Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021547.1 Corchorus olitorius cultivar O-4 contig21580, 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: 35745
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:901 original size:26 final size:26
Alignment explanation
Indices: 865--916 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
855 TGTTCTCTTC
*
865 AAGTTTTTTTTTTCAAATCAAAGCCA
1 AAGTTTTTTTTTTAAAATCAAAGCCA
891 AAGTTTTTTTTTTAAAATCAAAGCCA
1 AAGTTTTTTTTTTAAAATCAAAGCCA
917 GGAGTCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (26 bp):
AAGTTTTTTTTTTAAAATCAAAGCCA
Found at i:927 original size:27 final size:26
Alignment explanation
Indices: 871--930 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
861 CTTCAAGTTT
* **
871 TTTTTTTCAAATCAAAGCCAAAGTTT
1 TTTTTTTAAAATCAAAGCCAAAGTCA
*
897 TTTTTTTAAAATCAAAGCCAGGAGTCA
1 TTTTTTTAAAATCAAAGCCA-AAGTCA
924 TTTTTTT
1 TTTTTTT
931 CTTTTTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (26 bp):
TTTTTTTAAAATCAAAGCCAAAGTCA
Found at i:4622 original size:28 final size:28
Alignment explanation
Indices: 4583--4646 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
4573 CACTTGCGTG
4583 AGCTTGGTGAAGCTCGGTTG-TGTAACA
1 AGCTTGGTGAAGCTCGGTTGCTGTAACA
*
4610 AGCTTGGGTGAAGCTTGGTTGCTGTAAC-
1 AGCTT-GGTGAAGCTCGGTTGCTGTAACA
*
4638 GGCTTGGTG
1 AGCTTGGTG
4647 TAGCCCCGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 9 0.27
28 18 0.55
29 6 0.18
ACGTcount: A:0.17, C:0.14, G:0.38, T:0.31
Consensus pattern (28 bp):
AGCTTGGTGAAGCTCGGTTGCTGTAACA
Found at i:6830 original size:94 final size:94
Alignment explanation
Indices: 6664--6855 Score: 294
Period size: 94 Copynumber: 2.0 Consensus size: 94
6654 ATTCACATAA
* * * *
6664 AATTTGATAGATTGCAGACAAAGTAAGTGTTCTCACTACTTATAAACAGAAAATAGGATATAGCT
1 AATTTGATAAATTGCAGACAAAGTAAGAGTTCTCACAACTTATAAACAGAAAATAAGATATAGCT
* *
6729 TTTAGTTCTCAAAAAAGAAAGTTGGAATC
66 TTAAGTTCTCAAAAAAGAAAGGTGGAATC
* *
6758 AATTTGATAAATTGTAGACAAAGTAAGAGTTCTCACAACTTATAAACAGAAATTAAGATATAGCT
1 AATTTGATAAATTGCAGACAAAGTAAGAGTTCTCACAACTTATAAACAGAAAATAAGATATAGCT
* *
6823 TTAAGTTCTCAAAACAGAAAGGTGGACTC
66 TTAAGTTCTCAAAAAAGAAAGGTGGAATC
6852 AATT
1 AATT
6856 CGGAACAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 88 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (94 bp):
AATTTGATAAATTGCAGACAAAGTAAGAGTTCTCACAACTTATAAACAGAAAATAAGATATAGCT
TTAAGTTCTCAAAAAAGAAAGGTGGAATC
Found at i:13615 original size:11 final size:11
Alignment explanation
Indices: 13572--13609 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13562 TTCCTATATA
*
13572 AAATAAATTAT
1 AAATTAATTAT
13583 CAAA-TAATTAT
1 -AAATTAATTAT
13594 AAATTAATTAT
1 AAATTAATTAT
13605 AAATT
1 AAATT
13610 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:13857 original size:20 final size:20
Alignment explanation
Indices: 13815--13857 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
13805 CCCTTTTTTT
* *
13815 TCCATATTCTATTCTCTCTC
1 TCCATATTCAATTCTCTCAC
13835 TCCATATTTCAATTCTCT-AC
1 TCCATA-TTCAATTCTCTCAC
13855 TCC
1 TCC
13858 CTTGCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.47
Consensus pattern (20 bp):
TCCATATTCAATTCTCTCAC
Found at i:16760 original size:22 final size:22
Alignment explanation
Indices: 16732--16774 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16722 ATTTCCGCAA
* *
16732 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGACAGGACTTGTC
16754 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
16775 TTTGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:16830 original size:21 final size:21
Alignment explanation
Indices: 16804--16845 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
16794 TTCAACAGAC
16804 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
16825 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
16846 TCTGATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGAGTTGT
Found at i:16858 original size:71 final size:71
Alignment explanation
Indices: 16732--16916 Score: 284
Period size: 71 Copynumber: 2.6 Consensus size: 71
16722 ATTTCCGCAA
* * *
16732 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTTTGAATTTTCTTCCGTTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTC
16797 AACAGAC
65 AACAGAC
*
16804 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGAGTTGTTCTG-ATTCTTCTTCCGTCTTTC
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATT-TTCTTCCGTCTTTC
16868 AACAGAC
65 AACAGAC
*
16875 C-AGATCATGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
1 CAAG-TCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
16917 CCTGTTTTTA
Statistics
Matches: 105, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
70 5 0.05
71 79 0.75
72 21 0.20
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (71 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
ACAGAC
Found at i:20603 original size:26 final size:23
Alignment explanation
Indices: 20573--20619 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
20563 CTTGAAAATT
20573 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
20599 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
20620 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:21200 original size:22 final size:22
Alignment explanation
Indices: 21164--21206 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
21154 TTTTCCGCAA
* *
21164 CAAGTCATGGGCAGGAGTTGTC
1 CAAGTCATGGACAGGACTTGTC
*
21186 CAAGTCCTGGACAGGACTTGT
1 CAAGTCATGGACAGGACTTGT
21207 TCTGAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCATGGACAGGACTTGTC
Found at i:21265 original size:21 final size:21
Alignment explanation
Indices: 21239--21278 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21229 AACAGACCAG
*
21239 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
21260 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
21279 CTGTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:27257 original size:15 final size:16
Alignment explanation
Indices: 27226--27265 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
27216 TTACTCTGCT
27226 TTGTTTTCTAATTTAA
1 TTGTTTTCTAATTTAA
*
27242 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAATTTAA
27257 TTGTTTTCT
1 TTGTTTTCT
27266 TTCAACCTCT
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:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAATTTAA
Found at i:33939 original size:25 final size:25
Alignment explanation
Indices: 33893--33941 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
33883 ACCAAAAAGA
*
33893 TTTTTTTATTATTTATTCACTATTT
1 TTTTTTTATTATTTATTAACTATTT
*
33918 TTTTTGTTATT-TTTTTTAACTATT
1 TTTTT-TTATTATTTATTAACTATT
33942 ATCTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTTTTATTATTTATTAACTATTT
Found at i:33971 original size:4 final size:4
Alignment explanation
Indices: 33964--34092 Score: 85
Period size: 4 Copynumber: 34.0 Consensus size: 4
33954 ACTATACATC
* * * *
33964 TATT TATT TA-T T-TT TAAT TA-T TATC TATT TATT TA-C TATT TATC
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
* * * * *
34008 TATT TATT TATT AATT TAAT TA-T TATC TATT TATT TA-C AATT TATCT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT-T
* * *
34055 T-TT TATT TATT AATT TAGT TA-T TATC TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
34093 ATTATTAGTT
Statistics
Matches: 95, Mismatches: 21, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
3 18 0.19
4 75 0.79
5 2 0.02
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:34006 original size:19 final size:19
Alignment explanation
Indices: 33936--34017 Score: 76
Period size: 19 Copynumber: 4.1 Consensus size: 19
33926 ATTTTTTTTA
33936 ACTA-TTATCTATTTATTT
1 ACTATTTATCTATTTATTT
**
33954 ACTATACATCTATTTATTT
1 ACTATTTATCTATTTATTT
*
33973 ATTTTTAATTATTATCTATTTATTT
1 A---CT-A-T-TTATCTATTTATTT
33998 ACTATTTATCTATTTATTT
1 ACTATTTATCTATTTATTT
34017 A
1 A
34018 TTAATTTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
18 4 0.08
19 28 0.55
20 1 0.02
21 1 0.02
22 2 0.04
23 1 0.02
24 1 0.02
25 13 0.25
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (19 bp):
ACTATTTATCTATTTATTT
Found at i:34024 original size:27 final size:27
Alignment explanation
Indices: 33984--34093 Score: 94
Period size: 27 Copynumber: 4.4 Consensus size: 27
33974 TTTTTAATTA
* *
33984 TTATCTATTTATTTACTATTTATCTAT
1 TTATTTATTAATTTACTATTTATCTAT
34011 TTATTTATTAATTTA--A-TTAT-TAT
1 TTATTTATTAATTTACTATTTATCTAT
* * *
34034 CTA--T-TT-ATTTACAATTTATCTTT
1 TTATTTATTAATTTACTATTTATCTAT
*
34057 TTATTTATTAATTTAGT-TATTATCTAT
1 TTATTTATTAATTTACTAT-TTATCTAT
34084 TTATTTATTA
1 TTATTTATTA
34094 TTATTAGTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
19 5 0.08
20 2 0.03
21 2 0.03
22 4 0.06
23 9 0.14
24 4 0.06
25 2 0.03
26 3 0.05
27 35 0.53
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (27 bp):
TTATTTATTAATTTACTATTTATCTAT
Found at i:34033 original size:19 final size:20
Alignment explanation
Indices: 34011--34099 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 20
34001 ATTTATCTAT
34011 TTATTTATTAATTTAATTATTA
1 TTATTTATTAATTT-A-TATTA
* *
34033 TCTATTTATTTACAATTTATCTTT
1 T-TATTTA-TT--AATTTATATTA
*
34057 TTATTTATTAATTTA-GTTA
1 TTATTTATTAATTTATATTA
* *
34076 TTATCTATTTATTTATTATTA
1 TTATTTATTAATTTA-TATTA
34097 TTA
1 TTA
34100 GTTTTTAGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
19 15 0.28
20 6 0.11
21 6 0.11
22 3 0.06
23 12 0.22
24 6 0.11
25 1 0.02
26 5 0.09
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (20 bp):
TTATTTATTAATTTATATTA
Found at i:34043 original size:46 final size:46
Alignment explanation
Indices: 33932--34095 Score: 251
Period size: 46 Copynumber: 3.6 Consensus size: 46
33922 TGTTATTTTT
* **
33932 TTTAACTATTATCTATTTATTTACTATACATCTATTTATTTATT--
1 TTTAATTATTATCTATTTATTTACTATTTATCTATTTATTTATTAA
33976 TTTAATTATTATCTATTTATTTACTATTTATCTATTTATTTATTAA
1 TTTAATTATTATCTATTTATTTACTATTTATCTATTTATTTATTAA
* *
34022 TTTAATTATTATCTATTTATTTACAATTTATCTTTTTATTTATTAA
1 TTTAATTATTATCTATTTATTTACTATTTATCTATTTATTTATTAA
* *
34068 TTTAGTTATTATCTATTTATTTATTATT
1 TTTAATTATTATCTATTTATTTACTATT
34096 ATTAGTTTTT
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
44 41 0.37
46 69 0.63
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (46 bp):
TTTAATTATTATCTATTTATTTACTATTTATCTATTTATTTATTAA
Found at i:34116 original size:28 final size:28
Alignment explanation
Indices: 34058--34127 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
34048 TTTATCTTTT
* * **
34058 TATTTATTAAT-TTAGTTATTATCTATT
1 TATTTATTATTATTAGTTATTAGCTACC
*
34085 TATTTATTATTATTAGTTTTTAGCTACC
1 TATTTATTATTATTAGTTATTAGCTACC
34113 TATTTATCTATTATT
1 TATTTAT-TATTATT
34128 CTCTGTATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 10 0.28
28 19 0.53
29 7 0.19
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.61
Consensus pattern (28 bp):
TATTTATTATTATTAGTTATTAGCTACC
Found at i:34139 original size:24 final size:23
Alignment explanation
Indices: 34112--34173 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
34102 TTTTAGCTAC
*
34112 CTATTTATCTATTATTCTCTGTAT
1 CTATTTATCTATTATT-TCTATAT
34136 CTATTTATCTATTTATTTCTATAT
1 CTATTTATCTA-TTATTTCTATAT
34160 CT-TTT-T-TATTATTT
1 CTATTTATCTATTATTT
34174 TATTTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 6 0.17
21 2 0.06
22 1 0.03
23 3 0.08
24 19 0.53
25 5 0.14
ACGTcount: A:0.21, C:0.13, G:0.02, T:0.65
Consensus pattern (23 bp):
CTATTTATCTATTATTTCTATAT
Found at i:34146 original size:8 final size:8
Alignment explanation
Indices: 33961--34151 Score: 66
Period size: 8 Copynumber: 25.2 Consensus size: 8
33951 TTTACTATAC
33961 ATCTATTT
1 ATCTATTT
*
33969 ATTTATTT
1 ATCTATTT
*
33977 -T-TAATT
1 ATCTATTT
*
33983 AT-TATCT
1 ATCTATTT
*
33990 ATTTATTT
1 ATCTATTT
33998 A-CTATTT
1 ATCTATTT
34005 ATCTATTT
1 ATCTATTT
* *
34013 ATTTATTA
1 ATCTATTT
* *
34021 ATTTAATT
1 ATCTATTT
*
34029 AT-TATCT
1 ATCTATTT
*
34036 ATTTATTT
1 ATCTATTT
*
34044 A-CAATTT
1 ATCTATTT
*
34051 ATCTTTTT
1 ATCTATTT
* *
34059 ATTTATTA
1 ATCTATTT
* *
34067 ATTTAGTT
1 ATCTATTT
*
34075 AT-TATCT
1 ATCTATTT
*
34082 ATTTATTT
1 ATCTATTT
34090 AT-TA-TT
1 ATCTATTT
34096 AT-TAGTTT
1 ATCTA-TTT
**
34104 -T-TAGCT
1 ATCTATTT
*
34110 ACCTATTT
1 ATCTATTT
34118 ATCTA-TT
1 ATCTATTT
* *
34125 ATTCTCTGT
1 A-TCTATTT
34134 ATCTATTT
1 ATCTATTT
34142 ATCTATTT
1 ATCTATTT
34150 AT
1 AT
34152 TTCTATATCT
Statistics
Matches: 136, Mismatches: 35, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
6 11 0.08
7 36 0.26
8 87 0.64
9 2 0.01
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.62
Consensus pattern (8 bp):
ATCTATTT
Done.