Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024476.1 Corchorus olitorius cultivar O-4 contig24509, 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: 42782
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6598 original size:2 final size:2
Alignment explanation
Indices: 6591--6627 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6581 AAACATTTAC
6591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6628 AAGTACGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8522 original size:35 final size:35
Alignment explanation
Indices: 8457--8523 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
8447 GATCCTCTTT
* *
8457 GATATTGGAGTTAGTAGGATATTAATGTGTTTGGA
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
* * *
8492 GATATTGAAGTTAGTGGGGTTTTAAGGTGTTT
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTT
8524 AAAGAGCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (35 bp):
GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
Found at i:9484 original size:44 final size:44
Alignment explanation
Indices: 9436--9585 Score: 148
Period size: 44 Copynumber: 3.4 Consensus size: 44
9426 AAGCATAGGA
*
9436 AGGTTA-CAAAATTTCATA-GGAAAGTTTATTAAAATTTCATAGTT
1 AGGTTATCAAAATTTCATATGG--AGTTTATCAAAATTTCATAGTT
* * * *
9480 AGGTTATCAAAGTTTCTTATGGAGTTTATCACAATTTTATAGTT
1 AGGTTATCAAAATTTCATATGGAGTTTATCAAAATTTCATAGTT
* * * *
9524 A-ATTATCAAAATTTCATATGGTGGTTATCAAAATTT-AGTAGGAT
1 AGGTTATCAAAATTTCATATGGAGTTTATCAAAATTTCA-TA-GTT
9568 A-GTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
9586 AAAGTATTCA
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
42 1 0.01
43 31 0.35
44 45 0.51
45 10 0.11
46 2 0.02
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATATGGAGTTTATCAAAATTTCATAGTT
Found at i:9495 original size:22 final size:22
Alignment explanation
Indices: 9436--9585 Score: 96
Period size: 22 Copynumber: 6.9 Consensus size: 22
9426 AAGCATAGGA
**
9436 AGGTTA-CAAAATTTCATAGGAA
1 AGGTTATCAAAATTTCATA-GTT
* *
9458 AGTTTATTAAAATTTCATAGTT
1 AGGTTATCAAAATTTCATAGTT
* * *
9480 AGGTTATCAAAGTTTCTTA-TGG
1 AGGTTATCAAAATTTCATAGT-T
* * *
9502 AGTTTATCACAATTTTATAGTT
1 AGGTTATCAAAATTTCATAGTT
* *
9524 A-ATTATCAAAATTTCATATGGT
1 AGGTTATCAAAATTTCATA-GTT
*
9546 -GGTTATCAAAATTT-AGTAGGAT
1 AGGTTATCAAAATTTCA-TA-GTT
9568 A-GTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
9586 AAAGTATTCA
Statistics
Matches: 98, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
21 16 0.16
22 69 0.70
23 13 0.13
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTT
Found at i:9650 original size:2 final size:2
Alignment explanation
Indices: 9643--9686 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
9633 GCTAAACTAG
9643 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9685 TA
1 TA
9687 AAAGAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15351 original size:44 final size:45
Alignment explanation
Indices: 15301--15389 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 45
15291 AAAACAGTAT
15301 GGGATATAAAAGGTGTTTTAATATCTCCTCAAGACAAA-AAATAA
1 GGGATATAAAAGGTGTTTTAATATCTCCTCAAGACAAATAAATAA
* *
15345 GGGATATAAAAGGTTTTTTAATATCTCCTCTAGACAAATAAATAA
1 GGGATATAAAAGGTGTTTTAATATCTCCTCAAGACAAATAAATAA
15390 AACATCTGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 36 0.86
45 6 0.14
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (45 bp):
GGGATATAAAAGGTGTTTTAATATCTCCTCAAGACAAATAAATAA
Found at i:19711 original size:2 final size:2
Alignment explanation
Indices: 19706--19744 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19696 CTTTTTTTTC
19706 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19745 CCCCACACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20077 original size:108 final size:108
Alignment explanation
Indices: 19888--20092 Score: 374
Period size: 108 Copynumber: 1.9 Consensus size: 108
19878 AGGTGCCTTA
* *
19888 CATACTCGTAATTTTGGTTCATGACTGACGCGAAGGTTGATATTTGTGATACCGAACCCCGTGTG
1 CATACTCGTAATTTTGGTTCATGACTGACGCGAAGGTTGATATTTGTGAAACCGAACCCCATGTG
19953 CTCCACTTCCCAAAAACAGCGGAGTAATTTATAAGATGCTTTG
66 CTCCACTTCCCAAAAACAGCGGAGTAATTTATAAGATGCTTTG
*
19996 CATACTCGTAATTTTGGTTCGTGACTGACGCGAAGGTTGATATTTGTGAAACCGAACCCCATGTG
1 CATACTCGTAATTTTGGTTCATGACTGACGCGAAGGTTGATATTTGTGAAACCGAACCCCATGTG
*
20061 CTCCACTTCCCAAAAACAGCGGAGTAGTTTAT
66 CTCCACTTCCCAAAAACAGCGGAGTAATTTAT
20093 TAAATTCCCT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 93 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (108 bp):
CATACTCGTAATTTTGGTTCATGACTGACGCGAAGGTTGATATTTGTGAAACCGAACCCCATGTG
CTCCACTTCCCAAAAACAGCGGAGTAATTTATAAGATGCTTTG
Found at i:23531 original size:21 final size:21
Alignment explanation
Indices: 23507--23554 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
23497 TCTCATTTTA
*
23507 TTGTTGAGCCAATTTCCCCAC
1 TTGTTGAGCCAATTGCCCCAC
23528 TTGTTGAGCCAATTGCCCCAC
1 TTGTTGAGCCAATTGCCCCAC
23549 TTGTTG
1 TTGTTG
23555 CTCAAGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (21 bp):
TTGTTGAGCCAATTGCCCCAC
Found at i:29197 original size:12 final size:12
Alignment explanation
Indices: 29180--29214 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
29170 TTAAATTCAA
29180 GTCTCATTTAAT
1 GTCTCATTTAAT
29192 GTCTCATTTAAT
1 GTCTCATTTAAT
*
29204 GTCTCAATTAA
1 GTCTCATTTAA
29215 AAATCTATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.46
Consensus pattern (12 bp):
GTCTCATTTAAT
Found at i:29290 original size:109 final size:109
Alignment explanation
Indices: 29099--29413 Score: 630
Period size: 109 Copynumber: 2.9 Consensus size: 109
29089 AAAAACTTAA
29099 CAATTAAAAATCTATGGCTTCGGCTTCCCTTTGCTTTCATATTTTTGTCTTTACTCTTTACAAAT
1 CAATTAAAAATCTATGGCTTCGGCTTCCCTTTGCTTTCATATTTTTGTCTTTACTCTTTACAAAT
29164 CACAACTTAAATTCAAGTCTCATTTAATGTCTCATTTAATGTCT
66 CACAACTTAAATTCAAGTCTCATTTAATGTCTCATTTAATGTCT
29208 CAATTAAAAATCTATGGCTTCGGCTTCCCTTTGCTTTCATATTTTTGTCTTTACTCTTTACAAAT
1 CAATTAAAAATCTATGGCTTCGGCTTCCCTTTGCTTTCATATTTTTGTCTTTACTCTTTACAAAT
29273 CACAACTTAAATTCAAGTCTCATTTAATGTCTCATTTAATGTCT
66 CACAACTTAAATTCAAGTCTCATTTAATGTCTCATTTAATGTCT
29317 CAATTAAAAATCTATGGCTTCGGCTTCCCTTTGCTTTCATATTTTTGTCTTTACTCTTTACAAAT
1 CAATTAAAAATCTATGGCTTCGGCTTCCCTTTGCTTTCATATTTTTGTCTTTACTCTTTACAAAT
29382 CACAACTTAAATTCAAGTCTCATTTAATGTCT
66 CACAACTTAAATTCAAGTCTCATTTAATGTCT
29414 AAAAAAAAAA
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 206 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (109 bp):
CAATTAAAAATCTATGGCTTCGGCTTCCCTTTGCTTTCATATTTTTGTCTTTACTCTTTACAAAT
CACAACTTAAATTCAAGTCTCATTTAATGTCTCATTTAATGTCT
Found at i:29306 original size:12 final size:12
Alignment explanation
Indices: 29289--29323 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
29279 TTAAATTCAA
29289 GTCTCATTTAAT
1 GTCTCATTTAAT
29301 GTCTCATTTAAT
1 GTCTCATTTAAT
*
29313 GTCTCAATTAA
1 GTCTCATTTAA
29324 AAATCTATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.46
Consensus pattern (12 bp):
GTCTCATTTAAT
Found at i:30673 original size:15 final size:16
Alignment explanation
Indices: 30638--30677 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
30628 AAAAAAAAAA
* *
30638 TTTTATCAATGTTGTT
1 TTTTATTAATATTGTT
30654 TTTTATTAATATTG-T
1 TTTTATTAATATTGTT
30669 TTTTATTAA
1 TTTTATTAA
30678 GAGTTATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (16 bp):
TTTTATTAATATTGTT
Done.