Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1822
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: 27382
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:2389 original size:40 final size:40
Alignment explanation
Indices: 2343--2529 Score: 213
Period size: 39 Copynumber: 4.7 Consensus size: 40
2333 ACTACTTGCT
2343 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAG-CCCGGTTATAGTAACTCGCA
* *
2383 CAAATGCCTTCGGGACTCATCCCGGTTCA-A-TAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTT-ATAGTAACTCGCA
* * *
2422 CCAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * ** * *
2462 CAATTGCCTTCGGG-TTTAGCCC-GAAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
2501 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
2530 CATCCGAATA
Statistics
Matches: 123, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
38 4 0.03
39 62 0.50
40 54 0.44
41 3 0.02
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:2481 original size:39 final size:40
Alignment explanation
Indices: 2320--2525 Score: 210
Period size: 40 Copynumber: 5.2 Consensus size: 40
2310 CCTTTGAAAT
* *
2320 TTAG-CCGGATATAACT-ACTTGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-TAACTCGCACAAATGCCTTCGGGAC
* *
2359 TT-GACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAG-CCCGGATATAATAACTCGCACAAATGCCTTCGGGAC
* * *
2399 TCATCCCGG-T-TCAATAACTCGCACCAATGCCTTCGGGAC
1 TTAGCCCGGATAT-AATAACTCGCACAAATGCCTTCGGGAC
* *
2438 TTAGCCCGGATATAATAACTCGCACAATTGCCTTCGGG-T
1 TTAGCCCGGATATAATAACTCGCACAAATGCCTTCGGGAC
* * * *
2477 TTAGCCC-GAAATTAGTCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATA-TAATAACTCGCACAAATGCCTTCGGGAC
2517 TTAGCCCGG
1 TTAGCCCGG
2526 TTATCATCCG
Statistics
Matches: 138, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
38 5 0.04
39 65 0.47
40 66 0.48
41 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAATAACTCGCACAAATGCCTTCGGGAC
Found at i:2507 original size:79 final size:79
Alignment explanation
Indices: 2343--2525 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 79
2333 ACTACTTGCT
* * *
2343 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTCATCCCG
1 CAAATGCCTTCGGGACTTAG-CCCGGATATAATAACTCGCACAAATGCCTTCGGGACTCAGCCCG
* *
2407 GTTCAATAACTCGCA
65 ATTCAATAACTAGCA
* * * *
2422 CCAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAATTGCCTTCGGG-TTTAGCCCGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATGCCTTCGGGACTCAGCCCG-
* *
2486 AATT-AGTCACTAGCA
65 -ATTCAATAACTAGCA
2501 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
2526 TTATCATCCG
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
78 6 0.07
79 80 0.90
80 3 0.03
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATGCCTTCGGGACTCAGCCCGA
TTCAATAACTAGCA
Found at i:20105 original size:19 final size:19
Alignment explanation
Indices: 20083--20119 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20073 GGAATAGTAT
*
20083 ATATAGTAAAATATATAAC
1 ATATAATAAAATATATAAC
*
20102 ATATAATAAAATTTATAA
1 ATATAATAAAATATATAA
20120 ATAAAATGTA
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:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
ATATAATAAAATATATAAC
Found at i:20139 original size:21 final size:23
Alignment explanation
Indices: 20115--20170 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 23
20105 TAATAAAATT
20115 TATAAATAAAATG-T--ATAATAA
1 TATAAATAAAATGATAAATAAT-A
*
20136 TATAAATAATATGATAAATAATA
1 TATAAATAAAATGATAAATAATA
20159 TATAAATAAAAT
1 TATAAATAAAAT
20171 AATATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.40
22 1 0.03
23 12 0.40
24 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (23 bp):
TATAAATAAAATGATAAATAATA
Found at i:20144 original size:12 final size:11
Alignment explanation
Indices: 20129--20167 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 11
20119 AATAAAATGT
20129 ATAATAATATAA
1 ATAAT-ATATAA
20141 ATAATATGATAA
1 ATAATAT-ATAA
20153 ATAATATATAA
1 ATAATATATAA
20164 ATAA
1 ATAA
20168 AATAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
ATAATATATAA
Found at i:21949 original size:44 final size:44
Alignment explanation
Indices: 21812--22239 Score: 492
Period size: 44 Copynumber: 9.9 Consensus size: 44
21802 ATCAACTTAC
* *
21812 CTGCCCTCTGTCAATACAGAGAC-CCAAATCTGTTATCTTTGAT
1 CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAT
* * *
21855 -TGCTCTTTTTCAATACAGAGACGCCAAAT-TGCTATCTTCGAT
1 CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAT
*
21897 CTGCTCTCTGTCAATACAGAGACTCCAAATCTGTTATCTTCGAT
1 CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAT
* * * *
21941 CTGCTCTCTATCAATACAGAGAAGCCAAAT-TGTCATCTTTGAT
1 CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAT
* * * *
21984 TTGCTCTTTGTTCAATACAGAGACGCCAAATCTATTATCTTCAAT
1 CTGCTCTCTG-TCAATACAGAGACGCCAAATCTGTTATCTTCGAT
* * * * *
22029 CTACTCTCTGTCATTATAGAGATGCCAAATCTGTCATCTTCGAT
1 CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAT
* * * *
22073 CTGCTCTCTATCAATACAGAGACGCCAAATCTATCATCTTGGAT
1 CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAT
* * * *
22117 CTGCTTTCTGTAAATACAGAGACACCAAATCTGTTGTCTTCGAT
1 CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAT
* * * *
22161 CTGCT-TATG-CAATACAGAGACACCAAATCTGTCATCTTTGAT
1 CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAT
* * *
22203 CTGCTCTCTATCAATACAGAGATG-CAAATCTGCTATC
1 CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATC
22240 GGTGATCTAC
Statistics
Matches: 321, Mismatches: 57, Indels: 14
0.82 0.15 0.04
Matches are distributed among these distances:
42 64 0.20
43 66 0.21
44 175 0.55
45 16 0.05
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (44 bp):
CTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAT
Found at i:22050 original size:132 final size:133
Alignment explanation
Indices: 21760--22234 Score: 555
Period size: 132 Copynumber: 3.7 Consensus size: 133
21750 GTCAGATTGC
* * * * * * * * * *
21760 TATCTTTGATCTGCTCCCCGTCTAATATAGAGAC-ACAAATCTATCAACTT--ACCTGCCCTCTG
1 TATCTTCGATCTGCTCTCTGTC-AATACAGAGACTCCAAATCTGTCATCTTCGATCTGCTCTCTA
* *
21822 TCAATACAGAG-ACCCAAATCTGTTATCTTTGA-TTGCTCTTT-TTCAATACAGAGACGCCAAAT
65 TCAATACAGAGAAGCCAAATCTGTCATCTTTGATTTGCTCTTTGTTCAATACAGAGACGCCAAAT
*
21884 -TGC
130 CTGT
*
21887 TATCTTCGATCTGCTCTCTGTCAATACAGAGACTCCAAATCTGTTATCTTCGATCTGCTCTCTAT
1 TATCTTCGATCTGCTCTCTGTCAATACAGAGACTCCAAATCTGTCATCTTCGATCTGCTCTCTAT
21952 CAATACAGAGAAGCCAAAT-TGTCATCTTTGATTTGCTCTTTGTTCAATACAGAGACGCCAAATC
66 CAATACAGAGAAGCCAAATCTGTCATCTTTGATTTGCTCTTTGTTCAATACAGAGACGCCAAATC
*
22016 TAT
131 TGT
* * * *
22019 TATCTTCAATCTACTCTCTGTCATTATAGAGA-TGCCAAATCTGTCATCTTCGATCTGCTCTCTA
1 TATCTTCGATCTGCTCTCTGTCAATACAGAGACT-CCAAATCTGTCATCTTCGATCTGCTCTCTA
* * * * * *
22083 TCAATACAGAGACGCCAAATCTATCATCTTGGATCTGCT-TTCTG-TAAATACAGAGACACCAAA
65 TCAATACAGAGAAGCCAAATCTGTCATCTTTGATTTGCTCTT-TGTTCAATACAGAGACGCCAAA
22146 TCTGT
129 TCTGT
* * * *
22151 TGTCTTCGATCTGCT-TATG-CAATACAGAGACACCAAATCTGTCATCTTTGATCTGCTCTCTAT
1 TATCTTCGATCTGCTCTCTGTCAATACAGAGACTCCAAATCTGTCATCTTCGATCTGCTCTCTAT
*
22214 CAATACAGAGATG-CAAATCTG
66 CAATACAGAGAAGCCAAATCTG
22235 CTATCGGTGA
Statistics
Matches: 300, Mismatches: 37, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
126 10 0.03
127 31 0.10
129 38 0.13
130 67 0.22
131 25 0.08
132 112 0.37
133 17 0.06
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (133 bp):
TATCTTCGATCTGCTCTCTGTCAATACAGAGACTCCAAATCTGTCATCTTCGATCTGCTCTCTAT
CAATACAGAGAAGCCAAATCTGTCATCTTTGATTTGCTCTTTGTTCAATACAGAGACGCCAAATC
TGT
Done.