Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010742.1 Corchorus olitorius cultivar O-4 contig10774, 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: 17247
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:1987 original size:350 final size:352
Alignment explanation
Indices: 1342--2042 Score: 1230
Period size: 350 Copynumber: 2.0 Consensus size: 352
1332 TTCTACAGTC
*
1342 AATTTGGGATCGATAATTTAAATGCTCCGGTGTGACTTTGATCCAGTTCTCCAATTCACTCGCTT
1 AATTTGGGATCGATAATTTAAATGCTCCGGTGTGACTTTGATCCAGTTCCCCAATTCACTCGCTT
*
1407 TGATTTATTTTTGTGCTACGCGCACCACCAAAATATTTCTATAACTTCTTTGTCATTTTCAGCAA
66 TGATTTATTTTTGTGCTA-GCGCACCACCAAAATATTTCTACAACTTCTTTGTCATTTTCAGCAA
* *
1472 AATGACTGGTATGCCCCGCGCTGCTATTAAGTTTTTCACAAAAACTCTACCCAAAGAAATTTTTG
130 AATGACTGGCATGCCCCGCGCTGCTATTAAGTTTTTCACAAAAACTCTACCCAAAGAAATTTTCG
1537 GCGCAACATCTCTTTTTGGCACGCCCAGTGGGACTTAAAAGAATTGACTTCTCACTCCGCGTTTG
195 GCGCAACATCTCTTTTTGGCACGCCCAGTGGGACTTAAAAGAATTGACTTCTCACTCCGCGTTTG
1602 TCAAAAGATTTCTTGCTCCGTGTTCTTTGAAATTTTTTAATTTTTCTTTCGCAGATCTGGTGTCC
260 TCAAAAGATTTCTTGCTCCGTGTTCTTTGAAATTTTTT-ATTTTTCTTTCGCAGATCTGGTGTCC
1667 GCCTAGTCAGGCTCGCACCAAACCTTTTT
324 GCCTAGTCAGGCTCGCACCAAACCTTTTT
*
1696 AATTTGGGATCGATGATTTAAATGCTCCGGTGTGACTTTGATCCAGTTCCCGCAATTCACTCGCT
1 AATTTGGGATCGATAATTTAAATGCTCCGGTGTGACTTTGATCCAGTTCCC-CAATTCACTCGCT
* *
1761 TTGATTTA-TTTT-TG-T-GCGCACCACCAAAATGTTTCTACAAGTTCTTTGTCATTTTCAGCAA
65 TTGATTTATTTTTGTGCTAGCGCACCACCAAAATATTTCTACAACTTCTTTGTCATTTTCAGCAA
* * * *
1822 AATGACTTGCATGCCCCGCGCTGTTATTAAGTTTTTCGCAAAAACTTTACCCAAAGAAATTTTCG
130 AATGACTGGCATGCCCCGCGCTGCTATTAAGTTTTTCACAAAAACTCTACCCAAAGAAATTTTCG
1887 GCGCAACATCTCTTTTTGGCACGCCCAGTGGGACTTAAAAGAATTGACTTCTCACTCCGCGTTTG
195 GCGCAACATCTCTTTTTGGCACGCCCAGTGGGACTTAAAAGAATTGACTTCTCACTCCGCGTTTG
**
1952 TCAAAAGATTTCTTGCTCCGTGTTCTTTGAAATTTTTTATTTTTCTTTCGTGGATCTGGTGTCCG
260 TCAAAAGATTTCTTGCTCCGTGTTCTTTGAAATTTTTTATTTTTCTTTCGCAGATCTGGTGTCCG
2017 CCTAGTCAGGCTCGCACCAAACCTTT
325 CCTAGTCAGGCTCGCACCAAACCTTT
2043 ATCTTTTCTC
Statistics
Matches: 333, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
349 51 0.15
350 205 0.62
352 1 0.00
353 2 0.01
354 53 0.16
355 21 0.06
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (352 bp):
AATTTGGGATCGATAATTTAAATGCTCCGGTGTGACTTTGATCCAGTTCCCCAATTCACTCGCTT
TGATTTATTTTTGTGCTAGCGCACCACCAAAATATTTCTACAACTTCTTTGTCATTTTCAGCAAA
ATGACTGGCATGCCCCGCGCTGCTATTAAGTTTTTCACAAAAACTCTACCCAAAGAAATTTTCGG
CGCAACATCTCTTTTTGGCACGCCCAGTGGGACTTAAAAGAATTGACTTCTCACTCCGCGTTTGT
CAAAAGATTTCTTGCTCCGTGTTCTTTGAAATTTTTTATTTTTCTTTCGCAGATCTGGTGTCCGC
CTAGTCAGGCTCGCACCAAACCTTTTT
Found at i:12223 original size:2 final size:2
Alignment explanation
Indices: 12216--12250 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12206 ATTATATTTG
12216 AT AT AT AT AT AT AT AT AT 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 A
12251 GTTGATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12823 original size:16 final size:17
Alignment explanation
Indices: 12792--12825 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12782 GGGGACTATA
*
12792 TATATAGCCTGGGTATT
1 TATATAGCCCGGGTATT
12809 TATATA-CCCGGGTATT
1 TATATAGCCCGGGTATT
12825 T
1 T
12826 CACTTGGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.41
Consensus pattern (17 bp):
TATATAGCCCGGGTATT
Found at i:16188 original size:178 final size:178
Alignment explanation
Indices: 15866--16195 Score: 470
Period size: 178 Copynumber: 1.9 Consensus size: 178
15856 TAAGCTCAAA
* * ** **
15866 TTATGTAATCTTAAGTAGACCGTCTATTTTCGTTAACCGAAACAATTAATTGTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTTGGAAGCATTT
* *
15931 TTTATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGTATGAAAGTTGTAGATCATGGAACAAC
66 TTGATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGAATGAAAGTTGTAGATCATGGAACAAC
*
15996 CTTTCAAGAGACACTTGAATCATCATAATCAGACATCTAGAGCAAAAG
131 CTTTCAAGAGACACTTAAATCATCATAATCAGACATCTAGAGCAAAAG
*
16044 TTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAA-CTAT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTT-GGAAGC-AT
*
16107 TTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTT-AATGAAAGTTGTAGATCATGGAA
64 TTTTGATACCTTG-AACATTAAATTTAGTTTTCCAGT-CTTGAATGAAAGTTGTAGATCATGGAA
* * *
16170 CAATCTTTTAATAGACACTTAAATCA
127 CAACCTTTCAAGAGACACTTAAATCA
16196 CCTTTATTGG
Statistics
Matches: 134, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
177 8 0.06
178 123 0.92
179 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTTGGAAGCATTT
TTGATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGAATGAAAGTTGTAGATCATGGAACAAC
CTTTCAAGAGACACTTAAATCATCATAATCAGACATCTAGAGCAAAAG
Found at i:16228 original size:178 final size:177
Alignment explanation
Indices: 15863--16235 Score: 441
Period size: 178 Copynumber: 2.1 Consensus size: 177
15853 TCATAAGCTC
* * ** **
15863 AAATTATGTAATCTTAAGTAGACCGTCTATTTTCGTTAACCGAAACAATTAATTGTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTTGGAAGCA
* *
15928 TTTTTTATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGTATGAAAGTTGTAGATCATGGAAC
66 TTTTTGATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGAATGAAAGTTGTAGATCATGGAAC
* * * * *
15993 AACCTTTCAAGAGACACTTGAATCATCATAATCAGACATCTAGAGCA
131 AACCTTTCAAGAGACACTTAAATCACCATAATCAGAAACCAAGAGCA
*
16040 AAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAA-
1 AAA-TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTT-GGAAG
*
16103 CTATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTT-AATGAAAGTTGTAGATCAT
64 C-ATTTTTGATACCTTG-AACATTAAATTTAGTTTTCCAGT-CTTGAATGAAAGTTGTAGATCAT
* * * * * **
16166 GGAACAATCTTTTAATAGACACTTAAATCACCTTTATTGGATAACCAAAGAG-A
126 GGAACAACCTTTCAAGAGACACTTAAATCACCATAATCAGA-AACC-AAGAGCA
*
16219 AAATTATATAATGTTAA
1 AAATTATATAATATTAA
16236 ATATATCGTT
Statistics
Matches: 166, Mismatches: 23, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
177 11 0.07
178 142 0.86
179 9 0.05
180 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTGTTTGGAAGCA
TTTTTGATACCTTGAACATTAAATTTAGTTTTCCAGTCTTGAATGAAAGTTGTAGATCATGGAAC
AACCTTTCAAGAGACACTTAAATCACCATAATCAGAAACCAAGAGCA
Found at i:16808 original size:2 final size:2
Alignment explanation
Indices: 16803--16845 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
16793 AGTTGAAGTG
* *
16803 AT AT AT AT AT AT AT AT AT AT A- ACT TT AA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
16845 A
1 A
16846 AAGAAACCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.