Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016700.1 Corchorus olitorius cultivar O-4 contig16733, 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: 38502
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:9496 original size:28 final size:28
Alignment explanation
Indices: 9464--9539 Score: 127
Period size: 28 Copynumber: 2.8 Consensus size: 28
9454 ATGCATCTTG
*
9464 TACATGTTAGAATTGTCAAATGTAATTT
1 TACATGTTAGAATTGTCAAATGTAAATT
*
9492 TACATGTTAGAATTGTAAAATGTAAATT
1 TACATGTTAGAATTGTCAAATGTAAATT
9520 TACATGTTAGAATT-TCAAAT
1 TACATGTTAGAATTGTCAAAT
9540 TTTATATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 5 0.11
28 40 0.89
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (28 bp):
TACATGTTAGAATTGTCAAATGTAAATT
Found at i:10274 original size:18 final size:18
Alignment explanation
Indices: 10251--10287 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
10241 CAAAGAAAAC
*
10251 ATAATAAGTAAAATAAAT
1 ATAATAAGTAAAAGAAAT
10269 ATAATAAGTAAAAGAAAT
1 ATAATAAGTAAAAGAAAT
10287 A
1 A
10288 ATTTATTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
ATAATAAGTAAAAGAAAT
Found at i:12121 original size:42 final size:42
Alignment explanation
Indices: 12062--12161 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
12052 CTCAAGATCT
* *
12062 CAGCCTCTCTCTCCCTCTACCTCTGAATCTGAGCAGCAGCAG
1 CAGCCTCTCACTCCCTCTACCTCTGAATCTGAACAGCAGCAG
* * *
12104 CAGCCTCTGACTCCCTCTTCCTCTGACTCTGAACAGCAGCAG
1 CAGCCTCTCACTCCCTCTACCTCTGAATCTGAACAGCAGCAG
* *
12146 CAACCTCTCCCTCCCT
1 CAGCCTCTCACTCCCT
12162 TTGCAACTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.18, C:0.44, G:0.14, T:0.24
Consensus pattern (42 bp):
CAGCCTCTCACTCCCTCTACCTCTGAATCTGAACAGCAGCAG
Found at i:13740 original size:75 final size:74
Alignment explanation
Indices: 13572--13743 Score: 170
Period size: 75 Copynumber: 2.3 Consensus size: 74
13562 ACTCTCCTTC
* * * * * *
13572 TCAGGTTGCTAATTCGAATTCAAATAATGAGTTTTTTGATGGTGTTAGGAAAATCTTGAAGATGA
1 TCAGGTTTCTGATTCGAATTCAAATAATAAGTTCTCTGATGATGTTAGGAAAATCTTGAAGATGA
13637 TTCATCTGA
66 TTCATCTGA
* * * * * *
13646 TTA-GTTTCTTGTTTTGAATTCAAATACTAAGTTCTCTGATGATGATT-GGCAACATCTTGAAGC
1 TCAGGTTTC-TGATTCGAATTCAAATAATAAGTTCTCTGATGATG-TTAGG-AAAATCTTGAAGA
*
13709 TGATTCA-CTTTA
63 TGATTCATC-TGA
13721 TCAGGTTTCTGATTCGAATTCAA
1 TCAGGTTTCTGATTCGAATTCAA
13744 TTTTTGAGCA
Statistics
Matches: 77, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
73 4 0.05
74 32 0.42
75 36 0.47
76 5 0.06
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (74 bp):
TCAGGTTTCTGATTCGAATTCAAATAATAAGTTCTCTGATGATGTTAGGAAAATCTTGAAGATGA
TTCATCTGA
Found at i:13827 original size:75 final size:75
Alignment explanation
Indices: 13684--13827 Score: 164
Period size: 75 Copynumber: 1.9 Consensus size: 75
13674 AAGTTCTCTG
* * * * * * * **
13684 ATGATGATTGGCAACATCTTGAAGCTGATTCACTTTATCAGGTTTCTGATTCGAATTCAATTTTT
1 ATGATGATAGGCAACATCTTGAAACTGATTCACCTAATCAAGATGCTGATTCGAATTCAATTACT
13749 GAGCATCATA
66 GAGCATCATA
* * *
13759 ATGATGATAGGCAACATCTTGAAATTGATTCTCCTAATCAAGATGCTGTTTCGAATTCTAA-TAC
1 ATGATGATAGGCAACATCTTGAAACTGATTCACCTAATCAAGATGCTGATTCGAATTC-AATTAC
13823 TGAGC
65 TGAGC
13828 TTCCCAATGA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
75 54 0.96
76 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (75 bp):
ATGATGATAGGCAACATCTTGAAACTGATTCACCTAATCAAGATGCTGATTCGAATTCAATTACT
GAGCATCATA
Found at i:18380 original size:94 final size:94
Alignment explanation
Indices: 18191--18960 Score: 1107
Period size: 94 Copynumber: 8.2 Consensus size: 94
18181 TTGACTCCTC
* * * * *
18191 TTTATTACTTAGTTTAATTACCTAGAATTAAATTAATTTCTTCTTCTTTTATTAGTTAGTTGCAA
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTT-TAA
18256 TTACCTAGAATTAAACTAATTTCTTCTTCT
65 TTACCTAGAATTAAACTAATTTCTTCTTCT
* * * * * *
18286 TTTACTATTTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCTTTTATTACTTAGTTTAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAAT
* *
18351 TACCTGGAATTAAACTAATGTCTTCTTCT
66 TACCTAGAATTAAACTAATTTCTTCTTCT
* * *
18380 TTTACTATTTAGTTCAATTACCTAGAATTAAACTACTTTCTTCTTCTTTTACTATTTAGTTTAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAAT
*
18445 TACCTAGAATTAAACTAAATTTCTTCTCCT
66 TACCTAGAATTAAACT-AATTTCTTCTTCT
* * *
18475 TTTACTACTTAGTTCAATTACCTAGAATTAGACTACTTTCTTCTTCTTTTACTATTTAGTTTAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAAT
* * *
18540 TACCTAGAATTAAACTAATCTCCTCCTCT
66 TACCTAGAATTAAACTAATTTCTTCTTCT
* * *
18569 TTTATTACTTAGTTTAATTACCTGGAATTAAACTACTTTCTTCTTCTTTTACTATTTAGTTTAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAAT
18634 TACCTAGAATTAAACTAAATTTCTTCTTCT
66 TACCTAGAATTAAACT-AATTTCTTCTTCT
* * *
18664 TTTACTACTTAGTTCAATTACCTAGAATTAAACTAAATTTATTCTTCTTTTACTATTTAGTTCAA
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACT-AATTTCTTCTTCTTTTACTATTTAGTTTAA
*
18729 TTACCTAGAATTAAACTAATCTCTTC-TCT
65 TTACCTAGAATTAAACTAATTTCTTCTTCT
* * *
18758 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTC-TCTTTTACTACTTAGTTCAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAAT
18822 TACCTAGAATTAAACTAAATTTCTTCTTCT
66 TACCTAGAATTAAACT-AATTTCTTCTTCT
* * * *
18852 TTTACTATTTAGTTCAATTACCTAGAATTAAACTAATCTCTTC-TCTTTTACTACTTAGTTTAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAAT
* * *
18916 TACCTAGAATTAAACTAATCTATTC-TCC
66 TACCTAGAATTAAACTAATTTCTTCTTCT
18944 TTTACTACTTAGTTTAA
1 TTTACTACTTAGTTTAA
18961 AACTATCTTC
Statistics
Matches: 617, Mismatches: 53, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
92 53 0.09
93 22 0.04
94 305 0.49
95 193 0.31
96 44 0.07
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (94 bp):
TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAAT
TACCTAGAATTAAACTAATTTCTTCTTCT
Found at i:18536 original size:189 final size:188
Alignment explanation
Indices: 18191--18960 Score: 1177
Period size: 189 Copynumber: 4.1 Consensus size: 188
18181 TTGACTCCTC
* * * *
18191 TTTATTACTTAGTTTAATTACCTAGAATTAAATTAATTTCTTCTTCTTTTATTAGTTAGTTGCAA
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTT-CAA
* *
18256 TTACCTAGAATTAAACT-AATTTCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACT
65 TTACCTAGAATTAAACTAAATTTCTTCTTCTTTTACTACTTAGTTCAATTACCTAGAATTAAACT
* * * * *
18320 AATCTCCTCCTCTTTTATTACTTAGTTTAATTACCTGGAATTAAACTAATGTCTTCTTCT
130 AATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTC-TCT
* * * *
18380 TTTACTATTTAGTTCAATTACCTAGAATTAAACTACTTTCTTCTTCTTTTACTATTTAGTTTAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTCAAT
* *
18445 TACCTAGAATTAAACTAAATTTCTTCTCCTTTTACTACTTAGTTCAATTACCTAGAATTAGACTA
66 TACCTAGAATTAAACTAAATTTCTTCTTCTTTTACTACTTAGTTCAATTACCTAGAATTAAACTA
* * * *
18510 CTTTCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCT
131 ATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCT-CTTCTCT
* * * *
18569 TTTATTACTTAGTTTAATTACCTGGAATTAAACTACTTTCTTCTTCTTTTACTATTTAGTTTAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTCAAT
18634 TACCTAGAATTAAACTAAATTTCTTCTTCTTTTACTACTTAGTTCAATTACCTAGAATTAAACTA
66 TACCTAGAATTAAACTAAATTTCTTCTTCTTTTACTACTTAGTTCAATTACCTAGAATTAAACT-
* * * *
18699 AATTTATTCTTCTTTTACTATTTAGTTCAATTACCTAGAATTAAACTAATCTCTTCTCT
130 AATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTCT
* *
18758 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTC-TCTTTTACTACTTAGTTCAAT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTCAAT
*
18822 TACCTAGAATTAAACTAAATTTCTTCTTCTTTTACTATTTAGTTCAATTACCTAGAATTAAACTA
66 TACCTAGAATTAAACTAAATTTCTTCTTCTTTTACTACTTAGTTCAATTACCTAGAATTAAACTA
* *
18887 ATCTCTTC-TCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTATTCTCC
131 ATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTCT
18944 TTTACTACTTAGTTTAA
1 TTTACTACTTAGTTTAA
18961 AACTATCTTC
Statistics
Matches: 534, Mismatches: 44, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
186 62 0.12
187 7 0.01
188 101 0.19
189 312 0.58
190 52 0.10
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (188 bp):
TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTCAAT
TACCTAGAATTAAACTAAATTTCTTCTTCTTTTACTACTTAGTTCAATTACCTAGAATTAAACTA
ATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTCT
Found at i:18613 original size:236 final size:236
Alignment explanation
Indices: 18191--18957 Score: 1240
Period size: 236 Copynumber: 3.3 Consensus size: 236
18181 TTGACTCCTC
* * * * * *
18191 TTTATTACTTAGTTTAATTACCTAGAATTAAA-TTAATTTCTTCTTCTTTTATTAGTTAGTTGCA
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAATTTATTCTCCTTTTACTACTTAGTT-CA
18255 ATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACT
65 ATTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACT
*
18320 AATCTCCTCCTCTTTTATTACTTAGTTTAATTACCTGGAATTAAACTAATGTCTTCTTCTTTTAC
130 AATCTCCTCCTCTTTTATTACTTAGTTTAATTACCTGGAATTAAACTAATTTCTTCTTCTTTTAC
*
18385 TATTTAGTTCAATTACCTAGAATTAAACTACTTTCTTCTTCT
195 TATTTAGTTCAATTACCTAGAATTAAACTAATTTCTTCTTCT
* *
18427 TTTACTATTTAGTTTAATTACCTAGAATTAAACTAAATTTCTTCTCCTTTTACTACTTAGTTCAA
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAATTTATTCTCCTTTTACTACTTAGTTCAA
* *
18492 TTACCTAGAATTAGACTACTTTCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTA
66 TTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTA
*
18557 ATCTCCTCCTCTTTTATTACTTAGTTTAATTACCTGGAATTAAACTACTTTCTTCTTCTTTTACT
131 ATCTCCTCCTCTTTTATTACTTAGTTTAATTACCTGGAATTAAACTAATTTCTTCTTCTTTTACT
*
18622 ATTTAGTTTAATTACCTAGAATTAAACTAAATTTCTTCTTCT
196 ATTTAGTTCAATTACCTAGAATTAAACT-AATTTCTTCTTCT
* * *
18664 TTTACTACTTAGTTCAATTACCTAGAATTAAACTAAATTTATTCTTCTTTTACTATTTAGTTCAA
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAATTTATTCTCCTTTTACTACTTAGTTCAA
* *
18729 TTACCTAGAATTAAACTAATCTCTTC-TCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTA
66 TTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTA
* * * *
18793 ATCT-CTTCTCTTTTACTACTTAGTTCAATTACCTAGAATTAAACTAAATTTCTTCTTCTTTTAC
131 ATCTCCTCCTCTTTTATTACTTAGTTTAATTACCTGGAATTAAACT-AATTTCTTCTTCTTTTAC
*
18857 TATTTAGTTCAATTACCTAGAATTAAACTAATCTCTTC-TCT
195 TATTTAGTTCAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
18898 TTTACTACTTAGTTTAATTACCTAGAATTAAACT-AATCTATTCTCC-TTTACTACTTAGTT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAATTTATTCTCCTTTTACTACTTAGTT
18958 TAAAACTATC
Statistics
Matches: 496, Mismatches: 32, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
232 13 0.03
233 10 0.02
234 36 0.07
235 45 0.09
236 272 0.55
237 120 0.24
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (236 bp):
TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAATTTATTCTCCTTTTACTACTTAGTTCAA
TTACCTAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTA
ATCTCCTCCTCTTTTATTACTTAGTTTAATTACCTGGAATTAAACTAATTTCTTCTTCTTTTACT
ATTTAGTTCAATTACCTAGAATTAAACTAATTTCTTCTTCT
Found at i:22779 original size:27 final size:26
Alignment explanation
Indices: 22749--22817 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
22739 ACAGTAATTT
* *
22749 TGACCGAAATGCCCCTGGGGCGGAAAA
1 TGACCAAAATGCCCCTGAGG-GGAAAA
* *
22776 TGACCAAAATGCCCCCGAGGTGAAAA
1 TGACCAAAATGCCCCTGAGGGGAAAA
22802 TGACCAAAATGCCCCT
1 TGACCAAAATGCCCCT
22818 AGTGAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 20 0.54
27 17 0.46
ACGTcount: A:0.33, C:0.29, G:0.25, T:0.13
Consensus pattern (26 bp):
TGACCAAAATGCCCCTGAGGGGAAAA
Found at i:32873 original size:28 final size:28
Alignment explanation
Indices: 32809--32883 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
32799 TCCGGCATTT
32809 AAGGGCAAAACTGTAA-TTTAGTCAACC
1 AAGGGCAAAACTGTAATTTTAGTCAACC
* * **
32836 AGGGGTAAAA-TGGTAATTTTAGTTGACC
1 AAGGGCAAAACT-GTAATTTTAGTCAACC
32864 AAGGGCAAAACTGTAATTTT
1 AAGGGCAAAACTGTAATTTT
32884 GACATCTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 1 0.03
27 12 0.31
28 25 0.64
29 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (28 bp):
AAGGGCAAAACTGTAATTTTAGTCAACC
Found at i:35667 original size:33 final size:33
Alignment explanation
Indices: 35569--35699 Score: 145
Period size: 33 Copynumber: 3.8 Consensus size: 33
35559 AAAAACTGAA
* ****
35569 TGGGAACTTTCCCAATTTGAAAACTTAAAAGTTAA
1 TGGGAACTTTCCCAA-TTAAAAACTTAAAA-CCGG
35604 TGGGAACTTTCCCAATTTTTAAAAACTTAAAACCGG
1 TGGGAACTTTCCCAA---TTAAAAACTTAAAACCGG
* * *
35640 TGGGAACTTTCCCGATTAAAAATTTAAAACTGG
1 TGGGAACTTTCCCAATTAAAAACTTAAAACCGG
35673 TGGGAACTTTCCCAATTAAAAACTTAA
1 TGGGAACTTTCCCAATTAAAAACTTAA
35700 TGAAATTCTT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 41 0.49
35 15 0.18
36 14 0.17
37 14 0.17
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (33 bp):
TGGGAACTTTCCCAATTAAAAACTTAAAACCGG
Found at i:36422 original size:23 final size:23
Alignment explanation
Indices: 36376--36438 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
36366 GGAATTAAAT
* *
36376 CCAAAGTATAAACTAGAATCTAAG
1 CCAAAGCAT-AACTAAAATCTAAG
* * *
36400 CCCAAGCCTAACTAAAATTTAAG
1 CCAAAGCATAACTAAAATCTAAG
*
36423 CCAAAGTATAACTAAA
1 CCAAAGCATAACTAAA
36439 GTTCAAAGGC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (23 bp):
CCAAAGCATAACTAAAATCTAAG
Done.