Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020814.1 Corchorus olitorius cultivar O-4 contig20847, 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: 18050
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:272 original size:62 final size:62
Alignment explanation
Indices: 175--455 Score: 528
Period size: 62 Copynumber: 4.5 Consensus size: 62
165 TGAAGACACG
*
175 ACAGGCACGAAGGTGCACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
237 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
299 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
361 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCA-GAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
422 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAG
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAG
456 ACAGACACGA
Statistics
Matches: 217, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
61 46 0.21
62 171 0.79
ACGTcount: A:0.36, C:0.22, G:0.39, T:0.03
Consensus pattern (62 bp):
ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
Found at i:470 original size:34 final size:34
Alignment explanation
Indices: 427--517 Score: 173
Period size: 34 Copynumber: 2.7 Consensus size: 34
417 GGCCAGCAGG
427 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
461 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
*
495 CACGAAGGTAAACGAGAAGACAG
1 CACGAAGGTACACGAGAAGACAG
518 TGGTGCTCCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.47, C:0.18, G:0.32, T:0.03
Consensus pattern (34 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
Found at i:1396 original size:44 final size:45
Alignment explanation
Indices: 1346--1453 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
1336 GAAAACGTGC
* *
1346 AGGAGATCAAGGAAAG-TTAGAATCCATGACTGCCAAATGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
* * ** *
1390 AGGAGATCAAAGAGAGCTTTGGCCCCATGATTGCCAAATGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
* *
1435 AGGAAATCAAAGAGAGCTT
1 AGGAGATCAAAGAAAGCTT
1454 TGGCTCCATG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 14 0.25
45 41 0.75
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (45 bp):
AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
Found at i:1425 original size:45 final size:45
Alignment explanation
Indices: 1369--1469 Score: 175
Period size: 45 Copynumber: 2.2 Consensus size: 45
1359 AAGTTAGAAT
* *
1369 CCATGACTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
1 CCATGATTGCCAAATGCTTTAAGGAAATCAAAGAGAGCTTTGGCC
*
1414 CCATGATTGCCAAATGCTTTAAGGAAATCAAAGAGAGCTTTGGCT
1 CCATGATTGCCAAATGCTTTAAGGAAATCAAAGAGAGCTTTGGCC
1459 CCATGATTGCC
1 CCATGATTGCC
1470 GAGTGCACAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (45 bp):
CCATGATTGCCAAATGCTTTAAGGAAATCAAAGAGAGCTTTGGCC
Found at i:9362 original size:2 final size:2
Alignment explanation
Indices: 9355--9391 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9345 TTGGGGGAGG
9355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9392 TGAAATATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11521 original size:19 final size:19
Alignment explanation
Indices: 11475--11533 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
11465 CGTTGCTCTA
*
11475 ATAATCTCATTTGTACAGT
1 ATAATCTCATCTGTACAGT
*
11494 ACCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAGT
11515 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
11534 TGCTAAACAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:13953 original size:16 final size:16
Alignment explanation
Indices: 13923--13956 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
13913 AAGCTACTCG
13923 ATACAAATATATATAT
1 ATACAAATATATATAT
13939 ATACATAATAT-TATAT
1 ATACA-AATATATATAT
13955 AT
1 AT
13957 TTAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
ATACAAATATATATAT
Found at i:15701 original size:7 final size:7
Alignment explanation
Indices: 15689--15721 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
15679 GACAATCATA
*
15689 TATATAG
1 TATATAC
15696 TATATAC
1 TATATAC
15703 TATAT-C
1 TATATAC
15709 TATATAC
1 TATATAC
15716 TATATA
1 TATATA
15722 AGTCTAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (7 bp):
TATATAC
Found at i:15714 original size:13 final size:13
Alignment explanation
Indices: 15696--15720 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15686 ATATATATAG
15696 TATATACTATATC
1 TATATACTATATC
15709 TATATACTATAT
1 TATATACTATAT
15721 AAGTCTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATACTATATC
Found at i:15999 original size:21 final size:21
Alignment explanation
Indices: 15975--16041 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
15965 GTAACATAAA
15975 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* ** *
15996 TAATTAAATGTAATA-ATAC-T
1 TAA-TAACTAAAATACTTACAT
*
16016 ATAATAACTAAAACACTTACAT
1 -TAATAACTAAAATACTTACAT
16038 TAAT
1 TAAT
16042 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Found at i:16420 original size:202 final size:204
Alignment explanation
Indices: 16156--16568 Score: 674
Period size: 202 Copynumber: 2.0 Consensus size: 204
16146 TTCCTTATTA
* *
16156 ATAAATAAATCGGATCTTAATATTTTTAATTTATAATTTTGAAATTTTGTTTGACATTGATCTAA
1 ATAAATAAATCGGATCTTAATA-TTCT-ATTTATAATTTTGAAAATTTGTTTGACATTGATCTAA
*
16221 TTTAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATGTATATAA
64 TTTAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAG-T-TATATATATAA
* *
16286 TAGTAATGTGTTGTATCTTATT-CACTACAACTTTGTTAGTAATCTTAGATTTAAA-AATTAATA
127 TAATAATGTGTTGTATCTTATTACACTACAACTTTGTTAGTAATCTTAGACTTAAACAATTAATA
*
16349 ACATTCACCATTG
192 ACATTCACCATTC
16362 ATAAATAAATCGGATCTTTAATA-TCT-TTTATAATTTT-AAAATTTGTTTGACATTGATCTAAT
1 ATAAATAAATCGGATC-TTAATATTCTATTTATAATTTTGAAAATTTGTTTGACATTGATCTAAT
* *
16424 TTAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGTTATAGTTATATATATAATAA
65 TTAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTATATATATAATAA
16489 TAATGTGTTGTATCTTATTACACTACAACTTTGTTAGTAATCTTAGACTTAAACAATTAATAACA
130 TAATGTGTTGTATCTTATTACACTACAACTTTGTTAGTAATCTTAGACTTAAACAATTAATAACA
16554 TTCACCATTC
195 TTCACCATTC
16564 ATAAA
1 ATAAA
16569 GTTATTAAGC
Statistics
Matches: 196, Mismatches: 8, Indels: 10
0.92 0.04 0.05
Matches are distributed among these distances:
200 31 0.16
201 33 0.17
202 97 0.49
203 11 0.06
205 2 0.01
206 16 0.08
207 6 0.03
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (204 bp):
ATAAATAAATCGGATCTTAATATTCTATTTATAATTTTGAAAATTTGTTTGACATTGATCTAATT
TAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTATATATATAATAAT
AATGTGTTGTATCTTATTACACTACAACTTTGTTAGTAATCTTAGACTTAAACAATTAATAACAT
TCACCATTC
Done.