Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018678.1 Corchorus olitorius cultivar O-4 contig18711, 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: 27857
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:862 original size:204 final size:201
Alignment explanation
Indices: 474--883 Score: 741
Period size: 202 Copynumber: 2.0 Consensus size: 201
464 GCTTAATAAC
*
474 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGGCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
539 GATACAACACATTATTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
604 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
669 CGATTTA
195 CGATTTA
676 TTTATCAATGGTGAATGTTATTAATTTTTTAAGGCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGGCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
741 GATACAACACATTACTATTATATATATAGAACTATA-CAAAGATAAATTAGTTGAACATTAGTGG
66 GATACAACACATTACTATTATATATAT--AACTATACCAAA-AAAAAGTAGTTGAACATTAGTGG
805 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
128 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
870 TCCGATTTA
193 TCCGATTTA
879 TTTAT
1 TTTAT
884 TATTAAGGAA
Statistics
Matches: 201, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
202 90 0.45
203 22 0.11
204 89 0.44
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGGCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Found at i:1048 original size:39 final size:40
Alignment explanation
Indices: 994--1074 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
984 ATACCTAAGA
*
994 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
1033 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
1073 AT
1 AT
1075 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:1302 original size:2 final size:2
Alignment explanation
Indices: 1290--1322 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
1280 AGTTTAGACT
1290 TA TA TA GTA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
1323 TTAATTAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1865 original size:33 final size:33
Alignment explanation
Indices: 1828--1900 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
1818 CGCGGAGGCG
* *
1828 TGCCTCGCACTGTGGTAGGGCACCCCCTGGGGA
1 TGCCTCCCACCGTGGTAGGGCACCCCCTGGGGA
* *
1861 TGCCTCCCACCGTGGTGGGGCGCCCCCTGGGGA
1 TGCCTCCCACCGTGGTAGGGCACCCCCTGGGGA
*
1894 CGCCTCC
1 TGCCTCC
1901 GCGCCTAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.08, C:0.40, G:0.36, T:0.16
Consensus pattern (33 bp):
TGCCTCCCACCGTGGTAGGGCACCCCCTGGGGA
Found at i:5917 original size:46 final size:46
Alignment explanation
Indices: 5865--5957 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
5855 CTGTGTTTCA
5865 TTATCAGAATTCTTACAGTTGTGTTTCATCACATTCATTTTAATAG
1 TTATCAGAATTCTTACAGTTGTGTTTCATCACATTCATTTTAATAG
5911 TTATCAGAATTCTTACAGTTGTGTTTCATCACATTCATTTTAATAG
1 TTATCAGAATTCTTACAGTTGTGTTTCATCACATTCATTTTAATAG
5957 T
1 T
5958 ATTTGATATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (46 bp):
TTATCAGAATTCTTACAGTTGTGTTTCATCACATTCATTTTAATAG
Found at i:5941 original size:25 final size:25
Alignment explanation
Indices: 5867--5941 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
5857 GTGTTTCATT
5867 ATCAGAATTCTTACAGTTGTGTTTC
1 ATCAGAATTCTTACAGTTGTGTTTC
* ** * *
5892 ATCA-CATTCATTTTA-AT-AG-TT-
1 ATCAGAATTC-TTACAGTTGTGTTTC
5913 ATCAGAATTCTTACAGTTGTGTTTC
1 ATCAGAATTCTTACAGTTGTGTTTC
5938 ATCA
1 ATCA
5942 CATTCATTTT
Statistics
Matches: 34, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
21 7 0.21
22 7 0.21
23 2 0.06
24 7 0.21
25 11 0.32
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (25 bp):
ATCAGAATTCTTACAGTTGTGTTTC
Found at i:6745 original size:48 final size:48
Alignment explanation
Indices: 6692--6787 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
6682 TTAAAAAATT
6692 AATGAATCGACTACTTGGTTGAAAGCAATTATTTGTCTTTAGTCTTTA
1 AATGAATCGACTACTTGGTTGAAAGCAATTATTTGTCTTTAGTCTTTA
6740 AATGAATCGACTACTTGGTTGAAAGCAATTATTTGTCTTTAGTCTTTA
1 AATGAATCGACTACTTGGTTGAAAGCAATTATTTGTCTTTAGTCTTTA
6788 TGTTTGGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (48 bp):
AATGAATCGACTACTTGGTTGAAAGCAATTATTTGTCTTTAGTCTTTA
Found at i:10704 original size:7 final size:7
Alignment explanation
Indices: 10692--10720 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
10682 TGGAGGAATT
10692 GGAAAGA
1 GGAAAGA
10699 GGAAAGA
1 GGAAAGA
10706 GGAAAGA
1 GGAAAGA
10713 GGAAAGA
1 GGAAAGA
10720 G
1 G
10721 AGAGAGCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (7 bp):
GGAAAGA
Found at i:19307 original size:141 final size:138
Alignment explanation
Indices: 19051--19307 Score: 347
Period size: 138 Copynumber: 1.8 Consensus size: 138
19041 TCTAATAATG
* * *
19051 GTATCTCTTTAATATCATATTGTCGTGTATTCTATTAAGTAGCGCATCTAGAGAAAGGCTAGGGG
1 GTATCCCTTTAATATCATATTGCCGCGTATTCTATTAAGTAGCGCATCTAGAGAAAGGCTAGGGG
* * *
19116 CTATGTTGTGTCCCTTTAATATCATGTTGCCACGTATCCTATTCGATGGCGAATCTAGAGGAGGG
66 CTATGTTATGTCCCTTTAACATCACGTTGCCACGTATCCTATTCGATGGCGAATCTAGAGGAGGG
19181 ACCATGTT
131 ACCATGTT
* * *
19189 GTATCCCTTTGATATCATGTTGCCGCGTATTCTATTAAGT-GACGGATCTAGA-AGAAGGCTGGC
1 GTATCCCTTTAATATCATATTGCCGCGTATTCTATTAAGTAG-CGCATCTAGAGA-AAGGCT---
** *
19252 AGGGGCTATGTTATGTCCCTTTAACATCACGTTGCTGCGTATCCTATTCGGTGGCG
61 AGGGGCTATGTTATGTCCCTTTAACATCACGTTGCCACGTATCCTATTCGATGGCG
19308 CACGAATTTA
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
137 2 0.02
138 50 0.49
141 50 0.49
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (138 bp):
GTATCCCTTTAATATCATATTGCCGCGTATTCTATTAAGTAGCGCATCTAGAGAAAGGCTAGGGG
CTATGTTATGTCCCTTTAACATCACGTTGCCACGTATCCTATTCGATGGCGAATCTAGAGGAGGG
ACCATGTT
Found at i:19468 original size:76 final size:75
Alignment explanation
Indices: 19176--19474 Score: 239
Period size: 76 Copynumber: 3.9 Consensus size: 75
19166 GAATCTAGAG
* * * *
19176 GAGGGACCATGTTGTATCCCTTTGATATCATGTTGCCGCGTATTCTATTAAGTGACGGATCTAGA
1 GAGGG-CCATGTTGTGTCCCTTTAATATCATGTTGCCGCGTATTCTATTCAGTGACAGATCTAGA
* * **
19241 AGAAGGCTGGCA
65 GGAGGGCT-ATA
* * * * * * * * *
19253 G-GGGCTATGTTATGTCCCTTTAACATCACGTTGCTGCGTATCCTATTCGGTGGCGCACGAATTT
1 GAGGGCCATGTTGTGTCCCTTTAATATCATGTTGCCGCGTATTCTATTCAGT-G-ACA-G-ATCT
* *
19317 AGAGGATGGCTGACA
62 AGAGGAGGGCT-ATA
* * * *
19332 G-GGGTCATG-T-TGTCCTTTTAATATCATGTTGTCGCGTATTCTATTCAGTGACGGATCTAGAG
1 GAGGGCCATGTTGTGTCCCTTTAATATCATGTTGCCGCGTATTCTATTCAGTGACAGATCTAGAG
19394 GAGGGCTATA
66 GAGGGCTATA
* * *
19404 GTAGGGCCATGTTGTGTCCCTTTAATATTATGTTGCCGCGTATTCTAATT-GGTGGCAGATCTAG
1 G-AGGGCCATGTTGTGTCCCTTTAATATCATGTTGCCGCGTATTCT-ATTCAGTGACAGATCTAG
*
19468 AGTAGGG
64 AGGAGGG
19475 TTAGCAGGGT
Statistics
Matches: 175, Mismatches: 38, Indels: 19
0.75 0.16 0.08
Matches are distributed among these distances:
72 3 0.02
73 13 0.07
74 8 0.05
75 39 0.22
76 51 0.29
77 37 0.21
78 2 0.01
79 22 0.13
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (75 bp):
GAGGGCCATGTTGTGTCCCTTTAATATCATGTTGCCGCGTATTCTATTCAGTGACAGATCTAGAG
GAGGGCTATA
Found at i:22476 original size:23 final size:22
Alignment explanation
Indices: 22437--22479 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
22427 ATTCAAATGA
* *
22437 TTATTTAAAAATTTTATAAGAG
1 TTATTAAAAAATCTTATAAGAG
22459 TTATTAAAGAAATCTTATAAG
1 TTATTAAA-AAATCTTATAAG
22480 TTACTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (22 bp):
TTATTAAAAAATCTTATAAGAG
Found at i:22754 original size:20 final size:21
Alignment explanation
Indices: 22731--22770 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22721 GACTTATGGG
22731 GTTT-CTAAAAAACTTATATA
1 GTTTACTAAAAAACTTATATA
* *
22751 GTTTACTTAAAACCTTATAT
1 GTTTACTAAAAAACTTATAT
22771 GCTTACCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
GTTTACTAAAAAACTTATATA
Found at i:22776 original size:20 final size:21
Alignment explanation
Indices: 22738--22776 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22728 GGGGTTTCTA
*
22738 AAAAACTTATATAGTTTACTT
1 AAAAACTTATATAGCTTACTT
*
22759 AAAACCTTATAT-GCTTAC
1 AAAAACTTATATAGCTTAC
22777 CTTTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAACTTATATAGCTTACTT
Found at i:23080 original size:18 final size:17
Alignment explanation
Indices: 23048--23081 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23038 TATTTTTTTT
*
23048 AAAAAAAAAATTATTTC
1 AAAAAAAAAAGTATTTC
23065 AAAAAAAAGAAGTATTT
1 AAAAAAAA-AAGTATTT
23082 TTTTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAAAAAAAGTATTTC
Found at i:26322 original size:12 final size:12
Alignment explanation
Indices: 26307--26338 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
26297 TGCTTGTTAC
26307 TTATTATGTTTA
1 TTATTATGTTTA
26319 TTATTATGTTTA
1 TTATTATGTTTA
26331 TTATTATG
1 TTATTATG
26339 AATGTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATTATGTTTA
Found at i:27268 original size:62 final size:62
Alignment explanation
Indices: 27167--27292 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
27157 GATGAACAAT
27167 TGCATATTTGGATTCGGTTAGGGTGCGTGAAGGCCGAGATAGTGGGTTAAACCTAAACATTA
1 TGCATATTTGGATTCGGTTAGGGTGCGTGAAGGCCGAGATAGTGGGTTAAACCTAAACATTA
* * ** *
27229 TGCATATTTGGATTTGGTTAGGGTGTGTGAAGGTGGAGATGGTGGGTTAAACCTAAACATTA
1 TGCATATTTGGATTCGGTTAGGGTGCGTGAAGGCCGAGATAGTGGGTTAAACCTAAACATTA
27291 TG
1 TG
27293 AAGGAAAGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.26, C:0.10, G:0.33, T:0.32
Consensus pattern (62 bp):
TGCATATTTGGATTCGGTTAGGGTGCGTGAAGGCCGAGATAGTGGGTTAAACCTAAACATTA
Done.