Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018534.1 Corchorus olitorius cultivar O-4 contig18567, 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: 28284
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1334 original size:19 final size:18
Alignment explanation
Indices: 1310--1345 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1300 TGAAGACTTA
*
1310 TTGAAGACTATTTGAAGAT
1 TTGAAGACCA-TTGAAGAT
1329 TTGAAGACCATTGAAGA
1 TTGAAGACCATTGAAGA
1346 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGACCATTGAAGAT
Found at i:11946 original size:15 final size:16
Alignment explanation
Indices: 11923--11956 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11913 TCTAAATTGA
*
11923 TATTATTAAAATTTAT
1 TATTATTAAAATTAAT
11939 TATT-TTAAAATTAAT
1 TATTATTAAAATTAAT
11954 TAT
1 TAT
11957 AAAATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTATTAAAATTAAT
Found at i:12157 original size:44 final size:44
Alignment explanation
Indices: 12064--12254 Score: 167
Period size: 44 Copynumber: 4.4 Consensus size: 44
12054 ATAGAGATCA
* * * *
12064 GATTATCAAAATTT-ATAG-GAAGATAATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAG-AGGTTATCAAAATTTCATAATG-T
* * *
12108 G-TTATCAAAATTTCAAAGCGAGGTTTTCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * *
12151 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAGA-GA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATA-ATGT
* * * *
12195 GGTTATCAAAATTTCATAA-AAAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
12239 GATTATCAAAATTTCA
1 GATTATCAAAATTTCA
12255 TAGTGGCATT
Statistics
Matches: 117, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
43 15 0.13
44 99 0.85
45 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:12219 original size:22 final size:22
Alignment explanation
Indices: 11986--12256 Score: 137
Period size: 22 Copynumber: 12.4 Consensus size: 22
11976 TAAAAGTCTC
* *
11986 AATTTCATAAGGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
12006 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * *
12026 AATTTCATAGAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
* * *
12048 AATGTCATAGAGATCAGATTATCAA
1 AATTTCATA-A-A-GAGGTTATCAA
*
12073 AATTT-ATAGGAAGA--TAATCAA
1 AATTTCATA--AAGAGGTTATCAA
** **
12094 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
* *
12116 AATTTCA-AAGCGAGGTTTTCAA
1 AATTTCATAA-AGAGGTTATCAA
* * * *
12138 AATTACATAATGTGATTATCAA
1 AATTTCATAAAGAGGTTATCAA
* * * *
12160 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGAGGTTATCAA
*
12182 AATTTCATAGAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
12204 AATTTCATAAAAAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
* * *
12226 ATTTTCA-AAATGTGATTATCAA
1 AATTTCATAAA-GAGGTTATCAA
12248 AATTTCATA
1 AATTTCATA
12257 GTGGCATTTC
Statistics
Matches: 190, Mismatches: 46, Indels: 27
0.72 0.17 0.10
Matches are distributed among these distances:
19 1 0.01
20 21 0.11
21 24 0.13
22 121 0.64
23 4 0.02
24 5 0.03
25 14 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:12223 original size:66 final size:66
Alignment explanation
Indices: 12003--12812 Score: 227
Period size: 66 Copynumber: 12.3 Consensus size: 66
11993 TAAGGAGTAC
* * * * * *
12003 CAAAATTTGAT-AGAAGGTTATC-AAATTTCATAGAGTGATTATCGAAATGTCATAGAGATCAGA
1 CAAAATTTCATAAGAAGATTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAG---AGG
12066 TTAT
63 TTAT
* * * * * * *
12070 CAAAATTT-ATAGGAAGATAATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTT
1 CAAAATTTCATAAGAAGATTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAGAGGTTA
12134 T
66 T
* * * * *
12135 CAAAATTACATAATG-TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAGAGAGGTT
1 CAAAATTTCATAA-GAAGATTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAGAGGTT
12199 AT
65 AT
* * * * *
12201 CAAAATTTCATAAAAAGGTTATCAAATTTTCA-AAATGTGATTATCAAAATTTCATAGTGGCATT
1 CAAAATTTCATAAGAAGATTATCAAAATTTCATAGA-GTGGTTATCAAAATTTCATA---G-A--
12265 TCTGGGGAGGTTAT
59 ------GAGGTTAT
* * * * * * * * *
12279 CAAAATTTCAT-AGTATGGTTA-CCAAA-TT-A-GGA-AGGTTCTTAAACTTTTATA-ATG-GAG
1 CAAAATTTCATAAG-AAGATTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGA-GAG-G
*
12336 TAAT
63 TTAT
** * * *** *
12340 CAAAATTTCA-GGGAGGA-TATCAAAATTTCATATAAAAGTTATCAAAATTTCATA-ATTA-GTT
1 CAAAATTTCATAAGAAGATTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGA-GAGGTT
*
12401 TT
65 AT
* * * * * * * * * *
12403 CAAATTTTCATAATATG-TAGATCGAAATTTCATAGGGAGATTAACCAAATTTCATA-ATGAGGT
1 CAAAATTTCATAAGAAGAT-TATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGA-GAGGT
12466 TAT
64 TAT
** * * * *
12469 CAAAAAATCATAGGGAGGTTATCAAAATTT-AT--A---GTTATCAAGATTTCATA-AGGAGGTT
1 CAAAATTTCATAAGAAGATTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGA-GAGGTT
12527 AT
65 AT
* * * * * *
12529 CAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAG-GTTTATCAAAATTTCATA-ACGAG
1 CAAAATTTCATA-AGAAGATTATCAAAATTTCATA-G-AGTGGTTATCAAAATTTCATAGA-GAG
12592 GTTAT
62 GTTAT
* ** *
12597 CACAATTTCAT-AGTGTGATTATCAAAATTT--TAGGGTGTGATTAAT-AACAA-TTCATATG-G
1 CAAAATTTCATAAG-AAGATTATCAAAATTTCATAGAGTG-G-TT-ATCAA-AATTTCATA-GAG
*
12656 AGGTTTT
60 AGGTTAT
* * * * * * * * * *
12663 TAAATTTTCATAACGTAG-TTATCAATATATCATATG-GAGGTTATCAACATCTCATAGTGTTGG
1 CAAAATTTCATAA-GAAGATTATCAAAATTTCATA-GAGTGGTTATCAAAATTTCATAGAG-AGG
12726 TTAT
63 TTAT
** * * * * * *
12730 CAAAATTTCATTGGGAAG-TTATCAAAATTTCATAGTGAGGTTTTCAAAATTCCTTAGGGAGGTT
1 CAAAATTTCA-TAAGAAGATTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAGAGGTT
*
12794 AA
65 AT
12796 CAAAATTTCATAAGAAG
1 CAAAATTTCATAAGAAG
12813 GTTAAAAAAA
Statistics
Matches: 544, Mismatches: 140, Indels: 120
0.68 0.17 0.15
Matches are distributed among these distances:
59 2 0.00
60 38 0.07
61 33 0.06
62 3 0.01
63 14 0.03
64 20 0.04
65 58 0.11
66 174 0.32
67 85 0.16
68 68 0.12
69 2 0.00
70 1 0.00
73 13 0.02
75 2 0.00
76 2 0.00
77 4 0.01
78 25 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (66 bp):
CAAAATTTCATAAGAAGATTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAGAGGTTA
T
Found at i:12497 original size:44 final size:44
Alignment explanation
Indices: 12338--12816 Score: 295
Period size: 44 Copynumber: 11.0 Consensus size: 44
12328 TAATGGAGTA
* * *
12338 ATCAAAATTTC--AGGGAGGATATCAAAATTTCAT-ATAAAAGTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAAT-GAGGTT
*** * * * *
12380 ATCAAAATTTCATAATTA-GTTTTCAAATTTTCATAAT-ATGTAG
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGGT-T
* * * *
12423 ATCGAAATTTCATAGGGAGATTAACCAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTT
**
12467 ATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-AT-A-GTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTT
* * * **
12505 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGG-TT
* * *
12550 ATCAAAATTTTATAGGAAGGTTTATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATAGGGAGG-TTATCAAAATTTCATAATGAGGTT
* * * * * *** * *
12595 ATCACAATTTCATAGTGTGATTATCAAAATTTTAGGGTGTGATT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTT
* * * * *
12639 AAT-AACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGTA-GTT
1 -ATCAA-AATTTCATAGGGAGGTTATCAAAATTTCATAATG-AGGTT
* * * * * * *
12683 ATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATG-AGGTT
* * *
12728 ATCAAAATTTCATTGGGAAGTTATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTT
* * * *
12772 TTCAAAATTCCTTAGGGAGGTTAACAAAATTTCATAA-GAAGGTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATG-AGGTT
12816 A
1 A
12817 AAAAAAATTA
Statistics
Matches: 324, Mismatches: 92, Indels: 40
0.71 0.20 0.09
Matches are distributed among these distances:
38 28 0.09
39 3 0.01
40 2 0.01
41 2 0.01
42 14 0.04
43 34 0.10
44 146 0.45
45 76 0.23
46 19 0.06
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTT
Found at i:12555 original size:23 final size:22
Alignment explanation
Indices: 12338--12816 Score: 268
Period size: 22 Copynumber: 22.0 Consensus size: 22
12328 TAATGGAGTA
*
12338 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
*** *
12358 ATCAAAATTTCATATAAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
***
12380 ATCAAAATTTCATAATTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * ** * *
12401 TTCAAATTTTCATA-ATATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
* *
12423 ATCGAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* * **
12445 AACCAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
12467 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
12489 ATCAAAATTT-AT----A-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
12505 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
12527 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
12550 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
**
12573 ATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
12595 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
12617 ATCAAAATTT--TAGGGTGTGATT
1 ATCAAAATTTCATAGGGAG-G-TT
*
12639 AAT-AACAA-TTCATATGGAGGTT
1 -ATCAA-AATTTCATAGGGAGGTT
* * * * *
12661 TTTAAATTTTCATAACGTA-GTT
1 ATCAAAATTTCAT-AGGGAGGTT
* * *
12683 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
12705 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
12728 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
12750 ATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
12772 TTCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
12794 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
12816 A
1 A
12817 AAAAAAATTA
Statistics
Matches: 349, Mismatches: 87, Indels: 44
0.73 0.18 0.09
Matches are distributed among these distances:
16 12 0.03
17 3 0.01
20 19 0.05
21 25 0.07
22 218 0.62
23 67 0.19
24 5 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:12829 original size:21 final size:22
Alignment explanation
Indices: 12789--12829 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12779 TTCCTTAGGG
* *
12789 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTCATAAGA
12811 AGGTTAAAAAAAATT-ATAA
1 AGGTTAAAAAAAATTCATAA
12830 AAAGATTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (22 bp):
AGGTTAAAAAAAATTCATAAGA
Found at i:17454 original size:107 final size:104
Alignment explanation
Indices: 17290--17551 Score: 418
Period size: 107 Copynumber: 2.5 Consensus size: 104
17280 AGTTTAGCCT
*
17290 TAATTTCACTAAGTTTAGTCTCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
*
17355 AATAATTTATTGTTATAGGGTTTTATAAATAAAATATAAAAC
65 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATATAAAAC
*
17397 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCATAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
*
17462 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
65 AATAATATTGTTATAGGGTTTTAGAAATAAAATATAAAAC
** *
17502 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
17552 TAGAAAAATT
Statistics
Matches: 147, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
103 30 0.20
104 14 0.10
105 36 0.24
107 67 0.46
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.43
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTA
ATAATATTGTTATAGGGTTTTAGAAATAAAATATAAAAC
Found at i:24736 original size:20 final size:19
Alignment explanation
Indices: 24690--24736 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
24680 CGTCCTCAGG
24690 GGGCGCCTCCCACCGTGGT
1 GGGCGCCTCCCACCGTGGT
* *
24709 GGGCCGCCTTCTACCGTGGT
1 GGG-CGCCTCCCACCGTGGT
24729 CGGGCGCC
1 -GGGCGCC
24737 CCCTGGGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.04, C:0.40, G:0.38, T:0.17
Consensus pattern (19 bp):
GGGCGCCTCCCACCGTGGT
Found at i:26188 original size:14 final size:14
Alignment explanation
Indices: 26169--26195 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26159 TTTTTATGAC
26169 GTATTAAATTATTT
1 GTATTAAATTATTT
26183 GTATTAAATTATT
1 GTATTAAATTATT
26196 ATTATTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
GTATTAAATTATTT
Found at i:26198 original size:3 final size:3
Alignment explanation
Indices: 26190--26243 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
26180 TTTGTATTAA
26190 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
26238 A-T ATT A
1 ATT ATT A
26244 GATTAAATAC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:26303 original size:31 final size:31
Alignment explanation
Indices: 26257--26335 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
26247 TAAATACCAA
* * *
26257 AAAAT-ATCCTTTATGTTTTTCTTGTGGGAT
1 AAAATAATCCCTTATGTTTTTCTTGTCGGAC
*
26287 AAAATAATCCCTTATG--TTTCTTTTCGGAC
1 AAAATAATCCCTTATGTTTTTCTTGTCGGAC
26316 AAATATAATCCCTTATGTTT
1 AAA-ATAATCCCTTATGTTT
26336 CAAAAGTGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 13 0.32
30 18 0.44
31 9 0.22
32 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (31 bp):
AAAATAATCCCTTATGTTTTTCTTGTCGGAC
Done.