Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024106.1 Corchorus olitorius cultivar O-4 contig24139, 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: 4191
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Found at i:401 original size:8 final size:8
Alignment explanation
Indices: 384--432 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
374 ACTCGAGGCC
*
384 TTGAATAA
1 TTGAAGAA
392 TTGAAGAA
1 TTGAAGAA
*
400 TTGAAGCA
1 TTGAAGAA
* *
408 TCGAATAA
1 TTGAAGAA
416 CTTGAAGAA
1 -TTGAAGAA
425 TTGAAGAA
1 TTGAAGAA
433 AGACCACCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
8 27 0.82
9 6 0.18
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (8 bp):
TTGAAGAA
Found at i:581 original size:35 final size:35
Alignment explanation
Indices: 426--1475 Score: 872
Period size: 36 Copynumber: 29.5 Consensus size: 35
416 CTTGAAGAAT
** * **
426 TGAAGAAAGACCACCCTGGGTCGTTCTGGAATAATT
1 TGAAGAAAGACCACCCTGGGTC-AACTGAAATAAAC
* * *
462 TGAAGCAAGACCACCTTAGGTC-ACTTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
* * * ** * * **
497 TGAAAAAATGACCACCCTCGATCCTTCCGACACCAAC
1 TGAAGAAA-GACCACCCTGGGT-CAACTGAAATAAAC
* * * *
534 TAAAGAAAGACCACCCAGAGTCAATTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *** ** * *
569 TGAAGAACGACCACCCTTAATCATTTCGAACTGAAC
1 TGAAGAAAGACCACCCTGGGTCAACT-GAAATAAAC
* * * ** * * * *
605 TGAGGGACA-ACCACCCTCGACCATTCCGACATGAAC
1 TGA-AGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
* *
641 TGAAGAAAGACCTCCCTGGGTC-ACTTGGAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
* *
676 TGAAGAAAAGACCACCTTGGGTCGAACTGACATAAAC
1 TGAAG-AAAGACCACCCTGGGTC-AACTGAAATAAAC
* *
713 TGAAGAAAAGACCACCATGGGTCGACTGAAATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
749 TGAAGAACGACCGCCCTAGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * * **
784 TGAAGAACGACCACCCTTGATCATTCTGACATAAGT
1 TGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
* * * ** *
820 TGAAGAAAGACCGCCCTAGATCAATCCAAAATAAGC
1 TGAAGAAAGACCACCCTGGGTCAA-CTGAAATAAAC
*
856 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
*
891 TGAAGAAAAGACCACCCTGGGTCAACTAAAATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* *
927 TGAAAAAAGACCACCCTGGGTCAACTAAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
962 TGAAGAAAAGACCACCCTGAGTCAACTGAAATAAGC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* * * *
998 TGAGGAAAGACCACCCTGGGTCAACTAAAATGAAT
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * **
1033 TGAAGAAGGATCGCCCTGAATCAACTTGAAA-ACAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATA-AAC
* * * *
1069 TGAAGAAAGACCTCCTTGGGTCGATTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
*
1104 TGAAGAAAAGACCACCCTGGGTCAACTGAAATAAGC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* * ** *
1140 TGAAGAAAGACCGCCCTGGATCAATCCAAAATAAGC
1 TGAAGAAAGACCACCCTGGGTCAA-CTGAAATAAAC
*
1176 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
1211 TGAAGAAAAGACCA-CCTGGGTCAACTGAAATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* *
1246 TGAAGACAGACCACCCTGGGTCAACTAAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
*
1281 TGAAGAAAAGACCACCCTGGGTCAACTGAAATAAGC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* * * *
1317 TGAAGAAAGACCACCCTGGGTCGACTAAAATGAAT
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * *
1352 TGAAGAAGGATCGCCCTGGATCAACTTGAAA-ACAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATA-AAC
* * * *
1388 TGAAGAAAGACCGCCCTGGGTCAATTGAAGTAGAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * *
1423 TGAAGAATGATCGCCCTAGATCAACTTGAAA-ACAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATA-AAC
1459 TGAAGAAAGACCACCCT
1 TGAAGAAAGACCACCCT
1476 AGGTTGATTG
Statistics
Matches: 816, Mismatches: 169, Indels: 58
0.78 0.16 0.06
Matches are distributed among these distances:
34 9 0.01
35 356 0.44
36 402 0.49
37 46 0.06
38 3 0.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (35 bp):
TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
Found at i:581 original size:107 final size:107
Alignment explanation
Indices: 468--1475 Score: 535
Period size: 107 Copynumber: 9.4 Consensus size: 107
458 AATTTGAAGC
* **
468 AAGACCACCTTAGGTCACTTGAAATAAACTGAAAAAATGACCACCCTCGATCCTTCCGACACCAA
1 AAGACCACCTTAGGTCACTTGAAATAAACTGAAAAAA-GACCACCCTCGATCCTTCCGAAATAAA
* * * *
533 CTAAAGAAAGACCACCCAGAGTCAATTGAAATAAACTGAAG-A
65 CTGAAGAAAGACCGCCCAGGGTCAACTGAAATAAACTGAAGAA
* * * * * ** * *
575 ACGACCACCCTTA-ATCATTTCGAACTGAACTGAGGGACA-ACCACCCTCGA-CCATTCCGACAT
1 AAGACCA-CCTTAGGTCACTT-GAAATAAACTGA-AAAAAGACCACCCTCGATCC-TTCCGAAAT
* * * *
637 GAACTGAAGAAAGACCTCCCTGGGTC-ACTTGGAATAAACTGAAGAA
62 AAACTGAAGAAAGACCGCCCAGGGTCAAC-TGAAATAAACTGAAGAA
* * * * * ** *
683 AAGACCACCTTGGGTCGAAC-TGACATAAACTGAAGAAAAGACCACCATGGGT-CGACTGAAATA
1 AAGACCACCTTAGGTC--ACTTGAAATAAACTGAA-AAAAGACCACCCTCGATCCTTCCGAAATA
*
746 AACTGAAGAACGACCGCCCTA-GGTCAACTGAAATAAACTGAAG-A
63 AACTGAAGAAAGACCGCCC-AGGGTCAACTGAAATAAACTGAAGAA
* * * * ** * * * ** *
790 ACGACCACCCTT-GATCATTCTGACATAAGTTGAAGAAAGACCGCCCTAGATCAATCCAAAATAA
1 AAGACCA-CCTTAGGTCACT-TGAAATAAACTGAAAAAAGACCACCCTCGATCCTTCCGAAATAA
* *
854 GCTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAA
64 ACTGAAGAAAGACCGCCCAGGGTCAACTGAAATAAACTGAAGAA
* * * * * ** **
898 AAGACCACCCTGGGTCAAC-TAAAATAAACTGAAAAAAGACCACCCTGGGT-CAACTAAAATAAA
1 AAGACCACCTTAGGTC-ACTTGAAATAAACTGAAAAAAGACCACCCTCGATCCTTCCGAAATAAA
* * * * *
961 CTGAAGAAAAGACCACCCTGAGTCAACTGAAATAAGCTG-AGGA
65 CTGAAG-AAAGACCGCCCAGGGTCAACTGAAATAAACTGAAGAA
* * * * * * * * *
1004 AAGACCACCCTGGGTCAAC-TAAAATGAATTGAAGAAGGATCGCCCT-GAATCAACTT--GAAA-
1 AAGACCACCTTAGGTC-ACTTGAAATAAACTGAAAAAAGACCACCCTCG-ATC--CTTCCGAAAT
* ** * *
1064 ACAACTGAAGAAAGACCTCCTTGGGTCGATTGAAATAAACTGAAGAA
62 A-AACTGAAGAAAGACCGCCCAGGGTCAACTGAAATAAACTGAAGAA
* * * * * * ** * *
1111 AAGACCACCCTGGGTCAAC-TGAAATAAGCTGAAGAAAGACCGCCCTGGATCAATCCAAAATAAG
1 AAGACCACCTTAGGTC-ACTTGAAATAAACTGAAAAAAGACCACCCTCGATCCTTCCGAAATAAA
*
1175 CTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAA
65 CTGAAGAAAGACCGCCCAGGGTCAACTGAAATAAACTGAAGAA
* * * * * ** **
1218 AAGACCACC-TGGGTCAAC-TGAAATAAACTGAAGACAGACCACCCTGGGT-CAACTAAAATAAA
1 AAGACCACCTTAGGTC-ACTTGAAATAAACTGAAAAAAGACCACCCTCGATCCTTCCGAAATAAA
* * *
1280 CTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAGCTGAAG-A
65 CTGAAG-AAAGACCGCCCAGGGTCAACTGAAATAAACTGAAGAA
* * * * * * * * * *
1323 AAGACCACCCTGGGTCGAC-TAAAATGAATTGAAGAAGGATCGCCCTGGATCAACTT--GAAA-A
1 AAGACCACCTTAGGTC-ACTTGAAATAAACTGAAAAAAGACCACCCTCGATC--CTTCCGAAATA
* * * *
1384 CAACTGAAGAAAGACCGCCCTGGGTCAATTGAAGTAGACTGAAG-A
63 -AACTGAAGAAAGACCGCCCAGGGTCAACTGAAATAAACTGAAGAA
* * * * * *
1429 ATGATCGCCCTAGATCAACTTGAAA-ACAACTGAAGAAAGACCACCCT
1 AAGACCACCTTAGGTC-ACTTGAAATA-AACTGAAAAAAGACCACCCT
1476 AGGTTGATTG
Statistics
Matches: 714, Mismatches: 146, Indels: 82
0.76 0.15 0.09
Matches are distributed among these distances:
105 28 0.04
106 246 0.34
107 331 0.46
108 91 0.13
109 17 0.02
110 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (107 bp):
AAGACCACCTTAGGTCACTTGAAATAAACTGAAAAAAGACCACCCTCGATCCTTCCGAAATAAAC
TGAAGAAAGACCGCCCAGGGTCAACTGAAATAAACTGAAGAA
Found at i:824 original size:71 final size:70
Alignment explanation
Indices: 426--1475 Score: 872
Period size: 71 Copynumber: 14.7 Consensus size: 70
416 CTTGAAGAAT
** * ** * * *
426 TGAAGAAAGACCACCCTGGGTCGTTCTGGAATAATTTGAAGCAAGACCACCTTAGGTC-ACTTGA
1 TGAAGAAAGACCACCCTGGGTC-AACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAAC-TGA
490 AATAAAC
64 AATAAAC
* * * ** * * ** * * * *
497 TGAAAAAATGACCACCCTCGATCCTTCCGACACCAACTAAAGAAAGACCACCCAGAGTCAATTGA
1 TGAAGAAA-GACCACCCTGGGT-CAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGA
562 AATAAAC
64 AATAAAC
* *** ** * * * * * ** * *
569 TGAAGAACGACCACCCTTAATCATTTCGAACTGAACTGAGGGACA-ACCACCCTCGACCATTCCG
1 TGAAGAAAGACCACCCTGGGTCAACT-GAAATAAACTGA-AGAAAGACCACCCTGGGTCA-ACTG
* *
633 ACATGAAC
63 AAATAAAC
* * *
641 TGAAGAAAGACCTCCCTGGGTC-ACTTGGAATAAACTGAAGAAAAGACCACCTTGGGTCGAACTG
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAACTGAAG-AAAGACCACCCTGGGTC-AACTG
*
705 ACATAAAC
63 AAATAAAC
* * * * *
713 TGAAGAAAAGACCACCATGGGTCGACTGAAATAAACTGAAGAACGACCGCCCTAGGTCAACTGAA
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAA
778 ATAAAC
65 ATAAAC
* * * * * ** * * * **
784 TGAAGAACGACCACCCTTGATCATTCTGACATAAGTTGAAGAAAGACCGCCCTAGATCAATCCAA
1 TGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAA-CTGA
*
849 AATAAGC
64 AATAAAC
* *
856 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTAAA
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGGTCAACTGAA
921 ATAAAC
65 ATAAAC
* * *
927 TGAAAAAAGACCACCCTGGGTCAACTAAAATAAACTGAAGAAAAGACCACCCTGAGTCAACTGAA
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGGTCAACTGAA
*
992 ATAAGC
65 ATAAAC
* * * * * * * **
998 TGAGGAAAGACCACCCTGGGTCAACTAAAATGAATTGAAGAAGGATCGCCCTGAATCAACTTGAA
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAAC-TGAA
1063 A-ACAAC
65 ATA-AAC
* * * *
1069 TGAAGAAAGACCTCCTTGGGTCGATTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTGAA
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAG-AAAGACCACCCTGGGTCAACTGAA
*
1134 ATAAGC
65 ATAAAC
* * ** * *
1140 TGAAGAAAGACCGCCCTGGATCAATCCAAAATAAGCTGAAGAAAGACCGCCCTGGGTCAACTGAA
1 TGAAGAAAGACCACCCTGGGTCAA-CTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAA
1205 ATAAAC
65 ATAAAC
* *
1211 TGAAGAAAAGACCA-CCTGGGTCAACTGAAATAAACTGAAGACAGACCACCCTGGGTCAACTAAA
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAA
1275 ATAAAC
65 ATAAAC
* * *
1281 TGAAGAAAAGACCACCCTGGGTCAACTGAAATAAGCTGAAGAAAGACCACCCTGGGTCGACTAAA
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAA
* *
1346 ATGAAT
65 ATAAAC
* * * * * *
1352 TGAAGAAGGATCGCCCTGGATCAACTTGAAA-ACAACTGAAGAAAGACCGCCCTGGGTCAATTGA
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATA-AACTGAAGAAAGACCACCCTGGGTCAACTGA
* *
1416 AGTAGAC
64 AATAAAC
* * * * *
1423 TGAAGAATGATCGCCCTAGATCAACTTGAAA-ACAACTGAAGAAAGACCACCCT
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATA-AACTGAAGAAAGACCACCCT
1476 AGGTTGATTG
Statistics
Matches: 792, Mismatches: 163, Indels: 48
0.79 0.16 0.05
Matches are distributed among these distances:
70 104 0.13
71 463 0.58
72 191 0.24
73 32 0.04
74 2 0.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (70 bp):
TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAA
TAAAC
Found at i:3227 original size:14 final size:14
Alignment explanation
Indices: 3206--3238 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3196 TGAAAACAAA
3206 TTTT-AGAAACCAT
1 TTTTGAGAAACCAT
*
3219 TTTTGAGAAATCAT
1 TTTTGAGAAACCAT
3233 TTTTGA
1 TTTTGA
3239 AAAATCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (14 bp):
TTTTGAGAAACCAT
Done.