Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 121 of 135
Found at i:36511375 original size:21 final size:22
Alignment explanation
Indices: 36511323--36511385 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
36511313 GTTATGGGTC
36511323 AAAATTAAATTATAATTTTTACGA
1 AAAATTAAATT-TAATTTTTAC-A
*
36511347 TAAA--AAATTTAATTTTTA-A
1 AAAATTAAATTTAATTTTTACA
* *
36511366 AAAATTAAATTAAAATTTTA
1 AAAATTAAATTTAATTTTTA
36511386 TCATTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.12
21 21 0.64
22 5 0.15
24 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATTAAATTTAATTTTTACA
Found at i:36518848 original size:20 final size:19
Alignment explanation
Indices: 36518820--36518901 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 19
36518810 TTTAACATTC
*
36518820 TAAATTTTTTATATATATTT
1 TAAAATTTTTATA-ATATTT
36518840 TAAAATTTTTATAATATTT
1 TAAAATTTTTATAATATTT
* *
36518859 CAAAA---ATATAA-ATTT
1 TAAAATTTTTATAATATTT
* *
36518874 TGAACTTTTTATAAATATTT
1 TAAAATTTTTAT-AATATTT
36518894 T-AAATTTT
1 TAAAATTTT
36518902 GAAAGTTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 6 0.12
16 5 0.10
18 3 0.06
19 18 0.37
20 17 0.35
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (19 bp):
TAAAATTTTTATAATATTT
Found at i:36521497 original size:31 final size:31
Alignment explanation
Indices: 36521462--36521520 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
36521452 AAGGAAGGTT
* * *
36521462 AGAAAATTTTAAGGATTAAATAGTAAATGAG
1 AGAAAATATGAAGGACTAAATAGTAAATGAG
*
36521493 AGAAAATATGAGGGACTAAATAGTAAAT
1 AGAAAATATGAAGGACTAAATAGTAAAT
36521521 TATCCAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.20, T:0.25
Consensus pattern (31 bp):
AGAAAATATGAAGGACTAAATAGTAAATGAG
Found at i:36523181 original size:23 final size:23
Alignment explanation
Indices: 36523155--36523275 Score: 165
Period size: 23 Copynumber: 5.2 Consensus size: 23
36523145 ACACTAGCGC
36523155 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
36523178 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
36523201 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
36523226 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
36523249 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
36523272 GCTC
1 GCTC
36523276 AGTACTTTGT
Statistics
Matches: 88, Mismatches: 4, Indels: 12
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.05
23 63 0.72
24 1 0.01
25 17 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:36523224 original size:48 final size:46
Alignment explanation
Indices: 36523155--36523275 Score: 181
Period size: 48 Copynumber: 2.6 Consensus size: 46
36523145 ACACTAGCGC
*
36523155 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGT-GT
*
36523201 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGTGT
*
36523249 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
36523276 AGTACTTTGT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 26 0.38
48 42 0.61
49 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGTGT
Found at i:36523304 original size:39 final size:39
Alignment explanation
Indices: 36523240--36523314 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
36523230 TCTGATTAGC
*
36523240 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
*
36523279 ACTTTGTGTACTCTCT-ATTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGA-TTAGCACTTTGTGTGCTC
36523315 TTTGTTGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:36524246 original size:87 final size:88
Alignment explanation
Indices: 36524141--36524301 Score: 254
Period size: 87 Copynumber: 1.8 Consensus size: 88
36524131 GGGTTTCACT
* *
36524141 AAAAATTATCATTTTACCCTCGAACCTTCCAAAATTCC-GTTTTGACCTCGATTTCACCAAAAAT
1 AAAAATTATCATTTTACCCTCGAACCTTCCAAAATTCCAGTTTTAACCTCGATTTCACCAAAAAG
36524205 TACCATTTTACCCTTAAACTTTC
66 TACCATTTTACCCTTAAACTTTC
* * *
36524228 AAAAATTA-CATTTTTACCCTCGAACCTTCCCAAATTCCATTTTTAACCTCGATTTTACCAAAAA
1 AAAAATTATCA-TTTTACCCTCGAACCTTCCAAAATTCCAGTTTTAACCTCGATTTCACCAAAAA
36524292 GTACCATTTT
65 GTACCATTTT
36524302 GCCCGCGAGA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
86 2 0.03
87 34 0.51
88 31 0.46
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (88 bp):
AAAAATTATCATTTTACCCTCGAACCTTCCAAAATTCCAGTTTTAACCTCGATTTCACCAAAAAG
TACCATTTTACCCTTAAACTTTC
Found at i:36524262 original size:29 final size:29
Alignment explanation
Indices: 36524142--36524279 Score: 97
Period size: 29 Copynumber: 4.8 Consensus size: 29
36524132 GGTTTCACTA
36524142 AAAATTATCA-TTTTACCCTCGAACCTTCC
1 AAAATTA-CATTTTTACCCTCGAACCTTCC
* * * *
36524171 AAAATTCCGTTTTGA-CCTCG-A-TTTCACC
1 AAAATTACATTTTTACCCTCGAACCTT--CC
** * *
36524199 AAAAATTACCA-TTTTACCCTTAAACTTTCA
1 -AAAATTA-CATTTTTACCCTCGAACCTTCC
36524229 AAAATTACATTTTTACCCTCGAACCTTCC
1 AAAATTACATTTTTACCCTCGAACCTTCC
* * *
36524258 CAAATTCCATTTTTAACCTCGA
1 AAAATTACATTTTTACCCTCGA
36524280 TTTTACCAAA
Statistics
Matches: 83, Mismatches: 17, Indels: 18
0.70 0.14 0.15
Matches are distributed among these distances:
26 2 0.02
27 1 0.01
28 10 0.12
29 61 0.73
30 5 0.06
31 1 0.01
32 3 0.04
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTCGAACCTTCC
Found at i:36524330 original size:88 final size:86
Alignment explanation
Indices: 36524152--36524323 Score: 202
Period size: 87 Copynumber: 2.0 Consensus size: 86
36524142 AAAATTATCA
* *
36524152 TTTTACCCTCGAACCTTCCAAAATTCCGTTTTGACCTCGATTTCACCAAAAATTACCATTTTACC
1 TTTTACCCTCGAACCTTCCAAAATTCCGTTTTAACCTCGATTTCACCAAAAAGTACCATTTTACC
** * *
36524217 CTTAAACTTTCAAAAATTACAT
66 CCGAAAC-GTCAAAAATCACAT
* * * *
36524239 TTTTACCCTCGAACCTTCCCAAATTCCATTTTTAACCTCGATTTTACCAAAAAGTACCATTTTGC
1 TTTTACCCTCGAACCTTCCAAAATTCC-GTTTTAACCTCGATTTCACCAAAAAGTACCATTTTAC
* *
36524304 CCGCGAGA-GTCTAAAATCAC
65 CC-CGAAACGTCAAAAATCAC
36524324 CGTTTTTCCC
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
87 35 0.49
88 34 0.48
89 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (86 bp):
TTTTACCCTCGAACCTTCCAAAATTCCGTTTTAACCTCGATTTCACCAAAAAGTACCATTTTACC
CCGAAACGTCAAAAATCACAT
Found at i:36530032 original size:18 final size:18
Alignment explanation
Indices: 36530004--36530038 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36529994 TTTATGAAAT
36530004 GAAATGAAATGG-AGATG
1 GAAATGAAATGGCAGATG
36530021 GAAATGGAAATGGCAGAT
1 GAAAT-GAAATGGCAGAT
36530039 TAATTTAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.46, C:0.03, G:0.34, T:0.17
Consensus pattern (18 bp):
GAAATGAAATGGCAGATG
Found at i:36533494 original size:16 final size:17
Alignment explanation
Indices: 36533473--36533506 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
36533463 CATTGCATTA
36533473 TCAAAATATAT-TAAAT
1 TCAAAATATATATAAAT
*
36533489 TCAAAATTTATATAAAT
1 TCAAAATATATATAAAT
36533506 T
1 T
36533507 TGTGATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TCAAAATATATATAAAT
Found at i:36533577 original size:3 final size:3
Alignment explanation
Indices: 36533569--36533602 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
36533559 CATTTAACTG
36533569 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
36533603 CATAGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:36540467 original size:3 final size:3
Alignment explanation
Indices: 36540461--36540485 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36540451 TATTTAATAA
36540461 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
36540486 CATACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:36553186 original size:15 final size:14
Alignment explanation
Indices: 36553166--36553213 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 14
36553156 TAAATAAAAA
36553166 AAATATATAATTATT
1 AAATATATAA-TATT
36553181 AAATAT-TAA-ATT
1 AAATATATAATATT
*
36553193 AAA-AAATAATA-T
1 AAATATATAATATT
36553205 AAATATATA
1 AAATATATA
36553214 GATTTTAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.04
12 13 0.46
13 5 0.18
14 3 0.11
15 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATATAATATT
Found at i:36556237 original size:5 final size:5
Alignment explanation
Indices: 36556229--36556254 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
36556219 GGGCACACAT
36556229 TATTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA T
36556255 TAATAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:36559019 original size:18 final size:19
Alignment explanation
Indices: 36558986--36559024 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
36558976 TATTTTCCTA
*
36558986 TAAATATTATTAATGAAAT
1 TAAACATTATTAATGAAAT
*
36559005 TAAACATTA-TAATGATAT
1 TAAACATTATTAATGAAAT
36559023 TA
1 TA
36559025 TAGTATAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
TAAACATTATTAATGAAAT
Found at i:36559815 original size:29 final size:29
Alignment explanation
Indices: 36559783--36559858 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
36559773 ATGTATACTT
*
36559783 TTTTATATTT-GAAATTTAATCTCTTTTAC
1 TTTTATATTTAGAAATTTAATCT-ATTTAC
* *
36559812 TTTTATTTTTAGGAATTTAATCTATTTAC
1 TTTTATATTTAGAAATTTAATCTATTTAC
* *
36559841 TTTTCAAATTTAAAAATT
1 TTTT-ATATTTAGAAATT
36559859 CAACTATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 18 0.47
30 20 0.53
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTATATTTAGAAATTTAATCTATTTAC
Found at i:36561128 original size:191 final size:191
Alignment explanation
Indices: 36560792--36561138 Score: 523
Period size: 191 Copynumber: 1.8 Consensus size: 191
36560782 CCAACCACAT
* *
36560792 CATCATTGATAGAATGGCTCTTCCTAACTCTAGAGGAAGCTTGTACCTAGTTATCAATGTGAATT
1 CATCATTGATAGAATGACTCTTCCTAACTCTAGAGGAAGCTTGTACATAGTTATCAATGTGAATT
* * *
36560857 TGATTAGCTCCCCCATCAGCTTCCTCAATCTCATGAATTTCTTCCCCAGGTTCACTAGCAACTTG
66 TGATTAGCTCCCCCATCAGCTTCCTCAATCTCATGAATTTCTTCCCCAAGTTCACCAACAACTTG
36560922 CTCAATGCCTAAAGCAATGGGCACTAGATCAGGTTCACATCATCATTGAGATCACCAATCA
131 CTCAATGCCTAAAGCAATGGGCACTAGATCAGGTTCACATCATCATTGAGATCACCAATCA
* * * * * *
36560983 CATCATTGATAGAATGATTCTTCTTAACTCTAGAGTAAGGTTGTACATGGTTATCATTGTGAATT
1 CATCATTGATAGAATGACTCTTCCTAACTCTAGAGGAAGCTTGTACATAGTTATCAATGTGAATT
* ** *
36561048 TGATTAGCTTCCCCATCAGCTTCCTTGATCTCATGAATTTCTTCCTCAAGTTCACCAACAACTTG
66 TGATTAGCTCCCCCATCAGCTTCCTCAATCTCATGAATTTCTTCCCCAAGTTCACCAACAACTTG
** * *
36561113 CTCGGTGCTTAAAGCAGTGGGCACTA
131 CTCAATGCCTAAAGCAATGGGCACTA
36561139 ACTTAGGCAT
Statistics
Matches: 137, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
191 137 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (191 bp):
CATCATTGATAGAATGACTCTTCCTAACTCTAGAGGAAGCTTGTACATAGTTATCAATGTGAATT
TGATTAGCTCCCCCATCAGCTTCCTCAATCTCATGAATTTCTTCCCCAAGTTCACCAACAACTTG
CTCAATGCCTAAAGCAATGGGCACTAGATCAGGTTCACATCATCATTGAGATCACCAATCA
Found at i:36570042 original size:121 final size:121
Alignment explanation
Indices: 36569828--36570085 Score: 417
Period size: 121 Copynumber: 2.1 Consensus size: 121
36569818 TTTGGAAACA
* *
36569828 AAGCGCCGCAAAAGGTAAAGCATTAGCGGCGCTTTCCATAAAGCGCCGCAAAAGGTAAAGCATTA
1 AAGCGCCGCAAAAGGTAAAACATTAGCGGCGCTTTCCACAAAGCGCCGCAAAAGGTAAAGCATTA
* *
36569893 GCGGCGCTTTGTAAAAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTTCTAT
66 GCGGCGCTTAGTAAAAAGCGCCGCTAAAGGTCGGATCATTAGCGGCGCTTTTCTAT
* *
36569949 AAGCGTCGCAAAAGGTAAAACATTAGCGGCGCTTTTCACAAAGCGCCGCAAAAGGTAAAGCATTA
1 AAGCGCCGCAAAAGGTAAAACATTAGCGGCGCTTTCCACAAAGCGCCGCAAAAGGTAAAGCATTA
* * * *
36570014 GCGGCGCTTAGTAGAAAGCGCCGCTAAAGGTCGGATCATTAGCGGCGCTTATATAA
66 GCGGCGCTTAGTAAAAAGCGCCGCTAAAGGTCGGATCATTAGCGGCGCTTTTCTAT
*
36570070 AAGCGCCGCTAAAGGT
1 AAGCGCCGCAAAAGGT
36570086 CGGGTCATTA
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 125 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.19
Consensus pattern (121 bp):
AAGCGCCGCAAAAGGTAAAACATTAGCGGCGCTTTCCACAAAGCGCCGCAAAAGGTAAAGCATTA
GCGGCGCTTAGTAAAAAGCGCCGCTAAAGGTCGGATCATTAGCGGCGCTTTTCTAT
Found at i:36570166 original size:42 final size:41
Alignment explanation
Indices: 36569809--36570206 Score: 308
Period size: 41 Copynumber: 9.8 Consensus size: 41
36569799 AGCGGCACTT
* ** * **
36569809 TTAGCGGCGTTTGGAAACAAAGCGCCGCAAAAGGTAAAG-CA
1 TTAGCGGCGCTTATAAA-AAAGCGCCGCTAAAGGTAGGGTCA
* * * **
36569850 TTAGCGGCGCTT-TCCATAAAGCGCCGCAAAAGGTAAAG-CA
1 TTAGCGGCGCTTAT-AAAAAAGCGCCGCTAAAGGTAGGGTCA
* *
36569890 TTAGCGGCGCTT-TGTAAAAAGCGCCGCTAAAGGTCGGGTCA
1 TTAGCGGCGCTTAT-AAAAAAGCGCCGCTAAAGGTAGGGTCA
* ** * * * ***
36569931 TTAGCGGCGCTTTTCTATAAGCGTCGCAAAAGGTA-AAACA
1 TTAGCGGCGCTTATAAAAAAGCGCCGCTAAAGGTAGGGTCA
* * * * **
36569971 TTAGCGGCGCTTTTCACAAAGCGCCGCAAAAGGTAAAG-CA
1 TTAGCGGCGCTTATAAAAAAGCGCCGCTAAAGGTAGGGTCA
* * *
36570011 TTAGCGGCGCTTAGT-AGAAAGCGCCGCTAAAGGTCGGATCA
1 TTAGCGGCGCTTA-TAAAAAAGCGCCGCTAAAGGTAGGGTCA
* *
36570052 TTAGCGGCGCTTATATAAAAGCGCCGCTAAAGGTCGGGTCA
1 TTAGCGGCGCTTATAAAAAAGCGCCGCTAAAGGTAGGGTCA
*
36570093 TTAGCGGCACTTATAAAAAAGCGCCGCTAAAGGTAGGGTCA
1 TTAGCGGCGCTTATAAAAAAGCGCCGCTAAAGGTAGGGTCA
* * * *
36570134 ATAGTGGCGCTTATAAAAAAAGCGCCGCTAAAGGTAAGAG-AA
1 TTAGCGGCGCTTAT-AAAAAAGCGCCGCTAAAGGT-AGGGTCA
* ** *
36570176 TCAGCGGCGCTTATGGAAAAGCGCTGCTAAA
1 TTAGCGGCGCTTATAAAAAAGCGCCGCTAAA
36570207 AGTCTAAGCA
Statistics
Matches: 299, Mismatches: 49, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
40 119 0.40
41 144 0.48
42 33 0.11
43 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGCTTATAAAAAAGCGCCGCTAAAGGTAGGGTCA
Found at i:36571722 original size:40 final size:40
Alignment explanation
Indices: 36571677--36571757 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
36571667 ATCTCTTTTC
36571677 AATTAATGTTCTTATGATTGTTTTATTATTTTTGTTTATG
1 AATTAATGTTCTTATGATTGTTTTATTATTTTTGTTTATG
36571717 AATTAATGTTCTTATGATTGTTTTATTATTTTTGTTTATG
1 AATTAATGTTCTTATGATTGTTTTATTATTTTTGTTTATG
36571757 A
1 A
36571758 TGCTTGTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.62
Consensus pattern (40 bp):
AATTAATGTTCTTATGATTGTTTTATTATTTTTGTTTATG
Found at i:36572082 original size:8 final size:8
Alignment explanation
Indices: 36572069--36572120 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
36572059 TAATTCAAAA
36572069 TATTTAAT
1 TATTTAAT
36572077 TATTTAAT
1 TATTTAAT
36572085 TATTTAAT
1 TATTTAAT
** *
36572093 TAAATATT
1 TATTTAAT
* *
36572101 TAATTAAA
1 TATTTAAT
36572109 TATTTAAT
1 TATTTAAT
36572117 TATT
1 TATT
36572121 AAAACAACCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TATTTAAT
Found at i:36572100 original size:12 final size:12
Alignment explanation
Indices: 36572052--36572118 Score: 80
Period size: 12 Copynumber: 5.1 Consensus size: 12
36572042 AAAACAACCC
36572052 AAATATTTAATT
1 AAATATTTAATT
36572064 CAAAATATTTAATT
1 --AAATATTTAATT
36572078 ATTTAATTATTTAATT
1 A---AA-TATTTAATT
36572094 AAATATTTAATT
1 AAATATTTAATT
36572106 AAATATTTAATT
1 AAATATTTAATT
36572118 A
1 A
36572119 TTAAAACAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
12 23 0.47
13 2 0.04
14 12 0.24
15 2 0.04
16 10 0.20
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (12 bp):
AAATATTTAATT
Found at i:36572100 original size:20 final size:20
Alignment explanation
Indices: 36572055--36572120 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
36572045 ACAACCCAAA
36572055 TATTTAATTCAAAATATTTAAT
1 TATTTAATT--AAATATTTAAT
** * *
36572077 TATTTAATTATTTAATTAAA
1 TATTTAATTAAATATTTAAT
36572097 TATTTAATTAAATATTTAAT
1 TATTTAATTAAATATTTAAT
36572117 TATT
1 TATT
36572121 AAAACAACCC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 27 0.75
22 9 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTAATTAAATATTTAAT
Found at i:36572146 original size:163 final size:158
Alignment explanation
Indices: 36571958--36572277 Score: 471
Period size: 163 Copynumber: 2.0 Consensus size: 158
36571948 TAAGTTAGAA
* **
36571958 AAAACAACCGAAATACTTCATTATTTAATTACTTAAATCAACCCAATTAATTAATTAATTAATTT
1 AAAACAACCCAAATACTGAATTATTTAATTACTTAAATCAACCCAATTAATTAATTAATTAA---
* * *
36572023 TTTATTTATATAAATATTAAAAACAACCCAAATA-TTTAATTCAAAATATTTAATTATTTAATTA
63 TTAATTAAT-TAAATATTAAAAACAACCCAAATATTTTAATTCAAAATATTTAATTATTTAATCA
*
36572087 TTTAATTAAATATTTAATTAAATATTTAATTATT
127 TAT-A-TAAATATTTAATTAAATATTTAATTATT
* * *
36572121 AAAACAACCCAAATACTGAATTATTTTATTATTTAAATCAACTCAATTAATTAATTAATTAATTA
1 AAAACAACCCAAATACTGAATTATTTAATTACTTAAATCAACCCAATTAATTAATTAATTAATTA
*
36572186 ATTAATTAAATATTAAAAACAACTCAAATATTTTAATTCAAAATATTTAATTATTTAATCATATA
66 ATTAATTAAATATTAAAAACAACCCAAATATTTTAATTCAAAATATTTAATTATTTAATCATATA
*
36572251 TAATTATTTAATTAAATATTTAATTAT
131 TAAATATTTAATTAAATATTTAATTAT
36572278 ATTAAAGTAA
Statistics
Matches: 144, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
158 26 0.18
159 24 0.17
160 38 0.26
163 56 0.39
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (158 bp):
AAAACAACCCAAATACTGAATTATTTAATTACTTAAATCAACCCAATTAATTAATTAATTAATTA
ATTAATTAAATATTAAAAACAACCCAAATATTTTAATTCAAAATATTTAATTATTTAATCATATA
TAAATATTTAATTAAATATTTAATTATT
Found at i:36572243 original size:22 final size:21
Alignment explanation
Indices: 36572217--36572323 Score: 86
Period size: 18 Copynumber: 5.3 Consensus size: 21
36572207 ACTCAAATAT
36572217 TTTAATTCAAAATATTTAATTA
1 TTTAATTC-AAATATTTAATTA
*
36572239 TTTAA-TC--ATATATAATTA
1 TTTAATTCAAATATTTAATTA
36572257 TTTAATT-AAATATTTAATTA
1 TTTAATTCAAATATTTAATTA
* *
36572277 TATTAAAGT-AAATAATT-A-TA
1 T-TT-AATTCAAATATTTAATTA
**
36572297 AATAATT-AAATATTTAATTA
1 TTTAATTCAAATATTTAATTA
36572317 TTTAATT
1 TTTAATT
36572324 ATATTAAAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
18 25 0.37
19 3 0.04
20 20 0.29
21 5 0.07
22 15 0.22
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (21 bp):
TTTAATTCAAATATTTAATTA
Found at i:36572327 original size:18 final size:18
Alignment explanation
Indices: 36572228--36572812 Score: 103
Period size: 18 Copynumber: 35.1 Consensus size: 18
36572218 TTAATTCAAA
*
36572228 ATATTTAATTATTTAATC
1 ATATTTAATTATTTAATT
*
36572246 ATATATAATTATTTAATT
1 ATATTTAATTATTTAATT
36572264 AAATATTTAATTATATTAA--
1 --ATATTTAATTAT-TTAATT
** *
36572283 AGTAAATAATTATAAATAATT
1 A-TATTTAATTAT--TTAATT
36572304 AAATATTTAATTATTTAATT
1 --ATATTTAATTATTTAATT
* * **
36572324 ATATTAAAGTAAATAATT
1 ATATTTAATTATTTAATT
36572342 ATA-TTAAGTTA---AA--
1 ATATTTAA-TTATTTAATT
*
36572355 AGATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
* * * **
36572373 ATGTTAAAGTAAATAATT
1 ATATTTAATTATTTAATT
*
36572391 ATA-TT-A--AGTTAA--
1 ATATTTAATTATTTAATT
*
36572403 AGATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
* * **
36572421 ATATTAAAGTAAATAATT
1 ATATTTAATTATTTAATT
36572439 ATA-TTAAGTTA---AA--
1 ATATTTAA-TTATTTAATT
*
36572452 AGATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
* * * **
36572470 ATGTTAAAGTAAATAATT
1 ATATTTAATTATTTAATT
**
36572488 ATA-TT-A--AGCTAA--
1 ATATTTAATTATTTAATT
*
36572500 AGATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
** * **
36572518 ATATGAAAGTAAATAATT
1 ATATTTAATTATTTAATT
36572536 ATA-TTAA--A-TTAA--
1 ATATTTAATTATTTAATT
36572548 ATATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
* * * **
36572566 ATGTTAAAGTAAATAATT
1 ATATTTAATTATTTAATT
*
36572584 ATA-TT-A--ATTTAA-A
1 ATATTTAATTATTTAATT
* *
36572597 AGATATAATTATTT-ATT
1 ATATTTAATTATTTAATT
* * **
36572614 ATATTAAACTAAATAATT
1 ATATTTAATTATTTAATT
36572632 ATA-TTAA--A-TTAA--
1 ATATTTAATTATTTAATT
*
36572644 ATATTTAATTACTTAATT
1 ATATTTAATTATTTAATT
* * **
36572662 ATATTAAAGTAAATAATT
1 ATATTTAATTATTTAATT
36572680 ATA-TTAA--A-TTAA--
1 ATATTTAATTATTTAATT
*
36572692 ATATTTAATTACTTAATT
1 ATATTTAATTATTTAATT
* * **
36572710 ATATTAAAGTAAATAATT
1 ATATTTAATTATTTAATT
36572728 ATA-TTAA--A-TTAA--
1 ATATTTAATTATTTAATT
36572740 ATATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
* * **
36572758 ATATTAAAGTAAATAATT
1 ATATTTAATTATTTAATT
* *
36572776 ATATTAAATTTTTTAATT
1 ATATTTAATTATTTAATT
* *
36572794 AAATTTAATCATTTAATT
1 ATATTTAATTATTTAATT
36572812 A
1 A
36572813 AAAAAACAAC
Statistics
Matches: 399, Mismatches: 103, Indels: 130
0.63 0.16 0.21
Matches are distributed among these distances:
12 16 0.04
13 32 0.08
14 35 0.09
15 13 0.03
16 33 0.08
17 33 0.08
18 203 0.51
19 4 0.01
20 16 0.04
21 4 0.01
22 9 0.02
23 1 0.00
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (18 bp):
ATATTTAATTATTTAATT
Found at i:36572567 original size:30 final size:30
Alignment explanation
Indices: 36572531--36572685 Score: 114
Period size: 30 Copynumber: 4.9 Consensus size: 30
36572521 TGAAAGTAAA
36572531 TAATTATATTAAATTAAATATTTAATTATT
1 TAATTATATTAAATTAAATATTTAATTATT
* * *
36572561 TAATTATGTTAAAGTAAATAATTATATTAATT
1 TAATTATATTAAATTAAATATTTA-ATT-ATT
* * * * * **
36572593 TAAAAGATATAATT-ATTTATTATATTAAACTAAA
1 T--AA-TTAT-ATTAAATTA-AATATTTAATTATT
*
36572627 TAATTATATTAAATTAAATATTTAATTACT
1 TAATTATATTAAATTAAATATTTAATTATT
* *
36572657 TAATTATATTAAAGTAAATAATTATATTA
1 TAATTATATTAAATTAAATATTTA-ATTA
36572686 AATTAAATAT
Statistics
Matches: 94, Mismatches: 22, Indels: 17
0.71 0.17 0.13
Matches are distributed among these distances:
30 55 0.59
31 14 0.15
32 6 0.06
34 4 0.04
35 8 0.09
36 7 0.07
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (30 bp):
TAATTATATTAAATTAAATATTTAATTATT
Found at i:36572783 original size:48 final size:48
Alignment explanation
Indices: 36572262--36572785 Score: 809
Period size: 48 Copynumber: 10.9 Consensus size: 48
36572252 AATTATTTAA
* * *
36572262 TTAAATATTTAATTATATTAAAGTAAATAATTATA-AATAATTAAATAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTA-AATTAAAGAT
*
36572310 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT-AAAGAT
* *
36572359 TTAATTATTTAATTATGTTAAAGTAAATAATTATATTAAGTTAAAGAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAGAT
*
36572407 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT-AAAGAT
* **
36572456 TTAATTATTTAATTATGTTAAAGTAAATAATTATATTAAGCTAAAGAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAGAT
* *
36572504 TTAATTATTTAATTATATGAAAGTAAATAATTATATTAAATTAAATAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAGAT
* *
36572552 TTAATTATTTAATTATGTTAAAGTAAATAATTATATTAATTTAAAAGAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT-AAAGAT
* * *
36572601 ATAATTATTT-ATTATATTAAACTAAATAATTATATTAAATTAAATAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAGAT
* *
36572648 TTAATTACTTAATTATATTAAAGTAAATAATTATATTAAATTAAATAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAGAT
* *
36572696 TTAATTACTTAATTATATTAAAGTAAATAATTATATTAAATTAAATAT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAGAT
36572744 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
1 TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
36572786 TTTTAATTAA
Statistics
Matches: 445, Mismatches: 26, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
47 13 0.03
48 325 0.73
49 107 0.24
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (48 bp):
TTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAGAT
Found at i:36578435 original size:66 final size:66
Alignment explanation
Indices: 36578329--36578485 Score: 217
Period size: 66 Copynumber: 2.4 Consensus size: 66
36578319 CAAATTGCTC
*
36578329 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
36578393 AA
65 AA
* ** *
36578395 AACTTAAAGAGGAGGTTGCATTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
36578460 C
66 A
* * *
36578461 AACTTAAAGTGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAACGAG
36578486 GCAAGCGGAG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 1 0.01
66 78 0.99
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:36578497 original size:21 final size:21
Alignment explanation
Indices: 36578471--36578522 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
36578461 AACTTAAAGT
36578471 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
*
36578492 GGAGGCAGCAGCTAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
* *
36578513 GAAGGAAGCA
1 GGAGGCAGCA
36578523 AAGGCTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.21, G:0.44, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGGCAAGC
Found at i:36578861 original size:42 final size:43
Alignment explanation
Indices: 36578810--36578965 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 43
36578800 CTGTTATATT
*
36578810 AGCGGCGCTTTAT-CAAAAGCGCCGTTAAAGAACATGGCCTTC
1 AGCGGCGCTTTATCCAAAAGCGCCGCTAAAGAACATGGCCTTC
* *** *
36578852 AGCGACGC-TTATGGGAAAGCGCCGCTAAAGAACATGGCCTTT
1 AGCGGCGCTTTATCCAAAAGCGCCGCTAAAGAACATGGCCTTC
* * * ** ** *
36578894 AGCGGCGCTTTTTCCACAAGCGCCGCTGAAGGCCATGTTCTTT
1 AGCGGCGCTTTATCCAAAAGCGCCGCTAAAGAACATGGCCTTC
*
36578937 AGCGGCGCTTTTTCGCATAAA-CGCCGCTA
1 AGCGGCGCTTTATC-CA-AAAGCGCCGCTA
36578966 TTTTTTGCGG
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
41 4 0.04
42 39 0.42
43 38 0.41
44 9 0.10
45 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.23
Consensus pattern (43 bp):
AGCGGCGCTTTATCCAAAAGCGCCGCTAAAGAACATGGCCTTC
Found at i:36603224 original size:31 final size:31
Alignment explanation
Indices: 36603162--36603224 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
36603152 AATCTCAACA
*
36603162 TTATGTATATTATTATATATAAATTTCAATT
1 TTATGTATATTATTATACATAAATTTCAATT
* * *
36603193 TTATGTA-ATTTTTTTACATAATATTTTAATT
1 TTATGTATATTATTATACATAA-ATTTCAATT
36603224 T
1 T
36603225 AAGTTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
TTATGTATATTATTATACATAAATTTCAATT
Found at i:36605117 original size:6 final size:6
Alignment explanation
Indices: 36605092--36605130 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
36605082 ACAATTCATA
* * *
36605092 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
36605131 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:36606923 original size:22 final size:22
Alignment explanation
Indices: 36606879--36606919 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
36606869 ATGTTACAAT
*
36606879 TAAAAATTATTTTATTAAATAA
1 TAAAAATTATTTTATAAAATAA
36606901 TAAAAATTA-TTTATAAAAT
1 TAAAAATTATTTTATAAAAT
36606920 TAATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAAAATTATTTTATAAAATAA
Found at i:36606960 original size:36 final size:35
Alignment explanation
Indices: 36606881--36606949 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
36606871 GTTACAATTA
36606881 AAAATT-ATTTTATTAAATAATAAAAATTATTTAT
1 AAAATTAATTTTATTAAATAATAAAAATTATTTAT
* * *
36606915 AAAATTAATTTTATTAAGTAGTAAATACTTATTTA
1 AAAATTAATTTTATTAAATAATAAA-AATTATTTA
36606950 ATAAGATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 6 0.20
35 16 0.53
36 8 0.27
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (35 bp):
AAAATTAATTTTATTAAATAATAAAAATTATTTAT
Found at i:36607059 original size:23 final size:25
Alignment explanation
Indices: 36607033--36607086 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
36607023 TTTTTAAATC
36607033 TAATTAT-AAATACATATA-AATA-T
1 TAATTATAAAAT-CATATATAATATT
36607056 TAA-TATAAAATCATATATAATATT
1 TAATTATAAAATCATATATAATATT
36607080 TAATTAT
1 TAATTAT
36607087 TTAAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 9 0.33
23 11 0.41
24 4 0.15
25 3 0.11
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATTATAAAATCATATATAATATT
Found at i:36611109 original size:20 final size:19
Alignment explanation
Indices: 36611066--36611105 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
36611056 TAGTCAATTT
*
36611066 AATA-ATTTTATAAATTAA
1 AATATATTTTATAAAATAA
*
36611084 AATATATTTTTTAAAATAA
1 AATATATTTTATAAAATAA
36611103 AAT
1 AAT
36611106 TATAGGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATATTTTATAAAATAA
Found at i:36611578 original size:19 final size:19
Alignment explanation
Indices: 36611537--36611578 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
36611527 TAACTAATTG
*
36611537 AAAATGATTTATTTTATTG
1 AAAATGATTTATTTTATTA
36611556 AAAATGATTTATTCTT-TTA
1 AAAATGATTTATT-TTATTA
36611575 AAAA
1 AAAA
36611579 ATTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (19 bp):
AAAATGATTTATTTTATTA
Found at i:36623364 original size:41 final size:41
Alignment explanation
Indices: 36623305--36623396 Score: 166
Period size: 41 Copynumber: 2.2 Consensus size: 41
36623295 AATAAATATA
36623305 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTGAT
1 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTGAT
* *
36623346 TGCAAACATTCATTTCACCAATGTCAATATGCATATCTGAT
1 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTGAT
36623387 TGCAAACACT
1 TGCAAACACT
36623397 AGAATTATGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (41 bp):
TGCAAACACTCATCTCACCAATGTCAATATGCATATCTGAT
Found at i:36625195 original size:23 final size:23
Alignment explanation
Indices: 36625168--36625211 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
36625158 AATTACATAC
36625168 AAGGA-CAAATTAAATTTAAACAA
1 AAGGATCAAA-TAAATTTAAACAA
*
36625191 AAGGATGAAATAAATTTAAAC
1 AAGGATCAAATAAATTTAAAC
36625212 TAAACTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (23 bp):
AAGGATCAAATAAATTTAAACAA
Found at i:36626756 original size:17 final size:16
Alignment explanation
Indices: 36626706--36626758 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
36626696 ACTGAAACAT
*
36626706 TGTTCT-AAACATAAC
1 TGTTCTCAAACATAGC
*
36626721 TATTC-CAAACATAGC
1 TGTTCTCAAACATAGC
*
36626736 TGTTCTCAAACAATAGT
1 TGTTCTCAAAC-ATAGC
36626753 TGTTCT
1 TGTTCT
36626759 GAACAACAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 16 0.52
16 5 0.16
17 10 0.32
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (16 bp):
TGTTCTCAAACATAGC
Found at i:36627567 original size:16 final size:16
Alignment explanation
Indices: 36627542--36627573 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36627532 TTTTGTTGAG
*
36627542 CATTGTCAAGACAAGA
1 CATTGACAAGACAAGA
36627558 CATTGACAAGACAAGA
1 CATTGACAAGACAAGA
36627574 GACTAGTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (16 bp):
CATTGACAAGACAAGA
Found at i:36637032 original size:5 final size:5
Alignment explanation
Indices: 36637022--36637054 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
36637012 AACTTCTCCC
36637022 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATG
1 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATG
36637055 AGTTACACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (5 bp):
ATGTG
Found at i:36637267 original size:2 final size:2
Alignment explanation
Indices: 36637260--36637293 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
36637250 CTAAAAACAA
36637260 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
36637294 GATATATATT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36639623 original size:26 final size:26
Alignment explanation
Indices: 36639593--36639649 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
36639583 ATGCTATTTT
36639593 TTTTTAGTTTTTATGAACT-TTTTAT-AA
1 TTTTTA-TTTTT-TGAA-TATTTTATAAA
36639620 TTTTTATTTTTTGAATATTTTATAAA
1 TTTTTATTTTTTGAATATTTTATAAA
36639646 TTTT
1 TTTT
36639650 AAATTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 1 0.04
25 10 0.36
26 11 0.39
27 6 0.21
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (26 bp):
TTTTTATTTTTTGAATATTTTATAAA
Found at i:36639640 original size:25 final size:27
Alignment explanation
Indices: 36639593--36639650 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
36639583 ATGCTATTTT
36639593 TTTTTAGTTTTTATGAACTTTTTATAA
1 TTTTTAGTTTTTATGAACTTTTTATAA
36639620 TTTTTA-TTTTT-TGAA-TATTTTATAA
1 TTTTTAGTTTTTATGAACT-TTTTATAA
*
36639645 ATTTTA
1 TTTTTA
36639651 AATTATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 1 0.03
25 17 0.59
26 5 0.17
27 6 0.21
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (27 bp):
TTTTTAGTTTTTATGAACTTTTTATAA
Found at i:36642481 original size:19 final size:19
Alignment explanation
Indices: 36642459--36642497 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
36642449 TTTAATTTTG
*
36642459 TTAATTATTTATA-ATATTT
1 TTAATT-TTTAAACATATTT
36642478 TTAATTTTTAAACATATTT
1 TTAATTTTTAAACATATTT
36642497 T
1 T
36642498 GTCAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATTTTTAAACATATTT
Found at i:36651583 original size:3 final size:3
Alignment explanation
Indices: 36651575--36651601 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
36651565 AAATTTCAAT
36651575 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
36651602 ACAAATTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:36664570 original size:17 final size:18
Alignment explanation
Indices: 36664538--36664571 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36664528 TTCTATTTCA
*
36664538 TTTAATATTTTATTCTTC
1 TTTAATATTATATTCTTC
36664556 TTTAATATTAT-TTCTT
1 TTTAATATTATATTCTT
36664572 ACAAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTAATATTATATTCTTC
Found at i:36687675 original size:14 final size:14
Alignment explanation
Indices: 36687653--36687686 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
36687643 ATCATTTTGC
36687653 TATTATATTACTAT
1 TATTATATTACTAT
* *
36687667 TATTTTATTATTAT
1 TATTATATTACTAT
36687681 TATTAT
1 TATTAT
36687687 TAGGATATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATATTACTAT
Found at i:36687821 original size:23 final size:25
Alignment explanation
Indices: 36687794--36687839 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
36687784 AATTTTTTTT
36687794 AATATAT-TTTTAA-ATTGTTAGAA
1 AATATATATTTTAATATTGTTAGAA
* *
36687817 AATATTTATTTTAATATTTTTAG
1 AATATATATTTTAATATTGTTAG
36687840 TGTACCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 6 0.32
25 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (25 bp):
AATATATATTTTAATATTGTTAGAA
Found at i:36699776 original size:29 final size:28
Alignment explanation
Indices: 36699697--36699779 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 28
36699687 CAATTAATTA
*
36699697 ATTTTTTAAATTTTAAAAAAATTCAAAAAAT
1 ATTTTTAAAATTTT--AAAAATT-AAAAAAT
* *
36699728 A-TTTTAATAAGTATAAAAATTATAAAAAT
1 ATTTTTAA-AATTTTAAAAATTA-AAAAAT
36699757 ATTTTTAAAATTTTAAAAATTAA
1 ATTTTTAAAATTTTAAAAATTAA
36699780 TTTTGGGGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
28 2 0.05
29 26 0.59
30 11 0.25
31 5 0.11
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
ATTTTTAAAATTTTAAAAATTAAAAAAT
Found at i:36699924 original size:17 final size:17
Alignment explanation
Indices: 36699886--36699931 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
36699876 TCATTTTGCC
36699886 TTTAATTTTTATGAACTT
1 TTTAATTTTT-TGAACTT
36699904 TTTATATTTTTTGAA-TT
1 TTTA-ATTTTTTGAACTT
36699921 TTTAATTTTTT
1 TTTAATTTTTT
36699932 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 8 0.30
19 6 0.22
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (17 bp):
TTTAATTTTTTGAACTT
Found at i:36699931 original size:18 final size:18
Alignment explanation
Indices: 36699886--36699944 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 18
36699876 TCATTTTGCC
36699886 TTTAA-TTTTTATGAACTT
1 TTTAATTTTTTATGAA-TT
36699904 TTT-ATATTTTT-TGAATT
1 TTTAAT-TTTTTATGAATT
36699921 TTTAATTTTTTAT-AATT
1 TTTAATTTTTTATGAATT
*
36699938 TTAAATT
1 TTTAATT
36699945 ATTGTTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 21 0.58
18 10 0.28
19 5 0.14
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTAATTTTTTATGAATT
Found at i:36708663 original size:30 final size:30
Alignment explanation
Indices: 36708585--36708664 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
36708575 TTATTATTTA
* * *
36708585 ATTAAAAAACTATAATTT-ATTTATTAAATT
1 ATTAAAAAA-TTTTATTTAATTTATTAAACT
*
36708615 ATTTAAAAATTTTCATTTAATTTATTAAACT
1 ATTAAAAAATTTT-ATTTAATTTATTAAACT
36708646 ATTAAAAAATTTTATTTAA
1 ATTAAAAAATTTTATTTAA
36708665 GGTATTAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 2 0.05
30 18 0.42
31 23 0.53
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTAAAAAATTTTATTTAATTTATTAAACT
Found at i:36708671 original size:30 final size:31
Alignment explanation
Indices: 36708606--36708671 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
36708596 ATAATTTATT
* * **
36708606 TATTAAATTATTTAAAAATTTTCATTTAATT
1 TATTAAACTATTAAAAAATTTTCATTTAAGG
36708637 TATTAAACTATTAAAAAATTTT-ATTTAAGG
1 TATTAAACTATTAAAAAATTTTCATTTAAGG
36708667 TATTA
1 TATTA
36708672 GATTGTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (31 bp):
TATTAAACTATTAAAAAATTTTCATTTAAGG
Found at i:36711561 original size:20 final size:20
Alignment explanation
Indices: 36711521--36711562 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
36711511 TTAAAAAAAC
* * *
36711521 TTTTGTCTCAAAATTATTTT
1 TTTTATCTCAAAAATACTTT
36711541 TTTTATCTCAAAAATACTTT
1 TTTTATCTCAAAAATACTTT
36711561 TT
1 TT
36711563 AAAAGTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTATCTCAAAAATACTTT
Found at i:36713378 original size:27 final size:26
Alignment explanation
Indices: 36713313--36713380 Score: 102
Period size: 25 Copynumber: 2.6 Consensus size: 26
36713303 ACTTTGATAA
*
36713313 GACACTCTGAAAGGAATGCCTTTGTG
1 GACACTCTAAAAGGAATGCCTTTGTG
*
36713339 G-CACTCTAAAAGGAATGCTTTTGTG
1 GACACTCTAAAAGGAATGCCTTTGTG
36713364 GCACACTCTAAAAGGAA
1 G-ACACTCTAAAAGGAA
36713381 AGTCCATGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 23 0.61
26 1 0.03
27 14 0.37
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (26 bp):
GACACTCTAAAAGGAATGCCTTTGTG
Found at i:36713433 original size:27 final size:27
Alignment explanation
Indices: 36713403--36713455 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
36713393 TGGCACGCTT
* *
36713403 TGAATGGACCATCTTTGTGGCGTACTC
1 TGAATGGACCACCCTTGTGGCGTACTC
*
36713430 TGAATGGACTACCCTTGTGGCGTACT
1 TGAATGGACCACCCTTGTGGCGTACT
36713456 TTGATAAGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (27 bp):
TGAATGGACCACCCTTGTGGCGTACTC
Found at i:36714280 original size:23 final size:21
Alignment explanation
Indices: 36714249--36714294 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
36714239 AATTACTTGA
36714249 TTAACTCAAATAACTTGAATTAT
1 TTAACTC-AA-AACTTGAATTAT
* *
36714272 TTAATTCAAAATTTGAATTAT
1 TTAACTCAAAACTTGAATTAT
36714293 TT
1 TT
36714295 TTCGAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 2 0.10
23 6 0.29
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAACTCAAAACTTGAATTAT
Found at i:36716880 original size:2 final size:2
Alignment explanation
Indices: 36716873--36716901 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36716863 AATATTTTTC
36716873 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
36716902 GTCTCATTTT
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:36718197 original size:24 final size:24
Alignment explanation
Indices: 36718159--36718409 Score: 263
Period size: 24 Copynumber: 10.5 Consensus size: 24
36718149 TAACCCATAG
* *
36718159 GAGCCCATAATGGTTAGCTCTTAC
1 GAGCCCAAAATGGTTAGCTCCTAC
* *
36718183 AAGCCCAAAACGGTTAGCTCCTAC
1 GAGCCCAAAATGGTTAGCTCCTAC
* *
36718207 GAG-CCAAGAATAGTTAGCTCTTAC
1 GAGCCCAA-AATGGTTAGCTCCTAC
* *
36718231 GAGCCCAAAATGATTAGCT-CTCAT
1 GAGCCCAAAATGGTTAGCTCCT-AC
* * *
36718255 GGGCCCAGAATAGTTAGCTCCTAC
1 GAGCCCAAAATGGTTAGCTCCTAC
*
36718279 GAGCCCAAAACGGTTAGCTCCTAC
1 GAGCCCAAAATGGTTAGCTCCTAC
* * * *
36718303 GAGCCTAGAATAGTTAGCTCTTAC
1 GAGCCCAAAATGGTTAGCTCCTAC
*
36718327 GAGCCCAGAATGGTTAGCTCCTAC
1 GAGCCCAAAATGGTTAGCTCCTAC
**
36718351 GAGCCTGAAATGGTTAGCTCCTAC
1 GAGCCCAAAATGGTTAGCTCCTAC
* * * *
36718375 GAGCCCAGAATAGTTAGCTCTTAA
1 GAGCCCAAAATGGTTAGCTCCTAC
36718399 GAGCCCAAAAT
1 GAGCCCAAAAT
36718410 CAGTATAACG
Statistics
Matches: 184, Mismatches: 39, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
23 5 0.03
24 173 0.94
25 6 0.03
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (24 bp):
GAGCCCAAAATGGTTAGCTCCTAC
Found at i:36718451 original size:27 final size:27
Alignment explanation
Indices: 36718407--36718467 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
36718397 AAGAGCCCAA
*
36718407 AATCAGTATAACGCTCTTTTGAGCCAG
1 AATCAGAATAACGCTCTTTTGAGCCAG
* *
36718434 AATCAGAATAATGTTCTTTTGAGCCAG
1 AATCAGAATAACGCTCTTTTGAGCCAG
36718461 AATCAGA
1 AATCAGA
36718468 TTACTCCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (27 bp):
AATCAGAATAACGCTCTTTTGAGCCAG
Found at i:36723988 original size:6 final size:6
Alignment explanation
Indices: 36723977--36724009 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
36723967 TATTTAGCCC
36723977 TCCTTT TCCTTT TCCTTT TCCTTT TCCTTT TCC
1 TCCTTT TCCTTT TCCTTT TCCTTT TCCTTT TCC
36724010 CTCCCTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
TCCTTT
Found at i:36724151 original size:6 final size:6
Alignment explanation
Indices: 36724135--36724224 Score: 157
Period size: 6 Copynumber: 15.3 Consensus size: 6
36724125 CTTCGTACCT
*
36724135 ACTCTC TCTCTC ACTCTC -CTCTC ACTCTC ACTCTC ACTCTC ACTCTC
1 ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC
36724182 ACTCTC ACTCTC -CTCTC ACTCTC ACTCTC ACTCTC ACTCTC AC
1 ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC AC
36724225 ATGTGAAACT
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
5 10 0.12
6 70 0.88
ACGTcount: A:0.14, C:0.51, G:0.00, T:0.34
Consensus pattern (6 bp):
ACTCTC
Found at i:36724192 original size:41 final size:41
Alignment explanation
Indices: 36724135--36724224 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
36724125 CTTCGTACCT
*
36724135 ACTCTCTCTCTCACTCTCCTCTCACTCTCACTCTCACTCTC
1 ACTCTCACTCTCACTCTCCTCTCACTCTCACTCTCACTCTC
36724176 ACTCTCACTCTCACTCTCCTCTCACTCTCACTCTCACTCTC
1 ACTCTCACTCTCACTCTCCTCTCACTCTCACTCTCACTCTC
36724217 ACTCTCAC
1 ACTCTCAC
36724225 ATGTGAAACT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.14, C:0.51, G:0.00, T:0.34
Consensus pattern (41 bp):
ACTCTCACTCTCACTCTCCTCTCACTCTCACTCTCACTCTC
Found at i:36727312 original size:8 final size:8
Alignment explanation
Indices: 36727299--36727342 Score: 88
Period size: 8 Copynumber: 5.5 Consensus size: 8
36727289 GTCATTTCTG
36727299 ATTAAAAA
1 ATTAAAAA
36727307 ATTAAAAA
1 ATTAAAAA
36727315 ATTAAAAA
1 ATTAAAAA
36727323 ATTAAAAA
1 ATTAAAAA
36727331 ATTAAAAA
1 ATTAAAAA
36727339 ATTA
1 ATTA
36727343 TGCTTTCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
ATTAAAAA
Found at i:36731685 original size:2 final size:2
Alignment explanation
Indices: 36731678--36731702 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36731668 CTATCCTTTC
36731678 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
36731703 GACTAAGACA
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:36734461 original size:12 final size:12
Alignment explanation
Indices: 36734444--36734481 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
36734434 ATATATAAAA
36734444 TTTTTAACTATT
1 TTTTTAACTATT
36734456 TTTTTATA-TAATT
1 TTTTTA-ACT-ATT
36734469 TTTTTAACTATT
1 TTTTTAACTATT
36734481 T
1 T
36734482 ATTATTATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAACTATT
Found at i:36735808 original size:3 final size:3
Alignment explanation
Indices: 36735800--36735828 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
36735790 CCAATAGAAC
36735800 GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
36735829 GTCGTTATCA
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:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:36745523 original size:23 final size:23
Alignment explanation
Indices: 36745460--36745541 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
36745450 ACATTGTTTG
*
36745460 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCGATTA-ATGTTCA
* * *
36745484 TGAACATGTTAGTTTAATGTTCG
1 TGAACATGTTCGATTAATGTTCA
*
36745507 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT-CA
36745530 TGAACATGTTCG
1 TGAACATGTTCG
36745542 TGAACATTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 3 0.06
23 33 0.67
24 13 0.27
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTCA
Found at i:36745551 original size:23 final size:23
Alignment explanation
Indices: 36745507--36745552 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
36745497 TTAATGTTCG
* *
36745507 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
36745530 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
36745553 CAAGCGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:36746893 original size:24 final size:24
Alignment explanation
Indices: 36746866--36746916 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
36746856 ATTGATCTTA
36746866 TACTCCTATTCGAAAGAAATATTG
1 TACTCCTATTCGAAAGAAATATTG
* *
36746890 TACTCCTGTTCGAAATAAATATTG
1 TACTCCTATTCGAAAGAAATATTG
36746914 TAC
1 TAC
36746917 AACATTCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (24 bp):
TACTCCTATTCGAAAGAAATATTG
Found at i:36749069 original size:3 final size:3
Alignment explanation
Indices: 36749061--36749088 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
36749051 TTGTTTCAGA
36749061 GGC GGC GGC GGC GGC GGC GGC GGC GGC G
1 GGC GGC GGC GGC GGC GGC GGC GGC GGC G
36749089 TAGGAGAGGA
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:0.00, C:0.32, G:0.68, T:0.00
Consensus pattern (3 bp):
GGC
Found at i:36750893 original size:18 final size:18
Alignment explanation
Indices: 36750865--36750908 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
36750855 TTTGTTTAAC
*
36750865 AATAC-TTTTATCTCAAG
1 AATACTTTTTATCTCAAA
36750882 AATACTTTTTATCTCAAA
1 AATACTTTTTATCTCAAA
36750900 AATA-TTTTT
1 AATACTTTTT
36750909 GAAAAACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (18 bp):
AATACTTTTTATCTCAAA
Found at i:36750999 original size:3 final size:3
Alignment explanation
Indices: 36750991--36751038 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
36750981 ATTGAATGCC
36750991 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36751039 GAACGGAGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36751098 original size:14 final size:14
Alignment explanation
Indices: 36751079--36751105 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36751069 ACCTCATCTT
36751079 ATATATAAAGAAAA
1 ATATATAAAGAAAA
36751093 ATATATAAAGAAA
1 ATATATAAAGAAA
36751106 GCAGTTGACG
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:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (14 bp):
ATATATAAAGAAAA
Found at i:36753108 original size:23 final size:23
Alignment explanation
Indices: 36753082--36753145 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
36753072 AGATGATATG
* *
36753082 CAGATGTATTTTACCCTTGATTT
1 CAGATGTACTCTACCCTTGATTT
* *
36753105 CAGATTTACTCTCCCCTTGATTT
1 CAGATGTACTCTACCCTTGATTT
* * *
36753128 TAGATTTACTCTCCCCTT
1 CAGATGTACTCTACCCTT
36753146 TTGAAGATCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.27, G:0.09, T:0.45
Consensus pattern (23 bp):
CAGATGTACTCTACCCTTGATTT
Found at i:36753904 original size:16 final size:17
Alignment explanation
Indices: 36753883--36753919 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
36753873 AATAGAATGA
36753883 AAATAAATTT-TTAATT
1 AAATAAATTTATTAATT
36753899 AAATAAATTTAATTAATT
1 AAATAAATTT-ATTAATT
36753917 AAA
1 AAA
36753920 ATTGTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATTTATTAATT
Found at i:36754566 original size:20 final size:20
Alignment explanation
Indices: 36754537--36754582 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36754527 ACATATTTAA
36754537 TTTA-ATTTAAGAAATA-AT
1 TTTACATTTAAGAAATAGAT
*
36754555 TTTCACATTTAATAAATAGAT
1 TTT-ACATTTAAGAAATAGAT
36754576 TTTACAT
1 TTTACAT
36754583 AGGTTTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.12
19 1 0.04
20 15 0.62
21 5 0.21
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (20 bp):
TTTACATTTAAGAAATAGAT
Found at i:36758329 original size:38 final size:39
Alignment explanation
Indices: 36758256--36758330 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
36758246 AAGTTAGAAT
*
36758256 TGATAAACGGATTAAATTGTAAAAGAAGCTATAAATTTTG
1 TGATAAACGGATTAAATTG-AAAAGAAACTATAAATTTTG
* * *
36758296 TGATAAAGGGATTAAATTG-AAAGAAATTTTAAATT
1 TGATAAACGGATTAAATTGAAAAGAAACTATAAATT
36758331 ATGGTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 13 0.42
40 18 0.58
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (39 bp):
TGATAAACGGATTAAATTGAAAAGAAACTATAAATTTTG
Found at i:36761384 original size:18 final size:18
Alignment explanation
Indices: 36761356--36761410 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
36761346 TTTTATTTTA
*
36761356 AATATATAATTAATATATT
1 AATAAATAATTAA-ATATT
*
36761375 -ATAAATAATTAAATTTT
1 AATAAATAATTAAATATT
*
36761392 AATAAATATTTTAAATATT
1 AATAAATA-ATTAAATATT
36761411 TTTTTCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.13
18 18 0.60
19 8 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAAATAATTAAATATT
Found at i:36766650 original size:30 final size:31
Alignment explanation
Indices: 36766608--36766678 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
36766598 ATATTTAATT
* * *
36766608 TTAAAAAATTGAATGGCTAAAATAAAAAAAA
1 TTAAATAATTGAATGACCAAAATAAAAAAAA
**
36766639 TT-AATAATTGAATGACCAAAATAAAATGAA
1 TTAAATAATTGAATGACCAAAATAAAAAAAA
36766669 TTAAATAATT
1 TTAAATAATT
36766679 AGATGACTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.28
Consensus pattern (31 bp):
TTAAATAATTGAATGACCAAAATAAAAAAAA
Found at i:36774170 original size:48 final size:48
Alignment explanation
Indices: 36774084--36774176 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 48
36774074 TTTTTCTAGA
*
36774084 TTTTTTTAATTTATTATTAATTAATATTATAATATAATA-ATATAAAT
1 TTTTTTTAATTTAGTATTAATTAATATTATAATATAATATATATAAAT
* *
36774131 TTTTATTTAA-TTAGTATTATATTATTATTATTAA-CTAATATATATA
1 TTTT-TTTAATTTAGTATTA-ATTAATATTA-TAATATAATATATATA
36774177 TGTATATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
47 12 0.31
48 19 0.49
49 8 0.21
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (48 bp):
TTTTTTTAATTTAGTATTAATTAATATTATAATATAATATATATAAAT
Found at i:36779693 original size:48 final size:48
Alignment explanation
Indices: 36779606--36779699 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 48
36779596 ATTTTTCTAG
*
36779606 TTTTTTTTAATTTATTATTAATTAATATTATAATATAATA-ATATAAA
1 TTTTTTTTAATTTAGTATTAATTAATATTATAATATAATATATATAAA
* *
36779653 TTTTTATTTAA-TTAGTATTATATTATTATTATTAA-CTAATATATATA
1 TTTTT-TTTAATTTAGTATTA-ATTAATATTA-TAATATAATATATATA
36779700 TGTATATGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
47 13 0.32
48 19 0.47
49 8 0.20
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (48 bp):
TTTTTTTTAATTTAGTATTAATTAATATTATAATATAATATATATAAA
Found at i:36782276 original size:19 final size:19
Alignment explanation
Indices: 36782252--36782291 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
36782242 AATCTGACAT
36782252 ATACAATTAGACTCAAGTA
1 ATACAATTAGACTCAAGTA
*
36782271 ATACAATTAGGCTCAAGTA
1 ATACAATTAGACTCAAGTA
36782290 AT
1 AT
36782292 TGTAATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
ATACAATTAGACTCAAGTA
Found at i:36783250 original size:29 final size:31
Alignment explanation
Indices: 36783186--36783254 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
36783176 AATGGGCTCG
*
36783186 AGTGACTGATTTGTCACTTTTTATATATGTA
1 AGTGACTGATTTGTCACTTTTTATAAATGTA
* *
36783217 AGTGACTGATTTGTTA-TTTTTA-AAA-GTTT
1 AGTGACTGATTTGTCACTTTTTATAAATG-TA
36783246 AGTGACTGA
1 AGTGACTGA
36783255 AATATAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.03
29 12 0.35
30 6 0.18
31 15 0.44
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (31 bp):
AGTGACTGATTTGTCACTTTTTATAAATGTA
Found at i:36790338 original size:30 final size:31
Alignment explanation
Indices: 36790281--36790341 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
36790271 TTCTATAGGT
36790281 AATTTTATTTTTATATAAAAAATAACTTAAA
1 AATTTTATTTTTATATAAAAAATAACTTAAA
36790312 AATTTTATTTTTATATAAAAAA-AACTTAAA
1 AATTTTATTTTTATATAAAAAATAACTTAAA
36790342 TAAAGCTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
AATTTTATTTTTATATAAAAAATAACTTAAA
Found at i:36790359 original size:33 final size:31
Alignment explanation
Indices: 36790291--36790369 Score: 79
Period size: 33 Copynumber: 2.5 Consensus size: 31
36790281 AATTTTATTT
* * *
36790291 TTATATAAAAAATAACTTAAAAATTTTATTT
1 TTATATAAAAAATAACTTAAAAACTTAATTA
36790322 TTATATAAAAAA-AACTTAAATAAAGCTTAATTA
1 TTATATAAAAAATAACTT-AA-AAA-CTTAATTA
* *
36790355 TTATATTAATAATAA
1 TTATATAAAAAATAA
36790370 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 5 0.13
31 14 0.36
32 3 0.08
33 15 0.38
34 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (31 bp):
TTATATAAAAAATAACTTAAAAACTTAATTA
Found at i:36790497 original size:21 final size:19
Alignment explanation
Indices: 36790457--36790505 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
36790447 TTATTTATAT
36790457 TTAATCATA-TAATAAATTA
1 TTAAT-ATATTAATAAATTA
36790476 TTAATATATTAATATAATTTA
1 TTAATATATTAATA-AA-TTA
36790497 TTAAT-TATT
1 TTAATATATT
36790506 TAACATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 3 0.11
19 10 0.37
20 6 0.22
21 8 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAATATATTAATAAATTA
Found at i:36790537 original size:13 final size:13
Alignment explanation
Indices: 36790521--36790609 Score: 51
Period size: 14 Copynumber: 6.5 Consensus size: 13
36790511 TTTCAATTTT
36790521 ATTTTAATAATAA
1 ATTTTAATAATAA
*
36790534 ATTTTAAAAATAATA
1 ATTTTAATAAT-A-A
36790549 ATTTT-A-AATAA
1 ATTTTAATAATAA
36790560 TATTCTTCACAT-A-AA
1 -ATT-TT-A-ATAATAA
*
36790575 ATATTTAATATTAA
1 AT-TTTAATAATAA
36790589 TATTTTAATAATAA
1 -ATTTTAATAATAA
36790603 ATATTTA
1 AT-TTTA
36790610 TTACAATTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 25
0.68 0.03 0.28
Matches are distributed among these distances:
11 1 0.02
12 6 0.10
13 18 0.30
14 22 0.37
15 11 0.18
16 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTAATAATAA
Found at i:36790547 original size:16 final size:16
Alignment explanation
Indices: 36790525--36790561 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
36790515 AATTTTATTT
36790525 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
36790542 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
36790557 TAATA
1 TAATA
36790562 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:36790602 original size:29 final size:27
Alignment explanation
Indices: 36790523--36790609 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 27
36790513 TCAATTTTAT
36790523 TTTAATAATAA-ATTTTAAAAATAATAAT-
1 TTTAAT-ATAATATTTT-AAAATAA-AATA
* *
36790551 TTTAA-ATAATATTCTTCACATAAAATA
1 TTTAATATAATATT-TTAAAATAAAATA
36790578 TTTAATATTAATATTTTAATAAT-AAATA
1 TTTAATA-TAATATTTTAA-AATAAAATA
36790606 TTTA
1 TTTA
36790610 TTACAATTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
26 7 0.14
27 13 0.27
28 20 0.41
29 9 0.18
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTAATATAATATTTTAAAATAAAATA
Found at i:36790607 original size:15 final size:15
Alignment explanation
Indices: 36790520--36790643 Score: 70
Period size: 13 Copynumber: 8.4 Consensus size: 15
36790510 ATTTCAATTT
36790520 TATTTTAATAAT-AA
1 TATTTTAATAATAAA
*
36790534 -ATTTTAAAAAT-AA
1 TATTTTAATAATAAA
36790547 TAATTTT-A-AAT-AA
1 T-ATTTTAATAATAAA
36790560 TATTCTTCACAT-A-AAA
1 TATT-TT-A-ATAATAAA
*
36790576 TA-TTTAAT-ATTAA
1 TATTTTAATAATAAA
36790589 TATTTTAATAATAAA
1 TATTTTAATAATAAA
*
36790604 TATTTATTACAATTATAAA
1 TA-TT-TT--AATAATAAA
*
36790623 TATATTAATAATAAA
1 TATTTTAATAATAAA
36790638 TATTTT
1 TATTTT
36790644 GTAGTATAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
12 6 0.07
13 25 0.28
14 9 0.10
15 25 0.28
16 8 0.09
17 4 0.05
18 1 0.01
19 10 0.11
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTTTAATAATAAA
Found at i:36791708 original size:2 final size:2
Alignment explanation
Indices: 36791701--36791732 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36791691 TGTAGCCTCT
36791701 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
36791733 CTATGCTTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:36806661 original size:24 final size:25
Alignment explanation
Indices: 36806616--36806662 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
36806606 GGAGAAAGAA
36806616 GGAAAAAAGAAAGCAGAAAAATTAT
1 GGAAAAAAGAAAGCAGAAAAATTAT
*
36806641 GGAAGAAA-AAAG-AGAAGAAATT
1 GGAAAAAAGAAAGCAGAA-AAATT
36806663 GATGTCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 9 0.45
25 7 0.35
ACGTcount: A:0.64, C:0.02, G:0.23, T:0.11
Consensus pattern (25 bp):
GGAAAAAAGAAAGCAGAAAAATTAT
Found at i:36808757 original size:8 final size:8
Alignment explanation
Indices: 36808744--36808769 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
36808734 TAGACTTCTG
36808744 TTATTTTA
1 TTATTTTA
36808752 TTATTTTA
1 TTATTTTA
36808760 TTATTTTA
1 TTATTTTA
36808768 TT
1 TT
36808770 TTTGAGAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTTTA
Found at i:36811003 original size:30 final size:29
Alignment explanation
Indices: 36810930--36811003 Score: 69
Period size: 30 Copynumber: 2.4 Consensus size: 29
36810920 AAGATTCAAC
*
36810930 GAAAAATAAAATTTTCCAAAAATTTTAAGG
1 GAAAAAT-AAATTTTCCAAAAATTTCAAGG
* **
36810960 GACCTAAAT-AATTTTTTAAAAATTTCAAGG
1 GA--AAAATAAATTTTCCAAAAATTTCAAGG
36810990 GAAAAATCAAATTT
1 GAAAAAT-AAATTT
36811004 CTCGAAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
28 4 0.11
30 27 0.77
32 4 0.11
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.32
Consensus pattern (29 bp):
GAAAAATAAATTTTCCAAAAATTTCAAGG
Found at i:36820640 original size:19 final size:19
Alignment explanation
Indices: 36820618--36820665 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
36820608 ATTTTAACTT
*
36820618 TTTTTCAATTTTAAA-ATAA
1 TTTTTAAATTTTAAATAT-A
*
36820637 TTTTTAAAATTTAAATATA
1 TTTTTAAATTTTAAATATA
36820656 TTTTTAAATT
1 TTTTTAAATT
36820666 CTTTACAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTAAATTTTAAATATA
Found at i:36820686 original size:8 final size:8
Alignment explanation
Indices: 36820652--36820712 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
36820642 AAAATTTAAA
36820652 TATATTTT
1 TATATTTT
*
36820660 TAAATTCTT
1 TATATT-TT
*
36820669 TACAATTTT
1 TA-TATTTT
36820678 TATATTTT
1 TATATTTT
* *
36820686 TTTATATT
1 TATATTTT
36820694 TATAATTTT
1 TAT-ATTTT
*
36820703 TATAATTT
1 TATATTTT
36820711 TA
1 TA
36820713 AATATAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 24 0.56
9 15 0.35
10 4 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (8 bp):
TATATTTT
Found at i:36820717 original size:25 final size:25
Alignment explanation
Indices: 36820652--36820717 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
36820642 AAAATTTAAA
*
36820652 TATATTTTTAAATTCTTTACAATTTT
1 TATATTTTTAAA-TATTTACAATTTT
** *
36820678 TATATTTTTTTATATTTATAATTTT
1 TATATTTTTAAATATTTACAATTTT
*
36820703 TATAATTTTAAATAT
1 TATATTTTTAAATAT
36820718 AAAATATTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
25 23 0.70
26 10 0.30
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (25 bp):
TATATTTTTAAATATTTACAATTTT
Found at i:36820839 original size:3 final size:3
Alignment explanation
Indices: 36820831--36820880 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
36820821 TTAACAATTG
36820831 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36820878 AAT
1 AAT
36820881 CGGTTTTGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:36821430 original size:3 final size:3
Alignment explanation
Indices: 36821422--36821460 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
36821412 TTAAGTTTGA
36821422 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
36821461 GTATTACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:36821769 original size:22 final size:23
Alignment explanation
Indices: 36821743--36821786 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
36821733 AAACACCTCT
*
36821743 AAAGT-AATAAAATTTACTTTGA
1 AAAGTAAAAAAAATTTACTTTGA
36821765 AAAGTAAAAAAAAATTTACTTT
1 AAAGT-AAAAAAAATTTACTTT
36821787 TTTTAAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
24 14 0.74
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (23 bp):
AAAGTAAAAAAAATTTACTTTGA
Found at i:36822841 original size:22 final size:20
Alignment explanation
Indices: 36822808--36822848 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
36822798 CATTTACTTG
*
36822808 AATAATCATGACTATTTTTT
1 AATAATCATGACAATTTTTT
36822828 AATAATCAAGTGACAATTTTT
1 AATAATC-A-TGACAATTTTT
36822849 GAATTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
AATAATCATGACAATTTTTT
Found at i:36829610 original size:21 final size:22
Alignment explanation
Indices: 36829577--36829618 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
36829567 ATAATTTTGC
*
36829577 CAAAATTGTGATTT-ATGTCAT
1 CAAAATTGAGATTTCATGTCAT
*
36829598 CAAATTTGAGATTTCATGTCA
1 CAAAATTGAGATTTCATGTCA
36829619 CGTATGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
CAAAATTGAGATTTCATGTCAT
Found at i:36842699 original size:32 final size:32
Alignment explanation
Indices: 36842653--36842716 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
36842643 TACATAACTG
*
36842653 AAGTGGTGTTTCTTAACAAGTTGAGCCTGTAT
1 AAGTAGTGTTTCTTAACAAGTTGAGCCTGTAT
***
36842685 AAGTAGTGTTTCTTAATGTGTTGAGCCTGTAT
1 AAGTAGTGTTTCTTAACAAGTTGAGCCTGTAT
36842717 GAGTGGCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (32 bp):
AAGTAGTGTTTCTTAACAAGTTGAGCCTGTAT
Found at i:36858077 original size:20 final size:21
Alignment explanation
Indices: 36858054--36858102 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
36858044 TTAGTTGTTC
36858054 CGGTAGAAGC-ATACTTGTAT
1 CGGTAGAAGCTATACTTGTAT
*
36858074 CGGTAGAA-CTATAGTTGTAT
1 CGGTAGAAGCTATACTTGTAT
*
36858094 CAGTAGAAG
1 CGGTAGAAG
36858103 AGGAGTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (21 bp):
CGGTAGAAGCTATACTTGTAT
Found at i:36858334 original size:20 final size:20
Alignment explanation
Indices: 36858306--36858345 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
36858296 AATCTTCAAG
36858306 GTATAGGTAGAAGTGGAGTT
1 GTATAGGTAGAAGTGGAGTT
* *
36858326 GTATCGGTAGAAGTTGAGTT
1 GTATAGGTAGAAGTGGAGTT
36858346 CTACCGGTAA
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:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (20 bp):
GTATAGGTAGAAGTGGAGTT
Found at i:36858353 original size:20 final size:20
Alignment explanation
Indices: 36858311--36858354 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
36858301 TCAAGGTATA
* *
36858311 GGTAGAAGTGGAGTTGTATC
1 GGTAGAAGTGGAGTTCTACC
*
36858331 GGTAGAAGTTGAGTTCTACC
1 GGTAGAAGTGGAGTTCTACC
36858351 GGTA
1 GGTA
36858355 AAAATCTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.30
Consensus pattern (20 bp):
GGTAGAAGTGGAGTTCTACC
Found at i:36864626 original size:21 final size:21
Alignment explanation
Indices: 36864600--36864642 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
36864590 CGTGGCTGGG
36864600 TTAATTGAGGGTGAGTTTGGA
1 TTAATTGAGGGTGAGTTTGGA
36864621 TTAATTGAGGGTGAGTTTGGA
1 TTAATTGAGGGTGAGTTTGGA
36864642 T
1 T
36864643 GGATGAGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (21 bp):
TTAATTGAGGGTGAGTTTGGA
Found at i:36876682 original size:2 final size:2
Alignment explanation
Indices: 36876675--36876702 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36876665 ACATCCTTAA
36876675 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
36876703 GTGCTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:36890986 original size:7 final size:7
Alignment explanation
Indices: 36890974--36891016 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
36890964 GGCGACCAAG
36890974 AATTTTC
1 AATTTTC
*
36890981 AATTTTTT
1 AA-TTTTC
*
36890989 AATTTTTT
1 AA-TTTTC
36890997 AATTTTC
1 AATTTTC
36891004 AATTTTC
1 AATTTTC
36891011 AATTTT
1 AATTTT
36891017 AGATTCGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 19 0.58
8 14 0.42
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (7 bp):
AATTTTC
Found at i:36893831 original size:21 final size:21
Alignment explanation
Indices: 36893785--36893823 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
36893775 TATGAGCAGA
36893785 TTTGAATATTTCAGGAAGGTT
1 TTTGAATATTTCAGGAAGGTT
*
36893806 CTTGAA-A-TTCAGGAAGGT
1 TTTGAATATTTCAGGAAGGT
36893824 ACTTTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 1 0.06
21 5 0.29
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.36
Consensus pattern (21 bp):
TTTGAATATTTCAGGAAGGTT
Found at i:36904683 original size:13 final size:13
Alignment explanation
Indices: 36904665--36904692 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36904655 GTTAGAGCTC
36904665 CTCAACTTGTTGT
1 CTCAACTTGTTGT
36904678 CTCAACTTGTTGT
1 CTCAACTTGTTGT
36904691 CT
1 CT
36904693 TAGTCGCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.46
Consensus pattern (13 bp):
CTCAACTTGTTGT
Found at i:36911634 original size:29 final size:31
Alignment explanation
Indices: 36911568--36911641 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
36911558 AAATTTTAAA
* *
36911568 TTAATAATAAT-AAAATTATACTTTGATTCTT
1 TTAA-AATAATAAAAATTATAATTTGAATCTT
*
36911599 TCAAAATAATAAAAATT-TAATTT-AATCTT
1 TTAAAATAATAAAAATTATAATTTGAATCTT
*
36911628 TTAAAATTATAAAA
1 TTAAAATAATAAAA
36911642 TATAAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 17 0.46
30 11 0.30
31 9 0.24
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAATAATAAAAATTATAATTTGAATCTT
Found at i:36911647 original size:7 final size:8
Alignment explanation
Indices: 36911628--36911665 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
36911618 ATTTAATCTT
36911628 TTAAAAT-
1 TTAAAATA
36911635 TATAAAATA
1 T-TAAAATA
36911644 -TAAAATA
1 TTAAAATA
36911651 TTAAAATA
1 TTAAAATA
36911659 TTAAAAT
1 TTAAAAT
36911666 TATATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 8 0.29
8 20 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TTAAAATA
Found at i:36911647 original size:15 final size:16
Alignment explanation
Indices: 36911628--36911669 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
36911618 ATTTAATCTT
36911628 TTAAAATTATAAAATA
1 TTAAAATTATAAAATA
36911644 -TAAAA-TATTAAAATA
1 TTAAAATTA-TAAAATA
36911659 TTAAAATTATA
1 TTAAAATTATA
36911670 TTTTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.09
15 12 0.52
16 7 0.30
17 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAATTATAAAATA
Found at i:36911649 original size:44 final size:45
Alignment explanation
Indices: 36911601--36911687 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
36911591 TGATTCTTTC
* * *
36911601 AAAATAATAAAA-ATTTAATTTA-ATCTTTTAAAATTATAAAATAT
1 AAAATAATAAAATATTAAAATTATAT-TTTTAAAATCATAAAATAT
* *
36911645 AAAATATTAAAATATTAAAATTATATTTTTAATATCATAAAAT
1 AAAATAATAAAATATTAAAATTATATTTTTAAAATCATAAAAT
36911688 TATATAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 11 0.31
45 23 0.64
46 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (45 bp):
AAAATAATAAAATATTAAAATTATATTTTTAAAATCATAAAATAT
Done.