Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009784.1 Corchorus capsularis cultivar CVL-1 contig09805, 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: 23358
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Found at i:4048 original size:21 final size:21
Alignment explanation
Indices: 4022--4067 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4012 ACGAGTTCAA
*
4022 CAAATTTATAGA-CCTAAACTC
1 CAAATTTATAAATCC-AAACTC
4043 CAAATTTATAAATCCAAACTC
1 CAAATTTATAAATCCAAACTC
4064 CAAA
1 CAAA
4068 CGTGACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (21 bp):
CAAATTTATAAATCCAAACTC
Found at i:4224 original size:23 final size:22
Alignment explanation
Indices: 4198--4262 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
4188 AATTGGGGTA
*
4198 AGGTTTAATGTGGTTTGACTATT
1 AGGTTT-ATGGGGTTTGACTATT
* *
4221 AGGTTTTTGGGGTTTGTCTATT
1 AGGTTTATGGGGTTTGACTATT
** *
4243 AAATTTA-GGGGTTTAACTAT
1 AGGTTTATGGGGTTTGACTAT
4263 CAAATCGAGC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 11 0.32
22 17 0.50
23 6 0.18
ACGTcount: A:0.22, C:0.05, G:0.26, T:0.48
Consensus pattern (22 bp):
AGGTTTATGGGGTTTGACTATT
Found at i:4488 original size:22 final size:23
Alignment explanation
Indices: 4462--4518 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 23
4452 GGTTTAACAT
*
4462 GTTTTGACTATCAAA-TTTTGGA
1 GTTTTGACTATCAAACTTTCGGA
*
4484 GTTTT-ACTATTAAACTTTCGGA
1 GTTTTGACTATCAAACTTTCGGA
4506 --TTTGACTATCAAA
1 GTTTTGACTATCAAA
4519 ATGAAATGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 3 0.10
21 16 0.53
22 11 0.37
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (23 bp):
GTTTTGACTATCAAACTTTCGGA
Found at i:4854 original size:21 final size:21
Alignment explanation
Indices: 4820--4871 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
4810 AAGTTTTAAC
* *
4820 GTGGTTTAAATATTAAATTTT
1 GTGGTTTGAATATTAAACTTT
* *
4841 GTGGTTTGATTATTACACTTT
1 GTGGTTTGAATATTAAACTTT
*
4862 GGGGTTTGAA
1 GTGGTTTGAA
4872 ATTTAGAGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (21 bp):
GTGGTTTGAATATTAAACTTT
Found at i:4945 original size:20 final size:21
Alignment explanation
Indices: 4920--4967 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
4910 TGCTTTGTGT
* *
4920 GGTTTGACTATCAT-TTTTTG
1 GGTTTGACTATCATCCTTTGG
*
4940 GGTTTGCCTATCATCCTTTGG
1 GGTTTGACTATCATCCTTTGG
4961 GGTTTGA
1 GGTTTGA
4968 TAGTGCATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (21 bp):
GGTTTGACTATCATCCTTTGG
Found at i:6562 original size:2 final size:2
Alignment explanation
Indices: 6516--6542 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6506 CACCCATTTA
6516 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
6543 GGCAATACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:8162 original size:27 final size:25
Alignment explanation
Indices: 8105--8289 Score: 90
Period size: 27 Copynumber: 6.9 Consensus size: 25
8095 TATTTTTTGA
* *
8105 TTACTAATTACCATTTTTTACTCTT
1 TTACTGATTACCATATTTTACTCTT
8130 TGTACTGATTACCATATTTTACTCCGTT
1 T-TACTGATTACCATATTTTACT-C-TT
* * *
8158 TTACTGATTACCCCTTTTCTTACTGTTT
1 TTACTGATTA-CCATATT-TTACT-CTT
* *
8186 TTACTGAATATCACT-TTTTACTCTTT
1 TTACTGATTACCA-TATTTTACTC-TT
* *
8212 TTATTTAATTACCAT-TTCTTACTCTTT
1 TTA-CTGATTACCATATT-TTACTC-TT
* *
8239 ATTACTAATTACTC-TCTTTTACTCTTTT
1 -TTACTGATTAC-CATATTTTACTC--TT
*
8267 TTACTGATCACCACT-TTTTACTC
1 TTACTGATTACCA-TATTTTACTC
8290 ATTTCTTACT
Statistics
Matches: 128, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
25 1 0.01
26 33 0.26
27 59 0.46
28 30 0.23
29 5 0.04
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.53
Consensus pattern (25 bp):
TTACTGATTACCATATTTTACTCTT
Found at i:8510 original size:165 final size:165
Alignment explanation
Indices: 8317--8616 Score: 487
Period size: 165 Copynumber: 1.8 Consensus size: 165
8307 CCGATTACTC
*
8317 TTTTCTCTCTGAATTTAATTACTGACTATCATTTTACTCTTTACTGATTATTTCTTTACTTTTTT
1 TTTTCTCTCTGAACTTAATTACTGACTATCATTTTACTCTTTACTGATTATTTCTTTACTTTTTT
* *
8382 ATTAATTACTA-TTTCACTCTTACTGGTTACCATTA-CTTTTTAAACTTGAACACTGATTACCTT
66 ATTAATTACTACTTT-ACTCTCACTGATTACCATTATCTTTTTAAACTTGAACACTGATTACCTT
8445 TTTACTTCTCTTCTTTTTCTCTTTTACTGACTACCA
130 TTTACTTCTCTTCTTTTTCTCTTTTACTGACTACCA
*
8481 TTTTACTCTTTGAACTTAATTACTGACTATCATTTTACTCTTTACTGATTATTTCTTTACTTTTT
1 TTTT-CTCTCTGAACTTAATTACTGACTATCATTTTACTCTTTACTGATTATTTCTTTACTTTTT
* * * **
8546 TATTAATTACTACTTTACTCTCACTGATTATCATTATTTTTTTGAACTTGATTACTGATTACCTT
65 TATTAATTACTACTTTACTCTCACTGATTACCATTATCTTTTTAAACTTGAACACTGATTACCTT
8611 TTTACT
130 TTTACT
8617 GTTTACTGTT
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
164 4 0.03
165 87 0.70
166 33 0.27
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (165 bp):
TTTTCTCTCTGAACTTAATTACTGACTATCATTTTACTCTTTACTGATTATTTCTTTACTTTTTT
ATTAATTACTACTTTACTCTCACTGATTACCATTATCTTTTTAAACTTGAACACTGATTACCTTT
TTACTTCTCTTCTTTTTCTCTTTTACTGACTACCA
Found at i:8671 original size:22 final size:22
Alignment explanation
Indices: 8645--8800 Score: 130
Period size: 22 Copynumber: 7.4 Consensus size: 22
8635 CTAATTTCTA
* *
8645 TTACTCTTTACTGATTATCACT
1 TTACTCTTTACTGATTACCATT
*
8667 TTACTCTTTACTAATTACCATT
1 TTACTCTTTACTGATTACCATT
* * *
8689 TTACCCTTT-CAGA-TACCTTT
1 TTACTCTTTACTGATTACCATT
* *
8709 TTACTTTTTACTGATTACCTTT
1 TTACTCTTTACTGATTACCATT
* * *
8731 TTACTTTTTACTGTTTA-C-TA
1 TTACTCTTTACTGATTACCATT
* *
8751 TTACT-TCTTACTGATT-TC-TA
1 TTACTCT-TTACTGATTACCATT
8771 TTACTCTTTACTGATTACCATT
1 TTACTCTTTACTGATTACCATT
8793 TTAC-CTTT
1 TTACTCTTT
8801 TACTTATTGC
Statistics
Matches: 112, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.01
20 44 0.39
21 12 0.11
22 55 0.49
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.53
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCATT
Found at i:8717 original size:7 final size:7
Alignment explanation
Indices: 8705--8762 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
8695 TTTCAGATAC
8705 CTTTTTA
1 CTTTTTA
8712 CTTTTTA
1 CTTTTTA
**
8719 CTGATTA
1 CTTTTTA
8726 CCTTTTTA
1 -CTTTTTA
8734 CTTTTTA
1 CTTTTTA
*
8741 CTGTTTA
1 CTTTTTA
*
8748 C-TATTA
1 CTTTTTA
*
8754 CTTCTTA
1 CTTTTTA
8761 CT
1 CT
8763 GATTTCTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 4 0.10
7 32 0.78
8 5 0.12
ACGTcount: A:0.17, C:0.19, G:0.03, T:0.60
Consensus pattern (7 bp):
CTTTTTA
Found at i:8756 original size:20 final size:20
Alignment explanation
Indices: 8594--8788 Score: 108
Period size: 20 Copynumber: 9.3 Consensus size: 20
8584 TTTTTGAACT
8594 TGATTACTGATTACCTTTTTAC
1 TGATTACT-ATTA-CTTTTTAC
* * *
8616 TGTTTACTGTTACTTCTTAC
1 TGATTACTATTACTTTTTAC
* * *
8636 TAATTTCTATTACTCTTTAC
1 TGATTACTATTACTTTTTAC
*
8656 TGATTA-TCACTTTACTCTTTAC
1 TGATTACT-A--TTACTTTTTAC
* * **
8678 TAATTACCATTTTACCCTTT-C
1 TGATTA-C-TATTACTTTTTAC
* *
8699 AGA-TACCTTTTTACTTTTTAC
1 TGATTA-C-TATTACTTTTTAC
*
8720 TGATTACCTTTTTACTTTTTAC
1 TGATTA-C-TATTACTTTTTAC
* *
8742 TGTTTACTATTACTTCTTAC
1 TGATTACTATTACTTTTTAC
* *
8762 TGATTTCTATTACTCTTTAC
1 TGATTACTATTACTTTTTAC
8782 TGATTAC
1 TGATTAC
8789 CATTTTACCT
Statistics
Matches: 137, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.01
20 72 0.53
21 9 0.07
22 54 0.39
25 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.53
Consensus pattern (20 bp):
TGATTACTATTACTTTTTAC
Found at i:8804 original size:42 final size:43
Alignment explanation
Indices: 8625--8804 Score: 124
Period size: 42 Copynumber: 4.3 Consensus size: 43
8615 CTGTTTACTG
* * *
8625 TTACTTCTTACTAATT-TC-TATTACTCTTTACTGATTATCACT
1 TTACTT-TTACTAATTACCATATTACTCTTTACTGATTACCATT
* * * *
8667 TTACTCTTTACTAATTACCATTTTACCCTTT-CAGA-TACCTTT
1 TTACT-TTTACTAATTACCATATTACTCTTTACTGATTACCATT
* * * * * *
8709 TTACTTTTTACTGATTACCTTTTTACTTTTTACTGTTTA-C-TA
1 TTAC-TTTTACTAATTACCATATTACTCTTTACTGATTACCATT
* *
8751 TTACTTCTTACTGATT-TC-TATTACTCTTTACTGATTACCATT
1 TTACTT-TTACTAATTACCATATTACTCTTTACTGATTACCATT
8793 TTACCTTTTACT
1 TTA-CTTTTACT
8805 TATTGCATCT
Statistics
Matches: 109, Mismatches: 19, Indels: 20
0.74 0.13 0.14
Matches are distributed among these distances:
40 16 0.15
41 4 0.04
42 66 0.61
43 12 0.11
44 11 0.10
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (43 bp):
TTACTTTTACTAATTACCATATTACTCTTTACTGATTACCATT
Found at i:10309 original size:10 final size:10
Alignment explanation
Indices: 10294--10344 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
10284 CAATCGATGT
10294 CCGGTTGTGG
1 CCGGTTGTGG
10304 CCGGTTGGTGCG
1 CCGGTT-GTG-G
*
10316 CCAGG-CGATGG
1 CC-GGTTG-TGG
10327 CCGGTTGTGG
1 CCGGTTGTGG
10337 CCGGTTGT
1 CCGGTTGT
10345 CCCATACGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 19 0.56
11 8 0.24
12 5 0.15
13 2 0.06
ACGTcount: A:0.04, C:0.24, G:0.47, T:0.25
Consensus pattern (10 bp):
CCGGTTGTGG
Found at i:15885 original size:9 final size:8
Alignment explanation
Indices: 15867--15899 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
15857 GAATCGGCTA
15867 TGAATTTT
1 TGAATTTT
15875 TGAAGTTTT
1 TGAA-TTTT
15884 TGAATTTT
1 TGAATTTT
15892 TGAATTTT
1 TGAATTTT
15900 CAAGAAGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (8 bp):
TGAATTTT
Found at i:15889 original size:17 final size:16
Alignment explanation
Indices: 15867--15899 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
15857 GAATCGGCTA
15867 TGAATTTTTGAAGTTTT
1 TGAATTTTTGAA-TTTT
15884 TGAATTTTTGAATTTT
1 TGAATTTTTGAATTTT
15900 CAAGAAGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (16 bp):
TGAATTTTTGAATTTT
Found at i:16841 original size:10 final size:10
Alignment explanation
Indices: 16826--16876 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
16816 CAATCGATGT
16826 CCGGTTGTGG
1 CCGGTTGTGG
16836 CCGGTTGGTGCG
1 CCGGTT-GTG-G
*
16848 CCAGG-CGATGG
1 CC-GGTTG-TGG
16859 CCGGTTGTGG
1 CCGGTTGTGG
16869 CCGGTTGT
1 CCGGTTGT
16877 CCCATGCGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 19 0.56
11 8 0.24
12 5 0.15
13 2 0.06
ACGTcount: A:0.04, C:0.24, G:0.47, T:0.25
Consensus pattern (10 bp):
CCGGTTGTGG
Found at i:18978 original size:12 final size:13
Alignment explanation
Indices: 18953--18986 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
18943 ATAATTATTG
18953 TTTGCTTTATTAA
1 TTTGCTTTATTAA
18966 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
18978 TCTGCTTTA
1 TTTGCTTTA
18987 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:19020 original size:28 final size:25
Alignment explanation
Indices: 18980--19033 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
18970 CTTTATAATC
18980 TGCTTTAGATTTAGATTTAGATTTGTTT
1 TGCTTTAGATTTAG-TTTA-A-TTGTTT
**
19008 TGCTTTATTTTTAGTTTAATTGTTT
1 TGCTTTAGATTTAGTTTAATTGTTT
19033 T
1 T
19034 TAGGGGATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 1 0.04
27 4 0.17
28 12 0.50
ACGTcount: A:0.19, C:0.04, G:0.15, T:0.63
Consensus pattern (25 bp):
TGCTTTAGATTTAGTTTAATTGTTT
Found at i:19554 original size:2 final size:2
Alignment explanation
Indices: 19547--19578 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19537 CATCAGGTCC
19547 AT AT AT 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 AT AT AT
19579 GCTAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20676 original size:29 final size:29
Alignment explanation
Indices: 20634--20694 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
20624 GGTTGGTCAT
*
20634 CAACGCCTCTTGCATTTTGTCATGTGCTC
1 CAACGCCTCTTGCATCTTGTCATGTGCTC
20663 CAACGCCTCTTGCATCTTGTCATGTGCTC
1 CAACGCCTCTTGCATCTTGTCATGTGCTC
20692 CAA
1 CAA
20695 GCCCTTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.34
Consensus pattern (29 bp):
CAACGCCTCTTGCATCTTGTCATGTGCTC
Found at i:21954 original size:24 final size:24
Alignment explanation
Indices: 21912--21960 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
21902 ATTAGTTAAT
21912 TAAATTAGATTGGAACTACATGAA
1 TAAATTAGATTGGAACTACATGAA
* * *
21936 TAAATTATATTTGAGCTACATGAA
1 TAAATTAGATTGGAACTACATGAA
21960 T
1 T
21961 GCCGAAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (24 bp):
TAAATTAGATTGGAACTACATGAA
Found at i:22062 original size:26 final size:26
Alignment explanation
Indices: 22013--22062 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
22003 ATCTAGATGA
* *
22013 CTAAAAATGAATTAGCTCATCTAAGC
1 CTAAAAATGAATTAGCTAACCTAAGC
* *
22039 CTAAATATGAGTTAGCTAACCTAA
1 CTAAAAATGAATTAGCTAACCTAA
22063 ACTAAAAGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (26 bp):
CTAAAAATGAATTAGCTAACCTAAGC
Found at i:22117 original size:26 final size:27
Alignment explanation
Indices: 22078--22150 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
22068 AAGTGGTCCT
*
22078 CAAAATGACCAAAATGCCCCTA-GACT
1 CAAAATGACCAAAATGCCCCTAGGACC
* * ** *
22104 TAAAATGACTAAAACACCCCTAGGGCC
1 CAAAATGACCAAAATGCCCCTAGGACC
22131 CAAAATGACCAAAATGCCCC
1 CAAAATGACCAAAATGCCCC
22151 CCTAGATGAC
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
26 18 0.50
27 18 0.50
ACGTcount: A:0.42, C:0.32, G:0.12, T:0.14
Consensus pattern (27 bp):
CAAAATGACCAAAATGCCCCTAGGACC
Found at i:22882 original size:19 final size:19
Alignment explanation
Indices: 22855--22899 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
22845 CGCGACCCGC
22855 TGTTCTTCTTCTTTTTTTT
1 TGTTCTTCTTCTTTTTTTT
*
22874 TGTTTTTCTTCTTTTTTTT
1 TGTTCTTCTTCTTTTTTTT
*
22893 TCTTCTT
1 TGTTCTT
22900 TAAAGGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (19 bp):
TGTTCTTCTTCTTTTTTTT
Found at i:22888 original size:16 final size:16
Alignment explanation
Indices: 22860--22899 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
22850 CCCGCTGTTC
22860 TTCTTCTT-TTTTTTT
1 TTCTTCTTCTTTTTTT
*
22875 GTTTTTCTTCTTTTTTT
1 -TTCTTCTTCTTTTTTT
22892 TTCTTCTT
1 TTCTTCTT
22900 TAAAGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTCTTCTTCTTTTTTT
Found at i:22894 original size:13 final size:14
Alignment explanation
Indices: 22871--22900 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
22861 TCTTCTTTTT
22871 TTTTGTTTTTCTTC
1 TTTTGTTTTTCTTC
22885 TTTT-TTTTTCTTC
1 TTTTGTTTTTCTTC
22898 TTT
1 TTT
22901 AAAGGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTGTTTTTCTTC
Done.