Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009396.1 Hibiscus syriacus cultivar Beakdansim tig00113301_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: 283260
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:213815 original size:12 final size:11
Alignment explanation
Indices: 213795--213830 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
213785 GAAATCAGCT
213795 GCATTATTGCA
1 GCATTATTGCA
*
213806 GCACTTATTGCT
1 GCA-TTATTGCA
213818 GCATTATTGCA
1 GCATTATTGCA
213829 GC
1 GC
213831 CCGTGAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:214053 original size:8 final size:9
Alignment explanation
Indices: 214023--214060 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
214013 GGTAAGTTTT
214023 TTTTAATTA
1 TTTTAATTA
214032 TTTTAATTA
1 TTTTAATTA
*
214041 GTTT-ATTA
1 TTTTAATTA
214049 TTTTAAATTA
1 TTTT-AATTA
214059 TT
1 TT
214061 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:214182 original size:28 final size:27
Alignment explanation
Indices: 214143--214195 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
214133 ATATTAAAAA
214143 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
214171 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
214196 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:214201 original size:27 final size:29
Alignment explanation
Indices: 214142--214206 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
214132 TATATTAAAA
214142 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
214171 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
214197 AAATAGTTAA
1 AAATAATTAA
214207 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:214345 original size:18 final size:18
Alignment explanation
Indices: 214322--214376 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
214312 AATAATTATT
214322 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
214340 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
214352 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
214369 TAAATTAG
1 TAAATTAG
214377 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:214429 original size:21 final size:21
Alignment explanation
Indices: 214404--214443 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
214394 GTTAATTAGT
214404 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
214425 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
214444 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:214689 original size:30 final size:30
Alignment explanation
Indices: 214639--214716 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
214629 TAATAGTAAA
*
214639 TTATAATTAAA-AATCA-TTTATTAGTTTAA-T
1 TTAT-ATTAAAGAAT-AGTTTATTAG-TTAACG
214669 TTATATTAAAGAATAGTTTATTAGTTAACG
1 TTATATTAAAGAATAGTTTATTAGTTAACG
214699 TTATATTAAAGAATAGTT
1 TTATATTAAAGAATAGTT
214717 AAAGTTATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (30 bp):
TTATATTAAAGAATAGTTTATTAGTTAACG
Found at i:214715 original size:22 final size:22
Alignment explanation
Indices: 214690--214735 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
214680 AATAGTTTAT
*
214690 TAGTTAACGTTATATTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
214712 TAGTTAAAGTTATATTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
214734 TA
1 TA
214736 ATTTATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (22 bp):
TAGTTAAAGTTATATTAAAGAA
Found at i:217086 original size:14 final size:14
Alignment explanation
Indices: 217053--217101 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
217043 TTCAAGTCGT
*
217053 AAATCATTACTATC
1 AAATCATTAATATC
* *
217067 AAATTATT-A-CT-
1 AAATCATTAATATC
217078 AAATCATTAATATC
1 AAATCATTAATATC
217092 AAATCATTAA
1 AAATCATTAA
217102 ATATTAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
11 7 0.26
12 2 0.07
13 1 0.04
14 17 0.63
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:217108 original size:21 final size:22
Alignment explanation
Indices: 217052--217158 Score: 74
Period size: 25 Copynumber: 4.6 Consensus size: 22
217042 GTTCAAGTCG
* *
217052 TAAATCATTACTATCAAATTATT
1 TAAATCATTAATATCAAATCA-T
217075 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATCAAATCAT
* *
217099 TAAAT-ATTAATAATAAATTATTAT
1 TAAATCATTAAT-ATCAA--ATCAT
*
217123 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTAATATCAAATCAT
*
217147 TAAA-AATTAATA
1 TAAATCATTAATA
217159 ATAATTTCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
21 12 0.18
22 11 0.16
24 13 0.19
25 19 0.28
26 7 0.10
27 5 0.07
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:217126 original size:49 final size:48
Alignment explanation
Indices: 217069--217355 Score: 295
Period size: 60 Copynumber: 5.4 Consensus size: 48
217059 TTACTATCAA
* *
217069 ATTATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT
1 ATTATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAAATT
217118 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATT
1 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT-A----A--ATT
*
217173 ACTAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTT
1 A-T--T-ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAAATT
217226 CATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTGTT
1 -ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAA----A---TT
*
217282 ACTAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTT
1 A-T--T-ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAAATT
217335 CATTATTACTAATCATTACTA
1 -ATTATTACTAATCATTACTA
217356 AATCATTAAT
Statistics
Matches: 207, Mismatches: 5, Indels: 52
0.78 0.02 0.20
Matches are distributed among these distances:
48 32 0.15
49 57 0.28
50 12 0.06
51 2 0.01
53 7 0.03
54 2 0.01
55 6 0.03
56 4 0.02
58 2 0.01
59 13 0.06
60 70 0.34
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (48 bp):
ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAATT
Found at i:217261 original size:109 final size:109
Alignment explanation
Indices: 217072--217823 Score: 908
Period size: 109 Copynumber: 6.6 Consensus size: 109
217062 CTATCAAATT
* * *
217072 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
217136 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
217180 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
217245 TATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATC
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
217289 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA-T--
* *
217354 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATT
63 T--A-C-----TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
217409 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAAGTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
* * * * * * *
217473 --T-AAATCATTATTATCAAATCATTAAAAATTAATAATGATT--TCATT
66 TATCAAATCATTA--A--AAATTAATAATAATT--TCATTATTACTAATC
*
217518 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
* *
217582 TAAATCATTACTATCAAATAATTAAAAATTAATAACAATTTCATTATTTCTAATC
66 T--ATCA--A--ATC-----ATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
217637 ATTACTAAATTATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
217702 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
217746 ATTACTAAATCATTACTATCAAATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTA
1 ATTACTAAATCATTACTATCAAA-T-C-AT----T-A--AAA-ATTAATAATAATTTCATTATTA
217811 CTAATCATTACTA
55 CTAATCATTACTA
217824 AATCTTATAA
Statistics
Matches: 564, Mismatches: 34, Indels: 80
0.83 0.05 0.12
Matches are distributed among these distances:
105 9 0.02
106 1 0.00
107 1 0.00
108 43 0.08
109 253 0.45
110 2 0.00
111 7 0.01
112 3 0.01
113 2 0.00
114 6 0.01
115 1 0.00
116 4 0.01
117 7 0.01
118 8 0.01
119 76 0.13
120 136 0.24
121 1 0.00
123 4 0.01
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (109 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:217300 original size:60 final size:60
Alignment explanation
Indices: 217230--217534 Score: 533
Period size: 60 Copynumber: 5.1 Consensus size: 60
217220 TAATTTCATT
*
217230 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
217289 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
217349 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATT
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
217409 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAAGTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
217468 ATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
217528 ATTACTA
1 ATTACTA
217535 TCAAATCATT
Statistics
Matches: 233, Mismatches: 11, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
59 61 0.26
60 172 0.74
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:217411 original size:10 final size:10
Alignment explanation
Indices: 217396--217425 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
217386 TAATAATTTC
217396 ATTATTACTA
1 ATTATTACTA
217406 ATTATTACTA
1 ATTATTACTA
*
217416 ATCATTACTA
1 ATTATTACTA
217426 TCAAATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTATTACTA
Found at i:217462 original size:49 final size:49
Alignment explanation
Indices: 217406--217752 Score: 309
Period size: 60 Copynumber: 6.4 Consensus size: 49
217396 ATTATTACTA
*
217406 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAGTTC
1 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC
*
217455 ATTATTACTAATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTC
1 ATTATTACTAATCA-T--T--A-C-----TATCAAATCATTAAAAATTAATAATAATTTC
*
217515 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTT
1 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC
*
217564 ATTATTACTAATCATTACTAAATCATTACTATCAAATAATTAAAAATTAATAACAATTTC
1 ATTATTACTAATCATTACT--ATCA--A--ATC-----ATTAAAAATTAATAATAATTTC
* * * *
217624 ATTATTTCTAATCATTACTAAATTATTAAT-ATCAAATCATTAAATATTAATAATAATTTC
1 ATTATTACTAATCATTACT--ATCA--AATCATTAAA-AATT--A-A-TAA---TAATTTC
217684 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC
1 ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC
217733 ATTATTACTAATCATTACTA
1 ATTATTACTAATCATTACTA
217753 AATCATTACT
Statistics
Matches: 252, Mismatches: 15, Indels: 62
0.77 0.05 0.19
Matches are distributed among these distances:
49 89 0.35
50 1 0.00
51 4 0.02
52 9 0.04
53 5 0.02
54 3 0.01
55 6 0.02
56 7 0.03
57 9 0.04
58 5 0.02
59 1 0.00
60 113 0.45
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (49 bp):
ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC
Found at i:217501 original size:24 final size:24
Alignment explanation
Indices: 217453--217501 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
217443 AATAATAAGT
* *
217453 TCATTATTACTAATCATTACTAAA
1 TCATTATTACAAATCATTACAAAA
217477 TCATTATTATCAAATCATTA-AAAA
1 TCATTATTA-CAAATCATTACAAAA
217501 T
1 T
217502 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
TCATTATTACAAATCATTACAAAA
Found at i:217588 original size:60 final size:60
Alignment explanation
Indices: 217518--217827 Score: 341
Period size: 60 Copynumber: 5.2 Consensus size: 60
217508 TGATTTCATT
*
217518 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
217577 ATTACTAAATCATTACTATCAAATAATTAAAAATTAATAACAATTTCATTATTTCTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
217637 ATTACTAAATTATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * * * * * *
217697 ATTACTATCAAATCATTA--A--AAATTAATAATAATT--TCATTATTACTAATCATTACTAAAT
1 ATTAC--T-AAATCATTACTATCAAATCATTAAAAATTAATAATAATT--TCATTATTACT-AAT
217756 C
60 C
* *
217757 ATTACT--ATCAAATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
217817 ATTACTAAATC
1 ATTACTAAATC
217828 TTATAAATAC
Statistics
Matches: 208, Mismatches: 26, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
55 3 0.01
57 10 0.05
58 1 0.00
59 27 0.13
60 127 0.61
61 22 0.11
62 4 0.02
63 14 0.07
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:217603 original size:46 final size:48
Alignment explanation
Indices: 217468--217591 Score: 162
Period size: 49 Copynumber: 2.6 Consensus size: 48
217458 ATTACTAATC
* * *
217468 ATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATT
1 ATTACT-AATCATTA-CATCAAATCATTAAAAATAAATAATAATTTCATT
* *
217518 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATT
1 ATTACTAATCATTAC-ATCAAATCATTAAAAATAAATAATAATTTCATT
217567 ATTACTAATCATTAC-T-AAATCATTA
1 ATTACTAATCATTACATCAAATCATTA
217592 CTATCAAATA
Statistics
Matches: 70, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
46 9 0.13
47 1 0.01
49 54 0.77
50 6 0.09
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (48 bp):
ATTACTAATCATTACATCAAATCATTAAAAATAAATAATAATTTCATT
Found at i:217753 original size:169 final size:169
Alignment explanation
Indices: 217121--217769 Score: 873
Period size: 169 Copynumber: 3.8 Consensus size: 169
217111 ATAAATTATT
*
217121 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
* * * * * * *
217185 --T-AAATCATTACTATCAAATCATTAAAAATTAATAATAATT--TCATTATTACT-AATCATTA
66 TATCAAATCATTA--A--AAATTAATAATAATT--TCATTATTACTAATCATTACTAAATCATTA
* * * *
217244 CTATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATC
125 CTATCAAATAATTAAAAATTAATAACAAGTTCATTATTACTAATC
*
217289 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA-T--
* *
217354 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATTATTACT-AAT
63 T--A-C-----TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAAT
* *
217418 CATTACTATCAAATCATTAAAAATTAATAATAAGTTCATTATTACTAATC
120 CATTACTATCAAATAATTAAAAATTAATAACAAGTTCATTATTACTAATC
* *
217468 ATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
217533 TATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATCATTACTAAATCATTACTATCA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
* *
217598 AATAATTAAAAATTAATAACAATTTCATTATTTCTAATC
131 AATAATTAAAAATTAATAACAAGTTCATTATTACTAATC
* *
217637 ATTACTAAATTATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
217702 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
217767 AAT
131 AAT
217770 TACTATCAAA
Statistics
Matches: 440, Mismatches: 23, Indels: 35
0.88 0.05 0.07
Matches are distributed among these distances:
168 53 0.12
169 231 0.52
170 1 0.00
172 1 0.00
173 1 0.00
174 2 0.00
175 1 0.00
176 1 0.00
177 6 0.01
178 1 0.00
179 131 0.30
181 1 0.00
182 1 0.00
183 9 0.02
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (169 bp):
ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
AATAATTAAAAATTAATAACAAGTTCATTATTACTAATC
Found at i:217785 original size:49 final size:48
Alignment explanation
Indices: 217654--217760 Score: 164
Period size: 49 Copynumber: 2.2 Consensus size: 48
217644 AATTATTAAT
* *
217654 ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATCAAATCATTAAAAATTAATAATAATATCATTATTACTAATCATTAC
*
217702 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 -ATCAAATCATTAAAAATTAATAATAATATCATTATTACTAATCATTAC
217751 -T-AAATCATTA
1 ATCAAATCATTA
217761 CTATCAAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
46 9 0.16
47 1 0.02
49 47 0.82
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (48 bp):
ATCAAATCATTAAAAATTAATAATAATATCATTATTACTAATCATTAC
Found at i:217868 original size:288 final size:285
Alignment explanation
Indices: 217072--217872 Score: 1110
Period size: 288 Copynumber: 2.8 Consensus size: 285
217062 CTATCAAATT
*
217072 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
217136 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
217201 AATC-AT----T-A--AAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTA
131 AATCTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATTAC-ATCAAATCATTA
* *
217258 AAAATTAATAATAATTTCATTG-TTACTAATCATTACTAAATCATTACTATCAAATCATTAAAAA
195 AAAATTAATAATAA-TTCATAGATTACTAATCATTACTAAATCATTACTATCAAATAATTAAAAA
*
217322 TTAATAATAATTTCATTATTACTAATC
259 TTAATAACAATTTCATTATTACTAATC
217349 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATTATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAAT-A----A-T-TT-C--ATTATTAC
*
217414 TAATCATTACTATCAAATCATTAAAAATTAATAATAAGTTCATTATTACTAATCATTACTAAATC
56 TAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
* *
217479 ATTATTATCAAATC-AT----T-A--AAAATTAATAATGATTTCATTATTACTAATCATTACTAT
121 ATTACTATCAAATCTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATTAC-AT
* *
217536 CAAATCATTAAAAATTAATAATAATT-TTATTATTACTAATCATTACTAAATCATTACTATCAAA
185 CAAATCATTAAAAATTAATAATAATTCATA-GATTACTAATCATTACTAAATCATTACTATCAAA
*
217600 TAATTAAAAATTAATAACAATTTCATTATTTCTAATC
249 TAATTAAAAATTAATAACAATTTCATTATTACTAATC
*
217637 ATTACTAAATTATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
217702 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
*
217767 AATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTAC-T-AAATC-T
131 AA-T-CTATCAAATCATTAAA-ATTAATAATAATTTCATTATTACTAATCATTACATCAAATCAT
* *
217829 TATAAA-TACATAGA-AATTCATAGAAATACATATATCATTACTAA
193 TAAAAATTA-ATA-ATAATTCATAG-ATTAC-TA-ATCATTACTAA
217873 TGATGAGGCT
Statistics
Matches: 475, Mismatches: 19, Indels: 49
0.87 0.03 0.09
Matches are distributed among these distances:
277 41 0.09
278 84 0.18
279 1 0.00
280 2 0.00
281 4 0.01
282 2 0.00
283 1 0.00
284 4 0.01
285 14 0.03
286 14 0.03
287 6 0.01
288 271 0.57
289 31 0.07
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (285 bp):
ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
AATCTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATTACATCAAATCATTAA
AAATTAATAATAATTCATAGATTACTAATCATTACTAAATCATTACTATCAAATAATTAAAAATT
AATAACAATTTCATTATTACTAATC
Found at i:220917 original size:28 final size:28
Alignment explanation
Indices: 220886--220939 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
220876 ATAATCTAAT
*
220886 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
220914 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
220940 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:220946 original size:28 final size:28
Alignment explanation
Indices: 220882--220946 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
220872 TTATATAATC
*
220882 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
220910 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
220938 TAATTTATA
1 TAATATATA
220947 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:220949 original size:21 final size:21
Alignment explanation
Indices: 220916--220964 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
220906 TTAATATAAT
220916 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
220937 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
220958 ATTAACT
1 A-TAACT
220965 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:221696 original size:33 final size:33
Alignment explanation
Indices: 221655--221760 Score: 148
Period size: 33 Copynumber: 3.3 Consensus size: 33
221645 TGGGCGTACA
221655 TGGCGACCTACCATCTTGGTCGCCGGGATTGCT
1 TGGCGACCTACCATCTTGGTCGCCGGGATTGCT
* *
221688 TGGAGACCTACCATCTTGGTCGTCGGGATTGCT
1 TGGCGACCTACCATCTTGGTCGCCGGGATTGCT
* *
221721 TGGCGACCTA-CA---AGGTCGCTGGGATTGCT
1 TGGCGACCTACCATCTTGGTCGCCGGGATTGCT
221750 TGGCGACCTAC
1 TGGCGACCTAC
221761 AAGGTCGCTG
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
29 24 0.36
32 2 0.03
33 40 0.61
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.26
Consensus pattern (33 bp):
TGGCGACCTACCATCTTGGTCGCCGGGATTGCT
Found at i:221747 original size:29 final size:29
Alignment explanation
Indices: 221621--221817 Score: 144
Period size: 29 Copynumber: 6.5 Consensus size: 29
221611 GACATCGAGC
* * *
221621 GTGCATGGCGACCTATAAGGTCGCTGGGC
1 GTGCTTGGCGACCTACAAGGTCGCTGGGA
* * * *
221650 GTACATGGCGACCTACCATCTTGGTCGCCGGGA
1 GTGCTTGGCGACCTA-CA---AGGTCGCTGGGA
* * *
221683 TTGCTTGGAGACCTACCATCTTGGTCG-TCGGGA
1 GTGCTTGGCGACCTA-CA---AGGTCGCT-GGGA
*
221716 TTGCTTGGCGACCTACAAGGTCGCTGGGA
1 GTGCTTGGCGACCTACAAGGTCGCTGGGA
*
221745 TTGCTTGGCGACCTACAAGGTCGCTGGGA
1 GTGCTTGGCGACCTACAAGGTCGCTGGGA
* *** * *
221774 GTGCATGGCGACCTTGTAGGTCGCTTGAA
1 GTGCTTGGCGACCTACAAGGTCGCTGGGA
221803 GTGCTTGGCGACCTA
1 GTGCTTGGCGACCTA
221818 TGGTTGGGTT
Statistics
Matches: 141, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
29 87 0.62
30 2 0.01
32 2 0.01
33 50 0.35
ACGTcount: A:0.17, C:0.25, G:0.34, T:0.25
Consensus pattern (29 bp):
GTGCTTGGCGACCTACAAGGTCGCTGGGA
Found at i:221795 original size:58 final size:58
Alignment explanation
Indices: 221626--221817 Score: 161
Period size: 58 Copynumber: 3.2 Consensus size: 58
221616 CGAGCGTGCA
* * * * *
221626 TGGCGACCTATAAGGTCGCTGGGCGTACATGGCGACCTACCATCTTGGTCGCCGGGATTGCT
1 TGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCT----TCTAGGTCGCTGGGATTGCT
* * * * * *
221688 TGGAGACCTACCATCTTGGTCG-TCGGGATTGCTTGGCGACCTACAAGGTCGCTGGGATTGCT
1 TGGCGACCTA-CA---AGGTCGCT-GGGAGTGCATGGCGACCTTCTAGGTCGCTGGGATTGCT
* * * *
221750 TGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCTTGTAGGTCGCTTGAAGTGCT
1 TGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCTTCTAGGTCGCTGGGATTGCT
221808 TGGCGACCTA
1 TGGCGACCTA
221818 TGGTTGGGTT
Statistics
Matches: 103, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
58 45 0.44
59 1 0.01
61 2 0.02
62 34 0.33
63 1 0.01
65 1 0.01
66 19 0.18
ACGTcount: A:0.17, C:0.25, G:0.33, T:0.25
Consensus pattern (58 bp):
TGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCTTCTAGGTCGCTGGGATTGCT
Found at i:222403 original size:29 final size:29
Alignment explanation
Indices: 222363--222418 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
222353 GTGACCTACC
222363 TAGGTCGCTGGGCGTGCATGGCGACCTGG
1 TAGGTCGCTGGGCGTGCATGGCGACCTGG
222392 TAGGTCGCTGGGCGTGCATGGCGACCT
1 TAGGTCGCTGGGCGTGCATGGCGACCT
222419 ACCCCCGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.11, C:0.25, G:0.43, T:0.21
Consensus pattern (29 bp):
TAGGTCGCTGGGCGTGCATGGCGACCTGG
Found at i:226706 original size:18 final size:17
Alignment explanation
Indices: 226679--226737 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 17
226669 TATTAAGGAG
226679 TGGTCCTTCGGGACATAA
1 TGGT-CTTCGGGACATAA
*
226697 TGGTCATTCGGGACACAA
1 TGGTC-TTCGGGACATAA
*
226715 TGGTTCTTCGGGACATAG
1 TGG-TCTTCGGGACATAA
226733 TGGTC
1 TGGTC
226738 CTACGAGACA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.08
18 31 0.86
19 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (17 bp):
TGGTCTTCGGGACATAA
Found at i:229338 original size:11 final size:11
Alignment explanation
Indices: 229277--229339 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
229267 AAGATGAGAT
229277 TTAGTTAGTAA
1 TTAGTTAGTAA
*
229288 GTTTGTTAG---
1 -TTAGTTAGTAA
* *
229297 TTAGTTAGCAG
1 TTAGTTAGTAA
* *
229308 TTGGTTAGAAA
1 TTAGTTAGTAA
229319 TTAGTTAGTAA
1 TTAGTTAGTAA
229330 TTAGTTAGTA
1 TTAGTTAGTA
229340 TGTTAGCTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
8 7 0.17
11 27 0.66
12 7 0.17
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (11 bp):
TTAGTTAGTAA
Found at i:233898 original size:3 final size:3
Alignment explanation
Indices: 233890--234041 Score: 223
Period size: 3 Copynumber: 50.7 Consensus size: 3
233880 TTTTTATCCA
* * *
233890 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
233938 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
233986 TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
234034 TAT TAT TA
1 TAT TAT TA
234042 AATATATTAA
Statistics
Matches: 131, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 131 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:235386 original size:30 final size:29
Alignment explanation
Indices: 235351--235408 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
235341 ATAATTTAGA
235351 TTAATTATGAA-TTAGATT-TTTAATTTTATT
1 TTAATTAT-AATTTAG-TTATTT-ATTTTATT
235381 TTAATTATAATTTAGTTATTTATTTTAT
1 TTAATTATAATTTAGTTATTTATTTTAT
235409 ATGTCTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (29 bp):
TTAATTATAATTTAGTTATTTATTTTATT
Found at i:236232 original size:19 final size:18
Alignment explanation
Indices: 236190--236233 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
236180 TTTCAAATTA
236190 TTTATTTATTATTTTTAT
1 TTTATTTATTATTTTTAT
** *
236208 AATATTTATATGTTTTTAT
1 TTTATTTAT-TATTTTTAT
236227 TTTATTT
1 TTTATTT
236234 GCAAGCATTT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTATTTATTATTTTTAT
Found at i:246861 original size:5 final size:5
Alignment explanation
Indices: 246845--246929 Score: 72
Period size: 5 Copynumber: 17.2 Consensus size: 5
246835 ATTATGCTTG
* *
246845 AAGAA AAAAA AAGAA AAAAA AAGAA AAG-A AAGAA AAGAAAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAG--AA AAGAA AAGAA
*
246896 AA-AA TAGAA AATG-A AA-AA AA-AA AAGAAA AAGAA A
1 AAGAA AAGAA AA-GAA AAGAA AAGAA AAG-AA AAGAA A
246930 GGGGGTCAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
4 14 0.21
5 41 0.62
6 6 0.09
7 5 0.08
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:246863 original size:9 final size:9
Alignment explanation
Indices: 246849--246930 Score: 78
Period size: 9 Copynumber: 9.0 Consensus size: 9
246839 TGCTTGAAGA
246849 AAAAAAAAG
1 AAAAAAAAG
246858 AAAAAAAAAG
1 -AAAAAAAAG
*
246868 AAAAGAAAG
1 AAAAAAAAG
*
246877 AAAAGAAA-
1 AAAAAAAAG
*
246885 AAAGAAAAG
1 AAAAAAAAG
*
246894 AAAAAATAG
1 AAAAAAAAG
*
246903 AAAATGAAA-
1 AAAA-AAAAG
246912 AAAAAAAAG
1 AAAAAAAAG
246921 AAAAAGAAAG
1 AAAAA-AAAG
246931 GGGGTCAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
8 9 0.15
9 36 0.60
10 15 0.25
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:247951 original size:52 final size:53
Alignment explanation
Indices: 247873--247983 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
247863 TATGTGCTCA
*
247873 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
247925 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
247978 A-AGCAT
1 ATAGCAT
247984 TGAATTTGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 55 0.96
53 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (53 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
Found at i:248064 original size:83 final size:83
Alignment explanation
Indices: 247925--248149 Score: 416
Period size: 83 Copynumber: 2.7 Consensus size: 83
247915 TGGACAGAAC
247925 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
247990 TGGAAGATGAATTTGCCA
66 TGGAAGATGAATTTGCCA
*
248008 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
248073 TGGAAGATGAATTTGCCA
66 TGGAAGATGAATTTGCCA
*
248091 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CATAGCAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA-AGCAT
248150 CTTCTGGAAG
Statistics
Matches: 138, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
82 2 0.01
83 136 0.99
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
TGGAAGATGAATTTGCCA
Found at i:248147 original size:135 final size:135
Alignment explanation
Indices: 248008--249073 Score: 2105
Period size: 135 Copynumber: 7.9 Consensus size: 135
247998 GAATTTGCCA
*
248008 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
248073 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
66 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
248138 AGAAC
131 AGAAC
*
248143 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
248208 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
66 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
248273 AGAAC
131 AGAAC
248278 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
248343 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
66 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
248408 AGAAC
131 AGAAC
248413 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
248478 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
66 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
248543 AGAAC
131 AGAAC
248548 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
248613 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
66 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
248678 AGAAC
131 AGAAC
248683 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
248748 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
66 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
248813 AGAAC
131 AGAAC
248818 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
248883 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
66 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
248948 AGAAC
131 AGAAC
248953 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
*
249018 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
66 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
249074 CGAAGAAGTG
Statistics
Matches: 927, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 927 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (135 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
AGAAC
Found at i:248169 original size:52 final size:53
Alignment explanation
Indices: 248091--248201 Score: 190
Period size: 52 Copynumber: 2.1 Consensus size: 53
248081 GAATTTGCCA
*
248091 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
*
248143 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248196 A-AGCAT
1 ATAGCAT
248202 TGAATTTGGA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
52 54 0.96
53 2 0.04
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (53 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
Found at i:248249 original size:218 final size:218
Alignment explanation
Indices: 247871--248284 Score: 785
Period size: 218 Copynumber: 1.9 Consensus size: 218
247861 TATATGTGCT
247871 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
247936 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGAA
66 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGAA
248001 TTTGCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA-AGC
131 TTTGCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA-CATAGC
248065 ATTGAATTTGGAAGATGAATTTGC
195 ATTGAATTTGGAAGATGAATTTGC
248089 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
*
248154 TGGAAGTGTTCTTTGAGTTATTTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGAA
66 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGAA
* *
248219 TTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCA
131 TTTGCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCA
248284 T
196 T
248285 CTTCTGGAAG
Statistics
Matches: 192, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
217 2 0.01
218 190 0.99
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (218 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
TGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGAA
TTTGCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCA
TTGAATTTGGAAGATGAATTTGC
Found at i:248304 original size:52 final size:53
Alignment explanation
Indices: 248226--248336 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
248216 GAATTTGCCA
*
248226 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248278 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248331 A-AGCAT
1 ATAGCAT
248337 TGAATTTGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 55 0.96
53 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (53 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
Found at i:248367 original size:218 final size:214
Alignment explanation
Indices: 247871--248419 Score: 580
Period size: 218 Copynumber: 2.5 Consensus size: 214
247861 TATATGTGCT
*** * * * ** *
247871 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
1 CAATAGCATCTTCTGGAAGTAAGCATTGAATTATCGGAGATGATTGGACA-AACATAGCATCTTC
247936 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGAA
65 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGAA
248001 TTTGCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCA
130 TTTGCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCA
*
248066 TTGAATTTGGAAGATGAATTTG
195 TT--ATCTGGAAGATGAATTTG
*** * * * ** *
248088 CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTT
1 -CAATAGCATCTTCTGGAAGTAAGCATTGAATTATCGGAGATGATTGGACA-AACATAGCATCTT
*
248153 CTGGAAGTGTTCTTTGAGTTATTTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGA
64 CTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGA
* *
248218 ATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CATAG
129 ATTTGCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA-AG
**
248282 CATCT-TCTGGAAG-TGTTCTTTG
193 CAT-TATCTGGAAGATG-AATTTG
* * * *
248304 -AGTTATCTGATCTGAT-TGGACAGAATCAAGCATTGAATT-T-GGAAGATGAATTTG-C-CA-A
1 CA-ATAGC--ATCT--TCTGGA-AG--T-AAGCATTGAATTATCGG-AGATG-ATTGGACAAACA
*
248362 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CATAGCAT
55 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA-AGCAT
248420 CTTCTGGAAG
Statistics
Matches: 295, Mismatches: 21, Indels: 30
0.85 0.06 0.09
Matches are distributed among these distances:
214 1 0.00
215 5 0.02
216 11 0.04
217 8 0.03
218 248 0.84
219 5 0.02
220 1 0.00
221 6 0.02
222 10 0.03
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (214 bp):
CAATAGCATCTTCTGGAAGTAAGCATTGAATTATCGGAGATGATTGGACAAACATAGCATCTTCT
GGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGAAT
TTGCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCAT
TATCTGGAAGATGAATTTG
Found at i:248439 original size:52 final size:53
Alignment explanation
Indices: 248361--248471 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
248351 GAATTTGCCA
*
248361 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248413 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248466 A-AGCAT
1 ATAGCAT
248472 TGAATTTGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 55 0.96
53 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (53 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
Found at i:248574 original size:52 final size:53
Alignment explanation
Indices: 248496--248606 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
248486 GAATTTGCCA
*
248496 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248548 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248601 A-AGCAT
1 ATAGCAT
248607 TGAATTTGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 55 0.96
53 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (53 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
Found at i:248709 original size:52 final size:53
Alignment explanation
Indices: 248631--248741 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
248621 GAATTTGCCA
*
248631 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248683 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248736 A-AGCAT
1 ATAGCAT
248742 TGAATTTGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 55 0.96
53 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (53 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
Found at i:248844 original size:52 final size:53
Alignment explanation
Indices: 248766--248876 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
248756 GAATTTGCCA
*
248766 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248818 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248871 A-AGCAT
1 ATAGCAT
248877 TGAATTTGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 55 0.96
53 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (53 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
Found at i:248979 original size:52 final size:53
Alignment explanation
Indices: 248901--249011 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
248891 GAATTTGCCA
*
248901 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
248953 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
249006 A-AGCAT
1 ATAGCAT
249012 TGAATTTGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 55 0.96
53 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (53 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
Found at i:249836 original size:113 final size:111
Alignment explanation
Indices: 249667--250516 Score: 1207
Period size: 113 Copynumber: 7.5 Consensus size: 111
249657 TTGCAAGTTC
*
249667 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*** * * * *
249732 CAACCTTTTACCTGAATCCATCATTTAATGGATCAGCTTTTCCAGTTC
66 CAACCTTTTGTTTGAATTCATCATTTGATGGATCAACTTTTCCAG--A
*
249780 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*** * * * *
249845 CAACCTTTTACCTGAATCCATCATTTAATGGATCAGCTTTTCCAGTTC
66 CAACCTTTTGTTTGAATTCATCATTTGATGGATCAACTTTTCCAG--A
*
249893 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*** * * *
249958 CAACCTTTTACCTGAATCCATCATTTAATGGATCAGCTTTTCCAGA
66 CAACCTTTTGTTTGAATTCATCATTTGATGGATCAACTTTTCCAGA
*
250004 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
250069 CAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGA
66 CAACCTTTTGTTTGAATTCATCATTTGATGGATCAACTTTTCCAGA
250115 GAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 G-A-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
250180 TTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGA
64 TTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACTTTTCCAGA
250228 GAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 G-A-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * ** *
250293 TTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACAGTGCCAGA
64 TTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACTTTTCCAGA
250341 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 G--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* *
250406 TTCAACCTTTTGTTTGAATTCATCACTTGATGGATTAA-TTTTGCCAGA
64 TTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACTTTT-CCAGA
* *
250454 GAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGGAAAAAGTTCATAATGAGAAGAACT
1 G-A-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
250517 CATCAAGAGC
Statistics
Matches: 708, Mismatches: 24, Indels: 10
0.95 0.03 0.01
Matches are distributed among these distances:
111 99 0.14
112 4 0.01
113 603 0.85
114 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (111 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGTTTGAATTCATCATTTGATGGATCAACTTTTCCAGA
Found at i:250771 original size:3 final size:3
Alignment explanation
Indices: 250763--250898 Score: 202
Period size: 3 Copynumber: 45.7 Consensus size: 3
250753 TTTTTATCCA
* * *
250763 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
250811 TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
250859 TAT TAT T-T TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
250899 AATATTAAAT
Statistics
Matches: 118, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
2 2 0.02
3 116 0.98
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:252230 original size:30 final size:29
Alignment explanation
Indices: 252195--252252 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
252185 ATAATTTAGA
252195 TTAATTATGAA-TTAGATT-TTTAATTTTATT
1 TTAATTAT-AATTTAG-TTATTT-ATTTTATT
252225 TTAATTATAATTTAGTTATTTATTTTAT
1 TTAATTATAATTTAGTTATTTATTTTAT
252253 ATGTCTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (29 bp):
TTAATTATAATTTAGTTATTTATTTTATT
Found at i:253204 original size:24 final size:24
Alignment explanation
Indices: 253176--253230 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
253166 ATTTGATTGA
*
253176 TGGTGAGCAACGAGCCAATGATGT
1 TGGTGAGCAACGAGCCAACGATGT
253200 TGGTGAGCAACGAGCCAACGATGT
1 TGGTGAGCAACGAGCCAACGATGT
*
253224 TGATGAG
1 TGGTGAG
253231 GGAAGTCGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.20
Consensus pattern (24 bp):
TGGTGAGCAACGAGCCAACGATGT
Found at i:257651 original size:17 final size:17
Alignment explanation
Indices: 257629--257663 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
257619 CAAATGTCCC
257629 ATTTATTCAACATACAA
1 ATTTATTCAACATACAA
257646 ATTTATTCAACATACAA
1 ATTTATTCAACATACAA
257663 A
1 A
257664 CATTCACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTATTCAACATACAA
Found at i:261431 original size:12 final size:12
Alignment explanation
Indices: 261382--261433 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
261372 AAGAAAGAAA
*
261382 AAAAT-AAAGGT
1 AAAATAAAAGAT
*
261393 AAAATAAAAGGT
1 AAAATAAAAGAT
*
261405 ATAAT-AAA-AT
1 AAAATAAAAGAT
261415 AAAATAAAAGAT
1 AAAATAAAAGAT
261427 AAAATAA
1 AAAATAA
261434 TAAATAATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 5 0.14
11 11 0.31
12 19 0.54
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (12 bp):
AAAATAAAAGAT
Found at i:261442 original size:22 final size:22
Alignment explanation
Indices: 261382--261433 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
261372 AAGAAAGAAA
* *
261382 AAAATAAAGGTAAAATAAAAGGT
1 AAAATAAA-ATAAAATAAAAGAT
*
261405 ATAATAAAATAAAATAAAAGAT
1 AAAATAAAATAAAATAAAAGAT
261427 AAAATAA
1 AAAATAA
261434 TAAATAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (22 bp):
AAAATAAAATAAAATAAAAGAT
Found at i:261498 original size:18 final size:18
Alignment explanation
Indices: 261475--261517 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
261465 GTTGTTTTTA
*
261475 AAATAAAATATAAA-AATT
1 AAATAAAAGA-AAATAATT
261493 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
261511 AAATAAA
1 AAATAAA
261518 TAATCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:263160 original size:21 final size:21
Alignment explanation
Indices: 263136--263187 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
263126 AGTTGAGCTT
*
263136 TGAATTGAATATCC-TTCATTG
1 TGAATTGAATATCCAGTC-TTG
263157 TGAAGTTGAA-ATCCAGTCTTG
1 TGAA-TTGAATATCCAGTCTTG
*
263178 TAAATTGAAT
1 TGAATTGAAT
263188 TGCTTTGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 5 0.19
21 14 0.54
22 7 0.27
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (21 bp):
TGAATTGAATATCCAGTCTTG
Found at i:263160 original size:226 final size:224
Alignment explanation
Indices: 262611--263171 Score: 791
Period size: 224 Copynumber: 2.5 Consensus size: 224
262601 TGAAACTAAG
* * * *
262611 TCAATTTTTTGGGTATGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGATCCTTCGCTGTGA
1 TCAATCTTTTGGGTACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGCTGTGA
* * * * * *
262676 AGTTAAACTTCGAATTGGATGTCATTCGTTGTGAAATTGAATTCCAAAATTGCATTGCTTTCGAG
66 AGTTAAGCTTTGAATTGGATGTCCTTCGTTGTGAAGTTGAAATCCAAAATTGCATTGCTTCCGAG
* * *
262741 TTCAATATCTTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGTTTTTCATTGTTATGTC
131 TTCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAACGAAACTGGTTTTTCATTGTTATGTC
* * *
262806 TCAGATGACTCATTCGTCGTGAAGTTGGG
196 ACAAATGACTCATTCGTCGTGAAGTTGGA
*
262835 TCAATCTTTTGGGTACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCCCTGTGA
1 TCAATCTTTTGGGTACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGCTGTGA
* * *
262900 AGTTAAGTTTTGAATTGGATGTTCTTCGTTGTGAAGTTAAAATCCAAAATTGCATTGCTTCCGAG
66 AGTTAAGCTTTGAATTGGATGTCCTTCGTTGTGAAGTTGAAATCCAAAATTGCATTGCTTCCGAG
* *
262965 TTCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAACGAAACTGGTTTTTCATTTTTGTGTG
131 TTCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAACGAAACTGGTTTTTCA-TTGT-TATG
263030 TCACAAATGACTCATTCGTCGTGAAGTTGGA
194 TCACAAATGACTCATTCGTCGTGAAGTTGGA
* * * * ** *
263061 TCAATCTTTTGGGTACAATATCATTTGTTGTGAAGTCAAAATCGTAGG-TGGCTCATTCGTTGTG
1 TCAATCTTTTGGGTACGATATCCTTCGTCGTGAAGTTGAAATCGT-GGATGGCTCATTCGCTGTG
* * * *
263125 AAGTTGAGCTTTGAATTGAATATCCTTCATTGTGAAGTTGAAATCCA
65 AAGTTAAGCTTTGAATTGGATGTCCTTCGTTGTGAAGTTGAAATCCA
263172 GTCTTGTAAA
Statistics
Matches: 297, Mismatches: 37, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
224 168 0.57
225 3 0.01
226 124 0.42
227 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (224 bp):
TCAATCTTTTGGGTACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGCTGTGA
AGTTAAGCTTTGAATTGGATGTCCTTCGTTGTGAAGTTGAAATCCAAAATTGCATTGCTTCCGAG
TTCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAACGAAACTGGTTTTTCATTGTTATGTC
ACAAATGACTCATTCGTCGTGAAGTTGGA
Found at i:263300 original size:123 final size:123
Alignment explanation
Indices: 263077--263342 Score: 351
Period size: 123 Copynumber: 2.2 Consensus size: 123
263067 TTTTGGGTAC
*
263077 AATATCATTT-GTTGTGAAGTCAAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAAT
1 AATAT-ATTTCGTTGTGAAGTCAAAATCGTAGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAAT
* * *
263141 TGAATATCCTTCATTGTGAAGTTGAAATCCAGTCTTGTAAATTGA-ATT-GCTTTGAGATT
65 TGAATATCCTTCATTGTGAAGTTGAAATCCAATCTTGAAAATT-ACATTAGC-TCGAGATT
** *
263200 AATATATTTCGTTGTGAAGTTGAAATTGTAGATGGCTCATTCGCTT-TGAAGTTGAGCTTTGAAT
1 AATATATTTCGTTGTGAAGTCAAAATCGTAGATGGCTCATTCG-TTGTGAAGTTGAGCTTTGAAT
* * * *
263264 TGGATGTCCTTCGTTGTGAAGTTGAAATCCAATCTTGAAAATTACATTAGCTCGAGTTT
65 TGAATATCCTTCATTGTGAAGTTGAAATCCAATCTTGAAAATTACATTAGCTCGAGATT
**
263323 AATATCCTTCGTTGTGAAGT
1 AATATATTTCGTTGTGAAGT
263343 GGACATTGAC
Statistics
Matches: 126, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
122 5 0.04
123 117 0.93
124 4 0.03
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (123 bp):
AATATATTTCGTTGTGAAGTCAAAATCGTAGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
GAATATCCTTCATTGTGAAGTTGAAATCCAATCTTGAAAATTACATTAGCTCGAGATT
Found at i:270931 original size:5 final size:5
Alignment explanation
Indices: 270889--270972 Score: 57
Period size: 5 Copynumber: 16.4 Consensus size: 5
270879 AATTTTAAAG
* * * * *
270889 AAAAT ACAAT GAAAG AAAA- AAAAT AAAGGT ATAAT AAAAT AAAAT AAAAGAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT -AAA-AT
270941 AAAAT --AAT AAAAT AAAAT AAAAGAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT -AAA-AT AAAAT AA
270973 TAAATAATAA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
3 3 0.05
4 4 0.06
5 36 0.58
6 15 0.24
7 4 0.06
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:270942 original size:20 final size:18
Alignment explanation
Indices: 270919--270979 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 18
270909 AAATAAAGGT
270919 ATAATAAAATAAAATAAAA
1 ATAA-AAAATAAAATAAAA
270938 GATAAAATAATAAAAT-AAA
1 -ATAAAA-AATAAAATAAAA
*
270957 ATAAAAGATAAAATAATAA
1 ATAAAAAATAAAATAA-AA
270976 ATAA
1 ATAA
270980 TAATAGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 7 0.19
18 7 0.19
19 11 0.30
20 12 0.32
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAAATAAAATAAAA
Found at i:270944 original size:12 final size:12
Alignment explanation
Indices: 270927--270996 Score: 79
Period size: 12 Copynumber: 5.5 Consensus size: 12
270917 GTATAATAAA
270927 ATAAAATAAAAG
1 ATAAAATAAAAG
*
270939 ATAAAATAATAAA
1 ATAAAATAA-AAG
270952 ATAAAATAAAAG
1 ATAAAATAAAAG
270964 ATAAAATAATAA-
1 ATAAAATAA-AAG
270976 ATAATAATAGTAAAG
1 ATAA-AATA--AAAG
270991 ATAAAA
1 ATAAAA
270997 AGGTATTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
12 24 0.48
13 17 0.34
14 4 0.08
15 5 0.10
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:270947 original size:25 final size:25
Alignment explanation
Indices: 270919--270996 Score: 122
Period size: 25 Copynumber: 3.0 Consensus size: 25
270909 AAATAAAGGT
270919 ATAATAAAATAAAATAAAAGATAAA
1 ATAATAAAATAAAATAAAAGATAAA
270944 ATAATAAAATAAAATAAAAGATAAA
1 ATAATAAAATAAAATAAAAGATAAA
270969 ATAAT-AAATAATAATAGTAAAGATAAA
1 ATAATAAAATAA-AATA--AAAGATAAA
270996 A
1 A
270997 AGGTATTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
24 6 0.12
25 34 0.68
27 10 0.20
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (25 bp):
ATAATAAAATAAAATAAAAGATAAA
Found at i:271016 original size:13 final size:13
Alignment explanation
Indices: 270994--271023 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
270984 AGTAAAGATA
270994 AAAAGGTATTTTT
1 AAAAGGTATTTTT
*
271007 AAAAGTTATTTTT
1 AAAAGGTATTTTT
271020 AAAA
1 AAAA
271024 TAAAAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (13 bp):
AAAAGGTATTTTT
Found at i:271057 original size:17 final size:18
Alignment explanation
Indices: 271021--271062 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
271011 GTTATTTTTA
271021 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
271039 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
271056 AAATAAA
1 AAATAAA
271063 TAATATAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:271693 original size:85 final size:85
Alignment explanation
Indices: 271540--271702 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 85
271530 TTCAAATTCT
* * ** *
271540 TAAAAATAAACTAAAGATAATTTTTAAAATAATATTTTTATCGTAATTAAAAGACTTAAAACTTT
1 TAAAAATAAAATAAAAATAATTTTTAAAATAATATTTAAATCGTAATTAAAAGACTTAAAACTAT
271605 TTAAACTAAAATACCTAAAA
66 TTAAACTAAAATACCTAAAA
* * *
271625 TAAAGATAAAATAAAAATAA-TTTTAAAATAATATCTTAAATCTTAATTAAAATA-TTAATATA-
1 TAAAAATAAAATAAAAATAATTTTTAAAATAATAT-TTAAATCGTAATTAAAAGACTTAA-A-AC
271687 TATTTAAACTAAAATA
63 TATTTAAACTAAAATA
271703 TAAAGATAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 18 0.27
85 48 0.72
86 1 0.01
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (85 bp):
TAAAAATAAAATAAAAATAATTTTTAAAATAATATTTAAATCGTAATTAAAAGACTTAAAACTAT
TTAAACTAAAATACCTAAAA
Found at i:275593 original size:2 final size:2
Alignment explanation
Indices: 275586--275611 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
275576 TTTGGTTCAT
275586 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
275612 CTTTAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:276579 original size:22 final size:23
Alignment explanation
Indices: 276553--276602 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
276543 ATTATATTAT
276553 ATTATAAA-TTTAAGAACAAAAA
1 ATTATAAACTTTAAGAACAAAAA
* *
276575 ATTATAAAGCTTTAAGAATATAAA
1 ATTATAAA-CTTTAAGAACAAAAA
276599 ATTA
1 ATTA
276603 GATCATTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
24 16 0.67
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (23 bp):
ATTATAAACTTTAAGAACAAAAA
Found at i:278476 original size:20 final size:21
Alignment explanation
Indices: 278451--278543 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
278441 TTTTCCCAAT
*
278451 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
278471 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
278492 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
278512 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
278533 TCGCAATGCGA
1 TCGCAATGCGA
278544 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:278496 original size:41 final size:41
Alignment explanation
Indices: 278451--278543 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
278441 TTTTCCCAAT
278451 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
278492 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
278533 TCGCAATGCGA
1 TCGCAATGCGA
278544 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:278556 original size:41 final size:41
Alignment explanation
Indices: 278470--278604 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
278460 GAATAAGTAA
* *
278470 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
278511 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
278552 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
278593 TTCGCAACGCGA
1 ATCGCAACGCGA
278605 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:278557 original size:20 final size:20
Alignment explanation
Indices: 278532--278646 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
278522 AATTGGGAAA
*
278532 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
278552 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
278573 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
278593 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
278613 TTCGCAACACGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
278633 TTTGCAACGCGATA
1 ATCGCAACGCGATA
278647 ATATATAATC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:278861 original size:22 final size:22
Alignment explanation
Indices: 278833--278875 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
278823 ACTCTCTCAC
278833 CCATCTCCGACGAAATCCGTCA
1 CCATCTCCGACGAAATCCGTCA
*
278855 CCATCTCCGGCGAAATCCGTC
1 CCATCTCCGACGAAATCCGTC
278876 TATCTCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCA
Found at i:280527 original size:18 final size:18
Alignment explanation
Indices: 280506--280550 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
280496 TCCACTTCGG
*
280506 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
280524 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
280542 GAGCCATCA
1 GAGCCATCA
280551 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:281122 original size:19 final size:19
Alignment explanation
Indices: 281029--281126 Score: 71
Period size: 20 Copynumber: 5.3 Consensus size: 19
281019 TAGTTTACTT
* **
281029 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
281049 TCGCAACGCAGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
281069 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
281088 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
281102 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
281121 TCGCAA
1 TCGCAA
281127 TGCGTTTGTG
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 23 0.36
20 24 0.38
21 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:281161 original size:14 final size:14
Alignment explanation
Indices: 281142--281198 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
281132 TTGTGTTTCG
281142 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
281156 CGTTGCGATTTCAT-T
1 CGTTGCGATTT--TGT
281171 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
281187 CGTTGCGATTTT
1 CGTTGCGATTTT
281199 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 21 0.55
15 4 0.11
16 4 0.11
17 9 0.24
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:281179 original size:31 final size:33
Alignment explanation
Indices: 281137--281214 Score: 133
Period size: 31 Copynumber: 2.4 Consensus size: 33
281127 TGCGTTTGTG
*
281137 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
281169 -TTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
281201 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
281215 AGCCATTTCG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
31 25 0.58
32 5 0.12
33 13 0.30
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:281213 original size:19 final size:19
Alignment explanation
Indices: 281158--281255 Score: 75
Period size: 19 Copynumber: 5.5 Consensus size: 19
281148 GATTTTGTCG
281158 TTGCGA-TTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
*
281175 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
281189 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** *
281208 TTGCGATAGCCATTTCGCG
1 TTGCGATTTTCATTTCGCA
** *
281227 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
281246 TTGCGATTTT
1 TTGCGATTTT
281256 AAGTTTCGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
14 6 0.09
15 3 0.05
16 3 0.05
17 13 0.20
19 41 0.62
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:283039 original size:13 final size:14
Alignment explanation
Indices: 283023--283057 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
283013 ATTGTTTAAT
283023 TGATTTGTAAA-GA
1 TGATTTGTAAATGA
*
283036 TGATTTGTAAATGT
1 TGATTTGTAAATGA
283050 TGATTTGT
1 TGATTTGT
283058 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.49
Consensus pattern (14 bp):
TGATTTGTAAATGA
Done.