Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1898
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: 95539
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:798 original size:23 final size:24
Alignment explanation
Indices: 769--817 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
759 AGTCTATGTT
769 TAATATTAA-A-ATTAAATTTTTAA
1 TAATATTAATATATT-AATTTTTAA
*
792 TAATATTAATATATTATTTTTTAA
1 TAATATTAATATATTAATTTTTAA
816 TA
1 TA
818 TCAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 11 0.48
25 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATATTAATATATTAATTTTTAA
Found at i:1253 original size:16 final size:16
Alignment explanation
Indices: 1221--1268 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1211 CTTATATTTT
*
1221 TATAAA-TA-TAAAAA
1 TATAAATTATTAAATA
1235 TATAAATTATTAAATA
1 TATAAATTATTAAATA
1251 TATTAAATT-TTAAATA
1 TA-TAAATTATTAAATA
1267 TA
1 TA
1269 AATATGATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 6 0.20
15 2 0.07
16 16 0.53
17 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAATTATTAAATA
Found at i:1289 original size:29 final size:30
Alignment explanation
Indices: 1232--1289 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1222 ATAAATATAA
*
1232 AAATATAAATTATTAAATATATTAAATTTT
1 AAATATAAATTATGAAATATATTAAATTTT
* *
1262 AAATATAAA-TATGATATATATTATATTT
1 AAATATAAATTATGAAATATATTAAATTT
1290 ATTTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
AAATATAAATTATGAAATATATTAAATTTT
Found at i:1340 original size:22 final size:23
Alignment explanation
Indices: 1280--1340 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 23
1270 ATATGATATA
*
1280 TATTATATTTATTTAAA-AATATT
1 TATTATATTTA-TTAAATATTATT
1303 TATTAT-TTTATT--ATATTATT
1 TATTATATTTATTAAATATTATT
1323 T-TTATATTTATTAAATAT
1 TATTATATTTATTAAATAT
1341 ATCATATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 5 0.15
20 12 0.36
21 2 0.06
22 8 0.24
23 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATATTTATTAAATATTATT
Found at i:2582 original size:409 final size:408
Alignment explanation
Indices: 1797--2613 Score: 1546
Period size: 409 Copynumber: 2.0 Consensus size: 408
1787 TTTGTAATTT
*
1797 ATCATTTTTGCTTGTTTCTTTCTTTCTCTTAATATTCAGCAGCTTGTCACACTCGCGTGCGACTA
1 ATCATTTTTGCTTGTTTCTTTCTTTCTCTTAATATTCAGCAGCTTGTCACACTCGAGTGCGACTA
* *
1862 GTCTAGGTCCCGATAACTAACACTAAGCACGCGTAAAGGACTTTTATCATGGGACCACTGCTTAG
66 GTCTAGGTCCCGACAACCAACACTAAGCACGCGTAAAGGACTTTTATCATGGGACCACTGCTTAG
1927 GTACACCCAAGAGAATGATAAAGGACGCTTGACAAGGATGACATCTCTAGGCAGGACAACTCCAG
131 GTACACCCAAGAGAATGATAAAGGACGCTTGACAAGGATGACATCTCTAGGCAGGACAACTCCAG
1992 TACCTGTAGCACCATTTCACTATTTATCGTAGCAGACATCCAAGGGCAAGCAATTATGTTATCTG
196 TACCTGTAGCACCATTTCACTATTTATCGTAGCAGACATCCAAGGGCAAGCAATTATGTTATCTG
2057 GACTAATCGGTAGATTAGAATCCCAGGCATAAAAGGACGAGTTTACTATTCATAATTTTGTTACG
261 GACTAATCGGTAGATTAGAATCCCAGGCATAAAAGGACGAGTTTACTATTCATAATTTTGTTACG
*
2122 TTTTTAAAGATATTTGAACGTTTCGAAAAGAGTTTGATTTGTTTCATTAGATAGTTGTATAGATT
326 TTTTTAAAGATATTTGAACGTTTCGAAAAGAGTTTGATTTGTTTCATTAGATAGTTGTATAAATT
2187 ATCTCAAATTCGGTCTAA
391 ATCTCAAATTCGGTCTAA
2205 ATCATTTTTGCTTGTTTCTTAGTCTTT-TCTTAATATTCAGCAGCTTGTCACACTCGAGTGCGAC
1 ATCATTTTTGCTTGTTTCTT--TCTTTCTCTTAATATTCAGCAGCTTGTCACACTCGAGTGCGAC
*
2269 TAGTCTAGGTCCCGACAACCAACACTAAGCACGCGTAACGGACTTTTATCATGGGACCACTGCTT
64 TAGTCTAGGTCCCGACAACCAACACTAAGCACGCGTAAAGGACTTTTATCATGGGACCACTGCTT
*
2334 AGGTACACCCAGGAGAATGATAAAGGACGCTTGACAAGGATGACATCTCTAGGCAGGACAACTCC
129 AGGTACACCCAAGAGAATGATAAAGGACGCTTGACAAGGATGACATCTCTAGGCAGGACAACTCC
2399 AGTACCTGTAGCACCATTTCACTATTTATCGTAGCAGACATCCAAGGGCAAGCAATTATGTTATC
194 AGTACCTGTAGCACCATTTCACTATTTATCGTAGCAGACATCCAAGGGCAAGCAATTATGTTATC
*
2464 TGGACTAATCGGTAGATTAGAATTCCAGGCATAAAAGGACGAGTTTACTATTCATAATTTTGTTA
259 TGGACTAATCGGTAGATTAGAATCCCAGGCATAAAAGGACGAGTTTACTATTCATAATTTTGTTA
2529 CGTTTTTAAAGATATTTGAACGTTTCGAAAAGAGTTTGATTTGTTTCATTAGATAGTTGTATAAA
324 CGTTTTTAAAGATATTTGAACGTTTCGAAAAGAGTTTGATTTGTTTCATTAGATAGTTGTATAAA
2594 TTATCTCAAATTCGGTCTAA
389 TTATCTCAAATTCGGTCTAA
2614 GGCTTTACAT
Statistics
Matches: 400, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
408 20 0.05
409 375 0.94
410 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (408 bp):
ATCATTTTTGCTTGTTTCTTTCTTTCTCTTAATATTCAGCAGCTTGTCACACTCGAGTGCGACTA
GTCTAGGTCCCGACAACCAACACTAAGCACGCGTAAAGGACTTTTATCATGGGACCACTGCTTAG
GTACACCCAAGAGAATGATAAAGGACGCTTGACAAGGATGACATCTCTAGGCAGGACAACTCCAG
TACCTGTAGCACCATTTCACTATTTATCGTAGCAGACATCCAAGGGCAAGCAATTATGTTATCTG
GACTAATCGGTAGATTAGAATCCCAGGCATAAAAGGACGAGTTTACTATTCATAATTTTGTTACG
TTTTTAAAGATATTTGAACGTTTCGAAAAGAGTTTGATTTGTTTCATTAGATAGTTGTATAAATT
ATCTCAAATTCGGTCTAA
Found at i:5544 original size:9 final size:10
Alignment explanation
Indices: 5520--5544 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5510 TGGAATATAT
5520 GAAAAAGGTA
1 GAAAAAGGTA
5530 GAAAAAGGTA
1 GAAAAAGGTA
5540 GAAAA
1 GAAAA
5545 TGCATCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (10 bp):
GAAAAAGGTA
Found at i:8838 original size:27 final size:27
Alignment explanation
Indices: 8765--8832 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
8755 TTGATTGAAA
*
8765 AATGGGGTTGGAGTATCCTTTTGGAGG
1 AATGGGGTTGGAGTATCCCTTTGGAGG
8792 AATGGGGTTGGAGTATCCCTTTGGAGG
1 AATGGGGTTGGAGTATCCCTTTGGAGG
8819 AATGGGGTTGGAGT
1 AATGGGGTTGGAGT
8833 GGCCCTGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.19, C:0.07, G:0.43, T:0.31
Consensus pattern (27 bp):
AATGGGGTTGGAGTATCCCTTTGGAGG
Found at i:11059 original size:20 final size:20
Alignment explanation
Indices: 11034--11198 Score: 102
Period size: 20 Copynumber: 7.8 Consensus size: 20
11024 GAGAAAAAAC
11034 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
11054 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
11074 TGCATGTATCGATACATT--
1 AGAATGTATCGATACATTGA
** *
11092 -TTATGTATTGATACATTTGGGAAAAAAGA
1 AGAATGTATCGATACA-TT---------GA
11121 CAGAATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
11142 AGAATATATCGATACATTCA
1 AGAATGTATCGATACATTGA
* * *
11162 TGCATGTATTGATACATTGA
1 AGAATGTATCGATACATTGA
*
11182 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
11199 CTAGGTAAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 28
0.70 0.13 0.18
Matches are distributed among these distances:
17 12 0.11
18 2 0.02
20 81 0.73
21 2 0.02
30 2 0.02
31 12 0.11
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:11140 original size:88 final size:88
Alignment explanation
Indices: 11005--11229 Score: 319
Period size: 88 Copynumber: 2.5 Consensus size: 88
10995 AATACATAAA
* * *
11005 AAAATGTATTGATACATCTGAG-AAAAAACAGAATGTATCGATACATTGAAGAATGTATCGATAC
1 AAAATGTATTGATACATTTGGGAAAAAAACAGAATGTATCGATACATTGAAGAATATATCGATAC
11069 ATTCATGCATGTATCGATACATT
66 ATTCATGCATGTATCGATACATT
**
11092 -TTATGTATTGATACATTTGGGAAAAAAGACAGAATGTATCGATACATTGAAGAATATATCGATA
1 AAAATGTATTGATACATTTGGGAAAAAA-ACAGAATGTATCGATACATTGAAGAATATATCGATA
*
11156 CATTCATGCATGTATTGATACATT
65 CATTCATGCATGTATCGATACATT
* * *
11180 GAAAAATGTATCGATACATCTAGGTAAAAAAACAGAATGTATCGATACAT
1 --AAAATGTATTGATACAT-TTGGGAAAAAAACAGAATGTATCGATACAT
11230 CTGAGTAAAA
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
86 17 0.14
87 5 0.04
88 58 0.48
91 32 0.26
92 9 0.07
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (88 bp):
AAAATGTATTGATACATTTGGGAAAAAAACAGAATGTATCGATACATTGAAGAATATATCGATAC
ATTCATGCATGTATCGATACATT
Found at i:12074 original size:46 final size:46
Alignment explanation
Indices: 11966--12117 Score: 155
Period size: 46 Copynumber: 3.3 Consensus size: 46
11956 AGAGGAGTGC
** * * *
11966 CAATGTGCCAATTCAAGGCTAGCAACATCGAGCTAAGGGAAAA-GTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA---AAAAGGTGGA
* * *
12014 CAATGTGCTAATTCAGGGCCAGTGACATTGAGCTAAAAAAGGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAAAAAGGTGGA
* * *
12060 CAATGTGCTGATTCAAGGCCAGCGGCATTGAGCTAATAAAGGT-GC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAAAAAGGTGGA
*
12105 CAATATGCTGATT
1 CAATGTGCTGATT
12118 TAATACCAGG
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
45 17 0.19
46 43 0.48
48 30 0.33
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (46 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAAAAAGGTGGA
Found at i:12256 original size:28 final size:28
Alignment explanation
Indices: 12217--12791 Score: 633
Period size: 28 Copynumber: 20.5 Consensus size: 28
12207 CACTAAGTTA
*
12217 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
12245 TGTGGGCTTTGAAAAGAGTTGCCACCGACCT
1 TGTGGGCTTTG-AAAG-GATGCCACTGA-CT
* **
12276 GTGTGGGCTTTGAAAGGGTGCCACCAACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
12305 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** * *
12333 TGTGGGCTTTGAAAAAAAGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
12361 TGTGGGCTTTGAAAAGATGCCACT-A--
1 TGTGGGCTTTGAAAGGATGCCACTGACT
12386 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
12414 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
12442 TGTGGGCTTTGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
12470 TATGGCCTTTGAAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
12498 TGTGGGCTTTGAAAGGTTATGCCACTAACT
1 TGTGGGCTTTGAAAGG--ATGCCACTGACT
** * * *
12528 TGTGGATTTTGAAGGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
12556 TGTGGGCTTTGAAGGGGTAG-CACTGACT
1 TGTGGGCTTTGAAAGGAT-GCCACTGACT
* *
12584 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
12612 TGTGGGCTTTAAAAGG-TGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
12639 TGTGGTCTTTTG-AAGAGATGCCACTGACT
1 TGTGGGC-TTTGAAAG-GATGCCACTGACT
* ** *
12668 TATGGTTTTTGAAAGGATACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * **
12696 TATGGGCTTTGAAAAGATGCCACAAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
12724 TGTGGGCTTTGAAAAGATG-CACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
12751 TGTGGGCTTTGAAAGGATGCCACTGACC
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
12779 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
12792 GAGATGAATG
Statistics
Matches: 477, Mismatches: 54, Indels: 32
0.85 0.10 0.06
Matches are distributed among these distances:
25 23 0.05
26 1 0.00
27 47 0.10
28 325 0.68
29 24 0.05
30 40 0.08
31 6 0.01
32 11 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:12787 original size:223 final size:222
Alignment explanation
Indices: 12219--12793 Score: 708
Period size: 223 Copynumber: 2.6 Consensus size: 222
12209 CTAAGTTATG
* * * *
12219 TGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACCTGTGTGGGC
1 TGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGA--TGCCA-CAAACT-TGTGGGC
* *
12284 TTTGAAAGGGTGCCACCAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAA-AA
62 TTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAGAA
*
12348 AAAGCCACTAACTTGTGGGCTTTGAAAAGATGCCACTATGTGGGCTTTGAAAGGATGCCACTGAC
127 AAAGCCACTAACTTGTGGGCTTTGAAAAGATGCCACTATGTGGGCTTTAAAAGGATGCCACTGAC
*
12413 TTGTGGGCTTTGAAAAGATGCCACTGACTTG
192 TTGTGGGCTTTGAAAAGATGCCACTGACTTA
* * * * **
12444 TGGGCTTTGAAAGGATGCCACTGATTTATGGCCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACAAACTTGTGGGCTTTG
** * * ****
12509 AAAGGTTATGCCACTAACTTGTGGATTTTGAAGGGGTGCCACTAACTTGTGGGCTTTGAAGGGGT
66 AAAGG--ATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAGAAAA
* * * * *
12574 AG-CACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTAAAAGG-TGCCATTGA
129 AGCCACTAACTTGTGGGCTTTGAAAAGATGCCACT-A--TGTGGGCTTTAAAAGGATGCCACTGA
* *
12637 CTTGTGGTCTTTTGAAGAGATGCCACTGACTTA
191 CTTGTGGGC-TTTGAAAAGATGCCACTGACTTA
** *
12670 TGGTTTTTGAAAGGATACCACTGACTTATGGGCTTTGAAAAGATGCCACAAACTTGTGGGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACAAACTTGTGGGCTTTG
* * * *
12735 AAAAGATG-CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACCTATGGGCTTTGAAGA
66 AAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAGA
12794 GATGAATGTT
Statistics
Matches: 297, Mismatches: 46, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
221 16 0.05
222 3 0.01
223 123 0.41
224 6 0.02
225 53 0.18
226 96 0.32
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (222 bp):
TGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACAAACTTGTGGGCTTTG
AAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAGAAAAAG
CCACTAACTTGTGGGCTTTGAAAAGATGCCACTATGTGGGCTTTAAAAGGATGCCACTGACTTGT
GGGCTTTGAAAAGATGCCACTGACTTA
Found at i:12829 original size:13 final size:14
Alignment explanation
Indices: 12807--12839 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
12797 GAATGTTATA
12807 GACAAAAGTTT-TT
1 GACAAAAGTTTCTT
*
12820 GACAATAGTTTCTT
1 GACAAAAGTTTCTT
12834 GACAAA
1 GACAAA
12840 TGGCAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (14 bp):
GACAAAAGTTTCTT
Found at i:13039 original size:26 final size:26
Alignment explanation
Indices: 13010--13059 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
13000 AATGATGTAT
*
13010 GATGATATTATGAATGTATGATGCGA
1 GATGATATTATGAATATATGATGCGA
13036 GATGATATTATGAATATATGATGC
1 GATGATATTATGAATATATGATGC
13060 AGAATGCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (26 bp):
GATGATATTATGAATATATGATGCGA
Found at i:14085 original size:16 final size:16
Alignment explanation
Indices: 14066--14117 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
14056 ATCTGGACCC
14066 TTTTTTTGTTTGTTTG
1 TTTTTTTGTTTGTTTG
14082 TTTTTTTGTTTGTTT-
1 TTTTTTTGTTTGTTTG
*
14097 TTGTTTT-TTT-TTTG
1 TTTTTTTGTTTGTTTG
14111 TTTTTTT
1 TTTTTTT
14118 TGTACTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 3 0.09
14 9 0.27
15 6 0.18
16 15 0.45
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTTTTGTTTGTTTG
Found at i:14091 original size:12 final size:11
Alignment explanation
Indices: 14066--14118 Score: 72
Period size: 11 Copynumber: 4.7 Consensus size: 11
14056 ATCTGGACCC
14066 TTTTTTTGTTTG
1 TTTTTTT-TTTG
14078 TTTGTTTTTTTG
1 TTT-TTTTTTTG
*
14090 -TTTGTTTTTG
1 TTTTTTTTTTG
14100 TTTTTTTTTTG
1 TTTTTTTTTTG
14111 TTTTTTTT
1 TTTTTTTT
14119 GTACTAAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
10 7 0.19
11 19 0.51
12 7 0.19
13 4 0.11
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:14097 original size:26 final size:26
Alignment explanation
Indices: 14068--14120 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
14058 CTGGACCCTT
14068 TTTTTGTTTGTTTGTTT-TTTTGTTTG
1 TTTTTGTTT-TTTGTTTGTTTTGTTTG
* *
14094 TTTTTGTTTTTTTTTTGTTTTTTTTG
1 TTTTTGTTTTTTGTTTGTTTTGTTTG
14120 T
1 T
14121 ACTAAGGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (26 bp):
TTTTTGTTTTTTGTTTGTTTTGTTTG
Found at i:30119 original size:77 final size:78
Alignment explanation
Indices: 29958--30200 Score: 256
Period size: 80 Copynumber: 3.1 Consensus size: 78
29948 TTCATCGATG
* * * ** *
29958 TTTTTATTTCTAAAATACCAATTTTTCACTATCGGGGATACTCCAACCTCCTTATTTATGAGGGG
1 TTTTTATTTC-AAAACACTAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTTTGAGGGG
***
30023 ATACTCCAACCTTGG
65 ATACTCCAACC-CCA
* * * * *
30038 TTTTT-TTT-AGAACACTGATTTTTTACCATCGGAGATAGTCCAACCTTGTTATTTTTGAGGGGA
1 TTTTTATTTCAAAACACTAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTTTGAGGGGA
30101 TACTCCAACCCCAA
66 TACTCCAACCCC-A
* * * * * *
30115 TTTTTATTTCCAAAACATTAATTTTCCACCATCGGGGATACTCTAACCCTGTCATTTTTGAAGGG
1 TTTTTATTT-CAAAACACTAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTTTGAGGGG
30180 ATACTCCAACCCCA
65 ATACTCCAACCCCA
30194 TTTTTAT
1 TTTTTAT
30201 CTCCAAAATA
Statistics
Matches: 134, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
77 59 0.44
78 3 0.02
79 11 0.08
80 61 0.46
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (78 bp):
TTTTTATTTCAAAACACTAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTTTGAGGGGA
TACTCCAACCCCA
Found at i:30218 original size:80 final size:80
Alignment explanation
Indices: 30062--30219 Score: 219
Period size: 80 Copynumber: 2.0 Consensus size: 80
30052 CTGATTTTTT
* * * * *
30062 ACCATCGGAGATAGTCCAACCTTGTTATTTTTGAGGGGATACTCCAACCCCAATTTTTATTTCCA
1 ACCATCGGAGATACTCCAACCCTGTCATTTTTGAAGGGATACTCCAACCCCAATTTTTATCTCCA
*
30127 AAACATTAATTTTCC
66 AAACATAAATTTTCC
* *
30142 ACCATCGGGGATACTCTAACCCTGTCATTTTTGAAGGGATACTCCAACCCC-ATTTTTATCTCCA
1 ACCATCGGAGATACTCCAACCCTGTCATTTTTGAAGGGATACTCCAACCCCAATTTTTATCTCCA
*
30206 AAATATCAAATTTT
66 AAACAT-AAATTTT
30220 TTATCGAGGA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
79 17 0.25
80 51 0.75
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (80 bp):
ACCATCGGAGATACTCCAACCCTGTCATTTTTGAAGGGATACTCCAACCCCAATTTTTATCTCCA
AAACATAAATTTTCC
Found at i:36429 original size:30 final size:30
Alignment explanation
Indices: 36368--36429 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
36358 GCAACCTTTC
* * *
36368 TTCAAAGTCCATGACTTAGTGACATCTCTT
1 TTCAAAGTCCACGACTTAGTGACACCCCTT
*
36398 TTCAAAGTCCACGACTCT-GTGGCACCCCTT
1 TTCAAAGTCCACGACT-TAGTGACACCCCTT
36428 TT
1 TT
36430 AGCCCTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.34
Consensus pattern (30 bp):
TTCAAAGTCCACGACTTAGTGACACCCCTT
Found at i:36596 original size:62 final size:62
Alignment explanation
Indices: 36497--37030 Score: 584
Period size: 62 Copynumber: 8.6 Consensus size: 62
36487 GGTGGCACAT
* * * * * * * * ** *
36497 GCCTTTTTCTTTTCAAAACCAATACGAATTGGTGGCACCTTTTAGTCCTCAAAAAGAAAAAT
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCAGGAC
* * * * * *
36559 GTCTTTTTCTTTTCAAAGCTCACACGAGTTGCTGGCACCTTTTAGTCCTCAAAGAGCAGGAT
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCAGGAC
* * * * * * * *
36621 GCATTTTTATTTTTAAAGCCCATATGAGTTGGTGGCACCCTTTGGTCCTTAAAAAGCAAGAC
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCAGGAC
* * *
36683 GCCTTTTTCTTTTCGAAGCCCACATGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCATGAC
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCAGGAC
* *
36745 GCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTGGTCCTCAAAGAGTAGGAC
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCAGGAC
* * * * *
36807 TCATTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACCCTTTGGTCTTCAAGGAGCAGGAC
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCAGGAC
* * * *
36869 ACCTTTTTCTTTACAAAGCCCACACGAGTTGGTGGCACCTTTTGGTCCTCAAAGAGTAGGAC
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCAGGAC
* ** * * * *
36931 GCCCTTTTTTTTTTCAAAGTGCACACGAGTTGGTAGCACCCTTTAGTCCTC-AAGAAGTAGCAC
1 G-CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTGGTCCTCAAAG-AGCAGGAC
** * **
36994 AACTTTTTCTTTTTAAAGCCCACATAAGTTGGTGGCA
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
37031 GCATTTAGTC
Statistics
Matches: 399, Mismatches: 71, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
62 350 0.88
63 49 0.12
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (62 bp):
GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCAGGAC
Found at i:36814 original size:186 final size:186
Alignment explanation
Indices: 36497--37045 Score: 647
Period size: 186 Copynumber: 2.9 Consensus size: 186
36487 GGTGGCACAT
* * * * * * * * *
36497 GCCTTTTTCTTTTCAAAACCAATACGAATTGGTGGCACCTTTTAGTCCTCAAAAAGAAAAATGTC
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTGGTCCTCAAAGAGAAAGACGCC
* * * *
36562 TTTTTCTTTTCAAAGCTCACACGAGTTGCTGGCACCTTTTAGTCCTCAAAGAGCAGGA-TGCATT
66 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACT-CATT
* *
36626 TTTATTTTTAAAGCCCATATGAGTTGGTGGCACCCTTTGGTCCTTAAAAAGCAAGAC
130 TTTCTTTTTAAAGCCCACATGAGTTGGTGGCACCCTTTGGTCCTTAAAAAGCAAGAC
* * * * *
36683 GCCTTTTTCTTTTCGAAGCCCACATGAGTTGGTGGCACCCTTTGGTCCTCAAAGAGCATGACGCC
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTGGTCCTCAAAGAGAAAGACGCC
* *
36748 TTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTGGTCCTCAAAGAGTAGGACTCATTT
66 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACTCATTT
* * * ** *
36813 TTCTTTTCAAAGCCTACACGAGTTGGTGGCACCCTTTGGT-CTTCAAGGAGCAGGAC
131 TTCTTTTTAAAGCCCACATGAGTTGGTGGCACCCTTTGGTCCTT-AAAAAGCAAGAC
* * * *
36869 ACCTTTTTCTTTACAAAGCCCACACGAGTTGGTGGCACCTTTTGGTCCTCAAAGAGTAGGACGCC
1 GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTGGTCCTCAAAGAGAAAGACG-C
* ** * * *
36934 CTTTTTTTTTTCAAAGTGCACACGAGTTGGTAGCACCCTTTAGTCCTC-AAGAAGTAGCAC-AAC
65 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAG-AGTAGGACTCA-
* * * *
36997 TTTTTCTTTTTAAAGCCCACATAAGTTGGTGGCAGCATTTAGTCCTTAA
128 TTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCACCCTTTGGTCCTTAA
37046 GGAGTAGGAC
Statistics
Matches: 307, Mismatches: 50, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
185 3 0.01
186 212 0.69
187 89 0.29
188 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (186 bp):
GCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTGGTCCTCAAAGAGAAAGACGCC
TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACTCATTT
TTCTTTTTAAAGCCCACATGAGTTGGTGGCACCCTTTGGTCCTTAAAAAGCAAGAC
Found at i:37153 original size:45 final size:43
Alignment explanation
Indices: 37063--37450 Score: 284
Period size: 44 Copynumber: 9.1 Consensus size: 43
37053 GACACTTTTC
* * * *
37063 TCATTTCC-TTTTTTCCTTTGTCATTAAAGAGTAGGATGCACT
1 TCATTTCCTTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACT
* *
37105 TCATTTCCTTTTTTTCTCTTTTGTCCTCAAAGAGCAGGACACATT
1 TCATTTCCTTTTTTTC-C-TTTGTCCTCAAAGAGCAGGACGCACT
* *
37150 TCATTTCATTCTTTTTCCTTTTATCCTCAAAGAGCAGGACG----
1 TCATTTCCTT-TTTTTCC-TTTGTCCTCAAAGAGCAGGACGCACT
* * *
37191 -CA----CTTTTTTT-CTTTGTCCTCAAAGAGCAGGGCGCGCC
1 TCATTTCCTTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACT
* * *
37228 TCATTTCCTTATTTTCCCTTTGTCCTCAAAGAGCAGGGCGCATT
1 TCATTTCCTT-TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACT
* * *
37272 TCATTTCCTTCTCTTCTCTTTTGTCTTCAAAGAGCAGGACGCACT
1 TCATTTCCTT-T-TTTTCCTTTGTCCTCAAAGAGCAGGACGCACT
** * * * *
37317 TTGTTTCC--TTTTT-CTTTGTCCTCAAAGAGTAGGGCACACC
1 TCATTTCCTTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACT
* * * * * *
37357 TCATTTCCTTCTTTTCCCTTTGTCCTTAAAGAACAGGGCGTACC
1 TCATTTCCTT-TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACT
* * * *
37401 TCATTT-ATTTATTTTCCCTTTGTCCTCAAAGACCAGAATGCACT
1 TCATTTCCTTT-TTTT-CCTTTGTCCTCAAAGAGCAGGACGCACT
37445 TCATTT
1 TCATTT
37451 TTTTTCTTGT
Statistics
Matches: 275, Mismatches: 49, Indels: 42
0.75 0.13 0.11
Matches are distributed among these distances:
33 20 0.07
34 1 0.00
35 5 0.02
36 2 0.01
38 2 0.01
40 29 0.11
41 3 0.01
42 13 0.05
43 20 0.07
44 91 0.33
45 83 0.30
46 6 0.02
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.41
Consensus pattern (43 bp):
TCATTTCCTTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACT
Found at i:37213 original size:78 final size:79
Alignment explanation
Indices: 37114--37269 Score: 199
Period size: 78 Copynumber: 2.0 Consensus size: 79
37104 TTCATTTCCT
** * *
37114 TTTTTTCTCTTTTGTCCTCAAAGAGCAGGACACATTTCATTTCATTCTTTTTCCTTTTATCCTCA
1 TTTTTTCTCTTTTGTCCTCAAAGAGCAGGACACACCTCATTTCATT-ATTTTCCCTTTATCCTCA
37179 AAGAGCAGGACGCAC
65 AAGAGCAGGACGCAC
* * * * *
37194 TTTTTT-TC-TTTGTCCTCAAAGAGCAGGGCGCGCCTCATTTCCTTATTTTCCCTTTGTCCTCAA
1 TTTTTTCTCTTTTGTCCTCAAAGAGCAGGACACACCTCATTTCATTATTTTCCCTTTATCCTCAA
*
37257 AGAGCAGGGCGCA
66 AGAGCAGGACGCA
37270 TTTCATTTCC
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
77 28 0.42
78 30 0.45
79 2 0.03
80 6 0.09
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (79 bp):
TTTTTTCTCTTTTGTCCTCAAAGAGCAGGACACACCTCATTTCATTATTTTCCCTTTATCCTCAA
AGAGCAGGACGCAC
Found at i:37379 original size:129 final size:125
Alignment explanation
Indices: 37066--37396 Score: 391
Period size: 129 Copynumber: 2.6 Consensus size: 125
37056 ACTTTTCTCA
* * ** * * *
37066 TTTCCTTTTTTCCTTTGTCATTAAAGAGTAGGATGCACTTCATTTCCTTTTTTTCTCTTTTGTCC
1 TTTCC-TTTTT-CTTTGTCCTCAAAGAGTAGGGCGCACCTCATTTCCTTATTTTC-CCTTTGTCC
* * *
37131 TCAAAGAGCAGGACACATTTCATTTCATTCTTTTTCCTTTTATCCTCAAAGAGCAGGACGCAC
63 TCAAAGAGCAGGGCGCATTTCATTTCATTCTTTCTCCTTTTATCCTCAAAGAGCAGGACGCAC
* *
37194 -TT--TTTTTCTTTGTCCTCAAAGAGCAGGGCGCGCCTCATTTCCTTATTTTCCCTTTGTCCTCA
1 TTTCCTTTTTCTTTGTCCTCAAAGAGTAGGGCGCACCTCATTTCCTTATTTTCCCTTTGTCCTCA
* * *
37256 AAGAGCAGGGCGCATTTCATTTCCTTCTCTTCT-CTTTTGTCTTCAAAGAGCAGGACGCAC
66 AAGAGCAGGGCGCATTTCATTTCATTCT-TTCTCCTTTTATCCTCAAAGAGCAGGACGCAC
* *
37316 TTTGTTTCCTTTTTCTTTGTCCTCAAAGAGTAGGGCACACCTCATTTCCTTCTTTTCCCTTTGTC
1 ----TTTCCTTTTTCTTTGTCCTCAAAGAGTAGGGCGCACCTCATTTCCTTATTTTCCCTTTGTC
* *
37381 CTTAAAGAACAGGGCG
62 CTCAAAGAGCAGGGCG
37397 TACCTCATTT
Statistics
Matches: 174, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
122 61 0.35
123 38 0.22
124 5 0.03
127 4 0.02
129 66 0.38
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (125 bp):
TTTCCTTTTTCTTTGTCCTCAAAGAGTAGGGCGCACCTCATTTCCTTATTTTCCCTTTGTCCTCA
AAGAGCAGGGCGCATTTCATTTCATTCTTTCTCCTTTTATCCTCAAAGAGCAGGACGCAC
Found at i:43350 original size:52 final size:52
Alignment explanation
Indices: 43202--43330 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
43192 CGAAATATGA
* *
43202 AAATTTGCCTACATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
* *
43254 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATTGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
43306 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
43331 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
Found at i:43430 original size:19 final size:20
Alignment explanation
Indices: 43406--43458 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
43396 TAGCTTACAT
43406 TGTATCGATACAAAAC-TTA
1 TGTATCGATACAAAACTTTA
*
43425 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAACTTTA
43445 TGTATCGATACAAA
1 TGTATCGATACAAA
43459 TCGTTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (20 bp):
TGTATCGATACAAAACTTTA
Found at i:44513 original size:49 final size:48
Alignment explanation
Indices: 44361--45195 Score: 882
Period size: 49 Copynumber: 17.6 Consensus size: 48
44351 GTCAATGTGG
*
44361 TGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTT-AA-A--GAAAAGGTGCCAATATGC
* * * *
44413 TGATTCAAGGCCAGCTATACTGGACTT-----AAAGGTGCGAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAATATGC
44456 TGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGAA-AAGGTGCCAATATGC
* * ** *
44505 TGATTCAAGGCCAGCTATATAGGACTTAAAGGTGAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAA-GAAAAGGTGCCAATATGC
* * * * *
44554 TGATTCAAGGCTAGCGACATAGGACTTAAAGATGACAAAGGCGCCAATATGT
1 TGATTCAAGGCCAGCTACATTGGACTT-AA-A-GA-AAAGGTGCCAATATGC
* * * *
44606 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGA-AAAGGTGCCAATATGC
* *
44655 TGATTCAAGACCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGA-AAAGGTGCCAATATGC
* * * *
44704 TAATTCAAGGCCAACGATATTGGACTT-----AAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAATATGC
*
44747 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGA-AAAGGTGCCAATATGC
* * * *
44796 TGATTCAAGGCCAACGATATTGGACTT-----AAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAATATGC
*
44839 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGA-AAAGGTGCCAATATGC
* * *
44888 TGATTCAAGGCCAGCGATATTGGACTT-----AAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAATATGC
44931 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGA-AAAGGTGCCAATATGC
* * * * *
44980 TGATTCAAGGCCAGCGATATTGGACTT-----AAAGGTACCAATGTGT
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAATATGC
*
45023 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAATGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGA-AAAGGTGCCAATATGC
* * *
45072 TGATTCAAGGCCAGCGATATTGGACTT----AAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAATATGC
* *
45116 TGATTCAAGGCCACCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGA-AAAGGTGCCAATATGC
* * *
45165 TGATTCAAGGCTAGCGATATTGGACTTAAAG
1 TGATTCAAGGCCAGCTACATTGGACTTAAAG
45196 GTGATGCCAC
Statistics
Matches: 657, Mismatches: 87, Indels: 81
0.80 0.11 0.10
Matches are distributed among these distances:
43 192 0.29
44 38 0.06
45 1 0.00
48 2 0.00
49 356 0.54
50 4 0.01
51 4 0.01
52 60 0.09
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (48 bp):
TGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAATATGC
Found at i:44530 original size:92 final size:92
Alignment explanation
Indices: 44353--45198 Score: 1237
Period size: 92 Copynumber: 9.0 Consensus size: 92
44343 AAAAAGATGT
* * *
44353 CAATGTGGTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAATATGCTGATT
* *
44418 CAAGGCCAGCTATACTGGACTTAAAGGTGC
63 CAAGGCCAGCGATATTGGACTTAAAGGTGC
*
44448 GAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
* *
44513 GGCCAGCTATATAGGACTTAAAGGTGAAGGTGC
66 GGCCAGCGATATTGGACTT--A----AAGGTGC
* * * * * *
44546 CAATGTGCTGATTCAAGGCTAGCGACATAGGACTTAAAGATGACAAAGGCGCCAATATGTTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--A-GAAGGTGCCAATATGCTGATT
44611 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
63 CAAGGCCAGCGATATTGGACTT----A--AAGGTGC
* * *
44647 CAATGTGCTGATTCAAGACCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTAATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
*
44712 GGCCAACGATATTGGACTTAAAGGTGC
66 GGCCAGCGATATTGGACTTAAAGGTGC
* *
44739 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
*
44804 GGCCAACGATATTGGACTTAAAGGTGC
66 GGCCAGCGATATTGGACTTAAAGGTGC
*
44831 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
44896 GGCCAGCGATATTGGACTTAAAGGTGC
66 GGCCAGCGATATTGGACTTAAAGGTGC
44923 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGCTGATTCA
*
44987 AGGCCAGCGATATTGGACTTAAAGGTAC
65 AGGCCAGCGATATTGGACTTAAAGGTGC
* *
45015 CAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AATGTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGCTGATTCA
45079 AGGCCAGCGATATTGGACTTAAAAGGTGC
65 AGGCCAGCGATATTGGACTT-AAAGGTGC
* *
45108 CAATGTGCTGATTCAAGGCCACCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
*
45173 GGCTAGCGATATTGGACTTAAAGGTG
66 GGCCAGCGATATTGGACTTAAAGGTG
45199 ATGCCACCAA
Statistics
Matches: 696, Mismatches: 41, Indels: 31
0.91 0.05 0.04
Matches are distributed among these distances:
92 405 0.58
93 85 0.12
94 2 0.00
95 37 0.05
98 81 0.12
100 1 0.00
101 83 0.12
103 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGACTTAAAGGTGC
Found at i:44756 original size:21 final size:21
Alignment explanation
Indices: 44689--44756 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
44679 CTTAAAGATG
*
44689 AAGGTGCCAATATGCTAATTC
1 AAGGTGCCAATATGCTGATTC
* ** *
44710 AA-G-GCCAACGATATTGGACTTA
1 AAGGTGCCAA-TATGCT-GA-TTC
44732 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
44753 AAGG
1 AAGG
44757 CCAGCTACAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
21 9 0.27
22 6 0.18
23 4 0.12
24 5 0.15
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:45237 original size:33 final size:33
Alignment explanation
Indices: 45200--45361 Score: 197
Period size: 33 Copynumber: 5.0 Consensus size: 33
45190 TTAAAGGTGA
* * *
45200 TGCCACCAACTTGTGTTGGCTTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAGGT
*
45233 TGCCATCGACTTGTGTGGGCTTTAGAA-AAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAA-GGT
*
45266 TGCCACCGACTTGTGTGGGCTTTAG-AG-GGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAGG-T
*
45298 TGCCACCAACTTGTGTGGGCTTTAGAAGAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAGGT
** *
45331 TGTGACCGACTTGTGTGGGCTTTTG-AGAAGG
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAGG
45362 AGAAAGATGC
Statistics
Matches: 112, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
31 2 0.02
32 34 0.30
33 74 0.66
34 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGAAGGT
Found at i:45320 original size:65 final size:66
Alignment explanation
Indices: 45200--45361 Score: 197
Period size: 65 Copynumber: 2.5 Consensus size: 66
45190 TTAAAGGTGA
* * * * *
45200 TGCCACCAACTTGTGTTGGCTTTTGAAGAAGGTTGCCATCGACTTGTGTGGGCTTTAGAA-AAGG
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAAGAA-G
45264 GT
65 GT
*
45266 TGCCACCGACTTGTGTGGGCTTTAG-AG-GGGATTGCCACCAACTTGTGTGGGCTTTAGAAGAAG
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAGG-TTGCCACCAACTTGTGTGGGCTTTAGAAGAAG
45329 GT
65 GT
** *
45331 TGTGACCGACTTGTGTGGGCTTTTG-AGAAGG
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAGG
45362 AGAAAGATGC
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 2 0.02
65 55 0.66
66 26 0.31
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (66 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAAGAAGG
T
Found at i:45539 original size:33 final size:33
Alignment explanation
Indices: 45358--46019 Score: 459
Period size: 33 Copynumber: 20.5 Consensus size: 33
45348 GGCTTTTGAG
* * *
45358 AAGGAGAAAGATGCCACGAAGTTGTGGACTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
*
45391 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGAC-TT-AA
* *
45428 AA-GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGAC-TT-AA
* **
45462 AAGGGAAAAAGAGTGCCATGGAGTTGTGG-CTTTG
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGACTTAA
* * *
45496 AA--AAGAAGGTGCCACGAAGTCGTGGACTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* *
45527 AAGGAACAAGGTGCCACGGAGTCGTGGACTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* *
45560 AAGGAACAAGGTGCCACGGAGTCGTGGACTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* **
45593 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTG
1 AAGGAAAAAG-GTGCCACGGAGTTGTGGACTTAA
* * **
45627 AA--AAGAAGGTGCCACGAAGTCATGGACTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* * *
45658 AAGGAACAAGGTGCCACGGGGTTGTGAACTTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGAC-TTAA
* * *
45692 AAGGGAAAAATAGTGCCACAGAGTTGTGGGCTTTAA
1 AA-GGAAAAA-GGTGCCACGGAGTTGTGGAC-TTAA
*
45728 AA-G----A-GTGCCACGGAGTTGTGGACTTAG
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* *
45755 AAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTAA
1 AAGGAAAAAG-GTGCCACGGAGTTGTGGACTTAA
* *
45789 AAAGAAAAAGGTGCCATGGAGTTGTGGACTT-A
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* * *
45821 AACG-----GGTGCCACGAAGTTGTGGACTTTAG
1 AAGGAAAAAGGTGCCACGGAGTTGTGGAC-TTAA
* **
45850 AAGGAAAAAGAGTGCCACGGAGTCGTGGACTTTG
1 AAGGAAAAAG-GTGCCACGGAGTTGTGGACTTAA
* * *
45884 AA-G-AAAAGATGCCACTGAGTCGTGGACTT--
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* * * * *
45913 -TGGAAAGAGATGCCACTGAGTTGTGGGCTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
*
45945 AA-G----A-GTGCCACAGAGTTGTGGACTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
* ** **
45972 AAGG-AAAAGGATGCCACTGAGTCATGGACTTTG
1 AAGGAAAAAGG-TGCCACGGAGTTGTGGACTTAA
*
46005 AA-GAAAAAGATGCCA
1 AAGGAAAAAGGTGCCA
46020 TTGAGTCGTG
Statistics
Matches: 510, Mismatches: 76, Indels: 87
0.76 0.11 0.13
Matches are distributed among these distances:
27 45 0.09
28 22 0.04
29 4 0.01
30 38 0.07
31 49 0.10
32 23 0.05
33 133 0.26
34 98 0.19
35 47 0.09
36 31 0.06
37 20 0.04
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.19
Consensus pattern (33 bp):
AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAA
Found at i:45638 original size:131 final size:133
Alignment explanation
Indices: 45369--46019 Score: 617
Period size: 131 Copynumber: 5.0 Consensus size: 133
45359 AGGAGAAAGA
* *
45369 TGCCACGAAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAA
1 TGCCACGAAGTCGTGGACTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGACTTT-AAAAGAAA
* *
45434 AAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCATGGAGTTGTGG-CTTTGAA
63 AAAGTGCCACGGAGTTGTGGACTTT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAA
45498 -AAGAAGG
126 GAAGAAGG
* * *
45505 TGCCACGAAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAACAA
1 TGCCACGAAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAA-GAAAAA
* * *
45569 GGTGCCACGGAGTCGTGGAC-TTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA-AAG
65 AGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAGAAG
45632 AAGG
130 AAGG
* * * *
45636 TGCCACGAAGTCATGGACTTAAAAGGAACAAGGTGCCACGGGGTTGTGAACTTTAAAAGGGAAAA
1 TGCCACGAAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAA--GAAAA
* * *
45701 ATAGTGCCACAGAGTTGTGGGCTTT-------AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGG
64 A-AGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAA-G
*
45759 AAAAAGAG
127 AAGAAG-G
* * * * * *
45767 TGCCACGGAGTCGTGGGCTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGAC-TTAAACG-----G
1 TGCCACGAAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAAAAAA
* * *
45826 GTGCCACGAAGTTGTGGACTTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGACTTTGAAGAA-A
66 GTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAGAAGA
*
45890 AGA
131 AGG
* * * * *
45893 TGCCACTG-AGTCGTGGACTT---TGGAAAGAGATGCCACTGAGTTGTGGGC-TTAAAAG-----
1 TGCCAC-GAAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAAAAA
* * * ** *
45948 AGTGCCACAGAGTTGTGGAC-TTAAAAGGAAAAGGA-TGCCACTGAGTCATGGACTTTGAAGAAA
65 AGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAGAAG
*
46011 AAGA
130 AAGG
46015 TGCCA
1 TGCCA
46020 TTGAGTCGTG
Statistics
Matches: 444, Mismatches: 53, Indels: 50
0.81 0.10 0.09
Matches are distributed among these distances:
121 25 0.06
122 41 0.09
123 44 0.10
126 17 0.04
127 4 0.01
128 33 0.07
129 29 0.07
130 35 0.08
131 109 0.25
132 12 0.03
133 30 0.07
134 33 0.07
135 9 0.02
136 23 0.05
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (133 bp):
TGCCACGAAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAAAAAA
GTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAGAAGA
AGG
Found at i:45653 original size:98 final size:98
Alignment explanation
Indices: 45358--46006 Score: 554
Period size: 98 Copynumber: 6.7 Consensus size: 98
45348 GGCTTTTGAG
* * *
45358 AAGGAGAAAGA-TGCCACGAAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGAC
* *
45422 TTTGAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA
65 TTTGAAAAG----AGGTGCCACGGAGTTGTGGAC-TT-AA
* ** * * *
45462 AAGGGAAAAAGAGTGCCATGGAGTTGTGG-CTTTGAA--AAGAAG-GTGCCACGAAGTCGTGGAC
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC
** * *
45523 TTAAAAGGAACAAGGTGCCACGGAGTCGTGGACTTAA
65 TTTGAA--AA-GAGGTGCCACGGAGTTGTGGACTTAA
* * *
45560 AAGGAACAAG-GTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACT
* **
45624 TTGAAAAGAAGGTGCCACGAAGTCATGGACTTAA
66 TTGAAAAG-AGGTGCCACGGAGTTGTGGACTTAA
* * * * * *
45658 AAGGAACAAG-GTGCCACGGGGTTGTGAACTTTAAAAGGGAAAAATAGTGCCACAGAGTTGTGGG
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGAC-TTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGA
*
45722 CTTT-AAAAGA-GTGCCACGGAGTTGTGGACTTAG
64 CTTTGAAAAGAGGTGCCACGGAGTTGTGGACTTAA
* * * *
45755 AAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTAAAAAGAAAAAG-GTGCCATGGAGTTGTGGAC-
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACT
* * *
45818 TT-AAACG-GGTGCCACGAAGTTGTGGACTTTAG
66 TTGAAAAGAGGTGCCACGGAGTTGTGGAC-TTAA
* ** * *
45850 AAGGAAAAAGAGTGCCACGGAGTCGTGGACTTTGAA-G-AAAAGA-TGCCACTGAGTCGTGGACT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACT
* * * *
45912 TTGGAAAGAGATGCCACTGAGTTGTGGGCTT--
66 TTGAAAAGAGGTGCCACGGAGTTGTGGACTTAA
* * * **
45943 -----AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAAAAGGA-TGCCACTGAGTCATGGACT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACT
46002 TTGAA
66 TTGAA
46007 GAAAAAGATG
Statistics
Matches: 455, Mismatches: 69, Indels: 56
0.78 0.12 0.10
Matches are distributed among these distances:
88 27 0.06
89 1 0.00
90 27 0.06
93 20 0.04
94 27 0.06
95 58 0.13
96 37 0.08
97 46 0.10
98 71 0.16
99 18 0.04
100 67 0.15
101 20 0.04
102 5 0.01
103 2 0.00
104 2 0.00
105 13 0.03
106 14 0.03
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.20
Consensus pattern (98 bp):
AAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACT
TTGAAAAGAGGTGCCACGGAGTTGTGGACTTAA
Found at i:45763 original size:162 final size:160
Alignment explanation
Indices: 45402--46066 Score: 516
Period size: 167 Copynumber: 4.1 Consensus size: 160
45392 AGGGAAAAAG
* * *
45402 AGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAAGG
1 AGTGCCACGGAGTCGTGGAC-TT-AAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA--
* * ** * * *
45466 GAAAAAGAGTGCCATGGAGTTGTGG-CTTTGAA--AAGAAGGTGCCACGAAGTCGTGGAC-TTAA
60 G---AAG-GTGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAGTTGTGAACTTTAA
* * **
45527 AAGGAACAAG-GTGCCACGGAGTCGTGGACTTAAAAGGAACA
121 AAGGAAAAAGAGTGCCACAGAGTCGTGGACTTTGAA-GAA-A
45568 AGGTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGA
1 A-GTGCCACGGAGTCGTGGACTT-AAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGA
** **
45633 AGGTGCCACGAAGTCATGGACTTAAAAGGAACAAGGTGCCACGGGGTTGTGAACTTTAAAAGGGA
62 AGGTGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAGTTGTGAACTTTAAAA-GGA
* * * *
45698 AAAATAGTGCCACAGAGTTGTGGGCTTT-AA-AAG
126 AAAAGAGTGCCACAGAGTCGTGGACTTTGAAGAAA
* *
45731 AGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTAAAAAGAAA
1 AGTGCCACGGAGTCGTGGACTTA-AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-AAAAG---
* * * * *
45796 AAGGTGCCATGGAGTTGTGGACTT---A--AAC-GGGTGCCACGAAGTTGTGGACTTTAGAAGGA
61 AAGGTGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAGTTGTGAACTTTAAAAGGA
*
45855 AAAAGAGTGCCACGGAGTCGTGGACTTTGAAGAAA
126 AAAAGAGTGCCACAGAGTCGTGGACTTTGAAGAAA
* * * *
45890 AGATGCCACTGAGTCGTGGACTT--TGGAAAGAGA-TGCCACTGAGTTGTGGGCTTAAAAG-A-G
1 AG-TGCCACGGAGTCGTGGACTTAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAAGG
** * *
45950 TGCCAC-AGAGTTGTGGACTTAAAAGGAA-AAGGATGCCACTG-AGTCATGGACTTT-GAA-GAA
65 TGCCACGA-AGTTGTGGACTTAAAAGGAACAAGG-TGCCAC-GAAGTTGTGAACTTTAAAAGGAA
** *
46010 AAAGA-TGCCATTGAGTCGTGAACTTTGAAGAAA
127 AAAGAGTGCCACAGAGTCGTGGACTTTGAAGAAA
* *
46043 AGGATGCCACTGAGTCATGGACTT
1 A-G-TGCCACGGAGTCGTGGACTT
46067 TGAGAAGAGA
Statistics
Matches: 419, Mismatches: 55, Indels: 62
0.78 0.10 0.12
Matches are distributed among these distances:
150 18 0.04
151 1 0.00
153 27 0.06
154 29 0.07
155 12 0.03
156 35 0.08
157 36 0.09
158 25 0.06
159 7 0.02
160 18 0.04
161 22 0.05
162 57 0.14
163 1 0.00
164 42 0.10
165 7 0.02
166 20 0.05
167 62 0.15
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.20
Consensus pattern (160 bp):
AGTGCCACGGAGTCGTGGACTTAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAAGGT
GCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAGTTGTGAACTTTAAAAGGAAAAAG
AGTGCCACAGAGTCGTGGACTTTGAAGAAA
Found at i:45772 original size:62 final size:65
Alignment explanation
Indices: 45396--45822 Score: 221
Period size: 67 Copynumber: 6.5 Consensus size: 65
45386 CTTAAAAGGG
* * *
45396 AAAAAG-A-GTGCCACGGAGTTGTGGGCTTTGAAAA--GAAAAA-AGTGCCACGGAGTTGTGGGC
1 AAAAAGAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACAGAGTCGTGGGC
45456 TTT
64 -TT
* ** *
45459 AAAAAGGGAAAAAGAGTGCCATGGAGTTGTGG-CTTTGAA---AAGAAG-GTGCCAC-GAAGTCG
1 AAAAA--G---AAG-GTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACAG-AGTCG
*
45518 TGGACTT
59 TGGGCTT
* * * * *
45525 AAAAGGAACAAGGTGCCACGGAGTCGTGGACTTAAAA-GGAACAAG-GTGCCACGGAGTCGTGGA
1 -AAA--AAGAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACAGAGTCGTGGG
45588 CTT
63 CTT
* * ** * *
45591 AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA---AAGAAG-GTGCCAC-GAAGTCATG
1 -AAA--AAGAAG-GTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACAG-AGTCGTG
*
45651 GACTT
61 GGCTT
* * * * *
45656 AAAAGGAACAAGGTGCCACGGGGTTGTGAACTTTAAAAGGGAAAAATAGTGCCACAGAGTTGTGG
1 -AAA--AAGAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACAGAGTCGTGG
45721 GCTT
62 GCTT
* * *
45725 TAAAAG-A-GTGCCACGGAGTTGTGGACTTAGAA-GGAAAAAGAGTGCCACGGAGTCGTGGGCTT
1 AAAAAGAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACAGAGTCGTGGGCTT
*
45787 AAAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAA
1 AAAAAG---AAGGTGCCACGGAGTTGTGGACTTAAA
45823 CGGGTGCCAC
Statistics
Matches: 293, Mismatches: 41, Indels: 56
0.75 0.11 0.14
Matches are distributed among these distances:
62 32 0.11
63 25 0.09
64 42 0.14
65 40 0.14
66 41 0.14
67 66 0.23
68 8 0.03
69 21 0.07
70 2 0.01
71 16 0.05
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (65 bp):
AAAAAGAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACAGAGTCGTGGGCTT
Found at i:45961 original size:27 final size:28
Alignment explanation
Indices: 45855--45974 Score: 109
Period size: 30 Copynumber: 4.2 Consensus size: 28
45845 TTTAGAAGGA
* *
45855 AAAAGAG-TGCCACGGAGTCGTGGACTTT
1 AAAAGAGATGCCACAGAGTTGTGGAC-TT
* * *
45883 GAAGAAAAGATGCCACTGAGTCGTGGACTTT
1 -AA-AAGAGATGCCACAGAGTTGTGGAC-TT
* * *
45914 GGAAAGAGATGCCACTGAGTTGTGGGCTT
1 -AAAAGAGATGCCACAGAGTTGTGGACTT
45943 AAAAGAG-TGCCACAGAGTTGTGGACTT
1 AAAAGAGATGCCACAGAGTTGTGGACTT
45970 AAAAG
1 AAAAG
45975 GAAAAGGATG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
27 23 0.29
28 6 0.08
29 4 0.05
30 25 0.31
31 22 0.28
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.22
Consensus pattern (28 bp):
AAAAGAGATGCCACAGAGTTGTGGACTT
Found at i:45989 original size:60 final size:59
Alignment explanation
Indices: 45760--46066 Score: 196
Period size: 60 Copynumber: 5.0 Consensus size: 59
45750 CTTAGAAGGA
* *
45760 AAAAGAGTGCCACGGAGTCGTGGGCTTAAAAAGAAAAAGG-TGCCA-TGGAGTTGTGGACTT
1 AAAAGAGTGCCAC-GAGTCGTGGACTT-AAAAGGAAAAGGATGCCACT-GAGTTGTGGACTT
* * * * * * *
45820 AAACGGGTGCCACGAAGTTGTGGACTTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGACTTT
1 AAAAGAGTGCCACG-AGTCGTGGAC-TTAAAAGGAAAAGGA-TGCCACTGAGTTGTGGAC-TT
* * *
45883 GAAGAAAAGATGCCACTGAGTCGTGGACTT---TGG-AAAGAGATGCCACTGAGTTGTGGGCTT
1 -AA-AAGAG-TGCCAC-GAGTCGTGGACTTAAAAGGAAAAG-GATGCCACTGAGTTGTGGACTT
* **
45943 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAAAAGGATGCCACTGAGTCATGGACTTT
1 AAAAGAGTGCCAC-GAGTCGTGGACTTAAAAGGAAAAGGATGCCACTGAGTTGTGGAC-TT
* * * ** **
46004 GAAGAAAAAGATGCCATTGAGTCGTGAACTTTGAA-GAAAAGGATGCCACTGAGTCATGGACTT
1 --A-AAAGAG-TGCCA-CGAGTCGTGGACTTAAAAGGAAAAGGATGCCACTGAGTTGTGGACTT
46067 TGAGAAGAGA
Statistics
Matches: 195, Mismatches: 31, Indels: 39
0.74 0.12 0.15
Matches are distributed among these distances:
57 18 0.09
58 4 0.02
59 3 0.02
60 49 0.25
61 26 0.13
62 19 0.10
63 5 0.03
64 33 0.17
65 22 0.11
66 15 0.08
67 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (59 bp):
AAAAGAGTGCCACGAGTCGTGGACTTAAAAGGAAAAGGATGCCACTGAGTTGTGGACTT
Found at i:46017 original size:32 final size:32
Alignment explanation
Indices: 45364--46103 Score: 289
Period size: 33 Copynumber: 23.0 Consensus size: 32
45354 TGAGAAGGAG
* **
45364 AAAGATGCCAC-GAAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACTG-AGTCGTGGACTTTGAA--GAA
* * *
45398 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 AAAGA-TGCCACTGAGTCGTGGACTTTG--AAGAA
* * * *
45433 AAA-AGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
1 AAAGA-TGCCACTGAGTCGTGGACTTT--GAA--GAA
*
45469 AAAGAGTGCCA-TGGAGTTGTGG-CTTTGAA-AA
1 AAAGA-TGCCACT-GAGTCGTGGACTTTGAAGAA
* * **
45500 GAAGGTGCCAC-GAAGTCGTGGACTTAAAAGGAA
1 AAAGATGCCACTG-AGTCGTGGACTTTGAA-GAA
* * * **
45533 CAAGGTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGATGCCACTGAGTCGTGGACTTTGAA-GAA
* * * **
45566 CAAGGTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGATGCCACTGAGTCGTGGACTTTGAA-GAA
* * *
45599 AAAGAGTGCCACGGAGTTGTGGGCTTTGAA-AA
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAAGAA
* * * **
45631 GAAGGTGCCAC-GAAGTCATGGACTTAAAAGGAA
1 AAAGATGCCACTG-AGTCGTGGACTTTGAA-GAA
* * * * * * *
45664 CAAGGTGCCACGGGGTTGTGAACTTTAAAAGGGAA
1 AAAGATGCCACTGAGTCGTGGACTTT-GAA--GAA
* * * *
45699 AAATAGTGCCACAGAGTTGTGGGCTTT--A-AA
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAAGAA
* * * *
45729 AGAG-TGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGATGCCACTGAGTCGTGGACTTTGAA-GAA
* * **
45761 AAAGAGTGCCACGGAGTCGTGGGCTTAAAAAGAA
1 AAAGA-TGCCACTGAGTCGTGGACTT-TGAAGAA
* *
45795 AAAGGTGCCA-TGGAGTTGTGGAC-TT----AA
1 AAAGATGCCACT-GAGTCGTGGACTTTGAAGAA
** * *
45822 ACGGGTGCCAC-GAAGTTGTGGACTTTAGAAGGAA
1 AAAGATGCCACTG-AGTCGTGGACTTT-GAA-GAA
*
45856 AAAGAGTGCCACGGAGTCGTGGACTTTGAAG-A
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAAGAA
45888 AAAGATGCCACTGAGTCGTGGACTTTG--GAA
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGAA
* * *
45918 AGAGATGCCACTGAGTTGTGGGC-TT--A-AA
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGAA
* * * **
45946 AGAG-TGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAGATGCCACTGAGTCGTGGACTTTGAA-GAA
* *
45978 AAGGATGCCACTGAGTCATGGACTTTGAAGAA
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGAA
* *
46010 AAAGATGCCATTGAGTCGTGAACTTTGAAGAA
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGAA
* *
46042 AAGGATGCCACTGAGTCATGGACTTTG-AG-A
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGAA
* *
46072 AGAGATTGCCACTGAGTCGTAGACTTT-AAGAA
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAAGAA
46104 GGTATTTGAA
Statistics
Matches: 568, Mismatches: 84, Indels: 110
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.00
27 36 0.06
28 27 0.05
29 4 0.01
30 44 0.08
31 71 0.12
32 76 0.13
33 123 0.22
34 89 0.16
35 50 0.09
36 29 0.05
37 18 0.03
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (32 bp):
AAAGATGCCACTGAGTCGTGGACTTTGAAGAA
Found at i:46104 original size:31 final size:30
Alignment explanation
Indices: 45855--46103 Score: 236
Period size: 31 Copynumber: 8.1 Consensus size: 30
45845 TTTAGAAGGA
*
45855 AAAAGAGTGCCACGGAGTCGTGGACTTTGAAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTT-AAG
*
45887 AAAAGATGCCACTGAGTCGTGGACTTT-GG
1 AAAAGATGCCACTGAGTCGTGGACTTTAAG
* *
45916 AAAGAGATGCCACTGAGTTGTGGGC-TTAA-
1 AAA-AGATGCCACTGAGTCGTGGACTTTAAG
* * * *
45945 AAGAG-TGCCACAGAGTTGTGGACTTAAAAGG
1 AAAAGATGCCACTGAGTCGTGGACTT-TAA-G
*
45976 AAAAGGATGCCACTGAGTCATGGACTTTGAAG
1 AAAA-GATGCCACTGAGTCGTGGACTTT-AAG
* *
46008 AAAAAGATGCCATTGAGTCGTGAACTTTGAAG
1 -AAAAGATGCCACTGAGTCGTGGACTTT-AAG
* *
46040 AAAAGGATGCCACTGAGTCATGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTAAG
* *
46071 AAGAGATTGCCACTGAGTCGTAGACTTTAAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTAAG
46102 AA
1 AA
46104 GGTATTTGAA
Statistics
Matches: 180, Mismatches: 25, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
27 16 0.09
28 3 0.02
29 10 0.06
30 21 0.12
31 55 0.31
32 52 0.29
33 23 0.13
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.22
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTAAG
Found at i:46234 original size:16 final size:17
Alignment explanation
Indices: 46203--46240 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
46193 GATGCAAATA
* *
46203 ATGATGTTATTGATGTT
1 ATGATGTCATTGATGTC
46220 ATGATGTCA-TGATGTC
1 ATGATGTCATTGATGTC
46236 ATGAT
1 ATGAT
46241 TACAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTCATTGATGTC
Found at i:47107 original size:16 final size:15
Alignment explanation
Indices: 47065--47119 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
47055 CTTTCTTCTT
*
47065 TTTTTTGTTTTTTTG
1 TTTTTTGTTTTTTTC
47080 TTTCTTCT-TTTTTTTCC
1 TTT-TT-TGTTTTTTT-C
47097 TTTTTTGTTTTGTTTC
1 TTTTTTGTTTT-TTTC
47113 TTTTTTG
1 TTTTTTG
47120 GAAAAGAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 4 0.12
16 23 0.68
17 7 0.21
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (15 bp):
TTTTTTGTTTTTTTC
Found at i:47118 original size:24 final size:24
Alignment explanation
Indices: 47056--47106 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
47046 GGGTTTTTCC
**
47056 TTTCTTCTTTTTTTTGTTTTTTTG
1 TTTCTTCTTTTTTTTCCTTTTTTG
47080 TTTCTTCTTTTTTTTCCTTTTTTG
1 TTTCTTCTTTTTTTTCCTTTTTTG
47104 TTT
1 TTT
47107 TGTTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (24 bp):
TTTCTTCTTTTTTTTCCTTTTTTG
Found at i:47382 original size:9 final size:9
Alignment explanation
Indices: 47368--47403 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
47358 TTTTTCTGTG
*
47368 TTTTTTTTT
1 TTTTTTTTA
47377 TGTTTTTTTA
1 T-TTTTTTTA
47387 TTTTTTTTA
1 TTTTTTTTA
47396 TTTTTTTT
1 TTTTTTTT
47404 CATCACTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.06, C:0.00, G:0.03, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:47390 original size:17 final size:17
Alignment explanation
Indices: 47370--47402 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47360 TTTCTGTGTT
*
47370 TTTTTTTTGTTTTTTTA
1 TTTTTTTTATTTTTTTA
47387 TTTTTTTTATTTTTTT
1 TTTTTTTTATTTTTTT
47403 TCATCACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.03, T:0.91
Consensus pattern (17 bp):
TTTTTTTTATTTTTTTA
Found at i:47392 original size:18 final size:18
Alignment explanation
Indices: 47368--47403 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
47358 TTTTTCTGTG
*
47368 TTTTTTTTTTGTTTTTTTA
1 TTTTTTTTAT-TTTTTTTA
47387 TTTTTTTTATTTTTTTT
1 TTTTTTTTATTTTTTTT
47404 CATCACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.06, C:0.00, G:0.03, T:0.92
Consensus pattern (18 bp):
TTTTTTTTATTTTTTTTA
Found at i:54366 original size:52 final size:52
Alignment explanation
Indices: 54218--54346 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
54208 CGAAATATGA
*
54218 AAATTTGCCTGCATGTATCAATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
54270 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
54322 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
54347 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:54460 original size:32 final size:32
Alignment explanation
Indices: 54417--54484 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
54407 GGTAGTAGCT
54417 TACATTATATCGATACAAAACTTATGTATCGA
1 TACATTATATCGATACAAAACTTATGTATCGA
* * * *
54449 TACATTGTATCGATACTACATTTATGTATCGA
1 TACATTATATCGATACAAAACTTATGTATCGA
54481 TACA
1 TACA
54485 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (32 bp):
TACATTATATCGATACAAAACTTATGTATCGA
Found at i:55321 original size:80 final size:79
Alignment explanation
Indices: 55213--55398 Score: 264
Period size: 80 Copynumber: 2.3 Consensus size: 79
55203 CTTTATCGAT
* ** * * *
55213 ATTTTTATTTCTAAAATATTGATTTTCCACCATCGAGGATACTCTAACCCCGTTATTTTTGAGGG
1 ATTTTTATTTCCAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCATTATTTCTGAGGG
55278 GATACTCCAACCCC
66 GATACTCCAACCCC
* *
55292 GATTTTTATTTCCAAAATATCAATTTTCCACCATCGGGGATATTCCAACCCCATTATTTCTGAGG
1 -ATTTTTATTTCCAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCATTATTTCTGAGG
*
55357 GGATACTCCAACCTC
65 GGATACTCCAACCCC
*
55372 ATTTTTATCTCCAAAATATCAAATTTT
1 ATTTTTATTTCCAAAATATC-AATTTT
55399 TTATTGGGGA
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 19 0.20
80 76 0.80
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (79 bp):
ATTTTTATTTCCAAAATATCAATTTTCCACCATCGAGGATACTCCAACCCCATTATTTCTGAGGG
GATACTCCAACCCC
Found at i:59360 original size:11 final size:11
Alignment explanation
Indices: 59311--59363 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
59301 TATTCTTGTA
59311 TTTTTATTATT
1 TTTTTATTATT
*
59322 ATTTTATTTATT
1 TTTTTA-TTATT
*
59334 TTTTTGTTATCCT
1 TTTTTATTAT--T
59347 TTTTTATTATT
1 TTTTTATTATT
59358 TTTTTA
1 TTTTTA
59364 ATTTTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 16 0.46
12 9 0.26
13 10 0.29
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:60015 original size:85 final size:84
Alignment explanation
Indices: 59908--60632 Score: 532
Period size: 85 Copynumber: 8.6 Consensus size: 84
59898 GGGCCAACGG
* * * * * *
59908 GCAGACAAAAGGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTTGAGGGTAAGAAACTC
1 GCAGACTAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGA-GGTAAGGAAGTC
* * *
59973 TCCAAGGCCAAAGTCAACAA
65 TCCAGGGTCAAAGTCGACAA
* * * * *
59993 GCAGACTTAGGGTAAAAAAGTCTCCAAGGTCAAAGCCAACAGACAGACTTGGGGGTAAGAAAGTC
1 GCAGACTAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT-GAGGTAAGGAAGTC
** *
60058 TCCAAAGTCAAACT-GACAA
65 TCCAGGGTCAAAGTCGACAA
* * *** * * * * *
60077 GTAGACT-TGAGGTAAGGCAGTCTCCAAGGTTAAAGCCGATAGGCAAAC-TAAGGGTAAGAAAGT
1 GCAGACTAAG-GGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGA-GGTAAGGAAGT
*
60140 CTCTAGGGTCAAA-TCTGACAA
64 CTCCAGGGTCAAAGTC-GACAA
* * * * ** * * * *
60161 GCAAACT-TGAGATGAAGTAGTCTCCAAAGTCAAAGCCGACAGGCTA-ACTTGAGATGAGGTAGT
1 GCAGACTAAG-GGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGC-AGACTTGAGGTAAGGAAGT
* * * * *
60224 CTCTAGGGTCAAAGCCAATAG
64 CTCCAGGGTCAAAGTCGACAA
* * * *
60245 GCAAACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGCTGACAGGCAGACTTGAGGTAAGGCAGTC
1 GCAGACT-AAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGGAAGTC
* * *
60310 TCCAGGGTCAAAGCCGATAG
65 TCCAGGGTCAAAGTCGACAA
* * * * *
60330 GCAGACTGAAGGGTAAGAAAA-TCTCCAAGGTCAAAGCTGACAAGCGGACTTGAGGTGAGGCAGT
1 GCAGACT-AAGGGTAA-AAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGGAAGT
*
60394 CTCCAGGGTCAAAGTCGGCAA
64 CTCCAGGGTCAAAGTCGACAA
* * ** * * *
60415 GCAGAATGAGGGTAAAAAAGTCTTTAAGGTCAAAGCCAACAAGCAGACTTGAGGTAAGGCAGTCT
1 GCAGACTAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGGAAGTCT
* * *
60480 CCAGTGTCAAAGCCAACAA
66 CCAGGGTCAAAGTCGACAA
* * * ** * * **
60499 GTAGACTAAAGGGTAAGAAAGTCTCCAGGGTCAAAATCGACAGGCAGACTTAAGGTGAGGCTGTC
1 GCAGACT-AAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGGAAGTC
** *
60564 TTTAGAGG-CAAAGCCGAC-A
65 TCCAG-GGTCAAAGTCGACAA
* * * *
60583 GACAGACTGAGGGTAAAAAAGTCTCTAAGGTTAAAGTCGACAGGCAGACT
1 G-CAGACTAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACT
60633 GGGGATAAAA
Statistics
Matches: 519, Mismatches: 105, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
82 1 0.00
83 27 0.05
84 216 0.42
85 269 0.52
86 6 0.01
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (84 bp):
GCAGACTAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGGAAGTCT
CCAGGGTCAAAGTCGACAA
Found at i:60018 original size:42 final size:43
Alignment explanation
Indices: 59918--60533 Score: 346
Period size: 42 Copynumber: 14.6 Consensus size: 43
59908 GCAGACAAAA
* * * *
59918 GGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTTGAG
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
* * * *
59961 GGTAAGAAACTCTCCAAGGCCAAAGTCAACAAGCAGACTT-AG
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
*
60003 GGTAAAAAAGTCTCCAAGGTCAAAGCCAAC-AGACAGACTTGGG
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAG-CAGACTTGAG
* * ** *
60046 GGTAAGAAAGTCTCCAAAGTCAAA-CTGACAAGTAGACTTGA-
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
*** * * * * * *
60087 GGTAAGGCAGTCTCCAAGGTTAAAGCCGATAGGCAAAC-TAAG
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
* * * * ** *
60129 GGTAAGAAAGTCTCTAGGGTCAAATCTGACAAGCAAACTTGA-
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
* * ** * * *
60171 GATGAAGTAGTCTCCAAAGTCAAAGCCGACAGGCTA-ACTTGA-
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGC-AGACTTGAG
* * *** * * * * *
60213 GATGAGGTAGTCTCTAGGGTCAAAGCCAATAGGCAAAC-TGAAG
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTG-AG
* ** *
60256 GGTAAGAAAGTCTCCAAGGTCAAAGCTGACAGGCAGACTTGA-
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
*** * * * *
60298 GGTAAGGCAGTCTCCAGGGTCAAAGCCGATAGGCAGAC-TGAAG
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTG-AG
** *
60341 GGTAAGAAAA-TCTCCAAGGTCAAAGCTGACAAGCGGACTTGA-
1 GGTAA-AAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
* *** * * ** *
60383 GGTGAGGCAGTCTCCAGGGTCAAAGTCGGCAAGCAGA-ATGAG
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
**
60425 GGTAAAAAAGTCTTTAAGGTCAAAGCCAACAAGCAGACTTGA-
1 GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
*** * **
60467 GGTAAGGCAGTCTCC-AGTGTCAAAGCCAACAAGTAGACTAAAG
1 GGTAAAAAAGTCTCCAAG-GTCAAAGCCAACAAGCAGACTTGAG
* *
60510 GGTAAGAAAGTCTCCAGGGTCAAA
1 GGTAAAAAAGTCTCCAAGGTCAAA
60534 ATCGACAGGC
Statistics
Matches: 441, Mismatches: 111, Indels: 42
0.74 0.19 0.07
Matches are distributed among these distances:
41 35 0.08
42 260 0.59
43 140 0.32
44 6 0.01
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (43 bp):
GGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGAG
Found at i:60437 original size:169 final size:169
Alignment explanation
Indices: 59918--60632 Score: 529
Period size: 169 Copynumber: 4.2 Consensus size: 169
59908 GCAGACAAAA
* * * * ** * * *
59918 GGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTTGAGGGTAAGAAACTCTCCAAGGCCA
1 GGTAAAAAAGTCTCTAAGGTCAAAGCTGACAGGCAGACTTGA-GGTAAGGCAGTCTCCAGGGTCA
* * ** * *
59983 AAGTCAACAAGCAGACT-TAGGGTAA-AAAAGTCTCCAAGGTCAAAGCCAACAGACAGACTTGGG
65 AAGCCAACAAGCAGACTAAAGGGTAAGAAAA-TCTCCAAGGTCAAAGCTGACAGGCAGACTT-GA
* ** * ** * * *
60046 GGTAAGAAAGTCTCCAAAGTCAAA-CTGACAAGTAGACTTGA-
128 GGTGAGGCAGTCTCTAGGGTCAAAGCCGACAAGCAGA-ATGAG
*** * * * * * * ** *
60087 GGTAAGGCAGTCTCCAAGGTTAAAGCCGATAGGCAAAC-TAAGGGTAAGAAAGTCTCTAGGGTCA
1 GGTAAAAAAGTCTCTAAGGTCAAAGCTGACAGGCAGACTTGA-GGTAAGGCAGTCTCCAGGGTCA
* ** * ** * * * * *
60151 AATCTGACAAGCAAACTTGA-GATGAAG-TAGTCTCCAAAGTCAAAGCCGACAGGCTA-ACTTGA
65 AAGCCAACAAGCAGACTAAAGGGT-AAGAAAATCTCCAAGGTCAAAGCTGACAGGC-AGACTTGA
* * * * *
60213 GATGAGGTAGTCTCTAGGGTCAAAGCCAATAGGCA-AACTGAAG
128 GGTGAGGCAGTCTCTAGGGTCAAAGCCGACAAGCAGAA-TG-AG
* *
60256 GGTAAGAAAGTCTCCAAGGTCAAAGCTGACAGGCAGACTTGAGGTAAGGCAGTCTCCAGGGTCAA
1 GGTAAAAAAGTCTCTAAGGTCAAAGCTGACAGGCAGACTTGAGGTAAGGCAGTCTCCAGGGTCAA
* * * * * *
60321 AGCCGATAGGCAGACTGAAGGGTAAGAAAATCTCCAAGGTCAAAGCTGACAAGCGGACTTGAGGT
66 AGCCAACAAGCAGACTAAAGGGTAAGAAAATCTCCAAGGTCAAAGCTGACAGGCAGACTTGAGGT
* * *
60386 GAGGCAGTCTCCAGGGTCAAAGTCGGCAAGCAGAATGAG
131 GAGGCAGTCTCTAGGGTCAAAGCCGACAAGCAGAATGAG
* ** * *
60425 GGTAAAAAAGTCTTTAAGGTCAAAGCCAACAAGCAGACTTGAGGTAAGGCAGTCTCCAGTGTCAA
1 GGTAAAAAAGTCTCTAAGGTCAAAGCTGACAGGCAGACTTGAGGTAAGGCAGTCTCCAGGGTCAA
* * * * *
60490 AGCCAACAAGTAGACTAAAGGGTAAGAAAGTCTCCAGGGTCAAA-ATCGACAGGCAGACTTAAGG
66 AGCCAACAAGCAGACTAAAGGGTAAGAAAATCTCCAAGGTCAAAGCT-GACAGGCAGACTTGAGG
* * *
60554 TGAGGCTGTCTTTAGAGG-CAAAGCCGAC-AGACAGACTGAG
130 TGAGGCAGTCTCTAG-GGTCAAAGCCGACAAG-CAGAATGAG
*
60594 GGTAAAAAAGTCTCTAAGGTTAAAG-TCGACAGGCAGACT
1 GGTAAAAAAGTCTCTAAGGTCAAAGCT-GACAGGCAGACT
60633 GGGGATAAAA
Statistics
Matches: 429, Mismatches: 100, Indels: 34
0.76 0.18 0.06
Matches are distributed among these distances:
167 21 0.05
168 69 0.16
169 274 0.64
170 63 0.15
171 2 0.00
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (169 bp):
GGTAAAAAAGTCTCTAAGGTCAAAGCTGACAGGCAGACTTGAGGTAAGGCAGTCTCCAGGGTCAA
AGCCAACAAGCAGACTAAAGGGTAAGAAAATCTCCAAGGTCAAAGCTGACAGGCAGACTTGAGGT
GAGGCAGTCTCTAGGGTCAAAGCCGACAAGCAGAATGAG
Found at i:60912 original size:44 final size:44
Alignment explanation
Indices: 60744--60901 Score: 205
Period size: 44 Copynumber: 3.6 Consensus size: 44
60734 GTTAGCATAG
* *
60744 TTTGACTAGGGTGGTAACCATACGTCAAA-CAGAA-AAGAAGAGGA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAGAA-A-AA
* * *
60788 TTTGAC-GGGGTGGTAACCAGATGTCAAATCAGAATGAGAAAAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAGAAAAA
* * *
60831 TCTAACTAGGGTGGTAACCACACGTCAAATCAGAATGAGAAAAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAGAAAAA
60875 TTTGACTAGGGTGGTAACCATACGTCA
1 TTTGACTAGGGTGGTAACCATACGTCA
60902 CGCTGAAATG
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
43 24 0.24
44 70 0.71
45 4 0.04
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (44 bp):
TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAGAAAAA
Found at i:63980 original size:14 final size:15
Alignment explanation
Indices: 63958--63991 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
63948 GATATGAAAT
*
63958 TTTTTTATTTTTTA-
1 TTTTCTATTTTTTAC
63972 TTTTCTATTTTTTAC
1 TTTTCTATTTTTTAC
63987 TTTTC
1 TTTTC
63992 ATACCCCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTATTTTTTAC
Found at i:65709 original size:33 final size:34
Alignment explanation
Indices: 65662--65745 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 34
65652 ATTGCAGTAG
* * *
65662 TTTCTATTGCATTCATTTGC-CT-TTGAATTGCTA
1 TTTCAATTGCATTCATTT-CTCTCTTGAACTGATA
* *
65695 TTTCGATTGCATTCA-TTCTCTCTTGAACTGATG
1 TTTCAATTGCATTCATTTCTCTCTTGAACTGATA
65728 TTTCAATTGCATTCATTT
1 TTTCAATTGCATTCATTT
65746 ACAGTAGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
31 1 0.02
32 4 0.09
33 36 0.84
34 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (34 bp):
TTTCAATTGCATTCATTTCTCTCTTGAACTGATA
Found at i:66171 original size:29 final size:27
Alignment explanation
Indices: 66135--66225 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 27
66125 GAAACGAAAC
66135 GCATGAAATGAACATTACGTGAAATGCAT
1 GCATGAAATGAA-ATTAC-TGAAATGCAT
*
66164 GCATGAAATGTAATGTA-TG-AA---AT
1 GCATGAAATGAAAT-TACTGAAATGCAT
66187 GCATGAAATGAAAATTACATGAAATGCAT
1 GCATGAAATG-AAATTAC-TGAAATGCAT
*
66216 GTATGAAATG
1 GCATGAAATG
66226 TAATGCATGA
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
23 14 0.27
24 3 0.06
25 2 0.04
26 4 0.08
27 2 0.04
28 2 0.04
29 24 0.47
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (27 bp):
GCATGAAATGAAATTACTGAAATGCAT
Found at i:66197 original size:14 final size:14
Alignment explanation
Indices: 66105--66237 Score: 66
Period size: 14 Copynumber: 9.7 Consensus size: 14
66095 GAAAGAAAAC
66105 ATGCATGAAAT-ATA
1 ATGCATGAAATGA-A
* *
66119 AAGCATGAAACGAA
1 ATGCATGAAATGAA
*
66133 ACGCATGAAATGAA
1 ATGCATGAAATGAA
* * *
66147 CATTACGTGAAATG-C
1 -A-TGCATGAAATGAA
*
66162 ATGCATGAAATGTA
1 ATGCATGAAATGAA
66176 ATG--T---ATGAA
1 ATGCATGAAATGAA
66185 ATGCATGAAATGAAA
1 ATGCATGAAATG-AA
* *
66200 ATTACATGAAATG-C
1 A-TGCATGAAATGAA
* *
66214 ATGTATGAAATGTA
1 ATGCATGAAATGAA
66228 ATGCATGAAA
1 ATGCATGAAA
66238 GTAAAAGTAT
Statistics
Matches: 89, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
9 7 0.08
11 1 0.01
12 1 0.01
13 18 0.20
14 39 0.44
15 5 0.06
16 18 0.20
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.24
Consensus pattern (14 bp):
ATGCATGAAATGAA
Found at i:66212 original size:52 final size:52
Alignment explanation
Indices: 66130--66237 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
66120 AGCATGAAAC
* * *
66130 GAAACGCATGAAATGAACATTACGTGAAATGCATGCATGAAATGTAATGTAT
1 GAAACGCATGAAATGAAAATTACATGAAATGCATGCATGAAATGTAATGCAT
* *
66182 GAAATGCATGAAATGAAAATTACATGAAATGCATGTATGAAATGTAATGCAT
1 GAAACGCATGAAATGAAAATTACATGAAATGCATGCATGAAATGTAATGCAT
66234 GAAA
1 GAAA
66238 GTAAAAGTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (52 bp):
GAAACGCATGAAATGAAAATTACATGAAATGCATGCATGAAATGTAATGCAT
Found at i:66474 original size:3 final size:3
Alignment explanation
Indices: 66466--66509 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
66456 ATTAATTAAT
*
66466 TTA TTA TTA TTA TT- TTA TTA TTA TTA -TA TTA TTA ATA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
66510 TTTTTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:66482 original size:14 final size:14
Alignment explanation
Indices: 66460--66519 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 14
66450 TTGTTAATTA
*
66460 ATTAATTTATTATT
1 ATTATTTTATTATT
66474 ATTATTTTATTATT
1 ATTATTTTATTATT
66488 ATTA---TATTATT
1 ATTATTTTATTATT
*
66499 AATATTTTATT-TT
1 ATTATTTTATTATT
*
66512 TTTATTTT
1 ATTATTTT
66520 TTCATGTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 10 0.26
13 8 0.21
14 21 0.54
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTATTTTATTATT
Found at i:66483 original size:11 final size:11
Alignment explanation
Indices: 66469--66517 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
66459 AATTAATTTA
66469 TTATTATTATT
1 TTATTATTATT
66480 TTATTATTATT
1 TTATTATTATT
* *
66491 ATATTATTAATA
1 TTATTATT-ATT
*
66503 TT-TTATTTTT
1 TTATTATTATT
66513 TTATT
1 TTATT
66518 TTTTCATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 3 0.10
11 25 0.81
12 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTATT
Found at i:67310 original size:80 final size:80
Alignment explanation
Indices: 67051--67593 Score: 386
Period size: 80 Copynumber: 6.9 Consensus size: 80
67041 CATCACGACA
* * ** * *
67051 GTGGGGTTGGAGTATCCCCAAAGATGAAAAATTCAACATTTTGAAAGTAAAAAACAAGGTTAGAG
1 GTGGGATTGGAGTATCCCCAAAGATGAAAAATTTAATGTTTTGAAAGT-AAAAATAGGGTTAGAG
* *
67116 TACCCCCTCAAAGATG
65 TACCCTCTCAGAGATG
* * ** * *
67132 GTGGGGTTGGAGTAT-CCCAGAGATGAAAAATTTGGTGTTTTAAAAGTAAAAAAAGGGTT-GAAG
1 GTGGGATTGGAGTATCCCCAAAGATGAAAAATTTAATGTTTTGAAAGTAAAAATAGGGTTAG-AG
**
67195 TATCCC-CTC-GAAGAAA
65 TA-CCCTCTCAG-AGATG
* * *
67211 GT---A---GAGTATCCCCAAAGATGAAAATTTTAACGTTTTGAAAGTAAAAATGGGGTTAGAGT
1 GTGGGATTGGAGTATCCCCAAAGATGAAAAATTTAATGTTTTGAAAGTAAAAATAGGGTTAGAGT
*
67270 ACCCTCTCAGAGATT
66 ACCCTCTCAGAGATG
* * * * * * *
67285 GTGGGATTGAAGTATCCTCAAAGATGAAAATTTTGATATTTT-AGAAGTAAAAA-CGGGTTGGAG
1 GTGGGATTGGAGTATCCCCAAAGATGAAAAATTTAATGTTTTGA-AAGTAAAAATAGGGTTAGAG
*
67348 TATCCCT-TCTGAGATG
65 TA-CCCTCTCAGAGATG
* * *
67364 GTGGCAGTTGGAGTATCCCCAAA-AGTGAAAAATTTAATGTTTTGGAAGTAAAAAT-GAGGTTAA
1 GTGGGA-TTGGAGTATCCCCAAAGA-TGAAAAATTTAATGTTTTGAAAGTAAAAATAG-GGTTAG
* * *
67427 AGTATCCTTTTAGAGATG
63 AGTACCCTCTCAGAGATG
* * * * * *
67445 GTGGGTTTAGAGTATCCTCAAAGATGAAAATTTTAGTGTTTTGGAAGTAAAAATAGGGTT-GAAG
1 GTGGGATTGGAGTATCCCCAAAGATGAAAAATTTAATGTTTTGAAAGTAAAAATAGGGTTAG-AG
*
67509 TA-TCTCCTC-GAAGATG
65 TACCCT-CTCAG-AGATG
* * * * * * * * *
67525 GTTAGG-TTAGATTATCCCCAAAAATGAAAAATTTGACGTTTTAAAAGTAAAAATAGAGTTGGAG
1 G-TGGGATTGGAGTATCCCCAAAGATGAAAAATTTAATGTTTTGAAAGTAAAAATAGGGTTAGAG
67589 TACCC
65 TACCC
67594 CTTTTGACAT
Statistics
Matches: 367, Mismatches: 66, Indels: 58
0.75 0.13 0.12
Matches are distributed among these distances:
73 9 0.02
74 48 0.13
75 2 0.01
77 1 0.00
78 1 0.00
79 49 0.13
80 216 0.59
81 41 0.11
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (80 bp):
GTGGGATTGGAGTATCCCCAAAGATGAAAAATTTAATGTTTTGAAAGTAAAAATAGGGTTAGAGT
ACCCTCTCAGAGATG
Found at i:67461 original size:160 final size:156
Alignment explanation
Indices: 67060--67593 Score: 555
Period size: 160 Copynumber: 3.4 Consensus size: 156
67050 AGTGGGGTTG
* * ** *
67060 GAGTATCCCCAAAGATGAAAAATTCAACATTTTGAAAGTAAAAAACAAGGTTAGAGTACCCCCTC
1 GAGTATCCCCAAAGATGAAAAATTTAACGTTTTGAAAGT-AAAAATGAGGTTAGAGTACCCTCTC
* * * * * *
67125 AAAGATGGTGGGGTTGGAGTATCC-CAGAGATGAAAAATTTGGTGTTTTAAAAGTAAAAAAAGGG
65 AGAGATGGTGGGATT-GAGTATCCTCAAAGATGAAAATTTTGATGTTTTAGAAGT-AAAAAAGGG
*
67189 TTGAAGTATCCCCTCGA-A--G-AAAG-TA
128 TTGAAGTAT-CCCTCGAGATGGTGAAGTTA
* *
67214 GAGTATCCCCAAAGATGAAAATTTTAACGTTTTGAAAGTAAAAATGGGGTTAGAGTACCCTCTCA
1 GAGTATCCCCAAAGATGAAAAATTTAACGTTTTGAAAGTAAAAATGAGGTTAGAGTACCCTCTCA
* * *
67279 GAGATTGTGGGATTGAAGTATCCTCAAAGATGAAAATTTTGATATTTTAGAAGTAAAAACGGGTT
66 GAGATGGTGGGATTG-AGTATCCTCAAAGATGAAAATTTTGATGTTTTAGAAGTAAAAAAGGGTT
* * *
67344 GGAGTATCCCTTCTGAGATGGTGGCAGTTG
130 GAAGTATCCC-TC-GAGATGGT-GAAGTTA
* * * * * *
67374 GAGTATCCCCAAA-AGTGAAAAATTTAATGTTTTGGAAGTAAAAATGAGGTTAAAGTATCCTTTT
1 GAGTATCCCCAAAGA-TGAAAAATTTAACGTTTTGAAAGTAAAAATGAGGTTAGAGTACCCTCTC
* *
67438 AGAGATGGTGGGTTTAGAGTATCCTCAAAGATGAAAATTTT-AGTGTTTTGGAAGTAAAAATAGG
65 AGAGATGGTGGGATT-GAGTATCCTCAAAGATGAAAATTTTGA-TGTTTTAGAAGTAAAAA-AGG
* *
67502 GTTGAAGTATCTCCTCGAAGATGGTTAGGTTA
127 GTTGAAGTATC-CCTCG-AGATGGTGAAGTTA
* * * * *
67534 GATTATCCCCAAAAATGAAAAATTTGACGTTTTAAAAGTAAAAAT-AGAGTTGGAGTACCC
1 GAGTATCCCCAAAGATGAAAAATTTAACGTTTTGAAAGTAAAAATGAG-GTTAGAGTACCC
67594 CTTTTGACAT
Statistics
Matches: 316, Mismatches: 46, Indels: 30
0.81 0.12 0.08
Matches are distributed among these distances:
152 4 0.01
153 58 0.18
154 63 0.20
155 1 0.00
157 1 0.00
159 6 0.02
160 158 0.50
161 23 0.07
162 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (156 bp):
GAGTATCCCCAAAGATGAAAAATTTAACGTTTTGAAAGTAAAAATGAGGTTAGAGTACCCTCTCA
GAGATGGTGGGATTGAGTATCCTCAAAGATGAAAATTTTGATGTTTTAGAAGTAAAAAAGGGTTG
AAGTATCCCTCGAGATGGTGAAGTTA
Found at i:70452 original size:13 final size:13
Alignment explanation
Indices: 70434--70458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70424 ATATTACTTG
70434 GTATCGATACATT
1 GTATCGATACATT
70447 GTATCGATACAT
1 GTATCGATACAT
70459 GTTCTTTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:70559 original size:20 final size:20
Alignment explanation
Indices: 70534--70571 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
70524 TGTGCATGAT
*
70534 TGAATTCTATTGATACATGG
1 TGAATTCTATCGATACATGG
*
70554 TGAATTGTATCGATACAT
1 TGAATTCTATCGATACAT
70572 TGAGCCCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (20 bp):
TGAATTCTATCGATACATGG
Found at i:70623 original size:20 final size:20
Alignment explanation
Indices: 70595--70634 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
70585 TAGAATTTCA
*
70595 TATGCATTGTATCGATACAT
1 TATGAATTGTATCGATACAT
70615 TATGAATTGTATCGATACAT
1 TATGAATTGTATCGATACAT
70635 AGGAGTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (20 bp):
TATGAATTGTATCGATACAT
Found at i:70646 original size:20 final size:20
Alignment explanation
Indices: 70600--70638 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
70590 TTTCATATGC
*
70600 ATTGTATCGATACATTATGA
1 ATTGTATCGATACATTAGGA
70620 ATTGTATCGATACA-TAGGA
1 ATTGTATCGATACATTAGGA
70639 GTGTGTATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATTAGGA
Found at i:75370 original size:20 final size:21
Alignment explanation
Indices: 75345--75400 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
75335 CAAAACCCAG
75345 AATGTATCGATACAA-TG-AGA
1 AATGTATCGATACAATTGTA-A
75365 AATGTATCGATACAATTGTAA
1 AATGTATCGATACAATTGTAA
75386 ACATGTATCGATACA
1 A-ATGTATCGATACA
75401 TTTTCTAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.45
21 4 0.12
22 14 0.42
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACAATTGTAA
Found at i:75413 original size:20 final size:20
Alignment explanation
Indices: 75345--75423 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
75335 CAAAACCCAG
* *
75345 AATGTATCGATACA-ATGAGA
1 AATGTATCGATACATTTTA-A
*
75365 AATGTATCGATACAATTGTAA
1 AATGTATCGATAC-ATTTTAA
**
75386 ACATGTATCGATACATTTTCT
1 A-ATGTATCGATACATTTTAA
*
75407 AATGTATAGATACATTT
1 AATGTATCGATACATTT
75424 CCTTGACAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 28 0.57
21 8 0.16
22 13 0.27
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTTTAA
Found at i:76900 original size:11 final size:11
Alignment explanation
Indices: 76884--76925 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
76874 GAAAAAACCC
76884 AAAATTAAAAG
1 AAAATTAAAAG
76895 AAAATTAAAAG
1 AAAATTAAAAG
*
76906 AAAATTAAAATT
1 AAAATTAAAA-G
76918 AAAATTAA
1 AAAATTAA
76926 TAATCATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 21 0.72
12 8 0.28
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (11 bp):
AAAATTAAAAG
Found at i:76904 original size:6 final size:6
Alignment explanation
Indices: 76884--76925 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
76874 GAAAAAACCC
* *
76884 AAAATT AAAA-G AAAATT AAAA-G AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AA
76926 TAATCATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (6 bp):
AAAATT
Found at i:80653 original size:21 final size:21
Alignment explanation
Indices: 80628--80687 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
80618 TTATATTTGA
80628 ATAAATTATTAATGTA-TAAATT
1 ATAAA-TATTAAT-TATTAAATT
80650 -TAAATATT-ATTATTAAATT
1 ATAAATATTAATTATTAAATT
*
80669 ATAAAATATTATTTATTAA
1 AT-AAATATTAATTATTAA
80688 TAAATAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.06
19 8 0.24
20 5 0.15
21 11 0.33
22 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAAATATTAATTATTAAATT
Found at i:80691 original size:25 final size:22
Alignment explanation
Indices: 80656--80707 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
80646 AATTTAAATA
*
80656 TTATTATTAAATTATAAAATATTAT
1 TTATTAATAAA-TA-AAAATATT-T
*
80681 TTATTAATAAATAAAATTATTT
1 TTATTAATAAATAAAAATATTT
80703 TTATT
1 TTATT
80708 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 7 0.28
24 2 0.08
25 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATTAATAAATAAAAATATTT
Found at i:80694 original size:22 final size:22
Alignment explanation
Indices: 80651--80707 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
80641 GTATAAATTT
*
80651 AAATATTA-TTATTAAATTATA
1 AAATATTATTTATTAAATAATA
80672 AAATATTATTTATT-AATAAATA
1 AAATATTATTTATTAAAT-AATA
80694 AAATTATT-TTTATT
1 AAA-TATTATTTATT
80708 TATTTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.34
22 17 0.53
23 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATATTATTTATTAAATAATA
Done.