Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009638.1 Hibiscus syriacus cultivar Beakdansim tig00117047_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: 894601
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:141 original size:18 final size:18
Alignment explanation
Indices: 118--152 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
108 TTCCATCCGG
*
118 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
136 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
153 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1275 original size:13 final size:13
Alignment explanation
Indices: 1257--1319 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
1247 CGGTCGTCAA
1257 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1270 CGGGTCAACGAGTCGAGT
1 CGGGTCAAC--G--G-GT
*
1288 CAGGTCAACGGGT
1 CGGGTCAACGGGT
* *
1301 CGGATAAACGGGT
1 CGGGTCAACGGGT
1314 CGGGTC
1 CGGGTC
1320 GGGTAAACGG
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
13 25 0.64
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 10 0.26
ACGTcount: A:0.21, C:0.22, G:0.41, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1294 original size:31 final size:31
Alignment explanation
Indices: 1259--1336 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1249 GTCGTCAACG
*
1259 GGTCAACGGGTCGGGTCAACGAGTCGAGTCA
1 GGTCAACGGGTCGGGTAAACGAGTCGAGTCA
* * * *
1290 GGTCAACGGGTCGGATAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGAGTCGAGTCA
*
1321 GGTAAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
1337 TGTGACCGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.19, G:0.44, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGAGTCGAGTCA
Found at i:1317 original size:18 final size:18
Alignment explanation
Indices: 1296--1336 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1286 GTCAGGTCAA
1296 CGGGTCGGATAAACGGGT
1 CGGGTCGGATAAACGGGT
*
1314 CGGGTCGGGTAAACGGGT
1 CGGGTCGGATAAACGGGT
1332 CGGGT
1 CGGGT
1337 TGTGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGATAAACGGGT
Found at i:2156 original size:19 final size:19
Alignment explanation
Indices: 2132--2168 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2122 ACTAATGGAA
2132 CTTATGCAATAACGAAGAG
1 CTTATGCAATAACGAAGAG
*
2151 CTTATGCAATAATGAAGA
1 CTTATGCAATAACGAAGA
2169 CTACATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (19 bp):
CTTATGCAATAACGAAGAG
Found at i:3798 original size:22 final size:23
Alignment explanation
Indices: 3735--3788 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
3725 CTTAAAATCT
*
3735 TAAATTATAAA-CT-ATAACCTC
1 TAAATCATAAACCTCATAACCTC
*
3756 TAAACCAT-AACCTCATAACCTC
1 TAAATCATAAACCTCATAACCTC
3778 TAAATCATAAA
1 TAAATCATAAA
3789 TCCTAAACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.07
21 8 0.30
22 15 0.56
23 2 0.07
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAATCATAAACCTCATAACCTC
Found at i:11155 original size:28 final size:28
Alignment explanation
Indices: 11120--11184 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
11110 TATAAAGCAT
*
11120 AAGTTATGATTTAGGGTTTAAAGTTTAG
1 AAGTTATGATTTAAGGTTTAAAGTTTAG
*
11148 -AGATTATGATTTAAGGTTTAAGGTTTAG
1 AAG-TTATGATTTAAGGTTTAAAGTTTAG
11176 AAGTTATGA
1 AAGTTATGA
11185 GATAATAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.42
Consensus pattern (28 bp):
AAGTTATGATTTAAGGTTTAAAGTTTAG
Found at i:14261 original size:31 final size:31
Alignment explanation
Indices: 14208--14292 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
14198 AAACTACACA
* *
14208 TTTAATACTAAAACTATTAATTTTAATT-TAT
1 TTTAATACTTAAACTATCAATTTT-ATTCTAT
* *
14239 TTTAGTACTTAAACTATCAATTTTGTTCTAT
1 TTTAATACTTAAACTATCAATTTTATTCTAT
* *
14270 TTTATTA-TCTAAACTTTCAATTT
1 TTTAATACT-TAAACTATCAATTT
14293 CTTTTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 3 0.07
31 43 0.93
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (31 bp):
TTTAATACTTAAACTATCAATTTTATTCTAT
Found at i:16876 original size:4 final size:5
Alignment explanation
Indices: 16854--16884 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
16844 TTAACATTAT
*
16854 AAATA AAATA AAATA AAATA AATTA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
16885 TCATCTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:17441 original size:31 final size:31
Alignment explanation
Indices: 17405--17507 Score: 116
Period size: 32 Copynumber: 3.3 Consensus size: 31
17395 GAAGATGAAT
**
17405 TTTGATAAATTTAATAATTATTTTATAATAA
1 TTTGATAAATTTAATAACCATTTTATAATAA
* *
17436 TTTGATAAATTTTAGTGACCATTTTATAATAA
1 TTTGATAAA-TTTAATAACCATTTTATAATAA
* * * *
17468 TTTGATAAATTTTAGTGACCGTTTTATAACAA
1 TTTGATAAA-TTTAATAACCATTTTATAATAA
17500 TTTGATAA
1 TTTGATAA
17508 CCAACATCAT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
31 9 0.14
32 56 0.86
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (31 bp):
TTTGATAAATTTAATAACCATTTTATAATAA
Found at i:17460 original size:32 final size:32
Alignment explanation
Indices: 17424--17507 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
17414 TTTAATAATT
17424 ATTTTATAATAATTTGATAAATTTTAGTGACC
1 ATTTTATAATAATTTGATAAATTTTAGTGACC
17456 ATTTTATAATAATTTGATAAATTTTAGTGACC
1 ATTTTATAATAATTTGATAAATTTTAGTGACC
* *
17488 GTTTTATAACAATTTGATAA
1 ATTTTATAATAATTTGATAA
17508 CCAACATCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (32 bp):
ATTTTATAATAATTTGATAAATTTTAGTGACC
Found at i:21597 original size:14 final size:14
Alignment explanation
Indices: 21580--21606 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21570 ATATTAAATA
21580 ATAAATATAATTAT
1 ATAAATATAATTAT
21594 ATAAATATAATTA
1 ATAAATATAATTA
21607 AAAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATATAATTAT
Found at i:26742 original size:27 final size:28
Alignment explanation
Indices: 26689--26744 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
26679 CATATTAGAA
*
26689 AAATCAACAAACAATAACACTTATATTTTC
1 AAATCAACAAAC-A-AACACCTATATTTTC
26719 AAATCAACAAAC-AACACCTATATTTT
1 AAATCAACAAACAAACACCTATATTTT
26745 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
30 12 0.48
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (28 bp):
AAATCAACAAACAAACACCTATATTTTC
Found at i:28967 original size:21 final size:21
Alignment explanation
Indices: 28943--28993 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
28933 AGTAATGACG
28943 TGCTGATGTAGCGGTTCACAC
1 TGCTGATGTAGCGGTTCACAC
*
28964 TGCTGATGTAGCGGTTCACAG
1 TGCTGATGTAGCGGTTCACAC
28985 TGCTGATGT
1 TGCTGATGT
28994 GGTAGTCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (21 bp):
TGCTGATGTAGCGGTTCACAC
Found at i:29104 original size:21 final size:21
Alignment explanation
Indices: 29080--29121 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29070 GGACTGCCAT
*
29080 GTTAGCATCGT-AGACTATCAC
1 GTTACCATCGTGA-ACTATCAC
29101 GTTACCATCGTGAACTATCAC
1 GTTACCATCGTGAACTATCAC
29122 ATCAAAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (21 bp):
GTTACCATCGTGAACTATCAC
Found at i:30973 original size:60 final size:60
Alignment explanation
Indices: 30847--30973 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 60
30837 GATCGATTTG
* * *
30847 TAACTTTTAATAGTCGATGGACTCAAAAAAGCAATACTCAATAGCCAGAGTACTATATTG
1 TAACTTTTAATAGTCGATGGACTCAAAAAAGCAATACCCAATAGCCAGAGTACCATATTA
* * * * *
30907 TAACTTTTAGTAGTCGATGGACTTAATAAAA-TAATACCCTATAGTCGAGAG-ACCAT-TTA
1 TAACTTTTAATAGTCGATGGACTCAA-AAAAGCAATACCCAATAG-CCAGAGTACCATATTA
30966 TATACTTT
1 TA-ACTTT
30974 ACCCAAAGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
59 4 0.07
60 43 0.77
61 9 0.16
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (60 bp):
TAACTTTTAATAGTCGATGGACTCAAAAAAGCAATACCCAATAGCCAGAGTACCATATTA
Found at i:37025 original size:28 final size:29
Alignment explanation
Indices: 36989--37043 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
36979 TATTTTAGGT
*
36989 GGGGATGAACTTGAACTTATAAAATTTTA
1 GGGGATGAACTTAAACTTATAAAATTTTA
*
37018 GGGG-TGAACTTAAATTTATAAAATTT
1 GGGGATGAACTTAAACTTATAAAATTT
37044 ATAATGGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.36
Consensus pattern (29 bp):
GGGGATGAACTTAAACTTATAAAATTTTA
Found at i:42759 original size:31 final size:31
Alignment explanation
Indices: 42722--42789 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
42712 TCATATCCAA
42722 AACTTTAAACAATGTATCATTCATACCATTG
1 AACTTTAAACAATGTATCATTCATACCATTG
* *
42753 AGCTTTAGACAATGTATCATTCATACCATTG
1 AACTTTAAACAATGTATCATTCATACCATTG
42784 AACTTT
1 AACTTT
42790 CAATTGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (31 bp):
AACTTTAAACAATGTATCATTCATACCATTG
Found at i:43020 original size:31 final size:29
Alignment explanation
Indices: 42980--43049 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
42970 AAAAAAATTG
* * *
42980 AATACTTTAGGTACATATTTTGACCAAAA
1 AATATTTTAGGTACATATCTCGACCAAAA
*
43009 AGATAATTTTAGGTACTTATCTCGACCAAAA
1 A-AT-ATTTTAGGTACATATCTCGACCAAAA
43040 AATATTTTAG
1 AATATTTTAG
43050 TACTTAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.23
30 4 0.11
31 23 0.66
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (29 bp):
AATATTTTAGGTACATATCTCGACCAAAA
Found at i:43283 original size:15 final size:15
Alignment explanation
Indices: 43257--43298 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
43247 TCGATTTTGT
*
43257 CACTAAACTTTTAAA
1 CACTATACTTTTAAA
*
43272 CA-TATCACTTTTCAA
1 CACTAT-ACTTTTAAA
43287 CACTATACTTTT
1 CACTATACTTTT
43299 TTAGTGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 18 0.78
16 3 0.13
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (15 bp):
CACTATACTTTTAAA
Found at i:44215 original size:31 final size:31
Alignment explanation
Indices: 44177--44240 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
44167 CGATTGAGGT
* * * *
44177 ACTAAAATCGAATGGATCAATGATGTTATGG
1 ACTAAAATCAAACGGATCAATAATGTTACGG
*
44208 ACTAAAATCAAACGGATCGATAATGTTACGG
1 ACTAAAATCAAACGGATCAATAATGTTACGG
44239 AC
1 AC
44241 CATTCCTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (31 bp):
ACTAAAATCAAACGGATCAATAATGTTACGG
Found at i:45907 original size:30 final size:30
Alignment explanation
Indices: 45871--45930 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
45861 AACAAATCGA
45871 AACTGATAAATTAGATATTAAACTTGTAGT
1 AACTGATAAATTAGATATTAAACTTGTAGT
45901 AACTGATAAATTAGATATTAAACTTGTAGT
1 AACTGATAAATTAGATATTAAACTTGTAGT
45931 TTATCCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (30 bp):
AACTGATAAATTAGATATTAAACTTGTAGT
Found at i:47768 original size:5 final size:5
Alignment explanation
Indices: 47758--47783 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
47748 AATTCGATAG
47758 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
47784 ATTAAGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:59556 original size:2 final size:2
Alignment explanation
Indices: 59549--59587 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
59539 ATTAATTAAA
59549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59588 ATGACTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59649 original size:46 final size:46
Alignment explanation
Indices: 59596--59703 Score: 216
Period size: 46 Copynumber: 2.3 Consensus size: 46
59586 TAATGACTAT
59596 AACCCCTAATTTGACCAAATTCAAAAATGTAATAATAAAAGGACAA
1 AACCCCTAATTTGACCAAATTCAAAAATGTAATAATAAAAGGACAA
59642 AACCCCTAATTTGACCAAATTCAAAAATGTAATAATAAAAGGACAA
1 AACCCCTAATTTGACCAAATTCAAAAATGTAATAATAAAAGGACAA
59688 AACCCCTAATTTGACC
1 AACCCCTAATTTGACC
59704 TACAAAGAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.22
Consensus pattern (46 bp):
AACCCCTAATTTGACCAAATTCAAAAATGTAATAATAAAAGGACAA
Found at i:62111 original size:18 final size:19
Alignment explanation
Indices: 62076--62112 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
62066 TCCGGAATGT
62076 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
62096 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
62113 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:73985 original size:2 final size:2
Alignment explanation
Indices: 73978--74028 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
73968 AATTTAAAAT
* * *
73978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74020 TA TA TA TA T
1 TA TA TA TA T
74029 GTATGTATGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74029 original size:18 final size:18
Alignment explanation
Indices: 73984--74041 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
73974 AAATTATATA
* * *
73984 TATATATATATATATATA
1 TATATATATGTATGTATG
74002 TATATATATGTATGTATG
1 TATATATATGTATGTATG
74020 TATATATATGTATGTATG
1 TATATATATGTATGTATG
74038 TATA
1 TATA
74042 CATTTGAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (18 bp):
TATATATATGTATGTATG
Found at i:76053 original size:2 final size:2
Alignment explanation
Indices: 76048--76073 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
76038 ACACACACAC
76048 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
76074 GAAAGGGTAA
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:76658 original size:18 final size:19
Alignment explanation
Indices: 76623--76659 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
76613 CACGGAATGT
76623 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
76643 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
76660 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:76831 original size:15 final size:15
Alignment explanation
Indices: 76813--76843 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
76803 AAATTCTAAA
76813 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
76828 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
76843 T
1 T
76844 CTATTTGTTG
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:85011 original size:19 final size:19
Alignment explanation
Indices: 84987--85026 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
84977 TTCAAACTGC
84987 CGCCTGCGAGGTGACCCGT
1 CGCCTGCGAGGTGACCCGT
85006 CGCCTGCGAGGTGACCCGT
1 CGCCTGCGAGGTGACCCGT
85025 CG
1 CG
85027 TGTAATAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.38, G:0.38, T:0.15
Consensus pattern (19 bp):
CGCCTGCGAGGTGACCCGT
Found at i:85155 original size:3 final size:3
Alignment explanation
Indices: 85143--85233 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
85133 AAGATACTAA
* *
85143 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
85190 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
85234 AATATATTAA
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:86578 original size:19 final size:19
Alignment explanation
Indices: 86554--86594 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
86544 GTGATATTTT
*
86554 TATTTT-TATATTGTATAAA
1 TATTTTATATATT-CATAAA
86573 TATTTTATATATTCATAAA
1 TATTTTATATATTCATAAA
86592 TAT
1 TAT
86595 ACTTATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTTTATATATTCATAAA
Found at i:97990 original size:1 final size:1
Alignment explanation
Indices: 97974--98022 Score: 62
Period size: 1 Copynumber: 49.0 Consensus size: 1
97964 AAAAAGGGAG
* * * *
97974 AAAAGAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
98023 GGATTAAGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:99198 original size:83 final size:82
Alignment explanation
Indices: 99059--100023 Score: 1576
Period size: 83 Copynumber: 11.7 Consensus size: 82
99049 CATTAACTGA
* * *
99059 AAGATGAATTTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTCGGACAGA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT-GGACAGA
99124 ACCAATCATTGAATTTGG
65 ACCAATCATTGAATTTGG
* * **
99142 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTGGA-CAGA
99207 ACCAATCATTGAATTTGG
65 ACCAATCATTGAATTTGG
99225 AAGATGAATGTGCTAA-ATGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTCGGACAG
1 AAGATGAATGTGCTAATA-GCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT-GGACAG
99289 AACCAATCATTGAATTTGG
64 AACCAATCATTGAATTTGG
* * **
99308 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTGGA-CAGA
99373 ACCAATCATTGAATTTGG
65 ACCAATCATTGAATTTGG
99391 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TGGACAGA
99456 ACCAATCATTGAATTTGG
65 ACCAATCATTGAATTTGG
* **
99474 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTGGA-CAGA
99539 ACCAATCATTGAATTTGG
65 ACCAATCATTGAATTTGG
99557 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TGGACAGA
99622 ACCAATCATTGAATTTGG
65 ACCAATCATTGAATTTGG
* * **
99640 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTGGA-CAGA
99705 ACCAATCATTGAATTTGG
65 ACCAATCATTGAATTTGG
99723 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAG-TATCTGATCTGGTGGACAGAA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTGGACAGAA
99787 CCAATCATTGAATTTGG
66 CCAATCATTGAATTTGG
* *
99804 AAGATGAATGTGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TGGACAGA
99869 A-CAATCATTGAATTTGG
65 ACCAATCATTGAATTTGG
* * *
99886 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATAGA
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TGGACAGA
*
99951 ATCAATCATTGAATTTGG
65 ACCAATCATTGAATTTGG
* *
99969 AAGATGAATGTGCTAATAGCATCTTCTGGAATTTTTCTTTGAGTTATCTGATCTG
1 AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
100024 TTTTGGTAAG
Statistics
Matches: 828, Mismatches: 42, Indels: 24
0.93 0.05 0.03
Matches are distributed among these distances:
81 63 0.08
82 109 0.13
83 650 0.79
84 6 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (82 bp):
AAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTGGACAGAA
CCAATCATTGAATTTGG
Found at i:101039 original size:114 final size:114
Alignment explanation
Indices: 100709--101318 Score: 1123
Period size: 114 Copynumber: 5.4 Consensus size: 114
100699 GCCAGGTAGA
100709 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
100774 ACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG
66 ACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG
100823 GTTCATAATGAGAAGAAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 GTTCATAATGAGAAG-AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
100888 AACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG
65 AACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG
100938 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
101003 ACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG
66 ACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG
*
101052 GTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* *
101117 ACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAA
66 ACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG
101166 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* * * * * *
101231 ACCTTTTACTTGAATCCATC-ATTTGATGGATCAACTTTTCCAGAGAAA
66 ACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG
101279 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
101319 TTTGTTCAAC
Statistics
Matches: 487, Mismatches: 8, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
113 66 0.14
114 307 0.63
115 114 0.23
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (114 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
ACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG
Found at i:101652 original size:3 final size:3
Alignment explanation
Indices: 101640--101724 Score: 120
Period size: 3 Copynumber: 28.7 Consensus size: 3
101630 AAGATACTAA
* *
101640 TAT T-T TAT TAT TAT TAT TAT TAT TAT CAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
101687 TAT TGT TAT TAT TAT ATAT TAT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
101725 AATATATTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.05
3 66 0.90
4 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:101730 original size:18 final size:17
Alignment explanation
Indices: 101637--101733 Score: 83
Period size: 18 Copynumber: 5.6 Consensus size: 17
101627 CTGAAGATAC
*
101637 TAATATTTTATTATTAT
1 TAATATATTATTATTAT
*
101654 T-AT-TATTATTATCAT
1 TAATATATTATTATTAT
101669 T-ATCATTATTATTATTAT
1 TAAT-A-TATTATTATTAT
* *
101687 TATTGTTATTATTATATAT
1 TAAT-ATATTATTAT-TAT
*
101706 TATTATATTATTATTAT
1 TAATATATTATTATTAT
101723 TAAATATATTA
1 T-AATATATTA
101734 AATACATATA
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
15 13 0.20
16 2 0.03
17 5 0.08
18 38 0.58
19 8 0.12
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (17 bp):
TAATATATTATTATTAT
Found at i:113705 original size:22 final size:22
Alignment explanation
Indices: 113673--113716 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
113663 CATGTTATAT
*
113673 GGCACTACGGTGCAATTCTACG
1 GGCACTACGGTGCAATTATACG
*
113695 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
113717 AGCTGGGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (22 bp):
GGCACTACGGTGCAATTATACG
Found at i:116826 original size:21 final size:21
Alignment explanation
Indices: 116800--116844 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
116790 GATTTCTGGG
* *
116800 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
116821 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
116842 CAA
1 CAA
116845 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:118515 original size:149 final size:149
Alignment explanation
Indices: 118335--118649 Score: 605
Period size: 149 Copynumber: 2.1 Consensus size: 149
118325 GAGTCGAGGG
118335 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
118400 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
118465 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
118484 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
118549 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTGTTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
118614 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
118633 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
118650 TGTAATTATA
Statistics
Matches: 164, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 163 0.99
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:118650 original size:23 final size:23
Alignment explanation
Indices: 118617--118661 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
118607 ATTGTTATAT
*
118617 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
118640 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGCAATTATACG
118662 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:122748 original size:2 final size:2
Alignment explanation
Indices: 122741--122795 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
122731 GATATCTATC
*
122741 TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
122783 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
122796 TTAACGTAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:123940 original size:21 final size:21
Alignment explanation
Indices: 123910--123978 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
123900 CGTCCGTCAC
123910 TAACAACAATGATATCATATG
1 TAACAACAATGATATCATATG
* * *
123931 TAACATCAAT--TGGTC--A-C
1 TAACAACAATGAT-ATCATATG
123948 TAACAACAATGATATCATATG
1 TAACAACAATGATATCATATG
*
123969 TAACATCAAT
1 TAACAACAAT
123979 TGGTCACTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
17 9 0.26
18 3 0.09
19 2 0.06
20 3 0.09
21 18 0.51
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.29
Consensus pattern (21 bp):
TAACAACAATGATATCATATG
Found at i:123956 original size:38 final size:38
Alignment explanation
Indices: 123905--123986 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
123895 TTTTACGTCC
123905 GTCACTAACAACAATGATATCATATGTAACATCAATTG
1 GTCACTAACAACAATGATATCATATGTAACATCAATTG
123943 GTCACTAACAACAATGATATCATATGTAACATCAATTG
1 GTCACTAACAACAATGATATCATATGTAACATCAATTG
123981 GTCACT
1 GTCACT
123987 CTTAAACGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (38 bp):
GTCACTAACAACAATGATATCATATGTAACATCAATTG
Found at i:129006 original size:30 final size:30
Alignment explanation
Indices: 128972--129033 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
128962 GGATGGTTTA
128972 AAAATATTATAAACATACCTTAAATTTGAC
1 AAAATATTATAAACATACCTTAAATTTGAC
129002 AAAATATTATAAACATACCTTAAATTTGAC
1 AAAATATTATAAACATACCTTAAATTTGAC
129032 AA
1 AA
129034 TGAAATCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAATATTATAAACATACCTTAAATTTGAC
Found at i:132366 original size:12 final size:12
Alignment explanation
Indices: 132349--132375 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
132339 ATGTACCGTC
132349 CATCCATTCATA
1 CATCCATTCATA
132361 CATCCATTCATA
1 CATCCATTCATA
132373 CAT
1 CAT
132376 ACATGTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (12 bp):
CATCCATTCATA
Found at i:136632 original size:24 final size:25
Alignment explanation
Indices: 136600--136646 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
136590 CTATTCTTTC
136600 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
136624 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
136647 TTTTTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:140508 original size:26 final size:26
Alignment explanation
Indices: 140449--140511 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
140439 ATTGATATTT
140449 AATT-TAAAAAAAACTAAATTCCTAA
1 AATTATAAAAAAAACTAAATTCCTAA
*
140474 AATTA-AAAATAAAACTAAATT-C-GA
1 AATTATAAAA-AAAACTAAATTCCTAA
140498 AATGTATAAAAAAA
1 AAT-TATAAAAAAA
140512 TACAGGGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 4 0.12
25 14 0.42
26 15 0.45
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.25
Consensus pattern (26 bp):
AATTATAAAAAAAACTAAATTCCTAA
Found at i:141732 original size:38 final size:37
Alignment explanation
Indices: 141658--141733 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
141648 GTTAGAAAAT
*
141658 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTTAAAATCATAAA
*
141695 ATTTATATATATATT-TTTACAAAATTTAAAAAT-ATAAA
1 ATTTATATAT-T-TTCTTTAAAAAATTT-AAAATCATAAA
141733 A
1 A
141734 AAGTTTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 10 0.29
38 18 0.53
39 6 0.18
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTTAAAATCATAAA
Found at i:143389 original size:52 final size:52
Alignment explanation
Indices: 143327--143429 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 52
143317 ACATGTTTAA
* * *
143327 GGACAATATCTTTTACTGTTCTTGACACGGTTACACGTATAATGCATTGTCT
1 GGACAATATCTTTGACTGCTCTTCACACGGTTACACGTATAATGCATTGTCT
** * *
143379 GGACAATATCTTTGACTGCTCTTCACACTTTTCCATGTATAATGCATTGTC
1 GGACAATATCTTTGACTGCTCTTCACACGGTTACACGTATAATGCATTGTC
143430 CTCTTGTTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (52 bp):
GGACAATATCTTTGACTGCTCTTCACACGGTTACACGTATAATGCATTGTCT
Found at i:147197 original size:5 final size:5
Alignment explanation
Indices: 147189--147214 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
147179 TTTTTTTATT
147189 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
147215 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:147454 original size:2 final size:2
Alignment explanation
Indices: 147449--147477 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
147439 ATACACACGC
147449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
147478 GGTCATGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:147860 original size:2 final size:2
Alignment explanation
Indices: 147853--147878 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
147843 AATCCTTACC
147853 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
147879 TGTAATTGGC
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:149089 original size:17 final size:17
Alignment explanation
Indices: 149067--149106 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
149057 ACATACCTAC
149067 ATATAATACAATAA-AAT
1 ATATAATAC-ATAACAAT
*
149084 ATATAATACATAACCAT
1 ATATAATACATAACAAT
149101 ATATAA
1 ATATAA
149107 CATCATGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATAATACATAACAAT
Found at i:152444 original size:20 final size:20
Alignment explanation
Indices: 152400--152887 Score: 501
Period size: 20 Copynumber: 24.2 Consensus size: 20
152390 AATGACCAAC
*
152400 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
152419 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
152439 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
152459 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
152479 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
152500 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
152521 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
152542 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
152563 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
152585 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
152603 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
152623 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
152643 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
152665 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
152683 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
152703 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
152725 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
152743 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
152765 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
152785 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
152803 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
152825 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
152845 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
152863 AAAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTAAG
152883 AAAAT
1 AAAAT
152888 GAGTAAATTC
Statistics
Matches: 411, Mismatches: 27, Indels: 61
0.82 0.05 0.12
Matches are distributed among these distances:
18 14 0.03
19 15 0.04
20 325 0.79
21 14 0.03
22 43 0.10
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:152492 original size:60 final size:59
Alignment explanation
Indices: 152400--152887 Score: 580
Period size: 60 Copynumber: 8.1 Consensus size: 59
152390 AATGACCAAC
*** * * * *
152400 AAAATCGCAACGCGAAATAAAAATCGCAACGCGATTTAGAAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGATCCAAGAATCGCAACGCGATTAAGAAAATCGCAACG-CGATTAAG
* *** *
152459 AAAATCGCAACG-G-TCAAAAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATC-CAAG--AATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTAAG
*
152521 AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGA---TCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATT--AAG
* *
152585 --AATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATCCA-AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
*
152643 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGA-TCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
152703 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGA-TCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATT--AAG
152765 --AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGA-TCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATT--AAG
*
152825 --AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGA-TCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
152883 AAAAT
1 AAAAT
152888 GAGTAAATTC
Statistics
Matches: 386, Mismatches: 22, Indels: 41
0.86 0.05 0.09
Matches are distributed among these distances:
58 9 0.02
59 15 0.04
60 274 0.71
61 9 0.02
62 53 0.14
63 4 0.01
64 17 0.04
66 3 0.01
67 2 0.01
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (59 bp):
AAAATCGCAACGCGATCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
Found at i:152977 original size:6 final size:6
Alignment explanation
Indices: 152966--153022 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
152956 CGCACGTATT
152966 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
153014 ACCACG ACC
1 ACCACG ACC
153023 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:153534 original size:6 final size:6
Alignment explanation
Indices: 153523--153561 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
153513 TCTCGTCTCG
153523 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
153562 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:153682 original size:20 final size:20
Alignment explanation
Indices: 153657--153884 Score: 182
Period size: 20 Copynumber: 11.2 Consensus size: 20
153647 GAATTTACTC
153657 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
153677 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
153697 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
*
153717 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
153737 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* *
153759 ATTCTCTTAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
***
153779 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
*
153801 ATTTTCTT--TTGACCGTTGCG
1 ATTTTCTTAATCG--CGTTGCG
* *
153821 ATTTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
*
153841 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
153861 A-TTT-TTATTTCGCGTTGCG
1 ATTTTCTTA-ATCGCGTTGCG
153880 ATTTT
1 ATTTT
153885 GTTGGTCATT
Statistics
Matches: 166, Mismatches: 27, Indels: 30
0.74 0.12 0.13
Matches are distributed among these distances:
18 8 0.05
19 14 0.08
20 101 0.61
21 12 0.07
22 31 0.19
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:153713 original size:40 final size:42
Alignment explanation
Indices: 153666--153807 Score: 234
Period size: 42 Copynumber: 3.4 Consensus size: 42
153656 CATTTTCTTA
153666 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG-A-
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
153706 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
* * * *
153748 ATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAAT
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
153790 ATCGCGTTGCGATTTTCT
1 ATCGCGTTGCGATTTTCT
153808 TTTGACCGTT
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 39 0.41
41 1 0.01
42 55 0.58
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.38
Consensus pattern (42 bp):
ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
Found at i:155074 original size:20 final size:19
Alignment explanation
Indices: 155049--155104 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
155039 TCTCAAATAT
155049 AAATATAAGTTTTTAATTTA
1 AAATATAA-TTTTTAATTTA
*
155069 AAATATCATTTTTAATTT-
1 AAATATAATTTTTAATTTA
* *
155087 CATTATATATTTTTAATT
1 AAATATA-ATTTTTAATT
155105 GAATTATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 4 0.13
19 20 0.65
20 7 0.23
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (19 bp):
AAATATAATTTTTAATTTA
Found at i:155110 original size:19 final size:19
Alignment explanation
Indices: 155058--155118 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
155048 TAAATATAAG
*
155058 TTTTTAATTTAA-AATATCA
1 TTTTTAATTTAATTATAT-A
*
155077 TTTTTAATTTCATTATATA
1 TTTTTAATTTAATTATATA
*
155096 TTTTTAATTGAATTATGATA
1 TTTTTAATTTAATTAT-ATA
155116 TTT
1 TTT
155119 CCTATTCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 26 0.72
20 10 0.28
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTAATTTAATTATATA
Found at i:171098 original size:14 final size:14
Alignment explanation
Indices: 171081--171136 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
171071 GAGTTTATAA
171081 TTTA-AGGTTGATGG
1 TTTAGAGGTT-ATGG
*
171095 TTTAGAGGTTTTGG
1 TTTAGAGGTTATGG
*
171109 TTTAGAGGTTTTGG
1 TTTAGAGGTTATGG
171123 TTTAGAGGTTATGG
1 TTTAGAGGTTATGG
171137 GATTATGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
14 34 0.87
15 5 0.13
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (14 bp):
TTTAGAGGTTATGG
Found at i:171156 original size:14 final size:15
Alignment explanation
Indices: 171068--171136 Score: 76
Period size: 14 Copynumber: 4.9 Consensus size: 15
171058 AAATCATAAC
**
171068 TTAGA-GTTTATAAT
1 TTAGAGGTTTATGGT
*
171082 TTA-AGGTTGATGGT
1 TTAGAGGTTTATGGT
171096 TTAGAGGTTT-TGGT
1 TTAGAGGTTTATGGT
171110 TTAGAGGTTT-TGGT
1 TTAGAGGTTTATGGT
171124 TTAGAGG-TTATGG
1 TTAGAGGTTTATGG
171137 GATTATGGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.06
14 40 0.83
15 5 0.10
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (15 bp):
TTAGAGGTTTATGGT
Found at i:172601 original size:15 final size:16
Alignment explanation
Indices: 172568--172617 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
172558 GAGTAGTTAA
172568 AATTATTTTATATTTTT
1 AATTA-TTTATATTTTT
172585 AA-TATTTAT-TTTATT
1 AATTATTTATATTT-TT
*
172600 AATTATTTTATAATTTT
1 AATTA-TTTATATTTTT
172617 A
1 A
172618 TGAGGTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 3 0.11
15 9 0.32
16 4 0.14
17 10 0.36
18 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTATTTATATTTTT
Found at i:172605 original size:12 final size:11
Alignment explanation
Indices: 172568--172614 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 11
172558 GAGTAGTTAA
172568 AATTATTTTAT
1 AATTATTTTAT
*
172579 -ATT-TTTAAT
1 AATTATTTTAT
*
172588 ATTTATTTTATT
1 AATTATTTTA-T
172600 AATTATTTTAT
1 AATTATTTTAT
172611 AATT
1 AATT
172615 TTATGAGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 5 0.17
10 5 0.17
11 9 0.31
12 10 0.34
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
AATTATTTTAT
Found at i:172701 original size:17 final size:17
Alignment explanation
Indices: 172681--172713 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
172671 TGAGATCACA
172681 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
172698 ATATTATATTTTATAT
1 ATATTATATTTTATAT
172714 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:180397 original size:28 final size:29
Alignment explanation
Indices: 180307--180410 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
180297 AATATTATTT
* *
180307 TAAATTAATCCTCAAACTTTTGAGCATT-
1 TAAATTCATCCCCAAACTTTTGAGCATTC
* * * *
180335 TCAATTTCATCCCCATAC-TATGACCATTC
1 T-AAATTCATCCCCAAACTTTTGAGCATTC
* *
180364 TAAATTGATCCCTAAACTTTTGAGCATTC
1 TAAATTCATCCCCAAACTTTTGAGCATTC
* **
180393 TAATTTCATTTCCAAACT
1 TAAATTCATCCCCAAACT
180411 ATACATATAT
Statistics
Matches: 56, Mismatches: 17, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
28 21 0.38
29 35 0.62
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (29 bp):
TAAATTCATCCCCAAACTTTTGAGCATTC
Found at i:186718 original size:19 final size:19
Alignment explanation
Indices: 186682--186722 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
186672 ACAACATATA
186682 TTTAAATAAATATTTTAAAT
1 TTTAAATAAATATTTT-AAT
186702 TTTAAAT-AAT-TTCTTAAT
1 TTTAAATAAATATT-TTAAT
186720 TTT
1 TTT
186723 CTGCTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAAATAAATATTTTAAT
Found at i:189226 original size:7 final size:7
Alignment explanation
Indices: 189214--189253 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
189204 TATAAGTAAA
189214 GCATATT
1 GCATATT
189221 GCATATT
1 GCATATT
189228 GCATATT
1 GCATATT
189235 GCATATT
1 GCATATT
*
189242 GC-TTTT
1 GCATATT
189248 GCATAT
1 GCATAT
189254 GTCATTAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (7 bp):
GCATATT
Found at i:189240 original size:21 final size:20
Alignment explanation
Indices: 189214--189253 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
189204 TATAAGTAAA
189214 GCATATTGCATATTGCATATT
1 GCATATTGC-TATTGCATATT
*
189235 GCATATTGCTTTTGCATAT
1 GCATATTGCTATTGCATAT
189254 GTCATTAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (20 bp):
GCATATTGCTATTGCATATT
Found at i:191838 original size:4 final size:4
Alignment explanation
Indices: 191831--191877 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
191821 TGCATGCATG
191831 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
191878 GTTTCTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:196843 original size:12 final size:12
Alignment explanation
Indices: 196826--196850 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
196816 ACTAATTTAG
196826 AACGAATATCAT
1 AACGAATATCAT
196838 AACGAATATCAT
1 AACGAATATCAT
196850 A
1 A
196851 GTTTGGGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
AACGAATATCAT
Found at i:197479 original size:6 final size:6
Alignment explanation
Indices: 197468--197492 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
197458 TATGTACTTA
197468 AGGTTC AGGTTC AGGTTC AGGTTC A
1 AGGTTC AGGTTC AGGTTC AGGTTC A
197493 ACTGAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (6 bp):
AGGTTC
Found at i:197707 original size:43 final size:43
Alignment explanation
Indices: 197644--197730 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
197634 CGAACTCGAC
* *
197644 TCGTTTACGGTTCTAAGTGAGCTCCCACTTTCTCTGCAAATAT
1 TCGTTTACGGGTCTAAGTGAGCTCCCACTTCCTCTGCAAATAT
*
197687 TCGTTTACGGGTCTAGGTGAGCTCCCACTTCCTCTGCAAATAT
1 TCGTTTACGGGTCTAAGTGAGCTCCCACTTCCTCTGCAAATAT
197730 T
1 T
197731 TAAAGTACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (43 bp):
TCGTTTACGGGTCTAAGTGAGCTCCCACTTCCTCTGCAAATAT
Found at i:198112 original size:16 final size:17
Alignment explanation
Indices: 198093--198129 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
198083 ATTTAAGGTA
*
198093 AAATAT-ATTAAATAAT
1 AAATATAATTAAAAAAT
198109 AAATATAATTAAAAAAT
1 AAATATAATTAAAAAAT
198126 AAAT
1 AAAT
198130 TTGGGGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATATAATTAAAAAAT
Found at i:198172 original size:14 final size:14
Alignment explanation
Indices: 198153--198180 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
198143 ATCATAACAA
198153 AATTATATAACTAT
1 AATTATATAACTAT
198167 AATTATATAACTAT
1 AATTATATAACTAT
198181 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:205584 original size:2 final size:2
Alignment explanation
Indices: 205577--205631 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
205567 AATTTACGTT
205577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
205619 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
205632 GTCCTTAAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:206283 original size:2 final size:2
Alignment explanation
Indices: 206276--206301 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
206266 AAATAAATAA
206276 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
206302 GAGAAAATAA
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:206519 original size:21 final size:19
Alignment explanation
Indices: 206495--206547 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
206485 ATTCGTATTG
*
206495 CGATAGTCTAAGTTCGCGTTA
1 CGATAGTCCAAGTT--CGTTA
*
206516 CGATTTATTCCAAGTTCGTTA
1 CGA--TAGTCCAAGTTCGTTA
206537 CGATAGTCCAA
1 CGATAGTCCAA
206548 AATCGCAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 7 0.26
21 11 0.41
23 9 0.33
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (19 bp):
CGATAGTCCAAGTTCGTTA
Found at i:207041 original size:2 final size:2
Alignment explanation
Indices: 207034--207077 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
207024 TAATCCCATA
207034 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
207076 AT
1 AT
207078 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:218179 original size:137 final size:137
Alignment explanation
Indices: 217878--218162 Score: 570
Period size: 137 Copynumber: 2.1 Consensus size: 137
217868 GTGCAATCAT
217878 AGGGCACAAATATGACATATGGCTACAATCCACATGCAATTATGTTAAATATAGTACAGTACAGT
1 AGGGCACAAATATGACATATGGCTACAATCCACATGCAATTATGTTAAATATAGTACAGTACAGT
217943 GCACTTGTGGTGTAATCACATGGCACTAAATGTGTCATACAATCACATATTACAAGTAGCTCTAC
66 GCACTTGTGGTGTAATCACATGGCACTAAATGTGTCATACAATCACATATTACAAGTAGCTCTAC
218008 TGCACAC
131 TGCACAC
218015 AGGGCACAAATATGACATATGGCTACAATCCACATGCAATTATGTTAAATATAGTACAGTACAGT
1 AGGGCACAAATATGACATATGGCTACAATCCACATGCAATTATGTTAAATATAGTACAGTACAGT
218080 GCACTTGTGGTGTAATCACATGGCACTAAATGTGTCATACAATCACATATTACAAGTAGCTCTAC
66 GCACTTGTGGTGTAATCACATGGCACTAAATGTGTCATACAATCACATATTACAAGTAGCTCTAC
218145 TGCACAC
131 TGCACAC
218152 AGGGCACAAAT
1 AGGGCACAAAT
218163 GTGCCACATA
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 148 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (137 bp):
AGGGCACAAATATGACATATGGCTACAATCCACATGCAATTATGTTAAATATAGTACAGTACAGT
GCACTTGTGGTGTAATCACATGGCACTAAATGTGTCATACAATCACATATTACAAGTAGCTCTAC
TGCACAC
Found at i:219944 original size:82 final size:81
Alignment explanation
Indices: 219812--220005 Score: 255
Period size: 82 Copynumber: 2.4 Consensus size: 81
219802 CCAAATAATG
*
219812 GTGGTACATTATCATTTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT-TTT
1 GTGGTACATTATCATATTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAA-AA-TATTT
*
219876 CAGAAAACGAGTGAAATA
64 CAGAAAACGAGCGAAATA
* * *
219894 GTGGTGCATTATCATATTCTGCAACTTTTCAGATGTCATTCAATGCATAATTTAAATATATTTCA
1 GTGGTACATTATCATATTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAAAATATTTCA
*
219959 GACAACGAGCGAAATA
66 GAAAACGAGCGAAATA
* ** * * *
219975 GTGATATTTTATCATCTTCGGTAACTTTTCA
1 GTGGTACATTATCATATTCTGCAACTTTTCA
220006 ATGATGTATC
Statistics
Matches: 98, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.01
81 44 0.45
82 53 0.54
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (81 bp):
GTGGTACATTATCATATTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAAAATATTTCA
GAAAACGAGCGAAATA
Found at i:221080 original size:30 final size:29
Alignment explanation
Indices: 221046--221108 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
221036 ATGTGTCTTG
*
221046 TTGGACCAAATAATTAAAGTGGATGTCCTA
1 TTGGACCAAATAATTAAAG-CGATGTCCTA
221076 TTGGACCAAATAATTAAAGCGATGTCCTA
1 TTGGACCAAATAATTAAAGCGATGTCCTA
221105 TTGG
1 TTGG
221109 GAAAAAACAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (29 bp):
TTGGACCAAATAATTAAAGCGATGTCCTA
Found at i:223580 original size:30 final size:30
Alignment explanation
Indices: 223542--223622 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
223532 TCATGACTAT
*
223542 GCATGCATAGATACATGCATTGTCAATGAA
1 GCATGCATAGATACATGCATTGGCAATGAA
* *
223572 GTATGCATAGATACATGCACTGGCAATGAA
1 GCATGCATAGATACATGCATTGGCAATGAA
223602 GCATGCATAGATACATGCATT
1 GCATGCATAGATACATGCATT
223623 ATCCATTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (30 bp):
GCATGCATAGATACATGCATTGGCAATGAA
Found at i:230544 original size:31 final size:31
Alignment explanation
Indices: 230509--230567 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
230499 ATGATAATTT
230509 CGTTTTCATTTAATTAAGATATGGTCACTTC
1 CGTTTTCATTTAATTAAGATATGGTCACTTC
*
230540 CGTTTTCATTTAATTAAGATGTGGTCAC
1 CGTTTTCATTTAATTAAGATATGGTCAC
230568 CACGGGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.44
Consensus pattern (31 bp):
CGTTTTCATTTAATTAAGATATGGTCACTTC
Found at i:231746 original size:17 final size:17
Alignment explanation
Indices: 231724--231758 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
231714 TCGATCCGAC
*
231724 TTAAAATAATATTTTTA
1 TTAAAAAAATATTTTTA
231741 TTAAAAAAATATTTTTA
1 TTAAAAAAATATTTTTA
231758 T
1 T
231759 ATAGAGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAAAAAATATTTTTA
Found at i:234091 original size:101 final size:101
Alignment explanation
Indices: 233912--234111 Score: 319
Period size: 101 Copynumber: 2.0 Consensus size: 101
233902 ACTTCGGTTG
* * *
233912 AAAAAGAATTATAATTATTCTTTAAGGTTTTAAATTCGAGTATCTTAAATGTCAGGGGCATAAAC
1 AAAAAAAATTATAATTATTCTTTAAGGTTTTAAATTCGAGAATCATAAATGTCAGGGGCATAAAC
* * *
233977 GTTTAGTGTCATTAGTTAAGGGTTATATCTGAACCA
66 GTTCAGTGCCATTAGTTAAGAGTTATATCTGAACCA
* * *
234013 AAAAAAAATTATAGTTATTCTTTAAGGTTTTAAGTTCGAGAATCATAAATGTCAGGGGCATAAGC
1 AAAAAAAATTATAATTATTCTTTAAGGTTTTAAATTCGAGAATCATAAATGTCAGGGGCATAAAC
234078 GTTCAGTGCCATTAGTTAAGAGTTATATCTGAAC
66 GTTCAGTGCCATTAGTTAAGAGTTATATCTGAAC
234112 AAGTAAACAC
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (101 bp):
AAAAAAAATTATAATTATTCTTTAAGGTTTTAAATTCGAGAATCATAAATGTCAGGGGCATAAAC
GTTCAGTGCCATTAGTTAAGAGTTATATCTGAACCA
Found at i:238205 original size:20 final size:22
Alignment explanation
Indices: 238168--238209 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
238158 GTATCATGTT
*
238168 AAAAAATTAATGACAAGTTTAG
1 AAAAAATTAATGAAAAGTTTAG
238190 AAAAAA-TAAT-AAAAGTTTAG
1 AAAAAATTAATGAAAAGTTTAG
238210 GTACTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (22 bp):
AAAAAATTAATGAAAAGTTTAG
Found at i:239574 original size:3 final size:3
Alignment explanation
Indices: 239566--239643 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
239556 CGATTCTTAG
239566 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
239614 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
239644 GCTCGATTCG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:241198 original size:36 final size:36
Alignment explanation
Indices: 241165--241249 Score: 170
Period size: 36 Copynumber: 2.4 Consensus size: 36
241155 GACACTTGCC
241165 CCACAAGCAATCTAATTATACGAACAATGACTTGTT
1 CCACAAGCAATCTAATTATACGAACAATGACTTGTT
241201 CCACAAGCAATCTAATTATACGAACAATGACTTGTT
1 CCACAAGCAATCTAATTATACGAACAATGACTTGTT
241237 CCACAAGCAATCT
1 CCACAAGCAATCT
241250 TAACTAGTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.26
Consensus pattern (36 bp):
CCACAAGCAATCTAATTATACGAACAATGACTTGTT
Found at i:248898 original size:71 final size:71
Alignment explanation
Indices: 248782--248925 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
248772 TTGAATATGC
248782 TTTGGGTCTGTTAATCTTCATGCTGTTCCGCTGTTCTTTCTACCTCATCTTGGTTTTTTCATCCC
1 TTTGGGTCTGTTAATCTTCATGCTGTTCCGCTGTTCTTTCTACCTCATCTTGGTTTTTTCATCCC
248847 AAGAAT
66 AAGAAT
248853 TTTGGGTCTGTTAATCTTCATGCTGTTCCGCTGTTCTTTCTACCTCATCTTGGTTTTTTCATCCC
1 TTTGGGTCTGTTAATCTTCATGCTGTTCCGCTGTTCTTTCTACCTCATCTTGGTTTTTTCATCCC
248918 AAGAAT
66 AAGAAT
248924 TT
1 TT
248926 CATGGATTTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.14, C:0.24, G:0.15, T:0.47
Consensus pattern (71 bp):
TTTGGGTCTGTTAATCTTCATGCTGTTCCGCTGTTCTTTCTACCTCATCTTGGTTTTTTCATCCC
AAGAAT
Found at i:249874 original size:147 final size:147
Alignment explanation
Indices: 249565--250131 Score: 946
Period size: 147 Copynumber: 3.9 Consensus size: 147
249555 ATGTTATTCA
* *
249565 ATGATGTTACTTTTATCATGTTGCGAATTCGCAGTTTCGATTTTGTAGTTTCGAAATCTATATGG
1 ATGATGTTACTTTTATCATGTTGCAAATTCGCAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
*
249630 -TGTCATTGTTTTTGTCTAAAGTGTCCTGCAAAAT--G-AG-TGAAGAATACTAGATTCCAGTAG
66 TTGTCATTGCTTTT-TCTAAAGTGTCCTGCAAAATGAGTAGCTGAAGAATACTAGATTCCAGTAG
*
249690 GATTATGTAGCTTTGCAG
130 GATCATGTAGCTTTGCAG
* * * *
249708 ATGATGTTACTTTTATCATGTCGCAAATTTGCAGTTTCGATTTTGTATTTTCGAAATCTATATGG
1 ATGATGTTACTTTTATCATGTTGCAAATTCGCAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
249773 TTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAATGAGTAGCTGAAGAATACTAGATTCCAGTAGG
66 TTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAATGAGTAGCTGAAGAATACTAGATTCCAGTAGG
*
249838 ATCATGTAGCTTTACAG
131 ATCATGTAGCTTTGCAG
*
249855 ATGATGTTACTTTTATCATGTTGCAAATTCGAAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
1 ATGATGTTACTTTTATCATGTTGCAAATTCGCAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
*
249920 TTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAATCGAGTAGCGGAAGAATACTAGATTCCAGTAG
66 TTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAAT-GAGTAGCTGAAGAATACTAGATTCCAGTAG
249985 GATCATGTAGCTTTGCAG
130 GATCATGTAGCTTTGCAG
*
250003 ATGATGTTACTTTTATCATGTTGCAAATTCGCAGTTTCGATTTCGTAGTTTCGAATTCTATATGG
1 ATGATGTTACTTTTATCATGTTGCAAATTCGCAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
* * *
250068 TTGTCATTGCTTTTTCTAAGGTGTCCTGCAAAATGAGTAGCCGAAGAATACTAGATTCCGGTAG
66 TTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAATGAGTAGCTGAAGAATACTAGATTCCAGTAG
250132 TATTATATGC
Statistics
Matches: 399, Mismatches: 19, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
143 81 0.20
144 12 0.03
145 1 0.00
146 2 0.01
147 161 0.40
148 142 0.36
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (147 bp):
ATGATGTTACTTTTATCATGTTGCAAATTCGCAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
TTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAATGAGTAGCTGAAGAATACTAGATTCCAGTAGG
ATCATGTAGCTTTGCAG
Found at i:250094 original size:295 final size:290
Alignment explanation
Indices: 249565--250131 Score: 956
Period size: 295 Copynumber: 1.9 Consensus size: 290
249555 ATGTTATTCA
* * *
249565 ATGATGTTACTTTTATCATGTTGCGAATTCGCAGTTTCGATTTTGTAGTTTCGAAATCTATATGG
1 ATGATGTTACTTTTATCATGTTGCAAATTCGAAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
* *
249630 TGTCATTGTTTTTGTCTAAAGTGTCCTGCAAAATGAGTGAAGAATACTAGATTCCAGTAGGATTA
66 TGTCATTGCTTTTGTCTAAAGTGTCCTGCAAAATGAGTGAAGAATACTAGATTCCAGTAGGATCA
* * *
249695 TGTAGCTTTGCAGATGATGTTACTTTTATCATGTCGCAAATTTGCAGTTTCGATTTTGTATTTTC
131 TGTAGCTTTGCAGATGATGTTACTTTTATCATGTCGCAAATTCGCAGTTTCGATTTCGTAGTTTC
*
249760 GAAATCTATATGGTTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAATGAGTAGCTGAAGAATACT
196 GAAATCTATATGGTTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAATGAGTAGCCGAAGAATACT
249825 AGATTCCAGTAGGATCATGTAGCTTTACAG
261 AGATTCCAGTAGGATCATGTAGCTTTACAG
249855 ATGATGTTACTTTTATCATGTTGCAAATTCGAAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
1 ATGATGTTACTTTTATCATGTTGCAAATTCGAAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
249920 TTGTCATTGCTTTT-TCTAAAGTGTCCTGCAAAATCGAGTAGCGGAAGAATACTAGATTCCAGTA
66 -TGTCATTGCTTTTGTCTAAAGTGTCCTGCAAAAT-GAGT----GAAGAATACTAGATTCCAGTA
*
249984 GGATCATGTAGCTTTGCAGATGATGTTACTTTTATCATGTTGCAAATTCGCAGTTTCGATTTCGT
125 GGATCATGTAGCTTTGCAGATGATGTTACTTTTATCATGTCGCAAATTCGCAGTTTCGATTTCGT
* *
250049 AGTTTCGAATTCTATATGGTTGTCATTGCTTTTTCTAAGGTGTCCTGCAAAATGAGTAGCCGAAG
190 AGTTTCGAAATCTATATGGTTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAATGAGTAGCCGAAG
*
250114 AATACTAGATTCCGGTAG
255 AATACTAGATTCCAGTAG
250132 TATTATATGC
Statistics
Matches: 258, Mismatches: 13, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
290 82 0.32
291 16 0.06
295 160 0.62
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (290 bp):
ATGATGTTACTTTTATCATGTTGCAAATTCGAAGTTTCGATTTCGTAGTTTCGAAATCTATATGG
TGTCATTGCTTTTGTCTAAAGTGTCCTGCAAAATGAGTGAAGAATACTAGATTCCAGTAGGATCA
TGTAGCTTTGCAGATGATGTTACTTTTATCATGTCGCAAATTCGCAGTTTCGATTTCGTAGTTTC
GAAATCTATATGGTTGTCATTGCTTTTTCTAAAGTGTCCTGCAAAATGAGTAGCCGAAGAATACT
AGATTCCAGTAGGATCATGTAGCTTTACAG
Found at i:254655 original size:15 final size:15
Alignment explanation
Indices: 254635--254669 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
254625 AATACTCGGA
*
254635 TCGAATGGACTTGAC
1 TCGAATGGACTCGAC
254650 TCGAATGGACTCGAC
1 TCGAATGGACTCGAC
254665 TCGAA
1 TCGAA
254670 CTCGAGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (15 bp):
TCGAATGGACTCGAC
Found at i:259549 original size:20 final size:20
Alignment explanation
Indices: 259524--259570 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
259514 TGACTCGAGG
*
259524 TTAGTTCGATCTGATCCGAA
1 TTAGTTCGATCTGATCCAAA
259544 TTAGTTCGATCTGATCCAAA
1 TTAGTTCGATCTGATCCAAA
259564 TTAGTTC
1 TTAGTTC
259571 ATTAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (20 bp):
TTAGTTCGATCTGATCCAAA
Found at i:261730 original size:2 final size:2
Alignment explanation
Indices: 261723--261779 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
261713 CTGAATTTCA
261723 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
261765 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
261780 GTGCTTGAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:262620 original size:2 final size:2
Alignment explanation
Indices: 262613--262652 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
262603 GTATTCCTAT
262613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
262653 CCTTCATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:263619 original size:3 final size:3
Alignment explanation
Indices: 263613--263638 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
263603 AGAAAAAAAA
263613 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
263639 AGAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:264904 original size:48 final size:48
Alignment explanation
Indices: 264833--264928 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
264823 ATATATAGTG
264833 GTTAAAAAAGATAAAAGAACATGAGAATAAGGAAAAGAGTGTTCGCAC
1 GTTAAAAAAGATAAAAGAACATGAGAATAAGGAAAAGAGTGTTCGCAC
264881 GTTAAAAAAGATAAAAGAACATGAGAATAAGGAAAAGAGTGTTCGCAC
1 GTTAAAAAAGATAAAAGAACATGAGAATAAGGAAAAGAGTGTTCGCAC
264929 CCGCCATCCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.17
Consensus pattern (48 bp):
GTTAAAAAAGATAAAAGAACATGAGAATAAGGAAAAGAGTGTTCGCAC
Found at i:267370 original size:15 final size:15
Alignment explanation
Indices: 267346--267387 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
267336 CCTCGGTAAG
267346 TTTCTCTTCTTTCTT
1 TTTCTCTTCTTTCTT
*
267361 TTTCTTTTCTTTC-T
1 TTTCTCTTCTTTCTT
267375 TTTCTGCTTCTTT
1 TTTCT-CTTCTTT
267388 TCTGCTGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTCTCTTCTTTCTT
Found at i:267378 original size:20 final size:20
Alignment explanation
Indices: 267346--267390 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
267336 CCTCGGTAAG
**
267346 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGCTTCT
267366 TTTCT-TTCTTTTCTGCTTCT
1 TTTCTCTTC-TTTCTGCTTCT
267386 TTTCT
1 TTTCT
267391 GCTGAGATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGCTTCT
Found at i:267391 original size:11 final size:11
Alignment explanation
Indices: 267362--267393 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
267352 TTCTTTCTTT
267362 TTCTTTTCT--
1 TTCTTTTCTGC
267371 TTCTTTTCTGC
1 TTCTTTTCTGC
267382 TTCTTTTCTGC
1 TTCTTTTCTGC
267393 T
1 T
267394 GAGATCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (11 bp):
TTCTTTTCTGC
Found at i:267690 original size:16 final size:16
Alignment explanation
Indices: 267669--267741 Score: 128
Period size: 16 Copynumber: 4.6 Consensus size: 16
267659 ATCGTTAGCT
267669 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
*
267685 GAGGCGGCTGGAGGTA
1 GAGGCGGCTGGAGGCA
267701 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
*
267717 GAGGCAGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
267733 GAGGCGGCT
1 GAGGCGGCT
267742 AGGGTTAGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.19, C:0.18, G:0.55, T:0.08
Consensus pattern (16 bp):
GAGGCGGCTGGAGGCA
Found at i:267857 original size:3 final size:3
Alignment explanation
Indices: 267851--267941 Score: 128
Period size: 3 Copynumber: 30.0 Consensus size: 3
267841 TATATTTTTT
* * *
267851 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
267899 TAA TTA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
267942 ATTAATATGG
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
3 74 0.96
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:268405 original size:113 final size:112
Alignment explanation
Indices: 268176--269408 Score: 2006
Period size: 113 Copynumber: 10.9 Consensus size: 112
268166 CAGAGTCATT
* * ** *
268176 CAAAAGGTTGAATAAACTCTTCT-ATTTATGAACTTCTTCTT-CTTC-AGATGACGAGTTCTTCT
1 CAAAAGGTTGAACAAATTCTTCTCA-TTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCT
* * * * * *
268238 CATTATGAACTCTTC-CTGGCAATGTTAATCCATCAATTGATGAATTTAAA
64 CATTATGAACT-TTCTCTGGAAAAGATAATCCATCAAGTGATGAA-TTCAG
* *
268288 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAAATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * *
268353 TTATGAACTTCCTTTGGAAAAGCTGATCCATCAAGTAATAGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGAT-GAATTCAG
*
268401 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
268466 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCA-G
* *
268514 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
268579 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAG
268626 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
268691 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTAAGG
65 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCA-G
* *
268740 TAAAAGGTTGTACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
268805 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAG
268852 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
268917 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGG
65 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCA-G
* *
268966 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
269031 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAG
*
269078 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTC
1 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
269143 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGG
65 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCA-G
*
269192 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
269257 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAG
*
269304 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
269369 ATTATGAACTTTCTCTGGAAAAGACAATCCATCAAATGAT
65 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGAT
269409 AGATTTGAAT
Statistics
Matches: 1054, Mismatches: 54, Indels: 25
0.93 0.05 0.02
Matches are distributed among these distances:
112 47 0.04
113 1001 0.95
114 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAG
Found at i:270351 original size:83 final size:83
Alignment explanation
Indices: 270206--271527 Score: 2462
Period size: 83 Copynumber: 16.0 Consensus size: 83
270196 CTTATTTCTA
* * * * *
270206 CTATGAGCAAATTCATCTTCCAAATTTAATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
270271 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
270289 CTATTG-GCAAATTCATCTTCTAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCA
1 CTA-TGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCA
270352 AAGAACACTTCCAGAAGATG
64 AAGAACACTTCCAGAAGATG
* * *
270372 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
270437 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
270455 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
270520 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
270538 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
270603 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
270621 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
270686 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
270704 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
270769 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
270787 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
270852 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
270870 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
*
270935 GAACACTTTCAGAAGATG
66 GAACACTTCCAGAAGATG
*
270953 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCATATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
271018 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
271036 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
271101 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
271119 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGT--AACCAGATCAGATAACTTAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
271182 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
271200 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
271265 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
271283 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
271348 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
271366 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
271431 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
271449 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTC---
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
271511 -AACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
271528 ACTCAAAGAA
Statistics
Matches: 1216, Mismatches: 17, Indels: 16
0.97 0.01 0.01
Matches are distributed among these distances:
79 17 0.01
81 80 0.07
82 3 0.00
83 1113 0.92
84 3 0.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:271531 original size:21 final size:22
Alignment explanation
Indices: 271502--271552 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
271492 CAACCAGATC
*
271502 AGATAACTC-AACACTTCCAGA
1 AGATGACTCAAACACTTCCAGA
271523 AGATGACTCAAAGAACACTTCCAGA
1 AGATGACTC--A-AACACTTCCAGA
271548 AGATG
1 AGATG
271553 CTATTAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 8 0.32
25 17 0.68
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (22 bp):
AGATGACTCAAACACTTCCAGA
Found at i:271604 original size:104 final size:105
Alignment explanation
Indices: 271419--271635 Score: 355
Period size: 104 Copynumber: 2.0 Consensus size: 105
271409 CAACCAGATC
* *
271419 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAATGATTG
1 AGATGACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTG
*
271484 GTTCTGTCCAACCAGATCAGATAACTC-AACACTTCCAGA
66 GTTCTGTCCAACCAGATCAAATAACTCAAACACTTCCAGA
* *
271523 AGATGACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCTAAATTCAATGATTG
1 AGATGACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTG
271588 GTTCTGTCCAACCAGATCAAATAACTCAAAGAACACTTCCAGA
66 GTTCTGTCCAACCAGATCAAATAACTC--A-AACACTTCCAGA
271631 AGATG
1 AGATG
271636 CTATTAATAC
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
104 87 0.84
108 17 0.16
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (105 bp):
AGATGACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTG
GTTCTGTCCAACCAGATCAAATAACTCAAACACTTCCAGA
Found at i:283537 original size:30 final size:28
Alignment explanation
Indices: 283472--283539 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
283462 ATGAAATATT
* *
283472 AATAATATATATATATAAATACTATAAA
1 AATAATATATATATATAAAAAATATAAA
*
283500 AATAATATGTATATATAAAAAATATATAA
1 AATAATATATATATATAAAAAATATA-AA
*
283529 ATTAA-ATATAT
1 AATAATATATAT
283540 GAAATTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 28 0.82
29 6 0.18
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (28 bp):
AATAATATATATATATAAAAAATATAAA
Found at i:285104 original size:15 final size:15
Alignment explanation
Indices: 285080--285121 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
285070 CCTCGGTAAG
285080 TTTCTCTTCTTTCTT
1 TTTCTCTTCTTTCTT
*
285095 TTTCTTTTCTTTC-T
1 TTTCTCTTCTTTCTT
285109 TTTCTGCTTCTTT
1 TTTCT-CTTCTTT
285122 TCTGCTGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTCTCTTCTTTCTT
Found at i:285112 original size:20 final size:20
Alignment explanation
Indices: 285080--285124 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
285070 CCTCGGTAAG
**
285080 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGCTTCT
285100 TTTCT-TTCTTTTCTGCTTCT
1 TTTCTCTTC-TTTCTGCTTCT
285120 TTTCT
1 TTTCT
285125 GCTGAGATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGCTTCT
Found at i:285125 original size:11 final size:11
Alignment explanation
Indices: 285096--285127 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
285086 TTCTTTCTTT
285096 TTCTTTTCT--
1 TTCTTTTCTGC
285105 TTCTTTTCTGC
1 TTCTTTTCTGC
285116 TTCTTTTCTGC
1 TTCTTTTCTGC
285127 T
1 T
285128 GAGATCGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (11 bp):
TTCTTTTCTGC
Found at i:285536 original size:3 final size:3
Alignment explanation
Indices: 285528--285627 Score: 92
Period size: 3 Copynumber: 33.0 Consensus size: 3
285518 TATATATTTT
* * * * * *
285528 TAA TAA TAA TTA TAA TAA TAA TAA TTA TTA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
285576 TTA TAA TAA TTA TAA TAA TAA TAA TTA TTA TAA TTA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
285622 TAA TAA
1 TAA TAA
285628 ATTAATATGG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
3 81 0.96
4 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:285548 original size:15 final size:15
Alignment explanation
Indices: 285528--285627 Score: 119
Period size: 15 Copynumber: 6.4 Consensus size: 15
285518 TATATATTTT
285528 TAATAATAATTATAA
1 TAATAATAATTATAA
*
285543 TAATAATAATTATTA
1 TAATAATAATTATAA
285558 TAATAATAATTATTATTA
1 TAATAATAATTA-TA--A
*
285576 TTATAATAATTATAA
1 TAATAATAATTATAA
*
285591 TAATAATAATTATTA
1 TAATAATAATTATAA
* *
285606 TAATTATAATAATAAA
1 TAATAATAATTAT-AA
285622 TAATAA
1 TAATAA
285628 ATTAATATGG
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
15 51 0.71
16 7 0.10
17 2 0.03
18 12 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAATAATTATAA
Found at i:285549 original size:18 final size:18
Alignment explanation
Indices: 285528--285627 Score: 119
Period size: 18 Copynumber: 5.5 Consensus size: 18
285518 TATATATTTT
285528 TAATAATAATTATAATAA
1 TAATAATAATTATAATAA
*
285546 TAATAATTATTATAATAA
1 TAATAATAATTATAATAA
* * *
285564 TAATTATTATTATTATAA
1 TAATAATAATTATAATAA
* *
285582 TAATTATAATAATAATAA
1 TAATAATAATTATAATAA
* *
285600 TTATTATAATTATAATAA
1 TAATAATAATTATAATAA
285618 TAAATAATAA
1 T-AATAATAA
285628 ATTAATATGG
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
18 65 0.92
19 6 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATAATTATAATAA
Found at i:289408 original size:21 final size:20
Alignment explanation
Indices: 289374--289414 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
289364 CTATTCATTA
* *
289374 TACTTTTAATTTTTTTAATT
1 TACTTTTAAATTTTTGAATT
289394 TACTTATTAAATTTTTGAATT
1 TACTT-TTAAATTTTTGAATT
289415 GTCGAATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
TACTTTTAAATTTTTGAATT
Found at i:289946 original size:29 final size:30
Alignment explanation
Indices: 289890--289955 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
289880 TAAAGCAATC
* ** **
289890 AAAATAAGAACAATTCAAAAGTTTAATGGGT
1 AAAAT-AGAAAAATTCAAAAGTAAAATGAAT
289921 AAAATAGAAAAATT-AAAAGTAAAATGAAT
1 AAAATAGAAAAATTCAAAAGTAAAATGAAT
289950 AAAATA
1 AAAATA
289956 ATAGAGAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.57
30 8 0.27
31 5 0.17
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (30 bp):
AAAATAGAAAAATTCAAAAGTAAAATGAAT
Done.