Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019599.1 Corchorus olitorius cultivar O-4 contig19632, 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: 28922
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:1133 original size:22 final size:22
Alignment explanation
Indices: 1093--1134 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1083 GTTTATAATA
* *
1093 TTCTTGGGTCATTCGGGTTAAC
1 TTCTCGGGTCATTCAGGTTAAC
*
1115 TTCTCGGGTCATTTAGGTTA
1 TTCTCGGGTCATTCAGGTTA
1135 CGAATTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (22 bp):
TTCTCGGGTCATTCAGGTTAAC
Found at i:5070 original size:16 final size:16
Alignment explanation
Indices: 5049--5079 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5039 CTTAAAATTT
*
5049 TAAAGATTTTTAAAAA
1 TAAAGAATTTTAAAAA
5065 TAAAGAATTTTAAAA
1 TAAAGAATTTTAAAA
5080 TGTATCATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TAAAGAATTTTAAAAA
Found at i:28483 original size:27 final size:27
Alignment explanation
Indices: 28451--28502 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28441 ACTCAACTTT
* **
28451 TCCTACTCCTTTACATGACCAAACTGG
1 TCCTACTCCTTAACAACACCAAACTGG
28478 TCCTACTCCTTAACAACACCAAACT
1 TCCTACTCCTTAACAACACCAAACT
28503 ACACCAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.37, G:0.06, T:0.27
Consensus pattern (27 bp):
TCCTACTCCTTAACAACACCAAACTGG
Found at i:28799 original size:778 final size:777
Alignment explanation
Indices: 27305--28862 Score: 2814
Period size: 778 Copynumber: 2.0 Consensus size: 777
27295 CACTTGACTT
27305 ATATATGTTTACATACCTACAACTTCTAACTCTGTTAAGCAAACCCACCAGATAATAGCAGCAAG
1 ATATATGTTTACATACCTACAACTTCTAACTCTGTTAAGCAAACCCACCAGATAATAGCAGCAAG
* *
27370 CAACCAGTGTAGTGAAGGAAAGCAAGCCACAGCTACAAGTTTTTGTTTTCAATTTCTGTGTTTAT
66 CAACCAGTGTAGTGAAGGAAAGCAAGCCACAGCGACAAGTTTTTGTTTTCAATTTCAGTGTTTAT
*
27435 GTTATTTACTTTTTAAATTATGGTAAATGTTTATGGATTTTGTCTTTTCAGTTTAAGCATATGTA
131 GTTATTCACTTTTTAAATTATGGTAAATGTTTATGGATTTTGTCTTTTCAGTTTAAGCATATGTA
27500 ACTTTGAAGCAATATTTTTAGCAAAAAGTATCTATGCCTTTGCAACAATGTACTTACTAGAATGA
196 ACTTTGAAGCAATATTTTTAGCAAAAAGTATCTATGCCTTTGCAACAATGTACTTACTAGAATGA
* * *
27565 TTCAACGGAATCAAATTCATCCTAAGACTTCCTCTTTACATTTTACTCACTGTAGAGCATAGCTC
261 TTCAACGGAATCAAATTCAACCTAAGACTTCCTCTTTACATTTTACTCACCGTAGAGCATAACTC
* *
27630 ATATCAATCAATTTATTGCATTAAAAATTTGCTACTCAACTTTTCCTATTCCTTTACATTACCAA
326 ATATCAATCAATTTATTGCATTAAAAATTTGCTACTCAACTTTTCCTACTCCTTTACATGACCAA
* *
27695 ACTGTTCCTACTCCTTAACAACACTAAACTACACCAAACTGAAGGCAATTCATATAAAAGCAACA
391 ACTGGTCCTACTCCTTAACAACACCAAACTACACCAAACTGAAGGCAATTCATATAAAAGCAACA
* * *
27760 TTTAACAATTCAAATTTCAAAACGCTCGACGCACTACTCATAGATTTTCTAAAACCCTATCTCAA
456 TTTAACAATTCAAATTTCAAAACACTCGACGCACCACTCATAGATTTTCTAAAACCCTATCCCAA
* *
27825 TAATATCTCAAATTTGGGTACTTACCTTTTATACAGGATTTATTTTAAAAGGTGGCTAAACCTTG
521 TAATATCTCAAATTTGGGGACTTACCTTTTATACAGGATTTATTTTAAAAGGGGGCTAAACCTTG
27890 GGCTGAAATCGTGCCTAAATTTAAGGAAGTCATTTGACATGACAAGATTCTATTGGTTAGTCCCA
586 GGCTGAAATCGTGCCTAAATTTAAGGAAGTCATTTGACATGACAAGATTCTATTGGTTAGTCCCA
*
27955 TGGATGACGTGGTGGGTCCGTCCCACCTAATAATTTCTCCTTTAAAACCATTAGTACATTATTAT
651 TGGATGACGTGATGGGTCCGTCCCACCTAATAATTTCTCCTTTAAAACCATTAGTACATTATTAT
* * *
28020 TTTTGGGAGGGGGAGGTTTATTGTTTTTGGTATTATAAAACTCAAAATTATATGCTAAATACC
716 TTTGGGGAGGGGGAGCTTTATTGTTTTTGGTATCATAAAA-TCAAAATTATATGCTAAATACC
28083 ATATATGTTTACATACCTACAACTTCTAACTCTGTTAAGCAAACCCACCAGATAATAGCAGCAAG
1 ATATATGTTTACATACCTACAACTTCTAACTCTGTTAAGCAAACCCACCAGATAATAGCAGCAAG
*
28148 CAACCAGTGTAGTGAAGGAAAGCAAGCCACAGCGGCAAGTTTTATGTTTTCAATTTCAGTGTTTA
66 CAACCAGTGTAGTGAAGGAAAGCAAGCCACAGCGACAAGTTTT-TGTTTTCAATTTCAGTGTTTA
*
28213 TGTTATTCACTTTTTAAGTTATGGTAAATGTTTATGGATTTTGTCTTTTCAGTTTAAGCATATGT
130 TGTTATTCACTTTTTAAATTATGGTAAATGTTTATGGATTTTGTCTTTTCAGTTTAAGCATATGT
* * *
28278 AACTTTGAAGCATTATTTTTAGCAAAAA-TGTCTATGCCTTTGTAACAATGTACTTACTAGAATG
195 AACTTTGAAGCAATATTTTTAGCAAAAAGTATCTATGCCTTTGCAACAATGTACTTACTAGAATG
28342 ATTCAACAGG-ATCAAATTCAACCTAAGACTTCCTCTTTACATTTTACTCACCGTAGAGCATAAC
260 ATTCAAC-GGAATCAAATTCAACCTAAGACTTCCTCTTTACATTTTACTCACCGTAGAGCATAAC
28406 TCATATCAATCAATTTATTGCATTAAAAATTTGCTACTCAACTTTTCCTACTCCTTTACATGACC
324 TCATATCAATCAATTTATTGCATTAAAAATTTGCTACTCAACTTTTCCTACTCCTTTACATGACC
28471 AAACTGGTCCTACTCCTTAACAACACCAAACTACACCAAACTGAAGGCAATTCATATAAAAGCAA
389 AAACTGGTCCTACTCCTTAACAACACCAAACTACACCAAACTGAAGGCAATTCATATAAAAGCAA
* *
28536 CATTTAACAATTCAAATTTCAAAACACTCGACGCGCCACTCATCGATTTTCTAAAACCCTATCCC
454 CATTTAACAATTCAAATTTCAAAACACTCGACGCACCACTCATAGATTTTCTAAAACCCTATCCC
*
28601 AATAATATCTCAAATTTGGGGACTTACCTTTTATACATGATTTATTTTAAAAGGGGGCTAAACCT
519 AATAATATCTCAAATTTGGGGACTTACCTTTTATACAGGATTTATTTTAAAAGGGGGCTAAACCT
* *
28666 TGGGTTGAAATCGTGCCTAAATTTAAGGAAGTCATTTGACATGGCAAGATTCTATTGGTTAGTCC
584 TGGGCTGAAATCGTGCCTAAATTTAAGGAAGTCATTTGACATGACAAGATTCTATTGGTTAGTCC
28731 CATGGATGACGTGATGGGTCCGTCCCACCTAATAATTTCTCCTTTAAAACCATTAGTACATTATT
649 CATGGATGACGTGATGGGTCCGTCCCACCTAATAATTTCTCCTTTAAAACCATTAGTACATTATT
28796 ATTTTGGGGAGGGGGAGCTTTATTGTTTTTGGTATCATAAAATCAAAATTATATGCTAAATACC
714 ATTTTGGGGAGGGGGAGCTTTATTGTTTTTGGTATCATAAAATCAAAATTATATGCTAAATACC
28860 ATA
1 ATA
28863 AGTAAGCTAA
Statistics
Matches: 749, Mismatches: 29, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
777 25 0.03
778 612 0.82
779 112 0.15
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (777 bp):
ATATATGTTTACATACCTACAACTTCTAACTCTGTTAAGCAAACCCACCAGATAATAGCAGCAAG
CAACCAGTGTAGTGAAGGAAAGCAAGCCACAGCGACAAGTTTTTGTTTTCAATTTCAGTGTTTAT
GTTATTCACTTTTTAAATTATGGTAAATGTTTATGGATTTTGTCTTTTCAGTTTAAGCATATGTA
ACTTTGAAGCAATATTTTTAGCAAAAAGTATCTATGCCTTTGCAACAATGTACTTACTAGAATGA
TTCAACGGAATCAAATTCAACCTAAGACTTCCTCTTTACATTTTACTCACCGTAGAGCATAACTC
ATATCAATCAATTTATTGCATTAAAAATTTGCTACTCAACTTTTCCTACTCCTTTACATGACCAA
ACTGGTCCTACTCCTTAACAACACCAAACTACACCAAACTGAAGGCAATTCATATAAAAGCAACA
TTTAACAATTCAAATTTCAAAACACTCGACGCACCACTCATAGATTTTCTAAAACCCTATCCCAA
TAATATCTCAAATTTGGGGACTTACCTTTTATACAGGATTTATTTTAAAAGGGGGCTAAACCTTG
GGCTGAAATCGTGCCTAAATTTAAGGAAGTCATTTGACATGACAAGATTCTATTGGTTAGTCCCA
TGGATGACGTGATGGGTCCGTCCCACCTAATAATTTCTCCTTTAAAACCATTAGTACATTATTAT
TTTGGGGAGGGGGAGCTTTATTGTTTTTGGTATCATAAAATCAAAATTATATGCTAAATACC
Done.