Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014348.1 Corchorus olitorius cultivar O-4 contig14381, 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: 57748
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1103 original size:29 final size:30
Alignment explanation
Indices: 1050--1107 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1040 GGTTTATAGG
* *
1050 GCCAAAATTGGTAGTTTAAAGGCTTATTTA
1 GCCAAAATTGGAAGTTGAAAGGCTTATTTA
*
1080 GCCAAAATT-GAAGTTGAGAGGCTTATTT
1 GCCAAAATTGGAAGTTGAAAGGCTTATTT
1108 GACGGTTAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.34
Consensus pattern (30 bp):
GCCAAAATTGGAAGTTGAAAGGCTTATTTA
Found at i:22342 original size:29 final size:26
Alignment explanation
Indices: 22290--22342 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 26
22280 TTGGGGTAAA
*
22290 AATTACTTTTCATTTTTTTGAGATGT
1 AATTACTTTTCATTTTTTAGAGATGT
22316 AATTACTTTTCATCTTTGATTAGAGAT
1 AATTACTTTTCAT-TTT--TTAGAGAT
22343 ATTAAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 13 0.57
27 3 0.13
29 7 0.30
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.53
Consensus pattern (26 bp):
AATTACTTTTCATTTTTTAGAGATGT
Found at i:29898 original size:3 final size:3
Alignment explanation
Indices: 29890--29929 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
29880 ATGAACTATA
29890 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
29930 AACATTCCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:30437 original size:33 final size:33
Alignment explanation
Indices: 30399--30534 Score: 99
Period size: 33 Copynumber: 4.2 Consensus size: 33
30389 GTATATATTT
30399 TATTATAAATATTAAATATATTTAAGATATATG
1 TATTATAAATATTAAATATATTTAAGATATATG
*
30432 TATTATATATATT--ATATA-TT-AG-TA-ATCAG
1 TATTATAAATATTAAATATATTTAAGATATAT--G
* * * * * *
30461 T-TT-TTATTAATTATATATATATAAATATATATTT
1 TATTATAAAT-ATTAAATATAT-TTAAGATATA-TG
*
30495 TATTATAAATATTAAATATATTTAAGATATATA
1 TATTATAAATATTAAATATATTTAAGATATATG
30528 TATTATA
1 TATTATA
30535 TATTAGTAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 26
0.66 0.11 0.22
Matches are distributed among these distances:
27 4 0.05
28 7 0.09
29 4 0.05
30 7 0.09
31 5 0.06
32 1 0.01
33 21 0.27
34 11 0.14
35 13 0.17
36 4 0.05
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.50
Consensus pattern (33 bp):
TATTATAAATATTAAATATATTTAAGATATATG
Found at i:30438 original size:9 final size:9
Alignment explanation
Indices: 30399--30537 Score: 57
Period size: 9 Copynumber: 16.1 Consensus size: 9
30389 GTATATATTT
*
30399 TATTATAAA
1 TATTATATA
*
30408 TATTAAATA
1 TATTATATA
30417 TATT-TA-A
1 TATTATATA
* *
30424 GA-TATATG
1 TATTATATA
30432 TATTATATA
1 TATTATATA
30441 TATTATATA
1 TATTATATA
*
30450 TTAGTA-ATCA
1 -TATTATAT-A
*
30460 GT-TTTTAT-
1 -TATTATATA
30468 TAATTATATA
1 T-ATTATATA
*
30478 TA-TATAAA
1 TATTATATA
*
30486 TA-TATATTT
1 TATTATA-TA
*
30495 TATTATAAA
1 TATTATATA
*
30504 TATTAAATA
1 TATTATATA
30513 TATT-TA-A
1 TATTATATA
*
30520 GA-TATATA
1 TATTATATA
30528 TATTATATA
1 TATTATATA
30537 T
1 T
30538 TAGTAATTAG
Statistics
Matches: 94, Mismatches: 22, Indels: 28
0.65 0.15 0.19
Matches are distributed among these distances:
6 2 0.02
7 9 0.10
8 16 0.17
9 54 0.57
10 13 0.14
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (9 bp):
TATTATATA
Found at i:30535 original size:22 final size:21
Alignment explanation
Indices: 30475--30538 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
30465 TATTAATTAT
* *
30475 ATATATATAAATATATATTTTA
1 ATATATAT-ATTATATATTTAA
* *
30497 TTATAAATATTAAATATATTTAA
1 ATATATATATT--ATATATTTAA
30520 GATATATATATTATATATT
1 -ATATATATATTATATATT
30539 AGTAATTAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 2 0.06
22 13 0.39
23 9 0.27
24 9 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATATATATTATATATTTAA
Found at i:30772 original size:3 final size:3
Alignment explanation
Indices: 30764--30794 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30754 ACATTAGGTA
30764 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
30795 TAGGGAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:32606 original size:170 final size:170
Alignment explanation
Indices: 32324--32666 Score: 650
Period size: 170 Copynumber: 2.0 Consensus size: 170
32314 ATACCTTTGC
32324 GAAAATGTTTTATTTGAGGTTCCAATCGTTCAATTGGTTGAACCAAGCCATAACGTTCCAATTTT
1 GAAAATGTTTTATTTGAGGTTCCAATCGTTCAATTGGTTGAACCAAGCCATAACGTTCCAATTTT
32389 AGCCCAAATAAGGGGCTGGAGCCTGGTGTGTTTTTTAACCATTTTAACTATGGGTAATTATTTGA
66 AGCCCAAATAAGGGGCTGGAGCCTGGTGTGTTTTTTAACCATTTTAACTATGGGTAATTATTTGA
32454 TACACCGCGGTGTAACTTTTGGACTACACAAGCGCGTTGT
131 TACACCGCGGTGTAACTTTTGGACTACACAAGCGCGTTGT
* *
32494 GAAAATGTTTTATTTGAGGTTCTAATCGTTGAATTGGTTGAACCAAGCCATAACGTTCCAATTTT
1 GAAAATGTTTTATTTGAGGTTCCAATCGTTCAATTGGTTGAACCAAGCCATAACGTTCCAATTTT
32559 AGCCCAAATAAGGGGCTGGAGCCTGGTGTGTTTTTTAACCATTTTAACTATGGGTAATTATTTGA
66 AGCCCAAATAAGGGGCTGGAGCCTGGTGTGTTTTTTAACCATTTTAACTATGGGTAATTATTTGA
* *
32624 TACACCGCGGTGTAACTTTTGGACTCCACAAGCGGGTTGT
131 TACACCGCGGTGTAACTTTTGGACTACACAAGCGCGTTGT
32664 GAA
1 GAA
32667 GTTGATACAT
Statistics
Matches: 169, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 169 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (170 bp):
GAAAATGTTTTATTTGAGGTTCCAATCGTTCAATTGGTTGAACCAAGCCATAACGTTCCAATTTT
AGCCCAAATAAGGGGCTGGAGCCTGGTGTGTTTTTTAACCATTTTAACTATGGGTAATTATTTGA
TACACCGCGGTGTAACTTTTGGACTACACAAGCGCGTTGT
Found at i:33945 original size:9 final size:8
Alignment explanation
Indices: 33897--33969 Score: 59
Period size: 7 Copynumber: 9.8 Consensus size: 8
33887 CCGAATACTA
*
33897 ATATATAT
1 ATATATTT
33905 ATATA-TT
1 ATATATTT
*
33912 ATATTTTT
1 ATATATTT
33920 ATAT-TTT
1 ATATATTT
33927 ATAT-TTT
1 ATATATTT
33934 ATATATTAT
1 ATATATT-T
*
33943 ATATATCT
1 ATATATTT
*
33951 -GAT-TTT
1 ATATATTT
33957 AT-TATTT
1 ATATATTT
33964 ATATAT
1 ATATAT
33970 ATTAAAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
6 3 0.06
7 26 0.49
8 17 0.32
9 7 0.13
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (8 bp):
ATATATTT
Found at i:34514 original size:12 final size:12
Alignment explanation
Indices: 34492--34520 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34482 ATAAAGGTAC
34492 TTATT-ATTTGA
1 TTATTGATTTGA
34503 TTATTGATTTGA
1 TTATTGATTTGA
34515 TTATTG
1 TTATTG
34521 GCTTTTGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (12 bp):
TTATTGATTTGA
Found at i:35139 original size:31 final size:30
Alignment explanation
Indices: 35106--35202 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 30
35096 ATATATAATC
35106 AATTGACAGATTTTGTTAAGTAGAGGGACTC-
1 AATTGACAGA-TTTGTTAAGTAGAGGGAC-CA
* *
35137 AATTGACACCAAATTG-TAAGTAGAGGGACCA
1 AATTGACA--GATTTGTTAAGTAGAGGGACCA
35168 AATTGACAG-TTT-TTATAGTAGAGGGACCA
1 AATTGACAGATTTGTTA-AGTAGAGGGACCA
35197 AATTGA
1 AATTGA
35203 TCCTGTACAG
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
28 4 0.07
29 19 0.33
30 1 0.02
31 29 0.51
32 3 0.05
33 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (30 bp):
AATTGACAGATTTGTTAAGTAGAGGGACCA
Found at i:39223 original size:42 final size:42
Alignment explanation
Indices: 39176--39264 Score: 117
Period size: 45 Copynumber: 2.1 Consensus size: 42
39166 CATTACCTAA
*
39176 ATTCTA-CACCATCTCTAGGTAATTCATCAAAATAAAGCCAAT
1 ATTCTACCACCATCTCTAGATAATTCATCAAAATAAA-CCAAT
* *
39218 ATTCTACTCCCCCATCTCTAGATAATTCATCAAAATAAACTAAT
1 ATTCTA--CCACCATCTCTAGATAATTCATCAAAATAAACCAAT
39262 ATT
1 ATT
39265 GATTGTTGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
42 6 0.15
44 7 0.17
45 28 0.68
ACGTcount: A:0.39, C:0.25, G:0.04, T:0.31
Consensus pattern (42 bp):
ATTCTACCACCATCTCTAGATAATTCATCAAAATAAACCAAT
Found at i:41138 original size:26 final size:27
Alignment explanation
Indices: 41099--41156 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
41089 CTCATTATAG
* *
41099 GGGTAAAATCGTAACTTTATCAATCA-
1 GGGTAAAATAGTAAATTTATCAATCAC
* * *
41125 GGGTAATATAGTAAATTTGTCCATCAC
1 GGGTAAAATAGTAAATTTATCAATCAC
41152 GGGTA
1 GGGTA
41157 TTTTGGTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (27 bp):
GGGTAAAATAGTAAATTTATCAATCAC
Found at i:56417 original size:17 final size:17
Alignment explanation
Indices: 56395--56428 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56385 TATAATATAA
56395 TGAAACTTACATGGATT
1 TGAAACTTACATGGATT
56412 TGAAACTTACATGGATT
1 TGAAACTTACATGGATT
56429 AAGATCTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TGAAACTTACATGGATT
Done.