Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 176 of 313
Found at i:54643868 original size:30 final size:31
Alignment explanation
Indices: 54643829--54643888 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
54643819 GGAGGTGGGA
*
54643829 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
54643860 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
54643889 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:54648206 original size:44 final size:44
Alignment explanation
Indices: 54648156--54648245 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
54648146 GTTAAAATAA
* * * * * *
54648156 AATAGAAGTTGTGATAATTATACATTTAAAAATAATTATAATTT
1 AATAGAAATAGTGAAAATTACACATTTAAAAATAAATAGAATTT
54648200 AATAGAAATAGTGAAAATTACACATTTAAAAATAAATAGAATTT
1 AATAGAAATAGTGAAAATTACACATTTAAAAATAAATAGAATTT
54648244 AA
1 AA
54648246 ATTAAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.34
Consensus pattern (44 bp):
AATAGAAATAGTGAAAATTACACATTTAAAAATAAATAGAATTT
Found at i:54648509 original size:44 final size:45
Alignment explanation
Indices: 54648437--54648527 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 45
54648427 AAAGTTGGAA
* * *
54648437 AATAGAAGTTTGTCATAATTATAAATTTAAAAATAATTATAATTT
1 AATAGAAGTTTATAATAATTATAAATTTAAAAATAATTAGAATTT
54648482 AATAGAAG-TTATAATAATTA-AACATTTAAAAATAATTAGAATTT
1 AATAGAAGTTTATAATAATTATAA-ATTTAAAAATAATTAGAATTT
54648526 AA
1 AA
54648528 ATTATTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 2 0.05
44 32 0.76
45 8 0.19
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (45 bp):
AATAGAAGTTTATAATAATTATAAATTTAAAAATAATTAGAATTT
Found at i:54648527 original size:17 final size:18
Alignment explanation
Indices: 54648494--54648528 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54648484 TAGAAGTTAT
54648494 AATAATTAAACATTTAAA
1 AATAATTAAACATTTAAA
*
54648512 AATAATTAGA-ATTTAAA
1 AATAATTAAACATTTAAA
54648529 TTATTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
AATAATTAAACATTTAAA
Found at i:54648873 original size:20 final size:22
Alignment explanation
Indices: 54648839--54648884 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
54648829 GAATAAGTTA
54648839 AAAATTTTTTAATTAT-TATTT
1 AAAATTTTTTAATTATATATTT
54648860 AAAATTTTTT-ATTATAATATTT
1 AAAATTTTTTAATTAT-ATATTT
54648882 AAA
1 AAA
54648885 TTTATAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AAAATTTTTTAATTATATATTT
Found at i:54649557 original size:20 final size:20
Alignment explanation
Indices: 54649524--54649575 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
54649514 TTGCTATAAA
* * *
54649524 TATTTTAAAATTTTGAAAAT
1 TATTTTGAATTTTTGAAAAC
*
54649544 TATTTTGAATTTTTTTAAAAC
1 TATTTTGAA-TTTTTGAAAAC
54649565 TATTTTGAATT
1 TATTTTGAATT
54649576 GGTTTGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (20 bp):
TATTTTGAATTTTTGAAAAC
Found at i:54649563 original size:21 final size:21
Alignment explanation
Indices: 54649534--54649575 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54649524 TATTTTAAAA
*
54649534 TTTTGAAAATTATTTTGAATT
1 TTTTGAAAACTATTTTGAATT
*
54649555 TTTTTAAAACTATTTTGAATT
1 TTTTGAAAACTATTTTGAATT
54649576 GGTTTGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTGAAAACTATTTTGAATT
Found at i:54651193 original size:17 final size:17
Alignment explanation
Indices: 54651171--54651209 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
54651161 ACTTTATTGT
54651171 ATTTATTAATT-AATATA
1 ATTTATT-ATTAAATATA
*
54651188 ATTTATTATTAAATTTA
1 ATTTATTATTAAATATA
54651205 ATTTA
1 ATTTA
54651210 ATAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATTATTAAATATA
Found at i:54655792 original size:21 final size:22
Alignment explanation
Indices: 54655766--54655812 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
54655756 CTCTGCTCAA
*
54655766 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
54655787 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
54655809 ACTC
1 ACTC
54655813 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:54656835 original size:21 final size:22
Alignment explanation
Indices: 54656809--54656855 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
54656799 CTCTGCTCAA
*
54656809 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
54656830 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
54656852 ACTC
1 ACTC
54656856 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:54666198 original size:15 final size:15
Alignment explanation
Indices: 54666177--54666217 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
54666167 AACTAAACAC
54666177 AAATAAAATTAATA-
1 AAATAAAATTAATAG
*
54666191 ATAATAAAATAAATAG
1 A-AATAAAATTAATAG
54666207 AAA-AAAATTAA
1 AAATAAAATTAA
54666218 GAAGGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 8 0.35
15 14 0.61
16 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAATAAAATTAATAG
Found at i:54669809 original size:16 final size:15
Alignment explanation
Indices: 54669784--54669813 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54669774 ATTAAGTTAA
54669784 TTAACTAAATGCAAG
1 TTAACTAAATGCAAG
54669799 TTAACCTAAATGCAA
1 TTAA-CTAAATGCAA
54669814 ATGAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (15 bp):
TTAACTAAATGCAAG
Found at i:54681191 original size:29 final size:29
Alignment explanation
Indices: 54681128--54681195 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
54681118 TAATCAACCG
54681128 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
54681157 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
54681186 CGCACACTTA
1 CGCACACTTA
54681196 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:54681308 original size:174 final size:174
Alignment explanation
Indices: 54681017--54681344 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
54681007 AACTCAAGGT
* *
54681017 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
54681082 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
54681147 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
54681191 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
54681256 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
54681321 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
54681345 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:54681336 original size:29 final size:30
Alignment explanation
Indices: 54681297--54681375 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
54681287 CTTAATAATC
54681297 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
54681327 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
54681356 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
54681376 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:54708476 original size:11 final size:11
Alignment explanation
Indices: 54708460--54708502 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
54708450 GTTTTAATTA
54708460 AATAAAATATT
1 AATAAAATATT
54708471 AAT-AAATATCT
1 AATAAAATAT-T
54708482 AATTAAAATATT
1 AA-TAAAATATT
54708494 AATAAAATA
1 AATAAAATA
54708503 ATATTTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.21
11 13 0.45
12 4 0.14
13 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAAAATATT
Found at i:54709791 original size:38 final size:38
Alignment explanation
Indices: 54709740--54709815 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
54709730 TATATTGACT
54709740 TGTTTTAAAAACAGTTTGACTAATTGAAAGAATTCTAA
1 TGTTTTAAAAACAGTTTGACTAATTGAAAGAATTCTAA
54709778 TGTTTTAAAAACAGTTTGACTAATTGAAAGAATTCTAA
1 TGTTTTAAAAACAGTTTGACTAATTGAAAGAATTCTAA
54709816 CTTATTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (38 bp):
TGTTTTAAAAACAGTTTGACTAATTGAAAGAATTCTAA
Found at i:54709836 original size:38 final size:38
Alignment explanation
Indices: 54709744--54709825 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
54709734 TTGACTTGTT
*
54709744 TTAAAAACAGTTTGACTAATTGAAAGAATTCTAATGTT
1 TTAAAAACAGTTTGACTAATTGAAAGAATTCTAATGTA
54709782 TTAAAAACAGTTTGACTAATTGAAAGAATTCTAACT-TA
1 TTAAAAACAGTTTGACTAATTGAAAGAATTCTAA-TGTA
54709820 TTAAAA
1 TTAAAA
54709826 TTATTTTGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
38 41 0.98
39 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (38 bp):
TTAAAAACAGTTTGACTAATTGAAAGAATTCTAATGTA
Found at i:54709966 original size:22 final size:24
Alignment explanation
Indices: 54709940--54709983 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
54709930 ATTTTGTTCA
54709940 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
54709962 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
54709984 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:54715424 original size:18 final size:17
Alignment explanation
Indices: 54715392--54715426 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
54715382 TTTACAAACT
*
54715392 TAAAAAATATATTAAAA
1 TAAAAAATAAATTAAAA
54715409 TAAAAAATAAATTTAAAA
1 TAAAAAATAAA-TTAAAA
54715427 AAGGAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATAAATTAAAA
Found at i:54721231 original size:25 final size:25
Alignment explanation
Indices: 54721184--54721231 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
54721174 TAGGCTAACT
* *
54721184 AGAGTTTAAGTGAGAAACTAAAAAC
1 AGAGTTTAACTGAGAAACGAAAAAC
54721209 AGAGTTTAACTGAGAGAA-GAAAA
1 AGAGTTTAACTGAGA-AACGAAAA
54721232 CTAAAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (25 bp):
AGAGTTTAACTGAGAAACGAAAAAC
Found at i:54722804 original size:27 final size:27
Alignment explanation
Indices: 54722774--54722831 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
54722764 ATGATAATGA
*
54722774 ATTTAAATTTTTTTATTAGTT-TTTTAT
1 ATTTAAATTTATTTATT-GTTATTTTAT
* *
54722801 ATTTATATTTATTTATTGTTATTTTCT
1 ATTTAAATTTATTTATTGTTATTTTAT
54722828 ATTT
1 ATTT
54722832 TAGCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (27 bp):
ATTTAAATTTATTTATTGTTATTTTAT
Found at i:54741268 original size:4 final size:4
Alignment explanation
Indices: 54741259--54741286 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
54741249 TACTAGTCTC
54741259 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
54741287 CCATTTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:54743028 original size:45 final size:45
Alignment explanation
Indices: 54742964--54743056 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
54742954 AATTTGTTCA
54742964 CTCAAATACACTCACAAAATACATTCCACAATGAACAGACAAGTG
1 CTCAAATACACTCACAAAATACATTCCACAATGAACAGACAAGTG
*
54743009 CTCAAATACACTCACAAAATACGTTCCACAATGAACAGACAAGTG
1 CTCAAATACACTCACAAAATACATTCCACAATGAACAGACAAGTG
54743054 CTC
1 CTC
54743057 TCAATACTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.44, C:0.28, G:0.10, T:0.18
Consensus pattern (45 bp):
CTCAAATACACTCACAAAATACATTCCACAATGAACAGACAAGTG
Found at i:54744548 original size:20 final size:21
Alignment explanation
Indices: 54744525--54744563 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
54744515 ATATGTGTAT
*
54744525 AATAATTAGTGTT-TAAATGA
1 AATAAATAGTGTTATAAATGA
*
54744545 AATAAATATTGTTATAAAT
1 AATAAATAGTGTTATAAAT
54744564 TTATTGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (21 bp):
AATAAATAGTGTTATAAATGA
Found at i:54746599 original size:17 final size:17
Alignment explanation
Indices: 54746577--54746609 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54746567 GATGAATGAC
54746577 TTAATT-ACTATTTCATA
1 TTAATTGACT-TTTCATA
54746594 TTAATTGACTTTTCAT
1 TTAATTGACTTTTCAT
54746610 GAAGGAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (17 bp):
TTAATTGACTTTTCATA
Found at i:54749439 original size:26 final size:26
Alignment explanation
Indices: 54749401--54749506 Score: 124
Period size: 26 Copynumber: 4.1 Consensus size: 26
54749391 TGTACCTAAA
*
54749401 TAGCAGGCCTTGAGCCGGTGTTTATT
1 TAGCAGGCTTTGAGCCGGTGTTTATT
* * * *
54749427 TAGCAAGCTTTGAGCTGGTGATTACT
1 TAGCAGGCTTTGAGCCGGTGTTTATT
* * *
54749453 T-GCAGGCTATGAGCTGGTGCTTATT
1 TAGCAGGCTTTGAGCCGGTGTTTATT
*
54749478 TAGCAGGCTTTGAGCCAGTGTTTATT
1 TAGCAGGCTTTGAGCCGGTGTTTATT
54749504 TAG
1 TAG
54749507 TAGGTACTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
25 21 0.32
26 45 0.68
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.36
Consensus pattern (26 bp):
TAGCAGGCTTTGAGCCGGTGTTTATT
Found at i:54761633 original size:26 final size:26
Alignment explanation
Indices: 54761602--54761654 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
54761592 CCCAAATCAT
*
54761602 ATAAATAAACAAAATATAA-AAAAATA
1 ATAAATAAA-AAAATAAAACAAAAATA
54761628 ATAAATAAAAAAATAAAACAAAAATA
1 ATAAATAAAAAAATAAAACAAAAATA
54761654 A
1 A
54761655 AGTAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (26 bp):
ATAAATAAAAAAATAAAACAAAAATA
Found at i:54761651 original size:11 final size:11
Alignment explanation
Indices: 54761604--54761655 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
54761594 CAAATCATAT
54761604 AAAT-AAACAA
1 AAATAAAACAA
54761614 AATATAAAA-AA
1 AA-ATAAAACAA
*
54761625 ATAATAAATAAAA
1 A-AATAAA-ACAA
54761638 AAATAAAACAA
1 AAATAAAACAA
54761649 AAATAAA
1 AAATAAA
54761656 GTAATTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 2 0.06
11 20 0.56
12 11 0.31
13 3 0.08
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (11 bp):
AAATAAAACAA
Found at i:54763200 original size:14 final size:14
Alignment explanation
Indices: 54763181--54763207 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54763171 ATATAGATAT
54763181 ACTATTTTTATTAA
1 ACTATTTTTATTAA
54763195 ACTATTTTTATTA
1 ACTATTTTTATTA
54763208 TACATATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
ACTATTTTTATTAA
Found at i:54768349 original size:23 final size:23
Alignment explanation
Indices: 54768323--54768420 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
54768313 ATAAGTGCCA
54768323 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54768346 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
54768369 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54768391 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54768414 CACTGAT
1 CACTGAT
54768421 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54768388 original size:45 final size:45
Alignment explanation
Indices: 54768330--54768418 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
54768320 CCACACTGAT
* *
54768330 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
54768375 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
54768419 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:54777265 original size:145 final size:145
Alignment explanation
Indices: 54776999--54777323 Score: 526
Period size: 145 Copynumber: 2.2 Consensus size: 145
54776989 TGAAGTCGAT
* *
54776999 AATCCTATCTCCTTGAAGTTACAATAGAGCGGATTAAAATAAAGAATCTTATCTCTCTAAAATTA
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTAAAATTA
* * *
54777064 CAGTAGAATAGATCGCATCATGTCTTATCTCCTTGAGATTATAGTGAAATAAACCGAAGAATTCC
66 CAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAAACCGAAGAATTCC
54777129 TAATCGAAAATGGTG
131 TAATCGAAAATGGTG
*
54777144 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAATG-ATCTTATTTCTCTAAAATT
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAA-GAATCTTATCTCTCTAAAATT
* *
54777208 ACAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTC
65 ACAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAAACCGAAGAATTC
54777273 CTAATCGAAAATGGTG
130 CTAATCGAAAATGGTG
* * * *
54777289 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATT
54777324 GAAGCTAGAA
Statistics
Matches: 167, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
145 166 0.99
146 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (145 bp):
AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTAAAATTA
CAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAAACCGAAGAATTCC
TAATCGAAAATGGTG
Found at i:54777338 original size:145 final size:143
Alignment explanation
Indices: 54776999--54777366 Score: 493
Period size: 145 Copynumber: 2.5 Consensus size: 143
54776989 TGAAGTCGAT
* * * *
54776999 AATCCTATCTCCTTGAAGTTACAATAGAGCGGATTAAAATAAAGAATCTTATCTCTCTAAAATTA
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAT-AA-AATCTTATCTCTCTAAAATTA
* * *
54777064 CAGTAGAATAGATCGCATCATGTCTTATCTCCTTGAGATTATAGTGAAATAAACCGAAGAATTCC
64 CAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAAACCGAAGAATTCC
54777129 TAATCGAAAATGGTG
129 TAATCGAAAATGGTG
* * *
54777144 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAATGATCTTATTTCTCTAAAATTA
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAA--ATCTTATCTCTCTAAAATTA
* *
54777209 CAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCC
64 CAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAAACCGAAGAATTCC
54777274 TAATCGAAAATGGTG
129 TAATCGAAAATGGTG
* * ** * * *
54777289 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGATATTA
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATA-AAATCTTATCTCTCTAAAATTA
* *
54777354 CAGTGGAGTAGAT
64 CAGTAGAATAGAT
54777367 TGAAGCCGAT
Statistics
Matches: 199, Mismatches: 20, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
143 1 0.01
144 2 0.01
145 190 0.95
146 4 0.02
147 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (143 bp):
AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAATCTTATCTCTCTAAAATTACA
GTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAAACCGAAGAATTCCTA
ATCGAAAATGGTG
Found at i:54777355 original size:44 final size:44
Alignment explanation
Indices: 54777289--54777411 Score: 167
Period size: 44 Copynumber: 2.8 Consensus size: 44
54777279 GAAAATGGTG
54777289 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCTAGA-
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-AGAT
** * *
54777333 AATCTTATCTCCCTGATATTACAGTGGAGTAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCAGAT
** *
54777377 AATCCAATCTCCTTGAGGTTACAGTGGAGCAGATT
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
54777412 AAAATAAATG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.03
44 66 0.97
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCAGAT
Found at i:54777431 original size:44 final size:43
Alignment explanation
Indices: 54777290--54777431 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 43
54777280 AAAATGGTGA
**
54777290 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCTAGAA-
1 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-AAAATA-AAT
** * * ****
54777334 ATCTTATCTCCCTGATATTACAGTGGAGTAGATTGAAGCCGAT
1 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAATAAAT
** *
54777377 AATCCAATCTCCTTGAGGTTACAGTGGAGCAGATTAAAATAAAT
1 -ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAATAAAT
54777421 GATCTTATCTC
1 -ATCTTATCTC
54777432 TCTAAAATTA
Statistics
Matches: 73, Mismatches: 23, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 71 0.97
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAATAAAT
Found at i:54777440 original size:233 final size:232
Alignment explanation
Indices: 54777144--54777809 Score: 1131
Period size: 233 Copynumber: 2.9 Consensus size: 232
54777134 GAAAATGGTG
*
54777144 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAATGATCTTATTTCTCTAAAATTA
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAATAAATGATCTTA-TTCTCTAAAATTA
*
54777209 CAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCC
65 CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCC
*
54777274 TAATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCTAGAAATCTT
130 TAATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTT
* *
54777339 ATCTCCCTGATATTACAGTGGAGTAGATTGAAGCCGAT
195 ATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
* *
54777377 AATCCAATCTCCTTGAGGTTACAGTGGAGCAGATTAAAATAAATGATCTTATCTCTCTAAAATTA
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAATAAATGATCTTAT-TCTCTAAAATTA
* * *
54777442 CAGTAGAGTAGATCACATCAGGTCTTATCTCCCTAAGATTACAATGGAATAGACCGAAGAATTCC
65 CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCC
*
54777507 TAATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAAAATCTT
130 TAATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTT
*
54777572 ATCTCTCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
195 ATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
* *
54777610 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAATAAAAGATCTTA---TCTGAAATTAC
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAATAAATGATCTTATTCTCTAAAATTAC
* * *
54777672 AGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGATTACAGTGGAATAGATCGAAGAACTCCT
66 AGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCCT
*
54777737 AATCGAAAATGGTGAATCTTATCTCCTTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTA
131 AATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTA
54777802 TCTCCCTG
196 TCTCCCTG
54777810 CGGTATAGTG
Statistics
Matches: 407, Mismatches: 25, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
229 139 0.34
232 1 0.00
233 267 0.66
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (232 bp):
AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAATAAATGATCTTATTCTCTAAAATTAC
AGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCCT
AATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTA
TCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
Found at i:54777663 original size:44 final size:44
Alignment explanation
Indices: 54777522--54777644 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 44
54777512 GAAAATGGTG
* *
54777522 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAA
1 AATCTTATCTCCTTGAAGTTACAGTGGAGCAGATTGAAGCCAAA
* *
54777566 AATCTTATCT-CTCTG-AGATTACAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCT-TGAAG-TTACAGTGGAGCAGATTGAAGCCAAA
*
54777610 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATT
1 AATCTTATCTCCTTGAAGTTACAGTGGAGCAGATT
54777645 AAAATAAAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
43 2 0.03
44 64 0.91
45 4 0.06
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCTTGAAGTTACAGTGGAGCAGATTGAAGCCAAA
Found at i:54777967 original size:50 final size:49
Alignment explanation
Indices: 54777848--54777968 Score: 111
Period size: 50 Copynumber: 2.4 Consensus size: 49
54777838 ACGACAGATA
* * *
54777848 TTGCTTCCCCAACATTGCAGTTAGAAAGATTGAAGCTGCAATAGTGAATC
1 TTGCTTCCCCGACATTGCAG-TAGAAAGATTGAAGCTACAAAAGTGAATC
* * * ** *
54777898 TTACTGCCCAGTA-GGTGCAGTGGAACAGATTGAAGCTACAACAAG-GAATC
1 TTGCTTCCCCG-ACATTGCAGTAGAA-AGATTGAAGCTACAA-AAGTGAATC
54777948 TTGCTTCCCCGACATTGCAGT
1 TTGCTTCCCCGACATTGCAGT
54777969 TAAACGGATT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
49 5 0.09
50 45 0.85
51 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (49 bp):
TTGCTTCCCCGACATTGCAGTAGAAAGATTGAAGCTACAAAAGTGAATC
Found at i:54778250 original size:18 final size:18
Alignment explanation
Indices: 54778220--54778267 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
54778210 CAAATCAAAT
*
54778220 AAATAAACA-AAATATAAA
1 AAATAAAAATAAATA-AAA
*
54778238 AAA-AATAATAAATAAAA
1 AAATAAAAATAAATAAAA
54778255 AAATAAAAATAAA
1 AAATAAAAATAAA
54778268 GTTATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATAAAAATAAATAAAA
Found at i:54778390 original size:26 final size:27
Alignment explanation
Indices: 54778349--54778399 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
54778339 CAAACAGATC
*
54778349 CCAAATACCCACTTAACCTAGCCCAAA
1 CCAAATACCCAATTAACCTAGCCCAAA
*
54778376 CCAAA-ACCCAATTAACTTAGCCCA
1 CCAAATACCCAATTAACCTAGCCCA
54778400 GCTAATGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.41, C:0.39, G:0.04, T:0.16
Consensus pattern (27 bp):
CCAAATACCCAATTAACCTAGCCCAAA
Found at i:54779856 original size:14 final size:14
Alignment explanation
Indices: 54779837--54779863 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54779827 ATATAGATAT
54779837 ACTATTTTTATTAA
1 ACTATTTTTATTAA
54779851 ACTATTTTTATTA
1 ACTATTTTTATTA
54779864 TACATATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
ACTATTTTTATTAA
Found at i:54780052 original size:18 final size:18
Alignment explanation
Indices: 54780024--54780064 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
54780014 TGATGTGAGC
54780024 TTATTGTCTTATGTGTAT
1 TTATTGTCTTATGTGTAT
*
54780042 TGTATTG-CTTATTTGTAT
1 T-TATTGTCTTATGTGTAT
54780060 TTATT
1 TTATT
54780065 AATTATTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.63
Consensus pattern (18 bp):
TTATTGTCTTATGTGTAT
Found at i:54783175 original size:18 final size:20
Alignment explanation
Indices: 54783135--54783179 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
54783125 AATATGATAA
54783135 ATTTATAAACGATAAAATAT
1 ATTTATAAACGATAAAATAT
*
54783155 ATTTA-AAATGATAAAAT-T
1 ATTTATAAACGATAAAATAT
54783173 ATTTATA
1 ATTTATA
54783180 TAATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 12 0.52
20 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
ATTTATAAACGATAAAATAT
Found at i:54784188 original size:22 final size:24
Alignment explanation
Indices: 54784142--54784191 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
54784132 GAACCAAATA
*
54784142 TAAAAAACATATTAATTTAATAAT
1 TAAAAAACATATTAATTAAATAAT
*
54784166 TAAATAACATA-TAA-TAAATAAT
1 TAAAAAACATATTAATTAAATAAT
54784188 TAAA
1 TAAA
54784192 CATTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 3 0.12
24 10 0.42
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAAAAACATATTAATTAAATAAT
Found at i:54795053 original size:25 final size:25
Alignment explanation
Indices: 54795007--54795054 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
54794997 AAATACTATC
*
54795007 AAAAATTTTAAAAATATTTTTTCGT
1 AAAAATTTTAAAAATATCTTTTCGT
*
54795032 AAAACTTTTCAAAAATA-CTTTTC
1 AAAAATTTT-AAAAATATCTTTTC
54795055 AACTTCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAAATTTTAAAAATATCTTTTCGT
Found at i:54797033 original size:24 final size:22
Alignment explanation
Indices: 54796985--54797034 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
54796975 ATACTTATTC
*
54796985 TTTATATATAAATATATTTTCT
1 TTTATATATAAATAAATTTTCT
54797007 TTTATATGAATAAATAAAGTTTT-T
1 TTTATAT--ATAAATAAA-TTTTCT
54797031 TTTA
1 TTTA
54797035 AGATCTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
24 13 0.54
25 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTATATATAAATAAATTTTCT
Found at i:54798869 original size:309 final size:310
Alignment explanation
Indices: 54798250--54798882 Score: 1133
Period size: 309 Copynumber: 2.0 Consensus size: 310
54798240 GATGACATTT
54798250 AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
1 AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
*
54798315 AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCGATTCCATA
66 AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCAATTCCATA
54798380 AAATGAAAAATTATTGAAAGAAAAGAGAAAGAAATGAAGATGGTCATATGCTAAAGAAGGCGAGT
131 AAATGAAAAATTATT----------AGAAAGAAATGAAGATGGTCATATGCTAAAGAAGGCGAGT
*
54798445 ACTCATGAAGAGACCCAAGGCATAACTTTTGATAAAACCCTAACAGAGGTTCAGGTACATGAAAT
186 ACTCATGAAGAGACCCAAGGCATAACTCTTGATAAAACCCTAACAGAGGTTCAGGTACATGAAAT
54798510 TATAAATATAATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
251 TATAAATATAATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
54798570 AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
1 AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
54798635 AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCAATTCCATA
66 AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCAATTCCATA
*
54798700 AAATGAAAAATTATT-GAAAGAAATGAATATGGTCATATGCTAAAGAAGGCGAGTACTCATGAAG
131 AAATGAAAAATTATTAGAAAGAAATGAAGATGGTCATATGCTAAAGAAGGCGAGTACTCATGAAG
*
54798764 AGACCCAAGGCATAACTCTTGATAAACCCCTAACAGAGGTTCAGGTACATGAAATTATAAATATA
196 AGACCCAAGGCATAACTCTTGATAAAACCCTAACAGAGGTTCAGGTACATGAAATTATAAATATA
54798829 ATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
261 ATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
54798879 AAAG
1 AAAG
54798883 GAAATTATTG
Statistics
Matches: 309, Mismatches: 4, Indels: 11
0.95 0.01 0.03
Matches are distributed among these distances:
309 165 0.53
320 144 0.47
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (310 bp):
AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCAATTCCATA
AAATGAAAAATTATTAGAAAGAAATGAAGATGGTCATATGCTAAAGAAGGCGAGTACTCATGAAG
AGACCCAAGGCATAACTCTTGATAAAACCCTAACAGAGGTTCAGGTACATGAAATTATAAATATA
ATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
Found at i:54800366 original size:3 final size:3
Alignment explanation
Indices: 54800358--54800426 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
54800348 TTCTTTGCAG
* * * * *
54800358 TAT TAT TAT TGT TGT AAT TAT TAT TAC TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54800406 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
54800427 ATAAAACAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:54800761 original size:14 final size:14
Alignment explanation
Indices: 54800742--54800771 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54800732 TACCATTTTA
54800742 TTGCTAATTCTTCT
1 TTGCTAATTCTTCT
54800756 TTGCTAATTCTTCT
1 TTGCTAATTCTTCT
54800770 TT
1 TT
54800772 TACCATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.07, T:0.60
Consensus pattern (14 bp):
TTGCTAATTCTTCT
Found at i:54805040 original size:13 final size:13
Alignment explanation
Indices: 54805022--54805051 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
54805012 AACCCAAACT
54805022 CAATTACCCAACC
1 CAATTACCCAACC
54805035 CAATTACCCAACC
1 CAATTACCCAACC
54805048 CAAT
1 CAAT
54805052 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:54805132 original size:20 final size:20
Alignment explanation
Indices: 54805107--54805146 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54805097 CGTAAAATGA
*
54805107 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
54805127 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
54805147 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:54805136 original size:34 final size:35
Alignment explanation
Indices: 54805092--54805158 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54805082 CAGTAAAATA
* *
54805092 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
54805126 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
54805159 CTAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:54805824 original size:9 final size:9
Alignment explanation
Indices: 54805812--54805897 Score: 84
Period size: 9 Copynumber: 9.4 Consensus size: 9
54805802 AAATAAAAAA
54805812 AATTCGGGT
1 AATTCGGGT
54805821 AATTCGGGT
1 AATTCGGGT
*
54805830 ATTTTTC-GGT
1 A--ATTCGGGT
* *
54805840 AATTCAGTT
1 AATTCGGGT
*
54805849 AATTCGGTT
1 AATTCGGGT
*
54805858 AATTCGGTT
1 AATTCGGGT
*
54805867 AATTCGGTT
1 AATTCGGGT
54805876 AATTCGGGT
1 AATTCGGGT
*
54805885 AATTCGGAT
1 AATTCGGGT
54805894 AATT
1 AATT
54805898 TTTAACCAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
8 3 0.04
9 58 0.85
10 4 0.06
11 3 0.04
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:54805862 original size:18 final size:18
Alignment explanation
Indices: 54805834--54805897 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
54805824 TCGGGTATTT
*
54805834 TTCGG-TAATTCAGTTAA
1 TTCGGTTAATTCGGTTAA
54805851 TTCGGTTAATTCGGTTAA
1 TTCGGTTAATTCGGTTAA
*
54805869 TTCGGTTAATTCGGGTAA
1 TTCGGTTAATTCGGTTAA
*
54805887 TTCGGATAATT
1 TTCGGTTAATT
54805898 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 5 0.12
18 38 0.88
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (18 bp):
TTCGGTTAATTCGGTTAA
Found at i:54805876 original size:27 final size:26
Alignment explanation
Indices: 54805820--54805897 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 26
54805810 AAAATTCGGG
*
54805820 TAATTCGGGTATTTTTCGGTAATTCAGT
1 TAATTCGGGTA--ATTCGGTAATTCAGT
* *
54805848 TAATTCGGTTAATTCGGTTAATTCGGT
1 TAATTCGGGTAATTCGG-TAATTCAGT
54805875 TAATTCGGGTAATTCGGATAATT
1 TAATTCGGGTAATTCGG-TAATT
54805898 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
26 5 0.11
27 29 0.66
28 10 0.23
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (26 bp):
TAATTCGGGTAATTCGGTAATTCAGT
Found at i:54806571 original size:68 final size:67
Alignment explanation
Indices: 54806499--54806631 Score: 175
Period size: 63 Copynumber: 2.0 Consensus size: 67
54806489 TGGCACTTCT
*
54806499 ATTACTTGCTCTTTGAATTTCTCTTGAGTGTGGTTTTATTGTGGTAGTT-T-TTTTT-TTTTT-T
1 ATTACTTGCTCTTTGAA---CTC--GACTGTGGTTTTATTGTGGTAGTTCTCTTTTTGTTTTTAT
54806560 AGGTTCC
61 AGGTTCC
*
54806567 ATTACTTTCTCTTTGAACTCGACTGTGGTTTTATTGTGGTAGTTCTCTTTTTGTTTTTATAGGTT
1 ATTACTTGCTCTTTGAACTCGACTGTGGTTTTATTGTGGTAGTTCTCTTTTTGTTTTTATAGGTT
54806632 TAGAGAACCA
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
63 23 0.39
64 1 0.02
65 8 0.14
66 5 0.08
67 6 0.10
68 16 0.27
ACGTcount: A:0.13, C:0.11, G:0.19, T:0.57
Consensus pattern (67 bp):
ATTACTTGCTCTTTGAACTCGACTGTGGTTTTATTGTGGTAGTTCTCTTTTTGTTTTTATAGGTT
CC
Found at i:54811415 original size:11 final size:11
Alignment explanation
Indices: 54811379--54811417 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
54811369 TAAATAGTAA
*
54811379 TTTATTAATAT
1 TTTAATAATAT
54811390 TTTAATGAGATAT
1 TTTAAT-A-ATAT
54811403 TTTAATAATAT
1 TTTAATAATAT
54811414 TTTA
1 TTTA
54811418 TTTAAAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 13 0.52
12 2 0.08
13 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:54814639 original size:14 final size:14
Alignment explanation
Indices: 54814616--54814674 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 14
54814606 TATGAATAAT
54814616 AATATAATAAAACAA
1 AATATAATAAAAC-A
54814631 ATATCATAATAAAA-A
1 A-AT-ATAATAAAACA
*
54814646 AATATGATAATAA-A
1 AATATAATAA-AACA
54814660 AATA-AATAAAACA
1 AATATAATAAAACA
54814673 AA
1 AA
54814675 AAAGAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 2 0.05
13 13 0.34
14 9 0.24
15 3 0.08
16 2 0.05
17 9 0.24
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (14 bp):
AATATAATAAAACA
Found at i:54814650 original size:16 final size:16
Alignment explanation
Indices: 54814619--54814661 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
54814609 GAATAATAAT
54814619 ATAATAAAACAAATATC
1 ATAATAAAA-AAATATC
*
54814636 ATAATAAAAAAATATG
1 ATAATAAAAAAATATC
54814652 ATAATAAAAA
1 ATAATAAAAA
54814662 TAAATAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (16 bp):
ATAATAAAAAAATATC
Found at i:54814661 original size:17 final size:17
Alignment explanation
Indices: 54814619--54814667 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
54814609 GAATAATAAT
*
54814619 ATAATAAAACAAATATC
1 ATAATAAAAAAAATATC
*
54814636 ATAAT-AAAAAAATATG
1 ATAATAAAAAAAATATC
54814652 ATAATAAAAATAAATA
1 ATAATAAAAA-AAATA
54814668 AAACAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 14 0.50
17 9 0.32
18 5 0.18
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (17 bp):
ATAATAAAAAAAATATC
Found at i:54816790 original size:27 final size:30
Alignment explanation
Indices: 54816756--54816810 Score: 80
Period size: 27 Copynumber: 1.9 Consensus size: 30
54816746 TCTTTATTGA
54816756 TATATTTTTC-TCTTTT-TTT-ATTTTAAT
1 TATATTTTTCATCTTTTCTTTCATTTTAAT
*
54816783 TATATTTTTCATTTTTTCTTTCATTTTA
1 TATATTTTTCATCTTTTCTTTCATTTTA
54816811 TTTTTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 5 0.21
29 3 0.12
30 6 0.25
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (30 bp):
TATATTTTTCATCTTTTCTTTCATTTTAAT
Found at i:54816816 original size:12 final size:12
Alignment explanation
Indices: 54816771--54816816 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
54816761 TTTTCTCTTT
*
54816771 TTTTA-TTTTAA
1 TTTTATTTTTCA
*
54816782 TTATATTTTTCA
1 TTTTATTTTTCA
54816794 TTTT-TTCTTTCA
1 TTTTATT-TTTCA
54816806 TTTTATTTTTC
1 TTTTATTTTTC
54816817 CAATTTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 6 0.21
12 21 0.72
13 2 0.07
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:54826912 original size:2 final size:2
Alignment explanation
Indices: 54826905--54826929 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54826895 TTCCAATAGC
54826905 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
54826930 TTAAAATGGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54828364 original size:30 final size:31
Alignment explanation
Indices: 54828328--54828385 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
54828318 AAAAATCAAG
*
54828328 AAAATTAACATCACAAAC-AAAATCCATTAA
1 AAAATTAACATAACAAACAAAAATCCATTAA
54828358 AAAATTAACATAACAAACAAAAATCCAT
1 AAAATTAACATAACAAACAAAAATCCAT
54828386 CAATCTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (31 bp):
AAAATTAACATAACAAACAAAAATCCATTAA
Found at i:54830203 original size:21 final size:21
Alignment explanation
Indices: 54830174--54830213 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54830164 AATAAAAAAA
54830174 AAAGCCTTTACCAAGAATACT
1 AAAGCCTTTACCAAGAATACT
* *
54830195 AAAGGCTTTTCCAAGAATA
1 AAAGCCTTTACCAAGAATA
54830214 GCAAGAGCAT
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:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (21 bp):
AAAGCCTTTACCAAGAATACT
Found at i:54830862 original size:58 final size:59
Alignment explanation
Indices: 54830751--54830869 Score: 222
Period size: 58 Copynumber: 2.0 Consensus size: 59
54830741 ATAAAACAAA
*
54830751 AGAAAGAATCATCAGCTTCTTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
1 AGAAAGAATCATCAGCTTATTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
54830810 AGAAAGAATCATCAGCTTATTCATTTT-TTTTAACTCCCATCGAAAATCCATTGTTGTT
1 AGAAAGAATCATCAGCTTATTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
54830868 AG
1 AG
54830870 TCTCCAAGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 33 0.56
59 26 0.44
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (59 bp):
AGAAAGAATCATCAGCTTATTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
Found at i:54832819 original size:10 final size:11
Alignment explanation
Indices: 54832798--54832980 Score: 96
Period size: 11 Copynumber: 17.9 Consensus size: 11
54832788 GGCCCATTTT
54832798 TATTTT-AAAA
1 TATTTTAAAAA
54832808 -ATTTTAAAAA
1 TATTTTAAAAA
*
54832818 -A-TTAAAAAA
1 TATTTTAAAAA
54832827 GTATTTTAAAAA
1 -TATTTTAAAAA
54832839 TATTTTAAAAA
1 TATTTTAAAAA
54832850 TATTTT--AAA
1 TATTTTAAAAA
**
54832859 -ATTAAAAAAA
1 TATTTTAAAAA
* **
54832869 AATTAAAAAAA
1 TATTTTAAAAA
*
54832880 GTATTTTAAAAT
1 -TATTTTAAAAA
54832892 TATTTT--AAA
1 TATTTTAAAAA
54832901 -A--TTAAAAA
1 TATTTTAAAAA
* *
54832909 -AATTAAAAAA
1 TATTTTAAAAA
54832919 GTATTTTAAAAA
1 -TATTTTAAAAA
54832931 TA-TTT-AAAA
1 TATTTTAAAAA
54832940 -A-TTTAAAAA
1 TATTTTAAAAA
*
54832949 -AATTTAAAAA
1 TATTTTAAAAA
* *
54832959 GTATGTAAAAAA
1 -TATTTTAAAAA
54832971 TATTTTAAAA
1 TATTTTAAAA
54832981 TTAAAAAAAT
Statistics
Matches: 138, Mismatches: 17, Indels: 35
0.73 0.09 0.18
Matches are distributed among these distances:
6 2 0.01
8 12 0.09
9 26 0.19
10 25 0.18
11 44 0.32
12 29 0.21
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:54832878 original size:40 final size:41
Alignment explanation
Indices: 54832798--54832989 Score: 232
Period size: 40 Copynumber: 4.7 Consensus size: 41
54832788 GGCCCATTTT
* * * *
54832798 TATTTTAAAAAT-TTTAAAAAATTAAAAAAGTATTTTAAAAA-
1 TATTTTAAAAATATTT-TAAAATTAAAAAA-AAATTAAAAAAG
54832839 TATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAAAATT-AAAAAAG
*
54832881 TATTTTAAAATTATTTTAAAATT--AAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAAG
* * *
54832920 TATTTTAAAAATATTTAAAAATT-TAAAAAAATTTAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAAG
* *
54832960 TATGTAAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAA
54832990 TAAATATATT
Statistics
Matches: 134, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
39 28 0.21
40 47 0.35
41 34 0.25
42 25 0.19
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (41 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAAG
Found at i:54832902 original size:31 final size:30
Alignment explanation
Indices: 54832845--54832911 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
54832835 AAAATATTTT
54832845 AAAAATATTTTAAAATTAAAAAAAAATTAA
1 AAAAATATTTTAAAATTAAAAAAAAATTAA
****
54832875 AAAAAGTATTTTAAAATTATTTTAAAATTAA
1 AAAAA-TATTTTAAAATTAAAAAAAAATTAA
54832906 AAAAAT
1 AAAAAT
54832912 TAAAAAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAAATATTTTAAAATTAAAAAAAAATTAA
Found at i:54832916 original size:8 final size:9
Alignment explanation
Indices: 54832898--54832990 Score: 53
Period size: 9 Copynumber: 9.6 Consensus size: 9
54832888 AAATTATTTT
54832898 AAAATTAAA
1 AAAATTAAA
54832907 AAAATTAAA
1 AAAATTAAA
54832916 AAAGTATTTTAAA
1 AAA--A--TTAAA
* *
54832929 AATATTTAA
1 AAAATTAAA
*
54832938 AAATTTAAA
1 AAAATTAAA
54832947 AAAATTTAAA
1 AAAA-TTAAA
*
54832957 AAGTATGTAAA
1 AA-AAT-TAAA
**
54832968 AAATATT-TT
1 AAA-ATTAAA
54832977 AAAATTAAA
1 AAAATTAAA
54832986 AAAAT
1 AAAAT
54832991 AAATATATTT
Statistics
Matches: 63, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
8 3 0.05
9 33 0.52
10 9 0.14
11 11 0.17
13 7 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAATTAAA
Found at i:54840360 original size:15 final size:17
Alignment explanation
Indices: 54840325--54840363 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
54840315 AAGTTGATTT
*
54840325 TTTTTTTAGATTTGAGC
1 TTTTTTAAGATTTGAGC
54840342 TTTTTTAAG-TTTGAG-
1 TTTTTTAAGATTTGAGC
54840357 TTTTTTA
1 TTTTTTA
54840364 TATTCGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 6 0.29
17 8 0.38
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (17 bp):
TTTTTTAAGATTTGAGC
Found at i:54843808 original size:3 final size:3
Alignment explanation
Indices: 54843800--54843836 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
54843790 TCAGCTTCTT
54843800 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
54843837 ATAATATATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54849146 original size:4 final size:4
Alignment explanation
Indices: 54849129--54849176 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
54849119 TTATTCTATT
* * * * *
54849129 TTTA TTTA TCTA TTTA TTTA TGTA TTCA TTCA TTTA TTTA TTTC TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
54849177 CTCTTTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:54849274 original size:12 final size:12
Alignment explanation
Indices: 54849235--54849275 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
54849225 CATTTTATTA
54849235 TTATTGTTGTTG
1 TTATTGTTGTTG
*
54849247 TTGTTGTTG-TG
1 TTATTGTTGTTG
54849258 ATTATTGTTGTTG
1 -TTATTGTTGTTG
54849271 TTATT
1 TTATT
54849276 TATTTTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.10, C:0.00, G:0.24, T:0.66
Consensus pattern (12 bp):
TTATTGTTGTTG
Found at i:54866098 original size:4 final size:4
Alignment explanation
Indices: 54866089--54866134 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
54866079 TATTATTCTA
* * * *
54866089 TATT TATT TATT TATT TATG TATT CATT CATT TATT TATT TCTT TA
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TA
54866135 CTCTTTTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:54878476 original size:45 final size:47
Alignment explanation
Indices: 54878427--54878520 Score: 138
Period size: 50 Copynumber: 2.0 Consensus size: 47
54878417 TGCCGAAATT
*
54878427 ATTTAAGCAACT-AAAATT-AAAACAACTTAATTCATTAAACTAATG
1 ATTTAAGCAACTAAAAATTAAAAACAACTTAATTAATTAAACTAATG
54878472 ATTTAAGCAACTAAAGAAAATTAAAAACAACTTAATTAATTAAACTAAT
1 ATTTAAGCAACT--A-AAAATTAAAAACAACTTAATTAATTAAACTAAT
54878521 TTAATTAACC
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 12 0.28
49 6 0.14
50 25 0.58
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (47 bp):
ATTTAAGCAACTAAAAATTAAAAACAACTTAATTAATTAAACTAATG
Found at i:54893300 original size:34 final size:31
Alignment explanation
Indices: 54893248--54893313 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 31
54893238 ATCTCATTAT
54893248 TAAATAAAATAAAAAAAA-TAGTAAATAATTTA
1 TAAATAAAATAAAAAAAATTA-TAAAT-ATTTA
*
54893280 TAAATAATAATTAAATAAAATTATAAATATTTA
1 TAAATAA-AA-TAAAAAAAATTATAAATATTTA
54893313 T
1 T
54893314 TTACAAGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 7 0.23
33 8 0.27
34 13 0.43
35 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (31 bp):
TAAATAAAATAAAAAAAATTATAAATATTTA
Found at i:54903626 original size:25 final size:25
Alignment explanation
Indices: 54903598--54903651 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
54903588 AGCTCCGAAT
*
54903598 AGCCATATATTGGGAAG-TTCAAGCG
1 AGCCATATATTGGGAAGCTTC-AGAG
54903623 AGCC--ATATTGGGAAGCTTCAGAG
1 AGCCATATATTGGGAAGCTTCAGAG
54903646 AGCCAT
1 AGCCAT
54903652 TAATCAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 18 0.72
24 3 0.12
25 4 0.16
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (25 bp):
AGCCATATATTGGGAAGCTTCAGAG
Found at i:54903634 original size:23 final size:23
Alignment explanation
Indices: 54903604--54903651 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
54903594 GAATAGCCAT
*
54903604 ATATTGGGAAG-TTCAAGCGAGCC
1 ATATTGGGAAGCTTC-AGAGAGCC
54903627 ATATTGGGAAGCTTCAGAGAGCC
1 ATATTGGGAAGCTTCAGAGAGCC
54903650 AT
1 AT
54903652 TAATCAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (23 bp):
ATATTGGGAAGCTTCAGAGAGCC
Found at i:54903775 original size:26 final size:26
Alignment explanation
Indices: 54903738--54903810 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
54903728 CGTGATATAT
54903738 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* * ** *
54903764 GGCTCTTTGTGAGATTCTTGATTAAT
1 GGCTCTTCGTGAGCTTCCCGATTAAA
*
54903790 GGCTCTTCG-AAGCTTCCCGAT
1 GGCTCTTCGTGAGCTTCCCGAT
54903811 ATATAGTTAC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
25 8 0.22
26 29 0.78
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:54910819 original size:27 final size:27
Alignment explanation
Indices: 54910782--54910896 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 27
54910772 AGAGGTCAAT
*
54910782 AAATGATCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
54910809 AAATGACCGAATTATCCCCACAGGTTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * * *
54910836 AAATAACCGAATTACCCCTATAGGATA
1 AAATGACCGAATTACCCCCACAGGGTA
** * *
54910863 AAATGACTAAAATACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
54910890 AAATGAC
1 AAATGAC
54910897 TATTATACCC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCACAGGGTA
Found at i:54911254 original size:28 final size:28
Alignment explanation
Indices: 54911212--54911319 Score: 198
Period size: 28 Copynumber: 3.9 Consensus size: 28
54911202 ACTGTACCGA
*
54911212 TACTGTATTAGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
54911240 TGCTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
54911268 TACTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
54911296 TACTGTATTGGGCTAAGGCCCACA
1 TACTGTATTGGGCTAAGGCCCACA
54911320 CTATACTGCT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 77 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACATTGT
Found at i:54922320 original size:15 final size:16
Alignment explanation
Indices: 54922296--54922332 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
54922286 TTGAATTAAC
*
54922296 TTTA-TTTATTT-ATT
1 TTTATTTTATTTGACT
54922310 TTTATTTTATTTGACT
1 TTTATTTTATTTGACT
54922326 TTTATTT
1 TTTATTT
54922333 AGTGAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 9 0.45
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTTGACT
Found at i:54923583 original size:6 final size:6
Alignment explanation
Indices: 54923572--54923603 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
54923562 GAAGACTGAT
54923572 TTTGCA TTTGCA TTTGCA TTTCGCA TTTGCA T
1 TTTGCA TTTGCA TTTGCA TTT-GCA TTTGCA T
54923604 GAAAATTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (6 bp):
TTTGCA
Found at i:54923597 original size:13 final size:12
Alignment explanation
Indices: 54923572--54923603 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
54923562 GAAGACTGAT
54923572 TTTGCATTTGCA
1 TTTGCATTTGCA
54923584 TTTGCATTTCGCA
1 TTTGCATTT-GCA
54923597 TTTGCAT
1 TTTGCAT
54923604 GAAAATTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:54926443 original size:25 final size:25
Alignment explanation
Indices: 54926413--54926460 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
54926403 AGGTTTGTTT
54926413 GTGAAATTATTAAGGACTTTAATCA
1 GTGAAATTATTAAGGACTTTAATCA
**
54926438 GTGAAATTATTCGGGACTTTAAT
1 GTGAAATTATTAAGGACTTTAAT
54926461 GAGGACTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (25 bp):
GTGAAATTATTAAGGACTTTAATCA
Found at i:54933549 original size:9 final size:9
Alignment explanation
Indices: 54933535--54933576 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
54933525 AACTTTGAAA
54933535 AAAATATTT
1 AAAATATTT
54933544 AAAATA-TT
1 AAAATATTT
*
54933552 AAAATTTTT
1 AAAATATTT
54933561 AAATATATATT
1 AAA-ATAT-TT
54933572 AAAAT
1 AAAAT
54933577 GAGGTAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.25
9 11 0.39
10 5 0.18
11 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAAATATTT
Found at i:54933561 original size:17 final size:18
Alignment explanation
Indices: 54933535--54933568 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54933525 AACTTTGAAA
54933535 AAAATATTTAAA-ATATT
1 AAAATATTTAAATATATT
*
54933552 AAAATTTTTAAATATAT
1 AAAATATTTAAATATAT
54933569 ATTAAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATATTTAAATATATT
Found at i:54944143 original size:25 final size:24
Alignment explanation
Indices: 54944087--54944184 Score: 74
Period size: 25 Copynumber: 4.0 Consensus size: 24
54944077 ACCACAGGTT
*
54944087 GTATGAGCTTACCGATTTCAGCTC
1 GTATGAGCTTACCGATTACAGCTC
* *
54944111 ATGA-GAGCTTACTGATTCACAGCTC
1 GT-ATGAGCTTACCGATT-ACAGCTC
*
54944136 GTATGAGCTTACC-ATTTTTCAGCTC
1 GTATGAGCTTACCGA--TTACAGCTC
* * * *
54944161 GAAAGAGCTTACCGTTTACCGCTC
1 GTATGAGCTTACCGATTACAGCTC
54944185 TTATAAGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
24 22 0.39
25 33 0.58
26 2 0.04
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (24 bp):
GTATGAGCTTACCGATTACAGCTC
Found at i:54947037 original size:18 final size:17
Alignment explanation
Indices: 54947010--54947051 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
54947000 ACATAAATTC
*
54947010 AAATAACAAAACACCTAA
1 AAATAGCAAAACA-CTAA
*
54947028 AAATAGC-AAACACTGA
1 AAATAGCAAAACACTAA
54947044 AAATAGCA
1 AAATAGCA
54947052 GTCCTAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 6 0.29
ACGTcount: A:0.62, C:0.19, G:0.07, T:0.12
Consensus pattern (17 bp):
AAATAGCAAAACACTAA
Found at i:54955636 original size:20 final size:19
Alignment explanation
Indices: 54955596--54955646 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
54955586 TAATTTCGCC
*
54955596 ATTTTTTAGTTTAATATTT
1 ATTTTTTAATTTAATATTT
54955615 ATGTTTTTAATTTAAT-TATT
1 AT-TTTTTAATTTAATAT-TT
*
54955635 ATATTTTAATTT
1 ATTTTTTAATTT
54955647 TTTTTGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTTAATTTAATATTT
Found at i:54963499 original size:3 final size:3
Alignment explanation
Indices: 54963493--54963542 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
54963483 AAACTAATAA
* * * * *
54963493 ATT ATT ATT ATT AGT AGT ATT AAT ATT ATT ATT AAT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
54963541 AT
1 AT
54963543 CATCATATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:54963706 original size:18 final size:18
Alignment explanation
Indices: 54963675--54963709 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54963665 ATATATACGC
* *
54963675 TTATATTTTTTATATATT
1 TTATAATTTATATATATT
54963693 TTATAATTTATATATAT
1 TTATAATTTATATATAT
54963710 GTATGTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATAATTTATATATATT
Found at i:54964646 original size:10 final size:11
Alignment explanation
Indices: 54964621--54964645 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54964611 ATTTGGGAGC
54964621 AAAATGAATGA
1 AAAATGAATGA
54964632 AAAATGAATGA
1 AAAATGAATGA
54964643 AAA
1 AAA
54964646 TCGGAGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (11 bp):
AAAATGAATGA
Found at i:54965250 original size:22 final size:22
Alignment explanation
Indices: 54965225--54965283 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
54965215 GAAACATAAG
* *
54965225 ATATCAGATATAGTTACAGAAC
1 ATATTAGATATAGATACAGAAC
54965247 ATATTAGATATAGATACAGAAC
1 ATATTAGATATAGATACAGAAC
* *
54965269 AGATTAGATACAGAT
1 ATATTAGATATAGAT
54965284 GTAGATTCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.27
Consensus pattern (22 bp):
ATATTAGATATAGATACAGAAC
Found at i:54972411 original size:50 final size:50
Alignment explanation
Indices: 54972295--54972587 Score: 469
Period size: 50 Copynumber: 5.8 Consensus size: 50
54972285 GATCATAACA
* ** *
54972295 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* **
54972346 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
54972396 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
54972446 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTATCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54972496 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54972546 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
54972588 TTACCCAAAT
Statistics
Matches: 222, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
50 188 0.85
51 34 0.15
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54979723 original size:50 final size:50
Alignment explanation
Indices: 54979607--54979799 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
54979597 GATCATAACA
* ** *
54979607 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* **
54979658 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
54979708 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
54979758 TGCCCATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
54979800 TTACCCAAAT
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 91 0.73
51 34 0.27
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54979788 original size:100 final size:101
Alignment explanation
Indices: 54979607--54979788 Score: 303
Period size: 100 Copynumber: 1.8 Consensus size: 101
54979597 GATCATAACA
** *
54979607 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTACTCATGTCGGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTACTCATCTCGGTGCCCATGCCATGT
54979672 CCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
66 CCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
* * *
54979708 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCT-CTCGTCTCGGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTACTCATCTCGGTGCCCATGCCATGT
54979772 CCCAGACATGGTCTTAC
66 CCCAGACATGGTCTTAC
54979789 ATGGGATCTC
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
100 39 0.52
101 36 0.48
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.25
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTACTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
Found at i:54979915 original size:13 final size:13
Alignment explanation
Indices: 54979894--54979925 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54979884 GCTTGGATCA
*
54979894 TCATCAAATAAAT
1 TCATAAAATAAAT
54979907 TCATAAAATAAAT
1 TCATAAAATAAAT
54979920 TCATAA
1 TCATAA
54979926 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:54980172 original size:29 final size:30
Alignment explanation
Indices: 54980135--54980194 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
54980125 GCCCTCGACT
*
54980135 CTAACTTTTT-CAAAATTACAATTTTGCCC
1 CTAAATTTTTACAAAATTACAATTTTGCCC
* *
54980164 CTAAATTTTTACATAATTACATTTTTGCCC
1 CTAAATTTTTACAAAATTACAATTTTGCCC
54980194 C
1 C
54980195 AAGGCTCGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (30 bp):
CTAAATTTTTACAAAATTACAATTTTGCCC
Found at i:54982368 original size:431 final size:420
Alignment explanation
Indices: 54981566--54982401 Score: 1348
Period size: 431 Copynumber: 2.0 Consensus size: 420
54981556 GAAAATAAAG
* * **
54981566 GAGAAGGGAAAGGAAGAAACAACGCAAATGAGATAAAATGTAACAACATGTTTTCAGTAGTGTTG
1 GAGAAGGGAAAGGAAGAAACAACGCAAAGGAGATAAAATGTAACAACACGTTTTCAGTAGTGTCA
* * *
54981631 GAAATAGTGGTTTTAGGACCACGATTTCGATCATTGAGTCAGTATTTTATTATTTATAAGGTTAT
66 GAAATAGTGATTTCAGGACCACAATTTCGATCATTGAGTCAGTATTTTATTATTTATAAGGTTAT
**
54981696 TAATGTGTCGTATTAAAATTTGGTTAAGTAATTTTAATGTTTAGATAGTTAATTAAGTAAAAAGG
131 TAATGTGTCGTATTAAAATTTGGTTAAGTAATTTTAACATTTAGATAGTTAATTAAGTAAAAAGG
*
54981761 ACTAAAATGTAAAAACTAAAAAAGTTAATTGCTATTAGTTTAATTATACAAAATGGCTAAGGAAT
196 ACTAAAATGTAAAAACTAAAAAAGTTAATCGCTATTAGTTTAATTATACAAAATGGCTAAGGAAT
*
54981826 CATGATTTAATGGATTAAAATGGTAAATTTACCAATTTACATTATAGTGGACGGTTTAGGTAAGG
261 CATGATTTAATGGATTAAAATGGTAAATTTACCAATTTACATTATAGTGGACGATTTAGGTAAGG
*
54981891 TTTGGTATGAAATTTAATTTATTTTTAAAGGGAAAAATGGTAATTTAATAATGAAATAATATAAA
326 TTTGGTATGAAATTTAATTTATTTTTAAAGGGAAAAATGATAATTTAATAATGAAATAATATAAA
54981956 CAAAAGAAAACATTATCAAAGGAGATAGAA
391 CAAAAGAAAACATTATCAAAGGAGATAGAA
* * * *
54981986 GAGAAGGGAAAGGAAGAAACAATGGAAAGGAGATGAAATGTAACAACCCGTTTTCAGTAGTGTCA
1 GAGAAGGGAAAGGAAGAAACAACGCAAAGGAGATAAAATGTAACAACACGTTTTCAGTAGTGTCA
* * * *
54982051 GAAATAGTGATTTCAGGACTACAATTTCGATCATTAGGTTAATATTTTATTATTTATTATTTATT
66 GAAATAGTGATTTCAGGACCACAATTTCGATCATT--G-----A-GTCAGTA-TT-TTA-TTATT
*
54982116 TATAAGGTTATTAATGTGTCGTATTAAAATTTGGTTAGGTAATTTTAACATTTAGATAGTTAATT
120 TATAAGGTTATTAATGTGTCGTATTAAAATTTGGTTAAGTAATTTTAACATTTAGATAGTTAATT
* *
54982181 AAGTAAAAATGACTAAAATTTAAAAACTAAAAAAGTTAATCGCTATTAGTTTAATTATACAAAAT
185 AAGTAAAAAGGACTAAAATGTAAAAACTAAAAAAGTTAATCGCTATTAGTTTAATTATACAAAAT
*
54982246 GGCTAAGGAATCATGATTTAATGGATTAAAATGGTAAATTTTCCAATTTACATTATAGTGGACGA
250 GGCTAAGGAATCATGATTTAATGGATTAAAATGGTAAATTTACCAATTTACATTATAGTGGACGA
*
54982311 TTTAGGTAAGGTTTGGTATGAAATTTAATTTATTTTTAAAGGGCAAAATGATAATTTAATAATGA
315 TTTAGGTAAGGTTTGGTATGAAATTTAATTTATTTTTAAAGGGAAAAATGATAATTTAATAATGA
54982376 AATAATATAAACAAAAGAAAACATTA
380 AATAATATAAACAAAAGAAAACATTA
54982402 GCTATCATCT
Statistics
Matches: 380, Mismatches: 25, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
420 88 0.23
422 1 0.00
427 1 0.00
428 4 0.01
429 2 0.01
430 3 0.01
431 281 0.74
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (420 bp):
GAGAAGGGAAAGGAAGAAACAACGCAAAGGAGATAAAATGTAACAACACGTTTTCAGTAGTGTCA
GAAATAGTGATTTCAGGACCACAATTTCGATCATTGAGTCAGTATTTTATTATTTATAAGGTTAT
TAATGTGTCGTATTAAAATTTGGTTAAGTAATTTTAACATTTAGATAGTTAATTAAGTAAAAAGG
ACTAAAATGTAAAAACTAAAAAAGTTAATCGCTATTAGTTTAATTATACAAAATGGCTAAGGAAT
CATGATTTAATGGATTAAAATGGTAAATTTACCAATTTACATTATAGTGGACGATTTAGGTAAGG
TTTGGTATGAAATTTAATTTATTTTTAAAGGGAAAAATGATAATTTAATAATGAAATAATATAAA
CAAAAGAAAACATTATCAAAGGAGATAGAA
Found at i:54993404 original size:16 final size:16
Alignment explanation
Indices: 54993383--54993432 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 16
54993373 ATATCTAATC
54993383 ATATAATAAATTATTA
1 ATATAATAAATTATTA
54993399 ATATAAT--A-TATTA
1 ATATAATAAATTATTA
*
54993412 ATTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
54993429 ATAT
1 ATAT
54993433 TTCAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 1 0.04
16 9 0.32
17 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:54994396 original size:29 final size:29
Alignment explanation
Indices: 54994363--54994420 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
54994353 AAAATATTAT
* *
54994363 AAAATAAAATA-CTATTTGAAACTTTAAAC
1 AAAATAAAATATC-ACTGGAAACTTTAAAC
54994392 AAAATAAAATATCACTGGAAACTTTAAAC
1 AAAATAAAATATCACTGGAAACTTTAAAC
54994421 GAGAGGGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAATAAAATATCACTGGAAACTTTAAAC
Found at i:54994646 original size:24 final size:25
Alignment explanation
Indices: 54994577--54994653 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 25
54994567 ATTTAAATTT
* *
54994577 ATTTTTATAATATAAAATACATATTCA
1 ATTTTTAT-ATATAAAATA-ATTTTAA
54994604 ATTATTTAATATAATAAAATAATTTTAA
1 ATT-TTT-ATAT-ATAAAATAATTTTAA
*
54994632 ATTTTTATATA-AAAATATTTTT
1 ATTTTTATATATAAAATAATTTT
54994654 CAAAAATACA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
24 10 0.23
25 1 0.02
26 4 0.09
27 6 0.14
28 13 0.30
29 10 0.23
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTTTATATATAAAATAATTTTAA
Found at i:54996581 original size:40 final size:40
Alignment explanation
Indices: 54996516--54996648 Score: 189
Period size: 41 Copynumber: 3.3 Consensus size: 40
54996506 AATTTATTTT
*
54996516 AAAAATTAAAAAAAGTATTTT-AAAATATTTTTAAATTAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAATTAA
*
54996555 AAAAATTTTAAAAAGTATTTTAAAAATATTTTTAAAATT-A
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTT-AAATTAA
* * *
54996595 AAAAATAATAAAAAATTATTTTAAAAATATTTTAAAATTAA
1 AAAAAT-TTAAAAAAGTATTTTAAAAATATTTTTAAATTAA
54996636 AAAAATTTAAAAA
1 AAAAATTTAAAAA
54996649 TAAATATATT
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
39 19 0.23
40 29 0.35
41 35 0.42
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (40 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAATTAA
Found at i:54996592 original size:11 final size:11
Alignment explanation
Indices: 54996551--54996631 Score: 71
Period size: 11 Copynumber: 7.5 Consensus size: 11
54996541 TATTTTTAAA
*
54996551 TTAAAAAAATT
1 TTAAAAATATT
54996562 TTAAAAAGTATT
1 TTAAAAA-TATT
54996574 TTAAAAATATT
1 TTAAAAATATT
*
54996585 TT-TAAA-A-T
1 TTAAAAATATT
* *
54996593 TAAAAAATA-A
1 TTAAAAATATT
*
54996603 TAAAAAATTATT
1 TTAAAAA-TATT
54996615 TTAAAAATATT
1 TTAAAAATATT
54996626 TTAAAA
1 TTAAAA
54996632 TTAAAAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
8 2 0.03
9 4 0.07
10 11 0.19
11 25 0.43
12 16 0.28
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:54996593 original size:41 final size:41
Alignment explanation
Indices: 54996516--54996648 Score: 193
Period size: 40 Copynumber: 3.3 Consensus size: 41
54996506 AATTTATTTT
*
54996516 AAAAATTAAAAAAAGTATTTT-AAAATATTTTT-AAATTAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAAATTAA
*
54996555 AAAAATTTTAAAAAGTATTTTAAAAATATTTTTAAAATT-A
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAAATTAA
* *
54996595 AAAAATAATAAAAAATTATTTTAAAAATA-TTTTAAAATTAA
1 AAAAAT-TTAAAAAAGTATTTTAAAAATATTTTTAAAATTAA
54996636 AAAAATTTAAAAA
1 AAAAATTTAAAAA
54996649 TAAATATATT
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
39 19 0.23
40 34 0.40
41 31 0.37
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAAATTAA
Found at i:54996637 original size:17 final size:17
Alignment explanation
Indices: 54996615--54996659 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
54996605 AAAAATTATT
54996615 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
54996632 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
54996648 ATAAATATATTT
1 TTAAAAATATTT
54996660 ATTATATCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:55002508 original size:3 final size:3
Alignment explanation
Indices: 55002500--55002529 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55002490 CACGAACGAG
55002500 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
55002530 AATCTGGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:55004487 original size:31 final size:29
Alignment explanation
Indices: 55004452--55004511 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
55004442 TTTAACAGCC
*
55004452 TTTTATAACTTTTTGAATAGTTCAATGACCA
1 TTTTATAACCTTTTGAA-A-TTCAATGACCA
*
55004483 TTTTATAACCTTTTGAAATTGAATGACCA
1 TTTTATAACCTTTTGAAATTCAATGACCA
55004512 AAATGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 1 0.04
31 16 0.59
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (29 bp):
TTTTATAACCTTTTGAAATTCAATGACCA
Found at i:55004758 original size:16 final size:16
Alignment explanation
Indices: 55004737--55004775 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
55004727 TAAAATTGTT
55004737 TATTTGAGAA-TTAAAA
1 TATTTGA-AATTTAAAA
55004753 TATTTGAAATTTAAAA
1 TATTTGAAATTTAAAA
55004769 T-TTTGAA
1 TATTTGAA
55004776 TTAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (16 bp):
TATTTGAAATTTAAAA
Found at i:55005978 original size:15 final size:16
Alignment explanation
Indices: 55005952--55005982 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55005942 CAATTCTATC
55005952 TATTTTTAAATAATTT
1 TATTTTTAAATAATTT
55005968 TATTTTT-AATAATTT
1 TATTTTTAAATAATTT
55005983 ATTCAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAAATAATTT
Found at i:55019389 original size:23 final size:22
Alignment explanation
Indices: 55019348--55019397 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
55019338 GCTTTATTTG
*
55019348 TTAATATGTTTTGATATAACAAA
1 TTAAAATGTTTTGATATAA-AAA
*
55019371 TTAAAATGTTTTTGA-ATAAAAG
1 TTAAAATG-TTTTGATATAAAAA
55019393 TTAAA
1 TTAAA
55019398 GTTGAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 11 0.46
24 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (22 bp):
TTAAAATGTTTTGATATAAAAA
Found at i:55019635 original size:22 final size:21
Alignment explanation
Indices: 55019591--55019632 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55019581 TTCAATTTAC
*
55019591 ACAAAAAGTGTCGACACCTTT
1 ACAAAAAGTATCGACACCTTT
*
55019612 ACAAAAAGTATCGATACCTTT
1 ACAAAAAGTATCGACACCTTT
55019633 TACTAGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (21 bp):
ACAAAAAGTATCGACACCTTT
Found at i:55022620 original size:19 final size:19
Alignment explanation
Indices: 55022573--55022630 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
55022563 AAAATGATAA
55022573 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
**
55022593 AATTGAGTTAAACAT-TTTC
1 AATCAAGTTAAA-ATGTTTC
55022612 AATCAAGTTAAAACTGTTT
1 AATCAAGTTAAAA-TGTTT
55022631 TAAAACAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 13 0.42
21 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:55025669 original size:3 final size:3
Alignment explanation
Indices: 55025661--55025745 Score: 75
Period size: 3 Copynumber: 27.3 Consensus size: 3
55025651 ATATATAAGT
* * *
55025661 ATA ATA ATA TTA ATA TGTA AT- ATA ATA ATAA ATA ATA CTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
*
55025707 ATA CAGTA ATA ATA ACA ATA ATA ATA ATTA AT- ATA ATA A
1 ATA -A-TA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A
55025746 AATTAATGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
2 4 0.06
3 51 0.76
4 10 0.15
5 2 0.03
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:55025751 original size:14 final size:15
Alignment explanation
Indices: 55025724--55025761 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
55025714 AATAATAACA
55025724 ATAATAATAATTAAT-
1 ATAATAA-AATTAATG
55025739 ATAATAAAATTAATG
1 ATAATAAAATTAATG
55025754 AT-ATAAAA
1 ATAATAAAA
55025762 GAAATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATAATAAAATTAATG
Found at i:55027916 original size:25 final size:23
Alignment explanation
Indices: 55027865--55027909 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
55027855 GTAATTATAA
55027865 ATACATGTGTAATAAATATATGC
1 ATACATGTGTAATAAATATATGC
* *
55027888 ATACATTTGTAATTAATATATG
1 ATACATGTGTAATAAATATATG
55027910 TACATACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGC
Found at i:55027930 original size:25 final size:24
Alignment explanation
Indices: 55027865--55027930 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
55027855 GTAATTATAA
*
55027865 ATACATGTGTAA-TAAATATATGC
1 ATACATTTGTAATTAAATATATGC
55027888 ATACATTTGTAATT-AATATATGTAC
1 ATACATTTGTAATTAAATATATG--C
55027913 ATAC-TTAT-TAATTAAATA
1 ATACATT-TGTAATTAAATA
55027931 AAAGATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 19 0.51
24 8 0.22
25 10 0.27
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (24 bp):
ATACATTTGTAATTAAATATATGC
Done.