Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 134 of 185
Found at i:41136047 original size:28 final size:27
Alignment explanation
Indices: 41135969--41136065 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 27
41135959 TTCTTACAAC
*
41135969 TTTATAAAATTTTATAATTTTTTTATATT
1 TTTATAAAATTTTACAA--TTTTTATATT
* *
41135998 TCTAT-ATATTTT-CTAATTTTTATGATT
1 TTTATAAAATTTTAC-AATTTTTAT-ATT
41136025 TTTATAAAATTTTACAATTTTTATATAT
1 TTTATAAAATTTTACAATTTTTATAT-T
* *
41136053 TTTTTAAGATTTT
1 TTTATAAAATTTT
41136066 CATAACTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
26 7 0.12
27 9 0.16
28 35 0.62
29 5 0.09
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTATAAAATTTTACAATTTTTATATT
Found at i:41136056 original size:19 final size:19
Alignment explanation
Indices: 41135921--41136056 Score: 84
Period size: 19 Copynumber: 7.2 Consensus size: 19
41135911 AGTACGATAA
*
41135921 TTTTATAATTTTT-TATGAA
1 TTTTATAATTTTTATAT-AT
*
41135940 TTTTATATTTTTTATA-AT
1 TTTTATAATTTTTATATAT
** * *
41135958 TTTCT-TACAACTTTATAAAA
1 TTT-TATA-ATTTTTATATAT
*
41135978 TTTTATAATTTTTTTATAT
1 TTTTATAATTTTTATATAT
* *
41135997 TTCTAT-ATATTTTCTA-AT
1 TTTTATAAT-TTTTATATAT
* * *
41136015 TTTTATGATTTTTATAAAA
1 TTTTATAATTTTTATATAT
*
41136034 TTTTACAATTTTTATATAT
1 TTTTATAATTTTTATATAT
41136053 TTTT
1 TTTT
41136057 TAAGATTTTC
Statistics
Matches: 89, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
18 21 0.24
19 60 0.67
20 8 0.09
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTATATAT
Found at i:41136065 original size:56 final size:58
Alignment explanation
Indices: 41135969--41136076 Score: 150
Period size: 56 Copynumber: 1.9 Consensus size: 58
41135959 TTCTTACAAC
* * *
41135969 TTTATAAAATTTTATAATTTTTTTATATTTCTATATATTTTC-TAA-TTTTTATGATT
1 TTTATAAAATTTTACAATTTTTATATATTTCTATAGATTTTCATAACTTTTTATGATT
*
41136025 TTTATAAAATTTTACAATTTTTATATATTT-TTTAAGATTTTCATAACTTTTT
1 TTTATAAAATTTTACAATTTTTATATATTTCTAT-AGATTTTCATAACTTTTT
41136077 TGTAATATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
55 2 0.04
56 35 0.78
57 3 0.07
58 5 0.11
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (58 bp):
TTTATAAAATTTTACAATTTTTATATATTTCTATAGATTTTCATAACTTTTTATGATT
Found at i:41136142 original size:19 final size:19
Alignment explanation
Indices: 41136113--41136158 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41136103 TATTATATTT
41136113 TTTTTATTAAAATTTAATCA
1 TTTTTA-TAAAATTTAATCA
* * *
41136133 TTTTTATAAATTTTATTGA
1 TTTTTATAAAATTTAATCA
41136152 TTTTTAT
1 TTTTTAT
41136159 TTTTTATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTATAAAATTTAATCA
Found at i:41139452 original size:13 final size:13
Alignment explanation
Indices: 41139429--41139453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41139419 TTTATTTTAG
41139429 TATTTTATTTACT
1 TATTTTATTTACT
41139442 TATTTTATTTAC
1 TATTTTATTTAC
41139454 ATTTATACTT
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:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTATTTACT
Found at i:41139554 original size:16 final size:16
Alignment explanation
Indices: 41139529--41139563 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41139519 TAATTCTCAT
*
41139529 TTTATTTATTTACGTA
1 TTTATCTATTTACGTA
*
41139545 TTTATCTATTTACTTA
1 TTTATCTATTTACGTA
41139561 TTT
1 TTT
41139564 TTACAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTATCTATTTACGTA
Found at i:41141912 original size:31 final size:31
Alignment explanation
Indices: 41141876--41141937 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
41141866 AATCAAACTA
41141876 TATGTATATTAGCTAGTGTAGGTGAATCATG
1 TATGTATATTAGCTAGTGTAGGTGAATCATG
41141907 TATGTATATTAGCTAGTGTAGGTGAATCATG
1 TATGTATATTAGCTAGTGTAGGTGAATCATG
41141938 AAAGGTCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (31 bp):
TATGTATATTAGCTAGTGTAGGTGAATCATG
Found at i:41153842 original size:60 final size:61
Alignment explanation
Indices: 41153776--41153895 Score: 215
Period size: 61 Copynumber: 2.0 Consensus size: 61
41153766 CGTGAGATTT
* *
41153776 AAATGCTATATGA-TTTTTTTTATTCTGATCGTAATATTTAACACTTCATTTATGTAAATA
1 AAATGCTATATGATTTTTTTTTATTCTGATCATAATATTGAACACTTCATTTATGTAAATA
41153836 AAATGCTATATGATTTTTTTTTATTCTGATCATAATATTGAACACTTCATTTATGTAAAT
1 AAATGCTATATGATTTTTTTTTATTCTGATCATAATATTGAACACTTCATTTATGTAAAT
41153896 CGTGTTTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 13 0.23
61 44 0.77
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (61 bp):
AAATGCTATATGATTTTTTTTTATTCTGATCATAATATTGAACACTTCATTTATGTAAATA
Found at i:41158722 original size:82 final size:82
Alignment explanation
Indices: 41158573--41158728 Score: 267
Period size: 82 Copynumber: 1.9 Consensus size: 82
41158563 CCACCTAATT
* *
41158573 TGGAGTAGAAGTTGAGATTTCTTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTGTTCCAAA
1 TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTATTCCAAA
41158638 ATGCGTTTTTTAGTCCC
66 ATGCGTTTTTTAGTCCC
* *
41158655 TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATTTATTCCGAA
1 TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTATTCCAAA
*
41158720 ATGGGTTTT
66 ATGCGTTTT
41158729 AATTCTTCTA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.49
Consensus pattern (82 bp):
TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTATTCCAAA
ATGCGTTTTTTAGTCCC
Found at i:41162502 original size:22 final size:21
Alignment explanation
Indices: 41162459--41162506 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
41162449 TGATTTTTTT
41162459 AATTTTAATTTTATTAATATA
1 AATTTTAATTTTATTAATATA
41162480 ATATTTTATATTATT-TTAA-ATA
1 A-ATTTTA-ATT-TTATTAATATA
41162502 AATTT
1 AATTT
41162507 GGATGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 5 0.21
22 10 0.42
23 7 0.29
24 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTTAATTTTATTAATATA
Found at i:41163747 original size:19 final size:19
Alignment explanation
Indices: 41163718--41163759 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
41163708 TAGAAAATAA
41163718 TTTTTGAAAAATGATTTACT
1 TTTTTGAAAAATGATTTA-T
41163738 TTTTTG-AAAATGATTTAT
1 TTTTTGAAAAATGATTTAT
41163756 TTTT
1 TTTT
41163760 CTAATGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TTTTTGAAAAATGATTTAT
Found at i:41169445 original size:14 final size:14
Alignment explanation
Indices: 41169402--41169448 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
41169392 AAACCTAGAG
41169402 AATTTATAAA-TAT
1 AATTTATAAATTAT
* * *
41169415 -ATTAATAACTTAC
1 AATTTATAAATTAT
41169428 AATTTATAAATTAT
1 AATTTATAAATTAT
41169442 AATTTAT
1 AATTTAT
41169449 TAATATCAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
12 7 0.27
13 2 0.08
14 17 0.65
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTTATAAATTAT
Found at i:41169676 original size:22 final size:22
Alignment explanation
Indices: 41169633--41169679 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
41169623 TTCAATAAAT
* *
41169633 ATTAATATATATAATATTTTAG
1 ATTAATATATATAAGATATTAG
41169655 ATTAATATA-ATAGAGATATTAG
1 ATTAATATATATA-AGATATTAG
41169677 ATT
1 ATT
41169680 GGTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (22 bp):
ATTAATATATATAAGATATTAG
Found at i:41172364 original size:6 final size:6
Alignment explanation
Indices: 41172353--41172378 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41172343 AGATCAATGT
41172353 TCATAA TCATAA TCATAA TCATAA TC
1 TCATAA TCATAA TCATAA TCATAA TC
41172379 CTGAATCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (6 bp):
TCATAA
Found at i:41176752 original size:23 final size:23
Alignment explanation
Indices: 41176726--41176770 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
41176716 TGGAAAGAAA
* *
41176726 TGTAATATCTCGAAAATTACTAT
1 TGTAATACCCCGAAAATTACTAT
41176749 TGTAATACCCCGAAAATTACTA
1 TGTAATACCCCGAAAATTACTA
41176771 CAATAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAT
Found at i:41179293 original size:16 final size:16
Alignment explanation
Indices: 41179272--41179303 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41179262 CCCTTAGATG
41179272 GATCCTTGAGGCCCAA
1 GATCCTTGAGGCCCAA
41179288 GATCCTTGAGGCCCAA
1 GATCCTTGAGGCCCAA
41179304 TATTCACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (16 bp):
GATCCTTGAGGCCCAA
Found at i:41183373 original size:43 final size:43
Alignment explanation
Indices: 41183325--41183408 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
41183315 ATTTTCGATA
*
41183325 TGTGTTTTCATGTAAGACCATG-TCTGGGAC-GTTGGCATCGACT
1 TGTGTTTACATGTAAGACCATGTTC-GGGACAG-TGGCATCGACT
* *
41183368 TGTGTTTACGTGTAAGACCCTGTTCGGGACAGTGGCATCGA
1 TGTGTTTACATGTAAGACCATGTTCGGGACAGTGGCATCGA
41183409 TCTAAGAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 33 0.92
44 3 0.08
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (43 bp):
TGTGTTTACATGTAAGACCATGTTCGGGACAGTGGCATCGACT
Found at i:41184189 original size:15 final size:16
Alignment explanation
Indices: 41184171--41184208 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41184161 ATGGTTAAAT
*
41184171 TTTATATGG-ATAGTA
1 TTTATATGGTAAAGTA
41184186 TTTATATGGTAAAGTA
1 TTTATATGGTAAAGTA
*
41184202 TATATAT
1 TTTATAT
41184209 ATATGTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (16 bp):
TTTATATGGTAAAGTA
Found at i:41193137 original size:64 final size:64
Alignment explanation
Indices: 41193036--41193166 Score: 262
Period size: 64 Copynumber: 2.0 Consensus size: 64
41193026 GAATTATAAT
41193036 TCAGCCAATGAGGCTTGATTAAGATGGATGCCCTCGATTTTTAAGTATTTAAGTTTGAATTGAA
1 TCAGCCAATGAGGCTTGATTAAGATGGATGCCCTCGATTTTTAAGTATTTAAGTTTGAATTGAA
41193100 TCAGCCAATGAGGCTTGATTAAGATGGATGCCCTCGATTTTTAAGTATTTAAGTTTGAATTGAA
1 TCAGCCAATGAGGCTTGATTAAGATGGATGCCCTCGATTTTTAAGTATTTAAGTTTGAATTGAA
41193164 TCA
1 TCA
41193167 TATGAAATTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (64 bp):
TCAGCCAATGAGGCTTGATTAAGATGGATGCCCTCGATTTTTAAGTATTTAAGTTTGAATTGAA
Found at i:41197549 original size:25 final size:25
Alignment explanation
Indices: 41197521--41197610 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
41197511 CCTGATAATA
*
41197521 AGCTCTCATGAGCTTCTCGTTATTT
1 AGCTCTCATGAGCTTCTCGTTATGT
* * *
41197546 AGCTCTTATAAG-TATCCCGTTATGT
1 AGCTCTCATGAGCT-TCTCGTTATGT
* *
41197571 GGCTCTCACGAGCTTCTCGATTAATG-
1 AGCTCTCATGAGCTTCTCG-TT-ATGT
*
41197597 -GCTCTCTTGAGCTT
1 AGCTCTCATGAGCTT
41197611 TCCGTTTATG
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
24 1 0.02
25 43 0.86
26 3 0.06
27 3 0.06
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (25 bp):
AGCTCTCATGAGCTTCTCGTTATGT
Found at i:41197707 original size:25 final size:25
Alignment explanation
Indices: 41197570--41197759 Score: 117
Period size: 25 Copynumber: 7.7 Consensus size: 25
41197560 TCCCGTTATG
** *
41197570 TGGCTCTCACGAGCTTCTCGATTAA
1 TGGCTCTCTTGAGCTTCCCGATTAA
* *
41197595 TGGCTCTCTTGAGCTTTCCG-TTTA
1 TGGCTCTCTTGAGCTTCCCGATTAA
* *
41197619 TGGCT-TGTATGAGCTTTCCGA-TAA
1 TGGCTCTCT-TGAGCTTCCCGATTAA
** *
41197643 TTGGCTCTCCAGAGCTTCTCGA-TAA
1 -TGGCTCTCTTGAGCTTCCCGATTAA
41197668 TTGGCTCT-TATGAGCTTCCCGATTAA
1 -TGGCTCTCT-TGAGCTTCCCGATTAA
* * *
41197694 TGGCTCTCTGGAGCTTCCC-AATAT
1 TGGCTCTCTTGAGCTTCCCGATTAA
* * * *
41197718 TAGCTCGCATGAGCTTCCCGGTT-A
1 TGGCTCTCTTGAGCTTCCCGATTAA
*
41197742 CGGCTCT-TATGAGCTTCC
1 TGGCTCTCT-TGAGCTTCC
41197760 TGTTACATGG
Statistics
Matches: 127, Mismatches: 29, Indels: 19
0.73 0.17 0.11
Matches are distributed among these distances:
23 2 0.02
24 52 0.41
25 68 0.54
26 5 0.04
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (25 bp):
TGGCTCTCTTGAGCTTCCCGATTAA
Found at i:41197805 original size:25 final size:25
Alignment explanation
Indices: 41197752--41197806 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
41197742 CGGCTCTTAT
* * * *
41197752 GAGCTTCCTGTTACATGGCTTACAT
1 GAGCTTCATGTTACATGGCTCAAAA
*
41197777 GAGCTTCATGTTATATGGCTCAAAA
1 GAGCTTCATGTTACATGGCTCAAAA
41197802 GAGCT
1 GAGCT
41197807 ACCCATTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (25 bp):
GAGCTTCATGTTACATGGCTCAAAA
Found at i:41198701 original size:23 final size:23
Alignment explanation
Indices: 41198650--41198704 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
41198640 GCCCGGCCCG
41198650 ATTTTTAATAAACACAAAAAAATT
1 ATTTTTAA-AAACACAAAAAAATT
* *
41198674 A-TTTTAAAAATA-AAAAATATAT
1 ATTTTTAAAAACACAAAAAAAT-T
41198696 ATTTTTAAA
1 ATTTTTAAA
41198705 GTATTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.26
22 6 0.22
23 13 0.48
24 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTTTTAAAAACACAAAAAAATT
Found at i:41200512 original size:28 final size:28
Alignment explanation
Indices: 41200472--41200531 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
41200462 CCATGACATC
* *
41200472 CACAAAAATAGTCTA-TTGGGATAGTAAA
1 CACAAAAATAGTCTACCT-GGACAGTAAA
41200500 CACAAATAA-AGTCTACCTGGACAGTAAA
1 CACAAA-AATAGTCTACCTGGACAGTAAA
41200528 CACA
1 CACA
41200532 GGGTAAGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (28 bp):
CACAAAAATAGTCTACCTGGACAGTAAA
Found at i:41206625 original size:25 final size:25
Alignment explanation
Indices: 41206589--41206641 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
41206579 ATGACAATCT
*
41206589 AATCCTTCTTCAATCTATATCCTTA
1 AATCCTTATTCAATCTATATCCTTA
41206614 AATCCTTATTCAATCTATATCCTTA
1 AATCCTTATTCAATCTATATCCTTA
41206639 AAT
1 AAT
41206642 ATGGAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (25 bp):
AATCCTTATTCAATCTATATCCTTA
Found at i:41211146 original size:20 final size:22
Alignment explanation
Indices: 41211103--41211146 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
41211093 AAAAAATTTA
*
41211103 TTCTTTTGAAAAATTTTCGTAC
1 TTCTTTTGAAAAATTTTCGAAC
*
41211125 TTCTTTT-AAAAGTTTT-GAAC
1 TTCTTTTGAAAAATTTTCGAAC
41211145 TT
1 TT
41211147 TTTATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 8 0.40
22 7 0.35
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.52
Consensus pattern (22 bp):
TTCTTTTGAAAAATTTTCGAAC
Found at i:41213918 original size:18 final size:19
Alignment explanation
Indices: 41213881--41213920 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41213871 TATTTTGTAT
41213881 AAATTAAATATAAGATTAA
1 AAATTAAATATAAGATTAA
41213900 AAATTGAAA-ATAA-ATTAA
1 AAATT-AAATATAAGATTAA
41213918 AAA
1 AAA
41213921 CATATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 9 0.45
20 3 0.15
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATTAAATATAAGATTAA
Found at i:41232587 original size:15 final size:16
Alignment explanation
Indices: 41232559--41232589 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
41232549 AGGGGTTAAG
41232559 GGTTTAATGATTTTGA
1 GGTTTAATGATTTTGA
41232575 GGTTTAA-GATTTTGA
1 GGTTTAATGATTTTGA
41232590 TTTCAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (16 bp):
GGTTTAATGATTTTGA
Found at i:41232681 original size:62 final size:61
Alignment explanation
Indices: 41232561--41232689 Score: 143
Period size: 61 Copynumber: 2.1 Consensus size: 61
41232551 GGGTTAAGGG
* ** * * * *
41232561 TTTAATGATTTTGAGGTTTAAGATTTTGATTTCAAGTTTAGGAATGGTAATTAGGTTTAATA
1 TTTAATGATTTTAAGGTTTAAGAGGTTGATTTCAAGGTTAGGAACGATAATTAAGTTT-ATA
* *
41232623 TTTAATGATTTTAAGGTTTAAG-GGTTGATTTCGAGGTTAGGGACGATAATGTAAGTTTATA
1 TTTAATGATTTTAAGGTTTAAGAGGTTGATTTCAAGGTTAGGAACGATAAT-TAAGTTTATA
*
41232684 ATTAAT
1 TTTAAT
41232690 TTTTTAAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
61 29 0.52
62 27 0.48
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.44
Consensus pattern (61 bp):
TTTAATGATTTTAAGGTTTAAGAGGTTGATTTCAAGGTTAGGAACGATAATTAAGTTTATA
Found at i:41232830 original size:16 final size:16
Alignment explanation
Indices: 41232761--41232828 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
41232751 TTTGGTTCGC
41232761 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41232777 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41232793 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
41232809 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
41232825 TGTA
1 TGTA
41232829 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:41232860 original size:45 final size:44
Alignment explanation
Indices: 41232809--41232903 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
41232799 GGATTAGAGG
* * *
41232809 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
41232854 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
41232898 TGTAAT
1 TGTAAT
41232904 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:41233086 original size:18 final size:17
Alignment explanation
Indices: 41233065--41233099 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41233055 TTATTATTTA
*
41233065 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41233083 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41233100 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41233093 original size:28 final size:27
Alignment explanation
Indices: 41233023--41233095 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
41233013 TTTATTATCA
*
41233023 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
41233051 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
41233078 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
41233096 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:41233233 original size:18 final size:17
Alignment explanation
Indices: 41233212--41233246 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41233202 TTATTATTAA
*
41233212 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41233230 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41233247 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41233258 original size:147 final size:149
Alignment explanation
Indices: 41232984--41233258 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
41232974 ATGATTATTG
*
41232984 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
41233049 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
41233114 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
* *
41233133 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTACTCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
41233196 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
41233259 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 94 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:41233314 original size:147 final size:145
Alignment explanation
Indices: 41232990--41233297 Score: 357
Period size: 147 Copynumber: 2.1 Consensus size: 145
41232980 ATTGTTATTG
* * *
41232990 TTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAAACATAA
1 TTATTTAAATTATAATAAGA-TA-TAAATATC-AAAATAAATAATTTAATCATATTTAAACATAA
* * *
41233055 TTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAAT
63 TTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAAT
* * ** ** *
41233120 TTGTTTTGGTAAATTATT
128 ATGATTTACTAAACCATA
* * *
41233138 TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTACTCATATTTAAACATAAT
1 TTATTTAAATTATAATAAGA-TATAAATATCAA-AATAAATAATTTAATCATATTTAAACATAAT
* **
41233203 TATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTA
64 TATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACA--CAAA
41233268 TATGAATTTACTCAAACCATA
127 TATG-ATTTACT-AAACCATA
41233289 TTA-TTAAAT
1 TTATTTAAAT
41233298 ATGATACTGT
Statistics
Matches: 140, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
146 2 0.01
147 93 0.66
148 23 0.16
149 4 0.03
150 10 0.07
151 8 0.06
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (145 bp):
TTATTTAAATTATAATAAGATATAAATATCAAAATAAATAATTTAATCATATTTAAACATAATTA
TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATG
ATTTACTAAACCATA
Found at i:41233358 original size:18 final size:17
Alignment explanation
Indices: 41233337--41233371 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41233327 TTATTATTAA
41233337 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
41233355 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
41233372 TCTAATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:41233470 original size:119 final size:123
Alignment explanation
Indices: 41233195--41233491 Score: 417
Period size: 119 Copynumber: 2.4 Consensus size: 123
41233185 CTCATATTTA
*
41233195 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* * *
41233260 TATTCTTATATGAATTTACTCAAACCATATTATTAAATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTAAAACCATA-TATT-AATATGATACTATAAAAGATAAAAT
* *
41233320 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTC-TAATAATCAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
41233384 TATTCTTATATGAATTTACTAAAATCATA-A-T-ATATGATACTATAAAAGA-AAATT
66 TATTCTTATATGAATTTACTAAAACCATATATTAATATGATACTATAAAAGATAAAAT
* * *
41233438 GCAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGACTTAATAAAATT
1 --AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
41233492 TAAAATAATT
Statistics
Matches: 157, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
118 4 0.03
119 61 0.39
120 2 0.01
121 1 0.01
122 1 0.01
124 36 0.23
125 52 0.33
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (123 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTAAAACCATATATTAATATGATACTATAAAAGATAAAAT
Found at i:41233602 original size:91 final size:91
Alignment explanation
Indices: 41233507--41233714 Score: 285
Period size: 91 Copynumber: 2.3 Consensus size: 91
41233497 TAATTATAAC
* * * *
41233507 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
41233571 TAATATAAAATTTCATAAAATTCTTGA
65 TAATATAAAATTTCATAAAATTCTTAA
* *
41233598 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
41233663 GATATATAATTTCATAAAATTCTTAA
66 AATATAAAATTTCATAAAATTCTTAA
*
41233689 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
41233715 CTAAAATCAA
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
91 82 0.78
92 22 0.21
93 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATAAAATTTCATAAAATTCTTAA
Found at i:41233630 original size:47 final size:47
Alignment explanation
Indices: 41233574--41233721 Score: 128
Period size: 44 Copynumber: 3.2 Consensus size: 47
41233564 TTAATAATAA
*
41233574 TATAAAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATT
1 TATAAAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
* ** * * *
41233621 TATACAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATGA
1 TATAAAATTTCATAAAATTCTTAATAATAAAT-T-TTCTTATATGAAT-T
* *
41233665 TATATAATTTCATAAAATTCTTAATAATAAAATGTTCTTATATGAATT
1 TATAAAATTTCATAAAATTCTTAATAAT-AAATTTTCTTATATGAATT
41233713 TACTAAAAT
1 TA-TAAAAT
41233722 CAATATATAA
Statistics
Matches: 75, Mismatches: 15, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
43 3 0.04
44 24 0.32
45 6 0.08
46 4 0.05
47 22 0.29
48 8 0.11
49 8 0.11
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (47 bp):
TATAAAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
Found at i:41233674 original size:44 final size:43
Alignment explanation
Indices: 41233488--41233674 Score: 103
Period size: 44 Copynumber: 4.1 Consensus size: 43
41233478 GACTTAATAA
* * * *
41233488 AATTTAAAATAATTATAACTAATAAAT-TATATTTTATGAATTTGTAT
1 AATTTAAAATAA-T-TAA-TATTAAATATA-ATTTAAT-AATATATAT
* *
41233535 AATTTAAAATAA-TAATTATTACATATAATTTAATAATAATATAA
1 AATTTAAAATAATTAA-TATTAAATATAATTTAATAAT-ATATAT
** * * * * *
41233579 AATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTATAC
1 AA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATATAT
41233626 AATTTAAAATAATTAATATTAAATATAATTTAATAATGATATAT
1 AATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATATAT
41233670 AATTT
1 AATTT
41233675 CATAAAATTC
Statistics
Matches: 106, Mismatches: 22, Indels: 27
0.68 0.14 0.17
Matches are distributed among these distances:
43 6 0.06
44 47 0.44
45 9 0.08
46 7 0.07
47 32 0.30
48 5 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (43 bp):
AATTTAAAATAATTAATATTAAATATAATTTAATAATATATAT
Found at i:41236888 original size:18 final size:18
Alignment explanation
Indices: 41236867--41236901 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41236857 TTATATTATT
41236867 TATATGTATTTT-ATAATA
1 TATATGT-TTTTAATAATA
41236885 TATATGTTTTTAATAAT
1 TATATGTTTTTAATAAT
41236902 TTTTTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TATATGTTTTTAATAATA
Found at i:41237206 original size:21 final size:21
Alignment explanation
Indices: 41237168--41237208 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41237158 TGAATCATTA
**
41237168 TATATAAATATTTTATTATTC
1 TATATAAATATTCCATTATTC
*
41237189 TATATATATATTCCATTATT
1 TATATAAATATTCCATTATT
41237209 TATGTACTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATAAATATTCCATTATTC
Found at i:41240830 original size:3 final size:3
Alignment explanation
Indices: 41240822--41240850 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41240812 TTATCATCTT
41240822 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41240851 TTAATTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41241185 original size:22 final size:22
Alignment explanation
Indices: 41241157--41241203 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
41241147 ACAAATCCTA
41241157 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
*
41241179 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCCAAAATCC
41241201 TCT
1 TCT
41241204 TAAACTCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:41241235 original size:52 final size:52
Alignment explanation
Indices: 41241157--41241255 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
41241147 ACAAATCCTA
* *
41241157 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAATTCTCTTAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
*
41241209 TCTCAATTTCCTTTCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
41241256 CAAATCCATA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.39
Consensus pattern (52 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
Found at i:41241236 original size:22 final size:22
Alignment explanation
Indices: 41241208--41241258 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
41241198 TTCTCTTAAA
* *
41241208 CTCTCAATTTCCTTTC-AAAAT
1 CTCTCAATTTCATTCCAAAAAT
41241229 CCTCTCAATTTCATTCCAAAAAT
1 -CTCTCAATTTCATTCCAAAAAT
41241252 CTCTCAA
1 CTCTCAA
41241259 ATCCATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCTCAATTTCATTCCAAAAAT
Found at i:41253715 original size:108 final size:107
Alignment explanation
Indices: 41253526--41253727 Score: 289
Period size: 108 Copynumber: 1.9 Consensus size: 107
41253516 TAATCTTCAG
* *
41253526 TCTATTCCAATGTTTCCCAAGGAGATAGAATTATTGGCTTCAATATACTCCACTGCAACTTCAGG
1 TCTATTCCAATGTTGCCCAAGGAGATAGAATTACTGGCTTCAATATACTCCACTGCAAC-TCAGG
* *
41253591 GAGGTAAAATCTGCCATCTTTAATCTGCTCCACTACTGCTCAA
65 GAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTCAA
* * * *
41253634 TCTATTCCATTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAC-CACGA
1 TCTATTCCAATGTTGCCCAAGGAGATAGAATTACTGGCTTCAATATACTCCACTGCAACTCA-G-
*
41253698 GGAGGTAAAATCCGCCATCTTCGATCTGCT
64 GGAGGTAAAATCCGCCATCTTCAATCTGCT
41253728 TCGCTGTCTA
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
106 2 0.02
107 1 0.01
108 80 0.96
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (107 bp):
TCTATTCCAATGTTGCCCAAGGAGATAGAATTACTGGCTTCAATATACTCCACTGCAACTCAGGG
AGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTCAA
Found at i:41253813 original size:44 final size:44
Alignment explanation
Indices: 41253743--41253946 Score: 318
Period size: 44 Copynumber: 4.6 Consensus size: 44
41253733 GTCTATGCAG
* * * *
41253743 GAAGGCAAGATCTGATATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
*
41253787 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGTCAATACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
*
41253831 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
* *
41253875 GAAGACAATATCTGTTTTCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
* *
41253919 GAAGACAAGATTTACTTTCTTCGATCTA
1 GAAGACAAGATCTGCTTTCTTCGATCTA
41253947 TTCCACTGCC
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 146 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (44 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
Found at i:41253866 original size:88 final size:88
Alignment explanation
Indices: 41253715--41253946 Score: 320
Period size: 88 Copynumber: 2.6 Consensus size: 88
41253705 AAATCCGCCA
* * * * * * * * *
41253715 TCTTCGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTGATATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCAC-GTCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCC
41253780 AATACATGAAGACAAGATCTGCTT
65 AATACATGAAGACAAGATCTGCTT
41253804 TCTTCGATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCA
1 TCTTCGATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCA
* * *
41253869 GTACATGAAGACAATATCTGTTT
66 ATACATGAAGACAAGATCTGCTT
* * *
41253892 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATTTACTTTCTTCGATCTA
1 TCTTCGATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTTCGATCTA
41253947 TTCCACTGCC
Statistics
Matches: 128, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 113 0.88
89 15 0.12
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (88 bp):
TCTTCGATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCA
ATACATGAAGACAAGATCTGCTT
Found at i:41254033 original size:132 final size:129
Alignment explanation
Indices: 41253925--41254311 Score: 560
Period size: 132 Copynumber: 2.9 Consensus size: 129
41253915 ACATGAAGAC
* * *
41253925 AAGATTTACTTTCTTCGATCTATTCCACTGCCAACCAGGGAGATAGAATTACTGGCTTCAATATA
1 AAGATTTA-TATCTTC-ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATATA
41253990 CTCCACTGTAACTTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
64 CTCCACTGTAACTTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGC-TAGGGAG
41254055 AT
128 AT
* *
41254057 AAGATCTATAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATATA
1 AAGATTTAT-ATCTTC-ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATATA
* *
41254122 CTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCATTACTGCTTAGGGAG
64 CTCCACTGTAACTTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGC-TAGGGAG
41254187 AT
128 AT
* * * * *
41254189 AAGATCTGTA-ATCTTCAGTCTATTCCAATGTTTCCCAAGGAGATAGAATTATTGGCTTCAATAT
1 AAGAT-T-TATATCTTCA-TCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATAT
* *
41254253 ACTCCACTGCAACTTCAGGGAGGTAAAATCTGCCATCTTTAATCTGCTCCACTACTGCT
63 ACTCCACTGTAACTTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCT
41254312 CAATCTATTC
Statistics
Matches: 233, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
131 3 0.01
132 228 0.98
134 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (129 bp):
AAGATTTATATCTTCATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATATACT
CCACTGTAACTTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTAGGGAGAT
Found at i:41254053 original size:44 final size:44
Alignment explanation
Indices: 41254003--41254313 Score: 126
Period size: 44 Copynumber: 7.1 Consensus size: 44
41253993 CACTGTAACT
* ** *
41254003 TCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGC
1 TCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGC
* * *** * *
41254047 TTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCTGC
1 TCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGC
* * * *** *
41254091 CCAGGGAGATAGAAT-TACTGGCTTCAATATACTCCACTGTAAC--C
1 TCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCAC--T-ACTGC
* ** * *
41254135 TCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCATTACTGC
1 TCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGC
* * ** * * * ** *
41254179 TTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCAATGTTTC
1 TCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGC
* * * ***** * * **
41254223 CCAAGGAGATAGAAT-TATTGGCTTCAATATACTCCACTGCAAC
1 TCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGC
* * *
41254266 TTCAGGGAGGTAAAATCTGCCATCTTTAATCTGCTCCACTACTGC
1 -TCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGC
41254311 TCA
1 TCA
41254314 ATCTATTCCA
Statistics
Matches: 180, Mismatches: 79, Indels: 16
0.65 0.29 0.06
Matches are distributed among these distances:
42 2 0.01
43 34 0.19
44 112 0.62
45 31 0.17
46 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
TCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGC
Found at i:41254396 original size:108 final size:107
Alignment explanation
Indices: 41254207--41254408 Score: 289
Period size: 108 Copynumber: 1.9 Consensus size: 107
41254197 TAATCTTCAG
* *
41254207 TCTATTCCAATGTTTCCCAAGGAGATAGAATTATTGGCTTCAATATACTCCACTGCAACTTCAGG
1 TCTATTCCAATGTTGCCCAAGGAGATAGAATTACTGGCTTCAATATACTCCACTGCAAC-TCAGG
* *
41254272 GAGGTAAAATCTGCCATCTTTAATCTGCTCCACTACTGCTCAA
65 GAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTCAA
* * * *
41254315 TCTATTCCATTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAC-CACGA
1 TCTATTCCAATGTTGCCCAAGGAGATAGAATTACTGGCTTCAATATACTCCACTGCAACTCA-G-
*
41254379 GGAGGTAAAATCCGCCATCTTCGATCTGCT
64 GGAGGTAAAATCCGCCATCTTCAATCTGCT
41254409 TCGCTGTCTA
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
106 2 0.02
107 1 0.01
108 80 0.96
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (107 bp):
TCTATTCCAATGTTGCCCAAGGAGATAGAATTACTGGCTTCAATATACTCCACTGCAACTCAGGG
AGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTCAA
Found at i:41254516 original size:44 final size:45
Alignment explanation
Indices: 41254423--41254791 Score: 320
Period size: 44 Copynumber: 8.3 Consensus size: 45
41254413 TGTCTATGCA
* * * * * **
41254423 GGAAGGCAAGATCTGATATCTTTGATCTACTTCA-CGCCAATACA
1 GGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATG
* *
41254467 TGAAGACAAGATCTGCTTTC-TTAATCTACTTCACCACCAGTATG
1 GGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATG
* * * * **
41254511 GGAAGACAAGATCTGGTATCTTTGATCTATTTCA-CGCCAGTACA
1 GGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATG
* * ** *
41254555 TGAAGACAAGATCTACTTT-TTCAATCTACTTCGCCACCAGTATG
1 GGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATG
* * * **
41254599 GGAAGACAAGATCTAG-TATCTTTGATCTACTTCA-CGCCAATACA
1 GGAAGACAAGATCT-GCTTTCTTTGATCTACTTCACCACCAGTATG
* * *
41254643 TGAAGACAAGATCTACTTTCTTTGATCTGCTTCACCACCAGTATG
1 GGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATG
* * * * * **
41254688 GGAAGGCAAGATCTGGTATCTCTGATCTACTTCA-CATCAGTACA
1 GGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATG
* * *
41254732 TGAAGACAATATCTGCTTTCTTTGATCTGCTTCACCACCAGTATG
1 GGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATG
* *
41254777 GGAAGGCAATATCTG
1 GGAAGACAAGATCTG
41254792 GTATTTCTGA
Statistics
Matches: 249, Mismatches: 68, Indels: 15
0.75 0.20 0.05
Matches are distributed among these distances:
43 22 0.09
44 152 0.61
45 75 0.30
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (45 bp):
GGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATG
Found at i:41254715 original size:89 final size:89
Alignment explanation
Indices: 41254423--41254804 Score: 554
Period size: 88 Copynumber: 4.3 Consensus size: 89
41254413 TGTCTATGCA
* *
41254423 GGAAGGCAAGATCTGATATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC-
1 GGAAGGCAAGATCTGGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCT
41254487 TTAATCTACTTCACCACCAGTATG
66 TTAATCTACTTCACCACCAGTATG
* * *
41254511 GGAAGACAAGATCTGGTATCTTTGATCTATTTCACGCCAGTACATGAAGACAAGATCTACTTT-T
1 GGAAGGCAAGATCTGGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCT
* *
41254575 TCAATCTACTTCGCCACCAGTATG
66 TTAATCTACTTCACCACCAGTATG
* *
41254599 GGAAGACAAGATCTAGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCT
1 GGAAGGCAAGATCTGGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCT
* *
41254664 TTGATCTGCTTCACCACCAGTATG
66 TTAATCTACTTCACCACCAGTATG
* ** * * *
41254688 GGAAGGCAAGATCTGGTATCTCTGATCTACTTCACATCAGTACATGAAGACAATATCTGCTTTCT
1 GGAAGGCAAGATCTGGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCT
* *
41254753 TTGATCTGCTTCACCACCAGTATG
66 TTAATCTACTTCACCACCAGTATG
*
41254777 GGAAGGCAATATCTGGTAT-TTCTGATCT
1 GGAAGGCAAGATCTGGTATCTT-TGATCT
41254805 GTTCTCTGGG
Statistics
Matches: 267, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
88 141 0.53
89 126 0.47
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (89 bp):
GGAAGGCAAGATCTGGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCT
TTAATCTACTTCACCACCAGTATG
Found at i:41255918 original size:7 final size:7
Alignment explanation
Indices: 41255904--41255971 Score: 95
Period size: 7 Copynumber: 9.7 Consensus size: 7
41255894 TCCATTTTAT
41255904 TTTTTCA
1 TTTTTCA
*
41255911 TTTCTCA
1 TTTTTCA
41255918 TTTTTCA
1 TTTTTCA
41255925 TTTTTCA
1 TTTTTCA
41255932 -TTTTCA
1 TTTTTCA
41255938 TCTTTTCA
1 T-TTTTCA
41255946 TTTTTCA
1 TTTTTCA
41255953 -TTTTCA
1 TTTTTCA
41255959 TCTTTTCA
1 T-TTTTCA
41255967 TTTTT
1 TTTTT
41255972 TCACATCACT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
6 12 0.22
7 29 0.53
8 14 0.25
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTTCA
Found at i:41256718 original size:61 final size:61
Alignment explanation
Indices: 41256642--41256757 Score: 187
Period size: 61 Copynumber: 1.9 Consensus size: 61
41256632 TTTTTTGGTT
* **
41256642 ATGCATGTTACCTCAATGTCACAGTCTCTATTGTCTCCTTGTGAGGTAAAATTTCATTATC
1 ATGCATGTTACCTCAAGGTCACAGTCTCTATTGTCTCCTCATGAGGTAAAATTTCATTATC
* *
41256703 ATGCATGTTCCCTCAAGGTCACAGTTTCTATTGTCTCCTCATGAGGTAAAATTTC
1 ATGCATGTTACCTCAAGGTCACAGTCTCTATTGTCTCCTCATGAGGTAAAATTTC
41256758 CTTCCTGCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (61 bp):
ATGCATGTTACCTCAAGGTCACAGTCTCTATTGTCTCCTCATGAGGTAAAATTTCATTATC
Found at i:41261136 original size:21 final size:21
Alignment explanation
Indices: 41261111--41261152 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
41261101 CATATGCGTG
41261111 TATATATATAGATATAATAATAA
1 TATA-ATATA-ATATAATAATAA
41261134 TATAATATAATATAATAAT
1 TATAATATAATATAATAAT
41261153 GACAAAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 5 0.26
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TATAATATAATATAATAATAA
Found at i:41261140 original size:5 final size:5
Alignment explanation
Indices: 41261111--41261150 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
41261101 CATATGCGTG
41261111 TATATA TATAGA TATAA TAATAA TATAA TATAA TATAA TA
1 TATA-A TATA-A TATAA T-ATAA TATAA TATAA TATAA TA
41261151 ATGACAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
5 18 0.56
6 14 0.44
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:41263456 original size:9 final size:9
Alignment explanation
Indices: 41263442--41263470 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
41263432 CTCCTAATAG
41263442 AAAAATTAA
1 AAAAATTAA
41263451 AAAAATTAA
1 AAAAATTAA
41263460 AAAAATTAA
1 AAAAATTAA
41263469 AA
1 AA
41263471 GAGATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATTAA
Found at i:41266520 original size:43 final size:44
Alignment explanation
Indices: 41266435--41266532 Score: 144
Period size: 43 Copynumber: 2.2 Consensus size: 44
41266425 CCCCACGATC
* * *
41266435 AGGGTCTTTTGCGGCGTTTGTGGGGGAAAGCGCCGCTAAAGATT
1 AGGGTCTTTAGTGGCGTTTGTGGGCGAAAGCGCCGCTAAAGATT
* *
41266479 AGGTTCTTTAGTGGCGTTTGTGGTCG-AAGCGCCGCTAAAGATT
1 AGGGTCTTTAGTGGCGTTTGTGGGCGAAAGCGCCGCTAAAGATT
41266522 AGGGTCTTTAG
1 AGGGTCTTTAG
41266533 CGGCCAAACG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 27 0.56
44 21 0.44
ACGTcount: A:0.18, C:0.15, G:0.36, T:0.31
Consensus pattern (44 bp):
AGGGTCTTTAGTGGCGTTTGTGGGCGAAAGCGCCGCTAAAGATT
Found at i:41266585 original size:43 final size:43
Alignment explanation
Indices: 41266537--41266630 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
41266527 CTTTAGCGGC
* *
41266537 CAAACGCCGCGAAAG-ACCATGATCTTTAGGGGCACTTTTTCCA
1 CAAACGCCGCGAAAGAACC-TGATCTTTAGCGGCACTTTTACCA
* *
41266580 CAAACGCCGCGAAAGAACCTTATCTTTAGCGGCGCTTTTACCA
1 CAAACGCCGCGAAAGAACCTGATCTTTAGCGGCACTTTTACCA
*
41266623 AAAACGCC
1 CAAACGCC
41266631 ACTAAAGGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
43 42 0.93
44 3 0.07
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (43 bp):
CAAACGCCGCGAAAGAACCTGATCTTTAGCGGCACTTTTACCA
Found at i:41267032 original size:21 final size:21
Alignment explanation
Indices: 41266994--41267049 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
41266984 GCAGCCTTTG
* ** *
41266994 CTTCCCTCGCTGTAACCTGTA
1 CTTCTCTCGCTGCCACCTCTA
*
41267015 CTTCTCTCGCTGCCACCTCTG
1 CTTCTCTCGCTGCCACCTCTA
*
41267036 CTTCTCTTGCTGCC
1 CTTCTCTCGCTGCC
41267050 GCATCTGCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.07, C:0.43, G:0.14, T:0.36
Consensus pattern (21 bp):
CTTCTCTCGCTGCCACCTCTA
Found at i:41267056 original size:21 final size:21
Alignment explanation
Indices: 41267015--41267059 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
41267005 GTAACCTGTA
*
41267015 CTTCTCTCGCTGCCACCTCTG
1 CTTCTCTCGCTGCCACATCTG
* *
41267036 CTTCTCTTGCTGCCGCATCTG
1 CTTCTCTCGCTGCCACATCTG
41267057 CTT
1 CTT
41267060 TAAGCTGCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.42, G:0.16, T:0.38
Consensus pattern (21 bp):
CTTCTCTCGCTGCCACATCTG
Found at i:41267139 original size:66 final size:66
Alignment explanation
Indices: 41267029--41267195 Score: 203
Period size: 66 Copynumber: 2.5 Consensus size: 66
41267019 TCTCGCTGCC
* * **
41267029 ACCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATA-CTTTCGTT
1 ACCTCAGCTTCTCTCGCTGTTGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATATCTTT-GTT
41267093 GA
65 GA
* * * *
41267095 ACCTCAGCTTCTCTCGCTGTTGCATTTGCTTTCAGTTG-TAGCTGGAGTTCTTCATATCTTTTTT
1 ACCTCAGCTTCTCTCGCTGTTGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATATCTTTGTT
41267159 GA
65 GA
* * *
41267161 ACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAG
1 ACCTCAGCTTCTCTCGCTGTTGCATCTGCTTTAAG
41267196 TTGTGTGATT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 1 0.01
66 81 0.94
67 4 0.05
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.41
Consensus pattern (66 bp):
ACCTCAGCTTCTCTCGCTGTTGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATATCTTTGTTG
A
Found at i:41270910 original size:9 final size:9
Alignment explanation
Indices: 41270893--41271022 Score: 77
Period size: 9 Copynumber: 15.8 Consensus size: 9
41270883 TAAGTATAAT
*
41270893 TAAGCTATG
1 TAAGTTATG
41270902 TAAGTTATG
1 TAAGTTATG
41270911 T-A-TTATG
1 TAAGTTATG
41270918 TAAGTTAT-
1 TAAGTTATG
* **
41270926 TCA-TTACC
1 TAAGTTATG
*
41270934 CAAGTTATG
1 TAAGTTATG
*
41270943 TAAGTTGTG
1 TAAGTTATG
41270952 T-A-TTATG
1 TAAGTTATG
*
41270959 -AA--AAT-
1 TAAGTTATG
* *
41270964 TATGCTATG
1 TAAGTTATG
41270973 TAAGTTATG
1 TAAGTTATG
* *
41270982 TAAGTCATA
1 TAAGTTATG
41270991 TAAGTTATG
1 TAAGTTATG
41271000 T-A-TTATG
1 TAAGTTATG
41271007 TAAGTTATG
1 TAAGTTATG
41271016 TAAGTTA
1 TAAGTTA
41271023 AATGTATTAT
Statistics
Matches: 91, Mismatches: 19, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
6 3 0.03
7 20 0.22
8 10 0.11
9 58 0.64
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (9 bp):
TAAGTTATG
Found at i:41270919 original size:16 final size:16
Alignment explanation
Indices: 41270898--41271017 Score: 62
Period size: 16 Copynumber: 7.9 Consensus size: 16
41270888 ATAATTAAGC
41270898 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
41270914 TATGTAAGTTAT-TCAT
1 TATGTAAGTTATGT-AT
***
41270930 TACCCAAGTTATG---
1 TATGTAAGTTATGTAT
*
41270943 TA----AGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
41270955 TATGAAAATTATG-CT
1 TATGTAAGTTATGTAT
41270970 -ATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
41270987 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
41271003 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
41271018 AGTTAAATGT
Statistics
Matches: 78, Mismatches: 13, Indels: 26
0.67 0.11 0.22
Matches are distributed among these distances:
9 6 0.08
12 2 0.03
13 2 0.03
14 10 0.13
15 2 0.03
16 42 0.54
17 2 0.03
18 12 0.15
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.44
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:41271007 original size:25 final size:26
Alignment explanation
Indices: 41270977--41271035 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
41270967 GCTATGTAAG
41270977 TTATGTAAGTCATATAAGTT-ATGTA
1 TTATGTAAGTCATATAAGTTAATGTA
* *
41271002 TTATGTAAGTTATGTAAGTTAAATGTA
1 TTATGTAAGTCATATAAGTT-AATGTA
41271029 TTATGTA
1 TTATGTA
41271036 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 18 0.60
27 12 0.40
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.46
Consensus pattern (26 bp):
TTATGTAAGTCATATAAGTTAATGTA
Found at i:41273095 original size:12 final size:12
Alignment explanation
Indices: 41273052--41273095 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
41273042 TAAATTTTAG
41273052 ATTTTTT-TTTC
1 ATTTTTTATTTC
* *
41273063 ATTTTTTGTTTT
1 ATTTTTTATTTC
41273075 ATTTTTTATTTC
1 ATTTTTTATTTC
*
41273087 ATTTCTTAT
1 ATTTTTTAT
41273096 GTATTTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (12 bp):
ATTTTTTATTTC
Found at i:41273338 original size:57 final size:57
Alignment explanation
Indices: 41273275--41273402 Score: 231
Period size: 57 Copynumber: 2.2 Consensus size: 57
41273265 CTGACCTCTG
*
41273275 AAACCCTAAACCCTACATTCTAAACCACTAACCCTTAGCCCATAACTCGTAACCCCT
1 AAACCCTAAACCCTAAATTCTAAACCACTAACCCTTAGCCCATAACTCGTAACCCCT
41273332 AAACCCTAAACCCTAAATTCTAAACCACTAACCCTTAGCCCATAACTCGTAACCCCT
1 AAACCCTAAACCCTAAATTCTAAACCACTAACCCTTAGCCCATAACTCGTAACCCCT
41273389 AAACCCCT-AACCCT
1 AAA-CCCTAAACCCT
41273403 TATATCCCAA
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
57 65 0.94
58 4 0.06
ACGTcount: A:0.36, C:0.41, G:0.03, T:0.20
Consensus pattern (57 bp):
AAACCCTAAACCCTAAATTCTAAACCACTAACCCTTAGCCCATAACTCGTAACCCCT
Found at i:41273768 original size:7 final size:7
Alignment explanation
Indices: 41273756--41273785 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
41273746 CAAATCCATA
41273756 ACCCCTT
1 ACCCCTT
41273763 ACCCCTT
1 ACCCCTT
41273770 ACCCCTT
1 ACCCCTT
41273777 ACCCCTT
1 ACCCCTT
41273784 AC
1 AC
41273786 ACCTAAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.57, G:0.00, T:0.27
Consensus pattern (7 bp):
ACCCCTT
Found at i:41273804 original size:7 final size:7
Alignment explanation
Indices: 41273754--41273845 Score: 58
Period size: 7 Copynumber: 12.4 Consensus size: 7
41273744 TCCAAATCCA
41273754 TAACCCC
1 TAACCCC
*
41273761 TTACCCC
1 TAACCCC
*
41273768 TTACCCC
1 TAACCCC
*
41273775 TTACCCC
1 TAACCCC
* *
41273782 TTACACC
1 TAACCCC
41273789 TAAATCCCC
1 T-AA-CCCC
41273798 TAACCCC
1 TAACCCC
** *
41273805 TAAAGCA
1 TAACCCC
*
41273812 TAACCCT
1 TAACCCC
41273819 TAACCCC
1 TAACCCC
41273826 TAAATCCCTC
1 T-AA-CCC-C
41273836 TAACCCC
1 TAACCCC
41273843 TAA
1 TAA
41273846 ACATTAAATT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
7 50 0.72
8 8 0.12
9 9 0.13
10 2 0.03
ACGTcount: A:0.29, C:0.47, G:0.01, T:0.23
Consensus pattern (7 bp):
TAACCCC
Found at i:41274566 original size:15 final size:15
Alignment explanation
Indices: 41274546--41274584 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
41274536 ACCGTTGAAA
41274546 CCCTAAATTTCAAAC
1 CCCTAAATTTCAAAC
** *
41274561 CCCTAAACCTCTAAC
1 CCCTAAATTTCAAAC
41274576 CCCTAAATT
1 CCCTAAATT
41274585 AACCTTAAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (15 bp):
CCCTAAATTTCAAAC
Found at i:41275181 original size:41 final size:41
Alignment explanation
Indices: 41275112--41275332 Score: 196
Period size: 41 Copynumber: 5.4 Consensus size: 41
41275102 GCGTTTCGGC
* * * *
41275112 AAAAACGCCGCTAAAGGT-AAATACATTAGCGGCGCTTAGCT
1 AAAAACGCCGCTAAAGATCAGAGA-ATTAGCGGCGCTTAGAT
* * * * *
41275153 ACAAACGCCGCTGAAGA-CAAGAGAATTAGTGGCGCTAAGTT
1 AAAAACGCCGCTAAAGATC-AGAGAATTAGCGGCGCTTAGAT
* * * *
41275194 AAAAATGCCGCTAAAGATCCGAGCATTAGCGGCGCTTATAT
1 AAAAACGCCGCTAAAGATCAGAGAATTAGCGGCGCTTAGAT
* ** * *
41275235 AAAAACGCCGCCAAAGGCCAGAGCATTAGTGGCG-TTCAGAT
1 AAAAACGCCGCTAAAGATCAGAGAATTAGCGGCGCTT-AGAT
* * * *
41275276 AAAAACGCCGCGAAAGATCTGAGAATAAGCGGCGCTTATAT
1 AAAAACGCCGCTAAAGATCAGAGAATTAGCGGCGCTTAGAT
41275317 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
41275333 GTTTAAAAAT
Statistics
Matches: 142, Mismatches: 33, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
40 2 0.01
41 134 0.94
42 6 0.04
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGATCAGAGAATTAGCGGCGCTTAGAT
Found at i:41275241 original size:82 final size:82
Alignment explanation
Indices: 41275135--41275332 Score: 252
Period size: 82 Copynumber: 2.4 Consensus size: 82
41275125 AAGGTAAATA
** * * * *
41275135 CATTAGCGGCGCTTAGCTACAAACGCCGCTGAAGACAAGAGAATTAGTGGCGCTAAGTTAAAAAT
1 CATTAGCGGCGCTTATATAAAAACGCCGCTAAAGACAAGAGAATTAGTGGCGCTAAGATAAAAAC
*
41275200 GCCGCTAAAGATCCGAG
66 GCCGCGAAAGATCCGAG
* * * * * *
41275217 CATTAGCGGCGCTTATATAAAAACGCCGCCAAAGGCCAGAGCATTAGTGGCGTTCAGATAAAAAC
1 CATTAGCGGCGCTTATATAAAAACGCCGCTAAAGACAAGAGAATTAGTGGCGCTAAGATAAAAAC
*
41275282 GCCGCGAAAGATCTGAG
66 GCCGCGAAAGATCCGAG
* *
41275299 AATAAGCGGCGCTTATATAAAAACGCCGCTAAAG
1 CATTAGCGGCGCTTATATAAAAACGCCGCTAAAG
41275333 GTTTAAAAAT
Statistics
Matches: 99, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
82 99 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (82 bp):
CATTAGCGGCGCTTATATAAAAACGCCGCTAAAGACAAGAGAATTAGTGGCGCTAAGATAAAAAC
GCCGCGAAAGATCCGAG
Found at i:41276469 original size:13 final size:13
Alignment explanation
Indices: 41276451--41276475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41276441 CCCAATTGGT
41276451 AATTGAACTTGAA
1 AATTGAACTTGAA
41276464 AATTGAACTTGA
1 AATTGAACTTGA
41276476 GATCGTAAAT
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATTGAACTTGAA
Found at i:41276749 original size:26 final size:26
Alignment explanation
Indices: 41276713--41276764 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
41276703 TTGATGATTG
41276713 AGTGGTGGAAGAATTACACTCCTACT
1 AGTGGTGGAAGAATTACACTCCTACT
41276739 AGTGGTGGAAGAATTACACTCCTACT
1 AGTGGTGGAAGAATTACACTCCTACT
41276765 TGGACTCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (26 bp):
AGTGGTGGAAGAATTACACTCCTACT
Found at i:41280911 original size:44 final size:44
Alignment explanation
Indices: 41280862--41281321 Score: 168
Period size: 44 Copynumber: 10.5 Consensus size: 44
41280852 CCCTGGTTGG
*
41280862 CAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAAGCAA
1 CAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAGGCAA
* ** * * * * * **
41280906 TAGTGGAGCAGATCGAAGATGGT-AGATTTTACCTCCATGTGGTTA
1 CAGTGGAATAGATTGAAGAT-TTCAGATTTTATCTCCCT-AGGCAA
* * * ** * *
41280951 CAGTGGAGTACATTGAAGCCA-AT-A-ATTCCATCTCCCTGGGCAG
1 CAGTGGAATAGATTGAAG--ATTTCAGATTTTATCTCCCTAGGCAA
* * * *
41280994 CAGTGGAATAGATTGAAGATTACATATATTATCTCCCTAAGCAA
1 CAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAGGCAA
* * * ** * * **
41281038 TAGTGGAACAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTA
1 CAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCT-AGGCAA
* * * * * *
41281083 CAGTGGAGTATATTGAAGCCA-AT-A-ATTCTATCTCCCTGGGCAG
1 CAGTGGAATAGATTGAAG--ATTTCAGATTTTATCTCCCTAGGCAA
* * * *
41281126 CAGTGGAATAGATTGAAGATTACATATATTATCTCCCTAAGCAA
1 CAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAGGCAA
* * * ** * * **
41281170 TAGTGGAACAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTA
1 CAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCT-AGGCAA
* * * * * ***
41281215 TAGTGGAGTACATTGAAG---CCAGTAATTCTATCTCCCT-GGTTGG
1 CAGTGGAATAGATTGAAGATTTCAG--ATTTTATCTCCCTAGG-CAA
* * *
41281258 CAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
1 CAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAGGCAA
* * *
41281302 TAGTGGAGTAGATCGAAGAT
1 CAGTGGAATAGATTGAAGAT
41281322 GGAGAATTTT
Statistics
Matches: 294, Mismatches: 101, Indels: 42
0.67 0.23 0.10
Matches are distributed among these distances:
41 2 0.01
42 5 0.02
43 54 0.18
44 176 0.60
45 52 0.18
46 3 0.01
47 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (44 bp):
CAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAGGCAA
Found at i:41280984 original size:132 final size:132
Alignment explanation
Indices: 41280713--41281382 Score: 985
Period size: 132 Copynumber: 5.1 Consensus size: 132
41280703 CTGGGAAGAT
** *
41280713 AATAATTCTATCTCCCTGGGCAGCAGTAAAATAGATTGAAGATTTCAGATCTTATCTCCCT----
1 AATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGC
* * * *
41280774 -A-AGTGGAGAAGATTGAAGATGGCAAATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAG
66 AATAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
41280837 CC
131 CC
*** *
41280839 AATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAAGC
1 AATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGC
* *
41280904 AATAGTGGAGCAGATCGAAGATGGTAGATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAG
66 AATAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
41280969 CC
131 CC
* * *
41280971 AATAATTCCATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACATATATTATCTCCCTAAGC
1 AATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGC
* *
41281036 AATAGTGGAACAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAG
66 AATAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
41281101 CC
131 CC
* *
41281103 AATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACATATATTATCTCCCTAAGC
1 AATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGC
* *
41281168 AATAGTGGAACAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAG
66 AATAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
41281233 CC
131 CC
* *** *
41281235 AGTAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
1 AATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGC
* * * **
41281300 AGTAGTGGAGTAGATCGAAGATGG-AGAATTTTACCTCCCTATGACTACAGTGGAGTACATTGAA
66 AATAGTGGAGCAGATCGAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAA
41281364 GCC
130 GCC
*
41281367 AGTAATTCTATCTCCC
1 AATAATTCTATCTCCC
41281383 CGACATTGCG
Statistics
Matches: 497, Mismatches: 40, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
126 55 0.11
131 3 0.01
132 439 0.88
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (132 bp):
AATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGC
AATAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
CC
Found at i:41283612 original size:10 final size:9
Alignment explanation
Indices: 41283597--41283637 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
41283587 AGGTTGTTGC
41283597 TTTTTTTTA
1 TTTTTTTTA
*
41283606 TTTTTTTCA
1 TTTTTTTTA
*
41283615 TTCTTTTTA
1 TTTTTTTTA
41283624 TTTTATTTTA
1 TTTT-TTTTA
41283634 TTTT
1 TTTT
41283638 CCTATTTTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:41284339 original size:3 final size:3
Alignment explanation
Indices: 41284331--41284370 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
41284321 AAGTTAGTGC
* *
41284331 TAT TAT TAT TAT TAT TAT TATT TAA TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
41284371 CATCATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:41284850 original size:13 final size:13
Alignment explanation
Indices: 41284832--41284857 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41284822 CTTATTCCCA
41284832 TAATTTTATGTAT
1 TAATTTTATGTAT
41284845 TAATTTTATGTAT
1 TAATTTTATGTAT
41284858 ATACATACAT
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TAATTTTATGTAT
Found at i:41286145 original size:8 final size:9
Alignment explanation
Indices: 41286106--41286142 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
41286096 TGTAAGTAAT
41286106 TTATTTAAA
1 TTATTTAAA
41286115 TTATATTAAA
1 TTAT-TTAAA
41286125 TTATTTAAA
1 TTATTTAAA
41286134 -TATTTAAA
1 TTATTTAAA
41286142 T
1 T
41286143 ATTGCAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 8 0.31
9 9 0.35
10 9 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TTATTTAAA
Found at i:41286373 original size:23 final size:22
Alignment explanation
Indices: 41286319--41286374 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
41286309 GTATATTATT
*
41286319 TATAAAAGTT-TATATATGAAA
1 TATAAAAGTTGTTTATATGAAA
41286340 TATAAAA-TTGTTTATAT-AAA
1 TATAAAAGTTGTTTATATGAAA
41286360 TAATTAAAAGTTGTT
1 T-A-TAAAAGTTGTT
41286375 ATTTAGAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.20
21 14 0.47
22 5 0.17
23 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (22 bp):
TATAAAAGTTGTTTATATGAAA
Found at i:41287220 original size:21 final size:21
Alignment explanation
Indices: 41287196--41287258 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
41287186 AATATTTTTT
41287196 AATATTAAAAAGATATTATAA
1 AATATTAAAAAGATATTATAA
* *
41287217 AATATT-AAAATA-ATTACTAG
1 AATATTAAAAAGATATTA-TAA
41287237 AA-ATTATAAAAG-TATTATAA
1 AATATTA-AAAAGATATTATAA
41287257 AA
1 AA
41287259 AGTTTAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 7 0.21
20 13 0.38
21 14 0.41
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (21 bp):
AATATTAAAAAGATATTATAA
Found at i:41287242 original size:29 final size:29
Alignment explanation
Indices: 41287210--41287282 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
41287200 TTAAAAAGAT
41287210 ATTATAAAATATTA-AAATAA-TTACTAG-AA
1 ATTATAAAATATTATAAA-AAGTT--TAGAAA
41287239 ATTATAAAAGTATTATAAAAAGTTTAGAAA
1 ATTATAAAA-TATTATAAAAAGTTTAGAAA
*
41287269 ATTATAAAAAATTA
1 ATTATAAAATATTA
41287283 GAAACTTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 16 0.41
30 18 0.46
31 5 0.13
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.34
Consensus pattern (29 bp):
ATTATAAAATATTATAAAAAGTTTAGAAA
Found at i:41287283 original size:18 final size:19
Alignment explanation
Indices: 41287250--41287293 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
41287240 TTATAAAAGT
*
41287250 ATTATAAAAAGTTTAGAAA
1 ATTATAAAAAGATTAGAAA
41287269 ATTATAAAAA-ATTAGAAA
1 ATTATAAAAAGATTAGAAA
*
41287287 CTTATAA
1 ATTATAA
41287294 TTTTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (19 bp):
ATTATAAAAAGATTAGAAA
Found at i:41288168 original size:20 final size:20
Alignment explanation
Indices: 41288138--41288175 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41288128 AAGTGTGAAG
41288138 TATTATTGGATTGAATTGAGT
1 TATTATTGGATT-AATTGAGT
41288159 TATT-TTGGATTAATTGA
1 TATTATTGGATTAATTGA
41288176 TTGTGCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (20 bp):
TATTATTGGATTAATTGAGT
Found at i:41289104 original size:24 final size:24
Alignment explanation
Indices: 41289077--41289122 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41289067 AATCTATGTC
* *
41289077 TGCATTTGTATCTGAATCTGAATA
1 TGCATCTGTATCTGAACCTGAATA
*
41289101 TGCATCTGTATTTGAACCTGAA
1 TGCATCTGTATCTGAACCTGAA
41289123 AAATACATCT
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:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (24 bp):
TGCATCTGTATCTGAACCTGAATA
Found at i:41292735 original size:24 final size:24
Alignment explanation
Indices: 41292708--41292755 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
41292698 TATGCTGTAA
41292708 ACACTATTTCTTTAGTATTGTCTG
1 ACACTATTTCTTTAGTATTGTCTG
*
41292732 ACACTCTTTCTTTAGTATTGTCTG
1 ACACTATTTCTTTAGTATTGTCTG
41292756 CGGTACTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (24 bp):
ACACTATTTCTTTAGTATTGTCTG
Found at i:41303337 original size:32 final size:32
Alignment explanation
Indices: 41303282--41303364 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
41303272 GGGCCCACAT
*
41303282 GCCCGTGTAGGCCCACACACCCTACTTGGCCTA
1 GCCCGTGT-GGCCCACACGCCCTACTTGGCCTA
*
41303315 GCCCATGTGGCCCACACGCCCTACTTGGCCTA
1 GCCCGTGTGGCCCACACGCCCTACTTGGCCTA
* *
41303347 GCCTGTGTGGCCTACACG
1 GCCCGTGTGGCCCACACG
41303365 GCCACACCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 38 0.84
33 7 0.16
ACGTcount: A:0.16, C:0.41, G:0.24, T:0.19
Consensus pattern (32 bp):
GCCCGTGTGGCCCACACGCCCTACTTGGCCTA
Found at i:41315254 original size:9 final size:9
Alignment explanation
Indices: 41315240--41315277 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
41315230 TAAACAATTC
41315240 AATAATATA
1 AATAATATA
41315249 AATAATATA
1 AATAATATA
41315258 AATAATATA
1 AATAATATA
41315267 AATAATATA
1 AATAATATA
41315276 AA
1 AA
41315278 ATGTGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATATA
Found at i:41315787 original size:9 final size:9
Alignment explanation
Indices: 41315773--41315809 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41315763 TATAGTTTGA
41315773 TATTCGAAT
1 TATTCGAAT
41315782 TATTCGAAT
1 TATTCGAAT
*
41315791 TATTCGAGT
1 TATTCGAAT
41315800 TATTCGAAT
1 TATTCGAAT
41315809 T
1 T
41315810 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41315880 original size:9 final size:9
Alignment explanation
Indices: 41315863--41315893 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41315853 TCAAGTTGAT
41315863 TCGAATAAC
1 TCGAATAAC
*
41315872 TCGATTAAC
1 TCGAATAAC
41315881 TCGAATAAC
1 TCGAATAAC
41315890 TCGA
1 TCGA
41315894 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:41316467 original size:20 final size:20
Alignment explanation
Indices: 41316422--41316461 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41316412 TGGTGAATTA
*
41316422 TGTAGCGGCTGAAACATTTT
1 TGTAGCGGCCGAAACATTTT
*
41316442 TGTAGCGGCCGAAACGTTTT
1 TGTAGCGGCCGAAACATTTT
41316462 GTTAGCAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (20 bp):
TGTAGCGGCCGAAACATTTT
Found at i:41321089 original size:18 final size:17
Alignment explanation
Indices: 41321066--41321107 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
41321056 AGTAGTATAG
41321066 GTTCGC-TAGATACCAATA
1 GTTCGCATA-ATACCAA-A
*
41321084 GTTCGCATAATACCTAA
1 GTTCGCATAATACCAAA
41321101 GTTCGCA
1 GTTCGCA
41321108 ACAGGCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 12 0.55
19 2 0.09
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (17 bp):
GTTCGCATAATACCAAA
Found at i:41329519 original size:12 final size:12
Alignment explanation
Indices: 41329486--41329520 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
41329476 TGCTCATCCA
41329486 CCGCATCCAGCG
1 CCGCATCCAGCG
* *
41329498 CCACAACCAGCG
1 CCGCATCCAGCG
41329510 CCGCATCCAGC
1 CCGCATCCAGC
41329521 TGCACAGGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.51, G:0.20, T:0.06
Consensus pattern (12 bp):
CCGCATCCAGCG
Found at i:41342999 original size:44 final size:44
Alignment explanation
Indices: 41342891--41343321 Score: 417
Period size: 44 Copynumber: 9.9 Consensus size: 44
41342881 GTTATCGTGG
* * * **
41342891 CAAATTTTATCTCCCTAAAGTTGCAGTGGA-CAGACTAAAGCCA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
* * *
41342934 CATATCTTATCTCCCTGAAGTTGCAGTGGAGCTGATTGAAGTTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
* * * **
41342978 CAAATTTTATCTCCTTAAAGTTGTAGTGGAGCAGATTGAAAATA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
* * * *
41343022 GCAAATCTTATCTCTCTGAAGTTACAGTGGAACAGATTGAAGTTA
1 -CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
* * * * *
41343067 CAAATCTTATCTTCCTAAAGTTGAAATGGAGAAAATTGAAGTTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
* * *
41343111 CAAATCTTATCTCCCTGAA---GC--TGGAGTAAATTGAAGTTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
*
41343150 AAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
* * * * * ***
41343194 CAAATCTCATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGACG
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
* * * *
41343238 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGGTTAAAGCTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
* * * *
41343282 CAAATC-TAGTCTCTCTAAAGTTGTAGGGGAGTAGATTGAA
1 CAAATCTTA-TCTCCCTAAAGTTGCAGTGGAGCAGATTGAA
41343322 CAACAAATTC
Statistics
Matches: 315, Mismatches: 65, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
39 34 0.11
41 1 0.00
42 2 0.01
43 29 0.09
44 214 0.68
45 35 0.11
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (44 bp):
CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA
Found at i:41343199 original size:127 final size:130
Alignment explanation
Indices: 41342892--41343257 Score: 398
Period size: 127 Copynumber: 2.8 Consensus size: 130
41342882 TTATCGTGGC
* * * ** * *
41342892 AAATTTTATCTCCCTAAAGTTGCAGTGGACAGACTAAAGCCACATATCTTATCTCCCTGAAGTTG
1 AAATCTTATCTCCCTAAAGTTGCAGTGGACAGATTGAAGTTACAAATCTTATCTTCCTGAAGTTG
** * * * *
41342957 CAGTGGAGCTGATTGAAGTTACAAATTTTATCTCCTTAAAGTTGTAGTGGAGCAGATTGAAAATA
66 CAGTGGAGAAGATTGAAGTTACAAATCTTATCTCCCTAAAGCTGGAGT-GA-CAGATTGAAAATA
*
41343022 GC
129 GA
* * * *
41343024 AAATCTTATCTCTCTGAAGTTACAGTGGAACAGATTGAAGTTACAAATCTTATCTTCCTAAAGTT
1 AAATCTTATCTCCCTAAAGTTGCAGTGG-ACAGATTGAAGTTACAAATCTTATCTTCCTGAAGTT
* * * * **
41343089 GAAATGGAGAAAATTGAAGTTACAAATCTTATCTCCCTGAAGCTGGAGT-A-A-ATTGAAGTTA-
65 GCAGTGGAGAAGATTGAAGTTACAAATCTTATCTCCCTAAAGCTGGAGTGACAGATTGAAAATAG
41343150 A
130 A
* *
41343151 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTCATCTTCTTGAAGTT
1 AAATCTTATCTCCCTAAAGTTGCAGTGGA-CAGATTGAAGTTACAAATCTTATCTTCCTGAAGTT
* ***
41343216 GCAGTGGAGTAGATTGAAGACGCAAATCTTATCTCCCTAAAG
65 GCAGTGGAGAAGATTGAAGTTACAAATCTTATCTCCCTAAAG
41343258 TTGCAGTGGA
Statistics
Matches: 194, Mismatches: 38, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
126 1 0.01
127 91 0.47
128 8 0.04
129 1 0.01
131 1 0.01
132 24 0.12
133 68 0.35
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (130 bp):
AAATCTTATCTCCCTAAAGTTGCAGTGGACAGATTGAAGTTACAAATCTTATCTTCCTGAAGTTG
CAGTGGAGAAGATTGAAGTTACAAATCTTATCTCCCTAAAGCTGGAGTGACAGATTGAAAATAGA
Found at i:41343255 original size:88 final size:88
Alignment explanation
Indices: 41342891--41343507 Score: 431
Period size: 88 Copynumber: 7.0 Consensus size: 88
41342881 GTTATCGTGG
* * * * * * *
41342891 CAAATTTTATCTCCCTAAAGTTGCAGTGGA-CAGACTAAAGCCACATATCTTATCTCCCTGAAGT
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTTCTTGAAGT
41342955 TGCAGTGGAGCT-GATTGAAGTTA
66 TGCAGTGGAG-TAGATTGAAGTTA
* * * **
41342978 CAAATTTTATCTCCTTAAAGTTGTAGTGGAGCAGATTGAAAATAGCAAATCTTATC-TCTCTGAA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA-CAAATCTTATCTTCT-TGAA
* **
41343042 GTTACAGTGGAACAGATTGAAGTTA
64 GTTGCAGTGGAGTAGATTGAAGTTA
* * * * * * * *
41343067 CAAATCTTATCTTCCTAAAGTTGAAATGGAGAAAATTGAAGTTACAAATCTTATCTCCCTGAA--
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTTCTTGAAGT
*
41343130 -GC--TGGAGTAAATTGAAGTTA
66 TGCAGTGGAGTAGATTGAAGTTA
* * *
41343150 AAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTCATCTTCTTGAAGT
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTTCTTGAAGT
***
41343215 TGCAGTGGAGTAGATTGAAGACG
66 TGCAGTGGAGTAGATTGAAGTTA
* * * *
41343238 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGGTTAAAGCTACAAATC-TAGTC-TCTCTAAA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTA-TCTTCT-TGAA
* * **
41343301 GTTGTAGGGGAGTAGATTGAA-CAA
64 GTTGCAGTGGAGTAGATTGAAGTTA
* * * * * *
41343325 CAAAT-TCAATAC-CTCTAAAGTTGCAGTAGG-TCGGATTAAATCTACCATAGCAAGTCTTAT-T
1 CAAATCT-TAT-CTCCCTAAAGTTGCAGT-GGAGCAGATTGAAGCTA-C--A--AA-TCTTATCT
* * * * **
41343386 TCCCTGAAGCTACAGTAGAATAGAGTAAAGCTACAAGTTA
57 T-CTTGAAGTTGCAGT-G----GAGT--AGATTGAAGTTA
* * *
41343426 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCTACAAGTC-T-TCTTCTTGAAGT
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTTCTTGAAGT
*
41343489 TGCAGTGAAGTAGATTGAA
66 TGCAGTGGAGTAGATTGAA
41343508 ACTACTATTC
Statistics
Matches: 407, Mismatches: 87, Indels: 73
0.72 0.15 0.13
Matches are distributed among these distances:
83 69 0.17
85 1 0.00
86 8 0.02
87 62 0.15
88 114 0.28
89 71 0.17
90 1 0.00
92 3 0.01
93 23 0.06
94 7 0.02
95 2 0.00
96 1 0.00
98 5 0.01
100 9 0.02
101 30 0.07
102 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (88 bp):
CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTTCTTGAAGT
TGCAGTGGAGTAGATTGAAGTTA
Found at i:41344945 original size:21 final size:21
Alignment explanation
Indices: 41344921--41344960 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
41344911 TTACAAACTG
41344921 TTTTATTTATT-TATTATTTTA
1 TTTTATTTATTAT-TTATTTTA
41344942 TTTTATTTATTATTTATTT
1 TTTTATTTATTATTTATTT
41344961 AACTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTATTTATTATTTATTTTA
Found at i:41344948 original size:17 final size:17
Alignment explanation
Indices: 41344921--41344960 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
41344911 TTACAAACTG
41344921 TTTTA-TTTATTTATTA
1 TTTTATTTTATTTATTA
41344937 TTTTATTTTATTTATTA
1 TTTTATTTTATTTATTA
41344954 -TTTATTT
1 TTTTATTT
41344961 AACTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTTATTTATTA
Found at i:41345077 original size:3 final size:3
Alignment explanation
Indices: 41345022--41345062 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
41345012 TTATATTTTG
* * *
41345022 TTA TCA TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41345063 TTTTCCTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:41346652 original size:41 final size:40
Alignment explanation
Indices: 41346604--41346699 Score: 147
Period size: 41 Copynumber: 2.4 Consensus size: 40
41346594 GATTTAACCG
*
41346604 ATGAGACACTGGGTGTCAATTTACTACTTTGAATTTATTCA
1 ATGAGACACTGGGTGTCAATTTACTACTTCGAA-TTATTCA
*
41346645 ATGAGACACTGGGTGTCAATTTACTACTTCGAATTATTCG
1 ATGAGACACTGGGTGTCAATTTACTACTTCGAATTATTCA
* *
41346685 ATGAGGCACTAGGTG
1 ATGAGACACTGGGTG
41346700 CCAAACTGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 19 0.37
41 32 0.63
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAATTTACTACTTCGAATTATTCA
Found at i:41349412 original size:18 final size:20
Alignment explanation
Indices: 41349357--41349415 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
41349347 ACCTTTACAC
41349357 CACATTGTGGATAAACCACT
1 CACATTGTGGATAAACCACT
* *
41349377 CATCATTGTGTATGAACCACT
1 CA-CATTGTGGATAAACCACT
41349398 C-C-TTGTGGATAAACCACT
1 CACATTGTGGATAAACCACT
41349416 AGTAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 14 0.41
19 1 0.03
20 2 0.06
21 17 0.50
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (20 bp):
CACATTGTGGATAAACCACT
Found at i:41350288 original size:35 final size:34
Alignment explanation
Indices: 41350211--41350288 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
41350201 AAACACAAAA
****
41350211 AAATATTTTAAAAATAAAAAATAAAAATATTTTT
1 AAATATTTTAAAAATAAAAAATAAAAATAAAAGT
*
41350245 AAAGTATTTTAAAATTAAAAAATAAAAATAAAAAGT
1 AAA-TATTTTAAAAATAAAAAATAAAAAT-AAAAGT
*
41350281 ATATATTT
1 AAATATTT
41350289 ATTATATTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
34 3 0.08
35 29 0.81
36 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (34 bp):
AAATATTTTAAAAATAAAAAATAAAAATAAAAGT
Found at i:41354705 original size:46 final size:46
Alignment explanation
Indices: 41354653--41354759 Score: 196
Period size: 46 Copynumber: 2.3 Consensus size: 46
41354643 CCATGGAAAA
*
41354653 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAGCCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
*
41354699 TTGTGAAAAGTAGGTATGGTGTTTCAGTGATGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
41354745 TTGTGAAAAGTAGGT
1 TTGTGAAAAGTAGGT
41354760 GAAAACCATA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:41354765 original size:30 final size:30
Alignment explanation
Indices: 41354729--41354789 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
41354719 GTTTCAGTGA
41354729 TGAAAACCATACTGAGTTGTGAAAAGTAGG
1 TGAAAACCATACTGAGTTGTGAAAAGTAGG
41354759 TGAAAACCATACTGAGTTGTGAAAAGTAGG
1 TGAAAACCATACTGAGTTGTGAAAAGTAGG
41354789 T
1 T
41354790 ATGGTGTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.25
Consensus pattern (30 bp):
TGAAAACCATACTGAGTTGTGAAAAGTAGG
Found at i:41354780 original size:76 final size:76
Alignment explanation
Indices: 41354684--41354835 Score: 286
Period size: 76 Copynumber: 2.0 Consensus size: 76
41354674 TTTCAGTGAA
* *
41354684 GAAAGCCATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGATGAAAACCATACTGAGTTGT
1 GAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGT
41354749 GAAAAGTAGGT
66 GAAAAGTAGGT
41354760 GAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGT
1 GAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGT
41354825 GAAAAGTAGGT
66 GAAAAGTAGGT
41354836 ATGGTATTTC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (76 bp):
GAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGT
GAAAAGTAGGT
Found at i:41354812 original size:46 final size:46
Alignment explanation
Indices: 41354760--41354868 Score: 191
Period size: 46 Copynumber: 2.4 Consensus size: 46
41354750 AAAAGTAGGT
* *
41354760 GAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAA
1 GAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCAATGAA
41354806 GAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCAATGAA
1 GAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCAATGAA
*
41354852 GGAAACCATACTGAGTT
1 GAAAACCATACTGAGTT
41354869 ATAGTATTGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.28
Consensus pattern (46 bp):
GAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCAATGAA
Found at i:41357185 original size:16 final size:17
Alignment explanation
Indices: 41357164--41357197 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41357154 TATGTTTATA
41357164 GAATGTA-TGCATATTT
1 GAATGTATTGCATATTT
*
41357180 GAATGTATTGCATTTTT
1 GAATGTATTGCATATTT
41357197 G
1 G
41357198 CACATCCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (17 bp):
GAATGTATTGCATATTT
Found at i:41359742 original size:27 final size:26
Alignment explanation
Indices: 41359712--41359796 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
41359702 TTTATTTTTT
*
41359712 AAAAAAAATAAAATTCATAAAAATATA
1 AAAAAAAATAAAA-TCATTAAAATATA
**
41359739 AAAATGAATAAAAT-ATTAAAATATTA
1 AAAAAAAATAAAATCATTAAAATA-TA
*
41359765 AAAATAATATAAAATCATTTAAAA-ATA
1 AAAA-AAAATAAAATCA-TTAAAATATA
41359792 AAAAA
1 AAAAA
41359797 TAGAATTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
25 8 0.17
26 8 0.17
27 24 0.50
28 2 0.04
29 6 0.12
ACGTcount: A:0.71, C:0.02, G:0.01, T:0.26
Consensus pattern (26 bp):
AAAAAAAATAAAATCATTAAAATATA
Found at i:41359749 original size:10 final size:8
Alignment explanation
Indices: 41359713--41359798 Score: 50
Period size: 9 Copynumber: 9.9 Consensus size: 8
41359703 TTATTTTTTA
*
41359713 AAAAAAAT
1 AAAAATAT
*
41359721 AAAATTCAT
1 AAAAAT-AT
41359730 AAAAATAT
1 AAAAATAT
41359738 AAAAATGA-
1 AAAAAT-AT
41359746 ATAAAATAT
1 A-AAAATAT
*
41359755 TAAAATATT
1 AAAAATA-T
41359764 AAAAATAAT
1 AAAAAT-AT
41359773 ATAAAATCATTT
1 A-AAAAT-A--T
41359785 AAAAATA-
1 AAAAATAT
41359792 AAAAATA
1 AAAAATA
41359799 GAATTTTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
7 7 0.11
8 20 0.32
9 21 0.33
10 8 0.13
11 5 0.08
12 2 0.03
ACGTcount: A:0.70, C:0.02, G:0.01, T:0.27
Consensus pattern (8 bp):
AAAAATAT
Found at i:41359768 original size:17 final size:18
Alignment explanation
Indices: 41359710--41359791 Score: 62
Period size: 17 Copynumber: 4.5 Consensus size: 18
41359700 TTTTTATTTT
* *
41359710 TTAAAAAAAATAAAATTCA
1 TTAAAAATATTAAAA-TCA
* *
41359729 -TAAAAATATAAAAATGA
1 TTAAAAATATTAAAATCA
*
41359746 AT-AAAATATTAAAAT-A
1 TTAAAAATATTAAAATCA
41359762 TTAAAAATAATATAAAATCA
1 TTAAAAAT-AT-TAAAATCA
41359782 TTTAAAAATA
1 -TTAAAAATA
41359792 AAAAATAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
16 2 0.04
17 19 0.37
18 14 0.27
19 6 0.12
20 2 0.04
21 8 0.16
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (18 bp):
TTAAAAATATTAAAATCA
Found at i:41360242 original size:48 final size:48
Alignment explanation
Indices: 41360190--41360295 Score: 140
Period size: 48 Copynumber: 2.2 Consensus size: 48
41360180 GGAGGCGTTT
** * * * * *
41360190 GTGGGTTCACAATAGGTTGTGATGGTGGTGGTAGAATCGATGGTGTTG
1 GTGGGTTCACAATAGGAAGCGATAGAGGTGGTAGAACCGATGGTGTTA
*
41360238 GTGGGTTCACAATTGGAAGCGATAGAGGTGGTAGAACCGATGGTGTTA
1 GTGGGTTCACAATAGGAAGCGATAGAGGTGGTAGAACCGATGGTGTTA
41360286 GTGGGTTCAC
1 GTGGGTTCAC
41360296 TATTGCTGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (48 bp):
GTGGGTTCACAATAGGAAGCGATAGAGGTGGTAGAACCGATGGTGTTA
Found at i:41367090 original size:12 final size:12
Alignment explanation
Indices: 41367075--41367104 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41367065 TATTAAAATT
*
41367075 TAAAAGAAAAAC
1 TAAAAAAAAAAC
41367087 TAAAAAAAAAAC
1 TAAAAAAAAAAC
41367099 TAAAAA
1 TAAAAA
41367105 TTTCTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (12 bp):
TAAAAAAAAAAC
Found at i:41367528 original size:6 final size:6
Alignment explanation
Indices: 41367517--41367541 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41367507 TATTTTTCTC
41367517 CCGCCT CCGCCT CCGCCT CCGCCT C
1 CCGCCT CCGCCT CCGCCT CCGCCT C
41367542 ATCACCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.16, T:0.16
Consensus pattern (6 bp):
CCGCCT
Found at i:41367550 original size:6 final size:6
Alignment explanation
Indices: 41367541--41367567 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41367531 GCCTCCGCCT
41367541 CATCAC CATCAC CATCAC CATCAC CAT
1 CATCAC CATCAC CATCAC CATCAC CAT
41367568 ACTCTTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.19
Consensus pattern (6 bp):
CATCAC
Found at i:41370353 original size:126 final size:125
Alignment explanation
Indices: 41369950--41370412 Score: 552
Period size: 126 Copynumber: 3.7 Consensus size: 125
41369940 GATAAAATCA
* * * * * * * * *
41369950 AAGCAGGATGATTTATTAGAAGGATTTTTGAAGTCGTGCCCACGTGTACGCGCTTTTACTACAGT
1 AAGCAGAATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
41370015 AGGTCCTGGAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTTTAAAAAACGCTTT
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * *
41370075 AAGCAAAATGCTTTATGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGAATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * * *
41370140 TGGTCCTGGAAGAAATAATTTCGAGTTGATGTTTTTAAGCAAATAGTTTAAAAAAATGCTTC
66 AGGTCCT-GAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTT-AAAAAACGCTTC
* * * * *
41370202 AAGCAGGATGCTTTATAAGAAGAATTTGCGAAGTCGCGCCCACGTGGACGCGCTTTTGTTACAGT
1 AAGCAGAATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
41370267 AAGTCCTGAAAAAATAAATTT-GAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGC
66 AGGTCCTGAAAAAAT-AATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAA-AACGCTTC
* * * *
41370328 AAGCAGCATGCTATT-TGAGAAGAATTTGTGAAATTGTGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGAATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
*
41370392 TAGGTCCTGGAAAAATAATTT
65 TAGGTCCTGAAAAAATAATTT
41370413 ACAGTAGGTC
Statistics
Matches: 284, Mismatches: 49, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
125 68 0.24
126 137 0.48
127 79 0.28
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (125 bp):
AAGCAGAATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
Found at i:41370410 original size:252 final size:252
Alignment explanation
Indices: 41369950--41370412 Score: 680
Period size: 252 Copynumber: 1.8 Consensus size: 252
41369940 GATAAAATCA
* * ** * *
41369950 AAGCAGGATGATTTATTAGAAGGATTTTTGAAGTCGTGCCCACGTGTACGCGCTTTTACTACAGT
1 AAGCAGGATGATTTATAAGAAGAATTTGCGAAGTCGCGCCCACGTGGACGCGCTTTTACTACAGT
* * * **
41370015 AGGTCCTGGAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTTTAAAAAACGCTTTAAGCA
66 AAGTCCTGAAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTATAAAAAACGCTGCAAGCA
*
41370080 AAATGCTTTATGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTC
131 AAATGCTTTATGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTC
41370145 CTGGAAGAAATAATTTCGAGTTGATGTTTTTAAGCAAATAGTTTAAAAAAATGCTTC
196 CTGGAAGAAATAATTTCGAGTTGATGTTTTTAAGCAAATAGTTTAAAAAAATGCTTC
* **
41370202 AAGCAGGATGCTTTATAAGAAGAATTTGCGAAGTCGCGCCCACGTGGACGCGCTTTTGTTACAGT
1 AAGCAGGATGATTTATAAGAAGAATTTGCGAAGTCGCGCCCACGTGGACGCGCTTTTACTACAGT
* *
41370267 AAGTCCTGAAAAAATAAATTT-GAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGCAAG
66 AAGTCCTGAAAAAAT-AATTTCGACTTGACATTTCTGAGCAAATAGTATAAAA-AACGCTGCAAG
** ***
41370331 CAGCATGCTATT-TGAGAAGAATTTGTGAAATTGTGCCCTCGTGGACGCGCTTTTGCTACAGTAG
129 CAAAATGCT-TTATGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAGTAG
41370395 GTCCTGGAA-AAATAATTT
193 GTCCTGGAAGAAATAATTT
41370413 ACAGTAGGTC
Statistics
Matches: 186, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
252 106 0.57
253 78 0.42
254 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (252 bp):
AAGCAGGATGATTTATAAGAAGAATTTGCGAAGTCGCGCCCACGTGGACGCGCTTTTACTACAGT
AAGTCCTGAAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTATAAAAAACGCTGCAAGCA
AAATGCTTTATGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTC
CTGGAAGAAATAATTTCGAGTTGATGTTTTTAAGCAAATAGTTTAAAAAAATGCTTC
Done.