Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001134.1 Corchorus capsularis cultivar CVL-1 contig01134, 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: 3840
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Found at i:901 original size:30 final size:31
Alignment explanation
Indices: 843--911 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
833 GGGGAAACTT
* *
843 TATATTTCCGATTGTACCCTTATTTTTAAAA
1 TATATTTCCAATTGTACCCCTATTTTTAAAA
*
874 TATATTTTCAATTGTACCCCT-TTTTTAAAA
1 TATATTTCCAATTGTACCCCTATTTTTAAAA
*
904 CATATTTC
1 TATATTTC
912 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.49
Consensus pattern (31 bp):
TATATTTCCAATTGTACCCCTATTTTTAAAA
Found at i:918 original size:31 final size:31
Alignment explanation
Indices: 853--918 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
843 TATATTTCCG
* * *
853 ATTGTACCCTTATTTTTAAAATATATTTTCA
1 ATTGTACCCCTATTTTTAAAACATATTTTAA
884 ATTGTACCCCT-TTTTTAAAACATATTTCTAA
1 ATTGTACCCCTATTTTTAAAACATATTT-TAA
915 ATTG
1 ATTG
919 CCATTACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTGTACCCCTATTTTTAAAACATATTTTAA
Found at i:1481 original size:22 final size:22
Alignment explanation
Indices: 1409--1496 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
1399 CATGTCTTTA
1409 TGTGGTTATCAAAATTTCATAAG
1 TGTGGTTATCAAAATTTCAT-AG
* * * *
1432 -ATGATTATTATAATTTCAT-G
1 TGTGGTTATCAAAATTTCATAG
* *
1452 AAGAGGTTATCAAAATTTCATAG
1 -TGTGGTTATCAAAATTTCATAG
*
1475 TGTGGTTAGCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
1497 GATATTAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
20 1 0.02
22 48 0.96
23 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCATAG
Found at i:1707 original size:22 final size:21
Alignment explanation
Indices: 1658--1964 Score: 140
Period size: 22 Copynumber: 13.8 Consensus size: 21
1648 TTTCATGGGG
* *
1658 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
1680 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* * *
1702 ACGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
1727 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
1749 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
1768 AGTGATTATCAAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
*
1791 GATCGAATTATCAAAATTT-ATAGAA
1 -A--G-GTTATCAAAATTTCATAG-A
*
1816 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
1836 TGTTGTTATCAAAATTTCAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
*
1860 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
1880 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
1903 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
1925 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
1947 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
1965 AAATGTGATT
Statistics
Matches: 219, Mismatches: 41, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
19 2 0.01
20 12 0.05
21 26 0.12
22 138 0.63
23 5 0.02
24 8 0.04
25 18 0.08
26 6 0.03
27 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:1776 original size:21 final size:23
Alignment explanation
Indices: 1735--1989 Score: 155
Period size: 22 Copynumber: 11.6 Consensus size: 23
1725 TAAGGAGTAC
* *
1735 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
1756 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
1777 CAAAATTTCATAGAGATCGAATTAT
1 CAAAATTTCATAGAGAT-G-ATTAT
*
1802 CAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
1823 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
1845 CAAAATTTCAAAGCGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
1867 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * *
1889 CAGAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * *
1911 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
1933 CAAAATTTCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
1955 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
1976 CAAAAATTTCATAG
1 C-AAAATTTCATAG
1990 TGGTATTTCT
Statistics
Matches: 186, Mismatches: 31, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
20 10 0.05
21 25 0.13
22 127 0.68
23 5 0.03
24 6 0.03
25 13 0.07
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:1889 original size:44 final size:44
Alignment explanation
Indices: 1773--1986 Score: 177
Period size: 44 Copynumber: 4.8 Consensus size: 44
1763 CATAGAGTGA
* * *
1773 TTATCAAAATTTCATAGA-GATCGAATTATCAAAATTT-ATAGAAAGA
1 TTATCAAAATTTCATA-ATG-T-G-ATTATCAAAATTTCAAAGAGAGG
* *
1819 TTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAATG-TGATTATCAAAATTTCAAAGAGAGG
* * * *
1863 TTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAGG
* * * * * *
1907 TCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCATAATGTGATTATCAAAATTTCA-AAGAGAGG
* *
1951 TTATCAAATTTTCAAAATGTGATTA-CAAAAATTTCA
1 TTATCAAAATTTCATAATGTGATTATC-AAAATTTCA
1987 TAGTGGTATT
Statistics
Matches: 133, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
43 15 0.11
44 98 0.74
45 2 0.02
46 18 0.14
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAGG
Found at i:2100 original size:19 final size:19
Alignment explanation
Indices: 2070--2117 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
2060 TTATGGAGTA
2070 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
* *
2090 ATCGAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
2109 ATCAAAATT
1 ATCAAAATT
2118 TCATATGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:2134 original size:22 final size:22
Alignment explanation
Indices: 2108--2586 Score: 116
Period size: 22 Copynumber: 21.9 Consensus size: 22
2098 TCAGGGAGGA
2108 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
2130 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
2152 TTTCAAAATTTCACAAG-AGAGT
1 TATCAAAATTTCATATGAAG-GT
* * *
2174 TATGAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * * * *
2195 AGATCGAATTTTCATAGGTAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
2218 TAACAAAATTTCGTAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
2240 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
2263 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
2286 TATCAAAATTTC--AT--AGGT
1 TATCAAAATTTCATATGAAGGT
* * *
2304 TATCACAATTTCATAGTG-CGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
2326 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
2348 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* ** * * *
2370 TTTTTAATTTTTATAACGTAA--T
1 TATCAAAATTTCAT-ATG-AAGGT
* * *
2392 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
2414 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
2437 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
2459 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
2481 TAACCAAAA-TTCATAAGAAGGT
1 T-ATCAAAATTTCATATGAAGGT
** ** *
2503 TAAAAAAATTT-ATAAAAAAGT
1 TATCAAAATTTCATATGAAGGT
* * ***
2524 TCTCGAAA-TTC-TATAGTATCAT
1 TATCAAAATTTCATAT-G-AAGGT
* *
2546 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
2568 TATCAAAATTTCATATGAA
1 TATCAAAATTTCATATGAA
2587 TATTTTATTT
Statistics
Matches: 328, Mismatches: 95, Indels: 68
0.67 0.19 0.14
Matches are distributed among these distances:
18 12 0.04
19 2 0.01
20 7 0.02
21 32 0.10
22 198 0.60
23 74 0.23
24 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:2269 original size:23 final size:23
Alignment explanation
Indices: 2235--2302 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
2225 ATTTCGTAAT
2235 GAGG-TTATCAAAATTTTATAGG
1 GAGGTTTATCAAAATTTTATAGG
2257 GAGGTTTATCAAAATTTTATAGG
1 GAGGTTTATCAAAATTTTATAGG
* * *
2280 AAGATTTATCAAAATTTCATAGG
1 GAGGTTTATCAAAATTTTATAGG
2303 TTATCACAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 4 0.10
23 38 0.90
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (23 bp):
GAGGTTTATCAAAATTTTATAGG
Found at i:2308 original size:18 final size:21
Alignment explanation
Indices: 2239--2338 Score: 82
Period size: 23 Copynumber: 4.7 Consensus size: 21
2229 CGTAATGAGG
*
2239 TTATCAAAATTTTATAGG-GA
1 TTATCAAAATTTCATAGGCGA
* *
2259 GGTTTATCAAAATTTTATAGGAAGA
1 ---TTATCAAAATTTCATAGG-CGA
2284 TTTATCAAAATTTCATA-G-G-
1 -TTATCAAAATTTCATAGGCGA
*
2303 TTATCACAATTTCATAGTGCGA
1 TTATCAAAATTTCATAG-GCGA
2325 TTATCAAAATTTCA
1 TTATCAAAATTTCA
2339 GAGTGTGATT
Statistics
Matches: 68, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.22
20 2 0.03
21 1 0.01
22 14 0.21
23 34 0.50
25 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGCGA
Found at i:2314 original size:41 final size:40
Alignment explanation
Indices: 2221--2338 Score: 103
Period size: 41 Copynumber: 2.8 Consensus size: 40
2211 GGTAGATTAA
* * * *
2221 CAAAATTTCGTAATGAGGTTATCAAAATTTTATAGGGAGGTTTAT
1 CAAAATTTCATAGTGAGATTATCAAAATTTCAT----AGG-TTAT
*
2266 CAAAATTTTATAG-GAAGATTTATCAAAATTTCATAGGTTAT
1 CAAAATTTCATAGTG-AGA-TTATCAAAATTTCATAGGTTAT
* *
2307 CACAATTTCATAGTGCGATTATCAAAATTTCA
1 CAAAATTTCATAGTGAGATTATCAAAATTTCA
2339 GAGTGTGATT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
40 14 0.23
41 17 0.27
42 4 0.06
44 1 0.02
45 12 0.19
46 14 0.23
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (40 bp):
CAAAATTTCATAGTGAGATTATCAAAATTTCATAGGTTAT
Found at i:2512 original size:21 final size:22
Alignment explanation
Indices: 2477--2517 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2467 TTCCTTAGGG
*
2477 AGGTTAACCAAAATTCATAAGA
1 AGGTTAACAAAAATTCATAAGA
*
2499 AGGTTAA-AAAAATTTATAA
1 AGGTTAACAAAAATTCATAA
2518 AAAAGTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (22 bp):
AGGTTAACAAAAATTCATAAGA
Found at i:3808 original size:2 final size:2
Alignment explanation
Indices: 3797--3833 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3787 AATCATAGTG
3797 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3834 ATTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.