Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 46 of 230
Found at i:12315913 original size:41 final size:41
Alignment explanation
Indices: 12315798--12315920 Score: 167
Period size: 41 Copynumber: 3.0 Consensus size: 41
12315788 AATAATAATG
*
12315798 AATCGATTAAAGAAGCAAAGAATCGATTTAAAACAACAAAT
1 AATCGATTAAAGAAGCAAAGAATCGATTTAAAACAACAAAA
*
12315839 AATTGATTAAAGTAAGCAAAGAATCGATTTAAAACAA-AAAA
1 AATCGATTAAAG-AAGCAAAGAATCGATTTAAAACAACAAAA
* * **
12315880 AATCGATTCAAAGACGAAAAGAATTAATTTAAAACAACAAA
1 AATCGATT-AAAGAAGCAAAGAATCGATTTAAAACAACAAA
12315921 CAAACCTAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
41 41 0.57
42 31 0.43
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (41 bp):
AATCGATTAAAGAAGCAAAGAATCGATTTAAAACAACAAAA
Found at i:12316173 original size:47 final size:47
Alignment explanation
Indices: 12316112--12316229 Score: 137
Period size: 47 Copynumber: 2.5 Consensus size: 47
12316102 AGTCATTACC
* *
12316112 TGGTTTTCCATTTCAGCAACAACAACAATACCAACTATTACATAAAA
1 TGGTTTTCCATTTCAACAACAACAACAATACCAACTATCACATAAAA
* * * * * **
12316159 TGGTTTTCCATTTCAATAAAAACAACAGTACTAGCTATCACATAACC
1 TGGTTTTCCATTTCAACAACAACAACAATACCAACTATCACATAAAA
* *
12316206 TGGTTTTTCATTTAAACAACAACA
1 TGGTTTTCCATTTCAACAACAACA
12316230 CTATTACAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.31
Consensus pattern (47 bp):
TGGTTTTCCATTTCAACAACAACAACAATACCAACTATCACATAAAA
Found at i:12316522 original size:23 final size:22
Alignment explanation
Indices: 12316496--12316559 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
12316486 GACATCTTAA
* *
12316496 TTTCTTTTCTTCTTTTTCCTCTT
1 TTTCTCTTCTT-TTTTTACTCTT
*
12316519 TTTCTCTTCTTTTTCTTATTCTT
1 TTTCTCTTCTTTTT-TTACTCTT
12316542 TTTCTCTTCTTTTTTTAC
1 TTTCTCTTCTTTTTTTAC
12316560 CACCCAGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 6 0.17
23 30 0.83
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTCTCTTCTTTTTTTACTCTT
Found at i:12316531 original size:11 final size:11
Alignment explanation
Indices: 12316503--12316555 Score: 74
Period size: 11 Copynumber: 4.9 Consensus size: 11
12316493 TAATTTCTTT
12316503 TCTTCTTTTTC
1 TCTTCTTTTTC
12316514 -C-TCTTTTTC
1 TCTTCTTTTTC
12316523 TCTTCTTTTTC
1 TCTTCTTTTTC
*
12316534 TTATTCTTTTTC
1 -TCTTCTTTTTC
12316546 TCTTCTTTTT
1 TCTTCTTTTT
12316556 TTACCACCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 8 0.22
10 2 0.05
11 17 0.46
12 10 0.27
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TCTTCTTTTTC
Found at i:12319277 original size:184 final size:184
Alignment explanation
Indices: 12318963--12319315 Score: 499
Period size: 184 Copynumber: 1.9 Consensus size: 184
12318953 GTTGTGGAAT
* ** * * * *
12318963 GATGCTACATTATGCAGAAGTCATATACGTGATTTACCAACTTTTAGTTTCTTATCTATTTAAAC
1 GATGCTACATTATGCAGAACTCATATACCCGATGTACCAACTTTCAGTTCCTTATATATTTAAAC
* * * * * *
12319028 TTAGACTTTCATTTACATCAAAGTATATGAGTCACGCATGCATAGTTTATCATTCACTTAGGATT
66 TCAGACTTTCATTTACATCAAAGTATATGAGTCACACATACATAGTCTATCATCCACTCAGGATT
12319093 AAGGTATACCACATTATGAACATCACAAGTGAATAAATCCATAAACAAATATAG
131 AAGGTATACCACATTATGAACATCACAAGTGAATAAATCCATAAACAAATATAG
* * *
12319147 GATGCTACATTATGCAGAACTCGTATACCCGATGTATCAACTTTCAGTTCCTTATATATTTGAAC
1 GATGCTACATTATGCAGAACTCATATACCCGATGTACCAACTTTCAGTTCCTTATATATTTAAAC
* * * *
12319212 TCGGGCTTTCATTTACATCAAAGTATATGAGTTACACATACATAGTCTGTCATCCACTCAGGATT
66 TCAGACTTTCATTTACATCAAAGTATATGAGTCACACATACATAGTCTATCATCCACTCAGGATT
** *
12319277 AAGGTATGTCACATTATGAATATCACAAGTGAATAAATC
131 AAGGTATACCACATTATGAACATCACAAGTGAATAAATC
12319316 TTAAATCCAT
Statistics
Matches: 146, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
184 146 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (184 bp):
GATGCTACATTATGCAGAACTCATATACCCGATGTACCAACTTTCAGTTCCTTATATATTTAAAC
TCAGACTTTCATTTACATCAAAGTATATGAGTCACACATACATAGTCTATCATCCACTCAGGATT
AAGGTATACCACATTATGAACATCACAAGTGAATAAATCCATAAACAAATATAG
Found at i:12331735 original size:31 final size:31
Alignment explanation
Indices: 12331700--12331770 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
12331690 TGTTTGGTTT
*
12331700 AGGTACCAATTTGAACATTGAAACCAAATTC
1 AGGTACCAATTTGAACATTGAAACCAAACTC
* *
12331731 AGGTACCAATTTGAACATTGAATCTAAACTC
1 AGGTACCAATTTGAACATTGAAACCAAACTC
*
12331762 AAGTACCAA
1 AGGTACCAA
12331771 ATAGTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (31 bp):
AGGTACCAATTTGAACATTGAAACCAAACTC
Found at i:12333376 original size:17 final size:18
Alignment explanation
Indices: 12333346--12333391 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
12333336 ATTTAAATTA
12333346 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
12333364 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
12333380 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
12333392 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:12335362 original size:15 final size:17
Alignment explanation
Indices: 12335334--12335365 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
12335324 CGCCGCTGCT
12335334 GCACACACAGCCGCCGC
1 GCACACACAGCCGCCGC
12335351 GCACAC-CA-CCGCCGC
1 GCACACACAGCCGCCGC
12335366 CCCTGCTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (17 bp):
GCACACACAGCCGCCGC
Found at i:12335364 original size:18 final size:18
Alignment explanation
Indices: 12335313--12335366 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
12335303 CATCCTGTGA
* *
12335313 CGCACCACCAGCGCCGCTG
1 CGCA-CACCACCGCCGCCG
*
12335332 CTGCACA-CACAGCCGCCG
1 C-GCACACCACCGCCGCCG
12335350 CGCACACCACCGCCGCC
1 CGCACACCACCGCCGCC
12335367 CCTGCTGCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.17
18 18 0.62
19 3 0.10
20 3 0.10
ACGTcount: A:0.19, C:0.56, G:0.22, T:0.04
Consensus pattern (18 bp):
CGCACACCACCGCCGCCG
Found at i:12339630 original size:16 final size:18
Alignment explanation
Indices: 12339609--12339642 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
12339599 TTTTACATTT
12339609 ATCTTAA-AAT-TAATTA
1 ATCTTAATAATGTAATTA
12339625 ATCTTAATAATGTAATTA
1 ATCTTAATAATGTAATTA
12339643 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
ATCTTAATAATGTAATTA
Found at i:12341262 original size:138 final size:138
Alignment explanation
Indices: 12341084--12341343 Score: 475
Period size: 138 Copynumber: 1.9 Consensus size: 138
12341074 GAAAAAGGAA
* *
12341084 AATTGCTGATTAGACCTTGAACTTTTACTATCTATGCAATCTAACCCTAGTAAGTTTGTACGGTT
1 AATTGCTGATTAGACCTTGAACTTTTACTATCTATACAATCTAACCCTAGTAAGTTCGTACGGTT
12341149 TAAATTAGAATAATTTGTAATGTTATATTTGACTCGTGGATTATGATTTGTTGAATAATCAGCAA
66 TAAATTAGAATAATTTGTAATGTTATATTTGACTCGTGGATTATGATTTGTTGAATAATCAGCAA
12341214 TTACAAAT
131 TTACAAAT
* *
12341222 AATTGCTGATTAGACCTTGAACTTTTACTATCTCTACAATCTAACCCTTGTAAGTTCGTACGGTT
1 AATTGCTGATTAGACCTTGAACTTTTACTATCTATACAATCTAACCCTAGTAAGTTCGTACGGTT
*
12341287 TAAATTAGAATAATTTGTAATGTTATATTTGACTTGTGGATTATGATTTGTTGAATA
66 TAAATTAGAATAATTTGTAATGTTATATTTGACTCGTGGATTATGATTTGTTGAATA
12341344 TTCGTATTTT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 117 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (138 bp):
AATTGCTGATTAGACCTTGAACTTTTACTATCTATACAATCTAACCCTAGTAAGTTCGTACGGTT
TAAATTAGAATAATTTGTAATGTTATATTTGACTCGTGGATTATGATTTGTTGAATAATCAGCAA
TTACAAAT
Found at i:12343856 original size:25 final size:25
Alignment explanation
Indices: 12343827--12343885 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
12343817 GAAAAATATG
*
12343827 TATTGGGTTGGATTGAATCCTAAAA
1 TATTGGGTTGGATTGAATCATAAAA
* *
12343852 TATTGGGTTGGATTGAATTATAAAG
1 TATTGGGTTGGATTGAATCATAAAA
12343877 TATTGGGTT
1 TATTGGGTT
12343886 AAAAGTACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.27, T:0.41
Consensus pattern (25 bp):
TATTGGGTTGGATTGAATCATAAAA
Found at i:12344793 original size:70 final size:70
Alignment explanation
Indices: 12344596--12344771 Score: 255
Period size: 70 Copynumber: 2.5 Consensus size: 70
12344586 ACATATCGAT
* * *
12344596 AATCTCTACTAAT-TTAAAGCCCTGATTGAGTTTCGTGTCACTAGTCAAGTGAGACCAACTCAAT
1 AATCTCTACTAATATTAAAGCCCTGATTGAGTTTGGTGTCACAAGTCAAGTGACACCAACTCAAT
12344660 TAATA
66 TAATA
* * * *
12344665 AATCTCTACTAATATTAAAGCCCTGATTAAGTTTGATGTCACAAGTCAAGAGACACCAACTTAAT
1 AATCTCTACTAATATTAAAGCCCTGATTGAGTTTGGTGTCACAAGTCAAGTGACACCAACTCAAT
12344730 TAATA
66 TAATA
* * *
12344735 AATCTCTACTAATATTAAGGCCTTGACTGAGTTTGGT
1 AATCTCTACTAATATTAAAGCCCTGATTGAGTTTGGT
12344772 ATTAGGAGTT
Statistics
Matches: 94, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 13 0.14
70 81 0.86
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (70 bp):
AATCTCTACTAATATTAAAGCCCTGATTGAGTTTGGTGTCACAAGTCAAGTGACACCAACTCAAT
TAATA
Found at i:12357035 original size:2 final size:2
Alignment explanation
Indices: 12357028--12357052 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12357018 TCTTCTTCGA
12357028 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
12357053 TAGCCTGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12360155 original size:24 final size:24
Alignment explanation
Indices: 12360112--12360158 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12360102 TAACCACATC
*
12360112 TTTAATTCTTTACATCAAATTTAG
1 TTTAATTCTTTAAATCAAATTTAG
12360136 TTTAATTCATTTAAAT-AAATTTA
1 TTTAATTC-TTTAAATCAAATTTA
12360159 TCGCTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTAATTCTTTAAATCAAATTTAG
Found at i:12362584 original size:7 final size:7
Alignment explanation
Indices: 12362567--12362600 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
12362557 AGTCTCTTAT
12362567 AAAGTAAA
1 AAAG-AAA
*
12362575 AAAAAAA
1 AAAGAAA
12362582 AAAGAAA
1 AAAGAAA
12362589 AAAGAAA
1 AAAGAAA
12362596 AAAGA
1 AAAGA
12362601 TGTATATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.88
8 3 0.12
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:12367012 original size:91 final size:91
Alignment explanation
Indices: 12366843--12367050 Score: 292
Period size: 91 Copynumber: 2.3 Consensus size: 91
12366833 CGGACACTCC
* * * * *
12366843 AATTTGTGGATGAACCACCAGTG-TTGCAAGTTAATATGTTGCCAGTAAGTTGTGAATGCACAAT
1 AATTTGTGGATAAACCACCAGTGTTTGCAAGTTAATACGCTGCCAGTAAGTTGTGAATACACAAA
*
12366907 GGGTTTACAAATAAAAGCTGCCAGTA
66 GGGTTTACAAATAAAAGCTGCCAATA
* *
12366933 AATTTGTGGATAAACCACCAGTGTTTGCAGGTTAATACGCTGCCAGTAGGTTGTGAATACACAAA
1 AATTTGTGGATAAACCACCAGTGTTTGCAAGTTAATACGCTGCCAGTAAGTTGTGAATACACAAA
* ** *
12366998 GTGTTTGTAGATAAAAGCTGCCAATA
66 GGGTTTACAAATAAAAGCTGCCAATA
*
12367024 AATTTGTGGGTAAACCACCAGTGTTTG
1 AATTTGTGGATAAACCACCAGTGTTTG
12367051 TAGATAAACT
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 22 0.21
91 82 0.79
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (91 bp):
AATTTGTGGATAAACCACCAGTGTTTGCAAGTTAATACGCTGCCAGTAAGTTGTGAATACACAAA
GGGTTTACAAATAAAAGCTGCCAATA
Found at i:12367049 original size:46 final size:46
Alignment explanation
Indices: 12366917--12367058 Score: 155
Period size: 46 Copynumber: 3.1 Consensus size: 46
12366907 GGGTTTACAA
*
12366917 ATAAAAGCTGCCAGTAAATTTGTGGATAAACCACCAGTGTTTGCAGG
1 ATAAAAGCTGCCAGTAAATTTGTGGATAAACCACCAGTGTTTGTA-G
* * ** * * *
12366964 TTAATACGCTGCCAGT-AGGTTGTGAATACA-CA-AAGTGTTTGTAG
1 ATAA-AAGCTGCCAGTAAATTTGTGGATAAACCACCAGTGTTTGTAG
* *
12367008 ATAAAAGCTGCCAATAAATTTGTGGGTAAACCACCAGTGTTTGTAG
1 ATAAAAGCTGCCAGTAAATTTGTGGATAAACCACCAGTGTTTGTAG
12367054 ATAAA
1 ATAAA
12367059 CTACATTACT
Statistics
Matches: 74, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
43 9 0.12
44 13 0.18
45 11 0.15
46 18 0.24
47 13 0.18
48 10 0.14
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (46 bp):
ATAAAAGCTGCCAGTAAATTTGTGGATAAACCACCAGTGTTTGTAG
Found at i:12370888 original size:15 final size:15
Alignment explanation
Indices: 12370850--12370888 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
12370840 CAAGTTACAG
*
12370850 AAACCCAACTAGCCT
1 AAACCCAATTAGCCT
12370865 AAACCCAATTAGCCT
1 AAACCCAATTAGCCT
*
12370880 AAGCCCAAT
1 AAACCCAAT
12370889 ACCCTGGCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.36, G:0.08, T:0.15
Consensus pattern (15 bp):
AAACCCAATTAGCCT
Found at i:12372038 original size:4 final size:4
Alignment explanation
Indices: 12372029--12372055 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12372019 ATTAACTTAG
12372029 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
12372056 GTTTCTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:12374343 original size:3 final size:3
Alignment explanation
Indices: 12374335--12374362 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12374325 ATTCTTTTAG
12374335 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12374363 GGTAAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12378617 original size:18 final size:18
Alignment explanation
Indices: 12378594--12378629 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12378584 GGGAGATAAG
12378594 TGATTCTTGTTTCAGCTT
1 TGATTCTTGTTTCAGCTT
*
12378612 TGATTCTTGTTTCGGCTT
1 TGATTCTTGTTTCAGCTT
12378630 CGGCTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.17, G:0.19, T:0.56
Consensus pattern (18 bp):
TGATTCTTGTTTCAGCTT
Found at i:12383592 original size:31 final size:31
Alignment explanation
Indices: 12383546--12383607 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
12383536 AAATTTATGT
*
12383546 TAGTCAATTTTTACCAAGTCGCATAACAGCC
1 TAGTCAATTTGTACCAAGTCGCATAACAGCC
*
12383577 TAGTCGATTTGTACCAAGTCGCATAACAGCC
1 TAGTCAATTTGTACCAAGTCGCATAACAGCC
12383608 CATATTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (31 bp):
TAGTCAATTTGTACCAAGTCGCATAACAGCC
Found at i:12384705 original size:19 final size:19
Alignment explanation
Indices: 12384678--12384718 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12384668 TGGCAAAAAG
*
12384678 AATGAGAAATGAAATTTGA
1 AATGAGAAATGAAATGTGA
*
12384697 AATGGGAAATGAAATGTGA
1 AATGAGAAATGAAATGTGA
12384716 AAT
1 AAT
12384719 TGTGGATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (19 bp):
AATGAGAAATGAAATGTGA
Found at i:12390758 original size:4 final size:4
Alignment explanation
Indices: 12390749--12390792 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
12390739 TCTTTACTCG
* * * *
12390749 CTTA CTTA CTTA CTCA CTTA CTTG TTTA CTTA CTTG CTTA CTTA
1 CTTA CTTA CTTA CTTA CTTA CTTA CTTA CTTA CTTA CTTA CTTA
12390793 AATAACTCAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.50
Consensus pattern (4 bp):
CTTA
Found at i:12390779 original size:12 final size:12
Alignment explanation
Indices: 12390742--12390792 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
12390732 ATTAGAATCT
*
12390742 TTACTCGCTTAC
1 TTACTTGCTTAC
* *
12390754 TTACTTACTCAC
1 TTACTTGCTTAC
*
12390766 TTACTTGTTTAC
1 TTACTTGCTTAC
12390778 TTACTTGCTTAC
1 TTACTTGCTTAC
12390790 TTA
1 TTA
12390793 AATAACTCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.20, C:0.25, G:0.06, T:0.49
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:12391108 original size:50 final size:50
Alignment explanation
Indices: 12391041--12391230 Score: 227
Period size: 50 Copynumber: 3.7 Consensus size: 50
12391031 TTTTCTGTAC
* * **
12391041 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* ** *
12391091 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * *
12391141 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TC---GG
12391197 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
12391231 GGATCTCATT
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
50 82 0.69
53 2 0.02
56 34 0.29
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:12391174 original size:100 final size:103
Alignment explanation
Indices: 12391041--12391227 Score: 254
Period size: 100 Copynumber: 1.8 Consensus size: 103
12391031 TTTTCTGTAC
* * ** * *
12391041 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCAT-A-TC-GGTGCCCATGCCAT
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATAACTCAGATGCCAATGCCAT
12391103 GTCCCAGACATGGTCTTACGGGAGACCTCTCATCTCGG
66 GTCCCAGACATGGTCTTACGGGAGACCTCTCATCTCGG
* *
12391141 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATAA-CTC-A-GATGCCAATGC
12391206 CATGTCCCAGACATGGTCTTAC
63 CATGTCCCAGACATGGTCTTAC
12391228 ATGGGATCTC
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 39 0.53
101 1 0.01
103 2 0.03
106 31 0.42
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (103 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATAACTCAGATGCCAATGCCAT
GTCCCAGACATGGTCTTACGGGAGACCTCTCATCTCGG
Found at i:12418736 original size:9 final size:9
Alignment explanation
Indices: 12418711--12418786 Score: 54
Period size: 9 Copynumber: 8.3 Consensus size: 9
12418701 TACTTTTTCC
12418711 CATAAAAA-
1 CATAAAAAT
*
12418719 CGATTAAAAT
1 C-ATAAAAAT
12418729 CATAAAAAAT
1 CAT-AAAAAT
12418739 CATAAAAAT
1 CATAAAAAT
12418748 -ATAAAAAAT
1 CAT-AAAAAT
12418757 -ATAAAATTTAT
1 CATAAAA---AT
12418768 CA-AAAAAT
1 CATAAAAAT
12418776 -ATAAAAAT
1 CATAAAAAT
12418784 CAT
1 CAT
12418787 TAAATATTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 19
0.73 0.03 0.25
Matches are distributed among these distances:
7 1 0.02
8 15 0.27
9 24 0.43
10 9 0.16
11 6 0.11
12 1 0.02
ACGTcount: A:0.66, C:0.08, G:0.01, T:0.25
Consensus pattern (9 bp):
CATAAAAAT
Found at i:12418737 original size:10 final size:9
Alignment explanation
Indices: 12418724--12418782 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
12418714 AAAAACGATT
12418724 AAAATCATAA
1 AAAAT-ATAA
12418734 AAAATCAT-A
1 AAAAT-ATAA
12418743 AAAATATAA
1 AAAATATAA
12418752 AAAATATAA
1 AAAATATAA
**
12418761 AATTTATCAA
1 AAAATAT-AA
12418771 AAAATATAA
1 AAAATATAA
12418780 AAA
1 AAA
12418783 TCATTAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
8 2 0.05
9 26 0.60
10 15 0.35
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATATAA
Found at i:12418746 original size:19 final size:18
Alignment explanation
Indices: 12418724--12418800 Score: 86
Period size: 19 Copynumber: 4.3 Consensus size: 18
12418714 AAAAACGATT
12418724 AAAATCATAAAAAATCATA
1 AAAATCATAAAAAAT-ATA
12418743 AAAAT-ATAAAAAATATA
1 AAAATCATAAAAAATATA
* *
12418760 AAATTTATCAAAAAATATA
1 AAAATCAT-AAAAAATATA
* *
12418779 AAAATCATTAAATAT-TA
1 AAAATCATAAAAAATATA
12418796 AAAAT
1 AAAAT
12418801 ATATATGAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
17 14 0.27
18 16 0.31
19 21 0.41
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATCATAAAAAATATA
Found at i:12418852 original size:11 final size:10
Alignment explanation
Indices: 12418730--12418943 Score: 75
Period size: 9 Copynumber: 22.2 Consensus size: 10
12418720 GATTAAAATC
* *
12418730 ATAAAAAATC
1 ATAAAATATT
12418740 ATAAAA-A-T
1 ATAAAATATT
*
12418748 ATAAAA-AAT
1 ATAAAATATT
12418757 ATAAAAT-TT
1 ATAAAATATT
*
12418766 ATCAAAA-AAT
1 AT-AAAATATT
*
12418776 ATAAAA-ATC
1 ATAAAATATT
*
12418785 ATTAAATATT
1 ATAAAATATT
12418795 A-AAAATATAT
1 ATAAAATAT-T
* *
12418805 ATGAACAT-TG
1 AT-AAAATATT
* **
12418815 ATATAACCTT
1 ATAAAATATT
12418825 AT-AAATATT
1 ATAAAATATT
12418834 AT-AAATATT
1 ATAAAATATT
*
12418843 ATAAAAATATA
1 AT-AAAATATT
12418854 ATAAAATATGT
1 ATAAAATAT-T
*
12418865 GT-AAA-ATT
1 ATAAAATATT
*
12418873 ATAAAA-ATA
1 ATAAAATATT
12418882 ATAAAATATGT
1 ATAAAATAT-T
* *
12418893 GTAAAATTTT
1 ATAAAATATT
12418903 ATAAAA-ATTT
1 ATAAAATA-TT
12418913 ATTAAAAT-TCT
1 A-TAAAATAT-T
*
12418924 ATAAAA-ATC
1 ATAAAATATT
12418933 ATAAAAT-TT
1 ATAAAATATT
12418942 AT
1 AT
12418944 TTAAAAAATT
Statistics
Matches: 154, Mismatches: 29, Indels: 43
0.68 0.13 0.19
Matches are distributed among these distances:
8 9 0.06
9 66 0.43
10 51 0.33
11 24 0.16
12 4 0.03
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (10 bp):
ATAAAATATT
Found at i:12418861 original size:30 final size:31
Alignment explanation
Indices: 12418827--12418938 Score: 108
Period size: 30 Copynumber: 3.7 Consensus size: 31
12418817 ATAACCTTAT
12418827 AAATAT-TATAAATATTATAAAAATATAATA
1 AAATATGTATAAATATTATAAAAATATAATA
*
12418857 AAATATGTGTAAA-ATTAT-AAAA-ATAATA
1 AAATATGTATAAATATTATAAAAATATAATA
* * * *
12418885 AAATATGTGTAAAATTTTATAAAAATTTATTA
1 AAATATGTAT-AAATATTATAAAAATATAATA
* * *
12418917 AAAT-TCTATAAAAATCATAAAA
1 AAATATGTATAAATATTATAAAA
12418939 TTTATTTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
28 16 0.24
29 7 0.10
30 25 0.37
31 12 0.18
32 8 0.12
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (31 bp):
AAATATGTATAAATATTATAAAAATATAATA
Found at i:12418875 original size:22 final size:21
Alignment explanation
Indices: 12418827--12418936 Score: 63
Period size: 21 Copynumber: 5.4 Consensus size: 21
12418817 ATAACCTTAT
*
12418827 AAATATTAT-AAATATTATAA
1 AAATATAATAAAATATTATAA
*
12418847 AAATATAATAAAATATGTGT-A
1 AAATATAATAAAATAT-TATAA
*
12418868 AAAT-T-ATAAAA-ATAAT-A
1 AAATATAATAAAATATTATAA
** *
12418885 AAATATGTGTAAAATTTTATAA
1 AAATAT-AATAAAATATTATAA
* *
12418907 AAATTTATTAAAAT-TCTATAA
1 AAATATAATAAAATAT-TATAA
12418928 AAATCATAA
1 AAAT-ATAA
12418937 AATTTATTTA
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
17 6 0.09
18 3 0.04
19 6 0.09
20 15 0.22
21 29 0.42
22 10 0.14
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (21 bp):
AAATATAATAAAATATTATAA
Found at i:12419109 original size:18 final size:17
Alignment explanation
Indices: 12419069--12419111 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
12419059 GTTGAACCAA
12419069 TTTT-TTTATTTTTAAT
1 TTTTATTTATTTTTAAT
* *
12419085 ATATATTTATTTTTTAAT
1 TTTTATTTA-TTTTTAAT
12419103 TTTTATTTA
1 TTTTATTTA
12419112 ATTTAACTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 2 0.10
17 4 0.19
18 15 0.71
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTATTTTTAAT
Found at i:12419763 original size:31 final size:31
Alignment explanation
Indices: 12419728--12419828 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
12419718 ATAAAGGAGG
12419728 GGCTTAATTGATTATTTTAGTTAAGGGCAGA
1 GGCTTAATTGATTATTTTAGTTAAGGGCAGA
** **** * ** *
12419759 GGCTTAATTGGGT-GCGAATTTAA-TACATA
1 GGCTTAATTGATTATTTTAGTTAAGGGCAGA
12419788 GGCTTAATTGATTATTTTAGTTAAGGGCAGA
1 GGCTTAATTGATTATTTTAGTTAAGGGCAGA
*
12419819 GACTTAATTG
1 GGCTTAATTG
12419829 GGTGCGAATT
Statistics
Matches: 47, Mismatches: 21, Indels: 4
0.65 0.29 0.06
Matches are distributed among these distances:
29 14 0.30
30 10 0.21
31 23 0.49
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.38
Consensus pattern (31 bp):
GGCTTAATTGATTATTTTAGTTAAGGGCAGA
Found at i:12419796 original size:29 final size:29
Alignment explanation
Indices: 12419758--12419858 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
12419748 TTAAGGGCAG
12419758 AGGCTTAATTGGGTGCGAATTTAATACAT
1 AGGCTTAATTGGGTGCGAATTTAATACAT
** **** * ** *
12419787 AGGCTTAATTGATTATTTTAGTTAAGGGCAG
1 AGGCTTAATTGGGT-GCGAATTTAA-TACAT
*
12419818 AGACTTAATTGGGTGCGAATTTAATACAT
1 AGGCTTAATTGGGTGCGAATTTAATACAT
12419847 AGGCTTAATTGG
1 AGGCTTAATTGG
12419859 TTTTTTTTTT
Statistics
Matches: 48, Mismatches: 22, Indels: 4
0.65 0.30 0.05
Matches are distributed among these distances:
29 25 0.52
30 10 0.21
31 13 0.27
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.36
Consensus pattern (29 bp):
AGGCTTAATTGGGTGCGAATTTAATACAT
Found at i:12419798 original size:60 final size:60
Alignment explanation
Indices: 12419728--12419857 Score: 251
Period size: 60 Copynumber: 2.2 Consensus size: 60
12419718 ATAAAGGAGG
*
12419728 GGCTTAATTGATTATTTTAGTTAAGGGCAGAGGCTTAATTGGGTGCGAATTTAATACATA
1 GGCTTAATTGATTATTTTAGTTAAGGGCAGAGACTTAATTGGGTGCGAATTTAATACATA
12419788 GGCTTAATTGATTATTTTAGTTAAGGGCAGAGACTTAATTGGGTGCGAATTTAATACATA
1 GGCTTAATTGATTATTTTAGTTAAGGGCAGAGACTTAATTGGGTGCGAATTTAATACATA
12419848 GGCTTAATTG
1 GGCTTAATTG
12419858 GTTTTTTTTT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.37
Consensus pattern (60 bp):
GGCTTAATTGATTATTTTAGTTAAGGGCAGAGACTTAATTGGGTGCGAATTTAATACATA
Found at i:12422107 original size:31 final size:29
Alignment explanation
Indices: 12422042--12422156 Score: 90
Period size: 28 Copynumber: 3.9 Consensus size: 29
12422032 ATTATGTACC
* * * * *
12422042 GGTGATTATATTTATCAGGTACTTTGTATC
1 GGTG-TTATATTTATCAAGCACTATGTGTT
*
12422072 GGTGTTCATGTTGTATC-AGACACTATGTGTT
1 GGTGTT-ATATT-TATCAAG-CACTATGTGTT
12422103 GGTGTTATATTTATCAAGCACTATGTG-T
1 GGTGTTATATTTATCAAGCACTATGTGTT
* * * *
12422131 CGTGTTATAATTATCAGGTACTATGT
1 GGTGTTATATTTATCAAGCACTATGT
12422157 ACCGATGGTA
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
28 23 0.33
29 15 0.21
30 15 0.21
31 17 0.24
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.43
Consensus pattern (29 bp):
GGTGTTATATTTATCAAGCACTATGTGTT
Found at i:12424306 original size:22 final size:22
Alignment explanation
Indices: 12424280--12424321 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12424270 GTTTAATTTG
12424280 AGTATTA-ATTGTCTATTTAAGA
1 AGTATTACA-TGTCTATTTAAGA
*
12424302 AGTATTACATGTTTATTTAA
1 AGTATTACATGTCTATTTAA
12424322 AATAATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (22 bp):
AGTATTACATGTCTATTTAAGA
Found at i:12426175 original size:17 final size:17
Alignment explanation
Indices: 12426153--12426186 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12426143 ACATTTCTCT
12426153 TCTTTAGTAAATCCTCG
1 TCTTTAGTAAATCCTCG
12426170 TCTTTAGTAAATCCTCG
1 TCTTTAGTAAATCCTCG
12426187 ACGATTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
TCTTTAGTAAATCCTCG
Found at i:12430502 original size:44 final size:42
Alignment explanation
Indices: 12430447--12430569 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 42
12430437 AAATGCTATG
*
12430447 TCCCAGATATGGTCTTACATGGAAATCTCATATCGATGTCAATA
1 TCCCAGATATGGTCTTACAT-GAAATCTCATATCAATGTC-ATA
* * *
12430491 TCCCAGCTATGGTCTTACACGAAGTCTCATATCAATGTCATA
1 TCCCAGATATGGTCTTACATGAAATCTCATATCAATGTCATA
* * *
12430533 TCCCAGATATGATCTTATATGAAATCTCAAATCAATG
1 TCCCAGATATGGTCTTACATGAAATCTCATATCAATG
12430570 CCGATGCCAT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
42 34 0.49
43 17 0.25
44 18 0.26
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (42 bp):
TCCCAGATATGGTCTTACATGAAATCTCATATCAATGTCATA
Found at i:12430608 original size:48 final size:48
Alignment explanation
Indices: 12430529--12430712 Score: 210
Period size: 48 Copynumber: 3.8 Consensus size: 48
12430519 ATATCAATGT
* * * **
12430529 CATATCCCAGATATGATCTTATATGAAATCTCAAATCAATGCCGATGC
1 CATATCTCAGATATGGTCTTATACGGGATCTCAAATCAATGCCGATGC
* * * * *
12430577 CATATCTCAAATATGGTCTTATACGGGATCTCAAACCGATGCCAATTC
1 CATATCTCAGATATGGTCTTATACGGGATCTCAAATCAATGCCGATGC
* * *
12430625 CATATC-CTAGATATGGTCTTATACGGGATCTCAAATCGA-GACTGATGT
1 CATATCTC-AGATATGGTCTTATACGGGATCTCAAATCAATG-CCGATGC
*
12430673 TATATCTCAGATATGGTCTTATACGGGATCTCAAATCAAT
1 CATATCTCAGATATGGTCTTATACGGGATCTCAAATCAAT
12430713 TCGGCAATGT
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
47 2 0.02
48 111 0.97
49 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (48 bp):
CATATCTCAGATATGGTCTTATACGGGATCTCAAATCAATGCCGATGC
Found at i:12430645 original size:96 final size:96
Alignment explanation
Indices: 12430529--12430707 Score: 252
Period size: 96 Copynumber: 1.9 Consensus size: 96
12430519 ATATCAATGT
*
12430529 CATATCCCAGATATGATCTTATATGAAATCTCAAATCAATG-CCGATGCCATATCTCAAATATGG
1 CATATCCCAGATATGATCTTATACGAAATCTCAAATCAA-GACCGATGCCATATCTCAAATATGG
12430593 TCTTATACGGGATCTCAAACCGATGCCAATTC
65 TCTTATACGGGATCTCAAACCGATGCCAATTC
* * ** * * ** *
12430625 CATATCCTAGATATGGTCTTATACGGGATCTCAAATCGAGACTGATGTTATATCTCAGATATGGT
1 CATATCCCAGATATGATCTTATACGAAATCTCAAATCAAGACCGATGCCATATCTCAAATATGGT
12430690 CTTATACGGGATCTCAAA
66 CTTATACGGGATCTCAAA
12430708 TCAATTCGGC
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 71 0.99
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (96 bp):
CATATCCCAGATATGATCTTATACGAAATCTCAAATCAAGACCGATGCCATATCTCAAATATGGT
CTTATACGGGATCTCAAACCGATGCCAATTC
Found at i:12439036 original size:9 final size:9
Alignment explanation
Indices: 12439022--12439050 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12439012 TAAACAATTC
12439022 AATAATATA
1 AATAATATA
12439031 AATAATATA
1 AATAATATA
12439040 AATAATATA
1 AATAATATA
12439049 AA
1 AA
12439051 ATGTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATATA
Found at i:12439195 original size:20 final size:19
Alignment explanation
Indices: 12439169--12439221 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 19
12439159 GGGTGAGAAG
12439169 TAAAAGTTTAAGGGAAAAA
1 TAAAAGTTTAAGGGAAAAA
* *
12439188 TAAAAAGTTT--TGG-AGAA
1 T-AAAAGTTTAAGGGAAAAA
12439205 TAAAAGTTTAAGGGAAA
1 TAAAAGTTTAAGGGAAA
12439222 GTAAATAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
16 8 0.31
17 4 0.15
18 4 0.15
19 2 0.08
20 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.25
Consensus pattern (19 bp):
TAAAAGTTTAAGGGAAAAA
Found at i:12439596 original size:9 final size:9
Alignment explanation
Indices: 12439582--12439618 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
12439572 TATAGTTTGA
12439582 TATTCGAAT
1 TATTCGAAT
12439591 TATTCGAAT
1 TATTCGAAT
* *
12439600 TATTTGAGT
1 TATTCGAAT
12439609 TATTCGAAT
1 TATTCGAAT
12439618 T
1 T
12439619 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:12444098 original size:26 final size:26
Alignment explanation
Indices: 12444069--12444118 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
12444059 GCTGAGGCGG
12444069 TGGCCTTG-CGTTGCGAGCTGGGTCAT
1 TGGCCTTGTC-TTGCGAGCTGGGTCAT
* *
12444095 TGGCTTTGTCTTGCGAGCTTGGTC
1 TGGCCTTGTCTTGCGAGCTGGGTC
12444119 CACAAGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.06, C:0.22, G:0.36, T:0.36
Consensus pattern (26 bp):
TGGCCTTGTCTTGCGAGCTGGGTCAT
Found at i:12449984 original size:13 final size:13
Alignment explanation
Indices: 12449966--12449990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12449956 TAATTTATGT
12449966 GTGTGAAAATTTC
1 GTGTGAAAATTTC
12449979 GTGTGAAAATTT
1 GTGTGAAAATTT
12449991 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:12451206 original size:43 final size:42
Alignment explanation
Indices: 12451064--12451215 Score: 164
Period size: 43 Copynumber: 3.5 Consensus size: 42
12451054 TGATTTTGTA
12451064 TAAGACCACATCTGGGACATTGGCATCG-ATTTGGGATTTACATG
1 TAAGACCACATCTGGGACATTGGCATCGTATTT--GA-TTACATG
* ** * *
12451108 TAAAACCATGTCTGGGACATTGGCATCGTATATGATTACGTG
1 TAAGACCACATCTGGGACATTGGCATCGTATTTGATTACATG
* * *
12451150 TAAGACC-CTATCTGGGACAATGGCATTGTTATTTTATTACATG
1 TAAGACCAC-ATCTGGGACATTGGCATCG-TATTTGATTACATG
*
12451193 TAAGACCACATCTGGGACGTTGG
1 TAAGACCACATCTGGGACATTGG
12451216 TATTGTACGA
Statistics
Matches: 89, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 28 0.31
43 32 0.36
44 26 0.29
45 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
TAAGACCACATCTGGGACATTGGCATCGTATTTGATTACATG
Found at i:12452175 original size:8 final size:8
Alignment explanation
Indices: 12452162--12452189 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
12452152 ATGAGACGGG
12452162 TTTATAAA
1 TTTATAAA
12452170 TTTATAAA
1 TTTATAAA
12452178 TTTATAAA
1 TTTATAAA
12452186 TTTA
1 TTTA
12452190 AGTGTGCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTATAAA
Found at i:12455702 original size:19 final size:19
Alignment explanation
Indices: 12455678--12455724 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
12455668 AATTTTGATG
12455678 AAATTGTAATTTAGGGACT
1 AAATTGTAATTTAGGGACT
12455697 AAATTGTAATTTAGGGACT
1 AAATTGTAATTTAGGGACT
12455716 AAATTGTAA
1 AAATTGTAA
12455725 ATTTGTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.36
Consensus pattern (19 bp):
AAATTGTAATTTAGGGACT
Found at i:12460119 original size:58 final size:58
Alignment explanation
Indices: 12460029--12460287 Score: 349
Period size: 58 Copynumber: 4.5 Consensus size: 58
12460019 TCAGCAAATA
* * * ** *
12460029 GTTTTATACTTGAGAAAAATTTGAAAGATAATCAATTAGGGATGTGAATTTGTGAACT
1 GTTTTATACTTGTGAAAATTTTGAAAGATAATCAACTAGGGATGTGAATCCGCGAACT
* *
12460087 GTTTTATACTTGTGAAAATTTTGAAAGATAATCAACTAGGGATGTGAATCCACGAGCT
1 GTTTTATACTTGTGAAAATTTTGAAAGATAATCAACTAGGGATGTGAATCCGCGAACT
* * * * *
12460145 GTTTTATGCTTGTGAAAATTCTGAAAGATAATCAACTGGGGATGTGAATCCGTGAGCT
1 GTTTTATACTTGTGAAAATTTTGAAAGATAATCAACTAGGGATGTGAATCCGCGAACT
* * *
12460203 ATTTTATACTTGT-ACAAATTTTGAAAGATAACCAACTAGGGATGTGAATCCCCGAACT
1 GTTTTATACTTGTGA-AAATTTTGAAAGATAATCAACTAGGGATGTGAATCCGCGAACT
*
12460261 ATTTTATACTTGTGAAAATTTTGAAAG
1 GTTTTATACTTGTGAAAATTTTGAAAG
12460288 GTAACATAGT
Statistics
Matches: 178, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
57 1 0.01
58 176 0.99
59 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (58 bp):
GTTTTATACTTGTGAAAATTTTGAAAGATAATCAACTAGGGATGTGAATCCGCGAACT
Found at i:12460363 original size:21 final size:21
Alignment explanation
Indices: 12460337--12460376 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12460327 TAGAGGCTGC
12460337 GGTCTTTGACTGTAAGCTTTA
1 GGTCTTTGACTGTAAGCTTTA
* *
12460358 GGTCTTTGCCTGTGAGCTT
1 GGTCTTTGACTGTAAGCTT
12460377 CAGTATGACA
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:0.12, C:0.17, G:0.28, T:0.42
Consensus pattern (21 bp):
GGTCTTTGACTGTAAGCTTTA
Found at i:12460501 original size:69 final size:68
Alignment explanation
Indices: 12460380--12460659 Score: 328
Period size: 69 Copynumber: 4.1 Consensus size: 68
12460370 TGAGCTTCAG
* * * **
12460380 TATGACAGCTAGAGCTTTGCTCTCGCTAATTGTGTTGGAGGCTGCGGCTCTTCACCTACGAGTTT
1 TATGACAGGTAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCTCTTCACCTACGAGCCT
*
12460445 TAG
66 TAA
* * *
12460448 TATGATAGGTGAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGTGGCTCTTCGA-CTATGAGC
1 TATGACAGGT-AGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCTCTTC-ACCTACGAGC
12460512 CTTAA
64 CTTAA
* * * * * * * *
12460517 TATTACAGCTAGGAGCTTTGTTCTCGTTAACTATGTTGGAGGTTGTGGCTTTTCACCAACGAGCC
1 TATGACAGGTA-GAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCTCTTCACCTACGAGCC
12460582 TTAA
65 TTAA
* * * * *
12460586 TATGACAGGTAGAGCTTTGCTCTCGCTAATTGTGTTGGAGGCTGCGACTCTTCGCTTACGAGCCT
1 TATGACAGGTAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCTCTTCACCTACGAGCCT
12460651 TAA
66 TAA
12460654 TATGAC
1 TATGAC
12460660 TCGAATGTCG
Statistics
Matches: 177, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
68 62 0.35
69 114 0.64
70 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (68 bp):
TATGACAGGTAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCTCTTCACCTACGAGCCT
TAA
Found at i:12460623 original size:137 final size:137
Alignment explanation
Indices: 12460384--12460656 Score: 361
Period size: 137 Copynumber: 2.0 Consensus size: 137
12460374 CTTCAGTATG
* * * ** *
12460384 ACAGCTAGAGCTTTGCTCTCGCTAATTGTGTTGGAGGCTGCGGCTCTTCACCTACGAGTTTTAGT
1 ACAGCTAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCTCTTCACCAACGAGCCTTAAT
* * * *
12460449 ATGATAGGTGAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGTGGCTCTTCGAC-TATGAGCC
66 ATGACAGGTGAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGACTCTTCG-CTTACGAGCC
12460513 TTAATATT
130 TTAATATT
* * * * *
12460521 ACAGCTAGGAGCTTTGTTCTCGTTAACTATGTTGGAGGTTGTGGCTTTTCACCAACGAGCCTTAA
1 ACAGCTA-GAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCTCTTCACCAACGAGCCTTAA
* *
12460586 TATGACAGGT-AGAGCTTTGCTCTCGCTAATTGTGTTGGAGGCTGCGACTCTTCGCTTACGAGCC
65 TATGACAGGTGAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGACTCTTCGCTTACGAGCC
12460650 TTAATAT
130 TTAATAT
12460657 GACTCGAATG
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
136 1 0.01
137 61 0.52
138 55 0.47
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.34
Consensus pattern (137 bp):
ACAGCTAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCTCTTCACCAACGAGCCTTAAT
ATGACAGGTGAGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGACTCTTCGCTTACGAGCCT
TAATATT
Found at i:12470204 original size:54 final size:54
Alignment explanation
Indices: 12470121--12470230 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
12470111 TCTCGTCAGT
*
12470121 TGAAATCACACAAAAGAAATTATCTGACACATGACCTTGAGTTAGTTGCAATCG
1 TGAAATCACACAAAAGAAATTATCCGACACATGACCTTGAGTTAGTTGCAATCG
12470175 TGAAATCACACAAAAGAAATTATCCGACACATGACCTTGAGTTAGTTGCAATCG
1 TGAAATCACACAAAAGAAATTATCCGACACATGACCTTGAGTTAGTTGCAATCG
12470229 TG
1 TG
12470231 TTTGCTTTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (54 bp):
TGAAATCACACAAAAGAAATTATCCGACACATGACCTTGAGTTAGTTGCAATCG
Found at i:12475066 original size:39 final size:39
Alignment explanation
Indices: 12475023--12475159 Score: 132
Period size: 39 Copynumber: 3.5 Consensus size: 39
12475013 TATTCTGTTG
* * *
12475023 ATTTATGATCATGACCTTTGGCTTTCTTACAGTCCGCTA
1 ATTTACGATCACGACCTTTGGCTTTCTTACAGTCCACTA
* * * * *
12475062 ATTTACGATTATGATCTTTGACTTTCTTA-TGTTCCACTA
1 ATTTACGATCACGACCTTTGGCTTTCTTACAG-TCCACTA
* * * * * *
12475101 ATTTACGGTCACGATCTTCGGCATTCTTACAGTCTACTG
1 ATTTACGATCACGACCTTTGGCTTTCTTACAGTCCACTA
12475140 ATTTACGATCACGACCTTTG
1 ATTTACGATCACGACCTTTG
12475160 ATTTTCTAAC
Statistics
Matches: 78, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 76 0.97
40 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.41
Consensus pattern (39 bp):
ATTTACGATCACGACCTTTGGCTTTCTTACAGTCCACTA
Found at i:12475330 original size:134 final size:132
Alignment explanation
Indices: 12475177--12475532 Score: 435
Period size: 133 Copynumber: 2.7 Consensus size: 132
12475167 AACAATTTAC
* * *
12475177 TGATTTATGATCACGGCTTCAGTTCATTAATTTACAATTATGAACACTTCTTAAAGAGTTCATCG
1 TGATTTACGATCAC-GCTTCAGTTCATTGATTTATAATTATGAACACTTCTTAAAGAGTTCATCG
* * * * *
12475242 ATTTACGATCGCGACTCCACTTAA-ATAGTTCGCTAATTTACAATCACAATTGTCATTTTTAAAG
65 ATTTACAATCGCGACTCCACTTAACAT--TTCGCTAAGTTACAATCACAACTATCATGTTTAAAG
*
12475306 CTTGT
128 CCTGT
* * * * *
12475311 TGATTTACGATCACAGCTTCAGTTTATTGATTTATGATCATGAACACTTCTTGAAGAGTTCACCG
1 TGATTTACGATCAC-GCTTCAGTTCATTGATTTATAATTATGAACACTTCTTAAAGAGTTCATCG
** * * * ** *
12475376 ATTTACAATCATGACTACAATTAACATTTCGCTGAGTTAGTATCACGACTATCATGTTTAAAGCC
65 ATTTACAATCGCGACTCCACTTAACATTTCGCTAAGTTACAATCACAACTATCATGTTTAAAGCC
12475441 TGT
130 TGT
*
12475444 TGATTTACGATCACGACTTCAGTTCATTGATTTATAATTATGAACACTTCTTAAAGAATTCATCG
1 TGATTTACGATCACG-CTTCAGTTCATTGATTTATAATTATGAACACTTCTTAAAGAGTTCATCG
* *
12475509 ATTTACAATTGCGATTCCACTTAA
65 ATTTACAATCGCGACTCCACTTAA
12475533 GCAATTTGAT
Statistics
Matches: 185, Mismatches: 35, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
132 1 0.01
133 107 0.58
134 75 0.41
135 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (132 bp):
TGATTTACGATCACGCTTCAGTTCATTGATTTATAATTATGAACACTTCTTAAAGAGTTCATCGA
TTTACAATCGCGACTCCACTTAACATTTCGCTAAGTTACAATCACAACTATCATGTTTAAAGCCT
GT
Found at i:12477765 original size:124 final size:124
Alignment explanation
Indices: 12477545--12477792 Score: 496
Period size: 124 Copynumber: 2.0 Consensus size: 124
12477535 CTTTGATCTG
12477545 CTTCTTCACCAGAACATCCTCCCCCTCATTCTCCACTTCTGTTGATACTGTGTATCAACAAATTA
1 CTTCTTCACCAGAACATCCTCCCCCTCATTCTCCACTTCTGTTGATACTGTGTATCAACAAATTA
12477610 TATAATTATAAATTAATACAATAATAAAATTACATTTAAAAATTTAAAATTCAATTCTA
66 TATAATTATAAATTAATACAATAATAAAATTACATTTAAAAATTTAAAATTCAATTCTA
12477669 CTTCTTCACCAGAACATCCTCCCCCTCATTCTCCACTTCTGTTGATACTGTGTATCAACAAATTA
1 CTTCTTCACCAGAACATCCTCCCCCTCATTCTCCACTTCTGTTGATACTGTGTATCAACAAATTA
12477734 TATAATTATAAATTAATACAATAATAAAATTACATTTAAAAATTTAAAATTCAATTCTA
66 TATAATTATAAATTAATACAATAATAAAATTACATTTAAAAATTTAAAATTCAATTCTA
12477793 TAATTATAGG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (124 bp):
CTTCTTCACCAGAACATCCTCCCCCTCATTCTCCACTTCTGTTGATACTGTGTATCAACAAATTA
TATAATTATAAATTAATACAATAATAAAATTACATTTAAAAATTTAAAATTCAATTCTA
Found at i:12484875 original size:22 final size:23
Alignment explanation
Indices: 12484844--12484886 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12484834 GCTATCTACA
12484844 AATCAAATC-TCTAAAATTACCG
1 AATCAAATCTTCTAAAATTACCG
* *
12484866 AATCATATCTTCTAAGATTAC
1 AATCAAATCTTCTAAAATTAC
12484887 ATATCATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.33
Consensus pattern (23 bp):
AATCAAATCTTCTAAAATTACCG
Found at i:12486084 original size:17 final size:17
Alignment explanation
Indices: 12486058--12486090 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12486048 TTATTGAATC
12486058 AGCAAAAAAAATCAAAA
1 AGCAAAAAAAATCAAAA
*
12486075 AGCAATAAAAATCAAA
1 AGCAAAAAAAATCAAA
12486091 GTCTGCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.12, G:0.06, T:0.09
Consensus pattern (17 bp):
AGCAAAAAAAATCAAAA
Found at i:12486881 original size:22 final size:21
Alignment explanation
Indices: 12486827--12486881 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
12486817 ATAATTAAAC
* *
12486827 TTATTATTATAAATTTATTGT
1 TTATTATTTTAAATCTATTGT
12486848 TGATATTA-TTTAAATCTATTGT
1 T--TATTATTTTAAATCTATTGT
12486870 ATTATTATTTTA
1 -TTATTATTTTA
12486882 TTTTGTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
21 6 0.21
22 16 0.57
23 6 0.21
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (21 bp):
TTATTATTTTAAATCTATTGT
Found at i:12488466 original size:22 final size:22
Alignment explanation
Indices: 12488414--12488466 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
12488404 ATGCAATATA
*
12488414 AAAATATATGTAAGTATGTATAT
1 AAAATATATGT-AGTATGTAAAT
*
12488437 ATACATATATGT-GTATGTAAATT
1 A-AAATATATGTAGTATGTAAA-T
12488460 AAAATAT
1 AAAATAT
12488467 GTATATATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 13 0.52
23 3 0.12
24 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (22 bp):
AAAATATATGTAGTATGTAAAT
Found at i:12490265 original size:44 final size:44
Alignment explanation
Indices: 12490153--12490366 Score: 162
Period size: 44 Copynumber: 4.8 Consensus size: 44
12490143 CTATCAATGG
*
12490153 TCTGCTCCACTACAACTTTAGGGAGATAAGACTT-GTAGTCGGTCTTCAA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGA-TTGGTA-TC--T-TT-AA
* *
12490202 TCTACTCCACTACATCTTCAGGGAGATAAGATTGGTATCTTTAA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGATTGGTATCTTTAA
* * * * * *
12490246 TCTGCTCCATTAAAACTTCAGAGAGATAAGGTTTGTTAT-TTCAA
1 TCTGCTCCACTACAACTTCAGGGAGATAA-GATTGGTATCTTTAA
* * * * * ** *
12490290 CCTGCTCTACTGCAACTTCAGGGAGATAAGGTTTGTGGCTTTCA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGATTGGTATCTTTAA
** * *
12490334 TCTGCTCCACTGTAACTTTAGGGAGACAAGATT
1 TCTGCTCCACTACAACTTCAGGGAGATAAGATT
12490367 TGTAGCCTAT
Statistics
Matches: 132, Mismatches: 30, Indels: 11
0.76 0.17 0.06
Matches are distributed among these distances:
43 4 0.03
44 83 0.63
45 9 0.07
46 1 0.01
48 4 0.03
49 31 0.23
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (44 bp):
TCTGCTCCACTACAACTTCAGGGAGATAAGATTGGTATCTTTAA
Found at i:12490590 original size:44 final size:44
Alignment explanation
Indices: 12490414--12490591 Score: 107
Period size: 44 Copynumber: 4.0 Consensus size: 44
12490404 TTCGATCCGT
* *
12490414 TCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTAC
1 TCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTAC
* * * **** * * *
12490458 TCCACTGCTGCTCAGGGAGATAAGA-CTGGTGGCTTAAATCTGC
1 TCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTAC
* * * *
12490501 TTACCTACTAC--CTT-GGGAAAATAAGAT-T-CACCATCTTTAATCTAC
1 -T-CC-ACTACTGCTTAGGG-AGACAAGATCTGCA--ATCTTCAACCTAC
*
12490546 TCCACTACTGCTTAGGGAGACAGGATCTGCAATCTTCAACCTAC
1 TCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTAC
12490590 TC
1 TC
12490592 TACTGCAACT
Statistics
Matches: 96, Mismatches: 26, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
42 5 0.05
43 15 0.16
44 55 0.57
45 15 0.16
46 6 0.06
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (44 bp):
TCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTAC
Found at i:12491150 original size:177 final size:177
Alignment explanation
Indices: 12490563--12491307 Score: 571
Period size: 177 Copynumber: 4.2 Consensus size: 177
12490553 CTGCTTAGGG
* * * * * *
12490563 AGACAGGATCTGCAATCTTCAACCTACTCTACTGC-AACTTCAGGGAGATAAGGTTTGT-TATTT
1 AGACAAGATCTACAATCTTCAACCTACTCCACTGCAAAC-TCAGGGAGATAAGGCTAGTGT-CTT
* * * * * * * ** * ***
12490626 CGATCTGCTTCACTGCC-ATCACAAGAAGACAAGATCTGCTATTTTTCAGTCTGCTCCACTGAAA
64 CGATCTACTTCACTGCCAAT-ACAGGAAAACAAAATCTACAATCTTT-AACCTACTCCACTGCTG
*** * * * *
12490690 CTC-GGAGAGGCGAGGCTGGTGTCTTCGATCTGCTCCACTGCCAGTACAGAA
127 CTCAGG-GAGATAAGGCTGCTGTTTTCGATCTACTTCACTGCCAGTACAGAA
* ** * * ** * * *
12490741 AGACAAGATCTGC--TGCTTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGTTGGTGTATT
1 AGACAAGATCTACAAT-C-TTCAACCTACTCCACTGCAAACTCAGGGAGATAAGGCTAGTGTCTT
* * * * * * * **
12490804 CGATCTACTTCGCTGCCAATACAGGAAGATAAGATCTAC--TGCTTTCA-GT-CTGCTTTGCTGT
64 CGATCTACTTCACTGCCAATACAGGAAAACAAAATCTACAAT-CTTTAACCTACTCCACTGCTG-
* ** * * * * * *
12490865 AAACTCAAGGAGGCAAGGCCGGTGTTTTCGATCTACTTCGCTGCCAATATAGGA
127 ---CTCAGGGAGATAAGGCTGCTGTTTTCGATCTACTTCACTGCCAGTACAGAA
* *** * ** ** * *
12490919 AGATAAGATCTGTTA-CTTTTAGTCTGTTCAACTGCAAACTCAGGGAGGTAAGGCTAGTGTCTTC
1 AGACAAGATCTACAATC-TTCAACCTACTCCACTGCAAACTCAGGGAGATAAGGCTAGTGTCTTC
*
12490983 GATCTACTTCGCTGCCAATACAGGAAAACAAAATCTACAATCTTTAACCTACTCCACTGCTGCTC
65 GATCTACTTCACTGCCAATACAGGAAAACAAAATCTACAATCTTTAACCTACTCCACTGCTGCTC
*
12491048 AGGGAGATAAGGCTAG-TGTTTTCGATCTGCTTCACTGCCAGTACATG-A
130 AGGGAGATAAGGCT-GCTGTTTTCGATCTACTTCACTGCCAGTACA-GAA
* * * *
12491096 AGACAAGATCTACAATCTTTAACCTACTCCACTGCAAATTTAGGGAGATAAGGCTAGTGTTTTCG
1 AGACAAGATCTACAATCTTCAACCTACTCCACTGCAAACTCAGGGAGATAAGGCTAGTGTCTTCG
* * * *
12491161 ATCTGCTTCACTGCCAGTACAGGAAGACAAAATCTACAATCTTTAACCTACTCCATTGCTGCTCA
66 ATCTACTTCACTGCCAATACAGGAAAACAAAATCTACAATCTTTAACCTACTCCACTGCTGCTCA
*
12491226 GGGAGATAAGGCTGCTGTTTTTGATCTACTTCACTGCCAGTACAGAA
131 GGGAGATAAGGCTGCTGTTTTCGATCTACTTCACTGCCAGTACAGAA
*
12491273 AGACAAGATCTACAATCTTCAACCTACTCTACTGC
1 AGACAAGATCTACAATCTTCAACCTACTCCACTGC
12491308 TGCTTAAGGA
Statistics
Matches: 462, Mismatches: 83, Indels: 45
0.78 0.14 0.08
Matches are distributed among these distances:
174 5 0.01
175 1 0.00
176 4 0.01
177 227 0.49
178 203 0.44
179 12 0.03
180 2 0.00
181 8 0.02
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (177 bp):
AGACAAGATCTACAATCTTCAACCTACTCCACTGCAAACTCAGGGAGATAAGGCTAGTGTCTTCG
ATCTACTTCACTGCCAATACAGGAAAACAAAATCTACAATCTTTAACCTACTCCACTGCTGCTCA
GGGAGATAAGGCTGCTGTTTTCGATCTACTTCACTGCCAGTACAGAA
Found at i:12491196 original size:89 final size:88
Alignment explanation
Indices: 12490570--12491326 Score: 524
Period size: 89 Copynumber: 8.5 Consensus size: 88
12490560 GGGAGACAGG
* * * * * *
12490570 ATCTGCAATCTTCAACCTACTCTACTGCAACTTCAGGGAGATAAGGTTTGT-TATTTCGATCTGC
1 ATCTACAATCTTTAACCTACTCCACTGCAAC-TCAGGGAGATAAGGCTAGTGT-TTTCGATCTAC
* *
12490634 TTCACTGCCA-TCACAAGAAGACAAG
64 TTCACTGCCAGT-ACAGGAAGACAAA
* * * ** * * *** * * *
12490659 ATCTGCTATTTTTCAGTCTGCTCCACTGAAACTC-GGAGAGGCGAGGCTGGTGTCTTCGATCTGC
1 ATCTACAATCTTT-AACCTACTCCACTGCAACTCAGG-GAGATAAGGCTAGTGTTTTCGATCTAC
* * *
12490723 TCCACTGCCAGTACAGAAAGACAAG
64 TTCACTGCCAGTACAGGAAGACAAA
* ** * * ** * * *
12490748 ATCTGC--TGCTTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGTTGGTGTATTCGATCTA
1 ATCTACAAT-CTTT-AACCTACTCCACTGC-AACTCAGGGAGATAAGGCTAGTGTTTTCGATCTA
* * * *
12490811 CTTCGCTGCCAATACAGGAAGATAAG
63 CTTCACTGCCAGTACAGGAAGACAAA
** * *** * * ** **
12490837 ATCTAC--TGCTTTCAGTCTGCTTTGCTGTAAACTCAAGGAGGCAAGGCCGGTGTTTTCGATCTA
1 ATCTACAAT-CTTT-AACCTACTCCACTG-CAACTCAGGGAGATAAGGCTAGTGTTTTCGATCTA
* * * * *
12490900 CTTCGCTGCCAATATAGGAAGATAAG
63 CTTCACTGCCAGTACAGGAAGACAAA
*** ** ** * * *
12490926 ATCTGTTA-CTTTTAGTCTGTTCAACTGCAAACTCAGGGAGGTAAGGCTAGTGTCTTCGATCTAC
1 ATCTACAATC-TTTAACCTACTCCACTGC-AACTCAGGGAGATAAGGCTAGTGTTTTCGATCTAC
* * *
12490990 TTCGCTGCCAATACAGGAAAACAAA
64 TTCACTGCCAGTACAGGAAGACAAA
** *
12491015 ATCTACAATCTTTAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGTTTTCGATCTGCTT
1 ATCTACAATCTTTAACCTACTCCACTGCAACTCAGGGAGATAAGGCTAGTGTTTTCGATCTACTT
* *
12491080 CACTGCCAGTACATGAAGACAAG
66 CACTGCCAGTACAGGAAGACAAA
* * *
12491103 ATCTACAATCTTTAACCTACTCCACTGCAAATTTAGGGAGATAAGGCTAGTGTTTTCGATCTGCT
1 ATCTACAATCTTTAACCTACTCCACTGC-AACTCAGGGAGATAAGGCTAGTGTTTTCGATCTACT
12491168 TCACTGCCAGTACAGGAAGACAAA
65 TCACTGCCAGTACAGGAAGACAAA
* ** *
12491192 ATCTACAATCTTTAACCTACTCCATTGCTGCTCAGGGAGATAAGGCT-GCTGTTTTTGATCTACT
1 ATCTACAATCTTTAACCTACTCCACTGCAACTCAGGGAGATAAGGCTAG-TGTTTTCGATCTACT
* *
12491256 TCACTGCCAGTACAGAAAGACAAG
65 TCACTGCCAGTACAGGAAGACAAA
* * ** * *
12491280 ATCTACAATCTTCAACCTACTCTACTGCTGCTTAAGGAGATAAGGCT
1 ATCTACAATCTTTAACCTACTCCACTGCAACTCAGGGAGATAAGGCT
12491327 GGTGGCTTAA
Statistics
Matches: 561, Mismatches: 92, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
87 2 0.00
88 189 0.34
89 349 0.62
90 21 0.04
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (88 bp):
ATCTACAATCTTTAACCTACTCCACTGCAACTCAGGGAGATAAGGCTAGTGTTTTCGATCTACTT
CACTGCCAGTACAGGAAGACAAA
Found at i:12491327 original size:88 final size:89
Alignment explanation
Indices: 12490957--12491326 Score: 516
Period size: 88 Copynumber: 4.2 Consensus size: 89
12490947 CAACTGCAAA
* * * *
12490957 CTCAGGGAGGTAAGGCTAGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAA-ACAAAATCTAC
1 CTCAGGGAGATAAGGCTAGTGTTTTCGATCTACTTCACTGCCAGTACAGGAAAGACAAAATCTAC
12491021 AATCTTTAACCTACTCCACTGCTG
66 AATCTTTAACCTACTCCACTGCTG
* * *
12491045 CTCAGGGAGATAAGGCTAGTGTTTTCGATCTGCTTCACTGCCAGTACATG-AAGACAAGATCTAC
1 CTCAGGGAGATAAGGCTAGTGTTTTCGATCTACTTCACTGCCAGTACAGGAAAGACAAAATCTAC
**
12491109 AATCTTTAACCTACTCCACTGCAAA
66 AATCTTTAACCTACTCCACTGC-TG
* * *
12491134 TTTAGGGAGATAAGGCTAGTGTTTTCGATCTGCTTCACTGCCAGTACAGG-AAGACAAAATCTAC
1 CTCAGGGAGATAAGGCTAGTGTTTTCGATCTACTTCACTGCCAGTACAGGAAAGACAAAATCTAC
*
12491198 AATCTTTAACCTACTCCATTGCTG
66 AATCTTTAACCTACTCCACTGCTG
* *
12491222 CTCAGGGAGATAAGGCT-GCTGTTTTTGATCTACTTCACTGCCAGTACA-GAAAGACAAGATCTA
1 CTCAGGGAGATAAGGCTAG-TGTTTTCGATCTACTTCACTGCCAGTACAGGAAAGACAAAATCTA
* *
12491285 CAATCTTCAACCTACTCTACTGCTG
65 CAATCTTTAACCTACTCCACTGCTG
* *
12491310 CTTAAGGAGATAAGGCT
1 CTCAGGGAGATAAGGCT
12491327 GGTGGCTTAA
Statistics
Matches: 252, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
87 4 0.02
88 167 0.66
89 81 0.32
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (89 bp):
CTCAGGGAGATAAGGCTAGTGTTTTCGATCTACTTCACTGCCAGTACAGGAAAGACAAAATCTAC
AATCTTTAACCTACTCCACTGCTG
Found at i:12492768 original size:11 final size:11
Alignment explanation
Indices: 12492752--12492791 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
12492742 TCATCTTGGC
12492752 CTTTTTTTTTT
1 CTTTTTTTTTT
*
12492763 CTTTTTCTTTT
1 CTTTTTTTTTT
* *
12492774 CTTTTCTTCTT
1 CTTTTTTTTTT
12492785 CTTTTTT
1 CTTTTTT
12492792 GAAATATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:12492773 original size:16 final size:16
Alignment explanation
Indices: 12492754--12492791 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
12492744 ATCTTGGCCT
*
12492754 TTTTTTTTTCTTTTTC
1 TTTTTTTTTCTTCTTC
*
12492770 TTTTCTTTTCTTCTTC
1 TTTTTTTTTCTTCTTC
12492786 TTTTTT
1 TTTTTT
12492792 GAAATATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTCTTCTTC
Found at i:12495799 original size:9 final size:9
Alignment explanation
Indices: 12495788--12495881 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
12495778 TTTGGTTAAA
*
12495788 AATTAACCA
1 AATTAACCG
12495797 AATTAACCG
1 AATTAACCG
12495806 AATTAACCG
1 AATTAACCG
12495815 AATTAACCG
1 AATTAACCG
*
12495824 AATTAATCG
1 AATTAACCG
*
12495833 AATTACCCG
1 AATTAACCG
*
12495842 AATTACCCG
1 AATTAACCG
*
12495851 AATTACCCG
1 AATTAACCG
*
12495860 AATTACCCG
1 AATTAACCG
*
12495869 AATTAACCA
1 AATTAACCG
12495878 AATT
1 AATT
12495882 GAATCACTAC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 79 1.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:12497149 original size:22 final size:22
Alignment explanation
Indices: 12497097--12497149 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
12497087 ATGCAATATA
*
12497097 AAAATATATGTAAGTATGTATAT
1 AAAATATATGT-AGTATGTAAAT
*
12497120 ATACATATATGT-GTATGTAAATT
1 A-AAATATATGTAGTATGTAAA-T
12497143 AAAATAT
1 AAAATAT
12497150 GTATATATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 13 0.52
23 3 0.12
24 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (22 bp):
AAAATATATGTAGTATGTAAAT
Found at i:12504807 original size:3 final size:3
Alignment explanation
Indices: 12504799--12504823 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12504789 AGGTCCATTA
12504799 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
12504824 TTGTTGCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:12506227 original size:5 final size:6
Alignment explanation
Indices: 12506210--12506234 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12506200 ATTATAATAA
12506210 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
12506235 TTCCTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:12508599 original size:30 final size:24
Alignment explanation
Indices: 12508544--12508590 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
12508534 TAGGAGAATG
12508544 GGCAGCTATATTACAATCAATGTC
1 GGCAGCTATATTACAATCAATGTC
12508568 GGCAGCTATATTACAATCAATGT
1 GGCAGCTATATTACAATCAATGT
12508591 TCTAGTCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (24 bp):
GGCAGCTATATTACAATCAATGTC
Found at i:12515016 original size:24 final size:24
Alignment explanation
Indices: 12514966--12515017 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
12514956 TTTCTAGAAG
* * *
12514966 ATTTAGTATCTATTAGTATTATAT
1 ATTTAGCATCTATTAGCATAATAT
* *
12514990 ATTTAGCATTTATTAGCATAATGT
1 ATTTAGCATCTATTAGCATAATAT
12515014 ATTT
1 ATTT
12515018 TACCTACGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTAGCATCTATTAGCATAATAT
Found at i:12516957 original size:24 final size:24
Alignment explanation
Indices: 12516930--12516981 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
12516920 ATATTTTATT
*
12516930 TATAGAAGATTTAGTATCTATTAG
1 TATAGAAGATTTAGCATCTATTAG
* * *
12516954 TATAGTATATTTAGCATTTATTAG
1 TATAGAAGATTTAGCATCTATTAG
12516978 TATA
1 TATA
12516982 ATTTATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (24 bp):
TATAGAAGATTTAGCATCTATTAG
Found at i:12516988 original size:24 final size:24
Alignment explanation
Indices: 12516938--12516989 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
12516928 TTTATAGAAG
* *
12516938 ATTTAGTATCTATTAGTATAGTAT
1 ATTTAGCATCTATTAGTATAATAT
* *
12516962 ATTTAGCATTTATTAGTATAATTT
1 ATTTAGCATCTATTAGTATAATAT
12516986 ATTT
1 ATTT
12516990 TACCTACGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (24 bp):
ATTTAGCATCTATTAGTATAATAT
Found at i:12526185 original size:19 final size:19
Alignment explanation
Indices: 12526163--12526200 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12526153 GAATATAGAA
*
12526163 TAAAATATAT-GATATAAAT
1 TAAAA-ATATCGAAATAAAT
12526182 TAAAAATATCGAAATAAAT
1 TAAAAATATCGAAATAAAT
12526201 CAGATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAAAATATCGAAATAAAT
Found at i:12532566 original size:15 final size:16
Alignment explanation
Indices: 12532541--12532570 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12532531 GTTATATATA
12532541 TATATATATATATTTC
1 TATATATATATATTTC
12532557 TATA-ATATATATTT
1 TATATATATATATTT
12532571 ATACACGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATATATATATTTC
Found at i:12532661 original size:42 final size:42
Alignment explanation
Indices: 12532596--12532676 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
12532586 TTCATAATTT
* * *
12532596 ACTTATATATATACATACTTATATATATTTTTACATTTTATA
1 ACTTATATACATACATACATATATATATATTTACATTTTATA
* *
12532638 ACTTATATACATATC-TACATATATCTATATTTATATTTT
1 ACTTATATACATA-CATACATATATATATATTTACATTTT
12532677 TTATTTTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (42 bp):
ACTTATATACATACATACATATATATATATTTACATTTTATA
Found at i:12532825 original size:19 final size:19
Alignment explanation
Indices: 12532794--12532830 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12532784 ATATTTTATT
12532794 CATTTTTGTTTATTTATTTA
1 CATTTTTGTTTA-TTATTTA
12532814 CATTTTTG-TTATTATTT
1 CATTTTTGTTTATTATTT
12532831 TAAAAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (19 bp):
CATTTTTGTTTATTATTTA
Found at i:12533688 original size:71 final size:71
Alignment explanation
Indices: 12533572--12533713 Score: 248
Period size: 71 Copynumber: 2.0 Consensus size: 71
12533562 TATTTTCAAA
*
12533572 CTCAAGTTTTAAACGATATCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATCAT
1 CTCAAGTTTTAAACGATATCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCAT
12533637 TTTTTT
66 TTTTTT
* * *
12533643 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCT
1 CTCAAGTTTTAAACGATATCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCAT
12533708 TTTTTT
66 TTTTTT
12533714 TAAATCCAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (71 bp):
CTCAAGTTTTAAACGATATCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCAT
TTTTTT
Found at i:12536615 original size:9 final size:9
Alignment explanation
Indices: 12536601--12536653 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
12536591 GTTCAGTGGA
12536601 AAAAAAAAC
1 AAAAAAAAC
12536610 AAAAAAAAC
1 AAAAAAAAC
12536619 AAAAACAAA-
1 AAAAA-AAAC
* *
12536628 AAAAACAAT
1 AAAAAAAAC
12536637 AAAACAAAAC
1 AAAA-AAAAC
12536647 AAAAAAA
1 AAAAAAA
12536654 CCTCTATCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
8 2 0.05
9 26 0.68
10 10 0.26
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:12536624 original size:15 final size:15
Alignment explanation
Indices: 12536600--12536650 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
12536590 GGTTCAGTGG
12536600 AAAA-AAAAACAAAA
1 AAAACAAAAACAAAA
12536614 AAAACAAAAACAAAA
1 AAAACAAAAACAAAA
12536629 AAAACAATAAAACAAAA
1 AAAAC-A-AAAACAAAA
12536646 CAAAA
1 -AAAA
12536651 AAACCTCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.12
15 15 0.45
16 1 0.03
17 9 0.27
18 4 0.12
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (15 bp):
AAAACAAAAACAAAA
Found at i:12536628 original size:23 final size:23
Alignment explanation
Indices: 12536602--12536654 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
12536592 TTCAGTGGAA
12536602 AAAAAAACA-AAAAAAACAAAAAC
1 AAAAAAACACAAAAAAAC-AAAAC
*
12536625 AAAAAAA-ACAATAAAACAAAAC
1 AAAAAAACACAAAAAAACAAAAC
12536647 AAAAAAAC
1 AAAAAAAC
12536655 CTCTATCGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (23 bp):
AAAAAAACACAAAAAAACAAAAC
Found at i:12537109 original size:17 final size:17
Alignment explanation
Indices: 12537087--12537119 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12537077 TTCACTTGAA
*
12537087 AAAAAAGAAACGAAAAG
1 AAAAAAGAAAAGAAAAG
12537104 AAAAAAGAAAAGAAAA
1 AAAAAAGAAAAGAAAA
12537120 AGGAGAGGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGAAAAG
Found at i:12538056 original size:50 final size:50
Alignment explanation
Indices: 12538002--12538716 Score: 420
Period size: 50 Copynumber: 14.3 Consensus size: 50
12537992 GCAGTTAAAA
** *
12538002 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGCAGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTAGAAC
* * * * * * * * * *
12538052 AGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGTAAT-TAAT
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTAGAAC
* ** * * *
12538101 AAATTTGAAGCCACAACAACGAATCTTACTTCCCTGGCAGTGTACTGGAAC
1 AGA-TTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTAGAAC
* * * * ** * * *
12538152 AGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGATATTGCAATTA-AAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGC-AGTAGAAC
* * * *
12538202 AGATTGAAGCCACAACGGCAAATCTTACTTCCCTAGCGGTGCAGTGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTAGAAC
* * * * * * * * *
12538252 AGATTGAAGCTACAACGACGAATCTTGCTACCCCGACATTGCAATTA-AAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGC-AGTAGAAC
* * * * *
12538302 ATATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTACAGTGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTAGAAC
* * * *** * * * *
12538352 AGATTGAAGCTACAACGACGAATCTTGCTTCCCCAACATTGTAATTA-AAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG-CAGTAGAAC
* * * * * * *
12538402 AGATTGAAGCCACAACGGTGAATCTTACTTTCTTGGCGGTGTAATGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTAGAAC
* * ** * * * * * *
12538452 AGATTGAAGCTACGACGATGAATCTT-GTTTCCTCGACATTGCAATTA-AAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCT-GGCAGTGC-AGTAGAAC
* * * *
12538502 ATATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTACAGTGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTAGAAC
* * ** * * * * * *
12538552 AAATTGAAGCTACAACAACGAATCTTGCTTCCCCGACATTGCAATTA-AAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGC-AGTAGAAC
* * *
12538602 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTAGAAC
* * * * * * * *
12538652 AGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTGCAATTA-AAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGC-AGTAGAAC
12538702 AGATTGAAGCCACAA
1 AGATTGAAGCCACAA
12538717 AACTTCCCTG
Statistics
Matches: 479, Mismatches: 171, Indels: 30
0.70 0.25 0.04
Matches are distributed among these distances:
49 19 0.04
50 439 0.92
51 21 0.04
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTAGAAC
Found at i:12538178 original size:100 final size:100
Alignment explanation
Indices: 12537990--12538822 Score: 1060
Period size: 100 Copynumber: 8.4 Consensus size: 100
12537980 ACCCCTAAGG
* * * *
12537990 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGC-AGAACAG
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTA-CTGGAACAG
**
12538054 ATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACA
65 ATTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
* * ** *
12538090 TTGTAATTAATAAA-TTTGAAGCCACAACAACGAATCTTACTTCCCTGGCAGTGTACTGGAACAG
1 TTGCAATTAA-AAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTACTGGAACAG
* * *
12538154 ATTGAAGCTACAATGGCGAATCTTGCTTCCCCGATA
65 ATTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
* * * *
12538190 TTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTTCCCTAGCGGTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTACTGGAACAGA
*
12538255 TTGAAGCTACAACGACGAATCTTGCTACCCCGACA
66 TTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
* * ** *
12538290 TTGCAATTAAAAATATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTACAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTACTGGAACAGA
*
12538355 TTGAAGCTACAACGACGAATCTTGCTTCCCCAACA
66 TTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
* * * * *
12538390 TTGTAATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTTCTTGGCGGTGTAATGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTACTGGAACAGA
* * * *
12538455 TTGAAGCTACGACGATGAATCTTGTTTCCTCGACA
66 TTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
* ** * *
12538490 TTGCAATTAAAAATATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTACAGTGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTACTGGAACAGA
*
12538555 TTGAAGCTACAACAACGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
* * *
12538590 TTGCAATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTACTGGAACAGA
* *
12538655 TTGAAGCTACAATGGCGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
*
12538690 TTGCAATTAAAAAGATTGAAGCCAC-A-----AA----ACTTCCCTGGCGGTGTAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTACTGGAACAGA
* * * *
12538745 TTGAAGCTACGACGGCGAATCTCGTTTCCCCGACA
66 TTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
* * * * **
12538780 TTGCAGTTAAATAGATTGAAGCTACGACAACGAATCTTACTTC
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTC
12538823 TTTGGCATTA
Statistics
Matches: 647, Mismatches: 73, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
90 79 0.12
91 1 0.00
94 2 0.00
96 2 0.00
99 5 0.01
100 555 0.86
101 3 0.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTACTGGAACAGA
TTGAAGCTACAACGACGAATCTTGCTTCCCCGACA
Found at i:12538781 original size:90 final size:90
Alignment explanation
Indices: 12538628--12538801 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 90
12538618 GGTGAATCTT
* *
12538628 ACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTG
1 ACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACATTG
12538693 CAATTAAAAAGATTGAAGCCACAAA
66 CAATTAAAAAGATTGAAGCCACAAA
* * *
12538718 ACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTCGTTTCCCCGACATTG
1 ACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACATTG
* *
12538783 CAGTTAAATAGATTGAAGC
66 CAATTAAAAAGATTGAAGC
12538802 TACGACAACG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (90 bp):
ACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACATTG
CAATTAAAAAGATTGAAGCCACAAA
Found at i:12538961 original size:83 final size:83
Alignment explanation
Indices: 12538819--12538977 Score: 257
Period size: 83 Copynumber: 1.9 Consensus size: 83
12538809 ACGAATCTTA
* * * *
12538819 CTTCTTTGGCATTATAGTGGAGCAGATTAAAGCTGAAGGCAGCAGATCTTATCTTCCTGGCGTTA
1 CTTCTTTGGCATTATAGCGGAGCAGATTAAAGCTAAAGGCAGCAGATCTTATCTCCCTGGCATTA
12538884 AGACTGAAGACAGCTAGT
66 AGACTGAAGACAGCTAGT
*
12538902 CTTCTTTGGCATTGTAGCGGAGCAGATTAAAGCTAAAGGCAGC-GAATCTTATCTCCCTGGCATT
1 CTTCTTTGGCATTATAGCGGAGCAGATTAAAGCTAAAGGCAGCAG-ATCTTATCTCCCTGGCATT
12538966 AAGACTGAAGAC
65 AAGACTGAAGAC
12538978 GGCGAATCTT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
82 1 0.01
83 69 0.99
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (83 bp):
CTTCTTTGGCATTATAGCGGAGCAGATTAAAGCTAAAGGCAGCAGATCTTATCTCCCTGGCATTA
AGACTGAAGACAGCTAGT
Found at i:12541648 original size:71 final size:71
Alignment explanation
Indices: 12541532--12541673 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 71
12541522 TCTTTTCAAA
* *
12541532 CTCAAGTTTTAAACGATATCAGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATCCT
1 CTCAAGTTGTAAACGATATCAGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCT
12541597 TTTTTT
66 TTTTTT
* *
12541603 CTCAAGTTGTAAATGATCTC-GAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
1 CTCAAGTTGTAAACGATATCAG-GAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
12541667 TTTTTTT
65 TTTTTTT
12541674 AAATCCAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
70 1 0.02
71 65 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (71 bp):
CTCAAGTTGTAAACGATATCAGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCT
TTTTTT
Found at i:12556228 original size:21 final size:21
Alignment explanation
Indices: 12556202--12556257 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
12556192 AATAGCGGTG
*
12556202 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
12556223 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
12556244 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
12556258 AATAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:12556463 original size:30 final size:29
Alignment explanation
Indices: 12556426--12556551 Score: 180
Period size: 30 Copynumber: 4.2 Consensus size: 29
12556416 ATTCATTTAA
12556426 TAAAATACACTACATATATTTTTTTATTT
1 TAAAATACACTACATATATTTTTTTATTT
*
12556455 CTAGAATACACTACATATATTTTTTTATTT
1 -TAAAATACACTACATATATTTTTTTATTT
*
12556485 TGAAAATACACTACATGTATTTTTTTATTTT
1 T-AAAATACACTACATATATTTTTTTA-TTT
* *
12556516 TAAAATCCATTACATATATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTA-TTT
12556546 TAAAAT
1 TAAAAT
12556552 TTTAAATACA
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
29 1 0.01
30 83 0.94
31 4 0.05
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (29 bp):
TAAAATACACTACATATATTTTTTTATTT
Found at i:12556667 original size:28 final size:28
Alignment explanation
Indices: 12556627--12556729 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 28
12556617 GCAATAACAT
*
12556627 TCCCATTTCCCATTCCACCGTGCCCTCC
1 TCCCATTTCCCATTCCACCGTCCCCTCC
* *
12556655 TCCCATTTCCCATTCCCATC-TCCCCTCT
1 TCCCATTTCCCATT-CCACCGTCCCCTCC
* * *
12556683 TCCATCGATTCCCCTCTTCCACCGTTCCCTCC
1 TCC--C-ATTTCCC-ATTCCACCGTCCCCTCC
12556715 TCCCA-TTCCCATTCC
1 TCCCATTTCCCATTCC
12556730 CATTCCCATT
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.07
28 27 0.46
29 5 0.08
30 2 0.03
31 10 0.17
32 11 0.19
ACGTcount: A:0.11, C:0.53, G:0.04, T:0.32
Consensus pattern (28 bp):
TCCCATTTCCCATTCCACCGTCCCCTCC
Found at i:12556723 original size:21 final size:21
Alignment explanation
Indices: 12556634--12556723 Score: 50
Period size: 21 Copynumber: 4.4 Consensus size: 21
12556624 CATTCCCATT
*
12556634 TCCCATTCCACCGTGCCCTCC
1 TCCCATTCCACCGTTCCCTCC
* *
12556655 TCCCATTTC-CCATTCCCAT-C
1 TCCCATTCCACCGTTCCC-TCC
* *
12556675 TCCCCTCTTCCATCGATT-CC-CC
1 T-CCC-ATTCCACCG-TTCCCTCC
12556697 T--C-TTCCACCGTTCCCTCC
1 TCCCATTCCACCGTTCCCTCC
12556715 TCCCATTCC
1 TCCCATTCC
12556724 CATTCCCATT
Statistics
Matches: 50, Mismatches: 8, Indels: 22
0.62 0.10 0.28
Matches are distributed among these distances:
16 2 0.04
17 9 0.18
18 3 0.06
19 1 0.02
20 9 0.18
21 16 0.32
22 5 0.10
23 3 0.06
24 2 0.04
ACGTcount: A:0.10, C:0.54, G:0.04, T:0.31
Consensus pattern (21 bp):
TCCCATTCCACCGTTCCCTCC
Found at i:12556726 original size:6 final size:6
Alignment explanation
Indices: 12556715--12556739 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12556705 CGTTCCCTCC
12556715 TCCCAT TCCCAT TCCCAT TCCCAT T
1 TCCCAT TCCCAT TCCCAT TCCCAT T
12556740 ATCAACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.48, G:0.00, T:0.36
Consensus pattern (6 bp):
TCCCAT
Found at i:12558678 original size:19 final size:18
Alignment explanation
Indices: 12558656--12558717 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
12558646 AATTACATAA
12558656 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTTT
* *
12558675 AAAATTCAAAATATTTAT
1 AAAAATCAAAATATTTTT
*
12558693 AAAAATTCCAAATTATTTTT
1 AAAAA-T-CAAAATATTTTT
*
12558713 TAAAA
1 AAAAA
12558718 GTTTCAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 9 0.26
19 12 0.34
20 14 0.40
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATCAAAATATTTTT
Found at i:12558717 original size:20 final size:19
Alignment explanation
Indices: 12558656--12558717 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
12558646 AATTACATAA
* *
12558656 AAAAATCAAAATAATTTTT
1 AAAATTCAAAATATTTTTT
* *
12558675 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTTTT
*
12558694 AAAATTCCAAATTATTTTTT
1 AAAATT-CAAAATATTTTTT
12558714 AAAA
1 AAAA
12558718 GTTTCAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
19 21 0.60
20 14 0.40
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATATTTTTT
Found at i:12562229 original size:13 final size:13
Alignment explanation
Indices: 12562210--12562242 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12562200 AAATACCGGA
12562210 GAAAAGTGTTTTT
1 GAAAAGTGTTTTT
*
12562223 GAGAAGTGTTTTT
1 GAAAAGTGTTTTT
12562236 GAAAAGT
1 GAAAAGT
12562243 TTAGTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.39
Consensus pattern (13 bp):
GAAAAGTGTTTTT
Found at i:12566617 original size:5 final size:5
Alignment explanation
Indices: 12566607--12566656 Score: 50
Period size: 5 Copynumber: 10.4 Consensus size: 5
12566597 CTTTTTTTTC
* * * *
12566607 TTCTT TTCTT TTCTT TTCTT TACTT TAC-T TTCTT CTCTT TT-TT TCCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
12566655 TT
1 TT
12566657 GTTCTTTCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 6 0.16
5 31 0.84
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (5 bp):
TTCTT
Found at i:12568117 original size:3 final size:3
Alignment explanation
Indices: 12568109--12568165 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
12568099 TTTATAATGT
* * * * * *
12568109 TGC TGC TGC TGT TGT TGT TGC TGC TGT TGT TGA TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
12568157 TGC TGC TGC
1 TGC TGC TGC
12568166 ATATTATTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.02, C:0.23, G:0.33, T:0.42
Consensus pattern (3 bp):
TGC
Found at i:12568129 original size:18 final size:18
Alignment explanation
Indices: 12568105--12568155 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
12568095 CCAGTTTATA
12568105 ATGTTGCTGCTGCTGTTG
1 ATGTTGCTGCTGCTGTTG
* *
12568123 TTGTTGCTGCTGTTGTTG
1 ATGTTGCTGCTGCTGTTG
*
12568141 ATGCTGCTGCTGCTG
1 ATGTTGCTGCTGCTG
12568156 CTGCTGCTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.18, G:0.33, T:0.45
Consensus pattern (18 bp):
ATGTTGCTGCTGCTGTTG
Found at i:12568130 original size:15 final size:15
Alignment explanation
Indices: 12568106--12568164 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
12568096 CAGTTTATAA
12568106 TGTTGCTGCTGCTGT
1 TGTTGCTGCTGCTGT
*
12568121 TGTTGTTGCTGCTGT
1 TGTTGCTGCTGCTGT
* *
12568136 TGTTGATGCTGCTGC
1 TGTTGCTGCTGCTGT
*
12568151 TGCTGCTGCTGCTG
1 TGTTGCTGCTGCTG
12568165 CATATTATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.02, C:0.20, G:0.34, T:0.44
Consensus pattern (15 bp):
TGTTGCTGCTGCTGT
Found at i:12568905 original size:12 final size:12
Alignment explanation
Indices: 12568899--12568936 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
12568889 ATGTTGCTGT
*
12568899 TGCTGTTGTTGC
1 TGCTGCTGTTGC
*
12568911 TGCTGCTGGTGC
1 TGCTGCTGTTGC
12568923 TGCTGCTGTTGC
1 TGCTGCTGTTGC
12568935 TG
1 TG
12568937 ATGATGATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.37, T:0.42
Consensus pattern (12 bp):
TGCTGCTGTTGC
Found at i:12568910 original size:15 final size:15
Alignment explanation
Indices: 12568890--12568933 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
12568880 ATGCTGATGA
*
12568890 TGTTGCTGTTGCTGT
1 TGTTGCTGCTGCTGT
12568905 TGTTGCTGCTGCTG-
1 TGTTGCTGCTGCTGT
12568919 -G-TGCTGCTGCTGT
1 TGTTGCTGCTGCTGT
12568932 TG
1 TG
12568934 CTGATGATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 11 0.42
13 1 0.04
14 1 0.04
15 13 0.50
ACGTcount: A:0.00, C:0.18, G:0.36, T:0.45
Consensus pattern (15 bp):
TGTTGCTGCTGCTGT
Found at i:12572534 original size:30 final size:26
Alignment explanation
Indices: 12572500--12572574 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 26
12572490 TTAATTAAGT
12572500 TTTTAAAATTAAAAATAATTTTTTTTATAA
1 TTTTAAAATTAAAAAT-A--TTTTTT-TAA
* *
12572530 TTTTAATATTTTAAAATATTTTTTTAA
1 TTTTAA-AATTAAAAATATTTTTTTAA
12572557 TTTTAAAAATTAATAAAT
1 TTTT-AAAATTAA-AAAT
12572575 TGCTAATGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 11 0.29
28 12 0.32
30 7 0.18
31 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTAAAATTAAAAATATTTTTTTAA
Found at i:12573582 original size:18 final size:18
Alignment explanation
Indices: 12573532--12573582 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
12573522 AGATGAAAAA
12573532 AATTATATTTGAAAT-AT
1 AATTATATTTGAAATAAT
* * * *
12573549 -CTTACATATAAAATAAT
1 AATTATATTTGAAATAAT
12573566 AATTATATTTGAAATAA
1 AATTATATTTGAAATAA
12573583 CTATTTCATT
Statistics
Matches: 24, Mismatches: 8, Indels: 3
0.69 0.23 0.09
Matches are distributed among these distances:
16 10 0.42
17 2 0.08
18 12 0.50
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (18 bp):
AATTATATTTGAAATAAT
Found at i:12579362 original size:20 final size:20
Alignment explanation
Indices: 12579316--12579371 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
12579306 AGTTAATACA
* *
12579316 TATCTTAATATT-ATTTTAT
1 TATCTTAATATTAAATTGAT
12579335 TAAT-TTAATATTAAATTGAT
1 T-ATCTTAATATTAAATTGAT
*
12579355 TATCTTAATGTTAAATT
1 TATCTTAATATTAAATT
12579372 TAATTTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (20 bp):
TATCTTAATATTAAATTGAT
Found at i:12584107 original size:5 final size:5
Alignment explanation
Indices: 12584097--12584122 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12584087 GCTCACATAC
12584097 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
12584123 CAAACCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:12586819 original size:22 final size:21
Alignment explanation
Indices: 12586791--12586848 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
12586781 TGGTTTATTG
*
12586791 TTATTATTTTTATTGGTCATTA
1 TTATTATTTTTATTAGTC-TTA
* *
12586813 TTATTATTATTATTAGTCTTT
1 TTATTATTTTTATTAGTCTTA
*
12586834 TTATTTTATTTTATT
1 TTATTAT-TTTTATT
12586849 TTTCCTCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 8 0.27
22 22 0.73
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.69
Consensus pattern (21 bp):
TTATTATTTTTATTAGTCTTA
Found at i:12587394 original size:5 final size:5
Alignment explanation
Indices: 12587379--12587409 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
12587369 TAAATCTTCA
12587379 TATTAT TATTT TATTT TATTT TATTT TATTT
1 TATT-T TATTT TATTT TATTT TATTT TATTT
12587410 GTAATCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:12588319 original size:24 final size:25
Alignment explanation
Indices: 12588283--12588330 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
12588273 TTAAAATGAA
12588283 TTTTAAAAGATTT-TAAACTTTTAT
1 TTTTAAAAGATTTATAAACTTTTAT
* * *
12588307 TTTTATAATATTTATATACTTTTA
1 TTTTAAAAGATTTATAAACTTTTA
12588331 AAGAAAAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTAAAAGATTTATAAACTTTTAT
Found at i:12590300 original size:11 final size:11
Alignment explanation
Indices: 12590284--12590309 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12590274 ATTTAAGGAA
12590284 TTTTATCCTAT
1 TTTTATCCTAT
12590295 TTTTATCCTAT
1 TTTTATCCTAT
12590306 TTTT
1 TTTT
12590310 GACTGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATCCTAT
Found at i:12591296 original size:17 final size:17
Alignment explanation
Indices: 12591274--12591316 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
12591264 AATATATAAT
12591274 ATTATAATGCAAAATTA
1 ATTATAATGCAAAATTA
12591291 ATTATAATGCAAAATTA
1 ATTATAATGCAAAATTA
12591308 ATATATAAT
1 AT-TATAAT
12591317 ATTATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (17 bp):
ATTATAATGCAAAATTA
Found at i:12594257 original size:43 final size:42
Alignment explanation
Indices: 12594198--12594302 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 42
12594188 AATTTTTTTG
*
12594198 AAGGT-ATGTTTTTAGCGGCGTTTTTGCGAGAAGCGCCGCTA
1 AAGGTCATGTTTTTAGCGGCGTTTTTGCGAAAAGCGCCGCTA
* **
12594239 AAGGTCATGTTTTTTAGCGGCGTTTTTGGGAAAAGCGTTGCTA
1 AAGGTCATG-TTTTTAGCGGCGTTTTTGCGAAAAGCGCCGCTA
* *
12594282 AAGGTCGTGGTCTTTAGCGGC
1 AAGGTCAT-GTTTTTAGCGGC
12594303 ATTTGTTTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
41 5 0.09
42 3 0.05
43 46 0.84
44 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.32, T:0.33
Consensus pattern (42 bp):
AAGGTCATGTTTTTAGCGGCGTTTTTGCGAAAAGCGCCGCTA
Found at i:12596192 original size:16 final size:16
Alignment explanation
Indices: 12596171--12596210 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12596161 CGTTTGGTTC
*
12596171 GCTGTAATGGAATAGA
1 GCTGTAATGAAATAGA
12596187 GCTGTAATGAAATAGA
1 GCTGTAATGAAATAGA
*
12596203 ACTGTAAT
1 GCTGTAAT
12596211 AGTAATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (16 bp):
GCTGTAATGAAATAGA
Found at i:12596279 original size:44 final size:45
Alignment explanation
Indices: 12596197--12596281 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 45
12596187 GCTGTAATGA
12596197 AATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGGACTAG
1 AATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGGACTAG
* *
12596242 AATAGAACTGTAATGGT-ATTC-TTGTGTTTGGTTGAATGGA
1 AATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGGA
12596282 ATAATATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 1 0.03
44 20 0.54
45 16 0.43
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.38
Consensus pattern (45 bp):
AATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGGACTAG
Found at i:12599424 original size:15 final size:15
Alignment explanation
Indices: 12599401--12599441 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
12599391 TTTTGGTCTC
*
12599401 AAAATGTGAATCAGA
1 AAAAGGTGAATCAGA
12599416 AAAAGGTGAATCAGA
1 AAAAGGTGAATCAGA
12599431 AAAAGGTGAAT
1 AAAAGGTGAAT
12599442 AGCTATTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.54, C:0.05, G:0.24, T:0.17
Consensus pattern (15 bp):
AAAAGGTGAATCAGA
Done.