Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, whole genome shotgun sequence
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: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 12 of 14
Found at i:6159072 original size:19 final size:20
Alignment explanation
Indices: 6159040--6159128 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 20
6159030 ATAGATATAA
6159040 AATAATAAATATTATTTAAATT
1 AATAAT-AAT-TTATTTAAATT
*
6159062 AATAATAA-TTAATTAATTATT
1 AATAATAATTTATTTAA--ATT
*
6159083 AATTATATAAATTTATTTAATTT
1 AA-TA-AT-AATTTATTTAAATT
*
6159106 AA-AATAATTTTTTTAAACTT
1 AATAATAATTTATTTAAA-TT
6159126 AAT
1 AAT
6159129 TGTATGTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
19 17 0.31
20 6 0.11
21 8 0.15
22 8 0.15
23 6 0.11
24 2 0.04
25 7 0.13
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAATAATTTATTTAAATT
Found at i:6159177 original size:22 final size:21
Alignment explanation
Indices: 6159126--6159177 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
6159116 TTTTAAACTT
6159126 AATTGTATGTAATAAAAATTTA
1 AATT-TATGTAATAAAAATTTA
*
6159148 AGTATTATGCTAA-AAAAATTTA
1 AAT-TTATG-TAATAAAAATTTA
6159170 CAATTTAT
1 -AATTTAT
6159178 TAAGTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (21 bp):
AATTTATGTAATAAAAATTTA
Found at i:6161321 original size:28 final size:28
Alignment explanation
Indices: 6161290--6161347 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
6161280 GATTCTGAAG
*
6161290 TATGTATGTGCATTAGTTTTGCTCTTGA
1 TATGTATATGCATTAGTTTTGCTCTTGA
6161318 TATGTATATGCATTAGTTTTGCTCTTGA
1 TATGTATATGCATTAGTTTTGCTCTTGA
6161346 TA
1 TA
6161348 ATAAATTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.50
Consensus pattern (28 bp):
TATGTATATGCATTAGTTTTGCTCTTGA
Found at i:6164417 original size:2 final size:2
Alignment explanation
Indices: 6164410--6164444 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6164400 ATATACATGT
6164410 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 T
6164445 TAAAATAGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6168303 original size:5 final size:5
Alignment explanation
Indices: 6168293--6168317 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6168283 AATAGAAAAG
6168293 GGGTT GGGTT GGGTT GGGTT GGGTT
1 GGGTT GGGTT GGGTT GGGTT GGGTT
6168318 TGGGCAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
GGGTT
Found at i:6168762 original size:12 final size:12
Alignment explanation
Indices: 6168745--6168797 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
6168735 ATCTTTGACG
*
6168745 TTGATATTGGTA
1 TTGATATTGATA
**
6168757 TTGATATCAATA
1 TTGATATTGATA
*
6168769 TTGATACTGATA
1 TTGATATTGATA
6168781 TTGATATTGATA
1 TTGATATTGATA
*
6168793 CTGAT
1 TTGAT
6168798 GAGGAATATG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (12 bp):
TTGATATTGATA
Found at i:6168787 original size:18 final size:18
Alignment explanation
Indices: 6168745--6168797 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
6168735 ATCTTTGACG
* *
6168745 TTGATATTGGTATTGATA
1 TTGATATTGATACTGATA
**
6168763 TCAATATTGATACTGATA
1 TTGATATTGATACTGATA
6168781 TTGATATTGATACTGAT
1 TTGATATTGATACTGAT
6168798 GAGGAATATG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (18 bp):
TTGATATTGATACTGATA
Found at i:6169338 original size:3 final size:3
Alignment explanation
Indices: 6169330--6169371 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
6169320 TCAAAACTCC
* *
6169330 AAT AAT AAT AAT AAT AAT AAC AAT AAC AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6169372 CCTTCCATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:6169535 original size:18 final size:18
Alignment explanation
Indices: 6169514--6169556 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
6169504 GGCGGGTCAG
6169514 TGGTTAATGGTGGCTCAA
1 TGGTTAATGGTGGCTCAA
*
6169532 TGGTTAATGGTGGGTCAA
1 TGGTTAATGGTGGCTCAA
6169550 TGGTTAA
1 TGGTTAA
6169557 CGGGTCAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (18 bp):
TGGTTAATGGTGGCTCAA
Found at i:6179672 original size:34 final size:34
Alignment explanation
Indices: 6179629--6179697 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
6179619 AATGAAAATC
*
6179629 TTTTTTTGAGTGTCTAATCAGTGATTTGAAGCCA
1 TTTTTTTGAGGGTCTAATCAGTGATTTGAAGCCA
6179663 TTTTTTTGAGGGTCTAATCAGTGATTTGAAGCCA
1 TTTTTTTGAGGGTCTAATCAGTGATTTGAAGCCA
6179697 T
1 T
6179698 AAAACCTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (34 bp):
TTTTTTTGAGGGTCTAATCAGTGATTTGAAGCCA
Found at i:6185469 original size:6 final size:6
Alignment explanation
Indices: 6185458--6185484 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6185448 AAACCAACTG
6185458 AAAAGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA
6185485 TGAATAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:6186323 original size:38 final size:38
Alignment explanation
Indices: 6186272--6186345 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
6186262 GATATTTCTG
*
6186272 GGGTGTGTTCATCTCAGCTGCAGAACTGGTGGAGCCTT
1 GGGTGTGTTCATCTCAGCTACAGAACTGGTGGAGCCTT
6186310 GGGTGTGTTCATCTCAGCTACAGAACTGGTGGAGCC
1 GGGTGTGTTCATCTCAGCTACAGAACTGGTGGAGCC
6186346 CTCTTGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.18, C:0.22, G:0.34, T:0.27
Consensus pattern (38 bp):
GGGTGTGTTCATCTCAGCTACAGAACTGGTGGAGCCTT
Found at i:6205126 original size:17 final size:18
Alignment explanation
Indices: 6205068--6205129 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 18
6205058 CATGTGGAGC
*
6205068 TTAAATATTAATATTTTT
1 TTAAATATTAATATTTTA
* *
6205086 TTAATTTTTTAATATTTTTAA
1 TTAA-ATATTAATA-TTTT-A
6205107 TTAAATATTAATA-TTTA
1 TTAAATATTAATATTTTA
6205124 TTAAAT
1 TTAAAT
6205130 CTATAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.19
18 7 0.19
19 7 0.19
20 11 0.31
21 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATATTAATATTTTA
Found at i:6223835 original size:30 final size:30
Alignment explanation
Indices: 6223739--6223866 Score: 107
Period size: 31 Copynumber: 4.2 Consensus size: 30
6223729 TAAAAAATTT
* * * *
6223739 AAATAAATTTTTATTTTTTTATTAT-ATTC
1 AAATAAATTATTATATTTTTATTTTAAATC
* *
6223768 -AATCAAATTTTTATATTTTTATTTTTAAATT
1 AAAT-AAATTATTATATTTTTA-TTTTAAATC
* * *
6223799 ATATAAATTATTATACTTTTATTTTAAACC
1 AAATAAATTATTATATTTTTATTTTAAATC
* * *
6223829 AAATAAACTCTTATATTTTTTATTTTAAGTC
1 AAATAAATTATTATA-TTTTTATTTTAAATC
6223860 AAATAAA
1 AAATAAA
6223867 CTTTTATGAT
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
28 3 0.04
29 16 0.20
30 22 0.28
31 36 0.46
32 2 0.03
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (30 bp):
AAATAAATTATTATATTTTTATTTTAAATC
Found at i:6223855 original size:31 final size:31
Alignment explanation
Indices: 6223815--6223873 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
6223805 ATTATTATAC
6223815 TTTTATTTTAAACCAAATAAACTCTTATATT
1 TTTTATTTTAAACCAAATAAACTCTTATATT
** *
6223846 TTTTATTTTAAGTCAAATAAACTTTTAT
1 TTTTATTTTAAACCAAATAAACTCTTAT
6223874 GATTACTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (31 bp):
TTTTATTTTAAACCAAATAAACTCTTATATT
Found at i:6223987 original size:13 final size:13
Alignment explanation
Indices: 6223959--6223999 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
6223949 ATAATTGATT
6223959 ATATGCTGATAT-
1 ATATGCTGATATG
*
6223971 -TATGATGATATG
1 ATATGCTGATATG
*
6223983 ATATGCTGATTTG
1 ATATGCTGATATG
6223996 ATAT
1 ATAT
6224000 AATAACATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 10 0.42
13 14 0.58
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (13 bp):
ATATGCTGATATG
Found at i:6224402 original size:131 final size:130
Alignment explanation
Indices: 6224264--6224528 Score: 392
Period size: 131 Copynumber: 2.0 Consensus size: 130
6224254 AAGCAGCTAT
* * *
6224264 TTTTTTTATTTTTTATTAATTAAAAGTATTATAATTTAAATGTCTTTCCA-TACCA-AATAGATT
1 TTTTTTTAATTTTTATTAATTAAAAGTATTAAAATTTAAATGTC-TTCCAGTACCAGAACAGATT
* *
6224327 TGTTATGTAA-CTTTTCCATTCAACCATTCATAAAAAAACATTTTCAAGGAAGTCACTCTAAATC
65 TG-TATGTAATC-TTTCCATTCAACCATTCAT-AAAAAACATTTTCAAAGAAGTCACTATAAATC
6224391 AATA
127 AATA
* ** *
6224395 TTTTTTTAATTTTTATTAATTAAAAGTATTAAAATTTAATTGTCTTCCAGTTTCAGACCAGATTT
1 TTTTTTTAATTTTTATTAATTAAAAGTATTAAAATTTAAATGTCTTCCAGTACCAGAACAGATTT
6224460 GTATGTAATCTTTCCATTCAACCATTCATAAAAAACATTTTCAAAGAAGTCACTATAAATCAATA
66 GTATGTAATCTTTCCATTCAACCATTCATAAAAAACATTTTCAAAGAAGTCACTATAAATCAATA
6224525 TTTT
1 TTTT
6224529 AAATTTCACA
Statistics
Matches: 122, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
130 43 0.35
131 70 0.57
132 9 0.07
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (130 bp):
TTTTTTTAATTTTTATTAATTAAAAGTATTAAAATTTAAATGTCTTCCAGTACCAGAACAGATTT
GTATGTAATCTTTCCATTCAACCATTCATAAAAAACATTTTCAAAGAAGTCACTATAAATCAATA
Found at i:6230369 original size:182 final size:184
Alignment explanation
Indices: 6230022--6230369 Score: 495
Period size: 182 Copynumber: 1.9 Consensus size: 184
6230012 TCCTTCATCA
* * *
6230022 TCTTTAATTAATTTTCTTTTCGTATATATATATATATATATGACATGCGATATGTATTATACGAT
1 TCTTTAATTAATTTTC-TTTCATATATATATATATATATATGACACGCAATATGTATTATACGAT
* * **
6230087 TTGTTACAATATTGATGAAAAAATGTACAAATTTATATATTATATTGCTATCATTAAATATTGTA
65 TTGTTACAATATTAATGAAAAAATATACAAATTTATATATTATATTGCTATCATTAAATATCATA
* * *
6230152 TGTGTATCACATGATACACATATGATACAAAACAATGACTCTTAATCATTTACCC
130 TGTGTATCACACGACACACATACGATACAAAACAATGACTCTTAATCATTTACCC
6230207 TCTTTAATTAA-TTTC-TTCATATATATATATATATATATGACACGCAATATGTATTATACGATT
1 TCTTTAATTAATTTTCTTTCATATATATATATATATATATGACACGCAATATGTATTATACGATT
* * *
6230270 TGTTACAATATTAAT-AAAAAGTTATATAAATTTATATATTATATTGTTATCATTAAATATCATA
66 TGTTACAATATTAATGAAAAA-ATATACAAATTTATATATTATATTGCTATCATTAAATATCATA
** * **
6230334 TGTGTATTGCACGACACACGTACGATATGAAACAAT
130 TGTGTATCACACGACACACATACGATACAAAACAAT
6230370 ATATTATTTA
Statistics
Matches: 144, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
181 5 0.03
182 124 0.86
184 4 0.03
185 11 0.08
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (184 bp):
TCTTTAATTAATTTTCTTTCATATATATATATATATATATGACACGCAATATGTATTATACGATT
TGTTACAATATTAATGAAAAAATATACAAATTTATATATTATATTGCTATCATTAAATATCATAT
GTGTATCACACGACACACATACGATACAAAACAATGACTCTTAATCATTTACCC
Found at i:6231869 original size:16 final size:16
Alignment explanation
Indices: 6231829--6231863 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6231819 AATTTTTATT
*
6231829 TAATAATTAATATAAA
1 TAATAAATAATATAAA
6231845 TAATAAATAATA-AAA
1 TAATAAATAATATAAA
6231860 TAAT
1 TAAT
6231864 TTAATATGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATAAATAATATAAA
Found at i:6232175 original size:21 final size:22
Alignment explanation
Indices: 6232144--6232184 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
6232134 AAAAATTTAA
6232144 ATAATTTTTATATTATTTAATT
1 ATAATTTTTATATTATTTAATT
*
6232166 ATAA-TTTTATATTTTTTAA
1 ATAATTTTTATATTATTTAA
6232185 AATTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATAATTTTTATATTATTTAATT
Found at i:6236599 original size:27 final size:28
Alignment explanation
Indices: 6236545--6236600 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
6236535 CAAATATTCA
*
6236545 ACAACAACTTAAACAACATTACAAGTTT
1 ACAACAACGTAAACAACATTACAAGTTT
* *
6236573 ACAACAAGGTAAA-AACATTACAGGTTT
1 ACAACAACGTAAACAACATTACAAGTTT
6236600 A
1 A
6236601 ATTAACAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23
Consensus pattern (28 bp):
ACAACAACGTAAACAACATTACAAGTTT
Found at i:6236778 original size:16 final size:16
Alignment explanation
Indices: 6236735--6236785 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
6236725 TAAATATGTT
*
6236735 TATATTTAAAA-TAAA
1 TATATATAAAAGTAAA
*
6236750 TATA-ATAAAAGTATA
1 TATATATAAAAGTAAA
*
6236765 TATATATAATAGTAAA
1 TATATATAAAAGTAAA
6236781 TATAT
1 TATAT
6236786 TCTTATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 5 0.17
15 11 0.37
16 14 0.47
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (16 bp):
TATATATAAAAGTAAA
Found at i:6236982 original size:15 final size:15
Alignment explanation
Indices: 6236964--6237006 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
6236954 AAAGTATATA
6236964 TTTATAA-TTAATAAT
1 TTTATAAGTT-ATAAT
6236979 TTTATAAGTTATAAT
1 TTTATAAGTTATAAT
6236994 TTTGATAACGTTA
1 TTT-ATAA-GTTA
6237007 AACAAAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 15 0.60
16 6 0.24
17 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (15 bp):
TTTATAAGTTATAAT
Found at i:6242138 original size:46 final size:46
Alignment explanation
Indices: 6242081--6242169 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 46
6242071 AATATTATGT
6242081 ATAATAATT-AAATCTTTAACATAACGTATAATAATTATATTTTTCA
1 ATAATAATTAAAAT-TTTAACATAACGTATAATAATTATATTTTTCA
* * *
6242127 ATAATAATTAAAATTTTAATATTATGTATAATAATTATATTTT
1 ATAATAATTAAAATTTTAACATAACGTATAATAATTATATTTT
6242170 CAACATGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 35 0.90
47 4 0.10
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.47
Consensus pattern (46 bp):
ATAATAATTAAAATTTTAACATAACGTATAATAATTATATTTTTCA
Found at i:6242143 original size:19 final size:18
Alignment explanation
Indices: 6242108--6242147 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
6242098 AACATAACGT
* *
6242108 ATAATAATTATATTTTTCA
1 ATAATAATTAAAATTTT-A
6242127 ATAATAATTAAAATTTTA
1 ATAATAATTAAAATTTTA
6242145 ATA
1 ATA
6242148 TTATGTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATAATTAAAATTTTA
Found at i:6261913 original size:29 final size:27
Alignment explanation
Indices: 6261875--6261931 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
6261865 AATTCTAAAT
* *
6261875 TAATAA-AAAATATCTAATCATTTGTT
1 TAATAATAAAAAATCTAATCATTTGTC
*
6261901 TAATAATAAAAAATCTAATTATTTGTC
1 TAATAATAAAAAATCTAATCATTTGTC
6261928 TAAT
1 TAAT
6261932 TATTTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (27 bp):
TAATAATAAAAAATCTAATCATTTGTC
Found at i:6267348 original size:35 final size:37
Alignment explanation
Indices: 6267280--6267350 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 37
6267270 CATATCTCAA
* **
6267280 TTTTATTTTAATTTTGATAATTTTTTTGAAAATTATT
1 TTTTATTTTAATTTTGATAACTTTTCAGAAAATTATT
*
6267317 TTTTA-TTTAATTTT-ATAACTTTTCAGTAAATTAT
1 TTTTATTTTAATTTTGATAACTTTTCAGAAAATTAT
6267351 CGTTTCCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 16 0.53
36 9 0.30
37 5 0.17
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (37 bp):
TTTTATTTTAATTTTGATAACTTTTCAGAAAATTATT
Found at i:6275930 original size:3 final size:3
Alignment explanation
Indices: 6275924--6275971 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
6275914 AACAACAACG
* * * *
6275924 GCA GCA GCA ACA ACA GCA GCA GCA GCA GCA GCA GCA ACA GCA ACA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
6275972 ACAGTTACAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.42, C:0.33, G:0.25, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:6275934 original size:12 final size:12
Alignment explanation
Indices: 6275925--6275975 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
6275915 ACAACAACGG
*
6275925 CAGCAGCAACAA
1 CAGCAGCAGCAA
*
6275937 CAGCAGCAGCAG
1 CAGCAGCAGCAA
6275949 CAGCAGCAGCAA
1 CAGCAGCAGCAA
*
6275961 CAGCAACAGCAA
1 CAGCAGCAGCAA
6275973 CAG
1 CAG
6275976 TTACAGTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.43, C:0.33, G:0.24, T:0.00
Consensus pattern (12 bp):
CAGCAGCAGCAA
Found at i:6275934 original size:15 final size:15
Alignment explanation
Indices: 6275916--6275971 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
6275906 ACAACAAGAA
*
6275916 CAACAACGGCAGCAG
1 CAACAACAGCAGCAG
6275931 CAACAACAGCAGCAG
1 CAACAACAGCAGCAG
* * *
6275946 CAGCAGCAGCAGCAA
1 CAACAACAGCAGCAG
*
6275961 CAGCAACAGCA
1 CAACAACAGCA
6275972 ACAGTTACAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.43, C:0.34, G:0.23, T:0.00
Consensus pattern (15 bp):
CAACAACAGCAGCAG
Found at i:6275937 original size:18 final size:18
Alignment explanation
Indices: 6275914--6275974 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
6275904 CAACAACAAG
*
6275914 AACAACAACGGCAGCAGC
1 AACAACAACAGCAGCAGC
6275932 AACAACAGCAGCAGCAGCAGC
1 AACAACA--A-CAGCAGCAGC
* * *
6275953 AGCAGCAACAGCAACAGC
1 AACAACAACAGCAGCAGC
6275971 AACA
1 AACA
6275975 GTTACAGTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 19 0.54
19 1 0.03
20 1 0.03
21 14 0.40
ACGTcount: A:0.46, C:0.33, G:0.21, T:0.00
Consensus pattern (18 bp):
AACAACAACAGCAGCAGC
Found at i:6304046 original size:31 final size:29
Alignment explanation
Indices: 6304010--6304087 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
6304000 TCATAGGAAT
*
6304010 TAAATTCAATAAAAATATATAATATAGAAAC
1 TAAATT-AAAAAAAATATATAAT-TAGAAAC
* * **
6304041 TAAATTAAACAAAATTATGTTGTTAGAAAC
1 TAAATTAAA-AAAAATATATAATTAGAAAC
*
6304071 TAAATTGAAAAAAATAT
1 TAAATTAAAAAAAATAT
6304088 TTAAAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 7 0.18
30 17 0.44
31 15 0.38
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (29 bp):
TAAATTAAAAAAAATATATAATTAGAAAC
Found at i:6304636 original size:18 final size:18
Alignment explanation
Indices: 6304596--6304638 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6304586 TCTACCATTC
6304596 TAAT-TTTTTATTTATTT
1 TAATATTTTTATTTATTT
*
6304613 TTATATTTTTATTT-TGTT
1 TAATATTTTTATTTAT-TT
6304631 TAATATTT
1 TAATATTT
6304639 CAAGTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TAATATTTTTATTTATTT
Found at i:6304987 original size:107 final size:108
Alignment explanation
Indices: 6304846--6305047 Score: 354
Period size: 107 Copynumber: 1.9 Consensus size: 108
6304836 ATTTTAAGTA
*
6304846 AATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATTGT-AAAAGAATGTGTATTTGTAAA
1 AATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATT-TCAAAAGAATGTGTATTTATAAA
6304910 TTATGAAAGTTATAACTAAATCAACATATTTTACTAATTTAATG
65 TTATGAAAGTTATAACTAAATCAACATATTTTACTAATTTAATG
*
6304954 AATTTAAATAAAAA-GTAAATTGGGTAAGAGTTGAATAATTTCAAAAGAATGTGTTTTTATAAAT
1 AATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATTTCAAAAGAATGTGTATTTATAAAT
*
6305018 TATGAAAGTTGTAACTAAATCAACATATTT
66 TATGAAAGTTATAACTAAATCAACATATTT
6305048 AGTTATTTTA
Statistics
Matches: 90, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
106 1 0.01
107 75 0.83
108 14 0.16
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (108 bp):
AATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATTTCAAAAGAATGTGTATTTATAAAT
TATGAAAGTTATAACTAAATCAACATATTTTACTAATTTAATG
Found at i:6314141 original size:2 final size:2
Alignment explanation
Indices: 6314136--6314188 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
6314126 TATATATATA
6314136 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CTG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -TG TG TG TG
6314179 TG TG T- TG TG T
1 TG TG TG TG TG T
6314189 ACCTCCAAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.00, C:0.02, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:6332968 original size:6 final size:6
Alignment explanation
Indices: 6332957--6332982 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6332947 AGAAACCCTA
6332957 AAATCC AAATCC AAATCC AAATCC AA
1 AAATCC AAATCC AAATCC AAATCC AA
6332983 TTCAACTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATCC
Found at i:6338690 original size:14 final size:15
Alignment explanation
Indices: 6338673--6338701 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6338663 CTTTTAAAAG
6338673 ATTTTTA-AAATTTT
1 ATTTTTATAAATTTT
6338687 ATTTTTATAAATTTT
1 ATTTTTATAAATTTT
6338702 CAAGGTAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTTATAAATTTT
Found at i:6343895 original size:105 final size:105
Alignment explanation
Indices: 6343744--6344042 Score: 424
Period size: 105 Copynumber: 2.8 Consensus size: 105
6343734 ATTATCCCTC
* * *
6343744 TTCTGAAGAGACCTCTCTGCTTTCAGAATCTGAATTTCCTCAAGATTCTGAAGACACCAATTTGC
1 TTCTGAAGAAACCTCTCTGCCTTCAGAATCTGAATTTCCTCAAGATTCTGAAGACACCAGTTTGC
* * *
6343809 GCCTCCAGACCCAACAGGTGCCC-CTGAAAACACAGTCATT
66 CCCTCGAGACCCAACAGTTGCCCACTG-AAACACAGTCATT
* * *
6343849 TTCTGAAGAAACCTCTCTGCCTTCAGACTCTGAATTTCCCCAAGATTCTGAAGGCACCAGTTTGC
1 TTCTGAAGAAACCTCTCTGCCTTCAGAATCTGAATTTCCTCAAGATTCTGAAGACACCAGTTTGC
* *
6343914 CCCTTGAGACCCAACAGTTGCCCATTGAAACACAGTCATT
66 CCCTCGAGACCCAACAGTTGCCCACTGAAACACAGTCATT
* * *
6343954 TTCTGGAGAAACCTCTCTGCCTCCAGAATTCGTG--TTTCCTCAAGATTCTGAAGACAACAGTTT
1 TTCTGAAGAAACCTCTCTGCCTTCAGAA-TC-TGAATTTCCTCAAGATTCTGAAGACACCAGTTT
6344017 GCCCCTCGAGACCCAACAGTTGCCCA
64 GCCCCTCGAGACCCAACAGTTGCCCA
6344043 TCGAAACTGA
Statistics
Matches: 173, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
105 167 0.97
106 4 0.02
107 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (105 bp):
TTCTGAAGAAACCTCTCTGCCTTCAGAATCTGAATTTCCTCAAGATTCTGAAGACACCAGTTTGC
CCCTCGAGACCCAACAGTTGCCCACTGAAACACAGTCATT
Found at i:6348577 original size:17 final size:17
Alignment explanation
Indices: 6348555--6348588 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6348545 ATCCTCAATG
6348555 CATAATAACAACAATTA
1 CATAATAACAACAATTA
*
6348572 CATAATAACAGCAATTA
1 CATAATAACAACAATTA
6348589 GAGGCTGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.18, G:0.03, T:0.24
Consensus pattern (17 bp):
CATAATAACAACAATTA
Found at i:6356441 original size:19 final size:18
Alignment explanation
Indices: 6356403--6356441 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6356393 TAATACTTAA
* *
6356403 AAAAAAATTAAATTATTT
1 AAAAAAATTAAATCAATT
6356421 AAAAAAATTAAAATCAATT
1 AAAAAAATT-AAATCAATT
6356440 AA
1 AA
6356442 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAAATTAAATCAATT
Found at i:6363045 original size:28 final size:29
Alignment explanation
Indices: 6362987--6363045 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
6362977 CAAGTAGTTT
* *
6362987 TTTTTTTAATTAAAAAAATTAAAACTTTA
1 TTTTTTGAATTAAAAAAATTAAAACTGTA
6363016 TTTTTTGAA-TAAAAAAATTAAATA-TGTA
1 TTTTTTGAATTAAAAAAATTAAA-ACTGTA
6363044 TT
1 TT
6363046 AATGAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (29 bp):
TTTTTTGAATTAAAAAAATTAAAACTGTA
Found at i:6365306 original size:95 final size:96
Alignment explanation
Indices: 6365183--6365376 Score: 336
Period size: 96 Copynumber: 2.0 Consensus size: 96
6365173 TCCAATGCAT
*
6365183 TCAAAGTTGAAAAGCCAAAAGAATATTTAAAAAGTTAAGTAGTTTCCAT-AAACATAAATATCAT
1 TCAAAGTTGAAAAGCCAAAAGAATATTTAAAAAGTTAAGTAGTTTCCATAAAACAAAAATATCAT
6365247 CCAGCACTACCACCTCTCACCCTTGCATCAC
66 CCAGCACTACCACCTCTCACCCTTGCATCAC
* * * *
6365278 TCAAAGTTGAAAGGTCAAAAGAATATTTAATAAGTTGAGTAGTTTCCATAAAACAAAAATATCAT
1 TCAAAGTTGAAAAGCCAAAAGAATATTTAAAAAGTTAAGTAGTTTCCATAAAACAAAAATATCAT
6365343 CCAGCACTACCACCTCTCACCCTTGCATCAC
66 CCAGCACTACCACCTCTCACCCTTGCATCAC
6365374 TCA
1 TCA
6365377 TCTCTCATGT
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 45 0.48
96 48 0.52
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (96 bp):
TCAAAGTTGAAAAGCCAAAAGAATATTTAAAAAGTTAAGTAGTTTCCATAAAACAAAAATATCAT
CCAGCACTACCACCTCTCACCCTTGCATCAC
Found at i:6368959 original size:3 final size:3
Alignment explanation
Indices: 6368951--6368977 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6368941 TCTATGGCAA
6368951 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
6368978 CTGTTCTTTG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6369899 original size:19 final size:22
Alignment explanation
Indices: 6369870--6369921 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
6369860 ATTTAAAATA
6369870 AAAATACTTATTT-AA-ATTTTT
1 AAAATA-TTATTTAAAGATTTTT
6369891 AAAA-ATTATTTAAAGATTTTT
1 AAAATATTATTTAAAGATTTTT
6369912 AAAATATTAT
1 AAAATATTAT
6369922 ATACATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.21
20 3 0.11
21 14 0.50
22 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAATATTATTTAAAGATTTTT
Found at i:6369929 original size:20 final size:20
Alignment explanation
Indices: 6369870--6369929 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
6369860 ATTTAAAATA
*
6369870 AAAATACTTATTTAAATTTTT
1 AAAATA-TTATATAAATTTTT
*
6369891 AAAA-ATTATTTAAAGATTTTT
1 AAAATATTATAT-AA-ATTTTT
*
6369912 AAAATATTATATACATTT
1 AAAATATTATATAAATTT
6369930 ATTTTTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 6 0.18
20 7 0.21
21 15 0.44
22 6 0.18
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATATTATATAAATTTTT
Found at i:6370754 original size:16 final size:16
Alignment explanation
Indices: 6370733--6370768 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
6370723 TTAGTAATTA
6370733 AAATTT-TTTTATTAGT
1 AAATTTGTTTTATT-GT
6370749 AAATTTGTTTTATTGT
1 AAATTTGTTTTATTGT
6370765 AAAT
1 AAAT
6370769 GATATATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (16 bp):
AAATTTGTTTTATTGT
Found at i:6375532 original size:34 final size:34
Alignment explanation
Indices: 6375493--6375562 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 34
6375483 TATTATAAAA
6375493 TTTATT-TAATTTAAAATAAAAATATAAAA-ATTAT
1 TTTATTATAATTT-AAA-AAAAATATAAAATATTAT
*
6375527 TTTATTCAATAATTTAAAAAAAATTTAAAATATTAT
1 TTTATT--ATAATTTAAAAAAAATATAAAATATTAT
6375563 ATTAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
34 6 0.19
35 11 0.35
36 8 0.26
37 6 0.19
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (34 bp):
TTTATTATAATTTAAAAAAAATATAAAATATTAT
Found at i:6383911 original size:3 final size:3
Alignment explanation
Indices: 6383903--6383941 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
6383893 GGTTCTTTGG
* *
6383903 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAT GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
6383942 AGGGGTGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:6399577 original size:16 final size:16
Alignment explanation
Indices: 6399556--6399587 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6399546 AGATTTTAGG
6399556 AGAAAGAGGGGCTGTA
1 AGAAAGAGGGGCTGTA
6399572 AGAAAGAGGGGCTGTA
1 AGAAAGAGGGGCTGTA
6399588 GCTCAGGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.44, T:0.12
Consensus pattern (16 bp):
AGAAAGAGGGGCTGTA
Found at i:6417046 original size:18 final size:20
Alignment explanation
Indices: 6417012--6417049 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
6417002 AAGTTTATTA
6417012 ATTTTCAAAATAAATATTTT
1 ATTTTCAAAATAAATATTTT
6417032 ATTTT-AAAA-AAATATTTT
1 ATTTTCAAAATAAATATTTT
6417050 TTATTGGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTCAAAATAAATATTTT
Found at i:6417769 original size:2 final size:2
Alignment explanation
Indices: 6417762--6417792 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6417752 AGCTGCCTCT
6417762 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 T
6417793 GTATTCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6423216 original size:21 final size:21
Alignment explanation
Indices: 6423120--6423216 Score: 56
Period size: 21 Copynumber: 5.2 Consensus size: 21
6423110 TGATTGATTA
6423120 TTTTTTGAGTCTGAGTTAGGT
1 TTTTTTGAGTCTGAGTTAGGT
** *
6423141 TAATCTGA-T-TGA-TTA---
1 TTTTTTGAGTCTGAGTTAGGT
6423156 TTTTTTGAGTCTGAGTTAGGT
1 TTTTTTGAGTCTGAGTTAGGT
** *
6423177 TAATCTGA-T-TGA-TTA---
1 TTTTTTGAGTCTGAGTTAGGT
6423192 TTTTTTGAGTCTGAGTTAGGT
1 TTTTTTGAGTCTGAGTTAGGT
6423213 TTTT
1 TTTT
6423217 GTGTATTCGC
Statistics
Matches: 52, Mismatches: 12, Indels: 24
0.59 0.14 0.27
Matches are distributed among these distances:
15 10 0.19
16 2 0.04
17 6 0.12
18 12 0.23
19 6 0.12
20 2 0.04
21 14 0.27
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.53
Consensus pattern (21 bp):
TTTTTTGAGTCTGAGTTAGGT
Found at i:6423233 original size:42 final size:36
Alignment explanation
Indices: 6423104--6423213 Score: 220
Period size: 36 Copynumber: 3.1 Consensus size: 36
6423094 AACTTAGCAC
6423104 TTAATCTGATTGATTATTTTTTGAGTCTGAGTTAGG
1 TTAATCTGATTGATTATTTTTTGAGTCTGAGTTAGG
6423140 TTAATCTGATTGATTATTTTTTGAGTCTGAGTTAGG
1 TTAATCTGATTGATTATTTTTTGAGTCTGAGTTAGG
6423176 TTAATCTGATTGATTATTTTTTGAGTCTGAGTTAGG
1 TTAATCTGATTGATTATTTTTTGAGTCTGAGTTAGG
6423212 TT
1 TT
6423214 TTTGTGTATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (36 bp):
TTAATCTGATTGATTATTTTTTGAGTCTGAGTTAGG
Found at i:6431771 original size:29 final size:29
Alignment explanation
Indices: 6431738--6431794 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
6431728 ATATTCTTCG
6431738 GAATTAGCTTCTAATTCATTCTTCCCAAA
1 GAATTAGCTTCTAATTCATTCTTCCCAAA
6431767 GAATTAGCTTCTAATTCATTCTTCCCAA
1 GAATTAGCTTCTAATTCATTCTTCCCAA
6431795 TTGATTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (29 bp):
GAATTAGCTTCTAATTCATTCTTCCCAAA
Found at i:6431796 original size:25 final size:25
Alignment explanation
Indices: 6431730--6431796 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 25
6431720 TTTTGTCAAT
**
6431730 ATTCTTCGGAATTAGCTTCTAATTC
1 ATTCTTCCCAATTAGCTTCTAATTC
6431755 ATTCTTCCCAAAGAATTAGCTTCTAATTC
1 ATTCTTCCC----AATTAGCTTCTAATTC
6431784 ATTCTTCCCAATT
1 ATTCTTCCCAATT
6431797 GATTTTGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
25 11 0.31
29 25 0.69
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (25 bp):
ATTCTTCCCAATTAGCTTCTAATTC
Found at i:6458103 original size:17 final size:19
Alignment explanation
Indices: 6458072--6458110 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6458062 TCAATAGTGA
*
6458072 TTTTTAATTACTATAT-AT
1 TTTTTAAATACTATATAAT
6458090 TTTTTAAATA-TATATAAT
1 TTTTTAAATACTATATAAT
6458108 TTT
1 TTT
6458111 CTATGTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAAATACTATATAAT
Found at i:6459652 original size:19 final size:19
Alignment explanation
Indices: 6459628--6459666 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6459618 TTCACCAATG
6459628 AGGCTAA-GAGGATGAATCT
1 AGGCTAAGGA-GATGAATCT
6459647 AGGCTAAGGAGATGAATCT
1 AGGCTAAGGAGATGAATCT
6459666 A
1 A
6459667 AGGACAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (19 bp):
AGGCTAAGGAGATGAATCT
Found at i:6465932 original size:24 final size:24
Alignment explanation
Indices: 6465905--6465954 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
6465895 CGAGGACTGC
*
6465905 TCAACAAGTTTAGAATCGATAGAA
1 TCAACAAGTGTAGAATCGATAGAA
* * *
6465929 TCAAGAAGTGTGGAATCTATAGAA
1 TCAACAAGTGTAGAATCGATAGAA
6465953 TC
1 TC
6465955 TGCAGAATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (24 bp):
TCAACAAGTGTAGAATCGATAGAA
Found at i:6474359 original size:3 final size:3
Alignment explanation
Indices: 6474347--6474390 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
6474337 TTTACTACTT
* *
6474347 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6474391 GTTACATCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6495628 original size:3 final size:3
Alignment explanation
Indices: 6495620--6495648 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6495610 CTTTGTGTTT
6495620 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6495649 TCCATTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6508625 original size:16 final size:16
Alignment explanation
Indices: 6508600--6508645 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
6508590 TCGTTCCCCA
6508600 TTTTTTTTTTTACT-T
1 TTTTTTTTTTTACTGT
6508615 TTTTTTCTTTTTACTGT
1 TTTTTT-TTTTTACTGT
6508632 ATTTTTATTTTTTA
1 -TTTTT-TTTTTTA
6508646 TTAATAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.22
16 8 0.30
17 1 0.04
18 11 0.41
19 1 0.04
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTTTTTTTACTGT
Found at i:6511185 original size:2 final size:2
Alignment explanation
Indices: 6511178--6511202 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6511168 AACTCTATCC
6511178 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
6511203 CGTTTATTCA
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:6513917 original size:57 final size:58
Alignment explanation
Indices: 6513795--6513917 Score: 160
Period size: 57 Copynumber: 2.2 Consensus size: 58
6513785 GAAACTGGGG
* * *
6513795 ACAGGGATCGGGGAGTGAGAGATGATTACCGCTCCCTCAGGCGATCTAGATCAATTTC
1 ACAGGGATCGGGGAATGAGAGATGACTACCGCTCCCGCAGGCGATCTAGATCAATTTC
* * * * *
6513853 ACA-GGATCGGGGAATGAGAGATGACTATCGCTCTCGCAGTCGCTCTAGATCTATTTC
1 ACAGGGATCGGGGAATGAGAGATGACTACCGCTCCCGCAGGCGATCTAGATCAATTTC
6513910 A-AGGGATC
1 ACAGGGATC
6513918 ATGGGGCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 1 0.02
57 52 0.93
58 3 0.05
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (58 bp):
ACAGGGATCGGGGAATGAGAGATGACTACCGCTCCCGCAGGCGATCTAGATCAATTTC
Found at i:6519655 original size:7 final size:7
Alignment explanation
Indices: 6519643--6519668 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6519633 TGAAAAAACT
6519643 TTGCACC
1 TTGCACC
6519650 TTGCACC
1 TTGCACC
6519657 TTGCACC
1 TTGCACC
6519664 TTGCA
1 TTGCA
6519669 TCATCTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.38, G:0.15, T:0.31
Consensus pattern (7 bp):
TTGCACC
Found at i:6526483 original size:115 final size:115
Alignment explanation
Indices: 6526281--6526507 Score: 445
Period size: 115 Copynumber: 2.0 Consensus size: 115
6526271 TAATCAATAC
6526281 GTGTGGGGTGGCAGCTTGCAAGTGGAAGGAAAAGCTTCAAATGCACCATTCTCTTTATTAATGGA
1 GTGTGGGGTGGCAGCTTGCAAGTGGAAGGAAAAGCTTCAAATGCACCATTCTCTTTATTAATGGA
6526346 TAAAAAGATTTGGGGCATGTTTGACTTCACTTCCATTACAAATATTATAG
66 TAAAAAGATTTGGGGCATGTTTGACTTCACTTCCATTACAAATATTATAG
*
6526396 GTGTGGGGTGGCAGCTTGCAAGTGGAAGGTAAAGCTTCAAATGCACCATTCTCTTTATTAATGGA
1 GTGTGGGGTGGCAGCTTGCAAGTGGAAGGAAAAGCTTCAAATGCACCATTCTCTTTATTAATGGA
6526461 TAAAAAGATTTGGGGCATGTTTGACTTCACTTCCATTACAAATATTA
66 TAAAAAGATTTGGGGCATGTTTGACTTCACTTCCATTACAAATATTA
6526508 AAGAACTCCA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (115 bp):
GTGTGGGGTGGCAGCTTGCAAGTGGAAGGAAAAGCTTCAAATGCACCATTCTCTTTATTAATGGA
TAAAAAGATTTGGGGCATGTTTGACTTCACTTCCATTACAAATATTATAG
Found at i:6534780 original size:14 final size:14
Alignment explanation
Indices: 6534761--6534787 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6534751 CTTTATTTAT
6534761 AAATATATATATAA
1 AAATATATATATAA
6534775 AAATATATATATA
1 AAATATATATATA
6534788 TATTACACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATATATATATAA
Found at i:6553817 original size:27 final size:27
Alignment explanation
Indices: 6553775--6553833 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
6553765 ATCATCCAGC
* *
6553775 ACTTGTGTTTCACCGCCAAAGTTCAAA
1 ACTTGAGTTTCACCGCAAAAGTTCAAA
* *
6553802 ACTTGAGTTTCCCCGCAAAAGTTCACA
1 ACTTGAGTTTCACCGCAAAAGTTCAAA
6553829 ACTTG
1 ACTTG
6553834 GGTCTCGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (27 bp):
ACTTGAGTTTCACCGCAAAAGTTCAAA
Found at i:6561017 original size:12 final size:12
Alignment explanation
Indices: 6561000--6561024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6560990 ATATCAGTTT
6561000 TACTTTTATAAA
1 TACTTTTATAAA
6561012 TACTTTTATAAA
1 TACTTTTATAAA
6561024 T
1 T
6561025 TAAAATATAA
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TACTTTTATAAA
Found at i:6569574 original size:66 final size:66
Alignment explanation
Indices: 6569461--6569591 Score: 190
Period size: 66 Copynumber: 2.0 Consensus size: 66
6569451 TCTATGCATT
* ** * *
6569461 AGTTTCATCCGCACCCGATGAAGGGGCTTTTGTTTCTATGGGGTCTATTTCCATGTTGGAGACAT
1 AGTTTCATCCCCACCCGATGAAGAAGCTTTTGTTTCTATGGGATCTATTTCCATATTGGAGACAT
6569526 C
66 C
* * *
6569527 AGTTTCATCCCCACCTGGTGAAGAAGCTTTTGTTTCTGTGGGATCTATTTCCATATTGGAGACAT
1 AGTTTCATCCCCACCCGATGAAGAAGCTTTTGTTTCTATGGGATCTATTTCCATATTGGAGACAT
6569592 TGGTACTTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (66 bp):
AGTTTCATCCCCACCCGATGAAGAAGCTTTTGTTTCTATGGGATCTATTTCCATATTGGAGACAT
C
Found at i:6570998 original size:72 final size:71
Alignment explanation
Indices: 6570903--6571479 Score: 814
Period size: 72 Copynumber: 8.0 Consensus size: 71
6570893 GATTCCAAAG
* * * *
6570903 AAGGCTCTGCCTCACGTTCAGAATTAGTCTCAACCACAGAAGGTGCCTCCACCATGCCTGACTTA
1 AAGGCTCTGCTTCACATTCAGAATT-GTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
6570968 T-TAGGAC
65 TCT-GGAC
* *
6570975 AAGGCTCTGCTTCACATTCAGAATTATTCTCAACCATAACAGGTGCCTCCACCATGCCTGACTTA
1 AAGGCTCTGCTTCACATTCAGAATT-GTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
*
6571040 TCCGGAC
65 TCTGGAC
* * *
6571047 AGGGCTCTGCTTCACATTCAGAATTGTTTGCAACCATAGCAGGTGCCTCCACTATGCCTGACTTA
1 AAGGCTCTGCTTCACATTCAGAATTGTCT-CAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
6571112 TCTGGAC
65 TCTGGAC
*
6571119 AAGGCTCTGCTTCACATTCAGAATTGTTTGCAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
1 AAGGCTCTGCTTCACATTCAGAATTGTCT-CAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
6571184 TCTGGAC
65 TCTGGAC
*
6571191 AAGGCTCTGCTTCACATTCAGAATTGTTCTCAACCATAGCAGGTGCCTCCATCATGCCTGACTTA
1 AAGGCTCTGCTTCACATTCAGAATTG-TCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
6571256 TCTGGAC
65 TCTGGAC
* * * **
6571263 AAGGCTCTGCTTCACATTCAGGATTGTCCTCAACCACAGCAGGTGCCTCCATCACACCTGACTTA
1 AAGGCTCTGCTTCACATTCAGAATTGT-CTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
*
6571328 TCTGGAA
65 TCTGGAC
* *
6571335 AAGACTCTGCCTCACATTCAGAATTGTTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
1 AAGGCTCTGCTTCACATTCAGAATTG-TCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
6571400 TCTGGAC
65 TCTGGAC
* * *** * **
6571407 AAGGCTCTGCTTCACATTCAGAATTGTTCTCAAGCATAGCGGGTATGTCTACTGTGCCTGACTTA
1 AAGGCTCTGCTTCACATTCAGAATTG-TCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTA
6571472 TCTGGAC
65 TCTGGAC
6571479 A
1 A
6571480 CATGGTAATA
Statistics
Matches: 460, Mismatches: 40, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
71 3 0.01
72 454 0.99
73 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (71 bp):
AAGGCTCTGCTTCACATTCAGAATTGTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTAT
CTGGAC
Found at i:6591550 original size:14 final size:17
Alignment explanation
Indices: 6591529--6591565 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
6591519 GCATGAATTA
*
6591529 TAAAAA-ATTTATAAAC
1 TAAAAATATATATAAAC
6591545 -AAAAATATATATAAAC
1 TAAAAATATATATAAAC
6591561 TAAAA
1 TAAAA
6591566 CTTAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 9 0.50
17 4 0.22
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAATATATATAAAC
Found at i:6599847 original size:5 final size:5
Alignment explanation
Indices: 6599836--6599870 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
6599826 CCTTTTGCTT
*
6599836 TTTTGC TTTGC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
6599871 TTCACTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 24 0.89
6 3 0.11
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:6604924 original size:5 final size:6
Alignment explanation
Indices: 6604909--6604941 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
6604899 GTTTTCATCG
6604909 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
6604942 CGTTTCGCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:6605414 original size:29 final size:30
Alignment explanation
Indices: 6605381--6605443 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
6605371 CATTATTAAA
*
6605381 ATAATTAT-ATA-AATTATTTAATTAAGATT
1 ATAATTATAATATAATTATCTAATT-AGATT
*
6605410 ATAA-TATAATATTATTATCTAATTAGATT
1 ATAATTATAATATAATTATCTAATTAGATT
6605439 ATAAT
1 ATAAT
6605444 ATTTAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 3 0.10
29 16 0.55
30 10 0.34
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
ATAATTATAATATAATTATCTAATTAGATT
Found at i:6606612 original size:3 final size:3
Alignment explanation
Indices: 6606606--6606637 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6606596 TGATTATTGT
*
6606606 ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
6606638 TACAATCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:6607547 original size:2 final size:2
Alignment explanation
Indices: 6607540--6607573 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6607530 TTTGCTTTCA
6607540 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6607574 TTCATTTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6613601 original size:21 final size:20
Alignment explanation
Indices: 6613567--6613608 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
6613557 AAATATAATG
6613567 TTTATTATTTTTT-ATTTAC
1 TTTATTATTTTTTAATTTAC
6613586 TTTATATATATTTTTAATTTAC
1 TTTAT-TAT-TTTTTAATTTAC
6613608 T
1 T
6613609 CAAAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 5 0.25
22 7 0.35
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTATTTTTTAATTTAC
Found at i:6616242 original size:70 final size:69
Alignment explanation
Indices: 6616109--6616250 Score: 212
Period size: 70 Copynumber: 2.0 Consensus size: 69
6616099 TTGAAGAATA
*
6616109 AAACTAATTATTAAATAAAAAATTATTTTGAAGCCACTAAAAATATATAAAATAAATAAAATTGA
1 AAACTAATTATTAAACAAAAAATTATTTTGAAGCCACTAAAAATATATAAAATAAATAAAATTGA
6616174 ATTG
66 ATTG
* * * * *
6616178 AAACTAATTATTAAACCAAACATTATTTTGAAAGCTATTAAAAATATATATAATAAATAAAATTG
1 AAACTAATTATTAAACAAAAAATTATTTTG-AAGCCACTAAAAATATATAAAATAAATAAAATTG
*
6616243 TATTG
65 AATTG
6616248 AAA
1 AAA
6616251 GAAATACAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 27 0.42
70 38 0.58
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (69 bp):
AAACTAATTATTAAACAAAAAATTATTTTGAAGCCACTAAAAATATATAAAATAAATAAAATTGA
ATTG
Found at i:6616937 original size:13 final size:13
Alignment explanation
Indices: 6616921--6616946 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6616911 TTAGTTAATG
6616921 TATAAATAATTTA
1 TATAAATAATTTA
6616934 TATAAATAATTTA
1 TATAAATAATTTA
6616947 ATTGATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATAAATAATTTA
Found at i:6616965 original size:19 final size:19
Alignment explanation
Indices: 6616941--6616978 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6616931 TTATATAAAT
* *
6616941 AATTTAATTGATTAAATAA
1 AATTTAATTCAATAAATAA
6616960 AATTTAATTCAATAAATAA
1 AATTTAATTCAATAAATAA
6616979 TTTTATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
AATTTAATTCAATAAATAA
Found at i:6617021 original size:12 final size:12
Alignment explanation
Indices: 6617004--6617046 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
6616994 AAATGTTTAA
6617004 ATTAATTAATGT
1 ATTAATTAATGT
* *
6617016 ATTAATAAATTT
1 ATTAATTAATGT
*
6617028 ATTAAATAATGT
1 ATTAATTAATGT
6617040 AATTAAT
1 -ATTAAT
6617047 AAGATAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (12 bp):
ATTAATTAATGT
Found at i:6617126 original size:110 final size:110
Alignment explanation
Indices: 6617000--6617254 Score: 282
Period size: 110 Copynumber: 2.3 Consensus size: 110
6616990 TTTTAAATGT
* * ** *
6617000 TTAAATTAATTAATGTATTAATAAATTTATTAAATAATGTAATTAATAAGATAAAATAATGTATT
1 TTAAATTAATTAATGTACTAATAAATTAATTAAATAATACAATTAATAAAATAAAATAATGTATT
* *
6617065 AGTAAACAATTAATTAAATAAGTAATATTGTTTACTTTTCAACAA
66 AATAAACAAATAATTAAATAAGTAATATTGTTTACTTTTCAACAA
* * * *
6617110 TTAAATTAATTTATGTACTAATAACTTAATTAAATAGTACAATTAATAAAATAAATTAATGTATT
1 TTAAATTAATTAATGTACTAATAAATTAATTAAATAATACAATTAATAAAATAAAATAATGTATT
* * * * * *
6617175 AATTAATAAATAATTAATTAAGTAATAATATTTA-ATTT-AA-AA
66 AATAAACAAATAATTAAATAAGTAATATTGTTTACTTTTCAACAA
* * * * * *
6617217 ATAATTTAATTAATATATTAATAACTTATTTAAATAAT
1 TTAAATTAATTAATGTACTAATAAATTAATTAAATAAT
6617255 TTAATCGCTT
Statistics
Matches: 121, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
107 33 0.27
108 2 0.02
109 3 0.02
110 83 0.69
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (110 bp):
TTAAATTAATTAATGTACTAATAAATTAATTAAATAATACAATTAATAAAATAAAATAATGTATT
AATAAACAAATAATTAAATAAGTAATATTGTTTACTTTTCAACAA
Found at i:6617192 original size:15 final size:15
Alignment explanation
Indices: 6617172--6617231 Score: 59
Period size: 15 Copynumber: 3.7 Consensus size: 15
6617162 AAATTAATGT
6617172 ATTAATTAATAAATA
1 ATTAATTAATAAATA
6617187 ATTAATTAAGTAATAATA
1 ATTAATTAA-T-A-AATA
*
6617205 TTTAATTTAA-AAATA
1 ATTAA-TTAATAAATA
6617220 ATTTAATTAATA
1 A-TTAATTAATA
6617232 TATTAATAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
15 17 0.46
16 7 0.19
17 1 0.03
18 8 0.22
19 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTAATTAATAAATA
Found at i:6625653 original size:13 final size:13
Alignment explanation
Indices: 6625637--6625675 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
6625627 GTAATATATT
*
6625637 AATATTTATAATA
1 AATATTTATAAAA
* *
6625650 AATAATAATAAAA
1 AATATTTATAAAA
6625663 AATATTTATAAAA
1 AATATTTATAAAA
6625676 TAACATAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATTTATAAAA
Found at i:6625839 original size:26 final size:26
Alignment explanation
Indices: 6625802--6625865 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
6625792 ATAAAAACTT
* *
6625802 ATTTTATT-AAAATA-AAAATATAAAA
1 ATTTAATTAAAAATACAAAAAAT-AAA
6625827 ATTTAATTAAAAATACCAAAAAATAAA
1 ATTTAATTAAAAATA-CAAAAAATAAA
*
6625854 ATTTATTTAAAA
1 ATTTAATTAAAA
6625866 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 7 0.21
26 6 0.18
27 14 0.42
28 6 0.18
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (26 bp):
ATTTAATTAAAAATACAAAAAATAAA
Found at i:6625866 original size:26 final size:25
Alignment explanation
Indices: 6625804--6625866 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
6625794 AAAAACTTAT
*
6625804 TTTA-TTAAAATAAAAATATAAAAA
1 TTTATTTAAAATAAAAAAATAAAAA
*
6625828 TTTAATTAAAAATACCAAAAAAT-AAAA
1 TTT-ATTTAAAATA--AAAAAATAAAAA
6625855 TTTATTTAAAAT
1 TTTATTTAAAAT
6625867 TTTAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 3 0.09
25 1 0.03
26 15 0.47
27 7 0.22
28 6 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTATTTAAAATAAAAAAATAAAAA
Found at i:6637408 original size:2 final size:2
Alignment explanation
Indices: 6637401--6637431 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6637391 TCTGTTTATG
6637401 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
6637432 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:6637447 original size:2 final size:2
Alignment explanation
Indices: 6637442--6637487 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6637432 NNNNNNNNNN
6637442 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6637484 TC TC
1 TC TC
6637488 AGCCATTGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6662649 original size:15 final size:15
Alignment explanation
Indices: 6662629--6662658 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6662619 AGCTGCTGAT
*
6662629 TCTTCCTCCGCCTTC
1 TCTTCCTCCACCTTC
6662644 TCTTCCTCCACCTTC
1 TCTTCCTCCACCTTC
6662659 CGGTTGCTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.53, G:0.03, T:0.40
Consensus pattern (15 bp):
TCTTCCTCCACCTTC
Found at i:6663738 original size:21 final size:22
Alignment explanation
Indices: 6663714--6663766 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
6663704 TATTATTACA
6663714 ATTTTTTTAAAAAAAATTA-TT
1 ATTTTTTTAAAAAAAATTATTT
** * *
6663735 ATTTTCATAAATATAATTATTT
1 ATTTTTTTAAAAAAAATTATTT
*
6663757 AATTTTTTAA
1 ATTTTTTTAA
6663767 CTATATACAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTTTAAAAAAAATTATTT
Found at i:6669108 original size:17 final size:16
Alignment explanation
Indices: 6669082--6669114 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
6669072 AGCTTCCTTA
6669082 TTCCTCTTTGTTGCAT
1 TTCCTCTTTGTTGCAT
6669098 TTCCTTCTTTGTTGCAT
1 TTCC-TCTTTGTTGCAT
6669115 AACAGCCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.06, C:0.24, G:0.12, T:0.58
Consensus pattern (16 bp):
TTCCTCTTTGTTGCAT
Found at i:6678277 original size:32 final size:32
Alignment explanation
Indices: 6678241--6678306 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
6678231 TCCATTGCAT
6678241 AAACATTATTGATAACAACTTTCTCATGAAAG
1 AAACATTATTGATAACAACTTTCTCATGAAAG
*
6678273 AAACATTATTGATAACAGCTTTCTCATGAAAG
1 AAACATTATTGATAACAACTTTCTCATGAAAG
6678305 AA
1 AA
6678307 TGCAGGCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (32 bp):
AAACATTATTGATAACAACTTTCTCATGAAAG
Found at i:6680235 original size:2 final size:2
Alignment explanation
Indices: 6680228--6680263 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6680218 ATATGATTAA
*
6680228 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6680264 GAAATAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6689044 original size:11 final size:11
Alignment explanation
Indices: 6689028--6689052 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6689018 GAGAGTGAGA
6689028 GAGAGAGAAAG
1 GAGAGAGAAAG
6689039 GAGAGAGAAAG
1 GAGAGAGAAAG
6689050 GAG
1 GAG
6689053 GGTGAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (11 bp):
GAGAGAGAAAG
Found at i:6689189 original size:2 final size:2
Alignment explanation
Indices: 6689182--6689219 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6689172 CCTATTGGGC
6689182 TA TA TA TA TA TA 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 TA TA TA
6689220 GTTCTATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6691578 original size:2 final size:2
Alignment explanation
Indices: 6691571--6691599 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6691561 CATGTAGGTA
6691571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6691600 GTACTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6691798 original size:30 final size:31
Alignment explanation
Indices: 6691762--6691824 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
6691752 ACATTCAATC
*
6691762 AAGTTTTTGT-ATTTTTATTTTGAATTAAAT
1 AAGTTTTTGTCATTTTTATTTTGAATCAAAT
* *
6691792 AAGTTTTTTTCATTTTTATTTTGACTCAAAT
1 AAGTTTTTGTCATTTTTATTTTGAATCAAAT
6691823 AA
1 AA
6691825 ATCTTTATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 9 0.31
31 20 0.69
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (31 bp):
AAGTTTTTGTCATTTTTATTTTGAATCAAAT
Found at i:6692939 original size:61 final size:61
Alignment explanation
Indices: 6692867--6693023 Score: 240
Period size: 61 Copynumber: 2.7 Consensus size: 61
6692857 GATGAGGACA
* *
6692867 TCAAGGATTTGAGTGAGATTATGGTCTTGGGATTATGTGGCACCTAACATCCTCAGATCGC
1 TCAAGGATTTGAGTGAGATTATGGTCCTGGGATTATGTGGCACCTAACATCCTCACATCGC
6692928 TCAAGGATTTGAGTGAGATTATGGTCCTGGGATTATGTGGCACCTAACATCCTCACATCGC
1 TCAAGGATTTGAGTGAGATTATGGTCCTGGGATTATGTGGCACCTAACATCCTCACATCGC
6692989 TC-------T-AGTGAGATTATGGTCCTGGGATTATGTGGCAC
1 TCAAGGATTTGAGTGAGATTATGGTCCTGGGATTATGTGGCAC
6693024 TCACATCGCT
Statistics
Matches: 94, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
53 32 0.34
54 1 0.01
61 61 0.65
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (61 bp):
TCAAGGATTTGAGTGAGATTATGGTCCTGGGATTATGTGGCACCTAACATCCTCACATCGC
Found at i:6693042 original size:44 final size:44
Alignment explanation
Indices: 6692979--6693111 Score: 248
Period size: 44 Copynumber: 3.0 Consensus size: 44
6692969 ACCTAACATC
*
6692979 CTCACATCGCTCTAGTGAGATTATGGTCCTGGGATTATGTGGCA
1 CTCACATCGCTCTGGTGAGATTATGGTCCTGGGATTATGTGGCA
*
6693023 CTCACATCGCTCTGGTGAGATTATGGTCCTGGCATTATGTGGCA
1 CTCACATCGCTCTGGTGAGATTATGGTCCTGGGATTATGTGGCA
6693067 CTCACATCGCTCTGGTGAGATTATGGTCCTGGGATTATGTGGCA
1 CTCACATCGCTCTGGTGAGATTATGGTCCTGGGATTATGTGGCA
6693111 C
1 C
6693112 CTAACATTCC
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 86 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.32
Consensus pattern (44 bp):
CTCACATCGCTCTGGTGAGATTATGGTCCTGGGATTATGTGGCA
Found at i:6693387 original size:16 final size:16
Alignment explanation
Indices: 6693366--6693396 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6693356 CTATAATTGA
6693366 CTCAATGAAGATATGG
1 CTCAATGAAGATATGG
6693382 CTCAATGAAGATATG
1 CTCAATGAAGATATG
6693397 ACTAAACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (16 bp):
CTCAATGAAGATATGG
Found at i:6693461 original size:42 final size:42
Alignment explanation
Indices: 6693414--6693497 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
6693404 ATCAAAATGA
*
6693414 AATGAAAGAGGATTTGAGGCTTAGACCTGGCCACCTGTGCTC
1 AATGAAAGAGGATTTGAGGCTTAAACCTGGCCACCTGTGCTC
6693456 AATGAAAGAGGATTTGAGGCTTAAACCTGGCCACCTGTGCTC
1 AATGAAAGAGGATTTGAGGCTTAAACCTGGCCACCTGTGCTC
6693498 TTGTTTCAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (42 bp):
AATGAAAGAGGATTTGAGGCTTAAACCTGGCCACCTGTGCTC
Found at i:6695816 original size:4 final size:4
Alignment explanation
Indices: 6695783--6695831 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
6695773 TTCAATTTTA
* *
6695783 ATTT TTTT ATTT TTTT AATTT ATATT ATTT ATTT ATTT ATTT A-TT ATTT
1 ATTT ATTT ATTT ATTT -ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT
6695832 CTATTATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 3 0.08
4 28 0.74
5 7 0.18
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:6695830 original size:22 final size:21
Alignment explanation
Indices: 6695786--6695848 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
6695776 AATTTTAATT
*
6695786 TTTTTATTTTTTTAATTTA-TA
1 TTTTTATTTATTT-ATTTATTA
6695807 TTATTTATTTATTTATTTATTA
1 TT-TTTATTTATTTATTTATTA
* *
6695829 TTTCTATTATATTTACTTAT
1 TTTTTATT-TATTTATTTAT
6695849 ATGTTCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.33
22 24 0.67
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATTTATTTATTTATTA
Found at i:6695967 original size:26 final size:27
Alignment explanation
Indices: 6695918--6695974 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
6695908 TTTTATTACA
6695918 TCATATGTGAGTTGTATATTCTACTTG
1 TCATATGTGAGTTGTATATTCTACTTG
*
6695945 TCATATGTGA-TTTTATATTCTACTTG
1 TCATATGTGAGTTGTATATTCTACTTG
6695971 TCAT
1 TCAT
6695975 GTTTTTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (27 bp):
TCATATGTGAGTTGTATATTCTACTTG
Found at i:6700497 original size:1 final size:1
Alignment explanation
Indices: 6700491--6700521 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
6700481 TTATTCTCTT
6700491 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6700522 GCGCATGCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:6712884 original size:42 final size:42
Alignment explanation
Indices: 6712832--6712931 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
6712822 GGACAAAAAT
* * * *
6712832 AGAGGCCAAAGAAGGAATTGTGGAGGATAA-AA-AATTGGCTGA
1 AGAGACCAAAGAAGAAACTGTGCAGGA-AATAATAATT-GCTGA
*
6712874 AGAGACCAAAGAAGAAACTGTGCAGGAAATAATACTTGCTGA
1 AGAGACCAAAGAAGAAACTGTGCAGGAAATAATAATTGCTGA
*
6712916 AGAGACAAAAGAAGAA
1 AGAGACCAAAGAAGAA
6712932 GCTAAAGAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.04
42 45 0.90
43 3 0.06
ACGTcount: A:0.48, C:0.10, G:0.28, T:0.14
Consensus pattern (42 bp):
AGAGACCAAAGAAGAAACTGTGCAGGAAATAATAATTGCTGA
Found at i:6712972 original size:42 final size:42
Alignment explanation
Indices: 6712947--6713031 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
6712937 AGAAGATATC
*
6712947 GTGGAGGAT-AAAAACCTGGCTGAAGATGCAAAAGAACAAACT
1 GTGGAGGATGAAAAA-CTGGCTGAAGAAGCAAAAGAACAAACT
* * *
6712989 GTGGAGGGTGAAAAACTGGCTGAAG-AGAAAACAGAAGAAACT
1 GTGGAGGATGAAAAACTGGCTGAAGAAGCAAA-AGAACAAACT
6713031 G
1 G
6713032 CAAATGGTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 4 0.11
42 28 0.76
43 5 0.14
ACGTcount: A:0.45, C:0.12, G:0.31, T:0.13
Consensus pattern (42 bp):
GTGGAGGATGAAAAACTGGCTGAAGAAGCAAAAGAACAAACT
Found at i:6713011 original size:96 final size:93
Alignment explanation
Indices: 6712767--6713027 Score: 269
Period size: 96 Copynumber: 2.7 Consensus size: 93
6712757 TGAGAATGTG
* * *
6712767 AACCTGGCTGAAGAGACAAAAGAAAAAGCTGTGGAGGAAAACGAATTGGCTCAAGGGACAAAA-A
1 AACCTGGCTGAAGAGACAAAAGAAAAA-CTGTGGAGGAAAA--AACTGGCTGAAGAGACAAAAGA
* *
6712831 TAGAGGCCAAAGAAGGAATTGTGGAGGATAAA
63 -AGAAGCCAAAGAAGGAATCGTGGAGGATAAA
** * * *
6712863 AAATTGGCTGAAGAGACCAAAGAAGAAACTGTGCAGGAAATAATACTTGCTGAAGAGACAAAAGA
1 AACCTGGCTGAAGAGACAAAAGAA-AAACTGTGGAGGAAA-AA-ACTGGCTGAAGAGACAAAAGA
*
6712928 AGAAGCTAAAGAA-GATATCGTGGAGGATAAA
63 AGAAGCCAAAGAAGGA-ATCGTGGAGGATAAA
*
6712959 AACCTGGCTGAAGATG-CAAAAGAACAAACTGTGGAGGGTGAAAAACTGGCTGAAGAGA-AAACA
1 AACCTGGCTGAAGA-GACAAAAGAA-AAACTGTGGA-GG-AAAAAACTGGCTGAAGAGACAAA-A
6713022 GAAGAA
61 GAAGAA
6713028 ACTGCAAATG
Statistics
Matches: 138, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
95 6 0.04
96 120 0.87
97 10 0.07
98 2 0.01
ACGTcount: A:0.47, C:0.11, G:0.28, T:0.13
Consensus pattern (93 bp):
AACCTGGCTGAAGAGACAAAAGAAAAACTGTGGAGGAAAAAACTGGCTGAAGAGACAAAAGAAGA
AGCCAAAGAAGGAATCGTGGAGGATAAA
Found at i:6714934 original size:32 final size:32
Alignment explanation
Indices: 6714873--6714940 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 32
6714863 ATTAGATTAG
6714873 ATTTAAGATTAAAATTTTATTTAAATATTTTT
1 ATTTAAGATTAAAATTTTATTTAAATATTTTT
6714905 CATTTAA-ATT-AAATTTT-TTTAATATTATTTTT
1 -ATTTAAGATTAAAATTTTATTTAA-A-TATTTTT
6714937 ATTT
1 ATTT
6714941 TATAAATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 5 0.15
31 12 0.36
32 10 0.30
33 6 0.18
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (32 bp):
ATTTAAGATTAAAATTTTATTTAAATATTTTT
Found at i:6715047 original size:36 final size:36
Alignment explanation
Indices: 6714987--6715063 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
6714977 CAATCTTAAA
* *
6714987 TCTTACTCACTTGTTAAACCTAAACCCTAGCCTAGT
1 TCTTACTCACTTGTCAAACCTAAACCCTAACCTAGT
* * *
6715023 TCTTTCTCACTTGTCAAACGTAAACCTTAACCTAGT
1 TCTTACTCACTTGTCAAACCTAAACCCTAACCTAGT
*
6715059 CCTTA
1 TCTTA
6715064 TGTCACGGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.30, G:0.08, T:0.35
Consensus pattern (36 bp):
TCTTACTCACTTGTCAAACCTAAACCCTAACCTAGT
Found at i:6715387 original size:15 final size:13
Alignment explanation
Indices: 6715367--6715420 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
6715357 TATAGCTAAT
6715367 TTCCCTCCAAAACA
1 TTCCCTCCAAAA-A
6715381 GTTCCCTCCAAAAAAA
1 -TTCCCTCC--AAAAA
*
6715397 TTCCCTTCAAAAA
1 TTCCCTCCAAAAA
*
6715410 TTCCCTTCAAA
1 TTCCCTCCAAA
6715421 CATTTTTAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
13 16 0.44
15 15 0.42
16 1 0.03
17 4 0.11
ACGTcount: A:0.37, C:0.35, G:0.02, T:0.26
Consensus pattern (13 bp):
TTCCCTCCAAAAA
Found at i:6715410 original size:13 final size:13
Alignment explanation
Indices: 6715392--6715420 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6715382 TTCCCTCCAA
6715392 AAAAATTCCCTTC
1 AAAAATTCCCTTC
6715405 AAAAATTCCCTTC
1 AAAAATTCCCTTC
6715418 AAA
1 AAA
6715421 CATTTTTAGG
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:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATTCCCTTC
Found at i:6735995 original size:5 final size:5
Alignment explanation
Indices: 6735987--6736020 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
6735977 TAATATATTA
6735987 TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
6736021 ATTTGGGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:6741159 original size:5 final size:5
Alignment explanation
Indices: 6741149--6741194 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
6741139 ACGAGAAGGT
* * *
6741149 AAAGA AAAGA AAAAA AAAGA AAAAA AAAG- AGAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
6741195 TGAATAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
4 3 0.09
5 31 0.91
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:6750883 original size:2 final size:2
Alignment explanation
Indices: 6750876--6750906 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6750866 ACTGTACCTT
6750876 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 T
6750907 CTTTTAGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6751960 original size:2 final size:2
Alignment explanation
Indices: 6751953--6751985 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6751943 CTATTTTTCA
6751953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6751986 GAATAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6753799 original size:13 final size:13
Alignment explanation
Indices: 6753781--6753808 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6753771 ATAGTCCATT
6753781 AACTCTCACAAAA
1 AACTCTCACAAAA
6753794 AACTCTCACAAAA
1 AACTCTCACAAAA
6753807 AA
1 AA
6753809 GGCAACACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (13 bp):
AACTCTCACAAAA
Found at i:6757671 original size:2 final size:2
Alignment explanation
Indices: 6757659--6757695 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
6757649 TAATCGTTTG
6757659 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6757696 TTTATAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6766364 original size:18 final size:19
Alignment explanation
Indices: 6766343--6766383 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
6766333 TAAAAATAAA
*
6766343 ATTTTAAT-TAATTATTAT
1 ATTTTAATCAAATTATTAT
*
6766361 A-TTTAATCAAATTTTTAT
1 ATTTTAATCAAATTATTAT
6766379 ATTTT
1 ATTTT
6766384 TATTTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 6 0.32
18 10 0.53
19 3 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATCAAATTATTAT
Found at i:6766497 original size:28 final size:28
Alignment explanation
Indices: 6766461--6766516 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
6766451 GATATTAACA
6766461 TGTTATAATAGAA-AATATTGTTATATAT
1 TGTTATAATAGAATAATATT-TTATATAT
* * *
6766489 TGTTGTAATATAATAATATTTTTTATAT
1 TGTTATAATAGAATAATATTTTATATAT
6766517 GAAATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (28 bp):
TGTTATAATAGAATAATATTTTATATAT
Done.