Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007704.1 Hibiscus syriacus cultivar Beakdansim tig00109919_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: 612835
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 3
Found at i:11275 original size:28 final size:28
Alignment explanation
Indices: 11243--11318 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 28
11233 ATATATGACT
* **
11243 ATATAATAATAATAAAAATAATATTTAA
1 ATATAATAATAATAAAAATAAAACATAA
* *
11271 ATAT-ATAAACAAGTAAAATTAAAACATAA
1 ATATAAT-AATAA-TAAAAATAAAACATAA
*
11300 ATA-AACAATAATAAAAATA
1 ATATAATAATAATAAAAATA
11319 CAATTAGAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
27 9 0.24
28 12 0.32
29 16 0.43
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (28 bp):
ATATAATAATAATAAAAATAAAACATAA
Found at i:12680 original size:3 final size:3
Alignment explanation
Indices: 12674--12728 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
12664 TAATATTTTT
* *
12674 TAA TAA TAA -AA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12720 TAAA TAA TA
1 T-AA TAA TA
12729 TTTAAATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12688 original size:21 final size:25
Alignment explanation
Indices: 12661--12716 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
12651 TTTGGGCCTG
*
12661 TAATAATAT-TTTTTAATAATAA-AA
1 TAATAATATATTATT-ATAATAATAA
12685 TAATAATA-ATTATTATAATAATAA
1 TAATAATATATTATTATAATAATAA
12709 TAATAATA
1 TAATAATA
12717 ATATAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATAATATATTATTATAATAATAA
Found at i:12691 original size:24 final size:26
Alignment explanation
Indices: 12661--12720 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
12651 TTTGGGCCTG
*
12661 TAATAATATT-TTTTAATAATAA-AA
1 TAATAATATTATTATAATAATAATAA
12685 TAATAATAATTATTATAATAATAATAA
1 TAATAAT-ATTATTATAATAATAATAA
12712 TAATAATAT
1 TAATAATAT
12721 AAATAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 7 0.22
25 3 0.09
26 13 0.41
27 9 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATAATATTATTATAATAATAATAA
Found at i:17909 original size:15 final size:15
Alignment explanation
Indices: 17891--17920 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17881 CCACGGTGCT
*
17891 CCCGGAATCTTGCGC
1 CCCGGAATCCTGCGC
17906 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
17921 GATTGTGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.43, G:0.27, T:0.17
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:25099 original size:2 final size:2
Alignment explanation
Indices: 25092--25117 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25082 GTTGAATCAA
25092 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
25118 TTGATAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40321 original size:15 final size:15
Alignment explanation
Indices: 40301--40331 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40291 CAACAGATAA
40301 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
40316 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
40331 A
1 A
40332 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:40522 original size:20 final size:20
Alignment explanation
Indices: 40486--40523 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40476 ATCCTATTCC
**
40486 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
40506 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
40524 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:53061 original size:27 final size:29
Alignment explanation
Indices: 53022--53081 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
53012 ATTAAGATTT
* **
53022 ATTTTTTCTAATTAAATTGTAA-GATAAA
1 ATTTATTCTAATTAAATTAAAATGATAAA
53050 ATTTATTC-AATTAAATTAAAATGATAAA
1 ATTTATTCTAATTAAATTAAAATGATAAA
53078 ATTT
1 ATTT
53082 GTAAGTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTATTCTAATTAAATTAAAATGATAAA
Found at i:53395 original size:24 final size:24
Alignment explanation
Indices: 53341--53395 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
53331 TTAGTTTTCA
* *
53341 AAAATATATTTTATAAAATTTAGT
1 AAAATAAATTTTATAAAATTTAAT
* * *
53365 TATATAAATTTTTTAAAATTTAAT
1 AAAATAAATTTTATAAAATTTAAT
53389 AAAATAA
1 AAAATAA
53396 CTTTAATTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AAAATAAATTTTATAAAATTTAAT
Found at i:53775 original size:69 final size:70
Alignment explanation
Indices: 53688--53827 Score: 264
Period size: 71 Copynumber: 2.0 Consensus size: 70
53678 CATTAATTCT
53688 TTTTTTCAAATCCTCAATTTATT-GGGGGGGGGGTTTTGACCCATGATTTAGGCGATTGTGAAGT
1 TTTTTTCAAATCCTCAATTTATTGGGGGGGGGGGTTTTGACCCATGATTTAGGCGATTGTGAAGT
53752 TAATG
66 TAATG
53757 TTTTTTCAAATCCTCAATTTATTGGGGGGGGGGGGTTTTGACCCATGATTTAGGCGATTGTGAAG
1 TTTTTTCAAATCCTCAATTTATT-GGGGGGGGGGGTTTTGACCCATGATTTAGGCGATTGTGAAG
53822 TTAATG
65 TTAATG
53828 GAGCTTGTAA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
69 23 0.33
71 46 0.67
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (70 bp):
TTTTTTCAAATCCTCAATTTATTGGGGGGGGGGGTTTTGACCCATGATTTAGGCGATTGTGAAGT
TAATG
Found at i:54912 original size:21 final size:22
Alignment explanation
Indices: 54866--54963 Score: 68
Period size: 21 Copynumber: 4.7 Consensus size: 22
54856 TTTTAATTTC
* * *
54866 TATACTTATATATTAT-TATAT
1 TATAATTATTTATTATATATAA
*
54887 TTTAATTATTTATTATATATAA
1 TATAATTATTTATTATATATAA
*
54909 T-TAA-TA---ATAATA-ATAA
1 TATAATTATTTATTATATATAA
*
54925 TATATTTATTTATTATAATATAA
1 TATAATTATTTATTAT-ATATAA
54948 TATAATT-TTTCATTAT
1 TATAATTATTT-ATTAT
54964 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
16 5 0.08
17 7 0.12
18 2 0.03
20 2 0.03
21 20 0.33
22 9 0.15
23 15 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATAATTATTTATTATATATAA
Found at i:54932 original size:34 final size:33
Alignment explanation
Indices: 54889--54953 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 33
54879 TATTATATTT
54889 TAATTATTTA-TTATATATAAT-TAATAATAATAA
1 TAATTATTTATTTAT-TATAATATAAT-ATAATAA
54922 TAATATATTTATTTATTATAATATAATATAAT
1 TAAT-TATTTATTTATTATAATATAATATAAT
54954 TTTTCATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
33 4 0.14
34 17 0.59
35 8 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TAATTATTTATTTATTATAATATAATATAATAA
Found at i:54962 original size:23 final size:24
Alignment explanation
Indices: 54915--54963 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
54905 ATAATTAATA
*
54915 ATAATAATAATATATTTATTTATT
1 ATAATAATAATATATTTATTCATT
54939 ATAAT-ATAATATAATTT-TTCATT
1 ATAATAATAATAT-ATTTATTCATT
54962 AT
1 AT
54964 TTCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATAATAATAATATATTTATTCATT
Found at i:55016 original size:26 final size:26
Alignment explanation
Indices: 54971--55057 Score: 88
Period size: 26 Copynumber: 3.2 Consensus size: 26
54961 TATTTCAAAA
*
54971 TTTAT-AAA-ATATATTATAATTATT
1 TTTATAAAATATATATTTTAATTATT
54995 TTTATAAAATATATATTTTAATTACTAT
1 TTTATAAAATATATATTTTAATTA-T-T
* *
55023 ATTTATATATTATTATATTTTAATTATT
1 -TTTATAAAATA-TATATTTTAATTATT
55051 TATTATA
1 T-TTATA
55058 TTTTATAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
24 5 0.09
25 3 0.06
26 13 0.25
27 2 0.04
28 7 0.13
29 10 0.19
30 13 0.25
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTATAAAATATATATTTTAATTATT
Found at i:55023 original size:16 final size:15
Alignment explanation
Indices: 55003--55049 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
54993 TTTTTATAAA
55003 ATATATATTTTAATT
1 ATATATATTTTAATT
*
55018 ACTATAT-TTATATATT
1 A-TATATATTTTA-ATT
55034 AT-TATATTTTAATT
1 ATATATATTTTAATT
55048 AT
1 AT
55050 TTATTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.30
15 10 0.37
16 9 0.33
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATATATTTTAATT
Found at i:55179 original size:147 final size:146
Alignment explanation
Indices: 54807--55238 Score: 634
Period size: 147 Copynumber: 2.9 Consensus size: 146
54797 TTTAATTCAA
* * * *
54807 ATTTTAAAATTTTCAAAATATATTATAATTATTTTTTATAAAATATCTATTTTAATTTCTATACT
1 ATTTCAAAATTTACAAAATATATTATAATTA-TTTTTATAAAATATCTATTTTAATTACTATATT
* *
54872 TATATATTATTATATTTTAATTATTTATTATATATAATTAATAATAATAATAATATATTTATTTA
65 TATATATTATTATATTTTAATTATTTATTATAT-T--TT-ATAAT--TAATATTATA-ATATTTA
*
54937 TTATAATATAATATAATTTTTCATT
123 TT-TATTATAATATAATTTTTCATT
* *
54962 ATTTCAAAATTTATAAAATATATTATAATTATTTTTATAAAATATATATTTTAATTACTATATTT
1 ATTTCAAAATTTACAAAATATATTATAATTATTTTTATAAAATATCTATTTTAATTACTATATTT
55027 ATATATTATTATATTTTAATTATTTATTATATTTTATAATTAATATTATAATATTTATTTATTAT
66 ATATATTATTATATTTTAATTATTTATTATATTTTATAATTAATATTATAATATTTATTTATTAT
55092 AATATAATTTTTCATT
131 AATATAATTTTTCATT
*
55108 ATTTCAAAATTTACAAAATATATTATAATTATCTTTTATAAAATTTCTATTTTAATTACTATATT
1 ATTTCAAAATTTACAAAATATATTATAATTAT-TTTTATAAAATATCTATTTTAATTACTATATT
* *
55173 TATATATTATTATATTTTAATTATTTATTATATTTAATAATTCATATTATTAAT-TATTA-TTAT
65 TATATATTATTATATTTTAATTATTTATTATATTTTATAATTAATATTA-TAATAT-TTATTTAT
55236 TAT
128 TAT
55239 TATTATATTT
Statistics
Matches: 260, Mismatches: 14, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
146 52 0.20
147 93 0.36
148 16 0.06
150 5 0.02
151 2 0.01
153 1 0.00
154 63 0.24
155 28 0.11
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (146 bp):
ATTTCAAAATTTACAAAATATATTATAATTATTTTTATAAAATATCTATTTTAATTACTATATTT
ATATATTATTATATTTTAATTATTTATTATATTTTATAATTAATATTATAATATTTATTTATTAT
AATATAATTTTTCATT
Found at i:55185 original size:3 final size:3
Alignment explanation
Indices: 55172--55253 Score: 50
Period size: 3 Copynumber: 27.3 Consensus size: 3
55162 ATTACTATAT
* *
55172 TTA TATA TTA TTA -TA TT- TTAA TTA TTTA TTA -TA TT- TAA TAA TTCA
1 TTA T-TA TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA TTA TTA TT-A
55217 -TA TTA TTAA TTA TTA TTA TTA TTA TTA -TA TTTA TTA T
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA T
55254 AATATAATTT
Statistics
Matches: 65, Mismatches: 2, Indels: 24
0.71 0.02 0.26
Matches are distributed among these distances:
2 10 0.15
3 41 0.63
4 14 0.22
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:55186 original size:16 final size:16
Alignment explanation
Indices: 55162--55250 Score: 68
Period size: 16 Copynumber: 5.9 Consensus size: 16
55152 TTCTATTTTA
*
55162 ATTACTATATTTATAT
1 ATTATTATATTTATAT
55178 ATTATTATATTT-TA-
1 ATTATTATATTTATAT
55192 ATTATT-TA-TTATAT
1 ATTATTATATTTATAT
* *
55206 -TTAATA-ATTCATATT
1 ATTATTATATTTATA-T
55221 ATTAATTAT-TATTAT-T
1 ATT-ATTATAT-TTATAT
55237 ATTATTATATTTAT
1 ATTATTATATTTAT
55251 TATAATATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 21
0.69 0.06 0.25
Matches are distributed among these distances:
12 2 0.03
13 9 0.16
14 10 0.17
15 12 0.21
16 18 0.31
17 4 0.07
18 3 0.05
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:55206 original size:9 final size:9
Alignment explanation
Indices: 55167--55254 Score: 58
Period size: 9 Copynumber: 9.4 Consensus size: 9
55157 TTTTAATTAC
55167 TATATTTA-
1 TATATTTAT
55175 TATA-TTAT
1 TATATTTAT
55183 TATATTT-T
1 TATATTTAT
*
55191 AATTATTTAT
1 TA-TATTTAT
*
55201 TATATTTAA
1 TATATTTAT
55210 TA-ATTCATAT
1 TATATT--TAT
*
55220 TATTAATTAT
1 TA-TATTTAT
55230 TATTATTATTAT
1 TA-TA-T-TTAT
55242 TATATTTAT
1 TATATTTAT
55251 TATA
1 TATA
55255 ATATAATTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
7 3 0.05
8 13 0.20
9 23 0.36
10 15 0.23
11 2 0.03
12 8 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (9 bp):
TATATTTAT
Found at i:55263 original size:15 final size:15
Alignment explanation
Indices: 55167--55256 Score: 57
Period size: 13 Copynumber: 6.0 Consensus size: 15
55157 TTTTAATTAC
*
55167 TATATTTATATATTAT
1 TATATTTAT-TATAAT
*
55183 TATATTTTAATTATTTAT
1 TATA-TTT-ATTA-TAAT
55201 TATATTTA--ATAAT
1 TATATTTATTATAAT
55214 TCATA-TTA-T-TAAT
1 T-ATATTTATTATAAT
*
55227 TAT-TATTATTATTAT
1 TATAT-TTATTATAAT
55242 TATATTTATTATAAT
1 TATATTTATTATAAT
55257 ATAATTTTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 21
0.72 0.04 0.25
Matches are distributed among these distances:
12 2 0.03
13 15 0.25
14 5 0.08
15 15 0.25
16 6 0.10
17 8 0.13
18 10 0.16
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATTTATTATAAT
Found at i:59693 original size:26 final size:26
Alignment explanation
Indices: 59642--59693 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
59632 CAAAATAAAA
* *
59642 TAGTTTAGTACAAATATTTTAGTTTT
1 TAGTTTAGTACAAATATTTCAATTTT
59668 TAGTTTAGTACAAATATTTCAATTTT
1 TAGTTTAGTACAAATATTTCAATTTT
59694 GAAGATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.52
Consensus pattern (26 bp):
TAGTTTAGTACAAATATTTCAATTTT
Found at i:66499 original size:31 final size:31
Alignment explanation
Indices: 66461--66521 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
66451 CAATTTATGA
66461 TATAGATGAGTTTAGAGTGAGTTACATTTGG
1 TATAGATGAGTTTAGAGTGAGTTACATTTGG
*
66492 TATAGATGAGTTTAGAGTGAGTTACCTTTG
1 TATAGATGAGTTTAGAGTGAGTTACATTTG
66522 CTTACTAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.39
Consensus pattern (31 bp):
TATAGATGAGTTTAGAGTGAGTTACATTTGG
Found at i:70226 original size:169 final size:169
Alignment explanation
Indices: 69902--70782 Score: 987
Period size: 169 Copynumber: 5.2 Consensus size: 169
69892 TACTGCGAAT
* * * * * ** * *
69902 TTGACATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGT-ATTTGTTGACAGATAACCCTTTTT
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTC
* * ** ** * * * * * **
69966 ACCTTGAGTTATACTATAAATTTGATTTGCCTCTGAGCTGAATATAATCGAACTTAAAGGTC-TT
66 GCCTTGAGCTATGTTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTT
70030 GGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAA
129 GGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT-AAA
* * *
70072 TTGATATGCCTTTGAGCTAAATGTAATCGAACTCGAAGGTCTTTTGTT-GTAGATAGCCCTTCTC
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTC
* * *
70136 GCCTTGAGCTATGTTGCAAATGATGTGCATTTTTA-CTGAGGGTAATCAAACTCGAAGGTCTTTG
66 GCCTTGAGCTATGTTGCAAATGATGTGC-CTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTG
70200 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
130 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
* **
70240 TTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACTGTTCT
1 TT-GATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCT
* * *
70305 CGCCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTG
65 CGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTG
* * * *
70369 GTTAATAGATAACCCTTATCGCCTTGAGTTATGCTATAAA
130 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
* *
70409 TTAGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCT
1 TT-GATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCT
* * *
70474 CGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTT
65 CGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTG
* * * * * *
70539 GTTGGCATATAGCCCTTCTCGCCTTGAGCTATACTGCAAA
130 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
* * * * *
70579 -TGATATGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC-TTGGTTGATAGATAATCATTCTC
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTC
* * * *
70642 GCCTTGAGTTATGTTGTAAATTAGATATGCTTTTGAGCTGAGTGTAATCAAA--C-AA-GTCTTT
66 GCCTTGAGCTATGTTGCAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTT
* * * * ** **
70703 TGTTGA-ACGATAACCCTTCTCACCTTTAGCTACACTACAAA
129 GGTTGACA-GATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
*
70744 -TGATATGCCTTTGAGCTGAGTGTATTCGAACTCGAAGGT
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
70783 TGTCCGCTCG
Statistics
Matches: 619, Mismatches: 82, Indels: 25
0.85 0.11 0.03
Matches are distributed among these distances:
164 1 0.00
165 75 0.12
166 2 0.00
167 36 0.06
168 69 0.11
169 275 0.44
170 155 0.25
171 6 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (169 bp):
TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTC
GCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGG
TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
Found at i:70227 original size:84 final size:85
Alignment explanation
Indices: 69908--70782 Score: 954
Period size: 84 Copynumber: 10.4 Consensus size: 85
69898 GAATTTGACA
* * * * * **
69908 TGCCCTTGAGCTGAATGGAATCGAACTCGAAGGT-ATTTGTTGACAGATAACCCTTTTTACCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTG
* * * *
69972 AGTTATACTATAAATTTGATT
66 AGCTATGCTGTAAA-TTGATG
* * * ** *
69993 TGCCTCTGAGCTGAATATAATCGAACTTAAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTG
* *
70057 AGTTATGCTGTAAAATTGATA
66 AGCTATGCTGT-AAATTGATG
* * * *
70078 TGCCTTTGAGCTAAATGTAATCGAACTCGAAGGTCTTTTGTTG-TAGATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTG
* *
70142 AGCTATGTTGCAAA-TGATG
66 AGCTATGCTGTAAATTGATG
* * * * *
70161 TGCATTTTTA-CTGAGGGTAATCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGCCTT
1 TGC-CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
*
70225 GAGTTATGCTGTAAATTGGATG
65 GAGCTATGCTGTAAATT-GATG
** **
70247 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACTGTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTG
70312 AGCTATGCTGTAAA-TGATG
66 AGCTATGCTGTAAATTGATG
* * * *
70331 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTAATAGATAACCCTTATCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTG
* *
70395 AGTTATGCTATAAATTAGATG
66 AGCTATGCTGTAAATT-GATG
*
70416 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTG
* *
70481 AGCTATGTTGCAAA-TGATG
66 AGCTATGCTGTAAATTGATG
* * * *
70500 TGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCATATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTG
* * *
70565 AGCTATACTGCAAA-TGATA
66 AGCTATGCTGTAAATTGATG
* * * * *
70584 TGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC-TTGGTTGATAGATAATCATTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTG
* * *
70648 AGTTATGTTGTAAATTAGATA
66 AGCTATGCTGTAAATT-GATG
* * *
70669 TGCTTTTGAGCTGAGTGTAATC-AA-AC-AA-GTCTTTTGTTGA-ACGATAACCCTTCTCACCTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACA-GATAACCCTTCTCGCCTT
* ** ** *
70729 TAGCTACACTACAAA-TGATA
65 GAGCTATGCTGTAAATTGATG
*
70749 TGCCTTTGAGCTGAGTGTATTCGAACTCGAAGGT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
70783 TGTCCGCTCG
Statistics
Matches: 671, Mismatches: 100, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
80 24 0.04
81 7 0.01
82 33 0.05
83 105 0.16
84 197 0.29
85 194 0.29
86 111 0.17
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (85 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTG
AGCTATGCTGTAAATTGATG
Found at i:70395 original size:253 final size:252
Alignment explanation
Indices: 69913--70782 Score: 1040
Period size: 253 Copynumber: 3.4 Consensus size: 252
69903 TGACATGCCC
* * * * * * *
69913 TTGAGCTGAATGGAATCGAACTCGAAGGT-ATTTGTTGACAGATAACCCTTTTTACCTTGAGTTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTA
* * * * * ** * *
69977 TACTATAAATTTGATTTGCCTCTGAGCTGAATATAATCGAACTTAAAGGTC-TTGGTTGACAGAT
66 TACTACAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGAT
* * *
70041 AACCCTTCTCGCCTTGAGTTATGCTGTAAAATTGATATGCCTTTGAGCTAAATGTAATCGAACTC
129 AACCCTTCTCGCCTTGAGCTATGCTGT-AAA-TGATATGCCTTTGAGCTGAGTGTAATCGAACTC
* * * * *
70106 GAAGGTCTTTTGTTGTAGATAGCCCTTCTCGCCTTGAGCTATGTTGCAAA-T-GATGTGCATT
192 GAAGGTC-TTGGTTATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTAGATGTGC-TT
* * * * *
70167 TTTA-CTGAGGGTAATCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTA
* ** *
70231 TGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGAT
66 TACTACAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGAT
** *
70296 AACTGTTCTCGCCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
129 AACCCTTCTCGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGA
* * * *
70361 AGGTCTTGGTTAATAGATAACCCTTATCGCCTTGAGTTATGCTATAAATTAGATGTGCCT
194 AGGTCTTGGTT-ATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTAGATGTGCTT
* * *
70421 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTA
** * * * *
70486 TGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCATATAG
66 TACTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAA
* * *
70551 CCCTTCTCGCCTTGAGCTATACTGCAAATGATATGCCTTTGAGCTGAGTGTAATTGAACTCGAAG
131 CCCTTCTCGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* * *
70616 GTCTTGGTTGATAGATAATCATTCTCGCCTTGAGTTATGTTGTAAATTAGATATGCTT
196 GTCTTGGTT-ATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTAGATGTGCTT
*
70674 TTGAGCTGAGTGTAATCAAA--C-AA-GTCTTTTGTTGA-ACGATAACCCTTCTCACCTTTAGCT
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACA-GATAACCCTTCTCACCTTGAGCT
* * *
70734 ACACTACAAATGATATGCCTTTGAGCTGAGTGTATTCGAACTCGAAGGT
65 ATACTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
70783 TGTCCGCTCG
Statistics
Matches: 535, Mismatches: 73, Indels: 21
0.85 0.12 0.03
Matches are distributed among these distances:
248 1 0.00
249 74 0.14
250 2 0.00
251 1 0.00
252 5 0.01
253 267 0.50
254 82 0.15
255 103 0.19
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (252 bp):
TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTA
TACTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAA
CCCTTCTCGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
GTCTTGGTTATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTAGATGTGCTT
Found at i:72777 original size:86 final size:86
Alignment explanation
Indices: 72626--72811 Score: 248
Period size: 86 Copynumber: 2.2 Consensus size: 86
72616 GGAGTTATCA
** **
72626 AAGGTC-TTGGTTGACAGATAACCATTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCATTTG
1 AAGGTCTTTGGTTGACAGATAACCATTCTCGCCTTGAGCCATGCTACAAATTGGATGTGCATTTG
* *
72690 AGTTGAGTGTAATCAAACTCG
66 AGCTGAGGGTAATCAAACTCG
* * * *
72711 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTGAGCCATGCTACAAATTTGATGTGCCTTTG
1 AAGGTCTTTGGTTGACAGATAACCATTCTCGCCTTGAGCCATGCTACAAATTGGATGTGCATTTG
**
72776 AGCTGAGGGTAATTGAACTCG
66 AGCTGAGGGTAATCAAACTCG
*
72797 AAGGTCTTTTGTTGA
1 AAGGTCTTTGGTTGA
72812 ATATGCTTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 6 0.07
86 80 0.93
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (86 bp):
AAGGTCTTTGGTTGACAGATAACCATTCTCGCCTTGAGCCATGCTACAAATTGGATGTGCATTTG
AGCTGAGGGTAATCAAACTCG
Found at i:73197 original size:42 final size:43
Alignment explanation
Indices: 73151--73235 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
73141 TAATTCAGGC
73151 TCACAATCGAATC-AATCATAAACATGAGTTCACAGAAAATCA
1 TCACAATCGAATCAAATCATAAACATGAGTTCACAGAAAATCA
73193 TCACAATCGAATCAAATCATAAACATGAGTTCACAGAAAATCA
1 TCACAATCGAATCAAATCATAAACATGAGTTCACAGAAAATCA
73236 AAAGAATCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 13 0.31
43 29 0.69
ACGTcount: A:0.48, C:0.21, G:0.09, T:0.21
Consensus pattern (43 bp):
TCACAATCGAATCAAATCATAAACATGAGTTCACAGAAAATCA
Found at i:73866 original size:96 final size:96
Alignment explanation
Indices: 73687--73886 Score: 303
Period size: 96 Copynumber: 2.1 Consensus size: 96
73677 GGGACAGATC
* * * *
73687 ATATTATAATCACTTTATCAGGCTAGCTGACTATTATCCATAAAGCCGGGGTGTTTAGCCAATTA
1 ATATAATAATCACTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTA
73752 CATTAGAGGGACAACTCAAGCTTTATTGTAT
66 CATTAGAGGGACAACTCAAGCTTTATTGTAT
* *
73783 -TATAATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATT
1 ATATAATAATCA-CTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
* * *
73847 TCTTTAGAGGGACAGCTCAAGCTTTATTGTAT
65 ACATTAGAGGGACAACTCAAGCTTTATTGTAT
73879 ATATAATA
1 ATATAATA
73887 TTATAATATG
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
95 10 0.11
96 76 0.82
97 7 0.08
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (96 bp):
ATATAATAATCACTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTA
CATTAGAGGGACAACTCAAGCTTTATTGTAT
Found at i:77722 original size:142 final size:142
Alignment explanation
Indices: 77467--77750 Score: 552
Period size: 142 Copynumber: 2.0 Consensus size: 142
77457 ACACAGTGAC
77467 CAAAGTGTTACAATTCAAGAGAATGAAGCTACATCAAACTTCATTTAAACTAAAATGGTTAATGG
1 CAAAGTGTTACAATTCAAGAGAATGAAGCTACATCAAACTTCATTTAAACTAAAATGGTTAATGG
77532 ATTAATTTAACCAATGCATTAAACACATGTTCATAAACAAAACACAAAGAATGACT-ATCTTTAT
66 ATTAATTTAACCAATGCATTAAACACATGTTCATAAACAAAACACAAAGAATGACTCATCTTTAT
77596 CACTGCTTCACA
131 CACTGCTTCACA
77608 CAAAGTGTTACAATTCAAGAGAATGAAGCTACATCAAACTTCATTTAAAACTAAAATGGTTAATG
1 CAAAGTGTTACAATTCAAGAGAATGAAGCTACATCAAACTTCATTT-AAACTAAAATGGTTAATG
77673 GATTAATTTAACCAATGCATTAAACACATGTTCATAAACAAAACACAAAGAATGACTCATCTTTA
65 GATTAATTTAACCAATGCATTAAACACATGTTCATAAACAAAACACAAAGAATGACTCATCTTTA
77738 TCACTGCTTCACA
130 TCACTGCTTCACA
77751 TAAAACACAA
Statistics
Matches: 141, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
141 46 0.33
142 75 0.53
143 20 0.14
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (142 bp):
CAAAGTGTTACAATTCAAGAGAATGAAGCTACATCAAACTTCATTTAAACTAAAATGGTTAATGG
ATTAATTTAACCAATGCATTAAACACATGTTCATAAACAAAACACAAAGAATGACTCATCTTTAT
CACTGCTTCACA
Found at i:82602 original size:59 final size:58
Alignment explanation
Indices: 82536--82651 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
82526 GTAATCACAC
*
82536 TGGGCACATGACAAAGTAATGTCATTACTTTTAGACATGTGACATGTAAGATATATCAT
1 TGGGCACATGACAAAGTAATGTCATTAC-TTTAGACATGTGACATGTAAAATATATCAT
82595 TGGGCACATGACAAAGTAATGTCATTACTTTAGACATGTGACATGTAAAATATATCA
1 TGGGCACATGACAAAGTAATGTCATTACTTTAGACATGTGACATGTAAAATATATCA
82652 CTTTAGATAG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 28 0.50
59 28 0.50
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (58 bp):
TGGGCACATGACAAAGTAATGTCATTACTTTAGACATGTGACATGTAAAATATATCAT
Found at i:82631 original size:28 final size:29
Alignment explanation
Indices: 82541--82632 Score: 68
Period size: 29 Copynumber: 3.2 Consensus size: 29
82531 CACACTGGGC
*
82541 ACATGACAAAGTAATGTCATTACTTTTAG
1 ACATGACAAAGTAATGTCATTACATTTAG
* **
82570 ACATGTGAC-ATGTAA-G--ATATATCATTGGG
1 ACA--TGACAAAGTAATGTCAT-TA-CATTTAG
82599 CACATGACAAAGTAATGTCATTAC-TTTAG
1 -ACATGACAAAGTAATGTCATTACATTTAG
82628 ACATG
1 ACATG
82633 TGACATGTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 19
0.64 0.10 0.26
Matches are distributed among these distances:
27 2 0.04
28 11 0.23
29 16 0.34
30 10 0.21
31 6 0.13
32 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (29 bp):
ACATGACAAAGTAATGTCATTACATTTAG
Found at i:82637 original size:30 final size:30
Alignment explanation
Indices: 82544--82637 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
82534 ACTGGGCACA
82544 TGACAAAGTAATGTCATTACTTTTAGACATG
1 TGACAAAGTAATGTCATTAC-TTTAGACATG
* * * * **
82575 TGAC-ATGTAA-G--ATATATCATTGGGCACA
1 TGACAAAGTAATGTCAT-TA-CTTTAGACATG
82603 TGACAAAGTAATGTCATTACTTTAGACATG
1 TGACAAAGTAATGTCATTACTTTAGACATG
82633 TGACA
1 TGACA
82638 TGTAAAATAT
Statistics
Matches: 45, Mismatches: 12, Indels: 13
0.64 0.17 0.19
Matches are distributed among these distances:
27 2 0.04
28 11 0.24
29 7 0.16
30 17 0.38
31 6 0.13
32 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (30 bp):
TGACAAAGTAATGTCATTACTTTAGACATG
Found at i:83779 original size:16 final size:17
Alignment explanation
Indices: 83754--83795 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
83744 TGTGTTTGTT
*
83754 TTTATTTTATTAATTTA
1 TTTATCTTATTAATTTA
*
83771 -TTATCTTATTTATTTA
1 TTTATCTTATTAATTTA
83787 TTTATCTTA
1 TTTATCTTA
83796 GCTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATCTTATTAATTTA
Found at i:95005 original size:105 final size:105
Alignment explanation
Indices: 94823--95540 Score: 1039
Period size: 105 Copynumber: 7.0 Consensus size: 105
94813 AGGTTTTACC
94823 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
94888 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
94928 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
94993 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
***
95033 CAGAGCCAATTTTTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
95098 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
** **
95138 CAGAGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAATACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
95203 ACAAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
* ***
95243 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* **
95304 ACGAAGGGACCACTGACTGTCAACT-AA-A----T-AATTT
66 ACGAAGGGACCGCTGGTTGTCAA-TAAACATTTCTCAATTT
*
95338 CAGAGCCAATTTCAACTCCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
95403 ACGAAGGGACCGCTGGTTGTCAAT-AA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
* ***
95436 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
95497 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCTCAATTT
95538 CAG
1 CAG
95541 CTCCACAACG
Statistics
Matches: 566, Mismatches: 31, Indels: 33
0.90 0.05 0.05
Matches are distributed among these distances:
94 79 0.14
95 8 0.01
96 1 0.00
97 1 0.00
98 10 0.02
99 75 0.13
100 1 0.00
101 77 0.14
102 7 0.01
105 307 0.54
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
Found at i:97383 original size:21 final size:20
Alignment explanation
Indices: 97352--97401 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
97342 ACCAAACCTT
*
97352 TATCC-TTTTTTCAAA-TCTG
1 TATCCTTTTTTTTAAATTC-G
97371 TATCCTTTTTTTTAAATTCG
1 TATCCTTTTTTTTAAATTCG
97391 TATCCTTTTTT
1 TATCCTTTTTT
97402 CTATTTTCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.18
20 21 0.75
21 2 0.07
ACGTcount: A:0.18, C:0.18, G:0.04, T:0.60
Consensus pattern (20 bp):
TATCCTTTTTTTTAAATTCG
Found at i:97410 original size:20 final size:20
Alignment explanation
Indices: 97352--97410 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
97342 ACCAAACCTT
* *
97352 TATCCTTTTTTCAAATCT-G
1 TATCCTTTTTTCTAATTTCG
* *
97371 TATCCTTTTTTTTAAATTCG
1 TATCCTTTTTTCTAATTTCG
*
97391 TATCCTTTTTTCTATTTTCG
1 TATCCTTTTTTCTAATTTCG
97411 GTGGAGTGGC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.17, C:0.19, G:0.05, T:0.59
Consensus pattern (20 bp):
TATCCTTTTTTCTAATTTCG
Found at i:97629 original size:16 final size:17
Alignment explanation
Indices: 97604--97645 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
97594 TGTGTTTGTT
*
97604 TTTATTTTATTAATTTA
1 TTTATCTTATTAATTTA
*
97621 -TTATCTTATTTATTTA
1 TTTATCTTATTAATTTA
97637 TTTATCTTA
1 TTTATCTTA
97646 GCTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATCTTATTAATTTA
Found at i:98625 original size:61 final size:60
Alignment explanation
Indices: 98582--98707 Score: 180
Period size: 61 Copynumber: 2.1 Consensus size: 60
98572 ATGACACGTA
* * *
98582 ATCATACTGGACACATGACAAAGTAATGTCGTTACTTTTAGACATGTGACATGTAAGATAT
1 ATCACACTGGACACATGACAAAGTAATGTCATTAC-TTTAGACACGTGACATGTAAGATAT
* * * *
98643 ATCACACTGGGCACATGATAAAGTAATGTCATTACTTTAGACATGTGACATGTAAAATAT
1 ATCACACTGGACACATGACAAAGTAATGTCATTACTTTAGACACGTGACATGTAAGATAT
98703 ATCAC
1 ATCAC
98708 TTTAGATAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
60 29 0.48
61 31 0.52
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (60 bp):
ATCACACTGGACACATGACAAAGTAATGTCATTACTTTAGACACGTGACATGTAAGATAT
Found at i:100333 original size:44 final size:44
Alignment explanation
Indices: 100149--100648 Score: 321
Period size: 43 Copynumber: 11.7 Consensus size: 44
100139 GCCATTCAAT
* * *
100149 TTTTTAAC-TTTATAATTGAGGTCTCTAA-TTTTATCAATC-CTAG
1 TTTTT-ACTTTTATAATTGAGGTCCCTAATTTTTTTCAATCTC-AC
* * * *
100192 TTTTTA-TATTTATAATTGA-ATCCCTTAA-TTTTTT-AATTTAAA
1 TTTTTACT-TTTATAATTGAGGTCCC-TAATTTTTTTCAATCTCAC
* * *** *
100234 TTTTTACATTTATAATTAAGG-CCCTTAA-AAGTTTCAATCTCTC
1 TTTTTACTTTTATAATTGAGGTCCC-TAATTTTTTTCAATCTCAC
*
100277 TTTTTA-TCTTTATAATTGAGGTCCCTAATTTTTTTCAATATCAC
1 TTTTTACT-TTTATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
* * * * *
100321 TTTCTACTTTTATAATTAAAGCCCCTAGTTTTTTT-AATCTCAC
1 TTTTTACTTTTATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
* * *
100364 TTTTTACTTTTATAGTTGAGG----T-ATTTTTTTTAATTTCAC
1 TTTTTACTTTTATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
* * * * *
100403 CTTTTACATTTATAATTGA-ATCCCTTAATTTTTTT-AATCTAAT
1 TTTTTACTTTTATAATTGAGGTCCC-TAATTTTTTTCAATCTCAC
* * * *
100446 TTTTTACATTTATAATTAAGG-CCCTTAA-ATTTTTCAATCTCTC
1 TTTTTACTTTTATAATTGAGGTCCC-TAATTTTTTTCAATCTCAC
* **
100489 TTTTTTACCTTTATAATTGAGGTTTCTAATTTTTTTCAATCTCAC
1 -TTTTTACTTTTATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
* * * *
100534 TTTCTCCTTTTATAATTGAAG-CCCT--TTATTTTTTAATCTCAC
1 TTTTTACTTTTATAATTGAGGTCCCTAATT-TTTTTCAATCTCAC
* * ** * *
100576 TTTTTACCTTCATAATTGAAATCCCTAA--TTTTTCAATATAAC
1 TTTTTACTTTTATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
* *
100618 TTTTTACTTTTATAATTTAGGACCCTAATTT
1 TTTTTACTTTTATAATTGAGGTCCCTAATTT
100649 AATCATTTTC
Statistics
Matches: 352, Mismatches: 76, Indels: 57
0.73 0.16 0.12
Matches are distributed among these distances:
38 7 0.02
39 24 0.07
41 2 0.01
42 101 0.29
43 114 0.32
44 89 0.25
45 15 0.04
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.52
Consensus pattern (44 bp):
TTTTTACTTTTATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
Found at i:100472 original size:212 final size:211
Alignment explanation
Indices: 100193--100582 Score: 631
Period size: 212 Copynumber: 1.8 Consensus size: 211
100183 CAATCCTAGT
* *
100193 TTTTATATTTATAATTGAATCCCTTAATTTTTTAATTTAAATTTTTACATTTATAATTAAGGCCC
1 TTTTACATTTATAATTGAATCCCTTAATTTTTTAATCTAAATTTTTACATTTATAATTAAGGCCC
*
100258 TTAAAAGTTTCAATCTCTC-TTTTTATCTTTATAATTGAGGTCCCTAATTTTTTTCAATATCACT
66 TTAAAAGTTTCAATCTCTCTTTTTTACCTTTATAATTGAGGTCCCTAATTTTTTTCAATATCACT
100322 TTCTACTTTTATAATTAAAGCCCCTAGT-TTTTTTAATCTCACTTTTTACTTTTATAGTTGAGGT
131 TTCTACTTTTATAATTAAAG-CCCT-GTATTTTTTAATCTCACTTTTTACTTTTATAGTTGAGGT
100386 ATTTTTTTTAATTTCACC
194 ATTTTTTTTAATTTCACC
*
100404 TTTTACATTTATAATTGAATCCCTTAATTTTTTTAATCTAATTTTTTACATTTATAATTAAGGCC
1 TTTTACATTTATAATTGAATCCCTTAA-TTTTTTAATCTAAATTTTTACATTTATAATTAAGGCC
** ** *
100469 CTTAAATTTTTCAATCTCTCTTTTTTACCTTTATAATTGAGGTTTCTAATTTTTTTCAATCTCAC
65 CTTAAAAGTTTCAATCTCTCTTTTTTACCTTTATAATTGAGGTCCCTAATTTTTTTCAATATCAC
* * *
100534 TTTCTCCTTTTATAATTGAAGCCCTTTATTTTTTAATCTCACTTTTTAC
130 TTTCTACTTTTATAATTAAAGCCCTGTATTTTTTAATCTCACTTTTTAC
100583 CTTCATAATT
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
211 27 0.16
212 78 0.48
213 59 0.36
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (211 bp):
TTTTACATTTATAATTGAATCCCTTAATTTTTTAATCTAAATTTTTACATTTATAATTAAGGCCC
TTAAAAGTTTCAATCTCTCTTTTTTACCTTTATAATTGAGGTCCCTAATTTTTTTCAATATCACT
TTCTACTTTTATAATTAAAGCCCTGTATTTTTTAATCTCACTTTTTACTTTTATAGTTGAGGTAT
TTTTTTTAATTTCACC
Found at i:103911 original size:31 final size:33
Alignment explanation
Indices: 103876--103949 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 33
103866 TTTATTGCTC
103876 TCCGTT-GG-ATCGGGCTAGATCTATGGCTCTT
1 TCCGTTAGGTATCGGGCTAGATCTATGGCTCTT
103907 TCCGTTTGTCAGGTATCGGGCTAGATCTATGGCTCTT
1 TCCG--T-T-AGGTATCGGGCTAGATCTATGGCTCTT
103944 TCCGTT
1 TCCGTT
103950 TGTCAGGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
31 4 0.11
33 1 0.03
34 2 0.05
35 1 0.03
36 2 0.05
37 27 0.73
ACGTcount: A:0.12, C:0.23, G:0.27, T:0.38
Consensus pattern (33 bp):
TCCGTTAGGTATCGGGCTAGATCTATGGCTCTT
Found at i:103934 original size:37 final size:37
Alignment explanation
Indices: 103884--103958 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
103874 TCTCCGTTGG
103884 ATCGGGCTAGATCTATGGCTCTTTCCGTTTGTCAGGT
1 ATCGGGCTAGATCTATGGCTCTTTCCGTTTGTCAGGT
103921 ATCGGGCTAGATCTATGGCTCTTTCCGTTTGTCAGGT
1 ATCGGGCTAGATCTATGGCTCTTTCCGTTTGTCAGGT
103958 A
1 A
103959 AAACTCATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (37 bp):
ATCGGGCTAGATCTATGGCTCTTTCCGTTTGTCAGGT
Found at i:109629 original size:64 final size:64
Alignment explanation
Indices: 109551--109671 Score: 242
Period size: 64 Copynumber: 1.9 Consensus size: 64
109541 TTTCACATTC
109551 TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAATCAAGAAT
1 TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAATCAAGAAT
109615 TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAAT
1 TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAAT
109672 AAATTTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.36
Consensus pattern (64 bp):
TCAAATTTAAAGCTAGAAATTTTAATTTAATCGATCAAATCAATAAATCTTTAAAATCAAGAAT
Found at i:110547 original size:29 final size:29
Alignment explanation
Indices: 110514--110578 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
110504 ACAATATTCT
110514 ATAGTCGGATA-ACCATTATATAACTTTTG
1 ATAGTCGGA-AGACCATTATATAACTTTTG
* ** * *
110543 ATAGTTGGAAGATTATTTTGTAACTTTTG
1 ATAGTCGGAAGACCATTATATAACTTTTG
110572 ATAGTCG
1 ATAGTCG
110579 AGAGCTTTCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (29 bp):
ATAGTCGGAAGACCATTATATAACTTTTG
Found at i:114511 original size:42 final size:42
Alignment explanation
Indices: 114400--114551 Score: 118
Period size: 42 Copynumber: 3.7 Consensus size: 42
114390 TGGCGTAAAC
* *** * * *
114400 GCCACTAAAGTA-GAGTCTATAGC-GAAATTTATATAAAAAC
1 GCCACTAAAGTATGAGTCTTTAGCGGCGTTTTGTAGAAAAAT
* * *
114440 GCCACT-AA-TACGAGTCTATAGCGGTGTTTTGTA-AAGAAAT
1 GCCACTAAAGTATGAGTCTTTAGCGGCGTTTTGTAGAA-AAAT
* * *
114480 GCCACTAAAGTATGAGTCTTTAGTGGCGTTTTTTAGAATAAT
1 GCCACTAAAGTATGAGTCTTTAGCGGCGTTTTGTAGAAAAAT
* *
114522 GCCACTAAATTAT-AATCTTTAGCGGCGTTT
1 GCCACTAAAGTATGAGTCTTTAGCGGCGTTT
114552 ATAAAACGCT
Statistics
Matches: 92, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.02
39 15 0.16
40 21 0.23
41 17 0.18
42 35 0.38
43 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (42 bp):
GCCACTAAAGTATGAGTCTTTAGCGGCGTTTTGTAGAAAAAT
Found at i:115968 original size:20 final size:20
Alignment explanation
Indices: 115943--116117 Score: 172
Period size: 23 Copynumber: 8.2 Consensus size: 20
115933 CACAAAATAA
*
115943 TATATGAACAGTACCGATAC
1 TATATGAACAGTATCGATAC
115963 TATATGAACAGTA-CTGATAC
1 TATATGAACAGTATC-GATAC
*
115983 TATATGAACAATATCGATAC
1 TATATGAACAGTATCGATAC
*
116003 TGTATGAACAGTAGTATCGATAC
1 TATATGAAC---AGTATCGATAC
*
116026 TGTATGAACAATAGTATCGATAC
1 TATATGAAC---AGTATCGATAC
*
116049 TATATGAAAAATAGTATCGATAC
1 TATATG---AACAGTATCGATAC
116072 TATATGAACAATAGTATCGATAC
1 TATATGAAC---AGTATCGATAC
*
116095 TATATGAACAATATCGATAC
1 TATATGAACAGTATCGATAC
116115 TAT
1 TAT
116118 CAAGCCCAAC
Statistics
Matches: 136, Mismatches: 8, Indels: 22
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.01
20 58 0.43
21 1 0.01
23 74 0.54
26 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
TATATGAACAGTATCGATAC
Found at i:116024 original size:23 final size:23
Alignment explanation
Indices: 115952--116107 Score: 209
Period size: 23 Copynumber: 7.0 Consensus size: 23
115942 ATATATGAAC
*
115952 AGTACCGATACTATATGAAC---
1 AGTATCGATACTATATGAACAAT
115972 AGTA-CTGATACTATATGAAC-A-
1 AGTATC-GATACTATATGAACAAT
* *
115993 A-TATCGATACTGTATGAACAGT
1 AGTATCGATACTATATGAACAAT
*
116015 AGTATCGATACTGTATGAACAAT
1 AGTATCGATACTATATGAACAAT
*
116038 AGTATCGATACTATATGAAAAAT
1 AGTATCGATACTATATGAACAAT
116061 AGTATCGATACTATATGAACAAT
1 AGTATCGATACTATATGAACAAT
116084 AGTATCGATACTATATGAACAAT
1 AGTATCGATACTATATGAACAAT
116107 A
1 A
116108 TCGATACTAT
Statistics
Matches: 124, Mismatches: 6, Indels: 9
0.89 0.04 0.06
Matches are distributed among these distances:
19 1 0.01
20 33 0.27
21 2 0.02
22 1 0.01
23 87 0.70
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (23 bp):
AGTATCGATACTATATGAACAAT
Found at i:118660 original size:20 final size:20
Alignment explanation
Indices: 118599--118662 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
118589 CACAAAATAA
* *
118599 TGTATGAACAGAACTGATAT
1 TGTATGAACAGTACTGATAC
118619 TGTATGAACAATAGTA-TCGATAC
1 TGTATGAAC---AGTACT-GATAC
118642 TGTATGAACAGTACTGATAC
1 TGTATGAACAGTACTGATAC
118662 T
1 T
118663 CAAAATTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 19 0.51
21 1 0.03
22 1 0.03
23 16 0.43
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
TGTATGAACAGTACTGATAC
Found at i:121871 original size:23 final size:23
Alignment explanation
Indices: 121825--121974 Score: 177
Period size: 23 Copynumber: 6.8 Consensus size: 23
121815 AGGAGTCATT
*
121825 TGGTCCTTCGGGAC---TATATG
1 TGGTCCTTCGGGACAATTCTATG
121845 TGGTCCTTCGGGACAATTCTATG
1 TGGTCCTTCGGGACAATTCTATG
* *
121868 TGGTCTTTCGAGACAATTCTATG
1 TGGTCCTTCGGGACAATTCTATG
* *
121891 TGGTCATTCGGGACATTTCTATG
1 TGGTCCTTCGGGACAATTCTATG
* *
121914 TGGTCATTCGGGACATTTCTATG
1 TGGTCCTTCGGGACAATTCTATG
* *
121937 TGGTCCTTCTGGAC-A-TATATG
1 TGGTCCTTCGGGACAATTCTATG
121958 TGGTCCTTC-GGACAATT
1 TGGTCCTTCGGGACAATT
121975 TTACGAGGTT
Statistics
Matches: 115, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
20 18 0.16
21 15 0.13
22 1 0.01
23 81 0.70
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (23 bp):
TGGTCCTTCGGGACAATTCTATG
Found at i:133365 original size:76 final size:76
Alignment explanation
Indices: 133273--133424 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
133263 TGGCGCCTCC
133273 TCCACCTTTTCTGCTAATATACAAAGATCAACCACGTTTTAACATTCAACATATATAAGAAAGTA
1 TCCACCTTTTCTGCTAATATACAAAGATCAACCACGTTTTAACATTCAACATATATAAGAAAGTA
133338 TAAAATGGGAA
66 TAAAATGGGAA
133349 TCCACCTTTTCTGCTAATATACAAAGATCAACCACGTTTTAACATTCAACATATATAAGAAAGTA
1 TCCACCTTTTCTGCTAATATACAAAGATCAACCACGTTTTAACATTCAACATATATAAGAAAGTA
133414 TAAAATGGGAA
66 TAAAATGGGAA
133425 AAGTTATGAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (76 bp):
TCCACCTTTTCTGCTAATATACAAAGATCAACCACGTTTTAACATTCAACATATATAAGAAAGTA
TAAAATGGGAA
Found at i:135295 original size:77 final size:79
Alignment explanation
Indices: 135184--135339 Score: 282
Period size: 77 Copynumber: 2.0 Consensus size: 79
135174 CTTTGAAGAA
135184 GCTTAAATTAAGATTAACTTGGCAATTGACAATGTAATTTGGTATTAAAAGCAATAAAC-TTT-T
1 GCTTAAATTAAGATTAACTTGGCAATTGACAATGTAATTTGGTATTAAAAGCAATAAACTTTTAT
135247 ATGGAAAATTGAAGC
66 ATGG-AAATTGAAGC
135262 GCTT-AATTAAGATTAACTTGGCAATTGACAATGTAATTTGGTATTAAAAGCAATAAACTTTTAT
1 GCTTAAATTAAGATTAACTTGGCAATTGACAATGTAATTTGGTATTAAAAGCAATAAACTTTTAT
135326 ATGGAAATTGAAGC
66 ATGGAAATTGAAGC
135340 ACTGACCTTG
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
77 54 0.71
78 17 0.22
79 5 0.07
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (79 bp):
GCTTAAATTAAGATTAACTTGGCAATTGACAATGTAATTTGGTATTAAAAGCAATAAACTTTTAT
ATGGAAATTGAAGC
Found at i:135398 original size:31 final size:31
Alignment explanation
Indices: 135363--135425 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
135353 CACTCAGCAC
135363 GATTCTTTCCTTGACCATAGCAACGGTTGAA
1 GATTCTTTCCTTGACCATAGCAACGGTTGAA
135394 GATTCTTTCCTTGACCATAGCAACGGTTGAA
1 GATTCTTTCCTTGACCATAGCAACGGTTGAA
135425 G
1 G
135426 CGGGGTGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (31 bp):
GATTCTTTCCTTGACCATAGCAACGGTTGAA
Found at i:136266 original size:22 final size:22
Alignment explanation
Indices: 136240--136291 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
136230 TTAAAAATAT
136240 TTTG-AAATAATATAATATATAG
1 TTTGAAAAT-ATATAATATATAG
*
136262 TTTGAAAATATATATTATATAG
1 TTTGAAAATATATAATATATAG
*
136284 TTTTAAAA
1 TTTGAAAA
136292 CATTTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (22 bp):
TTTGAAAATATATAATATATAG
Found at i:136302 original size:34 final size:35
Alignment explanation
Indices: 136262--136509 Score: 140
Period size: 35 Copynumber: 7.1 Consensus size: 35
136252 TAATATATAG
136262 TTTGAAAATATATATTATATAGTTTT-AAAACATT
1 TTTGAAAATATATATTATATAGTTTTGAAAACATT
*
136296 TTTGAAAAAAATATATATAATATATAGTTTTGGAAA-ATAT
1 TTTG---AAAATATATAT--TATATAGTTTTGAAAACAT-T
* * * *
136336 TTTGAAAATGTATATAATATAATTTTGAAAATATT
1 TTTGAAAATATATATTATATAGTTTTGAAAACATT
* * * *
136371 TTGGAAATGTATATAATATATAATTTTGAAAA-ATAT
1 TTTGAAA-ATATATATTATATAGTTTTGAAAACAT-T
** * *
136407 TTTTCAAA-A-ATA-TATATGGTTTTAAAAACAATT
1 TTTGAAAATATATATTATATAGTTTTGAAAAC-ATT
* ** * *
136440 TTTGAAAATATTTCAAAATATA--TATAAAAACAATT
1 TTTGAAAATATAT-ATTATATAGTTTTGAAAAC-ATT
*
136475 TTTGAAAA-ATATA-TATTATAG-TTTGAAAATATT
1 TTTGAAAATATATATTA-TATAGTTTTGAAAACATT
136508 TT
1 TT
136510 AAAAGCATAT
Statistics
Matches: 168, Mismatches: 28, Indels: 37
0.72 0.12 0.16
Matches are distributed among these distances:
32 14 0.08
33 20 0.12
34 17 0.10
35 43 0.26
36 28 0.17
37 25 0.15
39 13 0.08
40 8 0.05
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (35 bp):
TTTGAAAATATATATTATATAGTTTTGAAAACATT
Found at i:136307 original size:37 final size:39
Alignment explanation
Indices: 136266--136423 Score: 140
Period size: 37 Copynumber: 4.3 Consensus size: 39
136256 ATATAGTTTG
136266 AAAATATATAT-TATATAGTTTT-AAAACAT-TTTTGAAA
1 AAAATATATATATATATAGTTTTGAAAA-ATATTTTGAAA
*
136303 AAAATATATATAATATATAGTTTTGGAAAATATTTTG---
1 AAAATATATAT-ATATATAGTTTTGAAAAATATTTTGAAA
* * *
136340 AAAATGTATATA-ATATAATTTTG-AAAATATTTTG-GA
1 AAAATATATATATATATAGTTTTGAAAAATATTTTGAAA
** * **
136376 AATGTATATA-ATATATAATTTTGAAAAATATTTT-TCA
1 AAAATATATATATATATAGTTTTGAAAAATATTTTGAAA
136413 AAAATATATAT
1 AAAATATATAT
136424 GGTTTTAAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
34 11 0.11
35 11 0.11
36 19 0.19
37 40 0.39
39 13 0.13
40 8 0.08
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (39 bp):
AAAATATATATATATATAGTTTTGAAAAATATTTTGAAA
Found at i:136309 original size:57 final size:57
Alignment explanation
Indices: 136204--136314 Score: 149
Period size: 56 Copynumber: 2.0 Consensus size: 57
136194 TAAATTGGTT
* *
136204 TTTGAAACATATATATAATATAATTTTTAAAAATATTTTGAAATAATATAATATATAG
1 TTTGAAACATATATATAATATAAGTTTTAAAAATATTTTGAAAAAATAT-ATATATAG
*
136262 TTTGAAA-ATATATATTATAT-AGTTTTAAAACAT-TTTTGAAAAAA-ATATATATA
1 TTTGAAACATATATATAATATAAGTTTTAAAA-ATATTTTGAAAAAATATATATATA
136315 ATATATAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
54 7 0.14
55 2 0.04
56 19 0.39
57 14 0.29
58 7 0.14
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (57 bp):
TTTGAAACATATATATAATATAAGTTTTAAAAATATTTTGAAAAAATATATATATAG
Found at i:136568 original size:31 final size:29
Alignment explanation
Indices: 136474--136589 Score: 88
Period size: 33 Copynumber: 3.7 Consensus size: 29
136464 TAAAAACAAT
* *
136474 TTTTGAAAAATATATATTATAGTTTGAAAATA
1 TTTT-AAAAATATATA--ATATTTTAAAAATA
136506 TTTTAAAAGCATATATAATATGGTTTAAAAATGA
1 TTTTAAAA--ATATATAATAT--TTTAAAAAT-A
* *
136540 TTTTCAAAAATATATAATATTTTCAAAATTT
1 TTTT-AAAAATATATAATATTTT-AAAAATA
**
136571 TTTTAAAACCATATAATAT
1 TTTTAAAAATATATAATAT
136590 GAAAATGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
30 13 0.18
31 14 0.20
32 9 0.13
33 26 0.37
34 5 0.07
35 4 0.06
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (29 bp):
TTTTAAAAATATATAATATTTTAAAAATA
Found at i:136710 original size:30 final size:28
Alignment explanation
Indices: 136651--136712 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
136641 TTTTTTTTTT
* * * *
136651 TATATGTTTTAAAAATTTTTGAAATATA
1 TATATGTTTGAAAAAATTTTAAAACATA
136679 TATATGTTTGAAAATAATTTTAAAAGCATA
1 TATATGTTTGAAAA-AATTTTAAAA-CATA
136709 TATA
1 TATA
136713 ATATATGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 13 0.46
29 8 0.29
30 7 0.25
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (28 bp):
TATATGTTTGAAAAAATTTTAAAACATA
Found at i:136749 original size:14 final size:14
Alignment explanation
Indices: 136732--136776 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 14
136722 TTTAAAAATG
136732 ATTTTTTATTTATT
1 ATTTTTTATTTATT
136746 A-TTTTT-TTT-TT
1 ATTTTTTATTTATT
*
136757 GTTTTTTATTTATT
1 ATTTTTTATTTATT
136771 ATTTTT
1 ATTTTT
136777 GAATATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 2 0.08
12 8 0.31
13 8 0.31
14 8 0.31
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (14 bp):
ATTTTTTATTTATT
Found at i:136786 original size:25 final size:25
Alignment explanation
Indices: 136733--136789 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
136723 TTAAAAATGA
** *
136733 TTTTTTATTTATTATTTTTTTTTTG
1 TTTTTTATTTATTATTTTTAATATG
*
136758 TTTTTTATTTATTATTTTTGAATATT
1 TTTTTTATTTATTATTTTT-AATATG
136784 TTTTTT
1 TTTTTT
136790 TCCCTTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.81
Consensus pattern (25 bp):
TTTTTTATTTATTATTTTTAATATG
Found at i:137549 original size:15 final size:14
Alignment explanation
Indices: 137529--137566 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
137519 CTACCCTTAG
137529 TTTTGGCTGTCTCGA
1 TTTTGGCT-TCTCGA
*
137544 TTTTGGC-TCTCGG
1 TTTTGGCTTCTCGA
137557 TTTTGGCTTC
1 TTTTGGCTTC
137567 GGGGTGACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 12 0.57
14 2 0.10
15 7 0.33
ACGTcount: A:0.03, C:0.21, G:0.26, T:0.50
Consensus pattern (14 bp):
TTTTGGCTTCTCGA
Found at i:138128 original size:6 final size:6
Alignment explanation
Indices: 138101--138206 Score: 53
Period size: 6 Copynumber: 17.2 Consensus size: 6
138091 AATTTAACCT
* *
138101 TTTTTC TTTTTA TTTCGT- TTTTTA -TTTTA TTTTATA CTTAATTTA -T-TTA
1 TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTT-TA -TT--TTTA TTTTTA
*
138150 TTTTTA TTTTTTA TTTTTA TTTTAATA TTTTTTA TTTTT- TTATT- TTTTTA
1 TTTTTA -TTTTTA TTTTTA TTTT--TA -TTTTTA TTTTTA TTTTTA TTTTTA
*
138200 TATTTA T
1 TTTTTA T
138207 ATATTTCACA
Statistics
Matches: 80, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
4 3 0.04
5 15 0.19
6 38 0.47
7 12 0.15
8 4 0.05
9 6 0.08
10 2 0.03
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:138161 original size:8 final size:8
Alignment explanation
Indices: 138150--138200 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
138140 AATTTATTTA
138150 TTTTTATT
1 TTTTTATT
*
138158 TTTTATTTT
1 TTTT-TATT
138167 TATTTTAATAT
1 T-TTTT-AT-T
138178 TTTTTATT
1 TTTTTATT
138186 TTTTTATT
1 TTTTTATT
138194 TTTTTAT
1 TTTTTAT
138201 ATTTATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 20 0.54
9 7 0.19
10 8 0.22
11 2 0.05
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTATT
Found at i:138162 original size:7 final size:7
Alignment explanation
Indices: 138141--138197 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
138131 TTTATACTTA
138141 ATTTATTT
1 ATTT-TTT
138149 A-TTTTT
1 ATTTTTT
138155 ATTTTTT
1 ATTTTTT
138162 A-TTTTT
1 ATTTTTT
*
138168 ATTTTAAT
1 ATTTT-TT
138176 ATTTTTT
1 ATTTTTT
138183 ATTTTTTT
1 A-TTTTTT
138191 ATTTTTT
1 ATTTTTT
138198 TATATTTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
6 10 0.23
7 19 0.44
8 14 0.33
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (7 bp):
ATTTTTT
Found at i:138162 original size:33 final size:34
Alignment explanation
Indices: 138118--138211 Score: 99
Period size: 33 Copynumber: 2.9 Consensus size: 34
138108 TTTTATTTCG
*
138118 TTTTTTATTTTATTTTATA-CTTAAT-TTATTTA
1 TTTTTTTTTTTATTTTATATCTTAATATTATTTA
* *
138150 TTTTTATTTTTTATTTT-TATTTTAATATTTTTTA
1 TTTTT-TTTTTTATTTTATATCTTAATATTATTTA
*
138184 TTTTTTTATTT-TTTTATAT-TTATATATT
1 TTTTTTTTTTTATTTTATATCTTA-ATATT
138212 TCACAATTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
32 14 0.26
33 28 0.53
34 11 0.21
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (34 bp):
TTTTTTTTTTTATTTTATATCTTAATATTATTTA
Found at i:138170 original size:39 final size:37
Alignment explanation
Indices: 138118--138206 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 37
138108 TTTTATTTCG
138118 TTTTTTA-TTTTATTTT-ATACTTAATTTATTTATTTT-T
1 TTTTTTATTTTTATTTTAATA-TT-ATTTATTT-TTTTAT
*
138155 ATTTTTTATTTTTATTTTAATATTTTTTATTTTTTTAT
1 -TTTTTTATTTTTATTTTAATATTATTTATTTTTTTAT
*
138193 TTTTTTATATTTAT
1 TTTTTTATTTTTAT
138207 ATATTTCACA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
37 17 0.37
38 15 0.33
39 11 0.24
40 3 0.07
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.78
Consensus pattern (37 bp):
TTTTTTATTTTTATTTTAATATTATTTATTTTTTTAT
Found at i:138178 original size:21 final size:20
Alignment explanation
Indices: 138100--138196 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 20
138090 AAATTTAACC
* *
138100 TTTTTTCTTTTTATTTCGTTTT
1 TTTTTTATTTTTATTT--TTTA
** *
138122 TTATTTTA-TTTTATACTTAA
1 TT-TTTTATTTTTATTTTTTA
138142 TTTATTTATTTTTATTTTTTA
1 TTT-TTTATTTTTATTTTTTA
138163 -TTTTTATTTTAATATTTTTTA
1 TTTTTTATTTT--TATTTTTTA
138184 TTTTTTTATTTTT
1 -TTTTTTATTTTT
138197 TTATATTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
19 9 0.15
20 10 0.17
21 19 0.32
22 8 0.13
23 14 0.23
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (20 bp):
TTTTTTATTTTTATTTTTTA
Found at i:139281 original size:16 final size:16
Alignment explanation
Indices: 139244--139281 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
139234 TCTCACTAAC
139244 TTTTTCTTTTCATTTT
1 TTTTTCTTTTCATTTT
139260 TGTTTTC-TTTCATTTT
1 T-TTTTCTTTTCATTTT
139276 ATTTTT
1 -TTTTT
139282 ATCATTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTCATTTT
Found at i:141065 original size:2 final size:2
Alignment explanation
Indices: 141058--141141 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
141048 CATGCATAAG
141058 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
141100 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
141142 GTTTATAGGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142696 original size:22 final size:22
Alignment explanation
Indices: 142671--142714 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
142661 ATGAGAAAGT
*
142671 ATATTGTTTTGTAAGAGTTTAA
1 ATATTGTTTTGTAAGAATTTAA
142693 ATATTGTTTTGTAAGAATTTAA
1 ATATTGTTTTGTAAGAATTTAA
142715 GAATGTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (22 bp):
ATATTGTTTTGTAAGAATTTAA
Found at i:153384 original size:18 final size:18
Alignment explanation
Indices: 153340--153396 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
153330 CTTTCCTAAC
* * *
153340 ATTTTTTTATTTATATAT
1 ATTTATTTATTTTTATTT
* *
153358 ATGTGTTTATTTTTATTT
1 ATTTATTTATTTTTATTT
*
153376 ATTTATTTA-TTTCATTT
1 ATTTATTTATTTTTATTT
153393 ATTT
1 ATTT
153397 TCTACATAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 11 0.34
18 21 0.66
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.72
Consensus pattern (18 bp):
ATTTATTTATTTTTATTT
Found at i:153809 original size:9 final size:9
Alignment explanation
Indices: 153797--153862 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
153787 ATATTTTTTC
153797 ATTTATATT
1 ATTTATATT
*
153806 ATTTTTATT
1 ATTTATATT
*
153815 TTTTATA-T
1 ATTTATATT
153823 ATATTATATAT
1 AT-TTATAT-T
153834 ATATTATA-T
1 AT-TTATATT
153843 ATTTAT-TT
1 ATTTATATT
153851 ATTTAT-TT
1 ATTTATATT
153859 ATTT
1 ATTT
153863 GTTTTCACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
8 19 0.39
9 21 0.43
11 9 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTATATT
Found at i:153832 original size:11 final size:11
Alignment explanation
Indices: 153818--153849 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
153808 TTTTATTTTT
153818 TATATATATTA
1 TATATATATTA
153829 TATATATATTA
1 TATATATATTA
*
153840 TATATTTATT
1 TATATATATT
153850 TATTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATATATTA
Found at i:153849 original size:4 final size:4
Alignment explanation
Indices: 153788--153862 Score: 52
Period size: 4 Copynumber: 19.2 Consensus size: 4
153778 TCCATTTTAA
* * *
153788 TATT T-TT TCATT TATAT TA-T T-TT TATT T-TT TATA TATAT TATA TATA
1 TATT TATT T-ATT TAT-T TATT TATT TATT TATT TATT TAT-T TATT TATT
*
153835 TA-T TATA TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
153863 GTTTTCACTT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
3 12 0.21
4 36 0.63
5 9 0.16
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:154404 original size:11 final size:11
Alignment explanation
Indices: 154388--154412 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
154378 TTTCATTATA
154388 GTTGTACTAAT
1 GTTGTACTAAT
154399 GTTGTACTAAT
1 GTTGTACTAAT
154410 GTT
1 GTT
154413 TTTTCAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (11 bp):
GTTGTACTAAT
Found at i:156947 original size:23 final size:24
Alignment explanation
Indices: 156903--156977 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 24
156893 TCCAATCAAG
* *
156903 AACAAAA-AAGAAA-AGAAGCAAA
1 AACAAAAGAAAAAAGAGAAACAAA
*
156925 AA-AAGAGAAAAAAGAGAAACAAA
1 AACAAAAGAAAAAAGAGAAACAAA
* *
156948 AACAAAAGGAAAAAGA-AATCAAA
1 AACAAAAGAAAAAAGAGAAACAAA
*
156971 AAGAAAA
1 AACAAAA
156978 AGGGACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
21 3 0.07
22 7 0.16
23 22 0.51
24 11 0.26
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (24 bp):
AACAAAAGAAAAAAGAGAAACAAA
Found at i:158559 original size:36 final size:36
Alignment explanation
Indices: 158519--158589 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
158509 TTAAAAGAAG
* *
158519 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
* *
158555 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
158590 TAAACTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
Found at i:159047 original size:106 final size:106
Alignment explanation
Indices: 158924--159449 Score: 688
Period size: 106 Copynumber: 5.0 Consensus size: 106
158914 ATCGTGCCAT
* *
158924 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACT-AGTTGTCAACAAACAATTTCCCA
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGA-TTGTCAACAAACAATTTCCCA
*
158988 ATTTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGGAC
65 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* ** * * *
159030 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGAAGACTGGTTGTCAACAAACAATTTTCCAG
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
* * *
159095 TTTCAAAGCCAATTTCAACTTCATAGTGAAGGATATTGGAC
66 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * * *
159136 TCAAGACAACACAAGATCAACTTCGCAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAA
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
* * *
159201 TTTCATAGCCAATTTCAACTTCCCAGCGAAGGATCTTGGAC
66 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * *
159242 CCAAGACAACACAAGCTCAACTTCACGACGAAGGGGTGGCTGATTGTCAAC-AA-AATTT--C-A
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
* *
159302 -TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGAC
66 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * * *
159342 TCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAATTTCCCAG
1 TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
* * *
159407 TTCCAGATCCAATTTCAACTTCACAGCGGAGGATATTGGAC
66 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
159448 TC
1 TC
159450 GGAACAATAC
Statistics
Matches: 362, Mismatches: 51, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
100 78 0.22
101 3 0.01
102 6 0.02
104 5 0.01
105 2 0.01
106 268 0.74
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
TCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCCCAA
TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
Found at i:161085 original size:2 final size:2
Alignment explanation
Indices: 161078--161103 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
161068 TTTCCGTTCC
161078 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
161104 TACTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:161175 original size:4 final size:4
Alignment explanation
Indices: 161164--161223 Score: 54
Period size: 4 Copynumber: 15.0 Consensus size: 4
161154 CTTTCCTAAC
* *
161164 ATTT -TTT ATTT ATATAT ATGT GTTT ATTT --TT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT AT-T-T ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
161211 ATTT CATTT ATTT
1 ATTT -ATTT ATTT
161224 TCTACATAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
2 2 0.04
3 3 0.07
4 33 0.72
5 5 0.11
6 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:161189 original size:18 final size:18
Alignment explanation
Indices: 161168--161212 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
161158 CCTAACATTT
*
161168 TTTATTTATATATATGTG
1 TTTATTTATATATATGTA
* * *
161186 TTTATTTTTATTTATTTA
1 TTTATTTATATATATGTA
161204 TTTATTTAT
1 TTTATTTAT
161213 TTCATTTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (18 bp):
TTTATTTATATATATGTA
Found at i:161650 original size:7 final size:7
Alignment explanation
Indices: 161640--161692 Score: 54
Period size: 7 Copynumber: 7.1 Consensus size: 7
161630 TTTATACATA
161640 TTTATTT
1 TTTATTT
161647 TTTATTT
1 TTTATTT
161654 ATTTATTT
1 -TTTATTT
161662 TTTATTT
1 TTTATTT
*
161669 GTTT-TCACT
1 -TTTAT--TT
161678 TTTATTT
1 TTTATTT
161685 TTTATTT
1 TTTATTT
161692 T
1 T
161693 CATGCATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 24 0.62
8 13 0.33
9 2 0.05
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTATTT
Found at i:161656 original size:15 final size:15
Alignment explanation
Indices: 161638--161668 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
161628 TTTTTATACA
161638 TATTTATTTTTTATT
1 TATTTATTTTTTATT
161653 TATTTATTTTTTATT
1 TATTTATTTTTTATT
161668 T
1 T
161669 GTTTTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TATTTATTTTTTATT
Found at i:161660 original size:38 final size:39
Alignment explanation
Indices: 161612--161691 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 39
161602 TATTTTGTCC
161612 TTTATATTA-TTTTGATTT-TTTAT-ACATATTTATTTTTTA
1 TTTATATTATTTTTGATTTGTTT-TCAC-T-TTTATTTTTTA
*
161651 TTTAT-TTATTTTTTATTTGTTTTCACTTTTATTTTTTA
1 TTTATATTATTTTTGATTTGTTTTCACTTTTATTTTTTA
161689 TTT
1 TTT
161692 TCATGCATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
38 17 0.46
39 15 0.41
40 5 0.14
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.74
Consensus pattern (39 bp):
TTTATATTATTTTTGATTTGTTTTCACTTTTATTTTTTA
Found at i:166080 original size:20 final size:20
Alignment explanation
Indices: 166051--166093 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
166041 ATTCCACCAC
166051 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
166071 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
166091 ATG
1 ATG
166094 AGATCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:176077 original size:85 final size:85
Alignment explanation
Indices: 175916--176509 Score: 776
Period size: 85 Copynumber: 7.0 Consensus size: 85
175906 AAACTATTCG
* * * * * *
175916 CAGCATAACTCAAGGCGAAAAGAGCTATCTGTCAGC-AAAACCTTTGAGTTCGATTACAGTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTCAGC
*
175980 TCAAGGTCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * * * **
176000 CAGCATAACTTAAGGCAAGAAGGGTTATTTGTCAACAAAAAACTTCGAGTTCGATTACATTCAAT
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTCAGC
176065 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * * * * * *
176085 CAGTATAGCTCAAGGCGAGAAAGGCTAACTATCAGCGGAAACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTCAGC
* *
176150 TAAAGGGCTTATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* *
176170 CAGCATAACTCAAGGCGAGAAGGATTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTAAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTCAGC
*
176235 TCAAGGGCTTATCAAATTTA
66 TCAAGGGCATATCAAATTTA
** * * ** * *
176255 CAATATAACTCAAGGCGAAAAGGGTTATTTGTCAGTGAAAACCTTCGAGTTCGATTATATTCAAC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTCAGC
176320 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
176340 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTCAGC
* *
176405 TCAAGGGCATATTAAATATA
66 TCAAGGGCATATCAAATTTA
* * * * * * * *
176425 CAACATAGCTCAAGGTGAGAAGGGCTATCTATCAACAAAAACCTTCGATTTCGATTACATACAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTCAGC
176490 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
176510 TTGCTCAAGG
Statistics
Matches: 437, Mismatches: 72, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
84 29 0.07
85 408 0.93
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (85 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACCTTCGAGTTCGATTACATTCAGC
TCAAGGGCATATCAAATTTA
Found at i:176524 original size:24 final size:24
Alignment explanation
Indices: 176488--176533 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
176478 ATTACATACA
176488 GCTCAAGGGCATATCAAATTTATT
1 GCTCAAGGGCATATCAAATTTATT
*
176512 GCTCAAGGTCATATCAAATTTA
1 GCTCAAGGGCATATCAAATTTA
176534 CAACATAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (24 bp):
GCTCAAGGGCATATCAAATTTATT
Found at i:176610 original size:109 final size:109
Alignment explanation
Indices: 176403--176613 Score: 300
Period size: 109 Copynumber: 1.9 Consensus size: 109
176393 ATTACATTCA
*
176403 GCTCAAGGGCATATTAAATATACAACATAGCTCAAGGTGAGAAGGGCTATCTATCAACAAAAACC
1 GCTCAAGGGCATATCAAATATACAACATAGCTCAAGGTGAGAAGGGCTATCTATCAACAAAAACC
* *
176468 TTCGATTTCGATTACATACAGCTCAAGGGCATATCAAATTTATT
66 TTCGAGTTCGATTACATACAGCTCAAGGACATATCAAATTTATT
* * * *
176512 GCTCAAGGTCATATCAAATTTACAACATAGCTTAAGGTGAGAAGGGCTATCTGTCAACAAAAA-C
1 GCTCAAGGGCATATCAAATATACAACATAGCTCAAGGTGAGAAGGGCTATCTATCAACAAAAACC
* * *
176576 TGTCGAGTTCGATT-CTATTCAGCTCGATGACATATCAA
66 T-TCGAGTTCGATTAC-ATACAGCTCAAGGACATATCAA
176614 CTGCATAGTA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
108 3 0.03
109 87 0.97
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (109 bp):
GCTCAAGGGCATATCAAATATACAACATAGCTCAAGGTGAGAAGGGCTATCTATCAACAAAAACC
TTCGAGTTCGATTACATACAGCTCAAGGACATATCAAATTTATT
Found at i:176828 original size:175 final size:175
Alignment explanation
Indices: 176532--177145 Score: 753
Period size: 175 Copynumber: 3.5 Consensus size: 175
176522 ATATCAAATT
* * *
176532 TACAACATAGCTTAAGGTGAGAAGGGCTATCTGTCAACAAAAACTGTCGAGTTCGATTCTATTCA
1 TACAACATAGCTCAAGGTAAGAAGGGCTATCTGTCAACAAAAACTGTCGAGTTCGATTCCATTCA
* * * * *
176597 GCTCGATGACATATCAACTGCATAGTAGCAGCGAGGAACTACTTTTCGGTTGGAGTTTAAACCGA
66 GCTCGAGGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGGAGTTTAAACCGA
*
176662 GGTCTTTAAGTCAAGAGGAAGATCTGGGGTAATCTCTCAGCTTAG
131 GGTCTTTAAGTCAAGAGGAAGATCTAGGGTAATCTCTCAGCTTAG
* * * * * *
176707 TATAGCATAGCTCAAGGTAAGAAGGGCTATCTGTCAATAAAAACTGTCAAGTTTGATTACATTCA
1 TACAACATAGCTCAAGGTAAGAAGGGCTATCTGTCAACAAAAACTGTCGAGTTCGATTCCATTCA
* * *
176772 ACTCGATGACATATCAACCGTATGGTAGCAGCGAGGAACTACTTTCCGATTGGAGTTTAAACCGA
66 GCTCGAGGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGGAGTTTAAACCGA
* * * *
176837 GCTCTTTAAGTCAGGAGGAAGGTCTAGGGCAATCTCTCAGCTTAG
131 GGTCTTTAAGTCAAGAGGAAGATCTAGGGTAATCTCTCAGCTTAG
* ** * *
176882 TACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACTTTCGAGTTCGATTCCATTCA
1 TACAACATAGCTCAAGGTAAGAAGGGCTATCTGTCAACAAAAACTGTCGAGTTCGATTCCATTCA
* * ** * *
176947 GCTCGAGGGCCTATCAACCGCATGGTAGCAGTAAGGAACTACTTTCCGTTTGAAGTTTAAACCGA
66 GCTCGAGGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGGAGTTTAAACCGA
* * * * * *
177012 GGTCTTTAAGTCAAGAAGAATATCCAGTGTAATCTCTTAGCCTAG
131 GGTCTTTAAGTCAAGAGGAAGATCTAGGGTAATCTCTCAGCTTAG
* * *** * * * * *
177057 TACATCATAGCTTAA-GTCAAGAAAATCTATCTTTCAACGAAAACTTTTGAGTTTGATTCCATTC
1 TACAACATAGCTCAAGGT-AAGAAGGGCTATCTGTCAACAAAAACTGTCGAGTTCGATTCCATTC
* *
177121 AGCTCGAGGGCATATCAACCACATG
65 AGCTCGAGGACATATCAACCGCATG
177146 ATAGTGTTGA
Statistics
Matches: 373, Mismatches: 65, Indels: 2
0.85 0.15 0.00
Matches are distributed among these distances:
174 1 0.00
175 372 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (175 bp):
TACAACATAGCTCAAGGTAAGAAGGGCTATCTGTCAACAAAAACTGTCGAGTTCGATTCCATTCA
GCTCGAGGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGGAGTTTAAACCGA
GGTCTTTAAGTCAAGAGGAAGATCTAGGGTAATCTCTCAGCTTAG
Found at i:178113 original size:12 final size:12
Alignment explanation
Indices: 178075--178120 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
178065 CGAACATAAC
178075 AAAAACACCAAG
1 AAAAACACCAAG
* *
178087 -AAAA-TCCAATC
1 AAAAACACCAA-G
178098 AAAAACACCAAG
1 AAAAACACCAAG
178110 AAAAACACCAA
1 AAAAACACCAA
178121 AATCTCGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
10 4 0.15
11 4 0.15
12 15 0.56
13 4 0.15
ACGTcount: A:0.65, C:0.26, G:0.04, T:0.04
Consensus pattern (12 bp):
AAAAACACCAAG
Found at i:178846 original size:10 final size:10
Alignment explanation
Indices: 178821--178896 Score: 64
Period size: 10 Copynumber: 7.4 Consensus size: 10
178811 AAATTTATCC
178821 ATTTTTCTTTT
1 ATTTTT-TTTT
178832 A-TTTTTTTT
1 ATTTTTTTTT
*
178841 ATTTTTTTACTC
1 ATTTTTTT--TT
*
178853 AATTTTTTTT
1 ATTTTTTTTT
* *
178863 AATATTTTTT
1 ATTTTTTTTT
*
178873 ATTTTATTTT
1 ATTTTTTTTT
*
178883 ATTTTTTTAT
1 ATTTTTTTTT
178893 ATTT
1 ATTT
178897 ATATATTTCG
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
9 5 0.09
10 39 0.74
11 1 0.02
12 8 0.15
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:178903 original size:18 final size:18
Alignment explanation
Indices: 178867--178904 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
178857 TTTTTTAATA
*
178867 TTTTTTATTTTATTTTAT
1 TTTTTTATTTTATTATAT
178885 TTTTTTATATTTA-TATAT
1 TTTTTTAT-TTTATTATAT
178903 TT
1 TT
178905 CGCAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTATTTTATTATAT
Found at i:180291 original size:52 final size:51
Alignment explanation
Indices: 180235--180380 Score: 150
Period size: 57 Copynumber: 2.7 Consensus size: 51
180225 TTCATTTATA
*
180235 ATTTAAAATAATTGTAAAAATATTTTAATTTATTTATTAGAA-GTTGTGAATC
1 ATTTAAAATAATTGTAAAAATA-TTTAATTTATTTATTA-AATGTTATGAATC
* * *
180287 ATTTAAAAATAATGGTAGAAAAAATTAATTTAATTAATTTATTAAATTTTATGAATC
1 ATTT-AAAATAAT--T-GTAAAAA-T-ATTTAATTTATTTATTAAATGTTATGAATC
* *
180344 ATGTAAAAATAATTGTAAAAACATTTAATTTATTTAT
1 AT-TTAAAATAATTGTAAAAATATTTAATTTATTTAT
180381 ATATAAACTA
Statistics
Matches: 78, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
52 18 0.23
53 8 0.10
54 6 0.08
55 2 0.03
56 8 0.10
57 34 0.44
58 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (51 bp):
ATTTAAAATAATTGTAAAAATATTTAATTTATTTATTAAATGTTATGAATC
Found at i:194465 original size:18 final size:18
Alignment explanation
Indices: 194418--194470 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
194408 ATTATCAGTG
*
194418 GTCCTTCGGGACATAATG
1 GTCCTTCGGGACATAATA
** * *
194436 GTTTTTCAGGACATAGTA
1 GTCCTTCGGGACATAATA
194454 GTCCTTCGGGACA-AATA
1 GTCCTTCGGGACATAATA
194471 TTCAGTGCCC
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (18 bp):
GTCCTTCGGGACATAATA
Found at i:204151 original size:60 final size:60
Alignment explanation
Indices: 204083--204205 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
204073 AACATAATGA
* * * * *
204083 ATAGTTGAGTGA-TCATTTTACAACTTTTAATAGTTGGGGGACTCAACAAAGTAACATCCT
1 ATAGTTGAGAGACT-ATTTTACAACTTTTAATAGTTAGAGGACCCAACAAAGTAACACCCT
**
204143 ATAGTTGAGAGACTATTTTGTAACTTTTAATAGTTAGAGGACCCAACAAAGTAACACCCT
1 ATAGTTGAGAGACTATTTTACAACTTTTAATAGTTAGAGGACCCAACAAAGTAACACCCT
204203 ATA
1 ATA
204206 ATAAGAAGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (60 bp):
ATAGTTGAGAGACTATTTTACAACTTTTAATAGTTAGAGGACCCAACAAAGTAACACCCT
Found at i:204480 original size:2 final size:2
Alignment explanation
Indices: 204473--204498 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
204463 GTTTTAAGAT
204473 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
204499 ATTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:205460 original size:20 final size:20
Alignment explanation
Indices: 205435--205480 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
205425 ACATGTTTAT
205435 GTACAAACAAACCACCACAA
1 GTACAAACAAACCACCACAA
205455 GTACAAACAAACCACCACAA
1 GTACAAACAAACCACCACAA
205475 GTACAA
1 GTACAA
205481 TGATTGGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.54, C:0.33, G:0.07, T:0.07
Consensus pattern (20 bp):
GTACAAACAAACCACCACAA
Found at i:220575 original size:32 final size:33
Alignment explanation
Indices: 220501--220577 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 33
220491 GTAGAGTGTT
*
220501 GCATTCAGATAATACACAATAGTGTCAATGTTC
1 GCATTCAGATAATACACAATAGTGTCAATGTCC
* * * * *
220534 -AATTTAGATAATGCACATTAGTGTCAGTG-CC
1 GCATTCAGATAATACACAATAGTGTCAATGTCC
220565 GCATTCAGATAAT
1 GCATTCAGATAAT
220578 CCATAGCAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
31 1 0.03
32 34 0.97
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (33 bp):
GCATTCAGATAATACACAATAGTGTCAATGTCC
Found at i:233482 original size:20 final size:17
Alignment explanation
Indices: 233445--233483 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
233435 AAACGATCAA
233445 ATCAATAAAATTAAAAT
1 ATCAATAAAATTAAAAT
233462 ATCAATGAACAATTGAAAAT
1 ATCAAT-AA-AATT-AAAAT
233482 AT
1 AT
233484 GCACATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 4 0.21
20 7 0.37
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (17 bp):
ATCAATAAAATTAAAAT
Found at i:236458 original size:21 final size:21
Alignment explanation
Indices: 236429--236470 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
236419 TACACTCTCC
*
236429 TCCTGTTCAACATCAACTCTT
1 TCCTATTCAACATCAACTCTT
236450 TCCTATTCAACATCAACTCTT
1 TCCTATTCAACATCAACTCTT
236471 AAGTCTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.38
Consensus pattern (21 bp):
TCCTATTCAACATCAACTCTT
Found at i:236741 original size:18 final size:17
Alignment explanation
Indices: 236707--236745 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
236697 TTGGCAGTAT
*
236707 TAAGCCCACTGCCAGCA
1 TAAGCCCACTACCAGCA
*
236724 CTAAGCCCACTACTAGCA
1 -TAAGCCCACTACCAGCA
236742 TAAG
1 TAAG
236746 GTATATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.36, G:0.15, T:0.15
Consensus pattern (17 bp):
TAAGCCCACTACCAGCA
Found at i:238485 original size:12 final size:13
Alignment explanation
Indices: 238457--238489 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
238447 ATCCTTTGAT
238457 ATTATATATTTGC
1 ATTATATATTTGC
*
238470 ATTATA-ATTTGG
1 ATTATATATTTGC
238482 ATTATATA
1 ATTATATA
238490 ATATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (13 bp):
ATTATATATTTGC
Found at i:249402 original size:43 final size:43
Alignment explanation
Indices: 249321--249404 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
249311 AGTACTTCTC
* * *
249321 TTAGGATGAAAACCTGAAAGGGCGTCCTAAGTAAAAAAAATGT
1 TTAGGATGAAAACCAGAAAGGGCGCCCTAAATAAAAAAAATGT
* **
249364 TTAGGGTGAAAACCAGAAAGGGCGCCCTAAATTGAAAAAAT
1 TTAGGATGAAAACCAGAAAGGGCGCCCTAAATAAAAAAAAT
249405 TAAAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19
Consensus pattern (43 bp):
TTAGGATGAAAACCAGAAAGGGCGCCCTAAATAAAAAAAATGT
Found at i:249433 original size:16 final size:16
Alignment explanation
Indices: 249412--249442 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
249402 AATTAAAAAA
249412 AAAAGAAAAAGAGAAC
1 AAAAGAAAAAGAGAAC
249428 AAAAGAAAAAGAGAA
1 AAAAGAAAAAGAGAA
249443 ATAACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAGAAC
Found at i:250562 original size:106 final size:105
Alignment explanation
Indices: 250429--250623 Score: 248
Period size: 106 Copynumber: 1.8 Consensus size: 105
250419 ATATCGTGCC
* * * * * ** *
250429 ACTCGAGACAACATAAGTTCAACTTCACAATGAAGGGAC-GACTGGTTGTCAATGAATAATTTCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACAG-CTGGCTGTCAACAAACAATTTCC
250493 CAGTTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAGTTT-AAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
250535 ACTCAAGACAACACAAGCTCAACTTCACGACGAAGGGGCAGTTGGCTGTTAACAAACAATTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACAGCTGGCTGTCAACAAACAATTTCCC
*
250600 AGTTTAGAGCCAATTTCAACTTCA
66 AGTTTAAAGCCAATTTCAACTTCA
250624 GGATGGAGGA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
105 18 0.24
106 56 0.75
107 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (105 bp):
ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACAGCTGGCTGTCAACAAACAATTTCCC
AGTTTAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:251188 original size:12 final size:13
Alignment explanation
Indices: 251160--251192 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
251150 ATCCTTTGAT
251160 ATTATATATTTGC
1 ATTATATATTTGC
*
251173 ATTATA-ATTTGG
1 ATTATATATTTGC
251185 ATTATATA
1 ATTATATA
251193 ATATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (13 bp):
ATTATATATTTGC
Found at i:253056 original size:11 final size:11
Alignment explanation
Indices: 253028--253057 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
253018 TTTTCTTTCG
253028 TTTGCATCATT
1 TTTGCATCATT
253039 TTT-CATCATT
1 TTTGCATCATT
253049 TTTGCATCA
1 TTTGCATCA
253058 CATTTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (11 bp):
TTTGCATCATT
Found at i:255981 original size:36 final size:36
Alignment explanation
Indices: 255941--256011 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
255931 ATGAGATTTT
*
255941 TTTCT-ACAAAACCAAATTTTGTCTCGCTTGAGACAA
1 TTTCTCACAAAA-CAAATTTCGTCTCGCTTGAGACAA
* *
255977 TTTCTCTCGAAACAAATTTCGTCTCGCTTGAGACA
1 TTTCTCACAAAACAAATTTCGTCTCGCTTGAGACA
256012 GTTTTCCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (36 bp):
TTTCTCACAAAACAAATTTCGTCTCGCTTGAGACAA
Found at i:256315 original size:137 final size:137
Alignment explanation
Indices: 256165--256431 Score: 367
Period size: 138 Copynumber: 1.9 Consensus size: 137
256155 GCAAACTTCG
*
256165 TCTCAATTGAGACATTTTCCCTCGGA-ATACAAATTTCAAATTTGTTTTACTTGAAACAAAATCA
1 TCTCAATTGAGACATTTTCCCTCGGAGATACAAATTTCAAATTTGTTTCACTTGAAACAAAATCA
* **
256229 ATCTCACTTGAGATTGTTT-TCTTAAAAACAAATTTTGTCTCGCTTGAGACACTTTCTTTCAAAA
66 ATCTCACTTGAGATTGTTTCT-TTAAAAAC-AATTTCGTCTCGCTTGAGACACTTTCCCTCAAAA
256293 CAATTTTCA
129 CAATTTTCA
* * ** * * * *
256302 TCTCACTTGAGACATTTTTCCTTTGAGATTCAAATTTCGAATTTGTTTCGCTTGAAACAAAATTA
1 TCTCAATTGAGACATTTTCCCTCGGAGATACAAATTTCAAATTTGTTTCACTTGAAACAAAATCA
* * *
256367 ATCTCACTTGAGATTGTTTCTTTCAAAACAGTTTCGTCTCGCTTGAGACAGTTTCCCTCAAAACA
66 ATCTCACTTGAGATTGTTTCTTTAAAAACAATTTCGTCTCGCTTGAGACACTTTCCCTCAAAACA
256432 CAAAATTTGG
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
137 53 0.47
138 59 0.52
139 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (137 bp):
TCTCAATTGAGACATTTTCCCTCGGAGATACAAATTTCAAATTTGTTTCACTTGAAACAAAATCA
ATCTCACTTGAGATTGTTTCTTTAAAAACAATTTCGTCTCGCTTGAGACACTTTCCCTCAAAACA
ATTTTCA
Found at i:256697 original size:30 final size:30
Alignment explanation
Indices: 256654--256764 Score: 78
Period size: 30 Copynumber: 3.5 Consensus size: 30
256644 CTTGAGACAA
* *
256654 TTTCTCTTAAAACAGAAGTCTTTGAGTCTG
1 TTTCCCTTGAAACAGAAGTCTTTGAGTCTG
* * *
256684 TTTCCCTTGAAACAAAGATTGGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC--AGA--AG--TCT-TTGAGTCTG
** * *
256721 TTTCTATTGAAACAAAAGTCTTTGAGTATG
1 TTTCCCTTGAAACAGAAGTCTTTGAGTCTG
256751 TTTCCCTTGAAACA
1 TTTCCCTTGAAACA
256765 AGATTTGTCT
Statistics
Matches: 60, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
30 29 0.48
31 3 0.05
32 3 0.05
33 1 0.02
34 1 0.02
35 2 0.03
36 3 0.05
37 18 0.30
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (30 bp):
TTTCCCTTGAAACAGAAGTCTTTGAGTCTG
Found at i:256697 original size:67 final size:67
Alignment explanation
Indices: 256468--256799 Score: 415
Period size: 67 Copynumber: 5.0 Consensus size: 67
256458 AATTAAATGT
*
256468 AAAATCTTTGAG-ATTGTTTCCCTTGAAA-AAAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAA
1 AAAATCTTTGAGTA-TGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTT--A
*
256531 ACAAAA
63 A-AACA
* *
256537 AAAATCTTTGAGTATGTTTCCCTTGAAACAAAG-TTT-TGTCTCTTGAGACAGTTTCTCTTGAAA
1 AAAATCTTTGAGTATGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTTAAAA
256600 C-
66 CA
* * * * *
256601 AAAATCTTTGAGTCTGTTTCCATTGAAACAAAGTTTTATCTCTCTTGAGACAATTTCTCTTAAAA
1 AAAATCTTTGAGTATGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTTAAAA
256666 CA
66 CA
* * * * * *
256668 GAAGTCTTTGAGTCTGTTTCCCTTGAAACAAAGATTGGTCTCTCTTGAGACAGTTTCTATTGAAA
1 AAAATCTTTGAGTATGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTTAAAA
256733 CA
66 CA
* * * *
256735 AAAGTCTTTGAGTATGTTTCCCTTGAAAC-AAGATTTGTCTCGCTTAAGACGGTTTCTCTTAAAA
1 AAAATCTTTGAGTATGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTTAAAA
256799 C
66 C
256800 CATTATCCCT
Statistics
Matches: 232, Mismatches: 26, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
64 31 0.13
65 5 0.02
66 56 0.24
67 85 0.37
68 22 0.09
69 29 0.12
70 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (67 bp):
AAAATCTTTGAGTATGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTTAAAA
CA
Found at i:256754 original size:134 final size:131
Alignment explanation
Indices: 256468--256799 Score: 436
Period size: 133 Copynumber: 2.5 Consensus size: 131
256458 AATTAAATGT
*
256468 AAAATCTTTGAG-ATTGTTTCCCTTGAAA-AAAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAA
1 AAAATCTTTGAGTA-TGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTT--A
* * * *
256531 ACAAAAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTTGAGACAGTTTCTCTT
63 A-AACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAGTTGTCTCTCTTGAGACAGTTTCTATT
256596 GAAAC
127 GAAAC
* * * * *
256601 AAAATCTTTGAGTCTGTTTCCATTGAAACAAAGTTTTATCTCTCTTGAGACAATTTCTCTTAAAA
1 AAAATCTTTGAGTATGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTTAAAA
* * *
256666 CAGAAGTCTTTGAGTCTGTTTCCCTTGAAACAAAGATTGGTCTCTCTTGAGACAGTTTCTATTGA
66 CAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAG-TT-GTCTCTCTTGAGACAGTTTCTATTGA
256731 AAC
129 AAC
* * *
256734 AAAAGTCTTTGAGTATGTTTCCCTTGAAAC-AAGATTTGTCTCGCTTAAGACGGTTTCTCTTAAA
1 AAAA-TCTTTGAGTATGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTTAAA
256798 AC
65 AC
256800 CATTATCCCT
Statistics
Matches: 173, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
131 33 0.19
132 4 0.02
133 85 0.49
134 51 0.29
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (131 bp):
AAAATCTTTGAGTATGTTTCCCTTGAAACAAAGATTTGTCTCTCTTGAGACAGTTTCTCTTAAAA
CAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAGTTGTCTCTCTTGAGACAGTTTCTATTGAAA
C
Found at i:257101 original size:135 final size:133
Alignment explanation
Indices: 256836--257195 Score: 411
Period size: 135 Copynumber: 2.7 Consensus size: 133
256826 CCTTATCATA
** * * *
256836 TAGGAACCGTGTCATCCACCAATAAGATCTCATCATCACGTAGGAGCCACGCCAATCC-TAGATA
1 TAGGAACAATGTCATCCACCAAT-AGATCTCCTCATCACGTAGGAGCCGCGTCAA-CCTTAGATA
* * *
256900 ACC-AGTCTTCCTCATCACGTAGGAACCGTGTTATCATCATCCCTAAAGATGGCCAATCTTCTTC
64 ACCAAAT-TTTCTCATCACGTAGGAACCGTGTTATCATCATCCCTAAAGATGGCCAACCTTCTTC
256964 ATCACG
128 ATCACG
*
256970 TAGGAACAATGTCATCCACCAACTAGATATCCTCATCACGTAGGAGCCGCGTCAACCTTAGATAA
1 TAGGAACAATGTCATCCACCAA-TAGATCTCCTCATCACGTAGGAGCCGCGTCAACCTTAGATAA
* * *
257035 CCAAATTGTTCTCATCACGTAGGAACTGTGTTATCATCATCCCTAAAGATGGTCAGCCGTTC-TC
65 CCAAATT-TTCTCATCACGTAGGAACCGTGTTATCATCATCCCTAAAGATGGCCAACC-TTCTTC
*
257099 ATCGCG
128 ATCACG
* * * ** * * * *
257105 TTGGAACTATATCATCCATAAAGTAGATCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAG
1 TAGGAACAATGTCATCCACCAA-TAGATCTCCTCATCACGTAGGAGCCGCGTCAACCTTAGATAA
* * *
257170 CCAGACTTTCTCATCATGTAGGAACC
65 CCAAATTTTCTCATCACGTAGGAACC
257196 ATATTGTCTC
Statistics
Matches: 193, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
133 2 0.01
134 74 0.38
135 114 0.59
136 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (133 bp):
TAGGAACAATGTCATCCACCAATAGATCTCCTCATCACGTAGGAGCCGCGTCAACCTTAGATAAC
CAAATTTTCTCATCACGTAGGAACCGTGTTATCATCATCCCTAAAGATGGCCAACCTTCTTCATC
ACG
Found at i:257461 original size:3 final size:3
Alignment explanation
Indices: 257401--257450 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
257391 TTTGTTGTTA
257401 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
257449 TA
1 TA
257451 AATAATTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:284194 original size:3 final size:3
Alignment explanation
Indices: 284186--284273 Score: 88
Period size: 3 Copynumber: 28.7 Consensus size: 3
284176 TTCATTTAAA
* * *
284186 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT TACT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * *
284232 AAT T-T TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
284274 CAAACGGGCC
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.03
3 60 0.86
4 8 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:284250 original size:19 final size:19
Alignment explanation
Indices: 284195--284267 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
284185 ATATTATTAT
* *
284195 TATTATTA-TAATTATTAT
1 TATTATTATTAATTACTAA
*
284213 TATTATAATTATAATTACTAA
1 TATTATTA-T-TAATTACTAA
* *
284234 TTTTATTATTTATTACTAA
1 TATTATTATTAATTACTAA
284253 TATTATTATTAATTA
1 TATTATTATTAATTA
284268 TTATTACAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
18 7 0.16
19 22 0.50
20 1 0.02
21 14 0.32
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTATTATTAATTACTAA
Found at i:285485 original size:17 final size:17
Alignment explanation
Indices: 285441--285486 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
285431 TAGATTTTTA
* *
285441 ATTTTATTTTTTCGTTT
1 ATTTTATTGTTTCATTT
285458 A-TTTATATGTTTCATTT
1 ATTTTAT-TGTTTCATTT
285475 ATTTTATTGTTT
1 ATTTTATTGTTT
285487 TTAATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.20
17 15 0.60
18 5 0.20
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.72
Consensus pattern (17 bp):
ATTTTATTGTTTCATTT
Found at i:287690 original size:8 final size:7
Alignment explanation
Indices: 287666--287706 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
287656 TTTTCATACA
287666 TGCA-TT
1 TGCATTT
287672 TGCATTT
1 TGCATTT
287679 TGCATCTT
1 TGCAT-TT
287687 TGCATTT
1 TGCATTT
*
287694 T-CATTG
1 TGCATTT
287700 TGCATTT
1 TGCATTT
287707 ATACTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
6 9 0.30
7 14 0.47
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (7 bp):
TGCATTT
Found at i:287791 original size:26 final size:25
Alignment explanation
Indices: 287762--287819 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
287752 CATTCACATA
*
287762 TTTACATTTGAATTTGCATTTGCATT
1 TTTACATTTGAATTTACATTT-CATT
* *
287788 TTTACGTTTGTATTTACATTTCATT
1 TTTACATTTGAATTTACATTTCATT
287813 TTTACAT
1 TTTACAT
287820 AATTACATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (25 bp):
TTTACATTTGAATTTACATTTCATT
Done.