Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010454.1 Corchorus capsularis cultivar CVL-1 contig10475, 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: 10750
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4841 original size:167 final size:165
Alignment explanation
Indices: 4478--4912 Score: 563
Period size: 167 Copynumber: 2.6 Consensus size: 165
4468 GTCATTTATC
*
4478 AATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAA
1 AATTGAGAAATGACCAAAAAGTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACATTTAA
* * * * ** * *
4543 GTAATCTGCCAAGTAGGTAAGAT--GAAAAAAATTAGTTTTGTAGCTCATCATCAATCCTTGATT
66 GTAATCTGCCAAGTAGG-AAAATACGAAAAAAATTAGTTGTCTAACTCAAAAGCAATCCTTGATA
* * *
4606 GGAATCTTTTATTAATTCCACTACTCTATTCAAGTC
130 GGAATCTTTTAGTAATTCCACTACTCTATTAAAGTA
* * *
4642 TATTGAAAAATGACCAAAAAGATTACTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACATTTA
1 AATTGAGAAATGACCAAAAAG-TTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACATTTA
* *
4707 AGTAATCTGCCAAGTAGGAAAATACGAAAAAAATAAGTTGTCTAACTCCAAAAGCAAGTCC-TGG
65 AGTAATCTGCCAAGTAGGAAAATACGAAAAAAATTAGTTGTCTAACT-CAAAAGCAA-TCCTTGA
*
4771 TAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTA
128 TAGGAATCTTTTAGTAATTCCACTACTCTATTAAAGTA
* **
4809 AATTGAGAAATGACCAAAAAGTCTAGTTATTTAA-TCACTTCAAGAATCAAAAGTTAGGGTATTT
1 AATTGAGAAATGACCAAAAAGT-TAGTTATTTAATTC-CCTCAAGAATCAAAAGTTAGGACATTT
* * * *
4873 AAGTAATCGGTCAAGTGGGAAAAGACGAAAAAAATTAGTT
64 AAGTAATCTGCCAAGTAGGAAAATACGAAAAAAATTAGTT
4913 CTCTCGCTCC
Statistics
Matches: 235, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
164 23 0.10
165 59 0.25
166 21 0.09
167 129 0.55
168 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (165 bp):
AATTGAGAAATGACCAAAAAGTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACATTTAA
GTAATCTGCCAAGTAGGAAAATACGAAAAAAATTAGTTGTCTAACTCAAAAGCAATCCTTGATAG
GAATCTTTTAGTAATTCCACTACTCTATTAAAGTA
Found at i:5046 original size:25 final size:25
Alignment explanation
Indices: 5022--5069 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
5012 TTAATGTTTA
5022 AATT-TTATTT-TTATTAAAAAATTT
1 AATTATTATTTATT-TTAAAAAATTT
5046 AATTATTATTTAATTTTAAAAAAT
1 AATTATTATTT-ATTTTAAAAAAT
5070 AAATATGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.19
25 6 0.29
26 9 0.43
27 2 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AATTATTATTTATTTTAAAAAATTT
Found at i:5652 original size:13 final size:13
Alignment explanation
Indices: 5625--5661 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5615 TATTAAATAT
5625 TTATTTATA--TA
1 TTATTTATATTTA
5636 TTATTTATATTTA
1 TTATTTATATTTA
*
5649 TTATTTACATTTA
1 TTATTTATATTTA
5662 CCATGTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 9 0.39
13 14 0.61
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTTATATTTA
Found at i:7472 original size:156 final size:156
Alignment explanation
Indices: 7195--7664 Score: 915
Period size: 156 Copynumber: 3.0 Consensus size: 156
7185 ATACCGCTCT
7195 ATAATGGTGTAGAAATTTTACTTTGAATGTTAAATAATTTTTTCTGAAAGCATCTTTGAATGTT-
1 ATAATGGTGTAGAAATTTTACTTTGAATGTTAAATAATTTTTTCTGAAAGCATCTTTGAATGTTA
* *
7259 GAATTAGTAAATACTCCCTCCGTCTCATATTATGGTTCCACTTTATCTGTCTATTTTTTCCCTAA
66 GAATTAGTAAATACTCCCTCCGTCCCATATTATGGTTCCACTTTATCTGTCCATTTTTTCCCTAA
7324 TAGAAGTGGTGTCCATTTTTTCCCTA
131 TAGAAGTGGTGTCCATTTTTTCCCTA
7350 ATAATGGTGTAGAAATTTTACTTTGAATGTTAAATAATTTTTTCTGAAAGCATCTTTGAATGTTA
1 ATAATGGTGTAGAAATTTTACTTTGAATGTTAAATAATTTTTTCTGAAAGCATCTTTGAATGTTA
7415 GAATTAGTAAATACTCCCTCCGTCCCATATTATGGTTCCACTTTATCTGTCCATTTTTTCCCTAA
66 GAATTAGTAAATACTCCCTCCGTCCCATATTATGGTTCCACTTTATCTGTCCATTTTTTCCCTAA
7480 TAGAAGTGGTGTCCATTTTTTCCCTA
131 TAGAAGTGGTGTCCATTTTTTCCCTA
7506 ATAATGGTGTAGAAATTTTACTTTGAATGTTAAATAATTTTTTCTGAAAGCATCTTTGAATGTTA
1 ATAATGGTGTAGAAATTTTACTTTGAATGTTAAATAATTTTTTCTGAAAGCATCTTTGAATGTTA
7571 GAATTAGTAAATACTCCCTCCGTCCCATATTATGGTTCCACTTTATCTGTCCATTTTTTCCCTAA
66 GAATTAGTAAATACTCCCTCCGTCCCATATTATGGTTCCACTTTATCTGTCCATTTTTTCCCTAA
7636 TAGAAGTGGTGTCCATTTTTTCCCTA
131 TAGAAGTGGTGTCCATTTTTTCCCTA
7662 ATA
1 ATA
7665 GAAGTGGTGG
Statistics
Matches: 312, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
155 64 0.21
156 248 0.79
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (156 bp):
ATAATGGTGTAGAAATTTTACTTTGAATGTTAAATAATTTTTTCTGAAAGCATCTTTGAATGTTA
GAATTAGTAAATACTCCCTCCGTCCCATATTATGGTTCCACTTTATCTGTCCATTTTTTCCCTAA
TAGAAGTGGTGTCCATTTTTTCCCTA
Found at i:7648 original size:27 final size:27
Alignment explanation
Indices: 7618--7673 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
7608 CCACTTTATC
7618 TGTCCATTTTTTCCCTAATAGAAGTGG
1 TGTCCATTTTTTCCCTAATAGAAGTGG
7645 TGTCCATTTTTTCCCTAATAGAAGTGG
1 TGTCCATTTTTTCCCTAATAGAAGTGG
7672 TG
1 TG
7674 GACAGATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (27 bp):
TGTCCATTTTTTCCCTAATAGAAGTGG
Found at i:7692 original size:23 final size:23
Alignment explanation
Indices: 7665--7708 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
7655 TTCCCTAATA
7665 GAAGTGGTGGACAGATAATATAG
1 GAAGTGGTGGACAGATAATATAG
*
7688 GAAGTGGTGGATAGATAATAT
1 GAAGTGGTGGACAGATAATAT
7709 GGGACGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.25
Consensus pattern (23 bp):
GAAGTGGTGGACAGATAATATAG
Found at i:8112 original size:55 final size:55
Alignment explanation
Indices: 8051--8162 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
8041 TACACTTTAT
*
8051 TTCTTAAATTTTGTAATCTTAAAAAGGGATAATAATGGAAGAAAAACGTGTTAAC
1 TTCTTAAATTTTGTAATCTTAAAAAGGGATAATAATGAAAGAAAAACGTGTTAAC
8106 TTCTTAAATTTTGTAATCTTAAAAAGGGATAATAATGAAAGAAAAACGTGTTAAC
1 TTCTTAAATTTTGTAATCTTAAAAAGGGATAATAATGAAAGAAAAACGTGTTAAC
8161 TT
1 TT
8163 ATTTATGTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (55 bp):
TTCTTAAATTTTGTAATCTTAAAAAGGGATAATAATGAAAGAAAAACGTGTTAAC
Found at i:10492 original size:21 final size:21
Alignment explanation
Indices: 10466--10508 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10456 AATATCTGAA
10466 TTGCTAAATACTGCCCCCTTT
1 TTGCTAAATACTGCCCCCTTT
** *
10487 TTGCTAGTTGCTGCCCCCTTT
1 TTGCTAAATACTGCCCCCTTT
10508 T
1 T
10509 GACACTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.33, G:0.14, T:0.42
Consensus pattern (21 bp):
TTGCTAAATACTGCCCCCTTT
Done.