Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013712.1 Corchorus capsularis cultivar CVL-1 contig13733, 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: 21324
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:787 original size:23 final size:23
Alignment explanation
Indices: 761--805 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
751 TTATTTTTGA
*
761 TAGAAAATAAGTTTAAATTTATT
1 TAGAAAAAAAGTTTAAATTTATT
784 TAGAAAAAAAGTTTAAATTTAT
1 TAGAAAAAAAGTTTAAATTTAT
806 CCAGAATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (23 bp):
TAGAAAAAAAGTTTAAATTTATT
Found at i:811 original size:23 final size:23
Alignment explanation
Indices: 762--811 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
752 TATTTTTGAT
* **
762 AGAAAATAAGTTTAAATTTATTT
1 AGAAAAAAAGTTTAAATTTATCC
785 AGAAAAAAAGTTTAAATTTATCC
1 AGAAAAAAAGTTTAAATTTATCC
808 AGAA
1 AGAA
812 TGTAAAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (23 bp):
AGAAAAAAAGTTTAAATTTATCC
Found at i:1472 original size:25 final size:26
Alignment explanation
Indices: 1427--1479 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
1417 AACCCTTAAT
*
1427 AACAACTGCATTTTTTAGTAACCTTG
1 AACAACTGCATTTTTTAGTAACATTG
1453 AACAACTGCA-TTTTTAGTAACATTG
1 AACAACTGCATTTTTTAGTAACATTG
1478 AA
1 AA
1480 TAAGAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (26 bp):
AACAACTGCATTTTTTAGTAACATTG
Found at i:2274 original size:18 final size:16
Alignment explanation
Indices: 2251--2290 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
2241 TAATACTATA
2251 TTTTTTCTTTCTTTTTTC
1 TTTTTTC-TT-TTTTTTC
2269 TTTTTTCTTTTTTTTC
1 TTTTTTCTTTTTTTTC
2285 TTTTTT
1 TTTTTT
2291 GTTAATTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.59
17 2 0.09
18 7 0.32
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTC
Found at i:2892 original size:25 final size:25
Alignment explanation
Indices: 2864--2916 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
2854 AGGACTTTAG
*
2864 TATTGGTTTTGAAATTTACTGAATT
1 TATTGATTTTGAAATTTACTGAATT
2889 TATTGATTTTGAAATTTACTGAATT
1 TATTGATTTTGAAATTTACTGAATT
2914 TAT
1 TAT
2917 CGATGATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (25 bp):
TATTGATTTTGAAATTTACTGAATT
Found at i:8066 original size:15 final size:15
Alignment explanation
Indices: 8026--8071 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
8016 TCTGAGTTGT
* *
8026 TTACACCGAAAATGT
1 TTACACTGAAAATGC
8041 TTACACTGAAAATGC
1 TTACACTGAAAATGC
8056 TTACA-TGGAAAATGC
1 TTACACT-GAAAATGC
8071 T
1 T
8072 CAGATCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 1 0.04
15 27 0.96
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (15 bp):
TTACACTGAAAATGC
Found at i:8264 original size:59 final size:59
Alignment explanation
Indices: 8073--8286 Score: 392
Period size: 60 Copynumber: 3.6 Consensus size: 59
8063 GAAAATGCTC
8073 AGATCTGTTATTTTACCTGTTTACATATATTTTATACATGGAAAATGCTCACATGGAAAT
1 AGATCTGTTATTTTACCTGTTTACATATATTTTATACAT-GAAAATGCTCACATGGAAAT
8133 AGATCTGTTATTTTACCTGTTTACATATATTTTATACATTGAAAATGCTCACATGGAAAT
1 AGATCTGTTATTTTACCTGTTTACATATATTTTATACA-TGAAAATGCTCACATGGAAAT
* *
8193 AGATCTGTTATTTTGCCTGTTTACATATATTTTATACATGAAAATGCTCACATAGAAAT
1 AGATCTGTTATTTTACCTGTTTACATATATTTTATACATGAAAATGCTCACATGGAAAT
8252 AGATCTGTTATTTTACCTGTTTACATATATTTTAT
1 AGATCTGTTATTTTACCTGTTTACATATATTTTAT
8287 GCCTTAAACT
Statistics
Matches: 150, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
59 54 0.36
60 95 0.63
61 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (59 bp):
AGATCTGTTATTTTACCTGTTTACATATATTTTATACATGAAAATGCTCACATGGAAAT
Found at i:8340 original size:24 final size:24
Alignment explanation
Indices: 8308--8364 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
8298 AGCATAGTTT
8308 CTCTCTTTTAATCATTAATTTCACC
1 CTCT-TTTTAATCATTAATTTCACC
* * *
8333 CTGTTTTTAATCATTAGTTTCTCC
1 CTCTTTTTAATCATTAATTTCACC
8357 CTCTTTTT
1 CTCTTTTT
8365 TCTTCCTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.54
Consensus pattern (24 bp):
CTCTTTTTAATCATTAATTTCACC
Found at i:10413 original size:13 final size:13
Alignment explanation
Indices: 10395--10421 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10385 TATCGACCTC
10395 GATCTATAAATCA
1 GATCTATAAATCA
10408 GATCTATAAATCA
1 GATCTATAAATCA
10421 G
1 G
10422 CACTAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (13 bp):
GATCTATAAATCA
Found at i:10608 original size:15 final size:15
Alignment explanation
Indices: 10568--10613 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
10558 TCTGAGTTGT
* *
10568 TTACACCGAAAATGT
1 TTACACTGAAAATGC
10583 TTACACTGAAAATGC
1 TTACACTGAAAATGC
10598 TTACA-TGGAAAATGC
1 TTACACT-GAAAATGC
10613 T
1 T
10614 CAGATCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 1 0.04
15 27 0.96
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (15 bp):
TTACACTGAAAATGC
Found at i:10661 original size:50 final size:50
Alignment explanation
Indices: 10599--10725 Score: 137
Period size: 60 Copynumber: 2.3 Consensus size: 50
10589 TGAAAATGCT
*
10599 TACATGGAAAATGCTCAGATCTGTTATTTTACCTGTTTACATATATTTTA
1 TACATGGAAAATGCTCAGATCTGTTATTTTACCTGTTTACATATACTTTA
*
10649 TACACGGAAAATGCTCACATGGAAATAGATCTGTTATTTTACCTGTTTACATATACTTTA
1 TACATGGAAAATGCT--C--------AGATCTGTTATTTTACCTGTTTACATATACTTTA
*
10709 TACATTGAAAATGCTCA
1 TACATGGAAAATGCTCA
10726 CATGGAAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
50 15 0.24
52 1 0.02
58 1 0.02
60 46 0.73
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (50 bp):
TACATGGAAAATGCTCAGATCTGTTATTTTACCTGTTTACATATACTTTA
Found at i:10697 original size:60 final size:60
Alignment explanation
Indices: 10615--10954 Score: 545
Period size: 60 Copynumber: 5.6 Consensus size: 60
10605 GAAAATGCTC
* **
10615 AGATCTGTTATTTTACCTGTTTACATATATTTTATACACGGAAAATGCTCACATGGAAAT
1 AGATCTGTTATTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAAT
10675 AGATCTGTTATTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAAT
1 AGATCTGTTATTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAAT
* * *
10735 AGATCTGTTATTATTTTACCTGTTTACATATATTTTATACATGGAAAATACTCACATGGAAAT
1 AGATCTG---TTATTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAAT
*
10798 AGATATGTTATTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAAT
1 AGATCTGTTATTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAAT
*
10858 AGATCTGTTATTTTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCAAATGGAAAT
1 AGATCTGTTA--TTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAAT
* *
10920 AGATCTGTTATTTTACCTATTTACATATATTTTAT
1 AGATCTGTTATTTTACCTGTTTACATATACTTTAT
10955 GTCTTAAACT
Statistics
Matches: 261, Mismatches: 14, Indels: 10
0.92 0.05 0.04
Matches are distributed among these distances:
60 146 0.56
62 59 0.23
63 56 0.21
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (60 bp):
AGATCTGTTATTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAAT
Found at i:10770 original size:123 final size:123
Alignment explanation
Indices: 10622--10954 Score: 587
Period size: 123 Copynumber: 2.7 Consensus size: 123
10612 CTCAGATCTG
*
10622 TTATTTTACCTGTTTACATATATTTTATACACGGAAAATGCTCACATGGAAATAGATCTGTTATT
1 TTATTTTACCTGTTTACATATATTTTATACATGGAAAATGCTCACATGGAAATAGATCTGTTATT
10687 TTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAATAGATCTGTTA
66 TTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAATAGATCTGTTA
* *
10745 TTATTTTACCTGTTTACATATATTTTATACATGGAAAATACTCACATGGAAATAGATATGTTATT
1 TTATTTTACCTGTTTACATATATTTTATACATGGAAAATGCTCACATGGAAATAGATCTGTTATT
10810 TTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAATAGATCTGTTA
66 TTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAATAGATCTGTTA
* * *
10868 TT-TTTTACCTGTTTACATATACTTTATACATTGAAAATGCTCAAATGGAAATAGATCTGTTATT
1 TTATTTTACCTGTTTACATATATTTTATACATGGAAAATGCTCACATGGAAATAGATCTGTTATT
* *
10932 TTACCTATTTACATATATTTTAT
66 TTACCTGTTTACATATACTTTAT
10955 GTCTTAAACT
Statistics
Matches: 200, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
122 78 0.39
123 122 0.61
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (123 bp):
TTATTTTACCTGTTTACATATATTTTATACATGGAAAATGCTCACATGGAAATAGATCTGTTATT
TTACCTGTTTACATATACTTTATACATTGAAAATGCTCACATGGAAATAGATCTGTTA
Found at i:11031 original size:24 final size:24
Alignment explanation
Indices: 10981--11032 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
10971 AGTTTCTTTC
* *
10981 TTTTAATCATTAATTTCAGCCTGT
1 TTTTAATCATTAATTTCACCCTCT
* *
11005 TTTTAATCATTAGTTTCTCCCTCT
1 TTTTAATCATTAATTTCACCCTCT
11029 TTTT
1 TTTT
11033 TCTTCCTCGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (24 bp):
TTTTAATCATTAATTTCACCCTCT
Found at i:11428 original size:12 final size:12
Alignment explanation
Indices: 11411--11436 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11401 CTTTTTTTTC
11411 TGTAATTTAAAT
1 TGTAATTTAAAT
11423 TGTAATTTAAAT
1 TGTAATTTAAAT
11435 TG
1 TG
11437 GTATTGTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (12 bp):
TGTAATTTAAAT
Found at i:11734 original size:17 final size:18
Alignment explanation
Indices: 11689--11739 Score: 50
Period size: 22 Copynumber: 2.6 Consensus size: 18
11679 TCTTCATTTG
11689 TTTCATTTTCTACTGAATTGT
1 TTTCATTTTCTACTGAA---T
11710 TGTTCATTTTCTACTGAA-
1 T-TTCATTTTCTACTGAAT
11728 TTTCATTGTTCT
1 TTTCATT-TTCT
11740 GTTCATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 5 0.18
21 1 0.04
22 16 0.57
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTCATTTTCTACTGAAT
Found at i:16667 original size:16 final size:16
Alignment explanation
Indices: 16626--16725 Score: 63
Period size: 16 Copynumber: 6.6 Consensus size: 16
16616 ACACCCGATA
*
16626 AATACTCACATGGTGC
1 AATACTCACCTGGTGC
16642 AATACTCACCTGGTG-
1 AATACTCACCTGGTGC
16657 AGATACTCACC-----C
1 A-ATACTCACCTGGTGC
* ** *
16669 -ACACTCACCCAGTAC
1 AATACTCACCTGGTGC
* *
16684 AATACTCACCCGGTGT
1 AATACTCACCTGGTGC
16700 AATACTCACCTGGTG-
1 AATACTCACCTGGTGC
16715 AGATACTCACC
1 A-ATACTCACC
16726 CACACTCACC
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
10 8 0.12
15 3 0.04
16 57 0.84
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (16 bp):
AATACTCACCTGGTGC
Found at i:16704 original size:58 final size:58
Alignment explanation
Indices: 16626--16767 Score: 239
Period size: 58 Copynumber: 2.4 Consensus size: 58
16616 ACACCCGATA
* *
16626 AATACTCACATGGTGCAATACTCACCTGGTGAGATACTCACCCACACTCACCCAGTAC
1 AATACTCACCTGGTGTAATACTCACCTGGTGAGATACTCACCCACACTCACCCAGTAC
*
16684 AATACTCACCCGGTGTAATACTCACCTGGTGAGATACTCACCCACACTCACCCAGTAC
1 AATACTCACCTGGTGTAATACTCACCTGGTGAGATACTCACCCACACTCACCCAGTAC
* *
16742 AATACTCATCTGGTATAATACTCACC
1 AATACTCACCTGGTGTAATACTCACC
16768 CACACTCACC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 78 1.00
ACGTcount: A:0.31, C:0.34, G:0.13, T:0.23
Consensus pattern (58 bp):
AATACTCACCTGGTGTAATACTCACCTGGTGAGATACTCACCCACACTCACCCAGTAC
Found at i:16733 original size:42 final size:42
Alignment explanation
Indices: 16700--16800 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
16690 CACCCGGTGT
16700 AATACTCACCTGGTGAGATACTCACCCACACTCACCCAGTAC
1 AATACTCACCTGGTGAGATACTCACCCACACTCACCCAGTAC
* *
16742 AATACTCATCTGGT-ATAATACTCACCCACACTCACCCAGTAC
1 AATACTCACCTGGTGA-GATACTCACCCACACTCACCCAGTAC
*
16784 AATACTCACCTAGTGAG
1 AATACTCACCTGGTGAG
16801 GCTATGCTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 1 0.02
42 50 0.96
43 1 0.02
ACGTcount: A:0.33, C:0.35, G:0.11, T:0.22
Consensus pattern (42 bp):
AATACTCACCTGGTGAGATACTCACCCACACTCACCCAGTAC
Found at i:16792 original size:16 final size:16
Alignment explanation
Indices: 16671--16793 Score: 56
Period size: 16 Copynumber: 8.4 Consensus size: 16
16661 ACTCACCCAC
16671 ACTCACCCAGTACAAT
1 ACTCACCCAGTACAAT
* **
16687 ACTCACCCGGTGTAAT
1 ACTCACCCAGTACAAT
** *
16703 ACTCACCTGGTGA-GAT
1 ACTCACCCAGT-ACAAT
16719 ACTCACCC---AC---
1 ACTCACCCAGTACAAT
16729 ACTCACCCAGTACAAT
1 ACTCACCCAGTACAAT
* ** *
16745 ACTCATCTGGTATAAT
1 ACTCACCCAGTACAAT
16761 ACTCACCC---AC---
1 ACTCACCCAGTACAAT
16771 ACTCACCCAGTACAAT
1 ACTCACCCAGTACAAT
16787 ACTCACC
1 ACTCACC
16794 TAGTGAGGCT
Statistics
Matches: 79, Mismatches: 14, Indels: 28
0.65 0.12 0.23
Matches are distributed among these distances:
10 16 0.20
12 1 0.01
13 5 0.06
16 57 0.72
ACGTcount: A:0.32, C:0.37, G:0.10, T:0.21
Consensus pattern (16 bp):
ACTCACCCAGTACAAT
Found at i:18392 original size:21 final size:22
Alignment explanation
Indices: 18366--18406 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
18356 AAATGATTCT
18366 TTTGAAAATTT-A-TTTTTAGGA
1 TTTG-AAATTTCAGTTTTTAGGA
18387 TTTGAAATTTCAGTTTTTAG
1 TTTGAAATTTCAGTTTTTAG
18407 TAAATGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (22 bp):
TTTGAAATTTCAGTTTTTAGGA
Found at i:20089 original size:16 final size:17
Alignment explanation
Indices: 20042--20092 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
20032 AATCTTGAGC
* *
20042 TAAAACATAACAAGACA
1 TAAAACCTAACAACACA
*
20059 TAAAA-CTAATTAACACA
1 TAAAACCTAA-CAACACA
20076 -AAAACCTAACAACACA
1 TAAAACCTAACAACACA
20092 T
1 T
20093 TAAGCCCAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.61, C:0.22, G:0.02, T:0.16
Consensus pattern (17 bp):
TAAAACCTAACAACACA
Done.