Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015437.1 Corchorus capsularis cultivar CVL-1 contig15458, 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: 29547
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:4415 original size:30 final size:31
Alignment explanation
Indices: 4381--4455 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
4371 CCGGTTGTGC
* ** *
4381 CCGGTCTTGTCCGATTGGC-CCATGCCATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
*
4411 CCGGTCATGTGCGA-TCCCTCCATGCAATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
4441 CCGGTCTTGTGCGAT
1 CCGGTCTTGTGCGAT
4456 GGCATCCTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.12, C:0.32, G:0.29, T:0.27
Consensus pattern (31 bp):
CCGGTCTTGTGCGATTCCCTCCATGCAATGG
Found at i:14266 original size:22 final size:22
Alignment explanation
Indices: 14240--14313 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
14230 TGCATGGGCA
14240 TGGCCGGGTCATGTGGTTGGTG
1 TGGCCGGGTCATGTGGTTGGTG
* **
14262 TGGCCGGG-CATGTGCGATCGGCA
1 TGGCCGGGTCATGTG-G-TTGGTG
* *
14285 TGGCCGGGTCATGTAGCTGGTG
1 TGGCCGGGTCATGTGGTTGGTG
14307 TGGCCGG
1 TGGCCGG
14314 TCAAGTGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
21 6 0.15
22 18 0.44
23 12 0.29
24 5 0.12
ACGTcount: A:0.08, C:0.20, G:0.47, T:0.24
Consensus pattern (22 bp):
TGGCCGGGTCATGTGGTTGGTG
Found at i:14291 original size:23 final size:24
Alignment explanation
Indices: 14213--14298 Score: 80
Period size: 23 Copynumber: 3.9 Consensus size: 24
14203 ATGGCTAAAG
14213 GATC-GCATGGCC-GGT--TGTGC
1 GATCGGCATGGCCGGGTCATGTGC
*
14233 -ATGGGCATGGCCGGGTCATGTG-
1 GATCGGCATGGCCGGGTCATGTGC
* **
14255 G-TTGGTGTGGCCGGG-CATGTGC
1 GATCGGCATGGCCGGGTCATGTGC
14277 GATCGGCATGGCCGGGTCATGT
1 GATCGGCATGGCCGGGTCATGT
14299 AGCTGGTGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.04
20 8 0.16
21 9 0.18
22 12 0.24
23 15 0.29
24 5 0.10
ACGTcount: A:0.10, C:0.21, G:0.44, T:0.24
Consensus pattern (24 bp):
GATCGGCATGGCCGGGTCATGTGC
Found at i:15318 original size:18 final size:17
Alignment explanation
Indices: 15291--15324 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
15281 TTTTCTAAGT
15291 TATTTTTGGAAAAGATA
1 TATTTTTGGAAAAGATA
15308 TATTCTTTGGAAAAGAT
1 TATT-TTTGGAAAAGAT
15325 CTTCATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TATTTTTGGAAAAGATA
Found at i:17370 original size:22 final size:22
Alignment explanation
Indices: 17323--17373 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
17313 ATGCTATGAC
**
17323 AAAACCTTTTATTTTTGTTCTT
1 AAAACCTTTTATTTTACTTCTT
*
17345 AAAATCTTTTATTTTACTT-TT
1 AAAACCTTTTATTTTACTTCTT
17366 GAAAACCT
1 -AAAACCT
17374 CCATTTTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AAAACCTTTTATTTTACTTCTT
Found at i:17670 original size:19 final size:19
Alignment explanation
Indices: 17628--17670 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
17618 CATTTTTTTC
**
17628 ATTTTTTCTTTTCCTTCTT
1 ATTTTTTCTTTTCCTTCAA
* *
17647 CTTTTTTCTTTTTCTTCAA
1 ATTTTTTCTTTTCCTTCAA
17666 ATTTT
1 ATTTT
17671 GACCTAAATA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTTCTTTTCCTTCAA
Found at i:20004 original size:36 final size:36
Alignment explanation
Indices: 19991--20108 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 36
19981 TCTCTTTTAG
19991 ATTAAGTTCTTTATTGACTTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATTGACTTCACTTAATTACCTTGA
* *
20027 ATTAAGTTCTTTATT--C-T-ACTTAATTACCCTAA
1 ATTAAGTTCTTTATTGACTTCACTTAATTACCTTGA
* *
20059 ATTAAG-CCTTTTATTGACCTCACTTAATTACCTTGA
1 ATTAAGTTC-TTTATTGACTTCACTTAATTACCTTGA
20095 ATTAAGTTCTTTAT
1 ATTAAGTTCTTTAT
20109 CTTACTTAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
31 1 0.01
32 25 0.36
33 1 0.01
34 2 0.03
35 1 0.01
36 39 0.56
37 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACTTCACTTAATTACCTTGA
Found at i:20053 original size:32 final size:35
Alignment explanation
Indices: 19991--20124 Score: 147
Period size: 36 Copynumber: 3.9 Consensus size: 35
19981 TCTCTTTTAG
19991 ATTAAGTTCTTTATTGACTTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATT-ACTTCACTTAATTACCTTGA
* *
20027 ATTAAGTTCTTTATT-C-T-ACTTAATTACCCTAA
1 ATTAAGTTCTTTATTACTTCACTTAATTACCTTGA
* *
20059 ATTAAG-CCTTTTATTGACCTCACTTAATTACCTTGA
1 ATTAAGTTC-TTTATT-ACTTCACTTAATTACCTTGA
*
20095 ATTAAGTTCTTTA-T-CTT-ACTTAATTTCCTT
1 ATTAAGTTCTTTATTACTTCACTTAATTACCTT
20125 TCCTGAAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
31 1 0.01
32 37 0.44
33 3 0.04
34 2 0.02
35 2 0.02
36 38 0.45
37 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.48
Consensus pattern (35 bp):
ATTAAGTTCTTTATTACTTCACTTAATTACCTTGA
Found at i:20202 original size:36 final size:36
Alignment explanation
Indices: 20157--20426 Score: 338
Period size: 36 Copynumber: 7.6 Consensus size: 36
20147 TTTTATTTAA
*
20157 TTTCCTTGAAACTAAGCCAGTCTTTTCTTCACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
20193 TTTCCTTGAAACTAAGCCAGT-TCTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCT-TTTCTTTACCTAG
* * * *
20229 TTTCCTTGAAACTAAGCTAGTC--TTGTTTACTTAA
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * *
20263 TTTCCTTGAAATTAAGCCAGTC--TTCTTTACTTAA
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* *
20297 TTTCTTTGAAATTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
20333 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * * *
20369 TTGT-CTTGAAACTAAGCCCGTCCTTT-TTTACTTAA
1 TT-TCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
*
20404 TTTCCTTGAAATTAAGCCAGTCT
1 TTTCCTTGAAACTAAGCCAGTCT
20427 ACTTTTTACT
Statistics
Matches: 208, Mismatches: 20, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
34 62 0.30
35 26 0.12
36 119 0.57
37 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
Found at i:20496 original size:36 final size:36
Alignment explanation
Indices: 20436--20694 Score: 301
Period size: 36 Copynumber: 7.3 Consensus size: 36
20426 TACTTTTTAC
* * *
20436 TAAGCAAGTCT-TGTTTTACTTAATTTCCTTGAAAT
1 TAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAAT
20471 TAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAAT
1 TAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAAT
* * *
20507 TAAGCCAGTCTA-TCTTTACCTAGTTTCCTTGAAAC
1 TAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAAT
* *
20542 TAAGCCCGTC-ATTTTTTACTTAATTTCCTTGAAAT
1 TAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAAT
* * *
20577 TAAACCAATCTATCTTTTACCTAATTTCCTTGAAAT
1 TAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAAT
* * * * * *
20613 TAAGTCGGTCTA-TCTTTACTTAATTTCTTTGGAAT
1 TAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAAT
* * * *
20648 TAAGCCAGTATATTCTTTACCTAGTTTCCTTGAAAC
1 TAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAAT
20684 TAAGCCAGTCT
1 TAAGCCAGTCT
20695 TTTATCAGTC
Statistics
Matches: 186, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
34 1 0.01
35 92 0.49
36 93 0.50
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.42
Consensus pattern (36 bp):
TAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAAT
Found at i:20558 original size:71 final size:70
Alignment explanation
Indices: 20450--20697 Score: 316
Period size: 71 Copynumber: 3.5 Consensus size: 70
20440 CAAGTCTTGT
* * *
20450 TTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAATTAAGCCAG
1 TTTACCTAATTTCCTTGAAACTAAGCCAGTCT-TTTTTTACTTAATTTCCTTGAAATTAAGCCAG
20515 TCTATC
65 TCTATC
* * * * *
20521 TTTACCTAGTTTCCTTGAAACTAAGCCCGTCATTTTTTACTTAATTTCCTTGAAATTAAACCAAT
1 TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
20586 CTATC
66 CTATC
* * * * * * *
20591 TTTTACCTAATTTCCTTGAAATTAAGTCGGTCTATCTTTACTTAATTTCTTTGGAATTAAGCCAG
1 -TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAGCCAG
*
20656 TATATTC
65 TCTA-TC
*
20663 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT
1 TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTT
20698 ATCAGTCTAA
Statistics
Matches: 149, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
70 35 0.23
71 112 0.75
72 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (70 bp):
TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
CTATC
Found at i:20624 original size:106 final size:106
Alignment explanation
Indices: 20449--20682 Score: 326
Period size: 106 Copynumber: 2.2 Consensus size: 106
20439 GCAAGTCTTG
* * *
20449 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTTTTTACCTAATTTCCTTGAAATTAAGCCA
1 TTTTACTTAATTTCCTTGAAATTAAACCAATCTATCTTTTACCTAATTTCCTTGAAATTAAGCCA
* *
20514 GTCTATCTTTACCTAGTTTCCTTGAAACTAAGCCCGTCAT-T
66 GTCTATCTTTACCTAATTTCCTTGAAACTAAGCCAGT-ATAT
* *
20555 TTTTACTTAATTTCCTTGAAATTAAACCAATCTATCTTTTACCTAATTTCCTTGAAATTAAGTCG
1 TTTTACTTAATTTCCTTGAAATTAAACCAATCTATCTTTTACCTAATTTCCTTGAAATTAAGCCA
* * * *
20620 GTCTATCTTTACTTAATTTCTTTGGAATTAAGCCAGTATAT
66 GTCTATCTTTACCTAATTTCCTTGAAACTAAGCCAGTATAT
* *
20661 TCTTTACCTAGTTTCCTTGAAA
1 T-TTTACTTAATTTCCTTGAAA
20683 CTAAGCCAGT
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
105 2 0.02
106 93 0.82
107 18 0.16
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (106 bp):
TTTTACTTAATTTCCTTGAAATTAAACCAATCTATCTTTTACCTAATTTCCTTGAAATTAAGCCA
GTCTATCTTTACCTAATTTCCTTGAAACTAAGCCAGTATAT
Found at i:20705 original size:11 final size:11
Alignment explanation
Indices: 20689--20895 Score: 117
Period size: 11 Copynumber: 18.5 Consensus size: 11
20679 GAAACTAAGC
*
20689 CAGTCTTTTAT
1 CAGTCTATTAT
20700 CAGTCTAATT-T
1 CAGTCT-ATTAT
20711 CAGTCTCATT-T
1 CAGTCT-ATTAT
*
20722 CAGTCTAATAT
1 CAGTCTATTAT
20733 CAGTCT-TATAT
1 CAGTCTAT-TAT
20744 CAGTCTAATT-T
1 CAGTCT-ATTAT
*
20755 CAGTCTAATAT
1 CAGTCTATTAT
* *
20766 CAGTCTTTTTTTTT
1 CAGTC---TATTAT
20780 CAGTCTAATT-T
1 CAGTCT-ATTAT
*
20791 CAGTCTATTTT
1 CAGTCTATTAT
20802 CAGTCTAATT-T
1 CAGTCT-ATTAT
*
20813 CAGTCTAATAT
1 CAGTCTATTAT
*
20824 TAGTCTAATT-T
1 CAGTCT-ATTAT
20835 CAGTCTGATT-T
1 CAGTCT-ATTAT
* *
20846 CAGTTTAATAT
1 CAGTCTATTAT
* *
20857 CAGTCTTTTTT
1 CAGTCTATTAT
* *
20868 CAATCTATTTT
1 CAGTCTATTAT
20879 CAGTCTAATT-T
1 CAGTCT-ATTAT
20890 CAGTCT
1 CAGTCT
20896 TCTCTTTCAG
Statistics
Matches: 157, Mismatches: 23, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
10 11 0.07
11 124 0.79
12 13 0.08
13 1 0.01
14 8 0.05
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (11 bp):
CAGTCTATTAT
Found at i:20714 original size:22 final size:22
Alignment explanation
Indices: 20699--20895 Score: 216
Period size: 22 Copynumber: 8.8 Consensus size: 22
20689 CAGTCTTTTA
*
20699 TCAGTCTAATTTCAGTCTCATT
1 TCAGTCTAATTTCAGTCTAATT
* * *
20721 TCAGTCTAATATCAGTCTTATA
1 TCAGTCTAATTTCAGTCTAATT
*
20743 TCAGTCTAATTTCAGTCTAATA
1 TCAGTCTAATTTCAGTCTAATT
**
20765 TCAGTCTTTTTTTTTCAGTCTAATT
1 TCAGTC---TAATTTCAGTCTAATT
*
20790 TCAGTCTATTTTCAGTCTAATT
1 TCAGTCTAATTTCAGTCTAATT
20812 TCAGTCTAATATT-AGTCTAATT
1 TCAGTCTAAT-TTCAGTCTAATT
* * *
20834 TCAGTCTGATTTCAGTTTAATA
1 TCAGTCTAATTTCAGTCTAATT
** * *
20856 TCAGTCTTTTTTCAATCTATTT
1 TCAGTCTAATTTCAGTCTAATT
20878 TCAGTCTAATTTCAGTCT
1 TCAGTCTAATTTCAGTCT
20896 TCTCTTTCAG
Statistics
Matches: 148, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
21 2 0.01
22 125 0.84
23 2 0.01
25 19 0.13
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (22 bp):
TCAGTCTAATTTCAGTCTAATT
Found at i:20786 original size:25 final size:23
Alignment explanation
Indices: 20699--20968 Score: 178
Period size: 22 Copynumber: 11.8 Consensus size: 23
20689 CAGTCTTTTA
* *
20699 TCAGTC-TAATTTCAGTCTCATT
1 TCAGTCTTATTTTCAGTCTAATT
* * * *
20721 TCAGTC-TAATATCAGTCTTATA
1 TCAGTCTTATTTTCAGTCTAATT
* *
20743 TCAGTC-TAATTTCAGTCTAATA
1 TCAGTCTTATTTTCAGTCTAATT
*
20765 TCAGTCTTTTTTTTTCAGTCTAATT
1 TCAGTC--TTATTTTCAGTCTAATT
20790 TCAGTC-TATTTTCAGTCTAATT
1 TCAGTCTTATTTTCAGTCTAATT
* *
20812 TCAGTCTAATATT-AGTCTAATT
1 TCAGTCTTATTTTCAGTCTAATT
* * *
20834 TCAGTCTGA-TTTCAGTTTAATA
1 TCAGTCTTATTTTCAGTCTAATT
* *
20856 TCAGTCTT-TTTTCAATCTATTT
1 TCAGTCTTATTTTCAGTCTAATT
* **
20878 TCAGTC-TAATTTCAGTCTTCTCTT
1 TCAGTCTTATTTTCAGTC-T-AATT
* * **
20902 TCAGTCTTGTTTTCAATCTTCTTT
1 TCAGTCTTATTTTCAGTC-TAATT
* **
20926 TCAGTCTTCTTTTCAGTCCTCTTT
1 TCAGTCTTATTTTCAGT-CTAATT
* *
20950 TTAGTCTTCTTTTCAGTCT
1 TCAGTCTTATTTTCAGTCT
20969 TCTTTTCAGT
Statistics
Matches: 205, Mismatches: 32, Indels: 21
0.79 0.12 0.08
Matches are distributed among these distances:
21 3 0.01
22 119 0.58
23 7 0.03
24 46 0.22
25 30 0.15
ACGTcount: A:0.21, C:0.20, G:0.09, T:0.51
Consensus pattern (23 bp):
TCAGTCTTATTTTCAGTCTAATT
Found at i:20896 original size:33 final size:33
Alignment explanation
Indices: 20699--20895 Score: 216
Period size: 33 Copynumber: 5.9 Consensus size: 33
20689 CAGTCTTTTA
* *
20699 TCAGTCTAATTTCAGTCTCATTTCAGTCTAATA
1 TCAGTCTAATTTCAGTCTAATTTCAGTCTAATT
* * *
20732 TCAGTCTTATATCAGTCTAATTTCAGTCTAATA
1 TCAGTCTAATTTCAGTCTAATTTCAGTCTAATT
** *
20765 TCAGTCTTTTTTTTTCAGTCTAATTTCAGTCTATTT
1 TCAGTC---TAATTTCAGTCTAATTTCAGTCTAATT
20801 TCAGTCTAATTTCAGTCTAATATT-AGTCTAATT
1 TCAGTCTAATTTCAGTCTAAT-TTCAGTCTAATT
* * * **
20834 TCAGTCTGATTTCAGTTTAATATCAGTCTTTTT
1 TCAGTCTAATTTCAGTCTAATTTCAGTCTAATT
* *
20867 TCAATCTATTTTCAGTCTAATTTCAGTCT
1 TCAGTCTAATTTCAGTCTAATTTCAGTCT
20896 TCTCTTTCAG
Statistics
Matches: 139, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.01
33 107 0.77
34 2 0.01
36 29 0.21
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (33 bp):
TCAGTCTAATTTCAGTCTAATTTCAGTCTAATT
Found at i:20984 original size:12 final size:12
Alignment explanation
Indices: 20856--20985 Score: 149
Period size: 12 Copynumber: 11.0 Consensus size: 12
20846 CAGTTTAATA
20856 TCAGTCTT-TTT
1 TCAGTCTTCTTT
* *
20867 TCAATC-TATTT
1 TCAGTCTTCTTT
**
20878 TCAGTC-TAATT
1 TCAGTCTTCTTT
20889 TCAGTCTTCTCTT
1 TCAGTCTTCT-TT
*
20902 TCAGTCTTGTTT
1 TCAGTCTTCTTT
*
20914 TCAATCTTCTTT
1 TCAGTCTTCTTT
20926 TCAGTCTTCTTT
1 TCAGTCTTCTTT
*
20938 TCAGTCCTCTTT
1 TCAGTCTTCTTT
*
20950 TTAGTCTTCTTT
1 TCAGTCTTCTTT
20962 TCAGTCTTCTTT
1 TCAGTCTTCTTT
*
20974 TCAGTCCTCTTT
1 TCAGTCTTCTTT
20986 CCTTGAAATT
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
10 1 0.01
11 23 0.23
12 67 0.66
13 11 0.11
ACGTcount: A:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (12 bp):
TCAGTCTTCTTT
Found at i:21059 original size:36 final size:35
Alignment explanation
Indices: 20983--21077 Score: 111
Period size: 36 Copynumber: 2.7 Consensus size: 35
20973 TTCAGTCCTC
* *
20983 TTTCCTTGAAATTAAAGTCAGTCTATATTTACTTAA
1 TTTCCTTGAAATT-AAGCCAGTCTATATTTACCTAA
* *
21019 TTTCCTTGAAATTAAGCCAGTCT-TTTCTTCACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTATAT-TT-ACCTAA
*
21055 TTTCCTTGAAACTAAGCCAGTCT
1 TTTCCTTGAAATTAAGCCAGTCT
21078 GTCTTCTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
34 2 0.04
35 11 0.21
36 39 0.75
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (35 bp):
TTTCCTTGAAATTAAGCCAGTCTATATTTACCTAA
Found at i:24458 original size:33 final size:33
Alignment explanation
Indices: 24408--24531 Score: 144
Period size: 33 Copynumber: 3.7 Consensus size: 33
24398 CCGCGCAACA
*
24408 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
24443 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
24476 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
24509 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
24532 CCTTTGTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 2 0.03
33 67 0.87
35 7 0.09
36 1 0.01
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.07
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:25447 original size:8 final size:8
Alignment explanation
Indices: 25434--25467 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
25424 CGCCTTCTTG
25434 AAAAATTC
1 AAAAATTC
25442 AAAAATTC
1 AAAAATTC
*
25450 AGAAACTTC
1 A-AAAATTC
25459 AAAAATTC
1 AAAAATTC
25467 A
1 A
25468 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Done.