Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024357.1 Corchorus olitorius cultivar O-4 contig24390, 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: 22998
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1291 original size:35 final size:35
Alignment explanation
Indices: 1231--1299 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
1221 GCTGGGTCAC
** ** *
1231 GACGCGGGTCGCGACCTTCTTCATGGCCGGGTCGA
1 GACGCGGGTCGCGACCCGCACCATGGCCAGGTCGA
1266 GACGCGGGTCGCGACCCGCACCATGGCCAGGTCG
1 GACGCGGGTCGCGACCCGCACCATGGCCAGGTCG
1300 CGACCCGGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.13, C:0.35, G:0.38, T:0.14
Consensus pattern (35 bp):
GACGCGGGTCGCGACCCGCACCATGGCCAGGTCGA
Found at i:3661 original size:22 final size:22
Alignment explanation
Indices: 3635--3686 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3625 TTTCTAGGAG
3635 TTTAGTTGTTGCAAATCATGGA
1 TTTAGTTGTTGCAAATCATGGA
* * * *
3657 TTTAGTGGTTGCAGATCGTGGC
1 TTTAGTTGTTGCAAATCATGGA
3679 TTTAGTTG
1 TTTAGTTG
3687 GTTTGTTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (22 bp):
TTTAGTTGTTGCAAATCATGGA
Found at i:8074 original size:22 final size:22
Alignment explanation
Indices: 8049--8098 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
8039 TCTAAGAGTG
8049 TAGTTGCTGCAAATCATGGATT
1 TAGTTGCTGCAAATCATGGATT
* * * *
8071 TAGTGGTTGCAAATCGTGGCTT
1 TAGTTGCTGCAAATCATGGATT
8093 TAGTTG
1 TAGTTG
8099 GTTTGTTGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (22 bp):
TAGTTGCTGCAAATCATGGATT
Found at i:10816 original size:11 final size:11
Alignment explanation
Indices: 10792--10826 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
10782 TTGACAGCGC
10792 AACAAAAACAA
1 AACAAAAACAA
* *
10803 AACGAAAACGA
1 AACAAAAACAA
10814 AACAAAAACAA
1 AACAAAAACAA
10825 AA
1 AA
10827 AACGAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:10818 original size:16 final size:16
Alignment explanation
Indices: 10797--10845 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
10787 AGCGCAACAA
10797 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
10813 AAACAAAAACAAAAAACG
1 AAAC-AAAAC-GAAAACG
10831 -AA-AAAACGAAAACG
1 AAACAAAACGAAAACG
10845 A
1 A
10846 TGCCAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 6 0.21
15 5 0.18
16 4 0.14
17 7 0.25
18 6 0.21
ACGTcount: A:0.73, C:0.16, G:0.10, T:0.00
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:15510 original size:3 final size:3
Alignment explanation
Indices: 15496--15542 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
15486 GGTGGATTAC
15496 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15541 AA
1 AA
15543 AACTAAGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:15971 original size:3 final size:3
Alignment explanation
Indices: 15965--15999 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
15955 TTTTTTCTTA
15965 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16000 ATTTAATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16737 original size:22 final size:22
Alignment explanation
Indices: 16708--16935 Score: 109
Period size: 22 Copynumber: 10.5 Consensus size: 22
16698 TGAATATTTT
16708 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* *
16730 TATTAAATTTTGATAAC-AGCGC
1 TATGAAATTTTGATAACTA-CCC
* *
16752 TAAGAAATTTTGATAATTTA-CC
1 TATGAAATTTTGATAA-CTACCC
* *
16774 TATGAAATTGTGATAAACT-CCA
1 TATGAAATTTTGAT-AACTACCC
* * *
16796 TATGAAACTTCGATAACCTA-AC
1 TATGAAATTTTGATAA-CTACCC
*
16818 TATGAAATTTTGATAAATCT-TCC
1 TATGAAATTTTGAT-AA-CTACCC
* ** *
16841 TATAAAATTTTG-TAACTTTCT
1 TATGAAATTTTGATAACTACCC
*
16862 TATG-ATTTTTGATAACCT-CCC
1 TATGAAATTTTGATAA-CTACCC
* * *
16883 TGTGAGATTTTGTTAATCT-CCC
1 TATGAAATTTTGATAA-CTACCC
* * *
16905 AAT-AAATTTTTGAT-ACTATCA
1 TATGAAA-TTTTGATAACTACCC
16926 TATGAAATTT
1 TATGAAATTT
16936 CGACAATCTC
Statistics
Matches: 153, Mismatches: 37, Indels: 33
0.69 0.17 0.15
Matches are distributed among these distances:
20 10 0.07
21 26 0.17
22 98 0.64
23 18 0.12
24 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:18904 original size:3 final size:3
Alignment explanation
Indices: 18896--18988 Score: 168
Period size: 3 Copynumber: 30.7 Consensus size: 3
18886 TGGGTTGGCC
18896 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
18944 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
18989 CATAATTTTA
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
3 84 0.97
4 3 0.03
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19214 original size:22 final size:22
Alignment explanation
Indices: 19168--19338 Score: 84
Period size: 22 Copynumber: 7.7 Consensus size: 22
19158 TGAATATTTT
**
19168 TATGAAATTTTGATAATTATCC
1 TATGAAATTTTGATAACCATCC
*
19190 TATTAAATTTTGATAACCA-CTC
1 TATGAAATTTTGATAACCATC-C
* *
19212 TATGAAATGTTGATAA--TTGCC
1 TATGAAATTTTGATAACCAT-CC
* * * * *
19233 TATGAAATCGTGATAATAAACTTCA
1 TATGAAAT--T-TTGATAACCATCC
**
19258 TATGAAATTTTGATAACC-TAAA
1 TATGAAATTTTGATAACCAT-CC
* *
19280 TATGAAATTGTAATAAACCATCC
1 TATGAAATTTTGAT-AACCATCC
* *
19303 TATGAAATTTTG-TAACCTTCA
1 TATGAAATTTTGATAACCATCC
*
19324 TATG-ATTTTTGATAA
1 TATGAAATTTTGATAA
19339 TCTCCCTATG
Statistics
Matches: 114, Mismatches: 23, Indels: 25
0.70 0.14 0.15
Matches are distributed among these distances:
20 6 0.05
21 24 0.21
22 52 0.46
23 15 0.13
24 6 0.05
25 9 0.08
26 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATCC
Found at i:19218 original size:44 final size:46
Alignment explanation
Indices: 19168--19273 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 46
19158 TGAATATTTT
* * ** **
19168 TATGAAATTTTGATAATTATCCTATTAAATTTTGATAA-CCAC-TC-
1 TATGAAATTTTGATAATT-GCCTATGAAATCGTGATAATAAACTTCA
*
19212 TATGAAATGTTGATAATTGCCTATGAAATCGTGATAATAAACTTCA
1 TATGAAATTTTGATAATTGCCTATGAAATCGTGATAATAAACTTCA
19258 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
19274 CCTAAATATG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 15 0.29
44 19 0.37
45 2 0.04
46 15 0.29
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (46 bp):
TATGAAATTTTGATAATTGCCTATGAAATCGTGATAATAAACTTCA
Found at i:20045 original size:3 final size:3
Alignment explanation
Indices: 20039--20086 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
20029 AAAAAAAAAG
* *
20039 TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20087 CATTATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20673 original size:22 final size:21
Alignment explanation
Indices: 20648--20833 Score: 100
Period size: 22 Copynumber: 8.6 Consensus size: 21
20638 GCACATTATG
20648 AAATTTTGATAACCTTTCGATA
1 AAATTTTGATAACCTTTC-ATA
* * * *
20670 AAATATTGGTTATCACATT-ATA
1 AAAT-TTTGATAAC-CTTTCATA
* *
20692 AAATTTTGATAACCATATCATG
1 AAATTTTGATAACC-TTTCATA
* **
20714 AAATTGTGAT-ACCTCACTATGA
1 AAATTTTGATAACCTTTC-AT-A
20736 AAATTTT-ATAAACCTCCTT-ATA
1 AAATTTTGAT-AACCT--TTCATA
* *
20758 AAATTTTGATAACC-TCCATTTG
1 AAATTTTGATAACCTTTCA--TA
20780 AAATTTTGATAACC--TCATA
1 AAATTTTGATAACCTTTCATA
20799 AAATTTTGATAACCATCTT-ATA
1 AAATTTTGATAACC-T-TTCATA
20821 AAATTTTGATAAC
1 AAATTTTGATAAC
20834 ATACCTACAA
Statistics
Matches: 125, Mismatches: 21, Indels: 36
0.69 0.12 0.20
Matches are distributed among these distances:
19 16 0.13
20 4 0.03
21 16 0.13
22 71 0.57
23 15 0.12
24 3 0.02
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (21 bp):
AAATTTTGATAACCTTTCATA
Found at i:20812 original size:41 final size:41
Alignment explanation
Indices: 20643--20833 Score: 124
Period size: 44 Copynumber: 4.4 Consensus size: 41
20633 TAAGCGCACA
* * * * *
20643 TTATGAAATTTTGATAACCTTTCGATAAAATATTGGTTATCA-C
1 TTATAAAATTTTGATAACC--TC-ATAAAATTTTGATAACCATC
* *
20686 ATTATAAAATTTTGATAACCATATCATGAAATTGTGAT-ACC-TC
1 -TTATAAAATTTTGATAACC---TCATAAAATTTTGATAACCATC
*
20729 ACTATGAAAATTTT-ATAAACCTCCTTATAAAATTTTGATAACC-TCC
1 -TTAT-AAAATTTTGAT-AACCT-C--ATAAAATTTTGATAACCAT-C
*
20775 ATT-TGAAATTTTGATAACCTCATAAAATTTTGATAACCATC
1 -TTATAAAATTTTGATAACCTCATAAAATTTTGATAACCATC
20816 TTATAAAATTTTGATAAC
1 TTATAAAATTTTGATAAC
20834 ATACCTACAA
Statistics
Matches: 122, Mismatches: 13, Indels: 27
0.75 0.08 0.17
Matches are distributed among these distances:
40 2 0.02
41 33 0.27
42 2 0.02
43 10 0.08
44 62 0.51
45 10 0.08
46 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (41 bp):
TTATAAAATTTTGATAACCTCATAAAATTTTGATAACCATC
Found at i:20855 original size:63 final size:62
Alignment explanation
Indices: 20687--20848 Score: 145
Period size: 63 Copynumber: 2.5 Consensus size: 62
20677 GGTTATCACA
* * *
20687 TTATAAAATTTTGATAACCATATCAT-GAAATTGTGAT-ACCTCACTATGAAAATTTTATAAACC
1 TTATAAAATTTTGATAA-CAT-CCATACAAATTTTGATAACCT--C-AT-AAAATTTTATAAACC
20750 TCC
60 TCC
* **
20753 TTATAAAATTTTGATAACCTCCATTTGAAATTTTGATAACCTCATAAAATTTTGAT-AACCAT-C
1 TTATAAAATTTTGATAACATCCA-TACAAATTTTGATAACCTCATAAAATTTT-ATAAACC-TCC
20816 TTATAAAATTTTGATAACATACC-TACAAATTTT
1 TTATAAAATTTTGATAACAT-CCATACAAATTTT
20849 CTATAACTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
62 8 0.10
63 32 0.38
64 9 0.11
65 4 0.05
66 27 0.32
67 4 0.05
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (62 bp):
TTATAAAATTTTGATAACATCCATACAAATTTTGATAACCTCATAAAATTTTATAAACCTCC
Found at i:20882 original size:22 final size:22
Alignment explanation
Indices: 20687--20882 Score: 144
Period size: 22 Copynumber: 9.0 Consensus size: 22
20677 GGTTATCACA
*
20687 TTATAAAATTTTGATAACCAT-A
1 TTATAAAATTTTGATAACC-TCC
* * *
20709 TCATGAAATTGTGAT-ACCTCAC
1 TTATAAAATTTTGATAACCTC-C
20731 -TATGAAAATTTT-ATAAACCTCC
1 TTAT-AAAATTTTGAT-AACCTCC
20753 TTATAAAATTTTGATAACCTCC
1 TTATAAAATTTTGATAACCTCC
*
20775 ATT-TGAAATTTTGATAACCT-C
1 -TTATAAAATTTTGATAACCTCC
20796 --ATAAAATTTTGATAACCAT-C
1 TTATAAAATTTTGATAACC-TCC
*
20816 TTATAAAATTTTGATAACATACC
1 TTATAAAATTTTGATAACCT-CC
* * *
20839 -TA-CAAATTTTCTATAACTTCC
1 TTATAAAATTTT-GATAACCTCC
* *
20860 TTATAGAATTTTGTTAACCTCC
1 TTATAAAATTTTGATAACCTCC
20882 T
1 T
20883 AGAGAACTTT
Statistics
Matches: 139, Mismatches: 18, Indels: 34
0.73 0.09 0.18
Matches are distributed among these distances:
19 15 0.11
20 3 0.02
21 18 0.13
22 84 0.60
23 19 0.14
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (22 bp):
TTATAAAATTTTGATAACCTCC
Found at i:21570 original size:2 final size:2
Alignment explanation
Indices: 21563--21595 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21553 AGTTACTCTT
21563 TA TA 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 TA TA T
21596 TTTGCAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.