Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010676.1 Corchorus capsularis cultivar CVL-1 contig10697, 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: 29269
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:2025 original size:33 final size:33
Alignment explanation
Indices: 1988--2063 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
1978 ACTGGCCATC
*
1988 ACCGGCCACGCGACAT-GGACATGCCCGGCCACA
1 ACCGGCCACACGAC-TCGGACATGCCCGGCCACA
* *
2021 ACCGGCCACATGACTCGGCCATGCCCGGCCACA
1 ACCGGCCACACGACTCGGACATGCCCGGCCACA
2054 ACCGGCCACA
1 ACCGGCCACA
2064 TGATCCTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
32 1 0.03
33 38 0.97
ACGTcount: A:0.24, C:0.45, G:0.25, T:0.07
Consensus pattern (33 bp):
ACCGGCCACACGACTCGGACATGCCCGGCCACA
Found at i:2027 original size:10 final size:10
Alignment explanation
Indices: 2012--2063 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
2002 ATGGACATGC
2012 CCGGCCACAA
1 CCGGCCACAA
2022 CCGGCCACATGA
1 CCGGCCACA--A
***
2034 CTCGGCCATGC
1 C-CGGCCACAA
2045 CCGGCCACAA
1 CCGGCCACAA
2055 CCGGCCACA
1 CCGGCCACA
2064 TGATCCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 2 0.06
13 6 0.18
ACGTcount: A:0.23, C:0.48, G:0.23, T:0.06
Consensus pattern (10 bp):
CCGGCCACAA
Found at i:6323 original size:27 final size:28
Alignment explanation
Indices: 6275--6332 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
6265 AAGCAAATTC
6275 AAAGCTAAAAGGTCCAAATGCAAGT-CA
1 AAAGCTAAAAGGTCCAAATGCAAGTCCA
* ** *
6302 AAAGCTAAAATGTGTAAGTGCAAGTCCA
1 AAAGCTAAAAGGTCCAAATGCAAGTCCA
6330 AAA
1 AAA
6333 TTAACCTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (28 bp):
AAAGCTAAAAGGTCCAAATGCAAGTCCA
Found at i:9030 original size:18 final size:18
Alignment explanation
Indices: 9007--9059 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
8997 AAAGGGTCGA
9007 ATGGCCGGTTGTGGCCGG
1 ATGGCCGGTTGTGGCCGG
9025 ATGGCC---TGT-G-C-G
1 ATGGCCGGTTGTGGCCGG
9037 ATGGCCGGTTGTGGCCGG
1 ATGGCCGGTTGTGGCCGG
9055 ATGGC
1 ATGGC
9060 TCGTGCGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
12 7 0.24
13 1 0.03
14 1 0.03
15 6 0.21
16 1 0.03
17 1 0.03
18 12 0.41
ACGTcount: A:0.08, C:0.23, G:0.47, T:0.23
Consensus pattern (18 bp):
ATGGCCGGTTGTGGCCGG
Found at i:9043 original size:30 final size:30
Alignment explanation
Indices: 9007--9072 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
8997 AAAGGGTCGA
9007 ATGGCCGGTTGTGGCCGGATGGC-CTGTGCG
1 ATGGCCGGTTGTGGCCGGATGGCTC-GTGCG
9037 ATGGCCGGTTGTGGCCGGATGGCTCGTGCG
1 ATGGCCGGTTGTGGCCGGATGGCTCGTGCG
9067 ATGGCC
1 ATGGCC
9073 CGTGCGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.08, C:0.24, G:0.45, T:0.23
Consensus pattern (30 bp):
ATGGCCGGTTGTGGCCGGATGGCTCGTGCG
Found at i:14939 original size:28 final size:25
Alignment explanation
Indices: 14883--14954 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 25
14873 CCTATACATA
*
14883 ATTAATTAAGAGATTTTTG--GTGC
1 ATTAATTAAGAGATTTTTGTTGAGC
14906 ATTAATTAAGAGATTTTTGTTTAGAGAC
1 ATTAATTAAGAGATTTTTG-TT-GAG-C
14934 ATTAATTAAGAGATTTTTGTT
1 ATTAATTAAGAGATTTTTGTT
14955 AATTTGATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
23 19 0.44
27 4 0.09
28 20 0.47
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (25 bp):
ATTAATTAAGAGATTTTTGTTGAGC
Found at i:24040 original size:1 final size:1
Alignment explanation
Indices: 24034--24060 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
24024 GGCTCATTTG
24034 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
24061 GTTGGCACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27788 original size:19 final size:19
Alignment explanation
Indices: 27764--27800 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
27754 TTACTATTAT
27764 TTTTAATTT-AATATTTTAC
1 TTTTAATTTCAAT-TTTTAC
27783 TTTTAATTTCAATTTTTA
1 TTTTAATTTCAATTTTTA
27801 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTCAATTTTTAC
Found at i:28036 original size:22 final size:22
Alignment explanation
Indices: 27967--28045 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
27957 GTCTCTATGT
* *
27967 GGTTATCAAAATTTCAT-AAGA
1 GGTTATCAAAATTCCATGAGGA
*
27988 TGATTATCAAAATTCCATGAGGA
1 -GGTTATCAAAATTCCATGAGGA
*
28011 GGTTATCAAAATTCCAT-AGTGC
1 GGTTATCAAAATTCCATGAG-GA
*
28033 GGTTACCAAAATT
1 GGTTATCAAAATT
28046 TCAGTGTAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.04
22 44 0.90
23 3 0.06
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (22 bp):
GGTTATCAAAATTCCATGAGGA
Found at i:28088 original size:24 final size:22
Alignment explanation
Indices: 28061--28118 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
28051 GTAGTTACCG
28061 AAATTTCATAGGATCAAGTTATTA
1 AAATTTCATAGG-T-AAGTTATTA
* * ** *
28085 AAATCTCTTAGGTTGGTTATTG
1 AAATTTCATAGGTAAGTTATTA
28107 AAATTTCATAGG
1 AAATTTCATAGG
28119 GTGGTTAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 16 0.59
23 1 0.04
24 10 0.37
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (22 bp):
AAATTTCATAGGTAAGTTATTA
Found at i:28110 original size:22 final size:22
Alignment explanation
Indices: 28078--28125 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
28068 ATAGGATCAA
* *
28078 GTTATTAAAATCTCTTAGGTTG
1 GTTATTAAAATCTCATAGGGTG
* *
28100 GTTATTGAAATTTCATAGGGTG
1 GTTATTAAAATCTCATAGGGTG
28122 GTTA
1 GTTA
28126 ATTATCACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (22 bp):
GTTATTAAAATCTCATAGGGTG
Found at i:28215 original size:22 final size:22
Alignment explanation
Indices: 28190--28295 Score: 92
Period size: 22 Copynumber: 4.8 Consensus size: 22
28180 AGATTATAAG
*
28190 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTGAGGTTAACAA
28212 AATTTCATTAG-GAGGTT-ACTAA
1 AATTTCA-TAGTGAGGTTAAC-AA
* * * *
28234 TATTTCATGGGGAGGTTATCAA
1 AATTTCATAGTGAGGTTAACAA
* * *
28256 AATTTTATAGTGTGGTTATCAA
1 AATTTCATAGTGAGGTTAACAA
28278 AATTTCATA-TGAAGGTTA
1 AATTTCATAGTG-AGGTTA
28296 TAAAAGTCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
21 6 0.09
22 58 0.85
23 4 0.06
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.39
Consensus pattern (22 bp):
AATTTCATAGTGAGGTTAACAA
Found at i:28296 original size:22 final size:21
Alignment explanation
Indices: 28161--28300 Score: 88
Period size: 22 Copynumber: 6.4 Consensus size: 21
28151 ATCAAAGAGA
* * *
28161 TTATCAAAATGTCATAGCGAGA
1 TTATCAAAATTTCATA-TGAGG
*
28183 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATA-TGAGG
* *
28205 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TATGAGG
* **
28227 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-ATGAGG
* *
28249 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATA-TGAGG
28271 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATG-AGG
28293 TTAT-AAAA
1 TTATCAAAA
28301 GTCTCAATTT
Statistics
Matches: 94, Mismatches: 16, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
21 10 0.11
22 79 0.84
23 5 0.05
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATATGAGG
Found at i:28362 original size:21 final size:22
Alignment explanation
Indices: 28338--28379 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28328 TTTGATAGAA
28338 GATTATC-AAATCTCATAGAGT
1 GATTATCGAAATCTCATAGAGT
*
28359 GATTATCGAAATTTCATAGAG
1 GATTATCGAAATCTCATAGAG
28380 GTTTCATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (22 bp):
GATTATCGAAATCTCATAGAGT
Found at i:28375 original size:22 final size:21
Alignment explanation
Indices: 28325--28379 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
28315 AGAAGTACCA
*
28325 AAATTTGATAGA-AGATTATC
1 AAATTTCATAGAGAGATTATC
* *
28345 AAATCTCATAGAGTGATTATC
1 AAATTTCATAGAGAGATTATC
28366 GAAATTTCATAGAG
1 -AAATTTCATAGAG
28380 GTTTCATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 10 0.34
21 7 0.24
22 12 0.41
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (21 bp):
AAATTTCATAGAGAGATTATC
Found at i:28418 original size:22 final size:21
Alignment explanation
Indices: 28393--28520 Score: 87
Period size: 22 Copynumber: 5.9 Consensus size: 21
28383 TCATAGTGTT
28393 GTTATCAAAATTTCAAAACGAG
1 GTTATCAAAATTTCAAAA-GAG
* *
28415 GTTATCAAAATTAT-ATAATGTG
1 GTTATCAAAATT-TCA-AAAGAG
* * * *
28437 ATTATCAGAATTTCATAGAGGG
1 GTTATCAAAATTTCA-AAAGAG
* * * *
28459 GTCAACGAAATTTTATAAAGAG
1 GTTATCAAAATTTCA-AAAGAG
*
28481 GTTATCAAAATTTAATAAAGAG
1 GTTATCAAAATTTCA-AAAGAG
*
28503 GTTATCAAATTTTCAAAA
1 GTTATCAAAATTTCAAAA
28521 TGTGATTACA
Statistics
Matches: 82, Mismatches: 21, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
21 4 0.05
22 75 0.91
23 3 0.04
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.33
Consensus pattern (21 bp):
GTTATCAAAATTTCAAAAGAG
Found at i:28651 original size:20 final size:20
Alignment explanation
Indices: 28623--28692 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 20
28613 TTATGGAGTA
28623 ATCAAAATTTAAGGGAGGAT
1 ATCAAAATTTAAGGGAGGAT
* *
28643 ATCAGAA-TTCAGGGAGGAT
1 ATCAAAATTTAAGGGAGGAT
* * *
28662 ATCAAAATTTCAATGAAGGTT
1 ATCAAAATTT-AAGGGAGGAT
28683 ATCAAAATTT
1 ATCAAAATTT
28693 CATAGTTTAG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 17 0.41
20 8 0.20
21 16 0.39
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTAAGGGAGGAT
Found at i:29031 original size:22 final size:22
Alignment explanation
Indices: 28655--29220 Score: 205
Period size: 22 Copynumber: 26.0 Consensus size: 22
28645 CAGAATTCAG
*
28655 GGAGGATATCAAAATTTCA-AT
1 GGAGGTTATCAAAATTTCATAT
*
28676 GAAGGTTATCAAAATTTCATAGT
1 GGAGGTTATCAAAATTTCATA-T
** *
28699 TTA-GTTTTCAAAATTTCATA-
1 GGAGGTTATCAAAATTTCATAT
* * *
28719 AGAGGGTTATCAAAGTGTCATA-
1 GGA-GGTTATCAAAATTTCATAT
* * * * *
28741 GTATGTAGATCAAAATTTTATAG
1 GGAGGT-TATCAAAATTTCATAT
*
28764 GGAGATTAAT-AAAATTTCATAAT
1 GGAGGTT-ATCAAAATTTCAT-AT
** *
28787 -GAGGTTATCAAAAAATCATAG
1 GGAGGTTATCAAAATTTCATAT
*
28808 GGACGTTATCAAAA--T--T-T
1 GGAGGTTATCAAAATTTCATAT
* * *
28825 GTA-GTTATCAAGATTTCATAA
1 GGAGGTTATCAAAATTTCATAT
* * * *
28846 GAAAGTTATCAAAATTTTATAG
1 GGAGGTTATCAAAATTTCATAT
**
28868 GGAGGTTTATCAAAATTTTGTA-
1 GGAGG-TTATCAAAATTTCATAT
*
28890 GGAAGATTTATCAAAATTTCATA-
1 GG-AG-GTTATCAAAATTTCATAT
*
28913 GCGAGGTTATCACAATTTCATAGT
1 G-GAGGTTATCAAAATTTCATA-T
*
28937 GTGA--TTATCAAAATTTCAGAGT
1 G-GAGGTTATCAAAATTTCATA-T
28959 GTGA--TTA-CTAACAA-TTCATAT
1 G-GAGGTTATC-AA-AATTTCATAT
**
28980 GGAGGTT-TTTAAATTTCCATAAT
1 GGAGGTTATCAAAATTT-CAT-AT
* * *
29003 GTA-GTTATCAATATATCATAT
1 GGAGGTTATCAAAATTTCATAT
* *
29024 GGAGGTTATCAACATCTCATAGT
1 GGAGGTTATCAAAATTTCATA-T
**
29047 GTTGGTTATCAAAATTTCAT-T
1 GGAGGTTATCAAAATTTCATAT
*
29068 GGGAAGTTATCAAAATTTCATAT
1 -GGAGGTTATCAAAATTTCATAT
* * * *
29091 TGAGGTCT-TCAAAATTCCTTAG
1 GGAGGT-TATCAAAATTTCATAT
* * *
29113 GGAGGTTAACCAAATTTCATAA
1 GGAGGTTATCAAAATTTCATAT
* ** * *
29135 GAAGGTTAAAAAAAATT-ATAA
1 GGAGGTTATCAAAATTTCATAT
** * * *
29156 AAAGGTTCTCGAAATTCCATA-
1 GGAGGTTATCAAAATTTCATAT
* * *
29177 GTATCGTTATTAAAATTTCATA-
1 GGA-GGTTATCAAAATTTCATAT
29199 GGAAGGTTATCAAAATTTCATA
1 GG-AGGTTATCAAAATTTCATA
29221 ATGGGATCAT
Statistics
Matches: 408, Mismatches: 97, Indels: 79
0.70 0.17 0.14
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
20 7 0.02
21 51 0.12
22 260 0.64
23 73 0.18
24 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
GGAGGTTATCAAAATTTCATAT
Done.