Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006087.1 Corchorus capsularis cultivar CVL-1 contig06105, 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: 18744
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:5310 original size:16 final size:17
Alignment explanation
Indices: 5275--5312 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5265 AACAAAATTA
5275 AAAACCCAACGGAAATAT
1 AAAACCCAAC-GAAATAT
*
5293 AAAACCCAAC-ATATAT
1 AAAACCCAACGAAATAT
5309 AAAA
1 AAAA
5313 AAGGGAAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
18 10 0.53
ACGTcount: A:0.61, C:0.21, G:0.05, T:0.13
Consensus pattern (17 bp):
AAAACCCAACGAAATAT
Found at i:9270 original size:20 final size:20
Alignment explanation
Indices: 9227--9266 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
9217 AATAATTATT
*
9227 ATAAGAAATTGAAATTAAAA
1 ATAAAAAATTGAAATTAAAA
9247 ATAAAAAATT-AAATTAAAA
1 ATAAAAAATTGAAATTAAAA
9266 A
1 A
9267 ATAATGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (20 bp):
ATAAAAAATTGAAATTAAAA
Found at i:10113 original size:62 final size:62
Alignment explanation
Indices: 9978--10251 Score: 311
Period size: 62 Copynumber: 4.3 Consensus size: 62
9968 AACTCTTTTA
* *
9978 CCGAAAGGGTATTTTAGGAAGAAAATTTAACCTAAATGCAAGATATATGACAAAACTGACCCTTT
1 CCGAAAGGGTATTTT-GG--G-AAATTGAATCTAAATGCAAGA-ATATGACAAAACTGACCCTTT
*
10043 TT
61 GT
* * * * **
10045 CTGAAAGGGTATTTTGGGAAATAT-AATCTAAATACAAGAATGTGATAAAACTGACCCTTCAT
1 CCGAAAGGGTATTTTGGGAAAT-TGAATCTAAATGCAAGAATATGACAAAACTGACCCTTTGT
* * *
10107 CCGAAAGGGTATTTTAGAAAATTGAATCTAAATGCGAAG-ATGTGACAAAACTGACCCTTTGT
1 CCGAAAGGGTATTTTGGGAAATTGAATCTAAATGC-AAGAATATGACAAAACTGACCCTTTGT
* * *
10169 CCGAAAGAGTATTTTGGGAAATTGAAACTAAATGC-TGAAATATGACAAAACTGACCCTTTGT
1 CCGAAAGGGTATTTTGGGAAATTGAATCTAAATGCAAG-AATATGACAAAACTGACCCTTTGT
*
10231 CCGAAAGGGTATTTTCGGAAA
1 CCGAAAGGGTATTTTGGGAAA
10252 GTAGAATAAA
Statistics
Matches: 180, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
60 1 0.01
61 1 0.01
62 140 0.78
63 20 0.11
64 2 0.01
66 2 0.01
67 14 0.08
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (62 bp):
CCGAAAGGGTATTTTGGGAAATTGAATCTAAATGCAAGAATATGACAAAACTGACCCTTTGT
Found at i:10304 original size:65 final size:66
Alignment explanation
Indices: 9958--10315 Score: 225
Period size: 62 Copynumber: 5.6 Consensus size: 66
9948 TACCGGAGAC
* * * * * * *
9958 ATGACAAAA-TAACTCTTTTACCGAAAGGGTATTTTAGG-AAG-AAAATTTAACCTAAATGCAAG
1 ATGACAAAACTGACCCTTTCACCGAAAGGGTATTTTCGGAAAGTAGAA--TAAACTAAATGC-TG
*
10020 ATAT
63 AAAT
** * * * * *
10024 ATGACAAAACTGACCCTTTTTCTGAAAGGGTATTTTGGGAAA-T---ATAATCTAAATAC-AAGA
1 ATGACAAAACTGACCCTTTCACCGAAAGGGTATTTTCGGAAAGTAGAATAAACTAAATGCTGA-A
10084 AT
65 AT
* * * * *
10086 GTGATAAAACTGACCC-TTCATCCGAAAGGGTATTTT-AGAAAATTGAAT---CTAAATGC-GAA
1 ATGACAAAACTGACCCTTTCA-CCGAAAGGGTATTTTCGGAAAGTAGAATAAACTAAATGCTGAA
10145 GAT
65 -AT
* ** * * *
10148 GTGACAAAACTGACCCTTTGTCCGAAAGAGTATTTTGGGAAA-TTG---AAACTAAATGCTGAAA
1 ATGACAAAACTGACCCTTTCACCGAAAGGGTATTTTCGGAAAGTAGAATAAACTAAATGCTGAAA
10209 T
66 T
**
10210 ATGACAAAACTGACCCTTTGTCCGAAAGGGTATTTTCGGAAAGTAGAATAAACTCAAATGC-GAA
1 ATGACAAAACTGACCCTTTCACCGAAAGGGTATTTTCGGAAAGTAGAATAAACT-AAATGCTGAA
10274 A-
65 AT
** * *
10275 ATGATGAAACTGACCCTTTCACCGGAAGGGTATTTTTGGAA
1 ATGACAAAACTGACCCTTTCACCGAAAGGGTATTTTCGGAA
10316 TTACAAATAC
Statistics
Matches: 239, Mismatches: 32, Indels: 43
0.76 0.10 0.14
Matches are distributed among these distances:
61 8 0.03
62 122 0.51
63 21 0.09
65 38 0.16
66 18 0.08
67 30 0.13
68 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (66 bp):
ATGACAAAACTGACCCTTTCACCGAAAGGGTATTTTCGGAAAGTAGAATAAACTAAATGCTGAAA
T
Found at i:11959 original size:21 final size:21
Alignment explanation
Indices: 11935--12004 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
11925 TACATGGTGA
11935 TTTTATTATCAAATGGGTAGT
1 TTTTATTATCAAATGGGTAGT
* * *
11956 TTTTATTATC--CTTGGT-GG
1 TTTTATTATCAAATGGGTAGT
11974 TTTTATTATCAAATGGGTAGT
1 TTTTATTATCAAATGGGTAGT
11995 TTTTATTATC
1 TTTTATTATC
12005 CTAGGTTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 11 0.28
19 4 0.10
20 4 0.10
21 21 0.52
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (21 bp):
TTTTATTATCAAATGGGTAGT
Found at i:11983 original size:39 final size:39
Alignment explanation
Indices: 11929--12040 Score: 161
Period size: 39 Copynumber: 2.9 Consensus size: 39
11919 GTTAAATACA
*
11929 TGGTGATTTTATTATCAAATGGGTAGTTTTTATTATCCT
1 TGGTGGTTTTATTATCAAATGGGTAGTTTTTATTATCCT
11968 TGGTGGTTTTATTATCAAATGGGTAGTTTTTATTATCCT
1 TGGTGGTTTTATTATCAAATGGGTAGTTTTTATTATCCT
* * * * * *
12007 AGGTTGTTTTATTTTTAAATGGATAGATTTTATT
1 TGGTGGTTTTATTATCAAATGGGTAGTTTTTATT
12041 TTTCGTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.53
Consensus pattern (39 bp):
TGGTGGTTTTATTATCAAATGGGTAGTTTTTATTATCCT
Found at i:12000 original size:18 final size:18
Alignment explanation
Indices: 11940--12000 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
11930 GGTGATTTTA
11940 TTATCAAATGGGTAGTTT
1 TTATCAAATGGGTAGTTT
* ** * *
11958 TTATTATCCTTGGTGGTTTT
1 TTATCA-AATGGGTAG-TTT
11978 ATTATCAAATGGGTAGTTT
1 -TTATCAAATGGGTAGTTT
11997 TTAT
1 TTAT
12001 TATCCTAGGT
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 9 0.30
19 8 0.27
20 8 0.27
21 5 0.17
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.51
Consensus pattern (18 bp):
TTATCAAATGGGTAGTTT
Found at i:12016 original size:18 final size:18
Alignment explanation
Indices: 11950--12019 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
11940 TTATCAAATG
*
11950 GGTAGTTTTTATTATCCTT
1 GGTAG-TTTTATTATCCTA
* * *
11969 GGTGGTTTTATTATCAAATG
1 GGTAGTTTTATTATC--CTA
11989 GGTAGTTTTTATTATCCTA
1 GGTAG-TTTTATTATCCTA
*
12008 GGTTGTTTTATT
1 GGTAGTTTTATT
12020 TTTAAATGGA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
18 17 0.41
19 9 0.22
20 5 0.12
21 10 0.24
ACGTcount: A:0.19, C:0.07, G:0.20, T:0.54
Consensus pattern (18 bp):
GGTAGTTTTATTATCCTA
Found at i:15139 original size:27 final size:26
Alignment explanation
Indices: 15079--15146 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
15069 GGTCACTTAG
*
15079 GGGCATTTTGGTCATTTTCGCACTCA
1 GGGCATTTTGGTCATTTGCGCACTCA
*
15105 TGGGCATTTTGGTCATTTGCAG-ATTCA
1 -GGGCATTTTGGTCATTTGC-GCACTCA
*
15132 GGGACATTTTAGTCA
1 GGG-CATTTTGGTCA
15147 ATTATTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 3 0.08
27 32 0.89
28 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTGCGCACTCA
Found at i:16866 original size:16 final size:17
Alignment explanation
Indices: 16845--16879 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16835 ATTTTTAGAC
16845 AGTTAC-AGAGAGAGAA
1 AGTTACAAGAGAGAGAA
*
16861 AGTTACAAGAGGGAGAA
1 AGTTACAAGAGAGAGAA
16878 AG
1 AG
16880 AAGATATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.49, C:0.06, G:0.34, T:0.11
Consensus pattern (17 bp):
AGTTACAAGAGAGAGAA
Found at i:18634 original size:22 final size:23
Alignment explanation
Indices: 18606--18679 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 23
18596 AGAAAGATGC
*
18606 AATCAGTAAAAG-GTAAAATGGT
1 AATCAGTAAAAGAGTAAAATGAT
*
18628 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAATGAT
*
18650 AATCAGT-AAAGAGTAATA-GA-
1 AATCAGTAAAAGAGTAAAATGAT
18670 AATCAGTAAA
1 AATCAGTAAA
18680 TCAGTAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 7 0.15
21 8 0.17
22 31 0.67
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAATGAT
Done.