Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007864.1 Hibiscus syriacus cultivar Beakdansim tig00110236_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: 1537186
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1212363 original size:20 final size:18
Alignment explanation
Indices: 1212338--1212391 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
1212328 CTTGTATGTT
1212338 TTTTTAATTTTTTTATTTTG
1 TTTTTAATTTTTTTA--TTG
*
1212358 TTTTTACTTTTTTTATTG
1 TTTTTAATTTTTTTATTG
*
1212376 TTATTTTATTTTTTTA
1 TT-TTTAATTTTTTTA
1212392 AAATTAGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.17
19 11 0.37
20 14 0.47
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.80
Consensus pattern (18 bp):
TTTTTAATTTTTTTATTG
Found at i:1217257 original size:12 final size:12
Alignment explanation
Indices: 1217240--1217270 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1217230 TCCAAATAAT
1217240 AAATTTATTTCA
1 AAATTTATTTCA
1217252 AAATTTATTTCA
1 AAATTTATTTCA
1217264 AAATTTA
1 AAATTTA
1217271 AAGTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTTATTTCA
Found at i:1217316 original size:20 final size:19
Alignment explanation
Indices: 1217288--1217335 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1217278 AAATGATTTG
*
1217288 ATTTTAAAAGCAAAAATTGA
1 ATTTTAAAAGC-AAAATTAA
* *
1217308 ATTTGAAAATCAAAATTAA
1 ATTTTAAAAGCAAAATTAA
1217327 ATTTTAAAA
1 ATTTTAAAA
1217336 AATGAATTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (19 bp):
ATTTTAAAAGCAAAATTAA
Found at i:1218496 original size:123 final size:123
Alignment explanation
Indices: 1218352--1218579 Score: 320
Period size: 123 Copynumber: 1.9 Consensus size: 123
1218342 ATTGTTATAT
* * * *
1218352 AACAAAAAGGGGGAGATGTATGGTTTGAAAACTTCAATATT-TTAATGAAAAG-GGAGAGTTGAA
1 AACAAAAAGGGGGAGAAGTATGGTTTGAAAAATTAAAT-TTCTTAATGAAAAGTGG-GAGCT-AA
* * *
1218415 A-ATTTTCATATTTTTCCAACAATTGGTATCCTTTTCATTAAATTAAGGGGAATTTTCCAAA
63 ATA-TTTCATATTTTTCCAACAAATGATATCATTTTCATTAAATTAAGGGGAATTTTCCAAA
1218476 AACAAAAA-GGGGAGAAGTATGGTTTGAAAAATTAAATTTCTTAATGAAAAGTGGGAGCTAAATA
1 AACAAAAAGGGGGAGAAGTATGGTTTGAAAAATTAAATTTCTTAATGAAAAGTGGGAGCTAAATA
*
1218540 TTTCATATTTTTCCAACAAATGATATTATTTTCATTAAAT
66 TTTCATATTTTTCCAACAAATGATATCATTTTCATTAAAT
1218580 ATTTATTAAG
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
122 41 0.44
123 42 0.45
124 10 0.11
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (123 bp):
AACAAAAAGGGGGAGAAGTATGGTTTGAAAAATTAAATTTCTTAATGAAAAGTGGGAGCTAAATA
TTTCATATTTTTCCAACAAATGATATCATTTTCATTAAATTAAGGGGAATTTTCCAAA
Found at i:1219899 original size:18 final size:19
Alignment explanation
Indices: 1219835--1219903 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
1219825 AAATAGTTGG
* *
1219835 GTATCGATACTCCTATAGGGA
1 GTATCGATACT-CTACA-TGA
*
1219856 GTATCGATACTCTACCT-A
1 GTATCGATACTCTACATGA
1219874 CGGTATCGATACT-TACATGA
1 --GTATCGATACTCTACATGA
1219894 GTATCGATAC
1 GTATCGATAC
1219904 CCAATTTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
18 11 0.27
19 4 0.10
20 15 0.37
21 11 0.27
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (19 bp):
GTATCGATACTCTACATGA
Found at i:1219962 original size:21 final size:20
Alignment explanation
Indices: 1219937--1219985 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1219927 AAAATACCCT
1219937 AGTATCGACACT-GACCCTCTG
1 AGTATCGACACTAGA--CTCTG
* *
1219958 AGTATCAATACTAGACTCTG
1 AGTATCGACACTAGACTCTG
1219978 AGTATCGA
1 AGTATCGA
1219986 TACTCCTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 10 0.42
22 2 0.08
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTATCGACACTAGACTCTG
Found at i:1221144 original size:15 final size:15
Alignment explanation
Indices: 1221113--1221156 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1221103 ATCGGGTCAA
*
1221113 ATTTTGGATCGGGTG
1 ATTTTGGATCGGATG
1221128 ATTTTCGGATC-GATG
1 ATTTT-GGATCGGATG
*
1221143 ATTTTGGTTCGGAT
1 ATTTTGGATCGGAT
1221157 CAATATTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.16
15 16 0.64
16 5 0.20
ACGTcount: A:0.16, C:0.09, G:0.32, T:0.43
Consensus pattern (15 bp):
ATTTTGGATCGGATG
Found at i:1222017 original size:17 final size:18
Alignment explanation
Indices: 1221997--1222045 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1221987 ATTACCAATT
1221997 TTATTTAAATTAA-TTTA
1 TTATTTAAATTAACTTTA
* *
1222014 TTATTCAAAATAACTTTTA
1 TTATTTAAATTAAC-TTTA
*
1222033 TTGTTTAAATTAA
1 TTATTTAAATTAA
1222046 AGTAAACTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
19 14 0.56
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTATTTAAATTAACTTTA
Found at i:1231783 original size:3 final size:3
Alignment explanation
Indices: 1231775--1231821 Score: 58
Period size: 3 Copynumber: 14.7 Consensus size: 3
1231765 TTTATTTATG
*
1231775 ATA ATA ATA ATA CTTA ATA ATA ATA ATTA ATA ATAA ATA ATA ATA AT
1 ATA ATA ATA ATA -ATA ATA ATA ATA A-TA ATA AT-A ATA ATA ATA AT
1231822 TAATTTTAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 31 0.79
4 8 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1231794 original size:13 final size:12
Alignment explanation
Indices: 1231776--1231821 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
1231766 TTATTTATGA
1231776 TAATAATAATACT
1 TAATAATAATA-T
1231789 TAATAATAATAAT
1 TAATAATAAT-AT
1231802 TAATAATAA-A-
1 TAATAATAATAT
1231812 TAATAATAAT
1 TAATAATAAT
1231822 TAATTTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
13 20 0.65
14 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:1231825 original size:10 final size:9
Alignment explanation
Indices: 1231775--1231821 Score: 58
Period size: 10 Copynumber: 4.9 Consensus size: 9
1231765 TTTATTTATG
1231775 ATAATAATA
1 ATAATAATA
*
1231784 ATACTTAATA
1 ATA-ATAATA
1231794 ATAATAATTA
1 ATAATAA-TA
1231804 ATAATAAATA
1 ATAAT-AATA
1231814 ATAATAAT
1 ATAATAAT
1231822 TAATTTTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 9 0.27
10 22 0.67
11 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
ATAATAATA
Found at i:1233869 original size:52 final size:54
Alignment explanation
Indices: 1233790--1234250 Score: 533
Period size: 53 Copynumber: 8.7 Consensus size: 54
1233780 CGTTTGATGG
*
1233790 AGATTGTT-GAGTCTTATACTCTCTGAAGAAAT-GGGGGCATACGCGATTTATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTT-TGA
* * *
1233843 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAAGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGAT-TTTGA
*
1233896 AGATTGTTCGAGTC-TATA--CTCTGAAGAAATAGGGGACAGACGCGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-TTGA
* *
1233948 AGATTGTTCGAGTCTTATACTCTCTGAAG-AATAGGGGGCATACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-TTGA
* *
1234002 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-TTGA
* * *
1234057 AGATTG-T-GGGTCTTATACTCTCT---GAAATA-GGGGCATACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-TTGA
* *
1234106 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-TTGA
* ** *
1234161 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGTAGCAGACACGATTATTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-TTGA
* * *
1234214 AGATTGTCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
1234251 AGCGAACCCG
Statistics
Matches: 356, Mismatches: 34, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
49 23 0.06
50 7 0.02
51 15 0.04
52 68 0.19
53 93 0.26
54 65 0.18
55 85 0.24
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (54 bp):
AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTTTGA
Found at i:1234124 original size:104 final size:105
Alignment explanation
Indices: 1233790--1234250 Score: 607
Period size: 104 Copynumber: 4.3 Consensus size: 105
1233780 CGTTTGATGG
* * *
1233790 AGATTGTTGAGTCTTATACTCTCTGAAGAAAT-GGGGGCATACGCGATTTATGAAGATTGTGGGT
1 AGATTGTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGGT
*
1233854 CTTATACTCTCTGAAGAAATAGGGGGCAGA-AGCGATCGTTGA
66 CTTATACTCTCT--AGAAATAGGGGGCAGACA-CGATTGTTGA
* *
1233896 AGATTGTTCGAGTC-TATA--CTCTGAAGAAATAGGGGACAGACGCGATTGTTGAAGATTGTTCG
1 AGATTG-TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-G
* *
1233958 AGTCTTATACTCTCT-GAAGAATAGGGGGCATACACGATTGTTGA
63 GGTCTTATACTCTCTAG-A-AATAGGGGGCAGACACGATTGTTGA
1234002 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTG-TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
*
1234067 TCTTATACTCTCT-GAAATA-GGGGCATACACGATTGTTGA
65 TCTTATACTCTCTAGAAATAGGGGGCAGACACGATTGTTGA
1234106 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTG-TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
** *
1234171 TCTTATACTCTCTGAAGAAATAGGTAGCAGACACGATTATTGA
65 TCTTATACTCTCT--AGAAATAGGGGGCAGACACGATTGTTGA
* *
1234214 AGATTGTCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGT-CGAGTCT-TATACTCTCTGAAGAAATAGGG
1234251 AGCGAACCCG
Statistics
Matches: 321, Mismatches: 18, Indels: 30
0.87 0.05 0.08
Matches are distributed among these distances:
104 111 0.35
105 28 0.09
106 46 0.14
107 50 0.16
108 48 0.15
109 38 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (105 bp):
AGATTGTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGGT
CTTATACTCTCTAGAAATAGGGGGCAGACACGATTGTTGA
Found at i:1234238 original size:159 final size:157
Alignment explanation
Indices: 1233790--1234238 Score: 613
Period size: 159 Copynumber: 2.8 Consensus size: 157
1233780 CGTTTGATGG
* *
1233790 AGATTGTTGAGTCTTATACTCTCTGAAGAAAT-GGGGGCATACGCGATTTATGAAGATTGTGGGT
1 AGATTGTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTGATGAAGATTGTGGGT
**
1233854 CTTATACTCTCTGAAGAAATAGGGGGCAGA-AGCGATCGTTGAAGATTGTTCGAGTCTATACTCT
66 CTTATACTCTCTGAAGAAATAGGGGGCAGACA-CGATTATTGAAGATTG-TCGAGTCTATACTCT
** *
1233918 GAAGAAATAGGGGACAGACGCGATTGTTGA
129 -CTGAAATAGGGGACAGACACGATTGTTGA
* *
1233948 AGATTGTTCGAGTCTTATACTCTCTGAAG-AATAGGGGGCATACACGATTGTTGAAGATTGCTCG
1 AGATTG-TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTGATGAAGATTG-T-G
* * *
1234012 AGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA-TGAAGATTGT-GGGTCTTATAC
63 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATT-ATTGAAGATTGTCGAGTC-TATAC
*
1234075 TCTCTGAAATAGGGG-CATACACGATTGTTGA
126 TCTCTGAAATAGGGGACAGACACGATTGTTGA
*
1234106 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTG-TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTGATGAAGATTGTGGG
**
1234171 TCTTATACTCTCTGAAGAAATAGGTAGCAGACACGATTATTGAAGATTGTCCGAGTTCTATACTC
65 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTATTGAAGATTGT-CGAG-TCTATACTC
1234236 TCT
128 TCT
1234239 AAAGAAAGAG
Statistics
Matches: 257, Mismatches: 22, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
156 1 0.00
157 47 0.18
158 52 0.20
159 99 0.39
160 12 0.05
161 46 0.18
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (157 bp):
AGATTGTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTGATGAAGATTGTGGGT
CTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTATTGAAGATTGTCGAGTCTATACTCTCT
GAAATAGGGGACAGACACGATTGTTGA
Found at i:1248747 original size:55 final size:55
Alignment explanation
Indices: 1248596--1249066 Score: 706
Period size: 55 Copynumber: 8.7 Consensus size: 55
1248586 CGTTTGATGG
*
1248596 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATT-TATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGT-TGA
* *
1248651 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
*
1248704 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
*
1248759 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* *
1248814 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* *
1248869 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* *
1248922 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * * *
1248977 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * *
1249030 AGATTGTCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
1249067 AGCGAACCCG
Statistics
Matches: 382, Mismatches: 26, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
53 143 0.37
54 7 0.02
55 232 0.61
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
Found at i:1249051 original size:163 final size:162
Alignment explanation
Indices: 1248596--1249066 Score: 732
Period size: 163 Copynumber: 2.9 Consensus size: 162
1248586 CGTTTGATGG
* *
1248596 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
**
1248661 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACTC
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGAAGATTG-TCGAGTCTTATACTC
*
1248726 TCTGAAGAAATAGGGGACAGACGCGATTGTTGA
130 TCTGAAGAAATAGGGGACAGACACGATTGTTGA
* *
1248759 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGCTCG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-G
* *
1248824 AGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA-TGAAGATTGT-GGGTCTTATAC
64 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-ATTGAAGATTGTCGAGTCTTATAC
*
1248887 TCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
128 TCTCTGAAGAAATAGGGGACAGACACGATTGTTGA
*
1248922 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
* *
1248987 TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTCCGAGT-TCTATACT
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGAAGATTGT-CGAGTCT-TATACT
* *
1249051 CTCTAAAGAAAGAGGG
129 CTCTGAAGAAATAGGG
1249067 AGCGAACCCG
Statistics
Matches: 282, Mismatches: 19, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
160 1 0.00
161 48 0.17
162 2 0.01
163 181 0.64
164 2 0.01
165 48 0.17
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (162 bp):
AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGAAGATTGTCGAGTCTTATACTCT
CTGAAGAAATAGGGGACAGACACGATTGTTGA
Found at i:1249089 original size:108 final size:108
Alignment explanation
Indices: 1248596--1249066 Score: 775
Period size: 108 Copynumber: 4.3 Consensus size: 108
1248586 CGTTTGATGG
* * *
1248596 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
* *
1248661 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
* * *
1248704 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGTTGAAGATTGTTCG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-G
*
1248769 AGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
64 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1248814 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1248879 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1248922 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
* *
1248987 TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGA
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
* *
1249030 AGATTG-TCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGCT-CGAGTCT-TATACTCTCTGAAGAAATAGGG
1249067 AGCGAACCCG
Statistics
Matches: 344, Mismatches: 15, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
107 2 0.01
108 239 0.69
109 2 0.01
110 101 0.29
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (108 bp):
AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
Found at i:1256070 original size:81 final size:81
Alignment explanation
Indices: 1255970--1257022 Score: 1468
Period size: 81 Copynumber: 13.0 Consensus size: 81
1255960 GTAAAAAAAA
* * * * *
1255970 TAATAGCTTAGTTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATAAAAGATTAAATA
1 TAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
1256035 CCTTTGAGTAAAAGAT
66 CCTTTGAGTAAAAGAT
* * * * *
1256051 TAATAACCTAG-AGTTGCATTTTACAGAAAGGTGTCAATTATGCTAGTTAGATGAAATGTTAAAT
1 TAATAGCCTAGTTG-TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
*
1256115 ACCTTTGGGTAAAAGAT
65 ACCTTTGAGTAAAAGAT
*
1256132 TAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTA
1 TAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
* *
1256197 CTTTTAAGTAAAAGAT
66 CCTTTGAGTAAAAGAT
* * * * * *
1256213 TAATAGCCTAGCTGTGCATTTTGGCAGAAAGATGTAAATTATGGCAGTTAGATGAAATGTTAAAT
1 TAATAGCCTAGTTGTGCA-TTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
1256278 ACCTTTGAGTAAAAGAT
65 ACCTTTGAGTAAAAGAT
*
1256295 TAATAGCCTAGTTGTTCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
1 TAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
1256360 CC-TTGAGTAAAAGAT
66 CCTTTGAGTAAAAGAT
* **
1256375 TAATAGCCTAGCTT-TGCATTTGATC-GAAAGGTGTCAATTATGACAGTTAGATGAAAGAATAAA
1 TAATAGCCTAG-TTGTGCATTTGA-CAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
* *
1256438 TACCATTAAGTAAAAGAT
64 TACCTTTGAGTAAAAGAT
* * *
1256456 TAATAGCCTAGTTGTGCATTTGAGAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATA
1 TAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
1256521 CCTTTGAGTAAAAGAT
66 CCTTTGAGTAAAAGAT
*
1256537 TAATAGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
1 TAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
1256602 CCTTTGAGTAAAAGAT
66 CCTTTGAGTAAAAGAT
* * * * *
1256618 TAATAGCCTAGTTTTGCATTTGATAGAAAATGTGCCAATTATGCCAGTTAGATGAAAAGTTAAAT
1 TAATAGCCTAGTTGTGCATTTGACAG-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
1256683 ACCTTTGAGTAAAAGAT
65 ACCTTTGAGTAAAAGAT
* ** *
1256700 TAATAGCCTAGTTGTGCATTTGAAAGAATTGTGTCAATTATGTCAGTTAGATGAAA-GTTAAATA
1 TAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
1256764 CCTTTGAGTAAAAGAT
66 CCTTTGAGTAAAAGAT
* * *
1256780 TAATAGCCTAGTTGTGCATTTGACAGGAGAGGTATCAATTATGTCAGTTAGATGAAAGGTTAAAT
1 TAATAGCCTAGTTGTGCATTTGACA-GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
*
1256845 TCCTTTGAGTAAAAGAT
65 ACCTTTGAGTAAAAGAT
* * * * * **
1256862 TAATAGCCAAGCTGTTCATTTGATAAAAAAAATGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
1 TAATAGCCTAGTTGTGCATTTGA-CAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
* *
1256927 ATCTTTGAGTAAAAGAA
65 ACCTTTGAGTAAAAGAT
* * * * * * *
1256944 TAATAGTCTAGCTGTGCATTTGACAGAAAGGTGTTAATCATGCAAGTTAGAGGAAAGGCTAAATA
1 TAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
*
1257009 CCTTTGGGTAAAAG
66 CCTTTGAGTAAAAG
1257023 GCTAAAGGAT
Statistics
Matches: 867, Mismatches: 93, Indels: 24
0.88 0.09 0.02
Matches are distributed among these distances:
80 122 0.14
81 486 0.56
82 258 0.30
83 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (81 bp):
TAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA
CCTTTGAGTAAAAGAT
Found at i:1256820 original size:244 final size:243
Alignment explanation
Indices: 1255970--1257022 Score: 1481
Period size: 244 Copynumber: 4.3 Consensus size: 243
1255960 GTAAAAAAAA
* * * * *
1255970 TAATAGCTTAGTTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATAAAAGATTAAATA
1 TAATAGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATA
* * * *
1256035 CCTTTGAGTAAAAGATTAATAACCTAG-AGTTGCATTTTACAGAAAGGTGTCAATTATGCTAGTT
66 CCTTTGAGTAAAAGATTAATAGCCTAGTTG-TGCATTTGACAGAAAGGTGTCAATTATGCCAGTT
* * * *
1256099 AGATGAAATGTTAAATACCTTTGGGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGT
130 AGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTTTGCATTTGATAGAAAGGT
* * *
1256164 GTCAATTATGCCAGTTAGATGAAAGGTTAAGTACTTTTAAGTAAAAGAT
195 GTCAATTATGCCAGTTAGATGAAAAGTTAAATACCTTTAAGTAAAAGAT
* * * * *
1256213 TAATAGCCTAGCTGTGCATTTTGGCAGAAA-GATGTAAATTATGGCAGTTAGATGAAATGTTAAA
1 TAATAGCCTAGTTGTGCA-TTTGACAGAAATG-TGTCAATTATGTCAGTTAGATGAAAGGTTAAA
*
1256277 TACCTTTGAGTAAAAGATTAATAGCCTAGTTGTTCATTTGACAGAAAGGTGTCAATTATGCCAGT
64 TACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGT
* *
1256342 TAGATGAAAGGTTAAATACC-TTGAGTAAAAGATTAATAGCCTAGCTTTGCATTTGATCGAAAGG
129 TAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTTTGCATTTGATAGAAAGG
* * *
1256406 TGTCAATTATGACAGTTAGATG-AAAGAATAAATACCATTAAGTAAAAGAT
194 TGTCAATTATGCCAGTTAGATGAAAAG-TTAAATACCTTTAAGTAAAAGAT
*
1256456 TAATAGCCTAGTTGTGCATTTGAGAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATA
1 TAATAGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATA
*
1256521 CCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTA
66 CCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTA
*
1256586 GATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTTTGCATTTGATAGAAAATGT
131 GATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTTTGCATTTGATAG-AAAGGT
* *
1256651 GCCAATTATGCCAGTTAGATGAAAAGTTAAATACCTTTGAGTAAAAGAT
195 GTCAATTATGCCAGTTAGATGAAAAGTTAAATACCTTTAAGTAAAAGAT
* *
1256700 TAATAGCCTAGTTGTGCATTTGAAAGAATTGTGTCAATTATGTCAGTTAGATGAAA-GTTAAATA
1 TAATAGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATA
* * *
1256764 CCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGGAGAGGTATCAATTATGTCAGTT
66 CCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACA-GAAAGGTGTCAATTATGCCAGTT
* * * * *
1256829 AGATGAAAGGTTAAATTCCTTTGAGTAAAAGATTAATAGCCAAGCTGTT-CATTTGATAAAAAAA
130 AGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAG-TTTTGCATTTGAT-AGAAAG
* * * * *
1256893 ATGTCAATTATGCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAGAA
193 GTGTCAATTATGCCAGTTAGATGAAAAGTTAAATACCTTTAAGTAAAAGAT
* * * * * * *
1256944 TAATAGTCTAGCTGTGCATTTGACAGAAAGGTGTTAATCATG-CAAGTTAGAGGAAAGGCTAAAT
1 TAATAGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGTC-AGTTAGATGAAAGGTTAAAT
*
1257008 ACCTTTGGGTAAAAG
65 ACCTTTGAGTAAAAG
1257023 GCTAAAGGAT
Statistics
Matches: 729, Mismatches: 68, Indels: 24
0.89 0.08 0.03
Matches are distributed among these distances:
242 124 0.17
243 200 0.27
244 376 0.52
245 29 0.04
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (243 bp):
TAATAGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATA
CCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTA
GATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTTTGCATTTGATAGAAAGGTG
TCAATTATGCCAGTTAGATGAAAAGTTAAATACCTTTAAGTAAAAGAT
Found at i:1257132 original size:47 final size:45
Alignment explanation
Indices: 1257067--1257185 Score: 125
Period size: 45 Copynumber: 2.6 Consensus size: 45
1257057 GTGCATTTAC
*
1257067 GGCATGAAAAGATGCCATATATAT-AAAATGTACA-ACAATGCATAATT
1 GGCATGAAAAGATACCATA-A-ATGAAAA--TACAGACAATGCATAATT
* *
1257114 GGTATGAAATGATACCATAAATGAAAATACAGACAATGCATAATT
1 GGCATGAAAAGATACCATAAATGAAAATACAGACAATGCATAATT
* * * *
1257159 GGCATGAAAGGATGCCACAATTGAAAA
1 GGCATGAAAAGATACCATAAATGAAAA
1257186 AAATTGGTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
44 4 0.06
45 37 0.60
46 5 0.08
47 16 0.26
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.23
Consensus pattern (45 bp):
GGCATGAAAAGATACCATAAATGAAAATACAGACAATGCATAATT
Found at i:1258786 original size:15 final size:15
Alignment explanation
Indices: 1258766--1258797 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1258756 ATACAAAAAT
*
1258766 AAAAATAGAAGATAA
1 AAAAATAAAAGATAA
1258781 AAAAATAAAAGATAA
1 AAAAATAAAAGATAA
1258796 AA
1 AA
1258798 TGAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAGATAA
Found at i:1258821 original size:16 final size:17
Alignment explanation
Indices: 1258800--1259036 Score: 97
Period size: 16 Copynumber: 13.8 Consensus size: 17
1258790 AGATAAAATG
1258800 AAATATATA-AAATAAT
1 AAATATATATAAATAAT
1258816 AAATATATATAACAT-AT
1 AAATATATATAA-ATAAT
1258833 -AAT-TATAGT-AATAA-
1 AAATATATA-TAAATAAT
1258847 AAATATATATAAATAAT
1 AAATATATATAAATAAT
* *
1258864 AATGATATATGAAAAAGAATT
1 AA--ATATAT-ATAAATAA-T
*
1258885 AAAAGTATATATATATATAT
1 -AAA-TATATATAAATA-AT
* *
1258905 AAATAAAGATAGAAT-AT
1 AAATATATATA-AATAAT
1258922 AGAA-A-ATA-AAAT-AT
1 A-AATATATATAAATAAT
* *
1258936 AAAAAAATATAAATATAT
1 AAATATATATAAATA-AT
1258954 ATATATATATATAAATAAT
1 A-A-ATATATATAAATAAT
* * *
1258973 AAAGATAGAATAAAGAATT
1 AAATATA-TATAAATAA-T
*
1258992 AAA-AGTATATATAT-AT
1 AAATA-TATATAAATAAT
* *
1259008 ATATATATATATAT-AT
1 AAATATATATAAATAAT
*
1259024 ATATATATATAAA
1 AAATATATATAAA
1259037 GATAGAATAT
Statistics
Matches: 174, Mismatches: 19, Indels: 56
0.70 0.08 0.22
Matches are distributed among these distances:
13 2 0.01
14 9 0.05
15 14 0.08
16 54 0.31
17 16 0.09
18 26 0.15
19 21 0.12
20 23 0.13
21 7 0.04
22 2 0.01
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
AAATATATATAAATAAT
Found at i:1258885 original size:48 final size:48
Alignment explanation
Indices: 1258800--1258910 Score: 122
Period size: 48 Copynumber: 2.3 Consensus size: 48
1258790 AGATAAAATG
* * *
1258800 AAATATATA-AAATAATAAATATATATAACATATAATT-ATAGTAATAA
1 AAATATATATAAATAATAAATATATATAACAAAGAATTAAAAGT-ATAA
*
1258847 AAATATATATAAATAAT-AATGATATATGAA-AAAGAATTAAAAGTATAT
1 AAATATATATAAATAATAAAT-ATATAT-AACAAAGAATTAAAAGTATAA
*
1258895 ATATATATATAAATAA
1 AAATATATATAAATAA
1258911 AGATAGAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
47 12 0.22
48 37 0.67
49 6 0.11
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (48 bp):
AAATATATATAAATAATAAATATATATAACAAAGAATTAAAAGTATAA
Found at i:1258951 original size:6 final size:6
Alignment explanation
Indices: 1258893--1259047 Score: 59
Period size: 6 Copynumber: 24.8 Consensus size: 6
1258883 TTAAAAGTAT
* * *
1258893 ATATAT ATATATA A-ATAA AGATAGA ATATAGA AAATAAA ATATAA A-A-AA
1 ATATAA ATATA-A ATATAA ATATA-A ATATA-A ATAT-AA ATATAA ATATAA
* * *
1258942 ATATAA ATATATA TATATAT ATATAA ATAATAA AGATAGA ATAAAGA AT-TAA
1 ATATAA ATATA-A -ATATAA ATATAA AT-ATAA ATATA-A ATATA-A ATATAA
* * * * * * *
1258994 A-AGTAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAA AGATAGA
1 ATA-TAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATA-A
1259043 ATATA
1 ATATA
1259048 GAAAATAAAA
Statistics
Matches: 121, Mismatches: 14, Indels: 27
0.75 0.09 0.17
Matches are distributed among these distances:
4 3 0.02
5 6 0.05
6 71 0.59
7 35 0.29
8 6 0.05
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:1259004 original size:2 final size:2
Alignment explanation
Indices: 1258997--1259034 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1258987 GAATTAAAAG
1258997 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
1259035 AAGATAGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1259178 original size:2 final size:2
Alignment explanation
Indices: 1259171--1259217 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1259161 AAGATAATTA
1259171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1259213 AT AT A
1 AT AT A
1259218 ATAAGAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1260828 original size:110 final size:110
Alignment explanation
Indices: 1260635--1260841 Score: 299
Period size: 110 Copynumber: 1.9 Consensus size: 110
1260625 GCTCTAGAAA
* * * * *
1260635 TTGTTTGTTGACAGTCAGCTGCCCCTTCGCTGTGAATTTGAGCTTGTGTTGTCTCAAGTTCAATA
1 TTGTTTATTGACAATCAGCTGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAATA
*
1260700 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAACG
66 TCCCTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAACG
* **
1260745 TTGTTTATTGACAATCAG-TCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAAT
1 TTGTTTATTGACAATCAGCT-GCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAAT
* *
1260809 ATCCCTCGGTGTGAAGTTGAAATTGGCTCTGAA
65 ATCCCTCGCTGTGAAGTTGAAATTGACTCTGAA
1260842 ACTGGGAAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
109 1 0.01
110 84 0.99
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (110 bp):
TTGTTTATTGACAATCAGCTGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAATA
TCCCTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAACG
Found at i:1261958 original size:11 final size:12
Alignment explanation
Indices: 1261937--1261962 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1261927 ACGTTTTTCA
1261937 TTTTTGTTTTTT
1 TTTTTGTTTTTT
1261949 TTTTTGTTTTTT
1 TTTTTGTTTTTT
1261961 TT
1 TT
1261963 ACTTAGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:1269095 original size:18 final size:19
Alignment explanation
Indices: 1269065--1269101 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1269055 TATGAATGTA
1269065 AAACATGGAAATATAAAAT
1 AAACATGGAAATATAAAAT
1269084 AAACAT-GAAATATAAAAT
1 AAACATGGAAATATAAAAT
1269102 GCAAAGTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.65, C:0.05, G:0.08, T:0.22
Consensus pattern (19 bp):
AAACATGGAAATATAAAAT
Found at i:1271888 original size:29 final size:29
Alignment explanation
Indices: 1271855--1271917 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1271845 AAAAATGTAG
*
1271855 TAAAAATGAATAAAATAAAGAAGGTG-AAA
1 TAAAAATAAATAAAATAAAGAAGG-GAAAA
** *
1271884 TAAAAATAAATGCAATAAAGTAGGGAAAA
1 TAAAAATAAATAAAATAAAGAAGGGAAAA
1271913 TAAAA
1 TAAAA
1271918 CAGATAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.65, C:0.02, G:0.16, T:0.17
Consensus pattern (29 bp):
TAAAAATAAATAAAATAAAGAAGGGAAAA
Found at i:1271992 original size:2 final size:2
Alignment explanation
Indices: 1271980--1272021 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1271970 ACAAAAACAA
1271980 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1272021 A
1 A
1272022 ATACATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1272084 original size:15 final size:15
Alignment explanation
Indices: 1272064--1272095 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1272054 ATACAAAAAT
*
1272064 AAAAATAGAAGATAA
1 AAAAATAAAAGATAA
1272079 AAAAATAAAAGATAA
1 AAAAATAAAAGATAA
1272094 AA
1 AA
1272096 TGAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAGATAA
Found at i:1272107 original size:14 final size:14
Alignment explanation
Indices: 1272090--1272157 Score: 63
Period size: 14 Copynumber: 4.8 Consensus size: 14
1272080 AAAATAAAAG
1272090 ATAAAATGAA-ATAT
1 ATAAAAT-AATATAT
1272104 ATAAAATAATATAT
1 ATAAAATAATATAT
1272118 ATAACATATAAT-TAT
1 ATAA-A-ATAATATAT
1272133 AGTAATAA-AATATAT
1 A-TAA-AATAATATAT
1272148 AT-AAATAATA
1 ATAAAATAATA
1272158 ATGATATATG
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
12 2 0.04
13 7 0.15
14 19 0.40
15 10 0.21
16 9 0.19
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (14 bp):
ATAAAATAATATAT
Found at i:1272121 original size:28 final size:29
Alignment explanation
Indices: 1272090--1272154 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1272080 AAAATAAAAG
1272090 ATAAA-ATGAAATATA-TAA-AATAATATAT
1 ATAAATAT-AAATATAGTAATAA-AATATAT
*
1272118 ATAACATATAATTATAGTAATAAAATATAT
1 ATAA-ATATAAATATAGTAATAAAATATAT
1272148 ATAAATA
1 ATAAATA
1272155 ATAATGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
28 4 0.12
29 10 0.31
30 16 0.50
31 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (29 bp):
ATAAATATAAATATAGTAATAAAATATAT
Found at i:1272159 original size:21 final size:21
Alignment explanation
Indices: 1272090--1272159 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
1272080 AAAATAAAAG
*
1272090 ATAA-AATGAAATATATA-AA
1 ATAATAATAAAATATATATAA
*
1272109 ATAATATATATAACATATA-AT-T
1 ATAATA-ATA-AA-ATATATATAA
*
1272131 ATAGTAATAAAATATATATAA
1 ATAATAATAAAATATATATAA
1272152 ATAATAAT
1 ATAATAAT
1272160 GATATATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
19 9 0.23
20 5 0.13
21 12 0.31
22 8 0.21
23 5 0.13
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (21 bp):
ATAATAATAAAATATATATAA
Found at i:1272274 original size:2 final size:2
Alignment explanation
Indices: 1272267--1272293 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1272257 AAGATAATTA
1272267 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1272294 ATAAGAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1274258 original size:23 final size:25
Alignment explanation
Indices: 1274227--1274282 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1274217 TACATCTTTG
*
1274227 ATTTGTCTAA-ATC-ATGTATTTTT
1 ATTTATCTAATATCAATGTATTTTT
*
1274250 ATTTATCTAATTTCAATGTATTTTT
1 ATTTATCTAATATCAATGTATTTTT
*
1274275 ATCTATCT
1 ATTTATCT
1274283 TGCAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 9 0.32
24 2 0.07
25 17 0.61
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (25 bp):
ATTTATCTAATATCAATGTATTTTT
Found at i:1275282 original size:20 final size:20
Alignment explanation
Indices: 1275253--1275295 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1275243 GTTACTAGCA
*
1275253 TATCCAATATACTTGTCATT
1 TATCCAATATACTTGCCATT
*
1275273 TATCCCATATACTTGCCATT
1 TATCCAATATACTTGCCATT
1275293 TAT
1 TAT
1275296 TACCATAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (20 bp):
TATCCAATATACTTGCCATT
Found at i:1275401 original size:44 final size:45
Alignment explanation
Indices: 1275279--1275408 Score: 208
Period size: 45 Copynumber: 2.9 Consensus size: 45
1275269 CATTTATCCC
* * *
1275279 ATATACTTGCCATTTATTACCATAAGATTGTAAGCTTATTTCACCA
1 ATATACTTACCATTTATT-CCATAAGCTCGTAAGCTTATTTCACCA
*
1275325 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTCACCA
1275370 ATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1275409 GCCAGTTTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
44 27 0.34
45 36 0.45
46 17 0.21
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.40
Consensus pattern (45 bp):
ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTCACCA
Found at i:1277852 original size:16 final size:16
Alignment explanation
Indices: 1277831--1277863 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1277821 AACGCTAGAG
*
1277831 TTGCTCTTAGTGGTAT
1 TTGCTCTTAATGGTAT
1277847 TTGCTCTTAATGGTAT
1 TTGCTCTTAATGGTAT
1277863 T
1 T
1277864 ATATAGTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.12, G:0.21, T:0.52
Consensus pattern (16 bp):
TTGCTCTTAATGGTAT
Found at i:1278351 original size:23 final size:21
Alignment explanation
Indices: 1278324--1278369 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
1278314 TCACTTAATT
1278324 ATTCAAATAATTTTGTTTTAGTA
1 ATTCAAATAATTTT-TTTTA-TA
* *
1278347 ATTCAACTAGTTTTTTTTATA
1 ATTCAAATAATTTTTTTTATA
1278368 AT
1 AT
1278370 CATACATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 5 0.24
23 12 0.57
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (21 bp):
ATTCAAATAATTTTTTTTATA
Found at i:1280437 original size:13 final size:12
Alignment explanation
Indices: 1280387--1280441 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 12
1280377 CTAATTACTT
1280387 TTTTAAATTTATA
1 TTTT-AATTTATA
1280400 -TTTAATTT-TA
1 TTTTAATTTATA
1280410 TGCTTTAATTT-TA
1 T--TTTAATTTATA
1280423 TTTTAATTATATA
1 TTTTAATT-TATA
1280436 TTTTAA
1 TTTTAA
1280442 AATTTAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
10 2 0.05
11 12 0.32
12 4 0.11
13 19 0.51
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (12 bp):
TTTTAATTTATA
Found at i:1280440 original size:24 final size:25
Alignment explanation
Indices: 1280387--1280447 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1280377 CTAATTACTT
* *
1280387 TTTTAAATTTATATTTAATTTTATG
1 TTTTAAATTTATATTTAATTATATA
* *
1280412 CTTTAATTTTAT-TTTAATTATATA
1 TTTTAAATTTATATTTAATTATATA
1280436 TTTTAAAATTTA
1 TTTT-AAATTTA
1280448 ATAATATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTAAATTTATATTTAATTATATA
Found at i:1283169 original size:18 final size:18
Alignment explanation
Indices: 1283142--1283176 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1283132 TGTTCGTCAA
*
1283142 ATTTTGTTATTGATTTGG
1 ATTTTGTTATTCATTTGG
*
1283160 ATTTTTTTATTCATTTG
1 ATTTTGTTATTCATTTG
1283177 CTGTGCAGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.03, G:0.14, T:0.66
Consensus pattern (18 bp):
ATTTTGTTATTCATTTGG
Found at i:1298123 original size:18 final size:19
Alignment explanation
Indices: 1298100--1298144 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
1298090 ATTTGGAACT
*
1298100 GATACT-CATAGGAGTATC
1 GATACTCCATAGAAGTATC
1298118 GATACTCCCCATAGAAGTATC
1 GATACT--CCATAGAAGTATC
1298139 GATACT
1 GATACT
1298145 GAGCCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
21 17 0.74
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (19 bp):
GATACTCCATAGAAGTATC
Found at i:1298218 original size:20 final size:20
Alignment explanation
Indices: 1298178--1298245 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
1298168 GCTATTTTAG
* *
1298178 GTATCGATACTC--TGGTGA
1 GTATCGATACCCAATGGTCA
1298196 GTATCGATACCCAATGGTCA
1 GTATCGATACCCAATGGTCA
1298216 GTATCGATACCCAATGGTCA
1 GTATCGATACCCAATGGTCA
*
1298236 GTATCAATAC
1 GTATCGATAC
1298246 TACTGACATA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 11 0.24
20 34 0.76
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCAATGGTCA
Found at i:1298869 original size:20 final size:21
Alignment explanation
Indices: 1298844--1298883 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1298834 CTTTATATAG
*
1298844 TAGTATCGATACCAT-AGGCT
1 TAGTATCAATACCATCAGGCT
1298864 TAGTATCAATACCATCAGGC
1 TAGTATCAATACCATCAGGC
1298884 CCAATGGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (21 bp):
TAGTATCAATACCATCAGGCT
Found at i:1302767 original size:14 final size:14
Alignment explanation
Indices: 1302748--1302800 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
1302738 TCGCTTATAT
1302748 GTTCATTTATGTTC
1 GTTCATTTATGTTC
1302762 GTTCATTTA---T-
1 GTTCATTTATGTTC
*
1302772 GTTCATTTATGTTT
1 GTTCATTTATGTTC
1302786 GTTCATTTATGTTC
1 GTTCATTTATGTTC
1302800 G
1 G
1302801 AACAGAGGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.15, C:0.11, G:0.15, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:1302777 original size:24 final size:24
Alignment explanation
Indices: 1302745--1302799 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
1302735 CGTTCGCTTA
1302745 TATGTTCATTTATGTTCGTTCATT
1 TATGTTCATTTATGTTCGTTCATT
*
1302769 TATGTTCATTTATGTTTGTTCATT
1 TATGTTCATTTATGTTCGTTCATT
1302793 TATGTTC
1 TATGTTC
1302800 GAACAGAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.11, G:0.13, T:0.60
Consensus pattern (24 bp):
TATGTTCATTTATGTTCGTTCATT
Found at i:1303236 original size:16 final size:16
Alignment explanation
Indices: 1303211--1303251 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1303201 CAAAAAAAAT
1303211 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
1303227 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
1303243 T-TT-ATTTAT
1 TGTTCATTTAT
1303252 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:1304666 original size:10 final size:10
Alignment explanation
Indices: 1304651--1304675 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1304641 TTATTCAATG
1304651 ATTGATGAAA
1 ATTGATGAAA
1304661 ATTGATGAAA
1 ATTGATGAAA
1304671 ATTGA
1 ATTGA
1304676 GGCAAACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (10 bp):
ATTGATGAAA
Found at i:1304784 original size:11 final size:11
Alignment explanation
Indices: 1304768--1304809 Score: 84
Period size: 11 Copynumber: 3.8 Consensus size: 11
1304758 TATTCTACTT
1304768 TTTTTTTCAAA
1 TTTTTTTCAAA
1304779 TTTTTTTCAAA
1 TTTTTTTCAAA
1304790 TTTTTTTCAAA
1 TTTTTTTCAAA
1304801 TTTTTTTCA
1 TTTTTTTCA
1304810 TTAAATCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:1309385 original size:31 final size:29
Alignment explanation
Indices: 1309322--1309385 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 29
1309312 AAAATGCGGG
*
1309322 AAAATTAAAGTGCAGAAAAATAAAATACT
1 AAAATTAAAGTGCAGAAAAATAAAATAAT
1309351 AAAATTTAAAGTGCAGGAAAAAT-AAATAAAT
1 AAAA-TTAAAGTGCA-GAAAAATAAAAT-AAT
1309382 AAAA
1 AAAA
1309386 AAGGAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 14 0.45
31 13 0.42
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (29 bp):
AAAATTAAAGTGCAGAAAAATAAAATAAT
Found at i:1309744 original size:120 final size:122
Alignment explanation
Indices: 1309596--1309886 Score: 385
Period size: 120 Copynumber: 2.4 Consensus size: 122
1309586 CGTAAGTTAG
* * * *
1309596 AAAAGTTAGTTGTTAGCAGAGTTCGAACCATAATAATGTCGATCTTACCCCAGATTAGGTCAAC-
1 AAAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCAGATCAGGTC-ACT
* *
1309660 ACAAGATTGAATCGAATAATGCAAAA-AATGTATAAAAATAAAATTAAA-TAAAAT-AA-
65 ACAAGATCGAATCGAATAATG-AAAACAATATATAAAAATAAAA-TAAATTAAAATAAAT
* *
1309716 AAAAGTTAGTGGTTAGCGGAGTCCGAACCATAATAATGTGGATCTTACCCCAGATCGGGTCACTA
1 AAAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCAGATCAGGTCACTA
* *
1309781 CAAGGTCGAATCGAATAATGAAAACGAATATATAAAAATAAAATAAATTAAATTAAATT
66 CAAGATCGAATCGAATAATGAAAAC-AATATATAAAAATAAAATAAATTAAAATAAA-T
* * *
1309840 AAAAGTTAGTGGTTAACAGAGTCCGAACTATAATAATATGGATCTTA
1 AAAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTA
1309887 TCTAGGATTT
Statistics
Matches: 150, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
119 6 0.04
120 78 0.52
121 21 0.14
122 2 0.01
124 43 0.29
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (122 bp):
AAAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCAGATCAGGTCACTA
CAAGATCGAATCGAATAATGAAAACAATATATAAAAATAAAATAAATTAAAATAAAT
Found at i:1319566 original size:156 final size:156
Alignment explanation
Indices: 1319280--1319566 Score: 385
Period size: 156 Copynumber: 1.8 Consensus size: 156
1319270 TTTCCGTAAA
**
1319280 CAAATATGTTATTCTAATTTATTGGGACTTTATTTTTAGTGGAAGCAAGGTCGTTAAGCTTTGAG
1 CAAATATGTTATTCTAATTTATTGGGACTTTATTTTTAGTGGAAGCAAGGTCGTTAAGCTTCAAG
* * * * * * * * *
1319345 CTCCCGAGTACAGTCTGATGCCTCTCTTGGGCAAGAAAGCACTCTATTTTGTCTGGTTAAGGAGA
66 CTCCCGAGTACAATATGAAGCCTCTCTTGGACAAGAAAACACCCTATTTTGGCTGGTCAAAGAGA
1319410 AAGATTGTTAAACACTTGACTCTACC
131 AAGATTGTTAAACACTTGACTCTACC
* * * * * * *
1319436 CAAATATTTTCTTCTCATTTATTGGGACTTTCTTTTTGGTGGAATCAAGGTTGTTAAGCTTCAAG
1 CAAATATGTTATTCTAATTTATTGGGACTTTATTTTTAGTGGAAGCAAGGTCGTTAAGCTTCAAG
** *
1319501 CTCCCGAGTGTAATATGAAGTCTCTCTTGGACAAGAAAACACCCTATTTTGGCTGGTCAAAGAGA
66 CTCCCGAGTACAATATGAAGCCTCTCTTGGACAAGAAAACACCCTATTTTGGCTGGTCAAAGAGA
1319566 A
131 A
1319567 CAAGACTGTT
Statistics
Matches: 110, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
156 110 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (156 bp):
CAAATATGTTATTCTAATTTATTGGGACTTTATTTTTAGTGGAAGCAAGGTCGTTAAGCTTCAAG
CTCCCGAGTACAATATGAAGCCTCTCTTGGACAAGAAAACACCCTATTTTGGCTGGTCAAAGAGA
AAGATTGTTAAACACTTGACTCTACC
Found at i:1324999 original size:66 final size:66
Alignment explanation
Indices: 1324888--1325012 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 66
1324878 CTTGAACTCA
* * *** *
1324888 AAATAAAAAATTGAAACTTGACTCGACTAAAAAGCTCATGCGCTTAAAACTTTCAAGTTGAACAT
1 AAATAAAAAATTGAAACTCGACTCGACTAAAAAGATCACAAGCTTAAAAATTTCAAGTTGAACAT
1324953 G
66 G
* * *
1324954 AAATAAAAAATT-AAAGCTCGACTCGACTCAAAATATCACAAGCTTAAAAATTTTAAGTT
1 AAATAAAAAATTGAAA-CTCGACTCGACTAAAAAGATCACAAGCTTAAAAATTTCAAGTT
1325013 TGACTTCGAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 3 0.06
66 46 0.94
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.26
Consensus pattern (66 bp):
AAATAAAAAATTGAAACTCGACTCGACTAAAAAGATCACAAGCTTAAAAATTTCAAGTTGAACAT
G
Found at i:1325716 original size:24 final size:24
Alignment explanation
Indices: 1325684--1325729 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1325674 TTTTAACAAG
1325684 TTAAAAAATATTTATATATTTTCT
1 TTAAAAAATATTTATATATTTTCT
1325708 TTAAAAAATATTTATATATTTT
1 TTAAAAAATATTTATATATTTT
1325730 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAAAAAATATTTATATATTTTCT
Found at i:1325736 original size:24 final size:24
Alignment explanation
Indices: 1325685--1325739 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1325675 TTTAACAAGT
***
1325685 TAAAAAATATTTATATATTTTCTT
1 TAAAAAATATTTATATATTTTAAA
1325709 TAAAAAATATTTATATATTTTAAA
1 TAAAAAATATTTATATATTTTAAA
1325733 TAAAAAA
1 TAAAAAA
1325740 ATTAAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TAAAAAATATTTATATATTTTAAA
Found at i:1327080 original size:61 final size:61
Alignment explanation
Indices: 1327015--1327134 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
1327005 GGGAATCGTG
* * * * *
1327015 TTCTGAAATATGTGTTATATGATTCATAGAGATTTTCTATAGACAGTGAATTTTATAGTAA
1 TTCTGAAATATATGCTATATGATCCATAGAGATTTTCTATAGACAGAGAAATTTATAGTAA
* * *
1327076 TTCTGAAGTATATGCTATATGATCCATGGAGATTTTCTATAGATAGAGAAATTTATAGT
1 TTCTGAAATATATGCTATATGATCCATAGAGATTTTCTATAGACAGAGAAATTTATAGT
1327135 TGGGGGTTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (61 bp):
TTCTGAAATATATGCTATATGATCCATAGAGATTTTCTATAGACAGAGAAATTTATAGTAA
Found at i:1327268 original size:107 final size:107
Alignment explanation
Indices: 1327079--1327346 Score: 421
Period size: 107 Copynumber: 2.5 Consensus size: 107
1327069 ATAGTAATTC
* * *
1327079 TGAAGTATATGCTATATGATCCATGGAGATTTTCTATAGATAGAGAAATTTATAGTTGGGGGTTA
1 TGAAGTATATGCTATATGATCCATGGAGATTTTCTATAGACAGTGAAATTTATAGTTAGGGGTTA
* * *
1327144 ATTAACTCTAATTTGACATT-AGGGTCAGAGGGAATCGAGTTA
66 ATTAACTCTAATCTGACATTGA-GGTCAAAGGGAATCCAGTTA
*
1327186 TGAAGTATATGCTATATGATCCATGGAGATTTCCTATAGACAGTGAAATTTATAGTTAGGGGTTA
1 TGAAGTATATGCTATATGATCCATGGAGATTTTCTATAGACAGTGAAATTTATAGTTAGGGGTTA
*
1327251 ATTAACTCTAATCTGACATTGAGGTCAAAGGGAATCCAGTTC
66 ATTAACTCTAATCTGACATTGAGGTCAAAGGGAATCCAGTTA
* * *
1327293 TGAAGTATATGCTATATGATCTATAGAGATTTTCTATACACAGTGAAATTTATA
1 TGAAGTATATGCTATATGATCCATGGAGATTTTCTATAGACAGTGAAATTTATA
1327347 CTTGGAGATT
Statistics
Matches: 148, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
107 147 0.99
108 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (107 bp):
TGAAGTATATGCTATATGATCCATGGAGATTTTCTATAGACAGTGAAATTTATAGTTAGGGGTTA
ATTAACTCTAATCTGACATTGAGGTCAAAGGGAATCCAGTTA
Found at i:1330116 original size:27 final size:29
Alignment explanation
Indices: 1330085--1330159 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 29
1330075 TTCCTTTCTT
*
1330085 TATTTATTTATTTTAAATT-T-TATGTTC
1 TATTTATTTATTTTAAATTATATATGTTA
* * *
1330112 TATTTATTTGTTTAAAATTATATATTTTA
1 TATTTATTTATTTTAAATTATATATGTTA
*
1330141 TATTCATTTA-TTTAAATTA
1 TATTTATTTATTTTAAATTA
1330160 AATTAATATG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 17 0.44
28 9 0.23
29 13 0.33
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (29 bp):
TATTTATTTATTTTAAATTATATATGTTA
Found at i:1330161 original size:34 final size:32
Alignment explanation
Indices: 1330083--1330168 Score: 77
Period size: 33 Copynumber: 2.7 Consensus size: 32
1330073 ATTTCCTTTC
* ** *
1330083 TTTATTTATTTATTTTAA-ATTTTATGTTCTA
1 TTTATTTAATTAAATTAATATTTTATATTCTA
**
1330114 TTTATTTGTTTAAAATTATATATTTTATATTC-A
1 TTTATTTAATT-AAATTA-ATATTTTATATTCTA
1330147 TTTATTTAAATTAAATTAATAT
1 TTTATTT-AATTAAATTAATAT
1330169 GTTCTTGATA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 10 0.22
32 8 0.18
33 15 0.33
34 12 0.27
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (32 bp):
TTTATTTAATTAAATTAATATTTTATATTCTA
Found at i:1330535 original size:25 final size:25
Alignment explanation
Indices: 1330470--1330526 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
1330460 TTTCAAGTTT
*
1330470 GACTCAAAATAAAAAACTGAAGCTC
1 GACTCAAAATCAAAAACTGAAGCTC
*
1330495 GACTCAAAATCAAAAACTGAAGCTT
1 GACTCAAAATCAAAAACTGAAGCTC
1330520 GACTCAA
1 GACTCAA
1330527 GCTTGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.49, C:0.21, G:0.12, T:0.18
Consensus pattern (25 bp):
GACTCAAAATCAAAAACTGAAGCTC
Found at i:1331099 original size:2 final size:2
Alignment explanation
Indices: 1331092--1331127 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1331082 TATCTTTGAG
1331092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1331128 TACAAGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1332702 original size:51 final size:52
Alignment explanation
Indices: 1332642--1332739 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 52
1332632 AAAAGACTCA
* * *
1332642 ACAATTGTTGTTAAGTTTAATTTGACACGAGTGATTAAAAT-AAAATCCCAC
1 ACAATTGTTGTCAAGTTTAATTTAACACGAATGATTAAAATGAAAATCCCAC
*
1332693 ACAATTGTTGTCATGTTTAATTTAACACGAATGATTAAAATGAAAAT
1 ACAATTGTTGTCAAGTTTAATTTAACACGAATGATTAAAATGAAAAT
1332740 AAAATCTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 37 0.88
52 5 0.12
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (52 bp):
ACAATTGTTGTCAAGTTTAATTTAACACGAATGATTAAAATGAAAATCCCAC
Found at i:1333710 original size:2 final size:2
Alignment explanation
Indices: 1333703--1333767 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1333693 TTTTGAGGAT
1333703 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
1333745 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1333768 TCACTAGAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1335601 original size:2 final size:2
Alignment explanation
Indices: 1335594--1335625 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1335584 TTACATATGT
1335594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1335626 TTAAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1341067 original size:43 final size:43
Alignment explanation
Indices: 1340912--1341067 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 43
1340902 CAGAGCCAAT
1340912 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
* * *** ** * * * *
1340955 TTCAACTTCACGACGAGGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGA-AGGA-TATTGG-ACTC--CAGACAA---CACAAG
*
1341006 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
*
1341049 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
1341068 GACCGCTGGT
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
43 37 0.45
44 3 0.04
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 19 0.23
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
Found at i:1341070 original size:94 final size:94
Alignment explanation
Indices: 1340801--1341775 Score: 1272
Period size: 94 Copynumber: 10.0 Consensus size: 94
1340791 AATTTTAGAG
* * *
1340801 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
**
1340866 GGGACTACTGGTTGTCAACAAACAACTTCTCAATTTC
66 GGGACCGCTGGTTGTCAAC--A-AA-----CAATTTC
* *
1340903 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
1340968 CGAGGGGACCGCTGGTTGTCAATAAACAATTTC
62 CGAAGGGACCGCTGGTTGTCAACAAACAATTTC
*
1341001 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1341066 GGGACCGCTGGTTGTCAATAAACAATTTTCC
66 GGGACCGCTGGTTGTCAACAAACAA-TTT-C
1341097 AATTCTAGAGTCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACT
1 ----C------CAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACT
1341162 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTC
56 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTC
* * *
1341201 CAAATTTCAACTTCACAACGAATGACATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1341266 GGGACCGCTGGTTGTCAACAAACAATTTC
66 GGGACCGCTGGTTGTCAACAAACAATTTC
1341295 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1341360 GGGACCGCTGGTTGTCAAAAAACAATTTC
66 GGGACCGCTGGTTGTCAACAAACAATTTC
*
1341389 CCAATTTCAACTTCACAACGAAGGGCATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1341454 GGGACCGCTGGTTGTCAACAAATAATTTC
66 GGGACCGCTGGTTGTCAACAAACAATTTC
1341483 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
**
1341548 GGGACCGCTGGTTGTCAACAAACAATTAG
66 GGGACCGCTGGTTGTCAACAAACAATTTC
* * * * *
1341577 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCGC-AGCGA
1 CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGA-CGA
* *
1341641 AGTGG-CGGCTGACTT-TCAACAAACAACTTCCCAATTTC
65 AG-GGACCGCTG-GTTGTCAAC--A-AA-----CAATTTC
* * * * *
1341679 AGAGCCAATTTTAACTTCACAATGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACAA
1 ----CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
1341744 CGAAGGGACCGCTGATTTTCAATAAACAATTT
62 CGAAGGGACCGCTGGTTGTCAACAAACAATTT
1341776 TCCAGTTCCA
Statistics
Matches: 795, Mismatches: 44, Indels: 68
0.88 0.05 0.07
Matches are distributed among these distances:
93 1 0.00
94 518 0.65
95 7 0.01
96 2 0.00
97 2 0.00
98 13 0.02
100 2 0.00
102 5 0.01
103 4 0.01
104 3 0.00
105 7 0.01
106 230 0.29
107 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (94 bp):
CCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACAAACAATTTC
Found at i:1341144 original size:200 final size:198
Alignment explanation
Indices: 1340801--1341775 Score: 1361
Period size: 200 Copynumber: 5.0 Consensus size: 198
1340791 AATTTTAGAG
* *
1340801 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
** *
1340866 GGGACTACTGGTTGTCAACAAACAACTTCTCAATT-TCAGAGCCAATTTCAACTTCACAACGAAG
66 GGGACCGCTGGTTGTCAACAAACAATTTC-CAATTCT-AGAG-CAATTTCAACTTCACAACGAAG
* * * *
1340930 GATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAGGGGACCGCTGGTTGTCAATAAAC
128 GACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
1340995 AATTTC
193 AATTTC
1341001 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1341066 GGGACCGCTGGTTGTCAATAAACAATTTTCCAATTCTAGAGTCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAACAAACAA-TTTCCAATTCTAGAG-CAATTTCAACTTCACAACGAAGG
1341131 ACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
129 ACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
1341196 ATTTC
194 ATTTC
* * * *
1341201 CAAATTTCAACTTCACAACGAATGACATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1341266 GGGACCGCTGGTTGTCAACAAACAATTT-C----C-----CAATTTCAACTTCACAACGAAGGAC
66 GGGACCGCTGGTTGTCAACAAACAATTTCCAATTCTAGAGCAATTTCAACTTCACAACGAAGGAC
*
1341321 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAAT
131 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAT
1341386 TTC
196 TTC
**
1341389 CCAATTTCAACTTCACAACGAAGGGCATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1341454 GGGACCGCTGGTTGTCAACAAATAATTT-C----C-----CAATTTCAACTTCACAACGAAGGAC
66 GGGACCGCTGGTTGTCAACAAACAATTTCCAATTCTAGAGCAATTTCAACTTCACAACGAAGGAC
1341509 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAT
131 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAT
**
1341574 TAG
196 TTC
* * * *
1341577 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCGC-AGCGA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA-CGA
* * * * *
1341641 AGTGG-CGGCTGACTT-TCAACAAACAACTTCCCAATT-TCAGAGCCAATTTTAACTTCACAATG
65 AG-GGACCGCTG-GTTGTCAACAAACAA-TTTCCAATTCT-AGAG-CAATTTCAACTTCACAACG
* * * * * *
1341703 AAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGATTTTCAATA
125 AAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
1341768 AACAATTT
190 AACAATTT
1341776 TCCAGTTCCA
Statistics
Matches: 713, Mismatches: 44, Indels: 36
0.90 0.06 0.05
Matches are distributed among these distances:
187 1 0.00
188 345 0.48
189 6 0.01
190 1 0.00
194 1 0.00
198 1 0.00
199 3 0.00
200 351 0.49
201 4 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (198 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACAAACAATTTCCAATTCTAGAGCAATTTCAACTTCACAACGAAGGAC
ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAT
TTC
Found at i:1342243 original size:84 final size:83
Alignment explanation
Indices: 1342013--1342470 Score: 501
Period size: 84 Copynumber: 5.5 Consensus size: 83
1342003 AGAAGGAGTG
* * * * * *
1342013 TCTGCCAACAAAAAACCTTTGAGTTCGACTACGCTCAGCT-CAATGGCACATCATTTACAGCATA
1 TCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGTATA
* *
1342077 GCTTAAGTCGAGAAGGGCTA
64 ACTTAAGTCGAGAAGGGTTA
** * * * * * * *
1342097 TCTG---CCAAAGACCCCCGAGTTTGATTGCACTCAGCTTCGAGGGCATATCATTTACAGTATAA
1 TCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGTATAA
* * *
1342159 CTCAAGGCTAGAAGGGTTA
65 CTTAAGTCGAGAAGGGTTA
* ** * *
1342178 TTTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCATATCATTTGCAGCATAA
1 TCTGCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAA
1342243 CTTAAGTCGAGAAGGGTTA
65 CTTAAGTCGAGAAGGGTTA
* *
1342262 TCTGCCAACCAAAGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAA
1 TCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAA
* *
1342327 CTTAAGTCTAGAAGGGTTG
65 CTTAAGTCGAGAAGGGTTA
** * *
1342346 TCTGCCAAGAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGACATATCATTTGCAGTATAA
1 TCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAA
1342411 CTTAAGTCGAGAAGGGTTA
65 CTTAAGTCGAGAAGGGTTA
* * *
1342430 TCTGCCAACCGAAGACCTTCGAGTTCGATTACACTCAGCTC
1 TCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1342471 AGAGGCAAAC
Statistics
Matches: 312, Mismatches: 55, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
80 22 0.07
81 37 0.12
82 1 0.00
84 226 0.72
85 26 0.08
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
TCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAAC
TTAAGTCGAGAAGGGTTA
Found at i:1342383 original size:168 final size:168
Alignment explanation
Indices: 1342003--1342470 Score: 606
Period size: 168 Copynumber: 2.8 Consensus size: 168
1341993 TCCAACTCAA
* *
1342003 AGAAGGAG-TGTCTGCCAACAAAAAACCTTTGAGTTCGACTACGCTCAGCT-CAATGGCACATCA
1 AGAAGG-GTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCATATCA
* * * ** * *
1342066 TTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTTGATTGCAC
64 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACAC
* * *
1342127 TCAGCTTCGAGGGCATATCATTTACAGTATAACTCAAGGCT
129 TCAGC-TCCAAGGCATATCATTTACAGTACAACTCAAGGCT
* * ** * * *
1342168 AGAAGGGTTATTTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
* * *
1342233 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAATTCGACTACGCTC
66 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTC
* * *
1342298 AGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCT
131 AGCTCCAAGGCATATCATTTACAGTACAACTCAAGGCT
* *
1342336 AGAAGGGTTGTCTGCCAAGAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGACATATCATT
1 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
* *
1342401 TGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCGAAGACCTTCGAGTTCGATTACACTC
66 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTC
1342466 AGCTC
131 AGCTC
1342471 AGAGGCAAAC
Statistics
Matches: 258, Mismatches: 39, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
164 1 0.00
165 80 0.31
166 3 0.01
168 150 0.58
169 24 0.09
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (168 bp):
AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTC
AGCTCCAAGGCATATCATTTACAGTACAACTCAAGGCT
Found at i:1355456 original size:27 final size:26
Alignment explanation
Indices: 1355403--1355458 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
1355393 TTTGATAATT
*
1355403 TTAAAAATTTTATTTAAAATCAAATAA
1 TTAAAAATTATATTTAAAA-CAAATAA
1355430 TTAAAAATTATATTTTAAAA-AACATAA
1 TTAAAAATTATA-TTTAAAACAA-ATAA
1355457 TT
1 TT
1355459 TTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 17 0.65
28 7 0.27
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAAAAATTATATTTAAAACAAATAA
Found at i:1368981 original size:28 final size:28
Alignment explanation
Indices: 1368934--1369003 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
1368924 GCCAACCTGG
* * * **
1368934 AACATATTACCTCCTTAAATTAACTTGA
1 AACACATTACCTTCTCAAATTAACCAGA
1368962 AACACATTACCTTCTCAAATTAACCAGA
1 AACACATTACCTTCTCAAATTAACCAGA
1368990 AACACATTACCTTC
1 AACACATTACCTTC
1369004 CCTAAATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (28 bp):
AACACATTACCTTCTCAAATTAACCAGA
Found at i:1373910 original size:17 final size:17
Alignment explanation
Indices: 1373888--1373927 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1373878 CGAAGTGTAG
* *
1373888 GTGCCCACCTGAGGGGA
1 GTGCCCACATGAGAGGA
*
1373905 GTGCCCACATGATAGGA
1 GTGCCCACATGAGAGGA
1373922 GTGCCC
1 GTGCCC
1373928 TATGGCCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.35, T:0.15
Consensus pattern (17 bp):
GTGCCCACATGAGAGGA
Found at i:1381045 original size:20 final size:20
Alignment explanation
Indices: 1381020--1381059 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1381010 TTTGTTAGTT
*
1381020 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
1381040 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
1381060 TTCTGTTGTT
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:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1387447 original size:23 final size:22
Alignment explanation
Indices: 1387421--1387465 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1387411 TTATTTATTG
1387421 TATTTTAA-AATATTAAAATAATA
1 TATTTTAATAATA-TAAAA-AATA
1387444 TATTTTAATAATATAAAAAATA
1 TATTTTAATAATATAAAAAATA
1387466 AAAATCCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTTTAATAATATAAAAAATA
Found at i:1389902 original size:29 final size:29
Alignment explanation
Indices: 1389866--1389933 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1389856 CATTTTACAC
* *
1389866 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
* *
1389895 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
*
1389924 GAATAGCACC
1 AAATAGCACC
1389934 AAAACCAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:1389954 original size:30 final size:29
Alignment explanation
Indices: 1389912--1389992 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 29
1389902 ACCCATTTCG
*
1389912 AATTAATTACCAGAATAGCACCAAAACCA
1 AATTATTTACCAGAATAGCACCAAAACCA
* * ***
1389941 AATTTATTTACCAGAATAACACTAAAATTG
1 AA-TTATTTACCAGAATAGCACCAAAACCA
*
1389971 AATTATTTACCATAATAGCACC
1 AATTATTTACCAGAATAGCACC
1389993 GGTCAACGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 19 0.45
30 23 0.55
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (29 bp):
AATTATTTACCAGAATAGCACCAAAACCA
Found at i:1397283 original size:29 final size:29
Alignment explanation
Indices: 1397247--1397314 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1397237 CATTTTACAC
*
1397247 AAATAGCATCC-TTTCTAAAATAATTACCA
1 AAATAGCACCCATTTC-AAAATAATTACCA
* *
1397276 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
*
1397305 GAATAGCACC
1 AAATAGCACC
1397315 AAAACTGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:1397324 original size:29 final size:29
Alignment explanation
Indices: 1397291--1397372 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1397281 GCACCCATTT
*
1397291 CGAATTAATTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
1397320 TGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
1397349 CGAATTATTTACCAGAATATCACC
1 CGAATTATTTACCAGAATAGCACC
1397373 TGTCAACGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:1397412 original size:18 final size:18
Alignment explanation
Indices: 1397380--1397426 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1397370 ACCTGTCAAC
*
1397380 GGTCAAC-GATCGGGTCG
1 GGTCAACGGGTCGGGTCG
1397397 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1397415 GGTCAACGGGTC
1 GGTCAACGGGTC
1397427 AGGTTGTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1401501 original size:2 final size:2
Alignment explanation
Indices: 1401494--1401538 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1401484 GGATCATTTG
1401494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1401536 AT A
1 AT A
1401539 ATTTTGCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1401738 original size:27 final size:27
Alignment explanation
Indices: 1401703--1401761 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
1401693 TATATTATTC
1401703 TATACAAAAACAATAAAT-TAATAATATAT
1 TATA-AAAAA-AATAAATCTAA-AATATAT
*
1401732 TATAAAAAAAATAAATCTAAAATATTT
1 TATAAAAAAAATAAATCTAAAATATAT
1401759 TAT
1 TAT
1401762 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 16 0.57
28 8 0.29
29 4 0.14
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (27 bp):
TATAAAAAAAATAAATCTAAAATATAT
Found at i:1404016 original size:26 final size:25
Alignment explanation
Indices: 1403985--1404044 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
1403975 AGTAAAATAA
1403985 TAATAATTAATT-ATTTATTAGAAAAT
1 TAATAATT-ATTCATTT-TTAGAAAAT
*
1404011 TAATAAATTATTCATTTTTAGTAAAT
1 TAAT-AATTATTCATTTTTAGAAAAT
*
1404037 TAGTAATT
1 TAATAATT
1404045 TTTAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 4 0.13
26 18 0.60
27 8 0.27
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
TAATAATTATTCATTTTTAGAAAAT
Found at i:1404037 original size:18 final size:18
Alignment explanation
Indices: 1404014--1404048 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1404004 AGAAAATTAA
* *
1404014 TAAATTATTCATTTTTAG
1 TAAATTAGTAATTTTTAG
1404032 TAAATTAGTAATTTTTA
1 TAAATTAGTAATTTTTA
1404049 ATGAAATGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (18 bp):
TAAATTAGTAATTTTTAG
Found at i:1407161 original size:2 final size:2
Alignment explanation
Indices: 1407154--1407200 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1407144 ATTTAAACAA
* * *
1407154 AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1407196 AT AT A
1 AT AT A
1407201 AGACTAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1407199 original size:16 final size:16
Alignment explanation
Indices: 1407156--1407200 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1407146 TTAAACAAAT
*
1407156 ATATATATATACATAC
1 ATATATATATATATAC
1407172 ATATATATATATATAC
1 ATATATATATATATAC
1407188 ATATATATATATA
1 ATATATATATATA
1407201 AGACTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATATATATAC
Found at i:1409546 original size:113 final size:112
Alignment explanation
Indices: 1409290--1409847 Score: 646
Period size: 113 Copynumber: 4.9 Consensus size: 112
1409280 TTAAGGCAAT
* *
1409290 GTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* * * ** *
1409354 ACACT-TCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGAT-AGAGTCAAAC-AAAG
66 ACTCTACCTGG--A-----ATGTTGATCCA--T-C--GAGTGATGA-ATTCAAACAAAAG
*
1409411 GTTGAACAAATTCTTCTTATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* * *
1409475 ACTCTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAA
66 ACTCTAC-CTGG-AATGTTGATCCATCGAGTGATGAATTCAAACAAAAG
* * *
1409524 GTTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* *
1409589 ACTCTACCTGGTAATGTTGATCCATCAAATGATGAATTCAAACAAAAG
66 ACTCTACCTGG-AATGTTGATCCATCGAGTGATGAATTCAAACAAAAG
* *
1409637 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATAAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* *
1409702 ACT-TTCTCTGGCAATGTTAATCCATCTG-GTGATGAATT-AAAGCAAAAG
66 ACTCTAC-CTGG-AATGTTGATCCATC-GAGTGATGAATTCAAA-CAAAAG
* * *
1409750 GTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* *
1409815 ACTCTACCTGGCATGTTGATCCATTGAGTGATG
66 ACTCTACCTGGAATGTTGATCCATCGAGTGATG
1409848 GATTTGAATC
Statistics
Matches: 388, Mismatches: 38, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
111 1 0.00
112 34 0.09
113 236 0.61
114 37 0.10
115 1 0.00
117 9 0.02
121 63 0.16
122 3 0.01
123 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (112 bp):
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
ACTCTACCTGGAATGTTGATCCATCGAGTGATGAATTCAAACAAAAG
Found at i:1409667 original size:226 final size:227
Alignment explanation
Indices: 1409290--1409838 Score: 745
Period size: 226 Copynumber: 2.4 Consensus size: 227
1409280 TTAAGGCAAT
1409290 GTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG-
** * * * ***
1409354 ACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAAACAAAGGTTGAACA
65 A-AC-TCT--ACCTGGTAATGTTGATCCA--TCCAAATGTGA-AGAGTCAAACAAAGGTTGAACA
*
1409419 AATTCTTCTTATTATGAACTTCTTCTTC-TTCTTCAGATAAGTTCTTCTCATTATGAACTCTTCT
123 AATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATAAGTTCTTCTCATTATGAACT-TTCT
*
1409483 CTGGAAAAGTTGATCCATC-GAGTGATGAATTCAAA-CAAAAA
187 CTGGAAAAGTTAATCCATCTG-GTGATGAATT-AAAGCAAAAA
*
1409524 GTTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
1409589 ACTCTACCTGGTAATGTTGATCCAT-CAAATGATG-A-ATTCAAACAAAAGGTTGAACAAGTTCT
66 ACTCTACCTGGTAATGTTGATCCATCCAAATG-TGAAGAGTCAAAC-AAAGGTTGAACAAATTCT
*
1409651 TCTCATTATGAACTTCTTCTTCATTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGCAA
129 TCTCATTATGAACTTCTTCTTCATTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
* *
1409716 TGTTAATCCATCTGGTGATGAATTAAAGCAAAAG
194 AGTTAATCCATCTGGTGATGAATTAAAGCAAAAA
* * *
1409750 GTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
1409815 ACTCTACCTGG-CATGTTGATCCAT
66 ACTCTACCTGGTAATGTTGATCCAT
1409839 TGAGTGATGG
Statistics
Matches: 288, Mismatches: 21, Indels: 21
0.87 0.06 0.06
Matches are distributed among these distances:
225 22 0.08
226 146 0.51
227 35 0.12
228 3 0.01
230 14 0.05
232 3 0.01
233 2 0.01
234 33 0.11
235 30 0.10
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (227 bp):
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTCTACCTGGTAATGTTGATCCATCCAAATGTGAAGAGTCAAACAAAGGTTGAACAAATTCTTC
TCATTATGAACTTCTTCTTCATTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
TTAATCCATCTGGTGATGAATTAAAGCAAAAA
Found at i:1414320 original size:72 final size:73
Alignment explanation
Indices: 1414150--1414350 Score: 262
Period size: 72 Copynumber: 2.7 Consensus size: 73
1414140 TAATTGAAAC
* * * *
1414150 TTATCCATAAAGCCGGGGCGATTAATCAATTGCTCTAGAGGGACAATTTTATTGCATATAATAGG
1 TTATCCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGACAA-CTTA-AGCATATAATA-G
* *
1414215 TTAGCTTAATA
63 CTAGCTGAATA
* *
1414226 TTATCCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGATAACTCAAGCATAATAA-A-CT
1 TTATCCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGACAACTTAAGCAT-ATAATAGCT
1414289 AGCTGAATA
65 AGCTGAATA
* *
1414298 TTATCCATAAAGCCGGGGCTATTAACCAATTGCTTTAGGGGGACAACTTAAGC
1 TTATCCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGACAACTTAAGC
1414351 TTTATTGTAT
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
72 58 0.52
74 5 0.04
75 6 0.05
76 43 0.38
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (73 bp):
TTATCCATAAAGCCGGGGCTATTAACCAATTGCTCTAGAGGGACAACTTAAGCATATAATAGCTA
GCTGAATA
Found at i:1417397 original size:43 final size:45
Alignment explanation
Indices: 1417310--1417399 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 45
1417300 TTTCCATGCA
* *
1417310 TCAAGCAAAACTTTTACATGCAGGGGAAAACTTTCAGTCATAACT
1 TCAAGCAAAACTTTTACATACAGGGGAAAACTTTCACTCATAACT
* * * *
1417355 TCAA-CAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACT
1 TCAAGCAAAACTTTTACATACAGGGGAAAACTTTCACTCATAACT
1417398 TC
1 TC
1417400 TCTAAAGCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 29 0.74
44 6 0.15
45 4 0.10
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (45 bp):
TCAAGCAAAACTTTTACATACAGGGGAAAACTTTCACTCATAACT
Found at i:1418851 original size:28 final size:29
Alignment explanation
Indices: 1418819--1418891 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
1418809 AATAATGTAC
*
1418819 ATATAAATATTATGAAAATAAA-AAGTAT
1 ATATAAATATTATGAAAAGAAAGAAGTAT
* * *
1418847 ATATAAAAATTTTGAAAAGAAAGAATTAT
1 ATATAAATATTATGAAAAGAAAGAAGTAT
*
1418876 AAATTAAATA-TATGAA
1 ATA-TAAATATTATGAA
1418892 TTTTTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 19 0.53
29 12 0.33
30 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (29 bp):
ATATAAATATTATGAAAAGAAAGAAGTAT
Found at i:1419841 original size:27 final size:28
Alignment explanation
Indices: 1419811--1419867 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
1419801 GTATTAAAAG
* *
1419811 TAAT-AATAAAATAATATTACAAATA-AA
1 TAATGAAT-AAATAAAATTAAAAATATAA
1419838 TAATGAATAAATAAAATTAAAAATATAA
1 TAATGAATAAATAAAATTAAAAATATAA
1419866 TA
1 TA
1419868 TAAACACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
TAATGAATAAATAAAATTAAAAATATAA
Found at i:1419850 original size:24 final size:23
Alignment explanation
Indices: 1419786--1419850 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
1419776 AAACAATAAT
1419786 TAAATAATAATTAAAGTATTAAAAG
1 TAAATAATAA-TAAA-TATTAAAAG
*
1419811 T-AATAATAAAATAATATTACAAA-
1 TAAATAATAATA-AATATTA-AAAG
1419834 TAAATAATGAATAAATA
1 TAAATAAT-AATAAATA
1419851 AAATTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
23 7 0.21
24 23 0.68
25 4 0.12
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (23 bp):
TAAATAATAATAAATATTAAAAG
Found at i:1419870 original size:23 final size:23
Alignment explanation
Indices: 1419803--1419871 Score: 59
Period size: 27 Copynumber: 2.8 Consensus size: 23
1419793 TAATTAAAGT
* *
1419803 ATTAAAAGTAATAATA-AAATAAT
1 ATTAAAAAT-ATAATATAAATAAA
*
1419826 ATTACAAATAAATAATGAATAAATAAA
1 ATTA-AAA-ATATAAT--ATAAATAAA
1419853 ATTAAAAATATAATATAAA
1 ATTAAAAATATAATATAAA
1419872 CACACTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
23 9 0.24
24 8 0.22
25 6 0.16
26 4 0.11
27 10 0.27
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (23 bp):
ATTAAAAATATAATATAAATAAA
Found at i:1422479 original size:20 final size:20
Alignment explanation
Indices: 1422456--1422507 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1422446 TGGACACAGT
*
1422456 AGTATCGATACCCCTATTGA
1 AGTATCAATACCCCTATTGA
1422476 AGTATCAATACCCCTATTGA
1 AGTATCAATACCCCTATTGA
1422496 AGTATCAATACC
1 AGTATCAATACC
1422508 AACATCTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.29
Consensus pattern (20 bp):
AGTATCAATACCCCTATTGA
Found at i:1437358 original size:19 final size:19
Alignment explanation
Indices: 1437334--1437371 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1437324 TTTTCATTGG
1437334 AAAAAAATA-AAAAAACAA
1 AAAAAAATATAAAAAACAA
1437352 AAAAAAATATAAAAAACAA
1 AAAAAAATATAAAAAACAA
1437371 A
1 A
1437372 TCGTAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.87, C:0.05, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAAAAATATAAAAAACAA
Found at i:1443676 original size:15 final size:16
Alignment explanation
Indices: 1443649--1443678 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1443639 TTTTTTGTCA
1443649 TAGTTACTAAAACTTT
1 TAGTTACTAAAACTTT
1443665 TAGTTA-TAAAACTT
1 TAGTTACTAAAACTT
1443679 GTCACTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (16 bp):
TAGTTACTAAAACTTT
Found at i:1447931 original size:18 final size:17
Alignment explanation
Indices: 1447890--1447946 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
1447880 CTTGTTTCAT
*
1447890 ATAATATTATT-TAAAA
1 ATAATATTATTAAAAAA
*
1447906 TTAA-ATTATCTAAAAAA
1 ATAATATTAT-TAAAAAA
1447923 ATAATATTATTTAAAATAA
1 ATAATATTA-TTAAAA-AA
1447942 ATAAT
1 ATAAT
1447947 TAATGTTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 5 0.15
16 4 0.12
17 7 0.21
18 9 0.27
19 8 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATATTATTAAAAAA
Found at i:1447938 original size:15 final size:15
Alignment explanation
Indices: 1447890--1447941 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1447880 CTTGTTTCAT
1447890 ATAATATTATTTAAA
1 ATAATATTATTTAAA
*
1447905 ATTAA-ATTATCTAAAAAA
1 A-TAATATTAT-T--TAAA
1447923 ATAATATTATTTAAA
1 ATAATATTATTTAAA
1447938 ATAA
1 ATAA
1447942 ATAATTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 13 0.43
16 4 0.13
17 4 0.13
18 9 0.30
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATATTATTTAAA
Found at i:1447942 original size:23 final size:23
Alignment explanation
Indices: 1447916--1447964 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1447906 TTAAATTATC
1447916 TAAAAAAATAATATTATTTAAAA
1 TAAAAAAATAATATTATTTAAAA
* * * *
1447939 TAAATAATTAATGTTGTTTAAAA
1 TAAAAAAATAATATTATTTAAAA
1447962 TAA
1 TAA
1447965 TAAATAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
TAAAAAAATAATATTATTTAAAA
Found at i:1447999 original size:30 final size:34
Alignment explanation
Indices: 1447936--1448004 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 34
1447926 ATATTATTTA
*
1447936 AAATAAATAATTAATGTTGTTTAAAATAATAAAT
1 AAATAAATAATTAATGATGTTTAAAATAATAAAT
*
1447970 AAATAAATAA-T-ATGAT-TTTAAAA-ATTAAAT
1 AAATAAATAATTAATGATGTTTAAAATAATAAAT
1448000 AAATA
1 AAATA
1448005 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 11 0.33
31 7 0.21
32 4 0.12
33 1 0.03
34 10 0.30
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (34 bp):
AAATAAATAATTAATGATGTTTAAAATAATAAAT
Found at i:1449835 original size:21 final size:22
Alignment explanation
Indices: 1449811--1449853 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1449801 TATAATAATA
1449811 TATTTTAATTTTTAG-TAATTT
1 TATTTTAATTTTTAGATAATTT
* *
1449832 TATTTTTATTTTTTGATAATTT
1 TATTTTAATTTTTAGATAATTT
1449854 ACATTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TATTTTAATTTTTAGATAATTT
Found at i:1449854 original size:21 final size:21
Alignment explanation
Indices: 1449805--1449854 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1449795 ATAAAGTATA
*
1449805 ATAATATATTTTAATTTTTAG
1 ATAATTTATTTTAATTTTTAG
* *
1449826 -TAATTTTATTTTTATTTTTTG
1 ATAA-TTTATTTTAATTTTTAG
1449847 ATAATTTA
1 ATAATTTA
1449855 CATTTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.12
21 18 0.75
22 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
ATAATTTATTTTAATTTTTAG
Found at i:1451015 original size:18 final size:18
Alignment explanation
Indices: 1450992--1451033 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1450982 CCTCAATAAT
1450992 ATTTCTAAAATTCCCTAA
1 ATTTCTAAAATTCCCTAA
1451010 ATTTCTAAAATTCCCTAA
1 ATTTCTAAAATTCCCTAA
1451028 ATTTCT
1 ATTTCT
1451034 TATTCTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTCTAAAATTCCCTAA
Found at i:1451095 original size:20 final size:20
Alignment explanation
Indices: 1451052--1451101 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1451042 GAACTGAGTT
* * *
1451052 AGTATCGATATTTACTTATC
1 AGTATCGATATTGACTAAGC
*
1451072 AGTATCGATATTGACTAAGG
1 AGTATCGATATTGACTAAGC
*
1451092 AGTATTGATA
1 AGTATCGATA
1451102 CCTCCATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (20 bp):
AGTATCGATATTGACTAAGC
Found at i:1453349 original size:35 final size:35
Alignment explanation
Indices: 1453303--1453380 Score: 156
Period size: 35 Copynumber: 2.2 Consensus size: 35
1453293 TATATATATA
1453303 TAAAAGTTAAGATCAACTTACACCCAGTATAAAAC
1 TAAAAGTTAAGATCAACTTACACCCAGTATAAAAC
1453338 TAAAAGTTAAGATCAACTTACACCCAGTATAAAAC
1 TAAAAGTTAAGATCAACTTACACCCAGTATAAAAC
1453373 TAAAAGTT
1 TAAAAGTT
1453381 TTACGCCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (35 bp):
TAAAAGTTAAGATCAACTTACACCCAGTATAAAAC
Found at i:1455076 original size:39 final size:39
Alignment explanation
Indices: 1455033--1455125 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 39
1455023 AATACAAATA
*
1455033 CCTTTTGGTTTAAGTTTATATTACTCATTATAAGATT-G
1 CCTTTTGGTTTAAGTTTATATTACCCATTATAAGATTAG
*
1455071 CCCTTTGGTTTAAGTTTATATTACCCATTATAAGATTAG
1 CCTTTTGGTTTAAGTTTATATTACCCATTATAAGATTAG
**
1455110 TTTTTTGGTTTAAGTT
1 CCTTTTGGTTTAAGTT
1455126 GATTCAGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 35 0.71
39 14 0.29
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.51
Consensus pattern (39 bp):
CCTTTTGGTTTAAGTTTATATTACCCATTATAAGATTAG
Found at i:1457967 original size:20 final size:21
Alignment explanation
Indices: 1457919--1457967 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1457909 TTAAACTTAA
1457919 GGGGTG-AACTAAAATTCTAG
1 GGGGTGAAACTAAAATTCTAG
*
1457939 GGGG-CAAACTAAAATGT-T-G
1 GGGGTGAAACTAAAAT-TCTAG
1457958 GGGGTGAAAC
1 GGGGTGAAAC
1457968 ATATTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 5 0.21
20 18 0.75
21 1 0.04
ACGTcount: A:0.35, C:0.10, G:0.35, T:0.20
Consensus pattern (21 bp):
GGGGTGAAACTAAAATTCTAG
Found at i:1458407 original size:18 final size:18
Alignment explanation
Indices: 1458384--1458419 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1458374 CAAGAAAATT
*
1458384 TGTTCATTTAGTTGTTCG
1 TGTTCATTCAGTTGTTCG
*
1458402 TGTTCATTCATTTGTTCG
1 TGTTCATTCAGTTGTTCG
1458420 GTTAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.19, T:0.56
Consensus pattern (18 bp):
TGTTCATTCAGTTGTTCG
Found at i:1459958 original size:19 final size:19
Alignment explanation
Indices: 1459914--1459951 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1459904 ACAATGTTCG
*
1459914 TAATAATTTGCTTATTAAGC
1 TAAT-ATTTGCTTATCAAGC
1459934 TAATATTTGCTTATCAAG
1 TAATATTTGCTTATCAAG
1459952 TTTATATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (19 bp):
TAATATTTGCTTATCAAGC
Found at i:1468798 original size:7 final size:7
Alignment explanation
Indices: 1468786--1468812 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1468776 TCCAAGAACC
1468786 GCGGTAA
1 GCGGTAA
1468793 GCGGTAA
1 GCGGTAA
1468800 GCGGTAA
1 GCGGTAA
1468807 GCGGTA
1 GCGGTA
1468813 TTTGTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.44, T:0.15
Consensus pattern (7 bp):
GCGGTAA
Found at i:1469181 original size:3 final size:3
Alignment explanation
Indices: 1469173--1469220 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1469163 TCTAAATTTC
1469173 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1469221 CGTACAAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1470213 original size:25 final size:27
Alignment explanation
Indices: 1470181--1470234 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
1470171 TTACGCACAA
1470181 CTTAAAATGTT-TTTTC-TTACTTTTT
1 CTTAAAATGTTATTTTCTTTACTTTTT
1470206 CTTAAAATGTTAACTTTTCTTTACTTTTT
1 CTTAAAATGTT-A-TTTTCTTTACTTTTT
1470235 TCTGGATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 11 0.44
28 5 0.20
29 9 0.36
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.61
Consensus pattern (27 bp):
CTTAAAATGTTATTTTCTTTACTTTTT
Found at i:1470398 original size:22 final size:22
Alignment explanation
Indices: 1470370--1470411 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1470360 TGTTATGTTG
1470370 TTTATAATATTTTAGGTCACAC
1 TTTATAATATTTTAGGTCACAC
1470392 TTTATAATATTTTAGGTCAC
1 TTTATAATATTTTAGGTCAC
1470412 GTATTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTATAATATTTTAGGTCACAC
Found at i:1472835 original size:29 final size:31
Alignment explanation
Indices: 1472803--1472867 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
1472793 AGAACATTAA
*
1472803 AAAAATTA-AAGTTTAA-TATGATTTTTTTT
1 AAAAATTAGAAGTTAAATTATGATTTTTTTT
** *
1472832 AAAAATTAGGGGTTAAATTATTATTTTTTTT
1 AAAAATTAGAAGTTAAATTATGATTTTTTTT
1472863 AAAAA
1 AAAAA
1472868 AATTTAAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.27
30 5 0.17
31 17 0.57
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (31 bp):
AAAAATTAGAAGTTAAATTATGATTTTTTTT
Found at i:1472893 original size:35 final size:31
Alignment explanation
Indices: 1472823--1472896 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 31
1472813 GTTTAATATG
* *
1472823 ATTTTTTTTAAAAATTAGGGGTTAAATTATT
1 ATTTTTTTTAAAAATTAAGGGTTAAATTATA
1472854 ATTTTTTTTAAAAAAATTTAAGGGTCTAAATTATA
1 ATTTTTTTT--AAAAA-TTAAGGGT-TAAATTATA
1472889 ATTTTTTT
1 ATTTTTTT
1472897 AATTTCGGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 9 0.24
33 5 0.14
34 7 0.19
35 16 0.43
ACGTcount: A:0.36, C:0.01, G:0.09, T:0.53
Consensus pattern (31 bp):
ATTTTTTTTAAAAATTAAGGGTTAAATTATA
Found at i:1472894 original size:34 final size:33
Alignment explanation
Indices: 1472823--1472898 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 33
1472813 GTTTAATATG
* *
1472823 ATTTTTTT-TAAAAATTAGGGGTTAAATTATTA
1 ATTTTTTTAAAAAAATTAAGGGTTAAATTATTA
*
1472855 TTTTTTTTAAAAAAATTTAAGGGTCTAAATTA-TA
1 ATTTTTTTAAAAAAA-TTAAGGGT-TAAATTATTA
1472889 ATTTTTTTAA
1 ATTTTTTTAA
1472899 TTTCGGGGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 7 0.19
33 5 0.14
34 18 0.49
35 7 0.19
ACGTcount: A:0.38, C:0.01, G:0.09, T:0.51
Consensus pattern (33 bp):
ATTTTTTTAAAAAAATTAAGGGTTAAATTATTA
Found at i:1473000 original size:49 final size:50
Alignment explanation
Indices: 1472945--1473052 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
1472935 GCCCCTGTAT
* *
1472945 AAAAATT-TGGATCATGAAA-TTCGTTATACTCACGTGACAAATTATAATA
1 AAAAATTATAGATCATAAAAGTT-GTTATACTCACGTGACAAATTATAATA
** * * *
1472994 AAAAATTATATTTTATAAAAGTTGTTATACTCATGTGACAAATTCTAAT-
1 AAAAATTATAGATCATAAAAGTTGTTATACTCACGTGACAAATTATAATA
1473043 AAAAATTATA
1 AAAAATTATA
1473053 TTTTATAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 17 0.34
50 31 0.62
51 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (50 bp):
AAAAATTATAGATCATAAAAGTTGTTATACTCACGTGACAAATTATAATA
Done.