Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017760.1 Corchorus olitorius cultivar O-4 contig17793, 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: 3151
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:1221 original size:331 final size:332
Alignment explanation
Indices: 1--1409 Score: 1960
Period size: 332 Copynumber: 4.2 Consensus size: 332
* * **
1 CTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACAAACGTTGTTCCACGGA-TTTT
1 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC---CAT-CAC-GATTTTT
65 GGCTAAAAACGCGTTCCGGGACCGCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGT-CTCCTTG
61 GGCTAAAAACGCGTTCCGGGACCGCGGCTCAGTTTTCAATGATTTTTGGCCCCGA-TACTCCTTG
* * * * * **
129 ACATAGCAATACTCATCTAACCAAATCTCAGTCAAGTTTTAATT-AAGGATTTGATTTTACGAGC
125 ACATATCTATATTCATCTAACCAAATCTCAGCCAA-ATTGGATTCAAGGATTTGATTTTACGAGC
* * * * *
193 ATCGGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACTTAAAGGAAAATAGATATTTGA
189 ATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGA
258 AGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAA
254 AGCGTGAAAAACCCTT-AATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAA
323 AGATTGTGGAAAAAA
318 AGATTGTGGAAAAAA
* * * * *
338 CTTTCAGGTCCATTTTTGCAAAATTTTAGCCGAAATCATATACTAACCATCACGGTTTTTGGCTA
1 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTA
** * * * * * *
403 AAAACGCAATCCGGGACCCCGACTCCGATTTCAATGATTTTTGGCCCTGAGACTCCTTGACATAT
66 AAAACGCGTTCCGGGACCGCGGCTCAGTTTTCAATGATTTTTGGCCCCGATACTCCTTGACATAT
* * * *
468 CTATA-TCATCTAACCAAATCTCAGCCAAATTGGATTTATGAATTTGATTTTACGGGCATCAGAA
131 CTATATTCATCTAACCAAATCTCAGCCAAATTGGATTCAAGGATTTGATTTTACGAGCATCAGAA
* * * *
532 TAATGTTTCGATTTAATTAGAAATTAATTCGGAAATATATAGGAAAATCGATATTAGAAGCTTGA
196 TCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGA
* *
597 AAAACCATTCAAACTTTTTGGCGTTGAATTATATATATATTCTATAAGTGTTTTGGCCAAAGATT
261 AAAACCCTT-AATCTTTTTGGCGTTGAA-T-TATATATATTCTATAAGTGTTTTGGCCAAAGATT
662 GTGTG-AAAAA
323 GTG-GAAAAAA
* * *
672 CTTTCGGGTCCA--TTTGCAAAATTTTAGCCGAAATCGTGTACGTTA-CATCACGGTTTTTGGCT
1 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGATTTTTGGCT
* * * *
734 AAAAACGCGTTCCGGGGCCTCGGCTTAGTTTTCAATGATTTTT-GCCCCTATACTCCTTGACATA
65 AAAAACGCGTTCCGGGACCGCGGCTCAGTTTTCAATGATTTTTGGCCCCGATACTCCTTGACATA
* * *
798 TCCATATTCATCTAACCAAATCTTAGCCAAATTGGATTCAAAGATTTGATTTTACGAGCATCAGA
130 TCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTCAAGGATTTGATTTTACGAGCATCAGA
* * *
863 ATCATGTTTCGATTTAATTAGAAATTAATTTGGAAACATATAGGAAAATTGATATTAGAAGCGTG
195 ATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTG
* * * *
928 AACAATCCTT-AGCTTTTCGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGT
260 AAAAACCCTTAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGT
992 GGATAAAAA
325 GGA-AAAAA
*
1001 -TTTCGGGTCAATTTTTGCGAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTA
1 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTA
* * *
1065 AAAACGCGTTCCGTGGTCC-CGGCTTAGTTTTCAATGATTTTTGGCCACGATACTCCTTGACATA
66 AAAACGCGTTCCG-GGACCGCGGCTCAGTTTTCAATGATTTTTGGCCCCGATACTCCTTGACATA
*
1129 TCTATATTCATCTAACCAAATCTCATCCAAATTGGATTCAAGGATTTGATTTTACGAGCATCAGA
130 TCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTCAAGGATTTGATTTTACGAGCATCAGA
* *
1194 ATCATGTTTCGATTTAATCATAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTC
195 ATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTG
* *
1259 AAAAACCCTTCAATCATTTTTGGCATTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATT
260 AAAAACCCTT-AATC-TTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATT
1324 GTGGAAAAAA
323 GTGGAAAAAA
*
1334 TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTTGGC
1 -CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GATTTTTGGC
*
1399 TAAAAATGCGT
64 TAAAAACGCGT
1410 ACTGGAAAAA
Statistics
Matches: 957, Mismatches: 94, Indels: 43
0.87 0.09 0.04
Matches are distributed among these distances:
327 1 0.00
328 47 0.05
329 8 0.01
330 96 0.10
331 180 0.19
332 327 0.34
333 81 0.08
334 105 0.11
335 52 0.05
336 19 0.02
337 41 0.04
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (332 bp):
CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTA
AAAACGCGTTCCGGGACCGCGGCTCAGTTTTCAATGATTTTTGGCCCCGATACTCCTTGACATAT
CTATATTCATCTAACCAAATCTCAGCCAAATTGGATTCAAGGATTTGATTTTACGAGCATCAGAA
TCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGGAAAATCGATATTAGAAGCGTGA
AAAACCCTTAATCTTTTTGGCGTTGAATTATATATATTCTATAAGTGTTTTGGCCAAAGATTGTG
GAAAAAA
Found at i:2417 original size:331 final size:330
Alignment explanation
Indices: 1906--3151 Score: 1541
Period size: 331 Copynumber: 3.8 Consensus size: 330
1896 GGAGTATATA
* * * *
1906 TTATGAGTATTTTAGCCAAAAATTGACAGAAAATTTTTTTGGGTCATTTTTTTGTAAAA--TT-G
1 TTATGAGTATTTTAGTCAAAAATTGACAGAAAATTTTTTCGGGTCATCTTTTTGCAAAATTTTAG
* ** * * * * *
1968 CCGAAATCGTGAACTAACCATAACGGTTTTTTACTAAAAAGGCATTTTGGGGCCCCGTCTTAGTT
66 CCGAAATCGTGAACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGGCTTAGTT
* * *
2033 TTGCAT-ATTTTTGGCATCGAGGCTCCA-AGAAATATCTATATTCATCTAATCAAATATCAGCCC
131 TTGCATGATTTTTGGCACCGAGACTCCATA-AAATATCTATATTCATCTAATCAAATATCAGCCA
* * * * *
2096 CACTGAATTTAAGAATTTATTTTTACGAGCATATGAATCTTATTTCGATTTAATTAGAAATTAAT
195 CATTGAATTTAAG-ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAAT
* *
2161 TCAAAAAATATGAAAAATGATATTAAAAGTGTGAAAATTTCTCCAATCTTTTTGGCGCTAAACTA
259 TCAAAAAATATGAAAAACGATATTAAAAGTGTGAAAA-TTCTCCAATCTTTTTGGCGTTAAACTA
2226 TATGTATT
323 TATGTATT
* *
2234 TTATGAGTATTTTATTCAAAAATTGAC-GGAAATATTTTTCGGGTCA-CTTTTTGCAAAATTTTA
1 TTATGAGTATTTTAGTCAAAAATTGACAGAAAAT-TTTTTCGGGTCATCTTTTTGCAAAATTTTA
* * *
2297 GCCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGGCTTAAT
65 GCCGAAATCGTGAACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGGCTTAGT
* * *
2362 TTTGCATGATTTTTGGCGCCGAGACTCCATAAAATATCTATATTCATCTAATCAAATTTCTA-AC
130 TTTGCATGATTTTTGGCACCGAGACTCCATAAAATATCTATATTCATCTAATCAAATATC-AGCC
* * * *
2426 ACATTGAAGTTAAGTTTCTGTTTTTACGAGCATCTGAATCTCGTTTCGATTTAATTAGAAATTAA
194 ACATTGAATTTAAGATT-TGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
2491 TTCAGGAAAATATGAAAAACGATATTAAAAGCGTGAAAATTCCCCAAATCTTTTGTTGACGTTAA
258 TTCA-AAAAATATGAAAAACGATATTAAAAGTGTGAAAATTCTCC-AATC-TTT-TTGGCGTTAA
* *
2556 A-T-TATATATA
319 ACTATATGTATT
* * * *
2566 TTATGAGTATTTTAG-CAAAAAAAGTGACAGAAAATTTTTTTGGGTCATTTTTTTGTAAAATTTT
1 TTATGAGTATTTTAGTC--AAAAATTGACAGAAAATTTTTTCGGGTCATCTTTTTGCAAAATTTT
* * * *
2630 AGCCGAAATCGTGAACTAACCATCACGGTTTTTGCCTAAAAAGGCGTTTCGGGGCCCCGTCTTAG
64 AGCCGAAATCGTGAACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGGCTTAG
** *
2695 TTTT-CAATGATTTTTGGCATTGAGACTCCATGAAATATCTATATTCATCTAATCAAATATCAGC
129 TTTTGC-ATGATTTTTGGCACCGAGACTCCATAAAATATCTATATTCATCTAATCAAATATCAGC
* *
2759 CACATTGAATTTAAGGATTTGTATTTACGAGCATCTAAATATTGTTTCGATTTAATTAGAAATTA
193 CACATTGAATTTAA-GATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTA
* *
2824 ATTCAAAAAA-ATGAAAAACGATATTAAAAGTGTGAAAAGTCCTCCAATCTTTTTGGCATTAAAC
257 ATTCAAAAAATATGAAAAACGATATTAAAAGTGTGAAAA-TTCTCCAATCTTTTTGGCGTTAAAC
*
2888 TATATGTCTT
321 TATATGTATT
* * * * * *
2898 TTATGAATATTTTAGTCAAAATTTGAC-GAAAAAATATTTCGGTTC-TCATTTTGCAAAATTTTA
1 TTATGAGTATTTTAGTCAAAAATTGACAG-AAAATTTTTTCGGGTCATCTTTTTGCAAAATTTTA
* * * * *
2961 GCCGAAATCTTGTACTAATCATCACGGTTTTTGGCTAAAAACACGTTTCGGGACCTCGGCTTAGT
65 GCCGAAATCGTGAACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGGCTTAGT
* * * * * * *
3026 TTTGCATGATTTTTTTGCGCCGAGACTCCATGAAATATCTATATTCATATAATCAAATTTCTGCT
130 TTTGCATGA-TTTTTGGCACCGAGACTCCATAAAATATCTATATTCATCTAATCAAATATCAGCC
* *
3091 ACATTGAATTTAAGTTTTGGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAA
194 ACATTGAATTTAAGATTT-GTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAA
Statistics
Matches: 788, Mismatches: 103, Indels: 51
0.84 0.11 0.05
Matches are distributed among these distances:
327 15 0.02
328 36 0.05
329 2 0.00
330 155 0.20
331 235 0.30
332 107 0.14
333 35 0.04
334 200 0.25
335 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (330 bp):
TTATGAGTATTTTAGTCAAAAATTGACAGAAAATTTTTTCGGGTCATCTTTTTGCAAAATTTTAG
CCGAAATCGTGAACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGGCTTAGTT
TTGCATGATTTTTGGCACCGAGACTCCATAAAATATCTATATTCATCTAATCAAATATCAGCCAC
ATTGAATTTAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTC
AAAAAATATGAAAAACGATATTAAAAGTGTGAAAATTCTCCAATCTTTTTGGCGTTAAACTATAT
GTATT
Done.