Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016243.1 Corchorus capsularis cultivar CVL-1 contig16264, 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: 27402
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:468 original size:29 final size:29
Alignment explanation
Indices: 426--482 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
416 ATGTTTATTG
*
426 ATCCAAGGCGATCTTTCTTGAGTTAATTA
1 ATCCAAGGCGATCTTTCTTCAGTTAATTA
*
455 ATCCAGGGCGATCTTTCTTCAGTTAATT
1 ATCCAAGGCGATCTTTCTTCAGTTAATT
483 TCAATTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (29 bp):
ATCCAAGGCGATCTTTCTTCAGTTAATTA
Found at i:494 original size:35 final size:35
Alignment explanation
Indices: 422--555 Score: 111
Period size: 35 Copynumber: 4.0 Consensus size: 35
412 GTTAATGTTT
* *
422 ATTGATCCAAGGCGATCTTTCTTGAGTTAA-TT--
1 ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
454 A---ATCCAGGGCGATCTTTCTTCAGTTAATTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
* * * *
486 ATTGATCCAGGGTGATATTTCTTGAGTTTATTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
* ** * *
521 GTTGA-CCTAGGATGGTCTTTCTTCAGTTTATTTCA
1 ATTGATCC-AGGGCGATCTTTCTTCAGTTAATTTCA
556 GTAAACCCAG
Statistics
Matches: 84, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
29 24 0.29
30 2 0.02
32 2 0.02
34 2 0.02
35 54 0.64
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (35 bp):
ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
Found at i:556 original size:35 final size:34
Alignment explanation
Indices: 457--591 Score: 135
Period size: 35 Copynumber: 3.9 Consensus size: 34
447 GTTAATTAAT
* * * *
457 CCAGGGCGATCTTTCTTCAGTTAATTTCAATTGA
1 CCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGA
* * *
491 TCCAGGGTGATATTTCTTGAGTTTATTTCAGTTGA
1 -CCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGA
* **
526 CCTAGGATGGTCTTTCTTCAGTTTATTTCAGTAAA
1 CC-AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGA
* *
561 CCCAGGGTGGTTTTTCTCCAGTTTATTTCAG
1 -CCAGGGTGGTCTTTCTTCAGTTTATTTCAG
592 AATGATCGAT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
34 2 0.02
35 80 0.95
36 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (34 bp):
CCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGA
Found at i:722 original size:49 final size:49
Alignment explanation
Indices: 650--745 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
640 AGTTTATCCA
* * *
650 AGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTCC
1 AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTCC
*
699 AGTTTAT-TTCAGGATGATCGATTCAGTCGACCCAGGGCGGTCTTTCT
1 AGTTTATGTT-AGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCT
746 TTAGTAGCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 2 0.05
49 40 0.95
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (49 bp):
AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTCC
Found at i:851 original size:49 final size:49
Alignment explanation
Indices: 769--869 Score: 139
Period size: 49 Copynumber: 2.1 Consensus size: 49
759 AGTTTATCCA
* * * *
769 AGTTTATGTTAGAATAATCGATTAAGTTGACCCAGGGTGGTTTTTCTTC
1 AGTTCATGTCAGAATAATCGATTAAGTCGACCCAGGGTGGTCTTTCTTC
* **
818 AGTTCATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTC
1 AGTTCATGTCAGAATAATCGATTAAGTCGACCCAGGGTGGTCTTTCTTC
867 AGT
1 AGT
870 AGTTTCCACG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.37
Consensus pattern (49 bp):
AGTTCATGTCAGAATAATCGATTAAGTCGACCCAGGGTGGTCTTTCTTC
Found at i:940 original size:119 final size:119
Alignment explanation
Indices: 560--933 Score: 640
Period size: 119 Copynumber: 3.1 Consensus size: 119
550 ATTTCAGTAA
560 ACCCAGGGTGGTTTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTT
1 ACCCAGGGTGGTTTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTT
625 CTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTG
66 CTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTG
*
679 ACCCAGGGTGGTTTTTCTCCAGTTTATTTCAGGATGATCGATTCAGTCGACCCAGGGCGGTCTTT
1 ACCCAGGGTGGTTTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTT
* *
744 CTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATAATCGATTAAGTTG
66 CTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTG
* * * * *
798 ACCCAGGGTGGTTTTTCTTCAGTTCATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTT
1 ACCCAGGGTGGTTTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTT
* * *
863 CTTCAGTAGTTTCCACGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTG
66 CTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTG
*
917 ACCCAGGGCGGTTTTTC
1 ACCCAGGGTGGTTTTTC
934 ATCAGTTGTT
Statistics
Matches: 240, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 240 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (119 bp):
ACCCAGGGTGGTTTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTT
CTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTG
Found at i:945 original size:70 final size:69
Alignment explanation
Indices: 818--956 Score: 188
Period size: 70 Copynumber: 2.0 Consensus size: 69
808 GTTTTTCTTC
* * * *
818 AGTTCATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTCATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCATCAGTAGTTTCCA-GTTG
883 ATCCA
65 ATCCA
* * * * *
888 AGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGCGGTTTTTCATCAGTTGTTTCCAGTTGA
1 AGTTCATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCATCAGTAGTTTCCAGTTGA
953 TCCA
66 TCCA
957 GGGTGGTCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
69 8 0.13
70 52 0.87
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (69 bp):
AGTTCATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCATCAGTAGTTTCCAGTTGA
TCCA
Found at i:958 original size:35 final size:33
Alignment explanation
Indices: 911--1005 Score: 93
Period size: 34 Copynumber: 2.8 Consensus size: 33
901 ATGATCGATT
* *
911 CAGTTGACCCAGGGCGGTTTTTCATCAGTTGTT-TC
1 CAGTTGATCCAGGGCGGTCTTT-ATCAG--GTTATC
* *
946 CAGTTGATCCAGGGTGGTCTTTATCAGGTTATT
1 CAGTTGATCCAGGGCGGTCTTTATCAGGTTATC
* *
979 CAGTTTGATCCAGGGTGGTCTTCATCA
1 CAG-TTGATCCAGGGCGGTCTTTATCA
1006 AAGATTCATG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
32 3 0.06
33 4 0.08
34 27 0.51
35 19 0.36
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (33 bp):
CAGTTGATCCAGGGCGGTCTTTATCAGGTTATC
Found at i:1013 original size:33 final size:34
Alignment explanation
Indices: 949--1018 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
939 TTGTTTCCAG
* *
949 TTGATCCAGGGTGGTCTTTATCAGGTTATTCA-GT
1 TTGATCCAGGGTGGTCTTCATCAAG-TATTCATGT
983 TTGATCCAGGGTGGTCTTCATCAAAG-ATTCATGT
1 TTGATCCAGGGTGGTCTTCATC-AAGTATTCATGT
1017 TT
1 TT
1019 AAATTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.16
34 25 0.78
35 2 0.06
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (34 bp):
TTGATCCAGGGTGGTCTTCATCAAGTATTCATGT
Found at i:1405 original size:57 final size:57
Alignment explanation
Indices: 1187--1407 Score: 190
Period size: 58 Copynumber: 3.7 Consensus size: 57
1177 CTGTTGGAGA
* * * *
1187 GTTTCATTTCAAATCCTGCTTAAGGTCTCTGGTCGAGAGTTTCTTGTTTCAATTCCAAAATATT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAG-----T-TTTCAA-CCCAAAATCTT
* * * * * ** * * *
1251 GTTTCATTTTAAATCATGCTTGAGATCTCTAGTCGAGAATTATCAATTCTAAGTCCT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAACCCAAAATCTT
* * *
1308 GTTTCATTTTCAAATCCTGCTCGAGGTCTCTAATTGAGAGTTTTCAACCCAAAATCTT
1 GTTTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAACCCAAAATCTT
* * *
1366 GTTTCATTTCAAATCCTGCTTGAGGTTTCTAGCCAAGAGTTT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT
1408 CTGTTTCAAT
Statistics
Matches: 125, Mismatches: 31, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
57 42 0.34
58 49 0.39
59 1 0.01
64 33 0.26
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (57 bp):
GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAACCCAAAATCTT
Found at i:5681 original size:30 final size:30
Alignment explanation
Indices: 5645--5704 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5635 AAAGGAGAGG
*
5645 ATGGAATCACAAAGTCTCATGAAGATGCCA
1 ATGGAATCACAAAGCCTCATGAAGATGCCA
* *
5675 ATGGAATCGCAAAGCCTCATGGAGATGCCA
1 ATGGAATCACAAAGCCTCATGAAGATGCCA
5705 TCAAGATGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (30 bp):
ATGGAATCACAAAGCCTCATGAAGATGCCA
Found at i:12135 original size:30 final size:30
Alignment explanation
Indices: 12099--12158 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
12089 AAAGGAGAGG
*
12099 ATGGAATCACAAAGTCTCATGAAGATGCCA
1 ATGGAATCACAAAGCCTCATGAAGATGCCA
*
12129 ATGGAATCGCAAAGCCTCATGAAGATGCCA
1 ATGGAATCACAAAGCCTCATGAAGATGCCA
12159 TTAAGATGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (30 bp):
ATGGAATCACAAAGCCTCATGAAGATGCCA
Found at i:22553 original size:24 final size:24
Alignment explanation
Indices: 22526--22669 Score: 122
Period size: 22 Copynumber: 6.2 Consensus size: 24
22516 ACTAAGGACT
22526 GTGGTCGTGAGATTCGACCACATA
1 GTGGTCGTGAGATTCGACCACATA
* * *
22550 GTGGCCGTGAGATTCG-GC-CATG
1 GTGGTCGTGAGATTCGACCACATA
* * * *
22572 GTGGTCATAAGATTCG-GC-CATG
1 GTGGTCGTGAGATTCGACCACATA
* * *
22594 GTGGTCATGAGATCCGACCACATG
1 GTGGTCGTGAGATTCGACCACATA
22618 GTGGTCGTGAGATTCGACCACA-A
1 GTGGTCGTGAGATTCGACCACATA
* *
22641 --GGTAGTGGAGATTTGACCACATA
1 GTGGTCGT-GAGATTCGACCACATA
22664 GTGGTC
1 GTGGTC
22670 ATTCAAAAAC
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.05
22 49 0.49
23 3 0.03
24 39 0.39
25 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (24 bp):
GTGGTCGTGAGATTCGACCACATA
Found at i:22905 original size:44 final size:43
Alignment explanation
Indices: 22857--22944 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 43
22847 TGGAGAATTC
*
22857 TAAAAAGCCATGTCGGGTTTTCAATTTGACCAAGGTGGCTGTGA
1 TAAAAAGCCATGTCGGGTTTTCAATTTGACCAAGGAGG-TGTGA
* * **
22901 TAAAAAGGCATGTTGTTTTTTCAATTTGACCAAGGAGGTGTGA
1 TAAAAAGCCATGTCGGGTTTTCAATTTGACCAAGGAGGTGTGA
22944 T
1 T
22945 GGCAAATCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 6 0.15
44 33 0.85
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.33
Consensus pattern (43 bp):
TAAAAAGCCATGTCGGGTTTTCAATTTGACCAAGGAGGTGTGA
Done.