Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018823.1 Corchorus olitorius cultivar O-4 contig18856, 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: 13443
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:175 original size:26 final size:26
Alignment explanation
Indices: 139--190 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
129 GAGGTCTTGG
139 GTTCAACTCTCACAGAATGTGAGTTT
1 GTTCAACTCTCACAGAATGTGAGTTT
*
165 GTTCAACTCTCACGGAATGTGAGTTT
1 GTTCAACTCTCACAGAATGTGAGTTT
191 ATTTGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (26 bp):
GTTCAACTCTCACAGAATGTGAGTTT
Found at i:684 original size:19 final size:19
Alignment explanation
Indices: 660--704 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
650 TGTGGCGTGA
660 TAATTATATTAATTAACGT
1 TAATTATATTAATTAACGT
** * *
679 TAATTACCTTAGTTAGCGT
1 TAATTATATTAATTAACGT
698 TAATTAT
1 TAATTAT
705 GTTTCTTTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (19 bp):
TAATTATATTAATTAACGT
Found at i:967 original size:23 final size:25
Alignment explanation
Indices: 943--990 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
933 CAGTCACCCT
943 CCGAAAAAACC-AGTCCAGCCACTC
1 CCGAAAAAACCTAGTCCAGCCACTC
** *
967 CCTCAAAAGCCTAGTCCAGCCACT
1 CCGAAAAAACCTAGTCCAGCCACT
991 ATCAAGACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.33, C:0.42, G:0.12, T:0.12
Consensus pattern (25 bp):
CCGAAAAAACCTAGTCCAGCCACTC
Found at i:3886 original size:22 final size:22
Alignment explanation
Indices: 3813--4029 Score: 128
Period size: 22 Copynumber: 9.8 Consensus size: 22
3803 CCTTATCTCT
3813 GTGTGGTTATCAAAAATTT-ATAA
1 GTGTGGTTATC-AAAATTTCAT-A
*
3836 G-ATGGTTAT-AATAATTTCATGA
1 GTGTGGTTATCAA-AATTTCAT-A
*
3858 G-GAGGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
3879 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
3901 -TG-GAACTTATCAAAATTTCAT-
1 GTGTG--GTTATCAAAATTTCATA
* * *
3922 GGGAAGGTTATCAAAAATTCATA
1 GTG-TGGTTATCAAAATTTCATA
* * *
3945 GTGTGCTTACCTAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
* *
3967 G-GATCAGGTTATTAAAATTTCTTA
1 GTG-T--GGTTATCAAAATTTCATA
* **
3991 G-GAAGGTTATTGAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
*
4013 GTGTGGTTATCACAATT
1 GTGTGGTTATCAAAATT
4030 ATATAGAAAG
Statistics
Matches: 151, Mismatches: 29, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
20 3 0.02
21 10 0.07
22 115 0.76
23 6 0.04
24 17 0.11
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:3919 original size:66 final size:68
Alignment explanation
Indices: 3848--4021 Score: 223
Period size: 66 Copynumber: 2.6 Consensus size: 68
3838 TGGTTATAAT
3848 AATTTCATGAGG-AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA-A-CTTA
1 AATTTCATGAGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-GGACAGCTTA
3910 TCAA
65 TCAA
* * * *
3914 AATTTCATG-GGAAGGTTATCAAAAATTCATAGTGTGCTTACCTAAATTTCATAGGATCAGGTTA
1 AATTTCATGAGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA-CAGCTTA
*
3978 TTAA
65 TCAA
* **
3982 AATTTC-TTAGGAAGGTTATTGAAATTTCATAGTGTGGTTA
1 AATTTCATGAGGAAGGTTATCAAAATTTCATAGTGTGGTTA
4022 TCACAATTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
65 5 0.05
66 47 0.51
67 2 0.02
68 39 0.42
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (68 bp):
AATTTCATGAGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGACAGCTTAT
CAA
Found at i:4155 original size:22 final size:22
Alignment explanation
Indices: 4102--4214 Score: 75
Period size: 22 Copynumber: 5.2 Consensus size: 22
4092 TGTGGTTAAC
* * *
4102 AAAATTTCATAAGGAGATTACT
1 AAAATTTCATAGGGAGGTTATT
* * *
4124 AATATATCATGGGGAGGTTATT
1 AAAATTTCATAGGGAGGTTATT
* * *
4146 AAAATTTCATAGTGTGGTTATC
1 AAAATTTCATAGGGAGGTTATT
** * * *
4168 AAAATTTTTTAGTGTGGTTATC
1 AAAATTTCATAGGGAGGTTATT
* *
4190 AAAATTTCATATGAAGGTTA-T
1 AAAATTTCATAGGGAGGTTATT
4211 AAAA
1 AAAA
4215 GTCTCAATTT
Statistics
Matches: 70, Mismatches: 21, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
21 4 0.06
22 66 0.94
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (22 bp):
AAAATTTCATAGGGAGGTTATT
Found at i:4289 original size:22 final size:22
Alignment explanation
Indices: 4238--4469 Score: 116
Period size: 22 Copynumber: 10.5 Consensus size: 22
4228 GAGGAGTACA
* **
4238 AAAATTTGATAGAAAGA-TATC
1 AAAATTTCATAGAGTGATTATC
*
4259 -AAATCTCATAGAGTGATTATC
1 AAAATTTCATAGAGTGATTATC
*
4280 GAAATTTCATAGAGATCGGATTATC
1 AAAATTTCATAGAG-T--GATTATC
4305 AAAATTT-ATAG-GTAGATTATC
1 AAAATTTCATAGAGT-GATTATC
* * * *
4326 AAAATTTCAAAGCGAGGTTATC
1 AAAATTTCATAGAGTGATTATC
* *
4348 AAAATTACATA-ATGTTATTATC
1 AAAATTTCATAGA-GTGATTATC
* * * * *
4370 AGAATTTCATAGAGGGGTCAAC
1 AAAATTTCATAGAGTGATTATC
* * * *
4392 AAAATTTTATCGAGGGGTTATC
1 AAAATTTCATAGAGTGATTATC
* * * *
4414 AAAATTTCATAAAGAGGTTTTC
1 AAAATTTCATAGAGTGATTATC
* * * *
4436 AAATTTTCA-AAATATGATTACC
1 AAAATTTCATAGA-GTGATTATC
4458 AAAATTTCATAG
1 AAAATTTCATAG
4470 TGTTATTTCT
Statistics
Matches: 159, Mismatches: 41, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
20 12 0.08
21 21 0.13
22 104 0.65
23 5 0.03
24 4 0.03
25 13 0.08
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
AAAATTTCATAGAGTGATTATC
Found at i:4763 original size:23 final size:23
Alignment explanation
Indices: 4731--4796 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
4721 AAGATTTCAT
4731 GAGG-TTATCAAAATTTTATAGG
1 GAGGTTTATCAAAATTTTATAGG
4753 GAGGTTTATCAAAATTTTATAGG
1 GAGGTTTATCAAAATTTTATAGG
*
4776 AAGGTTTATCAAAATTTTATA
1 GAGGTTTATCAAAATTTTATA
4797 ACGAGGTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
22 4 0.10
23 38 0.90
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (23 bp):
GAGGTTTATCAAAATTTTATAGG
Found at i:4803 original size:23 final size:23
Alignment explanation
Indices: 4731--4804 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
4721 AAGATTTCAT
*
4731 GAGG-TTATCAAAATTTTATAGG
1 GAGGTTTATCAAAATTTTATAAG
4753 GAGGTTTATCAAAATTTTAT-AG
1 GAGGTTTATCAAAATTTTATAAG
*
4775 GAAGGTTTATCAAAATTTTATAAC
1 G-AGGTTTATCAAAATTTTATAAG
4799 GAGGTT
1 GAGGTT
4805 ATTACAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.13
23 39 0.83
24 2 0.04
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
GAGGTTTATCAAAATTTTATAAG
Found at i:4950 original size:23 final size:22
Alignment explanation
Indices: 4561--5111 Score: 252
Period size: 22 Copynumber: 25.4 Consensus size: 22
4551 TCAAAATTTG
*
4561 AGGGAGGATATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* *
4583 ATGAAGGTTATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** *
4605 AGTTTA-GTTTTCAAAATTTCAT
1 AG-GGAGGTTATCAAAATTTCAT
*
4627 A-AGATGGTTATCAAAATTTCAT
1 AGGGA-GGTTATCAAAATTTCAT
* *
4649 AGGGAGATTAACAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** **
4671 AATGAGGTTATCAAAAAATCAT
1 AGGGAGGTTATCAAAATTTCAT
*
4693 AGGGAGATTATCAAAA-TT--T
1 AGGGAGGTTATCAAAATTTCAT
* * *
4712 --GTA-GTAATCAAGATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
*
4731 ---GAGGTTATCAAAATTTTAT
1 AGGGAGGTTATCAAAATTTCAT
*
4750 AGGGAGGTTTATCAAAATTTTAT
1 AGGGAGG-TTATCAAAATTTCAT
* *
4773 AGGAAGGTTTATCAAAATTTTAT
1 AGGGAGG-TTATCAAAATTTCAT
** * *
4796 AACGAGGTTATTACAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * * *
4818 AGTGTGATTATCAAAATTTCAG
1 AGGGAGGTTATCAAAATTTCAT
* * *
4840 AGTGTGATTA-CTAACAA-TTCAT
1 AGGGAGGTTATC-AA-AATTTCAT
* * * *
4862 ATGGAGGTTTTTAAATTTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** * * * *
4884 AACGTGGTTATCAATATATGAT
1 AGGGAGGTTATCAAAATTTCAT
** * *
4906 TTGGAGGTTATCAACATCTCAT
1 AGGGAGGTTATCAAAATTTCAT
**
4928 AGTGTTGGTTATCAAAATTTCAT
1 AG-GGAGGTTATCAAAATTTCAT
* *
4951 TGGGAAGTTATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** * *
4973 AATGAGGTCT-TCAAAATTCCTT
1 AGGGAGGT-TATCAAAATTTCAT
*
4995 AGGGAGGTTAACAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * * * * *
5017 AAGAATGTTA-AAAAAATTAAT
1 AGGGAGGTTATCAAAATTTCAT
*** * * *
5038 AAAAAGGTTTTCGATATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * * *
5060 A-GTATCGTCATTAAAATTTCAT
1 AGGGA-GGTTATCAAAATTTCAT
*
5082 AGGAAGGTTATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
*
5104 AAGGAGGT
1 AGGGAGGT
5112 CACAAAAAAA
Statistics
Matches: 389, Mismatches: 118, Indels: 44
0.71 0.21 0.08
Matches are distributed among these distances:
16 7 0.02
17 4 0.01
18 1 0.00
19 15 0.04
20 1 0.00
21 20 0.05
22 275 0.71
23 66 0.17
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
AGGGAGGTTATCAAAATTTCAT
Found at i:4961 original size:45 final size:45
Alignment explanation
Indices: 4888--4973 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
4878 TTTCATAACG
* * * * *
4888 TGGTTATCAATATATGATTTGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATAGTGT
* *
4933 TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATA
4974 ATGAGGTCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATAGTGT
Found at i:5739 original size:42 final size:44
Alignment explanation
Indices: 5688--5781 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 44
5678 AGTGCATTAT
*
5688 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
5729 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAAATAAAG
5774 CTAATATT
1 CTAATATT
5782 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 8 0.17
43 2 0.04
45 34 0.71
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
Found at i:6943 original size:16 final size:15
Alignment explanation
Indices: 6905--6946 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
6895 ACAGAGATTG
*
6905 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
6920 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
6935 ACTAGAAAACAA
1 AC-AGAAAACAA
6947 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:8359 original size:19 final size:18
Alignment explanation
Indices: 8326--8361 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8316 TTGAAATAAA
*
8326 TCTTCAATGGTCTTCAAG
1 TCTTCAATAGTCTTCAAG
8344 TCTTCAATTAGTCTTCAA
1 TCTTCAA-TAGTCTTCAA
8362 ACACGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAG
Found at i:9837 original size:14 final size:15
Alignment explanation
Indices: 9818--9847 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9808 CAATCAAAGC
9818 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
9832 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
9847 A
1 A
9848 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:10229 original size:21 final size:21
Alignment explanation
Indices: 10205--10254 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
10195 GGAATGGTAA
**
10205 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
10226 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
10247 TGGCACGG
1 TGGCACGG
10255 TGAATGGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Done.