Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 16 of 172
Found at i:5086949 original size:83 final size:83
Alignment explanation
Indices: 5086850--5087938 Score: 1829
Period size: 83 Copynumber: 13.2 Consensus size: 83
5086840 GAAGCAGATC
* * *
5086850 CAAGATGATTTGGCATCCTTGTACTTACAAGGAACAAATCGAGGACATAGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
* *
5086915 AACGTTCTCAAATAGACT
66 AATGTTCTCAAACAGACT
5086933 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
* *
5086998 AATGTTCTCAAATAGATT
66 AATGTTCTCAAACAGACT
* *
5087016 CAAGATGGTTTGGCATCCTTGTGCTTACAAGAAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
*
5087081 AATGTCCTCAAACAGACT
66 AATGTTCTCAAACAGACT
*
5087099 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
*
5087164 AATGTCCTCAAACAGACT
66 AATGTTCTCAAACAGACT
*
5087182 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
*
5087247 AATGTCCTCAAACAGACT
66 AATGTTCTCAAACAGACT
* * *
5087265 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATATGACTCTC-
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
*
5087329 -A-------AAATAGACT
66 AATGTTCTCAAACAGACT
*
5087339 CAAGATGATTTAGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
5087404 AATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
5087422 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
5087487 AATGTTCTCAAACAGA-T
66 AATGTTCTCAAACAGACT
* * *
5087504 TAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGTAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
*
5087569 AATGTCCTCAAACAGACT
66 AATGTTCTCAAACAGACT
*
5087587 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
*
5087652 AACGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
5087670 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
*
5087735 AACGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
5087753 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
*
5087818 AACGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
5087836 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
*
5087901 AATGTTCTCAAGCAGACT
66 AATGTTCTCAAACAGACT
* **
5087919 CAAGATAATTTAACATCCTT
1 CAAGATGATTTGGCATCCTT
5087939 ACAAATCGAA
Statistics
Matches: 962, Mismatches: 34, Indels: 20
0.95 0.03 0.02
Matches are distributed among these distances:
74 68 0.07
76 1 0.00
81 1 0.00
82 78 0.08
83 814 0.85
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (83 bp):
CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
AATGTTCTCAAACAGACT
Found at i:5093798 original size:36 final size:36
Alignment explanation
Indices: 5093747--5093828 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 36
5093737 ATGATGGCTG
* * * *
5093747 ATGTGAAAGTGAATATGAAGGTGTGTTGTTCATGCC
1 ATGTGACAGTAAATATGAAGGTATGTTATTCATGCC
* * **
5093783 CTGTTACAGTAAATATGTGGGTATGTTATTCATGCC
1 ATGTGACAGTAAATATGAAGGTATGTTATTCATGCC
5093819 ATGTGACAGT
1 ATGTGACAGT
5093829 GTTTATAATG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (36 bp):
ATGTGACAGTAAATATGAAGGTATGTTATTCATGCC
Found at i:5094733 original size:12 final size:12
Alignment explanation
Indices: 5094718--5094742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5094708 TGTTTACTTA
5094718 ATTAAGTGAATG
1 ATTAAGTGAATG
5094730 ATTAAGTGAATG
1 ATTAAGTGAATG
5094742 A
1 A
5094743 AGCATGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
ATTAAGTGAATG
Found at i:5096153 original size:31 final size:31
Alignment explanation
Indices: 5096115--5096176 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5096105 AGCAGGTAAG
*
5096115 GTTTAAAGTTAATTGCGGCTGTCATATATCC
1 GTTTAAAGTTAATTGCGACTGTCATATATCC
5096146 GTTTAAAGTTAATTGCGACTGTCATATATCC
1 GTTTAAAGTTAATTGCGACTGTCATATATCC
5096177 AAGAGCAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (31 bp):
GTTTAAAGTTAATTGCGACTGTCATATATCC
Found at i:5100924 original size:25 final size:25
Alignment explanation
Indices: 5100896--5100946 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
5100886 CATGTTAGTC
*
5100896 ACAAAATCTTCATATCAATTAAGTA
1 ACAAAATCTTCATATCAATCAAGTA
5100921 ACAAAATCTTCATATCAATCAAGTA
1 ACAAAATCTTCATATCAATCAAGTA
5100946 A
1 A
5100947 ATATAGATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (25 bp):
ACAAAATCTTCATATCAATCAAGTA
Found at i:5102048 original size:9 final size:9
Alignment explanation
Indices: 5101987--5102047 Score: 86
Period size: 9 Copynumber: 6.8 Consensus size: 9
5101977 GGTATTTTTC
5101987 GGTAATTCG
1 GGTAATTCG
*
5101996 GTTAATTCG
1 GGTAATTCG
*
5102005 GTTAATTCG
1 GGTAATTCG
5102014 GGTAATTCG
1 GGTAATTCG
*
5102023 GGTAATTCA
1 GGTAATTCG
*
5102032 GGTAATTTG
1 GGTAATTCG
5102041 GGTAATT
1 GGTAATT
5102048 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.39
Consensus pattern (9 bp):
GGTAATTCG
Found at i:5103766 original size:8 final size:8
Alignment explanation
Indices: 5103753--5103784 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
5103743 CACTCACGTA
5103753 TGATGAAG
1 TGATGAAG
5103761 TGATGAAG
1 TGATGAAG
5103769 TGATGAAG
1 TGATGAAG
5103777 TGATGAAG
1 TGATGAAG
5103785 AGTCTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (8 bp):
TGATGAAG
Found at i:5105242 original size:2 final size:2
Alignment explanation
Indices: 5105237--5105263 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5105227 TCTACTTTTT
5105237 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
5105264 TTTGAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5112068 original size:15 final size:15
Alignment explanation
Indices: 5112048--5112078 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5112038 CTTGTAGAAT
*
5112048 AAGAAACTATAATTA
1 AAGAAACTAAAATTA
5112063 AAGAAACTAAAATTA
1 AAGAAACTAAAATTA
5112078 A
1 A
5112079 GTGCTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (15 bp):
AAGAAACTAAAATTA
Found at i:5113519 original size:15 final size:15
Alignment explanation
Indices: 5113499--5113553 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
5113489 TGTGGAATAA
*
5113499 GAAACTACAATTAAT
1 GAAACTAAAATTAAT
5113514 GAAACTAAAATT-AT
1 GAAACTAAAATTAAT
* *
5113528 -ATA-TACAATTAAT
1 GAAACTAAAATTAAT
5113541 GAAACTAAAATTA
1 GAAACTAAAATTA
5113554 TATACTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 6 0.19
13 4 0.12
14 4 0.12
15 18 0.56
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.29
Consensus pattern (15 bp):
GAAACTAAAATTAAT
Found at i:5113536 original size:27 final size:27
Alignment explanation
Indices: 5113504--5113557 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5113494 AATAAGAAAC
5113504 TACAATTAATGAAACTAAAATTATATA
1 TACAATTAATGAAACTAAAATTATATA
5113531 TACAATTAATGAAACTAAAATTATATA
1 TACAATTAATGAAACTAAAATTATATA
5113558 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (27 bp):
TACAATTAATGAAACTAAAATTATATA
Found at i:5117310 original size:22 final size:23
Alignment explanation
Indices: 5117268--5117313 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5117258 TGATAGTGCA
*
5117268 TTAAATATATTTCCTTTATTTTT
1 TTAAATATATTTCATTTATTTTT
*
5117291 TTAAGTATATTT-ATTTATTTTT
1 TTAAATATATTTCATTTATTTTT
5117313 T
1 T
5117314 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TTAAATATATTTCATTTATTTTT
Found at i:5131618 original size:25 final size:25
Alignment explanation
Indices: 5131590--5131639 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5131580 TAATTAACGG
5131590 AAAATAATAAAATTAAATAAAGTTT
1 AAAATAATAAAATTAAATAAAGTTT
5131615 AAAATAATAAAATTAAATAAAGTTT
1 AAAATAATAAAATTAAATAAAGTTT
5131640 TGGTTGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (25 bp):
AAAATAATAAAATTAAATAAAGTTT
Found at i:5131898 original size:26 final size:24
Alignment explanation
Indices: 5131868--5131915 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
5131858 AAATAAAAAA
*
5131868 TTAAAAATATAATAAATCAAATATAT
1 TTAAAAACATAA-AAAT-AAATATAT
5131894 TTAAAAACATAAAAATAAATAT
1 TTAAAAACATAAAAATAAATAT
5131916 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 11 0.52
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
TTAAAAACATAAAAATAAATATAT
Found at i:5131927 original size:22 final size:22
Alignment explanation
Indices: 5131886--5131944 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
5131876 ATAATAAATC
* *
5131886 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
5131906 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
* *
5131928 AAAT-GATACTAAAACAA
1 AAATAAATATTAAAACAA
5131945 TTCTTAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 17 0.52
22 9 0.27
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:5134429 original size:12 final size:12
Alignment explanation
Indices: 5134412--5134437 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5134402 CTTCTCTTTT
5134412 TTTTTTCTTTCC
1 TTTTTTCTTTCC
5134424 TTTTTTCTTTCC
1 TTTTTTCTTTCC
5134436 TT
1 TT
5134438 GTTGCCCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTCTTTCC
Found at i:5134788 original size:9 final size:9
Alignment explanation
Indices: 5134760--5134814 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
5134750 AATTATCTCA
*
5134760 TTTATAACT
1 TTTATAATT
5134769 TTTAT-ATT
1 TTTATAATT
5134777 TTTATAATT
1 TTTATAATT
*
5134786 TTTTTAA--
1 TTTATAATT
*
5134793 TTTAAAATT
1 TTTATAATT
5134802 TTTAATAATT
1 TTT-ATAATT
5134812 TTT
1 TTT
5134815 TTATAATTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
7 5 0.14
8 7 0.19
9 17 0.46
10 8 0.22
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:5136674 original size:14 final size:14
Alignment explanation
Indices: 5136657--5136696 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
5136647 AATTGTGCAA
5136657 ATTTTTTAAAACTT
1 ATTTTTTAAAACTT
* *
5136671 ATTTTCTAAAAATT
1 ATTTTTTAAAACTT
5136685 ATTTTTTAAAAC
1 ATTTTTTAAAAC
5136697 AAACTTAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTTTAAAACTT
Found at i:5138333 original size:22 final size:22
Alignment explanation
Indices: 5138307--5138357 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5138297 CCCGTGTGGC
5138307 CCACACGGCCTCAATCGAGCCA
1 CCACACGGCCTCAATCGAGCCA
*
5138329 CCACACGGCCTCACTCGAGCCA
1 CCACACGGCCTCAATCGAGCCA
5138351 CCACACG
1 CCACACG
5138358 ACCGTGTGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.49, G:0.18, T:0.08
Consensus pattern (22 bp):
CCACACGGCCTCAATCGAGCCA
Found at i:5146104 original size:14 final size:14
Alignment explanation
Indices: 5146087--5146126 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
5146077 AATTGTGCAA
5146087 ATTTTTTAAAACTT
1 ATTTTTTAAAACTT
* *
5146101 ATTTTCTAAAAATT
1 ATTTTTTAAAACTT
5146115 ATTTTTTAAAAC
1 ATTTTTTAAAAC
5146127 AAACTTAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTTTAAAACTT
Found at i:5147763 original size:22 final size:22
Alignment explanation
Indices: 5147737--5147787 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5147727 CCCGTGTGGC
5147737 CCACACGGCCTCAATCGAGCCA
1 CCACACGGCCTCAATCGAGCCA
*
5147759 CCACACGGCCTCACTCGAGCCA
1 CCACACGGCCTCAATCGAGCCA
5147781 CCACACG
1 CCACACG
5147788 ACCGTGTGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.49, G:0.18, T:0.08
Consensus pattern (22 bp):
CCACACGGCCTCAATCGAGCCA
Found at i:5156891 original size:18 final size:17
Alignment explanation
Indices: 5156863--5156899 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
5156853 TTCTTTATAT
5156863 ATTTAAAAATATTAAAA
1 ATTTAAAAATATTAAAA
*
5156880 ATTTATAAAATATTTAAA
1 ATTTA-AAAATATTAAAA
5156898 AT
1 AT
5156900 AAATGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAAATATTAAAA
Found at i:5159562 original size:14 final size:14
Alignment explanation
Indices: 5159543--5159582 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5159533 TTGATTGGCA
5159543 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
5159557 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
5159571 GGAAAATGTTTT
1 GTAAAATGTTTT
5159583 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:5160992 original size:27 final size:27
Alignment explanation
Indices: 5160962--5161029 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
5160952 AATAATCAAT
*
5160962 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
5160989 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
5161017 TCAAAATCCAACA
1 TCAATATCCAACA
5161030 GTCTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 20 0.59
28 14 0.41
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.25
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:5170948 original size:24 final size:24
Alignment explanation
Indices: 5170921--5170967 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
5170911 GAACATCAAT
5170921 TTTTAAGCTCAAAGTTGACTCGAA
1 TTTTAAGCTCAAAGTTGACTCGAA
5170945 TTTTAAGCTCAAAGTTGACTCGA
1 TTTTAAGCTCAAAGTTGACTCGA
5170968 GATACAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (24 bp):
TTTTAAGCTCAAAGTTGACTCGAA
Found at i:5172824 original size:13 final size:14
Alignment explanation
Indices: 5172808--5172843 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5172798 CAATCTCATA
5172808 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
5172821 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
5172834 TCTC-ATTTCA
1 TCTCAATTTCA
5172844 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:5172833 original size:18 final size:19
Alignment explanation
Indices: 5172795--5172835 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
5172785 TGGTTCATGT
5172795 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
5172814 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
5172832 TTTC
1 TTTC
5172836 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:5172970 original size:23 final size:23
Alignment explanation
Indices: 5172940--5172997 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
5172930 GCGGATTCCT
*
5172940 CCCAAACACACTAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
5172963 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
5172986 CCCAAACACACC
1 CCCAAACACACC
5172998 CGGAATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.47, C:0.41, G:0.03, T:0.09
Consensus pattern (23 bp):
CCCAAACACACCAGAATATCCAA
Found at i:5173519 original size:15 final size:15
Alignment explanation
Indices: 5173499--5173575 Score: 100
Period size: 15 Copynumber: 5.1 Consensus size: 15
5173489 TAATATATAT
5173499 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
5173514 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
5173529 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
5173544 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
5173559 TTCAATCAATATAAA
1 TTCAATCAATATAAA
5173574 TT
1 TT
5173576 TGATAAATTC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:5173533 original size:30 final size:30
Alignment explanation
Indices: 5173497--5173575 Score: 158
Period size: 30 Copynumber: 2.6 Consensus size: 30
5173487 TATAATATAT
5173497 ATTTCAATCAATATAAATTCAATCAAAATG
1 ATTTCAATCAATATAAATTCAATCAAAATG
5173527 ATTTCAATCAATATAAATTCAATCAAAATG
1 ATTTCAATCAATATAAATTCAATCAAAATG
5173557 ATTTCAATCAATATAAATT
1 ATTTCAATCAATATAAATT
5173576 TGATAAATTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (30 bp):
ATTTCAATCAATATAAATTCAATCAAAATG
Found at i:5173999 original size:19 final size:19
Alignment explanation
Indices: 5173975--5174013 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5173965 AATACTTATT
*
5173975 TATTATTTATACATGTGTA
1 TATTATTAATACATGTGTA
5173994 TATTATTAATACATGTGTA
1 TATTATTAATACATGTGTA
5174013 T
1 T
5174014 CTATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAATACATGTGTA
Found at i:5174021 original size:19 final size:19
Alignment explanation
Indices: 5173978--5174021 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5173968 ACTTATTTAT
5173978 TATTT-ATACATGTGTATA
1 TATTTAATACATGTGTATA
*
5173996 T-TATTAATACATGTGTATC
1 TAT-TTAATACATGTGTATA
5174015 TATTTAA
1 TATTTAA
5174022 AACCATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 1 0.05
18 3 0.14
19 17 0.77
20 1 0.05
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (19 bp):
TATTTAATACATGTGTATA
Found at i:5183327 original size:5 final size:6
Alignment explanation
Indices: 5183312--5183361 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
5183302 CATAAATGTT
**
5183312 AAAAAG AAAAAG AAAAAG AAAAATG AAGAGTCG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAA-G AA-A-AAG AAAAAG AAAAAG AAAAA
5183362 TGAAGAGTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 29 0.78
7 4 0.11
8 4 0.11
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:5183347 original size:27 final size:27
Alignment explanation
Indices: 5183317--5183373 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
5183307 ATGTTAAAAA
5183317 GAAAAAGAAAAAGAAAAATGAAGAGTC
1 GAAAAAGAAAAAGAAAAATGAAGAGTC
5183344 GAAAAAGAAAAAGAAAAATGAAGAGTC
1 GAAAAAGAAAAAGAAAAATGAAGAGTC
5183371 GAA
1 GAA
5183374 GCAGTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.67, C:0.04, G:0.23, T:0.07
Consensus pattern (27 bp):
GAAAAAGAAAAAGAAAAATGAAGAGTC
Found at i:5183349 original size:15 final size:15
Alignment explanation
Indices: 5183329--5183373 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
5183319 AAAAGAAAAA
5183329 GAAAAATGAAGAGTC
1 GAAAAATGAAGAGTC
**
5183344 GAAAAA-GAA-A-AA
1 GAAAAATGAAGAGTC
5183356 GAAAAATGAAGAGTC
1 GAAAAATGAAGAGTC
5183371 GAA
1 GAA
5183374 GCAGTATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
12 6 0.26
13 4 0.17
14 4 0.17
15 9 0.39
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.09
Consensus pattern (15 bp):
GAAAAATGAAGAGTC
Found at i:5185372 original size:27 final size:28
Alignment explanation
Indices: 5185318--5185372 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
5185308 GAGTAATTAT
* **
5185318 TTAGTATTTTAAAGGTTAATTATGTAAA
1 TTAGTATTATAAAGGTTAATTAAATAAA
5185346 TTAGT-TTATAAAGGTTAATTAAATAAA
1 TTAGTATTATAAAGGTTAATTAAATAAA
5185373 ACAAATGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (28 bp):
TTAGTATTATAAAGGTTAATTAAATAAA
Found at i:5186304 original size:24 final size:24
Alignment explanation
Indices: 5186267--5186333 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
5186257 TGCCTATATA
* * *
5186267 TCAGCTCGTAAGAGCTTACTATTT
1 TCAGCTCATTAGAGCTTACTAGTT
*
5186291 TCAGCTCATTAGAGCTTAC-CGTT
1 TCAGCTCATTAGAGCTTACTAGTT
* *
5186314 TCAGTTCAATAGAGCTTACT
1 TCAGCTCATTAGAGCTTACT
5186334 GTCCATCAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (24 bp):
TCAGCTCATTAGAGCTTACTAGTT
Found at i:5189035 original size:43 final size:42
Alignment explanation
Indices: 5188979--5189107 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 42
5188969 AGCTCGTACA
* *
5188979 ATGCCATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCATGTCCCAGATATGGTCTTACATGTAATCACATATCG
* * * *
5189021 ATGCCACTGTCCCAGATAGGGTCTTACACGAAATCA-ATTAACG
1 ATGCCA-TGTCCCAGATATGGTCTTACATGTAATCACA-TATCG
* * * *
5189064 ATGCCAATGTCCAATACATGGTCTTACATGTAATCACATCTCG
1 ATGCC-ATGTCCCAGATATGGTCTTACATGTAATCACATATCG
5189107 A
1 A
5189108 CAACCTAATG
Statistics
Matches: 69, Mismatches: 14, Indels: 7
0.77 0.16 0.08
Matches are distributed among these distances:
42 7 0.10
43 60 0.87
44 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (42 bp):
ATGCCATGTCCCAGATATGGTCTTACATGTAATCACATATCG
Found at i:5192012 original size:130 final size:128
Alignment explanation
Indices: 5191765--5192097 Score: 402
Period size: 130 Copynumber: 2.6 Consensus size: 128
5191755 TTTTTATTTG
* * *
5191765 TCGTGCCCTAACGTGTTGGGTTGCAATTTCGTATTTGCTCAAAATAATCGAATTTTCCTTCGAAA
1 TCGTGCCCTAACGTGTTGGGTTGCAATTTCGTATTTGTTCAAAATAATCGAA-TATCCTTCAAAA
* * * * *
5191830 TTTCATTCATATCTTTTAAAATCCCTTAAATGAAGATGAGATTTGATGTTTGGCCATTCGCGGAA
65 TTTCACTCATATCTTTTAAAATACCTAAAATGAAGA-GAGATTTGATATTTGGCAATTCGCGGAA
*
5191895 TCGTGCCCTAACGTGTTGGGTTGCAATTTCGTATTTGTTCAAAATAATCGAATATCACTTTAAAA
1 TCGTGCCCTAACGTGTTGGGTTGCAATTTCGTATTTGTTCAAAATAATCGAATATC-CTTCAAAA
** * * * *
5191960 TTTTGCTCATGTCTTTTAAAATATCTAAAATGAAG-GAGATATGTGTTATTTGGCAATTCGCGGG
65 TTTCACTCATATCTTTTAAAATACCTAAAATGAAGAGAGAT-T-TGATATTTGGCAATTCGCGGA
5192024 A
128 A
* * * *
5192025 TCGTGCCTTAACGTGTTGGGTAGCAATTTCCCG-A-TTGTTTAAAATAATCAAATATCCCTTCAA
1 TCGTGCCCTAACGTGTTGGGTTGCAATTT--CGTATTTGTTCAAAATAATCGAATAT-CCTTCAA
5192088 AATTTCACTC
63 AATTTCACTC
5192098 GGCTCTTCTA
Statistics
Matches: 175, Mismatches: 22, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
128 5 0.03
129 4 0.02
130 162 0.93
131 2 0.01
132 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (128 bp):
TCGTGCCCTAACGTGTTGGGTTGCAATTTCGTATTTGTTCAAAATAATCGAATATCCTTCAAAAT
TTCACTCATATCTTTTAAAATACCTAAAATGAAGAGAGATTTGATATTTGGCAATTCGCGGAA
Found at i:5203054 original size:3 final size:3
Alignment explanation
Indices: 5203048--5203080 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5203038 TGAAAAAAAA
*
5203048 AAG AAG AAG AAG ATG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5203081 GAGAGGCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:5203938 original size:44 final size:44
Alignment explanation
Indices: 5203888--5204393 Score: 798
Period size: 44 Copynumber: 11.5 Consensus size: 44
5203878 GGTAAATCCT
* **
5203888 GCAGATTTGGCGTCTCCATATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
5203932 GCAGATTTGGCATCTCTGTATTGGCGGAGAACAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
5203976 GTAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
5204020 GCAGATTTGACATCTCTGTATTGGCGGAGAACAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
5204064 GTAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGGTCA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGAT-A
5204109 -CAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * * * *
5204152 GCATATTTGGCATCTCTGTATTGGCGGTGAACAGGTCGAAAATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
5204196 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATC
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
5204240 GTAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
5204284 GCAGATTTGGCATCTCTGTATTGGCGGAGAACAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
5204328 GTAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
5204372 GCAGATTTGGCGTCTTTGTATT
1 GCAGATTTGGCATCTCTGTATT
5204394 TACAAAAAAC
Statistics
Matches: 422, Mismatches: 38, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
43 1 0.00
44 420 1.00
45 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (44 bp):
GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATA
Found at i:5207576 original size:131 final size:131
Alignment explanation
Indices: 5207505--5207974 Score: 809
Period size: 131 Copynumber: 3.6 Consensus size: 131
5207495 AATACTCAGT
* * * *
5207505 GTTTGACGATTCGGGAATCATGCCCTATCGTGCTTGGTTGTGATTTCTCGTTTAGTCAAAACAAT
1 GTTTGGCGATTTGAGAATCCTGCCCTATCGTGCTTGGTTGTGATTTCTCGTTTAGTCAAAACAAT
5207570 CGAATATTCCTTGAGGTTTTCACTCGCTTTTAGAAAACATTCTTAAAAACGAAGACGATGTTCAA
66 CGAATATTCCTTGAGGTTTTCACTCGCTTTTAGAAAACATTCTTAAAAACGAAGACGATGTTCAA
5207635 C
131 C
5207636 GTTTGGCGATTTGAGAATCCTGCCCTATCGTGCTTGGTTGTGATTTCTCGTTTAGTCAAAACAAT
1 GTTTGGCGATTTGAGAATCCTGCCCTATCGTGCTTGGTTGTGATTTCTCGTTTAGTCAAAACAAT
5207701 CGAATATTCCTTGAGGTTTTCACTCGCTTTTAGAAAACATTCTTAAAAACGAAGACGATGTTCAA
66 CGAATATTCCTTGAGGTTTTCACTCGCTTTTAGAAAACATTCTTAAAAACGAAGACGATGTTCAA
5207766 C
131 C
5207767 GTTTGGCGATTTGAGAATCCTGCCCTATCGTGCTTGGTTGTGATTTCTCGTTTAGTCAAAACAAT
1 GTTTGGCGATTTGAGAATCCTGCCCTATCGTGCTTGGTTGTGATTTCTCGTTTAGTCAAAACAAT
5207832 CGAATATTCCTTGAGGTTTTCACTCGCTTTTAGAAAACATTCTTAAAAACGAAGACGATGTTCAA
66 CGAATATTCCTTGAGGTTTTCACTCGCTTTTAGAAAACATTCTTAAAAACGAAGACGATGTTCAA
5207897 C
131 C
* * * * * *
5207898 GTTTGGCGATTTGAGAATCGTGCCCTATCGTGC-TGGATTGCGTTTTTTCATTT-GTCTAAAATA
1 GTTTGGCGATTTGAGAATCCTGCCCTATCGTGCTTGG-TTGTGATTTCTCGTTTAGTC-AAAACA
5207961 ATCGAATATCTCCT
64 ATCGAATAT-TCCT
5207975 CGGAATTTTA
Statistics
Matches: 326, Mismatches: 10, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
130 6 0.02
131 316 0.97
132 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (131 bp):
GTTTGGCGATTTGAGAATCCTGCCCTATCGTGCTTGGTTGTGATTTCTCGTTTAGTCAAAACAAT
CGAATATTCCTTGAGGTTTTCACTCGCTTTTAGAAAACATTCTTAAAAACGAAGACGATGTTCAA
C
Found at i:5211095 original size:27 final size:27
Alignment explanation
Indices: 5211065--5211118 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
5211055 CGGTAAAATA
* *
5211065 ATTGTCCATGACCCTCAGGGTATTGGG
1 ATTGCCCACGACCCTCAGGGTATTGGG
*
5211092 ATTGCCCACGACCCTCTGGGTATTGGG
1 ATTGCCCACGACCCTCAGGGTATTGGG
5211119 GCTAACAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.28
Consensus pattern (27 bp):
ATTGCCCACGACCCTCAGGGTATTGGG
Found at i:5223871 original size:27 final size:25
Alignment explanation
Indices: 5223814--5223883 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 25
5223804 ACTCTATTAT
* *
5223814 ATTTTTCATATTATATCATGTATATAC
1 ATTTTTCATA-TAT-TCATGTACACAC
*
5223841 ATTTTTCATATATGTCATGTACACGC
1 ATTTTTCATATAT-TCATGTACACAC
5223867 AATTTTTCA-ATATTCAT
1 -ATTTTTCATATATTCAT
5223884 TTTATACATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 4 0.11
26 16 0.42
27 18 0.47
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (25 bp):
ATTTTTCATATATTCATGTACACAC
Found at i:5223872 original size:26 final size:27
Alignment explanation
Indices: 5223816--5223872 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
5223806 TCTATTATAT
* * *
5223816 TTTTCATATTATATCATGTATATACAT
1 TTTTCATATTATATCATGTACACACAA
* *
5223843 TTTTCATA-TATGTCATGTACACGCAA
1 TTTTCATATTATATCATGTACACACAA
5223869 TTTT
1 TTTT
5223873 TCAATATTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (27 bp):
TTTTCATATTATATCATGTACACACAA
Found at i:5224636 original size:72 final size:72
Alignment explanation
Indices: 5224515--5224653 Score: 260
Period size: 72 Copynumber: 1.9 Consensus size: 72
5224505 CGTAGACCTA
5224515 AACTCGGCCTTCTTTTTGTTTTAAAAATAAATTTATTAGGTGTCCGATCGTACCTATAAAAAAGA
1 AACTCGGCCTTCTTTTTGTTTTAAAAATAAATTTATTAGGTGTCCGATCGTACCTATAAAAAAGA
5224580 TCGGTGG
66 TCGGTGG
* *
5224587 AACTCGGCCTTCTTTTTGTTTTAAAAATAAATTTATTAGGTGTCTGATCGTACCTATAAAAAGGA
1 AACTCGGCCTTCTTTTTGTTTTAAAAATAAATTTATTAGGTGTCCGATCGTACCTATAAAAAAGA
5224652 TC
66 TC
5224654 AGTGACGACT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (72 bp):
AACTCGGCCTTCTTTTTGTTTTAAAAATAAATTTATTAGGTGTCCGATCGTACCTATAAAAAAGA
TCGGTGG
Found at i:5236204 original size:172 final size:169
Alignment explanation
Indices: 5235812--5236707 Score: 1057
Period size: 172 Copynumber: 5.2 Consensus size: 169
5235802 AAAGAGAAAA
* * * *
5235812 AAAAAGTCAACTCATATTGTGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTAACTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
*
5235877 CTGTTTTTCAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGCTC
65 CTG-TTTT-AATTCTGTTTT--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---
** * * * *
5235941 ACATACTGAGGTATCTTCAATTTCTATTTTTT-TAAT-TCATGTTTTC
123 ACACGCTGAGGTATTTTCAATTTCTGTTTTTTCCAATCT-ATATTTTC
*
5235987 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
**
5236052 CTGTTCTTAATGTCTGTTTTTGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
65 CTGTT-TTAAT-TCTGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
5236117 CTGAGGTATTTTCAATTTCTGTTTTTTCCAATCTATATTTTT
128 CTGAGGTATTTTCAATTTCTGTTTTTTCCAATCTATATTTTC
* *
5236159 AAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTTCAATTT
1 AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
* ** *
5236224 TTGTTCTTAATGTCTGTTTTTGAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
65 CTGTT-TTAAT-TCTGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
5236289 CTGATGTATTTTCAATTTCTGTTTTTTCCAATCTATATTTTTC
128 CTGAGGTATTTTCAATTTCTGTTTTTTCCAATCTATA-TTTTC
*
5236332 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTAATTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAAT
*
5236396 TTCTGTTTTCAATTTCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
63 TTCTGTTTT-AA-TTCT-GTTTT--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* * * *
5236461 ACACGCTGAGGTAATTTCAATTTCTG-TTTTTCAAATTCTA-CTTTGC
123 ACACGCTGAGGTATTTTCAATTTCTGTTTTTTCCAA-TCTATATTTTC
* * * *
5236507 AAAAAAATCAACTCATATTACGAGAGGTGAGTTGGGCCTCGGGGCACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* *** * *
5236572 TCT-ATTT--TTC---AAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGTCTCAGGACACGC
64 TCTGTTTTAATTCTGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* * *
5236631 TGAGGTATTTTCAAATTCTG-TTTTT--AATTTCTACTTTTC
129 TGAGGTATTTTCAATTTCTGTTTTTTCCAATCTATA-TTTTC
*
5236670 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
5236708 GGGTCACATG
Statistics
Matches: 648, Mismatches: 51, Indels: 57
0.86 0.07 0.08
Matches are distributed among these distances:
161 37 0.06
162 2 0.00
163 4 0.01
164 67 0.10
170 3 0.00
171 34 0.05
172 200 0.31
173 45 0.07
174 41 0.06
175 100 0.15
176 13 0.02
177 100 0.15
178 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (169 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTTTAATTCTGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
AGGTATTTTCAATTTCTGTTTTTTCCAATCTATATTTTC
Found at i:5236405 original size:89 final size:85
Alignment explanation
Indices: 5235812--5236826 Score: 1002
Period size: 89 Copynumber: 11.8 Consensus size: 85
5235802 AAAGAGAAAA
* * * **
5235812 AAAAAGTCAACTCATATTGTGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTAACTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
5235877 CTGTTTTTCAATTCT-GTTTTC
65 CTG-TTTTCAATTCTATTTTTC
* ** *
5235898 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGCTCACATACTGAGGTATCTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAAT
* *
5235962 TTCTATTTTTTTAATTC-ATGTTTTC
63 TTC--TGTTTTCAATTCTAT-TTTTC
5235987 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
5236052 CTGTTCTT-AATGTCTGTTTTT-
65 CTGTT-TTCAAT-TCTATTTTTC
*
5236073 --GAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
*
5236136 TGTTTTTTCCAA-TCTATATTTTT
66 TG--TTTT-CAATTCTAT-TTTTC
*
5236159 AAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTTCAATTT
1 AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
* *
5236224 TTGTTCTT-AATGTCTGTTTTT-
65 CTGTT-TTCAAT-TCTATTTTTC
* * *
5236245 --GAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGATGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
*
5236308 TGTTTTTTCCAATCTATATTTTTC
66 TG--TTTT-CAAT-TCTATTTTTC
* *
5236332 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTAATTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAAT
*
5236396 TTCTGTTTTCAATTTCTACTTTTC
63 TTCTGTTTTCAA-TTCTATTTTTC
*
5236420 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
5236485 TGTTTTTCAAATTCTACTTTGC
66 TG-TTTTC-AATTCTATTTTTC
* * * * *
5236507 AAAAAAATCAACTCATATTACGAGAGGTGAGTTGGGCCTCGGGGCACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
* *
5236572 TCT-ATTT---TTC-A-----A
64 TCTGTTTTCAATTCTATTTTTC
* * *
5236584 AAAAATCAATTCATATTGCGAGAGGTGAGTTGAGTCTCAGGACACGCTGAGGTATTTTCAAATTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
5236649 TGTTTTTAATTTCTACTTTTC
66 TGTTTTCAA-TTCTATTTTTC
* * * * *
5236670 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGGTCACATGAC-GAGGTACTTTCAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACG-CTGAGGTATTTTCAAT
** * * **
5236734 ACCTACTTTTCAAAT-TAAGTTTC
63 TTCT-GTTTTCAATTCTATTTTTC
* * *
5236757 AAAAAGACCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGATCACGCACTGAGTTATTTTCA
1 -AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA-CACG--CTGAGGTATTTTCA
5236821 ATTTCT
61 ATTTCT
5236827 TTATGTTATT
Statistics
Matches: 794, Mismatches: 75, Indels: 117
0.81 0.08 0.12
Matches are distributed among these distances:
75 58 0.07
76 3 0.00
80 3 0.00
81 1 0.00
82 1 0.00
83 126 0.16
84 11 0.01
85 40 0.05
86 89 0.11
87 61 0.08
88 118 0.15
89 220 0.28
90 37 0.05
91 26 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (85 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTTCAATTCTATTTTTC
Found at i:5236515 original size:177 final size:171
Alignment explanation
Indices: 5235811--5236826 Score: 1034
Period size: 172 Copynumber: 5.9 Consensus size: 171
5235801 AAAAGAGAAA
* * * *
5235811 AAAAAAGTCAACTCATATTGTGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTAACTTCAATT
1 AAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGACACGCTGAGGTAATTTCAATT
*
5235876 TCTGTTTTTCAA-TTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGC
64 TCTG-TTTT-AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-
** * * ** *
5235939 TCACATACTGAGGTATCTTCAATTTCTATTTTTTTAATTC-ATGTTTTC
126 --ACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAATTCTA-CTTTTC
*
5235987 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGACACGCTGAGGTAATTTCAATTT
* **
5236052 CTGTTCTTAATGTCTGTTTT--TGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
65 CTGTT-TTAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* * *
5236115 CGCTGAGGTATTTTCAATTTCTGTTTTTTCCAA-TCTATATTTTT
129 CGCTGAGGTATTTTCAATTTCTG-TTTTTCAAATTCTA-CTTTTC
* *
5236159 AAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TAGGACACGCTGAGGTAATTTCAATTT
* * ** *
5236224 TTGTTCTTAATGTCTGTTTT--TGAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACA
65 CTGTT-TTAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* * * *
5236287 CGCTGATGTATTTTCAATTTCTGTTTTTTCCAATCTATATTTTTC
129 CGCTGAGGTATTTTCAATTTCTG-TTTTTCAAAT-TCTACTTTTC
*
5236332 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTAATTTCAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGG---ACACGCTGAGGTAATTTCAAT
*
5236396 TTCTGTTTTCAATTTCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
63 TTCTGTTTT-AATTTCT-GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* *
5236461 ACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAATTCTACTTTGC
126 ACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAATTCTACTTTTC
* * * *
5236507 AAAAAAATCAACTCATATTACGAGAGGTGAGTTGGGCCTCGGGGCACGCTGAGGTAATTTCAATT
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGACACGCTGAGGTAATTTCAATT
*** * *
5236572 TC-----T-A-TT-T-TTCAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGTCTCAGGACA
64 TCTGTTTTAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* *
5236628 CGCTGAGGTATTTTCAAATTCTGTTTTT-AATTTCTACTTTTC
129 CGCTGAGGTATTTTCAATTTCTGTTTTTCAAATTCTACTTTTC
* * * *
5236670 -AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGGTCACATGAC-GAGGTACTTTCAA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGG--ACACG-CTGAGGTAATTTCAA
*** * * ** *
5236733 AACCTACTTTTCAAATTAAG-TTTCAAAAAGACCAACTCATATTGCGAGAGGTGAGTTGAGCCT-
62 TTTCT-GTTTT-AATTTCTGTTTTC-AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* *
5236796 TGGATCACGCACTGAGTTATTTTCAATTTCT
123 AGGA-CACG--CTGAGGTATTTTCAATTTCT
5236827 TTATGTTATT
Statistics
Matches: 732, Mismatches: 71, Indels: 73
0.84 0.08 0.08
Matches are distributed among these distances:
161 38 0.05
163 28 0.04
164 71 0.10
166 1 0.00
167 2 0.00
168 1 0.00
169 1 0.00
170 1 0.00
171 28 0.04
172 205 0.28
173 42 0.06
174 48 0.07
175 135 0.18
176 15 0.02
177 114 0.16
178 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (171 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGACACGCTGAGGTAATTTCAATTTC
TGTTTTAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
CTGAGGTATTTTCAATTTCTGTTTTTCAAATTCTACTTTTC
Found at i:5236606 original size:164 final size:159
Alignment explanation
Indices: 5236402--5236710 Score: 483
Period size: 164 Copynumber: 1.9 Consensus size: 159
5236392 CAATTTCTGT
5236402 TTTCAATTTCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
5236467 TGAGGTAATTTCAATTTCTGTTTTTCAAATTCTACTTTGCAAAAAAATCAACTCATATTACGAGA
66 TGAGGTAATTTCAAATTCTGTTTTT-AAATTCTACTTTGC--AAAAATCAACTCATATTACGAGA
* *
5236532 GGTGAGTTGGGCCTCGGGGCACGCTGAGGTAA
128 GATGAGTTGAGCCTCGGGGCACGCTGAGGTAA
* * *
5236564 TTTCAATTTCTATTTTTCAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGTCTCAGGACAC
1 TTTCAATTTCTACTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* * * *
5236629 GCTGAGGTATTTTCAAATTCTGTTTTTAATTTCTACTTTTCAAAAATCAACTCATATTGCGAGAG
64 GCTGAGGTAATTTCAAATTCTGTTTTTAAATTCTACTTTGCAAAAATCAACTCATATTACGAGAG
5236694 ATGAGTTGAGCCTCGGG
129 ATGAGTTGAGCCTCGGG
5236711 TCACATGACG
Statistics
Matches: 135, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
161 38 0.28
162 17 0.13
163 12 0.09
164 68 0.50
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (159 bp):
TTTCAATTTCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAATTTCAAATTCTGTTTTTAAATTCTACTTTGCAAAAATCAACTCATATTACGAGAGAT
GAGTTGAGCCTCGGGGCACGCTGAGGTAA
Found at i:5236612 original size:75 final size:75
Alignment explanation
Indices: 5236489--5236655 Score: 235
Period size: 75 Copynumber: 2.2 Consensus size: 75
5236479 AATTTCTGTT
* * * * *
5236489 TTTCAAATTCTACTTTGCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGGGCCTCGGGGCAC
1 TTTCAAATTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACAC
5236554 GCTGAGGTAA
66 GCTGAGGTAA
* * * *
5236564 TTTCAATTTCTATTTTTCAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGTCTCAGGACAC
1 TTTCAAATTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACAC
*
5236629 GCTGAGGTAT
66 GCTGAGGTAA
*
5236639 TTTCAAATTCTGTTTTT
1 TTTCAAATTCTATTTTT
5236656 AATTTCTACT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 80 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (75 bp):
TTTCAAATTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTAA
Found at i:5248846 original size:16 final size:14
Alignment explanation
Indices: 5248818--5248856 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
5248808 TTGAGTTAAG
*
5248818 AAATTATTTAATTGA
1 AAATTAATTAATT-A
5248833 AAATTTAATTAATTA
1 AAA-TTAATTAATTA
5248848 AAATTAATT
1 AAATTAATT
5248857 TAATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 7 0.32
16 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
AAATTAATTAATTA
Found at i:5248859 original size:15 final size:16
Alignment explanation
Indices: 5248818--5248860 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
5248808 TTGAGTTAAG
5248818 AAATT-ATTTAATTGA
1 AAATTAATTTAATTGA
5248833 AAATTTAA-TTAATT-A
1 AAA-TTAATTTAATTGA
5248848 AAATTAATTTAAT
1 AAATTAATTTAAT
5248861 AAATAATGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.16
15 12 0.48
16 8 0.32
17 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
AAATTAATTTAATTGA
Found at i:5250021 original size:33 final size:29
Alignment explanation
Indices: 5249958--5250022 Score: 76
Period size: 33 Copynumber: 2.1 Consensus size: 29
5249948 ATTAATGTTT
* *
5249958 TAAAATTTATTTTAATTTATAATTTCATA
1 TAAAATTTATTTTAATTTAAAATTTAATA
5249987 TAAATATTTATTATTAATTTTAAAATTTTAATA
1 TAAA-ATTTATT-TTAA-TTTAAAA-TTTAATA
5250020 TAA
1 TAA
5250023 TTATATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.13
30 7 0.23
31 4 0.13
32 6 0.20
33 9 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
TAAAATTTATTTTAATTTAAAATTTAATA
Found at i:5261865 original size:46 final size:46
Alignment explanation
Indices: 5261812--5261906 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
5261802 TTGGGTGAGA
*
5261812 AAGATGCATTGTTCTCTAGTGGCTGAAAGTTC-AGGAGAAACATATT
1 AAGATGCATTGTTCTCTAGTGGCTAAAAGTTCTA-GAGAAACATATT
*
5261858 AAGATGCATTTTTCTCTAGTGGCTAAAAGTTCTAGAGAAACATATT
1 AAGATGCATTGTTCTCTAGTGGCTAAAAGTTCTAGAGAAACATATT
5261904 AAG
1 AAG
5261907 GGTATGGAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (46 bp):
AAGATGCATTGTTCTCTAGTGGCTAAAAGTTCTAGAGAAACATATT
Found at i:5276011 original size:3 final size:3
Alignment explanation
Indices: 5276003--5276055 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
5275993 TATTTCCACT
* *
5276003 TTC TTC TTC GTT- TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC ATC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5276048 TTC TTC TT
1 TTC TTC TT
5276056 TGGCTTCTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5276062 original size:18 final size:18
Alignment explanation
Indices: 5276023--5276062 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5276013 TTTTCTTCTT
* **
5276023 CTTCTTCTTCTTCTTTTT
1 CTTCATCTTCTTCTTTGG
5276041 CTTCATCTTCTTCTTTGG
1 CTTCATCTTCTTCTTTGG
5276059 CTTC
1 CTTC
5276063 TCAATCTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.30, G:0.05, T:0.62
Consensus pattern (18 bp):
CTTCATCTTCTTCTTTGG
Found at i:5276540 original size:3 final size:3
Alignment explanation
Indices: 5276532--5276562 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5276522 TTCCTGTTAC
5276532 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
5276563 TGAAGAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:5276570 original size:3 final size:3
Alignment explanation
Indices: 5276564--5276591 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5276554 ATCATCATCT
5276564 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
5276592 CAGCTCCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5279774 original size:6 final size:6
Alignment explanation
Indices: 5279763--5279793 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5279753 GGCACAGTGT
5279763 GTAAAA GTAAAA GTAAAA GTAAAA GTAAAA G
1 GTAAAA GTAAAA GTAAAA GTAAAA GTAAAA G
5279794 GAGCAGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (6 bp):
GTAAAA
Found at i:5287682 original size:23 final size:22
Alignment explanation
Indices: 5287630--5287682 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
5287620 TCCACGTCTT
*
5287630 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
5287652 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
5287675 TTTCTTTT
1 TTTCTTTT
5287683 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:5290034 original size:4 final size:4
Alignment explanation
Indices: 5290025--5290056 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
5290015 TTAAACTAAG
5290025 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
5290057 AATAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:5290981 original size:22 final size:22
Alignment explanation
Indices: 5290956--5290999 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5290946 TAGTCTTATA
5290956 ATAACTTATTAATATAATAAAT
1 ATAACTTATTAATATAATAAAT
* * *
5290978 ATAATTTATTATTTTAATAAAT
1 ATAACTTATTAATATAATAAAT
5291000 TACTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAACTTATTAATATAATAAAT
Found at i:5291112 original size:15 final size:15
Alignment explanation
Indices: 5291078--5291148 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
5291068 ATATTATTGA
5291078 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
5291091 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
5291106 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
5291125 AAATATATTAATAAT
1 AAATATTTTAATAAT
*
5291140 AAATGTTTT
1 AAATATTTT
5291149 GTAGTTTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 18 0.40
16 2 0.04
17 4 0.09
18 1 0.02
19 10 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:5291625 original size:14 final size:13
Alignment explanation
Indices: 5291606--5291644 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
5291596 CTAGAAAAGT
5291606 AAATCATTTTCCAG
1 AAATCATTTTCC-G
*
5291620 AAATCATTTTTCG
1 AAATCATTTTCCG
5291633 AAAGTCATTTTC
1 AAA-TCATTTTC
5291645 AGTGAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (13 bp):
AAATCATTTTCCG
Found at i:5292114 original size:20 final size:20
Alignment explanation
Indices: 5292071--5292120 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5292061 TCGCACTACG
* *
5292071 GTGCCCCTGTTTGCACATTT
1 GTGCCCCTGTCTGCACATTA
5292091 GTGCCCCTGTCTGCAC-TTCA
1 GTGCCCCTGTCTGCACATT-A
*
5292111 GTGCTCCTGT
1 GTGCCCCTGT
5292121 TATGCATCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.08, C:0.34, G:0.22, T:0.36
Consensus pattern (20 bp):
GTGCCCCTGTCTGCACATTA
Found at i:5299686 original size:19 final size:18
Alignment explanation
Indices: 5299662--5299713 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 18
5299652 TTTTTTTAAA
5299662 CATATTTAATTTTA-T-T
1 CATATTTAATTTTATTAT
5299678 -ATATTT-ATTATTAATTAT
1 CATATTTAATT-TT-ATTAT
5299696 CATATTTAATTTTATTAT
1 CATATTTAATTTTATTAT
5299714 TAATTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.10
15 8 0.27
16 1 0.03
17 1 0.03
18 6 0.20
19 8 0.27
20 3 0.10
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (18 bp):
CATATTTAATTTTATTAT
Found at i:5299731 original size:29 final size:29
Alignment explanation
Indices: 5299663--5299731 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
5299653 TTTTTTAAAC
*
5299663 ATATTTAATTTTATTATATTTATTATTAA
1 ATATTTAATTTAATTATATTTATTATTAA
* * *
5299692 TTA-TCATATTTAATTTTA-TTATTAATTAA
1 ATATTTA-ATTTAATTATATTTATT-ATTAA
5299721 ATATTTAATTT
1 ATATTTAATTT
5299732 TTGAAAATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
28 7 0.23
29 22 0.71
30 2 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (29 bp):
ATATTTAATTTAATTATATTTATTATTAA
Found at i:5299733 original size:25 final size:25
Alignment explanation
Indices: 5299681--5299732 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
5299671 TTTTATTATA
*
5299681 TTTATTATTAATTATCATATTTAAT
1 TTTATTATTAATTATAATATTTAAT
5299706 TTTATTATTAATTA-AATATTTAAT
1 TTTATTATTAATTATAATATTTAAT
5299730 TTT
1 TTT
5299733 TGAAAATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATTATTAATTATAATATTTAAT
Found at i:5301893 original size:13 final size:13
Alignment explanation
Indices: 5301875--5301902 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5301865 AACTTCCACC
5301875 TCTTGCTTGTCTA
1 TCTTGCTTGTCTA
5301888 TCTTGCTTGTCTA
1 TCTTGCTTGTCTA
5301901 TC
1 TC
5301903 AAGAGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.25, G:0.14, T:0.54
Consensus pattern (13 bp):
TCTTGCTTGTCTA
Found at i:5314485 original size:38 final size:38
Alignment explanation
Indices: 5314434--5314510 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
5314424 CAGTCATGGC
*
5314434 AGTTTTTAATAGTAGAAGTGAAT-TAAATTTTTAAGAGA
1 AGTTTTTAATAGTAGAAATGAATGT-AATTTTTAAGAGA
*
5314472 AGTTTTTAATAGTAGAAATGAATGTAATTTTTAATAGA
1 AGTTTTTAATAGTAGAAATGAATGTAATTTTTAAGAGA
5314510 A
1 A
5314511 AGGGGCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 35 0.97
39 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (38 bp):
AGTTTTTAATAGTAGAAATGAATGTAATTTTTAAGAGA
Found at i:5314716 original size:5 final size:5
Alignment explanation
Indices: 5314706--5314731 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5314696 ACCTAAATAA
5314706 TGTAT TGTAT TGTAT TGTAT TGTAT T
1 TGTAT TGTAT TGTAT TGTAT TGTAT T
5314732 ACCATAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TGTAT
Found at i:5324962 original size:5 final size:5
Alignment explanation
Indices: 5324952--5324983 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5324942 CTCTGTGTGA
5324952 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
5324984 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:5329393 original size:5 final size:5
Alignment explanation
Indices: 5329383--5329414 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5329373 CAATTTGTGA
5329383 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
5329415 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:5329408 original size:9 final size:9
Alignment explanation
Indices: 5329384--5329414 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5329374 AATTTGTGAA
5329384 AAATAAAAT
1 AAATAAAAT
5329393 AAAATAAAAT
1 -AAATAAAAT
5329403 AAATAAAAT
1 AAATAAAAT
5329412 AAA
1 AAA
5329415 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5334540 original size:3 final size:3
Alignment explanation
Indices: 5334532--5334622 Score: 85
Period size: 3 Copynumber: 29.0 Consensus size: 3
5334522 ATTCAAACAC
* * *
5334532 TAT TAT TAT T-T CTAT TAT TGT CAT TAT TAC TAT TAT TGAAT TAT TGAAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT T--AT TAT T--AT
* *
5334581 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5334623 CTTAGCATTA
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
2 1 0.01
3 64 0.89
4 1 0.01
5 6 0.08
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:5334792 original size:20 final size:22
Alignment explanation
Indices: 5334755--5334803 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
5334745 AGTACTATTT
* *
5334755 TTATTACTATTACTATATTGTTA
1 TTATTACTA-TACTATATTATCA
5334778 TTATTACTA-AC-ATATTATCA
1 TTATTACTATACTATATTATCA
5334798 TTATTA
1 TTATTA
5334804 TAGTATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.54
21 2 0.08
23 9 0.38
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTACTATACTATATTATCA
Found at i:5336216 original size:20 final size:21
Alignment explanation
Indices: 5336188--5336226 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5336178 TCGTTATTAT
*
5336188 TATTATTAGTA-TATTTTTAC
1 TATTATTAGAATTATTTTTAC
*
5336208 TATTCTTAGAATTATTTTT
1 TATTATTAGAATTATTTTT
5336227 TAGTTTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (21 bp):
TATTATTAGAATTATTTTTAC
Found at i:5339939 original size:15 final size:14
Alignment explanation
Indices: 5339919--5339961 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
5339909 TCCAATATTC
5339919 AAAATAATTCAAATA
1 AAAATAATT-AAATA
*
5339934 AAAATATAATAAATA
1 AAAATA-ATTAAATA
*
5339949 CAAATAATTAAAT
1 AAAATAATTAAAT
5339962 TTTAACAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.25
15 16 0.67
16 2 0.08
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATAATTAAATA
Found at i:5343275 original size:21 final size:21
Alignment explanation
Indices: 5343236--5343276 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5343226 ATCTGCTCAA
* * *
5343236 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTAGAGTAC
5343257 ACTCCACCTGCTGTAGAGTA
1 ACTCCACCTGCTGTAGAGTA
5343277 TTGCTCGTTT
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:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTAGAGTAC
Found at i:5348022 original size:34 final size:35
Alignment explanation
Indices: 5347984--5348049 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 35
5347974 TATTATTTTA
* *
5347984 TTTTCCTTACGTTATTATTA-TATCGTATCATCTT
1 TTTTCCTTACATTATTATTATTATCATATCATCTT
* **
5348018 TTTTCGTTTTATTATTATTATTATCATATCAT
1 TTTTCCTTACATTATTATTATTATCATATCAT
5348050 TATTATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
34 16 0.62
35 10 0.38
ACGTcount: A:0.23, C:0.14, G:0.05, T:0.59
Consensus pattern (35 bp):
TTTTCCTTACATTATTATTATTATCATATCATCTT
Found at i:5348034 original size:3 final size:3
Alignment explanation
Indices: 5348026--5348168 Score: 53
Period size: 3 Copynumber: 47.0 Consensus size: 3
5348016 TTTTTTCGTT
* * * **
5348026 TTA TTA TTA TTA TTA TCA -TA TCA TTA TTA TTT TTCA TGTA CACA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA -TTA TTA
* * * * *
5348073 TT- TATA TTAA TT- TTA TGA TTA TTA TT- GTA TTTA TTT TTA CTA CTA
1 TTA T-TA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * * *
5348118 TTA TTA -TA TTTA TTA TTA GTA TTA GTA TTA GTA TTA TAA TTA CTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5348163 TTA TTA
1 TTA TTA
5348169 CTGTTGACGC
Statistics
Matches: 100, Mismatches: 28, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
2 7 0.07
3 81 0.81
4 11 0.11
5 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:5348146 original size:24 final size:24
Alignment explanation
Indices: 5348069--5348168 Score: 89
Period size: 24 Copynumber: 4.2 Consensus size: 24
5348059 TCATGTACAC
*
5348069 ATTATTTATATTAATT-TTA-TGATT
1 ATTA-TTATATTTATTATTACT-ATT
* * *
5348093 ATTATTGTATTTATTTTTACTACT
1 ATTATTATATTTATTATTACTATT
*
5348117 ATTATTATATTTATTATTAGTATT
1 ATTATTATATTTATTATTACTATT
* *
5348141 AGTATTAGTA-TTATAATTACTATT
1 ATTATTA-TATTTATTATTACTATT
5348165 ATTA
1 ATTA
5348169 CTGTTGACGC
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
23 9 0.15
24 50 0.81
25 3 0.05
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (24 bp):
ATTATTATATTTATTATTACTATT
Found at i:5349470 original size:14 final size:12
Alignment explanation
Indices: 5349458--5349503 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
5349448 CACGTATATG
5349458 TATATAAAAATA
1 TATATAAAAATA
5349470 TATATAAAAATTA
1 TATATAAAAA-TA
*
5349483 TAAAATATAAAATA
1 T-ATATA-AAAATA
5349497 TATATAA
1 TATATAA
5349504 GTATGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 7 0.24
15 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:5349517 original size:27 final size:26
Alignment explanation
Indices: 5349458--5349520 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
5349448 CACGTATATG
5349458 TATATA-AAAATATATATAAAAATTA
1 TATATATAAAATATATATAAAAATTA
* **
5349483 TAAAATATAAAATATATATAAGTATGTA
1 T-ATATATAAAATATATATAAAAAT-TA
5349511 TATATATAAA
1 TATATATAAA
5349521 TGAGGAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.13
27 23 0.74
28 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
TATATATAAAATATATATAAAAATTA
Found at i:5351669 original size:85 final size:85
Alignment explanation
Indices: 5351393--5351883 Score: 793
Period size: 85 Copynumber: 5.7 Consensus size: 85
5351383 CACTCGAGAG
* *
5351393 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTCAA
1 AGGCAAGGC-TTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTTAA
* *
5351458 CCAGCTCCACTGCAACCGATGG
64 CCAGCTCCACTGCAACCAATGA
* * *
5351480 AGGCAAGGCTTTGTTTTTCGATCTACTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTCA
1 AGGCAAGGC-TTG-TTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTTA
*
5351545 ACCAGCTCCACTGTAACCAATGA
63 ACCAGCTCCACTGCAACCAATGA
* *
5351568 AGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTACTTCTTTAACC
1 AGGCAAGGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACC
5351633 AGCTCCACTGCAACCAATGA
66 AGCTCCACTGCAACCAATGA
5351653 AGGCAAGGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACC
1 AGGCAAGGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACC
*
5351718 AGCTCCACTGTAACCAATGA
66 AGCTCCACTGCAACCAATGA
* * * *
5351738 AGGCAATGCTTGTTTTCGATCTGCTTCGCTGTTAACACAGGAAGACAAGATCTACTTCTTTAACC
1 AGGCAAGGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACC
5351803 AGCTCCACTGCAACCAATGA
66 AGCTCCACTGCAACCAATGA
5351823 AGGCAAGGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTGTCTT
1 AGGCAAGGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTT
5351884 CACTGATCTG
Statistics
Matches: 378, Mismatches: 24, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
85 241 0.64
86 45 0.12
87 16 0.04
88 76 0.20
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (85 bp):
AGGCAAGGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACC
AGCTCCACTGCAACCAATGA
Found at i:5352960 original size:21 final size:21
Alignment explanation
Indices: 5352934--5352980 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5352924 GGTATAGCAG
*
5352934 GATCACCACATGCCCCAATCT
1 GATCACCACATACCCCAATCT
** *
5352955 GATCACTTCATACCCCATTCT
1 GATCACCACATACCCCAATCT
5352976 GATCA
1 GATCA
5352981 ATATTTGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.26
Consensus pattern (21 bp):
GATCACCACATACCCCAATCT
Found at i:5356603 original size:19 final size:20
Alignment explanation
Indices: 5356574--5356622 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5356564 CACTTCGTGA
* *
5356574 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
5356593 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
5356613 AAATG-AATGC
1 AAATGTAATGC
5356623 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:5358953 original size:14 final size:12
Alignment explanation
Indices: 5358941--5358986 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
5358931 CACGTATATG
5358941 TATATAAAAATA
1 TATATAAAAATA
5358953 TATATAAAAATTA
1 TATATAAAAA-TA
*
5358966 TAAAATATAAAATA
1 T-ATATA-AAAATA
5358980 TATATAA
1 TATATAA
5358987 GTATGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 7 0.24
15 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:5359000 original size:27 final size:26
Alignment explanation
Indices: 5358941--5359003 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
5358931 CACGTATATG
5358941 TATATA-AAAATATATATAAAAATTA
1 TATATATAAAATATATATAAAAATTA
* **
5358966 TAAAATATAAAATATATATAAGTATGTA
1 T-ATATATAAAATATATATAAAAAT-TA
5358994 TATATATAAA
1 TATATATAAA
5359004 TGAGGAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.13
27 23 0.74
28 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
TATATATAAAATATATATAAAAATTA
Found at i:5359616 original size:63 final size:63
Alignment explanation
Indices: 5359529--5359653 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
5359519 TTTGGATTGC
5359529 CATAGCGCCGCCGCGCCACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAAA
1 CATAGCGCCGCCGCGCCACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAAA
* *
5359592 CATAGCGCCGCCGTGCTACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAA
1 CATAGCGCCGCCGCGCCACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAA
5359654 GCGCCAGATC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.17, C:0.50, G:0.26, T:0.08
Consensus pattern (63 bp):
CATAGCGCCGCCGCGCCACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAAA
Found at i:5359680 original size:82 final size:82
Alignment explanation
Indices: 5359592--5359754 Score: 308
Period size: 82 Copynumber: 2.0 Consensus size: 82
5359582 GCCGACGAAA
* *
5359592 CATAGCGCCGCCGTGCTACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAAGCG
1 CATAGCGCCGCCGCGCCACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAAGCG
5359657 CCAGATCGGCGTTTGAC
66 CCAGATCGGCGTTTGAC
5359674 CATAGCGCCGCCGCGCCACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAAGCG
1 CATAGCGCCGCCGCGCCACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAAGCG
5359739 CCAGATCGGCGTTTGA
66 CCAGATCGGCGTTTGA
5359755 AACTCCGTCA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.16, C:0.45, G:0.28, T:0.11
Consensus pattern (82 bp):
CATAGCGCCGCCGCGCCACCGCTGCGCCCGCCGCACCACCACCGTCTCCGACGGCCGACGAAGCG
CCAGATCGGCGTTTGAC
Found at i:5362627 original size:37 final size:37
Alignment explanation
Indices: 5362574--5362652 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 37
5362564 CTTAAATCTG
* *
5362574 TTTAAAAATAAATTCACTTACAATGTTCCTGGTGCT-T
1 TTTATAAATAAATTCACTTACAATGTTCATGGTG-TGT
5362611 TTTATAAATAAATTCACTTACAATGTTCATGGTGTGT
1 TTTATAAATAAATTCACTTACAATGTTCATGGTGTGT
5362648 TTTAT
1 TTTAT
5362653 CTCTAGCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 38 0.97
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTATAAATAAATTCACTTACAATGTTCATGGTGTGT
Found at i:5369973 original size:31 final size:31
Alignment explanation
Indices: 5369935--5369996 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
5369925 TTTTATTTAA
5369935 CCCAACAGTTTACGATGCCTTACCAACATAC
1 CCCAACAGTTTACGATGCCTTACCAACATAC
5369966 CCCAACAGTTTACGATGCCTTACCAACATAC
1 CCCAACAGTTTACGATGCCTTACCAACATAC
5369997 TCAAACTTAC
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:0.32, C:0.35, G:0.10, T:0.23
Consensus pattern (31 bp):
CCCAACAGTTTACGATGCCTTACCAACATAC
Found at i:5373015 original size:28 final size:29
Alignment explanation
Indices: 5372958--5373015 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
5372948 ATTAGTCTGG
* **
5372958 TTATCAAAAACAGAAGTATCAAAAGTTTT
1 TTATCAAAAACAGAAGCATCAAAAAATTT
5372987 TTATCAAAAA-AGAAAGCA-CAAAAAATTT
1 TTATCAAAAACAG-AAGCATCAAAAAATTT
5373015 T
1 T
5373016 GGAACCAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.28
Consensus pattern (29 bp):
TTATCAAAAACAGAAGCATCAAAAAATTT
Found at i:5390698 original size:54 final size:53
Alignment explanation
Indices: 5390634--5390763 Score: 145
Period size: 53 Copynumber: 2.4 Consensus size: 53
5390624 TAGTCCCTGA
* * * *
5390634 CTAGGTCTTACACTATGTGGTCTTCGTATTCCCATATGATGTCAT-GCCAAACAG
1 CTAGGCCTTACACTATATGGTCTTCAT-TTCCCATATGATGCCATAG-CAAACAG
* * * **
5390688 CTAGGCCTTACACTATATGGTATTCATTTTCCTTATGATGCCATAGCAAATGG
1 CTAGGCCTTACACTATATGGTCTTCATTTCCCATATGATGCCATAGCAAACAG
*
5390741 CTAGGCCTTACACAATATGGTCT
1 CTAGGCCTTACACTATATGGTCT
5390764 ACTTACCATG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
53 40 0.62
54 24 0.38
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (53 bp):
CTAGGCCTTACACTATATGGTCTTCATTTCCCATATGATGCCATAGCAAACAG
Found at i:5391203 original size:104 final size:104
Alignment explanation
Indices: 5391023--5391238 Score: 299
Period size: 104 Copynumber: 2.1 Consensus size: 104
5391013 GGGCAGTTTA
* * *
5391023 AACCTCAGATTCTTTACCTAGCCAGACACTGCAGCCTCCTTTTTCCCTCGATAGACAGAAAAATT
1 AACCTCAGATTCTTTACCTAACCAAACACTACAGCCTCCTTTTTCCCTCGATAGACAGAAAAATT
*
5391088 TCATTAAAACTCATTCAAGTAATCATTATCATCACTTTT
66 TCATTAAAACTCATTCAAGTAATCATTACCATCACTTTT
* * * * * *
5391127 AACCTTAGATTCTTTGCCTAACCAAACACTACAGCCTCCTTTTTCCCTTGATAGATAGATACATT
1 AACCTCAGATTCTTTACCTAACCAAACACTACAGCCTCCTTTTTCCCTCGATAGACAGAAAAATT
** * *
5391192 TCATTAAAACTCATTCGGGTAATCCTTGCCATCACTTTT
66 TCATTAAAACTCATTCAAGTAATCATTACCATCACTTTT
5391231 AACC-CAGA
1 AACCTCAGA
5391239 CATAGCTTCA
Statistics
Matches: 97, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
103 3 0.03
104 94 0.97
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (104 bp):
AACCTCAGATTCTTTACCTAACCAAACACTACAGCCTCCTTTTTCCCTCGATAGACAGAAAAATT
TCATTAAAACTCATTCAAGTAATCATTACCATCACTTTT
Found at i:5391428 original size:21 final size:21
Alignment explanation
Indices: 5391404--5391446 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5391394 AACCCTTTCC
*
5391404 TAACTTAACCTAAGTATTCTT
1 TAACTTAACCCAAGTATTCTT
*
5391425 TAACTTAACCCAAGTCTTCTT
1 TAACTTAACCCAAGTATTCTT
5391446 T
1 T
5391447 GGAACTGGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (21 bp):
TAACTTAACCCAAGTATTCTT
Found at i:5394130 original size:46 final size:46
Alignment explanation
Indices: 5394078--5394437 Score: 506
Period size: 46 Copynumber: 7.8 Consensus size: 46
5394068 AGTGTGCTCT
* *
5394078 CTGATATGGAATGTGTAAGACAATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
5394124 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
5394170 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
5394216 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
5394262 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
5394308 CTGACATGAAATGAGTAAGACCATGGTTGAAAGGTACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** **
5394354 ATGATGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
5394401 ATGACA-GAAAATGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
5394438 TATGACATCA
Statistics
Matches: 289, Mismatches: 24, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
46 249 0.86
47 40 0.14
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:5401130 original size:18 final size:19
Alignment explanation
Indices: 5401107--5401143 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
5401097 TATTCGTATC
5401107 TATTGTTGAAA-ATGAAAT
1 TATTGTTGAAATATGAAAT
5401125 TATTGTTGAAATATGAAAT
1 TATTGTTGAAATATGAAAT
5401144 CAAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (19 bp):
TATTGTTGAAATATGAAAT
Found at i:5401404 original size:101 final size:101
Alignment explanation
Indices: 5401222--5401409 Score: 286
Period size: 101 Copynumber: 1.9 Consensus size: 101
5401212 GAGTGTAAGG
* * * * *
5401222 CCATGGTTGGACCATGGTAGTATTTATATGTAAGACCATAGCTGGGCTATGGCATTTTAATGAAA
1 CCATGGTTAGACCATGGCAGTATCTATATGTAAAACCATAGCTGGGCTATGGCATTCTAATGAAA
5401287 AGACCATAACTAGGTTATGGCACCTTAAACGTAAAA
66 AGACCATAACTAGGTTATGGCACCTTAAACGTAAAA
* * *
5401323 CCATGGTTAGACCATGGCAGTATCTATATGTAAAACCGTAGCTGGGCTATGGCATTCTGATGATA
1 CCATGGTTAGACCATGGCAGTATCTATATGTAAAACCATAGCTGGGCTATGGCATTCTAATGAAA
* *
5401388 AGACCATAATTGGGTTATGGCA
66 AGACCATAACTAGGTTATGGCA
5401410 TTACGAATGT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 77 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (101 bp):
CCATGGTTAGACCATGGCAGTATCTATATGTAAAACCATAGCTGGGCTATGGCATTCTAATGAAA
AGACCATAACTAGGTTATGGCACCTTAAACGTAAAA
Found at i:5401408 original size:33 final size:33
Alignment explanation
Indices: 5401365--5401427 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5401355 AAACCGTAGC
5401365 TGGGCTATGGCATT-CTG-ATGATAAGACCATAAT
1 TGGGCTATGGCATTAC-GAATG-TAAGACCATAAT
*
5401398 TGGGTTATGGCATTACGAATGTAAGACCAT
1 TGGGCTATGGCATTACGAATGTAAGACCAT
5401428 GGCAGGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (33 bp):
TGGGCTATGGCATTACGAATGTAAGACCATAAT
Found at i:5401427 original size:101 final size:100
Alignment explanation
Indices: 5401215--5401429 Score: 279
Period size: 101 Copynumber: 2.1 Consensus size: 100
5401205 ATGAATTGAG
* * * * * *
5401215 TGTAAGGCCATGGTTGGACCATGGTAGTATTTATATGTAAGACCATAGCTGGGCTATGGCATTTT
1 TGTAAGACCATGGTTAGACCATGGCAGTATCTATATGTAAAACCATAGCTGGGCTATGGCATTCT
5401280 AATGAAAAGACCATAACTAGGTTATGGCACCTTAAA
66 AATGAAAAGACCATAACTAGGTTATGGCA-CTTAAA
* * *
5401316 CGTAAAACCATGGTTAGACCATGGCAGTATCTATATGTAAAACCGTAGCTGGGCTATGGCATTCT
1 TGTAAGACCATGGTTAGACCATGGCAGTATCTATATGTAAAACCATAGCTGGGCTATGGCATTCT
* * * *
5401381 GATGATAAGACCATAATTGGGTTATGGCA-TTACGAA
66 AATGAAAAGACCATAACTAGGTTATGGCACTTA--AA
5401417 TGTAAGACCATGG
1 TGTAAGACCATGG
5401430 CAGGGCCATG
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
99 3 0.03
101 94 0.97
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (100 bp):
TGTAAGACCATGGTTAGACCATGGCAGTATCTATATGTAAAACCATAGCTGGGCTATGGCATTCT
AATGAAAAGACCATAACTAGGTTATGGCACTTAAA
Found at i:5404401 original size:35 final size:34
Alignment explanation
Indices: 5404344--5404504 Score: 112
Period size: 35 Copynumber: 4.7 Consensus size: 34
5404334 GAATTGAGCT
* * *
5404344 TAAGACCATGGTTGGACCATGGCAGTATTTATATG
1 TAAGACCATAGTTGGGCTATGGCA-TATTTATATG
*
5404379 TAAGACCATAGCTGGGCTATGGCAT-TTTA-ATG
1 TAAGACCATAGTTGGGCTATGGCATATTTATATG
* * *** * ** * *
5404411 AAAAGACCGTAACCGGGTTATGGCA-CCTTAAACG
1 -TAAGACCATAGTTGGGCTATGGCATATTTATATG
* * * *
5404445 TAAGACCATGGTTGGACCATGGCAGTATCTATATG
1 TAAGACCATAGTTGGGCTATGGCA-TATTTATATG
5404480 TAAGACCATAGTTGGGCTATGGCAT
1 TAAGACCATAGTTGGGCTATGGCAT
5404505 TCTGATGACA
Statistics
Matches: 93, Mismatches: 28, Indels: 11
0.70 0.21 0.08
Matches are distributed among these distances:
32 3 0.03
33 41 0.44
34 4 0.04
35 45 0.48
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (34 bp):
TAAGACCATAGTTGGGCTATGGCATATTTATATG
Found at i:5404519 original size:101 final size:100
Alignment explanation
Indices: 5404344--5404602 Score: 317
Period size: 101 Copynumber: 2.6 Consensus size: 100
5404334 GAATTGAGCT
* * *
5404344 TAAGACCATGGTTGGACCATGGCAGTATTTATATGTAAGACCATAGCTGGGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAGTATCTATATGTAAGACCATAGTTGGGCTATGGCATTCTAA
*
5404409 TGAAAAGACCGTAACCGGGTTATGGCACCTTA-AACG
66 TGAAAAGACCATAACCGGGTTATGGCA-C-TACAACG
*
5404445 TAAGACCATGGTTGGACCATGGCAGTATCTATATGTAAGACCATAGTTGGGCTATGGCATTCTGA
1 TAAGACCATGGTTGGACCATGGCAGTATCTATATGTAAGACCATAGTTGGGCTATGGCATTCTAA
* ** *
5404510 TGACAAGACCATAATTGGGTTATGGCACTACGAATG
66 TGAAAAGACCATAACCGGGTTATGGCACTAC-AACG
* ** * * ** *
5404546 TAAGACCACGGCAGGGCCATGGCAATA-C-ACGTGTAAGACCATAGTTGGACTATGGCA
1 TAAGACCATGGTTGGACCATGGCAGTATCTATATGTAAGACCATAGTTGGGCTATGGCA
5404603 CAAGAAAAAT
Statistics
Matches: 139, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
99 28 0.20
100 2 0.01
101 109 0.78
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (100 bp):
TAAGACCATGGTTGGACCATGGCAGTATCTATATGTAAGACCATAGTTGGGCTATGGCATTCTAA
TGAAAAGACCATAACCGGGTTATGGCACTACAACG
Found at i:5404551 original size:33 final size:32
Alignment explanation
Indices: 5404477--5404553 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
5404467 CAGTATCTAT
* *
5404477 ATGTAAGACCATAGTTGGGCTATGGCATTCTG
1 ATGTAAGACCATAATTGGGCTATGGCATACTG
* *
5404509 ATGACAAGACCATAATTGGGTTATGGCACTAC-G
1 ATG-TAAGACCATAATTGGGCTATGGCA-TACTG
5404542 AATGTAAGACCA
1 -ATGTAAGACCA
5404554 CGGCAGGGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
32 3 0.08
33 29 0.78
34 5 0.14
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (32 bp):
ATGTAAGACCATAATTGGGCTATGGCATACTG
Found at i:5408084 original size:21 final size:21
Alignment explanation
Indices: 5408059--5408100 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5408049 AATAAATGCT
5408059 AAAACTCTAA-ATTCTAAACTC
1 AAAAC-CTAAGATTCTAAACTC
5408080 AAAACCTAAGATTCTAAACTC
1 AAAACCTAAGATTCTAAACTC
5408101 TTAAATCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAACCTAAGATTCTAAACTC
Found at i:5408165 original size:23 final size:23
Alignment explanation
Indices: 5408138--5408200 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 23
5408128 CTTAAATCCG
5408138 ATAATTATTAATATTTA-GTTATA
1 ATAATTATTAATATTTATGTT-TA
5408161 ATAATTA-TAA-A-TTATGTTTA
1 ATAATTATTAATATTTATGTTTA
5408181 ACTAAAATTATTAATATTTA
1 A-T--AATTATTAATATTTA
5408201 ATTTTAGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
20 6 0.18
21 5 0.15
22 3 0.09
23 12 0.36
24 3 0.09
25 1 0.03
26 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (23 bp):
ATAATTATTAATATTTATGTTTA
Found at i:5420431 original size:40 final size:40
Alignment explanation
Indices: 5420387--5420560 Score: 249
Period size: 40 Copynumber: 4.3 Consensus size: 40
5420377 GCGCTAATCC
5420387 GATAAACCGACAATATCAAATGTGGGCCCAGCACTAGTTG
1 GATAAACCGACAATATCAAATGTGGGCCCAGCACTAGTTG
5420427 GATAAACCGACAATATCAAATGTGGGCCCAGCACTAGTTG
1 GATAAACCGACAATATCAAATGTGGGCCCAGCACTAGTTG
* * * **
5420467 GATAAACCTACAATATCAAATGTGTGCCCATCACTAGTCA
1 GATAAACCGACAATATCAAATGTGGGCCCAGCACTAGTTG
* * * * * *
5420507 GATAAGCCGACAACATCAAATATGTGCCCAGCAGTAGTGG
1 GATAAACCGACAATATCAAATGTGGGCCCAGCACTAGTTG
5420547 GATAAACCGACAAT
1 GATAAACCGACAAT
5420561 TACATATGTA
Statistics
Matches: 119, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 119 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (40 bp):
GATAAACCGACAATATCAAATGTGGGCCCAGCACTAGTTG
Found at i:5437629 original size:25 final size:25
Alignment explanation
Indices: 5437587--5437637 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5437577 TTCAATTTCA
* *
5437587 AAAAATTATTTTATTTATTGAACTAT
1 AAAAATTATTATAATTATT-AACTAT
5437613 AAAAATT-TTATAATTATTAACTAT
1 AAAAATTATTATAATTATTAACTAT
5437637 A
1 A
5437638 TTAAACAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 9 0.39
26 7 0.30
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (25 bp):
AAAAATTATTATAATTATTAACTAT
Found at i:5438917 original size:136 final size:136
Alignment explanation
Indices: 5438672--5438939 Score: 455
Period size: 136 Copynumber: 2.0 Consensus size: 136
5438662 TATTTACTCT
* *
5438672 CCCTCATGAAAACATCACATGCTTCCTCATATTCTACATATTCAATCTTGAATACTAATATTTCA
1 CCCTCATGAAAACATCACATACTTCCTCATATTCTACATATTCAATCTTGAACACTAATATTTCA
5438737 AATGACTATTTGAATGTATTTGCTAAGCATTTATATCACCATTCTTTTGAAAGTCATGAGGAAGG
66 AATGACTATTTGAATGTATTTGCTAAGCATTTATATCACCATTCTTTTGAAAGTCATGAGGAAGG
5438802 GGCTCC
131 GGCTCC
* * * * *
5438808 CCCTCATGAAAACATTACATACTTTCTCATATTCTACGTATTCAATCTTGAACACTAGTCTTTCA
1 CCCTCATGAAAACATCACATACTTCCTCATATTCTACATATTCAATCTTGAACACTAATATTTCA
* *
5438873 AATGACTATTTGAATGTATTTGCTAAGCATTTATATCACTATTCTTTTGAAAGTCATGAGTAAGG
66 AATGACTATTTGAATGTATTTGCTAAGCATTTATATCACCATTCTTTTGAAAGTCATGAGGAAGG
5438938 GG
131 GG
5438940 AATTTTTGGG
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
136 123 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (136 bp):
CCCTCATGAAAACATCACATACTTCCTCATATTCTACATATTCAATCTTGAACACTAATATTTCA
AATGACTATTTGAATGTATTTGCTAAGCATTTATATCACCATTCTTTTGAAAGTCATGAGGAAGG
GGCTCC
Found at i:5446089 original size:10 final size:9
Alignment explanation
Indices: 5446076--5446150 Score: 53
Period size: 10 Copynumber: 7.8 Consensus size: 9
5446066 ATTTTAATTT
5446076 TTTTTCTAAA
1 TTTTT-TAAA
5446086 TTTTTTAAA
1 TTTTTTAAA
*
5446095 TGATTTTTGAA
1 T--TTTTTAAA
5446106 -TTTTTAAA
1 TTTTTTAAA
* *
5446114 TAATTTAAATA
1 T-TTTTTAA-A
5446125 TTTTTTATAA
1 TTTTTTA-AA
*
5446135 TTTTTTTAA
1 TTTTTTAAA
5446144 TTTTTTA
1 TTTTTTA
5446151 CAAAATTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
8 7 0.14
9 13 0.25
10 21 0.41
11 10 0.20
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:5450620 original size:21 final size:20
Alignment explanation
Indices: 5450582--5450620 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5450572 TTTACTAAAT
*
5450582 TAAATATATATTTCAAATAG
1 TAAATATATATTTAAAATAG
*
5450602 TAAATTATATGTTTAAAAT
1 TAAA-TATATATTTAAAAT
5450621 GCATTATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (20 bp):
TAAATATATATTTAAAATAG
Found at i:5451416 original size:70 final size:70
Alignment explanation
Indices: 5451327--5451474 Score: 210
Period size: 70 Copynumber: 2.1 Consensus size: 70
5451317 TCCTAAAATC
* * *
5451327 AAAAAACAACATGCATATGAATGAGCCA-TAAAAAAAT-AATTTGTTGAAAATTAATAGACTTAA
1 AAAAAAAAACATGCATATGAATGAGCCATTAAAAAAATAAATTT-TT-AAAATTAAAAGACATAA
5451390 TCATTAA
64 TCATTAA
*
5451397 AAAAAAAAACATGCATATGAATGAGCCATTAAAAAAATAAATTTTTAAAATTAAAAGACATAGTC
1 AAAAAAAAACATGCATATGAATGAGCCATTAAAAAAATAAATTTTTAAAATTAAAAGACATAATC
*
5451462 ATTAC
66 ATTAA
*
5451467 AATAAAAA
1 AAAAAAAA
5451475 TAAAAGATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
70 54 0.77
71 11 0.16
72 5 0.07
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (70 bp):
AAAAAAAAACATGCATATGAATGAGCCATTAAAAAAATAAATTTTTAAAATTAAAAGACATAATC
ATTAA
Found at i:5452880 original size:40 final size:40
Alignment explanation
Indices: 5452825--5452902 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
5452815 ATGGAACTCT
5452825 ATCTAAATTGGCAAAATAACTTATTTGCTTGAGTATCTGC
1 ATCTAAATTGGCAAAATAACTTATTTGCTTGAGTATCTGC
5452865 ATCTAAATTGGCAAAATAACTTATTTGCTTGAGTATCT
1 ATCTAAATTGGCAAAATAACTTATTTGCTTGAGTATCT
5452903 ACAGTGTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (40 bp):
ATCTAAATTGGCAAAATAACTTATTTGCTTGAGTATCTGC
Found at i:5455379 original size:24 final size:24
Alignment explanation
Indices: 5455349--5455434 Score: 69
Period size: 24 Copynumber: 3.8 Consensus size: 24
5455339 AATAATAATT
5455349 TTATATTAA-AATTATTATTAAAAA
1 TTATATTAATAA-TATTATTAAAAA
*
5455373 TTATATTAATAATGTTATT--AAA
1 TTATATTAATAATATTATTAAAAA
* *
5455395 TTATA-T-ATTATTTTATT--AAA
1 TTATATTAATAATATTATTAAAAA
5455415 TTATATTTAATAATAATTAT
1 TTATA-TTAATAAT-ATTAT
5455435 GTTAAAATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
20 17 0.33
21 1 0.02
22 9 0.17
23 4 0.08
24 19 0.37
25 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (24 bp):
TTATATTAATAATATTATTAAAAA
Found at i:5455659 original size:44 final size:46
Alignment explanation
Indices: 5455590--5455682 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 46
5455580 TTACAACATT
5455590 ATTCCATTCAACCAAACACAAGAATT-CT-ATTACAGCTCTACTCC
1 ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTACTCC
* *** * *
5455634 ATTCCATTCAACTAAACAGTTGAATTACTGATTACAGCTTTATTCC
1 ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTACTCC
5455680 ATT
1 ATT
5455683 ACAGCTCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 22 0.54
45 2 0.05
46 17 0.41
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.33
Consensus pattern (46 bp):
ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTACTCC
Found at i:5455685 original size:16 final size:16
Alignment explanation
Indices: 5455664--5455734 Score: 99
Period size: 16 Copynumber: 4.4 Consensus size: 16
5455654 TGAATTACTG
*
5455664 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
5455680 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
5455696 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
5455712 ATTACAAC-CTTATTCC
1 ATTACAGCTC-TATTCC
5455728 ATTACAG
1 ATTACAG
5455735 TGAACTAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
15 1 0.02
16 48 0.98
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:5456479 original size:10 final size:9
Alignment explanation
Indices: 5456453--5456543 Score: 53
Period size: 10 Copynumber: 9.6 Consensus size: 9
5456443 ATTACAAAGA
5456453 AAAT-TTAT
1 AAATATTAT
5456461 AAA-ATTAT
1 AAATATTAT
5456469 ACAATATTAT
1 A-AATATTAT
*
5456479 AAGATATTTTT
1 AA-ATA-TTAT
5456490 AAATATTAT
1 AAATATTAT
*
5456499 AAAATGTTAT
1 -AAATATTAT
*
5456509 AAA-AATAT
1 AAATATTAT
5456517 GAAAATATTATAT
1 --AAATA-T-TAT
*
5456530 AAATACTAT
1 AAATATTAT
5456539 AAATA
1 AAATA
5456544 AATTTAGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 21
0.70 0.08 0.23
Matches are distributed among these distances:
8 11 0.17
9 17 0.26
10 23 0.35
11 11 0.17
13 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (9 bp):
AAATATTAT
Found at i:5456516 original size:21 final size:20
Alignment explanation
Indices: 5456490--5456591 Score: 70
Period size: 19 Copynumber: 5.2 Consensus size: 20
5456480 AGATATTTTT
*
5456490 AAATATTATAAAATGTTATAA
1 AAATA-TATAAAATATTATAA
* *
5456511 AAATAT-GAAAATATTATAT
1 AAATATATAAAATATTATAA
* *
5456530 AAATACTATAAATAAATT-TAG
1 AAATA-TATAAA-ATATTATAA
*
5456551 AAAT-TATAGAATATT-TCAA
1 AAATATATAAAATATTAT-AA
*
5456570 AAATATATAAAA-ACTATAA
1 AAATATATAAAATATTATAA
5456589 AAA
1 AAA
5456592 AAAAGTTATT
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
18 5 0.08
19 32 0.50
20 9 0.14
21 14 0.22
22 4 0.06
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATATATAAAATATTATAA
Done.