Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000669.1 Hibiscus syriacus cultivar Beakdansim tig00001302_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: 144374
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6585 original size:19 final size:20
Alignment explanation
Indices: 6561--6611 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
6551 AATGACCAAT
6561 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
6580 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
6600 AAAATCGCAACG
1 AAAATCGCAACG
6612 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:6621 original size:20 final size:20
Alignment explanation
Indices: 6598--6651 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
6588 AACGCGATTT
*
6598 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
6618 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
6638 AGAAAATCGCAACG
1 AGAAAATCGCAACG
6652 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:6711 original size:20 final size:20
Alignment explanation
Indices: 6686--6936 Score: 351
Period size: 20 Copynumber: 12.4 Consensus size: 20
6676 TTTAGAAGAA
* *
6686 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGACTGAGAG
* * *
6706 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGACTGAGAG
*
6726 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGACTGAGAG
* *
6746 AGTCGCAACGCGA-TGTAGAAG
1 AATCGCAATGCGACTG-AG-AG
6767 AAAATCGCAATGCGACTGAGAG
1 --AATCGCAATGCGACTGAGAG
6789 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAG
6809 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAG
6829 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAG
6849 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAG
6869 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAG
6889 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAG
* * * *
6909 AATCGCAACGCGATTTAGAA
1 AATCGCAATGCGACTGAGAG
6929 AATCGCAA
1 AATCGCAA
6937 CGTTGAAAAT
Statistics
Matches: 215, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
19 2 0.01
20 194 0.90
21 2 0.01
22 2 0.01
23 13 0.06
24 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (20 bp):
AATCGCAATGCGACTGAGAG
Found at i:6965 original size:20 final size:20
Alignment explanation
Indices: 6927--6965 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6917 CGCGATTTAG
* *
6927 AAAATCGCAACGTTGAAAAT
1 AAAATCGCAACGGTCAAAAT
6947 AAAATCGCAACGGTCAAAA
1 AAAATCGCAACGGTCAAAA
6966 GAATAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGGTCAAAAT
Found at i:7057 original size:6 final size:6
Alignment explanation
Indices: 7046--7118 Score: 146
Period size: 6 Copynumber: 12.2 Consensus size: 6
7036 GACACGTATT
7046 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
7094 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
7119 GACGGCGACG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:7806 original size:6 final size:6
Alignment explanation
Indices: 7795--7893 Score: 198
Period size: 6 Copynumber: 16.5 Consensus size: 6
7785 TCTCGTCTCG
7795 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
7843 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
7891 GGT
1 GGT
7894 AATACGTGTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:8021 original size:20 final size:20
Alignment explanation
Indices: 7998--8168 Score: 198
Period size: 20 Copynumber: 8.4 Consensus size: 20
7988 ATTTTCAACG
* *
7998 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
8018 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
* *
8038 TTGCGATTCTCTCAGTCGCG
1 TTGCGATTCTCTCAATCGCA
* *
8058 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
* *
8081 TTGCGACTCTCTCAATCGCG
1 TTGCGATTCTCTCAATCGCA
*
8101 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
8121 TTGCGATTATATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
8141 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
8161 TTGCGATT
1 TTGCGATT
8169 TTCTTCTAAA
Statistics
Matches: 135, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
20 115 0.85
21 2 0.01
22 3 0.02
23 15 0.11
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:8098 original size:83 final size:83
Alignment explanation
Indices: 7996--8148 Score: 216
Period size: 83 Copynumber: 1.8 Consensus size: 83
7986 TTATTTTCAA
* * * * * * *
7996 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCGTTG
1 CGTTGCGACTCTATAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTG
8061 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
* * *
8079 CGTTGCGACTCTCTCAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTG
1 CGTTGCGACTCTATAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTG
8144 CGATT
66 CGATT
8149 CTATCAATCG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 60 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (83 bp):
CGTTGCGACTCTATAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTG
CGATTTTCTTCTAAATCG
Found at i:8165 original size:103 final size:103
Alignment explanation
Indices: 7996--8189 Score: 307
Period size: 103 Copynumber: 1.9 Consensus size: 103
7986 TTATTTTCAA
* * * * * * *
7996 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCGTTG
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
8061 CGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
66 CGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
* *
8099 CGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
8164 CGATTTTCTTCTAAATCGCGTTGCGA
66 CGATTTTCTTCTAAATCGCGTTGCGA
8190 ACTTGGAAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 82 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.36
Consensus pattern (103 bp):
CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
CGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
Found at i:8181 original size:83 final size:81
Alignment explanation
Indices: 7998--8189 Score: 208
Period size: 83 Copynumber: 2.3 Consensus size: 81
7988 ATTTTCAACG
* * * * * * * * *
7998 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCGTTGCG
1 TTGCGACTCTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCG
*
8063 ATTTTCTTCTAAATCGCG
66 A-TTTCTTC-AAATCGCA
*
8081 TTGCGACTCTCTCAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCG
1 TTGCGACTCTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCG
8146 A-TTCTATC-AATCGCA
66 ATTTCT-TCAAATCGCA
*
8161 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--CTC-TCTAAATCGCGTTGCGA
8190 ACTTGGAAGC
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
80 12 0.13
81 4 0.04
82 4 0.04
83 72 0.78
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (81 bp):
TTGCGACTCTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCG
ATTTCTTCAAATCGCA
Found at i:8230 original size:20 final size:20
Alignment explanation
Indices: 8205--8256 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
8195 GAAGCTCGCA
*
8205 TTGCGATTTTCTTTTGACCG
1 TTGCGATTTTCTTTTGAACG
*
8225 TTGCGATTTTCTTTTTAACG
1 TTGCGATTTTCTTTTGAACG
8245 TTGCGATTTTCT
1 TTGCGATTTTCT
8257 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTCTTTTGAACG
Found at i:8283 original size:19 final size:20
Alignment explanation
Indices: 8243--8293 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
8233 TTCTTTTTAA
*
8243 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
8263 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
8282 CGTTGCGATTTT
1 CGTTGCGATTTT
8294 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:12029 original size:14 final size:15
Alignment explanation
Indices: 12005--12034 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11995 ATATTAAAAA
12005 ATATGTTAAAATATT
1 ATATGTTAAAATATT
12020 ATAT-TTAAAATATT
1 ATATGTTAAAATATT
12034 A
1 A
12035 AAAATACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATATGTTAAAATATT
Found at i:12530 original size:20 final size:20
Alignment explanation
Indices: 12505--12546 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12495 GTTAAAGGCG
*
12505 AAGGTTTTGTTGTGACAGCA
1 AAGGTTTTGTTGTGACAACA
12525 AAGGTTTTGTTGTGACAACA
1 AAGGTTTTGTTGTGACAACA
12545 AA
1 AA
12547 AGGAAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (20 bp):
AAGGTTTTGTTGTGACAACA
Found at i:16788 original size:24 final size:24
Alignment explanation
Indices: 16761--16867 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
16751 AAACGGAGAT
*
16761 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
16785 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
16809 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
16833 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
16857 ATCAGAAATCA
1 ATCAGAAATCA
16868 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:16867 original size:48 final size:48
Alignment explanation
Indices: 16761--16869 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
16751 AAACGGAGAT
* * * **
16761 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
16809 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
16857 ATCAGAAATCAGA
1 ATCAGAAATCAGA
16870 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:19364 original size:13 final size:13
Alignment explanation
Indices: 19346--19406 Score: 77
Period size: 13 Copynumber: 4.3 Consensus size: 13
19336 TCCGGGCAAC
19346 GGTCAACGGGTCG
1 GGTCAACGGGTCG
19359 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
19377 GGTCAACGGGTCG
1 GGTCAACGGGTCG
19390 GGTCAACGGGTCG
1 GGTCAACGGGTCG
19403 GGTC
1 GGTC
19407 GGGTTGTGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
13 30 0.70
18 13 0.30
ACGTcount: A:0.13, C:0.23, G:0.48, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:19383 original size:31 final size:31
Alignment explanation
Indices: 19346--19410 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
19336 TCCGGGCAAC
19346 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
19377 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
19408 GGT
1 GGT
19411 TGTGACCGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:19410 original size:18 final size:18
Alignment explanation
Indices: 19352--19393 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
19342 CAACGGTCAA
19352 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
19370 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
19388 CGGGTC
1 CGGGTC
19394 AACGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:21566 original size:24 final size:24
Alignment explanation
Indices: 21539--21646 Score: 72
Period size: 24 Copynumber: 4.5 Consensus size: 24
21529 AAACGGAGAT
*
21539 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
21563 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
21587 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
21611 ATCAGATGTCAAAAACATAATTCAA
1 ATCAGAAATC-AAAACAGAATTCAG
*
21636 ATAAGAAATCA
1 ATCAGAAATCA
21647 GATAAAATAT
Statistics
Matches: 59, Mismatches: 24, Indels: 2
0.69 0.28 0.02
Matches are distributed among these distances:
24 42 0.71
25 17 0.29
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:24141 original size:8 final size:8
Alignment explanation
Indices: 24120--24198 Score: 59
Period size: 8 Copynumber: 10.8 Consensus size: 8
24110 TGGTCAACTC
24120 CGGG-CAA
1 CGGGTCAA
24127 C-GGTCAA
1 CGGGTCAA
24134 CGGGTCAA
1 CGGGTCAA
24142 C-GGTCAA
1 CGGGTCAA
24149 CGGGT---
1 CGGGTCAA
24154 CGGGTCAA
1 CGGGTCAA
**
24162 CGGGTCGGGT
1 CGGGTC--AA
24172 CGGGTCAA
1 CGGGTCAA
24180 CGGGT---
1 CGGGTCAA
24185 CGGGTCAA
1 CGGGTCAA
24193 CGGGTC
1 CGGGTC
24199 GGGTCGGGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 21
0.70 0.05 0.26
Matches are distributed among these distances:
5 10 0.18
6 2 0.04
7 12 0.21
8 27 0.47
10 6 0.11
ACGTcount: A:0.18, C:0.25, G:0.43, T:0.14
Consensus pattern (8 bp):
CGGGTCAA
Found at i:24144 original size:15 final size:15
Alignment explanation
Indices: 24120--24167 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
24110 TGGTCAACTC
24120 CGGG-CAACGGTCAA
1 CGGGTCAACGGTCAA
24134 CGGGTCAACGGTCAA
1 CGGGTCAACGGTCAA
*
24149 CGGGTC--GGGTCAA
1 CGGGTCAACGGTCAA
24162 CGGGTC
1 CGGGTC
24168 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 12 0.38
14 4 0.12
15 16 0.50
ACGTcount: A:0.21, C:0.27, G:0.40, T:0.12
Consensus pattern (15 bp):
CGGGTCAACGGTCAA
Found at i:24161 original size:13 final size:13
Alignment explanation
Indices: 24128--24203 Score: 80
Period size: 13 Copynumber: 5.3 Consensus size: 13
24118 TCCGGGCAAC
*
24128 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
24143 GGTCAACGGGTCG
1 GGTCAACGGGTCG
24156 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
24174 GGTCAACGGGTCG
1 GGTCAACGGGTCG
24187 GGTCAACGGGTCG
1 GGTCAACGGGTCG
24200 GGTC
1 GGTC
24204 GGGTTGTGAC
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
13 30 0.55
15 12 0.22
18 13 0.24
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:24181 original size:31 final size:31
Alignment explanation
Indices: 24143--24207 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
24133 ACGGGTCAAC
24143 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
24174 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
24205 GGT
1 GGT
24208 TGTGACCGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:24207 original size:18 final size:18
Alignment explanation
Indices: 24149--24190 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
24139 CAACGGTCAA
24149 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
24167 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
24185 CGGGTC
1 CGGGTC
24191 AACGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:34946 original size:17 final size:17
Alignment explanation
Indices: 34920--34955 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34910 ATATCATCCC
34920 TTATAAATTTTAAAAAT
1 TTATAAATTTTAAAAAT
* *
34937 TTATATATTTTAAATAT
1 TTATAAATTTTAAAAAT
34954 TT
1 TT
34956 TTATTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATAAATTTTAAAAAT
Found at i:59035 original size:24 final size:23
Alignment explanation
Indices: 59008--59072 Score: 58
Period size: 26 Copynumber: 2.7 Consensus size: 23
58998 CAAATTATTG
59008 AATATTTAAAAATATAAATAAAAT
1 AATATTTAAAAATATAAA-AAAAT
* * **
59032 AATAAATTTAAAATTATTAAAATCT
1 AAT--ATTTAAAAATATAAAAAAAT
59057 ATATATTTAAAAATAT
1 A-ATATTTAAAAATAT
59073 TTATAAACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
24 14 0.42
25 4 0.12
26 15 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATTTAAAAATATAAAAAAAT
Found at i:59073 original size:24 final size:23
Alignment explanation
Indices: 59009--59073 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
58999 AAATTATTGA
59009 ATATTTAAAAATATAAATAAAATAAT
1 ATATTTAAAAATAT---TAAAATAAT
* * *
59035 AAATTTAAAATTATTAAAATCTAT
1 ATATTTAAAAATATTAAAAT-AAT
59059 ATATTTAAAAATATT
1 ATATTTAAAAATATT
59074 TATAAACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 6 0.18
24 15 0.45
26 12 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATTTAAAAATATTAAAATAAT
Found at i:77737 original size:106 final size:106
Alignment explanation
Indices: 77549--77920 Score: 602
Period size: 106 Copynumber: 3.5 Consensus size: 106
77539 ACTAATTCAA
* *
77549 TAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATCAGCATAT
1 TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATCATCAGCTTAT
*
77614 AATATTCCAATCGGTAAACAGCAGCTAATTTTAAATATTAT
66 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
* *
77655 TAGAAACTCAAAATTTACTATCGGAAAGCCAGATAATCAATGAAAATTAACAATCATCAGCTTAT
1 TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATCATCAGCTTAT
77720 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
66 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
* * *
77761 TAGAAATTCAGAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACATTCATCAGCTTAT
1 TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATCATCAGCTTAT
77826 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
66 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
* ** * * * *
77867 TAGAAACTCATAATTTAAAAT-AGAAAACTAAATAATCAATTAAATTTAACAATC
1 TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATC
77921 CTAAGACCAA
Statistics
Matches: 247, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
105 28 0.11
106 219 0.89
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (106 bp):
TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATCATCAGCTTAT
AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
Found at i:77941 original size:212 final size:218
Alignment explanation
Indices: 77414--77949 Score: 622
Period size: 212 Copynumber: 2.5 Consensus size: 218
77404 TTAAAAACTA
* * * * * * * * *
77414 CAGCTAACTTTAAACATTACTAGAAACTCGACA-TTAACAATTAAAAAACCAACTAATCTATGAA
1 CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTAA-AATCAGAAAACCAAATAATCAATGAA
* * ** *
77478 AATTAACACTCCTCGGAACAA-AAATATTCCAATCAGTAAACAACAGCTAATATTTAGCATTACT
65 AATTAACAATCATAAG-CCAATAAA-ATTCCAATCAGTAAACAACAGCTAATATTTA-CA-TACT
77542 AATTCAATAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATC
126 AATTCAATAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATC
*
77607 AGCATATAATATTCCAATCGGTAAACAG
191 AGCATATAATATTCCAATCAGTAAACAG
** * * *
77635 CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTACTATCGGAAAGCCAGATAATCAATGAAA
1 CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTAAAATCAGAAAACCAAATAATCAATGAAA
* ** * *
77700 ATTAACAATCATCAGCTTATAATATTCCAATCAGTAAACAGCAGCTAAT-TTTA-A-A-T-ATT-
66 ATTAACAATCATAAGCCAATAAAATTCCAATCAGTAAACAACAGCTAATATTTACATACTAATTC
* * * * * *
77759 ATTAGAAATTCAGAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACATTCATCAGCTT
131 AATAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATCAGCAT
77824 ATAATATTCCAATCAGTAAACAG
196 ATAATATTCCAATCAGTAAACAG
* * *
77847 CAGCTAATTTTAAATATTATTAGAAACTCATAATTTAAAAT-AGAAAACTAAATAATCAATTAAA
1 CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTAAAATCAGAAAACCAAATAATCAATGAAA
* * *
77911 TTTAACAATCCTAAGACCAATAAAATTCCAACCAGTAAA
66 ATTAACAATCATAAG-CCAATAAAATTCCAATCAGTAAA
77950 TTAAAAATAA
Statistics
Matches: 268, Mismatches: 44, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
211 30 0.11
212 138 0.51
213 3 0.01
214 1 0.00
215 1 0.00
217 1 0.00
219 4 0.01
220 26 0.10
221 61 0.23
222 3 0.01
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (218 bp):
CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTAAAATCAGAAAACCAAATAATCAATGAAA
ATTAACAATCATAAGCCAATAAAATTCCAATCAGTAAACAACAGCTAATATTTACATACTAATTC
AATAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATCAGCAT
ATAATATTCCAATCAGTAAACAG
Found at i:78538 original size:14 final size:15
Alignment explanation
Indices: 78501--78538 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
78491 AAAGATTTTA
*
78501 TAAATTAATACTTAC
1 TAAATTAATACCTAC
78516 TAAATTAATACCT-C
1 TAAATTAATACCTAC
*
78530 TAAAATAAT
1 TAAATTAAT
78539 GATTTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATTAATACCTAC
Found at i:82084 original size:23 final size:23
Alignment explanation
Indices: 82058--82105 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
82048 ATAAAGTACA
*
82058 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
82081 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
82104 AT
1 AT
82106 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:82550 original size:23 final size:23
Alignment explanation
Indices: 82515--82587 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
82505 ATACTTTACA
*
82515 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
82538 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
82561 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
82584 ATAT
1 ATAT
82588 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:82986 original size:23 final size:23
Alignment explanation
Indices: 82960--83018 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
82950 AACCACTACC
82960 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
82983 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
83006 TATTACATCATAT
1 TATTACATTATAT
83019 TTTTATCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:83333 original size:430 final size:431
Alignment explanation
Indices: 82172--83650 Score: 2683
Period size: 430 Copynumber: 3.5 Consensus size: 431
82162 TATTACATTA
*
82172 TATTATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
82237 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
82302 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
82367 AATAATAATATATATCGTAACGTAAAAAATAAATCA-T-------TATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
* * *
82424 TTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
* * *
82489 TTTATAAAAATGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTA
326 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
*
82554 TTACATTATATAAGTGCTACCTATTACATCATATTTTTACC
391 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
* * *
82595 TATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATAATTTTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
82660 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
82725 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
82790 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
82855 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATGGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
82920 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATA
326 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
*
82985 TTACATTATATAAGCGCTACCTATTACATCATATTTTTATC
391 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
83026 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
83091 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
83155 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
83220 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
* *
83285 CTTAAAACTCACTCAAAGGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
83350 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
326 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
83415 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
83456 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
83521 TTATGTTTCAA-TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
83585 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
83649 AA
196 AA
83651 CAACATTAAC
Statistics
Matches: 1019, Mismatches: 29, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
423 225 0.22
424 1 0.00
429 10 0.01
430 529 0.52
431 254 0.25
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (431 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:83412 original size:23 final size:23
Alignment explanation
Indices: 83386--83448 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
83376 ATATAACCAC
83386 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
83409 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
83432 TACCTATTACATCATAT
1 TACCTATTACATTATAT
83449 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:83925 original size:39 final size:39
Alignment explanation
Indices: 83869--83955 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
83859 TCAAGTTGTA
* *
83869 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCATTTTGCTTGGCACCATATGAGATTTG
*
83908 GATTTTGATTTCATTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCATTTTGCTTGGCACCATATGAGATTTG
83947 GATTTTGAT
1 GATTTTGAT
83956 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCATTTTGCTTGGCACCATATGAGATTTG
Found at i:84249 original size:18 final size:18
Alignment explanation
Indices: 84226--84262 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
84216 CGAAATATAT
84226 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
84244 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
84262 A
1 A
84263 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:84683 original size:25 final size:25
Alignment explanation
Indices: 84649--84698 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
84639 ATTATTTTTC
*
84649 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
84674 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
84699 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:85006 original size:23 final size:23
Alignment explanation
Indices: 84980--85042 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
84970 ATATAAGCAC
84980 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
85003 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
85026 TACCTATTACATCATAT
1 TACCTATTACATTATAT
85043 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:85445 original size:25 final size:25
Alignment explanation
Indices: 85388--85453 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
85378 CACTCAAAAG
*
85388 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
85413 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
85438 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
85454 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:88448 original size:183 final size:182
Alignment explanation
Indices: 87923--88415 Score: 905
Period size: 183 Copynumber: 2.7 Consensus size: 182
87913 TTAAAATTAC
*
87923 CGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTGCCGACACAAT
1 CGACACTTTTTTAAA-TGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
87988 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
88053 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
88106 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
88171 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
88236 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
88289 CGACACTTTTTGAGAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTA-AATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
88354 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
88416 ATAGCATTGC
Statistics
Matches: 302, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
182 1 0.00
183 298 0.99
184 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (182 bp):
CGACACTTTTTTAAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:89931 original size:9 final size:9
Alignment explanation
Indices: 89916--89996 Score: 87
Period size: 9 Copynumber: 9.3 Consensus size: 9
89906 ACTTGTTTGG
*
89916 ATCATCATC
1 ATCATCGTC
* *
89925 TTCATCATC
1 ATCATCGTC
*
89934 ATCATCATC
1 ATCATCGTC
89943 ATCATCGTC
1 ATCATCGTC
89952 ATCATCGTC
1 ATCATCGTC
89961 ATCATC-T-
1 ATCATCGTC
89968 -TCATCGTC
1 ATCATCGTC
89976 ATCATCGTC
1 ATCATCGTC
* *
89985 GTCATCTTC
1 ATCATCGTC
89994 ATC
1 ATC
89997 GTCAGTTTCA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
6 5 0.08
7 1 0.02
8 1 0.02
9 56 0.89
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.37
Consensus pattern (9 bp):
ATCATCGTC
Found at i:89936 original size:15 final size:15
Alignment explanation
Indices: 89916--89996 Score: 78
Period size: 15 Copynumber: 5.6 Consensus size: 15
89906 ACTTGTTTGG
89916 ATCATCATCTTCATC
1 ATCATCATCTTCATC
89931 ATCATCA---TCATC
1 ATCATCATCTTCATC
* *
89943 ATCATCGTCATCATC
1 ATCATCATCTTCATC
*
89958 GTCATCATCTTCATC
1 ATCATCATCTTCATC
* * *
89973 GTCATCATCGTCGTC
1 ATCATCATCTTCATC
*
89988 ATCTTCATC
1 ATCATCATC
89997 GTCAGTTTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
12 11 0.20
15 44 0.80
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.37
Consensus pattern (15 bp):
ATCATCATCTTCATC
Found at i:89948 original size:24 final size:24
Alignment explanation
Indices: 89916--90000 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
89906 ACTTGTTTGG
* *
89916 ATCATCATCTTCATCATCATCATC
1 ATCATCATCGTCATCATCGTCATC
89940 ATCATCATCGTCATCATCGTCATC
1 ATCATCATCGTCATCATCGTCATC
* *
89964 ATCTTCATCGTCATCATCGTCGTC
1 ATCATCATCGTCATCATCGTCATC
*
89988 ATCTTCATCGTCA
1 ATCATCATCGTCA
90001 GTTTCATCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (24 bp):
ATCATCATCGTCATCATCGTCATC
Found at i:92422 original size:199 final size:198
Alignment explanation
Indices: 91469--92636 Score: 2156
Period size: 198 Copynumber: 5.9 Consensus size: 198
91459 TTTAAATTAG
*
91469 TATCGACACATACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
91534 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATATTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
*
91599 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
91664 AAA
196 AAA
*
91667 TATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
* *
91732 TTGTACCGATTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
*
91797 GACACTTTTTATATATGGATCGACACTTTATGGTTACACCCTGTTTTCCATTCATTCTGGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
*
91862 AAC
196 AAA
*
91865 TATCGACACAAACTAAAAAGTATCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
91930 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
*
91995 GACACTTTTTATATATGGATCGACACTTTATGGTTACACCCTGTTTTCCATTCATTCTGGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
92060 AAA
196 AAA
* *
92063 TATCGACACAAACTAAAACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAA
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
92128 TTATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
*
92193 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
92258 AAA
196 AAA
92261 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
92326 TTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
92391 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
92456 AAAA
195 AAAA
92460 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
92525 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGGA
92590 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
129 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
92637 GGCCATATTG
Statistics
Matches: 944, Mismatches: 24, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
198 593 0.63
199 288 0.31
200 63 0.07
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
AAA
Found at i:94613 original size:33 final size:33
Alignment explanation
Indices: 94574--94639 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
94564 CATCTTAATA
*
94574 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
94607 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
94640 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:94698 original size:21 final size:21
Alignment explanation
Indices: 94673--94716 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
94663 CCCCTTATGC
94673 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
94694 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
94715 CT
1 CT
94717 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:96900 original size:17 final size:18
Alignment explanation
Indices: 96878--96920 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
96868 ATATATCCGG
96878 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
96895 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
96915 TATCAT
1 TATCAT
96921 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:97090 original size:20 final size:20
Alignment explanation
Indices: 97063--97109 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
97053 TCCGGTAACG
97063 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
97082 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
97103 TTTTACC
1 TTTTACC
97110 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:97562 original size:228 final size:229
Alignment explanation
Indices: 97158--97875 Score: 1325
Period size: 228 Copynumber: 3.1 Consensus size: 229
97148 ACTTTTATAC
*
97158 GTATGAACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
97223 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
97288 TTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
*
97353 TATAATAATAAATATGTTTTTCACAGTGAAATAA
196 GATAATAATAAATATGTTTTTCACAGTGAAATAA
97387 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
97451 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
*
97516 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
*
97581 GATAATAATAAATATGTTTTCCACAGTGAAATAA
196 GATAATAATAAATATGTTTTTCACAGTGAAATAA
97615 GTATGGACACTTTTATAAAAATGATATATAC-TTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
*
97679 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
* *
97744 TTATTTAATTTTTTGATATTCTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
*
97809 GATAATAATAAATAT-ATTTTCACAGTGAAATAA
196 GATAATAATAAATATGTTTTTCACAGTGAAATAA
* *
97842 GTATGGACACTTTTATAAAAAGGATAGATACTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTT
97876 ACAATATAAC
Statistics
Matches: 475, Mismatches: 12, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
227 75 0.16
228 339 0.71
229 61 0.13
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.45
Consensus pattern (229 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
TTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
GATAATAATAAATATGTTTTTCACAGTGAAATAA
Found at i:107321 original size:2 final size:2
Alignment explanation
Indices: 107314--107341 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
107304 CCGATTAGTT
107314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
107342 AAATAGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:114821 original size:21 final size:21
Alignment explanation
Indices: 114792--114838 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
114782 ATTCTGACTA
*
114792 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCAATTTCCCAAAT
* * *
114813 TCGCGTTGCAATTTTCCTAAT
1 TCGCATTGCAATTTCCCAAAT
114834 TCGCA
1 TCGCA
114839 AAGCGAATAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (21 bp):
TCGCATTGCAATTTCCCAAAT
Found at i:114883 original size:20 final size:20
Alignment explanation
Indices: 114858--115005 Score: 169
Period size: 20 Copynumber: 7.2 Consensus size: 20
114848 CGTAAATAAT
*
114858 TCGCATTGTGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
*
114878 TCGCATTGCGATTTTTC-TAA
1 TCGCATTGCGA-TTTACGTAA
* *
114898 TTCGTATTGTGATTTACGTAA
1 -TCGCATTGCGATTTACGTAA
114919 TTCGCACTT-CGATTTACGTAA
1 -TCGCA-TTGCGATTTACGTAA
114940 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
114960 TTCGCACTT-CGATTTACGTAA
1 -TCGCA-TTGCGATTTACGTAA
114981 TCGCATTGCGATTTA-GTAAA
1 TCGCATTGCGATTTACGT-AA
115001 TCGCA
1 TCGCA
115006 ACGAGATTCT
Statistics
Matches: 112, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.05
20 53 0.47
21 49 0.44
22 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:114901 original size:41 final size:41
Alignment explanation
Indices: 114858--115005 Score: 196
Period size: 41 Copynumber: 3.6 Consensus size: 41
114848 CGTAAATAAT
* *
114858 TCGCATTGTGATTTACGTAA-TCGCA-TTGCGATTTTTC-TAA
1 TCGCATTGCGATTTACGTAATTCGCACTT-CGA-TTTACGTAA
* *
114898 TTCGTATTGTGATTTACGTAATTCGCACTTCGATTTACGTAA
1 -TCGCATTGCGATTTACGTAATTCGCACTTCGATTTACGTAA
114940 TCGCATTGCGATTTACGTAATTCGCACTTCGATTTACGTAA
1 TCGCATTGCGATTTACGTAATTCGCACTTCGATTTACGTAA
*
114981 TCGCATTGCGATTTA-GTAAATCGCA
1 TCGCATTGCGATTTACGTAATTCGCA
115006 ACGAGATTCT
Statistics
Matches: 99, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
40 9 0.09
41 77 0.78
42 11 0.11
43 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATTCGCACTTCGATTTACGTAA
Found at i:114911 original size:21 final size:22
Alignment explanation
Indices: 114854--114994 Score: 124
Period size: 21 Copynumber: 6.8 Consensus size: 22
114844 AATACGTAAA
114854 TAATTCGCATTGTGA-TTTACG
1 TAATTCGCATTGTGATTTTACG
* *
114875 TAA-TCGCATTGCGATTTTTC-
1 TAATTCGCATTGTGATTTTACG
*
114895 TAATTCGTATTGTGA-TTTACG
1 TAATTCGCATTGTGATTTTACG
*
114916 TAATTCGCACTT-CGA-TTTACG
1 TAATTCGCA-TTGTGATTTTACG
*
114937 TAA-TCGCATTGCGA-TTTACG
1 TAATTCGCATTGTGATTTTACG
*
114957 TAATTCGCACTT-CGA-TTTACG
1 TAATTCGCA-TTGTGATTTTACG
*
114978 TAA-TCGCATTGCGATTT
1 TAATTCGCATTGTGATTT
114995 AGTAAATCGC
Statistics
Matches: 104, Mismatches: 7, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.04
20 42 0.40
21 54 0.52
22 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (22 bp):
TAATTCGCATTGTGATTTTACG
Found at i:114936 original size:62 final size:62
Alignment explanation
Indices: 114854--115005 Score: 197
Period size: 62 Copynumber: 2.5 Consensus size: 62
114844 AATACGTAAA
* * * *
114854 TAATTCGCATTGTGATTTACGTAATCGCATTGCGATTTTTC-TAATTCGTA-TTGTGATTTACG
1 TAATTCGCATTGCGATTTACGTAATCGCATTGCGA-TTTACGTAATTCGCACTT-CGATTTACG
114916 TAATTCGCACTT-CGATTTACGTAATCGCATTGCGATTTACGTAATTCGCACTTCGATTTACG
1 TAATTCGCA-TTGCGATTTACGTAATCGCATTGCGATTTACGTAATTCGCACTTCGATTTACG
114978 TAA-TCGCATTGCGATTTA-GTAAATCGCA
1 TAATTCGCATTGCGATTTACGT-AATCGCA
115006 ACGAGATTCT
Statistics
Matches: 81, Mismatches: 4, Indels: 11
0.84 0.04 0.11
Matches are distributed among these distances:
60 4 0.05
61 23 0.28
62 50 0.62
63 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (62 bp):
TAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATTCGCACTTCGATTTACG
Found at i:118453 original size:20 final size:19
Alignment explanation
Indices: 118430--118484 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
118420 GCAATATCTT
*
118430 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
118450 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
118469 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
118485 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:118472 original size:19 final size:19
Alignment explanation
Indices: 118437--118587 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
118427 CTTAATGTCT
* **
118437 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
118457 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
118476 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
118490 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
118509 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
118523 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
118542 ATCGCAAT--G--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
118556 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
118575 ATCGCAACGCGAA
1 ATCGCAATGCGAA
118588 TTTAGTTTCG
Statistics
Matches: 101, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 28 0.28
15 3 0.03
16 5 0.05
17 5 0.05
18 3 0.03
19 48 0.48
20 9 0.09
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:118499 original size:33 final size:33
Alignment explanation
Indices: 118457--118583 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
118447 GGAAATGACT
118457 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
118490 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
118523 ATCGCAATGCGAAATGAAAATCGCAATGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
118556 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
118584 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:118637 original size:33 final size:33
Alignment explanation
Indices: 118593--118672 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
118583 GCGAATTTAG
* * *
118593 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
118626 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
118659 TTTTGCATTGCGAT
1 TTTCGCATTGCGAT
118673 AGTCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:118638 original size:19 final size:19
Alignment explanation
Indices: 118614--118672 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
118604 GATTTTGTCG
118614 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
118633 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
118647 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
118666 TTGCGAT
1 TTGCGAT
118673 AGTCATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 6 0.19
16 7 0.22
17 6 0.19
19 13 0.41
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:118756 original size:14 final size:14
Alignment explanation
Indices: 118737--118773 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
118727 CATCAATTAA
118737 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
118751 ACAAATCATCTTTT
1 ACAAATCAACTTTT
118765 ACAAATCAA
1 ACAAATCAA
118774 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:120758 original size:20 final size:20
Alignment explanation
Indices: 120733--120771 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
120723 GTTGCGATTA
120733 TCTCGTTGCGATTTTCATTC
1 TCTCGTTGCGATTTTCATTC
120753 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
120772 TCAACCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.15, T:0.51
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTC
Found at i:121008 original size:94 final size:93
Alignment explanation
Indices: 120862--121139 Score: 383
Period size: 94 Copynumber: 3.1 Consensus size: 93
120852 ATGGATTGCA
* * *
120862 TTACTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
120927 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAAACGAACAAAT
120955 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
121020 TTAGCAGAATTGGCAGC-AAC---CGAAT
65 TTAGCAGAATTGGCAGCAAACGAACAAAT
* * * *
121045 ATACTTCAACCAAAAGACAAAACAAAAGATAAATATTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
121106 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAAACGAACAAAT
121135 TTACT
1 TTACT
121140 AAGCAATCTA
Statistics
Matches: 166, Mismatches: 13, Indels: 15
0.86 0.07 0.08
Matches are distributed among these distances:
86 25 0.15
87 2 0.01
89 19 0.11
90 39 0.23
93 7 0.04
94 74 0.45
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAAACGAACAAAT
Found at i:122857 original size:20 final size:20
Alignment explanation
Indices: 122832--122927 Score: 84
Period size: 20 Copynumber: 5.2 Consensus size: 20
122822 TTTTGGTTGA
122832 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
122852 AATGAAAATCGCAACGCTGA-
1 AATGAAAATCGCAACG-AGAG
**
122872 AATGACTATCGCAAC--GAG
1 AATGAAAATCGCAACGAGAG
122890 -A-G--AATCGCAAC-ACGA-
1 AATGAAAATCGCAACGA-GAG
122905 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
122925 AAT
1 AAT
122928 CGCAATGCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 8 0.13
16 4 0.06
17 4 0.06
19 11 0.18
20 33 0.53
21 2 0.03
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:122873 original size:40 final size:38
Alignment explanation
Indices: 122829--122927 Score: 118
Period size: 40 Copynumber: 2.7 Consensus size: 38
122819 GTCTTTTGGT
*
122829 TGAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 TGAAATGAAAATCGCAACGAGAGAATG--AATCGCAACAC
**
122869 TGAAATGACTATCGCAAC--GAG-A-GAATCGCAACAC
1 TGAAATGAAAATCGCAACGAGAGAATGAATCGCAACAC
122903 -GAAATGAAAATCGCAACGAGAGAAT
1 TGAAATGAAAATCGCAACGAGAGAAT
122928 CGCAATGCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
33 15 0.30
34 10 0.20
35 3 0.06
36 2 0.04
37 1 0.02
38 3 0.06
40 16 0.32
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (38 bp):
TGAAATGAAAATCGCAACGAGAGAATGAATCGCAACAC
Found at i:122898 original size:14 final size:14
Alignment explanation
Indices: 122879--122932 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
122869 TGAAATGACT
122879 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
122893 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
122912 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
122926 ATCGCAA
1 ATCGCAA
122933 TGCGATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 15 0.45
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.24
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:122916 original size:33 final size:34
Alignment explanation
Indices: 122829--122932 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 34
122819 GTCTTTTGGT
*
122829 TGAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 TGAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACAC
**
122869 TGAAATGACTATCGCAACGAGAGAATCGCAACAC
1 TGAAATGAAAATCGCAACGAGAGAATCGCAACAC
122903 -GAAATGAAAATCGCAACGAGAGAATCGCAA
1 TGAAATGAAAATCGCAACGAGAGAATCGCAA
122933 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
33 28 0.47
34 10 0.17
36 1 0.02
37 1 0.02
38 3 0.05
40 16 0.27
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (34 bp):
TGAAATGAAAATCGCAACGAGAGAATCGCAACAC
Found at i:123585 original size:20 final size:20
Alignment explanation
Indices: 123562--123675 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
123552 CGATAGTCAG
*
123562 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
123582 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
123602 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
123622 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
123643 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
123663 ATTCGCATTGCGA
1 ATTCGCATTGCGA
123676 ATTAGGAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 65 0.78
21 18 0.22
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:123638 original size:41 final size:40
Alignment explanation
Indices: 123562--123675 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 40
123552 CGATAGTCAG
* *
123562 ATTCGTATTGCGATTTACGTATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
* * *
123602 ATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTACGT
* *
123643 AATCGCGTTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
123676 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 30 0.47
41 34 0.53
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
Found at i:123690 original size:61 final size:61
Alignment explanation
Indices: 123568--123690 Score: 156
Period size: 61 Copynumber: 2.0 Consensus size: 61
123558 TCAGATTCGT
* * * * * *
123568 ATTGCGATTTACGTATTCGTATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGC
1 ATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGC
* * **
123629 ATTGCGATTTACTTAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCGC
1 ATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGC
123690 A
1 A
123691 ACGCGAATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (61 bp):
ATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGC
Found at i:123696 original size:21 final size:21
Alignment explanation
Indices: 123672--123712 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
123662 TATTCGCATT
123672 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
123693 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
123713 TGCGGTAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:135809 original size:60 final size:59
Alignment explanation
Indices: 135701--135869 Score: 146
Period size: 60 Copynumber: 2.8 Consensus size: 59
135691 TTGGATGAAT
* * * * **
135701 TTAGAATATTCAAAAGTTTGGGGACCATTTTAGAAAGAGGGTAGTAGTTT-AGGGA-TAAAA
1 TTAGAATATTCAAAAGTTTGAGGACTAATTTAGAATGAGATTA-TAGTTTGA-GGACT-AAA
* *
135761 TTAGAATGTTCAAAAGTTTGATGACTAATTTAGAATGAGATTCATAGTTTGAGGACTAAA
1 TTAGAATATTCAAAAGTTTGAGGACTAATTTAGAATGAGATT-ATAGTTTGAGGACTAAA
* * * * *
135821 TTAAAATCTTCAAGAGTTTAAGGA-TCAATTTAAAATGAGAATTATAGTT
1 TTAGAATATTCAAAAGTTTGAGGACT-AATTTAGAATGAG-ATTATAGTT
135870 ATGGACATAT
Statistics
Matches: 90, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
59 1 0.01
60 83 0.92
61 6 0.07
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.34
Consensus pattern (59 bp):
TTAGAATATTCAAAAGTTTGAGGACTAATTTAGAATGAGATTATAGTTTGAGGACTAAA
Found at i:142244 original size:22 final size:22
Alignment explanation
Indices: 142219--142260 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
142209 TTGTGTCAAT
142219 GAAGAAAAGCCCATTGTTCTGA
1 GAAGAAAAGCCCATTGTTCTGA
142241 GAAGAAAAGCCCATTGTTCT
1 GAAGAAAAGCCCATTGTTCT
142261 CCACCACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (22 bp):
GAAGAAAAGCCCATTGTTCTGA
Done.