Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 130 of 235
Found at i:44067433 original size:22 final size:23
Alignment explanation
Indices: 44067379--44067447 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 23
44067369 GCTATCTGAT
*
44067379 TATTAGCACGTCAGTGCTATCTG
1 TATTAGCACGTCAGTGCTCTCTG
44067402 ATTATTAGCACGTCAGTGCTCTCTG
1 --TATTAGCACGTCAGTGCTCTCTG
* *
44067427 -ATTAGCACATCCGTGCTCTCT
1 TATTAGCACGTCAGTGCTCTCT
44067448 ATTCATTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
22 19 0.46
25 22 0.54
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (23 bp):
TATTAGCACGTCAGTGCTCTCTG
Found at i:44077183 original size:39 final size:42
Alignment explanation
Indices: 44077129--44077226 Score: 162
Period size: 44 Copynumber: 2.3 Consensus size: 42
44077119 TTTCTGCATT
*
44077129 TATTTA-TTTTAATAAAATAAGATATCATATTTTAATGATAA
1 TATTTAGTTATAATAAAATAAGATATCATATTTTAATGATAA
44077170 TATTTAGTTATAAAATAAAATAAGATATCATATTTTAATGATAA
1 TATTTAGTTAT--AATAAAATAAGATATCATATTTTAATGATAA
44077214 TATTTAGTTATAA
1 TATTTAGTTATAA
44077227 AATTATTAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
41 6 0.11
42 5 0.09
44 42 0.79
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (42 bp):
TATTTAGTTATAATAAAATAAGATATCATATTTTAATGATAA
Found at i:44077187 original size:44 final size:44
Alignment explanation
Indices: 44077139--44077229 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
44077129 TATTTATTTT
44077139 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
1 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
44077183 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
1 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
44077227 AAT
1 AAT
44077230 TATTAGTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (44 bp):
AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
Found at i:44077364 original size:19 final size:19
Alignment explanation
Indices: 44077324--44077369 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
44077314 TTTTTCAAAA
*
44077324 TTTAGAGAAATAAGCTATT
1 TTTAGAGAAATAAGCGATT
*
44077343 TTTAGAGAAATACATCGA-T
1 TTTAGAGAAATA-AGCGATT
44077362 TTTAGAGA
1 TTTAGAGA
44077370 TAGAGTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (19 bp):
TTTAGAGAAATAAGCGATT
Found at i:44077540 original size:18 final size:19
Alignment explanation
Indices: 44077494--44077540 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
44077484 TCTTAAATTT
*
44077494 AACTCTCTCTATTCTCTCTA
1 AACT-TCTCAATTCTCTCTA
44077514 AACTT-TCAATTCTCTC-A
1 AACTTCTCAATTCTCTCTA
*
44077531 AATTTCTCAA
1 AACTTCTCAA
44077541 GATTTATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 1 0.04
20 4 0.17
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (19 bp):
AACTTCTCAATTCTCTCTA
Found at i:44081082 original size:14 final size:14
Alignment explanation
Indices: 44081063--44081089 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44081053 TCAGAAAAAT
44081063 AAAAATATTTTTAG
1 AAAAATATTTTTAG
44081077 AAAAATATTTTTA
1 AAAAATATTTTTA
44081090 ACGTAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
AAAAATATTTTTAG
Found at i:44081143 original size:17 final size:18
Alignment explanation
Indices: 44081098--44081145 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
44081088 TAACGTAATT
*
44081098 AAATAATTATTAGTGAAAG
1 AAATAATT-TTAGTCAAAG
*
44081117 TAATTAATTTTAGTCAAA-
1 -AAATAATTTTAGTCAAAG
44081135 AAATAATTTTA
1 AAATAATTTTA
44081146 AAATAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
19 8 0.32
20 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (18 bp):
AAATAATTTTAGTCAAAG
Found at i:44083005 original size:20 final size:20
Alignment explanation
Indices: 44082973--44083010 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44082963 TGTTTCACAT
44082973 TCATATAACTAATATTTATA
1 TCATATAACTAATATTTATA
*
44082993 TCAT-TAACATAATTTTTA
1 TCATATAAC-TAATATTTA
44083011 ACTTAATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TCATATAACTAATATTTATA
Found at i:44083331 original size:454 final size:454
Alignment explanation
Indices: 44082484--44083394 Score: 1750
Period size: 454 Copynumber: 2.0 Consensus size: 454
44082474 CCCCTGCAAA
44082484 TTCAAACCAAAACAACCAACACCAATGTTTCACATTCATATAACTAATATTTATATCATTAACAA
1 TTCAAACCAAAACAACCAACACCAATGTTTCACATTCATATAACTAATATTTATATCATTAACAA
44082549 AATTTTTAACTTAATAACTATCATAGCATCATTCAAAATTGATTAAAAACTTCATTCATTTAACC
66 AATTTTTAACTTAATAACTATCATAGCATCATTCAAAATTGATTAAAAACTTCATTCATTTAACC
44082614 ATCTAAATCTTATAATTCATCTTTCACTACCCAATGTAACATACATATTCAAGTGACTAAACAAC
131 ATCTAAATCTTATAATTCATCTTTCACTACCCAATGTAACATACATATTCAAGTGACTAAACAAC
*
44082679 ACCTATGTACATGCCACCTTTACCCAAAAGAAAAATATACATCACCAAGTTTGTGTTGGAGTCGG
196 ACCTATGTACATGCCACCTTTACCCAAAAGAAAAATATACATCACCAAATTTGTGTTGGAGTCGG
* * ** *
44082744 GATTGTTCTGGATGCTGAGCCGGGACACTTGACTTCTACTAACCTGTGCACGGAAACAACCGTAC
261 GAATGTTCTAGATGCTGAGCCAAGACAATTGACTTCTACTAACCTGTGCACGGAAACAACCGTAC
44082809 GCTGAGTATGGATATACTCAGTGGTATTACCATAATTCAAAATATATCATCAATAATAATAATAT
326 GCTGAGTATGGATATACTCAGTGGTATTACCATAATTCAAAATATATCATCAATAATAATAATAT
44082874 AAATATTAAAATACATAACAATTAATTTTTTAAATACTAATTCATACTTTATTTTTATTTTTAT
391 AAATATTAAAATACATAACAATTAATTTTTTAAATACTAATTCATACTTTATTTTTATTTTTAT
*
44082938 TTCAAACCAAAACAACCAACACCAATGTTTCACATTCATATAACTAATATTTATATCATTAACAT
1 TTCAAACCAAAACAACCAACACCAATGTTTCACATTCATATAACTAATATTTATATCATTAACAA
44083003 AATTTTTAACTTAATAACTATCATAGCATCATTCAAAATTGATTAAAAACTTCATTCATTTAACC
66 AATTTTTAACTTAATAACTATCATAGCATCATTCAAAATTGATTAAAAACTTCATTCATTTAACC
44083068 ATCTAAATCTTATAATTCATCTTTCACTACCCAATGTAACATACATATTCAAGTGACTAAACAAC
131 ATCTAAATCTTATAATTCATCTTTCACTACCCAATGTAACATACATATTCAAGTGACTAAACAAC
44083133 ACCTATGTACATGCCACCTTTACCCAAAAGAAAAATATACATCACCAAATTTGTGTTGGAGTCGG
196 ACCTATGTACATGCCACCTTTACCCAAAAGAAAAATATACATCACCAAATTTGTGTTGGAGTCGG
44083198 GAATGTTCTAGATGCTGAGCCAAGACAATTGACTTCTACTAACCTGTGCACGGAAACAACCGTAC
261 GAATGTTCTAGATGCTGAGCCAAGACAATTGACTTCTACTAACCTGTGCACGGAAACAACCGTAC
*
44083263 GTTGAGTATGGATATACTCAGTGGTATTACCATAATTCAAAATATATCATCAATAATAATAATAT
326 GCTGAGTATGGATATACTCAGTGGTATTACCATAATTCAAAATATATCATCAATAATAATAATAT
44083328 AAATATTAAAATACATAACAATTAATTTTTTAAATACTAATTCATACTTTATTTTTATTTTTAT
391 AAATATTAAAATACATAACAATTAATTTTTTAAATACTAATTCATACTTTATTTTTATTTTTAT
44083392 TTC
1 TTC
44083395 CATCATTTCA
Statistics
Matches: 449, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
454 449 1.00
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.34
Consensus pattern (454 bp):
TTCAAACCAAAACAACCAACACCAATGTTTCACATTCATATAACTAATATTTATATCATTAACAA
AATTTTTAACTTAATAACTATCATAGCATCATTCAAAATTGATTAAAAACTTCATTCATTTAACC
ATCTAAATCTTATAATTCATCTTTCACTACCCAATGTAACATACATATTCAAGTGACTAAACAAC
ACCTATGTACATGCCACCTTTACCCAAAAGAAAAATATACATCACCAAATTTGTGTTGGAGTCGG
GAATGTTCTAGATGCTGAGCCAAGACAATTGACTTCTACTAACCTGTGCACGGAAACAACCGTAC
GCTGAGTATGGATATACTCAGTGGTATTACCATAATTCAAAATATATCATCAATAATAATAATAT
AAATATTAAAATACATAACAATTAATTTTTTAAATACTAATTCATACTTTATTTTTATTTTTAT
Found at i:44084103 original size:36 final size:36
Alignment explanation
Indices: 44084062--44084135 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
44084052 AATAAATAAC
44084062 TTGAATTATAGTAATACAAACCGTAATTCTCCCGTT
1 TTGAATTATAGTAATACAAACCGTAATTCTCCCGTT
*
44084098 TTGAATTATAGTAATACACACCGTAATTCTCCCGTT
1 TTGAATTATAGTAATACAAACCGTAATTCTCCCGTT
44084134 TT
1 TT
44084136 AGTCCTCGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
TTGAATTATAGTAATACAAACCGTAATTCTCCCGTT
Found at i:44085140 original size:23 final size:23
Alignment explanation
Indices: 44085097--44085155 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
44085087 AACTTAATTT
44085097 AAAAAAATAATAATAATTTAATA
1 AAAAAAATAATAATAATTTAATA
*
44085120 AAAAAACATACTAATAA-TTAATA
1 AAAAAA-ATAATAATAATTTAATA
* *
44085143 ATAATAATAATAA
1 AAAAAAATAATAA
44085156 AATCTTAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 6 0.19
23 16 0.52
24 9 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAAAATAATAATAATTTAATA
Found at i:44090738 original size:94 final size:94
Alignment explanation
Indices: 44090577--44090781 Score: 365
Period size: 94 Copynumber: 2.2 Consensus size: 94
44090567 TGGAAGCTTA
* *
44090577 GCACACGCCCATGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCTATTTGGT
1 GCACACGCCCGTGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCCATTTGGT
*
44090642 CATGAGCAAGTTAGGGTCACATGGCCAAG
66 CATGAACAAGTTAGGGTCACATGGCCAAG
* *
44090671 GCACACGCCCGTGTGCTAAGGACACGCCTGTGTCCCGTGCCCATAGAGCTCTTTGTCCATTTGGT
1 GCACACGCCCGTGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCCATTTGGT
44090736 CATGAACAAGTTAGGGTCACATGGCCAAG
66 CATGAACAAGTTAGGGTCACATGGCCAAG
44090765 GCACACGCCCGTGTGCT
1 GCACACGCCCGTGTGCT
44090782 TAAGCCATAT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 106 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.22
Consensus pattern (94 bp):
GCACACGCCCGTGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCCATTTGGT
CATGAACAAGTTAGGGTCACATGGCCAAG
Found at i:44092605 original size:22 final size:22
Alignment explanation
Indices: 44092577--44092650 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
44092567 TGTACCTGTC
*
44092577 CACACGGGCCTATTAGGGGTTG
1 CACACGGGCCTATGAGGGGTTG
44092599 CACACGGGCCTATGAGGGGTTG
1 CACACGGGCCTATGAGGGGTTG
*
44092621 CACACGGGCCTGTGAGGGGTTG
1 CACACGGGCCTATGAGGGGTTG
44092643 CACACGGG
1 CACACGGG
44092651 TGTGTGGGTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.41, T:0.18
Consensus pattern (22 bp):
CACACGGGCCTATGAGGGGTTG
Found at i:44092699 original size:30 final size:30
Alignment explanation
Indices: 44092665--44092729 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
44092655 TGGGTAAGTA
* *
44092665 ACACGGGCATGTGGAAACTAGAGCTATCAC
1 ACACGGGCATATGAAAACTAGAGCTATCAC
** * *
44092695 ACACGGGTGTATGAAAATTGGAGCTATCAC
1 ACACGGGCATATGAAAACTAGAGCTATCAC
44092725 ACACG
1 ACACG
44092730 AGTGTATGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (30 bp):
ACACGGGCATATGAAAACTAGAGCTATCAC
Found at i:44095053 original size:18 final size:18
Alignment explanation
Indices: 44095030--44095086 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
44095020 ACACTAAGAT
44095030 AAATGCAACTTAACAAGC
1 AAATGCAACTTAACAAGC
** *
44095048 AAATGCTTC-TAA-AA-T
1 AAATGCAACTTAACAAGC
44095063 AAATGCAACTTAACAAGC
1 AAATGCAACTTAACAAGC
44095081 AAATGC
1 AAATGC
44095087 TTCTAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 5 0.17
18 13 0.43
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (18 bp):
AAATGCAACTTAACAAGC
Found at i:44095068 original size:33 final size:33
Alignment explanation
Indices: 44095023--44095097 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
44095013 TTAAATAACA
*
44095023 CTAAGATAAATGCAACTTAACAAGCAAATGCTT
1 CTAAAATAAATGCAACTTAACAAGCAAATGCTT
44095056 CTAAAATAAATGCAACTTAACAAGCAAATGCTT
1 CTAAAATAAATGCAACTTAACAAGCAAATGCTT
44095089 CTAAAATAA
1 CTAAAATAA
44095098 TAAAAAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.24
Consensus pattern (33 bp):
CTAAAATAAATGCAACTTAACAAGCAAATGCTT
Found at i:44095139 original size:30 final size:31
Alignment explanation
Indices: 44095080--44095140 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
44095070 ACTTAACAAG
44095080 CAAATGCTTCTAAAATAATAAAAAAAATTAA
1 CAAATGCTTCTAAAATAATAAAAAAAATTAA
*
44095111 CAAATGCCTT-TAAAATAAT-AAGAAAATTAA
1 CAAATG-CTTCTAAAATAATAAAAAAAATTAA
44095141 TAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 10 0.36
31 15 0.54
32 3 0.11
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (31 bp):
CAAATGCTTCTAAAATAATAAAAAAAATTAA
Found at i:44096041 original size:19 final size:19
Alignment explanation
Indices: 44096017--44096064 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
44096007 TTCTCTTTTT
44096017 TTTCTATTCATTCTATCCA
1 TTTCTATTCATTCTATCCA
*
44096036 TTTCTATTCATTCTATTCA
1 TTTCTATTCATTCTATCCA
44096055 TTTCTATTCA
1 TTTCTATTCA
44096065 AACACACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTCTATTCATTCTATCCA
Found at i:44096042 original size:10 final size:10
Alignment explanation
Indices: 44096017--44096064 Score: 73
Period size: 9 Copynumber: 5.0 Consensus size: 10
44096007 TTCTCTTTTT
44096017 TTTCTATTCA
1 TTTCTATTCA
*
44096027 -TTCTATCCA
1 TTTCTATTCA
44096036 TTTCTATTCA
1 TTTCTATTCA
44096046 -TTCTATTCA
1 TTTCTATTCA
44096055 TTTCTATTCA
1 TTTCTATTCA
44096065 AACACACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 17 0.50
10 17 0.50
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:44098775 original size:39 final size:39
Alignment explanation
Indices: 44098729--44098907 Score: 286
Period size: 39 Copynumber: 4.6 Consensus size: 39
44098719 GCTCTGATGA
* *
44098729 GCTTCAGTTAGCCTTCGGGCTTCCGTATAGTACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
44098768 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
44098807 GCTTCACTTAGCCTTCGGGCTTCCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
44098846 GCTTCACTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
44098885 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
44098908 AGATCACGAT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 131 1.00
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:44100939 original size:13 final size:13
Alignment explanation
Indices: 44100921--44100945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44100911 TATTTTAATA
44100921 TTATTTTGTGTGT
1 TTATTTTGTGTGT
44100934 TTATTTTGTGTG
1 TTATTTTGTGTG
44100946 CATTCGATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:44102192 original size:41 final size:41
Alignment explanation
Indices: 44101893--44102181 Score: 569
Period size: 41 Copynumber: 7.0 Consensus size: 41
44101883 GTCTATTAGC
44101893 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
1 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
44101934 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
1 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
44101975 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
1 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
44102016 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
1 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
44102057 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
1 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
44102098 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
1 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
*
44102139 CTTAATGCCGGTGACACATTTCGGACTATAAGTCTAGCAGG
1 CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
44102180 CT
1 CT
44102182 AAGAGCCGGT
Statistics
Matches: 247, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 247 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
CTTAATGCCGGTGACACATTTCAGACTATAAGTCTAGCAGG
Found at i:44102452 original size:33 final size:32
Alignment explanation
Indices: 44102396--44102459 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
44102386 ATATATATAT
44102396 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
44102428 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
44102460 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:44102476 original size:33 final size:33
Alignment explanation
Indices: 44102403--44102476 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
44102393 TATATATATA
* * **
44102403 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
44102435 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
44102468 TGTATGTAT
1 TATATGTAT
44102477 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:44116575 original size:21 final size:21
Alignment explanation
Indices: 44116549--44116591 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
44116539 TATCATTATC
44116549 TAAATCCTCAAAGAAAGTAAT
1 TAAATCCTCAAAGAAAGTAAT
*
44116570 TAAATCCTCAGAGAAAGTAAT
1 TAAATCCTCAAAGAAAGTAAT
44116591 T
1 T
44116592 TGAACCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (21 bp):
TAAATCCTCAAAGAAAGTAAT
Found at i:44118742 original size:20 final size:20
Alignment explanation
Indices: 44118717--44118758 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
44118707 TTCTGCTGCC
*
44118717 AACTTTTCTAATGTTTTGCA
1 AACTTTTCTAATATTTTGCA
44118737 AACTTTTCTAATATTTTGCA
1 AACTTTTCTAATATTTTGCA
44118757 AA
1 AA
44118759 TTCTTGGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (20 bp):
AACTTTTCTAATATTTTGCA
Found at i:44125575 original size:51 final size:51
Alignment explanation
Indices: 44125499--44125600 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
44125489 TTGGAGATAG
44125499 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
1 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
44125550 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
1 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
44125601 ACCATATACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (51 bp):
GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
Found at i:44125853 original size:25 final size:25
Alignment explanation
Indices: 44125825--44125875 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
44125815 AGTTTCCAGC
44125825 ATGCTGATCTGGGTTGTTTGTTCTT
1 ATGCTGATCTGGGTTGTTTGTTCTT
44125850 ATGCTGATCTGGGTTGTTTGTTCTT
1 ATGCTGATCTGGGTTGTTTGTTCTT
44125875 A
1 A
44125876 GTCCCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.10, C:0.12, G:0.27, T:0.51
Consensus pattern (25 bp):
ATGCTGATCTGGGTTGTTTGTTCTT
Found at i:44137101 original size:23 final size:23
Alignment explanation
Indices: 44137052--44137101 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
44137042 GATTTTTTCT
* *
44137052 AAATATTATTACTAAATATTCCT
1 AAATATTATCACTAAATATTCCA
*
44137075 AAATGTTATCACTAAATAATT-CA
1 AAATATTATCACTAAAT-ATTCCA
44137098 AAAT
1 AAAT
44137102 TTAAAAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATATTATCACTAAATATTCCA
Found at i:44138815 original size:33 final size:33
Alignment explanation
Indices: 44138778--44138851 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
44138768 GAGTCAAATC
*
44138778 TAATAGGAAAATTCATAAATCGAGTTAATGTGA
1 TAATAGGAAAATCCATAAATCGAGTTAATGTGA
44138811 TAATAGGAAAATCCATAAATCGAGTTAATGTGA
1 TAATAGGAAAATCCATAAATCGAGTTAATGTGA
44138844 TAATAGGA
1 TAATAGGA
44138852 GTTTTAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (33 bp):
TAATAGGAAAATCCATAAATCGAGTTAATGTGA
Found at i:44140127 original size:15 final size:15
Alignment explanation
Indices: 44140104--44140138 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
44140094 CATTATCCTA
* *
44140104 AATATATTATAATTT
1 AATAAATTATAATAT
44140119 AATAAATTATAATAT
1 AATAAATTATAATAT
44140134 AATAA
1 AATAA
44140139 TTAATCAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATTATAATAT
Found at i:44141058 original size:14 final size:14
Alignment explanation
Indices: 44141021--44141063 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
44141011 TTAATTCTTA
*
44141021 AATATAAAAAATTT
1 AATATAAAATATTT
*
44141035 ATTA-ATAAATATTT
1 AATATA-AAATATTT
44141049 AATATAAAATATTT
1 AATATAAAATATTT
44141063 A
1 A
44141064 TCAGTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATAAAATATTT
Found at i:44144571 original size:26 final size:27
Alignment explanation
Indices: 44144541--44144606 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
44144531 TTTTTAATGG
*
44144541 TGCTCACACGAGCTA-TGAAATGGGTC
1 TGCTCACACGAGCTAGTGAAATGGGCC
*
44144567 TGCTCATACGAGC-AGTGAAATGGGCC
1 TGCTCACACGAGCTAGTGAAATGGGCC
44144593 TGCTCACACGAGCT
1 TGCTCACACGAGCT
44144607 GTAGGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (27 bp):
TGCTCACACGAGCTAGTGAAATGGGCC
Found at i:44155329 original size:18 final size:17
Alignment explanation
Indices: 44155298--44155333 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
44155288 AGGCCTTCCT
44155298 TTTATATAATAGTAGTA
1 TTTATATAATAGTAGTA
44155315 TTTATATATATAGTAGTA
1 TTTATATA-ATAGTAGTA
44155333 T
1 T
44155334 AGATACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTATATAATAGTAGTA
Found at i:44155526 original size:28 final size:28
Alignment explanation
Indices: 44155464--44155528 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
44155454 TCATATACAT
*
44155464 AAGTAAATTATATAAAATATTCAAAAAA
1 AAGTAAATTATATAAAAAATTCAAAAAA
* *
44155492 AAGTAAATTATATAAAAGAATTCACATAA
1 AAGTAAATTATATAAAA-AATTCAAAAAA
44155521 AA-TAAATT
1 AAGTAAATT
44155529 CAACAATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 23 0.70
29 10 0.30
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (28 bp):
AAGTAAATTATATAAAAAATTCAAAAAA
Found at i:44156214 original size:164 final size:169
Alignment explanation
Indices: 44155942--44156278 Score: 576
Period size: 164 Copynumber: 2.0 Consensus size: 169
44155932 ATAGTCTACC
* *
44155942 ATCAATCTCTTTTGTCTCCTCTATCTTCTAATCTCTTCCCATCCAGATTCTGTCATGCCAAAATT
1 ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
*
44156007 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTGCCATTGTTGTGTCG-C-CA-AA-TTTCAA
66 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCCACACAACTTTCAA
44156068 TCTTATGTCGCCAAAACTAAAAACACATATTGCAACCTA
131 TCTTATGTCGCCAAAACTAAAAACACATATTGCAACCTA
44156107 ATCAATCTCTTTTGTCTCCTCTATCTTCCAATC-CTCCCCATCCAGATTCTGTCATGCCAAAATT
1 ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
44156171 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCCAAATCACAACTTT
66 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCC--A-CACAACTTT
*
44156236 CAATCTTATGTCGCCAAAACTAGAAACACATATTGCAACCTA
128 CAATCTTATGTCGCCAAAACTAAAAACACATATTGCAACCTA
44156278 A
1 A
44156279 CTGCTTGTGA
Statistics
Matches: 161, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
164 79 0.49
165 33 0.20
169 2 0.01
170 2 0.01
171 45 0.28
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (169 bp):
ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCCACACAACTTTCAA
TCTTATGTCGCCAAAACTAAAAACACATATTGCAACCTA
Found at i:44156665 original size:9 final size:9
Alignment explanation
Indices: 44156646--44156689 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
44156636 ACTCTAGAAG
44156646 TTTTCTCTTC
1 TTTT-TCTTC
44156656 TTTTTCTTC
1 TTTTTCTTC
*
44156665 TTCTTCTTC
1 TTTTTCTTC
*
44156674 -TTTGCTTC
1 TTTTTCTTC
44156682 TTTTTCTT
1 TTTTTCTT
44156690 TTACTGTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 6 0.21
9 19 0.66
10 4 0.14
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:44157069 original size:22 final size:22
Alignment explanation
Indices: 44157025--44157070 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
44157015 ACCGTGGGAC
** * *
44157025 AATCCAAAAAATCAAGAATGAA
1 AATCCAAAAAAGAAAAAAAGAA
44157047 AATCCAAAAAAGAAAAAAAGAA
1 AATCCAAAAAAGAAAAAAAGAA
44157069 AA
1 AA
44157071 GAAAAGAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.72, C:0.11, G:0.09, T:0.09
Consensus pattern (22 bp):
AATCCAAAAAAGAAAAAAAGAA
Found at i:44161205 original size:28 final size:28
Alignment explanation
Indices: 44161165--44161222 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
44161155 AGGCCAACAG
44161165 ATAACACTTCTATTGCAGCATGATTCTT
1 ATAACACTTCTATTGCAGCATGATTCTT
*
44161193 ATAACCCTTCTATTGCAGCATGATTCTT
1 ATAACACTTCTATTGCAGCATGATTCTT
44161221 AT
1 AT
44161223 CCAAAAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (28 bp):
ATAACACTTCTATTGCAGCATGATTCTT
Found at i:44172626 original size:134 final size:133
Alignment explanation
Indices: 44172366--44172689 Score: 436
Period size: 134 Copynumber: 2.4 Consensus size: 133
44172356 CATTCTAACA
* * * *
44172366 GCTCATTGATTTACGATCACAACCTAAGTTTATTGATTTATGATCATGAATAATTTCTTTAAGTT
1 GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTCTTTAAGTT
* * *
44172431 AGCTGATTTACGATTGCAACTCCATTTTAACAACTCACTGATTTACGATCACGATTGATATTATT
66 AGCTGATTTACGATTGCAACTCCATTCTAACAACTCAATGATTTACAATCACGATTGATATTATT
44172496 AAG
131 AAG
* * * * *
44172499 GCTTATTGATTTATGATCATAGCCTAAGTTCATTGATTTACGATCACGAACAATTTCTTTTGAGT
1 GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTC-TTTAAGT
* *** *
44172564 TAGCTGATTTATGATTGCAACTCCATTCTAATTGC-CTAATGATTTACAATGAC-ATTTGATATT
65 TAGCTGATTTACGATTGCAACTCCATTCTAACAACTC-AATGATTTACAATCACGA-TTGATATT
44172627 ATTAAG
128 ATTAAG
* *
44172633 GCTCACTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACGATTTC
1 GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTC
44172690 ATCTGTTAAA
Statistics
Matches: 165, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
133 51 0.31
134 114 0.69
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (133 bp):
GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTCTTTAAGTT
AGCTGATTTACGATTGCAACTCCATTCTAACAACTCAATGATTTACAATCACGATTGATATTATT
AAG
Found at i:44172844 original size:19 final size:20
Alignment explanation
Indices: 44172808--44172850 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
44172798 AATTAAATTT
*
44172808 TTTTCAATTGAGTTAAAC-A
1 TTTTCAATTCAGTTAAACTA
44172827 TTTTCAA-TCAGTTAAAACTA
1 TTTTCAATTCAGTT-AAACTA
44172847 TTTT
1 TTTT
44172851 TAAACAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTTCAATTCAGTTAAACTA
Found at i:44173003 original size:21 final size:21
Alignment explanation
Indices: 44172977--44173016 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44172967 CAATCAACAT
*
44172977 AAAAAGTATTGATACCTTTCC
1 AAAAAGTATCGATACCTTTCC
*
44172998 AAAAAGTCTCGATACCTTT
1 AAAAAGTATCGATACCTTT
44173017 TAGCAGGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGTATCGATACCTTTCC
Found at i:44174221 original size:134 final size:133
Alignment explanation
Indices: 44173967--44174420 Score: 356
Period size: 134 Copynumber: 3.4 Consensus size: 133
44173957 TAAGGTTTGC
* * * * * ** * * *
44173967 TGATTTATGATCATGAACGATTTCATCTGATTTAGCTAATTTACAATCGCAACGCCATTCAAACA
1 TGATTTACGATCATGAA-AATTTCATCAGAGTTAGCTGATTTATGATTGCAACTCTATTCAAACA
* * * * * * * * * *
44174032 GCTCAC-AGATTTATGGTCACAATTGATATTATCAAGGCTCGCTGATTT-CTTATCACACCCTAA
65 ACTCGCTA-ACTTACGATCACAACTGATATTATTAAGGCTCGTTAATTTAC-AATCACACCCTAA
44174095 GTTCAT
128 GTTCAT
* * *
44174101 TAATTTACGATCATGAAAATTTTCTTCAGAGTTAGCTGATTTATGATCGCAACTCTATTCAAACA
1 TGATTTACGATCATGAAAA-TTTCATCAGAGTTAGCTGATTTATGATTGCAACTCTATTCAAACA
* *** * * * *
44174166 ACTTGCTGGTTTACGATTACAGCTGATATTATTGAGGCTCGTTAATTTACAATCACATCCTAAGT
65 ACTCGCTAACTTACGATCACAACTGATATTATTAAGGCTCGTTAATTTACAATCACACCCTAAGT
44174231 TCAT
130 TCAT
* * * * * * *
44174235 TGATTTATGATCATTAACAGTTTCAT-ATGAGTTAGCAGATTTACGATTGCAACTCTATTCTAAT
1 TGATTTACGATCATGAA-AATTTCATCA-GAGTTAGCTGATTTATGATTGCAACTCTATTCAAAC
* * ** * *** **
44174299 AGCTCGCTAACTTACTATCACAACTGATATTATTAAGGCTTTTTGATTTATGGTCACAGACTAAG
64 AACTCGCTAACTTACGATCACAACTGATATTATTAAGGCTCGTTAATTTACAATCACACCCTAAG
44174364 TTCAT
129 TTCAT
* * * *
44174369 TGATTTACAATCATGAACGATTTCATCTGAGTTAGCTTATTTATGATTGCAA
1 TGATTTACGATCATGAA-AATTTCATCAGAGTTAGCTGATTTATGATTGCAA
44174421 ATCCAGTCAA
Statistics
Matches: 251, Mismatches: 63, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
133 2 0.01
134 247 0.98
135 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (133 bp):
TGATTTACGATCATGAAAATTTCATCAGAGTTAGCTGATTTATGATTGCAACTCTATTCAAACAA
CTCGCTAACTTACGATCACAACTGATATTATTAAGGCTCGTTAATTTACAATCACACCCTAAGTT
CAT
Found at i:44177456 original size:9 final size:9
Alignment explanation
Indices: 44177442--44177473 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
44177432 TATTTGAATA
44177442 GAAATGAAC
1 GAAATGAAC
44177451 GAAATGAAC
1 GAAATGAAC
44177460 GAAATGAAC
1 GAAATGAAC
44177469 GAAAT
1 GAAAT
44177474 AAATAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.22, T:0.12
Consensus pattern (9 bp):
GAAATGAAC
Found at i:44177796 original size:26 final size:26
Alignment explanation
Indices: 44177734--44177796 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
44177724 ACGAATTTTC
*
44177734 TCGAAATTTTAACGAAGGTAAAATTG
1 TCGAAATTTTAACAAAGGTAAAATTG
* * *
44177760 TCAAAAATTTATCAAAGGTAAAATTTG
1 TCGAAATTTTAACAAAGGTAAAA-TTG
44177787 T-GAAATTTTA
1 TCGAAATTTTA
44177797 CTAGGGTAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.35
Consensus pattern (26 bp):
TCGAAATTTTAACAAAGGTAAAATTG
Found at i:44180552 original size:27 final size:27
Alignment explanation
Indices: 44180522--44180699 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
44180512 ATATTGAGTC
* * * *
44180522 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
44180549 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44180576 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
44180604 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
44180631 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
44180658 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44180685 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44180700 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:44180661 original size:82 final size:81
Alignment explanation
Indices: 44180543--44180698 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
44180533 TGCTATATAA
* *
44180543 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
44180608 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
44180625 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
44180689 CACTTAGTGC
65 CACTTAGTGC
44180699 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:44188615 original size:27 final size:27
Alignment explanation
Indices: 44188585--44188762 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
44188575 ATATTGAGTC
* * * *
44188585 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
44188612 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44188639 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
44188667 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
44188694 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
44188721 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44188748 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44188763 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:44188724 original size:82 final size:81
Alignment explanation
Indices: 44188606--44188761 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
44188596 TGCTATATAA
* *
44188606 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
44188671 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
44188688 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
44188752 CACTTAGTGC
65 CACTTAGTGC
44188762 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:44191496 original size:29 final size:29
Alignment explanation
Indices: 44191463--44191531 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
44191453 TGTGTGTACC
44191463 ATGTGAAAAGGGATAACTTCGACTATCGA
1 ATGTGAAAAGGGATAACTTCGACTATCGA
* *
44191492 ATGTGAAAAGGGATAGCTTCGGCTATCGA
1 ATGTGAAAAGGGATAACTTCGACTATCGA
44191521 ATGTGAAAAGG
1 ATGTGAAAAGG
44191532 AAAGAGATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (29 bp):
ATGTGAAAAGGGATAACTTCGACTATCGA
Found at i:44191633 original size:33 final size:33
Alignment explanation
Indices: 44191592--44191660 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
44191582 GTACACTTAA
*
44191592 AAAGGTATACTCTGTGTGTACCATTTGAAAAGG
1 AAAGGTATACTCTGTATGTACCATTTGAAAAGG
* *
44191625 AAAGGTATACTTTGTATTTACCATTTGAAAAGG
1 AAAGGTATACTCTGTATGTACCATTTGAAAAGG
44191658 AAA
1 AAA
44191661 TGTACAACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (33 bp):
AAAGGTATACTCTGTATGTACCATTTGAAAAGG
Found at i:44202199 original size:102 final size:102
Alignment explanation
Indices: 44202023--44202227 Score: 392
Period size: 102 Copynumber: 2.0 Consensus size: 102
44202013 CTCTTTAAAC
44202023 CCCATTTCAATCAAGTACTTATAAATTAGAACACATATTTTGCAACCTTTGCAATTTAGTCCTAA
1 CCCATTTCAATCAAGTACTTATAAATTAGAACACATATTTTGCAACCTTTGCAATTTAGTCCTAA
44202088 AAGTCCAATTAAGCACTTTATCAGTAAAATTACTTAA
66 AAGTCCAATTAAGCACTTTATCAGTAAAATTACTTAA
* *
44202125 CCCATTTCAATCAAGTACTTATGAATTAGAACACATATTTTGCAACTTTTGCAATTTAGTCCTAA
1 CCCATTTCAATCAAGTACTTATAAATTAGAACACATATTTTGCAACCTTTGCAATTTAGTCCTAA
44202190 AAGTCCAATTAAGCACTTTATCAGTAAAATTACTTAA
66 AAGTCCAATTAAGCACTTTATCAGTAAAATTACTTAA
44202227 C
1 C
44202228 GATATTTTTA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.35
Consensus pattern (102 bp):
CCCATTTCAATCAAGTACTTATAAATTAGAACACATATTTTGCAACCTTTGCAATTTAGTCCTAA
AAGTCCAATTAAGCACTTTATCAGTAAAATTACTTAA
Found at i:44203891 original size:48 final size:48
Alignment explanation
Indices: 44203836--44203937 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
44203826 TTCAAGAGGG
* *
44203836 GATAAATAGTGATAATAGTATAGACAGTGGAAAACCAAATTTAACAAT
1 GATAAATAGTGATAAGAGTATAGACAGTGGAAAACCAAATTTAAAAAT
* * * *
44203884 GATAAATAGTGATGAGAGTGTAGACAGTGGAAGACCAAGTTTAAAAAT
1 GATAAATAGTGATAAGAGTATAGACAGTGGAAAACCAAATTTAAAAAT
44203932 GCATAA
1 G-ATAA
44203938 CATAATTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 43 0.91
49 4 0.09
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.24
Consensus pattern (48 bp):
GATAAATAGTGATAAGAGTATAGACAGTGGAAAACCAAATTTAAAAAT
Found at i:44207529 original size:3 final size:3
Alignment explanation
Indices: 44207521--44207552 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
44207511 TGTTGTATCT
44207521 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
44207553 TTTTATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:44218596 original size:14 final size:14
Alignment explanation
Indices: 44218579--44218608 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44218569 ATTCAACTAA
*
44218579 ACTAAAATGATTAT
1 ACTAAAATGATCAT
44218593 ACTAAAATGATCAT
1 ACTAAAATGATCAT
44218607 AC
1 AC
44218609 ATACTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (14 bp):
ACTAAAATGATCAT
Found at i:44218985 original size:12 final size:11
Alignment explanation
Indices: 44218966--44218998 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
44218956 ATTTACCTAC
44218966 TGAAAAAAATT
1 TGAAAAAAATT
44218977 TGAAAAAAATT
1 TGAAAAAAATT
44218988 TGAAAAAAATT
1 TGAAAAAAATT
44218999 CTTAGGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (11 bp):
TGAAAAAAATT
Found at i:44228680 original size:52 final size:52
Alignment explanation
Indices: 44228618--44228720 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
44228608 TGCTGGTTAG
*
44228618 TTGTTTTCTATGCATTAAAAATATTCCAACTTTGTCTATTTTCGCTTCTATA
1 TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTATA
44228670 TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTAT
1 TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTAT
44228721 GTCAATGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (52 bp):
TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTATA
Found at i:44233199 original size:21 final size:21
Alignment explanation
Indices: 44233175--44233229 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
44233165 ATTTTACTTT
* * *
44233175 TAAAATTTTTAATAGTATTTA
1 TAAAATTTTAAAAAGTATATA
*
44233196 TAAAAATTTAAAAAGTATATA
1 TAAAATTTTAAAAAGTATATA
44233217 -AAAATTTTAAAAA
1 TAAAATTTTAAAAA
44233230 ATTAAATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAAATTTTAAAAAGTATATA
Found at i:44235051 original size:26 final size:25
Alignment explanation
Indices: 44235022--44235108 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
44235012 ATCTGGGAAG
*
44235022 CCTTTCTGGCTAATCTTGTGGAAAAA
1 CCTTTGTGGCTAAT-TTGTGGAAAAA
*
44235048 CCTTTGTGG-TGAATTCTCTGGAAAAA
1 CCTTTGTGGCT-AATT-TGTGGAAAAA
* * *
44235074 CCTATGTGACTAATATTGTGG-AAAG
1 CCTTTGTGGCTAAT-TTGTGGAAAAA
44235099 CCTTTGTGGC
1 CCTTTGTGGC
44235109 ATGTTATTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
25 13 0.27
26 34 0.69
27 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (25 bp):
CCTTTGTGGCTAATTTGTGGAAAAA
Found at i:44238216 original size:24 final size:21
Alignment explanation
Indices: 44238157--44238216 Score: 57
Period size: 24 Copynumber: 2.7 Consensus size: 21
44238147 GGATCAAAAT
44238157 TAAATTATAATTTTTACTATAA
1 TAAATTAT-ATTTTTACTATAA
* * *
44238179 AAAAATATAATTTTACTATTTTAA
1 TAAATTATATTTTTACTA---TAA
44238203 TAAATTATATTTTT
1 TAAATTATATTTTT
44238217 TAAAAGATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 9 0.31
22 6 0.21
24 14 0.48
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATTATATTTTTACTATAA
Found at i:44250709 original size:84 final size:84
Alignment explanation
Indices: 44250563--44250732 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
44250553 TGAGGGAGGT
*
44250563 AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCTCTAGATTGACTTGACATATCTTG
1 AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
44250628 GGAGAGATCTCAGTTAAAC
66 GGAGAGATCTCAGTTAAAC
*
44250647 AGTTTACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
1 AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
44250712 GGAGAGATCTCAGTTAAAC
66 GGAGAGATCTCAGTTAAAC
44250731 AG
1 AG
44250733 GGGTGTGCAT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (84 bp):
AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
GGAGAGATCTCAGTTAAAC
Found at i:44254674 original size:16 final size:15
Alignment explanation
Indices: 44254649--44254681 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
44254639 ATTCGGTTAC
44254649 TTTTTTTTGTTATTT
1 TTTTTTTTGTTATTT
44254664 TTTTTTCTTGTTATTT
1 TTTTTT-TTGTTATTT
44254680 TT
1 TT
44254682 CACTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTTTTTGTTATTT
Found at i:44254773 original size:17 final size:19
Alignment explanation
Indices: 44254740--44254774 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
44254730 ATTATTTGGA
44254740 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
44254759 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
44254775 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:44255596 original size:3 final size:3
Alignment explanation
Indices: 44255590--44255614 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
44255580 AGCAGCGGGC
44255590 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
44255615 AAGAAGGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:44268735 original size:6 final size:7
Alignment explanation
Indices: 44268720--44268744 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44268710 CACTACTTGT
44268720 AAAATAA
1 AAAATAA
44268727 AAAATAA
1 AAAATAA
44268734 AAAATAA
1 AAAATAA
44268741 AAAA
1 AAAA
44268745 AAGTTTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:44270656 original size:21 final size:23
Alignment explanation
Indices: 44270632--44270676 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
44270622 TTGAACTAAC
44270632 TGCTACTAACAACC-ATTA-TTA
1 TGCTACTAACAACCTATTAGTTA
*
44270653 TGCTACTAACGACCTATTAGTTA
1 TGCTACTAACAACCTATTAGTTA
44270676 T
1 T
44270677 CTTAACAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 4 0.19
23 4 0.19
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (23 bp):
TGCTACTAACAACCTATTAGTTA
Found at i:44272245 original size:21 final size:21
Alignment explanation
Indices: 44272200--44272247 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
44272190 AGATATATTT
*
44272200 TAAATAAATTTATACATTTTT
1 TAAATAAATTTATACATTTTA
*
44272221 TAAATAAATTTATTC-TTTTAA
1 TAAATAAATTTATACATTTT-A
44272242 TAAATA
1 TAAATA
44272248 GTATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATAAATTTATACATTTTA
Found at i:44273032 original size:25 final size:26
Alignment explanation
Indices: 44272998--44273047 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
44272988 TATTTTGATC
*
44272998 ATTAAGATAA-TATGAAAGTTTAAAA
1 ATTAAGATAATTATAAAAGTTTAAAA
* *
44273023 ATTAATATAATTTTAAAAGTTTAAA
1 ATTAAGATAATTATAAAAGTTTAAA
44273048 TGAAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (26 bp):
ATTAAGATAATTATAAAAGTTTAAAA
Found at i:44273094 original size:18 final size:17
Alignment explanation
Indices: 44273071--44273114 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
44273061 AATTTAAAAT
*
44273071 ATTTTAATTTGAATTTGA
1 ATTTTAATTTAAATTT-A
*
44273089 ATTTTAAATTAAATTTA
1 ATTTTAATTTAAATTTA
*
44273106 TTTTTAATT
1 ATTTTAATT
44273115 ATTTCACAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTTAATTTAAATTTA
Found at i:44273200 original size:21 final size:21
Alignment explanation
Indices: 44273159--44273200 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
44273149 TAAATAATAA
* *
44273159 TTTATTATTAAATTTTCTTTT
1 TTTATTATTAAATTATATTTT
44273180 TTTATTATTAAATTATATTTT
1 TTTATTATTAAATTATATTTT
44273201 AAATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATTATTAAATTATATTTT
Found at i:44288990 original size:44 final size:44
Alignment explanation
Indices: 44288927--44289014 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
44288917 AACAAAAAAA
44288927 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
1 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
44288971 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
1 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
44289015 CTTAATTCCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (44 bp):
AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
Found at i:44298408 original size:9 final size:9
Alignment explanation
Indices: 44298394--44298425 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
44298384 ATAAGTATAA
44298394 AATTAACCG
1 AATTAACCG
44298403 AATTAACCG
1 AATTAACCG
44298412 AATTAACCG
1 AATTAACCG
44298421 AATTA
1 AATTA
44298426 TTTGTACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:44298460 original size:5 final size:6
Alignment explanation
Indices: 44298445--44298485 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
44298435 AATTATATGT
*
44298445 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
44298486 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:44298526 original size:13 final size:13
Alignment explanation
Indices: 44298510--44298534 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44298500 AATTTTTATG
44298510 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
44298523 ATTGGGTTGGGT
1 ATTGGGTTGGGT
44298535 TGAGTTGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:44303601 original size:14 final size:14
Alignment explanation
Indices: 44303582--44303608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44303572 TCTGAAAATT
44303582 AAAAATATATATTA
1 AAAAATATATATTA
44303596 AAAAATATATATT
1 AAAAATATATATT
44303609 TATTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATATATATTA
Found at i:44303809 original size:21 final size:22
Alignment explanation
Indices: 44303763--44303820 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
44303753 AATATTTACG
*
44303763 ATTTTTTTAT-AATTTTAAGTT
1 ATTTTATTATAAATTTTAAGTT
* *
44303784 TTTTTATTATAAATTTTATG-T
1 ATTTTATTATAAATTTTAAGTT
*
44303805 ATTTTCTTA-AAATTTT
1 ATTTTATTATAAATTTT
44303821 TAGATGATGC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 7 0.23
21 16 0.52
22 8 0.26
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (22 bp):
ATTTTATTATAAATTTTAAGTT
Found at i:44303809 original size:22 final size:20
Alignment explanation
Indices: 44303763--44303820 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
44303753 AATATTTACG
44303763 ATTTTTTTATAATTTTAAGT
1 ATTTTTTTATAATTTTAAGT
* *
44303783 TTTTTTATTATAAATTTTATGT
1 ATTTTT-TTAT-AATTTTAAGT
* *
44303805 ATTTTCTTAAAATTTT
1 ATTTTTTTATAATTTT
44303821 TAGATGATGC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 11 0.35
21 7 0.23
22 13 0.42
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (20 bp):
ATTTTTTTATAATTTTAAGT
Found at i:44308681 original size:28 final size:26
Alignment explanation
Indices: 44308650--44308718 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
44308640 AAAACTTCAG
44308650 AAAATTATAAAAAAATATTAAAAATTAT
1 AAAATTA-AAAAAAA-ATTAAAAATTAT
* * *
44308678 AAAATGTAGATAAAAAATTCAAATTTAT
1 AAAAT-TA-AAAAAAAATTAAAAATTAT
*
44308706 AAACTTAAAAAAA
1 AAAATTAAAAAAA
44308719 TATGATTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 5 0.15
27 2 0.06
28 19 0.56
29 8 0.24
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (26 bp):
AAAATTAAAAAAAAATTAAAAATTAT
Found at i:44310026 original size:8 final size:8
Alignment explanation
Indices: 44310013--44310047 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
44310003 ATTCAACTCC
44310013 AAAAAGAA
1 AAAAAGAA
44310021 AAAAAGAA
1 AAAAAGAA
44310029 AAAAAGAA
1 AAAAAGAA
44310037 AAAAAGAA
1 AAAAAGAA
44310045 AAA
1 AAA
44310048 GACCCTGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:44313270 original size:28 final size:28
Alignment explanation
Indices: 44313237--44313298 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
44313227 TTGATAAGGG
**
44313237 TTATATTTAATGTGGCGTATGCTTTTAT
1 TTATATTTAATGTAACGTATGCTTTTAT
* *
44313265 TTATATTTAATGTAATGTATGGTTTTAT
1 TTATATTTAATGTAACGTATGCTTTTAT
44313293 TTATAT
1 TTATAT
44313299 ATAAGTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (28 bp):
TTATATTTAATGTAACGTATGCTTTTAT
Found at i:44315401 original size:29 final size:29
Alignment explanation
Indices: 44315349--44315404 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
44315339 TAGCTATTTG
* * *
44315349 AACTAATTAATTACACTGTTAAAATATTA
1 AACTAATTAATAACACTATAAAAATATTA
*
44315378 AACTAATTAATAACATTATAAAAATAT
1 AACTAATTAATAACACTATAAAAATAT
44315405 AGAGACCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTAATTAATAACACTATAAAAATATTA
Found at i:44322672 original size:81 final size:81
Alignment explanation
Indices: 44322534--44322699 Score: 260
Period size: 81 Copynumber: 2.0 Consensus size: 81
44322524 TGATCACACA
* **
44322534 AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCGAGGTGTTAAGCTACA
1 AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCAAAATGTTAAGCTACA
* *
44322599 CGATGTTGCTTATACG
66 CGATGCTGCTCATACG
* *
44322615 AGCTGTGACTGTAACATGTAACTGTATATGCTCACATGAGTTGTGGGTCAAAATGTTAAGCTACA
1 AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCAAAATGTTAAGCTACA
*
44322680 TGATGCTGCTCATACG
66 CGATGCTGCTCATACG
44322696 AGCT
1 AGCT
44322700 ATGAAAAATC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (81 bp):
AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCAAAATGTTAAGCTACA
CGATGCTGCTCATACG
Found at i:44324536 original size:19 final size:19
Alignment explanation
Indices: 44324499--44324538 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
44324489 TTATTGTTTC
* * *
44324499 TTGTTGTTTTTTTATTATT
1 TTGTTGTTTTCTCAGTATT
44324518 TTGTTGTTTTCTCAGTATT
1 TTGTTGTTTTCTCAGTATT
44324537 TT
1 TT
44324539 ACTATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.05, G:0.12, T:0.72
Consensus pattern (19 bp):
TTGTTGTTTTCTCAGTATT
Found at i:44329018 original size:18 final size:18
Alignment explanation
Indices: 44328995--44329030 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
44328985 TTAAAAAAAA
44328995 TCATGATAGGTTCTAGTT
1 TCATGATAGGTTCTAGTT
44329013 TCATGATAGGTTCTAGTT
1 TCATGATAGGTTCTAGTT
44329031 CCAACTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (18 bp):
TCATGATAGGTTCTAGTT
Found at i:44332261 original size:12 final size:12
Alignment explanation
Indices: 44332244--44332268 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44332234 GATTTACAGC
44332244 AAAAAAAGAAAG
1 AAAAAAAGAAAG
44332256 AAAAAAAGAAAG
1 AAAAAAAGAAAG
44332268 A
1 A
44332269 GGCACGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:44338268 original size:13 final size:13
Alignment explanation
Indices: 44338250--44338275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44338240 TGTACCTTAA
44338250 AACTCAAGTTTAC
1 AACTCAAGTTTAC
44338263 AACTCAAGTTTAC
1 AACTCAAGTTTAC
44338276 TAAATTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
AACTCAAGTTTAC
Found at i:44344268 original size:16 final size:17
Alignment explanation
Indices: 44344237--44344269 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44344227 TTTATAAGTA
44344237 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
44344254 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
44344270 GCTTCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:44356465 original size:16 final size:16
Alignment explanation
Indices: 44356446--44356484 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
44356436 AATTTTTCCC
*
44356446 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
*
44356462 TTTTCCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
44356478 TCTTTCC
1 TTTTTCC
44356485 CCTGCTCTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:44356542 original size:16 final size:18
Alignment explanation
Indices: 44356513--44356553 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
44356503 TCATCCTTTC
44356513 TTTCTTTTTCTATT-CTT
1 TTTCTTTTTCTATTCCTT
44356530 TTTCTTTTT-TATTCCTT
1 TTTCTTTTTCTATTCCTT
*
44356547 TTACTTT
1 TTTCTTT
44356554 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTTTTTCTATTCCTT
Found at i:44358174 original size:16 final size:16
Alignment explanation
Indices: 44358153--44358186 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
44358143 AATTGATCTA
44358153 TTGATGTTCTTCTCTC
1 TTGATGTTCTTCTCTC
44358169 TTGATGTTCTTCTCTC
1 TTGATGTTCTTCTCTC
44358185 TT
1 TT
44358187 AGGTACAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.24, G:0.12, T:0.59
Consensus pattern (16 bp):
TTGATGTTCTTCTCTC
Found at i:44375579 original size:161 final size:162
Alignment explanation
Indices: 44375313--44375794 Score: 896
Period size: 161 Copynumber: 3.0 Consensus size: 162
44375303 GACGAGTGTA
*
44375313 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGAAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
44375378 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGGTTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
44375443 GTAATAATCTTTTCCACCAATTAAATTTGATT
131 GTAATAATCTTTTCCACCAATTAAATTTGATT
*
44375475 AAGTGATGATCTATGTTACAGTGAATCC-CCTACAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
44375539 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGC
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
*
44375604 GTAATAATC-TTTCCTACCAATTAAATTTGCTT
131 GTAATAATCTTTTCC-ACCAATTAAATTTGATT
44375636 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
44375701 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
44375766 GTAATAATCTTTTCCACCAATTAAATTTG
131 GTAATAATCTTTTCCACCAATTAAATTTG
44375795 CTTACTTTTA
Statistics
Matches: 310, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
160 5 0.02
161 150 0.48
162 150 0.48
163 5 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (162 bp):
AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
GTAATAATCTTTTCCACCAATTAAATTTGATT
Found at i:44375746 original size:162 final size:162
Alignment explanation
Indices: 44375313--44375798 Score: 904
Period size: 162 Copynumber: 3.0 Consensus size: 162
44375303 GACGAGTGTA
*
44375313 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGAAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
44375378 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGGTTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
*
44375443 GTAATAATCTTTTCCACCAATTAAATTTGATT
131 GTAATAATCTTTTCCACCAATTAAATTTGCTT
*
44375475 AAGTGATGATCTATGTTACAGTGAATCC-CCTACAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
44375539 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGC
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
44375604 GTAATAATC-TTTCCTACCAATTAAATTTGCTT
131 GTAATAATCTTTTCC-ACCAATTAAATTTGCTT
44375636 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
44375701 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
44375766 GTAATAATCTTTTCCACCAATTAAATTTGCTT
131 GTAATAATCTTTTCCACCAATTAAATTTGCTT
44375798 A
1 A
44375799 CTTTTAAAAC
Statistics
Matches: 314, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
160 5 0.02
161 150 0.48
162 154 0.49
163 5 0.02
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (162 bp):
AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
GTAATAATCTTTTCCACCAATTAAATTTGCTT
Found at i:44376920 original size:18 final size:18
Alignment explanation
Indices: 44376893--44376985 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
44376883 TACGACCGTT
44376893 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
44376911 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
44376929 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
44376947 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
44376965 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
44376983 TAC
1 TAC
44376986 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:44384283 original size:3 final size:3
Alignment explanation
Indices: 44384275--44384309 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
44384265 TACCTTGTGC
44384275 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
44384310 GGCGGCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:44384847 original size:4 final size:4
Alignment explanation
Indices: 44384838--44384863 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
44384828 CCCTTTAACC
44384838 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
44384864 TAAAAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:44385887 original size:111 final size:111
Alignment explanation
Indices: 44385754--44385971 Score: 328
Period size: 111 Copynumber: 2.0 Consensus size: 111
44385744 TTCTTCCAAT
* * * * *
44385754 TTGGAATGATGAGAGGATAGAAAATAAGAGAGAAATATATGTTAGTTCAAAATTATGAATTTTTA
1 TTGGAATCATGAGAGGAGAGAAAATAAAAGAGAAATAGATGTTAGTTCAAAATTATGAATTTTCA
* * *
44385819 AATTTTTTATTTTATTTTCTTTCATTTTTCAATTCTACCAAGTAAA
66 AATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAGTAAA
* * *
44385865 TTGGAATCATGAGATGAGAGAAAATAAAAGAGAAGTGGATGTTAGTTCAAAATTATGAATTTTCA
1 TTGGAATCATGAGAGGAGAGAAAATAAAAGAGAAATAGATGTTAGTTCAAAATTATGAATTTTCA
*
44385930 GATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAG
66 AATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAG
44385972 CAACGAAGAA
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 95 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (111 bp):
TTGGAATCATGAGAGGAGAGAAAATAAAAGAGAAATAGATGTTAGTTCAAAATTATGAATTTTCA
AATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAGTAAA
Found at i:44393030 original size:29 final size:28
Alignment explanation
Indices: 44392997--44393054 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
44392987 CAATAAAAGC
*
44392997 CCATTTCTTACTTTATTTA-CGGAAATAGG
1 CCATTT-TTACATTATTTACCGG-AATAGG
*
44393026 CCATTTTTTCATTATTTACCGGAATAGG
1 CCATTTTTACATTATTTACCGGAATAGG
44393054 C
1 C
44393055 TGAAAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (28 bp):
CCATTTTTACATTATTTACCGGAATAGG
Found at i:44422497 original size:30 final size:30
Alignment explanation
Indices: 44422462--44422521 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
44422452 AAATTTCGAG
*
44422462 TTAGTCGAGTTGACGAATCCTATTTTAGCA
1 TTAGTCCAGTTGACGAATCCTATTTTAGCA
44422492 TTAGTCCAGTTGACGAATCCTATTTTAGCA
1 TTAGTCCAGTTGACGAATCCTATTTTAGCA
44422522 ACCTAACTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (30 bp):
TTAGTCCAGTTGACGAATCCTATTTTAGCA
Found at i:44426815 original size:46 final size:46
Alignment explanation
Indices: 44426763--44427128 Score: 491
Period size: 46 Copynumber: 8.0 Consensus size: 46
44426753 GCTTTCTGAA
* *
44426763 ATGAAATGTGTAAGAACATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
44426809 ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
44426855 ATGAAATGTGTAAGATCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
44426901 ATGAAATGTGTAAGACCACGGTTGAAAGATACCATGGCAATAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * *
44426947 ATAAAATGTGTAAGATCATGGTTAAAAGATACCATAGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* ** * *
44426993 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** *
44427039 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
44427085 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
44427129 TCAAAGATAA
Statistics
Matches: 281, Mismatches: 38, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
45 1 0.00
46 280 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:44427430 original size:16 final size:17
Alignment explanation
Indices: 44427409--44427441 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44427399 ATGATGGAGC
44427409 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
44427425 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
44427442 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:44436399 original size:19 final size:20
Alignment explanation
Indices: 44436372--44436409 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
44436362 TTTTATATTA
44436372 TTAAAAAAATTAA-ATTTTT
1 TTAAAAAAATTAATATTTTT
*
44436391 TTAACAAAATTAATATTTT
1 TTAAAAAAATTAATATTTT
44436410 AAAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAAAAAATTAATATTTTT
Found at i:44438373 original size:29 final size:30
Alignment explanation
Indices: 44438341--44438399 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
44438331 CTTATAATGA
44438341 ACATTTTA-AATAAATAA-TTATTTTAATTT
1 ACATTTTATAAT-AATAATTTATTTTAATTT
*
44438370 ACATTTTATAATAATAATTTTTTTTAATTT
1 ACATTTTATAATAATAATTTATTTTAATTT
44438400 TTTCAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (30 bp):
ACATTTTATAATAATAATTTATTTTAATTT
Found at i:44446478 original size:87 final size:86
Alignment explanation
Indices: 44446324--44446515 Score: 201
Period size: 88 Copynumber: 2.2 Consensus size: 86
44446314 CTTTAAAAAG
* * * * * * *
44446324 AAAAAAG-AATTAAACTCTTTTTTTTTGCACTTAATTGAGTACTTTAACTTTCAGAATGTATAAA
1 AAAAAAGCAATTAAACCCTTTTTTTTTCCACTTAACTGAGTAATTGAACTTTCAAAATATATAAA
* *
44446388 AAAAGGC-CTTCAAATTTTTTC
66 AAAAGACACTT-AAAATTTTTC
* * *
44446409 AAAAAAAGCAATTAAGCCCATTTTTTTTTCCACTTAACTGGGTAATTGAGCTTTCAAAATATAT-
1 -AAAAAAGCAATTAAACCC-TTTTTTTTTCCACTTAACTGAGTAATTGAACTTTCAAAATATATA
*
44446473 TAAAAAGACACTTAAAATTTTTC
64 AAAAAAGACACTTAAAATTTTTC
*
44446496 AAAAAAGCTATTAAAACCCT
1 AAAAAAGCAATT-AAACCCT
44446516 ACTCTTATTA
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
86 19 0.22
87 29 0.33
88 39 0.45
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.36
Consensus pattern (86 bp):
AAAAAAGCAATTAAACCCTTTTTTTTTCCACTTAACTGAGTAATTGAACTTTCAAAATATATAAA
AAAAGACACTTAAAATTTTTC
Found at i:44446584 original size:17 final size:18
Alignment explanation
Indices: 44446549--44446588 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
44446539 AATATAAAAA
44446549 TAAATTTTAGAAAAATTAT
1 TAAATTTTA-AAAAATTAT
*
44446568 TAAATTTT-AAAATTTAT
1 TAAATTTTAAAAAATTAT
44446585 TAAA
1 TAAA
44446589 AATAGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
19 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TAAATTTTAAAAAATTAT
Found at i:44446695 original size:20 final size:19
Alignment explanation
Indices: 44446670--44446717 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
44446660 GATTTTTGAT
44446670 ATAAAATGATAAAAAAATCA
1 ATAAAATGATAAAAAAAT-A
* * *
44446690 ATAAAAGTTATAGAAAAATT
1 ATAAAA-TGATAAAAAAATA
44446710 ATAAAATG
1 ATAAAATG
44446718 TTTCTTATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 12 0.52
21 10 0.43
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (19 bp):
ATAAAATGATAAAAAAATA
Found at i:44446846 original size:10 final size:10
Alignment explanation
Indices: 44446833--44446922 Score: 50
Period size: 9 Copynumber: 9.5 Consensus size: 10
44446823 CTTCTATATA
44446833 TTTTATAATT
1 TTTTATAATT
*
44446843 TTTTACAA-T
1 TTTTATAATT
**
44446852 TTTTATAAAA
1 TTTTATAATT
* *
44446862 GTTTACAATT
1 TTTTATAATT
44446872 TTTTAT-ATT
1 TTTTATAATT
44446881 TTTTACT-A--
1 TTTTA-TAATT
44446889 TTTTAT-ATT
1 TTTTATAATT
*
44446898 TTTTCTAA-T
1 TTTTATAATT
*
44446907 TGTTATTAATT
1 TTTTA-TAATT
44446918 TTTTA
1 TTTTA
44446923 ATATTTGAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 25 0.42
10 23 0.38
11 5 0.08
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:44446855 original size:19 final size:19
Alignment explanation
Indices: 44446833--44446922 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 19
44446823 CTTCTATATA
44446833 TTTTATAATTTTTTACAAT
1 TTTTATAATTTTTTACAAT
***
44446852 TTTTATAAAAGTTTACAAT
1 TTTTATAATTTTTTACAAT
*
44446871 TTTT-TATATTTTTTACTA-
1 TTTTATA-ATTTTTTACAAT
44446889 TTTTAT-ATTTTTT-CTAAT
1 TTTTATAATTTTTTAC-AAT
*
44446907 TGTTATTAATTTTTTA
1 TTTTA-TAATTTTTTA
44446923 ATATTTGAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
16 1 0.02
17 8 0.15
18 10 0.18
19 29 0.53
20 7 0.13
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:44446857 original size:56 final size:55
Alignment explanation
Indices: 44446780--44446901 Score: 140
Period size: 56 Copynumber: 2.2 Consensus size: 55
44446770 TTACATTTTG
* * * *
44446780 TATAATTTTCTTACGACTTTATAAAATTTTATATTTTTTTATACTTCTATA-TATTT
1 TATAATTTT-TTACAACTTTATAAAAGTTTACAATTTTTTATA-TTCTATACTATTT
* * *
44446836 TATAATTTTTTACAATTTTTATAAAAGTTTACAATTTTTTATATTTTTTACTATTT
1 TATAATTTTTTACAA-CTTTATAAAAGTTTACAATTTTTTATATTCTATACTATTT
44446892 TAT-ATTTTTT
1 TATAATTTTTT
44446902 CTAATTGTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
55 17 0.30
56 40 0.70
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (55 bp):
TATAATTTTTTACAACTTTATAAAAGTTTACAATTTTTTATATTCTATACTATTT
Found at i:44446894 original size:17 final size:17
Alignment explanation
Indices: 44446872--44446938 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 17
44446862 GTTTACAATT
44446872 TTTTATATTTTTTACTA
1 TTTTATATTTTTTACTA
44446889 TTTTATATTTTTT-CTAA
1 TTTTATATTTTTTACT-A
*
44446906 TTGTTATTAATTTTTTAATA
1 TT-TTA-T-ATTTTTTACTA
*
44446926 TTTGA-ATTTTTTA
1 TTTTATATTTTTTA
44446939 TTAAAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
16 10 0.23
17 16 0.37
18 3 0.07
19 3 0.07
20 10 0.23
21 1 0.02
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTATATTTTTTACTA
Found at i:44453350 original size:18 final size:18
Alignment explanation
Indices: 44453307--44453374 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
44453297 TTAGTAACAT
* *
44453307 TCAATCATTCAGTAGCAA
1 TCAATTATTCAGTAGCAG
*
44453325 TTAATTATTCAGTAGCAG
1 TCAATTATTCAGTAGCAG
* *
44453343 TCATTTATTCAATAGCAG
1 TCAATTATTCAGTAGCAG
44453361 TCAGA-TATTCAGTA
1 TCA-ATTATTCAGTA
44453375 CCTTTATTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TCAATTATTCAGTAGCAG
Found at i:44453594 original size:51 final size:53
Alignment explanation
Indices: 44453490--44453604 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 53
44453480 CCGTAATGGT
*
44453490 AATAGAAACAGTAACAGTAACGGTACACAGAATACCTCATCGGAACAAATCCGG
1 AATAGTAACAGTAACAGTAACGGTA-ACAGAATACCTCATCGGAACAAATCCGG
* * * **
44453544 AATAGTAACAGTAACAGTAA-GGT-ACGGAGTACCTCTTCGGAATGAATCCGG
1 AATAGTAACAGTAACAGTAACGGTAACAGAATACCTCATCGGAACAAATCCGG
*
44453595 AACAGTAACA
1 AATAGTAACA
44453605 ATAAGGCGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 32 0.59
53 3 0.06
54 19 0.35
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (53 bp):
AATAGTAACAGTAACAGTAACGGTAACAGAATACCTCATCGGAACAAATCCGG
Found at i:44454916 original size:20 final size:21
Alignment explanation
Indices: 44454893--44454940 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
44454883 TATAATTATT
*
44454893 TAATTAATAAATATCT-TTTA
1 TAATTAATAAATATCTATTAA
44454913 TAATTAATAAATATCTATTAA
1 TAATTAATAAATATCTATTAA
44454934 TAATTAA
1 TAATTAA
44454941 ATACATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATTAATAAATATCTATTAA
Found at i:44462363 original size:17 final size:17
Alignment explanation
Indices: 44462316--44462357 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
44462306 TTATCATTTA
* *
44462316 TTAAATAAAA-ATAATT
1 TTAATTAAAACATTATT
44462332 TTAATTAAAACATTATT
1 TTAATTAAAACATTATT
44462349 TT-ATTAAAA
1 TTAATTAAAA
44462358 TGATTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAACATTATT
Found at i:44463252 original size:20 final size:20
Alignment explanation
Indices: 44463227--44463276 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
44463217 TGGCTTAAAA
44463227 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
44463247 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
44463264 GTGGTAGTGGATT
1 TTGGTAGTGGATT
44463277 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:44467891 original size:20 final size:20
Alignment explanation
Indices: 44467866--44467915 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
44467856 TGGCTTAAAA
44467866 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
44467886 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
44467903 GTGGTAGTGGATT
1 TTGGTAGTGGATT
44467916 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:44469840 original size:22 final size:19
Alignment explanation
Indices: 44469795--44469844 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
44469785 TTTGTTTCAT
*
44469795 GAAAAATAATTTAGTCAAT
1 GAAAAATAATTTAGTCAAC
*
44469814 AAAAAATAACTTATAGATCAAC
1 GAAAAATAA-TT-TAG-TCAAC
44469836 GAAAAATAA
1 GAAAAATAA
44469845 ATTCATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 3 0.12
22 12 0.48
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (19 bp):
GAAAAATAATTTAGTCAAC
Found at i:44469989 original size:19 final size:17
Alignment explanation
Indices: 44469959--44470001 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
44469949 TAATATTACT
*
44469959 ATATTAATAATAATTTTAA
1 ATATTAAAAAT-A-TTTAA
*
44469978 ATTTTAAAAATATTTAA
1 ATATTAAAAATATTTAA
44469995 ATATTAA
1 ATATTAA
44470002 GATCAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 11 0.52
18 1 0.05
19 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTAAAAATATTTAA
Found at i:44474797 original size:24 final size:22
Alignment explanation
Indices: 44474754--44474797 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
44474744 AGAAAATTGA
**
44474754 TTTTTTTTTCAAATTTTTAAGT
1 TTTTTTTTTCAAATGATTAAGT
44474776 TTTTTTTTTCAAGAATGATTAA
1 TTTTTTTTTC-A-AATGATTAA
44474798 ATATAAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 1 0.06
24 7 0.39
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTTTTTTTCAAATGATTAAGT
Found at i:44483612 original size:26 final size:26
Alignment explanation
Indices: 44483581--44483688 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
44483571 TGAAATGCCC
*
44483581 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
44483607 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
44483633 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
44483659 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
44483685 ATCA
1 ATCA
44483689 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:44489683 original size:12 final size:12
Alignment explanation
Indices: 44489668--44489693 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44489658 TGGGTTTCTA
44489668 TGGACCTTACGG
1 TGGACCTTACGG
44489680 TGGACCTTACGG
1 TGGACCTTACGG
44489692 TG
1 TG
44489694 AGAATCTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.35, T:0.27
Consensus pattern (12 bp):
TGGACCTTACGG
Done.