Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 18 of 103
Found at i:6434650 original size:17 final size:17
Alignment explanation
Indices: 6434628--6434664 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6434618 GCTATTATTA
*
6434628 GGTCCAATTTTTTGTTG
1 GGTCCAATTTTCTGTTG
6434645 GGTCCAATTTTCTGTTG
1 GGTCCAATTTTCTGTTG
6434662 GGT
1 GGT
6434665 TAAAGCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.14, G:0.27, T:0.49
Consensus pattern (17 bp):
GGTCCAATTTTCTGTTG
Found at i:6438037 original size:29 final size:28
Alignment explanation
Indices: 6438003--6438074 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
6437993 AAGTTACATG
6438003 CCATGTTTAAAAAACAATATTGTTACACA
1 CCATGTTTAAAAAA-AATATTGTTACACA
* *
6438032 CCATG-TTCAAAAAAATATTGTTACACG
1 CCATGTTTAAAAAAAATATTGTTACACA
* *
6438059 CTATGTTGAAAAAAAA
1 CCATGTTTAAAAAAAA
6438075 GTTGTTAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 17 0.46
28 15 0.41
29 5 0.14
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (28 bp):
CCATGTTTAAAAAAAATATTGTTACACA
Found at i:6438046 original size:154 final size:154
Alignment explanation
Indices: 6437881--6438196 Score: 406
Period size: 153 Copynumber: 2.1 Consensus size: 154
6437871 CAAGTGCATG
* ** * *
6437881 TGTTCAAAAAAAATGTTGTTACATTCCATGTT-AAAAAAAAATTGTTGCACGTCATGTTTAAGGT
1 TGTTCAAAAAAAATATTGTTACACGCCATGTTGAAAAAAAAATTGTT-AACGCCATGTTTAAGGT
*
6437945 GTTTAACTCGAAGAGTTTATGTCATAGTAAAATACAAAGATAGAGACCAAGTTACATGCC-ATGT
65 ATTTAACTCGAAGAGTTTATGTCATAGTAAAATACAAAGATAGAGACCAAGTTACATGCCAATGT
* *
6438009 TTAAAAAACAATA-TTGTTACACACCA
130 TGAAAAAA-AA-ACTTGTTACACAACA
* * *
6438035 TGTTC-AAAAAAATATTGTTACACGCTATGTTGAAAAAAAAGTTGTTAATGCCATGTTTAAGGTA
1 TGTTCAAAAAAAATATTGTTACACGCCATGTTGAAAAAAAAATTGTTAACGCCATGTTTAAGGTA
* * * * * *
6438099 TTTGATTCTAAGAGTTTATGTCTTAGTGAAATACAAAGATAGAGACCAAGTTATATGCCAATGTT
66 TTTAACTCGAAGAGTTTATGTCATAGTAAAATACAAAGATAGAGACCAAGTTACATGCCAATGTT
*
6438164 GAAAAAAAAACTTGTTACGCAACA
131 GAAAAAAAAACTTGTTACACAACA
*
6438188 TGTTGAAAA
1 TGTTCAAAA
6438197 TATGAGTTAT
Statistics
Matches: 139, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
152 1 0.01
153 106 0.76
154 32 0.23
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (154 bp):
TGTTCAAAAAAAATATTGTTACACGCCATGTTGAAAAAAAAATTGTTAACGCCATGTTTAAGGTA
TTTAACTCGAAGAGTTTATGTCATAGTAAAATACAAAGATAGAGACCAAGTTACATGCCAATGTT
GAAAAAAAAACTTGTTACACAACA
Found at i:6438079 original size:27 final size:26
Alignment explanation
Indices: 6437995--6438091 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 26
6437985 TAGAGACCAA
* *
6437995 GTTACATGCCATGTTTAAAAAACAATATT
1 GTTACACGCCATG-TTCAAAAA-AA-ATT
*
6438024 GTTACACACCATGTTCAAAAAAATATT
1 GTTACACGCCATGTTCAAAAAAA-ATT
* *
6438051 GTTACACGCTATGTTGAAAAAAAAGTT
1 GTTACACGCCATGTTCAAAAAAAA-TT
*
6438078 GTTA-ATGCCATGTT
1 GTTACACGCCATGTT
6438092 TAAGGTATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
26 9 0.15
27 32 0.54
28 7 0.12
29 11 0.19
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (26 bp):
GTTACACGCCATGTTCAAAAAAAATT
Found at i:6438180 original size:126 final size:127
Alignment explanation
Indices: 6438034--6438275 Score: 285
Period size: 128 Copynumber: 1.9 Consensus size: 127
6438024 GTTACACACC
* * * ** *
6438034 ATGTTCAAAAAAATATTGTTACAC-GCTATGTTGAAAA-AAAAGTTGTTA-ATGCCATGTTTAAG
1 ATGTTCAAAAAAAAATTGTTACACAAC-ATGTTGAAAATAAAAGTTATTACACACCATATTTAAG
* * *
6438096 GTATTTGATTCTAAGAGTTTATG-TCTTAGTGAAATACAAAGATAGAGACCAAGTTATATGCCA
65 GTATTTAACTCCAAGAGTTTATGTTC-TAGTGAAATACAAAGATAGAGACCAAGTTATATGCCA
* * **
6438159 ATGTTGAAAAAAAAACTTGTTACGCAACATGTTGAAAATATGAGTTATTACACACCATATTTAAG
1 ATGTTCAAAAAAAAA-TTGTTACACAACATGTTGAAAATAAAAGTTATTACACACCATATTTAAG
* * *
6438224 GTGTTTAACTCCATGAGTTTATGTTCTAGTGAAATACAAATATAGAGACCAA
65 GTATTTAACTCCAAGAGTTTATGTTCTAGTGAAATACAAAGATAGAGACCAA
6438276 ATACATTTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
125 13 0.14
126 18 0.19
127 9 0.09
128 54 0.56
129 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (127 bp):
ATGTTCAAAAAAAAATTGTTACACAACATGTTGAAAATAAAAGTTATTACACACCATATTTAAGG
TATTTAACTCCAAGAGTTTATGTTCTAGTGAAATACAAAGATAGAGACCAAGTTATATGCCA
Found at i:6446716 original size:34 final size:34
Alignment explanation
Indices: 6446673--6446737 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
6446663 CTTGAGACAC
6446673 AAGTGGGCCAACTTGCTAATGCTCTAAATAATAG
1 AAGTGGGCCAACTTGCTAATGCTCTAAATAATAG
*
6446707 AAGTGGGCCAACTTGCTAATGTTCTAAATAA
1 AAGTGGGCCAACTTGCTAATGCTCTAAATAA
6446738 CAGACCTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (34 bp):
AAGTGGGCCAACTTGCTAATGCTCTAAATAATAG
Found at i:6454317 original size:17 final size:20
Alignment explanation
Indices: 6454295--6454334 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
6454285 CTTTTGTAGG
6454295 TTTAATGG-AGGA-AG-AAT
1 TTTAATGGAAGGAGAGCAAT
6454312 TTTAATGGAAGGAGAGCAAT
1 TTTAATGGAAGGAGAGCAAT
6454332 TTT
1 TTT
6454335 GAGGTGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 2 0.10
20 6 0.30
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.33
Consensus pattern (20 bp):
TTTAATGGAAGGAGAGCAAT
Found at i:6459832 original size:43 final size:42
Alignment explanation
Indices: 6459772--6459907 Score: 164
Period size: 43 Copynumber: 3.2 Consensus size: 42
6459762 ACCATCCCAC
* *
6459772 CATCATCAACTCATGTGCACTCCCTACTCGCACATAGTTGGGT
1 CATCATTAGCTCATGTGCACTCCC-ACTCGCACATAGTTGGGT
* * *
6459815 CATCATTAGCTCCTGTGCACTCCCATTCTACACATAGTTGGGT
1 CATCATTAGCTCATGTGCACTCCCACTC-GCACATAGTTGGGT
* * * **
6459858 CATCATCAGCTCATATGCACTCCCACACGCACATAGCCGGGT
1 CATCATTAGCTCATGTGCACTCCCACTCGCACATAGTTGGGT
6459900 CATCATTA
1 CATCATTA
6459908 TCACACAAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
42 21 0.27
43 57 0.73
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (42 bp):
CATCATTAGCTCATGTGCACTCCCACTCGCACATAGTTGGGT
Found at i:6480002 original size:22 final size:22
Alignment explanation
Indices: 6479968--6480023 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
6479958 GCAGTACTGG
** *
6479968 TTTTTAAACATTGTGTCACCGA
1 TTTTTAAGTATTGTGACACCGA
* *
6479990 TTTTTAAGTATTGTGAGACTGA
1 TTTTTAAGTATTGTGACACCGA
6480012 TTTTTAAGTATT
1 TTTTTAAGTATT
6480024 ACGTGATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (22 bp):
TTTTTAAGTATTGTGACACCGA
Found at i:6480139 original size:22 final size:23
Alignment explanation
Indices: 6480109--6480162 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
6480099 TTAGCAACAT
6480109 CTAAGTCACACAATACC-TAAAAA
1 CTAA-TCACACAATACCTTAAAAA
* **
6480132 CTAATCACGCAATACCTTAGTAA
1 CTAATCACACAATACCTTAAAAA
6480155 CTAATCAC
1 CTAATCAC
6480163 GAAATGCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (23 bp):
CTAATCACACAATACCTTAAAAA
Found at i:6480191 original size:23 final size:23
Alignment explanation
Indices: 6480130--6480180 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
6480120 AATACCTAAA
* * *
6480130 AACTAATCACGCAATACCTTAGT
1 AACTAATCACGAAATGCCTTACT
6480153 AACTAATCACGAAATGCCTTACT
1 AACTAATCACGAAATGCCTTACT
6480176 AACTA
1 AACTA
6480181 GTCATGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.25
Consensus pattern (23 bp):
AACTAATCACGAAATGCCTTACT
Found at i:6480256 original size:22 final size:22
Alignment explanation
Indices: 6480213--6480295 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
6480203 AATCATGCTT
* *
6480213 TACCTAAAAATCAGTCA-ACAA
1 TACCTAAAAATTAGTCACGCAA
6480234 TACCTAAAAATTAGTCACGCAA
1 TACCTAAAAATTAGTCACGCAA
* * *
6480256 TGCTTAAAAATTAATCACGCAA
1 TACCTAAAAATTAGTCACGCAA
* *
6480278 TACTTAAAAACTAGTCAC
1 TACCTAAAAATTAGTCAC
6480296 ATAATGTCCA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 16 0.30
22 37 0.70
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (22 bp):
TACCTAAAAATTAGTCACGCAA
Found at i:6480447 original size:9 final size:9
Alignment explanation
Indices: 6480433--6480460 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6480423 CTTGACGAAG
6480433 AATGTTCAA
1 AATGTTCAA
6480442 AATGTTCAA
1 AATGTTCAA
6480451 AATGTTCAA
1 AATGTTCAA
6480460 A
1 A
6480461 TATTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATGTTCAA
Found at i:6480508 original size:60 final size:60
Alignment explanation
Indices: 6480438--6480565 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
6480428 CGAAGAATGT
* * * *
6480438 TCAAAATGTTCAAAATGTTCAAATATTTTTATTCATATATCAAAAATCACTCAAAAATAC
1 TCAAAATGTTCAAAACGCTCAAAGATTTTTATTCATATATCAAAAATCAATCAAAAATAC
* * * * * * *
6480498 TTAAAATGTTCAAAACGCTCAAAGATTTTTCTTCGTGTATTAAAAATCAATCCAAAATGC
1 TCAAAATGTTCAAAACGCTCAAAGATTTTTATTCATATATCAAAAATCAATCAAAAATAC
6480558 TCAAAATG
1 TCAAAATG
6480566 CGTAAAGTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.34
Consensus pattern (60 bp):
TCAAAATGTTCAAAACGCTCAAAGATTTTTATTCATATATCAAAAATCAATCAAAAATAC
Found at i:6480695 original size:15 final size:16
Alignment explanation
Indices: 6480675--6480710 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
6480665 ATATAGGTCG
6480675 ATTTTA-TTAAAATTA
1 ATTTTATTTAAAATTA
6480690 ATTTTATTTAAAATTA
1 ATTTTATTTAAAATTA
6480706 ATTTT
1 ATTTT
6480711 TTTGACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTATTTAAAATTA
Found at i:6482564 original size:19 final size:18
Alignment explanation
Indices: 6482525--6482576 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
6482515 GCCTCACTTA
6482525 ATTTTAATTT-T-TTTAT
1 ATTTTAATTTATATTTAT
*
6482541 TTTTTCAATTTATATTTAT
1 ATTTT-AATTTATATTTAT
*
6482560 ATTTTTTATTTATATTT
1 A-TTTTAATTTATATTT
6482577 TTCTATACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.14
17 5 0.17
18 1 0.03
19 15 0.52
20 4 0.14
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTAATTTATATTTAT
Found at i:6482569 original size:13 final size:13
Alignment explanation
Indices: 6482553--6482578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6482543 TTTCAATTTA
6482553 TATTTATATTTTT
1 TATTTATATTTTT
6482566 TATTTATATTTTT
1 TATTTATATTTTT
6482579 CTATACTATT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTATATTTTT
Found at i:6486414 original size:2 final size:2
Alignment explanation
Indices: 6486407--6486440 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6486397 ATTAATCCCA
6486407 AT AT 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
6486441 GTTCATGGTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6486805 original size:4 final size:4
Alignment explanation
Indices: 6486796--6486826 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
6486786 AAAGGAGTAT
6486796 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
6486827 TATATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:6488960 original size:35 final size:35
Alignment explanation
Indices: 6488904--6489002 Score: 171
Period size: 35 Copynumber: 2.8 Consensus size: 35
6488894 TGTGCAGTGA
* *
6488904 GAGTTAAAGCTTGGGTATTTGCCGCCGGTTAGGAG
1 GAGTAAAAGCTTGGGTGTTTGCCGCCGGTTAGGAG
*
6488939 GGGTAAAAGCTTGGGTGTTTGCCGCCGGTTAGGAG
1 GAGTAAAAGCTTGGGTGTTTGCCGCCGGTTAGGAG
6488974 GAGTAAAAGCTTGGGTGTTTGCCGCCGGT
1 GAGTAAAAGCTTGGGTGTTTGCCGCCGGT
6489003 GAGAATGGGT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.18, C:0.15, G:0.39, T:0.27
Consensus pattern (35 bp):
GAGTAAAAGCTTGGGTGTTTGCCGCCGGTTAGGAG
Found at i:6491543 original size:2 final size:2
Alignment explanation
Indices: 6491536--6491571 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6491526 NNNNNNNNNN
6491536 AT AT AT 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
6491572 TCACTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6491867 original size:29 final size:29
Alignment explanation
Indices: 6491808--6491864 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
6491798 AAAACCTTAT
*
6491808 TTGTTTTAAAATAAAAAAAAATTAATTAA
1 TTGTTATAAAATAAAAAAAAATTAATTAA
* * *
6491837 TTGTTATAAAA-AATAAAAATTTATTTAA
1 TTGTTATAAAATAAAAAAAAATTAATTAA
6491865 ATTTTCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (29 bp):
TTGTTATAAAATAAAAAAAAATTAATTAA
Found at i:6505842 original size:168 final size:167
Alignment explanation
Indices: 6505563--6505899 Score: 665
Period size: 168 Copynumber: 2.0 Consensus size: 167
6505553 ACCATTATGT
6505563 TTTATATTGAGTAATTTTTAAACATTAATTTATTGATAAAATTCTAAATATTTAAAATTTAAATT
1 TTTATATTGAGTAATTTTTAAACATTAATTTATTGATAAAATTCTAAATATTTAAAATTTAAATT
6505628 TGTGTTTGTAACGACCCCTCCTCAGTCGCTACCGACGTCCGAGACCTCCGGGAGAGCTCGTCAAG
66 TGTGTTTGTAACGACCCCTCCTCAGTCGCTACCGACGTCCGAGACCTCCGGGAGAGCTCGTCAAG
6505693 TCCCAAACAAGCCTGAAAGAAATTTCTCAATAACTCA
131 TCCCAAACAAGCCTGAAAGAAATTTCTCAATAACTCA
6505730 TNTTATATTGAGTAATTTTTAAACATTAATTTATTGATAAAATTCTAAATATTTAAAATTTAAAT
1 T-TTATATTGAGTAATTTTTAAACATTAATTTATTGATAAAATTCTAAATATTTAAAATTTAAAT
6505795 TTGTGTTTGTAACGACCCCTCCTCAGTCGCTACCGACGTCCGAGACCTCCGGGAGAGCTCGTCAA
65 TTGTGTTTGTAACGACCCCTCCTCAGTCGCTACCGACGTCCGAGACCTCCGGGAGAGCTCGTCAA
6505860 GTCCCAAACAAGCCTGAAAGAAATTTCTCAATAACTCA
130 GTCCCAAACAAGCCTGAAAGAAATTTCTCAATAACTCA
6505898 TT
1 TT
6505900 GTACACTTTT
Statistics
Matches: 169, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
167 2 0.01
168 167 0.99
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (167 bp):
TTTATATTGAGTAATTTTTAAACATTAATTTATTGATAAAATTCTAAATATTTAAAATTTAAATT
TGTGTTTGTAACGACCCCTCCTCAGTCGCTACCGACGTCCGAGACCTCCGGGAGAGCTCGTCAAG
TCCCAAACAAGCCTGAAAGAAATTTCTCAATAACTCA
Found at i:6507657 original size:35 final size:35
Alignment explanation
Indices: 6507603--6507745 Score: 137
Period size: 35 Copynumber: 4.0 Consensus size: 35
6507593 TTTCCTCCTG
**
6507603 AATCGGGCAGCAAAACTCTTTCTTTTTCCCTCTCAA
1 AATC-GGCAGCAAGTCTCTTTCTTTTTCCCTCTCAA
* *
6507639 AA-CTGGCAGCAAGTCTCTTTCTTTTCCCCTTTCAA
1 AATC-GGCAGCAAGTCTCTTTCTTTTTCCCTCTCAA
* ** *
6507674 AATCGGCAGCAA-TTTCCCTCATTTCTCCCTCTCAA
1 AATCGGCAGCAAGTCTCTTTC-TTTTTCCCTCTCAA
* * *
6507709 AATCGACAGCAAGTTCTCTTCCTTTTTCCCTCACAA
1 AATCGGCAGCAAG-TCTCTTTCTTTTTCCCTCTCAA
6507745 A
1 A
6507746 CCAGTAGCCA
Statistics
Matches: 85, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
34 5 0.06
35 60 0.71
36 16 0.19
37 4 0.05
ACGTcount: A:0.24, C:0.33, G:0.10, T:0.34
Consensus pattern (35 bp):
AATCGGCAGCAAGTCTCTTTCTTTTTCCCTCTCAA
Found at i:6509156 original size:175 final size:175
Alignment explanation
Indices: 6508860--6509207 Score: 486
Period size: 175 Copynumber: 2.0 Consensus size: 175
6508850 ATATTCTCCT
* *
6508860 CTCCCTTCATTTTCTTCTTTCCCTTTCTCTCTCGACTCGCAGCCACCCTCTGACTTCTTTCTAAA
1 CTCCCTTCATTTTCTTATTTCCCTTTCTCTCTCGACTCGCAGCCACCCTCTCACTTCTTTCTAAA
*
6508925 CTTTTCCCTCCGTCAGCAGCTTTCTCATTCTCTCTCACCTTCCCCTCCACCGGTGGCTTGAAGCT
66 CTTTTCCCTCCGTCAGCAGCTTTCTCATTCTCTCTCACCTTCCCCGCCACCGGTGGCTTGAAGCT
*
6508990 CGGCCACACAAAACCCTAAATATCTCTTCCCTCCACCGACAATTC
131 CGACCACACAAAACCCTAAATATCTCTTCCCTCCACCGACAATTC
* * *
6509035 CTCCCTTCATTTTCTTATTTCCCTTTCTCTCTCTAGC-CGCGGCCTCCCTCTCACTT-TTCTCTA
1 CTCCCTTCATTTTCTTATTTCCCTTTCTCTCTCGA-CTCGCAGCCACCCTCTCACTTCTT-TCTA
* * * * * * *
6509098 AACTTTTCCCTTCGTCGGCCGCTTTGTC-TATCTTTGTCACCTTCCCCGCCATCGGTGGCTTGAA
64 AACTTTTCCCTCCGTCAGCAGCTTTCTCAT-TCTCTCTCACCTTCCCCGCCACCGGTGGCTTGAA
* * * *
6509162 GCTTGATCACCCAAAACCCTAAATATCTCTTCCTTCCACCGACAAT
128 GCTCGACCACACAAAACCCTAAATATCTCTTCCCTCCACCGACAAT
6509208 CCCTAGATCT
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
174 3 0.02
175 148 0.97
176 1 0.01
ACGTcount: A:0.16, C:0.39, G:0.10, T:0.35
Consensus pattern (175 bp):
CTCCCTTCATTTTCTTATTTCCCTTTCTCTCTCGACTCGCAGCCACCCTCTCACTTCTTTCTAAA
CTTTTCCCTCCGTCAGCAGCTTTCTCATTCTCTCTCACCTTCCCCGCCACCGGTGGCTTGAAGCT
CGACCACACAAAACCCTAAATATCTCTTCCCTCCACCGACAATTC
Found at i:6514160 original size:5 final size:5
Alignment explanation
Indices: 6514124--6514156 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
6514114 TGACCCCTAA
*
6514124 TTAAG TTAAG TTAAG TTAAG TTAAG TTAGG TTA
1 TTAAG TTAAG TTAAG TTAAG TTAAG TTAAG TTA
6514157 GGTTGAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (5 bp):
TTAAG
Found at i:6523733 original size:21 final size:20
Alignment explanation
Indices: 6523703--6523741 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
6523693 GGTTTTTCTC
6523703 TTTTCTTCTTTTACTCTCTA
1 TTTTCTTCTTTTACTCTCTA
*
6523723 TTTTCTCTCTTTTTCTCTC
1 TTTTCT-TCTTTTACTCTC
6523742 CTTATGGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCTTCTTTTACTCTCTA
Found at i:6523738 original size:10 final size:10
Alignment explanation
Indices: 6523695--6523741 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
6523685 TTTCCTTTGG
6523695 TTTT-TCTC-
1 TTTTCTCTCT
6523703 TTTTCT-TCT
1 TTTTCTCTCT
*
6523712 TTTACTCTCT
1 TTTTCTCTCT
6523722 ATTTTCTCTCT
1 -TTTTCTCTCT
6523733 TTTTCTCTC
1 TTTTCTCTC
6523742 CTTATGGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 6 0.18
9 6 0.18
10 12 0.36
11 9 0.27
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTCTCTCT
Found at i:6525790 original size:26 final size:25
Alignment explanation
Indices: 6525739--6525796 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
6525729 AAAATTTTAA
*
6525739 AAAATTTACAATTTTTGTGTTCTAT
1 AAAATTTACAATTTTTGTGTTATAT
* * *
6525764 AAAATTTACTATTTTCTTTTTTATAT
1 AAAATTTACAATTTT-TGTGTTATAT
*
6525790 AATATTT
1 AAAATTT
6525797 TTTTCAGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (25 bp):
AAAATTTACAATTTTTGTGTTATAT
Found at i:6529932 original size:30 final size:30
Alignment explanation
Indices: 6529896--6529963 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
6529886 TTTGATTGGT
6529896 GATGAAGACA-ATGACATGCAAAGAGATGAA
1 GATGAAGA-AGATGACATGCAAAGAGATGAA
* *
6529926 GATGAAGAAGATGACATGGAAGGAGATGAA
1 GATGAAGAAGATGACATGCAAAGAGATGAA
*
6529956 AATGAAGA
1 GATGAAGA
6529964 TGACGATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.50, C:0.06, G:0.31, T:0.13
Consensus pattern (30 bp):
GATGAAGAAGATGACATGCAAAGAGATGAA
Found at i:6529973 original size:18 final size:18
Alignment explanation
Indices: 6529950--6529984 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6529940 CATGGAAGGA
6529950 GATGAA-AATGAAGATGAC
1 GATGAAGAA-GAAGATGAC
6529968 GATGAAGAAGAAGATGA
1 GATGAAGAAGAAGATGA
6529985 ACTTGAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.51, C:0.03, G:0.31, T:0.14
Consensus pattern (18 bp):
GATGAAGAAGAAGATGAC
Found at i:6530726 original size:19 final size:20
Alignment explanation
Indices: 6530681--6530718 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6530671 AAGATATTTC
6530681 TAATATTTGTTAATGAAATTG
1 TAATATTTGTTAA-GAAATTG
*
6530702 TTATATTTGTTAA-AAAT
1 TAATATTTGTTAAGAAAT
6530719 ATTAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
21 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
TAATATTTGTTAAGAAATTG
Found at i:6537139 original size:20 final size:20
Alignment explanation
Indices: 6537114--6537159 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
6537104 TTTTGACCCC
6537114 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
6537134 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
6537154 ATTTGA
1 ATTTGA
6537160 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:6537235 original size:28 final size:27
Alignment explanation
Indices: 6537204--6537256 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
6537194 TTTGGAGTAT
*
6537204 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
6537232 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
6537257 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:6537262 original size:28 final size:28
Alignment explanation
Indices: 6537204--6537262 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
6537194 TTTGGAGTAT
* *
6537204 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
6537232 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
6537260 AGG
1 AGG
6537263 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:6545251 original size:22 final size:22
Alignment explanation
Indices: 6545225--6545268 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6545215 TTTAAAACAA
*
6545225 CTTTAAAACTAAAAACTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
*
6545247 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
6545269 ACCAATCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:6554184 original size:35 final size:35
Alignment explanation
Indices: 6554128--6554198 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
6554118 TTAGTTGTTG
* * * *
6554128 GGTTTTGGTTGATCCTGGTAAAAACCATTGTGAAA
1 GGTTTTGGCTGAGCCTAGTAAAAACCATTGTAAAA
*
6554163 GGTTTTGGCTGAGCCTAGTAAAAGCCATTGTAAAA
1 GGTTTTGGCTGAGCCTAGTAAAAACCATTGTAAAA
6554198 G
1 G
6554199 CTTGGTGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.31
Consensus pattern (35 bp):
GGTTTTGGCTGAGCCTAGTAAAAACCATTGTAAAA
Found at i:6562149 original size:17 final size:17
Alignment explanation
Indices: 6562116--6562150 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6562106 AATAAAATAC
*
6562116 GCACACACTAAGGGGGA
1 GCACACACTAAGAGGGA
*
6562133 GCACACACTTAGAGGGA
1 GCACACACTAAGAGGGA
6562150 G
1 G
6562151 GAAAACCTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.23, G:0.34, T:0.09
Consensus pattern (17 bp):
GCACACACTAAGAGGGA
Found at i:6565285 original size:21 final size:20
Alignment explanation
Indices: 6565267--6565308 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
6565257 ATAAATTTAC
*
6565267 TTAAGATTTGATTTGATTTGA
1 TTAAAATTT-ATTTGATTTGA
6565288 TTAAAATTTATTTGAATTTGA
1 TTAAAATTTATTTG-ATTTGA
6565309 ATATCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (20 bp):
TTAAAATTTATTTGATTTGA
Found at i:6567751 original size:15 final size:14
Alignment explanation
Indices: 6567722--6567755 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6567712 TTTCCGACGG
6567722 ATTTCCAACAGAAA
1 ATTTCCAACAGAAA
*
6567736 ATTTTCAACAGAAA
1 ATTTCCAACAGAAA
*
6567750 AATTCC
1 ATTTCC
6567756 GTTGAAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (14 bp):
ATTTCCAACAGAAA
Found at i:6567991 original size:101 final size:102
Alignment explanation
Indices: 6567812--6568033 Score: 279
Period size: 101 Copynumber: 2.2 Consensus size: 102
6567802 CTGACGGAAT
* *
6567812 TTCCAACGGAAAAA-TTTCCGTTGGAAAAATTTTTGATGAGCGAAAAAAAAACAGGAGACCACCA
1 TTCCAAC-GAAAAATTTTCTGTTGGAAAAATTTTTGAGGAGCGAAAAAAAAACAGGAGACCACCA
* * * * * * *
6567876 TTTCTGATGGAATTTTTAACGGAATTTTTGTTGAAAAA
65 TTTCAGACGAAATTTTCAACGAAACTTCTGTTGAAAAA
* * *
6567914 TTCCAACGCAAAATTTTCTGTTGGAAAAATTTTTG-GGAAGC-AAAAAAAGACAGGAGACTACCA
1 TTCCAACGAAAAATTTTCTGTTGGAAAAATTTTTGAGG-AGCGAAAAAAAAACAGGAGACCACCA
* *
6567977 TTTCAGACGAAATTTTCAACTAAACTTCTGTTGAAAAT
65 TTTCAGACGAAATTTTCAACGAAACTTCTGTTGAAAAA
6568015 TTCCAACGAAAAATTTTCT
1 TTCCAACGAAAAATTTTCT
6568034 ATTAGAAATC
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
101 73 0.71
102 30 0.29
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (102 bp):
TTCCAACGAAAAATTTTCTGTTGGAAAAATTTTTGAGGAGCGAAAAAAAAACAGGAGACCACCAT
TTCAGACGAAATTTTCAACGAAACTTCTGTTGAAAAA
Found at i:6569522 original size:21 final size:20
Alignment explanation
Indices: 6569470--6569523 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
6569460 TTACTTTTTC
*
6569470 TTTTATTTTATTATCATACT
1 TTTTATTTTTTTATCATACT
* **
6569490 TTTATATATTTTTATTTTACT
1 TTT-TATTTTTTTATCATACT
6569511 TGTTTATTTTTTT
1 T-TTTATTTTTTT
6569524 TAATTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 3 0.11
21 22 0.81
22 2 0.07
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTATTTTTTTATCATACT
Found at i:6570560 original size:13 final size:12
Alignment explanation
Indices: 6570541--6570599 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
6570531 AATTTTAATC
6570541 TTTATTATATTA
1 TTTATTATATTA
*
6570553 TTTGATTATTTTA
1 TTT-ATTATATTA
6570566 TTTATT-TATTTA
1 TTTATTATA-TTA
6570578 TTTTTATTATATATA
1 --TTTATTATAT-TA
6570593 TTT-TTAT
1 TTTATTAT
6570600 TTGGGGAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
11 1 0.03
12 13 0.33
13 14 0.36
14 7 0.18
15 4 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTATTATATTA
Found at i:6570596 original size:15 final size:14
Alignment explanation
Indices: 6570566--6570601 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
6570556 GATTATTTTA
*
6570566 TTTATTTATTTATT
1 TTTATTTATATATT
6570580 TTTATTATATATATT
1 TTTATT-TATATATT
6570595 TTTATTT
1 TTTATTT
6570602 GGGGAATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTATTTATATATT
Found at i:6570598 original size:21 final size:20
Alignment explanation
Indices: 6570541--6570601 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
6570531 AATTTTAATC
6570541 TTTATTATATTATTTGATTA-T
1 TTTATTATATTATTT--TTATT
*
6570562 TTTATT-TATT-TATTTATT
1 TTTATTATATTATTTTTATT
6570580 TTTATTATATATATTTTTATT
1 TTTATTATAT-TATTTTTATT
6570601 T
1 T
6570602 GGGGAATAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 5 0.15
20 5 0.15
21 14 0.41
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATTATATTATTTTTATT
Found at i:6571086 original size:23 final size:23
Alignment explanation
Indices: 6571056--6571101 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6571046 TGATGCATAA
* *
6571056 TCTCGTTACTGCTGCTTTTGATT
1 TCTCGTTACTGATGCCTTTGATT
6571079 TCTCGTTACTGATGCCTTTGATT
1 TCTCGTTACTGATGCCTTTGATT
6571102 ATAGCTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.22, G:0.17, T:0.50
Consensus pattern (23 bp):
TCTCGTTACTGATGCCTTTGATT
Found at i:6571250 original size:3 final size:3
Alignment explanation
Indices: 6571242--6571267 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6571232 TAAACCAACG
6571242 GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GC
6571268 CCAAGCATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.35, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:6578781 original size:28 final size:28
Alignment explanation
Indices: 6578750--6578805 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
6578740 AAGAGTTGGC
6578750 TGATTTTTTGCCAAGTATCAAATGAGGT
1 TGATTTTTTGCCAAGTATCAAATGAGGT
6578778 TGATTTTTTGCCAAGTATCAAATGAGGT
1 TGATTTTTTGCCAAGTATCAAATGAGGT
6578806 GCTACAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
TGATTTTTTGCCAAGTATCAAATGAGGT
Found at i:6583124 original size:3 final size:3
Alignment explanation
Indices: 6583116--6583142 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6583106 AAAGAAGTTC
6583116 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
6583143 TAGAAGTCTT
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:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:6586358 original size:45 final size:44
Alignment explanation
Indices: 6586281--6586370 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
6586271 GATAACTTGA
* **
6586281 AGTCACACAATCAACCAAGGATGAAAAATTGAATTAATCTTCAT
1 AGTCACAAAATCAACCAAGGATGAAAAATTGAACCAATCTTCAT
* *
6586325 AGTCATCAAAATCAACCAAGGAT-AAGTAGTTGAACCAATCTTCAT
1 AGTCA-CAAAATCAACCAAGGATGAA-AAATTGAACCAATCTTCAT
6586370 A
1 A
6586371 ATCGTAACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
44 7 0.18
45 32 0.82
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.24
Consensus pattern (44 bp):
AGTCACAAAATCAACCAAGGATGAAAAATTGAACCAATCTTCAT
Found at i:6604111 original size:44 final size:44
Alignment explanation
Indices: 6604063--6604154 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
6604053 TGGTGAATTC
6604063 AAGCCAAAGGTGGAGATTTGTTGTGATAATCTTGAATTCTAAGT
1 AAGCCAAAGGTGGAGATTTGTTGTGATAATCTTGAATTCTAAGT
*
6604107 AAGCCAAAGGTGGAGATTTGTTGTGATAGTCTTGAATTCTAAGT
1 AAGCCAAAGGTGGAGATTTGTTGTGATAATCTTGAATTCTAAGT
6604151 AAGC
1 AAGC
6604155 TAGGATATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.33
Consensus pattern (44 bp):
AAGCCAAAGGTGGAGATTTGTTGTGATAATCTTGAATTCTAAGT
Found at i:6617067 original size:15 final size:15
Alignment explanation
Indices: 6617018--6617068 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
6617008 TTTAAAGATC
*
6617018 AAAGATTTTGATTTT
1 AAAGTTTTTGATTTT
* * *
6617033 AAAGCTTTGGATTTC
1 AAAGTTTTTGATTTT
6617048 AAAGTTTTTGATTTT
1 AAAGTTTTTGATTTT
6617063 AAAGTT
1 AAAGTT
6617069 GTTTTAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (15 bp):
AAAGTTTTTGATTTT
Found at i:6617113 original size:5 final size:5
Alignment explanation
Indices: 6617103--6617142 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
6617093 TGCGTGGCCC
* *
6617103 AAGTT AAGTT AAGTT AAG-T AAGTC AAGTT AAGTT AGGTT A
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT A
6617143 TATCGAGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (5 bp):
AAGTT
Found at i:6619572 original size:28 final size:29
Alignment explanation
Indices: 6619531--6619590 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
6619521 GTCTATGGGC
*
6619531 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCAGTTTTAGGGGGCAAAAATGT
* * *
6619559 AATTTTTGATTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAGTTTTA-GGGGGCAAAAATGT
6619589 AA
1 AA
6619591 ATATCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (29 bp):
AATTTTTCAGTTTTAGGGGGCAAAAATGT
Found at i:6627860 original size:38 final size:38
Alignment explanation
Indices: 6627809--6627886 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
6627799 TACATTACCT
6627809 TAGTGTATCGATACATTTATTCAAAATTAGGGTAGATG
1 TAGTGTATCGATACATTTATTCAAAATTAGGGTAGATG
*
6627847 TAGTGTATCGATACATTTATTCAAGATTAGGGTAGATG
1 TAGTGTATCGATACATTTATTCAAAATTAGGGTAGATG
6627885 TA
1 TA
6627887 TCGATGCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (38 bp):
TAGTGTATCGATACATTTATTCAAAATTAGGGTAGATG
Found at i:6628554 original size:12 final size:12
Alignment explanation
Indices: 6628537--6628564 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6628527 GCTAGAAAAC
6628537 TATATATGTGTG
1 TATATATGTGTG
6628549 TATATATGTGTG
1 TATATATGTGTG
6628561 TATA
1 TATA
6628565 AGGTATGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (12 bp):
TATATATGTGTG
Found at i:6630180 original size:2 final size:2
Alignment explanation
Indices: 6630173--6630248 Score: 83
Period size: 2 Copynumber: 40.5 Consensus size: 2
6630163 ANTTATGGTG
*
6630173 TA TA TA TA TA TA TA TA T- TA TA TG TA T- TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
6630212 TA TA TA -A CTA TA -A TA TA TA TA TA TA TA -A CA 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
6630249 GAAATGTTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
1 6 0.09
2 57 0.89
3 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6630199 original size:9 final size:9
Alignment explanation
Indices: 6630173--6630237 Score: 69
Period size: 9 Copynumber: 7.0 Consensus size: 9
6630163 ANTTATGGTG
6630173 TATATATA-
1 TATATATAT
6630181 TATATATAT
1 TATATATAT
*
6630190 TATATGTAT
1 TATATATAT
*
6630199 TATATATAA
1 TATATATAT
6630208 TATATATAT
1 TATATATAT
*
6630217 AACTATAATAT
1 TA-TAT-ATAT
6630228 ATATATATAT
1 -TATATATAT
6630238 AACATATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
8 8 0.17
9 24 0.51
10 7 0.15
11 7 0.15
12 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (9 bp):
TATATATAT
Found at i:6630213 original size:11 final size:11
Alignment explanation
Indices: 6630173--6630248 Score: 77
Period size: 11 Copynumber: 6.8 Consensus size: 11
6630163 ANTTATGGTG
6630173 TATATATAT-A
1 TATATATATAA
*
6630183 TATATATTATATG
1 TATATA-TATA-A
6630196 TATTATATATAA
1 TA-TATATATAA
6630208 TATATATATAA
1 TATATATATAA
6630219 CTATA-ATAT-A
1 -TATATATATAA
6630229 TATATATATAA
1 TATATATATAA
*
6630240 CATATATAT
1 TATATATAT
6630249 GAAATGTTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
9 4 0.07
10 11 0.20
11 25 0.45
12 6 0.11
13 6 0.11
14 4 0.07
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (11 bp):
TATATATATAA
Found at i:6630227 original size:15 final size:15
Alignment explanation
Indices: 6630176--6630248 Score: 92
Period size: 15 Copynumber: 4.7 Consensus size: 15
6630166 TATGGTGTAT
*
6630176 ATATATATATATATT
1 ATATATATATATATA
*
6630191 ATATGTATTATATATA
1 ATATATA-TATATATA
6630207 ATATATATATAACTATA
1 ATATATATAT-A-TATA
6630224 ATATATATATATATA
1 ATATATATATATATA
*
6630239 ACATATATAT
1 ATATATATAT
6630249 GAAATGTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
15 22 0.43
16 15 0.29
17 14 0.27
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:6641551 original size:2 final size:2
Alignment explanation
Indices: 6641544--6641583 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
6641534 GATTTCTCCA
6641544 TC TC TC TC TC TC TC T- TC TC TC TC TC TC T- TC TC T- 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
6641583 T
1 T
6641584 GTGTCATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:6641564 original size:13 final size:13
Alignment explanation
Indices: 6641546--6641583 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
6641536 TTTCTCCATC
6641546 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
6641559 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
6641572 TCTCT-TCTCTCT
1 TCTCTCTCTCTCT
6641584 GTGTCATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (13 bp):
TCTCTCTCTCTCT
Found at i:6647398 original size:100 final size:100
Alignment explanation
Indices: 6647216--6647415 Score: 301
Period size: 100 Copynumber: 2.0 Consensus size: 100
6647206 GCTATTCTAT
* * * *
6647216 TCAAATGTATCAAAAATAGTTTGAAGAGTAAATTAAAGAATAAGCAAGTTAAGAATAAATTTTCA
1 TCAAATGTATCAAAAATAATTTGAAGAGTAAATTAAAGAATAAACAAATTAAGAACAAATTTTCA
* *
6647281 AAACTCTTCAAAGTAAAGTAAAATTCACAAGTATA
66 AAACTCTTCAAAATAAAGTAAAATGCACAAGTATA
* * *
6647316 TCAATTGTGTCAAAAATAATTTGAAGAGTAAATTAAAGAATAAACAAATTAAGAACAAATTTTCG
1 TCAAATGTATCAAAAATAATTTGAAGAGTAAATTAAAGAATAAACAAATTAAGAACAAATTTTCA
* *
6647381 AAATTCTTCAAAATAAAGTAAAATGCATAAGTATA
66 AAACTCTTCAAAATAAAGTAAAATGCACAAGTATA
6647416 AATAGTGAAG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.28
Consensus pattern (100 bp):
TCAAATGTATCAAAAATAATTTGAAGAGTAAATTAAAGAATAAACAAATTAAGAACAAATTTTCA
AAACTCTTCAAAATAAAGTAAAATGCACAAGTATA
Found at i:6651802 original size:21 final size:20
Alignment explanation
Indices: 6651777--6651835 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
6651767 AGATGTCTAA
*
6651777 AATAATTATTTGAAATGAAAT
1 AATAATTATTTG-AATAAAAT
* *
6651798 TATAATTGTTTGAATAAAAT
1 AATAATTATTTGAATAAAAT
6651818 AATAA-TATTT-AATAAAAT
1 AATAATTATTTGAATAAAAT
6651836 GTTCTATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 8 0.24
19 4 0.12
20 11 0.33
21 10 0.30
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.41
Consensus pattern (20 bp):
AATAATTATTTGAATAAAAT
Found at i:6664762 original size:37 final size:37
Alignment explanation
Indices: 6664720--6664836 Score: 182
Period size: 37 Copynumber: 3.2 Consensus size: 37
6664710 GCATTGATGA
6664720 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
1 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
*
6664757 ATGATGAT-AGAGTGTGCGAGTAGGGAGTGCACACATG
1 ATGATGTTGA-AGTGTGCGAGTAGGGAGTGCACACATG
* **
6664794 ATGATGTTGAAGTGTGCGAGTAGGGAATGTGCACATG
1 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
6664831 ATGATG
1 ATGATG
6664837 ATATTGCATT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
36 1 0.01
37 71 0.97
38 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.38, T:0.25
Consensus pattern (37 bp):
ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
Found at i:6665351 original size:19 final size:20
Alignment explanation
Indices: 6665327--6665364 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6665317 GAGGTTTTAA
*
6665327 TGAG-AAACCCTCGGCCAGT
1 TGAGAAAACCCTCGACCAGT
6665346 TGAGAAAACCCTCGACCAG
1 TGAGAAAACCCTCGACCAG
6665365 CTGATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.13
Consensus pattern (20 bp):
TGAGAAAACCCTCGACCAGT
Found at i:6668918 original size:20 final size:20
Alignment explanation
Indices: 6668893--6668930 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6668883 TTCTTACTTT
*
6668893 AACTTTAACTGATTAAAATA
1 AACTTTAACTAATTAAAATA
6668913 AACTTTAACTAATTAAAA
1 AACTTTAACTAATTAAAA
6668931 ATTCTTCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
AACTTTAACTAATTAAAATA
Found at i:6670433 original size:26 final size:24
Alignment explanation
Indices: 6670404--6670460 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
6670394 TTCCTGATCA
* *
6670404 TTTTTCTTTGTCATTTTCTCACTTTC
1 TTTTTCTTTCTCA-ATTCTCA-TTTC
6670430 TTTTTCTTTCTCAATTCTCATTTC
1 TTTTTCTTTCTCAATTCTCATTTC
*
6670454 TGTTTCT
1 TTTTTCT
6670461 ATTTCAAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 10 0.36
25 6 0.21
26 12 0.43
ACGTcount: A:0.09, C:0.23, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTTCTTTCTCAATTCTCATTTC
Found at i:6682499 original size:21 final size:22
Alignment explanation
Indices: 6682474--6682514 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
6682464 CCTAGGTGGA
*
6682474 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
6682495 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
6682515 AAAGAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:6682515 original size:20 final size:21
Alignment explanation
Indices: 6682474--6682517 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
6682464 CCTAGGTGGA
*
6682474 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
6682495 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
6682515 AAA
1 AAA
6682518 GAAAAGGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.55, C:0.07, G:0.23, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:6683458 original size:40 final size:40
Alignment explanation
Indices: 6683351--6683446 Score: 183
Period size: 40 Copynumber: 2.4 Consensus size: 40
6683341 GATTTTATGG
*
6683351 AAAATGAGTTTAAATGGTAAATCTTTATTTTTTTATAAAC
1 AAAATGTGTTTAAATGGTAAATCTTTATTTTTTTATAAAC
6683391 AAAATGTGTTTAAATGGTAAATCTTTATTTTTTTATAAAC
1 AAAATGTGTTTAAATGGTAAATCTTTATTTTTTTATAAAC
6683431 AAAATGTGTTTAAATG
1 AAAATGTGTTTAAATG
6683447 AAATGATTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (40 bp):
AAAATGTGTTTAAATGGTAAATCTTTATTTTTTTATAAAC
Found at i:6685065 original size:19 final size:20
Alignment explanation
Indices: 6685038--6685083 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6685028 AGGAGACAAG
*
6685038 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
6685057 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
6685076 ATAATATT
1 ATAATATT
6685084 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:6708613 original size:15 final size:15
Alignment explanation
Indices: 6708595--6708625 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6708585 AATCATGTTT
6708595 AGTTATTTTAATTTA
1 AGTTATTTTAATTTA
*
6708610 AGTTATTTTAGTTTA
1 AGTTATTTTAATTTA
6708625 A
1 A
6708626 TTTTATGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (15 bp):
AGTTATTTTAATTTA
Found at i:6716773 original size:42 final size:42
Alignment explanation
Indices: 6716690--6716850 Score: 205
Period size: 42 Copynumber: 3.8 Consensus size: 42
6716680 TCTCCGATCG
* * * *
6716690 TCATCAGCTCATGTGCACTCCCCACTAGCACATGGTTGGGTCA
1 TCATCAGCTTATGTACACT-CCCACTCGCACATAGTTGGGTCA
* * *
6716733 TCATCGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
1 TCATCAGCTTATGTACACTCCCACTCGCACATAGTTGGGTCA
* * *
6716775 TCATCAGCTTATGTACACTCCTACTCACACATAGTTAGGTCA
1 TCATCAGCTTATGTACACTCCCACTCGCACATAGTTGGGTCA
* *
6716817 TCATCGGCTTATGTACACTCCTACTCGCACATAG
1 TCATCAGCTTATGTACACTCCCACTCGCACATAG
6716851 CCGAGTCCAC
Statistics
Matches: 105, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 88 0.84
43 17 0.16
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (42 bp):
TCATCAGCTTATGTACACTCCCACTCGCACATAGTTGGGTCA
Found at i:6716826 original size:84 final size:85
Alignment explanation
Indices: 6716690--6716850 Score: 236
Period size: 84 Copynumber: 1.9 Consensus size: 85
6716680 TCTCCGATCG
* * * *
6716690 TCATCAGCTCATGTGCACTCCCCACTAGCACATGGTTGGGTCATCATCGGCTTATGTGCACTCCC
1 TCATCAGCTCATGTACACTCCCCACTAGCACATAGTTAGGTCATCATCGGCTTATGTACACTCCC
6716755 ACTCGCACATAGTCGGGTCA
66 ACTCGCACATAGTCGGGTCA
* *
6716775 TCATCAGCTTATGTACACT-CCTACTCA-CACATAGTTAGGTCATCATCGGCTTATGTACACTCC
1 TCATCAGCTCATGTACACTCCCCACT-AGCACATAGTTAGGTCATCATCGGCTTATGTACACTCC
*
6716838 TACTCGCACATAG
65 CACTCGCACATAG
6716851 CCGAGTCCAC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
84 50 0.74
85 18 0.26
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (85 bp):
TCATCAGCTCATGTACACTCCCCACTAGCACATAGTTAGGTCATCATCGGCTTATGTACACTCCC
ACTCGCACATAGTCGGGTCA
Found at i:6721917 original size:52 final size:51
Alignment explanation
Indices: 6721835--6721939 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 51
6721825 AATGTACCTA
*
6721835 GAATAAGATAAAGAAGTTATGAGTTTATCAAATCCACAATTTCATTA-TAAT
1 GAATAAGATAAAGAAGTTATAAGTTTATCAAATCCACAATTTCA-TAGTAAT
* *
6721886 GAATGAAGATCAAGAAGTTATAAGTTTATCAAATCCACACTTTCATAGTAAT
1 GAAT-AAGATAAAGAAGTTATAAGTTTATCAAATCCACAATTTCATAGTAAT
6721938 GA
1 GA
6721940 GTGATTATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 6 0.12
52 43 0.88
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (51 bp):
GAATAAGATAAAGAAGTTATAAGTTTATCAAATCCACAATTTCATAGTAAT
Found at i:6722211 original size:15 final size:16
Alignment explanation
Indices: 6722180--6722212 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6722170 TTTAAATAAG
6722180 ACTAAAAATAAGCCTA
1 ACTAAAAATAAGCCTA
*
6722196 ACTAAAATTAAG-CTA
1 ACTAAAAATAAGCCTA
6722211 AC
1 AC
6722213 AAGTTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.18, G:0.06, T:0.21
Consensus pattern (16 bp):
ACTAAAAATAAGCCTA
Found at i:6738217 original size:28 final size:28
Alignment explanation
Indices: 6738177--6738235 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
6738167 TGGTAAAGAT
6738177 GTTAAACACTGATCCTGAGGAAAAATGG
1 GTTAAACACTGATCCTGAGGAAAAATGG
6738205 GTTAAACACTGATCCTGAGGAAAAATGG
1 GTTAAACACTGATCCTGAGGAAAAATGG
6738233 GTT
1 GTT
6738236 TAGGTCTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (28 bp):
GTTAAACACTGATCCTGAGGAAAAATGG
Found at i:6752975 original size:22 final size:22
Alignment explanation
Indices: 6752950--6752995 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
6752940 TTTTTGAAAG
6752950 GGTTTGGGCTGTTCACAATGAA
1 GGTTTGGGCTGTTCACAATGAA
6752972 GGTTTGGGCTGTTCACAATGAA
1 GGTTTGGGCTGTTCACAATGAA
6752994 GG
1 GG
6752996 CTTAGTGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.35, T:0.30
Consensus pattern (22 bp):
GGTTTGGGCTGTTCACAATGAA
Found at i:6757481 original size:9 final size:10
Alignment explanation
Indices: 6757460--6757488 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
6757450 CTAAGGTAGT
6757460 TTTTATGAAA
1 TTTTATGAAA
6757470 TTTTAT-AAA
1 TTTTATGAAA
6757479 TTTTATGAAA
1 TTTTATGAAA
6757489 AATGGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TTTTATGAAA
Found at i:6773786 original size:28 final size:28
Alignment explanation
Indices: 6773734--6773792 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
6773724 GGAAAAATGT
** *
6773734 CCTGGTGGTGGAAAATTACTGTTTTGCC
1 CCTGGTGGTGGAAAATTACCATTTTACC
6773762 CCTGG-GGTGGTAAAATTACCATTTTACC
1 CCTGGTGGTGG-AAAATTACCATTTTACC
6773790 CCT
1 CCT
6773793 ATACTCCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACCATTTTACC
Found at i:6779859 original size:87 final size:87
Alignment explanation
Indices: 6779713--6779887 Score: 332
Period size: 87 Copynumber: 2.0 Consensus size: 87
6779703 TTATACAAGT
**
6779713 TAATCAAGGATTGAGAACAAGTGAGATACATCCCCTCATATCACTTGGGGTGATGAATCCTCTCT
1 TAATCAAGGATTGAGAACAAGTGAGATACATCCCCTCATATCACTTAAGGTGATGAATCCTCTCT
6779778 TGACCACTCATTCACCTTCGCA
66 TGACCACTCATTCACCTTCGCA
6779800 TAATCAAGGATTGAGAACAAGTGAGATACATCCCCTCATATCACTTAAGGTGATGAATCCTCTCT
1 TAATCAAGGATTGAGAACAAGTGAGATACATCCCCTCATATCACTTAAGGTGATGAATCCTCTCT
6779865 TGACCACTCATTCACCTTCGCA
66 TGACCACTCATTCACCTTCGCA
6779887 T
1 T
6779888 GCTTCATGGC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (87 bp):
TAATCAAGGATTGAGAACAAGTGAGATACATCCCCTCATATCACTTAAGGTGATGAATCCTCTCT
TGACCACTCATTCACCTTCGCA
Found at i:6784148 original size:12 final size:11
Alignment explanation
Indices: 6784115--6784158 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
6784105 CCTAGGGTTG
6784115 TTGTTCTT-C-
1 TTGTTCTTCCT
6784124 TT-TTCTTCCT
1 TTGTTCTTCCT
6784134 TTGTTCTTCCCT
1 TTGTTCTT-CCT
6784146 TTGTT-TTCCT
1 TTGTTCTTCCT
6784156 TTG
1 TTG
6784159 GCCGGCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.16
9 3 0.10
10 8 0.26
11 7 0.23
12 8 0.26
ACGTcount: A:0.00, C:0.25, G:0.09, T:0.66
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:6785035 original size:18 final size:19
Alignment explanation
Indices: 6785012--6785054 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
6785002 AGTTTCAAAC
*
6785012 AATATTAAGATAA-TATAT
1 AATATTAAAATAATTATAT
6785030 AATATTAAAATAATTATAT
1 AATATTAAAATAATTATAT
6785049 AA-ATTA
1 AATATTA
6785055 TTTAATTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AATATTAAAATAATTATAT
Found at i:6836414 original size:82 final size:81
Alignment explanation
Indices: 6836295--6836444 Score: 246
Period size: 82 Copynumber: 1.8 Consensus size: 81
6836285 CATATATATA
* * * *
6836295 ATTTTTATATAATTTTTGTTTTTGTAAATCAATAAAAATTATGGATATATATTACATCAAATTTA
1 ATTTTTATAAAATTTTTGTTATTGTAAATAAATAAAAATTATGGATATATAGTACATCAAATTTA
6836360 TCATTATATATTTAAT
66 TCATTATATATTTAAT
*
6836376 ATTTATTATAAAATTTTTGTTATTGTAAATAAATAAAAATTATGTATATATAGTACATCAAATTT
1 ATTT-TTATAAAATTTTTGTTATTGTAAATAAATAAAAATTATGGATATATAGTACATCAAATTT
6836441 ATCA
65 ATCA
6836445 AGAAATTATA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
81 4 0.06
82 59 0.94
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (81 bp):
ATTTTTATAAAATTTTTGTTATTGTAAATAAATAAAAATTATGGATATATAGTACATCAAATTTA
TCATTATATATTTAAT
Found at i:6836463 original size:82 final size:81
Alignment explanation
Indices: 6836295--6836473 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
6836285 CATATATATA
* * * *
6836295 ATTT-TTATATAATTTTTGTTTTTGTAAATCAATAAAAATTATGGATATATATTACATCAAATTT
1 ATTTATTATAAAATTTTTGTTATTGTAAATAAATAAAAATTATGGATATATAGTACATCAAATTT
* *
6836359 ATCATTATATATTTAAT
66 ATCA-TAGAAATTTAAT
*
6836376 ATTTATTATAAAATTTTTGTTATTGTAAATAAATAAAAATTATGTATATATAGTACATCAAATTT
1 ATTTATTATAAAATTTTTGTTATTGTAAATAAATAAAAATTATGGATATATAGTACATCAAATTT
6836441 ATCA-AGAAATTATAAT
66 ATCATAGAAATT-TAAT
*
6836457 ATTTTATTGT-AAATTTT
1 A-TTTATTATAAAATTTT
6836474 AATCGAAATT
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
80 5 0.06
81 16 0.18
82 66 0.76
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (81 bp):
ATTTATTATAAAATTTTTGTTATTGTAAATAAATAAAAATTATGGATATATAGTACATCAAATTT
ATCATAGAAATTTAAT
Found at i:6837369 original size:8 final size:8
Alignment explanation
Indices: 6837356--6837380 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6837346 AACAGGAACT
6837356 AATCCTAC
1 AATCCTAC
6837364 AATCCTAC
1 AATCCTAC
6837372 AATCCTAC
1 AATCCTAC
6837380 A
1 A
6837381 GAAATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (8 bp):
AATCCTAC
Found at i:6840677 original size:12 final size:12
Alignment explanation
Indices: 6840660--6840684 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6840650 TGAACATTTG
6840660 ATTACTCACAAT
1 ATTACTCACAAT
6840672 ATTACTCACAAT
1 ATTACTCACAAT
6840684 A
1 A
6840685 GCGGGAGTTT
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:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTACTCACAAT
Found at i:6842472 original size:80 final size:83
Alignment explanation
Indices: 6842337--6842553 Score: 280
Period size: 86 Copynumber: 2.6 Consensus size: 83
6842327 AAGAATAAGA
* * * **
6842337 GAAAGGGATTTTCTAATTTGATAAATGATAATTGTTTGATTAATTCAC-AAAAAAAAGGAGAAAT
1 GAAAGGGTTTTTCTAATTTCATAAATGATAATTGTTTGATTGATTCACAAAAAAAAAAAAGAAAT
6842401 GATTTTTT-AAATTTGAT
66 GATTTTTTCAAATTTGAT
* * *
6842418 G-AAGGGTTTTTCTAATTTCATGAATGATAATTATTTGATTGATTTACAAAAAAAAAAAAAAAGA
1 GAAAGGGTTTTTCTAATTTCATAAATGATAATTGTTTGATTGA-TT-C-ACAAAAAAAAAAAAGA
*
6842482 AATGATTTTTTCCAATTTGAT
63 AATGATTTTTTCAAATTTGAT
* *
6842503 GAAAGGTTTTTTTTAATTTCATAAATGATAATTGTTTGATTGATTCA-AAAA
1 GAAAGGGTTTTTCTAATTTCATAAATGATAATTGTTTGATTGATTCACAAAA
6842554 GAGAAAGAGA
Statistics
Matches: 117, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
80 36 0.31
81 3 0.03
82 5 0.04
83 2 0.02
84 23 0.20
85 11 0.09
86 37 0.32
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (83 bp):
GAAAGGGTTTTTCTAATTTCATAAATGATAATTGTTTGATTGATTCACAAAAAAAAAAAAGAAAT
GATTTTTTCAAATTTGAT
Found at i:6842660 original size:26 final size:26
Alignment explanation
Indices: 6842607--6842677 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
6842597 CAAAAGATTT
*
6842607 ATAAAAGAAAAAAAAAG--C-AGTAG
1 ATAAAAGAAAAAAAAAGTTCTAGCAG
6842630 ATAAAAGAAAAAAAAAGTTCTAGCCAG
1 ATAAAAGAAAAAAAAAGTTCTAG-CAG
*
6842657 -TAAAA-AAGGAAAAAAGTTCTA
1 ATAAAAGAA-AAAAAAAGTTCTA
6842678 AAATTTGAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 17 0.41
25 3 0.07
26 19 0.46
27 2 0.05
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.14
Consensus pattern (26 bp):
ATAAAAGAAAAAAAAAGTTCTAGCAG
Found at i:6849560 original size:15 final size:15
Alignment explanation
Indices: 6849529--6849590 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
6849519 GTTTGATATT
*
6849529 TTATAATATAATTTAA
1 TTATAAT-TAATATAA
6849545 TTATAATTAATATAA
1 TTATAATTAATATAA
* *
6849560 TTATAAGTAATATGA
1 TTATAATTAATATAA
* *
6849575 TTATAAATAAAATAA
1 TTATAATTAATATAA
6849590 T
1 T
6849591 ATTATAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
15 33 0.82
16 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TTATAATTAATATAA
Found at i:6849572 original size:35 final size:35
Alignment explanation
Indices: 6849532--6849608 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
6849522 TGATATTTTA
* * *
6849532 TAATATAATT-TAATTATAATTAATATAATTATAAG
1 TAATATAATTATAAATA-AAATAATATAATAATAAG
* * *
6849567 TAATATGATTATAAATAAAATAATATTATAATATG
1 TAATATAATTATAAATAAAATAATATAATAATAAG
6849602 TAATATA
1 TAATATA
6849609 TAAGTAAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
35 29 0.85
36 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (35 bp):
TAATATAATTATAAATAAAATAATATAATAATAAG
Found at i:6849609 original size:17 final size:16
Alignment explanation
Indices: 6849544--6849630 Score: 53
Period size: 15 Copynumber: 5.6 Consensus size: 16
6849534 ATATAATTTA
6849544 ATTAT-AAT-TAATAT
1 ATTATAAATGTAATAT
6849558 AATTAT-AA-GTAATAT
1 -ATTATAAATGTAATAT
**
6849573 GATTATAAATAAAATAAT
1 -ATTATAAATGTAAT-AT
6849591 ATTATAATATGTAATAT
1 ATTATAA-ATGTAATAT
*
6849608 ATAAGTAAAT-TAATA-
1 ATTA-TAAATGTAATAT
6849623 ATTA-AAAT
1 ATTATAAAT
6849631 ATATAAAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
13 4 0.07
15 21 0.36
16 7 0.12
17 17 0.29
18 10 0.17
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTATAAATGTAATAT
Found at i:6849830 original size:33 final size:32
Alignment explanation
Indices: 6849779--6849875 Score: 112
Period size: 33 Copynumber: 3.1 Consensus size: 32
6849769 CTCTTAAATA
6849779 TATTTTTTAT-T-ATC--ATATATTTTATTTT
1 TATTTTTTATATAATCTTATATATTTTATTTT
6849807 TATTTTTTATTATAATCTTATATATTTTTATTTT
1 TATTTTTTA-TATAATCTTATATA-TTTTATTTT
* * *
6849841 TATTTTTTATATAATTTTTTATATTATATATTT
1 TATTTTTTATATAATCTTATATATTTTAT-TTT
6849874 TA
1 TA
6849876 ATTTAATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
28 9 0.15
29 1 0.02
30 1 0.02
31 3 0.05
32 5 0.08
33 22 0.37
34 18 0.31
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (32 bp):
TATTTTTTATATAATCTTATATATTTTATTTT
Found at i:6849840 original size:34 final size:33
Alignment explanation
Indices: 6849779--6849879 Score: 113
Period size: 34 Copynumber: 3.2 Consensus size: 33
6849769 CTCTTAAATA
6849779 TATTTTTTAT-T-ATC--ATATA-TTTTATTTT
1 TATTTTTTATATAATCTTATATATTTTTATTTT
6849807 TATTTTTTATTATAATCTTATATATTTTTATTTT
1 TATTTTTTA-TATAATCTTATATATTTTTATTTT
* * *
6849841 TATTTTTTATATAATTTTTTATATTATATATTTT
1 TATTTTTTATATAATCTTATATATT-TTTATTTT
*
6849875 AATTT
1 TATTT
6849880 AATTTTTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.15
29 1 0.02
30 1 0.02
31 3 0.05
33 19 0.31
34 29 0.47
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (33 bp):
TATTTTTTATATAATCTTATATATTTTTATTTT
Found at i:6849851 original size:31 final size:28
Alignment explanation
Indices: 6849779--6849851 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 28
6849769 CTCTTAAATA
*
6849779 TATTTTTTATTATCATATATTTTATTTT
1 TATTTTTTATAATCATATATTTTATTTT
6849807 TATTTTTTATTATAATCTTATATATTTTTATTTT
1 TA--TTTT-TTATAATC--ATATA-TTTTATTTT
6849841 TATTTTTTATA
1 TATTTTTTATA
6849852 TAATTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
28 2 0.05
30 4 0.11
31 12 0.32
32 4 0.11
33 5 0.13
34 11 0.29
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (28 bp):
TATTTTTTATAATCATATATTTTATTTT
Found at i:6849860 original size:14 final size:16
Alignment explanation
Indices: 6849776--6849874 Score: 54
Period size: 16 Copynumber: 6.6 Consensus size: 16
6849766 TATCTCTTAA
6849776 ATATA-TTTTT-TATT
1 ATATATTTTTTATATT
*
6849790 ATCATATATTTTAT-TT
1 AT-ATATTTTTTATATT
6849806 -T-TA-TTTTT-TATT
1 ATATATTTTTTATATT
* *
6849818 ATA-ATCTTATATATT
1 ATATATTTTTTATATT
* * *
6849833 -TTTATTTTTATTTTTT
1 ATATATTTTT-TATATT
6849849 ATATAATTTTTTATATT
1 ATAT-ATTTTTTATATT
6849866 ATATATTTT
1 ATATATTTT
6849875 AATTTAATTT
Statistics
Matches: 61, Mismatches: 12, Indels: 22
0.64 0.13 0.23
Matches are distributed among these distances:
11 1 0.02
12 6 0.10
13 4 0.07
14 6 0.10
15 12 0.20
16 15 0.25
17 11 0.18
18 6 0.10
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
ATATATTTTTTATATT
Found at i:6849865 original size:27 final size:26
Alignment explanation
Indices: 6849775--6849889 Score: 82
Period size: 27 Copynumber: 4.6 Consensus size: 26
6849765 TTATCTCTTA
* *
6849775 AATATATTTTTTATTATCATATATTTT
1 AATATAATTTTT-TTATTATATATTTT
* * * *
6849802 ATTTTTA-TTTTTTATTATA-ATCTT
1 AATATAATTTTTTTATTATATATTTT
6849826 -ATAT-ATTTTTATT-TT-TAT-TTTT
1 AATATAATTTTT-TTATTATATATTTT
*
6849848 TATATAATTTTTTATATTATATATTTT
1 AATATAATTTTTT-TATTATATATTTT
*
6849875 AATTTAATTTTTTTA
1 AATATAATTTTTTTA
6849890 AAAAATAATA
Statistics
Matches: 68, Mismatches: 11, Indels: 19
0.69 0.11 0.19
Matches are distributed among these distances:
22 6 0.09
23 13 0.19
24 13 0.19
25 9 0.13
26 9 0.13
27 18 0.26
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (26 bp):
AATATAATTTTTTTATTATATATTTT
Found at i:6850807 original size:18 final size:21
Alignment explanation
Indices: 6850772--6850812 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
6850762 TATTTAGTTT
6850772 TTTTTTTTGTTGTGTTTCTGG
1 TTTTTTTTGTTGTGTTTCTGG
6850793 TTTTTTTT-TT-T-TTTCTGG
1 TTTTTTTTGTTGTGTTTCTGG
6850811 TT
1 TT
6850813 GATGAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 2 0.10
21 8 0.40
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.78
Consensus pattern (21 bp):
TTTTTTTTGTTGTGTTTCTGG
Found at i:6851453 original size:13 final size:14
Alignment explanation
Indices: 6851435--6851463 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6851425 CATGCAAGTT
6851435 TAAATTAAAA-AAA
1 TAAATTAAAACAAA
6851448 TAAATTAAAACAAA
1 TAAATTAAAACAAA
6851462 TA
1 TA
6851464 CTTGTATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAATTAAAACAAA
Found at i:6854075 original size:13 final size:13
Alignment explanation
Indices: 6854053--6854108 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
6854043 TTAAGAGATG
*
6854053 ATATTTTATAAAA
1 ATATTATATAAAA
6854066 ATATTATATAAAA
1 ATATTATATAAAA
6854079 AT-TTATAATAAAA
1 ATATTAT-ATAAAA
*
6854092 A-A-TATATAAAT
1 ATATTATATAAAA
6854103 ATATTA
1 ATATTA
6854109 CACTTACATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 6 0.16
12 8 0.22
13 23 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTATATAAAA
Found at i:6862976 original size:24 final size:22
Alignment explanation
Indices: 6862949--6863006 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
6862939 AACATTAAAT
6862949 ACATAATTAAAACACATAATAAGA
1 ACATAATTAAAACAC--AATAAGA
* *
6862973 ACATATCATTTAAATACAATAAGA
1 ACATA--ATTAAAACACAATAAGA
6862997 ACAT-ATTAAA
1 ACATAATTAAA
6863007 GTATCTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 5 0.17
24 16 0.55
26 8 0.28
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (22 bp):
ACATAATTAAAACACAATAAGA
Found at i:6863282 original size:14 final size:15
Alignment explanation
Indices: 6863258--6863288 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
6863248 TTCTATATTC
6863258 TTTTTATTCTTTTCA
1 TTTTTATTCTTTTCA
6863273 TTTTTA-TCTTTTCA
1 TTTTTATTCTTTTCA
6863287 TT
1 TT
6863289 ATTCATCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTCTTTTCA
Found at i:6869594 original size:16 final size:16
Alignment explanation
Indices: 6869572--6869608 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6869562 AAAGAAAGGT
6869572 AGAAGAAGAAAGAAGA
1 AGAAGAAGAAAGAAGA
* *
6869588 GGAAGAAGGAAGAAGA
1 AGAAGAAGAAAGAAGA
6869604 AGAAG
1 AGAAG
6869609 CTAGGAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AGAAGAAGAAAGAAGA
Found at i:6869608 original size:13 final size:13
Alignment explanation
Indices: 6869567--6869608 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
6869557 TACTTAAAGA
*
6869567 AAGGTAGAAGAAG
1 AAGGAAGAAGAAG
* *
6869580 AAAGAAGAGGAAG
1 AAGGAAGAAGAAG
6869593 AAGGAAGAAGAAG
1 AAGGAAGAAGAAG
6869606 AAG
1 AAG
6869609 CTAGGAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (13 bp):
AAGGAAGAAGAAG
Found at i:6883192 original size:24 final size:25
Alignment explanation
Indices: 6883151--6883200 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
6883141 TTAATTATAT
*
6883151 TAAAAATATATAAAAATTAA-AAAA
1 TAAAAATATAAAAAAATTAATAAAA
6883175 TAAAAATA-AAAAATAATTAATAAAA
1 TAAAAATATAAAAA-AATTAATAAAA
6883200 T
1 T
6883201 TACCTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (25 bp):
TAAAAATATAAAAAAATTAATAAAA
Found at i:6883199 original size:13 final size:13
Alignment explanation
Indices: 6883160--6883190 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
6883150 TTAAAAATAT
6883160 ATAAAAATTAAAAA
1 ATAAAAA-TAAAAA
6883174 ATAAAAATAAAAA
1 ATAAAAATAAAAA
6883187 ATAA
1 ATAA
6883191 TTAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:6888003 original size:19 final size:16
Alignment explanation
Indices: 6887971--6888021 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 16
6887961 AAATTAAAGG
*
6887971 AAATAAATATAAAATT
1 AAATAATTATAAAATT
6887987 AAAATAACTTAATAAAAATT
1 -AAATAA-TT-AT-AAAATT
6888007 AAATAATTATAAAAT
1 AAATAATTATAAAAT
6888022 AACTAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.17
17 8 0.27
18 3 0.10
19 8 0.27
20 6 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAATTATAAAATT
Found at i:6890613 original size:27 final size:27
Alignment explanation
Indices: 6890562--6890613 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
6890552 ATAGTGATTA
* *
6890562 AAGGTTGTGCTTGATCGTTGGAAAAGC
1 AAGGTTGTGCTTGACCGTTGAAAAAGC
* *
6890589 AAGGTTGTGCTTGGCCTTTGAAAAA
1 AAGGTTGTGCTTGACCGTTGAAAAA
6890614 CATTGTATAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.31
Consensus pattern (27 bp):
AAGGTTGTGCTTGACCGTTGAAAAAGC
Found at i:6892240 original size:36 final size:36
Alignment explanation
Indices: 6892135--6892243 Score: 146
Period size: 36 Copynumber: 3.0 Consensus size: 36
6892125 TCAACTTAGC
** * * * *
6892135 TCATGTGCACTCTTACACCACACATAGCTAATACCA
1 TCATGTGCACTCCCACACCGCACATGGCAAATATCA
*
6892171 TCATGTGCACTCCCACACTGCACATGGCAAATATCA
1 TCATGTGCACTCCCACACCGCACATGGCAAATATCA
*
6892207 TCATGTGCACTCCCACACCGCATATGGCAAATATCA
1 TCATGTGCACTCCCACACCGCACATGGCAAATATCA
6892243 T
1 T
6892244 TATCATCGTG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.31, C:0.33, G:0.12, T:0.24
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACATGGCAAATATCA
Found at i:6892261 original size:42 final size:38
Alignment explanation
Indices: 6892138--6892345 Score: 119
Period size: 36 Copynumber: 5.6 Consensus size: 38
6892128 ACTTAGCTCA
** * * * *
6892138 TGTGCACTCTTACACCACACATAGCTAATACCATCA--
1 TGTGCACTCCCACACCGCACATGGCAAATATCATCATC
*
6892174 TGTGCACTCCCACACTGCACATGGCAAATATCATCA--
1 TGTGCACTCCCACACCGCACATGGCAAATATCATCATC
*
6892210 TGTGCACTCCCACACCGCATATGGCAAATATCATTATCATC
1 TGTGCACTCCCACACCGCACATGGCAAATATC---ATCATC
* * * ** **
6892251 GTGTGCACTCCTATACCGCACA---C-CACGTCCCCATC
1 -TGTGCACTCCCACACCGCACATGGCAAATATCATCATC
* * * *
6892286 ATGTGCACTCCCACATCGCACATGAC-AATATCATTATTG
1 -TGTGCACTCCCACACCGCACATGGCAAATATCATCA-TC
*
6892325 TGTGCACTCCCACACTGCACA
1 TGTGCACTCCCACACCGCACA
6892346 CCACCCTCTG
Statistics
Matches: 132, Mismatches: 30, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
35 22 0.17
36 59 0.45
38 27 0.20
39 6 0.05
42 18 0.14
ACGTcount: A:0.28, C:0.35, G:0.12, T:0.24
Consensus pattern (38 bp):
TGTGCACTCCCACACCGCACATGGCAAATATCATCATC
Found at i:6892296 original size:77 final size:73
Alignment explanation
Indices: 6892205--6892349 Score: 200
Period size: 77 Copynumber: 1.9 Consensus size: 73
6892195 TGGCAAATAT
* * * *
6892205 CATCATGTGCACTCCCACACCGCATATGGCAAATATCATTATCATCGTGTGCACTCCTATACCGC
1 CATCATGTGCACTCCCACACCGCACATGAC-AATATCATTAT--T-GTGTGCACTCCCACACCGC
6892270 ACACCACGTCCC
62 ACACCACGTCCC
* *
6892282 CATCATGTGCACTCCCACATCGCACATGACAATATCATTATTGTGTGCACTCCCACACTGCACAC
1 CATCATGTGCACTCCCACACCGCACATGACAATATCATTATTGTGTGCACTCCCACACCGCACAC
6892347 CAC
66 CAC
6892350 CCTCTGCACA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
73 23 0.37
74 1 0.02
76 11 0.18
77 27 0.44
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.23
Consensus pattern (73 bp):
CATCATGTGCACTCCCACACCGCACATGACAATATCATTATTGTGTGCACTCCCACACCGCACAC
CACGTCCC
Found at i:6892358 original size:14 final size:14
Alignment explanation
Indices: 6892339--6892367 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6892329 CACTCCCACA
6892339 CTGCACACCACCCT
1 CTGCACACCACCCT
6892353 CTGCACACCACCCT
1 CTGCACACCACCCT
6892367 C
1 C
6892368 ATCGTCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.59, G:0.07, T:0.14
Consensus pattern (14 bp):
CTGCACACCACCCT
Found at i:6893647 original size:19 final size:19
Alignment explanation
Indices: 6893623--6893659 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6893613 AGAAGTAAGA
6893623 AAGGAAAGGAAAA-GAAAAT
1 AAGGAAA-GAAAATGAAAAT
6893642 AAGGAAAGAAAATGAAAA
1 AAGGAAAGAAAATGAAAA
6893660 AAAATTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.05
Consensus pattern (19 bp):
AAGGAAAGAAAATGAAAAT
Found at i:6905695 original size:42 final size:42
Alignment explanation
Indices: 6905633--6905729 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
6905623 TCCACATTAA
* * * * *
6905633 CACATGGCTGGGTCATCATCGGCTTATGCGCACTCCCACTCG
1 CACATAGCCGGGTCAGCATCGACTTATGCGAACTCCCACTCG
*
6905675 CACATAGCCGGGTCAGCATCGACTTATGCGAACTCTCACTCG
1 CACATAGCCGGGTCAGCATCGACTTATGCGAACTCCCACTCG
6905717 CACATAGCCGGGT
1 CACATAGCCGGGT
6905730 GAATATCATT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.22
Consensus pattern (42 bp):
CACATAGCCGGGTCAGCATCGACTTATGCGAACTCCCACTCG
Found at i:6908057 original size:2 final size:2
Alignment explanation
Indices: 6908052--6908077 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6908042 ACATTATGTG
6908052 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
6908078 ATNCAGCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6908096 original size:74 final size:73
Alignment explanation
Indices: 6908007--6908151 Score: 281
Period size: 74 Copynumber: 2.0 Consensus size: 73
6907997 CTCTACAAGA
6908007 CAGCTGCACATGCATATAAGAATTCATGTATATATACATTATGTGTATATATATATATATATATA
1 CAGCTGCACATGCATATAAGAATTCATGTATATATACATTATGTGTATATATATATATATATATA
6908072 TATATAAT
66 TATATAAT
6908080 NCAGCTGCACATGCATATAAGAATTCATGTATATATACATTATGTGTATATATATATATATATAT
1 -CAGCTGCACATGCATATAAGAATTCATGTATATATACATTATGTGTATATATATATATATATAT
6908145 ATATATA
65 ATATATA
6908152 TAAACATTTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (73 bp):
CAGCTGCACATGCATATAAGAATTCATGTATATATACATTATGTGTATATATATATATATATATA
TATATAAT
Found at i:6908131 original size:2 final size:2
Alignment explanation
Indices: 6908126--6908153 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6908116 ACATTATGTG
6908126 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
6908154 AACATTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6917649 original size:30 final size:31
Alignment explanation
Indices: 6917587--6917672 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 31
6917577 CACTATGGAA
* *
6917587 TTGGAACTTGATATTTGTTTTAAATC-TTGGACT
1 TTGGAA-TTGATATTTG-TCTAGA-CATTGGACT
6917620 TTGGAATTGATA-TTGTCTAGACATTGGACT
1 TTGGAATTGATATTTGTCTAGACATTGGACT
* * *
6917650 TTGGATTTGGTATTTGTTTAGAC
1 TTGGAATTGATATTTGTCTAGAC
6917673 TTCAATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
29 1 0.02
30 21 0.46
31 12 0.26
32 6 0.13
33 6 0.13
ACGTcount: A:0.23, C:0.08, G:0.22, T:0.47
Consensus pattern (31 bp):
TTGGAATTGATATTTGTCTAGACATTGGACT
Found at i:6920997 original size:179 final size:179
Alignment explanation
Indices: 6920757--6921085 Score: 500
Period size: 179 Copynumber: 1.8 Consensus size: 179
6920747 GCCACCTATG
* * * *
6920757 GACAAGGGTTACGGTTTTTGAATTTTTTGAATGGCCAAATCACCTCCTATAGTCTTGAAAAAATA
1 GACAAGGGTTACGGTTTTTGAATTTTTTGAATAGCCAAATCACCTCCTAAAATCCTGAAAAAATA
*
6920822 TTCTAGAATTGTTCCATGAGTTAGCTATCAAGATAAATTTTATT-AAAATTAAATTCCTAAAAAT
66 TTCTAGAATTGTTCCATGAGTTAGATATCAAGATAAATTTTATTGAAAA-TAAATTCCTAAAAAT
*
6920886 AGGCCACTATAATGTCATGTACTCGGGACATGCTTGTTGTTGTACTTGTA
130 AGGCCACCATAATGTCATGTACTCGGGACATGCTTGTTGTTGTACTTGTA
* * *
6920936 GACATGGGTTATC-GTTTTTGAATTTTTTGAATAGCCAAGTCACCTCCTAAAATCCTGAAAAATT
1 GACAAGGGTTA-CGGTTTTTGAATTTTTTGAATAGCCAAATCACCTCCTAAAATCCTGAAAAAAT
* * * * *
6921000 TTTTTGGAATTGTTTCATGAGTTAGATATCAGGATAAATTTTATTGAAAATAAATTCCTAAAAAT
65 ATTCTAGAATTGTTCCATGAGTTAGATATCAAGATAAATTTTATTGAAAATAAATTCCTAAAAAT
6921065 AGGCCACCATAATGTCATGTA
130 AGGCCACCATAATGTCATGTA
6921086 ATTAGGACAT
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
179 129 0.96
180 5 0.04
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (179 bp):
GACAAGGGTTACGGTTTTTGAATTTTTTGAATAGCCAAATCACCTCCTAAAATCCTGAAAAAATA
TTCTAGAATTGTTCCATGAGTTAGATATCAAGATAAATTTTATTGAAAATAAATTCCTAAAAATA
GGCCACCATAATGTCATGTACTCGGGACATGCTTGTTGTTGTACTTGTA
Done.