Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold685
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: 30552
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Found at i:3733 original size:39 final size:40
Alignment explanation
Indices: 3592--3733 Score: 268
Period size: 40 Copynumber: 3.6 Consensus size: 40
3582 TATTCGAATG
3592 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
3632 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
3672 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
3712 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
3734 TACTTGGGTT
Statistics
Matches: 101, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
39 15 0.15
40 86 0.85
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:11643 original size:39 final size:40
Alignment explanation
Indices: 11502--11643 Score: 216
Period size: 40 Copynumber: 3.6 Consensus size: 40
11492 TATTCGAATG
*
11502 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGAGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
11542 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
11582 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* * *
11622 ATTTTC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
11644 TACTTGGGTT
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 15 0.16
40 79 0.82
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:16230 original size:40 final size:40
Alignment explanation
Indices: 16025--16215 Score: 319
Period size: 40 Copynumber: 4.8 Consensus size: 40
16015 TATTCGAATG
*
16025 ATATCCGGGCTAAGTCCCGAAGGAATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
16065 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
16105 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
16145 ATATCTGGGCCAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
16185 ATATCCGGGCTAAGACCCAAAGCCATTTGTG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTG
16216 TGAGTTGCTA
Statistics
Matches: 142, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:26165 original size:49 final size:47
Alignment explanation
Indices: 26101--26460 Score: 542
Period size: 49 Copynumber: 7.6 Consensus size: 47
26091 GATAATTGTG
* *
26101 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
26148 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
26197 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
26246 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
26295 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
26342 ATGTGAAAGTGTATATATGTGAT-GGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * ** *
26388 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACATGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
26435 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
26461 TCCCGAAGGG
Statistics
Matches: 295, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
46 43 0.15
47 109 0.37
49 143 0.48
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:28884 original size:40 final size:40
Alignment explanation
Indices: 28721--29116 Score: 453
Period size: 40 Copynumber: 10.1 Consensus size: 40
28711 AAGTCTCAAC
28721 GATG-ATCC-GGCTAAGTCCCGCAAGAGCATTCGTGCT-GT
1 GATGTATCCGGGCTAAGTCCCG-AAGAGCATTCGTGCTAGT
*
28759 GATGTATCCGGGC---G-ACCGAAGAGCATTC-TGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
28794 GATGTA-CCCGGCTAAGTCCCGAAGAGCATTC--GCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
28831 GATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
28871 GATGTATCTGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
28911 GATGTACCCGCGGC-AAGTCCCGCAAG-GCATTCGTGCTAGT
1 GATGTATCCG-GGCTAAGTCCCG-AAGAGCATTCGTGCTAGT
*
28951 GATGTATCCGCGGCTAAGTCTCGAAGAGCATTCGTGCTAGT
1 GATGTATCCG-GGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
28992 GATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT-GT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* ** * *
29031 GATATATCCGTTCTAA-ACCCGAAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCG-AAGAGCATTCGTGCTAGT
* * * * * *
29071 GTTATATCCGGGCTAGGTCTCGAAGAGCAATCAATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTC-GTGCTAGT
29112 GATGT
1 GATGT
29117 GTGTTCGGGC
Statistics
Matches: 308, Mismatches: 32, Indels: 33
0.83 0.09 0.09
Matches are distributed among these distances:
34 9 0.03
35 18 0.06
36 3 0.01
37 14 0.05
38 43 0.14
39 34 0.11
40 138 0.45
41 49 0.16
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:28983 original size:121 final size:119
Alignment explanation
Indices: 28721--29116 Score: 471
Period size: 121 Copynumber: 3.4 Consensus size: 119
28711 AAGTCTCAAC
*
28721 GATG-ATCC-GGCTAAGTCCCGCAAGAGCATTCGTGCT-GTGATGTATCCGGGC---G-ACCGAA
1 GATGTATCCGGGCTAAGTCTCG-AAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTACCGAA
28779 GAGCATTCTGCTAGTGATGTACC-CGGCTAAGTCCCGAAGAGCATTC--GCTAGT
65 GAGCATTCTGCTAGTGATGTACCGCGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
28831 GATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCTGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTACCGAAG
28896 AGCATTCATGCTAGTGATGTACCCGCGGC-AAGTCCCGCAAG-GCATTCGTGCTAGT
66 AGCATTC-TGCTAGTGATGTA-CCGCGGCTAAGTCCCG-AAGAGCATTCGTGCTAGT
* *
28951 GATGTATCCGCGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAA
1 GATGTATCCG-GGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTACCGAA
* ** * *
29016 GAGCATTCGTGCT-GTGATATATCCG-TTCTAA-ACCCGAAAGAGCATTCGTGCTGGT
65 GAGCATTC-TGCTAGTGATGTA-CCGCGGCTAAGTCCCG-AAGAGCATTCGTGCTAGT
* * * * *
29071 GTTATATCCGGGCTAGGTCTCGAAGAGCAATCAATGCTAGTGATGT
1 GATGTATCCGGGCTAAGTCTCGAAGAGCATTC-GTGCTAGTGATGT
29117 GTGTTCGGGC
Statistics
Matches: 250, Mismatches: 19, Indels: 24
0.85 0.06 0.08
Matches are distributed among these distances:
110 4 0.02
111 19 0.08
112 25 0.10
115 1 0.00
116 13 0.05
117 13 0.05
118 16 0.06
119 35 0.14
120 61 0.24
121 63 0.25
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (119 bp):
GATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTACCGAAG
AGCATTCTGCTAGTGATGTACCGCGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Done.