Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011010.1 Corchorus capsularis cultivar CVL-1 contig11031, 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: 18420
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Found at i:607 original size:51 final size:51
Alignment explanation
Indices: 531--731 Score: 220
Period size: 51 Copynumber: 4.1 Consensus size: 51
521 CTTGTTATTT
*
531 ATTAAAAGAGTGCTGGATATTTAGTTTCAGTATCGAGTTTGAATCTCAGGA
1 ATTAAAAGAGTGCTGGACATTTAGTTTCAGTATCGAGTTTGAATCTCAGGA
* ** * *
582 ATTAAAAGAGTGTTGGATGTTTAGTTTCAGTATTGAGTTTGAATCTCGGGA
1 ATTAAAAGAGTGCTGGACATTTAGTTTCAGTATCGAGTTTGAATCTCAGGA
** * *
633 GCTAAAAGAGTG-TCGGACATTTAGTTTCAG---C-A---TAAATTTCAGGA
1 ATTAAAAGAGTGCT-GGACATTTAGTTTCAGTATCGAGTTTGAATCTCAGGA
* * *
677 ATTAAAAGAGTGCTGGACATTTAGTTTTAGTATCGAGTTTGAGTCTCGGGA
1 ATTAAAAGAGTGCTGGACATTTAGTTTCAGTATCGAGTTTGAATCTCAGGA
728 ATTA
1 ATTA
732 GTAAGTAAAA
Statistics
Matches: 122, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
44 34 0.28
45 1 0.01
47 2 0.02
48 1 0.01
50 1 0.01
51 83 0.68
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.35
Consensus pattern (51 bp):
ATTAAAAGAGTGCTGGACATTTAGTTTCAGTATCGAGTTTGAATCTCAGGA
Found at i:1152 original size:29 final size:30
Alignment explanation
Indices: 1113--1170 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1103 AATGACTTGA
1113 ATTTGGAAGTTCA-AGCGGCAAAATGTCCTG
1 ATTTGGAAGTTCAGAG-GGCAAAATGTCCTG
*
1143 ATTT-GAAGTTGAGAGGGCAAAATGTCCT
1 ATTTGGAAGTTCAGAGGGCAAAATGTCCT
1171 TGATGCACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (30 bp):
ATTTGGAAGTTCAGAGGGCAAAATGTCCTG
Found at i:14253 original size:76 final size:76
Alignment explanation
Indices: 14127--14277 Score: 302
Period size: 76 Copynumber: 2.0 Consensus size: 76
14117 TGCATCTCGG
14127 TGGGATTTGGAAGTTGTGGAAAAGGGTTGGGAAATTATTATTAATGTAGTAAGAAATCGGCATCA
1 TGGGATTTGGAAGTTGTGGAAAAGGGTTGGGAAATTATTATTAATGTAGTAAGAAATCGGCATCA
14192 TAATAATACTC
66 TAATAATACTC
14203 TGGGATTTGGAAGTTGTGGAAAAGGGTTGGGAAATTATTATTAATGTAGTAAGAAATCGGCATCA
1 TGGGATTTGGAAGTTGTGGAAAAGGGTTGGGAAATTATTATTAATGTAGTAAGAAATCGGCATCA
14268 TAATAATACT
66 TAATAATACT
14278 GTCTCAGTTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (76 bp):
TGGGATTTGGAAGTTGTGGAAAAGGGTTGGGAAATTATTATTAATGTAGTAAGAAATCGGCATCA
TAATAATACTC
Found at i:15888 original size:321 final size:320
Alignment explanation
Indices: 15073--18420 Score: 4594
Period size: 322 Copynumber: 10.4 Consensus size: 320
15063 GGAATCATAG
* ** *
15073 CCATCATAGTTTTTGGCTAAAAACGCGTTCTAGAGCCCCGGCTCAATTTTGCATGAATTTTGGCG
1 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGAATTTTGGCG
*
15138 CAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGAATATAAGGATTT
66 CAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAGGATTT
* *
15203 GTTTTTACGAGCATCTAAATCTTGTTTCGATTTAAGTAGTAATTAATTCAGAAAAAATTGGAAAA
131 GTTTTTACGAGCATCT-AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAA
* * * *
15268 ACGATATTGGAAGCGTGAAAAGCCCGTAAATGTTTTTGGCGTTGAATTATATATTTTTTTGAGTA
195 ACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAGTA
* * * * *
15333 TTGTGGCAAAAATTTGAGAAAAAGCTTTTTC-GGTCAATTTTTAGCCGAAACCATATACTAA
260 TTGTGGCAAAAAATTGAGAAAAAAC-TTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
* * * *
15394 CGTTACATCACAATTTTTGGCTAAAAACGTGTTCCGGAGCCTTGGCTCAATTTTGCACGAATTTT
1 C----CATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGAATTTT
* *
15459 GGCGCAAAGACTCCTTGAAATATCTATATTCATCGACGCAAATGTCAGCCACATTGGATATAAGA
62 GGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAGG
*
15524 ATTTGTTTTTACGAGCATCTAGATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGG
127 ATTTGTTTTTACGAGCATCTA-ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGG
* * *
15589 AAAAACGATATTAGAAGCGTGAAAAGCCCGTTAATCTTTTTAGCGTTGAATTATATATTGTTTCG
191 AAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATT-TTTCT
* *
15654 GAGTATTGTGG-AAAAAATTGAGAAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTATACT
255 GAGTATTGTGGCAAAAAATTGAG-AAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACT
15718 AA
319 AA
* * * * * * * *
15720 CTATCACAGTTTTTAG-TAAAATCGTGATCCGGAGCCCTGGCTCAATTTTGTATGATTTTTGGTG
1 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGAATTTTGGCG
* * * * *
15784 CAAATG-CTCTTTGAATTATCTATATTCATCTAATCAAAAT-TCAGCCAAATTGGATATAAGGAT
66 CAAA-GACTCCTTGAAATATCTATATTCATCGAAGC-AAATGTCAGCCACATTGGATATAAGGAT
* * * *
15847 TTGTTTTTTCGAGCATCTCAATCTTGTTTCAATTTAATTAGAAATTAATTC-GGAAAAGTATGGA
129 TTGTTTTTACGAGCATCT-AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAT-TGGA
*
15911 AAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTGAATTATATATTTTTCTCT
192 AAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATA-TTTT-TCT
** * * * * *
15976 GAGCGTTGTGGAAAAAAATTGAGAAAAAATTTTTCGGGTTAGTTTTTAACCGAAATCGTGTACTA
255 GAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTA
16041 A
320 A
* * * *
16042 TCGTCACAGTTTTTGGCTAAAAACGCGTTCCGGAG-CCTCAGCTCAATTTTGCAAGAATTTTGGC
1 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCT-GGCTCAATTTTGCATGAATTTTGGC
* * *
16106 GCAAAGATTCCTTGAAATATCTATATTCATTGAAGCAAATGTCAGCCACATTGGATATAATGATT
65 GCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAGGATT
*
16171 TGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTACAAATTAATTCAGAAAAAATTGGAAA
130 TGTTTTTACGAGCATCT-AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAA
**
16236 AACGATATTAGAAGCGTGAAAAGCTAGAT-AATCTTTTTGGCGTTGAATTATAAATATTTTTCTG
194 AACGATATTAGAAGCGTGAAAAGCCCG-TCAATCTTTTTGGCGTTGAATTAT--ATATTTTTCTG
16300 AGTATTGTGGC-AAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
256 AGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
* *
16364 CCATCACAGTTTTTGACTAAAAACGCGTTCCGGAGTCCC-GGCTCAATTTTGCATGAAGTTTGGC
1 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAG-CCCTGGCTCAATTTTGCATGAATTTTGGC
* * * * * * *
16428 GCAAACACTCCTTCAAATATGTATATTCATCAAACCAAATGTCAGTCACATTGAATATAAGGATT
65 GCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAGGATT
*
16493 TGTTTTTACGAGCATCTAGATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAATAATTGGAAA
130 TGTTTTTACGAGCATCTA-ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGG-AA
* * * *
16558 AAACGATATTAGAAGCGTGAAAAGTCCATCAATCTTTTTGGCGTTGAATTATATATCTTTTTTTA
193 AAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATAT-TTTTCTGA
* *
16623 GTATAGTGGCAAAAAATTGAGAAAAAACTCTTT-GGGTCAATATTTAGCCGAAATCGTGTACTAA
257 GTATTGTGGCAAAAAATTGAGAAAAAACT-TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
*
16687 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGAATTTTGGCG
1 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGAATTTT-G-G
* *
16752 CGAAGCAAAGACTTCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAA
64 C---GCAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAG
* *
16817 GATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTACAAATTAATTAAGAAAAAATTG
126 GATTTGTTTTTACGAGCATCT-AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTG
* * * *
16882 GAAAAACGATATTAGATGGGTGAAAATCCCGTTAATCTTTTTGGCGTTGAATTATATATTTTTCT
190 GAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCT
*
16947 GAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTA
255 GAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTA
17012 A
320 A
* * * * *
17013 TCATCACAGATTTTT-GCTAAAAACGTGTTCCGGAACCCTGGCTCAATTTTGTATGATTTTTGGC
1 CCATCACAG-TTTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGAATTTTGGC
* * * * * *
17077 GCACAA-ACTCTTTGAATTATCTATATTCATCGAACCAAATTTCAGCTATATTGGATATAAGGAT
65 GCA-AAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAGGAT
* * * *
17141 TTGTTTTTTCGAGCATCTCAATCTTGTTTCAATTCAATTAGAAATTAATTC-GGAAAAATATGGA
129 TTGTTTTTACGAGCATCT-AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAT-TGGA
* *
17205 AAAACGATATTAGAAGCGTGAAAAGCTCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTTTG
192 AAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTG
* *
17270 TGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCCGAAATCGTGTACTAA
256 AGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
* * *
17335 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGGCTCAATTTTGCACGAATTTTGGCG
1 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGAATTTTGGCG
* * * *
17400 CAAGGACTCCTTGAAATATGTATATTCATCAAAGCAAATGTCAACCACATTGGATATAAGGATTT
66 CAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAGGATTT
* * * * *
17465 GTTTTTACGAGAATCTAGATCTTGTTTCGATTTAATCAGAAATTAAATAAGAAAAAAATGGAAAA
131 GTTTTTACGAGCATCTA-ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGG--AA
* *
17530 AAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGA
193 AAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTGA
* *
17595 CTATTGTGGCAAAAAATTGAGAAAAAACTCTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
257 GTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
* * *
17659 CCATCACAGTTTTTGGCTAAAAGCGCGTAT-CGGAGCCCCGACTCAATTTTGCATGAATTTTGGC
1 CCATCACAGTTTTTGGCTAAAAACGCGT-TCCGGAGCCCTGGCTCAATTTTGCATGAATTTTGGC
* * *
17723 GCAAAGACTCCTTGAAATATCT-TTTTCATC-AGAGCAAATATCAGCAACATTGGATATAAGGAT
65 GCAAAGACTCCTTGAAATATCTATATTCATCGA-AGCAAATGTCAGCCACATTGGATATAAGGAT
* * * *
17786 TTGTTTTTCCGAGCATCTCAATCTTGTTTCAAATTAATTAGAAATTAATTC-GGAAAAATATGGA
129 TTGTTTTTACGAGCATCT-AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAT-TGGA
* * * *
17850 AAAACGATATTAGAAGCGTGAAAAGCTCGTCAACCTTTTTGGCGTTGAATTATATATTTTTTTGC
192 AAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGA
* *
17915 GTATTGTGGCAAAAAATTGAGAAAAAACTTTTCTGGTCAATTTTTAGCCGAAATCGTGTATTAA
257 GTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
* ** *
17979 CCATCACCGTTTTTGGCTAAAAACGCGTTCCGGAGCCCAAGCTTAATTTTGCATGAATTTTGGCG
1 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGAATTTTGGCG
* * * * *
18044 CAAATACTCCTTGAAATATGTATATTTATCAAAGCAAATGTTAGCCACATTGGATATAAGGATTT
66 CAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAGGATTT
* *
18109 GTTTTTACGAGCATCTAGATCTTGTTTCGATTTAATTAAAAATTAATTAAGAAAAAATTGGAAAA
131 GTTTTTACGAGCATCTA-ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAA
* * *
18174 ACGATATTAGAAGCGTGAAAATCCTGTTAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGT
195 ACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTGAGT
* * *
18239 ATTGTGGCAAAAAATTGAGAAAAAACTCTTCGGGACAGTTTTTAGCCGAAATCGTGTACTAA
259 ATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
* * * ** ** *
18301 CCATCACAGATTTTT-GCTAAAAACGTGTTCCGGAACCCTGACTTGATTTTGTTTGATTTTTGGC
1 CCATCACAG-TTTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGAATTTTGGC
* * * * *
18365 GCACAA-ACTCTTTGAATTATCTATATTCATCGAACCAAATTTCAGCCATATTGGAT
65 GCA-AAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGAT
Statistics
Matches: 2678, Mismatches: 288, Indels: 121
0.87 0.09 0.04
Matches are distributed among these distances:
319 1 0.00
320 157 0.06
321 547 0.20
322 716 0.27
323 450 0.17
324 222 0.08
325 254 0.09
326 160 0.06
327 57 0.02
328 113 0.04
329 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (320 bp):
CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGAATTTTGGCG
CAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAGGATTT
GTTTTTACGAGCATCTAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAAA
CGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAGTAT
TGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA
Done.