Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008874.1 Corchorus capsularis cultivar CVL-1 contig08895, 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: 55410
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1000 original size:12 final size:12
Alignment explanation
Indices: 980--1013 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
970 TTGCCTCATC
*
980 TTTTCTTTTCTT
1 TTTTTTTTTCTT
992 TTTTTTTTTCTT
1 TTTTTTTTTCTT
1004 TTTTGTTTTT
1 TTTT-TTTTT
1014 ACTTCTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:2564 original size:22 final size:22
Alignment explanation
Indices: 2539--2582 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2529 CAATATTCAG
2539 ACATCATAAATATGGATAGAAA
1 ACATCATAAATATGGATAGAAA
*
2561 ACATCATAAATCTGGATAGAAA
1 ACATCATAAATATGGATAGAAA
2583 TCCTTTCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (22 bp):
ACATCATAAATATGGATAGAAA
Found at i:14225 original size:30 final size:30
Alignment explanation
Indices: 14189--14247 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
14179 TGTCTTCAAG
14189 TCCATGATAAGTCCTT-GGCGCATCATTCCT
1 TCCATGATAAG-CCTTGGGCGCATCATTCCT
*
14219 TCCATGATAAGCGTTGGGCGCATCATTCC
1 TCCATGATAAGCCTTGGGCGCATCATTCC
14248 ATGAAAGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCT
Found at i:15666 original size:30 final size:30
Alignment explanation
Indices: 15626--15688 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
15616 TTTCTTAAGA
*
15626 AAAAACTTTCTA-GTTTTAAACTTTCTATAG
1 AAAAACTTTCTACCTTTT-AACTTTCTATAG
* *
15656 AAAAATTTTCTACCTTTTTACTTTCTATAG
1 AAAAACTTTCTACCTTTTAACTTTCTATAG
15686 AAA
1 AAA
15689 CTTCCAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (30 bp):
AAAAACTTTCTACCTTTTAACTTTCTATAG
Found at i:25939 original size:15 final size:16
Alignment explanation
Indices: 25919--25957 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
25909 GCTTTTTTAT
25919 TTTAA-TTGCTTTCTA
1 TTTAATTTGCTTTCTA
25934 TTTAATTTGCTTTCT-
1 TTTAATTTGCTTTCTA
*
25949 GTTAATTTG
1 TTTAATTTG
25958 AATTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (16 bp):
TTTAATTTGCTTTCTA
Found at i:26225 original size:6 final size:6
Alignment explanation
Indices: 26215--26258 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
26205 CCCTCCACGT
* *
26215 TTTTTT TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TGTTTG TT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
26259 AACTAGGTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:35609 original size:12 final size:12
Alignment explanation
Indices: 35592--35631 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
35582 ATAAAAAATT
*
35592 AAAAAAATGAAA
1 AAAAAAACGAAA
35604 AAAAAAACGAAA
1 AAAAAAACGAAA
35616 AAAAAAACAGAAA
1 AAAAAAAC-GAAA
35629 AAA
1 AAA
35632 GTAGGGCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.85, C:0.05, G:0.07, T:0.03
Consensus pattern (12 bp):
AAAAAAACGAAA
Found at i:36067 original size:19 final size:19
Alignment explanation
Indices: 36036--36079 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
36026 TAAACCACCA
36036 TTTTTTCTGCTTTTCT-TT
1 TTTTTTCTGCTTTTCTGTT
*
36054 TTTTTCTCTTCTTTTCTGTT
1 TTTTT-TCTGCTTTTCTGTT
36074 TTTTTT
1 TTTTTT
36080 TCAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 11 0.48
20 7 0.30
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTTTCTGCTTTTCTGTT
Found at i:37645 original size:11 final size:10
Alignment explanation
Indices: 37629--37681 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
37619 AAGTTCGTGT
37629 TTGAAGATTTA
1 TTGAAGA-TTA
*
37640 TTGAAGATAA
1 TTGAAGATTA
37650 TTTGAAGA--A
1 -TTGAAGATTA
37659 TTGAAGATTA
1 TTGAAGATTA
37669 TTGAAGAATTA
1 TTGAAG-ATTA
37680 TT
1 TT
37682 TCAAGAAGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 9 0.24
11 20 0.54
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:37674 original size:18 final size:19
Alignment explanation
Indices: 37639--37678 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
37629 TTGAAGATTT
37639 ATTGAAGATAATTTGAAGA
1 ATTGAAGATAATTTGAAGA
*
37658 ATTGAAGATTA-TTGAAGA
1 ATTGAAGATAATTTGAAGA
37676 ATT
1 ATT
37679 ATTTCAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (19 bp):
ATTGAAGATAATTTGAAGA
Found at i:37688 original size:30 final size:30
Alignment explanation
Indices: 37629--37688 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
37619 AAGTTCGTGT
*
37629 TTGAAGATTTATTGAAGATAATTTGAAGAA
1 TTGAAGATTTATTGAAGATAATTTCAAGAA
*
37659 TTGAAGA-TTATTGAAGAATTATTTCAAGAA
1 TTGAAGATTTATTGAAG-ATAATTTCAAGAA
37689 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (30 bp):
TTGAAGATTTATTGAAGATAATTTCAAGAA
Found at i:39645 original size:6 final size:6
Alignment explanation
Indices: 39629--39659 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
39619 CTAAGCAAAG
39629 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
39660 TGGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:41020 original size:11 final size:11
Alignment explanation
Indices: 41003--41034 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
40993 ATTGTCTTCA
41003 AATCTTCAAAT
1 AATCTTCAAAT
*
41014 TATCTTCAAAT
1 AATCTTCAAAT
41025 AATCTTCAAA
1 AATCTTCAAA
41035 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:41031 original size:22 final size:22
Alignment explanation
Indices: 40980--41034 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 22
40970 TTACTTCATG
*
40980 AAATAATTCTTC-AATTGTCTTC
1 AAATAA-TCTTCAAATTATCTTC
41002 --A-AATCTTCAAATTATCTTC
1 AAATAATCTTCAAATTATCTTC
41021 AAATAATCTTCAAA
1 AAATAATCTTCAAA
41035 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 1 0.04
21 1 0.04
22 10 0.36
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATAATCTTCAAATTATCTTC
Found at i:45748 original size:19 final size:18
Alignment explanation
Indices: 45724--45763 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
45714 TTGAAGATTT
*
45724 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
45743 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
45761 ATT
1 ATT
45764 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:51065 original size:24 final size:26
Alignment explanation
Indices: 51038--51085 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
51028 TACTGATTAC
51038 CATTTTTACT-TTTGC-TACTTTTAT
1 CATTTTTACTCTTTGCTTACTTTTAT
*
51062 CATTTTTACTCTTTTCTTACTTTT
1 CATTTTTACTCTTTGCTTACTTTT
51086 TTTACTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 4 0.19
26 7 0.33
ACGTcount: A:0.15, C:0.19, G:0.02, T:0.65
Consensus pattern (26 bp):
CATTTTTACTCTTTGCTTACTTTTAT
Found at i:51125 original size:28 final size:27
Alignment explanation
Indices: 51074--51144 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
51064 TTTTTACTCT
*
51074 TTTCTTACT-TTTTTTACTAATTACCC
1 TTTCTTACTCTCTTTTACTAATTACCC
* *
51100 TTTCCTTACTCTCTTTTATTGATTACCAC
1 TTT-CTTACTCTCTTTTACTAATTACC-C
51129 TTT-TTACTCTTCTTTT
1 TTTCTTACTC-TCTTTT
51145 TCTCTTATAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.08
27 12 0.32
28 19 0.50
29 4 0.11
ACGTcount: A:0.15, C:0.24, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTCTTACTCTCTTTTACTAATTACCC
Found at i:51236 original size:21 final size:21
Alignment explanation
Indices: 51206--51286 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
51196 TCTTTACTGA
*
51206 TTACTCCTTACTAATTACCATT
1 TTACT-CTTACTGATTACCATT
* *
51228 TTGCTCTTACTGATTACTATT
1 TTACTCTTACTGATTACCATT
*
51249 TTACTCTGACTGATTACC-TT
1 TTACTCTTACTGATTACCATT
*
51269 TTACTGATTACT-ATTACC
1 TTACT-CTTACTGATTACC
51287 TGATTACTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 13 0.26
21 33 0.66
22 4 0.08
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.47
Consensus pattern (21 bp):
TTACTCTTACTGATTACCATT
Found at i:51276 original size:14 final size:14
Alignment explanation
Indices: 51257--51301 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
51247 TTTTACTCTG
51257 ACTGATTACCTTTT
1 ACTGATTACCTTTT
*
51271 ACTGATTA-CTATT
1 ACTGATTACCTTTT
*
51284 ACCTGATTACTTTTT
1 A-CTGATTACCTTTT
51299 ACT
1 ACT
51302 ACTCTTTGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 5 0.19
14 17 0.65
15 4 0.15
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (14 bp):
ACTGATTACCTTTT
Found at i:51338 original size:14 final size:14
Alignment explanation
Indices: 51316--51361 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
51306 TTTGCCATTT
51316 TTACT-TTTACTGA
1 TTACTCTTTACTGA
**
51329 TTACTCTTTACTTT
1 TTACTCTTTACTGA
*
51343 TTCCTCTTTACTGA
1 TTACTCTTTACTGA
51357 TTACT
1 TTACT
51362 ATTTTACCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.17, C:0.22, G:0.04, T:0.57
Consensus pattern (14 bp):
TTACTCTTTACTGA
Found at i:51402 original size:26 final size:27
Alignment explanation
Indices: 51356--51423 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
51346 CTCTTTACTG
**
51356 ATTACTATTTT-ACCCTCTTGAACTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
*
51382 ATTACTATTTTCATTCT-TTGAATTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
* *
51408 ATCACCATTTGTCATT
1 ATTACTATTT-TCATT
51424 TTACTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTACTATTTTCATTCTCTTGAACTTA
Found at i:51457 original size:33 final size:32
Alignment explanation
Indices: 51396--51465 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
51386 CTATTTTCAT
51396 TCTTTGAATTTAATCACCATTTGTCATTTTAC
1 TCTTTGAATTTAATCACCATTTGTCATTTTAC
* *
51428 TCTTTGGATTTAATTACCATTT-TACCATTTTAC
1 TCTTTGAATTTAATCACCATTTGT--CATTTTAC
51461 TCTTT
1 TCTTT
51466 ACCGATTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 1 0.03
32 20 0.59
33 13 0.38
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (32 bp):
TCTTTGAATTTAATCACCATTTGTCATTTTAC
Found at i:51545 original size:40 final size:40
Alignment explanation
Indices: 51501--51616 Score: 207
Period size: 40 Copynumber: 2.9 Consensus size: 40
51491 TTTTTACTCT
51501 TTACCGA-TTAACTGATTACTTCTTTTACTTTTACTCTTAA
1 TTACCGACTT-ACTGATTACTTCTTTTACTTTTACTCTTAA
51541 TTACCGACTTACTGATTACTTCTTTTACTTTTACTCTTAA
1 TTACCGACTTACTGATTACTTCTTTTACTTTTACTCTTAA
*
51581 TTACCGACTTACTGATTACTTCTTTTACTTTCACTC
1 TTACCGACTTACTGATTACTTCTTTTACTTTTACTC
51617 CATTTTACTG
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
40 72 0.97
41 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.05, T:0.49
Consensus pattern (40 bp):
TTACCGACTTACTGATTACTTCTTTTACTTTTACTCTTAA
Found at i:51705 original size:16 final size:16
Alignment explanation
Indices: 51684--51747 Score: 78
Period size: 16 Copynumber: 4.1 Consensus size: 16
51674 ACTTCTTTTA
51684 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
**
51700 CTTTTACT--TTTGTT
1 CTTTTACTGATTACTT
51714 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
* *
51730 CCTCTACTGATTACTT
1 CTTTTACTGATTACTT
51746 CT
1 CT
51748 CTTGATTACC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 12 0.31
16 27 0.69
ACGTcount: A:0.16, C:0.22, G:0.06, T:0.56
Consensus pattern (16 bp):
CTTTTACTGATTACTT
Found at i:51744 original size:96 final size:99
Alignment explanation
Indices: 51589--51784 Score: 290
Period size: 96 Copynumber: 2.0 Consensus size: 99
51579 AATTACCGAC
* *
51589 TTACTGATTACTTCTTTTACTTTCACTCCATTTTACTGATTACTTCTTCTACGGGTTACTTCTCT
1 TTACTGATTACTTCTTTTACTTTCACTCCATTTTACTGATTACTTCCTCTACGGATTACTTCTCT
*
51654 TGATTATCATTTTTCCGATTAC-TTCTTTTACTT
66 TGATTACCATTTTTCCGATTACTTTCTTTTACTT
** * *
51687 TTACTGATTACTTCTTTTACTTT-TGTTC-TTTTACTGATTACTTCCTCTACTGATTACTTCTCT
1 TTACTGATTACTTCTTTTACTTTCACTCCATTTTACTGATTACTTCCTCTACGGATTACTTCTCT
* *
51750 TGATTACCATTTTTCTGATTACTTTTTTTTACTT
66 TGATTACCATTTTTCCGATTACTTTCTTTTACTT
51784 T
1 T
51785 GACTCTTTGA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
96 52 0.59
97 13 0.15
98 23 0.26
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.56
Consensus pattern (99 bp):
TTACTGATTACTTCTTTTACTTTCACTCCATTTTACTGATTACTTCCTCTACGGATTACTTCTCT
TGATTACCATTTTTCCGATTACTTTCTTTTACTT
Found at i:51871 original size:45 final size:47
Alignment explanation
Indices: 51794--51898 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 47
51784 TGACTCTTTG
* * * * *
51794 ATTACTGACTTTACTGATTAATCTCTTACCTTGATTCTTAATTTTTAA
1 ATTACTGA-TTAACTGATTAATCTATTACCTTGACTCTTAATTATCAA
*
51842 ATTACTGATTAACTGATT-A-CTATTACCTTGACTCTTGATTATCAA
1 ATTACTGATTAACTGATTAATCTATTACCTTGACTCTTAATTATCAA
*
51887 TTTACTGATTAA
1 ATTACTGATTAA
51899 TCTCCTTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 32 0.64
46 1 0.02
47 9 0.18
48 8 0.16
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.47
Consensus pattern (47 bp):
ATTACTGATTAACTGATTAATCTATTACCTTGACTCTTAATTATCAA
Found at i:51961 original size:37 final size:38
Alignment explanation
Indices: 51853--51993 Score: 147
Period size: 37 Copynumber: 3.8 Consensus size: 38
51843 TTACTGATTA
*
51853 ACTGATTACTAT-TACCTTGACTCTTGATTATCAATTT
1 ACTGATTACTATCTACCTTGACTCTTAATTATCAATTT
* *
51890 ACTGATTA--ATCT-CCTT--TTACTTAATTA-CTGATTT
1 ACTGATTACTATCTACCTTGACT-CTTAATTATC-AATTT
51924 ACTGATTACTAT-TACCTTGACTCTTAATTATCAATTT
1 ACTGATTACTATCTACCTTGACTCTTAATTATCAATTT
51961 ACTGATTAATCCT-TCTACCTTGACTCTTAATTA
1 ACTGATT-A--CTATCTACCTTGACTCTTAATTA
51994 CTGACTTACC
Statistics
Matches: 86, Mismatches: 5, Indels: 23
0.75 0.04 0.20
Matches are distributed among these distances:
33 2 0.02
34 19 0.22
35 7 0.08
36 7 0.08
37 27 0.31
38 3 0.03
39 1 0.01
40 20 0.23
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (38 bp):
ACTGATTACTATCTACCTTGACTCTTAATTATCAATTT
Found at i:52118 original size:38 final size:39
Alignment explanation
Indices: 52025--52118 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 39
52015 ACCCTTACTT
* * * *
52025 ACTGATTGCTACTTTTACTTCTTCTCTTAGTTATCAATTT
1 ACTGATTACTACTTTTACTTC-TCTCTTAATTACCAATTG
* *
52065 ACTGATTAATCCTTTTACTTC-CTCTTAATTACCAATTG
1 ACTGATTACTACTTTTACTTCTCTCTTAATTACCAATTG
*
52103 ACTGATTACTTCTTTT
1 ACTGATTACTACTTTT
52119 TCTTTTCACT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 28 0.61
40 18 0.39
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.50
Consensus pattern (39 bp):
ACTGATTACTACTTTTACTTCTCTCTTAATTACCAATTG
Found at i:52247 original size:23 final size:23
Alignment explanation
Indices: 52215--52260 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
52205 TTCATTAATC
* *
52215 CTTTTACTTTCCTTTTTTTGCTT
1 CTTTTACTTTCATTTTTTAGCTT
*
52238 CTTTTGCTTTCATTTTTTAGCTT
1 CTTTTACTTTCATTTTTTAGCTT
52261 AATCACTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.07, C:0.20, G:0.07, T:0.67
Consensus pattern (23 bp):
CTTTTACTTTCATTTTTTAGCTT
Done.