Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 95 of 187
Found at i:28394569 original size:68 final size:69
Alignment explanation
Indices: 28394451--28394584 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 69
28394441 ATTATTTTAA
*
28394451 TATATTTAATATTAAATTAAATATTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTAATT
1 TATATTTAATATTAAATTAAATATTTATCTTAATAGTATTATATTAATTTAATATTAAAGTAATT
28394516 ATCG
66 ATCG
* * * * *
28394520 TATA-TTAA-ATTTAATTTAATATTTATCTTGATAAGTATTATATTGATTTAATATTAAAGTGAT
1 TATATTTAATATTAAATTAAATATTTATCTTAAT-AGTATTATATTAATTTAATATTAAAGTAAT
28394583 TA
65 TA
28394585 AGAATAATCA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
67 21 0.36
68 33 0.57
69 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (69 bp):
TATATTTAATATTAAATTAAATATTTATCTTAATAGTATTATATTAATTTAATATTAAAGTAATT
ATCG
Found at i:28407507 original size:8 final size:8
Alignment explanation
Indices: 28407496--28407541 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
28407486 TTAATTTTTT
28407496 AAAATTTA
1 AAAATTTA
28407504 AAAATTTA
1 AAAATTTA
*
28407512 AAAATTCAA
1 AAAATT-TA
28407521 AAAATTTAA
1 AAAATTT-A
28407530 AAAATTTA
1 AAAATTTA
28407538 AAAA
1 AAAA
28407542 ATATGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 19 0.56
9 15 0.44
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (8 bp):
AAAATTTA
Found at i:28407550 original size:10 final size:9
Alignment explanation
Indices: 28407496--28407553 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
28407486 TTAATTTTTT
28407496 AAAATTT-A
1 AAAATTTAA
28407504 AAAATTT-A
1 AAAATTTAA
*
28407512 AAAATTCAA
1 AAAATTTAA
28407521 AAAATTTAA
1 AAAATTTAA
28407530 AAAATTTAA
1 AAAATTTAA
* *
28407539 AAAATATGA
1 AAAATTTAA
28407548 AAAATT
1 AAAATT
28407554 AATATTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
8 14 0.32
9 30 0.68
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTTAA
Found at i:28408569 original size:16 final size:17
Alignment explanation
Indices: 28408536--28408569 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28408526 GTAATTAATA
*
28408536 AAATATTGTAAAATTAT
1 AAATATTGTAAAACTAT
28408553 AAATATT-TAAAACTAT
1 AAATATTGTAAAACTAT
28408569 A
1 A
28408570 CAAATCTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATATTGTAAAACTAT
Found at i:28413507 original size:2 final size:2
Alignment explanation
Indices: 28413500--28413552 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
28413490 NNNNNNNNTA
28413500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28413542 AT AT AT AT AT A
1 AT AT AT AT AT A
28413553 GACACCCTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28415375 original size:32 final size:31
Alignment explanation
Indices: 28415317--28415383 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
28415307 AGGTTTTAAT
*
28415317 GTAATTATGATAATTTTTAAAGGTTAACTAA
1 GTAATTATGATAATTGTTAAAGGTTAACTAA
* *
28415348 GTAATT-TGATAATTAAGTTAAATGTTAATTAA
1 GTAATTATGATAATT--GTTAAAGGTTAACTAA
28415380 GTAA
1 GTAA
28415384 AAGATGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.26
31 6 0.19
32 17 0.55
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.42
Consensus pattern (31 bp):
GTAATTATGATAATTGTTAAAGGTTAACTAA
Found at i:28416134 original size:40 final size:40
Alignment explanation
Indices: 28416002--28416137 Score: 182
Period size: 40 Copynumber: 3.4 Consensus size: 40
28415992 AATTATTGTA
* * *
28416002 TGATTGCACATAAGTGCCCTTGTTTGTACTTCGGTACCCC
1 TGATTGCACATATGTGCCCTTGTTTGTACTTTGGTAACCC
* *
28416042 TGATTGCACATACGTGCCCTTGTTTGTACTTTGGCAACCC
1 TGATTGCACATATGTGCCCTTGTTTGTACTTTGGTAACCC
* * *
28416082 TGATTGCACATATGTACCCCTGTTTGTACTTTGGTATCCC
1 TGATTGCACATATGTGCCCTTGTTTGTACTTTGGTAACCC
* *
28416122 AGGTTGCACATATGTG
1 TGATTGCACATATGTG
28416138 TCTCTAATTG
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (40 bp):
TGATTGCACATATGTGCCCTTGTTTGTACTTTGGTAACCC
Found at i:28416154 original size:80 final size:80
Alignment explanation
Indices: 28416002--28416157 Score: 188
Period size: 80 Copynumber: 1.9 Consensus size: 80
28415992 AATTATTGTA
* * * **
28416002 TGATTGCACATAAGTGCCCTTGTTTGTACTTCGGTACCCCTGATTGCACATACGTGCCCTTGTTT
1 TGATTGCACATAAGTACCCCTGTTTGTACTTCGGTACCCCAGATTGCACATACGTGCCCTTAATT
28416067 GTACTTTGGCAACCC
66 GTACTTTGGCAACCC
* * * * * *
28416082 TGATTGCACATATGTACCCCTGTTTGTACTTTGGTATCCCAGGTTGCACATATGTG-TCTCTAAT
1 TGATTGCACATAAGTACCCCTGTTTGTACTTCGGTACCCCAGATTGCACATACGTGCCCT-TAAT
*
28416146 TGTGCTTTGGCA
65 TGTACTTTGGCA
28416158 CCTTGAATGC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
79 2 0.03
80 61 0.97
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (80 bp):
TGATTGCACATAAGTACCCCTGTTTGTACTTCGGTACCCCAGATTGCACATACGTGCCCTTAATT
GTACTTTGGCAACCC
Found at i:28427995 original size:2 final size:2
Alignment explanation
Indices: 28427988--28428013 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28427978 TTGGTTATCG
28427988 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
28428014 TTAATTTCAT
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):
AT
Found at i:28429976 original size:4 final size:4
Alignment explanation
Indices: 28429967--28430009 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
28429957 TAAAAGCTGT
* *
28429967 TTTA TTTA -TTA TTTA ATAA TTTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTT
28430010 CATTCTGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.85
5 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:28430212 original size:20 final size:21
Alignment explanation
Indices: 28430170--28430219 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
28430160 TATTAGTGCA
* *
28430170 TTTTTATTGTCATTATCTGTT
1 TTTTTATTGTCATTAGCTATT
*
28430191 TTTTTATTGTTATT-GCTATT
1 TTTTTATTGTCATTAGCTATT
*
28430211 TTATTATTG
1 TTTTTATTG
28430220 CTTTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.16, C:0.06, G:0.10, T:0.68
Consensus pattern (21 bp):
TTTTTATTGTCATTAGCTATT
Found at i:28430341 original size:15 final size:15
Alignment explanation
Indices: 28430323--28430359 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
28430313 TTATAATTTG
28430323 ATTATTAATAAAATT
1 ATTATTAATAAAATT
*
28430338 ATTATTAATTAAATT
1 ATTATTAATAAAATT
*
28430353 AGTATTA
1 ATTATTA
28430360 TTATAGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
ATTATTAATAAAATT
Found at i:28440637 original size:27 final size:27
Alignment explanation
Indices: 28440607--28440665 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
28440597 TTGAAAAAAA
28440607 GAAGTTTTGACAGTATTTAATAAGGAC
1 GAAGTTTTGACAGTATTTAATAAGGAC
28440634 GAAGTTTTGACAGTATTTAATAAGGAC
1 GAAGTTTTGACAGTATTTAATAAGGAC
28440661 GAAGT
1 GAAGT
28440666 GAGGAAGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (27 bp):
GAAGTTTTGACAGTATTTAATAAGGAC
Found at i:28441253 original size:27 final size:27
Alignment explanation
Indices: 28441221--28441275 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
28441211 ATTGATTCCG
*
28441221 CTGTTTTTGAGAAAAAACCTCATTCAC
1 CTGTTTCTGAGAAAAAACCTCATTCAC
28441248 CTGTTTCTGAGAAAAAACCTCATTCAC
1 CTGTTTCTGAGAAAAAACCTCATTCAC
28441275 C
1 C
28441276 ACAACAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (27 bp):
CTGTTTCTGAGAAAAAACCTCATTCAC
Found at i:28447033 original size:30 final size:29
Alignment explanation
Indices: 28446999--28447056 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
28446989 GAAACTAATC
28446999 TCAATTACTGATTCTTAGGAAATTAGGATA
1 TCAATTACTGATTCTTAGG-AATTAGGATA
28447029 TCAATTACTGATTCTTAGGAATTAGGAT
1 TCAATTACTGATTCTTAGGAATTAGGAT
28447057 TTATTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (29 bp):
TCAATTACTGATTCTTAGGAATTAGGATA
Found at i:28465429 original size:63 final size:62
Alignment explanation
Indices: 28465360--28465507 Score: 174
Period size: 62 Copynumber: 2.4 Consensus size: 62
28465350 GGCCGTGTGG
* *
28465360 CAGGCCGTGTAACTCACTATTTTTGAAT-TTGAG-GCACACGGGCTAAGGACACAAGCGTGTGTC
1 CAGGCCGTGTAACTCACTGTTTTT-AATATTG-GTG-ACACGGACTAAGGACACAAGCGTGTGTC
* * * * * *
28465423 CAGGCCGTGTAAGTCACTGTTTGTATTATTGGTGACACGGACTAGGGACACGAGTGTGTGTC
1 CAGGCCGTGTAACTCACTGTTTTTAATATTGGTGACACGGACTAAGGACACAAGCGTGTGTC
*
28465485 CAGGCCGTGCAACTCACTGTTTT
1 CAGGCCGTGTAACTCACTGTTTT
28465508 GGATTTAGGG
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
62 47 0.65
63 25 0.35
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (62 bp):
CAGGCCGTGTAACTCACTGTTTTTAATATTGGTGACACGGACTAAGGACACAAGCGTGTGTC
Found at i:28465534 original size:62 final size:61
Alignment explanation
Indices: 28465360--28465534 Score: 151
Period size: 62 Copynumber: 2.8 Consensus size: 61
28465350 GGCCGTGTGG
*
28465360 CAGGCCGTGTAACTCACTATTTTTGAATTT-GAGG-CACACGGGCTAAGGACACAAGCGTGTGTC
1 CAGGCCGTGTAACTCACT-GTTTTGAATTTAG-GGTCACAC-GGC-AAGGACACAAGCGTGTGTC
* * * * * * *
28465423 CAGGCCGTGTAAGTCACTG-TTTGTA-TTATTGGTGACACGGACTAGGGACACGAGTGTGTGTC
1 CAGGCCGTGTAACTCACTGTTTTGAATTTA-GGGTCACACGG-C-AAGGACACAAGCGTGTGTC
* * *
28465485 CAGGCCGTGCAACTCACTGTTTTGGATTTAGGGTCACACGAGCCAGGACA
1 CAGGCCGTGTAACTCACTGTTTTGAATTTAGGGTCACACG-GCAAGGACA
28465535 TGGACGTGTT
Statistics
Matches: 90, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
60 2 0.02
61 9 0.10
62 44 0.49
63 31 0.34
64 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (61 bp):
CAGGCCGTGTAACTCACTGTTTTGAATTTAGGGTCACACGGCAAGGACACAAGCGTGTGTC
Found at i:28468034 original size:46 final size:46
Alignment explanation
Indices: 28467984--28468142 Score: 282
Period size: 46 Copynumber: 3.5 Consensus size: 46
28467974 GTGATAAGTA
* *
28467984 CTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTTG
1 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAG
28468030 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAG
1 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAG
*
28468076 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
1 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAG
*
28468122 CTATACTTATCTGATCAAGTG
1 CTACACTTATCTGATCAAGTG
28468143 GCTACACTTA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 109 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (46 bp):
CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAG
Found at i:28468151 original size:22 final size:22
Alignment explanation
Indices: 28468121--28468164 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28468111 GGTAGCCTTA
*
28468121 GCTATACTTATCTGATCAAGTG
1 GCTACACTTATCTGATCAAGTG
28468143 GCTACACTTATCTGATCAAGTG
1 GCTACACTTATCTGATCAAGTG
28468165 ACAAAGTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (22 bp):
GCTACACTTATCTGATCAAGTG
Found at i:28468184 original size:68 final size:68
Alignment explanation
Indices: 28468075--28468210 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
28468065 GGTAGCTTTA
*
28468075 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTATACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
28468140 GTG
66 GTG
28468143 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
28468208 GTG
66 GTG
28468211 ACAAAGTGAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (68 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
GTG
Found at i:28468210 original size:46 final size:46
Alignment explanation
Indices: 28468143--28468269 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
28468133 TGATCAAGTG
28468143 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
28468189 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
* *
28468235 GCTGCACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
28468270 ATCATACATA
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
44 12 0.15
45 5 0.06
46 62 0.78
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
Found at i:28468229 original size:114 final size:114
Alignment explanation
Indices: 28468029--28468252 Score: 421
Period size: 114 Copynumber: 2.0 Consensus size: 114
28468019 GGTAGCTTTT
*
28468029 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
*
28468094 GTGACAAAGTGATAAGTGGTAGCCTTAGCTATACTTATCTGATCAAGTG
66 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTG
28468143 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
*
28468208 GTGACAAAGTGATAAGTGGTAGCCTTAGCTGCACTTATCTGATCA
66 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCA
28468253 GGGACAAGTG
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (114 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTG
Found at i:28468646 original size:11 final size:11
Alignment explanation
Indices: 28468630--28468659 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28468620 TTGCGAATTG
*
28468630 AATGAAATGGA
1 AATGAAACGGA
28468641 AATGAAACGGA
1 AATGAAACGGA
28468652 AATGAAAC
1 AATGAAAC
28468660 ATTGAATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.07, G:0.23, T:0.13
Consensus pattern (11 bp):
AATGAAACGGA
Found at i:28470011 original size:14 final size:14
Alignment explanation
Indices: 28469992--28470018 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28469982 TATTTTATAC
28469992 TATAAAATATTTAT
1 TATAAAATATTTAT
28470006 TATAAAATATTTA
1 TATAAAATATTTA
28470019 CAAATTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAAAATATTTAT
Found at i:28484466 original size:81 final size:81
Alignment explanation
Indices: 28484331--28484494 Score: 292
Period size: 81 Copynumber: 2.0 Consensus size: 81
28484321 AAAAATAAAA
* *
28484331 TTACTTATAGATGAACTCTTTTCCAAGGATGACTTACGCTTTTTAAAAGAGTAAGTCAATTTACA
1 TTACTCATAAATGAACTCTTTTCCAAGGATGACTTACGCTTTTTAAAAGAGTAAGTCAATTTACA
28484396 AGAAAACGGTCTTATT
66 AGAAAACGGTCTTATT
* *
28484412 TTACTCATAAATGAGCTCTTTTCCGAGGATGACTTACGCTTTTTAAAAGAGTAAGTCAATTTACA
1 TTACTCATAAATGAACTCTTTTCCAAGGATGACTTACGCTTTTTAAAAGAGTAAGTCAATTTACA
28484477 AGAAAACGGTCTTATT
66 AGAAAACGGTCTTATT
28484493 TT
1 TT
28484495 TCATTGACTT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (81 bp):
TTACTCATAAATGAACTCTTTTCCAAGGATGACTTACGCTTTTTAAAAGAGTAAGTCAATTTACA
AGAAAACGGTCTTATT
Found at i:28487140 original size:9 final size:9
Alignment explanation
Indices: 28487107--28487148 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
28487097 TAAAAATCTA
28487107 TAAAAAATAT
1 TAAAAAAT-T
* *
28487117 TTAAAATTT
1 TAAAAAATT
28487126 TAAAAAATT
1 TAAAAAATT
28487135 TAAAAAA-T
1 TAAAAAATT
28487143 TAAAAA
1 TAAAAA
28487149 GTTGTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 7 0.25
9 15 0.54
10 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAAAATT
Found at i:28487145 original size:17 final size:18
Alignment explanation
Indices: 28487109--28487148 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28487099 AAAATCTATA
**
28487109 AAAAATATTTAAAATTTT
1 AAAAATATTTAAAAAATT
28487127 AAAAA-ATTTAAAAAATT
1 AAAAATATTTAAAAAATT
28487144 AAAAA
1 AAAAA
28487149 GTTGTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATATTTAAAAAATT
Found at i:28488306 original size:15 final size:17
Alignment explanation
Indices: 28488271--28488308 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
28488261 ACAAATGACA
*
28488271 TAAAAATATAAATAAAT
1 TAAAAATATAAATAAAC
28488288 TAAAAATA-AAA-AAAC
1 TAAAAATATAAATAAAC
28488303 TAAAAA
1 TAAAAA
28488309 ATATGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 8 0.40
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAATATAAATAAAC
Found at i:28488320 original size:29 final size:29
Alignment explanation
Indices: 28488286--28488341 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
28488276 ATATAAATAA
28488286 ATTAAAAA-TAAAAAAACTAAAAAATATGT
1 ATTAAAAATTAAAAAAA-TAAAAAATATGT
*
28488315 ATTAAAAATTAAAAAAATAAAATATAT
1 ATTAAAAATTAAAAAAATAAAAAATAT
28488342 CAAATTATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (29 bp):
ATTAAAAATTAAAAAAATAAAAAATATGT
Found at i:28488695 original size:2 final size:2
Alignment explanation
Indices: 28488688--28488750 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
28488678 NNNNNNNNTA
28488688 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28488730 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
28488751 CCAATCAATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28488921 original size:44 final size:44
Alignment explanation
Indices: 28488867--28488950 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
28488857 TCATAAATGT
28488867 TAGTTTGTGTTTTAAACTGATCTACGTTATTTTCTTAAAGCCAC
1 TAGTTTGTGTTTTAAACTGATCTACGTTATTTTCTTAAAGCCAC
* *
28488911 TAGTTTGTGTTTTAAATTGATCTACTTTATTTTCTTAAAG
1 TAGTTTGTGTTTTAAACTGATCTACGTTATTTTCTTAAAG
28488951 TTGCAACCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (44 bp):
TAGTTTGTGTTTTAAACTGATCTACGTTATTTTCTTAAAGCCAC
Found at i:28488948 original size:23 final size:23
Alignment explanation
Indices: 28488878--28488949 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 23
28488868 AGTTTGTGTT
*
28488878 TTAAACTGATCTACGTTATTTTC
1 TTAAACTGATCTACTTTATTTTC
* * * *
28488901 TTAAAGC-CA-CTAGTTTGTGTT-
1 TTAAA-CTGATCTACTTTATTTTC
*
28488922 TTAAATTGATCTACTTTATTTTC
1 TTAAACTGATCTACTTTATTTTC
28488945 TTAAA
1 TTAAA
28488950 GTTGCAACCA
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
21 6 0.17
22 17 0.49
23 11 0.31
24 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.49
Consensus pattern (23 bp):
TTAAACTGATCTACTTTATTTTC
Found at i:28494664 original size:39 final size:39
Alignment explanation
Indices: 28494610--28494839 Score: 334
Period size: 39 Copynumber: 5.9 Consensus size: 39
28494600 ATAATTATAT
* * * *
28494610 CCCTGATTGCACTTACGTGCCTCTGTCGTACTTTGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* *
28494649 CCCTGATCGCACTTACGTGCCCCTATCGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * *
28494688 CCTTGATCGCACTTACGTGCCCTTGTTGTACTTCGGCAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* *
28494727 CCCTGATCGGACTTACGTGCCCCTGTTGTACTTCGATAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
*
28494766 CCCTGATCGCACTTACGTGCCTCTGTTGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* *
28494805 CCTTGATCGCACTTATGTGCCCCTGTTGTACTTCG
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCG
28494840 ATACTATTGA
Statistics
Matches: 171, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 171 1.00
ACGTcount: A:0.13, C:0.33, G:0.20, T:0.33
Consensus pattern (39 bp):
CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
Found at i:28504590 original size:19 final size:19
Alignment explanation
Indices: 28504568--28504630 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
28504558 CACTTACATG
28504568 CCCCTGTTGTACTTCGGTA
1 CCCCTGTTGTACTTCGGTA
* *
28504587 CCCCTGATCG-ACTTAC-GTG
1 CCCCTG-TTGTACTT-CGGTA
*
28504606 CCCCTATTGTACTTCGGTA
1 CCCCTGTTGTACTTCGGTA
28504625 CCCCTG
1 CCCCTG
28504631 ATCGCACTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 3 0.09
19 28 0.82
20 3 0.09
ACGTcount: A:0.13, C:0.37, G:0.19, T:0.32
Consensus pattern (19 bp):
CCCCTGTTGTACTTCGGTA
Found at i:28504651 original size:39 final size:39
Alignment explanation
Indices: 28504432--28504660 Score: 244
Period size: 39 Copynumber: 5.9 Consensus size: 39
28504422 ATAATTATAT
* *** *
28504432 CCCTGATCGGACTTACGTGCCCCTGGCATACTTTGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * ** *
28504471 CCGTGATCGCACTTACGTGCCCTTGTCATACTTTGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
** * * * * * *
28504510 CTGTTATCGCACTTACATGCCCTTCTAGTACTTTGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * *
28504549 TCCTGATCACACTTACATGCCCCTGTTGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
*
28504588 CCCTGATCG-ACTTACGTGCCCCTATTGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
*
28504626 CCCTGATCGCACTTACGTGCCCCTATTGTACTTCG
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCG
28504661 ATACTTTTGA
Statistics
Matches: 166, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
38 36 0.22
39 130 0.78
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (39 bp):
CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
Found at i:28511216 original size:27 final size:27
Alignment explanation
Indices: 28511186--28511328 Score: 153
Period size: 27 Copynumber: 5.3 Consensus size: 27
28511176 ATTCGTGGGC
* *
28511186 AAATTACCAAAATACCCTTGAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTA
** *
28511213 AAATTATTGAAATATCC-CGAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTA
* * *
28511239 AAATTACCAAAACAACCTCGAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTA
* *
28511266 AAATTATCGAAATACCCTCGAAAGGTA
1 AAATTACCGAAATACCCTCGAAGGGTA
* * *
28511293 AAATTACTGAAATACCCTCAAAGGTTA
1 AAATTACCGAAATACCCTCGAAGGGTA
*
28511320 AAATGACCG
1 AAATTACCG
28511329 TTATACCCCT
Statistics
Matches: 93, Mismatches: 22, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
26 20 0.22
27 73 0.78
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGAAGGGTA
Found at i:28511249 original size:53 final size:54
Alignment explanation
Indices: 28511186--28511323 Score: 179
Period size: 53 Copynumber: 2.6 Consensus size: 54
28511176 ATTCGTGGGC
* * * *
28511186 AAATTACCAAAATACCCTTGAAGGGTAAAATTATTGAAATATCC-CGAAGGGTA
1 AAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAAGGTA
* *
28511239 AAATTACCAAAACAACCTCGAAGGGTAAAATTATCGAAATACCCTCGAAAGGTA
1 AAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAAGGTA
** * *
28511293 AAATTACTGAAATACCCTCAAAGGTTAAAAT
1 AAATTACCAAAATACCCTCGAAGGGTAAAAT
28511324 GACCGTTATA
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
53 39 0.54
54 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.22
Consensus pattern (54 bp):
AAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAAGGTA
Found at i:28511598 original size:26 final size:26
Alignment explanation
Indices: 28511519--28511616 Score: 97
Period size: 26 Copynumber: 3.8 Consensus size: 26
28511509 TTGCCACAAA
* *
28511519 TACTGTTACTGGTAGCTTTGTTGTGA
1 TACTGATACTGGTAGCTTTGTTGTGT
* * * *
28511545 TACTGATACTAGTAGCTCTGCTGCGT
1 TACTGATACTGGTAGCTTTGTTGTGT
* *
28511571 TACTGTTACTGGCAGCTTTGTTGTGT
1 TACTGATACTGGTAGCTTTGTTGTGT
* * *
28511597 TATTGATACTGCTAGTTTTG
1 TACTGATACTGGTAGCTTTG
28511617 CAACGATATT
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.44
Consensus pattern (26 bp):
TACTGATACTGGTAGCTTTGTTGTGT
Found at i:28511796 original size:30 final size:29
Alignment explanation
Indices: 28511732--28511872 Score: 124
Period size: 30 Copynumber: 4.8 Consensus size: 29
28511722 ATTTGTACTG
*
28511732 ATTACTGTTTTGGGCTAAGG-CCACAC-T
1 ATTACTGTATTGGGCTAAGGCCCACACTT
* *
28511759 GTTACTGTATTGGGTTAAGGCCCACACATT
1 ATTACTGTATTGGGCTAAGGCCCACAC-TT
* *
28511789 ATTACTGTATTGGGCTAAGACCCATACTCT
1 ATTACTGTATTGGGCTAAGGCCCACACT-T
* * **
28511819 GTTACTGTATTGGGCTATGAACCACACATT
1 ATTACTGTATTGGGCTAAGGCCCACAC-TT
** * *
28511849 GCTACTGTATAGGGCTCAGGCCCA
1 ATTACTGTATTGGGCTAAGGCCCA
28511873 AACTGATTCT
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
27 17 0.18
28 6 0.07
29 1 0.01
30 67 0.73
31 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (29 bp):
ATTACTGTATTGGGCTAAGGCCCACACTT
Found at i:28511844 original size:60 final size:57
Alignment explanation
Indices: 28511732--28511864 Score: 149
Period size: 60 Copynumber: 2.3 Consensus size: 57
28511722 ATTTGTACTG
* * * **
28511732 ATTACTGTTTTGGGCTAAGGCCACACTGTTACTGTATTGGGTTAAGGCCCACACATT
1 ATTACTGTATTGGGCTAAGCCCACACTGTTACTGTATTGGGCTAAGAACCACACATT
* *
28511789 ATTACTGTATTGGGCTAAGACCCATACTCTGTTACTGTATTGGGCTATGAACCACACATT
1 ATTACTGTATTGGGCTAAG-CCC--ACACTGTTACTGTATTGGGCTAAGAACCACACATT
** *
28511849 GCTACTGTATAGGGCT
1 ATTACTGTATTGGGCT
28511865 CAGGCCCAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
57 18 0.29
58 2 0.03
60 43 0.68
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (57 bp):
ATTACTGTATTGGGCTAAGCCCACACTGTTACTGTATTGGGCTAAGAACCACACATT
Found at i:28513804 original size:21 final size:21
Alignment explanation
Indices: 28513778--28513820 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28513768 TGTGGGTCCA
28513778 AGGAGCATCAAGTTAAGGACT
1 AGGAGCATCAAGTTAAGGACT
28513799 AGGAGCATCAAGTTAAGGACT
1 AGGAGCATCAAGTTAAGGACT
28513820 A
1 A
28513821 TCCTCAGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.19
Consensus pattern (21 bp):
AGGAGCATCAAGTTAAGGACT
Found at i:28518728 original size:26 final size:27
Alignment explanation
Indices: 28518617--28518751 Score: 155
Period size: 27 Copynumber: 5.0 Consensus size: 27
28518607 GATTCGTGGG
** * *
28518617 AAAATTACTAAAATTCCCCCGAAAGGT
1 AAAATTACCGAAATACCCCCGAAGGGT
***
28518644 AAAATTATTTAAATACCCCCGAAGGGT
1 AAAATTACCGAAATACCCCCGAAGGGT
* **
28518671 AAAATTACCAAAATACCCTTGAAGGGT
1 AAAATTACCGAAATACCCCCGAAGGGT
*
28518698 AAAATTACCGAAATA-CCCCAAAGGGT
1 AAAATTACCGAAATACCCCCGAAGGGT
*
28518724 AAAATTACTGAAATACCCCCGAAGGGT
1 AAAATTACCGAAATACCCCCGAAGGGT
28518751 A
1 A
28518752 GAATATTTAT
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
26 22 0.24
27 70 0.76
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (27 bp):
AAAATTACCGAAATACCCCCGAAGGGT
Found at i:28518738 original size:53 final size:54
Alignment explanation
Indices: 28518617--28518751 Score: 173
Period size: 53 Copynumber: 2.5 Consensus size: 54
28518607 GATTCGTGGG
* * *** *
28518617 AAAATTACTAAAATTCCCCCGAAAGGTAAAATTATTTAAATACCCCCGAAGGGT
1 AAAATTACTAAAATACCCCCGAAGGGTAAAATTACCGAAATACCCCCAAAGGGT
* **
28518671 AAAATTACCAAAATACCCTTGAAGGGTAAAATTACCGAAATA-CCCCAAAGGGT
1 AAAATTACTAAAATACCCCCGAAGGGTAAAATTACCGAAATACCCCCAAAGGGT
*
28518724 AAAATTACTGAAATACCCCCGAAGGGTA
1 AAAATTACTAAAATACCCCCGAAGGGTA
28518752 GAATATTTAT
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 34 0.50
54 34 0.50
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (54 bp):
AAAATTACTAAAATACCCCCGAAGGGTAAAATTACCGAAATACCCCCAAAGGGT
Found at i:28518907 original size:26 final size:26
Alignment explanation
Indices: 28518878--28518950 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
28518868 TTTGTCACAA
*
28518878 ATACTGTTACTGGTAGCTTTGCTACG
1 ATACTGTTACTGGCAGCTTTGCTACG
* *
28518904 ATACTGATACTGGCAGCTCTGCTACG
1 ATACTGTTACTGGCAGCTTTGCTACG
* *
28518930 TTACTATTACTGGCAGCTTTG
1 ATACTGTTACTGGCAGCTTTG
28518951 TTGCGTTACT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTACG
Found at i:28518957 original size:26 final size:26
Alignment explanation
Indices: 28518879--28518960 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 26
28518869 TTGTCACAAA
* * *
28518879 TACTGTTACTGGTAGCTTTGCTACGA
1 TACTATTACTGGCAGCTTTGCTACGT
*
28518905 TACTGA-TACTGGCAGCTCTGCTACGT
1 TACT-ATTACTGGCAGCTTTGCTACGT
* *
28518931 TACTATTACTGGCAGCTTTGTTGCGT
1 TACTATTACTGGCAGCTTTGCTACGT
28518957 TACT
1 TACT
28518961 GGTAGCTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 1 0.02
26 46 0.98
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTACGT
Found at i:28518978 original size:20 final size:20
Alignment explanation
Indices: 28518936--28518981 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
28518926 TACGTTACTA
**
28518936 TTACTGGCAGCTTTGTTGCG
1 TTACTGGCAGCTTTCCTGCG
* *
28518956 TTACTGGTAGCTTTCCTGTG
1 TTACTGGCAGCTTTCCTGCG
28518976 TTACTG
1 TTACTG
28518982 ATACTGTCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.20, G:0.26, T:0.43
Consensus pattern (20 bp):
TTACTGGCAGCTTTCCTGCG
Found at i:28519180 original size:30 final size:30
Alignment explanation
Indices: 28519121--28519254 Score: 166
Period size: 30 Copynumber: 4.6 Consensus size: 30
28519111 GATTACTATT
*
28519121 TTGGGCTAAGG--C-CACACTGTTACTATA
1 TTGGGCTAAGGCCCACACACTGTTACTGTA
* * *
28519148 TTGGGCTAAGGCCAACAAACTGTTTCTGTA
1 TTGGGCTAAGGCCCACACACTGTTACTGTA
*
28519178 TTGGGCTAAGGCCCACACTCTGTTACTGTA
1 TTGGGCTAAGGCCCACACACTGTTACTGTA
* *
28519208 TTGGGCTATGGCCCACACACTGCTACTGTA
1 TTGGGCTAAGGCCCACACACTGTTACTGTA
* *
28519238 TAGGGCTCAGGCCCACA
1 TTGGGCTAAGGCCCACA
28519255 TTGATTCTAC
Statistics
Matches: 90, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
27 11 0.12
30 79 0.88
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (30 bp):
TTGGGCTAAGGCCCACACACTGTTACTGTA
Found at i:28520086 original size:18 final size:19
Alignment explanation
Indices: 28520051--28520087 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
28520041 CATGACATTG
28520051 AATGAAATGTATGTATACA
1 AATGAAATGTATGTATACA
28520070 AATG-AATGT-TGTGATACA
1 AATGAAATGTATGT-ATACA
28520088 TACGCTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 10 0.59
19 4 0.24
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (19 bp):
AATGAAATGTATGTATACA
Found at i:28527037 original size:40 final size:40
Alignment explanation
Indices: 28526941--28527257 Score: 264
Period size: 40 Copynumber: 7.9 Consensus size: 40
28526931 GTGCCCCTAC
* * * * *
28526941 TTGTGCTTCGATACCCTTGATTGCACATTCGTGCCC-TGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCTTGT
* *
28526980 TTGTACATCGGTGCCCCTGAATGCACATACGTGCCCTTGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCTTGT
* * ** *
28527020 TTGTACTTTGGTACCCCT-AATTTCACATACACGCCCCATGT
1 TTGTACTTCGGTACCCCTGAA-TGCACATACGTG-CCCTTGT
* * * * * *
28527061 TTGTACTTCGATACCCTTGATTGCACATCCGTGGCTTTGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCTTGT
* * *
28527101 TTGTACTTCGGTACTCGTGAATGCACATACGTGCCTTTGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCTTGT
* *
28527141 TTGTACTTCGGTACCCCTAAATGCACATACGT-ACCTCTGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCT-TGT
* * * * *
28527181 TTGTATTTCGGTATCCCTAAATGCACATTCATGACCC-TGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTG-CCCTTGT
* * * * * *
28527221 TTGCACTTTGGTACCCTTGAAAGCACTTACATGCCCT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCT
28527258 GCTTATACTC
Statistics
Matches: 220, Mismatches: 50, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
39 36 0.16
40 152 0.69
41 29 0.13
42 3 0.01
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (40 bp):
TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCTTGT
Found at i:28527141 original size:121 final size:120
Alignment explanation
Indices: 28526941--28527170 Score: 343
Period size: 121 Copynumber: 1.9 Consensus size: 120
28526931 GTGCCCCTAC
* * *
28526941 TTGTGCTTCGATACCCTTGATTGCACATTCGTGCCCTGTTTGTACATCGGTGCCCCTGAATGCAC
1 TTGTACTTCGATACCCTTGATTGCACATCCGTGCCCTGTTTGTACATCGGTACCCCTGAATGCAC
* * *
28527006 ATACGTGCCCTTGTTTGTACTTTGGTACCCCTAATTTCACATACACGCCCCATGT
66 ATACGTGCCCTTGTTTGTACTTCGGTACCCCTAAATGCACATACACGCCCCATGT
** * * *
28527061 TTGTACTTCGATACCCTTGATTGCACATCCGTGGCTTTGTTTGTACTTCGGTACTCGTGAATGCA
1 TTGTACTTCGATACCCTTGATTGCACATCCGT-GCCCTGTTTGTACATCGGTACCCCTGAATGCA
*
28527126 CATACGTGCCTTTGTTTGTACTTCGGTACCCCTAAATGCACATAC
65 CATACGTGCCCTTGTTTGTACTTCGGTACCCCTAAATGCACATAC
28527171 GTACCTCTGT
Statistics
Matches: 97, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
120 30 0.31
121 67 0.69
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (120 bp):
TTGTACTTCGATACCCTTGATTGCACATCCGTGCCCTGTTTGTACATCGGTACCCCTGAATGCAC
ATACGTGCCCTTGTTTGTACTTCGGTACCCCTAAATGCACATACACGCCCCATGT
Found at i:28528001 original size:30 final size:30
Alignment explanation
Indices: 28527967--28528030 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
28527957 GGCATAGCCG
* *
28527967 TGTGAGGCACATAGCCTGACAACACGGCCA
1 TGTGAGGCACACAGCCTGACAAAACGGCCA
* * *
28527997 TGTGAGGCACACGGCTTGACAAAACGGCCG
1 TGTGAGGCACACAGCCTGACAAAACGGCCA
28528027 TGTG
1 TGTG
28528031 TCATATGGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.31, T:0.16
Consensus pattern (30 bp):
TGTGAGGCACACAGCCTGACAAAACGGCCA
Found at i:28530730 original size:23 final size:23
Alignment explanation
Indices: 28530698--28530769 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
28530688 GATAAGATCG
* *
28530698 ATTCCGTGATGTCTTTGTAGCGT
1 ATTCCATGATGCCTTTGTAGCGT
** * * *
28530721 ATTCTTTGATGCCCTTATGGCGT
1 ATTCCATGATGCCTTTGTAGCGT
*
28530744 ATTCCATGATGCCTTTGTAGCAT
1 ATTCCATGATGCCTTTGTAGCGT
28530767 ATT
1 ATT
28530770 TTGTAATGAC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (23 bp):
ATTCCATGATGCCTTTGTAGCGT
Found at i:28533815 original size:25 final size:25
Alignment explanation
Indices: 28533787--28533850 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
28533777 AGTTGTAGAC
* *
28533787 CGGTATGCTTTCACGAGCTATAAAT
1 CGGTATGCTCTCACGAGATATAAAT
28533812 CGGTATGCTCTCACGAGATATAAAT
1 CGGTATGCTCTCACGAGATATAAAT
* * *
28533837 TGGCATGATCTCAC
1 CGGTATGCTCTCAC
28533851 AAGCGGTGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (25 bp):
CGGTATGCTCTCACGAGATATAAAT
Found at i:28543088 original size:22 final size:22
Alignment explanation
Indices: 28543031--28543089 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
28543021 CATGCCAAAG
*
28543031 TATTTTTTTTTCTTTATGTGTC
1 TATTTTTTTTTGTTTATGTGTC
*
28543053 TATTTTTTGGTTTTGTTTAT-TGTT
1 TA-TTTTT--TTTTGTTTATGTGTC
28543077 TATTTTTATTTTG
1 TATTTTT-TTTTG
28543090 CTTGCTTGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 7 0.23
23 10 0.32
24 5 0.16
25 9 0.29
ACGTcount: A:0.10, C:0.03, G:0.12, T:0.75
Consensus pattern (22 bp):
TATTTTTTTTTGTTTATGTGTC
Found at i:28547662 original size:27 final size:27
Alignment explanation
Indices: 28547620--28547825 Score: 169
Period size: 27 Copynumber: 7.6 Consensus size: 27
28547610 CCCTTGTAGG
* *
28547620 GTAAAATTATCGAAATACCCCCAGTTT
1 GTAAAATTACCGAAATACCCCCAATTT
* *
28547647 GTAAAATTACCAAAATACCCCTAATTT
1 GTAAAATTACCGAAATACCCCCAATTT
* *
28547674 GTAAAATTACTGAAATACCCACAATTT
1 GTAAAATTACCGAAATACCCCCAATTT
* * * *
28547701 TTAAAATCATCGAAATACCCCTAATTT
1 GTAAAATTACCGAAATACCCCCAATTT
* * * *** **
28547728 TTAAAATTATCGCAATATAACTGATTT
1 GTAAAATTACCGAAATACCCCCAATTT
* *****
28547755 GTAAAATTATCGAAATACCTTTGGTTT
1 GTAAAATTACCGAAATACCCCCAATTT
* * *
28547782 GCAAAATTACCGAAATACCCTCAGTTT
1 GTAAAATTACCGAAATACCCCCAATTT
28547809 GTAAAATTACCGAAATA
1 GTAAAATTACCGAAATA
28547826 TCAAAATACC
Statistics
Matches: 146, Mismatches: 33, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 146 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCCCAATTT
Found at i:28547689 original size:54 final size:54
Alignment explanation
Indices: 28547620--28547825 Score: 211
Period size: 54 Copynumber: 3.8 Consensus size: 54
28547610 CCCTTGTAGG
* *
28547620 GTAAAATTATCGAAATACCCCCAGTTTGTAAAATTACCAAAATACCCCTAATTT
1 GTAAAATTATCGAAATACCCTCAGTTTGTAAAATTACCGAAATACCCCTAATTT
* * * * *
28547674 GTAAAATTA-CTGAAATACCCACAATTTTTAAAATCATCGAAATACCCCTAATTT
1 GTAAAATTATC-GAAATACCCTCAGTTTGTAAAATTACCGAAATACCCCTAATTT
* * * * ** **
28547728 TTAAAATTATCGCAATATA-ACTGA-TTTGTAAAATTATCGAAATACCTTTGGTTT
1 GTAAAATTATCG-AA-ATACCCTCAGTTTGTAAAATTACCGAAATACCCCTAATTT
* *
28547782 GCAAAATTACCGAAATACCCTCAGTTTGTAAAATTACCGAAATA
1 GTAAAATTATCGAAATACCCTCAGTTTGTAAAATTACCGAAATA
28547826 TCAAAATACC
Statistics
Matches: 124, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
52 3 0.02
53 6 0.05
54 107 0.86
55 5 0.04
56 3 0.02
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
GTAAAATTATCGAAATACCCTCAGTTTGTAAAATTACCGAAATACCCCTAATTT
Found at i:28547826 original size:81 final size:80
Alignment explanation
Indices: 28547622--28547826 Score: 205
Period size: 81 Copynumber: 2.5 Consensus size: 80
28547612 CTTGTAGGGT
* ***
28547622 AAAATTATCGAAATACCCCCAGTTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACTGA
1 AAAATTATCGAAATA-CCCCAGTTTGTAAAATTACCGAAATATAACTAATTTGTAAAATTACTGA
**
28547687 AATACCCACAATTTTT
65 AATACCCACAATTTGC
* * * * * *
28547703 AAAATCATCGAAATACCCCTAATTTTTAAAATTATCGCAATATAACTGATTTGTAAAATTA-TCG
1 AAAATTATCGAAATACCCC-AGTTTGTAAAATTACCGAAATATAACTAATTTGTAAAATTACT-G
*****
28547767 AAATACCTTTGGTTTGC
64 AAATACCCACAATTTGC
*
28547784 AAAATTACCGAAATACCCTCAGTTTGTAAAATTACCGAAATAT
1 AAAATTATCGAAATACCC-CAGTTTGTAAAATTACCGAAATAT
28547827 CAAAATACCT
Statistics
Matches: 98, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
80 5 0.05
81 92 0.94
82 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (80 bp):
AAAATTATCGAAATACCCCAGTTTGTAAAATTACCGAAATATAACTAATTTGTAAAATTACTGAA
ATACCCACAATTTGC
Found at i:28547867 original size:27 final size:27
Alignment explanation
Indices: 28547827--28547916 Score: 135
Period size: 27 Copynumber: 3.3 Consensus size: 27
28547817 ACCGAAATAT
28547827 CAAAATACCTCTGTAGGGTAGGATTAC
1 CAAAATACCTCTGTAGGGTAGGATTAC
** * *
28547854 TGAAATACCTCTGTAGGGTAAGATCAC
1 CAAAATACCTCTGTAGGGTAGGATTAC
*
28547881 CAAAATACCTCTGTAGGGTAGAATTAC
1 CAAAATACCTCTGTAGGGTAGGATTAC
28547908 CAAAATACC
1 CAAAATACC
28547917 CCCAAAGGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (27 bp):
CAAAATACCTCTGTAGGGTAGGATTAC
Found at i:28548264 original size:22 final size:22
Alignment explanation
Indices: 28548236--28548295 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
28548226 GTAATTTGAT
28548236 TATGGCTTTGTGCCAACCTAAA
1 TATGGCTTTGTGCCAACCTAAA
* * * * *
28548258 TATGGCTCTGTGCCATCGTGAT
1 TATGGCTTTGTGCCAACCTAAA
28548280 TATGGCTTTGTGCCAA
1 TATGGCTTTGTGCCAA
28548296 TCGTTTTTAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
TATGGCTTTGTGCCAACCTAAA
Found at i:28550326 original size:16 final size:18
Alignment explanation
Indices: 28550298--28550344 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
28550288 GTGAAGAAGA
28550298 AAGGAGTTTCAAAAA-TT
1 AAGGAGTTTCAAAAACTT
28550315 AAGGAG-TTCAAAAACTT
1 AAGGAGTTTCAAAAACTT
* *
28550332 AAGAAATTTCAAA
1 AAGGAGTTTCAAA
28550345 TAATAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 8 0.31
17 12 0.46
18 6 0.23
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.26
Consensus pattern (18 bp):
AAGGAGTTTCAAAAACTT
Found at i:28555917 original size:20 final size:20
Alignment explanation
Indices: 28555890--28555938 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
28555880 TAAAATAGTT
28555890 TAAC-TGATTGAAAAAATTC
1 TAACTTGATTGAAAAAATTC
* *
28555909 TAACTTGATTGAAATAATTT
1 TAACTTGATTGAAAAAATTC
28555929 TAACTTGATT
1 TAACTTGATT
28555939 AAAGGTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (20 bp):
TAACTTGATTGAAAAAATTC
Found at i:28558438 original size:23 final size:23
Alignment explanation
Indices: 28558394--28558555 Score: 148
Period size: 23 Copynumber: 7.0 Consensus size: 23
28558384 CTTAATATAT
* *
28558394 TTTTAAATTTATCAT-CAATATTA
1 TTTT-AATTTATCATGTATTATTA
* *
28558417 TTTTAATTTATAATATATTATTA
1 TTTTAATTTATCATGTATTATTA
* **
28558440 TTTTAAGTTTATCA-ATAACATTA
1 TTTTAA-TTTATCATGTATTATTA
*
28558463 TTTTAAGTTTATCATGTATTTTTA
1 TTTTAA-TTTATCATGTATTATTA
* *
28558487 TTTAAAGTTATCATGTATTATTA
1 TTTTAATTTATCATGTATTATTA
* * *
28558510 TTTTGAACTTATCATCTATGATTA
1 TTTT-AATTTATCATGTATTATTA
*
28558534 TTTAAATTTATCATGTATTATT
1 TTTTAATTTATCATGTATTATT
28558556 TTATGCATTC
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
22 9 0.08
23 70 0.61
24 35 0.31
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTAATTTATCATGTATTATTA
Found at i:28558442 original size:47 final size:45
Alignment explanation
Indices: 28558394--28558558 Score: 156
Period size: 47 Copynumber: 3.6 Consensus size: 45
28558384 CTTAATATAT
*
28558394 TTTTAAATTTATCATCAATATTATTTTAATTTATAATATATTATTA
1 TTTTAAATTTATCAT-AATATTATTTTAATTTATCATATATTATTA
* * * *
28558440 TTTTAAGTTTATCAATAACATTATTTTAAGTTTATCATGTATTTTTA
1 TTTTAAATTTATC-ATAATATTATTTTAA-TTTATCATATATTATTA
* * * * *
28558487 -TTTAAAGTTATCATGTATTATTATTTTGAACTTATCATCTATGATTA
1 TTTTAAATTTATCA--TAATATTATTTT-AATTTATCATATATTATTA
*
28558534 -TTTAAATTTATCAT-GTATTATTTTA
1 TTTTAAATTTATCATAATATTATTTTA
28558559 TGCATTCTTG
Statistics
Matches: 99, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 9 0.09
45 2 0.02
46 34 0.34
47 51 0.52
48 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (45 bp):
TTTTAAATTTATCATAATATTATTTTAATTTATCATATATTATTA
Found at i:28558522 original size:70 final size:70
Alignment explanation
Indices: 28558395--28558552 Score: 169
Period size: 70 Copynumber: 2.3 Consensus size: 70
28558385 TTAATATATT
* * * * * *
28558395 TTTAAATTTATCAT-CAATATTATTTTAATTTATAATATATTATTATTTTAAGTTTATCA-ATAA
1 TTTAAATTTATCATGTATTTTTATTTAAAGTTATAATATATTATTATTTTAAGCTTATCATATAA
28558458 CATTA
66 CATTA
* * * *
28558463 TTTTAAGTTTATCATGTATTTTTATTTAAAGTTATCATGTATTATTATTTTGAA-CTTATCATCT
1 -TTTAAATTTATCATGTATTTTTATTTAAAGTTATAATATATTATTATTTT-AAGCTTATCATAT
**
28558527 ATGATTA
64 AACATTA
28558534 TTTAAATTTATCATGTATT
1 TTTAAATTTATCATGTATT
28558553 ATTTTATGCA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
69 13 0.18
70 52 0.71
71 8 0.11
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.54
Consensus pattern (70 bp):
TTTAAATTTATCATGTATTTTTATTTAAAGTTATAATATATTATTATTTTAAGCTTATCATATAA
CATTA
Found at i:28558759 original size:14 final size:14
Alignment explanation
Indices: 28558724--28558750 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28558714 TATTTTATAT
28558724 ATATTATTGCTTTC
1 ATATTATTGCTTTC
28558738 ATATTATTGCTTT
1 ATATTATTGCTTT
28558751 TTATTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.59
Consensus pattern (14 bp):
ATATTATTGCTTTC
Found at i:28558848 original size:14 final size:14
Alignment explanation
Indices: 28558829--28558859 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28558819 ACTTTTTACC
28558829 TATATTATTATATA
1 TATATTATTATATA
*
28558843 TATATTATTATCTA
1 TATATTATTATATA
28558857 TAT
1 TAT
28558860 TGAGTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATTATTATATA
Found at i:28566117 original size:51 final size:51
Alignment explanation
Indices: 28566073--28566299 Score: 291
Period size: 51 Copynumber: 4.5 Consensus size: 51
28566063 TTCCATAGCA
* *
28566073 TTGCAGTGGAACAGATTAAAGCTGAAAGCAGCAAATCTTATTTCCTTGGCG
1 TTGCAGTGGAACAGATTAAAGCTGAAAGCAGCGAATCTTATTTCCCTGGCG
** *
28566124 TTATAGTGGAACAGATTAAAGCT-AAAGGCAGCGAATCTTATTTCCCTGGTG
1 TTGCAGTGGAACAGATTAAAGCTGAAA-GCAGCGAATCTTATTTCCCTGGCG
* *
28566175 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCCTT-TTTCCCTAGTC-
1 TTGCAGTGGAACAGATTAAAGCTGAAAGCAGCGAAT-CTTATTTCCCT-GGCG
* * *
28566226 TTGC-GATGGAACGGATTAAAGCTGAAGGCAACGAATCTTATTTCCCTGGCG
1 TTGCAG-TGGAACAGATTAAAGCTGAAAGCAGCGAATCTTATTTCCCTGGCG
*
28566277 TTGCAGTGGAACAGGTTAAAGCT
1 TTGCAGTGGAACAGATTAAAGCT
28566300 ACAAATTATG
Statistics
Matches: 153, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
50 9 0.06
51 137 0.90
52 7 0.05
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (51 bp):
TTGCAGTGGAACAGATTAAAGCTGAAAGCAGCGAATCTTATTTCCCTGGCG
Found at i:28566753 original size:193 final size:192
Alignment explanation
Indices: 28566206--28566762 Score: 699
Period size: 193 Copynumber: 2.9 Consensus size: 192
28566196 CTGAAGGCAG
* * *
28566206 CGAATCCTTTTTCCCTAGTC-TTGC-GATGGAACGGATTAAAGCTGAAGGCA-ACGAATCTTATT
1 CGAATCTTTTTTCCCTAG-CATTGCAG-TGGAACAGATTAAAGCTGAAGGCAGA--AATTTTATT
* * *
28566268 TCCCTGGCGTTGCAGTGGAACAGGTTAAAGCTACAAATTATGGTGGATTTTATCTTCCTAAAGTT
62 TCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGAATTTTATCTTCCTAAAGTT
* * * *
28566333 GCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTTCTTAAAGTTGCAGCAGAGCAGATTGAAATA
127 GCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCATGAAGTTGCAGCAGAGCAGATTGAAACA
*
28566398 G
192 A
* * * * **
28566399 CGAATCTTTTTTCCCTAGCGTTGTAGTGGAACAGAATAAAGTTGAAGGCAGCGATTATTATTTCC
1 CGAATCTTTTTTCCCTAGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGAAATT-TTATTTCC
* *
28566464 CTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGC-AGATCTTATCTTCCCAAAGTTGC
65 CTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGA-ATTTTATCTTCCTAAAGTTGC
* * *
28566528 AATGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAACAA
129 AGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCATGAAGTTGCAGCAGAGCAGATTGAAACAA
* * *
28566592 CGAATCTTTTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAGGGCAGTAAATTTTATTTCC
1 CGAATCTTTTTTCCCTAGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAG-AAATTTTATTTCC
* * * * *
28566657 CTGGCGTTGCAGTGGAATAGATTAAAGTTACAAGTTATGGCGAATTTTATCTTCCTGAAGTTGTA
65 CTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGAATTTTATCTTCCTAAAGTTGCA
** * ** *
28566722 GTGGAGTGGATTGAAGCTAGAAGCTTTATCTCCATGAAGTT
130 GTGGAGCAGATTGAAGCCACCAGCCTTATCTCCATGAAGTT
28566763 ACAGTGGATT
Statistics
Matches: 313, Mismatches: 44, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
192 3 0.01
193 305 0.97
194 5 0.02
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (192 bp):
CGAATCTTTTTTCCCTAGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGAAATTTTATTTCCC
TGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGAATTTTATCTTCCTAAAGTTGCAG
TGGAGCAGATTGAAGCCACCAGCCTTATCTCCATGAAGTTGCAGCAGAGCAGATTGAAACAA
Found at i:28568194 original size:23 final size:22
Alignment explanation
Indices: 28568159--28568250 Score: 71
Period size: 23 Copynumber: 4.0 Consensus size: 22
28568149 TGTTTAAGCT
*
28568159 TAATA-TATTTTTAAATTTATCG
1 TAATATTA-TTTTAAATTTATCA
*
28568181 TCAATATTATTTTAATATATAAT-A
1 T-AATATTATTTTAA-AT-TTATCA
* *
28568205 TATTATTATTTTAAGTTTATCA
1 TAATATTATTTTAAATTTATCA
* *
28568227 TTAAAATTATTTTAAGTTTATCA
1 -TAATATTATTTTAAATTTATCA
28568250 T
1 T
28568251 GTATTTTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
21 3 0.05
22 4 0.07
23 42 0.74
24 5 0.09
25 3 0.05
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (22 bp):
TAATATTATTTTAAATTTATCA
Found at i:28568270 original size:23 final size:24
Alignment explanation
Indices: 28568205--28568285 Score: 103
Period size: 23 Copynumber: 3.5 Consensus size: 24
28568195 ATATATAATA
*
28568205 TATTATTATTTTAAGTTTATCAT-
1 TATTATTATTTGAAGTTTATCATG
** *
28568228 TAAAATTATTTTAAGTTTATCATG
1 TATTATTATTTGAAGTTTATCATG
*
28568252 TATTTTTATTTGAAG-TTATCATG
1 TATTATTATTTGAAGTTTATCATG
28568275 TATTATTATTT
1 TATTATTATTT
28568286 TGACCTTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 39 0.78
24 11 0.22
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (24 bp):
TATTATTATTTGAAGTTTATCATG
Found at i:28568283 original size:47 final size:46
Alignment explanation
Indices: 28568174--28568286 Score: 120
Period size: 47 Copynumber: 2.4 Consensus size: 46
28568164 TATTTTTAAA
* * *
28568174 TTTATCGTCAATATTATTTTAATATATAATATATTATTATTTTAAG
1 TTTATCATTAATATTATTTTAATATATAATATATTATTATTTGAAG
* * * * *
28568220 TTTATCATTAAAATTATTTTAAGTTTATCATGTATTTTTATTTGAAG
1 TTTATCATTAATATTATTTTAA-TATATAATATATTATTATTTGAAG
*
28568267 -TTATCATGTATTATTATTTT
1 TTTATCAT-TAATATTATTTT
28568287 GACCTTATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
46 26 0.47
47 29 0.53
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (46 bp):
TTTATCATTAATATTATTTTAATATATAATATATTATTATTTGAAG
Found at i:28568294 original size:24 final size:23
Alignment explanation
Indices: 28568244--28568294 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
28568234 TATTTTAAGT
* *
28568244 TTATCATGTATTTTTATTTGAAG
1 TTATCATGTATTATTATTTGAAC
*
28568267 TTATCATGTATTATTATTTTGACC
1 TTATCATGTATTATTA-TTTGAAC
28568291 TTAT
1 TTAT
28568295 TTAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (23 bp):
TTATCATGTATTATTATTTGAAC
Found at i:28574167 original size:19 final size:17
Alignment explanation
Indices: 28574122--28574170 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 17
28574112 GTGTCGTTCG
28574122 TTTCTAAAATATTATTCA
1 TTTC-AAAATATTATTCA
28574140 TTT-ACAAATCATTATTCAA
1 TTTCA-AAAT-ATTATTC-A
28574159 TTTCAAAATATT
1 TTTCAAAATATT
28574171 TTCTTATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 4 0.15
18 13 0.48
19 8 0.30
20 1 0.04
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTCAAAATATTATTCA
Found at i:28584692 original size:20 final size:20
Alignment explanation
Indices: 28584667--28584737 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
28584657 AAAACTTGAC
*
28584667 AGGTATCAATATTTTTAAAA
1 AGGTATCAATAATTTTAAAA
*
28584687 AGGTATCAATAATTTTATAA
1 AGGTATCAATAATTTTAAAA
*
28584707 AGGTATCAACAATTTTAAAA
1 AGGTATCAATAATTTTAAAA
28584727 TA-GTATCAATA
1 -AGGTATCAATA
28584738 CCAAATCACA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
20 44 0.98
21 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (20 bp):
AGGTATCAATAATTTTAAAA
Found at i:28588736 original size:49 final size:49
Alignment explanation
Indices: 28588677--28588771 Score: 156
Period size: 49 Copynumber: 1.9 Consensus size: 49
28588667 ATTAGGTATA
* *
28588677 TTTAGCTTAGGATAGTCGTGTC-AAAATTTATGCCTAAAAGTAGAATATT
1 TTTAACTTAGGATAGTCGTG-CGAAAATTGATGCCTAAAAGTAGAATATT
28588726 TTTAACTTAGGATAGTCGTGCGAAAATTGATGCCTAAAAGTAGAAT
1 TTTAACTTAGGATAGTCGTGCGAAAATTGATGCCTAAAAGTAGAAT
28588772 GACGTAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 1 0.02
49 42 0.98
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (49 bp):
TTTAACTTAGGATAGTCGTGCGAAAATTGATGCCTAAAAGTAGAATATT
Found at i:28590274 original size:21 final size:21
Alignment explanation
Indices: 28590248--28590287 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28590238 CATCGTCAAC
* *
28590248 AGAAGCTCGAAAGTGCTGAAA
1 AGAAGCTCAAAAGAGCTGAAA
28590269 AGAAGCTCAAAAGAGCTGA
1 AGAAGCTCAAAAGAGCTGA
28590288 TCCACCCGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.15, G:0.28, T:0.12
Consensus pattern (21 bp):
AGAAGCTCAAAAGAGCTGAAA
Found at i:28594714 original size:3 final size:3
Alignment explanation
Indices: 28594706--28594754 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
28594696 GCACTGCACT
28594706 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
28594754 G
1 G
28594755 GCTGAGTAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
GTA
Found at i:28609586 original size:21 final size:21
Alignment explanation
Indices: 28609560--28609612 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
28609550 AAGGTTCCAC
28609560 GAGTATCGATAATTTTT-AAA
1 GAGTATCGATAATTTTTCAAA
28609580 TGAGTATCGAT-ATTTTTCAAA
1 -GAGTATCGATAATTTTTCAAA
*
28609601 AAGTATCGATAA
1 GAGTATCGATAA
28609613 AATGGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (21 bp):
GAGTATCGATAATTTTTCAAA
Found at i:28617066 original size:24 final size:23
Alignment explanation
Indices: 28617031--28617081 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
28617021 TTTAAATATA
*
28617031 TTTTTTAGTTTTTAGTTTTTAAAT
1 TTTTTTAATTTTTA-TTTTTAAAT
*
28617055 TTTTTTAATTTTTATTTTTTAAT
1 TTTTTTAATTTTTATTTTTAAAT
28617078 TTTT
1 TTTT
28617082 ATGAATTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTTAATTTTTATTTTTAAAT
Found at i:28617072 original size:14 final size:14
Alignment explanation
Indices: 28617032--28617083 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
28617022 TTAAATATAT
* *
28617032 TTTTTAGTTTTTAG
1 TTTTTATTTTTTAA
28617046 TTTTTAAATTTTTTTAA
1 TTTTT--A-TTTTTTAA
28617063 TTTTTATTTTTTAA
1 TTTTTATTTTTTAA
28617077 TTTTTAT
1 TTTTTAT
28617084 GAATTAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 20 0.61
15 1 0.03
16 1 0.03
17 11 0.33
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTTTATTTTTTAA
Found at i:28617088 original size:24 final size:24
Alignment explanation
Indices: 28617030--28617088 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
28617020 TTTTAAATAT
*
28617030 ATTTTTT-AGTTTTTAGTTTTTAA
1 ATTTTTTGAATTTTTAGTTTTTAA
* *
28617053 ATTTTTTTAATTTTTA-TTTTTTA
1 ATTTTTTGAATTTTTAGTTTTTAA
28617076 ATTTTTATGAATT
1 ATTTTT-TGAATT
28617089 AAGATTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (24 bp):
ATTTTTTGAATTTTTAGTTTTTAA
Found at i:28619555 original size:23 final size:23
Alignment explanation
Indices: 28619529--28619585 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
28619519 TTCTCCCAAG
*
28619529 TTTCCCTTCTAGAGGTAATTTCT
1 TTTCCCTTCCAGAGGTAATTTCT
*
28619552 TTTCCCTTCCAGATGTAATTTCT
1 TTTCCCTTCCAGAGGTAATTTCT
28619575 TTTCCCTTCCA
1 TTTCCCTTCCA
28619586 TCGGTTCTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.16, C:0.28, G:0.09, T:0.47
Consensus pattern (23 bp):
TTTCCCTTCCAGAGGTAATTTCT
Found at i:28619665 original size:60 final size:61
Alignment explanation
Indices: 28619588--28619705 Score: 184
Period size: 62 Copynumber: 1.9 Consensus size: 61
28619578 CCCTTCCATC
* * *
28619588 GGTTCTGCCATCTGTTCTTTTCG-TTCGTTTCTTTTATTTTCTTCATGGATTATCTCGTTT
1 GGTTCTGCCATCGGTTCTTCTCGTTTAGTTTCTTTTATTTTCTTCATGGATTATCTCGTTT
*
28619648 GGTTCTGCCATCGGTTCTTCTCGTTTTATTTTCTTTTATTTTCTTCATGGATTATCTC
1 GGTTCTGCCATCGGTTCTTCTCG-TTTAGTTTCTTTTATTTTCTTCATGGATTATCTC
28619706 TGTAATTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 21 0.40
62 31 0.60
ACGTcount: A:0.09, C:0.20, G:0.14, T:0.56
Consensus pattern (61 bp):
GGTTCTGCCATCGGTTCTTCTCGTTTAGTTTCTTTTATTTTCTTCATGGATTATCTCGTTT
Found at i:28621184 original size:16 final size:16
Alignment explanation
Indices: 28621164--28621216 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
28621154 TTGGTTCGCT
*
28621164 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
*
28621180 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
28621196 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
28621212 GTAAT
1 GTAAT
28621217 ATGTAATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.04, G:0.34, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:28621281 original size:44 final size:46
Alignment explanation
Indices: 28621202--28621293 Score: 152
Period size: 44 Copynumber: 2.0 Consensus size: 46
28621192 ATGCGTAATG
* *
28621202 GAATAGAGGCGTAATATGTAATTCTTTTGTTTGGTTGAATGGAATA
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGGAATA
28621248 GAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGGAATA
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGGAATA
28621292 GA
1 GA
28621294 GGTGTAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 27 0.61
45 2 0.05
46 15 0.34
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (46 bp):
GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGGAATA
Found at i:28621291 original size:39 final size:41
Alignment explanation
Indices: 28621198--28621303 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
28621188 ATAGATGCGT
* *
28621198 AATGGAATAGAGGCGTAATATGTAATTCTTTTGTTTGGTTG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTG
28621239 AATGGAATAGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTG
1 AAT-G----GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTG
*
28621283 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
28621304 CATAAGGAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 14 0.25
40 1 0.02
41 3 0.05
42 1 0.02
43 1 0.02
44 19 0.34
45 2 0.04
46 15 0.27
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (41 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTG
Found at i:28621502 original size:18 final size:17
Alignment explanation
Indices: 28621450--28621502 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
28621440 TTATTATTAA
28621450 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
28621468 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
28621485 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
28621503 CATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28632471 original size:3 final size:3
Alignment explanation
Indices: 28632463--28632489 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
28632453 TAAGCTAAAC
28632463 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
28632490 TCTTTTATTT
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:28637526 original size:14 final size:13
Alignment explanation
Indices: 28637499--28637531 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28637489 CGCTGTTCCC
28637499 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
28637512 TTTTCTTTTTATCT
1 TTTTCTTTTT-TCT
28637526 TTTTCT
1 TTTTCT
28637532 GAGTGCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:28640852 original size:21 final size:20
Alignment explanation
Indices: 28640807--28640869 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
28640797 TATTTCTTGA
*
28640807 TTTTTAAATTTAAATTT-TTT
1 TTTTTAAATTT-AATTTCATT
*
28640827 ATTTTTAAATTTAATTTCAAT
1 -TTTTTAAATTTAATTTCATT
*
28640848 TTTTTAAAATTAATTTCATT
1 TTTTTAAATTTAATTTCATT
28640868 TT
1 TT
28640870 ACAACCATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 25 0.68
21 12 0.32
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTAAATTTAATTTCATT
Found at i:28640860 original size:26 final size:25
Alignment explanation
Indices: 28640813--28640868 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
28640803 TTGATTTTTA
***
28640813 AATTTAAATTTTTTATTTTTAAATTT
1 AATTTAAATTTTTTAAAATT-AATTT
*
28640839 AATTTCAATTTTTTAAAATTAATTT
1 AATTTAAATTTTTTAAAATTAATTT
*
28640864 CATTT
1 AATTT
28640869 TACAACCATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
AATTTAAATTTTTTAAAATTAATTT
Found at i:28641758 original size:140 final size:139
Alignment explanation
Indices: 28641506--28641971 Score: 700
Period size: 140 Copynumber: 3.3 Consensus size: 139
28641496 AAAATCACAT
* * *
28641506 ACGCTTAAATGAGAGTTGCCTTTGCCCAACACTATGCCGACACTTTTGGGCCAACACTTTCTTAA
1 ACGCTTAAATAAGAGTCGCCTTTGCCCAACACTATGCCGACACTTTTGGGCCAACACTTTCCTAA
28641571 GTGTTGGGATAGACTTGCTGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCAT
66 GTGTTGGGATAGACTTGCTGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCAT
*
28641636 GTCTAAGACA
131 GCCTAAG-CA
* *
28641646 ACGCTTAAATGAGAGTTGCCTTTGCCCAACACTATGCCGACACTTTTGGGCCAACACTTTCCTAA
1 ACGCTTAAATAAGAGTCGCCTTTGCCCAACACTATGCCGACACTTTTGGGCCAACACTTTCCTAA
* *
28641711 GTGTCGGGATAGACTTGCTGACATACGCTTTGGCCAACTCCTTGTATAAGGGTTGGGATATGCAT
66 GTGTTGGGATAGACTTGCTGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCAT
28641776 GCCTAAGGCA
131 GCCTAA-GCA
* * * * * * *
28641786 ATGTTTAAATAAGAGTCGGCTTTGTCCAACACTATGTCGACACTTATGGGCCGACACTTTCCTAA
1 ACGCTTAAATAAGAGTCGCCTTTGCCCAACACTATGCCGACACTTTTGGGCCAACACTTTCCTAA
* *
28641851 CTGTTGGGATAGACTTG-TCGAAATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCA
66 GTGTTGGGATAGACTTGCT-GACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCA
28641915 TGCCTAATGCA
130 TGCCTAA-GCA
* * * *
28641926 ATGCTTAAATAAAAGTCGACTTTGTCCAACACTATGCCGACACTTT
1 ACGCTTAAATAAGAGTCGCCTTTGCCCAACACTATGCCGACACTTT
28641972 CCTAAGTTTT
Statistics
Matches: 301, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
139 1 0.00
140 299 0.99
141 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (139 bp):
ACGCTTAAATAAGAGTCGCCTTTGCCCAACACTATGCCGACACTTTTGGGCCAACACTTTCCTAA
GTGTTGGGATAGACTTGCTGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCAT
GCCTAAGCA
Found at i:28642060 original size:126 final size:126
Alignment explanation
Indices: 28641835--28642088 Score: 386
Period size: 126 Copynumber: 2.0 Consensus size: 126
28641825 ACACTTATGG
*
28641835 GCCGACACTTTCCTAACTGTTGGGATAGACTTGTCGAAATACGCTTTGGCCAACTCTTTGTATAA
1 GCCGACACTTTCCTAACTGTTGGGATAGACTTGTCGAAATACACTTTGGCCAACTCTTTGTATAA
* *
28641900 GGGTTGGGATATGCATGCCTAATGCAATGCTTAAATAAAAGTCGACTTTGTCCAACACTAT
66 GGGTTGAGATATGCATGCCTAATGCAATACTTAAATAAAAGTCGACTTTGTCCAACACTAT
* * * *
28641961 GCCGACACTTTCCTAAGTTTTGGGATAGACTTGAT-GACATACACTTTGGTCAACTCTTTGTATA
1 GCCGACACTTTCCTAACTGTTGGGATAGACTTG-TCGAAATACACTTTGGCCAACTCTTTGTATA
* * *
28642025 AGGGTTGAGATATGCATGCCT-ATGGCAATACTTAAATAAGAGTTGGCTTTGTCCAACACTAT
65 AGGGTTGAGATATGCATGCCTAAT-GCAATACTTAAATAAAAGTCGACTTTGTCCAACACTAT
28642087 GC
1 GC
28642089 TTAAGGAAAC
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
125 2 0.02
126 113 0.97
127 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (126 bp):
GCCGACACTTTCCTAACTGTTGGGATAGACTTGTCGAAATACACTTTGGCCAACTCTTTGTATAA
GGGTTGAGATATGCATGCCTAATGCAATACTTAAATAAAAGTCGACTTTGTCCAACACTAT
Found at i:28644228 original size:13 final size:13
Alignment explanation
Indices: 28644202--28644238 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
28644192 TCAATTTATA
28644202 TTAATTAA-ATCT
1 TTAATTAATATCT
28644214 TTAATTAATATCT
1 TTAATTAATATCT
28644227 TTAATTAATATC
1 TTAATTAATATC
28644239 ATTTCAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAATTAATATCT
Found at i:28644541 original size:36 final size:36
Alignment explanation
Indices: 28644341--28644902 Score: 579
Period size: 36 Copynumber: 15.5 Consensus size: 36
28644331 ATGGGACCTG
* *
28644341 AGACAAGATCTATCCCAA-CTTTTTAAGTTTGCCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTT
* * *
28644376 AGA-TAGGTCTACCCCAACCTTTTTAGGGTTGCCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTT
* *
28644411 AGAC-AGGTCTA-CTCTAACCTTTTTAGGGTTGCCTT
1 AGACAAGGTCTATC-CCAACCTTTTTAAGGTTGCCTT
28644446 AGAC--GTGTCTATCCCAACCTTTTTAAGGTTGCCTT
1 AGACAAG-GTCTATCCCAACCTTTTTAAGGTTGCCTT
**
28644481 AGA-TGGGTCTATCCCAACCGTTTTTAAAGGTTGCCTT
1 AGACAAGGTCTATCCCAACC-TTTTT-AAGGTTGCCTT
* * *
28644518 AGAC-GGGTTTATCCCAACCTTTTTTAAAGGTTG-TTGT
1 AGACAAGGTCTATCCCAACC-TTTTT-AAGGTTGCCT-T
* * * * *
28644555 AGCCAAGATTTATCCCAACATTTTTAAGGTTG-TTGT
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCT-T
* * * * *
28644591 AGCCAAGATTTATCCCAACATTTTTAAGGTTACCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTT
* *
28644627 AGATAAGGTCTATCCCAACCTTTTTTATAAGTTGCCTT
1 AGACAAGGTCTATCCCAACC-TTTTTA-AGGTTGCCTT
*
28644665 AGACAAGGTCTATCCCAACCTTTTTAAGGTTACCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTT
* *
28644701 AGAC-GGGTCTATCCTAACCTTTTTTAAAGGTTGCCTT
1 AGACAAGGTCTATCCCAACC-TTTTT-AAGGTTGCCTT
* *
28644738 AAACAAGGTCTATCCCAATCTTTTTAAGGTTGCCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTT
* * *
28644774 TGACAAGGTCTATCCCAACTTTTTTTAAAAGTTGCCTT
1 AGACAAGGTCTATCCCAAC-CTTTTT-AAGGTTGCCTT
* * *
28644812 AGACAAGATTTATCCCAACCTTTTTAAGGTTTCCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTT
* * *
28644848 AGACAAGGTCTATCCCAACCATTTTAAGGTTACTTT
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTT
28644884 AGACAAGGTCTATCCCAAC
1 AGACAAGGTCTATCCCAAC
28644903 TTGTATAAGC
Statistics
Matches: 457, Mismatches: 50, Indels: 39
0.84 0.09 0.07
Matches are distributed among these distances:
34 13 0.03
35 107 0.23
36 169 0.37
37 91 0.20
38 77 0.17
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (36 bp):
AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTT
Found at i:28644679 original size:74 final size:72
Alignment explanation
Indices: 28644341--28644902 Score: 563
Period size: 74 Copynumber: 7.8 Consensus size: 72
28644331 ATGGGACCTG
* * * *
28644341 AGACAAGATCTATCCCAA-CTTTTT-AAGTTTGCCTTAGA-TAGGTCTACCCCAACCTTTTTAGG
1 AGACAAGGTCTATCCCAACCTTTTTAAAG-TTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAG
28644403 GTTGCCTT
65 GTTGCCTT
* **
28644411 AGAC-AGGTCTA-CTCTAACCTTTTTAGGGTTGCCTTAGAC--GTGTCTATCCCAACCTTTTTAA
1 AGACAAGGTCTATC-CCAACCTTTTTAAAGTTGCCTTAGACAAG-GTCTATCCCAACCTTTTTAA
28644472 GGTTGCCTT
64 GGTTGCCTT
** * *
28644481 AGA-TGGGTCTATCCCAACCGTTTTTAAAGGTTGCCTTAGAC-GGGTTTATCCCAACCTTTTTTA
1 AGACAAGGTCTATCCCAACC-TTTTTAAA-GTTGCCTTAGACAAGGTCTATCCCAACC-TTTTT-
*
28644544 AAGGTTG-TTGT
62 AAGGTTGCCT-T
* * * * * * * * * *
28644555 AGCCAAGATTTATCCCAACATTTTTAAGGTTG-TTGTAGCCAAGATTTATCCCAACATTTTTAAG
1 AGACAAGGTCTATCCCAACCTTTTTAAAGTTGCCT-TAGACAAGGTCTATCCCAACCTTTTTAAG
*
28644619 GTTACCTT
65 GTTGCCTT
*
28644627 AGATAAGGTCTATCCCAACCTTTTTTATAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAA
1 AGACAAGGTCTATCCCAACC-TTTTTA-AAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAA
*
28644692 GGTTACCTT
64 GGTTGCCTT
* * * *
28644701 AGAC-GGGTCTATCCTAACCTTTTTTAAAGGTTGCCTTAAACAAGGTCTATCCCAATCTTTTTAA
1 AGACAAGGTCTATCCCAACC-TTTTTAAA-GTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAA
28644765 GGTTGCCTT
64 GGTTGCCTT
* * * *
28644774 TGACAAGGTCTATCCCAACTTTTTTTAAAAGTTGCCTTAGACAAGATTTATCCCAACCTTTTTAA
1 AGACAAGGTCTATCCCAAC-CTTTTT-AAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAA
*
28644839 GGTTTCCTT
64 GGTTGCCTT
* * * *
28644848 AGACAAGGTCTATCCCAACCATTTTAAGGTTACTTTAGACAAGGTCTATCCCAAC
1 AGACAAGGTCTATCCCAACCTTTTTAAAGTTGCCTTAGACAAGGTCTATCCCAAC
28644903 TTGTATAAGC
Statistics
Matches: 408, Mismatches: 60, Indels: 46
0.79 0.12 0.09
Matches are distributed among these distances:
68 1 0.00
69 10 0.02
70 61 0.15
71 8 0.02
72 74 0.18
73 95 0.23
74 144 0.35
75 15 0.04
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (72 bp):
AGACAAGGTCTATCCCAACCTTTTTAAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGG
TTGCCTT
Found at i:28644733 original size:147 final size:144
Alignment explanation
Indices: 28644349--28644904 Score: 566
Period size: 147 Copynumber: 3.8 Consensus size: 144
28644339 TGAGACAAGA
* * *
28644349 TCTATCCCAA-C--TTTT-TAAGTTTGCCTTAGA-TAGGTCTACCCCAACCTTTTTAGGGTTGCC
1 TCTATCCCAACCTTTTTTATAAG-TTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTT-CC
* * **
28644409 TTAGAC-AGGTCTA-CTCTAACC-TTTTTAGGGTTGCCTTAGACGTGTCTATCCCAACCTTTTTA
64 TTAGACAAGGTCTATC-CCAACCATTTTTAAGGTTGCCTTAGACAAGTCTATCCCAA-CTTTTTA
*
28644471 AGGTTGCCTTAGAT-GGG
127 AGGTTGCCTTAGATAAGG
* * * *
28644488 TCTATCCCAACCGTTTTTA-AAGGTTGCCTTAGAC-GGGTTTATCCCAACCTTTTTTAAAGGTTG
1 TCTATCCCAACCTTTTTTATAA-GTTGCCTTAGACAAGGTCTATCCCAACC-TTTTT-AAGGTTC
* * * * * * *
28644551 TTGTAGCCAAGATTTATCCCAA-CATTTTTAAGGTTG-TTGTAGCCAAGATTTATCCCAACATTT
63 CT-TAGACAAGGTCTATCCCAACCATTTTTAAGGTTGCCT-TAGACAAG-TCTATCCCAAC-TTT
*
28644614 TTAAGGTTACCTTAGATAAGG
124 TTAAGGTTGCCTTAGATAAGG
28644635 TCTATCCCAACCTTTTTTATAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACCT
1 TCTATCCCAACCTTTTTTATAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTT-CCT
* * * *
28644700 TAGAC-GGGTCTATCCTAACCTTTTTTAAAGGTTGCCTTAAACAAGGTCTATCCCAATCTTTTTA
65 TAGACAAGGTCTATCCCAACCATTTTT-AAGGTTGCCTTAGACAA-GTCTATCCCAA-CTTTTTA
* *
28644764 AGGTTGCCTTTGACAAGG
127 AGGTTGCCTTAGATAAGG
* * * *
28644782 TCTATCCCAACTTTTTTTAAAAGTTGCCTTAGACAAGATTTATCCCAACCTTTTTAAGGTTTCCT
1 TCTATCCCAACCTTTTTTATAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGG-TTCCT
* *
28644847 TAGACAAGGTCTATCCCAACCA-TTTTAAGGTTACTTTAGACAAGGTCTATCCCAACTT
65 TAGACAAGGTCTATCCCAACCATTTTTAAGGTTGCCTTAGACAA-GTCTATCCCAACTT
28644905 GTATAAGCCC
Statistics
Matches: 345, Mismatches: 46, Indels: 46
0.79 0.11 0.11
Matches are distributed among these distances:
139 10 0.03
140 1 0.00
142 28 0.08
143 7 0.02
144 11 0.03
145 37 0.11
146 71 0.21
147 147 0.43
148 33 0.10
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (144 bp):
TCTATCCCAACCTTTTTTATAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTCCTT
AGACAAGGTCTATCCCAACCATTTTTAAGGTTGCCTTAGACAAGTCTATCCCAACTTTTTAAGGT
TGCCTTAGATAAGG
Found at i:28644904 original size:110 final size:108
Alignment explanation
Indices: 28644341--28644902 Score: 572
Period size: 110 Copynumber: 5.2 Consensus size: 108
28644331 ATGGGACCTG
* * * * *
28644341 AGACAAGATCTATCCCAA-CTTTTTAAGTTTGCCTTAGA-TAGGTCTACCCCAACCTTTTTAGGG
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGG
* * *
28644404 TTGCCTTAGAC-AGGTCTA-CTCTAACCTTTTTAGGGTTGCCTT
66 TTGCCTTAGACAAGGTCTATC-CCAACCTTTTTAAGGTTGCTTT
**
28644446 AGAC--GTGTCTATCCCAACCTTTTTAAGGTTGCCTTAGA-TGGGTCTATCCCAACCGTTTTTAA
1 AGACAAG-GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTT-A
* *
28644508 AGGTTGCCTTAGAC-GGGTTTATCCCAACCTTTTTTAAAGGTTG-TTGT
63 AGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTT-AAGGTTGCTT-T
* * * * * * * * *
28644555 AGCCAAGATTTATCCCAACATTTTTAAGGTTG-TTGTAGCCAAGATTTATCCCAACATTTTTAAG
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCT-TAGACAAGGTCTATCCCAACCTTTTTAAG
* * * *
28644619 GTTACCTTAGATAAGGTCTATCCCAACCTTTTTTATAAGTTGCCTT
65 GTTGCCTTAGACAAGGTCTATCCCAACC-TTTTTA-AGGTTGCTTT
* * *
28644665 AGACAAGGTCTATCCCAACCTTTTTAAGGTTACCTTAGAC-GGGTCTATCCTAACCTTTTTTAAA
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTT-AA
* *
28644729 GGTTGCCTTAAACAAGGTCTATCCCAATCTTTTTAAGGTTGCCTTT
64 GGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTG-CTTT
* * * *
28644775 -GACAAGGTCTATCCCAACTTTTTTTAAAAGTTGCCTTAGACAAGATTTATCCCAACCTTTTTAA
1 AGACAAGGTCTATCCCAAC-CTTTTT-AAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAA
* * *
28644839 GGTTTCCTTAGACAAGGTCTATCCCAACCATTTTAAGGTTACTTT
64 GGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCTTT
28644884 AGACAAGGTCTATCCCAAC
1 AGACAAGGTCTATCCCAAC
28644903 TTGTATAAGC
Statistics
Matches: 377, Mismatches: 57, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
103 1 0.00
104 10 0.03
105 37 0.10
106 5 0.01
107 24 0.06
108 7 0.02
109 62 0.16
110 161 0.43
111 59 0.16
112 11 0.03
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (108 bp):
AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGG
TTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCTTT
Found at i:28649453 original size:29 final size:30
Alignment explanation
Indices: 28649400--28649456 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28649390 TCCGAGCCTT
28649400 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGTAAAAGTTTA
* *
28649430 GGGGCAAAATTGTAATTTTG-AAAAGTT
1 GGGGCAAAAATGTAATTATGTAAAAGTT
28649457 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGTAAAAGTTTA
Found at i:28653490 original size:14 final size:14
Alignment explanation
Indices: 28653471--28653497 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28653461 TTCCAGCAAC
28653471 TATGAATTTATTTT
1 TATGAATTTATTTT
28653485 TATGAATTTATTT
1 TATGAATTTATTT
28653498 GATGATGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TATGAATTTATTTT
Found at i:28653672 original size:50 final size:50
Alignment explanation
Indices: 28653597--28653889 Score: 496
Period size: 50 Copynumber: 5.8 Consensus size: 50
28653587 ATTTGGGTAA
28653597 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
28653647 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
28653697 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
28653747 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
28653797 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
28653847 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28653890 TGTTATTATC
Statistics
Matches: 228, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
50 194 0.85
51 34 0.15
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28660244 original size:38 final size:38
Alignment explanation
Indices: 28660130--28660245 Score: 141
Period size: 36 Copynumber: 3.1 Consensus size: 38
28660120 GGGGTGTTAA
28660130 CAACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCC
1 CAACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCC
* *
28660168 CAACC-TTTTT-AAGGTTGCCTTAGACGA-CTCTATCC
1 CAACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCC
* * * *
28660203 CAACCTTTTTTAAAGGTCGGCCTT-GACTAGGTCTTTGC
1 CAACCTTTTTTAAAGGT-TGCCTTAGACAAGGTCTATCC
28660241 CAACC
1 CAACC
28660246 CTTCAATAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
35 12 0.18
36 21 0.31
37 14 0.21
38 20 0.30
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (38 bp):
CAACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCC
Found at i:28668251 original size:3 final size:3
Alignment explanation
Indices: 28668243--28668403 Score: 163
Period size: 3 Copynumber: 53.0 Consensus size: 3
28668233 TAATATTTCC
28668243 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
28668291 ATT ATT ATT ATT ATT ATT ATT ATT AGTT -TT -TT ACTT AAT CTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT A-TT ATT ATT ATT
* *
28668336 ATT A-T AGT ATT ACCTT -TT ATT -TT ATTT ATT ATT AGT ATT ATTT ATT
1 ATT ATT ATT ATT A--TT ATT ATT ATT A-TT ATT ATT ATT ATT A-TT ATT
*
28668382 -TT TTT ATGT ATT ATT ACTT ATT
1 ATT ATT AT-T ATT ATT A-TT ATT
28668404 TTACTAAATA
Statistics
Matches: 137, Mismatches: 8, Indels: 26
0.80 0.05 0.15
Matches are distributed among these distances:
2 12 0.09
3 106 0.77
4 17 0.12
5 2 0.01
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:28669597 original size:20 final size:20
Alignment explanation
Indices: 28669572--28669613 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
28669562 CAACCTTTTC
*
28669572 TTTTTTAAAAAACACGAATT
1 TTTTTTAAAAAACAAGAATT
*
28669592 TTTTTTAAAATACAAGAATT
1 TTTTTTAAAAAACAAGAATT
28669612 TT
1 TT
28669614 AGAAACACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTTTAAAAAACAAGAATT
Found at i:28669704 original size:17 final size:17
Alignment explanation
Indices: 28669678--28669789 Score: 82
Period size: 17 Copynumber: 6.3 Consensus size: 17
28669668 CGAGGATTTT
28669678 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* *
28669695 TTTATGAAACACGATCAAT
1 TTTTTGAAACACGA--AAA
28669714 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* * **
28669732 TTTTTTAAAGACGAATTTT
1 TTTTTGAAACACGAA--AA
* *
28669751 TTTTTGAAAATACGGAAA
1 TTTTTG-AAACACGAAAA
*
28669769 TTTATGAAACACG-AAA
1 TTTTTGAAACACGAAAA
28669785 TTTTT
1 TTTTT
28669790 TTTTTGAAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
16 7 0.10
17 27 0.37
18 12 0.16
19 12 0.16
20 15 0.21
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:28669726 original size:37 final size:37
Alignment explanation
Indices: 28669662--28669810 Score: 167
Period size: 37 Copynumber: 3.9 Consensus size: 37
28669652 GATAAAATAC
28669662 GAAACACGAGGATTTTTTTTTG-AAACACGAAAATTTAT
1 GAAACACGA--ATTTTTTTTTGAAAACACGAAAATTTAT
** *
28669700 GAAACACG-ATCAATTTTTTGAAAACACGAAAATTTTT
1 GAAACACGAAT-TTTTTTTTGAAAACACGAAAATTTAT
* * * *
28669737 TAAAGACGAATTTTTTTTTGAAAATACGGAAATTTAT
1 GAAACACGAATTTTTTTTTGAAAACACGAAAATTTAT
*
28669774 GAAACACGAAATTTTTTTTTTGAAAACAAGAAAATTT
1 GAAACACG-AA-TTTTTTTTTGAAAACACGAAAATTT
28669811 TCGAAATACG
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
35 2 0.02
36 7 0.08
37 48 0.53
38 12 0.13
39 22 0.24
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (37 bp):
GAAACACGAATTTTTTTTTGAAAACACGAAAATTTAT
Found at i:28669776 original size:74 final size:74
Alignment explanation
Indices: 28669673--28669811 Score: 199
Period size: 76 Copynumber: 1.9 Consensus size: 74
28669663 AAACACGAGG
*
28669673 ATTTTTTTTTGAAACACGAAAATTTATGAAACACG-ATCAATTTTTTGAAAACACGAAAATTTTT
1 ATTTTTTTTTGAAACACGAAAATTTATGAAACACGAATCAATTTTTTGAAAACAAGAAAATTTTT
28669737 TAAAGACGA
66 TAAAGACGA
* * ***
28669746 ATTTTTTTTTGAAAATACGGAAATTTATGAAACACGAAATTTTTTTTTTGAAAACAAGAAAATTT
1 ATTTTTTTTTG-AAACACGAAAATTTATGAAACACG-AATCAATTTTTTGAAAACAAGAAAATTT
28669811 T
64 T
28669812 CGAAATACGG
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
73 11 0.19
74 22 0.39
76 24 0.42
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.39
Consensus pattern (74 bp):
ATTTTTTTTTGAAACACGAAAATTTATGAAACACGAATCAATTTTTTGAAAACAAGAAAATTTTT
TAAAGACGA
Found at i:28669874 original size:18 final size:17
Alignment explanation
Indices: 28669838--28669888 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
28669828 TTAAAAATAC
*
28669838 GAAAACATGAAAATTTT
1 GAAAACACGAAAATTTT
28669855 GAAAACACGAAAACTTTT
1 GAAAACACGAAAA-TTTT
*
28669873 G-AAACACGAGAATTTT
1 GAAAACACGAAAATTTT
28669889 TTTTTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 4 0.13
17 22 0.71
18 5 0.16
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (17 bp):
GAAAACACGAAAATTTT
Found at i:28669907 original size:47 final size:44
Alignment explanation
Indices: 28669855--28669952 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 44
28669845 TGAAAATTTT
*
28669855 GAAAACACGAAAACTTTTGAAACACGAGAATTTTTTTTTGAAAACAC
1 GAAAACACGAAAACTTTTCAAACACGAGAA---TTTTTTGAAAACAC
** * *
28669902 GAAAACGTGAAAATTTTTCAAACACGGGAATTTTTTGAAAACAC
1 GAAAACACGAAAACTTTTCAAACACGAGAATTTTTTGAAAACAC
*
28669946 GATAACA
1 GAAAACA
28669953 TCAAAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
44 19 0.43
47 25 0.57
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (44 bp):
GAAAACACGAAAACTTTTCAAACACGAGAATTTTTTGAAAACAC
Found at i:28669914 original size:107 final size:105
Alignment explanation
Indices: 28669795--28670110 Score: 327
Period size: 106 Copynumber: 3.0 Consensus size: 105
28669785 TTTTTTTTTT
* * * * * ***
28669795 GAAAACAAGAAAA-TTTTCGAAATACGGGAATTTTTAAAAATACGAAAACATGAAAATTTTGAAA
1 GAAAACACGAAAATTTTTC-AAACACGGGAATTTTTGAAAACACGAAAACATCAAAAAAAT--AA
28669859 ACACGAA-A-ACTTTTGAAACACGAGAATTTTTTTTTGAAAACAC
63 ACAC-AAGAGACTTTTGAAACACGAGAA-TTTTTTTTGAAAACAC
** * **
28669902 GAAAACGTGAAAATTTTTCAAACACGGGAATTTTTTGAAAACACGATAACATCAAAAAAATATTC
1 GAAAACACGAAAATTTTTCAAACACGGGAA-TTTTTGAAAACACGAAAACATCAAAAAAATAAAC
**
28669967 ACAAGAGTTTTTTGAAACACGAGAATTTTTTTTGAAAACAC
65 ACAAGAGACTTTTGAAACACGAGAATTTTTTTTGAAAACAC
* * * **
28670008 GAAAACACGAAAATTTTTCAAACACGGAAATTTTTGAAAACACGATAACGTCAAAAAAAATATTC
1 GAAAACACGAAAATTTTTCAAACACGGGAATTTTTGAAAACACGAAAACATC-AAAAAAATAAAC
* **
28670073 ACGAGAGTTTTTTGAAACACGAGAA--TTTTTTGAAAACA
65 ACAAGAGACTTTTGAAACACGAGAATTTTTTTTGAAAACA
28670111 TTTTTCAAAC
Statistics
Matches: 185, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
104 13 0.07
105 23 0.12
106 84 0.45
107 37 0.20
108 28 0.15
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (105 bp):
GAAAACACGAAAATTTTTCAAACACGGGAATTTTTGAAAACACGAAAACATCAAAAAAATAAACA
CAAGAGACTTTTGAAACACGAGAATTTTTTTTGAAAACAC
Found at i:28670048 original size:18 final size:18
Alignment explanation
Indices: 28670008--28670052 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
28669998 TTGAAAACAC
28670008 GAAAACACGAAAATTTTT
1 GAAAACACGAAAATTTTT
* *
28670026 -CAAACACGGAAATTTTT
1 GAAAACACGAAAATTTTT
28670043 GAAAACACGA
1 GAAAACACGA
28670053 TAACGTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (18 bp):
GAAAACACGAAAATTTTT
Found at i:28670102 original size:105 final size:106
Alignment explanation
Indices: 28669869--28670110 Score: 400
Period size: 106 Copynumber: 2.3 Consensus size: 106
28669859 ACACGAAAAC
** *
28669869 TTTTGAAACACGAGAATTTTTTTTTGAAAACACGAAAACGTGAAAATTTTTCAAACACGGGAATT
1 TTTTGAAACACGAGAA-TTTTTTTTGAAAACACGAAAACACGAAAATTTTTCAAACACGGGAAAT
28669934 TTTTGAAAACACGATAACATCAAAAAAATATTCACAAGAGTT
65 TTTTGAAAACACGATAACATCAAAAAAATATTCACAAGAGTT
28669976 TTTTGAAACACGAGAATTTTTTTTGAAAACACGAAAACACGAAAATTTTTCAAACAC-GGAAATT
1 TTTTGAAACACGAGAATTTTTTTTGAAAACACGAAAACACGAAAATTTTTCAAACACGGGAAATT
* *
28670040 TTTGAAAACACGATAACGTCAAAAAAAATATTCACGAGAGTT
66 TTTGAAAACACGATAACATC-AAAAAAATATTCACAAGAGTT
28670082 TTTTGAAACACGAGAA--TTTTTTGAAAACA
1 TTTTGAAACACGAGAATTTTTTTTGAAAACA
28670111 TTTTTCAAAC
Statistics
Matches: 129, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
104 13 0.10
105 25 0.19
106 75 0.58
107 16 0.12
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (106 bp):
TTTTGAAACACGAGAATTTTTTTTGAAAACACGAAAACACGAAAATTTTTCAAACACGGGAAATT
TTTGAAAACACGATAACATCAAAAAAATATTCACAAGAGTT
Found at i:28670132 original size:29 final size:30
Alignment explanation
Indices: 28670081--28670139 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28670071 TCACGAGAGT
*
28670081 TTTTTGAAACACGAGAATTTTTTGAAAACA
1 TTTTTCAAACACGAGAATTTTTTGAAAACA
*
28670111 TTTTTCAAACACGGGAA-TTTTTGAAAACA
1 TTTTTCAAACACGAGAATTTTTTGAAAACA
28670140 CGAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (30 bp):
TTTTTCAAACACGAGAATTTTTTGAAAACA
Found at i:28670184 original size:17 final size:18
Alignment explanation
Indices: 28670072--28670184 Score: 93
Period size: 17 Copynumber: 6.8 Consensus size: 18
28670062 AAAAAATATT
*
28670072 CACGAGAGTTTTTTGAAA
1 CACGAGAATTTTTTGAAA
28670090 CACGAGAATTTTTTGAAA
1 CACGAGAATTTTTTGAAA
*
28670108 -AC----A-TTTTTCAAA
1 CACGAGAATTTTTTGAAA
*
28670120 CACGGGAA-TTTTTGAAAA
1 CACGAGAATTTTTTG-AAA
* **
28670138 CACGAAAATTTTTT-ATT
1 CACGAGAATTTTTTGAAA
28670155 CACGAGAA-TTTTTGAAA
1 CACGAGAATTTTTTGAAA
28670172 CACG-GAATTTTTT
1 CACGAGAATTTTTT
28670185 TTTTAAAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
12 8 0.11
13 3 0.04
16 8 0.11
17 26 0.34
18 26 0.34
19 5 0.07
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (18 bp):
CACGAGAATTTTTTGAAA
Found at i:28670286 original size:17 final size:17
Alignment explanation
Indices: 28670246--28670290 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
28670236 ATTATTATTA
28670246 TGAAACACGAGAAATTT
1 TGAAACACGAGAAATTT
*
28670263 TGAAAACATGA-AAATTTT
1 TG-AAACACGAGAAA-TTT
28670281 TGAAACACGA
1 TGAAACACGA
28670291 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (17 bp):
TGAAACACGAGAAATTT
Found at i:28671070 original size:7 final size:6
Alignment explanation
Indices: 28671043--28671126 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
28671033 TTATTATTAT
*
28671043 TTTTTC TTTCTC TTTTTC TTTGTTC TTTTT- TTTTTC --TTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * *
28671089 -CTTT- TTTCTC TTTTTTC TTCTTCC TTTTTC TTCTTC TT
1 TTTTTC TTTTTC -TTTTTC TT-TTTC TTTTTC TTTTTC TT
28671127 CTTCGGGCCG
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.07
5 10 0.16
6 31 0.51
7 16 0.26
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:28671078 original size:30 final size:31
Alignment explanation
Indices: 28671042--28671120 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 31
28671032 TTTATTATTA
28671042 TTTTTTCTTTCTCTTTTTCTTTGTTCT-TTT
1 TTTTTTCTTTCTCTTTTTCTTTGTTCTCTTT
* *
28671072 TTTTTTCTTTCT-TTTTCCTTTTTTCTCTTT
1 TTTTTTCTTTCTCTTTTTCTTTGTTCTCTTT
*
28671102 TTTCTTC-TTC-CTTTTTCTT
1 TTTTTTCTTTCTCTTTTTCTT
28671121 CTTCTTCTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.78
Consensus pattern (31 bp):
TTTTTTCTTTCTCTTTTTCTTTGTTCTCTTT
Found at i:28671087 original size:29 final size:30
Alignment explanation
Indices: 28671042--28671118 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
28671032 TTTATTATTA
*
28671042 TTTTTTCTTTCTCTTTTTCTTTGTTCT-TTT
1 TTTTTTCTTTCT-TTTTCCTTTGTTCTCTTT
*
28671072 TTTTTTCTTTCTTTTTCCTTTTTTCTCTTT
1 TTTTTTCTTTCTTTTTCCTTTGTTCTCTTT
* *
28671102 TTTCTTCTTCCTTTTTC
1 TTTTTTCTTTCTTTTTC
28671119 TTCTTCTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 12 0.29
30 30 0.71
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (30 bp):
TTTTTTCTTTCTTTTTCCTTTGTTCTCTTT
Found at i:28671118 original size:13 final size:13
Alignment explanation
Indices: 28671079--28671124 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
28671069 TTTTTTTTTC
*
28671079 TTTCTTTTTCC-T
1 TTTCTTCTTCCTT
*
28671091 TTT-TTC-TCTTT
1 TTTCTTCTTCCTT
28671102 TTTCTTCTTCCTT
1 TTTCTTCTTCCTT
28671115 TTTCTTCTTC
1 TTTCTTCTTC
28671125 TTCTTCGGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 2 0.07
11 6 0.21
12 6 0.21
13 14 0.50
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTTCTTCCTT
Found at i:28671123 original size:23 final size:21
Alignment explanation
Indices: 28671044--28671123 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 21
28671034 TATTATTATT
*
28671044 TTTTCTTTCTCTTTTTCTTTGTTC
1 TTTT-TTTCT-TTTTTCTTT-TCC
28671068 TTTTTTT-TTTCTTTCTTTTTCC
1 TTTTTTTCTTT-TTTC-TTTTCC
28671090 TTTTTTCTCTTTTTTCTTCTTCC
1 TTTTTT-TCTTTTTTCTT-TTCC
28671113 TTTTTCTTCTT
1 TTTTT-TTCTT
28671124 CTTCTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
21 2 0.04
22 15 0.31
23 24 0.49
24 8 0.16
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (21 bp):
TTTTTTTCTTTTTTCTTTTCC
Done.