Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019728.1 Corchorus olitorius cultivar O-4 contig19761, 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: 19786
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:607 original size:21 final size:21
Alignment explanation
Indices: 581--648 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
571 TTAATTACTA
581 AATTACTAAAAGTATAAGATT
1 AATTACTAAAAGTATAAGATT
*
602 AATTACTAAAGGCTACT-A-A--
1 AATTACTAAAAG-TA-TAAGATT
621 AATTACTAAAAGTATAAGATT
1 AATTACTAAAAGTATAAGATT
642 AATTACT
1 AATTACT
649 GAATTTATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
17 1 0.03
18 3 0.08
19 12 0.31
21 19 0.49
22 3 0.08
23 1 0.03
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (21 bp):
AATTACTAAAAGTATAAGATT
Found at i:1776 original size:22 final size:24
Alignment explanation
Indices: 1725--1776 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
1715 TATACTGAAA
*
1725 ATTAATATGTGATTTATTATATTT
1 ATTAATATGTGATTTATTATAATT
1749 ATTTAATA-GATGATTTA-TA-AATT
1 A-TTAATATG-TGATTTATTATAATT
1772 ATTAA
1 ATTAA
1777 CATACGTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 4 0.16
23 4 0.16
24 4 0.16
25 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTAATATGTGATTTATTATAATT
Found at i:12044 original size:2 final size:2
Alignment explanation
Indices: 12039--12070 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12029 GATGAGAGAG
12039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12071 CTAAATGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12977 original size:22 final size:22
Alignment explanation
Indices: 12949--13124 Score: 126
Period size: 22 Copynumber: 8.0 Consensus size: 22
12939 AACTTTGCAT
*
12949 GTTATCAAAATTTTATAGTGTA
1 GTTATCAAAATTTCATAGTGTA
* *
12971 GTTATCAAAATTTCATAATGTG
1 GTTATCAAAATTTCATAGTGTA
** *
12993 GTTCGCAAAAATTTCATA-T-AA
1 GTTATC-AAAATTTCATAGTGTA
* *
13014 GGTTATCCAAATTTCATACTGT-
1 -GTTATCAAAATTTCATAGTGTA
13036 GCTTATCAAAATTTCATAGTG-A
1 G-TTATCAAAATTTCATAGTGTA
* * * * * *
13058 GACTAACGAAATTCCATAGGGAA
1 G-TTATCAAAATTTCATAGTGTA
* *
13081 GTTATCAAACTTTCATAGTATA
1 GTTATCAAAATTTCATAGTGTA
* *
13103 GATATCCAAATTTCATAGTGTA
1 GTTATCAAAATTTCATAGTGTA
13125 CCAAATCAAC
Statistics
Matches: 116, Mismatches: 31, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
21 11 0.09
22 92 0.79
23 13 0.11
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTA
Found at i:13478 original size:22 final size:21
Alignment explanation
Indices: 13453--13513 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
13443 AGTTTCACAA
*
13453 GGAGATTATCACAATTTATTAG
1 GGAGATTATCAAAATTTA-TAG
* *
13475 GGAGGTTATCAAAATATCATAG
1 GGAGATTATCAAAAT-TTATAG
*
13497 TGAGATTATCAAAATTT
1 GGAGATTATCAAAATTT
13514 CACAATAGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 1 0.03
22 29 0.91
23 2 0.06
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (21 bp):
GGAGATTATCAAAATTTATAG
Found at i:13850 original size:44 final size:45
Alignment explanation
Indices: 13796--13901 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 45
13786 TAGAGCCTAA
* * *
13796 GGTTATCAAAATTTCATAGG-CAGGTAAGCAAAAATTCAAATTGT
1 GGTTACCAAAATTTCATAGGACAGATAAGCAAAAATTCAAATTAT
* * * * *
13840 GGTTACCAAAATTTCAT-GGATAGATTATCAAAATTTCATATTAT
1 GGTTACCAAAATTTCATAGGACAGATAAGCAAAAATTCAAATTAT
13884 GGTTACCAAAATTTCATA
1 GGTTACCAAAATTTCATA
13902 TGGGGTTATC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
43 2 0.04
44 50 0.96
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (45 bp):
GGTTACCAAAATTTCATAGGACAGATAAGCAAAAATTCAAATTAT
Found at i:13893 original size:22 final size:22
Alignment explanation
Indices: 13824--13902 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
13814 GGCAGGTAAG
* * *
13824 CAAAAATTCAAATTGTGGTTAC
1 CAAAATTTCATATTATGGTTAC
* *
13846 CAAAATTTCATGGA-TA-GATTAT
1 CAAAATTTCAT--ATTATGGTTAC
13868 CAAAATTTCATATTATGGTTAC
1 CAAAATTTCATATTATGGTTAC
13890 CAAAATTTCATAT
1 CAAAATTTCATAT
13903 GGGGTTATCA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 41 0.89
23 1 0.02
24 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (22 bp):
CAAAATTTCATATTATGGTTAC
Found at i:13946 original size:22 final size:22
Alignment explanation
Indices: 13914--14115 Score: 147
Period size: 22 Copynumber: 9.0 Consensus size: 22
13904 GGGTTATCAA
* * *
13914 ATAGTGAGGTTATTAAAATTAC
1 ATAGGGAGGTTATCAAAATTTC
*
13936 ATAGGGGGGTTATCAAAATTTC
1 ATAGGGAGGTTATCAAAATTTC
** * * *
13958 ATAATGTGGTTACCAAAATTCC
1 ATAGGGAGGTTATCAAAATTTC
** *
13980 ATA-ATATGATTATCAAAATTTC
1 ATAGGGA-GGTTATCAAAATTTC
***
14002 ATAGACTGGTTATCAAAATTTC
1 ATAGGGAGGTTATCAAAATTTC
* *
14024 ATAGTGAGGTTA-CTAAAATTAC
1 ATAGGGAGGTTATC-AAAATTTC
*
14046 ATAGGGAGGTTATCAAAAGTACTCC
1 ATAGGGAGGTTATCAAAA-T--TTC
14071 ATAGGGAGGTTATCAAAATTTC
1 ATAGGGAGGTTATCAAAATTTC
** * *
14093 ATAATGTGGTTATCAACATTTC
1 ATAGGGAGGTTATCAAAATTTC
14115 A
1 A
14116 CGAATTTATC
Statistics
Matches: 144, Mismatches: 29, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
21 1 0.01
22 119 0.83
23 3 0.02
24 1 0.01
25 20 0.14
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
ATAGGGAGGTTATCAAAATTTC
Found at i:14042 original size:44 final size:44
Alignment explanation
Indices: 13921--14108 Score: 175
Period size: 44 Copynumber: 4.2 Consensus size: 44
13911 CAAATAGTGA
* * *
13921 GGTTATTAAAATTACATAGGGGGGTTATCAAAATTTCATAATGT
1 GGTTATCAAAATTCCATAGGGAGGTTATCAAAATTTCATAATGT
* ** * *
13965 GGTTACCAAAATTCCATA-ATATGATTATCAAAATTTCATAGA-CT
1 GGTTATCAAAATTCCATAGGGA-GGTTATCAAAATTTCATA-ATGT
* * * ** *
14009 GGTTATCAAAATTTCATAGTGAGGTTA-CTAAAATTACATAGGGA
1 GGTTATCAAAATTCCATAGGGAGGTTATC-AAAATTTCATAATGT
14053 GGTTATCAAAAGTACTCCATAGGGAGGTTATCAAAATTTCATAATGT
1 GGTTATCAAAA-T--TCCATAGGGAGGTTATCAAAATTTCATAATGT
14100 GGTTATCAA
1 GGTTATCAA
14109 CATTTCACGA
Statistics
Matches: 112, Mismatches: 23, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
43 1 0.01
44 74 0.66
45 3 0.03
47 33 0.29
48 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (44 bp):
GGTTATCAAAATTCCATAGGGAGGTTATCAAAATTTCATAATGT
Found at i:14059 original size:66 final size:66
Alignment explanation
Indices: 13914--14104 Score: 204
Period size: 66 Copynumber: 2.8 Consensus size: 66
13904 GGGTTATCAA
* * * *
13914 ATAGTGAGGTTATTAAAATTACATAGGGGGGTTATCAAAATTTCATAATGTGGTTACCAAAATTC
1 ATAGAGAGGTTATCAAAATTACATAGGGAGGTTATCAAAATTTCATAATGTGGTTACCAAAATTA
13979 C
66 C
* * * *** * * *
13980 ATA-ATATGATTATCAAAATTTCATAGACTGGTTATCAAAATTTCATAGTGAGGTTACTAAAATT
1 ATAGAGA-GGTTATCAAAATTACATAGGGAGGTTATCAAAATTTCATAATGTGGTTACCAAAATT
14044 AC
65 AC
* *
14046 ATAGGGAGGTTATCAAAAGTACTCCATAGGGAGGTTATCAAAATTTCATAATGTGGTTA
1 ATAGAGAGGTTATCAAAA-T--TACATAGGGAGGTTATCAAAATTTCATAATGTGGTTA
14105 TCAACATTTC
Statistics
Matches: 99, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
65 1 0.01
66 65 0.66
67 2 0.02
69 31 0.31
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (66 bp):
ATAGAGAGGTTATCAAAATTACATAGGGAGGTTATCAAAATTTCATAATGTGGTTACCAAAATTA
C
Found at i:14365 original size:21 final size:22
Alignment explanation
Indices: 14341--14383 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
14331 TACCTTTATC
*
14341 TTTTTATATATTTACA-TAAAA
1 TTTTAATATATTTACATTAAAA
14362 TTTTAATATATTTACATTAAAA
1 TTTTAATATATTTACATTAAAA
14384 ATTGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAATATATTTACATTAAAA
Found at i:16202 original size:54 final size:54
Alignment explanation
Indices: 16139--16294 Score: 252
Period size: 48 Copynumber: 3.0 Consensus size: 54
16129 TATGAACAAC
16139 TGACTATCATTTTAGTTCCTAATTCAGATTTGTCATTTAAACTTTATCTTTATT
1 TGACTATCATTTTAGTTCCTAATTCAGATTTGTCATTTAAACTTTATCTTTATT
16193 TGACTATCATTTTAGTTCC----T-A-ATTTGTCATTTAAACTTTATCTTTATT
1 TGACTATCATTTTAGTTCCTAATTCAGATTTGTCATTTAAACTTTATCTTTATT
* *
16241 TGACTATCATTTTAGTTCCTAATTCAGATTTATCATTTAAACTTTGTCTTTATT
1 TGACTATCATTTTAGTTCCTAATTCAGATTTGTCATTTAAACTTTATCTTTATT
16295 GCTCTTAAAA
Statistics
Matches: 94, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
48 46 0.49
49 1 0.01
50 1 0.01
52 1 0.01
53 1 0.01
54 44 0.47
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.53
Consensus pattern (54 bp):
TGACTATCATTTTAGTTCCTAATTCAGATTTGTCATTTAAACTTTATCTTTATT
Found at i:16217 original size:24 final size:24
Alignment explanation
Indices: 16190--16264 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
16180 CTTTATCTTT
16190 ATTTGACTATCATTTTAGTTCCTA
1 ATTTGACTATCATTTTAGTTCCTA
* * * * * *
16214 ATTTGTCATTTAAACTTTA--TCTTT
1 ATTTGAC-TAT-CATTTTAGTTCCTA
16238 ATTTGACTATCATTTTAGTTCCTA
1 ATTTGACTATCATTTTAGTTCCTA
16262 ATT
1 ATT
16265 CAGATTTATC
Statistics
Matches: 35, Mismatches: 12, Indels: 8
0.64 0.22 0.15
Matches are distributed among these distances:
22 5 0.14
23 2 0.06
24 21 0.60
25 2 0.06
26 5 0.14
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (24 bp):
ATTTGACTATCATTTTAGTTCCTA
Found at i:18473 original size:76 final size:76
Alignment explanation
Indices: 18344--18495 Score: 184
Period size: 76 Copynumber: 2.0 Consensus size: 76
18334 TGATGAGCTA
* *
18344 TGACACAGCCCATCTGGGTGATCAGGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCC
1 TGACACAGCCCACCTGGGTGATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCC
*
18409 AGCTGGAGTCG
66 AGCTAGAGTCG
* ** *
18420 TGACACTGCCCACCTGGGTTCTCAAGC-AAACCACATGGGTGC-TCAAGAC-AACCATGTGGGCG
1 TGACACAGCCCACCTGGGTGATCAAGCGAAA-CACATGGGT-CTTC-AGACAAACCATGTGGGCA
*
18482 CCCAGGTAGAGTCG
63 CCCAGCTAGAGTCG
18496 GGGTCCTTGT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 3 0.05
76 57 0.88
77 5 0.08
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (76 bp):
TGACACAGCCCACCTGGGTGATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCC
AGCTAGAGTCG
Done.