Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1111
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: 14031
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Found at i:8711 original size:76 final size:78
Alignment explanation
Indices: 8580--8778 Score: 208
Period size: 76 Copynumber: 2.6 Consensus size: 78
8570 GAGATAATAA
* * ** * *
8580 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-
*
8644 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* * *
8656 CGGGATTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-
* *
8721 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * *
8735 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCC
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCC
8779 TCGATGAAAT
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
75 7 0.07
76 47 0.47
77 2 0.02
78 3 0.03
79 42 0.42
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.26
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:8807 original size:28 final size:28
Alignment explanation
Indices: 8738--8811 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
8728 ATAAAGCCGG
* *
8738 GGTTGGAGTATCCCCTCG--GAAGTAACGG
1 GGTTGGAGTAT--CCTCGATGAAATAACGA
8766 GGTTGGAGTATCCTCGATGAAATAACGA
1 GGTTGGAGTATCCTCGATGAAATAACGA
8794 GGTTGGAGTATCCTCGAT
1 GGTTGGAGTATCCTCGAT
8812 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.12
28 37 0.88
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCTCGATGAAATAACGA
Found at i:8864 original size:52 final size:50
Alignment explanation
Indices: 8795--8964 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
8785 AAATAACGAG
* * *
8795 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
8847 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
8900 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
8951 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
8965 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:8983 original size:28 final size:28
Alignment explanation
Indices: 8938--9019 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
8928 AGTGTTTTAA
* *
8938 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
8965 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
8992 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
9020 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:11456 original size:13 final size:13
Alignment explanation
Indices: 11438--11463 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11428 ACAAAGATCC
11438 ATGTATCGATACA
1 ATGTATCGATACA
11451 ATGTATCGATACA
1 ATGTATCGATACA
11464 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11459 original size:33 final size:33
Alignment explanation
Indices: 11417--11483 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11407 AAAATTTCCA
***
11417 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
11450 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
11483 A
1 A
11484 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:12155 original size:55 final size:55
Alignment explanation
Indices: 12071--12309 Score: 338
Period size: 55 Copynumber: 4.3 Consensus size: 55
12061 ATAAATTGTA
* * * * * *
12071 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
12126 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
12181 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
12236 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
12291 TCCTGTTCTTTGAGGACTG
1 TCCTGCTCTTTGAGGACTG
12310 GAAAATGTAT
Statistics
Matches: 165, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
54 3 0.02
55 156 0.95
56 6 0.04
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:12408 original size:21 final size:21
Alignment explanation
Indices: 12384--12440 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
12374 CATTTGTAGG
*
12384 ATGTATCTATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
12405 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
12426 ATGTATCGATACATT
1 ATGTATCGATACATT
12441 TTTTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:13053 original size:159 final size:158
Alignment explanation
Indices: 12859--14011 Score: 385
Period size: 159 Copynumber: 7.3 Consensus size: 158
12849 AAAAAATCCA
* * * * *
12859 TTCTTGCGAATCCAAACCATCAATTTCGTCTATCCTAATGAGTTGACTATGTTGATAGTGCCTAA
1 TTCTTGCGAA-CCAAAGCATCAATATCATTTATCCTAATGAATTGACTATGTTGATAGTGCCTAA
*
12924 TCCTGAAAAGATTAGGGATTAGTATAACTATTCATGTTTGTCTTATTTAAGAGGCAAACTTTGAT
65 TCCTGAAAAGAAT-GGGATTAGTATAACTATTCATGTTTGTCTTATTTAAGAGGCAAACTTTGAT
* *
12989 TCTAACAAAAACAGTAGAGGCGAAA-CCTT
129 TCTAACAAAAACGGTAGAGGAGAAATCCTT
* ** * ** ** * *
13018 TTCTTGCGACACCAAAGCATCAATATCATTTATCCTAAAGAACGGATTGGGTTCTTAGTTCCAAA
1 TTCTTGCGA-ACCAAAGCATCAATATCATTTATCCTAATGAATTGACTATGTTGATAGTGCCTAA
* * * * ** * * * *
13083 TCTTGAAAAGAATGGAGA-CAGT-T-ACGAGAATCGATAATTGTCATAATTCAG-GG-ATGAATT
65 TCCTGAAAAGAATGG-GATTAGTATAAC--TATTC-ATGTTTGTCTTATTTAAGAGGCA--AACT
* * * * **
13143 TTTATTTTAAGGAAAATAGGGTA-A--AGAAATGATT
124 TTGATTCTAA-CAAAA-ACGGTAGAGGAGAAATCCTT
* * * ** * * ** * * * *
13177 TCCATGCAAAAGAAAATCATCAATATCATTTATCCTACTGAAAAGAATGTGTTTATAGTGCGTAA
1 TTCTTGC-GAACCAAAGCATCAATATCATTTATCCTAATGAATTGACTATGTTGATAGTGCCTAA
* * ** *
13242 TCAC--AAAATGAATGAAGATTATTACTAGAACCCTT--T-TTTGTCTCATTT--GAGGCACAAA
65 TC-CTGAAAA-GAATG-GGATTAGTA-T--AACTATTCATGTTTGTCTTATTTAAGAGG--CAAA
* ** * * *
13300 CTTAGACTT-T-ACAGAAATTGG-AGTGAAGAAATCC-A
122 CTTTGA-TTCTAACA-AAAACGGTAGAGGAGAAATCCTT
* * * *
13335 TTCTTGCGAATCCAAAGCATCAATTTCGTCTATCCTAATGAGTTGACTATGTTGATAGTGCCTAA
1 TTCTTGCGAA-CCAAAGCATCAATATCATTTATCCTAATGAATTGACTATGTTGATAGTGCCTAA
* * *
13400 TCCTGAAAAGATTAGGGATTAGTATGACTATTCATGTTTGTCTTATTTAAGAGCCAAACTTTGAT
65 TCCTGAAAAGAAT-GGGATTAGTATAACTATTCATGTTTGTCTTATTTAAGAGGCAAACTTTGAT
*
13465 TCTAACAAAAACGGTAGAGGCGAAA-CCTT
129 TCTAACAAAAACGGTAGAGGAGAAATCCTT
* * * ** * *
13494 TACTTGCGACACCAAAGCATCAATATCATTTATCCTAATGAA-GGAAT-TGGGTTCTTAGTTCCA
1 TTCTTGCGA-ACCAAAGCATCAATATCATTTATCCTAATGAATTGACTAT--GTTGATAGTGCCT
* * * * ** * * *
13557 AATCTTGAAAAGAATGGAGA-CAGT-T-ACGAGAATCGATAATTGTCATAATTCAG-GG-AGGAA
63 AATCCTGAAAAGAATGG-GATTAGTATAAC--TATTC-ATGTTTGTCTTATTTAAGAGGCA--AA
* * * * **
13617 TTTTTATTTTAAGGAAAATACGGTA-A--AGAAATGATT
122 CTTTGATTCTAA-CAAAA-ACGGTAGAGGAGAAATCCTT
* * * ** * * ** * * * * *
13653 TCCATGCAAAAGAAAATCATCAATATCATTTATCCTACTGAAAAGAATGTTTTTATAGTGCGTAA
1 TTCTTGC-GAACCAAAGCATCAATATCATTTATCCTAATGAATTGACTATGTTGATAGTGCCTAA
* * * * * * * *
13718 T--TACAAAATGAATGAAGATCA-T-T-ACTTGAATCCTTTTTTATCTCATTT--GAGGCACAAA
65 TCCT-GAAAA-GAATG-GGATTAGTATAAC-T--ATTCATGTTTGTCTTATTTAAGAGG--CAAA
* ** * * * *
13776 CTTAGACTT-T-ACAGAAATTGG-AGTGAAGAAATAC-A
122 CTTTGA-TTCTAACA-AAAACGGTAGAGGAGAAATCCTT
* * * * *
13811 TTCTTGCGAATCTAAAGCTTCAATTTCTTTTATCCTAATGAGTTGACTATGTTGATAGTGCCTAA
1 TTCTTGCGAA-CCAAAGCATCAATATCATTTATCCTAATGAATTGACTATGTTGATAGTGCCTAA
* * * * *
13876 TCTTGAAAAGATTAGCGATTAGTATGACTATTCGTGTTTGTCTTATTTAAGAGGCAAACTTTGAT
65 TCCTGAAAAGAAT-GGGATTAGTATAACTATTCATGTTTGTCTTATTTAAGAGGCAAACTTTGAT
* *
13941 TCTAACAAAAACGGTAGA-GAGGAAGCCTT
129 TCTAACAAAAACGGTAGAGGAGAAATCCTT
* *
13970 TTCTTACAACACCAAAGCATCAATATCATTTATCCTAATGAA
1 TTCTTGCGA-ACCAAAGCATCAATATCATTTATCCTAATGAA
14012 GGGATTGGGT
Statistics
Matches: 695, Mismatches: 213, Indels: 172
0.64 0.20 0.16
Matches are distributed among these distances:
155 4 0.01
156 6 0.01
157 25 0.04
158 221 0.32
159 380 0.55
160 40 0.06
161 15 0.02
162 1 0.00
163 1 0.00
165 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (158 bp):
TTCTTGCGAACCAAAGCATCAATATCATTTATCCTAATGAATTGACTATGTTGATAGTGCCTAAT
CCTGAAAAGAATGGGATTAGTATAACTATTCATGTTTGTCTTATTTAAGAGGCAAACTTTGATTC
TAACAAAAACGGTAGAGGAGAAATCCTT
Found at i:13545 original size:476 final size:475
Alignment explanation
Indices: 12646--14030 Score: 2324
Period size: 476 Copynumber: 2.9 Consensus size: 475
12636 GGTGTCTACA
* * *
12646 GTCATAACTT-AGGGATGAATTTTTATTTTATGTAAAATAGGTTAAAGAAATGATTTCCATGCAA
1 GTCATAA-TTCAGGGATGAATTTTTATTTTAAGGAAAATAGGGTAAAGAAATGATTTCCATGCAA
* * * ** *
12710 AAGAAAGTCATGAATATCATTTATCATAAGGAAAAGAATGTATTTATAGTGCCTAATCACAAAAT
65 AAGAAAATCATCAATATCATTTATCCTACTGAAAAGAATGTATTTATAGTGCGTAATCACAAAAT
* * * * * * *
12775 TAATGAAGATCGTTACTAGAATCCTTGTTTGTCTCATTTGAAGCACGAACTTAGACTTTATACAA
130 GAATGAAGATCATTACTAGAATCCTTTTTTGTCTCATTTGAGGCACAAACTTAGACTTTACAGAA
* *
12840 ATTGGAGTGAAAAAATCCATTCTTGCGAATCCAAACCATCAATTTCGTCTATCCTAATGAGTTGA
195 ATTGGAGTGAAGAAATCCATTCTTGCGAATCCAAAGCATCAATTTCGTCTATCCTAATGAGTTGA
*
12905 CTATGTTGATAGTGCCTAATCCTGAAAAGATTAGGGATTAGTATAACTATTCATGTTTGTCTTAT
260 CTATGTTGATAGTGCCTAATCCTGAAAAGATTAGGGATTAGTATGACTATTCATGTTTGTCTTAT
*
12970 TTAAGAGGCAAACTTTGATTCTAACAAAAACAGTAGAGGCGAAACCTTTTCTTGCGACACCAAAG
325 TTAAGAGGCAAACTTTGATTCTAACAAAAACGGTAGAGGCGAAACCTTTTCTTGCGACACCAAAG
*
13035 CATCAATATCATTTATCCTAAAGAACGGATTGGGTTCTTAGTTCCAAATCTTGAAAAGAATGGAG
390 CATCAATATCATTTATCCTAATGAA-GGATTGGGTTCTTAGTTCCAAATCTTGAAAAGAATGGAG
13100 ACAGTTACGAGAATCGATAATT
454 ACAGTTACGAGAATCGATAATT
13122 GTCATAATTCAGGGATGAATTTTTATTTTAAGGAAAATAGGGTAAAGAAATGATTTCCATGCAAA
1 GTCATAATTCAGGGATGAATTTTTATTTTAAGGAAAATAGGGTAAAGAAATGATTTCCATGCAAA
*
13187 AGAAAATCATCAATATCATTTATCCTACTGAAAAGAATGTGTTTATAGTGCGTAATCACAAAATG
66 AGAAAATCATCAATATCATTTATCCTACTGAAAAGAATGTATTTATAGTGCGTAATCACAAAATG
* *
13252 AATGAAGATTATTACTAGAACCCTTTTTTGTCTCATTTGAGGCACAAACTTAGACTTTACAGAAA
131 AATGAAGATCATTACTAGAATCCTTTTTTGTCTCATTTGAGGCACAAACTTAGACTTTACAGAAA
13317 TTGGAGTGAAGAAATCCATTCTTGCGAATCCAAAGCATCAATTTCGTCTATCCTAATGAGTTGAC
196 TTGGAGTGAAGAAATCCATTCTTGCGAATCCAAAGCATCAATTTCGTCTATCCTAATGAGTTGAC
13382 TATGTTGATAGTGCCTAATCCTGAAAAGATTAGGGATTAGTATGACTATTCATGTTTGTCTTATT
261 TATGTTGATAGTGCCTAATCCTGAAAAGATTAGGGATTAGTATGACTATTCATGTTTGTCTTATT
* *
13447 TAAGAGCCAAACTTTGATTCTAACAAAAACGGTAGAGGCGAAACCTTTACTTGCGACACCAAAGC
326 TAAGAGGCAAACTTTGATTCTAACAAAAACGGTAGAGGCGAAACCTTTTCTTGCGACACCAAAGC
13512 ATCAATATCATTTATCCTAATGAAGGAATTGGGTTCTTAGTTCCAAATCTTGAAAAGAATGGAGA
391 ATCAATATCATTTATCCTAATGAAGG-ATTGGGTTCTTAGTTCCAAATCTTGAAAAGAATGGAGA
13577 CAGTTACGAGAATCGATAATT
455 CAGTTACGAGAATCGATAATT
* *
13598 GTCATAATTCAGGGAGGAATTTTTATTTTAAGGAAAATACGGTAAAGAAATGATTTCCATGCAAA
1 GTCATAATTCAGGGATGAATTTTTATTTTAAGGAAAATAGGGTAAAGAAATGATTTCCATGCAAA
* *
13663 AGAAAATCATCAATATCATTTATCCTACTGAAAAGAATGTTTTTATAGTGCGTAATTACAAAATG
66 AGAAAATCATCAATATCATTTATCCTACTGAAAAGAATGTATTTATAGTGCGTAATCACAAAATG
* *
13728 AATGAAGATCATTACTTGAATCCTTTTTTATCTCATTTGAGGCACAAACTTAGACTTTACAGAAA
131 AATGAAGATCATTACTAGAATCCTTTTTTGTCTCATTTGAGGCACAAACTTAGACTTTACAGAAA
* * * * *
13793 TTGGAGTGAAGAAATACATTCTTGCGAATCTAAAGCTTCAATTTCTTTTATCCTAATGAGTTGAC
196 TTGGAGTGAAGAAATCCATTCTTGCGAATCCAAAGCATCAATTTCGTCTATCCTAATGAGTTGAC
* * *
13858 TATGTTGATAGTGCCTAATCTTGAAAAGATTAGCGATTAGTATGACTATTCGTGTTTGTCTTATT
261 TATGTTGATAGTGCCTAATCCTGAAAAGATTAGGGATTAGTATGACTATTCATGTTTGTCTTATT
* * *
13923 TAAGAGGCAAACTTTGATTCTAACAAAAACGGTAGAGAG-GAAGCCTTTTCTTACAACACCAAAG
326 TAAGAGGCAAACTTTGATTCTAACAAAAACGGTAGAG-GCGAAACCTTTTCTTGCGACACCAAAG
13987 CATCAATATCATTTATCCTAATGAAGGGATTGGGTTCTTAGTTC
390 CATCAATATCATTTATCCTAATGAA-GGATTGGGTTCTTAGTTC
14031 A
Statistics
Matches: 858, Mismatches: 47, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
475 4 0.00
476 851 0.99
477 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (475 bp):
GTCATAATTCAGGGATGAATTTTTATTTTAAGGAAAATAGGGTAAAGAAATGATTTCCATGCAAA
AGAAAATCATCAATATCATTTATCCTACTGAAAAGAATGTATTTATAGTGCGTAATCACAAAATG
AATGAAGATCATTACTAGAATCCTTTTTTGTCTCATTTGAGGCACAAACTTAGACTTTACAGAAA
TTGGAGTGAAGAAATCCATTCTTGCGAATCCAAAGCATCAATTTCGTCTATCCTAATGAGTTGAC
TATGTTGATAGTGCCTAATCCTGAAAAGATTAGGGATTAGTATGACTATTCATGTTTGTCTTATT
TAAGAGGCAAACTTTGATTCTAACAAAAACGGTAGAGGCGAAACCTTTTCTTGCGACACCAAAGC
ATCAATATCATTTATCCTAATGAAGGATTGGGTTCTTAGTTCCAAATCTTGAAAAGAATGGAGAC
AGTTACGAGAATCGATAATT
Done.