Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021103.1 Corchorus olitorius cultivar O-4 contig21136, 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: 10611
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:1156 original size:95 final size:95
Alignment explanation
Indices: 1020--1194 Score: 278
Period size: 95 Copynumber: 1.8 Consensus size: 95
1010 ATAGTAACAG
* * * * *
1020 ATTTAGCCCCAATTTCACAGAGTGTCGATTTTCTGGGTAGTTCCAAAATTTAATATATCAATTAA
1 ATTTAGCCACAATTTCACAAAGTGTCGATTTCCTGGCTAGTTCCAAAATTTAATATATCAATCAA
1085 GGTTTTAGCTAGTAATTGTAAGAACAAATT
66 GGTTTTAGCTAGTAATTGTAAGAACAAATT
* * *
1115 ATTTAGCCACAATTTCACAAAGTGTGGGTTTCCTGGCTAGTTCCAAAATTTAATATATTAATCAA
1 ATTTAGCCACAATTTCACAAAGTGTCGATTTCCTGGCTAGTTCCAAAATTTAATATATCAATCAA
1180 GGTTTTAGCTAGTAA
66 GGTTTTAGCTAGTAA
1195 CTAGTTATTG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 72 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (95 bp):
ATTTAGCCACAATTTCACAAAGTGTCGATTTCCTGGCTAGTTCCAAAATTTAATATATCAATCAA
GGTTTTAGCTAGTAATTGTAAGAACAAATT
Found at i:4040 original size:330 final size:329
Alignment explanation
Indices: 1858--4454 Score: 2026
Period size: 330 Copynumber: 7.9 Consensus size: 329
1848 ACACACACAC
* * * * **
1858 AAATCATGCAAAACTGAG-CTGGGCCCCTAAACACATTTTTAACCCAAAACCGTGATG---A-TA
1 AAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTT-A-CCAAAAAAGTGATGATTAGTA
* * * * * *
1918 CACAATTTCGGCTAAAATTTTG-AAAAATATGACCCGAAATATTTTTCCTCAATTTTTAGCCACA
64 CACGATTTCGGCTAAAATTTTGCAAAAAT-TGACCCGAAAGATATTTCCTCAATTTTTGGCTAAA
* * * ** * * * * *
1982 ATAGTCATAATATATATATAATTCAATGCCAAAAAGATTG-GCACACTTTTTACGCATTTAATAT
128 ATACTCATAAAAAATATATAATTCAACACTAAAAAGATTGAG--GAGTTTTCACGCTTTTAATAT
* * * * *
2046 CGTTTTTCATA--TTTTCTGAATTAATTTCTAATTCAATCGAAACAAGATTAAGATGCACGTAAA
191 CGTATTTCATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAA
* * * * *
2109 AACAAATCCTTAAATACAATGTGGCT-GAGATTTGATTAAATAAATATAGATATTTCAAGGAGTC
256 AACAAATCCTTAAATCCAATG-CGATAGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
*
2173 TCGACGGCAAA
320 TCGTC-GCAAA
* ** * * *
2184 AAATCATGCAAAACTAAGTTGGGACCCCAAAACGCGTTTTTAGCCAAAAAACACCGTGATGATTC
1 AAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTA-CC-AAAAA-A--GTGATGATTA
* * * * * * * * *
2249 GTACACGATTTCAGCGAAAATTTTCCAAAAAATGACCCGAAAAATTTTTCCTCGATTTTT-TCCA
61 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTA
* * * ** * * *
2313 AGAATACTCATGAAATATATATAATTTAATGCTAAAAAGGTTGGAGGACTTTTCACGCTTTTCAT
126 A-AATACTCATAAAAAATATATAATTCAACACTAAAAAGATT-GAGGAGTTTTCACGCTTTTAAT
* * * * * *
2378 ATCGTTTTTCATATTTTTTTCTTTAATTAATTTTTTATTAAATCGAAACAAGATTCAGATGCTCA
189 ATCGTATTTCATA-TTTTTTC-TGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCG
* * * * * * * *
2443 TAAAAAC-AATCCTTAAATGCAATGTGGTTGAGATTTAATTAGATGAATATGGGTATCTCAAGGA
252 TAAAAACAAATCCTTAAATCCAATGCGATAGAGATTTGATTAGATGAATATAGATATTTCAAGGA
* *
2507 GTCTTGGT-GCCAA
317 GTC-TCGTCGCAAA
* * ** * * *
2520 AAATCATGAAAAACTGACCCGGGGCCTTGGAACGCGTTTTTAGCCAAAAACCA-TGAAGATTATT
1 AAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTA-CCAAAAA--AGTGATGATTAGT
* * *
2584 ACACGATTTCGGCTAACATTTTGCAAAAATTGAGCCGAAAGATATTTCCTCAATTTTTGGTTAAA
63 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAA
* * * * * * * *
2649 ATACTCAT-AAAAA-ATATAATTCAACGCCAAAAATATTAAAAGG-CTTTTTACACTTCTAATAT
128 ATACTCATAAAAAATATATAATTCAACACTAAAAAGATT--GAGGAGTTTTCACGCTTTTAATAT
* * * * * * * *
2711 CATTTTTCCTACTTTTTCGGAATTGATTTCAAATTAAATCAAAACAAGATTTAGATGCTCGTGAA
191 CGTATTTCATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGT--A
* * * *
2776 AAAAAAAATCCTTAAATCCAATGTGGCT-GAGATTTGATTAGATGAATATAGATATTTCAAGAAG
254 AAAACAAATCCTTAAATCCAATG-CGATAGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* *
2840 TCTTGGCGCAAA
318 TCTCGTCGCAAA
* * * * * * *
2852 AAATTATGCAAAACTTACCCCGGGGCCCTGGAATGCGTTTTTAGCCAAAATAA---A--ACT-GT
1 AAATCATGCAAAACTGA-GCCGGGGCCCCGAAACGCGTTTTTA-CCAAAA-AAGTGATGATTAGT
* * * * * * * * *
2911 -GACGAATTCGGCTAATATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTAGCCACA
63 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAA
* * * * * *
2975 ATACTCATTAAAAATATATAATTTAACGCTAAAAATATTGAATGG-CTTTTCACGCTTCTAATAT
128 ATACTCATAAAAAATATATAATTCAACACTAAAAAGATTG-A-GGAGTTTTCACGCTTTTAATAT
* * * * * *
3039 CGTTTTTCCTATTTATTTCCGAATTAATTTCTAATTAAATCGAAACATGATTTAGATGC-CTGT-
191 CGTATTTCATATTT-TTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTC-GTA
* * *
3102 ------AA-----AAA--CAATG-GCT-GTGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
254 AAAACAAATCCTTAAATCCAATGCGATAGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
* *
3152 CTCGGCGCCAA
319 CTCGTCGCAAA
* * * * * ** *
3163 AAATCATGTAAAACTGAACC-GGGTCCCGGAACACGTTTTTAGCCAAAATAAAACCG-TGA-TGG
1 AAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTA-CC--AA-AAAAGTGATGATTAG
* * * ** * ** *
3225 TACACGATTTGGGCTAAAATTTTGTAAAACTTGACCATAAAGATATTTTTCTCAATTTTTAACCA
62 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATA-TTTCCTCAATTTTTGGCTA
* * * *
3290 CAATACTCATAAAAAATATAGAATTCAACAC-AAAAATATAGAAGG-GCTTTTCACGCTTTTAAT
126 AAATACTCATAAAAAATATATAATTCAACACTAAAAAGATTG-AGGAG-TTTTCACGCTTTTAAT
* * * * *
3353 ATCGTTTTTCATATTTTTTCTGAATTAATTTCTATTTTAATCGAAACAAGATTCAGATGCTAGTA
189 ATCGTATTTCATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTA
* * * * *
3418 AAAATAAATCCTTAAATGCAATGTGGATA-AGATTTTATTAGTTGAATATAGATATTTCAAGGAG
254 AAAACAAATCCTTAAATCCAATG-CGATAGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* *
3482 TCTCGGCGCCAA
318 TCTCGTCGCAAA
* * * **
3494 AAATCACGCAAAACTGAGCC-GGGCCCCGAAACACGTTTTTAGCAAAAAACAG-TGATTACGTAC
1 AAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTACCAAAAAAGTGATGATTA-GTAC
* * * * * *
3557 ACGATTTTGGCTAAAATTTTACAAAAAATGACCCGAAA-ATTTTTTCCTCAATTTTTTGATAAAA
65 ACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA-TATTTCCTCAATTTTTGGCTAAAA
* * * * *
3621 TACTCAT--AATATATATAATTTAACACCAAAAAGATTGGAGGATTTTTCACGCTTTTAATATCT
129 TACTCATAAAAAATATATAATTCAACACTAAAAAGATT-GAGGAGTTTTCACGCTTTTAATATCG
* * * * *
3684 TTTTTCATACTTTTTCTGTATTAATTTCTAATTAAATCAAAACAAGATTTAGTTGCTCGTAAAAA
193 TATTTCATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAA
* * * * * *
3749 CAAATTCTTAAACCCAATGCAACAGAGATTTGATTAGATGAATAT-GAATATCTCAAGGAGTCTT
258 CAAATCCTTAAATCCAATGCGATAGAGATTTGATTAGATGAATATAG-ATATTTCAAGGAGTCTC
3813 GTCGCAAA
322 GTCGCAAA
* * * *
3821 AAATCATGCAAAACTAAGCCGGGGCCCCGAAACGCTTTTTTATCCAAAAATTGTGATGATTATTA
1 AAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTA-CCAAAAA-AGTGATGATTAGTA
*
3886 CACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAA
64 CACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAA
* * ** *
3951 TAATCATAAAAAATATATATTTCAACACTAAAATTATTGACGG-GTTTTGACG-TTTCTAATATC
129 TACTCATAAAAAATATATAATTCAACACTAAAAAGATTGA-GGAGTTTTCACGCTTT-TAATATC
* * * * *
4014 ATATTTCCTATTATTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTATAA
192 GTATTTCATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAA
* * * * * * * *
4078 ACATATCCTTAATTCCAGTGTGGTTGAGATTTGATTAGATGAACATAGATATTTCAAGTAGTCTC
257 ACAAATCCTTAAATCCAATGCGATAGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
* * *
4143 ATAGTAAA
322 GTCGCAAA
* * * * * *
4151 AAATCATTG-AAAATTGAGGCGAGTCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
1 AAATCA-TGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTA-CCAAAAA-AGTGAT-G--A-T
* * * *
4215 TAGTACACGATTTCGACTAAAATTTTGCAAAAACTGACACGAAAGAT-TTCTCCTTAATTTTTGG
59 TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATT-TCCTCAATTTTTGG
* * *
4279 CTAAAATACTCAT-AAAAATATATAATTCAACGCCT-AAAAGATTTGAGGACTTTTCATGCTTTT
123 CTAAAATACTCATAAAAAATATATAATTCAAC-ACTAAAAAGA-TTGAGGAGTTTTCACGCTTTT
* * * *
4342 AATATCGTATTTCTTATTTTTTCTAAATTAATTTCTAATTAAATCAAAATAAGATTCAAATGCTC
186 AATATCGTATTTCATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTC
* * * *
4407 GTAAAAACAAATTCTTAAATCCAATGTTGCT-GAGATTTAATTAGATGA
251 GTAAAAACAAATCCTTAAATCCAATG-CGATAGAGATTTGATTAGATGA
4455 TGTAAAGTAT
Statistics
Matches: 1852, Mismatches: 324, Indels: 181
0.79 0.14 0.08
Matches are distributed among these distances:
309 20 0.01
310 2 0.00
311 64 0.03
312 2 0.00
313 5 0.00
314 1 0.00
315 49 0.03
316 74 0.04
317 44 0.02
320 2 0.00
322 2 0.00
326 100 0.05
327 197 0.11
328 103 0.06
329 123 0.07
330 222 0.12
331 170 0.09
332 100 0.05
333 127 0.07
334 212 0.11
335 88 0.05
336 47 0.03
337 53 0.03
338 45 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (329 bp):
AAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTACCAAAAAAGTGATGATTAGTACA
CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATA
CTCATAAAAAATATATAATTCAACACTAAAAAGATTGAGGAGTTTTCACGCTTTTAATATCGTAT
TTCATATTTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAA
ATCCTTAAATCCAATGCGATAGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGTCG
CAAA
Found at i:7141 original size:13 final size:13
Alignment explanation
Indices: 7123--7151 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
7113 TTAAATGTTT
7123 AATTAATGGAGAA
1 AATTAATGGAGAA
7136 AATTAATGGAGAA
1 AATTAATGGAGAA
7149 AAT
1 AAT
7152 CTTTGCCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (13 bp):
AATTAATGGAGAA
Done.