Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold283
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: 2945114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 15
Found at i:2916252 original size:2 final size:2
Alignment explanation
Indices: 2916245--2916271 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2916235 CAAGTTATGA
2916245 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
2916272 ATTGTCTTTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2916893 original size:2 final size:2
Alignment explanation
Indices: 2916886--2916934 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
2916876 TTATAGCATT
* * *
2916886 AC AC AC AC CC AC CC AC CC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2916928 AC AC AC A
1 AC AC AC A
2916935 TATATATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.55, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2917265 original size:2 final size:2
Alignment explanation
Indices: 2917258--2917284 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2917248 AACAAACAAG
2917258 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 A
2917285 GTTTAGAAAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2921159 original size:2 final size:2
Alignment explanation
Indices: 2921147--2921181 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2921137 ATTAAAAAGA
*
2921147 AT AT A- AT AT AT AT TT 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 AT
2921182 GGTTTGCAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2921661 original size:2 final size:2
Alignment explanation
Indices: 2921656--2921682 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2921646 GAAAAAAAAC
2921656 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 A
2921683 AAAGACAAGA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2922990 original size:2 final size:2
Alignment explanation
Indices: 2922985--2923015 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2922975 TTTGAGTGTG
2922985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2923016 CCTTTGTGCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2923407 original size:17 final size:16
Alignment explanation
Indices: 2923385--2923419 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2923375 GAATTTGTAT
2923385 AATAAATGAAAATAAAA
1 AATAAATGAAAA-AAAA
*
2923402 AATAAATTAAAAAAAA
1 AATAAATGAAAAAAAA
2923418 AA
1 AA
2923420 GAATAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AATAAATGAAAAAAAA
Found at i:2923905 original size:106 final size:109
Alignment explanation
Indices: 2923773--2923979 Score: 269
Period size: 108 Copynumber: 1.9 Consensus size: 109
2923763 TGATGGTAAC
* * * **
2923773 GACAAATGAGAAGATTCCCATTTA-TTTTAAG-AAAATAAATTACTAT-GGACTATAATAAATTT
1 GACAAATGAGAAGATTCACATATATTTTTAAGAAAAAAAAATTACTATAGG-CTATAATAAATAC
* * * *
2923835 GATTTAATTTT-TATTAGATTTGTTTAATTTTATTTTGTTTTGTT
65 GATTCAATTTTATATTAAATTTATTTAATTTAATTTTGTTTTGTT
* * *
2923879 GACAAATGAGAAGATTCACATATATTTTTAAGAAAAAAAAATTATTATAGGCTATGATAAGTACG
1 GACAAATGAGAAGATTCACATATATTTTTAAGAAAAAAAAATTACTATAGGCTATAATAAATACG
2923944 ATTCAATTTTATATTAAATTTATTTAATTTAATTTT
66 ATTCAATTTTATATTAAATTTATTTAATTTAATTTT
2923980 TTTGTTAATT
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
106 22 0.26
107 7 0.08
108 32 0.38
109 24 0.28
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (109 bp):
GACAAATGAGAAGATTCACATATATTTTTAAGAAAAAAAAATTACTATAGGCTATAATAAATACG
ATTCAATTTTATATTAAATTTATTTAATTTAATTTTGTTTTGTT
Found at i:2924840 original size:6 final size:6
Alignment explanation
Indices: 2924829--2924874 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
2924819 CAGGTGAGGT
2924829 GATAGA GATAGA GATAGA GATAGA GATAGA GATAGA GATAGA GATA
1 GATAGA GATAGA GATAGA GATAGA GATAGA GATAGA GATAGA GATA
2924875 AAGAGATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
GATAGA
Found at i:2925551 original size:23 final size:22
Alignment explanation
Indices: 2925525--2925568 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2925515 CTCCTCTCCC
2925525 TTCCCCTCCTTTTTTCTTTTTTT
1 TTCCCCTCC-TTTTTCTTTTTTT
** *
2925548 TTCCTTTTCTTTTTCTTTTTT
1 TTCCCCTCCTTTTTCTTTTTT
2925569 AATTCTCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TTCCCCTCCTTTTTCTTTTTTT
Found at i:2925552 original size:18 final size:19
Alignment explanation
Indices: 2925531--2925568 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2925521 TCCCTTCCCC
2925531 TCCTTTT-TTCTTT-TTTTT
1 TCCTTTTCTT-TTTCTTTTT
2925549 TCCTTTTCTTTTTCTTTTT
1 TCCTTTTCTTTTTCTTTTT
2925568 T
1 T
2925569 AATTCTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TCCTTTTCTTTTTCTTTTT
Found at i:2927124 original size:16 final size:16
Alignment explanation
Indices: 2927103--2927148 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
2927093 CTATGAAAGA
2927103 TTTATAAAATATATTT
1 TTTATAAAATATATTT
* *
2927119 TTTATATAAT-T-TTA
1 TTTATAAAATATATTT
*
2927133 ATTATAAAATATATTT
1 TTTATAAAATATATTT
2927149 ATAAATATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTATAAAATATATTT
Found at i:2927157 original size:19 final size:19
Alignment explanation
Indices: 2927122--2927179 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
2927112 TATATTTTTT
*
2927122 ATATAATTTTAATTATAAA
1 ATATAATTTTAAATATAAA
2927141 ATAT-ATTTATAAATATAAA
1 ATATAATTT-TAAATATAAA
* *
2927160 A-ATAGTTTTTAATATTAAA
1 ATATAATTTTAAATA-TAAA
2927179 A
1 A
2927180 ACCGACTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATATAATTTTAAATATAAA
Found at i:2927435 original size:2 final size:2
Alignment explanation
Indices: 2927428--2927460 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2927418 CCAATGTTAA
2927428 AT 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 AT A
2927461 GTCCAACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2929858 original size:2 final size:2
Alignment explanation
Indices: 2929851--2929882 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2929841 ATTTAAAAAG
2929851 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2929883 ATACCACGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2931375 original size:2 final size:2
Alignment explanation
Indices: 2931368--2931404 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2931358 CTATTTACAA
2931368 AT AT AT 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 AT AT AT A
2931405 ATAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2936712 original size:2 final size:2
Alignment explanation
Indices: 2936707--2936753 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2936697 ATATATATAT
2936707 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- 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
2936748 AG AG AG
1 AG AG AG
2936754 GAATATTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2938805 original size:4 final size:4
Alignment explanation
Indices: 2938796--2938820 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2938786 CATATAATAT
2938796 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
2938821 TGACAGCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:2939115 original size:2 final size:2
Alignment explanation
Indices: 2939108--2939136 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2939098 GAAATATCGA
2939108 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 A
2939137 AATAGTACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2941244 original size:22 final size:22
Alignment explanation
Indices: 2941216--2941259 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2941206 TAAAACTCTA
2941216 AAGATATTCATCAATCCTGCTG
1 AAGATATTCATCAATCCTGCTG
2941238 AAGATATTCATCAATCCTGCTG
1 AAGATATTCATCAATCCTGCTG
2941260 TACTAGGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (22 bp):
AAGATATTCATCAATCCTGCTG
Done.