Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 95 of 168
Found at i:28211141 original size:10 final size:10
Alignment explanation
Indices: 28211126--28211151 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28211116 TCATTAAGTG
28211126 CTAACAAATA
1 CTAACAAATA
28211136 CTAACAAATA
1 CTAACAAATA
28211146 CTAACA
1 CTAACA
28211152 TATCAGTAAG
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:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (10 bp):
CTAACAAATA
Found at i:28211577 original size:243 final size:243
Alignment explanation
Indices: 28211142--28211642 Score: 903
Period size: 243 Copynumber: 2.1 Consensus size: 243
28211132 AATACTAACA
* * *
28211142 AATACTAACATATCAGTAAGTGCTAACCAGAGAAAGGCACATATGCCAATTCATACATTAATCAT
1 AATACTAACAGATCAATAAGTGCTAACCAGAGAAAGACACATATGCCAATTCATACATTAATCAT
*
28211207 ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATTAGTCCACATGC
66 ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATCAGTCCACATGC
* *
28211272 CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGGCACGTATGTATTT
131 CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGCCACATATGTATTT
*
28211337 ACCTACCATCAACCAAATATAACAGCTCATCACTGCCATTTCCCAAAT
196 ACCTACCATCAACCAAATAAAACAGCTCATCACTGCCATTTCCCAAAT
* *
28211385 AATACTAATAGATCAATAAGTGCTAATCAGAGAAAGACACATATGCCAATTCATACATTAATCAT
1 AATACTAACAGATCAATAAGTGCTAACCAGAGAAAGACACATATGCCAATTCATACATTAATCAT
28211450 ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATCAGTCCACATGC
66 ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATCAGTCCACATGC
28211515 CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGCCACATATGTATTT
131 CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGCCACATATGTATTT
*
28211580 ACCTACCATCAACCAAATAAAACAGCTCATCATTGCCATTTCCCAAAT
196 ACCTACCATCAACCAAATAAAACAGCTCATCACTGCCATTTCCCAAAT
*
28211628 AATACTAACAAATCA
1 AATACTAACAGATCA
28211643 GAGTAAAAAT
Statistics
Matches: 246, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
243 246 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (243 bp):
AATACTAACAGATCAATAAGTGCTAACCAGAGAAAGACACATATGCCAATTCATACATTAATCAT
ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATCAGTCCACATGC
CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGCCACATATGTATTT
ACCTACCATCAACCAAATAAAACAGCTCATCACTGCCATTTCCCAAAT
Found at i:28212126 original size:16 final size:16
Alignment explanation
Indices: 28212105--28212141 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
28212095 CAAACAAATT
28212105 TACTTAGAATTCTCAA
1 TACTTAGAATTCTCAA
28212121 TACTTAGAATTCTCAA
1 TACTTAGAATTCTCAA
28212137 TACTT
1 TACTT
28212142 GTATATCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (16 bp):
TACTTAGAATTCTCAA
Found at i:28214518 original size:11 final size:11
Alignment explanation
Indices: 28214504--28214529 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28214494 TTTTATGTGT
28214504 TTTTTTAAATA
1 TTTTTTAAATA
28214515 TTTTTTAAATA
1 TTTTTTAAATA
28214526 TTTT
1 TTTT
28214530 ATTATACTTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:28214829 original size:24 final size:24
Alignment explanation
Indices: 28214797--28214846 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
28214787 TGTTAGAATT
28214797 ATCTATACTATATTTAAGATTTTG
1 ATCTATACTATATTTAAGATTTTG
*
28214821 ATCTTTACTATATTTAAGATTTTG
1 ATCTATACTATATTTAAGATTTTG
28214845 AT
1 AT
28214847 TGAGTTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (24 bp):
ATCTATACTATATTTAAGATTTTG
Found at i:28216325 original size:3 final size:3
Alignment explanation
Indices: 28216312--28216377 Score: 62
Period size: 3 Copynumber: 21.0 Consensus size: 3
28216302 TGTACATGAA
* *
28216312 AAT AAT AAAT AAT AAT AAAT AAT AAT AAG AAT AAT AAAC AAGT AAT AAT
1 AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AA-T AAT AAT
*
28216361 AAA AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
28216378 GTAAAAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 2 0.04
3 40 0.77
4 10 0.19
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:28216333 original size:17 final size:18
Alignment explanation
Indices: 28216311--28216377 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 18
28216301 ATGTACATGA
28216311 AAATAATA-AATAATAAT
1 AAATAATACAATAATAAT
*
28216328 AAATAAT--AATAAGAAT
1 AAATAATACAATAATAAT
28216344 -AATAA-ACAAGTAATAAT
1 AAATAATACAA-TAATAAT
*
28216361 AAA-AATATAATAATAAT
1 AAATAATACAATAATAAT
28216378 GTAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
15 5 0.12
16 10 0.24
17 22 0.52
18 5 0.12
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (18 bp):
AAATAATACAATAATAAT
Found at i:28216337 original size:20 final size:19
Alignment explanation
Indices: 28216312--28216377 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
28216302 TGTACATGAA
28216312 AATAATAAATAATAATAAAT
1 AATAAT-AATAATAATAAAT
* *
28216332 AATAATAAGAATAATAAAC
1 AATAATAATAATAATAAAT
*
28216351 AAGTAATAATAAAAATATAAT
1 AA-TAATAATAATAATA-AAT
28216372 AATAAT
1 AATAAT
28216378 GTAAAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 13 0.33
20 22 0.56
21 4 0.10
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAATAATAATAATAAAT
Found at i:28216357 original size:23 final size:21
Alignment explanation
Indices: 28216312--28216377 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
28216302 TGTACATGAA
28216312 AATAAT-AAATAATAATAAAT
1 AATAATAAAATAATAATAAAT
28216332 AATAATAAGAATAATAA-ACAAGT
1 AATAATAA-AATAATAATA-AA-T
28216355 AATAATAAAA-ATATAAT-AAT
1 AATAATAAAATA-ATAATAAAT
28216375 AAT
1 AAT
28216378 GTAAAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
20 10 0.25
21 5 0.12
22 16 0.40
23 9 0.22
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (21 bp):
AATAATAAAATAATAATAAAT
Found at i:28216360 original size:14 final size:13
Alignment explanation
Indices: 28216329--28216376 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
28216319 AATAATAATA
*
28216329 AATAATAATAAG-
1 AATAATAAAAAGT
28216341 AATAATAAACAAGT
1 AATAATAAA-AAGT
*
28216355 AATAATAAAAATAT
1 AATAATAAAAA-GT
28216369 AATAATAA
1 AATAATAA
28216377 TGTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 8 0.26
13 5 0.16
14 18 0.58
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (13 bp):
AATAATAAAAAGT
Found at i:28216963 original size:15 final size:14
Alignment explanation
Indices: 28216940--28216972 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
28216930 TTTTAAACAA
28216940 AAAATAAAATAAAT
1 AAAATAAAATAAAT
28216954 AAAATGAAAATAAAT
1 AAAAT-AAAATAAAT
28216969 AAAA
1 AAAA
28216973 AACGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:28218098 original size:44 final size:44
Alignment explanation
Indices: 28218048--28218635 Score: 211
Period size: 44 Copynumber: 13.4 Consensus size: 44
28218038 GCTGCAACCC
* **
28218048 CAGGGAGGTAAAATCTACCATCTTTGATCTACTCCACTACTACT
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
* * *** * ** * *
28218092 TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCC
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
* *** * *
28218136 CAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACT-GTAACCT
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACT-A-CT
* * * ** * *
28218180 CAGAGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCT
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
* * *** * ** * *
28218224 TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCC
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
* * * * *
28218268 CAGGGAGATAGAAT-TACTAGCTTCAATGTACTCCACT-GTAACCT
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACT-A-CT
* * ** *
28218312 CAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTACT
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
* * *** * ** * *
28218356 TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCC
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
* **** * *
28218400 CAGGGAGATAGAAT-TATTGGCTTCAATGTACTCCACT-GTAACCT
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACT-A-CT
* * * * * *
28218444 CAGGGAGGTAAAATCCACCATCTTCGATCTGCTCAACTACTTCT
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
* * ** * ** * *
28218488 TAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCC
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
* *** *
28218532 CAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTA-TAACTT
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACT-AC-T
* * * * ** *
28218576 CAAGGAGGTAAAATCCACCATATTTGATCTGCTCCACTACTACT
1 CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
* * *
28218620 TAGGCAGATAAGATCT
1 CAGGGAGATAAAATCT
28218636 GTTATCTTCG
Statistics
Matches: 370, Mismatches: 158, Indels: 32
0.66 0.28 0.06
Matches are distributed among these distances:
42 4 0.01
43 68 0.18
44 231 0.62
45 63 0.17
46 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
CAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTACT
Found at i:28218188 original size:132 final size:132
Alignment explanation
Indices: 28218003--28218650 Score: 1062
Period size: 132 Copynumber: 4.9 Consensus size: 132
28217993 CCACTACCGA
* ** * * * * *
28218003 CCAGGGAAATAGAATTACTGGCACCAATATACTCCGCTGCAACCCCAGGGAGGTAAAATCTACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
*
28218068 TCTTTGATCTACTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
28218133 GC
131 GC
* **
28218135 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCTGCCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
*
28218200 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
28218265 GC
131 GC
*
28218267 CCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
28218332 TCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
28218397 GC
131 GC
*
28218399 CCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
* * * *
28218464 TCTTCGATCTGCTCAACTACTTCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
28218529 GC
131 GC
* * *
28218531 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTATAACTTCAAGGAGGTAAAATCCACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
* * * *
28218596 TATTTGATCTGCTCCACTACTACTTAGGCAGATAAGATCTGTTATCTTCGATCTA
66 TCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTA
28218651 CTTCACGCCA
Statistics
Matches: 482, Mismatches: 34, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 482 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (132 bp):
CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
TCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
GC
Found at i:28219987 original size:13 final size:13
Alignment explanation
Indices: 28219956--28219986 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
28219946 TGGCCTCTCC
28219956 ATTTTTCTTTTTT
1 ATTTTTCTTTTTT
28219969 ATTTTTC-TTTTT
1 ATTTTTCTTTTTT
28219981 ATTTTT
1 ATTTTT
28219987 TTGGACTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTCTTTTTT
Found at i:28222826 original size:19 final size:19
Alignment explanation
Indices: 28222802--28222847 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28222792 AACTGTGTTT
* *
28222802 AATGCATATG-ATGTAATG
1 AATGCAAATGCATGAAATG
28222820 AAATGCAAATGCATGAAATG
1 -AATGCAAATGCATGAAATG
28222840 AATGCAAA
1 AATGCAAA
28222848 AAAGAGACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (19 bp):
AATGCAAATGCATGAAATG
Found at i:28224135 original size:21 final size:21
Alignment explanation
Indices: 28224111--28224151 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28224101 TATTTTAAAG
28224111 AAATAATAAAATATTATTATA
1 AAATAATAAAATATTATTATA
28224132 AAATAATAAAATATTATTAT
1 AAATAATAAAATATTATTAT
28224152 TTTAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATAATAAAATATTATTATA
Found at i:28224152 original size:24 final size:24
Alignment explanation
Indices: 28224095--28224166 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
28224085 CTTAGTGTCG
*
28224095 AAAAT-TTATT-TTAAAGAAATAAT
1 AAAATATTATTATTATA-AAATAAT
28224118 -AAA-A-TATTATTATAAAATAAT
1 AAAATATTATTATTATAAAATAAT
*
28224139 AAAATATTATTATTTTAAAGA-AAT
1 AAAATATTATTATTATAAA-ATAAT
28224163 AAAA
1 AAAA
28224167 CATCACACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
21 11 0.27
22 10 0.24
23 1 0.02
24 18 0.44
25 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (24 bp):
AAAATATTATTATTATAAAATAAT
Found at i:28227181 original size:13 final size:13
Alignment explanation
Indices: 28227163--28227203 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
28227153 GAATTTTTGC
*
28227163 TTTCTTTTCCCTA
1 TTTCTTTTCCATA
*
28227176 TTTCTTCTCCAT-
1 TTTCTTTTCCATA
28227188 TTTCTTTTCCATA
1 TTTCTTTTCCATA
28227201 TTT
1 TTT
28227204 ATCTTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCTTTTCCATA
Found at i:28230416 original size:39 final size:37
Alignment explanation
Indices: 28230370--28230452 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 37
28230360 TTAAATTTAA
28230370 TATTAAGATAA-TCATTTTAATATTAAATTAATA-AAATAC
1 TATTAAGATAAGT-A-TTTAAT-TTAAATTAATATAAAT-C
*
28230409 TATTAAGATAAGTATTTAATTTAATTTAATATTAAATC
1 TATTAAGATAAGTATTTAATTTAAATTAATA-TAAATC
28230447 TATTAA
1 TATTAA
28230453 AATATTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
37 10 0.25
38 13 0.32
39 16 0.40
40 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (37 bp):
TATTAAGATAAGTATTTAATTTAAATTAATATAAATC
Found at i:28236353 original size:91 final size:91
Alignment explanation
Indices: 28236198--28236403 Score: 290
Period size: 91 Copynumber: 2.3 Consensus size: 91
28236188 AGTTTAAGTA
* * * * *
28236198 CAAACACTAGTGGTTTATCCATACACTTACTGACAAATTTTATCTGCAAACCCTTTATGCATTCA
1 CAAACACTGGTGGTTTATCCACAAAATTACTGACAAATTTTATCTGCAAACCCGTTATGCATTCA
* *
28236263 CAACCTACTGGCAGCGTATTAACTTG
66 CAACCTACTAGCAACGTATTAACTTG
* *
28236289 CAAACACTGGTGGTTTATCCACAAAATTACTGA-AAGCTTTTATCTGCAAACCCGTTGTGCATTC
1 CAAACACTGGTGGTTTATCCACAAAATTACTGACAA-ATTTTATCTGCAAACCCGTTATGCATTC
28236353 ACAACCTACTAGCAACGTATTAACTTG
65 ACAACCTACTAGCAACGTATTAACTTG
* *
28236380 C-GACACTGGTGGTTCATCCACAAA
1 CAAACACTGGTGGTTTATCCACAAA
28236404 CTGGAGTGTC
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 23 0.22
91 80 0.78
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (91 bp):
CAAACACTGGTGGTTTATCCACAAAATTACTGACAAATTTTATCTGCAAACCCGTTATGCATTCA
CAACCTACTAGCAACGTATTAACTTG
Found at i:28240103 original size:2 final size:2
Alignment explanation
Indices: 28240096--28240126 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28240086 NNTAGACTAC
28240096 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28240127 TAATCCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28242421 original size:19 final size:19
Alignment explanation
Indices: 28242397--28242435 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28242387 AACAAAATAA
*
28242397 ATACATTCTATATTTAATT
1 ATACATTCTATAATTAATT
*
28242416 ATACATTTTATAATTAATT
1 ATACATTCTATAATTAATT
28242435 A
1 A
28242436 AAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (19 bp):
ATACATTCTATAATTAATT
Found at i:28246009 original size:21 final size:21
Alignment explanation
Indices: 28245968--28246010 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28245958 ATTAATCAAC
*
28245968 TATTTCTAATGCATCCAAACA
1 TATTTCTAATGCATCAAAACA
*
28245989 TATTT-TAATGCATGAATAACA
1 TATTTCTAATGCATCAA-AACA
28246010 T
1 T
28246011 GAACGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (21 bp):
TATTTCTAATGCATCAAAACA
Found at i:28247971 original size:10 final size:10
Alignment explanation
Indices: 28247956--28247982 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28247946 GACAATTCTA
28247956 AAGACTATAT
1 AAGACTATAT
28247966 AAGACTATAT
1 AAGACTATAT
28247976 AAGACTA
1 AAGACTA
28247983 ATGAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (10 bp):
AAGACTATAT
Found at i:28252795 original size:27 final size:27
Alignment explanation
Indices: 28252745--28252796 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
28252735 TGTCGTATAA
**
28252745 CATATAATGCGATAAAATTTCCAATAT
1 CATATAATGCGATAAAATCGCCAATAT
28252772 CATATAATGCGATAAAATCGCCAAT
1 CATATAATGCGATAAAATCGCCAAT
28252797 CCCTTCGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (27 bp):
CATATAATGCGATAAAATCGCCAATAT
Found at i:28257274 original size:25 final size:22
Alignment explanation
Indices: 28257244--28257290 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
28257234 TTAAGACTGG
* *
28257244 TCGTGGTGGCTTCCTCTAATTC
1 TCGTGGTGGTTTCCTCCAATTC
28257266 TCGTGGTGGTTTCCTCCAATTC
1 TCGTGGTGGTTTCCTCCAATTC
28257288 TCG
1 TCG
28257291 CGGTTTCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.28, G:0.23, T:0.40
Consensus pattern (22 bp):
TCGTGGTGGTTTCCTCCAATTC
Found at i:28262005 original size:20 final size:20
Alignment explanation
Indices: 28261980--28262019 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28261970 CTTGTACAGG
*
28261980 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTTTGATGCCTCT
28262000 GTTTGCACTTTGATGCCTCT
1 GTTTGCACTTTGATGCCTCT
28262020 ATTCACACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.45
Consensus pattern (20 bp):
GTTTGCACTTTGATGCCTCT
Found at i:28262028 original size:20 final size:20
Alignment explanation
Indices: 28261985--28262029 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28261975 ACAGGGTTTG
* * **
28261985 CACTTTGGTGCCTCTGTTTG
1 CACTTTGATGCCTCTATTCA
28262005 CACTTTGATGCCTCTATTCA
1 CACTTTGATGCCTCTATTCA
28262025 CACTT
1 CACTT
28262030 CGGCACCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.13, C:0.29, G:0.16, T:0.42
Consensus pattern (20 bp):
CACTTTGATGCCTCTATTCA
Found at i:28264041 original size:27 final size:27
Alignment explanation
Indices: 28264011--28264124 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 27
28264001 TCAAGACAAC
* * * *
28264011 AAACACGGTGTAGTCTGCCAAGACAGT
1 AAACACGGGGTAGTCCGTCGAGACAGT
* * *
28264038 AAACATGAGGTAGTCCGTCGAGATAGCT
1 AAACACGGGGTAGTCCGTCGAGACAG-T
*
28264066 -AACACGGGGTAGTCCATCGAGACAGT
1 AAACACGGGGTAGTCCGTCGAGACAGT
* *
28264092 AAACACGGGGTAGTCTGTCGAGACAGA
1 AAACACGGGGTAGTCCGTCGAGACAGT
28264119 AAACAC
1 AAACAC
28264125 AAGGAAGCTC
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.01
27 69 0.97
28 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (27 bp):
AAACACGGGGTAGTCCGTCGAGACAGT
Found at i:28269044 original size:32 final size:32
Alignment explanation
Indices: 28269003--28269072 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
28268993 CAATATTCCA
28269003 ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
1 ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
28269035 ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
1 ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
28269067 ACACGT
1 ACACGT
28269073 TCATCTAACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.27
Consensus pattern (32 bp):
ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
Found at i:28281477 original size:16 final size:16
Alignment explanation
Indices: 28281456--28281507 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
28281446 TTTGGTTCGC
28281456 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28281472 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
28281488 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
28281504 TGTA
1 TGTA
28281508 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28281760 original size:16 final size:16
Alignment explanation
Indices: 28281723--28281764 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28281713 TTAATCATAT
*
28281723 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28281739 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28281754 TTAAAATATAT
1 TTAAAATATAT
28281765 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28284364 original size:13 final size:13
Alignment explanation
Indices: 28284327--28284392 Score: 89
Period size: 13 Copynumber: 4.8 Consensus size: 13
28284317 TGCCTACTGG
28284327 AGAAAGCAAAGGAGAA
1 AGAAAGCAAA-G-G-A
28284343 AGCAAAGCAAAGGA
1 AG-AAAGCAAAGGA
28284357 AGAAAGCAAAGGA
1 AGAAAGCAAAGGA
28284370 AGAAAGCAAAGG-
1 AGAAAGCAAAGGA
28284382 AGAAAGCAAAG
1 AGAAAGCAAAG
28284393 AAAACAAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.22
13 23 0.47
14 3 0.06
15 1 0.02
16 3 0.06
17 8 0.16
ACGTcount: A:0.61, C:0.09, G:0.30, T:0.00
Consensus pattern (13 bp):
AGAAAGCAAAGGA
Found at i:28284459 original size:19 final size:19
Alignment explanation
Indices: 28284435--28284554 Score: 86
Period size: 19 Copynumber: 6.1 Consensus size: 19
28284425 CAAATCGGGC
28284435 GAAACAGAAGAGGCAAAGG
1 GAAACAGAAGAGGCAAAGG
*
28284454 GAAACAGAAGAGGCAGAGG
1 GAAACAGAAGAGGCAAAGG
* *
28284473 AGAAAGCA-AAGAAAAG-AAA-A
1 -GAAA-CAGAAG--AGGCAAAGG
*
28284493 GAAACAG-AGGGAGCAAATCGGG
1 GAAACAGAAGAG-GCAAA---GG
28284515 CGAAACAGAAGAGGCAAAGG
1 -GAAACAGAAGAGGCAAAGG
*
28284535 GAAACAGAAGAGGCAGAGG
1 GAAACAGAAGAGGCAAAGG
28284554 G
1 G
28284555 TAAAACAGGG
Statistics
Matches: 79, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
17 1 0.01
18 7 0.09
19 41 0.52
20 9 0.11
21 4 0.05
22 2 0.03
23 12 0.15
24 3 0.04
ACGTcount: A:0.52, C:0.11, G:0.37, T:0.01
Consensus pattern (19 bp):
GAAACAGAAGAGGCAAAGG
Found at i:28284459 original size:42 final size:42
Alignment explanation
Indices: 28284412--28284542 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 42
28284402 GAAAAGAAAA
28284412 GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
1 GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
* * * * *
28284454 GAAACAGA-AGAGGCAGA---GGAGAAAGCA-AAGAAAAG-AAA-A
1 GAAACAGAGGGA-GCAAATCGGGCGAAA-CAGAAG--AGGCAAAGG
28284493 GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
1 GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
28284535 GAAACAGA
1 GAAACAGA
28284543 AGAGGCAGAG
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
39 21 0.31
40 9 0.13
41 9 0.13
42 29 0.43
ACGTcount: A:0.51, C:0.12, G:0.35, T:0.02
Consensus pattern (42 bp):
GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
Found at i:28284486 original size:81 final size:81
Alignment explanation
Indices: 28284399--28284553 Score: 310
Period size: 81 Copynumber: 1.9 Consensus size: 81
28284389 AAAGAAAACA
28284399 AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
1 AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
28284464 AGGCAGAGGAGAAAGC
66 AGGCAGAGGAGAAAGC
28284480 AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
1 AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
28284545 AGGCAGAGG
66 AGGCAGAGG
28284554 GTAAAACAGG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 74 1.00
ACGTcount: A:0.53, C:0.11, G:0.35, T:0.01
Consensus pattern (81 bp):
AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
AGGCAGAGGAGAAAGC
Found at i:28286689 original size:43 final size:43
Alignment explanation
Indices: 28286642--28286724 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
28286632 CCTAATCATT
** * *
28286642 ACAATTAGGGACTCAAATCCAATCTGGGCCCAACCTTTTGTGA
1 ACAATTACAGACTCAAATCCAACCGGGGCCCAACCTTTTGTGA
* *
28286685 ACAATTACAGACTCGAATCTAACCGGGGCCCAACCTTTTG
1 ACAATTACAGACTCAAATCCAACCGGGGCCCAACCTTTTG
28286725 CGAAGAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
ACAATTACAGACTCAAATCCAACCGGGGCCCAACCTTTTGTGA
Found at i:28300522 original size:29 final size:29
Alignment explanation
Indices: 28300480--28300537 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28300470 ACCACAATAG
28300480 AATATGTCTCTTCATAATCAATGTCGAGC
1 AATATGTCTCTTCATAATCAATGTCGAGC
28300509 AATATGTCTCTTCATAATCAATGTCGAGC
1 AATATGTCTCTTCATAATCAATGTCGAGC
28300538 CTTTGCGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (29 bp):
AATATGTCTCTTCATAATCAATGTCGAGC
Found at i:28305025 original size:32 final size:32
Alignment explanation
Indices: 28304968--28305079 Score: 93
Period size: 32 Copynumber: 3.5 Consensus size: 32
28304958 GAAGACAATT
*
28304968 TTTTTAATTAATTTATATATTTATATATTTTTA
1 TTTTT-ATTAATTTTTATATTTATATATTTTTA
* **
28305001 TTTTTTTTAATTTTTAT-TTGTATAT-TTTAGA
1 TTTTTATTAATTTTTATATT-TATATATTTTTA
* * * *
28305032 TTTTTAAATAATTTTTATCTTTACATATGTTTA
1 TTTTT-ATTAATTTTTATATTTATATATTTTTA
* *
28305065 ATTTTGTTAATTTTT
1 TTTTTATTAATTTTT
28305080 TGAAATTATA
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
31 11 0.18
32 37 0.60
33 14 0.23
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (32 bp):
TTTTTATTAATTTTTATATTTATATATTTTTA
Found at i:28319418 original size:100 final size:100
Alignment explanation
Indices: 28319277--28319551 Score: 379
Period size: 100 Copynumber: 2.8 Consensus size: 100
28319267 ACAGTGGAGC
* * *
28319277 AGATTAAAGCCGCAATGGCGAATCTTACTCCCCTGGCGGTGTAGTAGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* * * *
28319342 CGATGAATTTCGTTTCCCCAACATTGCAATTAAAA
66 AGACGAATCTCATTTCCCCAACATTGCAATTAAAA
**
28319377 AGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* *
28319442 AGGCGAATCTCATTTCCCCAACATTGCAATTTAAA
66 AGACGAATCTCATTTCCCCAACATTGCAATTAAAA
* * * * * * *
28319477 AGATTGAAGCCGCAACGGCGAATCTTATTTCCCTGGCGTTGTAGCGGAGCAGATTGAAGCCATGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
28319542 CGACGAATCT
66 AGACGAATCT
28319552 TATCTCCCTG
Statistics
Matches: 153, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 153 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (100 bp):
AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
AGACGAATCTCATTTCCCCAACATTGCAATTAAAA
Found at i:28319431 original size:50 final size:50
Alignment explanation
Indices: 28319269--28319436 Score: 126
Period size: 50 Copynumber: 3.4 Consensus size: 50
28319259 TTAGCATTAC
* * * **
28319269 AGTGGAGCAGATTAAAGCCGCAATGGCGAATCTTACTCCCCTGGCGGTGT
1 AGTGGAACAGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGT
* ** * ** ** *
28319319 AGTAGAACAGATTGAAGCTACGACGATGAAT-TT-CGTTTCCCC-AACATTGC
1 AGTGGAACAGATTGAAGCCGCAACGATGAATCTTAC---TCCCCTGGCGGTGT
* ** *
28319369 AATTAAAAAGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGT
1 AGTGGAACAGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGT
28319419 AGTGGAACAGATTGAAGC
1 AGTGGAACAGATTGAAGC
28319437 TACGAAGGCG
Statistics
Matches: 82, Mismatches: 30, Indels: 12
0.66 0.24 0.10
Matches are distributed among these distances:
48 1 0.01
49 7 0.09
50 66 0.80
51 7 0.09
52 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.23
Consensus pattern (50 bp):
AGTGGAACAGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGT
Found at i:28323759 original size:26 final size:27
Alignment explanation
Indices: 28323681--28323760 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
28323671 TTAACAATTA
*
28323681 ATAAATTATTTGTAAATTTAAT-TATAC
1 ATAAAATATTT-TAAATTTAATATATAC
28323708 ATAAAATATTTTAAAATTTTAA-ATATAC
1 ATAAAATATTTT-AAA-TTTAATATATAC
* *
28323736 ATTAAATA-TTTAAATCTAATATATA
1 ATAAAATATTTTAAATTTAATATATA
28323761 TTCTATAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 4 0.09
26 9 0.20
27 16 0.35
28 17 0.37
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (27 bp):
ATAAAATATTTTAAATTTAATATATAC
Found at i:28325292 original size:2 final size:2
Alignment explanation
Indices: 28325231--28325274 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
28325221 AAAGTGTAGA
28325231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT ACT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
28325272 AT A
1 AT A
28325275 GACGCTTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 36 0.92
3 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28325483 original size:3 final size:3
Alignment explanation
Indices: 28325469--28325543 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
28325459 AACTAACAAT
* * * * *
28325469 TAA TAG TAA TAA TAA TTA TAA TTA TAA TAA TGA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28325517 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
28325544 CCAAAATGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:28326268 original size:6 final size:7
Alignment explanation
Indices: 28326253--28326277 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28326243 CAGAAAACAG
28326253 AAAATAA
1 AAAATAA
28326260 AAAATAA
1 AAAATAA
28326267 AAAATAA
1 AAAATAA
28326274 AAAA
1 AAAA
28326278 GGGAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:28327261 original size:44 final size:44
Alignment explanation
Indices: 28327040--28327579 Score: 375
Period size: 44 Copynumber: 12.6 Consensus size: 44
28327030 GTTTTTTCTG
* * * * *
28327040 TCTGCTCCGCTACTGCTTAGGGAGATAAGA-CT--TG-ATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* *** * **
28327080 TCTACTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * * * * *
28327123 TCTGCTTCACTACTGTTTAGGAAGATAAGATTTACCTTCTTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* *
28327166 -CT--T-CACTACTGCTTAGGAAGAT-GAGAT-TCCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAG-GATCTACCGTCTTCGA
*
28327205 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * *** * **
28327249 CCTGCTCTACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * * * * *
28327292 TCTGCTTCACTATTACTTAGGAAGATAAGAT-T-CGTCGTCCTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTAC--CGTCTTCGA
* * *
28327336 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * *
28327380 CCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCCTT-GA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGT-CTTCGA
* ** * **
28327424 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTAGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * *
28327467 TCTGCTTCACTACTGCTTAGGAAGAT-GAGAT-TCGCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAG-GATCT-ACCGTCTTCGA
* ***
28327511 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT-TTCG-
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* *
28327553 TTTGCTCCGCTACTGCTTAGGGAGATA
1 TCTGCTCCACTACTGCTTAGGGAGATA
28327580 AGACTTGGTG
Statistics
Matches: 397, Mismatches: 79, Indels: 46
0.76 0.15 0.09
Matches are distributed among these distances:
38 9 0.02
39 21 0.05
40 32 0.08
42 34 0.09
43 112 0.28
44 183 0.46
45 5 0.01
46 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (44 bp):
TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
Found at i:28327357 original size:131 final size:130
Alignment explanation
Indices: 28327165--28327406 Score: 403
Period size: 131 Copynumber: 1.9 Consensus size: 130
28327155 TACCTTCTTC
* * *
28327165 GCTTCACTACTGCTTAGGAAGATGAGATTCCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 GCTTCACTACTACTTAGGAAGATAAGATTCCCGTCCTCGATCTGCTCCACTACTGCTTAGGGAGA
* *
28327230 TAGGATCTACCATCTTCGACCTGCTCTACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCT
66 TAAGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCT
* *
28327295 GCTTCACTATTACTTAGGAAGATAAGATTCGTCGTCCTCGATCTGCTCCACTACTGCTTAGGGAG
1 GCTTCACTACTACTTAGGAAGATAAGATTC-CCGTCCTCGATCTGCTCCACTACTGCTTAGGGAG
*
28327360 ATAAGATCTACCATCTTTGACCTGCTCCACTACTGCTTAGGGAGATA
65 ATAAGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATA
28327407 AGATCTACCA
Statistics
Matches: 103, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
130 27 0.26
131 76 0.74
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (130 bp):
GCTTCACTACTACTTAGGAAGATAAGATTCCCGTCCTCGATCTGCTCCACTACTGCTTAGGGAGA
TAAGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCT
Found at i:28327448 original size:175 final size:174
Alignment explanation
Indices: 28327041--28327582 Score: 696
Period size: 175 Copynumber: 3.2 Consensus size: 174
28327031 TTTTTTCTGT
* ** * *
28327041 CTGCTCCGCTACTGCTTAGGGAGATAAGA-CT-TGATGC--GATCTACTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACCAT-CTTGACCTGCTCCACTACTGCTTAGGG
*
28327102 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGTTTAGGAAGATAAGATT--TAC--CTTC-
65 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGT-CGTCTTCG
* * * * * * *
28327162 TTC-GCTTCACTACTGCTTAGGAAGATGAGAT-TCCCGTCTTCGAT
129 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGAC
* *
28327206 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCTACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTT-GACCTGCTCCACTACTGCTTAGGG
* * *
28327271 AGATAGGACTGGTGGCTTAAATCTGCTTCACTATTACTTAGGAAGATAAGATTCGTCGTCCTCGA
65 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTCGA
*
28327336 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTGAC
130 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGAC
28327381 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCCTTGACCTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACCAT-CTTGACCTGCTCCACTACTGCTTAGGG
* * *
28327446 AGATAGGACTAGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATGAGATTCGCCGTCTTCGA
65 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTCGA
**** *
28327511 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT-TTCG-T
130 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGAC
* *
28327554 TTGCTCCGCTACTGCTTAGGGAGATAAGA
1 CTGCTCCACTACTGCTTAGGGAGATAAGA
28327583 CTTGGTGCGA
Statistics
Matches: 329, Mismatches: 35, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
165 27 0.08
166 3 0.01
167 2 0.01
169 71 0.22
170 1 0.00
171 1 0.00
172 3 0.01
173 29 0.09
174 28 0.09
175 161 0.49
176 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (174 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTGACCTGCTCCACTACTGCTTAGGGA
GATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGTCGTCTTCGAT
CTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGAC
Found at i:28327470 original size:131 final size:132
Alignment explanation
Indices: 28327204--28327543 Score: 384
Period size: 131 Copynumber: 2.6 Consensus size: 132
28327194 CCCGTCTTCG
* *
28327204 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCTACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTGCTCCACTACTGCTTAG
* ** * * * * * * *
28327269 GGAGATAGGA-CTGGTGGCTTAAATCTGCTTCACTATTACTTAGGAAGATAAGATTCGTCGTCCT
66 GGAGATAAGATCTCATGCCTTAAACCTGCTCCACTACTACTTAGGAAGATAAGACTAGTCGGCCT
**
28327333 CG
131 AA
*
28327335 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTGACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTGCTCCACTACTGCTTAG
* * * *
28327400 GGAGATAAGATCTACCAT-CCTT-GACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGT-GGC
66 GGAGATAAGATCT--CATGCCTTAAACCTGCTCCACTACTACTTAGGAAGATAAGACTAGTCGGC
*
28327462 TTAA
129 CTAA
* * * * * *
28327466 ATCTGCTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGATCTGCTCCACTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACCATCTTCGACCTGCTCCACTACTGCTTA
28327530 GGGAGATAAGATCT
65 GGGAGATAAGATCT
28327544 GTGGTTTCGT
Statistics
Matches: 178, Mismatches: 27, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
130 1 0.01
131 143 0.80
132 30 0.17
133 3 0.02
134 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTGCTCCACTACTGCTTAG
GGAGATAAGATCTCATGCCTTAAACCTGCTCCACTACTACTTAGGAAGATAAGACTAGTCGGCCT
AA
Found at i:28327693 original size:44 final size:43
Alignment explanation
Indices: 28327597--28328150 Score: 324
Period size: 44 Copynumber: 12.7 Consensus size: 43
28327587 GTGCGATTTG
* * ** * * *
28327597 CTCCACTATAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAAC-TCAGGGAGATAAGATCTCTGGCTTCAATCTA
* *
28327640 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAA-CTCAGGGAGATAAGATCTCTGGCTTCAATCTA
* * **
28327684 CTCCACTGTAACCTCAGGGGGATAAGATCTTACAT-TCTTCGGTCTA
1 CTCCACTGTAA-CTCAGGGAGATAAGATC-T-C-TGGCTTCAATCTA
* * * *
28327730 CTCCACCGTAACCTCAGGGAGATAAGA-C-CT-GATGCGATCTA
1 CTCCACTGTAA-CTCAGGGAGATAAGATCTCTGGCTTCAATCTA
** * * *** * **
28327771 CTCTGCTGTAACTTCAGAGAGATAAGACCT-TTATTTTAATCCG
1 CTCCACTGTAAC-TCAGGGAGATAAGATCTCTGGCTTCAATCTA
* * *
28327814 CTCCACTGTAACTTCAGAGAGATAGGAT-TACTAGCTTCAATCTA
1 CTCCACTGTAAC-TCAGGGAGATAAGATCT-CTGGCTTCAATCTA
* *
28327858 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAA-CTCAGGGAGATAAGATCTCTGGCTTCAATCTA
* * * **
28327902 CTCTACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTCGGTCTA
1 CTCCACTGTAA-CTCAGGGAGATAAGATCT---CTGGCTTCAATCTA
* * * *
28327948 CTCCATTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGATCTA
1 CTCCACTGTAA-CTCAGGGAGATAAGATCTCTGGCTTCAATCTA
** * *** * *
28327989 CTCTGCTGTAACTTCAGAGAGATAAGA-CTCTTTAATTTAATCCA
1 CTCCACTGTAAC-TCAGGGAGATAAGATCTC-TGGCTTCAATCTA
* *
28328033 CTCCACTGTAACTTCAGGGAGATAGGAT-TACTAGCTTCAATCTA
1 CTCCACTGTAAC-TCAGGGAGATAAGATCT-CTGGCTTCAATCTA
* * *
28328077 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAACCTG
1 CTCCACTGTAA-CTCAGGGAGATAAGATCTCTGGCTTCAATCTA
*
28328121 CTCCACTGTAACTTCAGAGAGATAAGATCT
1 CTCCACTGTAAC-TCAGGGAGATAAGATCT
28328151 GAAATTCTTC
Statistics
Matches: 400, Mismatches: 86, Indels: 49
0.75 0.16 0.09
Matches are distributed among these distances:
40 2 0.00
41 59 0.15
42 5 0.01
43 53 0.13
44 206 0.51
45 8 0.02
46 65 0.16
47 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (43 bp):
CTCCACTGTAACTCAGGGAGATAAGATCTCTGGCTTCAATCTA
Found at i:28328145 original size:219 final size:218
Alignment explanation
Indices: 28327596--28328278 Score: 1181
Period size: 219 Copynumber: 3.1 Consensus size: 218
28327586 GGTGCGATTT
* * * *
28327596 GCTCCACTATAACTTCAGGGAGATAGGA-TAGT-GTCTTCGATCTGCTCCGCTGTAATCTCAGGG
1 GCTCCACTGTAACTTCAGGGAGATAGGATTACTAG-CTTCAATCTACTCCGCTGTAATCTCAGGG
* * *
28327659 AGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGGGATAAGATCTTACATTCTTC
65 AGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTC
**
28327724 GGTCTACTCCACCGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGA
130 GGTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGA
*
28327789 GAGATAAGACCTTTATTTTAATCC
195 GAGATAAGACCTTTAATTTAATCC
*
28327813 GCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGA
1 GCTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGA
*
28327878 GATAAGATCTCTGGCTTCAATCTGCTCTACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
66 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
28327943 GTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
131 GTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
28328008 AGATAAGACTCTTTAATTTAATCC
196 AGATAAGAC-CTTTAATTTAATCC
*
28328032 ACTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGA
1 GCTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGA
* * *
28328097 GATAAGATCTCTGGCTTCAACCTGCTCCACTGTAACTTCAGAGAGATAAGATCTGAAATTCTTCG
66 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
28328162 GTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
131 GTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
28328227 AGATAAGACCCTTTAATTTAATCC
196 AGATAAGA-CCTTTAATTTAATCC
28328251 GCTCCACTGTAACTTCAGGGAGATAGGA
1 GCTCCACTGTAACTTCAGGGAGATAGGA
28328279 CTTGTAACTT
Statistics
Matches: 443, Mismatches: 19, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
217 26 0.06
218 164 0.37
219 252 0.57
220 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (218 bp):
GCTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGA
GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
GTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
AGATAAGACCTTTAATTTAATCC
Found at i:28328450 original size:25 final size:25
Alignment explanation
Indices: 28328406--28328455 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28328396 CTTGGGAAGT
* *
28328406 AAGATTCGCCGTTGTAGCTTTAATC
1 AAGATTCACCGATGTAGCTTTAATC
*
28328431 AAGATTCACCGATGTGGCTTTAATC
1 AAGATTCACCGATGTAGCTTTAATC
28328456 TTTTCAACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (25 bp):
AAGATTCACCGATGTAGCTTTAATC
Found at i:28328465 original size:125 final size:126
Alignment explanation
Indices: 28328317--28328555 Score: 327
Period size: 125 Copynumber: 1.9 Consensus size: 126
28328307 GATTCGCCAT
* * * *
28328317 TGTGGCTTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCT
1 TGTGGCTTTTAATCTTTTCAACTGCAATGTAGGAGAAACAAGATGCACCAATGTGGCTTTAATCT
* * * *
28328382 ATTCCACTGCATCGCTTGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCAAGATTCACCGA
66 ATTCCACTGCACCACCTGGGAAGTAAGATTCGCCGCTGTAGCTTTAATCAAGATTCACCGA
* * * * *
28328443 TGTGGC-TTTAATCTTTTCAACTGCAATGTAGGGGAAGCAAGATGCATCGATGTGGTTTTAATCT
1 TGTGGCTTTTAATCTTTTCAACTGCAATGTAGGAGAAACAAGATGCACCAATGTGGCTTTAATCT
* * *
28328507 GTTCCACTGCACCACCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAATC
66 ATTCCACTGCACCACCTGGGAAGTAAGATTCGCCGCTGTAGCTTTAATC
28328556 TTTTTAATCG
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
125 91 0.94
126 6 0.06
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (126 bp):
TGTGGCTTTTAATCTTTTCAACTGCAATGTAGGAGAAACAAGATGCACCAATGTGGCTTTAATCT
ATTCCACTGCACCACCTGGGAAGTAAGATTCGCCGCTGTAGCTTTAATCAAGATTCACCGA
Found at i:28328587 original size:50 final size:50
Alignment explanation
Indices: 28328526--28328784 Score: 215
Period size: 50 Copynumber: 5.2 Consensus size: 50
28328516 CACCACCTGG
* *
28328526 GAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGT
1 GAGGCAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGA
* * * * * * *
28328576 GAGGCAAGATTCACCTTC-GTGGCTTTAATCTTTTTACT-GCACA-GCCTGG
1 GAGGCAAGATTC-GCTGCTGTAGCTTTAATCTTTTTAATCGCA-ATGTCAGA
** * *
28328625 GAGATAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACCGCGATGTCAGA
1 GAGGCAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGA
* * * * * * * * * *
28328675 GAGGCAAGATTCACCGTTGTGGCTTTAATC-TATTACT-GCACTGCCTGG
1 GAGGCAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGA
** *
28328723 GAGATAAGATTCGCTG-TAGTAGCTTTAATCTTTTTAACCGCAATGTCAGA
1 GAGGCAAGATTCGCTGCT-GTAGCTTTAATCTTTTTAATCGCAATGTCAGA
28328773 GAGGCAAGATTC
1 GAGGCAAGATTC
28328785 ATGGTTTTAG
Statistics
Matches: 154, Mismatches: 47, Indels: 16
0.71 0.22 0.07
Matches are distributed among these distances:
47 1 0.01
48 32 0.21
49 42 0.27
50 76 0.49
51 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (50 bp):
GAGGCAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGA
Found at i:28328648 original size:99 final size:99
Alignment explanation
Indices: 28328447--28328785 Score: 454
Period size: 99 Copynumber: 3.4 Consensus size: 99
28328437 CACCGATGTG
* * * * * * * * *
28328447 GCTTTAATCTTTTCAACTGCAATGT-AGGGGAAGCAAGATGCATCGATGTGGTTTTAATCTGTTC
1 GCTTTAATCTTTTTAACCGCAATGTCA-GAGAGGCAAGATTCACCGTTGTGGCTTTAATCT-TTT
* *
28328511 CACTGCACCA-CCTGGGAGGTAAGATTCGCTGCTGTA
64 TACTGCA-CAGCCTGGGAGATAAGATTCGCTGCTGTA
* *
28328547 GCTTTAATCTTTTTAATCGCAATGTCAGTGAGGCAAGATTCACC-TTCGTGGCTTTAATCTTTTT
1 GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTT-GTGGCTTTAATCTTTTT
28328611 ACTGCACAGCCTGGGAGATAAGATTCGCTGCTGTA
65 ACTGCACAGCCTGGGAGATAAGATTCGCTGCTGTA
* *
28328646 GCTTTAATCTTTTTAACCGCGATGTCAGAGAGGCAAGATTCACCGTTGTGGCTTTAATC-TATTA
1 GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGTGGCTTTAATCTTTTTA
*
28328710 CTGCACTGCCTGGGAGATAAGATTCGCTG-TAGTA
66 CTGCACAGCCTGGGAGATAAGATTCGCTGCT-GTA
28328744 GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCA
1 GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCA
28328786 TGGTTTTAGT
Statistics
Matches: 216, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
97 1 0.00
98 78 0.36
99 87 0.40
100 49 0.23
101 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (99 bp):
GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGTGGCTTTAATCTTTTTA
CTGCACAGCCTGGGAGATAAGATTCGCTGCTGTA
Found at i:28329124 original size:87 final size:87
Alignment explanation
Indices: 28328993--28329536 Score: 887
Period size: 87 Copynumber: 6.3 Consensus size: 87
28328983 TACCGCTTAG
* * * *
28328993 GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTACTATCTT
1 GGAGGCAAGGCTT-TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTT
28329058 TAACCAGCTCCACTGCAACCGAT
65 TAACCAGCTCCACTGCAACCGAT
* * * * *
28329081 GGAGGCAAGGCTTTATTTTTGATCTGCTTCGCTATTAACGCAGGAAGGCAAGATTTGCTATCTTC
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
* *
28329146 AACCAGCTCCAGTACAACCGAT
66 AACCAGCTCCACTGCAACCGAT
* * *
28329168 GGAGGCAATGCTTTATTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
28329233 AACCAGCTCCACTGCAACCGAT
66 AACCAGCTCCACTGCAACCGAT
28329255 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
*
28329319 AACCAGCTCCACTGCAACCTA-
66 AACCAGCTCCACTGCAACCGAT
* *
28329340 GAGAGGCAAGGCTTTGTTTTCGATTTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTT
1 G-GAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTT
28329405 TAACCAGCTCCACTGCAACCGAT
65 TAACCAGCTCCACTGCAACCGAT
28329428 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
*
28329492 AACCAGCTCCACTGCAACCTAT
66 AACCAGCTCCACTGCAACCGAT
28329514 GGAGGCAAGGCTTTGTTTTCGAT
1 GGAGGCAAGGCTTTGTTTTCGAT
28329537 TTTCACTGAT
Statistics
Matches: 424, Mismatches: 29, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
85 1 0.00
86 130 0.31
87 279 0.66
88 14 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (87 bp):
GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
AACCAGCTCCACTGCAACCGAT
Found at i:28329473 original size:260 final size:260
Alignment explanation
Indices: 28328993--28329536 Score: 885
Period size: 260 Copynumber: 2.1 Consensus size: 260
28328983 TACCGCTTAG
* *
28328993 GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTACTATCTT
1 GGAGGCAAGGCTT-TGTTTTCGATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTACTATCTT
*
28329058 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTTGATCTGCTTCGCTATTAACGCA
65 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTCGATCTGCTTCGCTATTAACGCA
* * *
28329123 GGAAGGCAAGATTTGCTATCTTCAACCAGCTCCAGTACAACCGATGGAGGCAATGCTTTATTTTC
130 GGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTATTTTC
*
28329188 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
195 GATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCG
28329253 AT
259 AT
* *
28329255 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTACTATCTTT
* * * * *
28329319 AACCAGCTCCACTGCAACCTA-GAGAGGCAAGGCTTTGTTTTCGATTTGCTTCGCTGTTAATGCA
66 AACCAGCTCCACTGCAACCGATG-GAGGCAAGGCTTTATTTTCGATCTGCTTCGCTATTAACGCA
* * *
28329383 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
130 GGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTATTTTC
*
28329448 GATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTA
195 GATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGA
28329513 T
260 T
28329514 GGAGGCAAGGCTTTGTTTTCGAT
1 GGAGGCAAGGCTTTGTTTTCGAT
28329537 TTTCACTGAT
Statistics
Matches: 263, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
259 50 0.19
260 158 0.60
261 42 0.16
262 13 0.05
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (260 bp):
GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTACTATCTTT
AACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTCGATCTGCTTCGCTATTAACGCAG
GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTATTTTCG
ATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGAT
Found at i:28329538 original size:173 final size:173
Alignment explanation
Indices: 28328993--28329536 Score: 928
Period size: 173 Copynumber: 3.1 Consensus size: 173
28328983 TACCGCTTAG
* * *
28328993 GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTACTATCTT
1 GGAGGCAAGGCTT-TGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTT
* * *
28329058 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTTGATCTGCTTCGCTATTAACGCA
65 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCA
* * * * *
28329123 GGAAGGCAAGATTTGCTATCTTCAACCAGCTCCAGTACAACCGAT
130 GGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCTAT
* *
28329168 GGAGGCAATGCTTTATTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTT
28329233 AACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
66 AACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
28329298 GAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTA-
131 GAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTAT
*
28329340 GAGAGGCAAGGCTTTGTTTTCGATTTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTT
1 G-GAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTT
28329405 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCA
65 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCA
28329470 GGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTAT
130 GGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTAT
28329514 GGAGGCAAGGCTTTGTTTTCGAT
1 GGAGGCAAGGCTTTGTTTTCGAT
28329537 TTTCACTGAT
Statistics
Matches: 351, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
172 1 0.00
173 212 0.60
174 126 0.36
175 12 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (173 bp):
GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTT
AACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
GAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTAT
Found at i:28330789 original size:13 final size:13
Alignment explanation
Indices: 28330771--28330809 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
28330761 TAGCCTCTCC
28330771 ATTTTTCATTTTT
1 ATTTTTCATTTTT
* *
28330784 ATTTTTCATTCTC
1 ATTTTTCATTTTT
*
28330797 ATTTTTTATTTTT
1 ATTTTTCATTTTT
28330810 TTGACTCAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTTCATTTTT
Found at i:28336302 original size:2 final size:2
Alignment explanation
Indices: 28336241--28336284 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
28336231 AAAGTGTAGA
28336241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT ACT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
28336282 AT A
1 AT A
28336285 GACGCTTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 36 0.92
3 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28336495 original size:3 final size:3
Alignment explanation
Indices: 28336481--28336555 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
28336471 AACTAACAAT
* * * * *
28336481 TAA TAG TAA TAA TAA TTA TAA TTA TAA TAA TGA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28336529 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
28336556 CCAAAATGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:28338531 original size:20 final size:21
Alignment explanation
Indices: 28338502--28338545 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
28338492 ATATATTATG
28338502 AAAATAATATACT-TATTTTAA
1 AAAATAATATA-TATATTTTAA
*
28338523 AAAAT-ATATATATTTTTTAA
1 AAAATAATATATATATTTTAA
28338543 AAA
1 AAA
28338546 TCTTAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 15 0.71
21 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATAATATATATATTTTAA
Found at i:28338536 original size:18 final size:19
Alignment explanation
Indices: 28338491--28338538 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
28338481 GTGTCCATGC
*
28338491 TATATATTATGAAAATAATA
1 TATATATT-TTAAAATAATA
28338511 TACT-TATTTTAAAA-AATA
1 TA-TATATTTTAAAATAATA
28338529 TATATATTTT
1 TATATATTTT
28338539 TTAAAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 12 0.48
19 5 0.20
20 6 0.24
21 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TATATATTTTAAAATAATA
Found at i:28348820 original size:18 final size:20
Alignment explanation
Indices: 28348797--28348836 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
28348787 ATTGGCCTAT
28348797 TACAGTAAC-AATAAT-CAG
1 TACAGTAACAAATAATACAG
28348815 TACAGTAACAAATAATACAG
1 TACAGTAACAAATAATACAG
28348835 TA
1 TA
28348837 TACAGGTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 6 0.30
20 5 0.25
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.23
Consensus pattern (20 bp):
TACAGTAACAAATAATACAG
Found at i:28353311 original size:28 final size:27
Alignment explanation
Indices: 28353255--28353320 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
28353245 CTATTCAGTA
*
28353255 ACAGT-ACAGTGTGGCATTAGCCCAAT
1 ACAGTAACAGTGTAGCATTAGCCCAAT
* * *
28353281 ACAGTAACAGTGTAAGCCTTAGTCCATT
1 ACAGTAACAGTGT-AGCATTAGCCCAAT
*
28353309 ACAGTATCAGTG
1 ACAGTAACAGTG
28353321 CAGTGTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 5 0.15
27 7 0.21
28 21 0.64
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (27 bp):
ACAGTAACAGTGTAGCATTAGCCCAAT
Found at i:28353449 original size:26 final size:26
Alignment explanation
Indices: 28353419--28353495 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 26
28353409 GCCAACACAC
28353419 CAATATCATAGCAAAGCTGCCAGTAAT
1 CAATATCA-AGCAAAGCTGCCAGTAAT
28353446 -AATAATGCAA-CAAAGCTGCCAGT-AT
1 CAAT-AT-CAAGCAAAGCTGCCAGTAAT
* *
28353471 CAGTATCGCAGCAAAGCTGCCAGTA
1 CAATATC-AAGCAAAGCTGCCAGTA
28353496 CAGTATACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
24 1 0.02
25 5 0.12
26 31 0.74
27 3 0.07
28 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (26 bp):
CAATATCAAGCAAAGCTGCCAGTAAT
Found at i:28359206 original size:26 final size:27
Alignment explanation
Indices: 28359177--28359242 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
28359167 AATATTGGAA
* *
28359177 CAAAGCTACCAGTAAT-AGCACCGTAG
1 CAAAGCTGCCAGTAATCAGCACCGCAG
* * *
28359203 CAAAGTTGCCAGT-ATCAGTATCGCAG
1 CAAAGCTGCCAGTAATCAGCACCGCAG
28359229 CAAAGCTGCCAGTA
1 CAAAGCTGCCAGTA
28359243 CAGTATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (27 bp):
CAAAGCTGCCAGTAATCAGCACCGCAG
Found at i:28361811 original size:41 final size:41
Alignment explanation
Indices: 28361676--28361840 Score: 222
Period size: 42 Copynumber: 4.0 Consensus size: 41
28361666 GAACATGGTC
28361676 TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTCTT
1 TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTT-TT
* * * * *
28361718 CTAAGCACTGCTAAAGAACATGGTCTTTAGTGGCCTTTTTT
1 TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT
** *
28361759 TCTAAGCGCCGCTAAAGAACATTATCTTTAGCAGCGTTTTTT
1 T-TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT
* *
28361801 TTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
28361841 ATACAAAAAC
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
41 37 0.35
42 68 0.65
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (41 bp):
TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT
Found at i:28367609 original size:9 final size:9
Alignment explanation
Indices: 28367592--28367824 Score: 170
Period size: 9 Copynumber: 26.9 Consensus size: 9
28367582 TATGTATTAA
*
28367592 GTAAATTAT
1 GTAAGTTAT
28367601 GTAAGTTAT
1 GTAAGTTAT
28367610 GTACA-TGTA-
1 GTA-AGT-TAT
28367619 -TAAGTTAT
1 GTAAGTTAT
28367627 GTAAGTTAT
1 GTAAGTTAT
*
28367636 GT-A-TTAA
1 GTAAGTTAT
*
28367643 GTAAGCTAT
1 GTAAGTTAT
* *
28367652 TTAAGTTGT
1 GTAAGTTAT
28367661 GT-A-TTAT
1 GTAAGTTAT
28367668 GTAAGTTAT
1 GTAAGTTAT
28367677 GTAAGTTAT
1 GTAAGTTAT
** *
28367686 CAAAGTAAT
1 GTAAGTTAT
*
28367695 GTATGTTAT
1 GTAAGTTAT
28367704 GTAAG-T-T
1 GTAAGTTAT
28367711 GTAAGTTAT
1 GTAAGTTAT
*
28367720 -TATGTATTAT
1 GTAAG--TTAT
*
28367730 GTAGGTTAT
1 GTAAGTTAT
28367739 GTAAGTTAT
1 GTAAGTTAT
*
28367748 GTAAGTTTT
1 GTAAGTTAT
28367757 GT-A-TTAT
1 GTAAGTTAT
*
28367764 GTAAGTTGT
1 GTAAGTTAT
28367773 GTAAGTTAT
1 GTAAGTTAT
* *
28367782 GTATGCTAT
1 GTAAGTTAT
*
28367791 GTAAGTAAT
1 GTAAGTTAT
28367800 GT-A-TTAT
1 GTAAGTTAT
28367807 GTAAGTTTAT
1 GTAAG-TTAT
*
28367817 ATAAGTTA
1 GTAAGTTA
28367825 ATATGTAAGT
Statistics
Matches: 174, Mismatches: 31, Indels: 38
0.72 0.13 0.16
Matches are distributed among these distances:
7 29 0.17
8 16 0.09
9 111 0.64
10 15 0.09
11 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:28367612 original size:25 final size:25
Alignment explanation
Indices: 28367581--28367685 Score: 113
Period size: 25 Copynumber: 4.2 Consensus size: 25
28367571 TGATATATAT
28367581 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* *
28367606 TTATGTA-CATGTATAAGTTATGTAAG
1 TTATGTATTAAGTA-AA-TTATGTAAG
** *
28367632 TTATGTATTAAGTAAGCTATTTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* * *
28367657 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
28367682 TTAT
1 TTAT
28367686 CAAAGTAATG
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
24 4 0.06
25 40 0.62
26 17 0.26
27 4 0.06
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (25 bp):
TTATGTATTAAGTAAATTATGTAAG
Found at i:28367681 original size:34 final size:34
Alignment explanation
Indices: 28367596--28367813 Score: 125
Period size: 34 Copynumber: 6.4 Consensus size: 34
28367586 TATTAAGTAA
28367596 ATTATGTAAGTTATGT-A-C-ATGTATAAGTTATGT
1 ATTATGTAAGTTATGTAAGCTAT-T-TAAGTTATGT
* *
28367629 AAGTTATGT-A-TTAAGTAAGCTATTTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAGCTATTTAAGTTATGT
* ** *
28367663 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 ATTATGTAAGTTATGTAAGCTATTTAAGTTATGT
* *
28367697 ATGTTATGTAAG-T-TGTAAGTTA-TTATGTATTATGT
1 A--TTATGTAAGTTATGTAAGCTATTTAAG--TTATGT
*
28367732 AGGTTATGTAAGTTATGTAAG-T-TTTGTA-TTATGT
1 A--TTATGTAAGTTATGTAAGCTATTT-AAGTTATGT
* * * *
28367766 AAGTTGTGTAAGTTATGTATGCTATGTAAGTAATGT
1 -A-TTATGTAAGTTATGTAAGCTATTTAAGTTATGT
28367802 ATTATGTAAGTT
1 ATTATGTAAGTT
28367814 TATATAAGTT
Statistics
Matches: 145, Mismatches: 21, Indels: 36
0.72 0.10 0.18
Matches are distributed among these distances:
32 6 0.04
33 9 0.06
34 73 0.50
35 29 0.20
36 22 0.15
37 6 0.04
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.46
Consensus pattern (34 bp):
ATTATGTAAGTTATGTAAGCTATTTAAGTTATGT
Found at i:28367742 original size:62 final size:63
Alignment explanation
Indices: 28367660--28367813 Score: 170
Period size: 62 Copynumber: 2.4 Consensus size: 63
28367650 ATTTAAGTTG
28367660 TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTAT-TA
1 TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTA--TTATGTAAGTTGTGTAAGTTATGTA
* ** **
28367722 TGTATTATGTAGGTTATGTAAGTTATGTAAGTTTTGTATTATGTAAGTTGTGTAAGTTATGTA
1 TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATTATGTAAGTTGTGTAAGTTATGTA
*
28367785 TGCTATGTAAGTAATGTATTATGTAAGTT
1 TG-TAT-TATGTAA-G--TTATGTAAGTT
28367814 TATATAAGTT
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
60 9 0.12
61 1 0.01
62 43 0.56
63 4 0.05
64 3 0.04
65 5 0.06
66 1 0.01
68 11 0.14
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (63 bp):
TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATTATGTAAGTTGTGTAAGTTATGTA
Found at i:28367744 original size:87 final size:87
Alignment explanation
Indices: 28367632--28367796 Score: 199
Period size: 87 Copynumber: 1.9 Consensus size: 87
28367622 GTTATGTAAG
* *
28367632 TTATGTATTAAGTAAGCTATTTAAGTTGTGT-A-TTATGTAAGTTATGTAAGTTATCAAAGTAAT
1 TTATGTATTAAGTAAGCTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATCAAAGTAAT
*
28367695 GTATGTTATGTAAGTTGTAAGTTA
64 GTATGCTATGTAAGTTGTAAGTTA
* * * * * ** *
28367719 TTATGTATTATGTAGGTTATGTAAGTTATGTAAGTTTTGTATTATGTAAGTTGTGTAAGTTATGT
1 TTATGTATTAAGTAAGCTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATCAAAGTAATGT
28367784 ATGCTATGTAAGT
66 ATGCTATGTAAGT
28367797 AATGTATTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 58 0.89
88 2 0.03
89 5 0.08
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (87 bp):
TTATGTATTAAGTAAGCTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATCAAAGTAATGT
ATGCTATGTAAGTTGTAAGTTA
Found at i:28367763 original size:25 final size:25
Alignment explanation
Indices: 28367719--28367824 Score: 90
Period size: 25 Copynumber: 4.1 Consensus size: 25
28367709 TTGTAAGTTA
*
28367719 TTATGTATTATGTAGGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
28367744 TTATGTAAGTTTTGT-A-TTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* * *
28367769 TTGTGTAAGTTATGTATGCTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
28367796 TAATGTATTATGTAAGTTTATATAAG
1 TTATGTATTATGTAAG-TTATGTAAG
28367822 TTA
1 TTA
28367825 ATATGTAAGT
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
25 36 0.56
26 11 0.17
27 17 0.27
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.48
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:28367792 original size:43 final size:43
Alignment explanation
Indices: 28367673--28367824 Score: 155
Period size: 43 Copynumber: 3.5 Consensus size: 43
28367663 ATTATGTAAG
** * *
28367673 TTATGTAAGTTATCAAAGTAATGTATGTTATGTAAGTTGTAAGTTA
1 TTATGTAAGTTATGTAAGTTATGTATGTTATGTAAGTT-T-TG-TA
* *
28367719 TTATGT-A-TTATGTAGGTTATGTAAGTTATGTAAGTTTTGTA
1 TTATGTAAGTTATGTAAGTTATGTATGTTATGTAAGTTTTGTA
* * **
28367760 TTATGTAAGTTGTGTAAGTTATGTATGCTATGTAAGTAATGTA
1 TTATGTAAGTTATGTAAGTTATGTATGTTATGTAAGTTTTGTA
*
28367803 TTATGTAAGTTTATATAAGTTA
1 TTATGTAAG-TTATGTAAGTTA
28367825 ATATGTAAGT
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
41 8 0.09
42 2 0.02
43 38 0.43
44 34 0.38
45 1 0.01
46 6 0.07
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAGTTATGTATGTTATGTAAGTTTTGTA
Found at i:28368184 original size:13 final size:12
Alignment explanation
Indices: 28368166--28368211 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
28368156 CAAATTTTAG
28368166 TAAGTAATGTATT
1 TAAGTAAT-TATT
28368179 TAAGTAAATTATT
1 TAAGT-AATTATT
28368192 TAAGTAATATATT
1 TAAGTAAT-TATT
*
28368205 CAAGTAA
1 TAAGTAA
28368212 ATTTTAGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 3 0.10
13 24 0.80
14 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (12 bp):
TAAGTAATTATT
Found at i:28368361 original size:52 final size:53
Alignment explanation
Indices: 28368255--28368367 Score: 137
Period size: 53 Copynumber: 2.2 Consensus size: 53
28368245 TAAGTCATGT
*
28368255 AAAATA-TACTTAAAATATATATATTTAAGTAATGTAATATATAAATTTTAAA
1 AAAATATTACTTAAAATATATATATTTAAGTAATGTAATATATAAATTGTAAA
28368307 AAAATATTACTTAACAATATATATATTATTAA-TAA-GTTAA-AT-TAAATTGTAAA
1 AAAATATTACTTAA-AATATATATA-T-TTAAGTAATG-TAATATATAAATTGTAAA
*
28368360 AATATATT
1 AAAATATT
28368368 TAAAAATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
52 6 0.11
53 24 0.44
54 13 0.24
55 7 0.13
56 4 0.07
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (53 bp):
AAAATATTACTTAAAATATATATATTTAAGTAATGTAATATATAAATTGTAAA
Found at i:28368512 original size:13 final size:13
Alignment explanation
Indices: 28368494--28368552 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
28368484 CAAATTTTAG
*
28368494 TAAGTAATGTATT
1 TAAGTAATATATT
28368507 TAAGTAA-ATTATT
1 TAAGTAATA-TATT
28368520 TAAGTAATATATT
1 TAAGTAATATATT
*
28368533 CAAGTAATATATT
1 TAAGTAATATATT
*
28368546 AAAGTAA
1 TAAGTAA
28368553 ATTTTAGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
13 40 0.98
14 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:28368532 original size:26 final size:27
Alignment explanation
Indices: 28368494--28368563 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 27
28368484 CAAATTTTAG
*
28368494 TAAGTAATGTATTTAAGTAAAT-TATT
1 TAAGTAATATATTTAAGTAAATATATT
*
28368520 TAAGTAATATATTCAAGT-AATATATT
1 TAAGTAATATATTTAAGTAAATATATT
*
28368546 AAAGTAA-AT-TTT-AGTAAA
1 TAAGTAATATATTTAAGTAAA
28368564 AAATATGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 3 0.08
24 4 0.11
25 5 0.13
26 26 0.68
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (27 bp):
TAAGTAATATATTTAAGTAAATATATT
Found at i:28368702 original size:328 final size:318
Alignment explanation
Indices: 28368059--28368705 Score: 1012
Period size: 328 Copynumber: 2.0 Consensus size: 318
28368049 ATTATTTTTA
*
28368059 AAATTATAATATATTTTAACAAGTTATGTAAGTAATGTAATATATACTTAAATTTTAGTAAGTAA
1 AAATTATAATATATTTTAACAAGTTATCTAAGTAATGTAATATATACTTAAATTTTAGTAAGTAA
28368124 TATATATTTAAGTAATGTATTTAAAATTTAAACAAATTTTAGTAAGTAATGTATTTAAGTAAATT
66 TATATATTTAAGTAATGTATTTAAAATTTAAACAAATTTTAGTAAGTAATGTATTTAAGTAAATT
28368189 ATTTAAGTAATATATTCAAGTAAATTTTAGTAAAAAATATGTTTTAGTAAGTAATGTAAGTCATG
131 ATTTAAGTAATATATTCAAGTAAATTTTAGTAAAAAATATGTTTTAGTAAGTAATGTAAGTCATG
*
28368254 TAAAATATACTTAAAATATATATATTTAAGTAATGTAATATATAAATTTTAAAAAAATATTACTT
196 TAAAATATACTTAAAATATATATATTTAAGTAATGTAAGATATAAATTTTAAAAAAATATTACTT
28368319 AACAATATATATATTATTAATAAGTTAAATTAAATTGTAAAAATATATTTAAAAATATAATAAAT
261 AACAATATATATATTATTAATAAGTTAAATTAAATTG---------A--TAAAAATATAATAAAT
28368384 ATTG
315 ATTG
28368388 AAATTATAATATATTTTAACAAGTTA-CTAAGTAATGTAATATATACTTAAATTTTAGTAAGTAA
1 AAATTATAATATATTTTAACAAGTTATCTAAGTAATGTAATATATACTTAAATTTTAGTAAGTAA
28368452 TATATATTTAAGTAATGTATTTAAAATTTAAACAAATTTTAGTAAGTAATGTATTTAAGTAAATT
66 TATATATTTAAGTAATGTATTTAAAATTTAAACAAATTTTAGTAAGTAATGTATTTAAGTAAATT
28368517 ATTTAAGTAATATATTCAAGTAATATATTAAAGTAAATTTTAGTAAAAAATATGTTTTAGTAAGT
131 ATTTAAGTAATATATTC-------------AAGTAAATTTTAGTAAAAAATATGTTTTAGTAAGT
* *
28368582 AATGTAAGTCATGTAGAATATACTTAAAA-ATATATATTTAAGTAATGTAAGATATCAATTTTAA
183 AATGTAAGTCATGTAAAATATACTTAAAATATATATATTTAAGTAATGTAAGATATAAATTTTAA
*
28368646 AAAATTATTACTTAACAATATATATATTATTAATAAGTTAAATTAAATTG-TAAAAATATA
248 AAAAATATTACTTAACAATATATATATTATTAATAAGTTAAATTAAATTGATAAAAATATA
28368706 TTTAAAAATA
Statistics
Matches: 300, Mismatches: 5, Indels: 27
0.90 0.02 0.08
Matches are distributed among these distances:
328 129 0.43
329 26 0.09
340 82 0.27
341 63 0.21
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (318 bp):
AAATTATAATATATTTTAACAAGTTATCTAAGTAATGTAATATATACTTAAATTTTAGTAAGTAA
TATATATTTAAGTAATGTATTTAAAATTTAAACAAATTTTAGTAAGTAATGTATTTAAGTAAATT
ATTTAAGTAATATATTCAAGTAAATTTTAGTAAAAAATATGTTTTAGTAAGTAATGTAAGTCATG
TAAAATATACTTAAAATATATATATTTAAGTAATGTAAGATATAAATTTTAAAAAAATATTACTT
AACAATATATATATTATTAATAAGTTAAATTAAATTGATAAAAATATAATAAATATTG
Found at i:28368837 original size:23 final size:23
Alignment explanation
Indices: 28368811--28368876 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 23
28368801 ATTGAGAATT
28368811 CATTATATAATCAATTTATTAAA
1 CATTATATAATCAATTTATTAAA
* *
28368834 CA-T-T-CAATCAA-TAATT---
1 CATTATATAATCAATTTATTAAA
28368850 CATTATATAATCAATTTATTAAA
1 CATTATATAATCAATTTATTAAA
28368873 CATT
1 CATT
28368877 CAATCAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.31
20 10 0.31
21 1 0.03
22 1 0.03
23 6 0.19
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (23 bp):
CATTATATAATCAATTTATTAAA
Found at i:28368847 original size:27 final size:26
Alignment explanation
Indices: 28368773--28368848 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
28368763 AAGTTATTTA
*
28368773 TATTAAACATGCAATCAAGTAATAATT
1 TATTAAACATTCAATCAA-TAATAATT
* *
28368800 TATTGAGA-ATTC-ATTATATAATCAATT
1 TATT-AAACATTCAATCA-ATAAT-AATT
28368827 TATTAAACATTCAATCAATAAT
1 TATTAAACATTCAATCAATAAT
28368849 TCATTATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
26 9 0.23
27 25 0.64
28 5 0.13
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (26 bp):
TATTAAACATTCAATCAATAATAATT
Found at i:28368851 original size:39 final size:39
Alignment explanation
Indices: 28368807--28368884 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
28368797 ATTTATTGAG
28368807 AATTCATTATATAATCAATTTATTAAACATTCAATCAAT
1 AATTCATTATATAATCAATTTATTAAACATTCAATCAAT
28368846 AATTCATTATATAATCAATTTATTAAACATTCAATCAAT
1 AATTCATTATATAATCAATTTATTAAACATTCAATCAAT
28368885 TAATCGATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (39 bp):
AATTCATTATATAATCAATTTATTAAACATTCAATCAAT
Found at i:28368959 original size:16 final size:16
Alignment explanation
Indices: 28368938--28368973 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28368928 ATTAATTGAA
*
28368938 ATAAAATTGTAAATCG
1 ATAAAATTGAAAATCG
28368954 ATAAAATTGAAAATCG
1 ATAAAATTGAAAATCG
28368970 ATAA
1 ATAA
28368974 TTATAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAAAATTGAAAATCG
Found at i:28370469 original size:44 final size:44
Alignment explanation
Indices: 28370411--28370498 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
28370401 TTAAAACATT
*
28370411 TTTGCGGCGTTTTAAGCAAAGCGCCACAAACTATAAGTCAAAAC
1 TTTGCGGCGTTTTAAACAAAGCGCCACAAACTATAAGTCAAAAC
* *
28370455 TTTGCGGCGTTTTAAACTAAGCGCCACTAACTATAAGTCAAAAC
1 TTTGCGGCGTTTTAAACAAAGCGCCACAAACTATAAGTCAAAAC
28370499 GCAGTCGCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (44 bp):
TTTGCGGCGTTTTAAACAAAGCGCCACAAACTATAAGTCAAAAC
Found at i:28370748 original size:147 final size:147
Alignment explanation
Indices: 28370473--28370778 Score: 328
Period size: 147 Copynumber: 2.1 Consensus size: 147
28370463 GTTTTAAACT
* * *
28370473 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGCTTCATCAACACTTACCTCAAACCCGTGGCAT
1 AAGCGCCACTAACTATAAGTCAAAACGAAGCCGCTTCACCAACACTTACCTCAAACCCGTGGCAT
* ** * * ** *
28370538 TTGCGAGAAAACGCCACTAATAACATTTACAAAACGGCAACGTTTCAACAAATGTTAGAACAATT
66 TTCCGAGAAAACGCCACTAATAACATAGACAAAACGACAACATTTCAACAAACATAAGAACAATT
* * *
28370603 TTGTGGCGTTTCAAGTA
131 TTGCGGAGTTTCAAGGA
* * * **** *
28370620 AAGCGCCACTAACTATAAGTCAAAACGAAGCCGTTTCCCCAACAGTTTACC-CAATGTTGTGGCG
1 AAGCGCCACTAACTATAAGTCAAAACGAAGCCGCTTCACCAACA-CTTACCTCAAACCCGTGGCA
* * **
28370684 TTTCCGA-AAAACGCCACTAATACCATAGACAAAAACGACAACATTTCAATAAACATAATTACAA
65 TTTCCGAGAAAACGCCACTAATAACATAGAC-AAAACGACAACATTTCAACAAACATAAGAACAA
*
28370748 TTTTGCGGAGTTTCATGGA
129 TTTTGCGGAGTTTCAAGGA
*
28370767 ACGCGCCACTAA
1 AAGCGCCACTAA
28370779 TAGCAACATA
Statistics
Matches: 129, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
146 20 0.16
147 104 0.81
148 5 0.04
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (147 bp):
AAGCGCCACTAACTATAAGTCAAAACGAAGCCGCTTCACCAACACTTACCTCAAACCCGTGGCAT
TTCCGAGAAAACGCCACTAATAACATAGACAAAACGACAACATTTCAACAAACATAAGAACAATT
TTGCGGAGTTTCAAGGA
Found at i:28371253 original size:21 final size:21
Alignment explanation
Indices: 28371220--28371260 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28371210 ATTATAATTT
** *
28371220 CTAAACCTTAAACCTCAAAAA
1 CTAAACCCCAAACCCCAAAAA
28371241 CTAAACCCCAAACCCCAAAA
1 CTAAACCCCAAACCCCAAAA
28371261 CTCCAAACAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (21 bp):
CTAAACCCCAAACCCCAAAAA
Found at i:28372238 original size:18 final size:18
Alignment explanation
Indices: 28372215--28372250 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28372205 ATTGAATTTT
28372215 AATT-AATATAAATAAACA
1 AATTAAATATAAA-AAACA
28372233 AATTAAATATAAAAAACA
1 AATTAAATATAAAAAACA
28372251 TATAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AATTAAATATAAAAAACA
Found at i:28372258 original size:18 final size:19
Alignment explanation
Indices: 28372219--28372258 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
28372209 AATTTTAATT
*
28372219 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
28372238 AATATAAA-AAACATATAA
1 AATATAAATAAACAAATAA
28372256 AAT
1 AAT
28372259 GATTTTGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:28372749 original size:114 final size:113
Alignment explanation
Indices: 28372464--28372756 Score: 392
Period size: 113 Copynumber: 2.6 Consensus size: 113
28372454 GTGGCGCTTA
* * * *
28372464 CCAA-AAAGCGCCACTAACTCTAATATACGTCAAGGCCAAACTCTGCGTTTTGGTTAAGATACTT
1 CCAATAAA-CGCCACTAATTCTAATATACATCAAGACCAAACTCTGCGTTTTGGTTAAGATATTT
* *
28372528 TGCGGCGCTTTCCACAAACGCCGCTACTACTATACTTTAGCGGCGTTTT
65 TGAGGCGCTTACCACAAACGCCGCTACTACTATACTTTAGCGGCGTTTT
* *
28372577 CCAATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTT
1 CCAATAAACGCCACTAATTCTAATATACATCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTT
* * * *
28372642 GAGGCGCTTACCACCAAACGCTGCTATTACTATGCTTTAGTGGCGTTTT
66 GAGGCGCTTACCA-CAAACGCCGCTACTACTATACTTTAGCGGCGTTTT
* * * * *
28372691 CC-TTAAACGCCACTAATTATAGTATACATCAAGACCAAAACGCTGCGTTTTGGTTAAGATGTTT
1 CCAATAAACGCCACTAATTCTAATATACATCAAGACC-AAACTCTGCGTTTTGGTTAAGATATTT
28372755 TG
65 TG
28372757 CGGCATTTTC
Statistics
Matches: 159, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
113 97 0.61
114 62 0.39
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (113 bp):
CCAATAAACGCCACTAATTCTAATATACATCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTT
GAGGCGCTTACCACAAACGCCGCTACTACTATACTTTAGCGGCGTTTT
Found at i:28372909 original size:190 final size:190
Alignment explanation
Indices: 28372580--28372934 Score: 505
Period size: 190 Copynumber: 1.9 Consensus size: 190
28372570 GCGTTTTCCA
* *
28372580 ATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGAG
1 ATAAGCGCCACTAATTCTAATATACATCAAGACCAAACTCTGCGTTTTGGTTAACATATTTTGAG
* * * ** *
28372645 GCGCTTACCACCAAACGCTGCTATTACTATGCTTTAGTGGCGTTTTCCTTAAACGCCACTAATTA
66 GCGCTTACCACCAAACGCCGCTAATACTATGCATTACCGGCGTTTTCCGTAAACGCCACTAATTA
* *
28372710 TAGTATACATCAAGACCAAAACGCTGCGTTTTGGTTAAGATGTTTTGCGGCATTTTCTTT
131 TAATATACATCAAGACCAAAACGCTGCGTGTTGGTTAAGATGTTTTGCGGCATTTTCTTT
* * * *
28372770 ATAAGCGCCACTAATTGTAATATACATCAAGACCAAACTTTGCGTTTTGGTTAACATCTTTTGCG
1 ATAAGCGCCACTAATTCTAATATACATCAAGACCAAACTCTGCGTTTTGGTTAACATATTTTGAG
* * * * *
28372835 GCGCTT-CCGCTAAGCGCCGCTAATACTATGCATTACCGGCGTTTGTTCGTAAGCGCCACTAATT
66 GCGCTTACCACCAAACGCCGCTAATACTATGCATTACCGGCGTTT-TCCGTAAACGCCACTAATT
* *
28372899 CTAATATACATCAAGACCAGAACGCTGCGTGTTGGT
130 ATAATATACATCAAGACCAAAACGCTGCGTGTTGGT
28372935 CTTGAGATTT
Statistics
Matches: 143, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
189 30 0.21
190 113 0.79
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (190 bp):
ATAAGCGCCACTAATTCTAATATACATCAAGACCAAACTCTGCGTTTTGGTTAACATATTTTGAG
GCGCTTACCACCAAACGCCGCTAATACTATGCATTACCGGCGTTTTCCGTAAACGCCACTAATTA
TAATATACATCAAGACCAAAACGCTGCGTGTTGGTTAAGATGTTTTGCGGCATTTTCTTT
Found at i:28373443 original size:21 final size:22
Alignment explanation
Indices: 28373398--28373444 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
28373388 AATAATTAAC
*
28373398 TTATACCAAATTTTCAAATAAA
1 TTATACCAAATTTTAAAATAAA
* *
28373420 TTATACCGAA-TTTAAAATATA
1 TTATACCAAATTTTAAAATAAA
28373441 TTAT
1 TTAT
28373445 TTTATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (22 bp):
TTATACCAAATTTTAAAATAAA
Found at i:28374705 original size:17 final size:18
Alignment explanation
Indices: 28374679--28374712 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28374669 TTTTATATTA
*
28374679 TTTTTGAAAAGTACAAAC
1 TTTTTGAAAAATACAAAC
28374697 TTTTT-AAAAATACAAA
1 TTTTTGAAAAATACAAA
28374713 AAATTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (18 bp):
TTTTTGAAAAATACAAAC
Found at i:28381628 original size:21 final size:22
Alignment explanation
Indices: 28381604--28381650 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
28381594 TGAAATTTAT
* *
28381604 TTTTTTATTTTTATTTTA-AAA
1 TTTTTAATTTTTATATTACAAA
28381625 TTTTTAATTTTTATATTACAAA
1 TTTTTAATTTTTATATTACAAA
28381647 TTTT
1 TTTT
28381651 AAAATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTAATTTTTATATTACAAA
Found at i:28384282 original size:25 final size:25
Alignment explanation
Indices: 28384254--28384320 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
28384244 AAATTTATTT
28384254 ATATATTATAATAGTTAAAGTTAAA
1 ATATATTATAATAGTTAAAGTTAAA
28384279 ATATATTATAATAGTTAAAGTTAAA
1 ATATATTATAATAGTTAAAGTTAAA
*
28384304 ATATGTTATAAT-GTTAA
1 ATATATTATAATAGTTAA
28384321 GAAATTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 5 0.12
25 36 0.88
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (25 bp):
ATATATTATAATAGTTAAAGTTAAA
Found at i:28387028 original size:69 final size:69
Alignment explanation
Indices: 28386914--28387711 Score: 600
Period size: 69 Copynumber: 11.6 Consensus size: 69
28386904 GTCACATCAA
* * * * * * * * * *
28386914 CTCTCACTAACTATGTTTGAAGCTGCGGCTCTTAGCCAACAAGCCTTAGTATGATAGTTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
28386979 TTTG
66 TTTG
* * * * **
28386983 CTCTCGTTAACTGTGTTAGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATAAAAATTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
28387048 TTTG
66 TTTG
* * * ** * * * *
28387052 CTCTTGCTAATTGTGTTGGAAGCTGCAACTCTTCG-CTGGCAAGCCTCAGTATGACAGCTGGGAG
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCT-ACGAGCCTTAATATGACAGCTGGGAG
*
28387116 TTTTG
65 CTTTG
* ** ** *** * *
28387121 CTCTCGCTAATTGTGTTGGAGATTGTAGCTCTTCGCCTGTAAACCTTAATATGACAGCTAGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
*
28387186 TTTA
66 TTTG
* * * * * *
28387190 CTCTCGCTAATTGTGTTGGAGGTTGCGGCTTTTTGCCTACAAGCCTTAATATGACAACTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
* *
28387255 CTTA
66 TTTG
* * * ** * * ** * * *
28387259 CTATTGCTAACTGTGTTAGAAACTGCAGCTCTTC-ACTGGTGAGCATTAGTATGACAGTTGGGAG
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCT-ACGAGCCTTAATATGACAGCTGGGAG
28387323 CTTTG
65 CTTTG
** ** ** * * * * *
28387328 CTCTTACTAACTACGTTGGAGGCTATGACTTTTTCTG--TACGAGCCATAATATAACAGCTAGGA
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGC-TCTTC-GCCTACGAGCCTTAATATGACAGCTGGGA
28387391 GCTTTG
64 GCTTTG
* * *
28387397 CTCTCGCTAACTGTGTTGGAGGCTGTGGCTCTTCGCCTACGAGCCTTAATATGATAGCTGGAAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
28387462 TTTG
66 TTTG
* * * * ** * * * *
28387466 GTCTCGTTAACTGTGGTGGAGGATGTAGCTATTCGCCTTCGAGCCTTAATATGATAACTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
*
28387531 TTTA
66 TTTG
* * * * * * * * * **
28387535 CTCTCGCTAATTGTATTGGAGGTTGCGGC-CTTCACCTGCAAGTCTTAATATGATAGTTGGGAAT
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
*
28387599 TTTT
66 TTTG
* * * *
28387603 CTCTCGCTAACTGTGTTGGAGGCTACGACTCTTCGCTTGCGAGCCTTAATATGA-ATGCTGGGAG
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACA-GCTGGGAG
*
28387667 TTTTG
65 CTTTG
* *
28387672 CTCTCGCTAACTGTGTTGGAGGCTACGACTCTTCGCCTAC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTAC
28387712 AAATCTTAAT
Statistics
Matches: 573, Mismatches: 146, Indels: 20
0.78 0.20 0.03
Matches are distributed among these distances:
67 1 0.00
68 62 0.11
69 503 0.88
70 7 0.01
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (69 bp):
CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
TTTG
Found at i:28399056 original size:9 final size:9
Alignment explanation
Indices: 28399042--28399066 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28399032 AGCAATTCAT
28399042 AATTCAACA
1 AATTCAACA
28399051 AATTCAACA
1 AATTCAACA
28399060 AATTCAA
1 AATTCAA
28399067 AATAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (9 bp):
AATTCAACA
Found at i:28399107 original size:17 final size:18
Alignment explanation
Indices: 28399087--28399120 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28399077 AAAAATACAT
28399087 AAATAAATTTA-AATTTA
1 AAATAAATTTATAATTTA
*
28399104 AAATATATTTATAATTT
1 AAATAAATTTATAATTT
28399121 TTTTGGTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAAATTTATAATTTA
Found at i:28406283 original size:26 final size:27
Alignment explanation
Indices: 28406254--28406306 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
28406244 ATTTTACATC
* * *
28406254 AATAAAATTATCAC-AATTTTTTTTAA
1 AATAAAACTAACACAAATTTTGTTTAA
28406280 AATAAAACTAACACAAATTTTGTTTAA
1 AATAAAACTAACACAAATTTTGTTTAA
28406307 GTGAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (27 bp):
AATAAAACTAACACAAATTTTGTTTAA
Found at i:28406498 original size:44 final size:44
Alignment explanation
Indices: 28406449--28406538 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
28406439 TAATTATAAC
* * * *
28406449 TTAAATTCTAATTATTTTTAAATGTGTAATTATCACAACTTTTA
1 TTAAATTCTAATAATTCTTAAATGTATAATTATCACAACTTCTA
* *
28406493 TTAAATTGTAATAATTCTTAAATGTATAATTATCATAACTTCTA
1 TTAAATTCTAATAATTCTTAAATGTATAATTATCACAACTTCTA
28406537 TT
1 TT
28406539 TCATTTCAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (44 bp):
TTAAATTCTAATAATTCTTAAATGTATAATTATCACAACTTCTA
Found at i:28407651 original size:16 final size:16
Alignment explanation
Indices: 28407630--28407664 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28407620 CAAATCGTAT
*
28407630 TTGTTTGAAGAATATA
1 TTGTTTGAAAAATATA
28407646 TTGTTTGAAAAATATA
1 TTGTTTGAAAAATATA
28407662 TTG
1 TTG
28407665 ACTAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (16 bp):
TTGTTTGAAAAATATA
Found at i:28414978 original size:19 final size:19
Alignment explanation
Indices: 28414953--28415004 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
28414943 AACACATGAC
28414953 AAATTTTAATAAAAA-ATAT
1 AAATTTT-ATAAAAATATAT
* *
28414972 TAATTTTTTAAAAATATAT
1 AAATTTTATAAAAATATAT
28414991 AAA-TTTATAAAAAT
1 AAATTTTATAAAAAT
28415005 TATCTTACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTTATAAAAATATAT
Found at i:28415976 original size:23 final size:24
Alignment explanation
Indices: 28415928--28415976 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
28415918 TTAATTAAAT
*
28415928 TAAAATTATTTTTTATTTATTTTA
1 TAAAATTATTTTTTATTTATTATA
28415952 TAAAA-TATTTTTTATTT-TGTATA
1 TAAAATTATTTTTTATTTAT-TATA
28415975 TA
1 TA
28415977 TCCTATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 1 0.04
23 17 0.74
24 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TAAAATTATTTTTTATTTATTATA
Found at i:28416415 original size:31 final size:31
Alignment explanation
Indices: 28416377--28416449 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
28416367 CAACAACTAC
*
28416377 CGCTGACATGGAGCACCACATCAATAGCTGT
1 CGCTGACATGGAGCACCACATCAATAACTGT
* * *
28416408 CGCTGACATGGAGCATCACGTCAATAATTGT
1 CGCTGACATGGAGCACCACATCAATAACTGT
*
28416439 CGTTGACATGG
1 CGCTGACATGG
28416450 TCAAAGTGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (31 bp):
CGCTGACATGGAGCACCACATCAATAACTGT
Found at i:28417815 original size:43 final size:42
Alignment explanation
Indices: 28417768--28417856 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
28417758 GCGTGTGCGT
* *
28417768 AGGCTATGTAAACCACACAGGTAGAGGACATGGGTGTGTTTCC
1 AGGCTATGTAAACCACACAGGCA-AGGACATGGGTGTGTGTCC
* * * *
28417811 AGGCTGTGTGAGCCACACGGGCAAGGACATGGGTGTGTGTCC
1 AGGCTATGTAAACCACACAGGCAAGGACATGGGTGTGTGTCC
28417853 AGGC
1 AGGC
28417857 CGTATGGCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 22 0.55
43 18 0.45
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (42 bp):
AGGCTATGTAAACCACACAGGCAAGGACATGGGTGTGTGTCC
Found at i:28418398 original size:24 final size:22
Alignment explanation
Indices: 28418355--28418398 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
28418345 GAATAACTGC
* *
28418355 ATATGAATCTAATTTGTTCTGT
1 ATATGAAACTAAATTGTTCTGT
28418377 ATATGAAACTGAAATTGCTTCT
1 ATATGAAACT-AAATTG-TTCT
28418399 ACGTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 5 0.28
24 4 0.22
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAACTAAATTGTTCTGT
Found at i:28418483 original size:25 final size:25
Alignment explanation
Indices: 28418449--28418501 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
28418439 CTTCTGTTAT
28418449 CTAACCGAATCTTGGGATTCAAAAA
1 CTAACCGAATCTTGGGATTCAAAAA
*
28418474 CTAACTGAATCTTGGGATTCAAAAA
1 CTAACCGAATCTTGGGATTCAAAAA
28418499 CTA
1 CTA
28418502 TATTATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (25 bp):
CTAACCGAATCTTGGGATTCAAAAA
Found at i:28419113 original size:27 final size:27
Alignment explanation
Indices: 28419091--28419143 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
28419081 TTTATATTAT
* *
28419091 TATTTTGAAAT-TAAAAATATATAAAA
1 TATTTTAAAATATAAAAAAATATAAAA
28419117 TATTTTAAAATATAAAAAAATATAAAA
1 TATTTTAAAATATAAAAAAATATAAAA
28419144 ATTATTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
TATTTTAAAATATAAAAAAATATAAAA
Found at i:28419844 original size:19 final size:18
Alignment explanation
Indices: 28419819--28419864 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
28419809 TAAGGTTAAT
28419819 ATTTAATATCTAAGTTTGA-
1 ATTTAATATC-AA-TTTGAC
*
28419838 TTTTAATATCAATTTGAC
1 ATTTAATATCAATTTGAC
28419856 ATTTAATAT
1 ATTTAATAT
28419865 TTTTTTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (18 bp):
ATTTAATATCAATTTGAC
Found at i:28420794 original size:22 final size:22
Alignment explanation
Indices: 28420762--28420814 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
28420752 TAAATGAATG
* *
28420762 AAAAT-ATTAAATATTTAAA-TC
1 AAAATAATTAAA-ATATAAATTA
28420783 AAAATAATTAAAATATAAATTA
1 AAAATAATTAAAATATAAATTA
28420805 AAAATAATTA
1 AAAATAATTA
28420815 CAAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATAATTAAAATATAAATTA
Found at i:28424191 original size:132 final size:132
Alignment explanation
Indices: 28423951--28424296 Score: 568
Period size: 132 Copynumber: 2.6 Consensus size: 132
28423941 NNNNNNNNNN
* *
28423951 AGATCTGAAATCTTCAATCTATTCCACTA-TTGCCTAGGGAAGTAGAATTACTAGCTTCAATGTA
1 AGATCTGAAATCTTCAATCTATTCCAC-AGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* *
28424015 CTCCACTGTAACCATAGGGAGGTAAAATCCGCAATCCTCAATCTGCTCCACTACTGCTTAGGGAG
65 CTCCACTATAACCACAGGGAGGTAAAATCCGCAATCCTCAATCTGCTCCACTACTGCTTAGGGAG
28424080 ATA
130 ATA
*
28424083 AGATCTGAAATCTTCAATCTATTCCACAGTTGCCCAGGGAAGTAGAATTATTGGCTTCAATGTAC
1 AGATCTGAAATCTTCAATCTATTCCACAGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTAC
* * * **
28424148 TCCACTATAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGA
66 TCCACTATAACCACAGGGAGGTAAAATCCGCAATCCTCAATCTGCTCCACTACTGCTTAGGGAGA
28424213 TA
131 TA
* *
28424215 AGATCTGAAATCTTCAATCTATTCCACTGTTGCCCTGGGAAGTAGAATTACTGGCTTCAATGTAC
1 AGATCTGAAATCTTCAATCTATTCCACAGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTAC
28424280 TCCACTATAACCACAGG
66 TCCACTATAACCACAGG
28424297 NNNNNNNNNN
Statistics
Matches: 200, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 199 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (132 bp):
AGATCTGAAATCTTCAATCTATTCCACAGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTAC
TCCACTATAACCACAGGGAGGTAAAATCCGCAATCCTCAATCTGCTCCACTACTGCTTAGGGAGA
TA
Found at i:28424716 original size:133 final size:133
Alignment explanation
Indices: 28424499--28424761 Score: 463
Period size: 133 Copynumber: 2.0 Consensus size: 133
28424489 TCTTCAATCT
* *
28424499 ATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAG
1 ATTCCACTGCTGCCCAGAGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGAGAG
* *
28424564 GTAAAATCCGCCATATTCGATTTGCTTCGCTGTCAATGCAGGAAGGTAAGATCTGCTATCTTTAA
66 GTAAAATCCGCCATATTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAA
28424629 TAA
131 TAA
28424632 ATTCCACTGCTGCCCAGAGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGAGAG
1 ATTCCACTGCTGCCCAGAGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGAGAG
* * *
28424697 GTAAAATCTGCCATCTTCGATCTGTTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAA
66 GTAAAATCCGCCATATTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAA
28424762 CCTGCTCCAC
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 123 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (133 bp):
ATTCCACTGCTGCCCAGAGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGAGAG
GTAAAATCCGCCATATTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAA
TAA
Found at i:28426154 original size:27 final size:27
Alignment explanation
Indices: 28426116--28426170 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
28426106 TAGACAAGTC
28426116 TTCGTTATCCCTTTCGATCAGAACCAA
1 TTCGTTATCCCTTTCGATCAGAACCAA
28426143 TTCGTTATCCCTTTCGATCAGAACCAA
1 TTCGTTATCCCTTTCGATCAGAACCAA
28426170 T
1 T
28426171 GTAAAATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.35
Consensus pattern (27 bp):
TTCGTTATCCCTTTCGATCAGAACCAA
Found at i:28430208 original size:98 final size:98
Alignment explanation
Indices: 28430036--28430230 Score: 363
Period size: 98 Copynumber: 2.0 Consensus size: 98
28430026 ACAATAAAAT
*
28430036 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
28430101 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
28430134 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
28430199 TTTAAAATCCCAAACTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTA
28430231 TTGTTTTTAG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:28431803 original size:19 final size:19
Alignment explanation
Indices: 28431779--28431910 Score: 219
Period size: 19 Copynumber: 6.8 Consensus size: 19
28431769 AATCATATAT
28431779 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
28431798 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
28431817 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
28431836 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
28431857 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
28431876 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
28431895 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
28431911 CTCAAAAATT
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
19 86 0.82
21 19 0.18
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:28431863 original size:59 final size:59
Alignment explanation
Indices: 28431772--28431909 Score: 221
Period size: 59 Copynumber: 2.4 Consensus size: 59
28431762 ATTACAAAAT
*
28431772 CATAT-AT-TCTAAGATTGC--ATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
* *
28431827 CATATCATATCTAAGATTGCATATATCATATCTAAGATTGCATATCATATCTAGGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
28431886 CATATCATATCTAAGATTGCATAT
1 CATATCATATCTAAGATTGCATAT
28431910 CCTCAAAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
55 5 0.07
56 2 0.03
57 11 0.14
59 58 0.76
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (59 bp):
CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:28433055 original size:63 final size:62
Alignment explanation
Indices: 28432951--28433148 Score: 200
Period size: 63 Copynumber: 3.1 Consensus size: 62
28432941 TGGCAGGCCA
* * * * *
28432951 TGTGACTCACTGTTTTCCATTAAAGACCACAGGGGCCAGAGACACAGGTGTGTGTCTAGGTCG
1 TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCTAGAGACACAGGTGTGTGTCCAGG-CG
* * ** **
28433014 TGTGACTCACTGTTTGCCATTAAGGACCATACAGGCTAGAGAC-TTGAGCATGTGTCCAGGCTG
1 TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCTAGAGACACAG-GTGTGTGTCCAGGC-G
* * * * * *
28433077 TGCGACTCACTGTTTGCCATTAGGGACCACATGGGCTAGAGACACGGGTGCGTGTCCAGGCCA
1 TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCTAGAGACACAGGTGTGTGTCCAGG-CG
28433140 TGTGACTCA
1 TGTGACTCA
28433149 TTATTTGGGA
Statistics
Matches: 108, Mismatches: 23, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
62 2 0.02
63 104 0.96
64 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (62 bp):
TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCTAGAGACACAGGTGTGTGTCCAGGCG
Found at i:28436122 original size:16 final size:16
Alignment explanation
Indices: 28436079--28436125 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
28436069 TTAAACATAC
*
28436079 ATATATAATT-AT-TT
1 ATATATAATTAATATA
*
28436093 ATATTTAA-TAATATA
1 ATATATAATTAATATA
28436108 ATATATAATTAATATA
1 ATATATAATTAATATA
28436124 AT
1 AT
28436126 TTATTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 9 0.33
15 8 0.30
16 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATAATTAATATA
Found at i:28439189 original size:18 final size:17
Alignment explanation
Indices: 28439148--28439181 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28439138 GTCGTTTGTT
28439148 TTTA-AAATATTATTCA
1 TTTACAAATATTATTCA
28439164 TTTACAAATAGTTATTCA
1 TTTACAAATA-TTATTCA
28439182 ATTTCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTACAAATATTATTCA
Found at i:28441647 original size:13 final size:13
Alignment explanation
Indices: 28441629--28441657 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28441619 CCACAGACAC
28441629 CCAAAGCACTTAA
1 CCAAAGCACTTAA
28441642 CCAAAGCACTTAA
1 CCAAAGCACTTAA
28441655 CCA
1 CCA
28441658 TTGAAGCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.34, G:0.07, T:0.14
Consensus pattern (13 bp):
CCAAAGCACTTAA
Done.