199 AATAACGGGGTTGG
66 AATAACGAGGTTAG
477213 AGTATCCCC
1 AGTATCCCC
477222 AATGAAATAA
Statistics
Matches: 203, Mismatches: 32, Indels: 21
0.79 0.12 0.08
Matches are distributed among these distances:
78 69 0.34
79 124 0.61
80 10 0.05
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (79 bp):
AGTATCCCCGATTATGAGAAATTGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAA
AATAACGAGGTTAG
Found at i:477313 original size:51 final size:51
Alignment explanation
Indices: 477240--477351 Score: 152
Period size: 51 Copynumber: 2.2 Consensus size: 51
477230 AATAGGGTTG
* * *
477240 GAGTATCCCCGATTGTGAAAAATTGGTGTTTCAAAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAAAATTAGTGTTTCAAAAATAAAACCGGAGTTA
* * * * *
477291 GAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTG
1 GAGTATCCCCGATTATGAAAAATTAGTGTTTCAAAAATAAAACCGGAGTTA
477342 GAGTATCCCC
1 GAGTATCCCC
477352 TTAGAAATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
GAGTATCCCCGATTATGAAAAATTAGTGTTTCAAAAATAAAACCGGAGTTA
Found at i:477429 original size:51 final size:51
Alignment explanation
Indices: 477370--477477 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
477360 AACGGGGTTA
* * * *
477370 GAGTATCCCCGATTATGAAAAATTGATA-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTACGAAAAATCGATACTTTAG-AAATAAAATCAGAGTTG
* * *
477421 GAGTATCCCCGATTGCGATAAATCGATGCTTTAGAAATAAAATCAGAGTTG
1 GAGTATCCCCGATTACGAAAAATCGATACTTTAGAAATAAAATCAGAGTTG
477472 GAGTAT
1 GAGTAT
477478 TGATGTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
51 45 0.92
52 4 0.08
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTACGAAAAATCGATACTTTAGAAATAAAATCAGAGTTG
Found at i:477454 original size:130 final size:130
Alignment explanation
Indices: 477204--477477 Score: 349
Period size: 130 Copynumber: 2.1 Consensus size: 130
477194 TCGAAAATAA
* * * * *
477204 CGGGGTTGGAGTATCCCCAATGAAATAATAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGT
1 CGGGGTTGGAGTATCCCCAATGAAATAACAGGGTTAGAGTATCCCCGATTATGAAAAATTGATAT
* *
477269 TTCAAAAATAAAATCGGAGTTAGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAAC
66 TTCAAAAATAAAATCGGAGTTAGAGTATCCCCGATTATGGAAAATGAGTGCTTTAGAAATAAAAC
* *
477334 CGGGGTTGGAGTATCCCC-TTAGAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATTGATA
1 CGGGGTTGGAGTATCCCCAAT-GAAATAACAGGGTTAGAGTATCCCCGATTATGAAAAATTGATA
** *
477398 TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGA-T-TGCGATAAATCGA-TGCTTTAGAAATA
65 TTTCAAAAATAAAATCGGAGTTAGAGTATCCCCGATTATG-GA-AAAT-GAGTGCTTTAGAAATA
*
477460 AAAT
127 AAAC
* *
477464 CAGAGTTGGAGTAT
1 CGGGGTTGGAGTAT
477478 TGATGTTTTA
Statistics
Matches: 125, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
128 2 0.02
129 4 0.03
130 118 0.94
131 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (130 bp):
CGGGGTTGGAGTATCCCCAATGAAATAACAGGGTTAGAGTATCCCCGATTATGAAAAATTGATAT
TTCAAAAATAAAATCGGAGTTAGAGTATCCCCGATTATGGAAAATGAGTGCTTTAGAAATAAAAC
Found at i:479820 original size:20 final size:19
Alignment explanation
Indices: 479795--479868 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
479785 AAAATGCCTG
*
479795 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
479815 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
479835 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
*
479855 AATGTATCAATACA
1 AATGTATCGATACA
479869 TCTGGGTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:480803 original size:20 final size:20
Alignment explanation
Indices: 480765--480803 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
480755 CTGGCAGCAC
* *
480765 TACAGTATAAGATTAGAAAT
1 TACAGTAAAAAATTAGAAAT
*
480785 TACAGTAAAAAATTTGAAA
1 TACAGTAAAAAATTAGAAA
480804 CGATTTTTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (20 bp):
TACAGTAAAAAATTAGAAAT
Found at i:481526 original size:51 final size:51
Alignment explanation
Indices: 481453--481570 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
481443 TTTTTTTAAG
* * * *
481453 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATTA
1 GGGATACTCAAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCA
* * * *
481504 GGGATACTCAAACTCCGATTTTATTTCCAAAACATCAATTTTTCACAATCA
1 GGGATACTCAAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCA
*
481555 CGGATACTTC-AACCCC
1 GGGATAC-TCAAACCCC
481571 ATTATTTTCG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 54 0.96
52 2 0.04
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.30
Consensus pattern (51 bp):
GGGATACTCAAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCA
Found at i:481647 original size:51 final size:51
Alignment explanation
Indices: 481582--481701 Score: 197
Period size: 51 Copynumber: 2.4 Consensus size: 51
481572 TTATTTTCGA
* *
481582 GGGGATACTCCAACCCCGGCTTTATTT-TCAAAATATTGATCTCTCATAATC
1 GGGGATACTTCAACCCCGGCTTTATTTCT-AAAATATTGATCTCTCACAATC
*
481633 GGGGATACTTCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATC
1 GGGGATACTTCAACCCCGGCTTTATTTCTAAAATATTGATCTCTCACAATC
481684 GGGGATACTTCAACCCCG
1 GGGGATACTTCAACCCCG
481702 TTATTTTCCA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
51 64 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (51 bp):
GGGGATACTTCAACCCCGGCTTTATTTCTAAAATATTGATCTCTCACAATC
Found at i:481690 original size:130 final size:129
Alignment explanation
Indices: 481523--481908 Score: 522
Period size: 130 Copynumber: 3.0 Consensus size: 129
481513 AAACTCCGAT
* * ** * **
481523 TTTATTTCCAAAACATCAATTTTTCACAATCACGGATACTTCAACCCCATTATTTTCGAGGGGAT
1 TTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTTCAACCCCATTATTTTC-AGGGGAT
481588 ACTCCAACCCCGGCTTTATTTTCAAAATATTGATCTCTCATAATCGGGGATACTTCAACCCCGGC
65 ACTCCAACCCCGGCTTTATTTTCAAAATATTGATCTCTCATAATCGGGGATACTTCAACCCCGGC
* *
481653 TTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTTCAACCCCGTTATTTTCCAGAGGAT
1 TTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTTCAACCCCATTATTTT-CAGGGGAT
* * *
481718 ACTCTAACCCCGGCTTTATTTCCAAAATATTGATCTCTCATAATTGGGGATACTTCAACCCCGGC
65 ACTCCAACCCCGGCTTTATTTTCAAAATATTGATCTCTCATAATCGGGGATACTTCAACCCCGGC
* * *
481783 CTTATTTCTAAAATATTGATTTCTCACGATCGGGGATACTCCAACCCCATTATTTTCATGGGGAT
1 TTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTTCAACCCCATTATTTTCA-GGGGAT
* * ** * * * *
481848 ACTCCAATCTCGATTTTATTTTCAAAACATCGAT-TTTCTATAATCGGGGATACTCCAACCC
65 ACTCCAACCCCGGCTTTATTTTCAAAATATTGATCTCTC-ATAATCGGGGATACTTCAACCC
481909 TGTTATTTTC
Statistics
Matches: 225, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
129 5 0.02
130 219 0.97
131 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (129 bp):
TTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTTCAACCCCATTATTTTCAGGGGATA
CTCCAACCCCGGCTTTATTTTCAAAATATTGATCTCTCATAATCGGGGATACTTCAACCCCGGC
Found at i:481718 original size:79 final size:79
Alignment explanation
Indices: 481635--481780 Score: 240
Period size: 79 Copynumber: 1.8 Consensus size: 79
481625 TCATAATCGG
* *
481635 GGATACT-TCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTTCAACC
1 GGATACTCT-AACCCCGGCTTTATTTCCAAAATATTGATCTCTCACAATCGGGGATACTTCAACC
481699 CCGTTATTTTCCAGA
65 CCGTTATTTTCCAGA
* *
481714 GGATACTCTAACCCCGGCTTTATTTCCAAAATATTGATCTCTCATAATTGGGGATACTTCAACCC
1 GGATACTCTAACCCCGGCTTTATTTCCAAAATATTGATCTCTCACAATCGGGGATACTTCAACCC
481779 CG
66 CG
481781 GCCTTATTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 61 0.98
80 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (79 bp):
GGATACTCTAACCCCGGCTTTATTTCCAAAATATTGATCTCTCACAATCGGGGATACTTCAACCC
CGTTATTTTCCAGA
Found at i:481790 original size:51 final size:51
Alignment explanation
Indices: 481714--481830 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
481704 ATTTTCCAGA
* * *
481714 GGATAC-TCTAACCCCGGCTTTATTTCCAAAATATTGATCTCTCATAATTGG
1 GGATACTTC-AACCCCGGCCTTATTTCCAAAATATTGATCTCTCACAATCGG
* * *
481765 GGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCACGATCGG
1 GGATACTTCAACCCCGGCCTTATTTCCAAAATATTGATCTCTCACAATCGG
*
481816 GGATACTCCAACCCC
1 GGATACTTCAACCCC
481831 ATTATTTTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 56 0.97
52 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (51 bp):
GGATACTTCAACCCCGGCCTTATTTCCAAAATATTGATCTCTCACAATCGG
Found at i:481845 original size:79 final size:79
Alignment explanation
Indices: 481762--481936 Score: 201
Period size: 79 Copynumber: 2.2 Consensus size: 79
481752 CTCTCATAAT
* * * * *
481762 TGGGGATACTTCAACCCCGGCCTTA-TTTCTAAAATATTGA-TTTCTCACGATCGGGGATACTCC
1 TGGGGATACTCCAACCCCGACCTTATTTTC-AAAACATCGATTTTCT-ACAATCGGGGATACTCC
481825 AACCCCATTATTTTCA
64 AACCCCATTATTTTCA
* * ** *
481841 TGGGGATACTCCAATCTCGATTTTATTTTCAAAACATCGATTTTCTATAATCGGGGATACTCCAA
1 TGGGGATACTCCAACCCCGACCTTATTTTCAAAACATCGATTTTCTACAATCGGGGATACTCCAA
**
481906 CCCTGTTATTTTCA
66 CCCCATTATTTTCA
*
481920 AGGGGATACTCCAACCC
1 TGGGGATACTCCAACCC
481937 TGATTTTTAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
79 70 0.89
80 9 0.11
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
TGGGGATACTCCAACCCCGACCTTATTTTCAAAACATCGATTTTCTACAATCGGGGATACTCCAA
CCCCATTATTTTCA
Found at i:481942 original size:79 final size:80
Alignment explanation
Indices: 481784--481981 Score: 233
Period size: 79 Copynumber: 2.5 Consensus size: 80
481774 AACCCCGGCC
* * * ** *
481784 TTATTTCTAAAATATTGATTTCTCACGATCGGGGATACTCCAACCCCATTATTTTCATGGGGATA
1 TTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACCCCATTATTTTCAAGGGGATA
*
481849 CTCCAATCTCGA-TT
66 CTCCAACCTCGATTT
**
481863 TTATTT-TCAAAACATCGA-TTTTCTATAATCGGGGATACTCCAACCCTGTTATTTTCAAGGGGA
1 TTATTTCT-AAAACATCGATTTTTC-ATAATCGGGGATACTCCAACCCCATTATTTTCAAGGGGA
481926 TACTCCAACC-CTGATTT
64 TACTCCAACCTC-GATTT
* * *
481943 TTATTTCTAGAACATCGATTTTTCATAATCAGGAATACT
1 TTATTTCTAAAACATCGATTTTTCATAATCGGGGATACT
481982 TCAGCCCCGT
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
78 6 0.06
79 59 0.58
80 30 0.30
81 6 0.06
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (80 bp):
TTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACCCCATTATTTTCAAGGGGATA
CTCCAACCTCGATTT
Found at i:488239 original size:61 final size:61
Alignment explanation
Indices: 488132--488894 Score: 930
Period size: 61 Copynumber: 12.5 Consensus size: 61
488122 CCCTTTTAGC
* * * *
488132 CCTT-TAGTCCTCAAAGAGTAGGACGTCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACGAGTTGGTGGCA
* * * *
488193 CCTTCTAATCCTCAAGGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACGAGTTAGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * * * * *
488254 CCTTTTAGTCCTCAAAGAGTAGGACGCTTTTTCTTTTTAAAACCCACACGAGTTAGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * * ** * *
488315 CCTTC-AGTCCTCAAAGAGTAGGACACTTTTTCCTTTTTAAAGCCCACATAAATTGATGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCC-TTTTAAAGCCCACACGAGTTGGTGGCA
* * *
488376 CCTTC-AGTCCTCAAAGAGCAGGACGTCTTTTCCTTTCAAAGCCCACACGAGTTTGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * * *
488436 CATTTTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* *
488497 CCTTC-AGTCCTCAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCC-TTTTAAAGCCCACACGAGTTGGTGGCA
** * *
488558 GATTC-AGTCCTCAAAAAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * * **
488618 CCTTTTAGTCCTCAAAGAGCAGGACGCATTCTCC-TCCAAAGCCCACACGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * * *
488678 CCCTCTAGTCCTCAAAGAGCTGGATGCCGTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCC-TTTTCC-TTTTAAAGCCCACACGAGTTGGTGGCA
* * * *
488741 CCTT-TAGTCCTTAAAGAGCAGGACACCTTCTCC-TTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * * * *
488800 CCCTCTAGTCCTCAAAGAGCAGGACGCATTTTTTCTTTTTAAGGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGC--CTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
488863 CCTTCTAGTCCTCAAAGAGCAGGACGCACTTT
1 CCTTCTAGTCCTCAAAGAGCAGGACGC-CTTT
488895 ATTTTCCTCT
Statistics
Matches: 602, Mismatches: 88, Indels: 23
0.84 0.12 0.03
Matches are distributed among these distances:
59 27 0.04
60 172 0.29
61 275 0.46
62 53 0.09
63 75 0.12
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (61 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
Found at i:488445 original size:182 final size:182
Alignment explanation
Indices: 488132--488887 Score: 1018
Period size: 182 Copynumber: 4.1 Consensus size: 182
488122 CCCTTTTAGC
* * * **
488132 CCTTTAGTCCTCAAAGAGTAGGACGTCTTTTT-CTTTTCAAAGCCCACATGAGTTGGTGGCACCT
1 CCTTCAGTCCTCAAAGAGTAGGAC-ACTTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCT
* * *
488196 TCTAATCCTCAAGGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACGAGTTAGTGGCACCTTTTA
65 TC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTA
* * *
488261 GTCCTCAAAGAGTAGGACGCTTTTTCTTTTTAAAACCCACACGAGTTAGTGGCA
129 GTCCTCAAAGAGCAGGACGCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA
* * *
488315 CCTTCAGTCCTCAAAGAGTAGGACACTTTTTCCTTTTTAAAGCCCACATAAATTGATGGCACCTT
1 CCTTCAGTCCTCAAAGAGTAGGACACTTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * *
488380 CAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTCAAAGCCCACACGAGTTTGTGGCACATTTTAGT
66 CAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGT
* *
488445 CCTCAAAGAGCAGGACACCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA
131 CCTCAAAGAGCAGGACGCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA
* * **
488497 CCTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCAGATT
1 CCTTCAGTCCTCAAAGAGTAGGACACTTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * *
488562 CAGTCCTCAAAAAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGT
66 CAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGT
* * * **
488627 CCTCAAAGAGCAGGACGCATTCTC-CTCCAAAGCCCACACGAGTTGGTGGCA
131 CCTCAAAGAGCAGGACGCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA
* *
488678 CCCTCTAGTCCTCAAAGAGCT-GGATGC-CGTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTC-AGTCCTCAAAGAG-TAGGA--CACTTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
488741 CCTTTAGTCCTTAAAGAGCAGGACACCTTCTCC-TTCAAAGCCCACACGAGTTGGTGGCACCCTC
62 CCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCTTT
* *
488805 TAGTCCTCAAAGAGCAGGACGCATTTTTTCTTTTTAAGGCCCACACAAGTTGGTGGCA
127 TAGTCCTCAAAGAGCAGGACGC--TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA
*
488863 CCTTCTAGTCCTCAAAGAGCAGGAC
1 CCTTC-AGTCCTCAAAGAGTAGGAC
488888 GCACTTTATT
Statistics
Matches: 506, Mismatches: 58, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
181 28 0.06
182 315 0.62
183 115 0.23
184 5 0.01
185 43 0.08
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (182 bp):
CCTTCAGTCCTCAAAGAGTAGGACACTTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT
CAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGT
CCTCAAAGAGCAGGACGCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA
Found at i:489023 original size:87 final size:85
Alignment explanation
Indices: 488870--489166 Score: 350
Period size: 87 Copynumber: 3.4 Consensus size: 85
488860 GCACCTTCTA
* * * *
488870 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTC-CCTCTTGTCCTCAAAGAGTAGGACACA
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCTCCTC-TGTCCTCAAAGAGCATGACGCA
*
488934 CTTCA-TTTCCTTATTTTCCTTTT
65 CTTTATTTTCC-T-TTTTCC-TTT
*
488957 GTCCTCAAAGAGTAGGACGCACTTTATTTTCCTTTTCTCCTCTGTCCTCAAAGAGCATGACGCAC
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCTCCTCTGTCCTCAAAGAGCATGACGCAC
*
489022 TTTATTTTCCTTTTCCCCTTT
66 TTTATTTTCCTTTT-TCCTTT
* * * * * * *
489043 GTCTTCAAAGAGTAGGACACACTTCA-TTTCCTTATTTTCCCTTTTAGTTCTCAAAGAGCATGAC
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTT-TTCT-CC-TCT-GTCCTCAAAGAGCATGAC
489107 GCACTTTATTTTCCTTTTTCCTTT
62 GCACTTTATTTTCCTTTTTCCTTT
489131 GTCCTCAAAGAGCAGGACGCA-TTTCATTTTCCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTT-ATTTTCCTTTT
489167 TTGCTTTATC
Statistics
Matches: 183, Mismatches: 18, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
85 7 0.04
86 32 0.17
87 65 0.36
88 37 0.20
89 42 0.23
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.40
Consensus pattern (85 bp):
GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCTCCTCTGTCCTCAAAGAGCATGACGCAC
TTTATTTTCCTTTTTCCTTT
Found at i:489182 original size:43 final size:43
Alignment explanation
Indices: 488870--489191 Score: 357
Period size: 43 Copynumber: 7.4 Consensus size: 43
488860 GCACCTTCTA
* *
488870 GTCCTCAAAGAGCAGGACGCACTTTATTTTCC-TCTTCCCTCTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTTTCCT-TT
* * *
488913 GTCCTCAAAGAGTAGGACACACTTCA-TTTCCTTATTTTCCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTT-TTTTCC-TTT
* * *
488957 GTCCTCAAAGAGTAGGACGCACTTTATTTTCCTTTTCTCCTCT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTTTCCTTT
* **
489000 GTCCTCAAAGAGCATGACGCACTTTATTTTCCTTTTCCCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTTTCCTTT
* * * *
489043 GTCTTCAAAGAGTAGGACACACTTCA-TTTCCTTATTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTT-TTTT-CC-TTT
* *
489088 AGTTCTCAAAGAGCATGACGCACTTTATTTTCC-TTTTTCCTTT
1 -GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTTTCCTTT
*
489131 GTCCTCAAAGAGCAGGACGCA-TTTCATTTTCCTTTTTTGCTTT
1 GTCCTCAAAGAGCAGGACGCACTTT-ATTTTCCTTTTTTCCTTT
* *
489174 ATCCTCAAAAAGCAGGAC
1 GTCCTCAAAGAGCAGGAC
489192 ATACTCTTTT
Statistics
Matches: 237, Mismatches: 31, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
41 3 0.01
42 38 0.16
43 116 0.49
44 39 0.16
45 15 0.06
46 21 0.09
47 5 0.02
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTTTCCTTT
Found at i:489863 original size:13 final size:13
Alignment explanation
Indices: 489847--489876 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
489837 ATACATTGTT
489847 CATTATATCGATA
1 CATTATATCGATA
*
489860 CATTGTATCGATA
1 CATTATATCGATA
489873 CATT
1 CATT
489877 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:489917 original size:20 final size:19
Alignment explanation
Indices: 489892--489965 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 19
489882 TTTACCCAAA
489892 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
489912 TGTATCGATACATTTCTCAT
1 TGTATCGATACATTT-TCAT
*
489932 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
489952 TGTATCGATACATT
1 TGTATCGATACATT
489966 CAGGCATTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 1 0.02
20 49 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:492402 original size:28 final size:29
Alignment explanation
Indices: 492362--492439 Score: 106
Period size: 28 Copynumber: 2.7 Consensus size: 29
492352 ATTTTTCACA
492362 ATCGAGGGATACTCCAACCCCGTTA-TTTC
1 ATCGA-GGATACTCCAACCCCGTTATTTTC
*
492391 ATCGAGGATACTCCAACCCCATTATTTTC
1 ATCGAGGATACTCCAACCCCGTTATTTTC
* *
492420 A-AGGGGATACTCCAACCCCG
1 ATCGAGGATACTCCAACCCCG
492440 GCTTTATTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 34 0.77
29 10 0.23
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (29 bp):
ATCGAGGATACTCCAACCCCGTTATTTTC
Found at i:492506 original size:51 final size:51
Alignment explanation
Indices: 492425--492540 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
492415 TTTTCAAGGG
**
492425 GATACTCCAACCCCGGCTTTATTTCCAAAATATTGATCTCTCACAATCGGA
1 GATACTCCAACCCCGGCCATATTTCCAAAATATTGATCTCTCACAATCGGA
* * *
492476 GATACTTCAACCCCGGCCATATTTCTAAAATATTGATTTCTCACAATCGGA
1 GATACTCCAACCCCGGCCATATTTCCAAAATATTGATCTCTCACAATCGGA
492527 GATACTCCAACCCC
1 GATACTCCAACCCC
492541 ATTATTTTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.28
Consensus pattern (51 bp):
GATACTCCAACCCCGGCCATATTTCCAAAATATTGATCTCTCACAATCGGA
Found at i:492610 original size:79 final size:79
Alignment explanation
Indices: 492495--492699 Score: 195
Period size: 79 Copynumber: 2.6 Consensus size: 79
492485 ACCCCGGCCA
* ** * *
492495 TATTTCTAAAATATTGATTTCTCACAATCGGAGATACTCCAACCCCATTA-TTTTCATGGGAATA
1 TATTTCTAAAACACCGATTTTTCATAATCGG-GATACTCCAACCCCATTATTTTTCA-GGGAATA
*
492559 CTCCAA-TCTCGA-TTT
64 CTCCAACCCT-GATTTT
* ** * *
492574 TATTT-TCAAAACATCGA-TTTTCTATAATCAGGGATACTCCAACCCTGTTATTTTTGAGGGGAT
1 TATTTCT-AAAACACCGATTTTTC-ATAATC-GGGATACTCCAACCCCATTATTTTTCAGGGAAT
492637 ACTCCAACCCTGATTTT
63 ACTCCAACCCTGATTTT
* *
492654 TATTTCTAGAACACCGATTTTTCATAATCGGGAATACTCCAGCCCC
1 TATTTCTAAAACACCGATTTTTCATAATCGGG-ATACTCCAACCCC
492700 GTTGTTATCT
Statistics
Matches: 104, Mismatches: 13, Indels: 17
0.78 0.10 0.13
Matches are distributed among these distances:
78 5 0.05
79 51 0.49
80 42 0.40
81 6 0.06
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (79 bp):
TATTTCTAAAACACCGATTTTTCATAATCGGGATACTCCAACCCCATTATTTTTCAGGGAATACT
CCAACCCTGATTTT
Found at i:494381 original size:4 final size:4
Alignment explanation
Indices: 494372--494406 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
494362 AAAATAAAAC
*
494372 TAAA TAAA TAAA CAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
494407 GCACCTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:494390 original size:12 final size:12
Alignment explanation
Indices: 494363--494406 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
494353 TGACTGTACA
494363 AAATAAAACTAAAT
1 AAAT-AAAC-AAAT
494377 AAATAAACAAAT
1 AAATAAACAAAT
*
494389 AAATAAATAAAT
1 AAATAAACAAAT
494401 AAATAA
1 AAATAA
494407 GCACCTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 21 0.72
13 4 0.14
14 4 0.14
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (12 bp):
AAATAAACAAAT
Found at i:496572 original size:28 final size:28
Alignment explanation
Indices: 496541--496611 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
496531 AAATAAAATC
*
496541 GGGGTTGGAGCATCCTTTAAAAAACAAT
1 GGGGTTGGAGCATCCTCTAAAAAACAAT
* *
496569 GGGGTTGGA-CTATCCTCTCAAAAATAAT
1 GGGGTTGGAGC-ATCCTCTAAAAAACAAT
*
496597 GGGGTTGGAGTATCC
1 GGGGTTGGAGCATCC
496612 CCAATGGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (28 bp):
GGGGTTGGAGCATCCTCTAAAAAACAAT
Found at i:496689 original size:106 final size:106
Alignment explanation
Indices: 496466--496690 Score: 252
Period size: 106 Copynumber: 2.1 Consensus size: 106
496456 TAAAAACATG
* * *
496466 GTTAGAGTATCCCCTCAAAAATAACGAGGTTGGAGTCTCTCCAATAGTGAAAATTGATATTTTAG
1 GTTAGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCAATAGTGAAAATCGATATTTTAG
* * * * *
496531 AAATAAAATCGGGGTTGGAGCATCCTTTAAAAAACAATGGG
66 AAATAAAATCAGAGTTGGAGCATCCCTTAAAAAACAACGGA
* * * * * * * *
496572 GTTGGACTATCCTCTCAAAAATAATGGGGTTGGAGTATCCCCAATGGTGAAAATCGGTGTTTTAG
1 GTTAGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCAATAGTGAAAATCGATATTTTAG
* * *** *
496637 AAATAAAATTAGAGTTGGAGTATCCCTTCGGAAATAACGGA
66 AAATAAAATCAGAGTTGGAGCATCCCTTAAAAAACAACGGA
496678 GTTAGAGTATCCC
1 GTTAGAGTATCCC
496691 TGATAGTGGA
Statistics
Matches: 94, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (106 bp):
GTTAGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCAATAGTGAAAATCGATATTTTAG
AAATAAAATCAGAGTTGGAGCATCCCTTAAAAAACAACGGA
Found at i:496897 original size:80 final size:79
Alignment explanation
Indices: 496579--497439 Score: 632
Period size: 80 Copynumber: 10.9 Consensus size: 79
496569 GGGGTTGGAC
** * * * * * * *
496579 TATCCTCTCAAAAATAATGGGGTTGGAGTATCCCCAATGGT-G-AAAATCGGTGTTTTAGAAATA
1 TATCC-CTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGATGCTTTAGAGATA
* *
496642 AAA-TTAGAGTTGGAG
65 AAACTGAG-GTTAGAG
** * * *
496657 TATCCCTTCGGAAATAAC-GGAGTTAGAGTATCC-CTGATAGTGG-AAAATCGATGTTTTAGAAA
1 TATCCC-TCAAAAATAACAGGA-TTAGAGTATCCTC-GATGGTGGAAAAATCGATGCTTTAGAGA
*
496719 TAAAA-TAGAGGTTGGAG
63 TAAAACT-GAGGTTAGAG
* * * * * * *
496736 TATCCCCTCGAAAATAATAAGATTTGAGTATCCCCGATGGT-GAAAAAT-TAGTGTTTTAGAGAT
1 TAT-CCCTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGA-TGCTTTAGAGAT
* *
496799 AAAACAGGGGTT-GTAG
64 AAAACTGAGGTTAG-AG
*
496815 TATCTTCTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGATGCTTTAGAGATA
1 TATC-CCTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGATGCTTTAGAGATA
496880 AAACTGAGGTTAGAG
65 AAACTGAGGTTAGAG
* * * * *
496895 TATTCCCTTAAAAATAACGAGG-TTGGAGTATCCCCTATGGTGAAAAAATCGATGCTTTAGAGAT
1 TA-TCCCTCAAAAATAAC-AGGATTAGAGTATCCTCGATGGTGGAAAAATCGATGCTTTAGAGAT
496959 AAAACTG-GGTTAGAG
64 AAAACTGAGGTTAGAG
* * *
496974 TATCCCTTCAAAAATAACAGAATTAGAGT-TTCTCCGATGGT-GAAAAATCGGTGCTTTAGAGAT
1 TATCCC-TCAAAAATAACAGGATTAGAGTATCCT-CGATGGTGGAAAAATCGATGCTTTAGAGAT
* *
497037 AAAA-TCGGGGTTGGAG
64 AAAACT-GAGGTTAGAG
* * * * * *
497053 TATCCCTTCGAAAATAATAGGGTTGGAGTATCC-CAGATGGTGAAAAAATCAATGCTTTAGAGAT
1 TATCCC-TCAAAAATAACAGGATTAGAGTATCCTC-GATGGTGGAAAAATCGATGCTTTAGAGAT
* *
497117 AAAACCGAGGTTGGAG
64 AAAACTGAGGTTAGAG
* * ** * * *
497133 TATCTCTTCAAAAATAAC-GAGATTTGAGTATCCTCTTTGGTGAAAAAATTGGTGCTTTAGAGAT
1 TATC-CCTCAAAAATAACAG-GATTAGAGTATCCTCGATGGTGGAAAAATCGATGCTTTAGAGAT
* *
497197 AAAACAGGGGTTAGAG
64 AAAACTGAGGTTAGAG
* * * * * * * *
497213 TATGCCCTCAGAAATAACGGGGTTGGGGTATCCTCGATGGTAGAAAAATCAATGTTTTAGAGATA
1 TAT-CCCTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGATGCTTTAGAGATA
*
497278 AAA-TCAGGGTTAGAG
65 AAACTGA-GGTTAGAG
* * * * *
497293 TATCCTCTCAAAAATAATAGGGTTAGAGTATCCTTGATGGTGG-AAAATC-AGTGTTTTAGAAAT
1 TATCC-CTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGA-TGCTTTAGAGAT
* *
497356 AAAACTGTGGTCAGAG
64 AAAACTGAGGTTAGAG
* * * * * * * * *
497372 TATCCCCTCGAAAATAACGGGGTTGGAGAATCCCCAATGGT-GAAAAAT-GAGTGCTTTAAAAAT
1 TAT-CCCTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGA-TGCTTTAGAGAT
497435 AAAAC
64 AAAAC
497440 ATTAATGAAA
Statistics
Matches: 640, Mismatches: 104, Indels: 77
0.78 0.13 0.09
Matches are distributed among these distances:
77 5 0.01
78 67 0.10
79 271 0.42
80 286 0.45
81 11 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
TATCCCTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGATGCTTTAGAGATAA
AACTGAGGTTAGAG
Found at i:496990 original size:238 final size:235
Alignment explanation
Indices: 496569--497439 Score: 868
Period size: 238 Copynumber: 3.7 Consensus size: 235
496559 AAAAAACAAT
* * * * * * *
496569 GGGGTTGGACTATCCTCTCAAAAATAATGGGGTTGGAGTATCCCCAATGGT-GAAAATCGGTGTT
1 GGGGTTGGAGTATCCTCTCAAAAATAATAGGGTTAGAGTATCCTCGATGGTGGAAAATCGATGCT
* * ** *
496633 TTAGAAATAAAA-TTAGAGTTGGAGTATCCCTTCGGAAATAACG-GAGTTAGAGTAT-CCCTGAT
66 TTAGAAATAAAACTGAG-GTTAGAGTATCCCTTCAAAAATAACGAG-GTTGGAGTATCCCCT-AT
* * * * *
496695 AGTGGAAAATCGATGTTTTAGAAATAAAA-TAGAGGTTGGAGTATCCCCTCGAAAATAATAAGAT
128 GGTGAAAAATCGATGCTTTAGAAATAAAACT-G-GGTTAGAGTAT-CCCTCAAAAATAA-AAGAT
* *
496759 TTGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAGATAAAA-CA
189 TAGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAGATAAAATCA
* * * *
496805 GGGGTTGTAGTATCTTCTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGATGC
1 GGGGTTGGAGTATCCTCTCAAAAATAATAGGGTTAGAGTATCCTCGATGGTGG-AAAATCGATGC
*
496870 TTTAGAGATAAAACTGAGGTTAGAGTATTCCCTT-AAAAATAACGAGGTTGGAGTATCCCCTATG
65 TTTAGAAATAAAACTGAGGTTAGAGTA-TCCCTTCAAAAATAACGAGGTTGGAGTATCCCCTATG
* *
496934 GTGAAAAAATCGATGCTTTAGAGATAAAACTGGGTTAGAGTATCCCTTCAAAAATAACAGAATTA
129 GTG-AAAAATCGATGCTTTAGAAATAAAACTGGGTTAGAGTATCCC-TCAAAAATAAAAG-ATTA
* * * *
496999 GAGTTTCTCCGATGGTGAAAAATCGGTGCTTTAGAGATAAAATC-
191 GAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAGATAAAATCA
* * * *
497043 GGGGTTGGAGTATCC-CTTCGAAAATAATAGGGTTGGAGTATCC-CAGATGGTGAAAAAATCAAT
1 GGGGTTGGAGTATCCTC-TCAAAAATAATAGGGTTAGAGTATCCTC-GATGGTG-GAAAATCGAT
* * * * * * * *
497106 GCTTTAGAGATAAAACCGAGGTTGGAGTATCTCTTCAAAAATAACGAGATTTGAGTATCCTCTTT
63 GCTTTAGAAATAAAACTGAGGTTAGAGTATCCCTTCAAAAATAACGAGGTTGGAGTATCCCCTAT
* * * * * ** *
497171 GGTGAAAAAATTGGTGCTTTAGAGATAAAACAGGGGTTAGAGTATGCCCTCAGAAATAACGGGGT
128 GGTG-AAAAATCGATGCTTTAGAAATAAAAC-TGGGTTAGAGTAT-CCCTCAAAAATAA-AAGAT
* * * *
497236 TGGGGTATCCTCGATGGTAGAAAAATCAATGTTTTAGAGATAAAATCA
189 TAGAGTATCCCCGATGGT-GAAAAATCAGTGTTTTAGAGATAAAATCA
* * *
497284 -GGGTTAGAGTATCCTCTCAAAAATAATAGGGTTAGAGTATCCTTGATGGTGGAAAATC-AGTGT
1 GGGGTTGGAGTATCCTCTCAAAAATAATAGGGTTAGAGTATCCTCGATGGTGGAAAATCGA-TGC
* * * * * * *
497347 TTTAGAAATAAAACTGTGGTCAGAGTATCCCCTCGAAAATAACGGGGTTGGAGAATCCCCAATGG
65 TTTAGAAATAAAACTGAGGTTAGAGTATCCCTTCAAAAATAACGAGGTTGGAGTATCCCCTATGG
*
497412 TGAAAAAT-GAGTGCTTTAAAAATAAAAC
130 TGAAAAATCGA-TGCTTTAGAAATAAAAC
497440 ATTAATGAAA
Statistics
Matches: 527, Mismatches: 84, Indels: 46
0.80 0.13 0.07
Matches are distributed among these distances:
236 42 0.08
237 14 0.03
238 263 0.50
239 133 0.25
240 74 0.14
241 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (235 bp):
GGGGTTGGAGTATCCTCTCAAAAATAATAGGGTTAGAGTATCCTCGATGGTGGAAAATCGATGCT
TTAGAAATAAAACTGAGGTTAGAGTATCCCTTCAAAAATAACGAGGTTGGAGTATCCCCTATGGT
GAAAAATCGATGCTTTAGAAATAAAACTGGGTTAGAGTATCCCTCAAAAATAAAAGATTAGAGTA
TCCCCGATGGTGAAAAATCAGTGTTTTAGAGATAAAATCA
Found at i:497439 original size:79 final size:79
Alignment explanation
Indices: 496579--497439 Score: 668
Period size: 79 Copynumber: 10.9 Consensus size: 79
496569 GGGGTTGGAC
* * * * *
496579 TATCCTCTCAAAAATAATGGGGTTGGAGTATCCCCAATGGTG-AAAATCG-GTGTTTTAGAAATA
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAAT-GAGTGCTTTAGAGATA
* *
496642 AAA-TTAGAGTTGGAG
65 AAACTGAG-GTTAGAG
* ** * * * * * * *
496657 TATCCCTTCGGAAATAACGGAGTTAGAGTATCCCTGATAGTGGAAAATCGA-TGTTTTAGAAATA
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAAT-GAGTGCTTTAGAGATA
*
496721 AAA-TAGAGGTTGGAG
65 AAACT-GAGGTTAGAG
* *** * * * *
496736 TATCCCCTCGAAAATAATAAGATTTGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAGATAA
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATGAGTGCTTTAGAGATAA
* *
496801 AACAGGGGTT-GTAG
66 AACTGAGGTTAG-AG
** * * * *
496815 TATCTTCTCAAAAATAACAGGATTAGAGTATCCTCGATGGTGGAAAAATCGA-TGCTTTAGAGAT
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGT-GAAAAAT-GAGTGCTTTAGAGAT
496879 AAAACTGAGGTTAGAG
64 AAAACTGAGGTTAGAG
* * * *
496895 TATTCCCTTAAAAATAACGAGGTTGGAGTATCCCCTATGGTGAAAAAATCGA-TGCTTTAGAGAT
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTG-AAAAAT-GAGTGCTTTAGAGAT
496959 AAAACTG-GGTTAGAG
64 AAAACTGAGGTTAGAG
* * ** * * *
496974 TATCCCTTCAAAAATAACAGAATTAGAGTTTCTCCGATGGTGAAAAATCG-GTGCTTTAGAGATA
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAAT-GAGTGCTTTAGAGATA
* *
497038 AAA-TCGGGGTTGGAG
65 AAACT-GAGGTTAGAG
* * ** * * *
497053 TATCCCTTCGAAAATAATAGGGTTGGAGTATCCCAGATGGTGAAAAAATCAATGCTTTAGAGATA
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTG-AAAAATGAGTGCTTTAGAGATA
* *
497118 AAACCGAGGTTGGAG
65 AAACTGAGGTTAGAG
* * * * * * **
497133 TATCTCTTCAAAAATAACGAGATTTGAGTATCCTCTTTGGTGAAAAAATTG-GTGCTTTAGAGAT
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTG-AAAAA-TGAGTGCTTTAGAGAT
* *
497197 AAAACAGGGGTTAGAG
64 AAAACTGAGGTTAGAG
* * * * * * *
497213 TATGCCCTCAGAAATAACGGGGTTGGGGTATCCTCGATGGTAGAAAAATCAATGTTTTAGAGATA
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGT-GAAAAATGAGTGCTTTAGAGATA
*
497278 AAA-TCAGGGTTAGAG
65 AAACTGA-GGTTAGAG
* ** * ** * * * *
497293 TATCCTCTCAAAAATAATAGGGTTAGAGTATCCTTGATGGTGGAAAATCAGTGTTTTAGAAATAA
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATGAGTGCTTTAGAGATAA
* *
497358 AACTGTGGTCAGAG
66 AACTGAGGTTAGAG
* * * * *
497372 TATCCCCTCGAAAATAACGGGGTTGGAGAATCCCCAATGGTGAAAAATGAGTGCTTTAAAAATAA
1 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATGAGTGCTTTAGAGATAA
497437 AAC
66 AAC
497440 ATTAATGAAA
Statistics
Matches: 632, Mismatches: 130, Indels: 41
0.79 0.16 0.05
Matches are distributed among these distances:
77 1 0.00
78 59 0.09
79 291 0.46
80 277 0.44
81 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
TATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATGAGTGCTTTAGAGATAA
AACTGAGGTTAGAG
Found at i:497901 original size:9 final size:9
Alignment explanation
Indices: 497889--497924 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
497879 GAAAAAATAT
497889 TCAAAAAAA
1 TCAAAAAAA
497898 TCAAAAAATA
1 TCAAAAAA-A
*
497908 TCAAAAATA
1 TCAAAAAAA
497917 TCAAAAAA
1 TCAAAAAA
497925 GACATTGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (9 bp):
TCAAAAAAA
Found at i:497911 original size:19 final size:20
Alignment explanation
Indices: 497880--497924 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
497870 AACTTCTTTG
497880 AAAAAATATTCAAAAAAATC
1 AAAAAATATTCAAAAAAATC
*
497900 AAAAAATA-TCAAAAATATC
1 AAAAAATATTCAAAAAAATC
497919 AAAAAA
1 AAAAAA
497925 GACATTGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAATATTCAAAAAAATC
Found at i:501330 original size:10 final size:10
Alignment explanation
Indices: 501297--501361 Score: 51
Period size: 10 Copynumber: 6.1 Consensus size: 10
501287 CTCCTTATAT
501297 TATAATATTA
1 TATAATATTA
*
501307 TATTATA-TA
1 TATAATATTA
* *
501316 AATAATTTTA
1 TATAATATTA
501326 TATAATATTA
1 TATAATATTA
501336 TAATTAAATATTTA
1 T-A-T-AATA-TTA
501350 TATAAATATTA
1 TAT-AATATTA
501361 T
1 T
501362 GTATTCTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 6 0.14
10 17 0.39
11 5 0.11
12 7 0.16
13 5 0.11
14 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TATAATATTA
Found at i:501333 original size:24 final size:24
Alignment explanation
Indices: 501297--501361 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 24
501287 CTCCTTATAT
501297 TATAATATTATATTATATAAATAATTTTA
1 TATAATATTATA--AT-TAAAT-A-TTTA
501326 TATAATATTATAATTAAATATTTA
1 TATAATATTATAATTAAATATTTA
501350 TATAAATATTAT
1 TAT-AATATTAT
501362 GTATTCTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.20
25 9 0.26
26 5 0.14
27 2 0.06
29 12 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATAATATTATAATTAAATATTTA
Found at i:501357 original size:12 final size:12
Alignment explanation
Indices: 501309--501359 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
501299 TAATATTATA
501309 TTATATAAATAAT
1 TTATATAAAT-AT
501322 TT-TATATAATA-
1 TTATATA-AATAT
501333 TTATAATTAAATAT
1 TTAT-A-TAAATAT
501347 TTATATAAATAT
1 TTATATAAATAT
501359 T
1 T
501360 ATGTATTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.06
12 14 0.42
13 11 0.33
14 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTATATAAATAT
Found at i:501440 original size:25 final size:26
Alignment explanation
Indices: 501390--501441 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
501380 ATCATATGAC
* * *
501390 TATTGATATTATAATATATGATATAT
1 TATTGATATTATAATAAATAAAATAT
501416 TATT-ATATTATAATAAATAAAATAT
1 TATTGATATTATAATAAATAAAATAT
501441 T
1 T
501442 TAGTAATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
TATTGATATTATAATAAATAAAATAT
Found at i:501657 original size:33 final size:32
Alignment explanation
Indices: 501614--501685 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
501604 AAATAGCTCG
*
501614 AACTCGAAAGAATCCCAACCCGAA-AGAACCCAA
1 AACTCAAAAGAATCCCAACCC-AAGAGAACCC-A
* * *
501647 AACTCAAAAGAATTCGAACCCAAGAGAACTCA
1 AACTCAAAAGAATCCCAACCCAAGAGAACCCA
501679 AACTCAA
1 AACTCAA
501686 GATTGACCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 10 0.29
33 24 0.71
ACGTcount: A:0.50, C:0.29, G:0.11, T:0.10
Consensus pattern (32 bp):
AACTCAAAAGAATCCCAACCCAAGAGAACCCA
Found at i:501912 original size:22 final size:22
Alignment explanation
Indices: 501882--501925 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
501872 AAATAATAAT
* *
501882 TTATCAAAAAGTAACTTATATC
1 TTATAAAAAAGTAAATTATATC
501904 TTATAAAAAAGTAAATTATATC
1 TTATAAAAAAGTAAATTATATC
501926 ATGAGCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (22 bp):
TTATAAAAAAGTAAATTATATC
Found at i:502849 original size:31 final size:32
Alignment explanation
Indices: 502814--502892 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 32
502804 ATTTATAAAT
*
502814 AAATATAGATTTTAAT-A-AATAAATATA-TTAA
1 AAATA-AGATTTTAATAACAAAAAAT-TACTTAA
*
502845 AAATAACATTTT-ATAACAAAAAATTACTTAA
1 AAATAAGATTTTAATAACAAAAAATTACTTAA
*
502876 AAATAAGAATTTAATAA
1 AAATAAGATTTTAATAA
502893 TTTACCTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 2 0.05
30 9 0.22
31 25 0.62
32 4 0.10
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (32 bp):
AAATAAGATTTTAATAACAAAAAATTACTTAA
Found at i:503022 original size:16 final size:16
Alignment explanation
Indices: 502989--503059 Score: 81
Period size: 16 Copynumber: 4.5 Consensus size: 16
502979 CTTGAACTCG
*
502989 AACCTGAAAA-GTCCA
1 AACCTGAAAAGGCCCA
*
503004 AACTTGAAAAGGCCCA
1 AACCTGAAAAGGCCCA
* *
503020 AACCCGAAAAGGCTCA
1 AACCTGAAAAGGCCCA
* *
503036 AACCTGAAGAGGCTCA
1 AACCTGAAAAGGCCCA
503052 AACCTGAA
1 AACCTGAA
503060 TAGACTCGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 9 0.19
16 39 0.81
ACGTcount: A:0.44, C:0.27, G:0.18, T:0.11
Consensus pattern (16 bp):
AACCTGAAAAGGCCCA
Found at i:503054 original size:32 final size:32
Alignment explanation
Indices: 502989--503077 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
502979 CTTGAACTCG
* *
502989 AACCTGAAAAGTC-CAAACTTGAAAAGGCCCA
1 AACCTGAAAAGACTCAAACCTGAAAAGGCCCA
* * * *
503020 AACCCGAAAAGGCTCAAACCTGAAGAGGCTCA
1 AACCTGAAAAGACTCAAACCTGAAAAGGCCCA
* *
503052 AACCTGAATAGACTCGAACCTGAAAA
1 AACCTGAAAAGACTCAAACCTGAAAA
503078 AGACCAAGCC
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 11 0.23
32 36 0.77
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.12
Consensus pattern (32 bp):
AACCTGAAAAGACTCAAACCTGAAAAGGCCCA
Found at i:503071 original size:16 final size:16
Alignment explanation
Indices: 503018--503075 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
503008 TGAAAAGGCC
* * *
503018 CAAACCCGAAAAGGCT
1 CAAACCTGAAGAGACT
*
503034 CAAACCTGAAGAGGCT
1 CAAACCTGAAGAGACT
*
503050 CAAACCTGAATAGACT
1 CAAACCTGAAGAGACT
*
503066 CGAACCTGAA
1 CAAACCTGAA
503076 AAAGACCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.41, C:0.28, G:0.19, T:0.12
Consensus pattern (16 bp):
CAAACCTGAAGAGACT
Found at i:503235 original size:20 final size:20
Alignment explanation
Indices: 503212--503288 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 20
503202 TTGTTACAAT
503212 TATATATATATATATATATA
1 TATATATATATATATATATA
*
503232 TATATATAT-TATACA-AT-
1 TATATATATATATATATATA
*
503249 TA-ATAGATATAT-TATATCA
1 TATATATATATATATATAT-A
*
503268 TATTTA-ATA-ATAT-TATA
1 TATATATATATATATATATA
503285 TATA
1 TATA
503289 CCATAAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
16 6 0.13
17 11 0.24
18 7 0.15
19 11 0.24
20 11 0.24
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (20 bp):
TATATATATATATATATATA
Found at i:503300 original size:2 final size:2
Alignment explanation
Indices: 503212--503288 Score: 62
Period size: 2 Copynumber: 42.0 Consensus size: 2
503202 TTGTTACAAT
*
503212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
503251 -A TA GA TA TA T- TA TA TCA TA TT TA -A TA -A TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
503289 CCATAAATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
1 8 0.13
2 51 0.84
3 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:503717 original size:36 final size:34
Alignment explanation
Indices: 503677--503830 Score: 118
Period size: 34 Copynumber: 4.4 Consensus size: 34
503667 TACCTTTGAG
*
503677 GCTAAGATATAACCTAACAACCCTATCTTTTCACAA
1 GCTAAGATA-AACCT-ACTACCCTATCTTTTCACAA
* * * *
503713 GCTAAGATAAAACCT-TTTCCCTATCTTTTCATAG
1 GCTAAGAT-AAACCTACTACCCTATCTTTTCACAA
* * *
503747 GCTAAGATAAAAC-ATCTCCCCTATTTTTTCACAA
1 GCTAAGATAAACCTA-CTACCCTATCTTTTCACAA
* *
503781 GCTAAGATAGAACCT-CTTCCTTATCTTTTTCA-AA
1 GCTAAGATA-AACCTACTACCCTATC-TTTTCACAA
503815 GGCTAAGATAGAACCT
1 -GCTAAGATA-AACCT
503831 CTCAATCACT
Statistics
Matches: 96, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
33 4 0.04
34 54 0.56
35 24 0.25
36 13 0.14
37 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (34 bp):
GCTAAGATAAACCTACTACCCTATCTTTTCACAA
Found at i:503786 original size:68 final size:69
Alignment explanation
Indices: 503697--503833 Score: 204
Period size: 68 Copynumber: 2.0 Consensus size: 69
503687 AACCTAACAA
* *
503697 CCCTATCTTTTCACAAGCTAAGATAAAACCTTTTCCCTATC-TTTTCATAGGCTAAGATAAAACA
1 CCCTATCTTTTCACAAGCTAAGATAAAACCTCTTCCCTATCTTTTTCAAAGGCTAAGATAAAACA
503761 TCTC
66 TCTC
* * * * *
503765 CCCTATTTTTTCACAAGCTAAGATAGAACCTCTTCCTTATCTTTTTCAAAGGCTAAGATAGAACC
1 CCCTATCTTTTCACAAGCTAAGATAAAACCTCTTCCCTATCTTTTTCAAAGGCTAAGATAAAACA
503830 TCTC
66 TCTC
503834 AATCACTTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
68 37 0.61
69 24 0.39
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (69 bp):
CCCTATCTTTTCACAAGCTAAGATAAAACCTCTTCCCTATCTTTTTCAAAGGCTAAGATAAAACA
TCTC
Found at i:503820 original size:35 final size:34
Alignment explanation
Indices: 503697--503832 Score: 166
Period size: 34 Copynumber: 4.0 Consensus size: 34
503687 AACCTAACAA
*
503697 CCCTATCTTTTCACAAGCTAAGATAAAACCTTTT
1 CCCTATCTTTTCACAAGCTAAGATAAAACCTCTT
* * * *
503731 CCCTATCTTTTCATAGGCTAAGATAAAACATCTC
1 CCCTATCTTTTCACAAGCTAAGATAAAACCTCTT
* *
503765 CCCTATTTTTTCACAAGCTAAGATAGAACCTCTT
1 CCCTATCTTTTCACAAGCTAAGATAAAACCTCTT
* *
503799 CCTTATCTTTTTCA-AAGGCTAAGATAGAACCTCT
1 CCCTATC-TTTTCACAA-GCTAAGATAAAACCTCT
503833 CAATCACTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
34 64 0.74
35 23 0.26
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.35
Consensus pattern (34 bp):
CCCTATCTTTTCACAAGCTAAGATAAAACCTCTT
Found at i:504308 original size:21 final size:20
Alignment explanation
Indices: 504260--504318 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
504250 CCATTGGGCC
*
504260 AAATGTATCGATACAATTTA
1 AAATGTATCGATACAATCTA
*
504280 TAATGTATCGATACAATCTA
1 AAATGTATCGATACAATCTA
504300 AACATGTATCGATACAATC
1 AA-ATGTATCGATACAATC
504319 GAAGGTTAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATGTATCGATACAATCTA
Found at i:505425 original size:32 final size:31
Alignment explanation
Indices: 505363--505425 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
505353 TTTTATGGTC
*
505363 TATCGATACAAAGAACATGTATCAATATAATG
1 TATCGATACAAAGAACATGTA-CAAAATAATG
*
505395 TATCGATACAAAGCAATATGTA-AACAATAAT
1 TATCGATACAAAG-AACATGTACAA-AATAAT
505426 CTGGGTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 2 0.07
32 18 0.67
33 7 0.26
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (31 bp):
TATCGATACAAAGAACATGTACAAAATAATG
Found at i:509395 original size:474 final size:474
Alignment explanation
Indices: 508505--509451 Score: 1671
Period size: 474 Copynumber: 2.0 Consensus size: 474
508495 ATCTCCCTTT
*
508505 TGGACATGATTTCTACATATTCAAGTCCTAGAGTATTGTATGAGATTTTTGGTAAGACAAATGGC
1 TGGACATGATTTCTACATATTCAAGTCCTAGAGTATTGTATGAGATTTTTAGTAAGACAAATGGC
*
508570 ACTAGTATTGTCAATTTAATGGGAATTTGATCCATGGTAATACCAAAATATTCCATTTGTTGTTT
66 ACTAGTATTGTCAATTTAATGGGAATATGATCCATGGTAATACCAAAATATTCCATTTGTTGTTT
*
508635 TATCCATAAAACTTAGGCACAACAACTTCCTGCAGATATGAATTTCGCTTCGGTTGTGGATAAGG
131 TATCCATAAAACTTAGGCACAACAACTTCCTGCAGATATGAATTTCGCTTCGGTTATGGATAAGG
508700 CAACACTATTTTGTTTCTTAGAAAACCATGATATGAGCATATTACCTAGAAATTGACATGTACTG
196 CAACACTATTTTGTTTCTTAGAAAACCATGATATGAGCATATTACCTAGAAATTGACATGTACTG
* **
508765 CAAGTGCTCTTTTTATCAACCTTACAACCACCAAAATTTGCATCTAAATAAGCATGTAAAGATAA
261 CAAGTGCTCTTTCTATCAACCTTACAACCACCAAAATCCGCATCTAAATAAGCATGTAAAGATAA
** **
508830 GGAGGATTCTTTTGGGTACCATAAACCTAAATTGGGAGTGTCTCATAAATATTTAAAAATTCTTT
326 GGAGGATTCTTTTAAGTACCATAAACCTAAATTGGGAGTGTCTCATAAATATTTAAAAACCCTTT
* * * *
508895 TTACAGCTAGTAAGTGAGATTCCCTAGGTGATAATTGAAACCGAGCACAAAGGCAAATGCTAAAC
391 TTACAGCTAGCAAGTGAGACTCCCTAGATGATAATTGAAACCGAGCACAAAGGCAAACGCTAAAC
*
508960 ATTATATCTGATCTACTTA
456 ATTATATCCGATCTACTTA
*
508979 TGGACATGATTTCTACATATTCAAGTCCTAGAGTATTGTATGAGATTTTTAGTAAGATAAATGGC
1 TGGACATGATTTCTACATATTCAAGTCCTAGAGTATTGTATGAGATTTTTAGTAAGACAAATGGC
509044 ACTAGTATTGTCAATTTAATGGGAATATGATCCATGGTAATACCAAAATATTCCATTTGTTGTTT
66 ACTAGTATTGTCAATTTAATGGGAATATGATCCATGGTAATACCAAAATATTCCATTTGTTGTTT
* * *
509109 TATCCATAAAACTTGGGCACAACAACTTCCTGCAGATATGTA-TTCTGCTTTGGTTATGGATAAG
131 TATCCATAAAACTTAGGCACAACAACTTCCTGCAGATATGAATTTC-GCTTCGGTTATGGATAAG
509173 GCAACACTATTTTGTTTCTTAGAAAACCATGATATGAGCATATTACCTAGAAATTGACATGTACT
195 GCAACACTATTTTGTTTCTTAGAAAACCATGATATGAGCATATTACCTAGAAATTGACATGTACT
*
509238 GCAAGTGCTCTTTCTATTAACCTTACAACCACCAAAATCCGCATCTAAATAAGCATGTAAAGATA
260 GCAAGTGCTCTTTCTATCAACCTTACAACCACCAAAATCCGCATCTAAATAAGCATGTAAAGATA
*
509303 AGGAGGATTCTTTTAAGTACCATAAACCTAAATTGGGAGTGTCTTATAAATATTTAAAAACCCTT
325 AGGAGGATTCTTTTAAGTACCATAAACCTAAATTGGGAGTGTCTCATAAATATTTAAAAACCCTT
*
509368 TTTACAGCTAGCAAGTGAGACTCCCTAGATGATAATTGAAACCGGGCACAAAGGCAAACGCTAAA
390 TTTACAGCTAGCAAGTGAGACTCCCTAGATGATAATTGAAACCGAGCACAAAGGCAAACGCTAAA
*
509433 CGTTATATCCGATCTACTT
455 CATTATATCCGATCTACTT
509452 GTGGCAAAAT
Statistics
Matches: 449, Mismatches: 23, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
473 3 0.01
474 446 0.99
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (474 bp):
TGGACATGATTTCTACATATTCAAGTCCTAGAGTATTGTATGAGATTTTTAGTAAGACAAATGGC
ACTAGTATTGTCAATTTAATGGGAATATGATCCATGGTAATACCAAAATATTCCATTTGTTGTTT
TATCCATAAAACTTAGGCACAACAACTTCCTGCAGATATGAATTTCGCTTCGGTTATGGATAAGG
CAACACTATTTTGTTTCTTAGAAAACCATGATATGAGCATATTACCTAGAAATTGACATGTACTG
CAAGTGCTCTTTCTATCAACCTTACAACCACCAAAATCCGCATCTAAATAAGCATGTAAAGATAA
GGAGGATTCTTTTAAGTACCATAAACCTAAATTGGGAGTGTCTCATAAATATTTAAAAACCCTTT
TTACAGCTAGCAAGTGAGACTCCCTAGATGATAATTGAAACCGAGCACAAAGGCAAACGCTAAAC
ATTATATCCGATCTACTTA
Found at i:517354 original size:11 final size:11
Alignment explanation
Indices: 517307--517359 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 11
517297 TAAGTGATTG
517307 GAATTTGAAG-
1 GAATTTGAAGA
*
517317 GAATTTGAAGCT
1 GAATTTGAAG-A
517329 G-ATTTGAAGA
1 GAATTTGAAGA
517339 -AATTTGAAGA
1 GAATTTGAAGA
*
517349 GTATTTGAAGA
1 GAATTTGAAGA
517360 TTTTAAAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 19 0.51
11 17 0.46
12 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.32
Consensus pattern (11 bp):
GAATTTGAAGA
Found at i:519685 original size:20 final size:21
Alignment explanation
Indices: 519660--519716 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
519650 GTTGAGCTCA
*
519660 ATGTATTGATACAATGC-ACT
1 ATGTATCGATACAATGCAACT
* *
519680 ATGTATCGATACAATTCAAGT
1 ATGTATCGATACAATGCAACT
519701 ATGTATCGATACAATG
1 ATGTATCGATACAATG
519717 TATCAATACT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACAATGCAACT
Found at i:519799 original size:19 final size:19
Alignment explanation
Indices: 519775--519823 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
519765 CTTTTCAAAG
*
519775 TGTATCAATACTATGAACA
1 TGTATCGATACTATGAACA
519794 TGTATCGATACTATGAACA
1 TGTATCGATACTATGAACA
*
519813 CGTATCGATAC
1 TGTATCGATAC
519824 AATGTATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (19 bp):
TGTATCGATACTATGAACA
Found at i:520235 original size:9 final size:9
Alignment explanation
Indices: 520221--520262 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
520211 GGTTATGCTT
520221 GCATTGATA
1 GCATTGATA
520230 GCATTGATA
1 GCATTGATA
*
520239 GCA-AGCATA
1 GCATTG-ATA
520248 GCATTGATA
1 GCATTGATA
*
520257 ACATTG
1 GCATTG
520263 GACAATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 1 0.04
9 26 0.93
10 1 0.04
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (9 bp):
GCATTGATA
Found at i:521518 original size:35 final size:34
Alignment explanation
Indices: 521434--521519 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 34
521424 TTTACAACTT
*
521434 TATCTTTTCATAA-ACTAAGATAGAACCTCTTCCC
1 TATCTTTTCA-AAGGCTAAGATAGAACCTCTTCCC
* *
521468 TATCTTTTCACAGGCTAAGATAGAACCTCTTTCC
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTTCCC
521502 TATCTTTTTCAAAGGCTA
1 TATC-TTTTCAAAGGCTA
521520 TTCCCTATCT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 1 0.02
34 33 0.72
35 12 0.26
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.37
Consensus pattern (34 bp):
TATCTTTTCAAAGGCTAAGATAGAACCTCTTCCC
Found at i:526818 original size:2 final size:2
Alignment explanation
Indices: 526811--526851 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
526801 GCTTGCTAAT
526811 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
526852 TGCTGGAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:535786 original size:89 final size:85
Alignment explanation
Indices: 535668--535826 Score: 210
Period size: 89 Copynumber: 1.8 Consensus size: 85
535658 TGTAATTGAA
* * *
535668 AATTGTGTAATTTATGCGATATGCATATGTATTATTATGCAAAATATTGTTATTATTTATTCTAT
1 AATTGTGTAATTTATGCGATATGCATATGTATCATTAT--AAAA-A-TATAATTATTTATTCTAT
535733 TATTTAATTGAGTATATATTGTAT
62 TATTTAATTGAGTATATATTGTAT
* * * * *
535757 AATTGTGTAATTTATGTGGTATGCGTATGTATCATTATAAAAATATAATTATTTATTTTGTTATT
1 AATTGTGTAATTTATGCGATATGCATATGTATCATTATAAAAATATAATTATTTATTCTATTATT
535822 TAATT
66 TAATT
535827 ATGTGTGTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 23 0.37
86 1 0.02
87 4 0.06
89 34 0.55
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.51
Consensus pattern (85 bp):
AATTGTGTAATTTATGCGATATGCATATGTATCATTATAAAAATATAATTATTTATTCTATTATT
TAATTGAGTATATATTGTAT
Found at i:535896 original size:32 final size:29
Alignment explanation
Indices: 535854--535921 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
535844 TTGGAAATTT
535854 TGTA-ATTTATGTGATACATAAGTCATTATTA
1 TGTATATTTATGTGAT--ATAAGT-ATTATTA
*
535885 TGTATATTTATGTGATATATGTATTATTA
1 TGTATATTTATGTGATATAAGTATTATTA
*
535914 TGCATATT
1 TGTATATT
535922 ATTAATTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 14 0.41
30 5 0.15
31 4 0.12
32 11 0.32
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.50
Consensus pattern (29 bp):
TGTATATTTATGTGATATAAGTATTATTA
Found at i:536903 original size:28 final size:26
Alignment explanation
Indices: 536838--536892 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
536828 TAATTTATTT
*
536838 TTTACACAAA-AAACTTTTTTTTATA
1 TTTACATAAATAAACTTTTTTTTATA
536863 TTTACATAAATAAACTTTATTTTTA-A
1 TTTACATAAATAAACTTT-TTTTTATA
536889 TTTA
1 TTTA
536893 TATCTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.33
26 12 0.44
27 6 0.22
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTACATAAATAAACTTTTTTTTATA
Found at i:537131 original size:2 final size:2
Alignment explanation
Indices: 537124--537169 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
537114 GATGATTCAG
*
537124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
537166 AT AT
1 AT AT
537170 TGTTAAGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:539722 original size:15 final size:17
Alignment explanation
Indices: 539702--539739 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
539692 CGGATACATA
539702 TTAAAA-TTAA-TTTTT
1 TTAAAATTTAACTTTTT
539717 TTAAAATTTAACTTTTT
1 TTAAAATTTAACTTTTT
539734 TTAAAA
1 TTAAAA
539740 GGATTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.29
16 4 0.19
17 11 0.52
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAAATTTAACTTTTT
Found at i:540194 original size:33 final size:33
Alignment explanation
Indices: 540157--540223 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
540147 TTCAACGATT
540157 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
540190 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
540223 T
1 T
540224 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:540195 original size:13 final size:13
Alignment explanation
Indices: 540177--540201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
540167 CATAAAATGT
540177 TGTATCGATACAA
1 TGTATCGATACAA
540190 TGTATCGATACA
1 TGTATCGATACA
540202 TATTTTTTTG
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:540282 original size:13 final size:13
Alignment explanation
Indices: 540264--540288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
540254 ATTACTCAAA
540264 TGTATCGATACAT
1 TGTATCGATACAT
540277 TGTATCGATACA
1 TGTATCGATACA
540289 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:540390 original size:52 final size:52
Alignment explanation
Indices: 540297--540420 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
540287 CACTGATCTT
*
540297 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
540348 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
540400 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
540421 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:544569 original size:10 final size:10
Alignment explanation
Indices: 544554--544580 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
544544 TGCTAACTAA
544554 GTTTTTGTTT
1 GTTTTTGTTT
544564 GTTTTTGTTT
1 GTTTTTGTTT
544574 GTTTTTG
1 GTTTTTG
544581 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:554282 original size:1 final size:1
Alignment explanation
Indices: 554276--554377 Score: 177
Period size: 1 Copynumber: 102.0 Consensus size: 1
554266 GGCGTCCTCC
* *
554276 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
554341 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
554378 CACAACAGGG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 95 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:586911 original size:13 final size:13
Alignment explanation
Indices: 586893--586918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
586883 CATTTTTTGG
586893 TGTATCGATACAT
1 TGTATCGATACAT
586906 TGTATCGATACAT
1 TGTATCGATACAT
586919 ACTTTGTGTA
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:586933 original size:32 final size:33
Alignment explanation
Indices: 586873--586936 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
586863 TACAAGCTAA
**
586873 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
586906 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
586937 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:588573 original size:8 final size:8
Alignment explanation
Indices: 588560--588593 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
588550 ATTTGATTAA
588560 ATTTTGTG
1 ATTTTGTG
588568 ATTTTGTG
1 ATTTTGTG
588576 ATTTTGTG
1 ATTTTGTG
588584 ATTTTGTG
1 ATTTTGTG
588592 AT
1 AT
588594 GAATGATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:588974 original size:20 final size:20
Alignment explanation
Indices: 588939--588979 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
588929 CAAATTTCTT
588939 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
588961 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
588980 AACAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:589273 original size:20 final size:21
Alignment explanation
Indices: 589241--589282 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
589231 CCTCTAGGCA
*
589241 GCACCCACCAGGTCGCGACCG
1 GCACCCACCAGGTCGCAACCG
589262 GCACCC-CCAGGTCGCAACCG
1 GCACCCACCAGGTCGCAACCG
589282 G
1 G
589283 GCAGCCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.19, C:0.48, G:0.29, T:0.05
Consensus pattern (21 bp):
GCACCCACCAGGTCGCAACCG
Found at i:590690 original size:22 final size:22
Alignment explanation
Indices: 590664--590708 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
590654 CGAAATTGTC
590664 AAATTATTTT-ACTAAGGGGGAG
1 AAATT-TTTTGACTAAGGGGGAG
*
590686 AAATTTTTTGATTAAGGGGGAG
1 AAATTTTTTGACTAAGGGGGAG
590708 A
1 A
590709 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (22 bp):
AAATTTTTTGACTAAGGGGGAG
Found at i:591266 original size:20 final size:19
Alignment explanation
Indices: 591221--591273 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
591211 AAACCCTGAA
591221 AAGTATCGATACACATTTG
1 AAGTATCGATACACATTTG
*
591240 AATGTATCGATACAGA-TTG
1 AA-GTATCGATACACATTTG
591259 CACAGTATCGATACA
1 -A-AGTATCGATACA
591274 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.17
20 24 0.80
21 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (19 bp):
AAGTATCGATACACATTTG
Found at i:591281 original size:13 final size:13
Alignment explanation
Indices: 591263--591287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
591253 AGATTGCACA
591263 GTATCGATACATT
1 GTATCGATACATT
591276 GTATCGATACAT
1 GTATCGATACAT
591288 GACCAAATGT
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):
GTATCGATACATT
Found at i:591300 original size:20 final size:21
Alignment explanation
Indices: 591275--591327 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
591265 ATCGATACAT
**
591275 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
591295 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
591316 TGTATCGATACA
1 TGTATCGATACA
591328 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:593269 original size:31 final size:32
Alignment explanation
Indices: 593218--593279 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
593208 ACGCAAAAAT
593218 ACTAAAAAAATTAACACTTTCAAAACGAAAGC
1 ACTAAAAAAATTAACACTTTCAAAACGAAAGC
* * *
593250 ACTAAAAAAA-TAACGCTTTCATAAGGAAAG
1 ACTAAAAAAATTAACACTTTCAAAACGAAAG
593280 TGTCGATGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (32 bp):
ACTAAAAAAATTAACACTTTCAAAACGAAAGC
Found at i:594127 original size:29 final size:29
Alignment explanation
Indices: 594085--594143 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
594075 CTTTGTGAGC
* *
594085 AAAATAGTAATATTTTGATAAATAGTTTT
1 AAAATAATAATATTTTAATAAATAGTTTT
* * *
594114 AAAATAATATTATTTTAATAATTTGTTTT
1 AAAATAATAATATTTTAATAAATAGTTTT
594143 A
1 A
594144 GAATTAAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (29 bp):
AAAATAATAATATTTTAATAAATAGTTTT
Found at i:598769 original size:32 final size:30
Alignment explanation
Indices: 598733--598791 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
598723 GAAATCAAAT
598733 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
598765 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
598792 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:599089 original size:13 final size:13
Alignment explanation
Indices: 599071--599096 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
599061 CAATTTTTTG
599071 TGTATCGATACAT
1 TGTATCGATACAT
599084 TGTATCGATACAT
1 TGTATCGATACAT
599097 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:599111 original size:32 final size:33
Alignment explanation
Indices: 599051--599114 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
599041 TACAAGCCAA
** *
599051 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
599084 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
599115 AGTTTGGCTA
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:600856 original size:23 final size:23
Alignment explanation
Indices: 600807--600863 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
600797 CTAAGCATTA
*
600807 TTAATATTTTTTAATTAAAAATTT
1 TTAATA-TTTTTAATTAAAAATAT
*
600831 TTAATATTTTTAACTT-AATATAT
1 TTAATATTTTTAA-TTAAAAATAT
*
600854 TTAACATTTT
1 TTAATATTTT
600864 AAAGTTTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAATATTTTTAATTAAAAATAT
Found at i:611156 original size:125 final size:126
Alignment explanation
Indices: 610932--611179 Score: 383
Period size: 125 Copynumber: 2.0 Consensus size: 126
610922 TAGCCGTTAG
* *
610932 AGAGTTTTGACTTTTGCTTTTGCGTTTAGCTCTTCATTGCTTGATTTTCTTGTACATAGAAAGCA
1 AGAGTTTTGAATTTTGCTTTTGCGTTTAGCTCTTCATTGCCTGATTTTCTTGTACATAGAAAGCA
*
610997 ACCAAAACATAAAACTAATAACAATTTCCTTTTT-CTTTTCTTAAATTTTGTTCAAGTCAA
66 ACAAAAACATAAAACTAATAACAATTTCCTTTTTCCTTTTCTTAAATTTTGTTCAAGTCAA
** * ***
611057 AGAGTTTTGAATTTTGCTTTTGTTTTTGGCTCTTCATTGCCTGATTTTCTTGTACATAGTGGGCA
1 AGAGTTTTGAATTTTGCTTTTGCGTTTAGCTCTTCATTGCCTGATTTTCTTGTACATAGAAAGCA
*
611122 ACAAAAACATAAAACTAATTACAAGTTTCC-TTTTCCTTTTCTTAAATTTTGTTCAAGT
66 ACAAAAACATAAAACTAATAACAA-TTTCCTTTTTCCTTTTCTTAAATTTTGTTCAAGT
611180 ATCTTACAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
125 83 0.75
126 28 0.25
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.44
Consensus pattern (126 bp):
AGAGTTTTGAATTTTGCTTTTGCGTTTAGCTCTTCATTGCCTGATTTTCTTGTACATAGAAAGCA
ACAAAAACATAAAACTAATAACAATTTCCTTTTTCCTTTTCTTAAATTTTGTTCAAGTCAA
Found at i:611951 original size:17 final size:18
Alignment explanation
Indices: 611923--611971 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
611913 GTAACTTAGA
*
611923 AATATATAAAAATATTAT
1 AATATATTAAAATATTAT
*
611941 AA-ATATTAAAAT-TTTT
1 AATATATTAAAATATTAT
611957 AATATATT-AAATATT
1 AATATATTAAAATATT
611972 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.33
17 16 0.59
18 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATATATTAAAATATTAT
Found at i:612525 original size:4 final size:4
Alignment explanation
Indices: 612516--612541 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
612506 AATTAACTAA
612516 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
612542 TAAGAAGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:614236 original size:21 final size:21
Alignment explanation
Indices: 614183--614238 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
614173 AATTTTAGAT
**
614183 GTTTTATTTAGATTTAATTAA
1 GTTTTATTTATTTTTAATTAA
* ** *
614204 TTTTTAAATATTTTTAATTTA
1 GTTTTATTTATTTTTAATTAA
614225 GTTTTATTTATTTT
1 GTTTTATTTATTTT
614239 CTTTATATTG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
GTTTTATTTATTTTTAATTAA
Found at i:615884 original size:23 final size:22
Alignment explanation
Indices: 615846--615897 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
615836 AACAATAAAC
615846 GAGCTTTAAACAAAATAAAAGAT
1 GAGCTTTAAACAAAAT-AAAGAT
** *
615869 GAGCTTTAAATGAAATATAGAT
1 GAGCTTTAAACAAAATAAAGAT
615891 GAG-TTTA
1 GAGCTTTA
615898 TTCGTGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 4 0.15
22 8 0.31
23 14 0.54
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (22 bp):
GAGCTTTAAACAAAATAAAGAT
Found at i:616837 original size:26 final size:27
Alignment explanation
Indices: 616798--616855 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
616788 CGTATGCTTA
*
616798 TATATAGAAAA-TTTTTAGATAAGTTT
1 TATATAGAAAATTTTTTAGACAAGTTT
*
616824 TATATAGAACATTTTTTAGACAAGTTT
1 TATATAGAAAATTTTTTAGACAAGTTT
616851 TATAT
1 TATAT
616856 GTTTTAAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (27 bp):
TATATAGAAAATTTTTTAGACAAGTTT
Found at i:619805 original size:2 final size:2
Alignment explanation
Indices: 619798--619839 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
619788 TATCTAGCTA
619798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
619840 TGTTTTCAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:621066 original size:22 final size:22
Alignment explanation
Indices: 621041--621108 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 22
621031 TATTTAAAAA
621041 TTAAAATATATTTATTATTAAT
1 TTAAAATATATTTATTATTAAT
* *
621063 TTAATTAATAATAATTATTA-TACT
1 TTAA--AAT-ATATTTATTATTAAT
*
621087 TTAAAATAT-TTTA-TATTTAT
1 TTAAAATATATTTATTATTAAT
621107 TT
1 TT
621109 GATGCTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
19 2 0.05
20 7 0.19
21 2 0.05
22 7 0.19
24 10 0.27
25 9 0.24
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAAAATATATTTATTATTAAT
Found at i:621364 original size:19 final size:20
Alignment explanation
Indices: 621340--621385 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
621330 ATAAATATAT
*
621340 ATATATATAA-ATATTTAAA
1 ATATATATAATAAATTTAAA
621359 ATATAT-TAATAAATTTAAA
1 ATATATATAATAAATTTAAA
621378 ATA-ATATA
1 ATATATATA
621386 TCAATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATATATAATAAATTTAAA
Found at i:622131 original size:26 final size:24
Alignment explanation
Indices: 622102--622150 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
622092 TTCATATATT
*
622102 ATAAATTATATTATATAAATAAATAA
1 ATAAATTATATAAT-TAAA-AAATAA
622128 ATAAATTATATAATTAAAAAATA
1 ATAAATTATATAATTAAAAAATA
622151 GTGTGAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 4 0.18
26 13 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAATTATATAATTAAAAAATAA
Found at i:622137 original size:21 final size:21
Alignment explanation
Indices: 622102--622150 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
622092 TTCATATATT
*
622102 ATAAATTATATTATATAAATAA
1 ATAAA-TAAATTATATAAATAA
*
622124 ATAAATAAATTATATAATTAA
1 ATAAATAAATTATATAAATAA
622145 A-AAATA
1 ATAAATA
622151 GTGTGAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 15 0.60
22 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAATAAATTATATAAATAA
Found at i:622243 original size:13 final size:14
Alignment explanation
Indices: 622218--622249 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
622208 TATATAGATT
622218 AATTT-TTTATTTA
1 AATTTATTTATTTA
622231 AATTTATTT-TTTA
1 AATTTATTTATTTA
622244 AATTTA
1 AATTTA
622250 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
AATTTATTTATTTA
Found at i:622248 original size:19 final size:19
Alignment explanation
Indices: 622226--622264 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
622216 TTAATTTTTT
*
622226 ATTTAA-ATTTATTTTTTAA
1 ATTTAATATTT-TTATTTAA
622245 ATTTAATATTTTTATTTAA
1 ATTTAATATTTTTATTTAA
622264 A
1 A
622265 ATCTCCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTAATATTTTTATTTAA
Found at i:622528 original size:21 final size:20
Alignment explanation
Indices: 622490--622528 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
622480 ATAAATAATA
* *
622490 AATTATTTTTATATTTTTAT
1 AATTATTTTTAAAATTTTAT
622510 AATTAATTTTTAAAATTTT
1 AATT-ATTTTTAAAATTTT
622529 TCAATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTATTTTTAAAATTTTAT
Found at i:623465 original size:2 final size:2
Alignment explanation
Indices: 623458--623485 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
623448 TCTTTCCAAA
623458 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
623486 TAATTAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:624671 original size:18 final size:17
Alignment explanation
Indices: 624648--624703 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
624638 ATTTAAAAAT
624648 TTAAAAATTTAAAATAAA
1 TTAAAAA-TTAAAATAAA
*
624666 TTAAAAAAT-AAATATAA
1 TTAAAAATTAAAATA-AA
624683 TTAAAAAATTATAAA-AAA
1 TT-AAAAATTA-AAATAAA
624701 TTA
1 TTA
624704 TTTTAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 5 0.16
17 6 0.19
18 17 0.53
19 1 0.03
20 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAATTAAAATAAA
Found at i:624677 original size:17 final size:17
Alignment explanation
Indices: 624659--624691 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
624649 TAAAAATTTA
624659 AAATA-AATTAAAAAAT
1 AAATATAATTAAAAAAT
624675 AAATATAATTAAAAAAT
1 AAATATAATTAAAAAAT
624692 TATAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATATAATTAAAAAAT
Found at i:624735 original size:9 final size:8
Alignment explanation
Indices: 624640--624868 Score: 54
Period size: 8 Copynumber: 25.6 Consensus size: 8
624630 TAAATGTCAT
*
624640 TTAAAAAT
1 TTAAAAAA
*
624648 TTAAAAAT
1 TTAAAAAA
624656 TTAAAATAAA
1 TT-AAA-AAA
624666 TTAAAAAA
1 TTAAAAAA
624674 -TAAATATAA
1 TTAAA-A-AA
624683 TTAAAAAA
1 TTAAAAAA
624691 TTATAAAAAA
1 -T-TAAAAAA
**
624701 TTATTTTAAA
1 TTA--AAAAA
624711 TTAAAAAA
1 TTAAAAAA
*
624719 TTTTAAAAA
1 -TTAAAAAA
*
624728 TTCAAAAACCC
1 TT-AAAAA--A
624739 TTAAAAATA
1 TTAAAAA-A
*
624748 GCTAAAAATTA
1 -TTAAAAA--A
624759 TTTTAAAAAA
1 --TTAAAAAA
* *
624769 TTTAAAAT
1 TTAAAAAA
624777 TTAAAAAA
1 TTAAAAAA
624785 TATAAATAAA
1 T-TAAA-AAA
*
624795 -TAATATAA
1 TTAA-AAAA
*
624803 --AAAAAT
1 TTAAAAAA
624809 TTAAAATACTA
1 TTAAAA-A--A
*
624820 TTAAAATA
1 TTAAAAAA
624828 TATAATTAAAA
1 T-TAA--AAAA
624839 TTAATAAAAA
1 TT-A-AAAAA
624849 TT-AAAAA
1 TTAAAAAA
624856 TTAAAAAA
1 TTAAAAAA
624864 TTAAA
1 TTAAA
624869 TTTGAAAAAA
Statistics
Matches: 168, Mismatches: 23, Indels: 60
0.67 0.09 0.24
Matches are distributed among these distances:
6 2 0.01
7 13 0.08
8 57 0.34
9 31 0.18
10 43 0.26
11 15 0.09
12 7 0.04
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (8 bp):
TTAAAAAA
Found at i:624846 original size:43 final size:39
Alignment explanation
Indices: 624763--624869 Score: 114
Period size: 39 Copynumber: 2.7 Consensus size: 39
624753 AAATTATTTT
624763 AAAAAATTTAAAATTTAAAAAATATAAATAAATAATATA
1 AAAAAATTTAAAATTTAAAAAATATAAATAAATAATATA
* * *
624802 AAAAAATTTAAAATACTATTAAAATATATAATTAA-AAT-TA
1 AAAAAATTTAAAAT-TTA-AAAAATATA-AATAAATAATATA
*
624842 ATAAAAA-TTAAAAATTAAAAAAT-TAAAT
1 A-AAAAATTTAAAATTTAAAAAATATAAAT
624870 TTGAAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
36 3 0.05
37 2 0.03
38 5 0.09
39 16 0.28
40 11 0.19
41 16 0.28
42 5 0.09
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (39 bp):
AAAAAATTTAAAATTTAAAAAATATAAATAAATAATATA
Found at i:624864 original size:15 final size:17
Alignment explanation
Indices: 624831--624868 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
624821 TAAAATATAT
624831 AATT-AAAATTAATAAA
1 AATTAAAAATTAATAAA
624847 AATTAAAAATT-A-AAA
1 AATTAAAAATTAATAAA
624862 AATTAAA
1 AATTAAA
624869 TTTGAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 5 0.24
17 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTAAAAATTAATAAA
Found at i:625249 original size:24 final size:25
Alignment explanation
Indices: 625196--625270 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 25
625186 TTCGCCCCTT
*
625196 TTTCCTCTCTCTTCC-CTTTTTTTCCCCC
1 TTTCCTCTCCCTTCCTC-TTTTTT---CC
*
625224 TTTCTTCTCCCTTCCT-TTTTTTCC
1 TTTCCTCTCCCTTCCTCTTTTTTCC
*
625248 TTTCCTCTCCTTTCCTCTTTTTT
1 TTTCCTCTCCCTTCCTCTTTTTT
625271 TTTTTTTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 16 0.39
25 6 0.15
27 6 0.15
28 13 0.32
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTCCTCTCCCTTCCTCTTTTTTCC
Found at i:625479 original size:22 final size:22
Alignment explanation
Indices: 625419--625483 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
625409 AATTTTTTGA
*
625419 TTTTACATTTTGATTTT-TAATT
1 TTTTACATTTTTATTTTAT-ATT
* *
625441 TTTTATA-TTTT-TCTTATATT
1 TTTTACATTTTTATTTTATATT
625461 TTTTACATTTTTATTTTATATT
1 TTTTACATTTTTATTTTATATT
625483 T
1 T
625484 GAATTCTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 12 0.34
21 8 0.23
22 15 0.43
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTACATTTTTATTTTATATT
Found at i:627908 original size:21 final size:21
Alignment explanation
Indices: 627882--627925 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
627872 TTAAATTTAA
* *
627882 TAAATAATTTTTAATCAAATT
1 TAAATAAATTTAAATCAAATT
*
627903 TAAATAAATTTAAATCAATTT
1 TAAATAAATTTAAATCAAATT
627924 TA
1 TA
627926 TCAATTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATAAATTTAAATCAAATT
Found at i:628251 original size:13 final size:13
Alignment explanation
Indices: 628225--628261 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
628215 TCCGGATACA
628225 GAAT-GGGT-GGG
1 GAATGGGGTGGGG
628236 GAATGGGGTGGGG
1 GAATGGGGTGGGG
*
628249 GAAGGGGGTGGGG
1 GAATGGGGTGGGG
628262 TGGGGCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 4 0.17
12 4 0.17
13 15 0.65
ACGTcount: A:0.16, C:0.00, G:0.70, T:0.14
Consensus pattern (13 bp):
GAATGGGGTGGGG
Found at i:630520 original size:20 final size:20
Alignment explanation
Indices: 630483--630520 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
630473 TCAAACTAAT
*
630483 AATTTAACCTAAAAAAATGA
1 AATTTAACCAAAAAAAATGA
630503 AATTTAA-CAAAAACAAAT
1 AATTTAACCAAAAA-AAAT
630521 AAAAACTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.24
Consensus pattern (20 bp):
AATTTAACCAAAAAAAATGA
Found at i:633605 original size:20 final size:20
Alignment explanation
Indices: 633580--633627 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
633570 TTGTTGTATT
633580 GATACATATCATTATGAATC
1 GATACATATCATTATGAATC
*
633600 GATACATATCATTATGTATC
1 GATACATATCATTATGAATC
*
633620 AATACATA
1 GATACATA
633628 GAGCCATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (20 bp):
GATACATATCATTATGAATC
Found at i:634758 original size:79 final size:79
Alignment explanation
Indices: 634664--634885 Score: 304
Period size: 79 Copynumber: 2.8 Consensus size: 79
634654 ATAAATCCCG
* * * *
634664 GGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGGAGTGTCTTCGATTGTGAAAAATCAGTGTTT
1 GGGTTGGAGTATCCCCTCGAAAATAATGAGGTTAGAGTATCTCCGATTGTGAAAAATCAGTGTTT
*
634729 TGGAAATAAAATC-
66 TGAAAATAAAATCA
* * * *
634742 GAGGTTGGAGTATCCCCTCGAAAATAATGAGGTTAGAATATCTCCGATTATGAAAAATCAATATT
1 G-GGTTGGAGTATCCCCTCGAAAATAATGAGGTTAGAGTATCTCCGATTGTGAAAAATCAGTGTT
634807 TTGAAAATAAAATCA
65 TTGAAAATAAAATCA
* **
634822 GGGTTGGAGTATCTCCTCGAAAATAACAAGGTTAGAGTATC-CCTGATTGTGAAAAATCAGTGTT
1 GGGTTGGAGTATCCCCTCGAAAATAATGAGGTTAGAGTATCTCC-GATTGTGAAAAATCAGTGTT
634886 CTACTCAAAA
Statistics
Matches: 125, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
78 3 0.02
79 121 0.97
80 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCTCGAAAATAATGAGGTTAGAGTATCTCCGATTGTGAAAAATCAGTGTTT
TGAAAATAAAATCA
Found at i:635057 original size:210 final size:209
Alignment explanation
Indices: 634679--635087 Score: 509
Period size: 210 Copynumber: 2.0 Consensus size: 209
634669 GGAGTATCCC
* * *
634679 CTCAAAAATAATGAGGTTGGAGTGTCTTCGATTGTGAAAAATCAGTGTTTTGGAAATAAAATCGA
1 CTCAAAAATAACGAGGTTGGAGTATCTTCGATTGTGAAAAATCAGTGTTTTGGAAATAAAACCGA
* * * *
634744 GGTTGGAGTATCCCCTCGAAAATAATGAGGTTAGAATATCTCCGATTATGAAAAATCAATATTTT
66 GGTTAGAGTATCCCCTCGAAAATAATGAGGTTAGAATATCCCCGATGATAAAAAATCAATATTTT
* * * *
634809 GAAAATAAAATCAGGGTTGGAGTATCTCCTCGAAAATAACAAGGTTAGAGTATCCCTGATTGTGA
131 GAAAATAAAATCAGGGTTGGAATATCTCCTCAAAAATAA-AAGGTTAGAGTATCCCCGATTATGA
634874 AAAATCAGTGTTCTA
195 AAAATCAGTGTTCTA
*
634889 CTCAAAAATAACGGGGTTGGAGTATCCTT-GATTGTGAAAAATCAGTGTTTTGGAAATAAAACCG
1 CTCAAAAATAACGAGGTTGGAGTAT-CTTCGATTGTGAAAAATCAGTGTTTTGGAAATAAAACCG
* * * * * * *** *
634953 AGGTTAGAGTATCCCCTTGGAAATAAT-AGGGTTGGAGTGTCCCCGATGGTAAAAAATGGGTGTT
65 AGGTTAGAGTATCCCCTCGAAAATAATGA-GGTTAGAATATCCCCGATGATAAAAAATCAATATT
* * * ** *
635017 TTGGAAATAAAATCGGGGTTGGAATATC-CTTTCAAAAATAATGGGTTGGAGTATCCCCGATTAT
129 TTGAAAATAAAATCAGGGTTGGAATATCTC-CTCAAAAATAAAAGGTTAGAGTATCCCCGATTAT
635081 GAAAAAT
193 GAAAAAT
635088 TAATGTTTTA
Statistics
Matches: 168, Mismatches: 28, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
209 27 0.16
210 138 0.82
211 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (209 bp):
CTCAAAAATAACGAGGTTGGAGTATCTTCGATTGTGAAAAATCAGTGTTTTGGAAATAAAACCGA
GGTTAGAGTATCCCCTCGAAAATAATGAGGTTAGAATATCCCCGATGATAAAAAATCAATATTTT
GAAAATAAAATCAGGGTTGGAATATCTCCTCAAAAATAAAAGGTTAGAGTATCCCCGATTATGAA
AAATCAGTGTTCTA
Found at i:635102 original size:78 final size:78
Alignment explanation
Indices: 634892--635184 Score: 293
Period size: 78 Copynumber: 3.7 Consensus size: 78
634882 TGTTCTACTC
** * *
634892 AAAAATAACGGGGTTGGAGTATCCTTGATTGTGAAAAATCAGTGTTTTGGAAATAAAACCGAGGT
1 AAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAGTGTTTTGGAAATAAAACCGGGGT
* *
634957 TAGAGTATCCCCTT
66 TGGAGTAT-CCTTT
** ** * ** * ** *
634971 GGAAATAATAGGGTTGGAGTGTCCCCGATGGTAAAAAATGGGTGTTTTGGAAATAAAATCGGGGT
1 AAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAGTGTTTTGGAAATAAAACCGGGGT
*
635036 TGGAATATCCTTT
66 TGGAGTATCCTTT
* * * * **
635049 CAAAAATAA-TGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAGGCCGGGG
1 -AAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAGTGTTTTGGAAATAAAACCGGGG
635113 -TGGAGTATCCTCTT
65 TTGGAGTATCCT-TT
** * *
635127 GGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGAAAATAAAA
1 AAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAGTGTTTTGGAAATAAAA
635185 ACATCGATGC
Statistics
Matches: 170, Mismatches: 41, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
77 16 0.09
78 90 0.53
79 64 0.38
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (78 bp):
AAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAGTGTTTTGGAAATAAAACCGGGGT
TGGAGTATCCTTT
Found at i:637583 original size:30 final size:30
Alignment explanation
Indices: 637547--637620 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
637537 TACATTGAGA
*
637547 AATGTATCGATACATCTGGGTAAAACCTAG
1 AATGTATCGATACATCTAGGTAAAACCTAG
*
637577 AATGTATCGATACATCTAGGTGAAACCTAG
1 AATGTATCGATACATCTAGGTAAAACCTAG
*
637607 AATGTATCAATACA
1 AATGTATCGATACA
637621 ATGAACAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (30 bp):
AATGTATCGATACATCTAGGTAAAACCTAG
Found at i:638300 original size:62 final size:61
Alignment explanation
Indices: 638210--638408 Score: 256
Period size: 62 Copynumber: 3.2 Consensus size: 61
638200 AGGGGTATCT
** *
638210 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTTGGTTTTGAAAAGAAAAAGGCATCC
1 TGCTCTTTGAGGACT-AAAGGTATCACCAACTCGTGTTGGCTTTGAAAAGAAAAAGGCATCC
* * **
638272 TGCTCTTTGAAGACTAAATGGTATCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGTGTCC
1 TGCTCTTTGAGGACTAAA-GGTATCACCAACTCGTGTTGGCTTTGAAAAGAAAAAGGCATCC
* * *
638334 TGTTCTTTGAGGACTAAAGG-ATGCCATCAACTCGTGTTGGCTTTGAAAAGAAAAAGGCATGC
1 TGCTCTTTGAGGACTAAAGGTAT--CACCAACTCGTGTTGGCTTTGAAAAGAAAAAGGCATCC
*
638396 TTCTCTTTGAGGA
1 TGCTCTTTGAGGA
638409 ATAAGGAAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
60 2 0.02
61 5 0.04
62 111 0.94
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (61 bp):
TGCTCTTTGAGGACTAAAGGTATCACCAACTCGTGTTGGCTTTGAAAAGAAAAAGGCATCC
Done.