Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 119 of 145
Found at i:39758214 original size:27 final size:26
Alignment explanation
Indices: 39758175--39758391 Score: 229
Period size: 27 Copynumber: 8.1 Consensus size: 26
39758165 GGTCATATCA
*
39758175 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCA-TTTACCCTATGGGGGTATTTCG
*
39758202 ATCATGTTACCCTATGGGGGTATTTCG
1 GTCAT-TTACCCTATGGGGGTATTTCG
* *
39758229 ATCATTTTACCCTAT-GGGGTATTTTG
1 GTCA-TTTACCCTATGGGGGTATTTCG
* *
39758255 GTCATTCTACCCTATGGGGCTATTTTG
1 GTCATT-TACCCTATGGGGGTATTTCG
*
39758282 GTCATTTTACCCTATGGGGGTGTTTCG
1 GTCA-TTTACCCTATGGGGGTATTTCG
*
39758309 GTCATTTTCACCTATGGGGGTATTTCG
1 GTCATTTAC-CCTATGGGGGTATTTCG
* ** *
39758336 GTTATTCTACCCTATAAGGGTATTTCA
1 GTCATT-TACCCTATGGGGGTATTTCG
* *
39758363 ATCATTCTACCCTATGGGGGGATTTCG
1 GTCATT-TACCCTATGGGGGTATTTCG
39758390 GT
1 GT
39758392 TGCAATAGTG
Statistics
Matches: 161, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.01
26 26 0.16
27 128 0.80
28 5 0.03
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.40
Consensus pattern (26 bp):
GTCATTTACCCTATGGGGGTATTTCG
Found at i:39758308 original size:80 final size:80
Alignment explanation
Indices: 39758175--39758389 Score: 272
Period size: 80 Copynumber: 2.7 Consensus size: 80
39758165 GGTCATATCA
* *
39758175 GTCATTTTACCCTATGAGGGTATTTCGATCATGTTACCCTATGGGGGTATTTCGATCATTTT-AC
1 GTCATTCTACCCTATG-GGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGATCATTTTCA-
*
39758239 CCTAT-GGGGTATTTTG
64 CCTATGGGGGTATTTCG
* * * *
39758255 GTCATTCTACCCTATGGGGCTATTTTGGTCATTTTACCCTATGGGGGTGTTTCGGTCATTTTCAC
1 GTCATTCTACCCTATGGGG-TATTTCGATCATTTTACCCTATGGGGGTATTTCGATCATTTTCAC
39758320 CTATGGGGGTATTTCG
65 CTATGGGGGTATTTCG
* * * * *
39758336 GTTATTCTACCCTATAAGGGTATTTCAATCATTCTACCCTATGGGGGGATTTCG
1 GTCATTCTACCCTAT-GGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCG
39758390 GTTGCAATAG
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
79 3 0.03
80 57 0.49
81 53 0.46
82 3 0.03
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (80 bp):
GTCATTCTACCCTATGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGATCATTTTCACC
TATGGGGGTATTTCG
Found at i:39758392 original size:54 final size:53
Alignment explanation
Indices: 39758175--39758391 Score: 265
Period size: 54 Copynumber: 4.0 Consensus size: 53
39758165 GGTCATATCA
39758175 GTCATTTTACCCTATGAGGGTATTTCGATCATGTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCGATCAT-TTACCCTATGGGGGTATTTCG
* * * * *
39758229 ATCATTTTACCCTATG-GGGTATTTTGGTCATTCTACCCTATGGGGCTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCGATCATT-TACCCTATGGGGGTATTTCG
* * * *
39758282 GTCATTTTACCCTATGGGGGTGTTTCGGTCATTTTCACCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCGATCATTTAC-CCTATGGGGGTATTTCG
* * * * *
39758336 GTTATTCTACCCTATAAGGGTATTTCAATCATTCTACCCTATGGGGGGATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCGATCATT-TACCCTATGGGGGTATTTCG
39758390 GT
1 GT
39758392 TGCAATAGTG
Statistics
Matches: 139, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
52 1 0.01
53 48 0.35
54 88 0.63
55 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.40
Consensus pattern (53 bp):
GTCATTTTACCCTATGAGGGTATTTCGATCATTTACCCTATGGGGGTATTTCG
Found at i:39773031 original size:27 final size:26
Alignment explanation
Indices: 39772994--39773108 Score: 97
Period size: 27 Copynumber: 4.3 Consensus size: 26
39772984 AGAGGTCAAT
*
39772994 AAATGATCGAATTACCCCCACAGGATA
1 AAATGACCGAATTACCCCCACAGG-TA
** *
39773021 AAATGACCGAATTACCCTTATACGGTA
1 AAATGACCGAATTACCCCCACA-GGTA
**
39773048 AAATGACCGAATTACCCTAATC-GGTTA
1 AAATGACCGAATTACCCCCA-CAGG-TA
* * *
39773075 AAATGACAGAAATACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCACA-GGTA
39773102 AAATGAC
1 AAATGAC
39773109 TGTTATACCC
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
26 2 0.03
27 66 0.92
28 4 0.06
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.21
Consensus pattern (26 bp):
AAATGACCGAATTACCCCCACAGGTA
Found at i:39773497 original size:28 final size:28
Alignment explanation
Indices: 39773457--39773530 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
39773447 ACCGATATTG
*
39773457 TATTGGGCTAAGGCCCATATTGTTACTA
1 TATTGGGCTAAGGCCCACATTGTTACTA
* *
39773485 TATTGGGCTAAGGCCCGCATTGTTACTG
1 TATTGGGCTAAGGCCCACATTGTTACTA
39773513 TATTGGGCTAAGGCCCAC
1 TATTGGGCTAAGGCCCAC
39773531 GCTGTATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (28 bp):
TATTGGGCTAAGGCCCACATTGTTACTA
Found at i:39777307 original size:31 final size:32
Alignment explanation
Indices: 39777271--39777335 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
39777261 CTTAGATAAT
39777271 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
39777302 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
39777334 TT
1 TT
39777336 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:39790439 original size:20 final size:21
Alignment explanation
Indices: 39790398--39790439 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
39790388 GAATTAAGCG
*
39790398 AAGTTACGGTTTATCCAACAC
1 AAGTTACGGTTTATCAAACAC
39790419 AAGTTACGGTTT-TCAAACAC
1 AAGTTACGGTTTATCAAACAC
39790439 A
1 A
39790440 CTACCATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (21 bp):
AAGTTACGGTTTATCAAACAC
Found at i:39802334 original size:15 final size:15
Alignment explanation
Indices: 39802296--39802334 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
39802286 AAAGGAAAAT
*
39802296 AATTTAAAAACTTAA
1 AATTTGAAAACTTAA
*
39802311 ATTTTTGAAAACTTAA
1 A-ATTTGAAAACTTAA
39802327 AATTTGAA
1 AATTTGAA
39802335 GAAACGAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (15 bp):
AATTTGAAAACTTAA
Found at i:39802585 original size:22 final size:23
Alignment explanation
Indices: 39802555--39802598 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
39802545 CACTCGTGTT
*
39802555 TTCTTGCCAG-GAATATTTCCTG
1 TTCTAGCCAGAGAATATTTCCTG
39802577 TTCTAGCCAGAGAATATTTCCT
1 TTCTAGCCAGAGAATATTTCCT
39802599 ATTCATCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (23 bp):
TTCTAGCCAGAGAATATTTCCTG
Found at i:39805519 original size:29 final size:29
Alignment explanation
Indices: 39805486--39805714 Score: 178
Period size: 29 Copynumber: 7.9 Consensus size: 29
39805476 TCATCGACCA
39805486 ATGAAAAGGGATGGTGACGACCATCAACT
1 ATGAAAAGGGATGGTGACGACCATCAACT
* *
39805515 ATGAAAAGGGATGGTGACGATCATCAATT
1 ATGAAAAGGGATGGTGACGACCATCAACT
* * * * * *
39805544 ATTAAAAGGGATAGCT-TCGACTA-CTGATT
1 ATGAAAAGGGAT-GGTGACGACCATC-AACT
* *
39805573 ATTAAAAGGGATGGTGATGACCATCAACT
1 ATGAAAAGGGATGGTGACGACCATCAACT
* ** *
39805602 GTGAAAAGCAATGGTGATGACCATCGAA-T
1 ATGAAAAGGGATGGTGACGACCATC-AACT
* * * * *
39805631 ATGAAAAGGGATAGTTG-CGGCTATCGATT
1 ATGAAAAGGGAT-GGTGACGACCATCAACT
* * *
39805660 ATGAAAAGGGACGGTGATGACCAGCAACT
1 ATGAAAAGGGATGGTGACGACCATCAACT
* *
39805689 ACGAAAAGGTATGGTGACGACCATCA
1 ATGAAAAGGGATGGTGACGACCATCA
39805715 TCTTTCCACT
Statistics
Matches: 153, Mismatches: 39, Indels: 16
0.74 0.19 0.08
Matches are distributed among these distances:
28 7 0.05
29 138 0.90
30 8 0.05
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACGACCATCAACT
Found at i:39805638 original size:87 final size:87
Alignment explanation
Indices: 39805486--39805714 Score: 293
Period size: 87 Copynumber: 2.6 Consensus size: 87
39805476 TCATCGACCA
* * * *
39805486 ATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTGACGATCATCAATTATTAAAA
1 ATGAAAAGGGATGGTGATGACCATCAACTATGAAAAGGAATGGTGACGACCATCAATTATGAAAA
39805551 GGGATAGCTT-CGACTA-CTGATT
66 GGGATAG-TTGCGACTATC-GATT
* * * *
39805573 ATTAAAAGGGATGGTGATGACCATCAACTGTGAAAAGCAATGGTGATGACCATCGAA-TATGAAA
1 ATGAAAAGGGATGGTGATGACCATCAACTATGAAAAGGAATGGTGACGACCATC-AATTATGAAA
*
39805637 AGGGATAGTTGCGGCTATCGATT
65 AGGGATAGTTGCGACTATCGATT
* * * *
39805660 ATGAAAAGGGACGGTGATGACCAGCAACTACGAAAAGGTATGGTGACGACCATCA
1 ATGAAAAGGGATGGTGATGACCATCAACTATGAAAAGGAATGGTGACGACCATCA
39805715 TCTTTCCACT
Statistics
Matches: 122, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
86 3 0.02
87 116 0.95
88 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (87 bp):
ATGAAAAGGGATGGTGATGACCATCAACTATGAAAAGGAATGGTGACGACCATCAATTATGAAAA
GGGATAGTTGCGACTATCGATT
Found at i:39813156 original size:42 final size:42
Alignment explanation
Indices: 39813097--39813181 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
39813087 AGAGAAGAAG
39813097 AAAATTCACTATGTCGAATTCGAATGATTACAAGAGTAGACT
1 AAAATTCACTATGTCGAATTCGAATGATTACAAGAGTAGACT
*
39813139 AAAATTCACTATGTCGAATTCGGATGATTACAAGAGTAGACT
1 AAAATTCACTATGTCGAATTCGAATGATTACAAGAGTAGACT
39813181 A
1 A
39813182 TGTCTATTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (42 bp):
AAAATTCACTATGTCGAATTCGAATGATTACAAGAGTAGACT
Found at i:39818472 original size:30 final size:30
Alignment explanation
Indices: 39818438--39818499 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
39818428 TCTTTTTGAA
* *
39818438 AATATTTACAAAAAGAGGAATCTAATTTTT
1 AATATTTACAAAAAGAGGAACCAAATTTTT
*
39818468 AATATTTACAAAAAGAGTAACCAAATTTTT
1 AATATTTACAAAAAGAGGAACCAAATTTTT
39818498 AA
1 AA
39818500 AAATAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGAACCAAATTTTT
Found at i:39818568 original size:7 final size:7
Alignment explanation
Indices: 39818556--39818596 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
39818546 GTTGCAACAT
39818556 AAAATTC
1 AAAATTC
39818563 AAAATTC
1 AAAATTC
39818570 AAAATTC
1 AAAATTC
39818577 AAAATTC
1 AAAATTC
39818584 AAAATTC
1 AAAATTC
39818591 AAAATT
1 AAAATT
39818597 GACCCTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATTC
Found at i:39819327 original size:32 final size:32
Alignment explanation
Indices: 39819284--39819351 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
39819274 GTGTCTTATA
39819284 TGCCTTCGATCTCCTTGTTTGCCAGTTCAGCT
1 TGCCTTCGATCTCCTTGTTTGCCAGTTCAGCT
*
39819316 TGCCTTTGATCTCCTTGTTTGCCAGTTCAGCT
1 TGCCTTCGATCTCCTTGTTTGCCAGTTCAGCT
39819348 TGCC
1 TGCC
39819352 GTTGGTTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.09, C:0.31, G:0.19, T:0.41
Consensus pattern (32 bp):
TGCCTTCGATCTCCTTGTTTGCCAGTTCAGCT
Found at i:39821793 original size:43 final size:41
Alignment explanation
Indices: 39821725--39821839 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 41
39821715 TATGTTCAGT
*
39821725 GATACGGGGAATCATCACATAGCAACCCCTTTCACAATCAAG
1 GATACGGGGAATCAGCACATAGCAACCCCTTT-ACAATCAAG
* * * *
39821767 GATACGGTGGATTCAGCACCTAGCAACCACCTTTAGAATCAAT
1 GATACGG-GGAATCAGCACATAGCAACC-CCTTTACAATCAAG
* * *
39821810 AATTCGGGGAATCAGCACTTAGCAACCCCT
1 GATACGGGGAATCAGCACATAGCAACCCCT
39821840 CAGGGAATCT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
41 3 0.05
42 25 0.40
43 29 0.47
44 5 0.08
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (41 bp):
GATACGGGGAATCAGCACATAGCAACCCCTTTACAATCAAG
Found at i:39821835 original size:42 final size:43
Alignment explanation
Indices: 39821687--39821836 Score: 139
Period size: 42 Copynumber: 3.6 Consensus size: 43
39821677 AACCGTTACT
* * * *
39821687 CGGTGGAATTAGCACTTAGCAACCAAC-TTATG-TTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-GAATCAATGATA
* * * *
39821729 CGG-GGAATCATCACATAGCAACC-CCTTTCACAATCAAGGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-AGAATCAATGATA
* * * *
39821771 CGGTGGATTCAGCACCTAGCAACCACCTTTAGAATCAATAATT
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATGATA
39821814 CGG-GGAATCAGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
39821837 CCTCAGGGAA
Statistics
Matches: 86, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
40 1 0.01
41 19 0.22
42 32 0.37
43 29 0.34
44 5 0.06
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATGATA
Found at i:39821845 original size:26 final size:26
Alignment explanation
Indices: 39821816--39821866 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
39821806 CAATAATTCG
39821816 GGGAATCAGCACTTAGCAACCCCTCA
1 GGGAATCAGCACTTAGCAACCCCTCA
*
39821842 GGGAATCTGCACTTAGCAACCCCTC
1 GGGAATCAGCACTTAGCAACCCCTC
39821867 TTTGATCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.35, G:0.20, T:0.18
Consensus pattern (26 bp):
GGGAATCAGCACTTAGCAACCCCTCA
Found at i:39821948 original size:41 final size:41
Alignment explanation
Indices: 39821839--39821948 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
39821829 TAGCAACCCC
* *
39821839 TCAGGGAATCTGCACTTAGCAACCCCTCTTTGATCAGTGAT
1 TCAGGGAATCTGCACTTAGCAACCCCTTTTTGATCAATGAT
39821880 TCAGGGAATCTGCACTTAGCAACCCCTTTTTGATCAATGAT
1 TCAGGGAATCTGCACTTAGCAACCCCTTTTTGATCAATGAT
* * *
39821921 TCGGGGAATCTGCAGTTTGCAACCCCTT
1 TCAGGGAATCTGCACTTAGCAACCCCTT
39821949 ACATTCAATG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (41 bp):
TCAGGGAATCTGCACTTAGCAACCCCTTTTTGATCAATGAT
Found at i:39822967 original size:42 final size:42
Alignment explanation
Indices: 39822823--39822973 Score: 159
Period size: 42 Copynumber: 3.6 Consensus size: 42
39822813 TAACCGTTAC
* * *
39822823 TCGGTGGAATCAGCACTTAGCAACCAAC-TTATATTCAGTGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCTTTATAATCAAT-AT
* * * *
39822865 ACGG-GGAATCAACACATAGCAACC-CCTTTCACAATCAAGTAT
1 TCGGTGGAATCAGCACTTAGCAACCACCTTT-ATAATCAA-TAT
39822907 AT-GGTGGAATCAGCACTTAGCAACCACCTTTATAATCAATAAT
1 -TCGGTGGAATCAGCACTTAGCAACCACCTTTATAATCAAT-AT
39822950 TCGG-GGAATCAGCACTTAGCAACC
1 TCGGTGGAATCAGCACTTAGCAACC
39822974 CCTCGGGGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
40 1 0.01
41 20 0.22
42 34 0.38
43 30 0.33
44 5 0.06
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (42 bp):
TCGGTGGAATCAGCACTTAGCAACCACCTTTATAATCAATAT
Found at i:39822995 original size:26 final size:26
Alignment explanation
Indices: 39822950--39823002 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
39822940 AATCAATAAT
*
39822950 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACGTAGCAACCCC
39822976 TCGGGGAATCTA-CACGTAGCAACCCC
1 TCGGGGAATC-AGCACGTAGCAACCCC
39823002 T
1 T
39823003 TTTTAATCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (26 bp):
TCGGGGAATCAGCACGTAGCAACCCC
Found at i:39823037 original size:41 final size:41
Alignment explanation
Indices: 39822976--39823085 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
39822966 TAGCAACCCC
*
39822976 TCGGGGAATCTACACGTAGCAACCCCTTTTTAATCAGTGAT
1 TCGGGGAATCTACACTTAGCAACCCCTTTTTAATCAGTGAT
* * *
39823017 TCGGGGAATTTGCACTTAGCAACCCCTTTTTGATCAGTGAT
1 TCGGGGAATCTACACTTAGCAACCCCTTTTTAATCAGTGAT
*
39823058 TCGGGGAATCTACGCTTAGCAACCCCTT
1 TCGGGGAATCTACACTTAGCAACCCCTT
39823086 ACATTTGATG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (41 bp):
TCGGGGAATCTACACTTAGCAACCCCTTTTTAATCAGTGAT
Found at i:39823174 original size:19 final size:19
Alignment explanation
Indices: 39823133--39823176 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
39823123 CGGGAACCTT
* *
39823133 ATTTTACAACATTTTACCA
1 ATTTTTCAACATTTAACCA
39823152 ATTTTTCAA-ATTTAACCA
1 ATTTTTCAACATTTAACCA
39823170 CATTTTT
1 -ATTTTT
39823177 TGTAATCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTTCAACATTTAACCA
Found at i:39837301 original size:15 final size:16
Alignment explanation
Indices: 39837281--39837313 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39837271 GAGAAAATTC
*
39837281 ATTCAATAT-TTCACT
1 ATTCAACATGTTCACT
39837296 ATTCAACATGTTCACT
1 ATTCAACATGTTCACT
39837312 AT
1 AT
39837314 GACCGAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTCAACATGTTCACT
Found at i:39838400 original size:17 final size:17
Alignment explanation
Indices: 39838373--39838417 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
39838363 TGATAAGTGG
*
39838373 CATTGTAAGAACGTTTA
1 CATTGTGAGAACGTTTA
* *
39838390 CTTTGTGAGAATGTTTA
1 CATTGTGAGAACGTTTA
39838407 CATTGTGAGAA
1 CATTGTGAGAA
39838418 AGGCAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (17 bp):
CATTGTGAGAACGTTTA
Found at i:39840105 original size:58 final size:57
Alignment explanation
Indices: 39839982--39840113 Score: 144
Period size: 58 Copynumber: 2.3 Consensus size: 57
39839972 TGATTATCTT
* * * * *
39839982 AATATTAAATTTAATTTAATGTTTTATCTTTAAATATTCTATTAATTTCATACGATTT
1 AATATTAAATTTAATCTAATGATTTATCTTTAAATATTATATTAATTTAATAC-ATTA
39840040 AATATTAAATTTAATCTAAT-ATTTATCTTGATAAATATTATATTAATTTAAT-C-TTA
1 AATATTAAATTTAATCTAATGATTTATCTT--TAAATATTATATTAATTTAATACATTA
*
39840096 AAGTGATTAAGTTTAATC
1 AA-T-ATTAAATTTAATC
39840114 ACAATTGAAC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
56 4 0.06
57 9 0.14
58 32 0.50
59 19 0.30
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (57 bp):
AATATTAAATTTAATCTAATGATTTATCTTTAAATATTATATTAATTTAATACATTA
Found at i:39840625 original size:22 final size:22
Alignment explanation
Indices: 39840600--39840644 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39840590 GGATCTATTT
* *
39840600 TGCTTGGGTCCTATCTGATGTA
1 TGCTTGAGTCCTATCCGATGTA
39840622 TGCTTGAGTCCTATCCGATGTA
1 TGCTTGAGTCCTATCCGATGTA
39840644 T
1 T
39840645 TGTAGTCCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (22 bp):
TGCTTGAGTCCTATCCGATGTA
Found at i:39848960 original size:151 final size:151
Alignment explanation
Indices: 39848686--39848988 Score: 491
Period size: 151 Copynumber: 2.0 Consensus size: 151
39848676 TATGCTTCGG
*
39848686 TGCTGTGTATTAAAATTCGAAGGCAATTGGGAAAAATACCTGCCTTTAGTCGAATTCACATATAA
1 TGCTGTGTATTAAAATTCAAAGGCAATTGGGAAAAATACCTGCCTTTAGTCGAATTCACATATAA
* * *
39848751 TAATAATTATCAGTCAAGTATTAATATGGCACCATATGAGGCTCTGTATGGTTCTAAATGTAGAA
66 TAACAATTATCAGTCAAGTATTAAGATGGCACCATATGAGGCTCTATATGGTTCTAAATGTAGAA
*
39848816 CTCCATTGTATTGGACTGAGC
131 CTCCATTGTATTGGACTAAGC
* * * *
39848837 TGCTGTGTGTTAGAATTCAAAGGCAATTGGGAAAAATACCTGTCTTTAGTCGAATTCGCATATAA
1 TGCTGTGTATTAAAATTCAAAGGCAATTGGGAAAAATACCTGCCTTTAGTCGAATTCACATATAA
* *
39848902 TAACAGTTATCAGTCAAGTATTAAGATGGCACCGTATGAGGCTCTATATGG-TCATAAATGTAGA
66 TAACAATTATCAGTCAAGTATTAAGATGGCACCATATGAGGCTCTATATGGTTC-TAAATGTAGA
39848966 ACTCCATTGTATTGGACTAAGC
130 ACTCCATTGTATTGGACTAAGC
39848988 T
1 T
39848989 CAGTGAGAAA
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
150 2 0.01
151 138 0.99
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (151 bp):
TGCTGTGTATTAAAATTCAAAGGCAATTGGGAAAAATACCTGCCTTTAGTCGAATTCACATATAA
TAACAATTATCAGTCAAGTATTAAGATGGCACCATATGAGGCTCTATATGGTTCTAAATGTAGAA
CTCCATTGTATTGGACTAAGC
Found at i:39850603 original size:20 final size:20
Alignment explanation
Indices: 39850575--39850612 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39850565 GCTTCGGCTA
* *
39850575 TAATGGGCCATGTTGGGCCG
1 TAATAGGCCATATTGGGCCG
39850595 TAATAGGCCATATTGGGC
1 TAATAGGCCATATTGGGC
39850613 AGAGATGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.26
Consensus pattern (20 bp):
TAATAGGCCATATTGGGCCG
Found at i:39850623 original size:20 final size:20
Alignment explanation
Indices: 39850575--39850623 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
39850565 GCTTCGGCTA
* *
39850575 TAATGGGCCATGTTGGGCCG
1 TAATGGGCCATATTGGGCAG
*
39850595 TAATAGGCCATATTGGGCAG
1 TAATGGGCCATATTGGGCAG
39850615 -AGATGGGCC
1 TA-ATGGGCC
39850624 TGTGGGCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (20 bp):
TAATGGGCCATATTGGGCAG
Found at i:39850909 original size:27 final size:27
Alignment explanation
Indices: 39850878--39850958 Score: 135
Period size: 27 Copynumber: 3.0 Consensus size: 27
39850868 ACCCTAAAAT
39850878 AGGTAAAATGACCGAAATACCCCCATA
1 AGGTAAAATGACCGAAATACCCCCATA
* *
39850905 AGGTAAAATGATCGAAATACCCCCGTA
1 AGGTAAAATGACCGAAATACCCCCATA
*
39850932 AGGTAAAATGACCGAAATACCCTCATA
1 AGGTAAAATGACCGAAATACCCCCATA
39850959 GGCTCTCATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.17
Consensus pattern (27 bp):
AGGTAAAATGACCGAAATACCCCCATA
Found at i:39851015 original size:27 final size:26
Alignment explanation
Indices: 39850965--39851040 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
39850955 CATAGGCTCT
* ***
39850965 CATAAGGTAAAATGACTAAAATACCCC
1 CATAGGGTAAAATGACTGTTATA-CCC
39850992 CATAGGGTAAAATGACTGTTATACCC
1 CATAGGGTAAAATGACTGTTATACCC
*
39851018 C-TAGGAGATGAAATGACTGTTAT
1 CATAGG-G-TAAAATGACTGTTAT
39851041 GGCATTATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 4 0.10
26 5 0.12
27 33 0.79
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (26 bp):
CATAGGGTAAAATGACTGTTATACCC
Found at i:39853970 original size:26 final size:26
Alignment explanation
Indices: 39853913--39853975 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
39853903 GTCCTGATAT
39853913 ATGGCTCTTCGTGAGCTTTCCGATTA
1 ATGGCTCTTCGTGAGCTTTCCGATTA
* * *
39853939 AAGGCTCTTTGTGAGC-TTCTTGATTA
1 ATGGCTCTTCGTGAGCTTTC-CGATTA
*
39853965 TTGGCTCTTCG
1 ATGGCTCTTCG
39853976 AAGATTCCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (26 bp):
ATGGCTCTTCGTGAGCTTTCCGATTA
Found at i:39857920 original size:18 final size:18
Alignment explanation
Indices: 39857880--39857917 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
39857870 ATATTAACAC
*
39857880 AAATTTACATTTAATACT
1 AAATTTACATTTAATAAT
*
39857898 AAATTTA-ATTTATTAAT
1 AAATTTACATTTAATAAT
39857915 AAA
1 AAA
39857918 ATTATGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTTACATTTAATAAT
Found at i:39861125 original size:1 final size:1
Alignment explanation
Indices: 39861119--39861215 Score: 113
Period size: 1 Copynumber: 97.0 Consensus size: 1
39861109 TAACCATTAC
* * * * *
39861119 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAACAAAAACAAAAACAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
39861184 ACAAACAAAAAACAAAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39861216 CATATTTTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 78 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39863619 original size:45 final size:46
Alignment explanation
Indices: 39863568--39863769 Score: 212
Period size: 46 Copynumber: 4.4 Consensus size: 46
39863558 ATGTCGTAGC
* * * * *
39863568 GTCTTTCATCCATGGTCTTATTTA-TTTCCATCGTGATGCCATAGT
1 GTCTTTCAACAATGGTCTTATTCATTTTCCGTCATGATGCCATAGT
* * * *
39863613 GTCTTTCAACTATGGTCTTATTCATTTT-TGTCATGTTGTCATAGT
1 GTCTTTCAACAATGGTCTTATTCATTTTCCGTCATGATGCCATAGT
* * *
39863658 GTCTTTCAACAATGGTCTTATTTATTTTCCGTTAT-ATTGTCATAGT
1 GTCTTTCAACAATGGTCTTATTCATTTTCCGTCATGA-TGCCATAGT
* * * * * *
39863704 GTCTTTCAACTATAGTTTTATTCATTTTTCGTCTTGTTGCCATAGT
1 GTCTTTCAACAATGGTCTTATTCATTTTCCGTCATGATGCCATAGT
39863750 GTCTTTCAACAATGGTCTTA
1 GTCTTTCAACAATGGTCTTA
39863770 CACGTTTGAA
Statistics
Matches: 128, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
45 59 0.46
46 69 0.54
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (46 bp):
GTCTTTCAACAATGGTCTTATTCATTTTCCGTCATGATGCCATAGT
Found at i:39863725 original size:91 final size:91
Alignment explanation
Indices: 39863559--39863769 Score: 282
Period size: 91 Copynumber: 2.3 Consensus size: 91
39863549 TTTCAAAGAA
* * * * *
39863559 TGTCGTAGCGTCTTTCATCCATGGTCTTATTTATTTCCATCGTGATGCCATAGTGTCTTTCAACT
1 TGTCATAGTGTCTTTCAACAATGGTCTTATTTATTTCCATCATGATGCCATAGTGTCTTTCAACT
*
39863624 ATGGTCTTATTCATTTTT-GTCATGT
66 ATAGTCTTATTCATTTTTCGTCATGT
* * *
39863649 TGTCATAGTGTCTTTCAACAATGGTCTTATTTATTTTCCGTTAT-ATTGTCATAGTGTCTTTCAA
1 TGTCATAGTGTCTTTCAACAATGGTCTTATTTA-TTTCCATCATGA-TGCCATAGTGTCTTTCAA
* *
39863713 CTATAGTTTTATTCATTTTTCGTCTTGT
64 CTATAGTCTTATTCATTTTTCGTCATGT
*
39863741 TGCCATAGTGTCTTTCAACAATGGTCTTA
1 TGTCATAGTGTCTTTCAACAATGGTCTTA
39863770 CACGTTTGAA
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
90 30 0.28
91 42 0.40
92 34 0.32
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (91 bp):
TGTCATAGTGTCTTTCAACAATGGTCTTATTTATTTCCATCATGATGCCATAGTGTCTTTCAACT
ATAGTCTTATTCATTTTTCGTCATGT
Found at i:39863790 original size:91 final size:90
Alignment explanation
Indices: 39863607--39863814 Score: 247
Period size: 91 Copynumber: 2.3 Consensus size: 90
39863597 ATCGTGATGC
* *
39863607 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTTGTCATGTTGTCATAGTGTCTTTCAACAATG
1 CATAGTGTCTTTCAACTATAGTCTTATTCATTTTTGTCATGTTGCCATAGTGTCTTTCAACAATG
* * ** * *
39863672 GTCTTATTTATTTTCCGTTATATTGT
66 GTCTTA-TCAGTTTCAATTACAATGT
* *
39863698 CATAGTGTCTTTCAACTATAGTTTTATTCATTTTTCGTCTTGTTGCCATAGTGTCTTTCAACAAT
1 CATAGTGTCTTTCAACTATAGTCTTATTCATTTTT-GTCATGTTGCCATAGTGTCTTTCAACAAT
* *
39863763 GGTCTTA-CACGTTTGAATTGCAATGT
65 GGTCTTATCA-GTTTCAATTACAATGT
** *
39863789 CATAACGTCTTTCAACTATGGTCTTA
1 CATAGTGTCTTTCAACTATAGTCTTA
39863815 CTCGTTTGAA
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
90 1 0.01
91 64 0.65
92 34 0.34
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (90 bp):
CATAGTGTCTTTCAACTATAGTCTTATTCATTTTTGTCATGTTGCCATAGTGTCTTTCAACAATG
GTCTTATCAGTTTCAATTACAATGT
Found at i:39863861 original size:45 final size:45
Alignment explanation
Indices: 39863741--39863866 Score: 162
Period size: 45 Copynumber: 2.8 Consensus size: 45
39863731 TTCGTCTTGT
* * * *
39863741 TGCCATAGTGTCTTTCAACAATGGTCTTACACGTTTGAATTGCAA
1 TGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTTGAACTGCAA
* * **
39863786 TGTCATAACGTCTTTCAACTATGGTCTTACTCGTTTGAACTGTGA
1 TGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTTGAACTGCAA
* *
39863831 TGCCATAGCGTCTTTCAGCTATGGTCTTACTTGTTT
1 TGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTT
39863867 TTCAACCAAC
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (45 bp):
TGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTTGAACTGCAA
Found at i:39877870 original size:24 final size:24
Alignment explanation
Indices: 39877838--39877888 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
39877828 TTATGTAAGT
*
39877838 GTTTCAGATTATGAGGACTCTATA
1 GTTTCAGATTATGAGGACTCTACA
* * *
39877862 GTTTTAGATTCTGTGGACTCTACA
1 GTTTCAGATTATGAGGACTCTACA
39877886 GTT
1 GTT
39877889 AAGGATATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (24 bp):
GTTTCAGATTATGAGGACTCTACA
Found at i:39882216 original size:18 final size:17
Alignment explanation
Indices: 39882182--39882235 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 17
39882172 GCAGTAAAAA
39882182 AATGTTTGGAAATTGAAT
1 AATGTTTGGAAA-TGAAT
*
39882200 AATGATTTGTAAATGAAT
1 AATG-TTTGGAAATGAAT
39882218 AATGTGTTGGAAATGAAT
1 AATGT-TTGGAAATGAAT
39882236 GACACGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 24 0.75
19 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (17 bp):
AATGTTTGGAAATGAAT
Found at i:39894464 original size:20 final size:18
Alignment explanation
Indices: 39894439--39894478 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
39894429 CTTAAAAGAT
39894439 AAATAAAACTAATACCTATA
1 AAATAAAACTAA-A-CTATA
*
39894459 AAATAAAATTAAACTATA
1 AAATAAAACTAAACTATA
39894477 AA
1 AA
39894479 CTTTAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATAAAACTAAACTATA
Found at i:39896423 original size:19 final size:19
Alignment explanation
Indices: 39896399--39896436 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39896389 GTGTTGGTAA
39896399 GTGAGCATCTAGTGATTTT
1 GTGAGCATCTAGTGATTTT
39896418 GTGAGCATCTAGTGATTTT
1 GTGAGCATCTAGTGATTTT
39896437 ATGTGCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (19 bp):
GTGAGCATCTAGTGATTTT
Found at i:39898314 original size:15 final size:16
Alignment explanation
Indices: 39898294--39898327 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
39898284 ACAAAAATGG
39898294 TATGAAATGT-ACATA
1 TATGAAATGTAACATA
*
39898309 TATGAAATTTAACATA
1 TATGAAATGTAACATA
39898325 TAT
1 TAT
39898328 AAGCATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (16 bp):
TATGAAATGTAACATA
Found at i:39899798 original size:15 final size:15
Alignment explanation
Indices: 39899778--39899829 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
39899768 CATGGACGAA
39899778 TGTGTGGTATGACCG
1 TGTGTGGTATGACCG
* * *
39899793 TGTGTGGCA-CACAG
1 TGTGTGGTATGACCG
*
39899807 ATGTGTGGTGTGACCG
1 -TGTGTGGTATGACCG
39899823 TGTGTGG
1 TGTGTGG
39899830 CACACGGCCA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 3 0.11
15 22 0.79
16 3 0.11
ACGTcount: A:0.13, C:0.13, G:0.42, T:0.31
Consensus pattern (15 bp):
TGTGTGGTATGACCG
Found at i:39899813 original size:30 final size:30
Alignment explanation
Indices: 39899777--39899834 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
39899767 ACATGGACGA
39899777 ATGTGTGGTATGACCGTGTGTGGCACACAG
1 ATGTGTGGTATGACCGTGTGTGGCACACAG
*
39899807 ATGTGTGGTGTGACCGTGTGTGGCACAC
1 ATGTGTGGTATGACCGTGTGTGGCACAC
39899835 GGCCATGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (30 bp):
ATGTGTGGTATGACCGTGTGTGGCACACAG
Found at i:39902278 original size:20 final size:20
Alignment explanation
Indices: 39902237--39902279 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39902227 TAAAAAATCA
* *
39902237 AAAGTATCGATACCTTTAAC
1 AAAGTATCAATACCTCTAAC
*
39902257 AAAGTATCAATACCTCTGAC
1 AAAGTATCAATACCTCTAAC
39902277 AAA
1 AAA
39902280 AGAACCGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (20 bp):
AAAGTATCAATACCTCTAAC
Found at i:39903377 original size:42 final size:42
Alignment explanation
Indices: 39903314--39903412 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
39903304 CTCTCGGTAT
* *
39903314 CGCACACTTAGTGCCCGTTATTCAACATCATTATTATAATTC
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
* * *
39903356 CGCACACTTAGTGCCTATTATTCAACATCATCATTTTAATTT
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
**
39903398 TACACACTTAGTGCC
1 CGCACACTTAGTGCC
39903413 ATTCATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (42 bp):
CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
Found at i:39905779 original size:10 final size:10
Alignment explanation
Indices: 39905764--39905826 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
39905754 TTTAGAATAC
39905764 TTTTTTTAAA
1 TTTTTTTAAA
39905774 TTTTTTT-AA
1 TTTTTTTAAA
*
39905783 --TTTTAAAA
1 TTTTTTTAAA
*
39905791 TATTTTTAAAA
1 T-TTTTTTAAA
*
39905802 TACTTTTTAAA
1 T-TTTTTTAAA
*
39905813 TTTTTTTTAA
1 TTTTTTTAAA
39905823 TTTT
1 TTTT
39905827 AAAATATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
7 4 0.09
8 2 0.05
9 2 0.05
10 18 0.41
11 18 0.41
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:39905780 original size:41 final size:41
Alignment explanation
Indices: 39905743--39905858 Score: 184
Period size: 40 Copynumber: 2.9 Consensus size: 41
39905733 TTTTTTTAAT
* *
39905743 TTTAAAATACTTTTAGAATACTTTTTTTAAATTTTTTTAAT
1 TTTAAAATATTTTTAAAATACTTTTTTTAAATTTTTTTAAT
39905784 TTTAAAATATTTTTAAAATAC--TTTTTAAATTTTTTTTAAT
1 TTTAAAATATTTTTAAAATACTTTTTTTAAA-TTTTTTTAAT
39905824 TTTAAAATATTTTTAAAATACTTTTTTT-AATTTTT
1 TTTAAAATATTTTTAAAATACTTTTTTTAAATTTTT
39905859 AAAATAAATT
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
39 8 0.11
40 36 0.51
41 21 0.30
42 5 0.07
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (41 bp):
TTTAAAATATTTTTAAAATACTTTTTTTAAATTTTTTTAAT
Found at i:39905837 original size:11 final size:11
Alignment explanation
Indices: 39905783--39905849 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
39905773 ATTTTTTTAA
39905783 TTTTAAAATAT
1 TTTTAAAATAT
39905794 TTTTAAAATACT
1 TTTTAAAATA-T
39905806 TTTT-AAAT-T
1 TTTTAAAATAT
* *
39905815 TTTT---TTAA
1 TTTTAAAATAT
39905823 TTTTAAAATAT
1 TTTTAAAATAT
39905834 TTTTAAAATACT
1 TTTTAAAATA-T
39905846 TTTT
1 TTTT
39905850 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 1 0.02
8 4 0.09
9 5 0.11
11 26 0.57
12 10 0.22
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:39905870 original size:21 final size:21
Alignment explanation
Indices: 39905832--39905871 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39905822 ATTTTAAAAT
**
39905832 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
39905853 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
39905872 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:39905878 original size:22 final size:20
Alignment explanation
Indices: 39905831--39905885 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
39905821 AATTTTAAAA
* *
39905831 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
39905851 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
39905874 TATTTATTAAAA
1 TATTT-TTAAAA
39905886 AATGGGCCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:39906420 original size:22 final size:20
Alignment explanation
Indices: 39906368--39906430 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 20
39906358 CCAGTAACCA
39906368 AAATGGCTAAGAGCCATAAAC
1 AAATGGCTAA-AGCCATAAAC
* *
39906389 AAGATAGCTATAAGCTATAAAC
1 AA-ATGGCTA-AAGCCATAAAC
39906411 AGAATGGCTACAAGCCATAA
1 A-AATGGCTA-AAGCCATAA
39906431 GTATAGTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (20 bp):
AAATGGCTAAAGCCATAAAC
Found at i:39906471 original size:32 final size:32
Alignment explanation
Indices: 39906422--39906528 Score: 146
Period size: 32 Copynumber: 3.4 Consensus size: 32
39906412 GAATGGCTAC
* *
39906422 AAGCCATAAGT-ATAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
39906453 AAGCCATCAGTAATAGTAATATGACCGACACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
39906485 CAGCCATCAGTAAT-GATAATATGATCGGCACA
1 AAGCCATCAGTAATAG-TAATATGATCGGCACA
39906517 AAGCCATCAGTA
1 AAGCCATCAGTA
39906529 GCATCGCAGC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
31 11 0.17
32 55 0.83
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:39906563 original size:26 final size:26
Alignment explanation
Indices: 39906531--39906584 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
39906521 CATCAGTAGC
* *
39906531 ATCGCAGCATAGCTGCTAGCAACAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
39906557 ATCGCAGCAAAGCTGCCAGCAACAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
39906583 AT
1 AT
39906585 ATGTGGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGCAACAGT
Found at i:39906607 original size:27 final size:26
Alignment explanation
Indices: 39906572--39906636 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
39906562 AGCAAAGCTG
*
39906572 CCAGCAACAGTATATGTGGCCA-AGCCA
1 CCAGTAACAGTAT-TGTGG-CAGAGCCA
39906599 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGT-ATTGTGGCAGAGCCA
39906626 CCAGT-ACAGTA
1 CCAGTAACAGTA
39906637 CTTCTTCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 7 0.20
27 25 0.71
28 2 0.06
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (26 bp):
CCAGTAACAGTATTGTGGCAGAGCCA
Found at i:39906725 original size:11 final size:11
Alignment explanation
Indices: 39906709--39906751 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
39906699 AACCAGTCAT
39906709 ACAAATCACAG
1 ACAAATCACAG
*
39906720 ACAAATCAGTCAT
1 ACAAATCA--CAG
*
39906733 ACTAATCACAG
1 ACAAATCACAG
39906744 ACAAATCA
1 ACAAATCA
39906752 ATCATGTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.51, C:0.26, G:0.07, T:0.16
Consensus pattern (11 bp):
ACAAATCACAG
Found at i:39906734 original size:24 final size:24
Alignment explanation
Indices: 39906702--39906774 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
39906692 TGCTTAGAAC
39906702 CAGTCATACAAATCACAGACAAAT
1 CAGTCATACAAATCACAGACAAAT
*
39906726 CAGTCATACTAATCACAGACAAAT
1 CAGTCATACAAATCACAGACAAAT
* ** *
39906750 CAATCATGTAAATCAGAGACAAAT
1 CAGTCATACAAATCACAGACAAAT
39906774 C
1 C
39906775 GATCATTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.19
Consensus pattern (24 bp):
CAGTCATACAAATCACAGACAAAT
Found at i:39906830 original size:24 final size:24
Alignment explanation
Indices: 39906713--39906831 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
39906703 AGTCATACAA
* *
39906713 ATCACAGACAAATCAGTCATACTA-
1 ATCACAGACAAATCAATCAT-TTAC
* *
39906737 ATCACAGACAAATCAATCATGTAA
1 ATCACAGACAAATCAATCATTTAC
* *
39906761 ATCAGAGACAAATCGATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
* * *
39906785 ATCTCGGACAAATCAATTATTTAC
1 ATCACAGACAAATCAATCATTTAC
39906809 ATCACAGACAAATCAATCATTTA
1 ATCACAGACAAATCAATCATTTA
39906832 ACCCCGATAG
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
23 2 0.03
24 78 0.98
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:39906871 original size:27 final size:27
Alignment explanation
Indices: 39906850--39907146 Score: 263
Period size: 27 Copynumber: 11.4 Consensus size: 27
39906840 AGGCAAAATA
*
39906850 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTATG
* *
39906877 GTTATTTTACCCTACAGCGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTATG
* * *
39906904 GTCATTTTACCATACAGGGGCGTTACG
1 GTCATTTTACCCTACAGGGGCATTATG
* *
39906931 GCCATTTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGCATTATG
* *
39906958 GTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTATG
* * * *
39906985 GTTATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTATG
39907012 GTCATTTTACCCT--A----CA--A-G
1 GTCATTTTACCCTACAGGGGCATTATG
* * * *
39907030 ATCATTTTACCTTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTATG
* * * *
39907057 ATCATTTTACCTTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTATG
* * * *
39907084 GTCATTTCACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTATG
** *
39907111 GTCATTTTACCCTACA-GGTTATTATA
1 GTCATTTTACCCTACAGGGGCATTATG
39907137 GTCATTTTAC
1 GTCATTTTAC
39907147 AAATACTGGG
Statistics
Matches: 227, Mismatches: 34, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
18 12 0.05
19 1 0.00
20 1 0.00
21 1 0.00
24 1 0.00
25 1 0.00
26 18 0.08
27 192 0.85
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTATG
Found at i:39906938 original size:54 final size:53
Alignment explanation
Indices: 39906850--39907128 Score: 306
Period size: 54 Copynumber: 5.3 Consensus size: 53
39906840 AGGCAAAATA
*
39906850 GTCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTACAGCGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTACAG-GGTATTATG
* * **
39906904 GTCATTTTACCATACAGGGGCGTTACGGCCATTTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTACA-GGGTATTATG
* *
39906958 GTCATTTTACCCTATAGGGGCATTACGGTTATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTAC-AGGGTATTATG
* * *
39907012 GTCATTTTACCCTACA--AG-A-T-C----ATTTTACCTTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTACA-GGGTATTATG
* * * * * *
39907057 ATCATTTTACCTTACAGGGGTATTACGGTCATTTCACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTAC-AGGGTATTATG
39907111 GTCATTTTACCCTACAGG
1 GTCATTTTACCCTACAGG
39907129 TTATTATAGT
Statistics
Matches: 191, Mismatches: 21, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
44 1 0.01
45 35 0.18
47 1 0.01
48 1 0.01
49 2 0.01
50 2 0.01
51 1 0.01
52 1 0.01
54 144 0.75
55 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (53 bp):
GTCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTACAGGGTATTATG
Found at i:39906944 original size:81 final size:81
Alignment explanation
Indices: 39906850--39907128 Score: 324
Period size: 81 Copynumber: 3.6 Consensus size: 81
39906840 AGGCAAAATA
* * * *
39906850 GTCATTTTACCCTACAGGGGCATTACGGTTATTTTACCCTACAGCGGCATTATGGTCATTTTACC
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACC
**
39906915 ATACAGGGGCGTTACG
66 ATACAGGGGTATTACG
* * * *
39906931 GCCATTTTACCCTACAGGGGTATTATGGTCATTTTACCCTATAGGGGCATTACGGTTATTTTACC
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACC
* *
39906996 CTACAAGGGTATTACG
66 ATACAGGGGTATTACG
* * * *
39907012 GTCATTTTACCCTAC------A--A-GATCATTTTACCTTACAGGGGTATTACGATCATTTTACC
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACC
*
39907068 TTACAGGGGTATTACG
66 ATACAGGGGTATTACG
* *
39907084 GTCATTTCACCCTACAAGGGTATTACGGTCATTTTACCCTACAGG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGG
39907129 TTATTATAGT
Statistics
Matches: 165, Mismatches: 24, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
72 61 0.37
73 1 0.01
75 1 0.01
78 1 0.01
80 1 0.01
81 100 0.61
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (81 bp):
GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACC
ATACAGGGGTATTACG
Found at i:39907078 original size:72 final size:72
Alignment explanation
Indices: 39906959--39907101 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
39906949 GGTATTATGG
* * * *
39906959 TCATTTTACCCTATAGGGGCATTACGGTTATTTTACCCTACAAGGGTATTACGGTCATTTTACCC
1 TCATTTTACCCTACAGGGGCATTACGATCATTTTACCCTACAAGGGTATTACGGTCATTTCACCC
39907024 TACAAGA
66 TACAAGA
* * * *
39907031 TCATTTTACCTTACAGGGGTATTACGATCATTTTACCTTACAGGGGTATTACGGTCATTTCACCC
1 TCATTTTACCCTACAGGGGCATTACGATCATTTTACCCTACAAGGGTATTACGGTCATTTCACCC
39907096 TACAAG
66 TACAAG
39907102 GGTATTACGG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (72 bp):
TCATTTTACCCTACAGGGGCATTACGATCATTTTACCCTACAAGGGTATTACGGTCATTTCACCC
TACAAGA
Found at i:39907104 original size:99 final size:99
Alignment explanation
Indices: 39906933--39907126 Score: 316
Period size: 99 Copynumber: 2.0 Consensus size: 99
39906923 GCGTTACGGC
* * * * *
39906933 CATTTTACCCTACAGGGGTATTATGGTCATTTTACCCTATAGGGGCATTACGGTTATTTTACCCT
1 CATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAGGGGCATTACGGTCATTTCACCCT
39906998 ACAAGGGTATTACGGTCATTTTACCCTACAAGAT
66 ACAAGGGTATTACGGTCATTTTACCCTACAAGAT
* * *
39907032 CATTTTACCTTACAGGGGTATTACGATCATTTTACCTTACAGGGGTATTACGGTCATTTCACCCT
1 CATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAGGGGCATTACGGTCATTTCACCCT
39907097 ACAAGGGTATTACGGTCATTTTACCCTACA
66 ACAAGGGTATTACGGTCATTTTACCCTACA
39907127 GGTTATTATA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 87 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (99 bp):
CATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAGGGGCATTACGGTCATTTCACCCT
ACAAGGGTATTACGGTCATTTTACCCTACAAGAT
Found at i:39912838 original size:19 final size:20
Alignment explanation
Indices: 39912789--39912842 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
39912779 TGAAAAAAAT
39912789 TGAGTGAATAAAAGCA-AGG
1 TGAGTGAATAAAAGCATAGG
*
39912808 TGAG-GGATAAAAGCATA-G
1 TGAGTGAATAAAAGCATAGG
39912826 TGAGTGAATAAAAGCAT
1 TGAGTGAATAAAAGCAT
39912843 TGAATGAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.46, C:0.06, G:0.30, T:0.19
Consensus pattern (20 bp):
TGAGTGAATAAAAGCATAGG
Found at i:39914157 original size:386 final size:385
Alignment explanation
Indices: 39913431--39914191 Score: 1371
Period size: 386 Copynumber: 2.0 Consensus size: 385
39913421 TTAACAAATC
* *
39913431 TATCATTCAGAATATATCTAAGGTAGTCTGATTCTTTCGAGAGTCAGACTTCAAGCTACCCTACC
1 TATCATTCACAACATATCTAAGGTAGTCTGATTCTTTCGAGAGTCAGACTTCAAGCTACCCTACC
* *
39913496 TAAGGCTTTGCATATCTACAAGCTTTAAGAAGGATACCTATCACTGTTTCTTCCTTTCCTTGTAC
66 TAAGGCTTTGCATATCTACAAGCTTTAAAAAGGATACCCATCACTGTTTCTTCCTTTCCTTGTAC
*
39913561 AGAGCGTAGCTCTATGTCTAGAGTGCTACGACTATTCTGTCGAATACTCGCTTGTATCATTCAAT
131 AGAGCGTAGCTCTATGTCTAGAGTGCTACGACTATTCTATCGAATACTCGCTTGTATCATTCAAT
* *
39913626 CACAATCCAACTCATCTAACCTTTTCAGAATTAAATCAAGTTTATGGACGTACCATATATTCATC
196 CACAATCCAACTCATCTAACCTTTTCAAAATTAAATCAAGTTTATGGACATACCATATATTCATC
39913691 TATGTCTAGAGACTGCATGCATACGTTTTAAAATAGCGCAAATCAAATGAAATAGTAAATCTAAT
261 TATGTCTAGAGACTGCATGCATACGTTTTAAAATAGCGCAAATCAAATGAAATAGTAAATCTAAT
39913756 CAGGATAATGCCTTGGTCATTAAAGGAACTAAAGATTCATCCAATAATCCAAAATAAAAG
326 CAGGATAATGCCTTGGTCATTAAAGGAACTAAAGATTCATCCAATAATCCAAAATAAAAG
* *
39913816 TATCATTCAACAACATATCTAAGGTAGTCTGCTTCTTTCGAGAGTTAGACTTCAAGCTACCCTAC
1 TATCATTC-ACAACATATCTAAGGTAGTCTGATTCTTTCGAGAGTCAGACTTCAAGCTACCCTAC
39913881 CTAAGGCTTTGCATATCTACAAGCTTTAAAAAGGATACCCATCACTGTTTCTTCCTTT-CTCTGT
65 CTAAGGCTTTGCATATCTACAAGCTTTAAAAAGGATACCCATCACTGTTTCTTCCTTTCCT-TGT
* *
39913945 ACAGAGCGTAGTTCTATGTCTAGAGTGCTACGACTATTCTATCGAATACTCGCTTGTATCATTCG
129 ACAGAGCGTAGCTCTATGTCTAGAGTGCTACGACTATTCTATCGAATACTCGCTTGTATCATTCA
* *
39914010 ATCACAATCCAACTCATCTAACCTTTTCAAAATTAAATCAAGTTTATGGATATAGCATATATTCA
194 ATCACAATCCAACTCATCTAACCTTTTCAAAATTAAATCAAGTTTATGGACATACCATATATTCA
39914075 TCTATGTCTAGAGACTGCATGCATACGTTTTAAAATAGCGCAAATCAAATGAAATAGTAAATCTA
259 TCTATGTCTAGAGACTGCATGCATACGTTTTAAAATAGCGCAAATCAAATGAAATAGTAAATCTA
*
39914140 ATCAGGATAATGCCTTGGTCATTAAAGGAACTAAAGATTCATCCAGTAATCC
324 ATCAGGATAATGCCTTGGTCATTAAAGGAACTAAAGATTCATCCAATAATCC
39914192 CAACCCAATG
Statistics
Matches: 360, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
385 10 0.03
386 350 0.97
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (385 bp):
TATCATTCACAACATATCTAAGGTAGTCTGATTCTTTCGAGAGTCAGACTTCAAGCTACCCTACC
TAAGGCTTTGCATATCTACAAGCTTTAAAAAGGATACCCATCACTGTTTCTTCCTTTCCTTGTAC
AGAGCGTAGCTCTATGTCTAGAGTGCTACGACTATTCTATCGAATACTCGCTTGTATCATTCAAT
CACAATCCAACTCATCTAACCTTTTCAAAATTAAATCAAGTTTATGGACATACCATATATTCATC
TATGTCTAGAGACTGCATGCATACGTTTTAAAATAGCGCAAATCAAATGAAATAGTAAATCTAAT
CAGGATAATGCCTTGGTCATTAAAGGAACTAAAGATTCATCCAATAATCCAAAATAAAAG
Found at i:39924728 original size:111 final size:111
Alignment explanation
Indices: 39924534--39924754 Score: 361
Period size: 111 Copynumber: 2.0 Consensus size: 111
39924524 CTTATTATTT
* * * **
39924534 AAATCTTCATTTCGAGAAACCGACACGTCACATCCAATACATTAGGACATGACGTATTGAATTCC
1 AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCAAATTCC
*
39924599 CGAAAGTGAGTTTTTGGTTTATACGTTTTGATTGTAGAAAATTTTA
66 CGAAAGTGAGTTTTTGGTTTATACGCTTTGATTGTAGAAAATTTTA
* *
39924645 AAATCTTCATTTTGAGAAAACGACACATCACATTCAATACATTAGGACACGACGTATCAAATTCC
1 AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCAAATTCC
*
39924710 CGAAAGTGAGTTTTTGGTTTATTCGCTTTGATTGTAGAAAATTTT
66 CGAAAGTGAGTTTTTGGTTTATACGCTTTGATTGTAGAAAATTTT
39924755 TGATTATTTA
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (111 bp):
AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCAAATTCC
CGAAAGTGAGTTTTTGGTTTATACGCTTTGATTGTAGAAAATTTTA
Found at i:39927393 original size:44 final size:44
Alignment explanation
Indices: 39926967--39927400 Score: 553
Period size: 44 Copynumber: 9.9 Consensus size: 44
39926957 CAGGATCCAT
* * ** * * * *
39926967 AATCTTTAACCTATTCCACTACTTTTTAGGGAGATAGGACATAC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
* *
39927011 AATCTTCCACCTATTCCACTGCTGGTCAAGGAGTTAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
* * *
39927055 AATCTTCAACCTATTCTACTGCTGGCCAGGGAGTTAGGACTTGA
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
* *
39927099 AATCTTCTACCTATTCCATTGCTGGTCAGGGAGTTAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
* * *
39927143 AATCCTCAACCTATTCCACTGCTGGTCAAGAAGTTAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
* * *
39927187 AATCTTCTACCTACTCCTCTGCTGGTCAGGGAGTTAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
* * *
39927231 AATCTTCAACATATTCCACTGTTGGTTAGGGAGTTAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
* * * * *
39927275 AATCTTCTACCTATTCCTCTGTTGGTCAGGGAGATAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
* * *
39927319 AATCTTCAACCTATTCCACTGTTGGTCAGGGAGCTAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
* * *
39927363 AATCTTCAACCTATTCCACTACTGGACAGGGAGCTAGG
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGG
39927401 TTTTGTGATT
Statistics
Matches: 341, Mismatches: 49, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 341 1.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGC
Found at i:39939490 original size:111 final size:111
Alignment explanation
Indices: 39939296--39939516 Score: 352
Period size: 111 Copynumber: 2.0 Consensus size: 111
39939286 CTTATTATTT
* **
39939296 AAATCTTCATTTCCAGAAAACGACACGTCACATCCAATACATTAGGACACGATGTATCGAATTCC
1 AAATCTTCATTTCCAGAAAACGACACATCACATCCAATACATTAGGACACGACATATCGAATTCC
*
39939361 CGAAAGTGAGTTTTTGGTTTATGTGTTTTGATTGTAGAAAATTTTA
66 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTTA
* * * * * *
39939407 AAATCTTCATTTCGAGAAAACGACACATCACATTCAATACATTAGGACATGGCATATTGAATTCT
1 AAATCTTCATTTCCAGAAAACGACACATCACATCCAATACATTAGGACACGACATATCGAATTCC
39939472 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTT
66 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTT
39939517 CGATTATTTA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 100 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (111 bp):
AAATCTTCATTTCCAGAAAACGACACATCACATCCAATACATTAGGACACGACATATCGAATTCC
CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTTA
Found at i:39941140 original size:17 final size:17
Alignment explanation
Indices: 39941120--39941152 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39941110 TTGATTTGGC
39941120 TTTATTTTA-TTTATTTG
1 TTTA-TTTAGTTTATTTG
39941137 TTTATTTAGTTTATTT
1 TTTATTTAGTTTATTT
39941153 CACTAACGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTATTTAGTTTATTTG
Found at i:39941714 original size:36 final size:36
Alignment explanation
Indices: 39941667--39941738 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
39941657 CTTTCTTTTT
39941667 CTTTCTTCTTTTTATAGGGTAGGTCTCCATTTCAGC
1 CTTTCTTCTTTTTATAGGGTAGGTCTCCATTTCAGC
39941703 CTTTCTTCTTTTTATAGGGTAGGTCTCCATTTCAGC
1 CTTTCTTCTTTTTATAGGGTAGGTCTCCATTTCAGC
39941739 ACACACTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (36 bp):
CTTTCTTCTTTTTATAGGGTAGGTCTCCATTTCAGC
Found at i:39941749 original size:36 final size:36
Alignment explanation
Indices: 39941671--39941750 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
39941661 CTTTTTCTTT
***
39941671 CTTCTTTTTATAGGGTAGGTCTCCATTTCAGCCTTT
1 CTTCTTTTTATAGGGTAGGTCTCCATTTCAGCCACA
39941707 CTTCTTTTTATAGGGTAGGTCTCCATTTCAGCACACA
1 CTTCTTTTTATAGGGTAGGTCTCCATTTCAGC-CACA
39941744 C-TCTTTT
1 CTTCTTTT
39941751 CTCCCTCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 38 0.95
37 2 0.05
ACGTcount: A:0.16, C:0.24, G:0.15, T:0.45
Consensus pattern (36 bp):
CTTCTTTTTATAGGGTAGGTCTCCATTTCAGCCACA
Found at i:39948415 original size:21 final size:21
Alignment explanation
Indices: 39948377--39948416 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39948367 TTAGAGATTA
** *
39948377 ATTTAATTTCTTTGAATTATT
1 ATTTAATTGATTTAAATTATT
39948398 ATTTAATTGATTTAAATTA
1 ATTTAATTGATTTAAATTA
39948417 AATAATTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTTAATTGATTTAAATTATT
Found at i:39948754 original size:20 final size:20
Alignment explanation
Indices: 39948696--39948754 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
39948686 GAGTGCAAAA
*
39948696 ATTAAAAATTAAAAAATAATTT
1 ATTAAAAATT-ATAAA-AATTT
* *
39948718 ATTAACAATTATTAAAATTT
1 ATTAAAAATTATAAAAATTT
39948738 A-TAAAAATATATAAAAA
1 ATTAAAAAT-TATAAAAA
39948755 ATTCAAATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 6 0.19
20 13 0.42
21 3 0.10
22 9 0.29
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAAAATTATAAAAATTT
Found at i:39962423 original size:16 final size:15
Alignment explanation
Indices: 39962398--39962431 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
39962388 AAAGTTGATA
*
39962398 ATAATTAATATATATT
1 ATAATAAATATA-ATT
39962414 ATAATAAATATAATT
1 ATAATAAATATAATT
39962429 ATA
1 ATA
39962432 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:39985728 original size:70 final size:69
Alignment explanation
Indices: 39985511--39985771 Score: 229
Period size: 70 Copynumber: 3.7 Consensus size: 69
39985501 ACAACATTTG
* * * * * * *
39985511 TGTCATACTAAGGTTCGTTA-GATAAAAAATTGCAGCCACCAACATAGCTAGTGAGAGTAAAGCT
1 TGTCATACTAAGGCTCG-CAGGATAAAAAA-CGCAGCCTCCAACATAGTTAGAGAGAGCAAAGCT
*
39985575 CCCAGC
64 CCAAGC
* ** ** * *
39985581 TATCATACTAAAACTCGCAGGATAAAAAAATCTTAGCCTTCAACACAGTTAGCA-AGAGCAAAGC
1 TGTCATACTAAGGCTCGCAGGAT-AAAAAA-CGCAGCCTCCAACATAGTTAG-AGAGAGCAAAGC
*
39985645 TCCTAGC
63 TCCAAGC
* * * *
39985652 TCTCATACTAAGGCTCGCAGGATAAAAAACGGCAGCCTTCAACAAAGTTAGAGAGAGCAAAACTC
1 TGTCATACTAAGGCTCGCAGGATAAAAAAC-GCAGCCTCCAACATAGTTAGAGAGAGCAAAGCTC
*
39985717 CAAGT
65 CAAGC
* * * *
39985722 TGTCATACTAAGGCTCACAGAATAAAAATCGTAGCCTCCAACATAGTTAG
1 TGTCATACTAAGGCTCGCAGGATAAAAAACGCAGCCTCCAACATAGTTAG
39985772 CGAAAGTTAA
Statistics
Matches: 155, Mismatches: 31, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
69 20 0.13
70 79 0.51
71 56 0.36
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (69 bp):
TGTCATACTAAGGCTCGCAGGATAAAAAACGCAGCCTCCAACATAGTTAGAGAGAGCAAAGCTCC
AAGC
Found at i:40003795 original size:14 final size:15
Alignment explanation
Indices: 40003778--40003806 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40003768 TACATTTTAA
40003778 TAATTTC-TATTTTC
1 TAATTTCATATTTTC
40003792 TAATTTCATATTTTC
1 TAATTTCATATTTTC
40003807 ACATGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTTCATATTTTC
Found at i:40018911 original size:21 final size:21
Alignment explanation
Indices: 40018887--40018927 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40018877 GGTGGATCAG
40018887 CTCTTATGAACTTCTGTTCAA
1 CTCTTATGAACTTCTGTTCAA
* *
40018908 CTCTTATGAGCTTTTGTTCA
1 CTCTTATGAACTTCTGTTCA
40018928 GCTTTCAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (21 bp):
CTCTTATGAACTTCTGTTCAA
Found at i:40019941 original size:13 final size:14
Alignment explanation
Indices: 40019915--40019949 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
40019905 AACCTGCCCC
*
40019915 ATATACATATACAG
1 ATATACAGATACAG
40019929 ATA-ACAGATACAG
1 ATATACAGATACAG
40019942 ATATACAG
1 ATATACAG
40019950 TGTTAACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.23
Consensus pattern (14 bp):
ATATACAGATACAG
Found at i:40023467 original size:16 final size:16
Alignment explanation
Indices: 40023446--40023476 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40023436 AAACATTATA
*
40023446 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
40023462 AATTAAATAATTTTC
1 AATTAAATAATTTTC
40023477 TCAACCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:40035172 original size:20 final size:20
Alignment explanation
Indices: 40035147--40035213 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
40035137 TTGTACGAGA
40035147 TTGCACTTTGGTGCCTCTAT
1 TTGCACTTTGGTGCCTCTAT
* *
40035167 TTGCACTTCGGTGCCTCTAA
1 TTGCACTTTGGTGCCTCTAT
*
40035187 TTGCACAATTT--CGCCTCTAT
1 TTGCAC--TTTGGTGCCTCTAT
40035207 TTGCACT
1 TTGCACT
40035214 ACAGTGCCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
20 37 0.93
22 2 0.05
ACGTcount: A:0.15, C:0.28, G:0.16, T:0.40
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTAT
Found at i:40035222 original size:20 final size:20
Alignment explanation
Indices: 40035157--40035222 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
40035147 TTGCACTTTG
* *
40035157 GTGCCTCTATTTGCACTTCG
1 GTGCCTCTATTTGCACTACA
*
40035177 GTGCCTCTAATTGCAC-A-A
1 GTGCCTCTATTTGCACTACA
*
40035195 TTTCGCCTCTATTTGCACTACA
1 -GT-GCCTCTATTTGCACTACA
40035217 GTGCCT
1 GTGCCT
40035223 ATGAATAGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 1 0.03
20 32 0.89
21 2 0.06
22 1 0.03
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (20 bp):
GTGCCTCTATTTGCACTACA
Found at i:40036419 original size:21 final size:22
Alignment explanation
Indices: 40036377--40036419 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
40036367 AATTTTACCT
*
40036377 TTTTTGAACTTTTGTATCGATA
1 TTTTTGAACTTTTGCATCGATA
* *
40036399 TTTTTGTAC-TTTGCATTGATA
1 TTTTTGAACTTTTGCATCGATA
40036420 CTTGACCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.21, C:0.09, G:0.14, T:0.56
Consensus pattern (22 bp):
TTTTTGAACTTTTGCATCGATA
Found at i:40044203 original size:23 final size:23
Alignment explanation
Indices: 40044138--40044421 Score: 304
Period size: 23 Copynumber: 12.6 Consensus size: 23
40044128 CGTGACCAAA
40044138 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
* *
40044161 GG-TTTTAGGGTT-AA--GGGTTAG
1 GGTTTTTA--ATTAAATTAGGTTAG
*
40044182 TGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
*
40044205 GGTTTTTAATTTAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
* * *
40044228 GG-TTTGAGGGTT-AA--GGGTTAG
1 GGTTTTTA--ATTAAATTAGGTTAG
40044249 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
40044272 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
*
40044295 GGTTTTTAATTAAATTAGGTTAA
1 GGTTTTTAATTAAATTAGGTTAG
* *
40044318 GG-TTTTAGGGTT-AA--GGGTTAG
1 GGTTTTTA--ATTAAATTAGGTTAG
* *
40044339 GGTTTTTAAGTAAATCAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
*
40044362 GGTTTTTAATTAAATTAGGTTAA
1 GGTTTTTAATTAAATTAGGTTAG
40044385 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
40044408 GGTTTTTAAGTTAA
1 GGTTTTTAA-TTAA
40044422 GGGTATTAAT
Statistics
Matches: 218, Mismatches: 24, Indels: 37
0.78 0.09 0.13
Matches are distributed among these distances:
20 5 0.02
21 28 0.13
22 28 0.13
23 147 0.67
24 10 0.05
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (23 bp):
GGTTTTTAATTAAATTAGGTTAG
Found at i:40044222 original size:67 final size:67
Alignment explanation
Indices: 40044138--40044300 Score: 299
Period size: 67 Copynumber: 2.4 Consensus size: 67
40044128 CGTGACCAAA
*
40044138 GGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTAAGGGTTAGTGTTTTTAATTAAATTAGGTT
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTAAGGGTTAGGGTTTTTAATTAAATTAGGTT
40044203 AG
66 AG
* *
40044205 GGTTTTTAATTTAATTAGGTTAGGGTTTGAGGGTTAAGGGTTAGGGTTTTTAATTAAATTAGGTT
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTAAGGGTTAGGGTTTTTAATTAAATTAGGTT
40044270 AG
66 AG
40044272 GGTTTTTAATTAAATTAGGTTAGGGTTTT
1 GGTTTTTAATTAAATTAGGTTAGGGTTTT
40044301 TAATTAAATT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 91 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (67 bp):
GGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTAAGGGTTAGGGTTTTTAATTAAATTAGGTT
AG
Found at i:40044425 original size:90 final size:90
Alignment explanation
Indices: 40044176--40044413 Score: 413
Period size: 90 Copynumber: 2.6 Consensus size: 90
40044166 TAGGGTTAAG
* * *
40044176 GGTTAGTGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTGAGGGTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTA
* *
40044241 AGGGTTAGGGTTTTTAATTAAATTA
66 AGGGTTAGGGTTTTTAAGTAAATCA
*
40044266 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTAGGGTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTA
40044331 AGGGTTAGGGTTTTTAAGTAAATCA
66 AGGGTTAGGGTTTTTAAGTAAATCA
*
40044356 GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTT
40044414 TAAGTTAAGG
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 140 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (90 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTA
AGGGTTAGGGTTTTTAAGTAAATCA
Found at i:40044470 original size:9 final size:9
Alignment explanation
Indices: 40044452--40044489 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
40044442 ATTCTCAAAT
40044452 AATA-TCAA
1 AATATTCAA
40044460 AATATTCAA
1 AATATTCAA
40044469 AATATTCAA
1 AATATTCAA
*
40044478 AATATTAAA
1 AATATTCAA
40044487 AAT
1 AAT
40044490 TTTCTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 4 0.14
9 24 0.86
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (9 bp):
AATATTCAA
Found at i:40044523 original size:25 final size:25
Alignment explanation
Indices: 40044491--40044607 Score: 99
Period size: 25 Copynumber: 4.9 Consensus size: 25
40044481 ATTAAAAATT
40044491 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
40044516 TTCTATTTTATTACACATCAAAT-AA-
1 TTCTATTTTATT--ACATCAAATAAAC
** * *
40044541 TATC-A--AAATAAC-T-AAA-AAAA
1 T-TCTATTTTATTACATCAAATAAAC
*
40044561 AT-TATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
40044585 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
40044608 TATCAAAATA
Statistics
Matches: 71, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
19 7 0.10
20 1 0.01
21 6 0.08
22 1 0.01
23 5 0.07
24 4 0.06
25 34 0.48
26 4 0.06
27 9 0.13
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:40044619 original size:28 final size:26
Alignment explanation
Indices: 40044553--40044619 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 26
40044543 TCAAAATAAC
*
40044553 TAAAAAAAATTATTTTATTACATCAAA
1 TAAACAAAA-TATTTTATTACATCAAA
***
40044580 TAAAC-TTCTATTTTATTACATCAAA
1 TAAACAAAATATTTTATTACATCAAA
40044605 TAATATCAAAATATT
1 TAA-A-CAAAATATT
40044620 CAAAATATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
25 20 0.67
26 1 0.03
27 5 0.17
28 4 0.13
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.40
Consensus pattern (26 bp):
TAAACAAAATATTTTATTACATCAAA
Found at i:40045059 original size:18 final size:18
Alignment explanation
Indices: 40045036--40045075 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
40045026 GACTCGGAAA
*
40045036 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
40045054 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
40045072 AGGA
1 AGGA
40045076 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:40047380 original size:13 final size:13
Alignment explanation
Indices: 40047362--40047391 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40047352 CATCGTTTTA
*
40047362 TTTTCTTTTATTT
1 TTTTCTATTATTT
40047375 TTTTCTATTATTT
1 TTTTCTATTATTT
40047388 TTTT
1 TTTT
40047392 ACTCTGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTATTATTT
Found at i:40048838 original size:17 final size:17
Alignment explanation
Indices: 40048816--40048850 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40048806 CCCTTATGTA
40048816 TATTTGTTTCAT-TTATT
1 TATTTGTTT-ATATTATT
40048833 TATTTGTTTATATTATT
1 TATTTGTTTATATTATT
40048850 T
1 T
40048851 CTATGCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TATTTGTTTATATTATT
Found at i:40057609 original size:13 final size:13
Alignment explanation
Indices: 40057587--40057648 Score: 115
Period size: 13 Copynumber: 4.8 Consensus size: 13
40057577 TTCTTTATTA
40057587 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
*
40057600 CTTTTTAGAAGTG
1 CTTTTGAGAAGTG
40057613 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
40057626 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
40057639 CTTTTGAGAA
1 CTTTTGAGAA
40057649 ATTTGAGTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.40
Consensus pattern (13 bp):
CTTTTGAGAAGTG
Found at i:40058948 original size:19 final size:19
Alignment explanation
Indices: 40058902--40058950 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
40058892 AACAGCTTCA
* *
40058902 AAATATTAAACAGAAGAGG
1 AAATATAAAACAGAAGAAG
* *
40058921 AACTAATAAAACAGAATAAG
1 AAAT-ATAAAACAGAAGAAG
40058941 AAATATAAAA
1 AAATATAAAA
40058951 GAAACTCTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.16
Consensus pattern (19 bp):
AAATATAAAACAGAAGAAG
Found at i:40061212 original size:26 final size:27
Alignment explanation
Indices: 40061183--40061251 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
40061173 ATATACATGT
*
40061183 ATACATATATACATT-TACATTTTATA
1 ATACATATATACATTCCACATTTTATA
* *
40061209 ATACATATATATATTCCATATTTTATA
1 ATACATATATACATTCCACATTTTATA
*
40061236 ATCCATGCATATACAT
1 ATACAT--ATATACAT
40061252 GCATTTTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 14 0.40
27 14 0.40
29 7 0.20
ACGTcount: A:0.41, C:0.14, G:0.01, T:0.43
Consensus pattern (27 bp):
ATACATATATACATTCCACATTTTATA
Found at i:40072643 original size:22 final size:22
Alignment explanation
Indices: 40072613--40072661 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
40072603 AAGTGGGGGG
* *
40072613 TTGAAATGGTAAGTATGCATGA
1 TTGATATGGTAAGTATACATGA
40072635 TTGATATGGTAAGTATACATGA
1 TTGATATGGTAAGTATACATGA
40072657 TTGAT
1 TTGAT
40072662 CGATTTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (22 bp):
TTGATATGGTAAGTATACATGA
Found at i:40074586 original size:17 final size:16
Alignment explanation
Indices: 40074564--40074598 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
40074554 TTTACGAAAT
40074564 TTGAATTTATTTCTCAA
1 TTGAATTTATTTC-CAA
40074581 TTGAATTTATTTCCAA
1 TTGAATTTATTTCCAA
40074597 TT
1 TT
40074599 TATTTAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (16 bp):
TTGAATTTATTTCCAA
Found at i:40080110 original size:34 final size:34
Alignment explanation
Indices: 40080056--40080130 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
40080046 TTGGTGATAC
*
40080056 TGTT-TTTTGTGCTGTTTTTTTATGCTGTTTTGA-
1 TGTTGTTTTGTGCTGTCTTTTTATGCTGTTTT-AT
* *
40080089 TGTTGTTTTGGTGCTG-CTTTTTGTGGTGTTTTAT
1 TGTTGTTTT-GTGCTGTCTTTTTATGCTGTTTTAT
40080123 TGTTGTTT
1 TGTTGTTT
40080131 CGCAGTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 5 0.14
34 25 0.69
35 6 0.17
ACGTcount: A:0.04, C:0.05, G:0.25, T:0.65
Consensus pattern (34 bp):
TGTTGTTTTGTGCTGTCTTTTTATGCTGTTTTAT
Found at i:40080387 original size:13 final size:13
Alignment explanation
Indices: 40080369--40080408 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
40080359 TAATTTATTA
40080369 TATTTAAAAAAAT
1 TATTTAAAAAAAT
*
40080382 TATTTAATAAAAT
1 TATTTAAAAAAAT
* *
40080395 AATCTAAAAAAAT
1 TATTTAAAAAAAT
40080408 T
1 T
40080409 TAATATGGGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTTAAAAAAAT
Found at i:40084469 original size:44 final size:44
Alignment explanation
Indices: 40084402--40084595 Score: 155
Period size: 51 Copynumber: 4.2 Consensus size: 44
40084392 TTTGAGTACT
*
40084402 TCTGATAAGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTA
* *
40084446 TCTGATCAGTGACAAGTGGTAAGTGATAAGTGATAGCTTCAGCTATACTTA
1 TCTGATCAGTGACAAGTGATAA--G-T-A--G-TAGCTTCAGCTACACTTA
* * *
40084497 TCTAATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TC---TGA-T--C-AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTA
* *
40084548 TCTGATCAGTG---A--GATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTA
40084587 TCTGATCAG
1 TCTGATCAG
40084596 GGAAGAGTGA
Statistics
Matches: 127, Mismatches: 9, Indels: 33
0.75 0.05 0.20
Matches are distributed among these distances:
39 36 0.28
41 1 0.01
44 24 0.19
45 1 0.01
46 1 0.01
47 2 0.02
48 3 0.02
50 1 0.01
51 37 0.29
52 1 0.01
54 2 0.02
55 2 0.02
56 1 0.01
57 1 0.01
58 14 0.11
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTA
Found at i:40084484 original size:51 final size:51
Alignment explanation
Indices: 40084408--40084559 Score: 234
Period size: 51 Copynumber: 3.0 Consensus size: 51
40084398 TACTTCTGAT
40084408 AAGTGACAAGTGATAAGT-AGTAGCTTCAGCTACACTTATCTGATCAGTGAC
1 AAGTGACAAGTGATAAGTGA-TAGCTTCAGCTACACTTATCTGATCAGTGAC
** * *
40084459 AAGTGGTAAGTGATAAGTGATAGCTTCAGCTATACTTATCTAATCAGTGAC
1 AAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGAC
* *
40084510 AAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGA
1 AAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGA
40084560 GATAAGTGGT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 89 0.99
52 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (51 bp):
AAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGAC
Found at i:40084570 original size:39 final size:39
Alignment explanation
Indices: 40084521--40084595 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
40084511 AGTGACAAGT
40084521 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGA
1 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGA
40084560 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
40084596 GGAAGAGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (39 bp):
GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGA
Found at i:40089115 original size:25 final size:25
Alignment explanation
Indices: 40089048--40089127 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
40089038 GTACATGTAT
40089048 GCTCATACGAGCATGTA-AACGGGAA
1 GCTCATACGAGC-TGTATAACGGGAA
* * *
40089073 GCTCTTCCGAG-TCATATAACGGGAA
1 GCTCATACGAGCT-GTATAACGGGAA
* *
40089098 GCTCATATGAGCTGTATAATGGGAA
1 GCTCATACGAGCTGTATAACGGGAA
40089123 GCTCA
1 GCTCA
40089128 AGAGTCAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
23 1 0.02
24 2 0.05
25 40 0.91
26 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGTATAACGGGAA
Found at i:40089167 original size:24 final size:24
Alignment explanation
Indices: 40089140--40089233 Score: 118
Period size: 24 Copynumber: 3.9 Consensus size: 24
40089130 AGTCAAATTG
*
40089140 GAGAAGCTCATGCGAGTCAATATC
1 GAGAAGCTCATGCGAGCCAATATC
40089164 GAGAAGCTCATGCGAGCCAATATC
1 GAGAAGCTCATGCGAGCCAATATC
* *
40089188 GAGAAGCTC-TGGAGAGCCATTAATC
1 GAGAAGCTCAT-GCGAGCCAAT-ATC
* *
40089213 GGGAAGCTCATGAGAGCCAAT
1 GAGAAGCTCATGCGAGCCAAT
40089234 TAACGGGAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.02
24 40 0.65
25 20 0.32
26 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (24 bp):
GAGAAGCTCATGCGAGCCAATATC
Found at i:40089223 original size:49 final size:50
Alignment explanation
Indices: 40089161--40089256 Score: 133
Period size: 49 Copynumber: 1.9 Consensus size: 50
40089151 GCGAGTCAAT
* *
40089161 ATCGAGAAGCTCATGCGAGCCAA-TATCGAGAAGCTCTG-GAGAGCCATTA
1 ATCGAGAAGCTCATGAGAGCCAATTAACGAGAAGCT-TGTGAGAGCCATTA
* *
40089210 ATCGGGAAGCTCATGAGAGCCAATTAACGGGAAGCTTGTGAGAGCCA
1 ATCGAGAAGCTCATGAGAGCCAATTAACGAGAAGCTTGTGAGAGCCA
40089257 AATAACGGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
49 23 0.56
50 18 0.44
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.18
Consensus pattern (50 bp):
ATCGAGAAGCTCATGAGAGCCAATTAACGAGAAGCTTGTGAGAGCCATTA
Found at i:40089277 original size:25 final size:25
Alignment explanation
Indices: 40089142--40089313 Score: 118
Period size: 25 Copynumber: 7.0 Consensus size: 25
40089132 TCAAATTGGA
* * * *
40089142 GAAGCTCATGCGAGTCAA-TATCGA
1 GAAGCTCATGAGAGCCAATTAACGG
* * *
40089166 GAAGCTCATGCGAGCCAA-TATCGA
1 GAAGCTCATGAGAGCCAATTAACGG
40089190 GAAGCTC-TGGAGAGCC-ATTAATCGG
1 GAAGCTCAT-GAGAGCCAATTAA-CGG
40089215 GAAGCTCATGAGAGCCAATTAACGG
1 GAAGCTCATGAGAGCCAATTAACGG
** *
40089240 GAAGCTTGTGAGAGCCAAATAACGG
1 GAAGCTCATGAGAGCCAATTAACGG
* * * * **
40089265 AAAGCTCAAGAGATCCATTTATTGG
1 GAAGCTCATGAGAGCCAATTAACGG
* * * *
40089290 GATGCTCATAAGAGCTAAATAACG
1 GAAGCTCATGAGAGCCAATTAACG
40089314 AGACGATCTT
Statistics
Matches: 117, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
23 2 0.02
24 38 0.32
25 71 0.61
26 6 0.05
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (25 bp):
GAAGCTCATGAGAGCCAATTAACGG
Found at i:40090842 original size:597 final size:597
Alignment explanation
Indices: 40089709--40090902 Score: 2388
Period size: 597 Copynumber: 2.0 Consensus size: 597
40089699 AAAATTGCCC
40089709 TTAATTTTTTACTTTTATTCAATTTAGTCCCTGAACCCAGAACATGCAAATTAACCATTTTTAAT
1 TTAATTTTTTACTTTTATTCAATTTAGTCCCTGAACCCAGAACATGCAAATTAACCATTTTTAAT
40089774 ACAAATCCAAGCTAGCTGAATATTCATGCCATTTAATACAGCTCATTTTTGCAATAATTTCACAA
66 ACAAATCCAAGCTAGCTGAATATTCATGCCATTTAATACAGCTCATTTTTGCAATAATTTCACAA
40089839 AAAAAACTTGTATTTTTACTATTTTAACAAATTAATCCTTAATCGAAAAATTCATCAAAATCACT
131 AAAAAACTTGTATTTTTACTATTTTAACAAATTAATCCTTAATCGAAAAATTCATCAAAATCACT
40089904 TAACAAAATACTTTTATTTAAAAAATAATTTCTCAAATTCATCATTTAACATCAAAAATCATATA
196 TAACAAAATACTTTTATTTAAAAAATAATTTCTCAAATTCATCATTTAACATCAAAAATCATATA
40089969 GATTCATCAATGGCAACATGCGAAAAAAAAGTATATTATATTTTAAACTTAAGTATATATATAAT
261 GATTCATCAATGGCAACATGCGAAAAAAAAGTATATTATATTTTAAACTTAAGTATATATATAAT
40090034 TTGTTTATATTTTCTAAAATTATTTTATCAATAACTTTTATTAATATGTTGTTATTTAAATAATA
326 TTGTTTATATTTTCTAAAATTATTTTATCAATAACTTTTATTAATATGTTGTTATTTAAATAATA
40090099 ATGATTTTATAAAATACACGAACAATTTGTGCATAGCATAAGATAGAAAATTAGTATATAATATG
391 ATGATTTTATAAAATACACGAACAATTTGTGCATAGCATAAGATAGAAAATTAGTATATAATATG
40090164 ATAAGATACACAAGCATTATATTGCGAGATGACAATTCTCCCTTTTTTTTATTTGATTTTTATGA
456 ATAAGATACACAAGCATTATATTGCGAGATGACAATTCTCCCTTTTTTTTATTTGATTTTTATGA
40090229 GATAAATTAAGTAATTTTAATATATTCCAATTTCAAATTTCTGATTTTATAGAAGTACAATATTT
521 GATAAATTAAGTAATTTTAATATATTCCAATTTCAAATTTCTGATTTTATAGAAGTACAATATTT
40090294 TTAATTTTATGT
586 TTAATTTTATGT
40090306 TTAATTTTTTACTTTTATTCAATTTAGTCCCTGAACCCAGAACATGCAAATTAACCATTTTTAAT
1 TTAATTTTTTACTTTTATTCAATTTAGTCCCTGAACCCAGAACATGCAAATTAACCATTTTTAAT
40090371 ACAAATCCAAGCTAGCTGAATATTCATGCCATTTAATACAGCTCATTTTTGCAATAATTTCACAA
66 ACAAATCCAAGCTAGCTGAATATTCATGCCATTTAATACAGCTCATTTTTGCAATAATTTCACAA
40090436 AAAAAACTTGTATTTTTACTATTTTAACAAATTAATCCTTAATCGAAAAATTCATCAAAATCACT
131 AAAAAACTTGTATTTTTACTATTTTAACAAATTAATCCTTAATCGAAAAATTCATCAAAATCACT
40090501 TAACAAAATACTTTTATTTAAAAAATAATTTCTCAAATTCATCATTTAACATCAAAAATCATATA
196 TAACAAAATACTTTTATTTAAAAAATAATTTCTCAAATTCATCATTTAACATCAAAAATCATATA
40090566 GATTCATCAATGGCAACATGCGAAAAAAAAGTATATTATATTTTAAACTTAAGTATATATATAAT
261 GATTCATCAATGGCAACATGCGAAAAAAAAGTATATTATATTTTAAACTTAAGTATATATATAAT
40090631 TTGTTTATATTTTCTAAAATTATTTTATCAATAACTTTTATTAATATGTTGTTATTTAAATAATA
326 TTGTTTATATTTTCTAAAATTATTTTATCAATAACTTTTATTAATATGTTGTTATTTAAATAATA
40090696 ATGATTTTATAAAATACACGAACAATTTGTGCATAGCATAAGATAGAAAATTAGTATATAATATG
391 ATGATTTTATAAAATACACGAACAATTTGTGCATAGCATAAGATAGAAAATTAGTATATAATATG
40090761 ATAAGATACACAAGCATTATATTGCGAGATGACAATTCTCCCTTTTTTTTATTTGATTTTTATGA
456 ATAAGATACACAAGCATTATATTGCGAGATGACAATTCTCCCTTTTTTTTATTTGATTTTTATGA
40090826 GATAAATTAAGTAATTTTAATATATTCCAATTTCAAATTTCTGATTTTATAGAAGTACAATATTT
521 GATAAATTAAGTAATTTTAATATATTCCAATTTCAAATTTCTGATTTTATAGAAGTACAATATTT
40090891 TTAATTTTATGT
586 TTAATTTTATGT
40090903 AAACATATCT
Statistics
Matches: 597, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
597 597 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (597 bp):
TTAATTTTTTACTTTTATTCAATTTAGTCCCTGAACCCAGAACATGCAAATTAACCATTTTTAAT
ACAAATCCAAGCTAGCTGAATATTCATGCCATTTAATACAGCTCATTTTTGCAATAATTTCACAA
AAAAAACTTGTATTTTTACTATTTTAACAAATTAATCCTTAATCGAAAAATTCATCAAAATCACT
TAACAAAATACTTTTATTTAAAAAATAATTTCTCAAATTCATCATTTAACATCAAAAATCATATA
GATTCATCAATGGCAACATGCGAAAAAAAAGTATATTATATTTTAAACTTAAGTATATATATAAT
TTGTTTATATTTTCTAAAATTATTTTATCAATAACTTTTATTAATATGTTGTTATTTAAATAATA
ATGATTTTATAAAATACACGAACAATTTGTGCATAGCATAAGATAGAAAATTAGTATATAATATG
ATAAGATACACAAGCATTATATTGCGAGATGACAATTCTCCCTTTTTTTTATTTGATTTTTATGA
GATAAATTAAGTAATTTTAATATATTCCAATTTCAAATTTCTGATTTTATAGAAGTACAATATTT
TTAATTTTATGT
Found at i:40091664 original size:30 final size:30
Alignment explanation
Indices: 40091623--40091695 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
40091613 CCTATTGTTC
40091623 TTTTT-TTTTTTTTCATT-T-ATTTATTATT
1 TTTTTATTTTTTTTCATTGTCATTT-TTATT
**
40091651 TTTTCTATTTTTTTTGTTTGTCATTTTTATT
1 TTTT-TATTTTTTTTCATTGTCATTTTTATT
*
40091682 TTTTTATTTGTTTT
1 TTTTTATTTTTTTT
40091696 AAAATATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 4 0.11
29 1 0.03
30 19 0.50
31 10 0.26
32 4 0.11
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.81
Consensus pattern (30 bp):
TTTTTATTTTTTTTCATTGTCATTTTTATT
Found at i:40091680 original size:34 final size:32
Alignment explanation
Indices: 40091620--40091686 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 32
40091610 CTGCCTATTG
40091620 TTCTTTTTTTTTTTTTCATTTATTTATTATTTT
1 TTCTTTTTTTTTTTTTCATTTATTTATT-TTTT
40091653 TTCTATTTTTTTTGTTTGTCA-TT-TTTATTTTTT
1 TTCT-TTTTTTTT-TTT-TCATTTATTTATTTTTT
40091686 T
1 T
40091687 ATTTGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
33 9 0.29
34 14 0.45
35 5 0.16
36 3 0.10
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (32 bp):
TTCTTTTTTTTTTTTTCATTTATTTATTTTTT
Found at i:40091717 original size:13 final size:13
Alignment explanation
Indices: 40091699--40091724 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40091689 TTGTTTTAAA
40091699 ATATTTTAAATGT
1 ATATTTTAAATGT
40091712 ATATTTTAAATGT
1 ATATTTTAAATGT
40091725 TTTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATATTTTAAATGT
Found at i:40091763 original size:22 final size:22
Alignment explanation
Indices: 40091692--40091766 Score: 80
Period size: 22 Copynumber: 3.3 Consensus size: 22
40091682 TTTTTATTTG
* *
40091692 TTTTAAAATATTTTAAATGTAT
1 TTTTTAAATATTTTAAATATAT
* *
40091714 ATTTTAAATGTTTTATAATATTAT
1 TTTTTAAATATTTTA-AATA-TAT
40091738 TTTTTAAA-ATTTTAAATATAAT
1 TTTTTAAATATTTTAAATAT-AT
40091760 TTTTTAA
1 TTTTTAA
40091767 CGTTATAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.02
22 25 0.57
23 8 0.18
24 10 0.23
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (22 bp):
TTTTTAAATATTTTAAATATAT
Found at i:40091775 original size:22 final size:22
Alignment explanation
Indices: 40091726--40091775 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
40091716 TTTAAATGTT
*
40091726 TTAT-AATATTATTTTTTAAAA
1 TTATAAATATAATTTTTTAAAA
* **
40091747 TTTTAAATATAATTTTTTAACG
1 TTATAAATATAATTTTTTAAAA
40091769 TTATAAA
1 TTATAAA
40091776 ATATTTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTATAAATATAATTTTTTAAAA
Found at i:40096985 original size:18 final size:18
Alignment explanation
Indices: 40096962--40097001 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
40096952 ATTATATTAC
40096962 AATAACTATAAAATACAA
1 AATAACTATAAAATACAA
40096980 AATAACTATAAAATACAA
1 AATAACTATAAAATACAA
40096998 AATA
1 AATA
40097002 CAAACTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (18 bp):
AATAACTATAAAATACAA
Found at i:40097332 original size:11 final size:10
Alignment explanation
Indices: 40097310--40097352 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
40097300 TCAATTCAAC
40097310 TTTCAATTTTT
1 TTTC-ATTTTT
*
40097321 TCTCATTTTT
1 TTTCATTTTT
40097331 TTTCAATTTTT
1 TTTC-ATTTTT
*
40097342 TTTTATTTTT
1 TTTCATTTTT
40097352 T
1 T
40097353 GGTCCTCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 16 0.57
11 12 0.43
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTCATTTTT
Found at i:40097334 original size:21 final size:21
Alignment explanation
Indices: 40097310--40097352 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
40097300 TCAATTCAAC
40097310 TTTCAATTTTTTCTCATTTTT
1 TTTCAATTTTTTCTCATTTTT
* *
40097331 TTTCAATTTTTTTTTATTTTT
1 TTTCAATTTTTTCTCATTTTT
40097352 T
1 T
40097353 GGTCCTCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCAATTTTTTCTCATTTTT
Found at i:40097586 original size:20 final size:19
Alignment explanation
Indices: 40097561--40097706 Score: 62
Period size: 19 Copynumber: 7.8 Consensus size: 19
40097551 AATAATAAAC
40097561 AAATAAAAAATAGAAAAATG
1 AAATAAAAAA-AGAAAAATG
*
40097581 AAAT----AAAGAAAAA-C
1 AAATAAAAAAAGAAAAATG
40097595 AAATAAAAAAGAGAAAAATG
1 AAATAAAAAA-AGAAAAATG
*
40097615 AAAT----AAAGAAAAA-C
1 AAATAAAAAAAGAAAAATG
*
40097629 AAATAAAAAACAGAAAAAGG
1 AAATAAAAAA-AGAAAAATG
* * *
40097649 ACAAACAAATAAAAAAACAAATA
1 --AAATAAA-AAAAGAA-AAATG
* *
40097672 AAATGAAATAAAGAAAAA-C
1 AAAT-AAAAAAAGAAAAATG
*
40097691 AAATAAAAAAGGAAAA
1 AAATAAAAAAAGAAAA
40097707 GGACAAACAA
Statistics
Matches: 95, Mismatches: 14, Indels: 36
0.66 0.10 0.25
Matches are distributed among these distances:
14 8 0.08
15 14 0.15
16 4 0.04
18 14 0.15
19 18 0.19
20 11 0.12
21 8 0.08
22 12 0.13
23 6 0.06
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.09
Consensus pattern (19 bp):
AAATAAAAAAAGAAAAATG
Found at i:40097600 original size:34 final size:34
Alignment explanation
Indices: 40097557--40097700 Score: 176
Period size: 34 Copynumber: 4.4 Consensus size: 34
40097547 TAAAAATAAT
40097557 AAACAAATAAAAAATAGAAAAATGAAATAAAGAA
1 AAACAAATAAAAAATAGAAAAATGAAATAAAGAA
*
40097591 AAACAAATAAAAAAGAGAAAAATGAAATAAAGAA
1 AAACAAATAAAAAATAGAAAAATGAAATAAAGAA
* * *
40097625 AAACAAATAAAAAACAGAAAAAGGACAA-ACA-AA
1 AAACAAATAAAAAATAGAAAAATGA-AATAAAGAA
* *
40097658 TAA-AAA-AACAAAT---AAAATGAAATAAAGAA
1 AAACAAATAAAAAATAGAAAAATGAAATAAAGAA
40097687 AAACAAATAAAAAA
1 AAACAAATAAAAAA
40097701 GGAAAAGGAC
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
27 2 0.02
28 8 0.09
29 4 0.04
30 3 0.03
31 10 0.11
32 3 0.03
33 4 0.04
34 58 0.62
35 2 0.02
ACGTcount: A:0.77, C:0.06, G:0.08, T:0.09
Consensus pattern (34 bp):
AAACAAATAAAAAATAGAAAAATGAAATAAAGAA
Found at i:40097646 original size:10 final size:11
Alignment explanation
Indices: 40097550--40097700 Score: 53
Period size: 11 Copynumber: 12.9 Consensus size: 11
40097540 AATATTATAA
*
40097550 AAATAATAAAC
1 AAATAAAAAAC
*
40097561 AAATAAAAAAT
1 AAATAAAAAAC
*
40097572 AGAA-AAATGAAAT
1 A-AATAAA--AAAC
*
40097585 AAA-GAAAAAC
1 AAATAAAAAAC
*
40097595 AAATAAAAAAG
1 AAATAAAAAAC
*
40097606 AGAA-AAATGAAAT
1 A-AATAAA--AAAC
*
40097619 AAA-GAAAAAC
1 AAATAAAAAAC
40097629 AAATAAAAAAC
1 AAATAAAAAAC
*
40097640 AGAAAAAGGACAAAC
1 A-AATAA--A-AAAC
40097655 AAATAAAAAAAC
1 AAAT-AAAAAAC
40097667 AAATAAAATGAA-
1 AAATAAAA--AAC
40097679 ATAA-AGAAAAAC
1 A-AATA-AAAAAC
40097691 AAATAAAAAA
1 AAATAAAAAA
40097701 GGAAAAGGAC
Statistics
Matches: 109, Mismatches: 12, Indels: 38
0.69 0.08 0.24
Matches are distributed among these distances:
10 12 0.11
11 42 0.39
12 28 0.26
13 17 0.16
14 3 0.03
15 7 0.06
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (11 bp):
AAATAAAAAAC
Found at i:40097655 original size:60 final size:59
Alignment explanation
Indices: 40097554--40097741 Score: 216
Period size: 62 Copynumber: 3.1 Consensus size: 59
40097544 TTATAAAAAT
* * * * * *
40097554 AATAAACAAATAAAAAATAGAAAAATGAAATAAAGAAAAACAAATAAAAAAGAGA-AAAATGA
1 AATAAAGAAA-AACAAATA-AAAAA-GAAA-AAGGACAAACAAATAAAAAACAAATAAAATGA
40097616 AATAAAGAAAAACAAATAAAAAACAGAAAAAGGACAAACAAATAAAAAAACAAATAAAATGA
1 AATAAAGAAAAACAAAT-AAAAA-AGAAAAAGGACAAACAAAT-AAAAAACAAATAAAATGA
* * *
40097678 AATAAAGAAAAACAAATAAAAAAGGAAAAGGACAAACAAATAAAAAATAAAAAAAATGA
1 AATAAAGAAAAACAAATAAAAAAGAAAAAGGACAAACAAATAAAAAACAAATAAAATGA
40097737 CAATA
1 -AATA
40097742 GGTAGTAGAA
Statistics
Matches: 112, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
59 16 0.14
60 34 0.30
61 27 0.24
62 35 0.31
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.10
Consensus pattern (59 bp):
AATAAAGAAAAACAAATAAAAAAGAAAAAGGACAAACAAATAAAAAACAAATAAAATGA
Done.