Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013313.1 Corchorus olitorius cultivar O-4 contig13346, 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: 65174
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1055 original size:109 final size:108
Alignment explanation
Indices: 865--1083 Score: 393
Period size: 109 Copynumber: 2.0 Consensus size: 108
855 ATTAGTCAGG
** **
865 ACTAAGCCCTGGATACTGGATGGGATAAAAAAAAAAGATAAACTAGTATTATAATATAATATAGT
1 ACTAAGCCCTGGATACCAGATAAGATAAAAAAAAAAGATAAACTAGTATTATAATATAATATAGT
930 AAGAAGTAAGATTAGAATTGTAACTCATGTGTGAATATAACCC
66 AAGAAGTAAGATTAGAATTGTAACTCATGTGTGAATATAACCC
973 ACTAAGCCCTGGATACCAGATAAGATAAAAAAAAAACGATAAACTAGTATTATAATATAATATAG
1 ACTAAGCCCTGGATACCAGATAAGATAAAAAAAAAA-GATAAACTAGTATTATAATATAATATAG
1038 TAAGAAGTAAGATTAGAATTGTAACTCATGTGTGAATATAACCC
65 TAAGAAGTAAGATTAGAATTGTAACTCATGTGTGAATATAACCC
1082 AC
1 AC
1084 AGTGAAAAGT
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
108 32 0.30
109 74 0.70
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (108 bp):
ACTAAGCCCTGGATACCAGATAAGATAAAAAAAAAAGATAAACTAGTATTATAATATAATATAGT
AAGAAGTAAGATTAGAATTGTAACTCATGTGTGAATATAACCC
Found at i:8993 original size:20 final size:19
Alignment explanation
Indices: 8957--8994 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
8947 TTGTTTGGTT
8957 TTTTTTTGGCAATATTTTG
1 TTTTTTTGGCAATATTTTG
* *
8976 TTTTTTTGTCAATAATTTG
1 TTTTTTTGGCAATATTTTG
8995 ATGTTCTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.63
Consensus pattern (19 bp):
TTTTTTTGGCAATATTTTG
Found at i:17385 original size:57 final size:57
Alignment explanation
Indices: 17267--17378 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 57
17257 CCTTTCACAC
* * *
17267 AATAAATGTTAAAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTTCACAC
1 AATAAATGTTAAAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTACAAAA
* * *
17324 AATAAATGTTATAATAAATCCTAT-TCCCCTATCTCTACTTAATTATTC-TACAAAA
1 AATAAATGTTAAAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTACAAAA
17379 TAAATAATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
55 4 0.08
56 23 0.47
57 22 0.45
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (57 bp):
AATAAATGTTAAAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTACAAAA
Found at i:17495 original size:42 final size:42
Alignment explanation
Indices: 17436--17518 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
17426 GCTAAAGATC
17436 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
*
17478 ATGATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
17519 AAGACTTAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
Found at i:18875 original size:2 final size:2
Alignment explanation
Indices: 18868--18901 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18858 AAAAATTAGA
18868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18902 GATTTCAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23297 original size:3 final size:3
Alignment explanation
Indices: 23289--23340 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
23279 ATATATATAT
23289 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23337 ATA A
1 ATA A
23341 ATCCTTTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23695 original size:119 final size:122
Alignment explanation
Indices: 23457--23701 Score: 345
Period size: 127 Copynumber: 2.0 Consensus size: 122
23447 TTTGGCTGAC
* *
23457 ACGTTAAGTTGGTTTTTTTTTTCACCGTTTGGGCTTTTTTTCTGGGCATAATTTTAGATTCTTCT
1 ACGTTAAGTTGGTTTTTTTTTTCACCGTTTGGGCTTCTTTTCTGGACATAATTTTAGATTCTTCT
* * **
23522 CCTCTCTTCCCCATTTTTCTTCCCTTCTTCTTTTTTAATTAGGGATGCAAGCGGGTAGCAT
66 CCTCTCTTCCCCA--TTTC-TCCC-TCTCCCTCCTTAATTAGGGATGCAAGCGGGTAGCAT
*
23583 ACGTTAGGTTGGTTTTTTTTTTTCACCGTTTGGGCTTCTTTTCTGGACATAATTTTAGATTCTTC
1 ACGTTAAGTTGG-TTTTTTTTTTCACCGTTTGGGCTTCTTTTCTGGACATAATTTTAGATTCTTC
*
23648 TCCTCTCTTTCCCA-TTC-CCC-C-CCCTCCTTAATTAGGGATGCAAGCGGGTAGCAT
65 TCCTCTCTTCCCCATTTCTCCCTCTCCCTCCTTAATTAGGGATGCAAGCGGGTAGCAT
23702 TTAATCGGAT
Statistics
Matches: 110, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
119 29 0.26
120 1 0.01
122 3 0.03
124 3 0.03
126 11 0.10
127 63 0.57
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (122 bp):
ACGTTAAGTTGGTTTTTTTTTTCACCGTTTGGGCTTCTTTTCTGGACATAATTTTAGATTCTTCT
CCTCTCTTCCCCATTTCTCCCTCTCCCTCCTTAATTAGGGATGCAAGCGGGTAGCAT
Found at i:25725 original size:11 final size:11
Alignment explanation
Indices: 25711--25748 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
25701 ATTCATAACA
25711 AATTTATAATT
1 AATTTATAATT
25722 AATTTATAATT
1 AATTTATAATT
25733 -ATTTGATAATT
1 AATTT-ATAATT
*
25744 TATTT
1 AATTT
25749 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:28183 original size:13 final size:13
Alignment explanation
Indices: 28165--28190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28155 AAGGTAACAA
28165 CAAAAATCATCAC
1 CAAAAATCATCAC
28178 CAAAAATCATCAC
1 CAAAAATCATCAC
28191 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:50806 original size:10 final size:10
Alignment explanation
Indices: 50793--50818 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
50783 AAAATGCATA
50793 AAAAAATTAC
1 AAAAAATTAC
50803 AAAAAATTAC
1 AAAAAATTAC
50813 AAAAAA
1 AAAAAA
50819 AGGGGGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTAC
Found at i:51555 original size:128 final size:128
Alignment explanation
Indices: 51400--51638 Score: 383
Period size: 128 Copynumber: 1.9 Consensus size: 128
51390 ATATATAAAG
51400 TATATAATAGTCATATATAAAGTATAACGGAAATTACAATAATGATTGTCATTTAGTATCAATGA
1 TATATAATAGTCATATATAAAGTATAACGGAAATTACAATAATGATTGTCATTTAGTATCAATGA
*
51465 TATTTGATATTAAGATAAAAAAAACAAACCAATAATTATAGGAATTAATTATAAAGTTGAATCCA
66 TATTTGATATTAAGAT--AAAAAACAAACCAATAATTATAAGAATTAATTATAAAGTTGAATCCA
* * * *
51530 TATAT-ATAGTC-TATATCAAGTATAACGGAAATTACAATAATTATTGTTATTTAGTATCATTGA
1 TATATAATAGTCATATATAAAGTATAACGGAAATTACAATAATGATTGTCATTTAGTATCAATGA
* *
51593 TATTTGATATTAAGATGAAAAATAAACCAATAATTATAAGAATTAA
66 TATTTGATATTAAGATAAAAAACAAACCAATAATTATAAGAATTAA
51639 CCTGATTCAA
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
126 27 0.26
128 64 0.63
129 6 0.06
130 5 0.05
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (128 bp):
TATATAATAGTCATATATAAAGTATAACGGAAATTACAATAATGATTGTCATTTAGTATCAATGA
TATTTGATATTAAGATAAAAAACAAACCAATAATTATAAGAATTAATTATAAAGTTGAATCCA
Found at i:62646 original size:19 final size:19
Alignment explanation
Indices: 62622--62658 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
62612 GTACATTACT
62622 TAATCTAATATGTACAGTG
1 TAATCTAATATGTACAGTG
* *
62641 TAATCTCATCTGTACAGT
1 TAATCTAATATGTACAGT
62659 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATATGTACAGTG
Found at i:62743 original size:18 final size:18
Alignment explanation
Indices: 62720--62754 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
62710 TCTAATGGCC
62720 CTCAAGATCTTAACAATT
1 CTCAAGATCTTAACAATT
62738 CTCAAGATCTTAACAAT
1 CTCAAGATCTTAACAAT
62755 GTTGGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (18 bp):
CTCAAGATCTTAACAATT
Found at i:63966 original size:31 final size:31
Alignment explanation
Indices: 63928--63990 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
63918 ACAAGTATAG
63928 AACAATTCTCATATCATTTCATATCATCAAA
1 AACAATTCTCATATCATTTCATATCATCAAA
63959 AACAATTCTCATATCATTTCATATCATCAAA
1 AACAATTCTCATATCATTTCATATCATCAAA
63990 A
1 A
63991 TTTTGTGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (31 bp):
AACAATTCTCATATCATTTCATATCATCAAA
Done.