Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 128 of 135
Found at i:41710996 original size:27 final size:26
Alignment explanation
Indices: 41710940--41711008 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
41710930 TTAATTAATT
41710940 TTTAAAATTAAAAA-AATAAAAATAC
1 TTTAAAATTAAAAATAATAAAAATAC
*
41710965 TTTTAAGAATTAAAAATCATTAAAAATA-
1 -TTTAA-AATTAAAAAT-AATAAAAATAC
41710993 TTTAAAATATAAAAAT
1 TTTAAAAT-TAAAAAT
41711009 TATTTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 8 0.21
27 21 0.55
29 9 0.24
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (26 bp):
TTTAAAATTAAAAATAATAAAAATAC
Found at i:41711362 original size:16 final size:16
Alignment explanation
Indices: 41711341--41711373 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41711331 TGTTTTTAAA
41711341 TTTTTAAAAAATATTT
1 TTTTTAAAAAATATTT
*
41711357 TTTTTAAAAATTATTT
1 TTTTTAAAAAATATTT
41711373 T
1 T
41711374 GTAAAAACAT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTAAAAAATATTT
Found at i:41711389 original size:16 final size:14
Alignment explanation
Indices: 41711341--41711395 Score: 58
Period size: 15 Copynumber: 3.8 Consensus size: 14
41711331 TGTTTTTAAA
41711341 TTTTTAAAAAATATT
1 TTTTTAAAAAAT-TT
*
41711356 TTTTTTAAAAATTAT
1 TTTTTAAAAAATT-T
*
41711371 TTTGTAAAAACA-TT
1 TTTTTAAAAA-ATTT
41711385 TTTTTAAAAAA
1 TTTTTAAAAAA
41711396 AATAGTAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 1 0.03
14 11 0.32
15 21 0.62
16 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
TTTTTAAAAAATTT
Found at i:41713989 original size:18 final size:18
Alignment explanation
Indices: 41713958--41713992 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41713948 TATTTGATAA
41713958 AAATAAATATTAATTTTT
1 AAATAAATATTAATTTTT
41713976 AAATATAATA-TAATTTT
1 AAATA-AATATTAATTTT
41713993 AACCTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATAAATATTAATTTTT
Found at i:41714826 original size:21 final size:23
Alignment explanation
Indices: 41714788--41714831 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
41714778 ACCTTAGTTT
41714788 AGGAGGAGATCGAATACAATGCTA
1 AGGAGGAGATCG-ATACAATGCTA
41714812 AGGA-GAGATCG-TACAATGCT
1 AGGAGGAGATCGATACAATGCT
41714832 GGATCGCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
23 7 0.35
24 4 0.20
ACGTcount: A:0.39, C:0.14, G:0.30, T:0.18
Consensus pattern (23 bp):
AGGAGGAGATCGATACAATGCTA
Found at i:41717344 original size:20 final size:20
Alignment explanation
Indices: 41717279--41717344 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
41717269 ACCTTGTACC
* *
41717279 CACCCCATCCCCACCCGCCT
1 CACCCCATCCTCGCCCGCCT
* * *
41717299 CGCCCCATCCTTGGCCGTCC-
1 CACCCCATCCTCGCCCG-CCT
*
41717319 CGCCCCATCCTCGCCCGCCT
1 CACCCCATCCTCGCCCGCCT
41717339 CACCCC
1 CACCCC
41717345 GCATAATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.09, C:0.65, G:0.12, T:0.14
Consensus pattern (20 bp):
CACCCCATCCTCGCCCGCCT
Found at i:41717405 original size:12 final size:12
Alignment explanation
Indices: 41717388--41717420 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41717378 AAAAATTTAA
41717388 TTTAATAATTAT
1 TTTAATAATTAT
41717400 TTTAAT-ATTAT
1 TTTAATAATTAT
*
41717411 TTTATTAATT
1 TTTAATAATT
41717421 TAATATTGAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTAATAATTAT
Found at i:41717693 original size:40 final size:40
Alignment explanation
Indices: 41717635--41717719 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
41717625 AAGATACGAA
*
41717635 ATGATCCTTATTCACTTTTATGTTAAAAAAGTAATTAATC
1 ATGATCCTTATTCACTTTTATGTTAAAAAAATAATTAATC
*
41717675 ATGATCCTTATTCGCTTTTATGTTAAAAAAATAATTAATC
1 ATGATCCTTATTCACTTTTATGTTAAAAAAATAATTAATC
41717715 ATGAT
1 ATGAT
41717720 GAAGCTGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (40 bp):
ATGATCCTTATTCACTTTTATGTTAAAAAAATAATTAATC
Found at i:41722262 original size:8 final size:8
Alignment explanation
Indices: 41722251--41722275 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41722241 AGCTTTTTGA
41722251 AGTTTAGT
1 AGTTTAGT
41722259 AGTTTAGT
1 AGTTTAGT
41722267 AGTTTAGT
1 AGTTTAGT
41722275 A
1 A
41722276 ACTTTGAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (8 bp):
AGTTTAGT
Found at i:41728078 original size:31 final size:30
Alignment explanation
Indices: 41728043--41728112 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
41728033 TAATTAAGGG
*
41728043 TAAATTATA-TTTATGTTCATTAAATTATTAA
1 TAAATTATACTTT-TGGTCATTAAATTA-TAA
*
41728074 TAAATT-TACGTTTTGGTCATTCAATTATAA
1 TAAATTATAC-TTTTGGTCATTAAATTATAA
*
41728104 AAAATTATA
1 TAAATTATA
41728113 AAATGATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 10 0.30
31 20 0.61
32 3 0.09
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (30 bp):
TAAATTATACTTTTGGTCATTAAATTATAA
Found at i:41730583 original size:51 final size:52
Alignment explanation
Indices: 41730500--41730597 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 52
41730490 AAAATTGAAT
41730500 AGTTGGGTGACCATTTTGTAACTTTTCATAGTTAAATGACCAAAAAAAAAAA
1 AGTTGGGTGACCATTTTGTAACTTTTCATAGTTAAATGACCAAAAAAAAAAA
* * * *
41730552 AGTTGGGTGCCCATTTTGTAAC-TTTCATAGTTGAGTGATCAAAAAA
1 AGTTGGGTGACCATTTTGTAACTTTTCATAGTTAAATGACCAAAAAA
41730598 GAAAGTTACC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 21 0.50
52 21 0.50
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (52 bp):
AGTTGGGTGACCATTTTGTAACTTTTCATAGTTAAATGACCAAAAAAAAAAA
Found at i:41732758 original size:31 final size:31
Alignment explanation
Indices: 41732723--41732811 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
41732713 GGACCCCAAA
*
41732723 AAGTTTAAGTATCAATTTAGAAAAAAGTATC
1 AAGTTTAAGTATCAAATTAGAAAAAAGTATC
* * *
41732754 AAGTTTAGGTATCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTATCAAATTAGAAAAAAGTATC
* * *
41732785 AAGTTTGAGTACCAAATTGGATAAAAA
1 AAGTTTAAGTATCAAATTAGA-AAAAA
41732812 AGTACAGGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
31 43 0.90
32 5 0.10
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (31 bp):
AAGTTTAAGTATCAAATTAGAAAAAAGTATC
Found at i:41738689 original size:23 final size:22
Alignment explanation
Indices: 41738651--41738722 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
41738641 TTTTTGATTT
*
41738651 ATTTAAATAATAAAATACTTTTAA
1 ATTT-AATATTAAAATA-TTTTAA
*
41738675 ATTTAAT-TCTAAAATATATTAA
1 ATTTAATAT-TAAAATATTTTAA
*
41738697 TATTTAATATAAAAATATTTTTAA
1 -ATTTAATATTAAAATA-TTTTAA
41738721 AT
1 AT
41738723 ATTTTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 5 0.12
23 25 0.62
24 10 0.25
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTAATATTAAAATATTTTAA
Found at i:41741105 original size:15 final size:16
Alignment explanation
Indices: 41741085--41741120 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
41741075 CTGTTCCGAA
41741085 AAAAAAC-AACAAAAC
1 AAAAAACAAACAAAAC
*
41741100 AAAAAACAAACAAAAT
1 AAAAAACAAACAAAAC
41741116 AAAAA
1 AAAAA
41741121 TAGATCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAAAACAAACAAAAC
Found at i:41741105 original size:16 final size:17
Alignment explanation
Indices: 41741084--41741120 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
41741074 TCTGTTCCGA
41741084 AAAAAAAC-AACAAAAC
1 AAAAAAACAAACAAAAC
*
41741100 -AAAAAACAAACAAAAT
1 AAAAAAACAAACAAAAC
41741116 AAAAA
1 AAAAA
41741121 TAGATCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 7 0.39
17 4 0.22
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAAAAACAAACAAAAC
Found at i:41742100 original size:29 final size:29
Alignment explanation
Indices: 41741995--41742188 Score: 139
Period size: 30 Copynumber: 6.6 Consensus size: 29
41741985 CCAGACAGTT
* *
41741995 CCCAAAC-TTTCTAAAAATTACATTTTAAC
1 CCCAAACTTTTC-CAAAATTACATTTTGAC
* **
41742024 CCTTAAACTTTTTTAAAATCT-CATTTTGAC
1 CC-CAAACTTTTCCAAAAT-TACATTTTGAC
* * *
41742054 CCTCAAACTTCTCTAAAATTATATTTTGAC
1 CC-CAAACTTTTCCAAAATTACATTTTGAC
*
41742084 CCCAAACTTTTCCAAAA-TCCAATTTTGAAC
1 CCCAAACTTTTCCAAAATTAC-ATTTTG-AC
* *
41742114 CCTAAACTTCTCCAAAATTACATTTTGAC
1 CCCAAACTTTTCCAAAATTACATTTTGAC
* *
41742143 CCCTGAA--TTTCCAAAATTCACATTTTCAAC
1 CCC-AAACTTTTCCAAAATT-ACATTTT-GAC
*
41742173 CTCAAA-TTTTCCAAAA
1 CCCAAACTTTTCCAAAA
41742189 GCTCGATTTC
Statistics
Matches: 133, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
28 11 0.08
29 35 0.26
30 81 0.61
31 6 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCAAACTTTTCCAAAATTACATTTTGAC
Found at i:41742109 original size:59 final size:60
Alignment explanation
Indices: 41741997--41742178 Score: 189
Period size: 59 Copynumber: 3.1 Consensus size: 60
41741987 AGACAGTTCC
* * **
41741997 CAAACTT-TCTAAAAATTACATTTTAACCCTTAAACTTTTTTAAAATCTCATTTTG-ACCCT
1 CAAACTTCTCT-AAAATTACATTTTGACCC-CAAACTTTTCCAAAATCTCATTTTGAACCCT
*
41742057 CAAACTTCTCTAAAATTATATTTTGACCCCAAACTTTTCCAAAATC-CAATTTTGAACCCT
1 CAAACTTCTCTAAAATTACATTTTGACCCCAAACTTTTCCAAAATCTC-ATTTTGAACCCT
* * * *
41742117 -AAACTTCTCCAAAATTACATTTTGACCCCTGAA--TTTCCAAAATTCACATTTTCAA-CCT
1 CAAACTTCTCTAAAATTACATTTTGACCCC-AAACTTTTCCAAAA-TCTCATTTTGAACCCT
41742175 CAAA
1 CAAA
41742179 TTTTCCAAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 15
0.82 0.07 0.12
Matches are distributed among these distances:
58 13 0.12
59 59 0.56
60 31 0.29
61 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (60 bp):
CAAACTTCTCTAAAATTACATTTTGACCCCAAACTTTTCCAAAATCTCATTTTGAACCCT
Found at i:41742186 original size:30 final size:29
Alignment explanation
Indices: 41742084--41742217 Score: 98
Period size: 30 Copynumber: 4.6 Consensus size: 29
41742074 ATATTTTGAC
* *
41742084 CCCAAACTTTTCCAAAATCCA-ATTTTGAA
1 CCCAAA-TTTTCCAAAATTCACATTTTCAA
* * *
41742113 CCCTAAACTTCTCCAAAATT-ACATTTTGAC
1 CCC-AAA-TTTTCCAAAATTCACATTTTCAA
*
41742143 CCCTGAA-TTTCCAAAATTCACATTTTCAA
1 CCC-AAATTTTCCAAAATTCACATTTTCAA
* *
41742172 CCTCAAATTTTCCAAAAGCTC-GA-TTTCAA
1 CC-CAAATTTTCCAAAA-TTCACATTTTCAA
41742201 TCCCAAATTTTCCAAAA
1 -CCCAAATTTTCCAAAA
41742218 ATTTCAATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
28 10 0.11
29 36 0.41
30 40 0.45
31 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
CCCAAATTTTCCAAAATTCACATTTTCAA
Found at i:41744997 original size:38 final size:39
Alignment explanation
Indices: 41744928--41745011 Score: 152
Period size: 38 Copynumber: 2.2 Consensus size: 39
41744918 ATTGGCGTCA
41744928 CAGTTAATTTTAAAAGAAAGAAAGAAAATGAAGAAGTTTT
1 CAGTTAATTTTAAAAG-AAGAAAGAAAATGAAGAAGTTTT
41744968 CAGTTAATTTTAAAAG-AGAAAGAAAATGAAGAAGTTTT
1 CAGTTAATTTTAAAAGAAGAAAGAAAATGAAGAAGTTTT
41745006 CAGTTA
1 CAGTTA
41745012 GAATGTGCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 28 0.64
40 16 0.36
ACGTcount: A:0.50, C:0.04, G:0.18, T:0.29
Consensus pattern (39 bp):
CAGTTAATTTTAAAAGAAGAAAGAAAATGAAGAAGTTTT
Found at i:41745760 original size:29 final size:29
Alignment explanation
Indices: 41745713--41745772 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
41745703 AAAATTGAAT
*
41745713 CAAAACAAAATTTTATATATAAAATTACA
1 CAAAACAAAATTCTATATATAAAATTACA
*
41745742 CAAAATCAAAATTCT-TATATAACATTACA
1 CAAAA-CAAAATTCTATATATAAAATTACA
41745771 CA
1 CA
41745773 CTGAAGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (29 bp):
CAAAACAAAATTCTATATATAAAATTACA
Found at i:41750681 original size:37 final size:37
Alignment explanation
Indices: 41750640--41750713 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
41750630 ATAAAAGATA
*
41750640 AAAGTTTAAGGTTAAAGTATAAATGTTGAGTAATGAG
1 AAAGTTTAAGGTAAAAGTATAAATGTTGAGTAATGAG
*
41750677 AAAGTTTAGGGTAAAAGTATAAATGTTGAGTAATGAG
1 AAAGTTTAAGGTAAAAGTATAAATGTTGAGTAATGAG
41750714 TCAATTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (37 bp):
AAAGTTTAAGGTAAAAGTATAAATGTTGAGTAATGAG
Found at i:41751206 original size:38 final size:38
Alignment explanation
Indices: 41751136--41751387 Score: 251
Period size: 38 Copynumber: 6.6 Consensus size: 38
41751126 TGATTTATCG
*
41751136 GGCTATGTGC-AAGTGTTTATCGGG-TTTAGTGCCTAGCA
1 GGCTATGTGCTGA-TGTTTATCGGGCTTT-GTGCCTAGCA
* * *
41751174 GGCTTTATGCTGATGTTTATCGAGCTTTGTGCCTAGCA
1 GGCTATGTGCTGATGTTTATCGGGCTTTGTGCCTAGCA
* * * *
41751212 GGCTATGTGCTAATGTTTATCGGGCTTAGTGCCCAACA
1 GGCTATGTGCTGATGTTTATCGGGCTTTGTGCCTAGCA
* * * * *
41751250 AGCTTTGTGCCGATATTTATCGGGCTTTGTGCCTAGTA
1 GGCTATGTGCTGATGTTTATCGGGCTTTGTGCCTAGCA
* * * *
41751288 GGCTATGTACCGGTGTTTATCGGGTTTTGTGCCTAGCA
1 GGCTATGTGCTGATGTTTATCGGGCTTTGTGCCTAGCA
*
41751326 TGCTATGTGCCTG-TGTTTATCGGGCTTTGTGCCTAGCA
1 GGCTATGTG-CTGATGTTTATCGGGCTTTGTGCCTAGCA
* * *
41751364 AGCTATATGC-CAGTGTTTATCGGG
1 GGCTATGTGCTGA-TGTTTATCGGG
41751388 TTTCATGCCA
Statistics
Matches: 175, Mismatches: 34, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
37 1 0.01
38 168 0.96
39 6 0.03
ACGTcount: A:0.16, C:0.19, G:0.29, T:0.37
Consensus pattern (38 bp):
GGCTATGTGCTGATGTTTATCGGGCTTTGTGCCTAGCA
Found at i:41751269 original size:76 final size:76
Alignment explanation
Indices: 41751136--41751390 Score: 307
Period size: 76 Copynumber: 3.4 Consensus size: 76
41751126 TGATTTATCG
* * * *
41751136 GGCTATGTG-CAAGTGTTTATCGGGTTTAGTGCCTAGCAGGCTTTATGCTGATGTTTATCGAGCT
1 GGCTATGTGCCAA-TGTTTATCGGGTTTAGTGCCTAGCAAGCTTTGTGCCGATGTTTATCGGGCT
41751200 TTGTGCCTAGCA
65 TTGTGCCTAGCA
* * * * *
41751212 GGCTATGTGCTAATGTTTATCGGGCTTAGTGCCCAACAAGCTTTGTGCCGATATTTATCGGGCTT
1 GGCTATGTGCCAATGTTTATCGGGTTTAGTGCCTAGCAAGCTTTGTGCCGATGTTTATCGGGCTT
*
41751277 TGTGCCTAGTA
66 TGTGCCTAGCA
* ** * * *
41751288 GGCTATGTACCGGTGTTTATCGGGTTTTGTGCCTAGCATGCTATGTGCCTG-TGTTTATCGGGCT
1 GGCTATGTGCCAATGTTTATCGGGTTTAGTGCCTAGCAAGCTTTGTGCC-GATGTTTATCGGGCT
41751352 TTGTGCCTAGCA
65 TTGTGCCTAGCA
* * *
41751364 AGCTATATGCCAGTGTTTATCGGGTTT
1 GGCTATGTGCCAATGTTTATCGGGTTT
41751391 CATGCCAAAT
Statistics
Matches: 151, Mismatches: 26, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
76 148 0.98
77 3 0.02
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.37
Consensus pattern (76 bp):
GGCTATGTGCCAATGTTTATCGGGTTTAGTGCCTAGCAAGCTTTGTGCCGATGTTTATCGGGCTT
TGTGCCTAGCA
Found at i:41751343 original size:114 final size:114
Alignment explanation
Indices: 41751151--41751390 Score: 288
Period size: 114 Copynumber: 2.1 Consensus size: 114
41751141 TGTGCAAGTG
* * *
41751151 TTTATCGGGTTTAGTGCCTAGCAGGCTTTATGCTGATGTTTATCGAGCTTTGTGCCTAGCAGGCT
1 TTTATCGGGTTTAGTGCCTAGCAGGCTATATACCGATGTTTATCGAGCTTTGTGCCTAGCAGGCT
41751216 ATGTGCTAATGTTTATCGGGCTTAGTGCCCAACAAGCTTTGTGCCGATA
66 ATGTGCTAATGTTTATCGGGCTTAGTGCCCAACAAGCTTTGTGCCGATA
* * * * * *
41751265 TTTATCGGGCTTT-GTGCCTAGTAGGCTATGTACCGGTGTTTATCGGGTTTTGTGCCTAGCATGC
1 TTTATCGGG-TTTAGTGCCTAGCAGGCTATATACCGATGTTTATCGAGCTTTGTGCCTAGCAGGC
* * * * * * *
41751329 TATGTGCCT-GTGTTTATCGGGCTTTGTGCCTAGCAAGCTATATGCC-AGTG
65 TATGTG-CTAATGTTTATCGGGCTTAGTGCCCAACAAGCTTTGTGCCGA-TA
41751379 TTTATCGGGTTT
1 TTTATCGGGTTT
41751391 CATGCCAAAT
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
113 4 0.04
114 98 0.92
115 5 0.05
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.38
Consensus pattern (114 bp):
TTTATCGGGTTTAGTGCCTAGCAGGCTATATACCGATGTTTATCGAGCTTTGTGCCTAGCAGGCT
ATGTGCTAATGTTTATCGGGCTTAGTGCCCAACAAGCTTTGTGCCGATA
Found at i:41751408 original size:114 final size:114
Alignment explanation
Indices: 41751187--41751428 Score: 276
Period size: 114 Copynumber: 2.1 Consensus size: 114
41751177 TTTATGCTGA
41751187 TGTTTATCGAGCTTTGTGCCTAGCAGGCTATGTGCTAATGTTTATCGGGCTTAGTGCCCAACAAG
1 TGTTTATCGAGCTTTGTGCCTAGCAGGCTATGTGCTAATGTTTATCGGGCTTAGTGCCCAACAAG
* * * * * *
41751252 CTTTGTGCCGATATTTATCGGGCTTTGTGCCTAGTAGGCTATGT-ACCGG
66 CTATATGCCGATATTTATCGGGCTTTATGCCAAATAGACTATGTGA-CGG
* * * * * * *
41751301 TGTTTATCGGGTTTTGTGCCTAGCATGCTATGTGCCT-GTGTTTATCGGGCTTTGTGCCTAGCAA
1 TGTTTATCGAGCTTTGTGCCTAGCAGGCTATGTG-CTAATGTTTATCGGGCTTAGTGCCCAACAA
* *
41751365 GCTATATGCC-AGTGTTTATCGGG-TTTCATGCCAAATAGACTATGTGATGG
65 GCTATATGCCGA-TATTTATCGGGCTTT-ATGCCAAATAGACTATGTGACGG
*
41751415 TGTTTATCAAGCTT
1 TGTTTATCGAGCTT
41751429 AGTTCCTAAT
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
113 4 0.04
114 99 0.93
115 3 0.03
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (114 bp):
TGTTTATCGAGCTTTGTGCCTAGCAGGCTATGTGCTAATGTTTATCGGGCTTAGTGCCCAACAAG
CTATATGCCGATATTTATCGGGCTTTATGCCAAATAGACTATGTGACGG
Found at i:41751418 original size:76 final size:74
Alignment explanation
Indices: 41751136--41751422 Score: 247
Period size: 76 Copynumber: 3.8 Consensus size: 74
41751126 TGATTTATCG
* * ** * * * *
41751136 GGCTATGTGCAAGTGTTTATCGGGTTTAGTGCCTAGCAGGCTTTATGCTGATGTTTATCGAGCTT
1 GGCTATGTGCCAGTGTTTATCGGGTTTA-TGCCAAATA-GCTATGTGCTGGTGTTTATCGGGCTT
41751201 TGTGCCTAGCA
64 TGTGCCTAGCA
* * * * * * *
41751212 GGCTATGTGCTAATGTTTATCGGGCTTAGTGCCCAACA-AGCTTTGTGCCGATATTTATCGGGCT
1 GGCTATGTGCCAGTGTTTATCGGGTTTA-TG-CCAA-ATAGCTATGTGCTGGTGTTTATCGGGCT
*
41751276 TTGTGCCTAGTA
63 TTGTGCCTAGCA
* * * *
41751288 GGCTATGTACCGGTGTTTATCGGGTTTTGTGCCTAGCAT-GCTATGTGCCT-GTGTTTATCGGGC
1 GGCTATGTGCCAGTGTTTATCGGG-TTTATGCC-A-AATAGCTATGTG-CTGGTGTTTATCGGGC
41751351 TTTGTGCCTAGCA
62 TTTGTGCCTAGCA
* * *
41751364 AGCTATATGCCAGTGTTTATCGGGTTTCATGCCAAATAGACTATGTGATGGTGTTTATC
1 GGCTATGTGCCAGTGTTTATCGGGTTT-ATGCCAAATAG-CTATGTGCTGGTGTTTATC
41751423 AAGCTTAGTT
Statistics
Matches: 171, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
74 2 0.01
75 8 0.05
76 154 0.90
77 7 0.04
ACGTcount: A:0.17, C:0.18, G:0.28, T:0.37
Consensus pattern (74 bp):
GGCTATGTGCCAGTGTTTATCGGGTTTATGCCAAATAGCTATGTGCTGGTGTTTATCGGGCTTTG
TGCCTAGCA
Found at i:41752031 original size:19 final size:20
Alignment explanation
Indices: 41751985--41752032 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
41751975 TTCTTTTTCC
*
41751985 TCATATTACTATAGTGTTCAT
1 TCATATTACTATA-TATTCAT
* *
41752006 ACTTATTACTAT-TATTCAT
1 TCATATTACTATATATTCAT
41752025 TCATATTA
1 TCATATTA
41752033 TAAGTCATAC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 12 0.55
21 10 0.45
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (20 bp):
TCATATTACTATATATTCAT
Found at i:41753332 original size:36 final size:36
Alignment explanation
Indices: 41753271--41753353 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
41753261 CACAATATAA
* *
41753271 TCACTGCCACATGGCATGAAAAACATATCCACATAT
1 TCACTGTCACATGGCATGAAAAACATACCCACATAT
* *
41753307 TTACTGTCACATGGCAT-AAATAACATACCCTCATAT
1 TCACTGTCACATGGCATGAAA-AACATACCCACATAT
*
41753343 TCACTTTCACA
1 TCACTGTCACA
41753354 ACAATCATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 3 0.08
36 37 0.93
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (36 bp):
TCACTGTCACATGGCATGAAAAACATACCCACATAT
Found at i:41759505 original size:12 final size:12
Alignment explanation
Indices: 41759485--41759518 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41759475 TAAATAAGTT
* *
41759485 ATAACAATATGC
1 ATAATAATATAC
41759497 ATAATAATATAC
1 ATAATAATATAC
41759509 ATAATAATAT
1 ATAATAATAT
41759519 TTGTATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (12 bp):
ATAATAATATAC
Found at i:41759639 original size:17 final size:16
Alignment explanation
Indices: 41759596--41759640 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
41759586 TATAGTTTAT
* *
41759596 TTTTTTAATTTGATCA
1 TTTTTTAATTTTATTA
41759612 -TTTTTAATTTTATTA
1 TTTTTTAATTTTATTA
41759627 TTTTTTAAATTTTA
1 TTTTTT-AATTTTA
41759641 AATTCTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTTTAATTTTATTA
Found at i:41759650 original size:31 final size:32
Alignment explanation
Indices: 41759592--41759654 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
41759582 AAATTATAGT
* * *
41759592 TTATTTTTTTAATTTGATCATTTTTAATTTTA
1 TTATTTTTTAAATTTGATAATTCTTAATTTTA
*
41759624 TTATTTTTTAAATTTTA-AATTCTTAATTTTA
1 TTATTTTTTAAATTTGATAATTCTTAATTTTA
41759655 ATCAAATGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (32 bp):
TTATTTTTTAAATTTGATAATTCTTAATTTTA
Found at i:41765067 original size:2 final size:2
Alignment explanation
Indices: 41765060--41765084 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41765050 TGTCTCTTTT
41765060 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
41765085 TAGACTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:41769802 original size:92 final size:92
Alignment explanation
Indices: 41769645--41769829 Score: 361
Period size: 92 Copynumber: 2.0 Consensus size: 92
41769635 AATCATTATA
41769645 GACATACACTGAAACTAGTAAAACTCGTAGCACAGAGGATAAAAAGAAAACCGATAAAAGCTTAC
1 GACATACACTGAAACTAGTAAAACTCGTAGCACAGAGGATAAAAAGAAAACCGATAAAAGCTTAC
*
41769710 CAATACTGTCCAGGTTGAATTGGTCCG
66 CAATACTGTCCAGGTTGAATTGGCCCG
41769737 GACATACACTGAAACTAGTAAAACTCGTAGCACAGAGGATAAAAAGAAAACCGATAAAAGCTTAC
1 GACATACACTGAAACTAGTAAAACTCGTAGCACAGAGGATAAAAAGAAAACCGATAAAAGCTTAC
41769802 CAATACTGTCCAGGTTGAATTGGCCCG
66 CAATACTGTCCAGGTTGAATTGGCCCG
41769829 G
1 G
41769830 CCATCTTTTC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (92 bp):
GACATACACTGAAACTAGTAAAACTCGTAGCACAGAGGATAAAAAGAAAACCGATAAAAGCTTAC
CAATACTGTCCAGGTTGAATTGGCCCG
Found at i:41778437 original size:17 final size:18
Alignment explanation
Indices: 41778406--41778439 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
41778396 AAAAACATTA
41778406 AAACAAATATTAAAATAT
1 AAACAAATATTAAAATAT
41778424 AAACAAAT-TTAAAATA
1 AAACAAATATTAAAATA
41778440 CATTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AAACAAATATTAAAATAT
Found at i:41778599 original size:21 final size:21
Alignment explanation
Indices: 41778575--41778619 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
41778565 AATAACATCC
* *
41778575 AAACAACCAAAACAACAGCAA
1 AAACAACAAAAACAACAACAA
*
41778596 AAACCACAAAAACAACAACAA
1 AAACAACAAAAACAACAACAA
41778617 AAA
1 AAA
41778620 TAGCAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.71, C:0.27, G:0.02, T:0.00
Consensus pattern (21 bp):
AAACAACAAAAACAACAACAA
Found at i:41778671 original size:18 final size:19
Alignment explanation
Indices: 41778633--41778673 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
41778623 CAATAAAAAT
*
41778633 AACAGTAAAACAACACTAA
1 AACAGTAAAACAACACCAA
41778652 AACAGTAAAA-AACACCAA
1 AACAGTAAAACAACACCAA
41778670 AACA
1 AACA
41778674 ACAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.66, C:0.22, G:0.05, T:0.07
Consensus pattern (19 bp):
AACAGTAAAACAACACCAA
Found at i:41778676 original size:21 final size:21
Alignment explanation
Indices: 41778575--41778683 Score: 62
Period size: 21 Copynumber: 5.1 Consensus size: 21
41778565 AATAACATCC
*
41778575 AAACAACCAAAACAACAGCAAA
1 AAAC-ACCAAAACAACAGTAAA
* * **
41778597 AACCACAAAAACAACAACAAA
1 AAACACCAAAACAACAGTAAA
** *
41778618 AATAGCAATAAAAATAACAGTAAA
1 AA-A-C-ACCAAAACAACAGTAAA
*
41778642 ACAACA-C-TAA-AACAGTAAA
1 A-AACACCAAAACAACAGTAAA
*
41778661 AAACACCAAAACAACAATAAA
1 AAACACCAAAACAACAGTAAA
41778682 AA
1 AA
41778684 TAGTAAAAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
18 4 0.06
19 11 0.16
20 4 0.06
21 27 0.40
22 4 0.06
23 2 0.03
24 15 0.22
25 1 0.01
ACGTcount: A:0.69, C:0.21, G:0.04, T:0.06
Consensus pattern (21 bp):
AAACACCAAAACAACAGTAAA
Found at i:41778692 original size:21 final size:21
Alignment explanation
Indices: 41778668--41778757 Score: 58
Period size: 21 Copynumber: 4.2 Consensus size: 21
41778658 AAAAAACACC
*
41778668 AAAACAACAATAAAAATAGTA
1 AAAACAACAACAAAAATAGTA
* * * *
41778689 AAAATAAGTATC-AAAACAGTA
1 AAAACAA-CAACAAAAATAGTA
*
41778710 AAAA-AACAACACAAAAATAGCAA
1 AAAACAAC-A-ACAAAAATAG-TA
* *
41778733 AAAACAGCAACCAAAATAGTA
1 AAAACAACAACAAAAATAGTA
41778754 AAAA
1 AAAA
41778758 AATAGCACTA
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
20 3 0.06
21 24 0.47
22 16 0.31
23 6 0.12
24 2 0.04
ACGTcount: A:0.69, C:0.13, G:0.07, T:0.11
Consensus pattern (21 bp):
AAAACAACAACAAAAATAGTA
Found at i:41778770 original size:22 final size:22
Alignment explanation
Indices: 41778680--41778772 Score: 75
Period size: 22 Copynumber: 4.3 Consensus size: 22
41778670 AACAACAATA
* *
41778680 AAAATAGTAAAAATA-AGTA-T
1 AAAATAGTAAAAAAACAGCACT
* * *
41778700 CAAAACAGTAAAAAAACAACACA
1 -AAAATAGTAAAAAAACAGCACT
* *
41778723 AAAATAG-CAAAAAACAGCAACC
1 AAAATAGTAAAAAAACAGC-ACT
*
41778745 AAAATAGTAAAAAAATAGCACT
1 AAAATAGTAAAAAAACAGCACT
41778767 AAAATA
1 AAAATA
41778773 ACAATATAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
21 22 0.39
22 25 0.45
23 9 0.16
ACGTcount: A:0.67, C:0.13, G:0.08, T:0.13
Consensus pattern (22 bp):
AAAATAGTAAAAAAACAGCACT
Found at i:41782644 original size:21 final size:21
Alignment explanation
Indices: 41782620--41782666 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41782610 TTAACACTAA
*
41782620 TTATACAAAACATTACAGAAT
1 TTATACAAAACATTACAAAAT
* * *
41782641 TTATGCAAATCATTATAAAAT
1 TTATACAAAACATTACAAAAT
41782662 TTATA
1 TTATA
41782667 ATACTTTATG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (21 bp):
TTATACAAAACATTACAAAAT
Found at i:41784104 original size:29 final size:29
Alignment explanation
Indices: 41783983--41784169 Score: 151
Period size: 30 Copynumber: 6.3 Consensus size: 29
41783973 AAATAAAACC
* * ** *
41783983 GGGTCAAACTTGAATTTTTGGAAGCTTCAG
1 GGGTCAAATTTGAATTTTTGAAAAATT-TG
*** * *
41784013 GGGTCAAATAAAAAGTTTTGGAAAATTTG
1 GGGTCAAATTTGAATTTTTGAAAAATTTG
* *
41784042 GGGATCAAATTCGAATTTTTGGAAAATTTAG
1 GGG-TCAAATTTGAATTTTTGAAAAATTT-G
*
41784073 GGGTCAAATTTGATTTTTTGAAAAATTTGG
1 GGGTCAAATTTGAATTTTTGAAAAATTT-G
* *
41784103 GGGTCAAATTTGAATTTTTTAAAAAATTG
1 GGGTCAAATTTGAATTTTTGAAAAATTTG
* *
41784132 GGGTTAACTTTGAATTTTT-AGAAAATTTG
1 GGGTCAAATTTGAATTTTTGA-AAAATTTG
*
41784161 AAGGTCAAA
1 -GGGTCAAA
41784170 ACATATTTTT
Statistics
Matches: 128, Mismatches: 25, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
28 1 0.01
29 29 0.23
30 94 0.73
31 4 0.03
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGAAAAATTTG
Found at i:41785095 original size:12 final size:13
Alignment explanation
Indices: 41785071--41785104 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
41785061 TTATTTATTT
41785071 ATAAAATAATAATAA
1 ATAAAATAAT-A-AA
41785086 ATAAAATAATAAA
1 ATAAAATAATAAA
41785099 ATAAAA
1 ATAAAA
41785105 ACAAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 1 0.05
15 10 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAAAATAATAAA
Found at i:41786020 original size:18 final size:19
Alignment explanation
Indices: 41785990--41786028 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
41785980 ATTAATCATA
41785990 TTTATTATTTATATTTTGT
1 TTTATTATTTATATTTTGT
41786009 TTTATT-TTTATATTTTGT
1 TTTATTATTTATATTTTGT
41786027 TT
1 TT
41786029 AAAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTATTATTTATATTTTGT
Found at i:41796654 original size:29 final size:29
Alignment explanation
Indices: 41796617--41796682 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
41796607 TTAAAATTGC
* * *
41796617 TCATTCAACTTTGATTTTTTTTTAAAT-GG
1 TCATCCAACTATGA-TTTTTTTTAAATCGA
41796646 TCATCCAACTATGATTTTTTTTAAATCGA
1 TCATCCAACTATGATTTTTTTTAAATCGA
41796675 TCATCCAA
1 TCATCCAA
41796683 TTAATTGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.47
Consensus pattern (29 bp):
TCATCCAACTATGATTTTTTTTAAATCGA
Found at i:41797750 original size:6 final size:6
Alignment explanation
Indices: 41797741--41797796 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
41797731 GGAGGTTTTT
** *
41797741 TTAATA TTAATA -TAATTA TTTTTA TTTAATA GTAATA TTAATA TTAATA
1 TTAATA TTAATA TTAA-TA TTAATA -TTAATA TTAATA TTAATA TTAATA
*
41797790 TCAATA T
1 TTAATA T
41797797 GAAATTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
5 3 0.08
6 32 0.80
7 5 0.12
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:41798077 original size:30 final size:29
Alignment explanation
Indices: 41798025--41798118 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 29
41798015 ACCAATTTAA
*
41798025 AAAAAATTCATAGTTGGATGACTAAAAAAG
1 AAAAAA-TCATAGTTGGGTGACTAAAAAAG
*
41798055 AAATAAATCATTGTTGGGTGACTAATATAAA-
1 AAA-AAATCATAGTTGGGTGACTAA-A-AAAG
** *
41798086 AAAAGTTCATAGTTGAGTGACTAAAAAAG
1 AAAAAATCATAGTTGGGTGACTAAAAAAG
41798115 AAAA
1 AAAA
41798119 TGACTCATAG
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
28 3 0.06
29 5 0.09
30 36 0.67
31 7 0.13
32 3 0.06
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (29 bp):
AAAAAATCATAGTTGGGTGACTAAAAAAG
Found at i:41798130 original size:31 final size:31
Alignment explanation
Indices: 41798032--41798137 Score: 96
Period size: 30 Copynumber: 3.5 Consensus size: 31
41798022 TAAAAAAAAT
*
41798032 TCATAGTTG-GATGACTAAAAAAG-AAATAAA
1 TCATAGTTGAG-TGACTAAAAAAGAAAATGAA
* * *
41798062 TCATTGTTGGGTGACTAATATAAA-AAAA-G-T
1 TCATAGTTGAGTGACTAA-A-AAAGAAAATGAA
*
41798092 TCATAGTTGAGTGACTAAAAAAGAAAATGAC
1 TCATAGTTGAGTGACTAAAAAAGAAAATGAA
*
41798123 TCATAGTTTAGTGAC
1 TCATAGTTGAGTGAC
41798138 CTTAAGGGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
28 3 0.05
29 5 0.08
30 32 0.52
31 16 0.26
32 6 0.10
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.28
Consensus pattern (31 bp):
TCATAGTTGAGTGACTAAAAAAGAAAATGAA
Found at i:41798527 original size:22 final size:22
Alignment explanation
Indices: 41798479--41798527 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
41798469 ATATCCAAAC
* *
41798479 AATAATAATAAAATAATATCAA
1 AATAATAATAAAATAACAACAA
* *
41798501 TATAATAATAAAATGACAACAA
1 AATAATAATAAAATAACAACAA
41798523 AATAA
1 AATAA
41798528 CAGCAAAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.24
Consensus pattern (22 bp):
AATAATAATAAAATAACAACAA
Found at i:41805016 original size:31 final size:30
Alignment explanation
Indices: 41804942--41805016 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
41804932 CTTTAAAATT
* *
41804942 TTTTTTAACAATTCAATGATTTAAATAAAA
1 TTTTTTAATAATTCAATGACTTAAATAAAA
* * *
41804972 ATTTTCAATTAATTCAATGACTTAAATGAGAA
1 TTTTTTAA-TAATTCAATGACTTAAAT-AAAA
41805004 TTTTTTAATAATT
1 TTTTTTAATAATT
41805017 TAATTACTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 6 0.17
31 21 0.58
32 9 0.25
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (30 bp):
TTTTTTAATAATTCAATGACTTAAATAAAA
Found at i:41805541 original size:3 final size:3
Alignment explanation
Indices: 41805533--41805558 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41805523 CGGTAACTCT
41805533 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
41805559 AACAATCTCT
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:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:41806662 original size:16 final size:18
Alignment explanation
Indices: 41806623--41806656 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41806613 TAAGTTTATA
41806623 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
41806640 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
41806657 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:41808347 original size:2 final size:2
Alignment explanation
Indices: 41808340--41808399 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
41808330 AGATTTACAA
41808340 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
41808382 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
41808400 TACCGTTTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41813681 original size:22 final size:22
Alignment explanation
Indices: 41813656--41813705 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
41813646 ATAATATTAT
* * *
41813656 TAAAATACCACTTTGGTTAACA
1 TAAAATAACAATTTAGTTAACA
* *
41813678 TAAATTAACAATTTATTTAACA
1 TAAAATAACAATTTAGTTAACA
41813700 TAAAAT
1 TAAAAT
41813706 TTGGTTAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (22 bp):
TAAAATAACAATTTAGTTAACA
Found at i:41822471 original size:29 final size:28
Alignment explanation
Indices: 41822431--41822648 Score: 153
Period size: 29 Copynumber: 7.5 Consensus size: 28
41822421 ACCCGAGGGC
41822431 AAAATGGTAATTTTGGTGAAATCGGGGTT
1 AAAATGG-AATTTTGGTGAAATCGGGGTT
* * ***
41822460 AAAAAAGGAATTTTGGAGGGTTCGAGGG-T
1 -AAAATGGAATTTTGGTGAAATCG-GGGTT
* *
41822489 AAAATGGTAATTTTAGTGAAATTGGGGTT
1 AAAATGG-AATTTTGGTGAAATCGGGGTT
*
41822518 AAAAATGGAATTTT-G-GAAAGTTTAGGGG-T
1 -AAAATGGAATTTTGGTGAAA---TCGGGGTT
*
41822547 AAAATGGTAATTTTTGGTGAAATTGGGGTT
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTT
*
41822577 AAAATGGAATTTT-G-GAAAGTTTGAGGG-T
1 AAAATGGAATTTTGGTGAAA--TCG-GGGTT
41822605 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTT
41822635 AAAAATGGAATTTT
1 -AAAATGGAATTTT
41822649 AGAAAGTTTA
Statistics
Matches: 152, Mismatches: 15, Indels: 43
0.72 0.07 0.20
Matches are distributed among these distances:
26 4 0.03
27 5 0.03
28 32 0.21
29 52 0.34
30 42 0.28
31 9 0.06
32 8 0.05
ACGTcount: A:0.34, C:0.01, G:0.30, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATCGGGGTT
Found at i:41822486 original size:58 final size:59
Alignment explanation
Indices: 41822389--41822680 Score: 362
Period size: 58 Copynumber: 5.0 Consensus size: 59
41822379 GAAGAAACGA
** * * ** *
41822389 TGAAATCGGGGTTGAAAACGGGACTTTTGGATA-CCCGAGGGCAAAATGGTAA-TTTTGG
1 TGAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
* ** *
41822447 TGAAATCGGGGTTAAAAAAGGAATTTTGGAGGGTTCGAGGGTAAAATGGTAA-TTTTAG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
* *
41822505 TGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTT-TAGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGG
* *
41822564 TGAAATTGGGGTT-AAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
* *
41822622 TGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT-TAGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGG
41822681 ACTGCTTGGG
Statistics
Matches: 209, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
57 15 0.07
58 134 0.64
59 60 0.29
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.32
Consensus pattern (59 bp):
TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
Found at i:41822644 original size:117 final size:117
Alignment explanation
Indices: 41822431--41822680 Score: 405
Period size: 117 Copynumber: 2.1 Consensus size: 117
41822421 ACCCGAGGGC
**
41822431 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGGAGGGTTCGAGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGGAAAGTTCGAGGGTAAAATG
* *
41822495 GTAATTTTAGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
66 GTAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
* * *
41822547 AAAATGGTAATTTTTGGTGAAATTGGGGTT-AAAATGGAATTTTGGAAAGTTTGAGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGGAAAGTTCGAGGGTAAAATG
*
41822611 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
66 GTAA-TTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
41822664 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
41822681 ACTGCTTGGG
Statistics
Matches: 124, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
116 44 0.35
117 80 0.65
ACGTcount: A:0.34, C:0.01, G:0.30, T:0.34
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGGAAAGTTCGAGGGTAAAATG
GTAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
Found at i:41822669 original size:59 final size:60
Alignment explanation
Indices: 41822425--41822680 Score: 382
Period size: 58 Copynumber: 4.4 Consensus size: 60
41822415 TTGGATACCC
* * * * *
41822425 GAGGGCAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGG-AGGGTTC
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
41822483 GAGGGTAAAATGGTAA-TTTTAGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
41822542 G-GGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT-AAAATGGAATTTTGGAAAGTTT-
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
41822599 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTA
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
41822659 G-GGGTAAAATGGTAATTTTTGG
1 GAGGGTAAAATGGTAATTTTTGG
41822681 ACTGCTTGGG
Statistics
Matches: 183, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
57 1 0.01
58 116 0.63
59 65 0.36
60 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (60 bp):
GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:41822691 original size:29 final size:28
Alignment explanation
Indices: 41822485--41822691 Score: 106
Period size: 30 Copynumber: 7.1 Consensus size: 28
41822475 GAGGGTTCGA
* *
41822485 GGGTAAAATGGTAATTTTAGTGA-AATTG
1 GGGTAAAATGGTAATTTTTG-GATGATTG
* *
41822513 GGGTTAAAAATGG-AA-TTTTGGAAAGTTTAG
1 GGG-T-AAAATGGTAATTTTTGG-ATGATT-G
41822543 GGGTAAAATGGTAATTTTTGG-TGAAATTG
1 GGGTAAAATGGTAATTTTTGGATG--ATTG
* *
41822572 GGGTTAAAATGG-AA-TTTTGGAAAGTTTG
1 GGG-TAAAATGGTAATTTTTGG-ATGATTG
*
41822600 AGGGTAAAATGGTAATTTTTGG-TGAAATCG
1 -GGGTAAAATGGTAATTTTTGGATG--ATTG
* * * *
41822630 GGGTTAAAAATGG-AATTTTAGAAAGTTTAG
1 GGG-T-AAAATGGTAATTTTTGGATGATT-G
*
41822660 GGGTAAAATGGTAATTTTTGGACTGCTTG
1 GGGTAAAATGGTAATTTTTGGA-TGATTG
41822689 GGG
1 GGG
41822692 ACCTATAAAC
Statistics
Matches: 137, Mismatches: 19, Indels: 45
0.68 0.09 0.22
Matches are distributed among these distances:
27 1 0.01
28 41 0.30
29 36 0.26
30 51 0.37
31 8 0.06
ACGTcount: A:0.33, C:0.01, G:0.31, T:0.35
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTGGATGATTG
Found at i:41823650 original size:22 final size:22
Alignment explanation
Indices: 41823602--41823651 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
41823592 CGACGTACGA
* * * *
41823602 GCGAAACTCCGGCGGTGGTGGT
1 GCGAGACTCCGACGATGGCGGT
41823624 GCGAGACTCCGACGATGGCGGT
1 GCGAGACTCCGACGATGGCGGT
41823646 GCGAGA
1 GCGAGA
41823652 TAGGGAAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.44, T:0.14
Consensus pattern (22 bp):
GCGAGACTCCGACGATGGCGGT
Found at i:41823707 original size:3 final size:3
Alignment explanation
Indices: 41823701--41823784 Score: 51
Period size: 3 Copynumber: 26.7 Consensus size: 3
41823691 TAATGGTTGA
* * * * *
41823701 TAT TAT TAAT TAT TAA TAT TAAT TAT AAT TAT AAA TATT TAT TAC TAT
1 TAT TAT T-AT TAT TAT TAT T-AT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * *
41823749 TAT TAAT TAT TAT GAT TAT TAA TAA TAT TTT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
41823785 ATGATATTTA
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
3 50 0.82
4 11 0.18
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:41823729 original size:6 final size:7
Alignment explanation
Indices: 41823702--41823771 Score: 67
Period size: 7 Copynumber: 10.3 Consensus size: 7
41823692 AATGGTTGAT
41823702 ATTATTA
1 ATTATTA
41823709 ATTATTA
1 ATTATTA
41823716 A-TATTA
1 ATTATTA
41823722 ATTA-TA
1 ATTATTA
41823728 ATTA-TA
1 ATTATTA
* *
41823734 AATATTT
1 ATTATTA
*
41823741 ATTACT-
1 ATTATTA
41823747 ATTATTA
1 ATTATTA
41823754 ATTATTA
1 ATTATTA
41823761 TGATTATTA
1 --ATTATTA
41823770 AT
1 AT
41823772 AATATTTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
6 22 0.42
7 24 0.45
9 7 0.13
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (7 bp):
ATTATTA
Found at i:41823731 original size:19 final size:19
Alignment explanation
Indices: 41823701--41823777 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
41823691 TAATGGTTGA
*
41823701 TATTATTAATTATTAATAT
1 TATTACTAATTATTAATAT
*
41823720 TAATTA-TAATTATAAATATT
1 T-ATTACTAATTATTAATA-T
41823740 TATTACT-ATTATT-A-AT
1 TATTACTAATTATTAATAT
* *
41823756 TATTA-TGATTATTAATAA
1 TATTACTAATTATTAATAT
41823774 TATT
1 TATT
41823778 TTTATTAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
15 1 0.02
16 12 0.24
17 2 0.04
18 6 0.12
19 21 0.43
20 7 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (19 bp):
TATTACTAATTATTAATAT
Found at i:41823784 original size:15 final size:15
Alignment explanation
Indices: 41823764--41823793 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41823754 ATTATTATGA
41823764 TTATTAATAATATTT
1 TTATTAATAATATTT
*
41823779 TTATTAATGATATTT
1 TTATTAATAATATTT
41823794 ATGAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTATTAATAATATTT
Found at i:41824463 original size:13 final size:12
Alignment explanation
Indices: 41824443--41824482 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
41824433 CCAATATGGG
41824443 TTTAATTGGACT
1 TTTAATTGGACT
41824455 TTGTAATTGGACAT
1 TT-TAATTGGAC-T
*
41824469 TTCAATTGGACT
1 TTTAATTGGACT
41824481 TT
1 TT
41824483 CTATTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 5 0.20
13 17 0.68
14 3 0.12
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.47
Consensus pattern (12 bp):
TTTAATTGGACT
Found at i:41824527 original size:16 final size:17
Alignment explanation
Indices: 41824506--41824544 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
41824496 TTAATATCCT
41824506 TTTAAATTT-AAATAAA
1 TTTAAATTTAAAATAAA
*
41824522 TTTAAATTTAAAATTAA
1 TTTAAATTTAAAATAAA
41824539 TTTAAA
1 TTTAAA
41824545 ATCAAAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:41826145 original size:18 final size:19
Alignment explanation
Indices: 41826118--41826153 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41826108 TTTTAAATAC
41826118 ATTTATAATATATAATATG
1 ATTTATAATATATAATATG
*
41826137 ATTTA-AATATATTATAT
1 ATTTATAATATATAATAT
41826154 TATATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
ATTTATAATATATAATATG
Found at i:41826321 original size:4 final size:4
Alignment explanation
Indices: 41826312--41826355 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
41826302 GGGGGCCTGG
*
41826312 CATA CATA CATA CATA TATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
41826356 TGTATAGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:41830244 original size:29 final size:28
Alignment explanation
Indices: 41830204--41830421 Score: 162
Period size: 29 Copynumber: 7.5 Consensus size: 28
41830194 ACCCGAGGGC
41830204 AAAATGGTAATTTTGGTGAAATCGGGGTT
1 AAAATGG-AATTTTGGTGAAATCGGGGTT
* * ***
41830233 AAAAAAGGAATTTTGGAGGGTTCGAGGG-T
1 -AAAATGGAATTTTGGTGAAATCG-GGGTT
*
41830262 AAAATGGTAATTTTAGTGAAATCGGGGTT
1 AAAATGG-AATTTTGGTGAAATCGGGGTT
*
41830291 AAAAATGGAATTTT-G-GAAAGTTTAGGGG-T
1 -AAAATGGAATTTTGGTGAAA---TCGGGGTT
*
41830320 AAAATGGTAATTTTTGGTGAAATTGGGGTT
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTT
*
41830350 AAAATGGAATTTT-G-GAAAGTTTGAGGG-T
1 AAAATGGAATTTTGGTGAAA--TCG-GGGTT
41830378 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTT
41830408 AAAAATGGAATTTT
1 -AAAATGGAATTTT
41830422 AGAAAGTTTA
Statistics
Matches: 153, Mismatches: 14, Indels: 43
0.73 0.07 0.20
Matches are distributed among these distances:
26 4 0.03
27 5 0.03
28 32 0.21
29 53 0.35
30 42 0.27
31 9 0.06
32 8 0.05
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATCGGGGTT
Found at i:41830259 original size:58 final size:59
Alignment explanation
Indices: 41830162--41830453 Score: 371
Period size: 58 Copynumber: 5.0 Consensus size: 59
41830152 GAAGAAACGA
** * * ** *
41830162 TGAAATCGGGGTTGAAAACGGGACTTTTGGATA-CCCGAGGGCAAAATGGTAA-TTTTGG
1 TGAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
* ** *
41830220 TGAAATCGGGGTTAAAAAAGGAATTTTGGAGGGTTCGAGGGTAAAATGGTAA-TTTTAG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
*
41830278 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT-TAGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGG
* *
41830337 TGAAATTGGGGTT-AAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
* *
41830395 TGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT-TAGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGG
41830454 ACTGCTTGGG
Statistics
Matches: 209, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
57 15 0.07
58 135 0.65
59 59 0.28
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (59 bp):
TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
Found at i:41830416 original size:117 final size:117
Alignment explanation
Indices: 41830204--41830453 Score: 414
Period size: 117 Copynumber: 2.1 Consensus size: 117
41830194 ACCCGAGGGC
**
41830204 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGGAGGGTTCGAGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGGAAAGTTCGAGGGTAAAATG
*
41830268 GTAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
66 GTAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
* * *
41830320 AAAATGGTAATTTTTGGTGAAATTGGGGTT-AAAATGGAATTTTGGAAAGTTTGAGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGGAAAGTTCGAGGGTAAAATG
*
41830384 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
66 GTAA-TTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
41830437 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
41830454 ACTGCTTGGG
Statistics
Matches: 125, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
116 44 0.35
117 81 0.65
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGGAAAGTTCGAGGGTAAAATG
GTAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
Found at i:41830442 original size:59 final size:60
Alignment explanation
Indices: 41830198--41830453 Score: 391
Period size: 58 Copynumber: 4.4 Consensus size: 60
41830188 TTGGATACCC
* * * * *
41830198 GAGGGCAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAAAGGAATTTTGG-AGGGTTC
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
41830256 GAGGGTAAAATGGTAA-TTTTAGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
41830315 G-GGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT-AAAATGGAATTTTGGAAAGTTT-
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
41830372 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTA
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
41830432 G-GGGTAAAATGGTAATTTTTGG
1 GAGGGTAAAATGGTAATTTTTGG
41830454 ACTGCTTGGG
Statistics
Matches: 183, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
57 1 0.01
58 117 0.64
59 64 0.35
60 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (60 bp):
GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:41830464 original size:29 final size:28
Alignment explanation
Indices: 41830258--41830464 Score: 97
Period size: 30 Copynumber: 7.1 Consensus size: 28
41830248 GAGGGTTCGA
* * *
41830258 GGGTAAAATGGTAATTTTAGTGA-AATCG
1 GGGTAAAATGGTAATTTTTG-GATGATTG
* *
41830286 GGGTTAAAAATGG-AA-TTTTGGAAAGTTTAG
1 GGG-T-AAAATGGTAATTTTTGG-ATGATT-G
41830316 GGGTAAAATGGTAATTTTTGG-TGAAATTG
1 GGGTAAAATGGTAATTTTTGGATG--ATTG
* *
41830345 GGGTTAAAATGG-AA-TTTTGGAAAGTTTG
1 GGG-TAAAATGGTAATTTTTGG-ATGATTG
*
41830373 AGGGTAAAATGGTAATTTTTGG-TGAAATCG
1 -GGGTAAAATGGTAATTTTTGGATG--ATTG
* * * *
41830403 GGGTTAAAAATGG-AATTTTAGAAAGTTTAG
1 GGG-T-AAAATGGTAATTTTTGGATGATT-G
*
41830433 GGGTAAAATGGTAATTTTTGGACTGCTTG
1 GGGTAAAATGGTAATTTTTGGA-TGATTG
41830462 GGG
1 GGG
41830465 ACCTATAAAC
Statistics
Matches: 136, Mismatches: 20, Indels: 45
0.68 0.10 0.22
Matches are distributed among these distances:
27 1 0.01
28 41 0.30
29 35 0.26
30 51 0.38
31 8 0.06
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTGGATGATTG
Found at i:41831421 original size:22 final size:22
Alignment explanation
Indices: 41831373--41831422 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
41831363 CGACGTACGA
* * * *
41831373 GCGAAACTTCGGCGGTGGTGGT
1 GCGAGACTCCGGCGATGGCGGT
41831395 GCGAGACTCCGGCGATGGCGGT
1 GCGAGACTCCGGCGATGGCGGT
41831417 GCGAGA
1 GCGAGA
41831423 TAGGGAAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (22 bp):
GCGAGACTCCGGCGATGGCGGT
Found at i:41831560 original size:17 final size:17
Alignment explanation
Indices: 41831530--41831606 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
41831520 TTAAATTGAT
41831530 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
41831546 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
41831563 TTTAAAATTAAATGTTTAAA
1 TTT-AAATT-TAT-TTTAAA
*
41831583 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
41831600 TTTAAAT
1 TTTAAAT
41831607 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.18
17 18 0.36
18 12 0.24
19 2 0.04
20 9 0.18
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:41831589 original size:5 final size:6
Alignment explanation
Indices: 41831530--41831637 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
41831520 TTAAATTGAT
* * *
41831530 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
41831575 TGTTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 --TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
41831625 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
41831638 AGTCCAAATG
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 55 0.66
7 11 0.13
8 5 0.06
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:41831596 original size:31 final size:31
Alignment explanation
Indices: 41831546--41831606 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
41831536 TTTATTTAAA
* *
41831546 TTTAGATTTATTTTAAATTTAAAATTAAATG
1 TTTAAATTTAATTTAAATTTAAAATTAAATG
* *
41831577 TTTAAATTTAATTTGAATTTAAATTTAAAT
1 TTTAAATTTAATTTAAATTTAAAATTAAAT
41831607 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTAAATTTAATTTAAATTTAAAATTAAATG
Found at i:41833302 original size:154 final size:160
Alignment explanation
Indices: 41833112--41833422 Score: 431
Period size: 154 Copynumber: 2.0 Consensus size: 160
41833102 CTTTTCAATT
* *
41833112 TAGTCCTTTGACTGTTTGACCGTACCATAGGCTGCCACGTGTCA-CTTTTTGGATTATTTATGCA
1 TAGTCCTTTGACTGTTTGACCGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCA
* *
41833176 TTTAGTCC-T-TTTTT-ATTTTTTTTAATTTAATCC-CAAATCAAC-TTTATTTTAATTAC-GAA
66 TTTAGTCCTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTA-TTTAATTACAAAA
41833235 TTGG-CCCAATAATTTTTCAAGGTTTATAAAC
130 TTGGTCCCAA-AATTTTTCAAGGTTTATAAAC
* * * *
41833266 TAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGTA
1 TAGTCCTTTGACTGTTTGACCGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCA
*
41833331 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAA
66 TTTAGTCC---TTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAA
*
41833396 AATTGGTCCTAAAATTTTTCAAGGTTT
128 AATTGGTCCCAAAATTTTTCAAGGTTT
41833423 TCAAATGGGT
Statistics
Matches: 136, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
154 40 0.29
155 26 0.19
159 1 0.01
160 5 0.04
161 18 0.13
162 17 0.12
163 25 0.18
164 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.47
Consensus pattern (160 bp):
TAGTCCTTTGACTGTTTGACCGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCA
TTTAGTCCTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAAT
TGGTCCCAAAATTTTTCAAGGTTTATAAAC
Found at i:41833579 original size:29 final size:29
Alignment explanation
Indices: 41833516--41833623 Score: 101
Period size: 30 Copynumber: 3.6 Consensus size: 29
41833506 AACAATCTAG
* * * *
41833516 AAATTATATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAA-TTTTCAA
41833546 AAATTACATTTTAACCCCAAAATTTTCAA
1 AAATTACATTTTAACCCCAAAATTTTCAA
* * *
41833575 AAATTACCATTTTACCCCCCAAATCTTT-TA
1 AAATTA-CATTTTAACCCCAAAAT-TTTCAA
*
41833605 AAATTCCATTTTTAACCCC
1 AAATTACA-TTTTAACCCC
41833624 GATTACACCA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
29 14 0.21
30 49 0.74
31 3 0.05
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (29 bp):
AAATTACATTTTAACCCCAAAATTTTCAA
Found at i:41833948 original size:59 final size:58
Alignment explanation
Indices: 41833541--41833948 Score: 543
Period size: 59 Copynumber: 6.9 Consensus size: 58
41833531 CCTAAAACTT
* * *
41833541 TTCCAAAATTACA-TTTTAACCCCAAAATTTTCA--AAAATTACCATTTTACCCCCCAAATC
1 TTCCAAAATTCCATTTTTAACCCC--GA-TTTCACCAAAATTACCATTTTACCCCCGAAA-C
** *
41833600 TTTTAAAATTCCATTTTTAACCCCGATTACACCAAAATTACCATTTTACCCCCGAAAC
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGAAAC
*
41833658 TTCCAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAAAC
1 TTCCAAAATTCCATTTTTAACCCCGATTTCA-CCAAAATTACCATTTTACCCCCGAAAC
*
41833717 TTCCAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAAAC
1 TTCCAAAATTCCATTTTTAACCCCGATTTCA-CCAAAATTACCATTTTACCCCCGAAAC
* *
41833776 TTCCAAAATTCTATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGC
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCGAAAC
* * * *
41833835 TTCAAAAATTTCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAATC
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCGAAAC
** * * *
41833894 TTTTAAAATTCCATTTTTAAACCTCGATTACACCAAAATTACCATTTTGCCCCCG
1 TTCCAAAATTCCATTTTT-AACCCCGATTTCACCAAAATTACCATTTTACCCCCG
41833949 GATATCCATA
Statistics
Matches: 317, Mismatches: 26, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
57 4 0.01
58 31 0.10
59 260 0.82
60 22 0.07
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (58 bp):
TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGAAAC
Found at i:41850408 original size:68 final size:68
Alignment explanation
Indices: 41850294--41850934 Score: 1032
Period size: 68 Copynumber: 9.4 Consensus size: 68
41850284 TTGCAGATCT
* * *
41850294 CAACATCATTCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
41850359 GAG
66 GAG
*
41850362 CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
*
41850427 GAA
66 GAG
41850430 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
41850495 GAAG
66 G-AG
* * * *
41850499 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTACCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
41850564 GAG
66 GAG
*
41850567 CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
*
41850632 GAA
66 GAG
*
41850635 CAACGTCATCCCCTTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCC-TTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA
41850700 AGAAG
65 AG-AG
* *
41850705 CAACGTCATTCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
*
41850770 GAA
66 GAG
*
41850773 CAACATCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT-A
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
41850837 GAAG
66 G-AG
** * * *
41850841 CAACGTCATCCCCTCAAAATTGAAGTAGAGTGGATAACACATCTTTACCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
41850906 GAG
66 GAG
* *
41850909 CAACGTCATCCTCTTGGAATTGAAGT
1 CAACGTCATCCCCTTGAAATTGAAGT
41850935 GAAGTTGGAC
Statistics
Matches: 534, Mismatches: 34, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
67 2 0.00
68 349 0.65
69 170 0.32
70 13 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (68 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
GAG
Found at i:41850571 original size:137 final size:138
Alignment explanation
Indices: 41850294--41850934 Score: 1053
Period size: 137 Copynumber: 4.7 Consensus size: 138
41850284 TTGCAGATCT
* *
41850294 CAACATCATTCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
*
41850359 G-AGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
66 GAAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
41850423 GTAAGAA-
131 GTAAGAAG
*
41850430 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
* * * *
41850495 GAAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTACCTCTGAAATTGAA
66 GAAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
41850560 GTAAG-AG
131 GTAAGAAG
41850567 CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
*
41850632 GAA-CAACGTCATCCCCTTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
66 GAAGCAACGTCATCCCC-TTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
41850696 AGTAAGAAG
130 AGTAAGAAG
*
41850705 CAACGTCATTCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
*
41850770 GAA-CAACATCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
66 GAAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
41850834 GT-AGAAG
131 GTAAGAAG
* ** * * *
41850841 CAACGTCATCCCCTCAAAATTGAAGTAGAGTGGATAACACATCTTTACCTCTGAAATTGAAGTAA
1 CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
* *
41850906 G-AGCAACGTCATCCTCTTGGAATTGAAGT
66 GAAGCAACGTCATCCCCTTGAAATTGAAGT
41850935 GAAGTTGGAC
Statistics
Matches: 473, Mismatches: 27, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
135 1 0.00
136 164 0.35
137 227 0.48
138 81 0.17
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (138 bp):
CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
GAAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAA
GTAAGAAG
Found at i:41851269 original size:17 final size:17
Alignment explanation
Indices: 41851239--41851315 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
41851229 TTAAATTGAT
41851239 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
41851255 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
41851272 TTTAAAATTAAATGTTTAAA
1 TTT-AAATT-TAT-TTTAAA
*
41851292 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
41851309 TTTAAAT
1 TTTAAAT
41851316 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.18
17 18 0.36
18 12 0.24
19 2 0.04
20 9 0.18
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:41851298 original size:5 final size:6
Alignment explanation
Indices: 41851239--41851346 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
41851229 TTAAATTGAT
* * *
41851239 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
41851284 TGTTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 --TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
41851334 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
41851347 AGTCCAAATG
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 55 0.66
7 11 0.13
8 5 0.06
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:41851305 original size:31 final size:31
Alignment explanation
Indices: 41851255--41851315 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
41851245 TTTATTTAAA
* *
41851255 TTTAGATTTATTTTAAATTTAAAATTAAATG
1 TTTAAATTTAATTTAAATTTAAAATTAAATG
* *
41851286 TTTAAATTTAATTTGAATTTAAATTTAAAT
1 TTTAAATTTAATTTAAATTTAAAATTAAAT
41851316 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTAAATTTAATTTAAATTTAAAATTAAATG
Found at i:41851394 original size:14 final size:14
Alignment explanation
Indices: 41851375--41851408 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41851365 CATGGCCCAC
*
41851375 GGCCCAATTACAAT
1 GGCCCAATTACAAA
*
41851389 GGCCCAATTTCAAA
1 GGCCCAATTACAAA
41851403 GGCCCA
1 GGCCCA
41851409 TTTTTCGGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (14 bp):
GGCCCAATTACAAA
Found at i:41853193 original size:162 final size:159
Alignment explanation
Indices: 41852832--41853197 Score: 413
Period size: 159 Copynumber: 2.3 Consensus size: 159
41852822 CTTTTCAATT
* * * * * *
41852832 TAGTCCTTTGACTGTTTGACCGTACCATAGGCTGCCACGTGTCACTTTTTGGATTATTTATGCAT
1 TAGTCCCTTGACTGCTAGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGATTATTTATGCAT
*
41852897 TTAGTCCTTTTTTATTTTTTTTATTTTAATTTAATCCCAAATCAACTTTATTTTAATTACGAATT
66 TTAGTCCTTTTTTATTTTTTTTATTTTAATTTAATCCCAAATCAACTTTATTTTAATTACAAATT
41852962 GGCCCAATAATTTTTCAAGGTTTATAAAC
131 GGCCCAATAATTTTTCAAGGTTTATAAAC
* * * * * *
41852991 TAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGTA
1 TAGTCCCTTGACTGCTAGACTGCACCAGAGGCTGCCACGTGTCA-CTTTTTGGATTATTTATGCA
* *
41853056 TTTAGTCC-TTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTT-TATTTAATTAC
65 TTTAGTCCTTTTTTATTTTT--TTTATTTTAATTTAATCC-CAAATCAACTTTAT-TTTAATTAC
* *
41853119 AAAATTCGTCCTAA-AATTTTTCAAGGTTT-TCAAA-
126 -AAATT-GGCCCAATAATTTTTCAAGGTTTAT-AAAC
* * *
41853153 TGGGTCCCTTGACTGCTAGA-TGC-CTATGGGGCTGCCACGTGTCAC
1 T-AGTCCCTTGACTGCTAGACTGCACCA-GAGGCTGCCACGTGTCAC
41853198 CCACTCTTTG
Statistics
Matches: 179, Mismatches: 18, Indels: 18
0.83 0.08 0.08
Matches are distributed among these distances:
159 51 0.28
160 26 0.15
161 21 0.12
162 40 0.22
163 36 0.20
164 5 0.03
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (159 bp):
TAGTCCCTTGACTGCTAGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGATTATTTATGCAT
TTAGTCCTTTTTTATTTTTTTTATTTTAATTTAATCCCAAATCAACTTTATTTTAATTACAAATT
GGCCCAATAATTTTTCAAGGTTTATAAAC
Found at i:41853276 original size:30 final size:29
Alignment explanation
Indices: 41853238--41853312 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
41853228 CCAAACAATC
* *
41853238 CAAAAATTATATTTTGAACCTAAAACTTTT
1 CAAAAATTACATTTTGAACCCAAAAC-TTT
* *
41853268 CCAAAATTACATTTTGACCCCAAAACTTT
1 CAAAAATTACATTTTGAACCCAAAACTTT
41853297 CAAAAATTACCATTTT
1 CAAAAATTA-CATTTT
41853313 ACCCCCCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 11 0.28
30 28 0.72
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.36
Consensus pattern (29 bp):
CAAAAATTACATTTTGAACCCAAAACTTT
Found at i:41853316 original size:29 final size:29
Alignment explanation
Indices: 41853238--41853566 Score: 124
Period size: 29 Copynumber: 11.2 Consensus size: 29
41853228 CCAAACAATC
* **
41853238 CAAAAATTA-TATTTTGAACCTAAAACTTTT
1 CAAAAATTACCATTTT-AACCCCAAAC-TTT
* *
41853268 CCAAAATTA-CATTTTGACCCCAAAACTTT
1 CAAAAATTACCATTTTAACCCC-AAACTTT
*
41853297 CAAAAATTACCATTTTACCCCCCAAATCTTT
1 CAAAAATTACCATTTTA-ACCCCAAA-CTTT
* * *
41853328 -TAAAATT-CCATTTTAAACCCC-GA-TTA
1 CAAAAATTACCATTTT-AACCCCAAACTTT
*
41853354 CACCAAAATTACCATTTTACCCCCGAAAC-TT
1 CA--AAAATTACCATTTTAACCCC-AAACTTT
*
41853385 CCAAAATT-CCATTTTTAACCCC-AA-TTT
1 CAAAAATTACCA-TTTTAACCCCAAACTTT
*
41853412 CACCGAAAATTACCATTTT-ACCCTTGAAAC-TT
1 CA---AAAATTACCATTTTAACCC--CAAACTTT
*
41853444 CAAAAATT-CCATTTTTAACCCC-GA-TTT
1 CAAAAATTACCA-TTTTAACCCCAAACTTT
41853471 CACCGAAAATTACCATTTT-ACCCCTGAAAC-TT
1 CA---AAAATTACCATTTTAACCCC--AAACTTT
* * *
41853503 CCAAAATT-CCATTTTTAACCTC-GA-TTT
1 CAAAAATTACCA-TTTTAACCCCAAACTTT
*
41853530 CACAGAAAATTACCATTTT-ACCCCGAAACTTC
1 --CA-AAAATTACCATTTTAACCCC-AAACTTT
41853562 CAAAA
1 CAAAA
41853567 TTCTATTTTT
Statistics
Matches: 226, Mismatches: 30, Indels: 87
0.66 0.09 0.25
Matches are distributed among these distances:
26 2 0.01
27 13 0.06
28 10 0.04
29 88 0.39
30 80 0.35
31 21 0.09
32 12 0.05
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTAACCCCAAACTTT
Found at i:41853590 original size:176 final size:175
Alignment explanation
Indices: 41853297--41853729 Score: 650
Period size: 176 Copynumber: 2.5 Consensus size: 175
41853287 CCAAAACTTT
* *
41853297 CAAAAATTACCATTTTACCCCCCAAATCTTTTAAAATTCCATTTTAAACCCCGATTACACCAAAA
1 CAAAAATTACCATTTTACCCCCGAAA-CTTTTAAAATTCCATTTTTAACCCCGATTACACCAAAA
41853362 TTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCAATTTCACCGAAAATTACCA
65 TTACCATTTTA-CCCCGAAACTTCCAAAATTCCATTTTTAACCCCAATTTCACCGAAAATTACCA
*
41853427 TTTTACCCTTGAAACTTCAAAAATTCCATTTTTAACCCCGATTTCAC
129 TTTTACCCTCGAAACTTCAAAAATTCCATTTTTAACCCCGATTTCAC
* * ** * * *
41853474 CGAAAATTACCATTTTACCCCTGAAACTTCCAAAATTCCATTTTTAACCTCGATTTCACAGAAAA
1 CAAAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCATTTTTAACCCCGATTACAC-CAAAA
* ** *
41853539 TTACCATTTTACCCCGAAACTTCCAAAATTCTATTTTTAACCCTGATTTCACTGAAAATTACCAT
65 TTACCATTTTACCCCGAAACTTCCAAAATTCCATTTTTAACCCCAATTTCACCGAAAATTACCAT
* * *
41853604 TTTACCCTCGAAGCTTCTAAAATTTCATTTTTAACCCCGATTTCAC
130 TTTACCCTCGAAACTTCAAAAATTCCATTTTTAACCCCGATTTCAC
* *
41853650 CAAAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAAACCCCGATTACACCAAAA
1 CAAAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCATTTTT-AACCCCGATTACACCAAAA
*
41853715 TTACCATTTTGCCCC
65 TTACCATTTTACCCC
41853730 CGGATATCCA
Statistics
Matches: 227, Mismatches: 27, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
176 177 0.78
177 50 0.22
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (175 bp):
CAAAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCATTTTTAACCCCGATTACACCAAAAT
TACCATTTTACCCCGAAACTTCCAAAATTCCATTTTTAACCCCAATTTCACCGAAAATTACCATT
TTACCCTCGAAACTTCAAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:41853731 original size:59 final size:58
Alignment explanation
Indices: 41853299--41853731 Score: 571
Period size: 59 Copynumber: 7.4 Consensus size: 58
41853289 AAAACTTTCA
* ** * *
41853299 AAAATTACCATTTTACCCCCCAAATCTTTTAAAATTCCATTTTAAACCCCGATTACACC
1 AAAATTACCATTTTACCCCCGAAA-CTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
41853358 AAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCAATTTCACC
1 AAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCACC
** *
41853416 GAAAATTACCATTTTACCCTTGAAACTTCAAAAATTCCATTTTTAACCCCGATTTCACC
1 -AAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
41853475 GAAAATTACCATTTTACCCCTGAAACTTCCAAAATTCCATTTTTAACCTCGATTTCACAG
1 -AAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCAC-C
* * *
41853535 AAAATTACCATTTTA-CCCCGAAACTTCCAAAATTCTATTTTTAACCCTGATTTCACTG
1 AAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCAC-C
* * * *
41853593 AAAATTACCATTTTACCCTCGAAGCTTCTAAAATTTCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * ** *
41853651 AAAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAAACCCCGATTACACC
1 -AAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTT-AACCCCGATTTCACC
*
41853711 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
41853732 GATATCCATA
Statistics
Matches: 335, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
58 82 0.24
59 239 0.71
60 14 0.04
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:41854931 original size:6 final size:7
Alignment explanation
Indices: 41854907--41854973 Score: 61
Period size: 6 Copynumber: 9.9 Consensus size: 7
41854897 TGGTTTCGAC
41854907 ATTAATT
1 ATTAATT
41854914 ATTAA-T
1 ATTAATT
41854920 ATTAATT
1 ATTAATT
41854927 A-TAATT
1 ATTAATT
*
41854933 A-TAAAT
1 ATTAATT
*
41854939 ATTTATT
1 ATTAATT
*
41854946 ACT-ATT
1 ATTAATT
41854952 ATTAATT
1 ATTAATT
41854959 ATTATGATT
1 ATTA--ATT
41854968 ATTAAT
1 ATTAAT
41854974 AATATTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
6 22 0.44
7 21 0.42
9 7 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (7 bp):
ATTAATT
Found at i:41854933 original size:19 final size:18
Alignment explanation
Indices: 41854909--41854979 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
41854899 GTTTCGACAT
41854909 TAATTATTAATATTAATTA
1 TAATTATTAATATT-ATTA
*
41854928 TAATTATAAATATTTATTA
1 TAATTATTAATA-TTATTA
41854947 CT-ATTATT-A-ATTATTA
1 -TAATTATTAATATTATTA
* *
41854963 TGATTATTAATAATATT
1 TAATTATTAATATTATT
41854980 TTTATTAATG
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
15 1 0.02
16 12 0.27
17 2 0.05
18 6 0.14
19 20 0.45
20 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TAATTATTAATATTATTA
Found at i:41854986 original size:15 final size:15
Alignment explanation
Indices: 41854966--41854995 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41854956 ATTATTATGA
41854966 TTATTAATAATATTT
1 TTATTAATAATATTT
*
41854981 TTATTAATGATATTT
1 TTATTAATAATATTT
41854996 ATGAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTATTAATAATATTT
Found at i:41857995 original size:8 final size:8
Alignment explanation
Indices: 41857982--41858008 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
41857972 TTGAGGTGAA
41857982 AAAATATT
1 AAAATATT
41857990 AAAATATT
1 AAAATATT
41857998 AAAATATT
1 AAAATATT
41858006 AAA
1 AAA
41858009 TGACATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATATT
Found at i:41858246 original size:18 final size:18
Alignment explanation
Indices: 41858215--41858249 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41858205 TTTATTTTAA
41858215 ATATATTTATAATATATG
1 ATATATTTATAATATATG
41858233 ATATGATTTA-AATATAT
1 ATAT-ATTTATAATATAT
41858250 TTTTATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
ATATATTTATAATATATG
Found at i:41858416 original size:13 final size:13
Alignment explanation
Indices: 41858398--41858429 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
41858388 AAATAAATTG
41858398 AATTGATCGAAAA
1 AATTGATCGAAAA
41858411 AATTGATCGAAAA
1 AATTGATCGAAAA
41858424 AATTGA
1 AATTGA
41858430 ATGCTCTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (13 bp):
AATTGATCGAAAA
Found at i:41860300 original size:11 final size:12
Alignment explanation
Indices: 41860276--41860305 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
41860266 CAATTTAAAT
41860276 TTTATTATTTTA
1 TTTATTATTTTA
41860288 TTTATTA-TTTA
1 TTTATTATTTTA
41860299 TTTATTA
1 TTTATTA
41860306 AATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:41860339 original size:16 final size:15
Alignment explanation
Indices: 41860302--41860344 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
41860292 TTATTTATTT
41860302 ATTAAATAAATAAACA
1 ATTAAA-AAATAAACA
* *
41860318 AATAAAAAATAATAGA
1 ATTAAAAAATAA-ACA
41860334 ATTAAAAAATA
1 ATTAAAAAATA
41860345 TATATAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (15 bp):
ATTAAAAAATAAACA
Found at i:41861573 original size:31 final size:30
Alignment explanation
Indices: 41861460--41861615 Score: 194
Period size: 30 Copynumber: 5.2 Consensus size: 30
41861450 TCATTTTTTG
41861460 ACCCCTAAAGTTTT-TAAAAATTCAAATTTA
1 ACCCCTAAA-TTTTCTAAAAATTCAAATTTA
* *
41861490 ACCCCCATATTTTCTAAAAATTCAAATTTA
1 ACCCCTAAATTTTCTAAAAATTCAAATTTA
*
41861520 ATCCCC-AAAGTTTTC-AAAAATTCAAATTTG
1 A-CCCCTAAA-TTTTCTAAAAATTCAAATTTA
41861550 ACCCCTTAAATTTTCTAAAAATTCAAATTTA
1 ACCCC-TAAATTTTCTAAAAATTCAAATTTA
**
41861581 ACCCCTAAAATTTTC-AAAAATAAAAATTTA
1 ACCCCT-AAATTTTCTAAAAATTCAAATTTA
41861611 ACCCC
1 ACCCC
41861616 GTTTTAATGT
Statistics
Matches: 112, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.07
30 65 0.58
31 39 0.35
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (30 bp):
ACCCCTAAATTTTCTAAAAATTCAAATTTA
Found at i:41861595 original size:61 final size:60
Alignment explanation
Indices: 41861460--41861615 Score: 224
Period size: 61 Copynumber: 2.6 Consensus size: 60
41861450 TCATTTTTTG
* *
41861460 ACCCCTAAAGTTTTTAAAAATTCAAATTTAACCCCCATATTTTCTAAAAATTCAAATTTA
1 ACCCCTAAAGTTTTCAAAAATTCAAATTTAACCCCCAAATTTTCTAAAAATTCAAATTTA
* *
41861520 ATCCCC-AAAGTTTTCAAAAATTCAAATTTGACCCCTTAAATTTTCTAAAAATTCAAATTTA
1 A-CCCCTAAAGTTTTCAAAAATTCAAATTTAACCCC-CAAATTTTCTAAAAATTCAAATTTA
* **
41861581 ACCCCTAAAATTTTCAAAAATAAAAATTTAACCCC
1 ACCCCTAAAGTTTTCAAAAATTCAAATTTAACCCC
41861616 GTTTTAATGT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
60 32 0.38
61 53 0.62
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (60 bp):
ACCCCTAAAGTTTTCAAAAATTCAAATTTAACCCCCAAATTTTCTAAAAATTCAAATTTA
Found at i:41863414 original size:23 final size:23
Alignment explanation
Indices: 41863344--41863491 Score: 149
Period size: 23 Copynumber: 6.4 Consensus size: 23
41863334 ACGGAACAAG
* *
41863344 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
41863365 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
41863390 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
41863413 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
41863436 CGGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
41863459 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
41863482 CAGAGAGCAC
1 CAGAGAGCAC
41863492 GAGACGTACT
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
21 15 0.14
23 73 0.68
25 13 0.12
26 6 0.06
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:41863446 original size:46 final size:46
Alignment explanation
Indices: 41863390--41863512 Score: 167
Period size: 46 Copynumber: 2.7 Consensus size: 46
41863380 TGCTGGGCAA
*
41863390 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * * *
41863436 CGGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* *
41863482 CAGAGAGCACGAGAC-GTACTAAACAGAGAGC
1 CAGAGAGCAC-ACACAGTGCTAAACAGAGAGC
41863513 GCGCTAGTGT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 64 0.97
47 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (46 bp):
CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:41863463 original size:69 final size:66
Alignment explanation
Indices: 41863344--41863512 Score: 187
Period size: 69 Copynumber: 2.4 Consensus size: 66
41863334 ACGGAACAAG
* *
41863344 CAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGTGC
1 CAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAAAGTGC
41863409 TAAA
63 TAAA
*
41863413 CAGAGAGTACACAAAGTACTAATCGGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAAGTG
*
41863477 CTAAT
62 CTAAA
* * *
41863482 CAGAGAGCACGAGACGTACTAAACAGAGAGC
1 CAGAGAGTACCA-AAGTACT-AACAGAGAGC
41863513 GCGCTAGTGT
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
68 3 0.03
69 53 0.62
70 13 0.15
71 10 0.12
72 7 0.08
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (66 bp):
CAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGTGCTAA
A
Found at i:41867349 original size:50 final size:50
Alignment explanation
Indices: 41867285--41867507 Score: 295
Period size: 50 Copynumber: 4.5 Consensus size: 50
41867275 ATCTTTTACC
* * *
41867285 CCTAAAGCTATAGAGGTGCAGATTGAAATCGCAAAGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAAAGGCAAATCTCATACA
* ** * *
41867335 CCTAAAGCTGTAGAGGGGCAGAATGATGCCGCAATGG-AAATCTCATACC
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAAAGGCAAATCTCATACA
* * *
41867384 CCTAAAGCTATAGAGGTGCAGATTGAAACTGCAAAGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAAAGGCAAATCTCATACA
* * * * *
41867434 CCTAAAGCTGTAGAGGGGCAGAATGAAGCCGCAATGACAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAAAGGCAAATCTCATACA
41867484 CCTAAAGCTGTAGAGGGGCAGATT
1 CCTAAAGCTGTAGAGGGGCAGATT
41867508 TAAGTCACAA
Statistics
Matches: 147, Mismatches: 25, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
49 41 0.28
50 106 0.72
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAAAGGCAAATCTCATACA
Found at i:41867445 original size:99 final size:100
Alignment explanation
Indices: 41867267--41867507 Score: 378
Period size: 99 Copynumber: 2.4 Consensus size: 100
41867257 ATGGCGATAG
* **
41867267 AATGACCAATCTTTTACCCCTAAAGCTATAGAGGTGCAGATTGAAATCGCAAAGGCAAATCTCAT
1 AATGACAAATCTCATACCCCTAAAGCTATAGAGGTGCAGATTGAAATCGCAAAGGCAAATCTCAT
*
41867332 ACACCTAAAGCTGTAGAGGGGCAGAATGATGCCGC
66 ACACCTAAAGCTGTAGAGGGGCAGAATGAAGCCGC
*
41867367 AATG-GAAATCTCATACCCCTAAAGCTATAGAGGTGCAGATTGAAA-CTGCAAAGGCAAATCTCA
1 AATGACAAATCTCATACCCCTAAAGCTATAGAGGTGCAGATTGAAATC-GCAAAGGCAAATCTCA
41867430 TACACCTAAAGCTGTAGAGGGGCAGAATGAAGCCGC
65 TACACCTAAAGCTGTAGAGGGGCAGAATGAAGCCGC
* * * *
41867466 AATGACAAATCTCATTCACCTAAAGCTGTAGAGGGGCAGATT
1 AATGACAAATCTCATACCCCTAAAGCTATAGAGGTGCAGATT
41867508 TAAGTCACAA
Statistics
Matches: 129, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
98 1 0.01
99 92 0.71
100 36 0.28
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.20
Consensus pattern (100 bp):
AATGACAAATCTCATACCCCTAAAGCTATAGAGGTGCAGATTGAAATCGCAAAGGCAAATCTCAT
ACACCTAAAGCTGTAGAGGGGCAGAATGAAGCCGC
Found at i:41867527 original size:50 final size:50
Alignment explanation
Indices: 41867285--41867532 Score: 263
Period size: 50 Copynumber: 5.0 Consensus size: 50
41867275 ATCTTTTACC
* * *
41867285 CCTAAAGCTATAGAGGTGCAGATTGAAATCGCAAAGG-CAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGTCGC-AAGGACAAATCTCATACA
* * * *
41867335 CCTAAAGCTGTAGAGGGGCAGAATGATGCCGCAATGG--AAATCTCATACC
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGTCGCAA-GGACAAATCTCATACA
* * *
41867384 CCTAAAGCTATAGAGGTGCAGATTGAA-ACTGCAAAGG-CAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGTC-GC-AAGGACAAATCTCATACA
* * * *
41867434 CCTAAAGCTGTAGAGGGGCAGAATGAAGCCGCAATGACAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGTCGCAAGGACAAATCTCATACA
* * * *
41867484 CCTAAAGCTGTAGAGGGGCAGATTTAAGTCACAAGGACGAATCTTATAC
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGTCGCAAGGACAAATCTCATAC
41867533 TCTTGAAGCT
Statistics
Matches: 165, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
48 1 0.01
49 43 0.26
50 120 0.73
51 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAGTCGCAAGGACAAATCTCATACA
Found at i:41867669 original size:87 final size:86
Alignment explanation
Indices: 41867568--41867765 Score: 273
Period size: 80 Copynumber: 2.4 Consensus size: 86
41867558 AACAACCTCC
* * *
41867568 AATCTTTTACCCCGATCATGGGGCAGATTGGAGATTGAAGAAATTTAATCTTTTACCCTAACCAG
1 AATCTTTTACCCCGATCATGGGGCAGATT-GAGATTGAAGAAACTCAATCTTTTACCCTAACCAA
* *
41867633 AGGGCAAGATTGAAGACCGTCT
65 AGGGCAAGATTAAAGACCATCT
* *
41867655 AATTTTTTACCCCGATCATGGGGC------AGATTGAAGAAACTCAATCTTTTACCCTAACTAAA
1 AATCTTTTACCCCGATCATGGGGCAGATTGAGATTGAAGAAACTCAATCTTTTACCCTAACCAAA
41867714 GGGCAAGATTAAAGACCATCT
66 GGGCAAGATTAAAGACCATCT
*
41867735 GATCTTTTACCCCGATCATGGGGCAGATTGA
1 AATCTTTTACCCCGATCATGGGGCAGATTGA
41867766 AGAAATCCAA
Statistics
Matches: 96, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
80 72 0.75
86 1 0.01
87 23 0.24
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (86 bp):
AATCTTTTACCCCGATCATGGGGCAGATTGAGATTGAAGAAACTCAATCTTTTACCCTAACCAAA
GGGCAAGATTAAAGACCATCT
Found at i:41867683 original size:40 final size:40
Alignment explanation
Indices: 41867562--41867768 Score: 145
Period size: 40 Copynumber: 5.0 Consensus size: 40
41867552 TGAAGTAACA
*
41867562 ACCTCCAATCTTTTACCCCGATCATGGGGCAGATTGGAGATTGAAG
1 ACCTCTAATCTTTTACCCCGATCATGGGGC--A----AGATTGAAG
** * ** *
41867608 AAATTTAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAG
1 ACCTCTAATCTTTTACCCCGATCATG-GGGCAAGATTGAAG
*
41867648 ACCGTCTAATTTTTTACCCCGATCATGGGGC-AGATTGAAG
1 ACC-TCTAATCTTTTACCCCGATCATGGGGCAAGATTGAAG
* * * ** *
41867688 AAACTC-AATCTTTTA-CCCTAACTAAAGGGCAAGATTAAAG
1 -ACCTCTAATCTTTTACCCCGATC-ATGGGGCAAGATTGAAG
*
41867728 ACCATCTGATCTTTTACCCCGATCATGGGGC-AGATTGAAG
1 ACC-TCTAATCTTTTACCCCGATCATGGGGCAAGATTGAAG
41867768 A
1 A
41867769 AATCCAATAT
Statistics
Matches: 124, Mismatches: 28, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
38 5 0.04
39 15 0.12
40 40 0.32
41 35 0.28
42 6 0.05
44 1 0.01
45 1 0.01
46 21 0.17
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
ACCTCTAATCTTTTACCCCGATCATGGGGCAAGATTGAAG
Found at i:41867743 original size:80 final size:79
Alignment explanation
Indices: 41867599--41867791 Score: 287
Period size: 80 Copynumber: 2.4 Consensus size: 79
41867589 GGCAGATTGG
* * * * * *
41867599 AGATTGAAGAAATTTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCGTCTAATTTTTTA
1 AGATTGAAGAAA-TCAATCTTTTACCCTAACTAAAGGGCAAGATTAAAGACCATCTAATCTTTTA
41867664 CCCCGATCATGGGGC
65 CCCCGATCATGGGGC
*
41867679 AGATTGAAGAAACTCAATCTTTTACCCTAACTAAAGGGCAAGATTAAAGACCATCTGATCTTTTA
1 AGATTGAAGAAA-TCAATCTTTTACCCTAACTAAAGGGCAAGATTAAAGACCATCTAATCTTTTA
41867744 CCCCGATCATGGGGC
65 CCCCGATCATGGGGC
*
41867759 AGATTGAAGAAATCCAATATTTTACCCTAACTA
1 AGATTGAAGAAAT-CAATCTTTTACCCTAACTA
41867792 TGAGGTAGAT
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 1 0.01
80 102 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (79 bp):
AGATTGAAGAAATCAATCTTTTACCCTAACTAAAGGGCAAGATTAAAGACCATCTAATCTTTTAC
CCCGATCATGGGGC
Found at i:41867883 original size:40 final size:40
Alignment explanation
Indices: 41867599--41867916 Score: 243
Period size: 40 Copynumber: 8.0 Consensus size: 40
41867589 GGCAGATTGG
** *
41867599 AGATTGAAGA-AATTTAATCTTTTACCCTAACCA-GAGGGC
1 AGATTGAAGACAATCCAATCTTTTACCCCAACCATG-GGGC
** * * * *
41867638 AAGATTGAAGACCGTCTAATTTTTTACCCCGATCATGGGGC
1 -AGATTGAAGACAATCCAATCTTTTACCCCAACCATGGGGC
* * **
41867679 AGATTGAAGA-AA-CTCAATCTTTTACCCTAACTAAAGGGC
1 AGATTGAAGACAATC-CAATCTTTTACCCCAACCATGGGGC
* * ** * *
41867718 AAGATTAAAGACCATCTGATCTTTTACCCCGATCATGGGGC
1 -AGATTGAAGACAATCCAATCTTTTACCCCAACCATGGGGC
* * * * *
41867759 AGATTGAAGA-AATCCAATATTTTACCCTAACTATGAGGT
1 AGATTGAAGACAATCCAATCTTTTACCCCAACCATGGGGC
* * ** ** *
41867798 AGATTGAAG-CAATTCAATCTTTTACCCTAATTAAAGGGT
1 AGATTGAAGACAATCCAATCTTTTACCCCAACCATGGGGC
*
41867837 AGATTGAAGACAATCCAATCTCTTACCCCAACCATGGGGC
1 AGATTGAAGACAATCCAATCTTTTACCCCAACCATGGGGC
* * *
41867877 ATATTGAAGACAATCCAATCTCTTACCCCGACCATGGGGC
1 AGATTGAAGACAATCCAATCTTTTACCCCAACCATGGGGC
41867917 GGGTTGAAAC
Statistics
Matches: 216, Mismatches: 54, Indels: 16
0.76 0.19 0.06
Matches are distributed among these distances:
38 1 0.00
39 77 0.36
40 98 0.45
41 38 0.18
42 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (40 bp):
AGATTGAAGACAATCCAATCTTTTACCCCAACCATGGGGC
Found at i:41867885 original size:79 final size:79
Alignment explanation
Indices: 41867759--41867904 Score: 195
Period size: 79 Copynumber: 1.8 Consensus size: 79
41867749 ATCATGGGGC
* * * * * *
41867759 AGATTGAAGAAATCCAATATTTTACCCTAACTATGAGGTAGATTGAAG-CAATTCAATCTTTTAC
1 AGATTGAAGAAATCCAATATCTTACCCCAACCATGAGGCAGATTGAAGACAATCCAATCTCTTAC
41867823 CCTAATTAAAGGGT
66 CCTAATTAAAGGGT
* * *
41867837 AGATTGAAGACAATCCAATCTCTTACCCCAACCATGGGGCATATTGAAGACAATCCAATCTCTTA
1 AGATTGAAGA-AATCCAATATCTTACCCCAACCATGAGGCAGATTGAAGACAATCCAATCTCTTA
41867902 CCC
65 CCC
41867905 CGACCATGGG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 10 0.18
79 31 0.54
80 16 0.28
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (79 bp):
AGATTGAAGAAATCCAATATCTTACCCCAACCATGAGGCAGATTGAAGACAATCCAATCTCTTAC
CCTAATTAAAGGGT
Found at i:41867924 original size:119 final size:120
Alignment explanation
Indices: 41867599--41867916 Score: 356
Period size: 119 Copynumber: 2.7 Consensus size: 120
41867589 GGCAGATTGG
* * ** * *
41867599 AGATTGAAGA-AATTTAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACCGTCTAATTTTT
1 AGATTGAAGACAATCTAATCTTTTACCCCAACCATG-GGGC-AGATTGAAGACAATCCAATATTT
*
41867662 TACCCCGATCATGGGGCAGATTGAAGAAACTCAATCTTTTACCCTAACTAAAGGGCA
64 TACCCCGACCATGGGGCAGATTGAAGAAACTCAATCTTTTACCCTAACTAAAGGGCA
* * * * *
41867719 AGATTAAAGACCATCTGATCTTTTACCCCGATCATGGGGCAGATTGAAGA-AATCCAATATTTTA
1 AGATTGAAGACAATCTAATCTTTTACCCCAACCATGGGGCAGATTGAAGACAATCCAATATTTTA
** * * * * * * *
41867783 CCCTAACTATGAGGTAGATTGAAGCAATTCAATCTTTTACCCTAATTAAAGGG-T
66 CCCCGACCATGGGGCAGATTGAAGAAACTCAATCTTTTACCCTAACTAAAGGGCA
* * * * *
41867837 AGATTGAAGACAATCCAATCTCTTACCCCAACCATGGGGCATATTGAAGACAATCCAATCTCTTA
1 AGATTGAAGACAATCTAATCTTTTACCCCAACCATGGGGCAGATTGAAGACAATCCAATATTTTA
41867902 CCCCGACCATGGGGC
66 CCCCGACCATGGGGC
41867917 GGGTTGAAAC
Statistics
Matches: 159, Mismatches: 36, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
118 42 0.26
119 76 0.48
120 19 0.12
121 21 0.13
122 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (120 bp):
AGATTGAAGACAATCTAATCTTTTACCCCAACCATGGGGCAGATTGAAGACAATCCAATATTTTA
CCCCGACCATGGGGCAGATTGAAGAAACTCAATCTTTTACCCTAACTAAAGGGCA
Found at i:41868417 original size:11 final size:12
Alignment explanation
Indices: 41868393--41868422 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
41868383 CAACCCAAAT
41868393 TTTATTATTTTA
1 TTTATTATTTTA
41868405 TTTATTA-TTTA
1 TTTATTATTTTA
41868416 TTTATTA
1 TTTATTA
41868423 AATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:41869270 original size:22 final size:22
Alignment explanation
Indices: 41869245--41869287 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41869235 TAAAAATAAA
*
41869245 AATGGGTTTTTTTAATAGAAAG
1 AATGAGTTTTTTTAATAGAAAG
* *
41869267 AATGATTTTTTTTAATGGAAA
1 AATGAGTTTTTTTAATAGAAA
41869288 TAATCAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (22 bp):
AATGAGTTTTTTTAATAGAAAG
Found at i:41869626 original size:31 final size:31
Alignment explanation
Indices: 41869578--41869733 Score: 203
Period size: 31 Copynumber: 5.1 Consensus size: 31
41869568 CATTTTTTGA
*
41869578 CCCTCAAAGTTTT-TAAAAATTTAAATTTAAC
1 CCCT-AAAGTTTTCTAAAAATTCAAATTTAAC
* * *
41869609 CCCCAAAATTTTCTAAAAATTCAAATTTAAT
1 CCCTAAAGTTTTCTAAAAATTCAAATTTAAC
*
41869640 CCCTAAAGTTTTC-AAAAATTCAAATTTGAC
1 CCCTAAAGTTTTCTAAAAATTCAAATTTAAC
*
41869670 CCCTTAAA-ATTTCTAAAAATTCAAATTTAAC
1 CCC-TAAAGTTTTCTAAAAATTCAAATTTAAC
*
41869701 CCCTAAAGTTTTC-AAAAATTAAAATTTAAC
1 CCCTAAAGTTTTCTAAAAATTCAAATTTAAC
41869731 CCC
1 CCC
41869734 ATTTTAATAT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
30 52 0.48
31 57 0.52
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.35
Consensus pattern (31 bp):
CCCTAAAGTTTTCTAAAAATTCAAATTTAAC
Found at i:41869648 original size:61 final size:61
Alignment explanation
Indices: 41869578--41869733 Score: 233
Period size: 61 Copynumber: 2.5 Consensus size: 61
41869568 CATTTTTTGA
* * *
41869578 CCCTCAAAGTTTTTAAAAATTTAAATTTAACCCC-CAAAATTTTCTAAAAATTCAAATTTAAT
1 CCCT-AAAGTTTTCAAAAATTAAAATTTAACCCCTCAAAA-TTTCTAAAAATTCAAATTTAAC
* * *
41869640 CCCTAAAGTTTTCAAAAATTCAAATTTGACCCCTTAAAATTTCTAAAAATTCAAATTTAAC
1 CCCTAAAGTTTTCAAAAATTAAAATTTAACCCCTCAAAATTTCTAAAAATTCAAATTTAAC
41869701 CCCTAAAGTTTTCAAAAATTAAAATTTAACCCC
1 CCCTAAAGTTTTCAAAAATTAAAATTTAACCCC
41869734 ATTTTAATAT
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
61 78 0.91
62 8 0.09
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.35
Consensus pattern (61 bp):
CCCTAAAGTTTTCAAAAATTAAAATTTAACCCCTCAAAATTTCTAAAAATTCAAATTTAAC
Found at i:41874758 original size:22 final size:21
Alignment explanation
Indices: 41874727--41874774 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
41874717 AATCTTGAGA
*
41874727 TTTTTCATAA-TACATATCCTAT
1 TTTTTCATAACT--ATATACTAT
*
41874749 TTTTTTATAACTATATACTAT
1 TTTTTCATAACTATATACTAT
41874770 TTTTT
1 TTTTT
41874775 AATTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 13 0.57
22 9 0.39
23 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTTCATAACTATATACTAT
Found at i:41874953 original size:17 final size:16
Alignment explanation
Indices: 41874931--41874963 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
41874921 CAAGATTATT
41874931 TATTATTAATATAATAA
1 TATTATTAATA-AATAA
41874948 TATTATTAATAAATAA
1 TATTATTAATAAATAA
41874964 AAAATTCGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTATTAATAAATAA
Found at i:41875054 original size:26 final size:26
Alignment explanation
Indices: 41875020--41875101 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
41875010 ATAATTGTCT
* *
41875020 GACAATAAGCTAAAGAAAAAGCACCT
1 GACAATAAGCTAAAGAAATAGCACCG
*
41875046 GACAATAAGCTAAAGAAATATCACCG
1 GACAATAAGCTAAAGAAATAGCACCG
*
41875072 GACAATAAGCTAGAGAAATAGCACCG
1 GACAATAAGCTAAAGAAATAGCACCG
41875098 GACA
1 GACA
41875102 TCTTTTATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.12
Consensus pattern (26 bp):
GACAATAAGCTAAAGAAATAGCACCG
Found at i:41876725 original size:38 final size:38
Alignment explanation
Indices: 41876683--41876760 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
41876673 CACTCTAGTT
41876683 AAATTTAATTTAAGTTAGCTACAGCTTAAGATAACAGA
1 AAATTTAATTTAAGTTAGCTACAGCTTAAGATAACAGA
41876721 AAATTTAATTTAAGTTAGCTACAGCTTAAGATAACAGA
1 AAATTTAATTTAAGTTAGCTACAGCTTAAGATAACAGA
41876759 AA
1 AA
41876761 CAACTCAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (38 bp):
AAATTTAATTTAAGTTAGCTACAGCTTAAGATAACAGA
Done.