Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008717.1 Hibiscus syriacus cultivar Beakdansim tig00111772_pilon, whole genome shotgun sequence
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: 3453450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:1390330 original size:4 final size:4
Alignment explanation
Indices: 1390321--1390365 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
1390311 TGGAATTTTG
* *
1390321 ATTT ATTT ATTT ATTT ATTT A-TT -TTT ATTT AATT AATT -TTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1390366 GATATTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 6 0.17
4 30 0.83
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:1390361 original size:15 final size:14
Alignment explanation
Indices: 1390330--1390365 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1390320 GATTTATTTA
*
1390330 TTTATTTATTTATT
1 TTTATTTATTAATT
1390344 TTTATTTAATTAATT
1 TTTATTT-ATTAATT
1390359 TTTATTT
1 TTTATTT
1390366 GATATTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTATTTATTAATT
Found at i:1390371 original size:22 final size:22
Alignment explanation
Indices: 1390324--1390372 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1390314 AATTTTGATT
* * *
1390324 TATTTATTTATTTATTTATTTT
1 TATTTAATTAATTATTTATTTA
1390346 TATTTAATTAATT-TTTATTTGA
1 TATTTAATTAATTATTTATTT-A
1390368 TATTT
1 TATTT
1390373 CTTTTACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTTAATTAATTATTTATTTA
Found at i:1392262 original size:29 final size:29
Alignment explanation
Indices: 1392220--1392299 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
1392210 ATTATACAGT
1392220 GACCAAAGAGGTCGCCATGCACGCCCAAC
1 GACCAAAGAGGTCGCCATGCACGCCCAAC
1392249 GACCAAAGAGGTCGCCATGCACGCCCAAC
1 GACCAAAGAGGTCGCCATGCACGCCCAAC
*
1392278 GACCAAGGAGGTCGCCATGCAC
1 GACCAAAGAGGTCGCCATGCAC
1392300 ACTCGGGGCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.30, C:0.36, G:0.26, T:0.07
Consensus pattern (29 bp):
GACCAAAGAGGTCGCCATGCACGCCCAAC
Found at i:1392384 original size:29 final size:29
Alignment explanation
Indices: 1392351--1392434 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
1392341 GGGGTGGGGT
*
1392351 GTAGGTCTCCATGGAGTCCCGGCGACATG
1 GTAGGTCACCATGGAGTCCCGGCGACATG
*
1392380 GTAGGTCGCCATGGAGTCCCGGCGACATG
1 GTAGGTCACCATGGAGTCCCGGCGACATG
* *
1392409 GTAGGTCACCATGGAGTTCTGGCGAC
1 GTAGGTCACCATGGAGTCCCGGCGAC
1392435 CAAGCTGTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.26, G:0.36, T:0.20
Consensus pattern (29 bp):
GTAGGTCACCATGGAGTCCCGGCGACATG
Found at i:1392498 original size:32 final size:32
Alignment explanation
Indices: 1392457--1392521 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1392447 TCCTGCACCA
1392457 CGACCAAACTTTAACCCTATCCCTCATGCATG
1 CGACCAAACTTTAACCCTATCCCTCATGCATG
1392489 CGACCAAACTTTAACCCTATCCCTCATGCATG
1 CGACCAAACTTTAACCCTATCCCTCATGCATG
1392521 C
1 C
1392522 ATTGCATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.25
Consensus pattern (32 bp):
CGACCAAACTTTAACCCTATCCCTCATGCATG
Found at i:1392592 original size:65 final size:65
Alignment explanation
Indices: 1392480--1392617 Score: 217
Period size: 65 Copynumber: 2.1 Consensus size: 65
1392470 ACCCTATCCC
*
1392480 TCATGCAT-GCGACCAAACTTTAACCCTATCCCTCATGCATGCATTGCATCCATAGC-TGAGAGA
1 TCATGCATCGCGACCAAACTTTAACCCTATCACTCATGCATGCATTGCATCCATAGCTTG-GAGA
1392543 T
65 T
* * *
1392544 TCCTGCATCGCGACCAAGCTTTAACCCTATCACTCATGCATGCGTTGCATCCATAGCTTGGAGAT
1 TCATGCATCGCGACCAAACTTTAACCCTATCACTCATGCATGCATTGCATCCATAGCTTGGAGAT
1392609 TCATGCATC
1 TCATGCATC
1392618 CGTAGCTGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
64 7 0.10
65 58 0.87
66 2 0.03
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (65 bp):
TCATGCATCGCGACCAAACTTTAACCCTATCACTCATGCATGCATTGCATCCATAGCTTGGAGAT
Found at i:1393080 original size:43 final size:39
Alignment explanation
Indices: 1393026--1393127 Score: 134
Period size: 43 Copynumber: 2.5 Consensus size: 39
1393016 TTGTTAGTAT
1393026 AAATT-ATTAGTTTGTTAGTTTAAGATATATTATATATATAAA
1 AAATTAATTAGTTTGTTAGTTTAAG-T-TATTA-A-ATATAAA
*
1393068 AAATTAATTAGTTTATTAGTTTAAGTTATTAAATATAAA
1 AAATTAATTAGTTTGTTAGTTTAAGTTATTAAATATAAA
*
1393107 AAATATAATTAATTTGTTAGT
1 AAAT-TAATTAGTTTGTTAGT
1393128 GTCTTTAAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
39 11 0.20
40 15 0.27
41 5 0.09
42 6 0.11
43 18 0.33
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (39 bp):
AAATTAATTAGTTTGTTAGTTTAAGTTATTAAATATAAA
Found at i:1393550 original size:17 final size:17
Alignment explanation
Indices: 1393528--1393589 Score: 70
Period size: 17 Copynumber: 3.4 Consensus size: 17
1393518 AGATAATTTC
1393528 TGTTTAAAAAAATATTG
1 TGTTTAAAAAAATATTG
*
1393545 TGTTTAAAAAAATTTAGTG
1 TGTTTAAAAAAA--TATTG
*
1393564 TTGTTTTAAAAAAATATTT
1 -TG-TTTAAAAAAATATTG
1393583 TGTTTAA
1 TGTTTAA
1393590 TTTATATGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 17 0.45
18 2 0.05
19 7 0.18
20 2 0.05
21 10 0.26
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (17 bp):
TGTTTAAAAAAATATTG
Found at i:1393825 original size:15 final size:15
Alignment explanation
Indices: 1393805--1393872 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
1393795 TAATCATGAC
1393805 TAAATCATATATTAT
1 TAAATCATATATTAT
*
1393820 TAAATCAT-TAAATAT
1 TAAATCATAT-ATTAT
*
1393835 CAAATCATA-A--AT
1 TAAATCATATATTAT
*
1393847 T-AATAATA-ATTAT
1 TAAATCATATATTAT
1393860 TAAATCAT-TATTA
1 TAAATCATATATTA
1393873 GTATATTAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
11 7 0.17
12 2 0.05
13 3 0.07
14 11 0.26
15 19 0.45
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATCATATATTAT
Found at i:1396808 original size:49 final size:50
Alignment explanation
Indices: 1396737--1396832 Score: 167
Period size: 49 Copynumber: 1.9 Consensus size: 50
1396727 GGCACCCATC
*
1396737 TATTATTGATATTTAATGATTTGATAGTAATGATTAGTAA-TAATAAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATTAATAAAAT
*
1396786 TATTATTAATATTTAATTATTTGATAGTAATGATTAGTAATTAATAA
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATTAATAA
1396833 TAATGAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 38 0.86
50 6 0.14
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (50 bp):
TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATTAATAAAAT
Found at i:1396838 original size:20 final size:19
Alignment explanation
Indices: 1396813--1396864 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
1396803 TATTTGATAG
1396813 TAATGATTAGTAATTAATAA
1 TAATGATTAGTAATT-ATAA
* *
1396833 TAATGA--AATTATTATAA
1 TAATGATTAGTAATTATAA
1396850 TAATGATTTAGTAAT
1 TAATGA-TTAGTAAT
1396865 AATCATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 10 0.40
18 5 0.20
20 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (19 bp):
TAATGATTAGTAATTATAA
Found at i:1396916 original size:59 final size:60
Alignment explanation
Indices: 1396852--1397028 Score: 201
Period size: 59 Copynumber: 3.0 Consensus size: 60
1396842 TATTATAATA
1396852 ATGATTTAGTAATAATCATTTAATAATGATTTAAT-ATGATTTAAATATTTAATGATTTG
1 ATGATTTAGTAATAATCATTTAATAATGATTTAATAATGATTTAAATATTTAATGATTTG
* * * * * *
1396911 ATGATTTAGTAATGAT--TTGATAAT-ATCATTATAATAATGATTT-GATA-ATAATCATTATA
1 ATGATTTAGTAATAATCATT--TAATAATGATT-TAATAATGATTTAAATATTTAATGATT-TG
1396970 ATGATTTAGTAATAATCA-TT-ATAATGA-TTAATAATGATTTAAATATTTAATGATTTG
1 ATGATTTAGTAATAATCATTTAATAATGATTTAATAATGATTTAAATATTTAATGATTTG
1397027 AT
1 AT
1397029 TTAGTAATGA
Statistics
Matches: 96, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
56 12 0.12
57 11 0.11
58 23 0.24
59 42 0.44
60 8 0.08
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (60 bp):
ATGATTTAGTAATAATCATTTAATAATGATTTAATAATGATTTAAATATTTAATGATTTG
Found at i:1396958 original size:14 final size:14
Alignment explanation
Indices: 1396920--1397259 Score: 69
Period size: 14 Copynumber: 24.1 Consensus size: 14
1396910 GATGATTTAG
1396920 TAATGATTTGATAA
1 TAATGATTTGATAA
*
1396934 T-ATCA-TT-ATAA
1 TAATGATTTGATAA
1396945 TAATGATTTGATAA
1 TAATGATTTGATAA
*
1396959 TAATCA--T--T-A
1 TAATGATTTGATAA
1396968 TAATGATTT-AGTAA
1 TAATGATTTGA-TAA
*
1396982 TAATCATTATAATGATTAA
1 TAATGA-T-T--TGA-TAA
* *
1397001 TAATGATTTAAATATT
1 TAATGATTT-GATA-A
*
1397017 TAATGATTTGATTTAG
1 TAATGATTTGA--TAA
1397033 TAATGATTTGATAA
1 TAATGATTTGATAA
*
1397047 TAAT-ATAATATGATTAG
1 TAATGAT--T-TGA-TAA
**
1397064 T-AT-AAAT-ATAA
1 TAATGATTTGATAA
1397075 TAATGA-TT--TAA
1 TAATGATTTGATAA
* *
1397086 TAATGATTTAAATATT
1 TAATGATTT-GATA-A
1397102 TAATGATTTGATGATTTA
1 TAATGATTTGAT-A---A
1397120 GTAATGATTTGATAA
1 -TAATGATTTGATAA
*
1397135 TAATCA-TT-ATAA
1 TAATGATTTGATAA
*
1397147 TAATGATTTAATAA
1 TAATGATTTGATAA
*
1397161 TAATCA-TT-ATAA
1 TAATGATTTGATAA
*
1397173 TAATTATATAATGATTTAA
1 TAATGAT-T--TGA--TAA
* *
1397192 TAATGATTTAATAG
1 TAATGATTTGATAA
* *
1397206 TAATTA-TT--TAG
1 TAATGATTTGATAA
*
1397217 TAATGATTTTATAA
1 TAATGATTTGATAA
* * *
1397231 TAATAATTTAATAT
1 TAATGATTTGATAA
*
1397245 TAATGATTTAATAA
1 TAATGATTTGATAA
1397259 T
1 T
1397260 TATTACTAAA
Statistics
Matches: 247, Mismatches: 35, Indels: 88
0.67 0.09 0.24
Matches are distributed among these distances:
9 6 0.02
10 1 0.00
11 26 0.11
12 32 0.13
13 18 0.07
14 70 0.28
15 11 0.04
16 41 0.17
17 7 0.03
18 5 0.02
19 30 0.12
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.45
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:1396968 original size:26 final size:26
Alignment explanation
Indices: 1396843--1397176 Score: 112
Period size: 23 Copynumber: 13.4 Consensus size: 26
1396833 TAATGAAATT
1396843 ATTATAATAATGATTT-AGTAATAATC
1 ATTATAATAATGATTTGA-TAATAATC
* *
1396869 ATT-TAATAATGATTTAAT-ATGAT-
1 ATTATAATAATGATTTGATAATAATC
* * * * * *
1396892 -TTA-AATATTTA-ATGAT-TTGATG
1 ATTATAATAATGATTTGATAATAATC
*
1396914 ATT-TAGTAATGATTTGATAAT-ATC
1 ATTATAATAATGATTTGATAATAATC
1396938 ATTATAATAATGATTTGATAATAATC
1 ATTATAATAATGATTTGATAATAATC
1396964 A-T-T-ATAATGATTT-AGTAATAATC
1 ATTATAATAATGATTTGA-TAATAATC
* *
1396987 A-T-T-ATAATGA-TTAATAATGAT-
1 ATTATAATAATGATTTGATAATAATC
* * *
1397008 -TTAAATATTTAATGATTTGATTTAGTAATG
1 ATT--ATA-ATAATGATTTGA--TAATAATC
* *
1397038 ATTTGATAATAAT-ATAATATGATTAGT-ATA
1 A-TT-ATAATAATGAT--T-TGA-TAATAATC
* * *
1397068 AATATAATAATGATTTAATAATGAT-
1 ATTATAATAATGATTTGATAATAATC
* * * * * *
1397093 -TTA-AATATTTA-ATGAT-TTGATG
1 ATTATAATAATGATTTGATAATAATC
*
1397115 ATT-TAGTAATGATTTGATAATAATC
1 ATTATAATAATGATTTGATAATAATC
*
1397140 ATTATAATAATGATTTAATAATAATC
1 ATTATAATAATGATTTGATAATAATC
1397166 ATTATAATAAT
1 ATTATAATAAT
1397177 TATATAATGA
Statistics
Matches: 235, Mismatches: 39, Indels: 68
0.69 0.11 0.20
Matches are distributed among these distances:
21 12 0.05
22 20 0.09
23 49 0.21
24 21 0.09
25 41 0.17
26 49 0.21
27 4 0.02
28 8 0.03
29 10 0.04
30 7 0.03
31 9 0.04
32 5 0.02
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
ATTATAATAATGATTTGATAATAATC
Found at i:1397075 original size:116 final size:118
Alignment explanation
Indices: 1396847--1397089 Score: 334
Period size: 116 Copynumber: 2.2 Consensus size: 118
1396837 GAAATTATTA
1396847 TAATAATGATTTAGTAATAATCATTTAATAATGATTTAATATGATTTAAATATTTAATGATTTGA
1 TAATAATGATTTAGTAATAATCATTTAATAATGATTTAATATGATTTAAATATTTAATGATTT-A
1396912 TGATTTAGTAATGATTTGATAATATCATTATAATAATGATTTGATAATAATCA-T
65 TGATTTAGTAATGATTTGATAATA-CATTATAATAATGATTTGATAATAATCATT
1396966 T-ATAATGATTTAGTAATAATCA-TT-ATAATGA-TTAATAATGATTTAAATATTTAATGA-TT-
1 TAATAATGATTTAGTAATAATCATTTAATAATGATTTAAT-ATGATTTAAATATTTAATGATTTA
* *
1397025 TGATTTAGTAATGATTTGATAATA-A-TATAAT-ATGATTAG-T-ATAA--ATA
65 TGATTTAGTAATGATTTGATAATACATTATAATAATGATTTGATAATAATCATT
*
1397072 TAATAATGATTTAATAAT
1 TAATAATGATTTAGTAAT
1397090 GATTTAAATA
Statistics
Matches: 118, Mismatches: 3, Indels: 18
0.85 0.02 0.13
Matches are distributed among these distances:
105 1 0.01
106 1 0.01
107 19 0.16
108 1 0.01
109 7 0.06
110 6 0.05
111 1 0.01
113 24 0.20
115 7 0.06
116 27 0.23
117 2 0.02
118 21 0.18
119 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (118 bp):
TAATAATGATTTAGTAATAATCATTTAATAATGATTTAATATGATTTAAATATTTAATGATTTAT
GATTTAGTAATGATTTGATAATACATTATAATAATGATTTGATAATAATCATT
Found at i:1397088 original size:85 final size:87
Alignment explanation
Indices: 1396945--1397235 Score: 349
Period size: 88 Copynumber: 3.2 Consensus size: 87
1396935 ATCATTATAA
*
1396945 TAATGATTTGATAATAATCATTATAATGATTTAGTAATAATCATTATAATGATTAATAATGATTT
1 TAATGATTTGATAATAAT-ATAATAATGATTTAGTAATAATCATTATAATGATTAATAATGATTT
1397010 AAATATTTAATGATTTGATTTAG
65 AAATATTTAATGATTTGATTTAG
*
1397033 TAATGATTTGATAATAATATAAT-ATGA-TTAGT-ATAAAT-ATAATAATGATTTAATAATGATT
1 TAATGATTTGATAATAATATAATAATGATTTAGTAAT-AATCATTATAATGA-TTAATAATGATT
1397094 TAAATATTTAATGATTTGATGATTTAG
64 TAAATATTTAATGA-TT--TGATTTAG
* *
1397121 TAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATTATATAATG
1 TAATGATTTGATAAT-A--A-TATAATAATGATTTAGTAATAATCATTATAATGATTA-ATAATG
*
1397186 ATTTAATAATGATTTAATAGTAATT-ATTTAG
61 ATTT-A-AAT-ATTTAAT-G-ATTTGATTTAG
*
1397217 TAATGATTTTATAATAATA
1 TAATGATTTGATAATAATA
1397236 ATTTAATATT
Statistics
Matches: 177, Mismatches: 7, Indels: 34
0.81 0.03 0.16
Matches are distributed among these distances:
84 11 0.06
85 34 0.19
86 6 0.03
87 4 0.02
88 41 0.23
89 1 0.01
91 1 0.01
92 8 0.05
93 5 0.03
94 10 0.06
95 21 0.12
96 21 0.12
97 4 0.02
98 7 0.04
99 2 0.01
100 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.45
Consensus pattern (87 bp):
TAATGATTTGATAATAATATAATAATGATTTAGTAATAATCATTATAATGATTAATAATGATTTA
AATATTTAATGATTTGATTTAG
Found at i:1397148 original size:12 final size:12
Alignment explanation
Indices: 1397131--1397176 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
1397121 TAATGATTTG
1397131 ATAATAATCATT
1 ATAATAATCATT
*
1397143 ATAATAATGATTT
1 ATAATAATCA-TT
1397156 AATAATAATCATT
1 -ATAATAATCATT
1397169 ATAATAAT
1 ATAATAAT
1397177 TATATAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 17 0.57
13 4 0.13
14 9 0.30
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (12 bp):
ATAATAATCATT
Found at i:1397184 original size:26 final size:26
Alignment explanation
Indices: 1397121--1397184 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
1397111 GATGATTTAG
* *
1397121 TAATGATTTGATAATAATCATTATAA
1 TAATGATATAATAATAATCATTATAA
*
1397147 TAATGATTTAATAATAATCATTATAA
1 TAATGATATAATAATAATCATTATAA
*
1397173 TAATTATATAAT
1 TAATGATATAAT
1397185 GATTTAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (26 bp):
TAATGATATAATAATAATCATTATAA
Found at i:1397227 original size:26 final size:24
Alignment explanation
Indices: 1396847--1397243 Score: 180
Period size: 25 Copynumber: 17.2 Consensus size: 24
1396837 GAAATTATTA
1396847 TAATAATGATTTAGTAATAATCATT
1 TAATAATGATTTA-TAATAATCATT
*
1396872 TAATAATGA-TT-TAAT-ATGATT
1 TAATAATGATTTATAATAATCATT
* * *
1396893 T-A-AAT-ATTTAATGATTTGATGATT
1 TAATAATGATTT-AT-A-ATAATCATT
*
1396917 TAGTAATGATTTGATAAT-ATCATT
1 TAATAATGATTT-ATAATAATCATT
1396941 ATAATAATGATTTGATAATAATCA-T
1 -TAATAATGATTT-ATAATAATCATT
1396966 T-ATAATGATTTAGTAATAATCA-T
1 TAATAATGATTTA-TAATAATCATT
*
1396989 T-ATAATGA--T-TAATAATGATT
1 TAATAATGATTTATAATAATCATT
* * *
1397009 T-A-AAT-ATTTAATGAT-TTGATT
1 TAATAATGATTT-ATAATAATCATT
*
1397030 TAGTAATGATTTGATAATAAT-A--
1 TAATAATGATTT-ATAATAATCATT
*
1397052 TAAT-ATGA-TTAGT-ATAA--ATA
1 TAATAATGATTTA-TAATAATCATT
*
1397072 TAATAATGA-TT-TAATAATGATT
1 TAATAATGATTTATAATAATCATT
* * *
1397094 T-A-AAT-ATTTAATGATTTGATGATT
1 TAATAATGATTT-AT-A-ATAATCATT
*
1397118 TAGTAATGATTTGATAATAATCATT
1 TAATAATGATTT-ATAATAATCATT
1397143 ATAATAATGATTTAATAATAATCA-T
1 -TAATAATGATTT-ATAATAATCATT
* *
1397168 T-ATAAT-AATTAT-ATAATGATT
1 TAATAATGATTTATAATAATCATT
* *
1397189 TAATAATGATTTAATAGTAATTATT
1 TAATAATGATTT-ATAATAATCATT
* *
1397214 TAGTAATGATTTTATAATAATAATT
1 TAATAATGA-TTTATAATAATCATT
1397239 TAATA
1 TAATA
1397244 TTAATGATTT
Statistics
Matches: 295, Mismatches: 34, Indels: 86
0.71 0.08 0.21
Matches are distributed among these distances:
18 3 0.01
19 23 0.08
20 27 0.09
21 29 0.10
22 24 0.08
23 41 0.14
24 35 0.12
25 65 0.22
26 36 0.12
27 12 0.04
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (24 bp):
TAATAATGATTTATAATAATCATT
Found at i:1397259 original size:11 final size:11
Alignment explanation
Indices: 1396847--1397259 Score: 144
Period size: 11 Copynumber: 35.6 Consensus size: 11
1396837 GAAATTATTA
1396847 TAATAATGATTT
1 TAATAATGA-TT
*
1396859 AGTAATAATCATT
1 --TAATAATGATT
1396872 TAATAATGATT
1 TAATAATGATT
1396883 TAAT-ATGATT
1 TAATAATGATT
1396893 T-A-AAT-ATT
1 TAATAATGATT
1396901 TAATGATTTGATGATT
1 TAAT-A----ATGATT
*
1396917 TAGTAATGATT
1 TAATAATGATT
* *
1396928 TGATAATATCATT
1 TAAT-A-ATGATT
1396941 ATAATAATGATT
1 -TAATAATGATT
* *
1396953 TGATAATAATCAT
1 TAATAATGAT--T
1396966 T-ATAATGATT
1 TAATAATGATT
* *
1396976 TAGTAATAATCAT
1 TAATAATGAT--T
1396989 T-ATAATGA-T
1 TAATAATGATT
1396998 TAATAATGATT
1 TAATAATGATT
1397009 T-A-AAT-ATT
1 TAATAATGATT
*
1397017 TAATGATTTGATT
1 TAAT-A-ATGATT
*
1397030 TAGTAATGATT
1 TAATAATGATT
* * *
1397041 TGATAATAATA
1 TAATAATGATT
1397052 TAAT-ATGA-T
1 TAATAATGATT
*
1397061 TAGTATAA--ATA
1 TA--ATAATGATT
1397072 TAATAATGATT
1 TAATAATGATT
1397083 TAATAATGATT
1 TAATAATGATT
1397094 T-A-AAT-ATT
1 TAATAATGATT
1397102 TAATGATTTGATGATT
1 TAAT-A----ATGATT
*
1397118 TAGTAATGATTT
1 TAATAATGA-TT
*
1397130 GATAATAATCATT
1 --TAATAATGATT
1397143 ATAATAATGATT
1 -TAATAATGATT
*
1397155 TAATAATAATCAT
1 TAATAATGAT--T
*
1397168 T-ATAAT-AAT
1 TAATAATGATT
1397177 TATATAATGATT
1 TA-ATAATGATT
1397189 TAATAATGATT
1 TAATAATGATT
*
1397200 TAATAGTAATTATT
1 T-A-A-TAATGATT
*
1397214 TAGTAATGATTTT
1 TAATAATGA--TT
*
1397227 ATAATAATAATT
1 -TAATAATGATT
1397239 TAATATTAATGATT
1 T-A-A-TAATGATT
1397253 TAATAAT
1 TAATAAT
1397260 TATTACTAAA
Statistics
Matches: 304, Mismatches: 40, Indels: 113
0.67 0.09 0.25
Matches are distributed among these distances:
8 12 0.04
9 22 0.07
10 22 0.07
11 113 0.37
12 48 0.16
13 28 0.09
14 41 0.13
15 6 0.02
16 12 0.04
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (11 bp):
TAATAATGATT
Found at i:1397422 original size:13 final size:15
Alignment explanation
Indices: 1397389--1397426 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1397379 TGATTTACTA
1397389 ATTATTATTAATAAT
1 ATTATTATTAATAAT
1397404 GATTATTATTAAT-AT
1 -ATTATTATTAATAAT
1397419 -TTATTATT
1 ATTATTATT
1397427 TGATACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
15 2 0.09
16 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATTATTATTAATAAT
Found at i:1400121 original size:30 final size:30
Alignment explanation
Indices: 1400087--1400192 Score: 135
Period size: 30 Copynumber: 3.5 Consensus size: 30
1400077 TTTCTTTAAA
1400087 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
1400117 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* *
1400147 AAACTAATAAA-TGATTTTTTAATTATAA-TT
1 CAACTAATAAACT-ATTCTTTAA-TATAACTT
*
1400177 CACTACTAAAAAACTA
1 CA--ACTAATAAACTA
1400193 ATTAACTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
29 1 0.01
30 51 0.76
31 5 0.07
32 9 0.13
33 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:1400139 original size:15 final size:16
Alignment explanation
Indices: 1400091--1400145 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1400081 TTTAAACAAC
1400091 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
1400106 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
1400121 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
1400136 TAATATAACT
1 TAATATAACT
1400146 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:1400348 original size:17 final size:17
Alignment explanation
Indices: 1400326--1400359 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1400316 TAAATTTTTT
1400326 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
*
1400343 ACCCTAACCCTGAACTA
1 ACCCTAACCCTAAACTA
1400360 TCAAACTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.41, G:0.03, T:0.18
Consensus pattern (17 bp):
ACCCTAACCCTAAACTA
Found at i:1400699 original size:22 final size:22
Alignment explanation
Indices: 1400668--1400721 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1400658 GGTGCATGGA
*
1400668 GCAGC-GGGAGCAGGCGAGCAT
1 GCAGCGGGGAGCAGACGAGCAT
*
1400689 GCAGTGGGGAGCAGACGAGCAT
1 GCAGCGGGGAGCAGACGAGCAT
1400711 GCAGCGGGGAG
1 GCAGCGGGGAG
1400722 TAGGGCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.24, C:0.20, G:0.50, T:0.06
Consensus pattern (22 bp):
GCAGCGGGGAGCAGACGAGCAT
Found at i:1400809 original size:29 final size:29
Alignment explanation
Indices: 1400777--1400877 Score: 175
Period size: 29 Copynumber: 3.5 Consensus size: 29
1400767 ATCGCCTGGC
*
1400777 GTGCATGGTGACCTCCTTGGTCACCCGGA
1 GTGCATGGCGACCTCCTTGGTCACCCGGA
1400806 GTGCATGGCGACCTCCTTGGTCACCCGGA
1 GTGCATGGCGACCTCCTTGGTCACCCGGA
*
1400835 GTGCATGGCGACCTCCTTGGTCGCCCGGA
1 GTGCATGGCGACCTCCTTGGTCACCCGGA
*
1400864 GGGCATGGCGACCT
1 GTGCATGGCGACCT
1400878 ATGTTTTGGG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.13, C:0.33, G:0.34, T:0.21
Consensus pattern (29 bp):
GTGCATGGCGACCTCCTTGGTCACCCGGA
Found at i:1400920 original size:15 final size:15
Alignment explanation
Indices: 1400900--1400930 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1400890 GTGCATGTCC
1400900 CATGCGACGTTAATT
1 CATGCGACGTTAATT
1400915 CATGCGACGTTAATT
1 CATGCGACGTTAATT
1400930 C
1 C
1400931 GATCTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (15 bp):
CATGCGACGTTAATT
Found at i:1401446 original size:3 final size:3
Alignment explanation
Indices: 1401440--1401494 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
1401430 AATTGGTGAC
1401440 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1401488 AA- AAT AA
1 AAT AAT AA
1401495 ACAATTAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1401678 original size:31 final size:31
Alignment explanation
Indices: 1401643--1401714 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1401633 TCGTTAAAAA
* *
1401643 TAGGTGTCTAACGTTTTCTCCGTTATATTTT
1 TAGGTGTCTAACGTTTTCTCCATTATACTTT
* * *
1401674 TAGGT-TCCGAACGTTTTTTCTATTATACTTT
1 TAGGTGT-CTAACGTTTTCTCCATTATACTTT
1401705 TAGGTGTCTA
1 TAGGTGTCTA
1401715 CACAATAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 1 0.03
31 31 0.94
32 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (31 bp):
TAGGTGTCTAACGTTTTCTCCATTATACTTT
Found at i:1405275 original size:134 final size:134
Alignment explanation
Indices: 1405052--1405787 Score: 945
Period size: 134 Copynumber: 5.5 Consensus size: 134
1405042 ATTCCACTGT
* * * * * *
1405052 TCTTCAGGGAAGATTGAATCGGAGTCGATTTGCTTCACTGTTGTTTAGGAAGACCAAATCTAAAA
1 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
*
1405117 GAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
66 GAAGAAGAATCTACTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
*
1405182 CTAT
131 CTAC
* * *
1405186 TCTTTAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATTTGAAA
1 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
* * * *
1405251 GAAGAAGAATTTACTCCACTACTCTTTATGAGAGATCAGACTCGAGAAAATTTTGATCCACTTCA
66 GAAGAAGAATCTACTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
1405316 CTAC
131 CTAC
* * * *
1405320 TCTTCAGGGAATATTGAATCAGGATCGATTTGATTCACTGCTCTTCAGGAAAACCAAATCTGAAA
1 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
** * * * * * * *
1405385 GAAGAAGCGTCTTCTCTATTACTCTCTAGGGGAGACCATACTCGAGGAAACTTTGATCCACTTCA
66 GAAGAAGAATCTACTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
1405450 CTAC
131 CTAC
* * * * ** *
1405454 TCATAAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGATATTTTGGAAGACCAAATTTGAAA
1 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
* * * * *
1405519 GAAGAATAATCTGCTCCACTACTGTTTAGGGGGAGATCAGACTAGAGAAAATTTTGATCCACTTC
66 GAAGAAGAATCTACTCCACTACTCTTTA-GGGGAGATCAGACTCGAGAAAACTTTGATCCACTTC
*
1405584 ACTGC
130 ACTAC
1405589 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
1 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
** * * *
1405654 GAAGAAGCGTCTATTCTACTACTCTTTAGGGGATATCAGACTCGAGAAAACTTTGATCCACTTCA
66 GAAGAAGAATCTACTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
*
1405719 CTGC
131 CTAC
* * * * * * *
1405723 TCTTTAGGGAAGATTGAATC-GAATTTGATTTGTTTCTCTTG-TCTTCAAGAAGACCGAATATGA
1 TCTTCAGGGAAGATTGAATCAGAA-TCGATTTGCTTCAC-TGCTCTTCAGGAAGACCAAATCTGA
1405786 AA
64 AA
1405788 ATCAAACATT
Statistics
Matches: 515, Mismatches: 84, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
133 3 0.01
134 396 0.77
135 116 0.23
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (134 bp):
TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
GAAGAAGAATCTACTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
CTAC
Found at i:1405777 original size:269 final size:266
Alignment explanation
Indices: 1405046--1405787 Score: 1009
Period size: 269 Copynumber: 2.8 Consensus size: 266
1405036 TGATTCATTC
* * * * * *
1405046 CACTGTTCTTCAGGGAAGATTGAATCGGAGTCGATTTGCTTCACTGTTGTTTAGGAAGACCAAAT
1 CACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
* ** * *
1405111 CTAAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCC
66 CTGAAAGAAGAAGCGTCT-TTCTACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCC
* * *
1405176 ACTTCACTATTCTTTAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAAGACC
130 ACTTCACTACTCTTTAGGGAAGATTGAATC-GAATCGATTTGCTTCACTGATCTTCAGGAAGACC
* * *
1405241 AAATTTGAAAGAAGAAGAATTTACTCCACTACTCTTTATGAGAGATCAGACTCGAGAAAATTTTG
194 AAATTTGAAAGAAGAAGAATCTACTCCACTACTCTTTAGGAGAGATCAGACTAGAGAAAATTTTG
1405306 ATCCACTT
259 ATCCACTT
* * * * *
1405314 CACTACTCTTCAGGGAATATTGAATCAGGATCGATTTGATTCACTGCTCTTCAGGAAAACCAAAT
1 CACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
* * * * *
1405379 CTGAAAGAAGAAGCGTCTTCTCTATTACTCTCTAGGGGAGACCATACTCGAGGAAACTTTGATCC
66 CTGAAAGAAGAAGCGTCTT-TCTACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCC
* * * **
1405444 ACTTCACTACTCATAAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGATATTTTGGAAGACC
130 ACTTCACTACTCTTTAGGGAAGATTGAATC-GAATCGATTTGCTTCACTGATCTTCAGGAAGACC
* * * *
1405509 AAATTTGAAAGAAGAATAATCTGCTCCACTACTGTTTAGGGGGAGATCAGACTAGAGAAAATTTT
194 AAATTTGAAAGAAGAAGAATCTACTCCACTACTCTTTA-GGAGAGATCAGACTAGAGAAAATTTT
1405574 GATCCACTT
258 GATCCACTT
1405583 CACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
1 CACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
*
1405648 CTGAAAGAAGAAGCGTCTATTCTACTACTCTTTAGGGGATATCAGACTCGAGAAAACTTTGATCC
66 CTGAAAGAAGAAGCGTCT-TTCTACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCC
* * * * *
1405713 ACTTCACTGCTCTTTAGGGAAGATTGAATCGAATTTGATTTGTTTCTCTTG-TCTTCAAGAAGAC
130 ACTTCACTACTCTTTAGGGAAGATTGAATCGAA-TCGATTTGCTTCAC-TGATCTTCAGGAAGAC
* *
1405777 CGAATATGAAA
193 CAAATTTGAAA
1405788 ATCAAACATT
Statistics
Matches: 410, Mismatches: 59, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
268 202 0.49
269 205 0.50
270 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (266 bp):
CACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
CTGAAAGAAGAAGCGTCTTTCTACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCA
CTTCACTACTCTTTAGGGAAGATTGAATCGAATCGATTTGCTTCACTGATCTTCAGGAAGACCAA
ATTTGAAAGAAGAAGAATCTACTCCACTACTCTTTAGGAGAGATCAGACTAGAGAAAATTTTGAT
CCACTT
Found at i:1406338 original size:45 final size:45
Alignment explanation
Indices: 1406224--1406431 Score: 163
Period size: 45 Copynumber: 4.6 Consensus size: 45
1406214 GATACTACTG
* * * * *
1406224 AAAAG-TTTACTCTTCTTCGTGAGAAAGTCAAGAAGGACAACATT
1 AAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGAAAACACT
** ** * **
1406268 AAACTATCAACTTCTCTTCTTGAGAAAGTCAAGAAGGAAAACACT
1 AAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGAAAACACT
* ** * * *
1406313 AAAATATTGACTCCAGTTCACGAGAAATTC---AAGGAAAACAAT
1 AAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGAAAACACT
* * * *
1406355 ACCGAAAGATTGACTCCTCTTCGTGAGAATGTCAAGAAGGACAATACT
1 A---AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGAAAACACT
1406403 AAAAGATTGACTCCTCTTCGCGAGAAAGT
1 AAAAGATTGACTCCTCTTCGCGAGAAAGT
1406432 ACTGAAAGAT
Statistics
Matches: 126, Mismatches: 31, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
42 12 0.10
44 3 0.02
45 101 0.80
48 10 0.08
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (45 bp):
AAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGAAAACACT
Found at i:1406445 original size:32 final size:32
Alignment explanation
Indices: 1406399--1406463 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1406389 AGAAGGACAA
1406399 TACTAAAAGATTGACTCCTCTTCGCGAGAAAG
1 TACTAAAAGATTGACTCCTCTTCGCGAGAAAG
*
1406431 TACTGAAAGATTGACTCCTCTTCGCGAGAAAG
1 TACTAAAAGATTGACTCCTCTTCGCGAGAAAG
1406463 T
1 T
1406464 CAAGAAGGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (32 bp):
TACTAAAAGATTGACTCCTCTTCGCGAGAAAG
Found at i:1406485 original size:77 final size:77
Alignment explanation
Indices: 1406358--1406506 Score: 244
Period size: 77 Copynumber: 1.9 Consensus size: 77
1406348 AAACAATACC
* * *
1406358 GAAAGATTGACTCCTCTTCGTGAGAATGTCAAGAAGGACAATACTAAAAGATTGACTCCTCTTCG
1 GAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCCTCTTCG
1406423 CGAGAAAGTACT
66 CGAGAAAGTACT
* *
1406435 GAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACATTAAAAGATTGACTCCTCTTTG
1 GAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCCTCTTCG
*
1406500 TGAGAAA
66 CGAGAAA
1406507 ATCAAGAATG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 66 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (77 bp):
GAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCCTCTTCG
CGAGAAAGTACT
Found at i:1406505 original size:45 final size:45
Alignment explanation
Indices: 1406431--1406647 Score: 233
Period size: 45 Copynumber: 4.9 Consensus size: 45
1406421 CGCGAGAAAG
1406431 TACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAA
1 TACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAA
* * * * * * * *
1406476 CATTAAAAGATTGACTCCTCTTTGTGAGAAAATCAAGAATGAAAA
1 TACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAA
*
1406521 TACTGAGAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGG-CAA
1 TACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAA-GGACAA
* * * **
1406566 TACTGAGAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAA
1 TACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAA
* * * * *
1406611 TATTG--AGATTGACTTCTCTTCACGAGGAAGCCAAGAA
1 TACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAA
1406648 TAACAGAGAT
Statistics
Matches: 146, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
43 30 0.21
45 115 0.79
46 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (45 bp):
TACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAA
Found at i:1406569 original size:167 final size:167
Alignment explanation
Indices: 1406289--1406598 Score: 419
Period size: 167 Copynumber: 1.9 Consensus size: 167
1406279 TTCTCTTCTT
* * *
1406289 GAGAAAGTCAAGAAGGAAAACACTAAAATATTGACTCCAGTTCACGAGAAATTCAAGGAAAACAA
1 GAGAAAGTCAAGAAGGAAAACACTAAAAGATTGACTCCACTTCACGAGAAAATCAAGGAAAACAA
* *
1406354 TACCGAAAGATTGACTCCTCTTCGTGAGAATGTCAAGAAGGACAATACTAAAAGATTGACTCCTC
66 TACCGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAATACTAAAAGATTGACTCCTC
*
1406419 TTCGCGAGAAAGTACTGAAAGATTGACTCCTCTTCGC
131 TTCACGAGAAAGTACTGAAAGATTGACTCCTCTTCGC
* * * ***
1406456 GAGAAAGTCAAGAAGGACAACATTAAAAGATTGACTCCTCTTTGTGAGAAAATCAA-GAATGAA-
1 GAGAAAGTCAAGAAGGAAAACACTAAAAGATTGACTCCACTTCACGAGAAAATCAAGGAA--AAC
* * * * *
1406519 AATACTGAGAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGG-CAATACTGAGAGATTGACTT
64 AATACCGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAA-GGACAATACTAAAAGATTGACTC
1406583 CTCTTCACGAGAAAGT
128 CTCTTCACGAGAAAGT
1406599 CAAGAATAAC
Statistics
Matches: 123, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
166 3 0.02
167 116 0.94
168 4 0.03
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (167 bp):
GAGAAAGTCAAGAAGGAAAACACTAAAAGATTGACTCCACTTCACGAGAAAATCAAGGAAAACAA
TACCGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAATACTAAAAGATTGACTCCTC
TTCACGAGAAAGTACTGAAAGATTGACTCCTCTTCGC
Found at i:1406587 original size:90 final size:91
Alignment explanation
Indices: 1406426--1406648 Score: 258
Period size: 90 Copynumber: 2.5 Consensus size: 91
1406416 CTCTTCGCGA
* * *
1406426 GAAAGTACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAA-GGACAACATTAAAAGATTGA
1 GAAAATACTGAGAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGGACAACACTAAAAGATTGA
***
1406490 CTCCTCTTTGTGAGAAAATCAAGAAT
66 CTCCTCTTCACGAGAAAATCAAGAAT
* * *
1406516 GAAAATACTGAGAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGG-CAATACTGAGAGATTGA
1 GAAAATACTGAGAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGGACAACACTAAAAGATTGA
* *
1406580 CTTCTCTTCACGAGAAAGTCAAGAAT
66 CTCCTCTTCACGAGAAAATCAAGAAT
* * * * *
1406606 -AACAATA-T-TGAGATTGACTTCTCTTCACGAGGAAGCCAAGAAT
1 GAA-AATACTGAGAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAT
1406649 AACAGAGATT
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
88 30 0.26
89 3 0.03
90 80 0.70
91 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (91 bp):
GAAAATACTGAGAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGGACAACACTAAAAGATTGA
CTCCTCTTCACGAGAAAATCAAGAAT
Found at i:1406603 original size:212 final size:212
Alignment explanation
Indices: 1406219--1406604 Score: 490
Period size: 212 Copynumber: 1.8 Consensus size: 212
1406209 GGAAGGATAC
* * * ** *
1406219 TACTGAAAAGTTTACTCTTCTTCGTGAGAAAGTCAAGAAGGACAACATTAAACTATCAACTTCTC
1 TACTGAAAAGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACATTAAAAGATCAACTCCTC
* * * *
1406284 TTCTTGAGAAAGTCAAGAAGGAAAACACTAAAATATTGACTCCAGTTCACGAGAAATTCAAGGAA
66 TTCTTGAGAAAATCAAGAAGGAAAACACTAAAAGATTGACTCCACTTCACGAGAAAGTCAAGGAA
** *
1406349 AACAATACCGAAAGATTGACTCCTCTTCGTGAGAATGTCAAGAAGGACAATACTAAAAGATTGAC
131 AACAATACCGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAATACTAAAAGATTGAC
1406414 TCCTCTTCGCGAGAAAG
196 TCCTCTTCGCGAGAAAG
**
1406431 TACTG-AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACATTAAAAGATTGACTCCT
1 TACTGAAAAG-TTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACATTAAAAGATCAACTCCT
* * * * * *
1406495 CTT-TGTGAGAAAATCAAGAATGAAAATACTGAGAGATTGACTCCTCTTCGCGAGAAAGTCAA-G
65 CTTCT-TGAGAAAATCAAGAAGGAAAACACTAAAAGATTGACTCCACTTCACGAGAAAGTCAAGG
** * * *
1406558 AATGGCAATACTGAGAGATTGACTTCTCTTCACGAGAAAGTCAAGAA
129 AA-AACAATACCGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
1406605 TAACAATATT
Statistics
Matches: 145, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
211 8 0.06
212 137 0.94
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (212 bp):
TACTGAAAAGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACATTAAAAGATCAACTCCTC
TTCTTGAGAAAATCAAGAAGGAAAACACTAAAAGATTGACTCCACTTCACGAGAAAGTCAAGGAA
AACAATACCGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAATACTAAAAGATTGAC
TCCTCTTCGCGAGAAAG
Found at i:1406797 original size:38 final size:38
Alignment explanation
Indices: 1406573--1407048 Score: 465
Period size: 38 Copynumber: 11.8 Consensus size: 38
1406563 CAATACTGAG
*
1406573 AGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAATA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-A-A
*
1406613 TTGAGATTGACTTCTCTTCACGAGGAAGCCAAGAATAACAGA
1 ---AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA-A
1406655 GATTGACTTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGA
1 -A--GA-TTGACTTCTCTTCACGAGGAAGTCAAGAATAACA-A
1406698 GATTGAATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAA
1 -A--G-ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AA
1406744 AGATTGAC-TCTTCTTCACGAGGGAA-TCAAGAATAACAA
1 AGATTGACTTC-TCTTCACGA-GGAAGTCAAGAATAACAA
* * *
1406782 AGATCGACTTCTCTTCACTAGGAAGCCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* ** * *
1406820 AGATCGACTTCTCTTCATAAGGAATTCAAGAATAAAAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-AACAA
1406859 AGATCT-ACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAA
1 AGAT-TGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AA
* * * * *
1406901 AGATTGACTCCTCTTCGCGAGGGAGTAAAAAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
1406939 GGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1406977 AGATTGACTTCTCTTCATGAGAAAGTCAAGAATAACATTGAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AA
*
1407019 AGATTGACTCCTCTTCACGATGG-AGTCAAG
1 AGATTGACTTCTCTTCACGA-GGAAGTCAAG
1407049 TCGAAGCTTC
Statistics
Matches: 375, Mismatches: 34, Indels: 49
0.82 0.07 0.11
Matches are distributed among these distances:
37 4 0.01
38 127 0.34
39 34 0.09
40 2 0.01
41 3 0.01
42 88 0.23
43 113 0.30
44 1 0.00
45 1 0.00
46 1 0.00
47 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (38 bp):
AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
Found at i:1406916 original size:157 final size:161
Alignment explanation
Indices: 1406530--1407048 Score: 595
Period size: 157 Copynumber: 3.2 Consensus size: 161
1406520 ATACTGAGAG
* * * * * * *
1406530 ATTGACTCCTCTTCGCGAGAAAGTCAAGAATGGCAATACTGAGAGATTGACTTCTCTTCACGA-G
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAAT---AACATTGAAAGATTGACTCCTCTTCACGAGG
*
1406594 AAAGTCAAGAATAACAATATTGAGATTGACTTCTCTTCACGAGGAAGCCAAGAATAACAGAGATT
63 GAA-TCAAGAATAAC-A-A---AGATTGACTTCTCTTCACGAGGAAGCCAAGAATAACA-A-A--
* **
1406659 GACTTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAGATTGA
118 GA-TTGACTTCTCTTCATGAGGAAGTCAAGAATAACAGAGAAAGA
*
1406704 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTTCTTCACGAGGGAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGAA
* * *
1406769 TCAAGAATAACAAAGATCGACTTCTCTTCACTAGGAAGCCAAGAATAACAAAGATCGACTTCTCT
66 TCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGCCAAGAATAACAAAGATTGACTTCTCT
* *
1406834 TCATAAGGAATTCAAGAATAA-A-A-AAAG-
131 TCATGAGGAAGTCAAGAATAACAGAGAAAGA
*
1406861 ATCT-ACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCGCGAGGGA
1 AT-TGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
* * * * *
1406925 GTAAAAAATAACAAGGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTC
65 ATCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGCCAAGAATAACAAAGATTGACTTCTC
* **
1406990 TTCATGAGAAAGTCAAGAATAACATTGAAAG-
130 TTCATGAGGAAGTCAAGAATAACAGAGAAAGA
*
1407021 ATTGACTCCTCTTCACGATGG-AGTCAAG
1 ATTGACTTCTCTTCACGA-GGAAGTCAAG
1407049 TCGAAGCTTC
Statistics
Matches: 306, Mismatches: 32, Indels: 28
0.84 0.09 0.08
Matches are distributed among these distances:
157 136 0.44
158 4 0.01
159 2 0.01
160 27 0.09
161 30 0.10
162 2 0.01
164 1 0.00
165 1 0.00
166 35 0.11
169 1 0.00
170 1 0.00
171 35 0.11
172 3 0.01
174 28 0.09
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (161 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGAA
TCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGCCAAGAATAACAAAGATTGACTTCTCT
TCATGAGGAAGTCAAGAATAACAGAGAAAGA
Found at i:1408275 original size:43 final size:45
Alignment explanation
Indices: 1408197--1408327 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 45
1408187 TGATCTCGGA
* *
1408197 TGATATGGGCCTTCAAAAAAATGTCCCGACATTTATTATTTCTT-G-C
1 TGATATGGGCCTTC---AAAATGCCCCAACATTTATTATTTCTTGGAC
1408243 TGATATGGGCCTTCAAAATGCCCCAACATTTATTATTT-TTGGAC
1 TGATATGGGCCTTCAAAATGCCCCAACATTTATTATTTCTTGGAC
*** * *
1408287 -GATACATGCCTTCAAAAGTGCCCCAACATTCATCATTTCTT
1 TGATATGGGCCTTCAAAA-TGCCCCAACATTTATTATTTCTT
1408328 ACTCCAGTAC
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
42 2 0.03
43 37 0.50
44 19 0.26
45 2 0.03
46 14 0.19
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (45 bp):
TGATATGGGCCTTCAAAATGCCCCAACATTTATTATTTCTTGGAC
Found at i:1416138 original size:2 final size:2
Alignment explanation
Indices: 1416131--1416174 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1416121 ATAAAAATCT
1416131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1416173 TA
1 TA
1416175 AACTTGATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1416724 original size:22 final size:22
Alignment explanation
Indices: 1416699--1416747 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1416689 AATAAGTGAT
* *
1416699 TTAATTAATATTATTTGA-ATAA
1 TTAAATAAT-TTATTTGACAAAA
*
1416721 TTAAATAATTTGTTTGACAAAA
1 TTAAATAATTTATTTGACAAAA
1416743 TTAAA
1 TTAAA
1416748 AAGTAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (22 bp):
TTAAATAATTTATTTGACAAAA
Found at i:1420267 original size:17 final size:18
Alignment explanation
Indices: 1420242--1420275 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1420232 GTTTTGTTGA
*
1420242 TTGGGCTTGTA-ATATAT
1 TTGGACTTGTACATATAT
1420259 TTGGACTTGTACATATA
1 TTGGACTTGTACATATA
1420276 AATAAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (18 bp):
TTGGACTTGTACATATAT
Found at i:1421277 original size:21 final size:21
Alignment explanation
Indices: 1421234--1421326 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
1421224 TTTTCCCAAT
** *
1421234 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
*
1421254 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
** *
1421275 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
1421295 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
1421316 TCGCAATGCGA
1 TCGCAATGCGA
1421327 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTGGGAAAA
Found at i:1421279 original size:41 final size:41
Alignment explanation
Indices: 1421234--1421326 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1421224 TTTTCCCAAT
1421234 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
1421275 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1421316 TCGCAATGCGA
1 TCGCAATGCGA
1421327 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1421339 original size:41 final size:41
Alignment explanation
Indices: 1421253--1421387 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
1421243 GAATAAGTAA
* *
1421253 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
*
1421294 ATCGCAATGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * *
1421335 ATCGCAATGCGATAAT-AAAAAATCGCAACGCGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1421376 TTCGCAACGCGA
1 ATCGCAACGCGA
1421388 TAATACATAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1421340 original size:20 final size:19
Alignment explanation
Indices: 1421315--1421409 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 19
1421305 AATTGGGAAA
*
1421315 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATAAT-ACT
**
1421335 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATAAT--ACT
* *
1421356 ATCGCAACGCGATACTTACT
1 ATCGCAATGCGATA-ATACT
* *
1421376 TTCGCAACGCGATAATACAT
1 ATCGCAATGCGATAATAC-T
1421396 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1421410 TTTCAAAGCG
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.05
20 30 0.51
21 25 0.42
22 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAATGCGATAATACT
Found at i:1421388 original size:41 final size:41
Alignment explanation
Indices: 1421312--1421409 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
1421302 GCGAATTGGG
*
1421312 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAA
* * * *
1421353 AAAATCGCAACGCGATACTTACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAA
*
1421394 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
1421410 TTTCAAAGCG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAA
Found at i:1421605 original size:22 final size:22
Alignment explanation
Indices: 1421577--1421620 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1421567 CACTCTCTCA
1421577 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1421599 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1421621 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1421908 original size:20 final size:20
Alignment explanation
Indices: 1421885--1421927 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1421875 GATAGTCGAA
1421885 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
1421905 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
1421925 TTC
1 TTC
1421928 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:1423268 original size:18 final size:18
Alignment explanation
Indices: 1423247--1423291 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1423237 TCCACTTCGG
* *
1423247 GAGCCATTACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1423265 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1423283 GAGCCATCA
1 GAGCCATCA
1423292 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1423827 original size:19 final size:20
Alignment explanation
Indices: 1423773--1423839 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1423763 TAGTTTACTT
* *
1423773 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1423793 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1423813 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1423832 TCGCAACG
1 TCGCAACG
1423840 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1423847 original size:14 final size:14
Alignment explanation
Indices: 1423828--1423885 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1423818 ATGCGAAATG
1423828 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1423842 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1423858 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1423874 AAAATCGCAACG
1 AAAATCGCAACG
1423886 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1423870 original size:32 final size:33
Alignment explanation
Indices: 1423812--1423902 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1423802 GGAAATGGCT
1423812 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1423845 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1423877 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1423903 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1423938 original size:14 final size:14
Alignment explanation
Indices: 1423919--1423976 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1423909 TTGTGTTTCG
1423919 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1423933 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1423949 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1423965 CGTTGCGATTTT
1 CGTTGCGATTTT
1423977 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1423953 original size:32 final size:33
Alignment explanation
Indices: 1423914--1423984 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 33
1423904 GCGATTTGTG
1423914 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1423946 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1423979 TTTCGC
1 TTTCGC
1423985 ATTACGATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 27 0.71
33 11 0.29
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1423999 original size:19 final size:19
Alignment explanation
Indices: 1423977--1424023 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1423967 TTGCGATTTT
1423977 CATTTCGCATTACGATAGC
1 CATTTCGCATTACGATAGC
* * *
1423996 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTACGATAGC
1424016 CATTTCGC
1 CATTTCGC
1424024 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (19 bp):
CATTTCGCATTACGATAGC
Found at i:1424026 original size:19 final size:19
Alignment explanation
Indices: 1423965--1424031 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1423955 GCGATTTTGT
**
1423965 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
1423984 CATTACGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1424004 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
1424023 CGTTGCGAT
1 CGTTGCGAT
1424032 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1425918 original size:14 final size:14
Alignment explanation
Indices: 1425899--1425934 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1425889 ATTGTTTAAT
1425899 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1425913 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1425927 TGATTTGT
1 TGATTTGT
1425935 TTAATTGATG
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:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1426060 original size:14 final size:14
Alignment explanation
Indices: 1426041--1426094 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1426031 CGAAATGGCT
1426041 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1426055 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1426074 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1426088 ATCGCAA
1 ATCGCAA
1426095 TGTGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1426087 original size:19 final size:19
Alignment explanation
Indices: 1426051--1426087 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1426041 ATCGCAACGA
* *
1426051 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
1426070 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
1426088 ATCGCAATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:1426143 original size:20 final size:20
Alignment explanation
Indices: 1426118--1426155 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1426108 TCGCATTGCG
*
1426118 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1426138 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1426156 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1427236 original size:24 final size:24
Alignment explanation
Indices: 1427209--1427254 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1427199 TATTCGAAAT
* *
1427209 TTGATCTTGGTCAATACCCGGACA
1 TTGATATTGGTCAATACACGGACA
1427233 TTGATATTGGTCAATACACGGA
1 TTGATATTGGTCAATACACGGA
1427255 TTTTGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
TTGATATTGGTCAATACACGGACA
Found at i:1427260 original size:24 final size:24
Alignment explanation
Indices: 1427208--1427261 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1427198 GTATTCGAAA
* *
1427208 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
* *
1427232 ATTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1427256 TTTGAT
1 TTTGAT
1427262 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1427453 original size:12 final size:12
Alignment explanation
Indices: 1427436--1427460 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1427426 ATATAATCCT
1427436 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1427448 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1427460 G
1 G
1427461 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1429795 original size:33 final size:33
Alignment explanation
Indices: 1429753--1429879 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1429743 GGAAATTACT
1429753 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1429786 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
1429818 TTTCGCAATGCGAAATAAAAATTGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1429852 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1429880 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1429860 original size:66 final size:66
Alignment explanation
Indices: 1429754--1429886 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1429744 GAAATTACTA
* *
1429754 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1429819 T
66 T
* *
1429820 TCGCAATGCGAAATAAAAATTGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1429885 T
66 T
1429886 T
1 T
1429887 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1429901 original size:19 final size:20
Alignment explanation
Indices: 1429879--1429922 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1429869 AAATCGCAAC
1429879 GCGA-ATTTAATTTCGCGTT
1 GCGATATTTAATTTCGCGTT
* *
1429898 GCGATTTTTATTTTCGCGTT
1 GCGATATTTAATTTCGCGTT
1429918 GCGAT
1 GCGAT
1429923 TCTCTCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (20 bp):
GCGATATTTAATTTCGCGTT
Found at i:1429912 original size:20 final size:20
Alignment explanation
Indices: 1429884--1429923 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1429874 GCAACGCGAA
1429884 TTTAATTTCGCGTTGCGATT
1 TTTAATTTCGCGTTGCGATT
*
1429904 TTTATTTTCGCGTTGCGATT
1 TTTAATTTCGCGTTGCGATT
1429924 CTCTCGTTGC
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:0.12, C:0.15, G:0.20, T:0.53
Consensus pattern (20 bp):
TTTAATTTCGCGTTGCGATT
Found at i:1430081 original size:14 final size:14
Alignment explanation
Indices: 1430062--1430098 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1430052 CATCAATTAA
1430062 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1430076 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1430090 ACAAATCAA
1 ACAAATCAA
1430099 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1431520 original size:21 final size:21
Alignment explanation
Indices: 1431454--1431520 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1431444 GTGAATCGGG
*
1431454 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1431474 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1431496 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1431517 CTCT
1 CTCT
1431521 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1431539 original size:42 final size:41
Alignment explanation
Indices: 1431454--1431576 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1431444 GTGAATCGGG
* * * * *
1431454 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1431496 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1431538 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1431577 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1433591 original size:20 final size:19
Alignment explanation
Indices: 1433560--1433739 Score: 83
Period size: 19 Copynumber: 9.8 Consensus size: 19
1433550 TCTTTTGGTT
1433560 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1433579 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1433600 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1433619 G--A-G--AATAGCAACGC
1 GAAATGAAAATCGCAACGA
**
1433633 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
1433649 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1433666 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
1433686 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* * *
1433705 GAAATAAAAAACGCAACGC
1 GAAATGAAAATCGCAACGA
**
1433724 GAAACAAAAATCGCAA
1 GAAATGAAAATCGCAA
1433740 TGCGATTTTT
Statistics
Matches: 126, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
14 16 0.13
15 1 0.01
16 4 0.03
17 4 0.03
18 1 0.01
19 51 0.40
20 47 0.37
21 2 0.02
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1433642 original size:33 final size:33
Alignment explanation
Indices: 1433585--1433683 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
1433575 ACGAGATAAT
*
1433585 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
1433619 GAGAATAGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1433652 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1433684 GCGAAATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1433677 original size:19 final size:19
Alignment explanation
Indices: 1433655--1433744 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
1433645 GCGACCAGAC
*
1433655 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
1433674 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATAAA
1433694 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
* *
1433713 AAACGCAACGCGAAACAAA
1 AATCGCAACGCGAAATAAA
*
1433732 AATCGCAATGCGA
1 AATCGCAACGCGA
1433745 TTTTTGTTTC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 47 0.72
20 18 0.28
ACGTcount: A:0.50, C:0.23, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:1433698 original size:39 final size:38
Alignment explanation
Indices: 1433655--1433744 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 38
1433645 GCGACCAGAC
* * *
1433655 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATAAAAAACGCAA-CGCGAAACAAA
1433694 AATCGCAACGCGAAATAAAAAACGCAACGCGAAACAAA
1 AATCGCAACGCGAAATAAAAAACGCAACGCGAAACAAA
*
1433732 AATCGCAATGCGA
1 AATCGCAACGCGA
1433745 TTTTTGTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 22 0.47
39 25 0.53
ACGTcount: A:0.50, C:0.23, G:0.18, T:0.09
Consensus pattern (38 bp):
AATCGCAACGCGAAATAAAAAACGCAACGCGAAACAAA
Found at i:1433776 original size:19 final size:19
Alignment explanation
Indices: 1433740--1433806 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1433730 AAAATCGCAA
*
1433740 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1433759 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1433778 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1433798 TGCGATTTT
1 TGCGATTTT
1433807 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1434373 original size:20 final size:20
Alignment explanation
Indices: 1434321--1434360 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1434311 GCGCTATGTA
1434321 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1434341 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1434361 TATCTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1434411 original size:20 final size:20
Alignment explanation
Indices: 1434382--1434435 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1434372 GATTTTGTAT
1434382 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
1434402 TATCGTATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1434422 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1434436 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1434546 original size:21 final size:21
Alignment explanation
Indices: 1434506--1434546 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1434496 ATTGTATACC
**
1434506 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1434527 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1434547 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1435810 original size:6 final size:5
Alignment explanation
Indices: 1435798--1435862 Score: 51
Period size: 5 Copynumber: 12.2 Consensus size: 5
1435788 TCTTGAACCC
* * *
1435798 TCTTT TCCTTT TCTTT TTTAATT TCTTTTT TCTTC TCTTT TTTTT TCTTT
1 TCTTT T-CTTT TCTTT TCT--TT TC-T-TT TCTTT TCTTT TCTTT TCTTT
1435848 T-TTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT T
1435863 TTCCTTTAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.08
5 30 0.62
6 6 0.12
7 7 0.15
8 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:1435838 original size:22 final size:21
Alignment explanation
Indices: 1435806--1435854 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1435796 CCTCTTTTCC
*
1435806 TTTTCTTTTTTAATTTCTTTT
1 TTTTCTCTTTTAATTTCTTTT
**
1435827 TTCTTCTCTTTTTTTTTCTTTT
1 TT-TTCTCTTTTAATTTCTTTT
1435849 TTTTCT
1 TTTTCT
1435855 TTTCTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTCTCTTTTAATTTCTTTT
Found at i:1435864 original size:12 final size:12
Alignment explanation
Indices: 1435800--1435865 Score: 71
Period size: 12 Copynumber: 5.5 Consensus size: 12
1435790 TTGAACCCTC
*
1435800 TTTTCCTTTTCT
1 TTTTTCTTTTCT
**
1435812 TTTTTAATTTCT
1 TTTTTCTTTTCT
*
1435824 TTTTTCTTCTCT
1 TTTTTCTTTTCT
*
1435836 TTTTT-TTTCTTT
1 TTTTTCTTT-TCT
1435848 TTTTTCTTTTCT
1 TTTTTCTTTTCT
1435860 TTTTTC
1 TTTTTC
1435866 CTTTAAGTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.88
13 3 0.07
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:1436015 original size:14 final size:14
Alignment explanation
Indices: 1435980--1436007 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1435970 AACAACATAA
1435980 GAGCATTCCCAGTT
1 GAGCATTCCCAGTT
1435994 GAGCATTCCCAGTT
1 GAGCATTCCCAGTT
1436008 CGACATTCAC
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:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
GAGCATTCCCAGTT
Found at i:1440765 original size:13 final size:13
Alignment explanation
Indices: 1440749--1440782 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1440739 AATATAAGTT
1440749 TATATATAAACTA
1 TATATATAAACTA
1440762 TATATATAAACTA
1 TATATATAAACTA
*
1440775 TATTTATA
1 TATATATA
1440783 TTATAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:1440766 original size:30 final size:31
Alignment explanation
Indices: 1440729--1440797 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 31
1440719 AATAATTATA
1440729 ATATATATATAA-TATAAGTTTATA-TATAAACT
1 ATATATATA-AACTAT-A-TTTATATTATAAACT
1440761 ATATATATAAACTATATTTATATTATAAACT
1 ATATATATAAACTATATTTATATTATAAACT
1440792 ATATAT
1 ATATAT
1440798 GTATAAGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
30 6 0.17
31 17 0.49
32 12 0.34
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (31 bp):
ATATATATAAACTATATTTATATTATAAACT
Found at i:1440789 original size:18 final size:19
Alignment explanation
Indices: 1440760--1440887 Score: 69
Period size: 18 Copynumber: 6.9 Consensus size: 19
1440750 ATATATAAAC
1440760 TATATATATAAACTATATT
1 TATATATATAAACTATATT
1440779 TATAT-TATAAACTATATAT
1 TATATATATAAACTATAT-T
1440798 GTATA-AGCTATAAA--A-ATT
1 -TATATA--TATAAACTATATT
* *
1440816 ATATAGTTTATAAACTATAAT
1 -TATA-TATATAAACTATATT
*
1440837 T-TATAT-T-AA-TATATA
1 TATATATATAAACTATATT
* *
1440852 TATATATATATA-TATATA
1 TATATATATAAACTATATT
**
1440870 TATATGCATAAACTATAT
1 TATATATATAAACTATAT
1440888 AAAATAATCA
Statistics
Matches: 85, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
15 5 0.06
16 7 0.08
17 2 0.02
18 41 0.48
19 15 0.18
20 7 0.08
21 2 0.02
22 6 0.07
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (19 bp):
TATATATATAAACTATATT
Found at i:1440795 original size:59 final size:57
Alignment explanation
Indices: 1440723--1440863 Score: 144
Period size: 59 Copynumber: 2.4 Consensus size: 57
1440713 ATTTGAAATA
*
1440723 ATTATAATATATATATAATATAAGTTTATATATAAACTATATA-TATAAACTAT-ATTTAT
1 ATTATAA-ATATATATAATATAAG-CTATA-A-AAACTATATATTATAAACTATAATTTAT
* *
1440782 ATTATAAACTATATAT-GTATAAGCTATAAAAATTATATAGTTTATAAACTATAATTTAT
1 ATTATAAA-TATATATAATATAAGCTATAAAAACTATATA--TTATAAACTATAATTTAT
*
1440841 ATTAATATATATATATATATATA
1 ATT-ATAAATATATATA-ATATA
1440864 TATATATATA
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
55 9 0.13
56 1 0.01
57 4 0.06
58 17 0.25
59 30 0.43
60 4 0.06
61 4 0.06
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (57 bp):
ATTATAAATATATATAATATAAGCTATAAAAACTATATATTATAAACTATAATTTAT
Found at i:1440888 original size:2 final size:2
Alignment explanation
Indices: 1440725--1440874 Score: 66
Period size: 2 Copynumber: 76.5 Consensus size: 2
1440715 TTGAAATAAT
* *
1440725 TA TA -A TA TA TA TA TA -A TA TA -A GTT TA TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * * **
1440766 TA TA AA CTA TA TT TA TA T- TA TA AA CTA TA TA TG TA TA -A GC TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
1440808 TA AA AA T- TA TA TA GTT TA TA AA CTA TA -A TT TA TA T- TA -A TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
1440848 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1440875 GCATAAACTA
Statistics
Matches: 110, Mismatches: 23, Indels: 30
0.67 0.14 0.18
Matches are distributed among these distances:
1 9 0.08
2 96 0.87
3 5 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1441029 original size:19 final size:18
Alignment explanation
Indices: 1441005--1441073 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
1440995 ATATTACTAA
1441005 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
1441024 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
1441042 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
1441064 ATTA-TAATAA
1 ATTATTAATAA
1441074 ATATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 3 0.08
21 2 0.05
22 7 0.17
23 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:1441080 original size:54 final size:53
Alignment explanation
Indices: 1440890--1441080 Score: 130
Period size: 54 Copynumber: 3.6 Consensus size: 53
1440880 AACTATATAA
* ** * *
1440890 AATAATC-AATTATATTATAAT-AATATAAGATATTATAT-TTTTAT-TTTAAT
1 AATAATCTAATAATATTATAATAAATATATTAT-TTATATATTTAATATTAAAT
* * *
1440940 AAT-ATATAATAA-ATTATTAATAAAATTTATATTATTTAT-TAATTTCATA-GAAAT
1 AATAATCTAATAATATTA-TAAT-AAA--TATATTATTTATAT-ATTTAATATTAAAT
* * *
1440994 AATATTACTAA-ATTATTAATAATGAATAATATTATTTATATATTTAATATTAATAT
1 AATAAT-CTAATAATATT-ATAATAAAT-ATATTATTTATATATTTAATATTAA-AT
1441050 AATAATCTAATAATATTATAATAAATATATT
1 AATAATCTAATAATATTATAATAAATATATT
1441081 TAAAATATAC
Statistics
Matches: 107, Mismatches: 16, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
49 6 0.06
50 11 0.10
52 3 0.03
53 5 0.05
54 40 0.37
55 19 0.18
56 22 0.21
57 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (53 bp):
AATAATCTAATAATATTATAATAAATATATTATTTATATATTTAATATTAAAT
Found at i:1441087 original size:23 final size:24
Alignment explanation
Indices: 1441044--1441111 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
1441034 TATTTAATAT
*
1441044 TAATATAATA-ATCTAATAATATTA-
1 TAATA-AATATATTTAA-AATATTAC
1441068 TAATAAATATATTTAAAATA-TAC
1 TAATAAATATATTTAAAATATTAC
* *
1441091 TAATTAATATTTTTAAAATAT
1 TAATAAATATATTTAAAATAT
1441112 AATATAACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 2 0.05
23 26 0.68
24 10 0.26
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATAAATATATTTAAAATATTAC
Found at i:1441112 original size:23 final size:23
Alignment explanation
Indices: 1441068--1441112 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1441058 AATAATATTA
1441068 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
1441091 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
1441113 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:1441265 original size:22 final size:22
Alignment explanation
Indices: 1441228--1441286 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1441218 TATTAATAAT
* *
1441228 AAATAAATTATTTTAATATTTTA
1 AAATAAATAATATTAAT-TTTTA
1441251 AAAT-AATAATATTAATTTTTA
1 AAATAAATAATATTAATTTTTA
**
1441272 TGATAAATAATATTA
1 AAATAAATAATATTA
1441287 TTTATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 20 0.65
23 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATAAATAATATTAATTTTTA
Found at i:1441477 original size:14 final size:14
Alignment explanation
Indices: 1441458--1441501 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1441448 CCAGAAATGT
**
1441458 AATTCAATTTCTGG
1 AATTCAATTTCCAG
*
1441472 AATTCAAATTCCAG
1 AATTCAATTTCCAG
1441486 AATTCAATTTCCAG
1 AATTCAATTTCCAG
1441500 AA
1 AA
1441502 AACCAATTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:1441583 original size:2 final size:2
Alignment explanation
Indices: 1441530--1441574 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1441520 AAACAGACCC
**
1441530 TA TA TA TA TA TA -A CC TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1441571 TA TA
1 TA TA
1441575 AACTATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1441890 original size:22 final size:22
Alignment explanation
Indices: 1441865--1441906 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1441855 TATGTATAGT
1441865 ATATA-TAAATTGTATATATAAC
1 ATATAGTAAA-TGTATATATAAC
*
1441887 ATATAGTATATGTATATATA
1 ATATAGTAAATGTATATATA
1441907 CAATCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (22 bp):
ATATAGTAAATGTATATATAAC
Found at i:1441949 original size:57 final size:55
Alignment explanation
Indices: 1441815--1441950 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 55
1441805 TGTATACATG
* * *
1441815 TAAACTATATATGTAACTTATAATACATGTATGTATAAACTATGTATAGTATATA
1 TAAACTATATATGTAACATATAGTACATGTATATATAAACTATGTATAGTATATA
* * * * *
1441870 TAAATTGTATATATAACATATAGTATATGTATATATACAATCTATTTATATGT-TATA
1 TAAACTATATATGTAACATATAGTACATGTATATATA-AA-CTATGTATA-GTATATA
1441927 TAAACTATATATGTAACATATAGT
1 TAAACTATATATGTAACATATAGT
1441951 TTATAAACAA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
55 30 0.45
56 2 0.03
57 33 0.49
58 2 0.03
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (55 bp):
TAAACTATATATGTAACATATAGTACATGTATATATAAACTATGTATAGTATATA
Found at i:1441965 original size:14 final size:15
Alignment explanation
Indices: 1441941--1441969 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1441931 CTATATATGT
1441941 AACATATAGTTTATA
1 AACATATAGTTTATA
1441956 AACA-ATAGTTTATA
1 AACATATAGTTTATA
1441970 TTAATGTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
AACATATAGTTTATA
Found at i:1441969 original size:21 final size:20
Alignment explanation
Indices: 1441945--1442035 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 20
1441935 ATATGTAACA
1441945 TATAGTTTATAAACAATAGTT
1 TATA-TTTATAAACAATAGTT
* **
1441966 TATATTAATGTACTATATAGTT
1 TATATTTATAAAC-A-ATAGTT
* * *
1441988 TATACTTTATAACCTATAGTA
1 TATA-TTTATAAACAATAGTT
*
1442009 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAAACAATAGTT
1442030 TATATT
1 TATATT
1442036 AATGTACTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
20 9 0.16
21 30 0.55
22 11 0.20
23 5 0.09
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (20 bp):
TATATTTATAAACAATAGTT
Found at i:1441985 original size:22 final size:21
Alignment explanation
Indices: 1441956--1442062 Score: 94
Period size: 22 Copynumber: 5.0 Consensus size: 21
1441946 ATAGTTTATA
1441956 AACA-ATAGTTTATATTAATG
1 AACATATAGTTTATATTAATG
* *
1441976 TACTATATAGTTTATACTTTAT-
1 AAC-ATATAGTTTATA-TTAATG
* * * *
1441998 AACCTATAGTATATAATTTATA
1 AACATATAGTTTAT-ATTAATG
1442020 AAC-TATAGTTTATATTAATG
1 AACATATAGTTTATATTAATG
*
1442040 TACTATATAGTTTATATTAATG
1 AAC-ATATAGTTTATATTAATG
1442062 A
1 A
1442063 TAATTATCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
20 9 0.13
21 24 0.34
22 33 0.47
23 4 0.06
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (21 bp):
AACATATAGTTTATATTAATG
Found at i:1442122 original size:21 final size:21
Alignment explanation
Indices: 1442078--1442181 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 21
1442068 ATCTTAACTG
*
1442078 TAATTTATATTAA-TATAGTATA
1 TAATTTATA--AACTATACTATA
*
1442100 TAGTTTATAAACTATA-TACTA
1 TAATTTATAAACTATACTA-TA
* *
1442121 T-ATTAATATAAATTATATTAATTA
1 TAATT--TATAAACTATACT-A-TA
1442145 TAATTTATAAACTATACTATA
1 TAATTTATAAACTATACTATA
*
1442166 TAATTTATAAAATATA
1 TAATTTATAAACTATA
1442182 GTTTATATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
20 6 0.09
21 24 0.35
22 19 0.28
23 12 0.18
24 4 0.06
25 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATTTATAAACTATACTATA
Found at i:1442123 original size:67 final size:66
Alignment explanation
Indices: 1442052--1442201 Score: 171
Period size: 66 Copynumber: 2.3 Consensus size: 66
1442042 CTATATAGTT
* * * * *
1442052 TATATTAATGAT-AATTATCTTAACTGTAATTTATATTAA-TATAGTATATAGTTTATAAACTAT
1 TATATTAAT-ATAAATTATATTAACTATAATTTATA--AACTATACTATATAATTTATAAAATAT
1442115 ATAC
63 ATAC
*
1442119 TATATTAATATAAATTATATTAATTATAATTTATAAACTATACTATATAATTTATAAAATATAGT
1 TATATTAATATAAATTATATTAACTATAATTTATAAACTATACTATATAATTTATAAAATATA-T
*
1442184 -T
65 AC
*
1442185 TATATTAATATTAATTA
1 TATATTAATATAAATTA
1442202 CAAATTATAA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
65 2 0.03
66 40 0.56
67 30 0.42
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (66 bp):
TATATTAATATAAATTATATTAACTATAATTTATAAACTATACTATATAATTTATAAAATATATA
C
Found at i:1442188 original size:21 final size:21
Alignment explanation
Indices: 1441980--1442188 Score: 70
Period size: 21 Copynumber: 9.6 Consensus size: 21
1441970 TTAATGTACT
* *
1441980 ATATAGTTTATACTTTATAAC
1 ATATAGTTTATAATTTATAAA
* *
1442001 CTATAGTATATAATTTATAAA
1 ATATAGTTTATAATTTATAAA
* * **
1442022 CTATAGTTTAT-ATTAATGTACT
1 ATATAGTTTATAATT--TATAAA
* *
1442044 ATATAGTTTAT-ATTAATGATA
1 ATATAGTTTATAATTTAT-AAA
*
1442065 AT-TA-TCTTAACTGTAATTTATATTA
1 ATATAGT-TT-A---TAATTTATA-AA
* *
1442090 ATATAGTATATAGTTTATAAA
1 ATATAGTTTATAATTTATAAA
* *
1442111 CTATA-TACTAT-ATTAATATAAA
1 ATATAGT-TTATAATT--TATAAA
* *
1442133 TTATATTAATTATAATTTATAAA
1 ATATAGT--TTATAATTTATAAA
* * *
1442156 CTATACTATATAATTTATAAA
1 ATATAGTTTATAATTTATAAA
1442177 ATATAGTTTATA
1 ATATAGTTTATA
1442189 TTAATATTAA
Statistics
Matches: 142, Mismatches: 28, Indels: 36
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.01
20 11 0.08
21 61 0.43
22 34 0.24
23 12 0.08
24 6 0.04
25 13 0.09
26 3 0.02
27 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATAGTTTATAATTTATAAA
Found at i:1442241 original size:16 final size:14
Alignment explanation
Indices: 1442217--1442283 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 14
1442207 TATAAACTAT
1442217 ATTATATTAATATA
1 ATTATATTAATATA
1442231 AGTTAATATTAATATTA
1 A-TT-ATATTAATA-TA
1442248 ATTATATTAATATTA
1 ATTATATTAATA-TA
*
1442263 ATTATAAT-ATATA
1 ATTATATTAATATA
1442276 ATTTATAT
1 A-TTATAT
1442284 ATATTTTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
13 3 0.06
14 9 0.19
15 21 0.45
16 11 0.23
17 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTATATTAATATA
Found at i:1442241 original size:21 final size:20
Alignment explanation
Indices: 1442215--1442297 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 20
1442205 ATTATAAACT
1442215 ATATTATATTAA-TATAAGTTA
1 ATATTATATTAATTAT-A-TTA
1442236 ATATTAATATTAATTATATTA
1 ATATT-ATATTAATTATATTA
*
1442257 ATATTA-ATT-ATAATATATA
1 ATATTATATTAATTATAT-TA
*
1442276 AT-TTATATATATTTTATATTA
1 ATATTATAT-TA-ATTATATTA
1442297 A
1 A
1442298 GGCGGGAACT
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
18 9 0.17
19 9 0.17
20 2 0.04
21 16 0.31
22 13 0.25
23 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (20 bp):
ATATTATATTAATTATATTA
Found at i:1442242 original size:6 final size:6
Alignment explanation
Indices: 1442215--1442277 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
1442205 ATTATAAACT
*
1442215 ATATT- ATATTA ATA-TA A-GTTA ATATTA ATATT- A-ATT- ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
1442257 ATATTA AT-TATA ATATATA AT
1 ATATTA ATAT-TA ATAT-TA AT
1442278 TTATATATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 16 0.33
6 23 0.47
7 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:1442277 original size:7 final size:7
Alignment explanation
Indices: 1442112--1442287 Score: 52
Period size: 7 Copynumber: 24.7 Consensus size: 7
1442102 GTTTATAAAC
*
1442112 TATATAC
1 TATATAA
1442119 TATATTAA
1 TATA-TAA
1442127 TATA-AA
1 TATATAA
1442133 TTATATTAA
1 -TATA-TAA
1442142 T-TATAA
1 TATATAA
*
1442148 TTTATAA
1 TATATAA
*
1442155 -ACTATAC
1 TA-TATAA
1442162 TATATAA
1 TATATAA
*
1442169 TTTATAA
1 TATATAA
* *
1442176 AATATAGTT
1 TATATA--A
1442185 TATATTAA
1 TATA-TAA
1442193 TAT-TAA
1 TATATAA
*
1442199 T-TACAA
1 TATATAA
1442205 -ATTATAA
1 TA-TATAA
*
1442212 -ACTATAT
1 TA-TATAA
1442219 TATATTAA
1 TATA-TAA
1442227 TATAAGTTAA
1 TAT-A--TAA
1442237 TAT-TAA
1 TATATAA
1442243 TAT-TAA
1 TATATAA
1442249 TTATATTAA
1 -TATA-TAA
1442258 TAT-TAA
1 TATATAA
1442264 T-TATAA
1 TATATAA
1442270 TATATAA
1 TATATAA
*
1442277 TTTAT-A
1 TATATAA
1442283 TATAT
1 TATAT
1442288 TTTATATTAA
Statistics
Matches: 130, Mismatches: 17, Indels: 45
0.68 0.09 0.23
Matches are distributed among these distances:
5 2 0.02
6 34 0.26
7 56 0.43
8 20 0.15
9 9 0.07
10 9 0.07
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (7 bp):
TATATAA
Found at i:1442537 original size:23 final size:24
Alignment explanation
Indices: 1442510--1442563 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
1442500 ATTATTTTTC
1442510 TTTACATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
1442533 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
1442557 TTTACAT
1 TTTACAT
1442564 TTAATCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:1442878 original size:16 final size:16
Alignment explanation
Indices: 1442857--1442913 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
1442847 GATCATTTAC
1442857 AGGTCAGGTTAAAAAT
1 AGGTCAGGTTAAAAAT
* ** *
1442873 AGGTCAGGTTCATCAC
1 AGGTCAGGTTAAAAAT
*
1442889 AGGTCAGGTTGAAAAT
1 AGGTCAGGTTAAAAAT
1442905 AGGTCAGGT
1 AGGTCAGGT
1442914 AATACTAGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (16 bp):
AGGTCAGGTTAAAAAT
Found at i:1455797 original size:27 final size:27
Alignment explanation
Indices: 1455758--1455814 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1455748 CATTAAAATA
**
1455758 TATTCAGTGATGATTCCGAAGATGATC
1 TATTCAGCAATGATTCCGAAGATGATC
1455785 TATTCAGCAATGATTCCGAAGATGATC
1 TATTCAGCAATGATTCCGAAGATGATC
1455812 TAT
1 TAT
1455815 GGATAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (27 bp):
TATTCAGCAATGATTCCGAAGATGATC
Found at i:1456186 original size:24 final size:24
Alignment explanation
Indices: 1456158--1456244 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
1456148 GAATATTTTA
* * *
1456158 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATATGATATGAATTCTGT
*
1456182 TCTGATATATGATATGGATTCTGT
1 TCTGATATATGATATGAATTCTGT
*
1456206 TATGATATATGATATGAATTCTGT
1 TCTGATATATGATATGAATTCTGT
* * *
1456230 TTTGATTTCTGATAT
1 TCTGATATATGATAT
1456245 ATCCATTTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.24, C:0.08, G:0.17, T:0.51
Consensus pattern (24 bp):
TCTGATATATGATATGAATTCTGT
Found at i:1457633 original size:226 final size:225
Alignment explanation
Indices: 1457225--1457924 Score: 983
Period size: 226 Copynumber: 3.1 Consensus size: 225
1457215 ATTTTGACTT
* * * ** * *
1457225 TAACATAATCGGTTAATTACTGGAAACATTATCAACCATAATAATATATTAGGTAGTGCTTATGT
1 TAACAAAATAGGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGTGCTTATTT
* * * *
1457290 AATGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCCTTAGAAATTCAACGATAACAAAATAGG
66 AACGTAATAGGTAGTGCCTGTTTAAAGCTGATGGGGCCTTAGAAATCCAACGATAACAAAATAGG
* * * * *
1457355 TTGATTACTTGATTTGTTATCAATATTATCAACATATTAGGTAACGCCTAAAATGTTAGCAAAGT
131 TTAATTACTTAATTTGTTATCAGTATTATCAACATATTA-GTAACACCTAAAATGTTACCAAAGT
*
1457420 TTAAGCTGATGGAGCCTTAGAAATCCGACGA
195 TTAAGCTGATGGAGCCTTAGAAATCTGACGA
* *
1457451 TAACAAAATAGGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTTTTT
1 TAACAAAATAGGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGTGCTTATTT
* * * * *
1457516 AACGCAATATGTAGTGCCTGTTTAAAGCTGGTGGGGCATTGGAAATCCAACGATAACAAAATAGG
66 AACGTAATAGGTAGTGCCTGTTTAAAGCTGATGGGGCCTTAGAAATCCAACGATAACAAAATAGG
* * * *
1457581 TTAATTCCTTAATTTTTTATCAGTATTATTAACATATTAGATAACACCTAAAATATTACCAAAGT
131 TTAATTACTTAATTTGTTATCAGTATTATCAACATATTAG-TAACACCTAAAATGTTACCAAAGT
1457646 TTAAGCTGATGGAGCCTTAGAAATCTGATC-A
195 TTAAGCTGATGGAGCCTTAGAAATCTGA-CGA
*
1457677 TAACAAAATAGGTTAATTACAGGAAACATTATCAACCATAATAACATAACAAGTAGTGCTTATTT
1 TAACAAAATAGGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGTGCTTATTT
* * *
1457742 -ACTGTAATAGGTA-TCGTCTGTTTAAAGCTGATGGGGCCTTAGAAATCCGATGATAACAAAATA
66 AAC-GTAATAGGTAGT-GCCTGTTTAAAGCTGATGGGGCCTTAGAAATCCAACGATAACAAAATA
* * *
1457805 GGTTAATTACTCAATTTGTTATCAGTATTATCAACGTATTATGTATCACCTAAAATGTTACCAAA
129 GGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTA-GTAACACCTAAAATGTTACCAAA
* *
1457870 GTTTAAAGATGATGGAGCCTTAGAAATCTGATGA
193 GTTT-AAGCTGATGGAGCCTTAGAAATCTGACGA
1457904 TAACAAAATAGGTTAATTACT
1 TAACAAAATAGGTTAATTACT
1457925 TGATTTGTTA
Statistics
Matches: 418, Mismatches: 49, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
225 4 0.01
226 366 0.88
227 48 0.11
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (225 bp):
TAACAAAATAGGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGTGCTTATTT
AACGTAATAGGTAGTGCCTGTTTAAAGCTGATGGGGCCTTAGAAATCCAACGATAACAAAATAGG
TTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGTAACACCTAAAATGTTACCAAAGTT
TAAGCTGATGGAGCCTTAGAAATCTGACGA
Found at i:1457954 original size:109 final size:110
Alignment explanation
Indices: 1457310--1457954 Score: 391
Period size: 118 Copynumber: 5.8 Consensus size: 110
1457300 GTAGCGCCTT
* * * * *
1457310 TTTAAAGCTGATGGGGCCTTAGAAAT-TCAACGATAACAAAATAGGTTGATTACTTGATTTGTTA
1 TTTAAAGCTGATGGAGCCTTAGAAATCT-GATGATAACAAAATAGGTTAATTACTTAATTTGTTA
* * * * *
1457374 TCAATATTATCAACATATTA-GGTAACGCCTAAAATGTTAGCAAAG
65 TCAGTATTATCAACATATTATGATATCACCTAAAATGTTACCAAAG
* * * ***
1457419 TTT-AAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTGGAA-ACATTA
1 TTTAAAGCTGATGGAGCCTTAGAAATCTGATGATAACAAAATAGGTTAATTACT-TAATTTGTTA
** * * ** * * * * *
1457482 TCAACCATAAT-AACATAACAAGTAGCGCTTTTTTAACGC-AATATGTAGTGCC--TG
65 TC-AGTATTATCAACAT----ATTA----TGATATCAC-CTAAAATGT--TACCAAAG
* * * * ** * * *
1457536 TTTAAAGCTGGTGGGGCATTGGAAATCCAACGATAACAAAATAGGTTAATTCCTTAATTTTTTAT
1 TTTAAAGCTGATGGAGCCTTAGAAATCTGATGATAACAAAATAGGTTAATTACTTAATTTGTTAT
* * *
1457601 CAGTATTATTAACATATTA-GATAACACCTAAAATATTACCAAAG
66 CAGTATTATCAACATATTATGATATCACCTAAAATGTTACCAAAG
* ** ***
1457645 TTT-AAGCTGATGGAGCCTTAGAAATCTGATCATAACAAAATAGGTTAATTACAGGAA-ACATTA
1 TTTAAAGCTGATGGAGCCTTAGAAATCTGATGATAACAAAATAGGTTAATTAC-TTAATTTGTTA
** * * * * ** * ****
1457708 TCAACCATAAT-AACATAACAAGTAGTGCTTATTTA-CTGTAATAGGTATCGTCTG
65 TC-AGTATTATCAACAT----ATTA-TG-ATA-TCACCTAAAAT-GTTA-CCAAAG
* * *
1457762 TTTAAAGCTGATGGGGCCTTAGAAATCCGATGATAACAAAATAGGTTAATTACTCAATTTGTTAT
1 TTTAAAGCTGATGGAGCCTTAGAAATCTGATGATAACAAAATAGGTTAATTACTTAATTTGTTAT
*
1457827 CAGTATTATCAACGTATTATG-TATCACCTAAAATGTTACCAAAG
66 CAGTATTATCAACATATTATGATATCACCTAAAATGTTACCAAAG
* *
1457871 TTTAAAGATGATGGAGCCTTAGAAATCTGATGATAACAAAATAGGTTAATTACTTGATTTGTTAT
1 TTTAAAGCTGATGGAGCCTTAGAAATCTGATGATAACAAAATAGGTTAATTACTTAATTTGTTAT
1457936 CAGTATTATCAACATATTA
66 CAGTATTATCAACATATTA
1457955 CCGTGTCCAT
Statistics
Matches: 397, Mismatches: 102, Indels: 74
0.69 0.18 0.13
Matches are distributed among these distances:
107 3 0.01
108 106 0.27
109 108 0.27
110 5 0.01
111 7 0.02
112 6 0.02
113 2 0.01
114 7 0.02
115 7 0.02
116 3 0.01
117 31 0.08
118 110 0.28
119 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (110 bp):
TTTAAAGCTGATGGAGCCTTAGAAATCTGATGATAACAAAATAGGTTAATTACTTAATTTGTTAT
CAGTATTATCAACATATTATGATATCACCTAAAATGTTACCAAAG
Found at i:1458464 original size:200 final size:199
Alignment explanation
Indices: 1458110--1459258 Score: 1588
Period size: 200 Copynumber: 5.8 Consensus size: 199
1458100 TTAGATCGAG
* * * *
1458110 AGTATCAATACCTATAAAAAATGTATCGAAACTTTATGTTTATGCCTATTATCATTAAACCAGTA
1 AGTATCGATACCTATACAAAA-GTATCGAAACTTTATGTTTACGCCTATTATCATTAAACCAATA
* * * *
1458175 TATTTTTACCATTTACATTGTAAATTTACTTATTACTTTAAAGTAATAGGTTTCGAAATTATAAA
65 GATTTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAG
* * *
1458240 TATCGATACTTGTGATACGTGTATTGATACTTTCTGCGTGCATGTTGTTTGAGAAGTATACTGGA
130 TATCGATACTTGTGATACGTGTATCGATACTTTCTGTGTGCATGTTGTTTGAGAAGCATACTGGA
1458305 CTAAA
195 CTAAA
* **
1458310 AGTATCGATACCTATACTAAAAGTATAGAAACTTTATGTTTACGCCTATTATCATTAAACCGGTA
1 AGTATCGATACCTATAC-AAAAGTATCGAAACTTTATGTTTACGCCTATTATCATTAAACCAATA
* * *
1458375 GATTTTTAGCGTTTACATTGTAAATTTACCTGTTACTTTAAAGTAATAGGTTTCAAAATTATAAG
65 GATTTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAG
* **
1458440 TATCGATACTTGTGATATGTGTATTAATACTTTCTGTGTGCATGTTGTTTGAGAAGCATACTGGA
130 TATCGATACTTGTGATACGTGTATCGATACTTTCTGTGTGCATGTTGTTTGAGAAGCATACTGGA
1458505 CTAAA
195 CTAAA
* *
1458510 AGTATCGATACCTATAC-AAAGTATCGAAACTTTATGTTTACGCCTATTATCATTAAATCGATAG
1 AGTATCGATACCTATACAAAAGTATCGAAACTTTATGTTTACGCCTATTATCATTAAACCAATAG
* * * *
1458574 ATTTTTACCATTTACATTGTATATTTACCTATTACTTTAATGTAATAGGTTTCAAAATTATTATT
66 ATTTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGT
* *
1458639 ATCGATACTTTTGATACGTGTATCGATACTTTCTGTGTGCATGTTGTTTTAGAAGCATACTGGAC
131 ATCGATACTTGTGATACGTGTATCGATACTTTCTGTGTGCATGTTGTTTGAGAAGCATACTGGAC
1458704 TAAA
196 TAAA
* *
1458708 AGTATCGATACCTATACAAAAAGTATC-AATAATTTATGTTTACGCCTATTATCATTAAACCGAT
1 AGTATCGATACCTATAC-AAAAGTATCGAA-ACTTTATGTTTACGCCTATTATCATTAAACCAAT
* * * *
1458772 AGATTTTTACCATTTACATTGTAAATTAACCTATAACTTTAAAGTAATCA-GTTTCGAAGTTATA
64 AGATTTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAAT-AGGTTTCAAAATTATA
* * * *
1458836 AGTATCGATACTTGTTATACATGTATCGATACTTTCTGTTTGCATGTTGTTTGAGAAGCATATTG
128 AGTATCGATACTTGTGATACGTGTATCGATACTTTCTGTGTGCATGTTGTTTGAGAAGCATACTG
1458901 GACTAAA
193 GACTAAA
* * * *
1458908 AGTATCG-----------AAAGTATCGATACTATATGTTTATGCCTATAATCATTAAACCAATAG
1 AGTATCGATACCTATACAAAAGTATCGAAACTTTATGTTTACGCCTATTATCATTAAACCAATAG
* * * *
1458962 ACTTTTACCGTTGACATTGTAAATTTACCTATTACTTTAAAGTAATCGGTTTCAAAATTATAAGT
66 ATTTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGT
* * * * * *
1459027 ATTGATACTTCTGATACGTCTATCAATACTTTCTGAGTGCATGTTGTTTGAGAAGCATACTAGAC
131 ATCGATACTTGTGATACGTGTATCGATACTTTCTGTGTGCATGTTGTTTGAGAAGCATACTGGAC
1459092 TAAA
196 TAAA
* * * * *
1459096 AGTATCGATACCTATACAAAGAGTATTGATACTTTATGTTTACGTCTATTATCATTAAATCAGTA
1 AGTATCGATACCTATACAAA-AGTATCGAAACTTTATGTTTACGCCTATTATCATTAAACCAATA
* * *
1459161 GATTTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATAGGTTTCGAAATTATAAG
65 GATTTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAG
* *
1459226 TATCGATACTTGTTATACATGTATCGATACTTT
130 TATCGATACTTGTGATACGTGTATCGATACTTT
1459259 TTTGCATGCA
Statistics
Matches: 841, Mismatches: 89, Indels: 38
0.87 0.09 0.04
Matches are distributed among these distances:
188 161 0.19
189 1 0.00
198 183 0.22
199 4 0.00
200 487 0.58
201 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (199 bp):
AGTATCGATACCTATACAAAAGTATCGAAACTTTATGTTTACGCCTATTATCATTAAACCAATAG
ATTTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGT
ATCGATACTTGTGATACGTGTATCGATACTTTCTGTGTGCATGTTGTTTGAGAAGCATACTGGAC
TAAA
Found at i:1458854 original size:19 final size:21
Alignment explanation
Indices: 1458830--1458869 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1458820 CAGTTTCGAA
1458830 GTTATA-A-GTATCGATACTT
1 GTTATACATGTATCGATACTT
1458849 GTTATACATGTATCGATACTT
1 GTTATACATGTATCGATACTT
1458870 TCTGTTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (21 bp):
GTTATACATGTATCGATACTT
Found at i:1458870 original size:398 final size:395
Alignment explanation
Indices: 1458110--1459258 Score: 1638
Period size: 398 Copynumber: 2.9 Consensus size: 395
1458100 TTAGATCGAG
* *
1458110 AGTATCAATACCTATAAAAAATGTATCGAAACTTTATGTTTATGCCTATTATCATTAAACCAGTA
1 AGTATCGATACCTAT--AAAA-GTATCGAAACTTTATGTTTATGCCTATTATCATTAAA-CAATA
* * *
1458175 TATTTTTACCATTTACATTGTAAATTTACTTATTACTTTAAAGTAATAGGTTTCGAAATTATAAA
62 GATTTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAA
* * * *
1458240 TATCGATACTTGTGATACGTGTATTGATACTTTCTGCGTGCATGTTGTTTGAGAAGTATACTGGA
127 TATCGATACTTCTGATACGTGTATCGATACTTTCTGAGTGCATGTTGTTTGAGAAGCATACTGGA
*
1458305 CTAAAAGTATCGATACCTATACTAAAAGTATAGA-AACTTTATGTTTACGCCTATTATCATTAAA
192 CTAAAAGTATCGATACCTATACAAAAAGTATA-ATAA-TTTATGTTTACGCCTATTATCATTAAA
* * * * *
1458369 CCGGTAGATTTTTAGCGTTTACATTGTAAATTTACCTGTTACTTTAAAGTAATAGGTTTCAAAAT
255 CCGATAGATTTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATAGGTTTCGAAAT
* ** **
1458434 TATAAGTATCGATACTTGTGATATGTGTATTAATACTTTCTGTGTGCATGTTGTTTGAGAAGCAT
320 TATAAGTATCGATACTTGTTATACATGTATCGATACTTTCTGTGTGCATGTTGTTTGAGAAGCAT
1458499 ACTGGACTAAA
385 ACTGGACTAAA
* *
1458510 AGTATCGATACCTATACAAAGTATCGAAACTTTATGTTTACGCCTATTATCATTAAATCGATAGA
1 AGTATCGATACCTATA-AAAGTATCGAAACTTTATGTTTATGCCTATTATCATTAAA-CAATAGA
* * * *
1458575 TTTTTACCATTTACATTGTATATTTACCTATTACTTTAATGTAATAGGTTTCAAAATTATTATTA
64 TTTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAATA
* * *
1458640 TCGATACTTTTGATACGTGTATCGATACTTTCTGTGTGCATGTTGTTTTAGAAGCATACTGGACT
129 TCGATACTTCTGATACGTGTATCGATACTTTCTGAGTGCATGTTGTTTGAGAAGCATACTGGACT
1458705 AAAAGTATCGATACCTATACAAAAAGTATCAATAATTTATGTTTACGCCTATTATCATTAAACCG
194 AAAAGTATCGATACCTATACAAAAAGTAT-AATAATTTATGTTTACGCCTATTATCATTAAACCG
* * *
1458770 ATAGATTTTTACCATTTACATTGTAAATTAACCTATAACTTTAAAGTAATCA-GTTTCGAAGTTA
258 ATAGATTTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAAT-AGGTTTCGAAATTA
* *
1458834 TAAGTATCGATACTTGTTATACATGTATCGATACTTTCTGTTTGCATGTTGTTTGAGAAGCATAT
322 TAAGTATCGATACTTGTTATACATGTATCGATACTTTCTGTGTGCATGTTGTTTGAGAAGCATAC
1458899 TGGACTAAA
387 TGGACTAAA
* * * *
1458908 AGTATCG---------AAAGTATCGATACTATATGTTTATGCCTATAATCATTAAACCAATAGAC
1 AGTATCGATACCTATAAAAGTATCGAAACTTTATGTTTATGCCTATTATCATTAAA-CAATAGAT
* * * *
1458964 TTTTACCGTTGACATTGTAAATTTACCTATTACTTTAAAGTAATCGGTTTCAAAATTATAAGTAT
65 TTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAATAT
* * * *
1459029 TGATACTTCTGATACGTCTATCAATACTTTCTGAGTGCATGTTGTTTGAGAAGCATACTAGACTA
130 CGATACTTCTGATACGTGTATCGATACTTTCTGAGTGCATGTTGTTTGAGAAGCATACTGGACTA
* * * * *
1459094 AAAGTATCGATACCTATACAAAGAGTATTGATACTTTATGTTTACGTCTATTATCATTAAATC-A
195 AAAGTATCGATACCTATACAAAAAGTA-TAATAATTTATGTTTACGCCTATTATCATTAAACCGA
1459158 GTAGATTTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATAGGTTTCGAAATTAT
259 -TAGATTTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATAGGTTTCGAAATTAT
1459223 AAGTATCGATACTTGTTATACATGTATCGATACTTT
323 AAGTATCGATACTTGTTATACATGTATCGATACTTT
1459259 TTTGCATGCA
Statistics
Matches: 680, Mismatches: 62, Indels: 26
0.89 0.08 0.03
Matches are distributed among these distances:
387 2 0.00
388 309 0.45
389 1 0.00
398 347 0.51
399 7 0.01
400 14 0.02
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (395 bp):
AGTATCGATACCTATAAAAGTATCGAAACTTTATGTTTATGCCTATTATCATTAAACAATAGATT
TTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAATATC
GATACTTCTGATACGTGTATCGATACTTTCTGAGTGCATGTTGTTTGAGAAGCATACTGGACTAA
AAGTATCGATACCTATACAAAAAGTATAATAATTTATGTTTACGCCTATTATCATTAAACCGATA
GATTTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATAGGTTTCGAAATTATAAG
TATCGATACTTGTTATACATGTATCGATACTTTCTGTGTGCATGTTGTTTGAGAAGCATACTGGA
CTAAA
Found at i:1462205 original size:18 final size:18
Alignment explanation
Indices: 1462149--1462196 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1462139 TTGTTCATCG
*
1462149 CATACATAATTTCATTCA
1 CATACAAAATTTCATTCA
1462167 CATACAAAATTTCATTCA
1 CATACAAAATTTCATTCA
1462185 CATACAAAATTT
1 CATACAAAATTT
1462197 GGATTACATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (18 bp):
CATACAAAATTTCATTCA
Done.