Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019444.1 Corchorus olitorius cultivar O-4 contig19477, 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: 7684
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:1815 original size:14 final size:14
Alignment explanation
Indices: 1790--1824 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1780 CCAAAAAAAA
1790 AAAATCATTATGAGC
1 AAAAT-ATTATGAGC
*
1805 CAAATATTATGAGC
1 AAAATATTATGAGC
1819 AAAATA
1 AAAATA
1825 AATATTTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (14 bp):
AAAATATTATGAGC
Found at i:2628 original size:14 final size:14
Alignment explanation
Indices: 2604--2637 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2594 CCAAAAAAGA
2604 AAATCATTATGAGCC
1 AAAT-ATTATGAGCC
2619 AAATATTATGAGCC
1 AAATATTATGAGCC
*
2633 TAATA
1 AAATA
2638 GATATTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (14 bp):
AAATATTATGAGCC
Found at i:2720 original size:812 final size:809
Alignment explanation
Indices: 933--3727 Score: 3793
Period size: 811 Copynumber: 3.5 Consensus size: 809
923 TATGACTCAT
* * * *
933 ATGTTAAAACTAAAGAATCATTATGAAATCCAAAAAAAAAAACAAAAAGTATTACATGACCCAAA
1 ATGTTAAAACTAATGAATCATTATGAATTCCAAAAAAAAAATC-------ATT--ATGAGCCAAA
*
998 TATTATGAGCCAAATAGATATTTGGTAGTTGTATAACTTATTAATAAGAAAACAAAA-TTATAGA
57 TATTATGAGCCAAATAGATATTTGGTAGTTGTATAACTTATTAACAAGAAAACAAAATTTA-AGA
** * * *
1062 CAAAGATGTCCCCAATCATGTATTTGAATATATAGGTGGTTCAGTAATGCACCTTTAATAATTTT
121 CAAAGATGTCTACAATCACGTATTCGAATATATAGGTGGTTCAATAATGCACCTTTAATAATTTT
* *
1127 CCACGTTAAATTTCATTTCGTTGCAGTA-TTATGTATGTACACTTTGGGGCAGATTTATATGTTT
186 CCACGTTAAATTTCATTTCGTTGCAG-ACTTATGTACGTACACTTAGGGGCAGATTTATATGTTT
* * * * * * * *
1191 GATATAATGGTTTAGTACAAGTTGACTTATTAAATTGTACATCAATTGAAAGATTTGCATGTTTA
250 GATATGATGGGTCAGTACATGCTGACTTATCAAATTGTACATTAATTGACAGATTTGCATGTTTA
* *
1256 ATAGGATGGGTCTATACATGCAGACTTCTAAGTAGGTTCCTTGAGGGGTAGATTTATAAATAAGG
315 ATAGGATGGGTCTATAGATGCAGACTTCTCAGTAGGTTCCTTGAGGGGTAGATTTATAAATAAGG
* * * *
1321 AGAGTTTACAGGGCAACTCCTTGATTCAATGATATTATGGAATATGTGTTTAGAAATTATCGTAA
380 AGAGTTTACTGGGCAACTCCTTGATTCAATGATAATATTGAATATGTGTTTAGAAATTATTGTAA
* *
1386 CTTTCTAATGACACGCTAGACGAGATATTAGCTAATAAAATTAGGCGTAGCAAGTAGCATTATTA
445 CTTTCTAATGACACGTTAGACGAGATATTAGCTAATAAAATTAGGCGGAGCAAGTAGCATTATTA
* * * *
1451 CAAAGGAGGTCCAAAGATGTACAAAATTTTTTGTTATACGTCATTATCGATCTCTATA-TTTCTC
510 TAAAGGAGGTCCAAAGATGTACAAAGTTTTTTG-TACACGTCATTATCGATCTCTACATTTTCTC
* * * *
1515 CATAATTTCTCTGCATGTGATATTAATACTGATGAAACATTATAACCCTTATGGATATTTGTTCG
574 CATAATTTCTCTGCATGTGATGTTAATACTGATGAATCATTATAACCCTTATGGATATTTGGTGG
*
1580 TTGTAGTACTAGTTAGTTGTAGTACTTATAACAAAATTTAAGACAAAATGCATAAAAAACGTACA
639 TTGTAGTACTAGTTAGTTGTAGTACTT-TAACAAAATTTAAGACAAAATGC-TAAAAAACGTATA
* * * * *
1645 TATAGGTGGCCCAACTTGGTGGTTATTGTATTTATTGACACGACAACAACTTTTCTGTTACACGC
702 TATAGGTGGCTCAACTTGGTAGTTATAGTATTTATTGACACGACAACAACTTTTCTGTCACACAC
* *
1710 CATTATCGATCTTTATA-TTTTTTTTCGTAATTTTTGTACGT-
767 CATTATCGATCTTTATATTTTTTTTTCTTAAATTTTGTACGTG
*
1751 ATGTTAATACTAATGAATCATTATGAATTCCAAAAAAAAAAAATCATTATGAGCCAAATATTATG
1 ATGTTAAAACTAATGAATCATTATGAATTCC--AAAAAAAAAATCATTATGAGCCAAATATTATG
* * * * * *
1816 AGCAAAATAAATATTTGGTAATTGTATTATTTATTAACAAGAAAACAAAATTTAAGACAAACATG
64 AGCCAAATAGATATTTGGTAGTTGTATAACTTATTAACAAGAAAACAAAATTTAAGACAAAGATG
** * ** * * *
1881 TCTACAATCACGTATTCTTATATATAGGTTGTTCAATAAAACACCTTTAAAAATTTTCCATGTTG
129 TCTACAATCACGTATTCGAATATATAGGTGGTTCAATAATGCACCTTTAATAATTTTCCACGTTA
* * *
1946 AGTTTCATTTCGTTGCAGACTTATGTATC-TACACTTAGGGACAGAGTTATATGTTTGATATGAT
194 AATTTCATTTCGTTGCAGACTTATGTA-CGTACACTTAGGGGCAGATTTATATGTTTGATATGAT
* * * * *
2010 GGGTTAGTACATGCTGAATTATCAAATTGTACATTATTTGACAGATTTGTATGTTTAATAGGATT
258 GGGTCAGTACATGCTGACTTATCAAATTGTACATTAATTGACAGATTTGCATGTTTAATAGGATG
*
2075 GGTCTATAGATGCAGACTTCTCAGTAGGTTCCTTGAGGGGTTGATTTATAAATAAGGAGAGTTTA
323 GGTCTATAGATGCAGACTTCTCAGTAGGTTCCTTGAGGGGTAGATTTATAAATAAGGAGAGTTTA
*
2140 CTGGGCAACTCCTTGATTTAATGATAATATTGAATATGTGTTTAGAAATTATTGTAACTTTTCTA
388 CTGGGCAACTCCTTGATTCAATGATAATATTGAATATGTGTTTAGAAATTATTGTAAC-TTTCTA
* *
2205 ATGACACGTTAGATGAGATATTAGCTAATAAAATTAGGCGGAGCAAGTAGCATTATTATAAAGGG
452 ATGACACGTTAGACGAGATATTAGCTAATAAAATTAGGCGGAGCAAGTAGCATTATTATAAAGGA
* *
2270 GGTCCAAAGATGTTCAAAGTTTTTTGCTAGACGTCATTATCGATCTCTACATTTTCTCCATAATT
517 GGTCCAAAGATGTACAAAGTTTTTTG-TACACGTCATTATCGATCTCTACATTTTCTCCATAATT
*
2335 TCTCTGCATGTGATGTTAATACTGATCAATCATTATAACCCTTATGGATATTTGGTGGTTGTAGT
581 TCTCTGCATGTGATGTTAATACTGATGAATCATTATAACCCTTATGGATATTTGGTGGTTGTAGT
*
2400 ACTAGTTAGTTGTAGTACTTTAACAAAATTTAAGACAAAATGCCGT-AAAAGCGTATATATAGGT
646 ACTAGTTAGTTGTAGTACTTTAACAAAATTTAAGACAAAATG-C-TAAAAAACGTATATATAGGT
*
2464 GGCTCAACTTGGTAGTTATAGTATTTATTGACACGACAACAACTATTCTGTCACACACCATTATC
709 GGCTCAACTTGGTAGTTATAGTATTTATTGACACGACAACAACTTTTCTGTCACACACCATTATC
* *
2529 GATCTTTATATTTTTTTTTCTTAAATTCTGCACGTG
774 GATCTTTATATTTTTTTTTCTTAAATTTTGTACGTG
*
2565 ATGTTAACACTAATGAATCATTATGAATTCCAAAAAAGAAAATCATTATGAGCCAAATATTATGA
1 ATGTTAAAACTAATGAATCATTATGAATTCCAAAAAA-AAAATCATTATGAGCCAAATATTATGA
* * * * *
2630 GCCTAATAGATATTTGGTAGTTGTATTACTTATTAACAA-CAAACAAAATTTAAGAAAAATATGT
65 GCCAAATAGATATTTGGTAGTTGTATAACTTATTAACAAGAAAACAAAATTTAAGACAAAGATGT
*
2694 CTACAATCACGTATTCGTATATATAGGTGGTTCAATAATGCACCTTTAATAATTTTCCACGTTAA
130 CTACAATCACGTATTCGAATATATAGGTGGTTCAATAATGCACCTTTAATAATTTTCCACGTTAA
* * *
2759 ATTTCACTTCATTGCAGACTTATGTACGTACACTTAGGGGCAGATTTATATGTTTAATATGATGG
195 ATTTCATTTCGTTGCAGACTTATGTACGTACACTTAGGGGCAGATTTATATGTTTGATATGATGG
* * *
2824 GCCAGTAGC-TGCTGACTTATCAAATTGTACATTAATTGGCAGATTTGTATGTTTAATAGGATGG
260 GTCAGTA-CATGCTGACTTATCAAATTGTACATTAATTGACAGATTTGCATGTTTAATAGGATGG
* *
2888 GTCTATAGATGCAGACTTCTCAGTAGGTTCCATGAGGGGTAGATTTATAAATAAGGAGAGTTTAA
324 GTCTATAGATGCAGACTTCTCAGTAGGTTCCTTGAGGGGTAGATTTATAAATAAGGAGAGTTTAC
*
2953 TGGGCAACTCCTTGATTCAATGATAATATTGAATATGTGTTTAGAAACTATTGTAACTTTCTAAT
389 TGGGCAACTCCTTGATTCAATGATAATATTGAATATGTGTTTAGAAATTATTGTAACTTTCTAAT
** * **
3018 GACATATTAGACGAGATATTAGCTAATAAAATTTGGCAGGA-CAAGTAGCATTATTATAAAGTTG
454 GACACGTTAGACGAGATATTAGCTAATAAAATTAGGC-GGAGCAAGTAGCATTATTATAAAGGAG
* * *
3082 ATCCAAAGATGTACAAAGTTTTTTGTCACACGTCATTATCGAACTCTACATTTTCTCCACAATTT
518 GTCCAAAGATGTACAAAGTTTTTTGT-ACACGTCATTATCGATCTCTACATTTTCTCCATAATTT
* * * * * * * *
3147 CGCTGCACGTGATGTTAATACTAATGACTCATTATGACTCATATAGATATTTGGTGG-TGTCAGT
582 CTCTGCATGTGATGTTAATACTGATGAATCATTATAACCCTTATGGATATTTGGTGGTTGT-AGT
** *
3211 ACTAGTTAGTCATAGTACTTTAACAAAATTTAAGACAAAATGGCTAAAAAATGTATATATAGGTG
646 ACTAGTTAGTTGTAGTACTTTAACAAAATTTAAGACAAAAT-GCTAAAAAACGTATATATAGGTG
* * * * * * *
3276 ACTCAACTTGGAAGTTGTAATATTTATTGTCACGGCAACAACTTTTCTGTCACA-AGTCATTATC
710 GCTCAACTTGGTAGTTATAGTATTTATTGACACGACAACAACTTTTCTGTCACACA-CCATTATC
*
3340 GATCTTTATATTTTTTTATTCTTAAATTTTGTACGAG
774 GATCTTTATATTTTTTT-TTCTTAAATTTTGTACGTG
* * *
3377 ATGTTAAAACTAATGAATCATTATGAAATCCAAAAAAAAAA--ATTAT--------TA-CATGAC
1 ATGTTAAAACTAATGAATCATTATGAATTCCAAAAAAAAAATCATTATGAGCCAAATATTATGAG
3431 CCAAATAGATATTTGGTAGTTGTATAACTTATTAACAAGAAAACAAAATTGT-AGACAAAGATGT
66 CCAAATAGATATTTGGTAGTTGTATAACTTATTAACAAGAAAACAAAATT-TAAGACAAAGATGT
* * * * * *
3495 C--C---C-C--AATC-AATATATAGGTGGTTCAGTCATGTATCTTTAATAATTTTCCACGTTGA
130 CTACAATCACGTATTCGAATATATAGGTGGTTCAATAATGCACCTTTAATAATTTTCCACGTTAA
* * * *
3551 ATTTCTTTTTGTTGCAGACTTATGTACGTACATTTAGGGGCGGATTTATATGTTTGATATGATGG
195 ATTTCATTTCGTTGCAGACTTATGTACGTACACTTAGGGGCAGATTTATATGTTTGATATGATGG
** * * * * *
3616 GTCAGTACATGCTGACTTATCAAATTGTACATCGATTGATAAATTTACATGTTTAACAGGATGAG
260 GTCAGTACATGCTGACTTATCAAATTGTACATTAATTGACAGATTTGCATGTTTAATAGGATGGG
* * *
3681 TCTATAAATACAGACTTCTCAGTAGGTTCCTTGAGGGGCAGATTTAT
325 TCTATAGATGCAGACTTCTCAGTAGGTTCCTTGAGGGGTAGATTTAT
3728 GGTAACTTTT
Statistics
Matches: 1772, Mismatches: 182, Indels: 72
0.87 0.09 0.04
Matches are distributed among these distances:
791 1 0.00
792 196 0.11
793 3 0.00
795 1 0.00
796 1 0.00
799 1 0.00
800 40 0.02
801 23 0.01
802 1 0.00
809 5 0.00
810 7 0.00
811 651 0.37
812 593 0.33
813 180 0.10
814 30 0.02
818 28 0.02
820 11 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (809 bp):
ATGTTAAAACTAATGAATCATTATGAATTCCAAAAAAAAAATCATTATGAGCCAAATATTATGAG
CCAAATAGATATTTGGTAGTTGTATAACTTATTAACAAGAAAACAAAATTTAAGACAAAGATGTC
TACAATCACGTATTCGAATATATAGGTGGTTCAATAATGCACCTTTAATAATTTTCCACGTTAAA
TTTCATTTCGTTGCAGACTTATGTACGTACACTTAGGGGCAGATTTATATGTTTGATATGATGGG
TCAGTACATGCTGACTTATCAAATTGTACATTAATTGACAGATTTGCATGTTTAATAGGATGGGT
CTATAGATGCAGACTTCTCAGTAGGTTCCTTGAGGGGTAGATTTATAAATAAGGAGAGTTTACTG
GGCAACTCCTTGATTCAATGATAATATTGAATATGTGTTTAGAAATTATTGTAACTTTCTAATGA
CACGTTAGACGAGATATTAGCTAATAAAATTAGGCGGAGCAAGTAGCATTATTATAAAGGAGGTC
CAAAGATGTACAAAGTTTTTTGTACACGTCATTATCGATCTCTACATTTTCTCCATAATTTCTCT
GCATGTGATGTTAATACTGATGAATCATTATAACCCTTATGGATATTTGGTGGTTGTAGTACTAG
TTAGTTGTAGTACTTTAACAAAATTTAAGACAAAATGCTAAAAAACGTATATATAGGTGGCTCAA
CTTGGTAGTTATAGTATTTATTGACACGACAACAACTTTTCTGTCACACACCATTATCGATCTTT
ATATTTTTTTTTCTTAAATTTTGTACGTG
Found at i:3971 original size:2 final size:2
Alignment explanation
Indices: 3964--3994 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3954 CATCATTATC
3964 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 A
3995 AACATTCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5946 original size:21 final size:21
Alignment explanation
Indices: 5920--5963 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5910 ATATATACTA
* *
5920 GTTAAAGTACGTGCGCTGCCC
1 GTTAAAGCACGTGCGCTACCC
5941 GTTAAAGCACGTGCGCTACCC
1 GTTAAAGCACGTGCGCTACCC
5962 GT
1 GT
5964 ATGTTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (21 bp):
GTTAAAGCACGTGCGCTACCC
Done.