Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011300.1 Corchorus capsularis cultivar CVL-1 contig11321, 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: 28389
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:9166 original size:13 final size:13
Alignment explanation
Indices: 9148--9177 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
9138 TAAGAGTAGT
9148 AAAAAAAAAT-CC
1 AAAAAAAAATACC
9160 AAAAAAAAATACC
1 AAAAAAAAATACC
9173 AAAAA
1 AAAAA
9178 TGCAAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAAAAAATACC
Found at i:10627 original size:50 final size:50
Alignment explanation
Indices: 10566--10903 Score: 391
Period size: 49 Copynumber: 6.8 Consensus size: 50
10556 AGTTTTCACT
*
10566 TGCTATGTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTTACTTTTACC
1 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTTACTTTTACC
10616 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTTACTTTTACC
1 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTTACTTTTACC
* **
10666 TGCTATTTTCCAAAAATGCCCTTCCCAGACGGAAGGCATTTGTTTTTACC
1 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTTACTTTTACC
* ** **
10716 TGCT-TTTTCCAAAAATGCTCTTCCCGGACGGAAGGTTTTTTTTTTGTTTTACC
1 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGG----CATTTACTTTTACC
* * * *
10769 TGCTATTTTCC-AAAATGCCCTTCCCAGATGGAAGGCATTTGA-TTTCATC
1 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT-ACTTTTACC
* * * * *
10818 TGCTA-TTTCCCAAAATGCCCTTCCCGGACGGAAGGAACTT-GTTTTCATC
1 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTTACTTTT-ACC
* * *
10867 TGCTA-ATTCCCAAAACGCCCTTCCCGGACGGAAGGCA
1 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCA
10904 CCGATTTTTA
Statistics
Matches: 253, Mismatches: 26, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
48 8 0.03
49 104 0.41
50 100 0.40
53 35 0.14
54 6 0.02
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (50 bp):
TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTTACTTTTACC
Found at i:10746 original size:49 final size:50
Alignment explanation
Indices: 10557--10903 Score: 405
Period size: 50 Copynumber: 6.9 Consensus size: 50
10547 TCATTTTTCA
* * *
10557 GTTTTCACTTGCTATGTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
1 GTTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
**
10607 ACTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
1 GTTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
** *
10657 ACTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCAGACGGAAGGCATTT
1 GTTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
* **
10707 GTTTTTACCTGCT-TTTTCCAAAAATGCTCTTCCCGGACGGAAGGTTTTTTTT
1 GTTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGG---CATTT
* * *
10759 TTGTTTTACCTGCTATTTTCC-AAAATGCCCTTCCCAGATGGAAGGCATTT
1 GT-TTTTACCTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
* * * * * *
10809 GATTTCATCTGCTA-TTTCCCAAAATGCCCTTCCCGGACGGAAGGAACTT
1 GTTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
* * * * *
10858 GTTTTCATCTGCTA-ATTCCCAAAACGCCCTTCCCGGACGGAAGGCA
1 GTTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCA
10904 CCGATTTTTA
Statistics
Matches: 261, Mismatches: 30, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
48 5 0.02
49 106 0.41
50 108 0.41
52 4 0.02
53 32 0.12
54 6 0.02
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (50 bp):
GTTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
Found at i:10821 original size:102 final size:99
Alignment explanation
Indices: 10556--10950 Score: 408
Period size: 102 Copynumber: 4.0 Consensus size: 99
10546 TTCATTTTTC
* * *
10556 AGTTTTCACTTGCTATGTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT-ACTTTTACCTGCT
1 AGTTTT-ACCTGCTATTTTCCAAAAATGCCCTTCCCAGACGGAAGGCATTTGA-TTTTACCTGCT
10620 ATTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
64 -TTTTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
* *
10657 ACTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCAGACGGAAGGCATTTGTTTTTACCTGCTTT
1 AGTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCAGACGGAAGGCATTTGATTTTACCTGCTTT
* **
10722 TTCCAAAAATGCTCTTCCCGGACGGAAGGTTTTTTTTT
66 TTCCAAAAATGCCCTTCCCGGACGGAAGG----CATTT
* * * * *
10760 TGTTTTACCTGCTATTTTCC-AAAATGCCCTTCCCAGATGGAAGGCATTTGATTTCATCTGCTAT
1 AGTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCAGACGGAAGGCATTTGATTTTACCTGCTTT
* * *
10824 TTCCCAAAATGCCCTTCCCGGACGGAAGGAACTT
66 TTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
* * * * * ** **
10858 -GTTTTCATCTGCTA-ATTCCCAAAACGCCCTTCCCGGACGGAAGGCA-CCGATTTTTATTTG--
1 AGTTTT-ACCTGCTATTTTCCAAAAATGCCCTTCCCAGACGGAAGGCATTTGA-TTTTACCTGCT
* *
10918 TTTTCCTAAAACGCCCCTTCCCGGACGGAAGGC
64 TTTTCCAAAAATG-CCCTTCCCGGACGGAAGGC
10951 GTTGCTTTTT
Statistics
Matches: 252, Mismatches: 33, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
96 10 0.04
97 29 0.12
98 39 0.15
99 30 0.12
100 52 0.21
101 5 0.02
102 66 0.26
103 21 0.08
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (99 bp):
AGTTTTACCTGCTATTTTCCAAAAATGCCCTTCCCAGACGGAAGGCATTTGATTTTACCTGCTTT
TTCCAAAAATGCCCTTCCCGGACGGAAGGCATTT
Found at i:11857 original size:155 final size:153
Alignment explanation
Indices: 11693--12077 Score: 485
Period size: 155 Copynumber: 2.5 Consensus size: 153
11683 TTTTCCGATT
* * * *
11693 GGAATCGGAATTTGAAACAGAAATTAAATTTTTGTTTCTAAGAATGTTGCTAGCTAATTATAAAA
1 GGAAACGGAATTTCAAACAGAAATTATATTTTCGTTTCTAAGAATGTTGCTAGCTAATTATAAAA
* * *
11758 GGAAAATTAATTTTATATATTTGGATTATTATAAAGACAAGAAGTTGAAATATTTAAAGAAATAA
66 TGAAAATTAATTTTAT-TATTTAGATTATTATAAAGACAAGAAGTGGAAATATTTAAAGAAATAA
*
11823 TTTCATCTATAAATTTTTATCAC-TA
130 TTTCATCTATAAA-TGTT-TCACTTA
* * * * * * *
11848 GGAAACGGAATTTCACACGGCAATTATATTTCCATTTCTAAGAACGTTGCTAGCTAATTATCAAA
1 GGAAACGGAATTTCAAACAGAAATTATATTTTCGTTTCTAAGAATGTTGCTAGCTAATTATAAAA
* * * *
11913 TGAAAATT-A-GTT-TTATTTAGATTATTATAAAGATAAGGAGTGGAAATATTTACAGAAATAAT
66 TGAAAATTAATTTTATTATTTAGATTATTATAAAGACAAGAAGTGGAAATATTTAAAGAAATAAT
11975 TTCATCTATAAATGTTTCACTTA
131 TTCATCTATAAATGTTTCACTTA
* **
11998 -GAAACGGAATTTCATACAGAAATTATA-TTTCGTTTCTAAGAATGTTGCTAATTAATTATAAAA
1 GGAAACGGAATTTCAAACAGAAATTATATTTTCGTTTCTAAGAATGTTGCTAGCTAATTATAAAA
* *
12061 TGAACATTAGTTTTATT
66 TGAAAATTAATTTTATT
12078 CAAATTATAA
Statistics
Matches: 195, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
148 37 0.19
149 28 0.14
150 7 0.04
151 58 0.30
152 1 0.01
153 2 0.01
154 1 0.01
155 61 0.31
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (153 bp):
GGAAACGGAATTTCAAACAGAAATTATATTTTCGTTTCTAAGAATGTTGCTAGCTAATTATAAAA
TGAAAATTAATTTTATTATTTAGATTATTATAAAGACAAGAAGTGGAAATATTTAAAGAAATAAT
TTCATCTATAAATGTTTCACTTA
Found at i:19093 original size:14 final size:14
Alignment explanation
Indices: 19074--19103 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19064 CCTTTGAATG
19074 ATTCTTTATTACTC
1 ATTCTTTATTACTC
*
19088 ATTCTTTGTTACTC
1 ATTCTTTATTACTC
19102 AT
1 AT
19104 CATATCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (14 bp):
ATTCTTTATTACTC
Found at i:19432 original size:61 final size:61
Alignment explanation
Indices: 19354--19479 Score: 182
Period size: 61 Copynumber: 2.0 Consensus size: 61
19344 GACATGTGAC
* *
19354 GATATTAGAAATAATATTAGTCCGATAAAATATTATATT-TCAAATAGCGTGATTTTGATTT
1 GATATTAGAAATAATATTAGTCCGATAAAATATTATATTAT-AAATAACATGATTTTGATTT
* * *
19415 GATATTAGAAGTGATATTAGTCCGATAAAATATTATATTAATTAATAACATGATTTTGATTT
1 GATATTAGAAATAATATTAGTCCGATAAAATATTATATT-ATAAATAACATGATTTTGATTT
19477 GAT
1 GAT
19480 TAAGGGTATG
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
61 37 0.64
62 20 0.34
63 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (61 bp):
GATATTAGAAATAATATTAGTCCGATAAAATATTATATTATAAATAACATGATTTTGATTT
Found at i:19759 original size:79 final size:79
Alignment explanation
Indices: 19627--19782 Score: 285
Period size: 79 Copynumber: 2.0 Consensus size: 79
19617 ACATAATAGG
* * *
19627 CAATGTTATGTAATGTGTATGTGTTCTCTTATAATCCTTAGACATTGCGTCGTAATAGTCATTTC
1 CAATGTTATGTAATGTGTATGTCTTCTCTTATAATCCTTAGACATTGCATCGTAATAGTCATTCC
19692 ATAGTTTCCTCAGT
66 ATAGTTTCCTCAGT
19706 CAATGTTATGTAATGTGTATGTCTTCTCTTATAATCCTTAGACATTGCATCGTAATAGTCATTCC
1 CAATGTTATGTAATGTGTATGTCTTCTCTTATAATCCTTAGACATTGCATCGTAATAGTCATTCC
19771 ATAGTTTCCTCA
66 ATAGTTTCCTCA
19783 CATCTTTCTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (79 bp):
CAATGTTATGTAATGTGTATGTCTTCTCTTATAATCCTTAGACATTGCATCGTAATAGTCATTCC
ATAGTTTCCTCAGT
Found at i:22680 original size:33 final size:33
Alignment explanation
Indices: 22638--22706 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
22628 GGCAAAACCC
* **
22638 ATAGGTTTACATATAGAAACTTGGGATCTAAAT
1 ATAGGTTTACAGATAGAAACTTGGGAAATAAAT
* * *
22671 ATAGTTTTACAGGTCGAAACTTGGGAAATAAAT
1 ATAGGTTTACAGATAGAAACTTGGGAAATAAAT
22704 ATA
1 ATA
22707 TTAATACATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.32
Consensus pattern (33 bp):
ATAGGTTTACAGATAGAAACTTGGGAAATAAAT
Found at i:23791 original size:2 final size:2
Alignment explanation
Indices: 23784--23812 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23774 ATATTTAGTG
23784 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 T
23813 CTTAAGTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.