Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002326.1 Corchorus capsularis cultivar CVL-1 contig02332, 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, 737
Length: 1229
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Found at i:770 original size:15 final size:16
Alignment explanation
Indices: 740--814 Score: 91
Period size: 15 Copynumber: 4.7 Consensus size: 16
730 TTAGAAATTA
*
740 TATTATATATATATTTC
1 TATT-TATAAATATTTC
757 TATTTA-AAATATTTC
1 TATTTATAAATATTTC
*
772 TATTTA-GAATATTTC
1 TATTTATAAATATTTC
*
787 TATTTATAAATTATATC
1 TATTTATAAA-TATTTC
804 TATTTATAAAT
1 TATTTATAAAT
815 TATCTAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
15 28 0.54
16 5 0.10
17 19 0.37
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (16 bp):
TATTTATAAATATTTC
Found at i:832 original size:32 final size:32
Alignment explanation
Indices: 761--832 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
751 TATTTCTATT
* * * *
761 TAAAATATTTCTATTTAGAATATTTCTATTTA
1 TAAATTATATCTATTTAGAATATTTCTAATAA
*
793 TAAATTATATCTATTTATAA-ATTATCTAATAA
1 TAAATTATATCTATTTAGAATATT-TCTAATAA
*
825 TATATTAT
1 TAAATTAT
833 TATTAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 3 0.09
32 30 0.91
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (32 bp):
TAAATTATATCTATTTAGAATATTTCTAATAA
Found at i:850 original size:14 final size:13
Alignment explanation
Indices: 831--926 Score: 70
Period size: 14 Copynumber: 6.9 Consensus size: 13
821 ATAATATATT
831 ATTATTAAATTAA
1 ATTATTAAATTAA
*
844 GATTATTAAGTTATTAT
1 -ATTATTAA---ATTAA
*
861 ATTATTAAGTTATA
1 ATTATTAAATTA-A
875 ATTTATTAAATTTAA
1 A-TTATTAAA-TTAA
*
890 ATTACTAAATT--
1 ATTATTAAATTAA
901 ATTATTATAATTAA
1 ATTATTA-AATTAA
*
915 ATTACTAAATTA
1 ATTATTAAATTA
927 TTATTATAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 19
0.72 0.08 0.21
Matches are distributed among these distances:
11 6 0.09
12 4 0.06
13 10 0.15
14 22 0.33
15 9 0.14
16 11 0.17
17 4 0.06
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (13 bp):
ATTATTAAATTAA
Found at i:866 original size:16 final size:16
Alignment explanation
Indices: 845--969 Score: 68
Period size: 16 Copynumber: 8.0 Consensus size: 16
835 TTAAATTAAG
*
845 ATTATTAAGTTATTAT
1 ATTATTAAGTTATAAT
861 ATTATTAAGTTATAAT
1 ATTATTAAGTTATAAT
*
877 -TTATTAAATT-TAA-
1 ATTATTAAGTTATAAT
* * *
890 ATTACTAAATTATTATT
1 ATTATTAAGTTA-TAAT
* *
907 ATAATTAAATTACTAA-
1 ATTATTAAGTTA-TAAT
923 ATTATT-A-TTATAAT
1 ATTATTAAGTTATAAT
* *
937 AATATT-AGATATTAGAT
1 ATTATTAAGTTA-TA-AT
954 ATTATTATA-TTATAAT
1 ATTATTA-AGTTATAAT
970 TATATCTAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
13 3 0.03
14 21 0.24
15 12 0.14
16 26 0.30
17 21 0.24
18 2 0.02
19 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTATTAAGTTATAAT
Found at i:943 original size:25 final size:25
Alignment explanation
Indices: 828--936 Score: 115
Period size: 25 Copynumber: 4.6 Consensus size: 25
818 CTAATAATAT
*
828 ATTATTATTA-AATTAAGATTATTAA
1 ATTATTATTATAATTAA-ATTACTAA
* * *
853 GTTATTA-TATTATTAAGTTA-T-A
1 ATTATTATTATAATTAAATTACTAA
875 A-T-TTATTA-AATTTAAATTACTAA
1 ATTATTATTATAA-TTAAATTACTAA
898 ATTATTATTATAATTAAATTACTAA
1 ATTATTATTATAATTAAATTACTAA
923 ATTATTATTATAAT
1 ATTATTATTATAAT
937 AATATTAGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
20 4 0.06
21 10 0.14
22 2 0.03
23 3 0.04
24 6 0.09
25 43 0.61
26 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (25 bp):
ATTATTATTATAATTAAATTACTAA
Found at i:971 original size:28 final size:30
Alignment explanation
Indices: 898--971 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 30
888 AAATTACTAA
898 ATTATTATTATAATTAAATTACTAAATTATT
1 ATTA-TATTATAATTAAATTACTAAATTATT
* * * *
929 ATTATAATA-ATATTAGA-TATTAGA-TATT
1 ATTATATTATA-ATTAAATTACTAAATTATT
957 ATTATATTATAATTA
1 ATTATATTATAATTA
972 TATCTAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
28 16 0.44
29 7 0.19
30 9 0.25
31 4 0.11
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (30 bp):
ATTATATTATAATTAAATTACTAAATTATT
Found at i:982 original size:15 final size:15
Alignment explanation
Indices: 964--997 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
954 ATTATTATAT
*
964 TATAATTATATCTAA
1 TATAATAATATCTAA
979 TATAATAATATCTAA
1 TATAATAATATCTAA
994 TATA
1 TATA
998 GATTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATAATATCTAA
Found at i:1025 original size:27 final size:29
Alignment explanation
Indices: 977--1034 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
967 AATTATATCT
*
977 AATATAATAATATCTAATATAGATTTATAA
1 AATATAATAATA-CTAAAATAGATTTATAA
1007 AATATAA-AATA-TAAAATAGATTTATAA
1 AATATAATAATACTAAAATAGATTTATAA
1034 A
1 A
1035 TCGAATAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 16 0.59
29 4 0.15
30 7 0.26
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (29 bp):
AATATAATAATACTAAAATAGATTTATAA
Found at i:1140 original size:26 final size:26
Alignment explanation
Indices: 1106--1172 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
1096 ATAGAATAAA
*
1106 AATAGAAATTAATAACAACTAAAACT
1 AATATAAATTAATAACAACTAAAACT
1132 AATATAAATTAATAACAACTAAAACT
1 AATATAAATTAATAACAACTAAAACT
1158 AATATAAATTAATAA
1 AATATAAATTAATAA
1173 TAATTGATAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.63, C:0.09, G:0.01, T:0.27
Consensus pattern (26 bp):
AATATAAATTAATAACAACTAAAACT
Found at i:1202 original size:18 final size:18
Alignment explanation
Indices: 1179--1214 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1169 ATAATAATTG
1179 ATAGTAAGAATTGATAAT
1 ATAGTAAGAATTGATAAT
1197 ATAGTAAGAATTGATAAT
1 ATAGTAAGAATTGATAAT
1215 CATTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
ATAGTAAGAATTGATAAT
Done.