Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020716.1 Corchorus olitorius cultivar O-4 contig20749, 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: 3284
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--30 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31 TCATCTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:942 original size:332 final size:325
Alignment explanation
Indices: 245--1590 Score: 1262
Period size: 332 Copynumber: 4.1 Consensus size: 325
235 ACTGTTTTGT
* * **
245 TCAATTTTTGCAAAATATTAGGCGAAATCGTGTACGTTAGTCGAAATCACGGTTTTTTTTCCTAA
1 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA---TA-TC---ATCACGG--TTTTTGGCTAA
* * * * * * * * *
310 AAACGCGTTTCGGGGCCCTGGTTCAGTGTTGTATGATTTTTTGCGCCGAGACTCCTTGAAATATC
57 AAACGCG-TTCCGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCG-CAACACTCCTT-AAATATC
* * * * ***
375 TATATTAATCTAACCAAATCTCATCCACAATGGATTTAAGGATTTG-TAAAACAAGCATCTGAAT
119 TATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAAT
* * * *
439 CATGTTTCAATTTAATTAGAAATTAA-TCTTGAAAATAATAGGAAAAACGATACTAGAAGCATGA
184 CATGTTTCAATTTAATTAGAAATTAATTC-AG-AAA-AATATGAAAAACGATATTAAAAGCATGA
* ** ** *
503 AAAGTCCTTCAATATTTTTGGCGTTGAATTATATGAT-TTTACTGAGTATTGCGGCTAAAACTTG
246 AAAGTCCTCCAATCCTTTTGGCGTTGAATTATAT-ATATTTA-TGAGTATTTAGGCTAAAAATTG
* **
567 AGGAAATAAT-TTTCAAG
309 AAGAAA-AATATTTCGGG
* * * *
584 TCAATTTTTGTAAAATTCTAGCCGAAATCGTGTAATGATCATCACAGTTTTTGGCTAAAAACACG
1 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-AT-ATCATCACGGTTTTTGGCTAAAAACGCG
* * * * *
649 CTCCAGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGTCGAA-ACTCTTTCAGATATCCACATT
64 TTCC-GGGCCCCGGCTAAGTTTTGCATGATTTTTGGCG-C-AACACTCCTT-AAATATCTATATT
* * * * *
713 CATCTAATCAAATCTCAGCTACATTGGATTTAAGAATTTGATTTTACGAGCATCTGAATCTTGTT
125 CATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCATGTT
* *
778 TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAGCGATATTAAAAGCATGAAAAGTCCTC
190 TCAATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTC
* * * *
843 CAATCCTTTTGGGGTTAAATTATATATATATTATGAGTATTTATGCCAAAAATTGACAGAAAAAT
255 CAATCCTTTTGGCGTTGAATTATATATAT-TTATGAGTATTTAGGCTAAAAATTGA-AGAAAAAT
*
908 TTTTCGGG
318 ATTTCGGG
* * * * *
916 TCATTTTTTACAAAATTTTTGCCGAAATTGTGTACTAATCATCACGGTTTTTGGCTAAAAATGCG
1 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-T-ATCATCACGGTTTTTGGCTAAAAACGCG
* * * * *
981 TTTCGGGAACCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTT
64 TTCCGGG-CCCCGGCTAAGTTTTGCATGATTTTTGGCG-CAACACTCCTT-AAATATCTATATTC
* * * ** * * * *
1046 ATCTAATCAAATATTAGCCACATTCAATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTT
126 ATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCATGTTT
* * *
1111 CGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAGAGTCCTCC
191 CAATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCC
* * * *
1176 AATCTTTTTGGC-TTTAATTATATATATTCTATGAGTA-TTATGGCTAAAAATGGAGGAAAAATA
256 AATCCTTTTGGCGTTGAATTATATATATT-TATGAGTATTTA-GGCTAAAAATTGAAGAAAAATA
*
1239 TTTCGGT
319 TTTCGGG
* * * *
1246 TCAATTTTTGGAAAATTTTAGCTGAAATCGTG--TACCATCACGGTTTTTTGGCTAAAAACGTGT
1 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATATCATCACGG-TTTTTGGCTAAAAACGCGT
* * * * *
1309 TCTGGGGCCCCGGGTCAGTTTTGCATGATTTTTAGTG-GCAACATTCCTTAAATATTTATATTCA
65 TC-CGGGCCCCGGCTAAGTTTTGCATGATTTTT-G-GCGCAACACTCCTTAAATATCTATATTCA
* * *
1373 TCTGACCAAATCTAAGCCACATTGGATTTAA-AGATTTGTTTTTACAAGCATTTGAATCATGTTT
127 TCTAACCAAATCTCAGCCACATTGGATTTAAGA-ATTTGTTTTTACAAGCATCTGAATCATGTTT
* * * * * *
1437 CAATTTAATTAGAAATTAATT-TGAAAACAAATTGGAAAAACGATATTAGAAGCGTGAGAAGCCC
191 CAATTTAATTAGAAATTAATTCAGAAAA-ATA-T-GAAAAACGATATTAAAAGCATGAAAAGTCC
* * * *
1501 TTCAATCTTTTTAGCGTTGAATTATATATTTTTTATGAGTATTGT-GGCTAAAAATTG-AGAAAA
253 TCCAATCCTTTTGGCGTTGAATTATATA-TATTTATGAGTATT-TAGGCTAAAAATTGAAGAAAA
*
1564 ATATTTCGGA
316 ATATTTCGGG
*
1574 TCAATTTTTGTAAAATT
1 TCAATTTTTGCAAAATT
1591 CGTCGAAAAG
Statistics
Matches: 842, Mismatches: 138, Indels: 65
0.81 0.13 0.06
Matches are distributed among these distances:
325 5 0.01
326 96 0.11
327 52 0.06
328 74 0.09
329 31 0.04
330 49 0.06
331 116 0.14
332 337 0.40
333 40 0.05
334 8 0.01
337 3 0.00
338 1 0.00
339 29 0.03
340 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (325 bp):
TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATATCATCACGGTTTTTGGCTAAAAACGCGTT
CCGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGCAACACTCCTTAAATATCTATATTCATCTA
ACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCATGTTTCAATT
TAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATCC
TTTTGGCGTTGAATTATATATATTTATGAGTATTTAGGCTAAAAATTGAAGAAAAATATTTCGGG
Found at i:3250 original size:2 final size:2
Alignment explanation
Indices: 3243--3283 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
3233 AGACTCCTTA
*
3243 AT AT AT AT AT AT AT AT AT -T CAT CT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT A
3284 A
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.