Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009587.1 Corchorus capsularis cultivar CVL-1 contig09608, 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: 9594
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:372 original size:29 final size:29
Alignment explanation
Indices: 324--397 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 29
314 TCAAGTAATT
*
324 AAAGGAAATGAAAGCGGAGGGAAGTTTTTC
1 AAAGGAAAAGAAAG-GGAGGGAAGTTTTTC
*
354 AAAGGAAAGGAAAGGGAGGGAAGTTTTTC
1 AAAGGAAAAGAAAGGGAGGGAAGTTTTTC
383 AAAGGAAAAGAAAGG
1 AAAGGAAAAGAAAGG
398 AAAGGATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 29 0.69
30 13 0.31
ACGTcount: A:0.46, C:0.04, G:0.35, T:0.15
Consensus pattern (29 bp):
AAAGGAAAAGAAAGGGAGGGAAGTTTTTC
Found at i:829 original size:15 final size:17
Alignment explanation
Indices: 803--835 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
793 ATCTACCTAC
803 CAAATATACAAA-TAAA
1 CAAATATACAAACTAAA
819 CAAAT-TACAAACTAAA
1 CAAATATACAAACTAAA
835 C
1 C
836 TCACATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAATATACAAACTAAA
Found at i:1829 original size:21 final size:22
Alignment explanation
Indices: 1797--1841 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1787 TCAAAAGTGT
*
1797 AAAAAATGGGGCAGTGTTTAGC
1 AAAAAATGGGGCAGTATTTAGC
*
1819 AAAAAAT-GGGCGGTATTTAGC
1 AAAAAATGGGGCAGTATTTAGC
1840 AA
1 AA
1842 CACCCTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (22 bp):
AAAAAATGGGGCAGTATTTAGC
Found at i:5537 original size:14 final size:14
Alignment explanation
Indices: 5504--5531 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5494 TTATAATTAG
5504 TATATATATAGATA
1 TATATATATAGATA
5518 TATATATATAGATA
1 TATATATATAGATA
5532 ATTATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TATATATATAGATA
Found at i:5967 original size:22 final size:20
Alignment explanation
Indices: 5942--5988 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
5932 AAAGTTTATT
5942 ATAATAAAAAAATTATACTAGA
1 ATAAT-AAAAAA-TATACTAGA
**
5964 ATAATTGAAAATATACTAGA
1 ATAATAAAAAATATACTAGA
5984 ATAAT
1 ATAAT
5989 TGAAAATCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
21 4 0.17
22 5 0.22
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (20 bp):
ATAATAAAAAATATACTAGA
Found at i:5980 original size:20 final size:20
Alignment explanation
Indices: 5950--5995 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 20
5940 TTATAATAAA
5950 AAAATTATACTAGAATAATTG
1 AAAA-TATACTAGAATAATTG
5971 AAAATATACTAGAATAATTG
1 AAAATATACTAGAATAATTG
5991 AAAAT
1 AAAAT
5996 CAGGATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (20 bp):
AAAATATACTAGAATAATTG
Found at i:6173 original size:31 final size:31
Alignment explanation
Indices: 6138--6210 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
6128 TATAAAAGTA
6138 CCAATTGTACCCTTAATTTTAAAGTATATTT
1 CCAATTGTACCCTTAATTTTAAAGTATATTT
6169 CCAATTGTACCCTTAATTTTAAAGTATATTT
1 CCAATTGTACCCTTAATTTTAAAGTATATTT
*
6200 CTAATTGTACC
1 CCAATTGTACC
6211 ACTTTTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (31 bp):
CCAATTGTACCCTTAATTTTAAAGTATATTT
Found at i:6229 original size:31 final size:30
Alignment explanation
Indices: 6140--6234 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 30
6130 TAAAAGTACC
** *
6140 AATTGTACCCTTAATTTTAAAGTATATTTCC
1 AATTGTACCCTT-ATTTTAAAACATATTTCT
**
6171 AATTGTACCCTTAATTTTAAAGTATATTTCT
1 AATTGTACCCTT-ATTTTAAAACATATTTCT
6202 AATTGTACCACTT-TTTTAAAAACATATTTCT
1 AATTGTACC-CTTATTTT-AAAACATATTTCT
6233 AA
1 AA
6235 ATTACCATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 4 0.07
31 52 0.88
32 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (30 bp):
AATTGTACCCTTATTTTAAAACATATTTCT
Found at i:6280 original size:20 final size:19
Alignment explanation
Indices: 6255--6293 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
6245 CTAAATAATA
6255 TTTTAATTATTCCATTATTT
1 TTTTAATTATTCC-TTATTT
6275 TTTTAATTATTCCTTATTT
1 TTTTAATTATTCCTTATTT
6294 CATAATTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTAATTATTCCTTATTT
Found at i:6399 original size:22 final size:22
Alignment explanation
Indices: 6345--6496 Score: 105
Period size: 22 Copynumber: 6.8 Consensus size: 22
6335 CTCTATGTGA
*
6345 TTATCAAAATTTCATAAGATAG
1 TTATCAAAATTTCATAGGATAG
* * *
6367 TTATTATAACTTCATGAGGAT-G
1 TTATCAAAATTTCAT-AGGATAG
* * *
6389 TTATCAAAACTCCATAGTG-TGG
1 TTATCAAAATTTCATAG-GATAG
*
6411 TTACCAAAATTTCATATGGA-AG
1 TTATCAAAATTTCATA-GGATAG
*
6433 TTATCAAAATTTCATAGTG-TGG
1 TTATCAAAATTTCATAG-GATAG
* *
6455 TTACCAAAATTTTATAGGATCAG
1 TTATCAAAATTTCATAGGAT-AG
* *
6478 ATTATTAAAATTTCTTAGG
1 -TTATCAAAATTTCATAGG
6497 TTGGTTATTG
Statistics
Matches: 100, Mismatches: 20, Indels: 18
0.72 0.14 0.13
Matches are distributed among these distances:
21 5 0.05
22 75 0.75
23 6 0.06
24 14 0.14
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGATAG
Found at i:6425 original size:44 final size:43
Alignment explanation
Indices: 6377--6474 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 43
6367 TTATTATAAC
6377 TTCATGAGGATGTTATCAAAACTCCATAGTGTGGTTACCAAAAT
1 TTCAT-AGGATGTTATCAAAACTCCATAGTGTGGTTACCAAAAT
* * *
6421 TTCATATGGAAGTTATCAAAATTTCATAGTGTGGTTACCAAAAT
1 TTCATA-GGATGTTATCAAAACTCCATAGTGTGGTTACCAAAAT
*
6465 TTTATAGGAT
1 TTCATAGGAT
6475 CAGATTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 4 0.08
44 44 0.92
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (43 bp):
TTCATAGGATGTTATCAAAACTCCATAGTGTGGTTACCAAAAT
Found at i:6510 original size:22 final size:22
Alignment explanation
Indices: 6479--6525 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6469 TAGGATCAGA
* *
6479 TTATTAAAATTTCTTAGGTTGG
1 TTATTAAAATTTCGTAGGGTGG
*
6501 TTATTGAAATTTCGTAGGGTGG
1 TTATTAAAATTTCGTAGGGTGG
6523 TTA
1 TTA
6526 ATTATCACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (22 bp):
TTATTAAAATTTCGTAGGGTGG
Found at i:6660 original size:22 final size:21
Alignment explanation
Indices: 6608--6660 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
6598 AGTGTACTTA
*
6608 ACAAAATTTCATTAGGAGGTT
1 ACAAAATTTCATGAGGAGGTT
* *
6629 ACTAATATTTCATGGGGAGGTT
1 AC-AAAATTTCATGAGGAGGTT
6651 ATCAAAATTT
1 A-CAAAATTT
6661 TATAGTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 23 0.88
23 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (21 bp):
ACAAAATTTCATGAGGAGGTT
Found at i:6935 original size:22 final size:22
Alignment explanation
Indices: 6732--6949 Score: 130
Period size: 22 Copynumber: 9.8 Consensus size: 22
6722 CTCAAAGAGT
* *
6732 GATTATCGAAATTTCATAGAGA
1 GATTATCAAAATTTCATAAAGA
*
6754 TCGGATTATCAAAATTT-AT-AGGAA
1 ---GATTATCAAAATTTCATAAAG-A
* ** *
6778 GACTATCAAAATTTCATAGCGTT
1 GATTATCAAAATTTCATAAAG-A
*
6801 G-TTATCAAAATTTCA-AATCGA
1 GATTATCAAAATTTCATAA-AGA
* * * *
6822 GGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAAAGA
6844 GATTAT-AAGAATTTCATAAAG-
1 GATTATCAA-AATTTCATAAAGA
*
6865 GATTCAACAAAATATT-ATAAAGA
1 GATT-ATCAAAAT-TTCATAAAGA
*
6888 GGTTATCAAAATTTCATAAAGA
1 GATTATCAAAATTTCATAAAGA
* *
6910 GATTATCAAATTTTCA-AAATGT
1 GATTATCAAAATTTCATAAA-GA
6932 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
6950 GTGGTATTTC
Statistics
Matches: 154, Mismatches: 24, Indels: 32
0.73 0.11 0.15
Matches are distributed among these distances:
21 27 0.18
22 98 0.64
23 13 0.08
24 3 0.02
25 13 0.08
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
GATTATCAAAATTTCATAAAGA
Found at i:7079 original size:22 final size:20
Alignment explanation
Indices: 7054--7279 Score: 100
Period size: 22 Copynumber: 10.6 Consensus size: 20
7044 AATTTAGTTT
7054 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCAT-AGA-GGTTA
* * *
7076 TCAAAATTTCATATATGTAGA
1 TCAAAATTTCATAGAGGT-TA
*
7097 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATA--GAGGTTA
*
7119 ACAAAATTTCATAATGAGGTTA
1 TCAAAATTTCAT-A-GAGGTTA
* *
7141 TTAAAATTT-GT--A-GTTA
1 TCAAAATTTCATAGAGGTTA
* * *
7157 TCAAGATTTTATAAGCAAGTTA
1 TCAAAATTTCAT-AG-AGGTTA
*
7179 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATA--GAGG-TTA
* *
7202 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATA-G-AG-GTTA
*
7225 TCAAAATTTCGTAGTGAGGTTA
1 TCAAAATTTCATA--GAGGTTA
* * *
7247 TCACAATTTCACAGTGTGATTA
1 TCAAAATTTCATAGAG-G-TTA
7269 TCAAAATTTCA
1 TCAAAATTTCA
7280 ATGTGTGATT
Statistics
Matches: 158, Mismatches: 28, Indels: 36
0.71 0.13 0.16
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
20 4 0.03
21 20 0.13
22 82 0.52
23 38 0.24
24 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (20 bp):
TCAAAATTTCATAGAGGTTA
Found at i:7248 original size:45 final size:44
Alignment explanation
Indices: 7031--7255 Score: 132
Period size: 43 Copynumber: 5.2 Consensus size: 44
7021 TTATGGAGTA
*** * *
7031 ATCAAAATTTTATAATTTAGTTTTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTTATAAGCAAGTTATCAAAATTTCATAGGGA-GGTT
* * *
7075 ATCAAAATTTCATATATG-TAG--ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTT--TATAAGCAAGTTATCAAAATTTCATAGGGAGGTT
* * * * *
7118 AACAAAATTTCATAATG-AGGTTATTAAAA-TT--T--GTA-GTT
1 ATCAAAATTTTATAA-GCAAGTTATCAAAATTTCATAGGGAGGTT
* *
7156 ATCAAGATTTTATAAGCAAGTTATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTTATAAGCAAGTTATCAAAATTTCATAGGGAGG-TT
* * *
7201 ATCAAAATTTTAT-AGGAAGATTTATCAAAATTTCGTAGTGAGGTT
1 ATCAAAATTTTATAAGCAAG--TTATCAAAATTTCATAGGGAGGTT
*
7246 ATCACAATTT
1 ATCAAAATTT
7256 CACAGTGTGA
Statistics
Matches: 140, Mismatches: 25, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
37 1 0.01
38 24 0.17
39 4 0.03
41 5 0.04
42 2 0.01
43 29 0.21
44 24 0.17
45 28 0.20
46 23 0.16
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (44 bp):
ATCAAAATTTTATAAGCAAGTTATCAAAATTTCATAGGGAGGTT
Found at i:7301 original size:22 final size:22
Alignment explanation
Indices: 7222--7290 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
7212 ATAGGAAGAT
* * *
7222 TTATCAAAATTTC-GTAGTGAGG
1 TTATCAAAATTTCAAT-GTGTGA
*
7244 TTATCACAATTTCACA-GTGTGA
1 TTATCAAAATTTCA-ATGTGTGA
7266 TTATCAAAATTTCAATGTGTGA
1 TTATCAAAATTTCAATGTGTGA
7288 TTA
1 TTA
7291 CTAACAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAATGTGTGA
Found at i:7367 original size:42 final size:42
Alignment explanation
Indices: 7295--7381 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
7285 TGATTACTAA
* * *
7295 CAATTCATATGGAGATTTTTAAATTTTCATAACG-TGGTTAT
1 CAATTCATATGGAGATTATCAAATTCTCATAACGTTGGTTAT
*
7336 CAATATCATATGGAGATTATCAACA-TCTCATAATGTTGGTTAT
1 CAAT-TCATATGGAGATTATCAA-ATTCTCATAACGTTGGTTAT
7379 CAA
1 CAA
7382 AATTTCATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 4 0.10
42 24 0.62
43 11 0.28
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (42 bp):
CAATTCATATGGAGATTATCAAATTCTCATAACGTTGGTTAT
Done.