Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003039.1 Hibiscus syriacus cultivar Beakdansim tig00006321_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: 177064
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:643 original size:21 final size:21
Alignment explanation
Indices: 619--692 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
609 CCTATCGTTT
619 AAGAGGCCCCTATCATCCTTC
1 AAGAGGCCCCTATCATCCTTC
** *
640 AAGAGGCCCCTCCCA-CCATTT
1 AAGAGGCCCCTATCATCC-TTC
* * *
661 AAGAGGCTCCTGTCATCGTTC
1 AAGAGGCCCCTATCATCCTTC
*
682 AAGAGGTCCCT
1 AAGAGGCCCCT
693 CCCACCGTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 2 0.05
21 38 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
AAGAGGCCCCTATCATCCTTC
Found at i:645 original size:42 final size:42
Alignment explanation
Indices: 585--698 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
575 GCCTGATTCA
* * * *
585 CCTATCATCGTT-AGAGAGGCCTCTCCTATCGTTTAAGAGGCC
1 CCTATCATCGTTCA-AGAGGCCCCTCCCACCATTTAAGAGGCC
* *
627 CCTATCATCCTTCAAGAGGCCCCTCCCACCATTTAAGAGGCT
1 CCTATCATCGTTCAAGAGGCCCCTCCCACCATTTAAGAGGCC
* *
669 CCTGTCATCGTTCAAGAGGTCCCTCCCACC
1 CCTATCATCGTTCAAGAGGCCCCTCCCACC
699 GTTTGAGATC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 61 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (42 bp):
CCTATCATCGTTCAAGAGGCCCCTCCCACCATTTAAGAGGCC
Found at i:701 original size:21 final size:20
Alignment explanation
Indices: 637--701 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
627 CCTATCATCC
*
637 TTCAAGAGGCCCCTCCCACCA
1 TTCAAGAGG-CCCTCCCACCG
* ** *
658 TTTAAGAGGCTCCTGTCATCG
1 TTCAAGAGGC-CCTCCCACCG
679 TTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGG-CCCTCCCACCG
700 TT
1 TT
702 TGAGATCCCG
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (20 bp):
TTCAAGAGGCCCTCCCACCG
Found at i:2102 original size:64 final size:64
Alignment explanation
Indices: 2025--2173 Score: 237
Period size: 64 Copynumber: 2.3 Consensus size: 64
2015 AAATTGATGT
*
2025 ATTTGTACAAGTTGATTTGTTTAATTGATGAGGAAATAAGA-ATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAA-ATATTATTTTTTGCTTGTTTAATTG
* * *
2089 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAATCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAATATTATTTTTTGCTTGTTTAATTG
*
2153 ATTTTTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
2174 GTTTTAAATT
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
63 1 0.01
64 78 0.99
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAATATTATTTTTTGCTTGTTTAATTG
Found at i:2532 original size:18 final size:18
Alignment explanation
Indices: 2509--2544 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2499 AAGCCGGTTG
2509 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
**
2527 TGATTGTTATTTTGATTT
1 TGATTGGGATTTTGATTT
2545 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.22, T:0.61
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:4809 original size:24 final size:24
Alignment explanation
Indices: 4782--4852 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
4772 CAAAATCCGA
4782 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
4806 GTATTGACCAAGATCAAAGTCCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
4830 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
4853 AATACTGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:4997 original size:12 final size:12
Alignment explanation
Indices: 4976--5009 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4966 TGTTGTGGGT
*
4976 TTTGAGATTGTG
1 TTTGATATTGTG
4988 TTTGATATTGTG
1 TTTGATATTGTG
*
5000 TTTGGTATTG
1 TTTGATATTG
5010 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:5818 original size:20 final size:19
Alignment explanation
Indices: 5774--5900 Score: 80
Period size: 20 Copynumber: 6.4 Consensus size: 19
5764 CAAAACATTT
*
5774 GTGTTGCGAAACTAAAA-C
1 GTGTTGCGAAATTAAAATC
*
5792 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
5812 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* **
5832 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAA-TC
*
5852 GCGTTGCG-AATTCAGAAATC
1 GTGTTGCGAAATT-A-AAATC
* * *
5872 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAAATC
5892 AGTGTTGCG
1 -GTGTTGCG
5901 GATTGGAAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
18 15 0.18
19 10 0.12
20 40 0.47
21 20 0.24
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:5925 original size:40 final size:40
Alignment explanation
Indices: 5794--5921 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 40
5784 ACTAAAACCT
*
5794 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGGAAATCGA
** * *
5834 GTTGCGAAAACAAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGGAAATCGA
* * * *
5874 GTTGCGAATTTGAAATTCAGTGTTGCGGATT-GGAAATCGC
1 GTTGCGAAATTAAAATTC-GTGTTGCGAATTCGGAAATCGA
5914 GTTGCGAA
1 GTTGCGAA
5922 TTTGGAAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 64 0.86
41 10 0.14
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCGGAAATCGA
Found at i:5928 original size:20 final size:20
Alignment explanation
Indices: 5850--5950 Score: 89
Period size: 21 Copynumber: 5.0 Consensus size: 20
5840 AAAACAAAAT
**
5850 TCGCGTTGCGAATTCAGAAA
1 TCGCGTTGCGAATTTGGAAA
*
5870 TCGAGTTGCGAATTT-GAAA
1 TCGCGTTGCGAATTTGGAAA
* *
5889 TTCAGTGTTGCGGA-TTGGAAA
1 -TC-GCGTTGCGAATTTGGAAA
5910 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGG-AAA
** *
5931 TCGCAATGCGTATTTGGAAA
1 TCGCGTTGCGAATTTGGAAA
5951 CTGAGTTGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
19 12 0.18
20 26 0.39
21 29 0.43
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGGAAA
Found at i:13699 original size:13 final size:13
Alignment explanation
Indices: 13681--13715 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
13671 ATGATATGTG
13681 GTTTATACAGATT
1 GTTTATACAGATT
13694 GTTTATACAGATT
1 GTTTATACAGATT
*
13707 GTTCATACA
1 GTTTATACA
13716 TTATGCCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (13 bp):
GTTTATACAGATT
Found at i:14467 original size:12 final size:12
Alignment explanation
Indices: 14452--14514 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
14442 ATGATTTATG
14452 AGGGACTTGTAA
1 AGGGACTTGTAA
* * *
14464 AGGGAGTCGTATG
1 AGGGACTTGTA-A
14477 AGGGACTTGTAA
1 AGGGACTTGTAA
* *
14489 AGGGAGTCGTATA
1 AGGGACTTGTA-A
14502 AGGGACTTG-AA
1 AGGGACTTGTAA
14513 AG
1 AG
14515 CTTAAATAGC
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
11 3 0.08
12 19 0.49
13 17 0.44
ACGTcount: A:0.32, C:0.08, G:0.38, T:0.22
Consensus pattern (12 bp):
AGGGACTTGTAA
Found at i:14482 original size:25 final size:25
Alignment explanation
Indices: 14448--14514 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
14438 TTTTATGATT
14448 TATGAGGGACTTGTAAAGGGAGTCG
1 TATGAGGGACTTGTAAAGGGAGTCG
14473 TATGAGGGACTTGTAAAGGGAGTCG
1 TATGAGGGACTTGTAAAGGGAGTCG
*
14498 TATAAGGGACTTG-AAAG
1 TATGAGGGACTTGTAAAG
14515 CTTAAATAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 4 0.10
25 37 0.90
ACGTcount: A:0.31, C:0.07, G:0.37, T:0.24
Consensus pattern (25 bp):
TATGAGGGACTTGTAAAGGGAGTCG
Found at i:14506 original size:13 final size:13
Alignment explanation
Indices: 14463--14506 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
14453 GGGACTTGTA
14463 AAGGGAGTCGTAT
1 AAGGGAGTCGTAT
* * *
14476 GAGGGACTTGTA-
1 AAGGGAGTCGTAT
14488 AAGGGAGTCGTAT
1 AAGGGAGTCGTAT
14501 AAGGGA
1 AAGGGA
14507 CTTGAAAGCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.32, C:0.07, G:0.41, T:0.20
Consensus pattern (13 bp):
AAGGGAGTCGTAT
Found at i:17081 original size:20 final size:21
Alignment explanation
Indices: 17056--17122 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 21
17046 ATGGGTACCA
17056 ATACCCATCA-TGTAGTATCG
1 ATACCCATCAGTGTAGTATCG
*
17076 ATACCCTAGGCAAGTGTAGTATCG
1 ATACCC-A-TC-AGTGTAGTATCG
* *
17100 ATA-CCATCAGGGTAGTACCG
1 ATACCCATCAGTGTAGTATCG
17120 ATA
1 ATA
17123 TCCCTATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 19 0.49
21 2 0.05
22 2 0.05
23 3 0.08
24 13 0.33
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (21 bp):
ATACCCATCAGTGTAGTATCG
Found at i:17632 original size:33 final size:33
Alignment explanation
Indices: 17586--17649 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
17576 AAGAGGTTTT
*
17586 GGTTCTAGCTTAGCCTGCT-AAAAACTAGGGAAA
1 GGTTCTAGCTTAGCCCG-TAAAAAACTAGGGAAA
*
17619 GGTTCTAGTTTAGCCCGTAAAAAACTAGGGA
1 GGTTCTAGCTTAGCCCGTAAAAAACTAGGGA
17650 GTTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (33 bp):
GGTTCTAGCTTAGCCCGTAAAAAACTAGGGAAA
Found at i:27497 original size:3 final size:3
Alignment explanation
Indices: 27489--27515 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27479 CAAGTATTCA
27489 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
27516 TTTCCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29652 original size:3 final size:3
Alignment explanation
Indices: 29644--29678 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29634 TGCTTTATTG
29644 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
29679 AACCCAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:38495 original size:5 final size:5
Alignment explanation
Indices: 38487--38564 Score: 142
Period size: 5 Copynumber: 16.0 Consensus size: 5
38477 CAAAAATGCT
38487 ATATA ATATA ATATA ATAT- A-ATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
38535 ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
38565 TTGAAAATTT
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 67 0.94
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:39720 original size:81 final size:81
Alignment explanation
Indices: 39585--39754 Score: 295
Period size: 81 Copynumber: 2.1 Consensus size: 81
39575 CTTAGGGTGG
* *
39585 GTTTGGTTAACGGAATGTAAGATTATCAGTGGGAGTAAAAAATTATCAGTGAATAGGATTACTGA
1 GTTTGGTTAACAGAATGTAAGATTATCAGTGGGAGTAAAAAATTATCAGGGAATAGGATTACTGA
39650 GAATATTATATTTTAT
66 GAATATTATATTTTAT
* *
39666 GTTTGGTTCACAGAATGTAAGATTATCAGTGGGAGTAAAAGATTATCAGGGAATAGGATTACTGA
1 GTTTGGTTAACAGAATGTAAGATTATCAGTGGGAGTAAAAAATTATCAGGGAATAGGATTACTGA
*
39731 GAATATTATATTTTGT
66 GAATATTATATTTTAT
39747 GTTTGGTT
1 GTTTGGTT
39755 GGTTTAGCAG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (81 bp):
GTTTGGTTAACAGAATGTAAGATTATCAGTGGGAGTAAAAAATTATCAGGGAATAGGATTACTGA
GAATATTATATTTTAT
Found at i:41861 original size:18 final size:18
Alignment explanation
Indices: 41838--41885 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
41828 ATGAAGATTC
41838 TGAAAATAAAACCGAAAA
1 TGAAAATAAAACCGAAAA
* **
41856 TGAAAA-AGAAAACGAAGC
1 TGAAAATA-AAACCGAAAA
41874 TGAAAATAAAAC
1 TGAAAATAAAAC
41886 TAACCAACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.65, C:0.10, G:0.15, T:0.10
Consensus pattern (18 bp):
TGAAAATAAAACCGAAAA
Found at i:43514 original size:21 final size:21
Alignment explanation
Indices: 43472--43514 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43462 GTAGAAGTTA
* * *
43472 TTTTATATTGCTTTTTATAAC
1 TTTTATATTGCATATTAAAAC
*
43493 TTTTCTATTGCATATTAAAAC
1 TTTTATATTGCATATTAAAAC
43514 T
1 T
43515 GTTAAATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTATATTGCATATTAAAAC
Found at i:44777 original size:4 final size:4
Alignment explanation
Indices: 44770--44795 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
44760 TTTTGGATGA
44770 GAGG GAGG GAGG GAGG GAGG GAGG GA
1 GAGG GAGG GAGG GAGG GAGG GAGG GA
44796 AATTTAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:50150 original size:19 final size:19
Alignment explanation
Indices: 50126--50162 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
50116 CTTTAAGTTT
50126 AATATTTTATTTTTATATG
1 AATATTTTATTTTTATATG
*
50145 AATATTTTCTTTTTATAT
1 AATATTTTATTTTTATAT
50163 TTTGATGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
AATATTTTATTTTTATATG
Found at i:50574 original size:22 final size:22
Alignment explanation
Indices: 50538--50582 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
50528 AATTTCTGAG
50538 TAAAAAAATTAAGAGAAGAAAAA
1 TAAAAAAATTAAGAGAA-AAAAA
*
50561 TAAAAAAA-TGAGAGAAAAAAA
1 TAAAAAAATTAAGAGAAAAAAA
50582 T
1 T
50583 GAGAGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 7 0.33
23 8 0.38
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (22 bp):
TAAAAAAATTAAGAGAAAAAAA
Found at i:50580 original size:13 final size:14
Alignment explanation
Indices: 50562--50596 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
50552 GAAGAAAAAT
50562 AAAAAAATGAGA-G
1 AAAAAAATGAGAGG
50575 AAAAAAATGAGAGG
1 AAAAAAATGAGAGG
50589 AAAAAAAT
1 AAAAAAAT
50597 TTAACCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (14 bp):
AAAAAAATGAGAGG
Found at i:54187 original size:25 final size:28
Alignment explanation
Indices: 54132--54187 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 28
54122 TTCCAAGTAA
* *
54132 ATCTTAGTGTTATTTGCTTTTATTTTTCG
1 ATCTTAGTGTTATTTGC-TTTATGTTCCG
54161 ATCTT-GT-TTATTTG-TTTATGTTCCG
1 ATCTTAGTGTTATTTGCTTTATGTTCCG
54186 AT
1 AT
54188 ATTATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 11 0.44
27 7 0.28
28 2 0.08
29 5 0.20
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.61
Consensus pattern (28 bp):
ATCTTAGTGTTATTTGCTTTATGTTCCG
Found at i:56268 original size:24 final size:23
Alignment explanation
Indices: 56215--56275 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
56205 CTTCCAAAAT
56215 AAATAATATA-ATATACTTAATA
1 AAATAATATATATATACTTAATA
* **
56237 AATTTAATATATATATACTATCCTA
1 AA-ATAATATATATATACT-TAATA
56262 AAATAATATATATA
1 AAATAATATATATA
56276 CATATAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.06
23 7 0.22
24 18 0.56
25 5 0.16
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATAATATATATATACTTAATA
Found at i:57026 original size:2 final size:2
Alignment explanation
Indices: 57019--57076 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
57009 AGTTAGCATA
57019 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57061 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
57077 CGAAAACCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68123 original size:45 final size:46
Alignment explanation
Indices: 68059--68163 Score: 158
Period size: 45 Copynumber: 2.3 Consensus size: 46
68049 TGCACCAAGT
* * *
68059 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGA
1 GTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATAGCCAGA
**
68104 GTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATATTCAGA
1 GTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATAGCCAGA
68150 GTGCATCGATGCAT
1 GTGCATCGATGCAT
68164 GGAGAATGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 27 0.50
46 27 0.50
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (46 bp):
GTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATAGCCAGA
Found at i:68182 original size:65 final size:65
Alignment explanation
Indices: 68105--68249 Score: 161
Period size: 65 Copynumber: 2.2 Consensus size: 65
68095 ATAGCCTGAG
* *
68105 TGCATCGATGCATCAAATGCATTCAATGTTTTGAAAAT-ATTCA-GAGTGCATCGATGCATGG-A
1 TGCATCGGTGCATCAAATGCATTCAATG-TTT-AAAATAATTCACGAATGCATCGATGCATGGTA
68167 GAA
64 G-A
** * * * * *
68170 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGGTGCATCAAATGCATTCAATGTTTAAAATAATTCACGAATGCATCGATGCATGGTAGA
68235 TGCATCGGTGCATCA
1 TGCATCGGTGCATCA
68250 CCTCAAATAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
63 3 0.05
64 8 0.12
65 54 0.82
66 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
TGCATCGGTGCATCAAATGCATTCAATGTTTAAAATAATTCACGAATGCATCGATGCATGGTAGA
Found at i:68189 original size:17 final size:19
Alignment explanation
Indices: 68151--68197 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
68141 ATATTCAGAG
68151 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
68170 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
68187 TGCATTCGATG
1 TGCA-TCGATG
68198 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:68440 original size:20 final size:21
Alignment explanation
Indices: 68417--68456 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
68407 GAATCGAATA
68417 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
68437 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
68457 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:72421 original size:77 final size:77
Alignment explanation
Indices: 72230--72423 Score: 290
Period size: 76 Copynumber: 2.6 Consensus size: 77
72220 CCGTTATACA
* * *
72230 AGGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
72293 GCAAAACTGTTT
66 GCAAAACTGTTT
* *
72305 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
72369 GCCAAAACCT-TTT
66 G-CAAAA-CTGTTT
72382 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTC
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTC
72424 TAAGCAATCT
Statistics
Matches: 109, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
75 25 0.23
76 54 0.50
77 28 0.26
78 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
GCAAAACTGTTT
Found at i:73038 original size:15 final size:15
Alignment explanation
Indices: 73020--73061 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
73010 AACATCCATA
*
73020 AATCCAAAATCCAAC
1 AATCCAAAATCAAAC
73035 AATCCACAAAATCAAAC
1 AAT-C-CAAAATCAAAC
73052 AATCCAAAAT
1 AATCCAAAAT
73062 ATAATGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 2 0.08
17 13 0.54
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (15 bp):
AATCCAAAATCAAAC
Found at i:73046 original size:17 final size:17
Alignment explanation
Indices: 73024--73057 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
73014 TCCATAAATC
*
73024 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
73041 CAAAATCAAACAATCCA
1 CAAAATCAAACAATCCA
73058 AAATATAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:80919 original size:75 final size:77
Alignment explanation
Indices: 80797--80995 Score: 280
Period size: 75 Copynumber: 2.6 Consensus size: 77
80787 CCGTTGTACA
* * * *
80797 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
**
80861 -C-AAACTGTTT
66 CCAAAACCATTT
* *
80871 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
80936 CCAAAACCATTT
66 CCAAAACCATTT
*
80948 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
80996 ATCTGTAATT
Statistics
Matches: 112, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
74 19 0.17
75 39 0.35
76 22 0.20
77 32 0.29
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
CCAAAACCATTT
Found at i:80995 original size:77 final size:76
Alignment explanation
Indices: 80797--81000 Score: 281
Period size: 77 Copynumber: 2.7 Consensus size: 76
80787 CCGTTGTACA
* * * *
80797 AGGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
**
80860 GCAAACTGTTT
66 GCAAACCATTT
*
80871 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
80935 GCCAAAACCATTT
66 G-C-AAACCATTT
* *
80948 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTG
81001 TAATTTTTGG
Statistics
Matches: 116, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
74 25 0.22
75 33 0.28
76 22 0.19
77 36 0.31
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.24
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
GCAAACCATTT
Found at i:84410 original size:22 final size:21
Alignment explanation
Indices: 84368--84407 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
84358 GAGTTTGTTT
*
84368 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
84389 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
84408 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:86386 original size:64 final size:64
Alignment explanation
Indices: 86333--86496 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
86323 CGGTGCACCA
*
86333 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
86397 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * * *
86462 AGAATGCATCGGTGCATGGAATGCATTCTATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
86497 CAATTAATTC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 32 0.38
65 53 0.62
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:86736 original size:20 final size:21
Alignment explanation
Indices: 86713--86752 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
86703 GAATCGAATA
86713 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
86733 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
86753 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:90128 original size:24 final size:23
Alignment explanation
Indices: 90075--90135 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
90065 CTTCCAAAAT
90075 AAATAATATA-ATATACTTAATA
1 AAATAATATATATATACTTAATA
* **
90097 AATTTAATATATATATACTATCCTA
1 AA-ATAATATATATATACT-TAATA
90122 AAATAATATATATA
1 AAATAATATATATA
90136 CATATAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.06
23 7 0.22
24 18 0.56
25 5 0.16
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATAATATATATATACTTAATA
Found at i:100269 original size:75 final size:77
Alignment explanation
Indices: 100160--100369 Score: 293
Period size: 75 Copynumber: 2.8 Consensus size: 77
100150 CCGTTATACA
* * *
100160 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
**
100224 -CAAAACTGTTT
66 CCAAAACCATTT
* * *
100235 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
100299 CCAAAACCATTT
66 CCAAAACCATTT
*
100311 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
100370 TTTGGCTTTG
Statistics
Matches: 119, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
74 17 0.14
75 40 0.34
76 10 0.08
77 21 0.18
78 31 0.26
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
CCAAAACCATTT
Found at i:102982 original size:20 final size:20
Alignment explanation
Indices: 102906--102990 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
102896 AACAGAACCC
*
102906 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGAATCGATTCCCT
* *
102925 CTGTGGAGGGAATCGGTTCCCATT
1 CAG-GG-GGGAATCGATTCCC--T
* *
102949 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
102970 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
102990 C
1 C
102991 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
19 2 0.04
20 19 0.37
21 14 0.27
23 14 0.27
24 3 0.06
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:108865 original size:75 final size:77
Alignment explanation
Indices: 108756--108965 Score: 284
Period size: 75 Copynumber: 2.8 Consensus size: 77
108746 CCGTTATACA
* * *
108756 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
**
108820 -CAAAACTGTTT
66 CCAAAACCATTT
* * * *
108831 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCAAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
108895 CCAAAACCATTT
66 CCAAAACCATTT
*
108907 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
108966 TTTGGCTTTG
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
74 17 0.15
75 39 0.33
76 10 0.09
77 21 0.18
78 30 0.26
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
CCAAAACCATTT
Found at i:110342 original size:19 final size:19
Alignment explanation
Indices: 110318--110358 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
110308 AGCACAAGGT
110318 ATCGATAATTCGCAACGCG
1 ATCGATAATTCGCAACGCG
110337 ATCGATAATTCGCAACGCG
1 ATCGATAATTCGCAACGCG
110356 ATC
1 ATC
110359 TCCGGTATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (19 bp):
ATCGATAATTCGCAACGCG
Found at i:110412 original size:21 final size:21
Alignment explanation
Indices: 110386--110438 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
110376 GTTTCCAGAT
*
110386 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCAACTA
*
110407 TCGCAACGCGAACTTCAACTA
1 TCGCAACGCGAACATCAACTA
*
110428 TCGCAATGCGA
1 TCGCAACGCGA
110439 TAGTCCAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCAACTA
Found at i:110458 original size:19 final size:19
Alignment explanation
Indices: 110434--110530 Score: 122
Period size: 19 Copynumber: 4.9 Consensus size: 19
110424 ACTATCGCAA
110434 TGCGATAGTCCAAGTTCGT
1 TGCGATAGTCCAAGTTCGT
110453 TGCGATAGTCCAAGTTCGT
1 TGCGATAGTCCAAGTTCGT
*
110472 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTT--CGT
* *
110493 TGCGATTTATTCCAAATTCGT
1 TGCGA--TAGTCCAAGTTCGT
*
110514 TGCGATAGTCGAAGTTC
1 TGCGATAGTCCAAGTTC
110531 ACTATTTAAG
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
19 43 0.64
21 16 0.24
23 8 0.12
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (19 bp):
TGCGATAGTCCAAGTTCGT
Found at i:110519 original size:42 final size:39
Alignment explanation
Indices: 110434--110530 Score: 133
Period size: 42 Copynumber: 2.4 Consensus size: 39
110424 ACTATCGCAA
* *
110434 TGCGATAGTCCAAGTT-CGTTGCGATAGTCCAAGTTCGT
1 TGCGATAGTCGAAGTTCCGTTGCGATAGTCCAAATTCGT
*
110472 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCGAAGTTC-CGTTGCGA--TAGTCCAAATTCGT
110514 TGCGATAGTCGAAGTTC
1 TGCGATAGTCGAAGTTC
110531 ACTATTTAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
38 15 0.29
40 8 0.15
42 29 0.56
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (39 bp):
TGCGATAGTCGAAGTTCCGTTGCGATAGTCCAAATTCGT
Found at i:110719 original size:6 final size:6
Alignment explanation
Indices: 110710--110734 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
110700 CTGTCTCGTC
110710 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
110735 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:110894 original size:21 final size:19
Alignment explanation
Indices: 110823--110958 Score: 128
Period size: 21 Copynumber: 6.7 Consensus size: 19
110813 CGTTGTGATT
110823 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
110842 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
* *
110861 TTGTAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
110884 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
**
110903 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
*
110924 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
*
110945 TTCGACTATCGCAA
1 TTGGACTATCGCAA
110959 TGCAAATATG
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
19 39 0.40
21 50 0.51
23 9 0.09
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:110912 original size:40 final size:42
Alignment explanation
Indices: 110830--110939 Score: 174
Period size: 40 Copynumber: 2.7 Consensus size: 42
110820 ATTTTGGACT
110830 ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGTAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGTAATAA
*
110870 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTG-GA-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGTAATAA
*
110910 ATCGCAACGCGAACTTCGACTATCGCAACG
1 ATCGCAACGCGAACTTGGACTATCGCAACG
110940 CGAACTTCGA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
40 38 0.58
41 1 0.02
42 27 0.41
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGTAATAA
Found at i:110918 original size:61 final size:60
Alignment explanation
Indices: 110823--110958 Score: 168
Period size: 61 Copynumber: 2.2 Consensus size: 60
110813 CGTTGTGATT
** *
110823 TTGGACTATCGCAACGAACTTGGACTATCGCAA-CGAA-TTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAAAATCGCAACCGAACTTCG-AAT--ATCGCAACGCGAAC
* *
110884 TTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAAAATCGCAAC-CGAACTTCGAATATCGCAACGCGAAC
*
110945 TTCGACTATCGCAA
1 TTGGACTATCGCAA
110959 TGCAAATATG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
61 57 0.86
63 6 0.09
64 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (60 bp):
TTGGACTATCGCAACGAACTTGGAAAATCGCAACCGAACTTCGAATATCGCAACGCGAAC
Found at i:113427 original size:21 final size:23
Alignment explanation
Indices: 113394--113435 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
113384 GGTTAAAATA
*
113394 AAAAATAAGAATT-AAATAAAAG
1 AAAAATAACAATTAAAATAAAAG
113416 AAAAA-AACAATTAAAATAAA
1 AAAAATAACAATTAAAATAAA
113436 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (23 bp):
AAAAATAACAATTAAAATAAAAG
Found at i:114218 original size:76 final size:75
Alignment explanation
Indices: 114084--114247 Score: 240
Period size: 76 Copynumber: 2.2 Consensus size: 75
114074 AAAAAATTAT
* * *
114084 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAAGATAAA-ATA
114149 TAAT-ATAAAA
65 TAATGATAAAA
*
114159 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATAAAATA
1 ATAATATCCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATAAAAAGATAAAATA
* *
114224 TAATGTTTAAA
65 TAATGATAAAA
*
114235 ATATTATCCTAAA
1 ATAATATCCTAAA
114248 TTTGAGTTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
75 33 0.41
76 47 0.59
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.30
Consensus pattern (75 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAAGATAAAATAT
AATGATAAAA
Found at i:115889 original size:18 final size:19
Alignment explanation
Indices: 115866--115908 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
115856 CGAACCAAAT
*
115866 CTGTTTTTTTTTC-CTGCA
1 CTGTTTTTTTTGCACTGCA
115884 CTGTTTTTTTTGCACTGCA
1 CTGTTTTTTTTGCACTGCA
*
115903 TTGTTT
1 CTGTTT
115909 GAATCTACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.07, C:0.19, G:0.14, T:0.60
Consensus pattern (19 bp):
CTGTTTTTTTTGCACTGCA
Found at i:116142 original size:8 final size:8
Alignment explanation
Indices: 116111--116156 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
116101 AAAGTTCGCT
116111 AAAAAATA
1 AAAAAATA
116119 AAAAATATA
1 AAAAA-ATA
*
116128 ACGAAAATA
1 A-AAAAATA
116137 AAAAAATA
1 AAAAAATA
116145 AAAAAATA
1 AAAAAATA
116153 AAAA
1 AAAA
116157 CAAAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 23 0.68
9 8 0.24
10 3 0.09
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:116161 original size:27 final size:26
Alignment explanation
Indices: 116111--116164 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
116101 AAAGTTCGCT
*
116111 AAAAAATAAAAAATATAACGAAAATA
1 AAAAAATAAAAAATAAAACGAAAATA
*
116137 AAAAAATAAAAAAATAAAAACAAAAATA
1 AAAAAAT-AAAAAAT-AAAACGAAAATA
116165 TAACGAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 7 0.29
28 10 0.42
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (26 bp):
AAAAAATAAAAAATAAAACGAAAATA
Found at i:116173 original size:22 final size:21
Alignment explanation
Indices: 116113--116173 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 21
116103 AGTTCGCTAA
116113 AAAATAAAAAATATAACG-AA-
1 AAAA-AAAAAATATAACGAAAT
* *
116133 AATAAAAAAATA-AA-AAAAT
1 AAAAAAAAAATATAACGAAAT
116152 AAAAACAAAAATATAACGAAAT
1 AAAAA-AAAAATATAACGAAAT
116174 GGGTTGCCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 4 0.12
19 12 0.38
20 10 0.31
21 2 0.06
22 4 0.12
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (21 bp):
AAAAAAAAAATATAACGAAAT
Found at i:122523 original size:76 final size:75
Alignment explanation
Indices: 122371--122534 Score: 213
Period size: 76 Copynumber: 2.2 Consensus size: 75
122361 AAAAAAATAT
* * *
122371 ATAATATTCTAAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACAAAGATAAAGATA
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACATATTTAAACTAAAATACAAAGATAAAGACA
122436 AAATATAAAA
66 AAATATAAAA
* * *
122446 ATAATATCCTAAAACTTAATTAAAATGCTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AC
1 ATAATATCCTAAAACCTAATTAAAATACT-AAAACATATTTAAACTAAAATACAAAGATAAAGAC
* * *
122510 ATAATGTTTAAA
65 AAAAT-ATAAAA
*
122522 ATATTATCCTAAA
1 ATAATATCCTAAA
122535 TTTGAGTTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
75 30 0.39
76 47 0.61
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (75 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACATATTTAAACTAAAATACAAAGATAAAGACA
AAATATAAAA
Found at i:129710 original size:21 final size:21
Alignment explanation
Indices: 129684--129726 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
129674 CTATACTTAG
129684 ATAATTTAGTTTTTGTGCTTT
1 ATAATTTAGTTTTTGTGCTTT
129705 ATAATTTAGTTTTTGTGCTTT
1 ATAATTTAGTTTTTGTGCTTT
129726 A
1 A
129727 ACTTAACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.14, T:0.60
Consensus pattern (21 bp):
ATAATTTAGTTTTTGTGCTTT
Found at i:130718 original size:15 final size:15
Alignment explanation
Indices: 130698--130726 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
130688 ACCAACAACT
130698 GCAGGAACTCCAGTC
1 GCAGGAACTCCAGTC
130713 GCAGGAACTCCAGT
1 GCAGGAACTCCAGT
130727 TGTGGAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (15 bp):
GCAGGAACTCCAGTC
Found at i:139416 original size:14 final size:15
Alignment explanation
Indices: 139298--139454 Score: 140
Period size: 15 Copynumber: 9.9 Consensus size: 15
139288 TATTTTAAAA
139298 TAAAATAATTTATTT
1 TAAAATAATTTATTT
139313 TAAAATAATTTATTT
1 TAAAATAATTTATTT
139328 TAAAATAATTT-TTT
1 TAAAATAATTTATTT
*
139342 ATAAAATAATTTACTT
1 -TAAAATAATTTATTT
*
139358 TAAAATAAATTATTAT
1 TAAAATAATTTATT-T
*
139374 AAAATATGGATTGATTTATTT
1 TAAA-AT--A---ATTTATTT
139395 TAAAATAATTTATTT
1 TAAAATAATTTATTT
139410 T-AAATAATTTATTAGT
1 TAAAATAATTTATT--T
* * *
139426 ATGAATTGATTTATTT
1 -TAAAATAATTTATTT
139442 T-AAATAATTTATT
1 TAAAATAATTTATT
139455 AGTATGGATT
Statistics
Matches: 119, Mismatches: 10, Indels: 27
0.76 0.06 0.17
Matches are distributed among these distances:
14 25 0.21
15 59 0.50
16 8 0.07
17 3 0.03
18 11 0.09
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (15 bp):
TAAAATAATTTATTT
Found at i:139439 original size:18 final size:18
Alignment explanation
Indices: 139416--139472 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
139406 ATTTTAAATA
139416 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
139434 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
139448 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
139466 ATTTATT
1 ATTTATT
139473 TTAAAATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:139441 original size:32 final size:32
Alignment explanation
Indices: 139402--139477 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
139392 TTTTAAAATA
139402 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
139434 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
139466 ATTTATTTTAAA
1 ATTTATTTTAAA
139478 ATATAGATTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:139550 original size:32 final size:32
Alignment explanation
Indices: 139509--139763 Score: 141
Period size: 32 Copynumber: 8.5 Consensus size: 32
139499 TAGTTGTGTG
139509 GATTGATTTATTTTAAATAATTTATTAGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
139541 GATTGATTTATTTT-AA-AA--TA-T-G----
1 GATTGATTTATTTTAAATAATTTATTAGTATA
139563 GATTGATTTATTTTAAATAATTTATTAGTAT-
1 GATTGATTTATTTTAAATAATTTATTAGTATA
139594 GTATTGATTTATTTT-AA-AA--TA-T-G---A
1 G-ATTGATTTATTTTAAATAATTTATTAGTATA
* * *
139618 -ATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 GATTGATTTATTTT-AAATA---ATTTA-TTAGTAT-A
* * * * *
139655 AATATGGATTGA-TTT--AT--TTTA-AAATATG
1 GAT-T-GATTTATTTTAAATAATTTATTAGTATA
*
139683 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATA
* *
139715 GATTGATTTATTTTAAATAATTTATTTGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATA
139747 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
139764 ATATGGATTG
Statistics
Matches: 175, Mismatches: 13, Indels: 70
0.68 0.05 0.27
Matches are distributed among these distances:
22 27 0.15
23 2 0.01
24 4 0.02
25 1 0.01
26 9 0.05
27 7 0.04
28 8 0.05
29 5 0.03
30 5 0.03
31 12 0.07
32 81 0.46
36 2 0.01
37 1 0.01
38 2 0.01
39 4 0.02
40 5 0.03
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAGTATA
Found at i:139607 original size:22 final size:22
Alignment explanation
Indices: 139591--139699 Score: 200
Period size: 22 Copynumber: 5.0 Consensus size: 22
139581 AATTTATTAG
*
139591 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
139613 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
139635 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
139657 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
139679 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
139700 TAATTTATTA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 85 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:139829 original size:80 final size:83
Alignment explanation
Indices: 139655--139843 Score: 287
Period size: 80 Copynumber: 2.3 Consensus size: 83
139645 TTTATTTTAA
*
139655 AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTA-TTT-AAT-ATGTATTAGTATGGATTG
139720 ATTTATTTTAAATAATTTATT
63 ATTTATTTTAAATAATTTATT
**
139741 TGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TT-AT-TGTAGTT-GTATGGATTGAT
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAATATGTA-TTAGTATGGATTGAT
139802 TTATTTTAAATAATTTATT
65 TTATTTTAAATAATTTATT
139821 AATATGGATTGATTTATTTTAAA
1 AATATGGATTGATTTATTTTAAA
139844 TAATTTATTA
Statistics
Matches: 97, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
80 55 0.57
81 2 0.02
82 2 0.02
84 2 0.02
86 36 0.37
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (83 bp):
AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTAATATGTATTAGTATGGATTGATT
TATTTTAAATAATTTATT
Found at i:139832 original size:32 final size:32
Alignment explanation
Indices: 139791--139875 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
139781 ATTGTAGTTG
139791 TATGGATTGATTTATTTTAAATAATTTATTAA
1 TATGGATTGATTTATTTTAAATAATTTATTAA
*
139823 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAA
*
139855 TATGGATTGAATTATTTTAAA
1 TATGGATTGATTTATTTTAAA
139876 ATATGAATTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAA
Found at i:139900 original size:21 final size:21
Alignment explanation
Indices: 139855--139920 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
139845 AATTTATTAG
*
139855 TATGGATTGAATTATTTTAAAA
1 TATGGATTGATTTATTTT-AAA
*
139877 TATGAATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
139898 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
139919 TA
1 TA
139921 ATTTATTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 25 0.61
22 16 0.39
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
TATGGATTGATTTATTTTAAA
Found at i:139936 original size:32 final size:32
Alignment explanation
Indices: 139898--139982 Score: 170
Period size: 32 Copynumber: 2.7 Consensus size: 32
139888 TTATTTTAAA
139898 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
139930 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
139962 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
139983 ATATGAATTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:140025 original size:80 final size:80
Alignment explanation
Indices: 139877--140159 Score: 426
Period size: 80 Copynumber: 3.5 Consensus size: 80
139867 TATTTTAAAA
* * * *
139877 TATGAATTGATTTATTTT-AAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGA
1 TATGGATTGATTTATTTTAAAATATGAATTGATTTA--TT--AT--TGTAGTT-GTATGAATTGA
139940 TTTATTTTAAATAATTTATTAG
59 TTTATTTTAAATAATTTATTAG
139962 TATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
1 TATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
140027 TAAATAATTTATTAG
66 TAAATAATTTATTAG
140042 TATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
1 TATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
140107 TAAATAATTTATTAG
66 TAAATAATTTATTAG
* * *
140122 CATGGATTGATTTATTTTTAAATATGGATTGATTTATT
1 TATGGATTGATTTATTTTAAAATATGAATTGATTTATT
140160 TTAAATAATT
Statistics
Matches: 189, Mismatches: 7, Indels: 9
0.92 0.03 0.04
Matches are distributed among these distances:
80 150 0.79
81 2 0.01
82 2 0.01
84 2 0.01
85 17 0.09
86 16 0.08
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
TAAATAATTTATTAG
Found at i:140163 original size:21 final size:22
Alignment explanation
Indices: 140123--140166 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
140113 ATTTATTAGC
140123 ATGGATTGATTTATTTTTAAAT
1 ATGGATTGATTTATTTTTAAAT
140145 ATGGATTGATTTA-TTTTAAAT
1 ATGGATTGATTTATTTTTAAAT
140166 A
1 A
140167 ATTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
ATGGATTGATTTATTTTTAAAT
Found at i:140224 original size:31 final size:31
Alignment explanation
Indices: 140189--140247 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
140179 AGTTGTATGG
* *
140189 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
140220 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
140248 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:140286 original size:16 final size:16
Alignment explanation
Indices: 140265--140307 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
140255 GTTTAAAAAA
140265 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
140281 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
* *
140297 TTAGTTCATTT
1 TCAGTTTATTT
140308 TAGCAGTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:146659 original size:21 final size:21
Alignment explanation
Indices: 146635--146674 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
146625 ACGCATCTAA
146635 TATCTAAATTATCATTTTTAG
1 TATCTAAATTATCATTTTTAG
* *
146656 TATCTAAATTTTTATTTTT
1 TATCTAAATTATCATTTTT
146675 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (21 bp):
TATCTAAATTATCATTTTTAG
Found at i:148503 original size:22 final size:22
Alignment explanation
Indices: 148473--148533 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 22
148463 CCCTATGAAG
148473 TTTT-TAAATTCTTCTCTAAAA
1 TTTTATAAATTCTTCTCTAAAA
148494 TTTTATAAA---TTCTCTAAAA
1 TTTTATAAATTCTTCTCTAAAA
*
148513 TTTTATAAATTCATCTACTAA
1 TTTTATAAATTCTTCT-CTAA
148534 CATAAAATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 19 0.56
21 4 0.12
22 7 0.21
23 4 0.12
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTATAAATTCTTCTCTAAAA
Found at i:148508 original size:19 final size:19
Alignment explanation
Indices: 148484--148529 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
148474 TTTTAAATTC
148484 TTCTCTAAAATTTTATAAA
1 TTCTCTAAAATTTTATAAA
148503 TTCTCTAAAATTTTATAAA
1 TTCTCTAAAATTTTATAAA
148522 TTCATCTA
1 TTC-TCTA
148530 CTAACATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (19 bp):
TTCTCTAAAATTTTATAAA
Found at i:159833 original size:18 final size:18
Alignment explanation
Indices: 159807--159849 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
159797 TTCAAACCCA
*
159807 AGAAGCATTGGAGATATC
1 AGAACCATTGGAGATATC
159825 AGAACCATTGGAGATATC
1 AGAACCATTGGAGATATC
159843 AGAACCA
1 AGAACCA
159850 CTTGCAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (18 bp):
AGAACCATTGGAGATATC
Found at i:160831 original size:18 final size:18
Alignment explanation
Indices: 160808--160850 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
160798 TGTCCCGAAG
*
160808 GACCACTATATCCTAAAA
1 GACCACTATATCCCAAAA
* *
160826 GACCACTATGTCCCGAAA
1 GACCACTATATCCCAAAA
160844 GACCACT
1 GACCACT
160851 GATAATCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.19
Consensus pattern (18 bp):
GACCACTATATCCCAAAA
Found at i:167716 original size:18 final size:18
Alignment explanation
Indices: 167693--167727 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
167683 ACTGAATATT
*
167693 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
167711 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
167728 GATAATCCCT
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:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:168391 original size:29 final size:29
Alignment explanation
Indices: 168358--168442 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 29
168348 TTTAACCAGT
168358 GGCTAAAATATAAGTTTTAAAAGTTTAGA
1 GGCTAAAATATAAGTTTTAAAAGTTTAGA
* * *
168387 GGCTAAAGTATAAGCTTTGAAAAGTTTAGG
1 GGCTAAAATATAAG-TTTTAAAAGTTTAGA
* *
168417 GAGC-AAAATTGTAATTTTTAAAAGTT
1 G-GCTAAAA-TATAAGTTTTAAAAGTT
168443 ATATATTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 13 0.28
30 27 0.59
31 6 0.13
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
GGCTAAAATATAAGTTTTAAAAGTTTAGA
Found at i:168412 original size:30 final size:29
Alignment explanation
Indices: 168358--168415 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
168348 TTTAACCAGT
*
168358 GGCTAAAATATAAGTTTTAAAAGTTTAGA
1 GGCTAAAATATAAGTTTGAAAAGTTTAGA
*
168387 GGCTAAAGTATAAGCTTTGAAAAGTTTAG
1 GGCTAAAATATAAG-TTTGAAAAGTTTAG
168416 GGAGCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (29 bp):
GGCTAAAATATAAGTTTGAAAAGTTTAGA
Found at i:169416 original size:26 final size:26
Alignment explanation
Indices: 169387--169443 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
169377 ATACAAAAAG
*
169387 ATAT-GAATTTATATATACGTGTTCAT
1 ATATCGAATTT-TATATACATGTTCAT
* *
169413 ATATCTAGTTTTATATACATGTTCAT
1 ATATCGAATTTTATATACATGTTCAT
169439 ATATC
1 ATATC
169444 AAACTATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (26 bp):
ATATCGAATTTTATATACATGTTCAT
Found at i:174887 original size:51 final size:51
Alignment explanation
Indices: 174822--174956 Score: 164
Period size: 51 Copynumber: 2.6 Consensus size: 51
174812 CACCCGTAGT
* * * *
174822 AGTAAAGCGCGCCCCCTGAACCGCGCTATATGCTGATTTGG-CACCACGTGG
1 AGTATAGCGCGCCCCCTGAACCGCGCTATACGCTGACTGGGTCA-CACGTGG
* * *
174873 AGTATAGCGCGCCCCCTGTACCTCGCTATACGCTGACTGGGTTACACGTGG
1 AGTATAGCGCGCCCCCTGAACCGCGCTATACGCTGACTGGGTCACACGTGG
* **
174924 GGTATAGCGCGCCCCCTGCCCCGCGCTATACGC
1 AGTATAGCGCGCCCCCTGAACCGCGCTATACGC
174957 CATGTACGGG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 71 0.99
52 1 0.01
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (51 bp):
AGTATAGCGCGCCCCCTGAACCGCGCTATACGCTGACTGGGTCACACGTGG
Done.