Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017600.1 Corchorus olitorius cultivar O-4 contig17633, 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: 23749
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:4893 original size:6 final size:6
Alignment explanation
Indices: 4882--4919 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
4872 TCTTCCTCCT
*
4882 CTGACC CTGACC CTGACC CTGACC C-GAACC CTAACC CT
1 CTGACC CTGACC CTGACC CTGACC CTG-ACC CTGACC CT
4920 AATCCTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 1 0.03
6 28 0.97
ACGTcount: A:0.21, C:0.50, G:0.13, T:0.16
Consensus pattern (6 bp):
CTGACC
Found at i:8638 original size:2 final size:2
Alignment explanation
Indices: 8631--8657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8621 CCAGCCAATT
8631 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
8658 TTTAGGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12211 original size:314 final size:311
Alignment explanation
Indices: 11645--12262 Score: 866
Period size: 314 Copynumber: 2.0 Consensus size: 311
11635 ATTGATTTGA
** ** *
11645 TTGGCCTTTCGTAACAGTTGTAATTCATGTTGGAGTCTAGCCACTGAAGTCCCAAGTCCTTTTTC
1 TTGGCCTTTCGTAACAGTTGTAATTCATGTTCAAGTCTAGCCACTGAAGTCAAAAGTCCCTTTTC
11710 ATTCCTTTCTCCATGTAGCTTTGTTTGCAAATTGCCATTTTCTTCCCGACATCCCTTAAGTTCAT
66 ATTCCTTTCTCCATGTAGCTTTGTTTGCAAATTGCCATTTTCTTCCCGACATCCCTTAAGTTCAT
* ** *
11775 TCATAACAGCTGAATAATCTTTTCCAAATCATCCATAGCTCTTCTCAGTTTGTCATTTTCCATTC
131 TCATAACAGCTGAATAATCTTTTCCAAATCATCAATAGCTCTTCTCAAATCGTCATTTTCCATTC
**
11840 TGAATTTGTTGTTTTCCTTTCCCTCTTGTCATGCCTCTGCCTTCAATCTTTCAACCTCTTTCAAA
196 CCAATTTGTTGTTTTCCTTTCCCTCTTGTCATGCCTCTGCCTTCAATCTTTCAACCTCTTTCAAA
* * **
11905 AGTTCATGATTCTGACGTGCTATCTCCGTATTCTCACCCTCAAGTGTTTCC
261 AGTTCATGACTCTGACGTGCTAACTCCACATTCTCACCCTCAAGTGTTTCC
* * *
11956 TTGGCCTTTTGTAACATTTGTAATTCATGTTCAAGTCTAGCCACTGATA-TCTAAAATTCTTCCT
1 TTGGCCTTTCGTAACAGTTGTAATTCATGTTCAAGTCTAGCCACTGA-AGTC-AAAAGTC--CCT
* * *
12020 TTTCATTCCTTTCTCCATGT-GCTTTGTTTGTAAATTGTCATTTTCTTCTCGACATCCCTTAAGT
62 TTTCATTCCTTTCTCCATGTAGCTTTGTTTGCAAATTGCCATTTTCTTCCCGACATCCCTTAAGT
* * * * *
12084 TCATTCATAACTGCTGAATGATCTTTTTCCAAATCATTAATTGCTCTTTTCAAATCGTCATTTTC
127 TCATTCATAACAGCTGAATAATC-TTTTCCAAATCATCAATAGCTCTTCTCAAATCGTCATTTTC
* * *
12149 CATTCCCATATTCTG-T-TTTTCCTTTCCCTCTTGTCTTGCCTCTGCTTTCCATCTTTCAACCTC
191 CATTCCCA-ATT-TGTTGTTTTCCTTTCCCTCTTGTCATGCCTCTGCCTTCAATCTTTCAACCTC
* *
12212 TTTCAGAAGTTCTTGACTCTGACGTGCTAACTCCACATTCTCACCCTCAAG
254 TTTCAAAAGTTCATGACTCTGACGTGCTAACTCCACATTCTCACCCTCAAG
12263 CTTTTTCTTG
Statistics
Matches: 269, Mismatches: 31, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
311 45 0.17
312 5 0.02
313 62 0.23
314 151 0.56
315 4 0.01
316 2 0.01
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.42
Consensus pattern (311 bp):
TTGGCCTTTCGTAACAGTTGTAATTCATGTTCAAGTCTAGCCACTGAAGTCAAAAGTCCCTTTTC
ATTCCTTTCTCCATGTAGCTTTGTTTGCAAATTGCCATTTTCTTCCCGACATCCCTTAAGTTCAT
TCATAACAGCTGAATAATCTTTTCCAAATCATCAATAGCTCTTCTCAAATCGTCATTTTCCATTC
CCAATTTGTTGTTTTCCTTTCCCTCTTGTCATGCCTCTGCCTTCAATCTTTCAACCTCTTTCAAA
AGTTCATGACTCTGACGTGCTAACTCCACATTCTCACCCTCAAGTGTTTCC
Found at i:21855 original size:6 final size:6
Alignment explanation
Indices: 21844--21870 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21834 TCCAATCCGT
21844 AAATTC AAATTC AAATTC AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAA
21871 AAAAAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTC
Found at i:22318 original size:84 final size:84
Alignment explanation
Indices: 22165--22492 Score: 543
Period size: 84 Copynumber: 3.9 Consensus size: 84
22155 AATAACCAAA
* *
22165 AAGTCCCCAAACACATATATAACACAGTGGCAATTCTATTCCAAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATATA
22230 ACACAGAGGCACCTATATCC
65 ACACAGAGGCACCTATATCC
* *
22250 AAGTCCCCAAACACATATATAACACAGGGACACCTT-TATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTACAAAGTCCTCAAACACATATATA
*
22314 ACACAGAGGCACCTATATTC
65 ACACAGAGGCACCTATATCC
22334 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
** *
22399 CACAGAGGCATTTATATCA
66 CACAGAGGCACCTATATCC
22418 AAGTCCCCAAACACATATATAACACAGGGGC-ATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATATA
22482 ACACAGAGGCA
65 ACACAGAGGCA
22493 TTTCTCCTTA
Statistics
Matches: 229, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
83 4 0.02
84 188 0.82
85 35 0.15
86 2 0.01
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (84 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
CACAGAGGCACCTATATCC
Found at i:22493 original size:43 final size:43
Alignment explanation
Indices: 22164--22493 Score: 412
Period size: 43 Copynumber: 7.8 Consensus size: 43
22154 CAATAACCAA
* *
22164 AAAGTCCCCAAACACATATATAACACAGTGGCAAT-TCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
*
22207 AAAAGTCCTCAAACACATATATAACACAGAGGCA-C-CTA-TATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
* * *
22249 CAAGTCCCCAAACACATATATAACACAG-GGACACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGG-CATCTCTATTAC
* * *
22292 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
22334 -AAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
*
22376 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
22417 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
22460 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
22494 TTCTCCTTAT
Statistics
Matches: 253, Mismatches: 19, Indels: 29
0.84 0.06 0.10
Matches are distributed among these distances:
40 4 0.02
41 98 0.39
42 12 0.05
43 103 0.41
44 36 0.14
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Done.