Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015316.1 Kokia drynarioides strain JFW-HI SEQ_130361, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 577508
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 343 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2376 original size:23 final size:23
Alignment explanation
Indices: 2319--2494 Score: 169
Period size: 23 Copynumber: 7.5 Consensus size: 23
2309 TATACGGAAC
*
2319 AAACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
2341 GGGAAACAAAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACACAGTGCT
* * *
2367 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* * *
2390 AATCAGATAGCACACAAAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
2413 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
2436 AATAACAGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
*
2461 AAACAGAGAGCATACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
2484 AATA-AGAGAGC
1 AA-ACAGAGAGC
2495 GCGCTAGTGT
Statistics
Matches: 129, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
22 3 0.02
23 84 0.65
24 3 0.02
25 30 0.23
26 9 0.07
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:13243 original size:13 final size:14
Alignment explanation
Indices: 13225--13253 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13215 AATACCTATA
13225 CGTTTT-GATTTAT
1 CGTTTTGGATTTAT
13238 CGTTTTGGATTTAT
1 CGTTTTGGATTTAT
13252 CG
1 CG
13254 ATATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.14, C:0.10, G:0.21, T:0.55
Consensus pattern (14 bp):
CGTTTTGGATTTAT
Found at i:17346 original size:12 final size:12
Alignment explanation
Indices: 17315--17346 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
17305 ATTACTATCC
17315 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
17327 TTCTTTTTCTTT
1 TTTTTTTTCTTT
17339 TTTTTTTT
1 TTTTTTTT
17347 GTAAAAGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:27685 original size:71 final size:71
Alignment explanation
Indices: 27533--27685 Score: 207
Period size: 71 Copynumber: 2.2 Consensus size: 71
27523 ATCTCTTGGT
* * * *
27533 TCTACCGATATAACCAATATTTCTATCAGTAGAACAAACTCCAGAGAGCAAAGAAGTTATGGTCT
1 TCTACCGATACAACCAAGACTTCTATCAGTAGAACAAACTCCAGAAAGCAAAGAAGTTATGGTCT
* *
27598 GGGACT
66 GAGACA
** * * *
27604 TCTATTGATACAACCAGGACTTCTATCAGTAGAAGAAACTCCAGAAAGCAAAGAAGTTGTGGTCT
1 TCTACCGATACAACCAAGACTTCTATCAGTAGAACAAACTCCAGAAAGCAAAGAAGTTATGGTCT
27669 GAGACA
66 GAGACA
27675 TCTACCGATAC
1 TCTACCGATAC
27686 CTAGAAGGCT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (71 bp):
TCTACCGATACAACCAAGACTTCTATCAGTAGAACAAACTCCAGAAAGCAAAGAAGTTATGGTCT
GAGACA
Found at i:33822 original size:18 final size:18
Alignment explanation
Indices: 33778--33830 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
33768 CCGACCTCTG
*
33778 ACCGAACTAAATCGATTA
1 ACCGAATTAAATCGATTA
33796 ACCGAATTAAATCGATTCA
1 ACCGAATTAAATCGATT-A
* *
33815 ATCG-ATTAATTCGATT
1 ACCGAATTAAATCGATT
33831 TTAACCGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 27 0.87
19 4 0.13
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (18 bp):
ACCGAATTAAATCGATTA
Found at i:40515 original size:15 final size:16
Alignment explanation
Indices: 40483--40515 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40473 TTAAAATTTT
40483 ATAAAAATTATTTAATA
1 ATAAAAATTA-TTAATA
40500 ATAAAAATTA-TAATA
1 ATAAAAATTATTAATA
40515 A
1 A
40516 CAATCTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAAAATTATTAATA
Found at i:42007 original size:25 final size:24
Alignment explanation
Indices: 41957--42015 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
41947 TTAAATTATA
41957 TTTATATTATTTTAGTATTTATAAT
1 TTTATA-TATTTTAGTATTTATAAT
*
41982 TTTATATATTTT-TTATTTATTAAAT
1 TTTATATATTTTAGTATTTA-T-AAT
*
42007 TTTTTATAT
1 TTTATATAT
42016 AATCATCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 6 0.20
24 7 0.23
25 17 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTATATATTTTAGTATTTATAAT
Found at i:50774 original size:22 final size:22
Alignment explanation
Indices: 50744--50785 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
50734 TACATACATG
50744 ACACCTGTTTAATATCAATGCT
1 ACACCTGTTTAATATCAATGCT
* *
50766 ACACTTGTTTAATATTAATG
1 ACACCTGTTTAATATCAATG
50786 GTTTTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
ACACCTGTTTAATATCAATGCT
Found at i:51349 original size:77 final size:76
Alignment explanation
Indices: 51218--51371 Score: 238
Period size: 77 Copynumber: 2.0 Consensus size: 76
51208 AACACTCCTT
*
51218 TTTTGTCAGATAAAAAATACAAATTTTTTTGTCGGTCATACAATGGTCGACACCCCTATTTATCT
1 TTTTATCAGATAAAAAATACAAATTTTTTTGTCGGTCATACAATGGTCGACACCCCTATTTATCT
51283 GATAAAAAAAA
66 GATAAAAAAAA
** * *
51294 TTTTATCAGATAAAAAAT-TTAATTTTTTGATGTTGGTCATGCAATGGTCGACACCCCTATTTAT
1 TTTTATCAGATAAAAAATACAAATTTTTT--TGTCGGTCATACAATGGTCGACACCCCTATTTAT
51358 CTGATAAAAAAAA
64 CTGATAAAAAAAA
51371 T
1 T
51372 CAAATTTTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
75 8 0.11
76 17 0.24
77 46 0.65
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (76 bp):
TTTTATCAGATAAAAAATACAAATTTTTTTGTCGGTCATACAATGGTCGACACCCCTATTTATCT
GATAAAAAAAA
Found at i:51438 original size:60 final size:61
Alignment explanation
Indices: 51295--51439 Score: 153
Period size: 60 Copynumber: 2.5 Consensus size: 61
51285 TAAAAAAAAT
* * *
51295 TTTATC-AGAT-AAAAAATTT-AATTTTTTGATGTTGGTCATGCAATGGTCGACACCCCTA
1 TTTATCTAGATAAAAAAATTTCAATTTTTAGATGTTGGCCATACAATGGTCGACACCCCTA
* *
51353 TTTATCT-GATAAAAAAA-ATCAAATTTTTAGGTGTTGGCCATACAATGG-CTGACACTCCCT-
1 TTTATCTAGATAAAAAAATTTC-AATTTTTAGATGTTGGCCATACAATGGTC-GACAC-CCCTA
*
51413 TTTCT-TAGATAAAAAAATTTCAATTTT
1 TTTATCTAGATAAAAAAATTTCAATTTT
51440 CTTTGTATTG
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
58 10 0.14
59 8 0.11
60 48 0.67
61 6 0.08
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (61 bp):
TTTATCTAGATAAAAAAATTTCAATTTTTAGATGTTGGCCATACAATGGTCGACACCCCTA
Found at i:51652 original size:60 final size:59
Alignment explanation
Indices: 51514--51655 Score: 189
Period size: 60 Copynumber: 2.4 Consensus size: 59
51504 AAATTTTTTA
* *
51514 ATTTTTTTATCAG-TAAATAGGAGTGTCGGCCATTGTATGGCCAACACAAAAAAATTGT
1 ATTTTTTTATCAGATAAAAAGGAGTGTCGGCCATTGCATGGCCAACACAAAAAAATTGT
* * * *
51572 ATTTTTTTATCAAACAAAAAAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAATT-T
1 ATTTTTTTATCAGA-TAAAAAGGAGTGTCGGCCATTGCATGGCCAACACAAAAAAATTGT
51631 GATTTTTTTATCAGATTAAAAAGGA
1 -ATTTTTTTATCAGA-TAAAAAGGA
51656 ATGGCCAACA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
58 12 0.17
59 1 0.01
60 58 0.82
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (59 bp):
ATTTTTTTATCAGATAAAAAGGAGTGTCGGCCATTGCATGGCCAACACAAAAAAATTGT
Found at i:54697 original size:18 final size:18
Alignment explanation
Indices: 54676--54715 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
54666 ATTTTAAATG
54676 AATTTAATTTTTTATTTA
1 AATTTAATTTTTTATTTA
*
54694 AATTTATTTTTTTATTTA
1 AATTTAATTTTTTATTTA
54712 AATT
1 AATT
54716 CTCTCAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTTAATTTTTTATTTA
Found at i:66303 original size:20 final size:20
Alignment explanation
Indices: 66280--66351 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
66270 AAATTACAAA
*
66280 AAAAATTAAAAATAATTTTC
1 AAAAATTCAAAATAATTTTC
*
66300 AAAATTTCAAAATAATTTT-
1 AAAAATTCAAAATAATTTTC
* *
66319 TAAAATTCAAAAT-ATTTAC
1 AAAAATTCAAAATAATTTTC
66338 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
66352 TTATATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.09
19 18 0.41
20 22 0.50
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTC
Found at i:71143 original size:52 final size:52
Alignment explanation
Indices: 71051--71150 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
71041 AATTATATAT
* * *
71051 TAAAAAGAAACCTGCTCTCAAAGACTTTTAGGTATATGTCTAAATCAAGTAG
1 TAAAAAGAAACCTGCCCTCAAAGACATTTACGTATATGTCTAAATCAAGTAG
* * *
71103 TAAACAGAAACCTGCCCTCAAAGGCATTTACGTATGTGTCTAAATCAA
1 TAAAAAGAAACCTGCCCTCAAAGACATTTACGTATATGTCTAAATCAA
71151 TGACAGATGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (52 bp):
TAAAAAGAAACCTGCCCTCAAAGACATTTACGTATATGTCTAAATCAAGTAG
Found at i:74793 original size:101 final size:101
Alignment explanation
Indices: 74618--74806 Score: 369
Period size: 101 Copynumber: 1.9 Consensus size: 101
74608 GAGAATGGCC
74618 CCGCACAATTTGGAATGGAGATAAATTGTTCAATCCCATATGAGAGGGGTTTCCCACATATTCAA
1 CCGCACAATTTGGAATGGAGATAAATTGTTCAATCCCATATGAGAGGGGTTTCCCACATATTCAA
74683 TGGATGAAAATGTCAGTCACCAAACGTACTAAATGG
66 TGGATGAAAATGTCAGTCACCAAACGTACTAAATGG
*
74719 CCGCACAATTTGGAATGGAGATAAATTGTTCAATCCCATATGAGAGGGGTTTCCCACGTATTCAA
1 CCGCACAATTTGGAATGGAGATAAATTGTTCAATCCCATATGAGAGGGGTTTCCCACATATTCAA
74784 TGGATGAAAATGTCAGTCACCAA
66 TGGATGAAAATGTCAGTCACCAA
74807 TTTTACAATA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (101 bp):
CCGCACAATTTGGAATGGAGATAAATTGTTCAATCCCATATGAGAGGGGTTTCCCACATATTCAA
TGGATGAAAATGTCAGTCACCAAACGTACTAAATGG
Found at i:78586 original size:21 final size:22
Alignment explanation
Indices: 78540--78587 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
78530 AATACTTGAA
* *
78540 ATTTTATAGGAATTGCTTAGAT
1 ATTTTATAGGAAATGATTAGAT
*
78562 -TTTTATAGGAAAT-ATTAGGT
1 ATTTTATAGGAAATGATTAGAT
78582 ATTTTA
1 ATTTTA
78588 AGAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (22 bp):
ATTTTATAGGAAATGATTAGAT
Found at i:96291 original size:15 final size:13
Alignment explanation
Indices: 96261--96292 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
96251 GTTATAGGTG
96261 TTTTTAAAATTAT
1 TTTTTAAAATTAT
96274 TTTTTAAAATTAT
1 TTTTTAAAATTAT
*
96287 ATTTTA
1 TTTTTA
96293 TTTAAGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAAAATTAT
Found at i:105854 original size:29 final size:28
Alignment explanation
Indices: 105820--105888 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
105810 GTTGAGGGTC
* *
105820 AAATTAAAAACCTTGATAGTCGGGTGACT
1 AAATTAAAAA-ATTGATAGTCGGATGACT
105849 AAATTACAAGAAATTGATAGTCGGATGACT
1 AAATTA-AA-AAATTGATAGTCGGATGACT
*
105879 ACAAATAAAA
1 A-AATTAAAA
105889 TGAGCAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 7 0.21
30 21 0.62
31 6 0.18
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (28 bp):
AAATTAAAAAATTGATAGTCGGATGACT
Found at i:108943 original size:42 final size:43
Alignment explanation
Indices: 108896--108988 Score: 179
Period size: 42 Copynumber: 2.2 Consensus size: 43
108886 AAAACATAGT
108896 CCATCAAGTTCATTAAGATACTTTCAATTATTGTATCAAA-CC
1 CCATCAAGTTCATTAAGATACTTTCAATTATTGTATCAAACCC
108938 CCATCAAGTTCATTAAGATACTTTCAATTATTGTATCAAACCC
1 CCATCAAGTTCATTAAGATACTTTCAATTATTGTATCAAACCC
108981 CCATCAAG
1 CCATCAAG
108989 ATAAGCACCA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 40 0.80
43 10 0.20
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (43 bp):
CCATCAAGTTCATTAAGATACTTTCAATTATTGTATCAAACCC
Found at i:117723 original size:211 final size:211
Alignment explanation
Indices: 117354--117779 Score: 728
Period size: 211 Copynumber: 2.0 Consensus size: 211
117344 ATTTTATCTA
*
117354 ATAAATTATTGTGGGTAAAAGTACCATTATCTCCTTATACTAGATCTTGAATCATAGTTTTTCAA
1 ATAAATTATTGTAGGTAAAAGTACCATTATCTCCTTATACTAGATCTTGAATCATAGTTTTTCAA
* * * *
117419 CCTTTTGAAAAGACAAGACACATTCATCTTGCACACACAAATGCTTGAATCCAAATCTTTAAAAA
66 CCCTTTGAAAAGACAAGACACATACATCTTGCACACACAAATGCTTGAACCCAAATCTCTAAAAA
* * *
117484 TGAATACCATTCTCTTTTTCATTAAAACCACTTGTTGAGTTTTGAATTACATTTTGATCCTTTTA
131 TGAACACCATTCTCTTTTTCACTAAAACCACTCGTTGAGTTTTGAATTACATTTTGATCCTTTTA
117549 CATTTATATATAAATC
196 CATTTATATATAAATC
117565 ATAAATTATTGTAGGTAAAAGTACCATTATCTCCTTATACTAGATCTTGAATCATAGTTTTTCAA
1 ATAAATTATTGTAGGTAAAAGTACCATTATCTCCTTATACTAGATCTTGAATCATAGTTTTTCAA
* * *
117630 CCCTTTGAAAGGACAAGACACATACATCTTGCACACACAAGTGCTTGAACCCGAATCTCTAAAAA
66 CCCTTTGAAAAGACAAGACACATACATCTTGCACACACAAATGCTTGAACCCAAATCTCTAAAAA
*
117695 TGAACACCA-TCTTTTTTTCCACTAAAACCACTCGTTGAGTTTTGAATTACATTTTGATCCTTTT
131 TGAACACCATTCTCTTTTT-CACTAAAACCACTCGTTGAGTTTTGAATTACATTTTGATCCTTTT
117759 ACATTTATATATAAATC
195 ACATTTATATATAAATC
117776 ATAA
1 ATAA
117780 TAATAAATTT
Statistics
Matches: 202, Mismatches: 12, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
210 8 0.04
211 194 0.96
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (211 bp):
ATAAATTATTGTAGGTAAAAGTACCATTATCTCCTTATACTAGATCTTGAATCATAGTTTTTCAA
CCCTTTGAAAAGACAAGACACATACATCTTGCACACACAAATGCTTGAACCCAAATCTCTAAAAA
TGAACACCATTCTCTTTTTCACTAAAACCACTCGTTGAGTTTTGAATTACATTTTGATCCTTTTA
CATTTATATATAAATC
Found at i:118762 original size:15 final size:17
Alignment explanation
Indices: 118740--118783 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
118730 AATTCAACAC
118740 TTAA-TTTTTCAATA-A
1 TTAATTTTTTCAATACA
*
118755 TT-ATTTTTT-AATACT
1 TTAATTTTTTCAATACA
118770 TTAATTTTTTCAAT
1 TTAATTTTTTCAAT
118784 TTATAAAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 5 0.21
15 9 0.38
16 7 0.29
17 3 0.12
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAATTTTTTCAATACA
Found at i:125984 original size:242 final size:238
Alignment explanation
Indices: 125355--126002 Score: 803
Period size: 242 Copynumber: 2.7 Consensus size: 238
125345 AGAAAAAAAA
*
125355 TAGTGGGTGAAATGGGCCTGATATTGGGATTGAATGATTGATATGGGCTTTTAAACTAAAAGTGG
1 TAGT-GGTGAAATGGGCCTGATATTGGGATTGAATGATTGATCT-GGCTTTTAAACTAAAAGTGG
* * ** * * * * *
125420 TAACGTGTTCCTTTTTGCCAAAAAGGCCGTTTGAGGAAATCAAACCCATGACCACGTGGTTAAAA
64 -AA-ATG----TGTTTGCTTAAAACGCCGTCTGTGGGAATCAAACCCACGACCACGTGGTTAAAA
* * * *
125485 GCCACGCGCTCTACCGGCTGAGTTAAGACAGCTGCTCTTTTGAATATAAATATTAATTTTTCTGA
123 GCCACGCGCTCTACCGGCTGAGCTAAGACGGCTGCTCATTTAAATATAAATATTAATTTTTCTGA
125550 TCATTCATTTTTGTCAGAAAATAATAAAACTTACCTTTTGGAGGAAAAAGG
188 TCATTCATTTTTGTCAGAAAATAATAAAACTTACCTTTTGGAGGAAAAAGG
* * * * * * *
125601 GAGTTGGTGAAATGGACCTGATATTAGGATTGAAAGATTGATCCCGGTTTTTAAACTGAAAGTGG
1 TAG-TGGTGAAATGGGCCTGATATTGGGATTGAATGATTGAT-CTGGCTTTTAAACTAAAAGTGG
* * ** * * * *
125666 TAATGTGTTTCGGCTTTAAACATCGTCTGTTGGAATCAAACCCACAATCGCGTGGTTAAAAGCCA
64 AAATGTGTTT--GCTTAAAACGCCGTCTGTGGGAATCAAACCCACGACCACGTGGTTAAAAGCCA
**
125731 CGCGCTCTACCGGCTGAGCTAAGACGGCTTTTCATTTAAATTATAAATATTAATTTTTCTGATCA
127 CGCGCTCTACCGGCTGAGCTAAGACGGCTGCTCATTTAAA-TATAAATATTAATTTTTCTGATCA
*
125796 -TCTATTTTTGTCAGAAAATAATAAAACTTACCTTTTGGCGGAAAAAGG
191 TTC-ATTTTTGTCAGAAAATAATAAAACTTACCTTTTGGAGGAAAAAGG
* ** *
125844 TAGTGAGTGAAACGGGCCTGATGCTGGGATTGAATGATTGATCTGGCCTTTCAAACTAAAAGTGG
1 TAGTG-GTGAAATGGGCCTGATATTGGGATTGAATGATTGATCTGG-CTTTTAAACTAAAAGTGG
*
125909 AAATGTGATTTGCTTAAAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCAC
64 AAATGTG-TTTGCTTAAAACGCCGTCTGTGGGAATCAAACCCACGACCACGTGGTTAAAAGCCAC
125974 GCGCTCTACCGGCTGAGCTAAGACGGCTG
128 GCGCTCTACCGGCTGAGCTAAGACGGCTG
126003 GTTGTTAAAA
Statistics
Matches: 340, Mismatches: 53, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
240 4 0.01
242 154 0.45
243 121 0.36
244 5 0.01
245 1 0.00
246 54 0.16
247 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (238 bp):
TAGTGGTGAAATGGGCCTGATATTGGGATTGAATGATTGATCTGGCTTTTAAACTAAAAGTGGAA
ATGTGTTTGCTTAAAACGCCGTCTGTGGGAATCAAACCCACGACCACGTGGTTAAAAGCCACGCG
CTCTACCGGCTGAGCTAAGACGGCTGCTCATTTAAATATAAATATTAATTTTTCTGATCATTCAT
TTTTGTCAGAAAATAATAAAACTTACCTTTTGGAGGAAAAAGG
Found at i:133673 original size:9 final size:9
Alignment explanation
Indices: 133659--133689 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
133649 CATTGAACTC
133659 AAAAATATA
1 AAAAATATA
133668 AAAAATATA
1 AAAAATATA
*
133677 AAAAAAATA
1 AAAAATATA
133686 AAAA
1 AAAA
133690 TCTACGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAATATA
Found at i:134286 original size:2 final size:2
Alignment explanation
Indices: 134281--134316 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
134271 TGATATTGAT
134281 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
134317 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:134321 original size:2 final size:2
Alignment explanation
Indices: 134316--134354 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
134306 ATATATATAT
*
134316 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
134355 ATTTGATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:136673 original size:20 final size:22
Alignment explanation
Indices: 136638--136679 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
136628 CAGCTAATGA
136638 TTTTAAAATTATTAAAATTATT
1 TTTTAAAATTATTAAAATTATT
136660 TTTTAAAA-TA-TAAAATTATT
1 TTTTAAAATTATTAAAATTATT
136680 AAAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAATTATTAAAATTATT
Found at i:136784 original size:12 final size:12
Alignment explanation
Indices: 136763--136804 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
136753 CTTTTTTCTG
136763 TTCCCTTTCCCC
1 TTCCCTTTCCCC
*
136775 TTCCCCTTCCCC
1 TTCCCTTTCCCC
*
136787 TTCCCTTTCCCT
1 TTCCCTTTCCCC
136799 TTCCCT
1 TTCCCT
136805 CCTCCTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (12 bp):
TTCCCTTTCCCC
Found at i:136804 original size:6 final size:6
Alignment explanation
Indices: 136763--136804 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
136753 CTTTTTTCTG
* * *
136763 TTCCCT TTCCCC TTCCCC TTCCCC TTCCCT TTCCCT TTCCCT
1 TTCCCT TTCCCT TTCCCT TTCCCT TTCCCT TTCCCT TTCCCT
136805 CCTCCTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
TTCCCT
Found at i:137119 original size:24 final size:24
Alignment explanation
Indices: 137087--137142 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
137077 AGATGAGTTT
*
137087 AGTATTTTCTTGAGAAACAAACAG
1 AGTATTTTCCTGAGAAACAAACAG
137111 AGTATTTTCCTGAGAAACAAACAG
1 AGTATTTTCCTGAGAAACAAACAG
137135 AGTATTTT
1 AGTATTTT
137143 TGTAACAGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (24 bp):
AGTATTTTCCTGAGAAACAAACAG
Found at i:139542 original size:52 final size:52
Alignment explanation
Indices: 139457--139849 Score: 592
Period size: 52 Copynumber: 7.6 Consensus size: 52
139447 TAAATGTTAA
* *
139457 AGGTCCGATGACTATGTGTCATCGTGTGCATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
139509 AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
139561 AGGTTCGATGATTATGTGCCATCGCGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
139613 AGGTCCGATGACTATGTGTTATCGTGAGTATATGAATCCTTTACGAATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
139665 ATGTTCGATGAGTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * **
139717 AGGTCCGATGACTATGTGCCATCGTGAGTATATGAATCGTTTAATGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
139769 AGGTCCGATGAC--TGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
139819 AGGTCCAATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
139850 TAAATGAGAA
Statistics
Matches: 304, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
50 45 0.15
52 259 0.85
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:140752 original size:21 final size:21
Alignment explanation
Indices: 140723--140762 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
140713 GATAATTGTG
140723 TCGTAAGTATCGGTAGAACCA
1 TCGTAAGTATCGGTAGAACCA
*
140744 TCGTGAGTATCGGTAGAAC
1 TCGTAAGTATCGGTAGAAC
140763 TCTGCACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (21 bp):
TCGTAAGTATCGGTAGAACCA
Found at i:143710 original size:17 final size:17
Alignment explanation
Indices: 143688--143721 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
143678 AATCTTGCTC
143688 GTTGTTAGTAATTTTTA
1 GTTGTTAGTAATTTTTA
143705 GTTGTTAGTAATTTTTA
1 GTTGTTAGTAATTTTTA
143722 TATTTTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (17 bp):
GTTGTTAGTAATTTTTA
Found at i:143916 original size:16 final size:16
Alignment explanation
Indices: 143895--143927 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
143885 TGATGATTTT
*
143895 AATGTTAAAGGACTAA
1 AATGTTAAAGGAATAA
143911 AATGTTAAAGGAATAA
1 AATGTTAAAGGAATAA
143927 A
1 A
143928 TTTGTAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGTTAAAGGAATAA
Found at i:145066 original size:52 final size:52
Alignment explanation
Indices: 144913--145306 Score: 592
Period size: 52 Copynumber: 7.6 Consensus size: 52
144903 TAAATGCAAA
* *
144913 AGGTCTGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * * *
144965 AGATCCGATGACTATGTAT-TTTGTGAGTATATGGATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
145016 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
145068 AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
145120 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * * *
145172 AGTTCCGATGGCTATATGTCATCGTGAGTGTAAGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
145224 AGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTTCGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
145276 AGGTCCGATGACTATATGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
145307 TAAATGAGAA
Statistics
Matches: 303, Mismatches: 38, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
51 45 0.15
52 258 0.85
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:148688 original size:21 final size:21
Alignment explanation
Indices: 148663--148702 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
148653 CTTAAATTTT
148663 TAAATT-TAAAAAATTAAAAAC
1 TAAATTCTAAAAAA-TAAAAAC
*
148684 TAAATTCTTAAAAATAAAA
1 TAAATTCTAAAAAATAAAA
148703 TATAAGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAATTCTAAAAAATAAAAAC
Found at i:149842 original size:35 final size:35
Alignment explanation
Indices: 149775--149842 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
149765 CGTATAAATC
* *
149775 CAAACCTTAAAAACAAAGCCCTAACTTTCATAGAG
1 CAAACCTTAAAAACAAAACCCTAACTTCCATAGAG
* *
149810 CAAACC-TGAAAACAAAACCTTAACTCTCCATAG
1 CAAACCTTAAAAACAAAACCCTAACT-TCCATAG
149843 TTACCACGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.19
Consensus pattern (35 bp):
CAAACCTTAAAAACAAAACCCTAACTTCCATAGAG
Found at i:152218 original size:26 final size:26
Alignment explanation
Indices: 152162--152225 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
152152 AGGCCTTGTG
* * * *
152162 CCGGTGATTATCTATCAAACTTTGTG
1 CCGGTGATTATATATCAAACCTTATA
* *
152188 TCGGTGATTATATATCAAGCCTTATA
1 CCGGTGATTATATATCAAACCTTATA
152214 CCGGTGTATTAT
1 CCGGTG-ATTAT
152226 TAGGCTTTGT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (26 bp):
CCGGTGATTATATATCAAACCTTATA
Found at i:152305 original size:41 final size:41
Alignment explanation
Indices: 152227--152378 Score: 153
Period size: 41 Copynumber: 3.7 Consensus size: 41
152217 GTGTATTATT
* * * * * * *
152227 AGGCTTTGTGCCTAGCAAGCTTCGTGTCGATGTATTGATTC
1 AGGCCTTGAGCCTAGCAGGCTTCGAGTCGGTGAATTGAATC
** * *
152268 AGGTTTTGTGCCTGGCAGGCTTCGAG-CTGGTGAATTGAATC
1 AGGCCTTGAGCCTAGCAGGCTTCGAGTC-GGTGAATTGAATC
152309 AGGCCTTGAGCCTAGCAGGCTTCGAGTCGGTGAATTGAATC
1 AGGCCTTGAGCCTAGCAGGCTTCGAGTCGGTGAATTGAATC
* * * *
152350 AGACCTTGAGCCTAACAGGTTTCGTGTCG
1 AGGCCTTGAGCCTAGCAGGCTTCGAGTCG
152379 TTTTATTGAA
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.01
41 92 0.98
42 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (41 bp):
AGGCCTTGAGCCTAGCAGGCTTCGAGTCGGTGAATTGAATC
Found at i:170504 original size:98 final size:98
Alignment explanation
Indices: 170279--170617 Score: 342
Period size: 98 Copynumber: 3.4 Consensus size: 98
170269 TCATCACCAT
* * *
170279 GAAGGGAAAGATTTAAGCCGCAACGGCGAATTCAGTACCAC-AAAAGTACAAAGGGAAAGGTTTA
1 GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGA-TACAAAGGGAAAGGTTTA
* ** * * *
170343 AGTCGCAATGGCAAACCTTATACCTTAGAGGATGT
65 AGTCGCAACGGTGAACCTTATACCTCAGAGCA-GC
* * * ** *
170378 GAAGGGAAAGATTTAAGCCGTAACGGCAAATCCAATATCACGAAGATACGTAGGGAAATGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATACAAAGGGAAAGGTTTAA
* *
170443 GTCACAACGGTGAACCTTATGCCTCAGAAGCA-C
66 GTCGCAACGGTGAACCTTATACCTCAG-AGCAGC
* * *
170476 GAAGGGAAAGATTTAAGCCGCAAGGGCAAATCCAGTACCATGAAGATGCAAAGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATACAAAGGGAAAGGTTTAA
* * * * *
170541 GTCGTAACGGTGAACCTTGTACCTCGAAAACA-T
66 GTCGCAACGGTGAACCTTATACCTC-AGAGCAGC
* * * * * *
170574 GAGGGGAAAGATCTAAGCCACAATGGCGAATCTAGTACCACGAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAA
170618 AATATTGCAA
Statistics
Matches: 197, Mismatches: 40, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
98 117 0.59
99 74 0.38
100 6 0.03
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (98 bp):
GAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATACAAAGGGAAAGGTTTAA
GTCGCAACGGTGAACCTTATACCTCAGAGCAGC
Found at i:173522 original size:11 final size:12
Alignment explanation
Indices: 173501--173535 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
173491 TTCTATCTTG
173501 ATTCATTTTTTT
1 ATTCATTTTTTT
*
173513 TTTC-TTTTTTT
1 ATTCATTTTTTT
173524 ATTCATTTTTTT
1 ATTCATTTTTTT
173536 CTTTTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTCATTTTTTT
Found at i:173547 original size:19 final size:20
Alignment explanation
Indices: 173509--173547 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
173499 TGATTCATTT
*
173509 TTTTTTTCTTTTTTTATTCA
1 TTTTTTTCTTTTTCTATTCA
173529 TTTTTTTCTTTTTCT-TTCA
1 TTTTTTTCTTTTTCTATTCA
173548 AATCTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTTCTTTTTCTATTCA
Found at i:178024 original size:135 final size:135
Alignment explanation
Indices: 177879--178121 Score: 364
Period size: 134 Copynumber: 1.8 Consensus size: 135
177869 AAAATTTTAG
* *
177879 TAAACTAAAAAAATAGTCACTAAACTTTGGTTATTTTTTATCACCAAATTATGAAAAGTTACA-T
1 TAAACT-AAAAAATAGTCACTAAACTTTGATTATTTTTTATCACCAAACTATGAAAAGTTACATT
* *
177943 TTTGATCATTTATCCATTAAT-TGTCGTTACAACATTAACGGAAGTAAAACCAATAAAAGTAATT
65 TTTGATCATCTATCCATTAATCT-TCATTACAACATTAACGGAAGTAAAACCAATAAAAGTAATT
178007 TTTTGAA
129 TTTTGAA
* * *
178014 TAAATTAAAAAATAGTCACTAAACTTTGATTATTTTTTATCACTAAACTATGAAATGTTACATTT
1 TAAACTAAAAAATAGTCACTAAACTTTGATTATTTTTTATCACCAAACTATGAAAAGTTACATTT
* **
178079 TTTATCATCTATTTATTAATCTTCATTACAACATTAACGGAAG
66 TTGATCATCTATCCATTAATCTTCATTACAACATTAACGGAAG
178122 AGTAACCCAA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
134 52 0.54
135 43 0.45
136 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (135 bp):
TAAACTAAAAAATAGTCACTAAACTTTGATTATTTTTTATCACCAAACTATGAAAAGTTACATTT
TTGATCATCTATCCATTAATCTTCATTACAACATTAACGGAAGTAAAACCAATAAAAGTAATTTT
TTGAA
Found at i:178253 original size:20 final size:20
Alignment explanation
Indices: 178192--178253 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
178182 TTTTAAAAAA
* *
178192 TATAAAAATA-TCTAAAATT
1 TATAAAAATATTTTTAAATT
*
178211 TCAT-AAAAT-TGTTTAAA-T
1 T-ATAAAAATATTTTTAAATT
178229 TATAAAAATATTTTTAAATT
1 TATAAAAATATTTTTAAATT
178249 TATAA
1 TATAA
178254 TTATATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
17 2 0.06
18 7 0.21
19 17 0.50
20 8 0.24
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (20 bp):
TATAAAAATATTTTTAAATT
Found at i:185965 original size:135 final size:135
Alignment explanation
Indices: 185820--186062 Score: 364
Period size: 134 Copynumber: 1.8 Consensus size: 135
185810 AAAATTTTAG
* *
185820 TAAACTAAAAAAATAGTCACTAAACTTTGGTTATTTTTTATCACCAAATTATGAAAAGTTACA-T
1 TAAACT-AAAAAATAGTCACTAAACTTTGATTATTTTTTATCACCAAACTATGAAAAGTTACATT
* *
185884 TTTGATCATTTATCCATTAAT-TGTCGTTACAACATTAACGGAAGTAAAACCAATAAAAGTAATT
65 TTTGATCATCTATCCATTAATCT-TCATTACAACATTAACGGAAGTAAAACCAATAAAAGTAATT
185948 TTTTGAA
129 TTTTGAA
* * *
185955 TAAATTAAAAAATAGTCACTAAACTTTGATTATTTTTTATCACTAAACTATGAAATGTTACATTT
1 TAAACTAAAAAATAGTCACTAAACTTTGATTATTTTTTATCACCAAACTATGAAAAGTTACATTT
* **
186020 TTTATCATCTATTTATTAATCTTCATTACAACATTAACGGAAG
66 TTGATCATCTATCCATTAATCTTCATTACAACATTAACGGAAG
186063 AGTAACCCAA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
134 52 0.54
135 43 0.45
136 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (135 bp):
TAAACTAAAAAATAGTCACTAAACTTTGATTATTTTTTATCACCAAACTATGAAAAGTTACATTT
TTGATCATCTATCCATTAATCTTCATTACAACATTAACGGAAGTAAAACCAATAAAAGTAATTTT
TTGAA
Found at i:186194 original size:20 final size:20
Alignment explanation
Indices: 186133--186194 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
186123 TTTTAAAAAA
* *
186133 TATAAAAATA-TCTAAAATT
1 TATAAAAATATTTTTAAATT
*
186152 TCAT-AAAAT-TGTTTAAA-T
1 T-ATAAAAATATTTTTAAATT
186170 TATAAAAATATTTTTAAATT
1 TATAAAAATATTTTTAAATT
186190 TATAA
1 TATAA
186195 TTATATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
17 2 0.06
18 7 0.21
19 17 0.50
20 8 0.24
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (20 bp):
TATAAAAATATTTTTAAATT
Found at i:196499 original size:19 final size:17
Alignment explanation
Indices: 196463--196497 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
196453 CGTCAATGCA
196463 ACTTTTCTAGATGAGAG
1 ACTTTTCTAGATGAGAG
*
196480 ACTTTTCTAGATAAGAG
1 ACTTTTCTAGATGAGAG
196497 A
1 A
196498 GATAAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (17 bp):
ACTTTTCTAGATGAGAG
Found at i:199074 original size:31 final size:32
Alignment explanation
Indices: 199000--199079 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
198990 ACTTCAAATG
*
199000 TGTATAATTGAATTAAAAATTAAAATTTCATG
1 TGTATAATTGAATTAAAAATTAAAATTTCATA
* * * * * *
199032 TATATATTTGAA-TCACAATTAAAGTTTTATA
1 TGTATAATTGAATTAAAAATTAAAATTTCATA
*
199063 TGTATAATTGAACTAAA
1 TGTATAATTGAATTAAA
199080 TCAAATTCAT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (32 bp):
TGTATAATTGAATTAAAAATTAAAATTTCATA
Found at i:203144 original size:20 final size:21
Alignment explanation
Indices: 203103--203145 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
203093 TAATTTACTA
203103 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
203124 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
203144 TA
1 TA
203146 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:207136 original size:281 final size:281
Alignment explanation
Indices: 206633--207397 Score: 1458
Period size: 281 Copynumber: 2.7 Consensus size: 281
206623 TTCAATTATG
206633 TATTGGATCGAAGATGACAGAATACATAATTGAACTTAGAGAAACAAGCCCTTTAAAATCGGTAA
1 TATTGGATCGAAGATGACAGAATACATAATTGAACTTAGAGAAACAAGCCCTTTAAAATCGGTAA
* *
206698 GCAAAGATTTTCTATGCTAATTTAAACAAGTTTTTTGAATTACGAGTGAAGGTAGCTAAGCTGAC
66 GCAAAGCTTTTCTATGCTAATTTAAACAAGTTTTTTGAATTATGAGTGAAGGTAGCTAAGCTGAC
206763 TGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGCTGCAAAAGGAATTATTGAGTGAGCAGAAATT
131 TGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGCTGCAAAAGGAATTATTGAGTGAGCAGAAATT
*
206828 GCAATTTATCTGAGTAATACAATATAGTTGTTTCTCAATTCGTCTTTTCTATATATCTTCAAGTA
196 GCAATTTATCTGAGTAATACAATATAGTTGTTTCTCAAATCGTCTTTTCTATATATCTTCAAGTA
206893 TTGTATGTATATGTTATAGGC
261 TTGTATGTATATGTTATAGGC
206914 TATTGGATCGAAGATGACAGAATACATAATTGAACTTAGAGAAACAAGCCCTTTAAAATCGGTAA
1 TATTGGATCGAAGATGACAGAATACATAATTGAACTTAGAGAAACAAGCCCTTTAAAATCGGTAA
*
206979 GCAAAGCTTTTCTATGCTAATTTAAACAAGTTTTTTGAATTATGAGTGAAGGTAGCAAAGCTGAC
66 GCAAAGCTTTTCTATGCTAATTTAAACAAGTTTTTTGAATTATGAGTGAAGGTAGCTAAGCTGAC
207044 TGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGCTGCAAAAGGAATTATTGAGTGAGCAGAAATT
131 TGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGCTGCAAAAGGAATTATTGAGTGAGCAGAAATT
*
207109 GCAATTTATCTGAGTAATACAATATAGTTGTTTCTCAAATCTTCTTTTCTATATATCTTCAAGTA
196 GCAATTTATCTGAGTAATACAATATAGTTGTTTCTCAAATCGTCTTTTCTATATATCTTCAAGTA
207174 TTGTATGTATATGTTATAGGC
261 TTGTATGTATATGTTATAGGC
207195 TATTGGATCGAAGATGACAGAATACATAATTGAACTTAGAGAAACAAGCCCTTTAAAATCGGTAA
1 TATTGGATCGAAGATGACAGAATACATAATTGAACTTAGAGAAACAAGCCCTTTAAAATCGGTAA
* **
207260 GCAAAGCTTTTCTGTGCTAATTTAAACAAGTTTTTTGAATTATGAGTGAAGGTAGCTAAGCTGTT
66 GCAAAGCTTTTCTATGCTAATTTAAACAAGTTTTTTGAATTATGAGTGAAGGTAGCTAAGCTGAC
207325 TGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGCTGCAAAAGGAATTATTGAGTGAGCAGAAATT
131 TGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGCTGCAAAAGGAATTATTGAGTGAGCAGAAATT
207390 GCAATTTA
196 GCAATTTA
207398 ACCAAGATTC
Statistics
Matches: 475, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
281 475 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (281 bp):
TATTGGATCGAAGATGACAGAATACATAATTGAACTTAGAGAAACAAGCCCTTTAAAATCGGTAA
GCAAAGCTTTTCTATGCTAATTTAAACAAGTTTTTTGAATTATGAGTGAAGGTAGCTAAGCTGAC
TGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGCTGCAAAAGGAATTATTGAGTGAGCAGAAATT
GCAATTTATCTGAGTAATACAATATAGTTGTTTCTCAAATCGTCTTTTCTATATATCTTCAAGTA
TTGTATGTATATGTTATAGGC
Found at i:209740 original size:3 final size:3
Alignment explanation
Indices: 209732--209766 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
209722 GAGTTGAAAC
209732 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
209767 AGAGGGCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:213058 original size:13 final size:13
Alignment explanation
Indices: 213042--213066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213032 GCACCTATAC
213042 GTGCAACCTAGGG
1 GTGCAACCTAGGG
213055 GTGCAACCTAGG
1 GTGCAACCTAGG
213067 AGTGTAAATG
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:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (13 bp):
GTGCAACCTAGGG
Found at i:213234 original size:12 final size:12
Alignment explanation
Indices: 213217--213249 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
213207 CACGAACAAG
213217 CTCGTTTATTAA
1 CTCGTTTATTAA
*
213229 CTCGTTTA-TAG
1 CTCGTTTATTAA
213240 CTCGTTTATT
1 CTCGTTTATT
213250 TATTAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (12 bp):
CTCGTTTATTAA
Found at i:213382 original size:23 final size:23
Alignment explanation
Indices: 213338--213383 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
213328 ACATTGTTCG
* *
213338 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
213361 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
213384 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:213674 original size:20 final size:20
Alignment explanation
Indices: 213649--213695 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
213639 CTGATTTGAT
*
213649 TTGATTTAAATTTTTTTAAC
1 TTGATTTAAATTTCTTTAAC
213669 TTGATTTAAATTTCTTTAAC
1 TTGATTTAAATTTCTTTAAC
213689 TTGATTT
1 TTGATTT
213696 GAACTTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (20 bp):
TTGATTTAAATTTCTTTAAC
Found at i:215129 original size:22 final size:23
Alignment explanation
Indices: 215099--215146 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
215089 AAATAGTGAG
* *
215099 AAACTAGTAGGAAAACAACAGCA
1 AAACTAGTAGAAAAACAACAACA
215122 AAAC-AGTAGAAAAACAACAACA
1 AAACTAGTAGAAAAACAACAACA
215144 AAA
1 AAA
215147 TAACTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.65, C:0.17, G:0.12, T:0.06
Consensus pattern (23 bp):
AAACTAGTAGAAAAACAACAACA
Found at i:236286 original size:29 final size:30
Alignment explanation
Indices: 236232--236289 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
236222 AGAATTAGAT
236232 CAAATCAAAATTTCATGTATAAAATTGCAC
1 CAAATCAAAATTTCATGTATAAAATTGCAC
* * *
236262 CAAATTAAAA-TTCATTTATACAATTGCA
1 CAAATCAAAATTTCATGTATAAAATTGCA
236290 TATTAAACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (30 bp):
CAAATCAAAATTTCATGTATAAAATTGCAC
Found at i:236611 original size:2 final size:2
Alignment explanation
Indices: 236599--236628 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
236589 ATTTAAAATT
*
236599 TA TA AA 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
236629 ATTTTTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:240692 original size:23 final size:23
Alignment explanation
Indices: 240623--240769 Score: 122
Period size: 23 Copynumber: 6.3 Consensus size: 23
240613 CGGAACAAAT
* *
240623 AGAGAGTAC-CAAAGTACT-AAC
1 AGAGAGCACACAAAGTGCTAAAC
* *
240644 AGAGAGCACA-TAAGTGCTGGGCAAC
1 AGAGAGCACACAAAGTGCT---AAAC
*
240669 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACAAAGTGCTAAAC
* * *
240692 AGAGAGTACACAAAGTACTAATC
1 AGAGAGCACACAAAGTGCTAAAC
240715 AGAGAGCACACAAAGTGCTAATAAC
1 AGAGAGCACACAAAGTGCT-A-AAC
* *
240740 AGAGAGCACGA-GACGTGCTAAAC
1 AGAGAGCAC-ACAAAGTGCTAAAC
240763 AGAGAGC
1 AGAGAGC
240770 GCGCTAGTGT
Statistics
Matches: 102, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
21 14 0.14
23 49 0.48
24 2 0.02
25 30 0.29
26 7 0.07
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAAAC
Found at i:240697 original size:25 final size:25
Alignment explanation
Indices: 240669--240768 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 25
240659 GCTGGGCAAC
240669 AGAGAGCACACACAGTGCTAAACAG
1 AGAGAGCACACACAGTGCTAAACAG
* *
240694 AGAGTA-CACA-A-AGTACTAATC--
1 AGAG-AGCACACACAGTGCTAAACAG
* *
240715 AGAGAGCACACAAAGTGCTAATA-AC
1 AGAGAGCACACACAGTGCTAA-ACAG
*
240740 AGAGAGCACGAGAC-GTGCTAAACAG
1 AGAGAGCAC-ACACAGTGCTAAACAG
240765 AGAG
1 AGAG
240769 CGCGCTAGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
20 1 0.02
21 8 0.14
22 1 0.02
23 15 0.25
24 2 0.03
25 29 0.49
26 3 0.05
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (25 bp):
AGAGAGCACACACAGTGCTAAACAG
Found at i:240741 original size:71 final size:69
Alignment explanation
Indices: 240623--240768 Score: 197
Period size: 71 Copynumber: 2.1 Consensus size: 69
240613 CGGAACAAAT
* **
240623 AGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCAC-ACACAGTGC
1 AGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAACAGAGAGCACGACAC-GTGC
240687 TAAAC
65 TAAAC
* *
240692 AGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATAACAGAGAGCACGAGACGT
1 AGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAACAACAGAGAGCACGACACGT
240756 GCTAAAC
63 GCTAAAC
240763 AGAGAG
1 AGAGAG
240769 CGCGCTAGTG
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
69 9 0.13
70 11 0.16
71 38 0.56
72 10 0.15
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.12
Consensus pattern (69 bp):
AGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAACAGAGAGCACGACACGTGCT
AAAC
Found at i:245787 original size:4 final size:4
Alignment explanation
Indices: 245778--245805 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
245768 ATTTAAATAG
245778 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
245806 GACAATATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:249735 original size:12 final size:12
Alignment explanation
Indices: 249718--249769 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
249708 ATAACATCCA
*
249718 AACAACCAAAAT
1 AACAACCAAAAC
249730 AACAACCAAAAC
1 AACAACCAAAAC
* * *
249742 AGCAACAAAAAT
1 AACAACCAAAAC
249754 AACAA-CAAAAC
1 AACAACCAAAAC
249765 AACAA
1 AACAA
249770 AACAACAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.69, C:0.25, G:0.02, T:0.04
Consensus pattern (12 bp):
AACAACCAAAAC
Found at i:249762 original size:23 final size:24
Alignment explanation
Indices: 249720--249765 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
249710 AACATCCAAA
*
249720 CAACCAAAATAACAACCAAAACAG
1 CAACAAAAATAACAACCAAAACAG
249744 CAACAAAAATAACAA-CAAAACA
1 CAACAAAAATAACAACCAAAACA
249766 ACAAAACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.67, C:0.26, G:0.02, T:0.04
Consensus pattern (24 bp):
CAACAAAAATAACAACCAAAACAG
Found at i:249767 original size:8 final size:8
Alignment explanation
Indices: 249754--249779 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
249744 CAACAAAAAT
249754 AACAACAA
1 AACAACAA
249762 AACAACAA
1 AACAACAA
249770 AACAACAA
1 AACAACAA
249778 AA
1 AA
249780 ATAGTAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (8 bp):
AACAACAA
Found at i:249769 original size:20 final size:20
Alignment explanation
Indices: 249704--249771 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
249694 AAAAACGCAT
* *
249704 AAAAATAACATCCAAACAAC
1 AAAAATAACAACAAAACAAC
*
249724 CAAAATAACAACCAAAACAGCAAC
1 AAAAATAACAA-C-AAA-A-CAAC
249748 AAAAATAACAACAAAACAAC
1 AAAAATAACAACAAAACAAC
249768 AAAA
1 AAAA
249772 CAACAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 17 0.43
21 2 0.05
22 5 0.12
23 2 0.05
24 14 0.35
ACGTcount: A:0.69, C:0.24, G:0.01, T:0.06
Consensus pattern (20 bp):
AAAAATAACAACAAAACAAC
Found at i:249778 original size:28 final size:29
Alignment explanation
Indices: 249744--249798 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
249734 ACCAAAACAG
249744 CAACAAAAATAACAAC-AAAACAACAAAA
1 CAACAAAAATAACAACAAAAACAACAAAA
**
249772 CAACAAAAATAGTAACAAAAACAACAA
1 CAACAAAAATAACAACAAAAACAACAA
249799 CATCAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.05
Consensus pattern (29 bp):
CAACAAAAATAACAACAAAAACAACAAAA
Found at i:249800 original size:12 final size:12
Alignment explanation
Indices: 249718--249800 Score: 58
Period size: 12 Copynumber: 6.6 Consensus size: 12
249708 ATAACATCCA
* *
249718 AACAACCAAAAT
1 AACAACAAAAAC
*
249730 AACAACCAAAAC
1 AACAACAAAAAC
* *
249742 AGCAACAAAAAT
1 AACAACAAAAAC
249754 AACAACAAAACAAC
1 AACAAC-AAA-AAC
*
249768 AAAACAACAAAAAT
1 --AACAACAAAAAC
**
249782 AGTAACAAAAAC
1 AACAACAAAAAC
249794 AACAACA
1 AACAACA
249801 TCAAAACAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
12 39 0.71
13 3 0.05
14 4 0.07
15 3 0.05
16 6 0.11
ACGTcount: A:0.70, C:0.23, G:0.02, T:0.05
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:249806 original size:26 final size:24
Alignment explanation
Indices: 249762--249848 Score: 78
Period size: 23 Copynumber: 3.8 Consensus size: 24
249752 ATAACAACAA
* *
249762 AACAACAA-AACAACAAAAATAGT
1 AACAAAAACAACAACAAAAACAGT
249785 AACAAAAACAACAACATCAAAACAGT
1 AACAAAAACAACAACA--AAAACAGT
*
249811 -A-AAAAA-AACATC-AAAACAGT
1 AACAAAAACAACAACAAAAACAGT
*
249831 AA-AAAAACAACATCAAAA
1 AACAAAAACAACAACAAAA
249849 TAGCAAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
20 8 0.15
21 6 0.11
22 6 0.11
23 15 0.27
24 12 0.22
25 1 0.02
26 7 0.13
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.08
Consensus pattern (24 bp):
AACAAAAACAACAACAAAAACAGT
Found at i:249808 original size:20 final size:20
Alignment explanation
Indices: 249785--249860 Score: 84
Period size: 20 Copynumber: 3.6 Consensus size: 20
249775 CAAAAATAGT
249785 AACA-AAAACAACAACATCAA
1 AACAGAAAA-AACAACATCAA
249805 AACAGTAAAAAA-AACATCAA
1 AACAG-AAAAAACAACATCAA
249825 AACAGTAAAAAAACAACATCAA
1 AACAG--AAAAAACAACATCAA
*
249847 AATAGCAAAAAACA
1 AACAG-AAAAAACA
249861 GTAAAAAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
20 17 0.35
21 16 0.33
22 16 0.33
ACGTcount: A:0.70, C:0.18, G:0.04, T:0.08
Consensus pattern (20 bp):
AACAGAAAAAACAACATCAA
Found at i:249836 original size:19 final size:20
Alignment explanation
Indices: 249797--249858 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
249787 CAAAAACAAC
249797 AACATCAAAACAGTAAAAAA
1 AACATCAAAACAGTAAAAAA
249817 AACATCAAAACAGTAAAAAAA
1 AACATCAAAACAGT-AAAAAA
* *
249838 CAACATCAAAATAGCAAAAAA
1 -AACATCAAAACAGTAAAAAA
249859 CAGTAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 14 0.37
21 12 0.32
22 12 0.32
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.10
Consensus pattern (20 bp):
AACATCAAAACAGTAAAAAA
Found at i:249842 original size:22 final size:22
Alignment explanation
Indices: 249788--249858 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
249778 AAATAGTAAC
249788 AAAAACAACAACATCAAAACAGT
1 AAAAA-AACAACATCAAAACAGT
249811 -AAAAAA-AACATCAAAACAGT
1 AAAAAAACAACATCAAAACAGT
* *
249831 AAAAAAACAACATCAAAATAGC
1 AAAAAAACAACATCAAAACAGT
249853 AAAAAA
1 AAAAAA
249859 CAGTAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 14 0.32
21 8 0.18
22 22 0.50
ACGTcount: A:0.70, C:0.17, G:0.04, T:0.08
Consensus pattern (22 bp):
AAAAAAACAACATCAAAACAGT
Found at i:259067 original size:3 final size:3
Alignment explanation
Indices: 259059--259084 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
259049 ATTTCCAGTC
259059 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
259085 GGTTTCTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:265772 original size:17 final size:17
Alignment explanation
Indices: 265750--265807 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
265740 CTTTTCAAGC
265750 TTGGGTTTGAGGAGTGG
1 TTGGGTTTGAGGAGTGG
** * *
265767 TTGGGTTT-CTGTGTGC
1 TTGGGTTTGAGGAGTGG
*
265783 TTGGGTTTGGGGAGTGG
1 TTGGGTTTGAGGAGTGG
265800 TTGGGTTT
1 TTGGGTTT
265808 CTGTGGTGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 12 0.38
17 20 0.62
ACGTcount: A:0.05, C:0.03, G:0.48, T:0.43
Consensus pattern (17 bp):
TTGGGTTTGAGGAGTGG
Found at i:265786 original size:33 final size:33
Alignment explanation
Indices: 265748--265812 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
265738 TTCTTTTCAA
265748 GCTTGGGTTTGAGGAGTGGTTGGGTTTCTGTGT
1 GCTTGGGTTTGAGGAGTGGTTGGGTTTCTGTGT
*
265781 GCTTGGGTTTGGGGAGTGGTTGGGTTTCTGTG
1 GCTTGGGTTTGAGGAGTGGTTGGGTTTCTGTG
265813 GTGTTCCCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.05, C:0.06, G:0.48, T:0.42
Consensus pattern (33 bp):
GCTTGGGTTTGAGGAGTGGTTGGGTTTCTGTGT
Found at i:265990 original size:81 final size:84
Alignment explanation
Indices: 265855--266473 Score: 596
Period size: 93 Copynumber: 7.0 Consensus size: 84
265845 TAAAATATTG
* ** *
265855 GGTTTAAAGTTATTCGTTTCTTTCTTTCCTTCAGAACTTGGTTTTGAAGGGTTT-TCC-CCT-C-
1 GGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGG-CCTGGAGGGTTTCTCCGCCTCCT
*
265916 GACTCAATTCAATAGCCTTT
65 GACTCAATTCAGTAGCCTTT
* *
265936 GGTTTAAAGTTGTTGGTTTCTTTCTTTCCTTCAGAACTTGGCGCTGGAGGGTTT-T-CTCCT--T
1 GGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGC-CTGGAGGGTTTCTCCGCCTCCT
*
265997 TACTCAATTCAGTAGCCTTT
65 GACTCAATTCAGTAGCCTTT
* *
266017 GGTTTAAAGTTATTGGTTTCTGTCTTTCCTTCAAAACTTGGCCTTGGAGGGTTTTCCCCCTGACT
1 GGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCC-TGGAGGG-TTT----CT--C-
*
266082 CTCCTCCTGACTCAATTCAGTAGCCTTT
57 CGCCTCCTGACTCAATTCAGTAGCCTTT
* * *
266110 GGTTTAAAGTTTTTGATTTCTTTCTTTCCTTCAGAATTTGGCCTTGGAGGGTTTTCATCCTGACT
1 GGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCC-TGGAGGG-TTTC-TCC-G-C-
266175 TTCTCCCTGACTCAATTCAGTAGCCTTT
60 --CT-CCTGACTCAATTCAGTAGCCTTT
* *
266203 GGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCTTTGGAAGGTTTTCATCCTGACT
1 GGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGC-CTGG-AGGGTTTC-TCC-G-C-
266268 CTCCCCCTGACTCAATTCAGTAGCCTTT
60 CT---CCTGACTCAATTCAGTAGCCTTT
* *
266296 GGTTTAAAGTTACTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTTGGAGAGTTTTCATCCTGGCT
1 GGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCC-TGGAG-GGTTTC-TCC--GC-
* *
266361 CTCCCCCTGACTCAATTCAATATCCTTT
60 CT---CCTGACTCAATTCAGTAGCCTTT
* *
266389 GGTTTAAAGTTGTTGGTTTCTTTCTTTCCTTCAGAACTTGGTCTTGGAGGGTTT-TCC-CCT--T
1 GGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGG-CCTGGAGGGTTTCTCCGCCTCCT
*
266450 GACTCAATTCTGTAGCCTTT
65 GACTCAATTCAGTAGCCTTT
266470 GGTT
1 GGTT
266474 CATCCCTCCA
Statistics
Matches: 473, Mismatches: 34, Indels: 62
0.83 0.06 0.11
Matches are distributed among these distances:
80 2 0.00
81 138 0.29
82 3 0.01
86 2 0.00
87 3 0.01
88 1 0.00
89 2 0.00
90 4 0.01
91 8 0.02
92 8 0.02
93 297 0.63
94 5 0.01
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.43
Consensus pattern (84 bp):
GGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTGGAGGGTTTCTCCGCCTCCTG
ACTCAATTCAGTAGCCTTT
Found at i:266107 original size:93 final size:93
Alignment explanation
Indices: 265998--266444 Score: 723
Period size: 93 Copynumber: 4.8 Consensus size: 93
265988 TTTCTCCTTT
* *
265998 ACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTCTGTCTTTCCTTCAAAACTTGGCCTTG
1 ACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTTG
** *
266063 GAGGGTTTTCCCCCTGACTCTCCTCCTG
66 GAGGGTTTTCATCCTGACTCTCCCCCTG
* * *
266091 ACTCAATTCAGTAGCCTTTGGTTTAAAGTTTTTGATTTCTTTCTTTCCTTCAGAATTTGGCCTTG
1 ACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTTG
* *
266156 GAGGGTTTTCATCCTGACTTTCTCCCTG
66 GAGGGTTTTCATCCTGACTCTCCCCCTG
*
266184 ACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCTTTG
1 ACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTTG
*
266249 GAAGGTTTTCATCCTGACTCTCCCCCTG
66 GAGGGTTTTCATCCTGACTCTCCCCCTG
*
266277 ACTCAATTCAGTAGCCTTTGGTTTAAAGTTACTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTTG
1 ACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTTG
* *
266342 GAGAGTTTTCATCCTGGCTCTCCCCCTG
66 GAGGGTTTTCATCCTGACTCTCCCCCTG
* * * *
266370 ACTCAATTCAATATCCTTTGGTTTAAAGTTGTTGGTTTCTTTCTTTCCTTCAGAACTTGGTCTTG
1 ACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTTG
266435 GAGGGTTTTC
66 GAGGGTTTTC
266445 CCCTTGACTC
Statistics
Matches: 326, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 326 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.43
Consensus pattern (93 bp):
ACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTTG
GAGGGTTTTCATCCTGACTCTCCCCCTG
Found at i:266411 original size:279 final size:267
Alignment explanation
Indices: 265907--266444 Score: 781
Period size: 279 Copynumber: 2.0 Consensus size: 267
265897 TTTGAAGGGT
*
265907 TTTCCCCTCGACTCAATTCAATAGCCTTTGGTTTAAAGTTGTTGGTTTCTTTCTTTCCTTCAGAA
1 TTTCCCCTCGACTCAATTCAATAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAA
* *
265972 CTTGGCGCTGGAGGGTTTTCTCCTTTACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTC
66 CTTGGCGCTGGAAGGTTTTCTCCTTTACTCAATTCAGTAGCCTTTGGTTTAAAGTTACTGGTTTC
* * * *
266037 TGTCTTTCCTTCAAAACTTGGCCTTGGAGGGTTTTCCCCCTGACTCTCCTCCTGACTCAATTCAG
131 TGTCTTTCCTTCAAAACTTGGCCTTGGAGAGTTTTCACCCTGACTCTCCCCCTGACTCAATTCAA
* *
266102 TAGCCTTTGGTTTAAAGTTTTTGATTTCTTTCTTTCCTTCAGAATTTGGCCTTGGAGGGTTTTCA
196 TAGCCTTTGGTTTAAAGTTGTTGATTTCTTTCTTTCCTTCAGAACTTGGCCTTGGAGGGTTTTCA
266167 TCCTGAC
261 TCCTGAC
*
266174 TTTCTCCCT-GACTCAATTCAGTAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGA
1 TTTC-CCCTCGACTCAATTCAATAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGA
**
266238 ACTTGGCTTTGGAAGGTTTTCATCCTGACTCTCCCCCTGACTCAATTCAGTAGCCTTTGGTTTAA
65 ACTTGGCGCTGGAAGGTTTTC-T-C---CT-T-----T-ACTCAATTCAGTAGCCTTTGGTTTAA
* * * *
266303 AGTTACTGGTTTCTTTCTTTCCTTCAGAACTTGGCCTTGGAGAGTTTTCATCCTGGCTCTCCCCC
118 AGTTACTGGTTTCTGTCTTTCCTTCAAAACTTGGCCTTGGAGAGTTTTCACCCTGACTCTCCCCC
* * *
266368 TGACTCAATTCAATATCCTTTGGTTTAAAGTTGTTGGTTTCTTTCTTTCCTTCAGAACTTGGTCT
183 TGACTCAATTCAATAGCCTTTGGTTTAAAGTTGTTGATTTCTTTCTTTCCTTCAGAACTTGGCCT
266433 TGGAGGGTTTTC
248 TGGAGGGTTTTC
266445 CCCTTGACTC
Statistics
Matches: 239, Mismatches: 19, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
267 75 0.31
268 5 0.02
269 1 0.00
272 2 0.01
273 1 0.00
278 1 0.00
279 154 0.64
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (267 bp):
TTTCCCCTCGACTCAATTCAATAGCCTTTGGTTTAAAGTTATTGGTTTCTTTCTTTCCTTCAGAA
CTTGGCGCTGGAAGGTTTTCTCCTTTACTCAATTCAGTAGCCTTTGGTTTAAAGTTACTGGTTTC
TGTCTTTCCTTCAAAACTTGGCCTTGGAGAGTTTTCACCCTGACTCTCCCCCTGACTCAATTCAA
TAGCCTTTGGTTTAAAGTTGTTGATTTCTTTCTTTCCTTCAGAACTTGGCCTTGGAGGGTTTTCA
TCCTGAC
Found at i:290831 original size:6 final size:6
Alignment explanation
Indices: 290820--290852 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
290810 ACTATATATA
290820 TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGT
1 TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGT
290853 AAAAGGAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.48, T:0.36
Consensus pattern (6 bp):
TGTGCG
Found at i:306736 original size:24 final size:25
Alignment explanation
Indices: 306672--306736 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
306662 TTTTCACAAA
* *
306672 TTAATTAACAACATATAAAAATGTT
1 TTAATAAAAAACATATAAAAATGTT
*
306697 TT-ATAAAATTAA-ATATAATAAT-TT
1 TTAATAAAA--AACATATAAAAATGTT
306721 TTAATAAAAAACATAT
1 TTAATAAAAAACATAT
306737 TCTTTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
23 2 0.06
24 12 0.36
25 17 0.52
26 2 0.06
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (25 bp):
TTAATAAAAAACATATAAAAATGTT
Found at i:307966 original size:17 final size:18
Alignment explanation
Indices: 307935--307968 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
307925 TCAAAAATTG
*
307935 AAAATAATTTTTAAAATC
1 AAAATAATTTATAAAATC
307953 AAAAT-ATTTATAAAAT
1 AAAATAATTTATAAAAT
307969 TTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAATTTATAAAATC
Found at i:313606 original size:15 final size:14
Alignment explanation
Indices: 313587--313625 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
313577 CGATTTAATA
313587 AATTTTTATTTTTT
1 AATTTTTATTTTTT
*
313601 AGATTTTTAATTTTT
1 A-ATTTTTATTTTTT
*
313616 AATTATTATT
1 AATTTTTATT
313626 GATCCAGCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
AATTTTTATTTTTT
Found at i:314422 original size:11 final size:11
Alignment explanation
Indices: 314406--314440 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
314396 TATACACCCA
* *
314406 TTCTTTTTCTC
1 TTCTTTCTCCC
314417 TTCTTTCTCCC
1 TTCTTTCTCCC
314428 TTCTTTCTCCC
1 TTCTTTCTCCC
314439 TT
1 TT
314441 TCCCCCTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (11 bp):
TTCTTTCTCCC
Found at i:315102 original size:5 final size:5
Alignment explanation
Indices: 315092--315117 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
315082 AGCTTCAAAA
315092 GTGAT GTGAT GTGAT GTGAT GTGAT G
1 GTGAT GTGAT GTGAT GTGAT GTGAT G
315118 AGAGGTCCCT
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:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTGAT
Found at i:315532 original size:22 final size:22
Alignment explanation
Indices: 315481--315560 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
315471 GCTGGGGAAA
* *
315481 CAGTAAGCACACACAATGCAAT
1 CAGTAGGCACACACAGTGCAAT
315503 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
315526 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
*
315549 CAATAGGCACAC
1 CAGTAGGCACAC
315561 GAGGTGCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.39, C:0.29, G:0.20, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:315585 original size:23 final size:23
Alignment explanation
Indices: 315555--315624 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
315545 AAATCAATAG
315555 GCACACGAGGTGCGAAACAGTAA
1 GCACACGAGGTGCGAAACAGTAA
315578 GCACACGAGGTGCGAAACAGTAA
1 GCACACGAGGTGCGAAACAGTAA
*
315601 GCACACGAAGTGCGAAACAGTAA
1 GCACACGAGGTGCGAAACAGTAA
315624 G
1 G
315625 TGCGCTAGCG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.40, C:0.21, G:0.30, T:0.09
Consensus pattern (23 bp):
GCACACGAGGTGCGAAACAGTAA
Found at i:317646 original size:43 final size:43
Alignment explanation
Indices: 317597--317696 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
317587 TTAAACGGAT
* * * *
317597 GGTCGGATCAATTTTGATCACTGATCTGATTTTAAAAATTTTG
1 GGTCGGAACAATTTCGATCACTGATCTAATATTAAAAATTTTG
317640 GGTCGGAACAATTTCGATCACTGATCTAATATTAAAAATTTTG
1 GGTCGGAACAATTTCGATCACTGATCTAATATTAAAAATTTTG
* *
317683 GATCAGAAC-ATTTC
1 GGTCGGAACAATTTC
317697 ATGCTAACAT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.10
43 46 0.90
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (43 bp):
GGTCGGAACAATTTCGATCACTGATCTAATATTAAAAATTTTG
Found at i:318103 original size:28 final size:30
Alignment explanation
Indices: 318072--318129 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
318062 TAAAAAAATT
318072 AAATATATATATTT-TT-TAATTTT-ATAAA
1 AAATATATA-ATTTATTATAATTTTCATAAA
*
318100 AAATGTATAATTTATTATAATTTTCATAAA
1 AAATATATAATTTATTATAATTTTCATAAA
318130 TTTTCATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.15
28 10 0.38
29 7 0.27
30 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
AAATATATAATTTATTATAATTTTCATAAA
Found at i:320393 original size:16 final size:15
Alignment explanation
Indices: 320362--320392 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
320352 TCTATTTTGA
*
320362 TATTTAATTTATTTT
1 TATTTAAATTATTTT
320377 TATTTAAATTATTTT
1 TATTTAAATTATTTT
320392 T
1 T
320393 TCTTAGTCAG
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTAAATTATTTT
Found at i:320644 original size:2 final size:2
Alignment explanation
Indices: 320637--320664 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
320627 TTGCTCTTAC
320637 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
320665 TCATTTTATT
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:320786 original size:16 final size:16
Alignment explanation
Indices: 320767--320808 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
320757 ATAAATTATT
320767 TAAAAAATTATAAAAA
1 TAAAAAATTATAAAAA
*
320783 TAAAAAATATTTAAAAA
1 TAAAAAAT-TATAAAAA
320800 -AAAAAATTA
1 TAAAAAATTA
320809 ATTTAACCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 1 0.04
16 15 0.65
17 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAAATTATAAAAA
Found at i:320812 original size:18 final size:18
Alignment explanation
Indices: 320768--320814 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
320758 TAAATTATTT
320768 AAAA-AATTATAAAAATAA
1 AAAATAATT-TAAAAATAA
320786 AAAAT-ATTTAAAAA-AA
1 AAAATAATTTAAAAATAA
320802 AAAATTAATTTAA
1 AAAA-TAATTTAA
320815 CCGGTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.23
17 7 0.27
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATAATTTAAAAATAA
Found at i:329840 original size:37 final size:37
Alignment explanation
Indices: 329797--329924 Score: 100
Period size: 37 Copynumber: 3.3 Consensus size: 37
329787 TATAACTATT
329797 ATTATATTATAGATTATAATAAAATATATAGTATTAC
1 ATTATATTATAGATTATAATAAAATATATAGTATTAC
* * *
329834 ATTATATTATA-ATGTTTAATCATTGATGCATATATAAACTATTA-
1 ATTATATTATAGAT-TATAAT-A---A---A-ATATATAGTATTAC
*
329878 A-TATATTATAGATTATAATAAAAGATATAGTATTAC
1 ATTATATTATAGATTATAATAAAATATATAGTATTAC
* *
329914 ATGATACTATA
1 ATTATATTATA
329925 ACGTTCAATC
Statistics
Matches: 70, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
35 10 0.14
36 4 0.06
37 23 0.33
38 1 0.01
39 1 0.01
41 1 0.01
42 1 0.01
43 14 0.20
44 4 0.06
45 11 0.16
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (37 bp):
ATTATATTATAGATTATAATAAAATATATAGTATTAC
Found at i:329874 original size:80 final size:81
Alignment explanation
Indices: 329783--329937 Score: 249
Period size: 80 Copynumber: 1.9 Consensus size: 81
329773 GCACTACTAT
* * * * *
329783 TATATATAACTATTATTATATTATAGATTATAATAAAATATATAGTATTACATTATATTATAATG
1 TATATATAACTATTAATATATTATAGATTATAATAAAAGATATAGTATTACATGATACTATAACG
*
329848 TTTAATCATTGATGCA
66 TTCAATCATTGATGCA
329864 TATATA-AACTATTAATATATTATAGATTATAATAAAAGATATAGTATTACATGATACTATAACG
1 TATATATAACTATTAATATATTATAGATTATAATAAAAGATATAGTATTACATGATACTATAACG
329928 TTCAATCATT
66 TTCAATCATT
329938 CAATCATTGA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 62 0.91
81 6 0.09
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (81 bp):
TATATATAACTATTAATATATTATAGATTATAATAAAAGATATAGTATTACATGATACTATAACG
TTCAATCATTGATGCA
Found at i:330110 original size:2 final size:2
Alignment explanation
Indices: 330105--330134 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
330095 ATAAAAATTA
330105 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
330135 GCATCACTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:333732 original size:4 final size:4
Alignment explanation
Indices: 333719--333761 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
333709 AAAATTGAAG
*
333719 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
333762 GAAGGGAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:334166 original size:20 final size:21
Alignment explanation
Indices: 334125--334167 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
334115 TAATTTACTT
334125 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
334146 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
334166 TA
1 TA
334168 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:335590 original size:22 final size:23
Alignment explanation
Indices: 335564--335606 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
335554 AATTGGAAAT
* *
335564 AAAATTATTTTATTA-TTTTAAA
1 AAAATAATTTTAATAGTTTTAAA
335586 AAAATAATTTTAATAGTTTTA
1 AAAATAATTTTAATAGTTTTA
335607 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AAAATAATTTTAATAGTTTTAAA
Found at i:339333 original size:12 final size:11
Alignment explanation
Indices: 339301--339329 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
339291 AAATATTAAA
339301 TTAAAAATAAT
1 TTAAAAATAAT
339312 TTAAAAATAAT
1 TTAAAAATAAT
339323 TTAAAAA
1 TTAAAAA
339330 ATAAAAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAAAATAAT
Found at i:339599 original size:16 final size:16
Alignment explanation
Indices: 339578--339612 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
339568 CAAACTGTTC
*
339578 ACAACTAACCTTCTTG
1 ACAACTAACCTTCATG
339594 ACAACTAACCTTCATG
1 ACAACTAACCTTCATG
339610 ACA
1 ACA
339613 CACGTCTCAG
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:0.37, C:0.31, G:0.06, T:0.26
Consensus pattern (16 bp):
ACAACTAACCTTCATG
Found at i:345316 original size:36 final size:37
Alignment explanation
Indices: 345263--345340 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 37
345253 TAAAAATGGA
* *
345263 TATAA-AAATTTTCAAAATCAATGAAAGAACTCAAAT
1 TATAATAAATTTTCAAAATAAATGAAAGAACTAAAAT
* * *
345299 TATAATAAATTTT-AAAATAAATTAAAGTATTAAAAT
1 TATAATAAATTTTCAAAATAAATGAAAGAACTAAAAT
345335 TATAAT
1 TATAAT
345341 CACGATTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 29 0.81
37 7 0.19
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (37 bp):
TATAATAAATTTTCAAAATAAATGAAAGAACTAAAAT
Found at i:345591 original size:49 final size:51
Alignment explanation
Indices: 345496--345597 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 51
345486 TAATTTAAGT
*
345496 ATAATTTTTTAAATATTTCAATAATTTAAATAGAAACTATTGAATAATTTA
1 ATAATTTTTTAAATATTTCAATAATTAAAATAGAAACTATTGAATAATTTA
* *
345547 ATAATTTTTTAAA-A-TT-AATTAATTAAAATATAAATTTATT-AATAATTTA
1 ATAATTTTTTAAATATTTCAA-TAATTAAAATAGAAA-CTATTGAATAATTTA
345596 AT
1 AT
345598 GGTTTTAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
48 2 0.04
49 26 0.57
50 5 0.11
51 13 0.28
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (51 bp):
ATAATTTTTTAAATATTTCAATAATTAAAATAGAAACTATTGAATAATTTA
Found at i:346112 original size:28 final size:30
Alignment explanation
Indices: 346079--346148 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 30
346069 TTTGATTTTT
*
346079 TTTTTTTTAAGATTAATAATTATATTCGAC
1 TTTTTTTAAAGATTAATAATTATATTCGAC
* *
346109 TTTTTTTCAAAGATTAATAATTATATTTGAT
1 TTTTTTT-AAAGATTAATAATTATATTCGAC
346140 TTTTTTTAA
1 TTTTTTTAA
346149 TATTGAGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 9 0.25
31 27 0.75
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (30 bp):
TTTTTTTAAAGATTAATAATTATATTCGAC
Found at i:348240 original size:47 final size:48
Alignment explanation
Indices: 348146--348240 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
348136 TTAAAATTTT
* *
348146 CTCTTCACATCTCTGCAACCCCTGCTGCTATTATTTTTTTCCGGCAAC
1 CTCTTCACATCTCTGCAACCCCTGCTACTATTATTTTTTTCCAGCAAC
*
348194 CTCTTCACGTC-CTGCAACCCCCTGCTACTATTATTTTTTT-CAGCAAC
1 CTCTTCACATCTCTGCAA-CCCCTGCTACTATTATTTTTTTCCAGCAAC
348241 AACTTTGCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 12 0.28
48 31 0.72
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.37
Consensus pattern (48 bp):
CTCTTCACATCTCTGCAACCCCTGCTACTATTATTTTTTTCCAGCAAC
Found at i:350498 original size:24 final size:24
Alignment explanation
Indices: 350471--350521 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
350461 TTGTTGTTAT
*
350471 TATGATGAATACTATTATTGTTGC
1 TATGATGAACACTATTATTGTTGC
350495 TATGATGAACACTATTATTGTTGC
1 TATGATGAACACTATTATTGTTGC
350519 TAT
1 TAT
350522 TCTTTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (24 bp):
TATGATGAACACTATTATTGTTGC
Found at i:350502 original size:27 final size:26
Alignment explanation
Indices: 350461--350521 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
350451 TTTTAAATTC
* *
350461 TTGTTGTTATTATGATGAATACTATTA
1 TTGTTGCTA-TATGATGAACACTATTA
350488 TTGTTGC--TATGATGAACACTATTA
1 TTGTTGCTATATGATGAACACTATTA
350512 TTGTTGCTAT
1 TTGTTGCTAT
350522 TCTTTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 23 0.77
26 1 0.03
27 6 0.20
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.49
Consensus pattern (26 bp):
TTGTTGCTATATGATGAACACTATTA
Found at i:353820 original size:24 final size:25
Alignment explanation
Indices: 353765--353820 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
353755 TATAATCACC
*
353765 CTATTTTTCTTTTTTTTTCTTCATT
1 CTATTTTTCTTTTTCTTTCTTCATT
* *
353790 TTGTTTTTC-TTTTCTTTCTTCCA-T
1 CTATTTTTCTTTTTCTTTCTT-CATT
353814 CTATTTT
1 CTATTTT
353821 CCTTAAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (25 bp):
CTATTTTTCTTTTTCTTTCTTCATT
Found at i:354551 original size:198 final size:197
Alignment explanation
Indices: 354231--354846 Score: 895
Period size: 198 Copynumber: 3.1 Consensus size: 197
354221 ACGATGAGTC
** **
354231 AGTCTAGTTTCATTTAGAATAAACGGAGATTGATTTTGATTTGTAG-TTAAAATATATGAATTTT
1 AGTCTAGTTTTGTTTAGAATAAACGGAGATTGATTTCAATTTGTAGTTTAAAATATATGAATTTT
* * * *
354295 TGAGTGTTG-AATGTCATAAAAATCTTGCAGCAGAATTCTTATAAAACAAATTTAGCAGTGACTT
66 TGAATGTTGAAAGGTCATAAAAATCTGGCAGCAGAATTCTTATAAAACAGATTTAGCAGTGACTT
* *
354359 TGAAAAATCACCAAAAATTAT-AAAAGATAAAGTAGGAAATGAAACTTATATCCCTATAACAGTA
131 TGAAAAATCACCAAAAATT-TCAAAAGATAAAATAGGAAATGAACCTTATATCCCTATAA-AGTA
354423 TGGA
194 TGGA
*
354427 AGTCTAGTTTTGTTTAGAATAAATGGAGATTGATTTCAATTTGTAGTTTAAAATATATGAATTTT
1 AGTCTAGTTTTGTTTAGAATAAACGGAGATTGATTTCAATTTGTAGTTTAAAATATATGAATTTT
*
354492 TGAATGTTGAAAGGTCATAAAAATCTGGCAGCAGAATTCTTATAAAACAGTTTTAGCAGTGACTT
66 TGAATGTTGAAAGGTCATAAAAATCTGGCAGCAGAATTCTTATAAAACAGATTTAGCAGTGACTT
* * * *
354557 TGAAAAATCACC--AAATGCTGAACAAGATAAAATAGGAAATGAGCCTTATATCCCTATAAATTT
131 TGAAAAATCACCAAAAAT-TTCAA-AAGATAAAATAGGAAATGAACCTTATATCCCTATAAA-GT
354620 ATGGA
193 ATGGA
* * *
354625 AGTCTAGTTTTGTTTAGAATAAACGAAGACTGAATTCAATTTGTAGTTTAAAATATATGAATTTT
1 AGTCTAGTTTTGTTTAGAATAAACGGAGATTGATTTCAATTTGTAGTTTAAAATATATGAATTTT
*
354690 TTAATGTTGAAAGGTCATAAAAATCTGGC-GCAGAATTCTTATAAAACAGATTTAGCAGTGACTT
66 TGAATGTTGAAAGGTCATAAAAATCTGGCAGCAGAATTCTTATAAAACAGATTTAGCAGTGACTT
* * * * *
354754 TGAAAAATCATCAAAAATTTCAAAAGATAAAATAGGAAGT-AAGCCTTATATCTCTATAATGTAC
131 TGAAAAATCACCAAAAATTTCAAAAGATAAAATAGGAAATGAA-CCTTATATCCCTATAAAGTAT
354818 GGA
195 GGA
*
354821 AGTCTAGTTTTGTTTAAAATAAACGG
1 AGTCTAGTTTTGTTTAGAATAAACGG
354847 TTCTCAATTT
Statistics
Matches: 379, Mismatches: 32, Indels: 18
0.88 0.07 0.04
Matches are distributed among these distances:
196 76 0.20
197 105 0.28
198 194 0.51
199 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (197 bp):
AGTCTAGTTTTGTTTAGAATAAACGGAGATTGATTTCAATTTGTAGTTTAAAATATATGAATTTT
TGAATGTTGAAAGGTCATAAAAATCTGGCAGCAGAATTCTTATAAAACAGATTTAGCAGTGACTT
TGAAAAATCACCAAAAATTTCAAAAGATAAAATAGGAAATGAACCTTATATCCCTATAAAGTATG
GA
Found at i:357158 original size:15 final size:16
Alignment explanation
Indices: 357133--357162 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
357123 TTTCACTTTA
357133 TTTGTTTCATTTTATG
1 TTTGTTTCATTTTATG
357149 TTTG-TTCATTTTAT
1 TTTGTTTCATTTTAT
357163 ATTATCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.70
Consensus pattern (16 bp):
TTTGTTTCATTTTATG
Found at i:360432 original size:26 final size:25
Alignment explanation
Indices: 360394--360448 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
360384 ACACATCAAC
*
360394 GAAAATTATGGAGATAAA-ATGAAAG
1 GAAAATTAAGGAGATAAATA-GAAAG
*
360419 GAAAGATTAAGGAGATATATAGAAAG
1 GAAA-ATTAAGGAGATAAATAGAAAG
360445 GAAA
1 GAAA
360449 TCAGAGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 21 0.81
27 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.18
Consensus pattern (25 bp):
GAAAATTAAGGAGATAAATAGAAAG
Found at i:363928 original size:13 final size:13
Alignment explanation
Indices: 363910--363934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
363900 ATTCAAGGGG
363910 AAGTTTGATTTTT
1 AAGTTTGATTTTT
363923 AAGTTTGATTTT
1 AAGTTTGATTTT
363935 GCAAAAGTGT
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (13 bp):
AAGTTTGATTTTT
Found at i:367045 original size:18 final size:19
Alignment explanation
Indices: 367022--367072 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
367012 CGAAAGGAAT
367022 AGCATACTGGCTCGTTTA-
1 AGCATACTGGCTCGTTTAG
*
367040 AGCATACTAGCTCG-TTAG
1 AGCATACTGGCTCGTTTAG
*
367058 AGCATACTGGATCGT
1 AGCATACTGGCTCGT
367073 AGGTTTATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 3 0.11
18 25 0.89
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (19 bp):
AGCATACTGGCTCGTTTAG
Found at i:368696 original size:21 final size:21
Alignment explanation
Indices: 368672--368717 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
368662 AGCTCTACTA
*
368672 ATACAAGT-ATGATTTCTACCG
1 ATACAAGTAATG-TATCTACCG
368693 ATACAAGTAATGTATCTACCG
1 ATACAAGTAATGTATCTACCG
368714 ATAC
1 ATAC
368718 CAATAACTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (21 bp):
ATACAAGTAATGTATCTACCG
Found at i:379190 original size:18 final size:18
Alignment explanation
Indices: 379167--379233 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
379157 GGAAAGGAAT
*
379167 AGCATACTAGCTCGTTTG
1 AGCATACTGGCTCGTTTG
*
379185 AGCATATTGGCTCGTTTG
1 AGCATACTGGCTCGTTTG
*
379203 AGCATACTGGCTCGTTAG
1 AGCATACTGGCTCGTTTG
*
379221 AGCATATTGGCTC
1 AGCATACTGGCTC
379234 ACAAGGGCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (18 bp):
AGCATACTGGCTCGTTTG
Found at i:379308 original size:27 final size:27
Alignment explanation
Indices: 379271--379331 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
379261 TATCTTCACT
*
379271 AGAAGACCCGAAAGGGGTGTTGAATAA
1 AGAAGACCCGAAAGGGGTATTGAATAA
379298 AGAAGACCCGAAAGGGGTATTGAATAA
1 AGAAGACCCGAAAGGGGTATTGAATAA
379325 AGAAGAC
1 AGAAGAC
379332 AGAAGAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.11, G:0.31, T:0.13
Consensus pattern (27 bp):
AGAAGACCCGAAAGGGGTATTGAATAA
Found at i:380031 original size:21 final size:21
Alignment explanation
Indices: 379971--380042 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
379961 AGAGTTTTTA
*
379971 GTATCGGTAGAAGC-ATGACTT
1 GTATCGGTAGAA-CTATCACTT
* * * * *
379992 GTTTCTGTATAAGTGTCACTT
1 GTATCGGTAGAACTATCACTT
*
380013 GTATCGGTAGAACTATCACTA
1 GTATCGGTAGAACTATCACTT
380034 GTATCGGTA
1 GTATCGGTA
380043 AAAGTTTGCT
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAACTATCACTT
Found at i:386206 original size:48 final size:48
Alignment explanation
Indices: 386135--386231 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
386125 CTAACCTGTC
*
386135 ACTGCATCTCTCGATGTTGGCGCACTGCAATTTCACTTGCGTGCTTAA
1 ACTGCATCTCTCAATGTTGGCGCACTGCAATTTCACTTGCGTGCTTAA
386183 ACTGCATCTCTCAATGTTGGCGCACTGCAATTTCACTTGCGTGCTTAA
1 ACTGCATCTCTCAATGTTGGCGCACTGCAATTTCACTTGCGTGCTTAA
386231 A
1 A
386232 GCAATTAGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.33
Consensus pattern (48 bp):
ACTGCATCTCTCAATGTTGGCGCACTGCAATTTCACTTGCGTGCTTAA
Found at i:388028 original size:13 final size:13
Alignment explanation
Indices: 388010--388053 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
388000 ACCCTTGAAC
388010 CTTGAACCTTAAA
1 CTTGAACCTTAAA
*
388023 CTTGAACCCTAAA
1 CTTGAACCTTAAA
*
388036 CTTCAAATCCTTAAA
1 CTT-GAA-CCTTAAA
388051 CTT
1 CTT
388054 TAAAATCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 2 0.08
15 9 0.35
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (13 bp):
CTTGAACCTTAAA
Found at i:388915 original size:23 final size:24
Alignment explanation
Indices: 388871--388915 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
388861 CTTTTGGTCG
*
388871 TATGTATCAATTTCACATATATTA
1 TATGAATCAATTTCACATATATTA
388895 TATGAATC-ATTTC-CATCATAT
1 TATGAATCAATTTCACAT-ATAT
388916 CATTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 9 0.47
24 7 0.37
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (24 bp):
TATGAATCAATTTCACATATATTA
Found at i:389416 original size:43 final size:42
Alignment explanation
Indices: 389344--389494 Score: 176
Period size: 43 Copynumber: 3.5 Consensus size: 42
389334 CGCAAAAAGA
* *
389344 CCGCTACAGAACATGATCTTTAGCGGCACTTCTCTCACAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCACTT-TCTCACAAACG
* * * * *
389387 CCGTTAAAGAACATGGTTTTTAGCAGCACTTTTTCCTCAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCACTTTCT-CACAAACG
*
389430 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCAC-TTTCTCACAAACG
* * *
389473 CCACTAAAGACCATTGTCTTTA
1 CCGCTAAAGAACATGGTCTTTA
389495 TGGTCTTTAG
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
42 2 0.02
43 84 0.93
44 4 0.04
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (42 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCACTTTCTCACAAACG
Found at i:389545 original size:51 final size:52
Alignment explanation
Indices: 389442--389545 Score: 131
Period size: 51 Copynumber: 2.0 Consensus size: 52
389432 GCTAAAGAAC
* * *
389442 ATGGTCTTTAGCGGCGCTTTTCTCACAAACGCCACTAAAGACCATTGTCTTT
1 ATGGTCTTTAGCGGCGCTTTTCTCACAAACGCCACTAAAAAACATGGTCTTT
* * *
389494 ATGGTCTTTAGTGGCGCTTTTAC-CA-TAACGCCGCTAAAAAACATGGTCTTT
1 ATGGTCTTTAGCGGCGCTTTT-CTCACAAACGCCACTAAAAAACATGGTCTTT
389545 A
1 A
389546 ATGGCGTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
51 22 0.49
52 22 0.49
53 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (52 bp):
ATGGTCTTTAGCGGCGCTTTTCTCACAAACGCCACTAAAAAACATGGTCTTT
Done.