Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 55 of 345
Found at i:15511512 original size:43 final size:42
Alignment explanation
Indices: 15511356--15511583 Score: 175
Period size: 43 Copynumber: 5.4 Consensus size: 42
15511346 AGCAAACGCT
* * *
15511356 ACTAAAGACCATGACTTTTAGCGGCGC-TTT-TCAAAAAGCC
1 ACTAAAGACCATGACCTTTAGCGACGCTTTTCTCCAAAAGCC
* * *
15511396 ACTAAAGACCATGACCTTTAGCGGCGCTGTTC-CCACAAATACC
1 ACTAAAGACCATGACCTTTAGCGACGCTTTTCTCCA-AAA-GCC
*
15511439 ACTAAAGACCATGACCTTTAGC-AGCGCTTTTCTCGCAAAGGCC
1 ACTAAAGACCATGACCTTTAGCGA-CGCTTTTCTC-CAAAAGCC
* * * * * *
15511482 GCTAAAGACCATGACCTTTAGCGACACTTTTGTTACGAACGCC
1 ACTAAAGACCATGACCTTTAGCGACGCTTTT-CTCCAAAAGCC
* *
15511525 ACTATAA-A--ATAGACCTTTAGCGACGCTTTTCTACAAACA-TC
1 ACTA-AAGACCAT-GACCTTTAGCGACGCTTTTCTCCAAA-AGCC
* *
15511566 ACTAAAAAACATGACCTT
1 ACTAAAGACCATGACCTT
15511584 CAAAAATATT
Statistics
Matches: 153, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
40 28 0.18
41 17 0.11
42 27 0.18
43 72 0.47
44 7 0.05
45 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (42 bp):
ACTAAAGACCATGACCTTTAGCGACGCTTTTCTCCAAAAGCC
Found at i:15516434 original size:14 final size:14
Alignment explanation
Indices: 15516418--15516471 Score: 67
Period size: 14 Copynumber: 3.8 Consensus size: 14
15516408 ATATTAAATA
15516418 TTTAAGTTTTTTAATT
1 TTTAA-TTTTTTAA-T
15516434 TTTAA-TTTTTAAT
1 TTTAATTTTTTAAT
15516447 TTTAA-TTTTTATAT
1 TTTAATTTTTTA-AT
15516461 TTTAATTTTTT
1 TTTAATTTTTT
15516472 TTGAAGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.33
14 14 0.39
15 5 0.14
16 5 0.14
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTAATTTTTTAAT
Found at i:15516435 original size:7 final size:7
Alignment explanation
Indices: 15516425--15516470 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
15516415 ATATTTAAGT
15516425 TTTTTAA
1 TTTTTAA
15516432 TTTTTAA
1 TTTTTAA
15516439 TTTTTAA
1 TTTTTAA
15516446 -TTTTAA
1 TTTTTAA
15516452 TTTTT-A
1 TTTTTAA
15516458 TATTTTAA
1 T-TTTTAA
15516466 TTTTT
1 TTTTT
15516471 TTTGAAGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 8 0.22
7 26 0.72
8 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:15516451 original size:20 final size:20
Alignment explanation
Indices: 15516426--15516469 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
15516416 TATTTAAGTT
15516426 TTTTAATTTTTA-ATTTTTAA
1 TTTTAATTTTTATA-TTTTAA
15516446 TTTTAATTTTTATATTTTAA
1 TTTTAATTTTTATATTTTAA
15516466 TTTT
1 TTTT
15516470 TTTTGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTAATTTTTATATTTTAA
Found at i:15517236 original size:7 final size:7
Alignment explanation
Indices: 15517224--15517333 Score: 55
Period size: 7 Copynumber: 15.4 Consensus size: 7
15517214 AACCAACCCT
15517224 TAAACCA
1 TAAACCA
15517231 TAAACCA
1 TAAACCA
*
15517238 T-AATCA
1 TAAACCA
15517244 CTAAACCCA
1 -TAAA-CCA
*
15517253 TAATCCA
1 TAAACCA
*
15517260 TAAACCT
1 TAAACCA
15517267 TAAA--A
1 TAAACCA
15517272 TAATAACTCA
1 T-A-AAC-CA
* **
15517282 TACACTT
1 TAAACCA
*
15517289 TAAACCC
1 TAAACCA
15517296 TAAACCA
1 TAAACCA
* *
15517303 TATACCC
1 TAAACCA
15517310 TAAACCA
1 TAAACCA
*
15517317 TAAACCC
1 TAAACCA
*
15517324 TAAACTA
1 TAAACCA
15517331 TAA
1 TAA
15517334 TGATAATTAA
Statistics
Matches: 75, Mismatches: 20, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
5 1 0.01
6 5 0.07
7 57 0.76
8 7 0.09
9 3 0.04
10 2 0.03
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCA
Found at i:15517263 original size:15 final size:15
Alignment explanation
Indices: 15517218--15517265 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
15517208 CTTAAAAACC
* *
15517218 AACCCTTAAACCATA
1 AACCCATAATCCATA
15517233 AA-CCATAAT-CACTA
1 AACCCATAATCCA-TA
15517247 AACCCATAATCCATA
1 AACCCATAATCCATA
15517262 AACC
1 AACC
15517266 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:15517270 original size:22 final size:21
Alignment explanation
Indices: 15517221--15517328 Score: 78
Period size: 22 Copynumber: 5.0 Consensus size: 21
15517211 AAAAACCAAC
*
15517221 CCTTAAACCATAAACCATAAT
1 CCTTAAACCATAAACCATAAA
*
15517242 CAC-TAAACCCATAATCCATAAA
1 C-CTTAAA-CCATAAACCATAAA
*
15517264 CCTTAAA--ATAATAACTCATACA
1 CCTTAAACCAT-A-AAC-CATAAA
* * *
15517286 CTTTAAACCCTAAACCATATA
1 CCTTAAACCATAAACCATAAA
* *
15517307 CCCTAAACCATAAACCCTAAA
1 CCTTAAACCATAAACCATAAA
15517328 C
1 C
15517329 TATAATGATA
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
19 2 0.03
20 1 0.01
21 30 0.45
22 32 0.48
23 1 0.01
24 1 0.01
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (21 bp):
CCTTAAACCATAAACCATAAA
Found at i:15517311 original size:14 final size:14
Alignment explanation
Indices: 15517289--15517333 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
15517279 TCATACACTT
15517289 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
15517303 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
15517317 TAAACCCTAAACTA
1 TAAACCCTAAACCA
15517331 TAA
1 TAA
15517334 TGATAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:15517439 original size:7 final size:7
Alignment explanation
Indices: 15517427--15517588 Score: 87
Period size: 7 Copynumber: 22.7 Consensus size: 7
15517417 ACTAATTAAT
15517427 CTAAACC
1 CTAAACC
15517434 CTAAACTC
1 CTAAAC-C
* *
15517442 CTAATCT
1 CTAAACC
15517449 CTAAACC
1 CTAAACC
*
15517456 ATAAACC
1 CTAAACC
15517463 CTAAACC
1 CTAAACC
*
15517470 ATAAACC
1 CTAAACC
15517477 CTAAACC
1 CTAAACC
* *
15517484 ATAAATC
1 CTAAACC
* *
15517491 ATAAAAC
1 CTAAACC
*
15517498 ATAAACC
1 CTAAACC
*
15517505 CTGAACC
1 CTAAACC
*
15517512 ATAAACCC
1 CTAAA-CC
15517520 CT-AACAC
1 CTAAAC-C
15517527 CTAAACC
1 CTAAACC
*
15517534 TTAAATCC
1 CTAAA-CC
15517542 C--AACC
1 CTAAACC
15517547 CTTAAACC
1 C-TAAACC
* * *
15517555 ATAATCT
1 CTAAACC
15517562 CTAAACC
1 CTAAACC
*
15517569 CATAATCC
1 C-TAAACC
*
15517577 ATAAACC
1 CTAAACC
*
15517584 TTAAA
1 CTAAA
15517589 ATAGTAACTC
Statistics
Matches: 117, Mismatches: 29, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
5 3 0.03
6 3 0.03
7 88 0.75
8 23 0.20
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:15517468 original size:14 final size:14
Alignment explanation
Indices: 15517428--15517588 Score: 121
Period size: 14 Copynumber: 11.3 Consensus size: 14
15517418 CTAATTAATC
*
15517428 TAAACCCTAAACTCC
1 TAAACCCTAAAC-CA
* *
15517443 TAATCTCTAAACCA
1 TAAACCCTAAACCA
15517457 TAAACCCTAAACCA
1 TAAACCCTAAACCA
15517471 TAAACCCTAAACCA
1 TAAACCCTAAACCA
* * *
15517485 TAAATCATAAAACA
1 TAAACCCTAAACCA
*
15517499 TAAACCCTGAACCA
1 TAAACCCTAAACCA
15517513 TAAACCCCTAACACC-
1 TAAA-CCCTAA-ACCA
*
15517528 TAAACCTTAAATCC-
1 TAAACCCTAAA-CCA
*
15517542 -CAACCCTTAAACCA
1 TAAACCC-TAAACCA
* *
15517556 TAATCTCTAAACCCA
1 TAAACCCTAAA-CCA
* * *
15517571 TAATCCATAAACCT
1 TAAACCCTAAACCA
15517585 TAAA
1 TAAA
15517589 ATAGTAACTC
Statistics
Matches: 116, Mismatches: 23, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
13 7 0.06
14 72 0.62
15 34 0.29
16 3 0.03
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:15517892 original size:40 final size:40
Alignment explanation
Indices: 15517847--15517953 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
15517837 AAATTCTTTT
15517847 GCGGCATTTTTTGAAAAA-CGCCGCTAAAGATGAAGCAT-TA
1 GCGGCATTTTTT-AAAAAGCGCCGCTAAAGATGAA-CATATA
* * *
15517887 GCGGCATTTTCTAAAAAGCGCCGCTAAAGGTGTACATATA
1 GCGGCATTTTTTAAAAAGCGCCGCTAAAGATGAACATATA
* *
15517927 GCGGCGTTTTTAAAAAAGCGCCGCTAA
1 GCGGCATTTTTTAAAAAGCGCCGCTAA
15517954 TACTCGATCT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
39 8 0.14
40 51 0.86
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (40 bp):
GCGGCATTTTTTAAAAAGCGCCGCTAAAGATGAACATATA
Found at i:15518016 original size:39 final size:38
Alignment explanation
Indices: 15517840--15518016 Score: 124
Period size: 40 Copynumber: 4.5 Consensus size: 38
15517830 TTTTTTAAAA
* *
15517840 TTCTTTTGCGGCATTTTTTGAAAAA-CGCCGCTAAAGATG
1 TTCTTTAGCGGCA-TTTTT-AAAAAGCGCCGCTAAAGCTG
** * *
15517879 AAGCATTAGCGGCATTTTCTAAAAAGCGCCGCTAAAGGTG
1 -TTCTTTAGCGGCATTTT-TAAAAAGCGCCGCTAAAGCTG
* * *
15517919 TACATATAGCGGCGTTTTTAAAAAAGCGCCGCTAATA-CTCG
1 TTC-TTTAGCGGCATTTTT-AAAAAGCGCCGCTAA-AGCT-G
* * ** * *
15517960 ATCTTTAACGGTGTTTTTGAAAAGCGCCGCTAATGCTCG
1 TTCTTTAGCGGCATTTTTAAAAAGCGCCGCTAAAGCT-G
15517999 TTCTTTAGCGGCATTTTT
1 TTCTTTAGCGGCATTTTT
15518017 CATTCAAACG
Statistics
Matches: 108, Mismatches: 22, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
39 43 0.40
40 62 0.57
41 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (38 bp):
TTCTTTAGCGGCATTTTTAAAAAGCGCCGCTAAAGCTG
Found at i:15524183 original size:12 final size:12
Alignment explanation
Indices: 15524168--15524197 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
15524158 TTCTCTTTTA
15524168 TTTTCTTTCCCT
1 TTTTCTTTCCCT
*
15524180 TTTTCTTTCTCT
1 TTTTCTTTCCCT
15524192 TTTTCT
1 TTTTCT
15524198 CCCCTGCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTCTTTCCCT
Found at i:15529208 original size:43 final size:43
Alignment explanation
Indices: 15529114--15529319 Score: 225
Period size: 43 Copynumber: 4.8 Consensus size: 43
15529104 AAACATCACA
* * * * * *
15529114 AAAGATCATAGCTTTTAGCGGCATTTGTGGGAAAAGCACTATT
1 AAAGGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCACT
* ** *
15529157 AAAAGTCATGTTTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
1 AAAGGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCACT
* * * * *
15529200 AAAGGTCATGGCTTTTAGCGCCGGTTGTAGGAGAAGCGCCGCT
1 AAAGGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCACT
* *
15529243 AAAGGTCATGGCTTTTAACGGTGTTTGTGGGAGAAA-CGCCACT
1 AAAGGTCATGGCTTTTAGCGGCGTTTGTGGGA-AAAGCGCCACT
* *
15529286 AAAGGTCATGGCTTTTAGCGACGTTTATGGGAAA
1 AAAGGTCATGGCTTTTAGCGGCGTTTGTGGGAAA
15529320 GCGTTTGTGG
Statistics
Matches: 134, Mismatches: 28, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
42 2 0.01
43 130 0.97
44 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (43 bp):
AAAGGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCACT
Found at i:15529783 original size:21 final size:21
Alignment explanation
Indices: 15529758--15529806 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
15529748 GCTGCCATCG
15529758 CTGCTGCCGCTACCTCCCTCA
1 CTGCTGCCGCTACCTCCCTCA
15529779 CTGCTGCCGCTACCTCCCTCA
1 CTGCTGCCGCTACCTCCCTCA
15529800 CTGCTGC
1 CTGCTGC
15529807 ATCCTCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.08, C:0.51, G:0.16, T:0.24
Consensus pattern (21 bp):
CTGCTGCCGCTACCTCCCTCA
Found at i:15531050 original size:41 final size:41
Alignment explanation
Indices: 15530861--15531040 Score: 252
Period size: 41 Copynumber: 4.4 Consensus size: 41
15530851 CGTTTTAGAT
* *
15530861 AAAAACACCGCTATTGATCAGTTTTTAGTGGTGTTTGGGCC
1 AAAAACACCACTATTGCTCAGTTTTTAGTGGTGTTTGGGCC
* * *
15530902 AAAAACGCCACTATTGCTCAGTTTTTAGTGTTGTTTGGGTC
1 AAAAACACCACTATTGCTCAGTTTTTAGTGGTGTTTGGGCC
* *
15530943 AAAAACACCACTATTGCTCAGTTTTTAGTGGTGCTCGGGCC
1 AAAAACACCACTATTGCTCAGTTTTTAGTGGTGTTTGGGCC
* *
15530984 AAAAACACCACTATTGCTCAGTTTTTAGTGGAGTTTGGACC
1 AAAAACACCACTATTGCTCAGTTTTTAGTGGTGTTTGGGCC
* * *
15531025 AAGAACGCCGCTATTG
1 AAAAACACCACTATTG
15531041 TTTAATTTTT
Statistics
Matches: 122, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 122 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (41 bp):
AAAAACACCACTATTGCTCAGTTTTTAGTGGTGTTTGGGCC
Found at i:15531937 original size:23 final size:23
Alignment explanation
Indices: 15531911--15531959 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
15531901 AATAGGAATT
*
15531911 TCAAGCGAGCCATATCAGGAAGC
1 TCAAGCAAGCCATATCAGGAAGC
15531934 TCAAGCAAGCCATATCAGGAAGC
1 TCAAGCAAGCCATATCAGGAAGC
15531957 TCA
1 TCA
15531960 TAAAGAGCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (23 bp):
TCAAGCAAGCCATATCAGGAAGC
Found at i:15531983 original size:25 final size:24
Alignment explanation
Indices: 15531917--15531992 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 24
15531907 AATTTCAAGC
* *
15531917 GAGCCATATCAGGAAGCTCA-AGCA
1 GAGCCATATCAAGAAGCTCATA-AA
*
15531941 -AGCCATATCAGGAAGCTCATAAA
1 GAGCCATATCAAGAAGCTCATAAA
*
15531964 GAGCCTATATCAAGACGCTCATAAA
1 GAGCC-ATATCAAGAAGCTCATAAA
15531989 GAGC
1 GAGC
15531993 TAGGTTTGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
23 20 0.43
24 5 0.11
25 21 0.46
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (24 bp):
GAGCCATATCAAGAAGCTCATAAA
Found at i:15535070 original size:35 final size:34
Alignment explanation
Indices: 15534982--15535070 Score: 124
Period size: 35 Copynumber: 2.6 Consensus size: 34
15534972 GCCATGGACG
* *
15534982 GGTCTATCCCAACCTTTTCAAAATTGCCTTAGAC
1 GGTCTATCCCAACCTTTTTAAAATTACCTTAGAC
**
15535016 GAGTCTATCCCAACCTTTTTAAGGTTACCTTAGAC
1 G-GTCTATCCCAACCTTTTTAAAATTACCTTAGAC
15535051 GGCTCTATCCCAACCTTTTT
1 GG-TCTATCCCAACCTTTTT
15535071 TAAACGTCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 2 0.04
35 47 0.96
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (34 bp):
GGTCTATCCCAACCTTTTTAAAATTACCTTAGAC
Found at i:15536458 original size:13 final size:14
Alignment explanation
Indices: 15536432--15536460 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
15536422 ACTAACGACA
15536432 AATTAAACCATTAT
1 AATTAAACCATTAT
15536446 AATTAAA-CATTAT
1 AATTAAACCATTAT
15536459 AA
1 AA
15536461 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:15539990 original size:13 final size:13
Alignment explanation
Indices: 15539972--15540000 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15539962 GGTTGCTTAT
15539972 TAAACTAATTAAC
1 TAAACTAATTAAC
15539985 TAAACTAATTAAC
1 TAAACTAATTAAC
15539998 TAA
1 TAA
15540001 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:15542421 original size:9 final size:9
Alignment explanation
Indices: 15542407--15542612 Score: 161
Period size: 9 Copynumber: 22.6 Consensus size: 9
15542397 CGGGTAAGTT
15542407 GTTATGTAA
1 GTTATGTAA
**
15542416 GTTATGTGT
1 GTTATGTAA
15542425 GTTATGTAA
1 GTTATGTAA
*
15542434 GGTATGTAA
1 GTTATGTAA
*
15542443 GGTATGTAA
1 GTTATGTAA
*
15542452 GTTATGATACG
1 GTTATG-TA-A
*
15542463 GTATATATAA
1 GT-TATGTAA
*
15542473 GTTA-CTAA
1 GTTATGTAA
**
15542481 GTTACATAA
1 GTTATGTAA
*
15542490 GTTATGTGA
1 GTTATGTAA
*
15542499 GGTATGTAA
1 GTTATGTAA
15542508 GTTATGTAA
1 GTTATGTAA
*
15542517 GTTATGTGA
1 GTTATGTAA
15542526 GTTATGTAA
1 GTTATGTAA
15542535 GTTATGTATCCAA
1 GTTATG--T--AA
*
15542548 GATATG--A
1 GTTATGTAA
*
15542555 -TATATATAA
1 GT-TATGTAA
15542564 GTTAT-TAA
1 GTTATGTAA
15542572 GTTATGTAA
1 GTTATGTAA
*
15542581 GTTATGTGA
1 GTTATGTAA
15542590 GTTATGTAA
1 GTTATGTAA
*
15542599 GTTATGTGA
1 GTTATGTAA
15542608 GTTAT
1 GTTAT
15542613 TTGAATCAAC
Statistics
Matches: 159, Mismatches: 25, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
7 4 0.03
8 15 0.09
9 120 0.75
10 5 0.03
11 5 0.03
12 3 0.02
13 7 0.04
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (9 bp):
GTTATGTAA
Found at i:15544516 original size:37 final size:37
Alignment explanation
Indices: 15544466--15544611 Score: 184
Period size: 37 Copynumber: 3.9 Consensus size: 37
15544456 TATGCAGCAA
*
15544466 ATGCATGGGGCGAAGGCGATGGAGGAGATGGGTTGCG
1 ATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGCG
** * ** *
15544503 ATGCACGGGGCGAAGGTAATGGAGGGGATTAGTTGCA
1 ATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGCG
* * *
15544540 ATGCATGGGGCGAAGGCGACGAAGGAGATGGGTTGCG
1 ATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGCG
*
15544577 ATGCACGGGGCGAAGGTGATGGAGGAGATAGGGTT
1 ATGCACGGGGCGAAGGCGATGGAGGAGAT-GGGTT
15544612 TTGGGGGAAT
Statistics
Matches: 88, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
37 83 0.94
38 5 0.06
ACGTcount: A:0.25, C:0.11, G:0.48, T:0.16
Consensus pattern (37 bp):
ATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGCG
Found at i:15545980 original size:41 final size:41
Alignment explanation
Indices: 15545935--15546124 Score: 202
Period size: 41 Copynumber: 4.6 Consensus size: 41
15545925 CATTTTAGAT
*
15545935 AAAAACACCGCTATTGATCAGTTTTTAGTGGTGTTTGGGCC
1 AAAAACACCGCTATTGCTCAGTTTTTAGTGGTGTTTGGGCC
** *
15545976 AAAAATGCCACTATTGCTCAGTTTTTAGT-GTCGTTTGGGCC
1 AAAAACACCGCTATTGCTCAGTTTTTAGTGGT-GTTTGGGCC
* * * * * *
15546017 AAAAAAACGGCTATTGTTCAGTTTTTAGTGGCGCTCGGGCC
1 AAAAACACCGCTATTGCTCAGTTTTTAGTGGTGTTTGGGCC
* * * *
15546058 AAAAACACCACTATTGCTCAGTTTTTAGTGGAGTTTGGACT
1 AAAAACACCGCTATTGCTCAGTTTTTAGTGGTGTTTGGGCC
* * * *
15546099 AAGAACGCCGCTATTGTTCAATTTTT
1 AAAAACACCGCTATTGCTCAGTTTTT
15546125 CGCGGCGTTT
Statistics
Matches: 121, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
40 2 0.02
41 118 0.98
42 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (41 bp):
AAAAACACCGCTATTGCTCAGTTTTTAGTGGTGTTTGGGCC
Found at i:15546112 original size:82 final size:82
Alignment explanation
Indices: 15545916--15546124 Score: 249
Period size: 82 Copynumber: 2.5 Consensus size: 82
15545906 TTTTAAATCA
* * * * * *
15545916 TTTTAGTGGCATTTTAGA-TAAAAACACCGCTATTGATCAGTTTTTAGTGGTGTTTGGGCCAAAA
1 TTTTAGTGG-AGTTTGGACTAAAAACACCGCTATTGTTCAGTTTTTAGTGGCGCTCGGGCCAAAA
**
15545980 ATGCCACTATTGCTCAGT
65 ACACCACTATTGCTCAGT
** * * * *
15545998 TTTTAGTGTCGTTTGGGCCAAAAAAACGGCTATTGTTCAGTTTTTAGTGGCGCTCGGGCCAAAAA
1 TTTTAGTGGAGTTTGGACTAAAAACACCGCTATTGTTCAGTTTTTAGTGGCGCTCGGGCCAAAAA
15546063 CACCACTATTGCTCAGT
66 CACCACTATTGCTCAGT
* * *
15546080 TTTTAGTGGAGTTTGGACTAAGAACGCCGCTATTGTTCAATTTTT
1 TTTTAGTGGAGTTTGGACTAAAAACACCGCTATTGTTCAGTTTTT
15546125 CGCGGCGTTT
Statistics
Matches: 103, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
81 4 0.04
82 99 0.96
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (82 bp):
TTTTAGTGGAGTTTGGACTAAAAACACCGCTATTGTTCAGTTTTTAGTGGCGCTCGGGCCAAAAA
CACCACTATTGCTCAGT
Found at i:15547005 original size:23 final size:23
Alignment explanation
Indices: 15546972--15547052 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
15546962 GCCATATAAT
*
15546972 AGGAAGTTCAAGCGAGCCATATC
1 AGGAAGCTCAAGCGAGCCATATC
*
15546995 AGGAAGCTCAAGCAAGCCATATC
1 AGGAAGCTCAAGCGAGCCATATC
**
15547018 AGGAAGCTCATAAAGAGCCTATATC
1 AGGAAGCTCA-AGCGAGCC-ATATC
*
15547043 AGGACGCTCA
1 AGGAAGCTCA
15547053 TAAAGAGCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 31 0.62
24 5 0.10
25 14 0.28
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (23 bp):
AGGAAGCTCAAGCGAGCCATATC
Found at i:15547051 original size:25 final size:24
Alignment explanation
Indices: 15546985--15547060 Score: 102
Period size: 25 Copynumber: 3.2 Consensus size: 24
15546975 AAGTTCAAGC
*
15546985 GAGCCATATCAGGAAGCTCA-AGCA
1 GAGCCATATCAGGAAGCTCATA-AA
15547009 -AGCCATATCAGGAAGCTCATAAA
1 GAGCCATATCAGGAAGCTCATAAA
*
15547032 GAGCCTATATCAGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
15547057 GAGC
1 GAGC
15547061 TGCGTTTGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
23 20 0.43
24 5 0.11
25 22 0.47
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:15554790 original size:173 final size:171
Alignment explanation
Indices: 15554521--15554847 Score: 444
Period size: 173 Copynumber: 1.9 Consensus size: 171
15554511 TAATTTTAAG
* *
15554521 TTATAAAAGAAAAAACATATCAACATAAATAGTTGATGTTTTTAAAAAATAAAATACATTTAACA
1 TTATAAAAGAAAAAACATATCAAAATAAATAGTTGA-GTTTTAAAAAAATAAAATACATTTAACA
* * * *
15554586 TATAATGCTATATTGAAAAAATATATTTTCATAATATAGTTACATATTTATTATTTTGTCTATAT
65 -ATAATGCTATATTGAAAAAATATATTTTCATAAGATAATTACATAATTATTATTTTATCTATAT
15554651 AAATAAAAAAGCTATTAATTAAAAAATAATTAAAAGTAAAAGAA
129 AAATAAAAAA-CTATTAATTAAAAAATAATTAAAAGTAAAAGAA
* * * *
15554695 TTATACAAGGAAAAATATATCAAAATAAATAGTTGA-TTTTAAAAAAATTAAAATATATTTAAC-
1 TTATAAAAGAAAAAACATATCAAAATAAATAGTTGAGTTTTAAAAAAA-TAAAATACATTTAACA
* * * *
15554758 ATAATGCTATATAT-ATTAAAAATGTTTTTTCATTAGATAATTATATAATTATTATTTTATCTAT
65 ATAATGCTATAT-TGA--AAAAATATATTTTCATAAGATAATTACATAATTATTATTTTATCTAT
15554822 ATAAATAAAAAACTATTAATTAAAAA
127 ATAAATAAAAAACTATTAATTAAAAA
15554848 GTGAAAATAT
Statistics
Matches: 135, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
171 13 0.10
172 25 0.19
173 65 0.48
174 32 0.24
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.38
Consensus pattern (171 bp):
TTATAAAAGAAAAAACATATCAAAATAAATAGTTGAGTTTTAAAAAAATAAAATACATTTAACAA
TAATGCTATATTGAAAAAATATATTTTCATAAGATAATTACATAATTATTATTTTATCTATATAA
ATAAAAAACTATTAATTAAAAAATAATTAAAAGTAAAAGAA
Found at i:15563029 original size:21 final size:21
Alignment explanation
Indices: 15562981--15563020 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
15562971 TTAAAATAAT
*
15562981 AATAATATTGATAATAATGAC
1 AATAATATTAATAATAATGAC
15563002 AATAATATTAATAATAATG
1 AATAATATTAATAATAATG
15563021 CTACAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (21 bp):
AATAATATTAATAATAATGAC
Found at i:15563165 original size:3 final size:3
Alignment explanation
Indices: 15563157--15563364 Score: 144
Period size: 3 Copynumber: 70.0 Consensus size: 3
15563147 CAAAAAGAAA
* *
15563157 AAT AAT AAT AGT AAT AAT AA- ATT AATT AAT AAGT AAAT AAT AAGT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA-T -AAT AAT AA-T -AAT
* * * ** *
15563206 AA- ACAC AA- AAG AA- AAT -AT AAT TAT AAT AGC AAT AAT AAT AAA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * *
15563248 AAT AAT AGC AAT AAT AAT AGT AGT AAT AAT AAT GAT AAT AGT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * **
15563295 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT CAT AAT GGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15563343 AAT AA- AA- AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
15563365 TTAGCAAAAA
Statistics
Matches: 163, Mismatches: 29, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
2 14 0.09
3 137 0.84
4 8 0.05
5 4 0.02
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:15563197 original size:11 final size:11
Alignment explanation
Indices: 15563160--15563207 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
15563150 AAAGAAAAAT
15563160 AATAAT-AGT-
1 AATAATAAGTA
*
15563169 AATAATAAATTA
1 AATAAT-AAGTA
*
15563181 ATTAATAAGTA
1 AATAATAAGTA
15563192 AATAATAAGTA
1 AATAATAAGTA
15563203 AATAA
1 AATAA
15563208 ACACAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 6 0.19
11 21 0.66
12 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (11 bp):
AATAATAAGTA
Found at i:15563208 original size:15 final size:15
Alignment explanation
Indices: 15563128--15563208 Score: 51
Period size: 15 Copynumber: 5.1 Consensus size: 15
15563118 TTTAAAGAAT
15563128 AATAATAAGTAAATA
1 AATAATAAGTAAATA
* *
15563143 AATACAAAAAG-AAAAA
1 AAT--AATAAGTAAATA
15563159 TAATAAT-AGTAATAATA
1 -AATAATAAGT-A-AATA
*
15563176 AATTAATTAA-TAAGTA
1 AA-TAA-TAAGTAAATA
15563192 AATAATAAGTAAATA
1 AATAATAAGTAAATA
15563207 AA
1 AA
15563209 CACAAAAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 20
0.66 0.08 0.26
Matches are distributed among these distances:
14 5 0.10
15 15 0.30
16 12 0.24
17 15 0.30
18 2 0.04
19 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAATAAGTAAATA
Found at i:15564015 original size:19 final size:20
Alignment explanation
Indices: 15563968--15564018 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
15563958 TTTATATTAT
*
15563968 ATATATAAAAGAGAGAAGAAA
1 ATATA-AAAAGAAAGAAGAAA
15563989 ATTCATAAAAAGAAAGAAGAAA
1 A-T-ATAAAAAGAAAGAAGAAA
15564011 A-ATAAAAA
1 ATATAAAAA
15564019 TAAAATAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 7 0.26
21 1 0.04
22 16 0.59
23 3 0.11
ACGTcount: A:0.71, C:0.02, G:0.14, T:0.14
Consensus pattern (20 bp):
ATATAAAAAGAAAGAAGAAA
Found at i:15564349 original size:10 final size:10
Alignment explanation
Indices: 15564334--15564367 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
15564324 TAGTTTTTGA
15564334 GCCATATTGG
1 GCCATATTGG
15564344 GCCATATTGG
1 GCCATATTGG
15564354 GCCATATTGG
1 GCCATATTGG
15564364 GCCA
1 GCCA
15564368 CTAGGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (10 bp):
GCCATATTGG
Found at i:15564867 original size:44 final size:44
Alignment explanation
Indices: 15564812--15564959 Score: 163
Period size: 44 Copynumber: 3.4 Consensus size: 44
15564802 CTCCGATGCC
15564812 ACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCA
1 ACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCA
* * ** ** * *
15564856 ATTTCAAGGAGATAAGGTTTGTGGCTTTAA-TCTGCTCCACGGCA
1 ACTTCAGGGAGATAAGACTTGTAACTTCAACT-TGCTCCACTGCA
* * * * *
15564900 ACTTCATGGAGATAAGACTTCTAACTTCAACCTGCTCCATTTCA
1 ACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCA
15564944 ACTTCAGGGAGATAAG
1 ACTTCAGGGAGATAAG
15564960 GTTTGCTATG
Statistics
Matches: 81, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
43 1 0.01
44 80 0.99
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
ACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCA
Found at i:15564988 original size:41 final size:41
Alignment explanation
Indices: 15564942--15565046 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
15564932 TGCTCCATTT
* *
15564942 CAACTTCAGGGAGATAAGGTTTGCTATGATCTGCTCTTCTG
1 CAACTTCAGGGAGATAAGGTTTGCTATGATCTACTCTACTG
*
15564983 CAACTTCAGGGAGATAAGGTTTCCTATGATCTACTCTACTG
1 CAACTTCAGGGAGATAAGGTTTGCTATGATCTACTCTACTG
* * * *
15565024 TAATTTCAGAGAGATAAGATTTG
1 CAACTTCAGGGAGATAAGGTTTG
15565047 TAATTTATAG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (41 bp):
CAACTTCAGGGAGATAAGGTTTGCTATGATCTACTCTACTG
Found at i:15565179 original size:44 final size:44
Alignment explanation
Indices: 15565131--15565363 Score: 113
Period size: 44 Copynumber: 5.2 Consensus size: 44
15565121 AACTTGAAGT
15565131 AGATAAGACTTATAACTTCAACTTGCTCCATTGCAACTTCAGGG
1 AGATAAGACTTATAACTTCAACTTGCTCCATTGCAACTTCAGGG
* * * * * * * * *
15565175 AGATAAG-GTT-T-CCTATGATC-TGCTCTACTACAACTTTAGAG
1 AGATAAGACTTATAACT-TCAACTTGCTCCATTGCAACTTCAGGG
* *
15565216 AGATAAGATCTGTAATTTATAACTTCAA-TCTGTTCCACTGCAACTTCAGGG
1 AGATAAGA-C------TTATAACTTCAACT-TGCTCCATTGCAACTTCAGGG
* * * * *
15565267 AAATATA-A-TTCGCTATCTTC-AGTCTGCTCCATTGTAACTTCAGGG
1 AGATA-AGACTT--ATAACTTCAACT-TGCTCCATTGCAACTTCAGGG
* * * *
15565312 AGATAAGACTTATAACTTCAACCTACTCTATTGTAACTTCAGGG
1 AGATAAGACTTATAACTTCAACTTGCTCCATTGCAACTTCAGGG
15565356 AGATAAGA
1 AGATAAGA
15565364 TCTACTATGA
Statistics
Matches: 138, Mismatches: 31, Indels: 40
0.66 0.15 0.19
Matches are distributed among these distances:
41 25 0.18
42 4 0.03
43 4 0.03
44 42 0.30
45 32 0.23
46 2 0.01
49 2 0.01
50 3 0.02
51 23 0.17
52 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (44 bp):
AGATAAGACTTATAACTTCAACTTGCTCCATTGCAACTTCAGGG
Found at i:15565286 original size:181 final size:181
Alignment explanation
Indices: 15564981--15565948 Score: 1088
Period size: 181 Copynumber: 5.3 Consensus size: 181
15564971 TCTGCTCTTC
* * *
15564981 TGCAACTTCAGGGAGATAAGGTTTCCTATGATCTACTCTACTGTAA-TTTCAGAGAGATAAGATT
1 TGCAACTTCAGGGAGATAAGGTTTCCTATGATCTGCTCTACTGCAACTTT-AGAGAGATAAGATC
* * * * * *
15565045 TGTAATTTATAGCTTCAATCTATTCCACTGCAACTTAAGGGAAATATGATTCGATATCTTCAGTC
65 TGTAATTTATAACTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATTTTCAGTC
* * * * *
15565110 TGCTACACTGCAACTTGAAGTAGATAAGACTTATAACTTCAACTTGCTCCAT
130 TGCTCCACTGCAACTTCAGGGAGATAAGACTTATAACTTCAACCTGCTCCAT
*
15565162 TGCAACTTCAGGGAGATAAGGTTTCCTATGATCTGCTCTACTACAACTTTAGAGAGATAAGATCT
1 TGCAACTTCAGGGAGATAAGGTTTCCTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCT
*
15565227 GTAATTTATAACTTCAATCTGTTCCACTGCAACTTCAGGGAAATATA-ATTCGCTATCTTCAGTC
66 GTAATTTATAACTTCAATCTGTTCCACTGCAACTTCAGGGAAATA-AGATTCGCTATTTTCAGTC
* * * *
15565291 TGCTCCATTGTAACTTCAGGGAGATAAGACTTATAACTTCAACCTACTCTAT
130 TGCTCCACTGCAACTTCAGGGAGATAAGACTTATAACTTCAACCTGCTCCAT
* * * *
15565343 TGTAACTTCAGGGAGATAAGATCTACTATGATCTGCT-TACTGCAACTTTAGAGAGATAAGATCT
1 TGCAACTTCAGGGAGATAAGGTTTCCTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCT
* * * * * *
15565407 GTAATATAT-ACTTTTAATCTATTCCATTGCAACTTTAGGGAAATAAGATTCTCTATTTTCAGTC
66 GTAATTTATAAC-TTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATTTTCAGTC
* * *
15565471 TGCTCTACTGCAACTTCAGAGAGATAAGACTTATAACTTCAGCCTGCTCCAT
130 TGCTCCACTGCAACTTCAGGGAGATAAGACTTATAACTTCAACCTGCTCCAT
* ** * * *
15565523 TCCAACTTCAAAGAAATAA--TATTCACTATGATCTGCTCTACTGTAACTTCAGAGAGATAAGAT
1 TGCAACTTCAGGGAGATAAGGT-TTC-CTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGAT
* * * * * * * *
15565586 TTATAATTTATACCTTCAATCTGTTCTACTACAACTTCAAGGAAATAAGATTTGCTATTTTCAAA
64 CTGTAATTTATAACTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATTTTC-AG
* * * * * *
15565651 TCTGTTCCACTGTAATTTTAGGGAGATGAGACTTATAACTTCAACCTGCTCCAC
128 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAACTTCAACCTGCTCCAT
* * * * * * *
15565705 TGCAATTTCAGGGAGATAATGTATGCTATGATTTGCTCTACTACAACTTCAGAGAGATAAGATCT
1 TGCAACTTCAGGGAGATAAGGTTTCCTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCT
* * ** * *
15565770 GTGATTTCTAGGTTCAATCCGTTCCATTGCAACTTCAGGGAAATAAGATTCGCTATTTTCAGTCT
66 GTAATTTATAACTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATTTTCAGTCT
* * * * * * *
15565835 ACTTCACTACAA-TTCCAGGGAGATAAGACTTATAACTTTAACCTTCTCTAC
131 GCTCCACTGCAACTT-CAGGGAGATAAGACTTATAACTTCAACCTGCTCCAT
* * * *
15565886 TACAACTTCAGGGAGATAAGGTTT-GTGACTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
1 TGCAACTTCAGGGAGATAAGGTTTCCT-A--T-GATCTGCTCTACTGCAACTTTAGAGAGATAA
15565949 AATTCGTCAT
Statistics
Matches: 659, Mismatches: 112, Indels: 29
0.82 0.14 0.04
Matches are distributed among these distances:
178 1 0.00
179 4 0.01
180 152 0.23
181 324 0.49
182 149 0.23
183 2 0.00
184 27 0.04
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (181 bp):
TGCAACTTCAGGGAGATAAGGTTTCCTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCT
GTAATTTATAACTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATTTTCAGTCT
GCTCCACTGCAACTTCAGGGAGATAAGACTTATAACTTCAACCTGCTCCAT
Found at i:15565440 original size:361 final size:360
Alignment explanation
Indices: 15564980--15565909 Score: 1104
Period size: 361 Copynumber: 2.6 Consensus size: 360
15564970 ATCTGCTCTT
* * * *
15564980 CTGCAACTTCAGGGAGATAAGGTTTCCTATGATCTACTCTACTGTAA-TTTCAGAGAGATAAGAT
1 CTGCAACTTCAGGGAGATAA-GTATACTATGATCTGCTCTACTGCAACTTT-AGAGAGATAAGAT
* * * * *
15565044 TTGTAATTTATAGCTTCAATCTATTCCACTGCAACTTAAGGGAAATATGATTCGATATCTTCAGT
64 CTGTAATTTATA-CTTCAATCTATTCCATTGCAACTTAAGGGAAATAAGATTCGCTATTTTCAGT
* *
15565109 CTGCTACACTGCAACTTGAAGTAGATAAGACTTATAACTTCAACTTGCTCCATTGCAACTTCAGG
128 CTGCT-CACTGCAACTTCAAG-AGATAAGACTTATAACTTCAACTTGCTCCATTACAACTTCAGG
* *
15565174 GAGATAAGGTTTC-CTATGATCTGCTCTACTACAACTTTAGAGAGATAAGATCTGTAATTTATAA
191 GAGATAAGGTTTCACTATGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATAATTTATAA
* * * *
15565238 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATATA-ATTCGCTATCTTC-AGTCTGCTCCATTG
256 CTTCAATCTGTTCCACTACAACTTCAAGGAAATA-AGATTCGCTATCTTCAAATCTGCTCCACTG
*
15565301 TAACTTCAGGGAGATAAGACTTATAACTTCAACCTACTCTA
320 TAACTTCAGGGAGATAAGACTTATAACTTCAACCTACTCCA
* * *
15565342 TTGTAACTTCAGGGAGATAAGATCTACTATGATCTGCT-TACTGCAACTTTAGAGAGATAAGATC
1 CTGCAACTTCAGGGAGATAAG-TATACTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATC
* * * *
15565406 TGTAATATATACTTTTAATCTATTCCATTGCAACTTTAGGGAAATAAGATTCTCTATTTTCAGTC
65 TGTAATTTATAC-TTCAATCTATTCCATTGCAACTTAAGGGAAATAAGATTCGCTATTTTCAGTC
* * * **
15565471 TGCTCTACTGCAACTTCAGAGAGATAAGACTTATAACTTCAGCCTGCTCCATTCCAACTTCAAAG
129 TGCTC-ACTGCAACTTCA-AGAGATAAGACTTATAACTTCAACTTGCTCCATTACAACTTCAGGG
* ** * *
15565536 AAATAA--TATTCACTATGATCTGCTCTACTGTAACTTCAGAGAGATAAGATTTATAATTTATAC
192 AGATAAGGT-TTCACTATGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATAATTTATAA
* * * *
15565599 CTTCAATCTGTTCTACTACAACTTCAAGGAAATAAGATTTGCTATTTTCAAATCTGTTCCACTGT
256 CTTCAATCTGTTCCACTACAACTTCAAGGAAATAAGATTCGCTATCTTCAAATCTGCTCCACTGT
* * * *
15565664 AATTTTAGGGAGATGAGACTTATAACTTCAACCTGCTCCA
321 AACTTCAGGGAGATAAGACTTATAACTTCAACCTACTCCA
* * * * *
15565704 CTGCAATTTCAGGGAGATAATGTATGCTATGATTTGCTCTACTACAACTTCAGAGAGATAAGATC
1 CTGCAACTTCAGGGAGATAA-GTATACTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATC
* * * ** *
15565769 TGTGATTTCTAGGTTCAATCCGTTCCATTGCAACTTCAGGGAAATAAGATTCGCTATTTTCAGTC
65 TGTAATTTATA-CTTCAATCTATTCCATTGCAACTTAAGGGAAATAAGATTCGCTATTTTCAGTC
* * * * * *
15565834 TACTTCACTACAA-TTCCAGGGAGATAAGACTTATAACTTTAACCTT-CTCTACTACAACTTCAG
129 TGC-TCACTGCAACTT-CA-AGAGATAAGACTTATAACTTCAA-CTTGCTCCATTACAACTTCAG
15565897 GGAGATAAGGTTT
190 GGAGATAAGGTTT
15565910 GTGACTTCAA
Statistics
Matches: 481, Mismatches: 70, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
359 1 0.00
360 6 0.01
361 222 0.46
362 115 0.24
363 130 0.27
364 6 0.01
365 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (360 bp):
CTGCAACTTCAGGGAGATAAGTATACTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCT
GTAATTTATACTTCAATCTATTCCATTGCAACTTAAGGGAAATAAGATTCGCTATTTTCAGTCTG
CTCACTGCAACTTCAAGAGATAAGACTTATAACTTCAACTTGCTCCATTACAACTTCAGGGAGAT
AAGGTTTCACTATGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATAATTTATAACTTCA
ATCTGTTCCACTACAACTTCAAGGAAATAAGATTCGCTATCTTCAAATCTGCTCCACTGTAACTT
CAGGGAGATAAGACTTATAACTTCAACCTACTCCA
Found at i:15569893 original size:10 final size:10
Alignment explanation
Indices: 15569870--15569922 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
15569860 CCACGATCTC
* *
15569870 TTTTTTATTA
1 TTTTTTTTTG
15569880 TTTTTTTTTG
1 TTTTTTTTTG
*
15569890 TTTTTGTTTG
1 TTTTTTTTTG
*
15569900 TTTTTTTATTT
1 TTTTTTT-TTG
15569911 TTCTTTTTTTG
1 TT-TTTTTTTG
15569922 T
1 T
15569923 GCCTCCATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
10 23 0.66
11 7 0.20
12 5 0.14
ACGTcount: A:0.06, C:0.02, G:0.08, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:15571217 original size:16 final size:16
Alignment explanation
Indices: 15571196--15571232 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
15571186 AATGCACATA
* *
15571196 ATGCAATGTAATGTAG
1 ATGCAATATAATGCAG
15571212 ATGCAATATAATGCAG
1 ATGCAATATAATGCAG
15571228 ATGCA
1 ATGCA
15571233 TGAATGCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (16 bp):
ATGCAATATAATGCAG
Found at i:15578471 original size:17 final size:17
Alignment explanation
Indices: 15578451--15578523 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
15578441 TCTCCTTTTC
15578451 TTTCCTTTTTCTTTCTT
1 TTTCCTTTTTCTTTCTT
* * *
15578468 TTTCCCTTCTGTTTCGTT
1 TTTCCTTTTTCTTTC-TT
* *
15578486 TTTATCTTGTTTCATTCTT
1 TTT-CCTT-TTTCTTTCTT
* *
15578505 TTTCTTTTTTGTTTCTT
1 TTTCCTTTTTCTTTCTT
15578522 TT
1 TT
15578524 ATTTATTATA
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
17 22 0.54
18 7 0.17
19 7 0.17
20 5 0.12
ACGTcount: A:0.03, C:0.19, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTCCTTTTTCTTTCTT
Found at i:15578553 original size:5 final size:5
Alignment explanation
Indices: 15578545--15578607 Score: 53
Period size: 5 Copynumber: 13.0 Consensus size: 5
15578535 TCAGTATAAT
* *
15578545 ATATA ATATA ATATA ATATA ATAT- ATATA CT-TA ATA-A TTA-A GATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA
*
15578592 ATATT ATAATA ATATA
1 ATATA AT-ATA ATATA
15578608 TATTTTAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
4 11 0.23
5 31 0.66
6 5 0.11
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:15578564 original size:22 final size:22
Alignment explanation
Indices: 15578539--15578607 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
15578529 TTATACTCAG
*
15578539 TATAATATATAATATAATATAA
1 TATAATATATAATATTATATAA
15578561 TATAATATAT-ATACTTA-ATAA
1 TATAATATATAATA-TTATATAA
*
15578582 T-TAAGATATAATATTATAATAA
1 TATAATATATAATATTAT-ATAA
15578604 TATA
1 TATA
15578608 TATTTTAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 10 0.25
21 11 0.28
22 17 0.43
23 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
TATAATATATAATATTATATAA
Found at i:15582583 original size:46 final size:46
Alignment explanation
Indices: 15582531--15582889 Score: 513
Period size: 46 Copynumber: 7.8 Consensus size: 46
15582521 GTGTGCTCTC
*
15582531 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* * *
15582577 TGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
*
15582623 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
*
15582669 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* *
15582715 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* *
15582761 TGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
*** * * *
15582807 TGACGGGAAAATGAATAAGACCATGGTTGAAAGATTCCATGGCAACA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* * * *
15582854 TGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
15582890 TATGACATCG
Statistics
Matches: 292, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 251 0.86
47 41 0.14
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
Found at i:15584175 original size:40 final size:40
Alignment explanation
Indices: 15584078--15584264 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 40
15584068 GAATTCTCGT
* * *
15584078 ACACTAAGTGCCAATACATAGCCGAAGCTATTTTAATCTCGC
1 ACACTAAGTGCC-ATACATAGCCGAAGCTATCTCAA-ATCGC
* * * *
15584120 ACATTAAGTGCCATACATAGCCGAAGCCATCTCAAAACGT
1 ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGC
* * * *
15584160 ACATTAAGTGGCATACATAGCCAAAGCTATCTCGAATCGC
1 ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGC
* * *
15584200 ACACTAAGTGCCATACATAGCCAAAGCTATCTCGAATTGC
1 ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGC
*
15584240 ACACTAAGTGTCATACATAGCCGAA
1 ACACTAAGTGCCATACATAGCCGAA
15584265 TTGTCATCAA
Statistics
Matches: 127, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
40 96 0.76
41 20 0.16
42 11 0.09
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (40 bp):
ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGC
Found at i:15589852 original size:20 final size:20
Alignment explanation
Indices: 15589827--15589866 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
15589817 TTAATGGATG
15589827 AAAAGTTATCGATAACGGTT
1 AAAAGTTATCGATAACGGTT
15589847 AAAAGTTATCGATAACGGTT
1 AAAAGTTATCGATAACGGTT
15589867 TTACATGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (20 bp):
AAAAGTTATCGATAACGGTT
Found at i:15591077 original size:3 final size:3
Alignment explanation
Indices: 15591069--15591109 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
15591059 GTTAGATGGC
15591069 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
15591110 ATTTAATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:15594115 original size:34 final size:31
Alignment explanation
Indices: 15594045--15594106 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
15594035 ATTTATTTTA
15594045 TTGTT-AATTTTCTTATTATTTTAAAGACAT
1 TTGTTAAATTTTCTTATTATTTTAAAGACAT
* *
15594075 TTGTTAAATTTTTTTATTATTTTAGAGACAT
1 TTGTTAAATTTTCTTATTATTTTAAAGACAT
15594106 T
1 T
15594107 GCTTGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (31 bp):
TTGTTAAATTTTCTTATTATTTTAAAGACAT
Found at i:15597947 original size:29 final size:28
Alignment explanation
Indices: 15597901--15597955 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
15597891 TTGAAAGTTA
*
15597901 AAAAATATAAAGACTAAATTCTTAAAAAT
1 AAAAATACAAAGACTAAATTC-TAAAAAT
* *
15597930 AAAAATACAATGAGTAAATTCTAAAA
1 AAAAATACAAAGACTAAATTCTAAAA
15597956 TTATGAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (28 bp):
AAAAATACAAAGACTAAATTCTAAAAAT
Found at i:15602098 original size:40 final size:40
Alignment explanation
Indices: 15602048--15602129 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
15602038 TGCCTTCCCT
15602048 ATGTAAGTACCATTCGTTTCTTGCACATAACTTGTCCTTC
1 ATGTAAGTACCATTCGTTTCTTGCACATAACTTGTCCTTC
15602088 ATGTAAGTACCATTCGTTTCTTGCACATAACTTGTCCTTC
1 ATGTAAGTACCATTCGTTTCTTGCACATAACTTGTCCTTC
15602128 AT
1 AT
15602130 ATCCAACCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.40
Consensus pattern (40 bp):
ATGTAAGTACCATTCGTTTCTTGCACATAACTTGTCCTTC
Found at i:15613726 original size:4 final size:4
Alignment explanation
Indices: 15613717--15613749 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
15613707 TCTACAGCCC
15613717 CAAA CAAA CAAA CAAA CAAA -AAA CGAAA CAAA C
1 CAAA CAAA CAAA CAAA CAAA CAAA C-AAA CAAA C
15613750 CCAGAATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.11
4 20 0.74
5 4 0.15
ACGTcount: A:0.73, C:0.24, G:0.03, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:15616505 original size:9 final size:9
Alignment explanation
Indices: 15616477--15616507 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
15616467 GACTCGTTAC
15616477 TTTTCTTCT
1 TTTTCTTCT
*
15616486 TCTTCTTCT
1 TTTTCTTCT
15616495 TTTTCTTCT
1 TTTTCTTCT
15616504 TTTT
1 TTTT
15616508 TATCAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:15621655 original size:25 final size:24
Alignment explanation
Indices: 15621620--15621668 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
15621610 ATATTAATAT
15621620 TTATATAAATATTAAATAATTATAA
1 TTATATAAATATTAAATAA-TATAA
*
15621645 TTATATTAATATTAAATAATATAA
1 TTATATAAATATTAAATAATATAA
15621669 AAATCCTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATATAAATATTAAATAATATAA
Found at i:15621663 original size:19 final size:19
Alignment explanation
Indices: 15621608--15621664 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
15621598 AATGTAAATT
*
15621608 TTATATTAATATTTATATAA
1 TTATATTAATA-TTAAATAA
15621628 --ATATTAA-A-TAATTATAA
1 TTATATTAATATTAA--ATAA
15621645 TTATATTAATATTAAATAA
1 TTATATTAATATTAAATAA
15621664 T
1 T
15621665 ATAAAAATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 13
0.68 0.02 0.30
Matches are distributed among these distances:
15 2 0.07
17 5 0.17
18 7 0.23
19 12 0.40
20 1 0.03
21 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATATTAATATTAAATAA
Found at i:15621836 original size:12 final size:13
Alignment explanation
Indices: 15621819--15621848 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
15621809 ATATTTATTT
15621819 AATATTAATA-AA
1 AATATTAATATAA
15621831 AATATTAATATAA
1 AATATTAATATAA
15621844 AATAT
1 AATAT
15621849 AAGATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATTAATATAA
Found at i:15622310 original size:18 final size:19
Alignment explanation
Indices: 15622273--15622315 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
15622263 CTAAAGATTT
* *
15622273 ATTTTAATTTTTTTTTTAC
1 ATTTTAATTTTTTATGTAC
15622292 ATTTTAA-TTTTTATGTAC
1 ATTTTAATTTTTTATGTAC
15622310 ATTTTA
1 ATTTTA
15622316 TTACCTTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTAATTTTTTATGTAC
Found at i:15622563 original size:23 final size:23
Alignment explanation
Indices: 15622537--15622581 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
15622527 TATATACTAA
**
15622537 ATATATATTTTTTATTTTTAATC
1 ATATATACATTTTATTTTTAATC
*
15622560 ATATTTACATTTTATTTTTAAT
1 ATATATACATTTTATTTTTAAT
15622582 TTTAATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATATACATTTTATTTTTAATC
Found at i:15623481 original size:18 final size:20
Alignment explanation
Indices: 15623458--15623501 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
15623448 CCAAAGTATT
15623458 ATTTTAATTTT-TT-TATAC
1 ATTTTAATTTTATTATATAC
*
15623476 ATTTTAATTTTATTATGTAC
1 ATTTTAATTTTATTATATAC
15623496 ATTTTA
1 ATTTTA
15623502 TTAACTCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.48
19 2 0.09
20 10 0.43
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTAATTTTATTATATAC
Found at i:15624143 original size:29 final size:29
Alignment explanation
Indices: 15624085--15624147 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
15624075 CACATAGGGC
* * *
15624085 TATTATTAATTCTAACGTTAATTGAGAAT
1 TATTATTAATTCGAACATTAATTGACAAT
15624114 TATTATTAATTCGAACATTAATT-ACCAAT
1 TATTATTAATTCGAACATTAATTGA-CAAT
15624143 TATTA
1 TATTA
15624148 CTCTATAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (29 bp):
TATTATTAATTCGAACATTAATTGACAAT
Found at i:15626009 original size:2 final size:2
Alignment explanation
Indices: 15626002--15626031 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15625992 ATAAATCTAA
15626002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15626032 GAGAATAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15626626 original size:2 final size:2
Alignment explanation
Indices: 15626614--15626645 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
15626604 GCTCAACTTT
*
15626614 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15626646 GGAGGTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:15628356 original size:29 final size:30
Alignment explanation
Indices: 15628323--15628384 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
15628313 ACTTAATAAG
15628323 CAAATGCCTCTAAAATAATAA-AAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
15628352 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
15628382 CAA
1 CAA
15628385 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:15631045 original size:29 final size:29
Alignment explanation
Indices: 15630995--15631051 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
15630985 ATTATATCAA
*
15630995 GTATGAACACTTCAATCTCTTTCTTGTTG
1 GTATGAACACTTCAATCCCTTTCTTGTTG
*
15631024 GTATGAACACTTCGATCCCTTTCTTGTT
1 GTATGAACACTTCAATCCCTTTCTTGTT
15631052 TAATATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (29 bp):
GTATGAACACTTCAATCCCTTTCTTGTTG
Found at i:15632089 original size:30 final size:32
Alignment explanation
Indices: 15632030--15632091 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
15632020 TAAGTCCGTC
* * *
15632030 CATATTATTTCTTTAATTTTTAATTTTTTTAT
1 CATATTATTTCTTAAATATTTAATATTTTTAT
15632062 CATATTA-TT-TTAAATATTTAATATTTTTAT
1 CATATTATTTCTTAAATATTTAATATTTTTAT
15632092 AATTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 18 0.67
31 2 0.07
32 7 0.26
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (32 bp):
CATATTATTTCTTAAATATTTAATATTTTTAT
Found at i:15638276 original size:10 final size:9
Alignment explanation
Indices: 15638245--15638274 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
15638235 ACATTTAATT
15638245 AATTTTTGAA
1 AATTTTT-AA
15638255 AATTTTTAA
1 AATTTTTAA
15638264 AATTTTTAA
1 AATTTTTAA
15638273 AA
1 AA
15638275 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.65
10 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (9 bp):
AATTTTTAA
Found at i:15653768 original size:26 final size:26
Alignment explanation
Indices: 15653660--15653767 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
15653650 TGGTACAAAT
15653660 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
15653686 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
15653712 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
15653738 TGATGATGGTTTAGGTAAATGTTCCG
1 TGATAATGGGTTAGGTAAATGTTCCA
15653764 TGAT
1 TGAT
15653768 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:15655469 original size:54 final size:53
Alignment explanation
Indices: 15655387--15655527 Score: 219
Period size: 54 Copynumber: 2.6 Consensus size: 53
15655377 AGGAAGCGTC
15655387 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCTATT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTACCACATATATCTATT
* *
15655441 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTACCACATATATCTATT
* *
15655495 CTGGTGGCTCTGCCACAATATCTGTATCTGGTG
1 CTGGTGGCTATGCCACATTATCTG-ATCTGGTG
15655528 ACTTCGTCAC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 7 0.09
54 74 0.91
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTACCACATATATCTATT
Found at i:15655523 original size:32 final size:27
Alignment explanation
Indices: 15655387--15655527 Score: 182
Period size: 27 Copynumber: 5.2 Consensus size: 27
15655377 AGGAAGCGTC
*
15655387 CTGGTGGCTATGCCACA-ATTATCTGAT
1 CTGGTGGCTCTGCCACATA-TATCTGAT
*
15655414 CTGGTGGCTCTACCACATATATCT-ATT
1 CTGGTGGCTCTGCCACATATATCTGA-T
*
15655441 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTGCCAC-ATATATCTGAT
*
15655468 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGAT
15655495 CTGGTGGCTCTGCCACA-ATATCTGTAT
1 CTGGTGGCTCTGCCACATATATCTG-AT
15655522 CTGGTG
1 CTGGTG
15655528 ACTTCGTCAC
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.10
27 87 0.86
28 4 0.04
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTGAT
Found at i:15655538 original size:27 final size:27
Alignment explanation
Indices: 15655387--15655545 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
15655377 AGGAAGCGTC
*
15655387 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
* *
15655414 CTGGTGGCTCTACCACATATATCTAT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
* *
15655441 CTGGTGGCTATGCCACGATTATCTG-AT
1 CTGGTGGCTCTGCCAC-AATATCTGTAT
15655468 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
15655495 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
15655522 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
15655546 GCAGTCTCGC
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.09
27 101 0.89
28 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:15660389 original size:26 final size:26
Alignment explanation
Indices: 15660360--15660469 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
15660350 TGGTACAAAT
15660360 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
15660386 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
15660412 TAATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
15660438 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
15660464 TGATAA
1 TGATAA
15660470 GCATTTCATG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:15662107 original size:27 final size:26
Alignment explanation
Indices: 15662067--15662203 Score: 168
Period size: 27 Copynumber: 5.1 Consensus size: 26
15662057 AGGAAGCGTC
*
15662067 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
15662094 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
15662121 TTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
15662148 CTGGTGGCTCTGCCACATATATCT-ATT
1 CTGGTGGCTCTGCCACAT-TATCTGA-T
*
15662175 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
15662202 CT
1 CT
15662204 AGTGACTTCG
Statistics
Matches: 96, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.10
27 83 0.86
28 3 0.03
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:15662150 original size:54 final size:53
Alignment explanation
Indices: 15662067--15662203 Score: 211
Period size: 54 Copynumber: 2.5 Consensus size: 53
15662057 AGGAAGCGTC
*
15662067 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
*
15662121 TTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
* *
15662175 CTGGTGGCTCTGCCACAATATCTGTATCT
1 CTGGTGGCTATGCCACATTATCTG-ATCT
15662204 AGTGACTTCG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
53 7 0.09
54 69 0.91
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
Found at i:15665502 original size:20 final size:20
Alignment explanation
Indices: 15665473--15665510 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15665463 AATTAAGATG
15665473 AAATTATTATAATATATTTTT
1 AAATTATTATAATA-ATTTTT
15665494 AAATT-TTATAATAATTT
1 AAATTATTATAATAATTT
15665511 ATTTTCATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATTATTATAATAATTTTT
Found at i:15672648 original size:12 final size:12
Alignment explanation
Indices: 15672631--15672655 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15672621 TGTGAAAAAT
15672631 AAAATAAAATAA
1 AAAATAAAATAA
15672643 AAAATAAAATAA
1 AAAATAAAATAA
15672655 A
1 A
15672656 GAACACACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:15675320 original size:22 final size:21
Alignment explanation
Indices: 15675287--15675341 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
15675277 CCTGGGTAGT
15675287 AGAAGAAA-AAGAGAA-AAAGA
1 AGAA-AAAGAAGAGAACAAAGA
15675307 AGAATAAGAGAAGA-AACAAAGA
1 AGAA-AA-AGAAGAGAACAAAGA
15675329 AGAAAAAGAAGAG
1 AGAAAAAGAAGAG
15675342 GGGGAGAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 12 0.40
21 5 0.17
22 13 0.43
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (21 bp):
AGAAAAAGAAGAGAACAAAGA
Found at i:15676422 original size:21 final size:20
Alignment explanation
Indices: 15676376--15676423 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
15676366 TTTTCTTATG
15676376 TCTTCTTCTTTGTCACCTTT
1 TCTTCTTCTTTGTCACCTTT
*
15676396 TCCTTCTTCATTTGT-AGCTTCT
1 T-CTTCTTC-TTTGTCACCTT-T
15676418 TCTTCT
1 TCTTCT
15676424 GCTGCTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.06, C:0.29, G:0.06, T:0.58
Consensus pattern (20 bp):
TCTTCTTCTTTGTCACCTTT
Found at i:15681338 original size:23 final size:24
Alignment explanation
Indices: 15681293--15681344 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
15681283 ATAATTTATT
**
15681293 TAAAATGTATTAAAATT-TTAAAA
1 TAAAATGTATTAAAATTAAAAAAA
15681316 TAAAATGTAGTT-AAATTAAAAAAA
1 TAAAATGTA-TTAAAATTAAAAAAA
15681340 TAAAA
1 TAAAA
15681345 AATGAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.33
Consensus pattern (24 bp):
TAAAATGTATTAAAATTAAAAAAA
Found at i:15703546 original size:20 final size:20
Alignment explanation
Indices: 15703518--15703558 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
15703508 TTCTGTTGGG
15703518 TTTTAAATCGAGTT-AAACAA
1 TTTTAAATCGA-TTCAAACAA
*
15703538 TTTTGAATCGATTCAAACAA
1 TTTTAAATCGATTCAAACAA
15703558 T
1 T
15703559 AAACAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (20 bp):
TTTTAAATCGATTCAAACAA
Found at i:15707874 original size:6 final size:6
Alignment explanation
Indices: 15707863--15707895 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
15707853 GCCTTTATAA
15707863 CTTGAG CTTGAG CTTGAG CTTGAG CTTGAG CTT
1 CTTGAG CTTGAG CTTGAG CTTGAG CTTGAG CTT
15707896 TCTCTACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.36
Consensus pattern (6 bp):
CTTGAG
Found at i:15709320 original size:15 final size:16
Alignment explanation
Indices: 15709297--15709342 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
15709287 CATTTTGGGG
*
15709297 AGCTCGCACTTTTGT-
1 AGCTTGCACTTTTGTC
*
15709312 AGCTTGCACATTTGTC
1 AGCTTGCACTTTTGTC
*
15709328 AACTTGCACTTTTGT
1 AGCTTGCACTTTTGT
15709343 TGAGTTCGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (16 bp):
AGCTTGCACTTTTGTC
Found at i:15710919 original size:6 final size:6
Alignment explanation
Indices: 15710901--15710929 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
15710891 TAAATTAATA
15710901 ATAAAT A-AAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
15710930 TATATAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:15713369 original size:16 final size:16
Alignment explanation
Indices: 15713348--15713407 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
15713338 TTTGGTTTAG
*
15713348 TGTAATGGAATATAGT
1 TGTAATGGAATAGAGT
*
15713364 TGTAATGGAATAGAAT
1 TGTAATGGAATAGAGT
15713380 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGT
* *
15713396 TATAATAGAATA
1 TGTAATGGAATA
15713408 TAACTGTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:15713389 original size:32 final size:32
Alignment explanation
Indices: 15713348--15713417 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
15713338 TTTGGTTTAG
* * * *
15713348 TGTAATGGAATATAGTTGTAATGGAATAGAAT
1 TGTAATGGAATAGAGTTATAATAGAATAGAAC
*
15713380 TGTAATGGAATAGAGTTATAATAGAATATAAC
1 TGTAATGGAATAGAGTTATAATAGAATAGAAC
15713412 TGTAAT
1 TGTAAT
15713418 AGAAATTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.01, G:0.21, T:0.34
Consensus pattern (32 bp):
TGTAATGGAATAGAGTTATAATAGAATAGAAC
Found at i:15713421 original size:16 final size:16
Alignment explanation
Indices: 15713348--15713417 Score: 77
Period size: 16 Copynumber: 4.4 Consensus size: 16
15713338 TTTGGTTTAG
* *
15713348 TGTAATGGAATATAGT
1 TGTAATGGAATAGAAT
15713364 TGTAATGGAATAGAAT
1 TGTAATGGAATAGAAT
*
15713380 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAAT
* * * *
15713396 TATAATAGAATATAAC
1 TGTAATGGAATAGAAT
15713412 TGTAAT
1 TGTAAT
15713418 AGAAATTCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.43, C:0.01, G:0.21, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAAT
Found at i:15713864 original size:12 final size:12
Alignment explanation
Indices: 15713834--15713868 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
15713824 TATATGTTAC
15713834 TTAAAGAATAAT
1 TTAAAGAATAAT
*
15713846 TTAAAAGAGTAAT
1 TT-AAAGAATAAT
15713859 TTAAAGAATA
1 TTAAAGAATA
15713869 TCTTGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (12 bp):
TTAAAGAATAAT
Found at i:15714685 original size:37 final size:37
Alignment explanation
Indices: 15714639--15714711 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
15714629 ATTGGACTTA
15714639 TTTCTTTTTTTCCAAAAAAAAGAAGGATAGTTCTTTC
1 TTTCTTTTTTTCCAAAAAAAAGAAGGATAGTTCTTTC
15714676 TTTCTTTTTTTCCAAAAAAAAGAAGGATAGTTCTTT
1 TTTCTTTTTTTCCAAAAAAAAGAAGGATAGTTCTTT
15714712 ATTGTCACTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTCTTTTTTTCCAAAAAAAAGAAGGATAGTTCTTTC
Found at i:15716012 original size:34 final size:34
Alignment explanation
Indices: 15715973--15716042 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
15715963 AATACACGGG
15715973 CATGATACTTTAGAAGCTCCAAGATTCCCAAAAC
1 CATGATACTTTAGAAGCTCCAAGATTCCCAAAAC
*
15716007 CATGATACTTTAGAAGCTCCAAGATTCCTAAAAC
1 CATGATACTTTAGAAGCTCCAAGATTCCCAAAAC
15716041 CA
1 CA
15716043 AGTCATTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (34 bp):
CATGATACTTTAGAAGCTCCAAGATTCCCAAAAC
Found at i:15717769 original size:25 final size:25
Alignment explanation
Indices: 15717741--15717793 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
15717731 TTAGAAAGAG
15717741 ATTTCAATTAATCAACCTAGAGTCA
1 ATTTCAATTAATCAACCTAGAGTCA
15717766 ATTTCAATTAATCAACCTAGAGTCA
1 ATTTCAATTAATCAACCTAGAGTCA
15717791 ATT
1 ATT
15717794 GTTTTTACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (25 bp):
ATTTCAATTAATCAACCTAGAGTCA
Found at i:15723945 original size:15 final size:15
Alignment explanation
Indices: 15723925--15723993 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 15
15723915 GAATCATAGA
*
15723925 TTTTATTTATTTTCT
1 TTTTATTTATTTTAT
15723940 TTTTATTTTATTTTAT
1 TTTTA-TTTATTTTAT
*
15723956 TTTT-TGTTATTTTTAG
1 TTTTAT-TTA-TTTTAT
* *
15723972 TTGT-TTTGTTTTAT
1 TTTTATTTATTTTAT
15723986 TTTTATTT
1 TTTTATTT
15723994 TCTTGTACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.20
15 13 0.30
16 22 0.50
ACGTcount: A:0.13, C:0.01, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTATTTATTTTAT
Found at i:15723946 original size:11 final size:10
Alignment explanation
Indices: 15723925--15723994 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
15723915 GAATCATAGA
*
15723925 TTTTATTTAT
1 TTTTTTTTAT
15723935 TTTCTTTTTAT
1 TTT-TTTTTAT
*
15723946 TTTATTTTAT
1 TTTTTTTTAT
*
15723956 TTTTTGTTAT
1 TTTTTTTTAT
** *
15723966 TTTTAGTTGT
1 TTTTTTTTAT
*
15723976 TTTGTTTTAT
1 TTTTTTTTAT
15723986 TTTTATTTT
1 TTTT-TTTT
15723995 CTTGTACTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
10 34 0.72
11 13 0.28
ACGTcount: A:0.13, C:0.01, G:0.06, T:0.80
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:15723948 original size:5 final size:5
Alignment explanation
Indices: 15723924--15724017 Score: 50
Period size: 5 Copynumber: 18.0 Consensus size: 5
15723914 AGAATCATAG
* *
15723924 ATTTT A-TTT ATTTT CTTTTT ATTTT ATTTT ATTTT -TTGTT ATTTT -TAGTT
1 ATTTT ATTTT ATTTT -ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT AT-TTT
* * * *
15723974 GTTTT GTTTT ATTTTT ATTTT CTTGT ACTTTT AATTATT ATTTT
1 ATTTT ATTTT A-TTTT ATTTT ATTTT A-TTTT -ATT-TT ATTTT
15724018 TTGAACTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
4 7 0.10
5 40 0.57
6 20 0.29
7 3 0.04
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:15723949 original size:20 final size:20
Alignment explanation
Indices: 15723924--15723968 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
15723914 AGAATCATAG
*
15723924 ATTTTA-TTTATTTTCTTTTT
1 ATTTTATTTTATTTT-TTGTT
15723944 ATTTTATTTTATTTTTTGTT
1 ATTTTATTTTATTTTTTGTT
15723964 ATTTT
1 ATTTT
15723969 TAGTTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (20 bp):
ATTTTATTTTATTTTTTGTT
Found at i:15726685 original size:2 final size:2
Alignment explanation
Indices: 15726678--15726709 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
15726668 GTACTTTTAA
15726678 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15726710 ATTTGTATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15734546 original size:25 final size:24
Alignment explanation
Indices: 15734509--15734555 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
15734499 TTATTAAATA
15734509 AAAATAAAATAATATATTTAAAAGT
1 AAAATAAAATAATAT-TTTAAAAGT
*
15734534 AAAATAAACTAATATTTTAAAA
1 AAAATAAAATAATATTTTAAAA
15734556 TTTCTTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
AAAATAAAATAATATTTTAAAAGT
Found at i:15740499 original size:16 final size:17
Alignment explanation
Indices: 15740478--15740515 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
15740468 TCCATTTCAA
* *
15740478 TTTAATTTTTTTTAT-T
1 TTTAATATTTTTAATAT
15740494 TTTAATATTTTTAATAT
1 TTTAATATTTTTAATAT
15740511 TTTAA
1 TTTAA
15740516 AGACAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATATTTTTAATAT
Found at i:15741605 original size:11 final size:11
Alignment explanation
Indices: 15741589--15741631 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
15741579 TAGAATATAT
15741589 CCCATACCTTG
1 CCCATACCTTG
*
15741600 CCCATACCTTT
1 CCCATACCTTG
*
15741611 CCCATA-CTTA
1 CCCATACCTTG
15741621 CCCATACCTTG
1 CCCATACCTTG
15741632 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.44, G:0.05, T:0.30
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:15741626 original size:21 final size:22
Alignment explanation
Indices: 15741588--15741630 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
15741578 TTAGAATATA
*
15741588 TCCCATACCTTGCCCATACCTT
1 TCCCATACCTTACCCATACCTT
15741610 TCCCATA-CTTACCCATACCTT
1 TCCCATACCTTACCCATACCTT
15741631 GGAAAGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.21, C:0.44, G:0.02, T:0.33
Consensus pattern (22 bp):
TCCCATACCTTACCCATACCTT
Found at i:15748450 original size:22 final size:22
Alignment explanation
Indices: 15748425--15748466 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15748415 ATATAAGTAC
* *
15748425 AATAACAATAATGGTAATAAAA
1 AATAAAAATAATAGTAATAAAA
15748447 AATAAAAATAATAGTAATAA
1 AATAAAAATAATAGTAATAA
15748467 TAGCACGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (22 bp):
AATAAAAATAATAGTAATAAAA
Found at i:15748677 original size:12 final size:12
Alignment explanation
Indices: 15748633--15748680 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
15748623 TATTCATGCG
*
15748633 TAAATATAAAGA
1 TAAATATAAACA
**
15748645 TAGGTATAATACA
1 TAAATATAA-ACA
15748658 TAAAATATAAACA
1 T-AAATATAAACA
15748671 TAAATATAAA
1 TAAATATAAA
15748681 GAGAAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 16 0.55
13 7 0.24
14 6 0.21
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (12 bp):
TAAATATAAACA
Found at i:15749440 original size:3 final size:3
Alignment explanation
Indices: 15749434--15749466 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
15749424 AAAAAAAAAA
15749434 AAG AAG AAG AAG AAG AAG AAG AA- AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
15749467 AACCTTAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:15755661 original size:19 final size:18
Alignment explanation
Indices: 15755634--15755671 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
15755624 GTTAATAGGG
*
15755634 TTTCTAATTCACTTTTCAA
1 TTTCAAATTCAC-TTTCAA
15755653 TTTCAAATTCACTTTCAA
1 TTTCAAATTCACTTTCAA
15755671 T
1 T
15755672 CACAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTCAAATTCACTTTCAA
Found at i:15757225 original size:2 final size:2
Alignment explanation
Indices: 15757218--15757256 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
15757208 GAATTCTAGT
15757218 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
15757257 GTTTCAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15759536 original size:26 final size:25
Alignment explanation
Indices: 15759500--15759573 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 25
15759490 ATGAATTTTT
15759500 TCAAAATTTTACCAGGGCTAAAATCG
1 TCAAAATTTTACCAGGG-TAAAATCG
*
15759526 TCAAAATTTTACC-GCGAGTAAAATTG
1 TCAAAATTTTACCAG-G-GTAAAATCG
15759552 TCAAAATTTTA-CAGGGTAAAAT
1 TCAAAATTTTACCAGGGTAAAAT
15759574 TAGGGTGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
24 7 0.16
25 3 0.07
26 33 0.75
27 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (25 bp):
TCAAAATTTTACCAGGGTAAAATCG
Found at i:15761166 original size:31 final size:31
Alignment explanation
Indices: 15761131--15761310 Score: 288
Period size: 31 Copynumber: 5.8 Consensus size: 31
15761121 CTTGTCACTT
*
15761131 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
15761162 GTAGCCGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
15761193 GTAGCTGAAGCCACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
15761224 GTAGCCGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
15761255 GTAGCCGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
15761286 GTAGTCGAAGCTACTACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
15761311 TGTCATTTGT
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 137 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:15761400 original size:52 final size:51
Alignment explanation
Indices: 15761306--15761464 Score: 241
Period size: 52 Copynumber: 3.1 Consensus size: 51
15761296 CTACTACTTT
* * * *
15761306 TCACTTGTCATTTGTCCTTGATC-AGATAGGTGTAGTCGAAGCTATCATTTA
1 TCACTT-TCACTTGTTCTTGATCAAGATAAGTGTAGCCGAAGCTATCATTTA
15761357 TCACTTTCACTTGTTCTTGATCAGAGATAAGTGTAGCCGAAGCTATCATTTA
1 TCACTTTCACTTGTTCTTGATCA-AGATAAGTGTAGCCGAAGCTATCATTTA
*
15761409 TCACTTTCACTTGTTCTTGATCAA-ATAAGTGTAGCCGAAGCTATCACTTA
1 TCACTTTCACTTGTTCTTGATCAAGATAAGTGTAGCCGAAGCTATCATTTA
15761459 TCACTT
1 TCACTT
15761465 GTTGTCATGG
Statistics
Matches: 101, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
50 45 0.45
51 7 0.07
52 49 0.49
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (51 bp):
TCACTTTCACTTGTTCTTGATCAAGATAAGTGTAGCCGAAGCTATCATTTA
Found at i:15761460 original size:50 final size:50
Alignment explanation
Indices: 15761286--15761464 Score: 234
Period size: 52 Copynumber: 3.5 Consensus size: 50
15761276 CACTGATTAG
* * * * * *
15761286 GTAGTCGAAGCTA-CTACTTTTCACTTGTCATTTGTCCTTGATCAGATAGGT
1 GTAGCCGAAGCTATC-ACTTATCACTT-TCACTTGTTCTTGATCAAATAAGT
* *
15761337 GTAGTCGAAGCTATCATTTATCACTTTCACTTGTTCTTGATCAGAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTTCTTGATCA-A-ATAAGT
*
15761389 GTAGCCGAAGCTATCATTTATCACTTTCACTTGTTCTTGATCAAATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTTCTTGATCAAATAAGT
15761439 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
15761465 GTTGTCATGG
Statistics
Matches: 117, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
50 46 0.39
51 23 0.20
52 48 0.41
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTGTTCTTGATCAAATAAGT
Found at i:15764103 original size:21 final size:20
Alignment explanation
Indices: 15764077--15764121 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
15764067 TGTTGATCTA
*
15764077 TCAATGTTAATCAACACTAAG
1 TCAATGTCAATCAACA-TAAG
* *
15764098 TCAATGTCGATCAACATAGG
1 TCAATGTCAATCAACATAAG
15764118 TCAA
1 TCAA
15764122 CTTGTGGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (20 bp):
TCAATGTCAATCAACATAAG
Found at i:15764298 original size:33 final size:34
Alignment explanation
Indices: 15764224--15764298 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
15764214 ATTTCTTTAG
* *
15764224 AATATATTTTTTATTTTTATTTTTCTAAAAGTTT
1 AATATATTTTATAATTTTATTTTTCTAAAAGTTT
* *
15764258 AA-GTATTTTATAATTTTATTTTT-TAGAA-TTT
1 AATATATTTTATAATTTTATTTTTCTAAAAGTTT
15764289 ATATATATTT
1 A-ATATATTT
15764299 AACTTTATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
31 4 0.12
32 5 0.15
33 23 0.68
34 2 0.06
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (34 bp):
AATATATTTTATAATTTTATTTTTCTAAAAGTTT
Found at i:15764660 original size:42 final size:42
Alignment explanation
Indices: 15764575--15764662 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
15764565 AATATCTAAT
* * *
15764575 TTTTTTAATTAATAGAAAATAATATTTTAAAATTGTAATCTA
1 TTTTTAAATTAATAGAAAATAATATCTTAAAATTATAATCTA
* *
15764617 TTTTTAAATTAATAGAACAT-A-ATCTTAAATTTATAATAACTA
1 TTTTTAAATTAATAGAAAATAATATCTTAAAATTATAAT--CTA
15764659 TTTT
1 TTTT
15764663 ACACCCCACT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 13 0.33
41 1 0.03
42 25 0.64
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (42 bp):
TTTTTAAATTAATAGAAAATAATATCTTAAAATTATAATCTA
Found at i:15764759 original size:20 final size:20
Alignment explanation
Indices: 15764713--15764759 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
15764703 TAAATTACTT
*
15764713 AAATTAAAAATATTTAAATA
1 AAATTAAAAATATTGAAATA
**
15764733 ATTTTAAAAA-ATTGAACATA
1 AAATTAAAAATATTGAA-ATA
15764753 AAATTAA
1 AAATTAA
15764760 TAGGAAATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AAATTAAAAATATTGAAATA
Found at i:15766010 original size:3 final size:3
Alignment explanation
Indices: 15766002--15766028 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
15765992 GTTTGCTTCG
15766002 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
15766029 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:15770300 original size:51 final size:51
Alignment explanation
Indices: 15770244--15770346 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
15770234 AGGAAAAATA
15770244 AAAAGGAAATAATCTCTAGAAATTAGCCTATCCCTAAAAATTAGTAATTTG
1 AAAAGGAAATAATCTCTAGAAATTAGCCTATCCCTAAAAATTAGTAATTTG
15770295 AAAAGGAAATAATCTCTAGAAATTAGCCTATCCCTAAAAATTAGTAATTTG
1 AAAAGGAAATAATCTCTAGAAATTAGCCTATCCCTAAAAATTAGTAATTTG
15770346 A
1 A
15770347 TTATGGCTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (51 bp):
AAAAGGAAATAATCTCTAGAAATTAGCCTATCCCTAAAAATTAGTAATTTG
Found at i:15772340 original size:60 final size:60
Alignment explanation
Indices: 15772247--15772366 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
15772237 ACAGTGGCTG
*
15772247 TAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGGGCTGATAGAGTCTTGAGGTATAATGA
1 TAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGGGCTGATAGAGTCTTAAGGTATAATGA
15772307 TAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGGGCTGATAGAGTCTTAAGGTATAATGA
1 TAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGGGCTGATAGAGTCTTAAGGTATAATGA
15772367 GAAGATTGCT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.24, C:0.07, G:0.34, T:0.35
Consensus pattern (60 bp):
TAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGGGCTGATAGAGTCTTAAGGTATAATGA
Found at i:15776188 original size:18 final size:18
Alignment explanation
Indices: 15776165--15776201 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
15776155 AGGCTTAAAA
15776165 GTTCAACTACTTAATCAT
1 GTTCAACTACTTAATCAT
15776183 GTTCAACTACTTAATCAT
1 GTTCAACTACTTAATCAT
15776201 G
1 G
15776202 CTCTTATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (18 bp):
GTTCAACTACTTAATCAT
Found at i:15776456 original size:18 final size:17
Alignment explanation
Indices: 15776429--15776462 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
15776419 CCCCAACACA
15776429 TATATATTATCTTTGATT
1 TATATATTAT-TTTGATT
*
15776447 TATATTTTATTTTGAT
1 TATATATTATTTTGAT
15776463 ATCTATGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (17 bp):
TATATATTATTTTGATT
Found at i:15781792 original size:24 final size:24
Alignment explanation
Indices: 15781765--15781823 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 24
15781755 GTAATTGAAG
* *
15781765 AAGAGAATAATAGGTAAA-AATAAT
1 AAGAGAATAA-AAGTAAATAAGAAT
15781789 AAGATG-ATAAAAGTAAATAAGAAT
1 AAGA-GAATAAAAGTAAATAAGAAT
15781813 AAGAAGAATAA
1 AAG-AGAATAA
15781824 GTAAAAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 6 0.21
24 17 0.59
25 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (24 bp):
AAGAGAATAAAAGTAAATAAGAAT
Found at i:15782022 original size:22 final size:22
Alignment explanation
Indices: 15781994--15782043 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
15781984 TAAGGGCAGC
15781994 GTAATAAAATAAA-ATAATAATA
1 GTAATAAAATAAAGA-AATAATA
*
15782016 GTAATAAAATAAAGAAGTAATA
1 GTAATAAAATAAAGAAATAATA
15782038 GTAATA
1 GTAATA
15782044 CTAGTAGTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (22 bp):
GTAATAAAATAAAGAAATAATA
Found at i:15784204 original size:87 final size:85
Alignment explanation
Indices: 15784019--15784210 Score: 206
Period size: 87 Copynumber: 2.2 Consensus size: 85
15784009 AATTTTCAGC
* * *
15784019 CTGTTACCCTACTGCTTAGGGGATTAAGGCTTGTCATCTTTGATCTGTTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGATTAAGGCTTGTCATCTTCGATCTGTCTCCCTACGGCTTAGGG
** * *
15784084 TTTCAGATCTATAAACTCAA
66 AATAAGATCTACAAACTCAA
* * *
15784104 CTAGTTACCCTACTGTTTAGGGGGTTAAGGTTTGTCAATCTTCGATCTG-CTCCACTACGGCTTA
1 CT-GTTACCCTACTGCTTAGGGGATTAAGGCTTGTC-ATCTTCGATCTGTCTCC-CTACGGCTTA
** ***
15784168 GGGAAATAAGATCTACAATTTGGT
63 GGG-AATAAGATCTACAAACTCAA
15784192 CTGTTACCCTACTGCTTAG
1 CTGTTACCCTACTGCTTAG
15784211 AGTTTAAGAT
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
85 2 0.02
86 33 0.38
87 39 0.45
88 13 0.15
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (85 bp):
CTGTTACCCTACTGCTTAGGGGATTAAGGCTTGTCATCTTCGATCTGTCTCCCTACGGCTTAGGG
AATAAGATCTACAAACTCAA
Found at i:15784780 original size:44 final size:44
Alignment explanation
Indices: 15784623--15784796 Score: 160
Period size: 44 Copynumber: 4.0 Consensus size: 44
15784613 GGGAGACAAA
** * * *
15784623 ATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAG
1 ATCTGTAAACTTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAG
* **
15784667 GTCTGTAAA-TTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAG
1 ATCTGTAAACTTCAGCTTGTTACCCTACTGCTTAGGGGGTT-AAG
* * * * *
15784711 CTCAT-T-ATCTTCGATCTAT-TT-CCCTACTGCTTAGGGTGATAAG
1 ATC-TGTAAACTTC-AGCT-TGTTACCCTACTGCTTAGGGGGTTAAG
15784754 ATCTGTAAACTTCAGCTTGTTACCCTACTGCTTAGGGGGTTAA
1 ATCTGTAAACTTCAGCTTGTTACCCTACTGCTTAGGGGGTTAA
15784797 AGCTTGGTGG
Statistics
Matches: 102, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
42 2 0.02
43 38 0.37
44 56 0.55
45 5 0.05
46 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (44 bp):
ATCTGTAAACTTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAG
Done.