Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 126 of 352
Found at i:40324697 original size:24 final size:25
Alignment explanation
Indices: 40324664--40324710 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
40324654 AACTAACATC
*
40324664 ACATAGCTC-AAATATTCATCAATG
1 ACATAACTCAAAATATTCATCAATG
40324688 ACATAACTCAAAATATTCATCAA
1 ACATAACTCAAAATATTCATCAA
40324711 AATCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (25 bp):
ACATAACTCAAAATATTCATCAATG
Found at i:40331085 original size:43 final size:43
Alignment explanation
Indices: 40330986--40331097 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 43
40330976 TTACTGAGGC
*
40330986 TACATGTAAGACCATATCTGGGATATGTCATCAATATGAGACT
1 TACATGTAAGACCATATCTGGGATATGTCATCAATACGAGACT
* * * *
40331029 T-CGTGTAAGACCATAGCTGGGCTATTGGT-ATCGATACGAGA-T
1 TACATGTAAGACCATATCTGGGATA-T-GTCATCAATACGAGACT
40331071 TACATGTAAGACCATATCTGGGATATG
1 TACATGTAAGACCATATCTGGGATATG
40331098 GCATTGGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
41 1 0.02
42 23 0.40
43 32 0.55
44 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (43 bp):
TACATGTAAGACCATATCTGGGATATGTCATCAATACGAGACT
Found at i:40334177 original size:47 final size:47
Alignment explanation
Indices: 40334099--40334363 Score: 379
Period size: 47 Copynumber: 5.6 Consensus size: 47
40334089 CCCTTCGGGA
* * * * * *
40334099 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40334145 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40334193 CTCATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40334240 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40334289 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40334338 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
40334364 CACAATTATC
Statistics
Matches: 202, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
46 2 0.01
47 103 0.51
48 2 0.01
49 95 0.47
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40334273 original size:49 final size:49
Alignment explanation
Indices: 40334099--40334363 Score: 386
Period size: 49 Copynumber: 5.6 Consensus size: 49
40334089 CCCTTCGGGA
* * * * *
40334099 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40334145 CTCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40334193 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40334240 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40334289 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40334338 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
40334364 CACAATTATC
Statistics
Matches: 203, Mismatches: 10, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
46 3 0.01
47 92 0.45
48 2 0.01
49 106 0.52
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40337689 original size:16 final size:16
Alignment explanation
Indices: 40337664--40337704 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
40337654 TTCGAATGTC
40337664 CACACAGCCTGTGACA
1 CACACAGCCTGTGACA
*
40337680 CACACGGCCTGTGACA
1 CACACAGCCTGTGACA
40337696 CACACAGCC
1 CACACAGCC
40337705 AGGCCACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.29, C:0.41, G:0.20, T:0.10
Consensus pattern (16 bp):
CACACAGCCTGTGACA
Found at i:40340619 original size:15 final size:15
Alignment explanation
Indices: 40340601--40340670 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
40340591 AACACTTATC
*
40340601 CTATTAGACACATCA
1 CTATCAGACACATCA
40340616 CTATCAGACACATCA
1 CTATCAGACACATCA
* ** * *
40340631 TTAAT-AGGGAGATAA
1 CT-ATCAGACACATCA
40340646 CTATCAGACACATCA
1 CTATCAGACACATCA
**
40340661 AAATCAGACA
1 CTATCAGACA
40340671 TTTCTTCTTC
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
14 2 0.05
15 36 0.90
16 2 0.05
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.21
Consensus pattern (15 bp):
CTATCAGACACATCA
Found at i:40345966 original size:30 final size:29
Alignment explanation
Indices: 40345932--40346003 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
40345922 CGGGTTAGAG
*
40345932 ACACGGACGTGTGTAGTACACGGACCGACC
1 ACACGG-CGTGTGTAGTACACGGACCAACC
* * *
40345962 ACACGGGCGCGTGTAGTGCACGGCCCAACC
1 ACAC-GGCGTGTGTAGTACACGGACCAACC
40345992 ACACAGGCGTGT
1 ACAC-GGCGTGT
40346004 AGGCCCTGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.12
Consensus pattern (29 bp):
ACACGGCGTGTGTAGTACACGGACCAACC
Found at i:40351226 original size:5 final size:6
Alignment explanation
Indices: 40351213--40351261 Score: 71
Period size: 6 Copynumber: 7.8 Consensus size: 6
40351203 ATAATTTAAT
*
40351213 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAATAA AAATA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAATA
40351262 TATAATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 34 0.87
8 5 0.13
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:40351292 original size:9 final size:9
Alignment explanation
Indices: 40351278--40351373 Score: 68
Period size: 9 Copynumber: 10.7 Consensus size: 9
40351268 TTTATACAAA
*
40351278 TAATTTGAT
1 TAATTTGGT
40351287 TAATTTGGT
1 TAATTTGGT
*
40351296 TAATTCGGT
1 TAATTTGGT
*
40351305 TAATTTGGG
1 TAATTTGGT
*
40351314 TAATTCAGG-
1 TAATT-TGGT
* *
40351323 TAATTCGGG
1 TAATTTGGT
40351332 TAATTTGGT
1 TAATTTGGT
* *
40351341 TAATTCGAT
1 TAATTTGGT
* *
40351350 TGATTCGGT
1 TAATTTGGT
**
40351359 TAATTCAGT
1 TAATTTGGT
40351368 TAATTT
1 TAATTT
40351374 TATACTTATT
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
8 2 0.03
9 66 0.94
10 2 0.03
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (9 bp):
TAATTTGGT
Found at i:40351307 original size:18 final size:18
Alignment explanation
Indices: 40351286--40351364 Score: 79
Period size: 18 Copynumber: 4.4 Consensus size: 18
40351276 AATAATTTGA
* *
40351286 TTAATTTGGTTAATTCGG
1 TTAATTCGGGTAATTCGG
*
40351304 TTAATTTGGGTAATTCAGG
1 TTAATTCGGGTAATTC-GG
*
40351323 -TAATTCGGGTAATTTGG
1 TTAATTCGGGTAATTCGG
** *
40351340 TTAATTCGATTGATTCGG
1 TTAATTCGGGTAATTCGG
40351358 TTAATTC
1 TTAATTC
40351365 AGTTAATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
17 2 0.04
18 48 0.92
19 2 0.04
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.46
Consensus pattern (18 bp):
TTAATTCGGGTAATTCGG
Found at i:40351317 original size:27 final size:27
Alignment explanation
Indices: 40351278--40351372 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 27
40351268 TTTATACAAA
* *
40351278 TAATTTGATTAATTTGGTTAATTCGGT
1 TAATTTGGTTAATTAGGTTAATTCGGT
* *
40351305 TAATTTGGGTAATTCAGG-TAATTCGGG
1 TAATTTGGTTAATT-AGGTTAATTCGGT
* * *
40351332 TAATTTGGTTAATTCGATTGATTCGGT
1 TAATTTGGTTAATTAGGTTAATTCGGT
**
40351359 TAATTCAGTTAATT
1 TAATTTGGTTAATT
40351373 TTATACTTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
26 1 0.02
27 52 0.95
28 2 0.04
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.46
Consensus pattern (27 bp):
TAATTTGGTTAATTAGGTTAATTCGGT
Found at i:40351644 original size:5 final size:5
Alignment explanation
Indices: 40351633--40351672 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
40351623 AAAATAAAAA
*
40351633 TTTAT TTCAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
40351673 GGTTGGTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:40357626 original size:23 final size:24
Alignment explanation
Indices: 40357599--40357643 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
40357589 CAAATTATTA
*
40357599 ATTTGAATTTTA-AGTTCGAATTG
1 ATTTGAATTTTACAATTCGAATTG
40357622 ATTTGAATTTTACAATTCGAAT
1 ATTTGAATTTTACAATTCGAAT
40357644 AACAGATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (24 bp):
ATTTGAATTTTACAATTCGAATTG
Found at i:40357761 original size:18 final size:19
Alignment explanation
Indices: 40357726--40357761 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40357716 TTACAAAAAA
*
40357726 TTCAAAATAATTTTTAAAC
1 TTCAAAATAATTTATAAAC
40357745 TTCAAAAT-ATTTATAAA
1 TTCAAAATAATTTATAAA
40357762 AATTCCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCAAAATAATTTATAAAC
Found at i:40358957 original size:16 final size:16
Alignment explanation
Indices: 40358936--40358966 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40358926 AGAAACGTCC
40358936 TTACCTAAGCTTACAA
1 TTACCTAAGCTTACAA
40358952 TTACCTAAGCTTACA
1 TTACCTAAGCTTACA
40358967 CCTATAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTACCTAAGCTTACAA
Found at i:40359466 original size:42 final size:42
Alignment explanation
Indices: 40359420--40359507 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
40359410 ATATTTCTAG
*
40359420 TGGATATTAAAATCATAAAGTATATTAAACTTCTTATAATAA
1 TGGATATTAAAATCATAAAGTACATTAAACTTCTTATAATAA
*
40359462 TGGATATTAAAATTATAAAGTACATTAAACTTCTTATAATAA
1 TGGATATTAAAATCATAAAGTACATTAAACTTCTTATAATAA
40359504 TGGA
1 TGGA
40359508 CATCTGCTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.38
Consensus pattern (42 bp):
TGGATATTAAAATCATAAAGTACATTAAACTTCTTATAATAA
Found at i:40359510 original size:24 final size:24
Alignment explanation
Indices: 40359443--40359510 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 24
40359433 CATAAAGTAT
*
40359443 ATTAAACTTCTTATAATAATGGAT
1 ATTAAACTTCTTATAATAATGGAC
* *
40359467 ATTAAA---ATTAT-A-AA-GTAC
1 ATTAAACTTCTTATAATAATGGAC
40359485 ATTAAACTTCTTATAATAATGGAC
1 ATTAAACTTCTTATAATAATGGAC
40359509 AT
1 AT
40359511 CTGCTTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 1 0.03
21 8 0.24
22 1 0.03
23 2 0.06
24 11 0.33
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (24 bp):
ATTAAACTTCTTATAATAATGGAC
Found at i:40363077 original size:39 final size:39
Alignment explanation
Indices: 40362994--40363090 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 39
40362984 TGAAACCAAT
* *
40362994 TACCAACAC-AAGCCTGCGGGAATTTAAACCCGGTATAA
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
* * * *
40363032 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCCGGACATAT
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGG-CATAA
* *
40363071 TTCCAGCACGTAGCCTGCGG
1 TACCAGCACGAAGCCTGCGG
40363091 ACCTTAAGTC
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 13 0.27
39 35 0.73
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.20
Consensus pattern (39 bp):
TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
Found at i:40363104 original size:39 final size:39
Alignment explanation
Indices: 40363061--40363186 Score: 207
Period size: 39 Copynumber: 3.2 Consensus size: 39
40363051 GGACTTTAGC
* * * *
40363061 CCGGACATATTTCCAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
40363100 CCGGATTTAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
40363139 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
40363178 CCGGATATA
1 CCGGATATA
40363187 CATCACTGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.22
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:40370813 original size:25 final size:25
Alignment explanation
Indices: 40370732--40370814 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
40370722 ATGTATGCTT
*
40370732 ATACGAGCTATA-AACAGGAAGCTC
1 ATACGAGCTATATAACGGGAAGCTC
* *
40370756 CTCCGAGCTGA-ATAACGGGAAGCTC
1 ATACGAGCT-ATATAACGGGAAGCTC
*
40370781 ATGCGAGCTATATAACGGGAAGCTC
1 ATACGAGCTATATAACGGGAAGCTC
*
40370806 ATAAGAGCT
1 ATACGAGCT
40370815 GTGGTGTGTC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
24 9 0.18
25 40 0.82
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (25 bp):
ATACGAGCTATATAACGGGAAGCTC
Found at i:40375484 original size:47 final size:47
Alignment explanation
Indices: 40375418--40375850 Score: 668
Period size: 47 Copynumber: 9.1 Consensus size: 47
40375408 GAAATGATAG
**
40375418 TAAGGCCTAATGGCCGATGTGATGAACATGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40375465 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
40375514 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40375561 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40375608 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
40375657 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* *
40375706 TAGGGCCTAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40375753 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
40375800 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40375847 TAAG
1 TAAG
40375851 TCCCGAAGGG
Statistics
Matches: 360, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
47 220 0.61
49 140 0.39
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40375582 original size:96 final size:96
Alignment explanation
Indices: 40375418--40375850 Score: 685
Period size: 96 Copynumber: 4.5 Consensus size: 96
40375408 GAAATGATAG
**
40375418 TAAGGCCTAATGGCCGATGTGATGAACATGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
40375483 GTGATGAATGTGAAAGTGTATATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATATGTGA
*
40375514 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
40375579 GTGATGAATGTGAAAGTG--TATATATGAGA
66 GTGATGAATGTGAAAGTGTATATATATGTGA
*
40375608 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
40375673 ATGTGATGAATGTGAAAGTGTATATATATGTGA
64 ATGTGATGAATGTGAAAGTGTATATATATGTGA
* *
40375706 TAGGGCCTAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
40375771 GTGATGAATGTGAAA--GTATATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * * *
40375800 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
40375851 TCCCGAAGGG
Statistics
Matches: 315, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
94 103 0.33
96 168 0.53
98 44 0.14
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (96 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:40375676 original size:143 final size:143
Alignment explanation
Indices: 40375418--40375850 Score: 708
Period size: 143 Copynumber: 3.0 Consensus size: 143
40375408 GAAATGATAG
**
40375418 TAAGGCCTAATGGCCGATGTGATGAACATGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
40375483 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
40375548 TGTATATACGTGA
131 TGTATATATGTGA
*
40375561 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
40375626 GTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAG
40375691 TGTATATATATGTGA
131 TG--TATATATGTGA
* *
40375706 TAGGGCCTAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * * * * *
40375771 GTGATGAATGTGAAA--GTATATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
40375834 TGTATAAATGTGA
131 TGTATATATGTGA
40375847 TAAG
1 TAAG
40375851 TCCCGAAGGG
Statistics
Matches: 272, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
141 13 0.05
143 172 0.63
145 87 0.32
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (143 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGA
Found at i:40376011 original size:37 final size:37
Alignment explanation
Indices: 40375969--40376047 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
40375959 CCGAGCTCTA
* * * *
40375969 AAGACCTGATGACTACGTGTGGGGATTTTATCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATATCCGGGT
* *
40376006 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATATCCGGGT
40376043 AAGAC
1 AAGAC
40376048 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATATCCGGGT
Found at i:40382457 original size:25 final size:25
Alignment explanation
Indices: 40382429--40382502 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
40382419 CTCCAAGATG
*
40382429 AATAACGGGAAGCTCATGCGAGCTA
1 AATAACGGAAAGCTCATGCGAGCTA
* * *
40382454 AATAATGGAAAGCTCATGTGAGCTG
1 AATAACGGAAAGCTCATGCGAGCTA
* ** *
40382479 TATAATAGAAAGCTCATGTGAGCT
1 AATAACGGAAAGCTCATGCGAGCT
40382503 GTCTAACAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (25 bp):
AATAACGGAAAGCTCATGCGAGCTA
Found at i:40382503 original size:25 final size:25
Alignment explanation
Indices: 40382438--40382533 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
40382428 GAATAACGGG
* ** *
40382438 AAGCTCATGCGAGCTAAATAATGGA
1 AAGCTCATGTGAGCTGTATAATAGA
40382463 AAGCTCATGTGAGCTGTATAATAGA
1 AAGCTCATGTGAGCTGTATAATAGA
* * *
40382488 AAGCTCATGTGAGCTGTCTAACAGG
1 AAGCTCATGTGAGCTGTATAATAGA
* **
40382513 AAGTTCATAAGAGCTGTATAA
1 AAGCTCATGTGAGCTGTATAA
40382534 CAGGAAGTTC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (25 bp):
AAGCTCATGTGAGCTGTATAATAGA
Found at i:40382534 original size:25 final size:25
Alignment explanation
Indices: 40382473--40382554 Score: 110
Period size: 25 Copynumber: 3.3 Consensus size: 25
40382463 AAGCTCATGT
* * * **
40382473 GAGCTGTATAATAGAAAGCTCATGT
1 GAGCTGTATAACAGGAAGTTCATAA
*
40382498 GAGCTGTCTAACAGGAAGTTCATAA
1 GAGCTGTATAACAGGAAGTTCATAA
40382523 GAGCTGTATAACAGGAAGTTCATAA
1 GAGCTGTATAACAGGAAGTTCATAA
40382548 GAGCTGT
1 GAGCTGT
40382555 GGTGTGTCCG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (25 bp):
GAGCTGTATAACAGGAAGTTCATAA
Found at i:40385970 original size:16 final size:16
Alignment explanation
Indices: 40385945--40385993 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
40385935 ACATAGTATT
*
40385945 TTTTAA-ATTATTTTA
1 TTTTAATATTATTATA
40385960 TTTTAATATTATTATA
1 TTTTAATATTATTATA
40385976 TTTTAATATTATTATA
1 TTTTAATATTATTATA
40385992 TT
1 TT
40385994 ATGTTTAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 6 0.19
16 26 0.81
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATATTATTATA
Found at i:40385974 original size:3 final size:3
Alignment explanation
Indices: 40385951--40386295 Score: 131
Period size: 3 Copynumber: 114.3 Consensus size: 3
40385941 TATTTTTTAA
* *
40385951 ATT ATT -TT ATT -TT AAT ATT ATT A-T ATT -TT AAT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
40385994 ATGT -TT AGTT TTT TTT GAATT -TCT AT- ATT ATT ATT ATT ATT GTT
1 AT-T ATT A-TT ATT ATT --ATT AT-T ATT ATT ATT ATT ATT ATT ATT
* * * *
40386038 ACTT ATT ATT ATT GTT ATGT ACAT ATT ATT -TAT ACT A-T ACTT AAT
1 A-TT ATT ATT ATT ATT AT-T A-TT ATT ATT AT-T ATT ATT A-TT ATT
* *
40386083 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT A-T ATTT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
* * * *
40386128 ATT ATT ATTT ATA AAT ATT AGTGT A-T ATT -TT ATT -TT AAT ATC ATT
1 ATT ATT A-TT ATT ATT ATT A-T-T ATT ATT ATT ATT ATT ATT ATT ATT
*
40386173 A-T ATT ATGT -TT ACTT -TT TTT GAATT -TCT A-T ATT ATT ATT ATT
1 ATT ATT AT-T ATT A-TT ATT ATT --ATT AT-T ATT ATT ATT ATT ATT
* * *
40386215 ATT ATT ATT ATT ATT -TT ACTT ATT ATT ATT ACT GTT ATGT ACAT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT AT-T A-TT ATT
* *
40386262 ATT -TAT ACT A-T ACTT AAT ATT ATT ATT ATT ATT A
1 ATT AT-T ATT ATT A-TT ATT ATT ATT ATT ATT ATT A
40386296 CATTTACTAT
Statistics
Matches: 259, Mismatches: 37, Indels: 92
0.67 0.10 0.24
Matches are distributed among these distances:
2 38 0.15
3 184 0.71
4 31 0.12
5 6 0.02
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:40386312 original size:3 final size:3
Alignment explanation
Indices: 40386019--40386295 Score: 132
Period size: 3 Copynumber: 90.7 Consensus size: 3
40386009 TGAATTTCTA
* * *
40386019 TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TGT TAT GTACA TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT -TA-T TAT TAT
* * *
40386067 T-T ATAC TA- TACT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
40386112 TAT TAT TA- TATT TAC TAT TAT TATT TAT AAA TAT TAGT GTA- TAT T-T
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TA-T -TAT TAT TAT
* * *
40386158 TAT T-T TAA TAT CAT TA- TAT TAT GT-T TACT T-T TTT TGAAT T-T CTA-
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT T--AT TAT -TAT
*
40386202 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TACT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* * * *
40386247 TGT TAT GTACA TAT TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT TAT
1 TAT TAT -TA-T TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT
40386294 TA
1 TA
40386296 CATTTACTAT
Statistics
Matches: 210, Mismatches: 31, Indels: 66
0.68 0.10 0.21
Matches are distributed among these distances:
2 24 0.11
3 155 0.74
4 27 0.13
5 4 0.02
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:40386483 original size:3 final size:3
Alignment explanation
Indices: 40386475--40386528 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
40386465 GTATTTTTAC
*
40386475 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TATT TAT ATAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT -TAT
40386521 TAT TAT TA
1 TAT TAT TA
40386529 ATAGGTACTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 40 0.87
4 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:40391757 original size:29 final size:28
Alignment explanation
Indices: 40391692--40391759 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
40391682 TTGTTTTTGT
40391692 ATTTTTTTAAATTTTAAATTTTAAAATTTA
1 ATTTTTTT--ATTTTAAATTTTAAAATTTA
* * * *
40391722 GTATTTTTATTTTTACTTTTAAAAATTTA
1 ATTTTTTTATTTTAAATTTT-AAAATTTA
40391751 ATTTTTTTA
1 ATTTTTTTA
40391760 GATTATTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 10 0.32
29 15 0.48
30 6 0.19
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
ATTTTTTTATTTTAAATTTTAAAATTTA
Found at i:40391912 original size:18 final size:16
Alignment explanation
Indices: 40391889--40391922 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
40391879 ACTCAAATCT
40391889 TAAAATTAATATAAAAAA
1 TAAAATT-ATA-AAAAAA
40391907 TAAAATTATAAAAAAA
1 TAAAATTATAAAAAAA
40391923 AAGTTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATTATAAAAAAA
Found at i:40398977 original size:24 final size:24
Alignment explanation
Indices: 40398927--40398980 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
40398917 AATCGAATTT
*
40398927 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
40398951 GCACACATAGTGCCATAGT-ACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
40398975 GCACAC
1 GCACAC
40398981 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 5 0.19
26 3 0.11
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:40401000 original size:19 final size:20
Alignment explanation
Indices: 40400976--40401020 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
40400966 TACATGGGTT
40400976 TGTGTTT-TGGACACACGGC
1 TGTGTTTGTGGACACACGGC
* *
40400995 TGTGTTTGGTGGGCACACGGG
1 TGTGTTT-GTGGACACACGGC
40401016 TGTGT
1 TGTGT
40401021 GAGACCCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
21 15 0.68
ACGTcount: A:0.11, C:0.16, G:0.40, T:0.33
Consensus pattern (20 bp):
TGTGTTTGTGGACACACGGC
Found at i:40401170 original size:43 final size:43
Alignment explanation
Indices: 40401120--40401211 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
40401110 TAGTTCACCC
* * * *
40401120 GGGCGTATGCCTCA-ATCACATGACCATGTGCCTCTCTACACAT
1 GGGCGTATGCCTCAGCT-ACACGACCATATGCCTCTCTACAAAT
* *
40401163 GGGCGTATGCCTCAGCTACACGGCCATATGCCTCTCTTCAAAT
1 GGGCGTATGCCTCAGCTACACGACCATATGCCTCTCTACAAAT
40401206 GGGCGT
1 GGGCGT
40401212 TTAACCTCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 41 0.98
44 1 0.02
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.25
Consensus pattern (43 bp):
GGGCGTATGCCTCAGCTACACGACCATATGCCTCTCTACAAAT
Found at i:40403745 original size:12 final size:12
Alignment explanation
Indices: 40403730--40403763 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
40403720 TATTTAACCA
40403730 TTTATTTATTAT
1 TTTATTTATTAT
40403742 TTTATTTATTAT
1 TTTATTTATTAT
40403754 TCTT-TTTATT
1 T-TTATTTATT
40403764 CTATTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.90
13 2 0.10
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTATTAT
Found at i:40406047 original size:31 final size:31
Alignment explanation
Indices: 40406009--40406072 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
40405999 GATTATAAAC
*
40406009 ATATGTGTATGTTTTGTTATATCATATTTAG
1 ATATGTGTATGTTTTGTTATACCATATTTAG
*
40406040 ATATGTGTATGTTTTGTTGTACCATATTTAG
1 ATATGTGTATGTTTTGTTATACCATATTTAG
40406071 AT
1 AT
40406073 GTTAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.05, G:0.17, T:0.53
Consensus pattern (31 bp):
ATATGTGTATGTTTTGTTATACCATATTTAG
Found at i:40408909 original size:32 final size:32
Alignment explanation
Indices: 40408868--40408930 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
40408858 AGACAACTCA
*
40408868 ACAAAGTTACAATAAAGAACAAGTATCCATTG
1 ACAAAGTTACAATAAAAAACAAGTATCCATTG
40408900 ACAAAGTTACAATAAAAAACAAGTATCCATT
1 ACAAAGTTACAATAAAAAACAAGTATCCATT
40408931 TCCTCGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (32 bp):
ACAAAGTTACAATAAAAAACAAGTATCCATTG
Found at i:40416234 original size:48 final size:48
Alignment explanation
Indices: 40416165--40416393 Score: 193
Period size: 48 Copynumber: 4.9 Consensus size: 48
40416155 TAGGGTTATG
*
40416165 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGGTA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATA
* ***
40416213 TGTGATCCCATGTAAGACCATGTCTGGGACATCGCATTGGCGTTGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATA
* * * ** *
40416261 TTTGATCCAATGTAAGACCATATCTGGGATGTGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATA
* * * * ** *
40416309 TGAGA-CATCGTGTAAGACCATAG-CTAGG-C-T---ATTGGCTTCGATC
1 TGTGATC-CCATGTAAGACCAT-GTCTGGGACATGGCATTGGCACCGATA
* * * *
40416352 TGTGATCCCATGTAAGAGCATATCTGGGATATGGAATTGGCA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40416394 TTTTACTATG
Statistics
Matches: 141, Mismatches: 31, Indels: 18
0.74 0.16 0.09
Matches are distributed among these distances:
43 30 0.21
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 107 0.76
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATA
Found at i:40423770 original size:43 final size:43
Alignment explanation
Indices: 40423702--40423829 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 43
40423692 CATATAGCTC
* * ***
40423702 ATACAATGCC-ATATCCCAGATATGGTCTTACATGTTTTCAC-
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAAACACA
* *
40423743 ATATCGATGCCAATGTCCCAGACATGGTCTTATATGTAAACACA
1 ATA-CAATGCCAATGTCCCAGACATGGTCTTACATGTAAACACA
** * *
40423787 ATACAATGCCAATGTCTTAGACATGGTCCTACATGTAATCACA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAAACACA
40423830 TCTCGGTAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
41 3 0.04
42 6 0.08
43 59 0.83
44 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (43 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAAACACA
Found at i:40423855 original size:25 final size:22
Alignment explanation
Indices: 40423813--40423871 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
40423803 TTAGACATGG
*
40423813 TCCTACATGTAATCACATCTCGGTAA
1 TCCTA-ATGTCATCACAT-T-GGT-A
* *
40423839 TCCTAATGTCATGACATTTGTA
1 TCCTAATGTCATCACATTGGTA
40423861 TCCTAATGTCA
1 TCCTAATGTCA
40423872 CTTTCAGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 12 0.40
23 2 0.07
24 1 0.03
25 10 0.33
26 5 0.17
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (22 bp):
TCCTAATGTCATCACATTGGTA
Found at i:40425283 original size:32 final size:32
Alignment explanation
Indices: 40425242--40425305 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
40425232 AGACAGCTCA
40425242 ACAAAGTTACAAAAAAGAACAAGTATCCATTG
1 ACAAAGTTACAAAAAAGAACAAGTATCCATTG
*
40425274 ACAAAGTTACAATAAAGAACAAGTATCCATTG
1 ACAAAGTTACAAAAAAGAACAAGTATCCATTG
40425306 CCTCATATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (32 bp):
ACAAAGTTACAAAAAAGAACAAGTATCCATTG
Found at i:40429261 original size:15 final size:15
Alignment explanation
Indices: 40429241--40429269 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40429231 TGTGTACTTG
40429241 AATTTGAAGGTAATT
1 AATTTGAAGGTAATT
40429256 AATTTGAAGGTAAT
1 AATTTGAAGGTAAT
40429270 GGGGAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (15 bp):
AATTTGAAGGTAATT
Found at i:40433574 original size:19 final size:19
Alignment explanation
Indices: 40433552--40433588 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40433542 TCCCACATGG
*
40433552 CCTAGGTATTTCCACACGT
1 CCTAGGCATTTCCACACGT
40433571 CCTAGGCATTTCCACACG
1 CCTAGGCATTTCCACACG
40433589 GCCAGAGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27
Consensus pattern (19 bp):
CCTAGGCATTTCCACACGT
Found at i:40439886 original size:32 final size:32
Alignment explanation
Indices: 40439850--40439915 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
40439840 ATAAATGAAA
40439850 GTCAATTCTCATGAGATAAATATTTCTTACAT
1 GTCAATTCTCATGAGATAAATATTTCTTACAT
40439882 GTCAATTCTCATGAGATAAATATTTCTTACAT
1 GTCAATTCTCATGAGATAAATATTTCTTACAT
40439914 GT
1 GT
40439916 GTCACACCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (32 bp):
GTCAATTCTCATGAGATAAATATTTCTTACAT
Found at i:40441985 original size:54 final size:53
Alignment explanation
Indices: 40441919--40442207 Score: 202
Period size: 54 Copynumber: 5.5 Consensus size: 53
40441909 TAAGGATATT
*
40441919 ATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGAAAATGATACC
1 ATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAA-GATACC
* *** * *
40441973 ATGCAAGACCATG-TTTGGAACATGGCATTTGGTAAG----ATAA-G---GATATC
1 ATGTAAGACCATGCCAAGG--CATGGCA-TTGATAAGTTCTATAAGGAAAGATACC
* * ** * *
40442020 ACGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGTAATTAAATC
1 ATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGG-AAAGATACC
* * * * *
40442074 ATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCC
1 ATGTAAGACCATGCCAAGGCATGGCATTGATAAGTT-CTATAAGG-AAAGATACC
* * * * *
40442129 ATGTAAAACCATGCCAAGGCATGACATTGGTTAGTTC-ATAAGGCAAGGATACC
1 ATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGG-AAAGATACC
* * *
40442182 ACGTAAGACCATGTCAAGACATGGCA
1 ATGTAAGACCATGCCAAGGCATGGCA
40442208 ATAGTAAGTT
Statistics
Matches: 179, Mismatches: 42, Indels: 29
0.72 0.17 0.12
Matches are distributed among these distances:
45 7 0.04
46 7 0.04
47 15 0.08
48 2 0.01
49 4 0.02
50 1 0.01
52 4 0.02
53 36 0.20
54 48 0.27
55 48 0.27
56 7 0.04
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (53 bp):
ATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGATACC
Found at i:40442082 original size:101 final size:101
Alignment explanation
Indices: 40441872--40442087 Score: 342
Period size: 101 Copynumber: 2.1 Consensus size: 101
40441862 CAAGGATACA
* * *
40441872 ATGTAAGACCATGTTTGGAACATGACATTTGGTAAGATAAGGATATTATGTAAGACCATGCCAAG
1 ATGTAAGACCATGTTTGGAACATGACATTTGGTAAGATAAGGATATCACGTAAAACCATGCCAAG
*
40441937 GCATGGCATTGATAAGTTCTATAAGAAAATGATACC
66 GCATGGCATTGATAAGTTCTATAAGAAAATGAAACC
* *
40441973 ATGCAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCACGTAAAACCATGCCAAG
1 ATGTAAGACCATGTTTGGAACATGACATTTGGTAAGATAAGGATATCACGTAAAACCATGCCAAG
** * *
40442038 GCATGGCATTGATAAGTTCTATAAGGTAATTAAATC
66 GCATGGCATTGATAAGTTCTATAAGAAAATGAAACC
40442074 ATGTAAGACCATGT
1 ATGTAAGACCATGT
40442088 CAAGACATGG
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (101 bp):
ATGTAAGACCATGTTTGGAACATGACATTTGGTAAGATAAGGATATCACGTAAAACCATGCCAAG
GCATGGCATTGATAAGTTCTATAAGAAAATGAAACC
Found at i:40442140 original size:55 final size:53
Alignment explanation
Indices: 40442022--40442207 Score: 171
Period size: 55 Copynumber: 3.5 Consensus size: 53
40442012 AGGATATCAC
* * **
40442022 GTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGTAATTAAAT-CAT
1 GTAAAACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAA--AGGTCCAT
* * *
40442076 GTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCAT
1 GTAAAACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGCAAAGGT-CCAT
* * * * *
40442131 GTAAAACCATGCCAAGGCATGACATTGGTTAGTTC-ATAAGGC-AAGGATACCAC
1 GTAAAACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGG-T-CCAT
* *
40442184 GTAAGACCATGTCAAGACATGGCA
1 GTAAAACCATGCCAAGACATGGCA
40442208 ATAGTAAGTT
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
52 4 0.04
53 33 0.30
54 31 0.28
55 41 0.38
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (53 bp):
GTAAAACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGGTCCAT
Found at i:40443610 original size:13 final size:13
Alignment explanation
Indices: 40443592--40443632 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
40443582 CTAAGCCACC
40443592 TCACACGGGCGTG
1 TCACACGGGCGTG
*
40443605 TCACACGGGCATG
1 TCACACGGGCGTG
*
40443618 TCACACGAGCGTG
1 TCACACGGGCGTG
40443631 TC
1 TC
40443633 CCTGTCGAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.17
Consensus pattern (13 bp):
TCACACGGGCGTG
Found at i:40445106 original size:40 final size:40
Alignment explanation
Indices: 40445069--40445253 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
40445059 GCTACTCGTT
*
40445069 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
40445109 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
40445149 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * * *
40445188 CAAAAGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
40445229 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40445254 CATCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 74 0.62
41 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40454167 original size:28 final size:29
Alignment explanation
Indices: 40454135--40454233 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 29
40454125 ATAATAAGCC
*
40454135 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
*
40454163 CGCACACTTAGTGC-TATATAATC-AACCT
1 CGCACACTTAGTGCTTACATAATCGAA-CT
* * *
40454191 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
40454220 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40454234 CAATCTCATG
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.07
28 35 0.57
29 17 0.28
30 5 0.08
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:40465744 original size:47 final size:47
Alignment explanation
Indices: 40465686--40465861 Score: 192
Period size: 47 Copynumber: 3.6 Consensus size: 47
40465676 GCATTGGCAC
*
40465686 TAAGATAAGGATACCATGTAAGACTATGTTTGGAACATGGCATTTGG
1 TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
** **** *
40465733 TAAGATAAGGATATTATGTAAGACCATGCCAAG-ACATGGCATTGATAAGTTC
1 TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATT--T--G--G
40465785 TATAGGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TA-A-GATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
40465834 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGATAAGGATACCATGTAAGACCATG
40465862 CCAAGGCATG
Statistics
Matches: 104, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
46 10 0.10
47 50 0.48
48 2 0.02
49 2 0.02
50 1 0.01
51 1 0.01
52 2 0.02
53 2 0.02
54 24 0.23
55 10 0.10
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (47 bp):
TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:40465795 original size:54 final size:55
Alignment explanation
Indices: 40465736--40466047 Score: 267
Period size: 54 Copynumber: 5.9 Consensus size: 55
40465726 CATTTGGTAA
*
40465736 GATAAGGATATTATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTAT-AG
1 GATAAGGATATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAG
* **** *
40465790 GATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATT--T--G----GTAA-
1 GATAAGGATATCATGTAAGACCATGCCAAG-ACATGGCATTGATAAGTTCTATAAG
* *
40465837 GATAAGGATATCATGTAAGACCATGCCAAGGCATGCCATTGATAAGTTCTATAAG
1 GATAAGGATATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAG
* * * * *
40465892 G-CAAGGAAATCATGTAAGACCTTGTCAAGACATGGCATTGATGAGTTACTATAAG
1 GATAAGGATATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAG
** * * *
40465947 GCA-AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAG
1 G-ATAAGGATATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAG
* * * * * *
40466000 G-CAAGGATAACACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 GATAAGGATATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC
40466048 AAAAAGGAAA
Statistics
Matches: 206, Mismatches: 36, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
46 8 0.04
47 26 0.13
48 2 0.01
50 1 0.00
51 1 0.00
52 4 0.02
53 41 0.20
54 67 0.33
55 52 0.25
56 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (55 bp):
GATAAGGATATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAG
Found at i:40465817 original size:101 final size:102
Alignment explanation
Indices: 40465689--40465912 Score: 371
Period size: 101 Copynumber: 2.2 Consensus size: 102
40465679 TTGGCACTAA
* *
40465689 GATAAGGATACCATGTAAGACTATGTTTGGAACATGGCATTTGGTAAGATAAGGATATTATGTAA
1 GATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATGTAA
*
40465754 GACCATGCCAAGACATGGCATTGATAAGTTCTAT-AG
66 GACCATGCCAAGACATGCCATTGATAAGTTCTATAAG
40465790 GATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATGTAA
1 GATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATGTAA
*
40465855 GACCATGCCAAGGCATGCCATTGATAAGTTCTATAAG
66 GACCATGCCAAGACATGCCATTGATAAGTTCTATAAG
* * *
40465892 G-CAAGGAAATCATGTAAGACC
1 GATAAGGATACCATGTAAGACC
40465913 TTGTCAAGAC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
101 112 0.97
102 3 0.03
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (102 bp):
GATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATGTAA
GACCATGCCAAGACATGCCATTGATAAGTTCTATAAG
Found at i:40465965 original size:55 final size:54
Alignment explanation
Indices: 40465840--40466036 Score: 238
Period size: 55 Copynumber: 3.6 Consensus size: 54
40465830 TTGGTAAGAT
* * * *
40465840 AAGGATATCATGTAAGACCATGCCAAGGCATGCCATTGATAAGTTCTATAAGGC
1 AAGGATAACATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
40465894 AAGGA-AATCATGTAAGACCTTGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATAA-CATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC
** * *
40465949 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATAACATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
40466002 AAGGATAACACGTAAGACCATGTCAAGACATGGCA
1 AAGGATAACATGTAAGACCATGCCAAGACATGGCA
40466037 ATGGTAAGTT
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
52 4 0.03
53 33 0.27
54 38 0.31
55 42 0.35
56 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGATAACATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:40467704 original size:13 final size:14
Alignment explanation
Indices: 40467677--40467707 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
40467667 AAATTTGTGA
40467677 TATGAATAGATGAT
1 TATGAATAGATGAT
40467691 TATGAATAGA-GAT
1 TATGAATAGATGAT
40467704 TATG
1 TATG
40467708 TGTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (14 bp):
TATGAATAGATGAT
Found at i:40469880 original size:84 final size:84
Alignment explanation
Indices: 40469734--40469909 Score: 298
Period size: 84 Copynumber: 2.1 Consensus size: 84
40469724 ACTATTATGA
* *
40469734 ATGTTAGAACTATTTAAGAATGTTTGCAAATATTTTGGATTTTTTTGGCTATAAACGGTGCAAAT
1 ATGTTATAACTATTTAAGAATGTTTGCAAATATTTTGGATTTTTTTGGCTATAAACGATGCAAAT
*
40469799 TTATTTTTAATTTCATTTG
66 TTATTTTCAATTTCATTTG
* * *
40469818 ATGTTATAACTATTTAGGAATGTTTGCAGATTTTTTGGATTTTTTTGGCTATAAACGATGCAAAT
1 ATGTTATAACTATTTAAGAATGTTTGCAAATATTTTGGATTTTTTTGGCTATAAACGATGCAAAT
40469883 TTATTTTCAATTTCATTTG
66 TTATTTTCAATTTCATTTG
40469902 ATGTTATA
1 ATGTTATA
40469910 TTTCATCATT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.48
Consensus pattern (84 bp):
ATGTTATAACTATTTAAGAATGTTTGCAAATATTTTGGATTTTTTTGGCTATAAACGATGCAAAT
TTATTTTCAATTTCATTTG
Found at i:40470695 original size:45 final size:45
Alignment explanation
Indices: 40470631--40470721 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
40470621 TCCTCACTTC
40470631 ATGAATAAATTTATATTTACTCCGCCTTTGATATTTACTCAAACA
1 ATGAATAAATTTATATTTACTCCGCCTTTGATATTTACTCAAACA
40470676 ATGAATAAATTTATATTTACTCCGCCTTTGATATTTACTCAAACA
1 ATGAATAAATTTATATTTACTCCGCCTTTGATATTTACTCAAACA
40470721 A
1 A
40470722 AATCACAGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (45 bp):
ATGAATAAATTTATATTTACTCCGCCTTTGATATTTACTCAAACA
Found at i:40474180 original size:63 final size:65
Alignment explanation
Indices: 40474096--40474227 Score: 250
Period size: 63 Copynumber: 2.1 Consensus size: 65
40474086 ATCTTTTCGA
40474096 ATTTCCTTAATTCTCTCATTTATTACGTTGAGTTTTCTCATAAAATTTCTACTCTCTGTTTTTCT
1 ATTTCCTTAATTCTCTCATTTATTACGTTGAGTTTTCTCATAAAATTTCTACTCTCTGTTTTTCT
40474161 ATTTCCTTAA-T-TCTCATTTATTACGTTGAGTTTTCTCATAAAATTTCTACTCTCTGTTTTTCT
1 ATTTCCTTAATTCTCTCATTTATTACGTTGAGTTTTCTCATAAAATTTCTACTCTCTGTTTTTCT
40474224 ATTT
1 ATTT
40474228 TGTACGTAGT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 56 0.84
64 1 0.01
65 10 0.15
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.55
Consensus pattern (65 bp):
ATTTCCTTAATTCTCTCATTTATTACGTTGAGTTTTCTCATAAAATTTCTACTCTCTGTTTTTCT
Found at i:40486815 original size:42 final size:44
Alignment explanation
Indices: 40486732--40486817 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
40486722 GTTAATTGAG
** * *
40486732 AAAGCACTAAGTGTGTGGAATTATTATAGCTTTGGCTAATCTTT
1 AAAGCACTAAGTGTGCAGAATTATTAAAGCATTGGCTAATCTTT
40486776 AAAGCACTAAGTGTGCAG-ATGT-TTAAAGCATTGG-TAATCTTT
1 AAAGCACTAAGTGTGCAGAAT-TATTAAAGCATTGGCTAATCTTT
40486818 GGAAAGTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 8 0.22
43 12 0.32
44 17 0.46
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (44 bp):
AAAGCACTAAGTGTGCAGAATTATTAAAGCATTGGCTAATCTTT
Found at i:40489218 original size:5 final size:5
Alignment explanation
Indices: 40489208--40489238 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
40489198 AATAATTAAG
40489208 TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TA-TAT TATAT
40489239 ATAAAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:40490891 original size:48 final size:48
Alignment explanation
Indices: 40490835--40490984 Score: 300
Period size: 48 Copynumber: 3.1 Consensus size: 48
40490825 TAGTCCGAGC
40490835 TTTGTTAATAGGGTAAATAATTGAAATGAAATTTTGAAAATGAGATTA
1 TTTGTTAATAGGGTAAATAATTGAAATGAAATTTTGAAAATGAGATTA
40490883 TTTGTTAATAGGGTAAATAATTGAAATGAAATTTTGAAAATGAGATTA
1 TTTGTTAATAGGGTAAATAATTGAAATGAAATTTTGAAAATGAGATTA
40490931 TTTGTTAATAGGGTAAATAATTGAAATGAAATTTTGAAAATGAGATTA
1 TTTGTTAATAGGGTAAATAATTGAAATGAAATTTTGAAAATGAGATTA
40490979 TTTGTT
1 TTTGTT
40490985 TTAGCACTAT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 102 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (48 bp):
TTTGTTAATAGGGTAAATAATTGAAATGAAATTTTGAAAATGAGATTA
Found at i:40495693 original size:20 final size:20
Alignment explanation
Indices: 40495657--40495695 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40495647 AAAATAGTAT
* *
40495657 TATTATTATGTACATTTTTA
1 TATTATTATGCAAATTTTTA
40495677 TATTATTATGCAAATTTTT
1 TATTATTATGCAAATTTTT
40495696 TCGTCCACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
TATTATTATGCAAATTTTTA
Found at i:40503232 original size:24 final size:25
Alignment explanation
Indices: 40503184--40503241 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
40503174 TACCGATCAA
40503184 GATGCTCGCAGGAACTATATAACAG
1 GATGCTCGCAGGAACTATATAACAG
*
40503209 GATGCTCG-AGAGAGCT-TATAACAG
1 GATGCTCGCAG-GAACTATATAACAG
40503233 GATTGCTCG
1 GA-TGCTCG
40503242 TCCGAGCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (25 bp):
GATGCTCGCAGGAACTATATAACAG
Found at i:40509119 original size:40 final size:40
Alignment explanation
Indices: 40509064--40509248 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
40509054 CTTGCACAAG
* * *
40509064 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
* *
40509104 GCCTTTGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
* * * *
40509144 GCCTTCGGGTCTTAGCCCAGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
40509184 GCCTTC-GGATCTTCGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAAT
40509225 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
40509249 CATTCGAATA
Statistics
Matches: 118, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.03
40 86 0.73
41 26 0.22
42 3 0.03
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:40511206 original size:20 final size:20
Alignment explanation
Indices: 40511181--40511220 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40511171 GAGAGTCTAC
40511181 ATAGATTACAGGAAGTTAAA
1 ATAGATTACAGGAAGTTAAA
*
40511201 ATAGATTACATGAAGTTAAA
1 ATAGATTACAGGAAGTTAAA
40511221 TTCTTTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (20 bp):
ATAGATTACAGGAAGTTAAA
Found at i:40517460 original size:3 final size:3
Alignment explanation
Indices: 40517454--40517498 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
40517444 TTTTTCCCTT
*
40517454 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
40517499 CCCAACTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:40519197 original size:46 final size:46
Alignment explanation
Indices: 40519144--40519272 Score: 186
Period size: 46 Copynumber: 2.8 Consensus size: 46
40519134 TATTTGGGCA
*
40519144 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
40519190 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
40519236 CCCGAGCTCGTCGAGTTGAGTCTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40519273 GCGGGTTACA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:40525326 original size:20 final size:21
Alignment explanation
Indices: 40525287--40525326 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40525277 TCATAGTGAA
*
40525287 CCACACGGGCGTGTTGCCCTT
1 CCACACGAGCGTGTTGCCCTT
40525308 CCACACGAGCGTG-TGCCCT
1 CCACACGAGCGTGTTGCCCT
40525327 GTTTCAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.12, C:0.40, G:0.28, T:0.20
Consensus pattern (21 bp):
CCACACGAGCGTGTTGCCCTT
Found at i:40542479 original size:48 final size:48
Alignment explanation
Indices: 40542409--40542731 Score: 438
Period size: 48 Copynumber: 6.7 Consensus size: 48
40542399 CCGTGCTGAA
* *
40542409 TGTGCCTGTGTAAGACCATGTCTGGGACAGGGCATCGGCGATGATATA
1 TGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATG
* * *
40542457 TGTGCCTGTGTAAGACCATGTCTGGGTCATGGCATCGGTGATGAGATG
1 TGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATG
*
40542505 TGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATG
1 TGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATG
* * *
40542553 TGTGCCTATGTAAGACCATGTCTGGGACATGGCATCAGTGATGATATG
1 TGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATG
*
40542601 TGTGCCAGTGTAAGACCATG-CTTGGGACATGGCATCGGCGATGATATG
1 TGTGCCTGTGTAAGACCATGTC-TGGGACATGGCATCGGCGATGATATG
* * * *
40542649 TGTGCCAGTGTAAGACCATGTTTGGGACATGGCATTGACGATGATATG
1 TGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATG
* *
40542697 TGAAT-TC-ATGTAAGACCATGTC-GAGGACATGGCAT
1 TG--TGCCTGTGTAAGACCATGTCTG-GGACATGGCAT
40542732 TGGTACTTTA
Statistics
Matches: 251, Mismatches: 19, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
47 2 0.01
48 247 0.98
49 1 0.00
50 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.28
Consensus pattern (48 bp):
TGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATG
Found at i:40547226 original size:38 final size:39
Alignment explanation
Indices: 40547142--40547276 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
40547132 ACCAATATGG
*
40547142 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
40547181 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
40547219 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
40547260 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
40547277 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:40548872 original size:11 final size:12
Alignment explanation
Indices: 40548836--40548873 Score: 62
Period size: 11 Copynumber: 3.3 Consensus size: 12
40548826 TTGTTTCTTT
40548836 TATATATAATAA
1 TATATATAATAA
40548848 TA-ATATAATAA
1 TATATATAATAA
40548859 TATATAT-ATAA
1 TATATATAATAA
40548870 TATA
1 TATA
40548874 CTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATAATAA
Found at i:40554375 original size:38 final size:39
Alignment explanation
Indices: 40554291--40554425 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
40554281 ACAAATATGG
*
40554291 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
40554330 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
40554368 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
40554409 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
40554426 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:40564628 original size:16 final size:15
Alignment explanation
Indices: 40564591--40564629 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
40564581 TAATACACTT
*
40564591 TTTATATATTTTTAA
1 TTTATATATTTTAAA
40564606 TTATATATATTTATAAA
1 TT-TATATATTT-TAAA
40564623 TTTATAT
1 TTTATAT
40564630 TATATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 14 0.67
17 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATATATTTTAAA
Found at i:40564646 original size:23 final size:22
Alignment explanation
Indices: 40564601--40564646 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
40564591 TTTATATATT
* *
40564601 TTTAATTATATATATTTATAAA
1 TTTAATTATATATATTGAAAAA
40564623 TTTATATTATATATATTGAAAAA
1 TTTA-ATTATATATATTGAAAAA
40564646 T
1 T
40564647 AATAATAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTAATTATATATATTGAAAAA
Found at i:40567557 original size:42 final size:42
Alignment explanation
Indices: 40567505--40567584 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
40567495 TACTTAATTT
* * *
40567505 AATACTTAAATTGTAAAAATATATCAATTAAATTATTTATTA
1 AATACTTAAATTATAAAAATACATCAATTAAATCATTTATTA
* *
40567547 AATATTTAAATTATGAAAATACATCAATTAAATCATTT
1 AATACTTAAATTATAAAAATACATCAATTAAATCATTT
40567585 GAACATTGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (42 bp):
AATACTTAAATTATAAAAATACATCAATTAAATCATTTATTA
Found at i:40567788 original size:19 final size:19
Alignment explanation
Indices: 40567745--40567790 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
40567735 AAAATGAATA
40567745 TATAAAAAT-TATCAAAAT
1 TATAAAAATATATCAAAAT
* *
40567763 T-TAAAAATATTTGAAAAT
1 TATAAAAATATATCAAAAT
40567781 TATAAAAATA
1 TATAAAAATA
40567791 ATAATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.29
18 9 0.38
19 8 0.33
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TATAAAAATATATCAAAAT
Found at i:40567816 original size:20 final size:20
Alignment explanation
Indices: 40567779--40567822 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
40567769 ATATTTGAAA
*
40567779 ATTATAAAAATAATAATATT
1 ATTATAAAAATAAAAATATT
40567799 ATTA-AAAAATAAAAAATATT
1 ATTATAAAAAT-AAAAATATT
40567819 -TTAT
1 ATTAT
40567823 TAAACATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATAAAAATAAAAATATT
Found at i:40567818 original size:17 final size:20
Alignment explanation
Indices: 40567779--40567818 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
40567769 ATATTTGAAA
*
40567779 ATTATAAAAATAATAATATT
1 ATTATAAAAATAATAATAAT
40567799 ATTA-AAAAATAA-AA-AAT
1 ATTATAAAAATAATAATAAT
40567816 ATT
1 ATT
40567819 TTATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 5 0.26
18 2 0.11
19 8 0.42
20 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTATAAAAATAATAATAAT
Found at i:40574691 original size:24 final size:24
Alignment explanation
Indices: 40574664--40574709 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40574654 TTATAGGAAA
40574664 ATTTCTAAAATTAAAAAAATTGAT
1 ATTTCTAAAATTAAAAAAATTGAT
* * *
40574688 ATTTTTAAATTTATAAAAATTG
1 ATTTCTAAAATTAAAAAAATTG
40574710 TAGCATTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTTCTAAAATTAAAAAAATTGAT
Found at i:40575627 original size:60 final size:59
Alignment explanation
Indices: 40575553--40575678 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 59
40575543 AATATATATA
* ** *
40575553 AAAAAATCAATAAATTCAAACCTCAATGTTTACAAAGTTTGTCAATTTAGTTTGAATTCT
1 AAAAATTCAATAAATTCAAACCTCAACATTTACAAA-TTGGTCAATTTAGTTTGAATTCT
* ** * * *
40575613 AAAAATTCAATAAATTTAGCCCTTAACATTTACAAATTGGTCGATTTAGTTTTAATTCT
1 AAAAATTCAATAAATTCAAACCTCAACATTTACAAATTGGTCAATTTAGTTTGAATTCT
40575672 AAAAATT
1 AAAAATT
40575679 TCAAAAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 27 0.48
60 29 0.52
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (59 bp):
AAAAATTCAATAAATTCAAACCTCAACATTTACAAATTGGTCAATTTAGTTTGAATTCT
Found at i:40583545 original size:27 final size:28
Alignment explanation
Indices: 40583461--40583558 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
40583451 CATGAGATTG
* * * *
40583461 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
40583490 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40583518 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40583545 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
40583559 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40583569 original size:27 final size:27
Alignment explanation
Indices: 40583489--40583571 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
40583479 TAAATTGTAC
* *
40583489 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
40583517 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
40583544 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
40583571 A
1 A
40583572 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:40583572 original size:29 final size:27
Alignment explanation
Indices: 40583461--40583572 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
40583451 CATGAGATTG
** * *
40583461 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
40583490 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
40583518 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
40583545 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
40583573 TTTGAATCAC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:40588643 original size:46 final size:44
Alignment explanation
Indices: 40588513--40588679 Score: 122
Period size: 46 Copynumber: 3.6 Consensus size: 44
40588503 ATGAGAGCTT
* * * ** *
40588513 GTGTAAGACTATGTATGGGACATGGCATCGGCTTTAAGACGAGTGCTA
1 GTGTAAGAC-ATGTCTGGGACAT-GCATCAGCCTCGAGAC--GTGCCA
* *
40588561 GTGTAAGACATGTGTGGGACATGCAT-TGTCCTCGAGACGTAAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCAG-CCTCGAGACGT--GCCA
* * *
40588607 GTGTAAGACATGTCTGGGATATGCATCAG-CTACGAGATGTGTCA
1 GTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGACGTGCCA
*
40588651 GTGTAAGACCATTTCTGGGACATGGCATC
1 GTGTAAGA-CATGTCTGGGACAT-GCATC
40588680 GGCATAGATA
Statistics
Matches: 99, Mismatches: 13, Indels: 16
0.77 0.10 0.12
Matches are distributed among these distances:
44 13 0.13
45 15 0.15
46 49 0.49
47 13 0.13
48 9 0.09
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (44 bp):
GTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTGCCA
Found at i:40595235 original size:17 final size:17
Alignment explanation
Indices: 40595210--40595255 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
40595200 ACTTCACAAA
*
40595210 TCATTTGATATCTCAAC
1 TCATATGATATCTCAAC
40595227 TCATATGATGATATCTCAAC
1 TC--AT-ATGATATCTCAAC
40595247 TCATATGAT
1 TCATATGAT
40595256 GATACATTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
19 2 0.08
20 14 0.56
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (17 bp):
TCATATGATATCTCAAC
Found at i:40595240 original size:20 final size:20
Alignment explanation
Indices: 40595215--40595259 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
40595205 ACAAATCATT
40595215 TGATATCTCAACTCATATGA
1 TGATATCTCAACTCATATGA
40595235 TGATATCTCAACTCATATGA
1 TGATATCTCAACTCATATGA
40595255 TGATA
1 TGATA
40595260 CATTCCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
TGATATCTCAACTCATATGA
Found at i:40597860 original size:32 final size:32
Alignment explanation
Indices: 40597819--40597888 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
40597809 AATTATGACA
*
40597819 CATAACCAAAATAACTAAGTCCCTATACATGT
1 CATAACCAAAATAAATAAGTCCCTATACATGT
40597851 CATAACCAAAATAAATAAGTCCCTATACATGT
1 CATAACCAAAATAAATAAGTCCCTATACATGT
40597883 CATAAC
1 CATAAC
40597889 TCAGAATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (32 bp):
CATAACCAAAATAAATAAGTCCCTATACATGT
Found at i:40598433 original size:42 final size:42
Alignment explanation
Indices: 40598321--40598474 Score: 188
Period size: 42 Copynumber: 3.6 Consensus size: 42
40598311 AATCGTACCA
* * * *
40598321 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
40598363 ATGCCA-ATAGCCAAACTATGGTCTTACACGAAATCTCATATCG
1 ATGCCATAT-CCCAGA-TATGGTCTTACACGAAATCTCATATCG
*
40598406 ATGCCATATCCTAGATATGGTCTTACAC-AAAGTCTCATA-CTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAA-TCTCATATC-G
40598448 ATGCCATATCCCAGATATGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
40598475 TATAGTTTCA
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
41 6 0.06
42 57 0.59
43 32 0.33
44 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:40611729 original size:13 final size:15
Alignment explanation
Indices: 40611699--40611730 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
40611689 AAAAGGAAAA
40611699 AAAAGAATTAGTAAT
1 AAAAGAATTAGTAAT
40611714 AAAA-AATTAG-AAT
1 AAAAGAATTAGTAAT
40611727 AAAA
1 AAAA
40611731 TTTAAATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (15 bp):
AAAAGAATTAGTAAT
Found at i:40613080 original size:17 final size:17
Alignment explanation
Indices: 40613055--40613100 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
40613045 ACTTCACAAA
*
40613055 TCATTTGATATCTCAAC
1 TCATATGATATCTCAAC
40613072 TCATATGATGATATCTCAAC
1 TC--AT-ATGATATCTCAAC
40613092 TCATATGAT
1 TCATATGAT
40613101 GATACATTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
19 2 0.08
20 14 0.56
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (17 bp):
TCATATGATATCTCAAC
Found at i:40613085 original size:20 final size:20
Alignment explanation
Indices: 40613060--40613104 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
40613050 ACAAATCATT
40613060 TGATATCTCAACTCATATGA
1 TGATATCTCAACTCATATGA
40613080 TGATATCTCAACTCATATGA
1 TGATATCTCAACTCATATGA
40613100 TGATA
1 TGATA
40613105 CATTCCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
TGATATCTCAACTCATATGA
Found at i:40615705 original size:32 final size:32
Alignment explanation
Indices: 40615664--40615733 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
40615654 AATTATGACA
*
40615664 CATAACCAAAATAACTAAGTCCCTATACATGT
1 CATAACCAAAATAAATAAGTCCCTATACATGT
40615696 CATAACCAAAATAAATAAGTCCCTATACATGT
1 CATAACCAAAATAAATAAGTCCCTATACATGT
40615728 CATAAC
1 CATAAC
40615734 TCAGAATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (32 bp):
CATAACCAAAATAAATAAGTCCCTATACATGT
Found at i:40616287 original size:42 final size:42
Alignment explanation
Indices: 40616224--40616319 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
40616214 ATAGCCAAAC
*
40616224 TATGGTCTTACACGAAATCTCATA-TCGATGCCATATCCTAGA
1 TATGGTCTTACACGAAATCTCATACT-GATGCCATATCCCAGA
*
40616266 TATGGTCTTACGC-AAAGTCTCATACTGATGCCATATCCCAGA
1 TATGGTCTTACACGAAA-TCTCATACTGATGCCATATCCCAGA
40616308 TATGGTCTTACA
1 TATGGTCTTACA
40616320 TATAGTTTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
41 3 0.06
42 45 0.92
43 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
TATGGTCTTACACGAAATCTCATACTGATGCCATATCCCAGA
Found at i:40626231 original size:58 final size:58
Alignment explanation
Indices: 40626161--40626280 Score: 240
Period size: 58 Copynumber: 2.1 Consensus size: 58
40626151 AGTATAAACG
40626161 ACAACTTTAGATAGTATTAGATATGGCCTAAATTTATCGAATGCAAAAACCACAGCTA
1 ACAACTTTAGATAGTATTAGATATGGCCTAAATTTATCGAATGCAAAAACCACAGCTA
40626219 ACAACTTTAGATAGTATTAGATATGGCCTAAATTTATCGAATGCAAAAACCACAGCTA
1 ACAACTTTAGATAGTATTAGATATGGCCTAAATTTATCGAATGCAAAAACCACAGCTA
40626277 ACAA
1 ACAA
40626281 TTCTTTCTCC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (58 bp):
ACAACTTTAGATAGTATTAGATATGGCCTAAATTTATCGAATGCAAAAACCACAGCTA
Found at i:40629962 original size:13 final size:15
Alignment explanation
Indices: 40629932--40629963 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
40629922 AAAAGGAAAA
40629932 AAAAGAATTAGTAAT
1 AAAAGAATTAGTAAT
40629947 AAAA-AATTAG-AAT
1 AAAAGAATTAGTAAT
40629960 AAAA
1 AAAA
40629964 TTTAAATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (15 bp):
AAAAGAATTAGTAAT
Found at i:40631976 original size:13 final size:13
Alignment explanation
Indices: 40631960--40631985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40631950 ACTTTTTTAA
40631960 TTCCTTTTTAATT
1 TTCCTTTTTAATT
40631973 TTCCTTTTTAATT
1 TTCCTTTTTAATT
40631986 GCTTCTGACA
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:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TTCCTTTTTAATT
Found at i:40635560 original size:13 final size:13
Alignment explanation
Indices: 40635544--40635568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40635534 ATAACTAGCC
40635544 ACGACCGTGCGAT
1 ACGACCGTGCGAT
40635557 ACGACCGTGCGA
1 ACGACCGTGCGA
40635569 ACAATAAGGC
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:0.24, C:0.32, G:0.32, T:0.12
Consensus pattern (13 bp):
ACGACCGTGCGAT
Found at i:40636453 original size:11 final size:11
Alignment explanation
Indices: 40636409--40636435 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40636399 TTTACATATT
40636409 TATTTCTTTGC
1 TATTTCTTTGC
40636420 TATTTCTTTGC
1 TATTTCTTTGC
40636431 TATTT
1 TATTT
40636436 TATTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.11, C:0.15, G:0.07, T:0.67
Consensus pattern (11 bp):
TATTTCTTTGC
Found at i:40638075 original size:6 final size:6
Alignment explanation
Indices: 40638066--40638093 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
40638056 TTGCTTTTCC
40638066 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
40638094 CAAGTTCTAA
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:40639862 original size:119 final size:120
Alignment explanation
Indices: 40639656--40639878 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 120
40639646 TACTCGTTCA
*
40639656 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
* *
40639721 TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * ** *
40639776 AATGCCTTCGGG-CTTAGCTCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGA
* * *
40639838 ATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
64 ATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
40639879 CATCATTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.05
119 64 0.73
120 20 0.23
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:40639878 original size:40 final size:40
Alignment explanation
Indices: 40639654--40639878 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
40639644 GCTACTCGTT
* *
40639654 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
40639694 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
40639734 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
40639774 CCAATGCCTTCGGG-CTTAGCTCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
40639813 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
40639854 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40639879 CATCATTCGA
Statistics
Matches: 160, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 116 0.73
41 12 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:40647901 original size:40 final size:39
Alignment explanation
Indices: 40647864--40648035 Score: 229
Period size: 40 Copynumber: 4.3 Consensus size: 39
40647854 GCTACTCGTT
* *
40647864 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGTT-TAGTAACTCGCA
40647904 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
* *
40647944 TAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCC-GGTTTAGTAACTCGCA
* * * *
40647984 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
40648023 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40648036 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.01
39 31 0.26
40 83 0.70
41 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGTTTAGTAACTCGCA
Found at i:40648072 original size:79 final size:78
Alignment explanation
Indices: 40647864--40648086 Score: 214
Period size: 80 Copynumber: 2.8 Consensus size: 78
40647854 GCTACTCGTT
* * * * * *
40647864 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCACAAA-GCCTTCGGG-CTTAGCCCGG
*
40647929 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* * * *
40647944 TAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCA-CAAAGCCTTCGGGCTTAGCCCGGA
*
40648009 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
** * * ** *
40648023 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCAGTTAGCACAAAGCCTTCGAGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAACCCAGATATAGT-AACTAGCACAAAGCCTTCG-GGCTTAGCCCG
40648087 AACATCATTC
Statistics
Matches: 118, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
78 3 0.03
79 54 0.46
80 58 0.49
81 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCACAAAGCCTTCGGGCTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:40648072 original size:119 final size:120
Alignment explanation
Indices: 40647866--40648081 Score: 269
Period size: 119 Copynumber: 1.8 Consensus size: 120
40647856 TACTCGTTCA
*
40647866 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* * * *
40647931 TTAGTAACTCGCATAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACAAATGCCTTCGAGACTTAACCCAGATTTAGTAACTCGCACC
* * **
40647986 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* **
40648048 ATATGGTCAGTTAGCACAAA-GCCTTCGAGACTTA
64 ATATAGT-AACTAGCACAAATGCCTTCGAGACTTA
40648082 GCCCGAACAT
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
118 4 0.05
119 57 0.70
120 20 0.25
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTAGCACAAATGCCTTCGAGACTTAACCCAGATTTAGTAACTCGCACC
Found at i:40651804 original size:20 final size:20
Alignment explanation
Indices: 40651779--40651828 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
40651769 TATATTTTGT
40651779 TGTTTTCCCCTACTTTGAGA
1 TGTTTTCCCCTACTTTGAGA
40651799 TGTTTTCCCCTACTTTGAGA
1 TGTTTTCCCCTACTTTGAGA
40651819 TGTTTTCCCC
1 TGTTTTCCCC
40651829 CATCATTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.28, G:0.14, T:0.46
Consensus pattern (20 bp):
TGTTTTCCCCTACTTTGAGA
Found at i:40656945 original size:48 final size:46
Alignment explanation
Indices: 40656892--40657046 Score: 134
Period size: 48 Copynumber: 3.2 Consensus size: 46
40656882 TAGCCCAACG
* *
40656892 ATGGTCTTACACAATGTCTCATATCGATGCCAATGCAATATCCCAGAT
1 ATGGTCTTACA-AA-GTCTCATATCGATGCCAATGCCATGTCCCAGAT
** ** * *
40656940 ATGGTCTTACATGGGATCAAATATCGATGCCAATGCCATGTTCCAGAC
1 ATGGTCTTACA-AAG-TCTCATATCGATGCCAATGCCATGTCCCAGAT
* *
40656988 ATGGACTTACATGGAA-TCTCATATCGATGCCAATGCCATGTCCTAG-T
1 ATGGTCTTACA---AAGTCTCATATCGATGCCAATGCCATGTCCCAGAT
40657035 CATGGTCTTACA
1 -ATGGTCTTACA
40657047 TTGGATAACA
Statistics
Matches: 84, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
47 1 0.01
48 83 0.99
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (46 bp):
ATGGTCTTACAAAGTCTCATATCGATGCCAATGCCATGTCCCAGAT
Found at i:40657047 original size:48 final size:47
Alignment explanation
Indices: 40656908--40657047 Score: 174
Period size: 48 Copynumber: 2.9 Consensus size: 47
40656898 TTACACAATG
* * *
40656908 TCTCATATCGATGCCAATGCAATATCCCAGAT-ATGGTCTTACATGGGA
1 TCTCATATCGATGCCAATGCCATGT-CCAG-TCATGGTCTTACATGGAA
** * *
40656956 TCAAATATCGATGCCAATGCCATGTTCCAGACATGGACTTACATGGAA
1 TCTCATATCGATGCCAATGCCATG-TCCAGTCATGGTCTTACATGGAA
40657004 TCTCATATCGATGCCAATGCCATGTCCTAGTCATGGTCTTACAT
1 TCTCATATCGATGCCAATGCCATGTCC-AGTCATGGTCTTACAT
40657048 TGGATAACAC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
47 3 0.04
48 74 0.95
49 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (47 bp):
TCTCATATCGATGCCAATGCCATGTCCAGTCATGGTCTTACATGGAA
Found at i:40660773 original size:28 final size:29
Alignment explanation
Indices: 40660663--40660766 Score: 131
Period size: 29 Copynumber: 3.7 Consensus size: 29
40660653 GTGAGCATGA
*
40660663 ATATGAATGTGA-TTGGGTCTAACGGGCC
1 ATATGAATGTGATTTGGGCCTAACGGGCC
*
40660691 ATATAAATGTGATTTGGGCCTAACGGGCC
1 ATATGAATGTGATTTGGGCCTAACGGGCC
** * *
40660720 ATATTCAGGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAACGGGCC
*
40660749 ATATGAATATGA-TTGGGC
1 ATATGAATGTGATTTGGGC
40660767 TTAATGGTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 17 0.26
29 48 0.74
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAACGGGCC
Found at i:40665579 original size:28 final size:28
Alignment explanation
Indices: 40665540--40665635 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
40665530 TAATTTTGCA
*
40665540 CACACACAGTGCCTTACATCAGATCTCG
1 CACACATAGTGCCTTACATCAGATCTCG
* *
40665568 CACACATAGTGCTCGGTTA-AT-A-ATTTCA
1 CACACATAGTGC-C--TTACATCAGATCTCG
* *
40665596 CACACATAGTGCCTTACACCCGATCTCG
1 CACACATAGTGCCTTACATCAGATCTCG
40665624 CACACATAGTGC
1 CACACATAGTGC
40665636 TTTGTTACTA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 1 0.02
28 43 0.78
29 2 0.04
30 2 0.04
31 3 0.05
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (28 bp):
CACACATAGTGCCTTACATCAGATCTCG
Found at i:40665621 original size:56 final size:58
Alignment explanation
Indices: 40665528--40665657 Score: 183
Period size: 56 Copynumber: 2.3 Consensus size: 58
40665518 ATATTCCCTA
*
40665528 AATAATTTTGCACACACACAGTGCCTTACATCAGATCTCGCACACATAGTGCTCGGTT
1 AATAATTTTGCACACACACAGTGCCTTACACCAGATCTCGCACACATAGTGCTCGGTT
* * **
40665586 AATAA-TTT-CACACACATAGTGCCTTACACCCGATCTCGCACACATAGTGCTTTGTT
1 AATAATTTTGCACACACACAGTGCCTTACACCAGATCTCGCACACATAGTGCTCGGTT
* *
40665642 ACTAATCTTGCACACA
1 AATAATTTTGCACACA
40665658 TAGTACATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
56 47 0.75
57 5 0.08
58 11 0.17
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (58 bp):
AATAATTTTGCACACACACAGTGCCTTACACCAGATCTCGCACACATAGTGCTCGGTT
Found at i:40665649 original size:28 final size:28
Alignment explanation
Indices: 40665562--40665661 Score: 85
Period size: 28 Copynumber: 3.6 Consensus size: 28
40665552 CTTACATCAG
** *
40665562 ATCTCGCACACATAGTGCTCGGTTAATA
1 ATCTCGCACACATAGTGCTTTGTTACTA
* * * ** **
40665590 ATTTCACACACATAGTGCCTT-ACACCCG
1 ATCTCGCACACATAGTGCTTTGTTA-CTA
40665618 ATCTCGCACACATAGTGCTTTGTTACTA
1 ATCTCGCACACATAGTGCTTTGTTACTA
*
40665646 ATCTTGCACACATAGT
1 ATCTCGCACACATAGT
40665662 ACATATATTC
Statistics
Matches: 52, Mismatches: 18, Indels: 4
0.70 0.24 0.05
Matches are distributed among these distances:
27 1 0.02
28 50 0.96
29 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (28 bp):
ATCTCGCACACATAGTGCTTTGTTACTA
Found at i:40676860 original size:46 final size:45
Alignment explanation
Indices: 40676793--40676966 Score: 167
Period size: 46 Copynumber: 3.8 Consensus size: 45
40676783 GTAACCCACC
* *
40676793 CATAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
*
40676838 GCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAATT-ACAT
1 -CATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--ATTCGCAT
* * **
40676888 C-TCACG-G-ACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CAT-AAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
* *
40676931 CCATAAGTAAACTCGGACTCAACTCAACGAGTTCGG
1 -CATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
40676967 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 4 0.04
45 1 0.01
46 59 0.56
47 24 0.23
48 3 0.03
49 4 0.04
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
Found at i:40676915 original size:93 final size:93
Alignment explanation
Indices: 40676802--40676970 Score: 266
Period size: 93 Copynumber: 1.8 Consensus size: 93
40676792 CCATAAGTGA
** * * *
40676802 ACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATGCATAAGTGAACTCGGACTCAACTCAACG
1 ACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTAAACTCGGACTCAACTCAACG
40676867 AGCTCGGATGCCTAATTACATCTCACGG
66 AGCTCGGATGCCTAATTACATCTCACGG
* *
40676895 ACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTAAACTCGGACTCAACTCAACG
1 ACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTAAACTCGGACTCAACTCAACG
*
40676960 AGTTCGGATGC
66 AGCTCGGATGC
40676971 TCAACCATCC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
ACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTAAACTCGGACTCAACTCAACG
AGCTCGGATGCCTAATTACATCTCACGG
Found at i:40679383 original size:17 final size:17
Alignment explanation
Indices: 40679361--40679395 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
40679351 CCTCACACGG
40679361 GCAGACCACACGGCCAT
1 GCAGACCACACGGCCAT
40679378 GCAGACCACACGGCCAT
1 GCAGACCACACGGCCAT
40679395 G
1 G
40679396 TCAATTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.40, G:0.26, T:0.06
Consensus pattern (17 bp):
GCAGACCACACGGCCAT
Found at i:40707546 original size:16 final size:16
Alignment explanation
Indices: 40707525--40707570 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
40707515 TCCTCCTATT
40707525 TTTTTATTTATTCTTA
1 TTTTTATTTATTCTTA
40707541 TTTTTATTTTATT-TTA
1 TTTTTA-TTTATTCTTA
40707557 TTTTTATTT-TTCTT
1 TTTTTATTTATTCTT
40707571 TTGATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 5 0.18
16 15 0.54
17 6 0.21
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTATTTATTCTTA
Found at i:40707552 original size:5 final size:5
Alignment explanation
Indices: 40707526--40707609 Score: 57
Period size: 5 Copynumber: 15.8 Consensus size: 5
40707516 CCTCCTATTT
*
40707526 TTTTA -TTTA TTCTTA TTTTTA TTTTA TTTTA TTTTTA TTTTTC TTTTGA
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTT-A
*
40707575 TTTTTA TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
40707610 GAAAGACATA
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
3 3 0.05
4 4 0.06
5 27 0.42
6 25 0.38
7 6 0.09
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:40707556 original size:22 final size:22
Alignment explanation
Indices: 40707526--40707578 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
40707516 CCTCCTATTT
40707526 TTTTA-TTTATTCTTATTTTTA
1 TTTTATTTTATTCTTATTTTTA
* *
40707547 TTTTATTTTATTTTTATTTTTC
1 TTTTATTTTATTCTTATTTTTA
40707569 TTTTGATTTT
1 TTTT-ATTTT
40707579 TATTTTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 5 0.18
22 18 0.64
23 5 0.18
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTATTTTATTCTTATTTTTA
Found at i:40707579 original size:7 final size:6
Alignment explanation
Indices: 40707521--40707589 Score: 72
Period size: 6 Copynumber: 11.8 Consensus size: 6
40707511 TGAATCCTCC
*
40707521 TATTTT T-TTATT TATTCT TATTTT TA-TTT TA-TTT TATTTT TATTTT
1 TATTTT TATT-TT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
* * *
40707567 TCTTTT GATTTT TATTTT CATTT
1 TATTTT TATTTT TATTTT TATTT
40707590 CAATTTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 12 0.23
6 39 0.74
7 2 0.04
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (6 bp):
TATTTT
Done.