Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 137 of 185
Found at i:42393261 original size:21 final size:22
Alignment explanation
Indices: 42393219--42393261 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
42393209 ACAAACTTTA
42393219 TCTAAGTTAAAATCATTTTTTT
1 TCTAAGTTAAAATCATTTTTTT
42393241 TCTAAGTTAAAATCATTTTTT
1 TCTAAGTTAAAATCATTTTTT
42393262 GGCAATCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (22 bp):
TCTAAGTTAAAATCATTTTTTT
Found at i:42395766 original size:20 final size:20
Alignment explanation
Indices: 42395741--42395778 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42395731 AGGAGTAGTT
*
42395741 TTTCAATCAATTTAAAAATG
1 TTTCAATCAAGTTAAAAATG
*
42395761 TTTCAATTAAGTTAAAAA
1 TTTCAATCAAGTTAAAAA
42395779 AAGTTTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTCAATCAAGTTAAAAATG
Found at i:42395784 original size:21 final size:20
Alignment explanation
Indices: 42395741--42395784 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
42395731 AGGAGTAGTT
* *
42395741 TTTCAATCAATTTAAAAATG
1 TTTCAATCAATTAAAAAAAG
*
42395761 TTTCAATTAAGTTAAAAAAAG
1 TTTCAATCAA-TTAAAAAAAG
42395782 TTT
1 TTT
42395785 AAACCATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (20 bp):
TTTCAATCAATTAAAAAAAG
Found at i:42399281 original size:33 final size:34
Alignment explanation
Indices: 42399223--42399314 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 34
42399213 TTATTAAATG
* *
42399223 CATCTTTAATTAATGTCTTGCATTAT-TGATCTA
1 CATCTTTAATTAATGACATGCATTATGTGATCTA
*
42399256 CATCATTTAATT-ATGACATGCATTATGTGGTCTA
1 CATC-TTTAATTAATGACATGCATTATGTGATCTA
* *
42399290 CA--TTTAA-TAAAGTCATGCATTATGT
1 CATCTTTAATTAATGACATGCATTATGT
42399315 TACTCTCATG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 19 0.37
33 16 0.31
34 15 0.29
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (34 bp):
CATCTTTAATTAATGACATGCATTATGTGATCTA
Found at i:42409924 original size:27 final size:27
Alignment explanation
Indices: 42409847--42409925 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 27
42409837 GTTAAATATA
*
42409847 AGATTGGTACCCGAACTTGTCCACTTATCCT
1 AGATTGGTACCCGAACTT-T---TTTATCCT
* *** *
42409878 AGATTGGTACCTGTGGTTTTTTTTCCT
1 AGATTGGTACCCGAACTTTTTTATCCT
42409905 AGATTGGTACCCGAACTTTTT
1 AGATTGGTACCCGAACTTTTT
42409926 CTCCGTCCAC
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
27 23 0.61
30 1 0.03
31 14 0.37
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (27 bp):
AGATTGGTACCCGAACTTTTTTATCCT
Found at i:42411171 original size:28 final size:29
Alignment explanation
Indices: 42411139--42411209 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
42411129 AAAAGTTTGG
* *
42411139 GTACCAATCTGGGA-TAAAAAAACCGTA-
1 GTACCAATCTGGGACAAAAAAAACCATAC
**
42411166 GCTACCAATCTAAGACAAAAAAAACCATAC
1 G-TACCAATCTGGGACAAAAAAAACCATAC
42411196 GTACCAATCTGGGA
1 GTACCAATCTGGGA
42411210 GAAGTGGACA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 1 0.03
28 11 0.31
29 22 0.63
30 1 0.03
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (29 bp):
GTACCAATCTGGGACAAAAAAAACCATAC
Found at i:42416904 original size:26 final size:26
Alignment explanation
Indices: 42416868--42417051 Score: 149
Period size: 26 Copynumber: 7.1 Consensus size: 26
42416858 ATGAAAAAGT
*
42416868 AGGCCTTGAACCGATGTTTATTTAGC
1 AGGCCTTGAGCCGATGTTTATTTAGC
* * * *
42416894 AGGCCTTGA-ACTAGTGGTTATTTAGT
1 AGGCCTTGAGCCGA-TGTTTATTTAGC
* *
42416920 AGGCCTCGAGCTTG-TGTTTATTTAGC
1 AGGCCTTGAGC-CGATGTTTATTTAGC
* * *
42416946 AGGCATTGAGCCAATG-TAATTTAGC
1 AGGCCTTGAGCCGATGTTTATTTAGC
* *
42416971 AGGCCTTGAGTCTATGTTTATTTAGC
1 AGGCCTTGAGCCGATGTTTATTTAGC
* * * * *
42416997 AGGCCTTGAGCAGGTGATTAGTTACC
1 AGGCCTTGAGCCGATGTTTATTTAGC
* * *
42417023 AGGCTTTGACCCGATGTATATTTAGC
1 AGGCCTTGAGCCGATGTTTATTTAGC
42417049 AGG
1 AGG
42417052 TACTACGTAC
Statistics
Matches: 119, Mismatches: 34, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
25 23 0.19
26 96 0.81
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (26 bp):
AGGCCTTGAGCCGATGTTTATTTAGC
Found at i:42416989 original size:51 final size:52
Alignment explanation
Indices: 42416881--42417007 Score: 159
Period size: 51 Copynumber: 2.5 Consensus size: 52
42416871 CCTTGAACCG
* * * * *
42416881 ATGTTTATTTAGCAGGCCTTGAACTAGTGGTTATTTAGTAGGCCTCGAGCTT
1 ATGTTTATTTAGCAGGCCTTGAGCCAATGGTAATTTAGCAGGCCTCGAGCTT
* * *
42416933 GTGTTTATTTAGCAGGCATTGAGCCAAT-GTAATTTAGCAGGCCTTGAG-TCT
1 ATGTTTATTTAGCAGGCCTTGAGCCAATGGTAATTTAGCAGGCCTCGAGCT-T
42416984 ATGTTTATTTAGCAGGCCTTGAGC
1 ATGTTTATTTAGCAGGCCTTGAGC
42417008 AGGTGATTAG
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 1 0.02
51 40 0.62
52 23 0.36
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (52 bp):
ATGTTTATTTAGCAGGCCTTGAGCCAATGGTAATTTAGCAGGCCTCGAGCTT
Found at i:42417026 original size:77 final size:78
Alignment explanation
Indices: 42416881--42417051 Score: 202
Period size: 77 Copynumber: 2.2 Consensus size: 78
42416871 CCTTGAACCG
* * ** * * *
42416881 ATGTTTATTTAGCAGGCCTTGAACTAGTGGTTATTTAGTAGGCCTCGAGCTTGTGTTTATTTAGC
1 ATGTATATTTAGCAGGCCTTGAACTAGTGGTTATTTAGCAGGCCTCGAGCAGGTGATTAGTTACC
*
42416946 AGGCATTGAGCCA
66 AGGCATTGACCCA
* * *
42416959 ATGTA-ATTTAGCAGGCCTTGAGTCTA-TGTTTATTTAGCAGGCCTTGAGCAGGTGATTAGTTAC
1 ATGTATATTTAGCAGGCCTTGA-ACTAGTGGTTATTTAGCAGGCCTCGAGCAGGTGATTAGTTAC
* *
42417022 CAGGCTTTGACCCG
65 CAGGCATTGACCCA
42417036 ATGTATATTTAGCAGG
1 ATGTATATTTAGCAGG
42417052 TACTACGTAC
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
77 61 0.78
78 17 0.22
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (78 bp):
ATGTATATTTAGCAGGCCTTGAACTAGTGGTTATTTAGCAGGCCTCGAGCAGGTGATTAGTTACC
AGGCATTGACCCA
Found at i:42434776 original size:62 final size:62
Alignment explanation
Indices: 42434705--42434829 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
42434695 ATGTCCGGAC
42434705 ATAGATTCTTTCTTTCTATGATATGACATATAATAATGTAGCTTGGAAAGTATCTATGTTAA
1 ATAGATTCTTTCTTTCTATGATATGACATATAATAATGTAGCTTGGAAAGTATCTATGTTAA
42434767 ATAGATTCTTTCTTTCTATGATATGACATATAATAATGTAGCTTGGAAAGTATCTATGTTAA
1 ATAGATTCTTTCTTTCTATGATATGACATATAATAATGTAGCTTGGAAAGTATCTATGTTAA
42434829 A
1 A
42434830 CATGTCCAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (62 bp):
ATAGATTCTTTCTTTCTATGATATGACATATAATAATGTAGCTTGGAAAGTATCTATGTTAA
Found at i:42437471 original size:14 final size:14
Alignment explanation
Indices: 42437452--42437478 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42437442 TTGGTAACTT
42437452 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
42437466 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
42437479 AGGCTTTTTT
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:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:42437635 original size:6 final size:6
Alignment explanation
Indices: 42437617--42437662 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
42437607 CGCGTTCTTC
* * *
42437617 TCCCCT CTCCCCT TCCCCT TCCCCT TTCCCT TTCCCT TTCCCT TCC
1 TCCCCT -TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCC
42437663 TCTTGGGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCCCT
Found at i:42437641 original size:19 final size:19
Alignment explanation
Indices: 42437617--42437658 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42437607 CGCGTTCTTC
42437617 TCCCCTCTCCCCTTCCCCT
1 TCCCCTCTCCCCTTCCCCT
* * *
42437636 TCCCCTTTCCCTTTCCCTT
1 TCCCCTCTCCCCTTCCCCT
42437655 TCCC
1 TCCC
42437659 TTCCTCTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (19 bp):
TCCCCTCTCCCCTTCCCCT
Found at i:42449131 original size:14 final size:14
Alignment explanation
Indices: 42449112--42449138 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42449102 TTGGTAACTT
42449112 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
42449126 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
42449139 AGGCTTTTTT
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:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:42449296 original size:6 final size:6
Alignment explanation
Indices: 42449278--42449323 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
42449268 CGCGTTCTTC
* * *
42449278 TCCCCT CTCCCCT TCCCCT TCCCCT TTCCCT TTCCCT TTCCCT TCC
1 TCCCCT -TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCC
42449324 TCTTGGGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCCCT
Found at i:42449302 original size:19 final size:19
Alignment explanation
Indices: 42449278--42449319 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42449268 CGCGTTCTTC
42449278 TCCCCTCTCCCCTTCCCCT
1 TCCCCTCTCCCCTTCCCCT
* * *
42449297 TCCCCTTTCCCTTTCCCTT
1 TCCCCTCTCCCCTTCCCCT
42449316 TCCC
1 TCCC
42449320 TTCCTCTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (19 bp):
TCCCCTCTCCCCTTCCCCT
Found at i:42451254 original size:29 final size:28
Alignment explanation
Indices: 42451222--42451282 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
42451212 AAAAACCTGT
*
42451222 TTTTTTCAAAATTTCCCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** *
42451251 TTTTTTGATTATTTACCGGAATGGGCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
42451279 TTTT
1 TTTT
42451283 CTACGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:42453163 original size:20 final size:20
Alignment explanation
Indices: 42453138--42453177 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
42453128 AAATATTTTC
*
42453138 AGTAAATCATTTTCTAGAAA
1 AGTAAATCATTTTCCAGAAA
42453158 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
42453178 TAATTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:42453184 original size:34 final size:33
Alignment explanation
Indices: 42453128--42453192 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
42453118 AAATACCAGA
*
42453128 AAATATTTTCAGTAAATCATTTTCTA-GAAAAGT
1 AAATATTTTCAGTAAATAATTTT-TAGGAAAAGT
42453161 AAATCATTTTCCAG-AAATAATTTTTAGGAAAA
1 AAAT-ATTTT-CAGTAAATAATTTTTAGGAAAA
42453193 CATTTTACTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 6 0.21
34 19 0.68
35 3 0.11
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (33 bp):
AAATATTTTCAGTAAATAATTTTTAGGAAAAGT
Found at i:42462119 original size:69 final size:69
Alignment explanation
Indices: 42462034--42462198 Score: 217
Period size: 69 Copynumber: 2.4 Consensus size: 69
42462024 AAGAGGTTTA
* *
42462034 ACCATAGCTCGACTATGGAAACCAATAGAGTCTGATGGGACAGTAAACACGGTGATTTTAAGGTG
1 ACCATAGCTCGACTATGGAAACCAATAGAGTCTGATGGGACAGTAAACACGGGGATTTCAAGGTG
42462099 TAAG
66 TAAG
* * * * * *
42462103 ACCATAGCTC-AGCTATGGCAACCGATAGAGTCTGCTGGGATAGTTAACATGGGGATTTCAAGGT
1 ACCATAGCTCGA-CTATGGAAACCAATAGAGTCTGATGGGACAGTAAACACGGGGATTTCAAGGT
42462167 GTAAG
65 GTAAG
*
42462172 ACAATAGCTCGACTAT-GACAACCAATA
1 ACCATAGCTCGACTATGGA-AACCAATA
42462199 AAGCTCGCAG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
68 2 0.02
69 79 0.96
70 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (69 bp):
ACCATAGCTCGACTATGGAAACCAATAGAGTCTGATGGGACAGTAAACACGGGGATTTCAAGGTG
TAAG
Found at i:42467521 original size:28 final size:28
Alignment explanation
Indices: 42467479--42467534 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
42467469 TACTTGATGT
42467479 CAATGCCCTCAAGATAATTAGATTTTCA
1 CAATGCCCTCAAGATAATTAGATTTTCA
* *
42467507 CAATGCCCTCTAGATAATTGGATTTTCA
1 CAATGCCCTCAAGATAATTAGATTTTCA
42467535 TTCTTAGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (28 bp):
CAATGCCCTCAAGATAATTAGATTTTCA
Found at i:42472120 original size:13 final size:13
Alignment explanation
Indices: 42472102--42472127 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42472092 TTGGTTCTCC
42472102 AAAATGAAAATGA
1 AAAATGAAAATGA
42472115 AAAATGAAAATGA
1 AAAATGAAAATGA
42472128 CTTGGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:42481390 original size:25 final size:25
Alignment explanation
Indices: 42481355--42481405 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
42481345 ACGGATTACC
*
42481355 TGTAAGGCCTTCATGGT-AGACTCTT
1 TGTAAGACCTTCATGGTGA-ACTCTT
*
42481380 TGTAAGACCTTTATGGTGAACTCTT
1 TGTAAGACCTTCATGGTGAACTCTT
42481405 T
1 T
42481406 ATAAAGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (25 bp):
TGTAAGACCTTCATGGTGAACTCTT
Found at i:42481416 original size:25 final size:25
Alignment explanation
Indices: 42481361--42481444 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 25
42481351 TACCTGTAAG
* * *
42481361 GCCTTCATGGTAGACTCTTTGT-AA
1 GCCTTTATGGTAAACTCTTTATAAA
*
42481385 GACCTTTATGGTGAACTCTTTATAAA
1 G-CCTTTATGGTAAACTCTTTATAAA
* ** * *
42481411 GTCTTTGGGGTAAACTTTTTGTAAA
1 GCCTTTATGGTAAACTCTTTATAAA
42481436 GCCTTTATG
1 GCCTTTATG
42481445 ACGAACTGTT
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
24 1 0.02
25 41 0.91
26 3 0.07
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (25 bp):
GCCTTTATGGTAAACTCTTTATAAA
Found at i:42483284 original size:14 final size:15
Alignment explanation
Indices: 42483259--42483289 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
42483249 ATTAACAAGG
42483259 TAAATAAAAAATATT
1 TAAATAAAAAATATT
42483274 TAAAT-AAAAATATT
1 TAAATAAAAAATATT
42483288 TA
1 TA
42483290 CTTAACTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATAAAAAATATT
Found at i:42485152 original size:17 final size:17
Alignment explanation
Indices: 42485125--42485157 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42485115 TCACTACATT
42485125 TTTATTTCACATATTCAC
1 TTTATTTCACA-ATTCAC
42485143 TTTA-TTCACAATTCA
1 TTTATTTCACAATTCA
42485158 TAAAATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTCACAATTCAC
Found at i:42485376 original size:21 final size:20
Alignment explanation
Indices: 42485339--42485382 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
42485329 TTCAACAATT
* *
42485339 ATTATATCACTTTACACTCC
1 ATTATATCACATAACACTCC
*
42485359 ATTACTATCACATAACACTTC
1 ATTA-TATCACATAACACTCC
42485380 ATT
1 ATT
42485383 TAAGTCTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATATCACATAACACTCC
Found at i:42488591 original size:24 final size:24
Alignment explanation
Indices: 42488556--42488601 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42488546 AATGTTACAT
42488556 AAATTTACTATGT-TCTATTATTCA
1 AAATTTACTATGTATC-ATTATTCA
*
42488580 AAATTTATTATGTATCATTATT
1 AAATTTACTATGTATCATTATT
42488602 TAAATTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (24 bp):
AAATTTACTATGTATCATTATTCA
Found at i:42488877 original size:28 final size:29
Alignment explanation
Indices: 42488844--42488922 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 29
42488834 TTCTTTCCGC
42488844 TATTTTAACATTTTAATTTATCTC-AACT
1 TATTTTAACATTTTAATTTATCTCAAACT
** *
42488872 TATTTTAGTATTGTTAATTTAT-TCAAATT
1 TATTTTAACATT-TTAATTTATCTCAAACT
*
42488901 TATTTTAACCTTTTAATTTATC
1 TATTTTAACATTTTAATTTATC
42488923 CATGTTATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 21 0.50
29 21 0.50
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (29 bp):
TATTTTAACATTTTAATTTATCTCAAACT
Found at i:42496422 original size:8 final size:8
Alignment explanation
Indices: 42496409--42496433 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42496399 TTTCGAGCAA
42496409 TTATTCTT
1 TTATTCTT
42496417 TTATTCTT
1 TTATTCTT
42496425 TTATTCTT
1 TTATTCTT
42496433 T
1 T
42496434 CCAAGCGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTCTT
Found at i:42500211 original size:44 final size:44
Alignment explanation
Indices: 42500143--42500236 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
42500133 TAGATCACAT
*
42500143 CAGATTGAAGCAAAAAATCTTATCTCCCTCAGATTACAGCGGAG
1 CAGATTGAAGCAAAAAATCCTATCTCCCTCAGATTACAGCGGAG
* ** * *
42500187 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCAAAAAATCCTATCTCCCTCAGATTACAGCGGAG
42500231 CAGATT
1 CAGATT
42500237 AAAATAAAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (44 bp):
CAGATTGAAGCAAAAAATCCTATCTCCCTCAGATTACAGCGGAG
Found at i:42500301 original size:142 final size:142
Alignment explanation
Indices: 42500068--42500337 Score: 434
Period size: 142 Copynumber: 1.9 Consensus size: 142
42500058 CAGGTCTTAG
*
42500068 CTCCCTGAGATTACAGTGGAGAGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAG
1 CTCCCTGAGATTACAGTGGAGAGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAG
* *
42500133 TAGATCACATCAGATTGAAGCAAAAAATCTTATCTCCCTCAGATTACAGCGGAGCAGATTGAAGC
66 TAGATCACATCAGATTGAAGCAAAAAATCTTATCTCCCTCAGATTACAACAGAGCAGATTGAAGC
42500198 TAGTAATCCTAT
131 TAGTAATCCTAT
*
42500210 CTCCCTGAGATTACAGTGGAGCA-GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACTGTAGA
1 CTCCCTGAGATTACAGTGGAG-AGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGA
* * * * * *
42500274 GTAGATCGCATTAGATTGAAGCTAAAAATCTTATCTCCCTGATATTACAACAGAGTAGATTGAA
65 GTAGATCACATCAGATTGAAGCAAAAAATCTTATCTCCCTCAGATTACAACAGAGCAGATTGAA
42500338 ACAAGTGTGT
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
142 116 0.99
143 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (142 bp):
CTCCCTGAGATTACAGTGGAGAGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAG
TAGATCACATCAGATTGAAGCAAAAAATCTTATCTCCCTCAGATTACAACAGAGCAGATTGAAGC
TAGTAATCCTAT
Found at i:42505059 original size:21 final size:20
Alignment explanation
Indices: 42505026--42505067 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
42505016 TGAAGATAGG
*
42505026 AGCATACATAAGA-GATATTC
1 AGCATACAAAAGATGAT-TTC
42505046 AGCAGTACAAAAGATGATTTC
1 AGCA-TACAAAAGATGATTTC
42505067 A
1 A
42505068 AAGCATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 12 0.63
22 3 0.16
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (20 bp):
AGCATACAAAAGATGATTTC
Found at i:42515639 original size:272 final size:272
Alignment explanation
Indices: 42515153--42515697 Score: 1063
Period size: 272 Copynumber: 2.0 Consensus size: 272
42515143 GGGGGGGAGC
42515153 TTTTTTCAGGAAGTGATATTCATCTGGCTTTTACTGAAATACAGGGAGGATAGTGCAGCCATATA
1 TTTTTTCAGGAAGTGATATTCATCTGGCTTTTACTGAAATACAGGGAGGATAGTGCAGCCATATA
*
42515218 AAGCTTTATACCTTTTAACTTTCAGCTATTTTCATTCTCTGTTGTACTTACTGCTGGTTATATGT
66 AAGCTTTATACCTGTTAACTTTCAGCTATTTTCATTCTCTGTTGTACTTACTGCTGGTTATATGT
42515283 TATGATTTAGTGCAACTAGAGAGTACTCGACAAAGTATACCCACTTCTCATGGCAGCTTTACTGG
131 TATGATTTAGTGCAACTAGAGAGTACTCGACAAAGTATACCCACTTCTCATGGCAGCTTTACTGG
42515348 GCATCAGTGATGGGGTATTGAATATGCAACTTAGTGCTTTACATGTTCTACTTTCTAAGCATGAC
196 GCATCAGTGATGGGGTATTGAATATGCAACTTAGTGCTTTACATGTTCTACTTTCTAAGCATGAC
42515413 ATGGTATGAACT
261 ATGGTATGAACT
42515425 TTTTTTCAGGAAGTGATATTCATCTGGCTTTTACTGAAATACAGGGAGGATAGTGCAGCCATATA
1 TTTTTTCAGGAAGTGATATTCATCTGGCTTTTACTGAAATACAGGGAGGATAGTGCAGCCATATA
42515490 AAGCTTTATACCTGTTAACTTTCAGCTATTTTCATTCTCTGTTGTACTTACTGCTGGTTATATGT
66 AAGCTTTATACCTGTTAACTTTCAGCTATTTTCATTCTCTGTTGTACTTACTGCTGGTTATATGT
*
42515555 TATGATTTAGTGCAACTAGAGAGTACTCGGCAAAGTATACCCACTTCTCATGGCAGCTTTACTGG
131 TATGATTTAGTGCAACTAGAGAGTACTCGACAAAGTATACCCACTTCTCATGGCAGCTTTACTGG
*
42515620 GCATCGGTGATGGGGTATTGAATATGCAACTTAGTGCTTTACATGTTCTACTTTCTAAGCATGAC
196 GCATCAGTGATGGGGTATTGAATATGCAACTTAGTGCTTTACATGTTCTACTTTCTAAGCATGAC
42515685 ATGGTATGAACT
261 ATGGTATGAACT
42515697 T
1 T
42515698 ATTTCCCTGT
Statistics
Matches: 270, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
272 270 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (272 bp):
TTTTTTCAGGAAGTGATATTCATCTGGCTTTTACTGAAATACAGGGAGGATAGTGCAGCCATATA
AAGCTTTATACCTGTTAACTTTCAGCTATTTTCATTCTCTGTTGTACTTACTGCTGGTTATATGT
TATGATTTAGTGCAACTAGAGAGTACTCGACAAAGTATACCCACTTCTCATGGCAGCTTTACTGG
GCATCAGTGATGGGGTATTGAATATGCAACTTAGTGCTTTACATGTTCTACTTTCTAAGCATGAC
ATGGTATGAACT
Found at i:42530780 original size:22 final size:22
Alignment explanation
Indices: 42530755--42530820 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 22
42530745 CATACATATT
42530755 TAATTATTTATATTTAATAATA
1 TAATTATTTATATTTAATAATA
* * *
42530777 TAATAAATTATTAGTATAATTAATA
1 TAATTATTTA-TA-TTTAA-TAATA
42530802 TAATT-TATTAT-TTTAATAA
1 TAATTAT-TTATATTTAATAA
42530821 ATTATTCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
21 3 0.09
22 12 0.35
23 2 0.06
24 5 0.15
25 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATTATTTATATTTAATAATA
Found at i:42530825 original size:16 final size:19
Alignment explanation
Indices: 42530777--42530826 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
42530767 TTTAATAATA
42530777 TAATAAATTATTAGTATAAT
1 TAATAAATTATTAGTAT-AT
42530797 TAATATAATTTATTA-T-T-T
1 TAATA-AA-TTATTAGTATAT
42530815 TAATAAATTATT
1 TAATAAATTATT
42530827 CAATATTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.18
17 2 0.07
18 6 0.21
20 6 0.21
21 3 0.11
22 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAGTATAT
Found at i:42530874 original size:15 final size:16
Alignment explanation
Indices: 42530847--42530877 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42530837 AATTTATTTG
42530847 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
42530863 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
42530878 GTTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:42531073 original size:31 final size:30
Alignment explanation
Indices: 42531011--42531074 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
42531001 ATAAATTTGG
* ** *
42531011 AATTTAGTCCTTATACTTTTATTTTTTAAA
1 AATTTAGTCCCTATACTTTTAGATTTCAAA
*
42531041 AATTTAGTCCCTCTACTTTTTAGATTTCAAA
1 AATTTAGTCCCTATAC-TTTTAGATTTCAAA
42531072 AAT
1 AAT
42531075 CCAGGTTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (30 bp):
AATTTAGTCCCTATACTTTTAGATTTCAAA
Found at i:42537128 original size:19 final size:20
Alignment explanation
Indices: 42537104--42537143 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
42537094 CTTATATAAC
42537104 TTAATTAA-TATTTTAAACT
1 TTAATTAATTATTTTAAACT
42537123 TTAATTAATTATTTTAAACT
1 TTAATTAATTATTTTAAACT
42537143 T
1 T
42537144 GATTAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATTAATTATTTTAAACT
Found at i:42537148 original size:19 final size:18
Alignment explanation
Indices: 42537101--42537149 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
42537091 TTCCTTATAT
42537101 AACTTAATTAATATTTTA
1 AACTTAATTAATATTTTA
42537119 AACTTTAATTAATTATTTTA
1 AAC-TTAATTAA-TATTTTA
*
42537139 AACTTGATTAA
1 AACTTAATTAA
42537150 CATAACACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 3 0.11
19 15 0.54
20 10 0.36
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (18 bp):
AACTTAATTAATATTTTA
Found at i:42544596 original size:32 final size:32
Alignment explanation
Indices: 42544545--42544741 Score: 197
Period size: 32 Copynumber: 6.3 Consensus size: 32
42544535 GAATGGCTAC
* * * *
42544545 AAGCCATAAGT-ACAGTAATATGATTGACACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
42544576 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
42544608 CAGTCATCAGTAATAGTAGTATGATCGGCATA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
42544640 AGGCCAT---TAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
42544669 CAA-CCATCAATAATGGTAATATGATCGGCACA
1 -AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
42544701 TAGCCATCAGTAATGGTAATATAATCGACACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
42544733 AAGCCATCA
1 AAGCCATCA
42544742 AAAGCATCGC
Statistics
Matches: 136, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
29 23 0.17
30 1 0.01
31 11 0.08
32 101 0.74
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:42544707 original size:61 final size:60
Alignment explanation
Indices: 42544558--42544712 Score: 175
Period size: 61 Copynumber: 2.5 Consensus size: 60
42544548 CCATAAGTAC
* * ** *
42544558 AGTAATATGATTGACACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGTCATCAGTAAT
1 AGTAATATGATCGGCAC-AAGCCAT---TAGTAGTAATATGATCGGCACACAACCATCAATAAT
* *
42544622 AGTAGTATGATCGGCATAAGGCCATTAGTAGTAATATGATCGGCACACAACCATCAATAAT
1 AGTAATATGATCGGCACAA-GCCATTAGTAGTAATATGATCGGCACACAACCATCAATAAT
* *
42544683 GGTAATATGATCGGCACATAGCCATCAGTA
1 AGTAATATGATCGGCACA-AGCCATTAGTA
42544713 ATGGTAATAT
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
61 57 0.73
62 1 0.01
63 2 0.03
64 18 0.23
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (60 bp):
AGTAATATGATCGGCACAAGCCATTAGTAGTAATATGATCGGCACACAACCATCAATAAT
Found at i:42544739 original size:93 final size:93
Alignment explanation
Indices: 42544558--42544739 Score: 231
Period size: 93 Copynumber: 2.0 Consensus size: 93
42544548 CCATAAGTAC
* * * *
42544558 AGTAATATGATTGACACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGTCATCAGTAATA
1 AGTAATATGATCGACACAAAGCCATCAATAATAGTAATATGATCGGCACACAGCCATCAGTAATA
* * * * *
42544623 GTAGTATGATCGGCATAAGGCCATTAGT
66 GTAATATAATCGACACAAAGCCATTAGT
* * *
42544651 AGTAATATGATCGGCACACAA-CCATCAATAATGGTAATATGATCGGCACATAGCCATCAGTAAT
1 AGTAATATGATCGACACA-AAGCCATCAATAATAGTAATATGATCGGCACACAGCCATCAGTAAT
*
42544715 GGTAATATAATCGACACAAAGCCAT
65 AGTAATATAATCGACACAAAGCCAT
42544740 CAAAAGCATC
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
93 73 0.97
94 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.24
Consensus pattern (93 bp):
AGTAATATGATCGACACAAAGCCATCAATAATAGTAATATGATCGGCACACAGCCATCAGTAATA
GTAATATAATCGACACAAAGCCATTAGT
Found at i:42544799 original size:26 final size:26
Alignment explanation
Indices: 42544750--42544801 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
42544740 CAAAAGCATC
*
42544750 GCAGCAAAGCAGCTAGCAACAGTATA
1 GCAGCAAAGCAGCCAGCAACAGTATA
* * *
42544776 GCAGCAAAGCTGCCAGTAATAGTATA
1 GCAGCAAAGCAGCCAGCAACAGTATA
42544802 TGTGGCCAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.15
Consensus pattern (26 bp):
GCAGCAAAGCAGCCAGCAACAGTATA
Found at i:42544947 original size:24 final size:24
Alignment explanation
Indices: 42544915--42544972 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
42544905 CCATGCACGG
42544915 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
**
42544939 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
42544963 AATTAGTCAT
1 AATCAGTCAT
42544973 TGACATCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.24
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:42544973 original size:24 final size:24
Alignment explanation
Indices: 42544927--42545024 Score: 106
Period size: 24 Copynumber: 4.1 Consensus size: 24
42544917 TCAGTCATAC
*
42544927 AAATCACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAATCATTT
* * *
42544951 AAATCACAGACAAATTAGTCATTG
1 AAATCACAGACAAATCAATCATTT
* * *
42544975 ACATCTCTGACAAATCAATCATTT
1 AAATCACAGACAAATCAATCATTT
* * *
42544999 ACATCACAGGCAAATTAATCATTT
1 AAATCACAGACAAATCAATCATTT
42545023 AA
1 AA
42545025 CTCCGAGGGG
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (24 bp):
AAATCACAGACAAATCAATCATTT
Found at i:42545072 original size:27 final size:27
Alignment explanation
Indices: 42545042--42545394 Score: 212
Period size: 27 Copynumber: 13.5 Consensus size: 27
42545032 GGGCAAAATA
*
42545042 GTCATTTTACCATACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* ** *
42545069 GTCATTTTATCCTACAGAAGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* * * *
42545096 ATAATTTTACTCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* ** *
42545123 GTTATTTTACATTAC--GGTCA-T---
1 GTCATTTTACCCTACAGGGGCATTACG
* *
42545144 -T--T--TACCTTTCAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* **
42545166 GTTATTTTACCCTTTAGGGGCATTAC-
1 GTCATTTTACCCTACAGGGGCATTACG
* * * *
42545192 GACTATATTACCTTACAGGGGCATTACA
1 GTC-ATTTTACCCTACAGGGGCATTACG
* *
42545220 GTTATTTTACCCTACAGGAGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
** *
42545247 GTCATTTTACCCTACAGGGGTGTTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* **
42545274 GTTATTTTACCCTACAGGGGTGTTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * *
42545301 GTTATTTTACCTTATAGGGGCGTTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
42545328 GTCATTTTACCCGT-C-GAGGGTATTTCA
1 GTCATTTTACCC-TACAG-GGGCATTACG
* * *
42545355 GTCATTTTACCCTTCAGGGGTATTTCG
1 GTCATTTTACCCTACAGGGGCATTACG
*
42545382 ATCATTTTACCCT
1 GTCATTTTACCCT
42545395 TCGAGGGTAT
Statistics
Matches: 254, Mismatches: 55, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
16 6 0.02
18 5 0.02
19 1 0.00
20 1 0.00
23 1 0.00
24 1 0.00
25 5 0.02
26 3 0.01
27 228 0.90
28 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:42545135 original size:16 final size:16
Alignment explanation
Indices: 42545116--42545148 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42545106 TCTATAGGGG
*
42545116 CATTACGGTTATTTTA
1 CATTACGGTCATTTTA
42545132 CATTACGGTCATTTTA
1 CATTACGGTCATTTTA
42545148 C
1 C
42545149 CTTTCAGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (16 bp):
CATTACGGTCATTTTA
Found at i:42545175 original size:70 final size:70
Alignment explanation
Indices: 42545062--42545192 Score: 174
Period size: 70 Copynumber: 1.9 Consensus size: 70
42545052 CATACAGGGG
*
42545062 CATTACGGTCATTTTATCCTACAGAAGCATTACAATAATTTTACTCTATAGGGGCATTACGGTTA
1 CATTACGGTCATTTTATCCTACAGAAGCATTACAATAATTTTACCCTATAGGGGCATTACGGTTA
42545127 TTTTA
66 TTTTA
* ** ** * *
42545132 CATTACGGTCATTTTA-CCTTTCAGGGGCATTACGGTTATTTTACCCTTTAGGGGCATTACG
1 CATTACGGTCATTTTATCC-TACAGAAGCATTACAATAATTTTACCCTATAGGGGCATTACG
42545193 ACTATATTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 2 0.04
70 50 0.96
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (70 bp):
CATTACGGTCATTTTATCCTACAGAAGCATTACAATAATTTTACCCTATAGGGGCATTACGGTTA
TTTTA
Found at i:42545212 original size:97 final size:97
Alignment explanation
Indices: 42545042--42545229 Score: 236
Period size: 97 Copynumber: 1.9 Consensus size: 97
42545032 GGGCAAAATA
* *
42545042 GTCATTTTACCATACAGGGGCATTACGGTCATTTTATCCTACAGAAGCATTACAATAATTTTACT
1 GTCATTTTACCATACAGGGGCATTACGGTCATTTTACCCTACAGAAGCATTACAATAATATTACT
* *
42545107 CTATAGGGGCATTACGGTTATTTTACATTACG
66 CTACAGGGGCATTACAGTTATTTTACATTACG
* * * ** ** *
42545139 GTCATTTTACCTTTCAGGGGCATTACGGTTATTTTACCCTTTAGGGGCATTACGACT-ATATTAC
1 GTCATTTTACCATACAGGGGCATTACGGTCATTTTACCCTACAGAAGCATTAC-AATAATATTAC
42545203 -CTTACAGGGGCATTACAGTTATTTTAC
65 TC-TACAGGGGCATTACAGTTATTTTAC
42545230 CCTACAGGAG
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
96 1 0.01
97 74 0.96
98 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (97 bp):
GTCATTTTACCATACAGGGGCATTACGGTCATTTTACCCTACAGAAGCATTACAATAATATTACT
CTACAGGGGCATTACAGTTATTTTACATTACG
Found at i:42545362 original size:81 final size:80
Alignment explanation
Indices: 42545133--42545392 Score: 256
Period size: 81 Copynumber: 3.2 Consensus size: 80
42545123 GTTATTTTAC
* * * * *
42545133 ATTACGGTCATTTTACCTT-TCAGGGGCATTACGGTTATTTTACCCTTTAGGGGCATTAC-GACT
1 ATTACGGTTATTTTACCTTAT-AGGGGCATTACGGTCATTTTACCC-TCAGGGGTATTACAGTC-
* * *
42545196 ATATTACCTTACAGGGGC
63 ATTTTACCCTACAGGGGT
* * * * * *
42545214 ATTACAGTTATTTTACCCTACAGGAGCATTACGGTCATTTTACCCTACAGGGGTGTTACAGTTAT
1 ATTACGGTTATTTTACCTTATAGGGGCATTACGGTCATTTTACCCT-CAGGGGTATTACAGTCAT
42545279 TTTACCCTACAGGGGT
65 TTTACCCTACAGGGGT
* * *
42545295 GTTACGGTTATTTTACCTTATAGGGGCGTTACGGTCATTTTACCCGTC-GAGGGTATTTCAGTCA
1 ATTACGGTTATTTTACCTTATAGGGGCATTACGGTCATTTTACCC-TCAG-GGGTATTACAGTCA
*
42545359 TTTTACCCTTCAGGGGT
64 TTTTACCCTACAGGGGT
* * *
42545376 ATTTCGATCATTTTACC
1 ATTACGGTTATTTTACC
42545393 CTTCGAGGGT
Statistics
Matches: 146, Mismatches: 28, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
80 2 0.01
81 142 0.97
82 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (80 bp):
ATTACGGTTATTTTACCTTATAGGGGCATTACGGTCATTTTACCCTCAGGGGTATTACAGTCATT
TTACCCTACAGGGGT
Found at i:42545433 original size:54 final size:54
Alignment explanation
Indices: 42545329--42545434 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
42545319 GGCGTTACGG
* *
42545329 TCATTTTACCCGTCGAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGA
1 TCATTTTACCCGTCGAGGGTATTTCAGGCATTTTACCCTTCAGGGCTATTTCGA
*
42545383 TCATTTTACCCTTCGAGGGTATTT-AGGCAATTTTACCCTTC-GAGGCTATTTC
1 TCATTTTACCCGTCGAGGGTATTTCAGGC-ATTTTACCCTTCAG-GGCTATTTC
42545435 AGTAATTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
53 4 0.09
54 43 0.91
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (54 bp):
TCATTTTACCCGTCGAGGGTATTTCAGGCATTTTACCCTTCAGGGCTATTTCGA
Found at i:42545441 original size:27 final size:27
Alignment explanation
Indices: 42545331--42545444 Score: 135
Period size: 27 Copynumber: 4.2 Consensus size: 27
42545321 CGTTACGGTC
* *
42545331 ATTTTACCCGTCGAGGGTATTTCAGTC
1 ATTTTACCCTTCGAGGGTATTTCAGTA
*
42545358 ATTTTACCCTTC-AGGGGTATTTC-GATC
1 ATTTTACCCTTCGA-GGGTATTTCAG-TA
*
42545385 ATTTTACCCTTCGAGGGTATTT-AGGCA
1 ATTTTACCCTTCGAGGGTATTTCA-GTA
*
42545412 ATTTTACCCTTCGAGGCTATTTCAGTA
1 ATTTTACCCTTCGAGGGTATTTCAGTA
42545439 ATTTTA
1 ATTTTA
42545445 TAGCCTTTTC
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
26 2 0.03
27 71 0.93
28 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCAGTA
Found at i:42551235 original size:29 final size:29
Alignment explanation
Indices: 42551201--42551266 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
42551191 AGTGAACAGG
*
42551201 TTCTTCTTTCTAACCTCAACATTCTCTTT
1 TTCTTCTTTCTAACCTCAACATTCTCTTC
42551230 TTCTTCTTTCTAACCTCAACATTCTCTTC
1 TTCTTCTTTCTAACCTCAACATTCTCTTC
42551259 TTCTTCTT
1 TTCTTCTT
42551267 CTTCTTTAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.53
Consensus pattern (29 bp):
TTCTTCTTTCTAACCTCAACATTCTCTTC
Found at i:42552190 original size:25 final size:25
Alignment explanation
Indices: 42552162--42552212 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
42552152 CCTTCGTGGC
42552162 GAATTCTTTGTAAAGCCTTTATGGT
1 GAATTCTTTGTAAAGCCTTTATGGT
*
42552187 GAATTCTTTGTAAAGTCTTTATGGT
1 GAATTCTTTGTAAAGCCTTTATGGT
42552212 G
1 G
42552213 TATTATCTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.45
Consensus pattern (25 bp):
GAATTCTTTGTAAAGCCTTTATGGT
Found at i:42560160 original size:19 final size:20
Alignment explanation
Indices: 42560136--42560174 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42560126 TTATATTCCG
*
42560136 TAATTAA-TATTTTAAACTT
1 TAATTAATTACTTTAAACTT
42560155 TAATTAATTACTTTAAACTT
1 TAATTAATTACTTTAAACTT
42560175 GATTAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTAATTACTTTAAACTT
Found at i:42561860 original size:24 final size:25
Alignment explanation
Indices: 42561833--42561879 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
42561823 GTAAATCAAA
42561833 AAAATATCTCTA-AAAATTTTCTGG
1 AAAATATCTCTAGAAAATTTTCTGG
* * *
42561857 AAAATCTCTTTAGAGAATTTTCT
1 AAAATATCTCTAGAAAATTTTCT
42561880 CTCTACAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (25 bp):
AAAATATCTCTAGAAAATTTTCTGG
Found at i:42562059 original size:59 final size:62
Alignment explanation
Indices: 42561987--42562104 Score: 152
Period size: 62 Copynumber: 2.0 Consensus size: 62
42561977 AATCACTTTA
* * * *
42561987 ATATTAAATTAATATAAT-ATT-TAT-CAAGAGAAATATTAGATTAAATTTAATACTAAATC
1 ATATTAAAATAATAGAATGATTATATACAAGAGAAACATTAAATTAAATTTAATACTAAATC
* * *
42562046 ATATTAAAATAATAGAATGCTTATCTACAAGATAAACATTAAATTAAATTTAATACTAA
1 ATATTAAAATAATAGAATGATTATATACAAGAGAAACATTAAATTAAATTTAATACTAA
42562105 GATAATAACT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 16 0.33
60 2 0.04
61 2 0.04
62 29 0.59
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (62 bp):
ATATTAAAATAATAGAATGATTATATACAAGAGAAACATTAAATTAAATTTAATACTAAATC
Found at i:42562130 original size:20 final size:19
Alignment explanation
Indices: 42562083--42562143 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
42562073 CAAGATAAAC
42562083 ATTAAATT-A-AATTTAAT
1 ATTAAATTAATAATTTAAT
*
42562100 ACTAAGA-TAATAACTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
**
42562120 ATTAAATTAATAAAATAAT
1 ATTAAATTAATAATTTAAT
42562139 ATTAA
1 ATTAA
42562144 GATAAGTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 5 0.14
18 2 0.06
19 12 0.34
20 16 0.46
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:42562650 original size:25 final size:25
Alignment explanation
Indices: 42562604--42562651 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42562594 AAATATTATA
***
42562604 TTAATTTTAATTGATTTGATTTACT
1 TTAATTTTAATTGATCAAATTTACT
*
42562629 TTAATTTTACTTGATCAAATTTA
1 TTAATTTTAATTGATCAAATTTA
42562652 TTTTTTCCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (25 bp):
TTAATTTTAATTGATCAAATTTACT
Found at i:42566754 original size:15 final size:15
Alignment explanation
Indices: 42566734--42566771 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
42566724 AGGATTTGGT
42566734 TTGTTTATTTTATTA
1 TTGTTTATTTTATTA
42566749 TTGTTTATTTTATTA
1 TTGTTTATTTTATTA
*
42566764 TTATTTAT
1 TTGTTTAT
42566772 CATTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (15 bp):
TTGTTTATTTTATTA
Found at i:42566791 original size:13 final size:13
Alignment explanation
Indices: 42566773--42566798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42566763 ATTATTTATC
42566773 ATTTAAATATATA
1 ATTTAAATATATA
42566786 ATTTAAATATATA
1 ATTTAAATATATA
42566799 TAAATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTAAATATATA
Found at i:42566799 original size:15 final size:14
Alignment explanation
Indices: 42566777--42566811 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
42566767 TTTATCATTT
*
42566777 AAATATATAATTTA
1 AAATATATAAATTA
42566791 AATATATATAAATTA
1 AA-ATATATAAATTA
42566806 AAATAT
1 AAATAT
42566812 TTTAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATATATAAATTA
Found at i:42566823 original size:11 final size:11
Alignment explanation
Indices: 42566803--42566833 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
42566793 TATATATAAA
42566803 TTAA-AATATT
1 TTAATAATATT
42566813 TTAATAATATT
1 TTAATAATATT
42566824 TTAATAATAT
1 TTAATAATAT
42566834 AGAAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTAATAATATT
Found at i:42570768 original size:20 final size:19
Alignment explanation
Indices: 42570744--42570814 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
42570734 TGTAAATTTG
42570744 TAAAATTTTATAAAAAATA
1 TAAAATTTTATAAAAAATA
** *
42570763 GTAAAAAATTATAAAATATA
1 -TAAAATTTTATAAAAAATA
42570783 TAGAAA---TATAAAAAATTA
1 TA-AAATTTTATAAAAAA-TA
42570801 TAAAATTTTATAAA
1 TAAAATTTTATAAA
42570815 GTCGTAAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 11 0.26
18 4 0.10
19 2 0.05
20 25 0.60
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
TAAAATTTTATAAAAAATA
Found at i:42570777 original size:10 final size:9
Alignment explanation
Indices: 42570752--42570805 Score: 56
Period size: 10 Copynumber: 5.8 Consensus size: 9
42570742 TGTAAAATTT
42570752 TATAAAAAA
1 TATAAAAAA
42570761 TAGTAAAAAA
1 TA-TAAAAAA
*
42570771 T-TATAAAA
1 TATAAAAAA
*
42570779 TATATAGAAA
1 TATA-AAAAA
42570789 TATAAAAAA
1 TATAAAAAA
42570798 TTATAAAA
1 -TATAAAA
42570806 TTTTATAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 22 0.59
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (9 bp):
TATAAAAAA
Found at i:42571073 original size:28 final size:26
Alignment explanation
Indices: 42571016--42571073 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
42571006 TTATTAATTT
* * *
42571016 TTTTTATGATTTTTATAAAATTTTAT
1 TTTTTACGATTTTTATAAAATTCTAA
42571042 TTTTTACGATTTTTATAAAAAATTCTAA
1 TTTTTACGATTTTTAT--AAAATTCTAA
42571070 TTTT
1 TTTT
42571074 AAATAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 15 0.56
28 12 0.44
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (26 bp):
TTTTTACGATTTTTATAAAATTCTAA
Found at i:42571113 original size:18 final size:20
Alignment explanation
Indices: 42571092--42571133 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
42571082 TTTAAATTCT
42571092 TTTATAT-A-TTTATTAAAA
1 TTTATATAATTTTATTAAAA
*
42571110 TTTA-ATAATTTTTTTAAAA
1 TTTATATAATTTTATTAAAA
42571129 TTTAT
1 TTTAT
42571134 GAATTCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 2 0.10
18 5 0.25
19 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATATAATTTTATTAAAA
Found at i:42571665 original size:21 final size:21
Alignment explanation
Indices: 42571641--42571690 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
42571631 TTTCGAATCG
*
42571641 AGTTGAGTAAAACGAAATTCA
1 AGTTAAGTAAAACGAAATTCA
* * *
42571662 AGTTAAGTGAAATGAAATTTA
1 AGTTAAGTAAAACGAAATTCA
42571683 AGTTAAGT
1 AGTTAAGT
42571691 CAAATCGAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (21 bp):
AGTTAAGTAAAACGAAATTCA
Found at i:42571695 original size:21 final size:21
Alignment explanation
Indices: 42571654--42571695 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42571644 TGAGTAAAAC
*
42571654 GAAATTCAAGTTAAGTGAAAT
1 GAAATTCAAGTTAAGTCAAAT
*
42571675 GAAATTTAAGTTAAGTCAAAT
1 GAAATTCAAGTTAAGTCAAAT
42571696 CGAGTGACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (21 bp):
GAAATTCAAGTTAAGTCAAAT
Found at i:42575371 original size:18 final size:18
Alignment explanation
Indices: 42575335--42575373 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42575325 GACTTTTGAC
*
42575335 AGACATAATCCCTAGTCT
1 AGACATAATCCATAGTCT
42575353 AGACATAATCACATA-TCT
1 AGACATAATC-CATAGTCT
42575371 AGA
1 AGA
42575374 GATATATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (18 bp):
AGACATAATCCATAGTCT
Found at i:42579782 original size:263 final size:261
Alignment explanation
Indices: 42579317--42579838 Score: 839
Period size: 263 Copynumber: 2.0 Consensus size: 261
42579307 ACTTAGTCCG
* *
42579317 CCGAGTACTATCTAAGAGGAGGTTAGTGGCACCAATGAGTCTCTTAAATAATATGCTCTAAGAGT
1 CCGAGTACTATCTAAGAGGAGGTCAGTGGCACCAATGAGTCTCTTAAATAATATGCTCCAAGAGT
* * * *
42579382 TTATATAAGGTGGGCTCGCACAATCCAGAAGATATATAAGGAAGATCTCCTGACATTATTTGTTA
66 TTATATAAGATGGGCTCGCACAATCCAGAAAATATATAAGGAAGATCTACTGACAGTATTTGTTA
* * * *
42579447 ATCCATTGCATCCTATGATTGGCGACACTTATCCAGACATCTCATATAGTTCCCTCACATCAAAT
131 ATCCATTGCATCCTAGGATTGGCGACACCTATCCAAACATCTCACATAGTTCCCTCACATCAAAT
* * * *
42579512 CCAATAATGTTCCTAGCTAACATTCACCACTCTACCCTTTGCACCTATGAAGTAGAGTGCTTGAC
196 CCAATAATGGTCCTAGCTAAAATTCACCACTCTACCCTCTACACCTATGAAGTAGAGTGCTTGAC
42579577 A
261 A
* *
42579578 CCGAGTACTCTCTAAGAGGAGGTCAGTGGCACCAATGAGTCTCTTCAATAATATGCTCCAAGAGT
1 CCGAGTACTATCTAAGAGGAGGTCAGTGGCACCAATGAGTCTCTTAAATAATATGCTCCAAGAGT
*
42579643 TTATATAAGATGGGCTTGCACAATCCCTAGAAAATATATAAGGAAGATCTACTGATC-GTATTTG
66 TTATATAAGATGGGCTCGCACAAT-CC-AGAAAATATATAAGGAAGATCTACTGA-CAGTATTTG
42579707 TTAATCCATTGCATCCTAGGATTGGCGACACCTATCCAAACATCTCACATAGTTCCCTCACATCA
128 TTAATCCATTGCATCCTAGGATTGGCGACACCTATCCAAACATCTCACATAGTTCCCTCACATCA
* *
42579772 ACTCCAATAATGGTCCTAGCTAAAATTCACCACTTTACCCTCTACACCTATGAAGTAGAGTGCTT
193 AATCCAATAATGGTCCTAGCTAAAATTCACCACTCTACCCTCTACACCTATGAAGTAGAGTGCTT
42579837 GA
258 GA
42579839 TGGTTAGGGT
Statistics
Matches: 239, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
261 83 0.35
262 2 0.01
263 153 0.64
264 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (261 bp):
CCGAGTACTATCTAAGAGGAGGTCAGTGGCACCAATGAGTCTCTTAAATAATATGCTCCAAGAGT
TTATATAAGATGGGCTCGCACAATCCAGAAAATATATAAGGAAGATCTACTGACAGTATTTGTTA
ATCCATTGCATCCTAGGATTGGCGACACCTATCCAAACATCTCACATAGTTCCCTCACATCAAAT
CCAATAATGGTCCTAGCTAAAATTCACCACTCTACCCTCTACACCTATGAAGTAGAGTGCTTGAC
A
Found at i:42595495 original size:97 final size:97
Alignment explanation
Indices: 42595329--42595516 Score: 331
Period size: 97 Copynumber: 1.9 Consensus size: 97
42595319 AGGAATTATT
* *
42595329 TGTATATGTGAAATTAAAATTTTAGGCTCCGAGCCTAACAGGTTTATTAACAGTGAAGTAATCCA
1 TGTATATATGAAATTAAAATTTTAGGCTCCGAGCCTAAAAGGTTTATTAACAGTGAAGTAATCCA
42595394 GACATTACGTCTAGCACGCTTGATGTTTCACC
66 GACATTACGTCTAGCACGCTTGATGTTTCACC
* *
42595426 TGTATATATGAAATTAAAATTTTAGGCTTCGAGCCTAAAATGTTTATTAACAGTGAAGTAATCCA
1 TGTATATATGAAATTAAAATTTTAGGCTCCGAGCCTAAAAGGTTTATTAACAGTGAAGTAATCCA
*
42595491 GACATTACGTCTAGCAGGCTTGATGT
66 GACATTACGTCTAGCACGCTTGATGT
42595517 CGTTGAAACA
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 86 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (97 bp):
TGTATATATGAAATTAAAATTTTAGGCTCCGAGCCTAAAAGGTTTATTAACAGTGAAGTAATCCA
GACATTACGTCTAGCACGCTTGATGTTTCACC
Found at i:42595545 original size:41 final size:41
Alignment explanation
Indices: 42595488--42595711 Score: 358
Period size: 41 Copynumber: 5.5 Consensus size: 41
42595478 GTGAAGTAAT
* *
42595488 CCAGACATTACGTCTAGCAGGCTTGATGTCGTTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
42595529 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
42595570 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
* * *
42595611 CCAGACTTTACGTCTAGCAAGCTTGATGCCGGTGAATCATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
* *
42595652 CCAGACTTTACGTCTAGTAGGCTTGATGCCGGTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
* * *
42595693 TCAGACTTTATGTCTAGCA
1 CCAGACATTACGTCTAGCA
42595712 AGCTATGTGT
Statistics
Matches: 172, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 172 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (41 bp):
CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
Found at i:42595743 original size:123 final size:123
Alignment explanation
Indices: 42595489--42595743 Score: 332
Period size: 123 Copynumber: 2.1 Consensus size: 123
42595479 TGAAGTAATC
* * * *
42595489 CAGACATTACGTCTAGCAGGCTTGATGTCGTTGAAACATACCAGACATTACGTCTAGCAGGCTTG
1 CAGACTTTACGTCTAGCAAGCTTGATGCCGGTGAAACATACCAGACATTACGTCTAGCAGGCTTG
* * * *
42595554 ATGCCGGTGAAACATACCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATAC
66 ATGCCGGTGAAACATACCAGACATTACGTCTAGCAAGCTTGATGCCGGTCAAACAAAA
* * *
42595612 CAGACTTTACGTCTAGCAAGCTTGATGCCGGTGAATCATACCAGACTTTACGTCTAGTAGGCTTG
1 CAGACTTTACGTCTAGCAAGCTTGATGCCGGTGAAACATACCAGACATTACGTCTAGCAGGCTTG
* * * * * *
42595677 ATGCCGGTGAAACATATCAGACTTTATGTCTAGCAAGCTATG-TGTCGGTCTACCAAAA
66 ATGCCGGTGAAACATACCAGACATTACGTCTAGCAAGCT-TGATGCCGGTCAAACAAAA
*
42595735 CAGGCTTTA
1 CAGACTTTA
42595744 AGCCTAGTAG
Statistics
Matches: 113, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
123 111 0.98
124 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (123 bp):
CAGACTTTACGTCTAGCAAGCTTGATGCCGGTGAAACATACCAGACATTACGTCTAGCAGGCTTG
ATGCCGGTGAAACATACCAGACATTACGTCTAGCAAGCTTGATGCCGGTCAAACAAAA
Found at i:42595751 original size:82 final size:82
Alignment explanation
Indices: 42595501--42595756 Score: 280
Period size: 82 Copynumber: 3.1 Consensus size: 82
42595491 GACATTACGT
* * * * * * *
42595501 CTAGCAGGCTTGATGTCGTTGAAACATACCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 CTAGTAGGCTTGATGCCGGTGAAACATACCAGACTTTACGTCTAGCAAGCTTGATGCCGGTCAAC
* * * * *
42595566 CATACCAGACATTACGT
66 CAAAACAGACTTTAAGC
* * *
42595583 CTAGCAGGCTTGATGCCGGTGAAACATACCAGACTTTACGTCTAGCAAGCTTGATGCCGGTGAAT
1 CTAGTAGGCTTGATGCCGGTGAAACATACCAGACTTTACGTCTAGCAAGCTTGATGCCGGTCAAC
* * * *
42595648 CATACCAGACTTTACGT
66 CAAAACAGACTTTAAGC
* * * *
42595665 CTAGTAGGCTTGATGCCGGTGAAACATATCAGACTTTATGTCTAGCAAGCTATG-TGTCGGTCTA
1 CTAGTAGGCTTGATGCCGGTGAAACATACCAGACTTTACGTCTAGCAAGCT-TGATGCCGGTCAA
*
42595729 CCAAAACAGGCTTTAAGC
65 CCAAAACAGACTTTAAGC
42595747 CTAGTAGGCT
1 CTAGTAGGCT
42595757 AAGTGCCGGT
Statistics
Matches: 155, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
82 153 0.99
83 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (82 bp):
CTAGTAGGCTTGATGCCGGTGAAACATACCAGACTTTACGTCTAGCAAGCTTGATGCCGGTCAAC
CAAAACAGACTTTAAGC
Found at i:42603776 original size:41 final size:41
Alignment explanation
Indices: 42603729--42603915 Score: 266
Period size: 41 Copynumber: 4.6 Consensus size: 41
42603719 GTGAAGTAAT
42603729 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
* *
42603770 CCAGACATTACGTCTAGTAGGCTTGATGCTGGTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
* *
42603811 CCAGACTTTACGTCTTGCAGGCTTGATGCCGGTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
* * *
42603852 CCAGACATTACGTCTAGCAGGGTTGATACCGGTGAAATATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
* * * * *
42603893 TCATACTTTATGTCTAGGAGGCT
1 CCAGACATTACGTCTAGCAGGCT
42603916 AAGTGCCGGT
Statistics
Matches: 129, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 129 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (41 bp):
CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
Found at i:42603925 original size:41 final size:41
Alignment explanation
Indices: 42603880--42603968 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 41
42603870 AGGGTTGATA
* * * * * *
42603880 CCGGTGAAATATATCATACTTTATGTCTAGGAGGCTAAGTG
1 CCGGTGAAATAAAACAAACTTTAAGCCTAGCAGGCTAAGTG
* *
42603921 CCGGTGTACTAAAACAAACTTTAAGCCTAGCAGGCTAAGTG
1 CCGGTGAAATAAAACAAACTTTAAGCCTAGCAGGCTAAGTG
42603962 CCGGTGA
1 CCGGTGA
42603969 TATTGTTTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (41 bp):
CCGGTGAAATAAAACAAACTTTAAGCCTAGCAGGCTAAGTG
Found at i:42603954 original size:123 final size:123
Alignment explanation
Indices: 42603729--42603956 Score: 271
Period size: 123 Copynumber: 1.9 Consensus size: 123
42603719 GTGAAGTAAT
* * *
42603729 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACCAGACATTACGTCTAGTAGGCTT
1 CCAGACATTACGTCTAGCAGGCTTGATACCGGTGAAACATACCAGACATTACGTCTAGGAGGCTA
* * * * * * *
42603794 GATGCTGGTGAAACATACCAGACTTTACGTCTTGCAGGCTTGATGCCGGTGAAACATA
66 GATGCCGGTGAAACAAAACAAACTTTAAGCCTAGCAGGCTTGATGCCGGTGAAACATA
* * * * * *
42603852 CCAGACATTACGTCTAGCAGGGTTGATACCGGTGAAATATATCATACTTTATGTCTAGGAGGCTA
1 CCAGACATTACGTCTAGCAGGCTTGATACCGGTGAAACATACCAGACATTACGTCTAGGAGGCTA
*
42603917 -AGTGCCGGTG-TACTAAAACAAACTTTAAGCCTAGCAGGCT
66 GA-TGCCGGTGAAAC-AAAACAAACTTTAAGCCTAGCAGGCT
42603957 AAGTGCCGGT
Statistics
Matches: 86, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
122 3 0.03
123 83 0.97
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (123 bp):
CCAGACATTACGTCTAGCAGGCTTGATACCGGTGAAACATACCAGACATTACGTCTAGGAGGCTA
GATGCCGGTGAAACAAAACAAACTTTAAGCCTAGCAGGCTTGATGCCGGTGAAACATA
Found at i:42608803 original size:37 final size:37
Alignment explanation
Indices: 42608747--42608879 Score: 144
Period size: 37 Copynumber: 3.6 Consensus size: 37
42608737 TAGGACATAG
*
42608747 GTTTAGCTCAAACGAGTAACCTAATGTTGTTTTAAAA
1 GTTTAGCTCAGACGAGTAACCTAATGTTGTTTTAAAA
* * * * *
42608784 GTTTAGCTCAGACGGGTAACCTGAT-ATGTGTTAATA
1 GTTTAGCTCAGACGAGTAACCTAATGTTGTTTTAAAA
* *
42608820 TTATTAGCTC-GAACAAGTAACCTAATGTTGTTTTAAAA
1 GT-TTAGCTCAG-ACGAGTAACCTAATGTTGTTTTAAAA
* *
42608858 GTTTAGCTCGGATGAGTAACCT
1 GTTTAGCTCAGACGAGTAACCT
42608880 GATATGTGTT
Statistics
Matches: 76, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
36 10 0.13
37 56 0.74
38 10 0.13
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (37 bp):
GTTTAGCTCAGACGAGTAACCTAATGTTGTTTTAAAA
Found at i:42608877 original size:74 final size:74
Alignment explanation
Indices: 42608749--42608906 Score: 253
Period size: 74 Copynumber: 2.1 Consensus size: 74
42608739 GGACATAGGT
* * *
42608749 TTAGCTCAAACGAGTAACCTAATGTTGTTTTAAAAGTTTAGCTCAGACGGGTAACCTGATATGTG
1 TTAGCTCGAACAAGTAACCTAATGTTGTTTTAAAAGTTTAGCTCAGACGAGTAACCTGATATGTG
42608814 TTAATATTA
66 TTAATATTA
* *
42608823 TTAGCTCGAACAAGTAACCTAATGTTGTTTTAAAAGTTTAGCTCGGATGAGTAACCTGATATGTG
1 TTAGCTCGAACAAGTAACCTAATGTTGTTTTAAAAGTTTAGCTCAGACGAGTAACCTGATATGTG
*
42608888 TTTATATTA
66 TTAATATTA
*
42608897 TTAGATCGAA
1 TTAGCTCGAA
42608907 TAAGCAATTG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (74 bp):
TTAGCTCGAACAAGTAACCTAATGTTGTTTTAAAAGTTTAGCTCAGACGAGTAACCTGATATGTG
TTAATATTA
Found at i:42613715 original size:46 final size:46
Alignment explanation
Indices: 42613648--42613740 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
42613638 AAATATACTT
42613648 AAATCTTTACAGCTACACAATTTTAAATATGAGTTTGATACAACGA
1 AAATCTTTACAGCTACACAATTTTAAATATGAGTTTGATACAACGA
42613694 AAATCTTTACAGCTACACAATTTTAAATATGAGTTTGATACAACGA
1 AAATCTTTACAGCTACACAATTTTAAATATGAGTTTGATACAACGA
42613740 A
1 A
42613741 CTAACCTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (46 bp):
AAATCTTTACAGCTACACAATTTTAAATATGAGTTTGATACAACGA
Found at i:42616763 original size:19 final size:19
Alignment explanation
Indices: 42616725--42616763 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42616715 AAATAGTGAG
*
42616725 AATTTATTTTCTGAGTATA
1 AATTTATTTTCTGAGAATA
42616744 AATTCTATTTTCTG-GAATA
1 AATT-TATTTTCTGAGAATA
42616763 A
1 A
42616764 CAATTCTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (19 bp):
AATTTATTTTCTGAGAATA
Found at i:42623764 original size:6 final size:6
Alignment explanation
Indices: 42623746--42623774 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
42623736 AGAAAAACTT
42623746 TCTTTC T-TTTC TCTTTC TCTTTC TCTTTC
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC
42623775 ATGTTAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TCTTTC
Found at i:42630150 original size:17 final size:17
Alignment explanation
Indices: 42630128--42630160 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42630118 CACTAACATG
*
42630128 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
42630145 AAAATGCAATGACAAT
1 AAAATGCAATGACAAT
42630161 GTGTCCTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:42630618 original size:18 final size:18
Alignment explanation
Indices: 42630586--42630624 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
42630576 CATTTTTATT
** *
42630586 TTCAGCAACTTCTTCTTC
1 TTCAGCAACAACTTCCTC
42630604 TTCAGCAACAACTTCCTC
1 TTCAGCAACAACTTCCTC
42630622 TTC
1 TTC
42630625 TGCAGTAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.05, T:0.38
Consensus pattern (18 bp):
TTCAGCAACAACTTCCTC
Found at i:42642072 original size:27 final size:28
Alignment explanation
Indices: 42642028--42642081 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
42642018 CTTGGAGTCA
** *
42642028 GTAGTCCACCGGGATAG-TAAACAAGGG
1 GTAGTCCACAAGGATAGTTAAAAAAGGG
*
42642055 GTAGTCCACAAGGTTAGTTAAAAAAGG
1 GTAGTCCACAAGGATAGTTAAAAAAGG
42642082 AAAATCACCG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.37, C:0.15, G:0.30, T:0.19
Consensus pattern (28 bp):
GTAGTCCACAAGGATAGTTAAAAAAGGG
Found at i:42642754 original size:20 final size:18
Alignment explanation
Indices: 42642729--42642767 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
42642719 TTACATGATT
*
42642729 TTCATGTATATTTATATTAA
1 TTCATGT-TAATT-TATTAA
42642749 TTCATGTTAATTTATTAA
1 TTCATGTTAATTTATTAA
42642767 T
1 T
42642768 GTTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (18 bp):
TTCATGTTAATTTATTAA
Found at i:42650117 original size:70 final size:70
Alignment explanation
Indices: 42650004--42650145 Score: 239
Period size: 70 Copynumber: 2.0 Consensus size: 70
42649994 GTAGGTACCA
* * **
42650004 AAGTTATAGTATTTACCGATCATGCTGCCATTAAGTGCTTACTCACGAAGAAAGATGCTAAATTG
1 AAGTTATAGTATTTACCGATCATGCTACCATTAAGTACTTACTCACGAAGAAAGATGCTAAACCG
42650069 AGGCT
66 AGGCT
*
42650074 AAGTTATAGTATTTACCGATCATGCTACCATTAAGTACTTACTCATGAAGAAAGATGCTAAACCG
1 AAGTTATAGTATTTACCGATCATGCTACCATTAAGTACTTACTCACGAAGAAAGATGCTAAACCG
42650139 AGGCT
66 AGGCT
42650144 AA
1 AA
42650146 TTCAATGGAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (70 bp):
AAGTTATAGTATTTACCGATCATGCTACCATTAAGTACTTACTCACGAAGAAAGATGCTAAACCG
AGGCT
Found at i:42651756 original size:19 final size:19
Alignment explanation
Indices: 42651725--42651767 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42651715 AAAAAAAATT
* *
42651725 ATTTTTAGTTTTATTTTTC
1 ATTTTTAGTTTTATCTTTA
42651744 ATTTTTA-TCTTTATCTTTA
1 ATTTTTAGT-TTTATCTTTA
42651763 ATTTT
1 ATTTT
42651768 AATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (19 bp):
ATTTTTAGTTTTATCTTTA
Found at i:42651775 original size:11 final size:11
Alignment explanation
Indices: 42651759--42651796 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
42651749 TATCTTTATC
42651759 TTTAATTTTAA
1 TTTAATTTTAA
42651770 TTTAATTTTAA
1 TTTAATTTTAA
42651781 TCTTTAATTTTAA
1 --TTTAATTTTAA
42651794 TTT
1 TTT
42651797 GTTTATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.56
13 11 0.44
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTAATTTTAA
Found at i:42651788 original size:13 final size:13
Alignment explanation
Indices: 42651756--42651794 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
42651746 TTTTATCTTT
42651756 ATCTTTAATTTTA
1 ATCTTTAATTTTA
42651769 A--TTTAATTTTA
1 ATCTTTAATTTTA
42651780 ATCTTTAATTTTA
1 ATCTTTAATTTTA
42651793 AT
1 AT
42651795 TTGTTTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.46
13 13 0.54
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (13 bp):
ATCTTTAATTTTA
Found at i:42651793 original size:6 final size:6
Alignment explanation
Indices: 42651727--42651796 Score: 63
Period size: 6 Copynumber: 11.5 Consensus size: 6
42651717 AAAAAATTAT
* * * *
42651727 TTTTAG TTTTAT TTTTCA TTTTTA TCTTT-A TCTTTAA TTTTAA -TTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA T-TTTAA T-TTTAA TTTTAA TTTTAA
42651775 TTTTAA TCTTTAA TTTTAA TTT
1 TTTTAA T-TTTAA TTTTAA TTT
42651797 GTTTATGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.09
6 40 0.71
7 11 0.20
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:42654961 original size:50 final size:50
Alignment explanation
Indices: 42654890--42655054 Score: 208
Period size: 50 Copynumber: 3.3 Consensus size: 50
42654880 GGAATGAGAT
* *
42654890 CCCATGTAAGACCATGCCTGGGACATGGTGTTGGCACCGAGATGAGAGGC
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGC
* **
42654940 CCCATGTAAGACCATTTCTGGGACATGGCGTTGGCACTAAGATGAGAGGTC
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG-C
* * * * *
42654991 CCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGA-AC
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGC
42655039 TCCCATGTAAGACCAT
1 -CCCATGTAAGACCAT
42655055 ATCCGGGGTA
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 90 0.92
51 4 0.04
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGC
Found at i:42655341 original size:12 final size:12
Alignment explanation
Indices: 42655324--42655362 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42655314 ATGAGTTATT
42655324 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
42655336 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
42655348 TAAGTGAGTAAG
1 TAAGTAAGCAAG
42655360 TAA
1 TAA
42655363 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:42662475 original size:25 final size:25
Alignment explanation
Indices: 42662446--42662560 Score: 135
Period size: 25 Copynumber: 4.6 Consensus size: 25
42662436 TTCGCCATAC
42662446 AGGCTTTCCAGATAACATG-CTACAA
1 AGGCTTTCCAGATAACATGTC-ACAA
*
42662471 AGGCTTTCTAGATAACATG-CGACAA
1 AGGCTTTCCAGATAACATGTC-ACAA
*
42662496 AGGCTATCCAGATAACATGTCACAA
1 AGGCTTTCCAGATAACATGTCACAA
* * *
42662521 AGGTTTTCCGGATAATATGTCACAA
1 AGGCTTTCCAGATAACATGTCACAA
* *
42662546 ACGCTTTCCAAATAA
1 AGGCTTTCCAGATAA
42662561 TATGAGATAA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
25 76 0.99
26 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (25 bp):
AGGCTTTCCAGATAACATGTCACAA
Found at i:42662561 original size:25 final size:25
Alignment explanation
Indices: 42662446--42662577 Score: 133
Period size: 25 Copynumber: 5.3 Consensus size: 25
42662436 TTCGCCATAC
*
42662446 AGGCTTTCCAGATAACATGCTACAA
1 AGGCTTTCCAGATAACATGCGACAA
*
42662471 AGGCTTTCTAGATAACATGCGACAA
1 AGGCTTTCCAGATAACATGCGACAA
*
42662496 AGGCTATCCAGATAACATGTC-ACAA
1 AGGCTTTCCAGATAACATG-CGACAA
* * *
42662521 AGGTTTTCCGGATAATATGTC-ACAA
1 AGGCTTTCCAGATAACATG-CGACAA
* * * * *
42662546 ACGCTTTCCAAATAATATGAGATAA
1 AGGCTTTCCAGATAACATGCGACAA
42662571 AGGCTTT
1 AGGCTTT
42662578 TTAGTTACCA
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
25 89 0.99
26 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (25 bp):
AGGCTTTCCAGATAACATGCGACAA
Found at i:42664577 original size:19 final size:20
Alignment explanation
Indices: 42664555--42664599 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
42664545 TTAAAAAATG
*
42664555 GAATTTTTATAAA-TATTTT
1 GAATTTTTAAAAATTATTTT
42664574 GAA-TTTTAAAAATTATTTT
1 GAATTTTTAAAAATTATTTT
42664593 -AATTTTT
1 GAATTTTT
42664600 TTTGTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
GAATTTTTAAAAATTATTTT
Found at i:42664580 original size:18 final size:18
Alignment explanation
Indices: 42664559--42664598 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
42664549 AAAATGGAAT
*
42664559 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTT-AA
42664577 TTTTAAAAATTATTTTAA
1 TTTTAAAAATTATTTTAA
42664595 TTTT
1 TTTT
42664599 TTTTGTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTAAAAATTATTTTAA
Found at i:42665965 original size:17 final size:17
Alignment explanation
Indices: 42665943--42665989 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
42665933 ATGAACCTGT
42665943 AGTTTATTACATGTATC
1 AGTTTATTACATGTATC
42665960 AGTTTATTACATGTATC
1 AGTTTATTACATGTATC
42665977 --TATTATTACATGT
1 AGT-TTATTACATGT
42665990 GAACCAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 1 0.03
16 11 0.38
17 17 0.59
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
AGTTTATTACATGTATC
Found at i:42666072 original size:15 final size:15
Alignment explanation
Indices: 42666052--42666081 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42666042 ACTTGTATTT
*
42666052 TATTACTTGCGAACC
1 TATTACATGCGAACC
42666067 TATTACATGCGAACC
1 TATTACATGCGAACC
42666082 CTAGGAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (15 bp):
TATTACATGCGAACC
Found at i:42666117 original size:34 final size:34
Alignment explanation
Indices: 42666073--42666172 Score: 137
Period size: 34 Copynumber: 2.9 Consensus size: 34
42666063 AACCTATTAC
*
42666073 ATGCGAACCCTAGGAACATGCGAGACTATATGTT
1 ATGCAAACCCTAGGAACATGCGAGACTATATGTT
* * *
42666107 GTGCAAACCCTAGGAACATGGGAGTCTATATGTT
1 ATGCAAACCCTAGGAACATGCGAGACTATATGTT
* * *
42666141 ATGCGAACCCTAGGTACATGCGAGCCTATATG
1 ATGCAAACCCTAGGAACATGCGAGACTATATG
42666173 CGAACCTCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (34 bp):
ATGCAAACCCTAGGAACATGCGAGACTATATGTT
Found at i:42669803 original size:43 final size:43
Alignment explanation
Indices: 42669747--42669937 Score: 265
Period size: 43 Copynumber: 4.4 Consensus size: 43
42669737 TTAGAAAAAA
* *
42669747 AAACGCCGCTAAAGACCAAGACATTTCGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * ** *
42669790 AAACGCCGTTAAAGACCAAAACCTTTAGCGGCGCTTTTATCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * **
42669833 AAACGCCGCGAAAGACCACGACCTTTAGCGGCATTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
42669876 ATACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
42669919 AAACGCCGCTAAAGACCAA
1 AAACGCCGCTAAAGACCAA
42669938 AACTAAAAGC
Statistics
Matches: 124, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 124 1.00
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:42670037 original size:42 final size:43
Alignment explanation
Indices: 42669942--42670041 Score: 112
Period size: 42 Copynumber: 2.3 Consensus size: 43
42669932 GACCAAAACT
* * * * * *
42669942 AAAAGCGCCGCGAAAGACCAAGACCTTTAGCGACACTTTTATC
1 AAAAACGCCGCTAAAGAACAAGACCTTTAGCAACACTTCTAGC
* * *
42669985 ACAAATGCCGCTAAAGAACAA-ACCTTTAGCAACGCTTCTAGC
1 AAAAACGCCGCTAAAGAACAAGACCTTTAGCAACACTTCTAGC
42670027 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
42670042 AATAGAATCT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
42 30 0.65
43 16 0.35
ACGTcount: A:0.39, C:0.28, G:0.16, T:0.17
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACAAGACCTTTAGCAACACTTCTAGC
Found at i:42671292 original size:12 final size:12
Alignment explanation
Indices: 42671275--42671299 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42671265 ATTTGATCTG
42671275 TATACTAAATGA
1 TATACTAAATGA
42671287 TATACTAAATGA
1 TATACTAAATGA
42671299 T
1 T
42671300 GCCAGTATCA
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TATACTAAATGA
Found at i:42671951 original size:13 final size:13
Alignment explanation
Indices: 42671930--42671969 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
42671920 ACTAACCTGG
*
42671930 TTTAGAATAATTA
1 TTTAAAATAATTA
42671943 TTTAAAATACTATTA
1 TTTAAAATA--ATTA
42671958 TTTAAAATAATT
1 TTTAAAATAATT
42671970 TTAAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (13 bp):
TTTAAAATAATTA
Found at i:42675868 original size:133 final size:132
Alignment explanation
Indices: 42675626--42675884 Score: 353
Period size: 133 Copynumber: 2.0 Consensus size: 132
42675616 AATAACTTAA
* * * *
42675626 TTAATATATAAATTAAAAAATACTAATTAATCTAAACCTTAAACCCTAACTCGACCCCGAATCTC
1 TTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAACTCAACACCGAATCTC
* * *
42675691 TAAATCCTAAATCACTAACTCTTAACATCTAATCTCTAACCCCTAACCCCTAACCCTTAAACTTT
66 TAAATCCTAAATCACTAACTCTTAACATCTAACCCCTAACCCCTAACCCCTAACCCCTAAACTTT
42675756 AT
131 AT
42675758 TTAATATATAAATTAAAAAAACACTAATTAATCTAAACCATAAACCCTAAC-CTAACACCGAATC
1 TTAATATATAAATT-AAAAAACACTAATTAATCTAAACCATAAACCCTAACTC-AACACCGAATC
* ** * *
42675822 -CATAAATCCTAAATCCCTAACTCTTAATC-TCTAACCCCTAGGCCCTAGCCCCTGACCCCTAAA
64 TC-TAAATCCTAAATCACTAACTCTTAA-CATCTAACCCCTAACCCCTAACCCCTAACCCCTAAA
42675885 TCACAACTCT
Statistics
Matches: 111, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
132 16 0.14
133 94 0.85
134 1 0.01
ACGTcount: A:0.41, C:0.29, G:0.03, T:0.27
Consensus pattern (132 bp):
TTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAACTCAACACCGAATCTC
TAAATCCTAAATCACTAACTCTTAACATCTAACCCCTAACCCCTAACCCCTAACCCCTAAACTTT
AT
Found at i:42675925 original size:14 final size:15
Alignment explanation
Indices: 42675903--42675935 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42675893 CTTAAACCAG
*
42675903 AATCTCTAA-TCCAT
1 AATCCCTAATTCCAT
42675917 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
42675932 AATC
1 AATC
42675936 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:42676459 original size:41 final size:41
Alignment explanation
Indices: 42676340--42676690 Score: 557
Period size: 41 Copynumber: 8.7 Consensus size: 41
42676330 AATATTTTTA
* *
42676340 CGGCGCATTCTCAAAAACGCCGCTAAAAGTCTGAGCATTAG
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
* *
42676381 TGGCGCTTT-TCAAAAACACCGCT-AAAGCCTGAGCATTAG
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
*
42676420 CGGCGCTTTCTCAAAAATGCCGCTAAAAGCCTGAGCATTAG
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
*
42676461 CGGCGCTTTCTCAAAAACGTCGCT-AAAGCCTGAGCATTAG
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
*
42676501 CGGTGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
* *
42676542 CGGCGCTTTTTCAAAAACGCCGCTAAAAGCTTGAGCATTAG
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
*
42676583 CGGCGCTTTCTC-AAAACGCCGTTAAAAGCCTGAGCATTAG
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
* *
42676623 CGGCGCTTTCTAAAAAACGCCGCTAAAAGCTTGAGCATTAG
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
*
42676664 CGGCGCTTTTTCAAAAACGCCGCTAAA
1 CGGCGCTTTCTCAAAAACGCCGCTAAA
42676691 GCCCCAAAAT
Statistics
Matches: 284, Mismatches: 22, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
39 23 0.08
40 100 0.35
41 161 0.57
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (41 bp):
CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
Found at i:42676513 original size:81 final size:82
Alignment explanation
Indices: 42676340--42676690 Score: 557
Period size: 81 Copynumber: 4.3 Consensus size: 82
42676330 AATATTTTTA
* * * *
42676340 CGGCGCATTCTCAAAAACGCCGCTAAAAGTCTGAGCATTAGTGGCGCTTT-TCAAAAACACCGCT
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT
42676404 -AAAGCCTGAGCATTAG
66 AAAAGCCTGAGCATTAG
* *
42676420 CGGCGCTTTCTCAAAAATGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGTCGCT
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT
42676485 -AAAGCCTGAGCATTAG
66 AAAAGCCTGAGCATTAG
* *
42676501 CGGTGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCT
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT
*
42676566 AAAAGCTTGAGCATTAG
66 AAAAGCCTGAGCATTAG
* *
42676583 CGGCGCTTTCTC-AAAACGCCGTTAAAAGCCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCT
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT
*
42676647 AAAAGCTTGAGCATTAG
66 AAAAGCCTGAGCATTAG
*
42676664 CGGCGCTTTTTCAAAAACGCCGCTAAA
1 CGGCGCTTTCTCAAAAACGCCGCTAAA
42676691 GCCCCAAAAT
Statistics
Matches: 251, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
80 46 0.18
81 166 0.66
82 39 0.16
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (82 bp):
CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT
AAAAGCCTGAGCATTAG
Found at i:42676568 original size:122 final size:123
Alignment explanation
Indices: 42676340--42676690 Score: 566
Period size: 122 Copynumber: 2.9 Consensus size: 123
42676330 AATATTTTTA
* * * *
42676340 CGGCGCATTCTCAAAAACGCCGCTAAAAGTCTGAGCATTAGTGGCGCTTT-TCAAAAACACCGCT
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT
* *
42676404 -AAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAATGCCGCTAAAAGCCTGAGCATTAG
66 AAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
* *
42676461 CGGCGCTTTCTCAAAAACGTCGCT-AAAGCCTGAGCATTAGCGGTGCTTTCTCAAAAACGCCGCT
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT
*
42676525 AAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCTTGAGCATTAG
66 AAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
* *
42676583 CGGCGCTTTCTC-AAAACGCCGTTAAAAGCCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCT
1 CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT
*
42676647 AAAAGCTTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
66 AAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
42676691 GCCCCAAAAT
Statistics
Matches: 213, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
120 22 0.10
121 44 0.21
122 147 0.69
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (123 bp):
CGGCGCTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT
AAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTAG
Found at i:42682285 original size:18 final size:18
Alignment explanation
Indices: 42682258--42682350 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
42682248 TACGACCGTT
42682258 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
42682276 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
42682294 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
42682312 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
42682330 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
42682348 TAC
1 TAC
42682351 AGTAGTTGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:42690201 original size:12 final size:12
Alignment explanation
Indices: 42690178--42690206 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42690168 ATTTTTTGTT
42690178 ATTTTTTTTCTC
1 ATTTTTTTTCTC
42690190 ATTTTTTTTCTC
1 ATTTTTTTTCTC
42690202 -TTTTT
1 ATTTTT
42690207 AGACCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTTTTCTC
Found at i:42696424 original size:44 final size:44
Alignment explanation
Indices: 42696376--42696497 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 44
42696366 CATCATTTTG
*
42696376 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTAT-TGCTTTA
1 ATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TATCGGCTTTA
* *
42696420 ATCCGTTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTTA
1 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
** * * * *
42696464 ATCTACCCCACTGCAACCTCAGGGAAATAAGATT
1 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
42696498 TGTCATCCTC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 3 0.05
44 63 0.95
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (44 bp):
ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
Found at i:42696665 original size:44 final size:44
Alignment explanation
Indices: 42696607--42696715 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 44
42696597 CACTCTACTG
** * *
42696607 CAACTTCAAAGAGATAAGATCTA-CTACTTTAATCCGCTCCACTA
1 CAACTTCAGGGAGATAAGAT-TATCGACTTCAATCCGCTCCACTA
* * * *
42696651 CAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTG
1 CAACTTCAGGGAGATAAGATTATCGACTTCAATCCGCTCCACTA
* *
42696695 CAACCTCAGGGAGATGAGATT
1 CAACTTCAGGGAGATAAGATT
42696716 CGCCATCTTC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 2 0.04
44 51 0.96
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATTATCGACTTCAATCCGCTCCACTA
Found at i:42696668 original size:218 final size:218
Alignment explanation
Indices: 42696375--42696770 Score: 614
Period size: 218 Copynumber: 1.8 Consensus size: 218
42696365 CCATCATTTT
* ** * * * *
42696375 GATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATTGCTTTAATCCGTTCCACTACAACTTC
1 GATCCACTCCACTGCAACTTCAAAGAGATAAGATCTACTACTTTAATCCGCTCCACTACAACTTC
* * *
42696440 AGGGAGATAGGATTATCGGCTTTAATCTACCCCACTGCAACCTCAGGGAAATAAGATTTGTCATC
66 AGGGAGATAGGATTATCGGCTTCAATCTACCCCACTGCAACCTCAGGGAAATAAGATTCGCCATC
*
42696505 CTCGATTTGTCCCACTGCAACTTCAGGGG-GATAAGACCTGCTTACTCAGTCTGCTTCGTTGCAA
131 CTCGATCTGTCCCACTGCAACTTC-GGGGAGATAAGACCTGCTTACTCAGTCTGCTTCGTTGCAA
42696569 CCTCAGGGAAATAAGATTTGATGC
195 CCTCAGGGAAATAAGATTTGATGC
*
42696593 GATCCACTCTACTGCAACTTCAAAGAGATAAGATCTACTACTTTAATCCGCTCCACTACAACTTC
1 GATCCACTCCACTGCAACTTCAAAGAGATAAGATCTACTACTTTAATCCGCTCCACTACAACTTC
* * * *
42696658 AGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATGAGATTCGCCATC
66 AGGGAGATAGGATTATCGGCTTCAATCTACCCCACTGCAACCTCAGGGAAATAAGATTCGCCATC
* *
42696723 TTCGATCTGTCCCACTGTAACTTCGGGGAGATAAGACCTGCTTACTCA
131 CTCGATCTGTCCCACTGCAACTTCGGGGAGATAAGACCTGCTTACTCA
42696771 TTGATTTGTT
Statistics
Matches: 159, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
217 4 0.03
218 155 0.97
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (218 bp):
GATCCACTCCACTGCAACTTCAAAGAGATAAGATCTACTACTTTAATCCGCTCCACTACAACTTC
AGGGAGATAGGATTATCGGCTTCAATCTACCCCACTGCAACCTCAGGGAAATAAGATTCGCCATC
CTCGATCTGTCCCACTGCAACTTCGGGGAGATAAGACCTGCTTACTCAGTCTGCTTCGTTGCAAC
CTCAGGGAAATAAGATTTGATGC
Found at i:42710688 original size:14 final size:14
Alignment explanation
Indices: 42710669--42710698 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42710659 ACATCAAAGT
42710669 AAAATAGGACTAAC
1 AAAATAGGACTAAC
42710683 AAAATAGGACTAAC
1 AAAATAGGACTAAC
42710697 AA
1 AA
42710699 GTTAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAATAGGACTAAC
Found at i:42715613 original size:30 final size:30
Alignment explanation
Indices: 42715552--42715613 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
42715542 TATCTTCACC
* * **
42715552 TCAACCGTCGTCTTCATTTTCATCTTTATT
1 TCAACCGTCATCTTCATCTTCATCTCCATT
* *
42715582 TCAATCGTCATCTTCATCTTCGTCTCCATT
1 TCAACCGTCATCTTCATCTTCATCTCCATT
42715612 TC
1 TC
42715614 CTTCCTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.31, G:0.06, T:0.47
Consensus pattern (30 bp):
TCAACCGTCATCTTCATCTTCATCTCCATT
Found at i:42718808 original size:24 final size:24
Alignment explanation
Indices: 42718780--42718831 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42718770 TTAGTAGGTC
* *
42718780 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
42718804 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
42718828 AAAT
1 AAAT
42718832 TTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:42725017 original size:12 final size:11
Alignment explanation
Indices: 42724989--42725018 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
42724979 ATATATTATT
42724989 TATTTTTAAAA
1 TATTTTTAAAA
42725000 TATTTTTAAAA
1 TATTTTTAAAA
42725011 TACTTTTT
1 TA-TTTTT
42725019 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Done.