Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013842.1 Corchorus olitorius cultivar O-4 contig13875, 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: 56124
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1833 original size:32 final size:32
Alignment explanation
Indices: 1797--1942 Score: 220
Period size: 32 Copynumber: 4.5 Consensus size: 32
1787 GTGTGGAAAG
* *
1797 AAAACGCCCTTATTTAGCGGCGTTTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAGAGAAC
*
1829 AAAACGCCCTTATTTAACGGCGTCTAGAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAGAGAAC
*
1861 AAAACGCCCTTATTTAGCGGCGTCTAGACAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAGAGAAC
**
1893 AAAACGCCCTTATTTAGCGGCGTCTTTAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAGAGAAC
1925 AAAACGCCGCTATATTTA
1 AAAACGCC-CT-TATTTA
1943 ACTGCTTTTA
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 96 0.92
33 2 0.02
34 6 0.06
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTAGAGAAC
Found at i:4647 original size:19 final size:19
Alignment explanation
Indices: 4607--4647 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
4597 TCTGTAATCA
*
4607 CACGCCCCTAGCGGATTCG
1 CACGCCCCTAGCGGATGCG
*
4626 CACGCCCCTAGCGGATGGG
1 CACGCCCCTAGCGGATGCG
4645 CAC
1 CAC
4648 ATCAGGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.41, G:0.29, T:0.12
Consensus pattern (19 bp):
CACGCCCCTAGCGGATGCG
Found at i:10043 original size:15 final size:16
Alignment explanation
Indices: 10019--10058 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
10009 AGAGGTTGAA
*
10019 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
10034 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
10050 AGAAAACAA
1 AGAAAACAA
10059 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:11438 original size:29 final size:31
Alignment explanation
Indices: 11401--11460 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
11391 AATTCTTTCC
* *
11401 TCTTGAAATAATTCTTC-AAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAAATGGTCTTCAAA
11430 TCTTCAAATAAGTCTTCAAATGGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAATGGTCTTCAAA
11461 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 15 0.56
30 3 0.11
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (31 bp):
TCTTCAAATAAGTCTTCAAATGGTCTTCAAA
Found at i:11880 original size:25 final size:25
Alignment explanation
Indices: 11852--11916 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
11842 TATCATTCAG
*
11852 GAACTGTCTTTAGATCCATCTTCGT
1 GAACTGTCTTCAGATCCATCTTCGT
* *
11877 GAACTGTCTTCAGATCCTTCTTTGT
1 GAACTGTCTTCAGATCCATCTTCGT
11902 GAACTGTCTTCAGAT
1 GAACTGTCTTCAGAT
11917 TCAATCTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (25 bp):
GAACTGTCTTCAGATCCATCTTCGT
Found at i:11953 original size:86 final size:86
Alignment explanation
Indices: 11799--12063 Score: 370
Period size: 86 Copynumber: 3.1 Consensus size: 86
11789 ACCATACCAA
* * * * *
11799 TTCAGATCCTTCTTCGTGAACAGTCTTCAGATTTACTCTTAAATATCATTCAGGAACTGTCTTTA
1 TTCAGATCCTTCTTTGTGAACTGTCTTCAGATTCACTCTTAAATATCTTTCAGGAACTGTCTTCA
11864 GATCCATCTTCGTGAACTGTC
66 GATCCATCTTCGTGAACTGTC
* * * *
11885 TTCAGATCCTTCTTTGTGAACTGTCTTCAGATTCAATCTTAAATATCTTTTAGGAGCTGCCTTCA
1 TTCAGATCCTTCTTTGTGAACTGTCTTCAGATTCACTCTTAAATATCTTTCAGGAACTGTCTTCA
11950 GATCCATCTTCGTGAACTGTC
66 GATCCATCTTCGTGAACTGTC
* * * * * *
11971 TTCAGATCCTTCTTTGTGAACTATCTTTAGATTCACTATTTAATATCATTCCA-AAACTGTCTTC
1 TTCAGATCCTTCTTTGTGAACTGTCTTCAGATTCACTCTTAAATATC-TTTCAGGAACTGTCTTC
*
12035 AGATCCATTTTCGTGAACTGTC
65 AGATCCATCTTCGTGAACTGTC
12057 TTCAGAT
1 TTCAGAT
12064 TCACTCTCAA
Statistics
Matches: 158, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 155 0.98
87 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (86 bp):
TTCAGATCCTTCTTTGTGAACTGTCTTCAGATTCACTCTTAAATATCTTTCAGGAACTGTCTTCA
GATCCATCTTCGTGAACTGTC
Found at i:11974 original size:25 final size:25
Alignment explanation
Indices: 11945--12002 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
11935 TAGGAGCTGC
*
11945 CTTCAGATCCATCTTCGTGAACTGT
1 CTTCAGATCCATCTTCGTGAACTAT
* *
11970 CTTCAGATCCTTCTTTGTGAACTAT
1 CTTCAGATCCATCTTCGTGAACTAT
*
11995 CTTTAGAT
1 CTTCAGAT
12003 TCACTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (25 bp):
CTTCAGATCCATCTTCGTGAACTAT
Found at i:12150 original size:36 final size:36
Alignment explanation
Indices: 12105--12224 Score: 136
Period size: 36 Copynumber: 3.6 Consensus size: 36
12095 CAGATCCATC
*
12105 TTCGTGAACTGTCTTCAGATTCACTTTCAAATATCA
1 TTCGGGAACTGTCTTCAGATTCACTTTCAAATATCA
*
12141 TTCGGGAACTGTCTTCAGA-TC-CATT----T-TCA
1 TTCGGGAACTGTCTTCAGATTCACTTTCAAATATCA
*
12170 -T---GAACTGTCTTCAGATTCACTCTCAAATATCA
1 TTCGGGAACTGTCTTCAGATTCACTTTCAAATATCA
12202 TTCGGGAACTGTCTTCAGATTCA
1 TTCGGGAACTGTCTTCAGATTCA
12225 TCTTCATGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
25 14 0.20
26 2 0.03
27 2 0.03
28 1 0.01
29 3 0.04
30 1 0.01
31 1 0.01
32 3 0.04
33 1 0.01
34 3 0.04
35 2 0.03
36 36 0.52
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (36 bp):
TTCGGGAACTGTCTTCAGATTCACTTTCAAATATCA
Found at i:12176 original size:147 final size:146
Alignment explanation
Indices: 11799--12185 Score: 424
Period size: 147 Copynumber: 2.6 Consensus size: 146
11789 ACCATACCAA
* * * * *
11799 TTCAGATCCTTCTTCGTGAACAGTCTTCAGATTTACTCTTAAATATCATTCAGGAACTGTCTTTA
1 TTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACT-TTAAATATCATTCGGGAACTGTCTTAA
* * * *
11864 GATCCATCTTCGTGAACTGTCTTCAGATCCTTCTTTGTGAACTGTCTTCAGATTCAATCTTAAAT
65 GATCCATTTTCATGAACTGTCTTCAGATCCTTCTTCGTGAACTGTCTTCAGATTCAATCTCAAAT
* * *
11929 ATCTTTTAGGAGCTGCC
130 ATCATTCAGGAACTGCC
* * * * * *** *
11946 TTCAGATCCATCTTCGTGAACTGTCTTCAGATCCTTCTTTGTGAACTATCTTTAGATTCACTAT-
1 TTCAGATCCATCTTCGTGAACTGTCTTCAGATTC-AC-TT-T-AAATATCATTCG-GGAACTGTC
* * * *
12010 TTAATAT-CA-TTCCA-AAACTGTCTTCAGATCCATT-TTCGTGAACTGTCTTCAGATTCACTCT
61 TTAAGATCCATTTTCATGAACTGTCTTCAGATCC-TTCTTCGTGAACTGTCTTCAGATTCAATCT
*
12071 CAAATATCATTCAGGAATTGCC
125 CAAATATCATTCAGGAACTGCC
*
12093 TTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTTTCAAATATCATTCGGGAACTGTCTTCA
1 TTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTTT-AAATATCATTCGGGAACTGTCTTAA
12158 GATCCATTTTCATGAACTGTCTTCAGAT
65 GATCCATTTTCATGAACTGTCTTCAGAT
12186 TCACTCTCAA
Statistics
Matches: 190, Mismatches: 40, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
143 4 0.02
144 15 0.08
145 4 0.02
146 5 0.03
147 135 0.71
148 6 0.03
149 4 0.02
150 13 0.07
151 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (146 bp):
TTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTTTAAATATCATTCGGGAACTGTCTTAAG
ATCCATTTTCATGAACTGTCTTCAGATCCTTCTTCGTGAACTGTCTTCAGATTCAATCTCAAATA
TCATTCAGGAACTGCC
Found at i:12275 original size:61 final size:61
Alignment explanation
Indices: 11963--12286 Score: 418
Period size: 61 Copynumber: 5.3 Consensus size: 61
11953 CCATCTTCGT
* * * * * *
11963 GAACTGTCTTCAGATCCTTCTTTGTGAACTATCTTTAGATTCACTATTTAATATCATTCCA-
1 GAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTCTTAAATATCATT-CAG
* * *
12024 AAACTGTCTTCAGATCCATTTTCGTGAACTGTCTTCAGATTCACTCTCAAATATCATTCAG
1 GAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTCTTAAATATCATTCAG
* * *
12085 GAATTGCCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACT-TTCAAATATCATTCGG
1 GAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTCTT-AAATATCATTCAG
* * * *
12146 GAACTGTCTTCAGATCCATTTTCATGAACTGTCTTCAGATTCACTCTCAAATATCATTCGG
1 GAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTCTTAAATATCATTCAG
* * *
12207 GAACTGTCTTCAGATTCATCTTCATGAACTGACTTCAGATTCACTCTTAAATATCATTCAG
1 GAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTCTTAAATATCATTCAG
* * *
12268 GAGCTGTCTCCAGACCCAT
1 GAACTGTCTTCAGATCCAT
12287 GAATTAGTCT
Statistics
Matches: 231, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
60 3 0.01
61 227 0.98
62 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (61 bp):
GAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTCTTAAATATCATTCAG
Found at i:20542 original size:6 final size:6
Alignment explanation
Indices: 20531--20560 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
20521 GCAACCCAAT
20531 TTTTAA TTTTAA TTTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA -TTTTAA TTTTAA TTTTA
20561 TCTAACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:20546 original size:13 final size:13
Alignment explanation
Indices: 20528--20559 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
20518 GAGGCAACCC
20528 AATTTTTAATTTT
1 AATTTTTAATTTT
20541 AATTTTTAATTTT
1 AATTTTTAATTTT
20554 AATTTT
1 AATTTT
20560 ATCTAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTTTAATTTT
Found at i:22309 original size:12 final size:12
Alignment explanation
Indices: 22292--22317 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22282 GATAATTTCA
22292 TTTCTTCTAGTT
1 TTTCTTCTAGTT
22304 TTTCTTCTAGTT
1 TTTCTTCTAGTT
22316 TT
1 TT
22318 AGGCTAAGGG
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTCTTCTAGTT
Found at i:23111 original size:15 final size:16
Alignment explanation
Indices: 23081--23120 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
23071 TTACTTTGCT
23081 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
23097 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
23112 TTGTTTTCT
1 TTGTTTTCT
23121 TTCAATCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:23418 original size:33 final size:32
Alignment explanation
Indices: 23364--23450 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
23354 TCTTAGTCTC
* *
23364 TGCG-TTTTCTCT-AAAAAAAAAAAACTTTTTT
1 TGCGTTTTTTTCTAAAAAAAAAAAAAC-TTCTT
23395 TGCGTTTTTTTCTAAAAAAAAAAAAAACTTCTT
1 TGCGTTTTTTTCT-AAAAAAAAAAAAACTTCTT
23428 TGCGTTTTTAATT-TAAAAAAAAA
1 TGCGTTTTT--TTCTAAAAAAAAA
23451 TTTAGTTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
31 4 0.08
32 7 0.14
33 22 0.45
34 14 0.29
35 2 0.04
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (32 bp):
TGCGTTTTTTTCTAAAAAAAAAAAAACTTCTT
Found at i:27716 original size:11 final size:12
Alignment explanation
Indices: 27690--27716 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27680 AGATAATTTC
27690 TTTTCTTCTAGT
1 TTTTCTTCTAGT
27702 TTTTCTTCTAGT
1 TTTTCTTCTAGT
27714 TTT
1 TTT
27717 AGGCTAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTCTTCTAGT
Found at i:28510 original size:15 final size:16
Alignment explanation
Indices: 28480--28519 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
28470 TTACTTTGCT
28480 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
28496 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
28511 TTGCTTTCT
1 TTGTTTTCT
28520 TTCAATCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:34306 original size:22 final size:23
Alignment explanation
Indices: 34258--34308 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
34248 TTTCTGATTC
** *
34258 ATTGTTTTCTTTAATTTTTTTTG
1 ATTGTTTTCTTTAATTAATTTTA
*
34281 ATTGTTTTC-TTAGTTAATTTTA
1 ATTGTTTTCTTTAATTAATTTTA
34303 ATTGTT
1 ATTGTT
34309 AGTTTGCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.18, C:0.04, G:0.10, T:0.69
Consensus pattern (23 bp):
ATTGTTTTCTTTAATTAATTTTA
Found at i:39020 original size:27 final size:27
Alignment explanation
Indices: 38967--39038 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
38957 ATCCAGGGGT
* *
38967 ATTTTGGTCATTTGCACGTCTAGGGGC
1 ATTTTGGTCATTTGCAAGTCTAAGGGC
*
38994 ATTTTGGTCATTTGCATATTC-AAGGGC
1 ATTTTGGTCATTTGCA-AGTCTAAGGGC
*
39021 ATTATGGTCATTT-CAAGT
1 ATTTTGGTCATTTGCAAGT
39039 TCACTCTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 2 0.05
26 2 0.05
27 33 0.85
28 2 0.05
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (27 bp):
ATTTTGGTCATTTGCAAGTCTAAGGGC
Found at i:40675 original size:21 final size:21
Alignment explanation
Indices: 40651--40754 Score: 190
Period size: 21 Copynumber: 5.0 Consensus size: 21
40641 ACTCACAACG
40651 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
40672 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
*
40693 ATGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
40714 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
*
40735 AGGTTTCAAGCTCATTGGAG
1 AAGTTTCAAGCTCATTGGAG
40755 TTGCCTAAGG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 80 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (21 bp):
AAGTTTCAAGCTCATTGGAGA
Found at i:53820 original size:9 final size:8
Alignment explanation
Indices: 53798--53823 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
53788 CAATAAGATA
53798 AGAAAAAT
1 AGAAAAAT
53806 AGAAAAAT
1 AGAAAAAT
53814 AGAAAAAT
1 AGAAAAAT
53822 AG
1 AG
53824 GATCTTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (8 bp):
AGAAAAAT
Done.