Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014311.1 Corchorus capsularis cultivar CVL-1 contig14332, 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: 4710
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Found at i:267 original size:20 final size:20
Alignment explanation
Indices: 238--291 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
228 AATGGGGATA
*
238 TTTGGCTAAAAGATGTAACC
1 TTTGGATAAAAGATGTAACC
* *
258 TTTGGTTAAAAGATTTAACC
1 TTTGGATAAAAGATGTAACC
*
278 TTTGAATAAAAGAT
1 TTTGGATAAAAGAT
292 TGAATTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (20 bp):
TTTGGATAAAAGATGTAACC
Found at i:332 original size:50 final size:50
Alignment explanation
Indices: 273--603 Score: 337
Period size: 51 Copynumber: 6.6 Consensus size: 50
263 TTAAAAGATT
* *
273 TAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATG
1 TAACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATG
* * * * * *
323 TCATCTTTGAGTAAAAGATTGAATTTTTAGAGTGATTAGTAAATAAAGATT
1 TAACCTTTGAGTAAAAGATTGAATTTTTA-AGTAATTAGTAAAGAAAAATG
* *
374 TAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATG
1 TAACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATG
* ** * * * ** *
424 TCATATTTGAGTAAAAGATTGAATTTTTTTAGAATAATTAGTGAATAAAGGTT
1 TAACCTTTGAGTAAAAGATTGAA--TTTTTA-AGTAATTAGTAAAGAAAAATG
* *
477 TAACCTTTGAATAAAAGATTG---TTTTAAGTAATTGGTAAAGAAAAATG
1 TAACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATG
* * * * ** *
524 TCATCTTTGAGTAAAAGATTGAATTTTTAGAATAATTAGTAAATAAAGGTT
1 TAACCTTTGAGTAAAAGATTGAATTTTTA-AGTAATTAGTAAAGAAAAATG
575 TAACCTTTGAGTAAAAGATTG-ATTTTTAA
1 TAACCTTTGAGTAAAAGATTGAATTTTTAA
604 AAAAAAAAAT
Statistics
Matches: 224, Mismatches: 49, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
47 32 0.14
48 5 0.02
49 1 0.00
50 73 0.33
51 76 0.34
52 6 0.03
53 31 0.14
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.37
Consensus pattern (50 bp):
TAACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATG
Found at i:441 original size:101 final size:100
Alignment explanation
Indices: 266--603 Score: 563
Period size: 101 Copynumber: 3.4 Consensus size: 100
256 CCTTTGGTTA
266 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
1 AAAGATTTAACCTTTGAATAAAAGATTG-ATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
* *
331 GAGTAAAAGATTGAATTTTTAGAGTGATTAGTAAAT
65 GAGTAAAAGATTGAATTTTTAGAATAATTAGTAAAT
*
367 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTCATATTT
1 AAAGATTTAACCTTTGAATAAAAGATTG-ATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
*
432 GAGTAAAAGATTGAATTTTTTTAGAATAATTAGTGAAT
65 GAGTAAAAGATTGAA--TTTTTAGAATAATTAGTAAAT
*
470 AAAGGTTTAACCTTTGAATAAAAGATTG--TTTTAAGTAATTGGTAAAGAAAAATGTCATCTTTG
1 AAAGATTTAACCTTTGAATAAAAGATTGATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTTG
533 AGTAAAAGATTGAATTTTTAGAATAATTAGTAAAT
66 AGTAAAAGATTGAATTTTTAGAATAATTAGTAAAT
* *
568 AAAGGTTTAACCTTTGAGTAAAAGATTGATTTTTAA
1 AAAGATTTAACCTTTGAATAAAAGATTGATTTTTAA
604 AAAAAAAAAT
Statistics
Matches: 225, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
98 47 0.21
100 54 0.24
101 79 0.35
103 45 0.20
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (100 bp):
AAAGATTTAACCTTTGAATAAAAGATTGATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTTG
AGTAAAAGATTGAATTTTTAGAATAATTAGTAAAT
Found at i:1377 original size:55 final size:55
Alignment explanation
Indices: 1288--1429 Score: 221
Period size: 55 Copynumber: 2.6 Consensus size: 55
1278 GAAAGGGGGC
* * *
1288 AATCAGTAATTAAGTAAAAAGGGATTAATTAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1343 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* * * *
1398 AATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAG
1430 TAAATTGATT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 80 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:1736 original size:21 final size:20
Alignment explanation
Indices: 1679--2057 Score: 170
Period size: 21 Copynumber: 17.4 Consensus size: 20
1669 AATAGCATGC
*
1679 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGT-AAGAGT-AAAAGGT
* * *
1701 -ATCTGAAAGGGTAAAATGGT
1 AATCAGTAAGAGTAAAA-GGT
* *
1721 AATTAGTAAGAGTAAAATAGT
1 AATCAGTAAGAGTAAAA-GGT
*
1742 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGT-AAGAGTAA-AAGGT
** *
1764 AATCAACAAGAGTAAAATAGT
1 AATCAGTAAGAGTAAAA-GGT
* *
1785 AGTCAGTAGAAAGTAAATA-GT
1 AATCAGTA-AGAGTAAA-AGGT
**
1806 AATCAGTAAGAGTAAAACAAT
1 AATCAGTAAGAGTAAAA-GGT
* *
1827 AATCGGTAAGAAGTAAAAGGC
1 AATCAGTAAG-AGTAAAAGGT
*
1848 GATCAGTAAAGAGTAAAAGGCT
1 AATCAGT-AAGAGTAAAAGG-T
1870 AATCAGTAAGAAGTAAAAGGT
1 AATCAGTAAG-AGTAAAAGGT
* * *
1891 AATCAGTAAAAAGCAAAAGGC
1 AATCAGT-AAGAGTAAAAGGT
* *
1912 AATCAGTAAAAGGTAAAACAGT
1 AATCAGTAAGA-GTAAAA-GGT
*
1934 AATCAGTAAAAAAGGAGTAGAAAATAGT
1 AATCAGT----AA-GAGT--AAAA-GGT
*
1962 AATCACTAAAAGAGTAAAAGGGT
1 AATCAGT--AAGAGTAAAA-GGT
*
1985 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGT-AAGAGTAA-AAGGT
** *
2007 AATCAACAAGAGTAAAATAGT
1 AATCAGTAAGAGTAAAA-GGT
* *
2028 AATCAGTACAAAGT-AAAGAAT
1 AATCAGTA-AGAGTAAAAG-GT
2049 AATCAGTAA
1 AATCAGTAA
2058 AATAGTGATG
Statistics
Matches: 277, Mismatches: 53, Indels: 56
0.72 0.14 0.15
Matches are distributed among these distances:
19 5 0.02
20 23 0.08
21 130 0.47
22 76 0.27
23 17 0.06
25 4 0.01
26 8 0.03
27 1 0.00
28 13 0.05
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (20 bp):
AATCAGTAAGAGTAAAAGGT
Found at i:1812 original size:64 final size:63
Alignment explanation
Indices: 1679--1945 Score: 176
Period size: 64 Copynumber: 4.2 Consensus size: 63
1669 AATAGCATGC
* * * * *
1679 AATCAGTAAAAAGTAAAAAGGTATCTGAAAGGGTAAAATGGTAATTAGTAAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAAAGGTATCTAAAAGAGTAAAATAGTAATCAGTAAAAGTAAAATAGT
* *
1742 AATCAGTAAAAAGTAAGAAGGTAATC-AACAAGAGTAAAATAGTAGTCAGTAGAAAGT-AAATAG
1 AATCAGTAAAAAGTAAAAAGGT-ATCTAA-AAGAGTAAAATAGTAATCAGTA-AAAGTAAAATAG
1805 T
63 T
* * * * **
1806 AATCAGT-AAGAGTAAAACA-ATAATCGGTAAGA-AGTAAAA-GGCGATCAGTAAAGAGTAAAA-
1 AATCAGTAAAAAGTAAAA-AGGT-ATC--TAAAAGAGTAAAATAGTAATCAGTAAA-AGTAAAAT
*
1866 GGCT
61 AG-T
* * * * *
1870 AATCAGTAAGAAGT-AAAAGGTAATCAGTAAAA-AGCAAAA-GGCAATCAGTAAAAGGTAAAACA
1 AATCAGTAAAAAGTAAAAAGGT-ATC--TAAAAGAGTAAAATAGTAATCAGTAAAA-GTAAAATA
1932 GT
62 GT
1934 AATCAGTAAAAA
1 AATCAGTAAAAA
1946 AGGAGTAGAA
Statistics
Matches: 165, Mismatches: 25, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
62 2 0.01
63 48 0.29
64 103 0.62
65 10 0.06
66 2 0.01
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (63 bp):
AATCAGTAAAAAGTAAAAAGGTATCTAAAAGAGTAAAATAGTAATCAGTAAAAGTAAAATAGT
Found at i:1860 original size:85 final size:85
Alignment explanation
Indices: 1714--1899 Score: 202
Period size: 85 Copynumber: 2.2 Consensus size: 85
1704 TGAAAGGGTA
* * * * *
1714 AAATGGTAATTAGTAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAA
1 AAATAGTAATCAGTAAGAGTAAAACAATAATCAGTAAAAAGTAAGAAGGCAATCAACAAGAGTAA
*
1779 AATAG-TAGTCAGT-AGAAAGT
66 AA-AGCTAATCAGTAAG-AAGT
* * *
1799 AAATAGTAATCAGTAAGAGTAAAACAATAATCGGTAAGAAGTAA-AAGGCGATCAGTA-AAGAGT
1 AAATAGTAATCAGTAAGAGTAAAACAATAATCAGTAAAAAGTAAGAAGGCAATCA--ACAAGAGT
*
1862 AAAAGGCTAATCAGTAAGAAGT
64 AAAAAGCTAATCAGTAAGAAGT
1884 AAA-AGGTAATCAGTAA
1 AAATA-GTAATCAGTAA
1900 AAAGCAAAAG
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
84 10 0.12
85 73 0.85
86 3 0.03
ACGTcount: A:0.52, C:0.06, G:0.22, T:0.20
Consensus pattern (85 bp):
AAATAGTAATCAGTAAGAGTAAAACAATAATCAGTAAAAAGTAAGAAGGCAATCAACAAGAGTAA
AAAGCTAATCAGTAAGAAGT
Found at i:2018 original size:43 final size:42
Alignment explanation
Indices: 1679--2044 Score: 162
Period size: 43 Copynumber: 8.4 Consensus size: 42
1669 AATAGCATGC
* * *
1679 AATCAGTAAAAAGTAAAAAGGT-ATC-TGAAAGGGTAAAATGGT
1 AATCAGTAAAAAGT-AAAAGGTAATCATAAAAGAGTAAAA-AGT
* * * *
1721 AATTAGT-AAGAGTAAAATAGTAATCAGTAAAA-AGTAAGAAGGT
1 AATCAGTAAAAAGTAAAA-GGTAATCA-TAAAAGAGTAA-AAAGT
* * * * *
1764 AATCA--ACAAGAGTAAAATAGTAGTCAGTAGAA-AGTAAATAGT
1 AATCAGTA-AAAAGTAAAA-GGTAATCA-TAAAAGAGTAAAAAGT
* ** * * * *
1806 AATCAGT-AAGAGTAAAACAATAATCGGTAAGA-AGTAAAAGGC
1 AATCAGTAAAAAGTAAAA-GGTAATC-ATAAAAGAGTAAAAAGT
* * * *
1848 GATCAGTAAAGAGTAAAAGGCTAATCAGTAAGA-AGTAAAAGGT
1 AATCAGTAAAAAGTAAAAGG-TAATCA-TAAAAGAGTAAAAAGT
* *
1891 AATCAGTAAAAAGCAAAAGGCAATCAGTAAAAG-GTAAAACAGT
1 AATCAGTAAAAAGTAAAAGGTAATCA-TAAAAGAGTAAAA-AGT
* *
1934 AATCAGTAAAAAAGGAGTAGAAAATAGTAATCACTAAAAGAGTAAAAGGGT
1 AATCAGT--AAAA--AGT--AAAA-GGTAATCA-TAAAAGAGTAAAA-AGT
*
1985 AATCAGTAAAAAGTAAGAAGGTAATCA-ACAAGAGTAAAATAGT
1 AATCAGTAAAAAGTAA-AAGGTAATCATAAAAGAGTAAAA-AGT
*
2028 AATCAGTACAAAGTAAA
1 AATCAGTAAAAAGTAAA
2045 GAATAATCAG
Statistics
Matches: 259, Mismatches: 41, Indels: 48
0.74 0.12 0.14
Matches are distributed among these distances:
40 4 0.02
41 7 0.03
42 65 0.25
43 122 0.47
44 6 0.02
45 13 0.05
46 2 0.01
47 5 0.02
49 8 0.03
50 12 0.05
51 15 0.06
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (42 bp):
AATCAGTAAAAAGTAAAAGGTAATCATAAAAGAGTAAAAAGT
Done.