Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 86 of 193
Found at i:28360050 original size:39 final size:39
Alignment explanation
Indices: 28359918--28360065 Score: 147
Period size: 39 Copynumber: 3.8 Consensus size: 39
28359908 AGTGATCAAA
* * * *
28359918 ATACTGAACTAGTAGTGACACTGGAAACACTGCAAAGTT
1 ATACTGAACTAGCAGTGACACTGTAAACACTGCGAAGCT
* * * * *
28359957 ATATTGAA-TAAGCAGTAACATTGTAAACATTGCGAAACT
1 ATACTGAACT-AGCAGTGACACTGTAAACACTGCGAAGCT
* * *
28359996 ACATTGAACTGGCAGTGACACTGTAAACACTGCGAAGCT
1 ATACTGAACTAGCAGTGACACTGTAAACACTGCGAAGCT
*
28360035 ATACTG-ACTTAGCAGTGACACTATAAACACT
1 ATACTGAAC-TAGCAGTGACACTGTAAACACT
28360066 ACAATGTTAT
Statistics
Matches: 87, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
38 3 0.03
39 83 0.95
40 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (39 bp):
ATACTGAACTAGCAGTGACACTGTAAACACTGCGAAGCT
Found at i:28371867 original size:123 final size:121
Alignment explanation
Indices: 28371648--28371875 Score: 323
Period size: 123 Copynumber: 1.9 Consensus size: 121
28371638 CAGGAACGAA
* * *
28371648 GAAAACCACTAGTCCCATCTGCACTAGTCTAGTTTCAACATAATCATAGAAAACGAATACAACCA
1 GAAAACCACTAGTCACATCTGCACTAGTCCAATTTCAACATAATCATAGAAAACGAATACAACCA
* **
28371713 AATATGGAGACAGCAATGTGATGGTTCGAAAGGGATTAGATTAAATCATGCACCAT
66 AATATGGAGACAGCAAGGCAATGGTTCGAAAGGGATTAGATTAAATCATGCACCAT
* **
28371769 GAAAACCACTAGTCACATCTGCACTCTAGTCCAATTTCAACATGATCATAGAAAACGAATAGTAC
1 GAAAACCACTAGTCACATCTGCA--CTAGTCCAATTTCAACATAATCATAGAAAACGAATACAAC
* *
28371834 CAGATATGGAGACAGCAAGGCAACT-GTTTGAAAGGGATTAGA
64 CAAATATGGAGACAGCAAGGCAA-TGGTTCGAAAGGGATTAGA
28371876 ATAGAGCATG
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
121 22 0.24
123 70 0.75
124 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (121 bp):
GAAAACCACTAGTCACATCTGCACTAGTCCAATTTCAACATAATCATAGAAAACGAATACAACCA
AATATGGAGACAGCAAGGCAATGGTTCGAAAGGGATTAGATTAAATCATGCACCAT
Found at i:28386309 original size:13 final size:13
Alignment explanation
Indices: 28386291--28386343 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
28386281 CTTAACTCAA
28386291 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
28386304 ACTTTTCAAAA-T
1 ACTTTTCAAAAGT
* **
28386316 CACTTTTTAAAAAC
1 -ACTTTTCAAAAGT
*
28386330 ACTTATCAAAAGT
1 ACTTTTCAAAAGT
28386343 A
1 A
28386344 ATACTAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 1 0.03
13 31 0.97
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:28386558 original size:19 final size:19
Alignment explanation
Indices: 28386534--28386573 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28386524 AATGCTTTTT
* *
28386534 AAAAATATTTTTGAGCTAA
1 AAAAATACTTTTGAGATAA
28386553 AAAAATACTTTTGAGATAA
1 AAAAATACTTTTGAGATAA
28386572 AA
1 AA
28386574 CTAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
AAAAATACTTTTGAGATAA
Found at i:28388810 original size:13 final size:13
Alignment explanation
Indices: 28388792--28388818 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28388782 ATATACCAAT
28388792 TATTAATATAACA
1 TATTAATATAACA
28388805 TATTAATATAACA
1 TATTAATATAACA
28388818 T
1 T
28388819 TTACCTTTAG
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
TATTAATATAACA
Found at i:28391389 original size:30 final size:30
Alignment explanation
Indices: 28391355--28391419 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
28391345 ACTTATTTTA
* *
28391355 TTGTTAATTTTATTATTATTGAAGAGGTAT
1 TTGTTAATTTTATTACTATTGAAGAGGCAT
* **
28391385 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTATTACTATTGAAGAGGCAT
28391415 TTGTT
1 TTGTT
28391420 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.55
Consensus pattern (30 bp):
TTGTTAATTTTATTACTATTGAAGAGGCAT
Found at i:28393785 original size:23 final size:23
Alignment explanation
Indices: 28393759--28393802 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28393749 GCTAAATCTA
*
28393759 GGAGCACCAAAGTGTTAAATACG
1 GGAGCACCAAAGTGCTAAATACG
* *
28393782 GGAGCACTAGAGTGCTAAATA
1 GGAGCACCAAAGTGCTAAATA
28393803 TAGAAGCGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (23 bp):
GGAGCACCAAAGTGCTAAATACG
Found at i:28396793 original size:13 final size:13
Alignment explanation
Indices: 28396770--28396812 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
28396760 CAAATATACA
28396770 AAAACAAATATGAG
1 AAAA-AAATATGAG
28396784 AAAAAAATATGA-
1 AAAAAAATATGAG
28396796 AAAAATAA-ATGAG
1 AAAAA-AATATGAG
28396809 AAAA
1 AAAA
28396813 TACAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.33
13 14 0.52
14 4 0.15
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (13 bp):
AAAAAAATATGAG
Found at i:28396799 original size:27 final size:25
Alignment explanation
Indices: 28396761--28396812 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
28396751 AATAATGAAC
28396761 AAATATACAAAAACAAATATGAGAAAA
1 AAATATACAAAAA-AAA-ATGAGAAAA
*
28396788 AAATATGA-AAAAATAAATGAGAAAA
1 AAATAT-ACAAAAAAAAATGAGAAAA
28396813 TACAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 9 0.39
26 2 0.09
27 11 0.48
28 1 0.04
ACGTcount: A:0.71, C:0.04, G:0.10, T:0.15
Consensus pattern (25 bp):
AAATATACAAAAAAAAATGAGAAAA
Found at i:28397029 original size:87 final size:86
Alignment explanation
Indices: 28396918--28397268 Score: 338
Period size: 87 Copynumber: 4.1 Consensus size: 86
28396908 TTAAAACATA
* ** * * * * *
28396918 ATTTTGGAAAGTTT-AGGGGAAAAATGACATTTTGGGAAAATT-TAGGGTAAAAACGTGATTTTT
1 ATTTTGAAAAGTTTAAGGGTTAAAATGAGATTTTTGG-AAGTTCTAGGGTAAAAATGTAATTTTT
*
28396981 GGAAG-TTCAGGGTAAAAATGT
65 GGAAGTTTTAGGGTAAAAATGT
* * * * *
28397002 GATTTTGGAAAAGTGTAAGGGTTAAAATGTGATTTTTAGAAGTTCGAGGGTAAAAATGAAATTTT
1 -ATTTT-GAAAAGTTTAAGGGTTAAAATGAGATTTTTGGAAGTTCTAGGGTAAAAATGTAATTTT
* *
28397067 TGGAAGTTTAAGGGCAAAAATGT
64 TGGAAGTTTTAGGGTAAAAATGT
* *
28397090 ATTTTTG-AAAGTTTAAGGGTAAAAATGTA-ATTTTTGAGAAGTT-TGAGGGTTAAAATGTAATT
1 A-TTTTGAAAAGTTTAAGGGTTAAAATG-AGATTTTTG-GAAGTTCT-AGGGTAAAAATGTAATT
* *
28397152 TTTGGAAG-TTTGGGGGAAAAATGT
62 TTTGGAAGTTTTAGGGTAAAAATGT
* * * * *
28397176 AATTTTTAAGAAGTTTGAGGGTTAAAATGTGATTTTTGGAAGTTCAAGGGCAAAAATGTAATTTT
1 -ATTTTGAA-AAGTTTAAGGGTTAAAATGAGATTTTTGGAAGTTCTAGGGTAAAAATGTAATTTT
*
28397241 TGGAAGTTTTGGGGTAAAAATGT
64 TGGAAGTTTTAGGGTAAAAATGT
28397264 ATTTT
1 ATTTT
28397269 TTGAGAAATT
Statistics
Matches: 219, Mismatches: 33, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
85 5 0.02
86 52 0.24
87 105 0.48
88 57 0.26
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (86 bp):
ATTTTGAAAAGTTTAAGGGTTAAAATGAGATTTTTGGAAGTTCTAGGGTAAAAATGTAATTTTTG
GAAGTTTTAGGGTAAAAATGT
Found at i:28397270 original size:58 final size:58
Alignment explanation
Indices: 28396919--28397333 Score: 351
Period size: 58 Copynumber: 7.1 Consensus size: 58
28396909 TAAAACATAA
* * * ** *
28396919 TTTTGGAAAGTT-TAGGGGAAAAATG-ACATTTTGGGAAAATTTAGGGTAAAAACGTGAT
1 TTTTGG-AAGTTCAAGGGTAAAAATGTA-ATTTTTGGAAGTTTTAGGGTAAAAATGTGAT
* * * *
28396977 TTTTGGAAGTTC-AGGGTAAAAATGTGA-TTTTGGAAAAGTGTAAGGGTTAAAATGTGAT
1 TTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGG--AAGTTTTAGGGTAAAAATGTGAT
* * * * *
28397035 TTTTAGAAGTTCGAGGGTAAAAATGAAATTTTTGGAAGTTTAAGGGCAAAAATGT-AT
1 TTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTAAAAATGTGAT
* * * * *
28397092 TTTTGAAAGTTTAAGGGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTAAT
1 TTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTG-GAAGTTTTAGGGTAAAAATGTGAT
** * * * *
28397151 TTTTGGAAGTT-TGGGGGAAAAATGTAATTTTTAAGAAGTTTGAGGGTTAAAATGTGAT
1 TTTTGGAAGTTCAAGGGTAAAAATGTAATTTTT-GGAAGTTTTAGGGTAAAAATGTGAT
* *
28397209 TTTTGGAAGTTCAAGGGCAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAATGT-ATT
1 TTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTAAAAATGTGA-T
* ** * * ** ** *
28397267 TTTTGAGAAATTTGAGAGCAAAAACATAATTTTTGAGAAGTTCGAGGGTCAAAATGTGA-
1 TTTTG-GAAGTTCAAGGGTAAAAATGTAATTTTTG-GAAGTTTTAGGGTAAAAATGTGAT
28397326 TTTTGGAA
1 TTTTGGAA
28397334 AAGCGTAGGG
Statistics
Matches: 297, Mismatches: 46, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
56 5 0.02
57 49 0.16
58 148 0.50
59 71 0.24
60 23 0.08
61 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (58 bp):
TTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTAAAAATGTGAT
Found at i:28397280 original size:29 final size:28
Alignment explanation
Indices: 28396919--28397333 Score: 291
Period size: 29 Copynumber: 14.3 Consensus size: 28
28396909 TAAAACATAA
28396919 TTTTGGAAAGTTTAGGGG-AAAAATG-ACAT
1 TTTTGG-AAGTTT-GGGGTAAAAATGTA-AT
* * * * *
28396948 TTTGGGAAAATTTAGGGTAAAAACGTGAT
1 TTTTGG-AAGTTTGGGGTAAAAATGTAAT
** *
28396977 TTTTGGAAGTTCAGGGTAAAAATGTGA-
1 TTTTGGAAGTTTGGGGTAAAAATGTAAT
** * *
28397004 TTTTGGAAAAGTGTAAGGGTTAAAATGTGAT
1 TTTTGG--AAGT-TTGGGGTAAAAATGTAAT
* * *
28397035 TTTTAGAAGTTCGAGGGTAAAAATGAAAT
1 TTTTGGAAGTTTG-GGGTAAAAATGTAAT
* *
28397064 TTTTGGAAGTTTAAGGGCAAAAATGT-AT
1 TTTTGGAAGTTT-GGGGTAAAAATGTAAT
* *
28397092 TTTTGAAAGTTTAAGGGTAAAAATGTAAT
1 TTTTGGAAGTTT-GGGGTAAAAATGTAAT
*
28397121 TTTTGAGAAGTTTGAGGGTTAAAATGTAAT
1 TTTTG-GAAGTTTG-GGGTAAAAATGTAAT
*
28397151 TTTTGGAAGTTTGGGGGAAAAATGTAAT
1 TTTTGGAAGTTTGGGGTAAAAATGTAAT
* * *
28397179 TTTTAAGAAGTTTGAGGGTTAAAATGTGAT
1 TTTT-GGAAGTTTG-GGGTAAAAATGTAAT
** *
28397209 TTTTGGAAGTTCAAGGGCAAAAATGTAAT
1 TTTTGGAAGTT-TGGGGTAAAAATGTAAT
*
28397238 TTTTGGAAGTTTTGGGGTAAAAATGTATT
1 TTTTGGAAG-TTTGGGGTAAAAATGTAAT
* * * **
28397267 TTTTGAGAAATTTGAGAGCAAAAACATAAT
1 TTTTG-GAAGTTTG-GGGTAAAAATGTAAT
* * *
28397297 TTTTGAGAAGTTCGAGGGTCAAAATGTGA-
1 TTTTG-GAAGTTTG-GGGTAAAAATGTAAT
28397326 TTTTGGAA
1 TTTTGGAA
28397334 AAGCGTAGGG
Statistics
Matches: 312, Mismatches: 57, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
27 6 0.02
28 68 0.22
29 141 0.45
30 92 0.29
31 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
TTTTGGAAGTTTGGGGTAAAAATGTAAT
Found at i:28398509 original size:18 final size:19
Alignment explanation
Indices: 28398479--28398527 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
28398469 ACGTTTAGAA
28398479 ATAATAAATAATAATGGTAAT
1 ATAATAAATAAT-A-GGTAAT
28398500 ATAATAAATAAATAGGT-AT
1 ATAATAAAT-AATAGGTAAT
28398519 -TAATAAATA
1 ATAATAAATA
28398528 TATGCAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 8 0.30
19 2 0.07
20 3 0.11
21 10 0.37
22 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
ATAATAAATAATAGGTAAT
Found at i:28399139 original size:6 final size:6
Alignment explanation
Indices: 28399128--28399210 Score: 86
Period size: 6 Copynumber: 14.3 Consensus size: 6
28399118 GGACAATATT
* *
28399128 AATTTA AATTTA GAA--TA AATTTA AATTTA AGA-ATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA
*
28399175 AA-TTA AATTTA AATTTA AA-ATA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
28399211 AACAAATTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 2 0.03
5 12 0.18
6 48 0.74
7 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:28399150 original size:17 final size:17
Alignment explanation
Indices: 28399128--28399239 Score: 152
Period size: 17 Copynumber: 6.5 Consensus size: 17
28399118 GGACAATATT
*
28399128 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
28399145 AATTTAAATTTAAGAATA
1 AATTTAAATTTAA-AATA
* *
28399163 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
28399180 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
28399197 AATTTAAATTTAAAAACA
1 AATTTAAATTT-AAAATA
*
28399215 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
28399232 AATCTAAA
1 AATTTAAA
28399240 AAAATGGGTT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
17 53 0.63
18 31 0.37
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:28399167 original size:35 final size:33
Alignment explanation
Indices: 28399128--28399239 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 33
28399118 GGACAATATT
28399128 AATTTAAATTTAGAATAAATTTAAATTTAAGAATA
1 AATTTAAATTTA-AATAAATTTAAATTTAA-AATA
*
28399163 AATTTAAACTTAAATTAAATTTAAATTTAAAATA
1 AATTTAAATTTAAA-TAAATTTAAATTTAAAATA
* *
28399197 AATTTAAATTTAAAAACAAATTTAAACTTAAAATA
1 AATTTAAATTT--AAATAAATTTAAATTTAAAATA
*
28399232 AATCTAAA
1 AATTTAAA
28399240 AAAATGGGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
34 16 0.23
35 50 0.72
36 3 0.04
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (33 bp):
AATTTAAATTTAAATAAATTTAAATTTAAAATA
Found at i:28399187 original size:23 final size:23
Alignment explanation
Indices: 28399129--28399228 Score: 71
Period size: 23 Copynumber: 4.3 Consensus size: 23
28399119 GACAATATTA
*
28399129 ATTTAAATTTAGAATAAATTTAA
1 ATTTAAATTTAAAATAAATTTAA
* * *
28399152 ATTTAAGA-ATAAATTTAAACTTAA
1 ATTTAA-ATTTAAA-ATAAATTTAA
* *
28399176 A-TTAAATTTAAATTTAAA-ATAA
1 ATTTAAATTTAAA-ATAAATTTAA
*
28399198 ATTTAAATTTAAAAACAAATTTAA
1 ATTTAAATTT-AAAATAAATTTAA
*
28399222 ACTTAAA
1 ATTTAAA
28399229 ATAAATCTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
22 5 0.08
23 34 0.56
24 22 0.36
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTTAAATTTAAAATAAATTTAA
Found at i:28399189 original size:52 final size:52
Alignment explanation
Indices: 28399128--28399239 Score: 179
Period size: 52 Copynumber: 2.2 Consensus size: 52
28399118 GGACAATATT
* * * *
28399128 AATTTAAATTTAGAATAAATTTAAATTTAAGAATAAATTTAAACTTAAATTA
1 AATTTAAATTTAAAATAAATTTAAATTTAAAAACAAATTTAAACTTAAAATA
28399180 AATTTAAATTTAAAATAAATTTAAATTTAAAAACAAATTTAAACTTAAAATA
1 AATTTAAATTTAAAATAAATTTAAATTTAAAAACAAATTTAAACTTAAAATA
*
28399232 AATCTAAA
1 AATTTAAA
28399240 AAAATGGGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (52 bp):
AATTTAAATTTAAAATAAATTTAAATTTAAAAACAAATTTAAACTTAAAATA
Found at i:28399716 original size:39 final size:39
Alignment explanation
Indices: 28399673--28400258 Score: 211
Period size: 39 Copynumber: 15.3 Consensus size: 39
28399663 CCATGATCAA
*
28399673 GGTAAGAGATTGGCTGATGATGATCTACCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* * * *
28399712 GGTAA-A-ATAT--CTAATGGTTGCAATCTACCCCAGGCTCGT
1 GGTAAGAGAT-TGGCTGAT-GATG--ATCTGCCCCAGGCTCGG
* * ** *
28399751 GGTAAGTGATTGGCTGAT-AGTGATCTGCCTCAAACTCAG
1 GGTAAGAGATTGGCTGATGA-TGATCTGCCCCAGGCTCGG
* * * ** * * * *
28399790 GGTAAGAGATCGGATGGCT-ACAATCTGTCCTATGATCGG
1 GGTAAGAGATTGGCT-GATGATGATCTGCCCCAGGCTCGG
28399829 GGTAAGAGAATT-GC------TGATCTGCCCCAGGCTCGG
1 GGTAAGAG-ATTGGCTGATGATGATCTGCCCCAGGCTCGG
* * * * **
28399862 GGTAAGAGATTTGCTAATAATGATCTGCCTCAATCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* ** * *
28399901 GGCAAGAGA-T--CAAATGGTTGCAATCTGCCCCAGGCTTGG
1 GGTAAGAGATTGGCTGAT-GATG--ATCTGCCCCAGGCTCGG
* **
28399940 GGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* ** * *
28399979 GGCAAGAGA-T--CAAATGGTTGCAATCTGCCCCAGGCT-TG
1 GGTAAGAGATTGGCTGAT-GATG--ATCTGCCCCAGGCTCGG
* **
28400017 GGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* * ** * * * *
28400056 GGTAAAAGATCGAATG--GTTGCAATCTGTCCCAAGCTTGG
1 GGTAAGAGATTGGCTGATGATG--ATCTGCCCCAGGCTCGG
* * * * *
28400095 GGTAAGAGATTTGTTGATGGTAATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
* * * * *
28400134 GATAAGAGATCGAACGGCTGCA--ATCTGCCCCAGGCTCGG
1 GGTAAGAGATTG-GCTGATG-ATGATCTGCCCCAGGCTCGG
** *
28400173 GGTAAGATCGAACGGCTG--CA--ATCTGCCCCAGGCTCGG
1 GGTAAGA--GATTGGCTGATGATGATCTGCCCCAGGCTCGG
* * *
28400210 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGTTCGG
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
*
28400249 GGTAAAAGAT
1 GGTAAGAGAT
28400259 CGAATCTTCA
Statistics
Matches: 400, Mismatches: 104, Indels: 86
0.68 0.18 0.15
Matches are distributed among these distances:
32 3 0.01
33 23 0.06
35 7 0.02
36 11 0.03
37 38 0.09
38 25 0.06
39 255 0.64
40 15 0.04
41 16 0.04
42 7 0.02
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (39 bp):
GGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGG
Found at i:28399793 original size:78 final size:78
Alignment explanation
Indices: 28399646--28399794 Score: 174
Period size: 78 Copynumber: 1.9 Consensus size: 78
28399636 TATTGCTTCG
* * ** *
28399646 AATGATTGCAATCTGCCCCATGATCAAGGTAAGAGATTGGCTGATGATGATCTACCCCAGGCTCG
1 AATGATTGCAATCTACCCCAGGATCAAGGTAAGAGATTGGCTGATGATGATCTACCCCAAACTCA
28399711 GGGTAAAATATCT
66 GGGTAAAATATCT
* * ** * * *
28399724 AATGGTTGCAATCTACCCCAGGCTCGTGGTAAGTGATTGGCTGAT-AGTGATCTGCCTCAAACTC
1 AATGATTGCAATCTACCCCAGGATCAAGGTAAGAGATTGGCTGATGA-TGATCTACCCCAAACTC
28399788 AGGGTAA
65 AGGGTAA
28399795 GAGATCGGAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
77 1 0.02
78 57 0.98
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (78 bp):
AATGATTGCAATCTACCCCAGGATCAAGGTAAGAGATTGGCTGATGATGATCTACCCCAAACTCA
GGGTAAAATATCT
Found at i:28399890 original size:111 final size:111
Alignment explanation
Indices: 28399734--28399957 Score: 277
Period size: 111 Copynumber: 2.0 Consensus size: 111
28399724 AATGGTTGCA
* * * * *
28399734 ATCTACCCCAGGCTCGTGGTAAGTGATTGGCTGATAGTGATCTGCCTCAAACTCAGGGTAAGAGA
1 ATCTACCCCAGGCTCGGGGTAAGAGATTGGCTAATAATGATCTGCCTCAAACTCAGGGCAAGAGA
** * * *
28399799 TCGGATGGCTACAATCTGTCCTATGATCGGGGTAAGAGAATTGCTG
66 TCAAATGGCTACAATCTGCCCCAGGATCGGGGTAAGAGAATTGCTG
* * * *
28399845 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAATAATGATCTGCCTCAATCTCGGGGCAAGAGA
1 ATCTACCCCAGGCTCGGGGTAAGAGATTGGCTAATAATGATCTGCCTCAAACTCAGGGCAAGAGA
* * * * *
28399910 TCAAATGGTTGCAATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTG
66 TCAAATGGCTACAATCTGCCCCAGGATCGGGGTAAGAGAATTGCTG
28399956 AT
1 AT
28399958 GATGATCTGC
Statistics
Matches: 94, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
111 94 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (111 bp):
ATCTACCCCAGGCTCGGGGTAAGAGATTGGCTAATAATGATCTGCCTCAAACTCAGGGCAAGAGA
TCAAATGGCTACAATCTGCCCCAGGATCGGGGTAAGAGAATTGCTG
Found at i:28399943 original size:78 final size:78
Alignment explanation
Indices: 28399845--28400179 Score: 492
Period size: 78 Copynumber: 4.3 Consensus size: 78
28399835 AGAATTGCTG
* * * *
28399845 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAATAATGATCTGCCTCAATCTCGGGGCAAGAGA
1 ATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGGGGCAAGAGA
28399910 TCAAATGGTTGCA
66 TCAAATGGTTGCA
28399923 ATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGGGGCAAGAGA
1 ATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGGGGCAAGAGA
28399988 TCAAATGGTTGCA
66 TCAAATGGTTGCA
* *
28400001 ATCTGCCCCAGGCTT-GGGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGGGGTAAAAGA
1 ATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGGGGCAAGAGA
*
28400065 TCGAATGGTTGCA
66 TCAAATGGTTGCA
* * * * * * **
28400078 ATCTGTCCCAAGCTTGGGGTAAGAGATTTGTTGATGGTAATCTGCCCCAAGCTCGGGATAAGAGA
1 ATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGGGGCAAGAGA
* * *
28400143 TCGAACGGCTGCA
66 TCAAATGGTTGCA
*
28400156 ATCTGCCCCAGGCTCGGGGTAAGA
1 ATCTGCCCCAGGCTTGGGGTAAGA
28400180 TCGAACGGCT
Statistics
Matches: 236, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
77 72 0.31
78 164 0.69
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (78 bp):
ATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGGGGCAAGAGA
TCAAATGGTTGCA
Found at i:28400055 original size:155 final size:156
Alignment explanation
Indices: 28399845--28400179 Score: 501
Period size: 155 Copynumber: 2.2 Consensus size: 156
28399835 AGAATTGCTG
* *
28399845 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAATAATGATCTGCCTCAATCTCGGGGCAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAATAATGATCTGCCCCAATCTCGGGGCAAAAGA
* * *
28399910 TCAAATGGTTGCAATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAATC
66 TCAAATGGTTGCAATCTGCCCCAAGCTTGGGGTAAGAGATTTGCTGATGATAATCTGCCCCAAGC
* * *
28399975 TCGGGGCAAGAGATCAAATGGTTGCA
131 TCGGGACAAGAGATCAAACGGCTGCA
* * * *
28400001 ATCTGCCCCAGGCT-TGGGTAAGAGATTTGCTGATGATGATCTGCCCCAATCTCGGGGTAAAAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAATAATGATCTGCCCCAATCTCGGGGCAAAAGA
* * * *
28400065 TCGAATGGTTGCAATCTGTCCCAAGCTTGGGGTAAGAGATTTGTTGATGGTAATCTGCCCCAAGC
66 TCAAATGGTTGCAATCTGCCCCAAGCTTGGGGTAAGAGATTTGCTGATGATAATCTGCCCCAAGC
* *
28400130 TCGGGATAAGAGATCGAACGGCTGCA
131 TCGGGACAAGAGATCAAACGGCTGCA
28400156 ATCTGCCCCAGGCTCGGGGTAAGA
1 ATCTGCCCCAGGCTCGGGGTAAGA
28400180 TCGAACGGCT
Statistics
Matches: 159, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
155 137 0.86
156 22 0.14
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (156 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTAATAATGATCTGCCCCAATCTCGGGGCAAAAGA
TCAAATGGTTGCAATCTGCCCCAAGCTTGGGGTAAGAGATTTGCTGATGATAATCTGCCCCAAGC
TCGGGACAAGAGATCAAACGGCTGCA
Found at i:28400190 original size:37 final size:37
Alignment explanation
Indices: 28400116--28400216 Score: 166
Period size: 37 Copynumber: 2.7 Consensus size: 37
28400106 TGTTGATGGT
* *
28400116 AATCTGCCCCAAGCTCGGGATAAGAGATCGAACGGCTGC
1 AATCTGCCCCAGGCTCGGGGT-A-AGATCGAACGGCTGC
28400155 AATCTGCCCCAGGCTCGGGGTAAGATCGAACGGCTGC
1 AATCTGCCCCAGGCTCGGGGTAAGATCGAACGGCTGC
28400192 AATCTGCCCCAGGCTCGGGGTAAGA
1 AATCTGCCCCAGGCTCGGGGTAAGA
28400217 GATTGGCTGA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
37 40 0.67
38 1 0.02
39 19 0.32
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.16
Consensus pattern (37 bp):
AATCTGCCCCAGGCTCGGGGTAAGATCGAACGGCTGC
Found at i:28402533 original size:3 final size:3
Alignment explanation
Indices: 28402525--28402566 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
28402515 GATCATCCCT
* * *
28402525 TTC TTC TTC TTT TTC TTT TTC TTC TTT TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
28402567 AATATCATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:28402548 original size:15 final size:15
Alignment explanation
Indices: 28402523--28402565 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
28402513 GCGATCATCC
28402523 CTTTCTTCTTCTTTTT
1 CTTT-TTCTTCTTTTT
28402539 CTTTTTCTTCTTTTT
1 CTTTTTCTTCTTTTT
*
28402554 CTTCTTCTTCTT
1 CTTTTTCTTCTT
28402566 CAATATCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTTCTTCTTTTT
Found at i:28411985 original size:14 final size:14
Alignment explanation
Indices: 28411966--28412013 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
28411956 AATAATGAAC
28411966 AAATATACAAAAAT
1 AAATATACAAAAAT
*
28411980 AAATATGAGAAAAAT
1 AAATAT-ACAAAAAT
28411995 AAA-ATACGAAAAAAT
1 AAATATAC--AAAAAT
28412010 AAAT
1 AAAT
28412014 GAGAAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 8 0.29
15 19 0.68
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (14 bp):
AAATATACAAAAAT
Found at i:28412359 original size:30 final size:28
Alignment explanation
Indices: 28412186--28412455 Score: 141
Period size: 29 Copynumber: 9.2 Consensus size: 28
28412176 TAAAAACATG
* * *
28412186 ATTTTTGAAAGTTTAGAGGTAAAAATGTG
1 ATTTTTGGAAGTTTAG-GTTAAAAATGTA
* *
28412215 A-TTTTGGAAAAGTTTAAGAG-TCAAAATGTG
1 ATTTTTGG--AAGTTT-AG-GTTAAAAATGTA
* ** *
28412245 GTTTTTGGAAGTTCGGGGCTAAAAATGTA
1 ATTTTTGGAAGTT-TAGGTTAAAAATGTA
* * * *
28412274 ATTTTTGAAAGTTCGAGGCTAAAAATGTG
1 ATTTTTGGAAGTT-TAGGTTAAAAATGTA
*
28412303 ATTTTT-GATGTTTAGGTTAAAAATGTA
1 ATTTTTGGAAGTTTAGGTTAAAAATGTA
* * *
28412330 TTTTTTGAGAAGTTTAAGGTTTAACATGTA
1 ATTTTTG-GAAGTTT-AGGTTAAAAATGTA
* ***
28412360 ATTTTTGGAAGTTTGGGGGCAAAATGTAA
1 ATTTTTGGAAGTTTAGGTTAAAAATGT-A
** *
28412389 ATTTTTGGAAGTTCGGGGGGTAAAAATGTA
1 ATTTTTGGAAGTT--TAGGTTAAAAATGTA
* * **
28412419 TTTTTTGTGAAATTTAGGGGCAAAAATGTA
1 ATTTTTG-GAAGTTTA-GGTTAAAAATGTA
28412449 ATTTTTG
1 ATTTTTG
28412456 AGTTTGAGAG
Statistics
Matches: 192, Mismatches: 35, Indels: 27
0.76 0.14 0.11
Matches are distributed among these distances:
27 17 0.09
28 18 0.09
29 73 0.38
30 58 0.30
31 26 0.14
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (28 bp):
ATTTTTGGAAGTTTAGGTTAAAAATGTA
Found at i:28412365 original size:115 final size:118
Alignment explanation
Indices: 28412184--28412484 Score: 286
Period size: 115 Copynumber: 2.6 Consensus size: 118
28412174 GGTAAAAACA
**
28412184 TGATTTTTGAAAGTTTAGAGGTAAAAATGTGATTTTGGAAAAGTTTAAGAGTCAAAATGTGGTTT
1 TGATTTTTGAAAGTTTAGAGGTAAAAATGTGATTTTGGAAAAGTTTAAGAGTCAAAATGTAATTT
28412249 TTGGAAG-TTCGGGGCTAAAAATGT-AATTTTTGAAAGTTC-GAGGCTAAAAATG
66 TTGGAAGTTTCGGGGC--AAAATGTAAATTTTTGAAAGTTCGGAGGCTAAAAATG
* * * * * *
28412301 TGATTTTTG-ATGTTTAG-GTTAAAAATGT-ATTTTTTGAGAAGTTTAAG-GTTTAACATGTAAT
1 TGATTTTTGAAAGTTTAGAGGTAAAAATGTGA-TTTTGGAAAAGTTTAAGAG-TCAAAATGTAAT
* * * *
28412362 TTTTGGAAGTTTGGGGGCAAAATGTAAATTTTTGGAAGTTCGGGGGGTAAAAATG
64 TTTTGGAAGTTTCGGGGCAAAATGTAAATTTTTGAAAGTTCGGAGGCTAAAAATG
* * * * * *
28412417 T-ATTTTTTGTGAAA-TTTAGGGGCAAAAATGTAATTTTTG---AGTTTGAGAGTCAAAATGTGA
1 TGA--TTTT-TGAAAGTTTAGAGGTAAAAATGTGATTTTGGAAAAGTTTAAGAGTCAAAATGTAA
28412477 -TTTTGGAA
63 TTTTTGGAA
28412485 AAGTGTCAGG
Statistics
Matches: 153, Mismatches: 19, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
114 9 0.06
115 65 0.42
116 41 0.27
117 14 0.09
118 7 0.05
119 16 0.10
120 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.39
Consensus pattern (118 bp):
TGATTTTTGAAAGTTTAGAGGTAAAAATGTGATTTTGGAAAAGTTTAAGAGTCAAAATGTAATTT
TTGGAAGTTTCGGGGCAAAATGTAAATTTTTGAAAGTTCGGAGGCTAAAAATG
Found at i:28412391 original size:29 final size:28
Alignment explanation
Indices: 28412236--28412484 Score: 114
Period size: 29 Copynumber: 8.7 Consensus size: 28
28412226 GTTTAAGAGT
** *
28412236 CAAAATGTGGTTTTTGGAAG-TTCGGGG
1 CAAAATGTAATTTTTGGAAGTTTGGGGG
* * *
28412263 CTAAAAATGTAATTTTTGAAAG-TTCGAGG
1 C--AAAATGTAATTTTTGGAAGTTTGGGGG
* * * **
28412292 CTAAAAATGTGATTTTT-GATGTTTAGGTT
1 C--AAAATGTAATTTTTGGAAGTTTGGGGG
* * * **
28412321 AAAAATGTATTTTTTGAGAAGTTTAAGGTT
1 CAAAATGTAATTTTTG-GAAGTTT-GGGGG
* *
28412351 TAACATGTAATTTTTGGAAGTTTGGGGG
1 CAAAATGTAATTTTTGGAAGTTTGGGGG
*
28412379 CAAAATGTAAATTTTTGGAAGTTCGGGGGG
1 CAAAATGT-AATTTTTGGAAGTT-TGGGGG
* * * *
28412409 TAAAAATGTATTTTTTGTGAAATTTAGGGG
1 -CAAAATGTAATTTTTG-GAAGTTTGGGGG
* *
28412439 CAAAAATGTAATTTTT-G-AGTTTGAGAGT
1 C-AAAATGTAATTTTTGGAAGTTTG-GGGG
*
28412467 CAAAATGTGA-TTTTGGAA
1 CAAAATGTAATTTTTGGAA
28412485 AAGTGTCAGG
Statistics
Matches: 172, Mismatches: 36, Indels: 27
0.73 0.15 0.11
Matches are distributed among these distances:
26 4 0.02
27 26 0.15
28 15 0.09
29 68 0.40
30 47 0.27
31 12 0.07
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.39
Consensus pattern (28 bp):
CAAAATGTAATTTTTGGAAGTTTGGGGG
Found at i:28413671 original size:18 final size:19
Alignment explanation
Indices: 28413641--28413689 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
28413631 GCGTTTAGAA
28413641 ATAATAAATAATAATGGTAAT
1 ATAATAAATAAT-A-GGTAAT
28413662 ATAATAAATAAATAGGT-AT
1 ATAATAAAT-AATAGGTAAT
28413681 -TAATAAATA
1 ATAATAAATA
28413690 TATGCAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 8 0.30
19 2 0.07
20 3 0.11
21 10 0.37
22 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
ATAATAAATAATAGGTAAT
Found at i:28416864 original size:52 final size:52
Alignment explanation
Indices: 28416780--28417019 Score: 345
Period size: 52 Copynumber: 4.6 Consensus size: 52
28416770 GTAAATGAAA
* * * *
28416780 GAGGTCTGATGACTATGTGTCATCATGCGTATATGAATCCTTTATGGATTAT
1 GAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* *
28416832 GAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTATGGATTAT
1 GAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* *
28416884 GAGGTCCGATGACTATGTGTCATCGAGAGTATATGAATCCCTTACGGATTAT
1 GAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * *
28416936 GAGGTCCGATGACTAAGTGTCATCGTGAGTATATGATTCCTTTACGGATGAA
1 GAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
28416988 GAGGTCCGATGACTATATGTCATTGTGGGTAT
1 GAGGTCCGATGACTATGTGTCATCGTGAGTAT
28417020 TAAATGAAAT
Statistics
Matches: 170, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 170 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (52 bp):
GAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:28426364 original size:10 final size:10
Alignment explanation
Indices: 28426334--28426373 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
28426324 GTATTGAGGT
28426334 AGAAGAAAAA
1 AGAAGAAAAA
28426344 A-AAGAAGAAA
1 AGAAGAA-AAA
28426354 AGGAAGAAAAA
1 A-GAAGAAAAA
28426365 AGAAGAAAA
1 AGAAGAAAA
28426374 CGTTGCCCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.19
10 13 0.48
11 4 0.15
12 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
AGAAGAAAAA
Found at i:28428546 original size:21 final size:22
Alignment explanation
Indices: 28428522--28428573 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 22
28428512 TCAATTCATC
*
28428522 TTTTATTAATTTGCTCTGACAT
1 TTTTATTAATTTGCACTGACAT
28428544 TTTATATTACATTTGCACTGACAT
1 TTT-TATTA-ATTTGCACTGACAT
28428568 ATTTTA
1 -TTTTA
28428574 ATCTTAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 3 0.12
23 5 0.19
24 15 0.58
25 3 0.12
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (22 bp):
TTTTATTAATTTGCACTGACAT
Found at i:28431665 original size:32 final size:32
Alignment explanation
Indices: 28431629--28431692 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
28431619 AGAGTAAGAA
28431629 CTTTTGGCTCCTATTCATTTAGCTTTACTGCT
1 CTTTTGGCTCCTATTCATTTAGCTTTACTGCT
28431661 CTTTTGGCTCCTATTCATTTAGCTTTACTGCT
1 CTTTTGGCTCCTATTCATTTAGCTTTACTGCT
28431693 TCTTCTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.50
Consensus pattern (32 bp):
CTTTTGGCTCCTATTCATTTAGCTTTACTGCT
Found at i:28441985 original size:20 final size:21
Alignment explanation
Indices: 28441948--28441986 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28441938 ACATTTTTTC
* *
28441948 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTATTTCACT
28441969 TTTACTTTT-GTTATTTCA
1 TTTACTTTTAGTTATTTCA
28441987 AATTCCTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTATTTCACT
Found at i:28442636 original size:28 final size:28
Alignment explanation
Indices: 28442595--28442648 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
28442585 TCGTACCATA
* *
28442595 AGCAGCCTTGGGTAGGAATTATTTTGCG
1 AGCAGCCTTAGGTAGAAATTATTTTGCG
*
28442623 AGCAGCCTTAGGTAGAAATTCTTTTG
1 AGCAGCCTTAGGTAGAAATTATTTTG
28442649 TGAACACCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (28 bp):
AGCAGCCTTAGGTAGAAATTATTTTGCG
Found at i:28442659 original size:28 final size:28
Alignment explanation
Indices: 28442600--28442659 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
28442590 CCATAAGCAG
* * * *
28442600 CCTTGGGTAGGAATTATTTTGCGAGCAG
1 CCTTAGGTAGAAATTATTTTGCGAACAC
* *
28442628 CCTTAGGTAGAAATTCTTTTGTGAACAC
1 CCTTAGGTAGAAATTATTTTGCGAACAC
28442656 CCTT
1 CCTT
28442660 CTGGTTTCTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (28 bp):
CCTTAGGTAGAAATTATTTTGCGAACAC
Found at i:28450752 original size:4 final size:4
Alignment explanation
Indices: 28450743--28450771 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
28450733 TTTACATCTA
28450743 TATC TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC TATC T
28450772 GTCTTGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:28451191 original size:21 final size:21
Alignment explanation
Indices: 28451167--28451206 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28451157 TTTGGTTTAA
28451167 TTTTTTTATATTAATTTTAGG
1 TTTTTTTATATTAATTTTAGG
* *
28451188 TTTTTTTATTTTTATTTTA
1 TTTTTTTATATTAATTTTA
28451207 ATACAATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (21 bp):
TTTTTTTATATTAATTTTAGG
Found at i:28464011 original size:69 final size:69
Alignment explanation
Indices: 28463895--28464025 Score: 190
Period size: 69 Copynumber: 1.9 Consensus size: 69
28463885 GGCCAATACT
* * * * *
28463895 CCTAGTGGGCCGATTATGAGGAGTGGATTTAATTCACCCAGTGCAAATTATATGGAATATGGCAA
1 CCTAGTGGACCGATTATGAGGAGTGGATTTAATCCACCAAATACAAATTATATGGAATATGGCAA
28463960 CAAG
66 CAAG
* * *
28463964 CCTAGTGGATCGATTGTGAGGAGTGGATTTAATCCACCAAATACAAATTATGTGGAATATGG
1 CCTAGTGGACCGATTATGAGGAGTGGATTTAATCCACCAAATACAAATTATATGGAATATGG
28464026 TAGAGTTACA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (69 bp):
CCTAGTGGACCGATTATGAGGAGTGGATTTAATCCACCAAATACAAATTATATGGAATATGGCAA
CAAG
Found at i:28467250 original size:69 final size:69
Alignment explanation
Indices: 28467135--28467283 Score: 273
Period size: 69 Copynumber: 2.2 Consensus size: 69
28467125 AGAAACAGCA
*
28467135 GGTT-GTGTCTCGATCGATAGTTGAAGCTGAATATCGAGGGTTGGCTACTGCAACTGTGGATGTT
1 GGTTAGTGTCTCGATCGACAGTTGAAGCTGAATATCGAGGGTTGGCTACTGCAACTGTGGATGTT
28467199 ACAT
66 ACAT
*
28467203 GGTTAGTGTCTCGATCGACAGTTGAGGCTGAATATCGAGGGTTGGCTACTGCAACTGTGGATGTT
1 GGTTAGTGTCTCGATCGACAGTTGAAGCTGAATATCGAGGGTTGGCTACTGCAACTGTGGATGTT
28467268 ACAT
66 ACAT
28467272 GGTTAGTGTCTC
1 GGTTAGTGTCTC
28467284 TTTTGAGTGA
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
68 4 0.05
69 74 0.95
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.32
Consensus pattern (69 bp):
GGTTAGTGTCTCGATCGACAGTTGAAGCTGAATATCGAGGGTTGGCTACTGCAACTGTGGATGTT
ACAT
Found at i:28475802 original size:17 final size:17
Alignment explanation
Indices: 28475780--28475813 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28475770 TAAGTGGATG
28475780 TCTAACTCCTTTAAACC
1 TCTAACTCCTTTAAACC
*
28475797 TCTAACTTCTTTAAACC
1 TCTAACTCCTTTAAACC
28475814 CTCGTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (17 bp):
TCTAACTCCTTTAAACC
Found at i:28481386 original size:17 final size:17
Alignment explanation
Indices: 28481364--28481397 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28481354 TAAGTGAATG
28481364 TCTAACTCCTTTAAACC
1 TCTAACTCCTTTAAACC
28481381 TCTAACTCCTTTAAACC
1 TCTAACTCCTTTAAACC
28481398 CTCATTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (17 bp):
TCTAACTCCTTTAAACC
Found at i:28489589 original size:14 final size:14
Alignment explanation
Indices: 28489570--28489596 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28489560 GATAGTTAAG
28489570 ATATTTTTTTAAAC
1 ATATTTTTTTAAAC
28489584 ATATTTTTTTAAA
1 ATATTTTTTTAAA
28489597 ATTGTATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTTTTTTAAAC
Found at i:28498615 original size:20 final size:20
Alignment explanation
Indices: 28498590--28498655 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
28498580 TGAATCAATT
28498590 TTTTATTTATTAAAATGGGG
1 TTTTATTTATTAAAATGGGG
*** *
28498610 TTTTATTTATTAGTTTGGAG
1 TTTTATTTATTAAAATGGGG
*
28498630 -TTTATTTATAAAAATGGGG
1 TTTTATTTATTAAAATGGGG
28498649 TTTTATT
1 TTTTATT
28498656 AATTCATCCC
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 14 0.39
20 22 0.61
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTTATTTATTAAAATGGGG
Found at i:28498651 original size:19 final size:19
Alignment explanation
Indices: 28498591--28498651 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
28498581 GAATCAATTT
28498591 TTTATTTATTAAAATGGGG
1 TTTATTTATTAAAATGGGG
*** *
28498610 TTTTATTTATTAGTTTGGAG
1 -TTTATTTATTAAAATGGGG
*
28498630 TTTATTTATAAAAATGGGG
1 TTTATTTATTAAAATGGGG
28498649 TTT
1 TTT
28498652 TATTAATTCA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (19 bp):
TTTATTTATTAAAATGGGG
Found at i:28500457 original size:17 final size:17
Alignment explanation
Indices: 28500401--28500459 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
28500391 AAAATTATTA
28500401 AAAATATT-TTTTGAAAT
1 AAAATATTATTTT-AAAT
*
28500418 AAAA-ATTA-TTAAAATT
1 AAAATATTATTTTAAA-T
**
28500434 ATTATATTATTTTAAAT
1 AAAATATTATTTTAAAT
28500451 AAAATATTA
1 AAAATATTA
28500460 AAATTATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 3 0.09
16 8 0.25
17 16 0.50
18 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AAAATATTATTTTAAAT
Found at i:28500462 original size:31 final size:33
Alignment explanation
Indices: 28500404--28500468 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 33
28500394 ATTATTAAAA
28500404 ATATTTTTTGAAATAAAAATTATTAAAATTATT
1 ATATTTTTTGAAATAAAAATTATTAAAATTATT
28500437 ATATTATTTT-AAAT-AAAA-TATTAAAATTATT
1 ATATT-TTTTGAAATAAAAATTATTAAAATTATT
28500468 A
1 A
28500469 AATCTATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 14 0.45
32 4 0.13
33 9 0.29
34 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (33 bp):
ATATTTTTTGAAATAAAAATTATTAAAATTATT
Found at i:28503831 original size:61 final size:59
Alignment explanation
Indices: 28503756--28503951 Score: 173
Period size: 61 Copynumber: 3.3 Consensus size: 59
28503746 GTAATTTGGT
* * * *
28503756 AATTTTTGAAAGTTTCGGGGTCAAAATTGGAATTTTAT-TAAGTTCGGGGGAGTAAAAATAG
1 AATTTTTGGAAGTTTTGGGGTCAAAATTGGAATTTT-TGAAAGTT-GGAGG-GTAAAAATAG
** * * *
28503817 AATTTTTGGAAGTTTTAAGGTTAAAATTGGAATTTTTGAAAGTTTGAGGGTAAAAATAT
1 AATTTTTGGAAGTTTTGGGGTCAAAATTGGAATTTTTGAAAGTTGGAGGGTAAAAATAG
* * * * *
28503876 AATTTTTGGAAGTTTTGGGGTTTAAAA-TGTAATTTTGGAGAAGTTCGAGGTTAAAATATA-
1 AATTTTTGGAAGTTTTGGGG-TCAAAATTGGAATTTTTGA-AAGTTGGAGGGTAAAA-ATAG
*
28503936 TATTTTTGGACAGTTT
1 AATTTTTGGA-AGTTT
28503952 AAGGACTTAC
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
59 37 0.32
60 33 0.29
61 44 0.39
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.40
Consensus pattern (59 bp):
AATTTTTGGAAGTTTTGGGGTCAAAATTGGAATTTTTGAAAGTTGGAGGGTAAAAATAG
Found at i:28503891 original size:59 final size:59
Alignment explanation
Indices: 28503807--28503955 Score: 178
Period size: 59 Copynumber: 2.5 Consensus size: 59
28503797 GTTCGGGGGA
* * *
28503807 GTAAAAATAGAATTTTTGGAAGTTTTAAGG-TTAAAATTGGAATTTTTGA-AAGTTTGAGG
1 GTAAAAATATAATTTTTGGAAGTTTTAAGGTTTAAAA-TGGAATTTTGGAGAAGTTCGA-G
** *
28503866 GTAAAAATATAATTTTTGGAAGTTTTGGGGTTTAAAATGTAATTTTGGAGAAGTTCGAG
1 GTAAAAATATAATTTTTGGAAGTTTTAAGGTTTAAAATGGAATTTTGGAGAAGTTCGAG
*
28503925 GTTAAAATATATATTTTTGGACAG-TTTAAGG
1 GTAAAAATATA-ATTTTTGGA-AGTTTTAAGG
28503956 ACTTACAGGG
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
59 48 0.62
60 27 0.35
61 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.40
Consensus pattern (59 bp):
GTAAAAATATAATTTTTGGAAGTTTTAAGGTTTAAAATGGAATTTTGGAGAAGTTCGAG
Found at i:28503909 original size:30 final size:29
Alignment explanation
Indices: 28503810--28503951 Score: 128
Period size: 30 Copynumber: 4.8 Consensus size: 29
28503800 CGGGGGAGTA
* *
28503810 AAAATAGAATTTTTGGAAGTTTTAAGGTT
1 AAAATATAATTTTTGGAAGTTTTGAGGTT
* *
28503839 AAAAT-TGGAATTTTTGAAAG-TTTGAGGGTA
1 AAAATAT--AATTTTTGGAAGTTTTGA-GGTT
*
28503869 AAAATATAATTTTTGGAAGTTTTGGGGTTT
1 AAAATATAATTTTTGGAAGTTTTGAGG-TT
* * *
28503899 AAAATGTAATTTTGGAGAAG-TTCGAGGTT
1 AAAATATAATTTTTG-GAAGTTTTGAGGTT
28503928 AAAATATATATTTTTGGACAGTTT
1 AAAATATA-ATTTTTGGA-AGTTT
28503952 AAGGACTTAC
Statistics
Matches: 90, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
29 33 0.37
30 50 0.56
31 7 0.08
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (29 bp):
AAAATATAATTTTTGGAAGTTTTGAGGTT
Found at i:28504715 original size:19 final size:20
Alignment explanation
Indices: 28504673--28504709 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
28504663 TTTTCTTTCT
*
28504673 TTTTTTCATCTTAAAAACCC
1 TTTTTTCATCTTAAAAAACC
28504693 TTTTTTC-TCTTAAAAAA
1 TTTTTTCATCTTAAAAAA
28504710 GGTTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTTTCATCTTAAAAAACC
Found at i:28505032 original size:3 final size:3
Alignment explanation
Indices: 28505024--28505120 Score: 99
Period size: 3 Copynumber: 32.7 Consensus size: 3
28505014 ATTTATTAAA
* * *
28505024 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT T-T TAGT CAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * ** *
28505069 TAT TAA TGT CGT TA- TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28505116 TAT TA
1 TAT TA
28505121 CCAATATCAA
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
2 4 0.05
3 71 0.92
4 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:28506169 original size:39 final size:39
Alignment explanation
Indices: 28506125--28506267 Score: 220
Period size: 39 Copynumber: 3.7 Consensus size: 39
28506115 TAAATAAAGT
* *
28506125 TTAAAAGTTGAAATTAAATAAAATGAAAATGTAATTTAA
1 TTAAAAGTTGAAATTAAATGAAATGAAAATGAAATTTAA
* *
28506164 TTAAAAGTTGAAATTAAATGAAATGAAAATGAAAATGAA
1 TTAAAAGTTGAAATTAAATGAAATGAAAATGAAATTTAA
28506203 TTAAAAGTTGAAATT--ATGAAATGAAAATGAAATTTAA
1 TTAAAAGTTGAAATTAAATGAAATGAAAATGAAATTTAA
28506240 TTAAAAGTTGAAATTGAAAT-AAATGAAA
1 TTAAAAGTTGAAATT-AAATGAAATGAAA
28506268 TTCAAATGAA
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
37 35 0.37
39 58 0.61
40 2 0.02
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (39 bp):
TTAAAAGTTGAAATTAAATGAAATGAAAATGAAATTTAA
Found at i:28506237 original size:76 final size:77
Alignment explanation
Indices: 28506124--28506284 Score: 238
Period size: 76 Copynumber: 2.1 Consensus size: 77
28506114 TTAAATAAAG
*
28506124 TTTAAAAGTTGAAATTAAATAAAATGAAAATGTAATTTAATTAAAAGTTGAAATT-AAATGAAAT
1 TTTAAAAGTTGAAATT-AATAAAATGAAAATGAAATTTAATTAAAAGTTGAAATTGAAAT-AAAT
28506188 GAAAATGAAAATGAA
64 G-AAATGAAAATGAA
*
28506203 -TTAAAAGTTGAAATT-ATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATTGAAATAAATGA
1 TTTAAAAGTTGAAATTAATAAAATGAAAATGAAATTTAATTAAAAGTTGAAATTGAAATAAATGA
**
28506266 AATTCAAATGAA
66 AATGAAAATGAA
28506278 TTTAAAA
1 TTTAAAA
28506285 AAACATAGGG
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
75 11 0.14
76 46 0.61
77 4 0.05
78 15 0.20
ACGTcount: A:0.56, C:0.01, G:0.12, T:0.31
Consensus pattern (77 bp):
TTTAAAAGTTGAAATTAATAAAATGAAAATGAAATTTAATTAAAAGTTGAAATTGAAATAAATGA
AATGAAAATGAA
Found at i:28506283 original size:39 final size:38
Alignment explanation
Indices: 28506125--28506284 Score: 184
Period size: 39 Copynumber: 4.2 Consensus size: 38
28506115 TAAATAAAGT
* * *
28506125 TTAAAAGTTGAAATTAAATAAAATGAAAATGTAATTTAA
1 TTAAAAGTTGAAATTAAATGAAATGAAAAT-TAAATGAA
*
28506164 TTAAAAGTTGAAATTAAATGAAATGAAAATGAAAATGAA
1 TTAAAAGTTGAAATTAAATGAAATGAAAAT-TAAATGAA
* *
28506203 TTAAAAGTTGAAATT--ATGAAATGAAAATGAAATTTAA
1 TTAAAAGTTGAAATTAAATGAAATGAAAATTAAA-TGAA
28506240 TTAAAAGTTGAAATTGAAAT-AAATG-AAATTCAAATGAA
1 TTAAAAGTTGAAATT-AAATGAAATGAAAATT-AAATGAA
28506278 TTTAAAA
1 -TTAAAA
28506285 AAACATAGGG
Statistics
Matches: 107, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
36 3 0.03
37 31 0.29
38 7 0.07
39 64 0.60
40 2 0.02
ACGTcount: A:0.56, C:0.01, G:0.12, T:0.31
Consensus pattern (38 bp):
TTAAAAGTTGAAATTAAATGAAATGAAAATTAAATGAA
Found at i:28506640 original size:23 final size:23
Alignment explanation
Indices: 28506589--28506637 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
28506579 AATTATTATT
* *
28506589 TGAATTGAAATTAAAAGTTGAAT
1 TGAATTGAAATTAAAAGTTCAAA
*
28506612 TGAATTGAAATTCAAA-TTCAAA
1 TGAATTGAAATTAAAAGTTCAAA
28506634 TGAA
1 TGAA
28506638 ATTCCCATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (23 bp):
TGAATTGAAATTAAAAGTTCAAA
Found at i:28506987 original size:17 final size:16
Alignment explanation
Indices: 28506967--28507000 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28506957 ATATTTAATT
*
28506967 TAAAATTTGAATTGAAA
1 TAAAATTT-AAATGAAA
28506984 TAAAATTTAAATGAAA
1 TAAAATTTAAATGAAA
28507000 T
1 T
28507001 TTAATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
TAAAATTTAAATGAAA
Found at i:28507074 original size:16 final size:15
Alignment explanation
Indices: 28507026--28507067 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
28507016 ATAAGTTAAC
28507026 TAATTTAAAAACAAAT
1 TAATTTAAAAA-AAAT
28507042 TAATTTGAAAAAAAAT
1 TAATTT-AAAAAAAAT
28507058 T-ATTTAAAAA
1 TAATTTAAAAA
28507068 GTAAATTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 11 0.44
17 5 0.20
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
TAATTTAAAAAAAAT
Found at i:28508295 original size:20 final size:22
Alignment explanation
Indices: 28508246--28508296 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 22
28508236 TCAATTAATA
28508246 TGTCTTAATTAATTTAAATTCTAT
1 TGTCTTAA--AATTTAAATTCTAT
28508270 T-T-TTAAAATTT-AATT-TAT
1 TGTCTTAAAATTTAAATTCTAT
28508288 TGTCTTAAA
1 TGTCTTAAA
28508297 TTGATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 4 0.16
19 5 0.20
20 10 0.40
22 4 0.16
23 1 0.04
24 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (22 bp):
TGTCTTAAAATTTAAATTCTAT
Found at i:28510332 original size:17 final size:19
Alignment explanation
Indices: 28510300--28510337 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28510290 TTAAATTTTA
28510300 TTAAATATTATTTTT-ATT
1 TTAAATATTATTTTTAATT
*
28510318 TTAATTATT-TTTTTAATT
1 TTAAATATTATTTTTAATT
28510336 TT
1 TT
28510338 TTAGATGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTAAATATTATTTTTAATT
Found at i:28510471 original size:19 final size:19
Alignment explanation
Indices: 28510444--28510495 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
28510434 TTTTCGAATT
*
28510444 TTTTAAAATATTTTTT-TA
1 TTTTCAAATATTTTTTATA
28510462 TTTTCGAAATATTTTTTATA
1 TTTTC-AAATATTTTTTATA
28510482 TTTTCAAAT-TTTTT
1 TTTTCAAATATTTTT
28510496 AAATAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 9 0.29
19 15 0.48
20 7 0.23
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTCAAATATTTTTTATA
Found at i:28510530 original size:11 final size:11
Alignment explanation
Indices: 28510441--28510548 Score: 51
Period size: 8 Copynumber: 10.5 Consensus size: 11
28510431 ATATTTTCGA
28510441 ATTTTTTAAAAT
1 ATTTTTT-AAAT
28510453 ATTTTTT---T
1 ATTTTTTAAAT
**
28510461 ATTTTCGAAAT
1 ATTTTTTAAAT
28510472 ATTTTTT--AT
1 ATTTTTTAAAT
*
28510481 A--TTTTCAA-
1 ATTTTTTAAAT
28510489 ATTTTTTAAAT
1 ATTTTTTAAAT
28510500 AATATTTTTGAAAT
1 -AT-TTTTT-AAAT
*
28510514 ACTTTTTTACAT
1 A-TTTTTTAAAT
28510526 ATTTTTT---T
1 ATTTTTTAAAT
28510534 ATTTTTTAAAT
1 ATTTTTTAAAT
28510545 -TTTT
1 ATTTT
28510549 AAAAAAATAT
Statistics
Matches: 75, Mismatches: 6, Indels: 32
0.66 0.05 0.28
Matches are distributed among these distances:
7 4 0.05
8 15 0.20
9 4 0.05
10 10 0.13
11 13 0.17
12 13 0.17
13 11 0.15
14 5 0.07
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (11 bp):
ATTTTTTAAAT
Found at i:28510634 original size:13 final size:13
Alignment explanation
Indices: 28510616--28510640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28510606 GAAATATTAA
28510616 AAATATTTTTTTG
1 AAATATTTTTTTG
28510629 AAATATTTTTTT
1 AAATATTTTTTT
28510641 ACAAATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
AAATATTTTTTTG
Found at i:28512145 original size:29 final size:30
Alignment explanation
Indices: 28512102--28512220 Score: 165
Period size: 30 Copynumber: 4.1 Consensus size: 30
28512092 ATTTTAATTT
* *
28512102 TTTCGTTTATTTTTTAAATTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
28512132 TTTCG-TTATATTTTAAATTTAATTT-TAAA
1 TTTCGTTTATATTTTAAATTTAATTTCT-AA
28512161 TTTCGTTTATATTTTAAATTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
* *
28512191 TTTCG-TTATA-TTTAATTTTCATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
28512219 TT
1 TT
28512221 ATTATTTTTT
Statistics
Matches: 83, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
28 19 0.23
29 31 0.37
30 32 0.39
31 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTCTAA
Found at i:28513164 original size:55 final size:56
Alignment explanation
Indices: 28513089--28513709 Score: 475
Period size: 55 Copynumber: 10.9 Consensus size: 56
28513079 AAAAAAAATT
* ** *
28513089 ATTTTTTTATCAGATATAAAAAAGGTAATGT-GGCTAAGCATTGGCCAACACCAAAAA
1 ATTTTTTTATCTG--ATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAA
* * *
28513146 ATTTTTTTATCTGATAAAAAAGATGGTGTCGACCAATGCA-TGGTCAACACCAAAAAAA
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAA-GCATTGGCCAACACC--AAAAA
* * *
28513204 TTTATTTTTTTATCTGAGAAAAAAAGTGGTG-CGACCAAGCATTGGCCAACACCAAAAAA
1 ---ATTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACC-AAAAA
* * **
28513263 ATTATTTTTTATCTGATAAAAAAAGTGGTGTTGATCAATGCA-TGGCCAACACCAAAAAAA
1 A-T-TTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAA-GCATTGGCCAACACC--AAAAA
* *
28513323 TTATTTTTTTAT-TAGATAAAAAAAGTGGTGTCGACC-AGACATTGGCCAACACCAAAAAA
1 --ATTTTTTTATCT-GATAAAAAAGGTGGTGTCGGCCAAG-CATTGGCCAACACC-AAAAA
* *
28513382 ATATTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACATCAAAAT
1 AT-TTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAA
* * * *
28513439 A-TTTTTTATCTGATAAAAAAAGTGGTGTCGGCCAAGCATTGGCTAACATCAAAAT
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAA
* * * * ** *
28513494 A-TTTTTTATTTGATAAAAAAGGTAGTGTCGACCAGGCATTGATCAACACTAAAAA
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAA
* * * * * *
28513549 ATTATTTTTTATCTGATTAAAAAGATAGTGTAGG-CAA-CAATTTGCTAACACC--AAA
1 A-T-TTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGC-ATTGGCCAACACCAAAAA
* * ** * ** *
28513604 TTTTTTTTATCTGATAAAAAATGCTGGTGTCAACCAATGC-GTGATCAACA-C--TAA
1 ATTTTTTTATCTGATAAAAAA-GGTGGTGTCGGCCAA-GCATTGGCCAACACCAAAAA
* * * *
28513658 TTTTTTTTATCTGAT-CAAAAGGTGGTGTCAGCCACGCATTGGCCAACACCAA
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCAA
28513710 TTTTTTTCAA
Statistics
Matches: 467, Mismatches: 64, Indels: 68
0.78 0.11 0.11
Matches are distributed among these distances:
51 2 0.00
52 19 0.04
53 23 0.05
54 25 0.05
55 121 0.26
56 16 0.03
57 34 0.07
58 97 0.21
59 38 0.08
60 65 0.14
61 26 0.06
62 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (56 bp):
ATTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCAAAAA
Found at i:28513289 original size:58 final size:59
Alignment explanation
Indices: 28513061--28513571 Score: 542
Period size: 55 Copynumber: 8.8 Consensus size: 59
28513051 TTGGTCTTGG
* * * ** *
28513061 CCAATGCA-TGGCTAACACAAAAAAAATTATTTTTTTATCAGATATAAAAAAGGTAATGT-GG
1 CCAA-GCATTGGCCAACACCAAAAAAATTA-TTTTTTATCTGATA-AAAAAA-GTGGTGTCGA
*
28513122 CTAAGCATTGGCCAACACC-AAAAAA-T-TTTTTTATCTGAT-AAAAAAGATGGTGTCGA
1 CCAAGCATTGGCCAACACCAAAAAAATTATTTTTTATCTGATAAAAAAAG-TGGTGTCGA
* *
28513178 CCAATGCA-TGGTCAACACCAAAAAAATTTATTTTTTTATCTGAGAAAAAAAGTGGTG-CGA
1 CCAA-GCATTGGCCAACACCAAAAAAA-TTA-TTTTTTATCTGATAAAAAAAGTGGTGTCGA
*
28513238 CCAAGCATTGGCCAACACCAAAAAAATTATTTTTTATCTGATAAAAAAAGTGGTGTTGA
1 CCAAGCATTGGCCAACACCAAAAAAATTATTTTTTATCTGATAAAAAAAGTGGTGTCGA
*
28513297 TCAATGCA-TGGCCAACACCAAAAAAATTATTTTTTTAT-TAGATAAAAAAAGTGGTGTCGA
1 CCAA-GCATTGGCCAACACCAAAAAAATTA-TTTTTTATCT-GATAAAAAAAGTGGTGTCGA
* *
28513357 CC-AGACATTGGCCAACACCAAAAAAA-TATTTTTTATCTGATAAAAAAGGTGGTGTCGG
1 CCAAG-CATTGGCCAACACCAAAAAAATTATTTTTTATCTGATAAAAAAAGTGGTGTCGA
* *
28513415 CCAAGCATTGGCCAACATC---AAAA-TATTTTTTATCTGATAAAAAAAGTGGTGTCGG
1 CCAAGCATTGGCCAACACCAAAAAAATTATTTTTTATCTGATAAAAAAAGTGGTGTCGA
* * * * *
28513470 CCAAGCATTGGCTAACATC---AAAA-TATTTTTTATTTGATAAAAAAGGTAGTGTCGA
1 CCAAGCATTGGCCAACACCAAAAAAATTATTTTTTATCTGATAAAAAAAGTGGTGTCGA
* ** * *
28513525 CCAGGCATTGATCAACA-CTAAAAAATTATTTTTTATCTGATTAAAAA
1 CCAAGCATTGGCCAACACCAAAAAAATTATTTTTTATCTGATAAAAAA
28513572 GATAGTGTAG
Statistics
Matches: 396, Mismatches: 31, Indels: 49
0.83 0.07 0.10
Matches are distributed among these distances:
54 2 0.01
55 108 0.27
56 14 0.04
57 25 0.06
58 86 0.22
59 43 0.11
60 82 0.21
61 29 0.07
62 7 0.02
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.30
Consensus pattern (59 bp):
CCAAGCATTGGCCAACACCAAAAAAATTATTTTTTATCTGATAAAAAAAGTGGTGTCGA
Found at i:28513634 original size:112 final size:112
Alignment explanation
Indices: 28513081--28513657 Score: 433
Period size: 118 Copynumber: 5.0 Consensus size: 112
28513071 GCTAACACAA
* * * * *
28513081 AAAAAATTATTTTTTTATCAGATATAAAAAAGGTAATGT-GGCTAAGCATTGGCCAACACCAAAA
1 AAAAAA-TA-TTTTTTATCTGATA-AAAAAA-GTAGTGTAGGCCAAGCATTGGCTAACATCAAAA
* * * *
28513145 AATTTTTTTATCTGATAAAAAAGATGGTGTCGACCAATGCA-TGGTCAACACCA
62 TA-TTTTTTATCTGATAAAAAAGGTGGTGTCGACCAA-GCATTGATCAACA-CT
* * * * * *
28513198 AAAAAATTTATTTTTTTATCTGAGAAAAAAAGTGGTG-CGACCAAGCATTGGCCAACACCAAAAA
1 AAAAAA--TA-TTTTTTATCTGATAAAAAAAGTAGTGTAGGCCAAGCATTGGCTAACATC---AA
* * * ** *
28513262 AATTATTTTTTATCTGATAAAAAAAGTGGTGTTGATCAATGCA-TGGCCAACACCA
60 AA-TATTTTTTATCTGATAAAAAAGGTGGTGTCGACCAA-GCATTGATCAACA-CT
* * * * *
28513317 AAAAAATTATTTTTTTAT-TAGATAAAAAAAGTGGTGTCGACC-AGACATTGGCCAACACCAAAA
1 AAAAAA-TA-TTTTTTATCT-GATAAAAAAAGTAGTGTAGGCCAAG-CATTGGCTAACATC---A
* **
28513380 AAATATTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACA-T
59 AAATATTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGATCAACACT
* * *
28513433 -CAAAATATTTTTTATCTGATAAAAAAAGTGGTGTCGGCCAAGCATTGGCTAACATCAAAATATT
1 AAAAAATATTTTTTATCTGATAAAAAAAGTAGTGTAGGCCAAGCATTGGCTAACATCAAAATATT
* * *
28513497 TTTTATTTGATAAAAAAGGTAGTGTCGACCAGGCATTGATCAACACT
66 TTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGATCAACACT
* * *
28513544 AAAAAATTATTTTTTATCTGAT-TAAAAAGATAGTGTAGG-CAA-CAATTTGCTAACA-CCAAAT
1 AAAAAA-TATTTTTTATCTGATAAAAAAAG-TAGTGTAGGCCAAGC-ATTGGCTAACATCAAAAT
* * * *
28513605 TTTTTTTATCTGATAAAAAATGCTGGTGTCAACCAATGC-GTGATCAACACT
63 ATTTTTTATCTGATAAAAAA-GGTGGTGTCGACCAA-GCATTGATCAACACT
28513656 AA
1 AA
28513658 TTTTTTTTAT
Statistics
Matches: 400, Mismatches: 41, Indels: 43
0.83 0.08 0.09
Matches are distributed among these distances:
110 47 0.12
111 25 0.06
112 47 0.12
113 65 0.16
114 5 0.01
115 4 0.01
116 23 0.06
117 16 0.04
118 86 0.22
119 81 0.20
120 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.30
Consensus pattern (112 bp):
AAAAAATATTTTTTATCTGATAAAAAAAGTAGTGTAGGCCAAGCATTGGCTAACATCAAAATATT
TTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGATCAACACT
Found at i:28517028 original size:17 final size:17
Alignment explanation
Indices: 28517006--28517041 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28516996 TATTCTTATT
28517006 ATTTAATTTAAAAATAA
1 ATTTAATTTAAAAATAA
* *
28517023 ATTTAATTTTAAGATAA
1 ATTTAATTTAAAAATAA
28517040 AT
1 AT
28517042 CCAAACTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTTAATTTAAAAATAA
Found at i:28519476 original size:23 final size:22
Alignment explanation
Indices: 28519450--28519550 Score: 121
Period size: 23 Copynumber: 4.4 Consensus size: 22
28519440 ATTAGCGTGT
28519450 TTACTGTTTAGCACTGTGTGTGC
1 TTACTGTTT-GCACTGTGTGTGC
* *
28519473 TTACTGATTTGCATTGTGTGTAC
1 TTACTG-TTTGCACTGTGTGTGC
*
28519496 TTACTGTTTTGTACTGTGTGTGC
1 TTACTG-TTTGCACTGTGTGTGC
* *
28519519 CTACTGATTTGCATTGTGTGTGC
1 TTACTG-TTTGCACTGTGTGTGC
28519542 TTACTGTTT
1 TTACTGTTT
28519551 CCCCAGCACT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 3 0.05
23 60 0.91
24 3 0.05
ACGTcount: A:0.13, C:0.15, G:0.24, T:0.49
Consensus pattern (22 bp):
TTACTGTTTGCACTGTGTGTGC
Found at i:28519517 original size:46 final size:46
Alignment explanation
Indices: 28519450--28519550 Score: 166
Period size: 46 Copynumber: 2.2 Consensus size: 46
28519440 ATTAGCGTGT
*
28519450 TTACTGTTTAGCACTGTGTGTGCTTACTGATTTGCATTGTGTGTAC
1 TTACTGTTTAGCACTGTGTGTGCCTACTGATTTGCATTGTGTGTAC
* * *
28519496 TTACTGTTTTGTACTGTGTGTGCCTACTGATTTGCATTGTGTGTGC
1 TTACTGTTTAGCACTGTGTGTGCCTACTGATTTGCATTGTGTGTAC
28519542 TTACTGTTT
1 TTACTGTTT
28519551 CCCCAGCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.13, C:0.15, G:0.24, T:0.49
Consensus pattern (46 bp):
TTACTGTTTAGCACTGTGTGTGCCTACTGATTTGCATTGTGTGTAC
Found at i:28528379 original size:182 final size:183
Alignment explanation
Indices: 28528072--28528439 Score: 657
Period size: 182 Copynumber: 2.0 Consensus size: 183
28528062 TGGTAAAAAG
*
28528072 ATATTTGAGTCTACTTTCAGAAACATCAAGTGGATATTAATTTAGAATTCTTTAGCTCAAGATAT
1 ATATTTGAGTCTACTTTCAGAAACATCAAGCGGATATTAATTTAGAATTCTTTAGCTCAAGATAT
*
28528137 AAATAATTTAGTGATTGTGACTCAAGTGAACAACTTTGAAAATACATGTGTGAAATGATATGTGA
66 AAATAATTTAGTGATTATGACTCAAGTGAACAACTTTGAAAATACATGTGTGAAATGATATGTGA
28528202 ATAATAATAAGTGAAAATCACATATGATGATATATGTGAAAAG-AATATATAT
131 ATAATAATAAGTGAAAATCACATATGATGATATATGTGAAAAGAAATATATAT
* * *
28528254 ATATTTGAGTCTAGTTTCAGAAACATCAAGCGGATATTAATTTTGAATTCTTTAGCTCTAGATAT
1 ATATTTGAGTCTACTTTCAGAAACATCAAGCGGATATTAATTTAGAATTCTTTAGCTCAAGATAT
* * *
28528319 AAATAATTTAGTGATTATGAGTCAAGTGAACAGCTTTGAAAATATATGTGTGAAATGATATGTGA
66 AAATAATTTAGTGATTATGACTCAAGTGAACAACTTTGAAAATACATGTGTGAAATGATATGTGA
28528384 ATAATAATAAGTGAAAATCACATATGATGATATATGTGAAAAGAAATATATAT
131 ATAATAATAAGTGAAAATCACATATGATGATATATGTGAAAAGAAATATATAT
28528437 ATA
1 ATA
28528440 AGTTGTGAAT
Statistics
Matches: 177, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
182 165 0.93
183 12 0.07
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.35
Consensus pattern (183 bp):
ATATTTGAGTCTACTTTCAGAAACATCAAGCGGATATTAATTTAGAATTCTTTAGCTCAAGATAT
AAATAATTTAGTGATTATGACTCAAGTGAACAACTTTGAAAATACATGTGTGAAATGATATGTGA
ATAATAATAAGTGAAAATCACATATGATGATATATGTGAAAAGAAATATATAT
Found at i:28528580 original size:23 final size:23
Alignment explanation
Indices: 28528554--28528610 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
28528544 CAGCATTGTG
28528554 TGTGCTTACTGATTCGTACTATA
1 TGTGCTTACTGATTCGTACTATA
28528577 TGTGCTTACTGATTCGTACTATA
1 TGTGCTTACTGATTCGTACTATA
*
28528600 TATGCTTACTG
1 TGTGCTTACTG
28528611 TTTTGCACTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (23 bp):
TGTGCTTACTGATTCGTACTATA
Found at i:28528627 original size:46 final size:46
Alignment explanation
Indices: 28528577--28528744 Score: 120
Period size: 46 Copynumber: 3.4 Consensus size: 46
28528567 TCGTACTATA
*
28528577 TGTGCTTACTGATTCGTACTATATATGCTTACTGTTTTGCACTGTG
1 TGTGCCTACTGATTCGTACTATATATGCTTACTGTTTTGCACTGTG
* * ** * * **
28528623 TGTGCCTACTGGTTTGCCATTAAGGAACATTAGCGCGATTACTGTTCAGCACTGTG
1 TGTGCCTACT-GATT--C-GT-A-CTATA-TA-TGC--TTACTGTTTTGCACTGTG
* * *
28528679 TGTGCTTACTGATTCGTACTATATGTGCTTACTGATTTGCACTGTG
1 TGTGCCTACTGATTCGTACTATATATGCTTACTGTTTTGCACTGTG
* *
28528725 TGTGCCTACTGGTTTGTACT
1 TGTGCCTACTGATTCGTACT
28528745 GTGTGCTTAC
Statistics
Matches: 89, Mismatches: 23, Indels: 20
0.67 0.17 0.15
Matches are distributed among these distances:
46 41 0.46
47 3 0.03
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
52 3 0.03
53 3 0.03
54 2 0.02
55 3 0.03
56 25 0.28
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (46 bp):
TGTGCCTACTGATTCGTACTATATATGCTTACTGTTTTGCACTGTG
Found at i:28528728 original size:23 final size:23
Alignment explanation
Indices: 28528671--28528756 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
28528661 TTACTGTTCA
*
28528671 GCACTGTGTGTGCTTACTGATTC
1 GCACTGTGTGTGCTTACTGATTT
* * *
28528694 GTACTATATGTGCTTACTGATTT
1 GCACTGTGTGTGCTTACTGATTT
* *
28528717 GCACTGTGTGTGCCTACTGGTTT
1 GCACTGTGTGTGCTTACTGATTT
*
28528740 GTAC--TGTGTGCTTACTG
1 GCACTGTGTGTGCTTACTG
28528757 TTTCCCCAGC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 12 0.23
23 40 0.77
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (23 bp):
GCACTGTGTGTGCTTACTGATTT
Found at i:28528735 original size:125 final size:125
Alignment explanation
Indices: 28528512--28528749 Score: 370
Period size: 125 Copynumber: 1.9 Consensus size: 125
28528502 ATTAGTGACA
* *
28528512 TGCCATTAAGGAATATTAGCGCACTTACTGTTCAGCATTGTGTGTGCTTACTGATTCGTACTATA
1 TGCCATTAAGGAACATTAGCGCACTTACTGTTCAGCACTGTGTGTGCTTACTGATTCGTACTATA
* * *
28528577 TGTGCTTACTGATTCGTACTATATATGCTTACTGTTTTGCACTGTGTGTGCCTACTGGTT
66 TGTGCTTACTGATTCGCACTATATATGCCTACTGGTTTGCACTGTGTGTGCCTACTGGTT
28528637 TGCCATTAAGGAACATTAGCGCGA-TTACTGTTCAGCACTGTGTGTGCTTACTGATTCGTACTAT
1 TGCCATTAAGGAACATTAGCGC-ACTTACTGTTCAGCACTGTGTGTGCTTACTGATTCGTACTAT
* * * * *
28528701 ATGTGCTTACTGATTTGCACTGTGTGTGCCTACTGGTTTGTACTGTGTG
65 ATGTGCTTACTGATTCGCACTATATATGCCTACTGGTTTGCACTGTGTG
28528750 CTTACTGTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
125 101 0.99
126 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (125 bp):
TGCCATTAAGGAACATTAGCGCACTTACTGTTCAGCACTGTGTGTGCTTACTGATTCGTACTATA
TGTGCTTACTGATTCGCACTATATATGCCTACTGGTTTGCACTGTGTGTGCCTACTGGTT
Found at i:28528751 original size:44 final size:45
Alignment explanation
Indices: 28528671--28528756 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
28528661 TTACTGTTCA
*
28528671 GCACTGTGTGTGCTTACTGATTCGTACTATATGTGCTTACTGATTT
1 GCACTGTGTGTGCCTACTGATTCGTAC-ATATGTGCTTACTGATTT
* * *
28528717 GCACTGTGTGTGCCTACTGGTTTGTAC-TGTGTGCTTACTG
1 GCACTGTGTGTGCCTACTGATTCGTACATATGTGCTTACTG
28528757 TTTCCCCAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 12 0.33
46 24 0.67
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (45 bp):
GCACTGTGTGTGCCTACTGATTCGTACATATGTGCTTACTGATTT
Found at i:28530885 original size:76 final size:75
Alignment explanation
Indices: 28530786--28530943 Score: 219
Period size: 76 Copynumber: 2.1 Consensus size: 75
28530776 TAATAATACG
* * * * * * *
28530786 CAACAAAATTGATTTATAGATACAAGAAAATATGAACATTCTAGAAAGTTGATATATGAAAATAT
1 CAACAAAAATGATTTACAAATACAAAAAAATATGAACATTCTAAAAAATTGACATATGAAAATAT
28530851 AAAATTCGAC
66 AAAATTCGAC
*
28530861 CAACTAAAAATGATTTACAAATACAAAAAAATATGAACATTTTAAAAAATTGACATATGAAAATA
1 CAAC-AAAAATGATTTACAAATACAAAAAAATATGAACATTCTAAAAAATTGACATATGAAAATA
28530926 TAAAATTCTG-C
65 TAAAATTC-GAC
28530937 CAACAAA
1 CAACAAA
28530944 TAATACAGAC
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 7 0.10
76 65 0.89
77 1 0.01
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.27
Consensus pattern (75 bp):
CAACAAAAATGATTTACAAATACAAAAAAATATGAACATTCTAAAAAATTGACATATGAAAATAT
AAAATTCGAC
Found at i:28531021 original size:92 final size:88
Alignment explanation
Indices: 28530863--28531150 Score: 357
Period size: 90 Copynumber: 3.2 Consensus size: 88
28530853 AATTCGACCA
* * *
28530863 ACTAAAAATGATTTACAAATACAAAAAAATATGAACATTTTAAAAAATTGACATATGAAAATATA
1 ACTAAAATTGATTTACAAATACAAAAAAATATGAACATTTT-AAAAATTGATATA-CAAAATATA
28530928 AAATTCTG-CCAACAAATAATACAG
64 AAATTCTGACCAACAAATAATACAG
* *
28530952 ACTAAAATTGATTTACAAATACAAAAAAACAATATGAACATTCTAAAAAGTGTGATACACAAAAT
1 ACTAAAATTGATTTACAAATAC--AAAAA-AATATGAACATTTTAAAAA-T-TGATATACAAAAT
** *
28531017 ATAAAATTC-GATTAACAAATATTACAG
61 ATAAAATTCTGACCAACAAATAATACAG
* * * *
28531044 ACTAAAATTGATTTACAAATCCAAAAATAATACGAACATTTTAGAAAATTAATATACGAAAGTAT
1 ACTAAAATTGATTTACAAATACAAAAA-AATATGAACATTTTA-AAAATTGATATAC-AAAATAT
28531109 AAAATT-TGACCAACAAATAATACAG
63 AAAATTCTGACCAACAAATAATACAG
28531134 ACTAAAATTGATTTACA
1 ACTAAAATTGATTTACA
28531151 GATGAGCCAT
Statistics
Matches: 172, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
89 27 0.16
90 63 0.37
91 15 0.09
92 62 0.36
93 5 0.03
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (88 bp):
ACTAAAATTGATTTACAAATACAAAAAAATATGAACATTTTAAAAATTGATATACAAAATATAAA
ATTCTGACCAACAAATAATACAG
Found at i:28533293 original size:30 final size:30
Alignment explanation
Indices: 28533270--28533350 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
28533260 TTTGGTTACT
*
28533270 TTTTAAATTTAATTTGTAATTTTGTTTATA
1 TTTTAAATTTAATTTCTAATTTTGTTTATA
*
28533300 TTTTAAATTTAATTTCTAATTTCGTTTATA
1 TTTTAAATTTAATTTCTAATTTTGTTTATA
* *
28533330 TTTTAAATTTCATTTTTAATT
1 TTTTAAATTTAATTTCTAATT
28533351 ATTATTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTTGTTTATA
Found at i:28534313 original size:62 final size:59
Alignment explanation
Indices: 28534211--28534488 Score: 229
Period size: 58 Copynumber: 4.8 Consensus size: 59
28534201 ATAAAAAATT
* * *
28534211 AAGCATTGGCCAACA-CAAAAAA--ATATTTTTTATCAAATAAAAAAAGTGGTGTCAACC
1 AAGCA-TGGCCAACACCAAAAAATTATTTTTTTTATCAGATAAAAAAAGTGGTGTCAGCC
* * ** *
28534268 AATACATGGGCAACACCAAAAAAGTTTATTTTTTTTATCAGATAAAAATGGTGGTGTCGGCC
1 AA-GCATGGCCAACACCAAAAAA--TTATTTTTTTTATCAGATAAAAAAAGTGGTGTCAGCC
* * * * *
28534330 AAGCATTAGCTAACACC---CAA--ATTTTTTTTATCTGATAAAAAAAGTTAGTGTCAGCC
1 AAGCA-TGGCCAACACCAAAAAATTATTTTTTTTATCAGATAAAAAAAG-TGGTGTCAGCC
* * *
28534386 AATGCATGGCCAACACAAAAAAATTA-TTTTTTTATCGGAT-AAAAAAGTGGTGTCGGCC
1 AA-GCATGGCCAACACCAAAAAATTATTTTTTTTATCAGATAAAAAAAGTGGTGTCAGCC
* * *
28534444 AAGCATTGGCCAACACCAAAAAA--AATATTTTTATCTGATAAAAAA
1 AAGCA-TGGCCAACACCAAAAAATTATTTTTTTTATCAGATAAAAAA
28534489 TACTAGTGTC
Statistics
Matches: 176, Mismatches: 28, Indels: 33
0.74 0.12 0.14
Matches are distributed among these distances:
55 21 0.12
56 20 0.11
57 28 0.16
58 41 0.23
59 11 0.06
60 13 0.07
61 3 0.02
62 39 0.22
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (59 bp):
AAGCATGGCCAACACCAAAAAATTATTTTTTTTATCAGATAAAAAAAGTGGTGTCAGCC
Found at i:28534439 original size:58 final size:57
Alignment explanation
Indices: 28534211--28534488 Score: 246
Period size: 57 Copynumber: 4.8 Consensus size: 57
28534201 ATAAAAAATT
* *
28534211 AAGCATTGGCCAACACAAAAAAATA-TTTTTTATCAAATAAAAAAAGTGGTGTCAACC
1 AAGCATTGGCCAACACAAAAAAATATTTTTTTATCAGAT-AAAAAAGTGGTGTCAGCC
* * * * *
28534268 AATACA-TGGGCAACACCAAAAAAGTTTATTTTTTTTATCAGATAAAAATGGTGGTGTCGGCC
1 AA-GCATTGGCCAACA-CAAAAAA--ATA-TTTTTTTATCAGATAAAAA-AGTGGTGTCAGCC
* * ** * *
28534330 AAGCATTAGCTAACAC--CCAAAT-TTTTTTTATCTGATAAAAAAAGTTAGTGTCAGCC
1 AAGCATTGGCCAACACAAAAAAATATTTTTTTATCAGAT-AAAAAAG-TGGTGTCAGCC
* *
28534386 AATGCA-TGGCCAACACAAAAAAATTATTTTTTTATCGGATAAAAAAGTGGTGTCGGCC
1 AA-GCATTGGCCAACACAAAAAAA-TATTTTTTTATCAGATAAAAAAGTGGTGTCAGCC
* *
28534444 AAGCATTGGCCAACACCAAAAAAA-ATATTTTTATCTGATAAAAAA
1 AAGCATTGGCCAACA-CAAAAAAATATTTTTTTATCAGATAAAAAA
28534489 TACTAGTGTC
Statistics
Matches: 177, Mismatches: 27, Indels: 34
0.74 0.11 0.14
Matches are distributed among these distances:
55 14 0.08
56 24 0.14
57 36 0.20
58 32 0.18
59 18 0.10
60 15 0.08
61 8 0.05
62 30 0.17
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (57 bp):
AAGCATTGGCCAACACAAAAAAATATTTTTTTATCAGATAAAAAAGTGGTGTCAGCC
Found at i:28534476 original size:117 final size:119
Alignment explanation
Indices: 28534211--28534498 Score: 356
Period size: 117 Copynumber: 2.4 Consensus size: 119
28534201 ATAAAAAATT
** *
28534211 AAGCATTGGCCAACA-CAAAAAAATATTTTTTATCAAATAAAAAAAGTGGTGTCAACCAATACAT
1 AAGCATTGGCCAACACCAAAAAAATA-TTTTTATCTGATAAAAAAAGTAGTGTCAACCAATACAT
* * *
28534275 GGGCAACACCAAAAAAGTTTATTTTTTTTATCAGATAAAAATGGTGGTGTCGGCC
65 GGCCAACACCAAAAAAGATTATTTTTTTTATCAGATAAAAATAGTGGTGTCGGCC
* * * * * * *
28534330 AAGCATTAGCTAACACC--CAAATTTTTTTTATCTGATAAAAAAAGTTAGTGTCAGCCAATGCAT
1 AAGCATTGGCCAACACCAAAAAAATATTTTTATCTGATAAAAAAAG-TAGTGTCAACCAATACAT
*
28534393 GGCCAACA-CAAAAAA-ATTA-TTTTTTTATCGGATAAAAA-AGTGGTGTCGGCC
65 GGCCAACACCAAAAAAGATTATTTTTTTTATCAGATAAAAATAGTGGTGTCGGCC
*
28534444 AAGCATTGGCCAACACCAAAAAAAATATTTTTATCTGATAAAAAATACTAGTGTC
1 AAGCATTGGCCAACACC-AAAAAAATATTTTTATCTGATAAAAAA-AGTAGTGTC
28534499 GGCTAATGCA
Statistics
Matches: 143, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
114 27 0.19
115 18 0.13
116 3 0.02
117 54 0.38
118 27 0.19
119 13 0.09
120 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (119 bp):
AAGCATTGGCCAACACCAAAAAAATATTTTTATCTGATAAAAAAAGTAGTGTCAACCAATACATG
GCCAACACCAAAAAAGATTATTTTTTTTATCAGATAAAAATAGTGGTGTCGGCC
Found at i:28534586 original size:55 final size:54
Alignment explanation
Indices: 28534295--28534639 Score: 230
Period size: 55 Copynumber: 6.2 Consensus size: 54
28534285 AAAAAAGTTT
* * * * * *
28534295 ATTTTTTTTATCAGATAAAAATGGTGGTGTCGGCCAAGCATTAGCTAACACCCAA
1 ATTTTTTTTATCTGATAAAAAAGCTAGTGTCGGCCAAGCATTGGCCAACA-CCAA
* * *
28534350 ATTTTTTTTATCTGATAAAAAAAGTTAGTGTCAGCCAATGCA-TGGCCAACACAAAAAA
1 ATTTTTTTTATCTGAT-AAAAAAGCTAGTGTCGGCCAA-GCATTGGCCAACAC---CAA
* *
28534408 ATTATTTTTTTATCGGATAAAAAAG-TGGTGTCGGCCAAGCATTGGCCAACACCAAAAAA
1 A-T-TTTTTTTATCTGATAAAAAAGCTAGTGTCGGCCAAGCATTGGCCAACACC----AA
* * * * *** * *
28534467 AATATTTTTATCTGATAAAAAATACTAGTGTCGGCTAATGCA-TAATCAAAAACAA
1 ATTTTTTTTATCTGATAAAAAA-GCTAGTGTCGGCCAA-GCATTGGCCAACACCAA
**** *
28534522 AAAAATTTTATCTGATAAAAAAAGCTAGTGTTGGCCAATGCA-TGGCCAACACCAA
1 ATTTTTTTTATCTGAT-AAAAAAGCTAGTGTCGGCCAA-GCATTGGCCAACACCAA
* * * * * *
28534577 ATTTTTTTTATTTGATTAAAAAGGTGGTGTCGACCAAGCATTGGCCCACACCAA
1 ATTTTTTTTATCTGATAAAAAAGCTAGTGTCGGCCAAGCATTGGCCAACACCAA
*
28534631 TTTTTTTTT
1 ATTTTTTTT
28534640 TTGAAAATAT
Statistics
Matches: 228, Mismatches: 45, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
53 3 0.01
54 36 0.16
55 67 0.29
56 30 0.13
57 24 0.11
58 24 0.11
59 28 0.12
60 16 0.07
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (54 bp):
ATTTTTTTTATCTGATAAAAAAGCTAGTGTCGGCCAAGCATTGGCCAACACCAA
Found at i:28545649 original size:21 final size:22
Alignment explanation
Indices: 28545612--28545663 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
28545602 TAAAAAATAA
* **
28545612 ATTATTAATATAATTTATTATT
1 ATTAATAATATAATTTACCATT
28545634 -TTAATAATA-AATTTTACCATT
1 ATTAATAATATAA-TTTACCATT
28545655 ATTAATAAT
1 ATTAATAAT
28545664 TTATATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 2 0.08
21 15 0.60
22 8 0.32
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTAATAATATAATTTACCATT
Found at i:28545842 original size:14 final size:16
Alignment explanation
Indices: 28545819--28545852 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28545809 CTATATATAA
28545819 AAAT-ATTTT-TGTAT
1 AAATAATTTTATGTAT
28545833 AAATAATTTTATGTAT
1 AAATAATTTTATGTAT
28545849 AAAT
1 AAAT
28545853 TTGAATAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 5 0.28
16 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
AAATAATTTTATGTAT
Found at i:28555892 original size:18 final size:18
Alignment explanation
Indices: 28555866--28555907 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28555856 GAAGGAATAT
28555866 CATACTGGCTCGATTGAG
1 CATACTGGCTCGATTGAG
* *
28555884 CATATTGGCTCGTTTGAG
1 CATACTGGCTCGATTGAG
28555902 CATACT
1 CATACT
28555908 AGCTTGTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (18 bp):
CATACTGGCTCGATTGAG
Found at i:28558202 original size:17 final size:17
Alignment explanation
Indices: 28558155--28558202 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
28558145 TCCAAAATAT
**
28558155 AATTAATTAATTAATTA
1 AATTAATTTTTTAATTA
28558172 AATTAATTTTTTAATTA
1 AATTAATTTTTTAATTA
28558189 AA-TAATTTTCTTAA
1 AATTAATTTT-TTAA
28558203 CTCAATCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTAATTTTTTAATTA
Found at i:28561579 original size:2 final size:2
Alignment explanation
Indices: 28561574--28561613 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28561564 GTGTTAATGG
28561574 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28561614 CGGGGAGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28565349 original size:171 final size:171
Alignment explanation
Indices: 28565057--28565386 Score: 552
Period size: 171 Copynumber: 1.9 Consensus size: 171
28565047 AGGGGGAACA
* *
28565057 TATTTGCTTCTCCAAAGAATTACCCAAAACTCAATCCCACGATCCTCTGCCACCTTCACATGGTG
1 TATTTGCTGCTCCAAAGAAATACCCAAAACTCAATCCCACGATCCTCTGCCACCTTCACATGGTG
* * * * *
28565122 AGATGGACCAGTTAGAGGAACGTAATTGTAGCAGCTCCTTTTCTCCTGCTTCTCTAGATACTCCA
66 AGATGGACCAGTTACAGGAACGTAATTGTAGCAGCTCCCTTTCTCCTACATCTCTAGATACTACA
28565187 TCCTCAGGTCAAAAGTTTGTATCTCCCATGGAAAAAGTTTG
131 TCCTCAGGTCAAAAGTTTGTATCTCCCATGGAAAAAGTTTG
* *
28565228 TATTTGCTGCTCCAAAGAAATACCCAAAACTCAATCCCATGATCCTGTGCCACCTTCACATGGTG
1 TATTTGCTGCTCCAAAGAAATACCCAAAACTCAATCCCACGATCCTCTGCCACCTTCACATGGTG
* * *
28565293 AGATGGATCAGTTACAGGATCGTAATTGTAGCAGCTCCCTTTCTCCTACATCTCTAGATCCTACA
66 AGATGGACCAGTTACAGGAACGTAATTGTAGCAGCTCCCTTTCTCCTACATCTCTAGATACTACA
28565358 TCCTCAGGTCAAAAGTTTGTATCTCCCAT
131 TCCTCAGGTCAAAAGTTTGTATCTCCCAT
28565387 AGCAAAGGAA
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
171 147 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (171 bp):
TATTTGCTGCTCCAAAGAAATACCCAAAACTCAATCCCACGATCCTCTGCCACCTTCACATGGTG
AGATGGACCAGTTACAGGAACGTAATTGTAGCAGCTCCCTTTCTCCTACATCTCTAGATACTACA
TCCTCAGGTCAAAAGTTTGTATCTCCCATGGAAAAAGTTTG
Found at i:28567808 original size:13 final size:13
Alignment explanation
Indices: 28567790--28567833 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
28567780 TCATTTTATC
28567790 AAAATAAATATAA
1 AAAATAAATATAA
*
28567803 AAAATAAAAATAA
1 AAAATAAATATAA
* *
28567816 AAACTTAATATAA
1 AAAATAAATATAA
28567829 AAAAT
1 AAAAT
28567834 CGAATCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAAATATAA
Found at i:28572892 original size:109 final size:110
Alignment explanation
Indices: 28572767--28572992 Score: 364
Period size: 109 Copynumber: 2.1 Consensus size: 110
28572757 TTTTGCTTAT
* * *
28572767 GCTGAATATATGATTCGATCTAATTTACCCATTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGT
1 GCTGAATATATGATTCGATCAAATTCACCCATTTTTTCTCTGCTTGTTTTAGGAAGTTGGTAAGT
28572832 ATTGA-TTTTTTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
66 ATTGATTTTTTTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
* *
28572876 GCTGAATATATGATTCGATCAAATTCGCCCCTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTAAGT
1 GCTGAATATATGATTCGATCAAATTCACCCATTTTTTCTCTGCTTGTTTTAGGAAGTTGGTAAGT
* * *
28572941 TTTTATTTTTTTAAGTTTAGTTTTACTCTCCCTTTTAGCAATTAG
66 ATTGATTTTTTTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
*
28572986 GTTGAAT
1 GCTGAAT
28572993 GTAACACCCA
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
109 63 0.59
110 44 0.41
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (110 bp):
GCTGAATATATGATTCGATCAAATTCACCCATTTTTTCTCTGCTTGTTTTAGGAAGTTGGTAAGT
ATTGATTTTTTTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
Found at i:28573421 original size:24 final size:23
Alignment explanation
Indices: 28573389--28573449 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
28573379 CAAGTGTGCA
*
28573389 AACTACCGATACATCTATACATAT-
1 AACTACCGATACATCTACA-AT-TC
28573413 AACTACCGATAC-TC-ACAATTC
1 AACTACCGATACATCTACAATTC
28573434 AACTACCGATACATCT
1 AACTACCGATACATCT
28573450 CAAGTCAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.42
22 4 0.12
23 2 0.06
24 12 0.36
ACGTcount: A:0.39, C:0.30, G:0.05, T:0.26
Consensus pattern (23 bp):
AACTACCGATACATCTACAATTC
Found at i:28574212 original size:52 final size:52
Alignment explanation
Indices: 28574046--28574217 Score: 249
Period size: 52 Copynumber: 3.3 Consensus size: 52
28574036 ACAATAACAT
**
28574046 ATAGTCATCGGACCTCT-TGTTCCGTATAGGAATTCATATACTCACGATGACAC
1 ATAGTCATCGGACCT-TATAATCCGTATAGG-ATTCATATACTCACGATGACAC
* * *
28574099 ATAGTCATCAGAACTCATAATCCGTATAGGATTCATATACTCACGATGACAC
1 ATAGTCATCGGACCTTATAATCCGTATAGGATTCATATACTCACGATGACAC
* *
28574151 ATAGTCATCGGACCTTATAATCCGTAAAGGATTCATATACTCGCGATGACAC
1 ATAGTCATCGGACCTTATAATCCGTATAGGATTCATATACTCACGATGACAC
28574203 ATAGTCATC-GACCTT
1 ATAGTCATCGGACCTT
28574218 TTTCATTTAC
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
51 6 0.06
52 78 0.72
53 24 0.22
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (52 bp):
ATAGTCATCGGACCTTATAATCCGTATAGGATTCATATACTCACGATGACAC
Found at i:28576526 original size:13 final size:13
Alignment explanation
Indices: 28576508--28576532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28576498 TTTTGAATTA
28576508 GAAGAGAAGAAGT
1 GAAGAGAAGAAGT
28576521 GAAGAGAAGAAG
1 GAAGAGAAGAAG
28576533 GAAAGGTGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.04
Consensus pattern (13 bp):
GAAGAGAAGAAGT
Found at i:28577251 original size:21 final size:21
Alignment explanation
Indices: 28577222--28577262 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28577212 GATACCTGAT
*
28577222 AAAAAGTATCGATACTTTTTG
1 AAAAAGTATCAATACTTTTTG
*
28577243 AAAATGTATCAATACTTTTT
1 AAAAAGTATCAATACTTTTT
28577263 TTTCATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (21 bp):
AAAAAGTATCAATACTTTTTG
Found at i:28583114 original size:24 final size:25
Alignment explanation
Indices: 28583073--28583120 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
28583063 ATTCACATAT
28583073 TTTCTTACTCATGATTCTT-TTTTA
1 TTTCTTACTCATGATTCTTCTTTTA
**
28583097 TTTCTTACTCATTTTTCTTCTTTT
1 TTTCTTACTCATGATTCTTCTTTT
28583121 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.12, C:0.19, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTCTTACTCATGATTCTTCTTTTA
Found at i:28583138 original size:28 final size:29
Alignment explanation
Indices: 28583090--28583146 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
28583080 CTCATGATTC
*
28583090 TTTTTTATTTCTTACTCATTTTTCTTCTT
1 TTTTTTATTTCTTACTCATTTCTCTTCTT
*
28583119 TTTTTTATTT-TT-CTATATTTCTCTTCTT
1 TTTTTTATTTCTTACT-CATTTCTCTTCTT
28583147 CTTCTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 13 0.52
29 10 0.40
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTTTATTTCTTACTCATTTCTCTTCTT
Found at i:28583533 original size:21 final size:22
Alignment explanation
Indices: 28583509--28583580 Score: 96
Period size: 21 Copynumber: 3.4 Consensus size: 22
28583499 GTGCAGACTC
*
28583509 CTACCGATACAAGTGA-TAGTT
1 CTACCGATACAAGTGACTACTT
28583530 CTACCGATACAAGTGACT-CTT
1 CTACCGATACAAGTGACTACTT
* *
28583551 CTACCAATACAAGT-ATTACTT
1 CTACCGATACAAGTGACTACTT
28583572 CTACCGATA
1 CTACCGATA
28583581 TTAAAAACTC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.04
21 42 0.93
22 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (22 bp):
CTACCGATACAAGTGACTACTT
Found at i:28591577 original size:17 final size:18
Alignment explanation
Indices: 28591555--28591595 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
28591545 GTCTCTACCA
28591555 AAAATAAAATATACA-TT
1 AAAATAAAATATACATTT
*
28591572 AAAATAAAATATATATTT
1 AAAATAAAATATACATTT
28591590 AAAATA
1 AAAATA
28591596 TTATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATAAAATATACATTT
Found at i:28592550 original size:10 final size:9
Alignment explanation
Indices: 28592520--28592548 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28592510 ATATATTCTC
28592520 TTTAA-ATT
1 TTTAATATT
28592528 TTTAATATT
1 TTTAATATT
28592537 TTTAATATT
1 TTTAATATT
28592546 TTT
1 TTT
28592549 TATGGTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTAATATT
Found at i:28592585 original size:19 final size:19
Alignment explanation
Indices: 28592563--28592706 Score: 85
Period size: 19 Copynumber: 7.9 Consensus size: 19
28592553 GTTCTAATTT
28592563 TTTTTATAATTTTATATAA
1 TTTTTATAATTTTATATAA
* *
28592582 TTTTTATAATTCTATCTTAA
1 TTTTTATAATTTTAT-ATAA
*
28592602 TTTATAATAATTTT-T-TCAA
1 TTT-TTATAATTTTATAT-AA
28592621 TTTTTAT-ATTTT-TATAA
1 TTTTTATAATTTTATATAA
28592638 --TTT-T-ATTTTATATAGA
1 TTTTTATAATTTTATATA-A
**
28592654 TTCATAT-ATTTTA-ATAA
1 TTTTTATAATTTTATATAA
* * *
28592671 TTTTCTATTATTGTAAATAA
1 TTTT-TATAATTTTATATAA
*
28592691 TTTTTA-ATTTTTATAT
1 TTTTTATAATTTTATAT
28592707 TTGTAATAGT
Statistics
Matches: 99, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
14 6 0.06
15 7 0.07
16 1 0.01
17 11 0.11
18 18 0.18
19 33 0.33
20 15 0.15
21 8 0.08
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTTATAATTTTATATAA
Found at i:28592589 original size:9 final size:9
Alignment explanation
Indices: 28592563--28592641 Score: 74
Period size: 9 Copynumber: 8.4 Consensus size: 9
28592553 GTTCTAATTT
28592563 TTTTTATAA
1 TTTTTATAA
28592572 TTTTATATAA
1 TTTT-TATAA
28592582 TTTTTATAA
1 TTTTTATAA
28592591 TTCTATCT-TAA
1 TT-T-T-TATAA
*
28592602 TTTATAATAA
1 TTT-TTATAA
28592612 TTTTT-TCAA
1 TTTTTAT-AA
28592621 TTTTTAT-A
1 TTTTTATAA
28592629 TTTTTATAA
1 TTTTTATAA
28592638 TTTT
1 TTTT
28592642 ATTTTATATA
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
8 9 0.15
9 24 0.40
10 20 0.33
11 6 0.10
12 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:28592595 original size:37 final size:36
Alignment explanation
Indices: 28592526--28592595 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 36
28592516 TCTCTTTAAA
* * **
28592526 TTTTTAATATTTTTAATATTTTTTATGGTTCTAATT
1 TTTTTAATAATTTTAATAATTTTTATAATTCTAATT
*
28592562 TTTTTTATAATTTTATATAATTTTTATAATTCTA
1 TTTTTAATAATTTTA-ATAATTTTTATAATTCTA
28592596 TCTTAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 13 0.46
37 15 0.54
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (36 bp):
TTTTTAATAATTTTAATAATTTTTATAATTCTAATT
Found at i:28594935 original size:19 final size:19
Alignment explanation
Indices: 28594911--28594949 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28594901 GAGTTATACC
*
28594911 AGAATTAGGAAGTAAACTT
1 AGAATTAAGAAGTAAACTT
28594930 AGAATTAAGAAGTAAACTT
1 AGAATTAAGAAGTAAACTT
28594949 A
1 A
28594950 CTTTCCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (19 bp):
AGAATTAAGAAGTAAACTT
Found at i:28595311 original size:4 final size:4
Alignment explanation
Indices: 28595282--28595357 Score: 111
Period size: 4 Copynumber: 19.5 Consensus size: 4
28595272 TGTGTGTGTG
* * *
28595282 TGTA TGTA TGTG TCTA TG-- TGTG TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
28595328 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
28595358 AGTTTTAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.03
4 63 0.97
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:28596660 original size:18 final size:18
Alignment explanation
Indices: 28596639--28596805 Score: 106
Period size: 18 Copynumber: 9.2 Consensus size: 18
28596629 CGAGTATGCA
28596639 AACCCTTATATGTATGTG
1 AACCCTTATATGTATGTG
* **
28596657 AACCCTTATATATATGCA
1 AACCCTTATATGTATGTG
* *
28596675 AACCCTTGTATGTAAGTG
1 AACCCTTATATGTATGTG
* **
28596693 AACCCTTATATTTATGCA
1 AACCCTTATATGTATGTG
* * *
28596711 AAACCTAATATGTATG-C
1 AACCCTTATATGTATGTG
* * * *
28596728 AAACCATATACTATATATG
1 AACCCTTATA-TGTATGTG
* *
28596747 AACCCTTAAATGTATGCG
1 AACCCTTATATGTATGTG
*
28596765 AACCC-TATTATGAATGTG
1 AACCCTTA-TATGTATGTG
*
28596783 AAACCC-TATAATGTACGTG
1 -AACCCTTAT-ATGTATGTG
28596802 AACC
1 AACC
28596806 AAAAAGTAAG
Statistics
Matches: 111, Mismatches: 33, Indels: 10
0.72 0.21 0.06
Matches are distributed among these distances:
17 10 0.09
18 80 0.72
19 21 0.19
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.32
Consensus pattern (18 bp):
AACCCTTATATGTATGTG
Found at i:28596680 original size:36 final size:36
Alignment explanation
Indices: 28596633--28596770 Score: 154
Period size: 36 Copynumber: 3.8 Consensus size: 36
28596623 AGTGCCCGAG
*
28596633 TATGCAAACCCTTATATGTATGTGAACCCTTATATA
1 TATGCAAACCCTTATATGTATGCGAACCCTTATATA
* * * *
28596669 TATGCAAACCCTTGTATGTAAGTGAACCCTTATATT
1 TATGCAAACCCTTATATGTATGCGAACCCTTATATA
* * * *
28596705 TATGCAAAACCTAATATGTATGCAAACCATATACTATA
1 TATGCAAACCCTTATATGTATGCGAACCCT-TA-TATA
*
28596743 TATG--AACCCTTAAATGTATGCGAACCCT
1 TATGCAAACCCTTATATGTATGCGAACCCT
28596771 ATTATGAATG
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
36 75 0.89
37 2 0.02
38 7 0.08
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (36 bp):
TATGCAAACCCTTATATGTATGCGAACCCTTATATA
Found at i:28596802 original size:19 final size:19
Alignment explanation
Indices: 28596765--28596803 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28596755 AATGTATGCG
* *
28596765 AACCCTATTATGAATGTGA
1 AACCCTATAATGAACGTGA
*
28596784 AACCCTATAATGTACGTGA
1 AACCCTATAATGAACGTGA
28596803 A
1 A
28596804 CCAAAAAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (19 bp):
AACCCTATAATGAACGTGA
Found at i:28599516 original size:68 final size:68
Alignment explanation
Indices: 28599401--28599577 Score: 178
Period size: 68 Copynumber: 2.6 Consensus size: 68
28599391 ACGACTCAAG
** * * *** ** *
28599401 AAGGTTGAAATATTTGAAAAGATAAGTGCTTGAGAATATAATGTACTTTAAGAAGTACT-TAACT
1 AAGGTTGAAAGCTTTGAAAAGTTAAGTGCATGAGAAGGCAAAATACTTTAAGAAGTA-TGCAACT
28599465 TGAA
65 TGAA
*
28599469 AAGGTTGAAAGCTTTGAAAAGTTAAGTGCATGAGAAGGCAAAATACTTTAATAAGTATGCAACTT
1 AAGGTTGAAAGCTTTGAAAAGTTAAGTGCATGAGAAGGCAAAATACTTTAAGAAGTATGCAACTT
*
28599534 GAG
66 GAA
* * * *
28599537 AAGG-TGGAAGACTTTGAAAAGTTAAGTTCCTGATAAGGCAA
1 AAGGTTGAAAG-CTTTGAAAAGTTAAGTGCATGAGAAGGCAA
28599578 TTTGTGGCAG
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
67 6 0.07
68 85 0.93
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (68 bp):
AAGGTTGAAAGCTTTGAAAAGTTAAGTGCATGAGAAGGCAAAATACTTTAAGAAGTATGCAACTT
GAA
Found at i:28602212 original size:21 final size:21
Alignment explanation
Indices: 28602187--28602245 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
28602177 AGCTCTGGCC
*
28602187 GAAACTGAGGCGAAGCCAGCT
1 GAAACTGAGGCGAAGCCAGCA
* * *
28602208 GAAACCGAGGTGAAACCAGCA
1 GAAACTGAGGCGAAGCCAGCA
*
28602229 GAAACTGAGGCAAAGCC
1 GAAACTGAGGCGAAGCC
28602246 CACAGAAGCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.31, T:0.07
Consensus pattern (21 bp):
GAAACTGAGGCGAAGCCAGCA
Found at i:28602581 original size:23 final size:23
Alignment explanation
Indices: 28602552--28602597 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28602542 TATAAATTTA
28602552 AAAAATTATGAAAATGATTCGAT
1 AAAAATTATGAAAATGATTCGAT
28602575 AAAAATTATGAAAATGATTCGAT
1 AAAAATTATGAAAATGATTCGAT
28602598 TTTAAGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (23 bp):
AAAAATTATGAAAATGATTCGAT
Found at i:28607791 original size:48 final size:49
Alignment explanation
Indices: 28607704--28607803 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 49
28607694 CCTCAAACCC
*
28607704 TTTACTTCCCCTAAAAAAAAAAATTTACTTCTCCTCAAACCCCAAAACT
1 TTTACTTCCCCTAAAAAAAAAAATTTACTTCTCCCCAAACCCCAAAACT
** * * *
28607753 TTTACTT-CCCTAAAAAAATTATTTTCCCTT-TCCCCAAACCCCTAAACT
1 TTTACTTCCCCTAAAAAAAAAAATTT-ACTTCTCCCCAAACCCCAAAACT
28607801 TTT
1 TTT
28607804 TTCCTTTGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
48 34 0.77
49 10 0.23
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.34
Consensus pattern (49 bp):
TTTACTTCCCCTAAAAAAAAAAATTTACTTCTCCCCAAACCCCAAAACT
Found at i:28624738 original size:39 final size:39
Alignment explanation
Indices: 28624694--28624769 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
28624684 GGATATAGAA
* *
28624694 GTAATTTTAGTCAAAAGCTCTCTTGTAAAAGCTAAAATT
1 GTAATTCTAGTCAAAAGCTCTATTGTAAAAGCTAAAATT
*
28624733 GTAATTCTAGTCAAAAGCTCTATTGTAAAAGTTAAAA
1 GTAATTCTAGTCAAAAGCTCTATTGTAAAAGCTAAAA
28624770 ATGGTGATCT
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:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (39 bp):
GTAATTCTAGTCAAAAGCTCTATTGTAAAAGCTAAAATT
Found at i:28630031 original size:9 final size:9
Alignment explanation
Indices: 28630019--28630059 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
28630009 GGGTTTTATA
28630019 TTTTTAAAT
1 TTTTTAAAT
28630028 TTTTTAAAT
1 TTTTTAAAT
*
28630037 TTTTTAGAT
1 TTTTTAAAT
*
28630046 TTTTATGAAT
1 TTTT-TAAAT
28630056 TTTT
1 TTTT
28630060 AATTATTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:28630060 original size:18 final size:17
Alignment explanation
Indices: 28630012--28630061 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
28630002 GTTGAATGGG
*
28630012 TTTTATATTTTTAAATT
1 TTTTAAATTTTTAAATT
*
28630029 TTTTAAATTTTTTAGATT
1 TTTTAAA-TTTTTAAATT
*
28630047 TTTATGAATTTTTAA
1 TTT-TAAATTTTTAA
28630062 TTATTGTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.22
18 18 0.67
19 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (17 bp):
TTTTAAATTTTTAAATT
Found at i:28632720 original size:36 final size:38
Alignment explanation
Indices: 28632655--28632738 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 38
28632645 AAATTATTTA
**
28632655 ATAA-TTTTAATAATTTTATATTTTTAAAAA-AA-TAT
1 ATAATTTTTAATAATTTTATATTTCAAAAAATAATTAT
* *
28632690 ATAATTTTTAATAATTTTTTATTTCAAAAAATAATTTT
1 ATAATTTTTAATAATTTTATATTTCAAAAAATAATTAT
*
28632728 AAAATTTTTAA
1 ATAATTTTTAA
28632739 AGTAATTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 4 0.10
36 23 0.56
37 2 0.05
38 12 0.29
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (38 bp):
ATAATTTTTAATAATTTTATATTTCAAAAAATAATTAT
Found at i:28633550 original size:23 final size:23
Alignment explanation
Indices: 28633519--28633565 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28633509 AGTGACAGTG
*
28633519 ATTCAGACTTTAAATGATTCGCC
1 ATTCAGACTTTAAACGATTCGCC
* *
28633542 ATTCGGACTTTAAACGATTTGCC
1 ATTCAGACTTTAAACGATTCGCC
28633565 A
1 A
28633566 ATACTCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (23 bp):
ATTCAGACTTTAAACGATTCGCC
Found at i:28635679 original size:24 final size:22
Alignment explanation
Indices: 28635647--28635700 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
28635637 AAGAAAAGAA
* *
28635647 AAAAAAGTGAAAAGAACAAAATG
1 AAAAGAGTGAAAA-AACAAAAAG
* *
28635670 AAAATGAGTGGAAATACAAAAAG
1 AAAA-GAGTGAAAAAACAAAAAG
28635693 AAAAGAGT
1 AAAAGAGT
28635701 AAGAAAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.15
23 15 0.58
24 7 0.27
ACGTcount: A:0.65, C:0.04, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAGAGTGAAAAAACAAAAAG
Done.