Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 3 of 127
Found at i:266232 original size:22 final size:23
Alignment explanation
Indices: 266189--266232 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
266179 TTTTTTTATT
* *
266189 TTTATATTTATGTATGATAAATG
1 TTTAAATTTATGTAGGATAAATG
266212 TTTAAATTTAT-TAGGATAAAT
1 TTTAAATTTATGTAGGATAAAT
266233 ATCTAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (23 bp):
TTTAAATTTATGTAGGATAAATG
Found at i:266634 original size:17 final size:18
Alignment explanation
Indices: 266598--266632 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
266588 CCTAAGTTTT
266598 TTTAAAAACCCCTAAAAA
1 TTTAAAAACCCCTAAAAA
*
266616 TTTAAAATCCCCTAAAA
1 TTTAAAAACCCCTAAAA
266633 TTCAAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (18 bp):
TTTAAAAACCCCTAAAAA
Found at i:266639 original size:17 final size:16
Alignment explanation
Indices: 266602--266655 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
266592 AGTTTTTTTA
*
266602 AAAACCCCTAAAAATTT
1 AAAACCCCT-AAAATTC
266619 AAAATCCCCTAAAATTC
1 AAAA-CCCCTAAAATTC
*
266636 AAAACCTCTTAAAATTC
1 AAAACC-CCTAAAATTC
266653 AAA
1 AAA
266656 GTTTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 2 0.06
17 26 0.79
18 5 0.15
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAACCCCTAAAATTC
Found at i:278007 original size:16 final size:16
Alignment explanation
Indices: 277988--278062 Score: 57
Period size: 17 Copynumber: 4.7 Consensus size: 16
277978 TATTTTGCTT
277988 AAAA-AAAAAGAAGGAA
1 AAAATAAAAAGAA-GAA
*
278004 AAAATGAAAAGAAGAA
1 AAAATAAAAAGAAGAA
*
278020 AAAATATACAA-AA-AA
1 AAAATA-AAAAGAAGAA
* *
278035 AAGATAAAAAAAATGAA
1 AAAATAAAAAGAA-GAA
*
278052 AAAATGAAAAG
1 AAAATAAAAAG
278063 GAAGTGACTC
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
14 3 0.07
15 9 0.20
16 14 0.30
17 20 0.43
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.08
Consensus pattern (16 bp):
AAAATAAAAAGAAGAA
Found at i:279213 original size:73 final size:73
Alignment explanation
Indices: 279094--279410 Score: 318
Period size: 73 Copynumber: 4.3 Consensus size: 73
279084 TCTTATATAT
* * * * * * *
279094 TTTTCTGACTTGCGGTTTAGTCGCAATCATCTTT-ATCTTTTTACTCGCGGTTTAATCTTGATCA
1 TTTTCTGACTTACGGTTCAGTCCCAGTCATCTTTAATC-TTTGACTCGCGATTTAATCTCGATCA
279158 TTTCATTAA
65 TTTCATTAA
* * * * *
279167 TTTTTTGACTTACAGTTCAGTCCCAGTAATCTTTAATTTTTGACTCGCGATTTAATCTCGGTCAT
1 TTTTCTGACTTACGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGCGATTTAATCTCGATCAT
*
279232 TTCATTTCA
66 TTCA-TTAA
* * * * * *
279241 TTCTCTGACTTACGATTTAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAAT-TCCGGTCA
1 TTTTCTGACTTACGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGCGATTTAATCT-CGATCA
*
279305 TTTTATTAA
65 TTTCATTAA
* ** * *
279314 -TTGCTTGACTTGTGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGCGATTTAATC-CCATCA
1 TTTTC-TGACTTACGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGCGATTTAATCTCGATCA
*
279377 TTTTATTAA
65 TTTCATTAA
**
279386 TTTTCTGACTTGTGGTTCAGTCCCA
1 TTTTCTGACTTACGGTTCAGTCCCA
279411 ATCAATTATC
Statistics
Matches: 202, Mismatches: 36, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
72 35 0.17
73 105 0.52
74 62 0.31
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (73 bp):
TTTTCTGACTTACGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGCGATTTAATCTCGATCAT
TTCATTAA
Found at i:279305 original size:35 final size:35
Alignment explanation
Indices: 279256--279381 Score: 105
Period size: 35 Copynumber: 3.6 Consensus size: 35
279246 TGACTTACGA
*
279256 TTTAGTCCCAGTCATCTTTAATCTTTGACTCGTGG
1 TTTAATCCCAGTCATCTTTAATCTTTGACTCGTGG
* * * *
279291 TTTAATTCCGGTCATTTTATTAAT-TGCTTGACTTGTGG
1 TTTAATCCCAGTCA-TCT-TTAATCT--TTGACTCGTGG
* * * * *
279329 TTCAGTCCCAATCATCTTTAATCTTTGACTCGCGA
1 TTTAATCCCAGTCATCTTTAATCTTTGACTCGTGG
279364 TTTAATCCCA-TCAT-TTTA
1 TTTAATCCCAGTCATCTTTA
279382 TTAATTTTCT
Statistics
Matches: 70, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
33 4 0.06
34 4 0.06
35 27 0.39
36 8 0.11
37 8 0.11
38 19 0.27
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.44
Consensus pattern (35 bp):
TTTAATCCCAGTCATCTTTAATCTTTGACTCGTGG
Found at i:279364 original size:147 final size:147
Alignment explanation
Indices: 279097--279370 Score: 363
Period size: 147 Copynumber: 1.9 Consensus size: 147
279087 TATATATTTT
* * * * *
279097 TCTGACTTGCGGTTTAGTCGCAATCATCTTTATCTTTTTACTCGCGGTTTAATCTTGATCATTTC
1 TCTGACTTACGATTTAGTCCCAATCATCTTTATCTTTTGACTCGCGGTTTAATCTCGATCATTTC
** * *
279162 ATTAATTTTTTGACTTACAGTTCAGTCCCAGTAATCTTTAATTTTTGACTCGCGATTTAATCTCG
66 ATTAATTGCTTGACTTACAGTTCAGTCCCAATAATCTTTAATCTTTGACTCGCGATTTAATCTCG
279227 GTCATTTCATTTCATTC
131 GTCATTTCATTTCATTC
* * *
279244 TCTGACTTACGATTTAGTCCCAGTCATCTTTAATC-TTTGACTCGTGGTTTAAT-TCCGGTCATT
1 TCTGACTTACGATTTAGTCCCAATCATCTTT-ATCTTTTGACTCGCGGTTTAATCT-CGATCATT
* *** *
279307 TTATTAATTGCTTGACTTGTGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGCGATTTAATC
64 TCATTAATTGCTTGACTTACAGTTCAGTCCCAATAATCTTTAATCTTTGACTCGCGATTTAATC
279371 CCATCATTTT
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
146 1 0.01
147 104 0.96
148 3 0.03
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (147 bp):
TCTGACTTACGATTTAGTCCCAATCATCTTTATCTTTTGACTCGCGGTTTAATCTCGATCATTTC
ATTAATTGCTTGACTTACAGTTCAGTCCCAATAATCTTTAATCTTTGACTCGCGATTTAATCTCG
GTCATTTCATTTCATTC
Found at i:279466 original size:68 final size:71
Alignment explanation
Indices: 279092--279466 Score: 249
Period size: 73 Copynumber: 5.2 Consensus size: 71
279082 AGTCTTATAT
* * * * * * * *
279092 ATTTTTCTGACTTGCGGTTTAGTCGCAATCATC-TTTATCTTTTTACTCGCGGTTTAATCTTGAT
1 ATTTTT-TGACTTGTGGTTCAGTCCCAATCA-CATTAATC-CTTGACTCGCGATTTAATC-CGAT
*
279156 CATTTCATTA
62 CATTTTATTA
*** * * * ** *
279166 ATTTTTTGACTTACAGTTCAGTCCCAGTAATCTTTAATTTTTGACTCGCGATTTAATCTCGGTCA
1 ATTTTTTGACTTGTGGTTCAGTCCCAATCA-CATTAATCCTTGACTCGCGATTTAATC-CGATCA
* *
279231 TTTCATTTC
64 TTTTA-TTA
* * ** * * * * * * * *
279240 ATTCTCTGACTTACGATTTAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATTCCGGTCA
1 ATTTTTTGACTTGTGGTTCAGTCCCAATCA-CATTAATCCTTGACTCGCGATTTAA-TCCGATCA
279305 TTTTATTA
64 TTTTATTA
** * * *
279313 ATTGCTTGACTTGTGGTTCAGTCCCAATCATCTTTAATCTTTGACTCGCGATTTAATCCCATCAT
1 ATTTTTTGACTTGTGGTTCAGTCCCAATCA-CATTAATCCTTGACTCGCGATTTAATCCGATCAT
279378 TTTATTA
65 TTTATTA
* *
279385 ATTTTCTGACTTGTGGTTCAGTCCCAATCA-ATT-ATCCTT-ACT-GATGATTTAATCCGATCA-
1 ATTTTTTGACTTGTGGTTCAGTCCCAATCACATTAATCCTTGACTCG-CGATTTAATCCGATCAT
279445 TTTATTA
65 TTTATTA
279452 ATTTTTTGGACTTGT
1 ATTTTTT-GACTTGT
279467 AGTCCCAGTC
Statistics
Matches: 252, Mismatches: 44, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
67 14 0.06
68 24 0.10
69 5 0.02
70 2 0.01
72 41 0.16
73 95 0.38
74 69 0.27
75 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (71 bp):
ATTTTTTGACTTGTGGTTCAGTCCCAATCACATTAATCCTTGACTCGCGATTTAATCCGATCATT
TTATTA
Found at i:279904 original size:105 final size:104
Alignment explanation
Indices: 279655--280291 Score: 579
Period size: 105 Copynumber: 6.1 Consensus size: 104
279645 TCATAAATTT
* *
279655 TTTTTAATCTCTGATT--CAGGTTCAATCTCGATCTTTTTAATTC-AAGTCACAGTTTTAATCTC
1 TTTTTATTCTCTGATTCGCA-GTTCAATC-CGATCTCTTTAATTCAAAGTCACAG-TTTAATCTC
* * * *
279717 AATTATTGTTGTTATCTTTCTGATTCCACGATTTAATCTTTGATC
63 GATTATTGTTGTTATC-TTCTGATT-CGCGGTTTAATC-TCGATC
* ***
279762 TTTTTATTCTCTGTTTCATGGTTCAATCCCGATCTCTTTAATTCAAAGTCACAGTTTAATCTCGA
1 TTTTTATTCTCTGATTCGCAGTTCAAT-CCGATCTCTTTAATTCAAAGTCACAGTTTAATCTCGA
*
279827 TTATTGTTGTTATCTTCTGATTCACGGTTTAATCTCGATC
65 TTATTGTTGTTATCTTCTGATTCGCGGTTTAATCTCGATC
* *
279867 TTTTTATTCTCTAATTCGTAGTTCAATTCCGATCTCTTTAATTCAAAGTCACAGTTTAATCTCGA
1 TTTTTATTCTCTGATTCGCAGTTCAA-TCCGATCTCTTTAATTCAAAGTCACAGTTTAATCTCGA
* * *
279932 TTATTGTTGTTATCTTTTGATTCGCGATTTAATCCCGATC
65 TTATTGTTGTTATCTTCTGATTCGCGGTTTAATCTCGATC
* * * * ***
279972 TTTTTATTCTCTGATTCGCGGTTCAATCCTAATCTTTTTAATTCAAAAATCGTTGTTTAATCTCG
1 TTTTTATTCTCTGATTCGCAGTTCAATCC-GATCTCTTTAATTC-AAAGTCACAGTTTAATCTCG
* * *
280037 ---ATTGTTGTTATCTTCTGACTCGTGGTTTAATCTTGATC
64 ATTATTGTTGTTATCTTCTGATTCGCGGTTTAATCTCGATC
* * * **
280075 ATTTCATTAATTCTCTGACTT-ACAATTCAATCTCGATCTCTTTAATTCAAAATCGTAGTTTAAT
1 -TTT--TT-ATTCTCTGA-TTCGCAGTTCAATC-CGATCTCTTTAATTCAAAGTCACAGTTTAAT
* * * *
280139 CTCGATTA---TTGTTATCTTTTGACTCGTGGTTTAATC-CATATC
60 CTCGATTATTGTTGTTATCTTCTGATTCGCGGTTTAATCTC-GATC
* * * *
280181 TCTTTA-TCTTTTCGATTCGCAGTTCAATCCCGATCCCTTTAATTCAAAGTCGCAGTTTAATCTC
1 TTTTTATTC-TCT-GATTCGCAGTTCAAT-CCGATCTCTTTAATTCAAAGTCACAGTTTAATCTC
* * *
280245 -A--ATTTTTGTTATCTTCTGACTT-GTGGTTTAACCTC-AGTC
63 GATTATTGTTGTTATCTTCTGA-TTCGCGGTTTAATCTCGA-TC
280284 TTTTTATT
1 TTTTTATT
280292 TTATTACTTG
Statistics
Matches: 451, Mismatches: 51, Indels: 59
0.80 0.09 0.11
Matches are distributed among these distances:
100 1 0.00
101 2 0.00
102 7 0.02
103 105 0.23
104 10 0.02
105 137 0.30
106 79 0.18
107 51 0.11
108 48 0.11
109 11 0.02
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.47
Consensus pattern (104 bp):
TTTTTATTCTCTGATTCGCAGTTCAATCCGATCTCTTTAATTCAAAGTCACAGTTTAATCTCGAT
TATTGTTGTTATCTTCTGATTCGCGGTTTAATCTCGATC
Found at i:281823 original size:16 final size:16
Alignment explanation
Indices: 281773--281824 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
281763 CAGGTAAATT
* *
281773 TTTTTTTTTTTTCTAAA
1 TTTTTTTATTTT-TATA
*
281790 TTTTTTTA-TATTATTA
1 TTTTTTTATTTTTA-TA
281806 TTTTTTTATTTTTATA
1 TTTTTTTATTTTTATA
281822 TTT
1 TTT
281825 ATGTATGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 2 0.07
16 16 0.55
17 11 0.38
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTATTTTTATA
Found at i:281858 original size:22 final size:24
Alignment explanation
Indices: 281815--281861 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
281805 ATTTTTTTAT
*
281815 TTTTATATTTATGTATGATAAATA
1 TTTTATATTTATGTAGGATAAATA
281839 TTTTA-ATTTAT-TAGGATAAATA
1 TTTTATATTTATGTAGGATAAATA
281861 T
1 T
281862 CTAATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 6 0.27
24 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTTATATTTATGTAGGATAAATA
Found at i:281883 original size:24 final size:22
Alignment explanation
Indices: 281821--281884 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
281811 TTATTTTTAT
*
281821 ATTTATGTATGATAAATATTTTA
1 ATTTAT-TATGATAAATATTCTA
*
281844 ATTTATTAGGATAAATA-TCTA
1 ATTTATTATGATAAATATTCTA
281865 ATTATTATTAATGATAAATA
1 A-T-TTATT-ATGATAAATA
281885 AATGAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 4 0.11
22 11 0.31
23 11 0.31
24 9 0.26
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (22 bp):
ATTTATTATGATAAATATTCTA
Found at i:282263 original size:17 final size:16
Alignment explanation
Indices: 282233--282286 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
282223 AGTTTTTTTA
282233 AAAACCCCTAAAAATTC
1 AAAACCCCT-AAAATTC
282250 AAAATCCCCTAAAATTC
1 AAAA-CCCCTAAAATTC
*
282267 AAAACCTCTTAAAATTC
1 AAAACC-CCTAAAATTC
282284 AAA
1 AAA
282287 GTCTTAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 2 0.06
17 27 0.79
18 5 0.15
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAACCCCTAAAATTC
Found at i:286166 original size:23 final size:25
Alignment explanation
Indices: 286113--286160 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
286103 ATTACACTCT
*
286113 AGAAATGTTAGAGAAGGCTAGAAGAG
1 AGAAATGTTAAAGAAGGC-AGAAGAG
286139 AGAAA-GTTAAAGAAGG-AGAAGA
1 AGAAATGTTAAAGAAGGCAGAAGA
286161 ACGAAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
25 10 0.48
26 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.33, T:0.12
Consensus pattern (25 bp):
AGAAATGTTAAAGAAGGCAGAAGAG
Found at i:292119 original size:45 final size:44
Alignment explanation
Indices: 292065--292385 Score: 229
Period size: 43 Copynumber: 7.5 Consensus size: 44
292055 TTGTTAAGTA
* *
292065 TCTGATTAGAGGAGCTTTGTTTATATTTTTCAAAGTCGTTGAGCC
1 TCTGATTAGAGGAGCTTTGATT-TATTTTTCAAAGTCATTGAGCC
* * * * * **
292110 TCTGTTTAGAAGAGC---AATTTA-TTTTAAAAGTCGTTGAATC
1 TCTGATTAGAGGAGCTTTGATTTATTTTTCAAAGTCATTGAGCC
* * ** * * *
292150 TCTAATTAGAGGAGCCTTTTA-TT-TTTTAAAAAGTCGTTAAACC
1 TCTGATTAGAGGAG-CTTTGATTTATTTTTCAAAGTCATTGAGCC
* * * *
292193 TCTGATTAGTGGAGCTTTG-TCTATCTTTCGAAAGTTATTGAGCC
1 TCTGATTAGAGGAGCTTTGATTTATTTTTC-AAAGTCATTGAGCC
* * *
292237 TCTGATTAGATGAGC---CATTTA-TTTTCAAAGTCTTTGAGCC
1 TCTGATTAGAGGAGCTTTGATTTATTTTTCAAAGTCATTGAGCC
* **
292277 TCT-ATTTAGAGGAGCTTT-ATTTATCTTTCAAAGTCATAAAGCC
1 TCTGA-TTAGAGGAGCTTTGATTTATTTTTCAAAGTCATTGAGCC
* **
292320 TCTGATTAGAGAAGCTTTG-TTTATGTCTTTCAAAGTCATAAAGCC
1 TCTGATTAGAGGAGCTTTGATTTAT-T-TTTCAAAGTCATTGAGCC
292365 TCTGATTAGAGGAGCTTTGAT
1 TCTGATTAGAGGAGCTTTGAT
292386 AAGAATTTTA
Statistics
Matches: 217, Mismatches: 40, Indels: 37
0.74 0.14 0.13
Matches are distributed among these distances:
39 1 0.00
40 51 0.24
41 7 0.03
42 15 0.07
43 68 0.31
44 25 0.12
45 49 0.23
46 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (44 bp):
TCTGATTAGAGGAGCTTTGATTTATTTTTCAAAGTCATTGAGCC
Found at i:292142 original size:40 final size:40
Alignment explanation
Indices: 292091--292330 Score: 158
Period size: 40 Copynumber: 5.8 Consensus size: 40
292081 TTGTTTATAT
* * * *
292091 TTTTCAAAGTCGTTGAGCCTCTGTTTAGAAGAGCAATTTA
1 TTTTAAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTA
** * *
292131 TTTTAAAAGTCGTTGAATCTCTAATTAGAGGAGCCTTTTA
1 TTTTAAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTA
* * * **
292171 TTTTTTAAAAAGTCGTTAAACCTCTGATTAGTGGAGCTTTGTCTA
1 --TTTT-AAAAGTCGTTGAGCCTCTGATTAGAGGAGCCAT-T-TA
* ** *
292216 TCTTTCGAAAGTTATTGAGCCTCTGATTAGATGAGCCATTTA
1 T-TTT-AAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTA
* * *
292258 TTTTCAAAGTCTTTGAGCCTCT-ATTTAGAGGAGCTTTATTTA
1 TTTTAAAAGTCGTTGAGCCTCTGA-TTAGAGGAGC--CATTTA
* * **
292300 TCTTTCAAAGTCATAAAGCCTCTGATTAGAG
1 T-TTTAAAAGTCGTTGAGCCTCTGATTAGAG
292331 AAGCTTTGTT
Statistics
Matches: 158, Mismatches: 31, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
39 1 0.01
40 56 0.35
41 3 0.02
42 13 0.08
43 54 0.34
44 29 0.18
45 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (40 bp):
TTTTAAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTA
Found at i:292201 original size:43 final size:42
Alignment explanation
Indices: 292065--292298 Score: 142
Period size: 40 Copynumber: 5.6 Consensus size: 42
292055 TTGTTAAGTA
* * *
292065 TCTGATTAGAGGAGCTTTGTTTATATTTTTCAAAGTCGTTGAGCC
1 TCTGATTAGAGGAGC-AT-TTTAT-TTTTTAAAAGTCGTTGAACC
* * * *
292110 TCTGTTTAGAAGAGCAATTTA--TTTTAAAAGTCGTTGAATC
1 TCTGATTAGAGGAGCATTTTATTTTTTAAAAGTCGTTGAACC
* * *
292150 TCTAATTAGAGGAGCCTTTTATTTTTTAAAAAGTCGTTAAACC
1 TCTGATTAGAGGAGCATTTTATTTTTT-AAAAGTCGTTGAACC
* * * ** ** *
292193 TCTGATTAGTGGAGCTTTGTCTATCTTTCGAAAGTTATTGAGCC
1 TCTGATTAGAGGAGCATT-T-TATTTTTTAAAAGTCGTTGAACC
* * * *
292237 TCTGATTAGATGAGCCA-TTTA--TTTTCAAAGTCTTTGAGCC
1 TCTGATTAGAGGAG-CATTTTATTTTTTAAAAGTCGTTGAACC
292277 TCT-ATTTAGAGGAGC--TTTATTT
1 TCTGA-TTAGAGGAGCATTTTATTT
292299 ATCTTTCAAA
Statistics
Matches: 148, Mismatches: 32, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
38 4 0.03
39 2 0.01
40 59 0.40
42 6 0.04
43 33 0.22
44 24 0.16
45 20 0.14
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (42 bp):
TCTGATTAGAGGAGCATTTTATTTTTTAAAAGTCGTTGAACC
Found at i:292280 original size:127 final size:126
Alignment explanation
Indices: 292065--292379 Score: 348
Period size: 127 Copynumber: 2.5 Consensus size: 126
292055 TTGTTAAGTA
* * *
292065 TCTGATTAGAGGAGCTTTGTTTATATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAAGAGCAATTT
1 TCTGATTAGAGGAGCTTTG--TATATCTTTCAAAGTCATTGAGCCTCTGATTAGAAGAGCAATTT
* *
292130 ATTTTAAAAGTCGTTGAATCTCTAATTAGAGGAGCCTTTTATTT-T-TTAAAAAGTCGTTAAA-C
64 ATTTTAAAAGTCGTTGAACCTCTAATTAGAGGAG-C-TTTATTTATCTTAAAAAGTC-ATAAAGC
292192 C
126 C
* * * * *
292193 TCTGATTAGTGGAGCTTTGTCTATCTTTCGAAAGTTATTGAGCCTCTGATTAGATGAGCCATTTA
1 TCTGATTAGAGGAGCTTTGTATATCTTTC-AAAGTCATTGAGCCTCTGATTAGAAGAGCAATTTA
* * * * **
292258 TTTTCAAAGTCTTTGAGCCTCTATTTAGAGGAGCTTTATTTATCTTTCAAAGTCATAAAGCC
65 TTTTAAAAGTCGTTGAACCTCTAATTAGAGGAGCTTTATTTATCTTAAAAAGTCATAAAGCC
* * ** *
292320 TCTGATTAGAGAAGCTTTGTTTATGTCTTTCAAAGTCATAAAGCCTCTGATTAGAGGAGC
1 TCTGATTAGAGGAGCTTTG--TATATCTTTCAAAGTCATTGAGCCTCTGATTAGAAGAGC
292380 TTTGATAAGA
Statistics
Matches: 157, Mismatches: 24, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
125 7 0.04
126 14 0.09
127 85 0.54
128 43 0.27
129 8 0.05
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (126 bp):
TCTGATTAGAGGAGCTTTGTATATCTTTCAAAGTCATTGAGCCTCTGATTAGAAGAGCAATTTAT
TTTAAAAGTCGTTGAACCTCTAATTAGAGGAGCTTTATTTATCTTAAAAAGTCATAAAGCC
Found at i:292374 original size:88 final size:84
Alignment explanation
Indices: 292187--292382 Score: 202
Period size: 88 Copynumber: 2.3 Consensus size: 84
292177 AAAAAGTCGT
* * * **
292187 TAAA-CCTCTGATTAGTGGAGCTTTGTCTATCTTTCGAAAGTTATTGAGCCTCTGATTAGATGAG
1 TAAAGCCTCTGATTAGAGGAGCTTTATCTATCTTTCGAAAGTCATAAAGCCTCTGATTAGATGAG
*
292251 CCATTTATTTTCAAAGTCT
66 CCATTTATTTTCAAAGTCA
** *
292270 TTGAGCCTCT-ATTTAGAGGAGCTTTATTTATCTTTC-AAAGTCATAAAGCCTCTGATTAGA-GA
1 TAAAGCCTCTGA-TTAGAGGAGCTTTATCTATCTTTCGAAAGTCATAAAGCCTCTGATTAGATG-
**
292332 AGCTTTGTTTATGTCTTTCAAAGTCA
64 AGC--CATTTA--T-TTTCAAAGTCA
292358 TAAAGCCTCTGATTAGAGGAGCTTT
1 TAAAGCCTCTGATTAGAGGAGCTTT
292383 GATAAGAATT
Statistics
Matches: 91, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
82 1 0.01
83 27 0.30
84 26 0.29
85 4 0.04
87 1 0.01
88 31 0.34
89 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (84 bp):
TAAAGCCTCTGATTAGAGGAGCTTTATCTATCTTTCGAAAGTCATAAAGCCTCTGATTAGATGAG
CCATTTATTTTCAAAGTCA
Found at i:292601 original size:4 final size:4
Alignment explanation
Indices: 292574--292770 Score: 84
Period size: 4 Copynumber: 47.8 Consensus size: 4
292564 TTCAGTTTGT
* * * *
292574 TTTA TTTTA TTTTA TTTT TTTA TTTA TTCTG TATTC TGTA TTTTA TTTA
1 TTTA -TTTA -TTTA TTTA TTTA TTTA TT-TA T-TTA TTTA -TTTA TTTA
* * * *
292623 TTTA -TTA TTTA TTTA TTTA TCTA -TTA TTACTA TTTA TTAA TATA TGTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA TTTA
* * * *
292671 TTT- TTTA -TTA -TTA CTTA TCTG TTTA TATA TTTA TTATA TATTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA T-TTA TTTA
* ** *
292717 TTTA TCTA TTTA CATA TTATCA TTTA TCTA TTAATA TTTA TTTA TTT-
1 TTTA TTTA TTTA TTTA TT-T-A TTTA TTTA TT--TA TTTA TTTA TTTA
292764 TTTA TTT
1 TTTA TTT
292771 TATTATTTTT
Statistics
Matches: 146, Mismatches: 29, Indels: 35
0.70 0.14 0.17
Matches are distributed among these distances:
3 20 0.14
4 90 0.62
5 23 0.16
6 13 0.09
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:292631 original size:23 final size:21
Alignment explanation
Indices: 292580--292778 Score: 58
Period size: 21 Copynumber: 9.0 Consensus size: 21
292570 TTGTTTTATT
292580 TTATTTTATTTT-TTTATTTA
1 TTATTTTATTTTATTTATTTA
292600 TTCTGTATTCTGTATTTTATTTATTTA
1 ---T-TATT-T-TATTTTATTTATTTA
*
292627 TTA-TTTA-TTTATTTATCTA
1 TTATTTTATTTTATTTATTTA
* * *
292646 TTATTACTA-TTTATTAATATA
1 TTATT-TTATTTTATTTATTTA
*
292667 TGTATTTT-TTATTA-TTACTTA
1 T-TATTTTATT-TTATTTATTTA
*
292688 TCTGTTTATATATTTATTATATATTA
1 T-TATTT-TAT-TTTATT-TAT-TTA
*
292714 TTA-TTTA-TCTATTTACATATTA
1 TTATTTTATTTTATTT--AT-TTA
* *
292736 TCATTTATCTATTAATATTTATTTA
1 TTA-TT-T-TATT-TTATTTATTTA
292761 TT-TTTTATTTTA-TTATTT
1 TTATTTTATTTTATTTATTT
292779 TTTTTCTTGG
Statistics
Matches: 136, Mismatches: 17, Indels: 50
0.67 0.08 0.25
Matches are distributed among these distances:
19 20 0.15
20 6 0.04
21 34 0.25
22 18 0.13
23 11 0.08
24 10 0.07
25 9 0.07
26 14 0.10
27 9 0.07
28 5 0.04
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATTTTATTTTATTTATTTA
Found at i:292734 original size:33 final size:34
Alignment explanation
Indices: 292612--292763 Score: 134
Period size: 33 Copynumber: 4.6 Consensus size: 34
292602 CTGTATTCTG
* *
292612 TATT-TTATTTATTTA-TTATTTATTTATTTATC
1 TATTATTATTTATCTATTTATATATTTATTTATC
* * * * *
292644 TATTATTA-CTATTTATTAATATATGTATTT-TT
1 TATTATTATTTATCTATTTATATATTTATTTATC
* * *
292676 TATTATTACTTATCTGTTTATATATTTA-TTATA
1 TATTATTATTTATCTATTTATATATTTATTTATC
*
292709 TATTATTATTTATCTATTTACATATTATCATTTATC
1 TATTATTATTTATCTATTTATATATT-T-ATTTATC
* *
292745 TATTAATATTTATTTATTT
1 TATTATTATTTATCTATTT
292764 TTTATTTTAT
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
32 21 0.22
33 52 0.54
34 1 0.01
35 1 0.01
36 21 0.22
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (34 bp):
TATTATTATTTATCTATTTATATATTTATTTATC
Found at i:293175 original size:19 final size:18
Alignment explanation
Indices: 293115--293175 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
293105 CAAATTTCGA
293115 TTGAATTTTTCTGTGAAGT
1 TTGAATTTTTCTGT-AAGT
293134 TTGAATTTTTC-G---G-
1 TTGAATTTTTCTGTAAGT
*
293147 -TGACTTTTTCTGTCAAGT
1 TTGAATTTTTCTGT-AAGT
293165 TTGAATTTTTC
1 TTGAATTTTTC
293176 GACCAGCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
12 9 0.27
13 1 0.03
14 1 0.03
17 1 0.03
18 1 0.03
19 20 0.61
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.54
Consensus pattern (18 bp):
TTGAATTTTTCTGTAAGT
Found at i:293667 original size:21 final size:21
Alignment explanation
Indices: 293647--293686 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
293637 AAATTGTTTA
293647 ATATTT-TTTATTTTATTTTT
1 ATATTTATTTATTTTATTTTT
*
293667 ATTTTTATTTATTTTATTTT
1 ATATTTATTTATTTTATTTT
293687 CTTTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (21 bp):
ATATTTATTTATTTTATTTTT
Found at i:293761 original size:57 final size:57
Alignment explanation
Indices: 293699--294033 Score: 381
Period size: 58 Copynumber: 5.8 Consensus size: 57
293689 TTAAAATTCA
*
293699 AAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGCTTTCCAAA
1 AAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGCTTT----T
* * * * *
293760 AAAAAAAATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAG-TTTT
1 AAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGCTTTT
* *
293816 CAAAAATGAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAG-TTTT
1 AAAAAAT--ATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGCTTTT
* * *
293873 CAAAAAAGGTTTTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGCTTTT
1 -AAAAAA--TATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGCTTTT
* * * * * * *
293933 TAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTACTCGAAATTAAAGTTTTT
1 AAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAAT-AAGCTTTT
*
293991 AAAAAATA-TTTTGAGAAAAAATTAAAAGTATCAATTTTTCTTG
1 AAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTG
294034 TACAAAAGTA
Statistics
Matches: 236, Mismatches: 30, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
56 5 0.02
57 78 0.33
58 85 0.36
59 13 0.06
60 8 0.03
61 47 0.20
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (57 bp):
AAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGCTTTT
Found at i:293807 original size:27 final size:27
Alignment explanation
Indices: 293777--293864 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
293767 ATTTTTGGGG
293777 AAAAGTTGAAAGTATCAATTTTTCTTAAA
1 AAAAGTTGAAAGTATCAATTTTTCTT--A
* * * ***
293806 AATAAGTTTTCAAA-AATGAATTTTTGAGA
1 AA-AAG--TTGAAAGTATCAATTTTTCTTA
293835 AAAAGTTGAAAGTATCAATTTTTCTTA
1 AAAAGTTGAAAGTATCAATTTTTCTTA
293862 AAA
1 AAA
293865 TAAGTTTTCA
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
26 5 0.12
27 13 0.30
28 3 0.07
29 5 0.12
30 3 0.07
31 9 0.21
32 5 0.12
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (27 bp):
AAAAGTTGAAAGTATCAATTTTTCTTA
Found at i:293847 original size:58 final size:57
Alignment explanation
Indices: 293700--294033 Score: 365
Period size: 57 Copynumber: 5.8 Consensus size: 57
293690 TAAAATTCAA
*
293700 AAAAAT-ATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGCTTTCC
1 AAAAATAATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAG-TTTTC
* * * * *
293757 AAAAAAAAAAATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTC
1 ---AAAAATAATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGTTTTC
*
293817 AAAAATGAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAGTTTTC
1 AAAAAT-AATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGTTTTC
* * * *
293874 AAAAA-AGGTTTTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGCTTTTT
1 AAAAATA---ATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAG-TTTTC
* * * * *
293934 AAAAAT-ATTTTTGGGAAAAAGTTGAAAGTATCAATTTTACTCGAAATTAAAGTTTT-
1 AAAAATAATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAAT-AAGTTTTC
* *
293990 TAAAA-AATATTTTGAGAAAAAATTAAAAGTATCAATTTTTCTTG
1 AAAAATAAT-TTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTG
294034 TACAAAAGTA
Statistics
Matches: 236, Mismatches: 27, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
55 1 0.00
56 6 0.03
57 92 0.39
58 70 0.30
59 8 0.03
60 18 0.08
61 41 0.17
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (57 bp):
AAAAATAATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGTTTTC
Found at i:294113 original size:16 final size:16
Alignment explanation
Indices: 294079--294113 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
294069 AACTGAATCA
*
294079 TTTTTTTCTTTTTCAT
1 TTTTTTTCTTTTCCAT
294095 TTTTTTTCTTTTCC-T
1 TTTTTTTCTTTTCCAT
294110 TTTT
1 TTTT
294114 ACTTTCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTCTTTTCCAT
Found at i:300553 original size:3 final size:3
Alignment explanation
Indices: 300545--300570 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
300535 TAATTGGATT
300545 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
300571 TCTAATCCCT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:306538 original size:28 final size:28
Alignment explanation
Indices: 306498--306554 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
306488 TTTTTTTTTA
306498 ATAGCATTAGGAGAAAAAGAGTTAGCAT
1 ATAGCATTAGGAGAAAAAGAGTTAGCAT
*
306526 ATAGCATTAGGAGAAAAAGAGTTTGCAT
1 ATAGCATTAGGAGAAAAAGAGTTAGCAT
306554 A
1 A
306555 CTTAAATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.23
Consensus pattern (28 bp):
ATAGCATTAGGAGAAAAAGAGTTAGCAT
Found at i:307616 original size:2 final size:2
Alignment explanation
Indices: 307609--307637 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
307599 CTGATTACCA
307609 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
307638 AGGATAACCA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:312614 original size:21 final size:20
Alignment explanation
Indices: 312579--312632 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
312569 TGATTGGTAA
*
312579 AAAATTT-AATTTTTTATAAGT
1 AAAATTTAAATTTTAT-TAA-T
*
312600 AAGATTTCAAATTTTATTAAT
1 AAAATTT-AAATTTTATTAAT
312621 AAAATTTAAATT
1 AAAATTTAAATT
312633 AAAAAAGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 13 0.46
22 3 0.11
23 7 0.25
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (20 bp):
AAAATTTAAATTTTATTAAT
Found at i:319148 original size:2 final size:2
Alignment explanation
Indices: 319141--319187 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
319131 GTAAAAGCTG
319141 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
319183 TC TC T
1 TC TC T
319188 TTTGCCCTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:321977 original size:19 final size:19
Alignment explanation
Indices: 321953--321991 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
321943 TTTGTAATAT
*
321953 ATTTTTAATGATCTTTTGG
1 ATTTTTAATGATCTTATGG
321972 ATTTTTAATGATCTTATGG
1 ATTTTTAATGATCTTATGG
321991 A
1 A
321992 GCAGTTAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (19 bp):
ATTTTTAATGATCTTATGG
Found at i:328945 original size:18 final size:18
Alignment explanation
Indices: 328891--328946 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
328881 CTTTGTTTTT
* *
328891 GATACATTTGAGGTGGAG
1 GATACATTTAAGGTGGAA
*
328909 GATATATTTGAGGAGGTGGAA
1 GATACATTT-A--AGGTGGAA
328930 GATACATTTAAGGTGGA
1 GATACATTTAAGGTGGA
328947 TAATAACCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 15 0.48
20 1 0.03
21 15 0.48
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.29
Consensus pattern (18 bp):
GATACATTTAAGGTGGAA
Found at i:331831 original size:86 final size:86
Alignment explanation
Indices: 331681--331846 Score: 296
Period size: 86 Copynumber: 1.9 Consensus size: 86
331671 CCACTAGTTC
* ** *
331681 TTTGTCTGAATTCTTGTCTTCTGTGCCACTCATGTTGTGATTGGATACTATCTCGTACGGCTTGT
1 TTTGTCTGAATTCTTATCTTCTGTGCCACTCATGTTGTGATTGGATACTATCTCACACGACTTGT
331746 CTAGTAGCAATGTCTGAATTA
66 CTAGTAGCAATGTCTGAATTA
331767 TTTGTCTGAATTCTTATCTTCTGTGCCACTCATGTTGTGATTGGATACTATCTCACACGACTTGT
1 TTTGTCTGAATTCTTATCTTCTGTGCCACTCATGTTGTGATTGGATACTATCTCACACGACTTGT
331832 CTAGTAGCAATGTCT
66 CTAGTAGCAATGTCT
331847 TCATCAATAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (86 bp):
TTTGTCTGAATTCTTATCTTCTGTGCCACTCATGTTGTGATTGGATACTATCTCACACGACTTGT
CTAGTAGCAATGTCTGAATTA
Found at i:332872 original size:26 final size:26
Alignment explanation
Indices: 332823--332871 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
332813 TTTCAAAAAT
*
332823 TAAAAGTTTTCAAACTTATATTTTAA
1 TAAAAGTTTTCAAACCTATATTTTAA
332849 TAAAA-TTTTCAAACCTATATTTT
1 TAAAAGTTTTCAAACCTATATTTT
332872 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (26 bp):
TAAAAGTTTTCAAACCTATATTTTAA
Found at i:333128 original size:20 final size:19
Alignment explanation
Indices: 333098--333138 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
333088 ACAACAAAAA
*
333098 AAAATTAAAATTCATATAT
1 AAAATTAAAATTAATATAT
333117 AAAATTATAAATTAATATAT
1 AAAATTA-AAATTAATATAT
333137 AA
1 AA
333139 CACAATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTAAAATTAATATAT
Found at i:334599 original size:2 final size:2
Alignment explanation
Indices: 334592--334628 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
334582 GAATATACAC
334592 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
334629 TGAACTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:334778 original size:2 final size:2
Alignment explanation
Indices: 334771--334820 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
334761 ATTTGACAAT
334771 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
334812 AG AG AG AG A
1 AG AG AG AG A
334821 TGAACTGATA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:334910 original size:192 final size:191
Alignment explanation
Indices: 334592--334964 Score: 728
Period size: 192 Copynumber: 1.9 Consensus size: 191
334582 GAATATACAC
334592 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGAACTGATACCAGAAAATTGCAGGGAC
1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGAACTGATACCAGAAAATTGCAGGGAC
334657 AGTGATATTGTAAGGATAAACAGCAATAGTATTGCTCAGCCAAAAGCCAGACATCTCACTTAAAT
66 AGTGATATTGTAAGGATAAACAGCAATAGTATTGCTCAGCCAAAAGCCAGACATCTCACTTAAAT
334722 GAAAGATTAAAAGCTTCATTAACAACTAATATCCCATCCATTTGACAATAGAGAGAGAGAG
131 GAAAGATTAAAAGCTTCATTAACAACTAATATCCCATCCATTTGACAATAGAGAGAGAGAG
334783 AGAGAGAGAGAGAGAGAGGAGAGAGAGAGAGAGAGAGATGAACTGATACCAGAAAATTGCAGGGA
1 AGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGATGAACTGATACCAGAAAATTGCAGGGA
*
334848 CAGTGATATTGTAAGGATAAACAGCAATAGTATTGCTCAGCCAAAAGCTAGACATCTCACTTAAA
65 CAGTGATATTGTAAGGATAAACAGCAATAGTATTGCTCAGCCAAAAGCCAGACATCTCACTTAAA
334913 TGAAAGATTAAAAGCTTCATTAACAACTAATATCCCATCCATTTGACAATAG
130 TGAAAGATTAAAAGCTTCATTAACAACTAATATCCCATCCATTTGACAATAG
334965 TACAATACAA
Statistics
Matches: 180, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
191 17 0.09
192 163 0.91
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (191 bp):
AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGAACTGATACCAGAAAATTGCAGGGAC
AGTGATATTGTAAGGATAAACAGCAATAGTATTGCTCAGCCAAAAGCCAGACATCTCACTTAAAT
GAAAGATTAAAAGCTTCATTAACAACTAATATCCCATCCATTTGACAATAGAGAGAGAGAG
Found at i:352674 original size:19 final size:20
Alignment explanation
Indices: 352632--352675 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
352622 TATATTATTT
*
352632 TTAATAAATTTTTACTTATT
1 TTAATAAATTTTTACTTATG
* *
352652 TTAATATATTTTTA-TTGTG
1 TTAATAAATTTTTACTTATG
352671 TTAAT
1 TTAAT
352676 TTCATGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (20 bp):
TTAATAAATTTTTACTTATG
Found at i:352742 original size:21 final size:22
Alignment explanation
Indices: 352707--352749 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
352697 AATGGCTATT
* *
352707 AAATTATATTTAAATTTTAAAA
1 AAATTATAGTTAAATGTTAAAA
352729 AAATTAT-GTTAAATGTTAAAA
1 AAATTATAGTTAAATGTTAAAA
352750 TTAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATTATAGTTAAATGTTAAAA
Found at i:352978 original size:19 final size:19
Alignment explanation
Indices: 352954--352990 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
352944 TGTTTACCTT
352954 GTTAAATT-TATATTTTTGG
1 GTTAAATTCTA-ATTTTTGG
352973 GTTAAATTCTAATTTTTG
1 GTTAAATTCTAATTTTTG
352991 AATATTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.57
Consensus pattern (19 bp):
GTTAAATTCTAATTTTTGG
Found at i:355589 original size:144 final size:143
Alignment explanation
Indices: 355316--355593 Score: 350
Period size: 144 Copynumber: 1.9 Consensus size: 143
355306 CTTTATGACT
*
355316 TAAAATTCGGATGCTTTTTTTGCTGAAATAGAGGAAGCGAATTGAGGAAGAAATGAAGTGAAAAA
1 TAAAATTCGGATGCTTTTTTTGCTAAAATAGAGGAAGCGAATTGAGGAAGAAATGAAGTGAAAAA
* * **
355381 GAAAATAAGGTGCAGGGTCTGGCTATGTGAAGAGATTAGGCACGCAGAAGGCAGAACTGTAGAAA
66 GAAAATAAGGTGCAGGGTCTGGCTATGTGAAGAGATTAGGCACGCAGAAGGCAAAAATACAGAAA
355446 GAAATTAAAAACCC
131 -AAATTAAAAACCC
* *
355460 TAAAA-TCTGGATGCTTTCTTTT-CTAAAATAGAGGAAGTGAATTGAGGAAGAAATGAAGTGGAG
1 TAAAATTC-GGATGCTTT-TTTTGCTAAAATAGAGGAAGCGAATTGAGGAAGAAATGAAGT-GAA
* * * * * *
355523 AAAG-AAATGAGGTGTAGGGTCTGGCTATGTGAGGAGA-TCGG-ACGGGTAGGAGGCAAAAATAC
63 AAAGAAAATAAGGTGCAGGGTCTGGCTATGTGAAGAGATTAGGCAC--GCAGAAGGCAAAAATAC
355585 AGAAAAAAT
126 AGAAAAAAT
355594 GAAGTGAAGA
Statistics
Matches: 116, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
142 2 0.02
143 9 0.08
144 95 0.82
145 10 0.09
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (143 bp):
TAAAATTCGGATGCTTTTTTTGCTAAAATAGAGGAAGCGAATTGAGGAAGAAATGAAGTGAAAAA
GAAAATAAGGTGCAGGGTCTGGCTATGTGAAGAGATTAGGCACGCAGAAGGCAAAAATACAGAAA
AAATTAAAAACCC
Found at i:355594 original size:80 final size:81
Alignment explanation
Indices: 355510--355677 Score: 257
Period size: 80 Copynumber: 2.1 Consensus size: 81
355500 ATTGAGGAAG
* * * *
355510 AAATGAAGTGGAGAAAGAAATGAGGTGTAGGGTCTGGCTATGTGAGGAGATCGGACGGGTAGGAG
1 AAATGAAGTGAAGAAAAAAATGAGGTGCAGGGTCTGACTATGTGAGGAGATCGGACGGGTAGGAG
355575 GCAAAAATACAG-AAA
66 GCAAAAATACAGAAAA
*
355590 AAATGAAGTGAAGAAAAAAATGAGGTGCAGGGTCTGATTATGTGAGGAGATCGGACGGGTAGGAG
1 AAATGAAGTGAAGAAAAAAATGAGGTGCAGGGTCTGACTATGTGAGGAGATCGGACGGGTAGGAG
* * *
355655 GCAGAATTGCAGAAAA
66 GCAAAAATACAGAAAA
355671 AAATGAA
1 AAATGAA
355678 AAATCCTAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
80 69 0.87
81 10 0.13
ACGTcount: A:0.40, C:0.07, G:0.36, T:0.17
Consensus pattern (81 bp):
AAATGAAGTGAAGAAAAAAATGAGGTGCAGGGTCTGACTATGTGAGGAGATCGGACGGGTAGGAG
GCAAAAATACAGAAAA
Found at i:364270 original size:2 final size:2
Alignment explanation
Indices: 364263--364293 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
364253 ATCACGGGCT
364263 TA 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 TA T
364294 GTTTCCTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:376154 original size:20 final size:19
Alignment explanation
Indices: 376131--376169 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
376121 ATAATAAAAA
*
376131 TATAAATATAATAATTTTTT
1 TATAAAAATAA-AATTTTTT
376151 TATAAAAATAAAATTTTTT
1 TATAAAAATAAAATTTTTT
376170 CAACTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATAAAAATAAAATTTTTT
Found at i:384568 original size:2 final size:2
Alignment explanation
Indices: 384561--384605 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
384551 TTTCTATTTG
*
384561 CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
384603 CT C
1 CT C
384606 GTACATCTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:390085 original size:2 final size:2
Alignment explanation
Indices: 390078--390112 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
390068 TCCGAAGTTC
390078 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 A
390113 GTGTAACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:390174 original size:2 final size:2
Alignment explanation
Indices: 390169--390201 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
390159 TATATATATA
*
390169 GT GT GT GT GT GT GT GT GT GT GT TT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
390202 ACTCTTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
GT
Found at i:393507 original size:2 final size:2
Alignment explanation
Indices: 393500--393536 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
393490 CCATATTTGC
*
393500 CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
393537 ACACACACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
CT
Found at i:393721 original size:9 final size:9
Alignment explanation
Indices: 393709--393739 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
393699 GAGGAGGAGG
393709 AGAAGAACA
1 AGAAGAACA
393718 AGAAGAACA
1 AGAAGAACA
393727 AGAAGAACA
1 AGAAGAACA
393736 AGAA
1 AGAA
393740 CAAGAAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.68, C:0.10, G:0.23, T:0.00
Consensus pattern (9 bp):
AGAAGAACA
Found at i:393738 original size:15 final size:15
Alignment explanation
Indices: 393711--393745 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
393701 GGAGGAGGAG
*
393711 AAGAACAAGAAGAAC
1 AAGAACAACAAGAAC
*
393726 AAGAAGAACAAGAAC
1 AAGAACAACAAGAAC
393741 AAGAA
1 AAGAA
393746 AAGGATGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.11, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAACAACAAGAAC
Found at i:396088 original size:12 final size:12
Alignment explanation
Indices: 396071--396095 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
396061 TAGATATCTT
396071 AGGTCCTAACTG
1 AGGTCCTAACTG
396083 AGGTCCTAACTG
1 AGGTCCTAACTG
396095 A
1 A
396096 AAATATGATG
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:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (12 bp):
AGGTCCTAACTG
Found at i:398673 original size:77 final size:78
Alignment explanation
Indices: 398529--398679 Score: 189
Period size: 77 Copynumber: 1.9 Consensus size: 78
398519 ATGTCAGCAT
* * * * * *
398529 CAAATAGAAAAGATATCCTAAAGAATAAAAATGCAAAGGTATCAATAACCATCTTTGAAAGATTA
1 CAAATAGAAAAGATAACCTAAAGAATAAAAAGGCAAAAGTAACAATAACCATCTTTCAAAGACTA
398594 TTATCAGCAAGAA
66 TTATCAGCAAGAA
* * * *
398607 CAAATA-AAAAGATAACCTTAAGAATGAAAAGGCAAAAGTAACAATAACCATC-TTCAAGTGGCT
1 CAAATAGAAAAGATAACCTAAAGAATAAAAAGGCAAAAGTAACAATAACCATCTTTCAA-AGACT
398670 ATTATCAGCA
65 ATTATCAGCA
398680 GAAAGGCCCA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
76 4 0.06
77 52 0.84
78 6 0.10
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.22
Consensus pattern (78 bp):
CAAATAGAAAAGATAACCTAAAGAATAAAAAGGCAAAAGTAACAATAACCATCTTTCAAAGACTA
TTATCAGCAAGAA
Found at i:407371 original size:43 final size:43
Alignment explanation
Indices: 407310--407397 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
407300 TGAGAAAATG
*
407310 ATTACAACCTAACAGTAGTTAACATTCAAGTATTTTGTAGAGT
1 ATTACAACCTAACAGTAGTTAACATTCAAGTATGTTGTAGAGT
* *
407353 ATTACAACCTATCGGTAGTTAACATTCAAGTATGTTGTAGAGT
1 ATTACAACCTAACAGTAGTTAACATTCAAGTATGTTGTAGAGT
407396 AT
1 AT
407398 CATAAGCTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (43 bp):
ATTACAACCTAACAGTAGTTAACATTCAAGTATGTTGTAGAGT
Found at i:409434 original size:18 final size:21
Alignment explanation
Indices: 409411--409449 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
409401 CCAAATTTTA
409411 CCATCAA-C-AAAA-TCAAAC
1 CCATCAATCGAAAACTCAAAC
409429 CCATCAATCGAAAACTCAAAC
1 CCATCAATCGAAAACTCAAAC
409450 AGTTGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 4 0.22
21 6 0.33
ACGTcount: A:0.51, C:0.33, G:0.03, T:0.13
Consensus pattern (21 bp):
CCATCAATCGAAAACTCAAAC
Found at i:418217 original size:2 final size:2
Alignment explanation
Indices: 418210--418259 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
418200 ATGAAGCAGA
* *
418210 AT AT AT AT AT AG AT AT AT CT 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
418252 AT AT AT AT
1 AT AT AT AT
418260 CTCCAATCCC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:419203 original size:2 final size:2
Alignment explanation
Indices: 419196--419227 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
419186 CTCTGCTTGC
419196 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
419228 TATTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:420160 original size:8 final size:8
Alignment explanation
Indices: 420147--420175 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
420137 GGGGCGCACT
420147 AGCACAGC
1 AGCACAGC
420155 AGCACAGC
1 AGCACAGC
420163 AGCACAGC
1 AGCACAGC
420171 AGCAC
1 AGCAC
420176 CGTTAACTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.38, G:0.24, T:0.00
Consensus pattern (8 bp):
AGCACAGC
Found at i:423087 original size:2 final size:2
Alignment explanation
Indices: 423082--423112 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
423072 TATATGTGTC
423082 TA 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 TA T
423113 TTACTACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:423561 original size:3 final size:3
Alignment explanation
Indices: 423553--423580 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
423543 TTAACAGTAT
423553 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
423581 CTTGTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:426526 original size:2 final size:2
Alignment explanation
Indices: 426492--426518 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
426482 AGACTTTAAG
426492 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
426519 CTTATATACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:428188 original size:3 final size:3
Alignment explanation
Indices: 428180--428228 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
428170 TCTATTCTCT
*
428180 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
428228 A
1 A
428229 GAACGTGGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:428975 original size:59 final size:58
Alignment explanation
Indices: 428888--429396 Score: 387
Period size: 59 Copynumber: 8.7 Consensus size: 58
428878 TACTTTTAAT
* * *
428888 TTTTCTTTAAAATTATTT-TTTT-AGGAAAATTGATACTTTTAA-TTTTTCTCAAAGATAC
1 TTTT-TTTGAAATT-TTTATTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAA-ATAA
* * *
428946 TTTTTTTGAAATTTTTATTTTCAAGGAAAATTAATATTTTCAAGTTTTTCTCAAAAT-A
1 TTTTTTTGAAATTTTTATTTT-AAGGAAAATTGATACTTTCAACTTTTTCTCAAAATAA
** * * *
429004 TTTTTTCAAAATTTTCATTTTTAAGGAAAGTTGATACTTTCAACTTTTCCTCAAAAATACA
1 TTTTTTTGAAATTTTTA-TTTTAAGGAAAATTGATACTTTCAACTTTTTCTC-AAAATA-A
* * *
429065 -TTTTTTGAGAATTTTTATTTTTAAGAAAAATTGATACTTTCAACATTTCCTC-AAA-AA
1 TTTTTTTGA-AATTTTTA-TTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAATAA
* * ** * * *
429122 TGTTTCTTG-AAGTTTTATTTTCAAAAAAAATTGTTACTTTCAATTTTTTCTTAAAA-AA
1 T-TTTTTTGAAATTTTTATTTT-AAGGAAAATTGATACTTTCAACTTTTTCTCAAAATAA
* * * * *
429180 TATCTTTTGAAAATTTTATCTTTAAGAAAAATTGATGCCTTT-AACTTTTCCTCAAAA-AA
1 T-TTTTTTGAAATTTTTAT-TTTAAGGAAAATTGAT-ACTTTCAACTTTTTCTCAAAATAA
* * * * *
429239 ATCTTTTGAAAATTTTATCTTTAAAGAAAATTGATACTTTCAAC-TTTTCTTCAAAAAAA
1 TTTTTTTGAAATTTTTAT-TTTAAGGAAAATTGATACTTTCAACTTTTTC-TCAAAATAA
* * * * * * *
429298 ATCTTTTAAAAATTTTATCTTTAAAGAAAATTGATACTTTCAACTTTTTTTCAAAA-ATT
1 TTTTTTTGAAATTTTTAT-TTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAATA-A
* * **
429357 TTTTTTTGAAGTTTTTATTTAAAAAAAAATTGATACTTTC
1 TTTTTTTGAAATTTTTATTTTAAGGAAAATTGATACTTTC
429397 CAACATTTCC
Statistics
Matches: 378, Mismatches: 52, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
56 7 0.02
57 52 0.14
58 117 0.31
59 134 0.35
60 28 0.07
61 40 0.11
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.47
Consensus pattern (58 bp):
TTTTTTTGAAATTTTTATTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAATAA
Found at i:429024 original size:58 final size:57
Alignment explanation
Indices: 428896--429396 Score: 320
Period size: 58 Copynumber: 8.6 Consensus size: 57
428886 ATTTTTCTTT
* * *
428896 AAAATTATT-TTTTT-AGGAAAATTGATACTTTTAATTTTTCTCAAAGATACTTTTTTT
1 AAAATTTTTATTTTTAAGGAAAATTGATACTTTCAATTTTTCTCAAA-ATA-TTTTTTC
* * * *
428953 GAAATTTTTATTTTCAAGGAAAATTAATATTTTCAAGTTTTTCTCAAAATATTTTTTC
1 AAAATTTTTATTTTTAAGGAAAATTGATACTTTCAA-TTTTTCTCAAAATATTTTTTC
* * * *
429011 AAAATTTTCATTTTTAAGGAAAGTTGATACTTTCAACTTTTCCTCAAAAATACATTTTTTG
1 AAAATTTTTATTTTTAAGGAAAATTGATACTTTCAA-TTTTTCTC-AAAAT--ATTTTTTC
* * * *
429072 AGAATTTTTATTTTTAAGAAAAATTGATACTTTCAACATTTCCTCAAAA-ATGTTTCTT-
1 AAAATTTTTATTTTTAAGGAAAATTGATACTTTCAA-TTTTTCTCAAAATAT-TTT-TTC
* * * ** * * * *
429130 -GAAGTTTTATTTTCAAAAAAAATTGTTACTTTCAATTTTTTCTTAAAAAATATCTTTTG
1 AAAATTTTTATTTTTAAGGAAAATTGATACTTTCAA-TTTTTC-T-CAAAATATTTTTTC
* * * * * * *
429189 AAAA-TTTTATCTTTAAGAAAAATTGATGCCTTT-AACTTTTCCTCAAAAAAATCTTTTG
1 AAAATTTTTATTTTTAAGGAAAATTGAT-ACTTTCAA-TTTTTCTC-AAAATATTTTTTC
* * * * *
429247 AAAA-TTTTATCTTTAAAGAAAATTGATACTTTCAACTTTTCTTCAAAAAAAATCTTTT-
1 AAAATTTTTATTTTTAAGGAAAATTGATACTTTCAATTTTTC-TC--AAAATATTTTTTC
* * * * * *
429305 AAAAATTTTATCTTTAAAGAAAATTGATACTTTCAACTTTTTTTCAAAAATTTTTTTTT
1 AAAATTTTTATTTTTAAGGAAAATTGATACTTTCAA-TTTTTCTC-AAAATATTTTTTC
* * * **
429364 GAAGTTTTTA-TTTAAAAAAAAATTGATACTTTC
1 AAAATTTTTATTTTTAAGGAAAATTGATACTTTC
429397 CAACATTTCC
Statistics
Matches: 367, Mismatches: 56, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
57 52 0.14
58 129 0.35
59 112 0.31
60 27 0.07
61 47 0.13
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (57 bp):
AAAATTTTTATTTTTAAGGAAAATTGATACTTTCAATTTTTCTCAAAATATTTTTTC
Found at i:429281 original size:117 final size:115
Alignment explanation
Indices: 428912--429396 Score: 451
Period size: 117 Copynumber: 4.1 Consensus size: 115
428902 ATTTTTTTAG
* * * * * *
428912 GAAAATTGATACTTTTAATTTTTC-TCAAAGATACTTTTTTTGAAATTTTTAT-TTTCAAGGAAA
1 GAAAATTGATACTTTCAATTTTTCTTAAAAAATA--TCTTTTGAAAATTTTATCTTT-AAGAAAA
* * * * * *
428975 ATTAATATTTTCAAGTTTTTCTC-AAAATATTTTTTCAAAATTTTCATTTTTAAG
63 ATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTT-A-TTTTAAA
* * * * * * *
429029 GAAAGTTGATACTTTCAACTTTTCCTCAAAAATACATTTTTTGAGAATTTTTATTTTTAAGAAAA
1 GAAAATTGATACTTTCAA-TTTTTCTTAAAAA-ATATCTTTTGA-AAATTTTATCTTTAAGAAAA
* * * *
429094 ATTGATACTTTCAACATTTCCTCAAAAATGTTTCTTG-AAGTTTTATTTTCAAA
63 ATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTATTTT-AAA
* *
429147 AAAAATTGTTACTTTCAATTTTTTCTTAAAAAATATCTTTTGAAAATTTTATCTTTAAGAAAAAT
1 GAAAATTGATACTTTCAA-TTTTTCTTAAAAAATATCTTTTGAAAATTTTATCTTTAAGAAAAAT
* * *
429212 TGATGCCTTT-AACTTTTCCTCAAAAAAATCTTTTGAAAATTTTATCTTTAAA
65 TGAT-ACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTAT-TTTAAA
* * *
429264 GAAAATTGATACTTTCAACTTTTCTTCAAAAAAAATCTTTTAAAAATTTTATCTTTAA-AGAAAA
1 GAAAATTGATACTTTCAATTTTTCTT-AAAAAATATCTTTTGAAAATTTTATCTTTAAGA-AAAA
** * ** *
429328 TTGATACTTTCAACTTTTTTTCAAAAATTTTTTTTTGAAGTTTTTATTTAAAA
64 TTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTGAAAATTTTATTTTAAA
*
429381 AAAAATTGATACTTTC
1 GAAAATTGATACTTTC
429397 CAACATTTCC
Statistics
Matches: 304, Mismatches: 50, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
116 56 0.18
117 132 0.43
118 59 0.19
119 42 0.14
120 15 0.05
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (115 bp):
GAAAATTGATACTTTCAATTTTTCTTAAAAAATATCTTTTGAAAATTTTATCTTTAAGAAAAATT
GATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTATTTTAAA
Found at i:429327 original size:29 final size:28
Alignment explanation
Indices: 429236--429328 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
429226 TTTCCTCAAA
429236 AAAATCTTTTGAAAATTTTATCTTTAAAG
1 AAAATCTTTT-AAAATTTTATCTTTAAAG
** * * *
429265 AAAAT-TGATACTTTCAACTTT-TCTTCAAAA
1 AAAATCT--T--TTAAAATTTTATCTTTAAAG
429295 AAAATCTTTTAAAAATTTTATCTTTAAAG
1 AAAATCTTTT-AAAATTTTATCTTTAAAG
429324 AAAAT
1 AAAAT
429329 TGATACTTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
27 2 0.04
28 6 0.13
29 18 0.38
30 13 0.28
31 6 0.13
32 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (28 bp):
AAAATCTTTTAAAATTTTATCTTTAAAG
Found at i:430217 original size:17 final size:18
Alignment explanation
Indices: 430178--430219 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
430168 TTTTTCACTT
430178 TTTTTGTTTCTGACTTCC
1 TTTTTGTTTCTGACTTCC
*
430196 TTTTTGTTTTTGA-TTCTC
1 TTTTTGTTTCTGACTTC-C
430214 TTTTTG
1 TTTTTG
430220 ACAGAAGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.05, C:0.14, G:0.12, T:0.69
Consensus pattern (18 bp):
TTTTTGTTTCTGACTTCC
Found at i:431193 original size:3 final size:3
Alignment explanation
Indices: 431185--431213 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
431175 AACACATGTA
431185 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
431214 CATTATCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:441073 original size:26 final size:26
Alignment explanation
Indices: 441037--441091 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
441027 TTACAAAGAA
*
441037 GAGGGGATTATTGCCATCATCATTTG
1 GAGGAGATTATTGCCATCATCATTTG
441063 GAGGAGATTATTGCCATCATCATTTG
1 GAGGAGATTATTGCCATCATCATTTG
441089 GAG
1 GAG
441092 CACATGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (26 bp):
GAGGAGATTATTGCCATCATCATTTG
Found at i:443580 original size:2 final size:2
Alignment explanation
Indices: 443573--443597 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
443563 ATTGTTTCTC
443573 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 A
443598 AATTCACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:445526 original size:2 final size:2
Alignment explanation
Indices: 445519--445552 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
445509 GCATTCTTAT
445519 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
445553 GGTTATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:452667 original size:26 final size:26
Alignment explanation
Indices: 452631--452682 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
452621 TAAGCTATGT
452631 AGCAATACTCCAACTCTCTAGTTGAA
1 AGCAATACTCCAACTCTCTAGTTGAA
452657 AGCAATACTCCAACTCTCTAGTTGAA
1 AGCAATACTCCAACTCTCTAGTTGAA
452683 CCATTTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (26 bp):
AGCAATACTCCAACTCTCTAGTTGAA
Found at i:452762 original size:2 final size:2
Alignment explanation
Indices: 452755--452781 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
452745 TAGTCCACCA
452755 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
452782 GATACATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:452790 original size:4 final size:4
Alignment explanation
Indices: 452783--452817 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
452773 ACACACACAG
452783 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
452818 ACAAGATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:474616 original size:22 final size:23
Alignment explanation
Indices: 474572--474617 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
474562 GATTTGTTTT
* *
474572 TCTTTATGTTGCTCTATATCTTC
1 TCTTTATGTTGCTCTAGAGCTTC
*
474595 TCTTTATGTT-TTCTAGAGCTTC
1 TCTTTATGTTGCTCTAGAGCTTC
474617 T
1 T
474618 AACTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.57
Consensus pattern (23 bp):
TCTTTATGTTGCTCTAGAGCTTC
Found at i:483062 original size:102 final size:102
Alignment explanation
Indices: 482885--483079 Score: 255
Period size: 102 Copynumber: 1.9 Consensus size: 102
482875 TTATTTGAAC
* * *
482885 ATGCAAATTCACTTCACGTGAATTTTGAAGAAAATCATCACGAACAGAATTTGGTAATGCTCAGA
1 ATGCAAACTCACTTCACATGAATTTTGAAGAAAATCATCACGAACAGAATTTGATAATGCTCAGA
** *
482950 ATGGAAAATCATGTTTCTAATCCTACAAGCTCTGGAT
66 ACAGAAAATCATGTTTCCAATCCTACAAGCTCTGGAT
* * ** * * *
482987 ATGCAAACTCACTTCACATGAATTTTGGAGAAAGTCATCGTGAACAGAGTTTGATAATGTTCAGG
1 ATGCAAACTCACTTCACATGAATTTTGAAGAAAATCATCACGAACAGAATTTGATAATGCTCAGA
* *
483052 ACAGAGAATCATGTTTCCAATCTTACAA
66 ACAGAAAATCATGTTTCCAATCCTACAA
483080 ATTCTGAACG
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
102 78 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (102 bp):
ATGCAAACTCACTTCACATGAATTTTGAAGAAAATCATCACGAACAGAATTTGATAATGCTCAGA
ACAGAAAATCATGTTTCCAATCCTACAAGCTCTGGAT
Found at i:492322 original size:2 final size:2
Alignment explanation
Indices: 492317--492351 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
492307 TCTCTCTCTC
*
492317 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
492352 GGTTCTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:493879 original size:25 final size:25
Alignment explanation
Indices: 493841--493908 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
493831 ATTTCAGAAG
*
493841 CTTCT-CTT-CTCTTTTCGTCCTTT
1 CTTCTCCTTCCTCTTTTCATCCTTT
493864 CTTCTCCTTCCTCTTTTCATCCTTT
1 CTTCTCCTTCCTCTTTTCATCCTTT
*
493889 CTTTTTCCTTCCTTCTTTTC
1 C-TTCTCCTTCC-TCTTTTC
493909 TGTTCTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.13
24 3 0.08
25 15 0.38
26 9 0.23
27 7 0.18
ACGTcount: A:0.01, C:0.37, G:0.01, T:0.60
Consensus pattern (25 bp):
CTTCTCCTTCCTCTTTTCATCCTTT
Found at i:499410 original size:205 final size:205
Alignment explanation
Indices: 499049--499469 Score: 790
Period size: 205 Copynumber: 2.1 Consensus size: 205
499039 TGGTGTATAA
499049 CCAACCACA-TCCTTGCCATTGTCATGAAACTATTGAAAACTTCAAAATTTTGTTCACTTTTCAT
1 CCAACC-CATTCCTTGCCATTGTCATGAAACTATTGAAAACTTCAAAATTTTGTTCACTTTTCAT
*
499113 TTTAACAACCTATAAAAAGTCATTTTTCATGGTAGAAGAAGCAAAAATATCTCCATTATCTTTAA
65 TTTAACAACCTATAAAAAGTCATTTTTCATGGTAGAAGAAGAAAAAATATCTCCATTATCTTTAA
* *
499178 CCAATAATATATTAATTTGATAATGGCATTCTATCTCTACAGTCTATATCTTTTTTAACATATAA
130 CCAATAATATATTAATTTGATAATGGCATTCTATCTCCACAGTCCATATCTTTTTTAACATATAA
499243 GAAAGAAAATT
195 GAAAGAAAATT
499254 CCAACCCATTCCTTGCCATTGTCATGAAACTATTGAAAACTTCAAAATTTTGTTCACTTTTCATT
1 CCAACCCATTCCTTGCCATTGTCATGAAACTATTGAAAACTTCAAAATTTTGTTCACTTTTCATT
*
499319 TTAACAACCTATAAAAAGTCATTTTTCATGGTAGAAGAAGAAAAAATATCTTCATTATCTTTAAC
66 TTAACAACCTATAAAAAGTCATTTTTCATGGTAGAAGAAGAAAAAATATCTCCATTATCTTTAAC
499384 CAATAATATATTAATTTGATAATGGCATTCTATCTCCACAGTCCATATCTTTTTTAACATATAAG
131 CAATAATATATTAATTTGATAATGGCATTCTATCTCCACAGTCCATATCTTTTTTAACATATAAG
499449 AAAGAAAATT
196 AAAGAAAATT
499459 CCAACCCATTC
1 CCAACCCATTC
499470 ATTTTCATAA
Statistics
Matches: 211, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
204 2 0.01
205 209 0.99
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (205 bp):
CCAACCCATTCCTTGCCATTGTCATGAAACTATTGAAAACTTCAAAATTTTGTTCACTTTTCATT
TTAACAACCTATAAAAAGTCATTTTTCATGGTAGAAGAAGAAAAAATATCTCCATTATCTTTAAC
CAATAATATATTAATTTGATAATGGCATTCTATCTCCACAGTCCATATCTTTTTTAACATATAAG
AAAGAAAATT
Found at i:502714 original size:2 final size:2
Alignment explanation
Indices: 502709--502751 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
502699 TTTTATTTCT
502709 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
502751 T
1 T
502752 TCACCCTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:510937 original size:19 final size:19
Alignment explanation
Indices: 510896--510939 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
510886 CCGGCCAAAT
*
510896 TCCGGCGAAATTTCCAGAT
1 TCCGGCGAAATTTCCAGAA
*
510915 TCCGGCG-ACTTTCCCAGAA
1 TCCGGCGAAATTT-CCAGAA
510934 TCCGGC
1 TCCGGC
510940 ACCGGTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (19 bp):
TCCGGCGAAATTTCCAGAA
Found at i:511230 original size:20 final size:19
Alignment explanation
Indices: 511202--511250 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
511192 TTTTTTTTTT
511202 TTTTTTATTTCT-TTGTTTA
1 TTTTTTATTT-TATTGTTTA
*
511221 TTTGTTTATTTTATTTTTTA
1 TTT-TTTATTTTATTGTTTA
511241 TTTTTTATTT
1 TTTTTTATTT
511251 ATTAGATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTTTATTTTATTGTTTA
Found at i:511266 original size:32 final size:32
Alignment explanation
Indices: 511202--511266 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
511192 TTTTTTTTTT
* * * *
511202 TTTTTTATTTCTTTGTTTATTTGTTTATTTTA
1 TTTTTTATTTCTTTATTTATTAGATTAGTTTA
511234 TTTTTTATTT-TTTATTTATTAGATTAGGTTTA
1 TTTTTTATTTCTTTATTTATTAGATTA-GTTTA
511266 T
1 T
511267 GTAATATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.74
Consensus pattern (32 bp):
TTTTTTATTTCTTTATTTATTAGATTAGTTTA
Found at i:511403 original size:60 final size:58
Alignment explanation
Indices: 511330--511784 Score: 604
Period size: 60 Copynumber: 7.7 Consensus size: 58
511320 AAAAAATTCT
511330 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCA
1 AAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCA
* *
511389 AAATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAATTTCC-
1 AAA-AAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCA
*
511448 AAAAAAGTATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTA-AGAATAAATTTCC-
1 AAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAGA-AATAAATTTCCA
*
511506 -AAAAAATATTTTTAGGGAAAAATTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCA
1 AAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCA
511564 AAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCAAAATTT-CA
1 AAAAAA-ATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCCA
*
511625 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCA
1 AAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCA
**** *
511684 AAAAATGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-GAAAATCGAAATTTCC-
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCCA
511744 -AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCC
511785 CTAAAAAAAA
Statistics
Matches: 359, Mismatches: 18, Indels: 38
0.87 0.04 0.09
Matches are distributed among these distances:
57 53 0.15
58 60 0.17
59 90 0.25
60 134 0.37
61 16 0.04
62 6 0.02
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (58 bp):
AAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCA
Found at i:511470 original size:118 final size:117
Alignment explanation
Indices: 511330--511795 Score: 639
Period size: 118 Copynumber: 4.0 Consensus size: 117
511320 AAAAAATTCT
511330 AAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT-AAATTTCCAAAA
1 AAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATCAAATTTCC--AA
*
511392 TAAAATATTTTTAGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAATTTCC
63 -AAAATATTTTT-GGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
*
511448 AAAAAA-GTATTTTT-GGGAAAAAGTTGAAAGTATCAATTTTCCTT-AAGAAT-AAATTTCCAAA
1 AAAAAATATATTTTTAGGG-AAAAGTTGAAAGTATCAATTTTCCTTGAA-AATCAAATTTCCAAA
*
511509 AAATATTTTTAGGGAAAAA-TTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
64 AAATATTTTT-GGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
*
511563 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCAAAA
1 -AAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTC-CAA
* *
511628 AAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
63 AAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
*** *
511683 AAAAAATGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCGAAATTTCCAAA
1 AAAAAATATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTCCAAA
*
511747 AAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCCTAAAAA-AAAT
64 AAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAT
511796 CATTCTTTCC
Statistics
Matches: 322, Mismatches: 14, Indels: 25
0.89 0.04 0.07
Matches are distributed among these distances:
115 48 0.15
116 12 0.04
117 44 0.14
118 103 0.32
119 68 0.21
120 47 0.15
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.34
Consensus pattern (117 bp):
AAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTCCAAAAA
ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
Found at i:527793 original size:39 final size:39
Alignment explanation
Indices: 527749--527827 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
527739 TTACCGGTTA
527749 ACAACAAGCTTATCTACAAACAATTATATGAATAATCAT
1 ACAACAAGCTTATCTACAAACAATTATATGAATAATCAT
527788 ACAACAAGCTTATCTACAAACAATTATATGAATAATCAT
1 ACAACAAGCTTATCTACAAACAATTATATGAATAATCAT
527827 A
1 A
527828 AGGGACATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (39 bp):
ACAACAAGCTTATCTACAAACAATTATATGAATAATCAT
Found at i:538038 original size:45 final size:45
Alignment explanation
Indices: 537989--538079 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
537979 TATAAAAACA
** *
537989 ATAATTTCTCATAAATTTGTTAGACTCGTAAACTTGTTTAAAATG
1 ATAATTTCTCATAAATTCATTAAACTCGTAAACTTGTTTAAAATG
* * *
538034 ATAATTTCTCATGAATTCATTAAATTCGTAAACTTGTTTAGAATG
1 ATAATTTCTCATAAATTCATTAAACTCGTAAACTTGTTTAAAATG
538079 A
1 A
538080 CCATGTCACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (45 bp):
ATAATTTCTCATAAATTCATTAAACTCGTAAACTTGTTTAAAATG
Found at i:543080 original size:67 final size:66
Alignment explanation
Indices: 542995--543194 Score: 220
Period size: 71 Copynumber: 2.9 Consensus size: 66
542985 TTCCAGGAAT
* * *
542995 TTTCATGACCATGAATTTTCTCCGAAAATTCCTTAATGGCAGACACGAGATTGTAAATACCAGGA
1 TTTCATGACCATGAATTTTCTCCGAAAATTCCTT-ATGGCAGAAATGAGACTGTAAATACCAGGA
543060 GC
65 GC
** * * * *
543062 TTTCATGGGCATGCATTTTCTCTGAAAATTCCTCTATGGCGGAAATTAGTGAGACTATAAATACC
1 TTTCATGACCATGAATTTTCTCCGAAAATTCCT-TATGGCAG-AA--A-TGAGACTGTAAATACC
*
543127 AGGAGT
61 AGGAGC
* * *
543133 TTTCATTACCATGAATTTTCCCCGAAAATTCCTCCATGGCAGAAATGAGACTGTAAATACCA
1 TTTCATGACCATGAATTTTCTCCGAAAATTCCT-TATGGCAGAAATGAGACTGTAAATACCA
543195 TGAACTTGCA
Statistics
Matches: 109, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
67 51 0.47
68 3 0.03
70 3 0.03
71 52 0.48
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (66 bp):
TTTCATGACCATGAATTTTCTCCGAAAATTCCTTATGGCAGAAATGAGACTGTAAATACCAGGAG
C
Found at i:549472 original size:19 final size:19
Alignment explanation
Indices: 549430--549472 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
549420 ATTCGTTATG
549430 ATTATTTATTTTTTATATA
1 ATTATTTATTTTTTATATA
* * * *
549449 TTTATTTTTTTTTTTTTTA
1 ATTATTTATTTTTTATATA
549468 ATTAT
1 ATTAT
549473 CATATAAATA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTATTTATTTTTTATATA
Found at i:561832 original size:6 final size:6
Alignment explanation
Indices: 561821--561856 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
561811 AAAATTATAA
* *
561821 AAATTT AAATTT AAATTT AAATCT AAATCT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
561857 GATTCAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:562322 original size:17 final size:17
Alignment explanation
Indices: 562297--562330 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
562287 GTATTCTGAA
*
562297 TTATGTAAAATTATTAT
1 TTATATAAAATTATTAT
*
562314 TTATATAAAATTTTTAT
1 TTATATAAAATTATTAT
562331 ACAAATAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTATATAAAATTATTAT
Found at i:569402 original size:249 final size:251
Alignment explanation
Indices: 568910--569404 Score: 692
Period size: 252 Copynumber: 2.0 Consensus size: 251
568900 CATCATCTTC
**
568910 CTCCTCCTCATAATCCTCATCTTCATCCTCTTCATCTGATACACTTTTTCGCTTTCGAGATTTTC
1 CTCCTCCTCATAATCCTCATCTTCATCCTCTTCATCTGATACACTTTTAAGCTTTCGAGATTTTC
* * * * * * * *
568975 TATCTACAATCTTCCTCTCTCTTGCTGAAGACATCTGCCTTGCTTTCAACCTAACAACCTTTTTC
66 TATCCAAAATATTCCTCTCCCTTGCTGAAGACATATGCCTTGCTTTCAACATAACAACATTTCTC
* ** * *
569040 AGCTCTTTCTCTTCCTCCTCCTCATCCTCCTCATTACTCCCAAAACCCTCTTCCGATCCCGATTC
131 AGCTCTTTCTCTTCCTCCTCCTCAT-CTCCGCAAAACTCCCAAAACCCTCTTCCGAGCACGATTC
* * *
569105 TTCTAAGGAAGAACAATAATCTTCTGCATCATCATCAGATTGTTCATTTCCCTCCAA
195 ATATAAGGAAGAACAATAATCTTCTGCATCATCATCAGATTCTTCATTTCCCTCCAA
* * *
569162 CTCCTCCTCATAATCTTCATCTTCCTCTTCTTCATCTGATACACTTTTAAGCTTTCGCA-ATTTT
1 CTCCTCCTCATAATCCTCATCTTCATCCTCTTCATCTGATACACTTTTAAGCTTTCG-AGATTTT
**
569226 CTATCCAAAATATTCCTCTCCCTTGCTGAAGACATATGTTTTGCTTTCAACATAACAACATTTCT
65 CTATCCAAAATATTCCTCTCCCTTGCTGAAGACATATGCCTTGCTTTCAACATAACAACATTTCT
* * * *
569291 CATCTCTTTCTCTTCCTCCTCCTCAT-T-GGCAAAACTCCCAGAACCCTCTTCTGAGGCAC-ATT
130 CAGCTCTTTCTCTTCCTCCTCCTCATCTCCGCAAAACTCCCAAAACCCTCTTCCGA-GCACGATT
569353 CATATAAGGAAGAACAATAATCTTCTGCATCATCATCAGATTCTTCATTTCC
194 CATATAAGGAAGAACAATAATCTTCTGCATCATCATCAGATTCTTCATTTCC
569405 TTCCTCTGAA
Statistics
Matches: 214, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
249 73 0.34
250 3 0.01
252 137 0.64
253 1 0.00
ACGTcount: A:0.23, C:0.32, G:0.07, T:0.37
Consensus pattern (251 bp):
CTCCTCCTCATAATCCTCATCTTCATCCTCTTCATCTGATACACTTTTAAGCTTTCGAGATTTTC
TATCCAAAATATTCCTCTCCCTTGCTGAAGACATATGCCTTGCTTTCAACATAACAACATTTCTC
AGCTCTTTCTCTTCCTCCTCCTCATCTCCGCAAAACTCCCAAAACCCTCTTCCGAGCACGATTCA
TATAAGGAAGAACAATAATCTTCTGCATCATCATCAGATTCTTCATTTCCCTCCAA
Found at i:571379 original size:7 final size:7
Alignment explanation
Indices: 571367--571392 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
571357 TAAATCAAAA
571367 TAAAATT
1 TAAAATT
571374 TAAAATT
1 TAAAATT
571381 TAAAATT
1 TAAAATT
571388 TAAAA
1 TAAAA
571393 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
TAAAATT
Found at i:576520 original size:20 final size:21
Alignment explanation
Indices: 576486--576548 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 21
576476 TCAATATTAG
* *
576486 AGAGAAACCGCGAGA-AAAAC
1 AGAGAAACAGAGAGAGAAAAC
576506 AGAGAAACAGAGAGAGAAAAAAC
1 AGAGAAACAGAGAGAG--AAAAC
*
576529 AGAGAGAA-AGTGAGAGAAAA
1 AGAGA-AACAGAGAGAGAAAA
576549 TCTTTTAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 13 0.36
21 4 0.11
23 17 0.47
24 2 0.06
ACGTcount: A:0.60, C:0.10, G:0.29, T:0.02
Consensus pattern (21 bp):
AGAGAAACAGAGAGAGAAAAC
Found at i:576530 original size:23 final size:23
Alignment explanation
Indices: 576500--576548 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
576490 AAACCGCGAG
576500 AAAAACAGAGA-AACAGAGAGAGA
1 AAAAACAGAGAGAA-AGAGAGAGA
*
576523 AAAAACAGAGAGAAAGTGAGAGA
1 AAAAACAGAGAGAAAGAGAGAGA
576546 AAA
1 AAA
576549 TCTTTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.65, C:0.06, G:0.27, T:0.02
Consensus pattern (23 bp):
AAAAACAGAGAGAAAGAGAGAGA
Found at i:590740 original size:34 final size:34
Alignment explanation
Indices: 590702--590767 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
590692 TTTTAAACTA
590702 ATTATTATTATTGATGAATATTAAAGAAATGGGC
1 ATTATTATTATTGATGAATATTAAAGAAATGGGC
*
590736 ATTATTATTATTGATGGATATTAAAGAAATGG
1 ATTATTATTATTGATGAATATTAAAGAAATGG
590768 AAAGTTAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (34 bp):
ATTATTATTATTGATGAATATTAAAGAAATGGGC
Found at i:591381 original size:18 final size:20
Alignment explanation
Indices: 591358--591407 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
591348 TAATTTATAA
591358 ATTTAATTAAT-TTTTTA-T
1 ATTTAATTAATATTTTTATT
*
591376 ATTTAAAT-ATATTTTTATT
1 ATTTAATTAATATTTTTATT
591395 ATTTTAATTAATA
1 A-TTTAATTAATA
591408 AAATATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.08
18 13 0.50
19 2 0.08
20 6 0.23
21 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAATTAATATTTTTATT
Found at i:592431 original size:21 final size:21
Alignment explanation
Indices: 592407--592446 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
592397 AAATTTCCCT
*
592407 GAATTAATTGGAGGTGAGACA
1 GAATTAATTGGACGTGAGACA
* *
592428 GAATTCATTTGACGTGAGA
1 GAATTAATTGGACGTGAGA
592447 AAAAGGAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (21 bp):
GAATTAATTGGACGTGAGACA
Found at i:598165 original size:104 final size:106
Alignment explanation
Indices: 597957--598167 Score: 266
Period size: 104 Copynumber: 2.0 Consensus size: 106
597947 GACTTCAGAA
* * * * *
597957 GTTTCCGCAAGAAAGAGATAATAAATAATAAATATAGGCGTTTTGGGAAATAGGCGTTTGGATCC
1 GTTTCCGCAAGAAAGAGAAAAAAAATAATAAAAAAAGGCGTTTTGGGAAATAGCCG-TTGGATCC
* * *
598022 TAAGCCTAATATGAAACCGCCTCTAAAACAGTTCGGCCCGTT
65 TAAGCCTAATATGAAACCACCGCTAAAACAATTCGGCCCGTT
* *
598064 GTTTCTGCAAGAAAGAGAAAAAAAATAATAAAAAAAAGGCGTTTTGGGAAATAGCCG-T-GAT-G
1 GTTTCCGCAAGAAAGAGAAAAAAAATAAT-AAAAAAAGGCGTTTTGGGAAATAGCCGTTGGATCC
* * *
598126 TAAGCCTAATTTGCAACTACCGCTAAAACAATTCGGCCCGTT
65 TAAGCCTAATATGAAACCACCGCTAAAACAATTCGGCCCGTT
598168 TTCAGAATCC
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
104 36 0.40
105 3 0.03
106 1 0.01
107 26 0.29
108 24 0.27
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (106 bp):
GTTTCCGCAAGAAAGAGAAAAAAAATAATAAAAAAAGGCGTTTTGGGAAATAGCCGTTGGATCCT
AAGCCTAATATGAAACCACCGCTAAAACAATTCGGCCCGTT
Found at i:598603 original size:2 final size:2
Alignment explanation
Indices: 598596--598624 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
598586 TTTATACTCC
598596 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
598625 ATTACAACTG
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:606843 original size:9 final size:9
Alignment explanation
Indices: 606829--606855 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
606819 ATTCACAAAA
606829 ATTTCCTTC
1 ATTTCCTTC
606838 ATTTCCTTC
1 ATTTCCTTC
606847 ATTTCCTTC
1 ATTTCCTTC
606856 TACTTGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTCCTTC
Found at i:608234 original size:22 final size:22
Alignment explanation
Indices: 608206--608247 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
608196 TTAAATCATA
* *
608206 AATAATTATTATAATCTTTTAG
1 AATAATTACTATAATATTTTAG
608228 AATAATTACTATAATATTTT
1 AATAATTACTATAATATTTT
608248 TATTTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
AATAATTACTATAATATTTTAG
Found at i:611603 original size:3 final size:3
Alignment explanation
Indices: 611595--611629 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
611585 GTTTCATGGT
611595 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
611630 TTATTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:611634 original size:3 final size:3
Alignment explanation
Indices: 611628--611667 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
611618 ATAATAATAA
611628 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
611668 GACTTAGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:622330 original size:2 final size:2
Alignment explanation
Indices: 622313--622350 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
622303 ATCAGGATGA
* *
622313 AT AT AA AT AA 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
622351 GCCTAAGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:624654 original size:28 final size:30
Alignment explanation
Indices: 624612--624684 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
624602 TTATATGTTT
** *
624612 TAAATAAATTTTTATATTTT-A-TTGTACC
1 TAAATAAATCATTATATTTTAATTTATACC
* *
624640 TAAATAAATCATTATTTTTTAATTTATATC
1 TAAATAAATCATTATATTTTAATTTATACC
*
624670 TAAATAAGTCATTAT
1 TAAATAAATCATTAT
624685 TTCAAATAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 17 0.46
29 1 0.03
30 19 0.51
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.51
Consensus pattern (30 bp):
TAAATAAATCATTATATTTTAATTTATACC
Found at i:624746 original size:30 final size:30
Alignment explanation
Indices: 624712--624809 Score: 137
Period size: 30 Copynumber: 3.3 Consensus size: 30
624702 TATGTTAAAA
*
624712 ATTTATTT-AAGTACAAATTAAAGGTTAATG
1 ATTTATTTGAA-TACAAATTAAAAGTTAATG
*
624742 ATTTATTTGAATACAAATTAAATGTTAA-G
1 ATTTATTTGAATACAAATTAAAAGTTAATG
624771 TATTTATTTGAATACAAATTAAAAGTTAATG
1 -ATTTATTTGAATACAAATTAAAAGTTAATG
*
624802 ACTTATTT
1 ATTTATTT
624810 TGATGTAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
29 1 0.02
30 58 0.94
31 3 0.05
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (30 bp):
ATTTATTTGAATACAAATTAAAAGTTAATG
Found at i:637295 original size:2 final size:2
Alignment explanation
Indices: 637288--637316 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
637278 ATACATACAT
637288 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
637317 TATAGATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:638817 original size:2 final size:2
Alignment explanation
Indices: 638810--638844 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
638800 ATATAAATTT
638810 TA TA TA 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 TA TA TA T
638845 CTAAGCATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:640957 original size:2 final size:2
Alignment explanation
Indices: 640950--640997 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
640940 TCAACTGCTT
640950 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
640992 TA TA TA
1 TA TA TA
640998 AACGAGCTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:652079 original size:91 final size:91
Alignment explanation
Indices: 651924--652102 Score: 277
Period size: 91 Copynumber: 2.0 Consensus size: 91
651914 CAATAGTTTC
* * **
651924 ATATTTTAGTTTCTTAAAAAGTTTTCCATGAAAAAGGTATGTACACTTAAGCAATGGTTTCATAT
1 ATATTTTAGTTTCTTAAAAAGTTGTCCATGAAAAAGGTATGTACACTCAAGCAATAATTTCATAT
*
651989 TTTAGTTTCTAGAAATAGTAAACCAT
66 TTTAGTTTCTAGAAATAATAAACCAT
* * *
652015 ATATTTTAGTTTTTTAAAAAGTTGTGCATGAAGAAGGTATGTACACTCAAGCAATAATTTCATAT
1 ATATTTTAGTTTCTTAAAAAGTTGTCCATGAAAAAGGTATGTACACTCAAGCAATAATTTCATAT
*
652080 TTTAGTTTCTAGAAGTAATAAAC
66 TTTAGTTTCTAGAAATAATAAAC
652103 GATTAAGTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 79 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (91 bp):
ATATTTTAGTTTCTTAAAAAGTTGTCCATGAAAAAGGTATGTACACTCAAGCAATAATTTCATAT
TTTAGTTTCTAGAAATAATAAACCAT
Found at i:663727 original size:15 final size:15
Alignment explanation
Indices: 663709--663748 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
663699 ATTAATTTTT
*
663709 AATTAAATTATTTAA
1 AATTAAATTAATTAA
663724 AATTAAATTAATT-A
1 AATTAAATTAATTAA
*
663738 AAGTAAATTAA
1 AATTAAATTAA
663749 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AATTAAATTAATTAA
Found at i:664094 original size:13 final size:13
Alignment explanation
Indices: 664076--664121 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
664066 CACTTTCGTT
664076 AATTAATTAATTC
1 AATTAATTAATTC
664089 AATTAAATTAATTC
1 AATT-AATTAATTC
*
664103 AATTTATTAATTC
1 AATTAATTAATTC
*
664116 TATTAA
1 AATTAA
664122 AATCAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.55
14 13 0.45
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAATTAATTC
Found at i:664860 original size:4 final size:4
Alignment explanation
Indices: 664851--664880 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
664841 ACCTAAGAAG
664851 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
664881 TATATGTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:668225 original size:81 final size:81
Alignment explanation
Indices: 668127--668290 Score: 301
Period size: 81 Copynumber: 2.0 Consensus size: 81
668117 CTCATGCCTT
*
668127 AAACAGTTTGATAAGAGTACAAAAATACAATCACATCTTAGTGCAAAAAACACATCCTCTTATTC
1 AAACAGTTTGATAAGAGTACAAAAAAACAATCACATCTTAGTGCAAAAAACACATCCTCTTATTC
668192 TTTTTACCTCTTGGAG
66 TTTTTACCTCTTGGAG
* *
668208 AAACAGTTTGATAAGAGTGCAAAAAAACAATCCCATCTTAGTGCAAAAAACACATCCTCTTATTC
1 AAACAGTTTGATAAGAGTACAAAAAAACAATCACATCTTAGTGCAAAAAACACATCCTCTTATTC
668273 TTTTTACCTCTTGGAG
66 TTTTTACCTCTTGGAG
668289 AA
1 AA
668291 GGCCCCATCA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (81 bp):
AAACAGTTTGATAAGAGTACAAAAAAACAATCACATCTTAGTGCAAAAAACACATCCTCTTATTC
TTTTTACCTCTTGGAG
Found at i:668736 original size:107 final size:109
Alignment explanation
Indices: 668548--668744 Score: 353
Period size: 107 Copynumber: 1.8 Consensus size: 109
668538 ATACCAAAAA
*
668548 AAAAAAAAAAAAAAATCAACACAAATTTATTAAAGTCCTGTCACCACAAAAACAAAAAATAGAAC
1 AAAAAAAAAAAAAAATCAACACAAATTTATTAAAGTCCTGTCACCACAAAAACAAAAAACAGAAC
*
668613 TTTCCTTCATTTTCTCGACAAGCAAACACCAATCAGCCAATACC
66 TGTCCTTCATTTTCTCGACAAGCAAACACCAATCAGCCAATACC
*
668657 AAAAAAAAAAAAAAATCAAC-CAAGTTTATTAAAGTCCTGTCACCAC-AAAACAAAAAACAGAAC
1 AAAAAAAAAAAAAAATCAACACAAATTTATTAAAGTCCTGTCACCACAAAAACAAAAAACAGAAC
668720 TGTCCTTCATTTTCTCGACAAGCAA
66 TGTCCTTCATTTTCTCGACAAGCAA
668745 GCACATACTA
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
107 40 0.47
108 25 0.29
109 20 0.24
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (109 bp):
AAAAAAAAAAAAAAATCAACACAAATTTATTAAAGTCCTGTCACCACAAAAACAAAAAACAGAAC
TGTCCTTCATTTTCTCGACAAGCAAACACCAATCAGCCAATACC
Found at i:670053 original size:21 final size:21
Alignment explanation
Indices: 670017--670059 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
670007 TTAATCGAAT
670017 TTTTATATTTTAATATAGATA
1 TTTTATATTTTAATATAGATA
*
670038 TTTT-TATTTTATATATATATA
1 TTTTATATTTTA-ATATAGATA
670059 T
1 T
670060 GAATTCAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTATATTTTAATATAGATA
Done.