Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010534.1 Corchorus capsularis cultivar CVL-1 contig10555, 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: 72768
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:784 original size:13 final size:13
Alignment explanation
Indices: 766--793 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
756 TATTTATATG
766 ATTGATTAATCAT
1 ATTGATTAATCAT
779 ATTGATTAATCAT
1 ATTGATTAATCAT
792 AT
1 AT
794 AAAAATAATG
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:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
ATTGATTAATCAT
Found at i:2365 original size:16 final size:17
Alignment explanation
Indices: 2333--2367 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2323 ATAAACTTAC
*
2333 AAAGAGAATCAAAGGAG
1 AAAGACAATCAAAGGAG
2350 AAAGACAATC-AAGGAG
1 AAAGACAATCAAAGGAG
2366 AA
1 AA
2368 TCCCAATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.60, C:0.09, G:0.26, T:0.06
Consensus pattern (17 bp):
AAAGACAATCAAAGGAG
Found at i:3522 original size:28 final size:28
Alignment explanation
Indices: 3478--3533 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3468 GGTACGTTCC
3478 ATTTTTCCTACTATTTCTTATATTAACG
1 ATTTTTCCTACTATTTCTTATATTAACG
*
3506 ATTTTTCCTACTGTTTCTTATATTAACG
1 ATTTTTCCTACTATTTCTTATATTAACG
3534 TATTAACGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.54
Consensus pattern (28 bp):
ATTTTTCCTACTATTTCTTATATTAACG
Found at i:6856 original size:2 final size:2
Alignment explanation
Indices: 6849--6879 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6839 TTGGAAAATG
*
6849 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6880 ATACTCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:23271 original size:1 final size:1
Alignment explanation
Indices: 23265--23292 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
23255 TGAGTAGTAG
23265 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
23293 GCCTTCTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:31099 original size:2 final size:2
Alignment explanation
Indices: 31092--31126 Score: 52
Period size: 2 Copynumber: 16.5 Consensus size: 2
31082 CTTTTTCTTA
31092 AT AT AT AT AT AT AT AT AT AT AT AT AGT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT A
31127 GGAGTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 27 0.87
3 4 0.13
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:44227 original size:196 final size:197
Alignment explanation
Indices: 43891--44335 Score: 738
Period size: 196 Copynumber: 2.3 Consensus size: 197
43881 GAAATTTTTC
43891 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAG-TAGGCCGAACGTGA
1 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCG-AACTAAGTTAGGCCGAACGTGA
* *
43955 TCTCTGGACTCTTTGTGAGAACGGCAACGTTCGCAATTGACCTTAGATTTCGATCCGGACTCGTC
65 GCCCTGGACTCTTTGTGAGAACGGCAACGTTCGCAATTGACCTTAGATTTCGATCCGGACTCGTC
44020 ATGAGAACATCGAAACTAAGTTGGCCGAACGTAGGCCCTGGACTCTTTGTGAGAACGACAACGTT
130 ATGAGAACATCGAAACTAAGTTGGCCGAACGTAGGCCCTGGACTCTTTGTGAGAACGACAACG-T
44085 TGCA-
194 T-CAG
*
44089 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAACTAAGTTCGG-CGAACGT-AG
1 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAACTAAGTTAGGCCGAACGTGA-
44152 GCCCTGGACTC-TTGTGAGAACGGCAACGTTCGCAATTGACCTTAGATTTCGATCCGGACTCGTC
65 GCCCTGGACTCTTTGTGAGAACGGCAACGTTCGCAATTGACCTTAGATTTCGATCCGGACTCGTC
*
44216 ATGAGAACATCGAAACTAAGTTGGCCGAACGTAGGCCCTGGACTCTTTGTGAGAACGGCAACGTT
130 ATGAGAACATCGAAACTAAGTTGGCCGAACGTAGGCCCTGGACTCTTTGTGAGAACGACAACGTT
44281 CATG
195 CA-G
* * *
44285 ATTAACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGACACTAAGT
1 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGA-ACTAAGT
44336 GGGCTGAGCG
Statistics
Matches: 235, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
194 2 0.01
195 2 0.01
196 156 0.66
197 30 0.13
198 45 0.19
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (197 bp):
ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAACTAAGTTAGGCCGAACGTGAG
CCCTGGACTCTTTGTGAGAACGGCAACGTTCGCAATTGACCTTAGATTTCGATCCGGACTCGTCA
TGAGAACATCGAAACTAAGTTGGCCGAACGTAGGCCCTGGACTCTTTGTGAGAACGACAACGTTC
AG
Found at i:44363 original size:99 final size:99
Alignment explanation
Indices: 43891--44335 Score: 736
Period size: 99 Copynumber: 4.5 Consensus size: 99
43881 GAAATTTTTC
*
43891 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGTAGGCCGAACGT-GA
1 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAG-
* *
43955 TCTCTGGACTCTTTGTGAGAACGGCAACGTTCGCA
65 GCCCTGGACTCTTTGTGAGAACGGCAACGTTCGCA
43990 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAGG
1 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAGG
* *
44055 CCCTGGACTCTTTGTGAGAACGACAACGTTTGCA
66 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGCA
44089 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCG-AACTAAGTTCGG-CGAACGTAG
1 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGTT-GGCCGAACGTAG
44152 GCCCTGGACTC-TTGTGAGAACGGCAACGTTCGCA
65 GCCCTGGACTCTTTGTGAGAACGGCAACGTTCGCA
44186 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAGG
1 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAGG
***
44251 CCCTGGACTCTTTGTGAGAACGGCAACGTTCATG
66 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGCA
* * * *
44285 ATTAACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGACACTAAGT
1 ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGT
44336 GGGCTGAGCG
Statistics
Matches: 327, Mismatches: 14, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
97 65 0.20
98 58 0.18
99 203 0.62
100 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (99 bp):
ATTGACCTTAGATTTCGATCCGGACTCGTCATGAGAACATCGAAACTAAGTTGGCCGAACGTAGG
CCCTGGACTCTTTGTGAGAACGGCAACGTTCGCA
Found at i:49358 original size:2 final size:2
Alignment explanation
Indices: 49353--49383 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49343 TGTGTGTGTT
49353 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 T
49384 TCAGAAGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59581 original size:18 final size:19
Alignment explanation
Indices: 59548--59585 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
59538 ACTCATTCCA
59548 TAGCCGATCACCTCCTCCG
1 TAGCCGATCACCTCCTCCG
*
59567 TAGCCG-TCGCCTCCTCCG
1 TAGCCGATCACCTCCTCCG
59585 T
1 T
59586 CGTCCACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.11, C:0.47, G:0.18, T:0.24
Consensus pattern (19 bp):
TAGCCGATCACCTCCTCCG
Found at i:62273 original size:62 final size:63
Alignment explanation
Indices: 62176--62301 Score: 236
Period size: 62 Copynumber: 2.0 Consensus size: 63
62166 AGAATGTTTT
62176 CTAAAAGAAAATTAAATGAGTATAAAATAAAAGTACAAATAATTGG-AAAAAAAGGAAAATGA
1 CTAAAAGAAAATTAAATGAGTATAAAATAAAAGTACAAATAATTGGAAAAAAAAGGAAAATGA
62238 CTAAAAGAAAATTAAATGAGTATAAAATAAAAGTACAAATAATTGGAAAAAAAAAGGAAAATGA
1 CTAAAAGAAAATTAAATGAGTATAAAATAAAAGTACAAATAATTGG-AAAAAAAAGGAAAATGA
62302 TAGAGAGCTC
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 46 0.74
64 16 0.26
ACGTcount: A:0.63, C:0.03, G:0.14, T:0.19
Consensus pattern (63 bp):
CTAAAAGAAAATTAAATGAGTATAAAATAAAAGTACAAATAATTGGAAAAAAAAGGAAAATGA
Found at i:63435 original size:14 final size:14
Alignment explanation
Indices: 63416--63446 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
63406 AAAAGCTAAG
*
63416 TATTAGTGTATTAT
1 TATTAGTGTATAAT
63430 TATTAGTGTATAAT
1 TATTAGTGTATAAT
63444 TAT
1 TAT
63447 ATGAGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (14 bp):
TATTAGTGTATAAT
Found at i:64396 original size:49 final size:49
Alignment explanation
Indices: 64339--64441 Score: 206
Period size: 49 Copynumber: 2.1 Consensus size: 49
64329 AATATATACA
64339 ATAATATATATAGAACATGACCTTTCTTTATTTTTCTTCTTTTGCTGCT
1 ATAATATATATAGAACATGACCTTTCTTTATTTTTCTTCTTTTGCTGCT
64388 ATAATATATATAGAACATGACCTTTCTTTATTTTTCTTCTTTTGCTGCT
1 ATAATATATATAGAACATGACCTTTCTTTATTTTTCTTCTTTTGCTGCT
64437 ATAAT
1 ATAAT
64442 TCCATTTCCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (49 bp):
ATAATATATATAGAACATGACCTTTCTTTATTTTTCTTCTTTTGCTGCT
Found at i:64799 original size:28 final size:28
Alignment explanation
Indices: 64759--64817 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
64749 GAAAAGCATG
64759 TATGGAAATTATAAGACGTAATTAGTAA
1 TATGGAAATTATAAGACGTAATTAGTAA
64787 TATGGAAATTATAAGACGTAATTAGTAA
1 TATGGAAATTATAAGACGTAATTAGTAA
64815 TAT
1 TAT
64818 TTCCTTGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (28 bp):
TATGGAAATTATAAGACGTAATTAGTAA
Found at i:68148 original size:2 final size:2
Alignment explanation
Indices: 68141--68173 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
68131 TACCTTTTTC
68141 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 T
68174 GTATTTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:70114 original size:83 final size:80
Alignment explanation
Indices: 70010--70171 Score: 227
Period size: 83 Copynumber: 2.0 Consensus size: 80
70000 ACAGTTTCAT
* * *
70010 TCTATGAATCCTATTTCAATCATTATGTTTGATTTTGTAACGTTA-TATAATAAATGTTTTTCAT
1 TCTATAAATCCTATTTAAATCATTATGTTTGATTTTGTAA---TAGAAT-ATAAATGTTTTTCAT
70074 TAAATGGAATTAATTTAGC
62 TAAATGGAATTAATTTAGC
* * *
70093 TCTATAAATTCTATTTAAATCATTATGTTTGATTTTTTAATAGAATATATATGTTTTTCATTAAA
1 TCTATAAATCCTATTTAAATCATTATGTTTGATTTTGTAATAGAATATAAATGTTTTTCATTAAA
70158 TGGAATTAATTTAG
66 TGGAATTAATTTAG
70172 GGTATTATTA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
80 34 0.47
81 2 0.03
83 36 0.50
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (80 bp):
TCTATAAATCCTATTTAAATCATTATGTTTGATTTTGTAATAGAATATAAATGTTTTTCATTAAA
TGGAATTAATTTAGC
Found at i:71978 original size:77 final size:73
Alignment explanation
Indices: 71846--71994 Score: 219
Period size: 77 Copynumber: 2.0 Consensus size: 73
71836 AGCAAATAAC
*
71846 AGTTACTTAGAAACTGTTCCACTTAAGAGTATACAAACTTTAGCATTAAACATTTAGATTTAGTA
1 AGTTACTTAGAAACTGTTCCACTTAAGAGTATACAAAATTTAGCATTAAACATTTAGATTTAGTA
71911 ACGCCTAT
66 ACGCCTAT
* *
71919 AGTTACTTAGGAAACTGTTCCAC-TAAGAGTCAATATATAGAATTTAGTATTAAACATTTAGATT
1 AGTTACTTA-GAAACTGTTCCACTTAAGAGT--ATACA-A-AATTTAGCATTAAACATTTAGATT
71983 TAGTAACGCCTA
61 TAGTAACGCCTA
71995 AAGGTCACAT
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
73 16 0.24
74 13 0.19
75 4 0.06
76 1 0.01
77 34 0.50
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (73 bp):
AGTTACTTAGAAACTGTTCCACTTAAGAGTATACAAAATTTAGCATTAAACATTTAGATTTAGTA
ACGCCTAT
Done.