Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold116_ERROPOS1184609
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: 202646
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1067 original size:9 final size:9
Alignment explanation
Indices: 1053--1204 Score: 53
Period size: 9 Copynumber: 16.7 Consensus size: 9
1043 TGAGTATAAT
1053 TAAGTTATG
1 TAAGTTATG
*
1062 TAAGTTATAA
1 TAAGTTAT-G
* * *
1072 TATGATATA
1 TAAGTTATG
*
1081 T-ATTTATG
1 TAAGTTATG
1089 T-A-TTATG
1 TAAGTTATG
1096 TAAGTTATG
1 TAAGTTATG
*
1105 TAAATTATG
1 TAAGTTATG
*
1114 TACGTTATG
1 TAAGTTATG
* * *
1123 AAATTTGATCTT
1 TAAGTT-A--TG
*
1135 TAAATTATG
1 TAAGTTATG
1144 TAAGTTATG
1 TAAGTTATG
* * *
1153 AAATTTGAACTT
1 TAAGTT--A-TG
*
1165 TAAATTATG
1 TAAGTTATG
1174 TAAGTTATG
1 TAAGTTATG
1183 T-A-TTATG
1 TAAGTTATG
*
1190 TAAATTATG
1 TAAGTTATG
*
1199 TGAGTT
1 TAAGTT
1205 GCTGGGGAAC
Statistics
Matches: 105, Mismatches: 27, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
7 12 0.11
8 8 0.08
9 65 0.62
10 8 0.08
11 2 0.02
12 10 0.10
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:1139 original size:30 final size:30
Alignment explanation
Indices: 1105--1182 Score: 138
Period size: 30 Copynumber: 2.6 Consensus size: 30
1095 GTAAGTTATG
* *
1105 TAAATTATGTACGTTATGAAATTTGATCTT
1 TAAATTATGTAAGTTATGAAATTTGAACTT
1135 TAAATTATGTAAGTTATGAAATTTGAACTT
1 TAAATTATGTAAGTTATGAAATTTGAACTT
1165 TAAATTATGTAAGTTATG
1 TAAATTATGTAAGTTATG
1183 TATTATGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (30 bp):
TAAATTATGTAAGTTATGAAATTTGAACTT
Found at i:1189 original size:16 final size:16
Alignment explanation
Indices: 1168--1199 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1158 TGAACTTTAA
*
1168 ATTATGTAAGTTATGT
1 ATTATGTAAATTATGT
1184 ATTATGTAAATTATGT
1 ATTATGTAAATTATGT
1200 GAGTTGCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (16 bp):
ATTATGTAAATTATGT
Found at i:4053 original size:15 final size:15
Alignment explanation
Indices: 4030--4061 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4020 AAATAATAAT
4030 TTATATATATTTATC
1 TTATATATATTTATC
*
4045 TTATTTATATTTATC
1 TTATATATATTTATC
4060 TT
1 TT
4062 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATATATTTATC
Found at i:4127 original size:14 final size:14
Alignment explanation
Indices: 4084--4135 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
4074 GCAAAATTAT
* *
4084 ACCTTAAACTTGAA
1 ACCTTAAACCTCAA
*
4098 ACCCTAAA-CTCTAA
1 ACCTTAAACCTC-AA
4112 ACCTTAAACCTCAA
1 ACCTTAAACCTCAA
*
4126 ACCTCAAACC
1 ACCTTAAACC
4136 ATAAACTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 1 0.03
14 27 0.87
15 3 0.10
ACGTcount: A:0.42, C:0.35, G:0.02, T:0.21
Consensus pattern (14 bp):
ACCTTAAACCTCAA
Found at i:4154 original size:21 final size:21
Alignment explanation
Indices: 4096--4160 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
4086 CTTAAACTTG
* * * *
4096 AAACCCTAAACTCTAAACCTT
1 AAACTCTAAACCCCAAACCAT
*
4117 AAACCTC-AAACCTCAAACCAT
1 AAA-CTCTAAACCCCAAACCAT
4138 AAACTCTAAACCCCAAAACCAT
1 AAACTCTAAACCCC-AAACCAT
4160 A
1 A
4161 CACCGTAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.09
21 22 0.63
22 10 0.29
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (21 bp):
AAACTCTAAACCCCAAACCAT
Found at i:9553 original size:11 final size:11
Alignment explanation
Indices: 9537--9562 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9527 GAAATCTAAA
9537 AAAATAATAAT
1 AAAATAATAAT
9548 AAAATAATAAT
1 AAAATAATAAT
9559 AAAA
1 AAAA
9563 AAGAGAAGAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:9676 original size:23 final size:23
Alignment explanation
Indices: 9646--9706 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
9636 ACCCGAAAAC
9646 GGGCAGCTCAAATTTTGAATATG
1 GGGCAGCTCAAATTTTGAATATG
9669 GGGCAGCTCAAATTTTGAATATG
1 GGGCAGCTCAAATTTTGAATATG
9692 GGGCAGCTCAAATTT
1 GGGCAGCTCAAATTT
9707 CAAATTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (23 bp):
GGGCAGCTCAAATTTTGAATATG
Found at i:10449 original size:44 final size:44
Alignment explanation
Indices: 10399--10804 Score: 670
Period size: 44 Copynumber: 9.2 Consensus size: 44
10389 GGTAAATCCT
*
10399 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
10443 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAAATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * * *
10487 GTAGATTTGGCGTCTCTGTATTGGCAGAGAACAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
10531 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
10575 GCAGATTTGGCATCTCTGTATTGACGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
10619 GCAGATTTGACGTCTCTGTATTGGCGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
10663 GCAGATTTGGCGTCTCTGTATTGGCGAAGAACAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
10707 ACAGATTTGGCATCT-TCGTATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCT-GTATTGGCGGAGAGCAGATCGAAGATA
10751 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
10795 GCAGATTTGG
1 GCAGATTTGG
10805 TATTCCTGAG
Statistics
Matches: 333, Mismatches: 27, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
43 1 0.00
44 331 0.99
45 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (44 bp):
GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
Found at i:14514 original size:130 final size:130
Alignment explanation
Indices: 14280--14651 Score: 422
Period size: 130 Copynumber: 2.9 Consensus size: 130
14270 AAAATTCTTC
*
14280 AAAACGAAGACGAAATTTGATGTTCGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * *
14345 TTTCGCATTTGCTCAAAAAAATCGAATTTCCCTTCAAAATTCCATTCATATCTTTTAAAATCCCT
66 TTTCGCATTTGCTCAAAAAAATCGAATATCACTTCAAAATTCCACTCATATCTTTTAAAATCCCT
* * * * *
14410 TAAACGAAGATGAGATTTGATGTTTGGCAATTCGCGGAGTCGTGCCCTAACATGTTGGGTTGCAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * * * * * *
14475 TTTCGTATTTGCTCGAAATAATCGAATATCACTTTAAAATTTCGCTCGTGTCTTTTAAAGTCCCT
66 TTTCGCATTTGCTCAAAAAAATCGAATATCACTTCAAAATTCCACTCATATCTTTTAAAATCCCT
* * * * * * ** *
14540 AAAACGAAGGCGATATCTGGTATTTGACAATTCATGGAATCGTGCCCTAACGTGTTGGGTAGCAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * * * *
14605 TTTCTCGA-TTGTTTAAAATAATCAAATATCCCTTCAAAATTTCACTC
66 TTTCGC-ATTTGCTCAAAAAAATCGAATATCACTTCAAAATTCCACTC
14652 GGCTCTTCTA
Statistics
Matches: 201, Mismatches: 40, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
130 200 1.00
131 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (130 bp):
AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCATTTGCTCAAAAAAATCGAATATCACTTCAAAATTCCACTCATATCTTTTAAAATCCCT
Found at i:14709 original size:130 final size:129
Alignment explanation
Indices: 14307--14757 Score: 354
Period size: 130 Copynumber: 3.5 Consensus size: 129
14297 TGATGTTCGG
* * * *
14307 CAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGC-ATTTGCTCAAAAAAATCGAA
1 CAATTCG-GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGA-TTGTTCAAAATAATCAAA
* * * * * * * * *** * ** *
14371 TTTCCCTTCAAAATTCCATTCATATCTTTTAAAATCCCTTAAACGAAGATGAGATTTGATGTTTG
64 TATCACTTCAAAATTTCACTCGTGTCTTTAAAAATCCCTAAAACGAAGGCAATATCCGGTGTTTG
*
14436 G
129 A
* * * * *
14437 CAATTCGCGGAGTCGTGCCCTAACATGTTGGGTTGCAA-TT-TCGTATTTGCTCGAAATAATCGA
1 CAATTCG-GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCG-A-TTGTTCAAAATAATCAA
* * * * * * *
14500 ATATCACTTTAAAATTTCGCTCGTGTCTTTTAAAGTCCCTAAAACGAAGGCGATATCTGGTATTT
63 ATATCACTTCAAAATTTCACTCGTGTCTTTAAAAATCCCTAAAACGAAGGCAATATCCGGTGTTT
14565 GA
128 GA
* * *
14567 CAATTCATGGAATCGTGCCCTAACGTGTTGGGTAGCAATTTCTCGATTGTTTAAAATAATCAAAT
1 CAATTC-GGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGATTGTTCAAAATAATCAAAT
* * * * *
14632 ATCCCTTCAAAATTTCACTCG-GCTCTTCTAAAAATCCTTTAAATGAGGGCAATA-CGCGGTGTT
65 ATCACTTCAAAATTTCACTCGTG-TCTT-TAAAAATCCCTAAAACGAAGGCAATATC-CGGTGTT
14695 TGA
127 TGA
* * * * ** * *
14698 CAATTCGGGAATCATGCCTTATCGTGCTGGGTTGTGATTTCTCGTTTGTTCAAAACAATC
1 CAATTCGGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGATTGTTCAAAATAATC
14758 GAGTATTCCT
Statistics
Matches: 260, Mismatches: 53, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
128 1 0.00
129 3 0.01
130 217 0.83
131 36 0.14
132 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (129 bp):
CAATTCGGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGATTGTTCAAAATAATCAAATA
TCACTTCAAAATTTCACTCGTGTCTTTAAAAATCCCTAAAACGAAGGCAATATCCGGTGTTTGA
Found at i:18466 original size:24 final size:24
Alignment explanation
Indices: 18438--18549 Score: 152
Period size: 24 Copynumber: 4.7 Consensus size: 24
18428 GATTCAACTT
* * * *
18438 CGCACACATAGTGCCAAATAATTC
1 CGCACACATAGTGCCATACAAATA
* *
18462 CGCACACATAGTGCCTTACATATA
1 CGCACACATAGTGCCATACAAATA
*
18486 CGCACACATAATGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
18510 CGCACACATAGTGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
*
18534 CACACACATAGTGCCA
1 CGCACACATAGTGCCA
18550 CTTAAATCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 77 1.00
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.19
Consensus pattern (24 bp):
CGCACACATAGTGCCATACAAATA
Found at i:22681 original size:26 final size:26
Alignment explanation
Indices: 22651--22701 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
22641 ACCAATGAAC
*
22651 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
22677 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
22702 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:22735 original size:103 final size:104
Alignment explanation
Indices: 22514--22779 Score: 446
Period size: 103 Copynumber: 2.6 Consensus size: 104
22504 TAACCGTTAT
* **
22514 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
22579 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
22618 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTC-GGG
1 TGGTGGATCA-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
22681 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* **
22721 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
22780 TTATATACAA
Statistics
Matches: 152, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
103 96 0.63
104 56 0.37
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (104 bp):
TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:23136 original size:29 final size:29
Alignment explanation
Indices: 23103--23166 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
23093 TAATCCACCA
23103 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
23132 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
23162 CCCAA
1 CCCAA
23167 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:23140 original size:30 final size:30
Alignment explanation
Indices: 23110--23166 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
23100 CCACCCAACT
23110 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
23139 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
23167 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:30141 original size:70 final size:72
Alignment explanation
Indices: 30027--30177 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
30017 GGGGAATCAT
* *
30027 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
30091 GATATCG
66 GATATCG
***
30098 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
30162 GATATCG
66 GATATCG
30169 CACTTAGCA
1 CACTTAGCA
30178 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:30208 original size:103 final size:103
Alignment explanation
Indices: 30097--30318 Score: 374
Period size: 103 Copynumber: 2.2 Consensus size: 103
30087 AATGGATATC
30097 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
30162 GAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
30200 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
30265 GATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
30303 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
30319 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 111 0.99
104 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:30220 original size:26 final size:26
Alignment explanation
Indices: 30190--30240 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
30180 ACCAATGAAC
*
30190 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
30216 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
30241 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:30680 original size:29 final size:29
Alignment explanation
Indices: 30647--30710 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
30637 TAATCCACCA
30647 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
30676 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
30706 CCCAA
1 CCCAA
30711 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:30684 original size:30 final size:30
Alignment explanation
Indices: 30654--30710 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
30644 CCACCCAACT
30654 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
30683 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
30711 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:32855 original size:20 final size:20
Alignment explanation
Indices: 32817--32859 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
32807 TAAATTCTGA
* **
32817 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
32837 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
32857 AAA
1 AAA
32860 AAAATCCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:32875 original size:17 final size:18
Alignment explanation
Indices: 32851--32891 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
32841 ATAAATAAAG
32851 ATAATTAAAAAAATCCTA
1 ATAATTAAAAAAATCCTA
*
32869 A-AATT-AAATAATCCTA
1 ATAATTAAAAAAATCCTA
32885 ATAATTA
1 ATAATTA
32892 TCTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 11 0.55
17 8 0.40
18 1 0.05
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATTAAAAAAATCCTA
Found at i:32906 original size:15 final size:15
Alignment explanation
Indices: 32886--32915 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32876 ATAATCCTAA
*
32886 TAATTATCTTAATAT
1 TAATTATCCTAATAT
32901 TAATTATCCTAATAT
1 TAATTATCCTAATAT
32916 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:45501 original size:20 final size:20
Alignment explanation
Indices: 45476--45516 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
45466 TCAATCTCAT
45476 TATTGCCGTTACATTTCTGC
1 TATTGCCGTTACATTTCTGC
45496 TATTGCCGTTACATTTCTGC
1 TATTGCCGTTACATTTCTGC
45516 T
1 T
45517 TTTACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.46
Consensus pattern (20 bp):
TATTGCCGTTACATTTCTGC
Found at i:50110 original size:42 final size:42
Alignment explanation
Indices: 50051--50134 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
50041 ACCCAATGGG
50051 CCCTTTCTGAGTTGAAATCGAGTTAACTTAGAGAGATGATTA
1 CCCTTTCTGAGTTGAAATCGAGTTAACTTAGAGAGATGATTA
50093 CCCTTTCTGAGTTGAAATCGAGTTAACTTAGAGAGATGATTA
1 CCCTTTCTGAGTTGAAATCGAGTTAACTTAGAGAGATGATTA
50135 TACCTGTCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (42 bp):
CCCTTTCTGAGTTGAAATCGAGTTAACTTAGAGAGATGATTA
Found at i:50447 original size:25 final size:25
Alignment explanation
Indices: 50413--50464 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
50403 CGTAAATTCT
**
50413 AAAATAAATTCTCAATGGTCCTCTC
1 AAAATAAATTCTCAACCGTCCTCTC
50438 AAAATAAATTCTCAACCGTCCTCTC
1 AAAATAAATTCTCAACCGTCCTCTC
50463 AA
1 AA
50465 TGCCCGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (25 bp):
AAAATAAATTCTCAACCGTCCTCTC
Found at i:52629 original size:24 final size:24
Alignment explanation
Indices: 52602--52650 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
52592 TGTTTGTATA
52602 CTTTCTCATGTCAACATTTTAGTT
1 CTTTCTCATGTCAACATTTTAGTT
52626 CTTTCTCATGTCAACATTTTAGTT
1 CTTTCTCATGTCAACATTTTAGTT
52650 C
1 C
52651 CAGAACCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.08, T:0.49
Consensus pattern (24 bp):
CTTTCTCATGTCAACATTTTAGTT
Found at i:58262 original size:17 final size:16
Alignment explanation
Indices: 58240--58276 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
58230 ATAATTTTGC
58240 AGTTTAAAGTCCAAAA
1 AGTTTAAAGTCCAAAA
*
58256 TAGTTTACAGTCCAAAA
1 -AGTTTAAAGTCCAAAA
58273 AGTT
1 AGTT
58277 CGAAAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (16 bp):
AGTTTAAAGTCCAAAA
Found at i:58535 original size:6 final size:6
Alignment explanation
Indices: 58526--58616 Score: 164
Period size: 6 Copynumber: 15.2 Consensus size: 6
58516 ATAAAAATAT
* *
58526 AGATTC AGATAT AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC
1 AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC
58574 AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC A
1 AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC A
58617 AATTCAGATC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.19
Consensus pattern (6 bp):
AGATAC
Found at i:62323 original size:4 final size:4
Alignment explanation
Indices: 62314--62340 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
62304 GCTATAAATA
62314 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
62341 TAATATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:71084 original size:21 final size:21
Alignment explanation
Indices: 71045--71084 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
71035 TGGCTAAATA
* * *
71045 ATGCAAGGGAGATGGATGGCT
1 ATGCAAGGGAAAAGAATGGCT
71066 ATGCAAGGGAAAAGAATGG
1 ATGCAAGGGAAAAGAATGG
71085 AGAAATGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.40, T:0.15
Consensus pattern (21 bp):
ATGCAAGGGAAAAGAATGGCT
Found at i:71113 original size:15 final size:15
Alignment explanation
Indices: 71089--71119 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
71079 GAATGGAGAA
71089 ATGAAAGAGAGAATG
1 ATGAAAGAGAGAATG
*
71104 ATGAATGAGAGAATG
1 ATGAAAGAGAGAATG
71119 A
1 A
71120 ATGAGAGATT
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:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (15 bp):
ATGAAAGAGAGAATG
Found at i:75314 original size:38 final size:38
Alignment explanation
Indices: 75264--75340 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
75254 TTTTGGATGT
*
75264 ATGTTAAATGACCGATAAGTTTACCTTTCCGTTATTCG
1 ATGTTAAATGACCGATAAGTTTACCTTTCCATTATTCG
*
75302 ATGTTAAATGACCGGTAAGTTTACCTTTCCATTATTCG
1 ATGTTAAATGACCGATAAGTTTACCTTTCCATTATTCG
75340 A
1 A
75341 ACTTACTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (38 bp):
ATGTTAAATGACCGATAAGTTTACCTTTCCATTATTCG
Found at i:86871 original size:85 final size:85
Alignment explanation
Indices: 86718--87128 Score: 543
Period size: 85 Copynumber: 4.8 Consensus size: 85
86708 AAGTACAATA
* * * * ** * * * * * *
86718 CCGACGTCCCAGACATGGTCTTACATGTAATTCAAAATTGATGCCTCTGGCCCAGACAGGGTCTT
1 CCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACACGATCTT
*
86783 ACACGAAATCAAATACGATG
66 ACACGAAATCAGATACGATG
* * * * *
86803 CTGATGTCCAAGACATGGTCTTATATGTAAACCTCAATCGAGGCCTGTGTCCCAAACACGATCTT
1 CCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACACGATCTT
86868 ACACGAAATCAGATACGATG
66 ACACGAAATCAGATACGATG
* * * * *
86888 CCGATGTCCTAGACATGGTCTTATATGTAAATCTCAATTGAGGCCTGTGTCCCTGACACGGTCTT
1 CCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACACGATCTT
*
86953 ACACGAAATCACATACGATG
66 ACACGAAATCAGATACGATG
* *
86973 CCGATGTCCCAGACATAGTCTTATACGTAAATCTCAATCGAGGTCTGTGTCCCAGACACGATCTT
1 CCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACACGATCTT
* *
87038 ACACAAAATTAGATACGATG
66 ACACGAAATCAGATACGATG
* * *
87058 CCAATGTCCCAGACACGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACACGGTCTT
1 CCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACACGATCTT
87123 ACACGA
66 ACACGA
87129 TGTCTCAAAC
Statistics
Matches: 286, Mismatches: 40, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 286 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (85 bp):
CCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACACGATCTT
ACACGAAATCAGATACGATG
Found at i:86951 original size:43 final size:43
Alignment explanation
Indices: 86723--87123 Score: 279
Period size: 43 Copynumber: 9.4 Consensus size: 43
86713 CAATACCGAC
* * * * ** * * *
86723 GTCCCAGACATGGTCTTACATGTAATTCAAAATTGATGCCTCT
1 GTCCCAGACACGGTCTTATACGTAAATCTCAATCGAGGCCTGT
* * * * *
86766 GGCCCAGACAGGGTCTTACACG-AAATC-AAATACGATG-CTGAT
1 GTCCCAGACACGGTCTTATACGTAAATCTCAAT-CGAGGCCTG-T
* * * *
86808 GTCCAAGACATGGTCTTATATGTAAACCTCAATCGAGGCCTGT
1 GTCCCAGACACGGTCTTATACGTAAATCTCAATCGAGGCCTGT
* * * *
86851 GTCCCAAACACGATCTTACACG-AAA--TCAGATACGATGCC-GAT
1 GTCCCAGACACGGTCTTATACGTAAATCTCA-AT-CGAGGCCTG-T
* * * *
86893 GTCCTAGACATGGTCTTATATGTAAATCTCAATTGAGGCCTGT
1 GTCCCAGACACGGTCTTATACGTAAATCTCAATCGAGGCCTGT
* * * *
86936 GTCCCTGACACGGTCTTACACG-AAATCAC-ATACGATGCC-GAT
1 GTCCCAGACACGGTCTTATACGTAAATCTCAAT-CGAGGCCTG-T
** *
86978 GTCCCAGACATAGTCTTATACGTAAATCTCAATCGAGGTCTGT
1 GTCCCAGACACGGTCTTATACGTAAATCTCAATCGAGGCCTGT
* * * * **
87021 GTCCCAGACACGATCTTACAC-AAAAT-T-AGATACGATGCCAAT
1 GTCCCAGACACGGTCTTATACGTAAATCTCA-AT-CGAGGCCTGT
87063 GTCCCAGACACGGTCTTATACGTAAATCTCAATCGAGGCCTGT
1 GTCCCAGACACGGTCTTATACGTAAATCTCAATCGAGGCCTGT
87106 GTCCCAGACACGGTCTTA
1 GTCCCAGACACGGTCTTA
87124 CACGATGTCT
Statistics
Matches: 277, Mismatches: 59, Indels: 44
0.73 0.16 0.12
Matches are distributed among these distances:
40 4 0.01
41 15 0.05
42 111 0.40
43 128 0.46
44 15 0.05
45 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
GTCCCAGACACGGTCTTATACGTAAATCTCAATCGAGGCCTGT
Found at i:94409 original size:85 final size:84
Alignment explanation
Indices: 94313--94586 Score: 422
Period size: 85 Copynumber: 3.2 Consensus size: 84
94303 GCCTCTATCT
* * * *
94313 CAGACAGGGTCTTACACGAAATCAAATACGATGCCTATGTCCCAGACATGGTCTTATATGTAAGT
1 CAGACACGGTCTTACACGAAATCAGATACGATG-CTATGTCCCAGACATGGTCTTATACGTAAAT
*
94378 GTCAATCGAGGCCTGTGTCC
65 CTCAATCGAGGCCTGTGTCC
* * *
94398 CAAACACGGTCTTACACGAAATCAGATACGATGTCGATGTCCCAAACATGGTCTTATACGTAAAT
1 CAGACACGGTCTTACACGAAATCAGATACGATG-CTATGTCCCAGACATGGTCTTATACGTAAAT
94463 CTCAATCGAGGCCTGTGTCC
65 CTCAATCGAGGCCTGTGTCC
* *
94483 CAGACACGGTCTTACACGAAATCAGATACGATGTTGATGTCCTAGACATGGTCTTATACGTAAAT
1 CAGACACGGTCTTACACGAAATCAGATACGATGCT-ATGTCCCAGACATGGTCTTATACGTAAAT
94548 CTCAATCGAGGCCTGTGTCC
65 CTCAATCGAGGCCTGTGTCC
*
94568 TAGACACGGTCTTACACGA
1 CAGACACGGTCTTACACGA
94587 TGTCTTAGAT
Statistics
Matches: 173, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
85 173 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (84 bp):
CAGACACGGTCTTACACGAAATCAGATACGATGCTATGTCCCAGACATGGTCTTATACGTAAATC
TCAATCGAGGCCTGTGTCC
Found at i:94568 original size:43 final size:43
Alignment explanation
Indices: 94266--94586 Score: 232
Period size: 43 Copynumber: 7.5 Consensus size: 43
94256 CAATGCCGAC
** * * * *
94266 GTCCCAGACGTGGTCTTACATGTAAT-TCAATATCGATGCCTCT
1 GTCCCAGACACGGTCTTACACGAAATCTCAATA-CGAGGCCTGT
* * * * * *
94309 ATCTCAGACAGGGTCTTACACGAAATC-AAATACGATGCCTAT
1 GTCCCAGACACGGTCTTACACGAAATCTCAATACGAGGCCTGT
* * * * *
94351 GTCCCAGACATGGTCTTATATGTAAGTGTCAAT-CGAGGCCTGT
1 GTCCCAGACACGGTCTTACACG-AAATCTCAATACGAGGCCTGT
* * *
94394 GTCCCAAACACGGTCTTACACGAAA--TCAGATACGATGTC-GAT
1 GTCCCAGACACGGTCTTACACGAAATCTCA-ATACGAGGCCTG-T
* * *
94436 GTCCCAAACATGGTCTTATACGTAAATCTCAAT-CGAGGCCTGT
1 GTCCCAGACACGGTCTTACACG-AAATCTCAATACGAGGCCTGT
* *
94479 GTCCCAGACACGGTCTTACACGAAA--TCAGATACGATG-TTGAT
1 GTCCCAGACACGGTCTTACACGAAATCTCA-ATACGAGGCCTG-T
* * *
94521 GTCCTAGACATGGTCTTATACGTAAATCTCAAT-CGAGGCCTGT
1 GTCCCAGACACGGTCTTACACG-AAATCTCAATACGAGGCCTGT
*
94564 GTCCTAGACACGGTCTTACACGA
1 GTCCCAGACACGGTCTTACACGA
94587 TGTCTTAGAT
Statistics
Matches: 220, Mismatches: 41, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
40 6 0.03
41 7 0.03
42 82 0.37
43 109 0.50
44 10 0.05
45 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (43 bp):
GTCCCAGACACGGTCTTACACGAAATCTCAATACGAGGCCTGT
Found at i:94874 original size:8 final size:8
Alignment explanation
Indices: 94861--94892 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
94851 TACAGTACAA
94861 ATTCAATC
1 ATTCAATC
94869 ATTCAATC
1 ATTCAATC
94877 ATTCATATC
1 ATTCA-ATC
94886 ATTCAAT
1 ATTCAAT
94893 TTAATCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTCAATC
Found at i:94888 original size:17 final size:16
Alignment explanation
Indices: 94861--94892 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
94851 TACAGTACAA
94861 ATTCAATCATTCAATC
1 ATTCAATCATTCAATC
94877 ATTCATATCATTCAAT
1 ATTCA-ATCATTCAAT
94893 TTAATCAATA
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:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTCAATCATTCAATC
Found at i:104503 original size:49 final size:50
Alignment explanation
Indices: 104447--104592 Score: 206
Period size: 49 Copynumber: 2.9 Consensus size: 50
104437 TAGCCAAAGC
*
104447 TATCTGGTACTCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA-T
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAGT
* * * *
104496 TATCTGGTACACATAGTAGCCTGGACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAAGT
*
104547 TAT-TGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TATCT-GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
104593 TCATAATAGA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
49 40 0.48
50 5 0.06
51 39 0.46
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (50 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAGT
Found at i:106935 original size:40 final size:40
Alignment explanation
Indices: 106851--107034 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
106841 TTAAATGCTG
* * * *
106851 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
106890 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
106931 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
106971 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
*
107011 TCCGGGTTAAGTCCTGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
107035 GAATGAGTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 110 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:106988 original size:80 final size:81
Alignment explanation
Indices: 106851--107031 Score: 212
Period size: 80 Copynumber: 2.3 Consensus size: 81
106841 TTAAATGCTG
* * *
106851 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
106915 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
106931 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
106992 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
*
107011 TCCGGGTTAAGTCCTGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
107032 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
79 4 0.05
80 75 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:107055 original size:39 final size:39
Alignment explanation
Indices: 106931--107081 Score: 126
Period size: 40 Copynumber: 3.8 Consensus size: 39
106921 AGTTATTAAT
* ** * *
106931 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
** *
106971 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* * *
107011 TCCGGGTTAAGTCCTGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
107051 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
107082 GAGCTATATC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 29 0.31
40 64 0.69
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:114877 original size:40 final size:40
Alignment explanation
Indices: 114793--114976 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
114783 TTAAATGCTG
* * * *
114793 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
114832 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
114873 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
114913 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
*
114953 TCCGGGTTAAGTCCTGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
114977 GAATGAGTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 110 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:114930 original size:80 final size:81
Alignment explanation
Indices: 114793--114973 Score: 212
Period size: 80 Copynumber: 2.3 Consensus size: 81
114783 TTAAATGCTG
* * *
114793 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
114857 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
114873 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
114934 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
*
114953 TCCGGGTTAAGTCCTGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
114974 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
79 4 0.05
80 75 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:114997 original size:39 final size:39
Alignment explanation
Indices: 114873--115023 Score: 126
Period size: 40 Copynumber: 3.8 Consensus size: 39
114863 AGTTATTAAT
* ** * *
114873 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
** *
114913 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* * *
114953 TCCGGGTTAAGTCCTGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
114993 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
115024 GAGCTATATC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 29 0.31
40 64 0.69
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:122468 original size:19 final size:19
Alignment explanation
Indices: 122440--122479 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
122430 CCCCTTATTA
122440 AACATAAAAAA-ATAAAATT
1 AACATAAAAAACAT-AAATT
*
122459 AACATTAAAAACATAAATT
1 AACATAAAAAACATAAATT
122478 AA
1 AA
122480 AGTGAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (19 bp):
AACATAAAAAACATAAATT
Found at i:126287 original size:39 final size:39
Alignment explanation
Indices: 126233--126312 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
126223 ACTCAAATGA
*
126233 CAAATGACATGCCTTTCCAAAAACTGGTCGATAAGGAGT
1 CAAATGACAAGCCTTTCCAAAAACTGGTCGATAAGGAGT
*
126272 CAAATGACAAGCCTTTCCAAAAACTGGTCGATAGGGAGT
1 CAAATGACAAGCCTTTCCAAAAACTGGTCGATAAGGAGT
126311 CA
1 CA
126313 TTCCTAACAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (39 bp):
CAAATGACAAGCCTTTCCAAAAACTGGTCGATAAGGAGT
Found at i:131517 original size:33 final size:33
Alignment explanation
Indices: 131472--131567 Score: 119
Period size: 33 Copynumber: 2.9 Consensus size: 33
131462 TCAAGCCCAT
*
131472 TGGGCCTAAGCCCTATTCAGATAACAGTATGTAC
1 TGGGCCTAAGCCCTTTTCAGATAACAGTATG-AC
131506 TGGGCC-AAGCCCTTTTCAGA-ATACAGTA--AC
1 TGGGCCTAAGCCCTTTTCAGATA-ACAGTATGAC
*
131536 TGGGCCTTAGCCTCTTTTCAGATAACAGTATG
1 TGGGCCTAAGCC-CTTTTCAGATAACAGTATG
131568 GCCTATAGGC
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
30 8 0.15
31 4 0.07
32 16 0.30
33 20 0.37
34 6 0.11
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (33 bp):
TGGGCCTAAGCCCTTTTCAGATAACAGTATGAC
Found at i:133163 original size:15 final size:16
Alignment explanation
Indices: 133143--133197 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 16
133133 AGGAAAGGAA
133143 GAAGAG-AAAGTAGAT
1 GAAGAGAAAAGTAGAT
* *
133158 GAAGAGAAAAG-AAAA
1 GAAGAGAAAAGTAGAT
133173 GAA-AGAAAAGTAGAT
1 GAAGAGAAAAGTAGAT
133188 GAAGA-AAAAG
1 GAAGAGAAAAG
133198 CTGAATCCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 7 0.21
15 21 0.64
16 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (16 bp):
GAAGAGAAAAGTAGAT
Found at i:139666 original size:28 final size:28
Alignment explanation
Indices: 139625--139678 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
139615 ATGCAGTTGA
*
139625 ATACTCAATGTCTCGCACACTAAGTGCC
1 ATACTCAATATCTCGCACACTAAGTGCC
* *
139653 ATACTCGATATCTCGTACACTAAGTG
1 ATACTCAATATCTCGCACACTAAGTG
139679 TCGTACATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (28 bp):
ATACTCAATATCTCGCACACTAAGTGCC
Found at i:139765 original size:43 final size:42
Alignment explanation
Indices: 139691--139809 Score: 163
Period size: 43 Copynumber: 2.9 Consensus size: 42
139681 GTACATAGAT
139691 GAAGCTATCTC-AA-ATCGCACACTAAGTGCCATATATAGCC
1 GAAGCTATCTCGAATATCGCACACTAAGTGCCATATATAGCC
* * *
139731 GAAGCTATGTCGAATATCGCACACCAAAGTGCCATATATAGTC
1 GAAGCTATCTCGAATATCGCACA-CTAAGTGCCATATATAGCC
* *
139774 GAAGCTATCTCG-ATCTCGCACGCTAAGTGCCATATA
1 GAAGCTATCTCGAATATCGCACACTAAGTGCCATATA
139810 AAGATGATTC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
40 10 0.14
41 15 0.22
42 16 0.23
43 28 0.41
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (42 bp):
GAAGCTATCTCGAATATCGCACACTAAGTGCCATATATAGCC
Found at i:147167 original size:28 final size:28
Alignment explanation
Indices: 147126--147185 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
147116 ATGTCGTTGA
*
147126 ATACTCAATGTCTTGCACACTAAGTGCC
1 ATACTCAATATCTTGCACACTAAGTGCC
* *
147154 ATACTCGATATCTTGCACACTAAGTGTC
1 ATACTCAATATCTTGCACACTAAGTGCC
147182 ATAC
1 ATAC
147186 ATAGCCGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (28 bp):
ATACTCAATATCTTGCACACTAAGTGCC
Found at i:147261 original size:42 final size:42
Alignment explanation
Indices: 147157--147311 Score: 199
Period size: 42 Copynumber: 3.7 Consensus size: 42
147147 AAGTGCCATA
* * *
147157 CTCGATATCTTGCACACTAAGTGTCATACATAGCCGAAGCTAT
1 CTCGA-ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTAT
* * * *
147200 CTC-AA-ATCACACATTAAGTGCCATATACAGCCGAAGCTAT
1 CTCGAATCTCGCACACTAAGTGCCATATATAGCCGAAGCTAT
*
147240 GTCGAATCTCGCACACTAAGTGCCATATATAGCCGAAGCTAT
1 CTCGAATCTCGCACACTAAGTGCCATATATAGCCGAAGCTAT
*
147282 CTCG-ATCTCGCACACTAAGTGCCACATATA
1 CTCGAATCTCGCACACTAAGTGCCATATATA
147312 CCTGATTCAT
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
40 30 0.31
41 28 0.29
42 35 0.36
43 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (42 bp):
CTCGAATCTCGCACACTAAGTGCCATATATAGCCGAAGCTAT
Found at i:152081 original size:13 final size:13
Alignment explanation
Indices: 152063--152088 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
152053 GGATATGTTT
152063 TGAAATAATCACA
1 TGAAATAATCACA
152076 TGAAATAATCACA
1 TGAAATAATCACA
152089 CTACATGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
TGAAATAATCACA
Found at i:160510 original size:40 final size:39
Alignment explanation
Indices: 160421--160643 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 39
160411 TTGAATGATG
* * * *
160421 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
160461 TCC-GACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
160500 TCCGGGCTAAGCCCAAAAGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
160539 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAGTAAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
*
160579 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
160620 -CCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
160644 AACGAGGAGC
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
39 67 0.43
40 86 0.55
41 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:160563 original size:79 final size:79
Alignment explanation
Indices: 160466--160643 Score: 234
Period size: 79 Copynumber: 2.2 Consensus size: 79
160456 CCATATCCGA
*
160466 CTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCAAAAGCATTGGTGCGA
1 CTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCAAAAGCATTGGTGCGA
160530 GTTACTA-AATCCGGG
65 GTTACTATAA-CCGGG
* * * * * * *
160545 TTAAGTCCCGAAGGCATTTGTGCGAGTTAGTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA
1 CTAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCAAAAGCATTGGTGCGA
160610 GTTACTATAACCGGG
65 GTTACTATAACCGGG
*
160625 CTATGTCCGAAGGCATTTG
1 CTAAGTCCGAAGGCATTTG
160644 AACGAGGAGC
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
78 1 0.01
79 51 0.59
80 32 0.37
81 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
CTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCAAAAGCATTGGTGCGAG
TTACTATAACCGGG
Found at i:160661 original size:79 final size:78
Alignment explanation
Indices: 160421--160662 Score: 226
Period size: 79 Copynumber: 3.1 Consensus size: 78
160411 TTGAATGATG
* * * * *
160421 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC-GACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCGAAGGCATT
*
160484 TGTGCGA-GATACTAA
64 TGTGCGAGGA-GCTAA
* * * *
160499 TTCCGGGCTAAG-CCCAAAAGCATTGGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCAT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGT-CCGAAGGCAT
*
160562 TTGTGCGAGTTAG-TAAA
63 TTGTGCGAG-GAGCT-AA
* *
160579 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGGCATTTG
**
160644 AACGAGGAGCTATA
66 TGCGAGGAGCTA-A
160658 TCCGG
1 TCCGG
160663 TTAAATTCCG
Statistics
Matches: 132, Mismatches: 20, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
77 1 0.01
78 19 0.14
79 75 0.57
80 34 0.26
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGGCATTTG
TGCGAGGAGCTAA
Found at i:171779 original size:26 final size:26
Alignment explanation
Indices: 171749--171800 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
171739 CACCGCTGAA
*
171749 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
171775 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
171801 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:171883 original size:26 final size:26
Alignment explanation
Indices: 171853--171903 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
171843 ACCAATGAAC
*
171853 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
171879 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
171904 CTTTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:171896 original size:103 final size:104
Alignment explanation
Indices: 171717--171982 Score: 446
Period size: 103 Copynumber: 2.6 Consensus size: 104
171707 TAACCGTTAT
* **
171717 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
171782 ATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
171820 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
171885 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
171924 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
171983 TTATATACAA
Statistics
Matches: 153, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 81 0.53
104 71 0.46
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:172343 original size:29 final size:29
Alignment explanation
Indices: 172310--172373 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
172300 TAATCCACCA
172310 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
172339 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
172369 CCCAA
1 CCCAA
172374 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:172347 original size:30 final size:30
Alignment explanation
Indices: 172317--172373 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
172307 CCACCCAACT
172317 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
172346 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
172374 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:177105 original size:24 final size:24
Alignment explanation
Indices: 177011--177110 Score: 91
Period size: 24 Copynumber: 4.2 Consensus size: 24
177001 GATTCAACTC
** * *
177011 CGCACACATAGTGCCAAATAATTC
1 CGCACACATAGTGCCACTTAAATA
177035 CGCACACATAGTG-C-CTTACATATA
1 CGCACACATAGTGCCACTTA-A-ATA
177059 CGCACACATAGTGCCGTAC--AAATA
1 CGCACACATAGTGCC--ACTTAAATA
*
177083 CGCACACATAGTGCCACTTAAATC
1 CGCACACATAGTGCCACTTAAATA
177107 CGCA
1 CGCA
177111 TATCTAGTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
22 4 0.06
23 2 0.03
24 53 0.84
25 2 0.03
26 1 0.02
28 1 0.02
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (24 bp):
CGCACACATAGTGCCACTTAAATA
Found at i:185573 original size:19 final size:20
Alignment explanation
Indices: 185514--185565 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
185504 AAAAATTACA
* *
185514 AAAAAAATCAAATTAATTT-T
1 AAAAAATTCAAAAT-ATTTAT
185534 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
*
185554 AAAAATTTCAAA
1 AAAAAATTCAAA
185566 TTTATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:185575 original size:21 final size:20
Alignment explanation
Indices: 185533--185575 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
185523 AAATTAATTT
*
185533 TAAAAAATTCAAAATATTTA
1 TAAAAAATTCAAAATATATA
* *
185553 TAAAAATTTCAAATTTATATA
1 TAAAAAATTCAAA-ATATATA
185574 TA
1 TA
185576 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAAATTCAAAATATATA
Found at i:185843 original size:25 final size:24
Alignment explanation
Indices: 185802--185848 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
185792 TATTTAATTT
*
185802 TTAAATTAACTCGAATAAATTTAC
1 TTAAATTAACTCAAATAAATTTAC
*
185826 TTAAATTTAATTCAAATAAATTT
1 TTAAA-TTAACTCAAATAAATTT
185849 CAAATCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAAATTAACTCAAATAAATTTAC
Found at i:193384 original size:7 final size:7
Alignment explanation
Indices: 193372--193397 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
193362 AAAATATATT
193372 TATTTAA
1 TATTTAA
193379 TATTTAA
1 TATTTAA
193386 TATTTAA
1 TATTTAA
193393 TATTT
1 TATTT
193398 TTATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TATTTAA
Done.