Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019471.1 Corchorus olitorius cultivar O-4 contig19504, 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: 32064
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--25 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
26 TTTAAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5307 original size:21 final size:22
Alignment explanation
Indices: 5272--5319 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
5262 ATGATTTGTT
*
5272 TAATTTAATACTTAATTTGCAA
1 TAATTTAATACTTAATTAGCAA
* *
5294 TAATTTAGTA-TTAATTAGCAT
1 TAATTTAATACTTAATTAGCAA
5315 TAATT
1 TAATT
5320 AATTTAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (22 bp):
TAATTTAATACTTAATTAGCAA
Found at i:5605 original size:3 final size:3
Alignment explanation
Indices: 5584--5664 Score: 121
Period size: 3 Copynumber: 27.3 Consensus size: 3
5574 AATTATGTTA
* *
5584 TAT TA- TAT TA- TAC TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5630 TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
5665 TTTAGTGACT
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.06
3 65 0.90
4 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:8731 original size:48 final size:48
Alignment explanation
Indices: 8657--8752 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
8647 TTAAACATGT
* *
8657 AGATACGAGAATGAAAATTTTGATATCCCAAAAAGTTGTTATTTTCGA
1 AGATACGAGAATGAAAATTTTAATATCCCAAAAAGTTGTAATTTTCGA
* *
8705 AGATAGGAGAATGAAAATTTTAATATCCCAAAGAGTTGTAATTTTCGA
1 AGATACGAGAATGAAAATTTTAATATCCCAAAAAGTTGTAATTTTCGA
8753 GAGCAATCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (48 bp):
AGATACGAGAATGAAAATTTTAATATCCCAAAAAGTTGTAATTTTCGA
Found at i:15154 original size:102 final size:104
Alignment explanation
Indices: 14919--15159 Score: 335
Period size: 106 Copynumber: 2.3 Consensus size: 104
14909 ATTTCACTAA
* *
14919 CCCAAATTAAAATTTTATTTTTATTTTAAT-GGTAAATTTCAAAATTAATAATTTATTGTTATAG
1 CCCAAATTAAAATTTTATTTTTATTTT-ATGGGTAAATTCCAAAATTAATAA--TATTGTTATAA
*
14983 GGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAG
63 GATTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAG
* *
15025 CCCAAATTAAAATTTTATTTTTATTTTATGGGTAAATTCCATAATTGATAA-ATTGTTATAAGAT
1 CCCAAATTAAAATTTTATTTTTATTTTATGGGTAAATTCCAAAATTAATAATATTGTTATAAGAT
* *
15089 TTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAG
66 TTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAG
** * *
15127 CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 CCCAAATTAAAATTTTATTTTTATTTTATGGGT
15160 TAGAAAAATT
Statistics
Matches: 123, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
102 43 0.35
103 33 0.27
105 2 0.02
106 45 0.37
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (104 bp):
CCCAAATTAAAATTTTATTTTTATTTTATGGGTAAATTCCAAAATTAATAATATTGTTATAAGAT
TTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAG
Found at i:19699 original size:21 final size:22
Alignment explanation
Indices: 19673--19726 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
19663 CTTGCGAGTG
*
19673 GTAATAGTAAGATAGTAA-CTA
1 GTAATAGTAAGATAGTAAGATA
*
19694 GTAATAG-AGATATAGTAAGATA
1 GTAATAGTA-AGATAGTAAGATA
19716 GTAACTAGTAA
1 GTAA-TAGTAA
19727 TAGAGATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 15 0.56
22 6 0.22
23 4 0.15
24 1 0.04
ACGTcount: A:0.48, C:0.04, G:0.20, T:0.28
Consensus pattern (22 bp):
GTAATAGTAAGATAGTAAGATA
Found at i:19718 original size:29 final size:29
Alignment explanation
Indices: 19676--19735 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
19666 GCGAGTGGTA
19676 ATAGTAAGATAGTAACTAGTAATAGAGAT
1 ATAGTAAGATAGTAACTAGTAATAGAGAT
19705 ATAGTAAGATAGTAACTAGTAATAGAGAT
1 ATAGTAAGATAGTAACTAGTAATAGAGAT
19734 AT
1 AT
19736 TGAGTGGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.28
Consensus pattern (29 bp):
ATAGTAAGATAGTAACTAGTAATAGAGAT
Found at i:20525 original size:13 final size:13
Alignment explanation
Indices: 20507--20536 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20497 TTTCAAAAAG
*
20507 TTCAATCTCCAAT
1 TTCAATCCCCAAT
20520 TTCAATCCCCAAT
1 TTCAATCCCCAAT
20533 TTCA
1 TTCA
20537 CTGGGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (13 bp):
TTCAATCCCCAAT
Found at i:20892 original size:29 final size:31
Alignment explanation
Indices: 20836--20909 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
20826 GTACCGTACA
20836 GGTCCCTCTACTTACAAAAAGGGATCAATTT
1 GGTCCCTCTACTTACAAAAAGGGATCAATTT
* **
20867 GGTCTCTCTA-TTACAAAAATTG-TCAATTT
1 GGTCCCTCTACTTACAAAAAGGGATCAATTT
*
20896 GATCCCTCTACTTA
1 GGTCCCTCTACTTA
20910 AAATTTGGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.41
30 13 0.35
31 9 0.24
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (31 bp):
GGTCCCTCTACTTACAAAAAGGGATCAATTT
Found at i:28645 original size:119 final size:118
Alignment explanation
Indices: 28410--28764 Score: 606
Period size: 118 Copynumber: 3.0 Consensus size: 118
28400 TGGAAGAACA
* *
28410 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTCAATTTTCCATTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
28475 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAACGC
66 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAACGC
* * * *
28528 TCTACCACAACCATTAATATTATTTTGAGGAATTTCTCGAGTCCTTAAATTTTCCACTTCAAACC
1 TCCACCACAACCATGAATATTGTTTTGAGGAA-TT-TCAAGTCCTTAAATTTTCCACTTCAAACC
*
28593 AACTCTTCC-ATTAAAATAGTATAAATTACTCCTTAATTCTTA-AGTCCCAAACGC
64 AACTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGA-TCCCAAACGC
28647 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
28712 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAACGC
66 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAACGC
28765 GTTAACAATA
Statistics
Matches: 220, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
117 37 0.17
118 74 0.34
119 74 0.34
120 35 0.16
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.34
Consensus pattern (118 bp):
TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAACGC
Found at i:29649 original size:17 final size:17
Alignment explanation
Indices: 29623--29658 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
29613 TTGATAATGG
*
29623 AAACTTAACTCAGTTTC
1 AAACTAAACTCAGTTTC
29640 AAACTAAACTCAGTTTC
1 AAACTAAACTCAGTTTC
29657 AA
1 AA
29659 TTACCCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (17 bp):
AAACTAAACTCAGTTTC
Found at i:30199 original size:22 final size:22
Alignment explanation
Indices: 30170--30310 Score: 125
Period size: 22 Copynumber: 6.6 Consensus size: 22
30160 TATGAAGAGG
30170 TTATCCAAATTTTCATAGTGTGA
1 TTAT-CAAATTTTCATAGTGTGA
*
30193 TTA-CCAATTTT-ATAGTGTGA
1 TTATCAAATTTTCATAGTGTGA
* * *
30213 TTATCAAAATTTCATAGGGAGA
1 TTATCAAATTTTCATAGTGTGA
* * * *
30235 TTATCAAAATTTCACAGTATGG
1 TTATCAAATTTTCATAGTGTGA
30257 TTATCAAATTTTCATA--G-G-
1 TTATCAAATTTTCATAGTGTGA
* *
30275 TTATCAAAATTTCATAATGATG-
1 TTATCAAATTTTCATAGTG-TGA
30297 TTATCAAATTTTCA
1 TTATCAAATTTTCA
30311 CATCATTATC
Statistics
Matches: 97, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
18 15 0.15
19 1 0.01
20 13 0.13
21 13 0.13
22 52 0.54
23 3 0.03
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCAAATTTTCATAGTGTGA
Found at i:30209 original size:20 final size:21
Alignment explanation
Indices: 30177--30229 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
30167 AGGTTATCCA
30177 AATTTTCATAGTGTGATTACC
1 AATTTTCATAGTGTGATTACC
*
30198 AATTTT-ATAGTGTGATTATCA
1 AATTTTCATAGTGTGATTA-CC
*
30219 AAATTTCATAG
1 AATTTTCATAG
30230 GGAGATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.43
21 12 0.43
22 4 0.14
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.43
Consensus pattern (21 bp):
AATTTTCATAGTGTGATTACC
Found at i:30278 original size:18 final size:20
Alignment explanation
Indices: 30145--30310 Score: 81
Period size: 22 Copynumber: 7.8 Consensus size: 20
30135 CTTAATGGTG
30145 TGGTTATCACAATTTT-ATGAA
1 TGGTTATCA-AATTTTCAT-AA
* *
30166 GAGGTTATCCAAATTTTCATAG
1 -TGGTTAT-CAAATTTTCATAA
* *
30188 TGTGATTA-CCAATTTT-ATAG
1 TG-G-TTATCAAATTTTCATAA
* *
30208 TGTGATTATCAAAATTTCATAG
1 TG-G-TTATCAAATTTTCATAA
* * *
30230 GGAGATTATCAAAATTTCACAGTA
1 TG-G-TTATCAAATTTTCATA--A
30254 TGGTTATCAAATTTTCAT-A
1 TGGTTATCAAATTTTCATAA
*
30273 -GGTTATCAAAATTTCATAA
1 TGGTTATCAAATTTTCATAA
30292 TGATGTTATCAAATTTTCA
1 TG--GTTATCAAATTTTCA
30311 CATCATTATC
Statistics
Matches: 117, Mismatches: 15, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
18 16 0.14
19 2 0.02
20 13 0.11
21 14 0.12
22 63 0.54
23 8 0.07
24 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (20 bp):
TGGTTATCAAATTTTCATAA
Found at i:30366 original size:11 final size:12
Alignment explanation
Indices: 30338--30363 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30328 AATGACATAC
30338 AAATTTATTGAA
1 AAATTTATTGAA
30350 AAATTTATTGAA
1 AAATTTATTGAA
30362 AA
1 AA
30364 TTTTGTACGT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (12 bp):
AAATTTATTGAA
Done.