Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024222.1 Corchorus olitorius cultivar O-4 contig24255, 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: 6521
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:563 original size:30 final size:30
Alignment explanation
Indices: 528--1075 Score: 741
Period size: 30 Copynumber: 18.2 Consensus size: 30
518 ACTGATGAAA
* *
528 CAATGATCCTCAACCAGGATTAAAACAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
558 TAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
588 CAAAT-ATCCTCAACCAGGATAAAAATAAAG
1 C-AATGATCCTCAAACAGGATTAAAATAAAG
*
618 CAATGATCCTCAAACAGGATTAAAATAGAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
648 CAAAT-ATCCTCAACCAGGATTAAAATAAAG
1 C-AATGATCCTCAAACAGGATTAAAATAAAG
*
678 CAATGATCCTCAAACAGGATTAAAATAGAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
708 TAAAT-ATCCTCAACCAGGATTAAAATAAAG
1 -CAATGATCCTCAAACAGGATTAAAATAAAG
*
738 CAATGATCCTCAAACAGGATTAAAACAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
768 CAATGATCCTCAAACAGGATTAAGATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
798 CAATGATCCTCAAACAGGATTAAGATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
828 CAAAT-ATCCTCAACCAGGATTAAAATAAAG
1 C-AATGATCCTCAAACAGGATTAAAATAAAG
858 CAATGATCCTCAAACAGGATTAACAATAAAG
1 CAATGATCCTCAAACAGGATTAA-AATAAAG
*
889 CAATGATCCTCAAACAGGATTAAAACAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * *
919 CAATGATCCTCAAATAGGATTAAGATGAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
949 CAATGATCCTCAAACAGGATTAAAAATGAAG
1 CAATGATCCTCAAACAGGATT-AAAATAAAG
* *
980 CAAAT-ATCCTCAACCAGGATAAAAATAAAG
1 C-AATGATCCTCAAACAGGATTAAAATAAAG
1010 CAATGATCCTCAAACAGGA-TAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* ** *
1039 CAATGATCC-GAAACCAGGATCGAAATGAAG
1 CAATGATCCTCAAA-CAGGATTAAAATAAAG
1069 CAATGAT
1 CAATGAT
1076 GCCATGATCC
Statistics
Matches: 466, Mismatches: 38, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
28 3 0.01
29 38 0.08
30 357 0.77
31 65 0.14
32 3 0.01
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.19
Consensus pattern (30 bp):
CAATGATCCTCAAACAGGATTAAAATAAAG
Found at i:1570 original size:158 final size:157
Alignment explanation
Indices: 1208--1688 Score: 703
Period size: 158 Copynumber: 3.0 Consensus size: 157
1198 GAAAAACTTG
* * *
1208 ATGAAATCAAATGGTACCCAGAGGTTTTATCAATTGCCTGGAGGACTTATCAGAATTAATACCCG
1 ATGAAATGAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCG
* * *
1273 AAGGTTTATGAATTTGTGCCCGGAGGACTTACCAATGCGAACTTTGAAATGAGACCTTGAACAAG
66 GAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCAAACTTTGAAATGAGACCTTGAACAAG
1338 GATTTTAAACTTAAACATGAATTTTGATGAAAACTTA
131 GATTTTAAACTTAAACATGAA--TT--T------TTA
* * *
1375 ATGAAATGAAATGGTACCCGGAGGTTTTACCGATTGCCCAGAGGACTTATCAGAATTAATACCCG
1 ATGAAATGAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCG
* * *
1440 GAGGTTTCTGAACTTGTGCCCGGAGGTCTCTACCAATGCAAACTCTG-AATAGAGACCTTGAACA
66 GAGGTTTCTGAATTTGTGCCCGGAGGACT-TACCAATGCAAACTTTGAAAT-GAGACCTTGAACA
*
1504 AGGATTTTAAACTTAAACATGAACTTTTA
129 AGGATTTTAAACTTAAACATGAATTTTTA
*
1533 ATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCG
1 ATGAAATGAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCG
*
1598 GAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATACAAACTTTGAAATGAGACCTTGAACAAG
66 GAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCAAACTTTGAAATGAGACCTTGAACAAG
*
1663 GATCTTAAACTTAAACATGAATTTTT
131 GATTTTAAACTTAAACATGAATTTTT
1689 GGTGAAAAAC
Statistics
Matches: 288, Mismatches: 23, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
157 54 0.19
158 94 0.33
164 1 0.00
166 1 0.00
167 87 0.30
168 51 0.18
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (157 bp):
ATGAAATGAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCG
GAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCAAACTTTGAAATGAGACCTTGAACAAG
GATTTTAAACTTAAACATGAATTTTTA
Found at i:3176 original size:22 final size:23
Alignment explanation
Indices: 3151--3205 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
3141 CTAGAGCTCA
3151 ATTCTTTCTTTTTTTC-TTTTTC
1 ATTCTTTCTTTTTTTCATTTTTC
*
3173 ATTC-TTCATTTTTTCATTTTTC
1 ATTCTTTCTTTTTTTCATTTTTC
3195 ATT-TTT-TTTTT
1 ATTCTTTCTTTTT
3206 GCACTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (23 bp):
ATTCTTTCTTTTTTTCATTTTTC
Found at i:3187 original size:15 final size:15
Alignment explanation
Indices: 3167--3201 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3157 TCTTTTTTTC
3167 TTTTTCATTCTTCAT
1 TTTTTCATTCTTCAT
*
3182 TTTTTCATTTTTCAT
1 TTTTTCATTCTTCAT
3197 TTTTT
1 TTTTT
3202 TTTTGCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCATTCTTCAT
Found at i:3201 original size:8 final size:7
Alignment explanation
Indices: 3161--3200 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
3151 ATTCTTTCTT
3161 TTTTTC-
1 TTTTTCA
3167 TTTTTCA
1 TTTTTCA
*
3174 TTCTTCA
1 TTTTTCA
3181 TTTTTTCA
1 -TTTTTCA
3189 TTTTTCA
1 TTTTTCA
3196 TTTTT
1 TTTTT
3201 TTTTTGCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 6 0.20
7 18 0.60
8 6 0.20
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:3546 original size:13 final size:13
Alignment explanation
Indices: 3530--3570 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
3520 TTTTCTTTGA
3530 TGATTTTTTTGTT
1 TGATTTTTTTGTT
*
3543 TGATTTTTTGTTTT
1 TGATTTTTT-TGTT
3557 TGATTTTTTTGTT
1 TGATTTTTTTGTT
3570 T
1 T
3571 TTGATTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.07, C:0.00, G:0.15, T:0.78
Consensus pattern (13 bp):
TGATTTTTTTGTT
Found at i:3548 original size:27 final size:26
Alignment explanation
Indices: 3511--3570 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
3501 TTAATTTTGA
3511 TTTT-TTTATTTTTCT-TTGATGATTT
1 TTTTGTTTATTTTT-TGTTGATGATTT
**
3536 TTTTGTTTGATTTTTTGTTTTTGATTT
1 TTTTGTTT-ATTTTTTGTTGATGATTT
3563 TTTTGTTT
1 TTTTGTTT
3571 TTGATTGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 22 0.73
ACGTcount: A:0.08, C:0.02, G:0.12, T:0.78
Consensus pattern (26 bp):
TTTTGTTTATTTTTTGTTGATGATTT
Found at i:3550 original size:14 final size:13
Alignment explanation
Indices: 3493--3576 Score: 71
Period size: 15 Copynumber: 6.1 Consensus size: 13
3483 TCAATTCCTC
*
3493 TTTTTTTTTTAAT
1 TTTTTTTTTTGAT
3506 TTTGATTTTTTT-AT
1 TTT--TTTTTTTGAT
**
3520 TTTTCTTTGATGAT
1 TTTT-TTTTTTGAT
*
3534 TTTTTTGTTTGAT
1 TTTTTTTTTTGAT
3547 TTTTTGTTTTTGATT
1 TTTTT-TTTTTGA-T
3562 TTTTTGTTTTTGAT
1 TTTTT-TTTTTGAT
3576 T
1 T
3577 GAATTTCTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
12 1 0.02
13 18 0.31
14 19 0.32
15 21 0.36
ACGTcount: A:0.11, C:0.01, G:0.11, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTGAT
Done.