Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014056.1 Kokia drynarioides strain JFW-HI SEQ_129087, 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: 156565
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:1316 original size:24 final size:23
Alignment explanation
Indices: 1289--1335 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1279 TTAAATCTTA
* *
1289 TCAGTGCAAATGTAATATAAAATG
1 TCAGAGCAAAT-TAATAGAAAATG
*
1313 TCAGAGTAAATTAATAGAAAATG
1 TCAGAGCAAATTAATAGAAAATG
1336 GATTGATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (23 bp):
TCAGAGCAAATTAATAGAAAATG
Found at i:6706 original size:12 final size:13
Alignment explanation
Indices: 6680--6736 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 13
6670 TGTTCAACCG
*
6680 TTCACCTT-TCAT
1 TTCACCTTGACAT
6692 TTC-CCTTGACAT
1 TTCACCTTGACAT
*
6704 TTCACCTT-TCAT
1 TTCACCTTGACAT
*
6716 CTC-CCTTGACAT
1 TTCACCTTGACAT
6728 TTCACCTTG
1 TTCACCTTG
6737 TAACTCATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
11 8 0.22
12 19 0.53
13 9 0.25
ACGTcount: A:0.16, C:0.35, G:0.05, T:0.44
Consensus pattern (13 bp):
TTCACCTTGACAT
Found at i:6712 original size:24 final size:24
Alignment explanation
Indices: 6680--6735 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
6670 TGTTCAACCG
*
6680 TTCACCTTTCATTTCCCTTGACAT
1 TTCACCTTTCATCTCCCTTGACAT
6704 TTCACCTTTCATCTCCCTTGACAT
1 TTCACCTTTCATCTCCCTTGACAT
6728 TTCACCTT
1 TTCACCTT
6736 GTAACTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.16, C:0.36, G:0.04, T:0.45
Consensus pattern (24 bp):
TTCACCTTTCATCTCCCTTGACAT
Found at i:12132 original size:21 final size:20
Alignment explanation
Indices: 12098--12138 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
12088 GAAAAAATTT
**
12098 AAATATAATTAAAAATACTAA
1 AAATATAAAAAAAAAT-CTAA
12119 AAATATAAAAAAAAATCTAA
1 AAATATAAAAAAAAATCTAA
12139 TTTATCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATATAAAAAAAAATCTAA
Found at i:15883 original size:28 final size:28
Alignment explanation
Indices: 15824--15883 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
15814 TACATGGATC
* *
15824 GATTATTTAACTAGTAGACGAAGTATAA
1 GATTATTTAACTAATAAACGAAGTATAA
15852 GATTATTTAACTACATAAAC-AA-TATAA
1 GATTATTTAACTA-ATAAACGAAGTATAA
15879 TGATT
1 -GATT
15884 TTGCCTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.18
28 19 0.68
29 4 0.14
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (28 bp):
GATTATTTAACTAATAAACGAAGTATAA
Found at i:16748 original size:20 final size:18
Alignment explanation
Indices: 16721--16773 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 18
16711 ATATATTACC
16721 AATTCGGTTAATTTTGTTT
1 AATTCGGTTAATTTTG-TT
16740 AATTTCGGTTAATTTTGTT
1 AA-TTCGGTTAATTTTGTT
*
16759 AATCCGGTTAATTTT
1 AATTCGGTTAATTTT
16774 AATTTGGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 12 0.38
19 6 0.19
20 14 0.44
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.55
Consensus pattern (18 bp):
AATTCGGTTAATTTTGTT
Found at i:16783 original size:24 final size:24
Alignment explanation
Indices: 16748--16793 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
16738 TTAATTTCGG
*
16748 TTAATTTTGTTAATCCGGTTAATT
1 TTAATTTGGTTAATCCGGTTAATT
16772 TTAATTTGGTTAATCCGGTTAA
1 TTAATTTGGTTAATCCGGTTAA
16794 ATAAACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (24 bp):
TTAATTTGGTTAATCCGGTTAATT
Found at i:21311 original size:21 final size:21
Alignment explanation
Indices: 21286--21348 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
21276 GATACCTGAT
*
21286 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCAATACTTTTTG
21307 AAAAGGTATCAATACTTTTTG
1 AAAAGGTATCAATACTTTTTG
21328 AAAAGGTATCAATACTTTTTG
1 AAAAGGTATCAATACTTTTTG
21349 TCATTGTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (21 bp):
AAAAGGTATCAATACTTTTTG
Found at i:21561 original size:19 final size:20
Alignment explanation
Indices: 21531--21573 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
21521 AATTGAAACC
21531 ATTTCAACTTGATTTTATCA
1 ATTTCAACTTGATTTTATCA
21551 ATTTC-ACTTGATTTTATCA
1 ATTTCAACTTGATTTTATCA
21570 ATTT
1 ATTT
21574 GTTCAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (20 bp):
ATTTCAACTTGATTTTATCA
Found at i:22503 original size:31 final size:31
Alignment explanation
Indices: 22465--22527 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
22455 CTCAATTTTG
22465 AAACATTTTTCTTGTGTTATGAAATCATGAC
1 AAACATTTTTCTTGTGTTATGAAATCATGAC
*
22496 AAACATTTTTCTTGTGTTTTGAAATCATGAC
1 AAACATTTTTCTTGTGTTATGAAATCATGAC
22527 A
1 A
22528 TCAAATTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (31 bp):
AAACATTTTTCTTGTGTTATGAAATCATGAC
Found at i:23916 original size:21 final size:21
Alignment explanation
Indices: 23887--23927 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23877 GATACTTGAT
23887 AAAAAGTATCGATACTTTTTG
1 AAAAAGTATCGATACTTTTTG
* *
23908 AAAAGGTATTGATACTTTTT
1 AAAAAGTATCGATACTTTTT
23928 ATCATTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (21 bp):
AAAAAGTATCGATACTTTTTG
Found at i:29629 original size:24 final size:24
Alignment explanation
Indices: 29561--29629 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
29551 AGTTTGACTC
* *
29561 AAACAAATAAACATAGTTTAGTTA
1 AAACAAATAAACAGAGTTTAATTA
*
29585 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTA
*
29609 AAACAATTAAACAGAGTTTAA
1 AAACAAATAAACAGAGTTTAA
29630 CCTGGAAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTA
Found at i:29641 original size:24 final size:24
Alignment explanation
Indices: 29549--29630 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
29539 TAGACTAATA
* * *
29549 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAATTAAAC
* ** * *
29573 ATAGTTTAGTTAAAACAAATAAAC
1 AGAGTTTAACTGAAACAATTAAAC
*
29597 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAATTAAAC
29621 AGAGTTTAAC
1 AGAGTTTAAC
29631 CTGGAAGATT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAATTAAAC
Found at i:30231 original size:64 final size:64
Alignment explanation
Indices: 30130--30265 Score: 263
Period size: 64 Copynumber: 2.1 Consensus size: 64
30120 AACCTTTTGA
30130 GTCTAAATTACTTAAGGAGATTAGATTCTTTCGTAAATCAGATACATACCTGACATCTGATAGT
1 GTCTAAATTACTTAAGGAGATTAGATTCTTTCGTAAATCAGATACATACCTGACATCTGATAGT
30194 GTCTAAATTACTTAAGGAGATTAGATTCTTTCGTAAATCAGATACATACCTGACATCTGATAGT
1 GTCTAAATTACTTAAGGAGATTAGATTCTTTCGTAAATCAGATACATACCTGACATCTGATAGT
*
30258 GTCCAAAT
1 GTCTAAAT
30266 CGTACCATCC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 71 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (64 bp):
GTCTAAATTACTTAAGGAGATTAGATTCTTTCGTAAATCAGATACATACCTGACATCTGATAGT
Found at i:31606 original size:24 final size:24
Alignment explanation
Indices: 31576--31664 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 24
31566 TAGATTAATA
* *
31576 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAAAAAATAAAT
* * *
31600 ATAGTTTAATTGAAAAAAATAAAT
1 AGAGTTTAACTCAAAAAAATAAAT
* * * * *
31624 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAAAAAATAAAT
*
31648 AGAGTTTAACTGAAAAA
1 AGAGTTTAACTCAAAAA
31665 TTATTTCTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTCAAAAAAATAAAT
Found at i:34902 original size:17 final size:17
Alignment explanation
Indices: 34880--34915 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
34870 AATTATTTCG
34880 TTATTTAATAATCATAT
1 TTATTTAATAATCATAT
*
34897 TTATTTAGTAATCATAT
1 TTATTTAATAATCATAT
34914 TT
1 TT
34916 CACTACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
TTATTTAATAATCATAT
Found at i:35424 original size:13 final size:14
Alignment explanation
Indices: 35406--35434 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
35396 GACATCGCTC
35406 TTCAATTGG-GAGG
1 TTCAATTGGAGAGG
35419 TTCAATTGGAGAGG
1 TTCAATTGGAGAGG
35433 TT
1 TT
35435 TCGGCTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.24, C:0.07, G:0.34, T:0.34
Consensus pattern (14 bp):
TTCAATTGGAGAGG
Found at i:39654 original size:86 final size:86
Alignment explanation
Indices: 39509--39741 Score: 306
Period size: 86 Copynumber: 2.7 Consensus size: 86
39499 TGGTGATTAT
* * * * *
39509 TAAAAGGAAGACTCATGTCTTGGATAAAGCATGAGATTATTTATAAATGGAAGACTTATGTCTTG
1 TAAAAGGAAGACTTATGTCTCGGATAAAGCATAAGATTATTTATAAAAGGAAGACTTATGTCTCG
39574 GTTAGAGCATAAGATTGTTTA
66 GTTAGAGCATAAGATTGTTTA
* * * * *
39595 TAAAAAGAAGGCTTATGTCTCGGTTAGAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCG
1 TAAAAGGAAGACTTATGTCTCGGATAAAGCATAAGATTATTTATAAAAGGAAGACTTATGTCTCG
39660 GTTAGAGCATAAGATTGTTTA
66 GTTAGAGCATAAGATTGTTTA
* * * * *
39681 TAAAAGGAAGACTTATGTCTC-AACAAGAGCATAAGGTTATTTGTAAATGGAAGAACTTATG
1 TAAAAGGAAGACTTATGTCTCGGATAA-AGCATAAGATTATTTATAAAAGGAAG-ACTTATG
39742 ACTCAGTCGG
Statistics
Matches: 125, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
85 1 0.01
86 117 0.94
87 7 0.06
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (86 bp):
TAAAAGGAAGACTTATGTCTCGGATAAAGCATAAGATTATTTATAAAAGGAAGACTTATGTCTCG
GTTAGAGCATAAGATTGTTTA
Found at i:39734 original size:43 final size:43
Alignment explanation
Indices: 39509--39701 Score: 296
Period size: 43 Copynumber: 4.5 Consensus size: 43
39499 TGGTGATTAT
* * * * * *
39509 TAAAAGGAAGACTCATGTCTTGGATAAAGCATGAGATTATTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
* *
39552 TAAATGGAAGACTTATGTCTTGGTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
* *
39595 TAAAAAGAAGGCTTATGTCTCGGTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
39638 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
39681 TAAAAGGAAGACTTATGTCTC
1 TAAAAGGAAGACTTATGTCTC
39702 AACAAGAGCA
Statistics
Matches: 138, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 138 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (43 bp):
TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
Found at i:42264 original size:43 final size:43
Alignment explanation
Indices: 42193--42529 Score: 449
Period size: 43 Copynumber: 7.8 Consensus size: 43
42183 TGGTGACTAC
* * * *
42193 TAAAAGGAAGACTCATGTCTCAGATAGAGCATAAGATTATTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
* *
42236 TAAATGGAAGACTTATGTCTCGATTAGAGCATAAGATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
*
42279 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGGTTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
* * * *
42322 TAAAATGATGACTTATGTCTTGGTTAGAGCATAAAATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
* *
42365 TAAAAGGAAGACTTATGTCTTGGTTAGAGCAAAAGATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
42408 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
* ** * * *
42451 TAAAGGGAAGACTTATGTCTCGGCAAGAGCATACGATTATTTG
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
* * * * *
42494 TAAATGGAAGTATTTATGACTCGGTCAGAGCTTAAG
1 TAAAAGGAAG-ACTTATGTCTCGGTTAGAGCATAAG
42530 GCTAATACAG
Statistics
Matches: 260, Mismatches: 33, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
43 241 0.93
44 19 0.07
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (43 bp):
TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
Found at i:47290 original size:28 final size:28
Alignment explanation
Indices: 47250--47306 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
47240 TATTTTGCTC
47250 TTTATTTTATAACCTCCACCATAATATG
1 TTTATTTTATAACCTCCACCATAATATG
47278 TTTATTTTATAACCTCCACCATAATATG
1 TTTATTTTATAACCTCCACCATAATATG
47306 T
1 T
47307 CTACTTACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.44
Consensus pattern (28 bp):
TTTATTTTATAACCTCCACCATAATATG
Found at i:49601 original size:13 final size:13
Alignment explanation
Indices: 49574--49606 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
49564 GCAAATATAA
49574 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
49587 TTTCTTTTC-TCTT
1 TTT-TTTTCTTCTT
49600 TTTTTTT
1 TTTTTTT
49607 AAGTGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 10 0.53
14 5 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:50689 original size:12 final size:12
Alignment explanation
Indices: 50674--50709 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
50664 CTTCTCTTTA
50674 TTCTCTTCTTCC
1 TTCTCTTCTTCC
50686 TTCTCTTCTT-C
1 TTCTCTTCTTCC
50697 TTC-CTT-TTCC
1 TTCTCTTCTTCC
50707 TTC
1 TTC
50710 AGCTGGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 4 0.17
12 10 0.43
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTCTTCTTCC
Found at i:65433 original size:25 final size:25
Alignment explanation
Indices: 65399--65449 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
65389 TAATATATAG
65399 AAGTTAGTACCACCATCTTACCTTT
1 AAGTTAGTACCACCATCTTACCTTT
*
65424 AAGTTAGTACCACCGTCTTACCTTT
1 AAGTTAGTACCACCATCTTACCTTT
65449 A
1 A
65450 TGTTTTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.35
Consensus pattern (25 bp):
AAGTTAGTACCACCATCTTACCTTT
Found at i:73551 original size:17 final size:20
Alignment explanation
Indices: 73521--73560 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
73511 TGTTCTATTG
73521 AAATATAATGAAATA-TTAA
1 AAATATAATGAAATATTTAA
73540 AAATA-AAT-AAATATTTAA
1 AAATATAATGAAATATTTAA
73558 AAA
1 AAA
73561 ACGAAAGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 10 0.50
19 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
AAATATAATGAAATATTTAA
Found at i:74888 original size:30 final size:30
Alignment explanation
Indices: 74854--74914 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
74844 GCTAGAATGT
74854 TTTTGATTTGAAAATTTGTCGAGCAAGTGA
1 TTTTGATTTGAAAATTTGTCGAGCAAGTGA
*
74884 TTTTGATTTGAAATTTTGTCGAGCAAGTGA
1 TTTTGATTTGAAAATTTGTCGAGCAAGTGA
74914 T
1 T
74915 GCAAGCTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.43
Consensus pattern (30 bp):
TTTTGATTTGAAAATTTGTCGAGCAAGTGA
Found at i:77515 original size:22 final size:21
Alignment explanation
Indices: 77477--77517 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
77467 TTGCCTGCTA
**
77477 TGTCGCGACACGGCTCCTGTG
1 TGTCGCGACACAACTCCTGTG
77498 TGTCGCGACATCAACTCCTG
1 TGTCGCGACA-CAACTCCTG
77518 AATGCGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (21 bp):
TGTCGCGACACAACTCCTGTG
Found at i:83732 original size:11 final size:11
Alignment explanation
Indices: 83716--83744 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
83706 AGAAATCAAG
83716 TATTTTCTTTA
1 TATTTTCTTTA
83727 TATTTTCTTTA
1 TATTTTCTTTA
83738 TATTTTC
1 TATTTTC
83745 ATAGGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTCTTTA
Found at i:88959 original size:24 final size:26
Alignment explanation
Indices: 88909--88960 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
88899 TCAAATTCTC
**
88909 TTTGAGTTTTTCTTTCCAGAATTGTT
1 TTTGAGTTTTTCTTTCCAGAAGAGTT
*
88935 TTTGAG-TTTTCTTT-TAGAAGAGTT
1 TTTGAGTTTTTCTTTCCAGAAGAGTT
88959 TT
1 TT
88961 AACAATCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.39
25 8 0.35
26 6 0.26
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (26 bp):
TTTGAGTTTTTCTTTCCAGAAGAGTT
Found at i:90945 original size:29 final size:29
Alignment explanation
Indices: 90910--90984 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
90900 TCCCTTTGAC
* * *
90910 ATAGATAGCCATAGAGGCAT-CATTGAGTA
1 ATAGATAGCCATAAAGGCATCCA-TAAGCA
**
90939 ATAGATAATCATAAAGGCATCCATAAGCA
1 ATAGATAGCCATAAAGGCATCCATAAGCA
*
90968 A-AGATAGCCATATAGGC
1 ATAGATAGCCATAAAGGC
90985 GTCTAATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 13 0.35
29 22 0.59
30 2 0.05
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (29 bp):
ATAGATAGCCATAAAGGCATCCATAAGCA
Found at i:91045 original size:26 final size:26
Alignment explanation
Indices: 90969--91036 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
90959 CCATAAGCAA
* * *
90969 AGATAGCCATATAGGCGTCTAATTAG
1 AGATAGCCACAAAGGCGTCCAATTAG
90995 AGATAGCCACAAAGGCGTCCAATTAG
1 AGATAGCCACAAAGGCGTCCAATTAG
*
91021 ATATAGCCACAAAGGC
1 AGATAGCCACAAAGGC
91037 TTTCCATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (26 bp):
AGATAGCCACAAAGGCGTCCAATTAG
Found at i:91109 original size:29 final size:29
Alignment explanation
Indices: 91069--91263 Score: 182
Period size: 29 Copynumber: 6.7 Consensus size: 29
91059 GATTCCCTTT
*
91069 ACAGAATT-AACCACAAAGGCTCACATATA
1 ACAG-ATTCAACCACAAAGGCTCTCATATA
*
91098 ACAGATTCAACCACAAAGACTCTCATATA
1 ACAGATTCAACCACAAAGGCTCTCATATA
* * *
91127 ACAAAATCAACTACAAAGGCTCTCATATA
1 ACAGATTCAACCACAAAGGCTCTCATATA
*
91156 ACAG-TATCAACCACAAATGCTCTCATATGA
1 ACAGAT-TCAACCACAAAGGCTCTCATAT-A
* * * * * *
91186 AAAAATT-AGCAACAAAAGCTTTCATATA
1 ACAGATTCAACCACAAAGGCTCTCATATA
* * *
91214 ATAGAATCAGA-CACAAAGCCTCTCATATA
1 ACAGATTCA-ACCACAAAGGCTCTCATATA
*
91243 ACAGATTCAGCCACAAAGGCT
1 ACAGATTCAACCACAAAGGCT
91264 TCACTTTTCG
Statistics
Matches: 131, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
28 8 0.06
29 118 0.90
30 4 0.03
31 1 0.01
ACGTcount: A:0.46, C:0.24, G:0.10, T:0.21
Consensus pattern (29 bp):
ACAGATTCAACCACAAAGGCTCTCATATA
Found at i:93509 original size:21 final size:21
Alignment explanation
Indices: 93468--93518 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
93458 ACTATTCACA
*
93468 TTTTTTCTTACTCATGATTCTT
1 TTTTTTC-TACTCATGATTCTC
**
93490 TTTTTTCTACTCATTTTTCTC
1 TTTTTTCTACTCATGATTCTC
*
93511 TTCTTTCT
1 TTTTTTCT
93519 GATTTTTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTTCTACTCATGATTCTC
Found at i:93534 original size:17 final size:18
Alignment explanation
Indices: 93502--93535 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
93492 TTTTCTACTC
*
93502 ATTTTTCTCTTCTTTCTG
1 ATTTTTCTCTTATTTCTG
93520 ATTTTTCTC-TATTTCT
1 ATTTTTCTCTTATTTCT
93536 TTCTTTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTTCTCTTATTTCTG
Found at i:108252 original size:18 final size:19
Alignment explanation
Indices: 108226--108263 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
108216 CGGTTGGTTC
*
108226 GAGGGACAA-GAAAAGAAA
1 GAGGCACAAGGAAAAGAAA
*
108244 GAGGCACAAGGGAAAGAAA
1 GAGGCACAAGGAAAAGAAA
108263 G
1 G
108264 TGAAGAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.37, T:0.00
Consensus pattern (19 bp):
GAGGCACAAGGAAAAGAAA
Found at i:113794 original size:21 final size:21
Alignment explanation
Indices: 113768--113808 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
113758 AGGTGTGTCG
113768 CAACATAGCAAGCAGTTTCAA
1 CAACATAGCAAGCAGTTTCAA
*
113789 CAACATAGCAAGTAGTTTCA
1 CAACATAGCAAGCAGTTTCA
113809 TTCTGAGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (21 bp):
CAACATAGCAAGCAGTTTCAA
Found at i:114642 original size:11 final size:11
Alignment explanation
Indices: 114626--114658 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
114616 ACACGAGGGT
114626 AATAAATTTAA
1 AATAAATTTAA
114637 AATAAA-TTAA
1 AATAAATTTAA
114647 ACATAAATTTAA
1 A-ATAAATTTAA
114659 CCCTCTGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 11 0.55
12 4 0.20
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAATTTAA
Found at i:126782 original size:28 final size:31
Alignment explanation
Indices: 126737--126805 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
126727 AATTATTTTG
126737 AAATTATTAAAATTATTTTTTT-AAAT-ATA
1 AAATTATTAAAATTATTTTTTTGAAATAATA
* *
126766 AAATTATT-GAATTATTTTTTTGATATAATA
1 AAATTATTAAAATTATTTTTTTGAAATAATA
126796 AAATT-TTAAA
1 AAATTATTAAA
126806 TAATTTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 12 0.35
29 13 0.38
30 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
AAATTATTAAAATTATTTTTTTGAAATAATA
Found at i:128029 original size:31 final size:29
Alignment explanation
Indices: 127994--128094 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
127984 ATTAAAATTA
127994 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-AAAAAAATAAT
** *
128025 TTTAATAATTTTACGTTT-TAAAAATAA-
1 TTTAATAATTTTATATTTAAAAAAATAAT
* * * *
128052 TTAAAAAAATTTATATTTTAAAATAATAAT
1 TTTAATAATTTTATA-TTTAAAAAAATAAT
128082 TTTAATAATTTTA
1 TTTAATAATTTTA
128095 AAATCATTTG
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
27 10 0.19
28 11 0.20
29 7 0.13
30 13 0.24
31 13 0.24
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (29 bp):
TTTAATAATTTTATATTTAAAAAAATAAT
Found at i:128048 original size:28 final size:27
Alignment explanation
Indices: 127994--128094 Score: 96
Period size: 28 Copynumber: 3.5 Consensus size: 27
127984 ATTAAAATTA
127994 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-T-TTT--AAAAAATAAT
128025 TTTAATAATTTTACGTTTT-AAAAATAAT
1 TTTAATAATTTTA--TTTTAAAAAATAAT
** *
128053 TAAAAAAATTTATATTTTAAAATAATAAT
1 TTTAATAATTT-TATTTTAAAA-AATAAT
128082 TTTAATAATTTTA
1 TTTAATAATTTTA
128095 AAATCATTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
27 4 0.07
28 22 0.37
29 16 0.27
31 16 0.27
32 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (27 bp):
TTTAATAATTTTATTTTAAAAAATAAT
Found at i:128064 original size:27 final size:27
Alignment explanation
Indices: 128016--128078 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
128006 ATTATTTCAA
* * * *
128016 AAAAATAATTTTAATAATTTTACGTTTT
1 AAAAATAA-TTAAAAAAATTTACATTTT
*
128044 AAAAATAATTAAAAAAATTTATATTTT
1 AAAAATAATTAAAAAAATTTACATTTT
128071 -AAAATAAT
1 AAAAATAAT
128079 AATTTTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 8 0.27
27 14 0.47
28 8 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
AAAAATAATTAAAAAAATTTACATTTT
Found at i:140014 original size:32 final size:28
Alignment explanation
Indices: 139955--140015 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 28
139945 TTTAGGGTTG
*
139955 GTTGGATGGTGATTGGTGGTTGCGGCAA
1 GTTGGATGGTGATTGGTGGTTGAGGCAA
*
139983 GTTGTGATGGTGGTGTGGTGTGTGTGAGGCAA
1 GTTG-GATGGTGAT-TGGTG-GT-TGAGGCAA
140015 G
1 G
140016 GACGCATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 8 0.30
30 5 0.19
31 2 0.07
32 8 0.30
ACGTcount: A:0.13, C:0.05, G:0.49, T:0.33
Consensus pattern (28 bp):
GTTGGATGGTGATTGGTGGTTGAGGCAA
Found at i:143305 original size:29 final size:29
Alignment explanation
Indices: 143272--143367 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 29
143262 CAATCATGCC
*
143272 ACAAATACAATCACGTCACATATACAGTT
1 ACAAATACAATCACGTCACAAATACAGTT
* * * *
143301 ACAAATACAGTCATGCCACAAATACAGTC
1 ACAAATACAATCACGTCACAAATACAGTT
* * *
143330 ACAGATA-AATTCACGTCATAGATACAGTT
1 ACAAATACAA-TCACGTCACAAATACAGTT
143359 ACAAATACA
1 ACAAATACA
143368 GTTATATCAC
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
28 1 0.02
29 50 0.96
30 1 0.02
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.22
Consensus pattern (29 bp):
ACAAATACAATCACGTCACAAATACAGTT
Found at i:143327 original size:17 final size:17
Alignment explanation
Indices: 143259--143330 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 17
143249 ACAGTTACAG
*
143259 ATACAATCATGCCACAA
1 ATACAGTCATGCCACAA
* * * *
143276 ATACAATCACGTCACAT
1 ATACAGTCATGCCACAA
143293 ATACAGT--T---ACAA
1 ATACAGTCATGCCACAA
143305 ATACAGTCATGCCACAA
1 ATACAGTCATGCCACAA
143322 ATACAGTCA
1 ATACAGTCA
143331 CAGATAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 10 0.23
14 1 0.02
17 33 0.75
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.21
Consensus pattern (17 bp):
ATACAGTCATGCCACAA
Found at i:143381 original size:29 final size:29
Alignment explanation
Indices: 143272--143389 Score: 103
Period size: 29 Copynumber: 4.1 Consensus size: 29
143262 CAATCATGCC
* * * *
143272 ACAAATACAATCACGTCACATATACAGTT
1 ACAAATACAGTTATGTCACAGATACAGTT
* * * *
143301 ACAAATACAGTCATGCCACAAATACAGTC
1 ACAAATACAGTTATGTCACAGATACAGTT
* * * *
143330 ACAGATA-AATTCACGTCATAGATACAGTT
1 ACAAATACAGTT-ATGTCACAGATACAGTT
*
143359 ACAAATACAGTTATATCACAGATACAGTT
1 ACAAATACAGTTATGTCACAGATACAGTT
143388 AC
1 AC
143390 GGATGCAAAC
Statistics
Matches: 69, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
28 2 0.03
29 64 0.93
30 3 0.04
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (29 bp):
ACAAATACAGTTATGTCACAGATACAGTT
Found at i:146792 original size:17 final size:17
Alignment explanation
Indices: 146770--146811 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
146760 TAGAAATAAT
* *
146770 ATAGATACAGTCATGCC
1 ATAGATACAATCACGCC
*
146787 ATAGATACAATCACGTC
1 ATAGATACAATCACGCC
146804 ATAGATAC
1 ATAGATAC
146812 GTTATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (17 bp):
ATAGATACAATCACGCC
Found at i:146899 original size:17 final size:17
Alignment explanation
Indices: 146858--146904 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
146848 ATATAGTCAC
146858 GTCATAGATACAGTTA-
1 GTCATAGATACAGTTAT
146874 --CA-A-ATACAGTTAT
1 GTCATAGATACAGTTAT
146887 GTCATAGATACAGTTAT
1 GTCATAGATACAGTTAT
146904 G
1 G
146905 GATGCAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
12 9 0.35
13 1 0.04
14 2 0.08
15 2 0.08
16 1 0.04
17 11 0.42
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (17 bp):
GTCATAGATACAGTTAT
Found at i:146900 original size:29 final size:29
Alignment explanation
Indices: 146791--146902 Score: 109
Period size: 29 Copynumber: 3.9 Consensus size: 29
146781 CATGCCATAG
* * *
146791 ATACAATCACGTCATAGATAC-GTTATAA
1 ATACAGTCATGTCATAGATACAGTTACAA
* * * * * *
146819 ATACAGTCATGCCAAAAATATAGTCACAG
1 ATACAGTCATGTCATAGATACAGTTACAA
* *
146848 ATATAGTCACGTCATAGATACAGTTACAA
1 ATACAGTCATGTCATAGATACAGTTACAA
*
146877 ATACAGTTATGTCATAGATACAGTTA
1 ATACAGTCATGTCATAGATACAGTTA
146903 TGGATGCAGA
Statistics
Matches: 63, Mismatches: 20, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
28 15 0.24
29 48 0.76
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (29 bp):
ATACAGTCATGTCATAGATACAGTTACAA
Done.