Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 19 of 349
Found at i:5374771 original size:26 final size:26
Alignment explanation
Indices: 5374735--5374808 Score: 81
Period size: 21 Copynumber: 3.1 Consensus size: 26
5374725 AATAAAAAGG
*
5374735 TTTGCATCTTTTCTTTTTTCTTTTCT
1 TTTGAATCTTTTCTTTTTTCTTTTCT
5374761 TTTGAA-----TCTTTTTTCTTTTCT
1 TTTGAATCTTTTCTTTTTTCTTTTCT
*
5374782 TTTGAATCTTTT-TTCTTTC-TTTCT
1 TTTGAATCTTTTCTTTTTTCTTTTCT
5374806 TTT
1 TTT
5374809 TATATACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
21 21 0.51
24 8 0.20
25 6 0.15
26 6 0.15
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTGAATCTTTTCTTTTTTCTTTTCT
Found at i:5374800 original size:20 final size:21
Alignment explanation
Indices: 5374746--5374803 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
5374736 TTGCATCTTT
5374746 TCTTTTTTCTTTTCTTTTGAA
1 TCTTTTTTCTTTTCTTTTGAA
5374767 TCTTTTTTCTTTTCTTTTGAA
1 TCTTTTTTCTTTTCTTTTGAA
5374788 TCTTTTTTC-TTTCTTT
1 TCTTTTTTCTTTTCTTT
5374804 CTTTTTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 7 0.19
21 30 0.81
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.74
Consensus pattern (21 bp):
TCTTTTTTCTTTTCTTTTGAA
Found at i:5375548 original size:32 final size:32
Alignment explanation
Indices: 5375508--5375576 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
5375498 CAATTAGTTA
5375508 TATATTTCTTATACTATTCCATGTATGTATTT
1 TATATTTCTTATACTATTCCATGTATGTATTT
5375540 TATATTTCTTATACTATTCCATGTATGTATTT
1 TATATTTCTTATACTATTCCATGTATGTATTT
5375572 TATAT
1 TATAT
5375577 CATCTTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.57
Consensus pattern (32 bp):
TATATTTCTTATACTATTCCATGTATGTATTT
Found at i:5375714 original size:27 final size:27
Alignment explanation
Indices: 5375655--5375714 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
5375645 GTATATATTA
5375655 TTATTACTAATTATTACTACTGCTAGTG
1 TTATTACTAATTATTACTACT-CTAGTG
*
5375683 TTATTA-TAATTATTATTACAT-TAGTG
1 TTATTACTAATTATTACTAC-TCTAGTG
5375709 TATATT
1 T-TATT
5375715 TTATGTACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.21
27 16 0.55
28 7 0.24
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (27 bp):
TTATTACTAATTATTACTACTCTAGTG
Found at i:5375741 original size:18 final size:20
Alignment explanation
Indices: 5375709--5375755 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
5375699 TACATTAGTG
5375709 TATATTTTATGTACATAT-A
1 TATATTTTATGTACATATCA
5375728 TATATTTT-TGTACATATCA
1 TATATTTTATGTACATATCA
5375747 T-TATTTTAT
1 TATATTTTAT
5375756 ATTATTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (20 bp):
TATATTTTATGTACATATCA
Found at i:5377455 original size:31 final size:31
Alignment explanation
Indices: 5377420--5377483 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
5377410 CCTTTTAATA
*
5377420 TTTCATATTTGATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
5377451 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
5377482 TT
1 TT
5377484 ATTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:5377740 original size:26 final size:26
Alignment explanation
Indices: 5377709--5377807 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
5377699 CTCTTTTAAT
* *
5377709 AACTGGTGCAAAAGCCCTTTTAGGTA
1 AACTGGGGCATAAGCCCTTTTAGGTA
*
5377735 AACTGGGGCATAAGCCCTTTTTGGTA
1 AACTGGGGCATAAGCCCTTTTAGGTA
* *
5377761 AACTGGGGCATAAGCCATTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTAGGTA
* *
5377787 AATTAGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
5377808 TGCACTTCCT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTAGGTA
Found at i:5377880 original size:20 final size:20
Alignment explanation
Indices: 5377857--5377923 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
5377847 TTATGAATAC
5377857 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
5377877 ATCATGTACATATCATACAT
1 ATCATGTGCATATCATACAT
*
5377897 ATCATGTGCATCTCATATCA-
1 ATCATGTGCATATCATA-CAT
5377917 ATCATGT
1 ATCATGT
5377924 ATATCAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:5377886 original size:11 final size:11
Alignment explanation
Indices: 5377857--5377924 Score: 58
Period size: 9 Copynumber: 6.7 Consensus size: 11
5377847 TTATGAATAC
*
5377857 ATCATGTGCAT
1 ATCATGTACAT
5377868 ATCA--TACAT
1 ATCATGTACAT
5377877 ATCATGTACAT
1 ATCATGTACAT
5377888 ATCA--TACAT
1 ATCATGTACAT
*
5377897 ATCATGTGCAT
1 ATCATGTACAT
* *
5377908 CTCATAT-CA-
1 ATCATGTACAT
5377917 ATCATGTA
1 ATCATGTA
5377925 TATCAAAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
9 22 0.48
10 2 0.04
11 22 0.48
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (11 bp):
ATCATGTACAT
Found at i:5388617 original size:4 final size:4
Alignment explanation
Indices: 5388610--5388651 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
5388600 ATATATATAT
5388610 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
5388652 TTGAAGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:5389890 original size:136 final size:137
Alignment explanation
Indices: 5389645--5389930 Score: 529
Period size: 136 Copynumber: 2.1 Consensus size: 137
5389635 CATTGGGCCT
**
5389645 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
5389710 AGCCCCTTATTCAGATAATAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
5389775 CATATGC
131 CATATGC
5389782 AAGCCCATTTGGGTAACAGTGGTACTGGGCC-GAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
5389846 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATTAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
5389911 CATATGC
131 CATATGC
5389918 AAGCCCATTTGGG
1 AAGCCCATTTGGG
5389931 GAGACTACTC
Statistics
Matches: 145, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 116 0.80
137 29 0.20
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:5390215 original size:25 final size:27
Alignment explanation
Indices: 5390178--5390230 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5390168 TCAAACATGC
5390178 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
5390204 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
5390230 A
1 A
5390231 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:5391753 original size:26 final size:26
Alignment explanation
Indices: 5391717--5391826 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5391707 CATGAAATTC
5391717 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5391743 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5391769 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
5391795 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5391821 TTATCA
1 TTATCA
5391827 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5394055 original size:228 final size:227
Alignment explanation
Indices: 5393659--5394229 Score: 932
Period size: 228 Copynumber: 2.5 Consensus size: 227
5393649 TCTACTTCAT
*
5393659 TGCAACTTCA-AGGAGATAAGA-TCTGTTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATA
1 TGCAACTTCAGA-GAGATAAGATTC-GTTATCTTCAGTTTGCTCCACTGCAACTTCAGGGAGATA
** * * * * * * *
5393722 AGACTTGTAACTTCAACTTGCCCTACTACAACTTCAGGGGGATAAGTTTTGTGGCTTTAATCTAC
64 AGACTCATAACTTTAACTTGCCCCACTGCAACTTCAAGGGAATAAGGTTTGTGGCTTCAATCTAC
5393787 TCCACTACAACTTCAGGGAGATAAGATTCACCATGGTAGGTTTGATCCGACCTACTGCAACTTCA
129 TCCACTACAACTTCAGGGAGATAAGATTCACCATGGTAGGTTTGATCCGACCTACTGCAACTTCA
*
5393852 GAGGTATAGGAATTATAGCTTTAATCTGCTCTAC
194 GAGGAATAGGAATTATAGCTTTAATCTGCTCTAC
** *
5393886 TGCAACTTCAGAGAGATAAGATTCACTATCTTCAGTTTGCTCCACTACAACTTCAGGGAGATAAG
1 TGCAACTTCAGAGAGATAAGATTCGTTATCTTCAGTTTGCTCCACTGCAACTTCAGGGAGATAAG
5393951 ACTCATAAGCTTTAACTTGCCCCACTGCAACTTCAAGGGAATAAGGTTTGTGGCTTCAATCTACT
66 ACTCATAA-CTTTAACTTGCCCCACTGCAACTTCAAGGGAATAAGGTTTGTGGCTTCAATCTACT
5394016 CCACTACAACTTCAGGGAGATAAGATTCACCATGGTAGGTTTGATCCGACCTACTGCAACTTCAG
130 CCACTACAACTTCAGGGAGATAAGATTCACCATGGTAGGTTTGATCCGACCTACTGCAACTTCAG
*
5394081 AGGAATAGGATTTATAGCTTTAATCTGCTCTAC
195 AGGAATAGGAATTATAGCTTTAATCTGCTCTAC
* *
5394114 TGCAACTTTAGAGAGATAAGATTCGTTATCTTCAGTTTGCTTCACTGCAACTTCAGGGAGATAAG
1 TGCAACTTCAGAGAGATAAGATTCGTTATCTTCAGTTTGCTCCACTGCAACTTCAGGGAGATAAG
5394179 ACTCATAACTTTAACTTGCCCCACTGCAACTTC-AGGGAGATAAGGTTTGTG
66 ACTCATAACTTTAACTTGCCCCACTGCAACTTCAAGGGA-ATAAGGTTTGTG
5394230 TATTTTTATC
Statistics
Matches: 320, Mismatches: 20, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
226 5 0.02
227 99 0.31
228 216 0.68
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (227 bp):
TGCAACTTCAGAGAGATAAGATTCGTTATCTTCAGTTTGCTCCACTGCAACTTCAGGGAGATAAG
ACTCATAACTTTAACTTGCCCCACTGCAACTTCAAGGGAATAAGGTTTGTGGCTTCAATCTACTC
CACTACAACTTCAGGGAGATAAGATTCACCATGGTAGGTTTGATCCGACCTACTGCAACTTCAGA
GGAATAGGAATTATAGCTTTAATCTGCTCTAC
Found at i:5394205 original size:89 final size:89
Alignment explanation
Indices: 5394068--5394361 Score: 301
Period size: 89 Copynumber: 3.3 Consensus size: 89
5394058 GATCCGACCT
* * * * *
5394068 ACTGCAACTTCAGAG-GAATAGGATTTATAGCTTTAATCTGCTCTACTGCAACTTTAGAGAGATA
1 ACTGCAACTTCAGAGAG-ATAAGACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
*
5394132 AGATTCGTTATCTTCAGTTTGCTTC
65 AGATTCGTTATCTTCAGTCTGCTTC
* * * *
5394157 ACTGCAACTTCAGGGAGATAAGACTCATAACTTTAA-CTTGCCCCACTGCAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGACTTATAGCTTTAATC-TGCTCCACTGCAACTTCAGGGAGATA
* * * * *
5394221 AGGTTTGTGTATTTTTA-TCCTGCTTT
65 AGATTCGT-TATCTTCAGT-CTGCTTC
* * * *
5394247 ATTGCAACTTCAGAAAGATAAGGA-TTATGGCTTTGATCTGCTCCACTGCAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAA-GACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
* *
5394311 AGA-TCTGTCATCTTCAGTCTGCTCC
65 AGATTC-GTTATCTTCAGTCTGCTTC
*
5394336 ACTGCAACTTTAGAGAGATAAGACTT
1 ACTGCAACTTCAGAGAGATAAGACTT
5394362 GCTACTTCAA
Statistics
Matches: 163, Mismatches: 33, Indels: 18
0.76 0.15 0.08
Matches are distributed among these distances:
88 3 0.02
89 89 0.55
90 68 0.42
91 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (89 bp):
ACTGCAACTTCAGAGAGATAAGACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
GATTCGTTATCTTCAGTCTGCTTC
Found at i:5394219 original size:44 final size:44
Alignment explanation
Indices: 5393659--5394358 Score: 261
Period size: 44 Copynumber: 15.5 Consensus size: 44
5393649 TCTACTTCAT
* ** * * * *
5393659 TGCAACTTCAAGGAGATAAGATCTGTTATCTTCAGTCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGAT-TCATAACTTTAATTTGCTCCAC
* * *
5393704 TGCAACTTCAGGGAGATAAGACTT-GTAACTTCAACTTGC-CCTAC
1 TGCAACTTCAGGGAGATAAGA-TTCATAACTTTAATTTGCTCC-AC
* * * ** ** * *
5393748 TACAACTTCAGGGGGATAAGTTTTGTGGCTTTAATCTACTCCAC
1 TGCAACTTCAGGGAGATAAGATTCATAACTTTAATTTGCTCCAC
* ** * * *
5393792 TACAACTTCAGGGAGATAAGATTCACCA-TGGTAGGTTTGATCCGACCTAC
1 TGCAACTTCAGGGAGATAAGATTCATAACT-TTA-ATTTG---C-TCC-AC
* * * * *
5393842 TGCAACTTCAGAGG-TATAGGAATT-ATAGCTTTAATCTGCTCTAC
1 TGCAACTTCAG-GGAGATAAG-ATTCATAACTTTAATTTGCTCCAC
* * * *
5393886 TGCAACTTCAGAGAGATAAGATTCACTATCTTCAGTTTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTCA-TAACTTTAATTTGCTCCAC
* * * *
5393931 TACAACTTCAGGGAGATAAGACTCATAAGCTTTAACTTGCCCCAC
1 TGCAACTTCAGGGAGATAAGATTCATAA-CTTTAATTTGCTCCAC
* ** ** * * *
5393976 TGCAACTTCAAGGGA-ATAAGGTTTGTGGCTTCAATCTACTCCAC
1 TGCAACTTC-AGGGAGATAAGATTCATAACTTTAATTTGCTCCAC
* ** * * *
5394020 TACAACTTCAGGGAGATAAGATTCACCA-TGGTAGGTTTGATCCGACCTAC
1 TGCAACTTCAGGGAGATAAGATTCATAACT-TTA-ATTTG---C-TCC-AC
* * * * *
5394070 TGCAACTTCAGAGGA-ATAGGATTTATAGCTTTAATCTGCTCTAC
1 TGCAACTTCAG-GGAGATAAGATTCATAACTTTAATTTGCTCCAC
* * * * * * *
5394114 TGCAACTTTAGAGAGATAAGATTCGTTATCTTCAGTTTGCTTCAC
1 TGCAACTTCAGGGAGATAAGATTC-ATAACTTTAATTTGCTCCAC
* * *
5394159 TGCAACTTCAGGGAGATAAGACTCATAACTTTAACTTGCCCCAC
1 TGCAACTTCAGGGAGATAAGATTCATAACTTTAATTTGCTCCAC
* ** * * * * ** *
5394203 TGCAACTTCAGGGAGATAAGGTTTGTGTATTTTTATCCTGCTTTAT
1 TGCAACTTCAGGGAGATAAGATTCAT-AACTTTAAT-TTGCTCCAC
** ** * *
5394249 TGCAACTTCAGAAAGATAAGGATT-ATGGCTTTGATCTGCTCCAC
1 TGCAACTTCAGGGAGATAA-GATTCATAACTTTAATTTGCTCCAC
* * *
5394293 TGCAACTTCAGGGAGATAAGATCTGTCAT--CTTCAGTCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGA--T-TCATAACTTTAATTTGCTCCAC
* *
5394338 TGCAACTTTAGAGAGATAAGA
1 TGCAACTTCAGGGAGATAAGA
5394359 CTTGCTACTT
Statistics
Matches: 475, Mismatches: 142, Indels: 76
0.69 0.20 0.11
Matches are distributed among these distances:
43 19 0.04
44 188 0.40
45 169 0.36
46 31 0.07
47 5 0.01
48 2 0.00
49 10 0.02
50 41 0.09
51 10 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGATTCATAACTTTAATTTGCTCCAC
Found at i:5398705 original size:8 final size:8
Alignment explanation
Indices: 5398692--5398730 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
5398682 ACCTATAAAT
5398692 TTTTTTTA
1 TTTTTTTA
5398700 TTTTTTTA
1 TTTTTTTA
*
5398708 TTTTTTTC
1 TTTTTTTA
* *
5398716 GTATTTTA
1 TTTTTTTA
5398724 TTTTTTT
1 TTTTTTT
5398731 TGTACTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:5399097 original size:14 final size:14
Alignment explanation
Indices: 5399075--5399112 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5399065 TCCAAGTTAG
5399075 ATAAAATAATTAAA
1 ATAAAATAATTAAA
*
5399089 A-AGAAATAACTAAA
1 ATA-AAATAATTAAA
5399103 ATAAAATAAT
1 ATAAAATAAT
5399113 AAATCCAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.05
14 18 0.90
15 1 0.05
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:5406277 original size:30 final size:30
Alignment explanation
Indices: 5406236--5406302 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
5406226 AAATCGAAAC
5406236 CCAACACGTTAGGGTACGATTTCTCAGATTT
1 CCAA-ACGTTAGGGTACGATTTCTCAGATTT
5406267 CCAAACGTTAGGGTACGATTTCTCAGATTT
1 CCAAACGTTAGGGTACGATTTCTCAGATTT
5406297 CCAAAC
1 CCAAAC
5406303 ATGGAACATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (30 bp):
CCAAACGTTAGGGTACGATTTCTCAGATTT
Found at i:5407092 original size:3 final size:3
Alignment explanation
Indices: 5407084--5407125 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5407074 TAATGTATAT
5407084 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5407126 TATGAAATGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5415449 original size:59 final size:59
Alignment explanation
Indices: 5415379--5415496 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
5415369 ATTATTTGAG
5415379 CCATTAATTAAGCTTTTAAAATAAATATTTTTTATTTAATAATTACATATATCATGGTT
1 CCATTAATTAAGCTTTTAAAATAAATATTTTTTATTTAATAATTACATATATCATGGTT
*
5415438 CCATTAGTTAAGCTTTTAAAATAAATATTTTTTATTTAATAATTACATATATCATGGTT
1 CCATTAATTAAGCTTTTAAAATAAATATTTTTTATTTAATAATTACATATATCATGGTT
5415497 TCAGTGTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.47
Consensus pattern (59 bp):
CCATTAATTAAGCTTTTAAAATAAATATTTTTTATTTAATAATTACATATATCATGGTT
Found at i:5424990 original size:16 final size:16
Alignment explanation
Indices: 5424969--5425026 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
5424959 TTTGTGAGGA
5424969 TTTATTTTTAAAATAT
1 TTTATTTTTAAAATAT
*
5424985 TTTATTTATAAAAT-T
1 TTTATTTTTAAAATAT
* *
5425000 ATTATTTTAATAAATAAAT
1 TTTATTTT--TAAA-ATAT
5425019 TTTATTTT
1 TTTATTTT
5425027 AGAAAAAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
15 7 0.21
16 13 0.39
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATTTTTAAAATAT
Found at i:5428332 original size:19 final size:19
Alignment explanation
Indices: 5428307--5428398 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
5428297 ATAATCTTCA
5428307 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
5428326 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5428345 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5428362 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5428381 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
5428399 AGATATGATT
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
17 17 0.25
19 52 0.75
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5428347 original size:14 final size:15
Alignment explanation
Indices: 5428328--5428384 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
5428318 TCTTAGATGT
5428328 GATATG-CAATCTTA
1 GATATGACAATCTTA
5428342 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
5428359 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
5428378 GATATGA
1 GATATGA
5428385 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:5428355 original size:36 final size:37
Alignment explanation
Indices: 5428307--5428405 Score: 150
Period size: 36 Copynumber: 2.7 Consensus size: 37
5428297 ATAATCTTCA
*
5428307 ATGATATGCAATCTTAGATGTGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
5428345 ATGATA-CAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
5428381 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
5428406 ATTTTGTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
36 41 0.71
37 1 0.02
38 16 0.28
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.35
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:5434129 original size:14 final size:14
Alignment explanation
Indices: 5434107--5434164 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
5434097 TTCTATTTCA
* *
5434107 AAAGCAAAAAAAAG
1 AAAGAAAAAAAAAC
**
5434121 AAAGAAAAAAAATT
1 AAAGAAAAAAAAAC
5434135 AAAGAAAAAGAGAAAAC
1 AAAG-AAAA-A-AAAAC
5434152 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
5434165 AAAAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 19 0.53
15 5 0.14
16 5 0.14
17 7 0.19
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAAAAC
Found at i:5434150 original size:8 final size:8
Alignment explanation
Indices: 5434113--5434175 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
5434103 TTCAAAAGCA
5434113 AAAAAAAG
1 AAAAAAAG
5434121 AAAGAAAA-
1 AAA-AAAAG
5434129 AAAATTAAAG
1 AAAA--AAAG
*
5434139 AAAAAGAG
1 AAAAAAAG
5434147 AAAACAAAG
1 AAAA-AAAG
5434156 AAAAAAA-
1 AAAAAAAG
*
5434163 AAAAAAAT
1 AAAAAAAG
5434171 AAAAA
1 AAAAA
5434176 TGGAGAGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
7 8 0.17
8 21 0.45
9 14 0.30
10 4 0.09
ACGTcount: A:0.84, C:0.02, G:0.10, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5435179 original size:43 final size:43
Alignment explanation
Indices: 5435131--5435357 Score: 148
Period size: 43 Copynumber: 5.3 Consensus size: 43
5435121 CGCCTTAATC
*
5435131 CCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAAGTTAAAATTGCAGATCTTATCT
* * * * * * *
5435174 CCCTAAGCAGTAGTGG-AGC-AGATCGAAGACT-C-G-CCTTAACC
1 CCCTAAGCAGTAG-GGTAACAAG-T-TAAAATTGCAGATCTTATCT
* * *
5435215 CCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAAGTTAAAATTGCAGATCTTATCT
* ** *
5435258 CCCTAAGCAGTAGTGG-AAC-AGATTAATGA-TGACTCACCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAAG-TTAA-AATTG-CAGATCTT-ATCT
* * * *
5435302 CCCTAAGCAGTAGGATAACAGGTCAAAATTGCGGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAAGTTAAAATTGCAGATCTTATCT
5435345 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
5435358 TGGAGCAGAT
Statistics
Matches: 136, Mismatches: 31, Indels: 34
0.68 0.15 0.17
Matches are distributed among these distances:
40 6 0.04
41 21 0.15
42 9 0.07
43 62 0.46
44 34 0.25
45 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAAGTTAAAATTGCAGATCTTATCT
Found at i:5435262 original size:84 final size:84
Alignment explanation
Indices: 5435121--5435412 Score: 415
Period size: 84 Copynumber: 3.4 Consensus size: 84
5435111 CAAAATTCAG
* * *
5435121 CGCCTTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAATTGCAGATCTTATCTCCCTAAGCAGTA
5435186 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* *
5435205 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAATTGCAGATCTTATCTCCCTAAGCAGTA
* * *
5435270 GTGGAACAGATTAATGATGACT
66 GTGGAGCAGA-T--CGAAGACT
* * * * *
5435292 CACCTTAATCCCCTAAGCAGTAGGATAACAGGTCAAAATTGCGGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAATTGCAGATCTTATCTCCCTAAGCAGTA
5435357 GTGGAGCAGATCGAAGA-T
66 GTGGAGCAGATCGAAGACT
*
5435375 GCGCCTTAACCCCCTAAGTAGTAGGGTAACAGGTTAAA
1 -CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAA
5435413 GCATAGCAGA
Statistics
Matches: 181, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
83 1 0.01
84 105 0.58
85 1 0.01
86 1 0.01
87 73 0.40
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (84 bp):
CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAATTGCAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAAGACT
Found at i:5435966 original size:207 final size:207
Alignment explanation
Indices: 5435414--5436412 Score: 1619
Period size: 207 Copynumber: 4.8 Consensus size: 207
5435404 CAGGTTAAAG
5435414 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
1 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
* *
5435479 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGAGGAAGCAAATC
66 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
* * *
5435544 TAAGATGATTTGGAATCTCTGTATTGTCAGAGAACAAATCAAATTTTGGCGTCTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
5435609 GGAGGGCAGACA
196 GGAGGGCAGACA
5435621 CATAGCAGATCTGGCCTTCA-ATGTTTATACTGAA-CAAGATCCAAGATGGTTTGGCATCCTTGT
1 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
* * *
5435684 GCTTACAAGGAACAAATCAAAGACATAGTTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
66 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
*
5435749 TAAGATGATTTGGCATTTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
5435814 GGAGGGCAGACA
196 GGAGGGCAGACA
* *
5435826 CATAGCAGATCTGGCCTTCAAATGTTTATACTGAAGCAAGATCCAAGCTGGTTTGGCATCCTTGT
1 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
* * *
5435891 GCTTACAAGGAACAAATTGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTC
66 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
*
5435956 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTTTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
5436021 GGAGGGCAGACA
196 GGAGGGCAGACA
* * *
5436033 CATAGCAGATCTGACCTTCAGATGTTTATACTGAAGTAAGATCCAAGATGGTTTGGCATCTTTGT
1 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
* * * *
5436098 GCTTACAAGGAGCAAATCGAAGACATAGTTGATTTGGCTTTCACGTGTTTACGCTGAAGCAAGTC
66 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
*
5436163 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATTGAAGTTTGGCGTCTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
* *
5436228 GGAGGACAAACA
196 GGAGGGCAGACA
* ** * * * *
5436240 TATAGCAGATCTAACCTTCAGATGATGAGACTGAAGC-AGATCCAAGATGGTTTGGTATCCTTGT
1 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
** * *
5436304 GCTTACAAGGAGTAAATCGAAGACATAGCTGATTTGGCTTTCGCGTGTTTACGCTGAAGCAAATC
66 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
* *
5436369 TAAGATGATTTGGCATCTCTGTATTTTCAG-GAAACAAATTGAAG
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAG-AACAAATCGAAG
5436413 AAGCAGATTT
Statistics
Matches: 747, Mismatches: 42, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
205 185 0.25
206 155 0.21
207 407 0.54
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (207 bp):
CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
GGAGGGCAGACA
Found at i:5436836 original size:18 final size:18
Alignment explanation
Indices: 5436769--5436947 Score: 247
Period size: 18 Copynumber: 9.9 Consensus size: 18
5436759 ATAATCTTCA
5436769 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
5436788 GTGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
5436807 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
5436824 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
5436842 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
5436859 ATGATTGCAATATTAGAT
1 ATGATTGCAATCTTAGAT
* *
5436877 ATGA-TACAATATTAGAT
1 ATGATTGCAATCTTAGAT
5436894 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
5436912 ATGATTGCAATATTAGAT
1 ATGATTGCAATCTTAGAT
5436930 ATGATATGCAATCTTAGA
1 ATGAT-TGCAATCTTAGA
5436948 AGATATGATT
Statistics
Matches: 144, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
17 48 0.33
18 64 0.44
19 32 0.22
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:5436839 original size:35 final size:35
Alignment explanation
Indices: 5436777--5436947 Score: 270
Period size: 35 Copynumber: 4.8 Consensus size: 35
5436767 CAATGATATG
*
5436777 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
5436813 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
*
5436848 CAATCTTAGATATGATTGCAATATTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
* *
5436883 CAATATTAGATATGATTGCAATCTTAGATATGATTG
1 CAATCTTAGATATGATTGCAATCTTAGATATGA-TA
*
5436919 CAATATTAGATATGATATGCAATCTTAGA
1 CAATCTTAGATATGAT-TGCAATCTTAGA
5436948 AGATATGATT
Statistics
Matches: 128, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
35 84 0.66
36 32 0.25
37 12 0.09
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:5438227 original size:43 final size:43
Alignment explanation
Indices: 5438163--5438271 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
5438153 TTACAGCGCT
* * ** *
5438163 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTTCAACAAACG
1 CCGCTAAAAAACATGACCTTTAACGGAACTTTTCCAACAAACG
* *
5438206 CCGCTAAAAAACATGATCTTTAACGGAACTTTTCCCACAAACG
1 CCGCTAAAAAACATGACCTTTAACGGAACTTTTCCAACAAACG
*
5438249 CCGCTAAAAAACATAACCTTTAA
1 CCGCTAAAAAACATGACCTTTAA
5438272 AAAATGTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.23
Consensus pattern (43 bp):
CCGCTAAAAAACATGACCTTTAACGGAACTTTTCCAACAAACG
Found at i:5439880 original size:15 final size:16
Alignment explanation
Indices: 5439846--5439882 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5439836 ACCCACCCTA
*
5439846 ACCCAAAACCCAGAAG
1 ACCCAAAACCCACAAG
5439862 -CCCAAAACCC-CAAG
1 ACCCAAAACCCACAAG
5439876 ACCCAAA
1 ACCCAAA
5439883 TCAGAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.49, C:0.43, G:0.08, T:0.00
Consensus pattern (16 bp):
ACCCAAAACCCACAAG
Found at i:5441191 original size:33 final size:36
Alignment explanation
Indices: 5441127--5441198 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 36
5441117 GTAAGTGTTC
*
5441127 TAATACTATATCATATATAAATATGCATTTTTCATAT
1 TAATACTATATCATATATAAATATG-ATTTTTAATAT
*
5441164 TAATA-TATAT-ATATATATATATG-TTTTTAATAT
1 TAATACTATATCATATATAAATATGATTTTTAATAT
5441197 TA
1 TA
5441199 TATTATCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 11 0.33
35 12 0.36
36 5 0.15
37 5 0.15
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (36 bp):
TAATACTATATCATATATAAATATGATTTTTAATAT
Found at i:5441193 original size:27 final size:27
Alignment explanation
Indices: 5441163--5441226 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
5441153 ATTTTTCATA
5441163 TTAATA-TATATATAT-ATATATATGTTT
1 TTAATATTATAT-TATCATATATATG-TT
*
5441190 TTAATATTATATTATCATGTATATGTT
1 TTAATATTATATTATCATATATATGTT
5441217 TTAATATTAT
1 TTAATATTAT
5441227 TAGCTATCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (27 bp):
TTAATATTATATTATCATATATATGTT
Found at i:5441403 original size:21 final size:21
Alignment explanation
Indices: 5441362--5441403 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5441352 TCTAATATAA
* *
5441362 ATATATATATCATATAGGTTT
1 ATATACATATCATACAGGTTT
*
5441383 ATATACATATCATACATGTTT
1 ATATACATATCATACAGGTTT
5441404 CTTTATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATACATATCATACAGGTTT
Found at i:5441802 original size:21 final size:20
Alignment explanation
Indices: 5441778--5441868 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 20
5441768 ACTATTATTT
*
5441778 TATTTATTTTTATTCCTAGTA
1 TATTTATTTTTATT-ATAGTA
* *
5441799 TATTTATTATTAATATTAGTA
1 TATTTATTTTTATTA-TAGTA
*
5441820 TATGTA-TTTTATTATACGTA
1 TATTTATTTTTATTATA-GTA
*
5441840 TATATATATTTTTATAAATAGTA
1 TAT-T-TATTTTTAT-TATAGTA
5441863 TTATTT
1 -TATTT
5441869 TCATATATTC
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
19 2 0.04
20 12 0.22
21 22 0.40
22 3 0.05
23 10 0.18
24 6 0.11
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.58
Consensus pattern (20 bp):
TATTTATTTTTATTATAGTA
Found at i:5441842 original size:20 final size:20
Alignment explanation
Indices: 5441817--5441855 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5441807 ATTAATATTA
*
5441817 GTATATGTAT-TTTATTATAC
1 GTATATATATATTT-TTATAC
5441837 GTATATATATATTTTTATA
1 GTATATATATATTTTTATA
5441856 AATAGTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (20 bp):
GTATATATATATTTTTATAC
Found at i:5441930 original size:21 final size:20
Alignment explanation
Indices: 5441904--5441950 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
5441894 TACTTATTAT
*
5441904 TTTATTCTAAATTACTATGTA
1 TTTATTCTAAAATA-TATGTA
*
5441925 TTTATTTTAAAATATATGTA
1 TTTATTCTAAAATATATGTA
*
5441945 TATATT
1 TTTATT
5441951 TGTGTAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTATTCTAAAATATATGTA
Found at i:5441944 original size:20 final size:21
Alignment explanation
Indices: 5441904--5441951 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
5441894 TACTTATTAT
* *
5441904 TTTATTCTAAATTACTATGTA
1 TTTATTTTAAAATACTATGTA
5441925 TTTATTTTAAAATA-TATGTA
1 TTTATTTTAAAATACTATGTA
*
5441945 TATATTT
1 TTTATTT
5441952 GTGTAGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTATTTTAAAATACTATGTA
Found at i:5442051 original size:19 final size:18
Alignment explanation
Indices: 5442027--5442070 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5442017 TTTTATATAT
5442027 TATGTATGTATA-TATTAC
1 TATGTAT-TATAGTATTAC
*
5442045 ATATGTATTTTAGTATTAC
1 -TATGTATTATAGTATTAC
5442064 TATGTAT
1 TATGTAT
5442071 ACACTTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (18 bp):
TATGTATTATAGTATTAC
Found at i:5457131 original size:15 final size:14
Alignment explanation
Indices: 5457100--5457135 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5457090 CGCTAAGGTA
*
5457100 TTTTCAATTTCTGC
1 TTTTCAAATTCTGC
5457114 TTTTCAAATTCTGC
1 TTTTCAAATTCTGC
*
5457128 CTTTCAAA
1 TTTTCAAA
5457136 AAAATCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (14 bp):
TTTTCAAATTCTGC
Found at i:5457149 original size:89 final size:87
Alignment explanation
Indices: 5457046--5457258 Score: 282
Period size: 89 Copynumber: 2.4 Consensus size: 87
5457036 TTCTGTTTTC
* ** *
5457046 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCTAAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTC
** *
5457111 TGCTTTTCAAATTCTGCCTTTCAA
66 CACTTTTCAAATTATG--TTTCAA
* *
5457135 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTC
* * *
5457200 CATTTTTCGATTTATGTTTCAA
66 CACTTTTCAAATTATGTTTCAA
* *
5457222 AGAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5457259 TTTAATTTCT
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
87 40 0.37
89 69 0.63
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTC
CACTTTTCAAATTATGTTTCAA
Found at i:5457471 original size:56 final size:54
Alignment explanation
Indices: 5457224--5457476 Score: 407
Period size: 54 Copynumber: 4.6 Consensus size: 54
5457214 TGTTTCAAAG
*
5457224 AAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAA
* *
5457278 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAATTTCTATTTTTCAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAA
5457332 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAA
* * * * *
5457386 AAATCGACTCATATTGCGAGAGGTGAGTTGAACCTTTCAATTTATATTTTTTCAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCT-GTTTTTC-AA
*
5457442 AAATCAACTCATATTGCGAGAGGTCAGTTGAGCCT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5457477 CGGGTCATAT
Statistics
Matches: 184, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
54 144 0.78
55 6 0.03
56 34 0.18
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (54 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAA
Found at i:5457781 original size:44 final size:44
Alignment explanation
Indices: 5457712--5457823 Score: 188
Period size: 44 Copynumber: 2.5 Consensus size: 44
5457702 ACCAGAGTTG
* *
5457712 GCCTCTCTGAAGTTGCGATGGAGCAGGTCAAAGTTGCAAGTCTT
1 GCCTCCCTGAAGTTGCGGTGGAGCAGGTCAAAGTTGCAAGTCTT
*
5457756 GCTTCCCTGAAGTTGCGGTGGAGCAGGTCAAAGTTGCAAGTCTT
1 GCCTCCCTGAAGTTGCGGTGGAGCAGGTCAAAGTTGCAAGTCTT
*
5457800 GCCTCCCTGAAGTTGCAGTGGAGC
1 GCCTCCCTGAAGTTGCGGTGGAGC
5457824 TGATCGAGGA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (44 bp):
GCCTCCCTGAAGTTGCGGTGGAGCAGGTCAAAGTTGCAAGTCTT
Found at i:5459576 original size:25 final size:23
Alignment explanation
Indices: 5459548--5459595 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5459538 ACTATATCAT
*
5459548 ATATACATATGCATTTTTCATATTA
1 ATATACATATG--TTTTTAATATTA
*
5459573 ATATATATATGTTTTTAATATTA
1 ATATACATATGTTTTTAATATTA
5459596 TATTATCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
25 10 0.48
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (23 bp):
ATATACATATGTTTTTAATATTA
Found at i:5459804 original size:21 final size:21
Alignment explanation
Indices: 5459763--5459804 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5459753 TCTAATATAA
* *
5459763 ATATATATATCATATAGGTTT
1 ATATACATATCATACAGGTTT
*
5459784 ATATACATATCATACATGTTT
1 ATATACATATCATACAGGTTT
5459805 CTTTATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATACATATCATACAGGTTT
Found at i:5460457 original size:19 final size:18
Alignment explanation
Indices: 5460433--5460476 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5460423 TTTTATATAT
5460433 TATGTATGTATA-TATTAC
1 TATGTAT-TATAGTATTAC
*
5460451 ATATGTATTTTAGTATTAC
1 -TATGTATTATAGTATTAC
5460470 TATGTAT
1 TATGTAT
5460477 ACACTTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (18 bp):
TATGTATTATAGTATTAC
Found at i:5462728 original size:20 final size:20
Alignment explanation
Indices: 5462703--5462764 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
5462693 CTCATTTTCA
5462703 ATTTTTTTTCTTTTTCTTTT
1 ATTTTTTTTCTTTTTCTTTT
5462723 ATTTTTTTTCTTTTTCTTTT
1 ATTTTTTTTCTTTTTCTTTT
5462743 ATTTTTTTCTTCTTTTTTCTTT
1 A-TTTTTT-TTC-TTTTTCTTT
5462765 CAAATTTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
20 21 0.54
21 6 0.15
22 3 0.08
23 9 0.23
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (20 bp):
ATTTTTTTTCTTTTTCTTTT
Found at i:5462730 original size:14 final size:13
Alignment explanation
Indices: 5462704--5462765 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
5462694 TCATTTTCAA
5462704 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
*
5462717 TCTTTTATT-TTTT
1 T-TTTTTTTCTTTT
*
5462730 TTCTTTTTCTTTT
1 TTTTTTTTCTTTT
*
5462743 ATTTTTTTCTTCTT
1 TTTTTTTTCTT-TT
*
5462757 TTTTCTTTC
1 TTTTTTTTC
5462766 AAATTTGTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 5 0.13
13 19 0.49
14 15 0.38
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:5466550 original size:20 final size:20
Alignment explanation
Indices: 5466527--5466564 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5466517 TTTAAACATT
5466527 AAAAATATTAAAAATTATAA
1 AAAAATATTAAAAATTATAA
* *
5466547 AAAAATTTTAAAATTTAT
1 AAAAATATTAAAAATTAT
5466565 TTAATTGCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATATTAAAAATTATAA
Found at i:5469231 original size:6 final size:6
Alignment explanation
Indices: 5469220--5469262 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
5469210 ATGTCCTTGG
* * *
5469220 TATTTT TATTTT TATTAT TATTTAT TACTAT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTT-T TATTTT TATTTT TATTTT
5469263 GATGCCACTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:5469518 original size:3 final size:3
Alignment explanation
Indices: 5469510--5469547 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5469500 GTATTTTTAC
*
5469510 ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5469548 ATATAGTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5470015 original size:22 final size:22
Alignment explanation
Indices: 5469990--5470031 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5469980 TTTTTTATAC
5469990 ATATTAT-TACTATTTTCAATAA
1 ATATTATATA-TATTTTCAATAA
*
5470012 ATATTGTATATATTTTCAAT
1 ATATTATATATATTTTCAAT
5470032 CTAGTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTATATATATTTTCAATAA
Found at i:5476510 original size:22 final size:22
Alignment explanation
Indices: 5476485--5476527 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5476475 AGGTTAATTA
5476485 TAAAAAAATATAAAAAATTCTT
1 TAAAAAAATATAAAAAATTCTT
* * *
5476507 TAAAAAATTCTAAAAATTTCT
1 TAAAAAAATATAAAAAATTCT
5476528 CTAATAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAAAATATAAAAAATTCTT
Found at i:5479434 original size:19 final size:19
Alignment explanation
Indices: 5479412--5479481 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
5479402 GTACCCGATT
*
5479412 ACTACCCTGCAGGCCTAAA
1 ACTACCCAGCAGGCCTAAA
* * **
5479431 ACTACCCAGCAGACCCATTT
1 ACTACCCAGCAGGCCTA-AA
*
5479451 ACTACCCAGCAGGCTTAAA
1 ACTACCCAGCAGGCCTAAA
5479470 ACTACCCAGCAG
1 ACTACCCAGCAG
5479482 ACCCATTTAC
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 26 0.65
20 14 0.35
ACGTcount: A:0.33, C:0.37, G:0.14, T:0.16
Consensus pattern (19 bp):
ACTACCCAGCAGGCCTAAA
Found at i:5479453 original size:39 final size:39
Alignment explanation
Indices: 5479410--5479496 Score: 149
Period size: 39 Copynumber: 2.3 Consensus size: 39
5479400 GTGTACCCGA
5479410 TTACTACCCTGCAGGCCTAAAACTACCCAGCAGACCCAT
1 TTACTACCCTGCAGGCCTAAAACTACCCAGCAGACCCAT
* *
5479449 TTACTACCCAGCAGGCTTAAAACTACCCAGCAGACCCAT
1 TTACTACCCTGCAGGCCTAAAACTACCCAGCAGACCCAT
5479488 TTAC-ACCCT
1 TTACTACCCT
5479497 TGACCCAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 4 0.09
39 41 0.91
ACGTcount: A:0.31, C:0.38, G:0.11, T:0.20
Consensus pattern (39 bp):
TTACTACCCTGCAGGCCTAAAACTACCCAGCAGACCCAT
Found at i:5479495 original size:19 final size:20
Alignment explanation
Indices: 5479431--5479495 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 20
5479421 CAGGCCTAAA
5479431 ACTACCCAGCAGACCCATTT
1 ACTACCCAGCAGACCCATTT
* ** **
5479451 ACTACCCAGCAGGCTTA-AA
1 ACTACCCAGCAGACCCATTT
5479470 ACTACCCAGCAGACCCATTT
1 ACTACCCAGCAGACCCATTT
5479490 AC-ACCC
1 ACTACCC
5479496 TTGACCCAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.40, G:0.11, T:0.17
Consensus pattern (20 bp):
ACTACCCAGCAGACCCATTT
Found at i:5481533 original size:22 final size:22
Alignment explanation
Indices: 5481508--5481551 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5481498 ATTAATTACT
* *
5481508 TATTTTATACTTATATTA-TATA
1 TATTATATAATTAT-TTACTATA
5481530 TATTATATAATTATTTACTATA
1 TATTATATAATTATTTACTATA
5481552 AATATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTATATAATTATTTACTATA
Found at i:5483556 original size:11 final size:11
Alignment explanation
Indices: 5483522--5483563 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
5483512 AAATCATTTT
5483522 GAAGAGAGAAA
1 GAAGAGAGAAA
* *
5483533 GAA-AAAAAAA
1 GAAGAGAGAAA
*
5483543 GAAGGGAGAAA
1 GAAGAGAGAAA
5483554 GAAGAGAGAA
1 GAAGAGAGAA
5483564 GGGAGGGGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAAA
Found at i:5484066 original size:28 final size:29
Alignment explanation
Indices: 5484035--5484098 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
5484025 TTCTTGGTTT
5484035 TTTTTTGGGGGGTTAGG-TTTTTCTTTTC
1 TTTTTTGGGGGGTTAGGTTTTTTCTTTTC
** *
5484063 TTTTTT-TTGGGTTAGGTTTTTTCTTTTT
1 TTTTTTGGGGGGTTAGGTTTTTTCTTTTC
5484091 TTTTTTGG
1 TTTTTTGG
5484099 TTAGGTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.03, C:0.05, G:0.23, T:0.69
Consensus pattern (29 bp):
TTTTTTGGGGGGTTAGGTTTTTTCTTTTC
Found at i:5484074 original size:27 final size:25
Alignment explanation
Indices: 5484044--5484112 Score: 104
Period size: 27 Copynumber: 2.7 Consensus size: 25
5484034 TTTTTTTGGG
5484044 GGGTTAGGTTTTTCTTTTCTTTTTTTT
1 GGGTTAGGTTTTT-TTTT-TTTTTTTT
5484071 GGGTTAGGTTTTTTCTTTTTTTTTTT
1 GGGTTAGGTTTTTT-TTTTTTTTTTT
5484097 -GGTTAGGTTTTTTTTT
1 GGGTTAGGTTTTTTTTT
5484113 GGGAGGGCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
24 3 0.07
25 13 0.32
26 9 0.22
27 16 0.39
ACGTcount: A:0.04, C:0.04, G:0.20, T:0.71
Consensus pattern (25 bp):
GGGTTAGGTTTTTTTTTTTTTTTTT
Found at i:5484100 original size:25 final size:28
Alignment explanation
Indices: 5484044--5484109 Score: 104
Period size: 25 Copynumber: 2.5 Consensus size: 28
5484034 TTTTTTTGGG
5484044 GGGTTAGG-TTTTTCTTTTCTTTTTTTT
1 GGGTTAGGTTTTTTCTTTTCTTTTTTTT
5484071 GGGTTAGGTTTTTTC-TTT-TTTTTTTT
1 GGGTTAGGTTTTTTCTTTTCTTTTTTTT
5484097 -GGTTAGGTTTTTT
1 GGGTTAGGTTTTTT
5484110 TTTGGGAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
25 13 0.34
26 8 0.21
27 11 0.29
28 6 0.16
ACGTcount: A:0.05, C:0.05, G:0.21, T:0.70
Consensus pattern (28 bp):
GGGTTAGGTTTTTTCTTTTCTTTTTTTT
Found at i:5484972 original size:30 final size:30
Alignment explanation
Indices: 5484936--5484993 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5484926 TTTTGAAAAA
*
5484936 CAGAAATTAAAAAACTTAACTCAACTCTCG
1 CAGAAATTAAAAAACTCAACTCAACTCTCG
* *
5484966 CAGAAATTAAAAAGCTCAACTCACCTCT
1 CAGAAATTAAAAAACTCAACTCAACTCT
5484994 AGCAATATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.45, C:0.26, G:0.07, T:0.22
Consensus pattern (30 bp):
CAGAAATTAAAAAACTCAACTCAACTCTCG
Found at i:5485110 original size:13 final size:13
Alignment explanation
Indices: 5485092--5485126 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
5485082 ATGAGTTGAT
5485092 TTTTGAAAACAGA
1 TTTTGAAAACAGA
5485105 TTTTGAAAACAGA
1 TTTTGAAAACAGA
5485118 TTTTGAAAA
1 TTTTGAAAA
5485127 TACCTCGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (13 bp):
TTTTGAAAACAGA
Found at i:5485315 original size:77 final size:75
Alignment explanation
Indices: 5485105--5485430 Score: 324
Period size: 77 Copynumber: 4.3 Consensus size: 75
5485095 TGAAAACAGA
** * * * *
5485105 TTTTGAAAACAGATTTTGAAAATACCTC-GACATGTGA-CCCGAGGCTCAACTCACATCTCGCAA
1 TTTTGAAAACAGAAATTGAAAATACCTCAGGC--GTGATCTCAAGGCTCAACTCACCTCTCGCAA
*
5485168 TGTGAGTTGATTTT
64 TATGAGTTGA--TT
* * * *
5485182 TTTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGC
1 TTTTG-AAAACAGAAATTG--AAAATACCTCAG-GCGTGATCTCAAGGCTCAACTCACCTCTCGC
5485246 AATATGAGTTGATTT
62 AATATGAGTTGA-TT
* *
5485261 TTTTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGC-CAAGGCTCAACTCACCTCTCGCAA
1 TTTTGAAA-ACAGAAATTGAAAATACCTCAG-GCGTGATCTCAAGGCTCAACTCACCTCTCGCAA
*
5485325 TATAAGTTGATT
64 TATGAGTTGATT
* ** **
5485337 TTTTGAAAACAGAAATTGAAAATACCTCA-ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATA
1 TTTTGAAAACAGAAATTGAAAATACCTCAGGCGTGATCTCAAGGCTCAACTCACCTCTCGCAATA
*
5485400 TGAGTTGA-A
66 TGAGTTGATT
5485409 TTTTGAAAACAGAAATTGAAAA
1 TTTTGAAAACAGAAATTGAAAA
5485431 ATAGAAATTG
Statistics
Matches: 212, Mismatches: 28, Indels: 23
0.81 0.11 0.09
Matches are distributed among these distances:
72 23 0.11
73 33 0.16
75 20 0.09
76 12 0.06
77 51 0.24
78 12 0.06
79 16 0.08
80 42 0.20
81 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (75 bp):
TTTTGAAAACAGAAATTGAAAATACCTCAGGCGTGATCTCAAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATT
Found at i:5485339 original size:244 final size:249
Alignment explanation
Indices: 5484768--5485358 Score: 772
Period size: 254 Copynumber: 2.4 Consensus size: 249
5484758 AACAGACATT
*
5484768 AAAAACAGAAATTGAAAATAGCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
** * * ** *
5484833 TTGATTTTTTG-AAACTTAACTTGAAAAGCAGATTTTGAAAATACCTCAATATGTGACTGGAGGT
66 TTGATTTTTTGAAAACAGAAATTGAAAAGCAGATTTTGAAAATACCTCAACATGTGACCCGAGGC
*
5484897 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAACTTAACTCAACT
131 TCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAAC-TAACTCAACT
5484962 CTCGCAGAAATTAAAAAGCTCAACTCACCTCTAGCAATATGAGTTGAATTTTTTTGAAAA
195 CTCGCAG-AATT-AAAAGCTCAACTCACCTCTAGCAATATGAGTTGAATTTTTTTG---A
* * *
5485022 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCTAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
** *
5485087 TTGA-TTTTTGAAAACAGATTTTGAAAA-CAGATTTTGAAAATACCTCGACATGTGACCCGAGGC
66 TTGATTTTTTGAAAACAGAAATTGAAAAGCAGATTTTGAAAATACCTCAACATGTGACCCGAGGC
* * * *
5485150 TCAACTCACATCTCGCAATGTGAGTTGATTTTTTTTGAAAAATATAAATTGAAAAAA-TACCTC-
131 TCAACTCACATCTCGCAATATGAGTTGA---TTTTTGAAAAACAGAAATT-AAAAAACTAACTCA
* * * * *
5485213 AGTGT-G-TG-ATCT-GAAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTG-
192 ACTCTCGCAGAAT-TAAAAGCTCAACTCACCTCTAGCAATATGAGTTGAATTTTTTTGA
* *
5485266 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
5485331 TTGATTTTTTGAAAACAGAAATTGAAAA
66 TTGATTTTTTGAAAACAGAAATTGAAAA
5485359 TACCTCAACG
Statistics
Matches: 300, Mismatches: 30, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
244 64 0.21
245 21 0.07
248 9 0.03
249 30 0.10
250 2 0.01
251 1 0.00
252 1 0.00
253 64 0.21
254 80 0.27
255 5 0.02
256 17 0.06
257 6 0.02
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (249 bp):
AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAAACAGAAATTGAAAAGCAGATTTTGAAAATACCTCAACATGTGACCCGAGGC
TCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAACTAACTCAACTC
TCGCAGAATTAAAAGCTCAACTCACCTCTAGCAATATGAGTTGAATTTTTTTGA
Found at i:5485445 original size:13 final size:13
Alignment explanation
Indices: 5485411--5485446 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
5485401 GAGTTGAATT
*
5485411 TTGAAAACAGAAA
1 TTGAAAATAGAAA
5485424 TTGAAAAATAGAAA
1 TTG-AAAATAGAAA
5485438 TTGAAAATA
1 TTGAAAATA
5485447 CCTCGGCGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.61, C:0.03, G:0.14, T:0.22
Consensus pattern (13 bp):
TTGAAAATAGAAA
Found at i:5485565 original size:84 final size:82
Alignment explanation
Indices: 5485374--5486203 Score: 518
Period size: 88 Copynumber: 9.7 Consensus size: 82
5485364 CAACGTGTCT
** *
5485374 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAAAATAGAAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG---AATA-AAA
*
5485438 TTGAAAATACCTCGGCGTGTGATC
62 --AAAAATACCTC-GCGTGTGATC
* * *
5485462 TGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAGTAAAAAAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA-TAAAAAAA
*
5485527 AATACCTCAGTGTGTGATC
65 AATACCTC-GCGTGTGATC
* * *
5485546 TGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAAACGGA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTGAATAA---A
5485611 AATTGAAAATACCTCGACGTGTGATC
61 AA---AAAATACCTCG-CGTGTGATC
*
5485637 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG--------A
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTGAATAAAAAA
* * *
5485694 AAATAGCTCAGCGCGTGAGC
64 AAATACCTC-GCGTGTGATC
** * * ** *
5485714 CAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTAAAGGCAGAAATTGAAAAACGA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAACAGAAATTG-AATA--A
*
5485779 AAATTGAAAATACCTCGGCGTGTGACC
60 AAA---AAAATACCTC-GCGTGTGATC
* * * *
5485806 TGAGGCTCAACTCGCCGCTCGCAATAGGAGTTGACTTTTTTG-ACAACAGAAATTG--------A
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTGAATAAAAAA
* *
5485862 AATTACCTCAGCGTGT--CC
64 AAATACCTC-GCGTGTGATC
** *
5485880 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAACG
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAAAACAGAAATTGAATAA--
*
5485945 GAAATTGAAAATACCTCGGCGTGTGACC
60 -AAA---AAAATACCTC-GCGTGTGATC
* * * * * *
5485973 TGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTCTTTCAAAAACATAATAATGAAAACAGAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGAAAAACAGAA-ATTGAATA-A-AA
* *
5486038 ATTGAAAATACCTCG-GCGTGACC
62 A---AAAATACCTCGCGTGTGATC
* * * * * *
5486061 TGAGGCTTAACTCACCTCTCGCAATATGAGCTGATTCTTTCAAAAACATAATAATGAAGACAGAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGAAAAACAGAA-ATTGAATA-A-AA
* *
5486126 ATTGAAAATACCTCG-GCGTGACC
62 A---AAAATACCTCGCGTGTGATC
*
5486149 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
5486204 ATTACCTCAG
Statistics
Matches: 624, Mismatches: 69, Indels: 101
0.79 0.09 0.13
Matches are distributed among these distances:
74 33 0.05
76 22 0.04
77 57 0.09
78 21 0.03
84 51 0.08
85 7 0.01
86 32 0.05
87 5 0.01
88 163 0.26
89 14 0.02
90 38 0.06
91 101 0.16
92 46 0.07
93 34 0.05
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (82 bp):
TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAATAAAAAAAA
ATACCTCGCGTGTGATC
Found at i:5485604 original size:14 final size:14
Alignment explanation
Indices: 5485585--5485619 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5485575 GTTGATTTTT
*
5485585 TTGAAAGACAGAAA
1 TTGAAAAACAGAAA
*
5485599 TTGAAAAACGGAAA
1 TTGAAAAACAGAAA
5485613 TTGAAAA
1 TTGAAAA
5485620 TACCTCGACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:5485646 original size:91 final size:89
Alignment explanation
Indices: 5485342--5485696 Score: 458
Period size: 91 Copynumber: 4.0 Consensus size: 89
5485332 TGATTTTTTG
* * **
5485342 AAAACAGAAATTGAAAATACCTCAACGTGT-CT-TGAGGCTCAACTCATTTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
5485405 TGAATTTTGAAA-ACAGAAATTGA
66 TGATTTTTGAAAGACAGAAATTGA
* * *
5485428 AAAATAGAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCAACTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
5485493 TGATTTTTGAAAAATATAAATTGA
66 TGATTTTTGAAAGACAGAAATTGA
** * *
5485517 AGTA-A-AAA---AAAATACCTC-AGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAG
1 AAAACAGAAATTGAAAATACCTCGA-CGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAG
5485576 TTGATTTTTTTGAAAGACAGAAATTGA
65 TTGA--TTTTTGAAAGACAGAAATTGA
*
5485603 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
5485668 TGATTTTTTTGAAAGACAGAAATTGA
66 TGA--TTTTTGAAAGACAGAAATTGA
5485694 AAA
1 AAA
5485697 TAGCTCAGCG
Statistics
Matches: 234, Mismatches: 23, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
84 50 0.21
86 47 0.20
87 4 0.02
88 44 0.19
89 11 0.05
91 77 0.33
92 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (89 bp):
AAAACAGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTGAAAGACAGAAATTGA
Found at i:5485680 original size:413 final size:399
Alignment explanation
Indices: 5485023--5486237 Score: 1072
Period size: 413 Copynumber: 2.9 Consensus size: 399
5485013 TTTTGAAAAA
* ** *
5485023 AAAACAGAAATTGAAAATAGCTCAGCACGTGAGCTAAGGCTCAACTC-ACTTCTCGCAATATGAG
1 AAAACAGAAATTGAAAATACCTCAG--CGTGTCCTGAGGCTCAACTCAAC-TCTCGCAATATGAG
** ** * * *
5485087 TTGA-TTTTTG-AAAACAGATTTTGAAAACAGATTTTGAAAATACCTC-GACATGTGACCCGAGG
63 TTGATTTTTTGAAAAACAGAAATTGAAAA-AGA-AAT-AAAATACCTCAG-CGTGTGACCTGAAG
* ** **** **
5485149 CTCAACTCACATCTCGCAATGTGAGTTGATT-TTTTTTGAA-A-AAT-AT--AAATTG-AA---A
124 CTCAACTCACCTCTCGCAATACGAGTTGATTCTTTCAAAAACAGAATAATGAAAACAGAAATTGA
* *
5485204 AAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
189 AAATACCTC-GAGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
*
5485269 GACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATAAGTTG
253 GACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
5485334 ATTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAAT
318 ATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAAT
*
5485399 ATGAGTTGAATTTTGAAAACAGAAATTG
383 AGGAGTTGAATTTT-----------TTG
* * *
5485427 AAAAATAGAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCAACTCTCGCAATATGAG
1 -AAAACAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCAACTCTCGCAATATGAG
* * * * *
5485492 TTGA-TTTTTGAAAAATATAAATTGAAGTAA-AAA-AAAATACCTCAGTGTGTGATCTGAAGCTC
63 TTGATTTTTTGAAAAACAGAAATTGAA-AAAGAAATAAAATACCTCAGCGTGTGACCTGAAGCTC
* * * * * *
5485554 AACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAA-ATTGAAAAACGGAAATTGAA
127 AACTCACCTCTCGCAATACGAGTTGA-TTCTTTCAAAAACAGAATAATG-AAAACAGAAATTGAA
5485618 AATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAG
190 AATACCTCGA-GTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAG
*
5485683 ACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGA
254 ACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * *
5485748 TTTTTTTTTAAAGGCAGAAATTGAAAAACGAAAATTGAAAATACCTCGGCGTGTGACCTGAGGCT
319 ---TTTTTT-------G--A---AAACA-G-AAATTGAAAATACCTCAGCGTGT--CTTGAGGCT
**** *
5485813 CAACTCGCCGCTCGCAATAGGAGTTGACTTTTTTG
365 CAACTCATTTCTCGCAATAGGAGTTGAATTTTTTG
* * *
5485848 ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAACTCTCGCAATATGAGTTG
** * *
5485913 ATTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGG
66 A---TTTTTTGAAAAACAGAAATTGAAAAA--GAAA-T-AAAATACCTCAGCGTGTGACCTGAAG
* *
5485978 CTCAACTCGCCTCTCGCAATACGAGTTGATTCTTTCAAAAACATAATAATGAAAACAGAAATTGA
124 CTCAACTCACCTCTCGCAATACGAGTTGATTCTTTCAAAAACAGAATAATGAAAACAGAAATTGA
* * * *
5486043 AAATACCTCG-GCGTGACCTGAGGCTTAACTCACCTCTCGCAATATGAGCTGATTCTTTCAAAAA
189 AAATACCTCGAGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTT------
* * *
5486107 CATAATAATGAAGACAGAAATTGAAAATACCTC-G-GCGTGA-CCTGAGGCTCAACTCACCTCTC
247 --T--TGA--AAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTC
* * *
5486169 GCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCCTGTCTTGAGGCTCAACT
305 GCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACT
5486233 CATTT
370 CATTT
5486238 TGAACAGAAA
Statistics
Matches: 664, Mismatches: 83, Indels: 116
0.77 0.10 0.13
Matches are distributed among these distances:
402 46 0.07
403 7 0.01
404 4 0.01
405 61 0.09
406 17 0.03
407 1 0.00
409 4 0.01
410 2 0.00
412 1 0.00
413 126 0.19
415 14 0.02
416 6 0.01
417 20 0.03
418 35 0.05
419 4 0.01
420 26 0.04
421 5 0.01
422 19 0.03
423 1 0.00
424 44 0.07
425 4 0.01
426 36 0.05
427 52 0.08
428 4 0.01
429 1 0.00
430 21 0.03
431 4 0.01
432 34 0.05
433 1 0.00
434 2 0.00
435 39 0.06
436 1 0.00
437 22 0.03
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (399 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAACTCTCGCAATATGAGTTG
ATTTTTTGAAAAACAGAAATTGAAAAAGAAATAAAATACCTCAGCGTGTGACCTGAAGCTCAACT
CACCTCTCGCAATACGAGTTGATTCTTTCAAAAACAGAATAATGAAAACAGAAATTGAAAATACC
TCGAGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAA
TTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG
AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATAGGAGTTG
AATTTTTTG
Found at i:5485726 original size:77 final size:78
Alignment explanation
Indices: 5485599--5485774 Score: 239
Period size: 77 Copynumber: 2.3 Consensus size: 78
5485589 AAGACAGAAA
* * * * **
5485599 TTGAAAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAGACAGAAATTGAAAATACCTCGACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
*
5485664 GAGTTGA-TTTTT
66 GAGTCGATTTTTT
*
5485676 TTGAAAGACAGAAATTGAAAATAGCTC-AGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAGACAGAAATTGAAAATACCTCGA-CGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATA
5485740 TGAGTCGATTTTTT
65 TGAGTCGATTTTTT
* *
5485754 TTTAAAGGCAGAAATTGAAAA
1 TTGAAAGACAGAAATTGAAAA
5485775 ACGAAAATTG
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
76 1 0.01
77 62 0.71
78 24 0.28
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (78 bp):
TTGAAAGACAGAAATTGAAAATACCTCGACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
GAGTCGATTTTTT
Found at i:5485902 original size:74 final size:75
Alignment explanation
Indices: 5485779--5485920 Score: 214
Period size: 74 Copynumber: 1.9 Consensus size: 75
5485769 TGAAAAACGA
* *
5485779 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATAGGAGTTGACTTT
1 AAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCGCTCGCAATAGGAGTTGACTTT
5485844 TTTGACAACAG
65 TTTGACAACAG
* * * *
5485855 AAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATAGGAGTTGACTTTT
5485919 TT
66 TT
5485921 TTGAAAGGCA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 39 0.65
76 21 0.35
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (75 bp):
AAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATAGGAGTTGACTTTT
TTGACAACAG
Found at i:5485922 original size:76 final size:75
Alignment explanation
Indices: 5485779--5485941 Score: 213
Period size: 74 Copynumber: 2.1 Consensus size: 75
5485769 TGAAAAACGA
* *
5485779 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATAGGAGTTGACTTT
1 AAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCGCTCGCAATAGGAGTTGACTTT
5485844 TTTGACAA-CAG
65 TTTGA-AAGCAG
* * * *
5485855 AAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATAGGAGTTGA--CTT
5485919 TTTTGAAAGGCAG
64 TTTTGAAA-GCAG
5485932 AAATTGAAAA
1 AAATTGAAAA
5485942 ACGGAAATTG
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
74 33 0.43
75 2 0.03
76 29 0.38
77 12 0.16
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (75 bp):
AAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATAGGAGTTGACTTTT
TTGAAAGCAG
Found at i:5485926 original size:336 final size:326
Alignment explanation
Indices: 5485263--5486234 Score: 1075
Period size: 336 Copynumber: 2.9 Consensus size: 326
5485253 GTTGATTTTT
* * * * *
5485263 TTGAAAGACAGAAATTGAAAATAGCTC-AGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACGGAAATTGAAAATACCTCGA-CGTGTGA-CCTGAGGCTCAACTCACCTCTCGCAAT
* * * * *
5485326 ATAAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTCA-ACGTGTCTTGAGGCTCAACTCAT
64 ATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAGGCGTGAC-CGAGGCTCAACTCAC
* * * * *
5485389 TTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAAAATAGAAATTGAAAATACCTCGG
128 CTCTCGCAATATGAGTCGATTTTTTCAAAACAGAAATTGAAAAACAGAAATTGAAAATACCTCGG
* * * *
5485453 CGTGTGATCTGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAA
193 CGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATT---
* * * *
5485518 GTAAAAAAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTT
254 G------AAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
5485583 TTTTGAAAGACAGAAA
311 TTTTGAAAGACAGAAA
*
5485599 TTGAAAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
* *
5485664 GAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCAC
66 GAGTTGATTTTTTTGAAA-ACAGAAATTGAAAATACCTCAG-GCGTGA-CCGAGGCTCAACTCAC
* *
5485729 CTCTCGCAATATGAGTCGATTTTTTTTTAAAGGCAGAAATTGAAAAAC-GAAAATTGAAAATACC
128 CTCTCGCAATATGAGTCGA--TTTTTTCAAA-ACAGAAATTGAAAAACAG-AAATTGAAAATACC
* * * *
5485793 TCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATAGGAGTTGACTTTTTTGACAACAGAAA
189 TCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAA
5485858 TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTT
252 TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTT
*
5485923 GAAAGGCAGAAA
315 GAAAGACAGAAA
* * *
5485935 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATAC
1 TTGAAAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
5486000 GAGTTGATTCTTTCAAAAACATAATAATGAAAACAGAAATTGAAAATACCTC-GGCGTGACCTGA
66 GAGTTGA-T-TTT--------T--T--TGAAAACAGAAATTGAAAATACCTCAGGCGTGACC-GA
* * * * *
5486064 GGCTTAACTCACCTCTCGCAATATGAG-CTGATTCTTTCAAAAACATAATAATG-AAGACAGAAA
116 GGCTCAACTCACCTCTCGCAATATGAGTC-GATTTTTTC-AAAACAGAA-ATTGAAAAACAGAAA
*
5486127 TTGAAAATACCTCGGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA
178 TTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
* *
5486190 AAACAGAAATTGAAATTACCTCAGCCTGTCTTGAGGCTCAACTCA
243 AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCA
5486235 TTTTGAACAG
Statistics
Matches: 549, Mismatches: 52, Indels: 65
0.82 0.08 0.10
Matches are distributed among these distances:
334 34 0.06
335 1 0.00
336 162 0.30
337 12 0.02
338 23 0.04
340 33 0.06
341 49 0.09
342 1 0.00
343 45 0.08
344 70 0.13
345 41 0.07
346 17 0.03
347 35 0.06
348 2 0.00
349 19 0.03
350 5 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (326 bp):
TTGAAAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAGGCGTGACCGAGGCTCAACTCACCTC
TCGCAATATGAGTCGATTTTTTCAAAACAGAAATTGAAAAACAGAAATTGAAAATACCTCGGCGT
GTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTA
CCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAA
A
Found at i:5486084 original size:181 final size:176
Alignment explanation
Indices: 5485850--5486182 Score: 470
Period size: 181 Copynumber: 1.9 Consensus size: 176
5485840 CTTTTTTGAC
* * *
5485850 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-
* * ** * *
5485915 TTTTTTTTGAAAGGCAGAA-ATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
65 --TTCTTTCAAAAACAGAATAATG-AAAACAGAAATTGAAAATACCTCGGC--GTGACCTGAGGC
*
5485979 TCAACTCGCCTCTCGCAATACGAGTTGATTCTTTCAAAAACATAATAATGAA
125 TCAACTCACCTCTCGCAATACGAGTTGATTCTTTCAAAAACATAATAATGAA
* *
5486031 AACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTTAACTCACCTCTCGCAATATGAGCTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
* *
5486096 TCTTTCAAAAACATAATAATGAAGACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACT
66 TCTTTCAAAAACAGAATAATGAAAACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACT
*
5486161 CACCTCTCGCAATATGAGTTGA
131 CACCTCTCGCAATACGAGTTGA
5486183 ATTTTGAAAA
Statistics
Matches: 136, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
176 38 0.28
178 36 0.26
179 3 0.02
181 59 0.43
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (176 bp):
AACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
TCTTTCAAAAACAGAATAATGAAAACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACT
CACCTCTCGCAATACGAGTTGATTCTTTCAAAAACATAATAATGAA
Found at i:5486248 original size:49 final size:49
Alignment explanation
Indices: 5486191--5486286 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
5486181 GAATTTTGAA
*
5486191 AACAGAAATTGAAATTACCTCAGCCTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATTACCTCAACCTGTCTTGAGGCTCAACTCATTTTG
*
5486240 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAATTACCTCAACCTGTCTTGAGGCTCAACTCATTT
5486287 CTCGCAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (49 bp):
AACAGAAATTGAAATTACCTCAACCTGTCTTGAGGCTCAACTCATTTTG
Found at i:5486320 original size:72 final size:72
Alignment explanation
Indices: 5486240--5486463 Score: 281
Period size: 72 Copynumber: 3.0 Consensus size: 72
5486230 ACTCATTTTG
5486240 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
5486305 TTTTGAA
66 TTTTGAA
5486312 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-
*
5486377 TTTTTTTTGAA
65 ---ATTTTGAA
* ** * * ** *
5486388 AGACAGAAATTGAAAATACCTCAGCATATGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAGC
1 A-ACAGAAATTGAAATTACCTCA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
5486452 TG-ATTTTGAA
62 TGAATTTTGAA
5486462 AA
1 AA
5486464 AGTAGAAATT
Statistics
Matches: 134, Mismatches: 10, Indels: 15
0.84 0.06 0.09
Matches are distributed among these distances:
72 64 0.48
73 1 0.01
74 8 0.06
76 8 0.06
77 20 0.15
79 32 0.24
80 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:5486341 original size:121 final size:121
Alignment explanation
Indices: 5486120--5486358 Score: 397
Period size: 121 Copynumber: 2.0 Consensus size: 121
5486110 AATAATGAAG
**
5486120 ACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAT
1 ACAGAAATTGAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAT
*
5486185 TTTGAAAACAGAAATTGAAATTACCTCAGCCTGTCTTGAGGCTCAACTCATTTTGA
66 TTTGAAAACAGAAATTGAAATTACCTCAACCTGTCTTGAGGCTCAACTCATTTTGA
* * * **
5486241 ACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 ACAGAAATTGAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAT
*
5486306 TTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
66 TTTGAAAACAGAAATTGAAATTACCTCAACCTGTCTTGAGGCTCAACTCATTT
5486359 CTCGCAATAT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 109 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (121 bp):
ACAGAAATTGAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAT
TTTGAAAACAGAAATTGAAATTACCTCAACCTGTCTTGAGGCTCAACTCATTTTGA
Found at i:5486527 original size:54 final size:54
Alignment explanation
Indices: 5486427--5486532 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
5486417 GAACCGAGGC
*
5486427 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
5486481 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
5486533 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:5486593 original size:140 final size:141
Alignment explanation
Indices: 5486383--5486731 Score: 612
Period size: 141 Copynumber: 2.5 Consensus size: 141
5486373 TGATTTTTTT
5486383 TTGAAAGACAGAAATTGAAAATACCTCAGCATATGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--ATG-ACCTGAGGCTCAACTCACCTCTCGCAATA
5486447 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCC-ACCTCTCGCAATATGAGTTGATT
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCAACCTCTCGCAATATGAGTTGATT
5486511 CTTGAACAACGTAAA
127 CTTGAACAACGTAAA
5486526 TTGAAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
5486591 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCAACCTCTCGCAATATGAGTTGATTCTTG
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCAACCTCTCGCAATATGAGTTGATTCTTG
*
5486656 AACAATGTAAA
131 AACAACGTAAA
* * *
5486667 TTGCAAACAGAAATTGAAAATACCTCATCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
5486732 TTAAAATTAA
Statistics
Matches: 200, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
139 3 0.01
140 69 0.34
141 99 0.50
142 23 0.12
143 6 0.03
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (141 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCAACCTCTCGCAATATGAGTTGATTCTTG
AACAACGTAAA
Found at i:5486788 original size:72 final size:72
Alignment explanation
Indices: 5486671--5486829 Score: 230
Period size: 72 Copynumber: 2.2 Consensus size: 72
5486661 TGTAAATTGC
* * * *
5486671 AAACAGAAATTGAAAATACCTCATCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAA
1 AAACAAAAATTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAA
5486736 AATTAAA
66 AATTAAA
* *
5486743 AAACAAAAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGA
1 AAACAAAAATTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAA
** *
5486808 TTTTGAA
66 AATTAAA
5486815 AAACAAAAATT-AAAA
1 AAACAAAAATTGAAAA
5486830 GGCTTAACTC
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 4 0.05
72 74 0.95
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (72 bp):
AAACAAAAATTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAA
AATTAAA
Found at i:5486905 original size:122 final size:123
Alignment explanation
Indices: 5486704--5486949 Score: 372
Period size: 122 Copynumber: 2.0 Consensus size: 123
5486694 TCGTGACCTG
* *
5486704 AGGCTCAACTCACCTCTCGCAATATGAGTTAAAATTAAAAAACAAAAATTGAAAATACCTCAACG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTAAAATTAAAAAACAAAAACTAAAAATACCTCAACG
5486769 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTG-AAAACAAAAATTAAA
* * * * *
5486829 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATT-TAAAACATAAACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTAAAATTAAAAAACAAAAACTAAAAATACCTCAACG
* *
5486891 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTGAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTGAAAACAAAAATTAAA
5486949 A
1 A
5486950 ATACCTCAAC
Statistics
Matches: 112, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
120 16 0.14
121 4 0.04
122 60 0.54
123 4 0.04
124 1 0.01
125 27 0.24
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (123 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTAAAATTAAAAAACAAAAACTAAAAATACCTCAACG
TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTGAAAACAAAAATTAAA
Found at i:5486971 original size:70 final size:69
Alignment explanation
Indices: 5486829--5487002 Score: 233
Period size: 70 Copynumber: 2.5 Consensus size: 69
5486819 AAAAATTAAA
* * ** * *
5486829 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAACAAAAACTAAAAATACCTCAACGTGC
5486894 CCCG
66 CCCG
*
5486898 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTGAAAACAAAAATTAAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTT-AAAACAAAAACTAAAAATACCTCAACGTG
* **
5486963 TCTTG
65 CCCCG
5486968 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
5487003 CCCTTGAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
69 32 0.34
70 61 0.66
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (69 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAACAAAAACTAAAAATACCTCAACGTGC
CCCG
Found at i:5495208 original size:12 final size:12
Alignment explanation
Indices: 5495188--5495223 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5495178 TGGGATATGC
*
5495188 AATGTATGAATG
1 AATGCATGAATG
5495200 AATGCATGAATG
1 AATGCATGAATG
5495212 AATGCATGAATG
1 AATGCATGAATG
5495224 TCAAAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:5497275 original size:13 final size:13
Alignment explanation
Indices: 5497253--5497294 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5497243 CTAATGGCAT
5497253 TAAA-AATATATA
1 TAAATAATATATA
*
5497265 TACATAATATATA
1 TAAATAATATATA
5497278 TAAAATACATATATA
1 T-AAATA-ATATATA
5497293 TA
1 TA
5497295 TACGTATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 3 0.12
13 9 0.36
14 5 0.20
15 8 0.32
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATAATATATA
Found at i:5497278 original size:15 final size:16
Alignment explanation
Indices: 5497258--5497297 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
5497248 GGCATTAAAA
5497258 ATATATATACATA-AT
1 ATATATATACATACAT
*
5497273 ATATATA-AAATACAT
1 ATATATATACATACAT
5497288 ATATATATAC
1 ATATATATAC
5497298 GTATTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 4 0.19
15 16 0.76
16 1 0.05
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATATATACATACAT
Found at i:5497634 original size:11 final size:11
Alignment explanation
Indices: 5497600--5497641 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
5497590 AAATCATTTT
5497600 GAAGAGAGAAA
1 GAAGAGAGAAA
* *
5497611 GAA-AAAAAAA
1 GAAGAGAGAAA
*
5497621 GAAGGGAGAAA
1 GAAGAGAGAAA
5497632 GAAGAGAGAA
1 GAAGAGAGAA
5497642 GGGAGGGGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAAA
Found at i:5498149 original size:25 final size:22
Alignment explanation
Indices: 5498113--5498185 Score: 105
Period size: 20 Copynumber: 3.4 Consensus size: 22
5498103 GGTTTCTTGG
**
5498113 TTTTTTTTTTTTGGGGTTAGGT
1 TTTTTTTTTTTTTTGGTTAGGT
5498135 TTTTCTTTTTTTTTTGGTTAGG-
1 TTTT-TTTTTTTTTTGGTTAGGT
5498157 -TTTTTTTTTTTTTGGTTAGGT
1 TTTTTTTTTTTTTTGGTTAGGT
5498178 TTTTTTTT
1 TTTTTTTT
5498186 GGGGAGGGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
20 17 0.37
21 3 0.07
22 11 0.24
23 15 0.33
ACGTcount: A:0.04, C:0.01, G:0.19, T:0.75
Consensus pattern (22 bp):
TTTTTTTTTTTTTTGGTTAGGT
Found at i:5499615 original size:13 final size:13
Alignment explanation
Indices: 5499597--5499624 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5499587 AAAAAATTTA
5499597 TTGATATTTTTTG
1 TTGATATTTTTTG
5499610 TTGATATTTTTTG
1 TTGATATTTTTTG
5499623 TT
1 TT
5499625 ATGAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (13 bp):
TTGATATTTTTTG
Found at i:5506539 original size:19 final size:21
Alignment explanation
Indices: 5506494--5506554 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
5506484 TTTTAAATTC
*
5506494 AAAAAATTTATAAAATTATTT
1 AAAAAATATATAAAATTATTT
* *
5506515 ATAAAATAT-TAAATTTA-TT
1 AAAAAATATATAAAATTATTT
5506534 AAAAAAGTATATAAAA-TATTT
1 AAAAAA-TATATAAAATTATTT
5506555 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 7 0.22
20 12 0.38
21 13 0.41
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAAATATATAAAATTATTT
Found at i:5507939 original size:41 final size:40
Alignment explanation
Indices: 5507840--5508018 Score: 227
Period size: 41 Copynumber: 4.4 Consensus size: 40
5507830 GCGTTTGAAA
* *
5507840 CAAAACGCCGCTAAAAACTGAGCAATAGTGGCGTTTTTTATC
1 CAAAACGCCGCAAAAAACTGAG-AATAGTGGCG-TTTTCATC
*
5507882 CAAAACGCCGCTAAAAACTGAGTAATAGTGGCGTTTTCATC
1 CAAAACGCCGCAAAAAACTGAG-AATAGTGGCGTTTTCATC
*
5507923 CAAAACGCCGCAAAAAACTGAGAAATAGTGGCGTTTT-ATT
1 CAAAACGCCGCAAAAAACTGAG-AATAGTGGCGTTTTCATC
* *
5507963 CAAAACGCCGCAAAAAACTGAGATATAGTGGCGCTTTCGTTC
1 CAAAACGCCGCAAAAAACTGAGA-ATAGTGGCGTTTTC-ATC
*
5508005 C-AAACGCCACAAAA
1 CAAAACGCCGCAAAA
5508019 GGTTGAGCTA
Statistics
Matches: 125, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 36 0.29
41 54 0.43
42 34 0.27
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (40 bp):
CAAAACGCCGCAAAAAACTGAGAATAGTGGCGTTTTCATC
Found at i:5507994 original size:81 final size:83
Alignment explanation
Indices: 5507840--5508018 Score: 249
Period size: 81 Copynumber: 2.2 Consensus size: 83
5507830 GCGTTTGAAA
* * *
5507840 CAAAACGCCGCTAAAAACTGAGCAATAGTGGCGTTTTTTATCCAAAACGCCGCTAAAAACTGAGT
1 CAAAACGCCGCAAAAAACTGAGAAATAGTGGCG-TTTTTATCCAAAACGCCGCAAAAAACTGAGT
*
5507905 AATAGTGGCGTTTTC-ATC
65 AATAGTGGCGCTTTCGATC
*
5507923 CAAAACGCCGCAAAAAACTGAGAAATAGTGGCG-TTTTATTCAAAACGCCGCAAAAAACTGAG-A
1 CAAAACGCCGCAAAAAACTGAGAAATAGTGGCGTTTTTATCCAAAACGCCGCAAAAAACTGAGTA
*
5507986 TATAGTGGCGCTTTCGTTC
66 -ATAGTGGCGCTTTCGATC
*
5508005 C-AAACGCCACAAAA
1 CAAAACGCCGCAAAA
5508019 GGTTGAGCTA
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
80 1 0.01
81 52 0.60
82 3 0.03
83 31 0.36
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (83 bp):
CAAAACGCCGCAAAAAACTGAGAAATAGTGGCGTTTTTATCCAAAACGCCGCAAAAAACTGAGTA
ATAGTGGCGCTTTCGATC
Found at i:5509822 original size:131 final size:130
Alignment explanation
Indices: 5509435--5509903 Score: 487
Period size: 131 Copynumber: 3.6 Consensus size: 130
5509425 GAAGAACCGA
* *
5509435 AACCCAGCACAG-TAGGGCACGATTCCTCGAATTGCCAAATGTCGAATACCGCCTTTGTTTTAAA
1 AACCCAGCAC-GTTAGGGCACGATT-CGCGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAA
* * * * * * *
5509499 GGA-TTTAAAAAAAATGAATGAAAACCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATC
64 GGATTTTAAAAGACATGAATGAAAATCTAAAGGGATATTCGATTATTTTGAGCAAACGAGAAATT
*
5509563 AC
129 GC
* * * * * * * *** *
5509565 AACCCAGCACGATAGGGCATGATTCCCGAATTTGTCGAACACCGAATATTTCCTTGGTTTTAAAG
1 AACCCAGCACGTTAGGGCACGATTCGCGAA-TTGCCAAATATCGAATACCGCCTTTGTTTTAAAG
* * * * * * *
5509630 AATTTTTAGAAGACATGCATGAAATTTTTAAGGGATA-TCGGATTATTTTAAGCAAACGAGAAAT
65 GA-TTTTAAAAGACATGAATGAAAATCTAAAGGGATATTC-GATTATTTTGAGCAAACGAGAAAT
5509694 TGC
128 TGC
* * * *
5509697 AACCCAGCACGTTAGGGCATGATTTCGCGAATTGCCAAATATCGCATATCGCCTTTG-TTTAAGG
1 AACCCAGCACGTTAGGGCACGA-TTCGCGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAAG
** * * *
5509761 GATCTTTAAAAGACATGGGTGAAAATCTAAAGGGACATTCAATTACTTTGAGCAAACGAGAAATT
65 GAT-TTTAAAAGACATGAATGAAAATCTAAAGGGATATTCGATTATTTTGAGCAAACGAGAAATT
5509826 GC
129 GC
5509828 AACCCAGCACGTTAGGGCACGATTCGTCGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAAG
1 AACCCAGCACGTTAGGGCACGATTCG-CGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAAG
*
5509893 GGTTTTCAAAA
65 GATTTT-AAAA
5509904 AGAATAGATA
Statistics
Matches: 275, Mismatches: 53, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
129 6 0.02
130 52 0.19
131 111 0.40
132 99 0.36
133 7 0.03
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (130 bp):
AACCCAGCACGTTAGGGCACGATTCGCGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAAGG
ATTTTAAAAGACATGAATGAAAATCTAAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGC
Found at i:5512625 original size:44 final size:43
Alignment explanation
Indices: 5512562--5513488 Score: 1001
Period size: 44 Copynumber: 21.1 Consensus size: 43
5512552 CGAGAACACC
*
5512562 AATCTG-TCATCTTTGATCTGCTCCCTGCCAATACAGAGATGCCA
1 AATCTGCT-ATCTTCGATCTGCTCCC-GCCAATACAGAGATGCCA
* *
5512606 AATCTG-TCATCTTCGATCTGCTCTCGTC-ATCACAGAGATGCCA
1 AATCTGCT-ATCTTCGATCTGCTCCCGCCAAT-ACAGAGATGCCA
* * * *
5512649 AATCTACTATCTTCGATCTGC-CCTCTGACGATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCC-C-GCCAATACAGAGATGCCA
* * *
5512693 AATCTGCTGTCTTCGATCTGCTCCCTGCCAATACAGAAACGCCA
1 AATCTGCTATCTTCGATCTGCTCCC-GCCAATACAGAGATGCCA
* *
5512737 AATCTGCTATCTTCGATCCGC-CCTCTGACAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCC-C-GCCAATACAGAGATGCCA
* * * *
5512781 AACCCGCTATTTTCGATCTGCTCTCCGCCAATACAGAGATGTCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
* * *
5512825 AATCTGC-ATCTTTGATCTGCTCTCCGACAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
*
5512868 AATCTGTTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
5512912 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
* * *
5512956 AATCTACTATCTTCGATCTGC-CCTCTGACAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCC-C-GCCAATACAGAGATGCCA
* * * *
5513000 AACCTGCTATCTTCGATCTACTCCCTGCCAATCCAGATATGCCA
1 AATCTGCTATCTTCGATCTGCTCCC-GCCAATACAGAGATGCCA
* * * *
5513044 AATCTGCTATCCTCGATCCGC-CCTCTGACAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCC-C-GCCAATACAGAGATGCCA
* * * *
5513088 AACCCGCTACCTTCGATCTACTCTCCGCCAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
* * *
5513132 AATCTG-TATCTTTGATCTACTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
** * *
5513175 AATCTATTATCTTCGATCTGCTCTCCGCCAATACAGATACGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
* *
5513219 AATCTGCTATCTTCGATCTGC-CCTCTGACAATACAGAGATGCAA
1 AATCTGCTATCTTCGATCTGCTCC-C-GCCAATACAGAGATGCCA
* *
5513263 AATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
* * * *
5513307 AATCTGTTATCTTCGATCTGCTCTACACCACTACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
* * * * * *
5513351 AATCTGCTATCTTCAATCTACTCTCTGCTAATATAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
*
5513395 AATCTGCTATCTTCGATCTGCTCTCCGCCAACACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
* *
5513439 AATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTC-CCGCCAATACAGAGATGCCA
5513483 AATCTG
1 AATCTG
5513489 TCTGGTCTTG
Statistics
Matches: 760, Mismatches: 102, Indels: 42
0.84 0.11 0.05
Matches are distributed among these distances:
42 5 0.01
43 117 0.15
44 623 0.82
45 12 0.02
46 3 0.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (43 bp):
AATCTGCTATCTTCGATCTGCTCCCGCCAATACAGAGATGCCA
Found at i:5512762 original size:88 final size:88
Alignment explanation
Indices: 5512562--5513488 Score: 1125
Period size: 88 Copynumber: 10.6 Consensus size: 88
5512552 CGAGAACACC
*
5512562 AATCTG-TCATCTTTGATCTGCTC-CCTGCCAATACAGAGATGCCAAATCTG-TCATCTTCGATC
1 AATCTGCT-ATCTTCGATCTGCTCTCC-GCCAATACAGAGATGCCAAATCTGCT-ATCTTCGATC
*
5512624 TGCTCT-CGTC-ATCACAGAGATGCCA
63 TGCTCTCCGCCAAT-ACAGAGATGCCA
* * * * * * *
5512649 AATCTACTATCTTCGATCTGCCCTCTGACGATACAGAGACGCCAAATCTGCTGTCTTCGATCTGC
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
* *
5512714 TC-CCTGCCAATACAGAAACGCCA
66 TCTCC-GCCAATACAGAGATGCCA
* * * * * * *
5512737 AATCTGCTATCTTCGATCCGCCCTCTGACAATACAGAGATGCCAAACCCGCTATTTTCGATCTGC
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
*
5512802 TCTCCGCCAATACAGAGATGTCA
66 TCTCCGCCAATACAGAGATGCCA
* * * *
5512825 AATCTGC-ATCTTTGATCTGCTCTCCGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGC
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
5512889 TCTCCGCCAATACAGAGATGCCA
66 TCTCCGCCAATACAGAGATGCCA
*
5512912 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTACTATCTTCGATCTGC
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
* * * *
5512977 CCTCTGACAATACAGAGACGCCA
66 TCTCCGCCAATACAGAGATGCCA
* * * * * *
5513000 AACCTGCTATCTTCGATCTACTC-CCTGCCAATCCAGATATGCCAAATCTGCTATCCTCGATCCG
1 AATCTGCTATCTTCGATCTGCTCTCC-GCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTG
* * * *
5513064 CCCTCTGACAATACAGAGACGCCA
65 CTCTCCGCCAATACAGAGATGCCA
* * * * * *
5513088 AACCCGCTACCTTCGATCTACTCTCCGCCAATACAGAGATGCCAAATCTG-TATCTTTGATCTAC
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
*
5513152 TCTCCGCCAATACAGAGACGCCA
66 TCTCCGCCAATACAGAGATGCCA
** * *
5513175 AATCTATTATCTTCGATCTGCTCTCCGCCAATACAGATACGCCAAATCTGCTATCTTCGATCTGC
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
* * * *
5513240 CCTCTGACAATACAGAGATGCAA
66 TCTCCGCCAATACAGAGATGCCA
* * *
5513263 AATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTATCTTCGATCTGC
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
* * *
5513328 TCTACACCACTACAGAGATGCCA
66 TCTCCGCCAATACAGAGATGCCA
* * * * * *
5513351 AATCTGCTATCTTCAATCTACTCTCTGCTAATATAGAGACGCCAAATCTGCTATCTTCGATCTGC
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
*
5513416 TCTCCGCCAACACAGAGATGCCA
66 TCTCCGCCAATACAGAGATGCCA
* *
5513439 AATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGACGCCAAATCTG
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTG
5513489 TCTGGTCTTG
Statistics
Matches: 726, Mismatches: 103, Indels: 21
0.85 0.12 0.02
Matches are distributed among these distances:
87 205 0.28
88 515 0.71
89 6 0.01
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (88 bp):
AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
TCTCCGCCAATACAGAGATGCCA
Found at i:5513067 original size:307 final size:307
Alignment explanation
Indices: 5512562--5513489 Score: 1328
Period size: 307 Copynumber: 3.0 Consensus size: 307
5512552 CGAGAACACC
* *
5512562 AATCTGTCATCTTTGATCTGCTC-CCTGCCAATACAGAGATGCCAAATCTG-TCATCTTCGATCT
1 AATCTGTTATCTTCGATCTGCTCTCC-GCCAATACAGAGATGCCAAATCTGCT-ATCTTCGATCT
* *
5512625 GCTCT-CGTC-ATCACAGAGATGCCAAATCTACTATCTTCGATCTGCCCTCTGACGATACAGAGA
64 GCTCTCCGACAAT-ACAGAGATGCCAAATCTACTATCTTCGATCTGCCCTCTGACAATACAGAGA
* *
5512688 CGCCAAATCTGCTGTCTTCGATCTGCTCCCTGCCAATACAGAAACGCCAAATCTGCTATCTTCGA
128 CGCCAAATCTGCTATCTTCGATCTGCTCCCTGCCAATACAGAAATGCCAAATCTGCTATCTTCGA
* *
5512753 TCCGCCCTCTGACAATACAGAGATGCCAAACCCGCTATTTTCGATCTGCTCTCCGCCAATACAGA
193 TCCGCCCTCTGACAATACAGAGACGCCAAACCCGCTATCTTCGATCTGCTCTCCGCCAATACAGA
* *
5512818 GATGTCAAATCTGCATCTTTGATCTGCTCTCCGACAATACAGAGACGCCA
258 GATGCCAAATCTGCATCTTTGATCTGCTCTCCGCCAATACAGAGACGCCA
5512868 AATCTGTTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
1 AATCTGTTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
*
5512933 TCTCCGCCAATACAGAGATGCCAAATCTACTATCTTCGATCTGCCCTCTGACAATACAGAGACGC
66 TCTCCGACAATACAGAGATGCCAAATCTACTATCTTCGATCTGCCCTCTGACAATACAGAGACGC
* * * * *
5512998 CAAACCTGCTATCTTCGATCTACTCCCTGCCAATCCAGATATGCCAAATCTGCTATCCTCGATCC
131 CAAATCTGCTATCTTCGATCTGCTCCCTGCCAATACAGAAATGCCAAATCTGCTATCTTCGATCC
* *
5513063 GCCCTCTGACAATACAGAGACGCCAAACCCGCTACCTTCGATCTACTCTCCGCCAATACAGAGAT
196 GCCCTCTGACAATACAGAGACGCCAAACCCGCTATCTTCGATCTGCTCTCCGCCAATACAGAGAT
* *
5513128 GCCAAATCTGTATCTTTGATCTACTCTCCGCCAATACAGAGACGCCA
261 GCCAAATCTGCATCTTTGATCTGCTCTCCGCCAATACAGAGACGCCA
* * *
5513175 AATCTATTATCTTCGATCTGCTCTCCGCCAATACAGATACGCCAAATCTGCTATCTTCGATCTGC
1 AATCTGTTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
* * * ** * * * * *
5513240 CCTCTGACAATACAGAGATGCAAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGATGC
66 TCTCCGACAATACAGAGATGCCAAATCTACTATCTTCGATCTGCCCTCTGACAATACAGAGACGC
* * * * * *
5513305 CAAATCTGTTATCTTCGATCTGCTCTAC-ACCACTACAGAGATGCCAAATCTGCTATCTTCAATC
131 CAAATCTGCTATCTTCGATCTGCTC-CCTGCCAATACAGAAATGCCAAATCTGCTATCTTCGATC
** * * * * *
5513369 TACTCTCTG-CTAATATAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCAACACAGAG
195 CGCCCTCTGAC-AATACAGAGACGCCAAACCCGCTATCTTCGATCTGCTCTCCGCCAATACAGAG
* *
5513433 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGACGCCA
259 ATGCCAAATCTGC-ATCTTTGATCTGCTCTCCGCCAATACAGAGACGCCA
5513483 AATCTGT
1 AATCTGT
5513490 CTGGTCTTGC
Statistics
Matches: 558, Mismatches: 57, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
306 62 0.11
307 454 0.81
308 42 0.08
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (307 bp):
AATCTGTTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
TCTCCGACAATACAGAGATGCCAAATCTACTATCTTCGATCTGCCCTCTGACAATACAGAGACGC
CAAATCTGCTATCTTCGATCTGCTCCCTGCCAATACAGAAATGCCAAATCTGCTATCTTCGATCC
GCCCTCTGACAATACAGAGACGCCAAACCCGCTATCTTCGATCTGCTCTCCGCCAATACAGAGAT
GCCAAATCTGCATCTTTGATCTGCTCTCCGCCAATACAGAGACGCCA
Found at i:5514386 original size:132 final size:131
Alignment explanation
Indices: 5513684--5515132 Score: 1682
Period size: 132 Copynumber: 11.0 Consensus size: 131
5513674 TATAATCTTC
* * * * *
5513684 AGCCCACTTCACTACAACTTTAGGGAGCTAGGACT--T-GCTTAAATCTGCTTCGCTGCATCTTC
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGG-TTGGTGGCTTAAATCTGCTTCACTGCAACTTC
* *** * * * * * * *
5513746 AAGAAGC-CAAGATTTATCGTCTTTGATTTCCCTCACTGCAACTTCAAGGAGACGAGATCTACAA
65 AGGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCTA-AA
* *
5513810 TCCTC
128 T-TTT
* * * * *
5513815 AGCCTACTCCACTATAACTTTAGAGAGCTAGGACT--T-GCTTAAATCTGCTTTACTGCAACATC
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGG-TTGGTGGCTTAAATCTGCTTCACTGCAACTTC
** * *
5513877 AGGAAGC-CTAGATTCGCCGTCTTCGATCTGCCCCACTGTAATCTT-AGGGAAATAAGATCTATA
65 AGGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTGCAA-CTTCAGGGAAACAAGATCTA-A
*
5513940 ATCTTC
127 AT-TTT
* ** * *
5513946 AGCCTACTCCACTACAACCTTAGGGAGCTA-G--AAT-GCTTAAATCTGCTTCGCTGCATCTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
*** * * * * * ** *
5514007 GGAAGC-CAAGATTTATCGTCTTTGATTTTCCTCACTGCAATTTCAGGGAGGCGAGATCTACAAT
66 GGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCTA-AAT
* *
5514071 CCTC
129 -TTT
** * * *
5514075 AGCCTACTCCACTACAACTTTAGAAAGCTAAGACTT-GT---TTAAATCTACTTCACTGCAACAT
1 AGCCTACTCCACTACAACTTTAGGGAGCT-AG-GTTGGTGGCTTAAATCTGCTTCACTGCAACTT
* ** *
5514136 CAAGAAGC-CTAGATTCGCCGTCTTCGATCTGCCCCACTACAA-TCTCAGGGAAACAAGATCTAT
64 CAGGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTGCAACT-TCAGGGAAACAAGATCTA-
*
5514199 AATCTTC
126 AAT-TTT
* * * *
5514206 AGCTTACTCCACTACAACCTTAGGAAGCTAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
* * * *
5514271 GGAAGCTCAGATTCGCCGTCTTCGATTTGTTTCACTGCAACTTTAGGAAAACAAGATCTGAAATT
66 GGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCT-AAATT
5514336 TT
130 TT
5514338 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
* * * * *
5514403 TGAACCTCAGATTCACCGTCTTCGATCTGTTTCACTGTAACTTCAGGGAAACAAGATCTAAAATT
66 GGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCT-AAATT
5514468 TT
130 TT
* *
5514470 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGACTTAAATCTGCTTCACTGCAACTTTA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
* * *
5514535 GGAAGCTCAGATTCGCTGTCTTCGATATGCTTCACTGCAACTTCAGGGAAACGAGATCTGAAATT
66 GGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCT-AAATT
5514600 TT
130 TT
* *
5514602 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGATGGCTTAAATCTGCTTTACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
* * * * * *
5514667 GGAAGCTCAAATTCGCCGTCTTCGATCTGTTTCATTTCAATTTCAGGGAAATAAGATCTAAAATT
66 GGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCT-AAATT
5514732 TT
130 TT
5514734 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
* * *
5514799 GGAAGCTCAGATTTGCCATCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAAATCTAAAATT
66 GGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCT-AAATT
5514864 TT
130 TT
5514866 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
* * * *
5514931 GGAAGCTCAG-TT-GCCATCTTCGATCTGCTTCATTACAACTTCAGGGAAACAAAATCTGAAATT
66 GGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCT-AAATT
5514994 TT
130 TT
* *
5514996 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGATGGCTTAAATCTACTTCACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
* *
5515061 GGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGTAACTTCAGGGAAATAAGATCTAAAATT
66 GGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCT-AAATT
5515126 TT
130 TT
5515128 AGCCT
1 AGCCT
5515133 CATAGGCTCA
Statistics
Matches: 1152, Mismatches: 147, Indels: 37
0.86 0.11 0.03
Matches are distributed among these distances:
128 2 0.00
129 100 0.09
130 130 0.11
131 232 0.20
132 611 0.53
133 74 0.06
134 3 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (131 bp):
AGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCA
GGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAGATCTAAATTT
T
Found at i:5514533 original size:43 final size:43
Alignment explanation
Indices: 5514479--5514673 Score: 113
Period size: 43 Copynumber: 4.5 Consensus size: 43
5514469 TAGCCTACTC
* *
5514479 CACTACAACTTTAGGGAGCTAGGTTGGTGACTTAAATCTGCTT
1 CACTGCAACTTTAGGGAGCTAGATTGGTGACTTAAATCTGCTT
* * * ** *
5514522 CACTGCAACTTTAGGAAGCTCAGATTCGCTGTCTTCGATATGCTT
1 CACTGCAACTTTAGGGAGCT-AGATT-GGTGACTTAAATCTGCTT
* * * ** * * ** * *
5514567 CACTGCAACTTCAGGGAAACGAGATCT-GAAATTTTAGCCTACTC
1 CACTGCAACTTTAGGG-AGCTAGAT-TGGTGACTTAAATCTGCTT
* * * *
5514611 CACTACAACTTTAGGGAGCTAGGTTGATGGCTTAAATCTGCTT
1 CACTGCAACTTTAGGGAGCTAGATTGGTGACTTAAATCTGCTT
* * *
5514654 TACTGCAACTTCAGGAAGCT
1 CACTGCAACTTTAGGGAGCT
5514674 CAAATTCGCC
Statistics
Matches: 104, Mismatches: 43, Indels: 10
0.66 0.27 0.06
Matches are distributed among these distances:
42 1 0.01
43 46 0.44
44 23 0.22
45 31 0.30
46 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (43 bp):
CACTGCAACTTTAGGGAGCTAGATTGGTGACTTAAATCTGCTT
Found at i:5514957 original size:43 final size:43
Alignment explanation
Indices: 5514773--5515107 Score: 142
Period size: 43 Copynumber: 7.7 Consensus size: 43
5514763 AGGTTGGTGG
*
5514773 CTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTTGCCAT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAG--TTGCCAT
* * ** * ***
5514818 CTTCGATCTGCTTCACTGCAACTTCAGGGAAACAAAATCTAAAAT
1 CTTAGATCTGCTTCACTGCAACTTCA-GGAAGCTCAGT-TGCCAT
* * * * * * * ****
5514863 TTTAG-CCTACTCCACTACAACTTTAGGGAGCT-AGGTTGGTGG
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCA-GTTGCCAT
*
5514905 CTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGTTGCCAT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGTTGCCAT
* * * * ** * **
5514948 CTTCGATCTGCTTCATTACAACTTCAGGGAAACAAAATCTGAAAT
1 CTTAGATCTGCTTCACTGCAACTTCA-GGAAGCTCAGT-TGCCAT
* * * * * * *
5514993 TTTAG-CCTACTCCACTACAACTTTAGGGAGCT-AGGTTG--AT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCA-GTTGCCAT
* * *
5515033 GGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
1 --CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAG-TT-GCCAT
* *
5515080 CTTCGATCTGCTTCACTGTAACTTCAGG
1 CTTAGATCTGCTTCACTGCAACTTCAGG
5515108 GAAATAAGAT
Statistics
Matches: 204, Mismatches: 70, Indels: 32
0.67 0.23 0.10
Matches are distributed among these distances:
40 2 0.01
42 11 0.05
43 80 0.39
44 42 0.21
45 62 0.30
46 6 0.03
47 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (43 bp):
CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGTTGCCAT
Found at i:5516814 original size:11 final size:10
Alignment explanation
Indices: 5516788--5516822 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
5516778 TATTGTTTGC
*
5516788 TTTTCCTTTT
1 TTTTCTTTTT
5516798 TTTTCTTTTT
1 TTTTCTTTTT
5516808 TTCTTCTTTTT
1 TT-TTCTTTTT
5516819 TTTT
1 TTTT
5516823 ATTTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:5518945 original size:5 final size:5
Alignment explanation
Indices: 5518935--5519043 Score: 126
Period size: 5 Copynumber: 22.6 Consensus size: 5
5518925 AATGCAAATG
5518935 ATGCA ATGCA ATGCA ATGCAA ATG-- ATGCA ATGCA ATGCA ATGCAA ATG--
1 ATGCA ATGCA ATGCA ATGC-A ATGCA ATGCA ATGCA ATGCA ATGC-A ATGCA
5518983 ATGCA ATGCA ATGCA ATGCA ATGCAA ATG-- ATGCA ATGCA ATGCAA ATG--
1 ATGCA ATGCA ATGCA ATGCA ATGC-A ATGCA ATGCA ATGCA ATGC-A ATGCA
5519031 ATGCA ATGCA ATG
1 ATGCA ATGCA ATG
5519044 TAAATGCATG
Statistics
Matches: 92, Mismatches: 0, Indels: 24
0.79 0.00 0.21
Matches are distributed among these distances:
3 12 0.13
5 64 0.70
6 16 0.17
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (5 bp):
ATGCA
Found at i:5518949 original size:19 final size:19
Alignment explanation
Indices: 5518940--5519049 Score: 135
Period size: 19 Copynumber: 6.0 Consensus size: 19
5518930 AAATGATGCA
5518940 ATGCAATGCAATGCAAATG
1 ATGCAATGCAATGCAAATG
5518959 ATGCAATGCAATGC--A--
1 ATGCAATGCAATGCAAATG
5518974 ATGCAAATG--ATGC-AATG
1 ATGC-AATGCAATGCAAATG
5518991 CAATGCAATGCAATGCAAATG
1 --ATGCAATGCAATGCAAATG
5519012 ATGCAATGCAATGCAAATG
1 ATGCAATGCAATGCAAATG
*
5519031 ATGCAATGCAATGTAAATG
1 ATGCAATGCAATGCAAATG
5519050 CATGGGATGA
Statistics
Matches: 81, Mismatches: 1, Indels: 18
0.81 0.01 0.18
Matches are distributed among these distances:
14 4 0.05
15 5 0.06
16 4 0.05
17 1 0.01
18 4 0.05
19 55 0.68
20 4 0.05
21 4 0.05
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (19 bp):
ATGCAATGCAATGCAAATG
Found at i:5518957 original size:24 final size:24
Alignment explanation
Indices: 5518925--5519043 Score: 190
Period size: 24 Copynumber: 5.0 Consensus size: 24
5518915 TGGGAAATTT
5518925 AATGCAAATGATGCAATGCAATGC
1 AATGCAAATGATGCAATGCAATGC
5518949 AATGCAAATGATGCAATGCAATGC
1 AATGCAAATGATGCAATGCAATGC
5518973 AATGCAAATGATGCAATGCAATGC
1 AATGCAAATGATGCAATGCAATGC
5518997 AATGC-AATGCAAATG--ATGCAATGC
1 AATGCAAATG---ATGCAATGCAATGC
5519021 AATGCAAATGATGCAATGCAATG
1 AATGCAAATGATGCAATGCAATG
5519044 TAAATGCATG
Statistics
Matches: 89, Mismatches: 0, Indels: 12
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.03
23 4 0.04
24 75 0.84
25 4 0.04
26 3 0.03
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (24 bp):
AATGCAAATGATGCAATGCAATGC
Found at i:5518977 original size:29 final size:29
Alignment explanation
Indices: 5518935--5519027 Score: 151
Period size: 29 Copynumber: 3.4 Consensus size: 29
5518925 AATGCAAATG
5518935 ATGCAATGCAATGCAATGC-AA--ATG--
1 ATGCAATGCAATGCAATGCAAATGATGCA
5518959 ATGCAATGCAATGCAATGCAAATGATGCA
1 ATGCAATGCAATGCAATGCAAATGATGCA
5518988 ATGCAATGCAATGCAATGCAAATGATGCA
1 ATGCAATGCAATGCAATGCAAATGATGCA
5519017 ATGCAATGCAA
1 ATGCAATGCAA
5519028 ATGATGCAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
24 19 0.30
25 2 0.03
27 3 0.05
29 40 0.62
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (29 bp):
ATGCAATGCAATGCAATGCAAATGATGCA
Found at i:5519049 original size:38 final size:38
Alignment explanation
Indices: 5518935--5519066 Score: 143
Period size: 38 Copynumber: 3.5 Consensus size: 38
5518925 AATGCAAATG
5518935 ATGCAATGCAATGCAATGCAAATGATGCAATGCAATGC-A
1 ATGC-ATGCAATG-AATGCAAATGATGCAATGCAATGCAA
5518974 ATGCA---AATG-ATGC-AATGCAATGCAATGCAATGCAA
1 ATGCATGCAATGAATGCAAATG--ATGCAATGCAATGCAA
*
5519009 ATG-ATGCAATGCAATGCAAATGATGCAATGCAATGTAA
1 ATGCATGCAATG-AATGCAAATGATGCAATGCAATGCAA
**
5519047 ATGCATGGGATGAATGCAAA
1 ATGCATGCAATGAATGCAAA
5519067 GGAAAGGAAG
Statistics
Matches: 80, Mismatches: 3, Indels: 21
0.77 0.03 0.20
Matches are distributed among these distances:
32 4 0.05
33 4 0.05
34 15 0.19
35 8 0.10
37 4 0.05
38 27 0.34
39 14 0.17
40 4 0.05
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (38 bp):
ATGCATGCAATGAATGCAAATGATGCAATGCAATGCAA
Found at i:5519064 original size:48 final size:47
Alignment explanation
Indices: 5518925--5519065 Score: 187
Period size: 48 Copynumber: 2.9 Consensus size: 47
5518915 TGGGAAATTT
*
5518925 AATGCAAATGATGCAATGCAATGCAATGCA-AATGATGCAATGCAATGC
1 AATGCAAATGATGCAATGCAATGCAATGCATGA-GATG-AATGCAATGC
*
5518973 AATGCAAATGATGCAATGCAATGCAATGCAATGCAAATG-ATGCAATGC
1 AATGCAAATGATGCAATGCAATGCAATGC-ATG-AGATGAATGCAATGC
* *
5519021 AATGCAAATGATGCAATGCAATGTAAATGCATGGGATGAATGCAA
1 AATGCAAATGATGCAATGCAATG-CAATGCATGAGATGAATGCAA
5519066 AGGAAAGGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
47 3 0.04
48 70 0.84
49 6 0.07
50 3 0.04
51 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (47 bp):
AATGCAAATGATGCAATGCAATGCAATGCATGAGATGAATGCAATGC
Found at i:5520927 original size:131 final size:131
Alignment explanation
Indices: 5520549--5521005 Score: 492
Period size: 131 Copynumber: 3.5 Consensus size: 131
5520539 CCCAACACAG
* * *
5520549 TAGGGCACGATTCCTCGAATTGCCAAATGTCGAATACCGCCTTTGTTTTAAAGGA-TTTAAAAAA
1 TAGGGCACGATTCCGCGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAAGGATTTTAAAAGA
* * * * * **
5520613 AATGAATGAAAACCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACG
66 CATGAATGAAAATCTAAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACG
*
5520678 A
131 T
* * * * * ** * * *
5520679 TAGGGCATGATTCC-CGAATTTGTCGAACACCGAATATTGCCTTGGTTTTAAAGAATTTTTAGAA
1 TAGGGCACGATTCCGCGAA-TTGCCAAATATCGAATACCGCCTTTGTTTTAAAGGA-TTTTAAAA
* * * * *
5520743 GACATGCATGAAATTTTTAAGGGATA-TCGGATTATTTTAAGCAAACGAGAAATTGCAACCCAGC
64 GACATGAATGAAAATCTAAAGGGATATTC-GATTATTTTGAGCAAACGAGAAATTGCAACCCAGC
5520807 ACGT
128 ACGT
* * * * *
5520811 TAGGGCATGATTCCGCGAATTTCCAAATATCGCATATCGCCTTTG-TTTAAGGGATCTTTAAAAG
1 TAGGGCACGATTCCGCGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAAGGAT-TTTAAAAG
** * * *
5520875 ACATGGGTGAAAATCTAAAGGGACATTCAATTACTTTGAGCAAACGAGAAATTGCAACCCAGCAC
65 ACATGAATGAAAATCTAAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCAC
5520940 GT
130 GT
*
5520942 TAGGGCACGATT-CGTCGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAAGGGTTTTCAAAA
1 TAGGGCACGATTCCG-CGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAAGGATTTT-AAAA
5521006 AGAATAGATA
Statistics
Matches: 266, Mismatches: 51, Indels: 18
0.79 0.15 0.05
Matches are distributed among these distances:
129 4 0.02
130 43 0.16
131 112 0.42
132 103 0.39
133 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (131 bp):
TAGGGCACGATTCCGCGAATTGCCAAATATCGAATACCGCCTTTGTTTTAAAGGATTTTAAAAGA
CATGAATGAAAATCTAAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACG
T
Found at i:5524403 original size:20 final size:20
Alignment explanation
Indices: 5524358--5524409 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
5524348 CCCCACCCAA
*
5524358 ATTTCCCCAAATCCCTAACT
1 ATTTCCCCAAATCCCTAAAT
*
5524378 -TTTCCCCTAATCCCTAAAT
1 ATTTCCCCAAATCCCTAAAT
*
5524397 ATTTCCCCGAATC
1 ATTTCCCCAAATC
5524410 AAAATCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.27, C:0.38, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTTCCCCAAATCCCTAAAT
Found at i:5526563 original size:10 final size:10
Alignment explanation
Indices: 5526533--5526562 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5526523 GGTTAGCTAC
5526533 TCTTTTATTT
1 TCTTTTATTT
5526543 TCTTTTATTT
1 TCTTTTATTT
5526553 TCTTTT-TTT
1 TCTTTTATTT
5526562 T
1 T
5526563 TAAATTACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (10 bp):
TCTTTTATTT
Found at i:5526989 original size:64 final size:64
Alignment explanation
Indices: 5526917--5527050 Score: 259
Period size: 64 Copynumber: 2.1 Consensus size: 64
5526907 TAATATTTCT
*
5526917 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
5526981 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
5527045 ATATTT
1 ATATTT
5527051 AATAAAATAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (64 bp):
ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
Found at i:5527063 original size:64 final size:64
Alignment explanation
Indices: 5526930--5527064 Score: 211
Period size: 64 Copynumber: 2.1 Consensus size: 64
5526920 TTTCTATCAC
* * * *
5526930 GATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAAATATTTCTATCAC
1 GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAAATATTTATATAAA
5526994 GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAAATATTTA-ATAAA
1 GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAAATATTTATATAAA
5527057 -ATATTTTA
1 GAT-TTTTA
5527065 TATAGTTTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
62 2 0.03
63 8 0.12
64 56 0.85
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.46
Consensus pattern (64 bp):
GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAAATATTTATATAAA
Found at i:5527137 original size:23 final size:24
Alignment explanation
Indices: 5527098--5527167 Score: 106
Period size: 23 Copynumber: 3.0 Consensus size: 24
5527088 ATTATTATTG
* *
5527098 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTTCGTTTTATCAC
*
5527122 AAATATTATTG-TCGTTTTATCAC
1 AAATATTATCGTTCGTTTTATCAC
5527145 AAATATTATCGTTCGTTTTATCA
1 AAATATTATCGTTCGTTTTATCA
5527168 TTTAAGTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.46
Consensus pattern (24 bp):
AAATATTATCGTTCGTTTTATCAC
Found at i:5527394 original size:15 final size:15
Alignment explanation
Indices: 5527341--5527424 Score: 95
Period size: 15 Copynumber: 5.8 Consensus size: 15
5527331 AACGACATGT
5527341 ATATTATTTAATTAA
1 ATATTATTTAATTAA
* ** *
5527356 A-ATAATTTTTTTCA
1 ATATTATTTAATTAA
5527370 ATATTATTTAATTAAA
1 ATATTATTTAATT-AA
5527386 ATATT-TTT-A-TAA
1 ATATTATTTAATTAA
5527398 ATATTATTTAATTAA
1 ATATTATTTAATTAA
5527413 ATATTATTTAAT
1 ATATTATTTAAT
5527425 CCGCAACTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
12 7 0.12
13 4 0.07
14 12 0.21
15 27 0.48
16 6 0.11
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:5527400 original size:28 final size:28
Alignment explanation
Indices: 5527341--5527422 Score: 121
Period size: 28 Copynumber: 2.9 Consensus size: 28
5527331 AACGACATGT
* *
5527341 ATATTATTTAATTAAAATAATTTTTTTCA
1 ATATTATTTAATTAAAAT-ATTTTTATAA
5527370 ATATTATTTAATTAAAATATTTTTATAA
1 ATATTATTTAATTAAAATATTTTTATAA
5527398 ATATTATTTAATT-AAATATTATTTA
1 ATATTATTTAATTAAAATATT-TTTA
5527423 ATCCGCAACT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
27 7 0.14
28 25 0.50
29 18 0.36
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATTATTTAATTAAAATATTTTTATAA
Found at i:5527553 original size:9 final size:9
Alignment explanation
Indices: 5527537--5527867 Score: 298
Period size: 9 Copynumber: 37.4 Consensus size: 9
5527527 AATATTTAAC
*
5527537 ATAACTTAC
1 ATAACTTAT
* *
5527546 AAAACTTAC
1 ATAACTTAT
5527555 ATAACTTAT
1 ATAACTTAT
*
5527564 ATAACTTAG
1 ATAACTTAT
**
5527573 A-AAAATAT
1 ATAACTTAT
*
5527581 AAAACTTAT
1 ATAACTTAT
*
5527590 ATAACTTAC
1 ATAACTTAT
5527599 ATAACTTAT
1 ATAACTTAT
*
5527608 ATAACTTAG
1 ATAACTTAT
*
5527617 ATAACTTAG
1 ATAACTTAT
*
5527626 ATAA-ATAT
1 ATAACTTAT
*
5527634 ATAACTTAC
1 ATAACTTAT
*
5527643 ATAACTTAC
1 ATAACTTAT
5527652 ATAACTTAT
1 ATAACTTAT
5527661 ATAACTTAT
1 ATAACTTAT
*
5527670 ATAACTTAG
1 ATAACTTAT
*
5527679 ATAA-ATAT
1 ATAACTTAT
*
5527687 ATAACTTAC
1 ATAACTTAT
*
5527696 ATAACTTAC
1 ATAACTTAT
5527705 ATAACTTAT
1 ATAACTTAT
*
5527714 ATAACTTAG
1 ATAACTTAT
*
5527723 ATAA-ATAT
1 ATAACTTAT
5527731 ATAACTTAT
1 ATAACTTAT
*
5527740 ATAACTTAC
1 ATAACTTAT
5527749 ATAACTTAT
1 ATAACTTAT
*
5527758 ATAACTGAT
1 ATAACTTAT
** *
5527767 ATGTCTTAG
1 ATAACTTAT
*
5527776 ATAA-ATAT
1 ATAACTTAT
*
5527784 ATAACTTAC
1 ATAACTTAT
5527793 ATAACTTAT
1 ATAACTTAT
*
5527802 ATAACTTAG
1 ATAACTTAT
*
5527811 ATAA-ATAT
1 ATAACTTAT
*
5527819 ATAACTTAC
1 ATAACTTAT
*
5527828 ATAA-ATAT
1 ATAACTTAT
* *
5527836 ATATCATAT
1 ATAACTTAT
*
5527845 CATAACTTAC
1 -ATAACTTAT
*
5527855 ATAACTTAC
1 ATAACTTAT
5527864 ATAA
1 ATAA
5527868 TACTTAAATA
Statistics
Matches: 261, Mismatches: 53, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
8 40 0.15
9 215 0.82
10 6 0.02
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (9 bp):
ATAACTTAT
Found at i:5527605 original size:53 final size:53
Alignment explanation
Indices: 5527537--5527867 Score: 421
Period size: 53 Copynumber: 6.4 Consensus size: 53
5527527 AATATTTAAC
* * *
5527537 ATAACTTACAAAACTTACATAACTTATATAACTTAGAAAAATATAAAACTTAT
1 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTAT
* * *
5527590 ATAACTTACATAACTTATATAACTTAGATAACTTAGATAAATATATAACTTAC
1 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTAT
*
5527643 ATAACTTACATAACTTATATAACTTATATAACTTAG------ATA-AA--TAT
1 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTAT
5527687 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTAT
1 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTAT
* * ** *
5527740 ATAACTTACATAACTTATATAACTGATATGTCTTAGATAAATATATAACTTAC
1 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTAT
* * * * * *
5527793 ATAACTTATATAACTTAGATAA-ATATATAACTTACATAAATATATATCATAT
1 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTAT
5527845 CATAACTTACATAACTTACATAA
1 -ATAACTTACATAACTTACATAA
5527868 TACTTAAATA
Statistics
Matches: 242, Mismatches: 26, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
44 37 0.15
46 2 0.01
47 3 0.01
50 3 0.01
51 2 0.01
52 22 0.09
53 173 0.71
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (53 bp):
ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTAT
Found at i:5527788 original size:35 final size:35
Alignment explanation
Indices: 5527599--5527867 Score: 155
Period size: 35 Copynumber: 7.9 Consensus size: 35
5527589 TATAACTTAC
* * *
5527599 ATAACTTATATAACTTAGATAACTTAGATAAATAT
1 ATAACTTACATAACTGATATAACTTAGATAAATAT
* * * *
5527634 ATAACTTACATAACTTACATAACTTATATAACTTAT
1 ATAACTTACATAACTGATATAACTTAGATAA-ATAT
* * *
5527670 ATAACTTAGATAAAT-ATATAAC-----T---TAC
1 ATAACTTACATAACTGATATAACTTAGATAAATAT
*
5527696 ATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTACATAACTGATATAACTTAGATAAATAT
* * * * *
5527731 ATAACTTATATAACTTACATAACTTATATAACTGAT
1 ATAACTTACATAACTGATATAACTTAGATAAAT-AT
** * * * *
5527767 ATGTCTTAGATAAAT-ATATAACTTACATAACTTAT
1 ATAACTTACATAACTGATATAACTTAGATAA-ATAT
* * *
5527802 ATAACTTAGATAAAT-ATATAACTTACATAAATAT
1 ATAACTTACATAACTGATATAACTTAGATAAATAT
* * * * *
5527836 ATATCATATCATAACTTACATAACTTACATAA
1 ATAACTTA-CATAACTGATATAACTTAGATAA
5527868 TACTTAAATA
Statistics
Matches: 190, Mismatches: 30, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
26 15 0.08
27 7 0.04
30 1 0.01
32 1 0.01
34 9 0.05
35 113 0.59
36 44 0.23
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (35 bp):
ATAACTTACATAACTGATATAACTTAGATAAATAT
Done.