Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012589.1 Corchorus olitorius cultivar O-4 contig12622, 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: 52836
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1263 original size:27 final size:27
Alignment explanation
Indices: 1232--1291 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
1222 TCTTCTCCAG
*
1232 TCTTAGTTTT-AAGTCGAAAACTTCTGA
1 TCTTA-TTTTGAAGGCGAAAACTTCTGA
* **
1259 TCTTATTTTGGAGGCTTAAACTTCTGA
1 TCTTATTTTGAAGGCGAAAACTTCTGA
1286 TCTTAT
1 TCTTAT
1292 ATGGTTCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (27 bp):
TCTTATTTTGAAGGCGAAAACTTCTGA
Found at i:3129 original size:18 final size:19
Alignment explanation
Indices: 3090--3130 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3080 CTTGTGAATG
*
3090 GAGAAAATCATTGTTGGGA
1 GAGAAAACCATTGTTGGGA
3109 GAGAAAACCATTGTT-GGA
1 GAGAAAACCATTGTTGGGA
3127 GAGA
1 GAGA
3131 TTTACCCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.39, C:0.07, G:0.32, T:0.22
Consensus pattern (19 bp):
GAGAAAACCATTGTTGGGA
Found at i:10286 original size:15 final size:15
Alignment explanation
Indices: 10266--10296 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10256 TTTCCTTTAT
10266 TTTCAAATAAGTCCC
1 TTTCAAATAAGTCCC
*
10281 TTTCAATTAAGTCCC
1 TTTCAAATAAGTCCC
10296 T
1 T
10297 GAAACTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
TTTCAAATAAGTCCC
Found at i:11184 original size:20 final size:18
Alignment explanation
Indices: 11161--11206 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
11151 ATATATATAT
11161 ATATATATAAAATTCCGATC
1 ATATATATAAAATT--GATC
**
11181 ATATATATATGATTGATC
1 ATATATATAAAATTGATC
11199 ATATATAT
1 ATATATAT
11207 GTATGTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
20 12 0.50
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (18 bp):
ATATATATAAAATTGATC
Found at i:11189 original size:2 final size:2
Alignment explanation
Indices: 11139--11169 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11129 CCAAATGTCC
11139 AT AT AT 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 AT AT AT A
11170 AAATTCCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29019 original size:24 final size:24
Alignment explanation
Indices: 28991--29066 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
28981 TATATTATAT
28991 ATGTAATTATTTGATACACTAACC
1 ATGTAATTATTTGATACACTAACC
* *
29015 ATGTAA--ATTTTAGT-CA-TATTA-T
1 ATGTAATTATTTGA-TACACTA--ACC
*
29037 ATATAATTATTTGATACACTAACC
1 ATGTAATTATTTGATACACTAACC
29061 ATGTAA
1 ATGTAA
29067 ATTTTAGTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
21 2 0.05
22 12 0.32
23 4 0.11
24 18 0.47
25 2 0.05
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (24 bp):
ATGTAATTATTTGATACACTAACC
Found at i:29045 original size:46 final size:47
Alignment explanation
Indices: 28982--29075 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 47
28972 TATTATATAT
28982 ATATTATATATGTAATTATTTGATACACTAACCATGTAAATTTTAGTC
1 ATATTATATA-GTAATTATTTGATACACTAACCATGTAAATTTTAGTC
29030 ATATTATATA-TAATTATTTGATACACTAACCATGTAAATTTTAGTC
1 ATATTATATAGTAATTATTTGATACACTAACCATGTAAATTTTAGTC
29076 TGCACAGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 36 0.78
48 10 0.22
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (47 bp):
ATATTATATAGTAATTATTTGATACACTAACCATGTAAATTTTAGTC
Found at i:35819 original size:8 final size:8
Alignment explanation
Indices: 35808--35837 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
35798 CTTTTTATTT
35808 TTTTTTTA
1 TTTTTTTA
35816 TTTTTTTA
1 TTTTTTTA
35824 -TTTTTTA
1 TTTTTTTA
35831 TTTTTTT
1 TTTTTTT
35838 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:35823 original size:19 final size:18
Alignment explanation
Indices: 35799--35841 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
35789 TTCTTCGTCC
*
35799 TTTTTATTTTTTTTTTATT
1 TTTTTATTTTTTATTT-TT
35818 TTTTTATTTTTTATTTTT
1 TTTTTATTTTTTATTTTT
35836 TTTTTA
1 TTTTTA
35842 AAATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTATTTTTTATTTTT
Found at i:35829 original size:15 final size:14
Alignment explanation
Indices: 35805--35840 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
35795 GTCCTTTTTA
35805 TTTTTTTTTTATTT
1 TTTTTTTTTTATTT
35819 TTTTATTTTTTATTT
1 TTTT-TTTTTTATTT
35834 TTTTTTT
1 TTTTTTT
35841 AAAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (14 bp):
TTTTTTTTTTATTT
Found at i:35848 original size:26 final size:26
Alignment explanation
Indices: 35799--35848 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
35789 TTCTTCGTCC
***
35799 TTTTTATTTTTTTTTTATTTTTTTAT
1 TTTTTATTTTTTTTTTAAAATTTTAT
35825 TTTTTATTTTTTTTTTAAAATTTT
1 TTTTTATTTTTTTTTTAAAATTTT
35849 TTTACAGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (26 bp):
TTTTTATTTTTTTTTTAAAATTTTAT
Found at i:37265 original size:1 final size:1
Alignment explanation
Indices: 37259--37286 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
37249 AGGTCGTAGC
37259 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
37287 CAATCATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38708 original size:49 final size:49
Alignment explanation
Indices: 38655--38750 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
38645 TCGATACCAG
* * *
38655 AGGAGGGATCGACTTACACTCGGTGTAAAACAATTTCTTTTACACCCAA
1 AGGAGGGATCAACTTACACCCGGTCTAAAACAATTTCTTTTACACCCAA
38704 AGGAGGGATCAACTTACACCCGGTCTAAAACAATTTCTTTTACACCC
1 AGGAGGGATCAACTTACACCCGGTCTAAAACAATTTCTTTTACACCC
38751 TTTTCTAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (49 bp):
AGGAGGGATCAACTTACACCCGGTCTAAAACAATTTCTTTTACACCCAA
Found at i:38848 original size:84 final size:79
Alignment explanation
Indices: 38707--38867 Score: 241
Period size: 84 Copynumber: 2.0 Consensus size: 79
38697 CACCCAAAGG
* * *
38707 AGGGATCAACTTACACCCGGTCTAAAACAATTTCTTTTACACCCTTTTCTAATTTAATCTAATCT
1 AGGGATAAACTTACAACCGGTCTAAAACAATTTCTTTTACACCCTTTTCTAACTTAA--T--T-T
38772 AGGATTAATATTTTTAAGA
61 AGGATTAATATTTTTAAGA
*
38791 AGGGATAAACTTACAACCGGTGTAAAACAATTTCTTTTACACCCTTTTCTAACTTAATTTAGGAT
1 AGGGATAAACTTACAACCGGTCTAAAACAATTTCTTTTACACCCTTTTCTAACTTAATTTAGGAT
38856 TAATATTTTTAA
66 TAATATTTTTAA
38868 AAATCAATCG
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
79 18 0.25
80 1 0.01
82 1 0.01
84 53 0.73
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (79 bp):
AGGGATAAACTTACAACCGGTCTAAAACAATTTCTTTTACACCCTTTTCTAACTTAATTTAGGAT
TAATATTTTTAAGA
Found at i:39674 original size:45 final size:45
Alignment explanation
Indices: 39620--39716 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 45
39610 AGTGCATTAG
* *
39620 CTAA-ATTCTACTCCTTCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
* *
39664 CTAATATTCTACTTCTCCATCTCTATATAATTCATCAAAATAAAA
1 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
39709 CTAATATT
1 CTAATATT
39717 AATTGTTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
44 4 0.08
45 44 0.92
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (45 bp):
CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:43466 original size:25 final size:25
Alignment explanation
Indices: 43438--43485 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
43428 AAGTCAAGAG
43438 CCATGCTATTTTATCAAAATTCTAA
1 CCATGCTATTTTATCAAAATTCTAA
43463 CCATGCTATTTTATCAAAATTCT
1 CCATGCTATTTTATCAAAATTCT
43486 GATATGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (25 bp):
CCATGCTATTTTATCAAAATTCTAA
Found at i:45069 original size:21 final size:19
Alignment explanation
Indices: 45043--45102 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
45033 TAGAGATTAG
45043 TTACACTAAAAATTGATACCA
1 TTACACTAAAAATTGAT--CA
45064 TTACACTAAATAA-TGATCA
1 TTACACTAAA-AATTGATCA
* *
45083 TTACACCAAACATTGATCA
1 TTACACTAAAAATTGATCA
45102 T
1 T
45103 ATTATCATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 18 0.51
21 14 0.40
22 2 0.06
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (19 bp):
TTACACTAAAAATTGATCA
Found at i:45386 original size:15 final size:15
Alignment explanation
Indices: 45366--45394 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45356 AAACGACGTA
45366 ATGAAGTGGAAGATC
1 ATGAAGTGGAAGATC
45381 ATGAAGTGGAAGAT
1 ATGAAGTGGAAGAT
45395 TATTATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.34, T:0.21
Consensus pattern (15 bp):
ATGAAGTGGAAGATC
Found at i:48302 original size:13 final size:15
Alignment explanation
Indices: 48284--48315 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
48274 CCTTATTACT
48284 TTAT-AACATA-ACA
1 TTATAAACATATACA
48297 TTATAAACATATACA
1 TTATAAACATATACA
48312 TTAT
1 TTAT
48316 TACTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 6 0.35
15 7 0.41
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
TTATAAACATATACA
Found at i:50123 original size:39 final size:40
Alignment explanation
Indices: 50070--50150 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
50060 TTTAATTCCT
50070 ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
* * *
50110 ATGTAATA-CTATAATAACTTAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
50149 AT
1 AT
50151 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
Found at i:50168 original size:24 final size:25
Alignment explanation
Indices: 50141--50187 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
50131 AATACTTACA
* *
50141 TTAA-TTAAATTCTTAGGTATTTTT
1 TTAATTTAAATTCGTAGGCATTTTT
50165 TTAATTTAAATTCGTAGGCATTT
1 TTAATTTAAATTCGTAGGCATTT
50188 GTGCAAACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (25 bp):
TTAATTTAAATTCGTAGGCATTTTT
Found at i:50501 original size:204 final size:200
Alignment explanation
Indices: 50258--50666 Score: 739
Period size: 204 Copynumber: 2.0 Consensus size: 200
50248 TTTCTTAATA
50258 ATAAATAAATTCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATTCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
50323 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACT-ACTTTTTTT-GTATAGTT-T-TATATATAATAA
50388 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACAT
127 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACAT
50453 TCACCATTG
192 TCACCATTG
50462 ATAAATAAATT-GGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
1 ATAAATAAATTCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
50526 TAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTGTATAGTTTTATATATAATAATAA
65 TAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTGTATAGTTTTATATATAATAATAA
*
50591 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCA
130 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATTCA
50656 CCATTG
195 CCATTG
50662 ATAAA
1 ATAAA
50667 GTTATTAAGC
Statistics
Matches: 201, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
200 89 0.44
201 1 0.00
202 8 0.04
203 13 0.06
204 90 0.45
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (200 bp):
ATAAATAAATTCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTGTATAGTTTTATATATAATAATAAT
GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATTCAC
CATTG
Found at i:51203 original size:36 final size:36
Alignment explanation
Indices: 51156--51225 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
51146 GAGATTTTAG
* *
51156 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
51192 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
51226 GGTTATTGAA
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:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.