Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023313.1 Corchorus olitorius cultivar O-4 contig23346, 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: 35925
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1155 original size:49 final size:49
Alignment explanation
Indices: 1040--1183 Score: 182
Period size: 49 Copynumber: 2.9 Consensus size: 49
1030 ATAAACACTA
* * **
1040 ATTTATATTACTAATTTGTTTGGCCCTTTAAAATGTAATAAACATTAGGTTAT
1 ATTTAAATTACTAATTTCTTTGGCCCTTTTTAATGTAAT----ATTAGGTTAT
*
1093 ATTTAAATTACTAATTTCTTTGGCTCTTTTTAATGTAATATTAGGTTAT
1 ATTTAAATTACTAATTTCTTTGGCCCTTTTTAATGTAATATTAGGTTAT
* *
1142 ATTTAGATTACTAATTTCCTTGGCCCTTTTTAATGTAA-ATTA
1 ATTTAAATTACTAATTTCTTTGGCCCTTTTTAATGTAATATTA
1184 ATAATTTCTT
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
48 4 0.05
49 45 0.54
53 34 0.41
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (49 bp):
ATTTAAATTACTAATTTCTTTGGCCCTTTTTAATGTAATATTAGGTTAT
Found at i:4023 original size:20 final size:21
Alignment explanation
Indices: 3988--4026 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3978 TTTCCTTTCT
*
3988 TTTCTTTTCTCTTTTCTTTTA
1 TTTCTTTTCACTTTTCTTTTA
4009 TTTCTTTT-ACTTTTCTTT
1 TTTCTTTTCACTTTTCTTT
4027 AAAATTTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTTTCACTTTTCTTTTA
Found at i:6400 original size:136 final size:139
Alignment explanation
Indices: 6235--6492 Score: 366
Period size: 136 Copynumber: 1.9 Consensus size: 139
6225 ATTTAAGAAA
* * *
6235 TATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGATA-AAACTAAA
1 TATATTTAAAAAATTATAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATACAAA-TAAA
6299 ATA-TGTATAA-G-TATATT-A-TAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAGATTGTA
65 ATAGT-TATAAGGATATATTAATTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAGATTGTA
6359 AAACTATAAAAG
128 AAACTATAAAAG
* * * *
6371 TATATTTAAAAAATTATAATGTATGTAAGTTTTTTAATTAAAATAGTAAAATGGTACAAATTAAA
1 TATATTTAAAAAATTATAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATACAAATAAAA
6436 TAGTTATAAGGATATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
66 TAGTTATAAGGATATATTA-A-TTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
6493 AACTATAAAA
Statistics
Matches: 107, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
136 61 0.57
137 5 0.05
138 6 0.06
140 1 0.01
141 25 0.23
142 9 0.08
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (139 bp):
TATATTTAAAAAATTATAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATACAAATAAAA
TAGTTATAAGGATATATTAATTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAGATTGTAAAA
CTATAAAAG
Found at i:6777 original size:2 final size:2
Alignment explanation
Indices: 6772--6796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6762 AAAGCTCTAC
6772 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6797 CACTACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7072 original size:56 final size:57
Alignment explanation
Indices: 6984--7093 Score: 186
Period size: 56 Copynumber: 1.9 Consensus size: 57
6974 ATCCGTTTCT
* *
6984 TTTCACACAATAAATGTTATAATAAATCCTATC-CTCTTATCTCTACTTAATTACTC
1 TTTCACACAATAAATGTTATAATAAATCCTATCACCCCTATCTCTACTTAATTACTC
*
7040 TTTCACACAATAAATGTTATAATAAATTCTATCACCCCTATCTCTACTTAATTA
1 TTTCACACAATAAATGTTATAATAAATCCTATCACCCCTATCTCTACTTAATTA
7094 TTCTACAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
56 32 0.64
57 18 0.36
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (57 bp):
TTTCACACAATAAATGTTATAATAAATCCTATCACCCCTATCTCTACTTAATTACTC
Found at i:7430 original size:27 final size:27
Alignment explanation
Indices: 7391--7444 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
7381 TGATCAATCC
*
7391 ATTATAAATAAGACTGTTTTTAGAAAA
1 ATTATAAACAAGACTGTTTTTAGAAAA
* *
7418 ATTATAGACAAGATTGTTTTTAGAAAA
1 ATTATAAACAAGACTGTTTTTAGAAAA
7445 CAAATGGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (27 bp):
ATTATAAACAAGACTGTTTTTAGAAAA
Found at i:7805 original size:12 final size:12
Alignment explanation
Indices: 7788--7813 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7778 CAAACAATTT
7788 AATTCGAATAGA
1 AATTCGAATAGA
7800 AATTCGAATAGA
1 AATTCGAATAGA
7812 AA
1 AA
7814 ATTGTGATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (12 bp):
AATTCGAATAGA
Found at i:9877 original size:13 final size:13
Alignment explanation
Indices: 9847--9901 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
9837 TTCACATCAT
*
9847 TATATCATCATAGC
1 TATATCAT-ATATC
9861 -ATATCATATATC
1 TATATCATATATC
9873 TATATC-TATATC
1 TATATCATATATC
*
9885 TATA-CTATCTATC
1 TATATC-ATATATC
9898 TATA
1 TATA
9902 CTATATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 1 0.03
12 14 0.39
13 21 0.58
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (13 bp):
TATATCATATATC
Found at i:9878 original size:6 final size:6
Alignment explanation
Indices: 9861--9907 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
9851 TCATCATAGC
9861 ATATCAT ATATCT ATATCT ATATCT ATA-CT ATCTATCT ATA-CT ATAT
1 ATATC-T ATATCT ATATCT ATATCT ATATCT A--TATCT ATATCT ATAT
9908 TAAAAAGTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 8 0.22
6 18 0.50
7 7 0.19
8 3 0.08
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (6 bp):
ATATCT
Found at i:11696 original size:22 final size:22
Alignment explanation
Indices: 11656--11697 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11646 GTTTATAATA
* *
11656 TTCTTGGGTCATTCGGGTTAAC
1 TTCTCGGGTCATTCAGGTTAAC
*
11678 TTCTCGGGTCATTTAGGTTA
1 TTCTCGGGTCATTCAGGTTA
11698 CGGATTTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (22 bp):
TTCTCGGGTCATTCAGGTTAAC
Found at i:18163 original size:16 final size:16
Alignment explanation
Indices: 18142--18172 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18132 TCATAACCAA
18142 AACAATTAGAAAAACC
1 AACAATTAGAAAAACC
*
18158 AACAATTATAAAAAC
1 AACAATTAGAAAAAC
18173 AATATCATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.16, G:0.03, T:0.16
Consensus pattern (16 bp):
AACAATTAGAAAAACC
Found at i:22968 original size:12 final size:12
Alignment explanation
Indices: 22951--22980 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
22941 AATATATAAA
22951 TTTATTTTTAAT
1 TTTATTTTTAAT
22963 TTTATTTTTAAT
1 TTTATTTTTAAT
22975 TTTATT
1 TTTATT
22981 ATAAATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTTTTAAT
Found at i:23086 original size:17 final size:15
Alignment explanation
Indices: 23054--23083 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
23044 CTAACAATTT
23054 TCTAAAAAAATTAAG
1 TCTAAAAAAATTAAG
23069 TCTAAGAAAAATTAA
1 TCTAA-AAAAATTAA
23084 AGTTTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (15 bp):
TCTAAAAAAATTAAG
Found at i:23487 original size:22 final size:22
Alignment explanation
Indices: 23459--23500 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
23449 ATGGGAAGTC
23459 TGGACAAAAGAAAATATATTAT
1 TGGACAAAAGAAAATATATTAT
* *
23481 TGGACAAAAGATAATTTATT
1 TGGACAAAAGAAAATATATT
23501 TTCTAGCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (22 bp):
TGGACAAAAGAAAATATATTAT
Found at i:29686 original size:2 final size:2
Alignment explanation
Indices: 29679--29754 Score: 72
Period size: 2 Copynumber: 39.5 Consensus size: 2
29669 CGACCGAATA
*
29679 AT AT AT AT AT AT AT A- AT CAT AT AT AT TT AT AT -T 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
* *
29720 GAT A- AT GT AT TT AT AT -T AT AT AT AT AT AT A- AT AT A
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29755 AATAATATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
1 5 0.08
2 52 0.85
3 4 0.07
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29700 original size:10 final size:9
Alignment explanation
Indices: 29679--29762 Score: 59
Period size: 9 Copynumber: 9.2 Consensus size: 9
29669 CGACCGAATA
29679 ATATAT-AT
1 ATATATAAT
29687 ATATATAAT
1 ATATATAAT
29696 CATATAT-AT
1 -ATATATAAT
*
29705 TTATATTATAT
1 ATATA-TA-AT
29716 ATATGATAAT
1 ATAT-ATAAT
* *
29726 GTAT-TTAT
1 ATATATAAT
29734 AT-TATATAT
1 ATATATA-AT
29743 ATATATAAT
1 ATATATAAT
*
29752 ATAAATAAT
1 ATATATAAT
29761 AT
1 AT
29763 TTATTTTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
7 1 0.02
8 15 0.25
9 21 0.35
10 15 0.25
11 7 0.12
12 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (9 bp):
ATATATAAT
Found at i:29715 original size:31 final size:29
Alignment explanation
Indices: 29679--29766 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 29
29669 CGACCGAATA
29679 ATATATATATATATAATCATATATATTTAT
1 ATATATATATATATAAT-ATATATATTTAT
* *
29709 AT-TATATATATGATAATGTATTTATATTAT
1 ATATATATATAT-ATAATATATATAT-TTAT
29739 ATATATATATAATATAA-ATA-ATATTTAT
1 ATATATATAT-ATATAATATATATATTTAT
29767 TTTTAAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
28 4 0.08
29 18 0.36
30 15 0.30
31 11 0.22
32 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (29 bp):
ATATATATATATATAATATATATATTTAT
Found at i:29730 original size:25 final size:27
Alignment explanation
Indices: 29679--29754 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 27
29669 CGACCGAATA
29679 ATATATATATATATAATCATATATATTT
1 ATAT-TATATATATAATCATATATATTT
* *
29707 ATATTATATATATGAT-A-ATGTATTT
1 ATATTATATATATAATCATATATATTT
*
29732 ATATTATATATATATATAATATA
1 ATATTATATATATA-ATCATATA
29755 AATAATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 20 0.49
26 3 0.07
27 12 0.29
28 6 0.15
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (27 bp):
ATATTATATATATAATCATATATATTT
Found at i:31276 original size:25 final size:27
Alignment explanation
Indices: 31236--31290 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
31226 AAATGTTAAA
*
31236 TCAATTGTTATATTCTGAATTTCTT-T
1 TCAATTGTAATATTCTGAATTTCTTAT
31262 TCAATTG-AATATTCTGAATTTCTTAT
1 TCAATTGTAATATTCTGAATTTCTTAT
31288 TCA
1 TCA
31291 TTCTGAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (27 bp):
TCAATTGTAATATTCTGAATTTCTTAT
Found at i:35326 original size:15 final size:17
Alignment explanation
Indices: 35288--35339 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 17
35278 AAAGGTTAGG
35288 TATTTATATTACATATA
1 TATTTATATTACATATA
35305 T-TATTATA-TA-ATATA
1 TAT-TTATATTACATATA
35320 TATTTAT-TT-CATTATA
1 TATTTATATTACA-TATA
35336 TATT
1 TATT
35340 ATTTCAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
15 12 0.40
16 12 0.40
17 6 0.20
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTATATTACATATA
Found at i:35326 original size:18 final size:17
Alignment explanation
Indices: 35288--35374 Score: 56
Period size: 18 Copynumber: 5.1 Consensus size: 17
35278 AAAGGTTAGG
*
35288 TATTTATAT-T-ACATA
1 TATTTATATATAATATA
35303 TA-TTATTATATAATATA
1 TATTTA-TATATAATATA
* *
35320 TATTTATTTCATTATATA
1 TATTTATAT-ATAATATA
*
35338 TTATTTCAGAT-TAATATA
1 -TATTT-ATATATAATATA
*
35356 TATATATATATTAATATA
1 TATTTATATA-TAATATA
35374 T
1 T
35375 TAAATATTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
14 3 0.05
15 5 0.09
16 4 0.07
17 12 0.22
18 24 0.44
19 5 0.09
20 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (17 bp):
TATTTATATATAATATA
Found at i:35341 original size:15 final size:16
Alignment explanation
Indices: 35316--35345 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35306 TATTATATAA
35316 TATATATTTATTTCAT
1 TATATATTTATTTCAT
35332 TATATA-TTATTTCA
1 TATATATTTATTTCA
35346 GATTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATATTTATTTCAT
Done.