Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015153.1 Kokia drynarioides strain JFW-HI SEQ_130197, whole genome shotgun sequence
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: 800050
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 392 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:332178 original size:89 final size:88
Alignment explanation
Indices: 331891--332251 Score: 370
Period size: 89 Copynumber: 4.0 Consensus size: 88
331881 CCTAATAGAT
* *
331891 CCCTAAAC-TTTCCAAAAATCATATTTTAACCCTTAAACTTCTCTAAAATTATATTTTAACCCTT
1 CCCTAAACTTTTCC-AAAATCATATTTTAACCC-TAAACTTTTC-AAAATTACATTTTAACCCTT
* *
331955 AAA-TAATTCTAAAATTACATTTTAAC
63 AAACT-TTTCCAAAATTACATTTTAAC
* * *
331981 CCTTCAAACTTTTCTAAAAT--TGAATTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCT
1 CCCT-AAACTTTTCCAAAATCAT-ATTTTAA-CCCTAAACTTTT-CAAAATTACATTTTAACCCT
* *
332044 TAAACTTTTCTAAAATTACATTTCAAC
62 TAAACTTTTCCAAAATTACATTTTAAC
* * * * * * * *
332071 CCTTAAAATTTTCTAAAATTACATTTTAACACCTAAACTTTTCTAAATTGCATTTCAACCCTTAA
1 CCCTAAACTTTTCCAAAATCATATTTTAAC-CCTAAACTTTTCAAAATTACATTTTAACCCTTAA
332136 ACTTTTCCAAAATTACATTTTAAC
65 ACTTTTCCAAAATTACATTTTAAC
* * * * * **
332160 CCCTAAACTTCTCCAAAATCATATTTTTATCCTTAAACCTTCCAAAATTACATTTTAACCCTCGA
1 CCCTAAACTTTTCCAAAATCATA-TTTTAACCCTAAACTTTTCAAAATTACATTTTAACCCTTAA
* *
332225 ACTTCTCCAAAATCACATTTTAAC
65 ACTTTTCCAAAATTACATTTTAAC
332249 CCC
1 CCC
332252 GTATTCTCCA
Statistics
Matches: 229, Mismatches: 32, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
89 126 0.55
90 85 0.37
91 14 0.06
92 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (88 bp):
CCCTAAACTTTTCCAAAATCATATTTTAACCCTAAACTTTTCAAAATTACATTTTAACCCTTAAA
CTTTTCCAAAATTACATTTTAAC
Found at i:333617 original size:38 final size:41
Alignment explanation
Indices: 333564--333640 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 41
333554 TTTTAAATAT
333564 AATATATA-TTCTTT-TATATTTGAAAGTGTACCGTATCTA
1 AATATATATTTCTTTATATATTTGAAAGTGTACCGTATCTA
*
333603 AATA-ATATTTTTTTATATATTTGAAAGTGTACCGTATC
1 AATATATATTTCTTTATATATTTGAAAGTGTACCGTATC
333641 CAAAATTATC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 3 0.09
39 9 0.26
40 23 0.66
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (41 bp):
AATATATATTTCTTTATATATTTGAAAGTGTACCGTATCTA
Found at i:334830 original size:19 final size:19
Alignment explanation
Indices: 334806--334871 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 19
334796 TATATTTTTT
334806 TCAT-AAAAATGATTAAAAA
1 TCATAAAAAAT-ATTAAAAA
334825 TCATAAAAAATATTAAAAAAA
1 TCATAAAAAATATT--AAAAA
*
334846 TCAGAAAAAAT-TATAAAAA
1 TCATAAAAAATAT-TAAAAA
334865 T-ATAAAA
1 TCATAAAA
334872 TGTATTACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 5 0.12
19 13 0.32
20 7 0.17
21 16 0.39
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (19 bp):
TCATAAAAAATATTAAAAA
Found at i:334844 original size:21 final size:20
Alignment explanation
Indices: 334820--334871 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
334810 AAAAATGATT
334820 AAAAATCATAAAAAATATTAA
1 AAAAATCATAAAAAA-ATTAA
* *
334841 AAAAATCA-GAAAAAATTAT
1 AAAAATCATAAAAAAATTAA
334860 AAAAAT-ATAAAA
1 AAAAATCATAAAA
334872 TGTATTACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 13 0.48
20 5 0.19
21 8 0.30
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAAATCATAAAAAAATTAA
Found at i:334967 original size:46 final size:47
Alignment explanation
Indices: 334909--335104 Score: 142
Period size: 47 Copynumber: 4.1 Consensus size: 47
334899 TGATATGACT
*
334909 TATAAATATTA-TAAAATGTTATAAATATTATAAAAATATAAAAAATC
1 TATAAA-ATTATTAAAATGTTATAAATATAATAAAAATATAAAAAATC
* * * *
334956 TA-ATAAATTA-TAAAA-ATTATAAGAT-TAATAAAATATATTTAAAATTT
1 TATA-AAATTATTAAAATGTTATAA-ATATAATAAAA-ATA-TAAAAAATC
** *
335003 TATAACAACGAATTAAAAT-TCTATAAAAATAATAAAAATATAAAAAAT-
1 TATAA-AA-TTATTAAAATGT-TATAAATATAATAAAAATATAAAAAATC
*
335051 TATAAAATTATTAAAATTGCTATAAACT-T-ATAAAAATTATAAAAAATC
1 TATAAAATTATTAAAA-TGTTATAAA-TATAATAAAAA-TATAAAAAATC
335099 -ATAAAA
1 TATAAAA
335105 ACATAAACTG
Statistics
Matches: 119, Mismatches: 14, Indels: 32
0.72 0.08 0.19
Matches are distributed among these distances:
45 13 0.11
46 29 0.24
47 39 0.33
48 8 0.07
49 7 0.06
50 10 0.08
51 13 0.11
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (47 bp):
TATAAAATTATTAAAATGTTATAAATATAATAAAAATATAAAAAATC
Found at i:335076 original size:20 final size:20
Alignment explanation
Indices: 335034--335088 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
335024 TATAAAAATA
* *
335034 ATAAAAATATAAAAAAT--T
1 ATAAAATTATAAAAATTGCT
*
335052 ATAAAATTATTAAAATTGCT
1 ATAAAATTATAAAAATTGCT
*
335072 ATAAACTTATAAAAATT
1 ATAAAATTATAAAAATT
335089 ATAAAAAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 14 0.47
20 16 0.53
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAATTATAAAAATTGCT
Found at i:335092 original size:9 final size:9
Alignment explanation
Indices: 334908--335105 Score: 100
Period size: 9 Copynumber: 21.0 Consensus size: 9
334898 TTGATATGAC
*
334908 TTATAAATA
1 TTATAAAAA
*
334917 TTATAAAATG
1 TTATAAAA-A
*
334927 TTATAAATA
1 TTATAAAAA
334936 TTATAAAAA
1 TTATAAAAA
334945 -TATAAAAA
1 TTATAAAAA
* *
334953 ATCTAATAAA
1 TTATAA-AAA
334963 TTATAAAAA
1 TTATAAAAA
*
334972 TTAT-AAGA
1 TTATAAAAA
334980 TTAATAAAATA
1 TT-ATAAAA-A
* *
334991 TATTTAAAATT
1 T-TATAAAA-A
335002 TTATAACAACGA
1 TTATAA-AA--A
* *
335014 AT-TAAAAT
1 TTATAAAAA
335022 TCTATAAAAA
1 T-TATAAAAA
*
335032 TAATAAAAA
1 TTATAAAAA
335041 -TATAAAAAA
1 TTAT-AAAAA
335050 TTAT-AAAA
1 TTATAAAAA
*
335058 TTATTAAAA
1 TTATAAAAA
* *
335067 TTGCTATAAAC
1 TT-ATA-AAAA
335078 TTATAAAAA
1 TTATAAAAA
335087 TTATAAAAAA
1 TTAT-AAAAA
*
335097 TCATAAAAA
1 TTATAAAAA
335106 CATAAACTGG
Statistics
Matches: 145, Mismatches: 27, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
8 23 0.16
9 59 0.41
10 42 0.29
11 19 0.13
12 2 0.01
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:335103 original size:47 final size:46
Alignment explanation
Indices: 334910--335104 Score: 132
Period size: 46 Copynumber: 4.1 Consensus size: 46
334900 GATATGACTT
* *
334910 ATAAATATTA-TAAAATGT-TATAAATATTATAAAAATATAAAAAATC
1 ATAAA-ATTATTAAAAT-TCTATAAAAATAATAAAAATATAAAAAATC
* * * ** *
334956 -TAATAAATTA-TAAAAAT-TATAAGATTAATAAAATATATTTAAAATTTT
1 AT-A-AAATTATTAAAATTCTATAAAAATAATAAAA-ATA--TAAAAAATC
** *
335004 ATAACAACGAATTAAAATTCTATAAAAATAATAAAAATATAAAAAATT
1 ATAA-AA-TTATTAAAATTCTATAAAAATAATAAAAATATAAAAAATC
* *
335052 ATAAAATTATTAAAATTGCTAT-AAACTTATAAAAATTATAAAAAATC
1 ATAAAATTATTAAAATT-CTATAAAAATAATAAAAA-TATAAAAAATC
335099 ATAAAA
1 ATAAAA
335105 ACATAAACTG
Statistics
Matches: 117, Mismatches: 20, Indels: 23
0.73 0.12 0.14
Matches are distributed among these distances:
45 14 0.12
46 33 0.28
47 25 0.21
48 20 0.17
49 2 0.02
50 9 0.08
51 14 0.12
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (46 bp):
ATAAAATTATTAAAATTCTATAAAAATAATAAAAATATAAAAAATC
Found at i:335704 original size:20 final size:21
Alignment explanation
Indices: 335668--335709 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
335658 ACAATTTTTA
335668 TAATTTTAATAAGTTT-ATAT
1 TAATTTTAATAAGTTTAATAT
**
335688 TAATTTTAATATTTTTAATAT
1 TAATTTTAATAAGTTTAATAT
335709 T
1 T
335710 TAATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATTTTAATAAGTTTAATAT
Found at i:335713 original size:16 final size:15
Alignment explanation
Indices: 335687--335716 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
335677 TAAGTTTATA
335687 TTAATTTTAATATTT
1 TTAATTTTAATATTT
335702 TTAATATTTAATATT
1 TTAAT-TTTAATATT
335717 ATTTTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAATTTTAATATTT
Found at i:335715 original size:28 final size:29
Alignment explanation
Indices: 335660--335731 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
335650 TAGTTTTTAC
*
335660 AATTTTTATAATTTTAATAAGTTTATATT
1 AATTTTTATATTTTTAATAAGTTTATATT
*
335689 AATTTTAATATTTTTAAT-A-TTTAATATT
1 AATTTTTATATTTTTAATAAGTTT-ATATT
335717 -ATTTTTATAATTTTT
1 AATTTTTAT-ATTTTT
335732 TATGATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 10 0.26
28 12 0.32
29 16 0.42
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (29 bp):
AATTTTTATATTTTTAATAAGTTTATATT
Found at i:335731 original size:9 final size:9
Alignment explanation
Indices: 335653--335746 Score: 59
Period size: 9 Copynumber: 10.2 Consensus size: 9
335643 AATGTATTAG
*
335653 TTTTTACAA
1 TTTTTATAA
335662 TTTTTATAA
1 TTTTTATAA
*
335671 TTTTAATAA
1 TTTTTATAA
*
335680 GTTTATATTAA
1 -TTTTTA-TAA
*
335691 TTTTAAT-A
1 TTTTTATAA
335699 TTTTTA-ATA
1 TTTTTATA-A
* *
335708 TTTAATATTA
1 TTT-TTATAA
335718 TTTTTATAA
1 TTTTTATAA
*
335727 TTTTTTATGA
1 -TTTTTATAA
335737 TTTTT-TAA
1 TTTTTATAA
335745 TT
1 TT
335747 ATTTTATGGG
Statistics
Matches: 65, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
8 10 0.15
9 30 0.46
10 22 0.34
11 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:335739 original size:19 final size:19
Alignment explanation
Indices: 335699--335754 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
335689 AATTTTAATA
*
335699 TTTTTAA-TATTTAATATTAT
1 TTTTTAATTATTT--TATGAT
335719 TTTTATAATT-TTTTATGAT
1 TTTT-TAATTATTTTATGAT
335738 TTTTTAATTATTTTATG
1 TTTTTAATTATTTTATG
335755 GGAAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.16
19 16 0.50
20 4 0.12
21 6 0.19
22 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (19 bp):
TTTTTAATTATTTTATGAT
Found at i:336109 original size:72 final size:72
Alignment explanation
Indices: 336028--336172 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
336018 TATGACATGA
336028 AACAACATTAGCAAGTTTAATATTTATTTATATTAAAAAAAAGTTTAATATTTATTTAAGGGAGT
1 AACAACATTAGCAAGTTTAATATTTATTTATATTAAAAAAAAGTTTAATATTTATTTAAGGGAGT
336093 AATTAGT
66 AATTAGT
336100 AACAACATTAGCAAGTTTAATATTTATTTATATTAAAAAAAAGTTTAATATTTATTTAAGGGAGT
1 AACAACATTAGCAAGTTTAATATTTATTTATATTAAAAAAAAGTTTAATATTTATTTAAGGGAGT
336165 AATTAGT
66 AATTAGT
336172 A
1 A
336173 TTGAATTTAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (72 bp):
AACAACATTAGCAAGTTTAATATTTATTTATATTAAAAAAAAGTTTAATATTTATTTAAGGGAGT
AATTAGT
Found at i:339798 original size:26 final size:26
Alignment explanation
Indices: 339769--339822 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
339759 ATTGTAAAAT
339769 GATTTTTGATAATTTTCAAAGTTAAG
1 GATTTTTGATAATTTTCAAAGTTAAG
339795 GATTTTTGATAATTTTCAAAGTTAAG
1 GATTTTTGATAATTTTCAAAGTTAAG
339821 GA
1 GA
339823 CCTATTTGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (26 bp):
GATTTTTGATAATTTTCAAAGTTAAG
Found at i:340036 original size:2 final size:2
Alignment explanation
Indices: 340029--340059 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
340019 TGTATATGTC
*
340029 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
340060 TAAATTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:341073 original size:21 final size:21
Alignment explanation
Indices: 341047--341089 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
341037 TGTTAGTGGA
341047 ATAGATGTTTAGATTCTAACT
1 ATAGATGTTTAGATTCTAACT
341068 ATAGATGTTTAGATTCTAACT
1 ATAGATGTTTAGATTCTAACT
341089 A
1 A
341090 AAATACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (21 bp):
ATAGATGTTTAGATTCTAACT
Found at i:341515 original size:54 final size:54
Alignment explanation
Indices: 341415--341538 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
341405 TGCAATATTC
* ** *
341415 ACACAGTCTGAGACATAGGTTAGGACATGGCCGTGAGTCTCGAGTCAGAGAGTT
1 ACACAGTCTGAGACACAGGTTAGGACACAGCCGTGAGTCTCAAGTCAGAGAGTT
* *
341469 ACACAGTCTGAGACACCGGTTAGGACACAGTCGTGTA-TCTCAAGTCAGAGAGTT
1 ACACAGTCTGAGACACAGGTTAGGACACAGCCGTG-AGTCTCAAGTCAGAGAGTT
* * *
341523 GCACAGTTTGACACAC
1 ACACAGTCTGAGACAC
341539 GGGCAGGGAC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
54 59 0.98
55 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (54 bp):
ACACAGTCTGAGACACAGGTTAGGACACAGCCGTGAGTCTCAAGTCAGAGAGTT
Found at i:341549 original size:54 final size:54
Alignment explanation
Indices: 341452--341558 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
341442 TGGCCGTGAG
* * **
341452 TCTCGAGTCAGAGAGTTACACAGTCTGAGACACCGGTTAGGACAC-AGTCGTGTA
1 TCTCAAGTCAGAGAGTTACACAGTCTGACACACCGGGCAGGACACGA-TCGTGTA
* *
341506 TCTCAAGTCAGAGAGTTGCACAGTTTGACACA-CGGGCAGGGACACGATCGTGT
1 TCTCAAGTCAGAGAGTTACACAGTCTGACACACCGGGCA-GGACACGATCGTGT
341559 GTCCCTACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 4 0.09
54 40 0.89
55 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (54 bp):
TCTCAAGTCAGAGAGTTACACAGTCTGACACACCGGGCAGGACACGATCGTGTA
Found at i:344466 original size:94 final size:94
Alignment explanation
Indices: 344302--344524 Score: 294
Period size: 94 Copynumber: 2.4 Consensus size: 94
344292 TTTGCATATT
* *
344302 CTCGTCAGCTTAGTGTGAGCAGCATC--AT--TAGGGAACAATTATATGTATAGATATCGTATCG
1 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTA-GTAACAATTATATGTACAGATATCGTATCG
344363 ATGGCTGAGGTACCGCATATGCTACGAGTC
65 ATGGCTGAGGTACCGCATATGCTACGAGTC
* *
344393 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTAGTAACAGTTATATGTACAGATA-CTGTATCT
1 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTAGTAACAATTATATGTACAGATATC-GTATCG
* * *
344457 ATTGCTGAGGTACCGCCTATGTTACGAGTC
65 ATGGCTGAGGTACCGCATATGCTACGAGTC
* * * *
344487 CTCATCAACTTAGTGTGAGCAACATCGTATACTGGTAA
1 CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTAGTAA
344525 TAGAGACAAT
Statistics
Matches: 116, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
91 26 0.22
93 3 0.03
94 85 0.73
95 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (94 bp):
CTCGTCAGCTTAGTGTGAGCAGCATCGTATACTAGTAACAATTATATGTACAGATATCGTATCGA
TGGCTGAGGTACCGCATATGCTACGAGTC
Found at i:349704 original size:94 final size:94
Alignment explanation
Indices: 349535--349771 Score: 284
Period size: 94 Copynumber: 2.6 Consensus size: 94
349525 GCATATTCTT
* * * * * *
349535 GTCAGCTTAGTGTGAGCAACATCG-CTA--GGGAACAATTATATATATAGATACTGTATCGATGG
1 GTCAGCTTAATGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACTGTATCGATGG
* *
349597 CTGAGGTAACGCATATGTTACGAGT-CCTC
66 CTCAAGTAACGCATATGTTACGAGTACC-C
** * *
349626 GTCAGCTTAATGTGAGCAGCATCGTATACTGGTAACGGTTATATGTACAGATATTGTATTGATGG
1 GTCAGCTTAATGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACTGTATCGATGG
* *
349691 CTCAAGTACCGCATATGTTGCGAGTACCC
66 CTCAAGTAACGCATATGTTACGAGTACCC
* * *
349720 GTTAGCTTAGTGTGAGTAGCATCGTATACTGGTAACAATTATATGTACAGAT
1 GTCAGCTTAATGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGAT
349772 TGAGGTACCG
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
91 22 0.18
92 2 0.02
94 97 0.79
95 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (94 bp):
GTCAGCTTAATGTGAGCAGCATCGTATACTGGTAACAATTATATGTACAGATACTGTATCGATGG
CTCAAGTAACGCATATGTTACGAGTACCC
Found at i:352515 original size:70 final size:68
Alignment explanation
Indices: 352372--352559 Score: 164
Period size: 70 Copynumber: 2.7 Consensus size: 68
352362 GCGTTGCATC
* * * * *
352372 ATCAACATGGCGGGAAAAAATTTGCAACCTCAACATGGTGAGAGGAAGGCCTATTTCCAACTCTG
1 ATCAACATGGCAGGAAAAAATTTGCAACTTCAACATGGTGAGAGG-AGGACTATCTCAAACTCTG
*
352437 CACC
65 CACA
* * * *
352441 ATCAACGTGGCAGGAAAAACCTTTGCAACTTCAACATGGTGAGAGGAGGAACT-GCTCTAAACTT
1 ATCAACATGGCAGGAAAAA-ATTTGCAACTTCAACATGGTGAGAGGAGG-ACTATCTC-AAACTC
*
352505 TGTACA
63 TGCACA
* ** * *
352511 ATCAACATGGTAGGAAGAAGTTTTGCACCCTT-AACATGGTGAAAGGAGG
1 ATCAACATGGCAGGAA-AAAATTTGCA-ACTTCAACATGGTGAGAGGAGG
352560 GGTCATTCTG
Statistics
Matches: 97, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
69 22 0.23
70 70 0.72
71 5 0.05
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (68 bp):
ATCAACATGGCAGGAAAAAATTTGCAACTTCAACATGGTGAGAGGAGGACTATCTCAAACTCTGC
ACA
Found at i:352635 original size:69 final size:70
Alignment explanation
Indices: 352511--352664 Score: 211
Period size: 69 Copynumber: 2.2 Consensus size: 70
352501 ACTTTGTACA
* * * ** * * *
352511 ATCAACATGGTAGGAAGAAGTTTTGCACCCTTAACATGGTGAAAGGAGGGGTCATTCTGAATTTT
1 ATCAACATGGCAGAAAAAAGTTTTGCACCCCCAACATGGCGAAAGGAGAGCTCATTCTGAATTTT
*
352576 TTACC
66 TCACC
*
352581 ATCAACATGGCAGAAAAAAG-TTTGCACCCCCAACATGGCGAGAGGAGAGCTCATTCTGAATTTT
1 ATCAACATGGCAGAAAAAAGTTTTGCACCCCCAACATGGCGAAAGGAGAGCTCATTCTGAATTTT
352645 TCACC
66 TCACC
352650 ATCAACATGGCAGAA
1 ATCAACATGGCAGAA
352665 GAGTTCAGAT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
69 57 0.77
70 17 0.23
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (70 bp):
ATCAACATGGCAGAAAAAAGTTTTGCACCCCCAACATGGCGAAAGGAGAGCTCATTCTGAATTTT
TCACC
Found at i:353992 original size:6 final size:6
Alignment explanation
Indices: 353981--354005 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
353971 GTAAAATAAA
353981 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
354006 GGGTATTGTA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:362631 original size:955 final size:951
Alignment explanation
Indices: 360786--362696 Score: 3026
Period size: 955 Copynumber: 2.0 Consensus size: 951
360776 ACCAACAAGG
* *
360786 TAAATAGCACCATTTGCAGATAAGTTAGACGGCAGCTGGGAGAAATATCTACCCTTAGTAGAGTT
1 TAAATAGCACCATTTGCAGATAAGTTAGACGGCAACTGAGAGAAATATCTACCCTTAGTAGAGTT
* *
360851 TGCTTATAGTAACAGTTATCAGTCCAGTATATAAATGGCACCATTTGAAGCACTTTATGGTAGAA
66 TGCTTATAATAACAGTTATCAGTCCAGTATATAAATGACACCATTTGAAGCACTTTATGGTAGAA
* *
360916 AATACAGAACACCTTTATACTGGTCAGAGTTGAGTGAACCGAAGCTAGTAGTGATTTGATCCATG
131 AATACAGAACACCTTTATACTGGTCAGAGTTGAGTGAACCGAAGCTAGTAGTGATCTAATCCATG
** * *
360981 AGACGAAAGATAAAGTTTAAGTAATTCTTGACTGCTTAAAAGCCGCATCTGACCGACAAAGATCT
196 AGACGAAAGATAAAGTTTAAGTAATTCGCGACTACTTAAAAGCCACATCTGACCGACAAAGATCT
* *
361046 TATGCAAATCTCAAAAGGAAAGATATAGAATTCATTGTCGAAGATAGAGTTTTTTTTAGAGTTTC
261 TATGCAAATCTCAAAAGGAAAGATATAGAATTCACTGTCGAAGATAGAGTTTTTTTTAGAGCTTC
* * *
361111 GCCTTGGAAGAAAGTGTTACGTTTTGGCTGGAAAGGAAAGTTGAGTCCGCGATTTATTAAACCGT
326 GCCTTAGAAGAAAGTGTTAAGTTTTGGCTAGAAAGGAAAGTTGAGTCCGCGATTTATTAAACCGT
* *
361176 ATGAAATCCTTAAGAGAGTAGGACCTGTAGCTTATAAGCTGGCTTTACCACCGGAACTGGAACAG
391 ATGAAATCCTTAAGAGAGTAGGACCTATAGCTTATAAGCTGGCTTTACCACCAGAACTGGAACAG
*
361241 ATTCATAATGTGTTTCATGTCTCGATGCTGAGACAGTACAGATCAGACCCTTCCCATGTGATTAC
456 ATTCATAATGTGTTTCATGTCTCGATGCTGAGACAGAACAGATCAGACCCTTCCCATGTGATTAC
*
361306 ACCTTATGAGGTTGAGATACAGTCGAATTTGACCTATTCAGAAGAACTAGTTAAGATTCTAGCTC
521 ACCTTATGAGGTTGAGATACAGTCGAATTTGACCTATTCAGAAGAACGAGTTAAGATTCTAGCTC
* * *
361371 TAAAGTGAAAAAGTTACGAAACAAACGAGTACCACTAGTAATGGTTTTCTGAAATCGACACGGGG
586 AAAAGTGAAAAAGTTACGAAACAAACGAGTACCACTAGAAAAGGTTTTCTGAAATCGACACGGGG
* * *
361436 TAGAGGAAGCAACATGGGAGATAGAGGCATCAATGAAATCACAGTACCATAATCTACTCACTAGT
651 TAGAGGAAGCAACATAGGAGATAGAGGCATCAATGAAATCACAGCACCATAATCTACTCACTAAT
361501 AAAAAATTTCAGGACGAAATTTCCCTAAGAGGAAGAGTTGTAACAATCCAATTTTTAGTAGTGTC
716 AAAAAATTTCAGGACGAAATTTCCCTAAGAGGAAGAGTTGTAACAATCCAATTTTTAGTAGTGTC
*
361566 GAAAATAGTGGTTTCGGGACCACAACTCCGACGAGTCGAGCTAAAATTTTCTTTATTTTAATATT
781 GAAAATAGTGGTTTCGGGACCACAACTCCGACGAGTCGAGCTAAAACTTTCTTTATTTTAATATT
*
361631 TATGATGTCATTAGCATTACATTAAAATTTGGATAAGAAATTTTAATGTCTAGTTAGTGAATTGA
846 TATGATGTCATTAGCATTACATTAAAATTTGGATAAGAAATTTTAATGTCTAGATAGTGAATTGA
* *
361696 GTAGAATGATTGAATCATAAAAGGTATTAAAGTAGAGTTGA
911 GTAGAAGGACTGAATCATAAAAGGTATTAAAGTAGAGTTGA
* *
361737 TAAATAGCACCATTTGCAGATAAGTTTGATGGCAACTGAGAGAAATATCTACCCTTAGTAGAGTT
1 TAAATAGCACCATTTGCAGATAAGTTAGACGGCAACTGAGAGAAATATCTACCCTTAGTAGAGTT
*
361802 TGCTTATAATAACAGTTATCAGTTCAGTAT-TAAAATGACACCATTTGAAGCACTTTATGGTAGA
66 TGCTTATAATAACAGTTATCAGTCCAGTATAT-AAATGACACCATTTGAAGCACTTTATGGTAGA
* * *
361866 AAATGCAGAACACCTTTATACTGGTCAGAGTTGAGTGAACTGAAGCTGGTTGAGACTGATCTAAT
130 AAATACAGAACACCTTTATACTGGTCAGAGTTGAGTGAACCGAAGCTAG-T-AG--TGATCTAAT
* * *
361931 CCATGAGATGGAAGATAAAGTTTAAGTAATTCGCGACTACTTAAAAGCCATATCTGACCGACAGA
191 CCATGAGACGAAAGATAAAGTTTAAGTAATTCGCGACTACTTAAAAGCCACATCTGACCGACA-A
*
361996 A-ATCTTATGCAGATCTCAAAAGGAAAGATATAGAATTCACTGTCGAAGATCA-AGTTTTTTTTA
255 AGATCTTATGCAAATCTCAAAAGGAAAGATATAGAATTCACTGTCGAAGAT-AGAGTTTTTTTTA
* * *
362059 GAGCTTCGCCTTAGAAGAAGGTGTTAAGTTTTGGCTAGAAA-GAAAGTTGAGTCTGCGTTTTATT
319 GAGCTTCGCCTTAGAAGAAAGTGTTAAGTTTTGGCTAGAAAGGAAAGTTGAGTCCGCGATTTATT
** * * * * *
362123 GGACCGTATGAAATCCTTGAGAGAGTAGGTCCTATAGCTTATAAGTTGTCTTTACCACCAGAATT
384 AAACCGTATGAAATCCTTAAGAGAGTAGGACCTATAGCTTATAAGCTGGCTTTACCACCAGAACT
**
362188 GGAACAGATTCATAATGTGTTTCATGTCTCGATGCTGAGATGGAACAGATCAGACCCTTCCCATG
449 GGAACAGATTCATAATGTGTTTCATGTCTCGATGCTGAGACAGAACAGATCAGACCCTTCCCATG
* * *
362253 TGATTACACCTTGTGAGGTTGAGATACAGTCGGATTTGACGTATTCAGAAGAACCGA-TTAAGAT
514 TGATTACACCTTATGAGGTTGAGATACAGTCGAATTTGACCTATTCAGAAGAA-CGAGTTAAGAT
* ** * * *
362317 TCTAGCTCAAGAAGTGAAAGAGTTACGAAACAAACGAGTACCGTTGGAAAAGGTTTTGTGGAATC
578 TCTAGCTCAA-AAGTGAAAAAGTTACGAAACAAACGAGTACCACTAGAAAAGGTTTTCTGAAATC
**
362382 GACGTGGGGTAGAGGAAGCAACATAGGAGATAGAGGCATCAATGAAATCACAGCATCC-TAATCT
642 GACACGGGGTAGAGGAAGCAACATAGGAGATAGAGGCATCAATGAAATCACAGCA-CCATAATCT
* * *
362446 ACTCACTAATAAGAAATTTC-GAGACGAAATTTCCCTAAGGGGAAGAGTTGTAACAATCCGATTT
706 ACTCACTAATAAAAAATTTCAG-GACGAAATTTCCCTAAGAGGAAGAGTTGTAACAATCCAATTT
* * * *
362510 TTAGTGGTGTCGAGAATAGTGGTTTTGGGACCACAACTCCGACGAGTCGAGCTAAAACTTTGTTT
770 TTAGTAGTGTCGAAAATAGTGGTTTCGGGACCACAACTCCGACGAGTCGAGCTAAAACTTTCTTT
* *
362575 ATTTTAATATTTATGATGTCATTAGCATTACATTAAAATTTGGATAATAAATTTTAATGTTTAGA
835 ATTTTAATATTTATGATGTCATTAGCATTACATTAAAATTTGGATAAGAAATTTTAATGTCTAGA
*
362640 TAGTGAATTGAGTAGAAGGACTGAATCGTAAAAGGTATTAAAGTAGAGTTGA
900 TAGTGAATTGAGTAGAAGGACTGAATCATAAAAGGTATTAAAGTAGAGTTGA
362692 TAAAT
1 TAAAT
362697 TAGAAGGACT
Statistics
Matches: 877, Mismatches: 72, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
950 1 0.00
951 166 0.19
952 1 0.00
953 2 0.00
954 206 0.23
955 496 0.57
956 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (951 bp):
TAAATAGCACCATTTGCAGATAAGTTAGACGGCAACTGAGAGAAATATCTACCCTTAGTAGAGTT
TGCTTATAATAACAGTTATCAGTCCAGTATATAAATGACACCATTTGAAGCACTTTATGGTAGAA
AATACAGAACACCTTTATACTGGTCAGAGTTGAGTGAACCGAAGCTAGTAGTGATCTAATCCATG
AGACGAAAGATAAAGTTTAAGTAATTCGCGACTACTTAAAAGCCACATCTGACCGACAAAGATCT
TATGCAAATCTCAAAAGGAAAGATATAGAATTCACTGTCGAAGATAGAGTTTTTTTTAGAGCTTC
GCCTTAGAAGAAAGTGTTAAGTTTTGGCTAGAAAGGAAAGTTGAGTCCGCGATTTATTAAACCGT
ATGAAATCCTTAAGAGAGTAGGACCTATAGCTTATAAGCTGGCTTTACCACCAGAACTGGAACAG
ATTCATAATGTGTTTCATGTCTCGATGCTGAGACAGAACAGATCAGACCCTTCCCATGTGATTAC
ACCTTATGAGGTTGAGATACAGTCGAATTTGACCTATTCAGAAGAACGAGTTAAGATTCTAGCTC
AAAAGTGAAAAAGTTACGAAACAAACGAGTACCACTAGAAAAGGTTTTCTGAAATCGACACGGGG
TAGAGGAAGCAACATAGGAGATAGAGGCATCAATGAAATCACAGCACCATAATCTACTCACTAAT
AAAAAATTTCAGGACGAAATTTCCCTAAGAGGAAGAGTTGTAACAATCCAATTTTTAGTAGTGTC
GAAAATAGTGGTTTCGGGACCACAACTCCGACGAGTCGAGCTAAAACTTTCTTTATTTTAATATT
TATGATGTCATTAGCATTACATTAAAATTTGGATAAGAAATTTTAATGTCTAGATAGTGAATTGA
GTAGAAGGACTGAATCATAAAAGGTATTAAAGTAGAGTTGA
Found at i:363651 original size:18 final size:18
Alignment explanation
Indices: 363630--363671 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
363620 AGGCTCGTTT
363630 GAGCATAAT-GACTCGTAA
1 GAGCATAATAG-CTCGTAA
*
363648 GAGCATACTAGCTCGTAA
1 GAGCATAATAGCTCGTAA
363666 GAGCAT
1 GAGCAT
363672 TATTGGATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (18 bp):
GAGCATAATAGCTCGTAA
Found at i:365803 original size:11 final size:11
Alignment explanation
Indices: 365789--365864 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
365779 GAAAATTATT
365789 TTAATATTAAA
1 TTAATATTAAA
365800 TTAATA--AAA
1 TTAATATTAAA
*
365809 -TATTATTAAA
1 TTAATATTAAA
*
365819 ATAAGTATTAAA
1 TTAA-TATTAAA
365831 TTTAAT-TTAATA
1 -TTAATATTAA-A
365843 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
365856 ATAATATTA
1 TTAATATTA
365865 TTTTTGGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 19 0.37
12 13 0.25
13 6 0.12
14 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:368872 original size:5 final size:6
Alignment explanation
Indices: 368857--368889 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
368847 ATGGCATATA
*
368857 AAAAAC AAAAAC AAAAAC -AAAAC AAAAAG AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
368890 TGAAGGGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:369161 original size:18 final size:18
Alignment explanation
Indices: 369138--369180 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
369128 GAATATGTTT
369138 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
369156 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
369174 TTAATTA
1 TTAATTA
369181 TATCTTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:374868 original size:16 final size:16
Alignment explanation
Indices: 374847--374903 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
374837 ATTAAATTAA
374847 TAATTAAATTATTTTT
1 TAATTAAATTATTTTT
*
374863 TAATTAAATAATTTTT
1 TAATTAAATTATTTTT
* *
374879 TCAATTCAATTCTTATTT
1 T-AATTAAATTATT-TTT
374897 T-ATTAAA
1 TAATTAAA
374904 GTCATGTCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 21 0.62
17 9 0.26
18 4 0.12
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTAAATTATTTTT
Found at i:377213 original size:9 final size:9
Alignment explanation
Indices: 377199--377277 Score: 55
Period size: 9 Copynumber: 9.2 Consensus size: 9
377189 ACAAATGATT
377199 TTAAAATTA
1 TTAAAATTA
377208 TTAAAATTA
1 TTAAAATTA
377217 TT----TT-
1 TTAAAATTA
377221 TTAAAA-TA
1 TTAAAATTA
*
377229 -TAAAAATA
1 TTAAAATTA
* *
377237 TAAAAATATT
1 TTAAAAT-TA
377247 TTAAAATTAA
1 TTAAAATT-A
377257 TTTAAAATTA
1 -TTAAAATTA
377267 TTAAAATTA
1 TTAAAATTA
377276 TT
1 TT
377278 TTTTGAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 6 0.11
8 2 0.04
9 27 0.49
10 8 0.15
11 8 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:377219 original size:20 final size:20
Alignment explanation
Indices: 377191--377279 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
377181 CCACATCAAC
*
377191 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
377211 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
* * *
377231 AAA--ATATAAAAATATTTTA
1 AAATTATTTTAAAAT-TATTA
*
377250 AAATTAATTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
377270 AAATTATTTT
1 AAATTATTTT
377280 TTGAAATAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
16 6 0.11
18 2 0.04
19 5 0.09
20 23 0.43
21 9 0.17
22 8 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:377235 original size:30 final size:30
Alignment explanation
Indices: 377201--377301 Score: 104
Period size: 30 Copynumber: 3.4 Consensus size: 30
377191 AAATGATTTT
377201 AAAATTATTAAAATTATTTTTTAAAATATA
1 AAAATTATTAAAATTATTTTTTAAAATATA
* *
377231 AAAA-TA-TAAAA--ATATTTTAAAATTAATTT
1 AAAATTATTAAAATTATTTTTTAAAA-T-A-TA
*
377260 AAAATTATTAAAATTATTTTTTGAAATA-A
1 AAAATTATTAAAATTATTTTTTAAAATATA
377289 TAAAATTATTAAA
1 -AAAATTATTAAA
377302 TAATTTTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
26 10 0.17
27 1 0.02
28 6 0.10
29 7 0.12
30 18 0.31
31 6 0.10
32 1 0.02
33 9 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (30 bp):
AAAATTATTAAAATTATTTTTTAAAATATA
Found at i:377303 original size:59 final size:60
Alignment explanation
Indices: 377198--377310 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 60
377188 AACAAATGAT
377198 TTTAAAATTATTAAAATTATTTTTTAAAATATAAAAATATAAAAAT-ATTTTAAAATTAA
1 TTTAAAATTATTAAAATTATTTTTTAAAATATAAAAATATAAAAATAATTTTAAAATTAA
* * *
377257 TTTAAAATTATTAAAATTATTTTTTGAAATAATAAAATTAT-TAAATAATTTTAA
1 TTTAAAATTATTAAAATTATTTTTTAAAAT-ATAAAAATATAAAAATAATTTTAA
377311 TTTTCAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
59 33 0.67
60 16 0.33
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (60 bp):
TTTAAAATTATTAAAATTATTTTTTAAAATATAAAAATATAAAAATAATTTTAAAATTAA
Found at i:378303 original size:9 final size:9
Alignment explanation
Indices: 378289--378350 Score: 50
Period size: 9 Copynumber: 7.8 Consensus size: 9
378279 TATTTAAAAA
378289 AATAATTTT
1 AATAATTTT
378298 AATAATTTT
1 AATAATTTT
*
378307 AAAAATTTT
1 AATAATTTT
378316 -AT-ATTTT
1 AATAATTTT
378323 AA-AA----
1 AATAATTTT
378327 AATAATTTT
1 AATAATTTT
*
378336 AATAAATTT
1 AATAATTTT
378345 AA-AATT
1 AATAATT
378351 ATTTGTTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 5 0.12
8 6 0.14
9 27 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATAATTTT
Found at i:378323 original size:16 final size:18
Alignment explanation
Indices: 378292--378327 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
378282 TTAAAAAAAT
378292 AATTTTAATAATTTTAAA
1 AATTTTAATAATTTTAAA
378310 AATTTT-AT-ATTTTAAA
1 AATTTTAATAATTTTAAA
378326 AA
1 AA
378328 ATAATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTTAATAATTTTAAA
Found at i:378329 original size:17 final size:19
Alignment explanation
Indices: 378287--378348 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
378277 ATTATTTAAA
378287 AAAATAATTTTAATAATTTT
1 AAAA-AATTTTAATAATTTT
378307 -AAAAATTTT-AT-ATTTT
1 AAAAAATTTTAATAATTTT
*
378323 AAAAAATAATTTTAATAAATTT
1 --AAAA-AATTTTAATAATTTT
378345 AAAA
1 AAAA
378349 TTATTTGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
16 5 0.14
17 2 0.06
18 6 0.17
19 6 0.17
20 10 0.29
21 2 0.06
22 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAAATTTTAATAATTTT
Found at i:378330 original size:38 final size:39
Alignment explanation
Indices: 378264--378348 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 39
378254 AATTAAAATT
*
378264 ATTTAATAATTTTATTATTTAAAAAAATAATTTTAATAA
1 ATTTAAAAATTTTATTATTTAAAAAAATAATTTTAATAA
* *
378303 TTTTAAAAATTTTA-TATTTTAAAAAATAATTTTAATAA
1 ATTTAAAAATTTTATTATTTAAAAAAATAATTTTAATAA
378341 ATTTAAAA
1 ATTTAAAA
378349 TTATTTGTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 30 0.71
39 12 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (39 bp):
ATTTAAAAATTTTATTATTTAAAAAAATAATTTTAATAA
Found at i:386207 original size:5 final size:5
Alignment explanation
Indices: 386194--386228 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
386184 AAAAAATGAA
*
386194 AAAAG AAAAT AAAAG AAAAG AAGAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAA
386229 AGGAGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:386207 original size:11 final size:11
Alignment explanation
Indices: 386193--386230 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
386183 AAAAAAATGA
386193 AAAAAGAAAA-
1 AAAAAGAAAAG
*
386203 TAAAAGAAAAG
1 AAAAAGAAAAG
*
386214 AAGAAGAAAAG
1 AAAAAGAAAAG
386225 AAAAAG
1 AAAAAG
386231 GAGGAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:386212 original size:16 final size:17
Alignment explanation
Indices: 386193--386244 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
386183 AAAAAAATGA
*
386193 AAAAAGAA-AATAAAAG
1 AAAAAGAAGAAGAAAAG
386209 -AAAAGAAGAAGAAAAG
1 AAAAAGAAGAAGAAAAG
*
386225 AAAAAGGAGGAA-AAAAG
1 AAAAA-GAAGAAGAAAAG
386242 AAA
1 AAA
386245 GTCAAGATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 7 0.23
16 7 0.23
17 12 0.39
18 5 0.16
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAAGAAGAAGAAAAG
Found at i:386267 original size:93 final size:90
Alignment explanation
Indices: 386109--386279 Score: 236
Period size: 93 Copynumber: 1.9 Consensus size: 90
386099 AGAGGAGATC
* *
386109 AAAAAAAAAAAAAGAAGAAGAAGAAGAAAAAAAGAAAGAAAAAGTCAAGATGAAAACCCGTAAAG
1 AAAAAAAAAAAAAGAAGAAGAAGAAGAAAAAAAGAAAAAAAAAGTCAAGATGAAAACCCGCAAAG
*
386174 GGCATCTTTAAAAAAATGAAAAAAG
66 GGCATCTTGAAAAAAATGAAAAAAG
* * **
386199 AAAATAAAAGAAAAGAAGAAGAA-AAGAAAAAGGAGGAAAAAAGAAAGTCAAGATGAAAACTTGC
1 AAAA-AAAAAAAAAGAAGAAGAAGAAGAAAAA--AAGAAAAAA-AAAGTCAAGATGAAAACCCGC
386263 AAAGGGCATCTTGAAAA
62 AAAGGGCATCTTGAAAA
386280 TCTATATATC
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
90 12 0.17
91 17 0.24
92 7 0.10
93 34 0.49
ACGTcount: A:0.64, C:0.06, G:0.20, T:0.09
Consensus pattern (90 bp):
AAAAAAAAAAAAAGAAGAAGAAGAAGAAAAAAAGAAAAAAAAAGTCAAGATGAAAACCCGCAAAG
GGCATCTTGAAAAAAATGAAAAAAG
Found at i:387121 original size:13 final size:12
Alignment explanation
Indices: 387103--387156 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 12
387093 ATTTCACCCT
387103 AAAAAAGAGAAGA
1 AAAAAAGA-AAGA
387116 AAAAAAGAAAGA
1 AAAAAAGAAAGA
387128 AAAAGAAGAAA-A
1 AAAA-AAGAAAGA
387140 AAGAAGAA-AAAGA
1 AA-AA-AAGAAAGA
387153 AAAA
1 AAAA
387157 GGAGAGGTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 16 0.42
13 22 0.58
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:387136 original size:9 final size:9
Alignment explanation
Indices: 387112--387153 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
387102 TAAAAAAGAG
387112 AAGAA-AAA
1 AAGAAGAAA
387120 AAGAAAGAAA
1 AAG-AAGAAA
387130 AAGAAGAAAA
1 AAGAAG-AAA
387140 AAGAAGAAA
1 AAGAAGAAA
387149 AAGAA
1 AAGAA
387154 AAAGGAGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 3 0.10
9 13 0.42
10 15 0.48
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:387144 original size:16 final size:16
Alignment explanation
Indices: 387104--387156 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
387094 TTTCACCCTA
387104 AAAAAGAGAAGAAAAA-
1 AAAAA-AGAAGAAAAAG
*
387120 AAGAAAGAA-AAAGAAG
1 AAAAAAGAAGAAA-AAG
387136 AAAAAAGAAGAAAAAG
1 AAAAAAGAAGAAAAAG
387152 AAAAA
1 AAAAA
387157 GGAGAGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 3 0.09
15 6 0.19
16 20 0.62
17 3 0.09
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAGAAAAAG
Found at i:388170 original size:49 final size:49
Alignment explanation
Indices: 388130--388506 Score: 285
Period size: 49 Copynumber: 7.7 Consensus size: 49
388120 CGTAATGGCA
* * *
388130 AACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGCCGTAACGATG
1 AACCTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACG
* * * * * * *
388179 AACCTTATACCTTAGAAAAATAATGGGAAAGATTAAAGTCGCAACAACG
1 AACCTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACG
* * * * * * *
388228 AATCTTGTACCATGGAGATATGGA-GGGAAAGGTCGAAGCTGTAACGACG
1 AACCTTGTACCTTAGAGATAT-GATGGGAAAGATTGAAGCCGCAACGACG
* * * * ** * *
388277 AACCTTATACCTTAGAGATATGATAGGAAATATTTAAGCCAAAATGATG
1 AACCTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACG
* * * * * *
388326 AATCTTGCACCATAAAGATATGGA-GGGAAATG-TTGAAGCCGCAATGACA
1 AACCTTGTACCTTAGAGATAT-GATGGGAAA-GATTGAAGCCGCAACGACG
* ** *
388375 AAACTTGTACCTTAGAGACCTGATGGGAAAGATTGAAGTCGCAACGACG
1 AACCTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACG
* *** * * *
388424 AATCTTGTACCACGGAGATATGGA-GGGAAAGGTTGAAGCCGCAAAGGCG
1 AACCTTGTACCTTAGAGATAT-GATGGGAAAGATTGAAGCCGCAACGACG
* **
388473 AACCTTATACCTTAGAGATATGAAAGGAAAGATT
1 AACCTTGTACCTTAGAGATATGATGGGAAAGATT
388507 AAGACCACAA
Statistics
Matches: 244, Mismatches: 76, Indels: 16
0.73 0.23 0.05
Matches are distributed among these distances:
48 7 0.03
49 232 0.95
50 5 0.02
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (49 bp):
AACCTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACG
Found at i:388246 original size:98 final size:98
Alignment explanation
Indices: 388133--388508 Score: 389
Period size: 98 Copynumber: 3.8 Consensus size: 98
388123 AATGGCAAAC
* * * * * *
388133 CTTGTACCTTAGAGATGT-GATGGGAAAGATTGAAGCCGTAACGATGAACCTTATACCTTAGAAA
1 CTTGTACCATAGAGATATGGA-GGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGA
*
388197 AATAATGGGAAAGATTAAAGTCGCAACAACGAAT
65 AATGATGGGAAAGATTAAAGTCGCAACAACGAAT
* * * * *
388231 CTTGTACCATGGAGATATGGAGGGAAAGGTCGAAGCTGTAACGACGAACCTTATACCTTAGAGAT
1 CTTGTACCATAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGAA
* * * * *
388296 ATGATAGGAAATATTTAAG-C-CAAAATGATGAAT
66 ATGATGGGAAAGATTAAAGTCGCAACA--ACGAAT
* * * * * * * *
388329 CTTGCACCATAAAGATATGGAGGGAAATGTTGAAGCCGCAATGACAAAACTTGTACCTTAGAGAC
1 CTTGTACCATAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGAA
* * *
388394 CTGATGGGAAAGATTGAAGTCGCAACGACGAAT
66 ATGATGGGAAAGATTAAAGTCGCAACAACGAAT
** * * *
388427 CTTGTACCACGGAGATATGGAGGGAAAGGTTGAAGCCGCAAAGGCGAACCTTATACCTTAGAGAT
1 CTTGTACCATAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGAA
**
388492 ATGAAAGGAAAGATTAA
66 ATGATGGGAAAGATTAA
388509 GACCACAACA
Statistics
Matches: 224, Mismatches: 49, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
96 4 0.02
97 1 0.00
98 213 0.95
99 3 0.01
100 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (98 bp):
CTTGTACCATAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGAA
ATGATGGGAAAGATTAAAGTCGCAACAACGAAT
Found at i:388797 original size:38 final size:39
Alignment explanation
Indices: 388746--389279 Score: 431
Period size: 38 Copynumber: 13.7 Consensus size: 39
388736 AACTACCACA
*
388746 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAG-CAT
1 CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACAT
* * * * * * *
388784 CCAATCTTTTACCCTAATTAGAGGGTAGATTCAAGACACA
1 CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACA-T
* *
388824 CCAATCTCTTACCCCGATCAT-GGAGTAGATTGAAG-CAT
1 CCAATCTCTTACCCCAATCATAGG-GCAGATTGAAGACAT
* * * *
388862 CCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACA
1 CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACA-T
**
388902 CCAATCTCTTACCCTGATCAT-GGGACAGATTGAAG-CAT
1 CCAATCTCTTACCCCAATCATAGGG-CAGATTGAAGACAT
* * ** * *
388940 CTAATCTTTTACCTTAATCAGAGGGTAGATTGAAGACA-
1 CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACAT
* * *
388978 CCAATCTCTTACCCCGATCAT-GAAGTAGATTGAAG-CAT
1 CCAATCTCTTACCCCAATCATAG-GGCAGATTGAAGACAT
* * * * *
389016 CCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACA
1 CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACA-T
* * * * * * * *
389056 CCAATCTTTTACCCTAATTAAATGGCAAATTAAAGATAT
1 CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACAT
* *
389095 ACCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-CAT
1 -CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACAT
* * * *
389134 CCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCAT
1 CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACAT
* * * * *
389173 CCAATCTTTTACCCTAATTAGAGGGCAAATTGAAGACAT
1 CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACAT
* * * *
389212 AACAATCTCTTACCCCAATCATGGGGTAGATTGAGGATCAT
1 -CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGA-CAT
*
389253 CCAATCTCTTA-CCCAATCATGGGGCAG
1 CCAATCTCTTACCCCAATCATAGGGCAG
389280 TTTTTTAAAG
Statistics
Matches: 393, Mismatches: 85, Indels: 35
0.77 0.17 0.07
Matches are distributed among these distances:
37 3 0.01
38 166 0.42
39 73 0.19
40 148 0.38
41 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (39 bp):
CCAATCTCTTACCCCAATCATAGGGCAGATTGAAGACAT
Found at i:388871 original size:78 final size:78
Alignment explanation
Indices: 388742--389351 Score: 614
Period size: 78 Copynumber: 7.7 Consensus size: 78
388732 GTGAAACTAC
* *
388742 CACACCAATCTCTTACCCCGATCATAGG-GCAGATTGAAGCATCCAATCTTTTACCCTAATTAGA
1 CACACCAATCTCTTACCCCGATCAT-GGAGTAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
* *
388806 GGGTAGATTCAAGA
65 GGGCAGATTGAAGA
388820 CACACCAATCTCTTACCCCGATCATGGAGTAGATTGAAGCATCCAATCTTTTACCCTAATCAGAG
1 CACACCAATCTCTTACCCCGATCATGGAGTAGATTGAAGCATCCAATCTTTTACCCTAATCAGAG
388885 GGCAGATTGAAGA
66 GGCAGATTGAAGA
* * * *
388898 CACACCAATCTCTTACCCTGATCATGG-GACAGATTGAAGCATCTAATCTTTTACCTTAATCAGA
1 CACACCAATCTCTTACCCCGATCATGGAG-TAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
*
388962 GGGTAGATTGAAG-
65 GGGCAGATTGAAGA
* *
388975 -ACACCAATCTCTTACCCCGATCATGAAGTAGATTGAAGCATCCAATCTTTTACCCTAACCAGAG
1 CACACCAATCTCTTACCCCGATCATGGAGTAGATTGAAGCATCCAATCTTTTACCCTAATCAGAG
389039 GGCAGATTGAAGA
66 GGCAGATTGAAGA
* ** * * * * **
389052 CACACCAATCTTTTACCCTAATTAAATGGCA--A-ATTAAAGATATACCAATCTCTTACCCCGAT
1 CACACCAATCTCTTACCCCGA-T-CATGG-AGTAGATTGAAG-CAT-CCAATCTTTTACCCTAAT
389114 CATG-GGGCAGATTGAAG-
61 CA-GAGGGCAGATTGAAGA
* * * * *
389131 CA-TCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAATTAGA
1 CACACCAATCTCTTACCCCGATCATGGAGTAGATTGAAG-CATCCAATCTTTTACCCTAATCAGA
*
389195 GGGCAAATTGAAGA
65 GGGCAGATTGAAGA
* * * * * *
389209 CATAACAATCTCTTACCCCAATCATGGGGTAGATTGAGGATCATCCAATCTCTTACCC-AATCAT
1 CACACCAATCTCTTACCCCGATCATGGAGTAGATTGA--AGCATCCAATCTTTTACCCTAATCA-
* *
389273 G-GGGCAGTTTTTTAAAGA
63 GAGGGCAG---ATTGAAGA
* * *
389291 CATCATCCAATCTCTTACCCTGATCATGGGGTAGATTAAAGACATTATCCAATCTTTTACC
1 CA-CA-CCAATCTCTTACCCCGATCATGGAGTAGATTGAAG-C---ATCCAATCTTTTACC
389352 TTGACCATGG
Statistics
Matches: 443, Mismatches: 60, Indels: 50
0.80 0.11 0.09
Matches are distributed among these distances:
76 72 0.16
77 33 0.07
78 188 0.42
79 44 0.10
80 49 0.11
81 3 0.01
82 9 0.02
83 2 0.00
84 29 0.07
86 14 0.03
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (78 bp):
CACACCAATCTCTTACCCCGATCATGGAGTAGATTGAAGCATCCAATCTTTTACCCTAATCAGAG
GGCAGATTGAAGA
Found at i:389166 original size:194 final size:194
Alignment explanation
Indices: 388746--389320 Score: 525
Period size: 194 Copynumber: 2.9 Consensus size: 194
388736 AACTACCACA
* * * *
388746 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTTTTACCCTAATTAGAGGGTA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCCAATCAGAGAGTA
* * * *
388811 GATTCAAGACACACCAATCTCTTACCCCGATCATGGAGTAGATTGAAGCATCCAATCTTTTACCC
66 GATTCAAGACACACCAATCTCTTACCCCAACCATGGAGCAGATTGAAGCAACCAATCTTTTACCC
* * * *
388876 TAATCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCTGATCATGGGACAGATTGAAGCAT
131 TAATCAAAGGGCAAATTAAAGACACACCAATCTCTTACCCCGATCATGGGACAGATTGAAGCAT
* * *** * * *
388940 CTAATCTTTTACCTTAATCA-GAGGGTAGATTGAAGACA-CCAATCTCTTACCCCGATCATGA-A
1 CCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG-CATCCAATCTTTTACCCCAATCA-GAGA
* * * * *
389002 GTAGATTGAAG-CA-TCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGACACACCAATCTT
63 GTAGATTCAAGACACACCAATCTCTTACCCCAACCATG-GAGCAGATTGAAG-CA-ACCAATCTT
* * * * *
389064 TTACCCTAATTAAATGGCAAATTAAAGATATACCAATCTCTTACCCCGATCATGGGGCAGATTGA
125 TTACCCTAATCAAAGGGCAAATTAAAGACACACCAATCTCTTACCCCGATCATGGGACAGATTGA
389129 AGCAT
190 AGCAT
* * * * *
389134 CCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAATTAGAGGGC
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-CATCCAATCTTTTACCCCAATCAGAGAGT
* * * * * * * * * *
389199 AAATTGAAGACATAACAATCTCTTACCCCAATCATGGGGTAGATTGAGGATCATCCAATCTCTTA
65 AGATTCAAGACACACCAATCTCTTACCCCAACCATGGAGCAGATTGA--AGCAACCAATCTTTTA
** ** *
389264 CCC-AATCATGGGGCAGTTTTTTAAAGACATCATCCAATCTCTTACCCTGATCATGGG
128 CCCTAATCAAAGGGCA---AATTAAAGACA-CA-CCAATCTCTTACCCCGATCATGGG
389321 GTAGATTAAA
Statistics
Matches: 299, Mismatches: 63, Indels: 31
0.76 0.16 0.08
Matches are distributed among these distances:
191 1 0.00
192 27 0.09
193 4 0.01
194 152 0.51
195 30 0.10
196 10 0.03
197 39 0.13
198 3 0.01
199 9 0.03
200 1 0.00
201 23 0.08
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (194 bp):
CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCCAATCAGAGAGTA
GATTCAAGACACACCAATCTCTTACCCCAACCATGGAGCAGATTGAAGCAACCAATCTTTTACCC
TAATCAAAGGGCAAATTAAAGACACACCAATCTCTTACCCCGATCATGGGACAGATTGAAGCAT
Found at i:389304 original size:44 final size:42
Alignment explanation
Indices: 388746--389372 Score: 300
Period size: 38 Copynumber: 15.8 Consensus size: 42
388736 AACTACCACA
** * *
388746 CCAATCTCTTACCCCGATCATAGGGCAGATT---GA-AGCAT
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
* * * *
388784 CCAATCTTTTACCCTAATTA-GAGGGTAGATTCAAGACA-CA-
1 CCAATCTCTTACCCTAATCATG-GGGCAGATTAAAGACATCAT
** * * *
388824 CCAATCTCTTACCCCGATCATGGAGTAGATT---GA-AGCAT
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
* *
388862 CCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACA-CA-
1 CCAATCTCTTACCCTAATCATG-GGGCAGATTAAAGACATCAT
* * *
388902 CCAATCTCTTACCCTGATCATGGGACAGATTGAAG-CATC-T
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
* * * *
388942 --AATCTTTTACCTTAATCA-GAGGGTAGATTGAAG--A-CA-
1 CCAATCTCTTACCCTAATCATG-GGGCAGATTAAAGACATCAT
** ** * *
388978 CCAATCTCTTACCCCGATCATGAAGTAGATT---GA-AGCAT
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
* * *
389016 CCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGACA-CA-
1 CCAATCTCTTACCCTAATCATG-GGGCAGATTAAAGACATCAT
* * *** * *
389056 CCAATCTTTTACCCTAATTAAATGGCAAATTAAAGATAT-A-
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
** *
389096 CCAATCTCTTACCCCGATCATGGGGCAGATT---GA-AGCAT
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
** * *
389134 CCAATCTCTTACCCCGACCATGGGGCAGATTGAAG-C--CAT
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
* * * *
389173 CCAATCTTTTACCCTAATTA-GAGGGCAAATTGAAGACAT-A-
1 CCAATCTCTTACCCTAATCATG-GGGCAGATTAAAGACATCAT
* * * * *
389213 ACAATCTCTTACCCCAATCATGGGGTAGATT-GAG-GATCAT
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
*
389253 CCAATCTCTTACCC-AATCATGGGGCAGTTTTTTAAAGACATCAT
1 CCAATCTCTTACCCTAATCATGGGGCAG---ATTAAAGACATCAT
* * *
389297 CCAATCTCTTACCCTGATCATGGGGTAGATTAAAGACATTAT
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
* * * * *
389339 CCAATCTTTTACCTTGACCATGGGGTAGATTAAA
1 CCAATCTCTTACCCTAATCATGGGGCAGATTAAA
389373 CCCACAATCC
Statistics
Matches: 459, Mismatches: 80, Indels: 96
0.72 0.13 0.15
Matches are distributed among these distances:
35 1 0.00
36 4 0.01
37 13 0.03
38 150 0.33
39 48 0.10
40 146 0.32
41 17 0.04
42 48 0.10
43 2 0.00
44 19 0.04
45 11 0.02
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (42 bp):
CCAATCTCTTACCCTAATCATGGGGCAGATTAAAGACATCAT
Found at i:389383 original size:42 final size:42
Alignment explanation
Indices: 389295--389392 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
389285 TAAAGACATC
* * * **
389295 ATCCAATCTCTTACCCTGATCATGGGGTAGATTAAAGACATT
1 ATCCAATCTTTTACCCTGACCATGGGGTAGATTAAACACACA
* *
389337 ATCCAATCTTTTACCTTGACCATGGGGTAGATTAAACCCACA
1 ATCCAATCTTTTACCCTGACCATGGGGTAGATTAAACACACA
389379 ATCCAATCTTTTAC
1 ATCCAATCTTTTAC
389393 TCTTAAATCA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (42 bp):
ATCCAATCTTTTACCCTGACCATGGGGTAGATTAAACACACA
Found at i:392678 original size:25 final size:27
Alignment explanation
Indices: 392650--392699 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
392640 TAAAAAATCA
*
392650 AAAACAA-GTAAAAA-AATAAAGAAGG
1 AAAACAATGTAAAAAGAAAAAAGAAGG
*
392675 AAAACAATTTAAAAAGAAAAAAGAA
1 AAAACAATGTAAAAAGAAAAAAGAA
392700 AATCAAACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 6 0.29
27 8 0.38
ACGTcount: A:0.74, C:0.04, G:0.12, T:0.10
Consensus pattern (27 bp):
AAAACAATGTAAAAAGAAAAAAGAAGG
Found at i:394962 original size:24 final size:24
Alignment explanation
Indices: 394935--394980 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
394925 ATCATCATTC
*
394935 TTATTCTTATTCTTATTATTTTAA
1 TTATTCTGATTCTTATTATTTTAA
* *
394959 TTATTCTGATTTTTTTTATTTT
1 TTATTCTGATTCTTATTATTTT
394981 CCTCTTCTCA
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:0.20, C:0.07, G:0.02, T:0.72
Consensus pattern (24 bp):
TTATTCTGATTCTTATTATTTTAA
Found at i:395378 original size:50 final size:49
Alignment explanation
Indices: 395242--395380 Score: 127
Period size: 49 Copynumber: 2.8 Consensus size: 49
395232 TTAAAAAAAA
* * * ** *
395242 AAAGAGAAAGCTTAGATTTTTAAAAATAAAAATTTATTTTTTAGTTATTTT
1 AAAGAAAAAGCTTAGATTTTT-AAAA-AAATATTGATTTTTTAACTATTTG
* * * *
395293 AAAGAAAAAGTTTAAATTTTTAACAAAATTTTGATTTTTTAACTATTTCG
1 AAAGAAAAAGCTTAGATTTTTAAAAAAATATTGATTTTTTAACTATTT-G
* *
395343 AAA-TAAAAGCTTAGATTTTTAAGAAAAATAGTGATTTT
1 AAAGAAAAAGCTTAGATTTTTAA-AAAAATATTGATTTT
395381 CTTTAAAAAA
Statistics
Matches: 70, Mismatches: 16, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
49 34 0.49
50 18 0.26
51 18 0.26
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (49 bp):
AAAGAAAAAGCTTAGATTTTTAAAAAAATATTGATTTTTTAACTATTTG
Found at i:395660 original size:149 final size:148
Alignment explanation
Indices: 395169--395828 Score: 850
Period size: 149 Copynumber: 4.4 Consensus size: 148
395159 TTGGGAAATG
* * * * * *
395169 TTTTGGTTTTTT-TAAACAATTTCGAAATAAGAA-CTTG-TTTTTTAAGCAAAATAGTAATTTTC
1 TTTTGATTTTTTCT-AACTATTTCGAAATAA-AAGTTTGAATTTTTAAGTAAAATAGTGATTTTC
* * *
395231 TTTAAAAAAAAAAAGAGAAAGCTTAGATTTTTAAAAATAAAAATTTATTTTTTAGTTATTTTAAA
64 TTT-----AAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAA
395296 GAAAAAGTTTAAATTTTTAACAAAA
124 GAAAAAGTTTAAATTTTTAACAAAA
* *
395321 TTTTGA-TTTTT-TAACTATTTCGAAATAAAAGCTT-AGATTTTTAAGAAAAATAGTGATTTTCT
1 TTTTGATTTTTTCTAACTATTTCGAAATAAAAGTTTGA-ATTTTTAAGTAAAATAGTGATTTTCT
*
395383 TTAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAA
65 TTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAA
*
395448 GTTTAAATTTTTAACAAAG
130 GTTTAAATTTTTAACAAAA
* *
395467 TTTTGATTTTTTCTAACTATTTCGAAATAAAAGTTTAAATTTTTTAGTAAAATAGTGATTTTCTT
1 TTTTGATTTTTTCTAACTATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAGTGATTTTCTT
* * *
395532 TAGAAAAGAGAAATTTTAGATTTTTAAAAA-ATAAAATCTGTTTTTTTAGTTACTTTAAAGAAAA
66 TAAAAAAGAGAAAGTTTAGATTTTTAAAAATA-AAAATCTG-TTTTTTAGTTATTTTAAAGAAAA
* * *
395596 AGTGTAAATTTTCAAGAAAA
129 AGTTTAAATTTTTAACAAAA
*
395616 TTTTGATTTTTTTCTAACTATTTCGAAATAAAAGTTTGAATTTTTAAG-CAAATAGTGATTTTCT
1 TTTTGA-TTTTTTCTAACTATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAGTGATTTTCT
* * *
395680 TTAAAAAAGAGAAGGTTTAAATTTTTAAAAAATAAAAATCTGTTTTTTATTTATTTTAAAGAAAA
65 TTAAAAAAGAGAAAGTTTAGATTTTT-AAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAA
* *
395745 AGTTTAAATCTTTAACAAAG
129 AGTTTAAATTTTTAACAAAA
* * * * *
395765 TTCTGAGTTTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTTATTTT
1 TTTTGA--TTTTTTCTAACTATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAGTGATTTT
395829 TGTTTAATCA
Statistics
Matches: 454, Mismatches: 41, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
146 83 0.18
147 6 0.01
148 82 0.18
149 125 0.28
150 110 0.24
151 43 0.09
152 5 0.01
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (148 bp):
TTTTGATTTTTTCTAACTATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAGTGATTTTCTT
TAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAG
TTTAAATTTTTAACAAAA
Found at i:400111 original size:148 final size:148
Alignment explanation
Indices: 399842--400141 Score: 521
Period size: 148 Copynumber: 2.0 Consensus size: 148
399832 CTTCTAAAAC
*
399842 GATGATGGATTCTATTGATGTTAAATGAATAAGAGAGTATCTTTTAATATTATATCATTTTCATT
1 GATGATGGATTCTACTGATGTTAAATGAATAAGAGAGTATCTTTTAATATTATATCATTTTCATT
399907 CTTATTTAACATTACTTGTCCGCTTATTCTTGGATTTAACCACTCTAAACACAAAAGTGAAATTG
66 CTTATTTAACATTACTTGTCCGCTTATTCTTGGATTTAACCACTCTAAACACAAAAGTGAAATTG
*
399972 CAGTACATCGAATCGAGA
131 CAGTACATCAAATCGAGA
* *
399990 GATGATGGATTCTGCTGATGTTAAATGAATACGAGAGTATCTTTTAATATTATATCA-TTTCGAT
1 GATGATGGATTCTACTGATGTTAAATGAATAAGAGAGTATCTTTTAATATTATATCATTTTC-AT
* * *
400054 TCTTATTTTACATTACTTGTCTGCTTATTCTTGGATTTAACCACTCTAAACAGAAAAGTGAAATT
65 TCTTATTTAACATTACTTGTCCGCTTATTCTTGGATTTAACCACTCTAAACACAAAAGTGAAATT
400119 GCAGTACATCAAATCGAGA
130 GCAGTACATCAAATCGAGA
400138 GATG
1 GATG
400142 CGATGACAGG
Statistics
Matches: 144, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
147 4 0.03
148 140 0.97
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (148 bp):
GATGATGGATTCTACTGATGTTAAATGAATAAGAGAGTATCTTTTAATATTATATCATTTTCATT
CTTATTTAACATTACTTGTCCGCTTATTCTTGGATTTAACCACTCTAAACACAAAAGTGAAATTG
CAGTACATCAAATCGAGA
Found at i:408461 original size:151 final size:146
Alignment explanation
Indices: 408169--408602 Score: 649
Period size: 151 Copynumber: 2.9 Consensus size: 146
408159 GCAAGACAGG
*
408169 AGTTTATATTTTTAAAAAATAAAAATCTGTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTA
1 AGTTTAGA-TTTTAAAAAATAAAAATCTGTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTA
408234 ACAAAGTTTTGATTTTTTCTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGAT
65 ACAAAGTTTTGATTTTTTCTAACTATTTCGAAATAAAAGTTTGGATTTTTAAG-AAAATAGTGAT
408299 TTTCTTTAAAAAAGAGAA
129 TTTCTTTAAAAAAGAGAA
* * *
408317 ATTTTAGATTTTAAAAAAATAAAAATCTGTTTTTTTTAGTTACTTTAAAAAAAAAGTTTAAATTT
1 AGTTTAGATTTT-AAAAAATAAAAATCTG---TTTTTAGTTATTTTAAAGAAAAAGTTTAAATTT
* * * *
408382 TTAACAAAGTTTTGATTTTTTCTAACTATTTCAAAAGACAAGTTTGGATTTTTAAGCAAATAGTG
62 TTAACAAAGTTTTGATTTTTTCTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAATAGTG
408447 ATTTTCTTTAAAAAAGAGAA
127 ATTTTCTTTAAAAAAGAGAA
*
408467 GGTTTAGA-TTTAAAAAA-AAAAATCTGTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAA
1 AGTTTAGATTTTAAAAAATAAAAATCTGTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAA
* * * *
408530 CAAAGTTTT-TTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATT
66 CAAAGTTTTGATTTTTTCTAACTATTTCGAAATAAAAGTTTGGATTTTTAAG-AAAATAGTGATT
*
408594 ATTGTTTAA
130 -TTCTTTAA
408603 TCAAATGAAA
Statistics
Matches: 259, Mismatches: 21, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
143 36 0.14
144 54 0.21
145 7 0.03
147 13 0.05
148 28 0.11
149 3 0.01
150 34 0.13
151 84 0.32
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (146 bp):
AGTTTAGATTTTAAAAAATAAAAATCTGTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAA
CAAAGTTTTGATTTTTTCTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAATAGTGATTT
TCTTTAAAAAAGAGAA
Found at i:421605 original size:34 final size:34
Alignment explanation
Indices: 421567--421632 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
421557 CTATAGTATA
*
421567 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* *
421601 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
421633 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:421606 original size:17 final size:17
Alignment explanation
Indices: 421575--421632 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
421565 TAATTGTCCC
* *
421575 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
421592 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
421609 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
421626 TGCATTT
1 TGCATTT
421633 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:429803 original size:11 final size:11
Alignment explanation
Indices: 429789--429823 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
429779 TTAAATCAAG
*
429789 AAAAAATATAA
1 AAAAAATAGAA
429800 AAAAAATAGAAA
1 AAAAAATAG-AA
429812 AAAAAATAGAA
1 AAAAAATAGAA
429823 A
1 A
429824 GAGAGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (11 bp):
AAAAAATAGAA
Found at i:429813 original size:12 final size:12
Alignment explanation
Indices: 429789--429823 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
429779 TTAAATCAAG
*
429789 AAAAAATA-TAA
1 AAAAAATAGAAA
429800 AAAAAATAGAAA
1 AAAAAATAGAAA
429812 AAAAAATAGAAA
1 AAAAAATAGAAA
429824 GAGAGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (12 bp):
AAAAAATAGAAA
Found at i:430935 original size:42 final size:42
Alignment explanation
Indices: 430225--430917 Score: 924
Period size: 42 Copynumber: 16.5 Consensus size: 42
430215 AAAGAAAGCA
430225 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
430267 TTCATTGCATTCAGAGGCCTAGGTGTGGAGG-CCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCC-ATTTACTT
* *
430309 TTTATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
430351 TTCATTGCATTCAGAGGCCTAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
430393 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
430435 TTCATTACATTCAGATGCCTAGGTGTAGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTC-CATTTACTT
** *
430477 TTCATCACATTTAGAGGCCTAGGTGTGGATGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * * *
430519 TTCATCGCATTTAGAGGTCGAAGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
430561 TTCATTACATTTAGAAGCCCAGGTGTAGAGGTCCATTTA-TT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
** *
430602 GTTCATTGCATTCCGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 -TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
430645 TTCATCGCATTCAGAGGCCCAGGTGTGGAGGTCCCTTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
430687 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
430729 TTCGTCGCATTTAGAGGCCTAGGTATGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
430771 TTCATTGCATTTAGAGGCCCATGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
430813 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
**
430855 TTCATTGCATTCGGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
430897 TTCATTGCAATTAGAGGCCTA
1 TTCATTGCATTTAGAGGCCTA
430918 AGCATAGAGG
Statistics
Matches: 576, Mismatches: 69, Indels: 12
0.88 0.11 0.02
Matches are distributed among these distances:
41 5 0.01
42 566 0.98
43 5 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
Found at i:431885 original size:31 final size:30
Alignment explanation
Indices: 431828--431885 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
431818 AAAGTTTAGA
* * **
431828 ATTTTAAAAATAAAAATTTATTTTTTAGTT
1 ATTTTAAAAAAAAAAATTAAAATTTTAGTT
431858 ATTTTAAAGAAAAAAAATTAAAATTTTA
1 ATTTTAAA-AAAAAAAATTAAAATTTTA
431886 ACAAAGTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 8 0.35
31 15 0.65
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
ATTTTAAAAAAAAAAATTAAAATTTTAGTT
Found at i:432161 original size:148 final size:147
Alignment explanation
Indices: 431747--432257 Score: 711
Period size: 149 Copynumber: 3.4 Consensus size: 147
431737 TTTTGGTTTT
* * *
431747 TTTTTTTAAACAATTTCAAAATAAAAGCTTTGATTTTTTTAAGCAAAATAGTGATTTTCTTTAAA
1 TTTTTTT-AACTATTTCGAAATAAAAG-TTTGA-ATTTTTAAGC-AAATAGTGATTTTCTTTAAA
*
431812 AAAGAGAAAGTTTAGAATTTT-AAAAATAAAAATTTATTTTTTAGTTATTTTAAAGAAAAAAAAT
62 AAAGAGAAAGTTTAGAATTTTAAAAAATAAAAATAT-TTTTTTAGTTATTTTAAAGAAAAAAAAT
431876 TAAAATTTTAACAAAGTTTTGA
126 TAAAATTTTAACAAAGTTTTGA
* * * *
431898 TTTTCTTAACTATTTCGAAATAAAAGCTTGGATTTTTAAGAAAATAGTGATTTTCTTTAAAAAAG
1 TTTTTTTAACTATTTCGAAATAAAAGTTTGAATTTTTAAGCAAATAGTGATTTTCTTTAAAAAAG
* * * *
431963 AGAAAATTTAGATTTTTAAAAAATAAAAAACTATTTTTTTAGTTACTTTAAAG-AAAAAATTTAA
66 AGAAAGTTTAGAATTTTAAAAAAT-AAAAA-TATTTTTTTAGTTATTTTAAAGAAAAAAAATTAA
*
432027 ATTTTTAACAAAGTTTTGA
129 AATTTTAACAAAGTTTTGA
*
432046 TTTTTTCTAACTATTTCGAAATAAAAGTTTGAATTTTTAAGCAAATAGTGATTTTCTTTAAAAAG
1 TTTTTT-TAACTATTTCGAAATAAAAGTTTGAATTTTTAAGCAAATAGTGATTTTCTTTAAAAAA
432111 GAGAAAGTTTAGAATTTTAAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAAAATTAA
65 GAGAAAGTTTAGAATTTTAAAAAATAAAAATAT-TTTTTTAGTTATTTTAAAGAAAAAAAATTAA
*
432176 AATTTTAACAAAGTTTTTA
129 AATTTTAACAAAGTTTTGA
* * * * * *
432195 TTTTTTTTAGCTAATTCGAAATAAAAAGTTTGGATTTTTAAGTAAGTAGTGATATTTATTTAA
1 -TTTTTTTAACTATTTCGAAAT-AAAAGTTTGAATTTTTAAGCAAATAGTGAT-TTTCTTTAA
432258 TCAAATGAAA
Statistics
Matches: 321, Mismatches: 30, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
147 42 0.13
148 70 0.22
149 143 0.45
150 52 0.16
151 14 0.04
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.42
Consensus pattern (147 bp):
TTTTTTTAACTATTTCGAAATAAAAGTTTGAATTTTTAAGCAAATAGTGATTTTCTTTAAAAAAG
AGAAAGTTTAGAATTTTAAAAAATAAAAATATTTTTTTAGTTATTTTAAAGAAAAAAAATTAAAA
TTTTAACAAAGTTTTGA
Found at i:438967 original size:3 final size:3
Alignment explanation
Indices: 438959--438987 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
438949 AACCTAGTTG
438959 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
438988 TTGGGCCCTT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:442054 original size:110 final size:111
Alignment explanation
Indices: 441910--442125 Score: 312
Period size: 110 Copynumber: 2.0 Consensus size: 111
441900 TCTCTCTTTT
*
441910 TTTTTCTTTTACATAAGAATATATTGGCCCTTTTGACACGAAATGGAATGACAACCCAAGCACCC
1 TTTTTCTTTTACATAAGAATATATTGACCCTTTTGACACGAAATGGAATGACAACCCAAGCACCC
*
441975 CATCCCAGTTACTCAAACCAACATACTCAC-AATTTATTATTCCTCC
66 CATCCCAGTTACTCAAACCAACACACTC-CTAATTTATTATTCCTCC
* * *
442021 TTTTT-TTTTACTTAAGAATGA-ATTGACCTTTTTGACGCGAAATGGAATGACAACCCAAGCACC
1 TTTTTCTTTTACATAAGAAT-ATATTGACCCTTTTGACACGAAATGGAATGACAACCCAAGCACC
* ** *
442084 CCATCCCGGTTACTCAGCCCAATACACTCCTAATTTATTATT
65 CCATCCCAGTTACTCAAACCAACACACTCCTAATTTATTATT
442126 ATATATTTTG
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
109 1 0.01
110 87 0.93
111 6 0.06
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (111 bp):
TTTTTCTTTTACATAAGAATATATTGACCCTTTTGACACGAAATGGAATGACAACCCAAGCACCC
CATCCCAGTTACTCAAACCAACACACTCCTAATTTATTATTCCTCC
Found at i:442318 original size:12 final size:13
Alignment explanation
Indices: 442295--442326 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
442285 AATCACCAGA
442295 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
442308 TTTTTTC-TTTTC
1 TTTTTTCTTTTTC
442320 TTTTTTC
1 TTTTTTC
442327 GAAAAGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:451894 original size:12 final size:12
Alignment explanation
Indices: 451879--451903 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
451869 AATAAAGAAT
451879 TAATAGCATTCA
1 TAATAGCATTCA
451891 TAATAGCATTCA
1 TAATAGCATTCA
451903 T
1 T
451904 CATATAACAA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:472835 original size:18 final size:18
Alignment explanation
Indices: 472812--472846 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
472802 TAAATTCACG
472812 CCTTTTGCCCTCAATTTT
1 CCTTTTGCCCTCAATTTT
*
472830 CCTTTTGCCTTCAATTT
1 CCTTTTGCCCTCAATTT
472847 AGTCCCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.31, G:0.06, T:0.51
Consensus pattern (18 bp):
CCTTTTGCCCTCAATTTT
Found at i:474094 original size:19 final size:20
Alignment explanation
Indices: 474070--474108 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
474060 GTAGGATCGA
*
474070 TTTTTA-AAAATTTGCATTG
1 TTTTTACAAAATATGCATTG
*
474089 TTTTTACGAAATATGCATTG
1 TTTTTACAAAATATGCATTG
474109 ACAGGATCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTTTACAAAATATGCATTG
Found at i:479025 original size:53 final size:53
Alignment explanation
Indices: 478936--479181 Score: 296
Period size: 53 Copynumber: 4.6 Consensus size: 53
478926 TTGTGCCAAA
* * *
478936 GATTAAAGGTCCGATGACTCTGTGTCAACGTCAGTTATATGAATCCTATCACG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCACG
** ** *
478989 GATTAAAGGTCTTATGGTTCTGTGTCATCGTGAGTTATATGAAAT-CTATCACG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATG-AATCCTATCACG
* *
479042 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGTATCCTATCATG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCACG
* * * * * * *
479095 TATTAAAGGTCTGATGACTATGTGTCATCTTAAGTTATATGAATACTATTACA
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCACG
* * *
479148 GATTAAGGGTCCGACGACTTTGTGTCATCGTGAG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAG
479182 ATACACGAAT
Statistics
Matches: 162, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
52 2 0.01
53 157 0.97
54 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCACG
Found at i:486152 original size:53 final size:53
Alignment explanation
Indices: 486072--486369 Score: 382
Period size: 53 Copynumber: 5.6 Consensus size: 53
486062 GTGCCAAAGC
* * * *
486072 TTAAAGGTTCGATGATTCTGTGTCATCGTGAGTTATATGAATCCTATCACGAA
1 TTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGA
* * * * * *
486125 TTAAAGATTCTATGGCTCTGTGTCATCGTGAGTTATATGAATCCTATCACGTA
1 TTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGA
* * *
486178 TTAAAGGTCCGATTACTGTGTGTCATCTTGAGTTATATGAATCCTATCATGGA
1 TTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGA
* * * * *
486231 TTAAAGGTCTGATGACTATGGGTCATTGTGAGTTATATGAATCCTATTATGGA
1 TTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGA
* * * * *
486284 TTAAGGGTCCGATGACTTTGTGTCATCGTGAGATACACGAATCC-ATCATGGA
1 TTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGA
486336 TTAAAGGTCCGATGACTCTGTGTCATCGTGAGTT
1 TTAAAGGTCCGATGACTCTGTGTCATCGTGAGTT
486370 GTCAAATGTG
Statistics
Matches: 212, Mismatches: 33, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
52 38 0.18
53 174 0.82
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (53 bp):
TTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGA
Found at i:487078 original size:21 final size:21
Alignment explanation
Indices: 487054--487110 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
487044 TAGAAATAAA
* *
487054 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
487075 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
*
487096 ACTTGTATCAGTAGA
1 ACTTGTATCGGTAGA
487111 GCTCTACACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:505502 original size:25 final size:25
Alignment explanation
Indices: 505469--505520 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
505459 AGATGTGCAT
* * *
505469 ATTAAAGAGCACTGATGTACTAATA
1 ATTAAAGAGAACTAAAGTACTAATA
* *
505494 ATTAGAGAGAACTAAAGTGCTAATA
1 ATTAAAGAGAACTAAAGTACTAATA
505519 AT
1 AT
505521 ATGGGAATGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (25 bp):
ATTAAAGAGAACTAAAGTACTAATA
Found at i:518339 original size:13 final size:13
Alignment explanation
Indices: 518321--518345 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518311 CCCATTTTAT
518321 CATTTTTAGCATG
1 CATTTTTAGCATG
518334 CATTTTTAGCAT
1 CATTTTTAGCAT
518346 TTTTAACTTA
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:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:522946 original size:144 final size:144
Alignment explanation
Indices: 522741--523198 Score: 482
Period size: 144 Copynumber: 3.1 Consensus size: 144
522731 TTAAAAAAAA
* * *
522741 AAAAAGAATGTGTGAATTTTTCAAAAATAAAAATATATTTTTTATTTATTTTAAAGGAAAAAGTT
1 AAAAAGAAAGT-T-AATTTTT-AAAAATAAAAATATATTTTTTAGTCATTTTAAAGGAAAAAGTT
* **
522806 TAAATTTTTAAACAAAGTTTTTATTTTTTTAAATATTTTGAAATAAAAACTTTGATTTTTAAGAA
63 TAAATTTTTAAACAAAGTTTTGATTTTTTT--ATATTTCAAAATAAAAACTTTGATTTTTAAGAA
**
522871 AAGTAATGATTTTTTT-TT
126 AAGTAATGATTTTTTTAAC
* * * *
522889 TAAAA-AAA-TTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCACTTAAAAGGAAAAAGTTTA
1 AAAAAGAAAGTTA-ATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGGAAAAAGTTTA
* * *
522952 AATTTTTAAATAAAGTTTTGATTTTTTTTAGCTATTTCAAAAT-AAAAGTTCTAATTTTTAAGAA
65 AATTTTTAAACAAAGTTTTGA-TTTTTTTA--TATTTCAAAATAAAAACTT-TGATTTTTAAGAA
* *
523016 AAGTAGTAAATTTTTTTAAAAC
126 AAGTAAT-GATTTTTTT--AAC
* * *
523038 AAAAAGAAAGTTTAAATTTTAAAAAT-AAAA-ATCTTTTTTAGTCATTTTAAAGGAAAAAATTTA
1 AAAAAGAAAG-TTAATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGGAAAAAGTTTA
* * *
523101 AATTTTTAAACAAAGTTTTGATTTTTTT-T-TTCTCAAAATAAAAATTTTGATCTTTAAGAAAAT
65 AATTTTTAAACAAAGTTTTGATTTTTTTATATT-TCAAAATAAAAACTTTGATTTTTAAGAAAAG
*
523164 TAATGATTTTTTTAAA
129 TAATGATTTTTTTAAC
* **
523180 AAAAAAAAAGAAAATTTTT
1 AAAAAGAAAGTTAATTTTT
523199 TATTTTGCAA
Statistics
Matches: 261, Mismatches: 35, Indels: 35
0.79 0.11 0.11
Matches are distributed among these distances:
141 6 0.02
142 11 0.04
143 1 0.00
144 76 0.29
145 65 0.25
146 15 0.06
147 2 0.01
148 11 0.04
149 53 0.20
150 7 0.03
151 11 0.04
152 3 0.01
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (144 bp):
AAAAAGAAAGTTAATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGGAAAAAGTTTAA
ATTTTTAAACAAAGTTTTGATTTTTTTATATTTCAAAATAAAAACTTTGATTTTTAAGAAAAGTA
ATGATTTTTTTAAC
Found at i:523753 original size:21 final size:21
Alignment explanation
Indices: 523728--523784 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
523718 CTTGTATAAT
*
523728 TTTTATTTATTTTTATTTC-A
1 TTTTATTTATTTTTATGTCTA
*
523748 TCTTTATTTATTTTCATGTCTA
1 T-TTTATTTATTTTTATGTCTA
523770 TTTATATTTATTTTT
1 TTT-TATTTATTTTT
523785 TTAACACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 18 0.58
22 12 0.39
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTATTTATTTTTATGTCTA
Found at i:523762 original size:16 final size:17
Alignment explanation
Indices: 523733--523778 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
523723 ATAATTTTTA
*
523733 TTTATTTTTATTTCATC
1 TTTATTTATATTTCATC
*
523750 TTTATTTAT-TTTCATG
1 TTTATTTATATTTCATC
*
523766 TCTATTTATATTT
1 TTTATTTATATTT
523779 ATTTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTATTTATATTTCATC
Found at i:524509 original size:3 final size:3
Alignment explanation
Indices: 524501--524525 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
524491 CTTTTAAAAG
524501 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
524526 AAGATTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:525329 original size:108 final size:101
Alignment explanation
Indices: 525137--525332 Score: 261
Period size: 101 Copynumber: 1.9 Consensus size: 101
525127 GAGTTCCTTT
* *
525137 TTTTTATTATTTATATTTACTTTTTTATTTTGGCATTTAATTTATTGATATTTTTGTTTATTTAT
1 TTTTTATTATTTATATTTACTTTTTTATTTTAGCATTTAATTTATTAATATTTTTGTTTATTTAT
*
525202 GTAGTTGTCATTTATTTTCATGCATAATCTCAGTTA
66 CTAGTTGTCATTTATTTTCATGCATAATCTCAGTTA
*
525238 TTTTTATTGTTTATATTTA-TTTGTTTATTTTAGCATTTAATTTTAATTTAATTTATTTTTTTGT
1 TTTTTATTATTTATATTTACTTT-TTTATTTTAGCATTTAA-TTT-A-TTAA--TA--TTTTTGT
525302 TTATTTATCTAGTTGGT-ATTTATTTTCATGC
58 TTATTTATCTAGTT-GTCATTTATTTTCATGC
525333 GATTTTATTG
Statistics
Matches: 82, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
100 3 0.04
101 34 0.41
102 3 0.04
103 1 0.01
104 3 0.04
106 2 0.02
108 34 0.41
109 2 0.02
ACGTcount: A:0.22, C:0.06, G:0.09, T:0.64
Consensus pattern (101 bp):
TTTTTATTATTTATATTTACTTTTTTATTTTAGCATTTAATTTATTAATATTTTTGTTTATTTAT
CTAGTTGTCATTTATTTTCATGCATAATCTCAGTTA
Found at i:525519 original size:15 final size:14
Alignment explanation
Indices: 525499--525544 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
525489 GCATTTCATA
525499 TATTTATTGTTTATT
1 TATTTATTG-TTATT
525514 TATTTATTGATTATT
1 TATTTATTG-TTATT
* *
525529 CATTTTTTGTTATT
1 TATTTATTGTTATT
525543 TA
1 TA
525545 CATTCTCGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.70
Consensus pattern (14 bp):
TATTTATTGTTATT
Found at i:525589 original size:21 final size:22
Alignment explanation
Indices: 525554--525595 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
525544 ACATTCTCGC
*
525554 TTTTATTTAATTTTATTTATTG
1 TTTTATATAATTTTATTTATTG
525576 TTTTATAT-ATTTTATTTATT
1 TTTTATATAATTTTATTTATT
525596 TATTATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATATAATTTTATTTATTG
Found at i:525636 original size:72 final size:72
Alignment explanation
Indices: 525512--525669 Score: 178
Period size: 72 Copynumber: 2.2 Consensus size: 72
525502 TTATTGTTTA
* * * * * *
525512 TTTATTTATTGATTATTCATTTTTTGTTATTTACATTCTCGCTTTTATTTAATTTTATTTA-TTG
1 TTTATTTATTTATTATTCA-TTTATGCTATTTACATTCTCGCCTTCATTTAATTTTATTTACTCG
*
525576 TTTTATATAT
65 -TTGATAT-T
* **
525586 TTTATTTATTTATTATTC-TTTATGCTATTTACATTTTTTCCTTCATTTAATTTTATTTACTCGT
1 TTTATTTATTTATTATTCATTTATGCTATTTACATTCTCGCCTTCATTTAATTTTATTTACTCGT
525650 TGATATT
66 TGATATT
525657 TTTATTT-TTTATT
1 TTTATTTATTTATT
525670 TATTTATATG
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
70 6 0.08
71 8 0.11
72 40 0.55
73 2 0.03
74 17 0.23
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.66
Consensus pattern (72 bp):
TTTATTTATTTATTATTCATTTATGCTATTTACATTCTCGCCTTCATTTAATTTTATTTACTCGT
TGATATT
Found at i:531219 original size:42 final size:42
Alignment explanation
Indices: 530802--531203 Score: 524
Period size: 42 Copynumber: 9.5 Consensus size: 42
530792 AAGGAAAGCA
* *
530802 TTCATTGCATTTAGAGGTCTC-GGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGG-CCCAAGTGTGGAGGTCCATTTACTT
* *
530844 TTCATTGCATTTAGAGGCCCAAGTGTGAAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
*
530886 TTCATTGCATTTAGAGACCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
530928 TTCAATT-CATTTAAAGG-CTAAGGTGTGGAGGTACATTTACTT
1 TTC-ATTGCATTTAGAGGCCCAA-GTGTGGAGGTCCATTTACTT
* * *
530970 TTCATCGCATTTAGATGTCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* *
531012 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTAATT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
*
531054 TTCATTGCATTT-GAAGGCCCATGTGTGGAGGTCCATTTACTTT
1 TTCATTGCATTTAG-AGGCCCAAGTGTGGAGGTCCATTTAC-TT
* * *
531097 TTCATTGCATTTAAAGACCCAAGTGTGGAAGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * * *
531139 TTTATTGCATTTAGAGGCCCAAGTTTGAAGATTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
*
531181 TTCACTGCATTTAGAGGCCCAAG
1 TTCATTGCATTTAGAGGCCCAAG
531204 CATAGAGGTC
Statistics
Matches: 316, Mismatches: 36, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
41 8 0.03
42 265 0.84
43 43 0.14
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
Found at i:546605 original size:10 final size:10
Alignment explanation
Indices: 546590--546620 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
546580 ATTGCTTTTA
546590 AGGCCAAAAG
1 AGGCCAAAAG
546600 AGGCCAAAAG
1 AGGCCAAAAG
*
546610 AGGCCTAAAG
1 AGGCCAAAAG
546620 A
1 A
546621 TTAGCTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.48, C:0.19, G:0.29, T:0.03
Consensus pattern (10 bp):
AGGCCAAAAG
Found at i:549358 original size:22 final size:22
Alignment explanation
Indices: 549332--549385 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
549322 AAAAGTTTCC
549332 TATAGTTTCACAATCACATTTA
1 TATAGTTTCACAATCACATTTA
* *
549354 TATAGTCTCACAATCACATTTC
1 TATAGTTTCACAATCACATTTA
549376 TATAGTTTCA
1 TATAGTTTCA
549386 AGATATATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (22 bp):
TATAGTTTCACAATCACATTTA
Found at i:552332 original size:153 final size:153
Alignment explanation
Indices: 552106--552415 Score: 620
Period size: 153 Copynumber: 2.0 Consensus size: 153
552096 TAATAAGCTC
552106 CCTTCCACTTTGCAACTCACTTCCCTAAATTTAAATTATGAGCAAAAAAAAATTAAGAATTAAGA
1 CCTTCCACTTTGCAACTCACTTCCCTAAATTTAAATTATGAGCAAAAAAAAATTAAGAATTAAGA
552171 TTTGATAGCCTCACCCTCTTATGACTTAATTAATTAATTGCTTAAAAAAAAGATGTGACAACACC
66 TTTGATAGCCTCACCCTCTTATGACTTAATTAATTAATTGCTTAAAAAAAAGATGTGACAACACC
552236 AAACTTCAAACCAAAATTCTCAT
131 AAACTTCAAACCAAAATTCTCAT
552259 CCTTCCACTTTGCAACTCACTTCCCTAAATTTAAATTATGAGCAAAAAAAAATTAAGAATTAAGA
1 CCTTCCACTTTGCAACTCACTTCCCTAAATTTAAATTATGAGCAAAAAAAAATTAAGAATTAAGA
552324 TTTGATAGCCTCACCCTCTTATGACTTAATTAATTAATTGCTTAAAAAAAAGATGTGACAACACC
66 TTTGATAGCCTCACCCTCTTATGACTTAATTAATTAATTGCTTAAAAAAAAGATGTGACAACACC
552389 AAACTTCAAACCAAAATTCTCAT
131 AAACTTCAAACCAAAATTCTCAT
552412 CCTT
1 CCTT
552416 AGGCTTACAT
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 157 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (153 bp):
CCTTCCACTTTGCAACTCACTTCCCTAAATTTAAATTATGAGCAAAAAAAAATTAAGAATTAAGA
TTTGATAGCCTCACCCTCTTATGACTTAATTAATTAATTGCTTAAAAAAAAGATGTGACAACACC
AAACTTCAAACCAAAATTCTCAT
Found at i:553520 original size:14 final size:14
Alignment explanation
Indices: 553466--553520 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 14
553456 TCGTTTTTTT
*
553466 AAATACTTCTAAAA
1 AAATACTTTTAAAA
*
553480 AAATA-TTTTGAAA
1 AAATACTTTTAAAA
* **
553493 AAGTAAATTT-AAA
1 AAATACTTTTAAAA
553506 AAATACTTTTAAAA
1 AAATACTTTTAAAA
553520 A
1 A
553521 CTTATTTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 20 0.62
14 12 0.38
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (14 bp):
AAATACTTTTAAAA
Found at i:553529 original size:26 final size:26
Alignment explanation
Indices: 553477--553532 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
553467 AATACTTCTA
*
553477 AAAAAATATTTTGAAAAAGTAAATTT
1 AAAAAATATTTTGAAAAACTAAATTT
* *
553503 AAAAAATACTTTT-AAAAACTTATTTT
1 AAAAAATA-TTTTGAAAAACTAAATTT
553529 AAAA
1 AAAA
553533 TTTAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (26 bp):
AAAAAATATTTTGAAAAACTAAATTT
Found at i:553732 original size:10 final size:11
Alignment explanation
Indices: 553713--553737 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
553703 TAATATACAA
553713 AAATATTTTTT
1 AAATATTTTTT
553724 AAATATTTTTT
1 AAATATTTTTT
553735 AAA
1 AAA
553738 CAATTAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATATTTTTT
Found at i:556342 original size:31 final size:30
Alignment explanation
Indices: 556304--556415 Score: 93
Period size: 31 Copynumber: 3.7 Consensus size: 30
556294 AAATATATAT
556304 TTTGGTACCTGAACTTGGCTTCAAGGTTCAA
1 TTTGGTACCTGAACTTGGCTTC-AGGTTCAA
* *** *
556335 TTTGGTACC-AAAGCTTATTTTCA-GTCCAA
1 TTTGGTACCTGAA-CTTGGCTTCAGGTTCAA
* * *
556364 TTAGATACCTGAACTTGGCTTCTTGGTTCAA
1 TTTGGTACCTGAACTTGGCTTC-AGGTTCAA
* *
556395 ATTGGTACTTGAACTTGGCTT
1 TTTGGTACCTGAACTTGGCTT
556416 TTTGGTCCAA
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
29 18 0.30
30 5 0.08
31 37 0.62
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (30 bp):
TTTGGTACCTGAACTTGGCTTCAGGTTCAA
Found at i:556421 original size:31 final size:31
Alignment explanation
Indices: 556358--556435 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
556348 CTTATTTTCA
*
556358 GTCC-AATTAGATACCTGAACTTGGCTTCTTG
1 GTCCAAATTAG-TACTTGAACTTGGCTTCTTG
* * *
556389 GTTCAAATTGGTACTTGAACTTGGCTTTTTG
1 GTCCAAATTAGTACTTGAACTTGGCTTCTTG
*
556420 GTCCAACTTAGTACTT
1 GTCCAAATTAGTACTT
556436 ACGATAAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 34 0.87
32 5 0.13
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (31 bp):
GTCCAAATTAGTACTTGAACTTGGCTTCTTG
Found at i:556522 original size:31 final size:31
Alignment explanation
Indices: 556463--556522 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
556453 TGAACTATGA
*
556463 AGCCAAGTTCAGGTACTGATTTGAACCAAAG
1 AGCCAAGTTCAGGTACTGAATTGAACCAAAG
*
556494 AGCCAAGTTCAGGTACCT-AATTGGACCAA
1 AGCCAAGTTCAGGTA-CTGAATTGAACCAA
556523 TAAAAAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (31 bp):
AGCCAAGTTCAGGTACTGAATTGAACCAAAG
Found at i:567927 original size:57 final size:59
Alignment explanation
Indices: 567829--567940 Score: 174
Period size: 58 Copynumber: 1.9 Consensus size: 59
567819 AATTCATATT
*
567829 TTAATAATAATTATATTAAAAATATTATTAAATTATATATTA-TTTCATTAAATTATAC
1 TTAATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTCATTAAATTATAC
* * *
567887 TTAATAATAATTATGTT-AAAATATAATTAAATTATTTATTATTTTTATTAAATT
1 TTAATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTCATTAAATT
567941 TAATTGGCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 22 0.45
58 27 0.55
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (59 bp):
TTAATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTCATTAAATTATAC
Found at i:568150 original size:16 final size:16
Alignment explanation
Indices: 568129--568166 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
568119 TGAATTACTG
568129 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCC
*
568145 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCC
568161 ATTACA
1 ATTACA
568167 ACGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.05, T:0.34
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:574348 original size:28 final size:28
Alignment explanation
Indices: 574286--574341 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
574276 TTGGTGAAAT
574286 ACTAAATGTGATCACAAAGTTAATGACA
1 ACTAAATGTGATCACAAAGTTAATGACA
574314 ACTAAATGTGATCACAAAGTTAATGACA
1 ACTAAATGTGATCACAAAGTTAATGACA
574342 TATAAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (28 bp):
ACTAAATGTGATCACAAAGTTAATGACA
Found at i:574941 original size:18 final size:18
Alignment explanation
Indices: 574918--574954 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
574908 TCTCCCTTTT
574918 TCTTTCTTTTTTCACCAG
1 TCTTTCTTTTTTCACCAG
*
574936 TCTTTCTTTTTTCATCAG
1 TCTTTCTTTTTTCACCAG
574954 T
1 T
574955 ATTTAACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.24, G:0.05, T:0.59
Consensus pattern (18 bp):
TCTTTCTTTTTTCACCAG
Found at i:575300 original size:20 final size:21
Alignment explanation
Indices: 575262--575301 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
575252 TAAACCAAAC
575262 ATCACTAAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
575283 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
575302 TAAAAATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:582294 original size:28 final size:28
Alignment explanation
Indices: 582246--582300 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
582236 TCTTATGGCA
*
582246 TGTACTAGGATGATATTATCTTTTATTTT
1 TGTACTAGGATGATA-TATCTCTTATTTT
*
582275 TGTATTAGAGATGATA-ATCTCTTATT
1 TGTACTAG-GATGATATATCTCTTATT
582301 ATGTTGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 7 0.30
30 7 0.30
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (28 bp):
TGTACTAGGATGATATATCTCTTATTTT
Found at i:589885 original size:21 final size:21
Alignment explanation
Indices: 589873--589930 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
589863 TAGATGCATG
589873 ACTTGTATCGGTAGAAGTTAT
1 ACTTGTATCGGTAGAAGTTAT
*
589894 ACTTGTATTGGTAGAAGTTAT
1 ACTTGTATCGGTAGAAGTTAT
589915 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
589931 CTAGCACAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGTTAT
Found at i:592845 original size:2 final size:2
Alignment explanation
Indices: 592840--592870 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
592830 TCATATATGT
592840 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
592871 TTACATATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:593618 original size:3 final size:3
Alignment explanation
Indices: 593610--593670 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
593600 ATGAACTATG
* *
593610 TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
593658 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
593671 TTCCTTTTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:596346 original size:14 final size:14
Alignment explanation
Indices: 596327--596362 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
596317 TTGAGAGATG
*
596327 TCAAGTGCCTAGAA
1 TCAAGTCCCTAGAA
596341 TCAAGTCCCTAGAA
1 TCAAGTCCCTAGAA
596355 TCAAGTCC
1 TCAAGTCC
596363 GTAAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (14 bp):
TCAAGTCCCTAGAA
Found at i:604324 original size:21 final size:21
Alignment explanation
Indices: 604312--604369 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
604302 TAGATGCATG
604312 ACTTGTATCGGTAGAAGTTAT
1 ACTTGTATCGGTAGAAGTTAT
*
604333 ACTTGTATTGGTAGAAGTTAT
1 ACTTGTATCGGTAGAAGTTAT
604354 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
604370 CTAGCACAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGTTAT
Found at i:607284 original size:2 final size:2
Alignment explanation
Indices: 607279--607309 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
607269 TCATATATGT
607279 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
607310 TTACATATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:608057 original size:3 final size:3
Alignment explanation
Indices: 608049--608109 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
608039 ATGAACTATG
* *
608049 TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
608097 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
608110 TTCCTTTTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:610785 original size:14 final size:14
Alignment explanation
Indices: 610766--610801 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
610756 TTGAGAGATG
*
610766 TCAAGTGCCTAGAA
1 TCAAGTCCCTAGAA
610780 TCAAGTCCCTAGAA
1 TCAAGTCCCTAGAA
610794 TCAAGTCC
1 TCAAGTCC
610802 GTAAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (14 bp):
TCAAGTCCCTAGAA
Found at i:613678 original size:55 final size:55
Alignment explanation
Indices: 613594--613709 Score: 225
Period size: 55 Copynumber: 2.1 Consensus size: 55
613584 AGTGTAAAGT
613594 AAGAATCAAAATGATCTAACATCAAAAGATACTCTTGTATTCATTTAAGATCATC
1 AAGAATCAAAATGATCTAACATCAAAAGATACTCTTGTATTCATTTAAGATCATC
613649 AAGAATCAAAATGATCTAACATCAAAAGATACTCTTGTATTCATTTAAGATCATC
1 AAGAATCAAAATGATCTAACATCAAAAGATACTCTTGTATTCATTTAAGATCATC
613704 AA-AATC
1 AAGAATC
613710 CGTCATTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 4 0.07
55 57 0.93
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (55 bp):
AAGAATCAAAATGATCTAACATCAAAAGATACTCTTGTATTCATTTAAGATCATC
Found at i:622149 original size:18 final size:19
Alignment explanation
Indices: 622118--622164 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
622108 CAAAAAAGTG
*
622118 ATAAAAAAGT-CGAGAAAA
1 ATAAAAAAATACGAGAAAA
*
622136 A-AGAAAAATACGAGAAAA
1 ATAAAAAAATACGAGAAAA
622154 ATAAAAAAATA
1 ATAAAAAAATA
622165 AAGAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 8 0.33
ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11
Consensus pattern (19 bp):
ATAAAAAAATACGAGAAAA
Found at i:622154 original size:19 final size:18
Alignment explanation
Indices: 622118--622164 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
622108 CAAAAAAGTG
*
622118 ATAAAAAAGT-CGAGAAA
1 ATAAAAAAATACGAGAAA
622135 A-AAGAAAAATACGAGAAAA
1 ATAA-AAAAATACGAG-AAA
622154 ATAAAAAAATA
1 ATAAAAAAATA
622165 AAGAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 2 0.08
17 6 0.24
18 4 0.16
19 11 0.44
20 2 0.08
ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11
Consensus pattern (18 bp):
ATAAAAAAATACGAGAAA
Found at i:622169 original size:18 final size:18
Alignment explanation
Indices: 622130--622171 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
622120 AAAAAAGTCG
* *
622130 AGAAAAAAGAAAAATACG
1 AGAAAAAAAAAAAATACA
622148 AGAAAAATAAAAAAATA-A
1 AGAAAAA-AAAAAAATACA
622166 AGAAAA
1 AGAAAA
622172 TTTTCTGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (18 bp):
AGAAAAAAAAAAAATACA
Found at i:629860 original size:50 final size:50
Alignment explanation
Indices: 629756--629865 Score: 116
Period size: 50 Copynumber: 2.2 Consensus size: 50
629746 CGTAATGGCG
* * **
629756 AATCTCATACACCTAAAGCTGTAGAGGGGCAAATTGAAGCTTCATTGGTG
1 AATCTCATACACCTAAAGCTGTAGAGGAGCAAATTGAAGCTTCATAGGAA
* * *
629806 AATCTCATTCACCTAAAGTTGTAGAGGAGCAGATTGAAG-TTGCA-AGGAAA
1 AATCTCATACACCTAAAGCTGTAGAGGAGCAAATTGAAGCTT-CATAGG-AA
*
629856 AATCTTATAC
1 AATCTCATAC
629866 TCTTGAAGCT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
49 4 0.08
50 45 0.92
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (50 bp):
AATCTCATACACCTAAAGCTGTAGAGGAGCAAATTGAAGCTTCATAGGAA
Found at i:629969 original size:40 final size:40
Alignment explanation
Indices: 629925--630051 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
629915 ACCAGAGGGT
629925 AGATTAAAGACCATCTGATCTCTTACCCCGACCATGGGGC
1 AGATTAAAGACCATCTGATCTCTTACCCCGACCATGGGGC
* * ** *
629965 AGATT-AAGTA--ATCTAATCTTTTACCCTAACCA-GAAGGC
1 AGATTAAAG-ACCATCTGATCTCTTACCCCGACCATG-GGGC
* * *
630003 AGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGAC
1 AGATTAAAGACCATCTGATCTCTTACCCCGACCATGGGGC
630043 AGATTAAAG
1 AGATTAAAG
630052 CAATCCAATC
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
37 1 0.01
38 27 0.40
39 6 0.09
40 33 0.49
41 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (40 bp):
AGATTAAAGACCATCTGATCTCTTACCCCGACCATGGGGC
Found at i:630030 original size:78 final size:79
Alignment explanation
Indices: 629901--630088 Score: 297
Period size: 78 Copynumber: 2.4 Consensus size: 79
629891 TACAACCCCG
* * * *
629901 AATCTTTTACCCTAACCAGAGGGTAGATTAAAGACCATCTGATCTCTTACCCCGACCATGGGGCA
1 AATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGACA
* *
629966 GATT-AAGTAATCT
66 GATTAAAGCAATCC
*
629979 AATCTTTTACCCTAACCAGAAGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGACA
1 AATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGACA
630044 GATTAAAGCAATCC
66 GATTAAAGCAATCC
*
630058 AATCTTTTACCCTAACCAGAGGGCAAATTGA
1 AATCTTTTACCCTAACCAGAGGGCAGATTGA
630089 GATAATCTAA
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 64 0.64
79 36 0.36
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (79 bp):
AATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGACA
GATTAAAGCAATCC
Found at i:630107 original size:78 final size:77
Alignment explanation
Indices: 629901--630109 Score: 283
Period size: 78 Copynumber: 2.7 Consensus size: 77
629891 TACAACCCCG
* * *
629901 AATCTTTTACCCTAACCAGAGGGTAGATTAAAGACCATCTGATCTCTTACCCCGACCATGGGGCA
1 AATCTTTTACCCTAACCAGAGGGCAGATT-GAGACCATCTGATCTCTTACCCCGACCATGGGACA
* *
629966 GATTAAGTAATCT
65 GATTAAGCAATCC
* *
629979 AATCTTTTACCCTAACCAGAAGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGACA
1 AATCTTTTACCCTAACCAGAGGGCAGATTG-AGACCATCTGATCTCTTACCCCGACCATGGGACA
630044 GATTAAAGCAATCC
65 GATT-AAGCAATCC
* ** * *
630058 AATCTTTTACCCTAACCAGAGGGCAAATTGAGATAATCTAATCTTTTACCCC
1 AATCTTTTACCCTAACCAGAGGGCAGATTGAGACCATCTGATCTCTTACCCC
630110 TAAAGTTATA
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
78 80 0.70
79 35 0.30
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (77 bp):
AATCTTTTACCCTAACCAGAGGGCAGATTGAGACCATCTGATCTCTTACCCCGACCATGGGACAG
ATTAAGCAATCC
Found at i:636542 original size:41 final size:42
Alignment explanation
Indices: 636497--636605 Score: 105
Period size: 41 Copynumber: 2.6 Consensus size: 42
636487 ATACCGACAC
* * * * *
636497 GAAGCCTGCTAGGCTTAAGGCTTGGTTCGTTTCACTGGCT-A
1 GAAGCCTGCTAGGCTCAAGGCTTGATTCATTCCACCGGCTCA
* * * *
636538 GAAGCTTGGTAGGCTCAAGTCTTGATTTATTCCACCGGCTCA
1 GAAGCCTGCTAGGCTCAAGGCTTGATTCATTCCACCGGCTCA
* *
636580 -AAGCCTGCTAGGCCCGAGGCTTGATT
1 GAAGCCTGCTAGGCTCAAGGCTTGATT
636606 TACTACATTA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 52 0.98
42 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (42 bp):
GAAGCCTGCTAGGCTCAAGGCTTGATTCATTCCACCGGCTCA
Found at i:636913 original size:12 final size:12
Alignment explanation
Indices: 636896--636936 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
636886 AATACAAAAA
636896 AAATATTAACCC
1 AAATATTAACCC
636908 AAATATTAA-CC
1 AAATATTAACCC
*
636919 TAATACTTAACCC
1 AAATA-TTAACCC
636932 AAATA
1 AAATA
636937 CACAAGCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.24
12 13 0.52
13 6 0.24
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATATTAACCC
Found at i:642072 original size:15 final size:13
Alignment explanation
Indices: 642048--642086 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
642038 TGCATATAAA
642048 TACATGCATTCAT
1 TACATGCATTCAT
642061 TAACATTGCATTTCAT
1 T-ACA-TGCA-TTCAT
642077 TACATGCATT
1 TACATGCATT
642087 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.13
14 7 0.30
15 7 0.30
16 6 0.26
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (13 bp):
TACATGCATTCAT
Found at i:644292 original size:21 final size:19
Alignment explanation
Indices: 644263--644313 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
644253 AGATTCGGTG
644263 AAAAA-AAAAAGAAAAGTAA
1 AAAAAGAAAAAGAAAAG-AA
* *
644282 AGAAAGGAAAAATAAAAGAA
1 A-AAAAGAAAAAGAAAAGAA
644302 AAAAAGAAAAAG
1 AAAAAGAAAAAG
644314 GAGAGGTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 10 0.38
20 6 0.23
21 10 0.38
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAAGAA
Done.