Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012213.1 Kokia drynarioides strain JFW-HI SEQ_127214, 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: 158941
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:4671 original size:49 final size:49
Alignment explanation
Indices: 4594--4696 Score: 179
Period size: 49 Copynumber: 2.1 Consensus size: 49
4584 TTTTTAGTAT
* * *
4594 ATCATTAATGAAGATAATTCAAGCAAGAATTAAGTCTAGTAAGGAATTC
1 ATCAATAATGAAGATAATTCAAGCAAGAATTAAGTCAAGTAAAGAATTC
4643 ATCAATAATGAAGATAATTCAAGCAAGAATTAAGTCAAGTAAAGAATTC
1 ATCAATAATGAAGATAATTCAAGCAAGAATTAAGTCAAGTAAAGAATTC
4692 ATCAA
1 ATCAA
4697 GACTTTGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (49 bp):
ATCAATAATGAAGATAATTCAAGCAAGAATTAAGTCAAGTAAAGAATTC
Found at i:4689 original size:17 final size:17
Alignment explanation
Indices: 4618--4690 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 17
4608 TAATTCAAGC
*
4618 AAGAATTAAGTCTAGTA
1 AAGAATTAAGTCAAGTA
* *
4635 AGGAATTCA-TCAA-TA
1 AAGAATTAAGTCAAGTA
* * * *
4650 ATGAAGATAATTCAAG-C
1 AAGAA-TTAAGTCAAGTA
4667 AAGAATTAAGTCAAGTA
1 AAGAATTAAGTCAAGTA
4684 AAGAATT
1 AAGAATT
4691 CATCAAGACT
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
15 6 0.15
16 13 0.32
17 22 0.54
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.26
Consensus pattern (17 bp):
AAGAATTAAGTCAAGTA
Found at i:5959 original size:5 final size:5
Alignment explanation
Indices: 5940--5985 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
5930 TTATAAAATC
*
5940 TATTT TA-TT TA-TT TATTT TATTTT TATTT CATTTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TA-TTT TATTT TA-TTT TATTT TATTT T
5986 GGATACATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 8 0.22
5 19 0.53
6 9 0.25
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:5967 original size:11 final size:11
Alignment explanation
Indices: 5940--5985 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
5930 TTATAAAATC
5940 TATTTTATTTATT
1 TATTTTA-TT-TT
5953 TATTTTATTTT
1 TATTTTATTTT
*
5964 TATTTCATTTT
1 TATTTTATTTT
5975 TATTTTATTTT
1 TATTTTATTTT
5986 GGATACATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 22 0.71
12 2 0.06
13 7 0.23
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:7150 original size:96 final size:96
Alignment explanation
Indices: 6971--7157 Score: 229
Period size: 96 Copynumber: 1.9 Consensus size: 96
6961 ACGAAAAAAA
* ** *
6971 TATTTGATTATCTCGATTCGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAACC
1 TATTCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAACC
*
7036 GAAGATAATGAAACATTGCCTCGATTAAGGG
66 GAAGATAAAGAAACATTGCCTCGATTAAGGG
* * *
7067 TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTC-GAAA
1 TATTCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTCAG-AA
*
7130 CTCGAA-ATATAAG-AATATTGCCTCGATT
64 C-CGAAGATA-AAGAAACATTGCCTCGATT
7158 TTAAAGCTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
95 2 0.03
96 70 0.90
97 6 0.08
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (96 bp):
TATTCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAACC
GAAGATAAAGAAACATTGCCTCGATTAAGGG
Found at i:7449 original size:28 final size:28
Alignment explanation
Indices: 7415--7760 Score: 196
Period size: 30 Copynumber: 11.8 Consensus size: 28
7405 TTTTGGGTTT
*
7415 AAAAATGGAATTTTTAGACA-TTCGGGGG
1 AAAAATGGAATTTTTGGA-AGTTCGGGGG
* **
7443 AAAAATGGAATTTTTGGAAATTTCGGGATA
1 AAAAATGGAATTTTTGG-AAGTTCGGG-GG
** **
7473 AAAAATGGTGTTTTTGGAAGTTCGGGAT
1 AAAAATGGAATTTTTGGAAGTTCGGGGG
*
7501 AAAAATGGAATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGAATTTTTGGAAG-TTCGGGG-G
*
7531 AAAAAT-GAGATTTTTGGAAGTTCGGGTG
1 AAAAATGGA-ATTTTTGGAAGTTCGGGGG
* * *
7559 TAAAATGGTAATTTTTAGAAGTTTCGAGGTCG
1 AAAAATGG-AATTTTTGGAAG-TTCG-GG-GG
* ** **
7591 -AAAATGGGATTTTTTAAAGTT-TTGGG
1 AAAAATGGAATTTTTGGAAGTTCGGGGG
* *
7617 ATCGAAAATGGGATTTTTTGGAAGTTCAGGGGT
1 A---AAAAT-GGAATTTTTGGAAGTTC-GGGGG
* ** * *
7650 AAAAATGGAAATTTTAAAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAAG-TTCGGGG-G
* * *
7680 AAAATTGGAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAG-TTCGGGGG
* * *
7709 CAAAATGGGATTTTTGGAAGTTCAGGGG
1 AAAAATGGAATTTTTGGAAGTTCGGGGG
*
7737 TAAAATGGTAATTTTTGGACAGTT
1 AAAAATGG-AATTTTTGGA-AGTT
7761 TAAGGACCTC
Statistics
Matches: 247, Mismatches: 49, Indels: 42
0.73 0.14 0.12
Matches are distributed among these distances:
26 1 0.00
27 1 0.00
28 52 0.21
29 82 0.33
30 86 0.35
31 21 0.09
32 1 0.00
33 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGG
Found at i:7479 original size:30 final size:30
Alignment explanation
Indices: 7384--7755 Score: 227
Period size: 29 Copynumber: 12.6 Consensus size: 30
7374 ACTCGAGGGT
* * * *
7384 AAAATGGTAATTTTGGGAAAATTTTGGGTTTA
1 AAAATGG-AATTTTTGG-AAATTTCGGGGTCA
* * *
7416 AAAATGGAATTTTTAGACA-TTCGGGG-GA
1 AAAATGGAATTTTTGGAAATTTCGGGGTCA
* *
7444 AAAATGGAATTTTTGGAAATTTCGGGATAA
1 AAAATGGAATTTTTGGAAATTTCGGGGTCA
** * *
7474 AAAATGGTGTTTTTGG-AAGTTCGGGAT-A
1 AAAATGGAATTTTTGGAAATTTCGGGGTCA
*
7502 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAATTTCGGGGTCA
*
7532 AAAAT-GAGATTTTTGG-AAGTTCGGGTGT--
1 AAAATGGA-ATTTTTGGAAATTTCGGG-GTCA
* * * *
7560 AAAATGGTAATTTTTAGAAGTTTCGAGGTCG
1 AAAATGG-AATTTTTGGAAATTTCGGGGTCA
* * * * *
7591 AAAATGGGATTTTT-TAAAGTTTTGGGATCG
1 AAAATGGAATTTTTGGAAA-TTTCGGGGTCA
* *
7621 AAAATGGGATTTTTTGG-AAGTTCAGGGGT-A
1 AAAAT-GGAATTTTTGGAAATTTC-GGGGTCA
* * *
7651 AAAATGGAAATTTT-AAAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAA-TTTCGGGGTCA
* * *
7681 AAATTGGAATTTTTGGAAGTTTTGGGGTC-
1 AAAATGGAATTTTTGGAAATTTCGGGGTCA
* *
7710 AAAATGGGATTTTTGG-AAGTTCAGGGGT--
1 AAAATGGAATTTTTGGAAATTTC-GGGGTCA
7738 AAAATGGTAATTTTTGGA
1 AAAATGG-AATTTTTGGA
7756 CAGTTTAAGG
Statistics
Matches: 266, Mismatches: 52, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
28 48 0.18
29 91 0.34
30 91 0.34
31 29 0.11
32 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAATTTCGGGGTCA
Found at i:7580 original size:59 final size:58
Alignment explanation
Indices: 7382--7761 Score: 292
Period size: 58 Copynumber: 6.4 Consensus size: 58
7372 ATACTCGAGG
* * * * * * *
7382 GTAAAATGGTAATTTTGGGAAAATTTTGGGTTTAAAAATGGAATTTTTAGACA-TTCGGGG
1 GTAAAATGG-AATTTTTGG-AAGTTTCGGGGTCAAAAATGGAATTTTTGGA-AGTTCGGGT
* * * * **
7442 GAAAAATGGAATTTTTGGAAATTTCGGGATAAAAAATGGTGTTTTTGGAAGTTCGGGAT
1 GTAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGG-T
*
7501 -AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAAT-GAGATTTTTGGAAGTTCGGGT
1 GTAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGA-ATTTTTGGAAGTTCGGGT
* * * * ** *
7558 GTAAAATGGTAATTTTTAGAAGTTTCGAGGTCGAAAATGGGATTTTTTAAAGTTTTGGGAT
1 GTAAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAG-TTCGGG-T
* * ** *
7619 CG-AAAATGGGATTTTTTGGAAG-TTCAGGGGT-AAAAATGGAAATTTTAAAAGTTTTGGG-
1 -GTAAAAT-GGAATTTTTGGAAGTTTC-GGGGTCAAAAATGGAATTTTTGGAAG-TTCGGGT
* *
7677 GTCAAAATTGGAATTTTTGGAAGTTTTGGGGTC-AAAATGGGATTTTTGGAAGTTCAGGG-
1 GT-AAAA-TGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTC-GGGT
7736 GTAAAATGGTAATTTTTGGACAGTTT
1 GTAAAATGG-AATTTTTGGA-AGTTT
7762 AAGGACCTCC
Statistics
Matches: 265, Mismatches: 36, Indels: 39
0.78 0.11 0.11
Matches are distributed among these distances:
57 7 0.03
58 103 0.39
59 89 0.34
60 43 0.16
61 20 0.08
62 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (58 bp):
GTAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGT
Found at i:9327 original size:12 final size:12
Alignment explanation
Indices: 9312--9363 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
9302 TTAATTAAGT
9312 TTTAAATACAAA
1 TTTAAATACAAA
**
9324 TTTAAATTTAAA
1 TTTAAATACAAA
*
9336 TTTAAA-ATAAA
1 TTTAAATACAAA
9347 TTTAAAT-C-AA
1 TTTAAATACAAA
9357 TTTAAAT
1 TTTAAAT
9364 CCAATAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
10 9 0.26
11 10 0.29
12 16 0.46
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTAAATACAAA
Found at i:9330 original size:6 final size:6
Alignment explanation
Indices: 9321--9353 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
9311 TTTTAAATAC
*
9321 AAATTT AAATTT AAATTT AAA-AT AAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
9354 CAATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AAATTT
Found at i:9348 original size:11 final size:11
Alignment explanation
Indices: 9321--9362 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
9311 TTTTAAATAC
*
9321 AAATTTAAATTT
1 AAATTTAAA-AT
9333 AAATTTAAAAT
1 AAATTTAAAAT
9344 AAATTT-AAAT
1 AAATTTAAAAT
*
9354 CAATTTAAA
1 AAATTTAAA
9363 TCCAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 9 0.33
11 9 0.33
12 9 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:10327 original size:2 final size:2
Alignment explanation
Indices: 10314--10360 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
10304 ATGTCATTAC
*
10314 TA TA TG TA TA TA 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
10356 TA TA T
1 TA TA T
10361 GAAAATTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12689 original size:30 final size:30
Alignment explanation
Indices: 12655--12975 Score: 262
Period size: 30 Copynumber: 10.7 Consensus size: 30
12645 ACCAAACTGA
*
12655 CCAAAAATTTGAATTTAACCCTCAAATTTG
1 CCAAAAATTTGAATTTAACCCTCAAATTTT
*
12685 CCAAAAATTTGAATTTGACCACT-AAATTTT
1 CCAAAAATTTGAATTTAACC-CTCAAATTTT
* *
12715 CCAAAAATTTAAATTTAACCC-CTAAGGTTTT
1 CCAAAAATTTGAATTTAACCCTC-AA-ATTTT
* *
12746 -TATAAATTTGAATTTAACCC-CAAATTTT
1 CCAAAAATTTGAATTTAACCCTCAAATTTT
*
12774 CCAAAAATTCGAATTTAACCCCTCAAATTTT
1 CCAAAAATTTGAATTTAA-CCCTCAAATTTT
* ** * *
12805 CCAAATATTCAAATTTCACCCT-GAATTTT
1 CCAAAAATTTGAATTTAACCCTCAAATTTT
* ** * *
12834 CCAAAAAATAAAATTTGA-CCTCGAATTTT
1 CCAAAAATTTGAATTTAACCCTCAAATTTT
* **
12863 CTAAAAATTCAAATTTAACCCCTCAAATTTT
1 CCAAAAATTTGAATTTAA-CCCTCAAATTTT
*
12894 CCAAAAATTTGAATTTGACCC-CTAAATTTT
1 CCAAAAATTTGAATTTAACCCTC-AAATTTT
* ** *
12924 CCAAGAATTCCAATATTGATCCC-CAAATTTT
1 CCAAAAATTTGAAT-TT-AACCCTCAAATTTT
* **
12955 CCAAAAAATCAAATTTAACCC
1 CCAAAAATTTGAATTTAACCC
12976 GATTTTAATT
Statistics
Matches: 240, Mismatches: 38, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
28 7 0.03
29 63 0.26
30 93 0.39
31 73 0.30
32 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (30 bp):
CCAAAAATTTGAATTTAACCCTCAAATTTT
Found at i:12861 original size:89 final size:92
Alignment explanation
Indices: 12677--12975 Score: 288
Period size: 89 Copynumber: 3.3 Consensus size: 92
12667 ATTTAACCCT
* ** * * * *
12677 CAAATTTGCCAAAAATTTGAATTTGACCACT-AAATTTTCCAAAAATTTAAATTTAACCCCTAAG
1 CAAATTTTCCAAAAATTCAAATTTAACCCCTCAAATTTTCCAAAAATTCAAATTTCACCCCTAA-
* * * * ** *
12741 GTTTT-TATAAATTTGAAT-TT-AACCC
65 ATTTTCCAAAAAATAAAATATTGATCCC
* * *
12766 CAAATTTTCCAAAAATTCGAATTTAACCCCTCAAATTTTCCAAATATTCAAATTTCA-CCCTGAA
1 CAAATTTTCCAAAAATTCAAATTTAACCCCTCAAATTTTCCAAAAATTCAAATTTCACCCCTAAA
*
12830 TTTTCCAAAAAATAAAAT-TTGA-CCT
66 TTTTCCAAAAAATAAAATATTGATCCC
* * ** *
12855 CGAATTTTCTAAAAATTCAAATTTAACCCCTCAAATTTTCCAAAAATTTGAATTTGACCCCTAAA
1 CAAATTTTCCAAAAATTCAAATTTAACCCCTCAAATTTTCCAAAAATTCAAATTTCACCCCTAAA
* * **
12920 TTTTCCAAGAATTCCAATATTGATCCC
66 TTTTCCAAAAAATAAAATATTGATCCC
*
12947 CAAATTTTCCAAAAAATCAAATTTAACCC
1 CAAATTTTCCAAAAATTCAAATTTAACCC
12976 GATTTTAATT
Statistics
Matches: 173, Mismatches: 31, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
88 4 0.02
89 94 0.54
90 43 0.25
91 4 0.02
92 28 0.16
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (92 bp):
CAAATTTTCCAAAAATTCAAATTTAACCCCTCAAATTTTCCAAAAATTCAAATTTCACCCCTAAA
TTTTCCAAAAAATAAAATATTGATCCC
Found at i:13002 original size:12 final size:13
Alignment explanation
Indices: 12983--13065 Score: 60
Period size: 14 Copynumber: 5.9 Consensus size: 13
12973 CCCGATTTTA
12983 ATTTTATTTATTT
1 ATTTTATTTATTT
12996 A-TTTATTTATTTT
1 ATTTTATTTA-TTT
13009 ATTTTATATGTATATT
1 ATTTTAT-T-TAT-TT
*
13025 ATTTTATTTTAATGT
1 ATTTTA-TTT-ATTT
* *
13040 ATTTTATGTATAT
1 ATTTTATTTATTT
*
13053 ATTATTTTTTATT
1 ATT-TTATTTATT
13066 ATGTATACTT
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
12 8 0.14
13 11 0.20
14 13 0.23
15 10 0.18
16 13 0.23
17 1 0.02
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:13007 original size:21 final size:21
Alignment explanation
Indices: 12983--13046 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
12973 CCCGATTTTA
* *
12983 ATTTTATTTATTTATTTAT-TT
1 ATTTTATTT-TATATGTATATT
13004 ATTTTATTTTATATGTATATT
1 ATTTTATTTTATATGTATATT
*
13025 ATTTTATTTTA-ATGTATTTT
1 ATTTTATTTTATATGTATATT
13045 AT
1 AT
13047 GTATATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 17 0.44
21 22 0.56
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
ATTTTATTTTATATGTATATT
Found at i:13009 original size:5 final size:5
Alignment explanation
Indices: 12977--13060 Score: 59
Period size: 5 Copynumber: 17.0 Consensus size: 5
12967 ATTTAACCCG
* *
12977 ATTTT AATTTT A-TTT A-TTT A-TTT A-TTT ATTTT ATTTT ATATGT ATATT
1 ATTTT -ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT
* * * *
13025 ATTTT ATTTT AATGT ATTTT ATGTAT ATATT ATTTT
1 ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT ATTTT
13061 TTATTATGTA
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
4 16 0.25
5 34 0.54
6 13 0.21
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (5 bp):
ATTTT
Found at i:13014 original size:26 final size:29
Alignment explanation
Indices: 12977--13065 Score: 87
Period size: 31 Copynumber: 3.1 Consensus size: 29
12967 ATTTAACCCG
12977 ATTTTAATTTTAT-T-TAT-TTATTTATTT
1 ATTTT-ATTTTATATATATATTATTTATTT
*
13004 ATTTTATTTTATATGTATATTATTTTATTTT
1 ATTTTATTTTATATATATATTA-TTTA-TTT
* * *
13035 AATGTATTTTATGTATATATTATTT-TTT
1 ATTTTATTTTATATATATATTATTTATTT
13063 ATT
1 ATT
13066 ATGTATACTT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
26 7 0.13
27 6 0.12
28 8 0.15
29 3 0.06
30 7 0.13
31 21 0.40
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (29 bp):
ATTTTATTTTATATATATATTATTTATTT
Found at i:13026 original size:16 final size:15
Alignment explanation
Indices: 12983--13064 Score: 68
Period size: 16 Copynumber: 5.7 Consensus size: 15
12973 CCCGATTTTA
12983 ATTTTATT-TAT-TT
1 ATTTTATTATATATT
*
12996 A-TTTATT-TATTTT
1 ATTTTATTATATATT
*
13009 ATTTTATATGTATATT
1 ATTTTAT-TATATATT
*
13025 ATTTTATTTTA-ATGT
1 ATTTTATTATATAT-T
13040 ATTTTATGTATATATT
1 ATTTTAT-TATATATT
13056 ATTTT-TTAT
1 ATTTTATTAT
13065 TATGTATACT
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
12 9 0.15
13 4 0.07
14 10 0.17
15 13 0.22
16 21 0.36
17 2 0.03
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (15 bp):
ATTTTATTATATATT
Found at i:15065 original size:31 final size:31
Alignment explanation
Indices: 15030--15101 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
15020 TGCATATGCA
*
15030 TTCATACGTTCATAAAA-TTCTGCATCGCATT
1 TTCATACATTCATAAAATTTC-GCATCGCATT
* * *
15061 TTCATGCATTTATAAAATTTCGCATTGCATT
1 TTCATACATTCATAAAATTTCGCATCGCATT
15092 TTCATACATT
1 TTCATACATT
15102 AAAATTTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.43
Consensus pattern (31 bp):
TTCATACATTCATAAAATTTCGCATCGCATT
Found at i:19815 original size:50 final size:50
Alignment explanation
Indices: 19735--19866 Score: 140
Period size: 50 Copynumber: 2.6 Consensus size: 50
19725 GACGAGTTCT
* * ** *
19735 ATACCCCTAAAGTTGTAGAGGAAC-GAATTGAAATCACAATGGCAAATCTC
1 ATACACCTAAAGCTGTAGAGGGGCAG-ATTGAAACCACAATGGCAAATCTC
* * *
19785 ATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCATTGGCAAATCTC
1 ATACACCTAAAGCTGTAGAGGGGCAGATTGAAACCACAATGGCAAATCTC
* * * *
19835 ATTCACCTAAAGCTGTAAAGCGGTAGATTGAA
1 ATACACCTAAAGCTGTAGAGGGGCAGATTGAA
19867 GTCGCAAGGA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
50 68 0.99
51 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (50 bp):
ATACACCTAAAGCTGTAGAGGGGCAGATTGAAACCACAATGGCAAATCTC
Found at i:19867 original size:50 final size:50
Alignment explanation
Indices: 19774--19872 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
19764 GAAATCACAA
* *
19774 TGGCAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAT
1 TGGCAAATCTCATACACCTAAAGCTGTAAAGCGGCAGATTGAAGCCGCAT
* * *
19824 TGGCAAATCTCATTCACCTAAAGCTGTAAAGCGGTAGATTGAAGTCGCA
1 TGGCAAATCTCATACACCTAAAGCTGTAAAGCGGCAGATTGAAGCCGCA
19873 AGGACGAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.22
Consensus pattern (50 bp):
TGGCAAATCTCATACACCTAAAGCTGTAAAGCGGCAGATTGAAGCCGCAT
Found at i:19963 original size:39 final size:40
Alignment explanation
Indices: 19920--20090 Score: 161
Period size: 39 Copynumber: 4.3 Consensus size: 40
19910 AAGATCATCA
* *
19920 AATCTTTTACCCCGACCATAGGGCAGATTGAA-ACAATCC
1 AATCTTTTACCCCAACCAGAGGGCAGATTGAAGACAATCC
* * * *
19959 AATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCAT-C
1 AATCTTTTACCCCAACCAGAGGGCAGATTGAAGACAATCC
* * * *
19998 AGATTTTTTACCTCGATCATG-GGGCAGATTGAAG-CAATCC
1 A-ATCTTTTACCCCAACCA-GAGGGCAGATTGAAGACAATCC
** * *
20038 AATCTTTTACCGTAACCAGAGAGCAGATTGAAGACCATCC
1 AATCTTTTACCCCAACCAGAGGGCAGATTGAAGACAATCC
*
20078 GATCTTTTACCCC
1 AATCTTTTACCCC
20091 TAAAGCTATA
Statistics
Matches: 102, Mismatches: 24, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
38 1 0.01
39 56 0.55
40 44 0.43
41 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (40 bp):
AATCTTTTACCCCAACCAGAGGGCAGATTGAAGACAATCC
Found at i:20007 original size:79 final size:79
Alignment explanation
Indices: 19909--20090 Score: 256
Period size: 79 Copynumber: 2.3 Consensus size: 79
19899 GAAGTGGAGC
* *
19909 GAAGATCATCAAATCTTTTACCCCGACCATAGGGCAGATTGAAACAATCCAATCTTTTACCCTAA
1 GAAGACCATCAGATCTTTTACCCCGACCATAGGGCAGATTGAAACAATCCAATCTTTTACCCTAA
* *
19974 CTAGAGGGCAAATT
66 CCAGAGAGCAAATT
* * * * * *
19988 GAAGACCATCAGATTTTTTACCTCGATCATGGGGCAGATTGAAGCAATCCAATCTTTTACCGTAA
1 GAAGACCATCAGATCTTTTACCCCGACCATAGGGCAGATTGAAACAATCCAATCTTTTACCCTAA
*
20053 CCAGAGAGCAGATT
66 CCAGAGAGCAAATT
*
20067 GAAGACCATCCGATCTTTTACCCC
1 GAAGACCATCAGATCTTTTACCCC
20091 TAAAGCTATA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 89 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (79 bp):
GAAGACCATCAGATCTTTTACCCCGACCATAGGGCAGATTGAAACAATCCAATCTTTTACCCTAA
CCAGAGAGCAAATT
Found at i:20688 original size:5 final size:5
Alignment explanation
Indices: 20678--20738 Score: 52
Period size: 5 Copynumber: 11.2 Consensus size: 5
20668 CAAAATCCAT
*
20678 TTTTA TTTTA TTTTA TTATTTA TTTCA TTTGTA TTTTA TTTT- TATTTA
1 TTTTA TTTTA TTTTA -T-TTTA TTTTA TTT-TA TTTTA TTTTA T-TTTA
20726 TTTATCA TTTTA T
1 TTT-T-A TTTTA T
20739 ATAAATAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
4 1 0.02
5 29 0.62
6 9 0.19
7 8 0.17
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:20701 original size:12 final size:11
Alignment explanation
Indices: 20678--20738 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
20668 CAAAATCCAT
20678 TTTTA-TTTTA
1 TTTTATTTTTA
20688 TTTTATTATTTA
1 TTTTATT-TTTA
* *
20700 TTTCATTTGTA
1 TTTTATTTTTA
20711 TTTTATTTTTA
1 TTTTATTTTTA
*
20722 -TTTATTTATCA
1 TTTTATTT-TTA
20733 TTTTAT
1 TTTTAT
20739 ATAAATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
10 12 0.29
11 15 0.36
12 15 0.36
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:20701 original size:17 final size:16
Alignment explanation
Indices: 20678--20724 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
20668 CAAAATCCAT
20678 TTTTATTTTATTT-TA
1 TTTTATTTTATTTGTA
*
20693 TTATTTATTTCATTTGTA
1 -T-TTTATTTTATTTGTA
20711 TTTTATTTTTATTT
1 TTTTA-TTTTATTT
20725 ATTTATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 19 0.73
18 2 0.08
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTATTTTATTTGTA
Found at i:20707 original size:22 final size:21
Alignment explanation
Indices: 20679--20738 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
20669 AAAATCCATT
20679 TTTATTT-TATTTTATTATTTA
1 TTTATTTATATTTTATT-TTTA
*
20700 TTTCATTTGTATTTTATTTTTA
1 TTT-ATTTATATTTTATTTTTA
20722 TTTATTTATCATTTTAT
1 TTTATTTAT-ATTTTAT
20739 ATAAATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 8 0.23
22 18 0.51
23 9 0.26
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTATTTATATTTTATTTTTA
Found at i:20733 original size:28 final size:27
Alignment explanation
Indices: 20675--20735 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
20665 TTACAAAATC
*
20675 CATTTTTATTTTATTTTATTATTTATTT
1 CATTTGTATTTTATTTTATTATTTA-TT
20703 CATTTGTATTTTATTTTTATTTATTTA-T
1 CATTTGTATTTTA-TTTTA-TTATTTATT
20731 CATTT
1 CATTT
20736 TATATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 18 0.60
29 5 0.17
30 7 0.23
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (27 bp):
CATTTGTATTTTATTTTATTATTTATT
Found at i:20870 original size:16 final size:17
Alignment explanation
Indices: 20849--20882 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20839 CTAATTACCT
20849 AGCCCAAA-TTTAACAA
1 AGCCCAAATTTTAACAA
20865 AGCCCAAATTTTAACAA
1 AGCCCAAATTTTAACAA
20882 A
1 A
20883 ACATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.21
Consensus pattern (17 bp):
AGCCCAAATTTTAACAA
Found at i:22072 original size:30 final size:29
Alignment explanation
Indices: 22028--22287 Score: 191
Period size: 30 Copynumber: 8.7 Consensus size: 29
22018 ATTTTTCGAC
* *
22028 CCCCAAACTATCCAAAAATTAGAATTTAA
1 CCCCAAATTTTCCAAAAATTAGAATTTAA
* *
22057 CTCTCAAATTTTCCAAAAATTTGAATTTAA
1 C-CCCAAATTTTCCAAAAATTAGAATTTAA
* ** *
22087 CCCCAAATTTTCCAAAAAATCTAATTTGA
1 CCCCAAATTTTCCAAAAATTAGAATTTAA
* * *
22116 CCCCTAAATTTTCCAAAAAATTCGAGTTTCA
1 CCCC-AAATTTTCC-AAAAATTAGAATTTAA
* *
22147 CCCTAAATTTTCCAAAAAATCA-AATTTAA
1 CCCCAAATTTTCC-AAAAATTAGAATTTAA
* * *
22176 CCCCAAATTTTCTAAAAAAATCA-AATTTGA
1 CCCCAAATTTTC--CAAAAATTAGAATTTAA
* * *
22206 CCCTCAAATTTTCCAAATATTTGAATTTTAC
1 CCC-CAAATTTTCCAAAAATTAGAA-TTTAA
* * ** *
22237 CCCCTAATTTTCCAAGAATTCCAATATTGAT
1 CCCCAAATTTTCCAAAAATTAGAAT-TT-AA
*
22268 CCCCAAAATTTCCAAAAATT
1 CCCCAAATTTTCCAAAAATT
22288 CCTACTTGAC
Statistics
Matches: 185, Mismatches: 36, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
29 50 0.27
30 87 0.47
31 48 0.26
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCCAAATTTTCCAAAAATTAGAATTTAA
Found at i:22105 original size:60 final size:58
Alignment explanation
Indices: 22028--22285 Score: 214
Period size: 60 Copynumber: 4.3 Consensus size: 58
22018 ATTTTTCGAC
* * * *
22028 CCCCAAACTATCC-AAAAATTAGAATTTAACTCTCAAATTTTCCAAAAATTTGAATTTAA
1 CCCCAAATTTTCCAAAAAATTA-AATTTAAC-CCCAAATTTTCCAAAAATTCGAATTTAA
* * *
22087 CCCCAAATTTTCCAAAAAATCT-AATTTGACCCCTAAATTTTCCAAAAAATTCGAGTTTCA
1 CCCCAAATTTTCCAAAAAAT-TAAATTTAACCCC-AAATTTTCC-AAAAATTCGAATTTAA
* * * * * *
22147 CCCTAAATTTTCCAAAAAATCAAATTTAACCCCAAATTTTCTAAAAAAATCAAATTTGA
1 CCCCAAATTTTCCAAAAAATTAAATTTAACCCCAAATTTTC-CAAAAATTCGAATTTAA
* * * * * * * *
22206 CCCTCAAATTTTCCAAATATTTGAATTTTACCCCCTAATTTTCCAAGAATTCCAATATTGAT
1 CCC-CAAATTTTCCAAAAAATT-AAATTTAACCCCAAATTTTCCAAAAATTCGAAT-TT-AA
*
22268 CCCCAAAATTTCCAAAAA
1 CCCCAAATTTTCCAAAAA
22286 TTCCTACTTG
Statistics
Matches: 159, Mismatches: 30, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
58 2 0.01
59 50 0.31
60 71 0.45
61 33 0.21
62 3 0.02
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.32
Consensus pattern (58 bp):
CCCCAAATTTTCCAAAAAATTAAATTTAACCCCAAATTTTCCAAAAATTCGAATTTAA
Found at i:22285 original size:90 final size:88
Alignment explanation
Indices: 22062--22286 Score: 222
Period size: 90 Copynumber: 2.5 Consensus size: 88
22052 TTTAACTCTC
* ** * *
22062 AAATTTTCCAAAAATTTGAATTTAACCCCAAATTTTCCAAAAAATCTAATTTGACCCCTAAATTT
1 AAATTTTCCAAAAAATCAAATTGAACCCCAAATTTTCC-AAAAATCAAATTTGACCCCTAAATTT
22127 TCCAAAAAATTCGAGTTTCACCCT
65 TCCAAAAAATTCGAGTTTCACCCT
* *
22151 AAATTTTCCAAAAAATCAAATTTAACCCCAAATTTTCTAAAAAAATCAAATTTGA-CCCTCAAAT
1 AAATTTTCCAAAAAATCAAATTGAACCCCAAATTTTC--CAAAAATCAAATTTGACCCCT-AAAT
* * * *
22215 TTTCC-AAATATTTGAATTTTACCCCCT
63 TTTCCAAAAAATTCG-AGTTT-CACCCT
* * * *
22242 -AATTTTCCAAGAATTCCAATATTGATCCCCAAAATTTCCAAAAAT
1 AAATTTTCCAAAAAAT-CAA-ATTGAACCCCAAATTTTCCAAAAAT
22287 TCCTACTTGA
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
89 45 0.39
90 46 0.40
91 8 0.07
92 15 0.13
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (88 bp):
AAATTTTCCAAAAAATCAAATTGAACCCCAAATTTTCCAAAAATCAAATTTGACCCCTAAATTTT
CCAAAAAATTCGAGTTTCACCCT
Found at i:22358 original size:5 final size:5
Alignment explanation
Indices: 22332--22395 Score: 53
Period size: 5 Copynumber: 13.2 Consensus size: 5
22322 TTGGACCCGG
* * * *
22332 TTTTA ATTT- TTTT- TTTT- TTTTA TTTTA TCTTA TATGTA TATTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA
*
22380 TTTTA TTGTA TTTTA T
1 TTTTA TTTTA TTTTA T
22396 GTATATATTG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
4 11 0.23
5 33 0.70
6 3 0.06
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:22384 original size:31 final size:27
Alignment explanation
Indices: 22345--22414 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 27
22335 TAATTTTTTT
*
22345 TTTTTTTTATTTTATCTTATATGTATATTA
1 TTTTTTTTATTGTAT-TT-TATGTATA-TA
22375 TTTTATTTTATTGTATTTTATGTATATA
1 TTTT-TTTTATTGTATTTTATGTATATA
22403 TTGTTTTTTATT
1 TT-TTTTTTATT
22415 ATGTATACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 11 0.30
29 10 0.27
30 6 0.16
31 10 0.27
ACGTcount: A:0.21, C:0.01, G:0.06, T:0.71
Consensus pattern (27 bp):
TTTTTTTTATTGTATTTTATGTATATA
Found at i:24856 original size:18 final size:17
Alignment explanation
Indices: 24820--24853 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
24810 ATATTTTTAT
24820 TAAATTTAATTATAAAA
1 TAAATTTAATTATAAAA
24837 TAAATATTAA-TATAAAA
1 TAAAT-TTAATTATAAAA
24854 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTAATTATAAAA
Found at i:48660 original size:16 final size:17
Alignment explanation
Indices: 48628--48661 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
48618 TATATTTTAA
*
48628 TTAATCATATTTTAATT
1 TTAATCATATCTTAATT
48645 TTAATCA-ATCTTAATT
1 TTAATCATATCTTAATT
48661 T
1 T
48662 ACTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATCATATCTTAATT
Found at i:48662 original size:21 final size:22
Alignment explanation
Indices: 48615--48662 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
48605 TATAAAACTT
*
48615 ATTTATATTTTAATTAATCATA
1 ATTTATATTTTAATCAATCATA
* *
48637 TTTTA-ATTTTAATCAATCTTA
1 ATTTATATTTTAATCAATCATA
48658 ATTTA
1 ATTTA
48663 CTTAATTAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTATATTTTAATCAATCATA
Found at i:53884 original size:3 final size:3
Alignment explanation
Indices: 53876--53911 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
53866 ACATAAATTG
53876 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
53912 AGGACACATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54964 original size:2 final size:2
Alignment explanation
Indices: 54957--54987 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54947 GAGATTCTTG
54957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54988 ACAATGTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57237 original size:25 final size:24
Alignment explanation
Indices: 57191--57238 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
57181 TATACATTAA
**
57191 AAAATGTTAAAAATAACTATATAC
1 AAAATGTTAAAAATAAAAATATAC
*
57215 AAAATTTTAATAAATAAAAATATA
1 AAAATGTTAA-AAATAAAAATATA
57239 TGATTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAATGTTAAAAATAAAAATATAC
Found at i:57296 original size:33 final size:38
Alignment explanation
Indices: 57223--57298 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 38
57213 ACAAAATTTT
*
57223 AATAAATAAAAATATATGATTATTAAATATTAAATTAAA
1 AATAAATAAAAATATAT-ATTATTAAATATTAAATAAAA
*
57262 AATAAATATAAATATAT-TT-TT-AAT-TTAAA-AAAA
1 AATAAATAAAAATATATATTATTAAATATTAAATAAAA
57295 AATA
1 AATA
57299 CAGATTAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
33 7 0.20
34 5 0.14
35 3 0.09
36 2 0.06
37 2 0.06
39 16 0.46
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (38 bp):
AATAAATAAAAATATATATTATTAAATATTAAATAAAA
Found at i:78873 original size:31 final size:29
Alignment explanation
Indices: 78838--78906 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
78828 TTTTTAAAAA
*
78838 TTAAAAATA-TTTGAAAAATATTTTTATATTT
1 TTAAAAATACTTT--AAAATATTTTT-TATAT
* *
78869 TTAAAAATACTTTTATATATTTTTTATAT
1 TTAAAAATACTTTAAAATATTTTTTATAT
78898 TTAAAAATA
1 TTAAAAATA
78907 ATTAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.38
30 9 0.26
31 9 0.26
32 3 0.09
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
TTAAAAATACTTTAAAATATTTTTTATAT
Found at i:78876 original size:20 final size:22
Alignment explanation
Indices: 78851--78892 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
78841 AAAATATTTG
78851 AAAAATA-TTTT-TATATTTTT
1 AAAAATACTTTTATATATTTTT
78871 AAAAATACTTTTATATATTTTT
1 AAAAATACTTTTATATATTTTT
78893 TATATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
22 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
AAAAATACTTTTATATATTTTT
Found at i:79152 original size:29 final size:30
Alignment explanation
Indices: 79107--79174 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
79097 GCTTTACAAA
79107 TTTAAAATTTAAACTCTATATATTT-AT-T
1 TTTAAAATTTAAACTCTATATATTTCATAT
* * * *
79135 TTTAAGAATTTTATCTCTCTATTTTTCATAT
1 TTTAA-AATTTAAACTCTATATATTTCATAT
79166 TTTAAAATT
1 TTTAAAATT
79175 CAAGTTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 5 0.15
29 16 0.48
30 6 0.18
31 6 0.18
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.56
Consensus pattern (30 bp):
TTTAAAATTTAAACTCTATATATTTCATAT
Found at i:97159 original size:19 final size:19
Alignment explanation
Indices: 97132--97178 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
97122 CTATAAGCCA
*
97132 GCAAAGCCATGGTCTCTTT
1 GCAATGCCATGGTCTCTTT
97151 GCAATGCCATGGTCTCTTT
1 GCAATGCCATGGTCTCTTT
97170 GCAATGCCA
1 GCAATGCCA
97179 ATGCAAATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (19 bp):
GCAATGCCATGGTCTCTTT
Found at i:97199 original size:18 final size:18
Alignment explanation
Indices: 97172--97206 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
97162 GTCTCTTTGC
97172 AATGCCAATGCAAATGCA
1 AATGCCAATGCAAATGCA
* *
97190 AATGCTAATGCTAATGC
1 AATGCCAATGCAAATGC
97207 CAATTGCAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (18 bp):
AATGCCAATGCAAATGCA
Found at i:98953 original size:45 final size:45
Alignment explanation
Indices: 98888--98975 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
98878 GATTTTTACC
*
98888 TAATATATATAATTAATAATAAATACCATGGAATTTAGTTAAAAT
1 TAATATAAATAATTAATAATAAATACCATGGAATTTAGTTAAAAT
** * *
98933 TAATATAAATAATTTGTAATAAATACCATGTAATTTATTTAAA
1 TAATATAAATAATTAATAATAAATACCATGGAATTTAGTTAAA
98976 CATTTACTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.40
Consensus pattern (45 bp):
TAATATAAATAATTAATAATAAATACCATGGAATTTAGTTAAAAT
Found at i:99102 original size:20 final size:19
Alignment explanation
Indices: 99073--99112 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
99063 TTATATTTTG
99073 AAAATAAAATA-TATGTATT
1 AAAATAAAATACTAT-TATT
99092 AAAATTAAAATACTATTATT
1 AAAA-TAAAATACTATTATT
99112 A
1 A
99113 TATAAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 12 0.63
21 3 0.16
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAATAAAATACTATTATT
Found at i:105936 original size:29 final size:29
Alignment explanation
Indices: 105904--106193 Score: 293
Period size: 29 Copynumber: 9.9 Consensus size: 29
105894 TTCAAGGTCG
*
105904 AAAATGGGATTTTTTGAAGTTTGAGGGTA
1 AAAATGGGATTTTTGGAAGTTTGAGGGTA
* *
105933 AAAATGGAATTTTTGGAAGTTTCGA-TGTCA
1 AAAATGGGATTTTTGGAAGTTT-GAGGGT-A
* * * *
105963 AAAACGGAATTTTTGGAAGTTCGAGGCTA
1 AAAATGGGATTTTTGGAAGTTTGAGGGTA
*
105992 AAAATGGGATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGGATTTTTGGAAGTTTGAGGGT-A
* * * *
106022 AAAA-GAGATTTTTTGAAGTTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTTGAGGGTA
* *
106050 AAAATGGAATTTTTGGAAGTTTCG-GGGTC
1 AAAATGGGATTTTTGGAAGTTT-GAGGGTA
* *
106079 AAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTTGAGGGTA
* *
106108 AAAATAGAATTTTTGGAAGTTTCGA-GGTAA
1 AAAATGGGATTTTTGGAAGTTT-GAGGGT-A
* * *
106138 AAAATGGTATTTTTGGAAGTTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTTGAGGGTA
106167 AAAATGGGATTTTTGGATAGTTT-AGGG
1 AAAATGGGATTTTTGGA-AGTTTGAGGG
106194 ACCTTCGGGG
Statistics
Matches: 214, Mismatches: 36, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.03
29 150 0.70
30 58 0.27
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34
Consensus pattern (29 bp):
AAAATGGGATTTTTGGAAGTTTGAGGGTA
Found at i:105944 original size:58 final size:58
Alignment explanation
Indices: 105891--106189 Score: 375
Period size: 58 Copynumber: 5.1 Consensus size: 58
105881 TAATTTTGAG
* * * *
105891 AGTTTCAAGGTCGAAAATGGGATTTTTTGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* * * * * *
105950 AGTTTCGATGTCAAAAACGGAATTTTTGGAAGTTCGAGGCTAAAAATGGGATTTTTGGA
1 AGTTTCGAGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* * * *
106009 AGTTT-TAGGGTCAAAAAGAGATTTTTTGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGA-GGTCAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* *
106067 AGTTTCGGGGTCAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGGA
1 AGTTTCGAGGTCAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* * *
106125 AGTTTCGAGGTAAAAAATGGTATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGA
1 AGTTTCGAGGT-CAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
106184 TAGTTT
1 -AGTTT
106190 AGGGACCTTC
Statistics
Matches: 207, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
58 101 0.49
59 101 0.49
60 5 0.02
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (58 bp):
AGTTTCGAGGTCAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
Found at i:105975 original size:59 final size:59
Alignment explanation
Indices: 105891--106189 Score: 372
Period size: 59 Copynumber: 5.1 Consensus size: 59
105881 TAATTTTGAG
* * * * * *
105891 AGTTTCAAGGTCGAAAATGGGATTTTTTGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* * * * *
105950 AGTTTCGATGTCAAAAACGGAATTTTTGGAAGTTCGAGGCTAAAAATGGGATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* *
106009 AGTTT-TAGGGTCAAAAA--GAGATTTTTTGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGA-GGTCAAAAATGGA-ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* * *
106067 AGTTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
* * *
106125 AGTTTCGAGGTAAAAAATGGTATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
106184 TAGTTT
1 -AGTTT
106190 AGGGACCTTC
Statistics
Matches: 208, Mismatches: 25, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
57 6 0.03
58 90 0.43
59 107 0.51
60 5 0.02
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (59 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
Found at i:106859 original size:33 final size:33
Alignment explanation
Indices: 106817--106884 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
106807 CGGCGTCCGT
106817 CGAGCGTAGGGCTACACGCGCACCGCTGATCCC
1 CGAGCGTAGGGCTACACGCGCACCGCTGATCCC
106850 CGAGCGTAGGGCTACACGCGCACCGCTGATCCC
1 CGAGCGTAGGGCTACACGCGCACCGCTGATCCC
106883 CG
1 CG
106885 CTGATCCCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.18, C:0.40, G:0.31, T:0.12
Consensus pattern (33 bp):
CGAGCGTAGGGCTACACGCGCACCGCTGATCCC
Found at i:107356 original size:3 final size:3
Alignment explanation
Indices: 107310--107338 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
107300 TCATTAATGC
107310 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
107339 AAACATCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:107992 original size:6 final size:6
Alignment explanation
Indices: 107984--108052 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
107974 GATTTTTTTT
*
107984 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAAA TTTAAA -TT-AA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
108030 TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
108053 ATAAATTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 2 0.04
5 11 0.20
6 39 0.72
7 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:108008 original size:11 final size:11
Alignment explanation
Indices: 107994--108059 Score: 73
Period size: 11 Copynumber: 5.9 Consensus size: 11
107984 TTTAATTTTG
107994 AAATTAAATTT
1 AAATTAAATTT
108005 AAATTTAAATTT
1 AAA-TTAAATTT
108017 AAATT-AATTT
1 AAATTAAATTT
*
108027 AAATTTAAA-AT
1 AAA-TTAAATTT
108038 AAATCTAAATTT
1 AAAT-TAAATTT
*
108050 AAAATAAATT
1 AAATTAAATT
108060 AAAAAGGGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
10 9 0.19
11 21 0.45
12 17 0.36
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:108023 original size:17 final size:17
Alignment explanation
Indices: 108004--108059 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
107994 AAATTAAATT
108004 TAAATTTAAATTT-AAA
1 TAAATTTAAATTTAAAA
*
108020 TTAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
108037 TAAATCTAAATTTAAAA
1 TAAATTTAAATTTAAAA
108054 TAAATT
1 TAAATT
108060 AAAAAGGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
16 12 0.34
17 23 0.66
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:108027 original size:16 final size:16
Alignment explanation
Indices: 108006--108062 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
107996 ATTAAATTTA
108006 AATTTAAATTTAAATT
1 AATTTAAATTTAAATT
*
108022 AATTTAAATTTAAAATA
1 AATTTAAATTT-AAATT
* *
108039 AATCTAAATTTAAAAT
1 AATTTAAATTTAAATT
*
108055 AAATTAAA
1 AATTTAAA
108063 AAGGGGACCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 20 0.59
17 14 0.41
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTAAATTTAAATT
Found at i:108761 original size:207 final size:207
Alignment explanation
Indices: 108402--109499 Score: 1881
Period size: 207 Copynumber: 5.3 Consensus size: 207
108392 TTTGTTCATC
* *
108402 GAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAAGACCGCATCGCTTGTTT
1 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
* * *
108467 CAATCCGCTTCTCTGTACCTCGTCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
66 CAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
*
108532 AGCTAACTGTTTATTGCTTCGACCTGCTTCTCGGTGTCTTATCAGGAAGCTGGGGTTTCAGAGAT
131 AGCTAACCGTTTATTGCTTCGACCTGCTTCTCGGTGTCTTATCAGGAAGCTGGGGTTTCAGAGAT
108597 TTTGCTCGCTTT
196 TTTGCTCGCTTT
*
108609 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTT
1 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
*
108674 CAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
66 CAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
* * *
108739 AGCTAACCATTTATTACTTCGACCTGCTTCTCGGTGTCTTATTAGGAAGCTGGGGTTTCAGAGAT
131 AGCTAACCGTTTATTGCTTCGACCTGCTTCTCGGTGTCTTATCAGGAAGCTGGGGTTTCAGAGAT
108804 TTTGCTCGCTTT
196 TTTGCTCGCTTT
* *
108816 GAGCGTGGGTTTGATTTAGTCTTCTTTTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
1 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
* * *
108881 TAATCCGCTTCTCTGTATCTCATCAAAAAGACGACTTTGGTTCACTTCTCAGTATCTCATCAGGA
66 CAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
* * *
108946 AGCTAACCGTTGATTGCTTTGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTTCAGAGAT
131 AGCTAACCGTTTATTGCTTCGACCTGCTTCTCGGTGTCTTATCAGGAAGCTGGGGTTTCAGAGAT
109011 TTTGCTCGCTTT
196 TTTGCTCGCTTT
* *
109023 GAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTATTT
1 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
* * * *
109088 CAATCCGCTTCTCTATATCTCATCAGAAAGACAAATTTAGTTCACTTCTCAGTATCTCATTAGGA
66 CAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
*
109153 AGCTAACCGTTTATTGCTTCGACCTGCTTCTCGGTGTCTTATCAGAAAGCTGGGGTTTCAGAGAT
131 AGCTAACCGTTTATTGCTTCGACCTGCTTCTCGGTGTCTTATCAGGAAGCTGGGGTTTCAGAGAT
109218 TTTGCTCGCTTT
196 TTTGCTCGCTTT
109230 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
1 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
* *
109295 CAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGATTCACTTCTCAGTATCTCATCAGAA
66 CAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
* * * *
109360 AGCTAACCGTTGATTGCTTTGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTTCAGAGAG
131 AGCTAACCGTTTATTGCTTCGACCTGCTTCTCGGTGTCTTATCAGGAAGCTGGGGTTTCAGAGAT
109425 TTTGCTCGCTTT
196 TTTGCTCGCTTT
* * *
109437 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAAATGACCGCGTCGTTTGT
1 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGT
109500 GGATAATCGC
Statistics
Matches: 838, Mismatches: 53, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
207 838 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (207 bp):
GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
CAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
AGCTAACCGTTTATTGCTTCGACCTGCTTCTCGGTGTCTTATCAGGAAGCTGGGGTTTCAGAGAT
TTTGCTCGCTTT
Found at i:110016 original size:26 final size:27
Alignment explanation
Indices: 109987--110039 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
109977 TCAAGAATTC
*
109987 TATT-AAAAGAGAATCAAAGGAAACAA
1 TATTAAAAAGAGAATCAAAGAAAACAA
* *
110013 TATTAAAAAGAGGATTAAAGAAAACAA
1 TATTAAAAAGAGAATCAAAGAAAACAA
110040 CCATTAGCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.17
Consensus pattern (27 bp):
TATTAAAAAGAGAATCAAAGAAAACAA
Found at i:121161 original size:29 final size:29
Alignment explanation
Indices: 121129--121453 Score: 236
Period size: 29 Copynumber: 11.1 Consensus size: 29
121119 TTTGGGAAAA
*
121129 TTTAGGGTTAAAAATGGGATTTTTAGACA-
1 TTTAGGGTTAAAAATGGGATTTTTGGA-AG
*
121158 TTTAAGGG-T-AAAA-GGGTAATTTT-GAGAG
1 TTT-AGGGTTAAAAATGGG-ATTTTTGGA-AG
* ** *
121186 TTTCGAGGTCGAAAATGAGATTTTTGGAAG
1 TTTAG-GGTTAAAAATGGGATTTTTGGAAG
**
121216 TTTGAGGG-TAAAAATGAAATTTTTGGAAG
1 TTT-AGGGTTAAAAATGGGATTTTTGGAAG
* *
121245 TTTGGGGCTAAAAATGGGATTTTTGGAAG
1 TTTAGGGTTAAAAATGGGATTTTTGGAAG
* * *
121274 TTTTAGAG-TAAAAAAGAGATTTTTGGAAG
1 -TTTAGGGTTAAAAATGGGATTTTTGGAAG
* * *
121303 TTTGGGGGTAAAAATGGAATTTTTGGAAG
1 TTTAGGGTTAAAAATGGGATTTTTGGAAG
* * *
121332 TTTCGGGGTAAAAAATGGGATTTTTAGAAG
1 TTT-AGGGTTAAAAATGGGATTTTTGGAAG
*
121362 TTTAGGGGTAAAAAT-GGATTTTTGGAAG
1 TTTAGGGTTAAAAATGGGATTTTTGGAAG
* * * *
121390 TTTTGGAGTCAAAAATGGTATTTTTAGAAG
1 TTTAGG-GTTAAAAATGGGATTTTTGGAAG
* * * *
121420 -TTCGGGAGTAAAAATGAGATTTTCGGACAG
1 TTTAGGG-TTAAAAATGGGATTTTTGGA-AG
121450 TTTA
1 TTTA
121454 AGGACCTCCA
Statistics
Matches: 235, Mismatches: 43, Indels: 34
0.75 0.14 0.11
Matches are distributed among these distances:
27 7 0.03
28 40 0.17
29 118 0.50
30 63 0.27
31 7 0.03
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
TTTAGGGTTAAAAATGGGATTTTTGGAAG
Found at i:121424 original size:87 final size:86
Alignment explanation
Indices: 121197--121442 Score: 318
Period size: 87 Copynumber: 2.8 Consensus size: 86
121187 TTCGAGGTCG
* *
121197 AAAATGAGATTTTTGGAAG-TTTGAGGGTAAAAATGAAATTTTTGGAAGTTTGGGGCTAAAAATG
1 AAAATGAGATTTTTGGAAGTTTTG-GGGTAAAAATGGAATTTTTGGAAGTTCGGGG-TAAAAATG
*
121261 GGATTTTTGGAAGTTTTAGAGTA
64 GGATTTTTAGAAGTTTTAGAGTA
* *
121284 AAAAAGAGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAAATG
1 AAAATGAGATTTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTGGAAG-TTCGGGGT-AAAAATG
*
121349 GGATTTTTAGAAG-TTTAGGGGTA
64 GGATTTTTAGAAGTTTTA-GAGTA
* * *
121372 AAAATG-GATTTTTGGAAGTTTTGGAGTCAAAAATGGTATTTTTAGAAGTTCGGGAGTAAAAATG
1 AAAATGAGATTTTTGGAAGTTTTGGGGT-AAAAATGGAATTTTTGGAAGTTCGGG-GTAAAAATG
*
121436 AGATTTT
64 GGATTTT
121443 CGGACAGTTT
Statistics
Matches: 141, Mismatches: 12, Indels: 12
0.85 0.07 0.07
Matches are distributed among these distances:
87 84 0.60
88 57 0.40
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.35
Consensus pattern (86 bp):
AAAATGAGATTTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTGGAAGTTCGGGGTAAAAATGGG
ATTTTTAGAAGTTTTAGAGTA
Found at i:123226 original size:11 final size:11
Alignment explanation
Indices: 123212--123274 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
123202 TTTAATTTTG
123212 AAATTAAATTT
1 AAATTAAATTT
123223 AAATTTAAA-TT
1 AAA-TTAAATTT
*
123234 AATTTAAATTT
1 AAATTAAATTT
* *
123245 AAAATAAATCT
1 AAATTAAATTT
*
123256 AAATTTAAA-AT
1 AAA-TTAAATTT
123267 AAATTAAA
1 AAATTAAA
123275 AAGGAAGCCC
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
10 10 0.23
11 24 0.56
12 9 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:123234 original size:17 final size:17
Alignment explanation
Indices: 123202--123271 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
123192 AACTTTTTTT
* *
123202 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
*
123220 TTTAAATTT-AAATTAA
1 TTTAAATTTAAAATAAA
123236 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
123253 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
123270 TT
1 TT
123272 AAAAAGGAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 14 0.31
17 23 0.51
18 8 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:123259 original size:33 final size:34
Alignment explanation
Indices: 123202--123274 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 34
123192 AACTTTTTTT
* * * *
123202 TTTAATTTTGAAATTAAATTTAAATTTAAATTAA
1 TTTAAATTTGAAAATAAATCTAAATTTAAAATAA
123236 TTTAAATTT-AAAATAAATCTAAATTTAAAATAA
1 TTTAAATTTGAAAATAAATCTAAATTTAAAATAA
*
123269 ATTAAA
1 TTTAAA
123275 AAGGAAGCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 26 0.76
34 8 0.24
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (34 bp):
TTTAAATTTGAAAATAAATCTAAATTTAAAATAA
Found at i:123266 original size:7 final size:6
Alignment explanation
Indices: 123202--123264 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
123192 AACTTTTTTT
*
123202 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAAA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
123248 -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
123265 ATAAATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
4 2 0.04
5 11 0.23
6 33 0.69
7 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:123475 original size:17 final size:16
Alignment explanation
Indices: 123452--123497 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
123442 AAAAAATATA
123452 ATAATTATAATTAATAT
1 ATAATTATAATTAA-AT
* *
123469 TTAATTATATTTAAAT
1 ATAATTATAATTAAAT
*
123485 AAAATTATAATTA
1 ATAATTATAATTA
123498 GTATAGTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATTATAATTAAAT
Found at i:124747 original size:31 final size:31
Alignment explanation
Indices: 124674--124745 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 31
124664 AGTTAGATCA
*
124674 AAATT-TTAAAATTTAAAAAATAGAAGGATT
1 AAATTCTTAAAATTTAAAAAATAGAAAGATT
124704 AAATTCTTAAAATTTAAAAAATA-AAAGATT
1 AAATTCTTAAAATTTAAAAAATAGAAAGATT
124734 AAATTCTTAAAA
1 AAATTCTTAAAA
124746 ATAAAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 23 0.57
31 17 0.43
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (31 bp):
AAATTCTTAAAATTTAAAAAATAGAAAGATT
Found at i:143649 original size:42 final size:42
Alignment explanation
Indices: 143585--143668 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
143575 AAACTGTGAT
*
143585 CAGTAGAGAGGCGATACAGGCTCTACTATTCATCATCCTTAC
1 CAGTAGAGAGGCGATACAGGCTCTACTATTAATCATCCTTAC
*
143627 CAGTCGAGAGGCGATACAGGCTCTACTATTAATCATCCTTAC
1 CAGTAGAGAGGCGATACAGGCTCTACTATTAATCATCCTTAC
143669 TCTCAAAGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (42 bp):
CAGTAGAGAGGCGATACAGGCTCTACTATTAATCATCCTTAC
Found at i:148317 original size:31 final size:31
Alignment explanation
Indices: 148282--148348 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
148272 GACTAATATA
* *
148282 TTAGTCATTGTATTTTATGAAATTTATAAAT
1 TTAGTCATTATATTTTACGAAATTTATAAAT
**
148313 TTAGTTGTTATATTTTACGAAATTTATAAAT
1 TTAGTCATTATATTTTACGAAATTTATAAAT
148344 TTAGT
1 TTAGT
148349 TTTTATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.52
Consensus pattern (31 bp):
TTAGTCATTATATTTTACGAAATTTATAAAT
Found at i:148349 original size:31 final size:31
Alignment explanation
Indices: 148292--148356 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
148282 TTAGTCATTG
*
148292 TATTTTATGAAATTTATAAATTTAGTTGTTA
1 TATTTTACGAAATTTATAAATTTAGTTGTTA
*
148323 TATTTTACGAAATTTATAAATTTAGTTTTTA
1 TATTTTACGAAATTTATAAATTTAGTTGTTA
148354 TAT
1 TAT
148357 ATTAATTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (31 bp):
TATTTTACGAAATTTATAAATTTAGTTGTTA
Found at i:157145 original size:6 final size:6
Alignment explanation
Indices: 157134--157168 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
157124 AATGAGTTTT
157134 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
157169 ATTCTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTTCC
Found at i:158106 original size:5 final size:5
Alignment explanation
Indices: 158096--158120 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
158086 AGCTTCAAAA
158096 GTGAT GTGAT GTGAT GTGAT GTGAT
1 GTGAT GTGAT GTGAT GTGAT GTGAT
158121 AAAAGATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
GTGAT
Found at i:158715 original size:23 final size:23
Alignment explanation
Indices: 158682--158803 Score: 92
Period size: 23 Copynumber: 5.3 Consensus size: 23
158672 GCTGGGGAAA
*
158682 CAGTAAACACACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCAAAT
*
158704 CCAGTAAGCACACACTGTGC-AAT
1 -CAGTAAGCACACACAGTGCAAAT
* * * * **
158727 CAGTAGGCGCAAATAGCACAAAT
1 CAGTAAGCACACACAGTGCAAAT
*
158750 CAGTAGGCACACGA-AGTGCGAAA-
1 CAGTAAGCACAC-ACAGTGC-AAAT
158773 CAGTAAGCACACACAGTGCTAAA-
1 CAGTAAGCACACACAGTGC-AAAT
158796 CAGTAAGC
1 CAGTAAGC
158804 GCGCTAGCGT
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
22 13 0.16
23 63 0.79
24 4 0.05
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Done.