Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008528.1 Corchorus capsularis cultivar CVL-1 contig08549, 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: 2075
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Found at i:271 original size:20 final size:20
Alignment explanation
Indices: 246--284 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
236 GGGATATTTG
*
246 GCTAAAAGGTGTAACCTTTT
1 GCTAAAAGATGTAACCTTTT
*
266 GCTAAAAGATTTAACCTTT
1 GCTAAAAGATGTAACCTTT
285 GAATAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
GCTAAAAGATGTAACCTTTT
Found at i:370 original size:51 final size:51
Alignment explanation
Indices: 281--641 Score: 258
Period size: 51 Copynumber: 7.2 Consensus size: 51
271 AAGATTTAAC
* ** *
281 CTTTGAATAAAAGATTGAATTTTTAAGTAA--ATGGGTAAACAAAAATGTCAT
1 CTTTGAATAAAAGATTGAATCTTT-AG-AATGATTAGTAAATAAAAATGTCAT
* * * * *
332 CTTTGAGTAAAAGATTGAATCTTTAGAATGATTAGTAAATAAAGATTTAAC
1 CTTTGAATAAAAGATTGAATCTTTAGAATGATTAGTAAATAAAAATGTCAT
* ** *
383 CTTTGAATAAAAGATTGAATTTTTAAGTAA--ATGGGTAAACAAAAATGTCAT
1 CTTTGAATAAAAGATTGAATCTTT-AG-AATGATTAGTAAATAAAAATGTCAT
* * * * *
434 CTTTGAGTAAAAGATTGAATCTTTAGAGTGATTAGTAAATAAAGAT-TTAA
1 CTTTGAATAAAAGATTGAATCTTTAGAATGATTAGTAAATAAAAATGTCAT
* * * *
484 CTTTTGAATAAAAGATTGAAT-TTTA-AGTAATTGGTAAGTAAAAATGTCAT
1 C-TTTGAATAAAAGATTGAATCTTTAGAATGATTAGTAAATAAAAATGTCAT
* * * * ** * * *
534 -GTTCAGGTAAAAGATTGAATCTTTAGAGTGATTAGTAAATAAAGCTTTAAC
1 CTTTGA-ATAAAAGATTGAATCTTTAGAATGATTAGTAAATAAAAATGTCAT
* * * * *
585 CTTTGAATGAAAGATTGAA-CTTTTA-AGTAATTAGTAAAT-AAAATGTTAC
1 CTTTGAATAAAAGATTGAATC-TTTAGAATGATTAGTAAATAAAAATGTCAT
634 CTTTGAAT
1 CTTTGAAT
642 TAGAAGTTTA
Statistics
Matches: 243, Mismatches: 54, Indels: 28
0.75 0.17 0.09
Matches are distributed among these distances:
48 3 0.01
49 46 0.19
50 31 0.13
51 156 0.64
52 5 0.02
53 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (51 bp):
CTTTGAATAAAAGATTGAATCTTTAGAATGATTAGTAAATAAAAATGTCAT
Found at i:388 original size:102 final size:102
Alignment explanation
Indices: 270--614 Score: 570
Period size: 102 Copynumber: 3.4 Consensus size: 102
260 CCTTTTGCTA
270 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAAATGGGTAAACAAAAATGTCATCTT
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAAATGGGTAAACAAAAATGTCATCTT
*
335 TGAGTAAAAGATTGAATCTTTAGAATGATTAGTAAAT
66 TGAGTAAAAGATTGAATCTTTAGAGTGATTAGTAAAT
372 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAAATGGGTAAACAAAAATGTCATCTT
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAAATGGGTAAACAAAAATGTCATCTT
437 TGAGTAAAAGATTGAATCTTTAGAGTGATTAGTAAAT
66 TGAGTAAAAGATTGAATCTTTAGAGTGATTAGTAAAT
* * ** *
474 AAAGATTTAACTTTTGAATAAAAGATTGAA-TTTTAAGT-AATTGGTAAGTAAAAATGTCAT-GT
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAAATGGGTAAACAAAAATGTCATCTT
*
536 TCAGGTAAAAGATTGAATCTTTAGAGTGATTAGTAAAT
66 TGA-GTAAAAGATTGAATCTTTAGAGTGATTAGTAAAT
* * *
574 AAAGCTTTAACCTTTGAATGAAAGATTGAACTTTTAAGTAA
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAA
615 TTAGTAAATA
Statistics
Matches: 230, Mismatches: 10, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
99 3 0.01
100 80 0.35
101 16 0.07
102 131 0.57
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.35
Consensus pattern (102 bp):
AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAAATGGGTAAACAAAAATGTCATCTT
TGAGTAAAAGATTGAATCTTTAGAGTGATTAGTAAAT
Found at i:656 original size:50 final size:51
Alignment explanation
Indices: 270--677 Score: 201
Period size: 51 Copynumber: 8.1 Consensus size: 51
260 CCTTTTGCTA
* * ** *
270 AAAGATTTAACCTTTGAATAAAAGATTGAA-TTTTTAAGTAAATGGGTAAAC
1 AAAGATTTAACCTTTGAATGAAAGATTAAACTTTTTAAGT-AATTAGTAAAT
* * * * * * * * * *
321 AAAAATGTCATCTTTGAGTAAAAGATTGAA-TCTTTAGAATGATTAGTAAAT
1 AAAGATTTAACCTTTGAATGAAAGATTAAACTTTTTA-AGTAATTAGTAAAT
* * ** *
372 AAAGATTTAACCTTTGAATAAAAGATTGAA-TTTTTAAGTAAATGGGTAAAC
1 AAAGATTTAACCTTTGAATGAAAGATTAAACTTTTTAAGT-AATTAGTAAAT
* * * * * * * * *
423 AAAAATGTCATCTTTGAGTAAAAGATTGAA-TCTTTAGAGTGATTAGTAAAT
1 AAAGATTTAACCTTTGAATGAAAGATTAAACTTTTTA-AGTAATTAGTAAAT
* * * * *
474 AAAGATTTAACTTTTGAATAAAAGATTGAA--TTTTAAGTAATTGGTAAGT
1 AAAGATTTAACCTTTGAATGAAAGATTAAACTTTTTAAGTAATTAGTAAAT
* * * * * * * * *
523 AAAAATGT--CATGTTCAGGTAAAAGATTGAA-TCTTTAGAGTGATTAGTAAAT
1 AAAGATTTAACCT-TTGA-ATGAAAGATTAAACTTTTTA-AGTAATTAGTAAAT
* *
574 AAAGCTTTAACCTTTGAATGAAAGATTGAAC-TTTTAAGTAATTAGTAAAT
1 AAAGATTTAACCTTTGAATGAAAGATTAAACTTTTTAAGTAATTAGTAAAT
* * * **
624 AAA-ATGTT-ACCTTTGAATTAGAAGTTTAAACTTTTTAGGCCATTAGTAAAT
1 AAAGAT-TTAACCTTTGAATGA-AAGATTAAACTTTTTAAGTAATTAGTAAAT
675 AAA
1 AAA
678 TTGATTAGTT
Statistics
Matches: 277, Mismatches: 67, Indels: 26
0.75 0.18 0.07
Matches are distributed among these distances:
47 2 0.01
48 3 0.01
49 41 0.15
50 36 0.13
51 185 0.67
52 8 0.03
53 2 0.01
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (51 bp):
AAAGATTTAACCTTTGAATGAAAGATTAAACTTTTTAAGTAATTAGTAAAT
Found at i:1474 original size:48 final size:47
Alignment explanation
Indices: 1281--1484 Score: 302
Period size: 47 Copynumber: 4.3 Consensus size: 47
1271 AAAAGGGGTG
* * * *
1281 ATCAGT-AATCAGTAAAAAGAGCTTAAACAGAGTCAAGGTGATGGTA
1 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
** *
1327 ATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGTT
1 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
1374 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
1 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
* * *
1421 ATCAGTAAATCAGTAAAAAGAGATTAATCAAAAGTCAAGGTAATAGTA
1 ATCAGTAAATCAGTAAAAAGAGATTAATC-AAAGTCAAAGTGATGGTA
1469 ATCAGTAAATCAGTAA
1 ATCAGTAAATCAGTAA
1485 TCAAGTAAAA
Statistics
Matches: 145, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 6 0.04
47 108 0.74
48 31 0.21
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.24
Consensus pattern (47 bp):
ATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTA
Found at i:1533 original size:71 final size:70
Alignment explanation
Indices: 1445--1600 Score: 174
Period size: 71 Copynumber: 2.2 Consensus size: 70
1435 AAAAAGAGAT
* * * *
1445 TAATCAAAAGTCAAGGTAATAG-TAATCAGTAAATCAGTAATCAA-GTAAAAACATAGTAATCAG
1 TAATTAAAAGTCAAGGTAAGAGATAATCAGTAAATAAG-AATCAAGGT-AAAA-ATACTAATCAG
*
1508 TAAAT-TG
63 TAAATCAG
* * *
1515 ATAATTAAGAGTCAAGGTAAGAGATTAATCAGTAATTAAGAGTCAAGGTAAAAATACTAATCAGT
1 -TAATTAAAAGTCAAGGTAAGAGA-TAATCAGTAAATAAGAATCAAGGTAAAAATACTAATCAGT
1580 AAATCAG
64 AAATCAG
1587 TAATTAAAAGTCAA
1 TAATTAAAAGTCAA
1601 TGGATTGATC
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
71 47 0.65
72 10 0.14
73 15 0.21
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (70 bp):
TAATTAAAAGTCAAGGTAAGAGATAATCAGTAAATAAGAATCAAGGTAAAAATACTAATCAGTAA
ATCAG
Found at i:1581 original size:32 final size:31
Alignment explanation
Indices: 1516--1581 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1506 AGTAAATTGA
*
1516 TAATTAAGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
1547 TAATTAAGAGTCAAGGTAA-AAATACTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAAT--TAATCAG
1579 TAA
1 TAA
1582 ATCAGTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 3 0.09
31 19 0.59
32 10 0.31
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:1723 original size:21 final size:22
Alignment explanation
Indices: 1699--1747 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1689 GAGAGTAATC
*
1699 AGTAAAAGAAAAAT-GGTAAAG
1 AGTAAAAGAAAAATCAGTAAAG
*
1720 AGT-AAAGAATAATCAGTAAAG
1 AGTAAAAGAAAAATCAGTAAAG
1741 AGTAAAA
1 AGTAAAA
1748 TAGTAATCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 12 0.50
22 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.16
Consensus pattern (22 bp):
AGTAAAAGAAAAATCAGTAAAG
Found at i:1888 original size:22 final size:21
Alignment explanation
Indices: 1840--1893 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
1830 AAGCAAAGTG
* * *
1840 GTAATTAGTAAGAGTCAAATA
1 GTAATCAGTAAGAGTAAAAGA
1861 GTAATCAGTAAGAAGTAAAAGA
1 GTAATCAGTAAG-AGTAAAAGA
1883 GTAATCAGTAA
1 GTAATCAGTAA
1894 AAAAGGAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.50, C:0.06, G:0.20, T:0.24
Consensus pattern (21 bp):
GTAATCAGTAAGAGTAAAAGA
Found at i:1892 original size:15 final size:15
Alignment explanation
Indices: 1874--1929 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1864 ATCAGTAAGA
*
1874 AGTAAAAGAGTAATC
1 AGTAAAATAGTAATC
* * *
1889 AGTAAAAAAG-GAGC
1 AGTAAAATAGTAATC
1903 AG-AAAATAGTAATC
1 AGTAAAATAGTAATC
1917 AGTAAAATAGTAA
1 AGTAAAATAGTAA
1930 AATGGTAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 6 0.18
14 8 0.24
15 19 0.58
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18
Consensus pattern (15 bp):
AGTAAAATAGTAATC
Found at i:1958 original size:22 final size:23
Alignment explanation
Indices: 1849--1995 Score: 101
Period size: 22 Copynumber: 6.4 Consensus size: 23
1839 GGTAATTAGT
* *
1849 AAGAGTCAAATAGTAATCAGTAA
1 AAGAGTAAAATGGTAATCAGTAA
*
1872 GA-AGTAAAA-GAGTAATCAGTAAAA
1 AAGAGTAAAATG-GTAATCAGT--AA
* *
1896 AAGGAGCAGAAAATAGTAATCAGTAA
1 AA-GAG--TAAAATGGTAATCAGTAA
*
1922 AATAGTAAAATGGTAATCAGTAA
1 AAGAGTAAAATGGTAATCAGTAA
*
1945 AA-AGTAGAAA-GGTAATCA--AC
1 AAGAGTA-AAATGGTAATCAGTAA
* *
1965 AAGAGTAAAATAGTAATCAGTAC
1 AAGAGTAAAATGGTAATCAGTAA
1988 AA-AGTAAA
1 AAGAGTAAA
1996 GAATAATCAG
Statistics
Matches: 100, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
20 6 0.06
21 11 0.11
22 33 0.33
23 26 0.26
24 3 0.03
25 2 0.02
26 6 0.06
28 13 0.13
ACGTcount: A:0.55, C:0.07, G:0.19, T:0.19
Consensus pattern (23 bp):
AAGAGTAAAATGGTAATCAGTAA
Done.