Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019659.1 Corchorus olitorius cultivar O-4 contig19692, 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: 10009
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1735 original size:66 final size:66
Alignment explanation
Indices: 1633--1762 Score: 251
Period size: 66 Copynumber: 2.0 Consensus size: 66
1623 ATTATCCATT
1633 AAAAAAATACACACTTCGAACATGTGTGAGATAATCTTTTATGATTTTTCGTACCATGCAAGATT
1 AAAAAAATACACACTTCGAACATGTGTGAGATAATCTTTTATGATTTTTCGTACCATGCAAGATT
1698 A
66 A
*
1699 AAAAAAATACACACTTCGAACATGTGTGAGATAATCTTTTATGATTTTTCGTATCATGCAAGAT
1 AAAAAAATACACACTTCGAACATGTGTGAGATAATCTTTTATGATTTTTCGTACCATGCAAGAT
1763 CTTCCTATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (66 bp):
AAAAAAATACACACTTCGAACATGTGTGAGATAATCTTTTATGATTTTTCGTACCATGCAAGATT
A
Found at i:7156 original size:37 final size:37
Alignment explanation
Indices: 7103--7208 Score: 167
Period size: 37 Copynumber: 2.9 Consensus size: 37
7093 TCAATCTTCT
* * *
7103 TTGATAATAATCCTCCATATACGTGAATCTTCAATCG
1 TTGAAAATAATCCTCCACATACGTGGATCTTCAATCG
*
7140 TTGAAAATAATCCTCCACATACGTGGATCTTCAATCT
1 TTGAAAATAATCCTCCACATACGTGGATCTTCAATCG
*
7177 TTGAAAATAATCCTCCACATATGTGGATCTTC
1 TTGAAAATAATCCTCCACATACGTGGATCTTC
7209 TTTCAATAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (37 bp):
TTGAAAATAATCCTCCACATACGTGGATCTTCAATCG
Found at i:8216 original size:333 final size:330
Alignment explanation
Indices: 7704--9603 Score: 2363
Period size: 333 Copynumber: 5.7 Consensus size: 330
7694 ACCTCGGAAT
* * * * *
7704 GCGTTTTTAGTCAAAAAACCGTGAT-G---GTACATGATTTCGGCTAAAATTTTGCA-AAAATAG
1 GCGTTTTTAG-CCAAAAACCGTGATGGTTAGTACACGATTCCAGCTTAAATTTTGCAGAAAAT-G
* * * * * *
7764 ACCCGAAATATTTTTCCTCAATTTTTAGCCACAATACTCACAAAATATATATAATTGAACTCCAA
64 ACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAA
* *
7829 AAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTCCATATTTTTTTGAATTAATTTTTAAT
129 AAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTGAATTAATTTCTAAT
* * * *
7894 TAAATAAAAACAAAATTCAGATGCTCGTAAAAACAAATCATTAAATTCAAATGTGGCTGAGATTT
193 TAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATGC-AATGTGGCTGAGATTT
* * * *
7959 TAATAGATGAGTATAGATATTTCAAGGAGTCTCGGTGACAAAAAATCATGCAAAACTAAGTCGGG
257 GATTAGATGAGTATAGATATTTCAAGGAGTCTCGGTG-CCAAAAATCATGCAAAACTAAGTCGGA
*
8024 GCCCCGAAAT
321 GCCCCGAAAC
* * * *
8034 GCGATTTTAGCCAAAACCCATGATGGTTAGTACACAATTCCAGCTTAAATTTTGCAGAAAATGAC
1 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTCCAGCTTAAATTTTGCAGAAAATGAC
* *
8099 CCGACAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATTTCTAATTTAACGCCAA
66 CCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATA--TATAATTTAACGCCAA
* *
8164 AAAGATTGGAGGACTTTTCACGCTTTTAATACCGTTGTTCAT-TTTTTTGAATTAATTTCTAATT
129 AAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTGAATTAATTTCTAATT
* * * * *
8228 AAATCGAAACAAGATTCAAATGCTCGTATAAACAAATCCTTAAATGCAATGTGACTGAGATTTAA
194 AAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATGCAATGTGGCTGAGATTTGA
* * * *
8293 TTAGATGAATATAGATATTTCAAGGATTCTCGATGCCAAAAAT-ATGC-AAACAAAGTCGGAGCC
259 TTAGATGAGTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGTCGGAGCC
*
8356 CTGAAAC
324 CCGAAAC
* *** * *
8363 GCGTTTTTA-CCAAAAAAACAGTGA----T-GTACACGATTTTGGCTAAAATTTTGCAAAAAATG
1 GCGTTTTTAGCC--AAAAACCGTGATGGTTAGTACACGATTCCAGCTTAAATTTTGCAGAAAATG
* * * *
8422 ACCCGAAAAATTTTTCTTCAA-TTTTGGCTAAAATACTCATGAAACATATATAATTTAACGCCAA
64 ACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAA
* * * *
8486 AAAGGTTGAAGGACTTTTTCGA-GCTTTTAATATCATTTTTCATATATTTCTGAATTAATTTCTA
129 AAAGATTGGAGGAC-TTTTC-ACGCTTTTAATATCGTTTTTCATAT-TTTTTGAATTAATTTCTA
* * * *
8550 ATTAAATCAAAACAAGATTCAGATACTCGTAAAAACAAATCATTAAATTCAAATGTGGATGAGAT
191 ATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATGC-AATGTGGCTGAGAT
*
8615 TTGATTAGATGAGTATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGT-GG
255 TTGATTAGATGAGTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGTCGG
* *
8679 GGTCCTCGAAAC
320 AG-CCCCGAAAC
* * *
8691 GCGTTATTAGCGAAAAACCCGTGATGGTTAATACACGATTCCAGCTTAAATTTTGCAGAAAATGA
1 GCGTTTTTAGCCAAAAA-CCGTGATGGTTAGTACACGATTCCAGCTTAAATTTTGCAGAAAATGA
* * *
8756 CCAGACAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATTTATAATTTTACGCCA
65 CCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATA--TATAATTTAACGCCA
*
8821 AAAAGATTGGAGGACTTTTCACGCTTTTAATACCGTTTTTCATATTTTTTTGAATTAATTTCTAA
128 AAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTGAATTAATTTCTAA
* * * * *
8886 TTAAATCGAAACAAGATTCAAATGCTCGTATAAACAAATCCTTAAATGCAATCTGACTGAGATTT
192 TTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATGCAATGTGGCTGAGATTT
* * * * * * *
8951 GATTAGATGAATATAGATATTTCAAGGATTCTCGATGCCAGAAATTATGCAAAATTGAGTCGGAG
257 GATTAGATGAGTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGTCGGAG
*
9016 CCCTGAAAC
322 CCCCGAAAC
* *** *
9025 GCGTTTTTA-CCAAAAAAACCGTGATGGTTACTACACGATTTTGGC-TAAACTTTTGCAAAAAAT
1 GCGTTTTTAGCC--AAAAACCGTGATGGTTAGTACACGATTCCAGCTTAAA-TTTTGCAGAAAAT
* * *
9088 GACCCGAAAAATTTTTCTTCAATTTTT-GACTAAAATACTCATGAAATATCTATAATTTAACGCC
63 GACCCGAAAAATTTTTCCTCAATTTTTAG-CTAAAATACTCATAAAATATATATAATTTAACGCC
* * * *
9152 AAAAAGGTTGAAGGACTTTTCGA-GTTTTTAATATCATTTTTCATATTTTTCTGAATTAATTTCT
127 AAAAAGATTGGAGGACTTTTC-ACGCTTTTAATATCGTTTTTCATATTTTT-TGAATTAATTTCT
* *
9216 AATTAAATCAAAACAAGATTCAAATGCTGGTAAAAACAAATCATTAAATTCAAATGTGGCTGAGA
190 AATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATGC-AATGTGGCTGAGA
* *
9281 TTTGATTAGATGAGTATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCG
254 TTTGATTAGATGAGTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGTCG
**
9346 GAGCATCGAAAC
319 GAGCCCCGAAAC
* * *
9358 GGGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTCCAGCTTAAATTTTGCAGGAAATGGC
1 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTCCAGCTTAAATTTTGCAGAAAATGAC
* * * * * *
9423 TCGAAAAATTTCTCCACAATTTTTGGCTAAAATAGTCAT--AATATATATAATTTAACTCCAAAA
66 CCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAAAA
* *
9486 GGATTGGAGGACTTTTCACGCTTTTAGTATCGTTTTTCATATTTTTCTGAATTAATGTT-TAATT
131 AGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTT-TGAATTAAT-TTCTAATT
* * * *
9550 AAATCGAAACAAGATTCAGATGCTCGTATAAACAAATCCTTAAATGCAATGTGG
194 AAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATGCAATGTGG
9604 TCATTAATTA
Statistics
Matches: 1345, Mismatches: 183, Indels: 85
0.83 0.11 0.05
Matches are distributed among these distances:
322 27 0.02
323 23 0.02
324 26 0.02
325 108 0.08
326 55 0.04
327 12 0.01
328 30 0.02
329 47 0.03
330 138 0.10
331 14 0.01
332 231 0.17
333 270 0.20
334 190 0.14
335 146 0.11
336 28 0.02
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (330 bp):
GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTCCAGCTTAAATTTTGCAGAAAATGAC
CCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAAAA
AGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTGAATTAATTTCTAATTAA
ATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATGCAATGTGGCTGAGATTTGATT
AGATGAGTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGTCGGAGCCCC
GAAAC
Found at i:9668 original size:148 final size:147
Alignment explanation
Indices: 9457--9752 Score: 422
Period size: 148 Copynumber: 2.0 Consensus size: 147
9447 GGCTAAAATA
* * *
9457 GTCATAATATATATAATTTAACTCCAAAAGGATTGGAGGACTTTTCACGCTTTTAGTATCGTTTT
1 GTCATAATATATATAATTTAACACAAAAAGGATTGAAGGACTTTTCACGCTTTTAGTATCGTTTT
* * *
9522 TCATATTTTTCTGAATTAATGTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTATAAACAAA
66 TCATATTTTTCTGAATTAAT-TTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAACAAA
*
9586 TCCTTAAATGC-AATGTG
130 TCATTAAATGCAAATGTG
9603 GTCATTAATTATATATAATTTAACACAAAAAAGG-TTGAAGGACTTTTCGA-GCTTTTCA-TATC
1 GTCA-TAA-TATATATAATTTAACAC-AAAAAGGATTGAAGGACTTTTC-ACGCTTTT-AGTATC
*
9665 GTTTTTTATATTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAA
61 GTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAA
*
9730 CAAATCATTAAATTCAAATGTG
126 CAAATCATTAAATGCAAATGTG
9752 G
1 G
9753 ATGAGATTTG
Statistics
Matches: 134, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
146 4 0.03
147 5 0.04
148 110 0.82
149 15 0.11
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (147 bp):
GTCATAATATATATAATTTAACACAAAAAGGATTGAAGGACTTTTCACGCTTTTAGTATCGTTTT
TCATATTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAACAAAT
CATTAAATGCAAATGTG
Done.