Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011718.1 Corchorus capsularis cultivar CVL-1 contig11739, 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: 7865
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:4960 original size:22 final size:22
Alignment explanation
Indices: 4932--5113 Score: 133
Period size: 22 Copynumber: 8.3 Consensus size: 22
4922 TGTCTCTATG
*
4932 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
4954 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
4977 -GGTTATC-AAATTTCCATA-G-
1 TGGTTATCAAAATTT-CATAGGA
*
4996 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* *
5019 -AGTTATCAAAATTTTATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
5040 TGGTTACCGAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
5062 TCAGGTAATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
5086 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
5108 TGGTTA
1 TGGTTA
5114 ATTATCACAA
Statistics
Matches: 125, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
20 11 0.09
21 14 0.11
22 81 0.65
23 3 0.02
24 16 0.13
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:5174 original size:22 final size:21
Alignment explanation
Indices: 5149--5475 Score: 108
Period size: 22 Copynumber: 14.7 Consensus size: 21
5139 ATCAAAGAGA
*
5149 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
**
5171 TTAT-AAGAATTTCATAGTGTCG
1 TTATCAA-AATTTCATAG-GAGG
*
5193 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
5215 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
** *
5237 TTATCAAAATTTCATATAAATG
1 TTATCAAAATTTCATA-GGAGG
*
5259 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
5284 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
5306 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
5326 ATTATCGAAATTTCATAGAGATCAGA
1 -TTATCAAAATTTCATAG-G---AGG
**
5352 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
*
5374 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
5396 TTATCAAAATTGCATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
* *
5418 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
5440 TCAACAAAATTTTATGAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
5462 TTATCAAATTTTCA
1 TTATCAAAATTTCA
5476 AAATGTGATT
Statistics
Matches: 222, Mismatches: 56, Indels: 54
0.67 0.17 0.16
Matches are distributed among these distances:
19 2 0.01
20 17 0.08
21 13 0.06
22 145 0.65
23 10 0.05
24 1 0.00
25 21 0.09
26 2 0.01
27 2 0.01
28 9 0.04
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:5448 original size:66 final size:65
Alignment explanation
Indices: 5350--5500 Score: 162
Period size: 66 Copynumber: 2.3 Consensus size: 65
5340 ATAGAGATCA
* ** * * *
5350 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTGCATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAGAA--GAGGTTATCAAAATTGCAAAAT
5414 GT
64 GT
* * * *
5416 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATGAAGAGGTTATCAAATTTTCAAAATG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCA-GAAGAGGTTATCAAAATTGCAAAATG
5481 T
65 T
5482 GATTA-CAAAAATTTCATAG
1 GATTATC-AAAATTTCATAG
5501 TGGTATTTCT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
65 1 0.01
66 68 0.96
68 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (65 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAGAAGAGGTTATCAAAATTGCAAAATGT
Found at i:5715 original size:44 final size:44
Alignment explanation
Indices: 5581--6051 Score: 242
Period size: 44 Copynumber: 10.8 Consensus size: 44
5571 TTATGGAGTA
*
5581 ATCAAAATTTC--AGGGAGGA-TATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATAG-TGAGGTT
* * * * * *
5623 TTCAAATTTTCATA-AGAGTGTTATCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCATAGGGAG-ATTATCAAAATTTCATAGTGAGGT-T
* *
5667 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTT
** * *
5711 ATCAAAAAATCATAGGAAGGTTATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTT
* * ** * * *
5749 GTCAAGATTTCA-AAAGAAAGTTATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGG-TT
* * *
5794 ATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGGTT
* * * * * * *
5839 ATCACAATTTCATAGTGTGAGTATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTT
* * * * * *
5883 A-CTAACAA-TTCATATGGA-AGTTTTTAAATTTTCATAATGTGGTT
1 ATC-AA-AATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGGTT
* * * * * * *
5927 ATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG-AGGTT
* * *
5972 ATCAAAATTTCATTGGGA-AGTTATCAAAATTCCATATTGAGGTCT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGGT-T
* * *
6017 -TCAAAATTCCTTAGGGACG-TTAACAAAATTTCATA
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATA
6052 AGAAGGTTAA
Statistics
Matches: 317, Mismatches: 84, Indels: 54
0.70 0.18 0.12
Matches are distributed among these distances:
37 2 0.01
38 20 0.06
39 3 0.01
40 1 0.00
41 2 0.01
42 12 0.04
43 11 0.03
44 171 0.54
45 72 0.23
46 23 0.07
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTT
Found at i:5716 original size:22 final size:22
Alignment explanation
Indices: 5595--6144 Score: 138
Period size: 22 Copynumber: 25.1 Consensus size: 22
5585 AAATTTCAGG
* *
5595 GAGGATATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATA-AT
* * *
5618 TA-GTTTTCAAATTTTCATAA-
1 GAGGTTATCAAAATTTCATAAT
*
5638 GAGTGTTATCAAAATTTCATAGT
1 GAG-GTTATCAAAATTTCATAAT
* * **
5661 -ATGTAGATCAAAATTTCATAGG
1 GAGGT-TATCAAAATTTCATAAT
* *
5683 GAGATTAACAAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAAT
** *
5705 GAGGTTATCAAAAAATCAT-AG
1 GAGGTTATCAAAATTTCATAAT
*
5726 GAAGGTTATCAAAA-TT--T-GT
1 G-AGGTTATCAAAATTTCATAAT
* * *
5745 -A-GTTGTCAAGATTTCA-AAA
1 GAGGTTATCAAAATTTCATAAT
* * **
5764 GAAAGTTATCAAAATTTTATAGG
1 G-AGGTTATCAAAATTTCATAAT
* *
5787 GAGGTTTATCAAAATTTTAT-AG
1 GAGG-TTATCAAAATTTCATAAT
* **
5809 GAAGATTTATCAAAATTTCATAGC
1 G-AG-GTTATCAAAATTTCATAAT
* *
5833 GAGGTTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATAAT
* * *
5855 GTGAG-TATCAAAATTTCAGAGT
1 GAG-GTTATCAAAATTTCATAAT
* *
5877 GTGATTA-CTAACAA-TTCAT-AT
1 GAGGTTATC-AA-AATTTCATAAT
* * * *
5898 GGAAGTTTTTAAATTTTCATAAT
1 -GAGGTTATCAAAATTTCATAAT
* * *
5921 GTGGTTATCAATATATCAT-AT
1 GAGGTTATCAAAATTTCATAAT
* * *
5942 GGAGGTTATCAACATCTCATAGT
1 -GAGGTTATCAAAATTTCATAAT
* ***
5965 GTTGGTTATCAAAATTTCATTGG
1 G-AGGTTATCAAAATTTCATAAT
* * *
5988 GAAGTTATCAAAATTCCATATT
1 GAGGTTATCAAAATTTCATAAT
* * **
6010 GAGGTCT-TCAAAATTCCTTAGG
1 GAGGT-TATCAAAATTTCATAAT
* *
6032 GACGTTAACAAAATTTCATAA-
1 GAGGTTATCAAAATTTCATAAT
** *
6053 GAAGGTTAAAAAAAATTT-ATAAA
1 G-AGGTT-ATCAAAATTTCATAAT
* * * *
6076 AAGGTTATCGAAATTCCATGGTAT
1 GAGGTTATCAAAATTTCAT--AAT
* *
6100 CA--TTATTAAAAATTTCATAGA-
1 GAGGTTA-TCAAAATTTCATA-AT
*
6121 AAGGTTATCAAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAAT
6143 GA
1 GA
6145 CATCATAAAA
Statistics
Matches: 381, Mismatches: 104, Indels: 85
0.67 0.18 0.15
Matches are distributed among these distances:
16 8 0.02
17 3 0.01
19 1 0.00
20 1 0.00
21 21 0.06
22 261 0.69
23 83 0.22
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAT
Found at i:5995 original size:45 final size:44
Alignment explanation
Indices: 5892--5998 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 44
5882 TACTAACAAT
* * * *
5892 TCATATGGAAGTTTTTAA-ATTTTCATAATGTGGTTATCAATATA
1 TCATATGGAAGTTATCAACA-TCTCATAATGTGGTTATCAAAATA
* * *
5936 TCATATGGAGGTTATCAACATCTCATAGTGTTGGTTATCAAAATT
1 TCATATGGAAGTTATCAACATCTCATAATG-TGGTTATCAAAATA
5981 TCAT-TGGGAAGTTATCAA
1 TCATAT-GGAAGTTATCAA
5999 AATTCCATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 24 0.46
45 28 0.54
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (44 bp):
TCATATGGAAGTTATCAACATCTCATAATGTGGTTATCAAAATA
Found at i:6156 original size:45 final size:44
Alignment explanation
Indices: 6062--6157 Score: 104
Period size: 45 Copynumber: 2.2 Consensus size: 44
6052 AGAAGGTTAA
* ** *
6062 AAAAAATTTATAAAAAGGTTATCGAAATTCCATGGTATCATTAT
1 AAAAAATTTATAAAAAGGTTATCAAAATTCCATAATATCATCAT
* * *
6106 TAAAAATTTCATAGAAAGGTTATCAAAATTTCATAATGA-CATCAT
1 AAAAAATTT-ATAAAAAGGTTATCAAAATTCCATAAT-ATCATCAT
6151 AAAAAAT
1 AAAAAAT
6158 AGTGTAATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
44 8 0.19
45 33 0.79
46 1 0.02
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (44 bp):
AAAAAATTTATAAAAAGGTTATCAAAATTCCATAATATCATCAT
Found at i:6252 original size:2 final size:2
Alignment explanation
Indices: 6245--6273 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6235 GTTAAAACTA
6245 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 A
6274 ACATGTAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7087 original size:15 final size:15
Alignment explanation
Indices: 7067--7100 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7057 AAAACAACTT
7067 ATAAAACAAGTTA-TA
1 ATAAAACAA-TTAGTA
7082 ATAAAACAATTAGTA
1 ATAAAACAATTAGTA
7097 ATAA
1 ATAA
7101 TAAATCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
ATAAAACAATTAGTA
Found at i:7573 original size:27 final size:27
Alignment explanation
Indices: 7517--7573 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
7507 TAATGCACCC
* * *
7517 AAAACATTTTAATAAAAATCATTTATA
1 AAAACACTTTAATAAAAATCAGTAATA
*
7544 AAAACACTTTACTAAAAAT-AGTAATA
1 AAAACACTTTAATAAAAATCAGTAATA
7570 AAAA
1 AAAA
7574 TAAGTCCCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAACACTTTAATAAAAATCAGTAATA
Done.