Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014145.1 Corchorus capsularis cultivar CVL-1 contig14166, 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: 63531
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:15948 original size:40 final size:39
Alignment explanation
Indices: 15886--16009 Score: 158
Period size: 40 Copynumber: 3.1 Consensus size: 39
15876 TGCACAATTA
15886 AAGCTTTAATTCAGTGTGATTAAGGAAAATTAAGAAAAGT
1 AAGC-TTAATTCAGTGTGATTAAGGAAAATTAAGAAAAGT
* ** *
15926 AAATCTTAATTCAGTGAAATTAAGGAAAACTAAGAAAAGT
1 -AAGCTTAATTCAGTGTGATTAAGGAAAATTAAGAAAAGT
* * *
15966 AAGCTTCAATCCAGTGTGATTAAGAAAAATTAAGAAAAGA
1 AAGCTT-AATTCAGTGTGATTAAGGAAAATTAAGAAAAGT
16006 AAGC
1 AAGC
16010 AGTCAAGAAC
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
39 5 0.07
40 63 0.89
41 3 0.04
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (39 bp):
AAGCTTAATTCAGTGTGATTAAGGAAAATTAAGAAAAGT
Found at i:16061 original size:37 final size:37
Alignment explanation
Indices: 16018--16326 Score: 383
Period size: 37 Copynumber: 8.4 Consensus size: 37
16008 GCAGTCAAGA
* *
16018 ACTTAATTCAAGGTAATTAAGTAAAAACAGTTAAAAG
1 ACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAAG
*
16055 ACTTAATTCAGGGAAATTAAGTAAAAGCAG-TAAAAGG
1 ACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAA-G
* *
16092 ACTTAATTCA-GGAAATTAAGTAAACACAGTTAAGA-
1 ACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAAG
* *
16127 ACTTAATTCAGGGCAATTAAGTAAAAGA-AGTTAAAGG
1 ACTTAATTCAGGGAAATTAAGTAAAA-ACAGTTAAAAG
* * *
16164 GCTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAAGG
1 ACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAAG
* *
16201 ACTTAATTCAGGGAAATTAAGTAAAACCAGTTAAAGG
1 ACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAAG
* * * *
16238 GCTTAATTCAGGGAAATTAAGTAAACACGGTTAAAGG
1 ACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAAG
* * **
16275 GCTTAATTCAGGGCAATTAAGTAAAAGTAGTTAAAAG
1 ACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAAG
*
16312 ACTTAATTCAAGGAA
1 ACTTAATTCAGGGAA
16327 GGAAATCAGG
Statistics
Matches: 238, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
35 10 0.04
36 41 0.17
37 187 0.79
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (37 bp):
ACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAAG
Found at i:16148 original size:109 final size:109
Alignment explanation
Indices: 16009--16326 Score: 444
Period size: 109 Copynumber: 2.9 Consensus size: 109
15999 GAAAAGAAAG
* * * * *
16009 CAGTCAAGAACTTAATTCAAGGTAATTAAGTAAAAACAGTTAAAAGACTTAATTCAGGGAAATTA
1 CAGTTAAGAACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAGGGCTTAATTCAGGGAAATTA
16074 AGTAAAAGCAGTAAAAGGACTTAATTCAGGAAATTAAGT-AAAC
66 AGTAAAAGCAGTAAAAGGACTTAATTCAGGAAATTAAGTAAAAC
*
16117 ACAGTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGA-AGTTAAAGGGCTTAATTCAGGGAAAT
1 -CAGTTAAGAACTTAATTCAGGGAAATTAAGTAAAA-ACAGTTAAAGGGCTTAATTCAGGGAAAT
*
16181 TAAGTAAAAGCAGTTAAAGGACTTAATTCAGGGAAATTAAGTAAAAC
64 TAAGTAAAAGCAGTAAAAGGACTTAATTCA-GGAAATTAAGTAAAAC
** * * *
16228 CAGTTAAAGGGCTTAATTCAGGGAAATTAAGTAAACACGGTTAAAGGGCTTAATTCAGGGCAATT
1 CAGTT-AAGAACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAGGGCTTAATTCAGGGAAATT
*
16293 AAGTAAAAGTAGTTAAAA-GACTTAATTCAAGGAA
65 AAGTAAAAGCAG-TAAAAGGACTTAATTC-AGGAA
16327 GGAAATCAGG
Statistics
Matches: 188, Mismatches: 14, Indels: 12
0.88 0.07 0.06
Matches are distributed among these distances:
109 85 0.45
110 18 0.10
111 80 0.43
112 5 0.03
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.25
Consensus pattern (109 bp):
CAGTTAAGAACTTAATTCAGGGAAATTAAGTAAAAACAGTTAAAGGGCTTAATTCAGGGAAATTA
AGTAAAAGCAGTAAAAGGACTTAATTCAGGAAATTAAGTAAAAC
Found at i:16394 original size:37 final size:37
Alignment explanation
Indices: 16353--16465 Score: 121
Period size: 37 Copynumber: 3.2 Consensus size: 37
16343 AAAACATAGG
*
16353 CTTAATTTCAAGGAAGGAAATTAAGT-AGAGTCAAGGA
1 CTTAATTTCAAGGAAAGAAATTAAGTCA-AGTCAAGGA
*
16390 CTTAATTTCAGGGAAAGAAATTAAGTCAAGTCAAGGA
1 CTTAATTTCAAGGAAAGAAATTAAGTCAAGTCAAGGA
* * * *
16427 TTTAA-TTC-AGG---GTAATTAAGTCAAGTGAGGGA
1 CTTAATTTCAAGGAAAGAAATTAAGTCAAGTCAAGGA
16459 CTTAATT
1 CTTAATT
16466 CAGGGTAATT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
32 22 0.33
33 1 0.02
35 2 0.03
36 3 0.05
37 37 0.56
38 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (37 bp):
CTTAATTTCAAGGAAAGAAATTAAGTCAAGTCAAGGA
Found at i:16444 original size:32 final size:32
Alignment explanation
Indices: 16371--16620 Score: 141
Period size: 37 Copynumber: 7.2 Consensus size: 32
16361 CAAGGAAGGA
*
16371 AATTAAGT-AGAGTCAAGGACTTAATTTCAGGGAAAGA
1 AATTAAGTCA-AGTCAAGGACTTAA-TTCA-GG---GT
*
16408 AATTAAGTCAAGTCAAGGATTTAATTCAGGGT
1 AATTAAGTCAAGTCAAGGACTTAATTCAGGGT
* *
16440 AATTAAGTCAAGTGAGGGACTTAATTCAGGGT
1 AATTAAGTCAAGTCAAGGACTTAATTCAGGGT
* *
16472 AATTAAGTAGCGTCAA-TAAAGGGACTTAATTAAGGGT
1 AATT-A--A--GTCAAGTCAA-GGACTTAATTCAGGGT
* *
16509 AATTAAGTAGCGTCAA-TAAAGAACTTAATTCAGGGT
1 AATT-A--A--GTCAAGTCAAGGACTTAATTCAGGGT
**
16545 AATTAAGTGGAGTCAATAAAAGG-CTTAATTCAGGGT
1 AATTAAGTCAAGTC-----AAGGACTTAATTCAGGGT
* * *
16581 AATTAAGT-AGAATAAAGAACTTAATTCAGGGT
1 AATTAAGTCA-AGTCAAGGACTTAATTCAGGGT
16613 AATTAAGT
1 AATTAAGT
16621 GGAGTCAATA
Statistics
Matches: 180, Mismatches: 18, Indels: 35
0.77 0.08 0.15
Matches are distributed among these distances:
31 6 0.03
32 56 0.31
33 2 0.01
35 4 0.02
36 47 0.26
37 64 0.36
38 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (32 bp):
AATTAAGTCAAGTCAAGGACTTAATTCAGGGT
Found at i:16544 original size:36 final size:36
Alignment explanation
Indices: 16458--16641 Score: 252
Period size: 36 Copynumber: 5.2 Consensus size: 36
16448 CAAGTGAGGG
* *
16458 ACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGGG
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA-GA
* *
16495 ACTTAATTAAGGGTAATTAAGTAGCGTCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
*
16531 ACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA-A
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
*
16566 GGCTTAATTCAGGGTAATTAAGT--AG--AATAAAGA
1 -ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
*
16599 ACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
16635 ACTTAAT
1 ACTTAAT
16642 CTAAAAAGAT
Statistics
Matches: 134, Mismatches: 7, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
32 27 0.20
33 1 0.01
34 4 0.03
35 1 0.01
36 68 0.51
37 33 0.25
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (36 bp):
ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
Found at i:16670 original size:104 final size:107
Alignment explanation
Indices: 16454--16679 Score: 239
Period size: 104 Copynumber: 2.1 Consensus size: 107
16444 AAGTCAAGTG
*
16454 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGGGACTTAATTAAGGGTAATTAAGTAG
1 AGGG-CTTAATTCAGGGTAATTAAGTA-CG-CAATAAAGGAACTTAATTAAGGGTAATTAAGTAG
* * ** * ***
16519 CGTCAATAAAGAACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
63 AGTCAATAAAGAACTTAATTAAAAG-AATTAAGTGAAAAAAATAAA
* *
16565 A-GGCTTAATTCAGGGTAATTAAGTA-G-AATAAA-GAACTTAATTCAGGGTAATTAAGTGGAGT
1 AGGGCTTAATTCAGGGTAATTAAGTACGCAATAAAGGAACTTAATTAAGGGTAATTAAGTAGAGT
*
16626 CAATAAAGAACTTAATCTAAAA-AGATTAGGT-AAAAAAATAAAA
66 CAATAAAGAACTTAAT-TAAAAGA-ATTAAGTGAAAAAAAT-AAA
16669 AGGGCTTAATT
1 AGGGCTTAATT
16680 TATGAAAATT
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
103 5 0.05
104 51 0.52
105 17 0.17
107 1 0.01
109 22 0.22
110 2 0.02
111 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (107 bp):
AGGGCTTAATTCAGGGTAATTAAGTACGCAATAAAGGAACTTAATTAAGGGTAATTAAGTAGAGT
CAATAAAGAACTTAATTAAAAGAATTAAGTGAAAAAAATAAA
Found at i:24674 original size:22 final size:22
Alignment explanation
Indices: 24649--24694 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
24639 CTTATTTACC
*
24649 TTAATTATTT-ATGCTTAACTTG
1 TTAATT-TTTAATGCCTAACTTG
*
24671 TTAATTTTTAATGCCTATCTTG
1 TTAATTTTTAATGCCTAACTTG
24693 TT
1 TT
24695 TCATTTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.57
Consensus pattern (22 bp):
TTAATTTTTAATGCCTAACTTG
Found at i:25899 original size:24 final size:25
Alignment explanation
Indices: 25853--25900 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
25843 ATTGGAGTAT
*
25853 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
25878 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
25901 TACTGTTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:31187 original size:60 final size:60
Alignment explanation
Indices: 31094--31213 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 60
31084 CAAATCTTCG
31094 TTGCTACTGATTAATCTAATTCCTTTCTTTTTCTTCTTCTTTCGATTCCTCCTTTTTAAT
1 TTGCTACTGATTAATCTAATTCCTTTCTTTTTCTTCTTCTTTCGATTCCTCCTTTTTAAT
* * *
31154 TTGCTATTGATTCATCTAATTGCTTTCTTTTTCTTCTTCTTTCGATTCCTCCTTTTTAAT
1 TTGCTACTGATTAATCTAATTCCTTTCTTTTTCTTCTTCTTTCGATTCCTCCTTTTTAAT
31214 CATCTGATCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.14, C:0.23, G:0.06, T:0.57
Consensus pattern (60 bp):
TTGCTACTGATTAATCTAATTCCTTTCTTTTTCTTCTTCTTTCGATTCCTCCTTTTTAAT
Found at i:32507 original size:12 final size:12
Alignment explanation
Indices: 32484--32532 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
32474 GTTAGGGCAG
32484 ATAATA-ATATA
1 ATAATATATATA
*
32495 ATGATATATATA
1 ATAATATATATA
32507 ATAATTATTATATAA
1 ATAA-TA-TATAT-A
32522 ATAATATATAT
1 ATAATATATAT
32533 TTATTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 5 0.16
12 8 0.25
13 7 0.22
14 7 0.22
15 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
ATAATATATATA
Found at i:32509 original size:20 final size:18
Alignment explanation
Indices: 32484--32529 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
32474 GTTAGGGCAG
32484 ATAATAATATAATGATATAT
1 ATAATAATATAAT--TATAT
32504 ATAATAAT-T-ATTATAT
1 ATAATAATATAATTATAT
32520 A-AATAATATA
1 ATAATAATATA
32530 TATTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
18 2 0.08
19 1 0.04
20 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
ATAATAATATAATTATAT
Found at i:32525 original size:18 final size:20
Alignment explanation
Indices: 32484--32531 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
32474 GTTAGGGCAG
*
32484 ATAATAATATAATGATATAT
1 ATAATAATATAATGATATAA
*
32504 ATAATAAT-T-ATTATATAA
1 ATAATAATATAATGATATAA
32522 ATAAT-ATATA
1 ATAATAATATA
32532 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 2 0.08
18 13 0.54
19 1 0.04
20 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAATAATATAATGATATAA
Found at i:34745 original size:7 final size:7
Alignment explanation
Indices: 34719--34751 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
34709 ACCTTCTGGG
34719 TTTTT-T
1 TTTTTGT
34725 TTTTTGT
1 TTTTTGT
34732 TTCTTTGT
1 TT-TTTGT
34740 TTTTTGT
1 TTTTTGT
34747 TTTTT
1 TTTTT
34752 CACTTTTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 5 0.20
7 13 0.52
8 7 0.28
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (7 bp):
TTTTTGT
Found at i:38559 original size:74 final size:74
Alignment explanation
Indices: 38423--38572 Score: 194
Period size: 74 Copynumber: 2.0 Consensus size: 74
38413 GGTAATTAAC
* * * *
38423 CAAGTGAGAAAAGATGAAAAGGGGGCGAAAAGGTTGTACCTCATAGAAAGTTAAAAGAAGCCTTT
1 CAAGCGAGAAAAGATCAAAAGGGGGCGAAAAGGTTCTACCACATAGAAAGTTAAAAGAAGCCTTT
38488 AGTAAATTT
66 AGTAAATTT
* * * * *
38497 CAAGCGAGAAAAGATCAAAATGGGGTGAAAAGGTTCTACCACATTA-AAAGTTGATAGGAGCCTT
1 CAAGCGAGAAAAGATCAAAAGGGGGCGAAAAGGTTCTACCACA-TAGAAAGTTAAAAGAAGCCTT
*
38561 TAGTAATTTT
65 TAGTAAATTT
38571 CA
1 CA
38573 GAGGGTATTC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
74 63 0.97
75 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.23
Consensus pattern (74 bp):
CAAGCGAGAAAAGATCAAAAGGGGGCGAAAAGGTTCTACCACATAGAAAGTTAAAAGAAGCCTTT
AGTAAATTT
Found at i:39717 original size:15 final size:15
Alignment explanation
Indices: 39697--39756 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
39687 TAATATGTAG
39697 TATATATAATAAATA
1 TATATATAATAAATA
*
39712 TATATAAAACTAATATA
1 TATATATAA-TAA-ATA
*
39729 TATTAATATAGTAAA-A
1 TA-T-ATATAATAAATA
*
39745 TTTATATAATAA
1 TATATATAATAA
39757 TAATCACAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
14 8 0.22
15 9 0.25
16 5 0.14
17 6 0.17
18 4 0.11
19 4 0.11
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
TATATATAATAAATA
Found at i:40252 original size:13 final size:15
Alignment explanation
Indices: 40190--40267 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 15
40180 TATTCAATCT
40190 TTATA-TATATATATA
1 TTATATTATAT-TATA
40205 TT-TA-TATATATATA
1 TTATATTATAT-TATA
* * *
40219 ATACATTGATAATTATG
1 TTATATT-AT-ATTATA
40236 TTATA-T-TATTATA
1 TTATATTATATTATA
40249 TTATATTATATTATA
1 TTATATTATATTATA
40264 TTAT
1 TTAT
40268 CAATAAACTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
13 10 0.20
14 15 0.29
15 14 0.27
16 2 0.04
17 8 0.16
18 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATATTATATTATA
Found at i:40266 original size:10 final size:10
Alignment explanation
Indices: 40190--40267 Score: 58
Period size: 10 Copynumber: 7.9 Consensus size: 10
40180 TATTCAATCT
40190 TTATA-TATA
1 TTATATTATA
40199 TATATATT-TA
1 T-TATATTATA
40209 -TATATATATA
1 TTATAT-TATA
* *
40219 ATACATTGATAA
1 TTATATT-AT-A
*
40231 TTATGTTATA
1 TTATATTATA
40241 -T-TATTATA
1 TTATATTATA
40249 TTATATTATA
1 TTATATTATA
40259 TTATATTAT
1 TTATATTAT
40268 CAATAAACTT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
8 11 0.20
9 4 0.07
10 26 0.47
11 9 0.16
12 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (10 bp):
TTATATTATA
Found at i:42164 original size:16 final size:16
Alignment explanation
Indices: 42143--42200 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
42133 CAACCTGAGA
42143 CCGAACCCGAA-AATAC
1 CCGAACCCGAACAA-AC
42159 CCGAACCC-AACAGAAC
1 CCGAACCCGAACA-AAC
* *
42175 CCAAACCCGAATAAAC
1 CCGAACCCGAACAAAC
42191 CCGAACCCGA
1 CCGAACCCGA
42201 GTGACCGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 2 0.06
16 30 0.83
17 4 0.11
ACGTcount: A:0.43, C:0.41, G:0.12, T:0.03
Consensus pattern (16 bp):
CCGAACCCGAACAAAC
Found at i:42730 original size:2 final size:2
Alignment explanation
Indices: 42723--42753 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42713 ATTGGTTAAC
42723 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 A
42754 CTAGTTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42893 original size:22 final size:20
Alignment explanation
Indices: 42867--42974 Score: 58
Period size: 22 Copynumber: 5.1 Consensus size: 20
42857 TTACACTATC
*
42867 TTTGATGATGTCCTTATGAAAT
1 TTTGATAAT-TCC-TATGAAAT
42889 TTTGATAACCTTCCTATGAAAT
1 TTTGATAA--TTCCTATGAAAT
* * *
42911 TATGATAATTACTAT--ATT
1 TTTGATAATTCCTATGAAAT
* **
42929 TTTTATGACGTCCTTATGAAAT
1 TTTGAT-AATTCC-TATGAAAT
*
42951 TTTGATAAGTTTCCAATGAAAT
1 TTTGATAA--TTCCTATGAAAT
42973 TT
1 TT
42975 CAATAACGAT
Statistics
Matches: 64, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
18 6 0.09
19 3 0.05
20 9 0.14
21 1 0.02
22 38 0.59
23 6 0.09
24 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (20 bp):
TTTGATAATTCCTATGAAAT
Found at i:42920 original size:62 final size:62
Alignment explanation
Indices: 42845--42973 Score: 188
Period size: 62 Copynumber: 2.1 Consensus size: 62
42835 ATTAAATTAA
* *
42845 AAATTATGATAATTAC-ACTATCTTTGATGATGTCCTTATGAAATTTTGATAACCTTCCTATG
1 AAATTATGATAATTACTA-TATCTTTGATGACGTCCTTATGAAATTTTGATAACCTTCCAATG
* * **
42907 AAATTATGATAATTACTATATTTTTTATGACGTCCTTATGAAATTTTGATAAGTTTCCAATG
1 AAATTATGATAATTACTATATCTTTGATGACGTCCTTATGAAATTTTGATAACCTTCCAATG
42969 AAATT
1 AAATT
42974 TCAATAACGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 59 0.98
63 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (62 bp):
AAATTATGATAATTACTATATCTTTGATGACGTCCTTATGAAATTTTGATAACCTTCCAATG
Found at i:43024 original size:20 final size:21
Alignment explanation
Indices: 43001--43047 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
42991 GAATTTCGAG
* *
43001 AACCTTTTTAT-AATTTTTTT
1 AACCTTCTTATAAATTTTGTT
43021 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTAT-AAATTTTGTT
43043 AACCT
1 AACCT
43048 CCCTAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
22 13 0.57
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (21 bp):
AACCTTCTTATAAATTTTGTT
Found at i:43069 original size:22 final size:22
Alignment explanation
Indices: 43044--43085 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
43034 AATTTTGTTA
* *
43044 ACCTCCCTAAGGAATTTTGAAG
1 ACCTCACTAAGAAATTTTGAAG
*
43066 ACCTCACTATGAAATTTTGA
1 ACCTCACTAAGAAATTTTGA
43086 TAGCTAACAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (22 bp):
ACCTCACTAAGAAATTTTGAAG
Found at i:43200 original size:22 final size:23
Alignment explanation
Indices: 43166--43222 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
43156 CCTCCATATG
*
43166 AATTGTCAGTAATCACACTC-TG-A
1 AATTGTGA-TAATCACAC-CATGAA
*
43189 AATTTTGATAATCACACCATGAA
1 AATTGTGATAATCACACCATGAA
43212 AATTGTGATAA
1 AATTGTGATAA
43223 CCTCGGTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 11 0.38
23 17 0.59
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (23 bp):
AATTGTGATAATCACACCATGAA
Found at i:43247 original size:23 final size:21
Alignment explanation
Indices: 43211--43479 Score: 174
Period size: 22 Copynumber: 12.5 Consensus size: 21
43201 CACACCATGA
* *
43211 AAATTGTGATAACCTCGGTATG
1 AAATTTTGATAACCTC-TTATG
*
43233 AAATTTTGATAAACCTTCTTATA
1 AAATTTTGAT-AACC-TCTTATG
* * *
43256 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGAT-AACCT-CTTATG
*
43279 AAATTTTGATGACCTCCTTATG
1 AAATTTTGATAACCT-CTTATG
* *
43301 AAAATCTTGATAA---C-TA-C
1 -AAATTTTGATAACCTCTTATG
*
43318 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCT-CTTATG
**
43340 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTC-TTATG
* * *
43362 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCT-CTTATG
* *
43384 AAATTTTGATCTACGTAC-TATG
1 AAATTTTGAT-AACCT-CTTATG
43406 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAA-CCTCTTATG
*
43428 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACC-TCTTATG
* * *
43450 AAATTTTGATATCCGCCT-TG
1 AAATTTTGATAACCTCTTATG
43470 AAATTTTGAT
1 AAATTTTGAT
43480 TACTCCATAA
Statistics
Matches: 198, Mismatches: 33, Indels: 34
0.75 0.12 0.13
Matches are distributed among these distances:
16 11 0.06
18 2 0.01
19 1 0.01
20 13 0.07
21 9 0.05
22 110 0.56
23 50 0.25
24 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (21 bp):
AAATTTTGATAACCTCTTATG
Found at i:43660 original size:21 final size:22
Alignment explanation
Indices: 43585--43659 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
43575 TATCACATTT
* *
43585 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
43607 TGAAATTTTGATAACCTATCTA
1 TGAAATTTTGATAACCTCTCTA
* *
43629 TAAAATTTTG-TAACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
43650 TGAAATTTTG
1 TGAAATTTTG
43660 TTCTCCTCTA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 18 0.39
22 28 0.61
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:50594 original size:33 final size:33
Alignment explanation
Indices: 50515--50617 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
50505 GCAAAGAGTG
* * *
50515 TTTTAGATGTTGTTTGCGATCATACTAAATCTA
1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
* * *
50548 ATTT-GAGTTTTGTTTGCGATGACACTAAATCTA
1 TTTTAG-GTGTTGTTTGCGATGAAACTAAATCTA
* * *
50581 TTTTAGGTGTTGTTTGTGATGAAACAAAATCTG
1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
50614 TTTT
1 TTTT
50618 GGACGCTAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 1 0.02
33 55 0.96
34 1 0.02
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (33 bp):
TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
Found at i:51738 original size:21 final size:20
Alignment explanation
Indices: 51699--51743 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
51689 AATTATCAAT
* *
51699 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
51719 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
51740 TAAA
1 TAAA
51744 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:52496 original size:18 final size:17
Alignment explanation
Indices: 52473--52508 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
52463 CTCAACCTAA
52473 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
52491 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
52508 A
1 A
52509 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:57029 original size:26 final size:25
Alignment explanation
Indices: 56967--57034 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
56957 TAATGCCCGG
*
56967 GGCATTTTTGTCA-TTTTGCCCAGG
1 GGCATTTTTGTCATTTTTGCCCAGC
* * *
56991 GGTATTTTGGTCATTTTTGCTTCAGC
1 GGCATTTTTGTCATTTTTGC-CCAGC
57017 GGCATTTTTGTCATTTTT
1 GGCATTTTTGTCATTTTT
57035 ACACTTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
24 11 0.31
25 6 0.17
26 19 0.53
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (25 bp):
GGCATTTTTGTCATTTTTGCCCAGC
Found at i:57049 original size:26 final size:25
Alignment explanation
Indices: 56990--57057 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
56980 TTTTGCCCAG
*
56990 GGGTATTTTGGTCATTTTTGCTTCA
1 GGGTATTTTGGTCATTTTTACTTCA
* *
57015 GCGGCATTTTTGTCATTTTTACACTT-A
1 G-GGTATTTTGGTCATTTTT--ACTTCA
*
57042 GGGTATTTCGGTCATT
1 GGGTATTTTGGTCATT
57058 CTCATGAGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 1 0.03
26 28 0.82
27 2 0.06
28 3 0.09
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (25 bp):
GGGTATTTTGGTCATTTTTACTTCA
Found at i:61993 original size:21 final size:20
Alignment explanation
Indices: 61917--62005 Score: 88
Period size: 21 Copynumber: 4.3 Consensus size: 20
61907 CTGATCACCC
61917 TTTACTCTTACTGATTACTAT
1 TTTACTCTTACTGATTA-TAT
* * *
61938 TTGACTCTTACTAATTATCAC
1 TTTACTCTTACTGATTAT-AT
* *
61959 TTTGCTCTTACTGGTTACTAT
1 TTTACTCTTACTGATTA-TAT
* *
61980 TTTACTCTTACTGGTTATCT
1 TTTACTCTTACTGATTATAT
62000 TTTACT
1 TTTACT
62006 GATTACTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.16
21 46 0.82
22 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTACTCTTACTGATTATAT
Found at i:62030 original size:22 final size:22
Alignment explanation
Indices: 62000--62357 Score: 170
Period size: 22 Copynumber: 16.1 Consensus size: 22
61990 CTGGTTATCT
*
62000 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACCATTTTACTC
* *
62022 TTTGCTGATTACC-TTCTTACTT
1 TTTACTGATTACCATT-TTACTC
62044 TTTACTGATTACCATTTTACTC
1 TTTACTGATTACCATTTTACTC
*
62066 TTTTACTGATTACCATTTTCTGCTCCC
1 -TTTACTGATTACCA-TTT-TACT--C
*
62093 TTTTTACTGATTACTC-TTTTACTT
1 --TTTACTGATTAC-CATTTTACTC
** * *
62117 TTTACTGATTGTC-TTTTGCTT
1 TTTACTGATTACCATTTTACTC
* *
62138 TTTACTGATTACCTTTTTA-TT
1 TTTACTGATTACCATTTTACTC
* *
62159 TCTTACTGATTAGCTTTTTACTC
1 T-TTACTGATTACCATTTTACTC
* *
62182 TTTACTGATCA-CTTTTTCACTC
1 TTTACTGATTACCATTTT-ACTC
* *
62204 -TTATTGATTTCC-TTTTACT-
1 TTTACTGATTACCATTTTACTC
**
62223 TCTTACTTG-TTACTTTTTTTTACTC
1 T-TTAC-TGATTAC--CATTTTACTC
** *
62248 -TTACTGATTAATATTTTACTTT
1 TTTACTGATTACCATTTTAC-TC
* ** *
62270 TTTACTGACTATTATTTCACTC
1 TTTACTGATTACCATTTTACTC
*
62292 TTGT--TGATTACC-TTCTTACTT
1 TT-TACTGATTACCATT-TTACTC
*
62313 TTTAATGATTACC-TTTTACTC
1 TTTACTGATTACCATTTTACTC
* * *
62334 -TTACTAACTACCATTTTACCC
1 TTTACTGATTACCATTTTACTC
62355 TTT
1 TTT
62358 CAGATACTTT
Statistics
Matches: 266, Mismatches: 40, Indels: 60
0.73 0.11 0.16
Matches are distributed among these distances:
20 15 0.06
21 77 0.29
22 98 0.37
23 42 0.16
24 10 0.04
25 3 0.01
26 3 0.01
27 4 0.02
28 13 0.05
29 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTACTGATTACCATTTTACTC
Found at i:62052 original size:44 final size:44
Alignment explanation
Indices: 61999--62335 Score: 230
Period size: 44 Copynumber: 7.6 Consensus size: 44
61989 ACTGGTTATC
*
61999 TTTTACTGATTACTATTTTACTCTTTGCTGATTACCTTCTTACT
1 TTTTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACT
* *
62043 TTTTACTGATTACCATTTTACTCTTTTACTGATTACCATTTTCTGCTCCCT
1 TTTTACTGATTACTATTTTACTC-TTTACTGATTACC---TTCT--T-ACT
* * ** *
62094 TTTTACTGATTACTCTTTTACTTTTTACTGATTGTCTT-TTGCT
1 TTTTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACT
* * *
62137 TTTTACTGATTACCT-TTTTA-TTTCTTACTGATTAGCTTTTTACT
1 TTTTACTGATTA-CTATTTTACTCT-TTACTGATTACCTTCTTACT
* * * *
62181 CTTTACTGATCACT-TTTTCACTC-TTATTGATTTCCTT-TTACT
1 TTTTACTGATTACTATTTT-ACTCTTTACTGATTACCTTCTTACT
* * * *
62223 TCTTACTTG-TTACTTTTTTTTACTC-TTACTGATTA-ATATTTTACTT
1 TTTTAC-TGATTAC--TATTTTACTCTTTACTGATTACCT-TCTTAC-T
* * *
62269 TTTTACTGACTATTATTTCACTCTTGT--TGATTACCTTCTTACT
1 TTTTACTGATTACTATTTTACTCTT-TACTGATTACCTTCTTACT
* *
62312 TTTTAATGATTAC-CTTTTACTCTT
1 TTTTACTGATTACTATTTTACTCTT
62336 ACTAACTACC
Statistics
Matches: 234, Mismatches: 36, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
42 24 0.10
43 62 0.26
44 73 0.31
45 25 0.11
46 10 0.04
47 2 0.01
48 4 0.02
50 12 0.05
51 22 0.09
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.56
Consensus pattern (44 bp):
TTTTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACT
Found at i:62078 original size:15 final size:15
Alignment explanation
Indices: 62060--62115 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
62050 GATTACCATT
62060 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
62075 TTAC-CATTTT-CTGC
1 TTACTC-TTTTACTGA
**
62089 TCCCT-TTTTACTGA
1 TTACTCTTTTACTGA
62103 TTACTCTTTTACT
1 TTACTCTTTTACT
62116 TTTTACTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
13 4 0.13
14 12 0.39
15 15 0.48
ACGTcount: A:0.16, C:0.25, G:0.05, T:0.54
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:62568 original size:22 final size:24
Alignment explanation
Indices: 62541--62584 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
62531 TTAACCACTC
62541 AACTCTTAATTAT-GA-TCACTTT
1 AACTCTTAATTATCGATTCACTTT
62563 AACTCTTAATTATCGATTCACT
1 AACTCTTAATTATCGATTCACT
62585 GATTACCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (24 bp):
AACTCTTAATTATCGATTCACTTT
Found at i:62713 original size:56 final size:56
Alignment explanation
Indices: 62666--62781 Score: 182
Period size: 56 Copynumber: 2.1 Consensus size: 56
62656 CTATCTTTAC
*
62666 CTGA-TTACTGATTACTATTACCTTAACTC-TGATTAATCTCTTTTTACTTAATTA
1 CTGATTTACTGATTACTACTACCTTAACTCATGATTAATCTCTTTTTACTTAATTA
* * *
62720 CTGATTTACTGATTACTGCTACTTTGACTCATGATTAATCTCTTTTTACTTAATTA
1 CTGATTTACTGATTACTACTACCTTAACTCATGATTAATCTCTTTTTACTTAATTA
62776 CTGATT
1 CTGATT
62782 GCCCCCTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
54 4 0.07
55 21 0.38
56 31 0.55
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (56 bp):
CTGATTTACTGATTACTACTACCTTAACTCATGATTAATCTCTTTTTACTTAATTA
Done.