Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold923
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: 16987
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:837 original size:39 final size:40
Alignment explanation
Indices: 776--956 Score: 189
Period size: 39 Copynumber: 4.7 Consensus size: 40
766 GGATGATAAC
* * *
776 CGGGCTAAGTCCCG-AGAGCATTTGAGCTAG-TGGCTAATTT
1 CGGGCTAAGTCCCGAAGA-CATTTGTGCGAGCT-ACTAATTT
* *
816 AGGGCTAAG-CCCGAAGACATTTGTGCGAGCTACTAATTC
1 CGGGCTAAGTCCCGAAGACATTTGTGCGAGCTACTAATTT
*
855 CGGGCTAAGT-CCGAAGGCATTTGTGCGAGCTACTAATTT
1 CGGGCTAAGTCCCGAAGACATTTGTGCGAGCTACTAATTT
* *
894 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TA-T-ATAT
1 -CGGGCTAAGTCCCGAAGACATTTGTGCGAGCTACTAATTT
* *
932 CAGGCTAAGT-CCGAAGGCATTTGTG
1 CGGGCTAAGTCCCGAAGACATTTGTG
957 AGTTATAACC
Statistics
Matches: 126, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
36 15 0.12
37 9 0.07
38 3 0.02
39 56 0.44
40 24 0.19
41 19 0.15
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGACATTTGTGCGAGCTACTAATTT
Found at i:952 original size:77 final size:78
Alignment explanation
Indices: 809--956 Score: 214
Period size: 77 Copynumber: 1.9 Consensus size: 78
799 GAGCTAGTGG
*
809 CTAATTTAGGGCTAAGCCCGAAGACATTTGTGCGAGCTACTAATTCCGGGCTAAGTCCGAAGGCA
1 CTAATTTAGGGCTAAGCCCGAAGACATTTGTGCGAGCTACTAATTCCAGGCTAAGTCCGAAGGCA
874 TTTGTGCGAGCTA
66 TTTGTGCGAGCTA
* *
887 CTAATTTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TA-T-ATAT-CAGGCTAAGTCCGAAG
1 CTAATTT-AGGGCTAAG-CCCGAAGACATTTGTGCGAGCTACTAAT-TCCAGGCTAAGTCCGAAG
948 GCATTTGTG
63 GCATTTGTG
957 AGTTATAACC
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
77 26 0.41
78 9 0.14
79 10 0.16
80 19 0.30
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (78 bp):
CTAATTTAGGGCTAAGCCCGAAGACATTTGTGCGAGCTACTAATTCCAGGCTAAGTCCGAAGGCA
TTTGTGCGAGCTA
Found at i:998 original size:30 final size:31
Alignment explanation
Indices: 901--1016 Score: 94
Period size: 33 Copynumber: 3.5 Consensus size: 31
891 TTTCCGGGCT
* *
901 AAGTCCCGAAGGCATTTGTGCGAGTATATATCAGGC
1 AAGT-CCG-AGGCATTTGT--GAGT-TATAACCGGC
937 TAAGTCCGAAGGCATTTGTGAGTTATAACCGG-
1 -AAGTCCG-AGGCATTTGTGAGTTATAACCGGC
969 AAGT-CGAGGCATTTGTGAAGTTACT-ACCGGC
1 AAGTCCGAGGCATTTGTG-AGTTA-TAACCGGC
*
1000 TAAGTCCGAAGCATTTG
1 -AAGTCCGAGGCATTTG
1017 AGCTAGTGGC
Statistics
Matches: 71, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
29 11 0.15
30 12 0.17
31 5 0.07
32 4 0.06
33 17 0.24
34 4 0.06
36 14 0.20
37 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (31 bp):
AAGTCCGAGGCATTTGTGAGTTATAACCGGC
Found at i:8881 original size:40 final size:39
Alignment explanation
Indices: 8821--9000 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 39
8811 CGGATGATAA
* * * *
8821 GGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAATTCC
1 GGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-ACTAATACC
*
8861 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAATACC
*
8901 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TTATACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAATACC
*
8940 GGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-ATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAT-ACC
8980 GGGCT-AGT-CCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
9001 AGCTAGTGGC
Statistics
Matches: 129, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
38 13 0.10
39 41 0.32
40 72 0.56
41 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAATACC
Found at i:8953 original size:39 final size:39
Alignment explanation
Indices: 8859--9000 Score: 207
Period size: 39 Copynumber: 3.6 Consensus size: 39
8849 GTGGCTAATT
* * *
8859 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TTATA
8899 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA
* *
8938 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAT-A
8978 CCGGGCT-AGT-CCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
9001 AGCTAGTGGC
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
38 13 0.14
39 42 0.44
40 41 0.43
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA
Found at i:12574 original size:28 final size:28
Alignment explanation
Indices: 12532--12589 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
12522 AGTGAAGAAA
12532 GGTCCAAACTATCAAACAGAGAAACAGG
1 GGTCCAAACTATCAAACAGAGAAACAGG
* * * *
12560 GGTCGAAACTGTCAAACAGCGAAATAGG
1 GGTCCAAACTATCAAACAGAGAAACAGG
12588 GG
1 GG
12590 AGACTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (28 bp):
GGTCCAAACTATCAAACAGAGAAACAGG
Found at i:15019 original size:39 final size:40
Alignment explanation
Indices: 14976--15144 Score: 216
Period size: 39 Copynumber: 4.3 Consensus size: 40
14966 TCCTCGTTCA
* * * *
14976 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
15015 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* *
15055 ACTGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * *
15094 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
15134 AAGGCCTTCGG
1 AATGCCTTCGG
15145 ATCTTAATCC
Statistics
Matches: 115, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 70 0.61
40 45 0.39
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:15103 original size:79 final size:78
Alignment explanation
Indices: 14974--15197 Score: 232
Period size: 79 Copynumber: 2.8 Consensus size: 78
14964 GCTCCTCGTT
* * * *
14974 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTC-GGACTTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGA
15039 TTTAACAACTCGCA
65 TTTAACAACTCGCA
* * * *
15053 CGACTGCCTTCGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGACTTAACCCGGATTTAATAACTCACAC-AATGCCTTCGGGACATAACCCGGA
** *
15118 TTTAGTATCTCGCA
65 TTTAACAACTCGCA
* * * * * * * * *
15132 CAAAGGCCTTCGGATCTTAATCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGA-CTTAACCCGGATTTAATAACTCA-CACAATGCCTTCGGGACATAACCCGG
15197 A
64 A
15198 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
78 24 0.20
79 54 0.45
80 39 0.32
81 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGACTTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGAT
TTAACAACTCGCA
Found at i:15119 original size:40 final size:39
Alignment explanation
Indices: 14976--15197 Score: 223
Period size: 40 Copynumber: 5.6 Consensus size: 39
14966 TCCTCGTTCA
* * * * *
14976 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
15015 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
*
15054 GACTGCCTTC-GGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
15093 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * * * * *
15133 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
15174 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
15198 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
39 73 0.47
40 75 0.48
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Done.