Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023885.1 Corchorus olitorius cultivar O-4 contig23918, 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: 29802
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1755 original size:331 final size:328
Alignment explanation
Indices: 1--2330 Score: 2958
Period size: 331 Copynumber: 7.1 Consensus size: 328
* * *
1 CCAAAAATTAAGGGAAAATTTTTCGGCTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
1 CCAAAAATTGAGGAAAAATTTTT-GGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
* *
66 CCATCACTGTTTTTGGCTAAAAACGTGTTCTAC-GGCCCCGGCTCAGTTTTGCATGATTTTCGGC
65 CCATCACGGTTTTTGGCTAAAAACGCGTTC--CGGGCCCCGGCTCAGTTTTGCATGATTTTCGGC
* * * * * *
130 GCAAAAACTCCTTCAAATATCTATATTCATCTAATAAAATCTCAGCCACATCGAATTTAAGGATT
128 GCCAAGACTCCATGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATT
195 TGTTTCTACGAGCATCAGAAATTGGTTTCAATTTAATTAGAAATTAATTTGGAAAAAATCGGAAA
193 TGTTTCTACGAGCATCAGAAATTGGTTTCAATTTAATTAGAAATTAATTTGGAAAAAAT-GG-AA
* **
260 AATGATATTAGAAGCTTGAAATGCCCTTCAATTTTTTTGGCGTTGAATTATTTATTTTTTACGAG
256 AATGATATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGCGTTGAATTATAGATTTTTTACGAG
325 TATTTTGG
321 TATTTTGG
* * * * *
333 TCTAAAATTTAGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG-GTA-T-A
1 CCAAAAATTGAGG-AAAAATTTTTGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
** *
395 CCATCATAGTTTTTGGCTAAAAACGTGTT-CGGTGCCCCGGCTCAGTTTTGCATGATTTTCGGCG
65 CCATCACGGTTTTTGGCTAAAAACGCGTTCCGG-GCCCCGGCTCAGTTTTGCATGATTTTCGGCG
* * * * *
459 CCGAGACTCCTTGAAATATCTATATTCACCTAATCAAATCTAAGCCACATTGGATTTAAGGATTT
129 CCAAGACTCCATGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATTT
* * * * *
524 GTTTCTACGAGTATCAGAATTTGGTTTCGATTTGATAAGAAATTAATTTGGAAAAAAATGGAAAA
194 GTTTCTACGAGCATCAGAAATTGGTTTCAATTTAATTAGAAATTAATTTGG-AAAAAATGG-AAA
* * * *
589 ATAATATTAGAAGCGTGAAATGCTCTTCAATTTTTTTGGTGTTCAATTAT---TTTTTTACGAGT
257 ATGATATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGCGTTGAATTATAGATTTTTTACGAGT
651 ATTTTGG
322 ATTTTGG
* * * *
658 CC-AAAATTAAGGAAAAACTTTTT-AGTTAGTTTTTGCAAAATTTTAGCCGAAATTGTGTACTAA
1 CCAAAAATTGAGGAAAAA-TTTTTGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
* * * * * * **
721 CCATAACGGTTTTTTGTTAAAATCGCGTTCCGGGGCCACGGCTCAGATTTGCATG-TTTTAATGC
65 CCATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTT-CGGC
* *
785 GCCAAGACTCCATGAAATATCAATGTTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATT
128 GCCAAGACTCCATGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATT
* * *
850 TGTTTCCACGAGCATCAAAAATTGGTTTCAATTTAATTAGAAATTATTTTGGAAAAAATGGAAAA
193 TGTTTCTACGAGCATCAGAAATTGGTTTCAATTTAATTAGAAATTAATTTGGAAAAAATGGAAAA
*
915 TGATATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGCGTCGAATTATAGATTTTTTACGAGTA
258 TGATATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGCGTTGAATTATAGATTTTTTACGAGTA
980 TTTTGG
323 TTTTGG
* * *
986 GCAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTTTGCGAAATTTTAGCCGAAATCG-GT-GT--
1 CCAAAAATTGAGGAAAAA-TTTTTGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
* * *
1047 --A-CACGGTTTTTGGCTAAAACCGCGTTCCATGGCCCCAGCTCAGTTTTGCATGA-TTTCGGCG
65 CCATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTCGGCG
* * * * *
1108 CCCAGACTCCTTAAAATATGTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTT
129 CCAAGACTCCATGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATTT
* * * * *
1173 GTTTCTATGAGCATCATAAATTGCTTCCGATTTAATTAGAAATTAATTTCGAAAAAAATGAAAAA
194 GTTTCTACGAGCATCAGAAATTGGTTTCAATTTAATTAGAAATTAATTT-G--------G-AAAA
* * * *
1238 TAATGAAAAAATGATATCAGAAGCGTGAAATGCCCTTCAATTTTTTTGGAGTTGAATTATATATT
249 -AATG-GAAAATGATATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGCGTTGAATTATAGATT
1303 TTTTACGAGTATTTTGG
312 TTTTACGAGTATTTTGG
* * *
1320 CCAAAAATTGAGGAAAAATTTTTCGGATCAGTTTTTGTAAAATTTTAGCCGAAATCGTGTGCTAA
1 CCAAAAATTGAGGAAAAATTTTT-GGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
* * * * * * * * *
1385 CAATCACGATTTTTGGTTGAAAACGCGTTTCGGGGCCCCGGCTCAGATTTGTAGGATTTTCGCCG
65 CCATCACGGTTTTTGGCTAAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCG
* * * *
1450 ACAAGACTCCATGATACATCTATGTTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATTT
129 CCAAGACTCCATGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATTT
* *
1515 GTTTCTACGAGCATCAGAAATTGGTTTCCATTTAATTAGAAATTAATTTTAGAAAAAATGGAAAA
194 GTTTCTACGAGCATCAGAAATTGGTTTCAATTTAATTAGAAATTAA-TTTGGAAAAAATGGAAAA
* *
1580 TGATATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGTGTTGAATTATAGATTTCTTACGAGTA
258 TGATATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGCGTTGAATTATAGATTTTTTACGAGTA
1645 TTTTGG
323 TTTTGG
* *
1651 CCAAAAATTTAGGAAAATATTTTTTGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGGTGTACTA
1 CCAAAAATTGAGGAAAA-ATTTTTGGGTCAGTTTTTGCAAAATTTTAGCCGAAATC-GTGTACTA
* * * *
1716 ACCATCACGGTTTTTGGCTAAAAACGTGTTCCAGGCCCCGGCTCAGTTTTGCATGGTTTTAC-AC
64 ACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTT-CGGC
* * * * * * *
1780 ACCCAGACTCCCTGAAATATCTATATTCATATAATCAAATCTCATCCACATTGGATTTAAGAATT
128 GCCAAGACTCCATGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATT
*
1845 TGTTTCTACGAGCATCAGAAATTGGTTTCAATTTAATTAAAAATTAATTTGGAAAAAATGGGAAA
193 TGTTTCTACGAGCATCAGAAATTGGTTTCAATTTAATTAGAAATTAATTTGGAAAAAAT-GGAAA
* * * *
1910 ATGTTATTAAAAGCGTGAAATGCCCTTCAATTTTTTTAGCATTGAATTATAGATTTTTTACGAGT
257 ATGATATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGCGTTGAATTATAGATTTTTTACGAGT
1975 ATTTTGG
322 ATTTTGG
* * * * * * **
1982 CCTAAAATTGAAGAAAAAATTTTCGGGACGGTTTTTGCCAAATTTTAGTTGAAATCGTGTACTAA
1 CCAAAAATTG-AGGAAAAATTTTTGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
* * *
2047 CCATCACGGTTTTTGGCTAAAAACGCGGTCCGGGGCCCCGACTCAGCTTTGCATGATTTTCGGCG
65 CCATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTCGGCG
* * *
2112 CCAAGACTCCATGAAATATCTTTGTTCATCTAATAAAATCTCATCCACATTGGATTTAAGGATTT
129 CCAAGACTCCATGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATTT
* *
2177 -TTGTCAACGAGCATCAGAAATTGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATGGAAA
194 GTT-TCTACGAGCATCAGAAATTGGTTTCAATTTAATTAGAAATTAATTTGG-AAAAAATGGAAA
* * * * * *
2241 ATGATACTAGAAGCGTAAAATGCCCTTCAATTTTCTTGGCGTTGAATGATAGATATTTTACAAGT
257 ATGATATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGCGTTGAATTATAGATTTTTTACGAGT
*
2306 ATTTTGA
322 ATTTTGG
2313 CC-AAAATTGAGGAAAAAT
1 CCAAAAATTGAGGAAAAAT
2331 CGAGTGGCAG
Statistics
Matches: 1733, Mismatches: 216, Indels: 101
0.85 0.11 0.05
Matches are distributed among these distances:
322 103 0.06
323 79 0.05
324 17 0.01
325 69 0.04
326 37 0.02
327 125 0.07
328 207 0.12
329 65 0.04
330 88 0.05
331 552 0.32
332 99 0.06
333 21 0.01
334 119 0.07
335 2 0.00
336 1 0.00
340 1 0.00
341 38 0.02
342 107 0.06
343 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (328 bp):
CCAAAAATTGAGGAAAAATTTTTGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
CATCACGGTTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCGCC
AAGACTCCATGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTTAAGGATTTGT
TTCTACGAGCATCAGAAATTGGTTTCAATTTAATTAGAAATTAATTTGGAAAAAATGGAAAATGA
TATTAGAAGCGTGAAATGCCCTTCAATTTTTTTGGCGTTGAATTATAGATTTTTTACGAGTATTT
TGG
Found at i:5310 original size:21 final size:21
Alignment explanation
Indices: 5286--5329 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5276 AAGTCATCTC
5286 ATTACAAAGTAATTTGCATAT
1 ATTACAAAGTAATTTGCATAT
*
5307 ATTATAAAGTAATTTGCATAT
1 ATTACAAAGTAATTTGCATAT
5328 AT
1 AT
5330 AAATGTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (21 bp):
ATTACAAAGTAATTTGCATAT
Found at i:24650 original size:30 final size:27
Alignment explanation
Indices: 24616--24689 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 27
24606 AGTTTGAGAA
* *
24616 GGGGCAAAACATCCAAAATTGAGAGTTTAG
1 GGGGCAAAACGTCCAAAATTGA-AG-TT-C
*
24646 GGGGCAAAATGTCCAAAATTGAAGTTC
1 GGGGCAAAACGTCCAAAATTGAAGTTC
24673 GGGGCAAAACGTCCAAA
1 GGGGCAAAACGTCCAAA
24690 CTTCAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 16 0.40
28 2 0.05
29 2 0.05
30 20 0.50
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (27 bp):
GGGGCAAAACGTCCAAAATTGAAGTTC
Done.