Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 123 of 345
Found at i:41336410 original size:18 final size:18
Alignment explanation
Indices: 41336387--41336421 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41336377 TACTTTTGTA
*
41336387 ATCTGAATCTAAATCTGG
1 ATCTGAATCCAAATCTGG
41336405 ATCTGAATCCAAATCTG
1 ATCTGAATCCAAATCTG
41336422 AAACTGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (18 bp):
ATCTGAATCCAAATCTGG
Found at i:41339774 original size:43 final size:43
Alignment explanation
Indices: 41339677--41339832 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 43
41339667 TATCGAGATG
* * *
41339677 TGATTACATGTAAGACTATGTCTGGGATATTGGCAT--TGTATT
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAT-TATT
* *
41339719 GTGAATATGTGTAAGACCATGTCTGGGACATTGGCATCATTATT
1 -TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCATTATT
* * * * *
41339763 TGATTTA-GTGTAAGACCCTGTCTAGGACAGTGACATCGA-TATG
1 TGA-TTACGTGTAAGACCATGTCTGGGACATTGGCATC-ATTATT
* *
41339806 TGATTACATGTAAGACCATATCTGGGA
1 TGATTACGTGTAAGACCATGTCTGGGA
41339833 TATAGCATTG
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 3 0.03
43 82 0.88
44 7 0.08
45 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.34
Consensus pattern (43 bp):
TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCATTATT
Found at i:41343646 original size:43 final size:43
Alignment explanation
Indices: 41343589--41343758 Score: 159
Period size: 43 Copynumber: 4.0 Consensus size: 43
41343579 GTTACCGAGA
* * *
41343589 TGTGATTACATGTAAGACCATGTCTGGAATATTGGCATTGTAT
1 TGTGAATACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* *
41343632 TGTGAATACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAT
1 TGTGAATACATGTAAGACCATGTCTGGGACATTGGCATTG-TAT
* * * * *
41343676 T-T-AATTTCGTTTAAGACCCTGTCTGGGACAGTGGCATTG-AT
1 TGTGAA-TACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * * *
41343717 ATGTGATTGCATGTAAGACCATATCTGGGATA-TGGCATTGTA
1 -TGTGAATACATGTAAGACCATGTCTGGGACATTGGCATTGTA
41343759 CGAGCTTTAT
Statistics
Matches: 104, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
41 2 0.02
42 11 0.11
43 86 0.83
44 5 0.05
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (43 bp):
TGTGAATACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:41347845 original size:112 final size:112
Alignment explanation
Indices: 41347648--41347881 Score: 441
Period size: 112 Copynumber: 2.1 Consensus size: 112
41347638 CATGGCTGAG
*
41347648 ACACACGGCCGTGTCTCTACCCATGTGTTTACTACTGGGTAATCTGTTTTGCATTAGTAGGGTGC
1 ACACACGGCCGTGTCTCTACCCATGTGTTTACTACTGGGAAATCTGTTTTGCATTAGTAGGGTGC
41347713 ATGGGACACACGACCGGATCACACACCCATGGGGAAGACCGTGTGTC
66 ATGGGACACACGACCGGATCACACACCCATGGGGAAGACCGTGTGTC
* *
41347760 ACACACGGCCGTGTCTCTGCCCATGTGTTTACTACTGGGAAATCTGTTTTGCATTATTAGGGTGC
1 ACACACGGCCGTGTCTCTACCCATGTGTTTACTACTGGGAAATCTGTTTTGCATTAGTAGGGTGC
41347825 ATGGGACACACGACCGGATCACACACCCATGGGGAAGACCGTGTGTC
66 ATGGGACACACGACCGGATCACACACCCATGGGGAAGACCGTGTGTC
41347872 ACACACGGCC
1 ACACACGGCC
41347882 AAGATACATG
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 119 1.00
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (112 bp):
ACACACGGCCGTGTCTCTACCCATGTGTTTACTACTGGGAAATCTGTTTTGCATTAGTAGGGTGC
ATGGGACACACGACCGGATCACACACCCATGGGGAAGACCGTGTGTC
Found at i:41349103 original size:45 final size:45
Alignment explanation
Indices: 41349033--41349120 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
41349023 AAACATGTGC
* *
41349033 CACATACATCATGAACTCAGGCCACAACTCAATGAGTTCAGATGT
1 CACATACATCATGAACTAAGACCACAACTCAATGAGTTCAGATGT
*
41349078 CACATATATCATGAACTAAGACCACAACTCAATGAGTTCAGAT
1 CACATACATCATGAACTAAGACCACAACTCAATGAGTTCAGAT
41349121 CACATAGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.23
Consensus pattern (45 bp):
CACATACATCATGAACTAAGACCACAACTCAATGAGTTCAGATGT
Found at i:41349124 original size:21 final size:21
Alignment explanation
Indices: 41349055--41349124 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
41349045 GAACTCAGGC
41349055 CACAACTCAATGAGTTCAGATGT
1 CACAACTCAATGAGTTCAGA--T
* ** * *
41349078 CACATATATC-ATGAACTAAGAC
1 CACA-A-CTCAATGAGTTCAGAT
41349100 CACAACTCAATGAGTTCAGAT
1 CACAACTCAATGAGTTCAGAT
41349121 CACA
1 CACA
41349125 TAGTTCCTAG
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
20 2 0.06
21 13 0.38
22 4 0.12
23 4 0.12
24 9 0.26
25 2 0.06
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (21 bp):
CACAACTCAATGAGTTCAGAT
Found at i:41358775 original size:15 final size:15
Alignment explanation
Indices: 41358755--41358786 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41358745 TATAAGTAGT
41358755 GTTGCCAAATCTTAA
1 GTTGCCAAATCTTAA
41358770 GTTGCCAAATCTTAA
1 GTTGCCAAATCTTAA
41358785 GT
1 GT
41358787 GTGAACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (15 bp):
GTTGCCAAATCTTAA
Found at i:41361768 original size:14 final size:14
Alignment explanation
Indices: 41361749--41361787 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
41361739 ATATTTAACT
41361749 TGTTCTTAATTATA
1 TGTTCTTAATTATA
41361763 TGTTCTTAATTATA
1 TGTTCTTAATTATA
41361777 TGTTCTTAATT
1 TGTTCTTAATT
41361788 CTTGTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (14 bp):
TGTTCTTAATTATA
Found at i:41365617 original size:55 final size:54
Alignment explanation
Indices: 41365514--41365639 Score: 148
Period size: 55 Copynumber: 2.3 Consensus size: 54
41365504 AAACTTTCCA
* *
41365514 AAACAACACGGGCGTGTGACACGCCCATGTCTAAAACCTGTGACCGAACCTGTC
1 AAACAACACGGGCGTGCGACACGCCCATGTCCAAAACCTGTGACCGAACCTGTC
* ** *
41365568 AAATCAACACGGGCGTGCGACACGCCCGTG-CCAAGCAACC-GTGGTCGAACCTGTT
1 AAA-CAACACGGGCGTGCGACACGCCCATGTCCAA--AACCTGTGACCGAACCTGTC
41365623 AAACTAACACGGGCGTG
1 AAAC-AACACGGGCGTG
41365640 GGCCTACATA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
54 7 0.11
55 51 0.82
56 4 0.06
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15
Consensus pattern (54 bp):
AAACAACACGGGCGTGCGACACGCCCATGTCCAAAACCTGTGACCGAACCTGTC
Found at i:41371220 original size:25 final size:25
Alignment explanation
Indices: 41371186--41371233 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
41371176 AACTAGGGTT
41371186 AGTTTTTTGGCTTTGGGTTTATACC
1 AGTTTTTTGGCTTTGGGTTTATACC
41371211 AGTTTTTTGGCTTTGGGTTTATA
1 AGTTTTTTGGCTTTGGGTTTATA
41371234 TCAAACAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.08, G:0.25, T:0.54
Consensus pattern (25 bp):
AGTTTTTTGGCTTTGGGTTTATACC
Found at i:41376542 original size:48 final size:48
Alignment explanation
Indices: 41376475--41376590 Score: 144
Period size: 48 Copynumber: 2.4 Consensus size: 48
41376465 TCACCCAGGT
* * * *
41376475 ATGGTCTTACATAGTATCACA-CATCGATGCCAATCCCATGGCCCAGAC
1 ATGGTCTTACATGGGATCACATAAT-GATGCCAATCCCATGGCCCACAC
** * *
41376523 ATGGTCTTACATGGGATCACATAATGATGCCAATTTCTTGTCCCACAC
1 ATGGTCTTACATGGGATCACATAATGATGCCAATCCCATGGCCCACAC
41376571 ATGGTCTTACATGGGATCAC
1 ATGGTCTTACATGGGATCAC
41376591 GCATAACCCT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
48 57 0.97
49 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (48 bp):
ATGGTCTTACATGGGATCACATAATGATGCCAATCCCATGGCCCACAC
Found at i:41378290 original size:16 final size:16
Alignment explanation
Indices: 41378238--41378290 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
41378228 TTTGACACAA
*
41378238 GTTAGAATCTA-CCAG
1 GTTAGAATCTATACAG
* *
41378253 TGTTAGAACCTATACAA
1 -GTTAGAATCTATACAG
*
41378270 ATTAGAATCTATACAG
1 GTTAGAATCTATACAG
41378286 GTTAG
1 GTTAG
41378291 TCAAATGCAC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 27 0.93
17 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (16 bp):
GTTAGAATCTATACAG
Found at i:41384530 original size:23 final size:23
Alignment explanation
Indices: 41384465--41384716 Score: 227
Period size: 23 Copynumber: 10.7 Consensus size: 23
41384455 CAAAGTGTCA
* * * *
41384465 CACTGTAATATAGTCGAAGCTAT
1 CACTGTATTGTAGCCGAAGCTAC
* ** *
41384488 CACTATAACGTAGCTGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
* *
41384511 CACTGTATTGTAACCAAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
*
41384534 CACTGTATTGTAACATGTAGTCGAAGCTAC
1 CACTGTA---T----TGTAGCCGAAGCTAC
* *
41384564 CACTATATTGTAGTCGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
* *
41384587 CACTATATTGTAGCGGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
* *
41384610 CACTGTATTGTGGCCGAAACTAC
1 CACTGTATTGTAGCCGAAGCTAC
*
41384633 CACTGTATTATAGCCGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
*
41384656 CACTATATTGTAGCCGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
* *
41384679 CACTG-AGATGTAGCCAAAGCTAC
1 CACTGTA-TTGTAGCCGAAGCTAC
*
41384702 CACTATATTGTAGCC
1 CACTGTATTGTAGCC
41384717 TATAGATTCC
Statistics
Matches: 188, Mismatches: 32, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.01
23 166 0.88
24 1 0.01
26 1 0.01
27 1 0.01
30 18 0.10
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (23 bp):
CACTGTATTGTAGCCGAAGCTAC
Found at i:41385554 original size:137 final size:137
Alignment explanation
Indices: 41385306--41385560 Score: 332
Period size: 137 Copynumber: 1.9 Consensus size: 137
41385296 ATTTTGGCTT
* * * *
41385306 TTGTTGTGGATACTCGTCAGCTTGTGTGAAAGGCATCGTGTAGCTACATTCTGACCGTCAGCTTG
1 TTGTTGTGGATACTCGTCAGCCTATGTGAAAGGCATCGTGTAGCTACATTCCGACCATCAGCTTG
* * * * *
41385371 TGTGAGAAAACCTAGGTTACCACATTTCGGGTGCTGGTGCTGAATGTCCTACCGACGATTGAGGT
66 TGTGAGAAAACCCAGGTTACCACATTTCGAGTGCTAGTCCTAAATGTCCTACCGACGATTGAGGT
41385436 CTGGTAC
131 CTGGTAC
*
41385443 TTGTTGTGGATACTCGTCAGCCTATGT-AAGTGGCATCGTGTAGCTACATTCCGACCATCAGCTT
1 TTGTTGTGGATACTCGTCAGCCTATGTGAA-AGGCATCGTGTAGCTACATTCCGACCATCAGCTT
* * * ** * * *
41385507 GTTTGAGTAGACCCAGGTTACCATGTTTTGATTGTTAGTCCTAAATGTCCTACC
65 GTGTGAGAAAACCCAGGTTACCACATTTCGAGTGCTAGTCCTAAATGTCCTACC
41385561 AATGGTTGAG
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
136 2 0.02
137 97 0.98
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (137 bp):
TTGTTGTGGATACTCGTCAGCCTATGTGAAAGGCATCGTGTAGCTACATTCCGACCATCAGCTTG
TGTGAGAAAACCCAGGTTACCACATTTCGAGTGCTAGTCCTAAATGTCCTACCGACGATTGAGGT
CTGGTAC
Found at i:41385584 original size:137 final size:137
Alignment explanation
Indices: 41385305--41385651 Score: 322
Period size: 137 Copynumber: 2.5 Consensus size: 137
41385295 CATTTTGGCT
* * * *
41385305 TTTGTTGTGGATACTCGTCAGCTTGTGTGAAAGGCATCGTGTAGCTACATTCTGACCGTCAGCTT
1 TTTGTTGTGGATACTCGTCAGCCTATGTGAAAGGCATCGTGTAGCTACATTCCGACCATCAGCTT
* * * * * *
41385370 GTGTGAGAAAACCTAGGTTACCACATTTCGGGTGCTGGTGCTGAATGTCCTACCGACGATTGAGG
66 GTGTGAGAAAACCCAGGTTACCACATTTCGAGTGCTAGTCCTAAATGTCCTACCAACGATTGAGG
* **
41385435 TCTGGTA
131 TCCGAAA
* *
41385442 CTTGTTGTGGATACTCGTCAGCCTATGT-AAGTGGCATCGTGTAGCTACATTCCGACCATCAGCT
1 TTTGTTGTGGATACTCGTCAGCCTATGTGAA-AGGCATCGTGTAGCTACATTCCGACCATCAGCT
* * * ** * * * * *
41385506 TGTTTGAGTAGACCCAGGTTACCATGTTTTGATTGTTAGTCCTAAATGTCCTACCAATGGTTGAG
65 TGTGTGAGAAAACCCAGGTTACCACATTTCGAGTGCTAGTCCTAAATGTCCTACCAACGATTGAG
41385571 GTCCGAAA
130 GTCCGAAA
** * * * * ** * *
41385579 TTTGTTACGGATGCTTGTCAGCTTGA-GTGAGCA-GCATCGTGTAGCTTACATTTTGATCATCAA
1 TTTGTTGTGGATACTCGTCAGCCT-ATGTGA-AAGGCATCGTGTAGC-TACATTCCGACCATCAG
41385642 CTTGTGTGAG
63 CTTGTGTGAG
41385652 TAGGCCCATT
Statistics
Matches: 167, Mismatches: 38, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
136 2 0.01
137 141 0.84
138 24 0.14
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (137 bp):
TTTGTTGTGGATACTCGTCAGCCTATGTGAAAGGCATCGTGTAGCTACATTCCGACCATCAGCTT
GTGTGAGAAAACCCAGGTTACCACATTTCGAGTGCTAGTCCTAAATGTCCTACCAACGATTGAGG
TCCGAAA
Found at i:41389237 original size:21 final size:20
Alignment explanation
Indices: 41389198--41389239 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
41389188 AATATGTTGT
* *
41389198 AAAATGAAATTTTTTGATAG
1 AAAATGAAAATTATTGATAG
41389218 AAAATGAAAGATTATTGATAG
1 AAAATGAAA-ATTATTGATAG
41389239 A
1 A
41389240 TAAACTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (20 bp):
AAAATGAAAATTATTGATAG
Found at i:41394357 original size:137 final size:137
Alignment explanation
Indices: 41394111--41394376 Score: 334
Period size: 137 Copynumber: 1.9 Consensus size: 137
41394101 ATGTCATTAG
** * * * ** *
41394111 GGTTACCATGTTTTGGGTGCTCGTCCTGAATGTCCTACCGATGGCTGAGTTCTGGCATTTATTGC
1 GGTTACCATGTTTCAGGTGCTCGTCCTGAATGTCCAACCAATGGCTGAGGTCCAGCATTTATTGA
** * * ** *
41394176 GGATACTCGTCAACTTATGTGGGGGACATTGTGTAGCTATATTCTGACCATCAACTTGTGTGAGA
66 GGATACTAATCAACTTATGTGAGCGACATCATGTAGCTATATTCTGACCATCAACTTCTGTGAGA
41394241 AGACCTA
131 AGACCTA
* *
41394248 GGTTACCATGTTTCAGGTGCTGGTCCTGAATGTCCAACCAATGGCTGAGGTCCAGCATTTGTTGA
1 GGTTACCATGTTTCAGGTGCTCGTCCTGAATGTCCAACCAATGGCTGAGGTCCAGCATTTATTGA
* * * * *
41394313 GGATACTAATCAGCTTGTTTGAGCGACATCATGTAGCTATATTCTGACCGTCAGCTTCTGTGAG
66 GGATACTAATCAACTTATGTGAGCGACATCATGTAGCTATATTCTGACCATCAACTTCTGTGAG
41394377 TAGCATCGTG
Statistics
Matches: 107, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
137 107 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (137 bp):
GGTTACCATGTTTCAGGTGCTCGTCCTGAATGTCCAACCAATGGCTGAGGTCCAGCATTTATTGA
GGATACTAATCAACTTATGTGAGCGACATCATGTAGCTATATTCTGACCATCAACTTCTGTGAGA
AGACCTA
Found at i:41400189 original size:55 final size:54
Alignment explanation
Indices: 41400096--41400207 Score: 215
Period size: 55 Copynumber: 2.1 Consensus size: 54
41400086 GAAGTAAGAG
41400096 AAATTTTATGTTTTAAGTTAGGGCATTTTGGTCATTTGGCTAATAAATGAATTA
1 AAATTTTATGTTTTAAGTTAGGGCATTTTGGTCATTTGGCTAATAAATGAATTA
41400150 AAATTTTATGTTTTAAGTTAAGGGCATTTTGGTCATTTGGCTAATAAATGAATTA
1 AAATTTTATGTTTTAAGTT-AGGGCATTTTGGTCATTTGGCTAATAAATGAATTA
41400205 AAA
1 AAA
41400208 ATCAAATTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 19 0.33
55 38 0.67
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (54 bp):
AAATTTTATGTTTTAAGTTAGGGCATTTTGGTCATTTGGCTAATAAATGAATTA
Found at i:41401161 original size:43 final size:42
Alignment explanation
Indices: 41401038--41401191 Score: 148
Period size: 42 Copynumber: 3.6 Consensus size: 42
41401028 TGAGTCTATG
* * *** **
41401038 TGTAAGACCATATCTAGGATATGGCATCAATATGAGACTT-CG
1 TGTAAGACCATATCTGGGATATGGCATCGATGCAAGA-TTAAA
* ** **
41401080 TGTAAGACCATATTTGGGATATGGCATCGATGTGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATGCAAGATTAAA
* *
41401122 TGTAAGACCATAGCTGGGCTATTGGCATCGATGCAAGATTAAA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATGCAAGATTAAA
*
41401165 TTTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
41401192 TGGTATGGTG
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.02
42 58 0.61
43 35 0.37
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATGCAAGATTAAA
Found at i:41404343 original size:18 final size:18
Alignment explanation
Indices: 41404320--41404354 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41404310 TCCTCGTCCT
* *
41404320 CTAAGGGGAAGCAGAAAG
1 CTAAGGGAAAGAAGAAAG
41404338 CTAAGGGAAAGAAGAAA
1 CTAAGGGAAAGAAGAAA
41404355 TCAACTAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.34, T:0.06
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:41409121 original size:25 final size:25
Alignment explanation
Indices: 41409093--41409151 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
41409083 TCAAAGCTCG
* * *
41409093 TGTGAGCATTCTGGTTCACAACTTA
1 TGTGAGCATTCTGATCCACAACTCA
*
41409118 TGTGAGCATTCTGATCCACAGCTCA
1 TGTGAGCATTCTGATCCACAACTCA
41409143 TGTGAGCAT
1 TGTGAGCAT
41409152 ACATGTACAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (25 bp):
TGTGAGCATTCTGATCCACAACTCA
Found at i:41409818 original size:20 final size:19
Alignment explanation
Indices: 41409795--41409836 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
41409785 TAAAGACGGT
41409795 AAATAC-AATGGAAAGTAATG
1 AAATACAAAT-GAAAGTAA-G
*
41409815 AAATTCAAATGAAAGTAAG
1 AAATACAAATGAAAGTAAG
41409834 AAA
1 AAA
41409837 ATTTGGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.19
Consensus pattern (19 bp):
AAATACAAATGAAAGTAAG
Found at i:41413236 original size:15 final size:15
Alignment explanation
Indices: 41413216--41413251 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
41413206 CATAATTTAG
41413216 TTCAATTTTATTCAA
1 TTCAATTTTATTCAA
41413231 TTCAATTTTATTCAA
1 TTCAATTTTATTCAA
41413246 TTCAAT
1 TTCAAT
41413252 ATCAATACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCAATTTTATTCAA
Found at i:41414162 original size:17 final size:16
Alignment explanation
Indices: 41414140--41414171 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41414130 TGTCATTATA
41414140 TTAATATAATATAATTT
1 TTAATATAATA-AATTT
41414157 TTAATATAATAAATT
1 TTAATATAATAAATT
41414172 AATAATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATATAATAAATTT
Found at i:41414187 original size:19 final size:18
Alignment explanation
Indices: 41414163--41414198 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41414153 ATTTTTAATA
*
41414163 TAATAAATTAATAATTTAG
1 TAATAAAATAAT-ATTTAG
41414182 TAATAAAATAATATTTA
1 TAATAAAATAATATTTA
41414199 CTTATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TAATAAAATAATATTTAG
Found at i:41416999 original size:22 final size:22
Alignment explanation
Indices: 41416958--41417011 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
41416948 ACGGCTCAAT
* * *
41416958 GCCATAGATAGGACAGCACATA
1 GCCATAAACAGGACAACACATA
*
41416980 GCCGTAAACAGGACAACACATA
1 GCCATAAACAGGACAACACATA
41417002 GCCATAAACA
1 GCCATAAACA
41417012 TCGCAGCAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (22 bp):
GCCATAAACAGGACAACACATA
Found at i:41417242 original size:22 final size:22
Alignment explanation
Indices: 41417214--41417278 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
41417204 GCAAATACGT
*
41417214 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
41417236 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
41417258 TTGGCGCAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
41417279 AATAATTGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:41417478 original size:41 final size:41
Alignment explanation
Indices: 41417421--41417502 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
41417411 AAAAGCCACC
* *
41417421 GGTGGATCTACGGTCGTCAAGCAACCATGCGATCCTCAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATT
41417462 GGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATT
41417503 TCTTCCTCCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (41 bp):
GGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATT
Found at i:41417819 original size:27 final size:27
Alignment explanation
Indices: 41417761--41417838 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
41417751 GGTAAATCTA
* *
41417761 CAAACCAAGGGTATTTCTGTAATTTTG
1 CAAATCAAGGGTATTTCTGTAATTTTC
*
41417788 TAAATC-AGGCGTATTTCTGTAATTTTC
1 CAAATCAAGG-GTATTTCTGTAATTTTC
* *
41417815 CAAATCAAGGTTATTTCGGTAATT
1 CAAATCAAGGGTATTTCTGTAATT
41417839 CTACCCTACA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.07
27 37 0.86
28 3 0.07
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCTGTAATTTTC
Found at i:41419278 original size:20 final size:20
Alignment explanation
Indices: 41419247--41419302 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
41419237 AGACGATGAA
41419247 CCATTCCATTTACTTACTTT
1 CCATTCCATTTACTTACTTT
*
41419267 CTACTT-CATTTACTTACTTT
1 CCA-TTCCATTTACTTACTTT
41419287 CCATTCCATTTACTTA
1 CCATTCCATTTACTTA
41419303 GCATAAGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (20 bp):
CCATTCCATTTACTTACTTT
Found at i:41419371 original size:21 final size:21
Alignment explanation
Indices: 41419347--41419387 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41419337 TAGTGTGTTT
*
41419347 ATTCATAACATAGGTAAATTC
1 ATTCATAACATAAGTAAATTC
*
41419368 ATTCATAGCATAAGTAAATT
1 ATTCATAACATAAGTAAATT
41419388 TCTCACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (21 bp):
ATTCATAACATAAGTAAATTC
Found at i:41425334 original size:46 final size:46
Alignment explanation
Indices: 41425267--41425442 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
41425257 ATGTAACCCG
*
41425267 TCCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCACA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACA
*
41425313 TCCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGATGCCTAGTT-ACA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCACA
* * * * *
41425363 TCTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCA
1 TC-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACA
*
41425406 TCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
41425443 ATGCTCAAAT
Statistics
Matches: 110, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
44 1 0.01
46 63 0.57
47 26 0.24
48 1 0.01
49 1 0.01
50 6 0.05
51 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACA
Found at i:41425408 original size:93 final size:93
Alignment explanation
Indices: 41425276--41425446 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
41425266 GTCCATAAGT
* * *
41425276 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCACATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGAACTCAACTCAA
41425341 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
41425369 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGAACTCAACTCAA
*
41425434 CGAGTTCGGATGC
66 CGAGCTCGGATGC
41425447 TCAAATATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGAACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:41426571 original size:9 final size:9
Alignment explanation
Indices: 41426557--41426581 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41426547 ACAAGTTTTG
41426557 CAATTTATT
1 CAATTTATT
41426566 CAATTTATT
1 CAATTTATT
41426575 CAATTTA
1 CAATTTA
41426582 GTCCCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (9 bp):
CAATTTATT
Found at i:41430764 original size:26 final size:26
Alignment explanation
Indices: 41430735--41430794 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
41430725 TCCCTTTGAA
* * *
41430735 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
41430761 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
41430789 CCATTC
1 TCATTC
41430795 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:41430820 original size:28 final size:28
Alignment explanation
Indices: 41430749--41430820 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
41430739 TCGATATTTT
**
41430749 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTACCATTCTCAATATCTC
* *
41430777 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTACCATTCTCAATATCTC
* * *
41430805 GTATACTGAGTACCAT
1 GCACACTAAGTACCAT
41430821 ATTTGATTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
GCACACTAAGTACCATTCTCAATATCTC
Found at i:41432603 original size:45 final size:45
Alignment explanation
Indices: 41432540--41432630 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
41432530 GAATTATGTA
* *
41432540 ATCTGAACTCAATGAGTTGTGGTTTGAGTTCATGATATATGTGAC
1 ATCTGAACTCAATAAGTTGTGGTCTGAGTTCATGATATATGTGAC
*
41432585 ATCTGAACTCATTAAGTTGTGGTCTGAGTTCATGATATATGTGAC
1 ATCTGAACTCAATAAGTTGTGGTCTGAGTTCATGATATATGTGAC
41432630 A
1 A
41432631 CATGTTTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.37
Consensus pattern (45 bp):
ATCTGAACTCAATAAGTTGTGGTCTGAGTTCATGATATATGTGAC
Found at i:41444129 original size:44 final size:44
Alignment explanation
Indices: 41444064--41444150 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
41444054 ATGATATCTT
* *
41444064 AAAGTCCATGGTTGTACCATGGCAATTAAGGAAGAATGGACGGA
1 AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATGGACGGA
* * *
41444108 AAAGTCCAT-GTTCATAACATGGCATTTAAGGAGGAATTGACGG
1 AAAGTCCATGGTT-ATAACATGGCAATTAAGGAAGAATGGACGG
41444151 TTAAGGATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 3 0.08
44 34 0.92
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.23
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATGGACGGA
Found at i:41445837 original size:47 final size:47
Alignment explanation
Indices: 41445779--41445900 Score: 199
Period size: 47 Copynumber: 2.6 Consensus size: 47
41445769 ACATTGGCAC
* *
41445779 TAAGACAAGGATACCATGTAAGACTATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATAACATGTAAGACCATGTTTGGAACATGGCATTTGG
41445826 TAAGACAAGGATAACATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATAACATGTAAGACCATGTTTGGAACATGGCATTTGG
* * *
41445873 TAAGATAAGAATATCATGTAAGACCATG
1 TAAGACAAGGATAACATGTAAGACCATG
41445901 CCAAGGCATG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (47 bp):
TAAGACAAGGATAACATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:41446006 original size:55 final size:53
Alignment explanation
Indices: 41445887--41446076 Score: 274
Period size: 53 Copynumber: 3.5 Consensus size: 53
41445877 ATAAGAATAT
* *
41445887 CATGTAAGACCATGCCAAGGCATGGGATTGGTGAGTTCATAAGGCAAGGATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGGTGAGTTCATAAGGCAAGGATAC
* ** *
41445940 CATGTAAGACCATGTCAAGACATGGCATTGACGAGTTACTATAAGGCAAAGG-TCC
1 CATGTAAGACCATGCCAAGACATGGCATTGGTGAGTT-C-ATAAGGC-AAGGATAC
*
41445995 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGGTGAGTTCATAAGGCAAGGATAC
*
41446048 CATGTAAGACCATGTCAAGACATGGCATT
1 CATGTAAGACCATGCCAAGACATGGCATT
41446077 ATAATGACCC
Statistics
Matches: 120, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
52 4 0.03
53 68 0.57
54 2 0.02
55 42 0.35
56 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (53 bp):
CATGTAAGACCATGCCAAGACATGGCATTGGTGAGTTCATAAGGCAAGGATAC
Found at i:41446493 original size:22 final size:24
Alignment explanation
Indices: 41446461--41446513 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 24
41446451 AGTTAATAAA
41446461 AGAAATAGAATAAAGAAAAGA-AAC
1 AGAAA-AGAATAAAGAAAAGAGAAC
*
41446485 A-AAAAGAATAGAGAAAAGAGAAC
1 AGAAAAGAATAAAGAAAAGAGAAC
41446508 AGAAAA
1 AGAAAA
41446514 CATTCGAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 14 0.54
23 7 0.27
24 5 0.19
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.06
Consensus pattern (24 bp):
AGAAAAGAATAAAGAAAAGAGAAC
Found at i:41446502 original size:27 final size:30
Alignment explanation
Indices: 41446458--41446512 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 30
41446448 TAAAGTTAAT
41446458 AAAAGAAATAGAATAAAGA-AA-AGAAACA
1 AAAAGAAATAGAATAAAGAGAACAGAAACA
41446486 AAAAG-AATAGAGA-AAAGAGAACAGAAA
1 AAAAGAAATAGA-ATAAAGAGAACAGAAA
41446513 ACATTCGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 11 0.46
28 8 0.33
29 5 0.21
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (30 bp):
AAAAGAAATAGAATAAAGAGAACAGAAACA
Found at i:41448055 original size:21 final size:22
Alignment explanation
Indices: 41447996--41448057 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
41447986 GCTTTACCGA
41447996 TTAGGCACTTTATGTGTCGTAT
1 TTAGGCACTTTATGTGTCGTAT
* **
41448018 TTCAGGCACGTCGTGTGTCGT-T
1 TT-AGGCACTTTATGTGTCGTAT
41448040 TTAGGCACTTTATGTGTC
1 TTAGGCACTTTATGTGTC
41448058 ATATGCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 13 0.39
22 5 0.15
23 15 0.45
ACGTcount: A:0.15, C:0.18, G:0.26, T:0.42
Consensus pattern (22 bp):
TTAGGCACTTTATGTGTCGTAT
Found at i:41449257 original size:53 final size:53
Alignment explanation
Indices: 41449159--41449286 Score: 150
Period size: 53 Copynumber: 2.4 Consensus size: 53
41449149 AGGGGGTGTT
* * *
41449159 ACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCATGCCAAG
1 ACATGGCATTGGTGAGTT-C-ATAAGGCAAAGGTACCACGTAAGACCATGCCAAG
* *
41449214 GCATGGCATTGGTGAGTTCATAAGGC-AAGGATACCACGTAAGACCATGTCAAG
1 ACATGGCATTGGTGAGTTCATAAGGCAAAGG-TACCACGTAAGACCATGCCAAG
* * *
41449267 ACATGACAATGGTAAGTTCA
1 ACATGGCATTGGTGAGTTCA
41449287 AAAAGGAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
52 4 0.06
53 42 0.67
54 1 0.02
55 16 0.25
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (53 bp):
ACATGGCATTGGTGAGTTCATAAGGCAAAGGTACCACGTAAGACCATGCCAAG
Found at i:41449421 original size:17 final size:16
Alignment explanation
Indices: 41449388--41449421 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41449378 CTTATTTAAT
*
41449388 ATTGAGATTCTAAGTA
1 ATTGAGATTATAAGTA
41449404 ATTGAGATTATCAAGTA
1 ATTGAGATTAT-AAGTA
41449421 A
1 A
41449422 GTGATGAGTT
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:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (16 bp):
ATTGAGATTATAAGTA
Found at i:41466285 original size:78 final size:80
Alignment explanation
Indices: 41466156--41466342 Score: 317
Period size: 78 Copynumber: 2.4 Consensus size: 80
41466146 TATTCGGATG
* *
41466156 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAG-CCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCA
41466220 TTTGT-CGAGTTACT
66 TTTGTGCGAGTTACT
*
41466234 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAGTCCCGAAGGC
41466298 ATTTGTGCGAGTTACT
65 ATTTGTGCGAGTTACT
41466314 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
41466343 AGCAAGTAGC
Statistics
Matches: 103, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
77 2 0.02
78 48 0.47
79 15 0.15
80 38 0.37
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:41466356 original size:80 final size:79
Alignment explanation
Indices: 41466156--41466375 Score: 315
Period size: 80 Copynumber: 2.8 Consensus size: 79
41466146 TATTCGGATG
*
41466156 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTA-ATTCCGGGCTAAG-CCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAG-CTATA-TCCGGGCTAAGTCCCGAAGG
41466218 CATTTGTCGAGTTACT
64 CATTTGTCGAGTTACT
* *
41466234 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TAGCTATATCCGGGCTAAGTCCCGAAGGC
41466298 ATTTGTGCGAGTTACT
65 ATTTGT-CGAGTTACT
* * *
41466314 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGCTATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTATATCCGGGCTAAGTCCCGAAGG
41466376 TACTTGGTTT
Statistics
Matches: 129, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
78 47 0.36
79 33 0.26
80 49 0.38
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTCGAGTTACT
Found at i:41466375 original size:39 final size:40
Alignment explanation
Indices: 41466156--41466342 Score: 317
Period size: 40 Copynumber: 4.7 Consensus size: 40
41466146 TATTCGGATG
* *
41466156 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
41466196 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGT-CGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
41466234 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
41466274 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
41466314 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
41466343 AGCAAGTAGC
Statistics
Matches: 139, Mismatches: 4, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
38 18 0.13
39 32 0.23
40 89 0.64
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:41468206 original size:22 final size:22
Alignment explanation
Indices: 41468181--41468225 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
41468171 TTGCAATTTG
41468181 ATCCACACAGTTTTGGAGACTT
1 ATCCACACAGTTTTGGAGACTT
41468203 ATCCACACAGTTTTGGAGACTT
1 ATCCACACAGTTTTGGAGACTT
41468225 A
1 A
41468226 CACGACTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (22 bp):
ATCCACACAGTTTTGGAGACTT
Found at i:41470447 original size:19 final size:19
Alignment explanation
Indices: 41470419--41470457 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41470409 GATTATATTC
*
41470419 CTTTTATTTTTTTTGATAT
1 CTTTTATTTTCTTTGATAT
*
41470438 CTTTTTTTTTCTTTGATAT
1 CTTTTATTTTCTTTGATAT
41470457 C
1 C
41470458 ACATATCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.05, T:0.72
Consensus pattern (19 bp):
CTTTTATTTTCTTTGATAT
Found at i:41472776 original size:26 final size:26
Alignment explanation
Indices: 41472742--41472792 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
41472732 AAATGTGAAA
*
41472742 GGGTTGCTATGTGCTGATTCCCCGAG
1 GGGTTGCTAAGTGCTGATTCCCCGAG
41472768 GGGTTGCTAAGTGCTGATTCCCCGA
1 GGGTTGCTAAGTGCTGATTCCCCGA
41472793 TTCATTGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29
Consensus pattern (26 bp):
GGGTTGCTAAGTGCTGATTCCCCGAG
Found at i:41472909 original size:103 final size:104
Alignment explanation
Indices: 41472665--41473030 Score: 600
Period size: 103 Copynumber: 3.6 Consensus size: 104
41472655 TGTATATAAA
** * * *
41472665 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
41472729 TTGAAATGTGAAA--GGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
41472766 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
41472831 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
41472870 AGGGGTTGCTAAGTGCTGATTCCCCG-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
**
41472934 TGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
41472972 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
41473031 ATAACGGTTA
Statistics
Matches: 251, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
101 70 0.28
102 57 0.23
103 93 0.37
104 31 0.12
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:41480355 original size:26 final size:26
Alignment explanation
Indices: 41480320--41480370 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
41480310 AATGTGAAAG
*
41480320 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
41480346 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
41480371 TTCATTGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:41480408 original size:102 final size:102
Alignment explanation
Indices: 41480242--41480606 Score: 610
Period size: 102 Copynumber: 3.6 Consensus size: 102
41480232 TGTATATAAA
** * * *
41480242 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
41480306 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAA--TGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
41480345 AGGGGTTGCTAAGTGCTGATTCCCCG-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
41480409 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
41480446 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
41480511 TGAAATAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
41480548 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
41480607 ATAACGGTTA
Statistics
Matches: 251, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
100 26 0.10
101 31 0.12
102 169 0.67
103 25 0.10
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:41495365 original size:59 final size:59
Alignment explanation
Indices: 41495287--41495420 Score: 205
Period size: 59 Copynumber: 2.3 Consensus size: 59
41495277 GTACAGTAAT
* * * *
41495287 GCACTTGGAGAATATTATTATGTGGTGAACTATTAATTATGTTGTTTAGTACTAAATAC
1 GCACTTGGACAATATTATTATGTGATGAACTATTAATTATGTGGTGTAGTACTAAATAC
* *
41495346 GTACTTGGACAATATTATTATGTGATGAACTATTAATTATGTGGTGTAGTACTAAATAT
1 GCACTTGGACAATATTATTATGTGATGAACTATTAATTATGTGGTGTAGTACTAAATAC
*
41495405 GCACTTGGGCAATATT
1 GCACTTGGACAATATT
41495421 GTAGTCATCA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 67 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (59 bp):
GCACTTGGACAATATTATTATGTGATGAACTATTAATTATGTGGTGTAGTACTAAATAC
Found at i:41495523 original size:3 final size:3
Alignment explanation
Indices: 41495515--41495591 Score: 129
Period size: 3 Copynumber: 25.7 Consensus size: 3
41495505 AGCTAATTTT
*
41495515 TTG TTG TTG TTG TTG TTG TT- TCTG TTG TTG TTG TTG TTG TTG CTG
1 TTG TTG TTG TTG TTG TTG TTG T-TG TTG TTG TTG TTG TTG TTG TTG
41495560 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
41495592 ATTATTATTA
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 1 0.01
3 68 0.97
4 1 0.01
ACGTcount: A:0.00, C:0.03, G:0.31, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:41500771 original size:65 final size:65
Alignment explanation
Indices: 41500684--41500835 Score: 205
Period size: 65 Copynumber: 2.3 Consensus size: 65
41500674 TGCGGACTAC
* * *
41500684 CGCAGTTCTTTGTAAGCGTCCTATTATATGATTGGTTGTGATCCTACATATATTGCGGACACAAA
1 CGCAGCTCTTTGTAAGCGTCCTATTATATGATCGGTTGTGATCCTACATATATTGCAGACACAAA
* * * * * *
41500749 CGTAGCTCTTTGTAAGTGTCCTATTTTATGATCGGTTGTGATCCTGCATATGTTGTAGACACAAA
1 CGCAGCTCTTTGTAAGCGTCCTATTATATGATCGGTTGTGATCCTACATATATTGCAGACACAAA
* *
41500814 CGCATCTCTTTGTTAGCGTCCT
1 CGCAGCTCTTTGTAAGCGTCCT
41500836 GATATGGCTC
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 74 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (65 bp):
CGCAGCTCTTTGTAAGCGTCCTATTATATGATCGGTTGTGATCCTACATATATTGCAGACACAAA
Found at i:41501042 original size:26 final size:26
Alignment explanation
Indices: 41500875--41501044 Score: 108
Period size: 26 Copynumber: 6.8 Consensus size: 26
41500865 TGGCTATCCG
* *
41500875 GAGC-TCCTGATTAAAGGCTCTTCGT
1 GAGCTTCCTGATTAATGGCTCTTTGT
** *
41500900 GAGCTTCCTGATTAAAAGTTCTTTGTT
1 GAGCTTCCTGATTAATGGCTCTTTG-T
* * * *
41500927 GAACTTCTTGATT-ATGACTC-TTAT
1 GAGCTTCCTGATTAATGGCTCTTTGT
* *
41500951 GAGCTTCCTG-TTATATAGCTC--AGAT
1 GAGCTTCCTGATTA-ATGGCTCTTTG-T
*
41500976 AAGCTTCCTGA-T-A-GGCTCTTTGT
1 GAGCTTCCTGATTAATGGCTCTTTGT
*
41500999 GAGCTTCTTGATTAATGGCTCTTTGT
1 GAGCTTCCTGATTAATGGCTCTTTGT
*
41501025 TAGCTTCCT-ATTATATGGCT
1 GAGCTTCCTGATTA-ATGGCT
41501045 TGAGAGAGGA
Statistics
Matches: 110, Mismatches: 23, Indels: 23
0.71 0.15 0.15
Matches are distributed among these distances:
22 4 0.04
23 13 0.12
24 11 0.10
25 27 0.25
26 43 0.39
27 12 0.11
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (26 bp):
GAGCTTCCTGATTAATGGCTCTTTGT
Found at i:41512173 original size:22 final size:23
Alignment explanation
Indices: 41512146--41512188 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
41512136 TTTTTATAAT
*
41512146 TTTAAAA-AATTCAATAATTTCC
1 TTTAAAATAATTAAATAATTTCC
*
41512168 TTTAAAATAATTAAATTATTT
1 TTTAAAATAATTAAATAATTT
41512189 TTGAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAAATAATTAAATAATTTCC
Found at i:41518899 original size:31 final size:31
Alignment explanation
Indices: 41518861--41518924 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
41518851 CCTTTTCATA
41518861 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
** *
41518892 TTTCATATTTCATATTACTGGGCTGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
41518923 TT
1 TT
41518925 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:41519164 original size:24 final size:24
Alignment explanation
Indices: 41519135--41519210 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
41519125 GAGGCTGCCT
* *
41519135 CTTTTAATAACTAGGGCAAAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
41519159 CTTTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
41519183 C-TTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
41519206 CTTTT
1 CTTTT
41519211 GCACTTCCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.47
24 26 0.53
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (24 bp):
CTTTTAATAACTGGGGCATAAGCC
Found at i:41519191 original size:23 final size:23
Alignment explanation
Indices: 41519137--41519209 Score: 119
Period size: 23 Copynumber: 3.1 Consensus size: 23
41519127 GGCTGCCTCT
* *
41519137 TTTAATAACTAGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
41519160 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
41519184 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
41519207 TTT
1 TTT
41519210 TGCACTTCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:41519285 original size:20 final size:20
Alignment explanation
Indices: 41519260--41519324 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
41519250 ATGAATACAC
41519260 CATGTGCATATCATACATAT
1 CATGTGCATATCATACATAT
*
41519280 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAT
*
41519300 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAT
41519320 CATGT
1 CATGT
41519325 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (20 bp):
CATGTGCATATCATACATAT
Found at i:41519291 original size:11 final size:11
Alignment explanation
Indices: 41519260--41519313 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
41519250 ATGAATACAC
41519260 CATGTGCATAT
1 CATGTGCATAT
*
41519271 CA--TACATAT
1 CATGTGCATAT
41519280 CATGTGCATAT
1 CATGTGCATAT
* *
41519291 CA--TACATGT
1 CATGTGCATAT
41519300 CATGTGCATAT
1 CATGTGCATAT
41519311 CAT
1 CAT
41519314 ACATACCATG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 15 0.45
11 18 0.55
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (11 bp):
CATGTGCATAT
Found at i:41522360 original size:40 final size:40
Alignment explanation
Indices: 41522305--41522496 Score: 277
Period size: 40 Copynumber: 4.9 Consensus size: 40
41522295 AGATATAGCT
* *
41522305 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATATTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
41522345 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
41522385 ACTCGCACAAATGCCTTC-GGACTTAG-CCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
41522423 AC-CGCA-AAATGCCTTCGGGACTTAGCCCGG-AATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
* *
41522461 ATTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
41522497 CATCCGAATA
Statistics
Matches: 137, Mismatches: 9, Indels: 12
0.87 0.06 0.08
Matches are distributed among these distances:
36 10 0.07
37 13 0.09
38 23 0.17
39 11 0.08
40 79 0.58
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:41522469 original size:76 final size:80
Alignment explanation
Indices: 41522312--41522496 Score: 272
Period size: 76 Copynumber: 2.4 Consensus size: 80
41522302 GCTACTCGCT
* *
41522312 CAAATGCCTTCGGGACTTAGCCCGGTTATATTAACTCGCACAATTGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
41522377 TTATAGTAACTCGCA
66 ATATAGTAACTAGCA
41522392 CAAATGCCTTC-GGACTTAG-CCGGTTATAGTAAC-CGCA-AAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
41522453 A-ATTAGTCATTAGCA
66 ATA-TAGTAACTAGCA
41522468 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
41522497 CATCCGAATA
Statistics
Matches: 96, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
75 1 0.01
76 43 0.45
77 12 0.12
78 21 0.22
79 8 0.08
80 11 0.11
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATATAGTAACTAGCA
Found at i:41524620 original size:28 final size:28
Alignment explanation
Indices: 41524588--41524645 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
41524578 ATGAACCTTG
41524588 GACTCAGTTTTCCCTTACGGCCAAATCT
1 GACTCAGTTTTCCCTTACGGCCAAATCT
41524616 GACTCAGTTTTCCCTTACGGCCAAATCT
1 GACTCAGTTTTCCCTTACGGCCAAATCT
41524644 GA
1 GA
41524646 GTATCTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (28 bp):
GACTCAGTTTTCCCTTACGGCCAAATCT
Found at i:41530460 original size:40 final size:40
Alignment explanation
Indices: 41530377--41530598 Score: 297
Period size: 40 Copynumber: 5.6 Consensus size: 40
41530367 CAACCAAGTA
** * *
41530377 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
* * *
41530416 CCTTCGGGACTTAGCCCGGTTATATTAACTCGCACAATTA
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
41530456 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCATAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
41530496 CCTTCGGGACTTAGCCCGGTTATTGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * *
41530536 CCTTCGGGACTTAGCCCGG-AATTAGTAATTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATG
41530576 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
41530599 CATCCGAATA
Statistics
Matches: 161, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
39 14 0.09
40 146 0.91
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:41533238 original size:19 final size:18
Alignment explanation
Indices: 41533201--41533244 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
41533191 ATACTTACAG
41533201 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
41533218 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
41533237 TACTAATT
1 TAATAATT
41533245 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:41534723 original size:22 final size:22
Alignment explanation
Indices: 41534698--41534743 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
41534688 TCTTATTCAA
41534698 CTGTGGATAATCGATGCACATT
1 CTGTGGATAATCGATGCACATT
41534720 CTGTGGATAATCGATGCACATT
1 CTGTGGATAATCGATGCACATT
41534742 CT
1 CT
41534744 CATAGTACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (22 bp):
CTGTGGATAATCGATGCACATT
Found at i:41540408 original size:5 final size:5
Alignment explanation
Indices: 41540398--41540442 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
41540388 GATAAAAACC
41540398 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
41540443 TTTTTATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:41546908 original size:47 final size:46
Alignment explanation
Indices: 41546806--41546977 Score: 136
Period size: 47 Copynumber: 3.7 Consensus size: 46
41546796 TCATATTGAT
* * * *
41546806 GCCATGTCCCAGACATCGTCTTACACTGACTATCATCTCGTA-GCC-AA
1 GCCATGTCCTAGACAT-GTCTTACACTGGCT-TCGTCTC-AAGGCCGAA
* *
41546853 TG-CTTGTCCTAGACATGTCTTACACTGGCTTACGTGTCAAAGGCCGAA
1 -GCCATGTCCTAGACATGTCTTACACTGGCTT-CGTCTC-AAGGCCGAA
* * * * *
41546901 G-CATGTCCTAGACATGTCTTACACTAGCACTCGTCTCGATGCCGAT
1 GCCATGTCCTAGACATGTCTTACACTGGC-TTCGTCTCAAGGCCGAA
*
41546947 GCCATGTCCCAGACATGGTCTTACACTGGCT
1 GCCATGTCCTAGACAT-GTCTTACACTGGCT
41546978 CTCATAATAT
Statistics
Matches: 101, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
45 1 0.01
46 25 0.25
47 59 0.58
48 16 0.16
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
GCCATGTCCTAGACATGTCTTACACTGGCTTCGTCTCAAGGCCGAA
Found at i:41562396 original size:49 final size:49
Alignment explanation
Indices: 41562291--41562418 Score: 134
Period size: 49 Copynumber: 2.6 Consensus size: 49
41562281 GCACATCAAA
* *
41562291 GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG
1 GTCGATGCCATGTCCCAGACAGGTCTTACACGGACTCTCATATATCGAG
* * * * *
41562340 G-CTGATGCCGTGTCCCAGACAGGTCTTACACGGGCTCTCATCTGTTG-G
1 GTC-GATGCCATGTCCCAGACAGGTCTTACACGGACTCTCATATATCGAG
* * *
41562388 TGTCGATGCCACGTCGCAGATAGGTCTTACA
1 -GTCGATGCCATGTCCCAGACAGGTCTTACA
41562419 TTGACACACA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
48 2 0.03
49 62 0.95
50 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (49 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACACGGACTCTCATATATCGAG
Found at i:41562501 original size:48 final size:48
Alignment explanation
Indices: 41562441--41562559 Score: 166
Period size: 48 Copynumber: 2.5 Consensus size: 48
41562431 AAGCTGACAC
* * * *
41562441 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCCAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGCATATCTCAAGGCCAATG
* * *
41562489 CATGTCCTAGACATGTCTTTCACTAGCTTGCATCTCTCAAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGCATATCTCAAGGCCAATG
*
41562537 TATGTCCCAGACATGTCTTACAC
1 CATGTCCCAGACATGTCTTACAC
41562560 CGGCTCTCGT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTGCATATCTCAAGGCCAATG
Found at i:41574447 original size:20 final size:20
Alignment explanation
Indices: 41574422--41574483 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
41574412 ATTATGTCAT
41574422 ATTTTTATGTTTGAGATGTG
1 ATTTTTATGTTTGAGATGTG
*
41574442 ATTTTTA---TT--GATAT-
1 ATTTTTATGTTTGAGATGTG
41574456 ATTTTTATGTTTGAGATGTG
1 ATTTTTATGTTTGAGATGTG
41574476 ATTTTTAT
1 ATTTTTAT
41574484 TGACTTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 7 0.21
15 4 0.12
17 4 0.12
19 4 0.12
20 15 0.44
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.60
Consensus pattern (20 bp):
ATTTTTATGTTTGAGATGTG
Found at i:41574458 original size:34 final size:34
Alignment explanation
Indices: 41574420--41574486 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
41574410 TCATTATGTC
41574420 ATATTTTTATGTTTGAGATGTGATTTTTATTGAT
1 ATATTTTTATGTTTGAGATGTGATTTTTATTGAT
41574454 ATATTTTTATGTTTGAGATGTGATTTTTATTGA
1 ATATTTTTATGTTTGAGATGTGATTTTTATTGA
41574487 CTTGTTAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (34 bp):
ATATTTTTATGTTTGAGATGTGATTTTTATTGAT
Found at i:41574486 original size:17 final size:17
Alignment explanation
Indices: 41574432--41574486 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
41574422 ATTTTTATGT
41574432 TTGAGATGTGATTTTTA
1 TTGAGATGTGATTTTTA
*
41574449 TT--GATAT-ATTTTTA
1 TTGAGATGTGATTTTTA
41574463 TGTTTGAGATGTGATTTTTA
1 ---TTGAGATGTGATTTTTA
41574483 TTGA
1 TTGA
41574487 CTTGTTAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
17 8 0.27
19 4 0.13
20 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (17 bp):
TTGAGATGTGATTTTTA
Found at i:41577570 original size:24 final size:25
Alignment explanation
Indices: 41577517--41577563 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
41577507 CACATTATAT
41577517 TATTATAATTATAATTATAAAAAAG
1 TATTATAATTATAATTATAAAAAAG
41577542 TATTATAA-TATAATTATAAAAA
1 TATTATAATTATAATTATAAAAA
41577564 TATATTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TATTATAATTATAATTATAAAAAAG
Found at i:41582504 original size:84 final size:84
Alignment explanation
Indices: 41582363--41582519 Score: 224
Period size: 84 Copynumber: 1.9 Consensus size: 84
41582353 GTCTTATAAG
* * * * * * *
41582363 GACTATCTTTTGTGGAAAGTCTGCCCAGGACTATCTTATGTGGAAAGTCCACCAAGGACTATCTT
1 GACTATCTTATGTGGAAAATCCGCCAAGGAATATCTTAGGTGGAAAGTCCACCAAGGACTACCTT
41582428 ATGTGGAAATTCCTCCAAT
66 ATGTGGAAATTCCTCCAAT
* * *
41582447 GACTATCTTATGTGGAAAATCCGCCAATGAATATCTTAGGTGGAATGTCTACCAAGGACTACCTT
1 GACTATCTTATGTGGAAAATCCGCCAAGGAATATCTTAGGTGGAAAGTCCACCAAGGACTACCTT
41582512 ATGTGGAA
66 ATGTGGAA
41582520 TTTTTCCAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 63 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (84 bp):
GACTATCTTATGTGGAAAATCCGCCAAGGAATATCTTAGGTGGAAAGTCCACCAAGGACTACCTT
ATGTGGAAATTCCTCCAAT
Found at i:41582520 original size:28 final size:28
Alignment explanation
Indices: 41582360--41582519 Score: 178
Period size: 28 Copynumber: 5.7 Consensus size: 28
41582350 GAAGTCTTAT
* *
41582360 AAGGACTATCTTTTGTGGAAAGTCTGCC
1 AAGGACTATCTTATGTGGAAAGTCTACC
* *
41582388 CAGGACTATCTTATGTGGAAAGTCCACC
1 AAGGACTATCTTATGTGGAAAGTCTACC
*
41582416 AAGGACTATCTTATGTGGAAATTCCT-CC
1 AAGGACTATCTTATGTGGAAAGT-CTACC
* * **
41582444 AATGACTATCTTATGTGGAAAATCCGCC
1 AAGGACTATCTTATGTGGAAAGTCTACC
* * * *
41582472 AATGAATATCTTAGGTGGAATGTCTACC
1 AAGGACTATCTTATGTGGAAAGTCTACC
*
41582500 AAGGACTACCTTATGTGGAA
1 AAGGACTATCTTATGTGGAA
41582520 TTTTTCCAGT
Statistics
Matches: 110, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 1 0.01
28 108 0.98
29 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (28 bp):
AAGGACTATCTTATGTGGAAAGTCTACC
Found at i:41585202 original size:29 final size:29
Alignment explanation
Indices: 41585169--41585242 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
41585159 GTTGTGAGAT
* *
41585169 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
41585198 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
41585227 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41585243 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:41601734 original size:44 final size:46
Alignment explanation
Indices: 41601662--41601783 Score: 115
Period size: 46 Copynumber: 2.7 Consensus size: 46
41601652 GGATAAGATA
* **
41601662 CCGATGCCAAGTCCC-GGACATGGTCTTACACTAACTTA-A-CTCGTAG
1 CCGATG-CATGTCCCAGG-CAT-GTCTTACACTAACTTACATCTCAAAG
**
41601708 CCGATGCATGTCCCAGGCATGTCTTACACTGGCTTACATCTCAAAG
1 CCGATGCATGTCCCAGGCATGTCTTACACTAACTTACATCTCAAAG
** * *
41601754 CTAATGCATGTCCCAGACGTGTCTTACACT
1 CCGATGCATGTCCCAGGCATGTCTTACACT
41601784 GGCTCTCGTC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
44 14 0.22
45 11 0.17
46 39 0.61
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (46 bp):
CCGATGCATGTCCCAGGCATGTCTTACACTAACTTACATCTCAAAG
Found at i:41607858 original size:34 final size:34
Alignment explanation
Indices: 41607815--41607882 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
41607805 AGACATTTCA
*
41607815 GAGTTTGTATCAAAATTTTTAGTGTGCCAACAAG
1 GAGTTTGTATCAAAATGTTTAGTGTGCCAACAAG
41607849 GAGTTTGTATCAAAATGTTTAGTGTGCCAACAAG
1 GAGTTTGTATCAAAATGTTTAGTGTGCCAACAAG
41607883 TGAAGGCAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (34 bp):
GAGTTTGTATCAAAATGTTTAGTGTGCCAACAAG
Found at i:41620984 original size:17 final size:17
Alignment explanation
Indices: 41620964--41621015 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
41620954 AACACATCAT
41620964 TCATATGCTACCATCTA
1 TCATATGCTACCATCTA
* *
41620981 TCATA--C-ACAAAC-A
1 TCATATGCTACCATCTA
41620994 TCATATGCTACCATCTA
1 TCATATGCTACCATCTA
41621011 TCATA
1 TCATA
41621016 CACAAACATC
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 2 0.07
16 4 0.15
17 11 0.41
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (17 bp):
TCATATGCTACCATCTA
Found at i:41620989 original size:30 final size:29
Alignment explanation
Indices: 41620951--41621026 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 29
41620941 CAACCAAGAC
*
41620951 ATCA-ACACATCATTCATATGCTACCATCT
1 ATCATACACAACA-TCATATGCTACCATCT
41620980 ATCATACACAAACATCATATGCTACCATCT
1 ATCATACAC-AACATCATATGCTACCATCT
41621010 ATCATACACAAACATCA
1 ATCATACAC-AACATCA
41621027 CATACTTATC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 4 0.09
30 37 0.84
31 3 0.07
ACGTcount: A:0.41, C:0.30, G:0.03, T:0.26
Consensus pattern (29 bp):
ATCATACACAACATCATATGCTACCATCT
Found at i:41624799 original size:6 final size:6
Alignment explanation
Indices: 41624788--41624815 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41624778 CTCTTGTTTG
41624788 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
41624816 CTTTGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:41627218 original size:42 final size:42
Alignment explanation
Indices: 41627099--41627218 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 42
41627089 CCGTACCAAC
* * *
41627099 GCCATATCCCAGGTATGGTCTTACATGTAATCTCGTATCGAT
1 GCCATATCCCAGATATGGTCTTACACGTAATCTCATATCGAT
* * * *
41627141 GCAAATAGCCCAGTTGTGGTCTTACACG-AAGTCTCATATCGAT
1 GC-CATATCCCAGATATGGTCTTACACGTAA-TCTCATATCGAT
*
41627184 GCCATATCCCAGATATGGTCTTGCACGTAATCTCA
1 GCCATATCCCAGATATGGTCTTACACGTAATCTCA
41627219 GTAACCCTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 29 0.45
43 35 0.55
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACACGTAATCTCATATCGAT
Found at i:41630234 original size:3 final size:3
Alignment explanation
Indices: 41630219--41630262 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
41630209 ATTATAGTAC
* * * *
41630219 AAT AAT GAT AAT AAT AAT ATT AAT AGT AAT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41630263 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41630808 original size:15 final size:15
Alignment explanation
Indices: 41630784--41630824 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
41630774 TATATACATG
41630784 AAAAATAATAATAAC
1 AAAAATAATAATAAC
*
41630799 AATAAA-AATAATAGC
1 AA-AAATAATAATAAC
41630814 AAAAATAATAA
1 AAAAATAATAA
41630825 AATTAACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 17 0.74
16 3 0.13
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAAATAATAATAAC
Found at i:41630824 original size:3 final size:3
Alignment explanation
Indices: 41630664--41630811 Score: 95
Period size: 3 Copynumber: 48.0 Consensus size: 3
41630654 GTAAAATAAG
* * * *
41630664 ATA ATA ATA ATA ATA AT- ATA TTG ATA ATA AGTA AAA ATA A-A AGGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A-TA
* * * * *
41630709 ATA AAA ATA ATA GTA ATA ATA AGA ATA TTTA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
* * *
41630755 ACA ATA AT- ATAA ATA ATA ATA TATA CATGA AAA ATA ATA ATA ACA ATA
1 ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A ATA ATA ATA ATA ATA ATA
*
41630803 AAA ATA ATA
1 ATA ATA ATA
41630812 GCAAAAATAA
Statistics
Matches: 110, Mismatches: 26, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
2 6 0.05
3 88 0.80
4 15 0.14
5 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:41630826 original size:9 final size:9
Alignment explanation
Indices: 41630708--41630826 Score: 62
Period size: 9 Copynumber: 12.8 Consensus size: 9
41630698 AAATAAAAGG
41630708 AATAAAAAT
1 AATAAAAAT
**
41630717 AATAGTAAT
1 AATAAAAAT
*
41630726 AATAAGAAT
1 AATAAAAAT
**
41630735 -AT-TTAAT
1 AATAAAAAT
**
41630742 AATAGTAAT
1 AATAAAAAT
*
41630751 AATAACAAT
1 AATAAAAAT
*
41630760 AATATAAAT
1 AATAAAAAT
*
41630769 AATAATATAT
1 AATAA-AAAT
41630779 ACATGAAAAAT
1 A-AT-AAAAAT
* *
41630790 AATAATAAC
1 AATAAAAAT
41630799 AATAAAAAT
1 AATAAAAAT
41630808 AATAGCAAAAAT
1 AAT---AAAAAT
41630820 AATAAAA
1 AATAAAA
41630827 TTAACTAATT
Statistics
Matches: 84, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
7 3 0.04
8 4 0.05
9 54 0.64
10 6 0.07
11 6 0.07
12 11 0.13
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (9 bp):
AATAAAAAT
Found at i:41632428 original size:88 final size:88
Alignment explanation
Indices: 41632191--41632915 Score: 615
Period size: 88 Copynumber: 8.5 Consensus size: 88
41632181 GGGAGATAAA
* *** * * *
41632191 ATCTG-AATTTCCAGCCTGTTACCCTACTGCTTAATAGGTTAAGGCCCTTCGTCTCCGATCTGCT
1 ATCTGAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGCT
41632255 CCACTACTGCTTA-GGGAGACAAG
66 CCACTACTGCTTAGGGGA-ACAAG
* * * * *
41632278 ATTTGTAATTTTCAG-CTGTTACCCTACTGTTTAGGAGGTTAAGGCCCTTCATCTTCGATCTGCT
1 ATCTGAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGCT
*
41632342 CCACTATTGCTTAGGGGAACAAG
66 CCACTACTGCTTAGGGGAACAAG
* * *
41632365 ATCTGAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTCGTCTTCGATCTGCT
1 ATCTGAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGCT
* *
41632430 CTACTTCTGCTTA-GGGAGACAAG
66 CCACTACTGCTTAGGGGA-ACAAG
* * * * * *
41632453 ATCTGTAAA-TTTCAGCCTGTTACCCTACTGCTTAGGAGGTCAAGGCTCACCGTCTTCGATCTAC
1 ATCTG-AAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGC
41632517 TCCACTACTGCTTAGGGAGAA-AAG
65 TCCACTACTGCTTAGGG-GAACAAG
* * * * * * * *
41632541 ATCTGTAATTTTTAGCCTAG-TACCCTACTGCTTAGGGGGTCAAGGCTCACCGTCCTCGATCTAC
1 ATCTGAAATTTTCAGCCT-GTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGC
** *
41632605 TCTGCTACTGCTTAGAGAGAA-AAG
65 TCCACTACTGCTTAG-GGGAACAAG
* * *
41632629 ATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCAT-A---T-G-T-T--T
1 ATCTGAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGCT
*
41632685 CC-CTACTGCTTAGGGTG-ATAAG
66 CCACTACTGCTTAGGG-GAACAAG
* * *
41632707 ATCTGTAAA--TTCATCCTGTTACCCTACTGCTTAGGAGTTTAAGG-CC--CATC-T-G-T-T--
1 ATCTG-AAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGC
*
41632761 TCC-CTACTGCTTAGGGTG-ATAAG
65 TCCACTACTGCTTAGGG-GAACAAG
* * *
41632784 ATCTGTAAA--TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGATCTGT
1 ATCTG-AAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTG-
* * * ***
41632847 TTCC-CTATTGTTTAGGGGGTTAAG
64 CTCCACTACTGCTTAGGGGAACAAG
41632871 ATCTGTAAA-TTT-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
1 ATCTG-AAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
41632916 TTCTGAATTT
Statistics
Matches: 557, Mismatches: 52, Indels: 58
0.84 0.08 0.09
Matches are distributed among these distances:
75 1 0.00
76 2 0.00
77 103 0.18
78 21 0.04
79 4 0.01
80 3 0.01
81 2 0.00
82 2 0.00
83 2 0.00
84 2 0.00
86 1 0.00
87 144 0.26
88 260 0.47
89 8 0.01
90 2 0.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (88 bp):
ATCTGAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCGATCTGCT
CCACTACTGCTTAGGGGAACAAG
Found at i:41632573 original size:176 final size:174
Alignment explanation
Indices: 41632178--41632915 Score: 733
Period size: 176 Copynumber: 4.3 Consensus size: 174
41632168 CACTGCAACT
* *** *
41632178 TTAGGGAGATAAA-ATCTG-AATTTCCAGCCTGTTACCCTACTGCTTAATAGGTTAAGGCCCTTC
1 TTAGGGAGA-AAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATC
* * * *
41632241 GTCTCCGATCTGCTCCACTACTGCTTAGGGAGACAAGATTTGTAATTTTCAG-CTGTTACCCTAC
65 GTCTTCGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGTAAATTTCAGCCTGTTACCCTAC
* * ** *
41632305 TGTTTAGGAGG-TTAAGGCCCTTCATCTTCGATCTGCTCCACTATTGC
130 TGCTTAGG-GGTTTAAGGCTCACCATCTTCGATCT-CTCC-CTACTGC
* * *
41632352 TTAGGG-GAACAAGATCTGAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTC
1 TTAGGGAGAA-AAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATC
*
41632416 GTCTTCGATCTGCTCTACTTCTGCTTAGGGAGACAAGATCTGTAAATTTCAGCCTGTTACCCTAC
65 GTCTTCGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGTAAATTTCAGCCTGTTACCCTAC
* *
41632481 TGCTTAGGAGG-TCAAGGCTCACCGTCTTCGATCTACTCCACTACTGC
130 TGCTTAGG-GGTTTAAGGCTCACCATCTTCGATCT-CTCC-CTACTGC
* * * *
41632528 TTAGGGAGAAAAGATCTGTAATTTTTAGCCTAG-TACCCTACTGCTTAGGGGGTCAAGGCTCACC
1 TTAGGGAGAAAAGATCTGTAATTTTCAGCCT-GTTACCCTACTGCTTAGGGGGTTAAGGCCCATC
* * * * *
41632592 GTCCTCGATCTACTCTGCTACTGCTTAGAGAGAAAAGATCTGT-AATTTCCAGCCTGTTACCCTA
65 GTCTTCGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGTAAATTT-CAGCCTGTTACCCTA
*
41632656 CTGCTTAGGGGTTTAAGG--C-CCAT-AT-G-T-T-TCCCTACTGC
129 CTGCTTAGGGGTTTAAGGCTCACCATCTTCGATCTCTCCCTACTGC
* * * * * *
41632694 TTAGGGTGATAAGATCTGTAA-ATTCATCCTGTTACCCTACTGCTTAGGAGTTTAAGGCCCA---
1 TTAGGGAGAAAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCG
* * *
41632755 TC-T-G-T-T--TC-CCTACTGCTTAGGGTGATAAGATCTGTAAA-TTCAGCCTGTTACCCTACT
66 TCTTCGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGTAAATTTCAGCCTGTTACCCTACT
* * * * *
41632812 GCTTAGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTATTGT
131 GCTTAGGGGTTTAAGGCTCACCATCTTCGATC--TCTCCCTACTGC
* ** *
41632858 TTAGGGGGTTAAGATCTGTAAATTT-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
1 TTAGGGAGAAAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
41632916 TTCTGAATTT
Statistics
Matches: 487, Mismatches: 56, Indels: 52
0.82 0.09 0.09
Matches are distributed among these distances:
154 33 0.07
155 25 0.05
156 5 0.01
157 2 0.00
158 2 0.00
159 2 0.00
160 2 0.00
161 1 0.00
162 2 0.00
163 1 0.00
164 58 0.12
165 33 0.07
166 26 0.05
167 3 0.01
169 1 0.00
170 1 0.00
171 1 0.00
172 2 0.00
173 7 0.01
174 12 0.02
175 94 0.19
176 170 0.35
177 4 0.01
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (174 bp):
TTAGGGAGAAAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCG
TCTTCGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGTAAATTTCAGCCTGTTACCCTACT
GCTTAGGGGTTTAAGGCTCACCATCTTCGATCTCTCCCTACTGC
Found at i:41632747 original size:77 final size:77
Alignment explanation
Indices: 41632609--41632915 Score: 398
Period size: 77 Copynumber: 3.8 Consensus size: 77
41632599 ATCTACTCTG
* * * *
41632609 CTACTGCTTAGAGAGAAAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGG
1 CTACTGCTTAGGGTGATAAGATCTGTAAATT-CAGCCTGTTACCCTACTGCTTAGGGGTTTAAGG
41632674 CCCATATGTTTCC
65 CCCATATGTTTCC
* *
41632687 CTACTGCTTAGGGTGATAAGATCTGTAAATTCATCCTGTTACCCTACTGCTTAGGAGTTTAAGGC
1 CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
*
41632752 CCATCTGTTTCC
66 CCATATGTTTCC
41632764 CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
1 CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
41632829 TCATCACCTTCGATCTGTTTCC
66 -C--CA---T--A--TGTTTCC
* * * * * *
41632851 CTATTGTTTAGGGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
1 CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
41632916 TTCTGAATTT
Statistics
Matches: 203, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
77 106 0.52
78 28 0.14
80 2 0.01
83 1 0.00
87 66 0.33
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (77 bp):
CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
CCATATGTTTCC
Found at i:41632817 original size:43 final size:42
Alignment explanation
Indices: 41632756--41632913 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 42
41632746 TAAGGCCCAT
* *
41632756 CTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGG-GTTAAGATCTGTAAATTCAGC
* * ** *
41632799 CTGTTACCCTACTGCTTAGGGGTTTAAGGCTCAT-CACCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGG-TTAA-GATC-TGTAAATTCAG-C
* * * *
41632843 CTGTTTCCCTATTGTTTAGGGGGTTAAGATCTGTAAATTTAGC
1 CTGTTACCCTACTGCTTA-GGGGTTAAGATCTGTAAATTCAGC
41632886 CTGTTACCCTACTGCTTAGGGGGTTAAG
1 CTGTTACCCTACTGCTTA-GGGGTTAAG
41632914 GCTTCTGAAT
Statistics
Matches: 89, Mismatches: 19, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
42 2 0.02
43 55 0.62
44 27 0.30
45 5 0.06
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (42 bp):
CTGTTACCCTACTGCTTAGGGGTTAAGATCTGTAAATTCAGC
Found at i:41632900 original size:87 final size:87
Alignment explanation
Indices: 41632754--41632916 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
41632744 TTTAAGGCCC
*
41632754 ATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGG
1 ATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGG
*
41632819 GGTTTAAGGCTCATCACCTTCG
66 GGGTTAAGGCTCATCACCTTCG
* * * *
41632841 ATCTGTTTCCCTATTGTTTAGGGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGG
1 ATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGG
41632906 GGGTTAAGGCT
66 GGGTTAAGGCT
41632917 TCTGAATTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (87 bp):
ATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGG
GGGTTAAGGCTCATCACCTTCG
Found at i:41642070 original size:40 final size:40
Alignment explanation
Indices: 41642025--41642216 Score: 219
Period size: 40 Copynumber: 4.8 Consensus size: 40
41642015 ATAACCACAA
* *
41642025 GCACAATTGCCTTCGGGTCTTAACCC-GAGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGA-TATAGCAACTC
*
41642065 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
41642105 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
41642145 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
41642185 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
41642217 CATTCAAATG
Statistics
Matches: 142, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 1 0.01
40 135 0.95
41 6 0.04
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:41650212 original size:40 final size:40
Alignment explanation
Indices: 41650137--41650347 Score: 248
Period size: 40 Copynumber: 5.3 Consensus size: 40
41650127 TCTTCAGAAT
* * * *
41650137 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * * * *
41650176 TTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
* *
41650216 TTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
* *
41650256 TTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* *
41650296 TTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
41650336 TTAGCCCGGATA
1 TTAGCCCGGATA
41650348 TCATTCAAAT
Statistics
Matches: 154, Mismatches: 15, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
39 5 0.03
40 145 0.94
41 4 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:41653492 original size:64 final size:63
Alignment explanation
Indices: 41653412--41653594 Score: 183
Period size: 67 Copynumber: 2.8 Consensus size: 63
41653402 AGACATTATG
* *
41653412 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAAGGGATAT
1 ATGTAGCTAGGTCGCATGGGTG-TACTATGTGTACACCATGTAGACAAGAGAGCTAAGAGATAA
* * * * * *
41653476 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-G-TACTA-TG-TGTACACCATGTAGACAAGAGAGCTAAGAGAT
41653541 AA
62 AA
* * *
41653543 ACTG--GCTAGGTCACATGGGTGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGTACTATGTGTACACCATGTAG-ACAAGAGAGC
41653595 CGAACTATAT
Statistics
Matches: 97, Mismatches: 17, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
61 1 0.01
62 19 0.20
63 1 0.01
64 23 0.24
65 5 0.05
66 16 0.16
67 30 0.31
68 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.23
Consensus pattern (63 bp):
ATGTAGCTAGGTCGCATGGGTGTACTATGTGTACACCATGTAGACAAGAGAGCTAAGAGATAA
Found at i:41657884 original size:68 final size:67
Alignment explanation
Indices: 41657812--41657961 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
41657802 CATCATGTGT
* * * *
41657812 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
41657874 ATGTAG
62 ATGTAG
** * *
41657880 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
41657945 AG
66 AG
41657947 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
41657962 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:41657917 original size:64 final size:64
Alignment explanation
Indices: 41657836--41658019 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
41657826 AGACATTATG
* * *
41657836 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
41657900 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGAGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
41657965 AA
63 AA
* * *
41657967 ACTG--GCTAGGTCACATGAGTGATACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
41658020 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:41660835 original size:22 final size:22
Alignment explanation
Indices: 41660791--41660835 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41660781 TGCAGTGCTA
* *
41660791 TTTTAAGTTCTTCTATCTTCTC
1 TTTTAAGTTCTTCAATCTACTC
41660813 TTTTAA-TTCTTCAATTCTACTC
1 TTTTAAGTTCTTCAA-TCTACTC
41660835 T
1 T
41660836 GACTAGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTAAGTTCTTCAATCTACTC
Found at i:41666391 original size:10 final size:10
Alignment explanation
Indices: 41666366--41666394 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
41666356 CATTTCTCTT
41666366 TTTCTATTCA
1 TTTCTATTCA
41666376 -TTCTATTCA
1 TTTCTATTCA
41666385 TTTCTATTCA
1 TTTCTATTCA
41666395 AACACGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:41677433 original size:131 final size:131
Alignment explanation
Indices: 41677199--41677494 Score: 358
Period size: 131 Copynumber: 2.3 Consensus size: 131
41677189 ACTGATTGGA
** * * * * *
41677199 AAATTAGCTAAAACAAATGAGATTGCTCATGATATTATATCGAATGAACTTATGTTGCAATCTTA
1 AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTACAATCTTA
* * *** **
41677264 AATTAGCCAACATTAACAATATCAGCTGTGATATTAAATCAACGGGCTATTTGGAGTAACAATAT
66 AATCAGACAACATTAACAATATCAGCTACAATATTAAATCAACAAGCTATTTGGAGTAACAATAT
41677329 T
131 T
*
41677330 AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTACGATCTTA
1 AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTACAATCTTA
* * * * * ***
41677395 AATCAGAGAACCTTTACAATATCAGCTACAATATTAAATCAGCAAGCTGTTTGGAGTAGTGATAT
66 AATCAGACAACATTAACAATATCAGCTACAATATTAAATCAACAAGCTATTTGGAGTAACAATAT
41677460 T
131 T
* * *
41677461 AAATAAGCTAACTCAGATAAGACTGTTCATGATA
1 AAATTAGCTAACTCAAATAAGATTGTTCATGATA
41677495 AATAAAGTAA
Statistics
Matches: 139, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
131 139 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (131 bp):
AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTACAATCTTA
AATCAGACAACATTAACAATATCAGCTACAATATTAAATCAACAAGCTATTTGGAGTAACAATAT
T
Found at i:41681092 original size:36 final size:36
Alignment explanation
Indices: 41681045--41681117 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
41681035 TTATGGAGTG
*
41681045 TTAATAAGATAGTATTAAAGTTTTGTTAGGAAATTT
1 TTAATAAGATAGTATTAAAGTCTTGTTAGGAAATTT
41681081 TTAATAAGATAGTATTAAAGTCTTGTTAGGAAATTT
1 TTAATAAGATAGTATTAAAGTCTTGTTAGGAAATTT
41681117 T
1 T
41681118 AACATTTCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (36 bp):
TTAATAAGATAGTATTAAAGTCTTGTTAGGAAATTT
Found at i:41685558 original size:28 final size:27
Alignment explanation
Indices: 41685495--41685564 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
41685485 ATATTAAGTC
*
41685495 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
41685522 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
*
41685550 TGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41685565 GTACAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:41693390 original size:21 final size:19
Alignment explanation
Indices: 41693361--41693401 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41693351 ACTCCCTTGA
41693361 CCCCAAAACATTTTTATTTCT
1 CCCCAAAAC--TTTTATTTCT
*
41693382 CCCCTAAACTTTTATTTCT
1 CCCCAAAACTTTTATTTCT
41693401 C
1 C
41693402 ACCTTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (19 bp):
CCCCAAAACTTTTATTTCT
Found at i:41703091 original size:10 final size:10
Alignment explanation
Indices: 41703074--41703130 Score: 60
Period size: 10 Copynumber: 5.4 Consensus size: 10
41703064 CATAAACACC
41703074 TAAAAATAAA
1 TAAAAATAAA
*
41703084 TCAAAATAAA
1 TAAAAATAAA
41703094 TAAAGAATAAA
1 TAAA-AATAAA
* *
41703105 GAATTGAATAAA
1 TAA--AAATAAA
41703117 TAAAAATAAA
1 TAAAAATAAA
41703127 TAAA
1 TAAA
41703131 CCAAATTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 22 0.58
11 8 0.21
12 8 0.21
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:41709679 original size:195 final size:194
Alignment explanation
Indices: 41709337--41709723 Score: 587
Period size: 195 Copynumber: 2.0 Consensus size: 194
41709327 CACTCCCATT
* * *
41709337 AAAATTACAAACGACAAGTTGATGTGGTAATTAAAAAATAGGTATAATAACAAATTTAGCCCGCC
1 AAAAATACAAACGACAAGATGATGTGGCAATTAAAAAATAGGTATAATAACAAATTTAGCCCGCC
* *
41709402 AATATTTACATATTATATCAATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAATA
66 AATATTTAAATATCATATCAATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAATA
* *
41709467 TTCTCAATTTGATCCTAATTCTAAAAAAATTCAAAGAAATATATAAAAATACATAAATATTTTCA
131 TTCTCAATTTAATCCTAATT-TAAAAAAATTCAAAGAAATATATAAAAACACATAAATATTTTCA
* * * * *
41709532 AAAAATACAAACGTCAAGATGATGTGGCAGTTAAAAATATATGTATAATAATAAATTTAGCCC-T
1 AAAAATACAAACGACAAGATGATGTGGCAATTAAAAA-ATAGGTATAATAACAAATTTAGCCCGC
* *
41709596 CAATTTTTAAATATCATATCGATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAAT
65 CAATATTTAAATATCATATCAATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAAT
* * * *
41709661 GTTCTCAATTTAATCCTAATTTTAAAAAGTTCAAAGAAATATATAAAAACACATACATATTTT
130 ATTCTCAATTTAATCCTAATTTAAAAAAATTCAAAGAAATATATAAAAACACATAAATATTTT
41709724 TTAAAATTTT
Statistics
Matches: 173, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
194 38 0.22
195 112 0.65
196 23 0.13
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (194 bp):
AAAAATACAAACGACAAGATGATGTGGCAATTAAAAAATAGGTATAATAACAAATTTAGCCCGCC
AATATTTAAATATCATATCAATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAATA
TTCTCAATTTAATCCTAATTTAAAAAAATTCAAAGAAATATATAAAAACACATAAATATTTTCA
Found at i:41709815 original size:27 final size:29
Alignment explanation
Indices: 41709785--41709856 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
41709775 TATTGTTCAC
* * *
41709785 AATAAATAATGATATATAAA-A-TTTAAA
1 AATATATAATAATAAATAAATATTTTAAA
*
41709812 AATATATAAAAATAAATAAATATTTTAAA
1 AATATATAATAATAAATAAATATTTTAAA
41709841 AATATATAATAATAAA
1 AATATATAATAATAAA
41709857 ATTTTTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 16 0.42
28 1 0.03
29 21 0.55
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (29 bp):
AATATATAATAATAAATAAATATTTTAAA
Found at i:41709821 original size:10 final size:10
Alignment explanation
Indices: 41709786--41709854 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
41709776 ATTGTTCACA
41709786 ATAAATAATGAT
1 ATAAA-AAT-AT
41709798 ATATAAAAT-T
1 ATA-AAAATAT
41709808 -TAAAAATAT
1 ATAAAAATAT
*
41709817 ATAAAAATAA
1 ATAAAAATAT
*
41709827 ATAAATAT-T
1 ATAAAAATAT
*
41709836 TTAAAAATAT
1 ATAAAAATAT
*
41709846 ATAATAATA
1 ATAAAAATA
41709855 AAATTTTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
8 5 0.11
9 9 0.20
10 24 0.52
12 6 0.13
13 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:41711901 original size:49 final size:49
Alignment explanation
Indices: 41711698--41711917 Score: 161
Period size: 49 Copynumber: 4.6 Consensus size: 49
41711688 ATGTGTGTGT
* * * * *
41711698 TAGTGTAAAACCTGTCTGGGACACGGCATCGATATAGATAAGTG-AGAGC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACACAAATAAGTGCA-AGC
* * * * * *
41711747 CAGTGTAAGACCTATCTGGGACATGGTATTGGCCTCAAA-ATA-TGCAAGC
1 TAGTGTAAGACCTGTCTGGGACATGGCA-TCGACACAAATA-AGTGCAAGC
* * * * * * *
41711796 TAGTGTAAAACCTGTCTGGGACATGGCATCG--GC--TTGAG-GTATGT
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACACAAATAAGTGCAAGC
*
41711840 TAGTGTAAGACCTGTCTAGGACATGGCATCGACACAAATAAGTG-AGAGC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACACAAATAAGTGCA-AGC
*
41711889 TAGTGTAAGACCTGTCTGGGACGTGGCAT
1 TAGTGTAAGACCTGTCTGGGACATGGCAT
41711918 TAACTTAGAT
Statistics
Matches: 129, Mismatches: 31, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
44 33 0.26
46 2 0.02
48 6 0.05
49 82 0.64
50 6 0.05
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (49 bp):
TAGTGTAAGACCTGTCTGGGACATGGCATCGACACAAATAAGTGCAAGC
Found at i:41719552 original size:49 final size:49
Alignment explanation
Indices: 41719478--41719608 Score: 217
Period size: 49 Copynumber: 2.7 Consensus size: 49
41719468 ATGTGTGTGT
*
41719478 TAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCATGATATGCAAAC
1 TAGTGTAAGACCTGTCTGGGGCATGGCATCGGCCTCATGATATGCAAAC
* *
41719527 TAGTGTAAGACCTGTCTGGGGCATGGCATCAGCCTCATGATATGCAAGC
1 TAGTGTAAGACCTGTCTGGGGCATGGCATCGGCCTCATGATATGCAAAC
* *
41719576 TAGTGTAAGACTTGTCTAGGGCATGGCATCGGC
1 TAGTGTAAGACCTGTCTGGGGCATGGCATCGGC
41719609 TTGAGGTGTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (49 bp):
TAGTGTAAGACCTGTCTGGGGCATGGCATCGGCCTCATGATATGCAAAC
Found at i:41724521 original size:219 final size:220
Alignment explanation
Indices: 41724134--41724576 Score: 595
Period size: 219 Copynumber: 2.0 Consensus size: 220
41724124 AATAGATTTT
* * * * *
41724134 TTTTATTCATGGGTAAACTCAGTCTTTCAGTGAGTAAGTCAACTAAGAATATCAAGACTGTTAAT
1 TTTTATTCATGGGTAAACTCAATCTCTCAATAAGTAAGTCAACTAAGAAGATCAAGACTGTTAAT
** * *
41724199 TCCAAAGACGTCCTAACAATGGGAGTAGCATAAGTAGTTGAGCAACAAATCAGTCAATGGAAAGG
66 TCCAAAGACGTCCTAACAATGCAAGTAGCACAAGGAGTTGAGCAACAAATCAGTCAATGGAAAGG
* * * * **
41724264 TAAGGAAGAATTCGAGGTAATCCACTTGGATGATTACGATTTTTTTATTGGCTTGAATTTTTTTG
131 AAAGGAAGAATTCGAGGTAATCCACTTGGATAATTACGATTTTATTATTGGCTTAAATTTCATTG
41724329 ACAAGATTAATGCTCTTTTGGTTCC
196 ACAAGATTAATGCTCTTTTGGTTCC
* *
41724354 TTTTA-TCATGGGTAAACTCAATCTCTCAATAAGTGAGTCAACTAAGAAGATTAAGACTGTTAAT
1 TTTTATTCATGGGTAAACTCAATCTCTCAATAAGTAAGTCAACTAAGAAGATCAAGACTGTTAAT
* * * * * *
41724418 TCCAAAGAGGT-CTCGACTATGCAAGTAGCACAAGGAGTTGAGCTATAGATC-GATCAATGGAAA
66 TCCAAAGACGTCCT-AACAATGCAAGTAGCACAAGGAGTTGAGCAACAAATCAG-TCAATGGAAA
* * * *
41724481 GGAAAGGAAGACTTTGAGGTAATCCACTTTGATAATTACGATTTTATTCTTGGCTTAAATTTCAT
129 GGAAAGGAAGAATTCGAGGTAATCCACTTGGATAATTACGATTTTATTATTGGCTTAAATTTCAT
*
41724546 TGACAAGATTAATGCTCTTTTGGTTCT
194 TGACAAGATTAATGCTCTTTTGGTTCC
41724573 TTTT
1 TTTT
41724577 TCCAACTATA
Statistics
Matches: 193, Mismatches: 28, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
218 3 0.02
219 185 0.96
220 5 0.03
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (220 bp):
TTTTATTCATGGGTAAACTCAATCTCTCAATAAGTAAGTCAACTAAGAAGATCAAGACTGTTAAT
TCCAAAGACGTCCTAACAATGCAAGTAGCACAAGGAGTTGAGCAACAAATCAGTCAATGGAAAGG
AAAGGAAGAATTCGAGGTAATCCACTTGGATAATTACGATTTTATTATTGGCTTAAATTTCATTG
ACAAGATTAATGCTCTTTTGGTTCC
Found at i:41726426 original size:22 final size:22
Alignment explanation
Indices: 41726355--41726431 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
41726345 GAAAATTATA
*
41726355 CGAACTCTATGTGTTATTCATG
1 CGAACCCTATGTGTTATTCATG
* * * *
41726377 CAAACCCTTCATG-ATTATTTATA
1 CGAACCC-T-ATGTGTTATTCATG
41726400 CGAACCCTATGTGTTATTCATG
1 CGAACCCTATGTGTTATTCATG
*
41726422 TGAACCCTAT
1 CGAACCCTAT
41726432 ATATTTGTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
21 3 0.07
22 22 0.52
23 14 0.33
24 3 0.07
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (22 bp):
CGAACCCTATGTGTTATTCATG
Found at i:41726428 original size:45 final size:44
Alignment explanation
Indices: 41726331--41726430 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 44
41726321 TATATATCCT
*
41726331 TGTGAACCCTACATGAAAATTATACGAACTCTATGTGTTATTCA
1 TGTGAACCCTACATGAAAATTATACGAACCCTATGTGTTATTCA
** * * *
41726375 TGCAAACCCTTCATGATTATTTATACGAACCCTATGTGTTATTCA
1 TGTGAACCCTACATGA-AAATTATACGAACCCTATGTGTTATTCA
41726420 TGTGAACCCTA
1 TGTGAACCCTA
41726431 TATATTTGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 13 0.28
45 33 0.72
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (44 bp):
TGTGAACCCTACATGAAAATTATACGAACCCTATGTGTTATTCA
Found at i:41731763 original size:40 final size:41
Alignment explanation
Indices: 41731716--41731817 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
41731706 ATGAATCGAT
41731716 TATATATGGCACTTAGTGTGCAA-ATCGGA-ATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCAAGA-CGGAGATAGCTTCGGC
* * *
41731756 TATATATGGCAGTTAATGTGCAAGACTGAGATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCAAGACGGAGATAGCTTCGGC
* *
41731797 TATAAAAGGCACTTAGTGTGC
1 TATATATGGCACTTAGTGTGC
41731818 GAGATTATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 24 0.45
41 29 0.55
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (41 bp):
TATATATGGCACTTAGTGTGCAAGACGGAGATAGCTTCGGC
Found at i:41741177 original size:40 final size:40
Alignment explanation
Indices: 41741130--41741315 Score: 171
Period size: 40 Copynumber: 4.6 Consensus size: 40
41741120 ATGAATCGAT
**
41741130 TATATATGGCACTTAGTGTGCGAATCGAAATAGCTTTGGC
1 TATATATGGCACTTAGTGTGCGAATCGAAATAGCTTCAGC
* *
41741170 TATATATGGCACTTAGTGTGTGAATCGGAATAGCTTCAGC
1 TATATATGGCACTTAGTGTGCGAATCGAAATAGCTTCAGC
* * * * *
41741210 TATATATGACACTTAGTGTGC-AAGACTAAAATAGTTTCGGC
1 TATATATGGCACTTAGTGTGCGAA-TC-GAAATAGCTTCAGC
* * *
41741251 TATGA-AAGGCACTTAGTGTACGAGAT-TATAATAGCTTCAGC
1 TAT-ATATGGCACTTAGTGTGCGA-ATCGA-AATAGCTTCAGC
* *
41741292 TATGCTTTGGCACTTAGTGTGCGA
1 TAT-ATATGGCACTTAGTGTGCGA
41741316 GATATTGAAT
Statistics
Matches: 117, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
39 2 0.02
40 57 0.49
41 40 0.34
42 17 0.15
43 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCGAATCGAAATAGCTTCAGC
Found at i:41745091 original size:24 final size:24
Alignment explanation
Indices: 41745059--41745105 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41745049 CAAACACTTG
41745059 GTGTACACTCTCTTTCTATGTCTA
1 GTGTACACTCTCTTTCTATGTCTA
*
41745083 GTGTACACTCTCTTTCTGTGTCT
1 GTGTACACTCTCTTTCTATGTCT
41745106 TTCTTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (24 bp):
GTGTACACTCTCTTTCTATGTCTA
Found at i:41747699 original size:27 final size:26
Alignment explanation
Indices: 41747639--41747700 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
41747629 ATAAGATTCC
41747639 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
41747665 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
41747693 ATTTTATT
1 ATTTTATT
41747701 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Done.