Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019221.1 Corchorus olitorius cultivar O-4 contig19254, 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: 51069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:19636 original size:2 final size:2
Alignment explanation
Indices: 19629--19653 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19619 AAGTTTGTAC
19629 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 A
19654 ATTTGATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22353 original size:15 final size:16
Alignment explanation
Indices: 22333--22366 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
22323 GTTTAATTTA
22333 TAGTAAAAGTT-TGAT
1 TAGTAAAAGTTGTGAT
22348 TAGTAAAAGTTGTGAT
1 TAGTAAAAGTTGTGAT
22364 TAG
1 TAG
22367 GCATGGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (16 bp):
TAGTAAAAGTTGTGAT
Found at i:27740 original size:3 final size:3
Alignment explanation
Indices: 27728--27761 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
27718 TGAGCAAATA
27728 TCT TCTT TCT TCTT TCT TCT TCT TCT TCT TCT TC
1 TCT TC-T TCT TC-T TCT TCT TCT TCT TCT TCT TC
27762 GGGGTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:27740 original size:7 final size:7
Alignment explanation
Indices: 27728--27760 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
27718 TGAGCAAATA
27728 TCTTCTT
1 TCTTCTT
27735 TCTTCTT
1 TCTTCTT
27742 TCTTC-T
1 TCTTCTT
27748 TCTTC-T
1 TCTTCTT
27754 TCTTCTT
1 TCTTCTT
27761 CGGGGTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
TCTTCTT
Found at i:31846 original size:3 final size:3
Alignment explanation
Indices: 31840--31874 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
31830 AAAAACAAAA
31840 AAG AAG AAG AAAG AAG AAG AAGG AAG AAG AAG AAG
1 AAG AAG AAG -AAG AAG AAG AA-G AAG AAG AAG AAG
31875 GGCCATGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31852 original size:10 final size:10
Alignment explanation
Indices: 31839--31874 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
31829 AAAAAACAAA
31839 AAAGAAGAAG
1 AAAGAAGAAG
31849 AAAGAAGAAG
1 AAAGAAGAAG
*
31859 AAGGAAGAAG
1 AAAGAAGAAG
31869 -AAGAAG
1 AAAGAAG
31875 GGCCATGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
AAAGAAGAAG
Found at i:31875 original size:13 final size:13
Alignment explanation
Indices: 31840--31875 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
31830 AAAAACAAAA
*
31840 AAGAAGAAGAAAG
1 AAGAAGAAGGAAG
31853 AAGAAGAAGGAAG
1 AAGAAGAAGGAAG
31866 AAGAAGAAGG
1 AAGAAGAAGG
31876 GCCATGACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGGAAG
Found at i:34819 original size:15 final size:15
Alignment explanation
Indices: 34799--34827 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34789 GGACCAGTAA
34799 GGGACGGGATGGGAC
1 GGGACGGGATGGGAC
34814 GGGACGGGATGGGA
1 GGGACGGGATGGGA
34828 GGTCCTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.62, T:0.07
Consensus pattern (15 bp):
GGGACGGGATGGGAC
Found at i:43954 original size:14 final size:14
Alignment explanation
Indices: 43935--43964 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
43925 TCGATTCACC
43935 TGAAGCGTATTTAT
1 TGAAGCGTATTTAT
43949 TGAAGCGTATTTAT
1 TGAAGCGTATTTAT
43963 TG
1 TG
43965 GGAGGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (14 bp):
TGAAGCGTATTTAT
Found at i:50340 original size:332 final size:331
Alignment explanation
Indices: 49618--51053 Score: 1541
Period size: 332 Copynumber: 4.3 Consensus size: 331
49608 TGATTTCAAT
* * * * **
49618 TAAAACTTTGCAAAAACTGTCCTGAAAATATTTTCTTCAATTTTTGGCCACAATACTTATACAAA
1 TAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCTT-AATTTTTGGCCACAATACTCGTA-AAA
* * ** * *
49683 AATATATAATTCAATACTAAAAAGAATGAACCGCTTTTCACGCTTCTAATATCGTATTTCCTATT
64 AATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCACACTTCTAATATCGTATTTCCTACT
** * * ** * *
49748 TTTTTCTGAATTAAATTCTTGATTAAATCGAAACATGATTCAAATGCTCGTAAAAATAAATCCTT
129 TTTTTCCAAATTAATTTC-TGATTAAATCGAAACATGATTCAGATGCAAGTAAAAAAAAAACCTT
* ** * * * *
49813 AAATCCAATATGGCTGAGATTTGGCAAGATGAATACATATATTT-TAGCGAGTCTTGGCGCAAAA
193 AAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCT-GTGAGTCTTGGCGCCAAA
* * * ** * *
49877 AACCATGCTAAACTGAG-CCAGGGACCTTGAACGAGTTTTTAGCCAAAAACTACGATAACTAGTA
257 AATCATGCAAAACTGAGTCGAGGGACCCAGAACGAGTTTTTAGCCAAAAACTATGAT--GTAGTA
* *
49941 CACGTTTTCAGC
320 CACGATTTCGGC
* * * *
49953 TACAATTTTGCAAAAACTTATCCGAAAAAATTTTCCTCAATTTTTGGCCACAATACTCGTAAAAA
1 TAAAATTTTGCAAAAACTGACCCGAAAAAATTTT-CTTAATTTTTGGCCACAATACTCGTAAAAA
* *
50018 ATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCACACTTCTAATACCGTATTTGCTA-TT
65 ATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCACACTTCTAATATCGTATTTCCTACTT
* *
50082 TTTTCCAAATCAATTTCTGATTAAATCGAAACATGATTCAGATGCAAGTAAAACAAAAAACCTCA
130 TTTTCCAAATTAATTTCTGATTAAATCGAAACATGATTCAGATGCAAGTAAAA-AAAAAACCTTA
* *
50147 AGTCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCTGTGAGTCTTGTCGCCAAAAA
194 AATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCTGTGAGTCTTGGCGCCAAAAA
* * * *
50212 TCATGTAAAAATGAGTCGA-GGACCC-GAAACGCGTTTTTAGCCAAAGAACTGTGATGTAGTACA
259 TCATGCAAAACTGAGTCGAGGGACCCAG-AACGAGTTTTTAGCCAAA-AACTATGATGTAGTACA
*
50275 TGATTTCGGC
322 CGATTTCGGC
* ** *
50285 TAAAATTTTGCAGAAACTGACCCGAAAATTTTTTTCTTAATTTTTGGCCACAATACCCGTAAAAA
1 TAAAATTTTGCAAAAACTGACCCGAAAA-AATTTTCTTAATTTTTGGCCACAATACTCGTAAAAA
* * * * * *
50350 ATAAATAATTCAATGTCAAAAAGAATGAAAGACTTTTCA-AGCTTCTAATATCTTATTTCCT-TT
65 ATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCACA-CTTCTAATATCGTATTTCCTACT
* * **
50413 TTTTTTCAAATTAATTTCTGATTAAATGGAAACATGATTCAGATGCTTGTAAAAAAGAAAAAAAA
129 TTTTTCCAAATTAATTTCTGATTAAATCGAAACATGATTCAGATGC-----AAGTA-AAAAAAAA
* * * * * * * * *
50478 ATTCTTAAATCCAAAGTGGCTAAGATTTAGTT-GATAAATATAAAAATTTCAGTGAGTTTTGGCG
188 A-CCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCTGTGAGTCTTGGCG
*
50542 -CAAAAACTCATGCAAAACTGAGTC-AGGGACCCAGAACGAGTTTTTTTGCCAAAAACTATGAT-
252 CCAAAAA-TCATGCAAAACTGAGTCGAGGGACCCAGAACGAG-TTTTTAGCCAAAAACTATGATG
50604 TAGTACACGATTTCGGC
315 TAGTACACGATTTCGGC
* *
50621 TAAAATTTTTGCAAAAACTGACCC-AAAATAATTTTCTTTAATTTTTAGCCACAATACCCGTAAA
1 TAAAA-TTTTGCAAAAACTGACCCGAAAA-AATTTTC-TTAATTTTTGGCCACAATACTCGTAAA
* * *
50685 AAATATATAATTCAATTCCAAAAAGAATGAAGGGTTTTTCACGCTTCTAATATCGTATTTCC-AC
63 AAATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCACACTTCTAATATCGTATTTCCTAC
* * * ** *
50749 TTTTTTCCGAATTAATTTCGGATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAAAATCT
128 TTTTTTCCAAATTAATTTCTGATTAAATCGAAACATGATTCAGATGCAAGTAAAAA-AAAAACCT
** * * * *
50814 TAAATTTAATGTGACTGAAATTTGTTTAGATGAATATAGATATTTCTGTGAGTCTTGTCGCCAAA
192 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCTGTGAGTCTTGGCGCCAAA
* * * * *
50879 AATCATGCAAAATTGAGTCG-GGGACCCAGAATGCGTTTTTAGCCAAAAAAGTGTGATTGTTAGT
257 AATCATGCAAAACTGAGTCGAGGGACCCAGAACGAGTTTTTAGCC-AAAAACTATGA-TG-TAGT
* *
50943 ATATGATTTCGGC
319 ACACGATTTCGGC
* * * *
50956 TAAATTTTTGCAAAAACTGACCCGAAAAAATTTTCGACTATGTTTTTGCCCACAATACTCGTAAA
1 TAAAATTTTGCAAAAACTGACCCGAAAAAATTTTC--TTA-ATTTTTGGCCACAATACTCGTAAA
** *
51021 CTATATATAATTCAATGCCAAAAAGAATAAAGG
63 AAATATATAATTCAATGCCAAAAAGAATGAAGG
51054 CTTCTAGAAT
Statistics
Matches: 924, Mismatches: 142, Indels: 69
0.81 0.13 0.06
Matches are distributed among these distances:
331 35 0.04
332 266 0.29
333 121 0.13
334 94 0.10
335 73 0.08
336 89 0.10
337 207 0.22
338 39 0.04
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (331 bp):
TAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCTTAATTTTTGGCCACAATACTCGTAAAAAA
TATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCACACTTCTAATATCGTATTTCCTACTTT
TTTCCAAATTAATTTCTGATTAAATCGAAACATGATTCAGATGCAAGTAAAAAAAAAACCTTAAA
TCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCTGTGAGTCTTGGCGCCAAAAATC
ATGCAAAACTGAGTCGAGGGACCCAGAACGAGTTTTTAGCCAAAAACTATGATGTAGTACACGAT
TTCGGC
Done.