Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017859.1 Corchorus olitorius cultivar O-4 contig17892, 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: 2806
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Found at i:1374 original size:330 final size:329
Alignment explanation
Indices: 562--1412 Score: 934
Period size: 337 Copynumber: 2.6 Consensus size: 329
552 GCACTGTATT
* *
562 CAAAAATTGAGGAAAAATCTTTCGGTTCAATTTTTACAAAATTTTAACTGAAATCATGTACTAAC
1 CAAAAATTGAGGAAAAATCTTTAGGTTCAATTTTTACAAAATTTTAAC-GAAATCGTGTACTAAC
* * * * * *
627 CATTACAG-TTTTCGACTAAAAATGCAT-TACGGGCCCCT-CCTTAGTTTTGCATGATTTTTCG-
65 CATCACGGTTTTTAG-CTAAAAA--CATGTTCGGGCCCCTGACTCAGTTTTGCATGATTTTT-GA
* * * * * *
688 GGCCATGACTCTTTTAAATATCTATATTCATCTAACCAAATCTCATCCATATTGGATTTAAGGAT
126 CGCCAAGACTCATTGAAATATCTATATTCATCTAACC-AATCTCAGCCAAATTGGATTTAAGGAT
* * *
753 TTGTTTTTACGAGTATCAAAATCCAGTTTCGATTTAATGATTAAATAATTCGAAAAAAAAAAGCA
190 TTGCTTTTACGAGCATCAAAATCCAGTTTCGATTTAATGATCAAATAATTCG--AAAAAAAA-CA
** * *
818 AGAAAGAAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTACTGTTGAATTATATTTT
252 AG--AGAAAAACCATATTAGAAGCGTGAAAAGCCCTTCAAAATTTTTACTGTTCAATTATATTTT
*
883 TTCTGAGTATTGTGG
315 TTATGAGTATTGTGG
* * *
898 AAAAAATTGAGGAAAAATCTTTAGGTTCAATTTTTACAAAATTATAACCGAAATCGTGTACTAAT
1 CAAAAATTGAGGAAAAATCTTTAGGTTCAATTTTTACAAAATTTTAA-CGAAATCGTGTACTAAC
* * * * *
963 CATCACGGTTTTAAGCTAAAAACGTGTATCGGGCCCCTGGCTCAGTTTTGAATGATTTTTTACGC
65 CATCACGGTTTTTAGCTAAAAACATGT-TCGGGCCCCTGACTCAGTTTTGCATGATTTTTGACGC
* **
1028 CAAGACTCCTTGAAATATCTATATTCATAAAACCACATCTCAGCCAAATTGGATTTAAGGATTTG
129 CAAGACTCATTGAAATATCTATATTCATCTAACCA-ATCTCAGCCAAATTGGATTTAAGGATTTG
* ** * * * * *
1093 CTTTTACGAGCATCAATATCTTGTTTCGATTTGATTATCAATTAATTCG-TAAAAAA-TAG-G-A
193 CTTTTACGAGCATCAAAATCCAGTTTCGATTTAATGATCAAATAATTCGAAAAAAAACAAGAGAA
* * *
1154 AAACCATATTAGAATCTTGAAAAGCCCTTTAAAATTTTTGAC-GTTCAATTGTATATTTTTTATG
258 AAACCATATTAGAAGCGTGAAAAGCCCTTCAAAATTTTT-ACTGTTCAA-T-TATATTTTTTATG
1218 AGTATTGTGG
320 AGTATTGTGG
* * * *
1228 CCAAAAATTGAGTAAAAATCCTTT-GGTTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTA
1 -CAAAAATTGAGGAAAAAT-CTTTAGGTTCAATTTTTACAAAATTTTA-ACGAAATCGTGTACTA
* * *
1292 ACCATCACGGTTTTTTGCTAAAAACATGTTCTAGG-TCCTGACTCAGTTTTGCATGATTTTTGAC
63 ACCATCACGGTTTTTAGCTAAAAACATGTTC-GGGCCCCTGACTCAGTTTTGCATGATTTTTGAC
* *
1356 GCCAAGACTCATTGAAATATTTATA-TCATTCTAACCGAATCTCAGCCACATTGGATT
127 GCCAAGACTCATTGAAATATCTATATTCA-TCTAACC-AATCTCAGCCAAATTGGATT
1413 GAACTATTTG
Statistics
Matches: 437, Mismatches: 62, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
328 39 0.09
329 7 0.02
330 95 0.22
331 79 0.18
332 6 0.01
334 8 0.02
335 1 0.00
336 81 0.19
337 121 0.28
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (329 bp):
CAAAAATTGAGGAAAAATCTTTAGGTTCAATTTTTACAAAATTTTAACGAAATCGTGTACTAACC
ATCACGGTTTTTAGCTAAAAACATGTTCGGGCCCCTGACTCAGTTTTGCATGATTTTTGACGCCA
AGACTCATTGAAATATCTATATTCATCTAACCAATCTCAGCCAAATTGGATTTAAGGATTTGCTT
TTACGAGCATCAAAATCCAGTTTCGATTTAATGATCAAATAATTCGAAAAAAAACAAGAGAAAAA
CCATATTAGAAGCGTGAAAAGCCCTTCAAAATTTTTACTGTTCAATTATATTTTTTATGAGTATT
GTGG
Found at i:1486 original size:330 final size:328
Alignment explanation
Indices: 563--1486 Score: 863
Period size: 330 Copynumber: 2.8 Consensus size: 328
553 CACTGTATTC
* * * *
563 AAAAATTGAGGAAAAATCTTTCGGTTCAATTTTTACAAAATTTTAACTGAAATCATGTACTAACC
1 AAAAATTGAGGAAAAATCTTTAGGTTCAATTTTTACAAAATTATAACCGAAATCGTGTACTAACC
* * * * * * *
628 ATTACAGTTTT-CGACTAAAAATGCAT-TA-CGGGCCCCT-CCTTAGTTTTGCATGATTTTTCG-
66 ATCACGGTTTTAAG-CTAAAAA--CATGTATCAGGCCCCTGACTCAGTTTTGAATGATTTTT-GA
* * * * ** * * * * *
688 GGCCATGACTCTTTTAAATATCTATATTCATCTAACCAAATCTCATCCATATTGGATTTAAGGAT
127 CGCCAAGACTCATTGAAATATCTATATTCATAAAACCACATCTCAGCCAAATTGGATTGAACGAT
* * * ** * * *
753 TTGTTTTTACGAGTATCAAAATCCAGTTTCGATTTAATGATTAAA-TAATTCGAAAAAAAAAAGC
192 TTGCTTTTACAAGCATCAAAATCTTGTTTCGATATAATTA-GAAATTAATTCG---AAAAAAA--
* ** * *
817 AAGAAAGAAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTACTGTTGAATTATATTT
251 TAG---G-AAAACCATATTAGAAGCGTGAAAAGCCCTTCAAAATTTTTACTGTTCAATTATATTT
*
882 TTTCTGAGTATTGTGGA
312 TTTATGAGTATTGTGGA
*
899 AAAAATTGAGGAAAAATCTTTAGGTTCAATTTTTACAAAATTATAACCGAAATCGTGTACTAATC
1 AAAAATTGAGGAAAAATCTTTAGGTTCAATTTTTACAAAATTATAACCGAAATCGTGTACTAACC
* * * *
964 ATCACGGTTTTAAGCTAAAAACGTGTATCGGGCCCCTGGCTCAGTTTTGAATGATTTTTTACGCC
66 ATCACGGTTTTAAGCTAAAAACATGTATCAGGCCCCTGACTCAGTTTTGAATGATTTTTGACGCC
* * *
1029 AAGACTCCTTGAAATATCTATATTCATAAAACCACATCTCAGCCAAATTGGATTTAAGGATTTGC
131 AAGACTCATTGAAATATCTATATTCATAAAACCACATCTCAGCCAAATTGGATTGAACGATTTGC
* * * * ** *
1094 TTTTACGAGCATCAATATCTTGTTTCGATTTGATTATCAATTAATTCGTAAAAAATAGGAAAACC
196 TTTTACAAGCATCAAAATCTTGTTTCGATATAATTAGAAATTAATTCGAAAAAAATAGGAAAACC
* * *
1159 ATATTAGAATCTTGAAAAGCCCTTTAAAATTTTTGAC-GTTCAATTGTATATTTTTTATGAGTAT
261 ATATTAGAAGCGTGAAAAGCCCTTCAAAATTTTT-ACTGTTCAA-T-TATATTTTTTATGAGTAT
*
1223 TGTGGCC
323 TGTGG-A
* * * * **
1230 AAAAATTGAGTAAAAATCCTTT-GGTTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC
1 AAAAATTGAGGAAAAAT-CTTTAGGTTCAATTTTTACAAAATTATAACCGAAATCGTGTACTAAC
** * *
1294 CATCACGGTTTTTTGCTAAAAACATGT-TCTAGG-TCCTGACTCAGTTTTGCATGATTTTTGACG
65 CATCACGGTTTTAAGCTAAAAACATGTATC-AGGCCCCTGACTCAGTTTTGAATGATTTTTGACG
* ** * *
1357 CCAAGACTCATTGAAATATTTATA-TCATTCTAACCGA-ATCTCAGCCACATTGGATTGAACTAT
129 CCAAGACTCATTGAAATATCTATATTCA-TAAAACC-ACATCTCAGCCAAATTGGATTGAACGAT
*
1420 TTGTTTTTACAAG-AGTCAGAAATCATT-TTTC-ATATAATTAGAAATTAATTC-AAAAAAATGA
192 TTGCTTTTACAAGCA-TCA-AAATC-TTGTTTCGATATAATTAGAAATTAATTCGAAAAAAAT-A
1481 GGAAAA
253 GGAAAA
1487 ATCATTCGGT
Statistics
Matches: 498, Mismatches: 72, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
328 39 0.08
329 15 0.03
330 136 0.27
331 87 0.17
332 8 0.02
334 8 0.02
335 2 0.00
336 88 0.18
337 115 0.23
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (328 bp):
AAAAATTGAGGAAAAATCTTTAGGTTCAATTTTTACAAAATTATAACCGAAATCGTGTACTAACC
ATCACGGTTTTAAGCTAAAAACATGTATCAGGCCCCTGACTCAGTTTTGAATGATTTTTGACGCC
AAGACTCATTGAAATATCTATATTCATAAAACCACATCTCAGCCAAATTGGATTGAACGATTTGC
TTTTACAAGCATCAAAATCTTGTTTCGATATAATTAGAAATTAATTCGAAAAAAATAGGAAAACC
ATATTAGAAGCGTGAAAAGCCCTTCAAAATTTTTACTGTTCAATTATATTTTTTATGAGTATTGT
GGA
Found at i:2381 original size:45 final size:45
Alignment explanation
Indices: 2330--2421 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
2320 AACTCTAGAA
2330 AAATCCTAATCCAAATCTAATCAGGAATTGGGTCAAAATCCTAAC
1 AAATCCTAATCCAAATCTAATCAGGAATTGGGTCAAAATCCTAAC
*
2375 AAATCCTAATCCAAATCTAATTAGGAATTGGGTCAAAATCCTAAC
1 AAATCCTAATCCAAATCTAATCAGGAATTGGGTCAAAATCCTAAC
2420 AA
1 AA
2422 GCATCTAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (45 bp):
AAATCCTAATCCAAATCTAATCAGGAATTGGGTCAAAATCCTAAC
Done.