Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019997.1 Corchorus olitorius cultivar O-4 contig20030, 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: 37705
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1106 original size:165 final size:166
Alignment explanation
Indices: 640--1123 Score: 588
Period size: 167 Copynumber: 2.9 Consensus size: 166
630 AAAACATGTA
** *
640 GAATTACTAAAAGATCCCCATCCTGGA-TT-A--ATGAG-TGAGAGAACTAATATTTTTCGTCTT
1 GAATTACTAAAAGATCCCCA-CCAAGACTTGATGATGAGCT-AGAGAACTAATCTTTTTCGTCTT
* ** * *
700 TTCTTACTTGTTAGATTATTTAAATAAATGTCCTAACTTTTGATTCTTAAGGGGATTAAATAACT
64 TTCCTACTTGACAGATTA-CT---TAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT
* *
765 AGACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTG
125 AAACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTG
* ** *
807 GAATTACTAAAAGATCCCCACCAAGACTTGCTTTTGGAGTTAGAGAACTAATCTTTTTCGTCTTT
1 GAATTACTAAAAGATCCCCACCAAGACTTGATGAT-GAGCTAGAGAACTAATCTTTTTCGTCTTT
* * ** * *
872 TTCTACTTGACAGATTACTTAAATGTTCTAACTTTTGATTCTTGAGCTGATTAAATAAGTAATCT
65 TCCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACT
937 TTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTG
130 TTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTG
* * * * *
974 GAATTAGTAAAAGATTCCCATCAAGGA-TTGATGAT-AGCTAGGGAACTAATCTTTTTCGTGTTT
1 GAATTACTAAAAGATCCCCACCAA-GACTTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTT
*
1037 TCCTACTTTG-CAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAAC
65 TCCTAC-TTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAAC
*
1101 TTTTTGATCATTTCTCAATTGAC
129 TTTTTGGTCATTTCTCAATTGAC
1124 AAATGATTAA
Statistics
Matches: 274, Mismatches: 35, Indels: 18
0.84 0.11 0.06
Matches are distributed among these distances:
165 100 0.36
166 7 0.03
167 123 0.45
168 2 0.01
170 2 0.01
171 39 0.14
172 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (166 bp):
GAATTACTAAAAGATCCCCACCAAGACTTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTT
CCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTT
TTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTG
Found at i:2368 original size:107 final size:107
Alignment explanation
Indices: 2254--2696 Score: 689
Period size: 107 Copynumber: 4.1 Consensus size: 107
2244 GTAATTTTTC
2254 ATTATAGGGTTTTAGAAATTAAATATAAAACTAATTTCACTAAGTTTAGCTCCAAATTAAAATTA
1 ATTATAGGGTTTTAGAAATTAAATATAAAACTAATTTCACTAAGTTTAGCTCCAAATTAAAATTA
2319 AAATTTTATTATAAGGGTAAATTCCAAAATTAATAACCTATT
66 AAATTTTATTATAAGGGTAAATTCCAAAATTAATAACCTATT
* *
2361 GTTATAGGGTTTTAGAAATTAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTA
1 ATTATAGGGTTTTAGAAATTAAATATAAAACTAATTTCACTAAGTTTAGCTCCAAATTAAAATTA
2426 AAATTTTATTATAAGGGTAAATTCCAAAATTAATAACCTATT
66 AAATTTTATTATAAGGGTAAATTCCAAAATTAATAACCTATT
*
2468 GTTATAGGGTTTTAGAAATTAAATATAAAACTAATTTCACTAAGTTTAG-TCCCAAATTAAAATT
1 ATTATAGGGTTTTAGAAATTAAATATAAAACTAATTTCACTAAGTTTAGCT-CCAAATTAAAATT
** * *
2532 TTAATTTTATTTTAAGGGTAAATTTCAAAATTAATAACCTATT
65 AAAATTTTATTATAAGGGTAAATTCCAAAATTAATAACCTATT
*
2575 ATTATAGGGTTTTAGAAA-TAAATTATAAAACTAATTTCACTAAGTTTATC-CCTAAATTAAAAT
1 ATTATAGGGTTTTAGAAATTAAA-TATAAAACTAATTTCACTAAGTTTAGCTCC-AAATTAAAAT
** * * *
2638 TTTAATTTTATTTTAAGAGTAAATTCTAAAATTAAT-ACCTTATT
64 TAAAATTTTATTATAAGGGTAAATTCCAAAATTAATAACC-TATT
*
2682 ATTATA-TGTTTTAGA
1 ATTATAGGGTTTTAGA
2697 TATACTTTTA
Statistics
Matches: 318, Mismatches: 13, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
106 17 0.05
107 301 0.95
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (107 bp):
ATTATAGGGTTTTAGAAATTAAATATAAAACTAATTTCACTAAGTTTAGCTCCAAATTAAAATTA
AAATTTTATTATAAGGGTAAATTCCAAAATTAATAACCTATT
Found at i:10075 original size:13 final size:13
Alignment explanation
Indices: 10057--10082 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10047 GTGACCTAGG
10057 TATTATATTATAT
1 TATTATATTATAT
10070 TATTATATTATAT
1 TATTATATTATAT
10083 ATATAATAAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATTATAT
Found at i:16054 original size:98 final size:98
Alignment explanation
Indices: 15952--16147 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
15942 CCTGTCCGGT
15952 TTTGTTATTCTATATTCAATTTTATATTTTTATATGGGATTAAGGGATTGGAATAGAAATT-AAA
1 TTTGTTATTCTATATTCAATTTTATATTTTTATATGGGATTAAGGGATTGGAATAGAAATTAAAA
*
16016 ATTTAAAATTTAAACCCTATCTAATATTAATCAA
66 AATTAAAATTTAAA-CCTATCTAATATTAATCAA
* *
16050 TTTGTTATTTTATATTCAATTTTATATTTTTATATGGGATTAAGGGATTGGAATAGAATTTAAAA
1 TTTGTTATTCTATATTCAATTTTATATTTTTATATGGGATTAAGGGATTGGAATAGAAATTAAAA
*
16115 AATTAAAATTTAAATCTATCTAATATTAATCAA
66 AATTAAAATTTAAACCTATCTAATATTAATCAA
16148 CTTAAATTTG
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
98 77 0.83
99 16 0.17
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (98 bp):
TTTGTTATTCTATATTCAATTTTATATTTTTATATGGGATTAAGGGATTGGAATAGAAATTAAAA
AATTAAAATTTAAACCTATCTAATATTAATCAA
Found at i:27092 original size:22 final size:22
Alignment explanation
Indices: 27067--27120 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
27057 AATGAAATAC
27067 TAATAACCTAACTAT-AAAATTT
1 TAATAACCTAACTATGAAAA-TT
**
27089 TAATAAACCTTTCTATGAAAATT
1 TAAT-AACCTAACTATGAAAATT
*
27112 TGATAACCT
1 TAATAACCT
27121 CCATATGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 9 0.33
23 14 0.52
24 4 0.15
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (22 bp):
TAATAACCTAACTATGAAAATT
Found at i:27156 original size:22 final size:22
Alignment explanation
Indices: 26967--27156 Score: 137
Period size: 22 Copynumber: 8.5 Consensus size: 22
26957 TAAATATTTT
* *
26967 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTCCC
* *
26989 TATGAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACCTCCC
**
27011 TATGAAATTTTGATATATTTACCC
1 TATGAAATTTTGATA-ACCT-CCC
* *
27035 TATGAAATTGTGATAAACTCCC
1 TATGAAATTTTGATAACCTCCC
* ** * **
27057 AATGAAATACTAATAACCTAAC
1 TATGAAATTTTGATAACCTCCC
* * **
27079 TATAAAATTTTAATAAACCTTTC
1 TATGAAATTTTGAT-AACCTCCC
* *
27102 TATGAAAATTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCC
** **
27124 TATGACTTTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCCC
27146 TATGAAATTTT
1 TATGAAATTTT
27157 ATTAATCTCC
Statistics
Matches: 131, Mismatches: 34, Indels: 6
0.77 0.20 0.04
Matches are distributed among these distances:
22 95 0.73
23 20 0.15
24 16 0.12
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:28266 original size:16 final size:16
Alignment explanation
Indices: 28245--28276 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28235 TTAATTTTCC
28245 TACGACAACTATACAT
1 TACGACAACTATACAT
28261 TACGACAACTATACAT
1 TACGACAACTATACAT
28277 GCTCCTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
TACGACAACTATACAT
Found at i:32902 original size:42 final size:44
Alignment explanation
Indices: 32851--32944 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 44
32841 AGTGCATTAC
*
32851 CTAA-ATTCTACT-C-CATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAA
32892 CTAATATTCTACTCCTTCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTACTCC-TCATCTCTAGATAATTCATCAAAATAAAA
32937 CTAATATT
1 CTAATATT
32945 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 8 0.17
43 1 0.02
45 35 0.73
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAA
Found at i:33549 original size:295 final size:292
Alignment explanation
Indices: 33017--33604 Score: 971
Period size: 295 Copynumber: 2.0 Consensus size: 292
33007 AATCTTGATT
*
33017 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACTAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACCAATCCTTTGGAATTCCGGCA
* *
33082 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATGTAACTAAAACACATTTAAT
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATATAACTAAAACACACTTAAT
* *
33147 CATAAATATAAAAATAGTAAATTACAAAAAAAGGCAGCAGGAAAAGTAAGGGAGGAAATTCATCG
131 CATAAATACAAAAATAGTAAATTACAAAAAAAGGCAGAAGGAAAAGTAAGGGAGGAAATTCATCG
* *
33212 AGGGCCTTTTTAGTCACCCGAAAAATGAGAAAAGACAAAAAAAAAGTCAAAAGGAGGCACCACAT
196 AAGGCCTTTTTAGTCACCCGAAAAATGAGAAAAG--AAAAAAAAAGCCAAAAGGAGGCACCACAT
* *
33277 TAATCCTCAAATTGGCCTTTTAAGTAATTTCCATA
259 TAATCCTCAAATTAGCC-TTTAAATAATTTCCATA
* * *
33312 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACCAATCCTTTGGAATTCCGGCA
* *
33377 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATTAATATATAATTAAAACACACTTAAT
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATATAACTAAAACACACTTAAT
* *
33442 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGAAGGAAAAGTAATGGAGGAAATTCATC-
131 CATAAATACAAAAATAGTAAATTACAAAAAAAGGCAGAAGGAAAAGTAAGGGAGGAAATTCATCG
*
33506 AAGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGATAAAAAAAAGCCAAAAGGAGGCACCACATT
196 AAGGCCTTTTTAGTCACCCGAAAAATGAGAAAAGA-AAAAAAAAGCCAAAAGGAGGCACCACATT
*
33571 AATCCTCAATTTAGCCTTTAAATAATTTCCATA
260 AATCCTCAAATTAGCCTTTAAATAATTTCCATA
33604 G
1 G
33605 TCACTAAAAA
Statistics
Matches: 274, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
292 18 0.07
293 42 0.15
294 32 0.12
295 182 0.66
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (292 bp):
GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACCAATCCTTTGGAATTCCGGCA
GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATATAACTAAAACACACTTAAT
CATAAATACAAAAATAGTAAATTACAAAAAAAGGCAGAAGGAAAAGTAAGGGAGGAAATTCATCG
AAGGCCTTTTTAGTCACCCGAAAAATGAGAAAAGAAAAAAAAAGCCAAAAGGAGGCACCACATTA
ATCCTCAAATTAGCCTTTAAATAATTTCCATA
Found at i:37239 original size:72 final size:72
Alignment explanation
Indices: 37122--37260 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
37112 CCACCCTGCG
*
37122 GGATATCCAATGATCTCATAGCACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCT
1 GGATATCCAATGATCTCATAACACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCT
37187 TGCAGCA
66 TGCAGCA
* * *
37194 GGATATCCAATGATCTCATAACATTGATCTTTCGTGTGCCCCATCTTTTGACAATGTTCACACCT
1 GGATATCCAATGATCTCATAACACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCT
37259 TG
66 TG
37261 GCTTGTCTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (72 bp):
GGATATCCAATGATCTCATAACACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCT
TGCAGCA
Done.