Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020763.1 Corchorus olitorius cultivar O-4 contig20796, 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: 24404
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:387 original size:2 final size:2
Alignment explanation
Indices: 380--421 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
370 CGTTCCATCA
380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
422 CCAAATAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2405 original size:41 final size:41
Alignment explanation
Indices: 2351--2613 Score: 357
Period size: 41 Copynumber: 6.3 Consensus size: 41
2341 AGGGTCGAAT
* * *
2351 GACTTGTTCTTGAATTGATAATTTAATTCAAGGGTGTTGAC
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAC
*
2392 GACTTGA-CATTGAATTGATAATTTAATTCAAGGGTCTTGAC
1 GACTTGATC-TTGAATTGATAATTTAATTCAAGGGTCTCGAC
* *
2433 GACTTGATCTTGAATTGATAATAATTCGATTCAAGGGTCTCGAT
1 GACTTGATCTTGAATTGATAAT--TT-AATTCAAGGGTCTCGAC
* *
2477 GACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAA
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAC
** *
2518 GACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAC
** *
2559 GACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGAT
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAC
2600 GACTTGATCTTGAA
1 GACTTGATCTTGAA
2614 CAAACGAAAA
Statistics
Matches: 203, Mismatches: 14, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
40 1 0.00
41 162 0.80
42 3 0.01
43 2 0.01
44 35 0.17
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (41 bp):
GACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCGAC
Found at i:2574 original size:126 final size:123
Alignment explanation
Indices: 2331--2613 Score: 401
Period size: 126 Copynumber: 2.3 Consensus size: 123
2321 GTTTAATTTG
* * *
2331 ATTTGATTCAAGGG--TCGAATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTGTTGACGA
1 ATTTGATTCAAGGGTCTCG-ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGA
** * **
2394 CTTGACATTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGATA
65 CTCAACATTGAATTGATAATTTAATTCAAGGGTCTCGACGACTCAATCTTGAATTGATA
2453 ATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAA
1 AT--TT-GATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAA
*
2518 GACTCAATC-TTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
63 GACTCAA-CATTGAATTGATAATTTAATTCAAGGGTCTCGACGACTCAATCTTGAATTGATA
* *
2579 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1 ATTTGATTCAAGGGTCTCGATGACTTGTTCTTGAA
2614 CAAACGAAAA
Statistics
Matches: 144, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
122 2 0.01
123 29 0.20
124 4 0.03
125 10 0.07
126 95 0.66
127 4 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (123 bp):
ATTTGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGAC
TCAACATTGAATTGATAATTTAATTCAAGGGTCTCGACGACTCAATCTTGAATTGATA
Found at i:2730 original size:16 final size:16
Alignment explanation
Indices: 2709--2743 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2699 TCTGAAAATA
2709 CTTCAGAG-TTTTTCTG
1 CTTCAGAGCTTTTT-TG
2725 CTTCAGAGCTTTTTTG
1 CTTCAGAGCTTTTTTG
2741 CTT
1 CTT
2744 TCTGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.51
Consensus pattern (16 bp):
CTTCAGAGCTTTTTTG
Found at i:7475 original size:111 final size:111
Alignment explanation
Indices: 7302--7525 Score: 385
Period size: 111 Copynumber: 2.0 Consensus size: 111
7292 TTTCTGAAAA
* *
7302 AAAAAAAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGTTCAAAGCCAAAGAAGA
1 AAAAAAAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGCTCAAAGCCAAAGAAAA
* *
7367 ACCAAATTGAAAACAAGAATTAGATGAAAATATTGACATCAGTGGC
66 ACCAAATTGAAAACAAAAATTAGATGAAAATATTGACATCAATGGC
*
7413 AAAAAGAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGCTCAAAGCCAAAGAAAA
1 AAAAAAAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGCTCAAAGCCAAAGAAAA
* *
7478 ACCAAATTGTAAACAAAAATTAGATGAAAATATTGACGTCAATGGC
66 ACCAAATTGAAAACAAAAATTAGATGAAAATATTGACATCAATGGC
7524 AA
1 AA
7526 TTTCTTCTTC
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (111 bp):
AAAAAAAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGCTCAAAGCCAAAGAAAA
ACCAAATTGAAAACAAAAATTAGATGAAAATATTGACATCAATGGC
Found at i:9102 original size:7 final size:7
Alignment explanation
Indices: 9092--9120 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
9082 GAAAATTGGC
9092 AACAGAA
1 AACAGAA
9099 AACAGAA
1 AACAGAA
9106 AACAGAA
1 AACAGAA
9113 AACAGAA
1 AACAGAA
9120 A
1 A
9121 CGATACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.14, G:0.14, T:0.00
Consensus pattern (7 bp):
AACAGAA
Found at i:9556 original size:51 final size:51
Alignment explanation
Indices: 9476--9612 Score: 204
Period size: 51 Copynumber: 2.7 Consensus size: 51
9466 TTTTGATTAA
* *
9476 TTAAATCTC-TAATATTGCAAAATCGGCTCAAATTAGTCATCAAAGTCAAT
1 TTAAGTCTCTTAATATTGCAAAATCGGCTCAAATCAGTCATCAAAGTCAAT
*
9526 TTAAGTCTCTTAATATTGCAAAATTGGCTCAAATCAGTCATCAAAGTCAAT
1 TTAAGTCTCTTAATATTGCAAAATCGGCTCAAATCAGTCATCAAAGTCAAT
* * * *
9577 TTAAGTCTTTTGATGTTGCAAAATCGACTCAAATCA
1 TTAAGTCTCTTAATATTGCAAAATCGGCTCAAATCA
9613 ATCTAGAGTC
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 8 0.10
51 70 0.90
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (51 bp):
TTAAGTCTCTTAATATTGCAAAATCGGCTCAAATCAGTCATCAAAGTCAAT
Found at i:12832 original size:33 final size:32
Alignment explanation
Indices: 12759--12850 Score: 111
Period size: 31 Copynumber: 2.9 Consensus size: 32
12749 TTTTGCTCGT
*
12759 CATACTTCGGAATATCATGAT-TTTTTTTTTGT
1 CATACTTCGG-ATATCATGATGTTTTTTTTTGG
*
12791 CA-A-ATCGGATATCATGCATGTTTTTTTTTGG
1 CATACTTCGGATATCATG-ATGTTTTTTTTTGG
*
12822 CATACTTCGGATATCAT-AGGTTTTTTTTT
1 CATACTTCGGATATCATGATGTTTTTTTTT
12851 TAATCGAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
29 8 0.15
30 6 0.12
31 24 0.46
32 3 0.06
33 11 0.21
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (32 bp):
CATACTTCGGATATCATGATGTTTTTTTTTGG
Found at i:12851 original size:33 final size:32
Alignment explanation
Indices: 12759--12851 Score: 93
Period size: 33 Copynumber: 2.9 Consensus size: 32
12749 TTTTGCTCGT
* *
12759 CATACTTCGGAATATCAT-GATTTTTTTTTTGT
1 CATACTTCGG-ATATCATGGTTTTTTTTTTTGG
* * *
12791 CA-A-ATCGGATATCATGCATGTTTTTTTTTGG
1 CATACTTCGGATATCATG-GTTTTTTTTTTTGG
12822 CATACTTCGGATATCATAGGTTTTTTTTTT
1 CATACTTCGGATATCAT-GGTTTTTTTTTT
12852 AATCGAAGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
29 7 0.15
30 4 0.08
31 13 0.27
32 3 0.06
33 20 0.42
34 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.51
Consensus pattern (32 bp):
CATACTTCGGATATCATGGTTTTTTTTTTTGG
Done.