Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010685.1 Corchorus capsularis cultivar CVL-1 contig10706, 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: 63644
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1308 original size:84 final size:80
Alignment explanation
Indices: 1192--1347 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 80
1182 GTTTGGTAGG
* * **
1192 ATTGTAGGGAATGAAATAGGTAAAAAAATGAAATAGTAAGGGAGGGAAGGAAAGTTGTTTTCCTT
1 ATTGTAGGGAAAGAAAAAGGTAAAAAAATGAAAT-G-AAAAG-GGGAAGGAAAGTTGTTTTCCTT
1257 CTTTTTGTTTATGGAAGA
63 CTTTTTGTTTATGGAAGA
* *
1275 ATTGTATGGAAAGAAAAAGGGTAAGAAAATGAAATGAAAAGGGGAAGGAAAGTTGTTTTCCTTCT
1 ATTGTAGGGAAAGAAAAA-GGTAAAAAAATGAAATGAAAAGGGGAAGGAAAGTTGTTTTCCTTCT
1340 TTTTGTTT
65 TTTTGTTT
1348 GGTATATATA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 32 0.48
82 3 0.05
83 16 0.24
84 15 0.23
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (80 bp):
ATTGTAGGGAAAGAAAAAGGTAAAAAAATGAAATGAAAAGGGGAAGGAAAGTTGTTTTCCTTCTT
TTTGTTTATGGAAGA
Found at i:4715 original size:191 final size:191
Alignment explanation
Indices: 4391--4776 Score: 745
Period size: 191 Copynumber: 2.0 Consensus size: 191
4381 ATACTAGCTA
4391 GCTATAGTACAAGTGTACAACAAATTAAAGAAAAAGGTAATTATTTGATACACCGGCGGTATAAA
1 GCTATAGTACAAGTGTACAACAAATTAAAGAAAAAGGTAATTATTTGATACACCGGCGGTATAAA
*
4456 TTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTCCATTTTTTGAATTAGTTAAGTTTTA
66 TTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTCCATTTTTTGAATTAGTTAACTTTTA
*
4521 AATATTTCAATCTAGTCCCTAGAGAACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCT
131 AATATTTCAATCTAGTCCCTAGAGAACACATGTCACCCTTCAGGACCCACTTGTGTAGTCT
4582 GCTATAGTACAAGTGTACAACAAATTAAAGAAAAAGGTAATTATTTGATACACCGGCGGTATAAA
1 GCTATAGTACAAGTGTACAACAAATTAAAGAAAAAGGTAATTATTTGATACACCGGCGGTATAAA
4647 TTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTCCATTTTTTGAATTAGTTAACTTTTA
66 TTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTCCATTTTTTGAATTAGTTAACTTTTA
*
4712 AATATTTCAATCTAGTCCCTAGAGGACACATGTCACCCTTCAGGACCCACTTGTGTAGTCT
131 AATATTTCAATCTAGTCCCTAGAGAACACATGTCACCCTTCAGGACCCACTTGTGTAGTCT
4773 GCTA
1 GCTA
4777 AACTCCACTG
Statistics
Matches: 192, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
191 192 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (191 bp):
GCTATAGTACAAGTGTACAACAAATTAAAGAAAAAGGTAATTATTTGATACACCGGCGGTATAAA
TTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTCCATTTTTTGAATTAGTTAACTTTTA
AATATTTCAATCTAGTCCCTAGAGAACACATGTCACCCTTCAGGACCCACTTGTGTAGTCT
Found at i:11017 original size:126 final size:125
Alignment explanation
Indices: 10749--10992 Score: 381
Period size: 126 Copynumber: 2.0 Consensus size: 125
10739 AATTATAATT
*
10749 CCCTAAATTAATAATTCAATGTAACAAGTTTAAGATGATATATGACTTTTTAATGAATTGAATAT
1 CCCTAAATT-ATAATTCAATGTAACAAGTTTAAGATGATATATGACTTTTTAATGAAATGAATAT
* *
10814 GATTCTAAGACAAAGAAAAAAAACGTTTGTTTTAATTTTTAGGGTTTTGTTCTAAACTATT
65 GATTCTAAGACAAAGAAAAAAAACGTTTGTTTTAATTTTTAGGGTCTTGTTCTAAACTATA
10875 CCCTAAATTAATAATTCAATGTAACAAGTTTAAGATGATATATGACTTTTTAATGAAATGAATAT
1 CCCTAAATT-ATAATTCAATGTAACAAGTTTAAGATGATATATGACTTTTTAATGAAATGAATAT
*
10940 GATTCTAA-A-ACA-AAAAAAAA-GTTT-TCTTTGAATTTTTAGGGTCTTGTTCTAAA
65 GATTCTAAGACAAAGAAAAAAAACGTTTGT-TTT-AATTTTTAGGGTCTTGTTCTAAA
10993 TTAACAAGGT
Statistics
Matches: 113, Mismatches: 3, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
121 1 0.01
122 7 0.06
123 30 0.27
124 2 0.02
125 1 0.01
126 72 0.64
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (125 bp):
CCCTAAATTATAATTCAATGTAACAAGTTTAAGATGATATATGACTTTTTAATGAAATGAATATG
ATTCTAAGACAAAGAAAAAAAACGTTTGTTTTAATTTTTAGGGTCTTGTTCTAAACTATA
Found at i:11119 original size:25 final size:25
Alignment explanation
Indices: 11080--11136 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
11070 CAGTCTGTCG
*
11080 CTTTTCTCTTCGATTATGCTATCTTC
1 CTTTT-TCTTCGATTATACTATCTTC
* *
11106 CTTTTTCTTGGATTCTACTATCTTC
1 CTTTTTCTTCGATTATACTATCTTC
11131 CTTTTT
1 CTTTTT
11137 TCTGCTCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.11, C:0.25, G:0.07, T:0.58
Consensus pattern (25 bp):
CTTTTTCTTCGATTATACTATCTTC
Found at i:26294 original size:2 final size:2
Alignment explanation
Indices: 26258--26312 Score: 60
Period size: 2 Copynumber: 26.5 Consensus size: 2
26248 TTAAAAAAAC
26258 AT AT ACT AT ACT AT ACT AT ACT AT A- AT AT -T AT AT AT AT AT AT
1 AT AT A-T AT A-T AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT
26300 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
26313 AAACTATAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
1 2 0.04
2 37 0.79
3 8 0.17
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:28001 original size:12 final size:13
Alignment explanation
Indices: 27984--28015 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
27974 ATTATATATG
27984 AATAATATG-AAT
1 AATAATATGTAAT
27996 AATAATA-GTAAT
1 AATAATATGTAAT
28008 AATAATAT
1 AATAATAT
28016 TTTTGACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 17 0.94
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (13 bp):
AATAATATGTAAT
Found at i:31931 original size:5 final size:6
Alignment explanation
Indices: 31900--31929 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
31890 TTTTCTTCTG
31900 GAAAAA GGAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA -GAAAAA GAAAAA GAAAAA GAAAA
31930 GATGATTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:36071 original size:16 final size:17
Alignment explanation
Indices: 36050--36081 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36040 CCATGAGAAA
36050 AACAA-CCAATATTTTG
1 AACAACCCAATATTTTG
36066 AACAACCCAATATTTT
1 AACAACCCAATATTTT
36082 CCATCTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (17 bp):
AACAACCCAATATTTTG
Found at i:38963 original size:21 final size:21
Alignment explanation
Indices: 38937--38983 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
38927 GTTAGCAATG
* *
38937 GGACCTGGTGGACCGGGCGGA
1 GGACCTGCTGGACCGGGAGGA
**
38958 GGACCTGCTGGATGGGGAGGA
1 GGACCTGCTGGACCGGGAGGA
38979 GGACC
1 GGACC
38984 GGGAGGGCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.21, G:0.51, T:0.11
Consensus pattern (21 bp):
GGACCTGCTGGACCGGGAGGA
Found at i:41314 original size:16 final size:16
Alignment explanation
Indices: 41293--41325 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41283 CCCAGGCGAA
41293 ATAGAGGGAGAGGGAG
1 ATAGAGGGAGAGGGAG
41309 ATAGAGGGAGAGGGAG
1 ATAGAGGGAGAGGGAG
41325 A
1 A
41326 GAGTAACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.55, T:0.06
Consensus pattern (16 bp):
ATAGAGGGAGAGGGAG
Found at i:43013 original size:31 final size:31
Alignment explanation
Indices: 42978--43043 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
42968 ATTACCCTCC
42978 AAAACAATGCAGACAAGCATAACTCCCAACT
1 AAAACAATGCAGACAAGCATAACTCCCAACT
43009 AAAACAATGCAGACAAGCATAACTCCCAACT
1 AAAACAATGCAGACAAGCATAACTCCCAACT
43040 AAAA
1 AAAA
43044 ATAGCATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.27, G:0.09, T:0.12
Consensus pattern (31 bp):
AAAACAATGCAGACAAGCATAACTCCCAACT
Found at i:44766 original size:7 final size:7
Alignment explanation
Indices: 44750--44781 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
44740 ATAAAAGTAA
44750 ATAT-AT
1 ATATAAT
44756 ATATAAT
1 ATATAAT
44763 ATATAAT
1 ATATAAT
44770 ATATAAT
1 ATATAAT
44777 ATATA
1 ATATA
44782 TAATTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATAAT
Found at i:44767 original size:25 final size:27
Alignment explanation
Indices: 44716--44783 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 27
44706 GTTATTTATT
44716 TATATATATATATATAATAAAGTTATAAAA
1 TATA-ATATATATATAAT-AAG-TATAAAA
*
44746 GTA-AATATATATATAAT-A-TATAATA
1 -TATAATATATATATAATAAGTATAAAA
44771 TATAATATATATA
1 TATAATATATATA
44784 ATTATACTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 2 0.06
25 16 0.46
27 1 0.03
29 13 0.37
30 1 0.03
31 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
TATAATATATATATAATAAGTATAAAA
Found at i:44771 original size:16 final size:16
Alignment explanation
Indices: 44749--44801 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
44739 TATAAAAGTA
44749 AATATATATATAATATAT
1 AATATATA-AT-ATATAT
44767 AATATATAATATATAT
1 AATATATAATATATAT
*
44783 AAT-TATACTATAGTAT
1 AATATATAATATA-TAT
44799 AAT
1 AAT
44802 TTACATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 8 0.24
16 15 0.45
17 2 0.06
18 8 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
AATATATAATATATAT
Found at i:61206 original size:15 final size:15
Alignment explanation
Indices: 61186--61215 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61176 ATCAGGCCGC
*
61186 CACGATACACGATAT
1 CACGATACACAATAT
61201 CACGATACACAATAT
1 CACGATACACAATAT
61216 TTCAACCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:63613 original size:2 final size:2
Alignment explanation
Indices: 63606--63644 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
63596 AGAGATCCCT
63606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.