Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011681.1 Corchorus capsularis cultivar CVL-1 contig11702, 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: 23734
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:675 original size:5 final size:5
Alignment explanation
Indices: 665--689 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
655 ATCGAAAAAT
665 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
690 TTTTCGACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:2120 original size:33 final size:33
Alignment explanation
Indices: 2078--2186 Score: 139
Period size: 33 Copynumber: 3.3 Consensus size: 33
2068 GTGTTTTAGA
2078 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
* * * * *
2111 TGTTGTTTGCAATGACACTAAATCT-GTTTTAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
* *
2143 ATGTTGTCTACGATGATACTAAACCTAATTTGAG
1 -TGTTGTTTGCGATGATACTAAACCTAATTTGAG
2177 TGTTGTTTGC
1 TGTTGTTTGC
2187 AATAAAACTA
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 5 0.08
33 50 0.83
34 5 0.08
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (33 bp):
TGTTGTTTGCGATGATACTAAACCTAATTTGAG
Found at i:2175 original size:66 final size:66
Alignment explanation
Indices: 2069--2211 Score: 241
Period size: 66 Copynumber: 2.2 Consensus size: 66
2059 TTGAAAAGAG
* * * *
2069 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATGACACTAAAT
1 TGTTTTAGATGTTGTCTACGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
2134 C
66 C
2135 TGTTTTAGATGTTGTCTACGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
1 TGTTTTAGATGTTGTCTACGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
2200 C
66 C
*
2201 TGTTTTGGATG
1 TGTTTTAGATG
2212 CTAATTGTGA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (66 bp):
TGTTTTAGATGTTGTCTACGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
C
Found at i:2261 original size:33 final size:33
Alignment explanation
Indices: 2224--2309 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
2214 AATTGTGATG
2224 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
* * ** *
2257 AAAACAATTATGTTCTGGTTGATTATAGCATTG
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
* * *
2290 CAAATAATCCTGTTTTGGTT
1 AAAACAATTCTGTTTTGGTT
2310 AATAGCATTG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (33 bp):
AAAACAATTCTGTTTTGGTTGAACATAGCATTA
Found at i:4283 original size:33 final size:33
Alignment explanation
Indices: 4239--4345 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 33
4229 AGCACAAGTG
4239 ACCGGCCACGCGACTTGGAAATGACCGACCATC
1 ACCGGCCACGCGACTTGGAAATGACCGACCATC
* * * * *
4272 ACCGGCTACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAAATGACCGACCATC
* * * *
4305 ACCGGCCACGCGACATGGACATGTCCGGCCA-C
1 ACCGGCCACGCGACTTGGAAATGACCGACCATC
4337 AACCGGCCA
1 -ACCGGCCA
4346 TCGCTTGGCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 1 0.02
33 62 0.98
ACGTcount: A:0.23, C:0.39, G:0.27, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAAATGACCGACCATC
Found at i:7862 original size:13 final size:15
Alignment explanation
Indices: 7839--7872 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
7829 AAAAAATTTA
7839 AAAAAATGAAAAA-G
1 AAAAAATGAAAAACG
7853 AAAAAA-GAAAAACG
1 AAAAAATGAAAAACG
7867 AAAAAA
1 AAAAAA
7873 AAATATCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAATGAAAAACG
Found at i:12092 original size:13 final size:13
Alignment explanation
Indices: 12076--12103 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12066 GATCTGATAA
12076 AAAAAATAAAAAT
1 AAAAAATAAAAAT
12089 AAAAAATAAAAAT
1 AAAAAATAAAAAT
12102 AA
1 AA
12104 CGGCGGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:22970 original size:6 final size:6
Alignment explanation
Indices: 22959--22990 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
22949 TGGTATCAAC
22959 TATCTA TATCTA TATCTA TATCTA TA-CTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TAT
22991 TAAAAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:23162 original size:70 final size:70
Alignment explanation
Indices: 23078--23320 Score: 236
Period size: 70 Copynumber: 3.2 Consensus size: 70
23068 TTGTTTAGGT
*
23078 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT
*
23142 ATTTTA
65 ATTATA
* *
23148 TTTTACTATTTTACTCAACTAAGAACTCTATTTTTATATAATTAAATCTAATATTATCCTTATAG
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAA--T-ATAATATCC-T-TA-
23213 GCTATAGCTATTATA
60 --TA-A-CTATTATA
* *
23228 TTTTACCATTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCT
1 TTTTA-C---TA----TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCT
*
23293 TATTACTATTATA
58 TATAACTATTATA
*
23306 TTTTACCATTTTACT
1 TTTTACTATTTTACT
23321 ATTTTAATTA
Statistics
Matches: 143, Mismatches: 11, Indels: 38
0.74 0.06 0.20
Matches are distributed among these distances:
70 48 0.34
71 2 0.01
72 1 0.01
73 8 0.06
74 1 0.01
75 2 0.01
77 1 0.01
78 15 0.10
79 2 0.01
80 13 0.09
81 1 0.01
83 2 0.01
84 2 0.01
85 7 0.05
86 1 0.01
88 37 0.26
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATA
Done.