Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 107 of 144
Found at i:25065289 original size:28 final size:29
Alignment explanation
Indices: 25065249--25065328 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
25065239 AACGGGGTCG
*
25065249 AAAATGAAGTTTTAGAGAA-TTTGGAGTT
1 AAAATGAAGTTTTAGAAAAGTTTGGAGTT
* *
25065277 AAAATGCAA-TTTTGGAAAAGTTTGGGGTT
1 AAAATG-AAGTTTTAGAAAAGTTTGGAGTT
** *
25065306 AAAATGTGGTTTTGGAAAAGTTT
1 AAAATGAAGTTTTAGAAAAGTTT
25065329 AAGGTCAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 14 0.32
29 30 0.68
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAATGAAGTTTTAGAAAAGTTTGGAGTT
Found at i:25065307 original size:29 final size:30
Alignment explanation
Indices: 25065274--25065540 Score: 178
Period size: 29 Copynumber: 9.0 Consensus size: 30
25065264 AGAATTTGGA
25065274 GTTAAAATGCAATTTTGGAAAAGTTT-GGG
1 GTTAAAATGCAATTTTGGAAAAGTTTAGGG
*** *
25065303 GTTAAAATGTGGTTTTGGAAAAGTTTA-AG
1 GTTAAAATGCAATTTTGGAAAAGTTTAGGG
* * * *
25065332 GTCAAAATGTC-ACTTTGGGAAAGTTTGGTGG
1 GTTAAAATG-CAATTTTGGAAAAGTTTAG-GG
*
25065363 GTTAAAATGCAATTTTGGAAAA-TTGTA-GT
1 GTTAAAATGCAATTTTGGAAAAGTT-TAGGG
*
25065392 GTT-AAATGCAATTTTAGG-AAAGTTTAAGG
1 GTTAAAATGCAATTTT-GGAAAAGTTTAGGG
** *
25065421 GTT-AAATGTGATTTTGGGAAAGTTTAGGG
1 GTTAAAATGCAATTTTGGAAAAGTTTAGGG
** * * *
25065450 GCCAAAATGTAATTTTAGAAAAGTTTTGGGG
1 GTTAAAATGCAATTTTGGAAAAG-TTTAGGG
** * * *
25065481 GCCAAAATGAAATTTTAGAAAAGTTTAAGG
1 GTTAAAATGCAATTTTGGAAAAGTTTAGGG
*
25065511 GTTCAAATATG--ATTTTGGGAAAG-TTAGGG
1 GTT-AAA-ATGCAATTTTGGAAAAGTTTAGGG
25065540 G
1 G
25065541 ACTGCTTGGG
Statistics
Matches: 190, Mismatches: 34, Indels: 28
0.75 0.13 0.11
Matches are distributed among these distances:
28 19 0.10
29 83 0.44
30 35 0.18
31 50 0.26
32 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (30 bp):
GTTAAAATGCAATTTTGGAAAAGTTTAGGG
Found at i:25065488 original size:118 final size:117
Alignment explanation
Indices: 25065249--25065502 Score: 282
Period size: 117 Copynumber: 2.2 Consensus size: 117
25065239 AACGGGGTCG
* * * * *
25065249 AAAATGAAGTTTTAGAGAATTTGGAGT-TAAAATGCAATTTTGGAAAAGTTTGGGGTTAAAATGT
1 AAAATGAAATTTTAGA-AAATTGTAGTGTTAAATGCAATTTTGGAAAAGTTTAGGGTTAAAATGT
* * * * * **
25065313 GGTTTTGGAAAAGTTTAAGGTCAAAATGTCACTTTGGGAAAGTTTGGTGGGTT
65 GATTTTGGAAAAGTTTAAGGCCAAAATGTAACTTTAGAAAAGTTTGGTGGGCC
* *
25065366 AAAATGCAATTTTGGAAAATTGTAGTGTTAAATGCAATTTTAGG-AAAGTTTAAGGGTT-AAATG
1 AAAATGAAATTTTAGAAAATTGTAGTGTTAAATGCAATTTT-GGAAAAGTTT-AGGGTTAAAATG
* * *
25065429 TGATTTTGGGAAAGTTTAGGGGCCAAAATGTAATTTTAGAAAAGTTTTGG-GGGCC
64 TGATTTTGGAAAAGTTTA-AGGCCAAAATGTAACTTTAGAAAAG-TTTGGTGGGCC
25065484 AAAATGAAATTTTAGAAAA
1 AAAATGAAATTTTAGAAAA
25065503 GTTTAAGGGT
Statistics
Matches: 113, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
116 8 0.07
117 54 0.48
118 46 0.41
119 5 0.04
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (117 bp):
AAAATGAAATTTTAGAAAATTGTAGTGTTAAATGCAATTTTGGAAAAGTTTAGGGTTAAAATGTG
ATTTTGGAAAAGTTTAAGGCCAAAATGTAACTTTAGAAAAGTTTGGTGGGCC
Found at i:25069004 original size:18 final size:18
Alignment explanation
Indices: 25068966--25069004 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25068956 ATTGCTTCTC
*
25068966 AAAAGCACTTTTGGGACA
1 AAAAGCACTTTTGAGACA
* *
25068984 AAAAGTACTTTTGAGATA
1 AAAAGCACTTTTGAGACA
25069002 AAA
1 AAA
25069005 GCTTTACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (18 bp):
AAAAGCACTTTTGAGACA
Found at i:25074762 original size:39 final size:39
Alignment explanation
Indices: 25074708--25074808 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 39
25074698 TGTTGGTTCA
* * *
25074708 GTATTGTAGTATTTACATTGTCACTACCAGTTCATTATT
1 GTATTGAAGTGTTTACATTGTCACTACCAGTTCAGTATT
* * ** *
25074747 GTATTGCAGTGTTTACATTGTCACTGCTGGTTTAGTATT
1 GTATTGAAGTGTTTACATTGTCACTACCAGTTCAGTATT
* *
25074786 GTTTTGAAGTGTTTACAGTGTCA
1 GTATTGAAGTGTTTACATTGTCA
25074809 ATGCCAGTCC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.46
Consensus pattern (39 bp):
GTATTGAAGTGTTTACATTGTCACTACCAGTTCAGTATT
Found at i:25077638 original size:6 final size:6
Alignment explanation
Indices: 25077614--25077677 Score: 73
Period size: 6 Copynumber: 11.2 Consensus size: 6
25077604 AAATCTTTAA
*
25077614 TTAAAT TT--AT TTAAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-ATT
1 TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
25077660 TTAAA- TTAATT TTAAAT T
1 TTAAAT TTAAAT TTAAAT T
25077678 GAATTCAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.08
5 8 0.16
6 33 0.67
7 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:25077644 original size:12 final size:12
Alignment explanation
Indices: 25077614--25077677 Score: 73
Period size: 11 Copynumber: 5.6 Consensus size: 12
25077604 AAATCTTTAA
25077614 TTAAATTT--AT
1 TTAAATTTAAAT
25077624 TTAAAATTTAAAT
1 TT-AAATTTAAAT
25077637 TTAAATTTAAAT
1 TTAAATTTAAAT
*
25077649 TTAAATTT-ATT
1 TTAAATTTAAAT
*
25077660 TTAAA-TTAATT
1 TTAAATTTAAAT
25077671 TTAAATT
1 TTAAATT
25077678 GAATTCAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
10 4 0.08
11 21 0.44
12 19 0.40
13 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:25078300 original size:30 final size:30
Alignment explanation
Indices: 25078264--25078324 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
25078254 AGTTTGTAAA
25078264 TATGTTCATTTATTATAATATTAAAATCAC
1 TATGTTCATTTATTATAATATTAAAATCAC
25078294 TATGTTCATTTATTATAATATTAAAATCAC
1 TATGTTCATTTATTATAATATTAAAATCAC
25078324 T
1 T
25078325 CATTATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (30 bp):
TATGTTCATTTATTATAATATTAAAATCAC
Found at i:25079499 original size:29 final size:30
Alignment explanation
Indices: 25079461--25079684 Score: 158
Period size: 29 Copynumber: 7.5 Consensus size: 30
25079451 CTCAATCTAA
25079461 CTAAAAATTACATTTTGACCCCTAAACTTT
1 CTAAAAATTACATTTTGACCCCTAAACTTT
* * *
25079491 -TTAGAATTACATTTTGA-CACTAAAACTTT
1 CTAAAAATTACATTTTGACCCCT-AAACTTT
* *
25079520 CTAAAAATTACATTTTAACCCTTAAACTTT
1 CTAAAAATTACATTTTGACCCCTAAACTTT
* * * *
25079550 CAAAAAAAATTACATTTAG-CCCCCAAACTTA
1 C--TAAAAATTACATTTTGACCCCTAAACTTT
* * *
25079581 CAAAAAATTACATTTT-AACCCTCAATCTTT
1 CTAAAAATTACATTTTGACCCCT-AAACTTT
*
25079611 C-CAAAATTACCATTTT-ACCCCTAAAC-TT
1 CTAAAAATTA-CATTTTGACCCCTAAACTTT
* * * * *
25079639 CCAAAAACT-CTATTTTTAACCCTAAATTTT
1 CTAAAAATTAC-ATTTTGACCCCTAAACTTT
* *
25079669 CCAAAAATTCCATTTT
1 CTAAAAATTACATTTT
25079685 TGAACCCGAT
Statistics
Matches: 154, Mismatches: 27, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.01
28 11 0.07
29 62 0.40
30 54 0.35
31 13 0.08
32 13 0.08
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (30 bp):
CTAAAAATTACATTTTGACCCCTAAACTTT
Found at i:25079656 original size:59 final size:60
Alignment explanation
Indices: 25079513--25079684 Score: 176
Period size: 59 Copynumber: 2.9 Consensus size: 60
25079503 TTTGACACTA
* * * *
25079513 AAACTTTCTAAAAATTACATTTTAACCCTTAAACTTTCAAAAAAAATTA-CA-TTTAGCCCCC
1 AAACTTACAAAAAATTACATTTTAACCC-TAAATTTTC--CAAAAATTACCATTTTAGCCCCC
* *
25079574 AAACTTACAAAAAATTACATTTTAACCCTCAATCTTTCC-AAAATTACCATTTTA-CCCCT
1 AAACTTACAAAAAATTACATTTTAACCCTAAAT-TTTCCAAAAATTACCATTTTAGCCCCC
* * *
25079633 AAACTTCCAAAAACTCTA-TTTTTAACCCTAAATTTTCCAAAAATT-CCATTTT
1 AAACTTACAAAAAAT-TACATTTTAACCCTAAATTTTCCAAAAATTACCATTTT
25079685 TGAACCCGAT
Statistics
Matches: 96, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
58 19 0.20
59 38 0.40
60 9 0.09
61 30 0.31
ACGTcount: A:0.40, C:0.24, G:0.01, T:0.35
Consensus pattern (60 bp):
AAACTTACAAAAAATTACATTTTAACCCTAAATTTTCCAAAAATTACCATTTTAGCCCCC
Found at i:25079752 original size:29 final size:28
Alignment explanation
Indices: 25079623--25079752 Score: 93
Period size: 29 Copynumber: 4.4 Consensus size: 28
25079613 AAAATTACCA
* * *
25079623 TTTTACCCCTAAACTTCCAAAAACTCTAT
1 TTTTAACCCGAAA-TTCCAAAAACTCCAT
* *
25079652 TTTTAACCCTAAATTTTCCAAAAATTCCAT
1 TTTTAACCCGAAA--TTCCAAAAACTCCAT
** *
25079682 TTTTGAACCCGATTTTTCC-AAAATTACCA-
1 TTTT-AACCCGA-AATTCCAAAAACT-CCAT
*
25079711 TTTTACCCCCGAAATTCCAAAAACTCCAT
1 TTTTA-ACCCGAAATTCCAAAAACTCCAT
25079740 TTTTGAACCCGAA
1 TTTT-AACCCGAA
25079753 CTTTTCGAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
28 8 0.10
29 42 0.52
30 25 0.31
31 6 0.07
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (28 bp):
TTTTAACCCGAAATTCCAAAAACTCCAT
Found at i:25079793 original size:88 final size:89
Alignment explanation
Indices: 25079610--25079810 Score: 221
Period size: 88 Copynumber: 2.3 Consensus size: 89
25079600 CCTCAATCTT
* * *
25079610 TCCAAAATTACCATTTTA-CCCCTAAACTTCCAAAAACTCTATTTTTAACCCTAAATTTTCCAAA
1 TCCAAAATTACCATTTTACCCCCGAAACTTCCAAAAACTCCATTTTTAACCCGAAATTTTCCAAA
****
25079674 AATTCCATTTTTGAACCCGATTTT
66 AATTCCATTTTTGAACCCGAAGCA
* *
25079698 TCCAAAATTACCATTTTACCCCCGAAA-TTCCAAAAACTCCATTTTTGAACCCGAACTTTT-CGA
1 TCCAAAATTACCATTTTACCCCCGAAACTTCCAAAAACTCCATTTTT-AACCCGAAATTTTCCAA
* ** *
25079761 AAGTTACCA-TTTTGTTCTCGAAGCA
65 AAATT-CCATTTTTGAACCCGAAGCA
* *
25079786 TCTAAAATTACCGTTTTACCCCCGA
1 TCCAAAATTACCATTTTACCCCCGA
25079811 GCATCCAAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
88 74 0.78
89 21 0.22
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.34
Consensus pattern (89 bp):
TCCAAAATTACCATTTTACCCCCGAAACTTCCAAAAACTCCATTTTTAACCCGAAATTTTCCAAA
AATTCCATTTTTGAACCCGAAGCA
Found at i:25092871 original size:49 final size:49
Alignment explanation
Indices: 25092749--25094101 Score: 859
Period size: 49 Copynumber: 27.6 Consensus size: 49
25092739 CTGCAGGTCT
* * * *
25092749 CAGTACCAC-GAAGATATGGAGGGAAAGGTTTTGAGTCGTAACGGCGAA-C
1 CAGTACCTCAGAAGATAT-GAGGGAAA-GATTTAAGTCGCAACGGCGAATC
* * * * * * *
25092798 CTTGTACCTAAGAAG-CATGAAGGGAAAGATTTCAGCCGCAACAGTGAATC
1 C-AGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTCGCAACGGCGAATC
* *
25092848 CAGTACCAC-GAAGATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAA-C
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * *
25092896 CTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
1 C-AGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * *
25092946 TAGTA-CT-ATGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGGC-AAAC
1 CAGTACCTCA-GAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * *
25092994 CTTGTACCTCAGAA-ACATGAAGGGAAAGATTTAAGCCGGAGCGGCGAATC
1 C-AGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * *
25093044 TAGTACCACA-AGGATATGGAGGGAAAGGTTTAAGTCGCAACGGC-AAAC
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * ** *
25093092 CTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAACCGCAACTGCGAATC
1 C-AGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTCGCAACGGCGAATC
* * *
25093142 CAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCGCAACAGCGAA-C
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * *
25093190 CTTGTACCTCAAAAGCT-TGAAGGGTAAGATTTAAG-CTGTAACGGCGAATC
1 C-AGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTC-GCAACGGCGAATC
* * * * * * *
25093240 CAATACCACAAAAGATATGGAAGGAAAGGTTTAAGTCGCAACGG-AAAAC
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * * *
25093289 CTTGTACCTCATAAG-CATGAAGGAAAGATTTAAGCCGCAACGACGAATC
1 C-AGTACCTCAGAAGATATGAGGGAAAGATTTAAGTCGCAACGGCGAATC
* *
25093338 CAGTACCAC-GAAGATATGGAGGGAAATG-TTTAAGTCGCAACGGTGAA-C
1 CAGTACCTCAGAAGATAT-GAGGGAAA-GATTTAAGTCGCAACGGCGAATC
** * * *
25093386 GTTGTACCTCAAAAG-CATGAAGGGAAA-ATTTTAAGCCGCAACGGCGAATC
1 -CAGTACCTCAGAAGATATG-AGGGAAAGA-TTTAAGTCGCAACGGCGAATC
* * *
25093436 CAGTACCTCAAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAA-C
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * * *
25093485 CTTGTACCTCAGAAGCATA-AAGGGAAAGATATAAGACACAATGGCGAATC
1 C-AGTACCTCAGAAG-ATATGAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * *
25093535 TAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA-C
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * *
25093583 CTTGTACCTCTGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGTGAATC
1 C-AGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * *
25093633 CAGTACCACA-AAGATATAGAGGGAAAGGTTTAAGTTGCAACGGC-AAAC
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * * *
25093681 CTTGTACCTTAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACTGTGAAT-
1 C-AGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * *
25093730 --TTACCAC-GAAGATATGGACGGAAAGGTTTAAGTCGCAACGGTGAA-C
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * *
25093776 CTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
1 C-AGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * *
25093826 TAGTACCACAAAAGATATAGAGGGAAAGGTTTAAGTCACAACGGCGAA-C
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * * *
25093875 CTTGTACCTCATAAG-CATGAAGGGAAAGATTTAAGCCCCAACGACGAATC
1 C-AGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTCGCAACGGCGAATC
* * *
25093925 CAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAATC
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
** * * * * * *
25093974 TTGTACCTCAAAAG-CATGAAGGGAAAAATTTAAGCCGCAACTGTGAATC
1 CAGTACCTCAGAAGATATG-AGGGAAAGATTTAAGTCGCAACGGCGAATC
* * *
25094023 TAGTACCTCAAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA-C
1 CAGTACCTCAGAAGATAT-GAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * *
25094072 CTTGTAACTCAGAAG-CATGAAGGGAAAGAT
1 C-AGTACCTCAGAAGATATG-AGGGAAAGAT
25094102 ACGGCGAATC
Statistics
Matches: 996, Mismatches: 223, Indels: 170
0.72 0.16 0.12
Matches are distributed among these distances:
45 4 0.00
46 30 0.03
47 8 0.01
48 83 0.08
49 647 0.65
50 211 0.21
51 13 0.01
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (49 bp):
CAGTACCTCAGAAGATATGAGGGAAAGATTTAAGTCGCAACGGCGAATC
Found at i:25092919 original size:98 final size:98
Alignment explanation
Indices: 25092749--25094101 Score: 1935
Period size: 98 Copynumber: 13.8 Consensus size: 98
25092739 CTGCAGGTCT
* * *
25092749 CAGTACCACGAAGATATGGAGGGAAAGGTTTTGAGTCGTAACGGCGAACCTTGTACCTAAGAAGC
1 CAGTACCACGAAGATATGGAGGGAAAGG-TTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGC
* * *
25092814 ATGAAGGGAAAGATTTCAGCCGCAACAGTGAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
*
25092848 CAGTACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
25092913 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * * *
25092946 TAGTACTATGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACCTCAGAAACA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* *
25093011 TGAAGGGAAAGATTTAAGCCGGAGCGGCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* *
25093044 TAGTACCAC-AAGGATATGGAGGGAAAGGTTTAAGTCGCAACGGCAAACCTTGTACCTCAGAAGC
1 CAGTACCACGAA-GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGC
* *
25093108 ATGAAGGGAAAGATTTAAACCGCAACTGCGAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
25093142 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACAGCGAACCTTGTACCTCAAAAGCT
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* * *
25093207 TGAAGGGTAAGATTTAAGCTGTAACGGCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * ** *
25093240 CAATACCACAAAAGATATGGAAGGAAAGGTTTAAGTCGCAACGGAAAACCTTGTACCTCATAAGC
1 CAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGC
*
25093305 ATGAA-GGAAAGATTTAAGCCGCAACGACGAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * *
25093338 CAGTACCACGAAGATATGGAGGGAAATGTTTAAGTCGCAACGGTGAACGTTGTACCTCAAAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
25093403 TGAAGGGAAA-ATTTTAAGCCGCAACGGCGAATC
66 TGAAGGGAAAGA-TTTAAGCCGCAACGGCGAATC
* * *
25093436 CAGTACCTCAAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGC
1 CAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGC
* * * * *
25093501 ATAAAGGGAAAGATATAAGACACAATGGCGAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* *
25093535 TAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCTGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
*
25093600 TGAAGGGAAAGATTTAAGCCGCAACGGTGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
25093633 CAGTACCACAAAGATATAGAGGGAAAGGTTTAAGTTGCAACGGCAAACCTTGTACCTTAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* *
25093698 TGAAGGGAAAGATTTAAGCCGCAACTGTGAAT-
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
25093730 --TTACCACGAAGATATGGACGGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
25093793 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
25093826 TAGTACCACAAAAGATATAGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCATAAGC
1 CAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGC
* *
25093891 ATGAAGGGAAAGATTTAAGCCCCAACGACGAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
25093925 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAATCTTGTACCTCAAAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* * *
25093990 TGAAGGGAAAAATTTAAGCCGCAACTGTGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * *
25094023 TAGTACCTCAAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTAACTCAGAAGC
1 CAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGC
25094088 ATGAAGGGAAAGAT
65 ATGAAGGGAAAGAT
25094102 ACGGCGAATC
Statistics
Matches: 1117, Mismatches: 125, Indels: 24
0.88 0.10 0.02
Matches are distributed among these distances:
95 85 0.08
97 56 0.05
98 658 0.59
99 317 0.28
100 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (98 bp):
CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:25094664 original size:12 final size:11
Alignment explanation
Indices: 25094599--25094679 Score: 57
Period size: 11 Copynumber: 7.6 Consensus size: 11
25094589 AAATCTTTAA
25094599 TTAAATTTATT
1 TTAAATTTATT
*
25094610 TTAAATTTGAAT
1 TTAAATTT-ATT
* *
25094622 TT-ATTTTAAGT
1 TTAAATTT-ATT
*
25094633 TTAAATTTAAT
1 TTAAATTTATT
25094644 TTAAA-TTA--
1 TTAAATTTATT
25094652 --AAATTTATT
1 TTAAATTTATT
25094661 TTAAATTTATTT
1 TTAAATTTA-TT
25094673 TTAAATT
1 TTAAATT
25094680 GAGTTCAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
6 3 0.05
7 3 0.05
10 3 0.05
11 30 0.54
12 17 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:25094675 original size:17 final size:17
Alignment explanation
Indices: 25094599--25094669 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
25094589 AAATCTTTAA
25094599 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
* *
25094616 TTGAATTTATTTTAAGT
1 TTAAATTTATTTTAAAT
*
25094633 TTAAATTTAATTTAAAT
1 TTAAATTTATTTTAAAT
*
25094650 TAAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
25094667 TTA
1 TTA
25094670 TTTTTAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:25096464 original size:30 final size:30
Alignment explanation
Indices: 25096428--25096736 Score: 287
Period size: 30 Copynumber: 10.5 Consensus size: 30
25096418 CAATCTATCT
25096428 AAAAATTACATTTTGACCCCTAAACTTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCC
* **
25096458 AAAAATTACATTTT-AACCCTCAAACTTTTT
1 AAAAATTACATTTTGACCCCT-AAACTTTCC
* * * *
25096488 AGAAATTACATTTTGACCCCCAAAATTTCT
1 AAAAATTACATTTTGACCCCTAAACTTTCC
* *
25096518 AAAAATTATATTTTGACCCTTAAAC-TTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCC
*
25096547 AAAAATTACATTTTAACCCCTAAACTTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCC
* *
25096577 AAAAATTATATTTAG-CCACC-AAACTTTCC
1 AAAAATTACATTTTGACC-CCTAAACTTTCC
* *
25096606 AAAAATTACATTTTGACCCTTAATCTTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCC
25096636 AAAAATTACTATTTTG-CCACC-AAAC-TTCC
1 AAAAATTAC-ATTTTGACC-CCTAAACTTTCC
* * * * **
25096665 AAAAACTCCATTTTCA-CCCTGATTTTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCC
* **
25096694 AAAAAATACCATTTT-ACCCCCGAAC-TTCC
1 AAAAATTA-CATTTTGACCCCTAAACTTTCC
*
25096723 AAAAATTCCATTTT
1 AAAAATTACATTTT
25096737 TGACTTCGAT
Statistics
Matches: 227, Mismatches: 39, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
27 2 0.01
28 13 0.06
29 87 0.38
30 114 0.50
31 11 0.05
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCTAAACTTTCC
Found at i:25096559 original size:29 final size:29
Alignment explanation
Indices: 25096428--25096793 Score: 228
Period size: 29 Copynumber: 12.5 Consensus size: 29
25096418 CAATCTATCT
*
25096428 AAAAATTACATTTTGACCCCTAAACTTTCC
1 AAAAATTACATTTTGACCCTTAAAC-TTCC
* * **
25096458 AAAAATTACATTTTAACCCTCAAACTTTTT
1 AAAAATTACATTTTGACCCTTAAAC-TTCC
* ** * *
25096488 AGAAATTACATTTTGACCCCCAAAATTTCT
1 AAAAATTACATTTTGA-CCCTTAAACTTCC
*
25096518 AAAAATTATATTTTGACCCTTAAACTTCC
1 AAAAATTACATTTTGACCCTTAAACTTCC
* *
25096547 AAAAATTACATTTTAACCCCTAAACTTTCC
1 AAAAATTACATTTTGACCCTTAAAC-TTCC
* * *
25096577 AAAAATTATATTTAG-CCAC-CAAACTTTCC
1 AAAAATTACATTTTGACC-CTTAAAC-TTCC
*
25096606 AAAAATTACATTTTGACCCTTAATCTTTCC
1 AAAAATTACATTTTGACCCTTAAAC-TTCC
*
25096636 AAAAATTACTATTTTG-CCAC-CAAACTTCC
1 AAAAATTAC-ATTTTGACC-CTTAAACTTCC
* * * * ***
25096665 AAAAACTCCATTTTCACCCTGATTTTTCC
1 AAAAATTACATTTTGACCCTTAAACTTCC
* ***
25096694 AAAAAATACCATTTT-ACCCCCGAACTTCC
1 AAAAATTA-CATTTTGACCCTTAAACTTCC
* * **
25096723 AAAAATTCCATTTTTGA--CTTCGATTTTCC
1 AAAAATTACA-TTTTGACCCTT-AAACTTCC
*
25096752 -AAAATTACCATTTT-ACCCTTGAACTTCC
1 AAAAATTA-CATTTTGACCCTTAAACTTCC
* *
25096780 AAAAACTCCATTTT
1 AAAAATTACATTTT
25096794 TGACTCCGAA
Statistics
Matches: 263, Mismatches: 56, Indels: 36
0.74 0.16 0.10
Matches are distributed among these distances:
27 1 0.00
28 31 0.12
29 114 0.43
30 104 0.40
31 13 0.05
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCTTAAACTTCC
Found at i:25096582 original size:59 final size:58
Alignment explanation
Indices: 25096428--25096736 Score: 302
Period size: 59 Copynumber: 5.2 Consensus size: 58
25096418 CAATCTATCT
* * **
25096428 AAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTACATTTTAACCCTCAAACTTTTT
1 AAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTATATTTTGACCC-CAAAC-TTCC
* * * * *
25096488 AGAAATTACATTTTGACCCCCAAAATTTCTAAAAATTATATTTTGACCCTTAAACTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTATATTTTGACCC-CAAACTTCC
* *
25096547 AAAAATTACATTTTAACCCCTAAACTTTCCAAAAATTATATTTAG-CCACCAAACTTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTATATTTTGACC-CCAAAC-TTCC
* *
25096606 AAAAATTACATTTTGACCCTTAATCTTTCCAAAAATTACTATTTTG-CCACCAAACTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTA-TATTTTGACC-CCAAACTTCC
* * * * ** * * *
25096665 AAAAACTCCATTTTCA-CCCTGATTTTTCCAAAAAATACCATTTT-ACCCCCGAACTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTA-TATTTTGA-CCCCAAACTTCC
*
25096723 AAAAATTCCATTTT
1 AAAAATTACATTTT
25096737 TGACTTCGAT
Statistics
Matches: 214, Mismatches: 30, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
58 51 0.24
59 100 0.47
60 63 0.29
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTATATTTTGACCCCAAACTTCC
Found at i:25096721 original size:58 final size:58
Alignment explanation
Indices: 25096540--25096793 Score: 212
Period size: 59 Copynumber: 4.4 Consensus size: 58
25096530 TTGACCCTTA
* * * * ** * * *
25096540 AACTTCCAAAAATTACATTTTAACCCCTAAACTTTCCAAAAATTA-TA-TTTAGCCACCA
1 AACTTCCAAAAACTCCATTTTGA-CCCTGATTTTTCCAAAAATTACCATTTTA-CCCCCG
* * * * * * * *
25096598 AACTTTCCAAAAATTACATTTTGACCCTTAATCTTTCCAAAAATTACTATTTTGCCACCA
1 AAC-TTCCAAAAACTCCATTTTGACCC-TGATTTTTCCAAAAATTACCATTTTACCCCCG
* *
25096658 AACTTCCAAAAACTCCATTTTCACCCTGATTTTTCCAAAAAATACCATTTTACCCCCG
1 AACTTCCAAAAACTCCATTTTGACCCTGATTTTTCCAAAAATTACCATTTTACCCCCG
* * **
25096716 AACTTCCAAAAATTCCATTTTTGA-CTTCGA-TTTTCC-AAAATTACCATTTTACCCTTG
1 AACTTCCAAAAACTCCA-TTTTGACCCT-GATTTTTCCAAAAATTACCATTTTACCCCCG
25096773 AACTTCCAAAAACTCCATTTT
1 AACTTCCAAAAACTCCATTTT
25096794 TGACTCCGAA
Statistics
Matches: 170, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
56 4 0.02
57 34 0.20
58 55 0.32
59 63 0.37
60 11 0.06
61 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (58 bp):
AACTTCCAAAAACTCCATTTTGACCCTGATTTTTCCAAAAATTACCATTTTACCCCCG
Found at i:25096790 original size:57 final size:60
Alignment explanation
Indices: 25096631--25096800 Score: 206
Period size: 57 Copynumber: 2.9 Consensus size: 60
25096621 ACCCTTAATC
* * * * * *
25096631 TTTCCAAAAATTACTATTTTGCCACCAAACTTCCAAAAACTCCA-TTTTCAC-CCTGATT
1 TTTCCAAAAAATACCATTTTACCCCCGAACTTCCAAAAACTCCATTTTTGACTCCTGATT
* *
25096689 TTTCCAAAAAATACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACTTC-GA-T
1 TTTCCAAAAAATACCATTTTACCCCCGAACTTCCAAAAACTCCATTTTTGACTCCTGATT
* **
25096747 TTTCC-AAAATTACCATTTTACCCTTGAACTTCCAAAAACTCCATTTTTGACTCC
1 TTTCCAAAAAATACCATTTTACCCCCGAACTTCCAAAAACTCCATTTTTGACTCC
25096801 GAACTTTGTA
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
57 44 0.45
58 44 0.45
59 8 0.08
60 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (60 bp):
TTTCCAAAAAATACCATTTTACCCCCGAACTTCCAAAAACTCCATTTTTGACTCCTGATT
Found at i:25101170 original size:6 final size:6
Alignment explanation
Indices: 25101159--25101197 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
25101149 AATTTGAAAA
*
25101159 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAGG TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TT
25101198 CCTGGGCCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:25101850 original size:99 final size:98
Alignment explanation
Indices: 25101646--25102061 Score: 405
Period size: 99 Copynumber: 4.2 Consensus size: 98
25101636 ATCATTGCAG
* * * * *
25101646 CTTAAATCTTTCCTTTCATG-TCTCTGAGGTACAAGGTTCGTCGTTACAACTTAAACCTTTCTCT
1 CTTAAATCTTTCCCTTCATGCT-TCTGA-GTGCAAGGTTCGCCGTTACGACTTAAACCTTTCCCT
** *
25101710 TTA-TATCTTCGTGGTACCGGATTCGTCGTTGCGA
64 CAATTATCTTCGTGGTACTGGATTCGTCGTTGCGA
* * * *
25101744 CTTAAATCTTT-ACTTCATGCTTCTGAGATGCGAGGTTCCCCATTACGACTTAAACCCTTTCCCT
1 CTTAAATCTTTCCCTTCATGCTTCTGAG-TGCAAGGTTCGCCGTTACGACTTAAA-CCTTTCCC-
* *
25101808 TC-ATTATCTTTGTCGTACTGGATTC-TCTGTTGCGA
63 TCAATTATCTTCGTGGTACTGGATTCGTC-GTTGCGA
* * * *
25101843 CTTAAATCTTTCCCTTCGTGCTTCTGAG-GCATAAGGTTTGCCGTTGCGACTTAAACATTTCCCT
1 CTTAAATCTTTCCCTTCATGCTTCTGAGTGC--AAGGTTCGCCGTTACGACTTAAACCTTTCCCT
* **
25101907 CAATTATCTTCGTGGTGCTGGATTCACCGTTGC-A
64 CAATTATCTTCGTGGTACTGGATTCGTCGTTGCGA
* * * ** *
25101941 GCTTAAATCTCTCCCTTTATGCTTCTGAGGTACAAGGTTCGCCGTTGTGACTTAAACCCTTTTCC
1 -CTTAAATCTTTCCCTTCATGCTTCTGA-GTGCAAGGTTCGCCGTTACGACTTAAA-CCTTTCCC
* * *
25102006 TCTATTAACTTCGTGGTACTGGATTCGTCGTTGCGG
63 TCAATTATCTTCGTGGTACTGGATTCGTCGTTGCGA
*
25102042 CATAAATCTTTCCCTTCATG
1 CTTAAATCTTTCCCTTCATG
25102062 GTAATGAAAC
Statistics
Matches: 260, Mismatches: 42, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
96 1 0.00
97 31 0.12
98 27 0.10
99 114 0.44
100 86 0.33
101 1 0.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (98 bp):
CTTAAATCTTTCCCTTCATGCTTCTGAGTGCAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCA
ATTATCTTCGTGGTACTGGATTCGTCGTTGCGA
Found at i:25102027 original size:199 final size:197
Alignment explanation
Indices: 25101646--25102061 Score: 462
Period size: 199 Copynumber: 2.1 Consensus size: 197
25101636 ATCATTGCAG
* * * * * *
25101646 CTTAAATCTTTCCTTTCATGTCTCTGAGGTACAAGGTTCGTCGTTACAACTTAAACCTTTCTCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGCACAAGGTTCGCCGTTACAACTTAAACATTTCCCTC
* ** * * *
25101711 TATATCTTCGTGGTACCGGATTCGTCGTTGCGACTTAAATCTTTACTTCATGCTTCTGAGATGCG
66 AATATCTTCGTGGTACCGGATTCACCGTTGCGACTTAAATCTTCACTTCATGCTTCTGAGATACA
* *
25101776 AGGTTCCCCATTACGACTTAAACCCTTTCCCTTCATTATCTTTGTCGTACTGGATTC-TCTGTTG
131 AGGTTCCCCATTACGACTTAAACCCTTTCCCTTCATTAACTTCGTCGTACTGGATTCGTC-GTTG
25101840 CGA
195 CGA
* * * * *
25101843 CTTAAATCTTTCCCTTCGTG-CTTCTGAGGCATAAGGTTTGCCGTTGCGACTTAAACATTTCCCT
1 CTTAAATCTTTCCCTTCATGTC-TCTGAGGCACAAGGTTCGCCGTTACAACTTAAACATTTCCCT
* * * * *
25101907 CAATTATCTTCGTGGTGCTGGATTCACCGTTGC-AGCTTAAATCTCTCCCTTTATGCTTCTGAGG
65 CAA-TATCTTCGTGGTACCGGATTCACCGTTGCGA-CTTAAATCT-TCACTTCATGCTTCTGAGA
* * ** * *
25101971 TACAAGGTTCGCCGTTGTGACTTAAACCCTTTTCC-TCTATTAACTTCGTGGTACTGGATTCGTC
127 TACAAGGTTCCCCATTACGACTTAAACCCTTTCCCTTC-ATTAACTTCGTCGTACTGGATTCGTC
*
25102035 GTTGCGG
191 GTTGCGA
*
25102042 CATAAATCTTTCCCTTCATG
1 CTTAAATCTTTCCCTTCATG
25102062 GTAATGAAAC
Statistics
Matches: 180, Mismatches: 33, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
196 1 0.01
197 54 0.30
198 36 0.20
199 87 0.48
200 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (197 bp):
CTTAAATCTTTCCCTTCATGTCTCTGAGGCACAAGGTTCGCCGTTACAACTTAAACATTTCCCTC
AATATCTTCGTGGTACCGGATTCACCGTTGCGACTTAAATCTTCACTTCATGCTTCTGAGATACA
AGGTTCCCCATTACGACTTAAACCCTTTCCCTTCATTAACTTCGTCGTACTGGATTCGTCGTTGC
GA
Found at i:25114021 original size:2 final size:2
Alignment explanation
Indices: 25114014--25114051 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25114004 TCTATCTATC
25114014 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25114052 ATAAATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25119944 original size:8 final size:8
Alignment explanation
Indices: 25119925--25119982 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 8
25119915 GAAAAAATTC
25119925 ATTTTTAT
1 ATTTTTAT
25119933 -TTTTTAT
1 ATTTTTAT
25119940 ATTTTTTAT
1 A-TTTTTAT
*
25119949 AATTTTAT
1 ATTTTTAT
*
25119957 AATTTT-T
1 ATTTTTAT
25119964 ATTTTTAT
1 ATTTTTAT
25119972 -TTTTT-T
1 ATTTTTAT
25119978 ATTTT
1 ATTTT
25119983 AAGCGTGTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
6 1 0.02
7 22 0.50
8 13 0.30
9 8 0.18
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
ATTTTTAT
Found at i:25120128 original size:18 final size:17
Alignment explanation
Indices: 25120092--25120140 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
25120082 TTATATTATA
*
25120092 ATTTTAAAATA-ATATAT
1 ATTTTAAAATATA-AAAT
25120109 ATATTTAAAATATAAAAT
1 AT-TTTAAAATATAAAAT
25120127 ATTTT-AAATATAAA
1 ATTTTAAAATATAAA
25120141 TTCCAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.31
17 5 0.17
18 14 0.48
19 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTTAAAATATAAAAT
Found at i:25120130 original size:16 final size:16
Alignment explanation
Indices: 25120094--25120140 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
25120084 ATATTATAAT
*
25120094 TTTAAAATAATATATATA
1 TTTAAAAT-ATA-AAATA
25120112 TTTAAAATATAAAATA
1 TTTAAAATATAAAATA
*
25120128 TTTTAAATATAAA
1 TTTAAAATATAAA
25120141 TTCCAGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 16 0.59
17 3 0.11
18 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAAATATAAAATA
Found at i:25122260 original size:40 final size:43
Alignment explanation
Indices: 25122207--25122285 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 43
25122197 GTGAGTTGTG
* *
25122207 AAAAATAATAAT-AAAA-TATGAAAAATATGAAA-AAGTAAAA
1 AAAAATAAAAATAAAAATTATGAAAAATAAGAAACAAGTAAAA
*
25122247 AAAAATAAAAATAAAAATTATTAAAAATAAGAAACAAGT
1 AAAAATAAAAATAAAAATTATGAAAAATAAGAAACAAGT
25122286 TATTTGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 11 0.33
41 4 0.12
42 14 0.42
43 4 0.12
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.20
Consensus pattern (43 bp):
AAAAATAAAAATAAAAATTATGAAAAATAAGAAACAAGTAAAA
Found at i:25124623 original size:15 final size:15
Alignment explanation
Indices: 25124599--25124632 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25124589 TAAAGCGTAG
*
25124599 TGGTAATGTTTTGAT
1 TGGTAATGTTTTGAA
*
25124614 TGGTAGTGTTTTGAA
1 TGGTAATGTTTTGAA
25124629 TGGT
1 TGGT
25124633 TGAATCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (15 bp):
TGGTAATGTTTTGAA
Found at i:25125826 original size:58 final size:57
Alignment explanation
Indices: 25125763--25126036 Score: 216
Period size: 58 Copynumber: 4.7 Consensus size: 57
25125753 GTAAAATGGT
*
25125763 AATTTTGGATAGTCGAGGGTAAAATGGTAATTTTGGGAAATTTTAGGGTCAAAAATAGA
1 AATTTTGGATAGTCGAGGGTAAAATGGTAATTTT-GGAAAATTTAGGGTCAAAAAT-GA
* * * * * * * ** ** *
25125822 ATTTTTAGACATTTGGGGGTAAAATGGTAATTTTGGAAAGTTCGGGGTTTAAAATGG
1 AATTTTGGATAGTCGAGGGTAAAATGGTAATTTTGGAAAATTTAGGGTCAAAAATGA
* * *
25125879 AATTTT-TAGTCA-TCCGGGGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGA
1 AATTTTGGA-T-AGT-CGAGGGTAAAATGGTAATTTTGGAAAATTTAGGGTCAAAAATGA
** * *
25125937 AATTTTTGGA-AGTTTAGGGGTAAAATGGTAATTTTTGGAAAATTGA-GGTAAAAAATGA
1 AA-TTTTGGATAGTCGA-GGGTAAAATGGTAA-TTTTGGAAAATTTAGGGTCAAAAATGA
* *
25125995 AAATTTGGAAAGTTCG-GAGGTAAAATGGTAATTTTTGGAAAA
1 AATTTTGGATAG-TCGAG-GGTAAAATGGTAA-TTTTGGAAAA
25126037 ATTGAGGTTA
Statistics
Matches: 171, Mismatches: 33, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
56 1 0.01
57 15 0.09
58 109 0.64
59 45 0.26
60 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (57 bp):
AATTTTGGATAGTCGAGGGTAAAATGGTAATTTTGGAAAATTTAGGGTCAAAAATGA
Found at i:25125853 original size:29 final size:29
Alignment explanation
Indices: 25125747--25126035 Score: 166
Period size: 28 Copynumber: 10.0 Consensus size: 29
25125737 TTTCTGATAC
* *
25125747 TCGGGGGTAAAATGGTAA-TTTTGGATAG
1 TCGGGGGTAAAATGGTAATTTTTGGAAAT
* *
25125775 TCGAGGGTAAAATGGTAATTTTGGGAAAT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAT
*** * * *
25125804 TTTAGGGTCAAAAATAG-AATTTTTAGACAT
1 TCGGGGGT--AAAATGGTAATTTTTGGAAAT
*
25125834 TTGGGGGTAAAATGGTAA-TTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAA-T
* * **
25125863 TCGGGGTTTAAAATGG-AATTTTTAGTCAT
1 TCGGGG-GTAAAATGGTAATTTTTGGAAAT
*
25125892 CCGGGGGTAAAATGGTAA-TTTTGGAAAAAT
1 TCGGGGGTAAAATGGTAATTTTTGG--AAAT
* *** * *
25125922 TAGGGTCAAAAAT-GAAATTTTTGGAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAT
**
25125950 TTAGGGGTAAAATGGTAATTTTTGGAAAAT
1 TCGGGGGTAAAATGGTAATTTTTGG-AAAT
* **
25125980 T--GAGGTAAAAAAT-G-AAAATTTGGAAAGT
1 TCGGGGGT--AAAATGGTAATTTTTGGAAA-T
*
25126008 TCGGAGGTAAAATGGTAATTTTTGGAAA
1 TCGGGGGTAAAATGGTAATTTTTGGAAA
25126036 AATTGAGGTT
Statistics
Matches: 197, Mismatches: 44, Indels: 38
0.71 0.16 0.14
Matches are distributed among these distances:
27 3 0.02
28 72 0.37
29 46 0.23
30 70 0.36
31 6 0.03
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTTTGGAAAT
Found at i:25125992 original size:116 final size:115
Alignment explanation
Indices: 25125779--25126093 Score: 311
Period size: 116 Copynumber: 2.7 Consensus size: 115
25125769 GGATAGTCGA
** *
25125779 GGGTAAAATGGTAATTTTGGGAAATTTTAGGGTCAAAAAT-AGAATTTTTAGACA-TTTGGGGGT
1 GGGTAAAATGGTAATTTT-GGAAAAATTAGGGTCAAAAATGA-AATTTTTGGA-AGTTT-GGGGT
* * ** ** **
25125842 AAAATGGTAATTTTGGAAAGTTCGGGGTTTAAAATGGAATTTTTAGTCA-TCCGG
62 AAAATGGTAATTTTGGAAAATTCGAGGTAAAAAAT-GAAAATTTAGAAAGTCCGG
25125896 GGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTTAGGGGTAAA
1 GGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTT-GGGGTAAA
* *
25125961 ATGGTAATTTTTGGAAAATT-GAGGTAAAAAATGAAAATTTGGAAAGTTCGG
65 ATGGTAA-TTTTGGAAAATTCGAGGTAAAAAATGAAAATTTAGAAAGTCCGG
* * * * *
25126012 AGGTAAAATGGTAATTTTTGGAAAAATT-GAGGT-TAAAATGGAAGTTTGGGAAGTTTGGGGCTA
1 GGGTAAAATGGTAA-TTTTGGAAAAATTAG-GGTCAAAAATGAAATTTTTGGAAGTTTGGGG-T-
*
25126075 AAAATAG-AATTTTGGAAAA
62 AAAATGGTAATTTTGGAAAA
25126094 GTTTAGGGAC
Statistics
Matches: 170, Mismatches: 20, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
115 23 0.14
116 95 0.56
117 52 0.31
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.32
Consensus pattern (115 bp):
GGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTTGGGGTAAAA
TGGTAATTTTGGAAAATTCGAGGTAAAAAATGAAAATTTAGAAAGTCCGG
Found at i:25126050 original size:58 final size:57
Alignment explanation
Indices: 25125895--25126093 Score: 212
Period size: 58 Copynumber: 3.5 Consensus size: 57
25125885 TAGTCATCCG
* *
25125895 GGGGTAAAATGGTAA-TTTTGGAAAAATT-AGGGTCAAAAATGAAATTTTTGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAAAATTGA-GGTAAAAAATGAAA-ATTTGGAAG-TTA
*
25125953 GGGGTAAAATGGTAATTTTTGG-AAAATTGAGGTAAAAAATGAAAATTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTTGGAAAAATTGAGGTAAAAAATGAAAATTTGG-AAGTTA
* * * *
25126010 GGAGGTAAAATGGTAATTTTTGGAAAAATTGAGGT-TAAAATGGAAGTTTGGGAAGTTT
1 GG-GGTAAAATGGTAATTTTTGGAAAAATTGAGGTAAAAAATGAAAATTT-GGAAGTTA
*
25126068 GGGGCTAAAAATAG-AA-TTTTGGAAAA
1 GGGG-T-AAAATGGTAATTTTTGGAAAA
25126094 GTTTAGGGAC
Statistics
Matches: 125, Mismatches: 8, Indels: 17
0.83 0.05 0.11
Matches are distributed among these distances:
57 21 0.17
58 78 0.62
59 26 0.21
ACGTcount: A:0.40, C:0.02, G:0.28, T:0.31
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGGAAAAATTGAGGTAAAAAATGAAAATTTGGAAGTTA
Found at i:25127989 original size:6 final size:6
Alignment explanation
Indices: 25127966--25128025 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
25127956 TCTAAATCAT
**
25127966 TTTAAA TTT-AA TTT-AA TTTAAA TTTAAAAA GATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT--AAA TTTAAA TTTAAA TTTAAA
**
25128014 AATAAA TTTAAA
1 TTTAAA TTTAAA
25128026 ATCGATTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
5 10 0.23
6 29 0.67
8 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:25128005 original size:20 final size:18
Alignment explanation
Indices: 25127980--25128025 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 18
25127970 AATTTAATTT
25127980 AATTTAAATTTAAAAAGATA
1 AATTTAAATTT-AAAA-ATA
25128000 AATTTAAATTTAAAAATA
1 AATTTAAATTTAAAAATA
25128018 AATTTAAA
1 AATTTAAA
25128026 ATCGATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 11 0.42
19 4 0.15
20 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATTTAAATTTAAAAATA
Found at i:25129713 original size:16 final size:17
Alignment explanation
Indices: 25129694--25129734 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
25129684 TAATTTTTTA
*
25129694 AAAATTATAAAAAT-GT
1 AAAATTATAAAAATAAT
*
25129710 AAAA-TATTAAAATAAT
1 AAAATTATAAAAATAAT
25129726 AAAATTATA
1 AAAATTATA
25129735 TTTTTACTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 8 0.40
16 9 0.45
17 3 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:25136443 original size:5 final size:6
Alignment explanation
Indices: 25136429--25136453 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25136419 GCTGAAATTT
25136429 AAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA A
25136454 GAGAGATAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:25140477 original size:3 final size:3
Alignment explanation
Indices: 25140469--25140512 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
25140459 AGACCTTTCT
25140469 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
25140513 TATTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:25140517 original size:3 final size:3
Alignment explanation
Indices: 25140511--25140557 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
25140501 AATAATAATA
25140511 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
25140558 CTTTTTATGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:25141324 original size:11 final size:11
Alignment explanation
Indices: 25141310--25141341 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
25141300 AATTAATCTT
25141310 AAATTATAAAA
1 AAATTATAAAA
25141321 AAATTAT--AA
1 AAATTATAAAA
25141330 AAATTATAAAA
1 AAATTATAAAA
25141341 A
1 A
25141342 TAATAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATTATAAAA
Found at i:25141340 original size:8 final size:9
Alignment explanation
Indices: 25141319--25141382 Score: 65
Period size: 9 Copynumber: 7.0 Consensus size: 9
25141309 TAAATTATAA
25141319 AAAAATTAT
1 AAAAATTAT
25141328 AAAAATTAT
1 AAAAATTAT
*
25141337 AAAAATAAT
1 AAAAATTAT
**
25141346 AAAAGAACAT
1 AAAA-ATTAT
*
25141356 TAAAATTAT
1 AAAAATTAT
*
25141365 AAAAAATAT
1 AAAAATTAT
*
25141374 GAAAATTAT
1 AAAAATTAT
25141383 TATAAATTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
9 38 0.86
10 6 0.14
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:25141340 original size:18 final size:18
Alignment explanation
Indices: 25141319--25141382 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
25141309 TAAATTATAA
*
25141319 AAAAATTATAAAAATTAT
1 AAAAATTATAAAAAATAT
* *
25141337 AAAAATAATAAAAGAACAT
1 AAAAATTATAAAA-AATAT
*
25141356 TAAAATTATAAAAAATAT
1 AAAAATTATAAAAAATAT
*
25141374 GAAAATTAT
1 AAAAATTAT
25141383 TATAAATTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 24 0.63
19 14 0.37
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAATTATAAAAAATAT
Found at i:25141389 original size:28 final size:28
Alignment explanation
Indices: 25141315--25141400 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
25141305 ATCTTAAATT
*
25141315 ATAA-AAAAATTATAAAAATTAT-AAAA
1 ATAATAAAAATTATTAAAATTATAAAAA
**
25141341 ATAATAAAAGAACATTAAAATTATAAAAA
1 ATAATAAAA-ATTATTAAAATTATAAAAA
*
25141370 AT-ATGAAAATTATTATAAATTAATTAAAAA
1 ATAATAAAAATTATTA-AAATT-A-TAAAAA
25141400 A
1 A
25141401 CATAAATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
26 4 0.08
27 9 0.19
28 21 0.44
29 7 0.15
30 7 0.15
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (28 bp):
ATAATAAAAATTATTAAAATTATAAAAA
Found at i:25141418 original size:18 final size:18
Alignment explanation
Indices: 25141384--25141418 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25141374 GAAAATTATT
*
25141384 ATAAATTAATTAAAAAAC
1 ATAAATTAATAAAAAAAC
*
25141402 ATAAATTTATAAAAAAA
1 ATAAATTAATAAAAAAA
25141419 ATATTTATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATTAATAAAAAAAC
Found at i:25143828 original size:27 final size:27
Alignment explanation
Indices: 25143790--25143852 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
25143780 CATCTTATTG
*
25143790 AAGGGAGAGTGTGTTGATGCTACAACT
1 AAGGGGGAGTGTGTTGATGCTACAACT
**
25143817 AAGGGGGAGTGTGTTGATGCTATTACT
1 AAGGGGGAGTGTGTTGATGCTACAACT
*
25143844 AAAGGGGAG
1 AAGGGGGAG
25143853 CCTTCTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.38, T:0.25
Consensus pattern (27 bp):
AAGGGGGAGTGTGTTGATGCTACAACT
Found at i:25145284 original size:35 final size:35
Alignment explanation
Indices: 25145245--25145319 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 35
25145235 AAATTTTATA
*
25145245 AAATATGTATAAAT-TGAAAAAATAAAA-ATTATTTT
1 AAATAT-TA-AAATGTGAAAAAATAAAATATAATTTT
* * *
25145280 AAATATTAATATGTGTAATAATAAAATATAATTTT
1 AAATATTAAAATGTGAAAAAATAAAATATAATTTT
25145315 AAATA
1 AAATA
25145320 AATTTCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 3 0.09
34 13 0.38
35 18 0.53
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (35 bp):
AAATATTAAAATGTGAAAAAATAAAATATAATTTT
Found at i:25145574 original size:16 final size:16
Alignment explanation
Indices: 25145555--25145617 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
25145545 GACAATATTG
25145555 ATCAAAGTCAACCCTA
1 ATCAAAGTCAACCCTA
**
25145571 ATCAAAGTCAACTTTA
1 ATCAAAGTCAACCCTA
* * *
25145587 TTTAAAGTCAACTCTA
1 ATCAAAGTCAACCCTA
25145603 ATCAAAGTCAACCCT
1 ATCAAAGTCAACCCT
25145618 TGTTAACTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.27
Consensus pattern (16 bp):
ATCAAAGTCAACCCTA
Found at i:25145985 original size:24 final size:24
Alignment explanation
Indices: 25145958--25146003 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
25145948 TTTAGTAGTA
*
25145958 TAATATATTTAGCATTTATTAGCT
1 TAATATATTTAGCATTGATTAGCT
*
25145982 TAATATATTTTGCATTGATTAG
1 TAATATATTTAGCATTGATTAG
25146004 AATTAGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.50
Consensus pattern (24 bp):
TAATATATTTAGCATTGATTAGCT
Found at i:25147773 original size:86 final size:86
Alignment explanation
Indices: 25147628--25147809 Score: 224
Period size: 86 Copynumber: 2.1 Consensus size: 86
25147618 GAAAAACGCT
* * * * ** *
25147628 GCTAAAGAACATGATCTTTAACGGTACTTTCCCCACAAACGTCACTAAAGAACATAATCTTTAGC
1 GCTAAAGAATATGATCTTTAACGGGACTTTACCAACAAACACCACTAAAGAACATAATCTTTAAC
*
25147693 GACGCTTTTCACACAAACCCC
66 GACGCTTTTCACACAAACACC
* * *
25147714 GCTAAAGAATATGATCTTTAACGGGGCTTTACCAAGAAATACCACTAAA-AACCATAATCTTTAA
1 GCTAAAGAATATGATCTTTAACGGGACTTTACCAACAAACACCACTAAAGAA-CATAATCTTTAA
* *
25147778 CGGCGCTTTTCACACAAACATC
65 CGACGCTTTTCACACAAACACC
25147800 GCTAAA-AATA
1 GCTAAAGAATA
25147810 ACAGATTTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
85 6 0.07
86 76 0.93
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (86 bp):
GCTAAAGAATATGATCTTTAACGGGACTTTACCAACAAACACCACTAAAGAACATAATCTTTAAC
GACGCTTTTCACACAAACACC
Found at i:25147807 original size:43 final size:43
Alignment explanation
Indices: 25147628--25147805 Score: 153
Period size: 43 Copynumber: 4.1 Consensus size: 43
25147618 GAAAAACGCT
* ** * * **
25147628 GCTAAAGAACATGATCTTTAACGGTACTTTCCCCACAAACGTC
1 GCTAAAGAACATAATCTTTAACGGCGCTTTTCACACAAACACC
* * * *
25147671 ACTAAAGAACATAATCTTTAGCGACGCTTTTCACACAAACCCC
1 GCTAAAGAACATAATCTTTAACGGCGCTTTTCACACAAACACC
* * * * * *
25147714 GCTAAAGAATATGATCTTTAACGGGGCTTTAC-CAAGAAATACC
1 GCTAAAGAACATAATCTTTAACGGCGCTTTTCAC-ACAAACACC
* *
25147757 ACTAAA-AACCATAATCTTTAACGGCGCTTTTCACACAAACATC
1 GCTAAAGAA-CATAATCTTTAACGGCGCTTTTCACACAAACACC
25147800 GCTAAA
1 GCTAAA
25147806 AATAACAGAT
Statistics
Matches: 103, Mismatches: 29, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
42 3 0.03
43 99 0.96
44 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (43 bp):
GCTAAAGAACATAATCTTTAACGGCGCTTTTCACACAAACACC
Found at i:25152486 original size:41 final size:41
Alignment explanation
Indices: 25152323--25152488 Score: 129
Period size: 41 Copynumber: 4.0 Consensus size: 41
25152313 TTATTGATTA
** * * * *
25152323 ACCTTTAACGGTGCTTTCCCATAAGCGACGTTAATGCTCTG
1 ACCTTTAACGGCACTTTCTCATAAGCGTCGCTAATCCTCTG
* * * * ** *
25152364 ACCTTTAGCGGTA-TTTTTCTATAAACACCGCTAATGCTCTG
1 ACCTTTAACGGCACTTTCTC-ATAAGCGTCGCTAATCCTCTG
* *
25152405 ACCTTTAACGGCACTTTCTCATAAGCGTTGCTAATTCTCTG
1 ACCTTTAACGGCACTTTCTCATAAGCGTCGCTAATCCTCTG
* * * *
25152446 ACCTTTAGCGGCGCTTT-TCAGTAAGTGTCGTTAATCCTCTG
1 ACCTTTAACGGCACTTTCTCA-TAAGCGTCGCTAATCCTCTG
25152487 AC
1 AC
25152489 TAAAAAAGCG
Statistics
Matches: 100, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
40 7 0.07
41 88 0.88
42 5 0.05
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (41 bp):
ACCTTTAACGGCACTTTCTCATAAGCGTCGCTAATCCTCTG
Found at i:25152571 original size:40 final size:41
Alignment explanation
Indices: 25152494--25152632 Score: 217
Period size: 41 Copynumber: 3.4 Consensus size: 41
25152484 CTGACTAAAA
* * *
25152494 AAGCGCCGCTAATG-TCTGACCTTTAACGGCGCTTTTTCAT
1 AAGCGCCGCTAATGCTCTGACCTTTAGCGGTGCTTTTCCAT
25152534 AAGCGCCGCTAATGCTCTGACCTTTAGCGGTGCTTTTCCAT
1 AAGCGCCGCTAATGCTCTGACCTTTAGCGGTGCTTTTCCAT
* * *
25152575 AAGTGCCGCTAATACTCTAACCTTTAGCGGTGCTTTTCCAT
1 AAGCGCCGCTAATGCTCTGACCTTTAGCGGTGCTTTTCCAT
25152616 AAGCGCCGCTAATGCTC
1 AAGCGCCGCTAATGCTC
25152633 GTTCCCATAT
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 14 0.16
41 76 0.84
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (41 bp):
AAGCGCCGCTAATGCTCTGACCTTTAGCGGTGCTTTTCCAT
Found at i:25154077 original size:41 final size:41
Alignment explanation
Indices: 25153989--25154107 Score: 118
Period size: 41 Copynumber: 3.0 Consensus size: 41
25153979 ACGCTTCCCC
* *
25153989 ATAAACGCCGCTATTACTCTAACCTTTAGCAGCGCTTTAAA
1 ATAAACGCCGCTATTGCTCTAACCTTTAGCGGCGCTTTAAA
* * * **
25154030 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGTGCTTATGTA
1 ATAAACGCCGCTATTGCTCTAACCTTTAGCGGCGCTT-TAAA
* * *
25154072 A-AAACGTCGCTATTGCT-TCACCTTTTGCGGCG-TTTA
1 ATAAACGCCGCTATTGCTCTAACCTTTAGCGGCGCTTTA
25154108 TTGTCCAAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
38 1 0.02
39 2 0.03
40 12 0.19
41 46 0.72
42 3 0.05
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (41 bp):
ATAAACGCCGCTATTGCTCTAACCTTTAGCGGCGCTTTAAA
Found at i:25161973 original size:17 final size:16
Alignment explanation
Indices: 25161951--25162005 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
25161941 CTAAAATTAT
25161951 TAAAAATATAAAAAAC
1 TAAAAATATAAAAAAC
*
25161967 TATAAAATATTAAAAAAT
1 TA-AAAATA-TAAAAAAC
25161985 TAAAAATATATAAAAA-
1 TAAAAATATA-AAAAAC
25162001 TAAAA
1 TAAAA
25162006 TTTATGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 9 0.26
17 17 0.49
18 9 0.26
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAAATATAAAAAAC
Found at i:25161979 original size:26 final size:27
Alignment explanation
Indices: 25161942--25161999 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
25161932 AAATACATTC
25161942 TAAAATTATT-AAAAATATAAAAA-ACTA
1 TAAAATTATTAAAAAAT-TAAAAATA-TA
25161969 TAAAA-TATTAAAAAATTAAAAATATA
1 TAAAATTATTAAAAAATTAAAAATATA
25161995 TAAAA
1 TAAAA
25162000 ATAAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 17 0.59
27 12 0.41
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (27 bp):
TAAAATTATTAAAAAATTAAAAATATA
Found at i:25162001 original size:10 final size:9
Alignment explanation
Indices: 25161942--25162002 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
25161932 AAATACATTC
*
25161942 TAAAATTAT
1 TAAAAATAT
25161951 TAAAAATA-
1 TAAAAATAT
*
25161959 TAAAAA-AC
1 TAAAAATAT
25161967 TATAAAATAT
1 TA-AAAATAT
25161977 TAAAAA-AT
1 TAAAAATAT
25161985 TAAAAATAT
1 TAAAAATAT
25161994 ATAAAAATA
1 -TAAAAATA
25162003 AAATTTATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
7 1 0.02
8 16 0.36
9 17 0.38
10 11 0.24
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
TAAAAATAT
Found at i:25162900 original size:5 final size:5
Alignment explanation
Indices: 25162890--25162916 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
25162880 ATTATTAAAT
25162890 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
25162917 ATCTCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:25167151 original size:23 final size:24
Alignment explanation
Indices: 25167125--25167172 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
25167115 AACGTGAAAA
*
25167125 TAAAA-GAATGAAGATCTCAATTT
1 TAAAACGAATAAAGATCTCAATTT
*
25167148 TAAAACGAATAAAGATTTCAATTT
1 TAAAACGAATAAAGATCTCAATTT
25167172 T
1 T
25167173 GAAGGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.33
Consensus pattern (24 bp):
TAAAACGAATAAAGATCTCAATTT
Found at i:25168437 original size:29 final size:28
Alignment explanation
Indices: 25168371--25168496 Score: 69
Period size: 29 Copynumber: 4.4 Consensus size: 28
25168361 GAAGAAACGA
* *
25168371 TGAAATCGGGGTGAAAATGGGACTTTT-G
1 TGAAATCGGGG-GAAAATGGTAATTTTGG
*
25168399 -GATACTCGGGGGCAAAATGGTAATTTTGG
1 TGA-AATCGGGGG-AAAATGGTAATTTTGG
** * *
25168428 TGAAATCGGGATTAAAAAT-GAAATTTTTG
1 TGAAATCGGG--GGAAAATGGTAATTTTGG
* ** *
25168457 AGAGTTCGAGGGTAAAATGGTAATTTTGG
1 TGAAATCG-GGGGAAAATGGTAATTTTGG
*
25168486 TGAAATTGGGG
1 TGAAATCGGGG
25168497 TTAAAAACGG
Statistics
Matches: 71, Mismatches: 19, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
27 3 0.04
28 27 0.38
29 32 0.45
30 9 0.13
ACGTcount: A:0.32, C:0.06, G:0.33, T:0.30
Consensus pattern (28 bp):
TGAAATCGGGGGAAAATGGTAATTTTGG
Found at i:25168568 original size:59 final size:57
Alignment explanation
Indices: 25168412--25168955 Score: 610
Period size: 59 Copynumber: 9.2 Consensus size: 57
25168402 ACTCGGGGGC
* * *
25168412 AAAATGGTAA-TTTTGGTGAAATCGGGATTAAAAATGAAATTTTTGAGAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAA-TTTT-AAAGTTCGAGGGT
* * *
25168470 AAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAACGGAATTTTAAGAGTTCGAGGCAT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAA-AGTTCGAGG-GT
* * *
25168528 AAAATGGTAATTTTTGGTTAAACCGGGGTTAAAAATGGAATTTTAAGAGTTCGGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAA-AGTTC-GAGGGT
* * * *
25168587 AAAATGGTAATTTTTGGTGAAACCAGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT--AAAGTTCGAGGGT
* * *
25168646 AAAATGGTAATTTTTAGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT--AAAGTTCGAGGGT
* * *
25168705 AAAATGGTAATTTTTGGAAGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
1 AAAATGGTAATTTTTGG-TGAAATCGGGGTTAAAAATGGAATTTT--AAAGTTCGAGGGT
* ** *
25168765 AAAATAGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT--AAAGTTCGAGGGT
* * *
25168824 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAGTTTTGGAAAGTTCAAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT--AAAGTTCGAGGGT
* **
25168883 AAAATGGTAATTTTT-G-GAAGTTTCGGGGTTAAAAATGGAATTTTAAAAGGTTTAAGGGT
1 AAAATGGTAATTTTTGGTGAA--ATCGGGGTTAAAAATGGAATTTT-AAA-GTTCGAGGGT
25168942 AAAATGGTAATTTT
1 AAAATGGTAATTTT
25168956 GGAAGTTTCG
Statistics
Matches: 434, Mismatches: 42, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
56 1 0.00
57 15 0.03
58 50 0.12
59 306 0.71
60 60 0.14
61 2 0.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGTTCGAGGGT
Found at i:25168570 original size:30 final size:31
Alignment explanation
Indices: 25168528--25168861 Score: 131
Period size: 29 Copynumber: 11.2 Consensus size: 31
25168518 TTCGAGGCAT
*
25168528 AAAATGGTAATTTTTGGTTAAACCGGGGTTA
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTA
** * ** * *
25168559 AAAATGG-AATTTTAAGAG-TTCGGGGGGT-
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTA
*
25168587 AAAATGGTAATTTTTGGTGAAACCAGGGTTA
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTA
* ** *
25168618 AAAATGG-AA-TTTT--AGAAAGTTTGGGGGT-
1 AAAATGGTAATTTTTGGTGAAA--CCGGGGTTA
* *
25168646 AAAATGGTAATTTTTAGTGAAATCGGGGTTA
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTA
** *
25168677 AAAATGG-AA-TTTT-G-GAAAGTTTGGGGGT-
1 AAAATGGTAATTTTTGGTGAAA--CCGGGGTTA
* * *
25168705 AAAATGGTAATTTTTGGAAGAAATCGAGGTTA
1 AAAATGGTAATTTTTGG-TGAAACCGGGGTTA
**
25168737 AAAATGG-AA-TTTT-G-GAAAGTTCAAGGG-T-
1 AAAATGGTAATTTTTGGTGAAA---CCGGGGTTA
* * **
25168765 AAAATAGTAATTTTTGGTGAAATCAAGGTTA
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTA
* *
25168796 AAAATGG-AA-TTTT-G-GAAAGTTCGGGGGT-
1 AAAATGGTAATTTTTGGTGAAA--CCGGGGTTA
* *
25168824 AAAATGGTAATTTTTGGTAAAATCGGGGTTA
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTA
25168855 AAAATGG
1 AAAATGG
25168862 AGTTTTGGAA
Statistics
Matches: 226, Mismatches: 43, Indels: 68
0.67 0.13 0.20
Matches are distributed among these distances:
27 16 0.07
28 36 0.16
29 54 0.24
30 54 0.24
31 44 0.19
32 18 0.08
33 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGTGAAACCGGGGTTA
Found at i:25168797 original size:178 final size:176
Alignment explanation
Indices: 25168412--25168955 Score: 706
Period size: 178 Copynumber: 3.1 Consensus size: 176
25168402 ACTCGGGGGC
* * * *
25168412 AAAATGGTAA-TTTTGGTGAAATC-GGGATTAAAAATGAAATTTTTGAGAGTTCGAGGGTAAAAT
1 AAAATGGTAATTTTTGGTGAAATCAGGG-TTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAAT
* * **
25168475 GGTAA-TTTTGGTGAAATTGGGGTTAAAAACGGAATTTT--AAGAGTTCGAGGCATAAAATGGTA
65 GGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAA-AGTTCG-GGGGTAAAATGGTA
** * **
25168537 ATTTTTGG-TTAAACCGGGGTTAAAAATGGAATTTTAAGAGTTCGGGGGGT
128 ATTTTTGGAAGAAATCGGGGTTAAAAATGGAATTTTAA-AGTTC-AAGGGT
* *
25168587 AAAATGGTAATTTTTGGTGAAACCAGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATG
* *
25168652 GTAATTTTTAGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATT
66 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
*
25168717 TTTGGAAGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
131 TTTGGAAGAAATCGGGGTTAAAAATGGAATTTT--AAAGTTCAAGGGT
* * *
25168765 AAAATAGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATG
* * **
25168830 GTAATTTTTGGTAAAATCGGGGTTAAAAATGGAGTTTTGGAAAGTTCAAGGGTAAAATGGTAATT
66 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
** *
25168895 TTTGGAAG-TTTCGGGGTTAAAAATGGAATTTTAAAAGGTTTAAGGGT
131 TTTGGAAGAAATCGGGGTTAAAAATGGAATTTT-AAA-GTTCAAGGGT
25168942 AAAATGGTAATTTT
1 AAAATGGTAATTTT
25168956 GGAAGTTTCG
Statistics
Matches: 325, Mismatches: 35, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
175 10 0.03
176 51 0.16
177 96 0.30
178 159 0.49
179 7 0.02
180 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (176 bp):
AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATG
GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
TTTGGAAGAAATCGGGGTTAAAAATGGAATTTTAAAGTTCAAGGGT
Found at i:25169217 original size:162 final size:162
Alignment explanation
Indices: 25169027--25169368 Score: 533
Period size: 162 Copynumber: 2.1 Consensus size: 162
25169017 AGGCATCCAG
* * * * *
25169027 CAGTCAAGGGATTAAATTGTAAACCTTGAAAAATTCTTGGGCCAATTTTATAATTAAATAAGAGT
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTCGGCCAATTTTATAATTAAATAAAAGT
*
25169092 TGATTT-GGAGATTAAATTAAAACAAATTCAAAATATCAAGGACTAAATGAATAAATAAGCCAAA
66 TGATTTAGG-GATTAAATTAAAACAAATTAAAAATATCAAGGACTAAATGAATAAATAAGCCAAA
25169156 AAGTGACACATGGCAGCCCCTGGTGCAGTCAAA
130 AAGTGACACATGGCAGCCCCTGGTGCAGTCAAA
* * *
25169189 CAGTCAAAGGACTAATTTATAAACCTTGAAAAATTGTTCGGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTCGGCCAATTTTATAATTAAATAAAAGT
* *
25169254 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGAATAAATAAGCCAAAA
66 TGATTTAGGGATTAAATTAAAACAAATTAAAAATATCAAGGACTAAATGAATAAATAAGCCAAAA
* * *
25169319 AGTGACACGTGGCAGTCTCTGGTGCAGTCAAA
131 AGTGACACATGGCAGCCCCTGGTGCAGTCAAA
*
25169351 CAGTCAAAGGATTAAATT
1 CAGTCAAAGGACTAAATT
25169369 GAAAACTAAT
Statistics
Matches: 163, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
162 161 0.99
163 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.27
Consensus pattern (162 bp):
CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTCGGCCAATTTTATAATTAAATAAAAGT
TGATTTAGGGATTAAATTAAAACAAATTAAAAATATCAAGGACTAAATGAATAAATAAGCCAAAA
AGTGACACATGGCAGCCCCTGGTGCAGTCAAA
Found at i:25170137 original size:13 final size:13
Alignment explanation
Indices: 25170119--25170144 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25170109 ATTATTATTG
25170119 TTAAAAATATTTA
1 TTAAAAATATTTA
25170132 TTAAAAATATTTA
1 TTAAAAATATTTA
25170145 CTCATCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAAAATATTTA
Found at i:25170625 original size:29 final size:29
Alignment explanation
Indices: 25170584--25170646 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
25170574 ACTGACTTGG
25170584 TTTTTATAGCCAAAATATTCAATCATTCT
1 TTTTTATAGCCAAAATATTCAATCATTCT
25170613 TTTTTATAGCCAAAATATTCAATCATTCT
1 TTTTTATAGCCAAAATATTCAATCATTCT
25170642 TTTTT
1 TTTTT
25170647 GTTTGTTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (29 bp):
TTTTTATAGCCAAAATATTCAATCATTCT
Found at i:25170986 original size:6 final size:6
Alignment explanation
Indices: 25170977--25171066 Score: 61
Period size: 6 Copynumber: 15.8 Consensus size: 6
25170967 GACTTTTCTT
25170977 TTTAAA TTTATAA --TAATA TT-AAA TTT-AA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
25171023 -TTAAA ATTGAA TTTAAA -ATAAA TTTAAGA -TTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAA
25171067 TTTTCAAATG
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
4 1 0.01
5 25 0.37
6 38 0.57
7 3 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:25171011 original size:11 final size:11
Alignment explanation
Indices: 25170990--25171049 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
25170980 AAATTTATAA
25170990 TAATATTAAATT
1 TAAT-TTAAATT
25171002 TAATTTAAATT
1 TAATTTAAATT
25171013 TAAATTTAAATT
1 T-AATTTAAATT
* * *
25171025 AAAATTGAATT
1 TAATTTAAATT
**
25171036 TAAAATAAATT
1 TAATTTAAATT
25171047 TAA
1 TAA
25171050 GATTAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
11 27 0.66
12 14 0.34
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATTTAAATT
Found at i:25171015 original size:17 final size:17
Alignment explanation
Indices: 25170977--25171066 Score: 87
Period size: 17 Copynumber: 5.3 Consensus size: 17
25170967 GACTTTTCTT
25170977 TTTAAATTTATAA-T-AA
1 TTTAAATTTA-AATTAAA
*
25170993 TATTAAATTTAATTTAAA
1 T-TTAAATTTAAATTAAA
25171011 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
* * *
25171028 ATTGAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
*
25171045 TTTAAGA-TTAAAATAAA
1 TTTAA-ATTTAAATTAAA
25171062 TTTAA
1 TTTAA
25171067 TTTTCAAATG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
16 2 0.03
17 57 0.90
18 4 0.06
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:25173326 original size:71 final size:71
Alignment explanation
Indices: 25173210--25173344 Score: 211
Period size: 71 Copynumber: 1.9 Consensus size: 71
25173200 CATGTCTCTG
* *
25173210 AGGTACAAGGTTCGCCGTTGTGACTTAAACCTTTCCCTTTGTATCTTCT-TGGTACTAGATTCAC
1 AGGTACAAGGTTCGCCATTGTCACTTAAACCTTTCCCTTTGTATC-TCTGTGGTACTAGATTCAC
25173274 GCTTTCA
65 GCTTTCA
*
25173281 AGGTACAGGGTTCGCCATTG-CATCTTAAACCTTTCCCTTTGTATCTCTGTGGTACTAGATTCAC
1 AGGTACAAGGTTCGCCATTGTCA-CTTAAACCTTTCCCTTTGTATCTCTGTGGTACTAGATTCAC
25173345 CGTTGCAGCT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
70 4 0.07
71 55 0.93
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (71 bp):
AGGTACAAGGTTCGCCATTGTCACTTAAACCTTTCCCTTTGTATCTCTGTGGTACTAGATTCACG
CTTTCA
Found at i:25173500 original size:48 final size:48
Alignment explanation
Indices: 25173281--25173709 Score: 278
Period size: 49 Copynumber: 8.8 Consensus size: 48
25173271 CACGCTTTCA
* ** ** * *
25173281 AGGTACAGGGTTCGCCATTGCATCTTAAACCTTTCCCTTTGTATCTCTG
1 AGGTACACGGTTCGCCATTGCGGCTTAAACCTTTCCCTTCAT-TTTTTG
* * * * * * * **
25173330 TGGTACTA-GATTCACCGTTGCAGCTTAAATCTTTCCCTTTACGCTTTTG
1 AGGTAC-ACGGTTCGCCATTGCGGCTTAAACCTTTCCCTTCA-TTTTTTG
** * * * * *
25173379 AGGTACAAAGTTCACCATTGCGACTTAAACCGTTCCCTTTGCA-TCTTCG
1 AGGTACACGGTTCGCCATTGCGGCTTAAACCTTTCCC-TT-CATTTTTTG
* * * *
25173428 TGGTATTA-GATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATTTTTTG
1 AGGTA-CACGGTTCGCCATTGCGGCTTAAACCTTTCCCTTCATTTTTTG
* * *
25173476 AGGTACACGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTTGCA-TCTTCG
1 AGGTACACGGTTCGCCATTGCGGCTTAAACCTTTCCC-TT-CATTTTTTG
* * * * *
25173525 TGGTAC-TGGATTCGCCATTGTGGCTTAAATCTTTCCCTTCATTTTTTA
1 AGGTACACGG-TTCGCCATTGCGGCTTAAACCTTTCCCTTCATTTTTTG
* * *
25173573 AGGTACACGGTTTGCCATTGCGGCTTAAACCTTTCCCTTTGCA-TCTTCG
1 AGGTACACGGTTCGCCATTGCGGCTTAAACCTTTCCC-TT-CATTTTTTG
* ** * * *
25173622 TGGTA-TTGGATTCGCCGTTGCGGCTTAAATCTTTCCCCTCATTTTTTG
1 AGGTACACGG-TTCGCCATTGCGGCTTAAACCTTTCCCTTCATTTTTTG
* * *
25173670 AGATACAAGGTTCTCCATTGCGGCTTAAACCTTTCCCTTC
1 AGGTACACGGTTCGCCATTGCGGCTTAAACCTTTCCCTTC
25173710 TTGTCTTCAT
Statistics
Matches: 291, Mismatches: 71, Indels: 37
0.73 0.18 0.09
Matches are distributed among these distances:
47 7 0.02
48 111 0.38
49 164 0.56
50 8 0.03
51 1 0.00
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.38
Consensus pattern (48 bp):
AGGTACACGGTTCGCCATTGCGGCTTAAACCTTTCCCTTCATTTTTTG
Found at i:25173518 original size:97 final size:97
Alignment explanation
Indices: 25173281--25173708 Score: 579
Period size: 97 Copynumber: 4.4 Consensus size: 97
25173271 CACGCTTTCA
* ** * *
25173281 AGGTACAGGGTTCGCCATTGCATCTTAAACCTTTCCCTTTGTATC-TCTGTGGTACTAGATTCAC
1 AGGTACAAGGTTCGCCATTGCGGCTTAAACCTTTCCCTTTGCATCTTC-GTGGTACTAGATTCGC
* * **
25173345 CGTTGCAGCTTAAATCTTTCCCTTTACGCTTTTG
65 CGTTGCGGCTTAAATCTTTCCCTTCA-TTTTTTG
* * * * *
25173379 AGGTACAAAGTTCACCATTGCGACTTAAACCGTTCCCTTTGCATCTTCGTGGTATTAGATTCGCC
1 AGGTACAAGGTTCGCCATTGCGGCTTAAACCTTTCCCTTTGCATCTTCGTGGTACTAGATTCGCC
*
25173444 GTTGCGGCTTAAACCTTTCCCTTCATTTTTTG
66 GTTGCGGCTTAAATCTTTCCCTTCATTTTTTG
* * *
25173476 AGGTACACGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTTGCATCTTCGTGGTACTGGATTCGCC
1 AGGTACAAGGTTCGCCATTGCGGCTTAAACCTTTCCCTTTGCATCTTCGTGGTACTAGATTCGCC
* * *
25173541 ATTGTGGCTTAAATCTTTCCCTTCATTTTTTA
66 GTTGCGGCTTAAATCTTTCCCTTCATTTTTTG
* * * *
25173573 AGGTACACGGTTTGCCATTGCGGCTTAAACCTTTCCCTTTGCATCTTCGTGGTATTGGATTCGCC
1 AGGTACAAGGTTCGCCATTGCGGCTTAAACCTTTCCCTTTGCATCTTCGTGGTACTAGATTCGCC
*
25173638 GTTGCGGCTTAAATCTTTCCCCTCATTTTTTG
66 GTTGCGGCTTAAATCTTTCCCTTCATTTTTTG
* *
25173670 AGATACAAGGTTCTCCATTGCGGCTTAAACCTTTCCCTT
1 AGGTACAAGGTTCGCCATTGCGGCTTAAACCTTTCCCTT
25173709 CTTGTCTTCA
Statistics
Matches: 292, Mismatches: 37, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
97 215 0.74
98 75 0.26
99 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (97 bp):
AGGTACAAGGTTCGCCATTGCGGCTTAAACCTTTCCCTTTGCATCTTCGTGGTACTAGATTCGCC
GTTGCGGCTTAAATCTTTCCCTTCATTTTTTG
Found at i:25176835 original size:17 final size:18
Alignment explanation
Indices: 25176797--25176889 Score: 79
Period size: 17 Copynumber: 5.4 Consensus size: 18
25176787 AAACCCATTT
25176797 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
* *
25176815 -TTAAGTTTGTTTTAA-A
1 TTTAAATTTATTTTAAGA
* *
25176831 TTTAAATTTAATTT-AGG
1 TTTAAATTTATTTTAAGA
*
25176848 TTTAAAGTTATTTTTAA-A
1 TTTAAATTTA-TTTTAAGA
* *
25176866 TTTAAAATTATTATAA-A
1 TTTAAATTTATTTTAAGA
25176883 TTTAAAT
1 TTTAAAT
25176890 AAATAAAAGT
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
16 2 0.03
17 44 0.75
18 12 0.20
19 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:25176863 original size:35 final size:34
Alignment explanation
Indices: 25176797--25176871 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 34
25176787 AAACCCATTT
*
25176797 TTTAAATTTATTTTAAGATTAAGTTTGTTTTAAA
1 TTTAAATTTAATTTAAGATTAAGTTTGTTTTAAA
* *
25176831 TTTAAATTTAATTTAGGTTTAAAGTTAT-TTTTAAA
1 TTTAAATTTAATTTAAGATT-AAGTT-TGTTTTAAA
25176866 TTTAAA
1 TTTAAA
25176872 ATTATTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 17 0.47
35 18 0.50
36 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (34 bp):
TTTAAATTTAATTTAAGATTAAGTTTGTTTTAAA
Found at i:25176911 original size:14 final size:15
Alignment explanation
Indices: 25176894--25176926 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25176884 TTAAATAAAT
25176894 AAAA-GTCCAACTAC
1 AAAATGTCCAACTAC
*
25176908 AAAATGTCCAATTAC
1 AAAATGTCCAACTAC
25176923 AAAA
1 AAAA
25176927 CCCATTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAATGTCCAACTAC
Found at i:25177633 original size:13 final size:13
Alignment explanation
Indices: 25177598--25177635 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
25177588 TTAATAACGG
*
25177598 TAATAATAAATAT
1 TAATAATTAATAT
25177611 TAATAATTAATAT
1 TAATAATTAATAT
*
25177624 TAATATTTAATA
1 TAATAATTAATA
25177636 AAAAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATAATTAATAT
Found at i:25178830 original size:29 final size:30
Alignment explanation
Indices: 25178761--25179020 Score: 218
Period size: 29 Copynumber: 8.9 Consensus size: 30
25178751 TAAGCCCTTA
*
25178761 AACTATCCAAAAATTACATTTTTACCCCTG
1 AACTTTCCAAAAATTACATTTTTACCCCTG
25178791 AAC-TTCACAAAAATTACATTTTTACCCCT-
1 AACTTTC-CAAAAATTACATTTTTACCCCTG
* * **
25178820 AATTTTCC-AAAATT-C-TATTTTCCCCCCA
1 AACTTTCCAAAAATTACAT-TTTTACCCCTG
* * *
25178848 AACTTTACAAAAATTATATTTTTACCCCCG
1 AACTTTCCAAAAATTACATTTTTACCCCTG
* * * * *
25178878 AACTTTCC-AAAAGTCCATTTTTACTCTTA
1 AACTTTCCAAAAATTACATTTTTACCCCTG
25178907 AACTTTCC-AAAATTACATTTTTACCCCTG
1 AACTTTCCAAAAATTACATTTTTACCCCTG
* * *
25178936 AACTTTCC-AAAATTCCATTTTTGCCCCCG
1 AACTTTCCAAAAATTACATTTTTACCCCTG
* *
25178965 AACTTT-CAAAAATTTCATTTTTGA-CCTTG
1 AACTTTCCAAAAATTACATTTTT-ACCCCTG
** *
25178994 ATTTTTCAAAAAATTACCA-TTTTACCC
1 AACTTTCCAAAAATTA-CATTTTTACCC
25179021 TCGAATGTCT
Statistics
Matches: 185, Mismatches: 33, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 9 0.05
28 13 0.07
29 102 0.55
30 57 0.31
31 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTTACCCCTG
Found at i:25178887 original size:58 final size:58
Alignment explanation
Indices: 25178761--25178986 Score: 240
Period size: 58 Copynumber: 3.9 Consensus size: 58
25178751 TAAGCCCTTA
* * ** * *
25178761 AACTATCCAAAAATTACATTTTTACCCCTGAACTTCACAAAAATTACATTTTTA-CCCCT
1 AACTTTCC-AAAATTCCATTTTTACCCCCAAACTT-TCAAAAATTACATTTTTACCCCCG
* * * *
25178820 AATTTTCCAAAATTCTA-TTTTCCCCCCAAACTTTACAAAAATTATATTTTTACCCCCG
1 AACTTTCCAAAATTCCATTTTTACCCCCAAACTTT-CAAAAATTACATTTTTACCCCCG
* * ** * *
25178878 AACTTTCCAAAAGTCCATTTTTACTCTTAAACTTTCCAAAATTACATTTTTACCCCTG
1 AACTTTCCAAAATTCCATTTTTACCCCCAAACTTTCAAAAATTACATTTTTACCCCCG
* * *
25178936 AACTTTCCAAAATTCCATTTTTGCCCCCGAACTTTCAAAAATTTCATTTTT
1 AACTTTCCAAAATTCCATTTTTACCCCCAAACTTTCAAAAATTACATTTTT
25178987 GACCTTGATT
Statistics
Matches: 136, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
57 29 0.21
58 88 0.65
59 19 0.14
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.38
Consensus pattern (58 bp):
AACTTTCCAAAATTCCATTTTTACCCCCAAACTTTCAAAAATTACATTTTTACCCCCG
Found at i:25179126 original size:59 final size:60
Alignment explanation
Indices: 25178997--25179197 Score: 153
Period size: 59 Copynumber: 3.4 Consensus size: 60
25178987 GACCTTGATT
* * * ** *
25178997 TTTCAAAAAATTACCATTTTACCCTCGAATGTCTTGAAATTTTATTTTTAACCTCGAATC
1 TTTCCAAAAATTACCATTTTACCCTAGAATATCTAAAAATTTTATTTTTAAACTCGAATC
* * *
25179057 CTTCC-TAAATTACCATTTTACCCCTAG-ATATCTAAAAATTTTGTTTTTAATAC-CGAA-C
1 TTTCCAAAAATTACCATTTTA-CCCTAGAATATCTAAAAATTTTATTTTTAA-ACTCGAATC
* ** * * ** * *
25179115 TTTCCAAAAATTATCATTTTATGCTCGGACGTCT-AAAATTTCATTTTTGAACTCTGAA-C
1 TTTCCAAAAATTACCATTTTACCCTAGAATATCTAAAAATTTTATTTTTAAACTC-GAATC
**
25179174 TTTTGAAAAATTACCATTTTACCC
1 TTTCCAAAAATTACCATTTTACCC
25179198 CCTCGAGTGT
Statistics
Matches: 110, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
57 2 0.02
58 22 0.20
59 77 0.70
60 9 0.08
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (60 bp):
TTTCCAAAAATTACCATTTTACCCTAGAATATCTAAAAATTTTATTTTTAAACTCGAATC
Found at i:25188218 original size:18 final size:18
Alignment explanation
Indices: 25188184--25188218 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25188174 CATTTAATAC
*
25188184 TGTTCCTTATAATTATTT
1 TGTTCCTTATAAATATTT
*
25188202 TGTTCCTTGTAAATATT
1 TGTTCCTTATAAATATT
25188219 CGGTAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (18 bp):
TGTTCCTTATAAATATTT
Found at i:25188728 original size:48 final size:49
Alignment explanation
Indices: 25188676--25189071 Score: 234
Period size: 49 Copynumber: 8.1 Consensus size: 49
25188666 TGGCAAACCT
* * * * **
25188676 AGTACCTCAAAGACGT-AAGGCAAAGATTTAAGCCGCAACAACGAATCC
1 AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC
* *
25188724 AGTACCACGAAGACTTGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC
1 AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC
* * * * *
25188773 AATACCACAAAGGCAT-AAGGGAAAGGTTTAAGTCGTAATGGCGAA-CC
1 AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC
* ** **
25188820 TAGTACCTCAAAGACATGAAGGGAAAGATTTAAGCTATAATAGCGAATCC
1 -AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC
* * * ** ** **
25188870 AGTACCACGAAGACA-CAAGGGAAAGGTTTAAATCACAATTGCGAA-CC
1 AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC
** * ** ***
25188917 TAGTACCTTAGAGACATGAAGGGAAAGAATTTAAGCCACAACAATGAATCC
1 -AGTACCACAAAGACATGAAGGGAAAG-ATTTAAGCCGTAACGGCGAATCC
* ** * * * * *
25188968 AGTACCGCGTAGACA-CAAGGGGAAAGGTTTAAGTCGTAATGGC-AAACC
1 AGTACCACAAAGACATGAA-GGGAAAGATTTAAGCCGTAACGGCGAATCC
* * * * **
25189016 ATATACCTCAGAAG-CATGAAAGGAAA-ATTTAAGCCGCAACGGCGAATTT
1 A-GTACCACA-AAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC
25189065 AGTACCA
1 AGTACCA
25189072 TGCGGATTGA
Statistics
Matches: 263, Mismatches: 72, Indels: 26
0.73 0.20 0.07
Matches are distributed among these distances:
47 4 0.02
48 108 0.41
49 112 0.43
50 37 0.14
51 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.18
Consensus pattern (49 bp):
AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC
Found at i:25188770 original size:49 final size:49
Alignment explanation
Indices: 25188676--25188973 Score: 228
Period size: 48 Copynumber: 6.1 Consensus size: 49
25188666 TGGCAAACCT
* * * * *
25188676 AGTACCTCAAAGACGT-AAGGCAAAGATTTAAGCCGCAACAACGAATCC
1 AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACAGCGAATCC
* * *
25188724 AGTACCACGAAGACTTGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC
1 AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACAGCGAATCC
* * * * **
25188773 AATACCACAAAGGCAT-AAGGGAAAGGTTTAAGTCGTAATGGCGAA-CC
1 AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACAGCGAATCC
* ** *
25188820 TAGTACCTCAAAGACATGAAGGGAAAGATTTAAGCTATAATAGCGAATCC
1 -AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACAGCGAATCC
* * * ** ** **
25188870 AGTACCACGAAGACA-CAAGGGAAAGGTTTAAATCACAATTGCGAA-CC
1 AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACAGCGAATCC
** * ** **
25188917 TAGTACCTTAGAGACATGAAGGGAAAGAATTTAAGCCACAACAATGAATCC
1 -AGTACCACAAAGACATGAAGGGAAAG-ATTTAAGCCGTAACAGCGAATCC
25188968 AGTACC
1 AGTACC
25188974 GCGTAGACAC
Statistics
Matches: 199, Mismatches: 43, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
47 4 0.02
48 86 0.43
49 86 0.43
50 21 0.11
51 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (49 bp):
AGTACCACAAAGACATGAAGGGAAAGATTTAAGCCGTAACAGCGAATCC
Found at i:25188792 original size:97 final size:97
Alignment explanation
Indices: 25188678--25189000 Score: 279
Period size: 97 Copynumber: 3.3 Consensus size: 97
25188668 GCAAACCTAG
* * * * * *
25188678 TACCTCAAAGACGTAAGGCAAAGATTTAAGCCGCAACAACGAATCC-AGTACCACGAAGACTTGA
1 TACCACAAAGACATAAGGGAAAGGTTTAAGCCGCAACAACGAA-CCTAGTACCACAAAGACATGA
* *
25188742 AGGGAAAGATTTAAGCCGTAACGGCGAATCCAA
65 AGGGAAAGATTTAAGCCATAACAGCGAATCCAA
* * * *** *
25188775 TACCACAAAGGCATAAGGGAAAGGTTTAAGTCGTAATGGCGAACCTAGTACCTCAAAGACATGAA
1 TACCACAAAGACATAAGGGAAAGGTTTAAGCCGCAACAACGAACCTAGTACCACAAAGACATGAA
* * *
25188840 GGGAAAGATTTAAGCTATAATAGCGAATCCAG
66 GGGAAAGATTTAAGCCATAACAGCGAATCCAA
* * ** * *** ** *
25188872 TACCACGAAGACACAAGGGAAAGGTTTAAATCACAATTGCGAACCTAGTACCTTAGAGACATGAA
1 TACCACAAAGACATAAGGGAAAGGTTTAAGCCGCAACAACGAACCTAGTACCACAAAGACATGAA
* ** *
25188937 GGGAAAGAATTTAAGCCACAACAATGAATCCAG
66 GGGAAAG-ATTTAAGCCATAACAGCGAATCCAA
* ** *
25188970 TACCGCGTAGACACAAGGGGAAAGGTTTAAG
1 TACCACAAAGACATAA-GGGAAAGGTTTAAG
25189001 TCGTAATGGC
Statistics
Matches: 188, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
96 2 0.01
97 139 0.74
98 34 0.18
99 13 0.07
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (97 bp):
TACCACAAAGACATAAGGGAAAGGTTTAAGCCGCAACAACGAACCTAGTACCACAAAGACATGAA
GGGAAAGATTTAAGCCATAACAGCGAATCCAA
Found at i:25195120 original size:23 final size:24
Alignment explanation
Indices: 25195094--25195141 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
25195084 AACGTGAAAA
*
25195094 TAAAA-GAATGAAGATCTC-AATTT
1 TAAAACGAATAAAGAT-TCGAATTT
25195117 TAAAACGAATAAAGATTCGAATTT
1 TAAAACGAATAAAGATTCGAATTT
25195141 T
1 T
25195142 GAAGGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (24 bp):
TAAAACGAATAAAGATTCGAATTT
Found at i:25198369 original size:17 final size:16
Alignment explanation
Indices: 25198347--25198394 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
25198337 CTAAAATTAT
*
25198347 TAAAAATGTAAAAAAC
1 TAAAAATATAAAAAAC
*
25198363 TATAAAATATTAAAAAAT
1 TA-AAAATA-TAAAAAAC
25198381 TAAAAATATAAAAA
1 TAAAAATATAAAAA
25198395 TAAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.29
17 11 0.39
18 9 0.32
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (16 bp):
TAAAAATATAAAAAAC
Found at i:25198375 original size:26 final size:25
Alignment explanation
Indices: 25198338--25198393 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
25198328 AAATACATTC
25198338 TAAAATTATT-AAAAATGTAAAAAACTA
1 TAAAATTATTAAAAAAT-T-AAAAA-TA
25198365 TAAAA-TATTAAAAAATTAAAAATA
1 TAAAATTATTAAAAAATTAAAAATA
25198389 TAAAA
1 TAAAA
25198394 ATAAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.25
25 5 0.18
26 5 0.18
27 11 0.39
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
TAAAATTATTAAAAAATTAAAAATA
Found at i:25200334 original size:12 final size:12
Alignment explanation
Indices: 25200300--25200336 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
25200290 AAGCCTAATC
25200300 TTTAATTTTAAA
1 TTTAATTTTAAA
*
25200312 TTT-ATTCTAAA
1 TTTAATTTTAAA
25200323 TTTAATTTTAAA
1 TTTAATTTTAAA
25200335 TT
1 TT
25200337 GAGTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:25201869 original size:29 final size:28
Alignment explanation
Indices: 25201818--25202187 Score: 213
Period size: 29 Copynumber: 12.8 Consensus size: 28
25201808 CCTTAAATTG
* *
25201818 TCCAAAAATCATATTTTGAACCCCAAACTT
1 TCCAAAAATTACATTTT--ACCCCAAACTT
*
25201848 TCCAAAAATTACATTTTAACCCCTAAACTA
1 TCCAAAAATTACATTTT-ACCCC-AAACTT
* * *
25201878 TCCAAAAATTATATTTTGACTCTCGAACTT
1 TCCAAAAATTACATTTT-AC-CCCAAACTT
*
25201908 TCTAAAAATTACATTTTACCCCTAAAC--
1 TCCAAAAATTACATTTTACCCC-AAACTT
* *
25201935 TCTAAAAATTATAGTTTTACCCTCAAACTT
1 TCCAAAAATTACA-TTTTACCC-CAAACTT
* * *
25201965 T-CAAAAATCACATTTTTATCCTAAAC-T
1 TCCAAAAATTACA-TTTTACCCCAAACTT
25201992 TCTCAAAAATTACATTTTTACCCCTAAAC-T
1 TC-CAAAAATTACA-TTTTACCCC-AAACTT
* * * * *
25202022 TCCAAAAATCACATTTCAACCCGAAC-A
1 TCCAAAAATTACATTTTACCCCAAACTT
* * * *
25202049 TCCAAAAATTACCATTTTGACCTC-GAGTG
1 TCCAAAAATTA-CATTTT-ACCCCAAACTT
* * * *
25202078 TCCAAAAATTACCATTTTGCCCTTAAAGTG
1 TCCAAAAATTA-CATTTTACCC-CAAACTT
*
25202108 TCC-AAAATTATCATTTTTAACCCCGAACTT
1 TCCAAAAATTA-CA-TTTT-ACCCCAAACTT
*
25202138 TCC-AAAATTACCATTTTACCCTCAAAC-A
1 TCCAAAAATTA-CATTTTACCC-CAAACTT
25202166 TCCAAAAATTACCA-TTTACCCC
1 TCCAAAAATTA-CATTTTACCCC
25202188 TGAAGTGTCC
Statistics
Matches: 274, Mismatches: 47, Indels: 41
0.76 0.13 0.11
Matches are distributed among these distances:
27 28 0.10
28 47 0.17
29 103 0.38
30 91 0.33
31 5 0.02
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.33
Consensus pattern (28 bp):
TCCAAAAATTACATTTTACCCCAAACTT
Found at i:25202201 original size:28 final size:29
Alignment explanation
Indices: 25202053--25202217 Score: 133
Period size: 29 Copynumber: 5.7 Consensus size: 29
25202043 CGAACATCCA
*
25202053 AAAATTACCATTTTGACCTC-G-AGTGTCC
1 AAAATTACCATTTT-ACCCCTGAAGTGTCC
* * *
25202081 AAAAATTACCATTTTGCCCTTAAAGTGTCC
1 -AAAATTACCATTTTACCCCTGAAGTGTCC
* * *
25202111 AAAATTATCATTTTTAACCCC-GAACTTTCC
1 AAAATTACCA-TTTT-ACCCCTGAAGTGTCC
* ***
25202141 AAAATTACCATTTTA-CCCTCAAACATCC
1 AAAATTACCATTTTACCCCTGAAGTGTCC
25202169 AAAAATTACCA-TTTACCCCTGAAGTGTCC
1 -AAAATTACCATTTTACCCCTGAAGTGTCC
* *
25202198 AAAATTATCATTTTGCCCCT
1 AAAATTACCATTTTACCCCT
25202218 ATGCATCAAA
Statistics
Matches: 107, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
27 3 0.03
28 21 0.20
29 54 0.50
30 26 0.24
31 3 0.03
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTGAAGTGTCC
Found at i:25205473 original size:29 final size:29
Alignment explanation
Indices: 25205435--25205615 Score: 199
Period size: 29 Copynumber: 6.1 Consensus size: 29
25205425 TGGACATTCG
* *
25205435 GGGGTAAAAATGGTAATTTTTGCAAGTTTC
1 GGGGTAAAAAT-GTAATTTTTGGAAGTTTA
*
25205465 GGGGTAAAAAAAAG-AA-TTTTGGAAGTTTA
1 GGGGT--AAAAATGTAATTTTTGGAAGTTTA
*
25205494 AGGGTAAAAATGTAATTTTTGGAAGTTTTA
1 GGGGTAAAAATGTAATTTTTGGAAG-TTTA
*
25205524 -GGGTCAAAAAATG-AATTTTTGGATGTTTA
1 GGGGT--AAAAATGTAATTTTTGGAAGTTTA
*
25205553 GGGGTAAAAATGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGTAATTTTTGGAAGTTTA
*
25205582 GGGGTTAAGAATGTAATTTTTGGATAGTTTA
1 GGGG-TAAAAATGTAATTTTTGGA-AGTTTA
25205613 GGG
1 GGG
25205616 ACCTCCAGGG
Statistics
Matches: 130, Mismatches: 10, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
27 6 0.05
28 9 0.07
29 50 0.38
30 44 0.34
31 16 0.12
32 5 0.04
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.37
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTA
Found at i:25205600 original size:59 final size:59
Alignment explanation
Indices: 25205411--25205615 Score: 243
Period size: 59 Copynumber: 3.4 Consensus size: 59
25205401 AATTAGGATC
** ** * *
25205411 AAAAATAGAATTTTTGGACATTCGGGGGTAAAAATGGTAATTTTTGCAAGTTTCGGGGTAA
1 AAAAAT-GAATTTTTGGATGTTTAGGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTAA
* * * * *
25205472 AAAAAAGAA-TTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTCA
1 AAAAATGAATTTTTGGATGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAA
*
25205530 AAAAATGAATTTTTGGATGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGT-T
1 AAAAATGAATTTTTGGATGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAA
*
25205588 AAGAATGTAATTTTTGGATAGTTTAGGG
1 AAAAATG-AATTTTTGGAT-GTTTAGGG
25205616 ACCTCCAGGG
Statistics
Matches: 125, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
58 35 0.28
59 74 0.59
60 11 0.09
61 5 0.04
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (59 bp):
AAAAATGAATTTTTGGATGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAA
Found at i:25206076 original size:16 final size:16
Alignment explanation
Indices: 25206053--25206108 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
25206043 CGTTTGGTTC
25206053 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
25206069 GGTGTAATGGAATATA
1 GCTGTAATGGAATAGA
25206085 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
25206101 GCTGTAAT
1 GCTGTAAT
25206109 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:25206143 original size:46 final size:44
Alignment explanation
Indices: 25206090--25206183 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
25206080 ATATAGCTGT
* *
25206090 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
25206136 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
25206180 AATG
1 AATG
25206184 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:25206345 original size:58 final size:55
Alignment explanation
Indices: 25206278--25206423 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 55
25206268 AATTTTAATG
*
25206278 ATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
25206336 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
25206394 ATTATTATTAAAATATGAATTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTAATAAAAAT
25206424 TATAATATAT
Statistics
Matches: 77, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
57 3 0.04
58 40 0.52
59 17 0.22
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (55 bp):
ATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:25209803 original size:15 final size:14
Alignment explanation
Indices: 25209775--25209862 Score: 54
Period size: 15 Copynumber: 6.0 Consensus size: 14
25209765 TTAATTTATT
*
25209775 TAATTATATTTTAACA
1 TAATTAT-TATTAA-A
25209791 TAATTATTATTAAA
1 TAATTATTATTAAA
* *
25209805 TACAATT-TAATAAAA
1 T--AATTATTATTAAA
* *
25209820 TAATATATAATTTAA
1 TAAT-TATTATTAAA
*
25209835 TAA-TATTTTTAATA
1 TAATTATTATTAA-A
25209849 TAATTATTATTAAA
1 TAATTATTATTAAA
25209863 ATATGAATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
13 9 0.16
14 8 0.14
15 29 0.51
16 11 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATTATTATTAAA
Found at i:25209804 original size:57 final size:58
Alignment explanation
Indices: 25209736--25209862 Score: 163
Period size: 58 Copynumber: 2.2 Consensus size: 58
25209726 TATTTTAATG
* *
25209736 ATTATTATTAAATATAATGTAA-AAAA-AAT-T-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATACAATGTAATAAAATAATATATAATTTA-ATAA-TAT-TTTTAACATA
* *
25209793 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATACAATGTAATAAAATAATATATAATTTAATAATATTTTTAACATA
25209851 ATTATTATTAAA
1 ATTATTATTAAA
25209863 ATATGAATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
57 20 0.32
58 25 0.40
59 6 0.10
60 4 0.06
61 7 0.11
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (58 bp):
ATTATTATTAAATACAATGTAATAAAATAATATATAATTTAATAATATTTTTAACATA
Found at i:25213349 original size:24 final size:24
Alignment explanation
Indices: 25213311--25213375 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
25213301 TTCTTTATTA
25213311 TTATTATTAATTATTAAAAAAATAT
1 TTATTATTAA-TATTAAAAAAATAT
* *
25213336 TTGTTATTAATATTAAAATAATAT
1 TTATTATTAATATTAAAAAAATAT
*
25213360 TTATTATTATTATTAA
1 TTATTATTAATATTAA
25213376 TACATTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 27 0.75
25 9 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATTATTAATATTAAAAAAATAT
Found at i:25216879 original size:50 final size:50
Alignment explanation
Indices: 25216748--25217202 Score: 435
Period size: 50 Copynumber: 9.3 Consensus size: 50
25216738 GCGGTTGCAA
* * * * * *
25216748 TGTCTTTGGGGTACTAGATTCACCATTGCAGCTTAAATCTTTCCCTCCAT
1 TGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* * * *
25216798 TCT-TTTGTGGTACTAGATTCGTCGTTGCGGCTTAAATTTTTCCCTTCAT
1 TGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* * *
25216847 TTTCTTCGTGGTACTAGATTTGCCGTTACGGCTTAAATCTTTCCCTTCAT
1 TGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* ** * * * * *
25216897 TTTC-T-AAGGTACAAGGTTCGCCGTTGTGGCTTAAACCTTT--C-TCTT
1 TGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* * * * *
25216942 TGCATCTTCGTGGTACTGGATTCGCCATCGCGGCTTGAATCTTTCCCTTTAT
1 TG--TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
*
25216994 TGTCTTCGTGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCAT
1 TGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* * *
25217044 TGTCTTCGTGGTACTAAATTCACCATTGCGGCTTAAATCTTTCCCTTCAT
1 TGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* * * *
25217094 TGTCTTCGTGGTACTAAATTCGCCATTGCAGCTTAGATCTTTCCC-T--T
1 TGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* * * * * * * *
25217141 TGTATTTGTGGTACTGGATTTGCTGTTGTGGCTTAAATCTTTCCGTTC-G
1 TGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
*
25217190 TGTCTTCATGGTA
1 TGTCTTCGTGGTA
25217203 ATGAAACCTG
Statistics
Matches: 333, Mismatches: 62, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
45 4 0.01
46 1 0.00
47 37 0.11
48 29 0.09
49 78 0.23
50 179 0.54
51 1 0.00
52 4 0.01
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (50 bp):
TGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
Found at i:25217152 original size:147 final size:147
Alignment explanation
Indices: 25216757--25217202 Score: 426
Period size: 147 Copynumber: 3.0 Consensus size: 147
25216747 ATGTCTTTGG
* * * * * *
25216757 GGTACTAGATTCACCATTGCAGCTTAAATCTTTCCCTCCATTCT-TTTGTGGTACTAGATTCGTC
1 GGTACTAAATTCACCATTGCGGCTTAAATCTTTCCCTTCATTGTCTTCGTGGTACTAGATTCGCC
* * * * *
25216821 GTTGCGGCTTAAATTTTTCCCTTCAT-TTTCTTCGTGGTACTAGATTTGCCGTTACGGCTTAAAT
66 ATTGCGGCTTAGATCTTTCCCTT--TGTAT-TT-GTGGTACTAGATTTGCCGTTGCGGCTTAAAT
* *
25216885 CTTTCCCTTCATTTTC-T-AA
127 CTTTCCCTTCATTGTCTTCAT
* * * * * * *
25216904 GGTAC-AAGGTTCGCCGTTGTGGCTTAAACCTTT--C-TCTTTGCATCTTCGTGGTACTGGATTC
1 GGTACTAA-ATTCACCATTGCGGCTTAAATCTTTCCCTTCATTG--TCTTCGTGGTACTAGATTC
* * * **
25216965 GCCATCGCGGCTT-GAATCTTTCCCTTTATTGTCTTCGTGGTACTAGATTCACCGTTGCGGCTTA
63 GCCATTGCGGCTTAG-ATCTTTCCC--T-TTGTATTTGTGGTACTAGATTTGCCGTTGCGGCTTA
*
25217029 AATCTTTCCCTTCATTGTCTTCGT
124 AATCTTTCCCTTCATTGTCTTCAT
*
25217053 GGTACTAAATTCACCATTGCGGCTTAAATCTTTCCCTTCATTGTCTTCGTGGTACTAAATTCGCC
1 GGTACTAAATTCACCATTGCGGCTTAAATCTTTCCCTTCATTGTCTTCGTGGTACTAGATTCGCC
* * * *
25217118 ATTGCAGCTTAGATCTTTCCCTTTGTATTTGTGGTACTGGATTTGCTGTTGTGGCTTAAATCTTT
66 ATTGCGGCTTAGATCTTTCCCTTTGTATTTGTGGTACTAGATTTGCCGTTGCGGCTTAAATCTTT
* *
25217183 CCGTTC-GTGTCTTCAT
131 CCCTTCATTGTCTTCAT
25217199 GGTA
1 GGTA
25217203 ATGAAACCTG
Statistics
Matches: 238, Mismatches: 45, Indels: 33
0.75 0.14 0.10
Matches are distributed among these distances:
144 3 0.01
145 1 0.00
146 14 0.06
147 141 0.59
148 4 0.02
149 28 0.12
150 40 0.17
151 2 0.01
152 5 0.02
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (147 bp):
GGTACTAAATTCACCATTGCGGCTTAAATCTTTCCCTTCATTGTCTTCGTGGTACTAGATTCGCC
ATTGCGGCTTAGATCTTTCCCTTTGTATTTGTGGTACTAGATTTGCCGTTGCGGCTTAAATCTTT
CCCTTCATTGTCTTCAT
Found at i:25217182 original size:197 final size:196
Alignment explanation
Indices: 25216757--25217184 Score: 493
Period size: 197 Copynumber: 2.2 Consensus size: 196
25216747 ATGTCTTTGG
* * * * * **
25216757 GGTACTAGATTCACCATTGCAGCTTAAATCTTTCCCTCCATTCTTTTGTGGTACTAGATTCGTCG
1 GGTACTGGATTCGCCATCGCGGCTTAAATCTTTCCCTCCATTCTTTCGTGGTACTAGATTCACCG
* * * ** *
25216822 TTGCGGCTTAAATTTTTCCCTTCATTTTCTTCGTGGTACTAGATTTGCCGTTACGGCTTAAATCT
66 TTGCGGCTTAAATCTTTCCCTTCATTGTCTTCGTGGTACTAAATTCACCATTACGGCTTAAATCT
* * * ** *
25216887 TTCCCTTCATTTTCTAAGGTACAAGGTTCGCCGTTGTGGCTTAAACCTTTCTCTTTGCATCTTCG
131 TTCCCTTCATTGTCTAAGGTACAAGATTCGCCATTGCAGCTTAAACCTTTCCCTTTGCATCTTCG
25216952 T
196 T
* ** *
25216953 GGTACTGGATTCGCCATCGCGGCTTGAATCTTTCCCTTTATTGTCTTCGTGGTACTAGATTCACC
1 GGTACTGGATTCGCCATCGCGGCTTAAATCTTTCCCTCCATTCT-TTCGTGGTACTAGATTCACC
*
25217018 GTTGCGGCTTAAATCTTTCCCTTCATTGTCTTCGTGGTACTAAATTCACCATTGCGGCTTAAATC
65 GTTGCGGCTTAAATCTTTCCCTTCATTGTCTTCGTGGTACTAAATTCACCATTACGGCTTAAATC
** * * *
25217083 TTTCCCTTCATTGTCTTCGTGGTACTAA-ATTCGCCATTGCAGCTTAGATCTTTCCCTTTGTAT-
130 TTTCCCTTCATTGTC-T-AAGGTAC-AAGATTCGCCATTGCAGCTTAAACCTTTCCCTTTGCATC
25217146 TT-GT
192 TTCGT
* ** * *
25217150 GGTACTGGATTTGCTGTTGTGGCTTAAATCTTTCC
1 GGTACTGGATTCGCCATCGCGGCTTAAATCTTTCC
25217185 GTTCGTGTCT
Statistics
Matches: 193, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
196 36 0.19
197 120 0.62
198 3 0.02
199 32 0.17
200 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (196 bp):
GGTACTGGATTCGCCATCGCGGCTTAAATCTTTCCCTCCATTCTTTCGTGGTACTAGATTCACCG
TTGCGGCTTAAATCTTTCCCTTCATTGTCTTCGTGGTACTAAATTCACCATTACGGCTTAAATCT
TTCCCTTCATTGTCTAAGGTACAAGATTCGCCATTGCAGCTTAAACCTTTCCCTTTGCATCTTCG
T
Found at i:25239620 original size:12 final size:12
Alignment explanation
Indices: 25239603--25239630 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
25239593 TAGAGCTTCA
25239603 AATGCCACAAGT
1 AATGCCACAAGT
25239615 AATGCCACAAGT
1 AATGCCACAAGT
25239627 AATG
1 AATG
25239631 GAGTTGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (12 bp):
AATGCCACAAGT
Found at i:25242780 original size:209 final size:208
Alignment explanation
Indices: 25242210--25242991 Score: 898
Period size: 209 Copynumber: 3.8 Consensus size: 208
25242200 AAACAACGAG
* * * *
25242210 GCGGTCATCTTCCTGATGAGATACTGAGAAGTGA-ACCAAATCAATGAAATC-AAGCTCAAAGTG
1 GCGGTCATCTTCCTGATGAGATACAGAGAAGT-ATACCAACTCAAT-AAAACAAAGCTCAAAGCG
** * * **
25242273 AGC-AAATCTTCAAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCCAAGCAATAAAGCGG
64 AGCGAAA-CTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGG
* * * * * *
25242337 TTACCTTCCTGATGAGATACATAGAAGTGGACCAAA-TCTGTCTTTCTGATGGGATACAGAGAAG
128 TCACCTTCCTGATAAGATACAGAGAAGTGGACCAAATTC-GTCTTCCTAATGAGATACAGAGAAG
* **
25242401 CGGATTAAAATAAACGA
192 CGGATTGAAATAAGTGA
* * * * * * * *
25242418 TGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAGTC---GAAACCAGGCTCAAAGTGA
1 -GCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATAAAACAAAGCTCAAAGCGA
* * * * * * *
25242480 GCTAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCAAAGTAATAAAGTGGTT
65 GCGAAACTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTC
* * * * *
25242545 ACCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCCTCTTCCTAATAAGATACAGAGAAGCAG
130 ACCTTCCTGATAAGATACAGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGG
*
25242610 ATTGAAACAAGTGA
195 ATTGAAATAAGTGA
* * * *
25242624 GATGGTCATCTTCTTGATGAGATACAAAGAAGTATACCAACTCAATAAAACAAAGCTCAAAGCAA
1 G-CGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATAAAACAAAGCTCAAAGCGA
** * *
25242689 GCGAAACTTTGAACCCCAGCTTATTGATGAGATACTGAGAAGCAGGTCGAAGTAGTAAAATGGTC
65 GCGAAACTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTC
* * *
25242754 AGCTTCCTGATAAGATACTA-AGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAATAAGCG
130 ACCTTCCTGATAAGATAC-AGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCG
25242818 GATTGAAATAAGTGA
194 GATTGAAATAAGTGA
* * * *
25242833 GGCAGT-ATTCTTCCTGATAAGATACAGAGAAGTATACCAACTCAATGAAACAAAGCTCAATGCG
1 -GCGGTCA-TCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATAAAACAAAGCTCAAAGCG
*
25242897 AGTGAAACTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
64 AGCGAAACTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
* *
25242962 CAGCTTTCTGATAAGATACAGAGAAGTGGA
129 CACCTTCCTGATAAGATACAGAGAAGTGGA
25242992 TTAAAACAAG
Statistics
Matches: 494, Mismatches: 67, Indels: 24
0.84 0.11 0.04
Matches are distributed among these distances:
205 4 0.01
206 166 0.34
207 4 0.01
208 3 0.01
209 315 0.64
210 2 0.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (208 bp):
GCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATAAAACAAAGCTCAAAGCGAG
CGAAACTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCA
CCTTCCTGATAAGATACAGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGA
TTGAAATAAGTGA
Found at i:25243100 original size:172 final size:172
Alignment explanation
Indices: 25242841--25243163 Score: 468
Period size: 172 Copynumber: 1.9 Consensus size: 172
25242831 GAGGCAGTAT
* * *
25242841 TCTTCCTGATAAGATACAGAGAAGTATACCAACTCAATGAAACAAAGCTCAATGCGAGTGAAACT
1 TCTTCCTGATAAGATACAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATGCGAGCGAAACT
*
25242906 TTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTT-C
66 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT-AGCTTTCC
25242970 TGATAAGATACAGAGAAGTGGATTAAAACAAGTAATGCGGTCA
130 TGATAAGATACAGAGAAGTGGATTAAAACAAGTAATGCGGTCA
* * * * *
25243013 TCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATTAAACCAAGCTCAATGTGAGCGAAACT
1 TCTTCCTGATAAGATACAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATGCGAGCGAAACT
* ** * * * * *
25243078 TCGAATCTTAGCTTCTTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAGTGGTTGTTTTCCT
66 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTAGCTTTCCT
*
25243143 GATGAGATACAGAGAAGTGGA
131 GATAAGATACAGAGAAGTGGA
25243164 CCAAATCTGT
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
171 4 0.03
172 128 0.97
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (172 bp):
TCTTCCTGATAAGATACAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATGCGAGCGAAACT
TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTAGCTTTCCT
GATAAGATACAGAGAAGTGGATTAAAACAAGTAATGCGGTCA
Found at i:25243295 original size:381 final size:381
Alignment explanation
Indices: 25242585--25243377 Score: 1024
Period size: 381 Copynumber: 2.1 Consensus size: 381
25242575 CAAATTCCTC
* ** * *
25242585 TTCCTAATAAGATACAGAGAAGCAGATTGAAACAAGTGAGATGGTCATCTTCTTGATGAGATACA
1 TTCCTGATAAGATACAGAGAAGTGGATTAAAACAAGTGAGATGGTCATCTTCCTGATGAGATACA
* * *
25242650 AAGAAGTATACCAACTCAATAAAACAAAGCTCAAAGCAAGCGAAACTTTGAACCCCAGCTTATTG
66 AAGAAGTAGACCAAATCAATAAAACAAAGCTCAAAGCAAGCGAAACTTCGAACCCCAGCTTATTG
* *
25242715 ATGAGATACTGAGAAGCAGGTCGAAGTAGTAAAATGGTCAGCTTCCTGATAAGATACTAAGAAGT
131 ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTGATAAGATACTAAGAAGT
* * *
25242780 GGACCAAATTCGTCTTCCTAATGAGATACAAATAAGCGGATTGAAATAAGTGAGGCAGTATTCTT
196 GGACCAAATTCGTCTTCCTAATGAGATACAAAGAAACGGATTAAAATAAGTGAGGCAGTATTCTT
* * * *
25242845 CCTGATAAGATACAGAGAAGTATACCAACTCAATGAAACAAAGCTCAATGCGAGTGAAACTTTGA
261 CCTGATAAGATACAGAGAAGAATACCAAATCAATGAAACAAAGCTCAATGCGAGCGAAACTTCGA
* *
25242910 ACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCT
326 ACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCGAAGCAAAAAAATGGTC-GCT
25242967 TT-CTGATAAGATACAGAGAAGTGGATTAAAACAAGT-A-ATGCGGTCATCTTCCTGATGAGATA
1 TTCCTGATAAGATACAGAGAAGTGGATTAAAACAAGTGAGAT--GGTCATCTTCCTGATGAGATA
** * * * ** * ** *
25243029 CTGAGAAGTAGACCAAATCAATTAAACCAAGCTCAATGTGAGCGAAACTTCGAATCTTAGCTTCT
64 CAAAGAAGTAGACCAAATCAATAAAACAAAGCTCAAAGCAAGCGAAACTTCGAACCCCAGCTTAT
* * * * *
25243094 TGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAGTGGT-TGTTTTCCTGATGAGATAC-AGAG
129 TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAG-CTTCCTGATAAGATACTA-AG
* * * * * * *
25243157 AAGTGGACCAAA-TCTGTCTTCTTGATTAGATACAGAGAAATGGATTAAAATAAGTGATGCGGTC
192 AAGTGGACCAAATTC-GTCTTCCTAATGAGATACAAAGAAACGGATTAAAATAAGTGAGGCAGT-
* * * * *
25243221 A-TCTTCTTGATGAGATACAGAGAAGAATACCAAATTAATGAAACAAGGCTCAATGTGAGCGAAA
255 ATTCTTCCTGATAAGATACAGAGAAGAATACCAAATCAATGAAACAAAGCTCAATGCGAGCGAAA
* *
25243285 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACATGTCGAAGCAAAAAAATGGTCGTT
320 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCGAAGCAAAAAAATGGTCGCT
*
25243347 TTCCTGATAAGATACAGAGAAGTGGACTAAA
1 TTCCTGATAAGATACAGAGAAGTGGATTAAA
25243378 TCCGTCTTCC
Statistics
Matches: 354, Mismatches: 50, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
379 2 0.01
380 9 0.03
381 340 0.96
382 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (381 bp):
TTCCTGATAAGATACAGAGAAGTGGATTAAAACAAGTGAGATGGTCATCTTCCTGATGAGATACA
AAGAAGTAGACCAAATCAATAAAACAAAGCTCAAAGCAAGCGAAACTTCGAACCCCAGCTTATTG
ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTGATAAGATACTAAGAAGT
GGACCAAATTCGTCTTCCTAATGAGATACAAAGAAACGGATTAAAATAAGTGAGGCAGTATTCTT
CCTGATAAGATACAGAGAAGAATACCAAATCAATGAAACAAAGCTCAATGCGAGCGAAACTTCGA
ACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCGAAGCAAAAAAATGGTCGCT
Found at i:25243350 original size:209 final size:209
Alignment explanation
Indices: 25242969--25243467 Score: 694
Period size: 209 Copynumber: 2.4 Consensus size: 209
25242959 GGTCAGCTTT
* *
25242969 CTGATAAGATACAGAGAAGTGGATTAAAACAAGTAATGCGGTCATCTTCCTGATGAGATACTGAG
1 CTGATAAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAG
* * * ** *
25243034 AAGTAGACCAAATCAATTAAACCAAGCTCAATGTGAGCGAAACTTCGAATCTTAGCTTCTTGATG
66 AAGAAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATG
* * * * * *
25243099 AGATACTGAGAAGCAGGTTGAAGCAATAAAGTGGTTGTTTTCCTGATGAGATACAGAGAAGTGGA
131 AGATACTGAGAAACAGGTCGAAGCAAAAAAATGGTCGTTTTCCTGATAAGATACAGAGAAGTGGA
*
25243164 CCAAATCTGTCTTC
196 CCAAATCCGTCTTC
* * * * *
25243178 TTGATTAGATACAGAGAAATGGATTAAAATAAGTGATGCGGTCATCTTCTTGATGAGATACAGAG
1 CTGATAAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAG
* *
25243243 AAGAATACCAAATTAATGAAA-CAAGGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGAT
66 AAGAAGACCAAATCAATGAAACCAA-GCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGAT
*
25243307 GAGATACTGAGAAACATGTCGAAGCAAAAAAATGGTCGTTTTCCTGATAAGATACAGAGAAGTGG
130 GAGATACTGAGAAACAGGTCGAAGCAAAAAAATGGTCGTTTTCCTGATAAGATACAGAGAAGTGG
*
25243372 ACTAAATCCGTCTTC
195 ACCAAATCCGTCTTC
* * * * *
25243387 CTGATAAGATACAAAGAAGCGGATTAAAACAAGTGAGGCGGTCATCTTCCTAATGAGATATAGAG
1 CTGATAAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAG
* * *
25243452 ATGTAGGCCAAATCAA
66 AAGAAGACCAAATCAA
25243468 ATGCGATTGA
Statistics
Matches: 250, Mismatches: 39, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
208 3 0.01
209 247 0.99
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (209 bp):
CTGATAAGATACAGAGAAGTGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAG
AAGAAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATG
AGATACTGAGAAACAGGTCGAAGCAAAAAAATGGTCGTTTTCCTGATAAGATACAGAGAAGTGGA
CCAAATCCGTCTTC
Found at i:25243970 original size:11 final size:12
Alignment explanation
Indices: 25243950--25243987 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25243940 AAGCTCAATC
25243950 TTTAATTTTAAA
1 TTTAATTTTAAA
*
25243962 TTT-ATTTTAAG
1 TTTAATTTTAAA
*
25243973 TTTAAATTTAAA
1 TTTAATTTTAAA
25243985 TTT
1 TTT
25243988 GACTTATTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:25243976 original size:17 final size:17
Alignment explanation
Indices: 25243950--25243982 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25243940 AAGCTCAATC
*
25243950 TTTAATTTTAAATTTAT
1 TTTAAGTTTAAATTTAT
25243967 TTTAAGTTTAAATTTA
1 TTTAAGTTTAAATTTA
25243983 AATTTGACTT
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:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTAAGTTTAAATTTAT
Found at i:25245214 original size:33 final size:31
Alignment explanation
Indices: 25245176--25245244 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
25245166 CATTGGGGGG
*
25245176 TTTTGAGAGAAAAAGAAAAGAAA-GAAAACTTTT
1 TTTTGAAAG-AAAAGAAAAGAAATG-AAA-TTTT
* *
25245209 TTTTGAAAGAAATGAAAGGAAATGAAATTTT
1 TTTTGAAAGAAAAGAAAAGAAATGAAATTTT
25245240 TTTTG
1 TTTTG
25245245 GAAAATTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 9 0.28
32 14 0.44
33 9 0.28
ACGTcount: A:0.48, C:0.01, G:0.19, T:0.32
Consensus pattern (31 bp):
TTTTGAAAGAAAAGAAAAGAAATGAAATTTT
Found at i:25245802 original size:29 final size:27
Alignment explanation
Indices: 25245767--25246017 Score: 202
Period size: 28 Copynumber: 8.9 Consensus size: 27
25245757 TCTCGAACTT
*
25245767 TTCAAAAATTACATTTTAACACTAAAC
1 TTCAAAAATTACATTTTAACCCTAAAC
*
25245794 TCTCAAAAATTACATTTTTACCCTTAAAC
1 T-TCAAAAATTACATTTTAACCC-TAAAC
* *
25245823 TTCCAAAAATCACATTTTTA-CCTCAAAC
1 TT-CAAAAATTACATTTTAACCCT-AAAC
* *
25245851 TTCTCAAAATTACATTTTACCCCTAAAC
1 TTC-AAAAATTACATTTTAACCCTAAAC
* *
25245879 TCTCAAAAATTATATTTTTATCCC-AAAC
1 T-TCAAAAATTACA-TTTTAACCCTAAAC
* * *
25245907 TTCCAAAAATCACATTTTTTACCTTAAAC
1 TT-CAAAAATTACA-TTTTAACCCTAAAC
*
25245936 TTCTTAAAAATTACATTTTTACCCCTAAAC
1 TTC--AAAAATTACA-TTTTAACCCTAAAC
* * * *
25245966 TTTAAAAAATCACATTTTTACCCTAAATA
1 -TTCAAAAATTACATTTTAACCCTAAA-C
25245995 TTCAAAAATTACCATTTT-ACCCT
1 TTCAAAAATTA-CATTTTAACCCT
25246018 CGAGGGTCCA
Statistics
Matches: 183, Mismatches: 26, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
27 4 0.02
28 100 0.55
29 56 0.31
30 21 0.11
31 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (27 bp):
TTCAAAAATTACATTTTAACCCTAAAC
Found at i:25245877 original size:85 final size:85
Alignment explanation
Indices: 25245730--25245989 Score: 326
Period size: 85 Copynumber: 3.0 Consensus size: 85
25245720 AGAAGGTTCC
* * * * * * *
25245730 TAAACTATCCAGAAATCATATTTTGACTCTCGAACTTTTCAAAAATTACATTTTAACACTAAACT
1 TAAACT-TCCAAAAATCACATTTTTAC-CTCAAACTTCTC-AAAATTACATTTTACCCCTAAACT
25245795 CTCAAAAATTACATTTTTACCCT
63 CTCAAAAATTACATTTTTACCCT
25245818 TAAACTTCCAAAAATCACATTTTTACCTCAAACTTCTCAAAATTACATTTTACCCCTAAACTCTC
1 TAAACTTCCAAAAATCACATTTTTACCTCAAACTTCTCAAAATTACATTTTACCCCTAAACTCTC
*
25245883 AAAAATTATATTTTTATCCC-
66 AAAAATTACATTTTTA-CCCT
* *
25245903 -AAACTTCCAAAAATCACATTTTTTACCTTAAACTTCTTAAAAATTACATTTTTACCCCTAAACT
1 TAAACTTCCAAAAATCACA-TTTTTACCTCAAACTTC-TCAAAATTACA-TTTTACCCCTAAACT
* * *
25245967 TTAAAAAATCACATTTTTACCCT
63 CTCAAAAATTACATTTTTACCCT
25245990 AAATATTCAA
Statistics
Matches: 153, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
84 18 0.12
85 56 0.37
86 26 0.17
87 47 0.31
88 6 0.04
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.37
Consensus pattern (85 bp):
TAAACTTCCAAAAATCACATTTTTACCTCAAACTTCTCAAAATTACATTTTACCCCTAAACTCTC
AAAAATTACATTTTTACCCT
Found at i:25246090 original size:29 final size:28
Alignment explanation
Indices: 25245762--25246093 Score: 137
Period size: 29 Copynumber: 11.6 Consensus size: 28
25245752 TTGACTCTCG
* * *
25245762 AACTTTTCAAAAATTACATTTTAACACTA
1 AACTTTTC-AAAATTCCATTTTTACCCTA
* *
25245791 AAC-TCTCAAAAATTACATTTTTACCCTTA
1 AACTTTTC-AAAATTCCATTTTTACCC-TA
* *
25245820 AAC-TTCCAAAAATCACATTTTTA-CCTCA
1 AACTTTTCAAAATTC-CATTTTTACCCT-A
* *
25245848 AACTTCTCAAAATTACA-TTTTACCCCTA
1 AACTTTTCAAAATTCCATTTTTA-CCCTA
* **
25245876 AAC-TCTCAAAAATTATATTTTTATCCC-A
1 AACTTTTC-AAAATTCCATTTTTA-CCCTA
* * *
25245904 AAC-TTCCAAAAATCACATTTTTTACCTTA
1 AACTTTTCAAAATTC-CA-TTTTTACCCTA
* *
25245933 AACTTCTTAAAAATTACATTTTTACCCCTA
1 AACTT-TTCAAAATTCCATTTTTA-CCCTA
* *
25245963 AAC-TTTAAAAAATCACATTTTTACCCTA
1 AACTTTTCAAAATTC-CATTTTTACCCTA
* *
25245991 AA-TATTCAAAAATTACCA-TTTTACCCTC
1 AACTTTTC-AAAATT-CCATTTTTACCCTA
* *** * ** *
25246019 GAGGGTCCAAAAATTACCATTTTGCCCCTG
1 AACTTTTC-AAAATT-CCATTTTTACCCTA
* *
25246049 AAGTATTT-GAAATTCCATTTTTGACCCTA
1 AACT-TTTCAAAATTCCATTTTT-ACCCTA
25246078 AACTTTTCAAAATTCC
1 AACTTTTCAAAATTCC
25246094 CATCTTACCC
Statistics
Matches: 233, Mismatches: 47, Indels: 46
0.71 0.14 0.14
Matches are distributed among these distances:
27 15 0.06
28 91 0.39
29 100 0.43
30 20 0.09
31 7 0.03
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.36
Consensus pattern (28 bp):
AACTTTTCAAAATTCCATTTTTACCCTA
Found at i:25246205 original size:30 final size:29
Alignment explanation
Indices: 25246144--25246245 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
25246134 GAACTTTCCA
* **
25246144 AAAATCACCATTTTACCCCCAAA-CATCC
1 AAAATTACCATTTTACCCCCAAAGTGTCC
*
25246172 AAAAATTACCATTTTGCCCCCAAAGTGTCC
1 -AAAATTACCATTTTACCCCCAAAGTGTCC
* *
25246202 AAAATTACTATTTTACCCCTCGAAGTGTCC
1 AAAATTACCATTTTACCCC-CAAAGTGTCC
25246232 AAAATTACCATTTT
1 AAAATTACCATTTT
25246246 GCTCTCGGGC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
29 38 0.60
30 25 0.40
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAAGTGTCC
Found at i:25247541 original size:28 final size:28
Alignment explanation
Indices: 25247438--25247546 Score: 94
Period size: 28 Copynumber: 3.8 Consensus size: 28
25247428 TTGGATGCCC
* *
25247438 GAGGGTAAAATGGTAATTTTGGACTCTC
1 GAGGGTAAAATGGTAATTTTGGACACTT
* *
25247466 GAGAGTAAAATGGTAATTTTGGGAAACTT
1 GAGGGTAAAATGGTAATTTT-GGACACTT
* * * * *
25247495 TAGGCTTAAAAAGAT-ATTTTAGACACTT
1 GAGG-GTAAAATGGTAATTTTGGACACTT
*
25247523 GAGGGTAAAACGGTAATTTATGGA
1 GAGGGTAAAATGGTAATTT-TGGA
25247547 AGAATCGAGA
Statistics
Matches: 61, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
27 7 0.11
28 32 0.52
29 15 0.25
30 7 0.11
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (28 bp):
GAGGGTAAAATGGTAATTTTGGACACTT
Found at i:25247603 original size:29 final size:29
Alignment explanation
Indices: 25247561--25247631 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 29
25247551 TCGAGAGAAA
* *
25247561 AAAATGGGACTTTTTGGATGCCCGAGGGC
1 AAAATGGTAATTTTTGGATGCCCGAGGGC
* ** *
25247590 AAAATGGTAA-TTTTGGATTCTTGGGGGC
1 AAAATGGTAATTTTTGGATGCCCGAGGGC
25247618 AAAATGGTAATTTT
1 AAAATGGTAATTTT
25247632 AGAAAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 24 0.69
29 11 0.31
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGATGCCCGAGGGC
Found at i:25247688 original size:28 final size:27
Alignment explanation
Indices: 25247590--25247689 Score: 67
Period size: 28 Copynumber: 3.5 Consensus size: 27
25247580 GCCCGAGGGC
* * * *
25247590 AAAATGGTAATTTTGGATTCTTGGGGGC
1 AAAATAGTAATTTTAGATT-TTTGGGGT
* **
25247618 AAAATGGTAATTTTAGAAAAATTTGGGGTT
1 AAAATAGTAATTTTAG--ATTTTTGGGG-T
*
25247648 AAAA-ATTACATTTTAGATTTTTGGAGGT
1 AAAATAGTA-ATTTTAGATTTTTGG-GGT
25247676 AAAATAGTAATTTT
1 AAAATAGTAATTTT
25247690 TGGAAGAATC
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 31 0.55
29 13 0.23
30 12 0.21
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (27 bp):
AAAATAGTAATTTTAGATTTTTGGGGT
Found at i:25247827 original size:147 final size:145
Alignment explanation
Indices: 25247427--25247894 Score: 500
Period size: 146 Copynumber: 3.2 Consensus size: 145
25247417 AAAATGAGAC
* * * * * *
25247427 TTTGGATGCCCGAGGGTAAAATGGTAATTTTGGACTCTCGAGAGTAAAATGGTAATTTT-GGGAA
1 TTTGGATACCCGAGGGTAAAATGGTAATTTTGGACTTTCGGGGGCAAAATGGTAATTTTAGGAAA
* * * * *
25247491 ACTTTAGGCTTAAAAA-GATATTTTAGACACTTGAGGGTAAAACGGTAATTTATGGAAGAATCGA
66 AATTTAGGGTTAAAAATGACATTTTAGACACTTGAGGGTAAAA-TGTAATTTTTGGAAGAATCG-
*
25247555 GAGAAAAAAATGGGACTT
129 G-GATAAAAATGGGACTT
* * *
25247573 TTTGGATGCCCGAGGGCAAAATGGTAATTTTGGA-TTCTTGGGGGCAAAATGGTAATTTTA-GAA
1 TTTGGATACCCGAGGGTAAAATGGTAATTTTGGACTT-TCGGGGGCAAAATGGTAATTTTAGGAA
* * ***
25247636 AAATTTGGGGTTAAAAATTACATTTTAGATTTTTG-GAGGTAAAATAGTAATTTTTGGAAGAATC
65 AAATTTAGGGTTAAAAATGACATTTTAGACACTTGAG-GGTAAAAT-GTAATTTTTGGAAGAATC
*
25247700 GGGATAAAAATGAGACTT
128 GGGATAAAAATGGGACTT
** * *
25247718 TTTGGATATTCGAAGGGTAAAATGGTAATCTTAGACTTTCGGGGGCAAAATGGTAATTTTAGGAA
1 TTTGGATACCCG-AGGGTAAAATGGTAATTTTGGACTTTCGGGGGCAAAATGGTAATTTTAGGAA
* * * *
25247783 AATTTTAGGGTTAAAAATGACATTTTAGACACTTGAGGGTAAAATGATAATTTTTAGAAAAATCA
65 AAATTTAGGGTTAAAAATGACATTTTAGACACTTGAGGGTAAAATG-TAATTTTTGGAAGAATCG
*
25247848 GAATCAAAAATGGGA-TT
129 GGAT-AAAAATGGGACTT
* * *
25247865 TTTGGACATCCG-GGCGTAAAATAGTAATTT
1 TTTGGATACCCGAGG-GTAAAATGGTAATTT
25247895 CGGGAGTTTC
Statistics
Matches: 269, Mismatches: 41, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
145 26 0.10
146 124 0.46
147 109 0.41
148 10 0.04
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.32
Consensus pattern (145 bp):
TTTGGATACCCGAGGGTAAAATGGTAATTTTGGACTTTCGGGGGCAAAATGGTAATTTTAGGAAA
AATTTAGGGTTAAAAATGACATTTTAGACACTTGAGGGTAAAATGTAATTTTTGGAAGAATCGGG
ATAAAAATGGGACTT
Found at i:25248077 original size:59 final size:58
Alignment explanation
Indices: 25247948--25248098 Score: 164
Period size: 59 Copynumber: 2.6 Consensus size: 58
25247938 TCAAAAATGG
* * ***
25247948 AATTTTTGGAAG-TTTGGGGT-AAGAATATAATTTTTTGAAGTTTTAAGGTCAAAAATAT
1 AATTTTTAGAAGTTTTAGGGTCAA-AATATAATTTTCAAAAGTTTTAAGGT-AAAAATAT
* * * *
25248006 AATTTTTGGAAGTTTTAGGGTTAAAATGTAATTTTCAAAAGTTTTAAGG-ATAAAATGT
1 AATTTTTAGAAGTTTTAGGGTCAAAATATAATTTTCAAAAGTTTTAAGGTA-AAAATAT
25248064 AATTTTATAGAAGTTTTAGGGTCAAAATATAATTT
1 AATTTT-TAGAAGTTTTAGGGTCAAAATATAATTT
25248099 ATGGATAGTT
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
57 1 0.01
58 24 0.30
59 53 0.66
60 2 0.03
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.42
Consensus pattern (58 bp):
AATTTTTAGAAGTTTTAGGGTCAAAATATAATTTTCAAAAGTTTTAAGGTAAAAATAT
Found at i:25248080 original size:30 final size:29
Alignment explanation
Indices: 25247971--25248098 Score: 141
Period size: 30 Copynumber: 4.3 Consensus size: 29
25247961 TTGGGGTAAG
*
25247971 AATATAATTTTTTGAAGTTTTAAGGTCAAA
1 AATATAATTTTTAGAAGTTTTAAGGTC-AA
* * *
25248001 AATATAATTTTTGGAAGTTTTAGGGTTAA
1 AATATAATTTTTAGAAGTTTTAAGGTCAA
* * *
25248030 AATGTAATTTTCAAAAGTTTTAAGGAT-AA
1 AATATAATTTTTAGAAGTTTTAAGG-TCAA
* *
25248059 AATGTAATTTTATAGAAGTTTTAGGGTCAA
1 AATATAATTTT-TAGAAGTTTTAAGGTCAA
25248089 AATATAATTT
1 AATATAATTT
25248099 ATGGATAGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
29 36 0.43
30 47 0.57
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (29 bp):
AATATAATTTTTAGAAGTTTTAAGGTCAA
Found at i:25248110 original size:29 final size:29
Alignment explanation
Indices: 25247919--25248113 Score: 168
Period size: 29 Copynumber: 6.7 Consensus size: 29
25247909 TCAAAAATGA
*
25247919 AATTTTTGAAAGTTTT-GGGTCAAAA-AT
1 AATTTTTGGAAGTTTTAGGGTCAAAATAT
*
25247946 GGAATTTTTGGAAG-TTTGGGGT-AAGAATAT
1 --AATTTTTGGAAGTTTTAGGGTCAA-AATAT
* *
25247976 AATTTTTTGAAGTTTTAAGGTCAAAAATAT
1 AATTTTTGGAAGTTTTAGGGTC-AAAATAT
* *
25248006 AATTTTTGGAAGTTTTAGGGTTAAAATGT
1 AATTTTTGGAAGTTTTAGGGTCAAAATAT
*** * *
25248035 AATTTTCAAAAGTTTTAAGGAT-AAAATGT
1 AATTTTTGGAAGTTTT-AGGGTCAAAATAT
*
25248064 AATTTTATAGAAGTTTTAGGGTCAAAATAT
1 AATTTT-TGGAAGTTTTAGGGTCAAAATAT
*
25248094 AATTTATGGATAG-TTTAGGG
1 AATTTTTGGA-AGTTTTAGGG
25248114 ACCTCTAAGG
Statistics
Matches: 138, Mismatches: 18, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
28 16 0.12
29 69 0.50
30 51 0.37
31 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (29 bp):
AATTTTTGGAAGTTTTAGGGTCAAAATAT
Found at i:25249244 original size:18 final size:16
Alignment explanation
Indices: 25249212--25249251 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
25249202 TATTTTATTT
25249212 ATTAATTATTATTATC
1 ATTAATTATTATTATC
*
25249228 ATTAATTACTGTATTATT
1 ATTAATTA-T-TATTATC
25249246 ATTAAT
1 ATTAAT
25249252 AAAGTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 12 0.57
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTAATTATTATTATC
Done.