Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013910.1 Corchorus olitorius cultivar O-4 contig13943, 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: 52660
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:494 original size:57 final size:57
Alignment explanation
Indices: 366--579 Score: 385
Period size: 57 Copynumber: 3.8 Consensus size: 57
356 GTGCGGTCTT
* *
366 TTGATCCTCAAATGATCCAGTGCGGTCATTCCAAGTAAGTTTTTTTTAAGGATTAGAG
1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGTAAG-TTTTTTTAATGATTAGAG
424 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGTAAGTTTTTTTAATGATTAGAG
1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGTAAGTTTTTTTAATGATTAGAG
481 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGTAAGTTTTTTTAATGATTAGAG
1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGTAAGTTTTTTTAATGATTAGAG
*
538 TTGATCCTCAGATGATCCAGTGCGGTCATTTCAAG-AAGTTTT
1 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGTAAGTTTT
580 CGGTGATCAG
Statistics
Matches: 153, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
56 7 0.05
57 108 0.71
58 38 0.25
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (57 bp):
TTGATCCTCAGATGATCCAGTGCGGTCATTCCAAGTAAGTTTTTTTAATGATTAGAG
Found at i:681 original size:38 final size:38
Alignment explanation
Indices: 564--705 Score: 224
Period size: 35 Copynumber: 3.9 Consensus size: 38
554 CCAGTGCGGT
*
564 CATTTCAAGAAGTTTTCGGTGATCAGAGTTGATC-TC-
1 CATTTCAAGAAGTTTTCGATGATCAGAGTTGATCATCG
600 C-TTTCAAGAAGTTTTCGATGATCAGAGTTG---ATCG
1 CATTTCAAGAAGTTTTCGATGATCAGAGTTGATCATCG
634 CATTTCAAGAAGTTTTCGATGATCAGAGTTGATCATCG
1 CATTTCAAGAAGTTTTCGATGATCAGAGTTGATCATCG
*
672 CATTTCAAGAAGTTTTCTATGATCAGAGTTGATC
1 CATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
706 TCATTGAAGC
Statistics
Matches: 98, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
33 2 0.02
34 1 0.01
35 57 0.58
36 1 0.01
38 37 0.38
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (38 bp):
CATTTCAAGAAGTTTTCGATGATCAGAGTTGATCATCG
Found at i:774 original size:26 final size:25
Alignment explanation
Indices: 690--789 Score: 102
Period size: 25 Copynumber: 4.0 Consensus size: 25
680 GAAGTTTTCT
*
690 ATGATCAGAGTTGATCT-CATTGAAGCG
1 ATGATCAGAGTTGATCTCCA-AGAA--G
717 ATGATCAGA---GATCTCGCAAGAA-
1 ATGATCAGAGTTGATCTC-CAAGAAG
*
739 ATGATCAGAGTTGGTCTCACAAGAAG
1 ATGATCAGAGTTGATCTC-CAAGAAG
765 ATGATCAGAGTTGATCTCCAAGAAG
1 ATGATCAGAGTTGATCTCCAAGAAG
790 TTTTGTCGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
22 9 0.14
24 5 0.08
25 21 0.33
26 19 0.30
27 9 0.14
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (25 bp):
ATGATCAGAGTTGATCTCCAAGAAG
Found at i:826 original size:34 final size:31
Alignment explanation
Indices: 767--831 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 31
757 ACAAGAAGAT
767 GATCAGAGTTGATCTCCAAGAAGTTT-TGTC
1 GATCAGAGTTGATCTCCAAGAAGTTTATGTC
797 GATCAGAGTTGATCTCGTTTCAAGAAGTTTATGTC
1 GATCAGAGTTGATCTC----CAAGAAGTTTATGTC
832 AGAGTTGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 16 0.53
34 10 0.33
35 4 0.13
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.35
Consensus pattern (31 bp):
GATCAGAGTTGATCTCCAAGAAGTTTATGTC
Found at i:2199 original size:86 final size:86
Alignment explanation
Indices: 1960--2175 Score: 405
Period size: 86 Copynumber: 2.5 Consensus size: 86
1950 ATAATCAATA
*
1960 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGATATATTTTAAGAA
1 AATAATAATGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGATATATTTTAAGAA
**
2025 ATAAATAAATCATAAAGGTTG
66 ATAAATAAATCATAAAGAATG
2046 AATAATAATGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGATATATTTTAAGAA
1 AATAATAATGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGATATATTTTAAGAA
2111 ATAAATAAATCATAAAGAATG
66 ATAAATAAATCATAAAGAATG
2132 AATAATAATGATAATATTTTCTAAATCTTGCCAAATTGTGGAAG
1 AATAATAATGATAATATTTTCTAAATCTTGCCAAATTGTGGAAG
2176 ATGTAGAAAT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 127 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (86 bp):
AATAATAATGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGATATATTTTAAGAA
ATAAATAAATCATAAAGAATG
Found at i:9492 original size:20 final size:20
Alignment explanation
Indices: 9467--9506 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9457 CACCCAGTTA
9467 GTTTTTAACATATGATTATC
1 GTTTTTAACATATGATTATC
9487 GTTTTTAACATATGATTATC
1 GTTTTTAACATATGATTATC
9507 TAACCTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
GTTTTTAACATATGATTATC
Found at i:12042 original size:27 final size:27
Alignment explanation
Indices: 12006--12079 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
11996 TCCGGCATTT
* *
12006 AAGGGCAAAATTGTAATTTAGTCAACC
1 AAGGGCAAAATAGTAATTTAGCCAACC
* * * * *
12033 AGGGGTAAAATGGTGATTTTAGCCTACC
1 AAGGGCAAAATAGT-AATTTAGCCAACC
12061 AAGGGCAAAATAGTAATTT
1 AAGGGCAAAATAGTAATTT
12080 TGACACCTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
27 15 0.42
28 21 0.58
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (27 bp):
AAGGGCAAAATAGTAATTTAGCCAACC
Found at i:15058 original size:13 final size:13
Alignment explanation
Indices: 15040--15065 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15030 GGGAGGATCA
15040 ATTGATCATTACC
1 ATTGATCATTACC
15053 ATTGATCATTACC
1 ATTGATCATTACC
15066 CACCTACAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ATTGATCATTACC
Found at i:15989 original size:2 final size:2
Alignment explanation
Indices: 15978--16015 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
15968 AGGTTGATCG
*
15978 TA TA TA -A TA TA TA TC TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16016 ATAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16209 original size:52 final size:52
Alignment explanation
Indices: 16131--16234 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
16121 GCAATATAAA
16131 GGCAGCATCTGTTAGCAGGTGATTAGAAATTCTTAGATCAGCCATTAAGTTC
1 GGCAGCATCTGTTAGCAGGTGATTAGAAATTCTTAGATCAGCCATTAAGTTC
*
16183 GGCAGCATCTGTTAGCAGGTGATTAGAAATTCTTAGATTAGCCATTAAGTTC
1 GGCAGCATCTGTTAGCAGGTGATTAGAAATTCTTAGATCAGCCATTAAGTTC
16235 AGCAATAAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (52 bp):
GGCAGCATCTGTTAGCAGGTGATTAGAAATTCTTAGATCAGCCATTAAGTTC
Found at i:18764 original size:53 final size:50
Alignment explanation
Indices: 18684--18788 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 50
18674 TGTTGTTGAA
* * *
18684 GACTCTTAATAAGAAAAGATGTGATAGAAAGTATGTAAAGCAAATATAGGTAG
1 GACTCTTAATAAGAAAACATGTAATAGAAAGTATG---AGCAAATATAGATAG
18737 GACTCTTAATAAGAAAACATGTAATAGAAAGTATGAGCAAATATAGATAG
1 GACTCTTAATAAGAAAACATGTAATAGAAAGTATGAGCAAATATAGATAG
18787 GA
1 GA
18789 ATGTAATAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
50 16 0.33
53 33 0.67
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.24
Consensus pattern (50 bp):
GACTCTTAATAAGAAAACATGTAATAGAAAGTATGAGCAAATATAGATAG
Found at i:22153 original size:2 final size:2
Alignment explanation
Indices: 22146--22181 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
22136 GCTTGTTTTC
*
22146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22182 GCATATTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36214 original size:10 final size:10
Alignment explanation
Indices: 36199--36223 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
36189 GACTCAAGTC
36199 TTTTTTCTTT
1 TTTTTTCTTT
36209 TTTTTTCTTT
1 TTTTTTCTTT
36219 TTTTT
1 TTTTT
36224 GGGTACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:36659 original size:2 final size:2
Alignment explanation
Indices: 36652--36687 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
36642 ATAGAATCTG
36652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36688 TTGTATTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51280 original size:42 final size:43
Alignment explanation
Indices: 51230--51323 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
51220 AATGCATTAT
*
51230 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
51271 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
51316 CTAATATT
1 CTAATATT
51324 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:52138 original size:2 final size:2
Alignment explanation
Indices: 52126--52169 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
52116 ACTAAAAATA
52126 AT AT A- 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 AT AT
52166 AT AT
1 AT AT
52170 GTGCAAAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.