Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015003.1 Corchorus olitorius cultivar O-4 contig15036, 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: 18162
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Found at i:297 original size:11 final size:11
Alignment explanation
Indices: 277--307 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
267 GCCATGGTCA
277 GGTCGCGATTC
1 GGTCGCGATTC
*
288 GGTCGTGATTC
1 GGTCGCGATTC
299 GGTCGCGAT
1 GGTCGCGAT
308 CGTCGCACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.39, T:0.29
Consensus pattern (11 bp):
GGTCGCGATTC
Found at i:1526 original size:5 final size:5
Alignment explanation
Indices: 1516--1571 Score: 85
Period size: 5 Copynumber: 10.6 Consensus size: 5
1506 TTGATGTCCC
1516 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATATAT ATATAT ATATAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT AT-TAT AT-TAT
1569 ATT
1 ATT
1572 GTCTGGTATC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 33 0.66
6 17 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATTAT
Found at i:1555 original size:2 final size:2
Alignment explanation
Indices: 1518--1570 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
1508 GATGTCCCAT
1518 TA TA T- TA TA T- TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1554 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1571 TGTCTGGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
1 6 0.13
2 39 0.87
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:2713 original size:182 final size:182
Alignment explanation
Indices: 2406--2768 Score: 681
Period size: 182 Copynumber: 2.0 Consensus size: 182
2396 CTTCTAGGAT
2406 CTGAAGTTTTAACTTTAGTTTATAGGTTACATTTTAAAGCAATGTATTCCGTAGTTAATACCAAG
1 CTGAAGTTTTAACTTTAGTTTATAGGTTACATTTTAAAGCAATGTATTCCGTAGTTAATACCAAG
* *
2471 GCTTTACTGTAAAGCCCAAAAGGAGAAACTAGCCTTCTAATAGAAACTGACACTACAAGAGCTCA
66 GCTTTACTGTAAAGCCCAAAAGGAGAAACTACCCTTCTAAGAGAAACTGACACTACAAGAGCTCA
* *
2536 TACGGTAATACCCAAGACTATCCAATGGCATGAAGTTAATCTTCCTGAAAGG
131 TACAGCAATACCCAAGACTATCCAATGGCATGAAGTTAATCTTCCTGAAAGG
2588 CTGAAGTTTTAACTTTAGTTTATAGGTTACATTTTAAAGCAATGTATTCCGTAGTTAATACCAAG
1 CTGAAGTTTTAACTTTAGTTTATAGGTTACATTTTAAAGCAATGTATTCCGTAGTTAATACCAAG
*
2653 GCTTTACTGTAAAGCCCAAAAGGAGAAACTACCCTTCTAGGAGAAACTGACACTACAAGAGCTCA
66 GCTTTACTGTAAAGCCCAAAAGGAGAAACTACCCTTCTAAGAGAAACTGACACTACAAGAGCTCA
2718 TACAGCAATACCCAAGACTATCCAATGGCATGAAGTTAATCTTCCTGAAAG
131 TACAGCAATACCCAAGACTATCCAATGGCATGAAGTTAATCTTCCTGAAAG
2769 ATGGAAATTA
Statistics
Matches: 176, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
182 176 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (182 bp):
CTGAAGTTTTAACTTTAGTTTATAGGTTACATTTTAAAGCAATGTATTCCGTAGTTAATACCAAG
GCTTTACTGTAAAGCCCAAAAGGAGAAACTACCCTTCTAAGAGAAACTGACACTACAAGAGCTCA
TACAGCAATACCCAAGACTATCCAATGGCATGAAGTTAATCTTCCTGAAAGG
Found at i:6301 original size:13 final size:13
Alignment explanation
Indices: 6283--6308 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6273 CAAAACAAGC
6283 AACATAGAATTAA
1 AACATAGAATTAA
6296 AACATAGAATTAA
1 AACATAGAATTAA
6309 GAAATACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
AACATAGAATTAA
Found at i:12680 original size:44 final size:44
Alignment explanation
Indices: 12630--12731 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 44
12620 TTTTCGAATC
12630 AGGGAAAGATCCCACCAAAAGTA-TTATT-CAAAGA-TTTCAAGATT
1 AGGGAAAGATCCCA-CAAAAGTATTTATTACAAAGATTTTC-AGA-T
* * *
12674 AGGGAAAGATCCCACTAAAGTATTTTTTTACAAAGATTTTCATAT
1 AGGGAAAGATCCCACAAAAGTA-TTTATTACAAAGATTTTCAGAT
12719 AGGGAAAGATCCC
1 AGGGAAAGATCCC
12732 TTCAAGTAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
43 7 0.14
44 14 0.27
45 18 0.35
46 8 0.16
47 4 0.08
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (44 bp):
AGGGAAAGATCCCACAAAAGTATTTATTACAAAGATTTTCAGAT
Found at i:12907 original size:118 final size:119
Alignment explanation
Indices: 12756--13012 Score: 380
Period size: 118 Copynumber: 2.2 Consensus size: 119
12746 AAAAGCCTTT
*
12756 AATTTAGGGAAAGATCCCATCTAGTATTTAAGTTTTTCAATTTAGGGAAAGATCCCATCCT-GTC
1 AATTTAGGGAAAGATCCCATCGAGTATTTAAG-TTTTCAATTTAGGGAAAGATCCCAT-CTAGTC
* *
12820 TTTTTCAGAGTTTT-AATTTAGGGAAAGATCCCATCTAGTCTTCTTCAAAATTTTA
64 TTTTTCAAAGTTTTCAATTAAGGGAAAGATCCCATCTAGTCTTCTTCAAAATTTTA
*
12875 AATTTA-GGAAAGATCCCGTCGAGT-TTTCAAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCT
1 AATTTAGGGAAAGATCCCATCGAGTATTT-AAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCT
* * *
12938 TTTTCAAAGTTTTCAATTAAGGGAAAGATCCCATCTAGTCTTTTTCAAAGTTTTC
65 TTTTCAAAGTTTTCAATTAAGGGAAAGATCCCATCTAGTCTTCTTCAAAATTTTA
12993 AA-TTAGGGGAAAGATCCCAT
1 AATTTA-GGGAAAGATCCCAT
13013 TAAAGATTTT
Statistics
Matches: 125, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
116 2 0.02
117 47 0.38
118 58 0.46
119 18 0.14
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (119 bp):
AATTTAGGGAAAGATCCCATCGAGTATTTAAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCTT
TTTCAAAGTTTTCAATTAAGGGAAAGATCCCATCTAGTCTTCTTCAAAATTTTA
Found at i:12954 original size:41 final size:41
Alignment explanation
Indices: 12656--13012 Score: 348
Period size: 41 Copynumber: 8.8 Consensus size: 41
12646 AAAAGTATTA
* * *
12656 TTCAAAGATTTCAAGATTAGGGAAAGATCCCA-CTAAAGTATTTTT
1 TTCAAAGTTTTCAA-TTTAGGGAAAGATCCCATCT--AG--TCTTT
* * * **
12701 TTACAAAGATTTTC-ATATAGGGAAAGATCCCTTCAAGTAGTT
1 TT-CAAAG-TTTTCAATTTAGGGAAAGATCCCATCTAGTCTTT
* *
12743 TTCAAAAGCCTTT-AATTTAGGGAAAGATCCCATCTAG--TAT
1 TTC-AAAG-TTTTCAATTTAGGGAAAGATCCCATCTAGTCTTT
12783 TT--AAGTTTTTCAATTTAGGGAAAGATCCCATCCT-GTCTTT
1 TTCAAAG-TTTTCAATTTAGGGAAAGATCCCAT-CTAGTCTTT
* *
12823 TTCAGAGTTTT-AATTTAGGGAAAGATCCCATCTAGTCTTC
1 TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCTTT
* * * *
12863 TTCAAAATTTTAAATTTA-GGAAAGATCCCGTCGAG---TT
1 TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCTTT
12900 TTC-AAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCTTT
1 TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCTTT
*
12940 TTCAAAGTTTTCAATTAAGGGAAAGATCCCATCTAGTCTTT
1 TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCTTT
12981 TTCAAAGTTTTCAA-TTAGGGGAAAGATCCCAT
1 TTCAAAGTTTTCAATTTA-GGGAAAGATCCCAT
13013 TAAAGATTTT
Statistics
Matches: 263, Mismatches: 30, Indels: 42
0.79 0.09 0.13
Matches are distributed among these distances:
36 12 0.05
37 25 0.10
38 21 0.08
39 4 0.02
40 63 0.24
41 75 0.29
42 34 0.13
44 2 0.01
45 16 0.06
46 7 0.03
47 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (41 bp):
TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCTTT
Found at i:15066 original size:13 final size:13
Alignment explanation
Indices: 15048--15077 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15038 TTGGTTTGCA
*
15048 AAAAGTGCTTTTT
1 AAAAGTGCTTTTG
15061 AAAAGTGCTTTTG
1 AAAAGTGCTTTTG
15074 AAAA
1 AAAA
15078 TAGCTGTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (13 bp):
AAAAGTGCTTTTG
Done.