Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3736
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: 42113
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:11240 original size:9 final size:9
Alignment explanation
Indices: 11226--11257 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
11216 GAGATCTATA
11226 AAACAGAGG
1 AAACAGAGG
11235 AAACAGAGG
1 AAACAGAGG
11244 AAACAGAGG
1 AAACAGAGG
11253 AAACA
1 AAACA
11258 AAGTAAACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.59, C:0.12, G:0.28, T:0.00
Consensus pattern (9 bp):
AAACAGAGG
Found at i:11265 original size:18 final size:18
Alignment explanation
Indices: 11226--11265 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
11216 GAGATCTATA
*
11226 AAACAGAGGAAACAGAGG
1 AAACAGAGGAAACAAAGG
*
11244 AAACAGAGGAAACAAAGT
1 AAACAGAGGAAACAAAGG
11262 AAAC
1 AAAC
11266 GGAGTAAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.12, G:0.25, T:0.03
Consensus pattern (18 bp):
AAACAGAGGAAACAAAGG
Found at i:11767 original size:37 final size:37
Alignment explanation
Indices: 11712--11814 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
11702 CAAATAGTCC
*
11712 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
* * *
11749 CTACGCGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
11786 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
11815 ATATATTTCC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:12013 original size:48 final size:48
Alignment explanation
Indices: 11955--12356 Score: 628
Period size: 48 Copynumber: 8.6 Consensus size: 48
11945 ATATACACAC
* *
11955 ATCTCCTACATATTTCACACTAGCCATTCGACTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
12003 ATCTCATACATTTTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12051 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
12099 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12147 ATCTCATACATATTTCACACTAGCCATTCGGCTTTA-C-C----AC--
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12187 A--T-ATACATATTTCACATTAGCCATTCGGCTCTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12232 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
12280 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12328 ATCTCATATATATTTCACATTAGCCATTC
1 ATCTCATACATATTTCACACTAGCCATTC
12357 TCCTGAGCAA
Statistics
Matches: 327, Mismatches: 16, Indels: 22
0.90 0.04 0.06
Matches are distributed among these distances:
37 29 0.09
38 2 0.01
39 1 0.00
40 1 0.00
42 2 0.01
43 2 0.01
45 1 0.00
46 1 0.00
47 2 0.01
48 286 0.87
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:12202 original size:37 final size:37
Alignment explanation
Indices: 12152--12233 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
12142 TACATATCTC
*
12152 ATACATATTTCACACTAGCCATTCGGCTTTACCACAT
1 ATACATATTTCACACTAGCCATTCGGCTCTACCACAT
*
12189 ATACATATTTCACATTAGCCATTCGGCTCTACCACAT
1 ATACATATTTCACACTAGCCATTCGGCTCTACCACAT
12226 ATACATAT
1 ATACATAT
12234 CTCATACATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33
Consensus pattern (37 bp):
ATACATATTTCACACTAGCCATTCGGCTCTACCACAT
Found at i:12202 original size:85 final size:88
Alignment explanation
Indices: 12104--12356 Score: 377
Period size: 85 Copynumber: 2.8 Consensus size: 88
12094 TACATATCTC
12104 ATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTA
1 ATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTA
12169 GCCATTCGGCTTTA-C-C-ACAT
66 GCCATTCGGCTTTACCACAACAT
*
12189 ATACATATTTCACATTAGCCATTCGGCTCTACCACATATACATATCTCATACATATTTCACACTA
1 ATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTA
12254 GCCATTCGGCTTTACCACATATACAT
66 GCCATTCGGCTTTACCAC--A-ACAT
* *
12280 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTTCA
1 A--T-A--CATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
12345 CATTAGCCATTC
61 CACTAGCCATTC
12357 TCCTGAGCAA
Statistics
Matches: 152, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
85 78 0.51
86 1 0.01
87 1 0.01
91 5 0.03
93 1 0.01
94 1 0.01
96 65 0.43
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (88 bp):
ATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTA
GCCATTCGGCTTTACCACAACAT
Found at i:12206 original size:133 final size:133
Alignment explanation
Indices: 12060--12329 Score: 513
Period size: 133 Copynumber: 2.0 Consensus size: 133
12050 TATCTCATAT
* *
12060 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCACATTAGCCATTCGGCTCTACCACATATACATATCTCATACATATTTCACACTAGCCA
12125 TTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATA
66 TTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATA
12190 TAC
131 TAC
12193 ATATTTCACATTAGCCATTCGGCTCTACCACATATACATATCTCATACATATTTCACACTAGCCA
1 ATATTTCACATTAGCCATTCGGCTCTACCACATATACATATCTCATACATATTTCACACTAGCCA
*
12258 TTCGGCTTTACCACATATACATATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATA
66 TTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATA
12323 TAC
131 TAC
12326 ATAT
1 ATAT
12330 CTCATATATA
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 134 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (133 bp):
ATATTTCACATTAGCCATTCGGCTCTACCACATATACATATCTCATACATATTTCACACTAGCCA
TTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATA
TAC
Found at i:12265 original size:181 final size:181
Alignment explanation
Indices: 12008--12356 Score: 617
Period size: 181 Copynumber: 1.9 Consensus size: 181
11998 TACATATCTC
* * * *
12008 ATACATTTTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTTCACATTA
1 ATACATATTTCACACTAGCCATTCGGCTCTACCACATATACATATCTCATACATATTTCACACTA
*
12073 GCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCA
66 GCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCA
12138 CATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACAT
131 CATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACAT
*
12189 ATACATATTTCACATTAGCCATTCGGCTCTACCACATATACATATCTCATACATATTTCACACTA
1 ATACATATTTCACACTAGCCATTCGGCTCTACCACATATACATATCTCATACATATTTCACACTA
*
12254 GCCATTCGGCTTTACCACATATACATATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCA
66 GCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCA
* *
12319 CATATACATATCTCATATATATTTCACATTAGCCATTC
131 CATATACATATCTCATACATATTTCACACTAGCCATTC
12357 TCCTGAGCAA
Statistics
Matches: 159, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
181 159 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (181 bp):
ATACATATTTCACACTAGCCATTCGGCTCTACCACATATACATATCTCATACATATTTCACACTA
GCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCA
CATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACAT
Found at i:15601 original size:40 final size:40
Alignment explanation
Indices: 15557--15915 Score: 594
Period size: 40 Copynumber: 9.0 Consensus size: 40
15547 GAATGCACAT
* * * *
15557 CACCAGCATGATTGCTTTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
15597 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
15637 CACCAGCACG-ATCGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAT-GCTCTTCGGGACTTAGCCCGGATATAA
* *
15677 CACCAGCATGAATGCTCTTCAGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
15717 CATCAGCACGAATGCTCTTCGGGACTTAGCTCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
15757 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
15797 CACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
15837 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
15877 CACCAGCACGAATACTCTTCGGGACTTAGCCCGGCTATA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
15916 TAACTCTCAA
Statistics
Matches: 299, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
39 2 0.01
40 295 0.99
41 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:19442 original size:22 final size:20
Alignment explanation
Indices: 19394--19442 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 20
19384 ATTTCACTAC
*
19394 TCAAATCCATAACCAAAACA
1 TCAAATCAATAACCAAAACA
19414 TACCAAATCAATATACCAAAATCA
1 T--CAAATCAATA-ACCAAAA-CA
19438 TCAAA
1 TCAAA
19443 CTTACATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
22 13 0.54
23 7 0.29
24 3 0.12
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (20 bp):
TCAAATCAATAACCAAAACA
Found at i:20255 original size:43 final size:43
Alignment explanation
Indices: 20221--20303 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
20211 CTTACATGTT
* * * *
20221 ATCACATATCGATGCCACTGTCCTAGACAGGGTCTTACACGAA
1 ATCAAATAACGATGCCAATGTCCCAGACAGGGTCTTACACGAA
* *
20264 ATCAAATAACGATGCTAATGTCCCAGACATGGTCTTACAC
1 ATCAAATAACGATGCCAATGTCCCAGACAGGGTCTTACAC
20304 ATAATCTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATCAAATAACGATGCCAATGTCCCAGACAGGGTCTTACACGAA
Found at i:20327 original size:43 final size:43
Alignment explanation
Indices: 20232--20345 Score: 106
Period size: 43 Copynumber: 2.7 Consensus size: 43
20222 TCACATATCG
* * * *
20232 ATGCCACTGTCCTAGACAGGGTCTTACACGAAATCAAATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATAACA
* * *
20275 ATGCTAATGTCCCAGACATGGTCTTACAC-ATAATCTCAAT-GCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGA-AATC-AAATAACA
* **
20318 ATGCCAATGTCTCAGATGTGGTCTTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
20346 TGTAATCACA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 54 0.93
44 3 0.05
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATAACA
Found at i:22267 original size:34 final size:34
Alignment explanation
Indices: 22218--22295 Score: 115
Period size: 34 Copynumber: 2.3 Consensus size: 34
22208 TGACCTTATG
22218 TTTCTTTTCAGACCTCTTACTTC-AGAGTTACTGA
1 TTTCTTTTCAGACCTCTTACTTCGA-AGTTACTGA
22252 TTTCTTTTCTA-ACCTCTTACTTCGAAGTTACTGA
1 TTTCTTTTC-AGACCTCTTACTTCGAAGTTACTGA
22286 TTTCTATTTC
1 TTTCT-TTTC
22296 CCCTTTATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
34 35 0.85
35 6 0.15
ACGTcount: A:0.19, C:0.23, G:0.09, T:0.49
Consensus pattern (34 bp):
TTTCTTTTCAGACCTCTTACTTCGAAGTTACTGA
Found at i:29315 original size:28 final size:27
Alignment explanation
Indices: 29252--29403 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
29242 ATATTAAGTC
* * *
29252 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
29279 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
29307 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
29334 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
29362 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
29389 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29404 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:29336 original size:55 final size:55
Alignment explanation
Indices: 29252--29403 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
29242 ATATTAAGTC
* * *
29252 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
29307 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
29362 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
29404 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:37319 original size:28 final size:27
Alignment explanation
Indices: 37256--37407 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
37246 ATATTAAGTC
* * *
37256 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
37283 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
37311 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
37338 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
37366 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
37393 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
37408 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:37340 original size:55 final size:55
Alignment explanation
Indices: 37256--37407 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
37246 ATATTAAGTC
* * *
37256 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
37311 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
37366 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
37408 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:40161 original size:40 final size:38
Alignment explanation
Indices: 40070--40285 Score: 175
Period size: 39 Copynumber: 5.4 Consensus size: 38
40060 CCTCGTTCAA
* * * * *
40070 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAAT-ACTCGCAC
40109 AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAAT-ACTCGCAC
40148 GAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATA-CTCGCAC
* * * *
40188 AAAGGCTTTGGGGCTTAACCCGGAACTTGT-AT-CTCGCAC
1 AATGCCTTCGGGACTTAACCCGG-A-TT-TAATACTCGCAC
* ** * * *
40227 AAATGCCTTCGAGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAAT-AC-TCGCAC
*
40269 AAAGCCTTCGGGACTTA
1 AATGCCTTCGGGACTTA
40286 GCCGGACAGC
Statistics
Matches: 144, Mismatches: 22, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
38 1 0.01
39 62 0.43
40 51 0.35
41 24 0.17
42 6 0.04
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (38 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATACTCGCAC
Found at i:40224 original size:79 final size:78
Alignment explanation
Indices: 40069--40285 Score: 195
Period size: 79 Copynumber: 2.7 Consensus size: 78
40059 TCCTCGTTCA
* * * *
40069 AAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGAT
1 AAATGCCTTCGGGACATAACCCGGATTTAATAACTCACACAAAGCCTTCGGGACTTAACCCGGAT
40134 TTAATGACTCGCAC
66 TTAAT-ACTCGCAC
* * * * * * *
40148 GAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACAAAGGCTTTGGGGCTTAACCCGGAA
1 AAATGCCTTCGGGACATAACCCGGATTTAATAACTCACACAAAGCCTTCGGGACTTAACCCGG-A
40213 CTTGT-AT-CTCGCAC
65 -TT-TAATACTCGCAC
* * ** * * * *
40227 AAATGCCTTCGAGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTA
1 AAATGCCTTCGGGA-CATAACCCGGATTTAATAACTCA-CACAAAGCCTTCGGGACTTA
40286 GCCGGACAGC
Statistics
Matches: 109, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
79 71 0.65
80 16 0.15
81 21 0.19
82 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (78 bp):
AAATGCCTTCGGGACATAACCCGGATTTAATAACTCACACAAAGCCTTCGGGACTTAACCCGGAT
TTAATACTCGCAC
Found at i:40300 original size:40 final size:42
Alignment explanation
Indices: 40223--40300 Score: 99
Period size: 40 Copynumber: 1.9 Consensus size: 42
40213 CTTGTATCTC
* *
40223 GCACAAATGCCTTCGAGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGAGATCTTAGTCCGGACACATTCACTTA
*
40265 GCACAAA-GCCTTCGGGA-CTTAG-CCGGACAGCATTCA
1 GCACAAATGCCTTCGAGATCTTAGTCCGGACA-CATTCA
40301 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 6 0.19
40 10 0.31
41 9 0.28
42 7 0.22
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (42 bp):
GCACAAATGCCTTCGAGATCTTAGTCCGGACACATTCACTTA
Done.