Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold398
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: 43222
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Found at i:80 original size:13 final size:13
Alignment explanation
Indices: 62--103 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
52 GGGGCGGGAA
62 AAAAAAAAGAAGG
1 AAAAAAAAGAAGG
75 AAAAAAAAGAA--
1 AAAAAAAAGAAGG
86 AAAAAAAA-AAGCG
1 AAAAAAAAGAAG-G
99 AAAAA
1 AAAAA
104 GCATCAAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.08
11 8 0.31
13 16 0.62
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAGG
Found at i:103 original size:15 final size:13
Alignment explanation
Indices: 60--96 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
50 ATGGGGCGGG
60 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
**
73 GGAAAAAAAAGAA
1 AAAAAAAAAAGAA
86 AAAAAAAAAAG
1 AAAAAAAAAAG
97 CGAAAAAGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:3215 original size:40 final size:40
Alignment explanation
Indices: 3114--3374 Score: 298
Period size: 40 Copynumber: 6.6 Consensus size: 40
3104 TCCTCGTTCA
* * * * *
3114 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
3153 AATGCCTTC-GGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
3192 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
3232 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
3272 AATGCCTTC-GGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
3311 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
3351 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3375 CAGCATTCAA
Statistics
Matches: 195, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
38 24 0.12
39 55 0.28
40 108 0.55
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:3297 original size:79 final size:78
Alignment explanation
Indices: 3114--3374 Score: 303
Period size: 79 Copynumber: 3.3 Consensus size: 78
3104 TCCTCGTTCA
* * * * *
3114 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGACATAACCCGGATTT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGACTTAACCCGGATTT
3179 AACAACTCGCACG
66 AACAACTCGCACG
* *
3192 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTC-GGACTTAACCCGGAT
*
3257 TTAATAACTCGCACG
64 TTAACAACTCGCACG
* * *
3272 AATGCCTTC-GGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAATCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGA-CTTAACCCGGAT
* * *
3336 ATATTC-ACTTAGCAC-
64 TTA-ACAAC-TCGCACG
* *
3351 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3375 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
78 36 0.23
79 67 0.43
80 54 0.34
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (78 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGACTTAACCCGGATTT
AACAACTCGCACG
Found at i:3307 original size:119 final size:118
Alignment explanation
Indices: 3114--3374 Score: 319
Period size: 119 Copynumber: 2.2 Consensus size: 118
3104 TCCTCGTTCA
* * *
3114 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGACATAACCCGGATTT
1 AATGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGACATAACCCGGATTT
* ** * *
3179 AACAACTCGCACGACTGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
66 AACAACTCGCACAAAGGCCTTC-GGATCTTAACCCGGATATAATAACTTAGCAC
* * *
3231 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGACTTAACCCGGAT
1 -AATGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AATGCCTTCGGACATAACCCGGAT
** * * * *
3296 TTAGTATCTCGCACAAAGGCCTTCGGATCTTAATCCGGATATATTCACTTAGCAC
64 TTAACAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATATAATAACTTAGCAC
*
3351 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
3375 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
118 37 0.31
119 79 0.65
120 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (118 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGACATAACCCGGATTT
AACAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATATAATAACTTAGCAC
Found at i:5519 original size:43 final size:43
Alignment explanation
Indices: 5471--5571 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
5461 ATTTCTCCTG
* * * *
5471 CTAGGCTTGAAGCCCGATATCATTTCACCGGCATGATAGCCTA
1 CTAGGCTCGAAGCCCAATATCATCTAACCGGCATGATAGCCTA
* * * *
5514 CTAGGCTCGAAGCCCAATATTATCTAACTGGCATTATAGCCTG
1 CTAGGCTCGAAGCCCAATATCATCTAACCGGCATGATAGCCTA
*
5557 CTAGGCCCGAAGCCC
1 CTAGGCTCGAAGCCC
5572 TATAATATTA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.24
Consensus pattern (43 bp):
CTAGGCTCGAAGCCCAATATCATCTAACCGGCATGATAGCCTA
Found at i:6762 original size:29 final size:28
Alignment explanation
Indices: 6721--6789 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
6711 ACACTCACAC
* *
6721 AACCCATATATTT-CACAATTTCACATTTT
1 AACCCA-AAATTTCCAC-ATTTCACAATTT
6750 AACCACAAAATTTCCACATTTCACAATTT
1 AACC-CAAAATTTCCACATTTCACAATTT
*
6779 AATCCAAAATT
1 AACCCAAAATT
6790 GACAGTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 7 0.20
29 23 0.66
30 5 0.14
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.35
Consensus pattern (28 bp):
AACCCAAAATTTCCACATTTCACAATTT
Found at i:7488 original size:6 final size:6
Alignment explanation
Indices: 7451--7634 Score: 108
Period size: 6 Copynumber: 29.8 Consensus size: 6
7441 TATCAAAACT
* * * * *
7451 AGAATC AAAATG AGAATT AGAATC AAAATC AGAATC AG-GTGAC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC
* * * * *
7500 AAAATC AGAATC AAAATC AAAATT AGGTAA-C AGAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC
* * *
7549 AGGTAA-C AGAATC AAAATC AGAACC AGAATC AGAATT AGGTAAT- AGAATC
1 A-G-AATC AGAATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC
* *
7599 AGAATT AGTATC AGGTAA-C AGAATC AGAATC AGAAT
1 AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAAT
7635 GTGAATGCAA
Statistics
Matches: 137, Mismatches: 26, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
5 10 0.07
6 107 0.78
7 12 0.09
8 8 0.06
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:7533 original size:37 final size:37
Alignment explanation
Indices: 7469--7549 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
7459 AATGAGAATT
* *
7469 AGAATCAAAATCAGAATCAGGTGACAGAATCAAAATC
1 AGAATCAAAATCAAAATCAGGTAACAGAATCAAAATC
* *
7506 AGAATCAAAATCAAAATTAGGTAACAGAATCAGAATC
1 AGAATCAAAATCAAAATCAGGTAACAGAATCAAAATC
*
7543 AGTATCA
1 AGAATCA
7550 GGTAACAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (37 bp):
AGAATCAAAATCAAAATCAGGTAACAGAATCAAAATC
Found at i:7550 original size:62 final size:62
Alignment explanation
Indices: 7469--7634 Score: 251
Period size: 62 Copynumber: 2.7 Consensus size: 62
7459 AATGAGAATT
* * *
7469 AGAATCAAAATCAGAATCAGGTGACAGAATCAAAATCAGAATCAAAATCAAAATTAGGTAAC
1 AGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAAAATCAAAATTAGGTAAC
* * * *
7531 AGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAACCAGAATCAGAATTAGGTAAT
1 AGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAAAATCAAAATTAGGTAAC
* *
7593 AGAATCAGAATTAGTATCAGGTAACAGAATCAGAATCAGAAT
1 AGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAAT
7635 GTGAATGCAA
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 94 1.00
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (62 bp):
AGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAAAATCAAAATTAGGTAAC
Found at i:7560 original size:19 final size:19
Alignment explanation
Indices: 7477--7631 Score: 84
Period size: 19 Copynumber: 7.6 Consensus size: 19
7467 TTAGAATCAA
*
7477 AATCAGAATCAGGTGACAG
1 AATCAGAATCAGGTAACAG
* *
7496 AATCAAAATCA-G-AATCAA
1 AATCAGAATCAGGTAA-CAG
* *
7514 AATCAAAATTAGGTAACAG
1 AATCAGAATCAGGTAACAG
7533 AATCAGAATCAGTATCAGGTAACAG
1 AATCAG----A--ATCAGGTAACAG
*
7558 AATCAAAATCA-G-AACCAG
1 AATCAGAATCAGGTAA-CAG
* *
7576 AATCAGAATTAGGTAATAG
1 AATCAGAATCAGGTAACAG
7595 AATCAGAATTAGTATCAGGTAACAG
1 AATCAG----A--ATCAGGTAACAG
7620 AATCAGAATCAG
1 AATCAGAATCAG
7632 AATGTGAATG
Statistics
Matches: 105, Mismatches: 13, Indels: 36
0.68 0.08 0.23
Matches are distributed among these distances:
17 3 0.03
18 26 0.25
19 36 0.34
20 4 0.04
21 2 0.02
23 2 0.02
25 32 0.30
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.19
Consensus pattern (19 bp):
AATCAGAATCAGGTAACAG
Found at i:7569 original size:25 final size:25
Alignment explanation
Indices: 7505--7571 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
7495 GAATCAAAAT
* *
7505 CAGAATCAAAATCAAAATTAGGTAA
1 CAGAATCAAAATCAGAATCAGGTAA
* *
7530 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAGGTAA
7555 CAGAATCAAAATCAGAA
1 CAGAATCAAAATCAGAA
7572 CCAGAATCAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (25 bp):
CAGAATCAAAATCAGAATCAGGTAA
Found at i:7599 original size:31 final size:31
Alignment explanation
Indices: 7502--7612 Score: 93
Period size: 31 Copynumber: 3.6 Consensus size: 31
7492 ACAGAATCAA
* * *
7502 AATCAGAATCAAAATCAAAATTAGGTAACAG
1 AATCAGAATCAGAATCAGAATTAGGTAATAG
* * *
7533 AATCAGAATCAGTATCAGGTAA-CA-G-AATCAA
1 AATCAGAATCAGAATCA-G-AATTAGGTAAT-AG
*
7564 AATCAGAACCAGAATCAGAATTAGGTAATAG
1 AATCAGAATCAGAATCAGAATTAGGTAATAG
* *
7595 AATCAGAATTAGTATCAG
1 AATCAGAATCAGAATCAG
7613 GTAACAGAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
29 2 0.03
30 4 0.07
31 49 0.80
32 4 0.07
33 2 0.03
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.21
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGAATTAGGTAATAG
Found at i:7601 original size:25 final size:25
Alignment explanation
Indices: 7567--7634 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
7557 GAATCAAAAT
* *
7567 CAGAACCAGAATCAGAATTAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
* * *
7592 TAGAATCAGAATTAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
7617 CAGAATCAGAATCAGAAT
1 CAGAATCAGAATCAGAAT
7635 GTGAATGCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAA
Found at i:7899 original size:27 final size:26
Alignment explanation
Indices: 7852--7902 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
7842 CGAGGCTGCC
*
7852 AGATATTGTGACGAAGTCACCAGAAT
1 AGATATTGTGACGAAGCCACCAGAAT
* *
7878 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
7903 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAT
Found at i:8177 original size:27 final size:27
Alignment explanation
Indices: 8147--8398 Score: 226
Period size: 27 Copynumber: 9.3 Consensus size: 27
8137 AGGGTAAAAT
* *
8147 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
8174 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* * * * *
8201 AGTAATTCTACCCTATAGGGGTATTTT
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
8228 GGT-ATTTCTACCTTACAAGGGTATTCC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* *
8255 AAG-AATTTTACCCTACAAGGGTATTTT
1 -GGTAATTTTACCCTACAAGGGTATTTC
* * *
8282 AGTAATTTTACCCTACAGGGGTATTTT
1 GGTAATTTTACCCTACAAGGGTATTTC
* * *
8309 GGT-ATTTCTACCTTACAGGGGTATTTT
1 GGTAATTT-TACCCTACAAGGGTATTTC
*
8336 GGT-ATTTCTACCCTACAAGGATATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
*
8363 AG-AATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
*
8390 GATAATTTT
1 GGTAATTTT
8399 GTAAATCGAG
Statistics
Matches: 189, Mismatches: 29, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
26 9 0.05
27 170 0.90
28 10 0.05
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:8206 original size:54 final size:54
Alignment explanation
Indices: 8148--8388 Score: 263
Period size: 54 Copynumber: 4.5 Consensus size: 54
8138 GGGTAAAATG
* * * *
8148 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTTTACCCTACAAGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCA
* * * * * *
8202 GTAATTCTACCCTATAGGGGTATTTTGGTATTTCTACCTTACAAGGGTATTCCAA
1 GTAATTTTACCCTACAAGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTC-A
* * * **
8257 G-AATTTTACCCTACAAGGGTATTTTAGTAATTTTACCCTACAGGGGTATTTTG
1 GTAATTTTACCCTACAAGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCA
* * * *
8310 GT-ATTTCTACCTTACAGGGGTATTTTGGTATTTCTACCCTACAAGGATATTTCA
1 GTAATTT-TACCCTACAAGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCA
8364 G-AATTTCTACCCTACAAGGGTATTT
1 GTAATTT-TACCCTACAAGGGTATTT
8389 CGATAATTTT
Statistics
Matches: 151, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
53 5 0.03
54 144 0.95
55 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (54 bp):
GTAATTTTACCCTACAAGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCA
Found at i:8277 original size:81 final size:80
Alignment explanation
Indices: 8177--8388 Score: 282
Period size: 81 Copynumber: 2.6 Consensus size: 80
8167 GTATCTCGGT
* * *
8177 AATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTTGGTATTTCTACCTT
1 AATTTTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTGGTATTTCTACCTT
8242 ACAAGGGTATTCCAAG
66 ACAAGGGTATT-CAAG
* *
8258 AATTTTACCCTACAAGGGTATTTTAGTAATTTTACCCTACAGGGGTATTTTGGTATTTCTACCTT
1 AATTTTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTGGTATTTCTACCTT
* ***
8323 ACAGGGGTATTTTGG
66 ACAAGGGTATTCAAG
* * *
8338 TATTTCTACCCTACAAGGATATTTCAG-AATTTCTACCCTACAAGGGTATTT
1 AATTT-TACCCTACAAGGGTATTTCAGTAA-TTCTACCCTACAGGGGTATTT
8389 CGATAATTTT
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
80 7 0.06
81 108 0.94
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (80 bp):
AATTTTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTGGTATTTCTACCTT
ACAAGGGTATTCAAG
Found at i:8410 original size:27 final size:27
Alignment explanation
Indices: 8380--8478 Score: 78
Period size: 27 Copynumber: 3.7 Consensus size: 27
8370 CTACCCTACA
8380 AGGGTATTTCGATAATTTTGTAAATCG
1 AGGGTATTTCGATAATTTTGTAAATCG
** * *
8407 AGGGTAAAATAG-TAATTTCGTAAATC-
1 AGGGT-ATTTCGATAATTTTGTAAATCG
* ** *
8433 AGGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCGATAATTTTGTAAATCG
*
8460 AGGGTATTTCAATAATTTT
1 AGGGTATTTCGATAATTTT
8479 ACAGGTCGAG
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
25 2 0.04
26 19 0.35
27 31 0.56
28 3 0.05
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTGTAAATCG
Found at i:8475 original size:80 final size:81
Alignment explanation
Indices: 8380--8536 Score: 199
Period size: 80 Copynumber: 2.0 Consensus size: 81
8370 CTACCCTACA
* ** **
8380 AGGGTATTTCGATAATTTTGTAAATCGAGGGTAAAATAGTAATTTCGTAAATC-AGGGTACTTTG
1 AGGGTATTTCAATAATTTTACAAATCGAGGGTAAAATAGTAATTTCACAAATCAAGGGTACTTTG
8444 GTAATTTTACAAGTCG
66 GTAATTTTACAAGTCG
** *** * *
8460 AGGGTATTTCAATAATTTTACAGGTCGAGGGTATTTTAGTAATTTTACAAATCAAGGGTAGTTTG
1 AGGGTATTTCAATAATTTTACAAATCGAGGGTAAAATAGTAATTTCACAAATCAAGGGTACTTTG
8525 GTAATTTTACAA
66 GTAATTTTACAA
8537 ACTAGGAGTA
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
80 42 0.66
81 22 0.34
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (81 bp):
AGGGTATTTCAATAATTTTACAAATCGAGGGTAAAATAGTAATTTCACAAATCAAGGGTACTTTG
GTAATTTTACAAGTCG
Found at i:8479 original size:27 final size:26
Alignment explanation
Indices: 8433--8644 Score: 133
Period size: 27 Copynumber: 7.8 Consensus size: 26
8423 TTCGTAAATC
*
8433 AGGGTACTTTGGTAATTTTACAAGTCG
1 AGGGTA-TTTAGTAATTTTACAAGTCG
* *
8460 AGGGTATTTCAATAATTTTACAGGTCG
1 AGGGTATTT-AGTAATTTTACAAGTCG
* *
8487 AGGGTATTTTAGTAATTTTACAAATCA
1 AGGGTA-TTTAGTAATTTTACAAGTCG
* * *
8514 AGGGTAGTTTGGTAATTTTACAA-ACT
1 AGGGTA-TTTAGTAATTTTACAAGTCG
* * *
8540 AGGAGTATTTTGGTAATTTTACAA-ACC
1 AGG-GTA-TTTAGTAATTTTACAAGTCG
* * ** *
8567 AGGGGTATTTTGGTAATTTTATAAACCA
1 A-GGGTA-TTTAGTAATTTTACAAGTCG
* *
8595 AGGGTATTTTAGTAATTTTACAA-ACC
1 AGGGTA-TTTAGTAATTTTACAAGTCG
*
8621 AGGGGTATTTTGGTAATTTTACAA
1 A-GGGTA-TTTAGTAATTTTACAA
8645 ACCAAGGGTA
Statistics
Matches: 158, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
26 9 0.06
27 142 0.90
28 7 0.04
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.39
Consensus pattern (26 bp):
AGGGTATTTAGTAATTTTACAAGTCG
Found at i:8767 original size:54 final size:54
Alignment explanation
Indices: 8434--8767 Score: 382
Period size: 54 Copynumber: 6.2 Consensus size: 54
8424 TCGTAAATCA
* ** * *** ***
8434 GGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAATAATTTTACAGGTC-G
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
* * * *
8487 AGGGTATTTTAGTAATTTTACAAATCAAGGGTAGTTTGGTAATTTTACAAACTAG
1 -GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
* * * *
8542 GAGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
* * *
8596 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
* * * * * *
8650 GGGTATTTTGGTGATTTTATAAACTAAGGGTATTATAGTAATTTTGCAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
** *
8704 GGGTATTTTGGTAATTTTGTAAACCACGGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
8758 GGGTATTTTG
1 GGGTATTTTG
8768 ATGATTTGGT
Statistics
Matches: 240, Mismatches: 39, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
54 239 1.00
55 1 0.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
Found at i:8781 original size:27 final size:27
Alignment explanation
Indices: 8488--8767 Score: 380
Period size: 27 Copynumber: 10.4 Consensus size: 27
8478 TACAGGTCGA
* * *
8488 GGGTATTTTAGTAATTTTACAAATCAA
1 GGGTATTTTGGTAATTTTACAAACCAG
* *
8515 GGGTAGTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
8542 GAGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* *
8569 GGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAG
*
8596 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
8623 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAG
* * * *
8650 GGGTATTTTGGTGATTTTATAAACTAA
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
8677 GGGTATTATAGTAATTTTGCAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
** *
8704 GGGTATTTTGGTAATTTTGTAAACCAC
1 GGGTATTTTGGTAATTTTACAAACCAG
8731 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
8758 GGGTATTTTG
1 GGGTATTTTG
8768 ATGATTTGGT
Statistics
Matches: 220, Mismatches: 33, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 220 1.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:11591 original size:18 final size:16
Alignment explanation
Indices: 11569--11620 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 16
11559 GACAATTCTT
11569 TTCTCTTCTTCTTTTC
1 TTCTCTTCTTCTTTTC
*
11585 TCATCTCTTCATCTATTTC
1 T--TCTCTTCTTCT-TTTC
11604 TTCTTCTTCTTCTTTTC
1 TTC-TCTTCTTCTTTTC
11621 CTCTATAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 1 0.03
17 6 0.20
18 18 0.60
19 5 0.17
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.63
Consensus pattern (16 bp):
TTCTCTTCTTCTTTTC
Found at i:12714 original size:27 final size:27
Alignment explanation
Indices: 12684--12741 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
12674 TAATAAAGTA
*
12684 CCCTAAGTATG-AAAATTACCATTATAC
1 CCCTAAG-ATGCAAAATGACCATTATAC
*
12711 CCCT-AGGTGCAAAATGACCATTATAC
1 CCCTAAGATGCAAAATGACCATTATAC
12737 CCCTA
1 CCCTA
12742 GGGTTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 2 0.07
26 21 0.78
27 4 0.15
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (27 bp):
CCCTAAGATGCAAAATGACCATTATAC
Found at i:12889 original size:28 final size:28
Alignment explanation
Indices: 12849--12909 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
12839 GGAAGCGTTC
* *
12849 TGGTGGCTCTGCCACAAATATCTGTTTT
1 TGGTGGCCCTGCCACAAATATCTGTATT
*
12877 TGGTGGCCCTGCCACAATTATCTGTATT
1 TGGTGGCCCTGCCACAAATATCTGTATT
12905 TGGTG
1 TGGTG
12910 ACTTTGTCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (28 bp):
TGGTGGCCCTGCCACAAATATCTGTATT
Found at i:12920 original size:28 final size:27
Alignment explanation
Indices: 12857--12928 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
12847 TCTGGTGGCT
* *
12857 CTGCCACAAATATCTGTTTTTGGTGGCC
1 CTGCCAC-AATATCTGTATTTGGTGACC
*
12885 CTGCCACAATTATCTGTATTTGGTGACT
1 CTGCCACAA-TATCTGTATTTGGTGACC
* *
12913 TTGTCACAATATCTGT
1 CTGCCACAATATCTGT
12929 TCTGGCACCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (27 bp):
CTGCCACAATATCTGTATTTGGTGACC
Found at i:19469 original size:18 final size:18
Alignment explanation
Indices: 19448--19498 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
19438 ACAATTCTTT
19448 TCTCTTCTTCTTTTCTCC
1 TCTCTTCTTCTTTTCTCC
* *
19466 TCTCTTCATCTATTTCTTC
1 TCTCTTCTTCT-TTTCTCC
19485 T-TCTTCTTCTTTTC
1 TCTCTTCTTCTTTTC
19499 CTCTATAGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 18 0.62
19 7 0.24
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.63
Consensus pattern (18 bp):
TCTCTTCTTCTTTTCTCC
Found at i:20739 original size:28 final size:28
Alignment explanation
Indices: 20702--20780 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 28
20692 AAGCGTTTTG
20702 GTGGCTCTGCCACAAATATCTGTTTCTA
1 GTGGCTCTGCCACAAATATCTGTTTCTA
* * * *
20730 GTGGCCCTGCCACAATTATCTGTATCTG
1 GTGGCTCTGCCACAAATATCTGTTTCTA
* *
20758 GTGACTCTGTCAC-AATATCTGTT
1 GTGGCTCTGCCACAAATATCTGTT
20781 CTGGCAGCCA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 8 0.19
28 34 0.81
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (28 bp):
GTGGCTCTGCCACAAATATCTGTTTCTA
Found at i:22529 original size:7 final size:7
Alignment explanation
Indices: 22519--22549 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
22509 AATGATGAAT
22519 GATGAGG
1 GATGAGG
22526 GATGAGG
1 GATGAGG
22533 GATGAGG
1 GATGAGG
22540 GATGAGG
1 GATGAGG
22547 GAT
1 GAT
22550 CATTAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.55, T:0.16
Consensus pattern (7 bp):
GATGAGG
Found at i:27247 original size:30 final size:30
Alignment explanation
Indices: 27212--27281 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
27202 TAGCATATAG
* * * *
27212 GCGTGTGGCCAGCTCGTTTGGCTGACACAA
1 GCGTGTGGCCAGCCCATGTGGCTCACACAA
*
27242 GCGTGTGGCCAGCCCATGTGGCTCACACAG
1 GCGTGTGGCCAGCCCATGTGGCTCACACAA
*
27272 GCGTGCGGCC
1 GCGTGTGGCC
27282 TACTGTGTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.19
Consensus pattern (30 bp):
GCGTGTGGCCAGCCCATGTGGCTCACACAA
Found at i:29333 original size:27 final size:27
Alignment explanation
Indices: 29299--29352 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
29289 CTTAAAAATG
29299 TTATTATATTTTATTCTTCTTCTTGTT
1 TTATTATATTTTATTCTTCTTCTTGTT
*
29326 TTATTATATTTTATTTTTCTTCTTGTT
1 TTATTATATTTTATTCTTCTTCTTGTT
29353 CGACCAAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (27 bp):
TTATTATATTTTATTCTTCTTCTTGTT
Found at i:32448 original size:39 final size:40
Alignment explanation
Indices: 32348--32532 Score: 173
Period size: 40 Copynumber: 4.7 Consensus size: 40
32338 TCGAATGATG
* * *
32348 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* * * *
32388 TTCGGACTAAGAT-CTGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
* *
32428 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
32467 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTA-AA
* *
32508 -CCGGGCTATGTTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
32533 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 33 0.28
40 74 0.62
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:40307 original size:39 final size:40
Alignment explanation
Indices: 40207--40388 Score: 198
Period size: 39 Copynumber: 4.7 Consensus size: 40
40197 TCGAATGATG
* * *
40207 TCCGGGCTAAGT-CCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
40245 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
40286 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
40325 TCCGGGTTAAGTCCCGAA-GCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
** *
40363 AACGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40389 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 15 0.12
39 69 0.56
40 30 0.24
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:40342 original size:79 final size:78
Alignment explanation
Indices: 40207--40386 Score: 204
Period size: 79 Copynumber: 2.3 Consensus size: 78
40197 TCGAATGATG
* * *
40207 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAA-GCATTT
40271 GTGCGAGTTACTAAT
65 GTGCGAGTTACT-AT
* * * **
40286 TCCGGGCTAAGCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGCATTT
40349 GTGCGAGTTACTAT
65 GTGCGAGTTACTAT
** *
40363 AACGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATT
40387 TGAACGAGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
77 10 0.11
78 31 0.36
79 40 0.46
80 6 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (78 bp):
TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGCATTTG
TGCGAGTTACTAT
Found at i:40395 original size:78 final size:77
Alignment explanation
Indices: 40259--40420 Score: 193
Period size: 78 Copynumber: 2.1 Consensus size: 77
40249 GGACTAAGAT
** **
40259 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTA-CTA
1 CCGAA-GCATTTGTGCGAGTTACTAATAACGGGCTAAGCCCGAAGGCATTGGAACGAG-TAGCTA
*
40323 AATCCGGGTTAAGTC
64 AATCC-GGTTAAATC
* * *
40338 CCGAAGCATTTGTGCGAGTTACT-ATAACGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTAT
1 CCGAAGCATTTGTGCGAGTTACTAATAACGGGCTAAG-CCCGAAGGCATTGGAACGAGTAGCTAA
*
40402 ATCCGGTTAAATT
65 ATCCGGTTAAATC
40415 CCGAAG
1 CCGAAG
40421 GTACATGATC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
77 25 0.35
78 42 0.58
79 5 0.07
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (77 bp):
CCGAAGCATTTGTGCGAGTTACTAATAACGGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTAAA
TCCGGTTAAATC
Done.