Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004204.1 Hibiscus syriacus cultivar Beakdansim tig00009201_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: 73689
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:761 original size:10 final size:10
Alignment explanation
Indices: 742--785 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
732 CAAAGAAAGT
*
742 AAAATGAATA
1 AAAATAAATA
752 AAAATAAATA
1 AAAATAAATA
762 AAAATAAA-A
1 AAAATAAATA
* *
771 GAAATAAGTA
1 AAAATAAATA
781 AAAAT
1 AAAAT
786 GTTTGGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 7 0.24
10 22 0.76
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (10 bp):
AAAATAAATA
Found at i:2788 original size:22 final size:25
Alignment explanation
Indices: 2745--2795 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
2735 AATTTCTATG
*
2745 ATTTTATTATAACATTATAGTAA-T
1 ATTTTATAATAACATTATAGTAATT
2769 ATTTTATAATAA-A-TATAGTAATT
1 ATTTTATAATAACATTATAGTAATT
2792 ATTT
1 ATTT
2796 AAATCTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 6 0.24
24 11 0.44
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
ATTTTATAATAACATTATAGTAATT
Found at i:3548 original size:25 final size:22
Alignment explanation
Indices: 3482--3557 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 22
3472 TATATACATA
*
3482 TATTTTTTATTTATTTATATTC
1 TATTTTTTATTTATTTATATAC
*
3504 -ATTTGGTTATTT-TTTA-ATAC
1 TATTT-TTTATTTATTTATATAC
3524 TATTTTATTATTTATATATATATAC
1 TATTTT-TTATTTAT-T-TATATAC
*
3549 TTTTTTTTA
1 TATTTTTTA
3558 AATATTTCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 3 0.07
21 18 0.42
22 7 0.16
23 1 0.02
24 5 0.12
25 9 0.21
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.67
Consensus pattern (22 bp):
TATTTTTTATTTATTTATATAC
Found at i:3722 original size:21 final size:22
Alignment explanation
Indices: 3690--3731 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3680 TCATTATATG
3690 TATACTTTTATA-TTTGGTTTA
1 TATACTTTTATATTTTGGTTTA
3711 TATA-TTTATATATTTTGGTTT
1 TATACTTT-TATATTTTGGTTT
3732 TTTTTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (22 bp):
TATACTTTTATATTTTGGTTTA
Found at i:3760 original size:18 final size:18
Alignment explanation
Indices: 3734--3768 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3724 TTTGGTTTTT
*
3734 TTTTTATATTATATTATA
1 TTTTCATATTATATTATA
3752 TTTTCATATTATATTAT
1 TTTTCATATTATATTAT
3769 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTCATATTATATTATA
Found at i:3810 original size:2 final size:2
Alignment explanation
Indices: 3805--3831 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3795 TTTTACTCAT
3805 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 T
3832 TTCATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8315 original size:29 final size:30
Alignment explanation
Indices: 8246--8315 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
8236 TCAAGAACAA
8246 AAAAGAAAAGAAGCAAAAAAACAAAAAAAC
1 AAAAGAAAAGAAGCAAAAAAACAAAAAAAC
* *
8276 -AAAGAAAA-AAGAGAAACAAGAAC-AAAAATC
1 AAAAGAAAAGAAG-CAAA-AA-AACAAAAAAAC
8306 AAAAGAAAAG
1 AAAAGAAAAG
8316 GGACAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
28 3 0.09
29 11 0.33
30 8 0.24
31 11 0.33
ACGTcount: A:0.77, C:0.09, G:0.13, T:0.01
Consensus pattern (30 bp):
AAAAGAAAAGAAGCAAAAAAACAAAAAAAC
Found at i:9212 original size:22 final size:22
Alignment explanation
Indices: 9092--9208 Score: 198
Period size: 22 Copynumber: 5.3 Consensus size: 22
9082 ACTACCCCAT
9092 CAAACCTATGAGCATCAAATGC
1 CAAACCTATGAGCATCAAATGC
9114 CAAACCTATGAGCATCAAATGC
1 CAAACCTATGAGCATCAAATGC
9136 CAAACCTATGAGCATCAAATGC
1 CAAACCTATGAGCATCAAATGC
*
9158 CAAACCTATGAGCATTAAATGC
1 CAAACCTATGAGCATCAAATGC
* * *
9180 CAAACCTTTGAGCATTAAATAC
1 CAAACCTATGAGCATCAAATGC
9202 CAAACCT
1 CAAACCT
9209 TTGACCAAAC
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 92 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (22 bp):
CAAACCTATGAGCATCAAATGC
Found at i:10174 original size:106 final size:106
Alignment explanation
Indices: 10029--11715 Score: 2739
Period size: 106 Copynumber: 15.9 Consensus size: 106
10019 CAAGATAACA
* *
10029 CAAGTTCAACTTCACAACGAAGTGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
10094 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
10135 CAAGTTCAACTTCATGACGAAGGGACCGCTGGTTTTCAACAAACAACTTCTCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
*
10200 ATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
10241 CAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTACTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
*
10306 ATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
10347 CAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTTAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* * *
10412 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGGCAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
10453 CAAGTTCAACTTCACGACGAAGGGACCTCTGGTTGTCAATAAACAACTTC-CTAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC-AATTTCAGAGCC
10517 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
65 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
10559 TAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTAAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* *
10624 ATTTCAACTTTACAACGAAGGATATTGGACCCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
10665 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* * *
10730 ATTTCAACTTCACAACGTAGGATATTGGACTCAAGATAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
10771 CAAGTTCAACTTCACGACAAAAGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* *
10836 ATTTCAACTTCACAGCGAAGGATATTGTACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
10877 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
*
10942 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
10983 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* *
11048 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
11089 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* *
11154 ATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAATG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
11195 CAATTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* * *
11260 ATTTTAACTTCACAACGAAAGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
11301 CAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAA-TTTTCCAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT-CAATTTCAGAGCC
* *
11365 AATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAGCG
65 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
11407 CAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
11472 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
11513 CAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* * *
11578 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * * ** *
11619 CAAGTTCAACTTCGCAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* *
11684 ATTTCAACTTCACGACGGAGGATATTGGACTC
66 ATTTCAACTTCACAACGAAGGATATTGGACTC
11716 AGAACAATGC
Statistics
Matches: 1463, Mismatches: 114, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
105 4 0.00
106 1456 1.00
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:12480 original size:37 final size:37
Alignment explanation
Indices: 12427--12531 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
12417 CCTTTTCGTC
12427 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
12464 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
12501 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
12532 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:13044 original size:21 final size:20
Alignment explanation
Indices: 13019--13072 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
13009 CATTTGGTTA
*
13019 TTTTTTAATACTATATTTA-T
1 TTTTTTAATA-TATATATACT
13039 TATTTTTATATATATATATACT
1 T-TTTTTA-ATATATATATACT
13061 TTTTTTAA-ATAT
1 TTTTTTAATATAT
13073 TTCACTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 4 0.13
20 2 0.07
21 19 0.63
22 5 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTTAATATATATATACT
Found at i:13052 original size:19 final size:19
Alignment explanation
Indices: 13016--13053 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
13006 ATTCATTTGG
13016 TTATTTTTTAATACTATAT
1 TTATTTTTTAATACTATAT
*
13035 TTATTATTTTTATA-TATAT
1 TTATT-TTTTAATACTATAT
13054 ATATACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTTTTAATACTATAT
Found at i:13236 original size:21 final size:22
Alignment explanation
Indices: 13204--13245 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
13194 TCATTATATG
13204 TATACTTTTATA-TTTGGTTTA
1 TATACTTTTATATTTTGGTTTA
13225 TATA-TTTATATATTTTGGTTT
1 TATACTTT-TATATTTTGGTTT
13246 TTGGTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (22 bp):
TATACTTTTATATTTTGGTTTA
Found at i:13278 original size:18 final size:19
Alignment explanation
Indices: 13252--13287 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
13242 GTTTTTGGTT
*
13252 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
13270 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
13288 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:13383 original size:16 final size:16
Alignment explanation
Indices: 13364--13404 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
13354 ATTTCATTTA
*
13364 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
13380 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
13395 TATT-TTTATT
1 T-TTATTTATT
13405 CTTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:13385 original size:29 final size:28
Alignment explanation
Indices: 13353--13430 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
13343 ATTTTTTTAA
*
13353 TATTTCATTTATTTATTTATTTTTCCTT-T
1 TATTTCATTTATTTATTT-TTATT-CTTAT
** *
13382 TATTTTTTTTACTTATTTTTATTCTTCAT
1 TATTTCATTTATTTATTTTTATTCTT-AT
*
13411 TTTTTCATTTATTTATTTTT
1 TATTTCATTTATTTATTTTT
13431 TCCCTCTAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
27 3 0.08
28 4 0.10
29 32 0.82
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (28 bp):
TATTTCATTTATTTATTTTTATTCTTAT
Found at i:15644 original size:71 final size:71
Alignment explanation
Indices: 15528--15670 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
15518 TTTAACTATG
15528 GTTGTGCATAACTTGAGGGCTAATGCATTATTGTTGAAGTAGAATTTTTTAGGTTGCAATAGAAT
1 GTTGTGCATAACTTGAGGGCTAATGCATTATTGTTGAAGTAGAATTTTTTAGGTTGCAATAGAAT
15593 TGAAAT
66 TGAAAT
*
15599 GTTGTGCATAACTTGAGGGCTAATGCATTATTGTTGAAGTAGAATTTTTTAGGTTGTAATAGAAT
1 GTTGTGCATAACTTGAGGGCTAATGCATTATTGTTGAAGTAGAATTTTTTAGGTTGCAATAGAAT
15664 TGAAAT
66 TGAAAT
15670 G
1 G
15671 GATTATGAAG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.38
Consensus pattern (71 bp):
GTTGTGCATAACTTGAGGGCTAATGCATTATTGTTGAAGTAGAATTTTTTAGGTTGCAATAGAAT
TGAAAT
Found at i:19362 original size:5 final size:5
Alignment explanation
Indices: 19348--19559 Score: 70
Period size: 5 Copynumber: 40.8 Consensus size: 5
19338 TAAGTTTTTT
* * * *
19348 TTATA CTATA TTATA TATGTA TTATT TTATA -TAGTA -TATA TTATA TAATA
1 TTATA TTATA TTATA T-TATA TTATA TTATA TTA-TA TTATA TTATA TTATA
* *
19398 TGATA TTATA -TAGCA TATATA TTATA --ATA TGTATA -TAGTA TTATACA
1 TTATA TTATA TTA-TA T-TATA TTATA TTATA T-TATA TTA-TA TTAT--A
* *
19445 TTATG TT-TA TGT-TA TTCATA TTCTATA TTATA TAGTATA TGTTTA -TATA
1 TTATA TTATA T-TATA TT-ATA -T-TATA TTATA T--TATA T-TATA TTATA
* *
19494 TTATA TTTTA TT-TA -TAGTA TTAT- TTATTA TTATA TATTTA TTATA
1 TTATA TTATA TTATA TTA-TA TTATA TTA-TA TTATA T-TATA TTATA
19539 TTATA TTATTA TTAATA TTAT
1 TTATA TTA-TA TT-ATA TTAT
19560 TTTTTTCAGT
Statistics
Matches: 160, Mismatches: 18, Indels: 58
0.68 0.08 0.25
Matches are distributed among these distances:
3 4 0.03
4 19 0.12
5 84 0.52
6 35 0.22
7 17 0.11
8 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:19478 original size:7 final size:7
Alignment explanation
Indices: 19354--19550 Score: 101
Period size: 7 Copynumber: 28.1 Consensus size: 7
19344 TTTTTTATAC
19354 TATATTA
1 TATATTA
19361 TATATGTA
1 TATAT-TA
*
19369 TTATTTTA
1 -TATATTA
*
19377 TATAGTA
1 TATATTA
19384 TATATTA
1 TATATTA
*
19391 TATAATA
1 TATATTA
19398 TGATATTA
1 T-ATATTA
*
19406 TATAGCATA
1 TATA--TTA
19415 TATATTA
1 TATATTA
19422 TA-A-TA
1 TATATTA
*
19427 TGTA-TA
1 TATATTA
19433 TAGTATTA
1 TA-TATTA
*
19441 TACATTA
1 TATATTA
*
19448 TGT-TTA
1 TATATTA
*
19454 TGTTATT-
1 T-ATATTA
* *
19461 CATATTC
1 TATATTA
19468 TATATTA
1 TATATTA
*
19475 TATAGTA
1 TATATTA
*
19482 TATGTTTA
1 TAT-ATTA
19490 TATATTA
1 TATATTA
19497 TAT-TT-
1 TATATTA
19502 TAT-TTA
1 TATATTA
19508 TAGTATTA
1 TA-TATTA
*
19516 TTTATTA
1 TATATTA
19523 T-TA-TA
1 TATATTA
19528 TAT-TTA
1 TATATTA
19534 TTATATTA
1 -TATATTA
19542 TATTATTA
1 TA-TATTA
19550 T
1 T
19551 TAATATTATT
Statistics
Matches: 147, Mismatches: 23, Indels: 39
0.70 0.11 0.19
Matches are distributed among these distances:
5 11 0.07
6 22 0.15
7 70 0.48
8 34 0.23
9 10 0.07
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (7 bp):
TATATTA
Found at i:19495 original size:29 final size:29
Alignment explanation
Indices: 19354--19560 Score: 111
Period size: 29 Copynumber: 7.3 Consensus size: 29
19344 TTTTTTATAC
*
19354 TATATTA-TATATGTATTATTTTATATAGTA
1 TATATTATTATA-GTATTA-TTTATATATTA
* * **
19384 TATATTA-TATAATATGATATTATATAGCA
1 TATATTATTATAGTATTAT-TTATATATTA
* *
19413 TATA-TATTATA--A-TATGTATATAGTA
1 TATATTATTATAGTATTATTTATATATTA
* *
19438 T-TATACATTAT-GT-TTATGTTATTCATATTC
1 TATAT-TATTATAGTATTAT-TTA-T-ATATTA
*
19468 TATATTA-TATAGTATATGTTTATATATTA
1 TATATTATTATAGTAT-TATTTATATATTA
*
19497 TATTTTATTTATAGTATTATTTAT-TATTA
1 TATATTA-TTATAGTATTATTTATATATTA
*
19526 TATATTTATTATATTA-TA-TTAT-TATTA
1 TATA-TTATTATAGTATTATTTATATATTA
19553 -ATATTATT
1 TATATTATT
19561 TTTTTCAGTT
Statistics
Matches: 143, Mismatches: 17, Indels: 39
0.72 0.09 0.20
Matches are distributed among these distances:
24 2 0.01
25 14 0.10
26 10 0.07
27 13 0.09
28 7 0.05
29 51 0.36
30 29 0.20
31 15 0.10
32 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (29 bp):
TATATTATTATAGTATTATTTATATATTA
Found at i:19519 original size:16 final size:16
Alignment explanation
Indices: 19354--19559 Score: 95
Period size: 16 Copynumber: 12.5 Consensus size: 16
19344 TTTTTTATAC
19354 TATATTATATATGTA-T
1 TATATTATATAT-TATT
* *
19370 TATTTTATATAGTA--
1 TATATTATATATTATT
*
19384 TATATTATATAATA-T
1 TATATTATATATTATT
* ** *
19399 GATATTATATAGCATA
1 TATATTATATATTATT
*
19415 TATATTATAATATGTATA
1 TATATTAT-ATAT-TATT
*
19433 TAGTATTATACATTATGTT
1 TA-TATTATATATTA--TT
*
19452 TATGTTAT-TCA-TATT
1 TATATTATAT-ATTATT
* *
19467 CTATATTATATAGTATA
1 -TATATTATATATTATT
*
19484 TGT-TTATATATTATAT
1 TATATTATATATTAT-T
*
19500 TTTATTTATAGTATTATT
1 TATA-TTATA-TATTATT
19518 TATTATTATATATT-TAT
1 TA-TATTATATATTAT-T
19535 TATATTATATTATTATT
1 TATATTATA-TATTATT
*
19552 AATATTAT
1 TATATTAT
19560 TTTTTTCAGT
Statistics
Matches: 148, Mismatches: 23, Indels: 37
0.71 0.11 0.18
Matches are distributed among these distances:
14 12 0.08
15 25 0.17
16 37 0.25
17 30 0.20
18 27 0.18
19 17 0.11
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (16 bp):
TATATTATATATTATT
Found at i:19523 original size:3 final size:3
Alignment explanation
Indices: 19511--19560 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
19501 TTATTTATAG
*
19511 TAT TATT TAT TAT TAT ATATT TAT TA- TAT TA- TAT TAT TAT TAA TAT
1 TAT TA-T TAT TAT TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
19557 TAT T
1 TAT T
19561 TTTTTCAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 4 0.10
3 28 0.70
4 7 0.17
5 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:19557 original size:26 final size:26
Alignment explanation
Indices: 19490--19557 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
19480 TATATGTTTA
*
19490 TATATTA-TATT-TTATTTATAGTAT
1 TATATTATTATTAATATTTATAGTAT
19514 TAT-TTATTATTATATATTTATTA-TAT
1 TATATTATTATTA-ATATTTA-TAGTAT
19540 TATATTATTATTAATATT
1 TATATTATTATTAATATT
19558 ATTTTTTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 3 0.08
24 7 0.18
26 17 0.45
27 11 0.29
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (26 bp):
TATATTATTATTAATATTTATAGTAT
Found at i:24077 original size:24 final size:24
Alignment explanation
Indices: 24050--24097 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
24040 TTCAAGGGGA
*
24050 CTCATCTGCTGCAAAAGTGCAAGC
1 CTCATCTGCTGCAAAAGTACAAGC
24074 CTCATCTGCTGCAAAAGTACAAGC
1 CTCATCTGCTGCAAAAGTACAAGC
24098 TTTTGTAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (24 bp):
CTCATCTGCTGCAAAAGTACAAGC
Found at i:27275 original size:2 final size:2
Alignment explanation
Indices: 27268--27304 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
27258 TCTCCTCTCG
27268 TA TA TA 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 TA TA TA T
27305 TTCCCCTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31548 original size:24 final size:26
Alignment explanation
Indices: 31521--31573 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
31511 ATCGGAAAAT
* *
31521 CAAGAA-CCAGAAA-ATCAAGATTGA
1 CAAGAATCAAGAAACATCAAGACTGA
*
31545 CAAGAATCAAGAAACGTCAAGACTGA
1 CAAGAATCAAGAAACATCAAGACTGA
31571 CAA
1 CAA
31574 AAAGAGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 6 0.25
26 12 0.50
ACGTcount: A:0.53, C:0.19, G:0.17, T:0.11
Consensus pattern (26 bp):
CAAGAATCAAGAAACATCAAGACTGA
Found at i:33202 original size:58 final size:59
Alignment explanation
Indices: 33134--33245 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 59
33124 ATTCCTTATT
33134 CATAGCAAGAAATTCTACCTTTTAATAA-AAAATATTTATTTCCTTAGTTAAGAATTAC
1 CATAGCAAGAAATTCTACCTTTTAATAATAAAATATTTATTTCCTTAGTTAAGAATTAC
* *
33192 CATAGCAAGAAATTCTACCTTTTCATAATAAATTATTTATTTCCTTAGTTAAGA
1 CATAGCAAGAAATTCTACCTTTTAATAATAAAATATTTATTTCCTTAGTTAAGA
33246 CTTAACATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
58 27 0.53
59 24 0.47
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (59 bp):
CATAGCAAGAAATTCTACCTTTTAATAATAAAATATTTATTTCCTTAGTTAAGAATTAC
Found at i:34276 original size:18 final size:20
Alignment explanation
Indices: 34243--34279 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
34233 TTTCTTTATA
34243 TTAATATAAGTATTTTCATT
1 TTAATATAAGTATTTTCATT
34263 TTAATAT-A-TATTTTCAT
1 TTAATATAAGTATTTTCAT
34280 ATTATGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (20 bp):
TTAATATAAGTATTTTCATT
Found at i:34656 original size:191 final size:192
Alignment explanation
Indices: 34332--34689 Score: 524
Period size: 191 Copynumber: 1.9 Consensus size: 192
34322 TTGTATAAGG
* * * *
34332 TGACGTTATGCATAATCATCATTCAAAATACTATTACATAACATTTTATTATGTCACTAAAAACA
1 TGACGTTATGCATAATCATCAATCAAAATAATATTACATAACATTATATTACGTCACTAAAAACA
*
34397 TGACAATATCTCTTACGTAACATATATGTTGATTTTATTGTATTATTCGTGACAATATAAATTAT
66 TGACAATATCTCTTACGTAACATATATGTTGATTTTAATGTATTATTCGTGACAATATAAATTAT
34462 TAATAA-AAATATTATATAATTTAGTGACGTAACTAGCTGTCATGCAATATAAGTTATAAAA
131 TAATAACAAATATTATATAATTTAGTGACGTAACTAGCTGTCATGCAATATAAGTTATAAAA
* * ** *
34523 TGACGTTATGCATAAGT-GTCAATCATAATAATATTAGGTAACATTATATTACGTCACTAAAAAT
1 TGACGTTATGCATAA-TCATCAATCAAAATAATATTACATAACATTATATTACGTCACTAAAAAC
* * * * * *
34587 GTGACAATATTTCTTTCGTCACATATA-GATTGATTTTAATGTATTATTCGTGACGATGTAAATT
65 ATGACAATATCTCTTACGTAACATATATG-TTGATTTTAATGTATTATTCGTGACAATATAAATT
*
34651 ATTAATAACAAATTTTATATAATTTAGTGACGTAACTAG
129 ATTAATAACAAATATTATATAATTTAGTGACGTAACTAG
34690 TTATCATTGA
Statistics
Matches: 147, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
190 1 0.01
191 116 0.79
192 30 0.20
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (192 bp):
TGACGTTATGCATAATCATCAATCAAAATAATATTACATAACATTATATTACGTCACTAAAAACA
TGACAATATCTCTTACGTAACATATATGTTGATTTTAATGTATTATTCGTGACAATATAAATTAT
TAATAACAAATATTATATAATTTAGTGACGTAACTAGCTGTCATGCAATATAAGTTATAAAA
Found at i:34845 original size:23 final size:23
Alignment explanation
Indices: 34819--34891 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 23
34809 GGTTTATCAA
34819 TGACGAAAATGTACATTATTTGG
1 TGACGAAAATGTACATTATTTGG
* * *
34842 TGAC-ATAAT-TA-ATTGTCATTGAA
1 TGACGAAAATGTACATTAT--TTG-G
34865 TGTA-GAAAATGTACATTATTTGG
1 TG-ACGAAAATGTACATTATTTGG
34888 TGAC
1 TGAC
34892 ATAATTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
20 4 0.11
21 2 0.06
22 8 0.22
23 8 0.22
24 8 0.22
25 2 0.06
26 4 0.11
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (23 bp):
TGACGAAAATGTACATTATTTGG
Found at i:34876 original size:46 final size:46
Alignment explanation
Indices: 34823--34912 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
34813 TATCAATGAC
34823 GAAAATGTACATTATTTGGTGACATAATTAATTGTCATTGAATGTA
1 GAAAATGTACATTATTTGGTGACATAATTAATTGTCATTGAATGTA
34869 GAAAATGTACATTATTTGGTGACATAATTAATTGTCATTGAATG
1 GAAAATGTACATTATTTGGTGACATAATTAATTGTCATTGAATG
34913 CAAATTATAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.39
Consensus pattern (46 bp):
GAAAATGTACATTATTTGGTGACATAATTAATTGTCATTGAATGTA
Found at i:35112 original size:5 final size:5
Alignment explanation
Indices: 35098--35327 Score: 88
Period size: 5 Copynumber: 47.4 Consensus size: 5
35088 GGGTTTCTTT
* * * *
35098 TTATA CTATA TTATA -TATA TCATT TTATA -TAGA -TATA TTATA -TAGTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA
* *
35145 TGATA TTATA TATCATAA TTATA --ATA TGTATA -TAGTA TTATA TTTTA
1 TTATA TTATA T-T-AT-A TTATA TTATA T-TATA TTA-TA TTATA TTATA
* *
35192 -TAT- TTATG TT-TA TGT-TA TTCATA TTATA -TAT- TATATA ATATA
1 TTATA TTATA TTATA T-TATA TT-ATA TTATA TTATA T-TATA TTATA
* * *
35234 TT-TT TTGATA GTATA -TATA TTATA -TATTA TT-TA TAATA TTAT- TTATTA
1 TTATA TT-ATA TTATA TTATA TTATA TTA-TA TTATA TTATA TTATA TTA-TA
35282 TTATA -TAT- TT-TA TTATA TTATA TTATA TTATTA TTAATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA TT-ATA TTATA TT
35328 TTTTGATTTT
Statistics
Matches: 172, Mismatches: 20, Indels: 66
0.67 0.08 0.26
Matches are distributed among these distances:
3 4 0.02
4 46 0.27
5 89 0.52
6 27 0.16
7 4 0.02
8 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:35157 original size:7 final size:7
Alignment explanation
Indices: 35104--35326 Score: 126
Period size: 7 Copynumber: 31.4 Consensus size: 7
35094 CTTTTTATAC
35104 TATATTA
1 TATATTA
35111 TATA-TA
1 TATATTA
*
35117 TCATTTTA
1 T-ATATTA
*
35125 TATA-GA
1 TATATTA
35131 TATATTA
1 TATATTA
*
35138 TATAGTA
1 TATATTA
35145 TGATATTA
1 T-ATATTA
*
35153 TATATCA
1 TATATTA
35160 TA-ATTA
1 TATATTA
35166 TAATATGTA
1 T-ATAT-TA
*
35175 TATAGTA
1 TATATTA
*
35182 TTATATTT
1 -TATATTA
35190 TATATT-
1 TATATTA
*
35196 TATGTT-
1 TATATTA
*
35202 TATGTTA
1 TATATTA
35209 TTCATATTA
1 -T-ATATTA
35218 TATATTA
1 TATATTA
*
35225 TATAATA
1 TATATTA
* *
35232 TATTTTT
1 TATATTA
35239 TGATAGTATA
1 T-ATA-T-TA
35249 TATATTA
1 TATATTA
35256 TATATTA
1 TATATTA
* *
35263 TTTATAA
1 TATATTA
35270 TATTATT-
1 TA-TATTA
35277 TATTATTA
1 TA-TATTA
35285 TATATT-
1 TATATTA
35291 T-TATTA
1 TATATTA
35297 TAT-TATA
1 TATAT-TA
35304 TTATATTA
1 -TATATTA
35312 T-TATTA
1 TATATTA
35318 -ATATTA
1 TATATTA
35324 TAT
1 TAT
35327 TTTTTGATTT
Statistics
Matches: 170, Mismatches: 23, Indels: 46
0.71 0.10 0.19
Matches are distributed among these distances:
5 4 0.02
6 36 0.21
7 81 0.48
8 34 0.20
9 13 0.08
10 2 0.01
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (7 bp):
TATATTA
Found at i:35199 original size:27 final size:28
Alignment explanation
Indices: 35169--35304 Score: 70
Period size: 27 Copynumber: 4.9 Consensus size: 28
35159 ATAATTATAA
*
35169 TATGTATATAG-TATT-ATATTTTATATT
1 TATGTATAT-GTTATTCATATTATATATT
*
35196 TATGTTTATGTTATTCATATTATATATT
1 TATGTATATGTTATTCATATTATATATT
* * * *
35224 ATATAATATAT-TTTTTGATAGTATATATAT
1 -TAT-GTATATGTTATTCATATTATATAT-T
* * *
35254 TATATATTAT-TTA-TAATATTATTTA-T
1 TATGTA-TATGTTATTCATATTATATATT
* *
35280 TATTATATATTTTATT-ATATTATAT
1 TA-TGTATATGTTATTCATATTATAT
35305 TATATTATTA
Statistics
Matches: 88, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
26 7 0.08
27 27 0.31
28 24 0.27
29 25 0.28
30 5 0.06
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (28 bp):
TATGTATATGTTATTCATATTATATATT
Found at i:35263 original size:38 final size:35
Alignment explanation
Indices: 35136--35327 Score: 119
Period size: 38 Copynumber: 5.2 Consensus size: 35
35126 ATAGATATAT
* *
35136 TATATAGTATGATATTATAT-ATCATAATTATAATATGTA
1 TATATATTAT-ATATTATATAAT-AT-ATT-TATTAT-TA
* * * *
35175 TATAGTATTATATTTTATAT-TTATGTTTA-TGTTA
1 TATA-TATTATATATTATATAATATATTTATTATTA
*
35209 T-TCATATTATATATTATATAATATATTTTTTGATAGTA
1 TAT-ATATTATATATTATATAATATATTTATT-AT--TA
35247 TATATATTATATATTATTTATAATATTATTTATTATTA
1 TATATATTATATATTA--TATAATA-TATTTATTATTA
*
35285 TATATTTTATTATATTATAT--TATA-TTATTATTAA
1 TATATATTA-TATATTATATAATATATTTATTATT-A
35319 TATTATATT
1 TA-TATATT
35328 TTTTGATTTT
Statistics
Matches: 126, Mismatches: 13, Indels: 32
0.74 0.08 0.19
Matches are distributed among these distances:
33 23 0.18
34 15 0.12
35 10 0.08
36 3 0.02
37 5 0.04
38 28 0.22
39 21 0.17
40 14 0.11
41 7 0.06
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (35 bp):
TATATATTATATATTATATAATATATTTATTATTA
Found at i:35276 original size:3 final size:3
Alignment explanation
Indices: 35251--35324 Score: 59
Period size: 3 Copynumber: 25.0 Consensus size: 3
35241 ATAGTATATA
*
35251 TAT TAT ATAT TAT T-T ATAA TAT TATT TAT TAT TAT ATAT T-T TAT TA-
1 TAT TAT -TAT TAT TAT -TAT TAT TA-T TAT TAT TAT -TAT TAT TAT TAT
*
35297 TAT TA- TAT TA- TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35325 ATTTTTTGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
2 9 0.16
3 40 0.69
4 9 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:35321 original size:22 final size:21
Alignment explanation
Indices: 35104--35327 Score: 96
Period size: 19 Copynumber: 11.3 Consensus size: 21
35094 CTTTTTATAC
*
35104 TATATTATA-TATATCATT-T
1 TATATTATATTATATTATTAT
*
35123 TATA-TAGA-TATATTA-TA-
1 TATATTATATTATATTATTAT
* *
35140 TAGTATGATATTATATATCATAAT
1 TA-TATTATATTATAT-T-ATTAT
* * *
35164 TATAATATGTATATAGTATTA-
1 TATATTATAT-TATATTATTAT
*
35185 TATTTTATATT-TATGT-TTAT
1 TATATTATATTATAT-TATTAT
35205 GT-TATTCATATTATA-TATTA-
1 -TATATT-ATATTATATTATTAT
* * *
35225 TATAATATATT-TTTTGA-TAG
1 TATATTATATTATATT-ATTAT
35245 TATA-TATATTATA-TATTAT
1 TATATTATATTATATTATTAT
*
35264 T-TATAATATTAT-TTATTAT
1 TATATTATATTATATTATTAT
35283 TATA-TAT-TT-TATTA-TAT
1 TATATTATATTATATTATTAT
*
35300 TATATTATATTATTATTAATAT
1 TATATTATATTA-TATTATTAT
35322 TATATT
1 TATATT
35328 TTTTGATTTT
Statistics
Matches: 154, Mismatches: 21, Indels: 57
0.66 0.09 0.25
Matches are distributed among these distances:
17 11 0.07
18 23 0.15
19 48 0.31
20 22 0.14
21 22 0.14
22 15 0.10
23 7 0.05
24 6 0.04
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (21 bp):
TATATTATATTATATTATTAT
Found at i:36954 original size:18 final size:18
Alignment explanation
Indices: 36931--36998 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 18
36921 GATGCAATTA
36931 GTATCGATACTGTTGTGG
1 GTATCGATACTGTTGTGG
* **
36949 GTATCGATACTAATTGCATCA
1 GTATCGATACT-GTTG--TGG
*
36970 GTATTGATACTGTTGTGG
1 GTATCGATACTGTTGTGG
36988 GTATCGATACT
1 GTATCGATACT
36999 AAGAGGAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 22 0.56
19 3 0.08
20 3 0.08
21 11 0.28
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (18 bp):
GTATCGATACTGTTGTGG
Found at i:36959 original size:39 final size:38
Alignment explanation
Indices: 36911--37036 Score: 141
Period size: 39 Copynumber: 3.3 Consensus size: 38
36901 GGATGAACAA
*
36911 TATCAATACTGATGCAATTAGTATCGATACTGTTGTGGG
1 TATCGATACTGATGCAATTAGTAT-GATACTGTTGTGGG
* *
36950 TATCGATACTAATTGC-ATCAGTATTGATACTGTTGTGGG
1 TATCGATACTGA-TGCAATTAGTA-TGATACTGTTGTGGG
* *
36989 TATCGATACTAAGAGGAAATTA-T-TGATACTGTTGTGGG
1 TATCGATACT--GATGCAATTAGTATGATACTGTTGTGGG
37027 TATCGATACT
1 TATCGATACT
37037 AAGAGGAAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
38 25 0.33
39 40 0.53
40 6 0.08
41 4 0.05
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.37
Consensus pattern (38 bp):
TATCGATACTGATGCAATTAGTATGATACTGTTGTGGG
Found at i:37022 original size:38 final size:38
Alignment explanation
Indices: 36930--37056 Score: 182
Period size: 38 Copynumber: 3.3 Consensus size: 38
36920 TGATGCAATT
* ** * *
36930 AGTATCGATACTGTTGTGGGTATCGATACTAATTGCATC
1 AGTATTGATACTGTTGTGGGTATCGATACTAAGAGGA-A
36969 AGTATTGATACTGTTGTGGGTATCGATACTAAGAGGAA
1 AGTATTGATACTGTTGTGGGTATCGATACTAAGAGGAA
*
37007 ATTATTGATACTGTTGTGGGTATCGATACTAAGAGGAA
1 AGTATTGATACTGTTGTGGGTATCGATACTAAGAGGAA
*
37045 AGTATCGATACT
1 AGTATTGATACT
37057 ATGGATTCCA
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 47 0.59
39 33 0.41
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (38 bp):
AGTATTGATACTGTTGTGGGTATCGATACTAAGAGGAA
Found at i:37051 original size:20 final size:20
Alignment explanation
Indices: 36988--37057 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
36978 ACTGTTGTGG
36988 GTATCGATACTAAGAGGAAA
1 GTATCGATACTAAGAGGAAA
* * ** *
37008 TTATTGATACTGTTGTGG---
1 GTATCGATACT-AAGAGGAAA
37026 GTATCGATACTAAGAGGAAA
1 GTATCGATACTAAGAGGAAA
37046 GTATCGATACTA
1 GTATCGATACTA
37058 TGGATTCCAG
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
17 3 0.08
18 9 0.25
20 21 0.58
21 3 0.08
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (20 bp):
GTATCGATACTAAGAGGAAA
Found at i:48743 original size:18 final size:18
Alignment explanation
Indices: 48701--48745 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
48691 CTGGAAGAAA
*
48701 GCCTCACCAGCCGTTATT
1 GCCTCATCAGCCGTTATT
*
48719 GCCTCATCAGCTGTTATT
1 GCCTCATCAGCCGTTATT
48737 GCCTCATCA
1 GCCTCATCA
48746 AGCAAGTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.36, G:0.16, T:0.31
Consensus pattern (18 bp):
GCCTCATCAGCCGTTATT
Found at i:49808 original size:65 final size:65
Alignment explanation
Indices: 49683--49810 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 65
49673 TAATAAAAAT
* * *
49683 GCCACTATATATGAACCTATTGCAACGTTTGTATTCAAAAACGCCACTAATATACTAAATTTGCA
1 GCCACTATATATGAACCTATTGCAACGCTTGTATTCAAAAACACCACTAACATACTAAATTTGCA
* *
49748 GCCACTATATATTAACCTATTGCAGA-GCTTGTA-T-AGAAAACACCACTAACGTACTAAAATTT
1 GCCACTATATATGAACCTATTGCA-ACGCTTGTATTCA-AAAACACCACTAACATACT-AAATTT
49810 G
63 G
49811 TGGCATTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.02
64 17 0.31
65 36 0.65
66 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.30
Consensus pattern (65 bp):
GCCACTATATATGAACCTATTGCAACGCTTGTATTCAAAAACACCACTAACATACTAAATTTGCA
Found at i:49918 original size:81 final size:81
Alignment explanation
Indices: 49750--49958 Score: 251
Period size: 81 Copynumber: 2.6 Consensus size: 81
49740 AATTTGCAGC
* * * **
49750 CACTATATATTAACCTATTGCAGAGCTTGTATAG-AAAACACCACTAACGTACTAAAATTTGTGG
1 CACTATATATTAACCTATTGCAGAGTTTGTATTGAAAAACGCCACTAACGTACTAAAATTTACGG
* *
49814 CATTTAATAAAAACAT
66 CATTTAATAAAAAAAG
* * *
49830 CACTATATATTAACCTATTGCAGCGTTTGTATTGAAAAACGCCACTAAGGTACTAATATTTACGG
1 CACTATATATTAACCTATTGCAGAGTTTGTATTGAAAAACGCCACTAACGTACTAAAATTTACGG
**
49895 TGTTTAATAAAAAAAG
66 CATTTAATAAAAAAAG
* * * *
49911 CATTATATTTTAACCTATTGC-GATGTGTGTTTTGAAAAACGCCACTAA
1 CACTATATATTAACCTATTGCAGA-GTTTGTATTGAAAAACGCCACTAA
49959 AGTGATAGTC
Statistics
Matches: 110, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
80 32 0.29
81 78 0.71
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (81 bp):
CACTATATATTAACCTATTGCAGAGTTTGTATTGAAAAACGCCACTAACGTACTAAAATTTACGG
CATTTAATAAAAAAAG
Found at i:54363 original size:21 final size:22
Alignment explanation
Indices: 54325--54366 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
54315 CAACGTTTTA
54325 CTCTTCAAAATAAAAATAAATC
1 CTCTTCAAAATAAAAATAAATC
54347 CTCTTCAAAAT-AAAATAAAT
1 CTCTTCAAAATAAAAATAAAT
54367 AAAATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.29
Consensus pattern (22 bp):
CTCTTCAAAATAAAAATAAATC
Found at i:56254 original size:17 final size:18
Alignment explanation
Indices: 56227--56260 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
56217 ACTAACCATT
56227 TTTTCTTTTCTTTTTTTC
1 TTTTCTTTTCTTTTTTTC
56245 TTTT-TTTTCTTTTTTT
1 TTTTCTTTTCTTTTTTT
56261 TCGTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTTTC
Found at i:56267 original size:10 final size:9
Alignment explanation
Indices: 56227--56269 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
56217 ACTAACCATT
56227 TTTTCTTTTC
1 TTTT-TTTTC
56237 -TTTTTTTC
1 TTTTTTTTC
56245 TTTTTTTTC
1 TTTTTTTTC
56254 TTTTTTTTC
1 TTTTTTTTC
56263 GTTTTTT
1 -TTTTTT
56270 CGCATGCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 5 0.16
9 20 0.65
10 6 0.19
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:56267 original size:17 final size:17
Alignment explanation
Indices: 56232--56270 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
56222 CCATTTTTTC
*
56232 TTTTCTTTTTTTCTTTT
1 TTTTCTTTTTTTCTGTT
56249 TTTTCTTTTTTT-TCGTT
1 TTTTCTTTTTTTCT-GTT
56266 TTTTC
1 TTTTC
56271 GCATGCTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTCTTTTTTTCTGTT
Found at i:56732 original size:16 final size:14
Alignment explanation
Indices: 56694--56728 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
56684 ATTTCTTCGC
*
56694 ATTTTTTATTATAA
1 ATTTTTAATTATAA
56708 ATTTTTAATTATAA
1 ATTTTTAATTATAA
*
56722 ATATTTA
1 ATTTTTA
56729 TAATATTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTTAATTATAA
Found at i:59034 original size:18 final size:19
Alignment explanation
Indices: 59001--59040 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
58991 ATTATTAAAG
59001 TTATAAAATAATTATTTGA
1 TTATAAAATAATTATTTGA
* *
59020 TTATAAAA-CATTATTTTA
1 TTATAAAATAATTATTTGA
59038 TTA
1 TTA
59041 AGTCTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TTATAAAATAATTATTTGA
Found at i:61796 original size:76 final size:77
Alignment explanation
Indices: 61652--61800 Score: 219
Period size: 76 Copynumber: 1.9 Consensus size: 77
61642 TAAAAAACTA
* ** * *
61652 TTAAAATATTTAAAATTTTGAAGTTAAAAATAATATGAAACTTTTACAAATTTTTATTAAATTTG
1 TTAAAATATTTAAAATTTTGAAGTTAAAAATAATATGAAACTTGTACAAATTTTTAACAAAATAG
61717 AAAAAAAATATT
66 AAAAAAAATATT
* * *
61729 TTAAAAT-TTTAAAATTTTGAAGTTAAAAATTATATGAAACTTGTAGAATTTTTTAACAAAATAG
1 TTAAAATATTTAAAATTTTGAAGTTAAAAATAATATGAAACTTGTACAAATTTTTAACAAAATAG
61793 AAAAAAAA
66 AAAAAAAA
61801 AACTTACATG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
76 57 0.89
77 7 0.11
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.39
Consensus pattern (77 bp):
TTAAAATATTTAAAATTTTGAAGTTAAAAATAATATGAAACTTGTACAAATTTTTAACAAAATAG
AAAAAAAATATT
Found at i:66737 original size:13 final size:13
Alignment explanation
Indices: 66721--66753 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
66711 AATACCTTTT
66721 AAAATAATTTTAA
1 AAAATAATTTTAA
66734 AAAATAATTTTAA
1 AAAATAATTTTAA
*
66747 AAGATAA
1 AAAATAA
66754 AAAATGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:68726 original size:25 final size:23
Alignment explanation
Indices: 68680--68727 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
68670 CTTGAAGTTG
* *
68680 GACTTGTTACCCAAATTGGACTT
1 GACTTGTTACCCAAACTAGACTT
68703 GACTTGTTAACCCCAAACTAGACTT
1 GACTTGTT-A-CCCAAACTAGACTT
68728 AGACCACCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 12 0.57
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (23 bp):
GACTTGTTACCCAAACTAGACTT
Found at i:68890 original size:24 final size:21
Alignment explanation
Indices: 68850--68895 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
68840 ATTAATACTA
*
68850 TATATATTTTTTTAAACTATAT
1 TATATATTTTTTAAAAC-ATAT
68872 TATATATTTTTTCCAAAACATAT
1 TATATATTTTTT--AAAACATAT
68895 T
1 T
68896 TTCTAAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
23 5 0.24
24 4 0.19
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (21 bp):
TATATATTTTTTAAAACATAT
Found at i:68969 original size:20 final size:20
Alignment explanation
Indices: 68899--68998 Score: 82
Period size: 20 Copynumber: 4.9 Consensus size: 20
68889 ACATATTTTC
68899 TAAAACTATAT-TATATATA
1 TAAAACTATATATATATATA
*
68918 TATATA-TATATATATATATA
1 TA-AAACTATATATATATATA
*
68938 TATATA-TATATATATATATA
1 TA-AAACTATATATATATATA
*
68958 TTCAAAACTATATATATAT-TT
1 -T-AAAACTATATATATATATA
*
68979 TCAAACCTATACTATATATA
1 T-AAAACTATA-TATATATA
68999 ACCAAATAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 7 0.10
20 40 0.57
21 11 0.16
22 12 0.17
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAACTATATATATATATA
Found at i:68976 original size:2 final size:2
Alignment explanation
Indices: 68905--68958 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
68895 TTTCTAAAAC
68905 TA TA T- 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
68946 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
68959 TCAAAACTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71212 original size:3 final size:3
Alignment explanation
Indices: 71206--71238 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
71196 TATAATAATA
71206 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
71239 TGTTCTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:71761 original size:18 final size:18
Alignment explanation
Indices: 71706--71763 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
71696 TTGTAGGTAA
71706 AAAGAAGAATTAGGAAAT
1 AAAGAAGAATTAGGAAAT
* *
71724 AAA-ATACGGAA-AAAGAAAT
1 AAAGA-A--GAATTAGGAAAT
71743 AAAGAAGAATTAGGAAAT
1 AAAGAAGAATTAGGAAAT
71761 AAA
1 AAA
71764 ATACGGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
17 4 0.13
18 13 0.42
19 10 0.32
20 4 0.13
ACGTcount: A:0.66, C:0.02, G:0.19, T:0.14
Consensus pattern (18 bp):
AAAGAAGAATTAGGAAAT
Done.