Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1922
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: 10680
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.18
Found at i:210 original size:102 final size:102
Alignment explanation
Indices: 34--220 Score: 315
Period size: 102 Copynumber: 1.8 Consensus size: 102
24 GGCCAGGTGC
* *
34 ACGGTGCGCGCCCTGCCCGCCCCCTGGTGTGGGGGCGGTCGGGGCGCACACCATGCGGAGCACCG
1 ACGGTGCGCGCCCTGCCCGCCCCCTGGGGTGGGGGCGGGCGGGGCGCACACCATGCGGAGCACCG
99 GTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGA
66 GTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGA
*
136 ACGGTGCGCGCCCAT-CCCGCCCCCTGGGGTCGGGGGCGGGCGGGGCGCACGCCATGCGGAGCA-
1 ACGGTGCGCGCCC-TGCCCGCCCCCTGGGGT-GGGGGCGGGCGGGGCGCACACCATGCGGAGCAC
199 CGGTGCGCGCCTCGCCCACCCT
64 CGGTGCGCGCCTCGCCCACCCT
221 GGGGGGTGCG
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
102 49 0.61
103 31 0.39
ACGTcount: A:0.09, C:0.41, G:0.41, T:0.10
Consensus pattern (102 bp):
ACGGTGCGCGCCCTGCCCGCCCCCTGGGGTGGGGGCGGGCGGGGCGCACACCATGCGGAGCACCG
GTGCGCGCCTCGCCCACCCTCGGCTGCGGGCGGGAGA
Found at i:291 original size:64 final size:62
Alignment explanation
Indices: 131--306 Score: 168
Period size: 64 Copynumber: 2.8 Consensus size: 62
121 GCTGCGGGCG
* ** *
131 GGAGAACGGTGCGCGCCCATCCCGCCCCCTGGGGT-CGGGGGCGG-GCGGGGCGCACGCCATGC
1 GGAGCACGGTGCGCGCCC-TCCCGCCCCCTGGGGTGC-GGGGCGGCGCGGCACGCACGCCAGGC
*
193 GGAGCACGGTGCGCG-CCTCGCC-CACCCTGGGGGGTGCGGGGCGGCCGCGGCACGCAC-CC-GG
1 GGAGCACGGTGCGCGCCCTC-CCGCCCCCT--GGGGTGCGGGGCGG-CGCGGCACGCACGCCAGG
254 CC
62 -C
256 AGGAGCACGGTGCGCGCCCTTCCCGCCCCCTGGGGTG-GGGGCGGTCGCGGC
1 -GGAGCACGGTGCGCGCCC-TCCCGCCCCCTGGGGTGCGGGGCGG-CGCGGC
307 GCACACCGTG
Statistics
Matches: 96, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
60 7 0.07
61 4 0.04
62 27 0.28
63 17 0.18
64 30 0.31
65 4 0.04
66 7 0.07
ACGTcount: A:0.08, C:0.39, G:0.45, T:0.09
Consensus pattern (62 bp):
GGAGCACGGTGCGCGCCCTCCCGCCCCCTGGGGTGCGGGGCGGCGCGGCACGCACGCCAGGC
Found at i:8353 original size:418 final size:404
Alignment explanation
Indices: 7557--8357 Score: 1081
Period size: 418 Copynumber: 1.9 Consensus size: 404
7547 CACTCAGCCC
* *
7557 GGGCGCGATCCATGCCAGGCGCATGGAGCGCAATCCCCGACGGCCAACCGGCAGGACGAACCCAG
1 GGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACGGCCAACCGGCAGGACGAACCCAC
*
7622 CGTTGCCGATGCAAGGGCCGCGAGACTGCCCCTGCTCGAGGGGCAACGGCCAGGCCAAGCCCGCA
66 CGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCTCGAGGGGCAACGGCCAGGCCAAGCCCGCA
7687 CCTGCAGCATCTGCCTGCACCACAACCGGGACCATCCACTCGAATTCGAGAACTTGGCAGCATCA
131 CCTGCAGCATCTGCCTGCACCACAACCGGGACCATCCACTCGAATTCGAGAACTTGGCAGCATCA
* * *
7752 CCGCAGGAGCAAGCCTAACCTTCCGGCACGACCACGCCCCGTTACCCACACACGCGTGCCAAGCG
196 CCGCAGGAGCAAGCCTAACCTTCCGGCACGACCACGCCCCATTACCCACACACGCGGGCCAACCG
* * * * *
7817 ATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGCCTTCATCACC
261 ATCGAGCACATAGCGACCGGGGACCTCACCACGGATCACTTGGACCGCGAAGGGCCTCCATCACC
*
7882 GCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATCGA
326 GCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCACGACCTGGATTTTAATCGA
7947 GAGGGACACTGCCG
391 GAGGGACACTGCCG
**
7961 GGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGG-CAACCGGCAGGACGTGCCCA
1 GGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGAC-GGCCAACCGGCAGGACGAACCCA
* * *
8025 CCGTTGCCGATGCAAGGGCCACGAGACTGCCCTTGCTCGAGGGGC-ATGGCCAGGCCAAGCCCTC
65 CCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCTCGAGGGGCAACGGCCAGGCCAAGCCCGC
* * * *
8089 ACCTGCAGCTTCTGCGC-GCGCCACAACCGGGACCCTCTACTCGATTAGGGGGCTTGGTCCTG-G
130 ACCTGCAGCATCTGC-CTGCACCACAACCGGGACCATCCACTCGA--A-------T--T-C-GAG
* * ** * * * * * *
8152 AGTCGTTGGCGGCATCGGCGCAGGTGCGAGCTTAACCTTCCGGCAGGACCACGCCTCATCTCCCC
181 A-AC-TTGGCAGCATCACCGCAGGAGCAAGCCTAACCTTCCGGCACGACCACGCCCCAT-TACCC
* * *
8217 ACACACGCGGGCCAACCGATCGAGCACATGGTGACCGGGGACCTCGCCACGGATCACTTGGACCG
243 ACACACGCGGGCCAACCGATCGAGCACATAGCGACCGGGGACCTCACCACGGATCACTTGGACCG
8282 CGAAGGGCCTCCATCACCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCAT-GCA
308 CGAAGGGCCTCCATCACCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGC-TCGCA
*
8346 TGACCTGGATTT
372 CGACCTGGATTT
8358 CACACGAGGC
Statistics
Matches: 343, Mismatches: 35, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
403 55 0.16
404 101 0.29
405 3 0.01
412 1 0.00
414 1 0.00
415 3 0.01
416 2 0.01
417 45 0.13
418 131 0.38
419 1 0.00
ACGTcount: A:0.21, C:0.36, G:0.30, T:0.13
Consensus pattern (404 bp):
GGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACGGCCAACCGGCAGGACGAACCCAC
CGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCTCGAGGGGCAACGGCCAGGCCAAGCCCGCA
CCTGCAGCATCTGCCTGCACCACAACCGGGACCATCCACTCGAATTCGAGAACTTGGCAGCATCA
CCGCAGGAGCAAGCCTAACCTTCCGGCACGACCACGCCCCATTACCCACACACGCGGGCCAACCG
ATCGAGCACATAGCGACCGGGGACCTCACCACGGATCACTTGGACCGCGAAGGGCCTCCATCACC
GCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCACGACCTGGATTTTAATCGA
GAGGGACACTGCCG
Found at i:9728 original size:358 final size:358
Alignment explanation
Indices: 9071--9787 Score: 1434
Period size: 358 Copynumber: 2.0 Consensus size: 358
9061 GCGTGCCAAA
9071 CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
1 CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
9136 CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
66 CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
9201 GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
131 GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
9266 GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCCCGAGGGGCATGGC
196 GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCCCGAGGGGCATGGC
9331 CAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACAACCTACTCGAATTCGGG
261 CAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACAACCTACTCGAATTCGGG
9396 AACTTGGCAGAATCACCGCAGGTGCGAGCCTTG
326 AACTTGGCAGAATCACCGCAGGTGCGAGCCTTG
9429 CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
1 CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
9494 CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
66 CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
9559 GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
131 GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
9624 GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCCCGAGGGGCATGGC
196 GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCCCGAGGGGCATGGC
9689 CAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACAACCTACTCGAATTCGGG
261 CAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACAACCTACTCGAATTCGGG
9754 AACTTGGCAGAATCACCGCAGGTGCGAGCCTTG
326 AACTTGGCAGAATCACCGCAGGTGCGAGCCTTG
9787 C
1 C
9788 CTTCCGGCAG
Statistics
Matches: 359, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
358 359 1.00
ACGTcount: A:0.21, C:0.35, G:0.30, T:0.13
Consensus pattern (358 bp):
CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCCCGAGGGGCATGGC
CAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACAACCTACTCGAATTCGGG
AACTTGGCAGAATCACCGCAGGTGCGAGCCTTG
Found at i:10562 original size:403 final size:403
Alignment explanation
Indices: 9429--10680 Score: 2014
Period size: 402 Copynumber: 3.1 Consensus size: 403
9419 GCGAGCCTTG
9429 CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
1 CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
9494 CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
66 CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
9559 GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
131 GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
*
9624 GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCCCGAGGGGCATGGC
196 GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCTCGAGGGGCATGGC
* *
9689 CAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACAACCTACTCGAATTCGGG
261 CAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACTACCAACTCGAATTCGGG
9754 AACTTGGCAGAATCACCGCAGGTGCGAGCCTTGCCTTCCGGCA-GACCACGCCCCGTTACCCGCA
326 AACTTGGCAGAATCACCGCAGGTGCGAGCCTTGCCTTCCGGCACGACCACGCCCCGTTACCCGCA
9818 CACGCGTGCCAAA
391 CACGCGTGCCAAA
9831 CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
1 CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
9896 CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
66 CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
9961 GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
131 GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
10026 GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCTCGAGGGGCATGGC
196 GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCTCGAGGGGCATGGC
* *
10091 CAGGCCAAGCCCTCACCTGCAGCCTCTGCCCACGCCACAACCGGGACTACCGACTCGAATTCGGG
261 CAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACTACCAACTCGAATTCGGG
*
10156 AACTTGGCAGCATCACCGCAGGTGCGAGCCTTGCCTTCCGGCACGACCACGCCCCGTTACCCGCA
326 AACTTGGCAGAATCACCGCAGGTGCGAGCCTTGCCTTCCGGCACGACCACGCCCCGTTACCCGCA
*
10221 CACGCGTGCCAAC
391 CACGCGTGCCAAA
* * ** * *
10234 CGATCGCGCACGCAGAGACCGACGGCCTCACCACGGATCACTTGGACCGCGAAGGGTC-CCGTCA
1 CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
* * * *
10298 CCGCAGCTGGGCATCCGGCCACCGAAAACCACGATCGCAAGGCACGCGCGACCTGGATCTTAACC
66 CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
* * * * *
10363 GAGAGGGACACTCTGCCGGGGCGCGATCAATGCCAGGCGCATCGAGCACAATCCCCGACAGACAA
131 GAGAGGGACA--CTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAA
* * * *
10428 CCGGCGGGACGAGCCCACCGTTGCCGAAGCAAGGGCCGCGAGACTGCCCCTGCTC-ACGGGGCAT
194 CCGGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCTCGA-GGGGCAT
10492 GGCCAGGCCAAGCCC-CACCTGCAGCTTCTGCCCACGCCACAACCGGGACTACCAACTCGAATTC
258 GGCCAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACTACCAACTCGAATTC
* * * * *
10556 GGGAACTTGGCAGAATCAGCGCAGGTG-GAAG-CTTAACCCTACGGCACGACCACGCCCCTTGTG
323 GGGAACTTGGCAGAATCACCGCAGGTGCG-AGCCTT-GCCTTCCGGCACGACCACGCCCC--GTT
* * **
10619 CCCCACACACGCGTGCCATG
384 ACCCGCACACGCGTGCCAAA
* * **
10639 CGATCG-GCAGCATACGGCGACCGGGGACCTTGCCACGGATCA
1 CGATCGCGCA-CGTA--GCGACCGGGGGCCTCACCACGGATCA
Statistics
Matches: 794, Mismatches: 45, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
402 443 0.56
403 181 0.23
404 124 0.16
405 26 0.03
407 20 0.03
ACGTcount: A:0.22, C:0.37, G:0.29, T:0.12
Consensus pattern (403 bp):
CGATCGCGCACGTAGCGACCGGGGGCCTCACCACGGATCACTTGGACCGCGTAGGGTCTCCATCA
CCGCAGCTGGGCATCCGGTCACCGAAAACCACGATCGCAAGGCTCGCGCGACCTGGATTTTAATC
GAGAGGGACACTGCCGGGGCGCGAACCATGCCAGGCGCATGGAGCGCAATCCCCGACAGGCAACC
GGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCCCCTGCTCGAGGGGCATGGC
CAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGACTACCAACTCGAATTCGGG
AACTTGGCAGAATCACCGCAGGTGCGAGCCTTGCCTTCCGGCACGACCACGCCCCGTTACCCGCA
CACGCGTGCCAAA
Done.