Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014895.1 Kokia drynarioides strain JFW-HI SEQ_129938, 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: 154167
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 498 characters in sequence are not A, C, G, or T
Found at i:4041 original size:20 final size:20
Alignment explanation
Indices: 4016--4058 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
4006 TATGAGTAAA
4016 ATAGTTTTTTACTCTGTTTT
1 ATAGTTTTTTACTCTGTTTT
4036 ATAGTTTTTTACTCTGTTTT
1 ATAGTTTTTTACTCTGTTTT
4056 ATA
1 ATA
4059 ATAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63
Consensus pattern (20 bp):
ATAGTTTTTTACTCTGTTTT
Found at i:12018 original size:45 final size:45
Alignment explanation
Indices: 11949--12060 Score: 188
Period size: 45 Copynumber: 2.5 Consensus size: 45
11939 TTCTCGAGCC
* **
11949 TTTTGCTTTCTTTTTGATCATCTTTCTTATGCAAAGACTCCTTAT
1 TTTTACTTTCTTTGCGATCATCTTTCTTATGCAAAGACTCCTTAT
11994 TTTTACTTTCTTTGCGATCATCTTTCTTATGCAAAGACTCCTTAT
1 TTTTACTTTCTTTGCGATCATCTTTCTTATGCAAAGACTCCTTAT
*
12039 TTTTACTTTCTTTGCTATCATC
1 TTTTACTTTCTTTGCGATCATC
12061 CTTGTTCTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.53
Consensus pattern (45 bp):
TTTTACTTTCTTTGCGATCATCTTTCTTATGCAAAGACTCCTTAT
Found at i:12993 original size:2 final size:2
Alignment explanation
Indices: 12986--13020 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12976 GCCTAATCAT
12986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13021 TTTTTTNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13768 original size:19 final size:19
Alignment explanation
Indices: 13740--13785 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
13730 GGTGTTAATT
*
13740 GGTGGTAAAATATGAGTTA
1 GGTGGCAAAATATGAGTTA
13759 GGTGGCAAAATATGAGTTA
1 GGTGGCAAAATATGAGTTA
13778 GGTGGCAA
1 GGTGGCAA
13786 TTTCCTCCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.35, T:0.26
Consensus pattern (19 bp):
GGTGGCAAAATATGAGTTA
Found at i:24176 original size:18 final size:20
Alignment explanation
Indices: 24136--24178 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
24126 ATTGAAGTTT
24136 AAAA-TTCAAAATATTTATA
1 AAAATTTCAAAATATTTATA
24155 AAAATTTCAAAAT-TTTA-A
1 AAAATTTCAAAATATTTATA
24173 AAAATT
1 AAAATT
24179 AAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.30
19 8 0.35
20 8 0.35
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTTCAAAATATTTATA
Found at i:31689 original size:15 final size:17
Alignment explanation
Indices: 31665--31702 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
31655 AAATAAAAAC
31665 ATATAAAATT-AATA-A
1 ATATAAAATTAAATATA
*
31680 ATATATAATTAAATATA
1 ATATAAAATTAAATATA
31697 ATATAA
1 ATATAA
31703 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 9 0.47
16 4 0.21
17 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATAAAATTAAATATA
Found at i:31699 original size:17 final size:15
Alignment explanation
Indices: 31652--31702 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
31642 AAAAATTTTA
*
31652 ATAAAA-TAAAAACAT
1 ATAAAATTAATAA-AT
31667 ATAAAATTAATAAAT
1 ATAAAATTAATAAAT
*
31682 ATATAATTAAATATAAT
1 ATAAAATT-AATA-AAT
31699 ATAA
1 ATAA
31703 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 15 0.50
16 9 0.30
17 6 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAATTAATAAAT
Found at i:35761 original size:21 final size:21
Alignment explanation
Indices: 35735--35775 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
35725 TATTTTCTAT
35735 ATTATAAGA-AAATAAAAAGAA
1 ATTATAA-ATAAATAAAAAGAA
35756 ATTATAAATTAAATAAAAAG
1 ATTATAAA-TAAATAAAAAG
35776 TAAAATTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 7 0.39
22 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (21 bp):
ATTATAAATAAATAAAAAGAA
Found at i:36218 original size:35 final size:34
Alignment explanation
Indices: 36137--36218 Score: 78
Period size: 35 Copynumber: 2.3 Consensus size: 34
36127 TGTATTTAAA
*
36137 AATTCTATTTAAGTAATAATTCTAATTTCGAATTT
1 AATT-TATTTAAGTAATAATTCTAATTTCAAATTT
* *
36172 ACATGTT-TTTAATTAATAATTGTAATTT-AAATTCT
1 A-AT-TTATTTAAGTAATAATTCTAATTTCAAATT-T
36207 AATTATATTTAA
1 AATT-TATTTAA
36219 ATGGATAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
33 1 0.03
34 7 0.18
35 27 0.69
36 3 0.08
37 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (34 bp):
AATTTATTTAAGTAATAATTCTAATTTCAAATTT
Found at i:38784 original size:24 final size:24
Alignment explanation
Indices: 38725--38785 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
38715 GACTAATAAA
* *
38725 AGTTTAACTCAAACAAATAAATAT
1 AGTTTAACTGAAACAAATAAATAG
*
38749 AGTTTAATTGAAACAAATAAATAG
1 AGTTTAACTGAAACAAATAAATAG
38773 AGTTTAACTGAAA
1 AGTTTAACTGAAA
38786 GATTATTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAATAG
Found at i:43607 original size:23 final size:23
Alignment explanation
Indices: 43505--43604 Score: 164
Period size: 23 Copynumber: 4.3 Consensus size: 23
43495 ACACTAGCGC
43505 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
43528 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
43551 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
43574 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
43597 GCTCTCTG
1 GCTCTCTG
43605 TTTTCCAGCA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:44996 original size:23 final size:23
Alignment explanation
Indices: 44894--44993 Score: 164
Period size: 23 Copynumber: 4.3 Consensus size: 23
44884 ACACTAGCGC
44894 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
44917 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
44940 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
44963 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
44986 GCTCTCTG
1 GCTCTCTG
44994 TTTTCCAGCA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:46255 original size:43 final size:43
Alignment explanation
Indices: 46207--46296 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
46197 TCTGCAATTG
46207 AGTGGCCAGCAAAGTAAAGGACGGATTGGATCCAAGTCATTTC
1 AGTGGCCAGCAAAGTAAAGGACGGATTGGATCCAAGTCATTTC
46250 AGTGGCCAGCAAAGTAAAGGACGGATTGGATCCAAGTCATTTC
1 AGTGGCCAGCAAAGTAAAGGACGGATTGGATCCAAGTCATTTC
46293 AGTG
1 AGTG
46297 CAGTTTTCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (43 bp):
AGTGGCCAGCAAAGTAAAGGACGGATTGGATCCAAGTCATTTC
Found at i:54107 original size:18 final size:19
Alignment explanation
Indices: 54076--54114 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
54066 CTGATAAAAT
* *
54076 ATTTATAAATTATAATTCA
1 ATTTATAAAATATAATACA
54095 ATTTA-AAAATATAATACA
1 ATTTATAAAATATAATACA
54113 AT
1 AT
54115 CATTCAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTATAAAATATAATACA
Found at i:59857 original size:2 final size:2
Alignment explanation
Indices: 59850--59895 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
59840 CAAATCAAAT
59850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59892 TA TA
1 TA TA
59896 AAATGATCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60303 original size:19 final size:19
Alignment explanation
Indices: 60262--60303 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
60252 TATATTTAGT
*
60262 TTTAAATTTAATTTTGATA
1 TTTAAATTTAATTTCGATA
* *
60281 TTTAAATTTAGTTTCGATG
1 TTTAAATTTAATTTCGATA
60300 TTTA
1 TTTA
60304 TTGAATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TTTAAATTTAATTTCGATA
Found at i:62444 original size:30 final size:30
Alignment explanation
Indices: 62408--62471 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
62398 AATTTGAGTG
62408 AAAAATAATAATTTAGATACCAAAATGTGA
1 AAAAATAATAATTTAGATACCAAAATGTGA
*
62438 AAAAATAATAATTTAGATACCGAAATGTGA
1 AAAAATAATAATTTAGATACCAAAATGTGA
62468 AAAA
1 AAAA
62472 TGATATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (30 bp):
AAAAATAATAATTTAGATACCAAAATGTGA
Found at i:62483 original size:31 final size:30
Alignment explanation
Indices: 62405--62483 Score: 117
Period size: 30 Copynumber: 2.6 Consensus size: 30
62395 ATCAATTTGA
62405 GTGAAAAATA-ATAATTTAGATACCAAAAT
1 GTGAAAAATATATAATTTAGATACCAAAAT
*
62434 GTGAAAAA-ATAATAATTTAGATACCGAAAT
1 GTGAAAAATAT-ATAATTTAGATACCAAAAT
62464 GTGAAAAATGATATAATTTA
1 GTGAAAAAT-ATATAATTTA
62484 AGTATTAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
28 1 0.02
29 8 0.18
30 26 0.58
31 8 0.18
32 2 0.04
ACGTcount: A:0.53, C:0.05, G:0.13, T:0.29
Consensus pattern (30 bp):
GTGAAAAATATATAATTTAGATACCAAAAT
Found at i:67789 original size:4 final size:4
Alignment explanation
Indices: 67765--67882 Score: 119
Period size: 4 Copynumber: 29.0 Consensus size: 4
67755 TTAAAAATAT
* * * * *
67765 TTTA TTTA GTTA GTTA TTTTA TTTA TTTA GTTA ATTA ATTA TTTA TTTA
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
67814 TTTTA TTTA TTTA GTTA ATTA TTTA GTTA TTTA TTTA TTTA CTTA TTTA
1 -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
67863 CTTA TTTA TTAA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA
67883 CATCGTAAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
4 89 0.93
5 7 0.07
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:71440 original size:2 final size:2
Alignment explanation
Indices: 71435--71469 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
71425 TTAAAAAATA
71435 AT AT AT AT AT 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 AT AT AT AT AT A
71470 ACATTATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72337 original size:24 final size:24
Alignment explanation
Indices: 72310--72357 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
72300 AATTATTTTT
72310 TAAATAATATTTAAATTAATTATA
1 TAAATAATATTTAAATTAATTATA
72334 TAAATAATATTTAAATTAATTATA
1 TAAATAATATTTAAATTAATTATA
72358 ATGTCTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAATAATATTTAAATTAATTATA
Found at i:72353 original size:12 final size:11
Alignment explanation
Indices: 72308--72349 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
72298 TTAATTATTT
72308 TTTAAATAATA
1 TTTAAATAATA
72319 TTTAAATTAATTA
1 TTTAAA-TAA-TA
*
72332 TATAAATAATA
1 TTTAAATAATA
72343 TTTAAAT
1 TTTAAAT
72350 TAATTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTAAATAATA
Found at i:75539 original size:31 final size:30
Alignment explanation
Indices: 75492--75591 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 30
75482 CAAAGACTAA
*
75492 AAAGTGTCTAAAATTTTGTTTTTTTAATTTTT
1 AAAG-GTCCAAAATTTT-TTTTTTTAATTTTT
* ** *
75524 AAAGGTTCAAAATTTTTTTTACTAACTTTT
1 AAAGGTCCAAAATTTTTTTTTTTAATTTTT
*
75554 AAGGGGTCCAAAATTTTTTTTTTTTTCAATTTTT
1 AA-AGGTCCAAAA--TTTTTTTTTTT-AATTTTT
75588 AAAG
1 AAAG
75592 AACCTAAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
30 13 0.25
31 18 0.34
32 4 0.08
33 10 0.19
34 8 0.15
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (30 bp):
AAAGGTCCAAAATTTTTTTTTTTAATTTTT
Found at i:77055 original size:32 final size:30
Alignment explanation
Indices: 77009--77204 Score: 104
Period size: 31 Copynumber: 6.4 Consensus size: 30
76999 ATTAAAAAAA
*
77009 TTAGGTACCAAATTAGAAAAAAATAGTCAAG
1 TTAGATACCAAATTAGAAAAAAAT-GTCAAG
**
77040 TTCAGATACCAAATTAGATCCCCAAAA-GT--A-
1 TT-AGATACCAAATTAGA---AAAAAATGTCAAG
* *
77070 TTAG-TACCAACTTA-AAAAAAAGTGTTAAG
1 TTAGATACCAAATTAGAAAAAAA-TGTCAAG
** *
77099 TTTAGGCACCAAATTAGAAAAAAGTGTCAAG
1 -TTAGATACCAAATTAGAAAAAAATGTCAAG
* * **
77130 TTTGAGTACCAAGTT-GAATAAAAA--AAAAG
1 TTAGA-TACCAAATTAGAA-AAAAATGTCAAG
*
77159 TTTAGATATCAAATTAGGAAAAAAATGTCAAG
1 -TTAGATACCAAATTA-GAAAAAAATGTCAAG
77191 TTCAGATACCAAAT
1 TT-AGATACCAAAT
77205 GTTATATTTA
Statistics
Matches: 122, Mismatches: 23, Indels: 39
0.66 0.12 0.21
Matches are distributed among these distances:
24 4 0.03
26 2 0.02
27 1 0.01
28 10 0.08
29 12 0.10
30 21 0.17
31 33 0.27
32 33 0.27
33 2 0.02
35 4 0.03
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (30 bp):
TTAGATACCAAATTAGAAAAAAATGTCAAG
Found at i:78876 original size:22 final size:25
Alignment explanation
Indices: 78851--78901 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
78841 TATTTTGGGT
*
78851 TTAT-TTTCAAAATT-TATTAA-AA
1 TTATATTTCAAAATTATATCAATAA
*
78873 TTATATTTCACAATTATATCAATAA
1 TTATATTTCAAAATTATATCAATAA
78898 TTAT
1 TTAT
78902 CATATGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 9 0.38
24 5 0.21
25 6 0.25
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (25 bp):
TTATATTTCAAAATTATATCAATAA
Found at i:81227 original size:48 final size:49
Alignment explanation
Indices: 81174--81274 Score: 116
Period size: 54 Copynumber: 2.0 Consensus size: 49
81164 AACTTTAGTC
81174 ATTTTAG-TATGCTTAAATTTAAGATTTAAT-TCTTATACTTTAATTTCA
1 ATTTTAGATATGCTTAAATTTAAGATTTAATCT-TTATACTTTAATTTCA
* *
81222 ATTTTAGTCCTAATATGCTTAAATTTGATATTTAATCTTTATACTTTAATTTC
1 ATTTTAG-----ATATGCTTAAATTTAAGATTTAATCTTTATACTTTAATTTC
81275 TAACATCATT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
48 7 0.16
54 36 0.82
55 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (49 bp):
ATTTTAGATATGCTTAAATTTAAGATTTAATCTTTATACTTTAATTTCA
Found at i:81516 original size:22 final size:24
Alignment explanation
Indices: 81471--81524 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
81461 TAAAATAATT
* *
81471 TTATAAAATGTATTCAAATTTTAA
1 TTATAAAATATATTCAAATATTAA
81495 TTATAAAATATA-T-AAATATTAA
1 TTATAAAATATATTCAAATATTAA
81517 -TATAAAAT
1 TTATAAAAT
81525 CATACTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.29
22 8 0.29
23 1 0.04
24 11 0.39
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TTATAAAATATATTCAAATATTAA
Found at i:91028 original size:24 final size:25
Alignment explanation
Indices: 91001--91048 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
90991 GTAAAAAAAA
*
91001 TATAAATT-TAAATATAGTTGAATT
1 TATAAATTCAAAATATAGTTGAATT
*
91025 TATAAATTCAAAATATTGTTGAAT
1 TATAAATTCAAAATATAGTTGAAT
91049 AGTTTATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (25 bp):
TATAAATTCAAAATATAGTTGAATT
Found at i:105016 original size:17 final size:17
Alignment explanation
Indices: 104985--105018 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
104975 TTTAATTAAC
**
104985 TTAATTTAATTTAATAA
1 TTAATTTAACATAATAA
105002 TTAATTTAACATAATAA
1 TTAATTTAACATAATAA
105019 ATTTCTTTTG
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTTAACATAATAA
Found at i:114478 original size:8 final size:8
Alignment explanation
Indices: 114465--114490 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
114455 TTAAACTCTC
114465 TTAAAATT
1 TTAAAATT
114473 TTAAAATT
1 TTAAAATT
114481 TTAAAATT
1 TTAAAATT
114489 TT
1 TT
114491 CAATTAAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTAAAATT
Found at i:118048 original size:16 final size:18
Alignment explanation
Indices: 118022--118055 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
118012 TTTTTTTAAA
118022 TTATGTAAAAATT-ATAT
1 TTATGTAAAAATTCATAT
118039 TTAT-TAAAAATTCATAT
1 TTATGTAAAAATTCATAT
118056 AAAAATCCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TTATGTAAAAATTCATAT
Found at i:118304 original size:2 final size:2
Alignment explanation
Indices: 118299--118330 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
118289 TTTAAAATAA
*
118299 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
118331 TAAATTACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:118772 original size:16 final size:16
Alignment explanation
Indices: 118735--118772 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
118725 AACGTAAACG
*
118735 CAAAATAATTTAAATT
1 CAAAATAATTTAAATC
*
118751 CGAAATAATTTAAATC
1 CAAAATAATTTAAATC
118767 CAAAAT
1 CAAAAT
118773 TAATCGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (16 bp):
CAAAATAATTTAAATC
Found at i:120967 original size:23 final size:22
Alignment explanation
Indices: 120916--121021 Score: 86
Period size: 23 Copynumber: 4.7 Consensus size: 22
120906 TGTTCAGTAG
* * *
120916 TGTGTGTGCTTACTGTTTCACAC
1 TGTGTGTGCCTACTGATT-GCAC
* *
120939 TTTGTGTGCCTACTGATTTGCGC
1 TGTGTGTGCCTACTGA-TTGCAC
* * * *
120962 TATGTGCGTCTACTGACTGCAC
1 TGTGTGTGCCTACTGATTGCAC
*
120984 TGTGTATGCCTACTGGATTGCAC
1 TGTGTGTGCCTACT-GATTGCAC
*
121007 TGTGTGTGCTTACTG
1 TGTGTGTGCCTACTG
121022 TTTCCCAGCA
Statistics
Matches: 64, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
22 15 0.23
23 47 0.73
24 2 0.03
ACGTcount: A:0.13, C:0.22, G:0.25, T:0.40
Consensus pattern (22 bp):
TGTGTGTGCCTACTGATTGCAC
Found at i:131398 original size:24 final size:24
Alignment explanation
Indices: 131364--131414 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
131354 AATTTGACTC
* *
131364 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
131388 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
131412 AAA
1 AAA
131415 GATTACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:133597 original size:37 final size:37
Alignment explanation
Indices: 133547--133630 Score: 141
Period size: 37 Copynumber: 2.3 Consensus size: 37
133537 AATTAATTAG
133547 GCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAA
1 GCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAA
* *
133584 GCTTTGTGCCTAGTAGGTTTCGTGCCGGTGTTTTCAG
1 GCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAA
*
133621 GCTTCGTGCC
1 GCTTTGTGCC
133631 GATGTTTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.08, C:0.23, G:0.31, T:0.38
Consensus pattern (37 bp):
GCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAA
Found at i:133645 original size:21 final size:21
Alignment explanation
Indices: 133602--133652 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
133592 CCTAGTAGGT
* *
133602 TTCGTGCCGGTGTTTTCAGGC
1 TTCGTGCCGATGTTTTCAAGC
133623 TTCGTGCCGATGTTTTCAAGC
1 TTCGTGCCGATGTTTTCAAGC
*
133644 TTTGTGCCG
1 TTCGTGCCG
133653 GTGACTCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.08, C:0.24, G:0.29, T:0.39
Consensus pattern (21 bp):
TTCGTGCCGATGTTTTCAAGC
Found at i:141666 original size:18 final size:19
Alignment explanation
Indices: 141637--141672 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
141627 AATTTCGTTG
141637 AAATTAAATTAATTGATTT
1 AAATTAAATTAATTGATTT
141656 AAATT-AATTAATTGATT
1 AAATTAAATTAATTGATT
141673 AATAATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
AAATTAAATTAATTGATTT
Found at i:142386 original size:23 final size:23
Alignment explanation
Indices: 142342--142388 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
142332 TATTTTTAAA
*
142342 GTTTATTTGAAAATATATATACT
1 GTTTATTTGAAAAAATATATACT
142365 GTTTATTTGAAAAAATATATACT
1 GTTTATTTGAAAAAATATATACT
142388 G
1 G
142389 ATACTATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (23 bp):
GTTTATTTGAAAAAATATATACT
Found at i:144603 original size:30 final size:27
Alignment explanation
Indices: 144512--144606 Score: 136
Period size: 27 Copynumber: 3.4 Consensus size: 27
144502 GGGATCTTCC
144512 TCATCTTCTTCCTCAGTTGAAGACCCT
1 TCATCTTCTTCCTCAGTTGAAGACCCT
144539 TCATCTTCTTCCTCAGTTGAAGACCCT
1 TCATCTTCTTCCTCAGTTGAAGACCCT
* **
144566 TCTTCTTCTTCCTCAGAAGAAGTCACCTCT
1 TCATCTTCTTCCTCAGTTGAAG--ACC-CT
144596 TCATCTTCTTC
1 TCATCTTCTTC
144607 AGAGGAAACA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
27 46 0.75
29 3 0.05
30 12 0.20
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (27 bp):
TCATCTTCTTCCTCAGTTGAAGACCCT
Found at i:145271 original size:18 final size:18
Alignment explanation
Indices: 145233--145273 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
145223 TAAAAAATTC
*
145233 ATAT-TTTTACATTTAAT
1 ATATATTTTACATTTAAA
145250 ATATATTTTA-ATTTCAAA
1 ATATATTTTACATTT-AAA
145268 ATATAT
1 ATATAT
145274 AGTAATAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATTTTACATTTAAA
Found at i:145919 original size:34 final size:34
Alignment explanation
Indices: 145876--145944 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
145866 TTTTTTCTTT
145876 TTCATTTTATAAATCGGTTAATTTTCAACTTTAG
1 TTCATTTTATAAATCGGTTAATTTTCAACTTTAG
145910 TTCATTTTATAAATCGGTTAATTTTCAACTTTAG
1 TTCATTTTATAAATCGGTTAATTTTCAACTTTAG
145944 T
1 T
145945 CCTTTTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.51
Consensus pattern (34 bp):
TTCATTTTATAAATCGGTTAATTTTCAACTTTAG
Found at i:145933 original size:17 final size:17
Alignment explanation
Indices: 145879--145934 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
145869 TTTCTTTTTC
145879 ATTTTATAAATCGGTTA
1 ATTTTATAAATCGGTTA
** ** *
145896 ATTTTCA-ACTTTAGTTC
1 ATTTT-ATAAATCGGTTA
145913 ATTTTATAAATCGGTTA
1 ATTTTATAAATCGGTTA
145930 ATTTT
1 ATTTT
145935 CAACTTTAGT
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
16 1 0.04
17 25 0.93
18 1 0.04
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (17 bp):
ATTTTATAAATCGGTTA
Found at i:146035 original size:54 final size:56
Alignment explanation
Indices: 145927--146035 Score: 125
Period size: 54 Copynumber: 1.9 Consensus size: 56
145917 TATAAATCGG
* * *
145927 TTAATTTTCAACTTTAGTCCTTTTAATATGCTTTAATTTGGGATTTAATTCTTATATT
1 TTAATTTTCAACTTTAGTCC--TTAATATGCTTTAATTTGAGATTAAATCCTTATATT
* *
145985 TTAA-TTTCAATTTTAGTCC-TAATATG-TTTAAATTTGATATTAAATCCTTAT
1 TTAATTTTCAACTTTAGTCCTTAATATGCTTT-AATTTGAGATTAAATCCTTAT
146036 GCTTTAATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
53 3 0.07
54 24 0.53
57 14 0.31
58 4 0.09
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.53
Consensus pattern (56 bp):
TTAATTTTCAACTTTAGTCCTTAATATGCTTTAATTTGAGATTAAATCCTTATATT
Found at i:146380 original size:19 final size:18
Alignment explanation
Indices: 146347--146382 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
146337 AAATAAATTT
146347 TATATTTATTGTATTAAA
1 TATATTTATTGTATTAAA
*
146365 TATATTATATTTTATTAA
1 TATATT-TATTGTATTAA
146383 TTTCAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TATATTTATTGTATTAAA
Found at i:147873 original size:19 final size:19
Alignment explanation
Indices: 147851--147909 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
147841 TTTTTTAATT
*
147851 TTTTTAAAAAACCTT-AAAA
1 TTTTTAAAAAA-ATTAAAAA
*
147870 TTTTGAATAAAAATTAAAAA
1 TTTTTAA-AAAAATTAAAAA
* *
147890 TTCTTAAAAAAATTAGAAA
1 TTTTTAAAAAAATTAAAAA
147909 T
1 T
147910 GTATAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (19 bp):
TTTTTAAAAAAATTAAAAA
Found at i:147934 original size:33 final size:33
Alignment explanation
Indices: 147892--147962 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
147882 ATTAAAAATT
*
147892 CTTAAAAAAATTAGAAATGTATAAATTATAAAA
1 CTTAAAAAAATAAGAAATGTATAAATTATAAAA
147925 CTTAAAAAAATAAGAAATGTATAAATTATAAAA
1 CTTAAAAAAATAAGAAATGTATAAATTATAAAA
147958 CTTAA
1 CTTAA
147963 TATATATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30
Consensus pattern (33 bp):
CTTAAAAAAATAAGAAATGTATAAATTATAAAA
Found at i:148321 original size:29 final size:29
Alignment explanation
Indices: 148289--148347 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 29
148279 TTTTTTGTAA
* *
148289 ATTTCTCAAAAAGTGATTTTT-TTATTTTT
1 ATTT-TCAAAAAATAATTTTTATTATTTTT
* *
148318 ATTTTTAAAAAATAATTTTTATTTTTTTT
1 ATTTTCAAAAAATAATTTTTATTATTTTT
148347 A
1 A
148348 AAGTTGAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (29 bp):
ATTTTCAAAAAATAATTTTTATTATTTTT
Done.