Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014631.1 Kokia drynarioides strain JFW-HI SEQ_129670, 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: 61769
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:2717 original size:29 final size:28
Alignment explanation
Indices: 2614--2717 Score: 75
Period size: 29 Copynumber: 3.5 Consensus size: 28
2604 ATTTTTGGTG
*
2614 TAAAATGGTAATTTTTGGAGAAATCGGGGT
1 TAAAATGG-AATTTTTGGA-AAATCGAGGT
* * *
2644 TAAAAATGGGA-TTTTGGAAAGTTCAAGGGT
1 T-AAAATGGAATTTTTGGAAA-ATCGA-GGT
* ** *
2674 AAAAATTTAACTTTTGGATAAATCGAGGT
1 TAAAATGGAATTTTTGGA-AAATCGAGGT
2703 TAAAATGGAATTTTT
1 TAAAATGGAATTTTT
2718 AAAAGTTTGG
Statistics
Matches: 55, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
28 2 0.04
29 29 0.53
30 15 0.27
31 9 0.16
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (28 bp):
TAAAATGGAATTTTTGGAAAATCGAGGT
Found at i:2793 original size:29 final size:30
Alignment explanation
Indices: 2762--2875 Score: 101
Period size: 30 Copynumber: 3.8 Consensus size: 30
2752 AATCAGGGTT
*
2762 AAAAATGGAATTTTGGAAAGTTTAGTGGT-
1 AAAAATGGAATTTTGGAAAGTTTAGAGGTC
* * *
2791 AAAAATGTAATTTTTAGAAAG-TTCGAGGTC
1 AAAAATGGAA-TTTTGGAAAGTTTAGAGGTC
* *
2821 AAAAATGG-ATTTTAGAAAAGTTTAGGGGTC
1 AAAAATGGAATTTT-GGAAAGTTTAGAGGTC
* *
2851 AAAATAT-GATTTTTGGATAGTTTAG
1 AAAA-ATGGAATTTTGGAAAGTTTAG
2876 GGACCTCTAG
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
28 4 0.06
29 20 0.30
30 37 0.55
31 6 0.09
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAAATGGAATTTTGGAAAGTTTAGAGGTC
Found at i:2813 original size:30 final size:29
Alignment explanation
Indices: 2761--2855 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
2751 AAATCAGGGT
* * *
2761 TAAAAATGGAATTTTGGAAAGTTTAGTGG
1 TAAAAATGTAATTTTAGAAAGTTTAGAGG
*
2790 TAAAAATGTAATTTTTAGAAAG-TTCGAGG
1 TAAAAATGTAA-TTTTAGAAAGTTTAGAGG
* *
2819 TCAAAAATG-GATTTTAGAAAAGTTTAGGGG
1 T-AAAAATGTAATTTTAG-AAAGTTTAGAGG
*
2849 TCAAAAT
1 TAAAAAT
2856 ATGATTTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
28 6 0.11
29 26 0.48
30 22 0.41
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (29 bp):
TAAAAATGTAATTTTAGAAAGTTTAGAGG
Found at i:2833 original size:117 final size:118
Alignment explanation
Indices: 2616--2849 Score: 314
Period size: 117 Copynumber: 2.0 Consensus size: 118
2606 TTTTGGTGTA
* * *
2616 AAATGGTAATTTTTGGAGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCAAGGGTAAAAATT
1 AAATGGTAATTTTTGGAGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAAATG
* * * *
2681 TAACTTTTGGATAAATCGAGGTTAAAATGGAATTTT-TAAAAGTTTGGGGGTG
66 TAACTTTTAGATAAATCGAGGTAAAAATGGAATTTTAGAAAAGTTTAGGGGTG
* *
2733 AAATGGTAATTTTTTGAGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTT-TAGTGGTAAAAAT
1 AAATGGTAATTTTTGGAGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAAG-GGTAAAAAT
* *
2797 GTAATTTTTAGA-AAGTTCGAGGTCAAAAATGG-ATTTTAGAAAAGTTTAGGGGT
65 GTAACTTTTAGATAA-ATCGAGGT-AAAAATGGAATTTTAGAAAAGTTTAGGGGT
2850 CAAAATATGA
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
116 4 0.04
117 78 0.76
118 20 0.20
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (118 bp):
AAATGGTAATTTTTGGAGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAAATG
TAACTTTTAGATAAATCGAGGTAAAAATGGAATTTTAGAAAAGTTTAGGGGTG
Found at i:2855 original size:59 final size:56
Alignment explanation
Indices: 2613--2865 Score: 206
Period size: 59 Copynumber: 4.3 Consensus size: 56
2603 AATTTTTGGT
* * * * *
2613 GTAAAATGGTAATTTTTGGAGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCAAGG
1 GTAAAAT-GTAATTTTT-GAGAAATCGAGG-TAAAAATGGAATTTTGAAAAGTTTAGGG
* * * * * *
2672 GTAAAAATTTAACTTTTGGATAAATCGAGGTTAAAATGGAATTTTTAAAAGTTTGGGG
1 GT-AAAATGTAA-TTTTTGAGAAATCGAGGTAAAAATGGAATTTTGAAAAGTTTAGGG
* * *
2730 GTGAAATGGTAATTTTTTGAGAAATC-AGGGTTAAAAATGGAATTTTGGAAAGTTTAGTG
1 GTAAAAT-GTAA-TTTTTGAGAAATCGA-GG-TAAAAATGGAATTTTGAAAAGTTTAGGG
2789 GTAAAAATGTAATTTTT-AGAAAGTTCGAGGTCAAAAATGG-ATTTTAGAAAAGTTTAGGG
1 GT-AAAATGTAATTTTTGAGAAA--TCGAGGT-AAAAATGGAATTTT-GAAAAGTTTAGGG
* *
2848 GTCAAAATATGATTTTTG
1 GT-AAAATGTAATTTTTG
2866 GATAGTTTAG
Statistics
Matches: 155, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
57 10 0.06
58 50 0.32
59 81 0.52
60 14 0.09
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (56 bp):
GTAAAATGTAATTTTTGAGAAATCGAGGTAAAAATGGAATTTTGAAAAGTTTAGGG
Found at i:4663 original size:18 final size:17
Alignment explanation
Indices: 4642--4691 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
4632 TATTTTGGGC
*
4642 TTTTAATTTAATATCAAG
1 TTTTAATTCAAT-TCAAG
*
4660 TTTTAAATCAATTCAAG
1 TTTTAATTCAATTCAAG
*
4677 -TTTAATTAAATTCAA
1 TTTTAATTCAATTCAA
4692 ATTTAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.46
17 5 0.18
18 10 0.36
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (17 bp):
TTTTAATTCAATTCAAG
Found at i:4688 original size:16 final size:16
Alignment explanation
Indices: 4643--4697 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
4633 ATTTTGGGCT
*
4643 TTTAATTTAATATCAAG
1 TTTAATTAAAT-TCAAG
* *
4660 TTTTAAATCAATTCAAG
1 -TTTAATTAAATTCAAG
*
4677 TTTAATTAAATTCAAA
1 TTTAATTAAATTCAAG
4693 TTTAA
1 TTTAA
4698 ACAAATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 18 0.56
17 5 0.16
18 9 0.28
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (16 bp):
TTTAATTAAATTCAAG
Found at i:4703 original size:16 final size:16
Alignment explanation
Indices: 4669--4714 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
4659 GTTTTAAATC
* **
4669 AATTCAAGTTTAATTA
1 AATTCAAATTTAAACA
4685 AATTCAAATTTAAACA
1 AATTCAAATTTAAACA
*
4701 AATTTAAATTTAAA
1 AATTCAAATTTAAA
4715 ATGATAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (16 bp):
AATTCAAATTTAAACA
Found at i:4709 original size:6 final size:6
Alignment explanation
Indices: 4682--4746 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
4672 TCAAGTTTAA
* * *
4682 TTAAAT TCAAAT TTAAA- -CAAAT TTAAAT TTAAAAT GATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT -TTAAAT TTAAAT
* *
4730 TTAAAA ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
4747 CCAATTTAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
4 3 0.07
6 33 0.73
7 8 0.18
8 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:4725 original size:20 final size:18
Alignment explanation
Indices: 4683--4746 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 18
4673 CAAGTTTAAT
*
4683 TAAATTCAAATTT--AAA
1 TAAATTTAAATTTAAAAA
*
4699 CAAATTTAAATTTAAAATGA
1 TAAATTTAAATTTAAAA--A
4719 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAAA
4737 TAAATTTAAA
1 TAAATTTAAA
4747 CCAATTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 11 0.27
18 13 0.32
20 17 0.41
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAA
Found at i:4755 original size:22 final size:22
Alignment explanation
Indices: 4727--4772 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4717 GATAAATTTA
4727 AATTTAAAAATAAATTTAAA-CC
1 AATTTAAAAAT-AATTTAAAGCC
*
4749 AATTTAAAACTAATTTAAAGCC
1 AATTTAAAAATAATTTAAAGCC
4771 AA
1 AA
4773 AGGCTTGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (22 bp):
AATTTAAAAATAATTTAAAGCC
Found at i:4757 original size:21 final size:23
Alignment explanation
Indices: 4727--4772 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
4717 GATAAATTTA
4727 AATTTAAAAA-TAAATTTAAA-CC
1 AATTTAAAAACT-AATTTAAAGCC
4749 AATTT-AAAACTAATTTAAAGCC
1 AATTTAAAAACTAATTTAAAGCC
4771 AA
1 AA
4773 AGGCTTGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (23 bp):
AATTTAAAAACTAATTTAAAGCC
Found at i:12997 original size:17 final size:17
Alignment explanation
Indices: 12975--13008 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12965 CTAAGAATTT
12975 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
12992 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
13009 GTATCAGTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:18909 original size:23 final size:25
Alignment explanation
Indices: 18883--18928 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
18873 CCAATTAGGG
18883 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
18906 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
18929 TATATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:19346 original size:15 final size:15
Alignment explanation
Indices: 19309--19347 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
19299 TTATGTGTGC
*
19309 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
19324 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
19338 TTAATTCTTG
1 TTAATTCTTG
19348 TTTGAAGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:20009 original size:13 final size:14
Alignment explanation
Indices: 19991--20020 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
19981 TTTAGCCATT
19991 TTTTTATTTT-TTA
1 TTTTTATTTTATTA
20004 TTTTTATTTTATTA
1 TTTTTATTTTATTA
20018 TTT
1 TTT
20021 GCATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTATTA
Found at i:20045 original size:14 final size:13
Alignment explanation
Indices: 20024--20055 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
20014 ATTATTTGCA
20024 TTTTTAATTTAAT
1 TTTTTAATTTAAT
20037 TTTTCTAATTTAAT
1 TTTT-TAATTTAAT
20051 TTTTT
1 TTTTT
20056 TCCCTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:22729 original size:5 final size:5
Alignment explanation
Indices: 22719--22761 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
22709 TTTATTATCA
*
22719 ATTTT ATTTT ATTTT ATCTT ATTTT ATTTT CAATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT --ATTTT ATTTT A
22762 GTTATGCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 29 0.85
7 5 0.15
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:24612 original size:23 final size:25
Alignment explanation
Indices: 24586--24631 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
24576 GCAATTAGGG
24586 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
24609 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
24632 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:25723 original size:18 final size:19
Alignment explanation
Indices: 25700--25742 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
25690 TTAGCCATTT
25700 TTTTATTATTT-ATTTTTA
1 TTTTATTATTTCATTTTTA
25718 TTTTATTATTTGCATTTTTA
1 TTTTATTATTT-CATTTTTA
*
25738 ATTTA
1 TTTTA
25743 ATTTCTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
20 11 0.50
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTATTATTTCATTTTTA
Found at i:26876 original size:28 final size:28
Alignment explanation
Indices: 26832--26913 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
26822 AAACTTTTGA
* *
26832 TTTTAAATTTATATTAAGTTTAAATTGG
1 TTTTAAATTTATTTTAAGTTTAAATTGC
* * * *
26860 TTTTCAATTTATTTTAAATTAAAATTTC
1 TTTTAAATTTATTTTAAGTTTAAATTGC
*
26888 TTTTAAATTTAAATTT-AGTTTAAATT
1 TTTTAAATTT-ATTTTAAGTTTAAATT
26914 TGAAATGGTT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
28 39 0.91
29 4 0.09
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (28 bp):
TTTTAAATTTATTTTAAGTTTAAATTGC
Found at i:26914 original size:17 final size:17
Alignment explanation
Indices: 26865--26919 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
26855 ATTGGTTTTC
*
26865 AATTTATTTTAAATTAA
1 AATTTATTTTAAATTTA
*
26882 AATTTCTTTTAAATTTA
1 AATTTATTTTAAATTTA
*
26899 AATTTAGTTTAAATTTGA
1 AATTTATTTTAAATTT-A
26917 AAT
1 AAT
26920 GGTTTTAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
17 29 0.88
18 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:27014 original size:40 final size:40
Alignment explanation
Indices: 26970--27045 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
26960 AAATACAAAA
*
26970 AAGGCCCAATTACAGGTTTAACTAGACAAACCCAAACACT
1 AAGGCCCAATTACAAGTTTAACTAGACAAACCCAAACACT
*
27010 AAGGCCCAATTACAAGTTTAACTAGACAGACCCAAA
1 AAGGCCCAATTACAAGTTTAACTAGACAAACCCAAA
27046 ACCTGACCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.17
Consensus pattern (40 bp):
AAGGCCCAATTACAAGTTTAACTAGACAAACCCAAACACT
Found at i:28628 original size:30 final size:30
Alignment explanation
Indices: 28594--28665 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
28584 TTAACCCCTA
*
28594 AACTTTTCCAAAATCACATATTAACCCTCG
1 AACTTTTCAAAAATCACATATTAACCCTCG
** * * *
28624 AACTTCACAAAAATTACATTTTTACCCTCG
1 AACTTTTCAAAAATCACATATTAACCCTCG
*
28654 AACTTTTTAAAA
1 AACTTTTCAAAA
28666 TTATATTTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (30 bp):
AACTTTTCAAAAATCACATATTAACCCTCG
Found at i:28693 original size:28 final size:29
Alignment explanation
Indices: 28599--29133 Score: 225
Period size: 29 Copynumber: 18.3 Consensus size: 29
28589 CCCTAAACTT
* * *
28599 TTCC-AAAATCACATATTAACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
28627 TTCACAAAAATTACATTTTTACCCTCGAAC
1 TTC-CAAAAATTACATTTTTACCCTCGAAC
*** * * *
28657 TTTTTAAAATTATA-TTTTACCCCCGACC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
*
28685 TTCCAAAAA-TATCATTCTTGACCC-CGAAC
1 TTCCAAAAATTA-CATT-TTTACCCTCGAAC
** * * *
28714 TTTTAAAAAATTACCCTTTTT-CTCTCGAAT
1 -TTCCAAAAATTA-CATTTTTACCCTCGAAC
* * ** *
28744 TTCCAACATTTACCGTTTT-CCCTTCGAAT
1 TTCCAAAAATTACATTTTTACCC-TCGAAC
* * *
28773 TTCCAAATATTCCATTTTTAACCCT-AAAC
1 TTCCAAAAATTACATTTTT-ACCCTCGAAC
* * *
28802 TTTCAAAAATTACCA-TTTTACCCT-TAAA
1 TTCCAAAAATTA-CATTTTTACCCTCGAAC
* * *
28830 TGTCAAAAAATTATATTTTTGACCCT-AAAC
1 T-TCCAAAAATTACATTTTT-ACCCTCGAAC
* *
28860 TTTCCAAAAACTACATTTTTACCACT-TAAC
1 -TTCCAAAAATTACATTTTTACC-CTCGAAC
* *
28890 TACCAAAAAATCACATTTTTA-CCTCGAAAC
1 TTCC-AAAAATTACATTTTTACCCTCG-AAC
* * * *
28920 TTTCAAAAATGACCA-CTTTACCCTTGAAC
1 TTCCAAAAATTA-CATTTTTACCCTCGAAC
*
28949 TTCCAAAAA-TATCATTTTTAACCCT--AAA
1 TTCCAAAAATTA-CATTTTT-ACCCTCGAAC
* *
28977 TTCTCTAAAATTACCA-TTTTACCC-CCAAGC
1 TTC-CAAAAATTA-CATTTTTACCCTCGAA-C
* * * * *
29007 TTCTAGAAATTACTTTTCTTACCCCCG-AG
1 TTCCAAAAATTACATTT-TTACCCTCGAAC
* *
29036 TGTCCAAAAACTATCA-TTTTACCCTCGAAG
1 T-TCCAAAAATTA-CATTTTTACCCTCGAAC
*
29066 TGTCC-AAAATTAGCA-TTTTACTCTCGAAC
1 T-TCCAAAAATTA-CATTTTTACCCTCGAAC
*
29095 TTCCAAAAATTACCA-TTTTACCCTCGAGC
1 TTCCAAAAATTA-CATTTTTACCCTCGAAC
*
29124 ATCCAAAAAT
1 TTCCAAAAAT
29134 CGTATTTTTA
Statistics
Matches: 385, Mismatches: 86, Indels: 71
0.71 0.16 0.13
Matches are distributed among these distances:
27 2 0.01
28 57 0.15
29 182 0.47
30 133 0.35
31 11 0.03
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCTCGAAC
Found at i:37915 original size:22 final size:24
Alignment explanation
Indices: 37873--37917 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
37863 AAAGGAAGCA
37873 TAGATGTGTGTTTGAATTAAAATG
1 TAGATGTGTGTTTGAATTAAAATG
*
37897 TAGATTTGTG-TT-AATTAAAAT
1 TAGATGTGTGTTTGAATTAAAAT
37918 AATGCTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 2 0.10
24 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (24 bp):
TAGATGTGTGTTTGAATTAAAATG
Found at i:38342 original size:17 final size:17
Alignment explanation
Indices: 38320--38353 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38310 CTAAGAATTT
38320 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
38337 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
38354 GTATCAGGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:39215 original size:23 final size:23
Alignment explanation
Indices: 39187--39240 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
39177 CGTCCATCCT
39187 TGCTGACTAGACCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
*
39210 TGCTGACTAGACCTTCTAGAAGT
1 TGCTGACTAGACCTTCTAGAAGC
39233 TGCTGACT
1 TGCTGACT
39241 GGATGCCACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAGAAGC
Found at i:42529 original size:15 final size:16
Alignment explanation
Indices: 42497--42530 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
42487 TGGGGTGGGT
42497 TTTATTATTTTATGAG
1 TTTATTATTTTATGAG
42513 TTTATTATTTT-TGAG
1 TTTATTATTTTATGAG
42528 TTT
1 TTT
42531 CTTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTATGAG
Found at i:42932 original size:20 final size:20
Alignment explanation
Indices: 42892--42966 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 20
42882 TAAATTACCA
42892 AAAATAAAAAATAAATAGAAAT
1 AAAAT-AAAAATAAAT-GAAAT
42914 AAAATAAAAATAAATGAAAT
1 AAAATAAAAATAAATGAAAT
42934 AATGAAGTATAAAATTAAAT-AAAT
1 AA--AA-TA-AAAA-TAAATGAAAT
42958 -AAATAAAAA
1 AAAATAAAAA
42967 CAATGGGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
19 4 0.08
20 9 0.19
21 12 0.25
22 7 0.15
23 3 0.06
24 8 0.17
25 5 0.10
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATAAAAATAAATGAAAT
Found at i:49214 original size:489 final size:489
Alignment explanation
Indices: 48296--49278 Score: 1576
Period size: 489 Copynumber: 2.0 Consensus size: 489
48286 GTTGGCCCTA
* * * *
48296 TGTTCAAGAAACTTTCACGAGTATTTTCGAGATAAGGAGTATCTCTAACAATTGTTGTGGCGAAC
1 TGTTCAAGAAACTTCCACGAGTATTTTCGAGACAAGGAGTATCTCTAACAAGTGTTGCGGCGAAC
* *
48361 TTGTTGCATTGGGAAAGGTTTGCCACACAGCATTACTAAAGAGGACTCTTGAGAATCCTCTATTC
66 TTGTTGCATTGGGAAAAGTTTGCCACACAGCATTACTAAAGAGGACTCTCGAGAATCCTCTATTC
* *
48426 AAAGAACTAAACCCAACTACAATTATAGCGAAGAGCTTCGAAACATAGAACAACTGCATGGCTTT
131 AAAGAACTAAACCCAACTACAATTATAGCGAAGAGCATCGAAACATAGAACAACTGCATGGCATT
* *
48491 GATCGATTCACCATCTCCGTCTGCTTAATGATATAGGATTGCTTCAACTAACAACAGGTTACAAG
196 GATCAATTCACCATCTCCGTCTGCTTAATGATATAGGATTGCTGCAACTAACAACAGGTTACAAG
* *
48556 ACGTGACGTGCTCAATACTATTCTTTTGTCATTACTTTCAACATTGTTCCCGAAGCTTCACTATT
261 ACGTGACGTGCTCAATACTATTCTTTTGTCATTACTTTCAACATTGTTCCCGAAGATTCACAATT
*
48621 GTCTGTCGTTAAATTTAAGTCGAGTTAAATTAATTTTTGTTCTACGAAAATTAAATGGTTCTAGA
326 GTCTGTCGTTAAATTTAAGTCGAGTTAAATTAATTTTAGTTCTACGAAAATTAAATGGTTCTAGA
*
48686 GAAGCCATTACTTAAAACACTATGATTTTATAAGGCCATTATTTTTAATTTTATAGCATTGGAAC
391 GAAGCCATTACTTAAAACACTATGATTTTATAAGGCCATTATTTTTAATTTTATAGAATTGGAAC
48751 TTGATAACCATCTCAAATCGAGTACTATATACTG
456 TTGATAACCATCTCAAATCGAGTACTATATACTG
* *
48785 TGTTCAAGAAACTTCCACGAGTATTTTCGAGACAGGGAGTATCTCTAACAAGTGTTGCGGTGAA-
1 TGTTCAAGAAACTTCCACGAGTATTTTCGAGACAAGGAGTATCTCTAACAAGTGTTGCGGCGAAC
* *** *
48849 TTGGTTGCCTTGGGAAAAGTTTGCCATGTAGCATTAGTAAAGAGGACTCTCGAGAATCCTCTATT
66 TT-GTTGCATTGGGAAAAGTTTGCCACACAGCATTACTAAAGAGGACTCTCGAGAATCCTCTATT
* * *
48914 CAAAGAACTAAACCCAACTATAATTATAGCGAAGAGCATCGAAACATGGAAGAACTGCATGGCAT
130 CAAAGAACTAAACCCAACTACAATTATAGCGAAGAGCATCGAAACATAGAACAACTGCATGGCAT
*
48979 TGATCAATTCACCATCTCCGTCTGCTTAATGATATAGGATTGCTGCAACTAACAACAGGTTATAA
195 TGATCAATTCACCATCTCCGTCTGCTTAATGATATAGGATTGCTGCAACTAACAACAGGTTACAA
* * * * * * *
49044 GACGTGATGTGC-CTAATATTGTTGTTTTGTCTTTATTTTCAACATTGTTCCGGAAGATTCACAA
260 GACGTGACGTGCTC-AATACTATTCTTTTGTCATTACTTTCAACATTGTTCCCGAAGATTCACAA
* * *
49108 TTTTCTGTCGTTAAATTTAAGTCGAGTTAAATTAATTTTAGTTGTACGAGAATTAAATGGTTCTA
324 TTGTCTGTCGTTAAATTTAAGTCGAGTTAAATTAATTTTAGTTCTACGAAAATTAAATGGTTCTA
* * *
49173 GAGAAGCCATTACTTAATACACTATGATTTTATAAGGCCATTGTTTTTAGTTTTATAGAATTGGA
389 GAGAAGCCATTACTTAAAACACTATGATTTTATAAGGCCATTATTTTTAATTTTATAGAATTGGA
*
49238 ACTTGATAACCATCTCGAATCGAGTACTATATACTG
454 ACTTGATAACCATCTCAAATCGAGTACTATATACTG
49274 T-TTCA
1 TGTTCA
49279 CATTGTTTAA
Statistics
Matches: 453, Mismatches: 39, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
488 7 0.02
489 446 0.98
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (489 bp):
TGTTCAAGAAACTTCCACGAGTATTTTCGAGACAAGGAGTATCTCTAACAAGTGTTGCGGCGAAC
TTGTTGCATTGGGAAAAGTTTGCCACACAGCATTACTAAAGAGGACTCTCGAGAATCCTCTATTC
AAAGAACTAAACCCAACTACAATTATAGCGAAGAGCATCGAAACATAGAACAACTGCATGGCATT
GATCAATTCACCATCTCCGTCTGCTTAATGATATAGGATTGCTGCAACTAACAACAGGTTACAAG
ACGTGACGTGCTCAATACTATTCTTTTGTCATTACTTTCAACATTGTTCCCGAAGATTCACAATT
GTCTGTCGTTAAATTTAAGTCGAGTTAAATTAATTTTAGTTCTACGAAAATTAAATGGTTCTAGA
GAAGCCATTACTTAAAACACTATGATTTTATAAGGCCATTATTTTTAATTTTATAGAATTGGAAC
TTGATAACCATCTCAAATCGAGTACTATATACTG
Found at i:56845 original size:23 final size:23
Alignment explanation
Indices: 56818--56863 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
56808 TAATCTAAAG
56818 AACGAAGAATAAGGAAATCAAGT
1 AACGAAGAATAAGGAAATCAAGT
56841 AACGAAGAATAAGGAAATCAAGT
1 AACGAAGAATAAGGAAATCAAGT
56864 TAAGACTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.09, G:0.22, T:0.13
Consensus pattern (23 bp):
AACGAAGAATAAGGAAATCAAGT
Done.