Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022142.1 Corchorus olitorius cultivar O-4 contig22175, 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: 6965
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:783 original size:105 final size:106
Alignment explanation
Indices: 603--887 Score: 416
Period size: 107 Copynumber: 2.7 Consensus size: 106
593 AATTTTTCTA
* ** *
603 ACCCTTAAAATAAAATTTTAATTTTAATTTGA--ATTAAATTTAGTG-AATTAGTTATATATTTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGA-TAAACTTAGTGAAATTAGTTATATATTTT
*
665 ATTTCTAAAACCCTATAACAAT-ATTATTAATTATGAAATTT
65 ATTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTC
* *
706 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGATAAACTTAGTGAAATTAGTTGTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGATAAACTTAGTGAAATTAGTTATATATTTTA
*
771 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTC
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTC
* * * *
813 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTTAAATTAGTTTTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGATAAACTTAGTGAAATTAGTTATATATTTTA
878 TTTCTAAAAC
66 TTTCTAAAAC
888 TCTACAATAA
Statistics
Matches: 164, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
103 29 0.18
104 10 0.06
105 38 0.23
107 87 0.53
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGATAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTC
Found at i:927 original size:107 final size:107
Alignment explanation
Indices: 603--929 Score: 371
Period size: 107 Copynumber: 3.1 Consensus size: 107
593 AATTTTTCTA
* ** * *
603 ACCCTTAAAATAAAATTTTAATTTTAATTTGA--ATTAAATTTAGTG-AATTAGTTATATATTTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGA-TAAACTTAGTGAAATTAGTTGTATATTTT
* * * * *
665 ATTTCTAAAACCCTATAAC--AATATTATTAATTATGAAATTT
65 ATTTCTAAAACCCTACAACAAAAAACTATTAATTTTCAAATTT
*
706 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGATAAACTTAGTGAAATTAGTTGTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGATAAACTTAGTGAAATTAGTTGTATATTTTA
* * * * *
771 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTC
66 TTTCTAAAACCCTACAACAAAAAACTATTAATTTTCAAATTT
* * * *
813 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTTAAATTAGTTTTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGATAAACTTAGTGAAATTAGTTGTATATTTTA
* *
878 TTTCTAAAACTCTACAATAAAAAACCT-TTAA-TTTCATAATTT
66 TTTCTAAAACCCTACAACAAAAAA-CTATTAATTTTCA-AATTT
*
920 ACTCTTAAAA
1 ACCCTTAAAA
930 ATTAAATTTC
Statistics
Matches: 194, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
103 29 0.15
104 10 0.05
105 35 0.18
106 4 0.02
107 115 0.59
108 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (107 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGATAAACTTAGTGAAATTAGTTGTATATTTTA
TTTCTAAAACCCTACAACAAAAAACTATTAATTTTCAAATTT
Found at i:1439 original size:31 final size:31
Alignment explanation
Indices: 1380--1450 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
1370 TTATTTAAAT
* *
1380 TATTATTTATATATTAGTAATTAGTAATATA
1 TATTATTTATAAATTAATAATTAGTAATATA
*
1411 TATTATTTATAAAATTAATATTATTAATAATTATA
1 TATTATTTAT-AAATTAATA--ATTAGTAA-TATA
1446 TATTA
1 TATTA
1451 AAGTTGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 10 0.30
32 7 0.21
34 7 0.21
35 9 0.27
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
TATTATTTATAAATTAATAATTAGTAATATA
Found at i:2940 original size:2 final size:2
Alignment explanation
Indices: 2933--2978 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
2923 TATATCCTAC
2933 TA TA TA TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2970 TA -A TA TA TA
1 TA TA TA TA TA
2979 ATTATAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
1 6 0.16
2 32 0.84
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:2966 original size:29 final size:30
Alignment explanation
Indices: 2934--3035 Score: 113
Period size: 29 Copynumber: 3.4 Consensus size: 30
2924 ATATCCTACT
2934 ATATATATAATATAATATAATATAAT-ATA
1 ATATATATAATATAATATAATATAATGATA
*
2963 ATATATATAATAT-ATA-ATTATAATGATA
1 ATATATATAATATAATATAATATAATGATA
*
2991 ATATAATAAGAATAATAATATAAATACTAATGATA
1 ATAT-AT-ATAAT-ATAATAT-AATA-TAATGATA
3026 ATATA-ATAAT
1 ATATATATAAT
3036 GATATAAACC
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
27 7 0.11
28 10 0.16
29 15 0.25
30 4 0.07
31 2 0.03
32 7 0.11
34 4 0.07
35 12 0.20
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (30 bp):
ATATATATAATATAATATAATATAATGATA
Found at i:3007 original size:3 final size:3
Alignment explanation
Indices: 2940--3080 Score: 79
Period size: 3 Copynumber: 49.0 Consensus size: 3
2930 TACTATATAT
*
2940 ATA AT- ATA AT- ATA AT- ATA AT- ATA AT- ATA TATA ATA TATA ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA -ATA ATA
* * * *
2982 ATA ATG ATA AT- ATA ATA AGA ATA ATA AT- ATAA ATA CTA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
* * *
3026 AT- ATA ATA ATG AT- ATA A-A CCCTA ATA ATA ATG ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA ATA ATA
*
3069 AGA ATA ATA ATA
1 ATA ATA ATA ATA
3081 TAAAATCACG
Statistics
Matches: 105, Mismatches: 17, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
2 21 0.20
3 75 0.71
4 8 0.08
5 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3029 original size:35 final size:34
Alignment explanation
Indices: 2940--3084 Score: 158
Period size: 35 Copynumber: 4.3 Consensus size: 34
2930 TACTATATAT
*
2940 ATAATAT-AATATAAT-ATAATATAATATA-TATA
1 ATAATATAAATATAATGATAATATAATA-AGAATA
*
2972 AT-ATATAATTATAATGATAATATAATAAGAATA
1 ATAATATAAATATAATGATAATATAATAAGAATA
3005 ATAATATAAATACTAATGATAATATAATAATGATATA
1 ATAATATAAATA-TAATGATAATATAATAA-GA-ATA
***
3042 A-ACCCT-AATAATAATGATAATATAATAAGAATA
1 ATAATATAAAT-ATAATGATAATATAATAAGAATA
3075 ATAATATAAA
1 ATAATATAAA
3085 ATCACGAACT
Statistics
Matches: 94, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
31 4 0.04
32 10 0.11
33 20 0.21
34 12 0.13
35 39 0.41
36 5 0.05
37 4 0.04
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (34 bp):
ATAATATAAATATAATGATAATATAATAAGAATA
Found at i:3040 original size:29 final size:30
Alignment explanation
Indices: 3001--3068 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
2991 ATATAATAAG
* *
3001 AATAATAATATAAATACTAATGATAAT-AT
1 AATAATAATATAAACACTAATAATAATGAT
* *
3030 AATAATGATATAAACCCTAATAATAATGAT
1 AATAATAATATAAACACTAATAATAATGAT
3060 AAT-ATAATA
1 AATAATAATA
3069 AGAATAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (30 bp):
AATAATAATATAAACACTAATAATAATGAT
Found at i:3056 original size:70 final size:66
Alignment explanation
Indices: 2940--3084 Score: 204
Period size: 70 Copynumber: 2.2 Consensus size: 66
2930 TACTATATAT
* *
2940 ATAATAT-AATATAATATAATATAATATATATAATATATAATTATAATGATAATATAATAAGAAT
1 ATAATATAAATATAATATAATATAATATATATAATACATAATAATAATGATAATATAATAAGAAT
3004 A
66 A
*
3005 ATAATATAAATACTAATGATAATATAATAATGATATAA-ACCCTAATAATAATGATAATATAATA
1 ATAATATAAATA-TAAT-ATAATATAAT-AT-ATATAATA-CATAATAATAATGATAATATAATA
3069 AGAATA
61 AGAATA
3075 ATAATATAAA
1 ATAATATAAA
3085 ATCACGAACT
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
65 7 0.10
66 4 0.06
67 4 0.06
68 10 0.14
69 3 0.04
70 43 0.61
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (66 bp):
ATAATATAAATATAATATAATATAATATATATAATACATAATAATAATGATAATATAATAAGAAT
A
Found at i:3061 original size:6 final size:5
Alignment explanation
Indices: 2933--3083 Score: 103
Period size: 5 Copynumber: 28.0 Consensus size: 5
2923 TATATCCTAC
*
2933 TATATA TATAA TATAA TATAA TATAA TATAA TAT-A TATAA TAT-A TA-AT
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
*
2981 TATAA TGATAA TATAA TAAGAA TAATAA TATAAA TACTAA TGATAA TATAA
1 TATAA T-ATAA TATAA T-ATAA T-ATAA TAT-AA TA-TAA T-ATAA TATAA
* *
3032 TAATGA TATAA -ACCCTAA TAATAA TGATAA TATAA TAAGAA TAATAA TATAA
1 T-ATAA TATAA TA---TAA T-ATAA T-ATAA TATAA T-ATAA T-ATAA TATAA
3084 AATCACGAAC
Statistics
Matches: 121, Mismatches: 9, Indels: 31
0.75 0.06 0.19
Matches are distributed among these distances:
4 10 0.08
5 54 0.45
6 51 0.42
7 5 0.04
9 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:3077 original size:14 final size:14
Alignment explanation
Indices: 2940--3039 Score: 77
Period size: 14 Copynumber: 7.2 Consensus size: 14
2930 TACTATATAT
2940 ATAATATAATATAAT-
1 ATAATAT-A-ATAATG
2955 ATAATATAATATAT-
1 ATAATATAATA-ATG
*
2969 ATAATAT-ATAATT
1 ATAATATAATAATG
*
2982 ATAATGATAAT-ATA
1 ATAAT-ATAATAATG
*
2996 ATAAGAATAATAAT-
1 ATAA-TATAATAATG
*
3010 ATAA-ATACTAATG
1 ATAATATAATAATG
3023 ATAATATAATAATG
1 ATAATATAATAATG
3037 ATA
1 ATA
3040 TAAACCCTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
12 9 0.12
13 15 0.21
14 38 0.52
15 11 0.15
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (14 bp):
ATAATATAATAATG
Found at i:3458 original size:2 final size:2
Alignment explanation
Indices: 3451--3587 Score: 60
Period size: 2 Copynumber: 72.0 Consensus size: 2
3441 AATAATTTAT
* * *
3451 TA TA TA TA T- TT TA TA TA TA TCA TA AA TA TA -A TT TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * * * * *
3491 TT TA CA TA TA T- TT TT TA TA TA TCA TA AA TA -A T- TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
* *
3531 T- TA TA TA TA TA TA TA T- TT TA TA TA T- TT TA TA TA TA TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* *
3571 AA TA TA T- TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
3588 ATAGCATAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
1 10 0.10
2 88 0.85
3 6 0.06
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3460 original size:9 final size:9
Alignment explanation
Indices: 3448--3586 Score: 81
Period size: 9 Copynumber: 15.3 Consensus size: 9
3438 AAAAATAATT
3448 TATTATATA
1 TATTATATA
*
3457 TATTTTATA
1 TATTATATA
3466 TA-TATCATA
1 TATTAT-ATA
*
3475 -AATATA-A
1 TATTATATA
3482 T-TTATATA
1 TATTATATA
*
3490 TTTTACATATA
1 TATT--ATATA
* *
3501 TTTTTTATA
1 TATTATATA
* *
3510 TATCATAAA
1 TATTATATA
*
3519 TAATTAAATA
1 T-ATTATATA
3529 TATTATATA
1 TATTATATA
3538 TA-TATATA
1 TATTATATA
*
3546 TTTTATATA
1 TATTATATA
*
3555 TTTTATATA
1 TATTATATA
*
3564 TATCATAAATA
1 TAT--TATATA
*
3575 TATTTTATA
1 TATTATATA
3584 TAT
1 TAT
3587 AATAGCATAA
Statistics
Matches: 102, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
7 5 0.05
8 13 0.13
9 61 0.60
10 6 0.06
11 17 0.17
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTATATA
Found at i:3466 original size:11 final size:11
Alignment explanation
Indices: 3450--3587 Score: 90
Period size: 11 Copynumber: 12.8 Consensus size: 11
3440 AAATAATTTA
3450 TTATATATATT
1 TTATATATATT
*
3461 TTATATATATC
1 TTATATATATT
* * *
3472 ATAAATATA-A
1 TTATATATATT
3482 TT-TATATATT
1 TTATATATATT
*
3492 TTACATATATT
1 TTATATATATT
*
3503 TT-T-TATATA
1 TTATATATATT
* * *
3512 TCATAAATA-A
1 TTATATATATT
*
3522 TTAAATATATT
1 TTATATATATT
3533 ATATATATATATAT
1 -T-TATATATAT-T
3547 TT-TATATATT
1 TTATATATATT
*
3557 TTATATATATC
1 TTATATATATT
* *
3568 ATAAATATATT
1 TTATATATATT
3579 TTATATATA
1 TTATATATA
3588 ATAGCATAAT
Statistics
Matches: 95, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
9 11 0.12
10 14 0.15
11 58 0.61
12 2 0.02
13 9 0.09
14 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
TTATATATATT
Found at i:4046 original size:41 final size:41
Alignment explanation
Indices: 4001--4081 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
3991 TTGCCTATAA
* *
4001 ATAAATAGATGATACTTCTCATCATTTTTGCAAAGTTGTAT
1 ATAAATAGATGACACTTCTCATCATTTTTGCAAAATTGTAT
4042 ATAAATAGATGACACTTCTCATCATTTTTGCAAAATTGTA
1 ATAAATAGATGACACTTCTCATCATTTTTGCAAAATTGTA
4082 CTCCCTCTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (41 bp):
ATAAATAGATGACACTTCTCATCATTTTTGCAAAATTGTAT
Found at i:4904 original size:22 final size:22
Alignment explanation
Indices: 4874--4918 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4864 AAAATATAAA
4874 AAAAATATTATCTTATTATTTT
1 AAAAATATTATCTTATTATTTT
*
4896 AAAATTATTATCTTATTATTTT
1 AAAAATATTATCTTATTATTTT
4918 A
1 A
4919 TCGAAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
AAAAATATTATCTTATTATTTT
Found at i:5791 original size:13 final size:13
Alignment explanation
Indices: 5773--5808 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5763 TCTGAACCCC
5773 TTCTTTTTTTTCT
1 TTCTTTTTTTTCT
*
5786 TTCTTTTTTTGCT
1 TTCTTTTTTTTCT
5799 TT-TTTTTTTT
1 TTCTTTTTTTT
5809 ATTTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (13 bp):
TTCTTTTTTTTCT
Found at i:5814 original size:13 final size:12
Alignment explanation
Indices: 5776--5814 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5766 GAACCCCTTC
5776 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
5788 CTTTTTTTGCTTT
1 -TTTTTTTTCTTT
*
5801 TTTTTTTTATTT
1 TTTTTTTTCTTT
5813 TT
1 TT
5815 GAAAGAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.87
Consensus pattern (12 bp):
TTTTTTTTCTTT
Done.