Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011966.1 Kokia drynarioides strain JFW-HI SEQ_126964, 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: 60668
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:2928 original size:34 final size:34
Alignment explanation
Indices: 2890--2977 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
2880 TAAAAATATT
*
2890 ATTTTTATTAAATTAGATTT-TGAATTGGGTTTTA
1 ATTTTTATTAAATTAGATTTGGGAATTGGG-TTTA
* *
2924 ATTTTTA-TAAATTATATTTGGGTATTGGGTTTA
1 ATTTTTATTAAATTAGATTTGGGAATTGGGTTTA
*
2957 ATTTTTTATT-ATTTAGATTTG
1 A-TTTTTATTAAATTAGATTTG
2978 AGATATAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
33 16 0.35
34 29 0.63
35 1 0.02
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (34 bp):
ATTTTTATTAAATTAGATTTGGGAATTGGGTTTA
Found at i:10981 original size:30 final size:30
Alignment explanation
Indices: 10945--11006 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
10935 GACCAAGGAG
10945 AAAGAAAGATGGGATGCAAATGATAAGACA
1 AAAGAAAGATGGGATGCAAATGATAAGACA
10975 AAAGAAAGATGGGATGCAAATGATAAGACA
1 AAAGAAAGATGGGATGCAAATGATAAGACA
11005 AA
1 AA
11007 TGCTCAATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.55, C:0.06, G:0.26, T:0.13
Consensus pattern (30 bp):
AAAGAAAGATGGGATGCAAATGATAAGACA
Found at i:17533 original size:2 final size:2
Alignment explanation
Indices: 17526--17550 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17516 TGTTCCATCA
17526 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17551 GATGAGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19524 original size:30 final size:29
Alignment explanation
Indices: 19394--19597 Score: 140
Period size: 30 Copynumber: 6.8 Consensus size: 29
19384 TTTTGAAGAA
*
19394 TTTGGGGTCAAAATGTAATTTTGGGAAA-
1 TTTGGGGTTAAAATGTAATTTTGGGAAAG
* * * * *
19422 TTTCAAGGATCAAAATGTAATTTTAGGAAAT
1 TTT--GGGGTTAAAATGTAATTTTGGGAAAG
* * * * *
19453 TTTAGGTGTTAAAAATGTGATTTCGAGAAGG
1 TTT-GGGGTT-AAAATGTAATTTTGGGAAAG
* * *
19484 TTTTGTGTTAAAATGTGATTTTGGGAAAG
1 TTTGGGGTTAAAATGTAATTTTGGGAAAG
* *
19513 CTTTGGGGTTAAAGTGTAATTTTGGAAAAG
1 -TTTGGGGTTAAAATGTAATTTTGGGAAAG
* * * *
19543 TTTAAGGGTCAAAATGTAATTTTAGAAAAG
1 TTT-GGGGTTAAAATGTAATTTTGGGAAAG
* *
19573 TTTGAGGGTTAAAATATGATTTTGG
1 TTTG-GGGTTAAAATGTAATTTTGG
19598 AAATTTTTAG
Statistics
Matches: 138, Mismatches: 31, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
28 3 0.02
29 20 0.14
30 95 0.69
31 20 0.14
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (29 bp):
TTTGGGGTTAAAATGTAATTTTGGGAAAG
Found at i:20792 original size:21 final size:21
Alignment explanation
Indices: 20768--20807 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20758 CTTCCATTTT
* *
20768 TATTTATTACTTATTTATTAA
1 TATTTATTAATTATGTATTAA
20789 TATTTATTAATTATGTATT
1 TATTTATTAATTATGTATT
20808 TATTATACTT
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:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTTATTAATTATGTATTAA
Found at i:20880 original size:12 final size:11
Alignment explanation
Indices: 20849--20881 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
20839 TAATAGTAAT
20849 AATTATA-ATA
1 AATTATATATA
20859 AATTATATATA
1 AATTATATATA
20870 AATATATATATA
1 AAT-TATATATA
20882 TTTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTATATATA
Found at i:21357 original size:7 final size:7
Alignment explanation
Indices: 21345--21370 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21335 TAAAAATAAT
21345 AATTTTA
1 AATTTTA
21352 AATTTTA
1 AATTTTA
21359 AATTTTA
1 AATTTTA
21366 AATTT
1 AATTT
21371 ATTATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:21663 original size:37 final size:37
Alignment explanation
Indices: 21621--21693 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
21611 GGCTTCATCT
**
21621 TTTGGTGCACTTCTCTGTATCTCT-TCAGGAAGATGAA
1 TTTGGTGCACTTCTCTACATCT-TGTCAGGAAGATGAA
*
21658 TTTGGTTCACTTCTCTACATCTTGTCAGGAAGATGA
1 TTTGGTGCACTTCTCTACATCTTGTCAGGAAGATGA
21694 TCACTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (37 bp):
TTTGGTGCACTTCTCTACATCTTGTCAGGAAGATGAA
Found at i:22090 original size:209 final size:201
Alignment explanation
Indices: 21628--22158 Score: 536
Period size: 209 Copynumber: 2.6 Consensus size: 201
21618 TCTTTTGGTG
* * **
21628 CACTTCTCTGTATCTC-TTCAGGAAGATGAATTTGGTTCACTTCTCTACATCTTGTCAGGAAGAT
1 CACTTCTCTGTATCTCATT-AGGAAGATGAATTTGGTCCACTTCTCT-TATCTCATCAGGAAGAT
* * * * *
21692 GATCACTTTATTGCTTCGA-CCACTTCTTTGTATCTCATCAGGAAGGTGGG-TTTGGAGTTTCAC
64 GATCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGATTTGAAGTTTCAC
* * * * **
21755 TCGCATTGAACTTTGCTTCATTTGATTTGGTCTTCTTCTCATCAGGAAGATGATTGCTTCATTAT
129 TCACATTGAACTTCGCTTCATTTAAATTGGTCTTCTTCTCATCAGGAAGATGATCACTTCATTAT
*
21820 TTGTGATC
194 TTGTAATC
* * * * * *
21828 CACTTCTCTATACCTAATCAGGAAGATGGATTTTGTCCACTTCTCATTATCTCATCAGGAAGATG
1 CACTTCTCTGTATCTCATTAGGAAGATGAATTTGGTCCACTTCTC-TTATCTCATCAGGAAGATG
* * * *
21893 ACCGCTTTATTGTTTTAACCCACTTCTCAGTATCTCATCAGGAAGATAGGGATTTGAAGTTTCAC
65 ATCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGAT-GGGATTTGAAGTTTCAC
* *
21958 TCACATTGAGCTTCGCTTCA-TTAAATTGGTCTGCTTCTTTGTATCTTATCAGGAAGATGA-CAC
129 TCACATTGAACTTCGCTTCATTTAAATTGG--T-CTTC----T-TCTCATCAGGAAGATGATCAC
22021 TTTCATTGA-TT-TAATC
186 -TTCATT-ATTTGTAATC
* * * * *
22037 CACTTCTTTGTATCTCATTAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAAGAAGGTG
1 CACTTCTCTGTATCTCATTAGGAAGATGAATTTGGTCCACTTCTCT-TATCTCATCAGGAAGATG
* * * * *
22102 ATAGCTTTATTGGTTTGACCCACTTTTCTGTATCTCATCAAGAAGATGAGATTTGAA
65 ATCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGATTTGAA
22159 AATTTTACTC
Statistics
Matches: 268, Mismatches: 47, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
200 64 0.24
201 27 0.10
202 10 0.04
203 29 0.11
204 1 0.00
205 4 0.01
208 10 0.04
209 98 0.37
210 24 0.09
211 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.38
Consensus pattern (201 bp):
CACTTCTCTGTATCTCATTAGGAAGATGAATTTGGTCCACTTCTCTTATCTCATCAGGAAGATGA
TCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGATTTGAAGTTTCACTC
ACATTGAACTTCGCTTCATTTAAATTGGTCTTCTTCTCATCAGGAAGATGATCACTTCATTATTT
GTAATC
Found at i:22136 original size:85 final size:86
Alignment explanation
Indices: 21991--22156 Score: 203
Period size: 85 Copynumber: 1.9 Consensus size: 86
21981 AATTGGTCTG
* * * * *
21991 CTTCTTTGTATCTTATCAGGAAGATGACACTTTCATTGATTTAATCCACTTCTTTGTATCTCATT
1 CTTCTCTGTATCTCATCAAGAAGATGACACTTTCATTGATTTAACCCACTTCTTTGTATCTCATC
22056 AAGAAGACGA-ATTTGGTCCA
66 AAGAAGACGAGATTTGGTCCA
* * * *
22076 CTTCTCTGTATCTCATCAAGAAGGTGATAGCTTT-ATTGGTTTGACCCACTT-TTCTGTATCTCA
1 CTTCTCTGTATCTCATCAAGAAGATGACA-CTTTCATTGATTTAACCCACTTCTT-TGTATCTCA
*
22139 TCAAGAAGATGAGATTTG
64 TCAAGAAGACGAGATTTG
22157 AAAATTTTAC
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
84 2 0.03
85 57 0.84
86 9 0.13
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (86 bp):
CTTCTCTGTATCTCATCAAGAAGATGACACTTTCATTGATTTAACCCACTTCTTTGTATCTCATC
AAGAAGACGAGATTTGGTCCA
Found at i:32550 original size:19 final size:21
Alignment explanation
Indices: 32501--32550 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
32491 CATGAGGGGT
32501 CGAAGAATAATGAGAAAATAA
1 CGAAGAATAATGAGAAAATAA
* *
32522 CG-AGATTAATTA-AAAAT-A
1 CGAAGAATAATGAGAAAATAA
32540 CGAAGAATAAT
1 CGAAGAATAAT
32551 AGTTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
19 12 0.48
20 8 0.32
21 2 0.08
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.20
Consensus pattern (21 bp):
CGAAGAATAATGAGAAAATAA
Found at i:32726 original size:29 final size:29
Alignment explanation
Indices: 32663--32879 Score: 197
Period size: 30 Copynumber: 7.3 Consensus size: 29
32653 TAATTTTAAG
32663 AAAGTTTAAGGGGTTAAAAATGTGATTTT-GA
1 AAAGTTT-A-GGGTT-AAAATGTGATTTTGGA
32694 GAAAGTTTAGGGTTAAAATGTGATTTTAGGA
1 -AAAGTTTAGGGTTAAAATGTGATTTT-GGA
* * * *
32725 AAGGTTTAGGG-T-CAGTGTAATTTTGGA
1 AAAGTTTAGGGTTAAAATGTGATTTTGGA
* * *
32752 AAAGTTTAAGGGGTAAAATGTAATTTTAGA
1 AAAGTTT-AGGGTTAAAATGTGATTTTGGA
* * *
32782 AAAGTTCAAGGGTCAAAATATGATTTTGGA
1 AAAGTT-TAGGGTTAAAATGTGATTTTGGA
* * *
32812 AAAATTTAAGGGTCAAAATGTAATTTTGGA
1 AAAGTTT-AGGGTTAAAATGTGATTTTGGA
* *
32842 AAAGTTTAGAGGTCAAAATATGATTTTGGA
1 AAAGTTTAG-GGTTAAAATGTGATTTTGGA
32872 AAAGTTTA
1 AAAGTTTA
32880 CGGACCTCTT
Statistics
Matches: 156, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
27 9 0.06
28 13 0.08
29 17 0.11
30 107 0.69
31 3 0.02
32 7 0.04
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAGTTTAGGGTTAAAATGTGATTTTGGA
Found at i:32753 original size:118 final size:119
Alignment explanation
Indices: 32621--32856 Score: 270
Period size: 118 Copynumber: 2.0 Consensus size: 119
32611 GGGGTCAAAA
* *
32621 TGTAATTTTGGGAAAA-TTCGA-GGATCAAAATATAATTTTA-AGAAAGTTTAAGGGGTTAAAAA
1 TGTAATTTTGGGAAAAGTTCAAGGGAT-AAAATATAATTTTAGA-AAAGTTCAA-GGG-TAAAAA
* * * * *
32683 TGTGATTTT-GAGAAAGTTT-AGGGTTAAAATGTGATTTTAGGAAAGGTTTAG-GGTCAG
62 TATGATTTTGGA-AAAATTTAAGGGTCAAAATGTAATTTT-GGAAAAGTTTAGAGGTCAG
* * * *
32740 TGTAATTTT-GGAAAAGTTTAAGGGGTAAAATGTAATTTTAGAAAAGTTCAAGGGTCAAAATATG
1 TGTAATTTTGGGAAAAGTTCAAGGGATAAAATATAATTTTAGAAAAGTTCAAGGGTAAAAATATG
32804 ATTTTGGAAAAATTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGTCA
66 ATTTTGGAAAAATTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGTCA
32857 AAATATGATT
Statistics
Matches: 100, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
117 30 0.30
118 33 0.33
119 33 0.33
120 4 0.04
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (119 bp):
TGTAATTTTGGGAAAAGTTCAAGGGATAAAATATAATTTTAGAAAAGTTCAAGGGTAAAAATATG
ATTTTGGAAAAATTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGTCAG
Found at i:32830 original size:60 final size:59
Alignment explanation
Indices: 32612--32879 Score: 244
Period size: 60 Copynumber: 4.5 Consensus size: 59
32602 CAATGAATTG
* ** * *
32612 GGGTCAAAATGTAATTTTGGGAAAA-TTCGAGGATCAAAATATAATTTTA-AGAAAGTTTAA
1 GGGTCAAAATGTGATTTT-GGAAAAGTTTAAGGGTCAAAATGTAATTTTAGA-AAAG-TTAA
* * * * *
32672 GGGGTTAAAAATGTGATTTT-GAGAAAGTTT-AGGGTTAAAATGTGATTTTAGGAAAGGTTTA
1 -GGG-TCAAAATGTGATTTTGGA-AAAGTTTAAGGGTCAAAATGTAATTTTA-GAAAAGTTAA
* *
32733 GGGTC--AGTGTAATTTTGGAAAAGTTTAAGGGGT-AAAATGTAATTTTAGAAAAGTTCAA
1 GGGTCAAAATGTGATTTTGGAAAAGTTTAA-GGGTCAAAATGTAATTTTAGAAAAGTT-AA
* * * *
32791 GGGTCAAAATATGATTTTGGAAAAATTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTA
1 GGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTAA
*
32850 GAGGTCAAAATATGATTTTGGAAAAGTTTA
1 G-GGTCAAAATGTGATTTTGGAAAAGTTTA
32880 CGGACCTCTT
Statistics
Matches: 172, Mismatches: 22, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
57 23 0.13
58 22 0.13
59 11 0.06
60 72 0.42
61 25 0.15
62 18 0.10
63 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (59 bp):
GGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTAA
Found at i:34057 original size:21 final size:21
Alignment explanation
Indices: 34018--34057 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
34008 CTTCCCTTTT
* * *
34018 TATTTATTACTTATTTATTAA
1 TATTTATTAATCATGTATTAA
34039 TATTTATTAATCATGTATT
1 TATTTATTAATCATGTATT
34058 TATTATACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (21 bp):
TATTTATTAATCATGTATTAA
Found at i:37447 original size:6 final size:6
Alignment explanation
Indices: 37438--37479 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
37428 AATTTTTTTG
* * *
37438 TTTTCT TTTTCT TTTTCG TTTTCT TTTTCG TTTTCG TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
37480 AGTGAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (6 bp):
TTTTCT
Found at i:37452 original size:18 final size:18
Alignment explanation
Indices: 37431--37479 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
37421 GTTCTACAAT
*
37431 TTTTTTGTTTTCTTTTTC
1 TTTTTCGTTTTCTTTTTC
37449 TTTTTCGTTTTCTTTTTC
1 TTTTTCGTTTTCTTTTTC
*
37467 GTTTTCGTTTTCT
1 TTTTTCGTTTTCT
37480 AGTGAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (18 bp):
TTTTTCGTTTTCTTTTTC
Found at i:37453 original size:12 final size:12
Alignment explanation
Indices: 37438--37478 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
37428 AATTTTTTTG
*
37438 TTTTCTTTTTCT
1 TTTTCGTTTTCT
37450 TTTTCGTTTTCT
1 TTTTCGTTTTCT
*
37462 TTTTCGTTTTCG
1 TTTTCGTTTTCT
37474 TTTTC
1 TTTTC
37479 TAGTGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTCGTTTTCT
Found at i:46680 original size:17 final size:17
Alignment explanation
Indices: 46658--46752 Score: 93
Period size: 17 Copynumber: 5.4 Consensus size: 17
46648 AACTTTTGAT
*
46658 TTTAAATTTATATTAAG
1 TTTAAATTTATATTAAA
** *
46675 TTTAAATTGGTTTTAAA
1 TTTAAATTTATATTAAA
*
46692 TTTAAATTTATTTTAAA
1 TTTAAATTTATATTAAA
*
46709 TTTAAATTTAAAATTTAAA
1 TTTAAATTT-ATA-TTAAA
46728 TTTAAATTTAGT-TTAAA
1 TTTAAATTTA-TATTAAA
46745 TTTGAAAT
1 TTT-AAAT
46753 GGTTTTAAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
17 45 0.69
18 6 0.09
19 14 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATATTAAA
Found at i:46695 original size:6 final size:6
Alignment explanation
Indices: 46686--46752 Score: 84
Period size: 6 Copynumber: 11.2 Consensus size: 6
46676 TTAAATTGGT
*
46686 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTAAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
*
46734 TTT-AG TTTAAA TTTGAAA T
1 TTTAAA TTTAAA TTT-AAA T
46753 GGTTTTAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
5 8 0.15
6 35 0.66
7 10 0.19
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:46706 original size:28 final size:28
Alignment explanation
Indices: 46657--46710 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
46647 AAACTTTTGA
*
46657 TTTTAAATTTATATTAAGTTTAAATTGG
1 TTTTAAATTTAAATTAAGTTTAAATTGG
* *
46685 TTTTAAATTTAAATTTATTTTAAATT
1 TTTTAAATTTAAATTAAGTTTAAATT
46711 TAAATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (28 bp):
TTTTAAATTTAAATTAAGTTTAAATTGG
Found at i:46742 original size:24 final size:24
Alignment explanation
Indices: 46686--46752 Score: 84
Period size: 23 Copynumber: 2.8 Consensus size: 24
46676 TTAAATTGGT
*
46686 TTTAAATTTAAATTT-ATTTTAAA
1 TTTAAATTTAAATTTAAATTTAAA
46709 TTTAAATTTAAAATTTAAATTTAAA
1 TTTAAATTT-AAATTTAAATTTAAA
*
46734 TTT-AGTTTAAATTTGAAAT
1 TTTAAATTTAAATTT-AAAT
46753 GGTTTTAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 15 0.38
24 14 0.36
25 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (24 bp):
TTTAAATTTAAATTTAAATTTAAA
Found at i:48394 original size:30 final size:29
Alignment explanation
Indices: 48360--48581 Score: 93
Period size: 30 Copynumber: 7.7 Consensus size: 29
48350 CTAAACTTTT
*
48360 CAAAAATTGCATTTTGCCCCTTGAACTTC
1 CAAAAATTACATTTTGCCCCTTGAACTTC
* * *
48389 ACAAAATTTACATTTTTG-ACCTTGAACTTTT
1 -CAAAAATTACA-TTTTGCCCCTTGAAC-TTC
* *
48420 CAAAAATT--ATTTTACCCC-TAAACTTC
1 CAAAAATTACATTTTGCCCCTTGAACTTC
* **
48446 CTAAAATTACATTTTTGACCCC-CAAAC-TC
1 CAAAAATTACA-TTTTG-CCCCTTGAACTTC
* * * *
48475 CTAAAATTGA-ATTTTG-ACTTTAAACTTC
1 CAAAAATT-ACATTTTGCCCCTTGAACTTC
* ** * *
48503 CAAAAATTACCTTTTTACCTTTAAACTTC
1 CAAAAATTACATTTTGCCCCTTGAACTTC
* * *
48532 CTAAAATTGCATTTTTGACCCC-TAAACTTC
1 CAAAAATTACA-TTTTG-CCCCTTGAACTTC
* * *
48562 CTAGAATTACATTTTTCCCC
1 CAAAAATTACATTTTGCCCC
48582 AAACTTTCTA
Statistics
Matches: 150, Mismatches: 28, Indels: 30
0.72 0.13 0.14
Matches are distributed among these distances:
26 10 0.07
27 13 0.09
28 26 0.17
29 38 0.25
30 54 0.36
31 9 0.06
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
CAAAAATTACATTTTGCCCCTTGAACTTC
Found at i:48477 original size:29 final size:29
Alignment explanation
Indices: 48429--48608 Score: 183
Period size: 29 Copynumber: 6.3 Consensus size: 29
48419 TCAAAAATTA
48429 TTTTACCCCTAAACTTCCTAAAATTACAT
1 TTTTACCCCTAAACTTCCTAAAATTACAT
*
48458 TTTTGACCCCCAAAC-TCCTAAAATTGA-AT
1 TTTT-ACCCCTAAACTTCCTAAAATT-ACAT
* ** * *
48487 TTTGA-CTTTAAACTTCCAAAAATTACCT
1 TTTTACCCCTAAACTTCCTAAAATTACAT
** *
48515 TTTTACCTTTAAACTTCCTAAAATTGCAT
1 TTTTACCCCTAAACTTCCTAAAATTACAT
*
48544 TTTTGACCCCTAAACTTCCTAGAATTACAT
1 TTTT-ACCCCTAAACTTCCTAAAATTACAT
*
48574 TTTT-CCCC-AAACTTTCTAAAATTACCA-
1 TTTTACCCCTAAACTTCCTAAAATTA-CAT
48601 TTTTACCC
1 TTTTACCC
48609 TCGAATGTCC
Statistics
Matches: 126, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
27 24 0.19
28 24 0.19
29 43 0.34
30 35 0.28
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTTACCCCTAAACTTCCTAAAATTACAT
Found at i:48586 original size:57 final size:57
Alignment explanation
Indices: 48428--48596 Score: 193
Period size: 57 Copynumber: 3.0 Consensus size: 57
48418 TTCAAAAATT
48428 ATTTT-ACCCCTAAACTTCCTAAAATTACATTTTTGACCCCCAAAC-TCCTAAAATTGA
1 ATTTTGACCCCTAAACTTCCTAAAATTACATTTTT-A-CCCCAAACTTCCTAAAATTGA
** * * **
48485 ATTTTGA-CTTTAAACTTCCAAAAATTACCTTTTTACCTTTAAACTTCCTAAAATTGCA
1 ATTTTGACCCCTAAACTTCCTAAAATTACATTTTTACC-CCAAACTTCCTAAAATTG-A
* * *
48543 TTTTTGACCCCTAAACTTCCTAGAATTACATTTTT-CCCCAAACTTTCTAAAATT
1 ATTTTGACCCCTAAACTTCCTAAAATTACATTTTTACCCCAAACTTCCTAAAATT
48597 ACCATTTTAC
Statistics
Matches: 92, Mismatches: 15, Indels: 10
0.79 0.13 0.09
Matches are distributed among these distances:
55 2 0.02
56 5 0.05
57 53 0.58
58 10 0.11
59 22 0.24
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (57 bp):
ATTTTGACCCCTAAACTTCCTAAAATTACATTTTTACCCCAAACTTCCTAAAATTGA
Found at i:48586 original size:86 final size:86
Alignment explanation
Indices: 48428--48608 Score: 222
Period size: 86 Copynumber: 2.1 Consensus size: 86
48418 TTCAAAAATT
48428 ATTTTACCCCTAAACTTCCTAAAATTACATTTTTGACCCCCAAACTCCTAAAATTGAATTTTGAC
1 ATTTTACCCCTAAACTTCCTAAAATTACATTTTTGACCCCCAAACTCCTAAAATTGAATTTTGAC
***
48493 TTTAAACTTCCAAAAATTACC
66 CCCAAACTTCCAAAAATTACC
* ** * * *
48514 TTTTTACCTTTAAACTTCCTAAAATTGCATTTTTGACCCCTAAACTTCCTAGAATT-ACATTTT-
1 ATTTTACCCCTAAACTTCCTAAAATTACATTTTTGACCCCCAAAC-TCCTAAAATTGA-ATTTTG
* * *
48577 TCCCCAAACTTTCTAAAATTACC
64 ACCCCAAACTTCCAAAAATTACC
48600 ATTTTACCC
1 ATTTTACCC
48609 TCGAATGTCC
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
86 65 0.82
87 14 0.18
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (86 bp):
ATTTTACCCCTAAACTTCCTAAAATTACATTTTTGACCCCCAAACTCCTAAAATTGAATTTTGAC
CCCAAACTTCCAAAAATTACC
Found at i:48633 original size:29 final size:29
Alignment explanation
Indices: 48591--48695 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 29
48581 CAAACTTTCT
48591 AAAATTACCA-TTTT-ACCCTCGAATGTCCA
1 AAAATT-CCATTTTTGA-CCTCGAATGTCCA
** * *
48620 AAAATTTTATTTTTGACCTCGAACTTTTCA
1 AAAATTCCATTTTTGACCTCGAA-TGTCCA
*
48650 AAAATTACCA-TTTT-ACCTCGGATGTCCA
1 AAAATT-CCATTTTTGACCTCGAATGTCCA
48678 AAAATTCCATTTTTGACC
1 AAAATTCCATTTTTGACC
48696 CTGAACCTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
27 3 0.05
28 15 0.25
29 27 0.44
30 15 0.25
31 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (29 bp):
AAAATTCCATTTTTGACCTCGAATGTCCA
Found at i:48661 original size:59 final size:58
Alignment explanation
Indices: 48583--48724 Score: 198
Period size: 58 Copynumber: 2.4 Consensus size: 58
48573 TTTTTCCCCA
* **
48583 AACTTTCTAAAATTACCATTTTACCCTCGAATGTCCAAAAATTTTATTTTTGA-CCTCG
1 AACTTTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACCCT-G
*
48641 AACTTTTCAAAAATTACCATTTTA-CCTCGGATGTCCAAAAATTCCATTTTTGACCCTG
1 AAC-TTTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACCCTG
* *
48699 AACCTTCAAAAATTACTATTTTACCC
1 AACTTTCAAAAATTACCATTTTACCC
48725 CCAAAGTATC
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
57 18 0.24
58 35 0.47
59 22 0.29
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.37
Consensus pattern (58 bp):
AACTTTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACCCTG
Found at i:50510 original size:114 final size:112
Alignment explanation
Indices: 50341--50569 Score: 352
Period size: 114 Copynumber: 2.0 Consensus size: 112
50331 CAGAAGCAAA
50341 TAAGACTCAATGCACCAGTAGAATTCTCCCAACAAAGTCTCCCCCCTTTGATAGTCTCCTCCTCA
1 TAAGACTCAATGCACCAGTAGAATTCTCCCAACAAAGTCTCCCCCCTTTGATAG--T-CTCCTCA
* *
50406 AAAATAGCTTCTAGCATCAT-CATCTTTTCTTTTCTCCCATTTTTTGATC
63 AAAATAGCTTCCAGCATCATACATCTCTTCTTTTCTCCCATTTTTTGATC
* * *
50455 TAAGTCTCAATGCAGCAGTAGAATTCTCCCAACAAAGTCTCCCCCCTTTGGTAGTCTCCTCAAAA
1 TAAGACTCAATGCACCAGTAGAATTCTCCCAACAAAGTCTCCCCCCTTTGATAGTCTCCTCAAAA
50520 ATAGCTTCCAGCATCATCAAGCATCTCTTCTTTTCTCCCATTTTTTGATC
66 ATAGCTTCCAGCATCAT--A-CATCTCTTCTTTTCTCCCATTTTTTGATC
50570 AACAAAATGC
Statistics
Matches: 106, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
111 26 0.25
112 1 0.01
114 51 0.48
115 28 0.26
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.34
Consensus pattern (112 bp):
TAAGACTCAATGCACCAGTAGAATTCTCCCAACAAAGTCTCCCCCCTTTGATAGTCTCCTCAAAA
ATAGCTTCCAGCATCATACATCTCTTCTTTTCTCCCATTTTTTGATC
Found at i:52689 original size:16 final size:17
Alignment explanation
Indices: 52643--52682 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
52633 TTAAAAAAAT
*
52643 TATATTTGTTAATTTTA
1 TATATTTATTAATTTTA
*
52660 -ATATTTAATAATTTTA
1 TATATTTATTAATTTTA
52676 TATATTT
1 TATATTT
52683 TTTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TATATTTATTAATTTTA
Done.