Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, 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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 30
Found at i:575 original size:12 final size:12
Alignment explanation
Indices: 548--583 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
538 AAGTGAAGAA
548 AAACTAAAGAAAGG
1 AAAC-AAAG-AAGG
562 AAACAAAGAAGG
1 AAACAAAGAAGG
574 AAACAAAGAA
1 AAACAAAGAA
584 AGCAAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.64
13 4 0.18
14 4 0.18
ACGTcount: A:0.69, C:0.08, G:0.19, T:0.03
Consensus pattern (12 bp):
AAACAAAGAAGG
Found at i:8395 original size:90 final size:90
Alignment explanation
Indices: 8215--8384 Score: 261
Period size: 90 Copynumber: 1.9 Consensus size: 90
8205 GGGAAATGAT
*
8215 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
8280 GGGCTGTTCACATGCTAAACACATG
66 GGGCTGGTCACATGCTAAACACATG
* * * *
8305 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGC-TATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
*
8369 GGGGCTGGTCATATGC
65 GGGGCTGGTCACATGC
8385 AAGGCACATG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
89 2 0.03
90 70 0.97
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.23
Consensus pattern (90 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGCTGGTCACATGCTAAACACATG
Found at i:9780 original size:15 final size:16
Alignment explanation
Indices: 9755--9784 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9745 TGAGCTAATG
9755 TAAACATAACATGAGC
1 TAAACATAACATGAGC
9771 TAAA-ATAACATGAG
1 TAAACATAACATGAG
9785 AGTTAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (16 bp):
TAAACATAACATGAGC
Found at i:9853 original size:30 final size:30
Alignment explanation
Indices: 9814--9872 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
9804 ACATGCTGCC
9814 ATGATATCT-AAATGATATGCAAACATAATAA
1 ATGATATCTAAAAT-ATATG-AAACATAATAA
*
9845 ATGA-ATCTAAAATATATGTAACATAATA
1 ATGATATCTAAAATATATGAAACATAATA
9873 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 9 0.35
30 9 0.35
31 8 0.31
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (30 bp):
ATGATATCTAAAATATATGAAACATAATAA
Found at i:10969 original size:24 final size:24
Alignment explanation
Indices: 10892--10974 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
10882 TGTAATGAAC
*
10892 TTGGAGCTTCAA-TGATCA-AACTT
1 TTGGAACTTCAAGTGA-CATAACTT
* *
10915 TTGGCACTTCAAGTGACATATCTT
1 TTGGAACTTCAAGTGACATAACTT
* * *
10939 TTTGAACTTCAAGTGGCATAACTG
1 TTGGAACTTCAAGTGACATAACTT
*
10963 TTGGAACGTCAA
1 TTGGAACTTCAA
10975 AGAACATGTC
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 12 0.25
24 36 0.75
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (24 bp):
TTGGAACTTCAAGTGACATAACTT
Found at i:13326 original size:19 final size:21
Alignment explanation
Indices: 13302--13355 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
13292 TTCGGCCAAG
*
13302 ATCATGTATCTTCA-TT-AAA
1 ATCATGTATTTTCATTTAAAA
13321 ATCATGTATTTTCATTTAAAA
1 ATCATGTATTTTCATTTAAAA
13342 ATCATGTATTTTCA
1 ATCATGTATTTTCA
13356 AAGGGGTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.41
20 2 0.06
21 17 0.53
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
ATCATGTATTTTCATTTAAAA
Found at i:17237 original size:19 final size:21
Alignment explanation
Indices: 17213--17264 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
17203 CGGCCAAGAG
*
17213 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
17232 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
17253 CATGTATTTTCA
1 CATGTATTTTCA
17265 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:18268 original size:19 final size:19
Alignment explanation
Indices: 18237--18278 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
18227 ATGGGATAAT
18237 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
18256 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
18275 AATA
1 AATA
18279 AAGAAAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:18733 original size:19 final size:21
Alignment explanation
Indices: 18690--18741 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
18680 GAAACCCCTT
18690 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
18711 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
18730 TGAAGATACATG
1 TGAAAATACATG
18742 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:19677 original size:30 final size:31
Alignment explanation
Indices: 19638--19697 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
19628 ACATGCTGCC
**
19638 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
19669 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
19698 TAAGCTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:20756 original size:24 final size:24
Alignment explanation
Indices: 20723--20806 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
20713 TGTAATGAAC
*
20723 TTGGAGCTTCAA-TGATCATAACTT
1 TTGGAACTTCAAGTGA-CATAACTT
* *
20747 TTGGCACTTCAAGTGACATATCTT
1 TTGGAACTTCAAGTGACATAACTT
* *
20771 TTTGAACTTCAAGTGGA-ATAACTG
1 TTGGAACTTCAAGT-GACATAACTT
*
20795 TTGGAACGTCAA
1 TTGGAACTTCAA
20807 AGGACATGTC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 44 0.90
25 5 0.10
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (24 bp):
TTGGAACTTCAAGTGACATAACTT
Found at i:25394 original size:16 final size:17
Alignment explanation
Indices: 25375--25406 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25365 TTTTTCTGAA
25375 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
25391 TTTTCTTTCTTTTTGT
1 TTTTCTTTCTTTTTGT
25407 ACTCCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:25403 original size:25 final size:24
Alignment explanation
Indices: 25346--25403 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
25336 TTTTCCTTGG
*
25346 CTTTCTTTTCTCTTTTTCTTTTTT
1 CTTTCTTTTCTCTTTTTCTCTTTT
*** *
25370 CTGAATTTTCTTCTTTTTGTCTTTT
1 CTTTCTTTTC-TCTTTTTCTCTTTT
25395 CTTTCTTTT
1 CTTTCTTTT
25404 TGTACTCCAA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.74
Consensus pattern (24 bp):
CTTTCTTTTCTCTTTTTCTCTTTT
Found at i:28254 original size:10 final size:11
Alignment explanation
Indices: 28239--28268 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
28229 TCTATTCTGA
28239 TTTTTTTTTCT
1 TTTTTTTTTCT
28250 TTTTTTTTTCT
1 TTTTTTTTTCT
28261 TTCTTTTT
1 TT-TTTTT
28269 GCACTCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:28263 original size:15 final size:14
Alignment explanation
Indices: 28239--28268 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28229 TCTATTCTGA
28239 TTTTTTTTTCTTTT
1 TTTTTTTTTCTTTT
28253 TTTTTTCTTTCTTTT
1 TTTTTT-TTTCTTTT
28268 T
1 T
28269 GCACTCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTCTTTT
Found at i:28557 original size:19 final size:19
Alignment explanation
Indices: 28522--28563 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
28512 AGGGGATAAT
28522 AATATAAGTAATAAAATGA
1 AATATAAGTAATAAAATGA
*
28541 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATAAAATGA
28560 AATA
1 AATA
28564 AAGAAACGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATAAAATGA
Found at i:29019 original size:19 final size:21
Alignment explanation
Indices: 28976--29027 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
28966 GAAACCCCTT
28976 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
28997 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
29016 TGAAGATACATG
1 TGAAAATACATG
29028 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:32214 original size:149 final size:148
Alignment explanation
Indices: 32030--32323 Score: 498
Period size: 149 Copynumber: 2.0 Consensus size: 148
32020 GTTGTGTTCT
32030 TACTAAGCATTTATTAACTACATAACAAGAATTCTTATCATAAAATGTATTATAAAAGCATATAG
1 TACTAAGCATTTATTAACTACATAACAAGAATTCTTATCATAAAATGTATTATAAAAGCATATAG
*
32095 TATATAACTAATATAAAGTAAATTCAATATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAAA
66 TATAGAACTAATATAAAGTAAATTCAATATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAAA
32160 ACGTGCTTGCATCATTCA
131 ACGTGCTTGCATCATTCA
* * * * *
32178 TACTAAGTTATTTATTAACTACATAACTAGTATTCTTATCATGAAATGTATTATAATAGCATATA
1 TACTAAG-CATTTATTAACTACATAACAAGAATTCTTATCATAAAATGTATTATAAAAGCATATA
* *
32243 GTATAGAACTAGTATAAAGTAAATTCAGTATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAA
65 GTATAGAACTAATATAAAGTAAATTCAATATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAA
*
32308 AATGTGCTTGCATCAT
130 AACGTGCTTGCATCAT
32324 CCCCCTTCTT
Statistics
Matches: 136, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
148 7 0.05
149 129 0.95
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (148 bp):
TACTAAGCATTTATTAACTACATAACAAGAATTCTTATCATAAAATGTATTATAAAAGCATATAG
TATAGAACTAATATAAAGTAAATTCAATATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAAA
ACGTGCTTGCATCATTCA
Found at i:33967 original size:11 final size:11
Alignment explanation
Indices: 33947--33973 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
33937 AACAAAAAAA
33947 CAAAAAAAAGC
1 CAAAAAAAAGC
33958 CAAAAAAAAGC
1 CAAAAAAAAGC
33969 CAAAA
1 CAAAA
33974 TTTCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.19, G:0.07, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGC
Found at i:42597 original size:14 final size:14
Alignment explanation
Indices: 42578--42617 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
42568 GTGCTTCAAG
42578 TTTTCTTTCTTTTC
1 TTTTCTTTCTTTTC
42592 TTTTCTTT-TTTTC
1 TTTTCTTTCTTTTC
42605 TTTT-TCTTCTTTT
1 TTTTCT-TTCTTTT
42618 TGAGTGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 11 0.46
14 12 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCTTTCTTTTC
Found at i:42633 original size:24 final size:24
Alignment explanation
Indices: 42606--42657 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
42596 CTTTTTTTCT
* *
42606 TTTTCTTCTTTTTGAGTGTTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
42630 TTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
42654 TTTT
1 TTTT
42658 ATTTGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.08, C:0.13, G:0.17, T:0.62
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTTGAC
Found at i:45806 original size:11 final size:13
Alignment explanation
Indices: 45775--45811 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
45765 GTGAAGTGCA
45775 AAGACAAAGAAATC
1 AAGA-AAAGAAATC
45789 AAGAAAA-AAATC
1 AAGAAAAGAAATC
45801 -AGAAAAGAAAT
1 AAGAAAAGAAAT
45812 TAAAGCACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.27
12 9 0.41
13 3 0.14
14 4 0.18
ACGTcount: A:0.70, C:0.08, G:0.14, T:0.08
Consensus pattern (13 bp):
AAGAAAAGAAATC
Found at i:68103 original size:15 final size:16
Alignment explanation
Indices: 68052--68104 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
68042 AGATGGTGAA
68052 ATAAGAAAAGATGAATG
1 ATAAGAAAA-ATGAATG
*
68069 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATG-AATG
68086 ATAAGAAAAATGAA-G
1 ATAAGAAAAATGAATG
68101 ATAA
1 ATAA
68105 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 9 0.29
17 13 0.42
18 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (16 bp):
ATAAGAAAAATGAATG
Found at i:73425 original size:19 final size:18
Alignment explanation
Indices: 73403--73461 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 18
73393 TTTTTTTGAA
73403 TTCTTTTTCTTTTCTTCTT
1 TTCTTTTTCTTTTCTT-TT
*
73422 TTCTGATTTTTCTCTTCTTTT
1 TTC---TTTTTCTTTTCTTTT
73443 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
73461 T
1 T
73462 ACACTCCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.24
19 9 0.26
21 3 0.09
22 14 0.41
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:77633 original size:15 final size:16
Alignment explanation
Indices: 77582--77634 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
77572 AGATAGTGAA
77582 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
77599 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
77616 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
77631 ATAA
1 ATAA
77635 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:77842 original size:7 final size:6
Alignment explanation
Indices: 77822--77867 Score: 65
Period size: 7 Copynumber: 7.2 Consensus size: 6
77812 GTTGTAGGAG
77822 TCTTTT TCTTTT TCTTCTT TCTTCTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTT-TT TCTT-TT TCTT-TT TCTTTT TCTTTT T
77868 TTTGTTGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 19 0.49
7 20 0.51
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:85981 original size:19 final size:22
Alignment explanation
Indices: 85931--85979 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
85921 TTTCTTTTCT
85931 TTTCTT-TTTGAGTGCTTTCAA
1 TTTCTTCTTTGAGTGCTTTCAA
* *
85952 TTTCTTCTTTGAGTGCTTTGAT
1 TTTCTTCTTTGAGTGCTTTCAA
85974 TTTCTT
1 TTTCTT
85980 TGCTGGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.61
Consensus pattern (22 bp):
TTTCTTCTTTGAGTGCTTTCAA
Found at i:93091 original size:19 final size:19
Alignment explanation
Indices: 93066--93109 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
93056 ATATCTTTTC
93066 TTTATTTCA-TTTCATT-CT
1 TTTATTT-ATTTTCATTACT
93084 TATTATTTATTTTCATTACT
1 T-TTATTTATTTTCATTACT
93104 TTTATT
1 TTTATT
93110 ATTATCCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.09
19 18 0.78
20 3 0.13
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTTATTTTCATTACT
Found at i:93878 original size:12 final size:13
Alignment explanation
Indices: 93858--93890 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
93848 GAGTGCTTTA
93858 ATTTCTTTTC-TG
1 ATTTCTTTTCTTG
*
93870 ATTTTTTTTCTTG
1 ATTTCTTTTCTTG
93883 ATTTCTTT
1 ATTTCTTT
93891 GACTTTGCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.73
Consensus pattern (13 bp):
ATTTCTTTTCTTG
Found at i:101750 original size:18 final size:17
Alignment explanation
Indices: 101682--101751 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 17
101672 GCTTGCTTTC
*
101682 TCTTTTTCTTTTCTTT-
1 TCTTTTTCTTTTTTTTG
*
101698 TC-TTTTCTTCTTTTCTG
1 TCTTTTTCTT-TTTTTTG
*
101715 ATTTTTTTCTCTTTTTTTG
1 -TCTTTTTCT-TTTTTTTG
101734 TCTTTTTCTTTCTTTTTG
1 TCTTTTTCTTT-TTTTTG
101752 CACTCCAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.16
16 6 0.14
17 2 0.05
18 15 0.35
19 12 0.28
20 1 0.02
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.77
Consensus pattern (17 bp):
TCTTTTTCTTTTTTTTG
Found at i:103609 original size:17 final size:17
Alignment explanation
Indices: 103589--103623 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
103579 TGTGGAACTA
*
103589 GCTAGGAAGCATGAGCT
1 GCTAGCAAGCATGAGCT
103606 GCTAGCAAGCATGAGCT
1 GCTAGCAAGCATGAGCT
103623 G
1 G
103624 TTTGTGAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.34, T:0.17
Consensus pattern (17 bp):
GCTAGCAAGCATGAGCT
Found at i:107737 original size:91 final size:91
Alignment explanation
Indices: 107582--107751 Score: 306
Period size: 91 Copynumber: 1.9 Consensus size: 91
107572 GTTGATGCTT
107582 GGCCGAATAGGGAGAACACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATGGGGG
1 GGCCGAATAGGGAGAACACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATGGGGG
107647 CTGGTCATATGCAAAACATATGGCTA
66 CTGGTCATATGCAAAACATATGGCTA
* *
107673 GGCCGAATAGGGAGATA-ACTCTTCATCTTGGTGCCTGAATGATCCACATGCAAGGCACATGGGG
1 GGCCGAATAGGGAGA-ACACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATGGGG
107737 GCTGGTCATATGCAA
65 GCTGGTCATATGCAA
107752 GGCACATGGG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 75 0.99
92 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (91 bp):
GGCCGAATAGGGAGAACACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATGGGGG
CTGGTCATATGCAAAACATATGGCTA
Found at i:111139 original size:15 final size:15
Alignment explanation
Indices: 111104--111132 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
111094 GTGGTTCAAC
111104 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
111118 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
111133 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:112146 original size:91 final size:91
Alignment explanation
Indices: 111964--112137 Score: 294
Period size: 91 Copynumber: 1.9 Consensus size: 91
111954 GGTAGTTGAT
* * *
111964 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTACCTAAATGATCCATATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATGCAAGGCACATA
112029 GGGGCTAGTCATATGCAAAACACATG
66 GGGGCTAGTCATATGCAAAACACATG
* *
112055 GCTTGGCCGAATATGGAGAGAACTCTTCATCTTGGCCCCTAAATGATCCACATGCAAGGCACATA
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATGCAAGGCACATA
*
112120 GGGGCTGGTCATATGCAA
66 GGGGCTAGTCATATGCAA
112138 GGTACATGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATGCAAGGCACATA
GGGGCTAGTCATATGCAAAACACATG
Found at i:117159 original size:83 final size:83
Alignment explanation
Indices: 117045--117211 Score: 307
Period size: 83 Copynumber: 2.0 Consensus size: 83
117035 CCATATGTTT
117045 TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGAATGTTCTTCAAAG
1 TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGAATGTTCTTCAAAG
117110 CTATTTCTAAGGGAGTTC
66 CTATTTCTAAGGGAGTTC
* *
117128 TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGGATGTTCTTCAAAT
1 TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGAATGTTCTTCAAAG
*
117193 CTGTTTCTAAGGGAGTTC
66 CTATTTCTAAGGGAGTTC
117211 T
1 T
117212 TCATTACCCT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (83 bp):
TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGAATGTTCTTCAAAG
CTATTTCTAAGGGAGTTC
Found at i:118290 original size:91 final size:91
Alignment explanation
Indices: 118135--118317 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
118125 CCTAGAACAC
*
118135 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
118200 AAGAGTTCTCTCCATATTCGGCCAAG
66 AAGAGTTCTCTCCATATTCGGCCAAG
** * * * *
118226 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
*
118291 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCATATTCGGCCAAG
118317 C
1 C
118318 ATCAACTACC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
AAGAGTTCTCTCCATATTCGGCCAAG
Found at i:119164 original size:10 final size:9
Alignment explanation
Indices: 119144--119182 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
119134 CCAACACTCA
119144 AAAAG-AAG
1 AAAAGAAAG
119152 AAAAGCAAAG
1 AAAAG-AAAG
119162 AAAAGAAAAG
1 AAAAG-AAAG
119172 AAAAGAAAG
1 AAAAGAAAG
119181 AA
1 AA
119183 GTTGAAGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 5 0.18
9 6 0.21
10 17 0.61
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:119166 original size:5 final size:5
Alignment explanation
Indices: 119149--119179 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
119139 ACTCAAAAAG
*
119149 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
119180 GAAGTTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:129946 original size:734 final size:733
Alignment explanation
Indices: 128533--130001 Score: 2769
Period size: 734 Copynumber: 2.0 Consensus size: 733
128523 ATATGAAAAA
128533 CATGATAAAATAAGCATAGGATGGAAATAATAATATGATAATTTATACTAACATATGAATGCATG
1 CATGATAAAATAAGCATAGGATGGAAATAATAATATGATAATTTATACTAACATATGAATGCATG
128598 CTTATGATAGAATAGAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAACTCCCTTAGA
66 CTTATGATAGAATAGAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAACTCCCTTAGA
*
128663 AATAGCTTTGAAGAACATCAATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTAGTTTGGATCG
131 AATAGCTTTGAAGAACATCAATGGTGTGTTCAAGTCATGGAGAAAATTGGAGCTAGTTTGGATCG
*
128728 TATAAGAACTTGTGGCATGACTTCTGGATTTGGGGTAGGTGTGACTATATCATCCCCCTTCTTTT
196 TATAAGAACTTGTGGCATGACTTCTGGATCTGGGGTAGGTGTGACTATATCATCCCCCTTCTTTT
* *
128793 AAGCGATTTGTCCCCAAATTGTGTCCATCCTCAAAGGGTGATAGGTCGGTGATATTAAATGAGGC
261 AAGCGATTTGTCCCCAAATCGTGTCCATCCTCAAAGGGTGATAAGTCGGTGATATTAAATGAGGC
128858 ACTGACACCACCAAACTCACTGGGCAATTCGAGTTTATAGGCATTGTTGTTGATCTTTTCTACAA
326 ACTGACACCACCAAACTCACTGGGCAATTCGAGTTTATAGGCATTGTTGTTGATCTTTTCTACAA
*
128923 TCTGAAATGGGCTATCTCCTCGGGGTAGTAGTTTAGACTTCCTTTGGTTTGAGAATCTTTCCTTC
391 TCTGAAATGGGCTATCTCCTCGGGGTAGTAGTTTAGACTTCCTTTCGTTTGAGAATCTTTCCTTC
*
128988 CTAAAGTGTACCCAAACCCAATCTCCCACGTCAAAAGTTACCTTTTTCCTTCCTTTGTTTGCTTG
456 CTAAAGTGTACCCAAACCCAATCTCCCACGTCAAAAGTTACCTTCTTCCTTCCTTTGTTTGCTTG
129053 TTGTTCATAATGTCTCGTTCTCCTTTCAATATTGACCTTGACTTGTTGATGGAGTCTTTTAACAA
521 TTGTTCATAATGTCTCGTTCTCCTTTCAATATTGACCTTGACTTGTTGATGGAGTCTTTTAACAA
* *
129118 ATTCTGCTTTGTTCTTTCCATCTTTTTTCACTATTTGATCATAAGGTAAAGGAAGTAAGTCCAAA
586 ATTCTGCTTTGTTCTTTCCATCTTTGTTCACTATTTGATCATAAGGTAAAGGAAGTAAATCCAAA
129183 GGAGTTAAAGGATTGAAACCATACACTACCTCAAATGGAGAATATTTGGTTGTCGAGTGAATGGT
651 GGAGTTAAAGGATTGAAACCATACACTACCTCAAATGGAGAATATTTGGTTGTCGAGTGAATGGT
*
129248 TTAGTTGTATGCAAACTC
716 TCAGTTGTATGCAAACTC
* *
129266 CATGATCAAATAAGCATAGGATGGAAATAATAATATGATAATTTATACTAACATATGAATGTATG
1 CATGATAAAATAAGCATAGGATGGAAATAATAATATGATAATTTATACTAACATATGAATGCATG
129331 CTTATGATAGAATAGAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAACTCCCTTAGA
66 CTTATGATAGAATAGAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAACTCCCTTAGA
*
129396 AATAGCTTTGAAGAACATCCATGGTGTGTTCAAGTCATGGAGAAAATTGGAGCTAGTTTGGATCG
131 AATAGCTTTGAAGAACATCAATGGTGTGTTCAAGTCATGGAGAAAATTGGAGCTAGTTTGGATCG
*
129461 TATCAGAACTTGTGGCATGACTT-TCGGATCTGGGGTAGGTGTGACTATATCATCCCCCCTTCTT
196 TATAAGAACTTGTGGCATGACTTCT-GGATCTGGGGTAGGTGTGACTATATCAT-CCCCCTTCTT
129525 TTAAGCGATTTGTCCCCAAATCGTGTCCATCCTCAAAGGGTGATAAGTCGGTGATATTAAATGAG
259 TTAAGCGATTTGTCCCCAAATCGTGTCCATCCTCAAAGGGTGATAAGTCGGTGATATTAAATGAG
*
129590 GCACTGACACCACCAAACTCACTGGGTAATTCGAGTTTATAGGCATTGTTGTTGATCTTTTCTAC
324 GCACTGACACCACCAAACTCACTGGGCAATTCGAGTTTATAGGCATTGTTGTTGATCTTTTCTAC
*
129655 AATCTGAAATGGGCTATCTCCTCGGGGTAGTAGTTTAGACTTCCTTTCTTTTGAGAATCTTTCCT
389 AATCTGAAATGGGCTATCTCCTCGGGGTAGTAGTTTAGACTTCCTTTCGTTTGAGAATCTTTCCT
129720 TCCTAAAGTGTACCCAAACCCAATCTCCCACGTCAAAAGTTACCTTCTTCCTTCCTTTGTTTGCT
454 TCCTAAAGTGTACCCAAACCCAATCTCCCACGTCAAAAGTTACCTTCTTCCTTCCTTTGTTTGCT
*
129785 TGTTGTTCATAATGTCTCGTTCTCCTTTCAATATTGTCCTTGACTTGTTGATGGAGTCTTTTAAC
519 TGTTGTTCATAATGTCTCGTTCTCCTTTCAATATTGACCTTGACTTGTTGATGGAGTCTTTTAAC
129850 AAATTCTGCTTTGTTCTTTCCATCTTTGTTCACTATTTGATCATAAGGTAAAGGAAGTAAATCCA
584 AAATTCTGCTTTGTTCTTTCCATCTTTGTTCACTATTTGATCATAAGGTAAAGGAAGTAAATCCA
129915 AAGGAGTTAAAGGATTGAAACCATACACTACCTCAAATGGAGAATATTTGGTTGTCGAGTGAATG
649 AAGGAGTTAAAGGATTGAAACCATACACTACCTCAAATGGAGAATATTTGGTTGTCGAGTGAATG
129980 GTTCAGTTGTATGCAAACTC
714 GTTCAGTTGTATGCAAACTC
130000 CA
1 CA
130002 CGTGTGGTAG
Statistics
Matches: 718, Mismatches: 16, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
732 1 0.00
733 240 0.33
734 477 0.66
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (733 bp):
CATGATAAAATAAGCATAGGATGGAAATAATAATATGATAATTTATACTAACATATGAATGCATG
CTTATGATAGAATAGAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAACTCCCTTAGA
AATAGCTTTGAAGAACATCAATGGTGTGTTCAAGTCATGGAGAAAATTGGAGCTAGTTTGGATCG
TATAAGAACTTGTGGCATGACTTCTGGATCTGGGGTAGGTGTGACTATATCATCCCCCTTCTTTT
AAGCGATTTGTCCCCAAATCGTGTCCATCCTCAAAGGGTGATAAGTCGGTGATATTAAATGAGGC
ACTGACACCACCAAACTCACTGGGCAATTCGAGTTTATAGGCATTGTTGTTGATCTTTTCTACAA
TCTGAAATGGGCTATCTCCTCGGGGTAGTAGTTTAGACTTCCTTTCGTTTGAGAATCTTTCCTTC
CTAAAGTGTACCCAAACCCAATCTCCCACGTCAAAAGTTACCTTCTTCCTTCCTTTGTTTGCTTG
TTGTTCATAATGTCTCGTTCTCCTTTCAATATTGACCTTGACTTGTTGATGGAGTCTTTTAACAA
ATTCTGCTTTGTTCTTTCCATCTTTGTTCACTATTTGATCATAAGGTAAAGGAAGTAAATCCAAA
GGAGTTAAAGGATTGAAACCATACACTACCTCAAATGGAGAATATTTGGTTGTCGAGTGAATGGT
TCAGTTGTATGCAAACTC
Found at i:132874 original size:19 final size:20
Alignment explanation
Indices: 132850--132892 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
132840 AGCATTTATC
*
132850 TTCATT-AAAATTATGTATT
1 TTCATTGAAAATCATGTATT
*
132869 TTCATTGAAAATCATGTGTT
1 TTCATTGAAAATCATGTATT
132889 TTCA
1 TTCA
132893 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
TTCATTGAAAATCATGTATT
Found at i:141119 original size:14 final size:14
Alignment explanation
Indices: 141081--141111 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
141071 TTCAAAGTCT
141081 TATAAAACTTTTCA
1 TATAAAACTTTTCA
141095 TATAAAACTTTTCA
1 TATAAAACTTTTCA
141109 TAT
1 TAT
141112 GCACCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (14 bp):
TATAAAACTTTTCA
Found at i:144790 original size:24 final size:21
Alignment explanation
Indices: 144755--144797 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
144745 GGCTCATTCT
*
144755 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
144778 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
144798 ATATTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:146024 original size:23 final size:23
Alignment explanation
Indices: 145983--146036 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
145973 TTTCTTTCTT
*
145983 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTT-TTTTCGAATGCTTTCAA
* * *
146007 TTTCTTTTTTTGAATGCTTTGAT
1 TTTCTTTTTTCGAATGCTTTCAA
146030 TTTCTTT
1 TTTCTTT
146037 GCTGGATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.11, C:0.15, G:0.11, T:0.63
Consensus pattern (23 bp):
TTTCTTTTTTCGAATGCTTTCAA
Found at i:153748 original size:8 final size:8
Alignment explanation
Indices: 153737--153761 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
153727 TCTTTTTCTT
153737 TTCTTTTC
1 TTCTTTTC
153745 TTCTTTTC
1 TTCTTTTC
153753 TTCTTTTC
1 TTCTTTTC
153761 T
1 T
153762 GATTTTTTTC
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:153797 original size:29 final size:29
Alignment explanation
Indices: 153731--153798 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
153721 GCTTTCTCTT
*
153731 TTTCTTTTCTTTTCTTCTTTTCTTCTTTTC
1 TTTCTTTT-TTCTCTTCTTTTCTTCTTTTC
* *
153761 TGAT-TTTTTTCTCTTCTTTT-GTCTTTTTC
1 T-TTCTTTTTTCTCTTCTTTTCTTC-TTTTC
153790 TTTCTTTTT
1 TTTCTTTTT
153799 GCACTCCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
28 3 0.10
29 22 0.71
30 5 0.16
31 1 0.03
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.76
Consensus pattern (29 bp):
TTTCTTTTTTCTCTTCTTTTCTTCTTTTC
Found at i:156716 original size:8 final size:8
Alignment explanation
Indices: 156705--156729 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
156695 TCTTTTTCTT
156705 TTCTTTTC
1 TTCTTTTC
156713 TTCTTTTC
1 TTCTTTTC
156721 TTCTTTTC
1 TTCTTTTC
156729 T
1 T
156730 GCTGTTTTGC
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:156716 original size:13 final size:12
Alignment explanation
Indices: 156691--156729 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
156681 CTTGGCTTGC
156691 TTTCTCTTTTTCT
1 TTTCT-TTTTTCT
156704 TTTCTTTTCTTCT
1 TTTCTTTT-TTCT
156717 TTTCTTCTTTTCT
1 TTTCTT-TTTTCT
156730 GCTGTTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 19 0.79
14 2 0.08
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:171895 original size:19 final size:20
Alignment explanation
Indices: 171871--171918 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
171861 CAGCCAAGAG
*
171871 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
*
171890 CATGTATTTTCTTTAAAAAT
1 CATGTATTTTCATTAAAAAT
171910 CATGTATTT
1 CATGTATTT
171919 GCAAAGGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:176086 original size:17 final size:15
Alignment explanation
Indices: 176034--176092 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 15
176024 TGAAATCTTT
*
176034 TTCTTTTTCTTTTTC
1 TTCTTTTTGTTTTTC
*
176049 TTCTTTTCTGAATTTTC
1 TTCTTTT-TG-TTTTTC
176066 TTCTTTTTGTCTTTTC
1 TTCTTTTTGT-TTTTC
176082 TTTCTTTTTGT
1 -TTCTTTTTGT
176093 ACTCCAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 7 0.19
16 8 0.22
17 22 0.59
ACGTcount: A:0.03, C:0.17, G:0.05, T:0.75
Consensus pattern (15 bp):
TTCTTTTTGTTTTTC
Found at i:179015 original size:27 final size:22
Alignment explanation
Indices: 178963--179005 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
178953 TGTTGGCGCA
178963 AAATTGGATGGGAGATGATGCC
1 AAATTGGATGGGAGATGATGCC
178985 AAATTGGATGGGAGATGATGC
1 AAATTGGATGGGAGATGATGC
179006 TTGGCCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.37, T:0.23
Consensus pattern (22 bp):
AAATTGGATGGGAGATGATGCC
Found at i:179484 original size:13 final size:13
Alignment explanation
Indices: 179466--179491 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
179456 TTATAGGCGT
179466 GAAAATGGTGATG
1 GAAAATGGTGATG
179479 GAAAATGGTGATG
1 GAAAATGGTGATG
179492 AACATGTAGT
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:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
GAAAATGGTGATG
Found at i:184307 original size:25 final size:25
Alignment explanation
Indices: 184279--184336 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 25
184269 AAAATCAGCA
184279 AAGAAAAAGTCAAGCACT-TCAAAAG
1 AAGAAAAAGTCAAGCACTCT-AAAAG
184304 AAG-AAAAGTCAAGCACTCTAAAAG
1 AAGAAAAAGTCAAGCACTCTAAAAG
184328 AAGAAAAAG
1 AAGAAAAAG
184337 AAAAGAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (25 bp):
AAGAAAAAGTCAAGCACTCTAAAAG
Found at i:187754 original size:19 final size:20
Alignment explanation
Indices: 187730--187781 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
187720 CGACCAAGAG
* *
187730 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
187749 CATGTATTTTCATAAAAAAAT
1 CATGTATTTTCAT-AAAAAAT
187770 CATGTATTTTCA
1 CATGTATTTTCA
187782 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
21 17 0.59
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:188511 original size:20 final size:21
Alignment explanation
Indices: 188486--188524 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
188476 AATTGGAGTG
188486 CAAAAAGAA-AAGAAAAAATA
1 CAAAAAGAAGAAGAAAAAATA
*
188506 CAAAAAGAAGAATAAAAAA
1 CAAAAAGAAGAAGAAAAAA
188525 AAATTCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.05
Consensus pattern (21 bp):
CAAAAAGAAGAAGAAAAAATA
Found at i:188533 original size:24 final size:24
Alignment explanation
Indices: 188490--188539 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
188480 GGAGTGCAAA
*
188490 AAGAAAAGAAAAAATACAAAA-AG
1 AAGAAAAAAAAAAATACAAAAGAG
*
188513 AAGAATAAAAAAAAATTCAAAAGAG
1 AAGAA-AAAAAAAAATACAAAAGAG
188538 AA
1 AA
188540 AGCAACCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 14 0.61
25 4 0.17
ACGTcount: A:0.76, C:0.04, G:0.12, T:0.08
Consensus pattern (24 bp):
AAGAAAAAAAAAAATACAAAAGAG
Found at i:191921 original size:19 final size:18
Alignment explanation
Indices: 191897--191932 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
191887 CGGCCAAGAG
191897 CATGTATCTTCATTAAAAT
1 CATGTATCTTCA-TAAAAT
*
191916 CATGTATTTTCATAAAA
1 CATGTATCTTCATAAAA
191933 AAATGATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (18 bp):
CATGTATCTTCATAAAAT
Found at i:191933 original size:19 final size:20
Alignment explanation
Indices: 191897--191948 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
191887 CGGCCAAGAG
* *
191897 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
191916 CATGTATTTTCATAAAAAAAT
1 CATGTATTTTCAT-AAAAAAT
*
191937 GATGTATTTTCA
1 CATGTATTTTCA
191949 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:195407 original size:5 final size:5
Alignment explanation
Indices: 195393--195432 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
195383 GTGCTTCAAC
*
195393 TTTC- TTTCT TTTCT TTTCT ATTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
195433 CTTTTTGAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:195418 original size:15 final size:14
Alignment explanation
Indices: 195393--195437 Score: 65
Period size: 15 Copynumber: 3.2 Consensus size: 14
195383 GTGCTTCAAC
195393 TTTCTTTCTTTTCT
1 TTTCTTTCTTTTCT
195407 TTTCTATTCTTTTCT
1 TTTCT-TTCTTTTCT
*
195422 TTTCTTT-TCTTCT
1 TTTCTTTCTTTTCT
195435 TTT
1 TTT
195438 TGAGTGCTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 8 0.28
14 7 0.24
15 14 0.48
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTTTCTTTTCT
Found at i:199114 original size:20 final size:18
Alignment explanation
Indices: 199048--199115 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 18
199038 AATTGGTGTG
199048 CAAAAAG-AAAGAAAATA
1 CAAAAAGAAAAGAAAATA
199065 C-AAAAG-AAAGAAAATA
1 CAAAAAGAAAAGAAAATA
199081 CAAAAAGAAGAAGAAAATTCA
1 CAAAAAGAA-AAGAAAA-T-A
*
199102 GAAAAAGAAAAGAA
1 CAAAAAGAAAAGAA
199116 GAAAGGAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
16 16 0.36
17 6 0.13
18 1 0.02
19 7 0.16
20 6 0.13
21 9 0.20
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.06
Consensus pattern (18 bp):
CAAAAAGAAAAGAAAATA
Found at i:202053 original size:23 final size:23
Alignment explanation
Indices: 202008--202053 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
201998 TTATACCTAT
*
202008 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
202031 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
202054 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:203664 original size:24 final size:25
Alignment explanation
Indices: 203618--203672 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
203608 ACAGTTATGC
*
203618 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
203642 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
203667 CA-TTGA
1 CACTTGA
203673 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:215816 original size:15 final size:16
Alignment explanation
Indices: 215765--215817 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
215755 AGATGGTGAA
215765 ATAAGAAAAGATGAATG
1 ATAAGAAAA-ATGAATG
*
215782 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATG-AATG
215799 ATAAGAAAAATGAA-G
1 ATAAGAAAAATGAATG
215814 ATAA
1 ATAA
215818 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 9 0.29
17 13 0.42
18 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (16 bp):
ATAAGAAAAATGAATG
Found at i:224093 original size:19 final size:18
Alignment explanation
Indices: 224071--224129 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 18
224061 TTTTTTTGAA
224071 TTCTTTTTCTTTTCTTCTT
1 TTCTTTTTCTTTTCTT-TT
*
224090 TTCTGATTTTTCTCTTCTTTT
1 TTC---TTTTTCTTTTCTTTT
224111 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
224129 T
1 T
224130 ACACTCCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.24
19 9 0.26
21 3 0.09
22 14 0.41
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:225069 original size:316 final size:316
Alignment explanation
Indices: 224496--225134 Score: 1269
Period size: 316 Copynumber: 2.0 Consensus size: 316
224486 TGATGAAATG
*
224496 GAAATGGTGGTGATATTGTATCTCAAACACGCCAAAGAGGAAACTATGCTATGAAGCACAATCCT
1 GAAATGGTGGTGATATTGTATCTCAAACACGCCAAAGAGGAAACTATGCTATGAAGCACAATCCC
224561 GGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATTTAGGA
66 GGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATTTAGGA
224626 ATTTTGGAATCAAAATGTGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGATGGCAACC
131 ATTTTGGAATCAAAATGTGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGATGGCAACC
224691 TTGTTATTTCCCGATCTAGGAGAGACACCAAATGCAACACCTTGAATTGAAAAGTAATCTGCTCA
196 TTGTTATTTCCCGATCTAGGAGAGACACCAAATGCAACACCTTGAATTGAAAAGTAATCTGCTCA
224756 AAAGAAGAATAATTGGTTAAGTAAATGAATAATTAAGAAAGGAAATGGAAATAATT
261 AAAGAAGAATAATTGGTTAAGTAAATGAATAATTAAGAAAGGAAATGGAAATAATT
224812 GAAATGGTGGTGATATTGTATCTCAAACACGCCAAAGAGGAAACTATGCTATGAAGCACAATCCC
1 GAAATGGTGGTGATATTGTATCTCAAACACGCCAAAGAGGAAACTATGCTATGAAGCACAATCCC
224877 GGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATTTAGGA
66 GGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATTTAGGA
224942 ATTTTGGAATCAAAATGTGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGATGGCAACC
131 ATTTTGGAATCAAAATGTGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGATGGCAACC
225007 TTGTTATTTCCCGATCTAGGAGAGACACCAAATGCAACACCTTGAATTGAAAAGTAATCTGCTCA
196 TTGTTATTTCCCGATCTAGGAGAGACACCAAATGCAACACCTTGAATTGAAAAGTAATCTGCTCA
225072 AAAGAAGAATAATTGGTTAAGTAAATGAATAATTAAGAAAGGAAATGGAAATAATT
261 AAAGAAGAATAATTGGTTAAGTAAATGAATAATTAAGAAAGGAAATGGAAATAATT
225128 GAAATGG
1 GAAATGG
225135 ATAGAATAGT
Statistics
Matches: 322, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
316 322 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.26
Consensus pattern (316 bp):
GAAATGGTGGTGATATTGTATCTCAAACACGCCAAAGAGGAAACTATGCTATGAAGCACAATCCC
GGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTTCAACCCACTAGATATCAATTTAGGA
ATTTTGGAATCAAAATGTGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGATGGCAACC
TTGTTATTTCCCGATCTAGGAGAGACACCAAATGCAACACCTTGAATTGAAAAGTAATCTGCTCA
AAAGAAGAATAATTGGTTAAGTAAATGAATAATTAAGAAAGGAAATGGAAATAATT
Found at i:227057 original size:15 final size:16
Alignment explanation
Indices: 227006--227058 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
226996 AGATAGTGAA
227006 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
227023 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
227040 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
227055 ATAA
1 ATAA
227059 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:227287 original size:7 final size:7
Alignment explanation
Indices: 227247--227283 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
227237 GTTGTAGGAG
227247 TCTT-TT
1 TCTTCTT
227253 TCTTCTT
1 TCTTCTT
227260 TCTTCTT
1 TCTTCTT
227267 TCTTCTT
1 TCTTCTT
227274 TCTT-TT
1 TCTTCTT
227280 TCTT
1 TCTT
227284 TTTTTTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 10 0.33
7 20 0.67
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TCTTCTT
Found at i:235438 original size:5 final size:5
Alignment explanation
Indices: 235424--235460 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
235414 GTGCTTCAAC
235424 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
235461 TGAGTGCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:235470 original size:21 final size:21
Alignment explanation
Indices: 235446--235502 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
235436 CTTTTCTTTT
*
235446 CTTTTCTTTTCTTTTTGAGTG
1 CTTTTCTTTTCTTTTTAAGTG
*
235467 C-TTTCAATTTCTTCTTTAAGTG
1 CTTTTC-TTTTCTT-TTTAAGTG
**
235489 CTTTGATTTTCTTT
1 CTTTTCTTTTCTTT
235503 GCTGGATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
20 4 0.14
21 8 0.29
22 14 0.50
23 2 0.07
ACGTcount: A:0.11, C:0.16, G:0.11, T:0.63
Consensus pattern (21 bp):
CTTTTCTTTTCTTTTTAAGTG
Found at i:235491 original size:22 final size:21
Alignment explanation
Indices: 235453--235502 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
235443 TTTCTTTTCT
*
235453 TTTCTTTTTGAGTGCTTTCAA
1 TTTCTTTTTAAGTGCTTTCAA
* *
235474 TTTCTTCTTTAAGTGCTTTGAT
1 TTTCTT-TTTAAGTGCTTTCAA
235496 TTTCTTT
1 TTTCTTT
235503 GCTGGATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.62
Consensus pattern (21 bp):
TTTCTTTTTAAGTGCTTTCAA
Found at i:247474 original size:2 final size:2
Alignment explanation
Indices: 247467--247496 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
247457 AGTTATTTTC
247467 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
247497 CCTATAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:254709 original size:12 final size:13
Alignment explanation
Indices: 254685--254709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
254675 CTTGAACTTC
254685 TTTTTGTATTTTT
1 TTTTTGTATTTTT
254698 TTTTTGTATTTT
1 TTTTTGTATTTT
254710 CGTTGTACGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTTGTATTTTT
Found at i:256154 original size:18 final size:18
Alignment explanation
Indices: 256129--256173 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
256119 ATTTTTTTTT
*
256129 CAAAAAAACAAAAAAAAAA
1 CAAAAAAA-TAAAAAAAAA
**
256148 CAAAAAAATCCAAAAAAA
1 CAAAAAAATAAAAAAAAA
256166 CAAAAAAA
1 CAAAAAAA
256174 AGTCAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.02
Consensus pattern (18 bp):
CAAAAAAATAAAAAAAAA
Found at i:256174 original size:11 final size:11
Alignment explanation
Indices: 256130--256155 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
256120 TTTTTTTTTC
256130 AAAAAAACAAA
1 AAAAAAACAAA
256141 AAAAAAACAAA
1 AAAAAAACAAA
256152 AAAA
1 AAAA
256156 TCCAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:256174 original size:19 final size:18
Alignment explanation
Indices: 256141--256183 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
256131 AAAAAACAAA
256141 AAAAAAACAAAAAAA-TCC
1 AAAAAAACAAAAAAAGT-C
256159 AAAAAAACAAAAAAAAGTC
1 AAAAAAAC-AAAAAAAGTC
256178 AAAAAA
1 AAAAAA
256184 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.35
19 14 0.61
20 1 0.04
ACGTcount: A:0.81, C:0.12, G:0.02, T:0.05
Consensus pattern (18 bp):
AAAAAAACAAAAAAAGTC
Found at i:256190 original size:19 final size:19
Alignment explanation
Indices: 256140--256190 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
256130 AAAAAAACAA
*
256140 AAAAAAAACAAAAAAATCC
1 AAAAAAACCAAAAAAATCC
*
256159 AAAAAAACAAAAAAAAGT-C
1 AAAAAAACCAAAAAAA-TCC
*
256178 AAAAAAGCCAAAA
1 AAAAAAACCAAAA
256191 TTTCAAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.78, C:0.14, G:0.04, T:0.04
Consensus pattern (19 bp):
AAAAAAACCAAAAAAATCC
Found at i:265247 original size:15 final size:15
Alignment explanation
Indices: 265236--265264 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
265226 ACTCAAAAAG
265236 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
265251 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
265265 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:270458 original size:19 final size:20
Alignment explanation
Indices: 270434--270484 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
270424 CGGCCAAGAG
* *
270434 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
270453 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
270473 CATGTATTTTCA
1 CATGTATTTTCA
270485 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:274104 original size:2 final size:2
Alignment explanation
Indices: 274093--274130 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
274083 TAACTATAGG
274093 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
274131 GAAAATAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:274508 original size:23 final size:23
Alignment explanation
Indices: 274478--274529 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
274468 ATTGAAGTCA
274478 TTTTGCTTTGAACGTTTGCGCCC
1 TTTTGCTTTGAACGTTTGCGCCC
274501 TTTTGCTTTGAACGTTTGCGCCC
1 TTTTGCTTTGAACGTTTGCGCCC
274524 TTTTGC
1 TTTTGC
274530 ATTCCAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.08, C:0.25, G:0.21, T:0.46
Consensus pattern (23 bp):
TTTTGCTTTGAACGTTTGCGCCC
Found at i:280278 original size:91 final size:91
Alignment explanation
Indices: 280123--280305 Score: 330
Period size: 91 Copynumber: 2.0 Consensus size: 91
280113 CCTAGAACAC
*
280123 CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATGTGGATCATTTAGGCATCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATGTGGATCATTTAGGCACCAAGATG
280188 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** *
280214 CCATGTGTTTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATGTGGATCATTTAGGCACCAAGATG
280279 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
280305 C
1 C
280306 ATCAACTACC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATGTGGATCATTTAGGCACCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:281199 original size:12 final size:12
Alignment explanation
Indices: 281182--281223 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
281172 CTCAGCTACT
281182 CAGCTACTCTCC
1 CAGCTACTCTCC
281194 CAGCTACT-T-C
1 CAGCTACTCTCC
281204 CAGCTACTCTCC
1 CAGCTACTCTCC
281216 CAGCTACT
1 CAGCTACT
281224 TCTAGCTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.32
11 2 0.07
12 17 0.61
ACGTcount: A:0.19, C:0.45, G:0.10, T:0.26
Consensus pattern (12 bp):
CAGCTACTCTCC
Found at i:281208 original size:10 final size:10
Alignment explanation
Indices: 281174--281232 Score: 59
Period size: 10 Copynumber: 5.7 Consensus size: 10
281164 CTCAGCTCCT
281174 CAGCTAC-T-
1 CAGCTACTTC
281182 CAGCTACTCTCC
1 CAGCTACT-T-C
281194 CAGCTACTTC
1 CAGCTACTTC
281204 CAGCTACTCTCC
1 CAGCTACT-T-C
281216 CAGCTACTTC
1 CAGCTACTTC
*
281226 TAGCTAC
1 CAGCTAC
281233 CTTTAGTCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
8 7 0.16
10 17 0.39
11 3 0.07
12 17 0.39
ACGTcount: A:0.20, C:0.42, G:0.10, T:0.27
Consensus pattern (10 bp):
CAGCTACTTC
Found at i:281210 original size:22 final size:22
Alignment explanation
Indices: 281169--281232 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
281159 GTCTTCTCAG
281169 CTCCTCAGCTAC-T-CAGCTACT
1 CTCC-CAGCTACTTCCAGCTACT
281190 CTCCCAGCTACTTCCAGCTACT
1 CTCCCAGCTACTTCCAGCTACT
*
281212 CTCCCAGCTACTTCTAGCTAC
1 CTCCCAGCTACTTCCAGCTAC
281233 CTTTAGTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
20 7 0.17
21 5 0.12
22 28 0.70
ACGTcount: A:0.19, C:0.44, G:0.09, T:0.28
Consensus pattern (22 bp):
CTCCCAGCTACTTCCAGCTACT
Found at i:284438 original size:81 final size:81
Alignment explanation
Indices: 284303--284464 Score: 288
Period size: 81 Copynumber: 2.0 Consensus size: 81
284293 CTTATATAAA
*
284303 ACATACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAGCAAGTATAA
1 ACATACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAACAAGTATAA
*
284368 TTCATATACTTGTGGC
66 TTCATATACTTATGGC
*
284384 ACATACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAACAAGTATAG
1 ACATACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAACAAGTATAA
*
284449 TTCCTATACTTATGGC
66 TTCATATACTTATGGC
284465 GTCATTCTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (81 bp):
ACATACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAACAAGTATAA
TTCATATACTTATGGC
Found at i:289198 original size:13 final size:13
Alignment explanation
Indices: 289176--289205 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
289166 ACTAAACACC
289176 TTTC-ACATACCT
1 TTTCAACATACCT
289188 TTTCAACATACCT
1 TTTCAACATACCT
289201 TTTCA
1 TTTCA
289206 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:299747 original size:13 final size:11
Alignment explanation
Indices: 299706--299790 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
299696 ACAATCTGTC
299706 CATCACCATTAT
1 CATCACCA-TAT
*
299718 CA-CGCCTATAT
1 CATCACC-ATAT
299729 CATCACCATAGT
1 CATCACCATA-T
299741 CCATCACCATTAT
1 -CATCACCA-TAT
*
299754 CA-CGCCTATAT
1 CATCACC-ATAT
299765 CATCACCATATT
1 CATCACCATA-T
299777 CCATCACCATAT
1 -CATCACCATAT
299789 CA
1 CA
299791 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:299750 original size:36 final size:36
Alignment explanation
Indices: 299703--299805 Score: 181
Period size: 36 Copynumber: 2.9 Consensus size: 36
299693 GATACAATCT
299703 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
299739 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
299775 TTCCATCACCA-TATCACGCCTATATTATCAC
1 GTCCATCACCATTATCACGCCTATATCATCAC
299806 TAACTTATAA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:300218 original size:26 final size:23
Alignment explanation
Indices: 300189--300236 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
300179 GTGCTACAAC
300189 AACAAAAAAGTAACAAGAAAGAAGAA
1 AACAAAAAAG-AA-AAGAAA-AAGAA
*
300215 AACAAAAGAGAAAAGAAAAAGA
1 AACAAAAAAGAAAAGAAAAAGA
300237 CTCCTACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 2 0.10
26 9 0.43
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.02
Consensus pattern (23 bp):
AACAAAAAAGAAAAGAAAAAGAA
Found at i:300458 original size:16 final size:15
Alignment explanation
Indices: 300432--300483 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
300422 GAGTTGTAAG
300432 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
300446 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
300462 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
300479 CTTAT
1 -TTAT
300484 TTCATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:302060 original size:16 final size:17
Alignment explanation
Indices: 302025--302070 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
302015 TTTGGGATGC
302025 CAAAGAACATGATCATT
1 CAAAGAACATGATCATT
302042 CAAAGTAACATG-T-ATT
1 CAAAG-AACATGATCATT
302058 CAACAG-ACATGAT
1 CAA-AGAACATGAT
302071 TTTTAACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.19
16 7 0.27
17 8 0.31
18 6 0.23
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (17 bp):
CAAAGAACATGATCATT
Found at i:303812 original size:36 final size:36
Alignment explanation
Indices: 303765--303869 Score: 160
Period size: 36 Copynumber: 2.9 Consensus size: 36
303755 GATACAATCT
303765 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
303801 GTCCATCACCATTATCACGCCTATATCATCACAATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
303837 TTCCATCACCA-TATCACGCC-AGTATTATCACCA
1 GTCCATCACCATTATCACGCCTA-TATCATCACCA
303870 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 1 0.02
35 18 0.28
36 45 0.70
ACGTcount: A:0.31, C:0.35, G:0.06, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:310322 original size:19 final size:20
Alignment explanation
Indices: 310298--310337 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
310288 TATCCTTTCT
310298 TTATTTCATTTT-ATT-CTTA
1 TTATTTC-TTTTCATTACTTA
310317 TTATTTCTTTTCATTACTTA
1 TTATTTCTTTTCATTACTTA
310337 T
1 T
310338 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTCTTTTCATTACTTA
Found at i:310461 original size:376 final size:375
Alignment explanation
Indices: 309768--310501 Score: 1281
Period size: 376 Copynumber: 2.0 Consensus size: 375
309758 ACACTATCAC
309768 CACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGCTTCATAACATAGTTTCCTCTTTGGCGTG
1 CACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGCTTCATAACATAGTTTCCTCTTTGGCGTG
* * * *
309833 TTTGAGATACAACATCACCATCATTTCCATTTCATCATCACTATCATCCATCTCTTCCATCAATT
66 TTTGAGATACAACATCACCACCATTGCCATTTCATCATCACAATCATCCATCTCTTCCATAAATT
* *
309898 CCGCAGCCATCTCTATCCTTTCTTTATTTCATTTCATTCTTATTATTTATTTTCATTACTTATAT
131 CCACAACCATCTCTATCCTTTCTTTATTTCATTTCATTCTTATTATTTATTTTCATTACTTATAT
309963 TATTATCCCCTTTATTAAATTCCATTATTAATCATTATTTTCTTATCATATTTTGCAGCCCAAAC
196 TATTATCCCCTTTATTAAATTCCATTATTAATCATTATTTTCTTATCATATTTTGCAGCCCAAAC
310028 TTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGGGACACAATAAGGCTATATACTCT
261 TTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGGGACACAATAAGGCTATATACTCT
*
310093 CTCCCATCAAAGTGTGTAGATTCGCCTTACATCATATTCGGCAAGGGTTTT
326 -TCCCATCAAAGTGTGTAGATTCACCTTACATCATATTCGGCAAGGGTTTT
*
310144 CACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCGTG
1 CACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGCTTCATAACATAGTTTCCTCTTTGGCGTG
* *
310209 TTTGAGATATAACATCACCACCATTGCCATTTCATCATGACCAATCATCCATCTCTTCCATAAAT
66 TTTGAGATACAACATCACCACCATTGCCATTTCATCATCA-CAATCATCCATCTCTTCCATAAAT
* *
310274 TCCACAACCATCTCTATCCTTTCTTTATTTCATTTTATTCTTATTATTTCTTTTCATTACTTATA
130 TCCACAACCATCTCTATCCTTTCTTTATTTCATTTCATTCTTATTATTTATTTTCATTACTTATA
* * *
310339 TTATTATCCTCTTTATT-AATTCCATTATTAATCATTCTTTTCTTATCTTATTTTGCAGCCCAAA
195 TTATTATCCCCTTTATTAAATTCCATTATTAATCATTATTTTCTTATCATATTTTGCAGCCCAAA
* *
310403 TTTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGGGACACAATAAGGCTATCTACTC
260 CTTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGGGACACAATAAGGCTATATACTC
*
310468 TTCTCATCAAAGTGTGTAGATTCACCTTACATCA
325 TTCCCATCAAAGTGTGTAGATTCACCTTACATCA
310502 GAAAGGGTGG
Statistics
Matches: 339, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
375 31 0.09
376 209 0.62
377 99 0.29
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (375 bp):
CACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGCTTCATAACATAGTTTCCTCTTTGGCGTG
TTTGAGATACAACATCACCACCATTGCCATTTCATCATCACAATCATCCATCTCTTCCATAAATT
CCACAACCATCTCTATCCTTTCTTTATTTCATTTCATTCTTATTATTTATTTTCATTACTTATAT
TATTATCCCCTTTATTAAATTCCATTATTAATCATTATTTTCTTATCATATTTTGCAGCCCAAAC
TTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGGGACACAATAAGGCTATATACTCT
TCCCATCAAAGTGTGTAGATTCACCTTACATCATATTCGGCAAGGGTTTT
Found at i:312748 original size:8 final size:8
Alignment explanation
Indices: 312735--312807 Score: 78
Period size: 8 Copynumber: 9.0 Consensus size: 8
312725 TATTTTTTAT
312735 CAAAAAAA
1 CAAAAAAA
312743 CAAAAAAA
1 CAAAAAAA
312751 CAAAAAAA
1 CAAAAAAA
*
312759 CAAAAAAGG
1 CAAAAAA-A
312768 C-AAAAAA
1 CAAAAAAA
**
312775 -AAAAAGG
1 CAAAAAAA
312782 CAAAAAAA
1 CAAAAAAA
312790 GGCAAAAAAA
1 --CAAAAAAA
312800 CAAAAAAA
1 CAAAAAAA
312808 GAGCCAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
7 4 0.07
8 41 0.76
9 1 0.02
10 8 0.15
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:312772 original size:24 final size:26
Alignment explanation
Indices: 312736--312818 Score: 62
Period size: 29 Copynumber: 3.0 Consensus size: 26
312726 ATTTTTTATC
312736 AAAAAAACAAAAAAA--CAAAAAAAC
1 AAAAAAACAAAAAAAGGCAAAAAAAC
*
312760 AAAAAAGGCAAAAAAAAAAAGGCAAAAAAAGGC
1 --AAAA---AAACAAAAAAAGGCAAAAAAA--C
*
312793 AAAAAAACAAAAAAAGAGCCAAAAAA
1 AAAAAAACAAAAAAAG-GCAAAAAAA
312819 GCCAAAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
26 4 0.09
28 11 0.24
29 18 0.39
31 12 0.26
33 1 0.02
ACGTcount: A:0.80, C:0.11, G:0.10, T:0.00
Consensus pattern (26 bp):
AAAAAAACAAAAAAAGGCAAAAAAAC
Found at i:312773 original size:10 final size:10
Alignment explanation
Indices: 312773--312825 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
312763 AAAGGCAAAA
312773 AAAAAAAGGC
1 AAAAAAAGGC
312783 AAAAAAAGGC
1 AAAAAAAGGC
312793 AAAAAAA--C
1 AAAAAAAGGC
312801 AAAAAAAGAGC
1 AAAAAAAG-GC
* *
312812 CAAAAAAGCC
1 AAAAAAAGGC
312822 AAAA
1 AAAA
312826 TTTCAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 8 0.22
10 21 0.57
11 8 0.22
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAGGC
Found at i:312799 original size:13 final size:14
Alignment explanation
Indices: 312754--312789 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
312744 AAAAAAACAA
312754 AAAAACAAAAAAGGC
1 AAAAA-AAAAAAGGC
312769 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
312783 AAAAAAA
1 AAAAAAA
312790 GGCAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:329726 original size:22 final size:22
Alignment explanation
Indices: 329701--329753 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
329691 TTTTCTTTTC
329701 TTTTCTTT-TCTTCTTTTCTGAT
1 TTTTCTTTCTCTTCTTTTCT-AT
* *
329723 TTTT-TTTCTCTTTTTTTCTCT
1 TTTTCTTTCTCTTCTTTTCTAT
329744 TTTTCTTTCT
1 TTTTCTTTCT
329754 TTTTGCATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTCTTTCTCTTCTTTTCTAT
Found at i:331617 original size:17 final size:17
Alignment explanation
Indices: 331591--331631 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
331581 CTTGCGTATG
*
331591 GAGCTAGCTAGGAAGCAT
1 GAGCT-GCTAGCAAGCAT
331609 GAGCTGCTAGCAAGCAT
1 GAGCTGCTAGCAAGCAT
331626 GAGCTG
1 GAGCTG
331632 TTTGTGAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.29, C:0.20, G:0.34, T:0.17
Consensus pattern (17 bp):
GAGCTGCTAGCAAGCAT
Found at i:336390 original size:14 final size:13
Alignment explanation
Indices: 336373--336422 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
336363 GTGCAAAAAG
336373 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
336387 AAAGAATAAGAAA
1 AAAGAAAAAGAAA
336400 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
336411 AAAGAAAAAGAA
1 AAAGAAAAAGAA
336423 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:336419 original size:19 final size:18
Alignment explanation
Indices: 336367--336422 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
336357 ATTGGAGTGC
336367 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
336384 CAAAAAGAATAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
336403 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
336422 A
1 A
336423 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:342814 original size:91 final size:91
Alignment explanation
Indices: 342659--342833 Score: 287
Period size: 91 Copynumber: 1.9 Consensus size: 91
342649 ATGCTTGGCC
*
342659 GAATAGGGAGAAAACTCTTCATCTTGGCACCTAAATGATCCACATGCAAGGTACATGGGGGCTGG
1 GAATAGGGAGAAAACTCTTCATCTTGGCACCTAAATGATCCACATGCAAGGCACATGGGGGCTGG
342724 TCATATGCAAAACACATGGCTAGGCT
66 TCATATGCAAAACACATGGCTAGGCT
* ** *
342750 GAATAGGGAGATAACTCTTCATCTTGGTGCCTGAATGATCCACATGCAAGGCACATGGGGGCTGG
1 GAATAGGGAGAAAACTCTTCATCTTGGCACCTAAATGATCCACATGCAAGGCACATGGGGGCTGG
**
342815 TCATATGCAAGGCACATGG
66 TCATATGCAAAACACATGG
342834 GTGTTCTAGG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (91 bp):
GAATAGGGAGAAAACTCTTCATCTTGGCACCTAAATGATCCACATGCAAGGCACATGGGGGCTGG
TCATATGCAAAACACATGGCTAGGCT
Found at i:347875 original size:83 final size:83
Alignment explanation
Indices: 347736--347902 Score: 307
Period size: 83 Copynumber: 2.0 Consensus size: 83
347726 CCATATGTTT
347736 TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGAATGTTCTTCAAAG
1 TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGAATGTTCTTCAAAG
347801 CTATTTCTAAGGGAGTTC
66 CTATTTCTAAGGGAGTTC
* *
347819 TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGGATGTTCTTCAAAT
1 TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGAATGTTCTTCAAAG
*
347884 CTGTTTCTAAGGGAGTTC
66 CTATTTCTAAGGGAGTTC
347902 T
1 T
347903 TCATTACCCT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (83 bp):
TGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGAATGTTCTTCAAAG
CTATTTCTAAGGGAGTTC
Found at i:349855 original size:10 final size:9
Alignment explanation
Indices: 349835--349873 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
349825 CCAACACTCA
349835 AAAAG-AAG
1 AAAAGAAAG
349843 AAAAGCAAAG
1 AAAAG-AAAG
349853 AAAAGAAAAG
1 AAAAG-AAAG
349863 AAAAGAAAG
1 AAAAGAAAG
349872 AA
1 AA
349874 GTTGAAGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 5 0.18
9 6 0.21
10 17 0.61
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:349857 original size:5 final size:5
Alignment explanation
Indices: 349840--349870 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
349830 ACTCAAAAAG
*
349840 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
349871 GAAGTTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:356108 original size:10 final size:11
Alignment explanation
Indices: 356087--356115 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
356077 GTGCTTCAAC
356087 TTCTTCTTCTT
1 TTCTTCTTCTT
356098 TTCTT-TTCTT
1 TTCTTCTTCTT
356108 TTCTTCTT
1 TTCTTCTT
356116 GTTGAGTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTCTTCTTCTT
Found at i:361391 original size:19 final size:20
Alignment explanation
Indices: 361367--361409 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
361357 AGCATTTATC
*
361367 TTCATT-AAAATTATGTATT
1 TTCATTGAAAATCATGTATT
*
361386 TTCATTGAAAATCATGTGTT
1 TTCATTGAAAATCATGTATT
361406 TTCA
1 TTCA
361410 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
TTCATTGAAAATCATGTATT
Found at i:368151 original size:8 final size:8
Alignment explanation
Indices: 368140--368164 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
368130 CTTTCTCTTT
368140 TTCTTTTC
1 TTCTTTTC
368148 TTCTTTTC
1 TTCTTTTC
368156 TTCTTTTC
1 TTCTTTTC
368164 T
1 T
368165 GCTGTTTTTC
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:383239 original size:14 final size:13
Alignment explanation
Indices: 383222--383271 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
383212 GTGCAAAAAG
383222 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
383236 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
383249 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
383260 AAAGAAAAAGAA
1 AAAGAAAAAGAA
383272 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:383268 original size:19 final size:18
Alignment explanation
Indices: 383216--383271 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
383206 ATTGGAGTGC
383216 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
383233 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
383252 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
383271 A
1 A
383272 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:383269 original size:11 final size:11
Alignment explanation
Indices: 383216--383271 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
383206 ATTGGAGTGC
383216 AAAAAG-AAAG
1 AAAAAGAAAAG
383226 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
383240 AAGAAGAAAAG
1 AAAAAGAAAAG
383251 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
383264 AAAAAGAA
1 AAAAAGAA
383272 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:395582 original size:19 final size:20
Alignment explanation
Indices: 395558--395605 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
395548 CAGCCAAGAG
*
395558 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
*
395577 CATGTATTTTCTTTAAAAAT
1 CATGTATTTTCATTAAAAAT
395597 CATGTATTT
1 CATGTATTT
395606 GCAAAGGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:398629 original size:27 final size:22
Alignment explanation
Indices: 398577--398619 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
398567 TGTTGGCGCA
398577 AAATTGGATGGGAGATGATGCC
1 AAATTGGATGGGAGATGATGCC
398599 AAATTGGATGGGAGATGATGC
1 AAATTGGATGGGAGATGATGC
398620 TTGGCCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.37, T:0.23
Consensus pattern (22 bp):
AAATTGGATGGGAGATGATGCC
Found at i:398864 original size:17 final size:15
Alignment explanation
Indices: 398840--398874 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
398830 AAAATAGAAT
398840 ATGAAAGAAAAAGGAA
1 ATGAAAG-AAAAGGAA
398856 ATGATAAGAAAAGGAA
1 ATGA-AAGAAAAGGAA
398872 ATG
1 ATG
398875 GATAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (15 bp):
ATGAAAGAAAAGGAA
Found at i:398878 original size:17 final size:15
Alignment explanation
Indices: 398848--398882 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
398838 ATATGAAAGA
398848 AAAAGGAAATGATAAG
1 AAAAGGAAATGAT-AG
398864 AAAAGGAAATGGATAG
1 AAAAGGAAAT-GATAG
398880 AAA
1 AAA
398883 TGATATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (15 bp):
AAAAGGAAATGATAG
Found at i:399097 original size:13 final size:13
Alignment explanation
Indices: 399079--399104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
399069 TTATAGGCGT
399079 GAAAATGGTGATG
1 GAAAATGGTGATG
399092 GAAAATGGTGATG
1 GAAAATGGTGATG
399105 AACAAATAGT
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:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
GAAAATGGTGATG
Found at i:403973 original size:24 final size:25
Alignment explanation
Indices: 403939--403997 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
403929 TCAGCAAAGA
*
403939 AAAAGTAAAGCACTTAAAAAGAAG-
1 AAAAGTAAAGCACTCAAAAAGAAGC
* *
403963 AAAAGTCAAGCACTCCAAAAGAAGC
1 AAAAGTAAAGCACTCAAAAAGAAGC
*
403988 AAAAGCAAAG
1 AAAAGTAAAG
403998 AAAAGAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 21 0.72
25 8 0.28
ACGTcount: A:0.59, C:0.15, G:0.17, T:0.08
Consensus pattern (25 bp):
AAAAGTAAAGCACTCAAAAAGAAGC
Found at i:407405 original size:19 final size:20
Alignment explanation
Indices: 407381--407432 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
407371 CGACCAAGAG
* *
407381 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
407400 CATGTATTTTTCATAAAAAAT
1 CATGTA-TTTTCATAAAAAAT
407421 CATGTATTTTCA
1 CATGTATTTTCA
407433 AATGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 12 0.41
21 11 0.38
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:408145 original size:22 final size:23
Alignment explanation
Indices: 408112--408158 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
408102 GGAGTGCAAA
408112 AAGAAAAGAAAAATACAAAA-AG
1 AAGAAAAGAAAAATACAAAAGAG
*
408134 AAGAATAA-AAAAATTCAAAAGAG
1 AAGAA-AAGAAAAATACAAAAGAG
408157 AA
1 AA
408159 AGCAACCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.74, C:0.04, G:0.13, T:0.09
Consensus pattern (23 bp):
AAGAAAAGAAAAATACAAAAGAG
Done.