Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015345.1 Kokia drynarioides strain JFW-HI SEQ_130392, 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: 58301
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 340 characters in sequence are not A, C, G, or T
Found at i:1066 original size:21 final size:22
Alignment explanation
Indices: 1019--1068 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1009 CCTTTAAAAT
**
1019 GTTAAAAAAAAAAAAATTCATC
1 GTTAAAAAAAAAAAAATTCAAA
* *
1041 TTTAAAAAATAAAAAATT-AAA
1 GTTAAAAAAAAAAAAATTCAAA
1062 GTTAAAA
1 GTTAAAA
1069 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (22 bp):
GTTAAAAAAAAAAAAATTCAAA
Found at i:2483 original size:19 final size:21
Alignment explanation
Indices: 2439--2483 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
2429 TTAAATTTTT
*
2439 ATTTTAATAATATATTTTAAC
1 ATTTTAATAATATATGTTAAC
2460 A--TTAATAATA-ATGTTAA-
1 ATTTTAATAATATATGTTAAC
2477 ATTTTAA
1 ATTTTAA
2484 ATTATATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
17 1 0.05
18 6 0.29
19 13 0.62
21 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTTAATAATATATGTTAAC
Found at i:2596 original size:24 final size:23
Alignment explanation
Indices: 2557--2602 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
2547 TATTACAATT
*
2557 TATAAATATTTAATAATATAAAA
1 TATAAACATTTAATAATATAAAA
2580 TATAAACATTATAATAATATAAA
1 TATAAACATT-TAATAATATAAA
2603 TATTAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TATAAACATTTAATAATATAAAA
Found at i:2598 original size:17 final size:16
Alignment explanation
Indices: 2573--2607 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2563 TATTTAATAA
2573 TATAAAATATAAACAT
1 TATAAAATATAAACAT
*
2589 TATAATAATATAAATAT
1 TATAA-AATATAAACAT
2606 TA
1 TA
2608 GTATTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TATAAAATATAAACAT
Found at i:2601 original size:40 final size:40
Alignment explanation
Indices: 2520--2606 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 40
2510 TATTTACATT
* * * *
2520 AATATTTTAATAATATATATATATATATATTACAATTTATA
1 AATA-TTTAATAATATATAAATATAAACATTACAATATATA
*
2561 AATATTTAATAATATA-AAATATAAACATTATAATAATATA
1 AATATTTAATAATATATAAATATAAACATTACAAT-ATATA
2601 AATATT
1 AATATT
2607 AGTATTTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 14 0.35
40 22 0.55
41 4 0.10
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (40 bp):
AATATTTAATAATATATAAATATAAACATTACAATATATA
Found at i:10709 original size:15 final size:17
Alignment explanation
Indices: 10683--10714 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10673 TTAGCAATAG
10683 AAAAGTAGATAT-TCAT
1 AAAAGTAGATATATCAT
10699 AAAAG-AGATATATCAT
1 AAAAGTAGATATATCAT
10715 CAATGACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.28
Consensus pattern (17 bp):
AAAAGTAGATATATCAT
Found at i:10858 original size:8 final size:8
Alignment explanation
Indices: 10840--10873 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
10830 AATTTTTTCA
10840 TTTAAATAT
1 TTTAAA-AT
10849 TTTAAAAT
1 TTTAAAAT
10857 TTTAAAAT
1 TTTAAAAT
10865 TTTAAAAT
1 TTTAAAAT
10873 T
1 T
10874 AATAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAAAT
Found at i:19967 original size:38 final size:40
Alignment explanation
Indices: 19881--19970 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 40
19871 TAAAAAGTAT
19881 TTATATTAAAAAAACACTAATATAAATATAATAAATATTTTA
1 TTATATT--AAAAACACTAATATAAATATAATAAATATTTTA
* *
19923 TTATATTAAAAACAC-AA-ATAAATATCATATATATTTTA
1 TTATATTAAAAACACTAATATAAATATAATAAATATTTTA
19961 TTATATTAAA
1 TTATATTAAA
19971 TATAAATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 29 0.63
39 2 0.04
40 8 0.17
42 7 0.15
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAACACTAATATAAATATAATAAATATTTTA
Found at i:20121 original size:29 final size:30
Alignment explanation
Indices: 20079--20138 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
20069 TTTAATATCA
*
20079 ATATAAATATAT-A-ATTATTTTTTAACAT
1 ATATAAATATATAATATTATTTTATAACAT
*
20107 ATATAATTAATATAATATTATTTTATAACAT
1 ATATAAAT-ATATAATATTATTTTATAACAT
20138 A
1 A
20139 ATATTCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 7 0.26
29 4 0.15
30 1 0.04
31 15 0.56
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
ATATAAATATATAATATTATTTTATAACAT
Found at i:22478 original size:83 final size:83
Alignment explanation
Indices: 22339--22506 Score: 309
Period size: 83 Copynumber: 2.0 Consensus size: 83
22329 TTATATTGTC
*
22339 TAATGTGATTAGCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGTTATG
1 TAATGTGATTAGCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGTTACG
22404 CTTCGACTTTAACTCAGT
66 CTTCGACTTTAACTCAGT
*
22422 TAATGTGATTATCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGTTACG
1 TAATGTGATTAGCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGTTACG
*
22487 CTTCGACTTTAACTCTGT
66 CTTCGACTTTAACTCAGT
22505 TA
1 TA
22507 TTACTCTTTC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (83 bp):
TAATGTGATTAGCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGTTACG
CTTCGACTTTAACTCAGT
Found at i:35961 original size:10 final size:10
Alignment explanation
Indices: 35946--35997 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
35936 ATATAACAAA
35946 TTTTAAATTT
1 TTTTAAATTT
35956 TTTTAAATTT
1 TTTTAAATTT
*
35966 ATTTAAA---
1 TTTTAAATTT
35973 TTTTAATATTT
1 TTTTAA-ATTT
*
35984 TTATAAATTT
1 TTTTAAATTT
35994 TTTT
1 TTTT
35998 TATATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 5 0.15
8 1 0.03
10 23 0.68
11 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:36002 original size:21 final size:21
Alignment explanation
Indices: 35947--36015 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
35937 TATAACAAAT
*
35947 TTTAAATTTTTTTAA-ATTTA
1 TTTAAATTTTTTTAATATATA
*
35967 TTTAAA---TTTTAATAT-TT
1 TTTAAATTTTTTTAATATATA
*
35984 TTATAAATTTTTTTTATATATA
1 TT-TAAATTTTTTTAATATATA
36006 TTTAAATTTT
1 TTTAAATTTT
36016 AATATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
17 9 0.22
18 6 0.15
20 6 0.15
21 16 0.40
22 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTAAATTTTTTTAATATATA
Found at i:36008 original size:39 final size:38
Alignment explanation
Indices: 35949--36025 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 38
35939 TAACAAATTT
*
35949 TAAATTTTTTTAAATTTATTTAAATTTTAATATTTTTA
1 TAAATTTTTTTAAATATATTTAAATTTTAATATTTTTA
*
35987 TAAATTTTTTTTATATATATTTAAATTTTAATATTTTTA
1 TAAA-TTTTTTTAAATATATTTAAATTTTAATATTTTTA
36026 ATATATAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 4 0.11
39 32 0.89
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (38 bp):
TAAATTTTTTTAAATATATTTAAATTTTAATATTTTTA
Found at i:36237 original size:43 final size:40
Alignment explanation
Indices: 36153--36284 Score: 106
Period size: 43 Copynumber: 3.1 Consensus size: 40
36143 GGTGGATACA
* * *
36153 AAAAAAAAAACATGAGAAAGTAGCAAAAAATATAAGGAATTAT
1 AAAAAAAAATCATGAG-AAGTAG-AAAAATTATGA-GAATTAT
*
36196 AAAAAAAAATCATGAGAGAGTACGAAAAATTATGAGTAATTAC
1 AAAAAAAAATCATGAGA-AGTA-GAAAAATTATGAG-AATTAT
* * * *
36239 CAAAAAAGAT-ACGAGAA-TATAAAAAATTATGAGAGATTAT
1 AAAAAAAAATCATGAGAAGTA-GAAAAATTATGAGA-ATTAT
36279 AAAAAA
1 AAAAAA
36285 TTTCGAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
39 1 0.01
40 23 0.31
41 1 0.01
42 7 0.09
43 41 0.55
44 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.14, T:0.19
Consensus pattern (40 bp):
AAAAAAAAATCATGAGAAGTAGAAAAATTATGAGAATTAT
Found at i:36299 original size:20 final size:19
Alignment explanation
Indices: 36254--36341 Score: 61
Period size: 20 Copynumber: 4.6 Consensus size: 19
36244 AAGATACGAG
* *
36254 AATATAAAAAATTATGAGAG
1 AATATAAAAAATT-TGAAAA
*
36274 ATTATAAAAAATTTCGAAAA
1 AATATAAAAAATTT-GAAAA
* * *
36294 AATATAACAAATATG-AAT
1 AATATAAAAAATTTGAAAA
* **
36312 ATTATAAAAAATACGAAAA
1 AATATAAAAAATTTGAAAA
*
36331 AGTATAAAAAA
1 AATATAAAAAA
36342 ATTTATGAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
18 14 0.26
19 14 0.26
20 26 0.48
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (19 bp):
AATATAAAAAATTTGAAAA
Found at i:36316 original size:38 final size:39
Alignment explanation
Indices: 36254--36353 Score: 123
Period size: 38 Copynumber: 2.5 Consensus size: 39
36244 AAGATACGAG
*
36254 AATATAAAAAATTATGAGAGATTATAAAAAATTTCGAAAA
1 AATATAAAAAATTATGAGAGATTATAAAAAA-TACGAAAA
* *
36294 AATATAACAAA-TATGA-ATATTATAAAAAATACGAAAA
1 AATATAAAAAATTATGAGAGATTATAAAAAATACGAAAA
*
36331 AGTATAAAAAAATTTATGAGAGA
1 AATAT-AAAAAA-TTATGAGAGA
36354 CTACCGCATA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
37 11 0.22
38 17 0.34
39 5 0.10
40 15 0.30
41 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.26
Consensus pattern (39 bp):
AATATAAAAAATTATGAGAGATTATAAAAAATACGAAAA
Found at i:38176 original size:18 final size:18
Alignment explanation
Indices: 38142--38192 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
38132 ATCACTTTCA
* *
38142 AATTTATTACTTAAATTT
1 AATTTATTCCTTTAATTT
*
38160 CATTTATTCCTTTAA-TT
1 AATTTATTCCTTTAATTT
38177 AATTT-TTCCTTTAATT
1 AATTTATTCCTTTAATT
38193 ATTTAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 9 0.32
17 7 0.25
18 12 0.43
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTATTCCTTTAATTT
Found at i:38187 original size:16 final size:17
Alignment explanation
Indices: 38142--38209 Score: 63
Period size: 16 Copynumber: 4.1 Consensus size: 17
38132 ATCACTTTCA
* *
38142 AATTTATTACTTAAATTT
1 AATTTATTCCTTTAA-TT
*
38160 CATTTATTCCTTTAATT
1 AATTTATTCCTTTAATT
38177 AATTT-TTCCTTTAATT
1 AATTTATTCCTTTAATT
38193 -ATTTAATT--TTTAATT
1 AATTT-ATTCCTTTAATT
38208 AA
1 AA
38210 AATAATGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 11 0.26
16 12 0.28
17 8 0.19
18 12 0.28
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTATTCCTTTAATT
Found at i:38559 original size:11 final size:11
Alignment explanation
Indices: 38545--38573 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
38535 ATTTTCAAAT
38545 ATTTAATGGCC
1 ATTTAATGGCC
38556 ATTTAATGGCC
1 ATTTAATGGCC
38567 ATTTAAT
1 ATTTAAT
38574 TTAAGGATAA
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:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (11 bp):
ATTTAATGGCC
Found at i:42118 original size:24 final size:22
Alignment explanation
Indices: 42088--42161 Score: 85
Period size: 24 Copynumber: 3.2 Consensus size: 22
42078 TCAAACAACC
42088 AAAATAGCAGCAAAAATAATAGAA
1 AAAATAGCA-CAAAAATAATA-AA
42112 AAAATAGCAACAAAAATAATAATA
1 AAAATAGC-ACAAAAATAATAA-A
* * *
42136 AAAACAACACAAAAATAGTAAA
1 AAAATAGCACAAAAATAATAAA
42158 AAAA
1 AAAA
42162 AAATTGCACC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.11
23 13 0.29
24 26 0.58
25 1 0.02
ACGTcount: A:0.72, C:0.09, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAATAGCACAAAAATAATAAA
Found at i:42568 original size:32 final size:34
Alignment explanation
Indices: 42509--42582 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 34
42499 TTCACACCGT
*
42509 ATTTAAATCTCATATTCTTTTCCTTCTTT-TTAA
1 ATTTAAATCTCATATTCTTTTCATTCTTTATTAA
42542 ATTTAAATC-C-TATTCATTTTCATTCTTTATTAA
1 ATTTAAATCTCATATTC-TTTTCATTCTTTATTAA
*
42575 CTTTAAAT
1 ATTTAAAT
42583 TCTTTTTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 5 0.14
32 12 0.32
33 20 0.54
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.55
Consensus pattern (34 bp):
ATTTAAATCTCATATTCTTTTCATTCTTTATTAA
Found at i:42642 original size:31 final size:30
Alignment explanation
Indices: 42607--42678 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 30
42597 AATTTATTAT
*
42607 TTTAAATTCATTTATCCTTTAATTAGAATCA
1 TTTAAATT-ATTTATCCTTTAATTAAAATCA
42638 TTT--A--ATTTATCCTTTAATTAAAATCA
1 TTTAAATTATTTATCCTTTAATTAAAATCA
*
42664 TTTAATTTGATTTAT
1 TTTAAATT-ATTTAT
42679 TACTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
26 24 0.71
29 1 0.03
31 9 0.26
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTAAATTATTTATCCTTTAATTAAAATCA
Found at i:42643 original size:14 final size:13
Alignment explanation
Indices: 42624--42670 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
42614 TCATTTATCC
42624 TTTAATTAGAATCA
1 TTTAATTA-AATCA
* *
42638 TTTAATT-TATCC
1 TTTAATTAAATCA
42650 TTTAATTAAAATCA
1 TTTAATT-AAATCA
42664 TTTAATT
1 TTTAATT
42671 TGATTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 10 0.37
14 17 0.63
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (13 bp):
TTTAATTAAATCA
Found at i:42645 original size:26 final size:26
Alignment explanation
Indices: 42616--42671 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
42606 TTTTAAATTC
*
42616 ATTTATCCTTTAATTAGAATCATTTA
1 ATTTATCCTTTAATTAAAATCATTTA
42642 ATTTATCCTTTAATTAAAATCATTTA
1 ATTTATCCTTTAATTAAAATCATTTA
42668 ATTT
1 ATTT
42672 GATTTATTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTTATCCTTTAATTAAAATCATTTA
Found at i:54293 original size:29 final size:30
Alignment explanation
Indices: 54250--54306 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
54240 GAATTTGATC
54250 AAATCAAAATTTCATATATAAAATTACACA
1 AAATCAAAATTTCATATATAAAATTACACA
* *
54280 AAATCAAAA-TTCATGTATATAATTACA
1 AAATCAAAATTTCATATATAAAATTACA
54307 TATTAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTACACA
Found at i:54697 original size:2 final size:2
Alignment explanation
Indices: 54690--54715 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54680 TAATTCACCA
54690 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54716 GATTATGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55061 original size:18 final size:19
Alignment explanation
Indices: 55038--55073 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55028 ATTAAAGTAT
55038 AATATAA-AAATTAATACG
1 AATATAAGAAATTAATACG
*
55056 AATATAAGAATTTAATAC
1 AATATAAGAAATTAATAC
55074 AGTACAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (19 bp):
AATATAAGAAATTAATACG
Found at i:55576 original size:6 final size:6
Alignment explanation
Indices: 55539--55619 Score: 53
Period size: 6 Copynumber: 14.2 Consensus size: 6
55529 CCAACAGAAT
* * * * *
55539 TTTAAA TTT-AT TTTAAA ATTAAA TTT-AT TTTAAG TTTAAA TTT-AC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
55584 TTAAAA TTTAAA TTT-AC TATAAA TTTAAG TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
55620 CTATTTAAAT
Statistics
Matches: 54, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
5 14 0.26
6 40 0.74
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:55600 original size:17 final size:17
Alignment explanation
Indices: 55539--55616 Score: 79
Period size: 17 Copynumber: 4.6 Consensus size: 17
55529 CCAACAGAAT
*
55539 TTTAAATTTATTTTAAAA
1 TTTAAATTTA-CTTAAAA
* * *
55557 -TTAAATTTATTTTAAG
1 TTTAAATTTACTTAAAA
55573 TTTAAATTTACTTAAAA
1 TTTAAATTTACTTAAAA
55590 TTTAAATTTAC-TATAAA
1 TTTAAATTTACTTA-AAA
*
55607 TTTAAGTTTA
1 TTTAAATTTA
55617 AATCTATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
16 7 0.13
17 45 0.87
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTACTTAAAA
Found at i:55611 original size:34 final size:34
Alignment explanation
Indices: 55539--55616 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
55529 CCAACAGAAT
* * * *
55539 TTTAAATTTATTTTAAAATTAAATTTATTTTAAG
1 TTTAAATTTATCTTAAAATTAAATTTACTATAAA
55573 TTTAAATTTA-CTTAAAATTTAAATTTACTATAAA
1 TTTAAATTTATCTTAAAA-TTAAATTTACTATAAA
*
55607 TTTAAGTTTA
1 TTTAAATTTA
55617 AATCTATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 6 0.16
34 32 0.84
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATCTTAAAATTAAATTTACTATAAA
Found at i:57628 original size:30 final size:29
Alignment explanation
Indices: 57572--57919 Score: 231
Period size: 29 Copynumber: 11.9 Consensus size: 29
57562 AAGCTATACG
*
57572 AAAATTCCATTTTCATCCC-CGAACTTCTA
1 AAAATTCCATTTTTA-CCCTCGAACTTCTA
*
57601 AAAATTCCATTTTTGACCCTTGAACTTCTA
1 AAAATTCCATTTTT-ACCCTCGAACTTCTA
* *
57631 AAAATTCC-GTTTTACCCTCGAACTT-TCG
1 AAAATTCCATTTTTACCCTCGAACTTCT-A
*
57659 AAAATTCCATTTTTGA-CCTCGAAACTTC-C
1 AAAATTCCATTTTT-ACCCTCG-AACTTCTA
57688 AAAATTCCATTTTTACCCTC-AATCTTCTA
1 AAAATTCCATTTTTACCCTCGAA-CTTCTA
* *
57717 AAAATTCCATTTTCAACCC-CGAAACTTCCA
1 AAAATTCCATTTT-TACCCTCG-AACTTCTA
* * *
57747 AAAATTACATTTTTACCCTCGAACCTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCTA
*
57776 AAATTTCCATTTTTGACCCT-GAACCTT-TCA
1 AAAATTCCATTTTT-ACCCTCGAA-CTTCT-A
* * * *
57806 AAAATTACCA--TTTGCCCCCGGA-TGTCCA
1 AAAATT-CCATTTTTACCCTCGAACT-TCTA
* * * *
57834 AAAACTCTATTTTCGA-CCTCGAAAC-TCCA
1 AAAATTCCATTTT-TACCCTCG-AACTTCTA
* *
57863 AAAATTTCATTTTTACCCCCGAA-TGTCTA
1 AAAATTCCATTTTTACCCTCGAACT-TCTA
* *
57892 AAAATTTCATCTTTTAACCTCGAACTTC
1 AAAATTCCAT-TTTTACCCTCGAACTTC
57920 CCCAAAATTA
Statistics
Matches: 252, Mismatches: 36, Indels: 61
0.72 0.10 0.17
Matches are distributed among these distances:
27 6 0.02
28 37 0.15
29 129 0.51
30 74 0.29
31 6 0.02
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCGAACTTCTA
Found at i:57882 original size:58 final size:59
Alignment explanation
Indices: 57572--57963 Score: 263
Period size: 58 Copynumber: 6.7 Consensus size: 59
57562 AAGCTATACG
* * * * * *
57572 AAAATTCCATTTTCATCCCCGAACT-TCTAAAAATTCCATTTTTGACCCTTG-AACTTCTA
1 AAAATTCCATTTTTACCCCCGAA-TGTCCAAAAATTCCATTTTCGA-CCTCGAAACTTCCA
* * * * *
57631 AAAATTCC-GTTTTACCCTCGAACT-TTCGAAAATTCCATTTTTGACCTCGAAACTTCC-
1 AAAATTCCATTTTTACCCCCGAA-TGTCCAAAAATTCCATTTTCGACCTCGAAACTTCCA
* * * * *
57688 AAAATTCCATTTTTACCCTC-AATCTTCTAAAAATTCCATTTTCAACCCCGAAACTTCCA
1 AAAATTCCATTTTTACCCCCGAAT-GTCCAAAAATTCCATTTTCGACCTCGAAACTTCCA
* * ** * * * *
57747 AAAATTACATTTTTACCCTCGAACCTCCAAAATTTCCATTTTTGACC-CTGAACCTTTCA
1 AAAATTCCATTTTTACCCCCGAATGTCCAAAAATTCCATTTTCGACCTC-GAAACTTCCA
* * * *
57806 AAAATTACCA--TTTGCCCCCGGATGTCCAAAAACTCTATTTTCGACCTCGAAAC-TCCA
1 AAAATT-CCATTTTTACCCCCGAATGTCCAAAAATTCCATTTTCGACCTCGAAACTTCCA
* * * ** *
57863 AAAATTTCATTTTTACCCCCGAATGTCTAAAAATTTCATCTTTTAACCTCG-AACTTCCCC
1 AAAATTCCATTTTTACCCCCGAATGTCCAAAAATTCCAT-TTTCGACCTCGAAACTT-CCA
* * *
57923 AAAATTACCA-TCTT-GCCCCGAAAGTCC-AAAATTACCATTTT
1 AAAATT-CCATTTTTACCCCCGAATGTCCAAAAATT-CCATTTT
57964 GCCCGGGGTA
Statistics
Matches: 264, Mismatches: 53, Indels: 33
0.75 0.15 0.09
Matches are distributed among these distances:
56 3 0.01
57 23 0.09
58 138 0.52
59 83 0.31
60 15 0.06
61 2 0.01
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (59 bp):
AAAATTCCATTTTTACCCCCGAATGTCCAAAAATTCCATTTTCGACCTCGAAACTTCCA
Found at i:57942 original size:117 final size:117
Alignment explanation
Indices: 57716--57953 Score: 270
Period size: 117 Copynumber: 2.0 Consensus size: 117
57706 TCAATCTTCT
* * *
57716 AAAAATTCCATTTTCAACCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACCTCCAAAATT
1 AAAAACTCCATTTTCAACCCCGAAACTTCCAAAAATTACATTTTTACCCCCGAACCTCAAAAATT
* * * *
57781 TCCATTTTTGACCCTGAACCTTTCAAAAATTACCATTTGCCCCCGGATGTCC
66 TCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTGCCCCCGAAAGTCC
* * * * **
57833 AAAAACTCTATTTTCGACCTCGAAAC-TCCAAAAATTTCATTTTTACCCCCGAATGTCTAAAAAT
1 AAAAACTCCATTTTCAACCCCGAAACTTCCAAAAATTACATTTTTACCCCCGAACCTC-AAAAAT
*
57897 TT-CATCTTTTAA-CCTCGAA-CTTCCCCAAAATTACCATCTTG-CCCCGAAAGTCC
65 TTCCAT-TTTTAACCCT-GAACCTT-CCAAAAATTACCAT-TTGCCCCCGAAAGTCC
57950 AAAA
1 AAAA
57954 TTACCATTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
116 36 0.35
117 63 0.62
118 3 0.03
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (117 bp):
AAAAACTCCATTTTCAACCCCGAAACTTCCAAAAATTACATTTTTACCCCCGAACCTCAAAAATT
TCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTGCCCCCGAAAGTCC
Done.