Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010777.1 Corchorus capsularis cultivar CVL-1 contig10798, 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: 22332
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:517 original size:2 final size:2
Alignment explanation
Indices: 512--537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
502 TGCATTGAAT
512 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
538 GTATTGTGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1172 original size:321 final size:319
Alignment explanation
Indices: 1--1737 Score: 1486
Period size: 321 Copynumber: 5.4 Consensus size: 319
* * ** * * * * *
1 ATGATTTTTGGCGTAAAGATTTTTTGAAATATATATATTCATAGAATCAAATCCCAGCCATATTG
1 ATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTG
* * * * * * * *
66 AATTTAGGGATTTGCTTTTACGAGCATCTTAA---TATTTCGATTTAATTAGAAGTTAATTCGGG
66 GATATAAGGATTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTC-GG
* * * *
128 AAAAAAAATGAAAAAACGAAATTAGAAGCGTGAAAAG-CCGGCAATCTTTTTGGC-ATGAGATTA
130 --AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA-ATTA
* * * * * *
191 TATATATTTCTT-T-AGTATTGTGGCAAAAAATTCAGAAAAATATTTTCGGATTAGTTTTTCGCC
192 TATAT-TTT-TTATAATTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCC
* * * * *
254 GAAATCGTGTACTAACCATCACAGTTTTTGGGTTAAAAACGCGTTTCGGGGCCCTGCTTTAGTTT
255 AAAATCGTGTACTAACCATCACGGTTTTT-GGCTAAAAACGCG-TTCAGGGCCCGGC-TTAGTTT
319 TGC
317 TGC
* * *
322 ATGATTTTTGGCGCAAAGGCTCCTTGAAATATCCATATTCATCGAACCAAATTTCAGCCACATTG
1 ATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTG
* * * * * *
387 GATACAAGGATTTGTTTTTAGGAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCGGA
66 GATATAAGGATTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-
* ** * *
452 AAAAAATGG-AAAACGATATTAGAAGCGTGAAAAACCTTTCACAAT-TTTTTTGCATTGAATTAT
130 AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGT--CAATCTTTTTGGCGTTGAA-T-T
* * *
515 ATATATATATATATATATATATAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGCCA-AT
191 ATATAT-T-T-T-T-TATA-AT--TATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTT
* * ** *
579 TTTAGCCGAAATTGTGTACTAGTCATCACGGTTTTTGACTAAAAACGCGTTCTAGAGG-CCGGAC
248 TTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTC-AG-GGCCCGG-C
*
643 TTAATTTTGC
310 TTAGTTTTGC
* * * * *
653 ATGCTTTTTTGCGCAAAGACTCCTAGAAATAGCTATATTCATCGAATCAAATCTCAGCCACATTG
1 ATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTG
* * *
718 GATATAAGGATCTTTTTTTTTAAC-AAGCATCTAAATCTTGTTTCTATTTAATTAGAAATAAATT
66 GATATAAGGA--TTTGTTTTT-ACGAA-CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATT
* * * * *
782 TGGAAAAAAATGAAAAAAAAACGATTTTAGAACCGTGAAAAGCCCATCAATCTTTTTGGCGTTGA
127 CGG-AAAAAATG---GAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
* *
847 ATTATATATTTTTTCTAATTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTGG
188 ATTATATATTTTTTATAATTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAG
912 CCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTACAGGGCCCTGGCTTAGTT
253 CCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTT-CAGGGCCC-GGCTTAGTT
*
977 TTGG
316 TTGC
* * * *
981 ATGATTTCTGGCAGAAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCGCATT
1 ATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATT
* * * *
1046 GGATTTAAGGGTTT-TTTTTACGAACATCTAAATCTTGTTTCGATTTAATTAGAAACTATTTCAG
65 GGATATAAGGATTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTC-G
* * *
1110 G-AAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGGTGAATTATA
129 GAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATA
* * ** * * * *
1174 TATTTTTTCTGATTATTACGGCAAAGAATTGAGGAAAAAATTTTCGGATCAGTTTTTAGTCAAAA
194 TATTTTTTATAATTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCAAAA
* * * * **
1239 TAGTGTACTAACCATCACGGTTTTT-GATAAAAAAACGCGTTCCATGGCTACAACTCT-GTTTTG
259 TCGTGTACTAACCATCACGGTTTTTGGCT--AAAAACGCGTT-CAGGGC-CCGGCT-TAGTTTTG
1302 C
319 C
* ** * ** * * *
1303 ATGATTTTTGACGCCGATACTCCTTGATTTATCTTTATTCATCTAATCAAATCTCAGCCACATTG
1 ATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTG
* ** * *
1368 GAT-TTAGTGATTTGTTTTTACGTGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG
66 GATATAAG-GATTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTC-G
* * * * * *
1432 AAAAAAATACGAAAAGCGATATTAAAAGCTTGAAAAGTCC-TCCAATCTTTTTGGCGTTGAATTA
129 GAAAAAAT-GGAAAAACGATATTAGAAGCGTGAAAAGCCCGT-CAATCTTTTTGGCGTTGAATTA
* * * * * * * *
1496 TATATATTTTATGAGTATTTTCGCCAAAAATGGAGGAAAAAA-TTTCGGGTCA-TTTTTA--C--
192 TATATTTTTTATAATTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCAA
* * * * *
1555 ---C----A-T-A--AT---GGTTTTTGGCTAAAAACACATTCCAGGCCCCGGCTCAGTTTTGT
257 AATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTT-CAGGGCCCGGCTTAGTTTTGC
** ** * * *
1605 ATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATT-ATTTAATCAAATCTCAGGCATATTG
1 ATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTG
* * ** * *
1669 GATTTAATGATTTGTTTTTACGAGTATATAAATCTTGATTCGATTTAATTAGAAATTAATTC--A
66 GATATAAGGATTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGA
1732 AAAAAT
131 AAAAAT
1738 ATGAAATAAA
Statistics
Matches: 1179, Mismatches: 189, Indels: 119
0.79 0.13 0.08
Matches are distributed among these distances:
298 7 0.01
301 74 0.06
302 45 0.04
303 14 0.01
304 7 0.01
305 2 0.00
307 2 0.00
309 1 0.00
310 1 0.00
311 1 0.00
320 6 0.01
321 283 0.24
322 94 0.08
323 27 0.02
324 117 0.10
325 44 0.04
326 10 0.01
327 43 0.04
328 69 0.06
329 61 0.05
330 6 0.01
331 92 0.08
332 36 0.03
333 42 0.04
334 46 0.04
335 7 0.01
336 5 0.00
337 12 0.01
338 25 0.02
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (319 bp):
ATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTG
GATATAAGGATTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGA
AAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATA
TTTTTTATAATTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCAAAATC
GTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCAGGGCCCGGCTTAGTTTTGC
Found at i:11494 original size:30 final size:29
Alignment explanation
Indices: 11418--11525 Score: 92
Period size: 30 Copynumber: 3.6 Consensus size: 29
11408 GGCATGTATC
* * *
11418 CTTTTGTGCACGTGGCATGCCACGTGCCA
1 CTTTTGTACACGTGGCATACCACGTGTCA
* *
11447 CTTTTTGAAACATGTGGCATACCACGTGTCA
1 C-TTTTG-TACACGTGGCATACCACGTGTCA
* *
11478 CTTTTGTTACACGTGGCGTGA-CATGTGTCA
1 CTTTTG-TACACGTGGCAT-ACCACGTGTCA
*
11508 CTTTTGGTACATGTGGCA
1 CTTTT-GTACACGTGGCA
11526 CGACTTTTGG
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
29 1 0.02
30 41 0.65
31 21 0.33
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (29 bp):
CTTTTGTACACGTGGCATACCACGTGTCA
Found at i:15021 original size:10 final size:11
Alignment explanation
Indices: 14996--15023 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
14986 TTCTTCTTCT
14996 TTTTTTGTTTA
1 TTTTTTGTTTA
15007 TTTTTTGTTTA
1 TTTTTTGTTTA
15018 TTTTTT
1 TTTTTT
15024 CTTTTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTTTGTTTA
Done.