Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold822
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: 6221
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Found at i:73 original size:27 final size:27
Alignment explanation
Indices: 6--478 Score: 540
Period size: 27 Copynumber: 17.6 Consensus size: 27
1 ACCAC
6 CCCTTTT-AGTTCCACAACTCCGTGGCCA
1 CCCTTTTAAG-TCCACAACTCCGTGG-CA
34 CCCTTTTAAGTCCACAACTCCGTGGGCA
1 CCCTTTTAAGTCCACAACTCCGT-GGCA
*
62 -CCTTTTAAGTCCACAA-TTCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
* * *
87 TCCTTGTAAGTCCACAACTTCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
114 CCCTTTT-AGTCCACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
* *
140 CCCTTTTAACGTCTAGAACTCCGTGGCA
1 CCCTTTTAA-GTCCACAACTCCGTGGCA
*
168 CCCTTTTAAAGTCCACAACTCTGTGGCA
1 CCCTTTT-AAGTCCACAACTCCGTGGCA
* *
196 TCCTTTTAAGTCCACAACTCTGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
*
223 CCCTTTTAAGTCCAC-ACTCCGTGTCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
* * **
249 CCTTTTTAAGTCCACCACTCTATGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
*
276 TCCCTTTT--GTCC-C-ACTTCGTGGCA
1 -CCCTTTTAAGTCCACAACTCCGTGGCA
300 CCCTTTTTAAGTCCACAACT-CGTGGCA
1 CCC-TTTTAAGTCCACAACTCCGTGGCA
327 CCCTTTT-AGTCCACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
* *
353 CCCTTTTAAAGTCTAGAAACTCCGTGGCA
1 CCCTTTT-AAGTCCA-CAACTCCGTGGCA
382 CCCTTTTAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
* *
409 CCATTTTAAGTCCACAACTCTGTGG-A
1 CCCTTTTAAGTCCACAACTCCGTGGCA
* * * *
435 TCCTTTTTAAGTTCACAACTTCATGG-A
1 -CCCTTTTAAGTCCACAACTCCGTGGCA
*
462 CCTTTTTTAAGTCCACA
1 CC-CTTTTAAGTCCACA
479 GGCGGTGGCA
Statistics
Matches: 391, Mismatches: 34, Indels: 41
0.84 0.07 0.09
Matches are distributed among these distances:
23 3 0.01
24 12 0.03
25 16 0.04
26 96 0.25
27 153 0.39
28 86 0.22
29 25 0.06
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.31
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:111 original size:53 final size:53
Alignment explanation
Indices: 6--478 Score: 484
Period size: 53 Copynumber: 8.8 Consensus size: 53
1 ACCAC
*
6 CCCTTTTAGTTCCACAACTCCGTGGCCACCCTTTTAAGTCCACAACTCCGTGGGCA
1 CCCTTTTAG-TCCACAACTCCGTGG-CACCCTTTTAAGTCCACAACTTCGT-GGCA
* * *
62 -CCTTTTAAGTCCACAA-TTCGTGGCATCCTTGTAAGTCCACAACTTCGTGGCA
1 CCCTTTT-AGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCA
* * *
114 CCCTTTTAGTCCACAACTCCGTGGCACCCTTTTAACGTCTAGAACTCCGTGGCA
1 CCCTTTTAGTCCACAACTCCGTGGCACCCTTTTAA-GTCCACAACTTCGTGGCA
* *
168 CCCTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAAC-TCTGTGGCA
1 CCCTTTT--AGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTC-GTGGCA
* * * *
223 CCCTTTTAAGTCCAC-ACTCCGTGTCACCTTTTTAAGTCCACCAC-TCTATGGCA
1 CCCTTTT-AGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTC-GTGGCA
*
276 TCCCTTTT-GTCC-C-ACTTCGTGGCACCCTTTTTAAGTCCACAAC-TCGTGGCA
1 -CCCTTTTAGTCCACAACTCCGTGGCACCC-TTTTAAGTCCACAACTTCGTGGCA
* * *
327 CCCTTTTAGTCCACAACTCCGTGGCACCCTTTTAAAGTCTAGAAACTCCGTGGCA
1 CCCTTTTAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCA-CAACTTCGTGGCA
*
382 CCCTTTTAAGTCCACAACTCCGTGGCACCATTTTAAGTCCACAAC-TCTGTGG-A
1 CCCTTTT-AGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTC-GTGGCA
* * * * *
435 TCCTTTTTAAGTTCACAACTTCATGG-ACCTTTTTTAAGTCCACA
1 -CCCTTTT-AGTCCACAACTCCGTGGCACC-CTTTTAAGTCCACA
479 GGCGGTGGCA
Statistics
Matches: 359, Mismatches: 39, Indels: 40
0.82 0.09 0.09
Matches are distributed among these distances:
50 7 0.02
51 21 0.06
52 38 0.11
53 99 0.28
54 88 0.25
55 53 0.15
56 53 0.15
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.31
Consensus pattern (53 bp):
CCCTTTTAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCA
Found at i:445 original size:213 final size:214
Alignment explanation
Indices: 6--478 Score: 649
Period size: 213 Copynumber: 2.2 Consensus size: 214
1 ACCAC
* *
6 CCCTTTT-AGTTCCACAACTCCGTGGCCACCCTTTTAAGTCCACAACTCCGTGGGCACCTTTTAA
1 CCCTTTTAAG-TCCACAACTCCGT-G-CACCTTTTTAAGTCCACAACTCCATGGGCACCTTTT-A
*
70 GTCCACAATTCGTGGCATCCTTGTAAGTCCACAACTTCGTGGCACCCTTTTAGTCCACAACTCCG
62 GTCCACAATTCGTGGCACCCTTGTAAGTCCACAACTTCGTGGCACCCTTTTAGTCCACAACTCCG
* *
135 TGGCACCCTTTTAACGTCTAGAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCATCCT
127 TGGCACCCTTTTAAAGTCTAGAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCT
200 TTTAAGTCCACAACTCTGTGGCA
192 TTTAAGTCCACAACTCTGTGGCA
* *
223 CCCTTTTAAGTCCAC-ACTCCGTGTCACCTTTTTAAGTCCACCACTCTAT-GGCATCCCTTTT-G
1 CCCTTTTAAGTCCACAACTCCGTG-CACCTTTTTAAGTCCACAACTCCATGGGCA--CCTTTTAG
* *
285 TCC-CACTTCGTGGCACCCTTTTTAAGTCCACAAC-TCGTGGCACCCTTTTAGTCCACAACTCCG
63 TCCACAATTCGTGGCACCC-TTGTAAGTCCACAACTTCGTGGCACCCTTTTAGTCCACAACTCCG
348 TGGCACCCTTTTAAAGTCTAGAAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCA-CC
127 TGGCACCCTTTTAAAGTCTAG-AACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCC
411 ATTTTAAGTCCACAACTCTGTGG-A
191 -TTTTAAGTCCACAACTCTGTGGCA
* * * * *
435 TCCTTTTTAAGTTCACAACTTCATGGACCTTTTTTAAGTCCACA
1 -CCCTTTTAAGTCCACAACTCCGTGCACC-TTTTTAAGTCCACA
479 GGCGGTGGCA
Statistics
Matches: 231, Mismatches: 16, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
212 3 0.01
213 119 0.52
214 60 0.26
215 22 0.10
216 13 0.06
217 12 0.05
218 2 0.01
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.31
Consensus pattern (214 bp):
CCCTTTTAAGTCCACAACTCCGTGCACCTTTTTAAGTCCACAACTCCATGGGCACCTTTTAGTCC
ACAATTCGTGGCACCCTTGTAAGTCCACAACTTCGTGGCACCCTTTTAGTCCACAACTCCGTGGC
ACCCTTTTAAAGTCTAGAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTA
AGTCCACAACTCTGTGGCA
Found at i:582 original size:31 final size:32
Alignment explanation
Indices: 519--942 Score: 545
Period size: 31 Copynumber: 13.4 Consensus size: 32
509 GTTAGTGTGC
519 ACCCATTTCAAAGCCCACACAAGTCCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGT-CGGTGGCA
552 ACCCATTTCAAAG-CCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
*
583 ATCCATTTCCAAAGCCCACACAAGTTCGGTGGC-
1 ACCCATTT-CAAAGCCCACACAAG-TCGGTGGCA
*
616 A-CTATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
*
647 ACCCTTTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
679 A-CCATTTCAAAGCCCACACCAAGTCTGGTGGCAA
1 ACCCATTTCAAAGCCCACA-CAAGTC-GGTGGC-A
713 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGC-A
746 ACCC--TTCAAAGCCCACACAAGTCGGGGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTC---GGTGGCA
779 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
* *
811 A-CCATTTCAAAGCCCACACACGTCAG-GGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
* *
841 ACCCATTTCAAAGCCCGCAC-AGTTGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
872 ACCC-TTTCAAAGCCCACAC-AGTCGGTGGC-
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
* * *
901 ACCCA-TTAAAAGCCCA-TCAAGTACAGTGGCA
1 ACCCATTTCAAAGCCCACACAAGT-CGGTGGCA
*
932 A-CCTTTTCAAA
1 ACCCATTTCAAA
943 AGCACCATTT
Statistics
Matches: 352, Mismatches: 18, Indels: 44
0.85 0.04 0.11
Matches are distributed among these distances:
28 1 0.00
29 17 0.05
30 47 0.13
31 120 0.34
32 63 0.18
33 46 0.13
34 22 0.06
35 36 0.10
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (32 bp):
ACCCATTTCAAAGCCCACACAAGTCGGTGGCA
Found at i:733 original size:66 final size:63
Alignment explanation
Indices: 519--942 Score: 560
Period size: 66 Copynumber: 6.7 Consensus size: 63
509 GTTAGTGTGC
519 ACCCATTTCAAAGCCCACACAAGTCCGGTGGCAACCCATTTCAAAG-CCACACAAGTCGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGT-CGGTGGCAA-CCATTTCAAAGCCCACACAAGTCGGTGGCA
* *
583 ATCCATTTCCAAAGCCCACACAAGTTCGGTGGC-ACTATTTCAAAGCCCACACAAGTCGGTGGCA
1 ACCCATTT-CAAAGCCCACACAAG-TCGGTGGCAACCATTTCAAAGCCCACACAAGTCGGTGGCA
*
647 ACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACACCAAGTCTGGTGGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACA-CAAGTC-GGTGGC-
712 A
63 A
*
713 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAAACC-CTTCAAAGCCCACACAAGTCGGGGGTGG
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGC-AACCATTTCAAAGCCCACACAAGTC---GGTGG
777 CA
62 CA
* *
779 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACACACGTCAG-GGCA
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACACAAGTCGGTGGCA
* * *
841 ACCCATTTCAAAGCCCGCAC-AGTTGGTGGCAACCCTTTCAAAGCCCACAC-AGTCGGTGGC-
1 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACACAAGTCGGTGGCA
* * * *
901 ACCCA-TTAAAAGCCCA-TCAAGTACAGTGGCAACCTTTTCAAA
1 ACCCATTTCAAAGCCCACACAAGT-CGGTGGCAACCATTTCAAA
943 AGCACCATTT
Statistics
Matches: 324, Mismatches: 22, Indels: 32
0.86 0.06 0.08
Matches are distributed among these distances:
58 1 0.00
59 12 0.04
60 25 0.08
61 31 0.10
62 31 0.10
63 43 0.13
64 38 0.12
65 38 0.12
66 95 0.29
67 10 0.03
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (63 bp):
ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACACAAGTCGGTGGCA
Found at i:1376 original size:27 final size:27
Alignment explanation
Indices: 1346--1621 Score: 356
Period size: 27 Copynumber: 10.0 Consensus size: 27
1336 TAAAAATAAT
* *
1346 AGGGTGCCATGGAGTTGTGGACTAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
*
1373 AGGGTGCCACAGAGTTGTGGACTTTAAA
1 AGGGTGCCACGGAGTTGTGGAC-TTAAA
* *
1401 AGGGTGTCACAGAGTTGTGGACTT-AA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
* *
1427 AGGATGCCACAGAGTTTGTGGACTTTAAA
1 AGGGTGCCACGGAG-TTGTGGAC-TTAAA
** * *
1456 AGAAAATGGCCACTGAGTCGTGGACTTAAA
1 AG--GGT-GCCACGGAGTTGTGGACTTAAA
1486 AGGGTGCCACGGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
1513 AGGGTGCCACGGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
* *
1540 AGGGTGCCACGAAGTTGTGAACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
*
1567 AGGGTGCCACAGAGTTGTGGACTTTAAA
1 AGGGTGCCACGGAGTTGTGGAC-TTAAA
1595 AGGGTGCCACGGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
1622 GAGGTCACGA
Statistics
Matches: 222, Mismatches: 19, Indels: 16
0.86 0.07 0.06
Matches are distributed among these distances:
26 14 0.06
27 126 0.57
28 54 0.24
29 4 0.02
30 7 0.03
31 9 0.04
32 8 0.04
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (27 bp):
AGGGTGCCACGGAGTTGTGGACTTAAA
Found at i:2110 original size:16 final size:16
Alignment explanation
Indices: 2089--2120 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2079 GATAAAGTGT
2089 TTGAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
2105 TTGAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
2121 AAAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
TTGAAAAAAAAAAAAA
Found at i:2156 original size:21 final size:21
Alignment explanation
Indices: 2132--2188 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2122 AAAAAATTTA
2132 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2153 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2174 AATGTATCGATACAT
1 AATGTATCGATACAT
2189 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2268 original size:19 final size:19
Alignment explanation
Indices: 2244--2311 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2234 AATTCAACAA
2244 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2263 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2278 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2295 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2312 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2283 original size:13 final size:13
Alignment explanation
Indices: 2265--2289 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2255 ACATAAGTTT
2265 TGTATCGATACAA
1 TGTATCGATACAA
2278 TGTATCGATACA
1 TGTATCGATACA
2290 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2287 original size:32 final size:32
Alignment explanation
Indices: 2246--2308 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2236 TTCAACAATT
*
2246 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2278 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2309 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2368 original size:13 final size:13
Alignment explanation
Indices: 2350--2375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2340 ACATTTTCTG
2350 TGTATCGATACAT
1 TGTATCGATACAT
2363 TGTATCGATACAT
1 TGTATCGATACAT
2376 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2392 original size:33 final size:32
Alignment explanation
Indices: 2331--2396 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
2321 GCCAAGGAAA
**
2331 TGTATCGATACATTTTCTGTGTATCGATACAT
1 TGTATCGATACATGATCTGTGTATCGATACAT
*
2363 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACAT-GATCTGTGTATCGATACAT
2396 T
1 T
2397 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGATCTGTGTATCGATACAT
Found at i:4913 original size:28 final size:27
Alignment explanation
Indices: 4846--4918 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
4836 CTTCACAATC
* *
4846 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
4873 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
4901 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
4919 ACGTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:4976 original size:50 final size:50
Alignment explanation
Indices: 4901--5069 Score: 160
Period size: 50 Copynumber: 3.3 Consensus size: 50
4891 TTATTTCTGA
** * *
4901 GGGGATACTCCAACCCCGACGTTATTTTCAAAATATCGATTTTTCATATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATATC
* * * * *
4951 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-AT-ATC
** * *
5004 GGGGATACT-CAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCA-TATC
*
5055 GAGGATACTCCAACC
1 GGGGATACTCCAACC
5070 TCGTTATTTC
Statistics
Matches: 92, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
50 35 0.38
51 13 0.14
52 21 0.23
53 23 0.25
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATATC
Found at i:5088 original size:28 final size:28
Alignment explanation
Indices: 5052--5133 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
5042 ATTTTTCACA
*
5052 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
5080 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
5108 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
5134 ATCTCCAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Done.