Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 88 of 356
Found at i:27596837 original size:39 final size:39
Alignment explanation
Indices: 27596742--27596840 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
27596732 GCTCTGATGA
* * *
27596742 GCTTCAGTTAGCCTCCGGGCTTCTGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTGCCGTTTAGCACTTATGT
27596781 GCTTCAGTTAGCCTTCGGGCTGCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTGCCGTTTAGCACTTATGT
**
27596820 GCTTCAGTTAGATTTCGGGCT
1 GCTTCAGTTAGCCTTCGGGCT
27596841 TCAGATCACG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.13, C:0.24, G:0.25, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTGCCGTTTAGCACTTATGT
Found at i:27598605 original size:15 final size:15
Alignment explanation
Indices: 27598585--27598616 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27598575 ATATAAATAG
27598585 AAATAGAAACATAAT
1 AAATAGAAACATAAT
*
27598600 AAATAGAAATATAAT
1 AAATAGAAACATAAT
27598615 AA
1 AA
27598617 TAGTAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (15 bp):
AAATAGAAACATAAT
Found at i:27598616 original size:18 final size:19
Alignment explanation
Indices: 27598566--27598646 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 19
27598556 TAATGAAAAT
*
27598566 AATATTAGTATATAAATAGA
1 AATATTAATA-ATAAATAGA
**
27598586 AATAGAAACATAATAAATAGA
1 AATA-TTA-ATAATAAATAGA
*
27598607 AATA-TAATAAT-AGTAGA
1 AATATTAATAATAAATAGA
*
27598624 AATATTAATAGATAAATAAA
1 AATATTAATA-ATAAATAGA
27598644 AAT
1 AAT
27598647 TAGATAAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
17 9 0.18
18 10 0.20
19 3 0.06
20 11 0.22
21 14 0.29
22 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.28
Consensus pattern (19 bp):
AATATTAATAATAAATAGA
Found at i:27598633 original size:29 final size:29
Alignment explanation
Indices: 27598601--27598714 Score: 77
Period size: 29 Copynumber: 3.9 Consensus size: 29
27598591 AAACATAATA
*
27598601 AATAGAAATATAATAATAGTAGAAATATT
1 AATAGAAATATAATAATAATAGAAATATT
* * * * *
27598630 AATAGATAA-ATAAAAATTAGATAAATAAT
1 AATAGA-AATATAATAATAATAGAAATATT
* * * * * * *
27598659 AATAGTATTAGAATAACAAAATAAATATA
1 AATAGAAATATAATAATAATAGAAATATT
* *
27598688 AATAGAAACATAATAATAATAGCAATA
1 AATAGAAATATAATAATAATAGAAATA
27598715 ATATATTAAA
Statistics
Matches: 60, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
28 1 0.02
29 57 0.95
30 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (29 bp):
AATAGAAATATAATAATAATAGAAATATT
Found at i:27599203 original size:5 final size:5
Alignment explanation
Indices: 27599195--27599219 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27599185 TAATTAATTT
27599195 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
27599220 TTTCTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:27607948 original size:180 final size:180
Alignment explanation
Indices: 27607646--27608000 Score: 480
Period size: 180 Copynumber: 2.0 Consensus size: 180
27607636 TATGGAACTT
* * *
27607646 CAAATTAAGATCCGTTAATTTTCCAAGAAACTAGACTCACATATATTCTTACCATAAAAATTTAA
1 CAAATTAAGAACCGCTAATTTTCCAAGAAACTAGACTCACATATATTCATACCATAAAAATTTAA
** * * * *
27607711 AATTTTTTTGTTTATTCAATTGGTACAGTTTATTCATTAAAGTTACCCCTATTTCACTTTCCAAC
66 AATTTTTTTGTTTAGCCAATTAGTACAGTTTATTCATTAAAGATACACCTATTTCACTGTCCAAC
* *
27607776 AGTTCCGACCTCTATTCACTAAAAATTATTTATCTCATGGTACAGGACTC
131 AGTTCCAACATCTATTCACTAAAAATTATTTATCTCATGGTACAGGACTC
* *
27607826 CAAATTAAGAACCGCTAATTTTCACAA-AAACTAGACTCACATATATTCATATCATAAAATTTTC
1 CAAATTAAGAACCGCTAATTTTC-CAAGAAACTAGACTCACATATATTCATACCATAAAAATTT-
* * * *
27607890 ATAA-TTTTTTGTTTAGCCAGTTAGTACAGTTTATTCATTAAAGATACACCTGTTTCACTGTCCG
64 AAAATTTTTTTGTTTAGCCAATTAGTACAGTTTATTCATTAAAGATACACCTATTTCACTGTCCA
* * * * *
27607954 ATAGTTCCAATATTTCTTCATTAAAAATTATTTATCTCATGGTACAG
129 ACAGTTCCAACATCTATTCACTAAAAATTATTTATCTCATGGTACAG
27608001 ATCTCGGATG
Statistics
Matches: 151, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
180 145 0.96
181 6 0.04
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (180 bp):
CAAATTAAGAACCGCTAATTTTCCAAGAAACTAGACTCACATATATTCATACCATAAAAATTTAA
AATTTTTTTGTTTAGCCAATTAGTACAGTTTATTCATTAAAGATACACCTATTTCACTGTCCAAC
AGTTCCAACATCTATTCACTAAAAATTATTTATCTCATGGTACAGGACTC
Found at i:27608632 original size:50 final size:50
Alignment explanation
Indices: 27608567--27608795 Score: 246
Period size: 50 Copynumber: 4.6 Consensus size: 50
27608557 CTGGTATGCA
*
27608567 TAGTAGCCTGCACTTAGTACTACACATGCGATCTATCAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
* * * * * * * *
27608617 TAGTAGCCTGAACTTAGTACTACACACGTGATCGAGGTTAA-C-GAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTA--TCAATCTG-GTACACG
* * * *
27608668 TAGTAGCCTGCACTTTGTACTACACATGCGACCTATCGATCCGCTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
* * * * **
27608718 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
27608768 TAGTAGCCTGCACTTAGTACTACACATG
1 TAGTAGCCTGCACTTAGTACTACACATG
27608796 TGTTTTCACA
Statistics
Matches: 147, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
49 2 0.01
50 106 0.72
51 36 0.24
52 3 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
Found at i:27608739 original size:101 final size:101
Alignment explanation
Indices: 27608564--27608748 Score: 316
Period size: 101 Copynumber: 1.8 Consensus size: 101
27608554 TCTCTGGTAT
* * *
27608564 GCATAGTAGCCTGCACTTAGTACTACACATGCGATCTATCAATCTGGTACACGTAGTAGCCTGAA
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCGCTACACGTAGTAGCCTGAA
27608629 CTTAGTACTACACACGTGATCGAGGTTAACGAGTAC
66 CTTAGTACTACACACGTGATCGAGGTTAACGAGTAC
* * *
27608665 GCATAGTAGCCTGCACTTTGTACTACACATGCGACCTATCGATCCGCTACACGTAGTAGCCTGCA
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCGCTACACGTAGTAGCCTGAA
27608730 CTTAGTACTACACACGTGA
66 CTTAGTACTACACACGTGA
27608749 CCTAACCATC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 78 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (101 bp):
GCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCGCTACACGTAGTAGCCTGAA
CTTAGTACTACACACGTGATCGAGGTTAACGAGTAC
Found at i:27615495 original size:39 final size:39
Alignment explanation
Indices: 27615445--27615520 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
27615435 TATTCTTATC
*
27615445 ATAAAATTTTTAGAATTTTTGGTTCAGTCAATTAGTACA
1 ATAAAAATTTTAGAATTTTTGGTTCAGTCAATTAGTACA
* *
27615484 ATAAAAATTTTAGAATTTTTTGTTTAGTCAATTAGTA
1 ATAAAAATTTTAGAATTTTTGGTTCAGTCAATTAGTA
27615521 TAGTTTATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (39 bp):
ATAAAAATTTTAGAATTTTTGGTTCAGTCAATTAGTACA
Found at i:27616227 original size:50 final size:50
Alignment explanation
Indices: 27616162--27616449 Score: 265
Period size: 50 Copynumber: 5.7 Consensus size: 50
27616152 ACCGAAGCTC
* * *
27616162 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
** * * * *
27616212 AGTGGTACACGTAGTAGCCTGCACTTAGTACTACACACATGACTTATCCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* ** ** * ** *
27616262 TCTGATACATGTAACAGCCTGCACTTAGTATTACACACGTGATCGAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAA
* * *** *
27616314 -CGGGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTATCGA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * *
27616363 TCCGCTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCA-CCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCT-ATCAA
**
27616413 TCTAATACACATAGTAGCCTGCACTTAGTACTACACA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
27616450 TGTGTTCTCA
Statistics
Matches: 186, Mismatches: 48, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
49 2 0.01
50 149 0.80
51 33 0.18
52 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
Found at i:27616382 original size:101 final size:101
Alignment explanation
Indices: 27616223--27616404 Score: 274
Period size: 101 Copynumber: 1.8 Consensus size: 101
27616213 GTGGTACACG
* * * *
27616223 TAGTAGCCTGCACTTAGTACTACACACATGACTTATCCATCTGATACATGTAACAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACACGACCTATCCATCCGATACACGTAACAGCCTGCACTT
*
27616288 AGTATTACACACGTGATCGAAGTTAACGGGTACGCA
66 AGTACTACACACGTGATCGAAGTTAACGGGTACGCA
* * * **
27616324 TAGTAGCCTGCACTTAGTACTACACATACGACCTATCGATCCGCTACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACACGACCTATCCATCCGATACACGTAACAGCCTGCACTT
27616389 AGTACTACACACGTGA
66 AGTACTACACACGTGA
27616405 CCTCACCATC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 71 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACACGACCTATCCATCCGATACACGTAACAGCCTGCACTT
AGTACTACACACGTGATCGAAGTTAACGGGTACGCA
Found at i:27616432 original size:151 final size:151
Alignment explanation
Indices: 27616165--27616449 Score: 428
Period size: 151 Copynumber: 1.9 Consensus size: 151
27616155 GAAGCTCTCT
* ** *
27616165 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAAAGTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAAACCGCTACACGTAGTAGC
* * ** *
27616230 CTGCACTTAGTACTACACACATGACTTATCCATCTGATACATGTAACAGCCTGCACTTAGTATTA
66 CTGCACTTAGTACTACACACATGACTCATCCATCTAATACACATAACAGCCTGCACTTAGTACTA
27616295 CACACGTGATCGAAGTTAACG
131 CACACGTGATCGAAGTTAACG
* *
27616316 GGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTATCGATCCGCTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAAACCGCTACACGTAGTAGC
* **
27616381 CTGCACTTAGTACTACACACGTGACCTCA-CCATCTAATACACATAGTAGCCTGCACTTAGTACT
66 CTGCACTTAGTACTACACACATGA-CTCATCCATCTAATACACATAACAGCCTGCACTTAGTACT
27616445 ACACA
130 ACACA
27616450 TGTGTTCTCA
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
151 116 0.97
152 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAAACCGCTACACGTAGTAGC
CTGCACTTAGTACTACACACATGACTCATCCATCTAATACACATAACAGCCTGCACTTAGTACTA
CACACGTGATCGAAGTTAACG
Found at i:27628872 original size:48 final size:48
Alignment explanation
Indices: 27628801--27628978 Score: 277
Period size: 48 Copynumber: 3.7 Consensus size: 48
27628791 CATTAAGGAA
*
27628801 TTCATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGGGC
1 TTCATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGC
* * *
27628849 TTCATTGATTTGGCTTCGAGCCATGATATTGGTACTTCGGGTGCGAG-
1 TTCATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGC
*
27628896 TTACATTGATTTGGCTTCGGGCTATGATATCGGCACTTCGGGTGCGAGC
1 TT-CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGC
* *
27628945 TTCATTGATTTGGCTTTGGGCCATGATATTGGCA
1 TTCATTGATTTGGCTTCGGGCCATGATATCGGCA
27628979 GTTAGGGTAC
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
47 2 0.02
48 113 0.97
49 2 0.02
ACGTcount: A:0.16, C:0.19, G:0.30, T:0.35
Consensus pattern (48 bp):
TTCATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGC
Found at i:27628968 original size:96 final size:96
Alignment explanation
Indices: 27628803--27628976 Score: 312
Period size: 96 Copynumber: 1.8 Consensus size: 96
27628793 TTAAGGAATT
*
27628803 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGGGCTTCATTGATTTGGCTTCGA
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGCTTCATTGATTTGGCTTCGA
27628868 GCCATGATATTGGTACTTCGGGTGCGAGTTA
66 GCCATGATATTGGTACTTCGGGTGCGAGTTA
* * *
27628899 CATTGATTTGGCTTCGGGCTATGATATCGGCACTTCGGGTGCGAGCTTCATTGATTTGGCTTTGG
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGCTTCATTGATTTGGCTTCGA
27628964 GCCATGATATTGG
66 GCCATGATATTGG
27628977 CAGTTAGGGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.16, C:0.19, G:0.31, T:0.34
Consensus pattern (96 bp):
CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGCTTCATTGATTTGGCTTCGA
GCCATGATATTGGTACTTCGGGTGCGAGTTA
Found at i:27631210 original size:20 final size:19
Alignment explanation
Indices: 27631165--27631202 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
27631155 GAGCGAAAGG
27631165 AATGAG-AAACGGGCCAAA
1 AATGAGAAAACGGGCCAAA
*
27631183 AATAGAGAAAATGGGCCAAA
1 AAT-GAGAAAACGGGCCAAA
27631203 GTATGAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 3 0.18
20 11 0.65
ACGTcount: A:0.53, C:0.13, G:0.26, T:0.08
Consensus pattern (19 bp):
AATGAGAAAACGGGCCAAA
Found at i:27631364 original size:13 final size:13
Alignment explanation
Indices: 27631346--27631372 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27631336 GAAGTAATCG
27631346 CACACGGGCGTGT
1 CACACGGGCGTGT
27631359 CACACGGGCGTGT
1 CACACGGGCGTGT
27631372 C
1 C
27631373 CCTGCTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:27637401 original size:43 final size:42
Alignment explanation
Indices: 27637320--27637458 Score: 140
Period size: 43 Copynumber: 3.3 Consensus size: 42
27637310 TGTGTTATCG
* * * *
27637320 TGTAAGACCACGTTTGGGACGTGGCATC-AACTTCTGATTTATA
1 TGTAAGACCACCTCTGGGACGTGGCATCGTA-TT-TGATTTACA
*
27637363 TGTAGGACCACCTCTGGGACGTTGGCATCGTATTTGATTT-CA
1 TGTAAGACCACCTCTGGGACG-TGGCATCGTATTTGATTTACA
***
27637405 TGTAAGACCTTTTCTGGGACAGTGGCATCGATATTTGA-TTACA
1 TGTAAGACCACCTCTGGGAC-GTGGCATCG-TATTTGATTTACA
27637448 TGTAAGACCAC
1 TGTAAGACCAC
27637459 GTTTGAGGCA
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
42 27 0.34
43 43 0.54
44 9 0.11
45 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (42 bp):
TGTAAGACCACCTCTGGGACGTGGCATCGTATTTGATTTACA
Found at i:27638620 original size:66 final size:66
Alignment explanation
Indices: 27638543--27638668 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
27638533 CTAGACACGC
* *
27638543 GGGCGTGTCTTGTGGCCGTGTGAACCAAGTCAGTA-GTCT-CCCTAATTTTCACACGGCCTGGCA
1 GGGCGTGTCTTGTGGACGTGTGAA-CAAGTCAGTATGTATGCCCT-ATTTTCACACGGCCTGGCA
27638606 CAT
64 CAT
* * * *
27638609 GGGCGTGTCTTGTGGATGTGTGGACAAGTCAGTATGTATGCCCTGTTTTGACACGGCCTG
1 GGGCGTGTCTTGTGGACGTGTGAACAAGTCAGTATGTATGCCCTATTTTCACACGGCCTG
27638669 TTCACACGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 10 0.19
66 38 0.73
67 4 0.08
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (66 bp):
GGGCGTGTCTTGTGGACGTGTGAACAAGTCAGTATGTATGCCCTATTTTCACACGGCCTGGCACA
T
Found at i:27638677 original size:13 final size:13
Alignment explanation
Indices: 27638659--27638687 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27638649 CCCTGTTTTG
27638659 ACACGGCCTGTTC
1 ACACGGCCTGTTC
27638672 ACACGGCCTGTTC
1 ACACGGCCTGTTC
27638685 ACA
1 ACA
27638688 ACTTTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (13 bp):
ACACGGCCTGTTC
Found at i:27640809 original size:48 final size:48
Alignment explanation
Indices: 27640733--27640923 Score: 251
Period size: 48 Copynumber: 4.0 Consensus size: 48
27640723 CATTAGGGAA
* * * *
27640733 TTCACTGATTTGGGTTCGGGCCATGATATCGGTACTTCGGGTGCGAGC
1 TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGAGC
* *
27640781 TTCATTGATTTGGCTTCAGGCCATGATATTGGCACTTCAGGTGCGAG-
1 TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGAGC
*
27640828 TTACATTGATTTGGCTTCGGGCC-TCGATATTGGCACTTCGGGTGCAAGC
1 TT-CATTGATTTGGCTTCGGGCCAT-GATATTGGCACTTCGGGTGCGAGC
* * * *
27640877 TTTATTGATTTCGCTTCGAGCCATGATATTGGCACTTAGGGTGCGAG
1 TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGAG
27640924 ACTGTCGAGT
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
47 3 0.02
48 119 0.95
49 3 0.02
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (48 bp):
TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGAGC
Found at i:27642606 original size:20 final size:20
Alignment explanation
Indices: 27642581--27642625 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
27642571 AGGGACTAAA
* *
27642581 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
27642601 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
27642621 ATGAA
1 ATGAA
27642626 TATATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:27645555 original size:19 final size:20
Alignment explanation
Indices: 27645518--27645555 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27645508 ATAAGGTGGT
27645518 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
27645538 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
27645556 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:27652705 original size:46 final size:46
Alignment explanation
Indices: 27652655--27652827 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
27652645 TGGTTGAGCA
*
27652655 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
27652701 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
27652748 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
27652794 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
27652828 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:27652811 original size:93 final size:93
Alignment explanation
Indices: 27652652--27652822 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
27652642 GGATGGTTGA
* *
27652652 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
27652717 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
27652745 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
27652810 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
27652823 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27653089 original size:19 final size:20
Alignment explanation
Indices: 27653052--27653089 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27653042 ATAAGGTGGT
27653052 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
27653072 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
27653090 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:27666964 original size:39 final size:40
Alignment explanation
Indices: 27666847--27667031 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
27666837 GCTACTCGTT
* *
27666847 CAAATGTCTTCGGGACGTAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * *
27666887 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
27666927 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
27666966 CAAATGCCTTC-AGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
27667007 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27667032 CATCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
38 1 0.01
39 32 0.27
40 75 0.62
41 12 0.10
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:27666991 original size:79 final size:82
Alignment explanation
Indices: 27666847--27667031 Score: 202
Period size: 79 Copynumber: 2.3 Consensus size: 82
27666837 GCTACTCGTT
* * * * *
27666847 CAAATGTCTTCGGGACGTAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCG
* * *
27666911 GATTTAGTAAC-TCGCG
66 GATATAGTAACTTAGCA
* **
27666927 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-AGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGAGA-CTTAACCC
* *
27666989 GGATATGGTCACTTAGCA
65 GGATATAGTAACTTAGCA
27667007 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27667032 CATCATTCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.02
79 54 0.61
80 32 0.36
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCG
GATATAGTAACTTAGCA
Found at i:27670548 original size:40 final size:40
Alignment explanation
Indices: 27670457--27670666 Score: 278
Period size: 40 Copynumber: 5.3 Consensus size: 40
27670447 TCCTCGTTCA
* * * * *
27670457 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
27670496 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
27670536 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
27670576 AATGCCCTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
27670616 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
27670656 AAGGCCTTCGG
1 AATGCCTTCGG
27670667 ATCTTAGTCC
Statistics
Matches: 152, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 32 0.21
40 120 0.79
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:27670707 original size:80 final size:80
Alignment explanation
Indices: 27670460--27670719 Score: 220
Period size: 80 Copynumber: 3.3 Consensus size: 80
27670450 TCGTTCAAAT
* * * * * * * * * *
27670460 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-CATGCCTTCGGGACGTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCCTCGGGACTTAACCCGGATATA
* * *
27670524 ACAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * * *
27670539 GCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCCTCGGGACTTAACCCGGATATA
* *
27670604 ATAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * * * **
27670619 GCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCCTCGGGA-CTTAACCCGGATAT
* **
27670683 ATTCGCTTAGCAC-AAA
65 AATAAC-TAGCACGAAA
*
27670699 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
27670720 CAGCATTCAA
Statistics
Matches: 152, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
79 34 0.22
80 113 0.74
81 5 0.03
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCCTCGGGACTTAACCCGGATATA
ATAACTAGCACGAAA
Found at i:27670707 original size:120 final size:118
Alignment explanation
Indices: 27670455--27670719 Score: 271
Period size: 120 Copynumber: 2.2 Consensus size: 118
27670445 GCTCCTCGTT
* * * * *
27670455 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACCATGCCTTCGGGACGTAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGA
* * * * *
27670520 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCA
65 TTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
* * * * *
27670574 CGAATGCCCTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AATGCCCTCGGGACGTAACCCGG
** * ** * **
27670639 ATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCGCTTAGCA
64 ATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATAATAAC-TAGCA
27670695 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
27670720 CAGCATTCAA
Statistics
Matches: 116, Mismatches: 26, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
119 34 0.29
120 77 0.66
121 5 0.04
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGAT
TTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
Found at i:27678501 original size:40 final size:40
Alignment explanation
Indices: 27678389--27678596 Score: 305
Period size: 40 Copynumber: 5.3 Consensus size: 40
27678379 TCCTCGTTCA
* * * * *
27678389 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
27678428 AATGCCTTCGGGAC-TAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
27678467 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
27678507 AATGCCTTCGGGACTTAACCCGGATTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
27678546 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
27678586 AAGGCCTTCGG
1 AATGCCTTCGG
27678597 ATCTTAGTCC
Statistics
Matches: 156, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
38 19 0.12
39 66 0.42
40 71 0.46
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:27678609 original size:40 final size:39
Alignment explanation
Indices: 27678389--27678648 Score: 285
Period size: 39 Copynumber: 6.6 Consensus size: 39
27678379 TCCTCGTTCA
* * * *
27678389 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTA-TAACTCGCACG
*
27678428 AATGCCTTCGGGAC-TAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTT-ATAACTCGCACG
27678467 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTT-ATAACTCGCACG
*
27678507 AATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTATAACTCGCACG
* *
27678546 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTA-TAACTCGCACG
* ** * ** *
27678586 AAGGCCTTC-GGATCTTAGTCCGGATATATTCCTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTATAAC-TCGCACG
* *
27678625 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27678649 CAGCATTCAA
Statistics
Matches: 196, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
38 18 0.09
39 91 0.46
40 87 0.44
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTATAACTCGCACG
Found at i:27678610 original size:79 final size:79
Alignment explanation
Indices: 27678389--27678596 Score: 321
Period size: 79 Copynumber: 2.6 Consensus size: 79
27678379 TCCTCGTTCA
* * * *
27678389 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGAC-TAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
27678453 TAACAACTCGCACG
66 TAACAACTCGCACG
*
27678467 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAT
27678532 TTAA-AACTCGCACG
65 TTAACAACTCGCACG
* *
27678546 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGG
27678597 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
78 34 0.29
79 71 0.60
80 14 0.12
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACG
Found at i:27678632 original size:79 final size:79
Alignment explanation
Indices: 27678392--27678648 Score: 261
Period size: 79 Copynumber: 3.3 Consensus size: 79
27678382 TCGTTCAAAT
* * * * * * *
27678392 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGAC-TAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
27678455 ACAACTCGCACGAAT
66 A-AACTAGCACGAAA
* * *
27678470 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
27678535 AAACTCGCACGAAT
66 AAACTAGCACGAAA
* * **
27678549 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
***
27678613 ATTCCTTAGCAC-AAA
65 AAAAC-TAGCACGAAA
*
27678628 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
27678649 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
78 34 0.22
79 104 0.66
80 19 0.12
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
AAACTAGCACGAAA
Found at i:27681310 original size:18 final size:19
Alignment explanation
Indices: 27681273--27681310 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
27681263 TACTCAGGGT
*
27681273 AATTTTACCGATACATTTTC
1 AATTATACCGATA-ATTTTC
27681293 AATTATACCGAT-ATTTTC
1 AATTATACCGATAATTTTC
27681311 TTGTGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (19 bp):
AATTATACCGATAATTTTC
Found at i:27688100 original size:43 final size:42
Alignment explanation
Indices: 27688039--27688144 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 42
27688029 ACAATGCCAA
*
27688039 TGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGTCAT
1 TGTCCCAGACGTGGTCTTACATGAAATCAAATA-CGATGTCAT
* * * *
27688082 TGTCCCAGACAG-GGTCTTATATGAAATCTAATACGATGCCAA
1 TGTCCCAGAC-GTGGTCTTACATGAAATCAAATACGATGTCAT
**
27688124 CATCCCAGACGTGGTCTTACA
1 TGTCCCAGACGTGGTCTTACA
27688145 CATAAATCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.02
42 23 0.43
43 28 0.53
44 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (42 bp):
TGTCCCAGACGTGGTCTTACATGAAATCAAATACGATGTCAT
Found at i:27691074 original size:27 final size:27
Alignment explanation
Indices: 27691043--27691099 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
27691033 AACGGTATTT
27691043 TACCCTACAAGG-GTATTTCGGTAATCC
1 TACCCTA-AAGGCGTATTTCGGTAATCC
*
27691070 TACCCTATAGGCGTATTTCGGTAATCC
1 TACCCTAAAGGCGTATTTCGGTAATCC
27691097 TAC
1 TAC
27691100 TACACAGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (27 bp):
TACCCTAAAGGCGTATTTCGGTAATCC
Found at i:27691112 original size:27 final size:27
Alignment explanation
Indices: 27691047--27691114 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
27691037 GTATTTTACC
* *
27691047 CTACAAGGGTATTTCGGTAATCCTACC
1 CTACAGGGGTATTTCGGTAATCCTACA
* *
27691074 CTATAGGCGTATTTCGGTAATCCTACTA
1 CTACAGGGGTATTTCGGTAATCCTAC-A
27691102 C-ACAGGGGTATTT
1 CTACAGGGGTATTT
27691115 TAGTAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 33 0.97
28 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (27 bp):
CTACAGGGGTATTTCGGTAATCCTACA
Found at i:27691134 original size:27 final size:27
Alignment explanation
Indices: 27691104--27691236 Score: 142
Period size: 27 Copynumber: 5.0 Consensus size: 27
27691094 TCCTACTACA
* *
27691104 CAGGGGTATTTTAGTAATTTTATAAAT
1 CAGGGGTATTTCAGTAATTTTACAAAT
* * *
27691131 CAGGGGTATTTCAATAACTTTACAAGT
1 CAGGGGTATTTCAGTAATTTTACAAAT
* *
27691158 CAAGGGTATTTCAGTAATTTCACAAAT
1 CAGGGGTATTTCAGTAATTTTACAAAT
* * * *
27691185 TAGGGGTATTTCAGCAGTTTTAC-AAC
1 CAGGGGTATTTCAGTAATTTTACAAAT
* *
27691211 CTGGGGTATTTTAGTAATTTTACAAA
1 CAGGGGTATTTCAGTAATTTTACAAA
27691237 GTAGAGGTCT
Statistics
Matches: 84, Mismatches: 21, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
26 20 0.24
27 64 0.76
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (27 bp):
CAGGGGTATTTCAGTAATTTTACAAAT
Found at i:27703799 original size:30 final size:30
Alignment explanation
Indices: 27703765--27703824 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
27703755 TATTTTATTA
27703765 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
27703795 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
27703825 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:27718007 original size:8 final size:8
Alignment explanation
Indices: 27717994--27718021 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
27717984 GAGGTTAATT
27717994 TGTAAAAA
1 TGTAAAAA
27718002 TGTAAAAA
1 TGTAAAAA
27718010 TGTAAAAA
1 TGTAAAAA
27718018 TGTA
1 TGTA
27718022 GGGTTAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (8 bp):
TGTAAAAA
Found at i:27718618 original size:43 final size:43
Alignment explanation
Indices: 27718518--27718619 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
27718508 ACCGAGATGT
* * * *
27718518 GATTACATGTAAGACCATGTTTGAGACATTGGCATTGTATTGA
1 GATTACGTGTAAGACCATGTCTGAGACATTGGCATCGTAATGA
* * *
27718561 GATTACGTGCAAGACCATGTCTGGGACATTGGCATCGTTAAT-C
1 GATTACGTGTAAGACCATGTCTGAGACATTGGCATCG-TAATGA
*
27718604 GATTTCGTGTAAGACC
1 GATTACGTGTAAGACC
27718620 CTATCTAGGA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 46 0.94
44 3 0.06
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGAGACATTGGCATCGTAATGA
Found at i:27721755 original size:37 final size:37
Alignment explanation
Indices: 27721700--27721802 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
27721690 CGAATAGTCC
*
27721700 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
* * *
27721737 CCACCCGTAGTCATCGGGTCTTATCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
27721774 CCACACGTAGTCATCGGGGCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
27721803 ATATATTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:27722001 original size:48 final size:48
Alignment explanation
Indices: 27721943--27722094 Score: 205
Period size: 48 Copynumber: 3.0 Consensus size: 48
27721933 ATATACACAC
* *
27721943 ATCTCCTACATATTTCACATTAGCCATTCGGATTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
** *
27721991 ATCTCATACATATTTCATGTTAGCCATTCGGCTTTACTACATATACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTAC--C----ACATATATAT
27722045 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
27722093 AT
1 AT
27722095 TTATCTTGTA
Statistics
Matches: 90, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
48 44 0.49
50 1 0.01
52 1 0.01
54 44 0.49
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
Found at i:27722115 original size:54 final size:50
Alignment explanation
Indices: 27721943--27722094 Score: 209
Period size: 54 Copynumber: 3.0 Consensus size: 50
27721933 ATATACACAC
* *
27721943 ATCTCCTACATATTTCACATTAGCCATTCGGATTTACCAC--ATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATATAT
** *
27721991 ATCTCATACATATTTCATGTTAGCCATTCGGCTTTACTACATATACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT--ATAT--AT
27722045 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATATAT
27722095 TTATCTTGTA
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
48 35 0.39
50 4 0.04
52 8 0.09
54 43 0.48
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (50 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATATAT
Found at i:27727446 original size:55 final size:54
Alignment explanation
Indices: 27727353--27727494 Score: 153
Period size: 55 Copynumber: 2.6 Consensus size: 54
27727343 AACACGGGCT
* * * * * *
27727353 GTGGGCGAACCTACCAAAATAGCAC-AGGCGTGCAACACGCCCGTGCCTTAA-ACCC
1 GTGGTCGAACCTATCAAATTAACACGA-GCGTGCAACACGCCCGTGCC--AACAACA
*
27727408 GTGGTCGAACCTATCAAATTAACACGAGCGTGCGACACGCCCGTGCCAAGCAACA
1 GTGGTCGAACCTATCAAATTAACACGAGCGTGCAACACGCCCGTGCCAA-CAACA
* *
27727463 GTGGTCGAACCTATTAAATTAACACGGGCGTG
1 GTGGTCGAACCTATCAAATTAACACGAGCGTG
27727495 GGCCTATATA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
53 2 0.03
55 72 0.96
56 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.16
Consensus pattern (54 bp):
GTGGTCGAACCTATCAAATTAACACGAGCGTGCAACACGCCCGTGCCAACAACA
Found at i:27738267 original size:50 final size:50
Alignment explanation
Indices: 27738213--27738555 Score: 287
Period size: 50 Copynumber: 6.8 Consensus size: 50
27738203 CAAAGATCTT
* *
27738213 TGGTACGCATAGTAGCCTGCACTTAGTACTACACATATGACCTATCAATC
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACATGACCTATCAATC
* * * * * * *
27738263 TGGTACACGTAGTAACCTTCACTTAGTACTACACACGTGACTTAACCATC
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACATGACCTATCAATC
* * * ** *
27738313 TGATACACGTAGTAGCATGCACTTAGTACTACACACATGATCGAAGTTAA-C
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACATGA-CCTA-TCAATC
* * ***
27738364 AGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATC
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACATGACCTATCAATC
* * * * *
27738414 TGGTACACGTAGTACCCTGCACTTAGTACTACACACATGA-TTGCAGTTAA-A
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACATGACCT--A-TCAATC
* *** *
27738465 GGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATT
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACATGACCTATCAATC
* ** * * * *
27738515 TGGTAAATGTAGTAGCCTACACTCAATACTACACACGTGAC
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACATGAC
27738556 TCACAACGGA
Statistics
Matches: 227, Mismatches: 58, Indels: 16
0.75 0.19 0.05
Matches are distributed among these distances:
49 7 0.03
50 145 0.64
51 70 0.31
52 5 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
TGGTACACATAGTAGCCTGCACTTAGTACTACACACATGACCTATCAATC
Found at i:27738392 original size:101 final size:101
Alignment explanation
Indices: 27738222--27738550 Score: 367
Period size: 101 Copynumber: 3.3 Consensus size: 101
27738212 TTGGTACGCA
* ** * * * * *
27738222 TAGTAGCCTGCACTTAGTACTACACATATGA-CCTA-TCAATCTGGTACACGTAGTAACCTTCAC
1 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAA-CAGGTACACATAGTAGCCTGCAC
* * *
27738285 TTAGTACTACACACGTGACTTAACCATCTGATACACG
65 TTAGTACTACACACGCGACCTAACAATCTGATACACG
* *
27738322 TAGTAGCATGCACTTAGTACTACACACATGATCGAAGTTAACAGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACAGGTACACATAGTAGCCTGCACT
* * *
27738387 TAGTACTACACATGCGACCTATCAATCTGGTACACG
66 TAGTACTACACACGCGACCTAACAATCTGATACACG
* * *
27738423 TAGTACCCTGCACTTAGTACTACACACATGATTGCAGTTAA-AGGGTACACATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACA-GGTACACATAGTAGCCTGCAC
* * * * * *
27738487 TTAGTACTACACATGCGACCTATCAATTTGGTAAATG
65 TTAGTACTACACACGCGACCTAACAATCTGATACACG
* * *
27738524 TAGTAGCCTACACTCAATACTACACAC
1 TAGTAGCCTGCACTTAGTACTACACAC
27738551 GTGACTCACA
Statistics
Matches: 198, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
100 30 0.15
101 165 0.83
102 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACAGGTACACATAGTAGCCTGCACT
TAGTACTACACACGCGACCTAACAATCTGATACACG
Found at i:27738532 original size:151 final size:149
Alignment explanation
Indices: 27738220--27738501 Score: 361
Period size: 151 Copynumber: 1.9 Consensus size: 149
27738210 CTTTGGTACG
* *
27738220 CATAGTAGCCTGCACTTAGTACTACACATATGACCTATCAATCTGGTACACGTAGTAACCTTCAC
1 CATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAATCTGGTACACGTAGTAACCTGCAC
* *** *
27738285 TTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCATGCACTTAGTACTACACACA
66 TTAGTACTACACACATGACTTAACCAAAGGATACACATAGTAGCATGCACTTAGTACTA-ACACA
* **
27738350 TGATCGAAGTTAACAGGTACG
130 TGA-CGAACTTAACAGGTAAA
* *
27738371 CATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTACCCTGCAC
1 CATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAATCTGGTACACGTAGTAACCTGCAC
*** * *
27738436 TTAGTACTACACACATGA-TTGCAGTTAAAGGGTACACATAGTAGCCTGCACTTAGTACT-ACAC
66 TTAGTACTACACACATGACTT--AACCAAAGGATACACATAGTAGCATGCACTTAGTACTAACAC
27738499 ATG
129 ATG
27738502 CGACCTATCA
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
150 9 0.08
151 78 0.68
152 28 0.24
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (149 bp):
CATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAATCTGGTACACGTAGTAACCTGCAC
TTAGTACTACACACATGACTTAACCAAAGGATACACATAGTAGCATGCACTTAGTACTAACACAT
GACGAACTTAACAGGTAAA
Found at i:27739199 original size:30 final size:30
Alignment explanation
Indices: 27739163--27739221 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
27739153 CAAAAATCAT
* *
27739163 ACTTTTACAAATTTTCATTTTGACCCCTAA
1 ACTTTTACAAATTTGCACTTTGACCCCTAA
* *
27739193 ACTTTTACATATTTGCACTTTGGCCCCTA
1 ACTTTTACAAATTTGCACTTTGACCCCTA
27739222 GGCTCGTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (30 bp):
ACTTTTACAAATTTGCACTTTGACCCCTAA
Found at i:27741535 original size:15 final size:14
Alignment explanation
Indices: 27741501--27741560 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
27741491 TATAGGTAAC
* *
27741501 AAGAAAACCAGGATT
1 AAGAAATCCAAGA-T
*
27741516 AAGAAGTCCAAGAT
1 AAGAAATCCAAGAT
27741530 AGAGAAATCCAAGAT
1 A-AGAAATCCAAGAT
27741545 CAAGAAATCCAAGAT
1 -AAGAAATCCAAGAT
27741560 A
1 A
27741561 CAATATCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
14 3 0.08
15 35 0.90
16 1 0.03
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.13
Consensus pattern (14 bp):
AAGAAATCCAAGAT
Found at i:27741550 original size:30 final size:30
Alignment explanation
Indices: 27741502--27741560 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
27741492 ATAGGTAACA
* * *
27741502 AGAAAACCAGGATTAAGAAGTCCAAGATAG
1 AGAAAACCAAGATCAAGAAATCCAAGATAG
*
27741532 AGAAATCCAAGATCAAGAAATCCAAGATA
1 AGAAAACCAAGATCAAGAAATCCAAGATA
27741561 CAATATCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.15, G:0.19, T:0.14
Consensus pattern (30 bp):
AGAAAACCAAGATCAAGAAATCCAAGATAG
Found at i:27744243 original size:53 final size:53
Alignment explanation
Indices: 27744182--27744288 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
27744172 GTGCACAACA
27744182 CCGTATGAATATCAAACAAGCATGAGTATTCCTCGTAACATAAACTTTTATCT
1 CCGTATGAATATCAAACAAGCATGAGTATTCCTCGTAACATAAACTTTTATCT
27744235 CCGTATGAATATCAAACAAGCATGAGTATTCCTCGTAACATAAACTTTTATCT
1 CCGTATGAATATCAAACAAGCATGAGTATTCCTCGTAACATAAACTTTTATCT
27744288 C
1 C
27744289 ACATGTTATC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (53 bp):
CCGTATGAATATCAAACAAGCATGAGTATTCCTCGTAACATAAACTTTTATCT
Found at i:27745936 original size:50 final size:50
Alignment explanation
Indices: 27745882--27746122 Score: 261
Period size: 50 Copynumber: 4.8 Consensus size: 50
27745872 CAAAGCTCTT
* **
27745882 TGGTACGCATAGTAGCCTGCACTTAGTACTACACATATGACCTATCAATC
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATC
* * * * * * *
27745932 TGGTACACGTAGTAACCTTCACTTAGTACTGCACACGTGACTTAACCATC
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATC
* * ** ** *
27745982 TGATACACGTAGTAGCCCACACTTAGTACTACACACGTGATCGAAGTTAA-C
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAATC
* * * *
27746033 -GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAGTC
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATC
27746082 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGAC
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGAC
27746123 TCACAACAGA
Statistics
Matches: 153, Mismatches: 34, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
48 2 0.01
49 3 0.02
50 144 0.94
51 3 0.02
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (50 bp):
TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATC
Found at i:27752849 original size:15 final size:15
Alignment explanation
Indices: 27752839--27752869 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27752829 TCGTGCGTCT
*
27752839 GACGAAGGTGCGGCC
1 GACGAAAGTGCGGCC
27752854 GACGAAAGTGCGGCC
1 GACGAAAGTGCGGCC
27752869 G
1 G
27752870 TACACAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.26, G:0.45, T:0.06
Consensus pattern (15 bp):
GACGAAAGTGCGGCC
Found at i:27755734 original size:19 final size:20
Alignment explanation
Indices: 27755710--27755747 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27755700 GGTACCACCA
27755710 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
27755729 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
27755748 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:27756085 original size:93 final size:93
Alignment explanation
Indices: 27755978--27756147 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
27755968 CCCCTAAGTG
* *
27755978 AACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
*
27756043 GAGTTCGGATGCCTAGTTACATCTCACA
66 AAGTTCGGATGCCTAGTTACATCTCACA
* *
27756071 AACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
27756136 AAGTTCGGATGC
66 AAGTTCGGATGC
27756148 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
AAGTTCGGATGCCTAGTTACATCTCACA
Found at i:27756144 original size:46 final size:46
Alignment explanation
Indices: 27755972--27756144 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
27755962 AACCCGCCCC
* * * *
27755972 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* *
27756018 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATC-CA
*
27756069 -CA---AACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
*
27756111 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
27756145 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 8 0.07
44 1 0.01
46 59 0.55
47 28 0.26
49 1 0.01
50 6 0.06
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:27759100 original size:23 final size:24
Alignment explanation
Indices: 27759074--27759118 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
27759064 CTTCGCTGTC
*
27759074 TCAA-ATTCAAGTCTTTTGTGACA
1 TCAATATTCAAGACTTTTGTGACA
*
27759097 TCAATATTTAAGACTTTTGTGA
1 TCAATATTCAAGACTTTTGTGA
27759119 TCGGTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (24 bp):
TCAATATTCAAGACTTTTGTGACA
Found at i:27765049 original size:41 final size:42
Alignment explanation
Indices: 27764975--27765054 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 42
27764965 ATTTTGAGTC
*
27764975 CACACGGCTTGTCACACGGGCGTGTGATCAGACCATGTGAGA
1 CACACGGCTTGTCACACGGGCATGTGATCAGACCATGTGAGA
*
27765017 CACACGGCTTG-CACACGGGCATGTTGAT-AGACCGTGTG
1 CACACGGCTTGTCACACGGGCATG-TGATCAGACCATGTG
27765055 TCCCCTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.20
Consensus pattern (42 bp):
CACACGGCTTGTCACACGGGCATGTGATCAGACCATGTGAGA
Found at i:27779178 original size:50 final size:49
Alignment explanation
Indices: 27779060--27779380 Score: 340
Period size: 50 Copynumber: 6.4 Consensus size: 49
27779050 TGAGGTCGCA
* * * * * *
27779060 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAGT-TGGTCACG
* * *
27779111 TGTGTAGTACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT-GGTCACG
* * *
27779161 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTC-CA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTGGTCACG
* * * * * * *
27779209 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAGT-TGGTCACG
** * *
27779260 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGT-TGGTCACG
* *
27779310 TGCGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GTTGGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAGTTGGTCACG
27779359 TGTGTAGTACTAAGTGCAGGCT
1 TGTGTAGTACTAAGTGCAGGCT
27779381 GCTATGCATA
Statistics
Matches: 225, Mismatches: 40, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
48 33 0.15
49 35 0.16
50 94 0.42
51 63 0.28
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTGGTCACG
Found at i:27779285 original size:99 final size:99
Alignment explanation
Indices: 27779060--27779380 Score: 317
Period size: 99 Copynumber: 3.2 Consensus size: 99
27779050 TGAGGTCGCA
* * * * * * * *
27779060 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TGAGGTCACATGCGTAGTACTAAG
* * * * *
27779125 TGCAGGCTATTACGTGTATCAGA-TGGTTAGGTCACG
65 TGCAGGCTACTACGCGTACCAAACT-GTT-GATCACG
* * * *
27779161 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAAT-TGGTC-CATGTGTAGTACTATGT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATGAGGTCACATGCGTAGTACTAAGT
*
27779224 GCAGGCTACTATGCGTACCCGAAAACTG-TGATCACG
66 GCAGGCTACTACGCGTA-CC--AAACTGTTGATCACG
** ** *
27779260 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTGAGGTCACGTGCGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATGAGGTCACATGCGTAGTACTAAGT
* * * *
27779325 GCAGGCTACTACGTGTACCAGACTGTTGGTCACA
66 GCAGGCTACTACGCGTACCAAACTGTTGATCACG
27779359 TGTGTAGTACTAAGTGCAGGCT
1 TGTGTAGTACTAAGTGCAGGCT
27779381 GCTATGCATA
Statistics
Matches: 186, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
98 34 0.18
99 75 0.40
100 8 0.04
101 68 0.37
102 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (99 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATGAGGTCACATGCGTAGTACTAAGT
GCAGGCTACTACGCGTACCAAACTGTTGATCACG
Found at i:27779328 original size:149 final size:150
Alignment explanation
Indices: 27779053--27779392 Score: 567
Period size: 149 Copynumber: 2.3 Consensus size: 150
27779043 TCTATTGTGA
*
27779053 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAG
* * *
27779118 TACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCT
66 TACTAAGTGCAGGCTACTACGTGTATCAGATGGTGAGGTCACGTGCGTAGTACTAAGTGCAGGCT
*
27779183 ACTACGTGTACCGGA-TAATT
131 ACTACGTGTACCAGACT-ATT
*
27779203 GGTC-CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAG
*
27779267 TACTAAGTGCAGGCTACTACGTGTATTAGATGGTGAGGTCACGTGCGTAGTACTAAGTGCAGGCT
66 TACTAAGTGCAGGCTACTACGTGTATCAGATGGTGAGGTCACGTGCGTAGTACTAAGTGCAGGCT
*
27779332 ACTACGTGTACCAGACTGTT
131 ACTACGTGTACCAGACTATT
* *
27779352 GGTCACATGTGTAGTACTAAGTGCAGGCTGCTATGCATACC
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
27779393 AAATAGCTTC
Statistics
Matches: 178, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
149 140 0.79
150 38 0.21
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (150 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAG
TACTAAGTGCAGGCTACTACGTGTATCAGATGGTGAGGTCACGTGCGTAGTACTAAGTGCAGGCT
ACTACGTGTACCAGACTATT
Found at i:27783213 original size:40 final size:40
Alignment explanation
Indices: 27783169--27783378 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
27783159 CGGACTAGAT
* * * **
27783169 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
27783209 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
27783249 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
27783289 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
* ** * * *
27783329 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
27783368 CCGAAGGCATT
1 CCGAAGGCATT
27783379 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
Found at i:27791125 original size:40 final size:40
Alignment explanation
Indices: 27791095--27791304 Score: 305
Period size: 40 Copynumber: 5.3 Consensus size: 40
27791085 GGACTAAGAT
* * * **
27791095 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
*
27791135 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
27791175 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
27791215 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
* ** * * *
27791255 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
27791294 CCGAAGGCATT
1 CCGAAGGCATT
27791305 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
39 33 0.21
40 124 0.79
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
Found at i:27793680 original size:21 final size:23
Alignment explanation
Indices: 27793644--27793685 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
27793634 AATACATTAA
27793644 TATGCAACCAAAACATGTCATTT
1 TATGCAACCAAAACATGTCATTT
27793667 TATGC-ACC-AAACATGTCAT
1 TATGCAACCAAAACATGTCAT
27793686 ACCAATTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (23 bp):
TATGCAACCAAAACATGTCATTT
Found at i:27797356 original size:48 final size:48
Alignment explanation
Indices: 27797285--27797805 Score: 481
Period size: 48 Copynumber: 11.0 Consensus size: 48
27797275 CAAGATAAAT
27797285 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
27797333 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
** *** *
27797381 ATATGTATATGTGGT--AGGAGATAT-G-TATATGTGGTAAAGCCGAATG-G
1 ATATGTATATGTGGTAAAGCCGA-ATGGCTA-ATGT-G-AAATATGTATGAG
* * * * * * *
27797428 CTAATGTGAAATAT-GT-ATG-AGATAT-G-TATATGTG--GTA-G-A-GCCG
1 AT-ATGT-ATATGTGGTAAAGCCGA-ATGGCTA-ATGTGAAATATGTATG-AG
*** * * * * *
27797471 A-ATGGCTA-ATGT-G-AAATATGTATGAGAT-ATGT-ATATGTGGTAGGAG
1 ATAT-G-TATATGTGGTAAAGCCGAATG-GCTAATGTGAAATAT-GTATGAG
*
27797517 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
27797565 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
27797613 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTGTGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * * * *
27797661 ATATGCATATGTGATAAAGCCGAATGGCTACTATGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
27797709 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * * *
27797757 ATACGTATATGTGGTAAAGCCGAAGGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
27797805 A
1 A
27797806 GGTGTGTATA
Statistics
Matches: 398, Mismatches: 47, Indels: 56
0.79 0.09 0.11
Matches are distributed among these distances:
41 10 0.03
42 8 0.02
43 5 0.01
44 1 0.00
45 5 0.01
46 17 0.04
47 12 0.03
48 331 0.83
49 9 0.02
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:27797401 original size:20 final size:20
Alignment explanation
Indices: 27797378--27797416 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27797368 AAATATGTAT
27797378 GAGATATGTATATGTGGTAG
1 GAGATATGTATATGTGGTAG
27797398 GAGATATGTATATGTGGTA
1 GAGATATGTATATGTGGTA
27797417 AAGCCGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (20 bp):
GAGATATGTATATGTGGTAG
Found at i:27797409 original size:68 final size:68
Alignment explanation
Indices: 27797330--27797465 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
27797320 AAATATGTAT
27797330 GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGG
1 GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGG
27797395 TAG
66 TAG
27797398 GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGG
1 GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGG
27797463 TAG
66 TAG
27797466 AGCCGAATGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (68 bp):
GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGG
TAG
Found at i:27797487 original size:116 final size:116
Alignment explanation
Indices: 27797285--27797628 Score: 670
Period size: 116 Copynumber: 3.0 Consensus size: 116
27797275 CAAGATAAAT
27797285 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
27797350 AGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAGGAG
66 AGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAGGAG
*
27797401 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
27797466 AGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAGGAG
66 AGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAGGAG
*
27797517 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
27797582 AGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTA
66 AGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTA
27797629 AAGCCGAATG
Statistics
Matches: 225, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 225 1.00
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (116 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
AGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAGGAG
Found at i:27797517 original size:20 final size:20
Alignment explanation
Indices: 27797494--27797532 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27797484 AAATATGTAT
27797494 GAGATATGTATATGTGGTAG
1 GAGATATGTATATGTGGTAG
27797514 GAGATATGTATATGTGGTA
1 GAGATATGTATATGTGGTA
27797533 AAGCCGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (20 bp):
GAGATATGTATATGTGGTAG
Found at i:27797518 original size:68 final size:68
Alignment explanation
Indices: 27797446--27797580 Score: 252
Period size: 68 Copynumber: 2.0 Consensus size: 68
27797436 AAATATGTAT
* *
27797446 GAGATATGTATATGTGGTAGAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGG
1 GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATGTATATGTGG
27797511 TAG
66 TAG
27797514 GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATGTATATGTGG
1 GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATGTATATGTGG
27797579 TA
66 TA
27797581 AAGCCGAATG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (68 bp):
GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATGTATATGTGG
TAG
Found at i:27797568 original size:164 final size:163
Alignment explanation
Indices: 27797285--27797690 Score: 561
Period size: 164 Copynumber: 2.5 Consensus size: 163
27797275 CAAGATAAAT
27797285 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGT-A
* * * * * * *
27797350 AGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAGGAGATATGTATATGTGG
65 AGCAGAATGGCTAATGTGAAAGACGAATGAGATATGTAAATATGGCAGGAGATATGTATATGTGG
27797415 TAAAGCCGAATGGCTAATGTGAAATATGTATGAG
130 TAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
27797449 ATATGTATATGTGGTAGAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGT-A
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
* * * *
27797513 GGAGATAT-G-TATATGTGGTAAAGCCGAATG-GCTAATGTGAAATAT-GCATGAGATATGTATA
66 GCAGA-ATGGCTA-ATGT-G-AAAGACGAATGAGAT-ATGT-AAATATGGCAGGAGATATGTATA
27797574 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
125 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
27797613 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTGTGAGATATGCATATGTGATAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGT-A
*
27797678 AGCCGAATGGCTA
65 AGCAGAATGGCTA
27797691 CTATGAAATA
Statistics
Matches: 214, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
161 2 0.01
162 9 0.04
163 5 0.02
164 185 0.86
165 6 0.03
166 5 0.02
167 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (163 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
GCAGAATGGCTAATGTGAAAGACGAATGAGATATGTAAATATGGCAGGAGATATGTATATGTGGT
AAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:27798092 original size:37 final size:37
Alignment explanation
Indices: 27797947--27798091 Score: 245
Period size: 37 Copynumber: 3.9 Consensus size: 37
27797937 GGGAATATAT
*
27797947 TCCGGGTAAGACCCGATGATTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
27797984 TCCGGGTAAGACCCGACGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
27798021 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
27798058 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
27798092 TCATCTGAGC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 102 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:27800073 original size:82 final size:82
Alignment explanation
Indices: 27799363--27800059 Score: 1173
Period size: 82 Copynumber: 8.5 Consensus size: 82
27799353 AGAATTGAGA
*
27799363 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTATTATATCCGGGCTAAGTCCCGA
1 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
27799428 AGAGCATTCGTGCTAGT
66 AGAGCATTCGTGCTAGT
*
27799445 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCTGGGCTAAGTCCCGA
1 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
*
27799510 AGAGCATTCGTACTAGT
66 AGAGCATTCGTGCTAGT
*
27799527 GATATATAGCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
1 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
27799592 AGAGCATTCGTGCTAGT
66 AGAGCATTCGTGCTAGT
* * *
27799609 GATATATAGCAGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGTTATATCTGGGCTAAGTCCCGA
1 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
27799674 AGAGCATTCGTGCTAGT
66 AGAGCATTCGTGCTAGT
*
27799691 GATATATAGCCGGGCTAAGTCCCGAAGAACATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
1 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
*
27799756 AGAGCATTCGTGTTAGT
66 AGAGCATTCGTGCTAGT
* * * * *
27799773 GATATATAGCCGGGATAAATCCTGAAGAGCATTCGTGCTAGTGTTATATCCGAGCTAAGTCCCGA
1 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
*
27799838 ACAGCATTCGTGCTAGT
66 AGAGCATTCGTGCTAGT
27799855 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
1 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
27799920 AGAGCATTCGTGCTAGT
66 AGAGCATTCGTGCTAGT
* *
27799937 GATATATAGCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCTCGA
1 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
* *
27800002 AGAGCTTTCGTGCTGGT
66 AGAGCATTCGTGCTAGT
* * * *
27800019 G-T-TATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTG
1 GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
27800060 ATGTGTATTC
Statistics
Matches: 577, Mismatches: 38, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
80 34 0.06
81 1 0.00
82 542 0.94
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (82 bp):
GATATATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
AGAGCATTCGTGCTAGT
Found at i:27800273 original size:25 final size:25
Alignment explanation
Indices: 27800223--27800273 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
27800213 TGTGTAACAA
* *
27800223 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
27800248 CAAATGATTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
27800273 C
1 C
27800274 GAGTTCTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:27803738 original size:20 final size:20
Alignment explanation
Indices: 27803715--27803821 Score: 81
Period size: 20 Copynumber: 5.0 Consensus size: 20
27803705 AAATATGTAT
27803715 GAGATATGTATATGTGGTAG
1 GAGATATGTATATGTGGTAG
27803735 GAGATATGTATATGTGGTAAAG
1 GAGATATGTATATGTGGT--AG
* * * *
27803757 CCGAATGGCTAATGTGAAATAT-GTAT
1 --G-A--GAT-ATGT-ATATGTGGTAG
27803783 GAGATATGTATATGTGGTAG
1 GAGATATGTATATGTGGTAG
*
27803803 GATATATGTATATGTGGTA
1 GAGATATGTATATGTGGTA
27803822 AAGTCGAATG
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
19 4 0.06
20 43 0.63
21 2 0.03
22 2 0.03
23 1 0.01
24 2 0.03
25 1 0.01
26 1 0.01
27 2 0.03
28 6 0.09
29 4 0.06
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (20 bp):
GAGATATGTATATGTGGTAG
Found at i:27803779 original size:68 final size:68
Alignment explanation
Indices: 27803670--27803869 Score: 382
Period size: 68 Copynumber: 2.9 Consensus size: 68
27803660 CAAGATAAAT
27803670 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAG
27803735 GAG
66 GAG
27803738 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAG
*
27803803 GAT
66 GAG
*
27803806 ATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTA
27803870 AAGCCGAATG
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 130 1.00
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (68 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAG
GAG
Found at i:27803859 original size:48 final size:48
Alignment explanation
Indices: 27803806--27804094 Score: 470
Period size: 48 Copynumber: 6.0 Consensus size: 48
27803796 GTGGTAGGAT
*
27803806 ATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
27803854 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
27803902 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTGTGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
27803950 ATATGTATATGTGATAAAGCCGAATGGCTACTGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
27803998 ATACGTATATGTCGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * * *
27804046 ATACGTATATGTGGTAAAGCCGAAGGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
27804094 A
1 A
27804095 GGTGTGTATA
Statistics
Matches: 227, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 227 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:27804344 original size:37 final size:37
Alignment explanation
Indices: 27804236--27804344 Score: 175
Period size: 37 Copynumber: 2.9 Consensus size: 37
27804226 GGAAATATAT
*
27804236 TCCGGGTAAGACCCGATGA-TTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTT-CGTGTGGAGATTTTG
*
27804273 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTTCGTGTGGAGATTTTG
*
27804310 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTTCGTGTGGAGATTT
27804345 CATCTAAGCT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 66 0.99
38 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTTCGTGTGGAGATTTTG
Found at i:27806679 original size:31 final size:31
Alignment explanation
Indices: 27806642--27806819 Score: 232
Period size: 31 Copynumber: 5.7 Consensus size: 31
27806632 TGTGTACAAT
*
27806642 GTGAAAAGTAGTAGCTTCGGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
*
27806673 GTGAAAAGTGGTAGCTTCGACTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* * *
27806704 ATGAAAAATGGTAGCTTTGGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* *
27806735 GTGAAAAGTAGTAGCTTCGGCTACCTGATTA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* * *
27806766 GTGAAAAGTGGTAGCTCCAGCTACCTGATTA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* *
27806797 GTGAATAA-TGATAGCTTCAGCTA
1 GTGAA-AAGTGGTAGCTTCGGCTA
27806820 TCGAATGTGA
Statistics
Matches: 130, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
31 128 0.98
32 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (31 bp):
GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
Found at i:27806812 original size:93 final size:93
Alignment explanation
Indices: 27806642--27806813 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
27806632 TGTGTACAAT
*
27806642 GTGAAAAGTAGTAGCTTCGGCTACCTGATCAGTGAAAAGTGGTAGCTTCGACTACCTGATCAATG
1 GTGAAAAGTAGTAGCTTCGGCTACCTGATCAGTGAAAAGTGGTAGCTCCGACTACCTGATCAATG
*
27806707 AAAAATGGTAGCTTTGGCTACCTGATCA
66 AAAAATGATAGCTTTGGCTACCTGATCA
* * *
27806735 GTGAAAAGTAGTAGCTTCGGCTACCTGATTAGTGAAAAGTGGTAGCTCC-AGCTACCTGATTAGT
1 GTGAAAAGTAGTAGCTTCGGCTACCTGATCAGTGAAAAGTGGTAGCTCCGA-CTACCTGATCAAT
*
27806799 GAATAATGATAGCTT
65 GAAAAATGATAGCTT
27806814 CAGCTATCGA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (93 bp):
GTGAAAAGTAGTAGCTTCGGCTACCTGATCAGTGAAAAGTGGTAGCTCCGACTACCTGATCAATG
AAAAATGATAGCTTTGGCTACCTGATCA
Found at i:27806890 original size:33 final size:33
Alignment explanation
Indices: 27806859--27806985 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 33
27806849 TCAAATTTGG
* *
27806859 AAAGGAAATGTATACTTTGTGTATACCATTTGA
1 AAAGGAAAGGTATACTTTGTGTATACCATATGA
** *
27806892 AAAGGTTAGGTATACTTTTTGTATACCATATGA
1 AAAGGAAAGGTATACTTTGTGTATACCATATGA
*
27806925 AAAGGAAAGGTATACTTTGTGTATATCATATGA
1 AAAGGAAAGGTATACTTTGTGTATACCATATGA
* *
27806958 AAAGGTAAGGTATACTTTGTGTGTACCA
1 AAAGGAAAGGTATACTTTGTGTATACCA
27806986 CTCAGAAAGA
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (33 bp):
AAAGGAAAGGTATACTTTGTGTATACCATATGA
Found at i:27808955 original size:43 final size:43
Alignment explanation
Indices: 27808887--27809010 Score: 164
Period size: 43 Copynumber: 2.9 Consensus size: 43
27808877 TGAGGGGTGT
*
27808887 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCGC-A
1 TACAATGCCAATGTCCCAGATATGGTCTTACACGTAATCGCAA
* * *
27808929 TA-ATGATGCCAATGTTCCAGATATGGTCTTACTCATAATCGCAA
1 TACA--ATGCCAATGTCCCAGATATGGTCTTACACGTAATCGCAA
*
27808973 TACAATGCCAATGTCCCA-ATATGGTCTTACATGTAATC
1 TACAATGCCAATGTCCCAGATATGGTCTTACACGTAATC
27809011 TCATCTCAGT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
41 1 0.01
42 19 0.27
43 46 0.66
44 3 0.04
45 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (43 bp):
TACAATGCCAATGTCCCAGATATGGTCTTACACGTAATCGCAA
Found at i:27815886 original size:43 final size:42
Alignment explanation
Indices: 27815839--27815948 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 42
27815829 ATAAAATCAT
* *
27815839 ATAATGATGCCAATGTCCCAGACAAAGTCTTACACTTAATCG
1 ATAATGATGCCAATGTCCCAGACAAAGTATTACACATAATCG
* *
27815881 CATAATGATGCCAATGTCCCAGACATAGTATTACCCATAATCG
1 -ATAATGATGCCAATGTCCCAGACAAAGTATTACACATAATCG
*
27815924 -TAATACAATGCCAATGTCCCAGACA
1 ATAAT--GATGCCAATGTCCCAGACA
27815949 TGATCTTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
41 4 0.07
43 56 0.93
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (42 bp):
ATAATGATGCCAATGTCCCAGACAAAGTATTACACATAATCG
Found at i:27836251 original size:18 final size:17
Alignment explanation
Indices: 27836230--27836267 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
27836220 TTTCATTAAA
*
27836230 TTTTTAGGATTCATTTG
1 TTTTTAAGATTCATTTG
27836247 TTTTTAAGATTCATTTG
1 TTTTTAAGATTCATTTG
27836264 TTTT
1 TTTT
27836268 CCTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.63
Consensus pattern (17 bp):
TTTTTAAGATTCATTTG
Found at i:27851338 original size:20 final size:20
Alignment explanation
Indices: 27851313--27851351 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27851303 TTAGAGAGGG
27851313 ACTAAAGATACAACAGTCAA
1 ACTAAAGATACAACAGTCAA
27851333 ACTAAAGATACAACAGTCA
1 ACTAAAGATACAACAGTCA
27851352 GATCTGAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.15
Consensus pattern (20 bp):
ACTAAAGATACAACAGTCAA
Found at i:27883487 original size:50 final size:49
Alignment explanation
Indices: 27883364--27883602 Score: 241
Period size: 50 Copynumber: 4.8 Consensus size: 49
27883354 CGAAGCTATA
* * * *
27883364 TGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-TCAACAATC
1 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTCAAC-ATC
* * * *
27883413 CGGTACACGTAGTAGCCTGCACTTAGAACTACACACGTGACCTCATCATC
1 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CTCAACATC
*
27883463 TGATACACGTAGTAGCCTCCACTTAGTACTACACACGTGA-TCGAAGTCAT-
1 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTC-AA--CATC
* * * * * *
27883513 TGAGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTTAACAGTA
1 TGA-TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTCAACA-TC
* *
27883564 TGATACACGTAGTAGCCTACACTTAGTGCTACACACGTG
1 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
27883603 TATTCACAAT
Statistics
Matches: 156, Mismatches: 25, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
48 2 0.01
49 36 0.23
50 73 0.47
51 44 0.28
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTCAACATC
Found at i:27883568 original size:101 final size:99
Alignment explanation
Indices: 27883361--27883602 Score: 274
Period size: 101 Copynumber: 2.4 Consensus size: 99
27883351 AGCCGAAGCT
* * * * * *
27883361 ATATGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGATCAACAATCCGGTACACGTAGT
1 ATATGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATCAACAATCCGGTACACATAGT
* *
27883426 AGCCTGCACTTAGAACTACACACGTGACCTCATC
66 AGCCTGCACTTAGAACTACACACGCGACCTCAAC
* * * *
27883460 ATCTGATACACGTAGTAGCCTCCACTTAGTACTACACACGTGATCGAAGTC-AT-TGAGTACGCA
1 ATATGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATC-AA--CAATCCG-GTACACA
* * *
27883523 TAGTAGCCTGCACTTAGTACTACACATGCGA-CTTAAC
62 TAGTAGCCTGCACTTAGAACTACACACGCGACCTCAAC
*
27883560 AGTATGATACACGTAGTAGCCTACACTTAGTGCTACACACGTG
1 A-TATGATACACGTAGTAGCCTACACTTAGTACTACACACGTG
27883603 TATTCACAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
99 39 0.32
100 8 0.07
101 73 0.60
102 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (99 bp):
ATATGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATCAACAATCCGGTACACATAGT
AGCCTGCACTTAGAACTACACACGCGACCTCAAC
Found at i:27892358 original size:13 final size:13
Alignment explanation
Indices: 27892342--27892374 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27892332 TTTAATTAAA
*
27892342 TTAGTTAATTAGT
1 TTAGATAATTAGT
27892355 TTAGATAATTAGT
1 TTAGATAATTAGT
27892368 TTA-ATAA
1 TTAGATAA
27892375 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:27893934 original size:21 final size:21
Alignment explanation
Indices: 27893909--27893977 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
27893899 TATAATGATT
27893909 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
27893930 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
27893950 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
27893970 ATTATTAT
1 ATTATTAT
27893978 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:27893990 original size:15 final size:14
Alignment explanation
Indices: 27893964--27893994 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
27893954 TATGGTTTTA
27893964 TATTAGATTATTAT
1 TATTAGATTATTAT
27893978 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
27893993 TA
1 TA
27893995 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:27900518 original size:6 final size:6
Alignment explanation
Indices: 27900491--27900575 Score: 68
Period size: 6 Copynumber: 14.3 Consensus size: 6
27900481 AATCCTCCTA
* * *
27900491 TTTTCT TTTTCT TTTTA- -TTTAT TCTTAT TTTTAT TTTTAT TTATT-T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT-TTAT
* * * *
27900537 ATTTTAT TCTTAT TTTTCT TTTGAT TTTTAT TTTCAT TT
1 -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
27900576 CAATTTTGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
4 4 0.06
6 55 0.86
7 5 0.08
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:27900539 original size:26 final size:25
Alignment explanation
Indices: 27900504--27900553 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
27900494 TCTTTTTCTT
*
27900504 TTTATTTATTCTTATTTTTATTTTTA
1 TTTATTTATT-TTATTCTTATTTTTA
27900530 TTTATTTATTTTATTCTTATTTTT
1 TTTATTTATTTTATTCTTATTTTT
27900554 CTTTTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTATTTATTTTATTCTTATTTTTA
Found at i:27900546 original size:31 final size:29
Alignment explanation
Indices: 27900502--27900570 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 29
27900492 TTTCTTTTTC
*
27900502 TTTTTA-TTTATTCTTATTTTTATTTTTA
1 TTTTTATTTTATTCTTATTTTTATTTTGA
*
27900530 TTTATTTATTTTATTCTTATTTTTCTTTTGA
1 -TT-TTTATTTTATTCTTATTTTTATTTTGA
27900561 TTTTTATTTT
1 TTTTTATTTT
27900571 CATTTCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 10 0.28
30 6 0.17
31 20 0.56
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (29 bp):
TTTTTATTTTATTCTTATTTTTATTTTGA
Found at i:27903966 original size:40 final size:40
Alignment explanation
Indices: 27903894--27904150 Score: 340
Period size: 40 Copynumber: 6.5 Consensus size: 40
27903884 ACCCAAGTAT
* * *
27903894 CTTCGGGAT-TTAG-CCAGATATAACAACACGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
27903933 CTTCGGGTCTTAGGCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
27903973 CTTCGGGTCTTAGGCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
27904013 CTTCGGGTCTTAGCCCGGATATAGCACCTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
27904053 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * * *
27904093 CTTCGGGACATAGCCCGGATATAGCAACTCACACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
27904133 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
27904151 TTATCATCCG
Statistics
Matches: 194, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
38 1 0.01
39 13 0.07
40 178 0.92
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:27912041 original size:40 final size:40
Alignment explanation
Indices: 27911974--27912145 Score: 224
Period size: 40 Copynumber: 4.3 Consensus size: 40
27911964 ACCCAAGTAT
*
27911974 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
27912013 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
27912053 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * * *
27912093 CTTCGGGACATAGCCTGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
27912133 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
27912146 TCCGATTATC
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 99 0.86
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:27935333 original size:35 final size:35
Alignment explanation
Indices: 27935293--27935363 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
27935283 TTTAAAAAGT
* *
27935293 TAAGAAACAAAAGCATAACATTAGTGAAAGTTCTA
1 TAAGAAACAAAAGCATAACATCAGTAAAAGTTCTA
27935328 TAAGAAACAAAAGCATAACATCAGTAAAAGTTCTA
1 TAAGAAACAAAAGCATAACATCAGTAAAAGTTCTA
27935363 T
1 T
27935364 GGCAACGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (35 bp):
TAAGAAACAAAAGCATAACATCAGTAAAAGTTCTA
Found at i:27952843 original size:62 final size:62
Alignment explanation
Indices: 27952773--27952890 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 62
27952763 GGTTCACATG
* **
27952773 GGCCAGGGACACGGGCGTACGCCTAGGCCATGTGACTCACTATTTGTGGTATAAAATCAAAT
1 GGCCAGGGACACGGGCGCACGCCTAGGCCATGCAACTCACTATTTGTGGTATAAAATCAAAT
* * *
27952835 GGCCAGGGACACGGGCGCATGCCTAGGCCGTGCAACTCACTTTTTGTGGTATAAAA
1 GGCCAGGGACACGGGCGCACGCCTAGGCCATGCAACTCACTATTTGTGGTATAAAA
27952891 CCACACAACC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (62 bp):
GGCCAGGGACACGGGCGCACGCCTAGGCCATGCAACTCACTATTTGTGGTATAAAATCAAAT
Found at i:27952903 original size:62 final size:62
Alignment explanation
Indices: 27952775--27952904 Score: 161
Period size: 62 Copynumber: 2.1 Consensus size: 62
27952765 TTCACATGGG
* ** * ***
27952775 CCAGGGACACGGGCGTACGCCTAGGCCATGTGACTCACTATTTGTGGTATAAAATCAAATGG
1 CCAGGGACACGGGCGCACGCCTAGGCCATGCAACTCACTATTTGTGGTATAAAACCAAACAA
* * * *
27952837 CCAGGGACACGGGCGCATGCCTAGGCCGTGCAACTCACTTTTTGTGGTATAAAACCACACAA
1 CCAGGGACACGGGCGCACGCCTAGGCCATGCAACTCACTATTTGTGGTATAAAACCAAACAA
27952899 CCAGGG
1 CCAGGG
27952905 GCACAGGTGT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (62 bp):
CCAGGGACACGGGCGCACGCCTAGGCCATGCAACTCACTATTTGTGGTATAAAACCAAACAA
Found at i:27966511 original size:18 final size:18
Alignment explanation
Indices: 27966490--27966526 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
27966480 TTGGTTTTCG
*
27966490 AATTCGAATAACTTGAAT
1 AATTCGAATAAATTGAAT
27966508 AATTCGAATAAATTGAAT
1 AATTCGAATAAATTGAAT
27966526 A
1 A
27966527 CTAAACTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (18 bp):
AATTCGAATAAATTGAAT
Found at i:27967156 original size:19 final size:19
Alignment explanation
Indices: 27967132--27967169 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
27967122 AAAGTTAATA
27967132 ACAAATTTAATTACAGTGG
1 ACAAATTTAATTACAGTGG
* *
27967151 ACAAATTTGATTACGGTGG
1 ACAAATTTAATTACAGTGG
27967170 GTGATAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
ACAAATTTAATTACAGTGG
Found at i:27967408 original size:28 final size:26
Alignment explanation
Indices: 27967357--27967410 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
27967347 ACTTCCCCTT
* *
27967357 ATATACCACATTAGACAAAAACAAAC
1 ATATACCACATTAAAAAAAAACAAAC
27967383 ATATACCACATTAAAAAAAGTAACAAAC
1 ATATACCACATTAAAAAAA--AACAAAC
27967411 TCAAGCACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 17 0.71
28 7 0.29
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (26 bp):
ATATACCACATTAAAAAAAAACAAAC
Found at i:27971169 original size:2 final size:2
Alignment explanation
Indices: 27971162--27971186 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27971152 ATTCATTTTC
27971162 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
27971187 AGATGTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27981485 original size:17 final size:17
Alignment explanation
Indices: 27981393--27981479 Score: 102
Period size: 17 Copynumber: 5.1 Consensus size: 17
27981383 CCAAACATTT
*
27981393 GTTCATATAAAATAATA
1 GTTCATACAAAATAATA
* * *
27981410 GTTCTTACCAAATGATA
1 GTTCATACAAAATAATA
27981427 GTTCATACAAAATAATA
1 GTTCATACAAAATAATA
* *
27981444 GTTCATACCAAATAACA
1 GTTCATACAAAATAATA
* *
27981461 ATTCATGCAAAATAATA
1 GTTCATACAAAATAATA
27981478 GT
1 GT
27981480 CCATGCTCCA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (17 bp):
GTTCATACAAAATAATA
Found at i:27981572 original size:21 final size:22
Alignment explanation
Indices: 27981546--27981588 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
27981536 TTATGAAACT
27981546 TATAA-GGACTATATCACCACA
1 TATAAGGGACTATATCACCACA
*
27981567 TATAAGTGGACTCTATCACCAC
1 TATAAG-GGACTATATCACCAC
27981589 CCATTAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (22 bp):
TATAAGGGACTATATCACCACA
Found at i:27982173 original size:18 final size:18
Alignment explanation
Indices: 27982147--27982221 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 18
27982137 CACAGTTTGA
*
27982147 CAAATTAATACAATTCAT
1 CAAATTAATACAATTCAC
*
27982165 CATATTAATACAGA-TCAC
1 CAAATTAATACA-ATTCAC
**
27982183 CAAATTAATACAATTTTC
1 CAAATTAATACAATTCAC
*
27982201 CATAA-TAATATAATTCAC
1 CA-AATTAATACAATTCAC
27982219 CAA
1 CAA
27982222 GTTATCATGG
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
17 2 0.04
18 41 0.89
19 3 0.07
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.32
Consensus pattern (18 bp):
CAAATTAATACAATTCAC
Found at i:27982641 original size:28 final size:29
Alignment explanation
Indices: 27982609--27982680 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
27982599 ACCCGCACAT
*
27982609 ATATATTATATATAT-AACACCAAAACCC
1 ATATATTATATATATAAACAACAAAACCC
*
27982637 ATATA-TATTATATATAAATAACAAAACCC
1 ATATATTA-TATATATAAACAACAAAACCC
* *
27982666 CTATACTTATCTATA
1 ATATA-TTATATATA
27982681 ATATATATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 2 0.06
28 12 0.33
29 15 0.42
30 5 0.14
31 2 0.06
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (29 bp):
ATATATTATATATATAAACAACAAAACCC
Found at i:27982642 original size:30 final size:29
Alignment explanation
Indices: 27982606--27982670 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
27982596 AAAACCCGCA
*
27982606 CATATATATTATATATATAACACCAAAACC
1 CATATATATTATATATA-AACAACAAAACC
*
27982636 CATATATATTATATATAAATAACAAAACC
1 CATATATATTATATATAAACAACAAAACC
*
27982665 CCTATA
1 CATATA
27982671 CTTATCTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (29 bp):
CATATATATTATATATAAACAACAAAACC
Found at i:27986021 original size:32 final size:31
Alignment explanation
Indices: 27985956--27986022 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
27985946 ACCTAAAATT
* * *
27985956 ATTAATTCTAATTATTTTAATATTTTATTTA
1 ATTAATTCTAATTATTTTAATATCTAATCTA
27985987 ATTAATTTCTAATTA-TTTAATTATCTAATCTA
1 ATTAA-TTCTAATTATTTTAA-TATCTAATCTA
27986019 ATTA
1 ATTA
27986023 CGGTTTTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTAATTCTAATTATTTTAATATCTAATCTA
Found at i:27987091 original size:22 final size:21
Alignment explanation
Indices: 27987049--27987092 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
27987039 ACTGGTTTTC
27987049 TTTTCTTTTCTTTTTACTCTTA
1 TTTTCTTTTCTTTTTA-TCTTA
27987071 TTTTACTTTTCCTTTTT-TCTTA
1 TTTT-CTTTT-CTTTTTATCTTA
27987093 CCTCGTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTCTTTTCTTTTTATCTTA
Found at i:27991733 original size:19 final size:20
Alignment explanation
Indices: 27991699--27991736 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27991689 TCATATAATT
*
27991699 AAAATAAATTTAAATTTTAA
1 AAAATAAAATTAAATTTTAA
27991719 AAAATAAAATT-AATTTTA
1 AAAATAAAATTAAATTTTA
27991737 TAATTCGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATAAAATTAAATTTTAA
Found at i:27995532 original size:12 final size:12
Alignment explanation
Indices: 27995515--27995541 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27995505 TTCGGGCCGC
27995515 GATAAGTTGTTT
1 GATAAGTTGTTT
27995527 GATAAGTTGTTT
1 GATAAGTTGTTT
27995539 GAT
1 GAT
27995542 TGTGTAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (12 bp):
GATAAGTTGTTT
Found at i:27995735 original size:27 final size:27
Alignment explanation
Indices: 27995705--27996009 Score: 92
Period size: 27 Copynumber: 11.3 Consensus size: 27
27995695 AAAATTCCTG
* *
27995705 AAATGCCCTCAATTTGTAAAATTACCA
1 AAATACCCTCAATTTATAAAATTACCA
* * *
27995732 AAATACTCTCGATTTATAGAATTACCA
1 AAATACCCTCAATTTATAAAATTACCA
*** ** *
27995759 TTTTACCCTTGATTTATAGAATTACCA
1 AAATACCCTCAATTTATAAAATTACCA
*** * *
27995786 TTTTACCCTCGATTTATAGAATTACC-
1 AAATACCCTCAATTTATAAAATTACCA
*** * * * * *
27995812 GTTTCACCCTCGATTTACAGAATTATCG
1 AAAT-ACCCTCAATTTATAAAATTACCA
*** * *
27995840 TTTTACCCTCGATTTATAGAATTACCA
1 AAATACCCTCAATTTATAAAATTACCA
*** * * * *
27995867 TTTTTCCCTCGATTTACAAAATTACCG
1 AAATACCCTCAATTTATAAAATTACCA
*** * * **
27995894 TTTTACCCTCGATTTATAGAATTACTG
1 AAATACCCTCAATTTATAAAATTACCA
*** * **
27995921 TTTTACCCTCAATTTACAAAATTACTG
1 AAATACCCTCAATTTATAAAATTACCA
*** *
27995948 AAATACCCTTGGTTTAAAAAATTACCA
1 AAATACCCTCAATTTATAAAATTACCA
*
27995975 AAATACCCTCGA-TTAGTAAAATTACCA
1 AAATACCCTCAATTTA-TAAAATTACCA
27996002 AAATACCC
1 AAATACCC
27996010 CTGGCTTGTA
Statistics
Matches: 234, Mismatches: 41, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
26 6 0.03
27 225 0.96
28 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (27 bp):
AAATACCCTCAATTTATAAAATTACCA
Found at i:27995806 original size:54 final size:54
Alignment explanation
Indices: 27995739--27995945 Score: 306
Period size: 54 Copynumber: 3.8 Consensus size: 54
27995729 CCAAAATACT
* * *
27995739 CTCGATTTATAGAATTACCATTTTACCCTTGATTTATAGAATTACCATTTTACC
1 CTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACC
* * *
27995793 CTCGATTTATAGAATTACCGTTTCACCCTCGATTTACAGAATTATCGTTTTACC
1 CTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACC
* *
27995847 CTCGATTTATAGAATTACCATTTTTCCCTCGATTTACAAAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACC
** * *
27995901 CTCGATTTATAGAATTACTGTTTTACCCTCAATTTACAAAATTAC
1 CTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTAC
27995946 TGAAATACCC
Statistics
Matches: 138, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 138 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (54 bp):
CTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACC
Found at i:27995845 original size:81 final size:80
Alignment explanation
Indices: 27995739--27995945 Score: 297
Period size: 81 Copynumber: 2.5 Consensus size: 80
27995729 CCAAAATACT
* * *
27995739 CTCGATTTATAGAATTACCATTTTACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTATA
1 CTCGATTTATAGAATTA-CGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACA
*
27995804 GAATTACCGTTTCACC
65 AAATTACCGTTTCACC
* *
27995820 CTCGATTTACAGAATTATCGTTTTACCCTCGATTTATAGAATTACCATTTTTCCCTCGATTTACA
1 CTCGATTTATAGAATTA-CGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACA
*
27995885 AAATTACCGTTTTACC
65 AAATTACCGTTTCACC
* * *
27995901 CTCGATTTATAGAATTACTGTTTTACCCTCAATTTACAAAATTAC
1 CTCGATTTATAGAATTAC-GTTTTACCCTCGATTTATAGAATTAC
27995946 TGAAATACCC
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 1 0.01
81 112 0.99
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (80 bp):
CTCGATTTATAGAATTACGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAA
AATTACCGTTTCACC
Found at i:27995969 original size:81 final size:81
Alignment explanation
Indices: 27995739--27995973 Score: 231
Period size: 81 Copynumber: 2.9 Consensus size: 81
27995729 CCAAAATACT
* * * ** * * ** *
27995739 CTCGATTTATAGAATTACCATTTTACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTATA
1 CTCGATTTACAGAATTATCGTTTTACCCTCAATTTACAAAATTACCATAATACCCTCGATTTAAA
*
27995804 GAATTACCGTTTCACC
66 AAATTACCGTTTCACC
* * * ** * *
27995820 CTCGATTTACAGAATTATCGTTTTACCCTCGATTTATAGAATTACCATTTTTCCCTCGATTTACA
1 CTCGATTTACAGAATTATCGTTTTACCCTCAATTTACAAAATTACCATAATACCCTCGATTTAAA
*
27995885 AAATTACCGTTTTACC
66 AAATTACCGTTTCACC
* * * *
27995901 CTCGATTTATAGAATTA-CTGTTTTACCCTCAATTTACAAAATTACTGA-AATACCCTTGGTTTA
1 CTCGATTTACAGAATTATC-GTTTTACCCTCAATTTACAAAATTAC-CATAATACCCTCGATTTA
27995964 AAAAATTACC
64 AAAAATTACC
27995974 AAAATACCCT
Statistics
Matches: 133, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
80 1 0.01
81 131 0.98
82 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.40
Consensus pattern (81 bp):
CTCGATTTACAGAATTATCGTTTTACCCTCAATTTACAAAATTACCATAATACCCTCGATTTAAA
AAATTACCGTTTCACC
Found at i:27995971 original size:54 final size:54
Alignment explanation
Indices: 27995710--27995972 Score: 168
Period size: 54 Copynumber: 4.9 Consensus size: 54
27995700 TCCTGAAATG
** * * * * **
27995710 CCCTCAATTTGTAAAATTACCAAAATACTCTCGATTTATAGAATTACCATTTTA
1 CCCTCAATTTACAAAATTACCGAAATACCCTCGATTTAAAAAATTACTGTTTTA
** * * ** * * * *
27995764 CCCTTGATTTATAGAATTACC-ATTTTACCCTCGATTTATAGAATTACCGTTTCA
1 CCCTCAATTTACAAAATTACCGA-AATACCCTCGATTTAAAAAATTACTGTTTTA
* * * *** * * ** *
27995818 CCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTATAGAATTACCATTTTT
1 CCCTCAATTTACAAAATTACCGAAATACCCTCGATTTAAAAAATTACTGTTTTA
* *** * *
27995872 CCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACTGTTTTA
1 CCCTCAATTTACAAAATTACCGAAATACCCTCGATTTAAAAAATTACTGTTTTA
* * *
27995926 CCCTCAATTTACAAAATTACTGAAATACCCTTGGTTTAAAAAATTAC
1 CCCTCAATTTACAAAATTACCGAAATACCCTCGATTTAAAAAATTAC
27995973 CAAAATACCC
Statistics
Matches: 177, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
53 1 0.01
54 176 0.99
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.39
Consensus pattern (54 bp):
CCCTCAATTTACAAAATTACCGAAATACCCTCGATTTAAAAAATTACTGTTTTA
Found at i:27995982 original size:54 final size:54
Alignment explanation
Indices: 27995924--27996036 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 54
27995914 ATTACTGTTT
** * *
27995924 TACCCTCAATTTA-CAAAATTACTGAAATACCCTTGGTTTAAAAAATTACCAAAA
1 TACCCTCAA-TTAGCAAAATTACCAAAATACCCCTGGCTTAAAAAATTACCAAAA
* * ** *
27995978 TACCCTCGATTAGTAAAATTACCAAAATACCCCTGGCTTGTAAAATTATCAAAA
1 TACCCTCAATTAGCAAAATTACCAAAATACCCCTGGCTTAAAAAATTACCAAAA
27996032 TACCC
1 TACCC
27996037 CTGATTTGTG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 3 0.06
54 46 0.94
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (54 bp):
TACCCTCAATTAGCAAAATTACCAAAATACCCCTGGCTTAAAAAATTACCAAAA
Found at i:27996020 original size:27 final size:27
Alignment explanation
Indices: 27995938--27996224 Score: 114
Period size: 27 Copynumber: 10.7 Consensus size: 27
27995928 CTCAATTTAC
** * * **
27995938 AAAATTACTGAAATACCCTTGGTTTAA
1 AAAATTACCAAAATACCCCTGGATTGT
*
27995965 AAAATTACCAAAATA-CCCTCGATTAGT
1 AAAATTACCAAAATACCCCTGGATT-GT
*
27995992 AAAATTACCAAAATACCCCTGGCTTGT
1 AAAATTACCAAAATACCCCTGGATTGT
*
27996019 AAAATTATCAAAATACCCCT-GATTTGT
1 AAAATTACCAAAATACCCCTGGA-TTGT
* *** * *
27996046 GAAATTATGGAAATA-CTCTCGATTTGT
1 AAAATTACCAAAATACCCCTGGA-TTGT
* *** * **
27996073 AGAATTATTGAAATACCCCTGTAGGGT
1 AAAATTACCAAAATACCCCTGGATTGT
* * * **
27996100 AGAATTACTAAAATACCCCTGTAGGGT
1 AAAATTACCAAAATACCCCTGGATTGT
* * * **
27996127 AGAATTACTAAAATACCCCTGTAGGGT
1 AAAATTACCAAAATACCCCTGGATTGT
* * * * **
27996154 AGAATTATCGAAATACCCCTGTAGGGT
1 AAAATTACCAAAATACCCCTGGATTGT
* ** * **
27996181 AGAATTACTGAAATACCCCTGTAGGGT
1 AAAATTACCAAAATACCCCTGGATTGT
*
27996208 -AGATTACCAAAATACCC
1 AAAATTACCAAAATACCC
27996225 TTGTAGGGTA
Statistics
Matches: 221, Mismatches: 34, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
26 23 0.10
27 187 0.85
28 11 0.05
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGATTGT
Done.