Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015127.1 Corchorus olitorius cultivar O-4 contig15160, 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: 19465
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:464 original size:18 final size:20
Alignment explanation
Indices: 437--476 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
427 TTGAGTAGAC
*
437 TTTAACTTTC-TGTTGGGCT
1 TTTAACTTTCTTATTGGGCT
456 TTTAA-TTTCTTATTGGGCT
1 TTTAACTTTCTTATTGGGCT
475 TT
1 TT
477 GCTAAGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.57
Consensus pattern (20 bp):
TTTAACTTTCTTATTGGGCT
Found at i:1413 original size:35 final size:35
Alignment explanation
Indices: 1374--1451 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 35
1364 GAGAATATCA
* * *
1374 TTAAGTTTTTTTTATTGGAAAAGTTCCCACCAGTT
1 TTAAGTTTTTGTAATCGGAAAAGTTCCCACCAGTT
* * *
1409 TTAAG-TTTTGTAATCGGGAAAGTTCTCACCGGTT
1 TTAAGTTTTTGTAATCGGAAAAGTTCCCACCAGTT
1443 TTAAGTTTT
1 TTAAGTTTT
1452 CAAATTGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 28 0.78
35 8 0.22
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (35 bp):
TTAAGTTTTTGTAATCGGAAAAGTTCCCACCAGTT
Found at i:1466 original size:34 final size:34
Alignment explanation
Indices: 1393--1470 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
1383 TTTTATTGGA
**
1393 AAAGTTCCCACCAGTTTTAAGTTTTGTAATCGGG
1 AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG
* * *
1427 AAAGTTCTCACCGGTTTTAAGTTTTCAAATTGGG
1 AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG
*
1461 CAAGTTCCCA
1 AAAGTTCCCA
1471 TTCAATTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (34 bp):
AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG
Found at i:3286 original size:27 final size:27
Alignment explanation
Indices: 3221--3297 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
3211 ATTAGGGCCA
* * *
3221 TCCAGGGGTACTTTGGTCATTTTGCACG
1 TCCAGGGGCATTTTGGTCA-TTTACACG
* *
3249 TCCAAGAGCATTTTGGTCATTTACACG
1 TCCAGGGGCATTTTGGTCATTTACACG
*
3276 TCCAGGGGCATTTTAGTCATTT
1 TCCAGGGGCATTTTGGTCATTT
3298 CAAGTACACT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 26 0.63
28 15 0.37
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (27 bp):
TCCAGGGGCATTTTGGTCATTTACACG
Found at i:8542 original size:187 final size:187
Alignment explanation
Indices: 8178--8606 Score: 689
Period size: 187 Copynumber: 2.3 Consensus size: 187
8168 ATTACCATTA
* * * ** *
8178 TATCCCCAAAGTAATATACATTAAACCCAAATTATCACATGCACCATCCCCAAATTCTTTAGAGA
1 TATCCCCAAAGTAATATACTTTATACCCAAATTGTTTC-T-CATCATCCCCAAATTCTTTAGAGA
* * *
8243 TGGACATTTTTTCTCATATACCCAAAATTGACTTTAAAAGTGTTTTAATCCATATATTAATTGAA
64 TGGACATTTTTTCTCATATACCCAAAATTAACTTTAAAACTGTTTTAATCCATATAATAATTGAA
* * *
8308 TAAACCCCGTCTATATGATTTTAGTGACATCCAATAATTAAACAAAATGCAAAATTCAG
129 TAAACCCCATCTATATGATTTTAGTGACATACAATAAATAAACAAAATGCAAAATTCAG
*
8367 TATCCCCAAAGTAATATACTTTATA-CGAAATTGTTTCTCATCATCCCCAAATTCTTTAGAGATG
1 TATCCCCAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCCAAATTCTTTAGAGATG
8431 GACATTTTTTCTCATATACCCAAAATTAACTTTAAAATCTGTTTTAATCCATATAATAATTGAAT
66 GACATTTTTTCTCATATACCCAAAATTAACTTTAAAA-CTGTTTTAATCCATATAATAATTGAAT
* *
8496 AAACCCCATCTATATGATTTTAGTGCCATATAATAAATAAACAAAATGCAAAATTCAG
130 AAACCCCATCTATATGATTTTAGTGACATACAATAAATAAACAAAATGCAAAATTCAG
8554 TATCCCCAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCCAAAT
1 TATCCCCAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCCAAAT
8607 AATCATATGC
Statistics
Matches: 222, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
186 61 0.27
187 104 0.47
188 34 0.15
189 23 0.10
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.34
Consensus pattern (187 bp):
TATCCCCAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCCAAATTCTTTAGAGATG
GACATTTTTTCTCATATACCCAAAATTAACTTTAAAACTGTTTTAATCCATATAATAATTGAATA
AACCCCATCTATATGATTTTAGTGACATACAATAAATAAACAAAATGCAAAATTCAG
Found at i:8861 original size:212 final size:211
Alignment explanation
Indices: 8408--9081 Score: 1177
Period size: 211 Copynumber: 3.2 Consensus size: 211
8398 TGTTTCTCAT
* **
8408 CATCCCCAAATTCTTTAGAGATGGACATTTTTTCTCATATACCCAAAATTAACTTTAAAATCTGT
1 CATCCCCAAATTCTTTAGAGATGGACATTTTTTCTCATATACCCAAAATTGACTTTAAAAGGTGT
* * *
8473 TTTAATCCATATAATAATTGAATAAACCCCATCTATATGATTTTAGTGCCATATAATAAATAAAC
66 TTTAATCCATATATTAATTGAATAAACCCCATCTATATGATTTTAGTGCCATCTAATAATTAAAC
8538 AAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCC
131 AAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCC
*
8603 AAATAATCATATGCAT
196 AAATAATCATATGCAC
*
8619 CATCCCCAAATTCTTTAGAGATGGACATTTTTTCTCATATACCCAAAATTGACCTTAAAAGGTGT
1 CATCCCCAAATTCTTTAGAGATGGACATTTTTTCTCATATACCCAAAATTGACTTTAAAAGGTGT
8684 TTTAATCCATATATTAATTGAATAAACCCCATCTATATGATTTTAGTGCCATCTAATTAATTAAA
66 TTTAATCCATATATTAATTGAATAAACCCCATCTATATGATTTTAGTGCCATCTAA-TAATTAAA
* * *
8749 GAAAATGCAAAATTCACTATCCCCAAAGTAATATACTTTATACCCAAATTATTTCTCATCATCCC
130 CAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCC
8814 CAAATAATCATATGCAC
195 CAAATAATCATATGCAC
**
8831 CATCCCCAAATTCTTTAGAGACAGACATTTTTTCTCATATACCCAAAATTGACTTTAAAAGGTGT
1 CATCCCCAAATTCTTTAGAGATGGACATTTTTTCTCATATACCCAAAATTGACTTTAAAAGGTGT
* * *
8896 TTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATCTACTAATTAAAC
66 TTTAATCCATATATTAATTGAATAAACCCCATCTATATGATTTTAGTGCCATCTAATAATTAAAC
*
8961 AAAATGCAAAATTCAGTATCCACAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCC
131 AAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCC
9026 AAATAATCATATGCAC
196 AAATAATCATATGCAC
*
9042 CATCCCCAAATTCTTTAGAGATGAACATTTTTTCTCATAT
1 CATCCCCAAATTCTTTAGAGATGGACATTTTTTCTCATAT
9082 TGTGGTTTAT
Statistics
Matches: 438, Mismatches: 24, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
211 238 0.54
212 200 0.46
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.34
Consensus pattern (211 bp):
CATCCCCAAATTCTTTAGAGATGGACATTTTTTCTCATATACCCAAAATTGACTTTAAAAGGTGT
TTTAATCCATATATTAATTGAATAAACCCCATCTATATGATTTTAGTGCCATCTAATAATTAAAC
AAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCC
AAATAATCATATGCAC
Found at i:9375 original size:29 final size:31
Alignment explanation
Indices: 9339--9408 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
9329 AAATTGTAAT
* *
9339 TAGAGGGACGAAATTGA-CAGTTTTT-ATAG
1 TAGAGGGACCAAATTGATCAGTTTTTGAAAG
**
9368 TAGAGGGACCAAATTGATCCTTTTTTGAAAG
1 TAGAGGGACCAAATTGATCAGTTTTTGAAAG
9399 TAGAGGGACC
1 TAGAGGGACC
9409 TGTTCGGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.46
30 6 0.17
31 13 0.37
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (31 bp):
TAGAGGGACCAAATTGATCAGTTTTTGAAAG
Found at i:15903 original size:18 final size:18
Alignment explanation
Indices: 15880--15915 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
15870 GGTTCAAGAA
15880 GTGTCATTGATTTTTATG
1 GTGTCATTGATTTTTATG
15898 GTGTCATTGATTTTTATG
1 GTGTCATTGATTTTTATG
15916 CACATGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.22, T:0.56
Consensus pattern (18 bp):
GTGTCATTGATTTTTATG
Done.