Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 86 of 131
Found at i:28790666 original size:133 final size:134
Alignment explanation
Indices: 28790503--28790773 Score: 526
Period size: 133 Copynumber: 2.0 Consensus size: 134
28790493 TTATATTTGT
*
28790503 AACTATTTAATTTTTAATAATATATTAATAATAAAAATTAGATAATTTTATCTAAATATAAAATT
1 AACTATTTAATTTTTAATAATATATTAATAATAAAAATAAGATAATTTTATCTAAATATAAAATT
28790568 CTGATTTTAATCTATTCCGTATCATTAATCTATCAATATAATGCTGTTTTATTCCATTTGTGCTG
66 CTGATTTTAATCTATTCCGTATCATTAATCTATCAATATAATGCTGTTTTATTCCATTTGTGCTG
28790633 CTCA
131 CTCA
28790637 AACTATTTAA-TTTTAATAATATATTAATAATAAAAATAAGATAATTTTATCTAAATATAAAATT
1 AACTATTTAATTTTTAATAATATATTAATAATAAAAATAAGATAATTTTATCTAAATATAAAATT
28790701 CTGATTTTAATCTATTCCGTATCATTAATCTATCAATATAATGCTGTTTTATTCCATTTGTGCTG
66 CTGATTTTAATCTATTCCGTATCATTAATCTATCAATATAATGCTGTTTTATTCCATTTGTGCTG
28790766 CTCA
131 CTCA
28790770 AACT
1 AACT
28790774 TCTTACCTCC
Statistics
Matches: 136, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
133 126 0.93
134 10 0.07
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (134 bp):
AACTATTTAATTTTTAATAATATATTAATAATAAAAATAAGATAATTTTATCTAAATATAAAATT
CTGATTTTAATCTATTCCGTATCATTAATCTATCAATATAATGCTGTTTTATTCCATTTGTGCTG
CTCA
Found at i:28794060 original size:24 final size:24
Alignment explanation
Indices: 28794045--28794096 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
28794035 AATTGATGTC
*
28794045 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
28794069 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
28794093 AAAT
1 AAAT
28794097 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:28802321 original size:20 final size:20
Alignment explanation
Indices: 28802183--28802322 Score: 120
Period size: 20 Copynumber: 7.0 Consensus size: 20
28802173 AATGCATAAC
* *
28802183 AGGGGCACTGAAGTGCAGAT
1 AGGGGCACCGAAGTGCAAAT
* *
28802203 AGGGGCA-CAAATGTGCAAAC
1 AGGGGCACCGAA-GTGCAAAT
* *
28802223 AGGGGCACCGTAGTGCGAAT
1 AGGGGCACCGAAGTGCAAAT
* *
28802243 AGGGGCACCGTAGTGCGAAT
1 AGGGGCACCGAAGTGCAAAT
* * * * ***
28802263 AGAGACACTGAAGTGTATGC
1 AGGGGCACCGAAGTGCAAAT
*
28802283 AGGGGCACCGAAGTACAAAT
1 AGGGGCACCGAAGTGCAAAT
28802303 AGGGGCACCGAAGTGCAAAT
1 AGGGGCACCGAAGTGCAAAT
28802323 CCCGTACAAG
Statistics
Matches: 92, Mismatches: 26, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
19 2 0.02
20 88 0.96
21 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.14
Consensus pattern (20 bp):
AGGGGCACCGAAGTGCAAAT
Found at i:28809144 original size:19 final size:18
Alignment explanation
Indices: 28809120--28809155 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28809110 GCAAATGAAT
*
28809120 CATTTCTCATTTTCATTTC
1 CATTTCT-ATTTCCATTTC
28809139 CATTTCTATTTCCATTT
1 CATTTCTATTTCCATTT
28809156 TGAGAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (18 bp):
CATTTCTATTTCCATTTC
Found at i:28809149 original size:12 final size:12
Alignment explanation
Indices: 28809119--28809156 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
28809109 TGCAAATGAA
28809119 TCATTTCTCATTT
1 TCATTTC-CATTT
28809132 TCATTTCCA-TT
1 TCATTTCCATTT
28809143 TCTATTTCCATTT
1 TC-ATTTCCATTT
28809156 T
1 T
28809157 GAGAAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 9 0.39
13 10 0.43
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:28811372 original size:28 final size:29
Alignment explanation
Indices: 28811308--28811385 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 29
28811298 ATTATTTTAG
* *
28811308 TTTTATTATTAATATTGTTTAATCTATTGTA
1 TTTTATTATT-ATATT-TTTAATATATTGAA
* *
28811339 TATTATTATTATATTTTTTATATATT-AA
1 TTTTATTATTATATTTTTAATATATTGAA
28811367 TTTTA-TATGTATTATTTTT
1 TTTTATTAT-TA-TATTTTT
28811386 CTAAGCTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 3 0.08
28 7 0.17
29 16 0.40
30 5 0.12
31 9 0.22
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (29 bp):
TTTTATTATTATATTTTTAATATATTGAA
Found at i:28811381 original size:22 final size:22
Alignment explanation
Indices: 28811332--28811381 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28811322 TTGTTTAATC
* *
28811332 TATTGTATATTATTATTATATT
1 TATTATATATTATTATTATATG
*
28811354 TTTTATATATTAATT-TTATATG
1 TATTATATATT-ATTATTATATG
28811376 TATTAT
1 TATTAT
28811382 TTTTCTAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TATTATATATTATTATTATATG
Found at i:28819309 original size:37 final size:37
Alignment explanation
Indices: 28819259--28819361 Score: 152
Period size: 37 Copynumber: 2.8 Consensus size: 37
28819249 CAATCACTCG
* *
28819259 TAAGAGTTAATCCACCCGATAACACGTCAGATGCTCA
1 TAAGAGCTAATCCACCCGATAACACGCCAGATGCTCA
28819296 TAAGAGCTAATCCACCCGATAACACGCCAGATGCTCA
1 TAAGAGCTAATCCACCCGATAACACGCCAGATGCTCA
* * * *
28819333 TAAGAGCTAGTCCAACCAAAAACACGCCA
1 TAAGAGCTAATCCACCCGATAACACGCCA
28819362 AAACAGGGAT
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:0.38, C:0.30, G:0.16, T:0.17
Consensus pattern (37 bp):
TAAGAGCTAATCCACCCGATAACACGCCAGATGCTCA
Found at i:28827229 original size:27 final size:27
Alignment explanation
Indices: 28827180--28827512 Score: 382
Period size: 27 Copynumber: 12.3 Consensus size: 27
28827170 CCTATCAGTC
*
28827180 ATTTTACCCTATCAAGGGTATTTCGGTA
1 ATTTTACCC-ATCGAGGGTATTTCGGTA
* *
28827208 ATTTTACCCATTGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
28827235 ATTTTACCCATCGAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
**
28827262 ATTTTACCCATC-AGGGGTATTTCAATA
1 ATTTTACCCATCGA-GGGTATTTCGGTA
* **
28827289 ATTTTACCCATCAAGGGTATTTTAGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* * ** *
28827316 ATTTTACCCATCAAAGGTATTTTAGCA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* * * *
28827343 ATTTTACTCGTGGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
**
28827370 ATTTTACCCATCGAGGGTATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
28827397 ATTTTACCCAT-GAAAGGTATTTCGGTA
1 ATTTTACCCATCG-AGGGTATTTCGGTA
** *
28827424 ATTTTACCCATCGAAAGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
28827451 ATTTTACCCATCGGGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
28827478 ATTTTTACCCATCTAGGGTATTTCGGTA
1 A-TTTTACCCATCGAGGGTATTTCGGTA
28827506 ATTTTAC
1 ATTTTAC
28827513 GACCCAAGCT
Statistics
Matches: 265, Mismatches: 35, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
26 2 0.01
27 227 0.86
28 36 0.14
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCGGTA
Found at i:28830257 original size:26 final size:26
Alignment explanation
Indices: 28830220--28830313 Score: 91
Period size: 26 Copynumber: 3.5 Consensus size: 26
28830210 TAATAACGCA
* *
28830220 GCAGAGCTACCAGTACAGTATTTGTG
1 GCAGAGCCACCAGTATAGTATTTGTG
* *
28830246 GCAAAGCCACCAGTAATAG-AATTGTG
1 GCAGAGCCACCAGT-ATAGTATTTGTG
*
28830272 GCAGAGCCACTAGTATTAGTATGTGTGTG
1 GCAGAGCCACCAGTA-TAGTAT-T-TGTG
*
28830301 GTAGAGCCACCAG
1 GCAGAGCCACCAG
28830314 AAGCAGTACT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.02
26 33 0.61
27 4 0.07
28 1 0.02
29 15 0.28
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (26 bp):
GCAGAGCCACCAGTATAGTATTTGTG
Found at i:28830483 original size:27 final size:27
Alignment explanation
Indices: 28830437--28830785 Score: 436
Period size: 27 Copynumber: 12.8 Consensus size: 27
28830427 CTTAGCGATC
*
28830437 ATTTTACCCTATCGAGGGTATTTCGGTA
1 ATTTTACCC-ATCGAGGGTATTTCAGTA
*
28830465 ATTTTACCCATCGGGGGTATTTC-GATA
1 ATTTTACCCATCGAGGGTATTTCAG-TA
*
28830492 ACTTTACCCATCGAGGGTATCTT-AGTA
1 ATTTTACCCATCGAGGGTAT-TTCAGTA
* *
28830519 ATTTTACCCATTGAAGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
28830546 ATTTTACCCATCGAGGGTATTTC-GATA
1 ATTTTACCCATCGAGGGTATTTCAG-TA
* * **
28830573 ATTCTACCCATTGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
*
28830600 ATTTTACTCATCGAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
* * *
28830627 ATTTTACCCATCAAAGGTATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCAGTA
** *
28830654 ATTTTACCCATCGATAGTATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCAGTA
*
28830681 ATATTACCCATCGAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
**
28830708 ATTTTACCCATTAAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
28830735 ACTTTTACCCATCGAGGGTATTTC-GATA
1 A-TTTTACCCATCGAGGGTATTTCAG-TA
28830763 ATTTTTACCCATCGAGGGTATTT
1 A-TTTTACCCATCGAGGGTATTT
28830786 TGATAATTTT
Statistics
Matches: 280, Mismatches: 33, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.01
27 219 0.78
28 57 0.20
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCAGTA
Found at i:28833134 original size:26 final size:26
Alignment explanation
Indices: 28833105--28833181 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
28833095 TTGTGGTTGG
* * *
28833105 TTTGACCAATTGATTCTAGTAATTGA
1 TTTGACCAACTGATTCTAGTAACTAA
28833131 TTTGACCAACTGATTCTAGTAACTAA
1 TTTGACCAACTGATTCTAGTAACTAA
* *
28833157 TTTGACCAACTAATTCTATTAACTA
1 TTTGACCAACTGATTCTAGTAACTA
28833182 TTTATTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (26 bp):
TTTGACCAACTGATTCTAGTAACTAA
Found at i:28859196 original size:51 final size:49
Alignment explanation
Indices: 28859116--28859303 Score: 223
Period size: 51 Copynumber: 3.7 Consensus size: 49
28859106 TGCCTATAAA
* * *
28859116 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGA-AGAT-TTGGT
* * *
28859167 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGAAGGCTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAA-GATTTGGT
* * *
28859218 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAAGTTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAGA-TTTGGT
* * *
28859268 CACGTGTTTAGTACTACGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
28859304 TCAAATGATA
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
50 40 0.34
51 74 0.63
52 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAGATTTGGT
Found at i:28865869 original size:22 final size:21
Alignment explanation
Indices: 28865844--28865889 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
28865834 TGATAAACTT
28865844 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
28865866 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
28865887 TAA
1 TAA
28865890 ACTTAGCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:28867476 original size:24 final size:22
Alignment explanation
Indices: 28867449--28867513 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
28867439 CCCCTTATTT
28867449 TTTCACAAACAAATATTCTCTCAA
1 TTTC-CAAACAAA-ATTCTCTCAA
***
28867473 TTTCCTTCCAAAATTCTCTCAA
1 TTTCCAAACAAAATTCTCTCAA
***
28867495 TTTCCTTCCAAAATTCTCT
1 TTTCCAAACAAAATTCTCT
28867514 TAAACTCTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 29 0.76
23 5 0.13
24 4 0.11
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTCCAAACAAAATTCTCTCAA
Found at i:28867491 original size:22 final size:22
Alignment explanation
Indices: 28867458--28867513 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
28867448 TTTTCACAAA
28867458 CAAATATTCTCTCAATTTCCTTC
1 CAAA-ATTCTCTCAATTTCCTTC
28867481 CAAAATTCTCTCAATTTCCTTC
1 CAAAATTCTCTCAATTTCCTTC
28867503 CAAAATTCTCT
1 CAAAATTCTCT
28867514 TAAACTCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41
Consensus pattern (22 bp):
CAAAATTCTCTCAATTTCCTTC
Found at i:28867524 original size:30 final size:30
Alignment explanation
Indices: 28867488--28867546 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
28867478 TTCCAAAATT
* *
28867488 CTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTTAAA
28867518 CTCTCAAATTCCTTCCAAAATCCTCTTAA
1 CTCTCAAATTCCTTCCAAAATCCTCTTAA
28867547 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.32, G:0.00, T:0.37
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTTAAA
Found at i:28867543 original size:22 final size:22
Alignment explanation
Indices: 28867518--28867570 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
28867508 TTCTCTTAAA
*
28867518 CTCTCAAATTCCTTC-CAAAAT
1 CTCTCAAATTCCTTCAAAAAAT
* *
28867539 CCTCTTAATTTCCTTCAAAAAAT
1 -CTCTCAAATTCCTTCAAAAAAT
28867562 CTCTCAAAT
1 CTCTCAAAT
28867571 CCATATTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (22 bp):
CTCTCAAATTCCTTCAAAAAAT
Found at i:28867549 original size:52 final size:52
Alignment explanation
Indices: 28867466--28867565 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
28867456 AACAAATATT
* * * *
28867466 CTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
*
28867518 CTCTCAAATTCCTTCCAAAATCCTCTTAATTTCCTTCAAAAAATCTCT
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCT
28867566 CAAATCCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.30, C:0.31, G:0.00, T:0.39
Consensus pattern (52 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
Found at i:28867635 original size:28 final size:27
Alignment explanation
Indices: 28867602--28867658 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
28867592 ATTCAATTTC
28867602 ATTTTTTAAAGAAAATTTTAAATATTTTT
1 ATTTTTTAAA-AAAATTTTAAA-ATTTTT
* *
28867631 ATTTTTTTAAATAATTTTAAAATTTTT
1 ATTTTTTAAAAAAATTTTAAAATTTTT
28867658 A
1 A
28867659 ATATTTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 7 0.27
28 10 0.38
29 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTTTTTAAAAAAATTTTAAAATTTTT
Found at i:28867656 original size:18 final size:18
Alignment explanation
Indices: 28867613--28867665 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
28867603 TTTTTTAAAG
*
28867613 AAAATTTTAAATATTTTT
1 AAAATTTTAAATAATTTT
***
28867631 ATTTTTTTAAATAATTTT
1 AAAATTTTAAATAATTTT
*
28867649 AAAATTTTTAAT-ATTTT
1 AAAATTTTAAATAATTTT
28867666 CAACAATGGC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AAAATTTTAAATAATTTT
Found at i:28867785 original size:14 final size:15
Alignment explanation
Indices: 28867756--28867789 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28867746 AAATTTTAAA
28867756 TTTTATTTAAGTTAT
1 TTTTATTTAAGTTAT
*
28867771 TTTTATTTATG-TAT
1 TTTTATTTAAGTTAT
28867785 TTTTA
1 TTTTA
28867790 GATAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTTATTTAAGTTAT
Found at i:28868758 original size:7 final size:7
Alignment explanation
Indices: 28868746--28868770 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28868736 AGTGGATTGA
28868746 TATTTAG
1 TATTTAG
28868753 TATTTAG
1 TATTTAG
28868760 TATTTAG
1 TATTTAG
28868767 TATT
1 TATT
28868771 ATATATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:28868934 original size:17 final size:17
Alignment explanation
Indices: 28868912--28868950 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28868902 AGCCCCACCA
*
28868912 GACAGACAGAGTGCTAC
1 GACAGACAGAGTCCTAC
*
28868929 GACAGACAGAGTCCTAG
1 GACAGACAGAGTCCTAC
28868946 GACAG
1 GACAG
28868951 TTTGGATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.31, T:0.10
Consensus pattern (17 bp):
GACAGACAGAGTCCTAC
Found at i:28869759 original size:24 final size:24
Alignment explanation
Indices: 28869732--28869787 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
28869722 GCATGGCTTT
* * *
28869732 CAAACTCCGTCGCCGTTCATGATG
1 CAAACACCGTCGCCATTCACGATG
28869756 CAAACACCGTCGCCATTCACGATG
1 CAAACACCGTCGCCATTCACGATG
28869780 CAAACACC
1 CAAACACC
28869788 TCCACATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.38, G:0.16, T:0.18
Consensus pattern (24 bp):
CAAACACCGTCGCCATTCACGATG
Found at i:28870123 original size:29 final size:29
Alignment explanation
Indices: 28870074--28870759 Score: 577
Period size: 29 Copynumber: 24.4 Consensus size: 29
28870064 TAATTTGTTT
*
28870074 AAAACCC-AACCCTAACCTAATTAAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
* **
28870102 AAAACTCTAACCCTAATTTAATTTAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
28870131 AAAACCCTAAACCCTAACCTAATTTAATTA
1 AAAACCCT-AACCCTAACCTAATTTAATTA
*
28870161 AAAACTCTAACCC--A--T--TTTAA-TA
1 AAAACCCTAACCCTAACCTAATTTAATTA
*
28870183 AAAA-CC-----CTAACCTAATTAAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
**
28870206 AAAACCCTAACCCTAATTTAATTTAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
28870235 AAAACCCTAAACCCTAACCTAATTTAATTA
1 AAAACCCT-AACCCTAACCTAATTTAATTA
*** *
28870265 AAAACCCTAACCCTAACCCTAACCCATTTTA
1 AAAACCCTAACCCTAA-CCTAATTTA-ATTA
* * *
28870296 ATGAA----AACCCTAATCTAATTAAATTA
1 A-AAACCCTAACCCTAACCTAATTTAATTA
** *
28870322 AAAACCCTAACCCTAATTTAATTTAATTT
1 AAAACCCTAACCCTAACCTAATTTAATTA
*
28870351 AATACCCTAAACCCTAACCTAATTTAATTA
1 AAAACCCT-AACCCTAACCTAATTTAATTA
**
28870381 AAAACCCTAACCCTAATTTAATTTAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
*
28870410 AAACCCCTAAACCCTAACCTAACCTAATTTAATTA
1 AAAACCCT-AA--C---CCTAACCTAATTTAATTA
* **
28870445 AAAACCCTAACCTTAATTTAATTTAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
28870474 AAAACCCTAAACCCTAACCTAATTTAATT-
1 AAAACCCT-AACCCTAACCTAATTTAATTA
*
28870503 -AAA----AACCCTAACCTAATTAAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
* *
28870527 AAAACCCTAAACCCTAACCCATTTTAA-T-
1 AAAACCCT-AACCCTAACCTAATTTAATTA
*
28870555 AAAA----AACCCTAACCTAATTAAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
* *
28870580 AAAACCCTAAACCCTAACCCATTTTAA-T-
1 AAAACCCT-AACCCTAACCTAATTTAATTA
*
28870608 AAAA----AACCCTAACCTAATTAAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
*
28870633 AAAACCCTAACCCTAA-TTGAATTTAATTA
1 AAAACCCTAACCCTAACCT-AATTTAATTA
*
28870662 AAAACCCTAACCCTAA-CTCATTTTAATTA
1 AAAACCCTAACCCTAACCT-AATTTAATTA
* **
28870691 AAAACTCTAA-CCTAATTTAATTTAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
* * * *
28870719 AAAGCTCTAACCCTAACCCATTTTAATTA
1 AAAACCCTAACCCTAACCTAATTTAATTA
28870748 AAAACCCTAACC
1 AAAACCCTAACC
28870760 ATTAACAAAA
Statistics
Matches: 530, Mismatches: 74, Indels: 107
0.75 0.10 0.15
Matches are distributed among these distances:
16 1 0.00
18 1 0.00
20 1 0.00
21 1 0.00
22 10 0.02
23 60 0.11
24 4 0.01
25 14 0.03
26 4 0.01
27 6 0.01
28 49 0.09
29 213 0.40
30 133 0.25
31 4 0.01
32 4 0.01
34 2 0.00
35 23 0.04
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (29 bp):
AAAACCCTAACCCTAACCTAATTTAATTA
Found at i:28870151 original size:59 final size:59
Alignment explanation
Indices: 28870074--28870757 Score: 669
Period size: 59 Copynumber: 12.2 Consensus size: 59
28870064 TAATTTGTTT
* *
28870074 AAAACCC--AACCCTAACCTAATTAAATTAAAAACTCTAACCCTAATTTAATTTAATTA
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
*
28870131 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACTCTAACCC--A--T--TTTAA-TA
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
*
28870183 AAAACCCT--A-----ACCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAATTA
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
** *** *
28870235 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCCTAACCCATTTTA
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA-TTTAATTTA-ATTA
** * * *
28870296 ATGA----AAACCCTAATCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAATTT
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
*
28870351 AATACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
* *
28870410 AAACCCCTAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTTAATTTAATTTAATTA
1 AAAACCCTAAA--C---CCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
28870474 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAA-TT-A---AATTA
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
* * *
28870527 AAAACCCTAAACCCTAACCCATTTTAATAAAAAACCCTAA-CCTAA-TT-A---AATTA
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
* * *
28870580 AAAACCCTAAACCCTAACCCATTTTAATAAAAAACCCTAA-CCTAA-TT-A---AATTA
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
* * * *
28870633 AAAACCCT-AACCCTAA-TTGAATTTAATTAAAAACCCTAACCCTAACTCATTTTAATTA
1 AAAACCCTAAACCCTAACCT-AATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
* ** * * *** *
28870691 AAAACTCT-AA-CCTAATTTAATTTAATTAAAAGCTCTAACCCTAACCCATTTTAATTA
1 AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
28870748 AAAACCCTAA
1 AAAACCCTAA
28870758 CCATTAACAA
Statistics
Matches: 546, Mismatches: 45, Indels: 71
0.82 0.07 0.11
Matches are distributed among these distances:
45 25 0.05
47 1 0.00
49 1 0.00
50 1 0.00
51 5 0.01
52 46 0.08
53 126 0.23
54 2 0.00
55 5 0.01
56 5 0.01
57 94 0.17
58 21 0.04
59 147 0.27
60 4 0.01
61 6 0.01
62 1 0.00
64 56 0.10
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (59 bp):
AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTA
Found at i:28870184 original size:22 final size:23
Alignment explanation
Indices: 28870139--28870228 Score: 119
Period size: 23 Copynumber: 3.9 Consensus size: 23
28870129 TAAAAACCCT
*
28870139 AAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCCAATTTAATTAA
* *
28870162 AAACTCTAACCCATTTTAA-TAA
1 AAACCCTAACCCAATTTAATTAA
* *
28870184 AAACCCTAACCTAATTAAATTAA
1 AAACCCTAACCCAATTTAATTAA
28870207 AAACCCTAACCCTAATTTAATT
1 AAACCCTAACCC-AATTTAATT
28870229 TAATTAAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
22 18 0.32
23 30 0.54
24 8 0.14
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (23 bp):
AAACCCTAACCCAATTTAATTAA
Found at i:28870205 original size:45 final size:46
Alignment explanation
Indices: 28870139--28870227 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 46
28870129 TAAAAACCCT
* * *
28870139 AAACCCTAACCTAATTTAATTAAAAACTCTAACCC-ATTTTAATAA
1 AAACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATAA
28870184 AAACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAAT
1 AAACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAAT
28870228 TTAATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 33 0.82
46 7 0.17
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (46 bp):
AAACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATAA
Found at i:28870454 original size:23 final size:23
Alignment explanation
Indices: 28870427--28870712 Score: 167
Period size: 23 Copynumber: 10.7 Consensus size: 23
28870417 TAAACCCTAA
28870427 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
28870450 CCTAACCTTAATTTAATTTAATTAAAAACCC
1 CCTAACC------TAATTTAATTAAAAA--C
28870481 TAAACCCTAACCTAATTTAATTAAAAAC
1 -----CCTAACCTAATTTAATTAAAAAC
*
28870509 CCTAACCTAATTAAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
28870532 CCTAAACCCTAACCCATTTTAATAAAAAAC
1 CCT-AA-CCT-A---A-TTTAATTAAAAAC
*
28870562 CCTAACCTAATTAAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
28870585 CCTAAACCCTAACCCATTTTAATAAAAAAC
1 CCT-AA-CCT-A---A-TTTAATTAAAAAC
*
28870615 CCTAACCTAATTAAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
28870638 CCTAACCCTAATTGAATTTAATTAAAAAC
1 CCTAA-CC----T-AATTTAATTAAAAAC
28870667 CCTAACCCTAACTCATTTTAATTAAAAAC
1 CCTAA-CCT-A---A-TTTAATTAAAAAC
*
28870696 TCTAACCTAATTTAATT
1 CCTAACCTAATTTAATT
28870713 TAATTAAAAG
Statistics
Matches: 214, Mismatches: 12, Indels: 74
0.71 0.04 0.25
Matches are distributed among these distances:
23 69 0.32
24 9 0.04
25 8 0.04
26 2 0.01
27 3 0.01
28 12 0.06
29 60 0.28
30 43 0.20
31 1 0.00
36 7 0.03
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (23 bp):
CCTAACCTAATTTAATTAAAAAC
Found at i:28870677 original size:53 final size:52
Alignment explanation
Indices: 28870184--28870673 Score: 410
Period size: 53 Copynumber: 8.6 Consensus size: 52
28870174 ATTTTAATAA
*
28870184 AAACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCT
1 AAACCCTAA-CTAATTTAATTAAAAACCCTAA-CCTAA-TT-A---AATTAAAAACCCT
* ** ***
28870243 AAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCCTAACCCATT-TTAA-TGA
1 AAACCCTAA-CTAATTTAATTAAAAACCCTAA-CCTAA--TTAA---ATTAAAAACCCT
* *
28870300 AAACCCTAATCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAATTTAATACCCT
1 AAACCCTAA-CTAATTTAATTAAAAACCCTAA-CCTAA-TTAAATTAA---AA-ACCCT
*
28870359 AAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAACCCCT
1 AAACCCTAA-CTAATTTAATTAAAAACCCTAA-CCTAA-TT-A---AATTAAAAACCCT
28870418 AAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTTAATTTAATTTAATTAAAAACCCT
1 AAA--C---CCTAA-CTAATTTAATTAAAAACCCTAACC-TAA-TT-A---AATTAAAAACCCT
28870482 AAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT
1 AAACCCTAA-CTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT
* * *
28870535 AAACCCTAACCCATTTTAATAAAAAACCCTAACCTAATTAAATTAAAAACCCT
1 AAACCCTAA-CTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT
* * *
28870588 AAACCCTAACCCATTTTAATAAAAAACCCTAACCTAATTAAATTAAAAACCCT
1 AAACCCTAA-CTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT
*
28870641 -AACCCTAATTGAATTTAATTAAAAACCCTAACC
1 AAACCCTAACT-AATTTAATTAAAAACCCTAACC
28870674 CTAACTCATT
Statistics
Matches: 380, Mismatches: 30, Indels: 49
0.83 0.07 0.11
Matches are distributed among these distances:
52 28 0.07
53 118 0.31
56 5 0.01
57 39 0.10
58 6 0.02
59 117 0.31
60 4 0.01
61 1 0.00
62 1 0.00
63 7 0.02
64 54 0.14
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.28
Consensus pattern (52 bp):
AAACCCTAACTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT
Found at i:28870729 original size:57 final size:57
Alignment explanation
Indices: 28870612--28870759 Score: 215
Period size: 57 Copynumber: 2.6 Consensus size: 57
28870602 TTTAATAAAA
* * *
28870612 AACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTGAATTTAATTAAAAACCCT
1 AACCCTAACCCATTTTAATTAAAAACCCTAA-CCTAATTGAATTTAATTAAAAACCCT
* * * * *
28870670 AACCCTAACTCATTTTAATTAAAAACTCTAACCTAATTTAATTTAATTAAAAGCTCT
1 AACCCTAACCCATTTTAATTAAAAACCCTAACCTAATTGAATTTAATTAAAAACCCT
28870727 AACCCTAACCCATTTTAATTAAAAACCCTAACC
1 AACCCTAACCCATTTTAATTAAAAACCCTAACC
28870760 ATTAACAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
57 54 0.68
58 26 0.32
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.30
Consensus pattern (57 bp):
AACCCTAACCCATTTTAATTAAAAACCCTAACCTAATTGAATTTAATTAAAAACCCT
Found at i:28873917 original size:124 final size:125
Alignment explanation
Indices: 28873691--28873956 Score: 371
Period size: 124 Copynumber: 2.1 Consensus size: 125
28873681 GCGATTTGAC
*
28873691 ACTATTTGCTCAGAAACATCAAAAAATAATTATTTCCTACATGACCAACTATAGCGAAATAGCGT
1 ACTATTTGCTCAGAAACATCAAAAAATAATTATTTCCTACATGACCAACTATAGCGAAATAGCAT
* **
28873756 CCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGATATTAGCAATTTTAT
66 CCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGATAGAAGCAATTTTAT
* * * *
28873816 ACTATTTGCTCATAAA-ATGTC-AAAAA-AATTATTTCTTACATGACCAACTGTAGCGAAATCGC
1 ACTATTTGCTCAGAAACA--TCAAAAAATAATTATTTCCTACATGACCAACTATAGCGAAATAGC
* *
28873878 ATCCACGAGGGCACGATTTCACAATTTCTTCTC-TGATAGCATCCTGGTAGAAGCGATTTTAT
64 ATCCACGAGGGCACGATTTCACAATTTCTTCTCAT-ATAGCATCCTGATAGAAGCAATTTTAT
28873940 ACTATTTGAC-CAGAAAC
1 ACTATTTG-CTCAGAAAC
28873957 GTCAGCTCGA
Statistics
Matches: 125, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
123 1 0.01
124 101 0.81
125 21 0.17
126 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (125 bp):
ACTATTTGCTCAGAAACATCAAAAAATAATTATTTCCTACATGACCAACTATAGCGAAATAGCAT
CCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGATAGAAGCAATTTTAT
Found at i:28876177 original size:18 final size:19
Alignment explanation
Indices: 28876154--28876191 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
28876144 TCATCTTTAA
28876154 ACCAAAATATTTT-ACATT
1 ACCAAAATATTTTAACATT
* *
28876172 ACCAAAGTGTTTTAACATT
1 ACCAAAATATTTTAACATT
28876191 A
1 A
28876192 ATTTCGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (19 bp):
ACCAAAATATTTTAACATT
Found at i:28880127 original size:17 final size:17
Alignment explanation
Indices: 28880105--28880137 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28880095 ATTAGTGCAC
*
28880105 ATTGTCGTTGCATTTTT
1 ATTGTCATTGCATTTTT
28880122 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
28880138 AATGTTAGTG
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:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:28883256 original size:2 final size:2
Alignment explanation
Indices: 28883249--28883296 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
28883239 GCTAAGCCAC
* *
28883249 AT AT AT AT AT AT AT AT AT AT AT AG AT AG AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28883291 AT AT AT
1 AT AT AT
28883297 CTGATTCTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:28887943 original size:42 final size:42
Alignment explanation
Indices: 28887896--28887988 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
28887886 TGGTGGTGAA
*
28887896 GCTTCTGCTCG-AGCCCAAAGCCAGGTC-CAACAAGGTCCC-CTT
1 GCTTCTG-TCGAAGCCCAAAGCCA-GTCTCAACAAGG-CCCTATT
* **
28887938 GCTTCTGTTGAAGCCCAAATTCAGTCTCAACAAGGCCCTATT
1 GCTTCTGTCGAAGCCCAAAGCCAGTCTCAACAAGGCCCTATT
28887980 GCTTCTGTC
1 GCTTCTGTC
28887989 TCATCCCGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
41 8 0.19
42 35 0.81
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (42 bp):
GCTTCTGTCGAAGCCCAAAGCCAGTCTCAACAAGGCCCTATT
Found at i:28893966 original size:23 final size:25
Alignment explanation
Indices: 28893939--28893999 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 25
28893929 CACTATTAAC
* *
28893939 TTAATTTAATTATATTATAT-AT-T
1 TTAATTTAATTATATTACATAATAA
* *
28893962 TTAATTTAATCACATTACATAATAA
1 TTAATTTAATTATATTACATAATAA
28893987 TTAATTTAATTAT
1 TTAATTTAATTAT
28894000 CATATTATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 17 0.57
24 2 0.07
25 11 0.37
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAATTTAATTATATTACATAATAA
Found at i:28898663 original size:31 final size:31
Alignment explanation
Indices: 28898628--28898692 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
28898618 AAAATAATAA
*
28898628 TCATTGAACTGTTCGAAAGTTTTTATTTAAG
1 TCATTGAACTATTCGAAAGTTTTTATTTAAG
28898659 TCATTGAACTATTCGAAAGTTTTTATTTAAG
1 TCATTGAACTATTCGAAAGTTTTTATTTAAG
28898690 TCA
1 TCA
28898693 CTGGGACGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (31 bp):
TCATTGAACTATTCGAAAGTTTTTATTTAAG
Found at i:28904913 original size:23 final size:25
Alignment explanation
Indices: 28904869--28904914 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
28904859 ATTTCGTTTT
*
28904869 TTAATCTCTTTTATTCTATTTTTCA
1 TTAATCTCTTTTATTATATTTTTCA
*
28904894 TTAATCT-TTTT-TTATTTTTTT
1 TTAATCTCTTTTATTATATTTTT
28904915 TATTTTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 4 0.21
25 7 0.37
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (25 bp):
TTAATCTCTTTTATTATATTTTTCA
Found at i:28905711 original size:20 final size:21
Alignment explanation
Indices: 28905674--28905715 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
28905664 TCTAAATTTT
28905674 TTATAAGTATATATATTTACG
1 TTATAAGTATATATATTTACG
28905695 TTATAAGTATA-ATATTTACG
1 TTATAAGTATATATATTTACG
28905715 T
1 T
28905716 ACTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (21 bp):
TTATAAGTATATATATTTACG
Found at i:28909263 original size:29 final size:29
Alignment explanation
Indices: 28909231--28909288 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28909221 GTTGAAAAGG
28909231 GATGGCAGTCACTCATCTTTGAAGGAGAT
1 GATGGCAGTCACTCATCTTTGAAGGAGAT
28909260 GATGGCAGTCACTCATCTTTGAAGGAGAT
1 GATGGCAGTCACTCATCTTTGAAGGAGAT
28909289 TCCCTCGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (29 bp):
GATGGCAGTCACTCATCTTTGAAGGAGAT
Found at i:28909666 original size:20 final size:20
Alignment explanation
Indices: 28909627--28909666 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28909617 GGAAAGTTTT
*
28909627 GAAAATGAAATCGTCAAAAG
1 GAAAATGAAATCGACAAAAG
28909647 GAAAATGAAAT-GACAGAAAG
1 GAAAATGAAATCGACA-AAAG
28909667 AGGAGAAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.57, C:0.07, G:0.23, T:0.12
Consensus pattern (20 bp):
GAAAATGAAATCGACAAAAG
Found at i:28910293 original size:24 final size:23
Alignment explanation
Indices: 28910264--28910308 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
28910254 TTTACGTATT
28910264 TAATTTTAAAATAACATATTTTAA
1 TAATTTTAAAAT-ACATATTTTAA
* *
28910288 TAATTTTTAAATATATATTTT
1 TAATTTTAAAATACATATTTT
28910309 CTAACTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATTTTAAAATACATATTTTAA
Found at i:28925308 original size:23 final size:25
Alignment explanation
Indices: 28925264--28925309 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
28925254 ATTTCGTTTT
*
28925264 TTAATCTCTTTTATTCTATTTTTCA
1 TTAATCTCTTTTATTATATTTTTCA
*
28925289 TTAATCT-TTTT-TTATTTTTTT
1 TTAATCTCTTTTATTATATTTTT
28925310 TATTTTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 4 0.21
25 7 0.37
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (25 bp):
TTAATCTCTTTTATTATATTTTTCA
Found at i:28929638 original size:29 final size:29
Alignment explanation
Indices: 28929606--28929663 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28929596 GTTGAAAAGG
28929606 GATGGCAGTCACTCATCTTTGAAGGAGAT
1 GATGGCAGTCACTCATCTTTGAAGGAGAT
28929635 GATGGCAGTCACTCATCTTTGAAGGAGAT
1 GATGGCAGTCACTCATCTTTGAAGGAGAT
28929664 TCCCTCGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (29 bp):
GATGGCAGTCACTCATCTTTGAAGGAGAT
Found at i:28930041 original size:20 final size:20
Alignment explanation
Indices: 28930002--28930041 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28929992 GGAAAGTTTT
*
28930002 GAAAATGAAATCGTCAAAAG
1 GAAAATGAAATCGACAAAAG
28930022 GAAAATGAAAT-GACAGAAAG
1 GAAAATGAAATCGACA-AAAG
28930042 AGGAGAAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.57, C:0.07, G:0.23, T:0.12
Consensus pattern (20 bp):
GAAAATGAAATCGACAAAAG
Found at i:28930488 original size:36 final size:37
Alignment explanation
Indices: 28930432--28930505 Score: 141
Period size: 36 Copynumber: 2.0 Consensus size: 37
28930422 TTTTTAAATG
28930432 TATATTATAAAAATGGGTACAAACAATATAATTATTT
1 TATATTATAAAAATGGGTACAAACAATATAATTATTT
28930469 TATATTAT-AAAATGGGTACAAACAATATAATTATTT
1 TATATTATAAAAATGGGTACAAACAATATAATTATTT
28930505 T
1 T
28930506 TAAATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 29 0.78
37 8 0.22
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (37 bp):
TATATTATAAAAATGGGTACAAACAATATAATTATTT
Found at i:28938520 original size:5 final size:5
Alignment explanation
Indices: 28938499--28938544 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
28938489 TTATTTAAGT
28938499 TATACA TATATA TATAA TATAA TAT-A -ATAA TATAA T-TAA TATAA TA
1 TATA-A TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA
28938545 CTTATTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 19 0.53
6 9 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:28938578 original size:28 final size:28
Alignment explanation
Indices: 28938510--28938578 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
28938500 ATACATATAT
* *
28938510 ATATAATATA-ATATAATAATATAATTA
1 ATATAATATATATTTAATAATATAATAA
*
28938537 ATATAATACT-TATTTATTAAGTA-AATAA
1 ATATAATA-TATATTTAATAA-TATAATAA
28938565 ATATAATATATATT
1 ATATAATATATATT
28938579 AACTAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
27 9 0.26
28 24 0.69
29 2 0.06
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (28 bp):
ATATAATATATATTTAATAATATAATAA
Found at i:28940789 original size:12 final size:11
Alignment explanation
Indices: 28940772--28940814 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
28940762 GATAAGAAGA
28940772 AATAATGAAAAT
1 AATAAT-AAAAT
28940784 AATAATAAAAAT
1 AATAAT-AAAAT
*
28940796 AATAGTACAAAT
1 AATAATA-AAAT
28940808 AATAATA
1 AATAATA
28940815 GGATTAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 1 0.04
12 26 0.96
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:28943414 original size:31 final size:31
Alignment explanation
Indices: 28943372--28943447 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
28943362 TGAAAAAAGA
*
28943372 TTAAGTACCAAATTAAGAATAAGCGTCAAGT
1 TTAAGTACCAAATTAAGAAAAAGCGTCAAGT
* * *
28943403 TTAGGTACCAAATTAGGAAAAAGTGTCAAGT
1 TTAAGTACCAAATTAAGAAAAAGCGTCAAGT
28943434 TTAAGTACCAAATT
1 TTAAGTACCAAATT
28943448 GGGCTAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (31 bp):
TTAAGTACCAAATTAAGAAAAAGCGTCAAGT
Found at i:28945272 original size:2 final size:2
Alignment explanation
Indices: 28945265--28945290 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28945255 CTGGGATTGG
28945265 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28945291 TATGTGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28947201 original size:33 final size:32
Alignment explanation
Indices: 28947129--28947204 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
28947119 ATGTTTAAAT
* * *
28947129 GTAAGACCATAGCTGGGCTATGACATTTTAAT
1 GTAAGACCATAACTGGGCTATGACATTTGAAC
* * *
28947161 GAAAAGACCATAACTGGGTTATGGCATCTTGAAC
1 G-TAAGACCATAACTGGGCTATGACAT-TTGAAC
28947195 GTAAGACCAT
1 GTAAGACCAT
28947205 GGTTGGACCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
32 1 0.03
33 29 0.83
34 5 0.14
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (32 bp):
GTAAGACCATAACTGGGCTATGACATTTGAAC
Found at i:28947273 original size:105 final size:101
Alignment explanation
Indices: 28947095--28947291 Score: 297
Period size: 105 Copynumber: 1.9 Consensus size: 101
28947085 AATTGAAAGA
* *
28947095 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTGGGCTATGACATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAGCTGGGCTATGACATTCTAA
28947160 TGAAAAGACCATAACTGGGTTATGGCATCTTGAACG
66 TGAAAAGACCATAACTGGGTTATGGCATCTTGAACG
* *
28947196 TAAGACCATGGTTGGACCATGGCAGTATAG-ATACATGTGTAAGACCATAGCTGGGCTATGGCAT
1 TAAGACCATGGTTGGACCATGGCA--AT-GTATA-A-ATGTAAGACCATAGCTGGGCTATGACAT
*
28947260 TCTAATGATAAGACCATAACTGGGTTATGGCA
61 TCTAATGAAAAGACCATAACTGGGTTATGGCA
28947292 CTACAAATGT
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
101 24 0.28
103 4 0.05
104 2 0.02
105 56 0.65
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAGCTGGGCTATGACATTCTAA
TGAAAAGACCATAACTGGGTTATGGCATCTTGAACG
Found at i:28947277 original size:33 final size:32
Alignment explanation
Indices: 28947233--28947357 Score: 108
Period size: 33 Copynumber: 3.8 Consensus size: 32
28947223 TAGATACATG
28947233 TGTAAGACCATAGCTGGGCTATGGCATTCTAA
1 TGTAAGACCATAGCTGGGCTATGGCATTCTAA
* * * *
28947265 TGATAAGACCATAACTGGGTTATGGCACTACAAA
1 TG-TAAGACCATAGCTGGGCTATGGCA-TTCTAA
* * * * *
28947299 TGTAAGATCATGGCAGGGCCATGGCAATAC-ATA
1 TGTAAGACCATAGCTGGGCTATGGC-ATTCTA-A
* *
28947332 TGTAAGACCATAGTTGGACTATGGCA
1 TGTAAGACCATAGCTGGGCTATGGCA
28947358 CAAAAAGAAC
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
32 4 0.05
33 62 0.85
34 7 0.10
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (32 bp):
TGTAAGACCATAGCTGGGCTATGGCATTCTAA
Found at i:28947304 original size:105 final size:101
Alignment explanation
Indices: 28947095--28947354 Score: 294
Period size: 105 Copynumber: 2.6 Consensus size: 101
28947085 AATTGAAAGA
* *
28947095 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTGGGCTATGACATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAGCTGGGCTATGACATTCTAA
**
28947160 TGAAAAGACCATAACTGGGTTATGGCATCTTGAACG
66 TGAAAAGACCATAACTGGGTTATGGCATCTCAAACG
* *
28947196 TAAGACCATGGTTGGACCATGGCAGTATAG-ATACATGTGTAAGACCATAGCTGGGCTATGGCAT
1 TAAGACCATGGTTGGACCATGGCA--AT-GTATA-A-ATGTAAGACCATAGCTGGGCTATGACAT
* *
28947260 TCTAATGATAAGACCATAACTGGGTTATGGCA-CTACAAATG
61 TCTAATGAAAAGACCATAACTGGGTTATGGCATCT-CAAACG
* ** * * * * *
28947301 TAAGATCATGGCAGGGCCATGGCAA--TACATATGTAAGACCATAGTTGGACTATG
1 TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAGCTGGGCTATG
28947355 GCACAAAAAG
Statistics
Matches: 135, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
99 21 0.16
101 26 0.19
103 5 0.04
104 4 0.03
105 79 0.59
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAGCTGGGCTATGACATTCTAA
TGAAAAGACCATAACTGGGTTATGGCATCTCAAACG
Found at i:28953006 original size:56 final size:56
Alignment explanation
Indices: 28952920--28953026 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 56
28952910 TATAGATTGC
*
28952920 AAATTAATTATTCATGAGCAATATTCAAATTAAAAGTGATGATTTATCATCTTACA
1 AAATTAATTATTCATAAGCAATATTCAAATTAAAAGTGATGATTTATCATCTTACA
*
28952976 AAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATC
1 AAATTAATTATTCATAAGCAATATTCAAATTAAAAGTGATGATTTATCATC
28953027 CAATGGATAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.37
Consensus pattern (56 bp):
AAATTAATTATTCATAAGCAATATTCAAATTAAAAGTGATGATTTATCATCTTACA
Found at i:28953552 original size:29 final size:29
Alignment explanation
Indices: 28953514--28953608 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 29
28953504 TTTTTAAAAA
* * *
28953514 AAATTGCATTTCGACCCCTAAATTTTTTG
1 AAATTACATTTTGACCCCTAAATTTCTTG
* * *
28953543 AAATTACATTTTAACCCTTAAAATTTCTCG
1 AAATTACATTTTGACCCCT-AAATTTCTTG
*
28953573 AAATTACATTTTGACCTCTAAACTTTCTTG
1 AAATTACATTTTGACCCCTAAA-TTTCTTG
28953603 AAATTA
1 AAATTA
28953609 TGTTTTGGCC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 18 0.33
30 36 0.67
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAATTTCTTG
Found at i:28953947 original size:21 final size:20
Alignment explanation
Indices: 28953923--28953973 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
28953913 CAACCAAGAG
28953923 GCAAGAAAAAAGAAAAAACAA
1 GCAAGAAAAAAGAAAAAA-AA
*
28953944 GCAAGCAAAAAGAAAAAAAA
1 GCAAGAAAAAAGAAAAAAAA
28953964 G-AAGAAAAAA
1 GCAAGAAAAAA
28953974 TAGCAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 8 0.29
20 3 0.11
21 17 0.61
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (20 bp):
GCAAGAAAAAAGAAAAAAAA
Found at i:28954324 original size:14 final size:12
Alignment explanation
Indices: 28954304--28954358 Score: 76
Period size: 12 Copynumber: 4.5 Consensus size: 12
28954294 GCAGGGCAGA
28954304 AAAAAAAGAGAGG
1 AAAAAAAGAGA-G
28954317 AGAAAAAAGAGAG
1 A-AAAAAAGAGAG
28954330 AAAAAAAGAGA-
1 AAAAAAAGAGAG
*
28954341 AAAAAAAGAAAG
1 AAAAAAAGAGAG
28954353 AAAAAA
1 AAAAAA
28954359 GGAAAAAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
11 10 0.26
12 16 0.41
13 3 0.08
14 10 0.26
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGAG
Found at i:28954332 original size:11 final size:11
Alignment explanation
Indices: 28954306--28954377 Score: 64
Period size: 11 Copynumber: 6.7 Consensus size: 11
28954296 AGGGCAGAAA
28954306 AAAAAGAGAGGAG
1 AAAAA-AGA-GAG
28954319 AAAAAAGAGAG
1 AAAAAAGAGAG
28954330 AAAAAA-AGAG
1 AAAAAAGAGAG
*
28954340 AAAAAAAAGA-
1 AAAAAAGAGAG
*
28954350 AAGAAAAAAG-G
1 AA-AAAAGAGAG
28954361 AAAAAAG-GA-
1 AAAAAAGAGAG
28954370 AAAAAAGA
1 AAAAAAGA
28954378 AAAAAGAGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
9 8 0.15
10 16 0.30
11 21 0.40
12 3 0.06
13 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:28954344 original size:9 final size:9
Alignment explanation
Indices: 28954316--28954391 Score: 74
Period size: 8 Copynumber: 9.0 Consensus size: 9
28954306 AAAAAGAGAG
28954316 GAGAAAAAA
1 GAGAAAAAA
28954325 GAGAGAAAAA
1 GAGA-AAAAA
* *
28954335 AAGAGAAAA
1 GAGAAAAAA
*
28954344 -A-AAAGAA
1 GAGAAAAAA
28954351 -AGAAAAAA
1 GAGAAAAAA
28954359 G-GAAAAAA
1 GAGAAAAAA
28954367 G-GAAAAAA
1 GAGAAAAAA
28954375 -AGAAAAAA
1 GAGAAAAAA
28954383 GAGAAAAAA
1 GAGAAAAAA
28954392 AAAGGTTCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
7 5 0.09
8 28 0.49
9 16 0.28
10 8 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
GAGAAAAAA
Found at i:28954584 original size:17 final size:16
Alignment explanation
Indices: 28954528--28954585 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
28954518 TTTTATGCAT
* *
28954528 TTTTATATTT-TTGTA
1 TTTTATTTTTATTTTA
28954543 TTTATATTTTTATTTTA
1 TTT-TATTTTTATTTTA
* *
28954560 ATTCATTTTTAATTTTA
1 TTTTATTTTT-ATTTTA
28954577 TTTTATTTT
1 TTTTATTTT
28954586 AAATAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 3 0.09
16 12 0.35
17 19 0.56
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTATTTTTATTTTA
Found at i:28955036 original size:21 final size:22
Alignment explanation
Indices: 28955002--28955044 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
28954992 TTCGTCTTTC
28955002 AAAATTCTCATGTTTTCAAAAA
1 AAAATTCTCATGTTTTCAAAAA
*
28955024 AAAATTCT-GTGTTTTCAAAAA
1 AAAATTCTCATGTTTTCAAAAA
28955045 TTTTCGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (22 bp):
AAAATTCTCATGTTTTCAAAAA
Found at i:28955067 original size:23 final size:22
Alignment explanation
Indices: 28955040--28955083 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28955030 CTGTGTTTTC
*
28955040 AAAAATTTTCGTATTTCAAAAA
1 AAAAAATTTCGTATTTCAAAAA
*
28955062 AAAAAATTTCGTGTTTCAAAAA
1 AAAAAATTTCGTATTTCAAAAA
28955084 TCCTCGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAAAATTTCGTATTTCAAAAA
Found at i:28955090 original size:17 final size:18
Alignment explanation
Indices: 28955063--28955307 Score: 163
Period size: 18 Copynumber: 13.9 Consensus size: 18
28955053 TTTCAAAAAA
28955063 AAAAATT-TCGTG-TTTC
1 AAAAATTCTCGTGTTTTC
*
28955079 AAAAATCCTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
28955097 AAAAATTCTGGTG-TTTC
1 AAAAATTCTCGTGTTTTC
*
28955114 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
* *
28955132 AAAAATTC-CG-GTGATCC
1 AAAAATTCTCGTGT-TTTC
* *
28955149 AAAAATTTTTGTGTTTTC
1 AAAAATTCTCGTGTTTTC
28955167 TAAAAATT-TCCGTG-TTTC
1 -AAAAATTCT-CGTGTTTTC
* *
28955185 AAAAATTTTTGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
28955203 ACAAATT-TACGTGTTTTC
1 AAAAATTCT-CGTGTTTTC
**
28955221 AACGA--CT-GTAGTCTTTC
1 AAAAATTCTCGT-GT-TTTC
* * *
28955238 ACAAATTTTCGTGTTTTA
1 AAAAATTCTCGTGTTTTC
* * *
28955256 AAAAATTTTTGTGTTTTGA
1 AAAAATTCTCGTGTTTT-C
*
28955275 AAAAATTCTCATG-TTTC
1 AAAAATTCTCGTGTTTTC
*
28955292 AAAAATTGTCGTGTTT
1 AAAAATTCTCGTGTTT
28955308 ATAAAAAAAT
Statistics
Matches: 178, Mismatches: 32, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
15 2 0.01
16 10 0.06
17 60 0.34
18 78 0.44
19 26 0.15
20 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (18 bp):
AAAAATTCTCGTGTTTTC
Found at i:28955096 original size:18 final size:17
Alignment explanation
Indices: 28955063--28955348 Score: 141
Period size: 18 Copynumber: 16.2 Consensus size: 17
28955053 TTTCAAAAAA
28955063 AAAAATT-TCGTGTTTC
1 AAAAATTCTCGTGTTTC
*
28955079 AAAAATCCTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
*
28955097 AAAAATTCTGGTGTTTC
1 AAAAATTCTCGTGTTTC
*
28955114 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
* *
28955132 AAAAATTC-CGGTGATCC
1 AAAAATTCTC-GTGTTTC
* *
28955149 AAAAATTTTTGTGTTTTC
1 AAAAATTCTCGTG-TTTC
28955167 TAAAAATT-TCCGTGTTTC
1 -AAAAATTCT-CGTGTTTC
* *
28955185 AAAAATTTTTGTGTTTTC
1 AAAAATTCTCGTG-TTTC
*
28955203 ACAAATT-TACGTGTTTTC
1 AAAAATTCT-CGTG-TTTC
** * * * *
28955221 AACGACTGTAGTCTTTC
1 AAAAATTCTCGTGTTTC
* * *
28955238 ACAAATTTTCGTGTTTTA
1 AAAAATTCTCGTG-TTTC
* * *
28955256 AAAAATTTTTGTGTTTTGA
1 AAAAATTCTCGTG-TTT-C
*
28955275 AAAAATTCTCATGTTTC
1 AAAAATTCTCGTGTTTC
* *
28955292 AAAAATTGTCGTGTTTATAA
1 AAAAATTCTCGTG-TT-T-C
*
28955312 AAAAATT-TTGTGTTTC
1 AAAAATTCTCGTGTTTC
* * *
28955328 TAAAATTTTTGTGTTTC
1 AAAAATTCTCGTGTTTC
28955345 AAAA
1 AAAA
28955349 TTTTCATTTA
Statistics
Matches: 209, Mismatches: 43, Indels: 35
0.73 0.15 0.12
Matches are distributed among these distances:
16 12 0.06
17 78 0.37
18 85 0.41
19 27 0.13
20 7 0.03
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTC
Found at i:28955097 original size:40 final size:40
Alignment explanation
Indices: 28954978--28955136 Score: 133
Period size: 39 Copynumber: 4.1 Consensus size: 40
28954968 TAACAAAACA
* *
28954978 AAAATAAAAAAGATTTCGTCTTTC-AAAATTCTCATGTTTTC
1 AAAA-AAAAAA-ATTTCGTGTTTCAAAAATTCTCGTGTTTTC
* *
28955019 --AAAAAAAAA-TTCTGTGTTTTCAAAAATTTTCGT-ATTTC
1 AAAAAAAAAAATTTC-GTG-TTTCAAAAATTCTCGTGTTTTC
*
28955057 AAAAAAAAAAATTTCGTGTTTCAAAAATCCTCGTGTTTTC
1 AAAAAAAAAAATTTCGTGTTTCAAAAATTCTCGTGTTTTC
* *
28955097 ------AAAAATTCTGGTGTTTCAAAAATTTTCGTGTTTTC
1 AAAAAAAAAAATT-TCGTGTTTCAAAAATTCTCGTGTTTTC
28955132 AAAAA
1 AAAAA
28955137 TTCCGGTGAT
Statistics
Matches: 95, Mismatches: 10, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
34 7 0.07
35 24 0.25
36 3 0.03
37 3 0.03
38 14 0.15
39 25 0.26
40 16 0.17
41 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (40 bp):
AAAAAAAAAAATTTCGTGTTTCAAAAATTCTCGTGTTTTC
Found at i:28955111 original size:35 final size:34
Alignment explanation
Indices: 28955063--28955353 Score: 226
Period size: 36 Copynumber: 8.3 Consensus size: 34
28955053 TTTCAAAAAA
**
28955063 AAAAATTTCGTGTTTCAAAAATCCTCGTGTTTTC
1 AAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTC
*
28955097 AAAAATTCTGGTGTTTCAAAAATTTTCGTGTTTTC
1 AAAAATT-TCGTGTTTCAAAAATTTTCGTGTTTTC
* * * *
28955132 AAAAATTCCGGTGATCCAAAAATTTTTGTGTTTTC
1 AAAAATTTC-GTGTTTCAAAAATTTTCGTGTTTTC
*
28955167 TAAAAATTTCCGTGTTTCAAAAATTTTTGTGTTTTC
1 -AAAAATTT-CGTGTTTCAAAAATTTTCGTGTTTTC
* ** * * * *
28955203 ACAAATTTACGTGTTTTCAACGACTGTAGT-CTTTC
1 AAAAATTT-CGTG-TTTCAAAAATTTTCGTGTTTTC
* * * *
28955238 ACAAATTTTCGTGTTTTAAAAAATTTTTGTGTTTTGA
1 A-AAAATTTCGTG-TTTCAAAAATTTTCGTGTTTT-C
* * *
28955275 AAAAATTCTCATGTTTCAAAAATTGTCGTGTTTATAA
1 AAAAATT-TCGTGTTTCAAAAATTTTCGTGTTT-T-C
* * *
28955312 AAAAATTTTGTGTTTCTAAAATTTTTGTG-TTTC
1 AAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTC
*
28955345 AAAATTTTC
1 AAAAATTTC
28955354 ATTTAAAAAA
Statistics
Matches: 204, Mismatches: 43, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
33 7 0.03
34 8 0.04
35 86 0.42
36 88 0.43
37 15 0.07
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (34 bp):
AAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTC
Found at i:28955332 original size:17 final size:17
Alignment explanation
Indices: 28955063--28955352 Score: 77
Period size: 17 Copynumber: 16.5 Consensus size: 17
28955053 TTTCAAAAAA
*
28955063 AAAAATTTCGTGTTTC-
1 AAAAATTTTGTGTTTCT
* *
28955079 AAAAATCCTCGTGTTT-T
1 AAAAAT-TTTGTGTTTCT
*
28955096 CAAAAATTCTGGTGTTTC-
1 -AAAAATT-TTGTGTTTCT
28955114 AAAAATTTTCGTGTTT-T
1 AAAAATTTT-GTGTTTCT
** * *
28955131 CAAAAATTCCG-GTGATCC
1 -AAAAATTTTGTGT-TTCT
28955149 AAAAATTTTTGTGTTTTCT
1 AAAAA-TTTTGTG-TTTCT
*
28955168 AAAAATTTCCGTGTTTC-
1 AAAAATTT-TGTGTTTCT
28955185 AAAAATTTTTGTGTTT-T
1 AAAAA-TTTTGTGTTTCT
* *
28955202 CACAAATTTACGTGTTT-T
1 -AAAAATTT-TGTGTTTCT
* * * * *
28955220 CAACGACTGTAGTCTTTC-
1 -AA-AAATTTTGTGTTTCT
*
28955238 ACAAATTTTCGTGTTT-T
1 AAAAATTTT-GTGTTTCT
28955255 AAAAAATTTTTGTGTTT-T
1 -AAAAA-TTTTGTGTTTCT
**
28955273 GAAAAAATTCTCATGTTTC-
1 --AAAAATT-TTGTGTTTCT
* *
28955292 AAAAATTGTCGTGTTTAT
1 AAAAATT-TTGTGTTTCT
28955310 AAAAAAATTTTGTGTTTCT
1 --AAAAATTTTGTGTTTCT
*
28955329 AAAATTTTTGTGTTTC-
1 AAAAATTTTGTGTTTCT
28955345 -AAAATTTT
1 AAAAATTTT
28955353 CATTTAAAAA
Statistics
Matches: 206, Mismatches: 38, Indels: 61
0.68 0.12 0.20
Matches are distributed among these distances:
15 7 0.03
16 12 0.06
17 77 0.37
18 64 0.31
19 38 0.18
20 8 0.04
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (17 bp):
AAAAATTTTGTGTTTCT
Found at i:28956556 original size:106 final size:106
Alignment explanation
Indices: 28956383--28956582 Score: 355
Period size: 106 Copynumber: 1.9 Consensus size: 106
28956373 ATTGGAAAAC
28956383 CATTAACTTAATATTCATCTGATGCAGCTTAAGGTCAAAATATTCCACTAAAGCCATTATAATCC
1 CATTAACTTAATATTCATCTGATGCAGCTTAAGGTCAAAATATTCCACTAAAGCCATTATAATCC
28956448 TTTCTCTAGTGGACCTTTTTTAATGACATCCATTGATCATA
66 TTTCTCTAGTGGACCTTTTTTAATGACATCCATTGATCATA
* * * * *
28956489 CATTAACTTAATATTCATCTGGTGTAGCTTAATGTCAAAATATTCCACTAAATCCTTTATAATCC
1 CATTAACTTAATATTCATCTGATGCAGCTTAAGGTCAAAATATTCCACTAAAGCCATTATAATCC
28956554 TTTCTCTAGTGGACCTTTTTTAATGACAT
66 TTTCTCTAGTGGACCTTTTTTAATGACAT
28956583 TCGTTCATGA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 89 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (106 bp):
CATTAACTTAATATTCATCTGATGCAGCTTAAGGTCAAAATATTCCACTAAAGCCATTATAATCC
TTTCTCTAGTGGACCTTTTTTAATGACATCCATTGATCATA
Found at i:28960395 original size:17 final size:18
Alignment explanation
Indices: 28960373--28960408 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28960363 AGTGAACGAA
*
28960373 AAATAATCAATA-AATAC
1 AAATAAGCAATACAATAC
28960390 AAATAAGCAATACAATAC
1 AAATAAGCAATACAATAC
28960408 A
1 A
28960409 CATGAGAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.64, C:0.14, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATAAGCAATACAATAC
Found at i:28980736 original size:3 final size:3
Alignment explanation
Indices: 28980728--28980789 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
28980718 CAAGCCCTAA
28980728 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
28980776 TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TA
28980790 ATAATAATAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:28981815 original size:24 final size:24
Alignment explanation
Indices: 28981764--28981819 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
28981754 TTAAAATACT
*
28981764 TTAAAAATATTTTTATTTTTTATT
1 TTAAAAATATTTTTATTTTTTATA
28981788 TTAAAAATATTTTT-TTTGTGTT-TA
1 TTAAAAATATTTTTATTT-T-TTATA
28981812 TTAAAAAT
1 TTAAAAAT
28981820 CGGGCCGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 3 0.10
24 24 0.83
25 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TTAAAAATATTTTTATTTTTTATA
Found at i:28990821 original size:15 final size:16
Alignment explanation
Indices: 28990791--28990824 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
28990781 AGACTTCAAT
28990791 TTTAAATTTGTGTTAA
1 TTTAAATTTGTGTTAA
28990807 TTTAAATTT-TGTTAA
1 TTTAAATTTGTGTTAA
28990822 TTT
1 TTT
28990825 TTTTATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (16 bp):
TTTAAATTTGTGTTAA
Found at i:28999916 original size:14 final size:14
Alignment explanation
Indices: 28999892--28999933 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
28999882 AATCAAAGTC
* *
28999892 AAAACAAAAAATGA
1 AAAAGAAAAAAGGA
*
28999906 AAATGAAAAAAGGA
1 AAAAGAAAAAAGGA
28999920 AAAAGAAAAAAGGA
1 AAAAGAAAAAAGGA
28999934 GAGGCCAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (14 bp):
AAAAGAAAAAAGGA
Found at i:29000819 original size:6 final size:7
Alignment explanation
Indices: 29000799--29000849 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
29000789 CAGAAAAATG
29000799 TGAAAAA
1 TGAAAAA
29000806 TGAAAAAA
1 TG-AAAAA
29000814 TG-AAAA
1 TGAAAAA
29000820 TGAAAAA
1 TGAAAAA
29000827 TGAAAAA
1 TGAAAAA
29000834 TGAAAAA
1 TGAAAAA
29000841 -GTAAAAA
1 TG-AAAAA
29000848 TG
1 TG
29000850 GAGAGGCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 7 0.17
7 25 0.62
8 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
TGAAAAA
Found at i:29002263 original size:44 final size:44
Alignment explanation
Indices: 29002160--29002270 Score: 159
Period size: 44 Copynumber: 2.5 Consensus size: 44
29002150 TATTGGTGGC
* * *
29002160 GAAGTAGATCGAAGAAAACAGATCTTGCCTTTATGTACTAGCAT
1 GAAGTAGATCGAAGATAGCAGATCTTGCCTTCATGTACTAGCAT
* * *
29002204 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTACTGGCAT
1 GAAGTAGATCGAAGATAGCAGATCTTGCCTTCATGTACTAGCAT
*
29002248 GAAGTAGATCGAAGATGGCAGAT
1 GAAGTAGATCGAAGATAGCAGAT
29002271 TTTACCTCCC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (44 bp):
GAAGTAGATCGAAGATAGCAGATCTTGCCTTCATGTACTAGCAT
Found at i:29002583 original size:50 final size:50
Alignment explanation
Indices: 29002474--29002768 Score: 302
Period size: 50 Copynumber: 5.9 Consensus size: 50
29002464 ACAGCGGAGT
* * * * * * * *
29002474 AGATTAAAGCCACAACGGTGAATCTTGCTTCTCTAAAATTACAGTTAAAA
1 AGATTAAAGCCACGACGGCGAATCTTACTTCCCTGACATTGCAGTGAAAA
* * * ** * *
29002524 AGACTAAAGCCACGACGGCGAGTCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACGACGGCGAATCTTACTTCCCTGACATTGCAGTGAAAA
* * * *
29002574 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACGACGGCGAATCTTACTTCCCTGACATTGCAGTGAAAA
* * * * * *
29002624 AGATTAAAGCCACGACGACAAATCTTACTTCCCTGGCATTGCATTGGAAT
1 AGATTAAAGCCACGACGGCGAATCTTACTTCCCTGACATTGCAGTGAAAA
* * * * * *
29002674 AGATTAAAGCCACAACGGCGACTCTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCCACGACGGCGAATCTTACTTCCCTGACATTGCAGTGAAAA
*
29002724 AGATTAAAGCCACGACGACGAATCTTACTTCCCTGACATTGCAGT
1 AGATTAAAGCCACGACGGCGAATCTTACTTCCCTGACATTGCAGT
29002769 CAGATAGAAG
Statistics
Matches: 191, Mismatches: 54, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 191 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACGACGGCGAATCTTACTTCCCTGACATTGCAGTGAAAA
Found at i:29002776 original size:100 final size:100
Alignment explanation
Indices: 29002473--29002768 Score: 439
Period size: 100 Copynumber: 3.0 Consensus size: 100
29002463 TACAGCGGAG
* * ** * * *
29002473 TAGATTAAAGCCACAACGGTGAATCTTGCTTCTCTAAAATTACAGTTAAAAAGACTAAAGCCACG
1 TAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACG
* * **
29002538 ACGGCGAGTCTTACTTCCCTGGCGGTGCAGTGGAA
66 ACGACGAATCTTACTTCCCTGGCATTGCAGTGGAA
*
29002573 CAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACG
1 TAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACG
* *
29002638 ACGACAAATCTTACTTCCCTGGCATTGCATTGGAA
66 ACGACGAATCTTACTTCCCTGGCATTGCAGTGGAA
* *
29002673 TAGATTAAAGCCACAACGGCGACTCTTGCTTCCCCGACATTGTAGTTAAAAAGATTAAAGCCACG
1 TAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACG
*
29002738 ACGACGAATCTTACTTCCCTGACATTGCAGT
66 ACGACGAATCTTACTTCCCTGGCATTGCAGT
29002769 CAGATAGAAG
Statistics
Matches: 176, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 176 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (100 bp):
TAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACG
ACGACGAATCTTACTTCCCTGGCATTGCAGTGGAA
Found at i:29003331 original size:16 final size:16
Alignment explanation
Indices: 29003310--29003346 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
29003300 AACCCAATAT
29003310 CCCAATCATAACTCAG
1 CCCAATCATAACTCAG
29003326 CCCAATCATAACTCAG
1 CCCAATCATAACTCAG
29003342 CCCAA
1 CCCAA
29003347 ATGACCTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.41, G:0.05, T:0.16
Consensus pattern (16 bp):
CCCAATCATAACTCAG
Found at i:29003547 original size:11 final size:11
Alignment explanation
Indices: 29003533--29003557 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29003523 GGGATTTCAT
29003533 TTTTATTTTTC
1 TTTTATTTTTC
29003544 TTTTATTTTTC
1 TTTTATTTTTC
29003555 TTT
1 TTT
29003558 GTTCGGCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:29006067 original size:4 final size:4
Alignment explanation
Indices: 29006058--29006111 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
29006048 TTTAAGCCTC
29006058 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
29006106 ATGT AT
1 ATGT AT
29006112 CCAAGTCCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:29014831 original size:42 final size:42
Alignment explanation
Indices: 29014785--29015179 Score: 479
Period size: 42 Copynumber: 9.4 Consensus size: 42
29014775 AAAAACAATA
* **
29014785 GAGGTCCATTTACCTTTCATAACATTTAGAGACCCAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
**
29014827 GAGGTCTGTTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
* *
29014869 GAGGTTCATTTAC-TTTAATTGCATTTAGAGACCCAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
*** * *
29014910 GAGGTTTGTTCACTTTTCATTGCATTTAGAGATCCAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
* *
29014952 GAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
* * * * *
29014994 GAGGTACATTTACTTTTCATTGCATTTAGAGGCCTAGGTATA
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
* * *
29015036 GAGGTCCATTTACTTTTCATTGCATTTAGAGACCTAGATGTA
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
* * * *
29015078 GAGGTCTATTCACTTTTCATTCCATTTAGAGGCCCAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
* * * *
29015120 GAGGCCCATTGACTTTTCATTGGATTTAGA-AGCCTAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGA-CCCAGGTGTG
* *
29015162 GAGGTCCGTCTACTTTTC
1 GAGGTCCATTTACTTTTC
29015180 TAGTTTAGAG
Statistics
Matches: 305, Mismatches: 46, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
41 37 0.12
42 268 0.88
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (42 bp):
GAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGTGTG
Found at i:29016059 original size:26 final size:27
Alignment explanation
Indices: 29016030--29016082 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
29016020 AGAAAGTTTA
29016030 GATTTTAAAAAAT-AAATATATTTTTT
1 GATTTTAAAAAATAAAATATATTTTTT
29016056 GATTTTAAAAAATAAAATATATTTTTT
1 GATTTTAAAAAATAAAATATATTTTTT
29016083 TAGTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
GATTTTAAAAAATAAAATATATTTTTT
Found at i:29017332 original size:16 final size:15
Alignment explanation
Indices: 29017308--29017341 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
29017298 ATTTGAGACC
*
29017308 TTTTTTTCTTTTCTT
1 TTTTTTTCTTTCCTT
29017323 TTTTTCTTCTTTCCTT
1 TTTTT-TTCTTTCCTT
29017339 TTT
1 TTT
29017342 GACAGTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTCTTTCCTT
Found at i:29021071 original size:150 final size:146
Alignment explanation
Indices: 29020885--29021194 Score: 383
Period size: 150 Copynumber: 2.1 Consensus size: 146
29020875 AAGTTTTGAT
* * * * *
29020885 TTTTTTTTAAAAAAAAAAGTTTAGATTTTAACAAATAAAAATATGTTTTTTTAGTTATTTTAAAG
1 TTTTTTTAAAAAAAAAAAGTTTAGATTTTAACAAATAAAAATATATTTTTTAAGTCATTTTAAAA
* *
29020950 GAAAGTAGAAATTTTTAGAACAAAATTTTAATTTTTTTCAACTATTT-TAAAGTAAAATCTTTAA
66 GAAAGTAGAAATTTTTAAAACAAAATTTTAATTTTTTT-AACTATTTCGAAA-TAAAAT-TTTAA
29021014 TCTTTAAGAAAAAT-AGTA
128 TCTTTAAGAAAAATAAGTA
29021032 TTTTTTTAAAAAAAGCAGAAAGTTTAGATTTTGAA-AAATAAAAATATATTTTTTAAGTCATTTT
1 TTTTTTTAAAAAAA--A-AAAGTTTAGATTTT-AACAAATAAAAATATATTTTTTAAGTCATTTT
** * * ** *
29021096 AAAAGAAAGTTTACATTTTTAAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAGGTTTTG
62 AAAAGAAAGTAGAAATTTTTAAAACAAAATTTTAATTTTTTTAACTATTTCGAAATAAAATTTTA
* * *
29021161 ATTTTTAAGAAAATTAATTA
127 ATCTTTAAGAAAAATAAGTA
29021181 TTTTTTTAAAAAAA
1 TTTTTTTAAAAAAA
29021195 CTTTGATTTT
Statistics
Matches: 140, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
147 13 0.09
148 16 0.11
149 30 0.21
150 79 0.56
151 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (146 bp):
TTTTTTTAAAAAAAAAAAGTTTAGATTTTAACAAATAAAAATATATTTTTTAAGTCATTTTAAAA
GAAAGTAGAAATTTTTAAAACAAAATTTTAATTTTTTTAACTATTTCGAAATAAAATTTTAATCT
TTAAGAAAAATAAGTA
Found at i:29024862 original size:14 final size:14
Alignment explanation
Indices: 29024843--29024877 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
29024833 CTTAATTAAA
29024843 TTTTTTATTTCTAT
1 TTTTTTATTTCTAT
*
29024857 TTTTTTATTTTTAT
1 TTTTTTATTTCTAT
29024871 TTATTTT
1 TT-TTTT
29024878 TTTAGAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTATTTCTAT
Found at i:29024869 original size:20 final size:18
Alignment explanation
Indices: 29024844--29024881 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
29024834 TTAATTAAAT
29024844 TTTTTATTTCTATTTTTTTA
1 TTTTTA-TT-TATTTTTTTA
29024864 TTTTTATTTATTTTTTTA
1 TTTTTATTTATTTTTTTA
29024882 GAGTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTATTTATTTTTTTA
Found at i:29027442 original size:6 final size:6
Alignment explanation
Indices: 29027431--29027482 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
29027421 ATCTAAAAAT
29027431 CTAATA CTAATA CTAATA CTAATA CTAATA CTAATA CTAATA CTAAT-
1 CTAATA CTAATA CTAATA CTAATA CTAATA CTAATA CTAATA CTAATA
29027478 CTAAT
1 CTAAT
29027483 GCAGAAATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 41 0.89
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (6 bp):
CTAATA
Found at i:29027529 original size:8 final size:8
Alignment explanation
Indices: 29027518--29027549 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
29027508 AACAAGTAGA
29027518 ATAATAAT
1 ATAATAAT
29027526 ATAAATAAT
1 AT-AATAAT
29027535 ATAATAAT
1 ATAATAAT
29027543 ATAATAA
1 ATAATAA
29027550 AATACACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
ATAATAAT
Found at i:29036250 original size:315 final size:315
Alignment explanation
Indices: 29035678--29036297 Score: 1240
Period size: 315 Copynumber: 2.0 Consensus size: 315
29035668 ATGCACCGGG
29035678 TAATTTTTTTCATGTGTCTTAAGTTGTCTCGAAGCATAGGCTATAAATTTACCTTCTTGCATCAA
1 TAATTTTTTTCATGTGTCTTAAGTTGTCTCGAAGCATAGGCTATAAATTTACCTTCTTGCATCAA
29035743 GACACAACCTAAACCATTTAATGATGTATCACTATAAATAATAAATTCTTTAGCCGGTTCAGGCT
66 GACACAACCTAAACCATTTAATGATGTATCACTATAAATAATAAATTCTTTAGCCGGTTCAGGCT
29035808 GTACCAACACAGGTGTTTTCGTTAACAAATCTATCAATCGATCGAAAATCTAGTGGCATTCATCA
131 GTACCAACACAGGTGTTTTCGTTAACAAATCTATCAATCGATCGAAAATCTAGTGGCATTCATCA
29035873 GTCCACAAGAATTTAACATCTTTCTGTAATAAACGGGTTATCGGAGAAGCTATCATAGAGAACCC
196 GTCCACAAGAATTTAACATCTTTCTGTAATAAACGGGTTATCGGAGAAGCTATCATAGAGAACCC
29035938 CTGTACAAATCTCCGATAATAACCAGCTAAACCCAAGAAATTTCTTCAGCTACAT
261 CTGTACAAATCTCCGATAATAACCAGCTAAACCCAAGAAATTTCTTCAGCTACAT
29035993 TAATTTTTTTCATGTGTCTTAAGTTGTCTCGAAGCATAGGCTATAAATTTACCTTCTTGCATCAA
1 TAATTTTTTTCATGTGTCTTAAGTTGTCTCGAAGCATAGGCTATAAATTTACCTTCTTGCATCAA
29036058 GACACAACCTAAACCATTTAATGATGTATCACTATAAATAATAAATTCTTTAGCCGGTTCAGGCT
66 GACACAACCTAAACCATTTAATGATGTATCACTATAAATAATAAATTCTTTAGCCGGTTCAGGCT
29036123 GTACCAACACAGGTGTTTTCGTTAACAAATCTATCAATCGATCGAAAATCTAGTGGCATTCATCA
131 GTACCAACACAGGTGTTTTCGTTAACAAATCTATCAATCGATCGAAAATCTAGTGGCATTCATCA
29036188 GTCCACAAGAATTTAACATCTTTCTGTAATAAACGGGTTATCGGAGAAGCTATCATAGAGAACCC
196 GTCCACAAGAATTTAACATCTTTCTGTAATAAACGGGTTATCGGAGAAGCTATCATAGAGAACCC
29036253 CTGTACAAATCTCCGATAATAACCAGCTAAACCCAAGAAATTTCT
261 CTGTACAAATCTCCGATAATAACCAGCTAAACCCAAGAAATTTCT
29036298 AACTTCAGCT
Statistics
Matches: 305, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
315 305 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (315 bp):
TAATTTTTTTCATGTGTCTTAAGTTGTCTCGAAGCATAGGCTATAAATTTACCTTCTTGCATCAA
GACACAACCTAAACCATTTAATGATGTATCACTATAAATAATAAATTCTTTAGCCGGTTCAGGCT
GTACCAACACAGGTGTTTTCGTTAACAAATCTATCAATCGATCGAAAATCTAGTGGCATTCATCA
GTCCACAAGAATTTAACATCTTTCTGTAATAAACGGGTTATCGGAGAAGCTATCATAGAGAACCC
CTGTACAAATCTCCGATAATAACCAGCTAAACCCAAGAAATTTCTTCAGCTACAT
Found at i:29044297 original size:32 final size:32
Alignment explanation
Indices: 29044256--29044320 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
29044246 TATACAAGCT
*
29044256 AAACATAATGGCTAATTGCATTAAACAAAGAC
1 AAACATAATGGCTAATTGCATCAAACAAAGAC
29044288 AAACATAATGGCTAATTGCATCAAACAAAGAC
1 AAACATAATGGCTAATTGCATCAAACAAAGAC
29044320 A
1 A
29044321 CCTATACATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (32 bp):
AAACATAATGGCTAATTGCATCAAACAAAGAC
Found at i:29051032 original size:15 final size:16
Alignment explanation
Indices: 29051012--29051041 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29051002 ATGACCCCCC
29051012 CCCCCCCTT-TTTTTT
1 CCCCCCCTTGTTTTTT
29051027 CCCCCCCTTGTTTTT
1 CCCCCCCTTGTTTTT
29051042 AACCTCTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (16 bp):
CCCCCCCTTGTTTTTT
Found at i:29052068 original size:65 final size:66
Alignment explanation
Indices: 29051992--29052125 Score: 234
Period size: 66 Copynumber: 2.0 Consensus size: 66
29051982 TCATAATTGG
* *
29051992 AATGTTAACATGGTA-TTTTATTTGCATCATGATAATTTTAGCTCTTAATTTTTGCACATTGCAT
1 AATGTCAACATGGTATTTTTATTTGCATCATGATAATTTTAACTCTTAATTTTTGCACATTGCAT
29052056 C
66 C
*
29052057 AATGTCAACATGGTATTTTTATTTGCATCATGATAATTTTAATTCTTAATTTTTGCACATTGCAT
1 AATGTCAACATGGTATTTTTATTTGCATCATGATAATTTTAACTCTTAATTTTTGCACATTGCAT
29052122 C
66 C
29052123 AAT
1 AAT
29052126 TTAATTTTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 14 0.22
66 51 0.78
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.46
Consensus pattern (66 bp):
AATGTCAACATGGTATTTTTATTTGCATCATGATAATTTTAACTCTTAATTTTTGCACATTGCAT
C
Found at i:29054280 original size:19 final size:20
Alignment explanation
Indices: 29054242--29054281 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
29054232 TTCTCTTATA
* *
29054242 TAAAATGTATTTTAATATTT
1 TAAAATGTATTTGAAAATTT
29054262 TAAAAT-TATTTGAAAATTT
1 TAAAATGTATTTGAAAATTT
29054281 T
1 T
29054282 GCTAGATTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TAAAATGTATTTGAAAATTT
Found at i:29056066 original size:47 final size:47
Alignment explanation
Indices: 29056011--29056140 Score: 188
Period size: 47 Copynumber: 2.8 Consensus size: 47
29056001 CAAAGTTGCT
* ***
29056011 AATATGTTGTGGATGAACCACTAGTCGAGCAGATGACTGTTGACTAA
1 AATATGTTGTGGATAAACCACTAGTCGAGCAGATGACTGCCAACTAA
* *
29056058 AATATGTTGTGGATAAACCACTGGTCGAGCAGATGACTGCCAACTAG
1 AATATGTTGTGGATAAACCACTAGTCGAGCAGATGACTGCCAACTAA
* *
29056105 AATACGTTGTGGATAAACCACTAGTCGAGTAGATGA
1 AATATGTTGTGGATAAACCACTAGTCGAGCAGATGA
29056141 ATTACCGACT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (47 bp):
AATATGTTGTGGATAAACCACTAGTCGAGCAGATGACTGCCAACTAA
Found at i:29060360 original size:12 final size:12
Alignment explanation
Indices: 29060343--29060372 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29060333 TGTAGCTAAT
29060343 ATGTGAACCTTC
1 ATGTGAACCTTC
*
29060355 ATGTGAACCTTT
1 ATGTGAACCTTC
29060367 ATGTGA
1 ATGTGA
29060373 TTTAGTACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (12 bp):
ATGTGAACCTTC
Found at i:29060415 original size:13 final size:13
Alignment explanation
Indices: 29060399--29060465 Score: 98
Period size: 13 Copynumber: 5.2 Consensus size: 13
29060389 TATATACAAG
29060399 CCCTATATGTGAA
1 CCCTATATGTGAA
29060412 CCCTATATGTGAA
1 CCCTATATGTGAA
** *
29060425 CTATATATGCGAA
1 CCCTATATGTGAA
29060438 CCCTATATGTGAA
1 CCCTATATGTGAA
*
29060451 CCCTATATGCGAA
1 CCCTATATGTGAA
29060464 CC
1 CC
29060466 TGTTATGTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (13 bp):
CCCTATATGTGAA
Found at i:29074218 original size:15 final size:17
Alignment explanation
Indices: 29074191--29074225 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
29074181 TTTCATTTTC
29074191 ATTTTATTTCACT-ATT
1 ATTTTATTTCACTCATT
29074207 ATTTTA-TTCACTCATT
1 ATTTTATTTCACTCATT
29074223 ATT
1 ATT
29074226 ATAACTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTTCACTCATT
Found at i:29075024 original size:43 final size:43
Alignment explanation
Indices: 29074973--29075132 Score: 205
Period size: 43 Copynumber: 3.7 Consensus size: 43
29074963 CTGGCACGTA
* *
29074973 AGTGCATCATTGGATAAACCGAAGAAAATATATTGGCACACAT
1 AGTGCATCATCGGATAAACCGAAGAAAATATATTGGCACACAC
* *
29075016 AGTGCATCATCGGAGAAACTGAAGAAAATATATTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGAAAATATATTGGCACACAC
* * * * *
29075059 AATGCATCATCGGATGAAACTGAAGATACTATACTGGCACACAC
1 AGTGCATCATCGGAT-AAACCGAAGAAAATATATTGGCACACAC
*
29075103 AGTGCATCA-CTGGATAAACCAAAGAAAATA
1 AGTGCATCATC-GGATAAACCGAAGAAAATA
29075133 AGATATACCG
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
43 64 0.63
44 37 0.37
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (43 bp):
AGTGCATCATCGGATAAACCGAAGAAAATATATTGGCACACAC
Found at i:29075166 original size:26 final size:24
Alignment explanation
Indices: 29075137--29075190 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
29075127 AAAATAAGAT
*
29075137 ATACCGAAGCAAATATACTAGCACAC
1 ATACCAAAGCAAATATACTA--ACAC
*
29075163 ATACCAAAGGAAATATACTAACAC
1 ATACCAAAGCAAATATACTAACAC
29075187 ATAC
1 ATAC
29075191 AGTGCATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 8 0.31
26 18 0.69
ACGTcount: A:0.50, C:0.24, G:0.09, T:0.17
Consensus pattern (24 bp):
ATACCAAAGCAAATATACTAACAC
Found at i:29078714 original size:38 final size:37
Alignment explanation
Indices: 29078659--29078736 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 37
29078649 GTTAACTTTC
* *
29078659 AATACACCGGCACAAAGCCTGCTAGGCACAGAGTCCG
1 AATACACCGGCACAAAGCCTACTAGGCACAGAGCCCG
*
29078696 AATATCACCGGCATAAAGCCTACTAGGCACAGAGCCCG
1 AATA-CACCGGCACAAAGCCTACTAGGCACAGAGCCCG
29078734 AAT
1 AAT
29078737 GACATTACGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 4 0.11
38 33 0.89
ACGTcount: A:0.35, C:0.31, G:0.22, T:0.13
Consensus pattern (37 bp):
AATACACCGGCACAAAGCCTACTAGGCACAGAGCCCG
Found at i:29080443 original size:19 final size:19
Alignment explanation
Indices: 29080404--29080443 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29080394 ATATGGGGTA
*
29080404 AATAATTCTTTCATCTAAC
1 AATAATTCTTTCACCTAAC
*
29080423 AATAATTCTTTCACCTTAC
1 AATAATTCTTTCACCTAAC
29080442 AA
1 AA
29080444 ACCATTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (19 bp):
AATAATTCTTTCACCTAAC
Found at i:29083167 original size:4 final size:4
Alignment explanation
Indices: 29083158--29083231 Score: 71
Period size: 4 Copynumber: 18.2 Consensus size: 4
29083148 TAAAACACCT
* * * *
29083158 AATA AATA AATA AA-A AATA AA-G AATA AATT AGTA GGATTAA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA --AAT-A AATA AATA
29083207 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
29083232 TTGTAAGAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
3 5 0.09
4 48 0.83
5 2 0.03
6 2 0.03
7 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:29086067 original size:21 final size:21
Alignment explanation
Indices: 29086034--29086084 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
29086024 TTTTTTTCAG
*
29086034 CAACTT-CTACTTCTTCAGCAA
1 CAACTTCCT-CTTCTGCAGCAA
* *
29086055 CAGCTTCCTCTTCTGCAGCAG
1 CAACTTCCTCTTCTGCAGCAA
29086076 CAACTTCCT
1 CAACTTCCT
29086085 TCTCAACAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.22, C:0.37, G:0.10, T:0.31
Consensus pattern (21 bp):
CAACTTCCTCTTCTGCAGCAA
Found at i:29089969 original size:68 final size:68
Alignment explanation
Indices: 29089869--29090011 Score: 182
Period size: 68 Copynumber: 2.1 Consensus size: 68
29089859 AAGCATGTCT
* * * *
29089869 TTTGCTATTCTATTTATTTGTTATAAATATATTAATTG-C-TACTGCATTGATCCGTTATAAGCA
1 TTTGCTATTCTATTGATTTGTTATAAACATATTAATTGTCAT-C-GCAATGATCCATTATAAGCA
29089932 TATTA
64 TATTA
* * * *
29089937 TTTGCTATTGTATTGATTTGTTATAAGCATATTAATTGTCATCGTAATGATTCATTATAAGCATA
1 TTTGCTATTCTATTGATTTGTTATAAACATATTAATTGTCATCGCAATGATCCATTATAAGCATA
29090002 TTA
66 TTA
29090005 TTTGCTA
1 TTTGCTA
29090012 CCGTATCAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
68 62 0.95
69 2 0.03
70 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (68 bp):
TTTGCTATTCTATTGATTTGTTATAAACATATTAATTGTCATCGCAATGATCCATTATAAGCATA
TTA
Found at i:29089988 original size:34 final size:34
Alignment explanation
Indices: 29089888--29090016 Score: 118
Period size: 34 Copynumber: 3.8 Consensus size: 34
29089878 CTATTTATTT
** * * *
29089888 GTTATAAATATATTAATTGCTA-CTGCATTGATCC
1 GTTATAAGCATATTAATTGCTATC-GTAATGATTC
* * * *
29089922 GTTATAAGCATATTATTTGCTATTGTATTGATTT
1 GTTATAAGCATATTAATTGCTATCGTAATGATTC
29089956 GTTATAAGCATATTAATTG-TCATCGTAATGATTC
1 GTTATAAGCATATTAATTGCT-ATCGTAATGATTC
* * *
29089990 ATTATAAGCATATTATTTGCTACCGTA
1 GTTATAAGCATATTAATTGCTATCGTA
29090017 TCAAGTTGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
33 1 0.01
34 76 0.97
35 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (34 bp):
GTTATAAGCATATTAATTGCTATCGTAATGATTC
Found at i:29090029 original size:34 final size:33
Alignment explanation
Indices: 29089922--29090031 Score: 98
Period size: 34 Copynumber: 3.2 Consensus size: 33
29089912 GCATTGATCC
* * *
29089922 GTTATAAGCATATTATTTGCTATTGTATTGATTT
1 GTTATAAGCATATTATTTGCTATCGTA-TAAGTT
* *
29089956 GTTATAAGCATATTAATTG-TCATCGTA-ATGATT
1 GTTATAAGCATATTATTTGCT-ATCGTATAAG-TT
* *
29089989 CATTATAAGCATATTATTTGCTACCGTATCAAGTT
1 -GTTATAAGCATATTATTTGCTATCGTAT-AAGTT
29090024 GTTATAAG
1 GTTATAAG
29090032 GAAATTAATT
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
33 3 0.05
34 52 0.87
35 3 0.05
36 2 0.03
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.45
Consensus pattern (33 bp):
GTTATAAGCATATTATTTGCTATCGTATAAGTT
Found at i:29090062 original size:68 final size:68
Alignment explanation
Indices: 29089914--29090068 Score: 161
Period size: 68 Copynumber: 2.3 Consensus size: 68
29089904 TTGCTACTGC
** ** ** * * * *
29089914 ATTGATCCGTTATAAGCATATTATTTGCTATTGTATTGATTTGTTATAAGCATATTAATTGTCAT
1 ATTGATCTATTATAAGCATATTATTTGCTACCGTATCAAGTTGTTATAAGCAAATTAATTCTCAC
*
29089979 CGT
66 CAT
* *
29089982 AATGAT-TCATTATAAGCATATTATTTGCTACCGTATCAAGTTGTTATAAGGAAATTAATTACT-
1 ATTGATCT-ATTATAAGCATATTATTTGCTACCGTATCAAGTTGTTATAAGCAAATTAATT-CTC
29090045 ACCAT
64 ACCAT
29090050 ATTGATCTATTATAAGCAT
1 ATTGATCTATTATAAGCAT
29090069 GTCATATTGC
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
68 68 0.97
69 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.43
Consensus pattern (68 bp):
ATTGATCTATTATAAGCATATTATTTGCTACCGTATCAAGTTGTTATAAGCAAATTAATTCTCAC
CAT
Found at i:29093178 original size:23 final size:23
Alignment explanation
Indices: 29093152--29093199 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
29093142 TGTGCAGTGA
29093152 AAGTTTGTAGAAAACAGTAAGAG
1 AAGTTTGTAGAAAACAGTAAGAG
29093175 AAGTTTGTAGAAAACAGTAAGAG
1 AAGTTTGTAGAAAACAGTAAGAG
29093198 AA
1 AA
29093200 TGTATGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.25, T:0.21
Consensus pattern (23 bp):
AAGTTTGTAGAAAACAGTAAGAG
Found at i:29094679 original size:15 final size:14
Alignment explanation
Indices: 29094645--29094685 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
29094635 ATTCCTTGTT
29094645 AAAAATAACATCCC
1 AAAAATAACATCCC
29094659 AAAAATAACATCCC
1 AAAAATAACATCCC
29094673 AACAAATAA-ATCC
1 AA-AAATAACATCC
29094686 AAAGGTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATAACATCCC
Found at i:29099947 original size:101 final size:103
Alignment explanation
Indices: 29099772--29099979 Score: 375
Period size: 101 Copynumber: 2.0 Consensus size: 103
29099762 GGCAACATAC
29099772 CAAAATAGTTTTGACTTTCAGAACCACTTTGATTATCGAAACTATGATAGTTGATAGACATTAAC
1 CAAAATAGTTTTGACTTTCAGAACCACTTTGATTATCGAAACTATGATAGTTGATAGACATTAAC
*
29099837 TGACCCTGATCACCATGTAATCC-AAAAAAAA-TTAAT
66 TGACCCTGATCACCAGGTAATCCAAAAAAAAATTTAAT
* *
29099873 CAAAATAGTTTTTACTTTCAGAACCACTTTGATTATCGAAACTATGATAGTTGATTGACATTAAC
1 CAAAATAGTTTTGACTTTCAGAACCACTTTGATTATCGAAACTATGATAGTTGATAGACATTAAC
29099938 TGACCCTGATCACCAGGTAATCCAAAAAAAAATTTAAT
66 TGACCCTGATCACCAGGTAATCCAAAAAAAAATTTAAT
29099976 CAAA
1 CAAA
29099980 CCTGTAGTAA
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 85 0.83
102 8 0.08
103 9 0.09
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (103 bp):
CAAAATAGTTTTGACTTTCAGAACCACTTTGATTATCGAAACTATGATAGTTGATAGACATTAAC
TGACCCTGATCACCAGGTAATCCAAAAAAAAATTTAAT
Found at i:29101138 original size:16 final size:16
Alignment explanation
Indices: 29101117--29101147 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29101107 ATTAACTATA
29101117 GCTAACAACCCTAACT
1 GCTAACAACCCTAACT
*
29101133 GCTAACAACCTTAAC
1 GCTAACAACCCTAAC
29101148 AGCTTCTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.35, G:0.06, T:0.19
Consensus pattern (16 bp):
GCTAACAACCCTAACT
Found at i:29102118 original size:42 final size:42
Alignment explanation
Indices: 29102037--29102120 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
29102027 ATATTTTATT
* *
29102037 TTATCTTTTAGTAGTTTATTAGAATAAGGAAATTATTTTCCC
1 TTATCTTTTAGTAGATTATTAAAATAAGGAAATTATTTTCCC
* *
29102079 TTATGTTTTAGTAGATTATTAAAATAAGGGAATTATTTTCCC
1 TTATCTTTTAGTAGATTATTAAAATAAGGAAATTATTTTCCC
29102121 AAGTAGGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.46
Consensus pattern (42 bp):
TTATCTTTTAGTAGATTATTAAAATAAGGAAATTATTTTCCC
Found at i:29112476 original size:16 final size:17
Alignment explanation
Indices: 29112439--29112476 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
29112429 ATTAGGAGAA
* *
29112439 CTTTAATTAAAAGTCTT
1 CTTTAATTAAAAATCAT
29112456 CTTTAATTAAAAAT-AT
1 CTTTAATTAAAAATCAT
29112472 CTTTA
1 CTTTA
29112477 TGGTATTACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (17 bp):
CTTTAATTAAAAATCAT
Found at i:29120173 original size:27 final size:28
Alignment explanation
Indices: 29120143--29120199 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
29120133 TTCTTTAATC
29120143 TCTTT-CCAACCGCTAC-CTTCTTTTTCT
1 TCTTTCCCAACCGCTACTC-TCTTTTTCT
*
29120170 TCTTTGCCCAGCCGCTACTCTCTTTTTCT
1 TCTTT-CCCAACCGCTACTCTCTTTTTCT
29120199 T
1 T
29120200 TTCTATTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 5 0.19
29 20 0.77
30 1 0.04
ACGTcount: A:0.09, C:0.37, G:0.07, T:0.47
Consensus pattern (28 bp):
TCTTTCCCAACCGCTACTCTCTTTTTCT
Found at i:29121066 original size:128 final size:128
Alignment explanation
Indices: 29120836--29121093 Score: 489
Period size: 128 Copynumber: 2.0 Consensus size: 128
29120826 TGAAATTAGA
* *
29120836 TATTCTTAAAGTTTACTTTGCTTTCTAGTTTTGAATGAATTTAAATATAGTTGTGCTCTTTGAAT
1 TATTCTTAAAGTTTACTTTGCTTTCTAGTTTTCAATGAATTTAAATACAGTTGTGCTCTTTGAAT
29120901 AAATTTGGCTTGTGACATTTCTAGTACTTAGCAGTTGCATGTTACCTCTTTCACCTTCTAAGC
66 AAATTTGGCTTGTGACATTTCTAGTACTTAGCAGTTGCATGTTACCTCTTTCACCTTCTAAGC
29120964 TATTCTTAAAGTTTACTTTGCTTTCTAGTTTTCAATGAATTTAAATACAGTTGTGCTCTTTGAAT
1 TATTCTTAAAGTTTACTTTGCTTTCTAGTTTTCAATGAATTTAAATACAGTTGTGCTCTTTGAAT
*
29121029 AAATTTGGCTTGTGACATTTCTAGTACTTAGCGGTTGCATGTTACCTCTTTCACCTTCTAAGC
66 AAATTTGGCTTGTGACATTTCTAGTACTTAGCAGTTGCATGTTACCTCTTTCACCTTCTAAGC
29121092 TA
1 TA
29121094 CTACTATAAA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (128 bp):
TATTCTTAAAGTTTACTTTGCTTTCTAGTTTTCAATGAATTTAAATACAGTTGTGCTCTTTGAAT
AAATTTGGCTTGTGACATTTCTAGTACTTAGCAGTTGCATGTTACCTCTTTCACCTTCTAAGC
Found at i:29122679 original size:1 final size:1
Alignment explanation
Indices: 29122668--29122706 Score: 69
Period size: 1 Copynumber: 39.0 Consensus size: 1
29122658 TGATTTTGCA
*
29122668 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29122707 GTAGTTGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Done.