Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016890.1 Corchorus olitorius cultivar O-4 contig16923, 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: 22915
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:2226 original size:22 final size:21
Alignment explanation
Indices: 2201--2243 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2191 TGAATGGACA
* *
2201 AAATATAATTAATGAATAATTT
1 AAATAAAAATAATGAA-AATTT
2223 AAATAAAAATAATGAAAATTT
1 AAATAAAAATAATGAAAATTT
2244 TTTTAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
AAATAAAAATAATGAAAATTT
Found at i:3118 original size:30 final size:30
Alignment explanation
Indices: 3054--3109 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3044 TTATTTATAA
**
3054 TAATATTTATTGTATATTAAATAAATAATC
1 TAATATTTATTACATATTAAATAAATAATC
3084 TAATATTTATTACATATT-AATAAATA
1 TAATATTTATTACATATTAAATAAATA
3110 TTTTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (30 bp):
TAATATTTATTACATATTAAATAAATAATC
Found at i:10156 original size:80 final size:80
Alignment explanation
Indices: 10019--10189 Score: 225
Period size: 80 Copynumber: 2.1 Consensus size: 80
10009 TCTGACTCAG
* * *
10019 AAAAATCCAATTTTCCTTGATCCATTTATAATGACCTGAATCAAAATTTCAATAATTAAAATTGC
1 AAAAATCCAATTTTCCTTGATCCATTTACAATGACCTGAATCAAAATTTAAAAAATTAAAATTGC
*
10084 AATAAAGAGAAACTA
66 AATAAAGAGAAAATA
* * ** * *
10099 AAAAATCCAGTTTTCCTTGATCCGTTTACCTTGACTTGAATCTAAATTTAAAAAATTAAAATTGC
1 AAAAATCCAATTTTCCTTGATCCATTTACAATGACCTGAATCAAAATTTAAAAAATTAAAATTGC
* *
10164 TATAAAGAGAAAATG
66 AATAAAGAGAAAATA
*
10179 AAAAATACAAT
1 AAAAATCCAAT
10190 CAATTCGAAG
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.32
Consensus pattern (80 bp):
AAAAATCCAATTTTCCTTGATCCATTTACAATGACCTGAATCAAAATTTAAAAAATTAAAATTGC
AATAAAGAGAAAATA
Found at i:12407 original size:9 final size:9
Alignment explanation
Indices: 12393--12419 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
12383 GTTTAGTTTC
12393 TAGTGATGA
1 TAGTGATGA
12402 TAGTGATGA
1 TAGTGATGA
12411 TAGTGATGA
1 TAGTGATGA
12420 CCAGCAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (9 bp):
TAGTGATGA
Found at i:15441 original size:117 final size:120
Alignment explanation
Indices: 15221--15458 Score: 328
Period size: 117 Copynumber: 2.0 Consensus size: 120
15211 AATTCAGAAA
*
15221 AGTTATATTTTCATTGATCAATTGGTATGCTAATACAGGAATTAGAAGAAGTTTGCACTATGGGA
1 AGTTATATTTTCATTGATCAATTGGTATGCTAATACAGGAATTAGAAGAAGTTTGCACTATGGCA
* * *
15286 GTGAAAGAGTATCATTCCCATTGGAATTGCTTTTCAAAAATAACAAAATGAAGCC
66 GTGAAAGAGAATCATTCCCATTGGAATTGCTTTTCAAAAACAACAAAATAAAGCC
* *
15341 AGTTATATTTTCATTGATC-ATTGGGTATGCTACA-ACAGGAATTA-CA-AA--TTGTTACTATG
1 AGTTATATTTTCATTGATCAATT-GGTATGCTA-ATACAGGAATTAGAAGAAGTTTG-CACTATG
*
15400 GCAGTGACAGA-AATCCATTCCCATTGGAATTGCTTTTCAAAAACAACAAAATAAAGCC
63 GCAGTGAAAGAGAAT-CATTCCCATTGGAATTGCTTTTCAAAAACAACAAAATAAAGCC
15458 A
1 A
15459 TTTAATACAC
Statistics
Matches: 107, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
116 5 0.05
117 57 0.53
118 2 0.02
119 4 0.04
120 38 0.36
121 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (120 bp):
AGTTATATTTTCATTGATCAATTGGTATGCTAATACAGGAATTAGAAGAAGTTTGCACTATGGCA
GTGAAAGAGAATCATTCCCATTGGAATTGCTTTTCAAAAACAACAAAATAAAGCC
Found at i:16193 original size:9 final size:9
Alignment explanation
Indices: 16181--16214 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
16171 CTTTTTTACG
*
16181 TTTTTTAAT
1 TTTTTTATT
*
16190 TTTTTGATT
1 TTTTTTATT
16199 TTTTTTATT
1 TTTTTTATT
16208 TTTTTTA
1 TTTTTTA
16215 CTTTAGGCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (9 bp):
TTTTTTATT
Found at i:20968 original size:56 final size:56
Alignment explanation
Indices: 20906--21364 Score: 582
Period size: 56 Copynumber: 8.5 Consensus size: 56
20896 GAATAAAATT
*
20906 TAAGTTAATTAAGATAAAAGGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
1 TAAGTTAATTAAGATAAAAAGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* *
20962 TAAGTTAATTAAGATAAAAAGATGGTAATCCGTAAATTAGCTTAATCAAAGTTGAG
1 TAAGTTAATTAAGATAAAAAGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
*
21018 TAAGTTAA-T-A-A-AAAAGGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
1 TAAGTTAATTAAGATAAAAAGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* *
21070 TAAGTTAA-T-A-A-AAAAGGATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAG
1 TAAGTTAATTAAGATAAAAAGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* *
21122 TAAGTTAATTAAGATGAAAA-ATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAG
1 TAAGTTAATTAAGATAAAAAGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* *
21177 TAAG---A-T--G---AAAA-ATGGTAATCGGTAAATTAATTTAATCAAAGTTGAG
1 TAAGTTAATTAAGATAAAAAGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* * *
21223 TAAGTTAATAAAGATAAAAAAAGATAGTAATCAGTAAATTAACTTAATCAAAGTTGAA
1 TAAGTTAATTAAGAT--AAAAAGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* * * *
21281 TAACTTAACTAAGATAAAAATATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAG
1 TAAGTTAATTAAGATAAAAAGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* *
21337 TAAGTTAATCAAG-TAAAAA-AAGGTAATC
1 TAAGTTAATTAAGATAAAAAGATGGTAATC
21365 GATAATTGGC
Statistics
Matches: 359, Mismatches: 28, Indels: 34
0.85 0.07 0.08
Matches are distributed among these distances:
46 40 0.11
49 2 0.01
51 1 0.00
52 99 0.28
53 2 0.01
54 10 0.03
55 47 0.13
56 111 0.31
57 4 0.01
58 43 0.12
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (56 bp):
TAAGTTAATTAAGATAAAAAGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
Found at i:21092 original size:160 final size:160
Alignment explanation
Indices: 20921--21345 Score: 639
Period size: 160 Copynumber: 2.7 Consensus size: 160
20911 TAATTAAGAT
20921 AAAAGGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAGTAAGTTAATTAAGATAAAAAGATG
1 AAAAGGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAGTAAGTTAATTAAGATAAAAA-ATG
*
20986 GTAATCCGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAATAAAAAAGGATGGTAATCAGTAAAT
65 GTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAAT-AAAAA--ATGGTAATCAGTAAAT
21051 TAACTTAATCAAAGTTGAGTAAG-T-T-A-ATAA
127 TAACTTAATCAAAGTTGAGTAAGTTATAAGATAA
* *
21081 AAAAGGATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAATTAAGATGAAAAATGG
1 AAAAGGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAGTAAGTTAATTAAGATAAAAAATGG
* * *
21146 TAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAG---ATGAAAAATGGTAATCGGTAAATTAAT
66 TAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAATAAAAAATGGTAATCAGTAAATTAAC
21208 TTAATCAAAGTTGAGTAAGTTAATAAAGATAA
131 TTAATCAAAGTTGAGTAAGTT-AT-AAGATAA
* * * * *
21240 AAAAAGATAGTAATCAGTAAATTAACTTAATCAAAGTTGAATAACTTAACTAAGATAAAAATATG
1 AAAAGGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAGTAAGTTAATTAAGATAAAAA-ATG
21305 GTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAAT
65 GTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAAT
21346 CAAGTAAAAA
Statistics
Matches: 242, Mismatches: 13, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
153 37 0.15
154 1 0.00
155 4 0.02
156 3 0.01
158 1 0.00
159 96 0.40
160 98 0.40
163 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (160 bp):
AAAAGGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAGTAAGTTAATTAAGATAAAAAATGG
TAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAATAAAAAATGGTAATCAGTAAATTAAC
TTAATCAAAGTTGAGTAAGTTATAAGATAA
Found at i:21188 original size:104 final size:103
Alignment explanation
Indices: 20971--21364 Score: 460
Period size: 104 Copynumber: 3.7 Consensus size: 103
20961 GTAAGTTAAT
*
20971 TAAGAT-AAAAAGATGGTAATCCGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAA-TAA-A-AA
1 TAAGATGAAAAAGATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAATTAAGATAA
**
21032 AGGATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
66 AAAATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
*
21070 TAAGTTAATAAAAAAGGATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAATTAAG
1 TAAG---ATGAAAAA-GATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAATTAAG
* *
21135 ATGAAAAATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAG
62 ATAAAAAATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* ** *
21177 TAAGATG-AAAA-ATGGTAATCGGTAAATTAATTTAATCAAAGTTGAGTAAGTTAATAAAGATAA
1 TAAGATGAAAAAGATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAATTAAGAT--
* *
21240 AAAAAGATAGTAATCAGTAAATTAACTTAATCAAAGTTGAA
64 AAAAA-ATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* *
21281 TAACTTAACTAAGATAAAAATATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAAT
1 TAA---GA-T--G--AAAAAGATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAAT
* *
21346 CAAG-TAAAAAAAGGTAATC
58 TAAGATAAAAAATGGTAATC
21365 GATAATTGGC
Statistics
Matches: 253, Mismatches: 21, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
99 4 0.02
101 46 0.18
102 2 0.01
103 13 0.05
104 80 0.32
105 3 0.01
106 1 0.00
107 41 0.16
108 1 0.00
110 8 0.03
111 5 0.02
113 5 0.02
114 44 0.17
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (103 bp):
TAAGATGAAAAAGATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAGTAAGTTAATTAAGATAA
AAAATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
Found at i:21190 original size:46 final size:46
Alignment explanation
Indices: 21131--21226 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 46
21121 GTAAGTTAAT
*
21131 TAAGATGAAAAATGGTAATCAGTAAATTAGCTTAATCAAAGTTGAG
1 TAAGATGAAAAATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
* *
21177 TAAGATGAAAAATGGTAATCGGTAAATTAATTTAATCAAAGTTGAG
1 TAAGATGAAAAATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
21223 TAAG
1 TAAG
21227 TTAATAAAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (46 bp):
TAAGATGAAAAATGGTAATCAGTAAATTAACTTAATCAAAGTTGAG
Found at i:22609 original size:32 final size:32
Alignment explanation
Indices: 22556--22651 Score: 151
Period size: 31 Copynumber: 3.1 Consensus size: 32
22546 AAGGGACTAA
22556 TTTGTCCCAAAA-AAAAACATAAGGGATTTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTTT
*
22587 TTTGTCCCAAAAGAAAAACATAAGGGA-TATT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTTT
* *
22618 TTTGTTCCAAAAGAAAAACATAATGGATTTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTTT
22650 TT
1 TT
22652 AGTATTTAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
31 40 0.68
32 19 0.32
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (32 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTTT
Done.