Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 127 of 128
Found at i:42370291 original size:30 final size:27
Alignment explanation
Indices: 42370235--42370292 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
42370225 TAGAACTACA
*
42370235 TAATTTAAAATAAAACAAATACTTTTT
1 TAATTTAAAATAAAAAAAATACTTTTT
*
42370262 TAATTTAAAAATTAAAAAAAAATATTTTTT
1 TAATTT-AAAA-T-AAAAAAAATACTTTTT
42370292 T
1 T
42370293 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 4 0.15
29 1 0.04
30 15 0.58
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATTTAAAATAAAAAAAATACTTTTT
Found at i:42380402 original size:12 final size:12
Alignment explanation
Indices: 42380385--42380415 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
42380375 CTTCGAATAC
42380385 CCGCCACCGCTG
1 CCGCCACCGCTG
42380397 CCGCCACCGCTG
1 CCGCCACCGCTG
42380409 CCGCCAC
1 CCGCCAC
42380416 TGCCACCGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.61, G:0.23, T:0.06
Consensus pattern (12 bp):
CCGCCACCGCTG
Found at i:42383173 original size:21 final size:22
Alignment explanation
Indices: 42383132--42383178 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
42383122 AGCAGAGGCG
42383132 TTTTATTCATTTTACTCAAAAA
1 TTTTATTCATTTTACTCAAAAA
*
42383154 TTTTATT-ATTTT-CATTAAAAA
1 TTTTATTCATTTTAC-TCAAAAA
42383175 TTTT
1 TTTT
42383179 GTCCTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.65
22 7 0.30
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTATTCATTTTACTCAAAAA
Found at i:42383594 original size:19 final size:19
Alignment explanation
Indices: 42383562--42383598 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42383552 TGTCATGTCA
* *
42383562 ATAAATATTTAAAAAAATC
1 ATAAAAATTAAAAAAAATC
42383581 ATAAAAATTAAAAAAAAT
1 ATAAAAATTAAAAAAAAT
42383599 AAGTATACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAAATTAAAAAAAATC
Found at i:42388189 original size:15 final size:15
Alignment explanation
Indices: 42388169--42388203 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
42388159 ACCTGACCAG
*
42388169 CAAACCCAAATGAAT
1 CAAACCCAAATGAAC
42388184 CAAACCCAAATGAAC
1 CAAACCCAAATGAAC
42388199 CAAAC
1 CAAAC
42388204 ATAAAGTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.54, C:0.31, G:0.06, T:0.09
Consensus pattern (15 bp):
CAAACCCAAATGAAC
Found at i:42389756 original size:8 final size:8
Alignment explanation
Indices: 42389733--42389786 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
42389723 AACTTTACAC
*
42389733 ACACACAC
1 ACACACAT
42389741 ACACACAT
1 ACACACAT
42389749 ACACACAT
1 ACACACAT
*
42389757 ACATACAT
1 ACACACAT
* *
42389765 ACA-TCGT
1 ACACACAT
*
42389772 ACACATAT
1 ACACACAT
42389780 ACACACA
1 ACACACA
42389787 CATGTACGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
7 5 0.14
8 32 0.86
ACGTcount: A:0.48, C:0.35, G:0.02, T:0.15
Consensus pattern (8 bp):
ACACACAT
Found at i:42392633 original size:6 final size:7
Alignment explanation
Indices: 42392616--42392640 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42392606 TAGTTACCTT
42392616 TTTTTCC
1 TTTTTCC
42392623 TTTTTCC
1 TTTTTCC
42392630 TTTTTCC
1 TTTTTCC
42392637 TTTT
1 TTTT
42392641 ATTATCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCC
Found at i:42395565 original size:264 final size:263
Alignment explanation
Indices: 42395084--42395586 Score: 801
Period size: 264 Copynumber: 1.9 Consensus size: 263
42395074 GGGAAGAAAT
* * *
42395084 TGTCATATTTCAAATTTTGTGCTTGTTTCAAGCCCAAATAGACCATTATAGTTACTTTTAACATA
1 TGTCAGATTTCAAATATTGTGCTTGTTTCAAGCCCAAATAGACCATCATAGTTACTTTTAACATA
* *
42395149 TGAAAAAATAGATCAATGATCATCCTTCAACATATGACATTAATACTATATGTCCAGAAAGGCCA
66 TGAAAAAATAGATCAAAGATCATCCTTCAACATATGACATTAATACTATATGTCCACAAA-GCCA
*
42395214 CCGAAGCCTTGTAAACCAATGCCTGGTCTTTATGGATACTGGTTTTCTAACATTATGCCCGTCTC
130 CCGAAGCCTTGTAAACCAATGCCTGGTCTTTATGGATACTGGTTTTCTAACATTATGCCCGCCTC
* *
42395279 CACAATTGCAACTTACTGATATGTTCTGTTTTTCTGCCAAAACATATATAATACATAAGTGGAAC
195 CACAATTGCAACTTACTGATATGTTCTATTTTTCTACCAAAACATATATAATACATAAGTGGAAC
42395344 TTAG
260 TTAG
*
42395348 TGTCAGATTTCAAATATTGTGCTTGTTTCAAGTCCAAATAGACCATCATAGTTACTTTTAACATA
1 TGTCAGATTTCAAATATTGTGCTTGTTTCAAGCCCAAATAGACCATCATAGTTACTTTTAACATA
* *
42395413 TGAAAAGATAGATCAAAGATCATCCTTCAACATATGACATTAATACTATATGTCTACAAA-CCAC
66 TGAAAAAATAGATCAAAGATCATCCTTCAACATATGACATTAATACTATATGTCCACAAAGCCAC
* * * ***
42395477 TGAAGCCTTTTAAACCAATGTCTGGTCTTTATGGATTACTGGTTTTCTAACATTAATGTTTGCCT
131 CGAAGCCTTGTAAACCAATGCCTGGTCTTTATGGA-TACTGGTTTTCTAACATT-ATGCCCGCCT
* *
42395542 CCATAATTGCAACTTAGTGATATGTTCTATTTTTCTACCAAAACA
194 CCACAATTGCAACTTACTGATATGTTCTATTTTTCTACCAAAACA
42395587 GGAAATTTAG
Statistics
Matches: 218, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
262 36 0.17
263 18 0.08
264 164 0.75
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (263 bp):
TGTCAGATTTCAAATATTGTGCTTGTTTCAAGCCCAAATAGACCATCATAGTTACTTTTAACATA
TGAAAAAATAGATCAAAGATCATCCTTCAACATATGACATTAATACTATATGTCCACAAAGCCAC
CGAAGCCTTGTAAACCAATGCCTGGTCTTTATGGATACTGGTTTTCTAACATTATGCCCGCCTCC
ACAATTGCAACTTACTGATATGTTCTATTTTTCTACCAAAACATATATAATACATAAGTGGAACT
TAG
Found at i:42402801 original size:4 final size:4
Alignment explanation
Indices: 42402792--42402816 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
42402782 ACTCATAAAC
42402792 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
42402817 ATTTTGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:42402964 original size:2 final size:2
Alignment explanation
Indices: 42402955--42402983 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
42402945 AATATATTTT
42402955 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42402984 AAATAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42403710 original size:30 final size:32
Alignment explanation
Indices: 42403648--42403717 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
42403638 GACCTCCAAA
*
42403648 AAATTTAAGTACCAACTTAAGAAAAAAGTGTC
1 AAATTTAAGTACCAAATTAAGAAAAAAGTGTC
*
42403680 AAATTTAAGTACTAAATTAA-AAAAAA-TGTC
1 AAATTTAAGTACCAAATTAAGAAAAAAGTGTC
42403710 AAATTTAA
1 AAATTTAA
42403718 ATGTCAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 12 0.33
31 6 0.17
32 18 0.50
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (32 bp):
AAATTTAAGTACCAAATTAAGAAAAAAGTGTC
Found at i:42408647 original size:188 final size:190
Alignment explanation
Indices: 42408300--42408673 Score: 576
Period size: 188 Copynumber: 2.0 Consensus size: 190
42408290 TCCCGAACCG
* * **
42408300 TGGAACTGGAATGTGTATTTGTTTCCTCTTTGGTGTTGTGGTGTGGTAATCCGATACTTGATTTT
1 TGGAACTGAAATGTGTATTTGCTTCCTCTCCGGTGTTGTGGTGTGGTAATCCGATACTTGATTTT
* *
42408365 ATTCCCTGTGAGGTTAGCTATTGAACTTCTCGAAAGTAACATTGAATTGTTTGATGCGTGATGGT
66 ATTCCCTGTGAGGTTAGCCATTGAACTTCTCGAAAGTAACATTGAATTGTTTGATGCATGATGGT
*
42408430 TAATGTTTGAATGAAAGTTTACTTTATGTTCGTTTTCGAGGTTAGTTAGGTAGTGTATTA
131 TAATGTTTGAATAAAAGTTTACTTTATGTTCGTTTTCGAGGTTAGTTAGGTAGTGTATTA
*
42408490 TGGAACTGAAATGTGTATTTGCTTCCTCTCCGGTG-T-T-GTGTGGTAATCCGTTACTTGATTTT
1 TGGAACTGAAATGTGTATTTGCTTCCTCTCCGGTGTTGTGGTGTGGTAATCCGATACTTGATTTT
* * * *
42408552 ATTCTCTGTGAGGTTAGCCATTGAACTTTTTC-ATAAGTAACATTGCATTGTTTGATGCATGTTG
66 ATTCCCTGTGAGGTTAGCCATTGAAC-TTCTCGA-AAGTAACATTGAATTGTTTGATGCATGATG
* *
42408616 GTTCATGTTTGAATAAAAGTTTACTTTATGTTTGTTTTCGAGGTTAGTTAGGTAGTGT
129 GTTAATGTTTGAATAAAAGTTTACTTTATGTTCGTTTTCGAGGTTAGTTAGGTAGTGT
42408674 CTCATAGTTG
Statistics
Matches: 168, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
187 49 0.29
188 87 0.52
189 1 0.01
190 31 0.18
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.44
Consensus pattern (190 bp):
TGGAACTGAAATGTGTATTTGCTTCCTCTCCGGTGTTGTGGTGTGGTAATCCGATACTTGATTTT
ATTCCCTGTGAGGTTAGCCATTGAACTTCTCGAAAGTAACATTGAATTGTTTGATGCATGATGGT
TAATGTTTGAATAAAAGTTTACTTTATGTTCGTTTTCGAGGTTAGTTAGGTAGTGTATTA
Found at i:42415639 original size:31 final size:31
Alignment explanation
Indices: 42415589--42415664 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
42415579 GATTTAGTCT
*
42415589 TTGTAC-TTT-AATTTGGTCAATTTTAATCC
1 TTGTACTTTTCAAATTGGTCAATTTTAATCC
* *
42415618 TTGTACTTTTCGAATTGGTCAATTTTAGTCC
1 TTGTACTTTTCAAATTGGTCAATTTTAATCC
42415649 TTGTACTTTTCAAATT
1 TTGTACTTTTCAAATT
42415665 CTTTTAGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 6 0.15
30 3 0.07
31 32 0.78
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.51
Consensus pattern (31 bp):
TTGTACTTTTCAAATTGGTCAATTTTAATCC
Found at i:42423810 original size:5 final size:5
Alignment explanation
Indices: 42423800--42423841 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
42423790 AGTTTATAAC
*
42423800 ATATT ATATT ATATT ATATT ATA-T ATATT -TTTT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
42423842 AATTTATAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 7 0.21
5 26 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATATT
Found at i:42423836 original size:18 final size:17
Alignment explanation
Indices: 42423813--42423846 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
42423803 TTATATTATA
42423813 TTATATTATATATATTTT
1 TTATATTATATA-ATTTT
42423831 TTATATTATATAATTT
1 TTATATTATATAATTT
42423847 ATAACACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTATATAATTTT
Found at i:42423857 original size:28 final size:28
Alignment explanation
Indices: 42423803--42423857 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
42423793 TTATAACATA
* * *
42423803 TTATATTATATTATATTATATATATTTT
1 TTATATTATATAATATTATACACATTTT
42423831 TTATATTATATAAT-TTATAACACATTT
1 TTATATTATATAATATTAT-ACACATTT
42423858 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TTATATTATATAATATTATACACATTTT
Found at i:42424431 original size:36 final size:36
Alignment explanation
Indices: 42424390--42424461 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
42424380 CTTTAGACAA
42424390 AACTCTTTTAATGTTATTTTTTCCATTCACAAAATT
1 AACTCTTTTAATGTTATTTTTTCCATTCACAAAATT
*
42424426 AACTCTTTTAATGTTATTTTTTCGATTCACAAAATT
1 AACTCTTTTAATGTTATTTTTTCCATTCACAAAATT
42424462 TTAAAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (36 bp):
AACTCTTTTAATGTTATTTTTTCCATTCACAAAATT
Found at i:42428796 original size:8 final size:7
Alignment explanation
Indices: 42428756--42428795 Score: 71
Period size: 7 Copynumber: 5.6 Consensus size: 7
42428746 CATGCTATTT
42428756 TTTTGAA
1 TTTTGAA
42428763 TTTTGAA
1 TTTTGAA
42428770 TTTTGAA
1 TTTTGAA
42428777 TTTTGAA
1 TTTTGAA
42428784 TTTTTGAA
1 -TTTTGAA
42428792 TTTT
1 TTTT
42428796 TATCATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 25 0.78
8 7 0.22
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TTTTGAA
Found at i:42431589 original size:16 final size:16
Alignment explanation
Indices: 42431570--42431604 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
42431560 TGTATCTTTG
*
42431570 ATTGATATAATCTTCA
1 ATTGAAATAATCTTCA
42431586 ATTGAAATAATCTTCA
1 ATTGAAATAATCTTCA
42431602 ATT
1 ATT
42431605 CTGACTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTGAAATAATCTTCA
Found at i:42436610 original size:2 final size:2
Alignment explanation
Indices: 42436603--42436640 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
42436593 GTATTTAGTT
42436603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42436641 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42455423 original size:75 final size:75
Alignment explanation
Indices: 42455333--42455471 Score: 269
Period size: 75 Copynumber: 1.9 Consensus size: 75
42455323 TAAAAGAATG
42455333 TAAATCCTAAAATGAGAATCTTTTTACTTTGTAGGATTAAATATCAAAATCAAAAGAATGTAAAA
1 TAAATCCTAAAATGAGAATCTTTTTACTTTGTAGGATTAAATATCAAAATCAAAAGAATGTAAAA
42455398 TGTAAATCAT
66 TGTAAATCAT
*
42455408 TAAATCCTAAAATGAGAATCTTTTTACTTTGTAGGATTAAATATCAAAATTAAAAGAATGTAAA
1 TAAATCCTAAAATGAGAATCTTTTTACTTTGTAGGATTAAATATCAAAATCAAAAGAATGTAAA
42455472 TCACATCATG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.34
Consensus pattern (75 bp):
TAAATCCTAAAATGAGAATCTTTTTACTTTGTAGGATTAAATATCAAAATCAAAAGAATGTAAAA
TGTAAATCAT
Found at i:42469392 original size:59 final size:58
Alignment explanation
Indices: 42469325--42469435 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 58
42469315 TAAAGGTTTA
42469325 ATTAAAATTTTCAAAACTTGTAGA-GGGCTTAATAAGAAATTTCAAAAAAATTGGGGGTG
1 ATTAAAATTTT-AAAACTTGTAGAGGGGCTTAATAAGAAA-TTCAAAAAAATTGGGGGTG
** * * * *
42469384 ATTAAAATTTTTTAATTTTTTGAGGGGCTTAATAAGAAATTCTAAAAAATTG
1 ATTAAAATTTTAAAACTTGTAGAGGGGCTTAATAAGAAATTCAAAAAAATTG
42469436 AAAGGCCTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
58 19 0.42
59 26 0.58
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.36
Consensus pattern (58 bp):
ATTAAAATTTTAAAACTTGTAGAGGGGCTTAATAAGAAATTCAAAAAAATTGGGGGTG
Found at i:42469633 original size:13 final size:13
Alignment explanation
Indices: 42469615--42469641 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42469605 ATATGGTGAG
42469615 TCAAAAAAGACGT
1 TCAAAAAAGACGT
42469628 TCAAAAAAGACGT
1 TCAAAAAAGACGT
42469641 T
1 T
42469642 TATAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (13 bp):
TCAAAAAAGACGT
Found at i:42472344 original size:19 final size:20
Alignment explanation
Indices: 42472312--42472363 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
42472302 TATTGATATT
* *
42472312 AAACACAT-TAAAATGATCG
1 AAACACATCGAAATTGATCG
42472331 AAACACATCGAAATTTTGATCG
1 AAACACATCGAAA--TTGATCG
*
42472353 AAACACTTCGA
1 AAACACATCGA
42472364 TATTAACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.30
20 3 0.11
22 16 0.59
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (20 bp):
AAACACATCGAAATTGATCG
Found at i:42473855 original size:73 final size:74
Alignment explanation
Indices: 42473760--42473907 Score: 289
Period size: 73 Copynumber: 2.0 Consensus size: 74
42473750 ACTTTATTTT
42473760 AATTATTATTATATATTCAATTTGGTGAAATATATTATAATTGGTATTAAATAATATTAATTTTA
1 AATTATTATTATATATTCAATTTGGTGAAATATATTATAATTGGTATTAAATAATATTAATTTTA
42473825 TGTTAGAAA
66 TGTTAGAAA
42473834 AATTATTATTA-ATATTCAATTTGGTGAAATATATTATAATTGGTATTAAATAATATTAATTTTA
1 AATTATTATTATATATTCAATTTGGTGAAATATATTATAATTGGTATTAAATAATATTAATTTTA
42473898 TGTTAGAAA
66 TGTTAGAAA
42473907 A
1 A
42473908 TAAAGGAATG
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 63 0.85
74 11 0.15
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (74 bp):
AATTATTATTATATATTCAATTTGGTGAAATATATTATAATTGGTATTAAATAATATTAATTTTA
TGTTAGAAA
Found at i:42474108 original size:17 final size:20
Alignment explanation
Indices: 42474080--42474123 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
42474070 GCAAATAATT
*
42474080 TAAAAATAATAAATA-TTCA
1 TAAAAATAATAAAAAGTTCA
42474099 -AAAAAT-ATAAAAAGTTCA
1 TAAAAATAATAAAAAGTTCA
42474117 TAAAAAT
1 TAAAAAT
42474124 TTCAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
19 6 0.27
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAAATAATAAAAAGTTCA
Found at i:42477434 original size:16 final size:16
Alignment explanation
Indices: 42477413--42477446 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42477403 ATTCATATAT
42477413 ATGTATGTATGTATGC
1 ATGTATGTATGTATGC
*
42477429 ATGTATGTTTGTATGC
1 ATGTATGTATGTATGC
42477445 AT
1 AT
42477447 ACACTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (16 bp):
ATGTATGTATGTATGC
Found at i:42483321 original size:59 final size:60
Alignment explanation
Indices: 42483184--42483329 Score: 208
Period size: 60 Copynumber: 2.5 Consensus size: 60
42483174 GTTAGCCGTG
* * * *
42483184 TGACCAAAAAAGACAGAATTA--AATAGTTGAGTGATTATTTTGTAATTTTTCATAGTTTGA
1 TGACCAAAAAAGA-A-ATTTACTAATAGTTGAATGATCATTTTGTAATTTTTCATAGTTGGA
*
42483244 TGACCAAAAAAGAAATTTACTAATAGTTGAATGATCATTTTGTATTTTTTCATAGTTGGA
1 TGACCAAAAAAGAAATTTACTAATAGTTGAATGATCATTTTGTAATTTTTCATAGTTGGA
42483304 TGACC-AAAAAGAAATTTACTAATAGT
1 TGACCAAAAAAGAAATTTACTAATAGT
42483330 AGGATTACTA
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
58 4 0.05
59 22 0.28
60 53 0.67
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (60 bp):
TGACCAAAAAAGAAATTTACTAATAGTTGAATGATCATTTTGTAATTTTTCATAGTTGGA
Found at i:42483564 original size:22 final size:20
Alignment explanation
Indices: 42483539--42483587 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
42483529 TCACCACTTG
42483539 AATTTTTTTAAAATATATTTA
1 AATTTTTTTAAAATAT-TTTA
* * *
42483560 TAATTTCTTTATAATCTTTTA
1 -AATTTTTTTAAAATATTTTA
42483581 AATTTTT
1 AATTTTT
42483588 AGGTGATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.26
21 4 0.17
22 13 0.57
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTTTTAAAATATTTTA
Found at i:42485588 original size:2 final size:2
Alignment explanation
Indices: 42485581--42485609 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42485571 CATGTATTTC
42485581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42485610 CAAGTAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42487720 original size:23 final size:23
Alignment explanation
Indices: 42487684--42487729 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42487674 ATTTTAAATT
* *
42487684 ATTTTAAATTAAATTTAATAAAA
1 ATTTTAAATAAAATTCAATAAAA
*
42487707 ATTTTAAGTAAAATTCAATAAAA
1 ATTTTAAATAAAATTCAATAAAA
42487730 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTTTAAATAAAATTCAATAAAA
Found at i:42487993 original size:17 final size:17
Alignment explanation
Indices: 42487971--42488003 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42487961 ATATTTAATA
42487971 TATATTTAATTAAAAAG
1 TATATTTAATTAAAAAG
*
42487988 TATATTTGATTAAAAA
1 TATATTTAATTAAAAA
42488004 TAAAAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
TATATTTAATTAAAAAG
Found at i:42488599 original size:22 final size:21
Alignment explanation
Indices: 42488558--42488600 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
42488548 TAAAAGGATC
42488558 TAAAAAAATATTTAGTAAAAAA
1 TAAAAAAATATTTAG-AAAAAA
42488580 TAAAAAAAGTAATTTA-AAAAA
1 TAAAAAAA-T-ATTTAGAAAAA
42488601 TTATTTCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.68
23 1 0.05
24 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
TAAAAAAATATTTAGAAAAAA
Found at i:42494664 original size:49 final size:49
Alignment explanation
Indices: 42494611--42494718 Score: 207
Period size: 49 Copynumber: 2.2 Consensus size: 49
42494601 CAGAGTGGAA
*
42494611 CTGTTCTTCAGTTCTCAGGATTTTTTCACGGACATTGGACATTGTTTAT
1 CTGTTCTTCAGTTCTCAGGATTTTTTCACAGACATTGGACATTGTTTAT
42494660 CTGTTCTTCAGTTCTCAGGATTTTTTCACAGACATTGGACATTGTTTAT
1 CTGTTCTTCAGTTCTCAGGATTTTTTCACAGACATTGGACATTGTTTAT
42494709 CTGTTCTTCA
1 CTGTTCTTCA
42494719 AAGGCATAGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 58 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (49 bp):
CTGTTCTTCAGTTCTCAGGATTTTTTCACAGACATTGGACATTGTTTAT
Found at i:42498549 original size:6 final size:6
Alignment explanation
Indices: 42498538--42498579 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
42498528 AAAATGAAAC
* * *
42498538 AAATTA AAATTA AGATTA AGATTA AAATTA TAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
42498580 GACAGCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (6 bp):
AAATTA
Found at i:42502895 original size:228 final size:229
Alignment explanation
Indices: 42502489--42502945 Score: 907
Period size: 228 Copynumber: 2.0 Consensus size: 229
42502479 CAATAAAAAA
42502489 TTAAAAATAAAATATTTATTTTTATTATTTATTATTTTATATTAATGATGTGTTTTCTTATTATT
1 TTAAAAATAAAATATTTATTTTTATTATTTATTATTTTATATTAATGATGTGTTTTCTTATTATT
42502554 TATCAATGATGCATAAAATTTATCATATATTAATTTAATTGTAAAATATTTTTTTATACTATGGA
66 TATCAATGATGCATAAAATTTATCATATATTAATTTAATTGTAAAATATTTTTTTATACTATGGA
42502619 TGTGAAATGAATCAAATTTCAATGTTTTAATGTATTTTTTTAACAAACAACATTTAATCTTTAAA
131 TGTGAAATGAATCAAATTTCAATGTTTTAATGTATTTTTTTAACAAACAACATTTAATCTTTAAA
42502684 TTTATCTTTATTATGGTAAATAAAGTTTAGTTAG
196 TTTATCTTTATTATGGTAAATAAAGTTTAGTTAG
42502718 TTAAAAAT-AAATATTTATTTTTATTATTTATTATTTTATATTAATGATGTGTTTTCTTATTATT
1 TTAAAAATAAAATATTTATTTTTATTATTTATTATTTTATATTAATGATGTGTTTTCTTATTATT
42502782 TATCAATGATGCATAAAATTTATCATATATTAATTTAATTGTAAAATATTTTTTTATACTATGGA
66 TATCAATGATGCATAAAATTTATCATATATTAATTTAATTGTAAAATATTTTTTTATACTATGGA
42502847 TGTGAAATGAATCAAATTTCAATGTTTTAATGTATTTTTTTAACAAACAACATTTAATCTTTAAA
131 TGTGAAATGAATCAAATTTCAATGTTTTAATGTATTTTTTTAACAAACAACATTTAATCTTTAAA
42502912 TTTATCTTTATTATGGTAAATAAAGTTTAGTTAG
196 TTTATCTTTATTATGGTAAATAAAGTTTAGTTAG
42502946 ATTTGAACTA
Statistics
Matches: 228, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
228 220 0.96
229 8 0.04
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (229 bp):
TTAAAAATAAAATATTTATTTTTATTATTTATTATTTTATATTAATGATGTGTTTTCTTATTATT
TATCAATGATGCATAAAATTTATCATATATTAATTTAATTGTAAAATATTTTTTTATACTATGGA
TGTGAAATGAATCAAATTTCAATGTTTTAATGTATTTTTTTAACAAACAACATTTAATCTTTAAA
TTTATCTTTATTATGGTAAATAAAGTTTAGTTAG
Found at i:42514763 original size:3 final size:3
Alignment explanation
Indices: 42514757--42514783 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42514747 TCTTAAATAA
42514757 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
42514784 TACATACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42520770 original size:30 final size:30
Alignment explanation
Indices: 42520736--42520800 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
42520726 CGAATATAAT
42520736 AAATATATATTTTTTA-ATTTTTTAATTTTA
1 AAATATATA-TTTTTACATTTTTTAATTTTA
* *
42520766 AAATATATATTTTTACTTTTTTTATTTTTA
1 AAATATATATTTTTACATTTTTTAATTTTA
42520796 AAATA
1 AAATA
42520801 AAATTTTCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
AAATATATATTTTTACATTTTTTAATTTTA
Found at i:42521603 original size:22 final size:23
Alignment explanation
Indices: 42521554--42521603 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
42521544 AATCATATTG
*
42521554 ATAATAAAAATAAAATTGAATCT
1 ATAATTAAAATAAAATTGAATCT
* *
42521577 A-AATTAAAATAAATTTTAAT-T
1 ATAATTAAAATAAAATTGAATCT
42521598 ATAATT
1 ATAATT
42521604 TACGTATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 20 0.87
23 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
ATAATTAAAATAAAATTGAATCT
Found at i:42528343 original size:23 final size:23
Alignment explanation
Indices: 42528316--42528362 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
42528306 ATTATACAAG
*
42528316 AATGGTTAGGTTTTAGTTTTAAT
1 AATGGTTAGATTTTAGTTTTAAT
42528339 AATGGTTAGATTTTAGTTTTAAT
1 AATGGTTAGATTTTAGTTTTAAT
42528362 A
1 A
42528363 CTTATATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (23 bp):
AATGGTTAGATTTTAGTTTTAAT
Found at i:42528816 original size:30 final size:30
Alignment explanation
Indices: 42528754--42528820 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
42528744 AAAAATTGAA
*
42528754 TGACTAAAATGAAAAAAAACTAATAGTTAGG
1 TGACTAAAAT-AAAAAAAACTAATAGTCAGG
*
42528785 TGACTAAAAT-AAAACAACTGAATAGTCAGG
1 TGACTAAAATAAAAAAAACT-AATAGTCAGG
42528815 TGACTA
1 TGACTA
42528821 TTCTTATACT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 8 0.24
30 15 0.45
31 10 0.30
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.22
Consensus pattern (30 bp):
TGACTAAAATAAAAAAAACTAATAGTCAGG
Found at i:42529026 original size:23 final size:23
Alignment explanation
Indices: 42528981--42529026 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
42528971 AATTTAATTG
*
42528981 TTAATTCAGTTAATGTTATTTTT
1 TTAATTCAGTTAATGTAATTTTT
* *
42529004 TTAATTC-GTTAGTGTAATATTT
1 TTAATTCAGTTAATGTAATTTTT
42529026 T
1 T
42529027 GAAATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (23 bp):
TTAATTCAGTTAATGTAATTTTT
Found at i:42530568 original size:31 final size:31
Alignment explanation
Indices: 42530533--42530592 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
42530523 GTAACAACCC
*
42530533 AATGACTTAAATAAAAATTTTTGAATAGTCA
1 AATGACTTAAATAAAAATTTTCGAATAGTCA
*
42530564 AATGACTTAAATGAAAATTTTCGAATAGT
1 AATGACTTAAATAAAAATTTTCGAATAGT
42530593 TCAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (31 bp):
AATGACTTAAATAAAAATTTTCGAATAGTCA
Found at i:42536895 original size:4 final size:4
Alignment explanation
Indices: 42536886--42536923 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
42536876 AACCTCATCA
42536886 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
42536924 TGCATTACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:42541034 original size:15 final size:15
Alignment explanation
Indices: 42541016--42541059 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
42541006 CATCAAAATA
*
42541016 ATCATCATCATCTCC
1 ATCATCATCACCTCC
42541031 ATCATCATCACCTCC
1 ATCATCATCACCTCC
42541046 ATC-TC--CACCTCC
1 ATCATCATCACCTCC
42541058 AT
1 AT
42541060 GATTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
14 2 0.07
15 17 0.61
ACGTcount: A:0.25, C:0.45, G:0.00, T:0.30
Consensus pattern (15 bp):
ATCATCATCACCTCC
Found at i:42542650 original size:5 final size:5
Alignment explanation
Indices: 42542640--42542665 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42542630 TACAAGCCAG
42542640 ACCCA ACCCA ACCCA ACCCA ACCCA A
1 ACCCA ACCCA ACCCA ACCCA ACCCA A
42542666 TCAGATTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.58, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCA
Found at i:42554631 original size:11 final size:11
Alignment explanation
Indices: 42554589--42554629 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
42554579 TGTTTTCTCC
42554589 CTATTTTGCTA
1 CTATTTTGCTA
*
42554600 CTATTTTACTA
1 CTATTTTGCTA
* *
42554611 CTATGTTGTTA
1 CTATTTTGCTA
42554622 CTATTTTG
1 CTATTTTG
42554630 TTGTTATTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:42558473 original size:6 final size:6
Alignment explanation
Indices: 42558462--42558496 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
42558452 CAAACATTAC
42558462 ATACAT ATACAT ATACAT ATACAT ATACAT ATACA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACA
42558497 AAGAAAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (6 bp):
ATACAT
Found at i:42565716 original size:9 final size:10
Alignment explanation
Indices: 42565700--42565783 Score: 74
Period size: 9 Copynumber: 8.9 Consensus size: 10
42565690 TTTTGGTTAA
42565700 AAATTACCCG
1 AAATTACCCG
*
42565710 -GATTACCCG
1 AAATTACCCG
42565719 AAATTACCCG
1 AAATTACCCG
*
42565729 --A-TAACCG
1 AAATTACCCG
*
42565736 -AATTAACCG
1 AAATTACCCG
42565745 -AATTACCCG
1 AAATTACCCG
42565754 AAAATTACCC-
1 -AAATTACCCG
42565764 AAATTACCCG
1 AAATTACCCG
42565774 AAAATTACCC
1 -AAATTACCC
42565784 AAAAAATTCG
Statistics
Matches: 63, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
7 5 0.08
8 2 0.03
9 31 0.49
10 8 0.13
11 17 0.27
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (10 bp):
AAATTACCCG
Found at i:42565768 original size:20 final size:20
Alignment explanation
Indices: 42565699--42565786 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 20
42565689 TTTTTGGTTA
**
42565699 AAAATTACCCGGATTACCCG
1 AAAATTACCCAAATTACCCG
* *
42565719 -AAATTACCC-GA-TAACCG
1 AAAATTACCCAAATTACCCG
* *
42565736 --AATTAACCGAATTACCCG
1 AAAATTACCCAAATTACCCG
42565754 AAAATTACCCAAATTACCCG
1 AAAATTACCCAAATTACCCG
42565774 AAAATTACCCAAA
1 AAAATTACCCAAA
42565787 AAATTCGGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
16 7 0.12
17 6 0.10
18 7 0.12
19 9 0.16
20 29 0.50
ACGTcount: A:0.43, C:0.28, G:0.09, T:0.19
Consensus pattern (20 bp):
AAAATTACCCAAATTACCCG
Found at i:42565788 original size:11 final size:11
Alignment explanation
Indices: 42565745--42565787 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
42565735 GAATTAACCG
42565745 AATTACCCGAA
1 AATTACCCGAA
42565756 AATTACCC--A
1 AATTACCCGAA
42565765 AATTACCCGAA
1 AATTACCCGAA
42565776 AATTACCC-AA
1 AATTACCCGAA
42565786 AA
1 AA
42565788 AATTCGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.30
10 4 0.13
11 17 0.57
ACGTcount: A:0.49, C:0.28, G:0.05, T:0.19
Consensus pattern (11 bp):
AATTACCCGAA
Found at i:42567861 original size:1 final size:1
Alignment explanation
Indices: 42567855--42567888 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
42567845 AGATAGCCTC
42567855 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42567889 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:42568164 original size:1 final size:1
Alignment explanation
Indices: 42568160--42568184 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
42568150 TAAATAGCCC
42568160 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
42568185 CCTTTTCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:42571818 original size:2 final size:2
Alignment explanation
Indices: 42571811--42571836 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42571801 ATTCATATGT
42571811 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
42571837 GGTTGAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42572371 original size:21 final size:21
Alignment explanation
Indices: 42572347--42572398 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
42572337 ATTTAAATAG
42572347 TTTAATAACTTAAATAA-AATT
1 TTTAATAACTTAAATAATAA-T
*
42572368 TTTAAATAA-TTCAATAATAAT
1 TTT-AATAACTTAAATAATAAT
42572389 TTT-ATAACTT
1 TTTAATAACTT
42572399 TTTAAAGTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.15
20 2 0.07
21 14 0.52
22 7 0.26
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAATAACTTAAATAATAAT
Found at i:42572374 original size:30 final size:31
Alignment explanation
Indices: 42572318--42572384 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
42572308 TTTAACAGTC
* * *
42572318 CAATGACTTTAATAAAATAATTTAAATAGTT
1 CAATAACTTAAATAAAATAATTTAAATAATT
* *
42572349 TAATAACTTAAATAAAAT-TTTTAAATAATT
1 CAATAACTTAAATAAAATAATTTAAATAATT
42572379 CAATAA
1 CAATAA
42572385 TAATTTTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (31 bp):
CAATAACTTAAATAAAATAATTTAAATAATT
Found at i:42572375 original size:22 final size:22
Alignment explanation
Indices: 42572350--42572391 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
42572340 TAAATAGTTT
42572350 AATAACTTAAATAA-AATTTTTA
1 AATAA-TTAAATAATAATTTTTA
*
42572372 AATAATTCAATAATAATTTT
1 AATAATTAAATAATAATTTT
42572392 ATAACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAATTAAATAATAATTTTTA
Found at i:42575532 original size:14 final size:15
Alignment explanation
Indices: 42575504--42575540 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
42575494 ATAAAATTTC
*
42575504 AAAGTAATT-TTAAT
1 AAAGTATTTCTTAAT
42575518 AAA-TATTTCTTAAT
1 AAAGTATTTCTTAAT
42575532 AAAGTATTT
1 AAAGTATTT
42575541 TTCATGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (15 bp):
AAAGTATTTCTTAAT
Found at i:42581667 original size:4 final size:4
Alignment explanation
Indices: 42581660--42581693 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
42581650 GGTACGTACG
*
42581660 TACA TACA TACA TACA TACA TACA TATA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
42581694 TGTGTCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (4 bp):
TACA
Found at i:42582467 original size:19 final size:18
Alignment explanation
Indices: 42582428--42582462 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42582418 ATAATAGTAT
42582428 TTAAAATTTAATTATTAAA
1 TTAAAATTT-ATTATTAAA
42582447 TTAAAATTT-TTATTAA
1 TTAAAATTTATTATTAA
42582463 CAATTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAAATTTATTATTAAA
Found at i:42600110 original size:29 final size:30
Alignment explanation
Indices: 42600072--42600150 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 30
42600062 AAATTAAAAA
*
42600072 TTAATATATAGTAAAATTATATTTTAA-CCT
1 TTAA-ATATAGTAAAATTATATTTAAATCCT
** * * **
42600102 TTAAATATAAAAAAAATCTATTTAAATTTT
1 TTAAATATAGTAAAATTATATTTAAATCCT
42600132 TTAAA-ATAGTAAAATTATA
1 TTAAATATAGTAAAATTATA
42600151 AAATTATATT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (30 bp):
TTAAATATAGTAAAATTATATTTAAATCCT
Found at i:42600423 original size:21 final size:21
Alignment explanation
Indices: 42600399--42600443 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42600389 ATTTTTTTTT
* * *
42600399 ATTTAAATTATTTAAAGTAAA
1 ATTTAAATTAATAAAAATAAA
*
42600420 ATTTTAATTAATAAAAATAAA
1 ATTTAAATTAATAAAAATAAA
42600441 ATT
1 ATT
42600444 ATACTTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATTTAAATTAATAAAAATAAA
Found at i:42604948 original size:2 final size:2
Alignment explanation
Indices: 42604936--42604982 Score: 67
Period size: 2 Copynumber: 22.5 Consensus size: 2
42604926 TGATGTTGCA
*
42604936 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT
42604980 AT A
1 AT A
42604983 ACGAAATCTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 37 0.90
3 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42605056 original size:2 final size:2
Alignment explanation
Indices: 42605044--42605090 Score: 67
Period size: 2 Copynumber: 22.5 Consensus size: 2
42605034 TGATGTTGCA
*
42605044 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT
42605088 AT A
1 AT A
42605091 ACGAAATCTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 37 0.90
3 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42605104 original size:108 final size:108
Alignment explanation
Indices: 42604915--42605130 Score: 423
Period size: 108 Copynumber: 2.0 Consensus size: 108
42604905 GTCGTGCATG
42604915 CAGGTGTTGCCTGATGTTGCAATATGTATATATATATATATATATATATATATATATGATATGAT
1 CAGGTGTTGCCTGATGTTGCAATATGTATATATATATATATATATATATATATATATGATATGAT
*
42604980 ATAACGAAATCTGATAATGTTCCTGACTCCTAAAATGAAAGGA
66 ATAACGAAATCTGATAATGTTCCTGAATCCTAAAATGAAAGGA
42605023 CAGGTGTTGCCTGATGTTGCAATATGTATATATATATATATATATATATATATATATGATATGAT
1 CAGGTGTTGCCTGATGTTGCAATATGTATATATATATATATATATATATATATATATGATATGAT
42605088 ATAACGAAATCTGATAATGTTCCTGAATCCTAAAATGAAAGGA
66 ATAACGAAATCTGATAATGTTCCTGAATCCTAAAATGAAAGGA
42605131 ATTGATGGAG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (108 bp):
CAGGTGTTGCCTGATGTTGCAATATGTATATATATATATATATATATATATATATATGATATGAT
ATAACGAAATCTGATAATGTTCCTGAATCCTAAAATGAAAGGA
Found at i:42615122 original size:33 final size:33
Alignment explanation
Indices: 42615081--42615147 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
42615071 GATATATTTT
*
42615081 ATTCTATTATATTTGAAATATTATATTTTAATC
1 ATTCTATTATATTTAAAATATTATATTTTAATC
*
42615114 ATTCTATTATATTTAAAATGTTATATTTTAATC
1 ATTCTATTATATTTAAAATATTATATTTTAATC
42615147 A
1 A
42615148 CTTATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (33 bp):
ATTCTATTATATTTAAAATATTATATTTTAATC
Found at i:42646893 original size:33 final size:32
Alignment explanation
Indices: 42646856--42646975 Score: 123
Period size: 33 Copynumber: 3.7 Consensus size: 32
42646846 TAAGAGGCTA
* * *
42646856 GAAGAAGAGGAGCATGAAGGAGCAATAAAACAC
1 GAAGAAGAGGAGCAGGAAGAAGGAAT-AAACAC
* * * **
42646889 GAAGAAGAGGAACGGGTAGAAGGAATCAAACGT
1 GAAGAAGAGGAGCAGGAAGAAGGAAT-AAACAC
42646922 GAAGAAGAGGAGCAGGAAGAAGGAAGTAAACAC
1 GAAGAAGAGGAGCAGGAAGAAGGAA-TAAACAC
* *
42646955 GAAGAAGAGGAGGAAGAAGAA
1 GAAGAAGAGGAGCAGGAAGAA
42646976 ACAAACAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
33 69 0.99
34 1 0.01
ACGTcount: A:0.51, C:0.08, G:0.36, T:0.05
Consensus pattern (32 bp):
GAAGAAGAGGAGCAGGAAGAAGGAATAAACAC
Found at i:42646985 original size:66 final size:66
Alignment explanation
Indices: 42646856--42646995 Score: 160
Period size: 66 Copynumber: 2.1 Consensus size: 66
42646846 TAAGAGGCTA
* * * ** * *
42646856 GAAGAAGAGGAGCATGAAGGAGCAATAAAACACGAAGAAGAGGAACGGGTAGAAGGAATCAAACG
1 GAAGAAGAGGAGCAGGAAGAAGCAATAAAACACGAAGAAGAGGAACGGGAAGAAACAAACAAACA
42646921 T
66 T
*
42646922 GAAGAAGAGGAGCAGGAAGAAGGAAGT-AAACACGAAGAAGAGG-A-GGAAGAAGAAACAAACAA
1 GAAGAAGAGGAGCAGGAAGAAGCAA-TAAAACACGAAGAAGAGGAACGG--GAAGAAACAAACAA
42646984 ACAT
63 ACAT
42646988 GAAGAAGA
1 GAAGAAGA
42646996 AGAAGAGGCT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
64 2 0.03
65 1 0.02
66 59 0.94
67 1 0.02
ACGTcount: A:0.53, C:0.09, G:0.33, T:0.05
Consensus pattern (66 bp):
GAAGAAGAGGAGCAGGAAGAAGCAATAAAACACGAAGAAGAGGAACGGGAAGAAACAAACAAACA
T
Found at i:42646986 original size:33 final size:33
Alignment explanation
Indices: 42646856--42646995 Score: 93
Period size: 33 Copynumber: 4.2 Consensus size: 33
42646846 TAAGAGGCTA
* * *
42646856 GAAGAAGAGGAGCATGAAGGAGCAATA-AAACAC
1 GAAGAAGAGGAGCAAGAAGAAACAA-ACAAACAC
* ** * ** * **
42646889 GAAGAAGAGGAACGGGTAGAAGGAATCAAACGT
1 GAAGAAGAGGAGCAAGAAGAAACAAACAAACAC
* ** **
42646922 GAAGAAGAGGAGCAGGAAGAAGGAAGTAAACAC
1 GAAGAAGAGGAGCAAGAAGAAACAAACAAACAC
* *
42646955 GAAGAAGAGGAGGAAGAAGAAACAAACAAACAT
1 GAAGAAGAGGAGCAAGAAGAAACAAACAAACAC
42646988 GAAGAAGA
1 GAAGAAGA
42646996 AGAAGAGGCT
Statistics
Matches: 83, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
33 83 1.00
ACGTcount: A:0.53, C:0.09, G:0.33, T:0.05
Consensus pattern (33 bp):
GAAGAAGAGGAGCAAGAAGAAACAAACAAACAC
Found at i:42652311 original size:18 final size:18
Alignment explanation
Indices: 42652265--42652314 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
42652255 AACCCGAAAT
* *
42652265 CTGATCCTGATCCGGATC
1 CTGATCCTGACCCGGAAC
* *
42652283 CTGGTCTTGACCCGGAAC
1 CTGATCCTGACCCGGAAC
*
42652301 GTGATCCTGACCCG
1 CTGATCCTGACCCG
42652315 AAATCACCAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.24
Consensus pattern (18 bp):
CTGATCCTGACCCGGAAC
Found at i:42662665 original size:17 final size:18
Alignment explanation
Indices: 42662640--42662676 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
42662630 TTATTTAAAA
42662640 ATTATAAAT-ATATAAATT
1 ATTATAAATAATA-AAATT
42662658 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
42662675 AT
1 AT
42662677 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:42664708 original size:150 final size:152
Alignment explanation
Indices: 42664513--42664814 Score: 518
Period size: 150 Copynumber: 2.0 Consensus size: 152
42664503 AATGGACTAA
42664513 ATTGAAATTCTAGCATTTGGGGGGGGGGGGGCAAACTATAATTTTACCATATATTAACTTGAGAT
1 ATTGAAATTCTAGCATTTGGGGGGGGGGGGGCAAACTATAATTTTACCATATATTAACTTGAGAT
* * *
42664578 TTTATAAAATTTGGGTGACTAAAGTAGCTATTTTCCATTTTGGAGGGGACAATGGCCTCTGTCTC
66 TTTATAAAATTTGGGTGACTAAAGTAGCAATTTTCCACTTTGGAGGGGACAAGGGCCTCTGTCTC
42664643 CCCCCTTCCCTTCGCCCCCTGC
131 CCCCCTTCCCTTCGCCCCCTGC
*
42664665 ATTGAAATTCTTGCA-TT-GGGGGGGGGGGGCAAACTATAATTTTACCATATATTAACTTGAGAT
1 ATTGAAATTCTAGCATTTGGGGGGGGGGGGGCAAACTATAATTTTACCATATATTAACTTGAGAT
* * *
42664728 TTTATAAATTTTTGGTGATTAAAGTAGCAATTTTCCACTTTGGAGGGGACAAGGGCCTCTGTCTC
66 TTTATAAAATTTGGGTGACTAAAGTAGCAATTTTCCACTTTGGAGGGGACAAGGGCCTCTGTCTC
*
42664793 TCCCCTTCCCTTCGCCCCCTGC
131 CCCCCTTCCCTTCGCCCCCTGC
42664815 TTGTATGTCT
Statistics
Matches: 142, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
150 126 0.89
151 2 0.01
152 14 0.10
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (152 bp):
ATTGAAATTCTAGCATTTGGGGGGGGGGGGGCAAACTATAATTTTACCATATATTAACTTGAGAT
TTTATAAAATTTGGGTGACTAAAGTAGCAATTTTCCACTTTGGAGGGGACAAGGGCCTCTGTCTC
CCCCCTTCCCTTCGCCCCCTGC
Found at i:42666832 original size:31 final size:31
Alignment explanation
Indices: 42666797--42666860 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
42666787 TTAACATAAT
*
42666797 ATGCAAATTAATCCTTTTATATTTGATAAAA
1 ATGCAAATCAATCCTTTTATATTTGATAAAA
42666828 ATGCAAATCAATCCTTTTATATTTGATAAAA
1 ATGCAAATCAATCCTTTTATATTTGATAAAA
42666859 AT
1 AT
42666861 TTCATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (31 bp):
ATGCAAATCAATCCTTTTATATTTGATAAAA
Found at i:42666945 original size:148 final size:149
Alignment explanation
Indices: 42666729--42667025 Score: 542
Period size: 148 Copynumber: 2.0 Consensus size: 149
42666719 AGGAACTTTG
* * **
42666729 AACTGTACATAAGCCAGACGTTGGGCCTTTTTTTTTTTTTTTTTTTTTTTTGTCTTTTTTAACAT
1 AACTGTACATAAGCCAGACGTTGGGCCTTTTTTTTTTTTTTTTCTTATGATGTCTTTTTTAACAT
42666794 AATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTTTTATATTTGATAAAA
66 AATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTTTTATATTTGATAAAA
42666859 ATTTCATTATTTTTATTGT
131 ATTTCATTATTTTTATTGT
*
42666878 AACTGTACAT-AGCCAGGCGTTGGGCCTTTTTTTTTTTTTTTTCTTATGATGTCTTTTTTAACAT
1 AACTGTACATAAGCCAGACGTTGGGCCTTTTTTTTTTTTTTTTCTTATGATGTCTTTTTTAACAT
42666942 AATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTTTTATATTTGATAAAA
66 AATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTTTTATATTTGATAAAA
42667007 ATTTCATTATTTTTATTGT
131 ATTTCATTATTTTTATTGT
42667026 TAGAAATTGG
Statistics
Matches: 143, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
148 133 0.93
149 10 0.07
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (149 bp):
AACTGTACATAAGCCAGACGTTGGGCCTTTTTTTTTTTTTTTTCTTATGATGTCTTTTTTAACAT
AATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTTTTATATTTGATAAAA
ATTTCATTATTTTTATTGT
Found at i:42666980 original size:31 final size:31
Alignment explanation
Indices: 42666945--42667008 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
42666935 TTAACATAAT
*
42666945 ATGCAAATTAATCCTTTTATATTTGATAAAA
1 ATGCAAATCAATCCTTTTATATTTGATAAAA
42666976 ATGCAAATCAATCCTTTTATATTTGATAAAA
1 ATGCAAATCAATCCTTTTATATTTGATAAAA
42667007 AT
1 AT
42667009 TTCATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (31 bp):
ATGCAAATCAATCCTTTTATATTTGATAAAA
Found at i:42667067 original size:148 final size:147
Alignment explanation
Indices: 42666779--42667067 Score: 350
Period size: 148 Copynumber: 2.0 Consensus size: 147
42666769 TTTTTTTTTT
42666779 TGTCTTTTTTAACATAATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTT
1 TGTCTTTTTTAACATAATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTT
* *** ** * ****
42666844 TTATATTTGATAAAAATTTCATTATTTTTATTGTAACTGTACATAGCCAGGCGTTGGGCCTTTTT
66 TTATATTTGATAAAAATTTCATTATTTTTATTGTAAC-GTAAATAGCCAGAAATTGAACATAAGG
* ***
42666909 TTTTTTTTTTTCTTATGA
130 TATAGGTTTTTCTTATGA
42666927 TGTCTTTTTTAACATAATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTT
1 TGTCTTTTTTAACATAATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTT
* * *
42666992 TTATATTTGATAAAAATTTCATTATTTTTATTGTTA-G-AAATTGGTCTCTATAAATT-AACATA
66 TTATATTTGATAAAAATTTCATTATTTTTATTGTAACGTAAA-TAG-C-C-AGAAATTGAACATA
42667054 AGGTATAGGTTTTT
127 AGGTATAGGTTTTT
42667068 TAATAAAAAT
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
145 2 0.02
146 3 0.03
147 1 0.01
148 110 0.92
149 3 0.03
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (147 bp):
TGTCTTTTTTAACATAATATGCAAATTAATCCTTTTATATTTGATAAAAATGCAAATCAATCCTT
TTATATTTGATAAAAATTTCATTATTTTTATTGTAACGTAAATAGCCAGAAATTGAACATAAGGT
ATAGGTTTTTCTTATGA
Found at i:42672908 original size:5 final size:5
Alignment explanation
Indices: 42672896--42672928 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
42672886 TAAAATGAAA
42672896 TAAA- TAAAC TAAAC TAAAC TAAAC TAAAC TAAA
1 TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAA
42672929 GAAATACCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAC
Found at i:42673531 original size:14 final size:15
Alignment explanation
Indices: 42673509--42673585 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
42673499 CAATCAAACA
42673509 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
42673523 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
42673538 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
42673558 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
42673572 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
42673586 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:42673550 original size:20 final size:20
Alignment explanation
Indices: 42673525--42673564 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42673515 AATATTTTCC
*
42673525 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
42673545 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
42673565 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:42673570 original size:34 final size:35
Alignment explanation
Indices: 42673513--42673579 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
42673503 CAAACACCAG
*
42673513 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
42673548 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
42673580 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:42677133 original size:30 final size:30
Alignment explanation
Indices: 42677097--42677165 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
42677087 TTAACATAGG
*
42677097 ATAAAATTACACTTTAA-CTCTTCTAAAAATA
1 ATAAAATTACA-TTTAATCCCTTC-AAAAATA
**
42677128 A-AAAATTTTATTTAATCCCTTCAAAAATA
1 ATAAAATTACATTTAATCCCTTCAAAAATA
42677157 ATAAAATTA
1 ATAAAATTA
42677166 TAAATTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 13 0.41
30 18 0.56
31 1 0.03
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (30 bp):
ATAAAATTACATTTAATCCCTTCAAAAATA
Found at i:42677408 original size:26 final size:26
Alignment explanation
Indices: 42677369--42677423 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
42677359 ACATTTAGAA
*
42677369 GAAAATCTCAAATCTACGAAGCCAATG
1 GAAAATCTAAAATCTACGAA-CCAATG
* *
42677396 GAAAA-CTAAAATCTAGGGACCAATG
1 GAAAATCTAAAATCTACGAACCAATG
42677421 GAA
1 GAA
42677424 TACAAGTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.36
26 11 0.44
27 5 0.20
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (26 bp):
GAAAATCTAAAATCTACGAACCAATG
Found at i:42677641 original size:31 final size:31
Alignment explanation
Indices: 42677606--42677702 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 31
42677596 GGTTAATTAA
*
42677606 AATTTGGTACCTAAATTTGATTTTAATATTC
1 AATTTGATACCTAAATTTGATTTTAATATTC
* * * **
42677637 AATTTGATACTTAAGTTT-TTCTTTTGT-TTC
1 AATTTGATACCTAAATTTGAT-TTTAATATTC
* * *
42677667 AATTTGATACGTGAATTTGGTTTTAATATTC
1 AATTTGATACCTAAATTTGATTTTAATATTC
42677698 AATTT
1 AATTT
42677703 AACACCTGTG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
30 23 0.45
31 28 0.55
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (31 bp):
AATTTGATACCTAAATTTGATTTTAATATTC
Found at i:42682320 original size:4 final size:4
Alignment explanation
Indices: 42682311--42682337 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
42682301 GGGTATATAT
42682311 GGAG GGAG GGAG GGAG GGAG GGAG GGA
1 GGAG GGAG GGAG GGAG GGAG GGAG GGA
42682338 TGAATAGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:42701094 original size:17 final size:18
Alignment explanation
Indices: 42701074--42701110 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
42701064 TATGTAATAC
*
42701074 ATATACAAATAATTT-AT
1 ATATAAAAATAATTTGAT
42701091 ATATAAAAATAATTTGAT
1 ATATAAAAATAATTTGAT
42701109 AT
1 AT
42701111 GTTTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
ATATAAAAATAATTTGAT
Found at i:42703306 original size:42 final size:42
Alignment explanation
Indices: 42703230--42703344 Score: 158
Period size: 42 Copynumber: 2.7 Consensus size: 42
42703220 TCGTGTTTAC
* *
42703230 TTTCTGTTTAGCTCTCACGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACCCTTATAGG
* * * *
42703272 TTTCCGTTCAGCTCTCACGAGTTTCTATTCAACCCTTATAGG
1 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACCCTTATAGG
* *
42703314 TTTCTGTTTTGCTCTCATGAGCTTCTGTTCA
1 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCA
42703345 GCCTTCGAGT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.43
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACCCTTATAGG
Found at i:42704182 original size:40 final size:39
Alignment explanation
Indices: 42704119--42704225 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 39
42704109 AGCTTTAGTG
* *
42704119 GCATTAGCGGCATTATTTTAAAAACGCCGCTATAGATCGA
1 GCATTAGCGGCGTT-TTTGAAAAACGCCGCTATAGATCGA
* *
42704159 GCATTAGCGGCGCTTTTTGAAAAATGCCGCTATAGGTCGA
1 GCATTAGCGGCG-TTTTTGAAAAACGCCGCTATAGATCGA
* * *
42704199 CCTTTAGCAGCGTTTTTCGAAAAACGC
1 GCATTAGCGGCGTTTTT-GAAAAACGC
42704226 AAACGCTGCA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
39 5 0.09
40 50 0.88
41 2 0.04
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (39 bp):
GCATTAGCGGCGTTTTTGAAAAACGCCGCTATAGATCGA
Found at i:42704502 original size:14 final size:15
Alignment explanation
Indices: 42704465--42704505 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
42704455 TACTATTTAA
* *
42704465 GGTTTATGGATTATG
1 GGTTTAGGGGTTATG
42704480 GGTTTAGGGGTTATG
1 GGTTTAGGGGTTATG
42704495 GG-TTAGGGGTT
1 GGTTTAGGGGTT
42704506 TACGGTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (15 bp):
GGTTTAGGGGTTATG
Found at i:42705072 original size:15 final size:15
Alignment explanation
Indices: 42705052--42705085 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
42705042 AAAATCATGA
42705052 TTAACGTCTCAATCT
1 TTAACGTCTCAATCT
42705067 TTAACGTCTCAATCT
1 TTAACGTCTCAATCT
42705082 TTAA
1 TTAA
42705086 TCTTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (15 bp):
TTAACGTCTCAATCT
Found at i:42705382 original size:12 final size:13
Alignment explanation
Indices: 42705351--42705385 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
42705341 AAACGGCGAT
42705351 TCTTATAACTTCTG
1 TCTTATAACTTC-G
42705365 TCTTATAACTTC-
1 TCTTATAACTTCG
42705377 TCTTATAAC
1 TCTTATAAC
42705386 AAAAAGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
14 12 0.57
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (13 bp):
TCTTATAACTTCG
Found at i:42705728 original size:2 final size:2
Alignment explanation
Indices: 42705721--42705748 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42705711 ATCGGTGTGG
42705721 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
42705749 TTAGTAAATC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42708162 original size:42 final size:42
Alignment explanation
Indices: 42708082--42708363 Score: 304
Period size: 42 Copynumber: 6.6 Consensus size: 42
42708072 CCTTGAATAC
* *
42708082 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTAT
1 AAAGG-GGTTGCTATGTGCTGATTCCATCGTATCTTTGATTAT
*
42708125 AAAAGGGGCTT-CTATGTGCTGATTCC-TCGTATCTTTGAATAT
1 -AAAGGGG-TTGCTATGTGCTGATTCCATCGTATCTTTGATTAT
* * *
42708167 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTAT
1 AAAGG-GGTTGCTATGTGCTGATTCCATCGTATCTTTGATTAT
* *
42708210 AAAAGGGGTTGATATGTGCTGATTCC--CAGTATCATTGATTAT
1 -AAAGGGGTTGCTATGTGCTGATTCCATC-GTATCTTTGATTAT
* * * * *
42708252 AGAGGTGGTTGCTAAGTGCTGATTCCATCGTAACCTTGATTTT
1 AAAGG-GGTTGCTATGTGCTGATTCCATCGTATCTTTGATTAT
* *
42708295 AAAAGGGGTTTCTATGTGCTGATTCC-TCGTATCCTTGATTAT
1 -AAAGGGGTTGCTATGTGCTGATTCCATCGTATCTTTGATTAT
*
42708337 AAGGGTGGTTGCTATGTGCTGATTCCA
1 AAAGG-GGTTGCTATGTGCTGATTCCA
42708364 CCATATATCA
Statistics
Matches: 202, Mismatches: 24, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
41 16 0.08
42 93 0.46
43 76 0.38
44 17 0.08
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (42 bp):
AAAGGGGTTGCTATGTGCTGATTCCATCGTATCTTTGATTAT
Found at i:42708217 original size:85 final size:84
Alignment explanation
Indices: 42708069--42708365 Score: 425
Period size: 85 Copynumber: 3.5 Consensus size: 84
42708059 TTAGAACGGA
*
42708069 TATCCTTGAATACAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTATAAAAGGGGC
1 TATCCTTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTATAAAAGGGG-
42708134 TTCTATGTGCTGATTCCTCG
65 TTCTATGTGCTGATTCCTCG
* *
42708154 TATCTTTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTATAAAAGGGGT
1 TATCCTTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTATAAAAGGGGT
*
42708219 TGATATGTGCTGATTCC-CAG
66 T-CTATGTGCTGATTCCTC-G
* * * * * * *
42708239 TATCATTGATTATAGAGGTGGTTGCTAAGTGCTGATTCCATCGTAACCTTGATTTTAAAAGGGGT
1 TATCCTTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTATAAAAGGGG-
42708304 TTCTATGTGCTGATTCCTCG
65 TTCTATGTGCTGATTCCTCG
* * *
42708324 TATCCTTGATTATAAGGGTGGTTGCTATGTGCTGATTCCACC
1 TATCCTTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACC
42708366 ATATATCATT
Statistics
Matches: 190, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
84 3 0.02
85 184 0.97
86 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (84 bp):
TATCCTTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTATAAAAGGGGT
TCTATGTGCTGATTCCTCG
Found at i:42709580 original size:27 final size:28
Alignment explanation
Indices: 42709550--42709608 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
42709540 TACTAGCAGG
42709550 CCTAA-ACCCACCCAAGC-CCAAACTAAA
1 CCTAATACCCA-CCAAGCTCCAAACTAAA
*
42709577 CCTAATACCCACCAAGCTCCAAACTAAC
1 CCTAATACCCACCAAGCTCCAAACTAAA
42709605 CCTA
1 CCTA
42709609 GCCCAGCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.41, C:0.44, G:0.03, T:0.12
Consensus pattern (28 bp):
CCTAATACCCACCAAGCTCCAAACTAAA
Found at i:42723819 original size:44 final size:44
Alignment explanation
Indices: 42723762--42723954 Score: 106
Period size: 44 Copynumber: 4.4 Consensus size: 44
42723752 TGAGGATTTT
* * *
42723762 AGATCTTATCTCCCTAAACGGTAGTGGAGCAGATCGAAGATGAC
1 AGATTTTACCTCCCTAAACGGTAGTGGAACAGATCGAAGATGAC
* * * * *
42723806 AGATTTTACCTCCCT-AAGGGTGCAGTGGAATACATTG-A-A-GCC
1 AGATTTTACCTCCCTAAACGGT--AGTGGAACAGATCGAAGATGAC
* *** * * * * * * ***
42723848 AGAATTTCTACTTCCCTGGGCCGCAGTGGAATAAATTGAGGATTTT
1 AG-ATTT-TACCTCCCTAAACGGTAGTGGAACAGATCGAAGATGAC
* * *
42723894 AGATCTTATCTCCCTAAACGGTAGTGGAGCAGATCGAAGATGAC
1 AGATTTTACCTCCCTAAACGGTAGTGGAACAGATCGAAGATGAC
42723938 AGATTTTACCTCCCTAA
1 AGATTTTACCTCCCTAA
42723955 GGGTGCAGTG
Statistics
Matches: 104, Mismatches: 37, Indels: 16
0.66 0.24 0.10
Matches are distributed among these distances:
42 4 0.04
43 23 0.22
44 60 0.58
45 15 0.14
46 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
AGATTTTACCTCCCTAAACGGTAGTGGAACAGATCGAAGATGAC
Found at i:42724021 original size:88 final size:88
Alignment explanation
Indices: 42723660--42724041 Score: 214
Period size: 88 Copynumber: 4.3 Consensus size: 88
42723650 GTAGTGGAGC
* * *
42723660 AGATCGAAGATGGCAGATTTTACCTCCCTAAGGTTGCAGTGGAATACATTGA-A-GCCAGAATTT
1 AGATTGAAGATGACAGATTTTACCTCCCTAAGGGTGCAGTGGAATACATTGAGATGCCAG-ATTT
42723723 CTACTTCCCTGGGCAGCAGTGGAAT
65 -TACTTCCCTGGGCAGCAGTGGAAT
* * *** * * * ** * * *
42723748 AAATTGAGGATTTTAGATCTTATCTCCCTAAACGGT--AGTGGAGCAGATCGAAGATGACAGATT
1 AGATTGAAGATGACAGATTTTACCTCCCT-AAGGGTGCAGTGGAATACATTG-AGATGCCAGATT
* *
42723811 TTACCTCCCTAAGGG-TGCAGTGGAAT
64 TTACTTCCCT--GGGCAGCAGTGGAAT
* * * * * ***
42723837 ACATTG-A-A-GCCAGAATTTCTACTTCCCT--GGGCCGCAGTGGAATAAATTGAGGATTTTAGA
1 AGATTGAAGATGACAG-ATTT-TACCTCCCTAAGGG-TGCAGTGGAATACATTGA-GATGCCAGA
* *** * * **
42723897 TCTTA-TCTCCCTAAACGGTAGTGGAGC
62 TTTTACT-TCCCTGGGCAGCAGTGGAAT
*
42723924 AGATCGAAGATGACAGATTTTACCTCCCTAAGGGTGCAGTGGAATACATTGA-A-GCCAGAATTT
1 AGATTGAAGATGACAGATTTTACCTCCCTAAGGGTGCAGTGGAATACATTGAGATGCCAG-ATTT
42723987 CTACTTCCCTGGGCAGCAGTGGAAT
65 -TACTTCCCTGGGCAGCAGTGGAAT
* * *
42724012 AGATTGAAGATTACAGATCTTATCTCCCTA
1 AGATTGAAGATGACAGATTTTACCTCCCTA
42724042 GGCAGTAGTG
Statistics
Matches: 208, Mismatches: 64, Indels: 44
0.66 0.20 0.14
Matches are distributed among these distances:
85 2 0.01
86 4 0.02
87 30 0.14
88 112 0.54
89 46 0.22
90 14 0.07
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (88 bp):
AGATTGAAGATGACAGATTTTACCTCCCTAAGGGTGCAGTGGAATACATTGAGATGCCAGATTTT
ACTTCCCTGGGCAGCAGTGGAAT
Found at i:42724249 original size:133 final size:133
Alignment explanation
Indices: 42723486--42724653 Score: 1257
Period size: 132 Copynumber: 8.8 Consensus size: 133
42723476 GTGGAGCAGG
** * * *
42723486 TTGAAGATAGCAGATCTTGCCTTCCTGCATAGACAGTGAAACAGATCAAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGTCTTCCTACATAGACAGTGAAGCAGATCAAAGATGGCAGATTTTAC
42723551 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAG-AATTTCTACTTCCCTGGGCAGCAGTGGAA
66 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-TTCTACTTCCCTGGGCAGCAGTGGAA
*
42723615 TAAA
130 TAGA
* * * * * * * * *
42723619 TTGAGGATTTTAGATCTTATCTCCCTAAACAG-TAGTGGAGCAGATCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGTCTTCCTACATAGACAGTGAAGCAGATCAAAGATGGCAGATTTTAC
** * *
42723683 CTCCCTAAGGTTGCAGTGGAATACATTGAAGCCAG-AATTTCTACTTCCCTGGGCAGCAGTGGAA
66 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-TTCTACTTCCCTGGGCAGCAGTGGAA
*
42723747 TAAA
130 TAGA
* * * * ** * * *
42723751 TTGAGGATTTTAGATCTTATCTCCCTA-A-ACGGTAGTGGAGCAGATCGAAGATGACAGATTTTA
1 TTGAAGATTTCAGATCTTGTCTTCCTACATA-GACAGTGAAGCAGATCAAAGATGGCAGATTTTA
** * * * *
42723814 CCTCCCTAAGGGTGCAGTGGAATACATTGAAGCCAG-AATTTCTACTTCCCTGGGCCGCAGTGGA
65 CCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-TTCTACTTCCCTGGGCAGCAGTGGA
*
42723878 ATAAA
129 ATAGA
* * * * ** * * *
42723883 TTGAGGATTTTAGATCTTATCTCCCTA-A-ACGGTAGTGGAGCAGATCGAAGATGACAGATTTTA
1 TTGAAGATTTCAGATCTTGTCTTCCTACATA-GACAGTGAAGCAGATCAAAGATGGCAGATTTTA
** * * *
42723946 CCTCCCTAAGGGTGCAGTGGAATACATTGAAGCCAG-AATTTCTACTTCCCTGGGCAGCAGTGGA
65 CCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-TTCTACTTCCCTGGGCAGCAGTGGA
42724010 ATAGA
129 ATAGA
* * * *** * * * * * *
42724015 TTGAAGATTACAGATCTTATCTCCCTAGGCAG-TAGTGGAGTAGATCGAAGATGGCGGATTTTTC
1 TTGAAGATTTCAGATCTTGTCTTCCTACATAGACAGTGAAGCAGATCAAAGATGGCAGATTTTAC
* * * *
42724079 CTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGAGCTA-TAGTGGA
66 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGC-AGCAGTGGA
42724142 ATAGA
129 ATAGA
* *
42724147 TTGAAGATTTCAGATCTTGCCTTCCTACATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGTCTTCCTACATAGACAGTGAAGCAGATCAAAGATGGCAGATTTTAC
* *** *
42724212 CTCCTTGTGGTTACAGTGGAGTACATTGAAAATAGTAATTCTA-TCTCCCTGGGCAGCAGCGGAA
66 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAA
42724276 TAGA
130 TAGA
* * * * * * *
42724280 TTGAAGATTTCAGATATTGTCTTCATGCATAAACAGCGAAGCAGATCAAAGATGGCGGATTATAC
1 TTGAAGATTTCAGATCTTGTCTTCCTACATAGACAGTGAAGCAGATCAAAGATGGCAGATTTTAC
* * * *
42724345 CTCCATGTGGTTACAGTGGAGTACATTAAAGCTAGTAATTCTA-TCTCCCTGGGCAGCAGCGGAA
66 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAA
42724409 TAGA
130 TAGA
* ** * * *
42724413 TTGAAGATTTCAGATCTTGCCTTCCTGTATAGACAGCGAAGCAGATCAAAGATGACATATTTTAC
1 TTGAAGATTTCAGATCTTGTCTTCCTACATAGACAGTGAAGCAGATCAAAGATGGCAGATTTTAC
* * * *
42724478 CTCCCTGTGGTTACAGTGGAGTATATTGAAACCAGTAATTCTACATCCCTGGGCAGCAGTAGAAT
66 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
42724543 AGA
131 AGA
* * * *
42724546 TTGGAGATTTCAGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGTCTTCCTACATAGACAGTGAAGCAGATCAAAGATGGCAGATTTTAC
*
42724611 CTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTA
66 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
42724654 TCTCCCGTGG
Statistics
Matches: 929, Mismatches: 96, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
130 1 0.00
131 3 0.00
132 478 0.51
133 446 0.48
134 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (133 bp):
TTGAAGATTTCAGATCTTGTCTTCCTACATAGACAGTGAAGCAGATCAAAGATGGCAGATTTTAC
CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
AGA
Found at i:42724673 original size:43 final size:43
Alignment explanation
Indices: 42724611--42724706 Score: 176
Period size: 43 Copynumber: 2.2 Consensus size: 43
42724601 CAGATTTTAC
42724611 CTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCC-GTGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTAT
42724655 CTCCCGTGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCGTGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTAT
42724698 CTCCC-TGGT
1 CTCCCGTGGT
42724707 CGGCAGTAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 4 0.08
43 43 0.83
44 5 0.10
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (43 bp):
CTCCCGTGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTAT
Found at i:42725357 original size:28 final size:28
Alignment explanation
Indices: 42725313--42725372 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
42725303 TACTAGCAGG
*
42725313 CCTAAACCCGCCCAAGC-CCAAACTAAA
1 CCTAAACCCACCCAAGCTCCAAACTAAA
* *
42725340 CCTAATACCCACCTAAGCTCCAAACTAAC
1 CCTAA-ACCCACCCAAGCTCCAAACTAAA
42725369 CCTA
1 CCTA
42725373 GCCCAGCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
28 10 0.36
29 13 0.46
ACGTcount: A:0.38, C:0.43, G:0.05, T:0.13
Consensus pattern (28 bp):
CCTAAACCCACCCAAGCTCCAAACTAAA
Found at i:42731271 original size:21 final size:21
Alignment explanation
Indices: 42731247--42731354 Score: 58
Period size: 21 Copynumber: 5.1 Consensus size: 21
42731237 CCGAAGGTTG
42731247 AACAGAAGCTCATGAAAGCTA
1 AACAGAAGCTCATGAAAGCTA
* * * * *
42731268 AACAGAAAC-CTATTAAGGTTG
1 AACAGAAGCTC-ATGAAAGCTA
* * *
42731289 AACGGAAGCTCGTGAGAGCTA
1 AACAGAAGCTCATGAAAGCTA
* * * * *
42731310 AACGGAAACCCAT-AAGGGTTA
1 AACAGAAGCTCATGAA-AGCTA
*
42731331 AACAGAAGCTCGTGAAAGCTA
1 AACAGAAGCTCATGAAAGCTA
42731352 AAC
1 AAC
42731355 GGAAAGTTCG
Statistics
Matches: 58, Mismatches: 25, Indels: 8
0.64 0.27 0.09
Matches are distributed among these distances:
20 2 0.03
21 53 0.91
22 3 0.05
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATGAAAGCTA
Found at i:42731288 original size:42 final size:41
Alignment explanation
Indices: 42731232--42731359 Score: 168
Period size: 42 Copynumber: 3.1 Consensus size: 41
42731222 ATCGTTATTA
* * *
42731232 GAAACCC-GAAGGTTGAACAGAAGCTCATGAAAGCTAAACA
1 GAAACCCATAAGGTTGAACAGAAGCTCGTGAAAGCTAAACG
* * *
42731272 GAAACCTATTAAGGTTGAACGGAAGCTCGTGAGAGCTAAACG
1 GAAACCCA-TAAGGTTGAACAGAAGCTCGTGAAAGCTAAACG
*
42731314 GAAACCCATAAGGGTTAAACAGAAGCTCGTGAAAGCTAAACG
1 GAAACCCATAA-GGTTGAACAGAAGCTCGTGAAAGCTAAACG
42731356 GAAA
1 GAAA
42731360 GTTCGCAACA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 6 0.08
41 3 0.04
42 66 0.88
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (41 bp):
GAAACCCATAAGGTTGAACAGAAGCTCGTGAAAGCTAAACG
Found at i:42733412 original size:33 final size:33
Alignment explanation
Indices: 42733365--42733531 Score: 145
Period size: 33 Copynumber: 4.7 Consensus size: 33
42733355 TATACGTTAC
* *
42733365 TCGGTGGATTCAACACTTAGCAACCACCAGTGAT
1 TCGG-GGAATCAACACTTAGCAACCACCAATGAT
*
42733399 TCGGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGAT
1 TCGGGGAATCAACACTTAGCAA---C---CAC---CAATGAT
* * *
42733441 ACGGTGGAATCAGCACTTAACAACCACCAATGAT
1 TCGG-GGAATCAACACTTAGCAACCACCAATGAT
* * *
42733475 TCGGGGAATCAGCACTTAGCAACTACCAATGAA
1 TCGGGGAATCAACACTTAGCAACCACCAATGAT
*
42733508 TCGGGGAATCAAAACTTAGCAACC
1 TCGGGGAATCAACACTTAGCAACC
42733532 CCTTGACGGA
Statistics
Matches: 109, Mismatches: 14, Indels: 21
0.76 0.10 0.15
Matches are distributed among these distances:
33 64 0.59
34 13 0.12
36 1 0.01
37 3 0.03
39 3 0.03
40 1 0.01
42 8 0.07
43 16 0.15
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (33 bp):
TCGGGGAATCAACACTTAGCAACCACCAATGAT
Found at i:42733492 original size:76 final size:75
Alignment explanation
Indices: 42733366--42733636 Score: 279
Period size: 76 Copynumber: 3.8 Consensus size: 75
42733356 ATACGTTACT
* *
42733366 CGGTGGATTCAACACTTAGCAACCACCAGTGATTCGGGGAATCAACACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCC-TTCAC
42733431 ATTCAAAGATA
65 ATTCAAAGATA
* * *
42733442 CGGTGGAATCAGCACTTAACAACCACCAATGATTCGGGGAATCAGCACTTAGCAA---C-T-AC-
1 CGGTGGAATCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTCACA
*
42733501 --CAATGA-A
66 TTCAAAGATA
* * *
42733508 TCGG-GGAATCAAAACTTAGCAACC-CC-TTGA--C--GGAATCAGCACTTAGCAACTCCTTCAC
1 -CGGTGGAATCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTCAC
*
42733566 ATTTAAA-ATA
65 ATTCAAAGATA
* * * *
42733576 CTGTGGGATCAGCACTTAGCAACCACCAGTGAATCGGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTT
42733637 GGGGGAATTA
Statistics
Matches: 160, Mismatches: 18, Indels: 36
0.75 0.08 0.17
Matches are distributed among these distances:
60 18 0.11
62 1 0.01
63 1 0.01
64 4 0.03
65 4 0.03
66 18 0.11
67 11 0.07
68 20 0.12
69 2 0.01
70 5 0.03
71 1 0.01
72 1 0.01
73 1 0.01
74 23 0.14
76 50 0.31
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (75 bp):
CGGTGGAATCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTCACA
TTCAAAGATA
Found at i:42740939 original size:33 final size:34
Alignment explanation
Indices: 42740888--42741096 Score: 147
Period size: 33 Copynumber: 5.7 Consensus size: 34
42740878 TATCCGTTAC
* *
42740888 TCGGTGGATTCAGCACTTAGCAACCACCAGTTAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAATTAT
*
42740922 TCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGAT
1 TCGGTGGAATCAGCACTTAGCAACCAC---CA-ATT-----AT
* * *
42740964 ACGGTGGAATCAGCATTTAGCAACCACCAATGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAATTAT
*
42740998 TCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTCAAGT
1 TCGGTGGAATCAGCACTTAGCAACCAC---CA-ATT--A-T
* *
42741038 TATGGTGGAATCAGCACTTAGCAACCACCAATGAAT
1 T-CGGTGGAATCAGCACTTAGCAACCACCAAT-TAT
42741074 T-GG-GGAATCAGCACTTAGCAACC
1 TCGGTGGAATCAGCACTTAGCAACC
42741097 CCTTGGGGGA
Statistics
Matches: 141, Mismatches: 14, Indels: 41
0.72 0.07 0.21
Matches are distributed among these distances:
33 60 0.43
34 11 0.08
36 6 0.04
37 5 0.04
38 2 0.01
39 5 0.04
40 4 0.03
41 2 0.01
42 26 0.18
43 20 0.14
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (34 bp):
TCGGTGGAATCAGCACTTAGCAACCACCAATTAT
Found at i:42741084 original size:75 final size:76
Alignment explanation
Indices: 42740889--42741100 Score: 347
Period size: 76 Copynumber: 2.8 Consensus size: 76
42740879 ATCCGTTACT
* * *
42740889 CGGTGGATTCAGCACTTAGCAACCACCAGTTATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
42740954 ATTCAAAGATA
66 ATTCAAAGATA
*
42740965 CGGTGGAATCAGCATTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
42741030 ATTC-AAGTTA
66 ATTCAAAGATA
*
42741040 TGGTGGAATCAGCACTTAGCAACCACCAATGAATT-GGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATG-ATTCGGGGAATCAGCACTTAGCAACCCCTT
42741101 GGGGGAATCA
Statistics
Matches: 128, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
75 60 0.47
76 68 0.53
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTCAAAGATA
Found at i:42741121 original size:102 final size:102
Alignment explanation
Indices: 42741000--42741239 Score: 363
Period size: 102 Copynumber: 2.4 Consensus size: 102
42740990 CCAATGATTC
* ** *
42741000 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGTTATGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAAATACGGTGGAATCAGCACTTAGCAACCA
* *
42741065 CCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATTGAGGAATCAACACTTAGCAACCCCTTG
* * *
42741102 GGGGAATCATCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGGATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAAATACGGTGGAATCAGCACTTAGCAACCA
* *
42741167 CCAATGAATTGAGGAATCAACACTTAGTAGCCCCTTG
66 CCAATGAATTGAGGAATCAACACTTAGCAACCCCTTG
* *
42741204 GGGGAATCAGCACTTAGCAACCCCCTTTATATTCAA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAA
42741240 TGTACTCCGG
Statistics
Matches: 123, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 123 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATTGAGGAATCAACACTTAGCAACCCCTTG
Found at i:42752845 original size:28 final size:28
Alignment explanation
Indices: 42752788--42752845 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
42752778 GTCTAATTTG
* *
42752788 TAATTTTAGACATAAATTTAGTTTTGTA
1 TAATTTTAGACATAAATTTAGTATTCTA
* *
42752816 TAATTTTATACATAAAATTTTG-ATTCTA
1 TAATTTTAGACAT-AAATTTAGTATTCTA
42752844 TA
1 TA
42752846 CAATTTTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (28 bp):
TAATTTTAGACATAAATTTAGTATTCTA
Found at i:42758688 original size:42 final size:42
Alignment explanation
Indices: 42758632--42758746 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 42
42758622 TCGTGTTTAC
* ** *
42758632 TTTCTGTTTC-GCTCTCACGAGCTTCTGTTTAACGTTTATGGG
1 TTTCTG-TTCAGCTCTCACGAGCTTCTGTTCAACCCTTATAGG
*
42758674 TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATAGG
1 TTTCTGTTCAGCTCTCACGAGCTTCTGTTCAACCCTTATAGG
* *
42758716 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCA
1 TTTCTGTTCAGCTCTCACGAGCTTCTGTTCA
42758747 GCCTTCGGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 3 0.05
42 61 0.95
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTCACGAGCTTCTGTTCAACCCTTATAGG
Found at i:42758743 original size:21 final size:21
Alignment explanation
Indices: 42758633--42758744 Score: 66
Period size: 21 Copynumber: 5.3 Consensus size: 21
42758623 CGTGTTTACT
* *
42758633 TTCTGTTTCGCTCTCACGAGC
1 TTCTGTTTAGCTCTCATGAGC
* * * *
42758654 TTCTGTTTAACGT-TTATGGGT
1 TTCTGTTTAGC-TCTCATGAGC
* *
42758675 TTCTGTTCAGCTCTCACGAGC
1 TTCTGTTTAGCTCTCATGAGC
* * * * * *
42758696 TTCCGTTCAACCCTTAT-AGGT
1 TTCTGTTTAGCTCTCATGA-GC
42758717 TTCTGTTTAGCTCTCATGAGC
1 TTCTGTTTAGCTCTCATGAGC
42758738 TTCTGTT
1 TTCTGTT
42758745 CAGCCTTCGG
Statistics
Matches: 63, Mismatches: 24, Indels: 8
0.66 0.25 0.08
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (21 bp):
TTCTGTTTAGCTCTCATGAGC
Found at i:42764492 original size:13 final size:14
Alignment explanation
Indices: 42764474--42764507 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
42764464 AAAGGGTACA
42764474 TTAATTTTTTTA-T
1 TTAATTTTTTTACT
*
42764487 TTAATTATTTTACT
1 TTAATTTTTTTACT
42764501 TTAATTT
1 TTAATTT
42764508 ATCAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
TTAATTTTTTTACT
Found at i:42767544 original size:14 final size:14
Alignment explanation
Indices: 42767525--42767559 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
42767515 AAAGGGTACA
42767525 TTAATTTTTTTAAT
1 TTAATTTTTTTAAT
* *
42767539 TTAATTATTTTACT
1 TTAATTTTTTTAAT
42767553 TTAATTT
1 TTAATTT
42767560 ATCAAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTAATTTTTTTAAT
Found at i:42774549 original size:5 final size:5
Alignment explanation
Indices: 42774539--42774567 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
42774529 ATATTGCTCT
42774539 TTATA TTATA TTATA TTATA TTATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTAT
42774568 GCATGCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:42778068 original size:22 final size:20
Alignment explanation
Indices: 42778042--42778083 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
42778032 AATTATTTTA
42778042 ATTTAATTTATCAAAATTTGAT
1 ATTT-ATTT-TCAAAATTTGAT
*
42778064 ATTTATTTTTAAAATTTGAT
1 ATTTATTTTCAAAATTTGAT
42778084 GTTAAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTATTTTCAAAATTTGAT
Found at i:42786176 original size:13 final size:13
Alignment explanation
Indices: 42786158--42786183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42786148 TTTATCAATT
42786158 AATATTTTTCTAA
1 AATATTTTTCTAA
42786171 AATATTTTTCTAA
1 AATATTTTTCTAA
42786184 GCTAAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTTTTCTAA
Found at i:42786630 original size:32 final size:32
Alignment explanation
Indices: 42786589--42786654 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
42786579 GATGAATCAC
*
42786589 TCTCTCCCATTGCATCACATCAAAATTCAAAA
1 TCTCTCCCATTGCAGCACATCAAAATTCAAAA
*
42786621 TCTCTCCCATTGCAGCACATCAAGATTCAAAA
1 TCTCTCCCATTGCAGCACATCAAAATTCAAAA
42786653 TC
1 TC
42786655 GAAATGATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.32, G:0.06, T:0.27
Consensus pattern (32 bp):
TCTCTCCCATTGCAGCACATCAAAATTCAAAA
Found at i:42786879 original size:13 final size:15
Alignment explanation
Indices: 42786860--42786896 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
42786850 TTAATCTTTA
42786860 AAATTATAAAAT-AT
1 AAATTATAAAATAAT
42786874 -AATTATTAAAATAAT
1 AAATTA-TAAAATAAT
42786889 AAATTATA
1 AAATTATA
42786897 TTTTTACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.25
14 6 0.30
15 4 0.20
16 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTATAAAATAAT
Found at i:42786882 original size:22 final size:22
Alignment explanation
Indices: 42786857--42786921 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
42786847 AATTTAATCT
42786857 TTAAAATTATAAAATATAATTA
1 TTAAAATTATAAAATATAATTA
* * *
42786879 TTAAAATAATAAATTAT-ATTT
1 TTAAAATTATAAAATATAATTA
*
42786900 TTACAATTATAAAATTATAATT
1 TTAAAATTATAAAA-TATAATT
42786922 TAATTTCTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 14 0.40
22 18 0.51
23 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAATTATAAAATATAATTA
Found at i:42799749 original size:21 final size:22
Alignment explanation
Indices: 42799720--42799766 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
42799710 CAGAAGGAGT
*
42799720 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
42799742 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
42799763 GAGT
1 GAGT
42799767 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:42801591 original size:15 final size:15
Alignment explanation
Indices: 42801571--42801599 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42801561 CAAGGTGGAG
42801571 ATTATTAGTAGCATA
1 ATTATTAGTAGCATA
42801586 ATTATTAGTAGCAT
1 ATTATTAGTAGCAT
42801600 CTTTGACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (15 bp):
ATTATTAGTAGCATA
Found at i:42804904 original size:27 final size:27
Alignment explanation
Indices: 42804874--42804941 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
42804864 AAGGGAACAC
*
42804874 TGTTAGCGGCACCAAACAAGGAAACCT
1 TGTTGGCGGCACCAAACAAGGAAACCT
**
42804901 TGTTGGCGGCACCAAACAAGGATTCCT
1 TGTTGGCGGCACCAAACAAGGAAACCT
42804928 TGTTGGCGGCACCA
1 TGTTGGCGGCACCA
42804942 CCTTAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (27 bp):
TGTTGGCGGCACCAAACAAGGAAACCT
Done.