Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021556.1 Corchorus olitorius cultivar O-4 contig21589, 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: 17224
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Found at i:5866 original size:24 final size:24
Alignment explanation
Indices: 5839--5916 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
5829 AGGCCATTGC
*
5839 AGCAGCCACCACCTTCTCTAGTTG
1 AGCAGCCACCACCTCCTCTAGTTG
** * * *
5863 AGCAGCCAATACCTCCTCCATTTC
1 AGCAGCCACCACCTCCTCTAGTTG
* *
5887 AGCAGCCACCACCTCCTCTTGTCG
1 AGCAGCCACCACCTCCTCTAGTTG
5911 AGCAGC
1 AGCAGC
5917 ATCGATAAGA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (24 bp):
AGCAGCCACCACCTCCTCTAGTTG
Found at i:8525 original size:31 final size:31
Alignment explanation
Indices: 8490--8550 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
8480 TTGACTGACA
8490 TATTGTAAATTTAAATTTACAAACCTTGAAG
1 TATTGTAAATTTAAATTTACAAACCTTGAAG
*
8521 TATTGTAAATTTTAATTTACAAACCTTGAA
1 TATTGTAAATTTAAATTTACAAACCTTGAA
8551 TTTTAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
TATTGTAAATTTAAATTTACAAACCTTGAAG
Found at i:9287 original size:402 final size:399
Alignment explanation
Indices: 8546--9349 Score: 1464
Period size: 402 Copynumber: 2.0 Consensus size: 399
8536 TTTACAAACC
8546 TTGAATTTTAATATAGTATTATTCATAATTCTAGTTTATTTCAATTTTTTTTACCAGAATAATAT
1 TTGAATTTTAATATAGTATTATTCATAATTCTAGTTTATTTCAATTTTTTTTACCAGAATAATAT
* *
8611 AATCCTCAAAAGTTGTTCCTAGAACAATCATTCCTAAATTTTGGAATGGCTTGGAATGACATTTT
66 AATCCTCAAAAGTTGTTCCTAGAACAATCATTCCTAAATTTTGGAATGGCTTGCAATGACATCTT
*
8676 AGGAACAATTATAATCTTTTGTTGTAAATTTTAGATGTTTCAAAAGTCATTCCAAAGTGGAGGAA
131 AGGAACAATTATAATCTTTTGTTGTAAATTTTAGATGTTTCAAAAGTCATTCCAAAGTAGAGGAA
*
8741 TGAGTTTAGCAATGATAAATAATTGTTCCAAAAATCATTCTTGAAATAGGGTCGTTCCTGTCTTT
196 TGAGTTTAGCAATGATAAATAATTGTTCCAAAAATCATTCCTGAAATAGGGTCGTTCCTGTCTTT
* *
8806 AGGAATGGGCTTTTGAAACGGGAACTAACCCGTTCCTGACTTCAGGAACGAGATTCATTTTTTTC
261 AGGAATGAGCTTTTGAAACGGAAACTAACCCGTTCCTGACTTCAGGAACGAGATTCATTTTTTTC
*
8871 ATTCCTATTTGCTCTGGAACGAGCCATATAGGAACGACCAGGTTTCCCGTTCCTCAACCTGTTCC
326 ATTCCTATTTGCTCTGGAACGAGCCATATAGGAACGACCAGGTTTCCCGTTCCTCAACATGTTCC
8936 TGACTAAGT
391 TGACTAAGT
*
8945 TTGAATTTTAATATAGTATTATTCATAATTCTAGTTTATTTCAATTTTTTTTACCAGAATGATAT
1 TTGAATTTTAATATAGTATTATTCATAATTCTAGTTTATTTCAATTTTTTTTACCAGAATAATAT
*
9010 AATCCTTAAAAGTTGTTCCTAGAACAATCATTCCTAAATTTTGGAATGGCATTTGCAATGACATC
66 AATCCTCAAAAGTTGTTCCTAGAACAATCATTCCTAAATTTTGGAATGGC--TTGCAATGACATC
*
9075 TTAGGAACAATTATAATTTTTTTGTTGTAAATTTTAGATGTTTCAAAAGTCATTCCAAAGTAGAG
129 TTAGGAACAATTATAA-TCTTTTGTTGTAAATTTTAGATGTTTCAAAAGTCATTCCAAAGTAGAG
**
9140 GAATGAGTTTAGCAATGATAAATAATTGTTCCGTAAATCATTCCTGAAATAGGGTCGTTCCTGTC
193 GAATGAGTTTAGCAATGATAAATAATTGTTCCAAAAATCATTCCTGAAATAGGGTCGTTCCTGTC
9205 TTTAGGAATGAGCTTTTGAAACGGAAACTAACCCGTTCCTGACTTCAGGAACGAGATTCATTTTT
258 TTTAGGAATGAGCTTTTGAAACGGAAACTAACCCGTTCCTGACTTCAGGAACGAGATTCATTTTT
*
9270 TTCATTCCTATTTGCTCTGGAACGAGCCATATAGGAACGACTAGGTTTCCCGTTCCTCAACATGT
323 TTCATTCCTATTTGCTCTGGAACGAGCCATATAGGAACGACCAGGTTTCCCGTTCCTCAACATGT
9335 TCCTGACTAAGT
388 TCCTGACTAAGT
9347 TTG
1 TTG
9350 GAACGAGATT
Statistics
Matches: 389, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
399 113 0.29
401 27 0.07
402 249 0.64
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (399 bp):
TTGAATTTTAATATAGTATTATTCATAATTCTAGTTTATTTCAATTTTTTTTACCAGAATAATAT
AATCCTCAAAAGTTGTTCCTAGAACAATCATTCCTAAATTTTGGAATGGCTTGCAATGACATCTT
AGGAACAATTATAATCTTTTGTTGTAAATTTTAGATGTTTCAAAAGTCATTCCAAAGTAGAGGAA
TGAGTTTAGCAATGATAAATAATTGTTCCAAAAATCATTCCTGAAATAGGGTCGTTCCTGTCTTT
AGGAATGAGCTTTTGAAACGGAAACTAACCCGTTCCTGACTTCAGGAACGAGATTCATTTTTTTC
ATTCCTATTTGCTCTGGAACGAGCCATATAGGAACGACCAGGTTTCCCGTTCCTCAACATGTTCC
TGACTAAGT
Found at i:9694 original size:43 final size:41
Alignment explanation
Indices: 9563--9891 Score: 382
Period size: 43 Copynumber: 7.8 Consensus size: 41
9553 CCAATAACCA
* *
9563 AAAGTCCCCAATCACATATATAACACAAGGGCACCTCTATTCC
1 AAAGTCCCCAAACACATATATAACAC-AGGGCA-CTCTATTAC
* *
9606 AAAAGTCCTCAAACACATATATAACACAGAG-ACATCTA-TATC
1 -AAAGTCCCCAAACACATATATAACACAGGGCAC-TCTATTA-C
*
9648 AAAGTCCCCAAACACATATATAACACATGGACACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACA-GGGCA-CTCTATTAC
* *
9691 AAAGTCCTCAAACACATATATAACACAGAG-ACATCTA-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGCAC-TCTATTA-C
9732 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACA-GGGCA-CTCTATTAC
* *
9775 AAAGTCCTCAAACACATATATAACACAGAGGCA-TTTA-TATC
1 AAAGTCCCCAAACACATATATAACACAG-GGCACTCTATTA-C
9816 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACA-GGGCA-CTCTATTAC
*
9859 AAAGTCCTCAAACACATATATAACACAGAGGCA
1 AAAGTCCCCAAACACATATATAACACAG-GGCA
9892 TTTCTCCTTA
Statistics
Matches: 249, Mismatches: 17, Indels: 39
0.82 0.06 0.13
Matches are distributed among these distances:
40 5 0.02
41 94 0.38
42 13 0.05
43 105 0.42
44 32 0.13
ACGTcount: A:0.43, C:0.27, G:0.09, T:0.21
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGGGCACTCTATTAC
Found at i:9892 original size:43 final size:43
Alignment explanation
Indices: 9563--9892 Score: 417
Period size: 41 Copynumber: 7.8 Consensus size: 43
9553 CCAATAACCA
* * *
9563 AAAGTCCCCAATCACATATATAACACA-AGGGCACCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGA-GGCATCTCTATTAC
* * *
9606 AAAAGTCCTCAAACACATATATAACACAGAGACATCTATA-T-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
9648 AAAGTCCCCAAACACATATATAACACATG-GACACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACA-GAGGCATCTCTATTAC
* * *
9691 AAAGTCCTCAAACACATATATAACACAGAGACATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
9732 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
9775 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
9816 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
9859 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
9893 TTCTCCTTAT
Statistics
Matches: 252, Mismatches: 23, Indels: 23
0.85 0.08 0.08
Matches are distributed among these distances:
40 2 0.01
41 104 0.41
42 8 0.03
43 103 0.41
44 34 0.13
45 1 0.00
ACGTcount: A:0.43, C:0.27, G:0.09, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:9894 original size:84 final size:84
Alignment explanation
Indices: 9563--9888 Score: 571
Period size: 84 Copynumber: 3.9 Consensus size: 84
9553 CCAATAACCA
* * *
9563 AAAGTCCCCAATCACATATATAACACAAGGGCACCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC-AAAGTCCTCAAACACATATAT
9628 AACACAGAGACATCTATATC
65 AACACAGAGACATCTATATC
* *
9648 AAAGTCCCCAAACACATATATAACACATGGACACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
9713 ACACAGAGACATCTATATC
66 ACACAGAGACATCTATATC
9732 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
* *
9797 ACACAGAGGCATTTATATC
66 ACACAGAGACATCTATATC
*
9816 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
9881 ACACAGAG
66 ACACAGAG
9889 GCATTTCTCC
Statistics
Matches: 232, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
84 193 0.83
85 39 0.17
ACGTcount: A:0.43, C:0.27, G:0.09, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGACATCTATATC
Found at i:10014 original size:2 final size:2
Alignment explanation
Indices: 10001--10039 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
9991 ACCAAATTCC
* *
10001 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10040 GTGACAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14782 original size:18 final size:19
Alignment explanation
Indices: 14749--14784 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14739 TGAAGACCAT
14749 TTGAAGATACTTTGGAGAC
1 TTGAAGATACTTTGGAGAC
*
14768 TTGAAGAT-TTTTGGAGA
1 TTGAAGATACTTTGGAGA
14785 TTTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.36
Consensus pattern (19 bp):
TTGAAGATACTTTGGAGAC
Done.