Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 19 of 167
Found at i:5632066 original size:22 final size:21
Alignment explanation
Indices: 5632031--5632193 Score: 81
Period size: 19 Copynumber: 8.5 Consensus size: 21
5632021 AAAAGGTATC
* *
5632031 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
5632052 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
5632075 TGCACATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5632094 T--ATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5632111 TACATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5632130 TGC-AATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5632148 T--GAATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5632165 TGCATATCATAT-T-TAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5632184 TGCATATCAT
1 TACAAATCAT
5632194 TGAAGATTAT
Statistics
Matches: 125, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
17 32 0.26
18 15 0.12
19 49 0.39
20 1 0.01
21 3 0.02
22 15 0.12
23 10 0.08
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:5632074 original size:23 final size:22
Alignment explanation
Indices: 5632031--5632088 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
5632021 AAAAGGTATC
* *
5632031 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
5632052 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
5632075 TGCACATCATATCT
1 TACAAATCATATCT
5632089 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:5632091 original size:19 final size:19
Alignment explanation
Indices: 5632067--5632193 Score: 192
Period size: 19 Copynumber: 6.9 Consensus size: 19
5632057 AATCATATCT
*
5632067 TCTAAGATTGCACATCATA
1 TCTAAGATTGCATATCATA
5632086 TCTAAGATT--ATATCATA
1 TCTAAGATTGCATATCATA
*
5632103 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
5632122 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
5632140 TCTAAGATTG-A-ATCATA
1 TCTAAGATTGCATATCATA
5632157 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
5632176 TTTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
5632194 TGAAGATTAT
Statistics
Matches: 101, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
17 33 0.33
18 17 0.17
19 51 0.50
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5632145 original size:54 final size:55
Alignment explanation
Indices: 5632044--5632205 Score: 206
Period size: 54 Copynumber: 2.9 Consensus size: 55
5632034 AAATTAAATC
*
5632044 TCTAAGATTACAAAATCATATCTTCTAAGATTGCACATCATATCTAAGATTATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCACATCATATCTAAGATTATATCATA
5632103 TCTAAGATTACATATCATATCTAAGATTGCA-ATCATATCTAAGATTGA-ATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCACATCATATCTAAGATT-ATATCATA
* * * *
5632157 TCTAAGATTGCATATCATATTTAAGATTGCATATCAT-T-GAAGATTATAT
1 TCTAAGATTACATATCATATCTAAGATTGCACATCATATCTAAGATTATAT
5632206 TTCCATATGA
Statistics
Matches: 96, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
52 1 0.01
53 8 0.08
54 51 0.53
55 18 0.19
58 7 0.07
59 11 0.11
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (55 bp):
TCTAAGATTACATATCATATCTAAGATTGCACATCATATCTAAGATTATATCATA
Found at i:5632201 original size:36 final size:38
Alignment explanation
Indices: 5632060--5632193 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 38
5632050 ATTACAAAAT
*
5632060 CATATC-T-TCTAAGATTGCACATCATATCTAAGATT-
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
*
5632095 -ATATCATATCTAAGATTACATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
5632132 CA-ATCATATCTAAGATTG-A-ATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
*
5632167 CATATCATATTTAAGATTGCATATCAT
1 CATATCATATCTAAGATTGCATATCAT
5632194 TGAAGATTAT
Statistics
Matches: 88, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
34 5 0.06
35 19 0.22
36 42 0.48
37 16 0.18
38 6 0.07
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGATTG
Found at i:5633051 original size:129 final size:128
Alignment explanation
Indices: 5632806--5633055 Score: 349
Period size: 129 Copynumber: 1.9 Consensus size: 128
5632796 AGAATTTAGA
* * * *
5632806 AAACATGAGTGAAATTCTAAAGGAATATTCAATTATTTGAACAAACAGGAAATTGCAACCCAGCA
1 AAACATGAGTGAAATTCCAAAGGAATATGCAATCATTTGAACAAACAGGAAATTGAAACCCAGCA
* * * *
5632871 CGATAGGGCACGATTCCCCGAATTTCAAAACTTCGAACGTTGCCTTCGTTTTAAGGAATTTTT
66 CGATAGGGCACGATTCCCCGAATTTCAAAACATCAAACATCGCCTTCGTTTTAAGGAATTTTT
*
5632934 AAACATGAGTGAAATTCCAAAGGAATATGCGATCATTTTGAACAAAC-GAGAAATTGAAACCCAG
1 AAACATGAGTGAAATTCCAAAGGAATATGCAATCA-TTTGAACAAACAG-GAAATTGAAACCCAG
** * * *
5632998 CACGATAGGGCACGATTCCTTGAATTTCTAAACATCAAACATCGCTTTTGTTTTAAGG
64 CACGATAGGGCACGATTCCCCGAATTTCAAAACATCAAACATCGCCTTCGTTTTAAGG
5633056 TTTAGAAAAC
Statistics
Matches: 106, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
128 32 0.30
129 74 0.70
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (128 bp):
AAACATGAGTGAAATTCCAAAGGAATATGCAATCATTTGAACAAACAGGAAATTGAAACCCAGCA
CGATAGGGCACGATTCCCCGAATTTCAAAACATCAAACATCGCCTTCGTTTTAAGGAATTTTT
Found at i:5633716 original size:25 final size:26
Alignment explanation
Indices: 5633688--5633782 Score: 86
Period size: 25 Copynumber: 3.7 Consensus size: 26
5633678 AGCATAAAAT
5633688 AAAAAGTTTAAAATAAATAATATATAA
1 AAAAAGTTTAAAATAAATAATATAT-A
*
5633715 AAAAAGGTTTAAAAT-AATAATATATG
1 AAAAA-GTTTAAAATAAATAATATATA
** * **
5633741 AAAGGGTTCAAAATAAGCAATATAT-
1 AAAAAGTTTAAAATAAATAATATATA
* *
5633766 ATAAATTTTAAAATAAA
1 AAAAAGTTTAAAATAAA
5633783 GTATAAATCA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
25 19 0.35
26 11 0.20
27 15 0.28
28 9 0.17
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (26 bp):
AAAAAGTTTAAAATAAATAATATATA
Found at i:5633733 original size:27 final size:27
Alignment explanation
Indices: 5633688--5633739 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
5633678 AGCATAAAAT
5633688 AAAAAGTTTAAAATAAATAATATATAA
1 AAAAAGTTTAAAATAAATAATATATAA
5633715 AAAAAGGTTTAAAAT-AATAATATAT
1 AAAAA-GTTTAAAATAAATAATATAT
5633740 GAAAGGGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (27 bp):
AAAAAGTTTAAAATAAATAATATATAA
Found at i:5636029 original size:45 final size:45
Alignment explanation
Indices: 5635969--5636260 Score: 184
Period size: 45 Copynumber: 6.5 Consensus size: 45
5635959 TTTCAACCTG
5635969 CTCCACTGCAACTTCAGAGAGATAAGGTCTGCTATCTTCAGTCTA
1 CTCCACTGCAACTTCAGAGAGATAAGGTCTGCTATCTTCAGTCTA
* * * *
5636014 CTCCACTGCAACTTCAG-GAAGATAA-GACTTG-TAACTTCA-ACTTG
1 CTCCACTGCAACTTCAGAG-AGATAAGGTC-TGCTATCTTCAGTC-TA
* * * * *
5636058 CCCCACTGCAACTTCAGGGGGATAAGGTTTGCTATCTTTAGTCTA
1 CTCCACTGCAACTTCAGAGAGATAAGGTCTGCTATCTTCAGTCTA
* * * * * ** * * * *
5636103 CTCCACTGTACCTTTAGGGGGATAAGGT-TTATAGCTTTAACTCTG
1 CTCCACTGCAACTTCAGAGAGATAAGGTCTGCTATC-TTCAGTCTA
* * * * * * *
5636148 CTCTACTGTAATTTCGGAGAGATAAGATTTGCTATCTTCAGTGTA
1 CTCCACTGCAACTTCAGAGAGATAAGGTCTGCTATCTTCAGTCTA
* * * * *
5636193 CTCTACTGCAACTTCAGAGAGACAAGATCT-ATAATCTTCAGCCTA
1 CTCCACTGCAACTTCAGAGAGATAAGGTCTGCT-ATCTTCAGTCTA
* *
5636238 CTCCACTACAACTT-AGGGAGATA
1 CTCCACTGCAACTTCAGAGAGATA
5636261 GGATGGTGGC
Statistics
Matches: 188, Mismatches: 49, Indels: 21
0.73 0.19 0.08
Matches are distributed among these distances:
43 1 0.01
44 46 0.24
45 136 0.72
46 5 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGAGAGATAAGGTCTGCTATCTTCAGTCTA
Found at i:5636066 original size:89 final size:88
Alignment explanation
Indices: 5635887--5636219 Score: 325
Period size: 89 Copynumber: 3.8 Consensus size: 88
5635877 TTCAATCTGT
* * * * *
5635887 TCCATTGCAACTTCAGAGAAATAAGGTTTGCTA---TGA-TCTGCTCTACTGCAACTTCA-GAGA
1 TCCACTGCAACTTCAGAGAGATAAGGTTTGCTATCTTCAGTCTACTCCACTGCAACTTCAGGAGA
* * *
5635947 TAATACTTGTAATTTCAACCTGC
66 TAAGACTTGTAACTTCAACTTGC
*
5635970 TCCACTGCAACTTCAGAGAGATAAGGTCTGCTATCTTCAGTCTACTCCACTGCAACTTCAGGAAG
1 TCCACTGCAACTTCAGAGAGATAAGGTTTGCTATCTTCAGTCTACTCCACTGCAACTTCAGG-AG
5636035 ATAAGACTTGTAACTTCAACTTGC
65 ATAAGACTTGTAACTTCAACTTGC
* * * * * * * *
5636059 CCCACTGCAACTTCAGGGGGATAAGGTTTGCTATCTTTAGTCTACTCCACTGTACCTTTAGGGGG
1 TCCACTGCAACTTCAGAGAGATAAGGTTTGCTATCTTCAGTCTACTCCACTGCAACTTCA-GGAG
** * * *
5636124 ATAAGGTTTATAGCTTTAACTCTGC
65 ATAAGACTTGTAACTTCAACT-TGC
* * * * * * *
5636149 TCTACTGTAATTTCGGAGAGATAAGATTTGCTATCTTCAGTGTACTCTACTGCAACTTCAGAGAG
1 TCCACTGCAACTTCAGAGAGATAAGGTTTGCTATCTTCAGTCTACTCCACTGCAACTTCAG-GAG
*
5636214 ACAAGA
65 ATAAGA
5636220 TCTATAATCT
Statistics
Matches: 201, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
83 30 0.15
86 2 0.01
87 18 0.09
88 1 0.00
89 93 0.46
90 57 0.28
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (88 bp):
TCCACTGCAACTTCAGAGAGATAAGGTTTGCTATCTTCAGTCTACTCCACTGCAACTTCAGGAGA
TAAGACTTGTAACTTCAACTTGC
Found at i:5636075 original size:44 final size:43
Alignment explanation
Indices: 5635925--5636074 Score: 153
Period size: 45 Copynumber: 3.4 Consensus size: 43
5635915 TGCTATGATC
* * * *
5635925 TGCTCTACTGCAACTTCAG-AGATAATACTTGTAATTTCAACC
1 TGCTCCACTGCAACTTCAGAAGATAAGACTTGTAACTTCAACT
* * *
5635967 TGCTCCACTGCAACTTCAGAGAGATAAG-GTCTGCTATCTTC-AGT
1 TGCTCCACTGCAACTTCAGA-AGATAAGACT-TG-TAACTTCAACT
*
5636011 CTACTCCACTGCAACTTCAGGAAGATAAGACTTGTAACTTCAACT
1 -TGCTCCACTGCAACTTCA-GAAGATAAGACTTGTAACTTCAACT
*
5636056 TGCCCCACTGCAACTTCAG
1 TGCTCCACTGCAACTTCAG
5636075 GGGGATAAGG
Statistics
Matches: 87, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
42 18 0.21
43 2 0.02
44 31 0.36
45 33 0.38
46 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (43 bp):
TGCTCCACTGCAACTTCAGAAGATAAGACTTGTAACTTCAACT
Found at i:5636082 original size:44 final size:44
Alignment explanation
Indices: 5635925--5636083 Score: 155
Period size: 44 Copynumber: 3.6 Consensus size: 44
5635915 TGCTATGATC
* * * *
5635925 TGCTCTACTGCAACTTCA--GAGATAATACTTGTAATTTCAACC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACT
* * * *
5635967 TGCTCCACTGCAACTTCAGAGAGATAAG-GTCTGCTATCTTC-AGT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACT-TG-TAACTTCAACT
* *
5636011 CTACTCCACTGCAACTTCAGGAAGATAAGACTTGTAACTTCAACT
1 -TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACT
* *
5636056 TGCCCCACTGCAACTTCAGGGGGATAAG
1 TGCTCCACTGCAACTTCAGGGAGATAAG
5636084 GTTTGCTATC
Statistics
Matches: 93, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
42 17 0.18
43 1 0.01
44 40 0.43
45 34 0.37
46 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACT
Found at i:5636341 original size:132 final size:132
Alignment explanation
Indices: 5636197--5636880 Score: 1039
Period size: 132 Copynumber: 5.2 Consensus size: 132
5636187 AGTGTACTCT
* * * * **
5636197 ACTGCAACTTCAGAGAGACAAGATCTATAATCTTCAGCCTACTCCACTACAACTTAGGGAGATAG
1 ACTGCAACTTCAGGGAGGCAAGATCTATAATCTTTAACCTACTCCACTACTGCTTAGGGAGATAG
*
5636262 GATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGAAAGACAAGATTTGCCGTATTCGATCTGCT
66 GATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGAAAGACAAGATTTGCCGTCTTCGATCTGCT
5636327 CC
131 CC
* * *
5636329 ACTGCAACTTCAGTGAGGCAAGATCTACAATCTTTAACCTACTCCACTACTTCTTAGGGAGATAG
1 ACTGCAACTTCAGGGAGGCAAGATCTATAATCTTTAACCTACTCCACTACTGCTTAGGGAGATAG
* * * *
5636394 GATGGTGGCTTAAATCTACTTCACTGCAACTTCAGAAAGACAAGATCTGTCGTCTTTGATCTGCT
66 GATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGAAAGACAAGATTTGCCGTCTTCGATCTGCT
5636459 CC
131 CC
* *
5636461 ACTGCAACTTCAGGGAGGCAAGATCTACAATGTTTAACCTACTCCACTACTGCTTAGGGAGATAG
1 ACTGCAACTTCAGGGAGGCAAGATCTATAATCTTTAACCTACTCCACTACTGCTTAGGGAGATAG
* * * * *
5636526 GATGGTGGCTTAAATCCGCTTCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCT
66 GATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGAAAGACAAGATTTGCCGTCTTCGATCTGCT
*
5636591 CT
131 CC
* * * *
5636593 ACTGCAACTTCAGGGAGACAGGATCTATAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAG
1 ACTGCAACTTCAGGGAGGCAAGATCTATAATCTTTAACCTACTCCACTACTGCTTAGGGAGATAG
* *
5636658 GATGGTGGCTTAAATCTACTTCACTGCAACTTCA-AGAAGACAAGATTCGCCGTCTTCGATCTGC
66 GATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGA-AAGACAAGATTTGCCGTCTTCGATCTGC
5636722 TCC
130 TCC
*
5636725 ACTGCAACTTCAGGGAGGCAAGAT-TTTCAATCTTTAACCTACTCCACTACTGCTTAGGGAGATA
1 ACTGCAACTTCAGGGAGGCAAGATCTAT-AATCTTTAACCTACTCCACTACTGCTTAGGGAGATA
* *
5636789 GGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACAAGATCTGCCGTCTTCGATCTGC
65 GGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGAAAGACAAGATTTGCCGTCTTCGATCTGC
*
5636854 TTC
130 TCC
*
5636857 ACTGTAACTTCAGGGAGGCAAGAT
1 ACTGCAACTTCAGGGAGGCAAGAT
5636881 TTGTAGAATT
Statistics
Matches: 501, Mismatches: 48, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
131 2 0.00
132 499 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (132 bp):
ACTGCAACTTCAGGGAGGCAAGATCTATAATCTTTAACCTACTCCACTACTGCTTAGGGAGATAG
GATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGAAAGACAAGATTTGCCGTCTTCGATCTGCT
CC
Found at i:5636747 original size:45 final size:45
Alignment explanation
Indices: 5636274--5636881 Score: 163
Period size: 45 Copynumber: 13.8 Consensus size: 45
5636264 TGGTGGCTTA
* ** * *
5636274 AATCTGCTTCACTGCAACTTCAGAAAGACAAGATTTGCCGTATTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTCGCCGTCTTC
* * * * ** *
5636319 GATCTGCTCCACTGCAACTTCAGTGAGGCAAGA-TCTACAATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTC-GCCGTCTTC
* * * ** * * ** * *
5636364 AACCTACTCCACTACTTCTT-AGGGAGATAGGA-T-GGTGGCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTCGCCGTCTTC
* * ** * *
5636406 AATCTACTTCACTGCAACTTCAGAAAGACAAGA-TCTGTCGTCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTC-GCCGTCTTC
* * ***
5636451 GATCTGCTCCACTGCAACTTCAGGGAGGCAAGATCTACAATGT-TT-
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGAT-T-CGCCGTCTTC
* * * ** * * ** * *
5636496 AACCTACTCCACTACTGCTT-AGGGAGATAGGA-T-GGTGGCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTCGCCGTCTTC
* * * * *
5636538 AATCCGCTTCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTCGCCGTCTTC
* * * ****
5636583 GATCTGCTCTACTGCAACTTCAGGGAGACAGGA-TCTATAATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTC-GCCGTCTTC
** * * ** * * ** * *
5636628 AGCCTACTCCACTACTGCTT-AGGGAGATAGGA-T-GGTGGCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTCGCCGTCTTC
* * * *
5636670 AATCTACTTCACTGCAACTTCAAGAAGACAAGATTCGCCGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTCGCCGTCTTC
* * ** ** *
5636715 GATCTGCTCCACTGCAACTTCAGGGAGGCAAGATTTTCAATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTCGCCGTCTTC
* * * ** * * ** * *
5636760 AACCTACTCCACTACTGCTT-AGGGAGATAGGA-T-GGTGGCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTCGCCGTCTTC
* *
5636802 AATCTGCTTCACTGCAACTTCAGGAAGACAAGA-TCTGCCGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTC-GCCGTCTTC
* * * *
5636847 GATCTGCTTCACTGTAACTTCAGGGAGGCAAGATT
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATT
5636882 TGTAGAATTG
Statistics
Matches: 384, Mismatches: 159, Indels: 39
0.66 0.27 0.07
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 65 0.17
43 37 0.10
44 44 0.11
45 227 0.59
46 3 0.01
47 3 0.01
48 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTCGCCGTCTTC
Found at i:5639578 original size:43 final size:43
Alignment explanation
Indices: 5639506--5639587 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
5639496 AGATGCCAAA
* * * * *
5639506 GAATAAATGATTCTAAGGATGATTATTTGTATGGTATGATCAT
1 GAATAAAAGAATCTAAGAATAATTATTTGTACGGTATGATCAT
*
5639549 GAATAAAAGAATCTAAGAATAATTGTTTGTACGGTATGA
1 GAATAAAAGAATCTAAGAATAATTATTTGTACGGTATGA
5639588 AATTGAAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (43 bp):
GAATAAAAGAATCTAAGAATAATTATTTGTACGGTATGATCAT
Found at i:5643543 original size:130 final size:128
Alignment explanation
Indices: 5643231--5643555 Score: 372
Period size: 130 Copynumber: 2.6 Consensus size: 128
5643221 AAATCGAAAT
* * * * * ** *
5643231 CCAGCACG-TAGGGCACGTTTTCTCGGATTCCTAAACGTTGAACATTGTCTTGTTTT-A-GAATT
1 CCAGCACGATAGGGCACGATTCCTCGAATTTCTAAACATTGAACATACTTTTGTTTTAAGGAATT
* * * * *
5643293 TAGAAAACATGAGTGATATTCTAAAGGAATATTCGATTATTTGAACAAACGGGAAATTGCAAC
66 TAGAAAACATAAGTGAAATTCCAAAGGAATATTCGATCATTTGAACAAACGAGAAATTGCAAC
* * * * * * * *
5643356 CCAGCACGATAGGGCACGATTCCCCAAATTTCCAAACTTTGAACGTTGCCTTCGTTTTAAGGAAT
1 CCAGCACGATAGGGCACGATTCCTCGAATTTCTAAACATTGAAC-ATACTTTTGTTTTAAGGAAT
**
5643421 TTTTAAAACATAAGTGAAATTCCAAAGGAATATTCGATCATTTTGAACAAACGAGAAATTGCAAC
65 TTAGAAAACATAAGTGAAATTCCAAAGGAATATTCGATCA-TTTGAACAAACGAGAAATTGCAAC
*
5643486 CCAGCACGATAGGGCACGATTCCTCGAATTTCTAAACATTAAACATCACTTTTGTTTTAAGG--T
1 CCAGCACGATAGGGCACGATTCCTCGAATTTCTAAACATTGAACAT-ACTTTTGTTTTAAGGAAT
5643549 TTAGAAA
65 TTAGAAA
5643556 GCAGGGACGA
Statistics
Matches: 162, Mismatches: 32, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
125 8 0.05
126 27 0.17
127 7 0.04
128 7 0.04
129 39 0.24
130 74 0.46
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (128 bp):
CCAGCACGATAGGGCACGATTCCTCGAATTTCTAAACATTGAACATACTTTTGTTTTAAGGAATT
TAGAAAACATAAGTGAAATTCCAAAGGAATATTCGATCATTTGAACAAACGAGAAATTGCAAC
Found at i:5644207 original size:25 final size:26
Alignment explanation
Indices: 5644179--5644273 Score: 86
Period size: 25 Copynumber: 3.7 Consensus size: 26
5644169 AGTGTAAAAT
5644179 AAAAAGTTTAAAATAAATAATATATAA
1 AAAAAGTTTAAAATAAATAATATAT-A
*
5644206 AAAAAGGTTTAAAAT-AATAATATATG
1 AAAAA-GTTTAAAATAAATAATATATA
* * * **
5644232 AAACAGTTCAGAATAAGCAATATAT-
1 AAAAAGTTTAAAATAAATAATATATA
* *
5644257 ATAAATTTTAAAATAAA
1 AAAAAGTTTAAAATAAA
5644274 GTATAAATCA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
25 18 0.33
26 12 0.22
27 15 0.28
28 9 0.17
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.29
Consensus pattern (26 bp):
AAAAAGTTTAAAATAAATAATATATA
Found at i:5644224 original size:27 final size:27
Alignment explanation
Indices: 5644179--5644230 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
5644169 AGTGTAAAAT
5644179 AAAAAGTTTAAAATAAATAATATATAA
1 AAAAAGTTTAAAATAAATAATATATAA
5644206 AAAAAGGTTTAAAAT-AATAATATAT
1 AAAAA-GTTTAAAATAAATAATATAT
5644231 GAAACAGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (27 bp):
AAAAAGTTTAAAATAAATAATATATAA
Found at i:5644430 original size:53 final size:53
Alignment explanation
Indices: 5644372--5644479 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
5644362 AAAATAAAAA
*
5644372 AGGGACCCTTTCGAATACATATAAAAGAGCTTAAAATAAATAATGTATAAATG
1 AGGGACCCTTTCAAATACATATAAAAGAGCTTAAAATAAATAATGTATAAATG
5644425 AGGGACCCTTTCAAATACATATAAAAGAGCTTAAAATAAATAATGTATAAATG
1 AGGGACCCTTTCAAATACATATAAAAGAGCTTAAAATAAATAATGTATAAATG
5644478 AG
1 AG
5644480 AAAATTAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (53 bp):
AGGGACCCTTTCAAATACATATAAAAGAGCTTAAAATAAATAATGTATAAATG
Found at i:5644619 original size:25 final size:25
Alignment explanation
Indices: 5644566--5644622 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
5644556 ATATAAGTTT
*
5644566 AAAATAAGTAGTATAAAAATATTTT
1 AAAATAAGTAGTATAAAAATATTTC
*
5644591 AAAATAAGTAAAGTATAGAAA-A-TTC
1 AAAATAAGT--AGTATAAAAATATTTC
5644616 AAAATAA
1 AAAATAA
5644623 ATAATGACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 18 0.64
26 1 0.04
27 9 0.32
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.28
Consensus pattern (25 bp):
AAAATAAGTAGTATAAAAATATTTC
Found at i:5644987 original size:26 final size:26
Alignment explanation
Indices: 5644958--5645037 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
5644948 AATAAAATAA
5644958 GCAAAGAGGGACCAAAATGAAAGGTC
1 GCAAAGAGGGACCAAAATGAAAGGTC
* * * * *
5644984 GCAAATGGGAGGA-GACAAT-AAA-ATAA
1 GCAAA-GAG-GGACCAAAATGAAAGGT-C
5645010 GCAAAGAGGGACCAAAATGAAAGGTC
1 GCAAAGAGGGACCAAAATGAAAGGTC
5645036 GC
1 GC
5645038 GAATGGGAGG
Statistics
Matches: 38, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
24 3 0.08
25 7 0.18
26 18 0.47
27 7 0.18
28 3 0.08
ACGTcount: A:0.47, C:0.14, G:0.30, T:0.09
Consensus pattern (26 bp):
GCAAAGAGGGACCAAAATGAAAGGTC
Found at i:5645004 original size:52 final size:52
Alignment explanation
Indices: 5644948--5645049 Score: 195
Period size: 52 Copynumber: 2.0 Consensus size: 52
5644938 GAAAACTGCA
5644948 AATAAAATAAGCAAAGAGGGACCAAAATGAAAGGTCGCAAATGGGAGGAGAC
1 AATAAAATAAGCAAAGAGGGACCAAAATGAAAGGTCGCAAATGGGAGGAGAC
*
5645000 AATAAAATAAGCAAAGAGGGACCAAAATGAAAGGTCGCGAATGGGAGGAG
1 AATAAAATAAGCAAAGAGGGACCAAAATGAAAGGTCGCAAATGGGAGGAG
5645050 GACCAAACGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.49, C:0.11, G:0.30, T:0.10
Consensus pattern (52 bp):
AATAAAATAAGCAAAGAGGGACCAAAATGAAAGGTCGCAAATGGGAGGAGAC
Found at i:5668638 original size:39 final size:40
Alignment explanation
Indices: 5668590--5668692 Score: 172
Period size: 40 Copynumber: 2.6 Consensus size: 40
5668580 AAGATTAAAT
* *
5668590 TGTAATTTGGGTGATTGTGTACTTGATTAC-AGAAAGAAA
1 TGTATTTTGGGTGATTGTGTACTTGATTACAAAAAAGAAA
*
5668629 TGTATTTTGGGTGATTGCGTACTTGATTACAAAAAAGAAA
1 TGTATTTTGGGTGATTGTGTACTTGATTACAAAAAAGAAA
5668669 TGTATTTTGGGTGATTGTGTACTT
1 TGTATTTTGGGTGATTGTGTACTT
5668693 CTATGAAGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 28 0.47
40 31 0.53
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.40
Consensus pattern (40 bp):
TGTATTTTGGGTGATTGTGTACTTGATTACAAAAAAGAAA
Found at i:5673262 original size:38 final size:38
Alignment explanation
Indices: 5673211--5673557 Score: 514
Period size: 38 Copynumber: 9.1 Consensus size: 38
5673201 ATATTCGACG
* *
5673211 TATATCCGGGTTAAATCCCGCAGGCTTCGTACTAGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* *
5673249 TATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* * *
5673287 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
*
5673325 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* * *
5673363 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
*
5673401 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* * *
5673439 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
*
5673477 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* * * *
5673515 TATATCCGGGTTAAATCTCGCAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
5673553 TATAT
1 TATAT
5673558 TTGGGCCTTT
Statistics
Matches: 277, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 277 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
Found at i:5673557 original size:76 final size:76
Alignment explanation
Indices: 5673211--5673538 Score: 602
Period size: 76 Copynumber: 4.3 Consensus size: 76
5673201 ATATTCGACG
* * ** * *
5673211 TATATCCGGGTTAAATCCCGCAGGCTTCGTACTAGTAATATATCCGGGTTAAATCCTGCAGGCTT
1 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
5673276 CGTGCTGGTAT
66 CGTGCTGGTAT
5673287 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
1 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
5673352 CGTGCTGGTAT
66 CGTGCTGGTAT
5673363 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
1 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
5673428 CGTGCTGGTAT
66 CGTGCTGGTAT
5673439 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
1 TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
5673504 CGTGCTGGTAT
66 CGTGCTGGTAT
5673515 TATATCCGGGTTAAATCTCGCAGG
1 TATATCCGGGTTAAATCTCGCAGG
5673539 CCTAGTGCTG
Statistics
Matches: 246, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 246 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (76 bp):
TATATCCGGGTTAAATCTCGCAGGTTTCGTGTTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
CGTGCTGGTAT
Found at i:5675912 original size:16 final size:17
Alignment explanation
Indices: 5675891--5675924 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5675881 ATTAAAAGAA
5675891 AAGGAAAGATT-TTTAC
1 AAGGAAAGATTGTTTAC
*
5675907 AAGGAAAGGTTGTTTAC
1 AAGGAAAGATTGTTTAC
5675924 A
1 A
5675925 GAGAGAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (17 bp):
AAGGAAAGATTGTTTAC
Found at i:5677596 original size:18 final size:18
Alignment explanation
Indices: 5677569--5677621 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
5677559 TGTTAATATA
*
5677569 GGAGTAAATCCCTGATTG
1 GGAGTAAATCCTTGATTG
*
5677587 GGAGTCAATCCTTGATTG
1 GGAGTAAATCCTTGATTG
*
5677605 GTAGTAAATCCTTGATT
1 GGAGTAAATCCTTGATT
5677622 AGGATTTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (18 bp):
GGAGTAAATCCTTGATTG
Found at i:5682981 original size:16 final size:17
Alignment explanation
Indices: 5682960--5682993 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5682950 ATTAAAAGAA
5682960 AAGGAAAGATT-TTTAC
1 AAGGAAAGATTGTTTAC
*
5682976 AAGGAAAGGTTGTTTAC
1 AAGGAAAGATTGTTTAC
5682993 A
1 A
5682994 GAAAGAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (17 bp):
AAGGAAAGATTGTTTAC
Found at i:5689820 original size:13 final size:13
Alignment explanation
Indices: 5689802--5689830 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5689792 CTTAGTTTAA
5689802 TTAGTTAATTAGT
1 TTAGTTAATTAGT
5689815 TTAGTTAATTAGT
1 TTAGTTAATTAGT
5689828 TTA
1 TTA
5689831 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:5695251 original size:8 final size:7
Alignment explanation
Indices: 5695238--5695286 Score: 54
Period size: 6 Copynumber: 7.6 Consensus size: 7
5695228 CATTGAATCC
5695238 TTTTATCT
1 TTTTAT-T
5695246 TTTTA-T
1 TTTTATT
5695252 TTTTA-T
1 TTTTATT
5695258 TTTTA-T
1 TTTTATT
5695264 TTTTA-T
1 TTTTATT
5695270 TTTTA-T
1 TTTTATT
5695276 TTTTATT
1 TTTTATT
5695283 TTTT
1 TTTT
5695287 TTCAATTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 30 0.75
7 5 0.12
8 5 0.12
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:5695256 original size:6 final size:6
Alignment explanation
Indices: 5695245--5695285 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
5695235 TCCTTTTATC
5695245 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
5695286 TTTCAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:5707508 original size:21 final size:20
Alignment explanation
Indices: 5707480--5707519 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5707470 CAAAACTTGT
5707480 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
5707500 ATAATCTATCATCAATCATT
1 ATAA-CTATCATCAAACATT
5707520 AAAATACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:5715947 original size:45 final size:45
Alignment explanation
Indices: 5715880--5715968 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
5715870 GGTTGATAAA
* *
5715880 GTGTGCAAGAACTGTCCGTTGATGA-TTCGGGATAATTGTTTTCCT
1 GTGTGCAAGAACTGTCCATTGATGACTT-GAGATAATTGTTTTCCT
* *
5715925 GTGTGCAAGAATTGTCTATTGATGACTTGAGATAATTGTTTTCC
1 GTGTGCAAGAACTGTCCATTGATGACTTGAGATAATTGTTTTCC
5715969 GGCCAATCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 37 0.95
46 2 0.05
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.39
Consensus pattern (45 bp):
GTGTGCAAGAACTGTCCATTGATGACTTGAGATAATTGTTTTCCT
Found at i:5720447 original size:43 final size:43
Alignment explanation
Indices: 5720358--5720458 Score: 134
Period size: 43 Copynumber: 2.3 Consensus size: 43
5720348 TGTGATTACA
* *
5720358 TGTAAGACCATGTTTGGGACATTGGCATCGTATTGAGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTAATGAGATTATG
*
5720401 TGTAAGACCATGTCTGGGACATTGGCATCGTTAAT-CGATT-TCG
1 TGTAAGACCATGTCTGGGACATTGGCATCG-TAATGAGATTAT-G
*
5720444 TGTAAGACCCTGTCT
1 TGTAAGACCATGTCT
5720459 AGGATGGTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
42 1 0.02
43 48 0.92
44 3 0.06
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTAATGAGATTATG
Found at i:5721609 original size:11 final size:11
Alignment explanation
Indices: 5721593--5721619 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5721583 CTACAGTTTT
5721593 GACACGGCCTA
1 GACACGGCCTA
5721604 GACACGGCCTA
1 GACACGGCCTA
5721615 GACAC
1 GACAC
5721620 TTGGGCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.37, G:0.26, T:0.07
Consensus pattern (11 bp):
GACACGGCCTA
Found at i:5731503 original size:24 final size:24
Alignment explanation
Indices: 5731471--5731521 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5731461 GAGGATCCAC
* *
5731471 GTCCGGCTTCGGCTCTGACTCCGA
1 GTCCGGCTTCAGCTCCGACTCCGA
*
5731495 GTCCGGCTTCAGCTCCGACTCTGA
1 GTCCGGCTTCAGCTCCGACTCCGA
5731519 GTC
1 GTC
5731522 TGGTTTCGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.25
Consensus pattern (24 bp):
GTCCGGCTTCAGCTCCGACTCCGA
Found at i:5736910 original size:13 final size:13
Alignment explanation
Indices: 5736878--5736904 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5736868 TATATTGTAC
5736878 TCAATTTAACCTT
1 TCAATTTAACCTT
5736891 TCAATTTAACCTT
1 TCAATTTAACCTT
5736904 T
1 T
5736905 ATATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAATTTAACCTT
Found at i:5749957 original size:13 final size:13
Alignment explanation
Indices: 5749941--5749966 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5749931 AGGGATTTGT
5749941 TTAACTAAACTAA
1 TTAACTAAACTAA
5749954 TTAACTAAACTAA
1 TTAACTAAACTAA
5749967 GGGTGCACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACTAAACTAA
Found at i:5754489 original size:30 final size:30
Alignment explanation
Indices: 5754455--5754521 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
5754445 TCCCTAACTC
* *
5754455 AATTAAGCCCTTC-TAAAATAACTAAAAATA-
1 AATTAAG-CCATCATAAAATAA-TAAAAAAAT
5754485 AATTAAGCCATCATAAAATAATAAAAAAAT
1 AATTAAGCCATCATAAAATAATAAAAAAAT
5754515 AATTAAG
1 AATTAAG
5754522 TCCTCCACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 11 0.33
30 22 0.67
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.25
Consensus pattern (30 bp):
AATTAAGCCATCATAAAATAATAAAAAAAT
Found at i:5761544 original size:20 final size:21
Alignment explanation
Indices: 5761519--5761574 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
5761509 ATATTAAAAT
5761519 ATTAAAAACAA-AAAAATATC
1 ATTAAAAACAATAAAAATATC
*
5761539 ATTAAAAATAATAAAAATAT-
1 ATTAAAAACAATAAAAATATC
*
5761559 A-TAAAAA-ATTAAAAAT
1 ATTAAAAACAATAAAAAT
5761575 TATGACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 11 0.33
21 8 0.24
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (21 bp):
ATTAAAAACAATAAAAATATC
Found at i:5761963 original size:3 final size:3
Alignment explanation
Indices: 5761955--5761986 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5761945 TATCAAGCGG
5761955 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5761987 AGGACACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5767525 original size:47 final size:47
Alignment explanation
Indices: 5767464--5767558 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
5767454 ATGAATCACC
5767464 TTCTGAGCTTTTCATTGCTAATTCTTTCCCATTATACAAATGAACTA
1 TTCTGAGCTTTTCATTGCTAATTCTTTCCCATTATACAAATGAACTA
5767511 TTCTGAGCTTTTCATTGCTAATTCTTTCCCATTATACAAATGAACTA
1 TTCTGAGCTTTTCATTGCTAATTCTTTCCCATTATACAAATGAACTA
5767558 T
1 T
5767559 GTCCCATTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.43
Consensus pattern (47 bp):
TTCTGAGCTTTTCATTGCTAATTCTTTCCCATTATACAAATGAACTA
Found at i:5770485 original size:14 final size:13
Alignment explanation
Indices: 5770468--5770504 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
5770458 TTTTTCCTTC
5770468 TTTTGTTTTTTTT
1 TTTTGTTTTTTTT
5770481 GTTTTGTTTTTTTT
1 -TTTTGTTTTTTTT
5770495 TTTT-TTTTTT
1 TTTTGTTTTTT
5770505 CGGGATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.26
13 4 0.17
14 13 0.57
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTGTTTTTTTT
Found at i:5771891 original size:5 final size:5
Alignment explanation
Indices: 5771881--5771913 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
5771871 AGAAATTAGA
5771881 ATATT ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATA
5771914 CATATAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:5772526 original size:69 final size:69
Alignment explanation
Indices: 5772423--5772560 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
5772413 TTCAATAAAA
5772423 AGTCAACCTGACCCACCGCAAAACCCAATTAAAAAAAAAAACCTATAGGATTGGGATGTAAAAAT
1 AGTCAACCTGACCCACCGCAAAACCCAATTAAAAAAAAAAACCTATAGGATTGGGATGTAAAAAT
5772488 GATG
66 GATG
5772492 AGTCAACCTGACCCACCGCAAAACCCAATTAAAAAAAAAAACCTATAGGATTGGGATGTAAAAAT
1 AGTCAACCTGACCCACCGCAAAACCCAATTAAAAAAAAAAACCTATAGGATTGGGATGTAAAAAT
5772557 GATG
66 GATG
5772561 TCGGTTTAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.17
Consensus pattern (69 bp):
AGTCAACCTGACCCACCGCAAAACCCAATTAAAAAAAAAAACCTATAGGATTGGGATGTAAAAAT
GATG
Found at i:5778181 original size:12 final size:12
Alignment explanation
Indices: 5778156--5778190 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
5778146 TAAGGAGGAA
*
5778156 AAAAAGCAAAAAG
1 AAAAAG-AAGAAG
5778169 AAAAAGAAGAAG
1 AAAAAGAAGAAG
5778181 AAAAAGAAGA
1 AAAAAGAAGA
5778191 GAGAGTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:5779776 original size:48 final size:48
Alignment explanation
Indices: 5779698--5779799 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 48
5779688 AATATTTACT
** *
5779698 AAATTAAAATTAATATAACATCAAAATTAAAACCCAAAGTTAAAACTTA
1 AAATTAAAAAAAATATAACATCAAAATTAAAACCCAAAGTTAAAAC-CA
* * ** *
5779747 AAATTAAAAAAAAT-TAACATCACAGTTAAAATTCAAATTTAAAACCA
1 AAATTAAAAAAAATATAACATCAAAATTAAAACCCAAAGTTAAAACCA
5779794 AAATTA
1 AAATTA
5779800 GCTTAAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
47 7 0.16
48 26 0.58
49 12 0.27
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (48 bp):
AAATTAAAAAAAATATAACATCAAAATTAAAACCCAAAGTTAAAACCA
Found at i:5788890 original size:9 final size:9
Alignment explanation
Indices: 5788876--5788900 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5788866 CAGATGCAAA
5788876 TATATAGTG
1 TATATAGTG
5788885 TATATAGTG
1 TATATAGTG
5788894 TATATAG
1 TATATAG
5788901 ATATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (9 bp):
TATATAGTG
Found at i:5792379 original size:22 final size:24
Alignment explanation
Indices: 5792354--5792397 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
5792344 ATTTCTCAAA
5792354 TTTATAATTTT-CCCTT-TTTTAT
1 TTTATAATTTTGCCCTTATTTTAT
*
5792376 TTTATAGTTTTGCCCTTATTTT
1 TTTATAATTTTGCCCTTATTTT
5792398 TTAGATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 5 0.26
24 4 0.21
ACGTcount: A:0.16, C:0.14, G:0.05, T:0.66
Consensus pattern (24 bp):
TTTATAATTTTGCCCTTATTTTAT
Found at i:5792405 original size:28 final size:28
Alignment explanation
Indices: 5792374--5792442 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
5792364 TCCCTTTTTT
** *
5792374 ATTTTATAGTTTTG-CCCTTATTTTTTAG
1 ATTTTATAGTTTTGTCCC-TATTTTCCAA
* *
5792402 ATTTTACAATTTTGTCCCTATTTTCCAA
1 ATTTTATAGTTTTGTCCCTATTTTCCAA
5792430 ATTTTATAGTTTT
1 ATTTTATAGTTTT
5792443 ACCCAAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (28 bp):
ATTTTATAGTTTTGTCCCTATTTTCCAA
Found at i:5795936 original size:20 final size:20
Alignment explanation
Indices: 5795907--5795948 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
5795897 AGGGACACAC
*
5795907 GCCCGTGTGGACAAAAATAG
1 GCCCGCGTGGACAAAAATAG
5795927 GCCCGCGTGGACAAAAATAG
1 GCCCGCGTGGACAAAAATAG
5795947 GC
1 GC
5795949 TAATTGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.31, T:0.12
Consensus pattern (20 bp):
GCCCGCGTGGACAAAAATAG
Found at i:5796959 original size:43 final size:43
Alignment explanation
Indices: 5796892--5797060 Score: 164
Period size: 43 Copynumber: 4.0 Consensus size: 43
5796882 TAAGCTCGTA
* * * *
5796892 CAATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATAT
* * * * * * *
5796934 CGATGCCACTGTTCCAGACAGGGTCTTGCACGAAATCATA-AT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATAT
* *
5796976 ACAATGCCAATATCCCAGACATGGTCTTACACATAATCACAGTAT
1 -CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCACA-TAT
* *
5797021 -AATGCCAATGTCCCAGACATGGTCTTACATGTCATCACAT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAT
5797061 CTCGATAACC
Statistics
Matches: 99, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
42 9 0.09
43 88 0.89
45 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (43 bp):
CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATAT
Found at i:5797045 original size:86 final size:85
Alignment explanation
Indices: 5796890--5797046 Score: 217
Period size: 86 Copynumber: 1.8 Consensus size: 85
5796880 CATAAGCTCG
* ** * * * *
5796890 TACAATGCCATATCCCAGATATGGTCTTACATGTTATCACATATCGATGCCACTGTTCCAGACAG
1 TACAATGCCATATCCCAGACATGGTCTTACACATAATCACATATCAATGCCAATGTCCCAGACAG
5796955 GGTCTTGCACGAAATCATAA
66 GGTCTTGCACGAAATCATAA
5796975 TACAATGCCAATATCCCAGACATGGTCTTACACATAATCACAGTAT-AATGCCAATGTCCCAGAC
1 TACAATGCC-ATATCCCAGACATGGTCTTACACATAATCACA-TATCAATGCCAATGTCCCAGAC
*
5797039 ATGGTCTT
64 AGGGTCTT
5797047 ACATGTCATC
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
85 9 0.15
86 50 0.81
87 3 0.05
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (85 bp):
TACAATGCCATATCCCAGACATGGTCTTACACATAATCACATATCAATGCCAATGTCCCAGACAG
GGTCTTGCACGAAATCATAA
Found at i:5800541 original size:28 final size:28
Alignment explanation
Indices: 5800510--5800566 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5800500 GGATATCAAA
5800510 AACTAAAAAATGAAAATATAGAATTTTG
1 AACTAAAAAATGAAAATATAGAATTTTG
5800538 AACTAAAAAATGAAAATATAGAATTTTG
1 AACTAAAAAATGAAAATATAGAATTTTG
5800566 A
1 A
5800567 GAAAACCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.28
Consensus pattern (28 bp):
AACTAAAAAATGAAAATATAGAATTTTG
Found at i:5814288 original size:9 final size:9
Alignment explanation
Indices: 5814276--5814301 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5814266 TTTTAGGCCC
5814276 TTTAAATTT
1 TTTAAATTT
5814285 TTTAAATTT
1 TTTAAATTT
5814294 TTTAAATT
1 TTTAAATT
5814302 AGTAAAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTAAATTT
Found at i:5815789 original size:20 final size:20
Alignment explanation
Indices: 5815766--5815805 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5815756 GTAAAAAATA
5815766 AAGTCAAATTATAAATAATT
1 AAGTCAAATTATAAATAATT
*
5815786 AAGTCGAATTATAAATAATT
1 AAGTCAAATTATAAATAATT
5815806 TATATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (20 bp):
AAGTCAAATTATAAATAATT
Found at i:5817537 original size:22 final size:21
Alignment explanation
Indices: 5817499--5817539 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5817489 AATTTTTTAA
* *
5817499 ATATATAATTTTTTATGTAAT
1 ATATATAATTATATATGTAAT
5817520 ATATAGTAATTATATATGTA
1 ATATA-TAATTATATATGTA
5817540 CCTTTTACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
ATATATAATTATATATGTAAT
Found at i:5821836 original size:14 final size:15
Alignment explanation
Indices: 5821807--5821847 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
5821797 TTTAGGTTTG
5821807 AAAATTTTAATTAATT
1 AAAATTTT-ATTAATT
5821823 AAAATTTT-TTAATT
1 AAAATTTTATTAATT
*
5821837 AAAAATTTATT
1 AAAATTTTATT
5821848 TTCATCCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 13 0.57
15 2 0.09
16 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAAATTTTATTAATT
Found at i:5822780 original size:154 final size:154
Alignment explanation
Indices: 5822498--5822776 Score: 384
Period size: 154 Copynumber: 1.8 Consensus size: 154
5822488 AAGTATATAG
*
5822498 ATTAAATCTCAAATTTGAGCCAAATAAAGGGATAAAAAATAAAATTTAACCAATCTTATATAATC
1 ATTAAATCTCAAATTTGAGCCAAATAAA-GGATAAAAAATAAAATTTAACCAATCTTATACAATC
* * * ***
5822563 TTTAAAAGGTAGATGGATTAGAACTGAAATTTAGCCATTATTTTCTCATGTCAAAAGAAAAGAAA
65 TTAAAAAGATAGATGGATTAGAACTGAAATTTAGCCATTAATTTCTCAAACCAAAAGAAAAGAAA
5822628 AGAAAAGTGTCTAAATTATGTCAAA
130 AGAAAAGTGTCTAAATTATGTCAAA
** * * * *
5822653 ATTAAATCTCAAATTTGAGTGAAATATAA-GATCAGAACTAAAATTTAACCATTCTTATACAATC
1 ATTAAATCTCAAATTTGAGCCAAATA-AAGGATAAAAAATAAAATTTAACCAATCTTATACAATC
*
5822717 TTAAAAAGATAGA-GGATTAGAACTGAAATTTAGCTATTACATTT-TCAAACCAAAAGAAAA
65 TTAAAAAGATAGATGGATTAGAACTGAAATTTAGCCATTA-ATTTCTCAAACCAAAAGAAAA
5822777 AGAATGAATA
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
153 38 0.35
154 44 0.41
155 24 0.22
156 2 0.02
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (154 bp):
ATTAAATCTCAAATTTGAGCCAAATAAAGGATAAAAAATAAAATTTAACCAATCTTATACAATCT
TAAAAAGATAGATGGATTAGAACTGAAATTTAGCCATTAATTTCTCAAACCAAAAGAAAAGAAAA
GAAAAGTGTCTAAATTATGTCAAA
Found at i:5823259 original size:12 final size:13
Alignment explanation
Indices: 5823242--5823270 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5823232 TTTTTCTTTT
5823242 TATACTATTTA-A
1 TATACTATTTATA
5823254 TATACTATTTATA
1 TATACTATTTATA
5823267 TATA
1 TATA
5823271 TACATACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (13 bp):
TATACTATTTATA
Found at i:5824853 original size:18 final size:18
Alignment explanation
Indices: 5824830--5824875 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
5824820 TATGATAATG
5824830 CATATATAAAATCATGGA
1 CATATATAAAATCATGGA
5824848 CATATATAAAATCATGGA
1 CATATATAAAATCATGGA
5824866 CATATA-AAAA
1 CATATATAAAA
5824876 CTGTTTTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.26
Consensus pattern (18 bp):
CATATATAAAATCATGGA
Found at i:5829315 original size:23 final size:25
Alignment explanation
Indices: 5829275--5829328 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
5829265 TGAGGTTATG
5829275 TTGGTATGCTAGCCTAGTTT-ATATT
1 TTGGTATGCTAGCCTAGTTTCATA-T
*
5829300 TTGGTATG-T-GCTTAGTTTCATAT
1 TTGGTATGCTAGCCTAGTTTCATAT
5829323 TTGGTA
1 TTGGTA
5829329 ACTTTAGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 15 0.56
24 4 0.15
25 8 0.30
ACGTcount: A:0.19, C:0.09, G:0.22, T:0.50
Consensus pattern (25 bp):
TTGGTATGCTAGCCTAGTTTCATAT
Found at i:5829396 original size:30 final size:30
Alignment explanation
Indices: 5829360--5829419 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5829350 GTTCAAATAT
5829360 GGTAAGTGCGATATGAATGAAAGTCTTGAA
1 GGTAAGTGCGATATGAATGAAAGTCTTGAA
*
5829390 GGTAAGTGTGATATGAATGAAAGTCTTGAA
1 GGTAAGTGCGATATGAATGAAAGTCTTGAA
5829420 TGTTTGATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.30, T:0.28
Consensus pattern (30 bp):
GGTAAGTGCGATATGAATGAAAGTCTTGAA
Found at i:5830094 original size:49 final size:49
Alignment explanation
Indices: 5830017--5830117 Score: 166
Period size: 49 Copynumber: 2.1 Consensus size: 49
5830007 TCTAGAAGGG
* * *
5830017 ATAAATAGTGATAAGAGTGTAGATAGTGGAAGACTAAATTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAATTTAGAAATGT
*
5830066 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGAAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAATTTAGAAATGT
5830115 ATA
1 ATA
5830118 GCATAATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.44, C:0.05, G:0.25, T:0.27
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAATTTAGAAATGT
Found at i:5831695 original size:28 final size:28
Alignment explanation
Indices: 5831654--5831708 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5831644 AATCTTACTT
* * *
5831654 ATAAGATATTCCTGACGGACTTCCACAC
1 ATAACATAGTCCTGACGAACTTCCACAC
*
5831682 ATAACATAGTCCTGGCGAACTTCCACA
1 ATAACATAGTCCTGACGAACTTCCACA
5831709 TATTTTTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.24
Consensus pattern (28 bp):
ATAACATAGTCCTGACGAACTTCCACAC
Found at i:5838681 original size:19 final size:18
Alignment explanation
Indices: 5838645--5838685 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
5838635 AGATTAAAGT
*
5838645 TTAATTAATTATGATTAAA
1 TTAATTAATTAGGATT-AA
*
5838664 TTAATTAATTAGGTTTAA
1 TTAATTAATTAGGATTAA
5838682 TTAA
1 TTAA
5838686 AATTAAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (18 bp):
TTAATTAATTAGGATTAA
Found at i:5845935 original size:40 final size:38
Alignment explanation
Indices: 5845824--5845943 Score: 134
Period size: 38 Copynumber: 3.1 Consensus size: 38
5845814 ATATGCTAGA
* *
5845824 ATTATATTCGGGTTAAAT-CCGCAGGCTTCGTGCTGGT
1 ATTATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGT
* * * *
5845861 AATATATCCGTGTTAAATCCCGCAGGCCTAGTGCTGGT
1 ATTATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGT
* *
5845899 ATTATATCTGAGTTTAAAGTCCCGTAGGCTTCGTGCTGGT
1 ATTATATCCGAG-TTAAA-TCCCGCAGGCTTCGTGCTGGT
*
5845939 GTTAT
1 ATTAT
5845944 GTTTGGGTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
37 15 0.22
38 26 0.38
39 5 0.07
40 22 0.32
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (38 bp):
ATTATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGT
Found at i:5846992 original size:16 final size:16
Alignment explanation
Indices: 5846971--5847030 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
5846961 TAAACACTCA
5846971 ATTTATTTTTTTATTC
1 ATTTATTTTTTTATTC
** *
5846987 ATTTATTTTTAACACTC
1 ATTTATTTTT-TTATTC
5847004 AATTTATTTTTTTATTC
1 -ATTTATTTTTTTATTC
5847021 ATTTATTTTT
1 ATTTATTTTT
5847031 ACTCTCCTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 20 0.56
17 6 0.17
18 10 0.28
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTATTTTTTTATTC
Found at i:5847004 original size:34 final size:34
Alignment explanation
Indices: 5846963--5847031 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5846953 ACTGGGTATA
5846963 AACACTCAATTTATTTTTTTATTCATTTATTTTT
1 AACACTCAATTTATTTTTTTATTCATTTATTTTT
5846997 AACACTCAATTTATTTTTTTATTCATTTATTTTT
1 AACACTCAATTTATTTTTTTATTCATTTATTTTT
5847031 A
1 A
5847032 CTCTCCTCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.61
Consensus pattern (34 bp):
AACACTCAATTTATTTTTTTATTCATTTATTTTT
Found at i:5847013 original size:17 final size:17
Alignment explanation
Indices: 5846963--5847013 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
5846953 ACTGGGTATA
5846963 AACACTCAATTTATTTT
1 AACACTCAATTTATTTT
*** *
5846980 TTTATTC-ATTTATTTTT
1 AACACTCAATTTA-TTTT
5846997 AACACTCAATTTATTTT
1 AACACTCAATTTATTTT
5847014 TTTATTCATT
Statistics
Matches: 24, Mismatches: 8, Indels: 4
0.67 0.22 0.11
Matches are distributed among these distances:
16 5 0.21
17 14 0.58
18 5 0.21
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (17 bp):
AACACTCAATTTATTTT
Found at i:5851480 original size:6 final size:6
Alignment explanation
Indices: 5851460--5851511 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
5851450 TTCAAAATAG
* * * * *
5851460 AAAGAC AAA-AT AAAGAT AAAGAT AAAAAT AAACAT AAAAAT AAACAT
1 AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT
5851507 AAAGA
1 AAAGA
5851512 GAAATGGACT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
5 4 0.10
6 35 0.90
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (6 bp):
AAAGAT
Found at i:5851489 original size:18 final size:18
Alignment explanation
Indices: 5851466--5851511 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5851456 ATAGAAAGAC
*
5851466 AAAATAAAGATAAAGATA
1 AAAATAAAGATAAAAATA
*
5851484 AAAATAAACATAAAAATA
1 AAAATAAAGATAAAAATA
*
5851502 AACATAAAGA
1 AAAATAAAGA
5851512 GAAATGGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAATAAAGATAAAAATA
Found at i:5851490 original size:12 final size:12
Alignment explanation
Indices: 5851469--5851509 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
5851459 GAAAGACAAA
* *
5851469 ATAAAGATAAAG
1 ATAAAAATAAAC
5851481 ATAAAAATAAAC
1 ATAAAAATAAAC
5851493 ATAAAAATAAAC
1 ATAAAAATAAAC
5851505 ATAAA
1 ATAAA
5851510 GAGAAATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (12 bp):
ATAAAAATAAAC
Found at i:5853187 original size:16 final size:16
Alignment explanation
Indices: 5853168--5853202 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5853158 TAAAGAAATG
5853168 TAATAAATAA-TAAGCA
1 TAATAAATAACTAA-CA
5853184 TAATAAATAACTAACA
1 TAATAAATAACTAACA
5853200 TAA
1 TAA
5853203 AATATCTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.63, C:0.09, G:0.03, T:0.26
Consensus pattern (16 bp):
TAATAAATAACTAACA
Found at i:5865585 original size:30 final size:29
Alignment explanation
Indices: 5865530--5865607 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 29
5865520 TAACATAAGT
* *
5865530 TTAGCCTGTACGAGCAACCTAATATAAAA
1 TTAGCTTGTATGAGCAACCTAATATAAAA
* * *
5865559 TTAGCTTGTGTGAGCAATCTTAATATAAAT
1 TTAGCTTGTATGAGCAA-CCTAATATAAAA
5865589 TTAGCTTGTATGAGCAACC
1 TTAGCTTGTATGAGCAACC
5865608 CTGATGTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (29 bp):
TTAGCTTGTATGAGCAACCTAATATAAAA
Found at i:5867687 original size:29 final size:29
Alignment explanation
Indices: 5867638--5867712 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
5867628 AGAGCTTAAT
*
5867638 TAAAATATTTTAAAAAATTAAAAGGTATAA
1 TAAAA-ATTTTCAAAAATTAAAAGGTATAA
*** * * *
5867668 TGTGAATTTTCAAAATTTAAAGGGTCTAA
1 TAAAAATTTTCAAAAATTAAAAGGTATAA
5867697 TAAAAATTTTCAAAAA
1 TAAAAATTTTCAAAAA
5867713 ATTTCAAGGA
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
29 32 0.94
30 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (29 bp):
TAAAAATTTTCAAAAATTAAAAGGTATAA
Found at i:5876899 original size:30 final size:30
Alignment explanation
Indices: 5876863--5876922 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
5876853 ATTGATTTCC
5876863 AAGTTTATAACACCCTTGTTTCTTGCATAA
1 AAGTTTATAACACCCTTGTTTCTTGCATAA
5876893 AAGTTTATAACACCCTTGTTTCTTGCATAA
1 AAGTTTATAACACCCTTGTTTCTTGCATAA
5876923 CTTTCTCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (30 bp):
AAGTTTATAACACCCTTGTTTCTTGCATAA
Found at i:5886720 original size:21 final size:21
Alignment explanation
Indices: 5886695--5886759 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
5886685 TAGCCTCCGG
5886695 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
* * *
5886716 GCTTCAG-TTAGC-CTT-CGG
1 GCTTCCGTTTAGCACTTATGT
*
5886734 GCTGCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
5886755 GCTTC
1 GCTTC
5886760 AGCTAGATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 8 0.24
21 11 0.33
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.38
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTATGT
Found at i:5886720 original size:39 final size:39
Alignment explanation
Indices: 5886677--5886761 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
5886667 GCTCTGATGA
*
5886677 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTGCCGTTTAGCACTTATGT
*
5886716 GCTTCAGTTAGCCTTCGGGCTGCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTGCCGTTTAGCACTTATGT
5886755 GCTTCAG
1 GCTTCAG
5886762 CTAGATTTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.13, C:0.27, G:0.25, T:0.35
Consensus pattern (39 bp):
GCTTCAGTTAGCCTCCGGGCTGCCGTTTAGCACTTATGT
Found at i:5886772 original size:39 final size:39
Alignment explanation
Indices: 5886677--5886775 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
5886667 GCTCTGATGA
* * * *
5886677 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGCTAGACTTCGGGCTGCCGTTTAGCACTTATGT
* *
5886716 GCTTCAGTTAGCCTTCGGGCTGCCGTTTAGCACTTATGT
1 GCTTCAGCTAGACTTCGGGCTGCCGTTTAGCACTTATGT
*
5886755 GCTTCAGCTAGATTTCGGGCT
1 GCTTCAGCTAGACTTCGGGCT
5886776 TCAGATCACG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.13, C:0.26, G:0.25, T:0.35
Consensus pattern (39 bp):
GCTTCAGCTAGACTTCGGGCTGCCGTTTAGCACTTATGT
Found at i:5891968 original size:24 final size:24
Alignment explanation
Indices: 5891923--5891969 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5891913 AACATTATTA
*
5891923 TTTTTAATATATCAAATGATATAT
1 TTTTTAACATATCAAATGATATAT
5891947 TTTTTAACATA-CAAATGA-ATAT
1 TTTTTAACATATCAAATGATATAT
5891969 T
1 T
5891970 AATATTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 7 0.32
24 10 0.45
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTTTAACATATCAAATGATATAT
Found at i:5894122 original size:18 final size:19
Alignment explanation
Indices: 5894089--5894124 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5894079 TTATTCAAAT
*
5894089 TATAATTGATTATTTTTTA
1 TATAAATGATTATTTTTTA
5894108 TATAAATGA-TATTTTTT
1 TATAAATGATTATTTTTT
5894125 GGGTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TATAAATGATTATTTTTTA
Found at i:5894447 original size:7 final size:7
Alignment explanation
Indices: 5894435--5894471 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
5894425 CTCAAACTCT
5894435 AATATTA
1 AATATTA
5894442 AATATTA
1 AATATTA
5894449 AATATTA
1 AATATTA
**
5894456 AAGCTTA
1 AATATTA
5894463 AATATTA
1 AATATTA
5894470 AA
1 AA
5894472 GCTTAAACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (7 bp):
AATATTA
Found at i:5894454 original size:14 final size:14
Alignment explanation
Indices: 5894435--5894478 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
5894425 CTCAAACTCT
*
5894435 AATATTAAATATTA
1 AATATTAAAGATTA
*
5894449 AATATTAAAGCTTA
1 AATATTAAAGATTA
*
5894463 AATATTAAAGCTTA
1 AATATTAAAGATTA
5894477 AA
1 AA
5894479 CCCTATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (14 bp):
AATATTAAAGATTA
Found at i:5894477 original size:21 final size:21
Alignment explanation
Indices: 5894439--5894478 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5894429 AACTCTAATA
*
5894439 TTAAATATTAAATATTAAAGC
1 TTAAATATTAAAGATTAAAGC
*
5894460 TTAAATATTAAAGCTTAAA
1 TTAAATATTAAAGATTAAA
5894479 CCCTATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
TTAAATATTAAAGATTAAAGC
Found at i:5894845 original size:20 final size:19
Alignment explanation
Indices: 5894801--5894845 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5894791 TATAGTTTTA
* *
5894801 TAATTAATAAAAATTAAAT
1 TAATTAAAAAAAATTAAAG
5894820 TAAATTAAAAAAAATTTAAAG
1 T-AATTAAAAAAAA-TTAAAG
5894841 TAATT
1 TAATT
5894846 TTGATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 15 0.68
21 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TAATTAAAAAAAATTAAAG
Found at i:5904381 original size:24 final size:24
Alignment explanation
Indices: 5904349--5904417 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
5904339 ATTATCTTCG
*
5904349 TCTTCTTCATCTTCACCTCGACCC
1 TCTTCTTCATCTTCACCTCCACCC
* *
5904373 TCTTCTTCATCTTTATCTCCACCC
1 TCTTCTTCATCTTCACCTCCACCC
* * *
5904397 CCGTCTTCATCTTCATCTCCA
1 TCTTCTTCATCTTCACCTCCA
5904418 TCTCTTTCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.13, C:0.43, G:0.03, T:0.41
Consensus pattern (24 bp):
TCTTCTTCATCTTCACCTCCACCC
Found at i:5904427 original size:24 final size:23
Alignment explanation
Indices: 5904351--5904428 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
5904341 TATCTTCGTC
* *
5904351 TTCTTCATCTTCACCTCGACCCT
1 TTCTTCATCTTCATCTCCACCCT
* *
5904374 CTTCTTCATCTTTATCTCCACCCCC
1 -TTCTTCATCTTCATCTCCA-CCCT
* *
5904399 GTCTTCATCTTCATCTCCATCTCT
1 TTCTTCATCTTCATCTCCA-CCCT
5904423 TTCTTC
1 TTCTTC
5904429 TGTGGTTAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 40 0.93
25 3 0.07
ACGTcount: A:0.12, C:0.42, G:0.03, T:0.44
Consensus pattern (23 bp):
TTCTTCATCTTCATCTCCACCCT
Found at i:5908046 original size:155 final size:154
Alignment explanation
Indices: 5907812--5908121 Score: 530
Period size: 155 Copynumber: 2.0 Consensus size: 154
5907802 ACATTAAAAA
* * *
5907812 TATTAAAATAAATGTTTCCTAACAAATTGAAAATACAAAAAAAAATATAGCATGTGATTTGCGCT
1 TATTAAAATAAATATTTCCCAACAAATTGAAAATACAAAAAAAAATATAACATGTGATTTGCGCT
* * *
5907877 GGGCTCAGGCCGAAAAGAAATTTGTCCAATTCCTTACCCTTTTTTAGGTTTATATTTTTACCTAA
66 GGGCCCAGGCCGAAAAGAAATTTGTCCAATTCCTTACCCATTTTTAGGTCTATATTTTTACCTAA
5907942 ACCCTCCCAATTTTCAGCTAACCT
131 ACCCTCCCAATTTTCAGCTAACCT
*
5907966 TATTAAAATAAATATTTCCCAACAAATTGAAAATACAAAAAAAAAATATAACATGTGATTTGGGC
1 TATTAAAATAAATATTTCCCAACAAATTGAAAATAC-AAAAAAAAATATAACATGTGATTTGCGC
* *
5908031 TGGGCCCAGGCCGAAAAGAAATTTGTCCAATTCCTTGCCCATTTTTAGGTCTATATTTTTGCCTA
65 TGGGCCCAGGCCGAAAAGAAATTTGTCCAATTCCTTACCCATTTTTAGGTCTATATTTTTACCTA
5908096 AACCCTCCCAATTTTCAGCTAACCT
130 AACCCTCCCAATTTTCAGCTAACCT
5908121 T
1 T
5908122 TGAGTCTAGA
Statistics
Matches: 146, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
154 34 0.23
155 112 0.77
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (154 bp):
TATTAAAATAAATATTTCCCAACAAATTGAAAATACAAAAAAAAATATAACATGTGATTTGCGCT
GGGCCCAGGCCGAAAAGAAATTTGTCCAATTCCTTACCCATTTTTAGGTCTATATTTTTACCTAA
ACCCTCCCAATTTTCAGCTAACCT
Found at i:5910742 original size:14 final size:14
Alignment explanation
Indices: 5910723--5910750 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5910713 AGGTAAAAAA
5910723 AATTAGGGTAAATT
1 AATTAGGGTAAATT
5910737 AATTAGGGTAAATT
1 AATTAGGGTAAATT
5910751 GTACAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
AATTAGGGTAAATT
Found at i:5919603 original size:27 final size:27
Alignment explanation
Indices: 5919573--5919627 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5919563 TTACCAATAA
*
5919573 AAGAGAACCTTTTGCTATTATGTATTT
1 AAGAGAACCTTTTGCTATTACGTATTT
5919600 AAGAGAACCTTTTGCTATTACGTATTT
1 AAGAGAACCTTTTGCTATTACGTATTT
5919627 A
1 A
5919628 CAGTTTTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (27 bp):
AAGAGAACCTTTTGCTATTACGTATTT
Found at i:5935019 original size:30 final size:31
Alignment explanation
Indices: 5934985--5935047 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
5934975 TTCAAGTCTC
* *
5934985 AATATATAAATAATTGTCT-AATTT-AAAATT
1 AATATAAAAATAATT-ACTAAATTTAAAAATT
5935015 AATATAAAAATAATTACTAAATTTAAAAATT
1 AATATAAAAATAATTACTAAATTTAAAAATT
5935046 AA
1 AA
5935048 CATACACTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 19 0.66
31 8 0.28
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (31 bp):
AATATAAAAATAATTACTAAATTTAAAAATT
Found at i:5935677 original size:16 final size:17
Alignment explanation
Indices: 5935652--5935684 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5935642 TAATTAAAAA
5935652 TTATTAAAAT-ATTCTT
1 TTATTAAAATAATTCTT
*
5935668 TTATTTAAATAATTCTT
1 TTATTAAAATAATTCTT
5935685 GTTGGAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATTAAAATAATTCTT
Found at i:5949614 original size:25 final size:25
Alignment explanation
Indices: 5949582--5949629 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5949572 TCTTAAGTCT
* * *
5949582 AAATATATATATTTATTATATTTTA
1 AAATATATAAATATATTAAATTTTA
5949607 AAATATATAAATATATTAAATTT
1 AAATATATAAATATATTAAATTT
5949630 AAATGATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AAATATATAAATATATTAAATTTTA
Found at i:5949625 original size:18 final size:16
Alignment explanation
Indices: 5949607--5949654 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
5949597 TTATATTTTA
5949607 AAATATATAAATATATT
1 AAAT-TATAAATATATT
5949624 AAATT-TAAATGATATT
1 AAATTATAAAT-ATATT
5949640 CAAATTCATAAATAT
1 -AAATT-ATAAATAT
5949655 TATAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.19
16 6 0.22
17 9 0.33
18 2 0.07
19 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATTATAAATATATT
Found at i:5949633 original size:23 final size:24
Alignment explanation
Indices: 5949581--5949638 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
5949571 GTCTTAAGTC
* * *
5949581 TAAATATATATATTTATTATATTT
1 TAAATATATAAATATATTATAATT
5949605 TAAAATATATAAATATATTA-AATT
1 T-AAATATATAAATATATTATAATT
5949629 TAAATGATAT
1 TAAAT-ATAT
5949639 TCAAATTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.14
24 9 0.31
25 16 0.55
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TAAATATATAAATATATTATAATT
Found at i:5950336 original size:12 final size:12
Alignment explanation
Indices: 5950319--5950346 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5950309 CATCAAGAAT
5950319 TATTTATTATAA
1 TATTTATTATAA
5950331 TATTTATTATAA
1 TATTTATTATAA
5950343 TATT
1 TATT
5950347 GTTATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTTATTATAA
Found at i:5955180 original size:25 final size:25
Alignment explanation
Indices: 5955124--5955392 Score: 101
Period size: 25 Copynumber: 10.8 Consensus size: 25
5955114 CAGTTCGAAA
* * * *
5955124 GAGCTTCCCATTAT-TAGCTCTCAT
1 GAGCTTCCCGTTATATGGCTCTTAC
* *
5955148 GAGCTTCCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTATATGGCTCTTAC
* * *
5955173 GAGTTTCCCATT-TATGGCTCTTAT
1 GAGCTTCCCGTTATATGGCTCTTAC
*
5955197 GAGCTTCCCGATATATGGCTCTT-C
1 GAGCTTCCCGTTATATGGCTCTTAC
* *
5955221 GGAGCTTCCCGATTA-AAGGCTCTTTC
1 -GAGCTTCCCG-TTATATGGCTCTTAC
* * *
5955247 TTGAGCTTCCTGATATATGGATCTT-C
1 --GAGCTTCCCGTTATATGGCTCTTAC
* * *
5955273 GGAACTTTCCGATTA-ATGGCTCTCT-G
1 -GAGCTTCCCG-TTATATGGCTCT-TAC
*
5955299 GAGCTTCCC--TATATTGGCTCTCT-T
1 GAGCTTCCCGTTATA-TGGCTCT-TAC
* ** * *
5955323 GAACTTCTTGAT-TATGGCTCTTAT
1 GAGCTTCCCGTTATATGGCTCTTAC
* * ** *
5955347 GAGCTTCCTGTTACATGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCTTAC
* *
5955372 AAGCTTCCCATTATATGGCTC
1 GAGCTTCCCGTTATATGGCTC
5955393 GAAAGACCTT
Statistics
Matches: 185, Mismatches: 45, Indels: 29
0.71 0.17 0.11
Matches are distributed among these distances:
22 2 0.01
23 2 0.01
24 63 0.34
25 92 0.50
26 10 0.05
27 16 0.09
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCTTAC
Found at i:5955230 original size:49 final size:49
Alignment explanation
Indices: 5955124--5955354 Score: 168
Period size: 49 Copynumber: 4.7 Consensus size: 49
5955114 CAGTTCGAAA
* * * *
5955124 GAGCTTCCCA-TTATTAGCTCTCATGAGCTTCCCGTTATATGGTTCTT-G
1 GAGCTTCCCATTTA-TGGCTCTTATGAGCTTCCCGATATATGGCTCTTCG
*
5955172 CGAGTTTCCCATTTATGGCTCTTATGAGCTTCCCGATATATGGCTCTTCG
1 -GAGCTTCCCATTTATGGCTCTTATGAGCTTCCCGATATATGGCTCTTCG
* * * * *
5955222 GAGCTTCCCGATTAAAGGCTCTTTCTTGAGCTTCCTGATATATGGATCTTCG
1 GAGCTTCCC-ATTTATGGCTC-TT-ATGAGCTTCCCGATATATGGCTCTTCG
* * * * * *
5955274 GAACTTTCCGATTAATGGCTCTCT-GGAGCTTCCCTATAT-TGGCTC-TCTT
1 GAGC-TTCCCATTTATGGCTCT-TATGAGCTTCCCGATATATGGCTCTTC-G
* **
5955323 GAACTTCTTGA-TTATGGCTCTTATGAGCTTCC
1 GAGCTTC-CCATTTATGGCTCTTATGAGCTTCC
5955355 TGTTACATGG
Statistics
Matches: 150, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
47 1 0.01
48 22 0.15
49 57 0.38
50 25 0.17
51 3 0.02
52 38 0.25
53 4 0.03
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (49 bp):
GAGCTTCCCATTTATGGCTCTTATGAGCTTCCCGATATATGGCTCTTCG
Found at i:5955271 original size:27 final size:26
Alignment explanation
Indices: 5955147--5955354 Score: 118
Period size: 25 Copynumber: 8.3 Consensus size: 26
5955137 TTAGCTCTCA
* * *
5955147 TGAGCTTCCCGTTATATGGTTCTTGC
1 TGAGCTTCCCGATATATGGCTCTTTC
* * *
5955173 -GAGTTTCCC-ATTTATGGCTC-TTA
1 TGAGCTTCCCGATATATGGCTCTTTC
5955196 TGAGCTTCCCGATATATGGCTC-TTC
1 TGAGCTTCCCGATATATGGCTCTTTC
* *
5955221 GGAGCTTCCCGAT-TAAAGGCTCTTTC
1 TGAGCTTCCCGATAT-ATGGCTCTTTC
* *
5955247 TTGAGCTTCCTGATATATGGATC-TTC
1 -TGAGCTTCCCGATATATGGCTCTTTC
* * *
5955273 GGAACTTTCCGAT-TAATGGCTC--TC
1 TGAGCTTCCCGATAT-ATGGCTCTTTC
* *
5955297 TGGAGCTTCCCTATAT-TGGCTCTCT-
1 T-GAGCTTCCCGATATATGGCTCTTTC
* ** *
5955322 TGAACTTCTTGAT-TATGGCTC-TTA
1 TGAGCTTCCCGATATATGGCTCTTTC
5955346 TGAGCTTCC
1 TGAGCTTCC
5955355 TGTTACATGG
Statistics
Matches: 138, Mismatches: 31, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
23 3 0.02
24 47 0.34
25 63 0.46
26 8 0.06
27 16 0.12
28 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (26 bp):
TGAGCTTCCCGATATATGGCTCTTTC
Found at i:5957233 original size:16 final size:16
Alignment explanation
Indices: 5957212--5957245 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5957202 GTGTTCGACT
*
5957212 TTATTTTATTTGTTCG
1 TTATTTTACTTGTTCG
5957228 TTATTTTACTTGTTCG
1 TTATTTTACTTGTTCG
5957244 TT
1 TT
5957246 GCCTAACCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.68
Consensus pattern (16 bp):
TTATTTTACTTGTTCG
Found at i:5960816 original size:73 final size:73
Alignment explanation
Indices: 5960697--5960917 Score: 424
Period size: 73 Copynumber: 3.0 Consensus size: 73
5960687 TGGAGGAGGA
*
5960697 TTACTAATTGTGTTTAGTGGAAGCTATTTGACAGCAAGTGTAATACATTTTCCTTCAATAGGGAA
1 TTACTAATTGTTTTTAGTGGAAGCTATTTGACAGCAAGTGTAATACATTTTCCTTCAATAGGGAA
5960762 TACAATAG
66 TACAATAG
5960770 TTACTAATTGTTTTTAGTGGAAGCTATTTGACAGCAAGTGTAATACATTTTCCTTCAATAGGGAA
1 TTACTAATTGTTTTTAGTGGAAGCTATTTGACAGCAAGTGTAATACATTTTCCTTCAATAGGGAA
5960835 TACAATAG
66 TACAATAG
*
5960843 TTACTAATTGTTTTTAGTGGAAGCTATTTGACAGCAAGTGTAATGCATTTTCCTTCAATAGGGAA
1 TTACTAATTGTTTTTAGTGGAAGCTATTTGACAGCAAGTGTAATACATTTTCCTTCAATAGGGAA
5960908 TACAATAG
66 TACAATAG
5960916 TT
1 TT
5960918 GATCATTGGC
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 146 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (73 bp):
TTACTAATTGTTTTTAGTGGAAGCTATTTGACAGCAAGTGTAATACATTTTCCTTCAATAGGGAA
TACAATAG
Found at i:5965183 original size:33 final size:33
Alignment explanation
Indices: 5965128--5965283 Score: 129
Period size: 33 Copynumber: 4.7 Consensus size: 33
5965118 AATTGACGGA
* * *
5965128 TAAGACCATGGCTGGGCCATGGCAATATATGTG
1 TAAGACCATAGCTGGGCTATGGCAATAGATGTG
* * *
5965161 TAAGACCATAGCTAGGCTATGGC-ATCCTGATG-A
1 TAAGACCATAGCTGGGCTATGGCAAT--AGATGTG
** * * *
5965194 TAAGACCATAATTTGGATATGGCACTACGA-GTG
1 TAAGACCATAGCTGGGCTATGGCAATA-GATGTG
* *
5965227 TAAGACCATGGCTGGGCCATGGCAATAGATGTG
1 TAAGACCATAGCTGGGCTATGGCAATAGATGTG
* *
5965260 TAAGACCATAGTTGGACTATGGCA
1 TAAGACCATAGCTGGGCTATGGCA
5965284 TCATACTAGA
Statistics
Matches: 93, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
32 5 0.05
33 84 0.90
34 4 0.04
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (33 bp):
TAAGACCATAGCTGGGCTATGGCAATAGATGTG
Found at i:5965344 original size:45 final size:45
Alignment explanation
Indices: 5965295--5965415 Score: 145
Period size: 45 Copynumber: 2.7 Consensus size: 45
5965285 CATACTAGAA
* * * *
5965295 ACGAGTAAGACCATCGTTGAAAGACGCTATGGCTTCGCGATTCAG
1 ACGAGTAAGACCATAGTTGAAAGACACTATGGCATCACGATTCAG
*
5965340 ACGAGTAAGACCATAGTTGAAAGACATTATGGCATCACGATTCAG
1 ACGAGTAAGACCATAGTTGAAAGACACTATGGCATCACGATTCAG
** * *
5965385 ATTTA-TAAGACTATAGTTGAAAGATACTATG
1 A-CGAGTAAGACCATAGTTGAAAGACACTATG
5965416 ACAGTATGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 64 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (45 bp):
ACGAGTAAGACCATAGTTGAAAGACACTATGGCATCACGATTCAG
Found at i:5965450 original size:46 final size:46
Alignment explanation
Indices: 5965428--5966422 Score: 1882
Period size: 46 Copynumber: 21.6 Consensus size: 46
5965418 AGTATGATGA
*
5965428 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965474 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965520 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965566 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
*
5965612 GAAATGAATAGGACCATGGTTGAAAGATACCATGGAAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
*
5965658 GAAATGAATATGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965704 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965750 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965796 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965842 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965888 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965934 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5965980 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5966026 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5966072 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5966118 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5966164 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5966210 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
5966256 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
* * * *
5966302 GAAATGAATAAGACCATAGTTGAAAGATACCATAGCAACATGATAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
* *
5966348 GAAATGAATAAGACCATGGTTAAAAGATACCATGGCAACATGACAG
1 GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
* * *
5966394 GAAATAAATAAGACTATGGTTGAAAGATA
1 GAAATGAATAGGACCATGGTTGAAAGATA
5966423 GAAATGAATA
Statistics
Matches: 933, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 933 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (46 bp):
GAAATGAATAGGACCATGGTTGAAAGATACCATGGCAACATGACAG
Found at i:5966444 original size:29 final size:29
Alignment explanation
Indices: 5966394--5966449 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5966384 AACATGACAG
* *
5966394 GAAATAAATAAGACTATGGTTGAAAGATA
1 GAAATAAATAAGACGATAGTTGAAAGATA
* *
5966423 GAAATGAATAAGACGATAGTTGGAAGA
1 GAAATAAATAAGACGATAGTTGAAAGA
5966450 CACTATGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.25, T:0.21
Consensus pattern (29 bp):
GAAATAAATAAGACGATAGTTGAAAGATA
Found at i:5967744 original size:43 final size:43
Alignment explanation
Indices: 5967683--5967771 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
5967673 ATGGCGAAAG
* *
5967683 TAAATTGGTTAGCAAATGGAGATAAAAATACTACTTTCTTTCA
1 TAAATTAGTTAGCAAATGGAGATAAAAATACCACTTTCTTTCA
5967726 TAAATTAGTTAGCAAATGGAGATAAAAATACCACTTTCTTTCA
1 TAAATTAGTTAGCAAATGGAGATAAAAATACCACTTTCTTTCA
5967769 TAA
1 TAA
5967772 TTATGCATCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (43 bp):
TAAATTAGTTAGCAAATGGAGATAAAAATACCACTTTCTTTCA
Found at i:5972076 original size:15 final size:15
Alignment explanation
Indices: 5972053--5972082 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5972043 TATGTACATT
*
5972053 GCCCTCAATGTACAA
1 GCCCCCAATGTACAA
5972068 GCCCCCAATGTACAA
1 GCCCCCAATGTACAA
5972083 AGATAGGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.37, G:0.13, T:0.17
Consensus pattern (15 bp):
GCCCCCAATGTACAA
Found at i:5982813 original size:21 final size:20
Alignment explanation
Indices: 5982776--5982828 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
5982766 TTTATTTAAA
* *
5982776 AAAAAGAACAATAATATACG
1 AAAAAGAAAAAAAATATACG
*
5982796 AAAAAGAAAAAAAGATATATG
1 AAAAAGAAAAAAA-ATATACG
5982817 AAGAATAGAAAA
1 AA-AA-AGAAAA
5982829 TATTTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 2 0.07
23 6 0.22
ACGTcount: A:0.70, C:0.04, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAAAGAAAAAAAATATACG
Found at i:5983754 original size:7 final size:8
Alignment explanation
Indices: 5983742--5983767 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5983732 ATCAAAAATG
5983742 AAAAAAGA
1 AAAAAAGA
5983750 AAAAAAGA
1 AAAAAAGA
5983758 AAAAAAGA
1 AAAAAAGA
5983766 AA
1 AA
5983768 TCAGAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:5984566 original size:68 final size:68
Alignment explanation
Indices: 5984446--5984650 Score: 286
Period size: 68 Copynumber: 3.0 Consensus size: 68
5984436 TTCAATCTAC
* * *
5984446 TCCGCTGAAACTTCAAGGAGATCTATTATGGCTTCG-AGCCGCTTCAACGCCATTTTAGGGAGAA
1 TCCGCTGAAACTTCAAGGAGATCTGTTGTGGCTT-GTAGCCGCTCCAACGCCATTTTAGGGAGAA
5984510 GAGA
65 GAGA
* * *
5984514 TCCGCTGAAACTTCAAGGAGATCTGTTGTGGCTTGTAGCCTCTCCAATGCCATTTTAGGGAAAAG
1 TCCGCTGAAACTTCAAGGAGATCTGTTGTGGCTTGTAGCCGCTCCAACGCCATTTTAGGGAGAAG
5984579 AGA
66 AGA
* * * * * *
5984582 TCCGCTGAAACTTTAAGAAGATCTGTTGTGGCTTTTAGTCGCTCCAACGCCATTTAAGGGGGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGTTGTGGCTTGTAGCCGCTCCAACGCCATTTTAGGGAGAAG
5984647 AGA
66 AGA
5984650 T
1 T
5984651 TTGTAGCTTC
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 1 0.01
68 120 0.99
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (68 bp):
TCCGCTGAAACTTCAAGGAGATCTGTTGTGGCTTGTAGCCGCTCCAACGCCATTTTAGGGAGAAG
AGA
Found at i:5984825 original size:86 final size:87
Alignment explanation
Indices: 5984658--5984988 Score: 450
Period size: 87 Copynumber: 3.8 Consensus size: 87
5984648 GATTTGTAGC
* * * * ** *
5984658 TTCAGCCTCTTACCCTACTGTTTAGGGGGTTAAGGCCTATTGCCTTCGATCTGCTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGC
* *
5984723 TTAGAGTGATAAGATCTGTAAA
66 TTAGGGTGGTAAGATCTGTAAA
* * *
5984745 TTCAACCTGTTACCCTACTGCTTAGGGG-TTAAGGCCCATCACCTTTGATCTATTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGC
*
5984809 TTAGGGTGGTAGGATCTGTAAA
66 TTAGGGTGGTAAGATCTGTAAA
* * * *
5984831 TTCGGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATTAGCTTCGATCTGTTTCCCTACTAC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGC
5984896 TTAGGG-GGTTAAGATCTGTAAA
66 TTAGGGTGG-TAAGATCTGTAAA
* * * *
5984918 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCATCTTCGATCTGTTACCCAATTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGC
5984983 TTAGGG
66 TTAGGG
5984989 GTTTAAGGCC
Statistics
Matches: 215, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
86 77 0.36
87 138 0.64
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.34
Consensus pattern (87 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGC
TTAGGGTGGTAAGATCTGTAAA
Found at i:5984899 original size:44 final size:43
Alignment explanation
Indices: 5984667--5985256 Score: 260
Period size: 44 Copynumber: 13.7 Consensus size: 43
5984657 CTTCAGCCTC
* * * **
5984667 TTACCCTACTGTTTAGGGGGTTAAGGCCTATTGCCTTCGATCTG
1 TTACCCTACTGCTTAGGGGTTTAAGGCC-CTTAACTTCGATCTG
* * ** * * *
5984711 CTT-CCCTACTGCTTA-GAGTGATAA-GATCTGTAAATTCAACCTG
1 -TTACCCTACTGCTTAGGGGT-TTAAGGCCCT-TAACTTCGATCTG
* * * *
5984754 TTACCCTACTGCTTAGGGG-TTAAGGCCCATCACCTTTGATCTA
1 TTACCCTACTGCTTAGGGGTTTAAGGCCC-TTAACTTCGATCTG
* * ** * **
5984797 TTTCCCTACTGCTTA-GGGTGGT-AGGATCTGTAAATTCGGCCTG
1 TTACCCTACTGCTTAGGGGT-TTAAGGCCCT-TAACTTCGATCTG
*
5984840 TTACCCTACTGCTTAGGGGTTTAAGGCCCATTAGCTTCGATCTG
1 TTACCCTACTGCTTAGGGGTTTAAGGCCC-TTAACTTCGATCTG
* * * ** * *
5984884 TTTCCCTACTACTTAGGGGGTTAA-GATCTGTAAATTC-AGCCTG
1 TTACCCTACTGCTTAGGGGTTTAAGGCCCT-TAACTTCGA-TCTG
* *
5984927 TTACCCTACTGCTTAGGGGTTTAAGGCCCATCATCTTCGATCTG
1 TTACCCTACTGCTTAGGGGTTTAAGGCCC-TTAACTTCGATCTG
* * ** *
5984971 TTACCCAATTGCTTAGGGGTTTAAGGCCCTTCGCCTTCGATTTG
1 TTACCCTACTGCTTAGGGGTTTAAGGCCCTT-AACTTCGATCTG
* * * * * ** * *
5985015 TTTCCTTACTACTTA-AGGTGATAA-GATCTGTAAATTC-AGCCTG
1 TTACCCTACTGCTTAGGGGT-TTAAGGCCCT-TAACTTCGA-TCTG
* * *
5985058 TTACCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGATCTG
1 TTACCCTACTGCTTAGGGGTTTAAGGC-CCTTAACTTCGATCTG
* * * * * *
5985102 TTTCCCTACTACTTAGGGGGTT-A---TCTGTAAATTC-AGCCTG
1 TTACCCTACTGCTTAGGGGTTTAAGGCCCT-TAACTTCGA-TCTG
* * * *
5985142 TTACTCTACTGCTTAAGGGTTTAAGGCCCATCACCTTCGATCTG
1 TTACCCTACTGCTTAGGGGTTTAAGGCCC-TTAACTTCGATCTG
* * ** * ** *
5985186 TTTCCCTACTGCTTAGGGGGTTAA-GATCTGTAAATTTAACCTG
1 TTACCCTACTGCTTAGGGGTTTAAGGCCCT-TAACTTCGATCTG
*
5985229 TTACCCTACTGCTTAGAGGTTTAAGGCC
1 TTACCCTACTGCTTAGGGGTTTAAGGCC
5985257 TGTGGCTTCA
Statistics
Matches: 383, Mismatches: 127, Indels: 71
0.66 0.22 0.12
Matches are distributed among these distances:
39 2 0.01
40 24 0.06
41 1 0.00
42 14 0.04
43 159 0.42
44 174 0.45
45 9 0.02
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (43 bp):
TTACCCTACTGCTTAGGGGTTTAAGGCCCTTAACTTCGATCTG
Found at i:5984996 original size:131 final size:131
Alignment explanation
Indices: 5984837--5985120 Score: 435
Period size: 131 Copynumber: 2.2 Consensus size: 131
5984827 TAAATTCGGC
* *
5984837 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATTAG-CTTCGATCTGTTTCCCTACTACTTAGG
1 CTGTTACCCAACTGCTTAGGGGTTTAAGGCCC-TTAGCCTTCGATCTGTTTCCCTACTACTTAAG
* *
5984901 GGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCATCTTCG
65 GGGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCG
5984966 AT
130 AT
* * * *
5984968 CTGTTACCCAATTGCTTAGGGGTTTAAGGCCCTTCGCCTTCGATTTGTTTCCTTACTACTTAAGG
1 CTGTTACCCAACTGCTTAGGGGTTTAAGGCCCTTAGCCTTCGATCTGTTTCCCTACTACTTAAGG
* *
5985033 TGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGA
66 GGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGA
5985098 T
131 T
* * *
5985099 CTGTTTCCCTACTACTTAGGGG
1 CTGTTACCCAACTGCTTAGGGG
5985121 GTTATCTGTA
Statistics
Matches: 138, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
130 3 0.02
131 135 0.98
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (131 bp):
CTGTTACCCAACTGCTTAGGGGTTTAAGGCCCTTAGCCTTCGATCTGTTTCCCTACTACTTAAGG
GGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGA
T
Found at i:5985062 original size:87 final size:87
Alignment explanation
Indices: 5984968--5985256 Score: 395
Period size: 87 Copynumber: 3.4 Consensus size: 87
5984958 CATCTTCGAT
* * * * * *
5984968 CTGTTACCCAATTGCTTAGGGGTTTAAGGCCCTTCGCCTTCGATTTGTTTCCTTACTACTTAAGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTACTTAAGG
*
5985033 TGATAAGATCTGTAAATTCAGC
66 GGATAAGATCTGTAAATTCAGC
*
5985055 CTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTACTT-AGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTACTTAAGG
* *
5985119 GGGT--TATCTGTAAATTCAGC
66 GGATAAGATCTGTAAATTCAGC
* * * *
5985139 CTGTTACTCTACTGCTTAAGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTACTTAAGG
* * *
5985204 GGTTAAGATCTGTAAATTTAAC
66 GGATAAGATCTGTAAATTCAGC
*
5985226 CTGTTACCCTACTGCTTAGAGGTTTAAGGCC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCC
5985257 TGTGGCTTCA
Statistics
Matches: 177, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
84 72 0.41
85 5 0.03
86 5 0.03
87 95 0.54
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (87 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTACTTAAGG
GGATAAGATCTGTAAATTCAGC
Found at i:5989820 original size:9 final size:10
Alignment explanation
Indices: 5989807--5989852 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
5989797 GGGAAAGTCT
5989807 AATGCAAAT-
1 AATGCAAATG
5989816 AATGC-AATG
1 AATGCAAATG
5989825 CAATGCAAATG
1 -AATGCAAATG
*
5989836 CATG-AAATG
1 AATGCAAATG
5989845 AATGCAAA
1 AATGCAAA
5989853 AAGAAAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
8 3 0.10
9 13 0.42
10 11 0.35
11 4 0.13
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (10 bp):
AATGCAAATG
Found at i:5989831 original size:19 final size:19
Alignment explanation
Indices: 5989807--5989852 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5989797 GGGAAAGTCT
*
5989807 AATGCAAAT-AATGCAATG
1 AATGCAAATGAATGAAATG
*
5989825 CAATGCAAATGCATGAAATG
1 -AATGCAAATGAATGAAATG
5989845 AATGCAAA
1 AATGCAAA
5989853 AAGAAAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (19 bp):
AATGCAAATGAATGAAATG
Found at i:5992776 original size:16 final size:16
Alignment explanation
Indices: 5992750--5992787 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5992740 CCCTAAATTC
*
5992750 ATAGAAGAAAAGAAAAA
1 ATAGAACAAAA-AAAAA
5992767 A-AGAACAAAAAAAAA
1 ATAGAACAAAAAAAAA
5992782 ATAGAA
1 ATAGAA
5992788 TGTTAAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 12 0.63
17 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (16 bp):
ATAGAACAAAAAAAAA
Found at i:5993689 original size:29 final size:31
Alignment explanation
Indices: 5993639--5993705 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
5993629 TATTAATTTT
**
5993639 AAAATAACATTAATTTACTTAT-TTCAAATA
1 AAAATAACATTAATGCACTTATCTTCAAATA
* * *
5993669 AAAATAA-ATTAATGCATTTATCTTCAATTT
1 AAAATAACATTAATGCACTTATCTTCAAATA
5993699 AAAATAA
1 AAAATAA
5993706 TTTTTAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (31 bp):
AAAATAACATTAATGCACTTATCTTCAAATA
Found at i:5997741 original size:22 final size:22
Alignment explanation
Indices: 5997713--5997760 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
5997703 ATTGACCCTA
5997713 AGATCCTGCCATATGAAAATGG
1 AGATCCTGCCATATGAAAATGG
5997735 AGATCCTGCCATATGAAAATGG
1 AGATCCTGCCATATGAAAATGG
5997757 AGAT
1 AGAT
5997761 GGAAGGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (22 bp):
AGATCCTGCCATATGAAAATGG
Done.