Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017566.1 Corchorus olitorius cultivar O-4 contig17599, 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: 15079
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:846 original size:323 final size:322
Alignment explanation
Indices: 3--1033 Score: 1548
Period size: 320 Copynumber: 3.2 Consensus size: 322
1 TT
* * * *
3 TTTTTTTTTCATGTTTTGCCACACTACTCTTTAAAAAATATATAATTTAAAGCCAAAAAAAGTTA
1 TTTTTTTTTCATTTTTTGCCACACTAATC-TGAAAAAATATATAATTTAAAGCCAAAAAAATTTA
* * * *
68 AGGGTTTTTCACGCTTCGAGTTTCGTTTTTCCAATTTTTTTTCCAAATTTATATCTAATTAAATC
65 AGGGTTTTTCACGCTTCGAATATCGATTTTCCAA-TTTTTTTCCGAATTTATATCTAATTAAATC
* *
133 GAAACAAAATTCAGATGCTTGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGCTTATA
129 GAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATA
*
198 TGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTTAGTCGGGGCCCCGAA
194 TGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGTCGGGGCCCCGAA
* * * * *
263 AAGCGTTTTTAGC-CAAAAACTGTGATGGTTAGTACACGATTTCTG-CTAAATATTGACCCGAAA
259 ACGCGTTTTTAGCAAAAAAACTGTGATGGTTTGTACACGATTTCGGCCCAAA-ATTGACCCGAAA
* * * * *
326 TTTTTTTTTTCAATTTTT-CCACACTACTCTGGAAAATTATATAATTCAAAGCC-AAAAAATTTA
1 -TTTTTTTTTCATTTTTTGCCACACTAATCTGAAAAAATATATAATTTAAAGCCAAAAAAATTTA
* * * *
389 AGGGTTTTTCGCGCTTCGAATATCGCTTTTCTAATTTTTTTCCGAATTTATTTCTAATTAAATCG
65 AGGGTTTTTCACGCTTCGAATATCGATTTTCCAATTTTTTTCCGAATTTATATCTAATTAAATCG
* *
454 TAACGAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATAT
130 AAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATAT
* * *
519 GAATATAGATATTTCAAGGAGTCTTTCTGCCAAGAATCATGCAAGACTGAGTCGGGGCCCCGAAA
195 GAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGTCGGGGCCCCGAAA
* *
584 CGCATTTTTAGCAAAAAAACCGTGATGGTTTGTACACGATTTCGGCCCAAAATTGACCCGAAA
260 CGCGTTTTTAGCAAAAAAACTGTGATGGTTTGTACACGATTTCGGCCCAAAATTGACCCGAAA
647 TTTTTTTTTCATTTTTTGCCACACTAATCTGAAAAAATATATAATTTAAAGCCAAAAAAATTTAA
1 TTTTTTTTTCATTTTTTGCCACACTAATCTGAAAAAATATATAATTTAAAGCCAAAAAAATTTAA
* *
712 GGGTTTTTAACGCTTCGAATATCGATTTTCCAATTTTTCTCCGAAGTTTATATCTAATTAAATCG
66 GGGTTTTTCACGCTTCGAATATCGATTTTCCAATTTTTTTCCGAA-TTTATATCTAATTAAATCG
*
777 AAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATTCAAATTGGCTGAGATTTGGTTATAT
130 AAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATAT
* *
842 GAATATAGATATTTCAACGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAA
195 GAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGTCGGGGCCCCGAAA
* * * *
907 CTCGTTTTTAGCAAAAAAAAAACTGTGATGTTTTGTACACAATTTCGACCCAAAATTGACCCGAA
260 CGCGTTTTTAGC---AAAAAAACTGTGATGGTTTGTACACGATTTCGGCCCAAAATTGACCCGAA
*
972 TTTT
322 ---A
*
976 TTTTTTTTTCAGTTTTTGCCACACTAATCTGAAAAAATATATAATTTAAAGCCAAAAA
1 TTTTTTTTTCATTTTTTGCCACACTAATCTGAAAAAATATATAATTTAAAGCCAAAAA
1034 TCTGAAAATG
Statistics
Matches: 641, Mismatches: 55, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
320 178 0.28
321 109 0.17
322 75 0.12
323 161 0.25
324 15 0.02
326 46 0.07
329 57 0.09
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (322 bp):
TTTTTTTTTCATTTTTTGCCACACTAATCTGAAAAAATATATAATTTAAAGCCAAAAAAATTTAA
GGGTTTTTCACGCTTCGAATATCGATTTTCCAATTTTTTTCCGAATTTATATCTAATTAAATCGA
AACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATATG
AATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGTCGGGGCCCCGAAAC
GCGTTTTTAGCAAAAAAACTGTGATGGTTTGTACACGATTTCGGCCCAAAATTGACCCGAAA
Found at i:3487 original size:84 final size:83
Alignment explanation
Indices: 3399--3635 Score: 312
Period size: 84 Copynumber: 2.8 Consensus size: 83
3389 ATAGAAGTCG
* * * * * * ***
3399 TAGGACCTGGTTGACGCTGATTATGGGATGAAACAGAAGCGGTAAAACCTTGTTGAGGCTGATTT
1 TAGGACCT-TTTGAGGCTGATTTTTGGCTGAAACAGAAGTGGTGGGACCTTGTTGAGGCTGATTT
*
3464 TGGGAGGGTAGAGCAGTAT
65 TGGGAGGCTAGAGCAGTAT
* * *
3483 TAGGACTTTTTTTAGGCTGATTTTTGGCTGAAACAGAAGTGGTGGGACCTTGTTGATGCTGATTT
1 TAGGAC-CTTTTGAGGCTGATTTTTGGCTGAAACAGAAGTGGTGGGACCTTGTTGAGGCTGATTT
3548 TGGGAGGCTAGAGCAGTAT
65 TGGGAGGCTAGAGCAGTAT
* *
3567 TTGGACCTTTCTGAGGCTGATTTTTGGCTGAAACAGAAGTGCTGGGACCTTGTTGAGGCTGATTT
1 TAGGACCTTT-TGAGGCTGATTTTTGGCTGAAACAGAAGTGGTGGGACCTTGTTGAGGCTGATTT
3632 TGGG
65 TGGG
3636 CCTCGACAGA
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
83 3 0.02
84 129 0.97
85 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.33, T:0.32
Consensus pattern (83 bp):
TAGGACCTTTTGAGGCTGATTTTTGGCTGAAACAGAAGTGGTGGGACCTTGTTGAGGCTGATTTT
GGGAGGCTAGAGCAGTAT
Found at i:3544 original size:42 final size:42
Alignment explanation
Indices: 3346--3635 Score: 197
Period size: 42 Copynumber: 6.9 Consensus size: 42
3336 CGGTAGTTGG
** * * *
3346 AACAGAAGTCATAGGACCTGGTTGACGCTGATTATT-GGCTGA
1 AACAGAAGTGGTAGGACCTTGTTGAGGCTGATT-TTGGGATGA
* * * * *
3388 AATAGAAGTCGTAGGACCTGGTTGACGCTGATTATGGGATGA
1 AACAGAAGTGGTAGGACCTTGTTGAGGCTGATTTTGGGATGA
* ** * *
3430 AACAGAAGCGGTAAAACCTTGTTGAGGCTGATTTTGGGAGGG
1 AACAGAAGTGGTAGGACCTTGTTGAGGCTGATTTTGGGATGA
* * * ** * * * * *
3472 TAGAGCAGTATTAGGACTTTTTTTAGGCTGATTTTTGGCTGA
1 AACAGAAGTGGTAGGACCTTGTTGAGGCTGATTTTGGGATGA
* * * *
3514 AACAGAAGTGGTGGGACCTTGTTGATGCTGATTTTGGGAGGC
1 AACAGAAGTGGTAGGACCTTGTTGAGGCTGATTTTGGGATGA
* * * ** * * *
3556 TAGAGCAGTATTTGGACCTT-TCTGAGGCTGATTTTTGGCTGA
1 AACAGAAGTGGTAGGACCTTGT-TGAGGCTGATTTTGGGATGA
* *
3598 AACAGAAGTGCTGGGACCTTGTTGAGGCTGATTTTGGG
1 AACAGAAGTGGTAGGACCTTGTTGAGGCTGATTTTGGG
3636 CCTCGACAGA
Statistics
Matches: 184, Mismatches: 61, Indels: 6
0.73 0.24 0.02
Matches are distributed among these distances:
41 2 0.01
42 181 0.98
43 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.31
Consensus pattern (42 bp):
AACAGAAGTGGTAGGACCTTGTTGAGGCTGATTTTGGGATGA
Found at i:3658 original size:84 final size:84
Alignment explanation
Indices: 3445--3659 Score: 231
Period size: 84 Copynumber: 2.6 Consensus size: 84
3435 AAGCGGTAAA
** * * *
3445 ACCTTGTTGAGGCTGATTTTGGGA-G-GGTAG-AGCAGTATTAGGACTTTTTTTAGGCTGATTTT
1 ACCTTGTTGAGGCTGATTTTGGGACGCGACAGAAGCA-TA-T-GGACCTTTCTGAGGCTGATTTT
*
3507 TGGCTGAAACAGAAGTGGTGGG
63 TGGCTGAAACAGAAGTGCTGGG
* * * * * * *
3529 ACCTTGTTGATGCTGATTTTGGGAGGCTAGAGCAGTATTTGGACCTTTCTGAGGCTGATTTTTGG
1 ACCTTGTTGAGGCTGATTTTGGGACGCGACAGAAGCATATGGACCTTTCTGAGGCTGATTTTTGG
3594 CTGAAACAGAAGTGCTGGG
66 CTGAAACAGAAGTGCTGGG
* *
3613 ACCTTGTTGAGGCTGATTTTGGGCCTCGACAGAAGCA-ATGCGACCTT
1 ACCTTGTTGAGGCTGATTTTGGGACGCGACAGAAGCATATG-GACCTT
3660 GTCGTAGCCA
Statistics
Matches: 108, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
83 2 0.02
84 98 0.91
85 2 0.02
86 3 0.03
87 3 0.03
ACGTcount: A:0.21, C:0.14, G:0.32, T:0.33
Consensus pattern (84 bp):
ACCTTGTTGAGGCTGATTTTGGGACGCGACAGAAGCATATGGACCTTTCTGAGGCTGATTTTTGG
CTGAAACAGAAGTGCTGGG
Found at i:14654 original size:5 final size:5
Alignment explanation
Indices: 14644--14668 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
14634 ATTTCCACCT
14644 CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA
14669 AAGGAGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:14961 original size:2 final size:2
Alignment explanation
Indices: 14954--14999 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
14944 ATCGAGAAGC
* *
14954 AG AG AG AG TG AG AG -G AA AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
14995 AG AG A
1 AG AG A
15000 AGGAAGGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Done.