Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016478.1 Corchorus capsularis cultivar CVL-1 contig16499, 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: 32017
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2895 original size:432 final size:432
Alignment explanation
Indices: 2092--2954 Score: 1708
Period size: 432 Copynumber: 2.0 Consensus size: 432
2082 CTTTATAAAT
2092 ATAGATAACAGTATTCTTTCCCTTAACCTTTCCTTGAAAATATTTGACTAACTCCATTAGTCCAT
1 ATAGATAACAGTATTCTTTCCCTTAACCTTTCCTTGAAAATATTTGACTAACTCCATTAGTCCAT
2157 GATCCATGAATTTAACCTTTTCATCATAACTTTATATTCTCATTGACCATATTGGTTCCAACTTT
66 GATCCATGAATTTAACCTTTTCATCATAACTTTATATTCTCATTGACCATATTGGTTCCAACTTT
2222 CAAGTCTTACCTTTGACTTTGTTGTTCGTCTTCCCTCCTTGCACTTGCATATAGAGAGTTTTAAG
131 CAAGTCTTACCTTTGACTTTGTTGTTCGTCTTCCCTCCTTGCACTTGCATATAGAGAGTTTTAAG
2287 TTTTAACACAACTCATGACTTCTCTCGCTATTCTCATATACCATAAGTTTTAATTGTCATTTTAC
196 TTTTAACACAACTCATGACTTCTCTCGCTATTCTCATATACCATAAGTTTTAATTGTCATTTTAC
2352 AAAGTTAAGAAGGCATTAATTATTTATTTTTCAAACGTGTCTTTTAATTAAGGAGAGACGGCGAG
261 AAAGTTAAGAAGGCATTAATTATTTATTTTTCAAACGTGTCTTTTAATTAAGGAGAGACGGCGAG
2417 TATGTGTGTAGGTGAATTTTTTTTTTTAGTATTAACCGTCTGGTATTAGGTGACCACATTAAACC
326 TATGTGTGTAGGTGAATTTTTTTTTTTAGTATTAACCGTCTGGTATTAGGTGACCACATTAAACC
2482 CCGATTATTTCAAATTCGAGCCACGTTGGAACCCATATGAAC
391 CCGATTATTTCAAATTCGAGCCACGTTGGAACCCATATGAAC
2524 ATAGATAACAGTATTCTTTCCCTTAACCTTTCCTTGAAAATATTTGACTAACTCCATTAGTCCAT
1 ATAGATAACAGTATTCTTTCCCTTAACCTTTCCTTGAAAATATTTGACTAACTCCATTAGTCCAT
2589 GATCCATGAATTTAACCTTTTCATCATAACTTTATATTCTCATTGACCATATTGGTTCCAACTTT
66 GATCCATGAATTTAACCTTTTCATCATAACTTTATATTCTCATTGACCATATTGGTTCCAACTTT
2654 CAAGTCTTACCTTTGACTTTGTTGTTCGTCTTCCCTCCTTGCACTTGCATATAGAGAGTTTTAAG
131 CAAGTCTTACCTTTGACTTTGTTGTTCGTCTTCCCTCCTTGCACTTGCATATAGAGAGTTTTAAG
2719 TTTTAACACAACTCATGACTTCTCTCGCTATTCTCATATACCATAAGTTTTAATTGTCATTTTAC
196 TTTTAACACAACTCATGACTTCTCTCGCTATTCTCATATACCATAAGTTTTAATTGTCATTTTAC
2784 AAAGTTAAGAAGGCATTAATTATTTATTTTTCAAACGTGTCTTTTAATTAAGGAGAGACGGCGAG
261 AAAGTTAAGAAGGCATTAATTATTTATTTTTCAAACGTGTCTTTTAATTAAGGAGAGACGGCGAG
*
2849 TATGTGTGTAGGTGAATTTTTTTTTTTGGTATTAACCGTCTGGTATTAGGTGACCACATTAAACC
326 TATGTGTGTAGGTGAATTTTTTTTTTTAGTATTAACCGTCTGGTATTAGGTGACCACATTAAACC
*
2914 CCGATTATTTCAGATTCGAGCCACGTTGGAACCCATATGAA
391 CCGATTATTTCAAATTCGAGCCACGTTGGAACCCATATGAA
2955 GGACGCTCTT
Statistics
Matches: 429, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
432 429 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (432 bp):
ATAGATAACAGTATTCTTTCCCTTAACCTTTCCTTGAAAATATTTGACTAACTCCATTAGTCCAT
GATCCATGAATTTAACCTTTTCATCATAACTTTATATTCTCATTGACCATATTGGTTCCAACTTT
CAAGTCTTACCTTTGACTTTGTTGTTCGTCTTCCCTCCTTGCACTTGCATATAGAGAGTTTTAAG
TTTTAACACAACTCATGACTTCTCTCGCTATTCTCATATACCATAAGTTTTAATTGTCATTTTAC
AAAGTTAAGAAGGCATTAATTATTTATTTTTCAAACGTGTCTTTTAATTAAGGAGAGACGGCGAG
TATGTGTGTAGGTGAATTTTTTTTTTTAGTATTAACCGTCTGGTATTAGGTGACCACATTAAACC
CCGATTATTTCAAATTCGAGCCACGTTGGAACCCATATGAAC
Found at i:11392 original size:42 final size:42
Alignment explanation
Indices: 11345--11429 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
11335 TAGATATTAA
*
11345 TTTTGAATATTAAATACATAATTGATTATCAAGTGAGATATG
1 TTTTGAATATTAAATACATAATTAATTATCAAGTGAGATATG
*
11387 TTTTGAATATTAAATACATAATTAATTATCATGTGAGATATG
1 TTTTGAATATTAAATACATAATTAATTATCAAGTGAGATATG
11429 T
1 T
11430 GTCAACATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAAGTGAGATATG
Found at i:12786 original size:16 final size:16
Alignment explanation
Indices: 12765--12851 Score: 95
Period size: 16 Copynumber: 5.4 Consensus size: 16
12755 GGTTAACTTC
*
12765 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
12781 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
*
12797 TCGGGTCACTCGGGTT
1 TCGGGTCATTCGGGTT
*
12813 ACGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
12829 TTGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
12845 TCGGGTC
1 TCGGGTC
12852 GGACGGGTTC
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
15 2 0.03
16 54 0.93
17 2 0.03
ACGTcount: A:0.08, C:0.21, G:0.38, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:12801 original size:32 final size:32
Alignment explanation
Indices: 12763--12866 Score: 113
Period size: 32 Copynumber: 3.3 Consensus size: 32
12753 CGGGTTAACT
*
12763 TCTCGGGTTATTCGGGTTTCGGGTCATACGGG
1 TCTCGGGTCATTCGGGTTTCGGGTCATACGGG
* *
12795 TCTCGGGTCACTCGGGTTACGGGTCAT-CTGGG
1 TCTCGGGTCATTCGGGTTTCGGGTCATAC-GGG
* * * **
12827 TTTTGGGTCATTCGGGTCTCGGGTCGGACGGG
1 TCTCGGGTCATTCGGGTTTCGGGTCATACGGG
12859 T-TCGGGTC
1 TCTCGGGTC
12867 GTTTACTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
31 7 0.12
32 51 0.86
33 1 0.02
ACGTcount: A:0.08, C:0.21, G:0.39, T:0.32
Consensus pattern (32 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATACGGG
Found at i:12859 original size:48 final size:47
Alignment explanation
Indices: 12776--12866 Score: 128
Period size: 48 Copynumber: 1.9 Consensus size: 47
12766 CGGGTTATTC
*
12776 GGGTTTCGGGTCATACGGGTCTCGGGTCACTCGGGTTACGGGTCATCT
1 GGGTTTCGGGTCATACGGGTCTCGGGTCACACGGGTT-CGGGTCATCT
* * **
12824 GGGTTTTGGGTCATTCGGGTCTCGGGTCGGACGGGTTCGGGTC
1 GGGTTTCGGGTCATACGGGTCTCGGGTCACACGGGTTCGGGTC
12867 GTTTACTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 6 0.16
48 32 0.84
ACGTcount: A:0.08, C:0.21, G:0.42, T:0.30
Consensus pattern (47 bp):
GGGTTTCGGGTCATACGGGTCTCGGGTCACACGGGTTCGGGTCATCT
Found at i:12918 original size:16 final size:15
Alignment explanation
Indices: 12887--12921 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
12877 TCTGATCAAA
*
12887 TCGGGTTGGGCGGGT
1 TCGGGTTGGACGGGT
12902 TCGGGTTCGGACGGGT
1 TCGGGTT-GGACGGGT
12918 TCGG
1 TCGG
12922 ATCAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.03, C:0.17, G:0.54, T:0.26
Consensus pattern (15 bp):
TCGGGTTGGACGGGT
Found at i:25992 original size:22 final size:23
Alignment explanation
Indices: 25952--26002 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
25942 TTAAAATAAT
*
25952 TTAAACACTAAAAATTTAAAGAA
1 TTAAATACTAAAAATTTAAAGAA
25975 TTAAATACTAAAAA-TTAAAGAA
1 TTAAATACTAAAAATTTAAAGAA
25997 TTAAAT
1 TTAAAT
26003 TATATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (23 bp):
TTAAATACTAAAAATTTAAAGAA
Found at i:26961 original size:22 final size:21
Alignment explanation
Indices: 26927--27043 Score: 103
Period size: 22 Copynumber: 5.3 Consensus size: 21
26917 CTAATCCCTG
*
26927 TGAAACTTTGATACCCACACTA
1 TGAAA-TTTGATAACCACACTA
26949 TGAAATTTCGATAACCATC-CTA
1 TGAAATTT-GATAACCA-CACTA
* *
26971 TTAAATTTTGATTACCACACTA
1 TGAAA-TTTGATAACCACACTA
26993 TGAAACTTTGATAACCACACTA
1 TGAAA-TTTGATAACCACACTA
* * *
27015 TAAAATAGTGATAACCTCTAC-A
1 TGAAAT-TTGATAACCAC-ACTA
27037 TGAAATT
1 TGAAATT
27044 AATTTTGCTA
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
21 5 0.06
22 67 0.86
23 6 0.08
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.32
Consensus pattern (21 bp):
TGAAATTTGATAACCACACTA
Found at i:27135 original size:22 final size:22
Alignment explanation
Indices: 27109--27150 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
27099 GATTTGGTAC
27109 ACTATGAAATTTGGATAACCAT
1 ACTATGAAATTTGGATAACCAT
*
27131 ACTATGAAATTTTGATAACC
1 ACTATGAAATTTGGATAACC
27151 TCCCTAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
ACTATGAAATTTGGATAACCAT
Found at i:27166 original size:21 final size:21
Alignment explanation
Indices: 27136--27177 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
27126 ACCATACTAT
*
27136 GAAATTTTGATAACCTCCCTA
1 GAAATGTTGATAACCTCCCTA
*
27157 GAAATGTTGATAACTTCCCTA
1 GAAATGTTGATAACCTCCCTA
27178 TAGAATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (21 bp):
GAAATGTTGATAACCTCCCTA
Found at i:27270 original size:22 final size:22
Alignment explanation
Indices: 27245--27326 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
27235 GATTACCTTC
*
27245 TATGAATTTTTTG-TAACCACAT
1 TATGAA-TTTTGGATAACCACAT
* *
27267 TATGAAATTTGGATAATCACAT
1 TATGAATTTTGGATAACCACAT
** *
27289 TATGAAATTTT-GATAGTCACAC
1 TATG-AATTTTGGATAACCACAT
27311 TATGAAATTTT-GATAA
1 TATG-AATTTTGGATAA
27327 TCTGCAAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
21 4 0.08
22 42 0.82
23 5 0.10
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (22 bp):
TATGAATTTTGGATAACCACAT
Found at i:27293 original size:44 final size:44
Alignment explanation
Indices: 27111--27328 Score: 113
Period size: 43 Copynumber: 4.9 Consensus size: 44
27101 TTTGGTACAC
* * * * * **
27111 TATGAAATTTGGATAACCATACTATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACACTATGAAATTTGGATAATCACAT
* ** * * * * *
27155 TA-GAAATGTTGATAACTTCCCTATAGAATTTTGTTAATTAATCTCAC
1 TATGAAATTTTGATAACCACACTAT-GAAATTTG--GA-TAATCACAT
* * * * *
27202 TATGAAATTTTGATAAGCACAAC-ATCAAATTTTGATTA-C-CTT
1 TATGAAATTTTGATAACCAC-ACTATGAAATTTGGATAATCACAT
* *
27244 CTATGAATTTTTTG-TAACCACATTATGAAATTTGGATAATCACAT
1 -TATGAA-ATTTTGATAACCACACTATGAAATTTGGATAATCACAT
** *
27289 TATGAAATTTTGATAGTCACACTATGAAATTTTGATAATC
1 TATGAAATTTTGATAACCACACTATGAAATTTGGATAATC
27329 TGCAAAGTGA
Statistics
Matches: 127, Mismatches: 35, Indels: 24
0.68 0.19 0.13
Matches are distributed among these distances:
42 2 0.02
43 46 0.36
44 45 0.35
45 3 0.02
46 1 0.01
47 14 0.11
48 15 0.12
49 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACACTATGAAATTTGGATAATCACAT
Found at i:27819 original size:29 final size:30
Alignment explanation
Indices: 27760--27853 Score: 145
Period size: 29 Copynumber: 3.1 Consensus size: 30
27750 TAATGGCAAT
*
27760 TTAGAAATATGTTTTTAAAAAAAGGATACAA
1 TTAGAAATATG-TTTTAAAAAAAGGGTACAA
*
27791 TTGGAAATATGTTTT-AAAAAAGGGTACAA
1 TTAGAAATATGTTTTAAAAAAAGGGTACAA
27820 TTAGAAATATGTTTTAAAAATAAGGGTACAA
1 TTAGAAATATGTTTTAAAAA-AAGGGTACAA
27851 TTA
1 TTA
27854 AATAGTTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
29 27 0.47
30 8 0.14
31 23 0.40
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.33
Consensus pattern (30 bp):
TTAGAAATATGTTTTAAAAAAAGGGTACAA
Done.