Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017180.1 Corchorus olitorius cultivar O-4 contig17213, 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: 24920
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1309 original size:22 final size:22
Alignment explanation
Indices: 1279--1401 Score: 87
Period size: 22 Copynumber: 5.8 Consensus size: 22
1269 CTTTGCAGAT
*
1279 TATCGAAATTTCATAGTGTAGC
1 TATCAAAATTTCATAGTGTAGC
* * * *
1301 TATTAAAATTTCATAATGTGGT
1 TATCAAAATTTCATAGTGTAGC
* * * *
1323 TGTCAAAATTTCATAATGTGGT
1 TATCAAAATTTCATAGTGTAGC
*
1345 TA-CAAAAATTTCAAAGT-TA--
1 TATC-AAAATTTCATAGTGTAGC
*
1364 -ATCAAAATTTCATATTGT-GC
1 TATCAAAATTTCATAGTGTAGC
1384 TTATCAAAATTTCATAGT
1 -TATCAAAATTTCATAGT
1402 TAGATTAACG
Statistics
Matches: 80, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
18 12 0.15
19 2 0.03
21 2 0.03
22 64 0.80
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTAGC
Found at i:1393 original size:40 final size:40
Alignment explanation
Indices: 1325--1403 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
1315 AATGTGGTTG
*
1325 TCAAAATTTCATAATGTGGTTACAAAAATTTCAAAGTTAA
1 TCAAAATTTCATAATGTGCTTACAAAAATTTCAAAGTTAA
* *
1365 TCAAAATTTCATATTGTGCTTATC-AAAATTTCATAGTTA
1 TCAAAATTTCATAATGTGCTTA-CAAAAATTTCAAAGTTA
1404 GATTAACGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (40 bp):
TCAAAATTTCATAATGTGCTTACAAAAATTTCAAAGTTAA
Found at i:1439 original size:22 final size:22
Alignment explanation
Indices: 1414--1456 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1404 GATTAACGAA
1414 ATTCTATAGGGAAGTTATCAAC
1 ATTCTATAGGGAAGTTATCAAC
*
1436 ATTCTATAGGGAGGTTATCAA
1 ATTCTATAGGGAAGTTATCAA
1457 AATTTCATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (22 bp):
ATTCTATAGGGAAGTTATCAAC
Found at i:1466 original size:22 final size:22
Alignment explanation
Indices: 1364--1466 Score: 75
Period size: 22 Copynumber: 4.7 Consensus size: 22
1354 TTCAAAGTTA
** * *
1364 ATCAAAATTTCATATTGTGCTT
1 ATCAAAATTTCATAGGGAGGTT
** *
1386 ATCAAAATTTCATAGTTAGATT
1 ATCAAAATTTCATAGGGAGGTT
* * *
1408 AACGAAA-TTCTATAGGGAAGTT
1 ATCAAAATTTC-ATAGGGAGGTT
*
1430 ATCAACA-TTCTATAGGGAGGTT
1 ATCAAAATTTC-ATAGGGAGGTT
1452 ATCAAAATTTCATAG
1 ATCAAAATTTCATAG
1467 TATACCAAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
21 3 0.05
22 58 0.91
23 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:1586 original size:22 final size:22
Alignment explanation
Indices: 1561--1617 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
1551 TCACAGTTTT
*
1561 ATAGTGTGGTTATCTAAATTTC
1 ATAGTGTGGTTATCGAAATTTC
1583 ATAG-GATGG-TATCGAAATTTC
1 ATAGTG-TGGTTATCGAAATTTC
*
1604 ATAGTGTAGTTATC
1 ATAGTGTGGTTATC
1618 AAAGTTCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (22 bp):
ATAGTGTGGTTATCGAAATTTC
Found at i:1695 original size:22 final size:22
Alignment explanation
Indices: 1531--1695 Score: 70
Period size: 22 Copynumber: 7.5 Consensus size: 22
1521 TCATCAGAAA
* *
1531 AAAATTTCATATAGAGGTTATC
1 AAAATTTCATAGAGAGATTATC
* * * * * *
1553 ACAGTTTTATAGTGTGGTTATC
1 AAAATTTCATAGAGAGATTATC
* *
1575 TAAATTTCATAG-GATG-GTATC
1 AAAATTTCATAGAGA-GATTATC
* *
1596 GAAATTTCATAGTGTAG-TTATC
1 AAAATTTCATAGAG-AGATTATC
* * * * *
1618 AAAGTTCCACAGGGAGGTTATC
1 AAAATTTCATAGAGAGATTATC
* * *
1640 ACAATTTCTTAGAGAGGTTATC
1 AAAATTTCATAGAGAGATTATC
*
1662 AAAATAAT-ATAGCA-AGATTATC
1 AAAAT-TTCATAG-AGAGATTATC
1684 AAAATTTCATAG
1 AAAATTTCATAG
1696 TAAGTAGGAG
Statistics
Matches: 106, Mismatches: 30, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
21 19 0.18
22 84 0.79
23 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGAGAGATTATC
Found at i:4771 original size:16 final size:17
Alignment explanation
Indices: 4750--4783 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
4740 TAAGTCATTT
4750 AAGCGCCCCAAGT-CCC
1 AAGCGCCCCAAGTGCCC
4766 AAGCGCCCCAAGTGCCC
1 AAGCGCCCCAAGTGCCC
4783 A
1 A
4784 TCTTTTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.26, C:0.47, G:0.21, T:0.06
Consensus pattern (17 bp):
AAGCGCCCCAAGTGCCC
Found at i:10420 original size:11 final size:11
Alignment explanation
Indices: 10404--10429 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10394 AGATATTTTC
10404 TTTTCTTCTAG
1 TTTTCTTCTAG
10415 TTTTCTTCTAG
1 TTTTCTTCTAG
10426 TTTT
1 TTTT
10430 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:11186 original size:16 final size:15
Alignment explanation
Indices: 11165--11221 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
11155 TTACTTTGCT
*
11165 TTGTTTTTTAGTTTAA
1 TTGTTTTCT-GTTTAA
11181 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
11196 TTGCTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
11211 TTGCTTTCTGT
1 TTGTTTTCTGT
11222 CAACCCCTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 31 0.79
16 8 0.21
ACGTcount: A:0.12, C:0.09, G:0.14, T:0.65
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:11193 original size:15 final size:15
Alignment explanation
Indices: 11175--11221 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
11165 TTGTTTTTTA
*
11175 GTTTAATTGTTTTCT
1 GTTTAATTGCTTTCT
11190 GTTTAATTGCTTTCT
1 GTTTAATTGCTTTCT
11205 GTTTAATTGCTTTCT
1 GTTTAATTGCTTTCT
11220 GT
1 GT
11222 CAACCCCTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.13, C:0.11, G:0.15, T:0.62
Consensus pattern (15 bp):
GTTTAATTGCTTTCT
Found at i:11611 original size:33 final size:32
Alignment explanation
Indices: 11566--11629 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
11556 CGTTTTTTAA
*
11566 TTTTTGTGTTTGCGTCATAAAAAAAAAAATTTG
1 TTTTTGTGTTTGCGTC-GAAAAAAAAAAATTTG
*
11599 TTTTATGT-TTTGCGTCGAAAAAAAAATATTT
1 TTTT-TGTGTTTGCGTCGAAAAAAAAAAATTT
11630 TTGCGTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.46
33 12 0.43
34 3 0.11
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (32 bp):
TTTTTGTGTTTGCGTCGAAAAAAAAAAATTTG
Found at i:16720 original size:29 final size:31
Alignment explanation
Indices: 16667--16727 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
16657 CGAAGTTCGT
* *
16667 ATTTGAAGACCATATGAAGATTTATTTGAAG
1 ATTTGAAGACCATATGAAAATTTATTTCAAG
*
16698 ATTTGAAGA-C-TTTGAAAATTTATTTCAAG
1 ATTTGAAGACCATATGAAAATTTATTTCAAG
16727 A
1 A
16728 GGAAGAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 17 0.63
30 1 0.04
31 9 0.33
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (31 bp):
ATTTGAAGACCATATGAAAATTTATTTCAAG
Found at i:17322 original size:11 final size:11
Alignment explanation
Indices: 17306--17331 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17296 AGATATTTTC
17306 TTTTCTTCTAG
1 TTTTCTTCTAG
17317 TTTTCTTCTAG
1 TTTTCTTCTAG
17328 TTTT
1 TTTT
17332 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:18105 original size:15 final size:15
Alignment explanation
Indices: 18066--18108 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
18056 TTTACTTTGC
18066 TTTGTTTTCTAGTTTA
1 TTTGTTTTCT-GTTTA
*
18082 ATTGTTTTCTGTTTA
1 TTTGTTTTCTGTTTA
*
18097 TTTGCTTTCTGT
1 TTTGTTTTCTGT
18109 CAACCTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.09, C:0.09, G:0.14, T:0.67
Consensus pattern (15 bp):
TTTGTTTTCTGTTTA
Found at i:23916 original size:11 final size:11
Alignment explanation
Indices: 23900--23924 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23890 GGGGAATAAT
23900 CAATCCAAAAA
1 CAATCCAAAAA
23911 CAATCCAAAAA
1 CAATCCAAAAA
23922 CAA
1 CAA
23925 ACAATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Done.