Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003463.1 Hibiscus syriacus cultivar Beakdansim tig00007318_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: 94900
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1882 original size:12 final size:12
Alignment explanation
Indices: 1865--1889 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1855 TCTTTGGGGA
1865 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1877 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1889 C
1 C
1890 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3143 original size:19 final size:20
Alignment explanation
Indices: 3105--3154 Score: 93
Period size: 19 Copynumber: 2.5 Consensus size: 20
3095 ATTCATTTGA
3105 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
3125 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
3144 CTATCGCAACG
1 CTATCGCAACG
3155 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:3225 original size:19 final size:19
Alignment explanation
Indices: 3201--3244 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3191 TTTTCTCGTT
*
3201 GCGATTTTCATTTTGCATA
1 GCGATTTTCATTTCGCATA
*
3220 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATA
3239 GCGATT
1 GCGATT
3245 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (19 bp):
GCGATTTTCATTTCGCATA
Found at i:3275 original size:20 final size:20
Alignment explanation
Indices: 3250--3288 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3240 CGATTCTCTC
3250 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
3270 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
3289 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:3390 original size:14 final size:14
Alignment explanation
Indices: 3371--3407 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3361 CATCAATTAA
3371 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3385 ACAAATCATCTTTT
1 ACAAATCAACATTT
3399 ACAAATCAA
1 ACAAATCAA
3408 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5300 original size:20 final size:20
Alignment explanation
Indices: 5258--5323 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
5248 TAGTTTACTT
* * **
5258 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGACTA
5278 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
5298 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
5318 TCGCAA
1 TCGCAA
5324 TGCTAAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:5352 original size:14 final size:14
Alignment explanation
Indices: 5333--5390 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
5323 ATGCTAAATG
5333 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
5347 AAAATCACAATGCGAA
1 AAAATCGCAA--CGAC
5363 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
5379 AAAATCGCAACG
1 AAAATCGCAACG
5391 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5375 original size:32 final size:33
Alignment explanation
Indices: 5321--5395 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 33
5311 ATGGCTATCG
*
5321 CAATGCTAAATGAAAATCGCAACGACAAAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
5354 CAATGCGAAATG-AAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
5386 CAACGCGAAA
1 CAATGCGAAA
5396 CACAAATCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 28 0.72
33 11 0.28
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:5443 original size:14 final size:14
Alignment explanation
Indices: 5424--5481 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5414 TTTCATTTCG
5424 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
5438 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
*
5454 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
5470 CGTTGCGATTTT
1 CGTTGCGATTTT
5482 CATTTCGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:5488 original size:33 final size:33
Alignment explanation
Indices: 5407--5497 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
5397 ACAAATCGCA
* *
5407 TTGCGATTTTCATTTCGCGTTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
5440 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
5472 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
5498 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:5516 original size:20 final size:19
Alignment explanation
Indices: 5482--5536 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5472 TTGCGATTTT
*
5482 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5501 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
5521 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
5537 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:6044 original size:18 final size:18
Alignment explanation
Indices: 6018--6062 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6008 GTCGATCAGA
*
6018 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
6036 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
6054 TGATGGCTC
1 TGATGGCTC
6063 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:7440 original size:20 final size:20
Alignment explanation
Indices: 7382--7440 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
7372 AATAGTTTCT
** *
7382 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
*
7402 GAAAATGACTATCGTAACGC
1 GAAAATGACTATCGCAACGC
**
7422 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
7441 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:7719 original size:20 final size:21
Alignment explanation
Indices: 7694--7742 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
7684 TTTGAGAGAT
7694 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
7714 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
7736 AGAGATG
1 GGAGATG
7743 GGTGAGAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:7728 original size:22 final size:22
Alignment explanation
Indices: 7701--7744 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
7691 GATGGAGATA
*
7701 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
7723 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
7745 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:7962 original size:20 final size:20
Alignment explanation
Indices: 7912--8046 Score: 130
Period size: 20 Copynumber: 6.7 Consensus size: 20
7902 CGCTTTGAAA
*
7912 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
7933 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
7953 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
7973 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
7994 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
8014 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
8034 ATCGCATTGCGAT
1 ATCGCATTGCGAT
8047 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 64 0.68
21 23 0.24
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:8018 original size:61 final size:61
Alignment explanation
Indices: 7912--8049 Score: 204
Period size: 61 Copynumber: 2.3 Consensus size: 61
7902 CGCTTTGAAA
* * *
7912 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
7973 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
8034 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
8050 CCCAATTCGC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:8065 original size:61 final size:61
Alignment explanation
Indices: 7912--8067 Score: 170
Period size: 61 Copynumber: 2.6 Consensus size: 61
7902 CGCTTTGAAA
* ** * * *
7912 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
7973 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
8034 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
8068 TTACTTATTC
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
61 78 0.98
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:8886 original size:35 final size:35
Alignment explanation
Indices: 8834--8905 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
8824 AAACCAAAAA
*
8834 AATAAGTTCATTAACCAAGTGACATGACTTATTAT
1 AATAAGTTCATTAACCAAATGACATGACTTATTAT
*
8869 AATAAG-TCTATTTACCAAATGACATGACTTATTAT
1 AATAAGTTC-ATTAACCAAATGACATGACTTATTAT
8904 AA
1 AA
8906 ATAACATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.35
Consensus pattern (35 bp):
AATAAGTTCATTAACCAAATGACATGACTTATTAT
Found at i:10043 original size:30 final size:30
Alignment explanation
Indices: 10007--10066 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
9997 GGCCATAAGA
*
10007 TATGTCCCATATCTCAGCTTGAAACACCGT
1 TATGTCCCATATATCAGCTTGAAACACCGT
10037 TATGTCCCATATATCAGCTTGAAACACCGT
1 TATGTCCCATATATCAGCTTGAAACACCGT
10067 GAAACTACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (30 bp):
TATGTCCCATATATCAGCTTGAAACACCGT
Found at i:11139 original size:112 final size:111
Alignment explanation
Indices: 10925--11147 Score: 410
Period size: 112 Copynumber: 2.0 Consensus size: 111
10915 TTTCCTTGAT
*
10925 CCGATACAAACCTACTGGGTCTATTTTGATCTAACATTCGGTTGGATTATTCATCGCAGTTTTCT
1 CCGATACAAACCTACTGGGTCTATTTTGATCTAACATTCAGTTGGATTATTCATCGCAGTTTTCT
10990 ATAACATCAATGATTGATGGAAGGGACGTGTGGAAACAATTGTCTC
66 ATAACATCAATGATTGATGGAAGGGACGTGTGGAAACAATTGTCTC
*
11036 CCGATACAAACCTACTGGGTCTATTTTGATCTAGCATTCAGTTGGATTATCTCATCGCAGTTTTC
1 CCGATACAAACCTACTGGGTCTATTTTGATCTAACATTCAGTTGGATTAT-TCATCGCAGTTTTC
*
11101 TATAACATCAATGATTGATGGAAGGGACGTGTGTAAACAATTGTCTC
65 TATAACATCAATGATTGATGGAAGGGACGTGTGGAAACAATTGTCTC
11148 TATCAAAATT
Statistics
Matches: 108, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
111 48 0.44
112 60 0.56
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (111 bp):
CCGATACAAACCTACTGGGTCTATTTTGATCTAACATTCAGTTGGATTATTCATCGCAGTTTTCT
ATAACATCAATGATTGATGGAAGGGACGTGTGGAAACAATTGTCTC
Found at i:11171 original size:2 final size:2
Alignment explanation
Indices: 11164--11210 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
11154 AATTTCAAAT
* * *
11164 TA TA TA TA TA TA TA TA TA TA TT TA AA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11206 TA TA T
1 TA TA T
11211 TTATTTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11200 original size:30 final size:30
Alignment explanation
Indices: 11164--11222 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
11154 AATTTCAAAT
11164 TATATATATATATATATATATTTAAATTTA
1 TATATATATATATATATATATTTAAATTTA
*
11194 TATATATATATATATATTTATTTAAATTT
1 TATATATATATATATATATATTTAAATTT
11223 TTTTCTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TATATATATATATATATATATTTAAATTTA
Found at i:12105 original size:28 final size:26
Alignment explanation
Indices: 12066--12124 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
12056 AGATAAATAG
* *
12066 ATAAAATT-AAAAAAGATAAAGGAGAA
1 ATAAAATTAAAAAAAGA-AAAAGAAAA
12092 ATAAAATTGAAAAAAAAGAAAAAGAAAA
1 ATAAAATT--AAAAAAAGAAAAAGAAAA
12120 ATAAA
1 ATAAA
12125 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.29
28 12 0.43
29 8 0.29
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.14
Consensus pattern (26 bp):
ATAAAATTAAAAAAAGAAAAAGAAAA
Found at i:12117 original size:26 final size:26
Alignment explanation
Indices: 12066--12118 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
12056 AGATAAATAG
* * *
12066 ATAAAATTAAAAAAGATAAAGGAGAA
1 ATAAAATTAAAAAAAAGAAAGAAGAA
12092 ATAAAATTGAAAAAAAAGAAA-AAGAA
1 ATAAAATT-AAAAAAAAGAAAGAAGAA
12118 A
1 A
12119 AATAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (26 bp):
ATAAAATTAAAAAAAAGAAAGAAGAA
Found at i:12137 original size:16 final size:16
Alignment explanation
Indices: 12090--12137 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
12080 GATAAAGGAG
*
12090 AAATAAAATTGAAAAA-
1 AAATAAAAAT-AAAAAT
* *
12106 AAAGAAAAAGAAAAAT
1 AAATAAAAATAAAAAT
12122 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
12138 TAGATGAAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:18799 original size:23 final size:23
Alignment explanation
Indices: 18732--18808 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 23
18722 TTTTAATTCC
18732 AATAAAAGAACTATTAAATCTCTTTT
1 AATAAAAGAA--A-TAAATCTCTTTT
*
18758 AAACAAAAGAGGTAATAAATCTCTTTT
1 -AATAAAAGA---AATAAATCTCTTTT
*
18785 AATAAAAGAAATAAATCTATTTT
1 AATAAAAGAAATAAATCTCTTTT
18808 A
1 A
18809 TCTTTATCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
23 14 0.32
26 8 0.18
27 20 0.45
28 1 0.02
30 1 0.02
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (23 bp):
AATAAAAGAAATAAATCTCTTTT
Found at i:25607 original size:3 final size:3
Alignment explanation
Indices: 25599--25667 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
25589 TTAATATATT
*
25599 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25647 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
25668 ATCAATATGG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:26192 original size:113 final size:112
Alignment explanation
Indices: 25924--26560 Score: 918
Period size: 113 Copynumber: 5.6 Consensus size: 112
25914 GCTCTTGATG
*
25924 AGTTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTTCT
* * * **
25988 CTAGAAGAGTTGATCCATCAAGTGATGGATTTGAGCAAAAAATATGAACA
65 CTGGAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGT-TGAACA
* * * ***
26038 AATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTGAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
26103 TGGAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
66 TGGAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGTTGAACA
*
26151 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-T
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCT
* * *
26215 CTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAATGTTGAACA
65 CTGGAAAAGCTGATCCATCAAGTGAT-GATTTGAGCAAAAGGTTGAACA
26264 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * * *
26329 TGGAAAGGCTGATCTATCAATTGATGAATTCAGGTAAAAGGTTGAACA
66 TGGAAAAGCTGATCCATCAAGTGATGATTTGA-GCAAAAGGTTGAACA
26377 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * * *
26442 TGGAAAGGCTGATCCATCAATTGATGAATTCAGGTAAATGGTTGAACA
66 TGGAAAAGCTGATCCATCAAGTGATGATTTGA-GCAAAAGGTTGAACA
26490 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
26555 TGGAAA
66 TGGAAA
26561 TGTCAATCCA
Statistics
Matches: 487, Mismatches: 32, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
112 7 0.01
113 389 0.80
114 91 0.19
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (112 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGCTGATCCATCAAGTGATGATTTGAGCAAAAGGTTGAACA
Found at i:27541 original size:105 final size:105
Alignment explanation
Indices: 27354--27651 Score: 569
Period size: 105 Copynumber: 2.8 Consensus size: 105
27344 CCAGAAGATG
*
27354 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
27419 AAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTTTA
66 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTTTA
27459 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
27524 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTTTA
66 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTTTA
*
27564 CTATGAGTAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
27629 GAACACTTCCAGAAGATGCTATT
66 GAACACTTCCAGAAGATGCTATT
27652 AGCAAATTGC
Statistics
Matches: 190, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 190 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.31
Consensus pattern (105 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTTTA
Found at i:28476 original size:16 final size:19
Alignment explanation
Indices: 28433--28478 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
28423 CATATAAAAG
*
28433 AATAAATTGAATTTTCGAA
1 AATAAATTGAATTCTCGAA
28452 AATAAATTGAA-TCTC-AA
1 AATAAATTGAATTCTCGAA
28469 AA-AAATTGAA
1 AATAAATTGAA
28479 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.31
17 4 0.15
18 3 0.12
19 11 0.42
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (19 bp):
AATAAATTGAATTCTCGAA
Found at i:28818 original size:1 final size:1
Alignment explanation
Indices: 28808--28865 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
28798 TTGTCCCCAC
* * * ** * *
28808 TTTTTCTTTTTTTTTCTTTTTTCTTTTTTCCTTCTTTTTTTTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28866 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:28827 original size:7 final size:7
Alignment explanation
Indices: 28817--28868 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
28807 CTTTTTCTTT
28817 TTTTTTC
1 TTTTTTC
28824 TTTTTTC
1 TTTTTTC
28831 TTTTTTCC
1 TTTTTT-C
28839 TTCTTTT-
1 TT-TTTTC
*
28846 TTTTTTT
1 TTTTTTC
28853 TTTTTTC
1 TTTTTTC
28860 TTTTTTC
1 TTTTTTC
28867 TT
1 TT
28869 CAAGCATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
6 4 0.10
7 30 0.73
8 3 0.07
9 4 0.10
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTC
Found at i:28829 original size:18 final size:18
Alignment explanation
Indices: 28808--28865 Score: 82
Period size: 17 Copynumber: 3.2 Consensus size: 18
28798 TTGTCCCCAC
28808 TTTTTCTTTTTTTTTC-T
1 TTTTTCTTTTTTTTTCTT
*
28825 TTTTTCTTTTTTCCTTCTT
1 TTTTTCTTTTTT-TTTCTT
*
28844 TTTTTTTTTTTTTTTCTT
1 TTTTTCTTTTTTTTTCTT
28862 TTTT
1 TTTT
28866 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.33
18 12 0.33
19 12 0.33
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTCTT
Found at i:41615 original size:3 final size:3
Alignment explanation
Indices: 41607--41675 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
41597 TTAATATATT
41607 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41655 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
41676 ATCAAGATGG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42153 original size:37 final size:37
Alignment explanation
Indices: 42080--42154 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
42070 GTTGGAAAAT
*
42080 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
42117 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
42154 A
1 A
42155 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:43134 original size:2 final size:2
Alignment explanation
Indices: 43127--43152 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43117 AGCAAACATA
43127 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
43153 TTGTGCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44946 original size:15 final size:16
Alignment explanation
Indices: 44905--44947 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
44895 TATTTTTATG
44905 ATTTTGTTTATTTGTT
1 ATTTTGTTTATTTGTT
**
44921 ATTTTAATTATTT-TT
1 ATTTTGTTTATTTGTT
*
44936 ATTTGGTTTATT
1 ATTTTGTTTATT
44948 AATTTTTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (16 bp):
ATTTTGTTTATTTGTT
Found at i:44949 original size:22 final size:21
Alignment explanation
Indices: 44905--44955 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
44895 TATTTTTATG
*
44905 ATTTTGTTTATTTGTTATTTTA
1 ATTTT-TTTATTTGTTATATTA
44927 ATTATTTTTATTTGGTT-TATTA
1 ATT-TTTTTATTT-GTTATATTA
44949 ATTTTTT
1 ATTTTTT
44956 ATATATAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 17 0.65
23 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.73
Consensus pattern (21 bp):
ATTTTTTTATTTGTTATATTA
Found at i:48502 original size:4 final size:4
Alignment explanation
Indices: 48495--48574 Score: 97
Period size: 4 Copynumber: 20.0 Consensus size: 4
48485 ACACACACAC
* * * * * * *
48495 ATAT ATAT ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAT ACAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
48543 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
48575 CCCTTGTTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 72 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:48524 original size:12 final size:12
Alignment explanation
Indices: 48479--48533 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
48469 ATATGTATAT
* *
48479 ATACACACACAC
1 ATACATACATAC
* * *
48491 ACACATATATAT
1 ATACATACATAC
*
48503 ATATATACATAC
1 ATACATACATAC
48515 ATACATACATAC
1 ATACATACATAC
48527 ATACATA
1 ATACATA
48534 TACATATATA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (12 bp):
ATACATACATAC
Found at i:48899 original size:19 final size:19
Alignment explanation
Indices: 48875--48917 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
48865 AGAGGAGAAG
48875 AGAAAAAAGAAGAAAAAAT-
1 AGAAAAAAG-AGAAAAAATA
*
48894 AGAAAAAAGAGAAGAAATA
1 AGAAAAAAGAGAAAAAATA
48913 AGAAA
1 AGAAA
48918 GAAATCGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (19 bp):
AGAAAAAAGAGAAAAAATA
Found at i:48906 original size:33 final size:33
Alignment explanation
Indices: 48813--48920 Score: 105
Period size: 33 Copynumber: 3.2 Consensus size: 33
48803 ACACATAGAG
48813 AAAGAAGAAAATATATAGAAAAA-A-AAGACATAA
1 AAAGAAGAAAA-A-ATAGAAAAAGAGAAGACATAA
* * *
48846 AAAGATAGCAAAAAATAGAAGAGGAGAAGAGA-AA
1 AAAGA-AG-AAAAAATAGAAAAAGAGAAGACATAA
*
48880 AAAGAAGAAAAAATAGAAAAAAGAGAAGAAATAA
1 AAAGAAGAAAAAATAG-AAAAAGAGAAGACATAA
48914 GAAAGAA
1 -AAAGAA
48921 ATCGATCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
32 9 0.15
33 25 0.40
34 13 0.21
35 15 0.24
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.07
Consensus pattern (33 bp):
AAAGAAGAAAAAATAGAAAAAGAGAAGACATAA
Found at i:49359 original size:181 final size:181
Alignment explanation
Indices: 49055--49421 Score: 707
Period size: 181 Copynumber: 2.0 Consensus size: 181
49045 ACAGTAGGGC
49055 AAATTGATCCTTGGTTCAATCCTTAAACACTTATTTAGACCTATTTATCTCTTTATTTCATAACC
1 AAATTGATCCTTGGTTCAATCCTTAAACACTTATTTAGACCTATTTATCTCTTTATTTCATAACC
*
49120 GTGAGCTCCGACCTACATTACATGCCTGAAAAATCCTTTCTAATCATATATGGGTTTCTAAGTGG
66 GTGAGCTCCGACCTACATTACATGCCTAAAAAATCCTTTCTAATCATATATGGGTTTCTAAGTGG
*
49185 AAAGACTATCTTCAGATTTCATTCCGCCCCTCAGGGTTAATTTTATTTGTA
131 AAAGACTATCTTCAGATTTCATTCCACCCCTCAGGGTTAATTTTATTTGTA
49236 AAATTGATCCTTGGTTCAATCCTTAAACACTTATTTAGACCTATTTATCTCTTTATTTCATAACC
1 AAATTGATCCTTGGTTCAATCCTTAAACACTTATTTAGACCTATTTATCTCTTTATTTCATAACC
49301 GTGAGCTCCGACCTACATTACATGCCTAAAAAATCCTTTCTAATCATATATGGGTTTCTAAGTGG
66 GTGAGCTCCGACCTACATTACATGCCTAAAAAATCCTTTCTAATCATATATGGGTTTCTAAGTGG
*
49366 AAAGACTATCTTCAGATTTTATTCCACCCCTCAGGGTTAATTTTATTTGTA
131 AAAGACTATCTTCAGATTTCATTCCACCCCTCAGGGTTAATTTTATTTGTA
49417 AAATT
1 AAATT
49422 AGTTTTCTAA
Statistics
Matches: 183, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
181 183 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (181 bp):
AAATTGATCCTTGGTTCAATCCTTAAACACTTATTTAGACCTATTTATCTCTTTATTTCATAACC
GTGAGCTCCGACCTACATTACATGCCTAAAAAATCCTTTCTAATCATATATGGGTTTCTAAGTGG
AAAGACTATCTTCAGATTTCATTCCACCCCTCAGGGTTAATTTTATTTGTA
Found at i:52392 original size:91 final size:90
Alignment explanation
Indices: 52282--52543 Score: 391
Period size: 91 Copynumber: 2.9 Consensus size: 90
52272 ACATTTCTGA
* *
52282 TGGAGAGTTCGTAATGAGAAGAACTCATCCAACGAGGGAGAGGAAGTTCATAATGAGAGGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAGGAAGTTCATAATGAGAAGAACTT
*
52347 GTTCTACCTTGGCTTAACATTTCCAG
66 GTTCAACCTTGGCTT-ACATTTCCAG
* *
52373 TGTAGAGTTCATAATGAGAATAACTCATCCAACGAGGGAGAGGAAGTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAGGAAGTTCATAATGAGAAGAACTT
*
52438 GTTCGAA-CTTGGATCTACATTTCCAG
66 GTTC-AACCTTGGCT-TACATTTCCAG
* * * *
52464 TGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTAATAATGAGAAGAATTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAGGAAGTTCATAATGAGAAGAACTT
*
52529 GTTCAACCTTAGCTT
66 GTTCAACCTTGGCTT
52544 GTTTCCATCA
Statistics
Matches: 154, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
90 3 0.02
91 149 0.97
92 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (90 bp):
TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAGGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTGGCTTACATTTCCAG
Found at i:52653 original size:117 final size:115
Alignment explanation
Indices: 52447--52720 Score: 361
Period size: 117 Copynumber: 2.4 Consensus size: 115
52437 TGTTCGAACT
* * * *
52447 TGGATCTACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTT
1 TGGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAACTT
* * * * * *
52512 AATAATGAGAAGAATTTGTTCAACCTTAGCTTGTTTCCATCACAGAAGGAGG
66 AATAATGAGAAGAATTTGCTCAACCCT-G-GTGATTCCATCACACAAGGAAG
* *
52564 TGGATCAACATTTCCGGTGAAGAGTTCATAATAAGAAGAACTCATCCGACAAGGGAGAAGAACTT
1 TGGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAACTT
*
52629 CATAATGAGAAGAATTTGCTCAACCCTGGTGATTCCATCACACAAGGAAG
66 AATAATGAGAAGAATTTGCTCAACCCTGGTGATTCCATCACACAAGGAAG
** * **
52679 TGGATTGACA-TCCCAACGAAGAGTTCATAATGAGAAGAACTC
1 TGGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTC
52721 GCAGCTAGAA
Statistics
Matches: 137, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
114 27 0.20
115 26 0.19
116 1 0.01
117 83 0.61
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (115 bp):
TGGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAACTT
AATAATGAGAAGAATTTGCTCAACCCTGGTGATTCCATCACACAAGGAAG
Found at i:63016 original size:20 final size:19
Alignment explanation
Indices: 62993--63059 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
62983 TATTTTTATG
62993 ATTTTGTTATTGTTTTATTT
1 ATTTT-TTATTGTTTTATTT
* * *
63013 ATTTATTTGTTATTTTAATT
1 ATTT-TTTATTGTTTTATTT
* *
63033 ATTTTTTATTTGGTTTATTA
1 ATTTTTTA-TTGTTTTATTT
63053 ATTTTTT
1 ATTTTTT
63060 TATATATAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.08
20 33 0.89
21 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.73
Consensus pattern (19 bp):
ATTTTTTATTGTTTTATTT
Found at i:63021 original size:23 final size:22
Alignment explanation
Indices: 62977--63044 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
62967 GAATGTATGT
* *
62977 TTATTTTATT-TTTATGATTTTG
1 TTATTTTATTATTTTTTA-TTTG
62999 TTATTGTT-TTATTTATTTATTTG
1 TTATT-TTATTATTT-TTTATTTG
63022 TTATTTTAATTATTTTTTATTTG
1 TTATTTT-ATTATTTTTTATTTG
63045 GTTTATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 9 0.23
23 22 0.56
24 8 0.21
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (22 bp):
TTATTTTATTATTTTTTATTTG
Found at i:63051 original size:16 final size:16
Alignment explanation
Indices: 62976--63043 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 16
62966 TGAATGTATG
62976 TTTATTTTATTTTTATGAT
1 TTTA-TTTATTTTT-T-AT
*
62995 TTT-GTTATTGTTTTA-
1 TTTATTTATT-TTTTAT
*
63010 TTTATTTATTTGTTAT
1 TTTATTTATTTTTTAT
*
63026 TTTAATTATTTTTTAT
1 TTTATTTATTTTTTAT
63042 TT
1 TT
63044 GGTTTATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.17
16 22 0.54
17 6 0.15
18 3 0.07
19 3 0.07
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTATTTATTTTTTAT
Found at i:66499 original size:31 final size:31
Alignment explanation
Indices: 66461--66520 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
66451 TGTAGATATT
66461 AAAAAATAACATTTGTTAGATACTATATGTA
1 AAAAAATAACATTTGTTAGATACTATATGTA
* *
66492 AAAAAATAATATTTGTTGGATACTATATG
1 AAAAAATAACATTTGTTAGATACTATATG
66521 AAGTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (31 bp):
AAAAAATAACATTTGTTAGATACTATATGTA
Found at i:66691 original size:21 final size:20
Alignment explanation
Indices: 66667--66713 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
66657 ATTTGAATTG
*
66667 ATTTGACTTATAATTTTATAA
1 ATTTGACTTAAAATTTT-TAA
*
66688 ATTTAACTTAAAATTTTTAA
1 ATTTGACTTAAAATTTTTAA
66708 ATTTGA
1 ATTTGA
66714 ATCGAGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTTGACTTAAAATTTTTAA
Found at i:69694 original size:32 final size:31
Alignment explanation
Indices: 69629--69734 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 31
69619 GGGCTTGAGA
* * * * * *
69629 GCCTACCCAAGATAGATTTCAGAGCCGTGGG
1 GCCTACCTAAGAAACATCTCAGGGCCGTAGG
*
69660 GCCTACCTAAGAACACATCTTAGGGCCGTAGG
1 GCCTACCTAAGAA-ACATCTCAGGGCCGTAGG
** ** *
69692 GCCTACCCGAGAATGATCTCAGGGCCGTAGA
1 GCCTACCTAAGAAACATCTCAGGGCCGTAGG
*
69723 GCCTAGCTAAGA
1 GCCTACCTAAGA
69735 GTCACATTAG
Statistics
Matches: 58, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
31 34 0.59
32 24 0.41
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (31 bp):
GCCTACCTAAGAAACATCTCAGGGCCGTAGG
Found at i:69719 original size:63 final size:63
Alignment explanation
Indices: 69611--69734 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
69601 ACTTAAGCGA
* * * *
69611 ACATCTTAGGGCTTGAGAGCCTACCCAAGATAGATTTCAGAGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCGTGAGAGCCTACCCAAGATAGATCTCAGAGCCGTAGAGCCTACCTAAGAAC
* * * *
69674 ACATCTTAGGGCCGT-AGGGCCTACCCGAGA-ATGATCTCAGGGCCGTAGAGCCTAGCTAAGA
1 ACATCTTAGGG-CGTGAGAGCCTACCCAAGATA-GATCTCAGAGCCGTAGAGCCTACCTAAGA
69735 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.94
64 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.19
Consensus pattern (63 bp):
ACATCTTAGGGCGTGAGAGCCTACCCAAGATAGATCTCAGAGCCGTAGAGCCTACCTAAGAAC
Found at i:71263 original size:18 final size:18
Alignment explanation
Indices: 71240--71275 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
71230 CTTTCATCCG
*
71240 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
71258 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
71276 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:74279 original size:2 final size:2
Alignment explanation
Indices: 74272--74343 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
74262 ATATAAATTC
74272 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
74344 CAAAACTTCA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78240 original size:24 final size:25
Alignment explanation
Indices: 78208--78258 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
78198 TATGGGTTAA
78208 AAAAATTAT-TTAAAATAATCATTT
1 AAAAATTATGTTAAAATAATCATTT
78232 AAAAATTATGGGTTAAAATAATCATTT
1 AAAAATTAT--GTTAAAATAATCATTT
78259 TGGTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
27 15 0.62
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (25 bp):
AAAAATTATGTTAAAATAATCATTT
Found at i:78512 original size:3 final size:3
Alignment explanation
Indices: 78504--78540 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
78494 TGTTAAGGGT
78504 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
78541 ATATGCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:78729 original size:3 final size:3
Alignment explanation
Indices: 78721--78747 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
78711 AGTTTCATTG
78721 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
78748 GCAGACTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:81007 original size:20 final size:21
Alignment explanation
Indices: 80967--81019 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
80957 TACTAATGGG
*
80967 GGTATCGATACCATGAGGAGA
1 GGTATCGATACTATGAGGAGA
80988 GGTATCGATACTAT-AGGAGA
1 GGTATCGATACTATGAGGAGA
81008 GGTA-CGATACTA
1 GGTATCGATACTA
81020 CTGCGTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 8 0.26
20 10 0.32
21 13 0.42
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (21 bp):
GGTATCGATACTATGAGGAGA
Found at i:81582 original size:23 final size:23
Alignment explanation
Indices: 81552--81634 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
81542 GTTGAGGGTT
*
81552 CTATGTGGTCATTCGGGA-AAATC
1 CTATGTGGTCATTCGGGACAAA-A
*
81575 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
**
81598 CTATGTGGTCATTTAGGA-AAAA
1 CTATGTGGTCATTCGGGACAAAA
81620 -TATGTGG-CAGTTCGG
1 CTATGTGGTCA-TTCGG
81635 TGTAAATTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.04
21 10 0.20
22 4 0.08
23 32 0.63
24 3 0.06
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:83738 original size:7 final size:7
Alignment explanation
Indices: 83726--83768 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
83716 ATTTTCAGAA
83726 ATTTCAT
1 ATTTCAT
83733 ATTTCAT
1 ATTTCAT
83740 ATTTCAT
1 ATTTCAT
83747 -TTTCAT
1 ATTTCAT
*
83753 CTTTCA-
1 ATTTCAT
*
83759 CTTTCAT
1 ATTTCAT
83766 ATT
1 ATT
83769 CATTTACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTCAT
Found at i:83752 original size:13 final size:13
Alignment explanation
Indices: 83726--83778 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
83716 ATTTTCAGAA
83726 ATTTCATATTTCAT
1 ATTTCAT-TTTCAT
83740 ATTTCATTTTCAT
1 ATTTCATTTTCAT
* *
83753 CTTTCACTTTCAT
1 ATTTCATTTTCAT
*
83766 A-TTCATTTACAT
1 ATTTCATTTTCAT
83778 A
1 A
83779 ACAAGTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
12 10 0.29
13 17 0.50
14 7 0.21
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTCATTTTCAT
Found at i:83839 original size:19 final size:18
Alignment explanation
Indices: 83813--83874 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
83803 TCATTTTCTG
83813 AATT-ATAACTTACTTTC
1 AATTCATAACTTACTTTC
* *
83830 ATATTCATAACTTAATTTT
1 A-ATTCATAACTTACTTTC
*
83849 AGATTCATAGCTTACTTTC
1 A-ATTCATAACTTACTTTC
83868 AATTCAT
1 AATTCAT
83875 CACCCAATGC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 1 0.03
18 9 0.24
19 27 0.73
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTCATAACTTACTTTC
Found at i:87757 original size:19 final size:20
Alignment explanation
Indices: 87729--87771 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
87719 TTGCTATTTT
*
87729 GTATTGATA-CAAAGGGTGA
1 GTATTAATACCAAAGGGTGA
* *
87748 GTATTAATACCCAAGGGTTA
1 GTATTAATACCAAAGGGTGA
87768 GTAT
1 GTAT
87772 CGATACTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (20 bp):
GTATTAATACCAAAGGGTGA
Done.