Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 131 of 210
Found at i:39842780 original size:27 final size:27
Alignment explanation
Indices: 39842742--39842872 Score: 167
Period size: 27 Copynumber: 4.9 Consensus size: 27
39842732 CCATAATAGT
39842742 TAATTTTACCCATCGGGGGTATTTCGA
1 TAATTTTACCCATCGGGGGTATTTCGA
* * *
39842769 TAATTTTACCCAT-TGGGGTATTTTGG
1 TAATTTTACCCATCGGGGGTATTTCGA
* **
39842795 TAATTTTACCTATCAAGGGTATTTC-A
1 TAATTTTACCCATCGGGGGTATTTCGA
*
39842821 GTAATTTTACCTATCGGGGGTATTTCGA
1 -TAATTTTACCCATCGGGGGTATTTCGA
*
39842849 TAATTTTACCCATCGAGGGTATTT
1 TAATTTTACCCATCGGGGGTATTT
39842873 TGGTATAGTC
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
26 22 0.25
27 66 0.74
28 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (27 bp):
TAATTTTACCCATCGGGGGTATTTCGA
Found at i:39842826 original size:53 final size:54
Alignment explanation
Indices: 39842742--39842872 Score: 176
Period size: 53 Copynumber: 2.4 Consensus size: 54
39842732 CCATAATAGT
* * * *
39842742 TAATTTTACCCATCGGGGGTATTTCGATAATTTTACCCAT-TGGGGTATTTTGG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGGGGGTATTTCGA
* * *
39842795 TAATTTTACCTATCAAGGGTATTTC-AGTAATTTTACCTATCGGGGGTATTTCGA
1 TAATTTTACCCATCGAGGGTATTTCGA-TAATTTTACCCATCGGGGGTATTTCGA
39842849 TAATTTTACCCATCGAGGGTATTT
1 TAATTTTACCCATCGAGGGTATTT
39842873 TGGTATAGTC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
52 1 0.01
53 34 0.51
54 32 0.48
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (54 bp):
TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGGGGGTATTTCGA
Found at i:39844408 original size:25 final size:25
Alignment explanation
Indices: 39844371--39844424 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
39844361 TGAACCTCTG
39844371 ACCTCCTTACCACACCTGTGACGCC
1 ACCTCCTTACCACACCTGTGACGCC
* * * **
39844396 ACCTCTTTGCCACACTTGTGTTGCC
1 ACCTCCTTACCACACCTGTGACGCC
39844421 ACCT
1 ACCT
39844425 TGCCGTTACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.17, C:0.43, G:0.13, T:0.28
Consensus pattern (25 bp):
ACCTCCTTACCACACCTGTGACGCC
Found at i:39846646 original size:114 final size:113
Alignment explanation
Indices: 39846367--39846646 Score: 373
Period size: 114 Copynumber: 2.5 Consensus size: 113
39846357 ATAGTCTATA
* * * * * * *
39846367 AATTTTAGGTTCAATGTTTG-AACATTTTAGTAAAAAATAAATGTATCGATACCCTTTCCATAGT
1 AATTTAAGCTTCAATGTTTGAAAAAATTTAGCAAAAAACAAATGTATCGATACCCTTGCCATAGT
* * * * *
39846431 ATTGATACTAGGGTCAAAGTATCGATACCTTTTCCTGGTATCGATACC
66 ATTAATACCAGGGTCAAAGTATCGACACCCTTGCCTGGTATCGATACC
* * * *
39846479 AATTTGAGCTTCGATGTTTGAAAAAATTTAGCAAAAGAACAAAGGTGTCGATACCCTTGCCATAG
1 AATTTAAGCTTCAATGTTTGAAAAAATTTAGCAAAA-AACAAATGTATCGATACCCTTGCCATAG
*
39846544 TATTAATACCAGGGTCATAGTATCGACACCCTTGCCTGGTATCGATACC
65 TATTAATACCAGGGTCAAAGTATCGACACCCTTGCCTGGTATCGATACC
*
39846593 AATTTAAGCTTCAATGTTTGAAAAAAATTTAGCAAAAAACAAATGTATTGATAC
1 AATTTAAGCTTCAATGTTTG-AAAAAATTTAGCAAAAAACAAATGTATCGATAC
39846647 AGGTATCGAT
Statistics
Matches: 144, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
112 17 0.12
113 12 0.08
114 99 0.69
115 16 0.11
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (113 bp):
AATTTAAGCTTCAATGTTTGAAAAAATTTAGCAAAAAACAAATGTATCGATACCCTTGCCATAGT
ATTAATACCAGGGTCAAAGTATCGACACCCTTGCCTGGTATCGATACC
Found at i:39850021 original size:2 final size:2
Alignment explanation
Indices: 39850016--39850043 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39850006 AAATTATAAG
39850016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39850044 TCAAGTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39850144 original size:44 final size:41
Alignment explanation
Indices: 39850068--39850153 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 41
39850058 ATATTTATGA
*
39850068 AAGTTAAAAAAAATATGTACATAAATATATATAGACATGTATAT
1 AAGTTAAAAAAAATATGTA-ATAAATACATAT--ACATGTATAT
*
39850112 AAGTTAAAAAATAAGTATGT-ATATATACATATACATGTATAT
1 AAGTTAAAAAA-AA-TATGTAATAAATACATATACATGTATAT
39850154 GCATTAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
42 10 0.26
44 21 0.55
45 2 0.05
46 5 0.13
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (41 bp):
AAGTTAAAAAAAATATGTAATAAATACATATACATGTATAT
Found at i:39850166 original size:30 final size:31
Alignment explanation
Indices: 39850131--39850193 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
39850121 AATAAGTATG
39850131 TATATATACATATACATGTATATGCAT-TAAAA
1 TATAT-TA-ATATACATGTATATGCATGTAAAA
* *
39850163 TATATTAATATATATGTATATGTATGTAAAA
1 TATATTAATATACATGTATATGCATGTAAAA
39850194 GTGTGCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 16 0.57
31 7 0.25
32 5 0.18
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (31 bp):
TATATTAATATACATGTATATGCATGTAAAA
Found at i:39851778 original size:44 final size:44
Alignment explanation
Indices: 39851706--39851821 Score: 162
Period size: 44 Copynumber: 2.7 Consensus size: 44
39851696 TGTTGGTTCG
* * *
39851706 ATCCGCTCTACTGC-ACTTCAGAGAGATACAATTTGTAGCTTCA
1 ATCCACTCTACTGCAAATTCAGAGAGATACAACTTGTAGCTTCA
* *
39851749 ATTCACTCTGCTGCAAATTCAGAGAGATACAACTTGTAGCTTCA
1 ATCCACTCTACTGCAAATTCAGAGAGATACAACTTGTAGCTTCA
* *
39851793 ATCCACTCTACTGCAACTTCAAAGAGATA
1 ATCCACTCTACTGCAAATTCAGAGAGATA
39851822 AGATTCATGG
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
43 11 0.17
44 52 0.83
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (44 bp):
ATCCACTCTACTGCAAATTCAGAGAGATACAACTTGTAGCTTCA
Found at i:39852011 original size:50 final size:48
Alignment explanation
Indices: 39851954--39852148 Score: 113
Period size: 45 Copynumber: 4.1 Consensus size: 48
39851944 TGCTCCACTA
39851954 CAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCCAACCTACTG
1 CAACTTTAGGGAGATAAGACTCGTTAT-GTAGATTTAATCC-ACCTACTG
* * * * * * *
39852004 CAACTTTAGAGG-TATAGGA-T--TCAT-CA-TTTTAATCCGCTCCACTG
1 CAACTTTAG-GGAGATAAGACTCGTTATGTAGATTTAATCCAC-CTACTG
* * * * * * **
39852048 CAACTTCAGGGAGATAAGATTTGTTATCTACAGTCTGCTCCA-CTA-T-
1 CAACTTTAGGGAGATAAGACTCGTTATGTAGA-TTTAATCCACCTACTG
39852094 -AACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCCAACCTACTG
1 CAACTTTAGGGAGATAAGACTCGTTAT-GTAGATTTAATCC-ACCTACTG
*
39852143 TAACTT
1 CAACTT
39852149 CAGAGGTATA
Statistics
Matches: 104, Mismatches: 26, Indels: 30
0.65 0.16 0.19
Matches are distributed among these distances:
43 3 0.03
44 26 0.25
45 30 0.29
46 4 0.04
47 10 0.10
48 4 0.04
49 1 0.01
50 24 0.23
51 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (48 bp):
CAACTTTAGGGAGATAAGACTCGTTATGTAGATTTAATCCACCTACTG
Found at i:39852173 original size:139 final size:138
Alignment explanation
Indices: 39851933--39852247 Score: 486
Period size: 139 Copynumber: 2.3 Consensus size: 138
39851923 TAAGATCCGC
* *
39851933 TATCTACAGCCTGCTCCACTACAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCCAAC
1 TATCTACAGTCTGCTCCACTATAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCCAAC
* *
39851998 CTACTGCAACTTTAGAGGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
66 CTACTGCAACTTCAGAGGTATAGGATTCAACATTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
*
39852063 AAGATTTG
131 AAGATTAG
39852071 TTATCTACAGTCTGCTCCACTATAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCCAA
1 -TATCTACAGTCTGCTCCACTATAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCCAA
* * * *
39852136 CCTACTGTAACTTCAGAGGTATAGGATTCAACGTTTTAATCTGCTCCACTGCAACTTTAGGGAGA
65 CCTACTGCAACTTCAGAGGTATAGGATTCAACATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
39852201 TAAGATTAG
130 TAAGATTAG
* * * * * *
39852210 TAGCTTCAATTTGCTCCGCTATAACTTCAGGGAGATAA
1 TATCTACAGTCTGCTCCACTATAACTTTAGGGAGATAA
39852248 CATTGGTATC
Statistics
Matches: 161, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
138 32 0.20
139 129 0.80
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (138 bp):
TATCTACAGTCTGCTCCACTATAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCCAAC
CTACTGCAACTTCAGAGGTATAGGATTCAACATTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
AAGATTAG
Found at i:39852242 original size:44 final size:44
Alignment explanation
Indices: 39852173--39852517 Score: 282
Period size: 44 Copynumber: 7.8 Consensus size: 44
39852163 TCAACGTTTT
* * *
39852173 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTAGTAGCTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTAGTATCTTC
* * * * *
39852217 AATTTGCTCCGCTATAACTTCAGGGAGATAACATTGGTATCTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTAGTATCTTC
* * * * * *
39852261 AACCTGCTCCACTGCAACTCCAGGGAGATAAGGTTTGTTATCTAC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTAG-TATCTTC
* * * * * *
39852306 AATATACTCCACTACAACTTTAGTGAGATAAGATCAGTAGCTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTAGTATCTTC
* * ** * *
39852350 AGTCTGCTCCTCTGTAACTTCAGGGCGATAAGACTCA-TATCTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGA-TTAGTATCTTC
* * * * *
39852394 AGTCTACTCCACTGCAACTTCATGGAAATAAGACTTA-TATCTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGA-TTAGTATCTTC
* * * *
39852438 AA-CTTGCTCCACCACAACTTCAAGGAGATAAGGTTTGCTATCTTC
1 AATC-TGCTCCACTACAACTTCAGGGAGATAAGATTAG-TATCTTC
* * *
39852483 AGTCTGTTCCACTATAACTTCAGGGAGATAAGATT
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATT
39852518 TGATTTGATA
Statistics
Matches: 234, Mismatches: 61, Indels: 11
0.76 0.20 0.04
Matches are distributed among these distances:
43 3 0.01
44 160 0.68
45 70 0.30
46 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTACAACTTCAGGGAGATAAGATTAGTATCTTC
Found at i:39852338 original size:133 final size:131
Alignment explanation
Indices: 39852179--39852513 Score: 348
Period size: 133 Copynumber: 2.5 Consensus size: 131
39852169 TTTTAATCTG
* * * *
39852179 CTCCACTGCAACTTTAGGGAGATAAGATTAGTAGCTTCAATTTGCTCCGCTATAACTTCAGGGAG
1 CTCCACTACAACTTTA-GGAGATAAGATTAGTAGCTTCAGTCTGCTCCACTATAACTTCAGGGAG
* ** * * ** *
39852244 ATAACATTGGTATCTTCAACCTGCTCCACTGCAACTCCAGGGAGATAAGGTTTGTTATCTACAA-
65 ATAACACTCATATCTTCAACCTACTCCACTGCAACTCCAGGGAAATAAGACTT-ATATCTACAAC
39852308 TATA
129 T-TA
* * * *
39852312 CTCCACTACAACTTTAGTGAGATAAGATCAGTAGCTTCAGTCTGCTCCTCTGTAACTTCAGGGCG
1 CTCCACTACAACTTTAG-GAGATAAGATTAGTAGCTTCAGTCTGCTCCACTATAACTTCAGGGAG
* ** * * *
39852377 ATAAGACTCATATCTTCAGTCTACTCCACTGCAACTTCATGGAAATAAGACTTATATCTTCAACT
65 ATAACACTCATATCTTCAACCTACTCCACTGCAACTCCAGGGAAATAAGACTTATATCTACAACT
*
39852442 TG
130 TA
* * * * * *
39852444 CTCCACCACAACTTCAAGGAGATAAGGTTTGCTATCTTCAGTCTGTTCCACTATAACTTCAGGGA
1 CTCCACTACAACTT-TAGGAGATAAGATTAG-TAGCTTCAGTCTGCTCCACTATAACTTCAGGGA
39852509 GATAA
64 GATAA
39852514 GATTTGATTT
Statistics
Matches: 166, Mismatches: 32, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
132 33 0.20
133 133 0.80
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (131 bp):
CTCCACTACAACTTTAGGAGATAAGATTAGTAGCTTCAGTCTGCTCCACTATAACTTCAGGGAGA
TAACACTCATATCTTCAACCTACTCCACTGCAACTCCAGGGAAATAAGACTTATATCTACAACTT
A
Found at i:39852708 original size:41 final size:44
Alignment explanation
Indices: 39852642--39852757 Score: 112
Period size: 45 Copynumber: 2.7 Consensus size: 44
39852632 ATTTTGGTTC
* * * * *
39852642 GCTCCACTACAACTTCTGGGAGATAAGACT-C-ATC-GTGGTCT
1 GCTCTACTGCAACTTCAGAGAGATAAGACTGCTATCTGTAGTCT
*
39852683 GCTCTACTGCAACTTCAGAGAGATAAGATCTGCTATCTTTAGTCT
1 GCTCTACTGCAACTTCAGAGAGATAAGA-CTGCTATCTGTAGTCT
** * *
39852728 ATTCTACTGCAACCTCAGTGAGATAAGACT
1 GCTCTACTGCAACTTCAGAGAGATAAGACT
39852758 TGTAGCTTCA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 24 0.39
42 2 0.03
43 1 0.02
44 5 0.08
45 29 0.48
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
GCTCTACTGCAACTTCAGAGAGATAAGACTGCTATCTGTAGTCT
Found at i:39852973 original size:103 final size:102
Alignment explanation
Indices: 39852683--39852974 Score: 311
Period size: 103 Copynumber: 2.8 Consensus size: 102
39852673 ATCGTGGTCT
* *** * *
39852683 GCTCTACTGCAACTTCAGAGAGATAAGATCTGCTATC-TTTAG-TCTATTCTACTGCAACCTCAG
1 GCTCTACTGCAACTTCAGAGAGATAAGATC--C-ATCATTTTGATCCGCTCCACTGCAACTTCAG
* * * *
39852746 TGAGATA-AGACTTGTAGCTTCAATAAAGTCTGATACAATCT
63 GGAGATAGA-AC-TATAACTTCAATAAAGTCTGATACAATCC
* * ** * * *
39852787 ACTCTACTACAACTTTGGAGAGATAAGATCCATCATTTTAATCCGCTTCACTGCAACTTCAGGAA
1 GCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTGATCCGCTCCACTGCAACTTCAGGGA
* *
39852852 GATAGGACTAGTAACTTCAATAAAGTCTGATACGATCC
66 GATAGAACTA-TAACTTCAATAAAGTCTGATACAATCC
*
39852890 GCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTGACCCGCTCCACTGCAACTTCAGGGA
1 GCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTGATCCGCTCCACTGCAACTTCAGGGA
*
39852955 GATAGAACTCATATCTTCAA
66 GATAGAACT-ATAACTTCAA
39852975 GTTGCCCCAC
Statistics
Matches: 154, Mismatches: 29, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
101 3 0.02
102 5 0.03
103 119 0.77
104 27 0.18
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (102 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTGATCCGCTCCACTGCAACTTCAGGGA
GATAGAACTATAACTTCAATAAAGTCTGATACAATCC
Found at i:39853245 original size:44 final size:44
Alignment explanation
Indices: 39852934--39853454 Score: 253
Period size: 44 Copynumber: 11.6 Consensus size: 44
39852924 ATTTTGACCC
**
39852934 GCTCCACTGCAACTTCAGGGAGAT-AGAACTCATATCTTCAAGT-T
1 GCTCCACTGCAACTTCAGGGAGATAAG-ACTTGTATCTTCAA-TCT
* *
39852978 GCCCCACTGCAACTTCAGAGG-GATAAGACTTGTAAT-TTCAACCT
1 GCTCCACTGCAACTTCAG-GGAGATAAGACTTGT-ATCTTCAATCT
* * * *
39853022 GCTCTACTACAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-C--T--TGTAT--CTTCAATCT
* * * * *
39853073 GTTCCACCGCAGCTTCAGGGAAATAAGA-TTCGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTT-G-TATCTTCAATCT
* * ** * *
39853118 ACTCCACTGCAACTTCAGGGAGATAGGA--TCCATCATTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTATC--TTCAATCT
** * * * *
39853162 ATTCCACTACAACTTCAGGGAGGTAGGA-TTAGTAACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTT-GTATCTTCAATCT
*
39853206 GCTCCACTACAACTTCAGGGAGATAAGACTTGTATCTTCAA-CTT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAATC-T
* ** *
39853250 GCCCCACTGCAACTTCATGGG-GATAAGGTTTGCTAT-TTGAATCT
1 GCTCCACTGCAACTTCA-GGGAGATAAGACTTG-TATCTTCAATCT
* * * * * *
39853294 GCTCTATTGCAACTTCAGAGAGATAA-AGTT-TGAT-AT-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGT-ATCTTCAATCT
* * ** * ** *
39853335 GCTCTAATGCAACTTCAGAAAGATGAGATCTGTTATGGTAGATTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-C---T-T-GTATCTTCAATCT
* * * * *
39853385 GTTCCACTACAACTTCAGGGAAATAAGATTTGCTATCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTG-TATCTTCAATCT
39853430 GCTCCACTGCAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
39853455 GAATCCACAA
Statistics
Matches: 363, Mismatches: 77, Indels: 73
0.71 0.15 0.14
Matches are distributed among these distances:
41 28 0.08
42 7 0.02
43 6 0.02
44 172 0.47
45 81 0.22
46 4 0.01
47 6 0.02
48 3 0.01
49 4 0.01
50 24 0.07
51 28 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAATCT
Found at i:39853468 original size:45 final size:45
Alignment explanation
Indices: 39853377--39853486 Score: 105
Period size: 45 Copynumber: 2.4 Consensus size: 45
39853367 TTATGGTAGA
* * *** *
39853377 TTTAATCTGTTCCACTACAACTTCAGGGAAATAAGATTTGCTATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATCCACAATC
*
39853422 TTTAATCTGCTCCACTGCAACTTCAGGGAGAT-AGAATCCACAATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAAATAAG-ATCCACAATC
* * * *
39853467 TTCAACCTACTCTACTGCAA
1 TTTAATCTGCTCCACTGCAA
39853487 ACTCGGAGAG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
44 2 0.04
45 51 0.96
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (45 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATCCACAATC
Found at i:39854011 original size:24 final size:24
Alignment explanation
Indices: 39853961--39854018 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
39853951 CGGATTGCCC
*
39853961 CCACTGTAATCTTTAAAGTTCAAT
1 CCACTGTAATCTTCAAAGTTCAAT
* *
39853985 CCATTGTAATCTTCAAGGTT-AAGT
1 CCACTGTAATCTTCAAAGTTCAA-T
39854009 CCACTGTAAT
1 CCACTGTAAT
39854019 TTTGGGACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGTTCAAT
Found at i:39855086 original size:7 final size:7
Alignment explanation
Indices: 39855074--39855117 Score: 52
Period size: 7 Copynumber: 5.7 Consensus size: 7
39855064 TGGCCTCTCC
39855074 TTTTTCT
1 TTTTTCT
39855081 TTTTTCT
1 TTTTTCT
39855088 CCTTTTTCT
1 --TTTTTCT
39855097 TTTTTCTT
1 TTTTTC-T
39855105 CTTTTTCT
1 -TTTTTCT
39855113 TTTTT
1 TTTTT
39855118 TGACTCAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 18 0.55
8 2 0.06
9 13 0.39
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:39855090 original size:16 final size:16
Alignment explanation
Indices: 39855069--39855117 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
39855059 CACCTTGGCC
39855069 TCTCCTTTTTCTTTTT
1 TCTCCTTTTTCTTTTT
39855085 TCTCCTTTTTCTTTTT
1 TCTCCTTTTTCTTTTT
*
39855101 TCTTCTTTTTCTTTTT
1 TCTCCTTTTTCTTTTT
39855117 T
1 T
39855118 TGACTCAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TCTCCTTTTTCTTTTT
Found at i:39855174 original size:62 final size:67
Alignment explanation
Indices: 39855093--39855226 Score: 165
Period size: 68 Copynumber: 2.1 Consensus size: 67
39855083 TTTCTCCTTT
39855093 TTCTTTTTTCTTC-TTTT-T-C-TTTTTTT-GACTCAAAGCGCCCTTTGCAGGTTTTCACCTTGG
1 TTCTTTTTTCTTCTTTTTCTCCTTTTTTTTAGACTCAAAGCGCCCTTTGCAGGTTTTCACCTTGG
39855153 TC
66 TC
* **
39855155 TTCTCTTTTT-TTCTTTTTCTCCTTTTTTTTAGGACTCAAGGCGCCCTTTGTGGGTTTTCACCTT
1 TTCT-TTTTTCTTCTTTTTCTCCTTTTTTTTA-GACTCAAAGCGCCCTTTGCAGGTTTTCACCTT
*
39855219 AGT-
64 GGTC
39855222 TTCTT
1 TTCTT
39855227 CCTTTTCAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
62 7 0.11
63 9 0.15
64 1 0.02
65 1 0.02
66 8 0.13
67 4 0.07
68 31 0.51
ACGTcount: A:0.09, C:0.23, G:0.13, T:0.54
Consensus pattern (67 bp):
TTCTTTTTTCTTCTTTTTCTCCTTTTTTTTAGACTCAAAGCGCCCTTTGCAGGTTTTCACCTTGG
TC
Found at i:39855821 original size:22 final size:21
Alignment explanation
Indices: 39855781--39855821 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39855771 TGAAAAGTGT
*
39855781 TTTTATTAATAAACAATTTAG
1 TTTTATTAAAAAACAATTTAG
*
39855802 TTTTATTAAAACAACGATTT
1 TTTTATTAAAA-AACAATTT
39855822 TGGTCCACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTTATTAAAAAACAATTTAG
Found at i:39856761 original size:30 final size:31
Alignment explanation
Indices: 39856726--39856788 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
39856716 AATAAGTATG
39856726 TATATATACATATACATGTATATGCAT-TAAAA
1 TATAT-TA-ATATACATGTATATGCATGTAAAA
* *
39856758 TATATTAATATATATGTATATGTATGTAAAA
1 TATATTAATATACATGTATATGCATGTAAAA
39856789 GTGTGCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 16 0.57
31 7 0.25
32 5 0.18
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (31 bp):
TATATTAATATACATGTATATGCATGTAAAA
Found at i:39858976 original size:19 final size:20
Alignment explanation
Indices: 39858934--39858985 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
39858924 TTCAAGGATG
39858934 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGA-ATA
39858955 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
39858974 TGCAATCTTAGA
1 TGCAATCTTAGA
39858986 AGATGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:39859571 original size:13 final size:14
Alignment explanation
Indices: 39859552--39859589 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
39859542 CAATGGCATA
39859552 GAAATAATATAAAC
1 GAAATAATATAAAC
39859566 -AAATAA-ATAAAC
1 GAAATAATATAAAC
39859578 GAAATTAATATA
1 GAAA-TAATATA
39859590 TGTAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:39859646 original size:30 final size:31
Alignment explanation
Indices: 39859612--39859669 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
39859602 TATTTGTTTT
* *
39859612 TATATATATGTA-ATTATCTTTTTTATAATC
1 TATATATATCTAGATAATCTTTTTTATAATC
*
39859642 TATATATATCTAGATAATTTTTTTTATA
1 TATATATATCTAGATAATCTTTTTTATA
39859670 TATGTACATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (31 bp):
TATATATATCTAGATAATCTTTTTTATAATC
Found at i:39860550 original size:12 final size:12
Alignment explanation
Indices: 39860533--39860565 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39860523 AAACAGGCTT
39860533 TTAGCGGCGTTC
1 TTAGCGGCGTTC
*
39860545 TTAGCGGCGTTT
1 TTAGCGGCGTTC
39860557 TTAGCGGCG
1 TTAGCGGCG
39860566 GTTGATACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.36, T:0.33
Consensus pattern (12 bp):
TTAGCGGCGTTC
Found at i:39860852 original size:114 final size:115
Alignment explanation
Indices: 39860652--39860961 Score: 400
Period size: 114 Copynumber: 2.7 Consensus size: 115
39860642 GCGATTTCCA
* *
39860652 GAAAGCGCCGC-AAAATACCTAAGCCCAACGACGCCGTTTT-TCGAGCTTTCGAGGGATTTAGCG
1 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCT-GAGCTTTCG-GGGATTTAGCG
* * *
39860715 G-TGTTTTTAAGAAAGCGCCGCTAATG-CTCAGGGCTTTAGTGGCGTTTTTAC
64 GCTGTTTTTAAGAAAGCGCCGCTAATGCCT-AGGGCTTTAGCGACGATTTTAC
* *
39860766 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGTCGTTTTCTAAGCTTTCGGGGATTTAGCGGC
1 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
** * *
39860831 T-TTTTTGGGGAAGCGCCGCTAATGCCTAGGGCTTTAGCGACGATTTTGC
66 TGTTTTTAAGAAAGCGCCGCTAATGCCTAGGGCTTTAGCGACGATTTTAC
* * *
39860880 GAAAGTGCCACAAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCTTTCGGGGATTTGGCGGC
1 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
*
39860945 -GCTTTTT-ATAAAGCGCC
66 TG-TTTTTAAGAAAGCGCC
39860962 ACAAAAACCT
Statistics
Matches: 171, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
114 127 0.74
115 43 0.25
116 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (115 bp):
GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
TGTTTTTAAGAAAGCGCCGCTAATGCCTAGGGCTTTAGCGACGATTTTAC
Found at i:39861001 original size:185 final size:186
Alignment explanation
Indices: 39860757--39861146 Score: 568
Period size: 185 Copynumber: 2.1 Consensus size: 186
39860747 GCTTTAGTGG
**
39860757 CGTTTTTACGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGTCGTTTTCTAAGCTTTCGGGGA
1 CGTTTTTAATAAAGCGCCAC-AAAAAACCTAAGCCCAACGACGTCGTTTTCTAAGCTTTCGGGGA
* * * * * * * *
39860822 TTTAGCGGCTTTTTTGGGGAAGCGCCGCTAATGCCTAGGGCTTTAGCGACGATTTTGCGAAAGTG
65 TTTAGCAGCATTTTTCGGGAAGCGACGCTAATACCCAAGGCTTTAGCGACGATTTTGCGAAAGCG
* * *
39860887 CCACAAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCTTTCGGGGATTTGGCGG
130 CCACAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCGGGGATTTAGCGA
* * *
39860944 CGCTTTTT-ATAAAGCGCCAC-AAAAACCTAATCCCAACGATGTCGTTTTCTGAGCTTTCGGGGA
1 CG-TTTTTAATAAAGCGCCACAAAAAACCTAAGCCCAACGACGTCGTTTTCTAAGCTTTCGGGGA
* * *
39861007 TTTAGCAGCATTTTTCGGGAAGCGACGCTAATACCCAAGGCTTTAGCGGCGTTTTTGCTAAAGCG
65 TTTAGCAGCATTTTTCGGGAAGCGACGCTAATACCCAAGGCTTTAGCGACGATTTTGCGAAAGCG
39861072 CCACAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCGGGGATTTAGCGA
130 CCACAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCGGGGATTTAGCGA
*
39861129 CGTTTTTAATTAAGCGCC
1 CGTTTTTAATAAAGCGCC
39861147 GCTAATGCTC
Statistics
Matches: 181, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
184 5 0.03
185 159 0.88
187 12 0.07
188 5 0.03
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.26
Consensus pattern (186 bp):
CGTTTTTAATAAAGCGCCACAAAAAACCTAAGCCCAACGACGTCGTTTTCTAAGCTTTCGGGGAT
TTAGCAGCATTTTTCGGGAAGCGACGCTAATACCCAAGGCTTTAGCGACGATTTTGCGAAAGCGC
CACAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCGGGGATTTAGCGA
Found at i:39861144 original size:114 final size:114
Alignment explanation
Indices: 39860940--39861523 Score: 698
Period size: 115 Copynumber: 5.1 Consensus size: 114
39860930 CGGGGATTTG
* * *
39860940 GCGGCGCTTTTT-ATAAAGCGCCAC--AAAAACCTAATCCCAACGATGTCGTTTTCTGAGCTTTC
1 GCGGCG-TTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTC
* ** * * * *
39861002 GGGGATTTAGC-AGCATTTTTCGGGAAGCGACGCTAATACCCAAGGCTTTA
65 GGGGATTTAGCGA-CGTTTTTAAGTAAGCGCCGCTAATGCTCAAGGCTTTA
* * *
39861052 GCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCG
1 GCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCG
* *
39861117 GGGATTTAGCGACGTTTTTAATTAAGCGCCGCTAATGCTCAGGGGCTTTA
66 GGGATTTAGCGACGTTTTTAAGTAAGCGCCGCTAATGCTCA-AGGCTTTA
* *
39861167 GCGGTGTTTTT-ACTAAAGCGCCACAAAAAAACCTAAGCCCGACGACGCCGTTTTCTGAGCTTTC
1 GCGGCGTTTTTGA-TAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTC
* *
39861231 GGGGATTTTGCGACGTTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTA
65 GGGGATTTAGCGACG-TTTTTAAGTAAGCGCCGCTAATGCTCAAGGCTTTA
* * * * *
39861282 GCAGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACACCGTTTTTTGAGTTTTCA
1 GCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCG
*
39861347 GGGATTTAGCGGCGTTTTTTAAGTAAGCGCCGCTAATGCTC-AGGCTTTTA
66 GGGATTTAGCGACG-TTTTTAAGTAAGCGCCGCTAATGCTCAAGGC-TTTA
** * * * *
39861397 GCGGCGTTTTTGGGAAGGCGCCGCAAAAAAACCTAAGCCCAACGACGCCATTTTCTTAGCTTTCG
1 GCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCG
* * * * *
39861462 TGGATTTAGTGGCATTTTTAA-TAAAGTGCCGCTAATGCTC-AGTGCTTTA
66 GGGATTTAGCGACGTTTTTAAGT-AAGCGCCGCTAATGCTCAAG-GCTTTA
*
39861511 GCGGCATTTTTGA
1 GCGGCGTTTTTGA
39861524 GGATGCGCCG
Statistics
Matches: 412, Mismatches: 49, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
111 5 0.01
112 17 0.04
113 1 0.00
114 108 0.26
115 254 0.62
116 27 0.07
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (114 bp):
GCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCG
GGGATTTAGCGACGTTTTTAAGTAAGCGCCGCTAATGCTCAAGGCTTTA
Found at i:39862153 original size:24 final size:24
Alignment explanation
Indices: 39862126--39862206 Score: 99
Period size: 24 Copynumber: 3.2 Consensus size: 24
39862116 AATAAACAAA
39862126 TAAATAAATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
* *
39862150 TAAATTAATTTTTAGGTAATTAATTGTT
1 TAAA-TAA---ATAGGTAATTAATTATT
*
39862178 TAAATAGATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
39862202 TAAAT
1 TAAAT
39862207 GAATGATACA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 24 0.50
25 3 0.06
27 2 0.04
28 19 0.40
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (24 bp):
TAAATAAATAGGTAATTAATTATT
Found at i:39862154 original size:28 final size:28
Alignment explanation
Indices: 39862123--39862206 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
39862113 ATAAATAAAC
39862123 AAATAAATAAATAGGTAATTAATTATTT
1 AAATAAATAAATAGGTAATTAATTATTT
* *** *
39862151 AAATTAATTTTTAGGTAATTAATT-GTT
1 AAATAAATAAATAGGTAATTAATTATTT
*
39862178 ---TAAATAGATAGGTAATTAATTATTT
1 AAATAAATAAATAGGTAATTAATTATTT
39862203 AAAT
1 AAAT
39862207 GAATGATACA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
24 17 0.40
25 2 0.05
27 2 0.05
28 21 0.50
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (28 bp):
AAATAAATAAATAGGTAATTAATTATTT
Found at i:39862943 original size:365 final size:365
Alignment explanation
Indices: 39862256--39862961 Score: 1171
Period size: 365 Copynumber: 1.9 Consensus size: 365
39862246 GATTTTGCGG
*
39862256 CGTTTTGATAAAAAAACGCCACAAAAATTTATTGCATTTACCGATACGGCTTCGTTTCGGCTTAG
1 CGTTTTGATAAAAAAACGCCACAAAAATTTATTGCATTTACCGATACGGCGTCGTTTCGGCTTAG
* *
39862321 GGAATAAGTTTTAGTTGTGGCATTTTTCCGAAAAGCGCCGTAAATAATATTTAAACTTTGCCAAA
66 GGAATAAATTTTAGTTGTGGCATTTTTCCGAAAAGCACCGTAAATAATATTTAAACTTTGCCAAA
* * * *
39862386 ATAGCGTCGTTTCAGTTGAAGGATGGAATATTTTAGTGGCGTTTTATTATAAACGCCGCAATGAT
131 ACAGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGGCGTTTTATTAAAAACGCCGCAAGGAT
** ** *
39862451 GTATAAAATTTTTTGAAAACGGTGCCGGTTCGATAATATATTAATTGTGGCGTTTTTGGGAAAAC
196 GTATAAAATTTACTGAAAACGACGCCGGTTCGATAATATATTAATTGTGGCGTGTTTGGGAAAAC
* *
39862516 GCTAGAATGTTTCCTTATATTTTAATAAAATGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTG
261 GCCAGAATGTTTCCTTATATTTTAATAAAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTG
*
39862581 GCGTTTTTAATTCAAAAACCGTAAAAGGTAGACATTACCAA
326 GCATTTTTAATT-AAAAACCGTAAAAGGTAGACATTACCAA
* *
39862622 CGTTTTGAT-AAAAAATGCCACAAATATTTATTGCATTTACCGATACGGCGTCGTTTCGGCTTAG
1 CGTTTTGATAAAAAAACGCCACAAAAATTTATTGCATTTACCGATACGGCGTCGTTTCGGCTTAG
* * * *
39862686 GGAATAAATTTTAGTTGTGGCATTTTTCCTAAAAGCACTGTAAATAATATTTGAACTTTGCGAAA
66 GGAATAAATTTTAGTTGTGGCATTTTTCCGAAAAGCACCGTAAATAATATTTAAACTTTGCCAAA
* * *
39862751 ACAGCGCCGTTTCAGTTGAAGGATGGAATCTTTTAGTGGCGTTTTATTAAAAATGTCGCAAGGAT
131 ACAGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGGCGTTTTATTAAAAACGCCGCAAGGAT
39862816 GTATAAAATTTACTGAAAACGACGCCGGTTCGATAATATATTAATTGTGGCGTGTTTGGGAAAAC
196 GTATAAAATTTACTGAAAACGACGCCGGTTCGATAATATATTAATTGTGGCGTGTTTGGGAAAAC
*
39862881 GCCAGAATGTTTCCTTATATTTTTATAAAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTG
261 GCCAGAATGTTTCCTTATATTTTAATAAAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTG
39862946 GCATTTTTAATTAAAA
326 GCATTTTTAATTAAAA
39862962 CGCCGCAAAT
Statistics
Matches: 315, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
364 4 0.01
365 302 0.96
366 9 0.03
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (365 bp):
CGTTTTGATAAAAAAACGCCACAAAAATTTATTGCATTTACCGATACGGCGTCGTTTCGGCTTAG
GGAATAAATTTTAGTTGTGGCATTTTTCCGAAAAGCACCGTAAATAATATTTAAACTTTGCCAAA
ACAGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGGCGTTTTATTAAAAACGCCGCAAGGAT
GTATAAAATTTACTGAAAACGACGCCGGTTCGATAATATATTAATTGTGGCGTGTTTGGGAAAAC
GCCAGAATGTTTCCTTATATTTTAATAAAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTG
GCATTTTTAATTAAAAACCGTAAAAGGTAGACATTACCAA
Found at i:39863656 original size:18 final size:18
Alignment explanation
Indices: 39863633--39863670 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
39863623 CGTTTGTTAG
*
39863633 TTACTTGCTGTGTTAATA
1 TTACTTGCAGTGTTAATA
39863651 TTACTTGCAGTGTTAATA
1 TTACTTGCAGTGTTAATA
39863669 TT
1 TT
39863671 TTTGAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (18 bp):
TTACTTGCAGTGTTAATA
Found at i:39864743 original size:23 final size:23
Alignment explanation
Indices: 39864715--39864758 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
39864705 CTTATATGTA
*
39864715 AACTTACATAATACATTACTTTT
1 AACTTACATAATACATAACTTTT
39864738 AACTTACATAATACATAACTT
1 AACTTACATAATACATAACTT
39864759 ATAAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (23 bp):
AACTTACATAATACATAACTTTT
Found at i:39864898 original size:9 final size:9
Alignment explanation
Indices: 39864866--39865202 Score: 271
Period size: 9 Copynumber: 38.8 Consensus size: 9
39864856 ATAACATAAC
39864866 AACTTACAT
1 AACTTACAT
39864875 AA--TACAT
1 AACTTACAT
* *
39864882 AGCATACAT
1 AACTTACAT
39864891 AACTTACAT
1 AACTTACAT
*
39864900 AA--TACAA
1 AACTTACAT
39864907 AACTTACAT
1 AACTTACAT
*
39864916 AACTTAAAT
1 AACTTACAT
* *
39864925 ATCTTACAC
1 AACTTACAT
39864934 AACTTACAT
1 AACTTACAT
*
39864943 AACCTACAT
1 AACTTACAT
39864952 AA--TACATTT
1 AACTTACA--T
39864961 AACTTACAT
1 AACTTACAT
39864970 AACTTACAT
1 AACTTACAT
39864979 AACTTACAT
1 AACTTACAT
*
39864988 AA--TACAA
1 AACTTACAT
39864995 AACTTACAT
1 AACTTACAT
* *
39865004 AACCTAAAT
1 AACTTACAT
* *
39865013 ATCTTACAC
1 AACTTACAT
39865022 AACTTACAT
1 AACTTACAT
*
39865031 AACCTACAT
1 AACTTACAT
39865040 AA--TACATTT
1 AACTTACA--T
39865049 AACTTACAT
1 AACTTACAT
39865058 AACTTACAT
1 AACTTACAT
*
39865067 AATACATA-AT
1 -A-ACTTACAT
39865077 AACTTAC--
1 AACTTACAT
39865084 AACTTACAT
1 AACTTACAT
*
39865093 AACATACAT
1 AACTTACAT
* **
39865102 TACTTTGAT
1 AACTTACAT
39865111 AACTTACAT
1 AACTTACAT
39865120 AACTTACAT
1 AACTTACAT
*
39865129 AA--TACAC
1 AACTTACAT
39865136 AACTTACAT
1 AACTTACAT
* *
39865145 AGCTTACTT
1 AACTTACAT
39865154 AA--TACAT
1 AACTTACAT
39865161 AACTTACAT
1 AACTTACAT
39865170 AACTT--AT
1 AACTTACAT
*
39865177 ACACGTACAT
1 A-ACTTACAT
39865187 AACTTACAT
1 AACTTACAT
*
39865196 AATTTAC
1 AACTTAC
39865203 TTATCTATGA
Statistics
Matches: 260, Mismatches: 42, Indels: 52
0.73 0.12 0.15
Matches are distributed among these distances:
7 48 0.18
8 7 0.03
9 187 0.72
10 6 0.02
11 12 0.05
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:39864910 original size:70 final size:68
Alignment explanation
Indices: 39864855--39865171 Score: 172
Period size: 70 Copynumber: 4.7 Consensus size: 68
39864845 TAACTTACGC
39864855 AATAACATA-ACAACTTACATAA-TACATAGCATACA-TAACTTACATAATACAAAACTTACATA
1 AATAACATACACAACTTACATAACTACATA--ATACATTAACTTACATAATACAAAACTTACATA
39864917 ACTTA
64 ACTTA
* * *
39864922 AATATCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAACTTACA
1 AATAACATACACAACTTACATAA-CTACATAATACA-TTAACTTACATAA--TACAAAACTTACA
39864987 TAA--TA
62 TAACTTA
* * * * * * * *
39864992 CAA-AACTTACATAACCTAAATATCTTACACAACTTACA-TAACCTACATAATACATTTAACTTA
1 -AATAACATACACAACTTACATAAC-TACATAA--TACATTAACTTACATAATACA--AAACTTA
39865055 CATAACTTA
60 CATAACTTA
* * *
39865064 CATAATACATA-ATAACTTAC--AACTTACATAACATACATT-ACTT---TGAT----AACTTAC
1 AAT-A-ACATACACAACTTACATAAC-TACAT-A-ATACATTAACTTACATAATACAAAACTTAC
39865118 ATAACTTA
61 ATAACTTA
* * *
39865126 CAT-A-ATACACAACTTACATAGCTTACTTAATACA-TAACTTACATAA
1 AATAACATACACAACTTACATAAC-TACATAATACATTAACTTACATAA
39865172 CTTATACACG
Statistics
Matches: 200, Mismatches: 22, Indels: 61
0.71 0.08 0.22
Matches are distributed among these distances:
58 4 0.02
59 18 0.09
60 1 0.00
61 7 0.04
62 20 0.10
67 7 0.04
68 25 0.12
69 1 0.00
70 64 0.32
71 17 0.09
72 23 0.12
73 9 0.05
74 4 0.02
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (68 bp):
AATAACATACACAACTTACATAACTACATAATACATTAACTTACATAATACAAAACTTACATAAC
TTA
Found at i:39864978 original size:88 final size:88
Alignment explanation
Indices: 39864877--39865151 Score: 371
Period size: 88 Copynumber: 3.1 Consensus size: 88
39864867 ACTTACATAA
* * *
39864877 TACATAGCATACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
1 TACATAACTTACATAACTTACATAATACAAAACTTACATAACATAAATATCTTACACAACTTACA
39864942 TAACCTACATAATACATTTAACT
66 TAACCTACATAATACATTTAACT
*
39864965 TACATAACTTACATAACTTACATAATACAAAACTTACATAACCTAAATATCTTACACAACTTACA
1 TACATAACTTACATAACTTACATAATACAAAACTTACATAACATAAATATCTTACACAACTTACA
39865030 TAACCTACATAATACATTTAACT
66 TAACCTACATAATACATTTAACT
* * ** *
39865053 TACATAACTTACATAA--TACATAATAACTTACAACTTACATAACATACAT-TACTTTGATAACT
1 TACATAACTTACATAACTTACATAAT-AC--AAAACTTACATAACATAAATAT-CTTACACAACT
* *
39865115 TACATAACTTACATAATACA--CAACT
62 TACATAACCTACATAATACATTTAACT
*
39865140 TACATAGCTTAC
1 TACATAACTTAC
39865152 TTAATACATA
Statistics
Matches: 171, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
86 8 0.05
87 17 0.10
88 102 0.60
89 44 0.26
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (88 bp):
TACATAACTTACATAACTTACATAATACAAAACTTACATAACATAAATATCTTACACAACTTACA
TAACCTACATAATACATTTAACT
Found at i:39865145 original size:25 final size:25
Alignment explanation
Indices: 39865109--39865202 Score: 107
Period size: 25 Copynumber: 3.7 Consensus size: 25
39865099 CATTACTTTG
*
39865109 ATAACTTACATAACTTACATAATAC
1 ATAACTTACATAACTTACACAATAC
* * **
39865134 ACAACTTACATAGCTTACTTAATAC
1 ATAACTTACATAACTTACACAATAC
* *
39865159 ATAACTTACATAACTTATACACGTAC
1 ATAACTTACATAACTTACACA-ATAC
*
39865185 ATAACTTACATAATTTAC
1 ATAACTTACATAACTTAC
39865203 TTATCTATGA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
25 38 0.67
26 19 0.33
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (25 bp):
ATAACTTACATAACTTACACAATAC
Found at i:39865174 original size:34 final size:34
Alignment explanation
Indices: 39864866--39865197 Score: 197
Period size: 34 Copynumber: 9.6 Consensus size: 34
39864856 ATAACATAAC
*
39864866 AACTTACATAA-TACATAGCATACATAACTTACAT
1 AACTTACATAACTACATAAC-TACATAACTTACAT
* * * *
39864900 AA--TACAAAACTTACATAACTTAAATATCTTACAC
1 AACTTACATAAC-TACATAAC-TACATAACTTACAT
39864934 AACTTACATAACCTACATAA-TACATTTAACTTACAT
1 AACTTACATAA-CTACATAACTACA--TAACTTACAT
*
39864970 AACTTACATAACTTACATAA-TACAAAACTTACAT
1 AACTTACATAAC-TACATAACTACATAACTTACAT
* * * * *
39865004 AACCTAAATATCTTACACAACTTACATAACCTACAT
1 AACTTACATAAC-TACATAAC-TACATAACTTACAT
39865040 AA--TACATTTAACTTACATAACTTACATAA--TACAT
1 AACTTACA--TAAC-TACATAAC-TACATAACTTACAT
* * * **
39865074 AA-TAACTTACAACTTACATAACATACATTACTTTGAT
1 AACTTAC--ATAAC-TACATAAC-TACATAACTTACAT
*
39865111 AACTTACATAACTTACATAA-TACACAACTTACAT
1 AACTTACATAAC-TACATAACTACATAACTTACAT
* *
39865145 AGCTTACTTAA-TACATAACTTACATAACTT--AT
1 AACTTACATAACTACATAAC-TACATAACTTACAT
*
39865177 ACACGTACATAACTTACATAA
1 A-ACTTACATAAC-TACATAA
39865198 TTTACTTATC
Statistics
Matches: 237, Mismatches: 38, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
32 16 0.07
33 7 0.03
34 88 0.37
35 28 0.12
36 88 0.37
37 7 0.03
38 3 0.01
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.31
Consensus pattern (34 bp):
AACTTACATAACTACATAACTACATAACTTACAT
Found at i:39867768 original size:21 final size:21
Alignment explanation
Indices: 39867744--39867817 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
39867734 AACTTAAAGT
* *
39867744 AGAGGCGGCAACGAGGGAAGC
1 AGAGGCTGCAGCGAGGGAAGC
*
39867765 AGAGGCTGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGGGAAGC
* *
39867786 AGAGGCTACAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGGGAAGC
39867807 AGAGGCTGCAG
1 AGAGGCTGCAG
39867818 GGCGAGAAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.32, C:0.18, G:0.45, T:0.05
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGGGAAGC
Found at i:39867824 original size:21 final size:21
Alignment explanation
Indices: 39867744--39867829 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
39867734 AACTTAAAGT
* * *
39867744 AGAGGCGGCAACGAGGGAAGC
1 AGAGGCTGCAGCGAGAGAAGC
* *
39867765 AGAGGCTGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGAGAAGC
*
39867786 AGAGGCTACAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGC
* *
39867807 AGAGGCTGCAGGGCGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGC
39867828 AG
1 AG
39867830 CGAGAGAAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.33, C:0.17, G:0.45, T:0.05
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGC
Found at i:39868329 original size:42 final size:42
Alignment explanation
Indices: 39868238--39868397 Score: 216
Period size: 43 Copynumber: 3.8 Consensus size: 42
39868228 AATAGTGCCA
* * **
39868238 CTAAAGAACATTA-CTTTTCGCGGCATTTGTGATGAAAGCGCCG
1 CTAAAGAACATGATC-TTTAGCGGCATTT-TTTTGAAAGCGCCG
*
39868281 CTAAAGAACATGATCTCTAGCGGCATTTTTTTGAAAGCGCCG
1 CTAAAGAACATGATCTTTAGCGGCATTTTTTTGAAAGCGCCG
39868323 CTAAAGAACATGATCTTTAGCGGCATTTTTTTTTG-AAGCGCCG
1 CTAAAGAACATGATCTTTAGCGGCA--TTTTTTTGAAAGCGCCG
*
39868366 CTAAAGAACATGACCTTTAGCGGCATTTTTTT
1 CTAAAGAACATGATCTTTAGCGGCATTTTTTT
39868398 CTGTAAACGC
Statistics
Matches: 107, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
41 7 0.07
42 36 0.34
43 55 0.51
44 9 0.08
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (42 bp):
CTAAAGAACATGATCTTTAGCGGCATTTTTTTGAAAGCGCCG
Found at i:39869633 original size:14 final size:14
Alignment explanation
Indices: 39869612--39869648 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
39869602 ACTTAATAAA
39869612 AGAAGAACAATTA-
1 AGAAGAACAATTAT
39869625 AGAAAGAAC-ATTAT
1 AG-AAGAACAATTAT
39869639 AGAAGAACAA
1 AGAAGAACAA
39869649 ACATGCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.62, C:0.08, G:0.16, T:0.14
Consensus pattern (14 bp):
AGAAGAACAATTAT
Found at i:39884023 original size:24 final size:24
Alignment explanation
Indices: 39883996--39884055 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
39883986 TATCATATTC
*
39883996 AAGCTATCACAAAACATACCACAT
1 AAGCTATCACAAAACATACAACAT
* *
39884020 AAGCCATTC-CAAAACATGCAACAT
1 AAGCTA-TCACAAAACATACAACAT
* *
39884044 AAGATAGCACAA
1 AAGCTATCACAA
39884056 TGACATAAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
23 1 0.04
24 25 0.89
25 2 0.07
ACGTcount: A:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (24 bp):
AAGCTATCACAAAACATACAACAT
Found at i:39886147 original size:19 final size:19
Alignment explanation
Indices: 39886099--39886154 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
39886089 CAGAGTAAAT
* *
39886099 ATACTAGCACATATAGTGC
1 ATACTAGCACACAAAGTGC
*
39886118 ATA-TTGACACACAAAGTGC
1 ATACTAG-CACACAAAGTGC
*
39886137 ATACTAGCACACGAAGTG
1 ATACTAGCACACAAAGTG
39886155 AATAAACCCG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.07
19 26 0.87
20 2 0.07
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (19 bp):
ATACTAGCACACAAAGTGC
Found at i:39893903 original size:13 final size:13
Alignment explanation
Indices: 39893887--39893911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39893877 GATGAAGTTT
39893887 CCTGATTCAGAAA
1 CCTGATTCAGAAA
39893900 CCTGATTCAGAA
1 CCTGATTCAGAA
39893912 TGCGCTACCT
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:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (13 bp):
CCTGATTCAGAAA
Found at i:39895479 original size:12 final size:12
Alignment explanation
Indices: 39895462--39895487 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39895452 CTTTGCCAGA
39895462 TCCCTTTTCTCT
1 TCCCTTTTCTCT
39895474 TCCCTTTTCTCT
1 TCCCTTTTCTCT
39895486 TC
1 TC
39895488 TCCACCGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
TCCCTTTTCTCT
Found at i:39896384 original size:27 final size:27
Alignment explanation
Indices: 39896162--39896384 Score: 306
Period size: 27 Copynumber: 8.3 Consensus size: 27
39896152 GAGTCGTGGC
*
39896162 AAATAACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
**
39896189 AAATGAATGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
39896216 AAATGACTGAAATACTCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
39896243 AAATGATCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* **
39896270 AAATGATCGAAATACCCTTAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
39896297 AAATAACCAAAATACCCTCGAAAGGGT-
1 AAATGACCGAAATACCCTCG-AAGGGTA
39896324 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
39896351 AAATGACCGAAATACCC-CCATAGGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
39896378 AAATGAC
1 AAATGAC
39896385 TATTATACCC
Statistics
Matches: 175, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
26 8 0.05
27 161 0.92
28 6 0.03
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:39898558 original size:13 final size:13
Alignment explanation
Indices: 39898542--39898594 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
39898532 TTTAAACCAA
39898542 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
39898555 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
39898568 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
39898581 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
39898594 A
1 A
39898595 ATGAAGATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39903935 original size:40 final size:40
Alignment explanation
Indices: 39903885--39904320 Score: 442
Period size: 40 Copynumber: 10.9 Consensus size: 40
39903875 TACTCTGTAG
* * *
39903885 TTGGTGTGTTTTGGTTGGACCAGCTCTTATGAGCTTCTGT
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
* ** *
39903925 TTGGCGTGTTTCGGTTGAATCAAATCTTATGAGCTTCTAT
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
* * * * *
39903965 TTGGTGTGTTTCAGTTGGATAAACTCTTATGAGCATCTGT
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
* * * * * * *
39904005 CTAGCGTGTTTTAGG-TGGACCAGCTCTAATTAGCTTTTGT
1 TTGGCGTG-TTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
* * *
39904045 TTGGTGTGTTTTGGTTGGATCAGCTCTTATGAGCTTTTGT
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
*
39904085 TTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGCTTCTGT
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
*
39904125 TTGGCGTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTGT
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
* * * * * *
39904165 TTCGCATGTTTTGGGTGGATCAGCTTTTATGAGCTTTTGT
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
* * * *
39904205 TTCGCATGTTTCGGTTGGATCAGCTCTTATAAGCTTCTAT
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
* * * * * * * *
39904245 TTGGCATATTTTGATTAGATCAGCACTTATGAGCTTTTGC
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
* * * *
39904285 TCGGCGTGTTTCGGTTGGATTAGTTGTTATGAGCTT
1 TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTT
39904321 TTATCTGGTG
Statistics
Matches: 322, Mismatches: 72, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
39 5 0.02
40 313 0.97
41 4 0.01
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.44
Consensus pattern (40 bp):
TTGGCGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGT
Found at i:39905001 original size:29 final size:30
Alignment explanation
Indices: 39904931--39905029 Score: 132
Period size: 30 Copynumber: 3.3 Consensus size: 30
39904921 TACTATTTAT
39904931 ATTTTGGCCCCTCAC-TTTTTCTAAAATTAC
1 ATTTTGGCCCC-CACTTTTTTCTAAAATTAC
39904961 ATTTTGGCCCCCACTTTTTTCTGAAAA-TAC
1 ATTTTGGCCCCCACTTTTTTCT-AAAATTAC
**
39904991 ATTTTGG-CCCCTTTTTTTTCTAAAATTAC
1 ATTTTGGCCCCCACTTTTTTCTAAAATTAC
*
39905020 ATTTTAGCCC
1 ATTTTGGCCC
39905030 TTGGAGCTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
28 4 0.06
29 24 0.39
30 30 0.48
31 4 0.06
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.44
Consensus pattern (30 bp):
ATTTTGGCCCCCACTTTTTTCTAAAATTAC
Found at i:39906035 original size:10 final size:10
Alignment explanation
Indices: 39906017--39906076 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
39906007 GGAAAGAGTT
39906017 AAAG-AAGAA
1 AAAGAAAGAA
*
39906026 AAAGGAAGAA
1 AAAGAAAGAA
*
39906036 AATA-AAAAAA
1 AA-AGAAAGAA
39906046 AGAAGAAAGAAA
1 A-AAGAAAG-AA
39906058 AAAGAAAGAA
1 AAAGAAAGAA
*
39906068 AAAGGAAGA
1 AAAGAAAGA
39906077 GAAATAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
9 4 0.10
10 23 0.55
11 12 0.29
12 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:39906057 original size:21 final size:22
Alignment explanation
Indices: 39906021--39906083 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
39906011 AGAGTTAAAG
*
39906021 AAGAAAAAGGAAGAAAATAA-A
1 AAGAAAAAGAAAGAAAATAAGA
39906042 AA-AAAGAAGAAAGAAAA-AAGA
1 AAGAAA-AAGAAAGAAAATAAGA
*
39906063 AAGAAAAAGGAAGAGAAATAA
1 AAGAAAAAGAAAGA-AAATAA
39906084 TCAGGTCCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 5 0.14
21 22 0.63
22 6 0.17
23 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (22 bp):
AAGAAAAAGAAAGAAAATAAGA
Found at i:39906059 original size:17 final size:17
Alignment explanation
Indices: 39906017--39906071 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
39906007 GGAAAGAGTT
* *
39906017 AAAGAAGAAAAAGGAAG
1 AAAGAAAAAAAAAGAAG
39906034 AAA-ATAAAAAAAAGAAG
1 AAAGA-AAAAAAAAGAAG
39906051 AAAGAAAAAAGAAAGAA-
1 AAAGAAAAAA-AAAGAAG
39906068 AAAG
1 AAAG
39906072 GAAGAGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 1 0.03
17 25 0.76
18 7 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAAAAAGAAG
Found at i:39906064 original size:11 final size:11
Alignment explanation
Indices: 39906024--39906080 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
39906014 GTTAAAGAAG
*
39906024 AAAAAGGAAGA
1 AAAAAGAAAGA
39906035 AAATAA-AAA-A
1 AAA-AAGAAAGA
*
39906045 AAGAAGAAAGA
1 AAAAAGAAAGA
39906056 AAAAAGAAAGA
1 AAAAAGAAAGA
*
39906067 AAAAGGAAGAGA
1 AAAAAGAA-AGA
39906079 AA
1 AA
39906081 TAATCAGGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 2 0.05
10 6 0.16
11 23 0.61
12 7 0.18
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:39906069 original size:27 final size:27
Alignment explanation
Indices: 39906017--39906070 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
39906007 GGAAAGAGTT
** *
39906017 AAAGAAGAAAAAGGAAGAAAATAAAAA
1 AAAGAAGAAAAAAAAAGAAAAGAAAAA
39906044 AAAGAAGAAAGAAAAAAG-AAAGAAAAA
1 AAAGAAGAAA-AAAAAAGAAAAGAAAAA
39906071 GGAAGAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (27 bp):
AAAGAAGAAAAAAAAAGAAAAGAAAAA
Found at i:39906173 original size:31 final size:31
Alignment explanation
Indices: 39906138--39906235 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 31
39906128 CCCAATAGCG
39906138 GCCCAACCCAGCAGACCCAACAACAGCAGTA
1 GCCCAACCCAGCAGACCCAACAACAGCAGTA
* *
39906169 GCCCAATCCAGTCAG-CCCAAC-A-A-TAGTA
1 GCCCAACCCAG-CAGACCCAACAACAGCAGTA
* * * * *
39906197 GACCAACCTAGTAGACCCAACAGCAGCAGCAA
1 GCCCAACCCAGCAGACCCAACAACAGCAG-TA
39906229 GCCCAAC
1 GCCCAAC
39906236 TCAGTTAGCC
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
27 2 0.04
28 18 0.35
29 1 0.02
30 2 0.04
31 18 0.35
32 10 0.20
ACGTcount: A:0.38, C:0.39, G:0.16, T:0.07
Consensus pattern (31 bp):
GCCCAACCCAGCAGACCCAACAACAGCAGTA
Found at i:39917961 original size:75 final size:74
Alignment explanation
Indices: 39917810--39917963 Score: 175
Period size: 76 Copynumber: 2.1 Consensus size: 74
39917800 TCATTTCCTT
* *
39917810 TTTCATTTTTCAAAAATCAACTATAATCTGAGAAGTGAATTGAGCCTCGGGTCACACGTCGAGGT
1 TTTCATTTTTCAAAAATCAACTATAATCTGAGAAGTGAATGGAGCCTCGGGTCACACGCCGAGGT
*
39917875 ATTTTTTAA
66 ATTTTTAAA
* * * * * * ** *
39917884 TTTCTATTTTTCAAAGATCAACTCATGATCTGAGAGGTGAGTGGAGCTTTGGGTTGCATGCCGAG
1 TTTC-ATTTTTCAAAAATCAACT-ATAATCTGAGAAGTGAATGGAGCCTCGGGTCACACGCCGAG
39917949 GTA-TTTTAAA
64 GTATTTTTAAA
39917959 TTTCA
1 TTTCA
39917964 GTCTTTTATT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
74 5 0.08
75 27 0.41
76 34 0.52
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (74 bp):
TTTCATTTTTCAAAAATCAACTATAATCTGAGAAGTGAATGGAGCCTCGGGTCACACGCCGAGGT
ATTTTTAAA
Found at i:39926766 original size:23 final size:23
Alignment explanation
Indices: 39926733--39926784 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
39926723 ATGAGTGCCA
* *
39926733 CACTGATATGTAGTCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
39926756 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
39926779 CACTGA
1 CACTGA
39926785 TCAATAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:39933273 original size:12 final size:10
Alignment explanation
Indices: 39933245--39933289 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
39933235 TTGAAAATAG
39933245 TCAAAATTAA
1 TCAAAATTAA
39933255 TCAAAATTAA
1 TCAAAATTAA
39933265 CTACAAAATTAA
1 -T-CAAAATTAA
* *
39933277 TTAAAATTCA
1 TCAAAATTAA
39933287 TCA
1 TCA
39933290 TGTTCATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.63
11 2 0.07
12 9 0.30
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (10 bp):
TCAAAATTAA
Found at i:39942981 original size:13 final size:13
Alignment explanation
Indices: 39942963--39942987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39942953 TAGATTGAAT
39942963 TTGATTATGTAAA
1 TTGATTATGTAAA
39942976 TTGATTATGTAA
1 TTGATTATGTAA
39942988 TCTTGTAAAT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:39943410 original size:11 final size:11
Alignment explanation
Indices: 39943382--39943431 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
39943372 CCGTGACACA
*
39943382 ATGGTGGTGAT
1 ATGGTGGTGCT
39943393 A-GGTGGTGCT
1 ATGGTGGTGCT
39943403 ATGGTGGTAG-T
1 ATGGTGGT-GCT
39943414 ATGGTGGTGCT
1 ATGGTGGTGCT
*
39943425 TTGGTGG
1 ATGGTGG
39943432 AGAAGTGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 10 0.29
11 23 0.68
12 1 0.03
ACGTcount: A:0.12, C:0.04, G:0.48, T:0.36
Consensus pattern (11 bp):
ATGGTGGTGCT
Found at i:39943422 original size:22 final size:21
Alignment explanation
Indices: 39943382--39943431 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
39943372 CCGTGACACA
39943382 ATGGTGGTGATAGGTGGTGCT
1 ATGGTGGTGATAGGTGGTGCT
39943403 ATGGTGGT-AGTATGGTGGTGCT
1 ATGGTGGTGA-TA-GGTGGTGCT
*
39943425 TTGGTGG
1 ATGGTGG
39943432 AGAAGTGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 10 0.38
22 15 0.58
ACGTcount: A:0.12, C:0.04, G:0.48, T:0.36
Consensus pattern (21 bp):
ATGGTGGTGATAGGTGGTGCT
Found at i:39943440 original size:22 final size:22
Alignment explanation
Indices: 39943382--39943440 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
39943372 CCGTGACACA
39943382 ATGGTGGT-G-ATAGGTGGTGCT
1 ATGGTGGTAGAAT-GGTGGTGCT
*
39943403 ATGGTGGTAGTATGGTGGTGCT
1 ATGGTGGTAGAATGGTGGTGCT
*
39943425 TTGGTGG-AGAAGTGGT
1 ATGGTGGTAGAA-TGGT
39943441 AGTTTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 11 0.33
22 20 0.61
23 2 0.06
ACGTcount: A:0.15, C:0.03, G:0.47, T:0.34
Consensus pattern (22 bp):
ATGGTGGTAGAATGGTGGTGCT
Found at i:39958814 original size:31 final size:31
Alignment explanation
Indices: 39958757--39958815 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
39958747 ATAGAATTAA
* *
39958757 AATCAAAATTTTATGTATACATTTGAACCAT
1 AATCAAAATTTCATGTATACAATTGAACCAT
* *
39958788 AATCAAAATTTCATGTTTATAATTGAAC
1 AATCAAAATTTCATGTATACAATTGAAC
39958816 AAAATTAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (31 bp):
AATCAAAATTTCATGTATACAATTGAACCAT
Found at i:39958999 original size:8 final size:8
Alignment explanation
Indices: 39958986--39959012 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
39958976 CCACCATCTT
39958986 ATATTAAA
1 ATATTAAA
39958994 ATATTAAA
1 ATATTAAA
39959002 ATATTAAA
1 ATATTAAA
39959010 ATA
1 ATA
39959013 CTCGAACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATTAAA
Found at i:39960230 original size:44 final size:44
Alignment explanation
Indices: 39960172--39960255 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
39960162 AATTGTATTT
* * *
39960172 TAAATTATATTTATTTTTAAAT-TCGTAATTATCATAACTTGTAC
1 TAAATTATAGTTATTTTTAAATGT-ATAATTATCACAACTTGTAC
39960216 TAAATTATAGTTATTTTTAAATGTATAATTATCACAACTT
1 TAAATTATAGTTATTTTTAAATGTATAATTATCACAACTT
39960256 CTATTTTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (44 bp):
TAAATTATAGTTATTTTTAAATGTATAATTATCACAACTTGTAC
Found at i:39965971 original size:27 final size:26
Alignment explanation
Indices: 39965915--39966011 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 26
39965905 TCGTGCGTCT
* **
39965915 CCTATTTTTCAGATTTTATGGTTTTAC
1 CCTATTTTTCAGATTTTCTAATTTT-C
*
39965942 CCTGATTTTTTAGATTTTCTAATTTTC
1 CCT-ATTTTTCAGATTTTCTAATTTTC
*
39965969 CCTTATTTTTCAAATTTTAC-AATTTTC
1 CC-TATTTTTCAGATTTT-CTAATTTTC
*
39965996 CCT-TTTTTTAGATTTT
1 CCTATTTTTCAGATTTT
39966012 ATAGTTTTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
25 11 0.19
26 1 0.02
27 27 0.46
28 20 0.34
ACGTcount: A:0.20, C:0.15, G:0.06, T:0.59
Consensus pattern (26 bp):
CCTATTTTTCAGATTTTCTAATTTTC
Found at i:39966307 original size:34 final size:34
Alignment explanation
Indices: 39966268--39966344 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
39966258 ATGACTTTTG
* * *
39966268 GCTACTG-AGTTGATCTGTTATAAGCGTATT-ATTT
1 GCTACTGTA-TTGAACTATTATAAGCATATTGA-TT
39966302 GCTACTGTATTGAACTATTATAAGCATATTGATT
1 GCTACTGTATTGAACTATTATAAGCATATTGATT
*
39966336 GCTATTGTA
1 GCTACTGTA
39966345 CTGTTCTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (34 bp):
GCTACTGTATTGAACTATTATAAGCATATTGATT
Found at i:39966417 original size:35 final size:35
Alignment explanation
Indices: 39966346--39966417 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
39966336 GCTATTGTAC
*
39966346 TGTTCTGTTAAAAGCATAATTAAATGATATCATAT
1 TGTTCTGTTAAAAGCATAATTAAATGATACCATAT
* *
39966381 TGTTCTGTTAAAAGCATAATTAAATGCTACCGTAT
1 TGTTCTGTTAAAAGCATAATTAAATGATACCATAT
39966416 TG
1 TG
39966418 ACCTATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (35 bp):
TGTTCTGTTAAAAGCATAATTAAATGATACCATAT
Found at i:39966612 original size:18 final size:18
Alignment explanation
Indices: 39966589--39966646 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 18
39966579 TTTTATTACT
39966589 AGTGGTTTATCCACAATG
1 AGTGGTTTATCCACAATG
*
39966607 AGTGGTTCATCCACGACGATG
1 AGTGGTTTATCCAC-A--ATG
39966628 AGTGGTTTTATCCACAATG
1 AGTGG-TTTATCCACAATG
39966647 TGGTGTAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
21 9 0.26
22 8 0.24
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (18 bp):
AGTGGTTTATCCACAATG
Found at i:39967611 original size:6 final size:6
Alignment explanation
Indices: 39967606--39967635 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39967596 ATAATAAATT
39967606 TTAAT- TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA TTAATA T
39967636 GAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAATA
Found at i:39968089 original size:24 final size:23
Alignment explanation
Indices: 39968062--39968109 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
39968052 TTAATATTAA
* *
39968062 TATAATTATATTTATTATATATTT
1 TATAATTATATATACTAT-TATTT
*
39968086 TATAATTTTATATACTATTATTT
1 TATAATTATATATACTATTATTT
39968109 T
1 T
39968110 TTGTCAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TATAATTATATATACTATTATTT
Found at i:39969611 original size:23 final size:24
Alignment explanation
Indices: 39969574--39969624 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
39969564 AGGGAGTAGC
39969574 AAAAGAAAATAGAAAAT-AAAGAAA
1 AAAAGAAAATAGAAAATGAAA-AAA
* *
39969598 AAAAGAAAA-GGAAAGTGAAAAAA
1 AAAAGAAAATAGAAAATGAAAAAA
39969621 AAAA
1 AAAA
39969625 CATAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAAGAAAATAGAAAATGAAAAAA
Found at i:39978853 original size:26 final size:28
Alignment explanation
Indices: 39978793--39978854 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
39978783 CGGACTTATC
* *
39978793 CTATGTTTACTGTCTCGGTAGACTCTAT
1 CTATGTTTACTGTCTCAGTAGACACTAT
* *
39978821 TTGTGTTTACTGTCTCAGT-GA-ACTAT
1 CTATGTTTACTGTCTCAGTAGACACTAT
39978847 CTATGTTT
1 CTATGTTT
39978855 TGTGTTTACT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
26 10 0.36
27 2 0.07
28 16 0.57
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (28 bp):
CTATGTTTACTGTCTCAGTAGACACTAT
Found at i:39997281 original size:22 final size:22
Alignment explanation
Indices: 39997239--39997281 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39997229 TTTCATCTCT
*
39997239 TGTCTTTTATTTTCACGACATC
1 TGTCTTTTATTTTCACAACATC
* *
39997261 TGTCTTTTTTTTTCCCAACAT
1 TGTCTTTTATTTTCACAACAT
39997282 GTTTACTGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.53
Consensus pattern (22 bp):
TGTCTTTTATTTTCACAACATC
Found at i:40000445 original size:27 final size:27
Alignment explanation
Indices: 40000415--40000505 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
40000405 TTTATTTCAA
40000415 TATTTTACAAACCATAAAAATACTTAT
1 TATTTTACAAACCATAAAAATACTTAT
* * **
40000442 TATTTTAC--TCTCGTAATATAATTGTTCAT
1 TATTTTACAAAC-CATAA-A-AATACTT-AT
40000471 TATTTTACAAACCATAAAAATACTTAT
1 TATTTTACAAACCATAAAAATACTTAT
*
40000498 TGTTTTAC
1 TATTTTAC
40000506 TCTCGTAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 18 0.37
28 10 0.20
29 11 0.22
30 4 0.08
31 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.44
Consensus pattern (27 bp):
TATTTTACAAACCATAAAAATACTTAT
Found at i:40000482 original size:56 final size:56
Alignment explanation
Indices: 40000410--40000521 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
40000400 GATATTTTAT
40000410 TTCAATATTTTACAAACCATAAAAATACTTATTATTTTACTCTCGTAATATAATTG
1 TTCAATATTTTACAAACCATAAAAATACTTATTATTTTACTCTCGTAATATAATTG
* *
40000466 TTCATTATTTTACAAACCATAAAAATACTTATTGTTTTACTCTCGTAATATAATTG
1 TTCAATATTTTACAAACCATAAAAATACTTATTATTTTACTCTCGTAATATAATTG
40000522 ACTTAAAGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (56 bp):
TTCAATATTTTACAAACCATAAAAATACTTATTATTTTACTCTCGTAATATAATTG
Found at i:40009720 original size:20 final size:20
Alignment explanation
Indices: 40009678--40009721 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40009668 TTGAGAGCAA
*
40009678 TTCTCTCTACTAAATAAGAC
1 TTCTCTCTACTAAATAACAC
*
40009698 TTCTCTCATA-TAAATAACCC
1 TTCTCTC-TACTAAATAACAC
40009718 TTCT
1 TTCT
40009722 TGCATGGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (20 bp):
TTCTCTCTACTAAATAACAC
Found at i:40025797 original size:107 final size:106
Alignment explanation
Indices: 40025570--40025783 Score: 331
Period size: 107 Copynumber: 2.0 Consensus size: 106
40025560 CCAAAACCCA
* * * *
40025570 TACTTTGAAACTTTAAGAGGGTATTTGGCTATTTGGCTAAACGAGAAATCGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGACTATTTGGCTAAACGAGAAATCGAAACCCAGCACATT
40025635 AGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
66 AGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* *
40025676 TACTTTGAAATTTTAAAAGGATATTTGACTATTTGG-TCGAACGAAGAAATCGAAACCTAGCACA
1 TACTTTGAAATTTTAAAAGGATATTTGACTATTTGGCT-AAACG-AGAAATCGAAACCCAGCACA
* *
40025740 TTAGGGCACGTTTTCTCGAATTTCCAAATGTAAAATATTGCCT
64 TTAGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
40025783 T
1 T
40025784 TATTATTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 1 0.01
106 36 0.37
107 61 0.62
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (106 bp):
TACTTTGAAATTTTAAAAGGATATTTGACTATTTGGCTAAACGAGAAATCGAAACCCAGCACATT
AGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
Found at i:40026403 original size:3 final size:3
Alignment explanation
Indices: 40026388--40026454 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
40026378 AAAAGGTATT
* * ** * **
40026388 TAA TAA TAT TAA TAA TGA TGC TAA TAA TAA TAA TAA TAA TAG TTT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40026436 TAA TAA TATA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA
40026455 AAAATGATAG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:40026419 original size:24 final size:24
Alignment explanation
Indices: 40026388--40026453 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
40026378 AAAAGGTATT
40026388 TAATAATATTAATAAT-GATGCTAA
1 TAATAATATTAATAATAG-TGCTAA
* **
40026412 TAATAATAATAATAATAGTTTTAA
1 TAATAATATTAATAATAGTGCTAA
40026436 TAATAATATATAATAATA
1 TAATAATAT-TAATAATA
40026454 AAAAATGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 27 0.75
25 9 0.25
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (24 bp):
TAATAATATTAATAATAGTGCTAA
Found at i:40034944 original size:24 final size:26
Alignment explanation
Indices: 40034917--40034975 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 26
40034907 TAAATGTGTA
40034917 AGCTAATAAAT-AATATATA-AGTTG
1 AGCTAATAAATAAATATATACAGTTG
**
40034941 AGCT-CGAAATAAATATATACAGTTG
1 AGCTAATAAATAAATATATACAGTTG
40034966 AG-TAACTAAA
1 AGCTAA-TAAA
40034976 ATAAGGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 7 0.26
26 3 0.11
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (26 bp):
AGCTAATAAATAAATATATACAGTTG
Found at i:40037039 original size:20 final size:21
Alignment explanation
Indices: 40037004--40037043 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
40036994 TCCAAAACAC
40037004 TTCAAGAATAATTTTCTAAAAA
1 TTCAAGAATAATTTTC-AAAAA
40037026 TTCAA-AAT-ATTTTCAAAA
1 TTCAAGAATAATTTTCAAAA
40037044 CCCATTCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 3 0.17
22 5 0.28
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (21 bp):
TTCAAGAATAATTTTCAAAAA
Found at i:40038023 original size:18 final size:18
Alignment explanation
Indices: 40038000--40038040 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
40037990 ATTAGCATCG
40038000 ATTGCGGCACTAAACAAT
1 ATTGCGGCACTAAACAAT
40038018 ATTGCGGCACTAAACAAT
1 ATTGCGGCACTAAACAAT
40038036 ATTGC
1 ATTGC
40038041 AACACAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (18 bp):
ATTGCGGCACTAAACAAT
Found at i:40038329 original size:27 final size:27
Alignment explanation
Indices: 40038299--40038623 Score: 382
Period size: 27 Copynumber: 12.1 Consensus size: 27
40038289 TATAACACTA
*
40038299 ATTTTACCCTATGGGGGCATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
40038326 ATTTTACCCTATAGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
40038353 ATTTTACCCTATCGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
** *
40038380 ATTTTACATTATGGGGGTATTTCGGTT
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * **
40038407 ATTTTACCCTCTAGGGGTATTTTAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
40038434 ATTTTACCCTATAGAGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
40038461 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
40038488 ATTTTACCATATTGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
40038515 ATTTTACCCTCT-GGGGTATTTCGGCC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * *
40038541 ATGTTACTCTACGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * **
40038568 ATTTTACCTTATGAGGGTATTTCAATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
40038595 ATTTTACCCTATGGGGGTATATCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
40038622 AT
1 AT
40038624 AAAAGTGTAA
Statistics
Matches: 247, Mismatches: 50, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
26 20 0.08
27 227 0.92
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:40040778 original size:25 final size:25
Alignment explanation
Indices: 40040750--40040801 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
40040740 CTTTAGATAA
40040750 TTATT-TTCTTTAATTATTGTTTATT
1 TTATTATTCTTT-ATTATTGTTTATT
*
40040775 TTATTATTGTTTATTATTGTTTATT
1 TTATTATTCTTTATTATTGTTTATT
40040800 TT
1 TT
40040802 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (25 bp):
TTATTATTCTTTATTATTGTTTATT
Found at i:40040789 original size:10 final size:10
Alignment explanation
Indices: 40040774--40040799 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40040764 TATTGTTTAT
40040774 TTTATTATTG
1 TTTATTATTG
40040784 TTTATTATTG
1 TTTATTATTG
40040794 TTTATT
1 TTTATT
40040800 TTTCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (10 bp):
TTTATTATTG
Found at i:40041918 original size:20 final size:22
Alignment explanation
Indices: 40041879--40041919 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
40041869 GTGGTTGGAT
40041879 TCAAATTCTAATACTAGATTGTA
1 TCAAATTC-AATACTAGATTGTA
40041902 TCAAATTC-ATA-TAGATTG
1 TCAAATTCAATACTAGATTG
40041920 ATACATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
23 8 0.44
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (22 bp):
TCAAATTCAATACTAGATTGTA
Found at i:40045567 original size:31 final size:32
Alignment explanation
Indices: 40045532--40045594 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
40045522 CACTTTCATG
40045532 TTGGAAGTGGGTAA-TTTTAATCTTTCTTTTT
1 TTGGAAGTGGGTAATTTTTAATCTTTCTTTTT
40045563 TTGGAAGTGGGTAATTTTTAATCTTTCTTTTT
1 TTGGAAGTGGGTAATTTTTAATCTTTCTTTTT
40045595 GCTATCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (32 bp):
TTGGAAGTGGGTAATTTTTAATCTTTCTTTTT
Found at i:40050536 original size:101 final size:101
Alignment explanation
Indices: 40050401--40050613 Score: 327
Period size: 101 Copynumber: 2.1 Consensus size: 101
40050391 CATAGCCTTG
* * * * *
40050401 CCATGGTCTTATGTTCATAGTGCCATAACCCAGTTATGGTCTTACCATCAGAATGCCATAGCCCA
1 CCATGGTCTTACGTCCATAGTGACATAACCCAGTTATGGTCTTACCATCAAAATGCCATAACCCA
* *
40050466 GCTATGGTCTTACATATAAACACTACCATGGTCTAA
66 GCAATGGTCTTACATATAAACACTACCATGGTCCAA
* *
40050502 CCATTGTCTTACGTCCATAGTGACATAACTCAGTTATGGTCTTACCATCAAAATGCCATAACCCA
1 CCATGGTCTTACGTCCATAGTGACATAACCCAGTTATGGTCTTACCATCAAAATGCCATAACCCA
* *
40050567 GCAATGGTCTTACATATATACACTGCCATGGTCCAA
66 GCAATGGTCTTACATATAAACACTACCATGGTCCAA
40050603 CCATGGTCTTA
1 CCATGGTCTTA
40050614 AATACTTCAA
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (101 bp):
CCATGGTCTTACGTCCATAGTGACATAACCCAGTTATGGTCTTACCATCAAAATGCCATAACCCA
GCAATGGTCTTACATATAAACACTACCATGGTCCAA
Found at i:40050662 original size:27 final size:27
Alignment explanation
Indices: 40050609--40050681 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
40050599 CCAACCATGG
40050609 TCTTAAATACTTCAA-TTTTTTATTAT
1 TCTTAAATACTTCAATTTTTTTATTAT
*
40050635 TTTTAAATACTTCAATTTTTTTATTAT
1 TCTTAAATACTTCAATTTTTTTATTAT
40050662 TCTTAAATACTTCAATTTTT
1 TCTTAAATACTTCAATTTTT
40050682 AAATTTCTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 14 0.32
27 30 0.68
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (27 bp):
TCTTAAATACTTCAATTTTTTTATTAT
Found at i:40051597 original size:11 final size:11
Alignment explanation
Indices: 40051581--40051606 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40051571 ATCAAATTAA
40051581 ATAAATATCCT
1 ATAAATATCCT
40051592 ATAAATATCCT
1 ATAAATATCCT
40051603 ATAA
1 ATAA
40051607 TTTTATACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAAATATCCT
Found at i:40052078 original size:59 final size:59
Alignment explanation
Indices: 40051986--40052104 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
40051976 TAAATATAAG
40051986 ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCATCCGAATTAATTGTT
1 ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCATCCGAATTAATTGTT
40052045 ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCATCCGAATTAATTGTT
1 ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCATCCGAATTAATTGTT
40052104 A
1 A
40052105 AAAATAAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.37
Consensus pattern (59 bp):
ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCATCCGAATTAATTGTT
Found at i:40058291 original size:29 final size:29
Alignment explanation
Indices: 40058249--40058321 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
40058239 ACCTCTCAAT
40058249 ACACTTAAATCAATGAGCCGAAACACACA
1 ACACTTAAATCAATGAGCCGAAACACACA
40058278 ACACTTAAATCAATGAGCCGAAACACACA
1 ACACTTAAATCAATGAGCCGAAACACACA
*
40058307 ACACTCAAATCAATG
1 ACACTTAAATCAATG
40058322 GAAGAGCATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.48, C:0.27, G:0.10, T:0.15
Consensus pattern (29 bp):
ACACTTAAATCAATGAGCCGAAACACACA
Found at i:40060457 original size:24 final size:25
Alignment explanation
Indices: 40060430--40060482 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
40060420 GTACATGTAT
*
40060430 GCTCATATGAGCTGTA-AACGGTAA
1 GCTCATATGAGCTGAATAACGGTAA
* * *
40060454 GCTCCTCTGAGTTGAATAACGGTAA
1 GCTCATATGAGCTGAATAACGGTAA
40060479 GCTC
1 GCTC
40060483 CTTCAAGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (25 bp):
GCTCATATGAGCTGAATAACGGTAA
Found at i:40062932 original size:25 final size:25
Alignment explanation
Indices: 40062904--40062951 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
40062894 GGACAAGATT
40062904 TTGTTAAATGAAATAATAAAAATAA
1 TTGTTAAATGAAATAATAAAAATAA
40062929 TTGTTAAATGAAATAATAAAAAT
1 TTGTTAAATGAAATAATAAAAAT
40062952 TGAGCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTGTTAAATGAAATAATAAAAATAA
Found at i:40064210 original size:122 final size:123
Alignment explanation
Indices: 40064002--40064291 Score: 393
Period size: 122 Copynumber: 2.4 Consensus size: 123
40063992 AAAAAATGCT
*** * *
40064002 GCTATTGCTTTACCTTTTGCGATGTTTATGGGAAAAACGCCACTATTGCTTTACCTTTTGTGGCG
1 GCTATTGCTTTACCTTTTGCGGCATTTATGGGAAAAATGCCACTATTGCTTTACCTTTTGTGGCA
40064067 TTTATGGGAAAAACGCCGCTATTGC-TTACCTTTTACAGCGTGTATAGGAAAAACACC
66 TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTTACAGCGTGTATAGGAAAAACACC
* *
40064124 GCTATTGCTTTACCTTTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCTTTTGTGGCA
1 GCTATTGCTTTACCTTTTGCGGCATTTATGGGAAAAATGCCACTATTGCTTTACCTTTTGTGGCA
* * * * * * * * * *
40064189 TTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGCGGTGTTTATGGGCAATATACC
66 TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTTACAGCGTGTATAGGAAAAACACC
* * *
40064247 ACTATTGCTTTACCTTTTGCGGCATTTATAGGAAAAATTCCACTA
1 GCTATTGCTTTACCTTTTGCGGCATTTATGGGAAAAATGCCACTA
40064292 ATGGTATATA
Statistics
Matches: 145, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
122 81 0.56
123 64 0.44
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (123 bp):
GCTATTGCTTTACCTTTTGCGGCATTTATGGGAAAAATGCCACTATTGCTTTACCTTTTGTGGCA
TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTTACAGCGTGTATAGGAAAAACACC
Found at i:40064291 original size:41 final size:41
Alignment explanation
Indices: 40063976--40064284 Score: 368
Period size: 41 Copynumber: 7.6 Consensus size: 41
40063966 AGTAAATAAA
* * *
40063976 TTTGCGGTGTTTATGGAAAAAATGCTGCTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
** * *
40064017 TTTGCGATGTTTATGGGAAAAACGCCACTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* *
40064058 TTTGTGGCGTTTATGGGAAAAACGCCGCTATTGC-TTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* * * * **
40064098 TTTACAGCGTGTATAGGAAAAACACCGCTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* *
40064139 TTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* * *
40064180 TTTGTGGCATTTATGGGCAAAATGCCGCTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* * * * *
40064221 TTTGCGGTGTTTATGGGCAATATACCACTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* *
40064262 TTTGCGGCATTTATAGGAAAAAT
1 TTTGCGGCGTTTATGGGAAAAAT
40064285 TCCACTAATG
Statistics
Matches: 232, Mismatches: 35, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 34 0.15
41 198 0.85
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (41 bp):
TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
Found at i:40073856 original size:29 final size:27
Alignment explanation
Indices: 40073823--40073877 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
40073813 GTGATTAAAT
40073823 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
40073852 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
40073878 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:40075316 original size:12 final size:13
Alignment explanation
Indices: 40075292--40075320 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40075282 GGGCTATAAG
40075292 TATTGCATTTATT
1 TATTGCATTTATT
40075305 TATTGC-TTTATT
1 TATTGCATTTATT
40075317 TATT
1 TATT
40075321 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:40087946 original size:26 final size:26
Alignment explanation
Indices: 40087912--40087962 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
40087902 CAGTAGCATC
40087912 GCAACAAAGCTGCCAGCAACAGTATT
1 GCAACAAAGCTGCCAGCAACAGTATT
* *
40087938 GCAATAAAGCTGCCAGTAACAGTAT
1 GCAACAAAGCTGCCAGCAACAGTAT
40087963 ATGTGGCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
GCAACAAAGCTGCCAGCAACAGTATT
Found at i:40087984 original size:27 final size:27
Alignment explanation
Indices: 40087954--40088006 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40087944 AAGCTGCCAG
* *
40087954 TAACAGT-ATATGTGGCCAAGCCACCAA
1 TAACAGTGAT-TGTGGCAAAACCACCAA
40087981 TAACAGTGATTGTGGCAAAACCACCA
1 TAACAGTGATTGTGGCAAAACCACCA
40088007 GTATAGTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (27 bp):
TAACAGTGATTGTGGCAAAACCACCAA
Found at i:40088104 original size:11 final size:11
Alignment explanation
Indices: 40088088--40088130 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
40088078 AATCTGCCAT
40088088 ACAAATCACAG
1 ACAAATCACAG
*
40088099 ACAAATCAGTCAT
1 ACAAATCA--CAG
*
40088112 ACCAATCACAG
1 ACAAATCACAG
40088123 ACAAATCA
1 ACAAATCA
40088131 GTCATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.51, C:0.28, G:0.07, T:0.14
Consensus pattern (11 bp):
ACAAATCACAG
Found at i:40088105 original size:24 final size:24
Alignment explanation
Indices: 40088078--40088154 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
40088068 TCATGCTCAG
*
40088078 AATCTGCCATACAAATCACAGACA
1 AATCAGCCATACAAATCACAGACA
* *
40088102 AATCAGTCATACCAATCACAGACA
1 AATCAGCCATACAAATCACAGACA
* ** * *
40088126 AATCAGTCATTTAAATCACAAAAA
1 AATCAGCCATACAAATCACAGACA
40088150 AATCA
1 AATCA
40088155 ATCATTTACC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.49, C:0.25, G:0.06, T:0.19
Consensus pattern (24 bp):
AATCAGCCATACAAATCACAGACA
Found at i:40088159 original size:24 final size:24
Alignment explanation
Indices: 40088115--40088162 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40088105 CAGTCATACC
* * *
40088115 AATCACAGACAAATCAGTCATTTA
1 AATCACAAAAAAATCAATCATTTA
40088139 AATCACAAAAAAATCAATCATTTA
1 AATCACAAAAAAATCAATCATTTA
40088163 CCCTATAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.04, T:0.25
Consensus pattern (24 bp):
AATCACAAAAAAATCAATCATTTA
Found at i:40088193 original size:27 final size:27
Alignment explanation
Indices: 40088159--40088220 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
40088149 AAATCAATCA
*
40088159 TTTACCCTATAGGGGCATTATGGTCAT
1 TTTACCCTATAGGGGCATTACGGTCAT
40088186 TTTACCCTATAGGGGCATTACGGTCAT
1 TTTACCCTATAGGGGCATTACGGTCAT
40088213 TTTACCCT
1 TTTACCCT
40088221 TCGAGGGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (27 bp):
TTTACCCTATAGGGGCATTACGGTCAT
Found at i:40088241 original size:27 final size:27
Alignment explanation
Indices: 40088211--40088325 Score: 108
Period size: 27 Copynumber: 4.3 Consensus size: 27
40088201 CATTACGGTC
40088211 ATTTTACCCTTCGAGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCAATA
*
40088238 ATTTTACCCAGT-GAGGGTATTTCAATA
1 ATTTTACCC-TTCGAGGGTATTTCAATA
* * ***
40088265 ATCTTACCCATC-AGGGGTATTTTTGTA
1 ATTTTACCCTTCGA-GGGTATTTCAATA
** * *
40088292 ATTTTACCCTTTAAGGGTATTTTAGTA
1 ATTTTACCCTTCGAGGGTATTTCAATA
40088319 ATTTTAC
1 ATTTTAC
40088326 AACCTTTCCG
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.03
27 70 0.95
28 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCAATA
Found at i:40102877 original size:24 final size:24
Alignment explanation
Indices: 40102850--40102902 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
40102840 ACATTGTTGT
*
40102850 AAACAAGAATAAAGAACACATAGA
1 AAACAAGAACAAAGAACACATAGA
*
40102874 AAACAAGAACAAAGAACACATAGC
1 AAACAAGAACAAAGAACACATAGA
40102898 AAACA
1 AAACA
40102903 TCTTTAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.66, C:0.17, G:0.11, T:0.06
Consensus pattern (24 bp):
AAACAAGAACAAAGAACACATAGA
Found at i:40105522 original size:34 final size:33
Alignment explanation
Indices: 40105468--40105531 Score: 78
Period size: 32 Copynumber: 1.9 Consensus size: 33
40105458 TGCATAATAT
40105468 TTTTAACATATATTAATAC-AACA-TTTACCAC
1 TTTTAACATATATTAATACAAACAGTTTACCAC
*
40105499 TTTTACACATATATACTATTACAAACAGTTTAC
1 TTTTA-ACATATAT--TAATACAAACAGTTTAC
40105532 TGTTTCACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 5 0.19
32 8 0.30
34 5 0.19
35 4 0.15
36 5 0.19
ACGTcount: A:0.41, C:0.19, G:0.02, T:0.39
Consensus pattern (33 bp):
TTTTAACATATATTAATACAAACAGTTTACCAC
Found at i:40107671 original size:51 final size:51
Alignment explanation
Indices: 40107595--40107697 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
40107585 TGATTCATTT
40107595 ACTTAAAAATTAATTCATCTACTACTAGACCAATTGCTCTGAATGCACTGC
1 ACTTAAAAATTAATTCATCTACTACTAGACCAATTGCTCTGAATGCACTGC
*
40107646 ACTTAAAAATTAATTCTTCTACTACTAGACCAATTGCTCTGAATGCACTGC
1 ACTTAAAAATTAATTCATCTACTACTAGACCAATTGCTCTGAATGCACTGC
40107697 A
1 A
40107698 TAAAGGTCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (51 bp):
ACTTAAAAATTAATTCATCTACTACTAGACCAATTGCTCTGAATGCACTGC
Found at i:40110791 original size:18 final size:18
Alignment explanation
Indices: 40110768--40110807 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40110758 GATGTGTGCT
* * *
40110768 TTTGTCCTATCTCCTATC
1 TTTGTCCAAACTCCTATA
40110786 TTTGTCCAAACTCCTATA
1 TTTGTCCAAACTCCTATA
40110804 TTTG
1 TTTG
40110808 AACTTCTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.28, G:0.07, T:0.47
Consensus pattern (18 bp):
TTTGTCCAAACTCCTATA
Found at i:40112892 original size:12 final size:12
Alignment explanation
Indices: 40112854--40112895 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
40112844 ATTGGTCATA
40112854 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
40112866 GAGGGATATT-TG
1 GAGAGAT-TTGAG
40112878 GAGAGATTTGAG
1 GAGAGATTTGAG
40112890 GAGAGA
1 GAGAGA
40112896 ATATTGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:40112902 original size:24 final size:24
Alignment explanation
Indices: 40112854--40112900 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
40112844 ATTGGTCATA
*
40112854 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
40112878 GAGAGATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
40112901 GGGATTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:40113600 original size:27 final size:27
Alignment explanation
Indices: 40113566--40113788 Score: 277
Period size: 27 Copynumber: 8.3 Consensus size: 27
40113556 AGAGGTCGAT
*
40113566 AAATGATCGAAATACCCCCATAGGATA
1 AAATGATCGAAATACCCCCATAGGGTA
*
40113593 AAATGATCGAAATACCCCCATAAGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
40113620 AAATGATCGAAATACCTCAATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
40113647 AAATGATTGAAATACCCCCATAGTGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
40113674 AAATGACCGAAATA-CCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
40113700 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * * *
40113727 GAATGACCAAAATACCCCTAATAGGGTA
1 AAATGATCGAAATACCCC-CATAGGGTA
* * * *
40113755 AAATGACCAAAATAACCCCATAAGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
40113782 AAATGAT
1 AAATGAT
40113789 TTTTATACCC
Statistics
Matches: 174, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 24 0.14
27 126 0.72
28 24 0.14
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:40114201 original size:28 final size:28
Alignment explanation
Indices: 40114156--40114303 Score: 192
Period size: 28 Copynumber: 5.3 Consensus size: 28
40114146 TGCACTGCAT
40114156 TGTTACTGTATTGGGCTAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
*
40114184 TGATT-CTGTACTGGGCTAAGGCCCACAC
1 TG-TTACTGTATTGGGCTAAGGCCCACAC
* * * *
40114212 TGATT-TTGTATTGGGCTAAGTCTCATAC
1 TG-TTACTGTATTGGGCTAAGGCCCACAC
*
40114240 TGTTACTGTATTGGGCTAAGGCCCACAT
1 TGTTACTGTATTGGGCTAAGGCCCACAC
* *
40114268 TGTTACTGTATTAGGCTAAGGCCCAGAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
40114296 TGTTACTG
1 TGTTACTG
40114304 CATGTTGTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
27 2 0.02
28 100 0.96
29 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:40114317 original size:14 final size:14
Alignment explanation
Indices: 40114298--40114335 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
40114288 GCCCAGACTG
* *
40114298 TTACTGCATGTTGT
1 TTACTGAATGCTGT
40114312 TTACTGAATGCTGT
1 TTACTGAATGCTGT
40114326 TTACTGAATG
1 TTACTGAATG
40114336 ACTGATAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (14 bp):
TTACTGAATGCTGT
Found at i:40116038 original size:7 final size:7
Alignment explanation
Indices: 40116026--40116051 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40116016 ATATTTTAAT
40116026 TTTAAAA
1 TTTAAAA
40116033 TTTAAAA
1 TTTAAAA
40116040 TTTAAAA
1 TTTAAAA
40116047 TTTAA
1 TTTAA
40116052 TTTCTAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:40126064 original size:20 final size:21
Alignment explanation
Indices: 40126018--40126064 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
40126008 TTATAGAGTT
*
40126018 ATAAAAACTAAAAATAATTAA
1 ATAAAAACTAAAAATAATGAA
*
40126039 AGAAAAA-T-AAAATAAATGAA
1 ATAAAAACTAAAAAT-AATGAA
40126059 ATAAAA
1 ATAAAA
40126065 TATCAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.23
20 11 0.50
21 6 0.27
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (21 bp):
ATAAAAACTAAAAATAATGAA
Found at i:40144026 original size:13 final size:13
Alignment explanation
Indices: 40144010--40144039 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40144000 ATATAACTGA
40144010 TTCATATAGCCAT
1 TTCATATAGCCAT
*
40144023 TTCATATAGTCAT
1 TTCATATAGCCAT
40144036 TTCA
1 TTCA
40144040 AAGTGCTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
TTCATATAGCCAT
Done.