Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017597.1 Corchorus olitorius cultivar O-4 contig17630, 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: 64724
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:246 original size:29 final size:30
Alignment explanation
Indices: 204--261 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
194 TTTAATTATG
* *
204 ATTTTAAAAAATATG-TGGGCCTTGGACAT
1 ATTTTAAAAAATATGAGGGGCCTTAGACAT
*
233 ATTTTTAAAAATATGAGGGGCCTTAGACA
1 ATTTTAAAAAATATGAGGGGCCTTAGACA
262 AAAGTTGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (30 bp):
ATTTTAAAAAATATGAGGGGCCTTAGACAT
Found at i:6442 original size:2 final size:2
Alignment explanation
Indices: 6426--6469 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
6416 ATGTTAGATC
6426 AT AT AT CAT AT -T AT AT AT AT AT AT AT AT AT AT AT 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
6468 AT
1 AT
6470 CTGAAATCCC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8155 original size:2 final size:2
Alignment explanation
Indices: 8148--8242 Score: 181
Period size: 2 Copynumber: 47.5 Consensus size: 2
8138 AAATCTGTAA
8148 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
8190 AC AC AC AC AC AC AC AC TC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
8232 AC AC AC AC AC A
1 AC AC AC AC AC A
8243 TATATATATA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:8247 original size:2 final size:2
Alignment explanation
Indices: 8242--8266 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8232 ACACACACAC
8242 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
8267 GTTAGTTAGT
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:8438 original size:109 final size:109
Alignment explanation
Indices: 8247--8465 Score: 438
Period size: 109 Copynumber: 2.0 Consensus size: 109
8237 CACACATATA
8247 TATATATATATATATATATAGTTAGTTAGTCACTGTAGATTATAATTAGAAGAAATAAGAGCTTG
1 TATATATATATATATATATAGTTAGTTAGTCACTGTAGATTATAATTAGAAGAAATAAGAGCTTG
8312 AAAAACTTTAAAAGAAAACTTTACCTTTAACGAGTTTATCAAAC
66 AAAAACTTTAAAAGAAAACTTTACCTTTAACGAGTTTATCAAAC
8356 TATATATATATATATATATAGTTAGTTAGTCACTGTAGATTATAATTAGAAGAAATAAGAGCTTG
1 TATATATATATATATATATAGTTAGTTAGTCACTGTAGATTATAATTAGAAGAAATAAGAGCTTG
8421 AAAAACTTTAAAAGAAAACTTTACCTTTAACGAGTTTATCAAAC
66 AAAAACTTTAAAAGAAAACTTTACCTTTAACGAGTTTATCAAAC
8465 T
1 T
8466 TATGTATCTC
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (109 bp):
TATATATATATATATATATAGTTAGTTAGTCACTGTAGATTATAATTAGAAGAAATAAGAGCTTG
AAAAACTTTAAAAGAAAACTTTACCTTTAACGAGTTTATCAAAC
Found at i:13211 original size:16 final size:17
Alignment explanation
Indices: 13187--13222 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
13177 GTTACTTTCT
*
13187 TTTCTTTTCCTT-CCTA
1 TTTCATTTCCTTCCCTA
13203 TTTCATTTCCTTCCCTA
1 TTTCATTTCCTTCCCTA
13220 TTT
1 TTT
13223 TCTTTCTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTCATTTCCTTCCCTA
Found at i:13228 original size:17 final size:17
Alignment explanation
Indices: 13186--13228 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
13176 TGTTACTTTC
*
13186 TTTTCTTTTCCTTCCTA
1 TTTTCATTTCCTTCCTA
13203 -TTTCATTTCCTTCCCTA
1 TTTTCATTTCCTT-CCTA
13220 TTTTC-TTTC
1 TTTTCATTTC
13229 TATGCAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTCATTTCCTTCCTA
Found at i:20605 original size:18 final size:18
Alignment explanation
Indices: 20582--20616 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20572 CAACTTTATT
20582 AATATTACCCTAACAATG
1 AATATTACCCTAACAATG
20600 AATATTACCCTAACAAT
1 AATATTACCCTAACAAT
20617 CGGTACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (18 bp):
AATATTACCCTAACAATG
Found at i:22760 original size:53 final size:53
Alignment explanation
Indices: 22680--22789 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
22670 TGTTTATTCA
22680 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATACAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATACAATGAACT
*
22733 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATACAATGAACT
22786 ATTG
1 ATTG
22790 GATTTAAAGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATACAATGAACT
Found at i:27956 original size:18 final size:19
Alignment explanation
Indices: 27933--27976 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
27923 GACAAGAGTC
27933 GACCAT-CTCCAAGTTCAA
1 GACCATACTCCAAGTTCAA
*
27951 GACCATCAACTCCAAGTTCTA
1 GACCAT--ACTCCAAGTTCAA
27972 GACCA
1 GACCA
27977 CAAATCAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
21 16 0.73
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.20
Consensus pattern (19 bp):
GACCATACTCCAAGTTCAA
Found at i:42844 original size:43 final size:43
Alignment explanation
Indices: 42783--42873 Score: 182
Period size: 43 Copynumber: 2.1 Consensus size: 43
42773 ACAAAATAAG
42783 GTAAAACCCCGTCATGTATGGAAAAACTCACAGAATATTAGCT
1 GTAAAACCCCGTCATGTATGGAAAAACTCACAGAATATTAGCT
42826 GTAAAACCCCGTCATGTATGGAAAAACTCACAGAATATTAGCT
1 GTAAAACCCCGTCATGTATGGAAAAACTCACAGAATATTAGCT
42869 GTAAA
1 GTAAA
42874 CCCTACATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (43 bp):
GTAAAACCCCGTCATGTATGGAAAAACTCACAGAATATTAGCT
Found at i:46628 original size:17 final size:17
Alignment explanation
Indices: 46606--46641 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
46596 ATACAAAGAG
46606 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
46623 CTATCTGGTCTAACAAA
1 CTATCTAGTATAACAAA
46640 CT
1 CT
46642 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Found at i:48434 original size:18 final size:18
Alignment explanation
Indices: 48411--48479 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
48401 CAAAGGTTCT
*
48411 TGCGGCAGCGGAACATCC
1 TGCGGCAGTGGAACATCC
* * *
48429 TGCGGCAATGCAACATTC
1 TGCGGCAGTGGAACATCC
* *
48447 TGCAGTAGTGGAACATCC
1 TGCGGCAGTGGAACATCC
*
48465 TGCGGTAGTGGAACA
1 TGCGGCAGTGGAACA
48480 ATATTTTGTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.26, C:0.25, G:0.30, T:0.19
Consensus pattern (18 bp):
TGCGGCAGTGGAACATCC
Found at i:51271 original size:17 final size:17
Alignment explanation
Indices: 51249--51284 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
51239 TGATTTGTAA
51249 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
51266 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
51283 AG
1 AG
51285 CTCTTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:53493 original size:21 final size:21
Alignment explanation
Indices: 53469--53535 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
53459 AATTCTCTGT
53469 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
53490 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
53511 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
53532 AAAT
1 AAAT
53536 CCAGATCCTG
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:53515 original size:42 final size:42
Alignment explanation
Indices: 53456--53536 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
53446 GCTAAGTCTT
53456 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
53498 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
53537 CAGATCCTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:53672 original size:55 final size:56
Alignment explanation
Indices: 53602--53707 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 56
53592 TTTATTTTGT
* **
53602 AGAATAATCAAGTAGAGATA-GGGGATAGGATTTACCATAACATTTATTGTGTGAA
1 AGAATAATCAAGTAGAAATAGGGGGATAAAATTTACCATAACATTTATTGTGTGAA
* **
53657 AGAATAATTAAGTAGAAATAGGGGGATAAAATTTATTATAACATTTATTGT
1 AGAATAATCAAGTAGAAATAGGGGGATAAAATTTACCATAACATTTATTGT
53708 ATGGAGGGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 18 0.41
56 26 0.59
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (56 bp):
AGAATAATCAAGTAGAAATAGGGGGATAAAATTTACCATAACATTTATTGTGTGAA
Found at i:54641 original size:12 final size:11
Alignment explanation
Indices: 54601--54658 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 11
54591 AGAAAATATT
54601 AAATTAAATT-
1 AAATTAAATTA
54611 AAATTAAA-TA
1 AAATTAAATTA
54621 AAATAATAAATTA
1 AAAT--TAAATTA
*
54634 AAATATAAATAA
1 AAAT-TAAATTA
*
54646 AAATCAAA-TA
1 AAATTAAATTA
54656 AAA
1 AAA
54659 GAACTAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 1 0.02
10 16 0.39
11 3 0.07
12 15 0.37
13 6 0.15
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATTAAATTA
Found at i:54654 original size:17 final size:17
Alignment explanation
Indices: 54610--54658 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
54600 TAAATTAAAT
*
54610 TAAATTAAATAAAATAA
1 TAAATAAAATAAAATAA
54627 TAAATTAAAATATAAATAA
1 TAAA-TAAAATA-AAATAA
*
54646 -AAATCAAATAAAA
1 TAAATAAAATAAAA
54659 GAACTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 3 0.11
17 10 0.36
18 9 0.32
19 6 0.21
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATAAAATAAAATAA
Found at i:55030 original size:14 final size:14
Alignment explanation
Indices: 55011--55043 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55001 TTTCTCTTGC
55011 TTTCTC-TCTAGGT
1 TTTCTCTTCTAGGT
55024 ATTTCTCTTCTAGGT
1 -TTTCTCTTCTAGGT
55039 TTTCT
1 TTTCT
55044 TTGTTCTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.09, C:0.21, G:0.12, T:0.58
Consensus pattern (14 bp):
TTTCTCTTCTAGGT
Found at i:61234 original size:6 final size:6
Alignment explanation
Indices: 61223--61247 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61213 AAGTTCACTC
61223 CAAACT CAAACT CAAACT CAAACT C
1 CAAACT CAAACT CAAACT CAAACT C
61248 CACCGTTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (6 bp):
CAAACT
Found at i:61597 original size:18 final size:18
Alignment explanation
Indices: 61574--61608 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
61564 ATATATATAT
61574 ATATACACACACACACAC
1 ATATACACACACACACAC
61592 ATATACACACACACACA
1 ATATACACACACACACA
61609 ACAAAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.11
Consensus pattern (18 bp):
ATATACACACACACACAC
Found at i:61774 original size:3 final size:3
Alignment explanation
Indices: 61768--61793 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61758 GATGCAAAAA
61768 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
61794 GATTATCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:64421 original size:36 final size:36
Alignment explanation
Indices: 64374--64443 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
64364 TTCAATAACC
* *
64374 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
64410 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
64444 CTAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.