Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007950.1 Hibiscus syriacus cultivar Beakdansim tig00110372_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: 1941792
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1105000 original size:11 final size:11
Alignment explanation
Indices: 1104984--1105034 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
1104974 TAAAGTTTGC
1104984 TAAAAATAAAA
1 TAAAAATAAAA
*
1104995 TAAAAATCAAA
1 TAAAAATAAAA
**
1105006 CGAAAATAAAA
1 TAAAAATAAAA
*
1105017 T-GAAATAAAA
1 TAAAAATAAAA
1105027 TAAAAATA
1 TAAAAATA
1105035 GAACGAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:1105034 original size:6 final size:5
Alignment explanation
Indices: 1104925--1105031 Score: 72
Period size: 5 Copynumber: 20.8 Consensus size: 5
1104915 TGTTTAGAGA
* * *
1104925 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT AAAAT -AAAT AGAAT GAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
* **** ** *
1104975 AAAGT TTGCT AAAAAT AAAAT AAAAAT CAAACG AAAAT AAAAT GAAAT
1 AAAAT AAAAT -AAAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT
1105023 AAAAT AAAA
1 AAAAT AAAA
1105032 ATAGAACGAA
Statistics
Matches: 76, Mismatches: 22, Indels: 8
0.72 0.21 0.08
Matches are distributed among these distances:
4 4 0.05
5 59 0.78
6 13 0.17
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:1107894 original size:21 final size:21
Alignment explanation
Indices: 1107840--1107900 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1107830 ATGAAGTTGA
*
1107840 AAAGATATAATAAAATAAAAAT
1 AAAGA-ATAATAAAATAAAAAG
* * **
1107862 AAATAATTATAATTTAAAAAG
1 AAAGAATAATAAAATAAAAAG
1107883 AAAGAATAATAAAATAAA
1 AAAGAATAATAAAATAAA
1107901 TAATAATAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAGAATAATAAAATAAAAAG
Found at i:1107903 original size:36 final size:34
Alignment explanation
Indices: 1107857--1107942 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
1107847 TAATAAAATA
* *
1107857 AAAATAAATAATTATAATTTAAAAAGAAAGAATAAT
1 AAAATAAATAATAATAA-ATAAAAAGAAA-AATAAT
**
1107893 AAAATAAATAATAATAAATAAAAAGGGAAATAAT
1 AAAATAAATAATAATAAATAAAAAGAAAAATAAT
1107927 AAAAT-AATAAATAATA
1 AAAATAAAT-AATAATA
1107943 GTAGTAAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 3 0.07
34 18 0.40
35 8 0.18
36 16 0.36
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (34 bp):
AAAATAAATAATAATAAATAAAAAGAAAAATAAT
Found at i:1107928 original size:37 final size:36
Alignment explanation
Indices: 1107848--1107942 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 36
1107838 GAAAAGATAT
* *
1107848 AATAA-AATAAAAATAAATAATTATAATTTAAAAAGA
1 AATAATAAT-AAAATAAATAATAATAATATAAAAAGA
*
1107884 AAGAATAATAAAATAAATAATAATAA-ATAAAAAGGGA
1 AATAATAATAAAATAAATAATAATAATATAAAAA--GA
1107921 AATAATAA-AATAATAAATAATA
1 AATAATAATAA-AATAAATAATA
1107943 GTAGTAAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
35 6 0.12
36 22 0.43
37 23 0.45
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (36 bp):
AATAATAATAAAATAAATAATAATAATATAAAAAGA
Found at i:1108003 original size:18 final size:18
Alignment explanation
Indices: 1107982--1108024 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1107972 GTTATTTTTA
* *
1107982 AAATAAAAGATAAGAGTT
1 AAATAAAAGAAAAGAATT
*
1108000 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1108018 AAATAAA
1 AAATAAA
1108025 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1109165 original size:5 final size:5
Alignment explanation
Indices: 1109155--1109179 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1109145 TAAAAGAGAT
1109155 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
1109180 CTATTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:1109956 original size:18 final size:18
Alignment explanation
Indices: 1109912--1109959 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
1109902 TTTTTAAAGA
*
1109912 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
1109931 AACT-TATAATATTATAC
1 AAATATATAATATTATAC
1109948 AAATATATAATA
1 AAATATATAATA
1109960 AGGACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 12 0.48
18 10 0.40
19 3 0.12
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:1112969 original size:36 final size:37
Alignment explanation
Indices: 1112922--1112993 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
1112912 AATTCATGTT
1112922 CAAAAATCC-AAAATACTTCAATTACATTCTAAACCC
1 CAAAAATCCAAAAATACTTCAATTACATTCTAAACCC
* ** *
1112958 CAAAATTCCAAAAATACTTTGATTATATTCTAAACC
1 CAAAAATCCAAAAATACTTCAATTACATTCTAAACC
1112994 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 8 0.26
37 23 0.74
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (37 bp):
CAAAAATCCAAAAATACTTCAATTACATTCTAAACCC
Found at i:1116042 original size:15 final size:15
Alignment explanation
Indices: 1115972--1116044 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
1115962 ATTAAAATAG
1115972 AATAA-AATAATTTAT
1 AATAATAAT-ATTTAT
* *
1115987 -ATAA-AAGATTTAAA
1 AATAATAATATTT-AT
1116001 AATAATAATTATTTAT
1 AATAATAA-TATTTAT
*
1116017 -AT-AT-GTATTTAT
1 AATAATAATATTTAT
1116029 AATAATAATATTTAT
1 AATAATAATATTTAT
1116044 A
1 A
1116045 TATATATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
12 7 0.16
13 6 0.13
14 11 0.24
15 14 0.31
16 3 0.07
17 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
AATAATAATATTTAT
Found at i:1116049 original size:31 final size:29
Alignment explanation
Indices: 1115977--1116060 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 29
1115967 AATAGAATAA
* *
1115977 AATAATT-TATATAAAAG-ATTTAAAAAT
1 AATAATTATATATATATGTATTTAAAAAT
*
1116004 AATAATTATTTATATATGTATTTATAATAAT
1 AATAATTATATATATATGTATTTA-AA-AAT
* * *
1116035 AATATTTATATATATATATATATAAA
1 AATAATTATATATATATGTATTTAAA
1116061 GTTTAAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 7 0.15
28 7 0.15
29 5 0.11
30 4 0.09
31 23 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
AATAATTATATATATATGTATTTAAAAAT
Found at i:1117322 original size:3 final size:3
Alignment explanation
Indices: 1117314--1117425 Score: 135
Period size: 3 Copynumber: 37.7 Consensus size: 3
1117304 GGCCTGTTTG
**
1117314 TAA TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
1117359 TAA TATA TAA -AA TAA TAA TAA TAA TAA TATA TAA -AA T-A TAA -AA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
1117402 TAA TAA TAA TAAA TAA TAA TAA TA
1 TAA TAA TAA T-AA TAA TAA TAA TA
1117426 GAAAATGGAG
Statistics
Matches: 96, Mismatches: 4, Indels: 18
0.81 0.03 0.15
Matches are distributed among these distances:
2 10 0.10
3 74 0.77
4 12 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1117350 original size:24 final size:24
Alignment explanation
Indices: 1117315--1117425 Score: 150
Period size: 24 Copynumber: 4.5 Consensus size: 24
1117305 GCCTGTTTGT
**
1117315 AATAATAATAATTTTAATAATAATA
1 AATAA-AATAATAATAATAATAATA
1117340 AATAAAATAATAATAATAATAATA
1 AATAAAATAATAATAATAATAATA
*
1117364 TATAAAATAATAATAATAATAATA
1 AATAAAATAATAATAATAATAATA
* *
1117388 TATAAAATATAAAATAATAATAATA
1 AATAAAATA-ATAATAATAATAATA
1117413 AATAATAATAATA
1 AATAA-AATAATA
1117426 GAAAATGGAG
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
24 49 0.63
25 25 0.32
26 4 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATAAAATAATAATAATAATAATA
Found at i:1117914 original size:101 final size:105
Alignment explanation
Indices: 1117785--1118033 Score: 337
Period size: 113 Copynumber: 2.3 Consensus size: 105
1117775 TAGAGTCATG
* *
1117785 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC-
*
1117849 ATT-TG-A-C-AATGCTGATCCATCGAATGATGAATTCAAG
65 ATTATGAACCGAATGCTGATCCATCGAATGATGAATTCAAA
* *
1117886 TAAAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1117951 TTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAA
66 TTATG-A----ACC--G-AATGCTGATCCATCGAATGATGAATTCAAA
1117999 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
1118034 TCTCTGGAAA
Statistics
Matches: 128, Mismatches: 7, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
101 42 0.33
102 22 0.17
108 1 0.01
109 1 0.01
113 62 0.48
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (105 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACCGAATGCTGATCCATCGAATGATGAATTCAAA
Found at i:1118291 original size:113 final size:111
Alignment explanation
Indices: 1118085--1118420 Score: 458
Period size: 113 Copynumber: 3.0 Consensus size: 111
1118075 AAGTCATGCC
* *
1118085 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
* *
1118150 TGAACT-TTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTTAGCA
66 TGAACTCTAC-CTGGAAATGCTGATCCATCAA-TGATGGATTTGAGCA
1118197 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATT
* * * *
1118262 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCGAGCA
65 ATGAACTCTACCTGGAAATGCTGATCCATC-AATGATGGATTTGAGCA
* *
1118310 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTGTTCTTCTT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGA---GTTCTTCTC
* * * *
1118375 ATTATGAACTCTAACTGAAAATGTTGATCCATTAAATGATGGATTT
62 ATTATGAACTCTACCTGGAAATGCTGATCCA-TCAATGATGGATTT
1118421 AAATCTTTGC
Statistics
Matches: 198, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
112 39 0.20
113 110 0.56
114 4 0.02
116 44 0.22
117 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (111 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTACCTGGAAATGCTGATCCATCAATGATGGATTTGAGCA
Found at i:1118320 original size:309 final size:299
Alignment explanation
Indices: 1117715--1118342 Score: 890
Period size: 309 Copynumber: 2.1 Consensus size: 299
1117705 TCTTCAGATG
* * * *
1117715 AGTTCTTCTCATTATGAA--TTCTACCTGGAAATATTGATGATGATCTATCTATTTCTGTGATAG
1 AGTTCTTCTCATTATGAACTTTCTA-CTGGAAATAGTGATGATAATCTATCTACTTCTGTGATAA
*
1117778 AGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
65 AGTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
* *
1117843 TTCTCTATTTGACAATGCTGATCCATCGAATGATGAATTCAAGTAAAAATTTGAACAAGTTCTTC
130 TTCTCTATTTGACAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTC
* *
1117908 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATG
195 TCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAATG
1117973 CTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACA
260 CTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACA
* *
1118013 AGTTCTTCTCATTATGAACTTTCT-CTGGAAA-AGTGTATGCTAATCTATCTCCTTCTGTGATAA
1 AGTTCTTCTCATTATGAACTTTCTACTGGAAATAGTG-ATGATAATCTATCTACTTCTGTGATAA
* *
1118076 AGTCATGCCAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
65 AGTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
* ** *
1118141 TTCTC-ATTATGAACTTTCTCTGGAAATGCTGATCCATC-AAGTGATGGATTTTAGCAAAAGGTT
130 TTCTCTATT-TG-A------C----AATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAAGTT
1118204 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACT
182 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * *
1118269 CGACCTGGCAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTGAACA
247 CGACCTGGAAATGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACA
1118322 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
1118343 CTTCTTCCTT
Statistics
Matches: 293, Mismatches: 21, Indels: 21
0.87 0.06 0.06
Matches are distributed among these distances:
297 6 0.02
298 116 0.40
299 1 0.00
300 4 0.01
305 1 0.00
308 2 0.01
309 163 0.56
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (299 bp):
AGTTCTTCTCATTATGAACTTTCTACTGGAAATAGTGATGATAATCTATCTACTTCTGTGATAAA
GTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT
TCTCTATTTGACAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCT
CATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAATGC
TGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACA
Found at i:1118847 original size:22 final size:22
Alignment explanation
Indices: 1118822--1118876 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1118812 GATAAAGCTT
*
1118822 TCATCTTTGAAAAGAGAATATG
1 TCATCTTTGAAAAGAGAATATA
* * * *
1118844 TCATGTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATATA
1118866 TCATCTTTGAA
1 TCATCTTTGAA
1118877 GAGTGTAGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:1119338 original size:54 final size:53
Alignment explanation
Indices: 1119244--1119455 Score: 270
Period size: 54 Copynumber: 4.0 Consensus size: 53
1119234 AGAATAGTAG
* *
1119244 GTTCGTAAAACATTTGACAGCACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT-CTTTTCTGTGGCTTCTGCTCAGAT
* * * * *
1119298 GTTCGTAAAACATTTGACAACACATTCTTCATCTCATGTGGTTTCAGCTCAGA-
1 GTTCGTAAAACATTTGACAACACATTCATCTTTTC-TGTGGCTTCTGCTCAGAT
*
1119351 --T-GTAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT-CTTTTCTGTGGCTTCTGCTCAGAT
* *
1119402 GTTCGTAAAGCATTTGACAATACATTCATCTTTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATC-TTTTCTGTGGCTTCTGCTCAGAT
1119456 TTCTCAATTA
Statistics
Matches: 135, Mismatches: 16, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
50 38 0.28
51 5 0.04
53 5 0.04
54 87 0.64
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCTTTTCTGTGGCTTCTGCTCAGAT
Found at i:1119442 original size:104 final size:104
Alignment explanation
Indices: 1119248--1119455 Score: 310
Period size: 104 Copynumber: 2.0 Consensus size: 104
1119238 TAGTAGGTTC
* *
1119248 GTAAAACATTTGACAGCACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTCGTAAAACATTT
1 GTAAAACACTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTCGTAAAACATTT
* *
1119313 GACAACACATTCTTCATCTCATGTGGTTTCAGCTCAGAT
66 GACAACACATTCATCATCTCATGTGGCTTCAGCTCAGAT
* *
1119352 GTAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAGCATTT
1 GTAAAACACTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTCGTAAAACATTT
* * * *
1119417 GACAATACATTCATCTTTTTC-TGTGGCTTCTGCTCAGAT
66 GACAACACATTCATC-ATCTCATGTGGCTTCAGCTCAGAT
1119456 TTCTCAATTA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
104 90 0.97
105 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (104 bp):
GTAAAACACTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTCGTAAAACATTT
GACAACACATTCATCATCTCATGTGGCTTCAGCTCAGAT
Found at i:1121790 original size:114 final size:114
Alignment explanation
Indices: 1121590--1121924 Score: 521
Period size: 114 Copynumber: 2.9 Consensus size: 114
1121580 GATCATGCAG
* * *
1121590 TTCATCTTTCAATTTCAATGATTGGTTCTGGGGTTCC-TA-CTGAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGG-TCCATACCT-AACCAGATCAGATAACTCAAA
*
1121653 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAC
64 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
1121704 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTCCATACCTAACCAGATCAGATAACTTAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTCCATACCTAACCAGATCAGATAACTCAAAGA
1121769 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * * * *
1121818 TTTATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATTAGATAATCTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTCCATACCTAACCAGATCAGATAA-CTCAAAG
* *
1121883 AACACTTCCAGAAGATGCTATTGTGTCTTCTTATTTCTACTA
65 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
1121925 CGAGAACATG
Statistics
Matches: 205, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
113 3 0.01
114 154 0.75
115 48 0.23
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTCCATACCTAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1126633 original size:12 final size:12
Alignment explanation
Indices: 1126618--1126645 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1126608 AACGTAAAAA
1126618 AAATGCAAATGT
1 AAATGCAAATGT
1126630 AAATGCAAATGT
1 AAATGCAAATGT
1126642 AAAT
1 AAAT
1126646 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:1129056 original size:28 final size:28
Alignment explanation
Indices: 1129014--1129071 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1129004 AAGATTTAAA
* * *
1129014 AATAATAATTATTTATATATGTATTTAT
1 AATAATAATTATTTAAATATATATATAT
1129042 AATAATAA-TATTTTAAATATATATATAT
1 AATAATAATTA-TTTAAATATATATATAT
1129070 AA
1 AA
1129072 AGTTTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
AATAATAATTATTTAAATATATATATAT
Found at i:1129064 original size:22 final size:22
Alignment explanation
Indices: 1129039--1129090 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
1129029 TATATGTATT
*
1129039 TATAATA-ATAATATTTTAAATA
1 TATAATATATAA-AGTTTAAATA
1129061 TAT-ATATATAAAGTTTAAATA
1 TATAATATATAAAGTTTAAATA
1129082 -ATAACTATA
1 TATAA-TATA
1129091 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
21 13 0.50
22 11 0.42
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TATAATATATAAAGTTTAAATA
Found at i:1130383 original size:3 final size:3
Alignment explanation
Indices: 1130375--1130509 Score: 195
Period size: 3 Copynumber: 44.7 Consensus size: 3
1130365 GGCCTGTTTG
**
1130375 TAA TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
1130420 TAA TATA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1130465 TAA TAA TATA TAA -AA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
1130510 GAAAATGGAG
Statistics
Matches: 121, Mismatches: 4, Indels: 14
0.87 0.03 0.10
Matches are distributed among these distances:
2 6 0.05
3 103 0.85
4 12 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1135435 original size:35 final size:35
Alignment explanation
Indices: 1135394--1135468 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
1135384 TTCATGTTCA
*
1135394 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTACATTCAAAACCCC
* * * *
1135429 AAATTCCAAAATACTTTAATTATATTCAAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCAAAACCCC
1135464 AAATT
1 AAATT
1135469 GAAGTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCAAAACCCC
Found at i:1135539 original size:35 final size:34
Alignment explanation
Indices: 1135463--1135540 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
1135453 TTCAAAACCC
1135463 TAAATTGAAGTATTTTAAAATTTAGGGTTTAAAA
1 TAAATTGAAGTATTTTAAAATTTAGGGTTTAAAA
* ** *
1135497 TATAATTGAATTATTTTGGAATTT-GGAGTTTAGAA
1 TA-AATTGAAGTATTTTAAAATTTAGG-GTTTAAAA
1135532 TGAAATTGA
1 T-AAATTGA
1135541 GGATTGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 4 0.11
35 32 0.86
36 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (34 bp):
TAAATTGAAGTATTTTAAAATTTAGGGTTTAAAA
Found at i:1138164 original size:14 final size:14
Alignment explanation
Indices: 1138145--1138173 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1138135 AACCAACCTT
1138145 TTGTGATAAATTTA
1 TTGTGATAAATTTA
1138159 TTGTGATAAATTTA
1 TTGTGATAAATTTA
1138173 T
1 T
1138174 AGGGAACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TTGTGATAAATTTA
Found at i:1151143 original size:2 final size:2
Alignment explanation
Indices: 1151136--1151165 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1151126 TTGATCTTTC
*
1151136 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1151166 TAATATGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1151356 original size:19 final size:19
Alignment explanation
Indices: 1151332--1151370 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1151322 TATTCCTATT
1151332 TCGGGAACTAAAGTGTAAA
1 TCGGGAACTAAAGTGTAAA
1151351 TCGGGAACTAAAGTGTAAA
1 TCGGGAACTAAAGTGTAAA
1151370 T
1 T
1151371 ATGTACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.23
Consensus pattern (19 bp):
TCGGGAACTAAAGTGTAAA
Found at i:1153371 original size:140 final size:136
Alignment explanation
Indices: 1153086--1153437 Score: 410
Period size: 140 Copynumber: 2.6 Consensus size: 136
1153076 TAAAAAGTTA
* *
1153086 AACAAGTTCTTATCATTATAAACTTCTT-TT-TTCTCATCAGATGAGTTCTTCTCATTATGAAC-
1 AACAAGTTCTTATCATTATGAACTTCTTCTTATT-T-TTCAGATGAGTTCTTCTCATTATGAACT
* *
1153148 TCCTTCTGGAAATGCTGATCCTCGAAAGGGGTATTATTAATTCAACTTCATATGTAATGAATTAA
64 TCC-TCTGGAAATACTGATCCTC-AAAGGGGTATTATTAATTCAACTTCATATGTAATGAATCAA
* ** *
1153213 GGCAGGGTTG
127 GACAAAGTCG
1153223 AACAAGTTCTTATCATTATGAACTTCTTCTTCATTTTTCAGATGAGTTCTTCTCATTATGAACTT
1 AACAAGTTCTTATCATTATGAACTTCTTCTT-ATTTTTCAGATGAGTTCTTCTCATTATGAACTT
* * * * * *
1153288 CCTCTGAAAATATTGATCCTC-AAGTGAGGTTCTTCTTTCATTCAACTTCATA-GATGATGAATC
65 CCTCTGGAAATACTGATCCTCAAAG-G-GG-TATT-ATTAATTCAACTTCATATG-TAATGAATC
1153351 AA-ACTAAAGTCG
125 AAGAC-AAAGTCG
* * *
1153363 AACAAGTTCTTCTCATTATGAACTTATTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTC
1 AACAAGTTCTTATCATTATGAACTTCTTCTTATTTTTCAGATGAGTTCTTCTCATTATGAACTTC
1153428 CTCTGGAAAT
66 CTCTGGAAAT
1153438 GTTGGTGTTG
Statistics
Matches: 187, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
136 3 0.02
137 28 0.15
138 46 0.25
139 51 0.27
140 59 0.32
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (136 bp):
AACAAGTTCTTATCATTATGAACTTCTTCTTATTTTTCAGATGAGTTCTTCTCATTATGAACTTC
CTCTGGAAATACTGATCCTCAAAGGGGTATTATTAATTCAACTTCATATGTAATGAATCAAGACA
AAGTCG
Found at i:1153492 original size:123 final size:123
Alignment explanation
Indices: 1153362--1153810 Score: 729
Period size: 123 Copynumber: 3.7 Consensus size: 123
1153352 AACTAAAGTC
* *
1153362 GAACAAGTTCTTCTCATTATGAACTTATTCTT-ATTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCATT-TTCAGATGAGTTATTCTCATTATGAACT
*
1153426 TCCTCTGGAAATGTTGGTGTTGATTTATCTCCTTCTGGGTTAGAATCGAGCAAAAGGTT
65 TCCTCTGGAAATGTTGGTGTTGATTTATCTCATTCTGGGTTAGAATCGAGCAAAAGGTT
* * *
1153485 GAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTTTCAGATGAGTTATTCTTATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTTTCAGATGAGTTATTCTCATTATGAACTT
*
1153550 CCACTGGAAATGTTGGTGTTGATTTATCTCATTCTGGGTTAGAATCGAGCAAAAGGTT
66 CCTCTGGAAATGTTGGTGTTGATTTATCTCATTCTGGGTTAGAATCGAGCAAAAGGTT
* * * *
1153608 GAACAAGTTCTTCTCATTGTGAATTTCTTATTCCTTTTCAGATGAGTTATTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTTTCAGATGAGTTATTCTCATTATGAACTT
* * *
1153673 CCTCTGAAAATGTTGGTGTTGATTTATCTCATTCTGGGATAGAATCGAGCAAAATGTT
66 CCTCTGGAAATGTTGGTGTTGATTTATCTCATTCTGGGTTAGAATCGAGCAAAAGGTT
* * *
1153731 GACCAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTTTCAGATGAGTTATTCTCATTATGAACTT
1153796 CCTCTGGAAATGTTG
66 CCTCTGGAAATGTTG
1153811 ATCCATCGAG
Statistics
Matches: 305, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
123 303 0.99
124 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (123 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTTTCAGATGAGTTATTCTCATTATGAACTT
CCTCTGGAAATGTTGGTGTTGATTTATCTCATTCTGGGTTAGAATCGAGCAAAAGGTT
Found at i:1153928 original size:37 final size:36
Alignment explanation
Indices: 1153827--1154124 Score: 195
Period size: 37 Copynumber: 8.1 Consensus size: 36
1153817 CGAGTGATGG
* * *
1153827 AAATTTCTGTTTCTAGTGAAACTGTCTCAAGCGAGAC
1 AAATTT-TGTTTCAAGTAAAACTATCTCAAGCGAGAC
* * * * * ** *
1153864 GAATCTTGTTTTAAGAAAAACAATCTCAAGTTAGAT
1 AAATTTTGTTTCAAGTAAAACTATCTCAAGCGAGAC
* *
1153900 AAATTATTGTTTCAAGTGAAACTGTCTCAAGCGAGAC
1 AAATT-TTGTTTCAAGTAAAACTATCTCAAGCGAGAC
* * * * * *
1153937 AAATTTTTTTTTTAAGAAAAACAATCTCAAGTGAGAT
1 AAA-TTTTGTTTCAAGTAAAACTATCTCAAGCGAGAC
* *
1153974 AAATTTCTGTTTCAAGTAAAAATATCTCAAGAGAGAC
1 AAATTT-TGTTTCAAGTAAAACTATCTCAAGCGAGAC
** * * * * *
1154011 GCAGTTTGTTTTAAG-AAAAATAATCTCAAGTGAGAT
1 AAATTTTGTTTCAAGTAAAACT-ATCTCAAGCGAGAC
* * *
1154047 AAATTTCTGTTTCGAGTAAAACTGTCTCAAGAGAGAC
1 AAATTT-TGTTTCAAGTAAAACTATCTCAAGCGAGAC
* * * * *
1154084 GCAA-TTTGTTTTAAGTAAAACAATCTCAAGTGAGAT
1 -AAATTTTGTTTCAAGTAAAACTATCTCAAGCGAGAC
1154120 AAATT
1 AAATT
1154125 ACTATTTGAA
Statistics
Matches: 194, Mismatches: 59, Indels: 17
0.72 0.22 0.06
Matches are distributed among these distances:
35 8 0.04
36 75 0.39
37 102 0.53
38 9 0.05
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (36 bp):
AAATTTTGTTTCAAGTAAAACTATCTCAAGCGAGAC
Found at i:1154050 original size:73 final size:73
Alignment explanation
Indices: 1153827--1154124 Score: 413
Period size: 73 Copynumber: 4.1 Consensus size: 73
1153817 CGAGTGATGG
* * *
1153827 AAATTTCTGTTTCTAGTGAAACTGTCTCAAGCGAGACG-AATCTTGTTTTAAGAAAAACAATCTC
1 AAATTTCTGTTTCAAGTAAAACTGTCTCAAGAGAGACGCAAT-TTGTTTTAAGAAAAACAATCTC
*
1153891 AAGTTAGAT
65 AAGTGAGAT
* * * *
1153900 AAATTAT-TGTTTCAAGTGAAACTGTCTCAAGCGAGAC-AAATTTTTTTTTTAAGAAAAACAATC
1 AAATT-TCTGTTTCAAGTAAAACTGTCTCAAGAGAGACGCAA--TTTGTTTTAAGAAAAACAATC
1153963 TCAAGTGAGAT
63 TCAAGTGAGAT
* * * *
1153974 AAATTTCTGTTTCAAGTAAAAATATCTCAAGAGAGACGCAGTTTGTTTTAAGAAAAATAATCTCA
1 AAATTTCTGTTTCAAGTAAAACTGTCTCAAGAGAGACGCAATTTGTTTTAAGAAAAACAATCTCA
1154039 AGTGAGAT
66 AGTGAGAT
* *
1154047 AAATTTCTGTTTCGAGTAAAACTGTCTCAAGAGAGACGCAATTTGTTTTAAGTAAAACAATCTCA
1 AAATTTCTGTTTCAAGTAAAACTGTCTCAAGAGAGACGCAATTTGTTTTAAGAAAAACAATCTCA
1154112 AGTGAGAT
66 AGTGAGAT
1154120 AAATT
1 AAATT
1154125 ACTATTTGAA
Statistics
Matches: 202, Mismatches: 17, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
73 139 0.69
74 61 0.30
75 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (73 bp):
AAATTTCTGTTTCAAGTAAAACTGTCTCAAGAGAGACGCAATTTGTTTTAAGAAAAACAATCTCA
AGTGAGAT
Found at i:1154869 original size:22 final size:22
Alignment explanation
Indices: 1154844--1154922 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
1154834 AATAAAGTTT
* *
1154844 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATATA
*
1154866 TCATCTTTGAAGAGAGAATTTA
1 TCATCTTTGAAGAGAGAATATA
1154888 TCATCTTTGAAGAGAGAATATA
1 TCATCTTTGAAGAGAGAATATA
1154910 TCATCTTTGAAGA
1 TCATCTTTGAAGA
1154923 ATGTAGATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATATA
Found at i:1156498 original size:41 final size:40
Alignment explanation
Indices: 1156411--1156502 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
1156401 ATTGAAATGG
* * **
1156411 GCTTTCAACATGCCTCAACATTTGCTTCTTGTTGATGTGA
1 GCTTTCAAAATGCCTCAACATTTGCTTCATACTGATGTGA
**
1156451 GCTTTCAAAATGCCTCAACATTTTTTTTCATACTGATGTGA
1 GCTTTCAAAATGCCTCAACA-TTTGCTTCATACTGATGTGA
1156492 GCTTTCAAAAT
1 GCTTTCAAAAT
1156503 ACCCCATATG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 19 0.42
41 26 0.58
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (40 bp):
GCTTTCAAAATGCCTCAACATTTGCTTCATACTGATGTGA
Found at i:1158876 original size:21 final size:20
Alignment explanation
Indices: 1158852--1158896 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1158842 CTTGATTCAA
1158852 TTTTTTCTT-TTTTTCTTATTC
1 TTTTTT-TTCTTTTTCTT-TTC
1158873 TTTTTTTTCTTTTTCTTTTC
1 TTTTTTTTCTTTTTCTTTTC
1158893 TTTT
1 TTTT
1158897 CTGATGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTTTCTTTTTCTTTTC
Found at i:1158879 original size:15 final size:15
Alignment explanation
Indices: 1158859--1158898 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
1158849 CAATTTTTTC
1158859 TTTTTTTCTTATTCT
1 TTTTTTTCTTATTCT
*
1158874 TTTTTTTCTTTTTCT
1 TTTTTTTCTTATTCT
1158889 TTTCTTTTCT
1 TTT-TTTTCT
1158899 GATGAATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTCTTATTCT
Found at i:1158891 original size:5 final size:5
Alignment explanation
Indices: 1158854--1158898 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
1158844 TGATTCAATT
1158854 TTTTC -TTT- TTTTC TTATTC TTTT- TTTTC TTTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC -TTTTC TTTTC TTTTC T
1158899 GATGAATGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
4 10 0.29
5 15 0.43
6 10 0.29
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:1159190 original size:2 final size:2
Alignment explanation
Indices: 1159183--1159267 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
1159173 ACAACAAGGG
1159183 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
1159225 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
1159267 A
1 A
1159268 GATAAATGAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1163807 original size:2 final size:2
Alignment explanation
Indices: 1163800--1163865 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
1163790 TAATTAAATA
1163800 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
*
1163842 AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
1163866 TAATATGACT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1164134 original size:15 final size:16
Alignment explanation
Indices: 1164093--1164134 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
1164083 TTAAAATGGC
1164093 TAAAATATA-ATAAAA
1 TAAAATATAGATAAAA
1164108 TAAAGCATATAGATAAAA
1 TAAA--ATATAGATAAAA
1164126 -AAAATATAG
1 TAAAATATAG
1164135 CAACTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 10 0.42
17 8 0.33
18 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (16 bp):
TAAAATATAGATAAAA
Found at i:1167486 original size:27 final size:28
Alignment explanation
Indices: 1167456--1167508 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
1167446 ATATATTTAT
*
1167456 ATTTTTTTCATTA-TTTATT-TATTATTA
1 ATTTTTTT-ATCATTTTATTCTATTATTA
1167483 ATTTTTTTATCATTTTATTCTATTAT
1 ATTTTTTTATCATTTTATTCTATTAT
1167509 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 14 0.61
28 6 0.26
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (28 bp):
ATTTTTTTATCATTTTATTCTATTATTA
Found at i:1167513 original size:2 final size:2
Alignment explanation
Indices: 1167506--1167534 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1167496 TTTATTCTAT
1167506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1167535 CTATTTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1167613 original size:33 final size:34
Alignment explanation
Indices: 1167576--1167661 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 34
1167566 TGTATATATA
*
1167576 TATATATATATATATTATTTTTAT-TATTTTCT-T
1 TATATATGTATATATTATTTTTATCTATTTT-TAT
* *
1167609 TATATATGT-TCTATT-TATTTATCTATTTTTAT
1 TATATATGTATATATTATTTTTATCTATTTTTAT
1167641 T-TACTATGTATATATTATTTT
1 TATA-TATGTATATATTATTTT
1167662 CACTATTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
31 9 0.21
32 18 0.42
33 13 0.30
34 3 0.07
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (34 bp):
TATATATGTATATATTATTTTTATCTATTTTTAT
Found at i:1167692 original size:17 final size:17
Alignment explanation
Indices: 1167665--1167707 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1167655 TTATTTTCAC
1167665 TATTATTTTCCTATAT-TT
1 TATT-TTTTCCT-TATCTT
*
1167683 TATTTTTTCCTTGTCTT
1 TATTTTTTCCTTATCTT
1167700 TATTTTTT
1 TATTTTTT
1167708 TTTCATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (17 bp):
TATTTTTTCCTTATCTT
Found at i:1167710 original size:20 final size:20
Alignment explanation
Indices: 1167685--1167725 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1167675 CTATATTTTA
*
1167685 TTTTTTCCTTGTCTTTATTT
1 TTTTTTCATTGTCTTTATTT
* *
1167705 TTTTTTCATTTTGTTTATTT
1 TTTTTTCATTGTCTTTATTT
1167725 T
1 T
1167726 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTTTCATTGTCTTTATTT
Found at i:1167756 original size:30 final size:29
Alignment explanation
Indices: 1167698--1167788 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 29
1167688 TTTCCTTGTC
*
1167698 TTTATTTTTTTTTCATTTTGTTTATTTTA
1 TTTATTTATTTTTCATTTTGTTTATTTTA
1167727 TTTATTTATTTTTC-TTATT-TCTTATTTTTA
1 TTTATTTATTTTTCATT-TTGT-TTA-TTTTA
* * *
1167757 TTTCTTTA-TTATCGTTTTGTTTATTTTA
1 TTTATTTATTTTTCATTTTGTTTATTTTA
1167785 TTTA
1 TTTA
1167789 CTTGTAGTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
28 11 0.21
29 27 0.51
30 15 0.28
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.76
Consensus pattern (29 bp):
TTTATTTATTTTTCATTTTGTTTATTTTA
Found at i:1169461 original size:11 final size:11
Alignment explanation
Indices: 1169445--1169489 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1169435 TTGGTGCTGG
1169445 AAATAAGATAA
1 AAATAAGATAA
*
1169456 AAATAAGATTA
1 AAATAAGATAA
*
1169467 AAACAAGATAA
1 AAATAAGATAA
1169478 AGAA-AAGATAA
1 A-AATAAGATAA
1169489 A
1 A
1169490 TGAATTGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (11 bp):
AAATAAGATAA
Found at i:1174032 original size:11 final size:11
Alignment explanation
Indices: 1174008--1174052 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1173998 TTGGTGCTGG
1174008 AAACAAGATAA
1 AAACAAGATAA
* *
1174019 AAATAAGATTA
1 AAACAAGATAA
1174030 AAACAAGATAA
1 AAACAAGATAA
1174041 AGAA-AAGATAA
1 A-AACAAGATAA
1174052 A
1 A
1174053 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:1174036 original size:22 final size:22
Alignment explanation
Indices: 1174008--1174049 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1173998 TTGGTGCTGG
1174008 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
1174030 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
1174050 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:1178594 original size:10 final size:10
Alignment explanation
Indices: 1178566--1178605 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
1178556 TGCTGGAAAC
*
1178566 AAGATAAAAT
1 AAGATAAAAA
1178576 AAGATTAAAAA
1 AAGA-TAAAAA
1178587 AAGATAAAGAA
1 AAGATAAA-AA
1178598 AAGATAAA
1 AAGATAAA
1178606 TGAATTGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (10 bp):
AAGATAAAAA
Found at i:1184810 original size:18 final size:17
Alignment explanation
Indices: 1184789--1184839 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
1184779 CCCTGAATTG
1184789 AAAAAAGAGAAAAAT-A
1 AAAAAAGAGAAAAATAA
*
1184805 ACAAAAGAGAAAAGA-AA
1 AAAAAAGAGAAAA-ATAA
*
1184822 AAAGAAAAAGAAAAATAA
1 AAA-AAAGAGAAAAATAA
1184840 GGTGGGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 12 0.43
17 5 0.18
18 11 0.39
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (17 bp):
AAAAAAGAGAAAAATAA
Found at i:1185790 original size:58 final size:60
Alignment explanation
Indices: 1185648--1185797 Score: 193
Period size: 58 Copynumber: 2.5 Consensus size: 60
1185638 GACTTACTCG
* * *
1185648 AGATTGGATTTCAACTTCACAACGAAGGATA-TCTAACTCAATACCAAATTGTTGAAACAA
1 AGATTGGATTTCAACTTCACGACGAAGGATATTCTAAC-CAATACCAAATTGGTGAAAAAA
* *
1185708 AGATTGGATTTCAACTTCAGGACGAAGGATATTC-AA-C-A-ACCAATTTGGTGAAGCAAAA
1 AGATTGGATTTCAACTTCACGACGAAGGATATTCTAACCAATACCAAATTGGTGAA--AAAA
1185766 AGATTGGATTTCAACTTCACGACGAAGGATAT
1 AGATTGGATTTCAACTTCACGACGAAGGATAT
1185798 CCAATTTGAG
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
56 12 0.15
57 1 0.01
58 35 0.43
60 31 0.38
61 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (60 bp):
AGATTGGATTTCAACTTCACGACGAAGGATATTCTAACCAATACCAAATTGGTGAAAAAA
Found at i:1186531 original size:31 final size:32
Alignment explanation
Indices: 1186465--1186555 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 32
1186455 GAAGAACCTA
* *
1186465 TCCATATGTTCCGAAGAACATAGGTAACACTG
1 TCCATATGTCCCGAAGGACATAGGTAACACTG
*
1186497 TCCATATGTCCCGAAGGGCATAGGTAA-ACTG
1 TCCATATGTCCCGAAGGACATAGGTAACACTG
* * *
1186528 TCCATATATCTCGAAAGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGGTAAC
1186556 CCTCGACTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 27 0.53
32 24 0.47
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (32 bp):
TCCATATGTCCCGAAGGACATAGGTAACACTG
Found at i:1190241 original size:16 final size:16
Alignment explanation
Indices: 1190222--1190258 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1190212 ATATATTTAA
1190222 TTATTATTTATTTTC-T
1 TTATTATTT-TTTTCAT
1190238 TTATTATTTTTTTCAT
1 TTATTATTTTTTTCAT
1190254 TTATT
1 TTATT
1190259 TATTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTATTTTTTTCAT
Found at i:1190298 original size:2 final size:2
Alignment explanation
Indices: 1190291--1190355 Score: 64
Period size: 2 Copynumber: 33.5 Consensus size: 2
1190281 TTTATTCTAT
* * * *
1190291 TA TA TA TA TA TA TA TA TA TC TA T- TT TT TA TA TCA T- TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
1190331 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1190356 TATTTTTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.05
2 50 0.91
3 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1190461 original size:19 final size:19
Alignment explanation
Indices: 1190437--1190477 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1190427 TTCACTATTA
1190437 TTTTCCTATAT-TTTATTTT
1 TTTTCCT-TATCTTTATTTT
*
1190456 TTTTCCTTGTCTTTATTTT
1 TTTTCCTTATCTTTATTTT
1190475 TTT
1 TTT
1190478 ATTTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTCCTTATCTTTATTTT
Found at i:1190480 original size:42 final size:44
Alignment explanation
Indices: 1190434--1190549 Score: 105
Period size: 45 Copynumber: 2.6 Consensus size: 44
1190424 ATTTTCACTA
* *
1190434 TTATTTTCCTATATTTTATTTTTTTTC-CTTG-TCTTTATTTTT
1 TTATTTTCCTATATTTTATTTTTTTTCACTTGTTATTTATTTAT
* * *
1190476 TTATTTT-TTTTCATTTTA-TTTTTTTCATTTTGTTTATTTATTTAT
1 TTATTTTCCTAT-ATTTTATTTTTTTTCA-CTTG-TTATTTATTTAT
*
1190521 TTATTTTCCTTATTTTTTATTTTTGTTTC
1 TTATTTTCC-TATATTTTATTTTT-TTTC
1190550 TTTATTATCA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
41 10 0.18
42 13 0.23
43 3 0.05
45 16 0.28
46 5 0.09
47 6 0.11
48 4 0.07
ACGTcount: A:0.13, C:0.09, G:0.03, T:0.76
Consensus pattern (44 bp):
TTATTTTCCTATATTTTATTTTTTTTCACTTGTTATTTATTTAT
Found at i:1190512 original size:41 final size:41
Alignment explanation
Indices: 1190446--1190576 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
1190436 ATTTTCCTAT
* * *
1190446 ATTTTATTTTTTTTCCTTGTCTTTATTTTTTTATTTTTTTTC
1 ATTTTA-TTTTTTTCATTTTGTTTATTTTTTTATTTTTTTTC
* *
1190488 ATTTTATTTTTTTCATTTTGTTTATTTATTTATTTATTTTC
1 ATTTTATTTTTTTCATTTTGTTTATTTTTTTATTTTTTTTC
* * *
1190529 --CTTA-TTTTTT-ATTTTTGTTTCTTTATTATCATTTTTTTT-
1 ATTTTATTTTTTTCA-TTTTGTTTATTT-TT-TTATTTTTTTTC
1190568 ATTTTATTT
1 ATTTTATTT
1190577 ACTTGTTATC
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
37 1 0.01
38 17 0.24
39 4 0.06
40 9 0.12
41 33 0.46
42 8 0.11
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (41 bp):
ATTTTATTTTTTTCATTTTGTTTATTTTTTTATTTTTTTTC
Found at i:1190544 original size:8 final size:8
Alignment explanation
Indices: 1190467--1190527 Score: 61
Period size: 8 Copynumber: 7.4 Consensus size: 8
1190457 TTTCCTTGTC
1190467 TTTATTTT
1 TTTATTTT
1190475 TTTATTTT
1 TTTATTTT
**
1190483 TTT-TCAT
1 TTTATTTT
1190490 TTTATTTT
1 TTTATTTT
1190498 TTTCATTTT
1 TTT-ATTTT
*
1190507 GTTTATTTA
1 -TTTATTTT
1190516 TTTATTTAT
1 TTTATTT-T
1190525 TTT
1 TTT
1190528 CCTTATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
7 5 0.12
8 23 0.53
9 12 0.28
10 3 0.07
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTATTTT
Found at i:1190554 original size:30 final size:29
Alignment explanation
Indices: 1190434--1190665 Score: 104
Period size: 29 Copynumber: 7.8 Consensus size: 29
1190424 ATTTTCACTA
* * *
1190434 TTATTTTC-CTATATTTTATTTTTTTTCC
1 TTATTTTCATTATTTTTTATTTTTTTTCT
*
1190462 TTGTCTTT-A-T-TTTTTTATTTTTTTTCATT
1 TTAT-TTTCATTATTTTTTATTTTTTTTC--T
* * *
1190491 TTATTTT-TTTCATTTTGTT-TATTTATTTAT
1 TTATTTTCATT-ATTTT-TTAT-TTTTTTTCT
*
1190521 TTATTTTCCTTATTTTTTATTTTTGTTTCT
1 TTATTTTCATTATTTTTTATTTTT-TTTCT
* *
1190551 TTATTATCATT-TTTTTTATTTTATTTAC-
1 TTATTTTCATTATTTTTTATTTT-TTTTCT
* * * *
1190579 TTGTTATCTTTATTTTATTATTAATATTTTCT
1 TTATTTTCATTATTTT-TTATT--TTTTTTCT
* * *
1190611 TTATTTTTCTTTACTCATTTTATTTTATCTTCT
1 TTA-TTTTCATTA-T-TTTTTATTTT-TTTTCT
*
1190644 TTA-TTTCATTTTTTTTTATTTT
1 TTATTTTCATTATTTTTTATTTT
1190666 GTTGGGTTTA
Statistics
Matches: 157, Mismatches: 25, Indels: 43
0.70 0.11 0.19
Matches are distributed among these distances:
27 15 0.10
28 16 0.10
29 39 0.25
30 34 0.22
31 17 0.11
32 12 0.08
33 16 0.10
34 6 0.04
35 2 0.01
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.74
Consensus pattern (29 bp):
TTATTTTCATTATTTTTTATTTTTTTTCT
Found at i:1190569 original size:45 final size:44
Alignment explanation
Indices: 1190540--1190665 Score: 87
Period size: 48 Copynumber: 2.7 Consensus size: 44
1190530 TTATTTTTTA
* * *
1190540 TTTTTGTTTCTTTATTATCATTTTTTTTATTTTATTTACTTGTTA
1 TTTTT-TTTCTTTATTATCATTTTTTTTATTTTCTTTATTTTTTA
* * *
1190585 TCTTTATTTT-ATTATTAAT-ATTTTCTTTATTTTTCTTTACTCATTTTA
1 T-TTT-TTTTCTTTATT-ATCATTTTTTTTA-TTTTCTTTA-T-TTTTTA
*
1190633 TTTTATCTTCTTTATT-TCATTTTTTTTTATTTT
1 TTTT-TTTTCTTTATTATCA-TTTTTTTTATTTT
1190666 GTTGGGTTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
45 15 0.24
46 17 0.27
47 13 0.21
48 18 0.29
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.73
Consensus pattern (44 bp):
TTTTTTTTCTTTATTATCATTTTTTTTATTTTCTTTATTTTTTA
Found at i:1190577 original size:4 final size:5
Alignment explanation
Indices: 1190474--1190665 Score: 63
Period size: 5 Copynumber: 38.8 Consensus size: 5
1190464 GTCTTTATTT
* *
1190474 TTTTA TTTT- TTTTCA TTTTA TTTT- TTTCA TTTT- GTTTA -TTTA -TTTA
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * *
1190520 -TTTA TTTTCC TTATT- TTTTA TTTT- TGTTT- CTTTA TTATCA TTTT-
1 TTTTA TTTT-A TT-TTA TTTTA TTTTA T-TTTA TTTTA TT-TTA TTTTA
1190564 TTTTA TTTTA -TTTA CTTGTTA TCTTTA TTTTA TTATTAA TATTT- TCTTTA
1 TTTTA TTTTA TTTTA -TT-TTA T-TTTA TTTTA TT-TT-A T-TTTA T-TTTA
* * * * * *
1190614 TTTT- TCTTTA -CTCA TTTTA TTTTA TCTT- CTTTA TTTCA TTTTT TTTTA
1 TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1190662 TTTT
1 TTTT
1190666 GTTGGGTTTA
Statistics
Matches: 142, Mismatches: 21, Indels: 48
0.67 0.10 0.23
Matches are distributed among these distances:
4 41 0.29
5 71 0.50
6 19 0.13
7 10 0.07
8 1 0.01
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:1190643 original size:23 final size:24
Alignment explanation
Indices: 1190617--1190662 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1190607 TTCTTTATTT
1190617 TTCTTTA-CTCATTTTATTTTATC
1 TTCTTTATCTCATTTTATTTTATC
* *
1190640 TTCTTTATTTCATTTTTTTTTAT
1 TTCTTTATCTCATTTTATTTTAT
1190663 TTTGTTGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (24 bp):
TTCTTTATCTCATTTTATTTTATC
Found at i:1196924 original size:39 final size:39
Alignment explanation
Indices: 1196841--1196921 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
1196831 ATTTAATGTT
* * * *
1196841 AAATTTTAAACGATAATATTAAAGTGAAATAAAAACTAA
1 AAATTTTAAACGATAATACTAAAATAAAACAAAAACTAA
1196880 AAATTTT-AACGATATGATACTAAAATAAAACAAAAACTAA
1 AAATTTTAAACGATA--ATACTAAAATAAAACAAAAACTAA
1196920 AA
1 AA
1196922 TTTCTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 7 0.19
39 7 0.19
40 22 0.61
ACGTcount: A:0.60, C:0.07, G:0.06, T:0.26
Consensus pattern (39 bp):
AAATTTTAAACGATAATACTAAAATAAAACAAAAACTAA
Found at i:1208891 original size:2 final size:2
Alignment explanation
Indices: 1208884--1208919 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1208874 CCGCCCCGAT
*
1208884 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1208920 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1210985 original size:21 final size:21
Alignment explanation
Indices: 1210959--1210999 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1210949 GACTATTGCA
1210959 TTGCGATTTCCCAAATTCGCG
1 TTGCGATTTCCCAAATTCGCG
* *
1210980 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTCCCAAATTCGC
1211000 AATGCGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGCG
Found at i:1211005 original size:21 final size:21
Alignment explanation
Indices: 1210960--1211006 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1210950 ACTATTGCAT
**
1210960 TGCGATTTCCCAAATTCGCGT
1 TGCGATTTCCCAAATTCGCAA
* *
1210981 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTCCCAAATTCGCAA
1211002 TGCGA
1 TGCGA
1211007 ATACGTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TGCGATTTCCCAAATTCGCAA
Found at i:1211021 original size:20 final size:20
Alignment explanation
Indices: 1210996--1211069 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1210986 TTTTCCTAAT
1210996 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1211016 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1211037 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1211057 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1211070 CTGACTATCG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1211291 original size:22 final size:22
Alignment explanation
Indices: 1211266--1211331 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
1211256 GGCGACATCC
1211266 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
1211288 GTCCCCATCGCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
1211310 GTCTCCATCTCCGGCAAAATCA
1 GTCCCCATCTCCGACGAAATCA
1211332 TTCATGGATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.26, C:0.39, G:0.15, T:0.20
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1211727 original size:20 final size:20
Alignment explanation
Indices: 1211702--1211748 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1211692 GATTCTTGCT
1211702 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
1211722 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
1211742 TTGCGAT
1 TTGCGAT
1211749 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:1211754 original size:20 final size:20
Alignment explanation
Indices: 1211716--1211770 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1211706 GATAGTCAAA
* **
1211716 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
1211736 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
1211756 TTCATGTTGCGATTT
1 TTCGTGTTGCGATTT
1211771 AAAGTTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1211778 original size:20 final size:20
Alignment explanation
Indices: 1211735--1211779 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1211725 CGATAGTCAT
* ** *
1211735 TTTCGTGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTAAAG
1211755 TTTCATGTTGCGATTTAAAG
1 TTTCATGTTGCGATTTAAAG
1211775 TTTCA
1 TTTCA
1211780 GAAACTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGATTTAAAG
Found at i:1213680 original size:20 final size:20
Alignment explanation
Indices: 1213655--1213837 Score: 236
Period size: 20 Copynumber: 9.5 Consensus size: 20
1213645 ATAATAGTTT
1213655 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1213675 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1213695 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1213711 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
1213728 AAAATCGTAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1213748 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1213768 ACTATTGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1213788 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1213808 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1213828 ACTATCGCAA
1 ACTATCGCAA
1213838 CGAAAGAATC
Statistics
Matches: 144, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
14 7 0.05
16 6 0.04
17 4 0.03
18 2 0.01
19 10 0.07
20 115 0.80
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1213739 original size:19 final size:19
Alignment explanation
Indices: 1213711--1213869 Score: 112
Period size: 20 Copynumber: 8.4 Consensus size: 19
1213701 GCAACGAGAG
1213711 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
1213730 AATCGTAATGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* *
1213750 TATCGCAATGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* * *
1213770 TATTGCAATGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* * *
1213790 TATCGCAATGTGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* * *
1213810 TATCGCAATGCGAATTTGAC
1 AATCGCAATGCGAA-ATGAA
*
1213830 TATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1213844 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1213863 AATCGCA
1 AATCGCA
1213870 TTGTGATTCT
Statistics
Matches: 122, Mismatches: 11, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.06
16 6 0.05
17 1 0.01
18 4 0.03
19 20 0.16
20 84 0.69
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.21
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1213780 original size:40 final size:40
Alignment explanation
Indices: 1213655--1213858 Score: 236
Period size: 40 Copynumber: 5.4 Consensus size: 40
1213645 ATAATAGTTT
*
1213655 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
*
1213695 ACTATCGCAA--CG-AGA-GA--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
1213728 AAAATCGTAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* *
1213768 ACTATTGCAATGCGAAAATGACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
**
1213808 ACTATCGCAATGCGAATTTGACTATCGCAA--CG-AAA-G
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1213844 A--ATCGCAATGCGAAA
1 ACTATCGCAATGCGAAA
1213859 TGAAAATCGC
Statistics
Matches: 141, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
33 12 0.09
34 23 0.16
35 2 0.01
36 6 0.04
37 7 0.05
38 3 0.02
39 11 0.08
40 77 0.55
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.20
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
Found at i:1213909 original size:20 final size:20
Alignment explanation
Indices: 1213884--1213930 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1213874 GATTCTCTCG
1213884 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
1213904 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
1213924 TTGCGAT
1 TTGCGAT
1213931 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:1213984 original size:33 final size:33
Alignment explanation
Indices: 1213902--1213997 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 33
1213892 GTCAAATTCG
* * *
1213902 CATTGCGATAGTCATTTTCGCGTTGCGATTTTGT
1 CATTGCGATAGTCA-TTTCGCATTGCGATTCTCT
** ** *
1213936 TGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CATTGCGATAGTCATTTCGCATTGCGATTCTCT
*
1213969 CATTGCGATAGTCATTTTCGCGTTGCGAT
1 CATTGCGATAGTCA-TTTCGCATTGCGAT
1213998 AGTCATTTTC
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
33 25 0.53
34 22 0.47
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.45
Consensus pattern (33 bp):
CATTGCGATAGTCATTTCGCATTGCGATTCTCT
Found at i:1213996 original size:20 final size:20
Alignment explanation
Indices: 1213971--1214017 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1213961 GATTCTCTCA
1213971 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
*
1213991 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCG
1214011 TTGCGAT
1 TTGCGAT
1214018 TTTAAGTTTC
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:0.15, C:0.17, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:1216017 original size:14 final size:14
Alignment explanation
Indices: 1215985--1216019 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1215975 GATTGTTTAA
1215985 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
1215999 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
1216013 TTGATTT
1 TTGATTT
1216020 ATTTAATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1216256 original size:33 final size:34
Alignment explanation
Indices: 1216201--1216274 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 34
1216191 TGATTTCGCG
1216201 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
* *
1216235 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
1216268 TTGCGAT
1 TTGCGAT
1216275 AGTCAATTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 26 0.68
34 12 0.32
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
Found at i:1216292 original size:20 final size:21
Alignment explanation
Indices: 1216259--1216324 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 21
1216249 TCGCATTGCG
1216259 ATTC-TCTCGTTGCGATAGTCA
1 ATTCTTCT-GTTGCGATAGTCA
1216280 ATTCTT-TGTTGCGATAGTC-
1 ATTCTTCTGTTGCGATAGTCA
1216299 ATT-TTCGTGTTGCGATAGTCA
1 ATTCTTC-TGTTGCGATAGTCA
1216320 TATTC
1 -ATTC
1216325 GCGTTGCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 25 0.64
21 5 0.13
22 4 0.10
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (21 bp):
ATTCTTCTGTTGCGATAGTCA
Found at i:1216325 original size:20 final size:20
Alignment explanation
Indices: 1216267--1216334 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
1216257 CGATTCTCTC
*
1216267 GTTGCGATAGTCA-ATTCTTT
1 GTTGCGATAGTCATATTC-GT
*
1216287 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATATTCGT
*
1216307 GTTGCGATAGTCATATTCGC
1 GTTGCGATAGTCATATTCGT
1216327 GTTGCGAT
1 GTTGCGAT
1216335 TTCCGCATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 40 0.93
21 3 0.07
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (20 bp):
GTTGCGATAGTCATATTCGT
Found at i:1218558 original size:14 final size:14
Alignment explanation
Indices: 1218539--1218565 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1218529 TCCCGTGGTA
1218539 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
1218553 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
1218566 TTTCTTCTTC
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:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:1218804 original size:24 final size:24
Alignment explanation
Indices: 1218777--1218823 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1218767 CAAAATCCGA
1218777 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1218801 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1218824 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1218832 original size:24 final size:24
Alignment explanation
Indices: 1218781--1218832 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1218771 ATCCGAGTAT
** *
1218781 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
1218805 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
1218829 TGAC
1 TGAC
1218833 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:1219716 original size:20 final size:20
Alignment explanation
Indices: 1219691--1219817 Score: 202
Period size: 20 Copynumber: 6.3 Consensus size: 20
1219681 GCGATAGTCG
1219691 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1219711 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1219731 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
1219751 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* *
1219771 TTGCGATTTTC-TAAATTCGCG
1 TTGCGATTTACGT--ATTCGCA
1219792 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1219812 TTGCGA
1 TTGCGA
1219818 ATTAGGAAAA
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
19 1 0.01
20 81 0.83
21 15 0.15
22 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1219813 original size:61 final size:60
Alignment explanation
Indices: 1219691--1219817 Score: 202
Period size: 61 Copynumber: 2.1 Consensus size: 60
1219681 GCGATAGTCG
*
1219691 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
* *
1219751 TTGCGATTTACGTAATCGCATTGCGATTTTC-TAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGT--ATTCGCATTGCGATTTACGTATTCGCA
1219812 TTGCGA
1 TTGCGA
1219818 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
59 1 0.02
60 29 0.47
61 32 0.52
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (60 bp):
TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
Found at i:1219838 original size:21 final size:21
Alignment explanation
Indices: 1219814--1219859 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1219804 TATTCGCATT
1219814 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1219835 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1219856 GCGA
1 GCGA
1219860 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1220703 original size:16 final size:16
Alignment explanation
Indices: 1220682--1220714 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1220672 TAATAAATAG
1220682 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1220698 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1220714 A
1 A
1220715 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1220800 original size:16 final size:16
Alignment explanation
Indices: 1220779--1220817 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
1220769 CATTTAATAA
1220779 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
1220795 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
1220811 ATAAACG
1 ATAAACG
1220818 TTAGAGACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:1221573 original size:10 final size:10
Alignment explanation
Indices: 1221558--1221605 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1221548 ATAAATGAAT
1221558 GAACATAAAC
1 GAACATAAAC
1221568 GAACATAATCGAAC
1 GAACAT-A---AAC
1221582 GAACATAAAC
1 GAACATAAAC
*
1221592 GAACATAACC
1 GAACATAAAC
1221602 GAAC
1 GAAC
1221606 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1221582 original size:14 final size:14
Alignment explanation
Indices: 1221565--1221595 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1221555 AATGAACATA
*
1221565 AACGAACATAATCG
1 AACGAACATAAACG
1221579 AACGAACATAAACG
1 AACGAACATAAACG
1221593 AAC
1 AAC
1221596 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1221585 original size:24 final size:24
Alignment explanation
Indices: 1221545--1221606 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
1221535 GATTGGGTTA
*
1221545 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1221569 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
1221593 AACATAACCGAACG
1 AACATAATCGAACG
1221607 TTCACGAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1230009 original size:22 final size:22
Alignment explanation
Indices: 1229984--1230025 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1229974 AAAACCCACT
* *
1229984 AAAAATGAA-AAAAAATTGAAC
1 AAAAAAGAAGAAAAAAATGAAC
1230005 AAAAAAGAAGAAAAAAATGAA
1 AAAAAAGAAGAAAAAAATGAA
1230026 GTTGTGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAAAGAAGAAAAAAATGAAC
Found at i:1235013 original size:20 final size:20
Alignment explanation
Indices: 1234988--1235037 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1234978 TATCAAGTTG
*
1234988 TTATGTTTCTTTTTATGT-TT
1 TTATGTTT-TTATTATGTATT
* *
1235008 TTATGTATTTATTATTTATT
1 TTATGTTTTTATTATGTATT
1235028 TTATGTTTTT
1 TTATGTTTTT
1235038 GTCGCTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.74
Consensus pattern (20 bp):
TTATGTTTTTATTATGTATT
Found at i:1236942 original size:84 final size:84
Alignment explanation
Indices: 1236768--1236950 Score: 246
Period size: 84 Copynumber: 2.2 Consensus size: 84
1236758 TCCAAAAGAT
* * * *
1236768 GTGTTTTTTCATTATTGTTCAGAGAATCTCTGGATTATAATAGTGATCCACCTCATCCGAAATGA
1 GTGTTTTTCCATTATTATTCAAAGAATCTCTAGATTATAATAGTGATCCACCTCATCCGAAATGA
* *
1236833 AAGGTACTTTCAAGGGGAA
66 AAGGCACTTTCAAGGAGAA
*
1236852 GCGTTTTTCCATTATTATTCAAAGAATCTCTAGATTATAATAGTGATCCATCC-CATCCGAAATG
1 GTGTTTTTCCATTATTATTCAAAGAATCTCTAGATTATAATAGTGATCCA-CCTCATCCGAAATG
* *
1236916 AAAGGCGCATTTCGA-GAGAA
65 AAAGGCAC-TTTCAAGGAGAA
1236936 GTG-TTTTCCATTATT
1 GTGTTTTTCCATTATT
1236951 TAAGATAATC
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
83 12 0.14
84 68 0.78
85 7 0.08
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (84 bp):
GTGTTTTTCCATTATTATTCAAAGAATCTCTAGATTATAATAGTGATCCACCTCATCCGAAATGA
AAGGCACTTTCAAGGAGAA
Found at i:1236998 original size:81 final size:84
Alignment explanation
Indices: 1236900--1237291 Score: 435
Period size: 83 Copynumber: 4.8 Consensus size: 84
1236890 AATAGTGATC
* *** * *
1236900 CATCCCATCCGAAATGAAAGGCGCATTTCGAGAG-AAGTGTTTTCCATTA-T-TTAAGATAATCT
1 CATCCCATCCGAAATGAAAGGCGCATTTCGAGGGAAAACATTTTCCATTATTATTCAGAGAATCT
*
1236962 TTGTCATGTCAGAGTGTTT
66 TTGCCATGTCAGAGTGTTT
** * * *
1236981 CATCCCATCAAAAATGAAAGACGTATTTC-AGGGAAAGCATTTTCCATTATTATTCAGAGAATCT
1 CATCCCATCCGAAATGAAAGGCGCATTTCGAGGGAAAACATTTTCCATTATTATTCAGAGAATCT
*
1237045 TTGCCATGTCAGAGTGTTC
66 TTGCCATGTCAGAGTGTTT
* * * * *
1237064 CATCCCATCTGAAATGAAAGGTGCGTTT-TAGGGAAAATATTTTCCATTATTATTCAGAGAATCT
1 CATCCCATCCGAAATGAAAGGCGCATTTCGAGGGAAAACATTTTCCATTATTATTCAGAGAATCT
*
1237128 TTACCA--TCAGAGTG-TT
66 TTGCCATGTCAGAGTGTTT
* * * * *
1237144 CTATCACATCTGAAATGAAAGACGTATTTCG-GGGAAAACATTTTCCATTATTATTCAGAGAATA
1 C-ATCCCATCCGAAATGAAAGGCGCATTTCGAGGGAAAACATTTTCCATTATTATTCAGAGAATC
*
1237208 TTTGTCATGTCAGAGTGTTT
65 TTTGCCATGTCAGAGTGTTT
* * * * *
1237228 CATCCCATCCGAAATAAAAGGTGCATTTCG-GGGAAAACGTTTTTCATTATTATTTAGAGAATCT
1 CATCCCATCCGAAATGAAAGGCGCATTTCGAGGGAAAACATTTTCCATTATTATTCAGAGAATCT
1237292 CTGTGTAACA
Statistics
Matches: 261, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
80 5 0.02
81 104 0.40
82 1 0.00
83 148 0.57
84 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (84 bp):
CATCCCATCCGAAATGAAAGGCGCATTTCGAGGGAAAACATTTTCCATTATTATTCAGAGAATCT
TTGCCATGTCAGAGTGTTT
Found at i:1237140 original size:164 final size:164
Alignment explanation
Indices: 1236893--1237291 Score: 482
Period size: 164 Copynumber: 2.4 Consensus size: 164
1236883 AGATTATAAT
* * * * *** *
1236893 AGTGATCCATCCCATCCGAAATGAAAGGCGCATTTC-GAGAGAAGTGTTTTCCATTA-T-TTAAG
1 AGTGTTCCATCCCATCCGAAATAAAAGGTGCATTTCAGGGA-AAACATTTTCCATTATTATTCAG
* ** * *
1236955 ATAATCTTTGTCATGTCAGAGTGTT-TCATCCCATCAAAAATGAAAGACGTATTTCAGGGAAAGC
65 AGAATCTTTACCA--TCAGAGTGTTCT-ATCACATCAAAAATGAAAGACGTATTTCAGGGAAAAC
*
1237019 ATTTTCCATTATTATTCAGAGAATCTTTGCCATGTCAG
127 ATTTTCCATTATTATTCAGAGAATATTTGCCATGTCAG
* * * * *
1237057 AGTGTTCCATCCCATCTGAAATGAAAGGTGCGTTTTAGGGAAAATATTTTCCATTATTATTCAGA
1 AGTGTTCCATCCCATCCGAAATAAAAGGTGCATTTCAGGGAAAACATTTTCCATTATTATTCAGA
** *
1237122 GAATCTTTACCATCAGAGTGTTCTATCACATCTGAAATGAAAGACGTATTTCGGGGAAAACATTT
66 GAATCTTTACCATCAGAGTGTTCTATCACATCAAAAATGAAAGACGTATTTCAGGGAAAACATTT
*
1237187 TCCATTATTATTCAGAGAATATTTGTCATGTCAG
131 TCCATTATTATTCAGAGAATATTTGCCATGTCAG
* * * * *
1237221 AGTGTTTCATCCCATCCGAAATAAAAGGTGCATTTCGGGGAAAACGTTTTTCATTATTATTTAGA
1 AGTGTTCCATCCCATCCGAAATAAAAGGTGCATTTCAGGGAAAACATTTTCCATTATTATTCAGA
1237286 GAATCT
66 GAATCT
1237292 CTGTGTAACA
Statistics
Matches: 202, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
164 183 0.91
165 5 0.02
166 14 0.07
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (164 bp):
AGTGTTCCATCCCATCCGAAATAAAAGGTGCATTTCAGGGAAAACATTTTCCATTATTATTCAGA
GAATCTTTACCATCAGAGTGTTCTATCACATCAAAAATGAAAGACGTATTTCAGGGAAAACATTT
TCCATTATTATTCAGAGAATATTTGCCATGTCAG
Found at i:1238106 original size:23 final size:23
Alignment explanation
Indices: 1238080--1238148 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1238070 CACCACAGCT
* *
1238080 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1238103 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1238126 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1238149 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1243342 original size:23 final size:23
Alignment explanation
Indices: 1243316--1243384 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1243306 CACCACAGCT
*
1243316 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1243339 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
1243362 CATAGAAATGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1243385 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1245065 original size:64 final size:63
Alignment explanation
Indices: 1244978--1245137 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 63
1244968 TTTCTAACAT
* * * *
1244978 GTGCATCGATACACTACCCATGCATCGATACATAAATCACCTTCGATGTTTTAATTTTAAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACATAAATCACATTCGATGTTTCAATTTTAAAGGG
* * ** * * *
1245042 GTGCATCGATGCACTCCTTATGCATCGATGCATTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACATAAATCACATTCGATGTTTCAATTTTAAAGGG
*
1245106 GTGCATCGATGCACTTCCTATACATCGATACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACA
1245138 CACTGAACAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.02
64 76 0.94
65 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACATAAATCACATTCGATGTTTCAATTTTAAAGGG
Found at i:1248140 original size:21 final size:20
Alignment explanation
Indices: 1248088--1248141 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1248078 AATTCTGACT
1248088 ATCGCATTGCGATTTTCCAA
1 ATCGCATTGCGATTTTCCAA
* *
1248108 ATTGGCGTTGCGATTTTCCGAA
1 A-TCGCATTGCGATTTTCC-AA
*
1248130 ATCGCAATGCGA
1 ATCGCATTGCGA
1248142 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.85
22 3 0.11
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATTTTCCAA
Found at i:1248153 original size:20 final size:20
Alignment explanation
Indices: 1248128--1248201 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
1248118 CGATTTTCCG
1248128 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGAATATGT
*
1248148 AAATCGCAATGTGAATATGT
1 AAATCGCAATGCGAATATGT
*
1248168 AAATCGCAATGCGATTATG-
1 AAATCGCAATGCGAATATGT
*
1248187 ATTATCGCAATGCGA
1 A-AATCGCAATGCGA
1248202 TTCTGACTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (20 bp):
AAATCGCAATGCGAATATGT
Found at i:1248212 original size:20 final size:20
Alignment explanation
Indices: 1248170--1248229 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
1248160 GAATATGTAA
* *
1248170 ATCGCAATGCGATTATGATT
1 ATCGCAATGCGATTCTGACT
1248190 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATTCTGACT
*
1248210 ATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATTCTGACT
1248230 GTTACAACAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
ATCGCAATGCGATTCTGACT
Found at i:1249090 original size:24 final size:24
Alignment explanation
Indices: 1249058--1249111 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1249048 GTATTCGAAA
1249058 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1249082 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1249106 TTTGAT
1 TTTGAT
1249112 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1249330 original size:14 final size:14
Alignment explanation
Indices: 1249301--1249337 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1249291 AGAAAAAGAA
1249301 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1249316 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1249330 GAAGAAAA
1 GAAGAAAA
1249338 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1251345 original size:18 final size:18
Alignment explanation
Indices: 1251313--1251347 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1251303 AGAAAAAGGC
**
1251313 AATCAAAATTGCAATCAA
1 AATCAAAATCCCAATCAA
1251331 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1251348 CAACCGGCTT
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:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1251676 original size:20 final size:20
Alignment explanation
Indices: 1251647--1251686 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1251637 TACACATTCT
1251647 TTTGAATATCGCAACGCAAA
1 TTTGAATATCGCAACGCAAA
* *
1251667 TTTGATTATCGCAACTCAAA
1 TTTGAATATCGCAACGCAAA
1251687 AATCGCAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (20 bp):
TTTGAATATCGCAACGCAAA
Found at i:1251795 original size:20 final size:20
Alignment explanation
Indices: 1251732--1251810 Score: 104
Period size: 20 Copynumber: 4.0 Consensus size: 20
1251722 CAAAAATTTC
*
1251732 AACGCGAATTTGTCTATCGT
1 AACGCGAATTTGACTATCGT
* *
1251752 AACACGAATTTTACTATCGT
1 AACGCGAATTTGACTATCGT
*
1251772 AACGCGAATTTGATTATCGT
1 AACGCGAATTTGACTATCGT
* *
1251792 AACGGGTATTTGACTATCG
1 AACGCGAATTTGACTATCG
1251811 CAATGAGAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (20 bp):
AACGCGAATTTGACTATCGT
Found at i:1251883 original size:20 final size:21
Alignment explanation
Indices: 1251854--1251911 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
1251844 GCAACGCGAA
1251854 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
* *
1251874 TTG-GCTTTCGCATTGTGATT
1 TTGAGCTTTCGCGTTGCGATT
*
1251894 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
1251912 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.45
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:1252070 original size:14 final size:14
Alignment explanation
Indices: 1252033--1252071 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1252023 TCAATATTAA
*
1252033 ACAAATCAACTTTT
1 ACAAATCAATTTTT
1252047 ACAAATCAATTTTT
1 ACAAATCAATTTTT
*
1252061 ATAAATCAATT
1 ACAAATCAATT
1252072 AAACAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:1254068 original size:18 final size:19
Alignment explanation
Indices: 1254045--1254090 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1254035 GAAACTTAAA
1254045 ATCGCAACACGAA-TGACT
1 ATCGCAACACGAATTGACT
**
1254063 ATCGCAATGCGAATTTGACT
1 ATCGCAACACGAA-TTGACT
1254083 ATCGCAAC
1 ATCGCAAC
1254091 GAGAGAATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 11 0.48
20 12 0.52
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (19 bp):
ATCGCAACACGAATTGACT
Found at i:1254179 original size:20 final size:20
Alignment explanation
Indices: 1254134--1254179 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1254124 GTGATTCTTT
*
1254134 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
* **
1254154 CTTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
1254174 CGTTGC
1 CGTTGC
1254180 AAAAGTAAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1254338 original size:18 final size:18
Alignment explanation
Indices: 1254315--1254364 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
1254305 ATTTACTAAG
1254315 TAATCTAAGTGAAATGAT
1 TAATCTAAGTGAAATGAT
*
1254333 TAATCTAAGTGAAATGGT
1 TAATCTAAGTGAAATGAT
1254351 TAATCTAAGTGAAA
1 TAATCTAAGTGAAA
1254365 ATACGAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (18 bp):
TAATCTAAGTGAAATGAT
Found at i:1256164 original size:19 final size:19
Alignment explanation
Indices: 1256137--1256180 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1256127 GAATTTGACT
*
1256137 ATCGTAACGCGAAA-TAAAA
1 ATCGCAACGCGAAACT-AAA
1256156 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
1256175 ATCGCA
1 ATCGCA
1256181 TTGCAATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:1256817 original size:20 final size:20
Alignment explanation
Indices: 1256794--1256867 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
1256784 ATCGCATTGT
*
1256794 GATAGTCAGTATCGTGTTGC
1 GATAGTCAGAATCGTGTTGC
* *
1256814 GATAGTCAGCATCGCGTTGC
1 GATAGTCAGAATCGTGTTGC
1256834 GATAGTCAGAATC-TCGTTGC
1 GATAGTCAGAATCGT-GTTGC
1256854 GATAGTCAGAATCG
1 GATAGTCAGAATCG
1256868 CATTGTGATT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
GATAGTCAGAATCGTGTTGC
Found at i:1256839 original size:40 final size:40
Alignment explanation
Indices: 1256783--1256872 Score: 128
Period size: 40 Copynumber: 2.2 Consensus size: 40
1256773 GCGCTTTGAA
* *
1256783 AATCGCATTGTGATAGTCAGTATCGT-GTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATC-TCGTTGCGATAGTCAG
* *
1256823 CATCGCGTTGCGATAGTCAGAATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATCTCGTTGCGATAGTCAG
1256863 AATCGCATTG
1 AATCGCATTG
1256873 TGATTTACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.02
40 42 0.98
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAGAATCTCGTTGCGATAGTCAG
Found at i:1259398 original size:64 final size:64
Alignment explanation
Indices: 1259243--1259401 Score: 171
Period size: 63 Copynumber: 2.5 Consensus size: 64
1259233 TCTTTAACAT
* * * * *
1259243 GTGCATCGATACACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTAATTTTAAGGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCAATTTTAAGGGG
* * ** * *
1259307 GTGCAT-GATGCAC-TCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAA-TG
1 GTGCATCGATGCACTTCC-TATGCATCGATACACAAATCACATTCGATGTTT-CAATTTTAAGGG
1259369 G
64 G
*
1259370 GTGCATCGATGCACTTCCTGTGCATCGATACA
1 GTGCATCGATGCACTTCCTATGCATCGATACA
1259402 GACTGAACAA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
62 2 0.03
63 41 0.53
64 32 0.41
65 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCAATTTTAAGGGG
Found at i:1260080 original size:22 final size:23
Alignment explanation
Indices: 1260050--1260093 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1260040 TACTTCATTT
*
1260050 AATAATTACCAATAA-TCCCTAA
1 AATAATTACAAATAAGTCCCTAA
*
1260072 AATATTTACAAATAAGTCCCTA
1 AATAATTACAAATAAGTCCCTA
1260094 CATTCTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (23 bp):
AATAATTACAAATAAGTCCCTAA
Done.