Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1224
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: 31074
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:106 original size:43 final size:43
Alignment explanation
Indices: 17--163 Score: 251
Period size: 43 Copynumber: 3.4 Consensus size: 43
7 GCATTTTCAA
*
17 GCCCGCACACTTAGTGCCAACTCTCACAA-CGTGAACACTTTCTT
1 GCCCGCACACTTAGTGCCAA-TCTCACAACCGTGAACAC-TTATT
*
61 GCCCGCACATTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
104 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
147 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
164 TGAAAACCAA
Statistics
Matches: 99, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
43 71 0.72
44 28 0.28
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.24
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:2072 original size:37 final size:37
Alignment explanation
Indices: 2022--2100 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
2012 TTATTACGAA
* * *
2022 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
2059 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
2096 GTCTT
1 GTCTT
2101 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:2362 original size:46 final size:47
Alignment explanation
Indices: 2216--2434 Score: 406
Period size: 47 Copynumber: 4.7 Consensus size: 47
2206 TGCCCTTCGG
*
2216 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
2264 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
2311 ACTTTCACATTCATCACATCGGCCATTAGG-CTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
2357 ACTTTCACATTCATCACATC-GCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
2403 ACTTTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
2435 ATACTATCAT
Statistics
Matches: 168, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
45 9 0.05
46 72 0.43
47 83 0.49
48 4 0.02
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:4178 original size:40 final size:40
Alignment explanation
Indices: 4134--4248 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
4124 TGAGTTACCA
* *
4134 TAGTGAATCAGGAACAAATCCTATCCATTTTATATAT-TTC
1 TAGTGAATCAGGAATAAATCCTATTCATTTTA-ATATCTTC
* * * *
4174 TAGTGAATCAGGAATAATTCCTATTCACTTTAATTTCTTT
1 TAGTGAATCAGGAATAAATCCTATTCATTTTAATATCTTC
4214 TAGTGAATCAGGAATAAATCCTATTCACTTTTAAT
1 TAGTGAATCAGGAATAAATCCTATTCA-TTTTAAT
4249 TCTCGAGAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
39 3 0.05
40 56 0.86
41 6 0.09
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (40 bp):
TAGTGAATCAGGAATAAATCCTATTCATTTTAATATCTTC
Found at i:4991 original size:17 final size:17
Alignment explanation
Indices: 4969--5002 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4959 TATAAACCAT
*
4969 GTCCAAAAATCTACTAA
1 GTCCAAAAATATACTAA
4986 GTCCAAAAATATACTAA
1 GTCCAAAAATATACTAA
5003 CTTTCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.06, T:0.24
Consensus pattern (17 bp):
GTCCAAAAATATACTAA
Found at i:5211 original size:13 final size:13
Alignment explanation
Indices: 5173--5216 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
5163 TCCCCTGTTT
*
5173 TTTCGTTTCTATTC
1 TTTC-TTTCTTTTC
*
5187 TGTTCTTCCTTTTC
1 T-TTCTTTCTTTTC
5201 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
5214 TTT
1 TTT
5217 TTTGTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 14 0.54
14 9 0.35
15 3 0.12
ACGTcount: A:0.02, C:0.23, G:0.05, T:0.70
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Found at i:5216 original size:18 final size:20
Alignment explanation
Indices: 5167--5217 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
5157 CCTTTCTCCC
*
5167 CTGTT-TTTTCGTTTCTATT
1 CTGTTCTTTTCTTTTCTATT
*
5186 CTGTTC-TTCCTTTTCT-TT
1 CTGTTCTTTTCTTTTCTATT
5204 CT-TTCTTTTCTTTT
1 CTGTTCTTTTCTTTT
5218 TTGTTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.11
18 11 0.41
19 13 0.48
ACGTcount: A:0.02, C:0.22, G:0.06, T:0.71
Consensus pattern (20 bp):
CTGTTCTTTTCTTTTCTATT
Found at i:5411 original size:8 final size:8
Alignment explanation
Indices: 5398--5428 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
5388 TTTAATTAAT
5398 ATAATATA
1 ATAATATA
5406 ATAATATA
1 ATAATATA
5414 ATAATATA
1 ATAATATA
5422 ATAATAT
1 ATAATAT
5429 TTACTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAATATA
Found at i:6065 original size:91 final size:91
Alignment explanation
Indices: 5941--6317 Score: 318
Period size: 91 Copynumber: 4.1 Consensus size: 91
5931 AAAGTGCAGC
* *
5941 AAATTGAAGTGTTTAAATGCTGTAAATTTAAGTGTTAAAGTGCTGCAAATTGAAGT-ATTAAATG
1 AAATTGAAGTG-TTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATG
6005 CTATAAATTGAAGTGTTTAAATGCTGT
65 CTATAAATTGAAGTGTTTAAATGCTGT
* * * **
6032 AAATTGAAGTGCTTAAATGTTGTAAATTGAAGTGTTTAAGTACTGCAAATTGAAGTGTTTAGTTG
1 AAATTGAAGTG-TTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATG
* *
6097 CTAAAAATTG-AGATGTTT-TATCGCTGT
65 CTATAAATTGAAG-TGTTTAAAT-GCTGT
* ** * * *
6124 -AATTGAGGAATATAAATGTTGTTAATTG-AGATGTTAAAATGCTGCAAATTGAAGTGTTTAAAT
1 AAATTGAAGTGT-TAAATGCTGTAAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAAT
* * * *
6187 GTTGTAAATTGAAGTG-TTAAAGTTCTGC
64 GCTATAAATTGAAGTGTTTAAA-TGCTGT
* ** * * * * * *
6215 AAATTCAAGTGTTAAAAGTGCTGCGATTTCAAGTGTTTAAA-TGTTGTAAATTGAAGTTTTTAAG
1 AAATTGAAGTGTT-AAA-TGCTGTAAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAA
* ** * *
6279 TACTGCAAATTCAAGTGTTTAAATGTTGT
63 TGCTATAAATTGAAGTGTTTAAATGCTGT
6308 AAATTGAAGT
1 AAATTGAAGT
6318 TTTTAAGTAC
Statistics
Matches: 226, Mismatches: 46, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
90 5 0.02
91 119 0.53
92 37 0.16
93 53 0.23
94 12 0.05
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (91 bp):
AAATTGAAGTGTTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGC
TATAAATTGAAGTGTTTAAATGCTGT
Found at i:6252 original size:70 final size:69
Alignment explanation
Indices: 5903--6323 Score: 284
Period size: 68 Copynumber: 6.1 Consensus size: 69
5893 GTTACATGAG
* * * * * * * *
5903 GTGTATAAATGTTATTAATTG-AGATGTTAAAGTGCAGCAAATTGAAGTGTTTAAATGCTGTAAA
1 GTGTTTAAATGTTGTAAATTGAAG-TGTTAAAGTACTGCAAATTCAAGTGTTAAAATGCTGCAAA
*
5967 TTTAA
65 TTCAA
* * * * ** * * *
5972 GTG-TTAAAGTGCTGCAAATTGAAGTATTAAA-TGCTATAAATTGAAGTGTTTAAATGCTGTAAA
1 GTGTTTAAA-TGTTGTAAATTGAAGTGTTAAAGTACTGCAAATTCAAGTGTTAAAATGCTGCAAA
*
6035 TTGAA
65 TTCAA
* * * * ** **
6040 GTGCTTAAATGTTGTAAATTGAAGTGTTTAAGTACTGCAAATTGAAGTGTTTAGTTGCTAAAAAT
1 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTACTGCAAATTCAAGTGTTAAAATGCTGCAAAT
*
6105 T-GA
66 TCAA
* * * ** ** *
6108 GATGTTT-TATCGCTGT-AATTGAGGAATATAAATGT--TGTTAATT-GAGATGTTAAAATGCTG
1 G-TGTTTAAAT-GTTGTAAATTGAAGTGT-TAAA-GTACTGCAAATTCAAG-TGTTAAAATGCTG
*
6168 CAAATTGAA
61 CAAATTCAA
* * *
6177 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTTCTGCAAATTCAAGTGTTAAAAGTGCTGCGAT
1 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTACTGCAAATTCAAGTGTTAAAA-TGCTGCAAA
6242 TTCAA
65 TTCAA
* * * * *
6247 GTGTTTAAATGTTGTAAATTGAAGTTTTTAAGTACTGCAAATTCAAGTGTTTAAATGTTGTAAAT
1 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTACTGCAAATTCAAGTGTTAAAATGCTGCAAAT
*
6312 TGAA
66 TCAA
*
6316 GTTTTTAA
1 GTGTTTAA
6324 GTACTATAAA
Statistics
Matches: 277, Mismatches: 59, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
67 4 0.01
68 103 0.37
69 102 0.37
70 68 0.25
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (69 bp):
GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTACTGCAAATTCAAGTGTTAAAATGCTGCAAAT
TCAA
Found at i:6322 original size:23 final size:23
Alignment explanation
Indices: 5941--6345 Score: 320
Period size: 23 Copynumber: 17.7 Consensus size: 23
5931 AAAGTGCAGC
5941 AAATTGAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTTAAATGCTGT
* *
5964 AAATTTAAGTG-TTAAAGTGCTGC
1 AAATTGAAGTGTTTAAA-TGCTGT
* *
5987 AAATTGAAGT-ATTAAATGCTAT
1 AAATTGAAGTGTTTAAATGCTGT
6009 AAATTGAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTTAAATGCTGT
* *
6032 AAATTGAAGTGCTTAAATGTTGT
1 AAATTGAAGTGTTTAAATGCTGT
* * *
6055 AAATTGAAGTGTTTAAGTACTGC
1 AAATTGAAGTGTTTAAATGCTGT
** **
6078 AAATTGAAGTGTTTAGTTGCTAA
1 AAATTGAAGTGTTTAAATGCTGT
*
6101 AAATTG-AGATGTTT-TATCGCTGT
1 AAATTGAAG-TGTTTAAAT-GCTGT
* ** * *
6124 -AATTGAGGAATATAAATGTTGT
1 AAATTGAAGTGTTTAAATGCTGT
* * *
6146 TAATTG-AGATGTTAAAATGCTGC
1 AAATTGAAG-TGTTTAAATGCTGT
*
6169 AAATTGAAGTGTTTAAATGTTGT
1 AAATTGAAGTGTTTAAATGCTGT
* *
6192 AAATTGAAGTG-TTAAAGTTCTGC
1 AAATTGAAGTGTTTAAA-TGCTGT
* * *
6215 AAATTCAAGTGTTAAAAGTGCTGC
1 AAATTGAAGTGTTTAAA-TGCTGT
* * * *
6239 GATTTCAAGTGTTTAAATGTTGT
1 AAATTGAAGTGTTTAAATGCTGT
* * * *
6262 AAATTGAAGTTTTTAAGTACTGC
1 AAATTGAAGTGTTTAAATGCTGT
* *
6285 AAATTCAAGTGTTTAAATGTTGT
1 AAATTGAAGTGTTTAAATGCTGT
* * * *
6308 AAATTGAAGTTTTTAAGTACTAT
1 AAATTGAAGTGTTTAAATGCTGT
*
6331 AAATTGAATTGTTTA
1 AAATTGAAGTGTTTA
6346 GTTGCTGAAA
Statistics
Matches: 297, Mismatches: 73, Indels: 24
0.75 0.19 0.06
Matches are distributed among these distances:
22 39 0.13
23 232 0.78
24 26 0.09
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (23 bp):
AAATTGAAGTGTTTAAATGCTGT
Found at i:7094 original size:85 final size:85
Alignment explanation
Indices: 6980--7184 Score: 207
Period size: 85 Copynumber: 2.4 Consensus size: 85
6970 TTTTCATGAC
* * * * * *
6980 CTTTCGCGGCATTTTTGGAAAAAGCGCCGCTAAAGAACATGACT-ATTAATGGCGTTTTTGAAAA
1 CTTTAGCGACATTTGTGGAGAAAGCGCCGCTAAAGAACATG-CTGATTAATGACGTTTTAGAAAA
* * *
7044 AGCATCGCT-AAAGATCATGTT
65 AGCACCGCTAAAAG-TCAGGAT
** * * * *
7065 CTTTAGCGACATTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTGTTTAGTGACGTTTTAGGAAAA
1 CTTTAGCGACATTTGTGGAGAAAGCGCCGCTAAAGAACATGCTGATTAATGACGTTTTAGAAAAA
**
7130 GTGCCGCTAAAAGTCAGGAT
66 GCACCGCTAAAAGTCAGGAT
* *
7150 CTTTAGCAACGTTTGTGGAGAAAGCGCCGCTAAAG
1 CTTTAGCGACATTTGTGGAGAAAGCGCCGCTAAAG
7185 GTTATGTTCT
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
84 1 0.01
85 94 0.95
86 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (85 bp):
CTTTAGCGACATTTGTGGAGAAAGCGCCGCTAAAGAACATGCTGATTAATGACGTTTTAGAAAAA
GCACCGCTAAAAGTCAGGAT
Found at i:7185 original size:85 final size:86
Alignment explanation
Indices: 7064--7231 Score: 248
Period size: 85 Copynumber: 2.0 Consensus size: 86
7054 AAGATCATGT
* * * *
7064 TCTTTAGCGACATTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTGTTTAGTGACGTTT-TAGGAA
1 TCTTTAGCAACATTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTGTAGCAA
*
7128 AAGTGCCGCTAAAAGTCAGGA
66 AAGCGCCGCTAAAAGTCAGGA
* * **
7149 TCTTTAGCAACGTTTGTGGAGAAAGCGCCGCTAAAGGTTATGTTCTTTAGCGGTGTTTGTAGCAA
1 TCTTTAGCAACATTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTGTAGCAA
7214 AAGCGCCGCTAAAAGTCA
66 AAGCGCCGCTAAAAGTCA
7232 TGTTCTATAG
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
85 51 0.70
86 22 0.30
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (86 bp):
TCTTTAGCAACATTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTGTAGCAA
AAGCGCCGCTAAAAGTCAGGA
Found at i:7244 original size:43 final size:43
Alignment explanation
Indices: 7049--7243 Score: 209
Period size: 43 Copynumber: 4.6 Consensus size: 43
7039 GAAAAAGCAT
*
7049 CGCT-AAAGATCATGTTCTTTAGCGACATTTGT-GGAGAAAGCGC
1 CGCTAAAAG-TCATGTTCTTTAGCGACGTTTGTAGGA-AAAGCGC
* * * *
7092 CGCTAAAGGTCATGTTGTTTAGTGACGTTT-TAGGAAAAGTGC
1 CGCTAAAAGTCATGTTCTTTAGCGACGTTTGTAGGAAAAGCGC
* * *
7134 CGCTAAAAGTCAGGATCTTTAGCAACGTTTGT-GGAGAAAGCGC
1 CGCTAAAAGTCATGTTCTTTAGCGACGTTTGTAGGA-AAAGCGC
* * ** *
7177 CGCTAAAGGTTATGTTCTTTAGCGGTGTTTGTAGCAAAAGCGC
1 CGCTAAAAGTCATGTTCTTTAGCGACGTTTGTAGGAAAAGCGC
*
7220 CGCTAAAAGTCATGTTCTATAGCG
1 CGCTAAAAGTCATGTTCTTTAGCG
7244 GCATTTTTTT
Statistics
Matches: 124, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
42 34 0.27
43 85 0.69
44 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (43 bp):
CGCTAAAAGTCATGTTCTTTAGCGACGTTTGTAGGAAAAGCGC
Found at i:16508 original size:55 final size:55
Alignment explanation
Indices: 16381--16508 Score: 152
Period size: 55 Copynumber: 2.3 Consensus size: 55
16371 TGCGACATGG
** * *
16381 CCGTGGTCGAACCTGCCAAAACAACACGGGCGTGTGACACGCCCGTGTGGAAGAA
1 CCGTGGTCGAACCTGTTAAAACAACACGGGCGTGCGACACGCCCGTGTGCAAGAA
* * *
16436 CCGTGGGT-GAACCTGTTAAAACAGCACGGGCGTGCGACACGCCCGTGT-CTAGCAC
1 CCGT-GGTCGAACCTGTTAAAACAACACGGGCGTGCGACACGCCCGTGTGCAAG-AA
*
16491 CCGTGGTCGAACTTGTTA
1 CCGTGGTCGAACCTGTTA
16509 GATTGACACA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
54 5 0.08
55 54 0.87
56 3 0.05
ACGTcount: A:0.23, C:0.29, G:0.30, T:0.17
Consensus pattern (55 bp):
CCGTGGTCGAACCTGTTAAAACAACACGGGCGTGCGACACGCCCGTGTGCAAGAA
Found at i:24694 original size:40 final size:40
Alignment explanation
Indices: 24610--24793 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
24600 TTGAATGCTG
* * * *
24610 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
24649 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
24690 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
24730 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
24770 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
24794 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:24747 original size:80 final size:81
Alignment explanation
Indices: 24610--24790 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
24600 TTGAATGCTG
* * *
24610 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
24674 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
24690 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
24751 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
24770 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
24791 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:24814 original size:39 final size:38
Alignment explanation
Indices: 24691--24840 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
24681 GTTATTAATT
* ** * *
24691 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
24731 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
24770 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
24810 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
24841 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Done.