Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 15 of 26
Found at i:2512853 original size:20 final size:20
Alignment explanation
Indices: 2512828--2512880 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
2512818 GTTCATTTTC
2512828 AAATTTTAATTTAATTTAAT
1 AAATTTTAATTTAATTTAAT
2512848 AAA-TTTAGGA-TTAATTTAAT
1 AAATTTTA--ATTTAATTTAAT
* *
2512868 AATTTTTATTTTA
1 AAATTTTAATTTA
2512881 TTAAGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
19 4 0.15
20 18 0.67
21 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
AAATTTTAATTTAATTTAAT
Found at i:2514655 original size:10 final size:10
Alignment explanation
Indices: 2514642--2514676 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2514632 TATTTGAGTG
*
2514642 TATGTATATG
1 TATGTATATA
2514652 TATGTATATA
1 TATGTATATA
*
2514662 TATATATATA
1 TATGTATATA
2514672 TATGT
1 TATGT
2514677 GTGTGTGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (10 bp):
TATGTATATA
Found at i:2514679 original size:2 final size:2
Alignment explanation
Indices: 2514674--2514712 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2514664 TATATATATA
2514674 TG TG TG TG TG TG TG TG TG TG 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 TG TG TG TG T
2514713 TGCATATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2516979 original size:15 final size:15
Alignment explanation
Indices: 2516959--2516988 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2516949 AACTTCTCTT
2516959 TCCTTGTCTGTTAGA
1 TCCTTGTCTGTTAGA
2516974 TCCTTGTCTGTTAGA
1 TCCTTGTCTGTTAGA
2516989 GTATCAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (15 bp):
TCCTTGTCTGTTAGA
Found at i:2519339 original size:5 final size:5
Alignment explanation
Indices: 2519329--2519354 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2519319 GGTGCTCTCG
2519329 CTCTT CTCTT CTCTT CTCTT CTCTT C
1 CTCTT CTCTT CTCTT CTCTT CTCTT C
2519355 CCTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (5 bp):
CTCTT
Found at i:2519632 original size:17 final size:18
Alignment explanation
Indices: 2519599--2519632 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2519589 CTCTGAGTTA
2519599 GCTTTCAGATCATCTGTC
1 GCTTTCAGATCATCTGTC
2519617 GCTTTCAGAT-ATCTGT
1 GCTTTCAGATCATCTGT
2519633 ACTTTATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (18 bp):
GCTTTCAGATCATCTGTC
Found at i:2521881 original size:20 final size:19
Alignment explanation
Indices: 2521832--2521883 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 19
2521822 TGATGTTATA
2521832 ATTTTAAAATATATAATTAAT
1 ATTTT-AAAT-TATAATTAAT
2521853 ATTTT-AATTATAAGTTAAT
1 ATTTTAAATTATAA-TTAAT
2521872 -TTATTAAATTAT
1 ATT-TTAAATTAT
2521884 TATAACTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 7 0.25
19 10 0.36
20 6 0.21
21 5 0.18
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTTAAATTATAATTAAT
Found at i:2523452 original size:22 final size:22
Alignment explanation
Indices: 2523426--2523486 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
2523416 TAATTATAAA
*
2523426 ATTTATTATTATGTTA-CTAATT
1 ATTTATTATTATGTTATC-AATC
*
2523448 ATTTATTATTACGTTATCAATC
1 ATTTATTATTATGTTATCAATC
*
2523470 ATTTGTTATTATGTTAT
1 ATTTATTATTATGTTAT
2523487 TTTATTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (22 bp):
ATTTATTATTATGTTATCAATC
Found at i:2523517 original size:22 final size:22
Alignment explanation
Indices: 2523489--2523538 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
2523479 TATGTTATTT
*
2523489 TATTAATAATTTACTACTATGA
1 TATTAATAATTTACTAATATGA
* *
2523511 TATTAATAATTTATTAATATGT
1 TATTAATAATTTACTAATATGA
2523533 TATTAA
1 TATTAA
2523539 CTGTTAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (22 bp):
TATTAATAATTTACTAATATGA
Found at i:2523575 original size:22 final size:23
Alignment explanation
Indices: 2523550--2523610 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 23
2523540 TGTTAAGTAT
2523550 TATATTATCATTTATTTATTA-A
1 TATATTATCATTTATTTATTACA
*
2523572 TATATTATC-TATTATTTTTTACA
1 TATATTATCAT-TTATTTATTACA
2523595 TATTATTAATCATTTA
1 TA-TATT-ATCATTTA
2523611 CTATTTTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 1 0.03
22 18 0.55
23 3 0.09
24 4 0.12
25 6 0.18
26 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTATCATTTATTTATTACA
Found at i:2524599 original size:264 final size:264
Alignment explanation
Indices: 2524129--2524646 Score: 973
Period size: 264 Copynumber: 2.0 Consensus size: 264
2524119 AAAAAGGAGA
* *
2524129 AAGAAAAAAAAGTGACCTAAGTTTCGAACACAAACCACATTGATAAAACTCCATTATGACTTCTA
1 AAGAAAAAAAAGTGACCTAAGTTTCAAACACAAACCACATTGATAAAACTCCATTATGACCTCTA
2524194 CGCCAAAGCCTAACTTTGGTCATAAAATGACAAAAATAAAAGGGTTTAAACGGGTTTAAGCACCA
66 CGCCAAAGCCTAACTTTGGTCATAAAATGACAAAAATAAAAGGGTTTAAACGGGTTTAAGCACCA
2524259 TTATTTTCTGATTAAAAGGGTTTAAGCGCTTATTTAAAAAATCTGAACGGTAAAAAAAAAGCTCA
131 TTATTTTCTGATTAAAAGGGTTTAAGCGCTTATTTAAAAAATCTGAACGGTAAAAAAAAAGCTCA
*
2524324 CACGGAGGGGAAAAACATATTAAAATTTGGGAATGATCCAACGATAGACGGTGATCGGAATGATC
196 CACGGAGGGGAAAAACATATTAAAATTTGGGAATGATCCAACGATAGACGATGATCGGAATGATC
2524389 CAAC
261 CAAC
* *
2524393 AAGAAAAAAAAGTGACCTAAGTTTCAAACCCAAGCCACATTGATAAAACTCCATTATGACCTCTA
1 AAGAAAAAAAAGTGACCTAAGTTTCAAACACAAACCACATTGATAAAACTCCATTATGACCTCTA
2524458 CGCCAAAGCCTAACTTTGGTCATAAAATGACAAAAATAAAAGGGTTTAAACGGGTTTAAGCACCA
66 CGCCAAAGCCTAACTTTGGTCATAAAATGACAAAAATAAAAGGGTTTAAACGGGTTTAAGCACCA
*
2524523 TTATTTTCTGATTAAAAGGGTTTAAGCGCTTATTTAAAAAATCTGAACGGTAAAAAAGAAGCTCA
131 TTATTTTCTGATTAAAAGGGTTTAAGCGCTTATTTAAAAAATCTGAACGGTAAAAAAAAAGCTCA
*
2524588 CATGGAGGGGAAAAACATATTAAAATTTGGGAATGATCCAACGATAGACGATGATCGGA
196 CACGGAGGGGAAAAACATATTAAAATTTGGGAATGATCCAACGATAGACGATGATCGGA
2524647 TTTGAGGGAT
Statistics
Matches: 247, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
264 247 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (264 bp):
AAGAAAAAAAAGTGACCTAAGTTTCAAACACAAACCACATTGATAAAACTCCATTATGACCTCTA
CGCCAAAGCCTAACTTTGGTCATAAAATGACAAAAATAAAAGGGTTTAAACGGGTTTAAGCACCA
TTATTTTCTGATTAAAAGGGTTTAAGCGCTTATTTAAAAAATCTGAACGGTAAAAAAAAAGCTCA
CACGGAGGGGAAAAACATATTAAAATTTGGGAATGATCCAACGATAGACGATGATCGGAATGATC
CAAC
Found at i:2524895 original size:14 final size:15
Alignment explanation
Indices: 2524871--2524903 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2524861 TTGAGGTGAG
*
2524871 AAAGAAAGAAGGAAA
1 AAAGAAAGAAGAAAA
2524886 AAAG-AAGAAGAAAA
1 AAAGAAAGAAGAAAA
2524900 AAAG
1 AAAG
2524904 GAAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAAAA
Found at i:2527568 original size:78 final size:79
Alignment explanation
Indices: 2527444--2527591 Score: 187
Period size: 78 Copynumber: 1.9 Consensus size: 79
2527434 ATTTATGTGG
* *
2527444 ACTCTATTTTTAATATTTAGTTCATTTGGATTTAAATAAATTAATAA-A-AATTACATATTTAAA
1 ACTCTATTTTTAATATTTAGTTAATTTAGATTTAAATAAA-TAATAATAGAATTACATATTTAAA
2527507 AAAATGTATTCATAA
65 AAAATGTATTCATAA
* *
2527522 ACTCTATTTTTAAATATTTA-TTAATTTAGATTTAAATTTTAA-AATAATAGAATTATATATTTA
1 ACTCTATTTTT-AATATTTAGTTAATTTAGATTTAAA--TAAATAATAATAGAATTACATATTTA
*
2527585 AATAAAT
63 AAAAAAT
2527592 TTTTTTATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
78 30 0.50
79 9 0.15
80 21 0.35
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (79 bp):
ACTCTATTTTTAATATTTAGTTAATTTAGATTTAAATAAATAATAATAGAATTACATATTTAAAA
AAATGTATTCATAA
Found at i:2527739 original size:107 final size:105
Alignment explanation
Indices: 2527519--2527724 Score: 235
Period size: 107 Copynumber: 2.0 Consensus size: 105
2527509 AATGTATTCA
* *
2527519 TAAACTCT-ATTTTTAAATATTTATTAATTTAGATTTAAATTTTAAAATAATAGAATTATATATT
1 TAAACT-TGATTTTTAAATATTTATTAATTTAGATTTAAA-TATAAAATAATAAAATTATATATT
** *
2527583 TAAATAAATTTTTTTATTAATTTTAAAACATATTGATATAATG
64 TAAATAAATTTTTAAATT-ATTTTAAAAAATATTGATATAATG
* *
2527626 TAAACTTGATTTTTTAATATTTATTAATTTTA-ATTTAAA-AT-ATATAATAAAATTATATATTT
1 TAAACTTGATTTTTAAATATTTATTAA-TTTAGATTTAAATATAAAATAATAAAATTATATATTT
* *
2527688 AGATATTAA-TTTTAAATT-TTTTAAAAAATATTTATAT
65 A-A-ATAAATTTTTAAATTATTTTAAAAAATATTGATAT
2527725 CAATTGTTAA
Statistics
Matches: 86, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
103 17 0.20
104 20 0.23
105 9 0.10
106 5 0.06
107 31 0.36
108 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (105 bp):
TAAACTTGATTTTTAAATATTTATTAATTTAGATTTAAATATAAAATAATAAAATTATATATTTA
AATAAATTTTTAAATTATTTTAAAAAATATTGATATAATG
Found at i:2527827 original size:2 final size:2
Alignment explanation
Indices: 2527820--2527853 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2527810 ACAGATCGAG
2527820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2527854 GACAGATCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2531894 original size:20 final size:20
Alignment explanation
Indices: 2531871--2531908 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2531861 GCAATTTATC
2531871 ATATTATA-ATTGTATTTAAA
1 ATATTATATATT-TATTTAAA
*
2531891 ATATTTTATATTTATTTA
1 ATATTATATATTTATTTA
2531909 TTAATTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATATTATATATTTATTTAAA
Found at i:2531971 original size:25 final size:25
Alignment explanation
Indices: 2531943--2531995 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2531933 TATTAAATAA
*
2531943 ATTTTGAAATA-TATATTTGTATCAT
1 ATTTT-AAATATTATATTTATATCAT
* *
2531968 ATTTTAATTATTTTATTTATATCAT
1 ATTTTAAATATTATATTTATATCAT
2531993 ATT
1 ATT
2531996 CATTTAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (25 bp):
ATTTTAAATATTATATTTATATCAT
Found at i:2535742 original size:13 final size:13
Alignment explanation
Indices: 2535724--2535759 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
2535714 CATTGCCGTA
2535724 TATTATTATAAAT
1 TATTATTATAAAT
2535737 TATTA-TAT-AAT
1 TATTATTATAAAT
2535748 TA-TATTATAAAT
1 TATTATTATAAAT
2535760 ATAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.10
11 8 0.38
12 6 0.29
13 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTATTATAAAT
Found at i:2540092 original size:129 final size:129
Alignment explanation
Indices: 2539862--2540121 Score: 520
Period size: 129 Copynumber: 2.0 Consensus size: 129
2539852 GGGAAATTAG
2539862 GTCACATGAAAAGGAATTATAGAATTCTGAAATAAGTAATAGATAAAAACCAATAAAAGGAAGAC
1 GTCACATGAAAAGGAATTATAGAATTCTGAAATAAGTAATAGATAAAAACCAATAAAAGGAAGAC
2539927 GACAAAAATACTTTGCAATGAAGAAGATTGTTGTCACATAGTAGAACAAGTTGTCGACTGGGTA
66 GACAAAAATACTTTGCAATGAAGAAGATTGTTGTCACATAGTAGAACAAGTTGTCGACTGGGTA
2539991 GTCACATGAAAAGGAATTATAGAATTCTGAAATAAGTAATAGATAAAAACCAATAAAAGGAAGAC
1 GTCACATGAAAAGGAATTATAGAATTCTGAAATAAGTAATAGATAAAAACCAATAAAAGGAAGAC
2540056 GACAAAAATACTTTGCAATGAAGAAGATTGTTGTCACATAGTAGAACAAGTTGTCGACTGGGTA
66 GACAAAAATACTTTGCAATGAAGAAGATTGTTGTCACATAGTAGAACAAGTTGTCGACTGGGTA
2540120 GT
1 GT
2540122 GGACTCGGCA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 131 1.00
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.23
Consensus pattern (129 bp):
GTCACATGAAAAGGAATTATAGAATTCTGAAATAAGTAATAGATAAAAACCAATAAAAGGAAGAC
GACAAAAATACTTTGCAATGAAGAAGATTGTTGTCACATAGTAGAACAAGTTGTCGACTGGGTA
Found at i:2544863 original size:23 final size:23
Alignment explanation
Indices: 2544814--2544863 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2544804 TTTTATATGC
*
2544814 TTATTTAATTAAATTATTTAAGT
1 TTATTTAATTAAATTATTTAAGA
* *
2544837 TTATTTTATTTAATTATATT-AGA
1 TTATTTAATTAAATTAT-TTAAGA
2544860 TTAT
1 TTAT
2544864 AAATTATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTATTTAATTAAATTATTTAAGA
Found at i:2547595 original size:50 final size:50
Alignment explanation
Indices: 2547541--2547639 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
2547531 TTACTTATTA
* *
2547541 CATGTTTTTTTTCTTAGTGACAGCTTTGCATTCATGTTTGACAAAATTGG
1 CATGTTTTTTTTCTTAGTGACAACTTTGCATACATGTTTGACAAAATTGG
*
2547591 CATGTTTTTTTTCTTAGTGACAACTTTGCATACATGTTTGACAAGATTG
1 CATGTTTTTTTTCTTAGTGACAACTTTGCATACATGTTTGACAAAATTG
2547640 AATTTTCTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.45
Consensus pattern (50 bp):
CATGTTTTTTTTCTTAGTGACAACTTTGCATACATGTTTGACAAAATTGG
Found at i:2549072 original size:42 final size:42
Alignment explanation
Indices: 2548981--2549072 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
2548971 TTAAACTGGT
*
2548981 ATTTAAAAATAAAAAATATTTTTATTTAAATTTAATTATAAA
1 ATTTAAAAATAAAAAATATTTTTATTTAAATTTAAATATAAA
* *
2549023 ATATT-AAAATAAAAAATATATTTT-TATTAATTTTTAAATAT-TA
1 AT-TTAAAAATAAAAAATAT-TTTTAT-TTAA-ATTTAAATATAAA
2549066 ATTTAAA
1 ATTTAAA
2549073 TTTTTTGATG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
42 19 0.45
43 15 0.36
44 8 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (42 bp):
ATTTAAAAATAAAAAATATTTTTATTTAAATTTAAATATAAA
Found at i:2551225 original size:2 final size:2
Alignment explanation
Indices: 2551218--2551254 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2551208 CTTTTTAGAA
2551218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2551255 ATTTTCTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2554248 original size:20 final size:20
Alignment explanation
Indices: 2554220--2554274 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2554210 CTGTCAAGGA
*
2554220 AATGCATCGATACATT-ATT
1 AATGTATCGATACATTGATT
*
2554239 CAATGTATCGATATATTGATT
1 -AATGTATCGATACATTGATT
**
2554260 TTTGTATCGATACAT
1 AATGTATCGATACAT
2554275 CTGAGAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTGATT
Found at i:2554317 original size:20 final size:20
Alignment explanation
Indices: 2554292--2554345 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
2554282 TTTTACCTAG
2554292 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
2554312 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
2554332 ATGTATCGATACAT
1 ATGTATCGATACAT
2554346 GCAGGCAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTATTCA
Found at i:2561150 original size:17 final size:17
Alignment explanation
Indices: 2561101--2561151 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
2561091 AAAATTAAAT
2561101 TTTACTTATATTTA-TTA
1 TTTACTTAT-TTTATTTA
**
2561118 TTTACTTAAATTATTTA
1 TTTACTTATTTTATTTA
*
2561135 TTTATTTATTTTATTTA
1 TTTACTTATTTTATTTA
2561152 AATACATATC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 3 0.11
17 25 0.89
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTACTTATTTTATTTA
Found at i:2563186 original size:11 final size:11
Alignment explanation
Indices: 2563172--2563197 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2563162 ATTTAATATC
2563172 TTAATTTTTTA
1 TTAATTTTTTA
2563183 TTAATTTTTTA
1 TTAATTTTTTA
2563194 TTAA
1 TTAA
2563198 AATATCGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTAATTTTTTA
Found at i:2563544 original size:11 final size:11
Alignment explanation
Indices: 2563528--2563552 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2563518 ATTTTCTTTT
2563528 ATTTTAAATAA
1 ATTTTAAATAA
2563539 ATTTTAAATAA
1 ATTTTAAATAA
2563550 ATT
1 ATT
2563553 ATCAGGACTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTTAAATAA
Found at i:2566199 original size:19 final size:19
Alignment explanation
Indices: 2566175--2566223 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2566165 ATTATACTCT
* *
2566175 TTATTTTTATTCTTTTTA-A
1 TTATTTATATT-TTTATATA
2566194 TTATTTATATTTTTATATA
1 TTATTTATATTTTTATATA
2566213 TTATTTA-ATTT
1 TTATTTATATTT
2566224 CGCCCACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTATATTTTTATATA
Found at i:2567607 original size:9 final size:9
Alignment explanation
Indices: 2567593--2567632 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
2567583 AATTACTAAT
2567593 AATTAAATA
1 AATTAAATA
2567602 AATTAAAT-
1 AATTAAATA
2567610 AATTAAAATA
1 AATT-AAATA
2567620 TAATTAAATA
1 -AATTAAATA
2567630 AAT
1 AAT
2567633 CTAATATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.14
9 15 0.54
10 5 0.18
11 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AATTAAATA
Found at i:2567638 original size:19 final size:19
Alignment explanation
Indices: 2567597--2567642 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
2567587 ACTAATAATT
*
2567597 AAATA-AATTAAATAATTA
1 AAATATAATTAAATAAATA
*
2567615 AAATATAATTAAATAAATC
1 AAATATAATTAAATAAATA
*
2567634 TAATATAAT
1 AAATATAAT
2567643 ATTCTATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATAATTAAATAAATA
Found at i:2567837 original size:22 final size:21
Alignment explanation
Indices: 2567806--2567849 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
2567796 TATTTTTATT
2567806 TAAATTTAAT-TATAAAATATA
1 TAAATTTAATATA-AAAATATA
2567827 TAAATATTAATATAAAAATATA
1 TAAAT-TTAATATAAAAATATA
2567849 T
1 T
2567850 TTTTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTAATATAAAAATATA
Found at i:2568232 original size:2 final size:2
Alignment explanation
Indices: 2568225--2568276 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
2568215 AATGTGTATG
2568225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2568267 TA TA CA TA TA
1 TA TA TA TA TA
2568277 AATCCTGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2570275 original size:3 final size:3
Alignment explanation
Indices: 2570267--2570304 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2570257 AATAATGTAA
*
2570267 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2570305 AATGTTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2587551 original size:279 final size:279
Alignment explanation
Indices: 2587051--2588727 Score: 3354
Period size: 279 Copynumber: 6.0 Consensus size: 279
2587041 AAGAGATCAT
2587051 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
1 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
2587116 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
66 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
2587181 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
131 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
2587246 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
196 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
2587311 CAGGAAGCAGTAAGTTGCC
261 CAGGAAGCAGTAAGTTGCC
2587330 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
1 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
2587395 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
66 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
2587460 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
131 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
2587525 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
196 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
2587590 CAGGAAGCAGTAAGTTGCC
261 CAGGAAGCAGTAAGTTGCC
2587609 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
1 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
2587674 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
66 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
2587739 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
131 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
2587804 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
196 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
2587869 CAGGAAGCAGTAAGTTGCC
261 CAGGAAGCAGTAAGTTGCC
2587888 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
1 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
2587953 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
66 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
2588018 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
131 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
2588083 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
196 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
2588148 CAGGAAGCAGTAAGTTGCC
261 CAGGAAGCAGTAAGTTGCC
2588167 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
1 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
2588232 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
66 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
2588297 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
131 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
2588362 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
196 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
2588427 CAGGAAGCAGTAAGTTGCC
261 CAGGAAGCAGTAAGTTGCC
2588446 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
1 CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
2588511 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
66 AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
2588576 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
131 AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
2588641 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
196 TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
2588706 CAGGAAGCAGTAAGTTGCC
261 CAGGAAGCAGTAAGTTGCC
2588725 CAT
1 CAT
2588728 TCATTTGGTC
Statistics
Matches: 1398, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
279 1398 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (279 bp):
CATAAGCTACAAATGAAGGTTTCAGTTCATTTCTAGGTAAAGTGACAAGGAGGAAAGAGACCATG
AGATACATGTGAAAACCATCTAGCTAGAAATTGACAAATTAATTTTGTTTCTAAATCTAATTACC
AGAATCAAAAACAAATTAGGAACAGAAAAAGAGGGGTATAAACTCAAACTAGTAGGTCTATTTGA
TCAATTTTGGCAGCTGTCATTTGTTGGGAGAAGTCAAATTGGAGTTATAAGAACAGAGAATGAAT
CAGGAAGCAGTAAGTTGCC
Found at i:2590363 original size:2 final size:2
Alignment explanation
Indices: 2590358--2590387 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2590348 ATCTGGGGGG
2590358 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2590388 AGGAAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2590893 original size:13 final size:15
Alignment explanation
Indices: 2590853--2590894 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2590843 ATATAATATA
* *
2590853 TATTAATTTTATATT
1 TATTTATTTTATAAT
2590868 TATTTATTTTATAAT
1 TATTTATTTTATAAT
2590883 T-TTTA-TTTATAA
1 TATTTATTTTATAA
2590895 AAAATAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 7 0.28
14 4 0.16
15 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTATTTTATAAT
Found at i:2590979 original size:15 final size:15
Alignment explanation
Indices: 2590959--2590989 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2590949 ATATTTTAAA
2590959 ATTAAAAATTAAATT
1 ATTAAAAATTAAATT
*
2590974 ATTAAATATTAAATT
1 ATTAAAAATTAAATT
2590989 A
1 A
2590990 AAAAATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAAAAATTAAATT
Found at i:2590994 original size:29 final size:29
Alignment explanation
Indices: 2590937--2590993 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
2590927 TAAAAAATAT
* *
2590937 ATTAAATTATTTATATTTTAAAATTAAAA
1 ATTAAATTATTTAAATATTAAAATTAAAA
2590966 ATTAAATTA-TTAAATATT-AAATTAAAA
1 ATTAAATTATTTAAATATTAAAATTAAAA
2590993 A
1 A
2590994 ATTTGTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 10 0.38
28 7 0.27
29 9 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATTAAATTATTTAAATATTAAAATTAAAA
Found at i:2592297 original size:27 final size:28
Alignment explanation
Indices: 2592266--2592333 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
2592256 AATTAGAATA
*
2592266 TATAATATTTTTATAAATG-TAA-ATATT
1 TATAATATTTATATAAA-GATAATATATT
*
2592293 TATAAT-TTTATATATAGATAATATATT
1 TATAATATTTATATAAAGATAATATATT
2592320 TA-AATATTATATAT
1 TATAATATT-TATAT
2592334 TATATAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 1 0.03
26 14 0.40
27 15 0.43
28 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
TATAATATTTATATAAAGATAATATATT
Found at i:2592333 original size:15 final size:17
Alignment explanation
Indices: 2592313--2592349 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2592303 TATATAGATA
2592313 ATATATT-TA-AATATT
1 ATATATTATATAATATT
*
2592328 ATATATTATATAATTTT
1 ATATATTATATAATATT
2592345 ATATA
1 ATATA
2592350 ACATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 2 0.11
17 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATATTATATAATATT
Found at i:2592355 original size:15 final size:14
Alignment explanation
Indices: 2592300--2592360 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 14
2592290 ATTTATAATT
*
2592300 TTATATATAGATAA
1 TTATATATAAATAA
*
2592314 -TATATTTAAAT-A
1 TTATATATAAATAA
*
2592326 TTATATATTATATAA
1 TTATATA-TAAATAA
*
2592341 TTTTATATAACATAA
1 TTATATATAA-ATAA
2592356 TTATA
1 TTATA
2592361 ATATGAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
12 1 0.03
13 14 0.39
14 6 0.17
15 15 0.42
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (14 bp):
TTATATATAAATAA
Found at i:2593029 original size:31 final size:32
Alignment explanation
Indices: 2592981--2593049 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
2592971 TAATATACCT
* **
2592981 TTATA-AAATTATATTTTATGTTACAATGTTA
1 TTATATAAATTATATTTTACGTTACAACATTA
* *
2593012 TTATATAAA-TATGTTTTACGTTACCACATTA
1 TTATATAAATTATATTTTACGTTACAACATTA
2593043 TTATATA
1 TTATATA
2593050 CTGTATGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (32 bp):
TTATATAAATTATATTTTACGTTACAACATTA
Found at i:2593088 original size:23 final size:22
Alignment explanation
Indices: 2593062--2593114 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2593052 GTATGTTACT
*
2593062 AATAGCTTTTAGTTTATGAAACA
1 AATA-CTTTTAATTTATGAAACA
* *
2593085 AATATTTTTAATTTATGAAACT
1 AATACTTTTAATTTATGAAACA
*
2593107 AATTCTTT
1 AATACTTT
2593115 GTACAATCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (22 bp):
AATACTTTTAATTTATGAAACA
Found at i:2593166 original size:21 final size:23
Alignment explanation
Indices: 2593136--2593191 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 23
2593126 CTTGTTTTCG
*
2593136 GTATCTTAAAATTGTTATTTTGT
1 GTATTTTAAAATTGTTATTTTGT
*
2593159 -TA-TTT-AAATTGTTATTTTTT
1 GTATTTTAAAATTGTTATTTTGT
2593179 GTATTTTAAAATT
1 GTATTTTAAAATT
2593192 TATTTGTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 14 0.50
21 4 0.14
22 5 0.18
23 5 0.18
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.61
Consensus pattern (23 bp):
GTATTTTAAAATTGTTATTTTGT
Found at i:2593194 original size:21 final size:21
Alignment explanation
Indices: 2593136--2593196 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
2593126 CTTGTTTTCG
* *
2593136 GTATCTTAAAATTGT-TATTTT
1 GTATTTTAAAATT-TATTTTTT
*
2593157 GT-TATTTAAATTGTTATTTTTT
1 GTAT-TTTAAAAT-TTATTTTTT
2593179 GTATTTTAAAATTTATTT
1 GTATTTTAAAATTTATTT
2593197 GTTGGTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.03
21 15 0.47
22 15 0.47
23 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (21 bp):
GTATTTTAAAATTTATTTTTT
Found at i:2593369 original size:6 final size:6
Alignment explanation
Indices: 2593358--2593382 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2593348 AAAATAATTT
2593358 TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
2593383 ATTATAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:2597576 original size:12 final size:13
Alignment explanation
Indices: 2597553--2597628 Score: 54
Period size: 14 Copynumber: 5.9 Consensus size: 13
2597543 TACGCGATTT
*
2597553 AAATAAAATATAAA
1 AAATAATATAT-AA
2597567 AAATAATATATAA
1 AAATAATATATAA
2597580 AAAT-ATGATA-AA
1 AAATAAT-ATATAA
*
2597592 TAA-AAT-TATAA
1 AAATAATATATAA
2597603 TAAA-AATATATAA
1 -AAATAATATATAA
*
2597616 ATATATATATATA
1 AAATA-ATATATA
2597629 TGAATCAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
10 2 0.04
11 2 0.04
12 15 0.29
13 15 0.29
14 17 0.33
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (13 bp):
AAATAATATATAA
Found at i:2597590 original size:25 final size:25
Alignment explanation
Indices: 2597560--2597618 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
2597550 TTTAAATAAA
2597560 ATATAAA-AAATAATAT-ATAAAAAT
1 ATATAAATAAA-AATATAATAAAAAT
*
2597584 ATGATAAATAAAATTATAATAAAAAT
1 AT-ATAAATAAAAATATAATAAAAAT
2597610 ATATAAATA
1 ATATAAATA
2597619 TATATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 2 0.06
25 16 0.52
26 13 0.42
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
ATATAAATAAAAATATAATAAAAAT
Found at i:2597594 original size:15 final size:14
Alignment explanation
Indices: 2597565--2597628 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
2597555 ATAAAATATA
*
2597565 AAAAATA-ATATAT
1 AAAAATATATAAAT
2597578 AAAAATATGATAAAT
1 AAAAATAT-ATAAAT
2597593 -AAAAT-TAT-AAT
1 AAAAATATATAAAT
2597604 AAAAATATATAAAT
1 AAAAATATATAAAT
* *
2597618 ATATATATATA
1 AAAAATATATA
2597629 TGAATCAGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
11 3 0.07
12 7 0.16
13 11 0.26
14 17 0.40
15 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AAAAATATATAAAT
Found at i:2597611 original size:36 final size:36
Alignment explanation
Indices: 2597552--2597621 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
2597542 ATACGCGATT
2597552 TAAATAAAATATAAAAAATAATATATAAAAATATGA
1 TAAATAAAATATAAAAAATAATATATAAAAATATGA
* *
2597588 TAAATAAAATTATAATAAA-AATATATAAATATAT
1 TAAATAAAA-TATAAAAAATAATATATAAAAATAT
2597622 ATATATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 23 0.74
37 8 0.26
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (36 bp):
TAAATAAAATATAAAAAATAATATATAAAAATATGA
Found at i:2597830 original size:11 final size:10
Alignment explanation
Indices: 2597810--2597856 Score: 53
Period size: 9 Copynumber: 4.7 Consensus size: 10
2597800 GGCAGCTGAG
2597810 AAAG-AAAAA
1 AAAGAAAAAA
*
2597819 AAGGAAAAAA
1 AAAGAAAAAA
2597829 AAAG-AAAAA
1 AAAGAAAAAA
2597838 AAAGAAAGAAA
1 AAAGAAA-AAA
2597849 GAAAGAAA
1 -AAAGAAA
2597857 GAATGGAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 12 0.38
10 10 0.31
11 3 0.09
12 7 0.22
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:2597831 original size:12 final size:12
Alignment explanation
Indices: 2597809--2597882 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 12
2597799 GGGCAGCTGA
2597809 GAAAGAAAAAAAG
1 GAAA-AAAAAAAG
2597822 G-AAAAAAAAAG
1 GAAAAAAAAAAG
*
2597833 AAAAAAAAGAAAG
1 GAAAAAAA-AAAG
*
2597846 AAAGAAAGAAAGAATGG
1 GAA-AAA-AAA-AA--G
2597863 AGAAAAAAAAAAG
1 -GAAAAAAAAAAG
2597876 GAAAAAA
1 GAAAAAA
2597883 TTTATATGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
11 8 0.16
12 15 0.29
13 9 0.18
14 4 0.08
15 6 0.12
16 3 0.06
17 4 0.08
18 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.01
Consensus pattern (12 bp):
GAAAAAAAAAAG
Found at i:2597845 original size:4 final size:4
Alignment explanation
Indices: 2597808--2597859 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
2597798 TGGGCAGCTG
* *
2597808 AGAA AGAA AAAA AGGAA A-AA A-AA AGAAA AAAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA A-GAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA
2597856 AGAA
1 AGAA
2597860 TGGAGAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 6 0.15
4 29 0.71
5 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2597951 original size:23 final size:22
Alignment explanation
Indices: 2597921--2597963 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2597911 TATATGTAAA
* *
2597921 ATATTATATTTTTATTTATTTT
1 ATATTATATTTATATATATTTT
2597943 ATATATATATTTATATATATT
1 ATAT-TATATTTATATATATT
2597964 GGTGTTGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATATTATATTTATATATATTTT
Found at i:2598000 original size:12 final size:11
Alignment explanation
Indices: 2597973--2598015 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
2597963 TGGTGTTGTG
*
2597973 TTTATATAATT
1 TTTAAATAATT
2597984 TTTAAATAATAT
1 TTTAAATAAT-T
*
2597996 TTTAAATATTT
1 TTTAAATAATT
2598007 TTATAAATA
1 TT-TAAATA
2598016 TCGTATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 12 0.43
12 16 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAAATAATT
Found at i:2598084 original size:4 final size:4
Alignment explanation
Indices: 2598075--2598102 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2598065 TTTTTATACG
2598075 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
2598103 ATTTTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:2598628 original size:18 final size:19
Alignment explanation
Indices: 2598586--2598632 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
2598576 TATATATTTT
2598586 TATATTTTTTACATATTAA
1 TATATTTTTTACATATTAA
*
2598605 TA-ATTTATTT-CAT-TTCA
1 TATATTT-TTTACATATTAA
2598622 TATATTTTTTA
1 TATATTTTTTA
2598633 TATGTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
17 8 0.33
18 11 0.46
19 5 0.21
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTTTTTACATATTAA
Found at i:2598645 original size:19 final size:19
Alignment explanation
Indices: 2598621--2598671 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
2598611 ATTTCATTTC
*
2598621 ATATATTTTTTATATGTAT
1 ATATATTTATTATATGTAT
*
2598640 ATATATTCATATTATGTGTAT
1 ATATATT--TATTATATGTAT
2598661 ATCATATTTAT
1 AT-ATATTTAT
2598672 GTTATGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 7 0.26
20 3 0.11
21 12 0.44
22 5 0.19
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (19 bp):
ATATATTTATTATATGTAT
Found at i:2598661 original size:17 final size:17
Alignment explanation
Indices: 2598641--2598673 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2598631 TATATGTATA
2598641 TATATTCATA-TTATGTG
1 TATA-TCATATTTATGTG
2598658 TATATCATATTTATGT
1 TATATCATATTTATGT
2598674 TATGTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (17 bp):
TATATCATATTTATGTG
Found at i:2599263 original size:16 final size:15
Alignment explanation
Indices: 2599226--2599292 Score: 61
Period size: 16 Copynumber: 4.6 Consensus size: 15
2599216 TTACGTGGTG
2599226 GAAA-AAAAAA-AAA
1 GAAAGAAAAAAGAAA
* *
2599239 GGAAGAAAAAGGAAA
1 GAAAGAAAAAAGAAA
2599254 GAAAGAAAAAAAGAAA
1 GAAAG-AAAAAAGAAA
*
2599270 GACAGAAGAAAA-AAA
1 GAAAGAA-AAAAGAAA
2599285 GAAA-AAAA
1 GAAAGAAAA
2599293 TTACAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 5 0.11
14 7 0.16
15 15 0.34
16 17 0.39
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAAAGAAA
Found at i:2599271 original size:27 final size:27
Alignment explanation
Indices: 2599227--2599292 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
2599217 TACGTGGTGG
*
2599227 AAAAA-AAAAAAAGGAAGA-AAAAGGAA
1 AAAAAGAAAAAAAGAAAGACAAAA-GAA
* *
2599253 AGAAAGAAAAAAAGAAAGACAGAAGAA
1 AAAAAGAAAAAAAGAAAGACAAAAGAA
2599280 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
2599293 TTACAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.12
27 27 0.79
28 3 0.09
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAAAAAGAAAGACAAAAGAA
Found at i:2599353 original size:35 final size:35
Alignment explanation
Indices: 2599314--2599419 Score: 101
Period size: 38 Copynumber: 2.9 Consensus size: 35
2599304 AAATTATATG
2599314 TTTTTATTTATATTTTTTATATTTAA-AATATTA-TA
1 TTTTTA-TTATATTTTTTATATTTAATAAT-TTATTA
*
2599349 TTTTTA-TATATTTTTTATATATTAATAATTTATTT
1 TTTTTATTATATTTTTTATAT-TTAATAATTTATTA
* * *
2599384 TATTTTATGTATATTTTTATGTATTTATTATTTTAT
1 T-TTTTAT-TATATTTTT-TATATTTAATAATTTAT
2599420 ATATGAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
33 14 0.23
34 7 0.12
35 11 0.18
36 5 0.08
38 19 0.32
39 4 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (35 bp):
TTTTTATTATATTTTTTATATTTAATAATTTATTA
Found at i:2599401 original size:37 final size:34
Alignment explanation
Indices: 2599315--2599408 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 34
2599305 AATTATATGT
*
2599315 TTTTATTTATATTTTT-TATATTTAAAATATTATA
1 TTTTATATATATTTTTATATA-TTAAAATATTATA
*
2599349 TTTT-TATATATTTTTTATATATTAATAATTTATTTTA
1 TTTTATATATA-TTTTTATATATTAA-AA--TATTATA
* *
2599386 TTTTATGTATATTTTTATGTATT
1 TTTTATATATATTTTTATATATT
2599409 TATTATTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
33 5 0.10
34 13 0.26
35 6 0.12
37 21 0.42
38 5 0.10
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (34 bp):
TTTTATATATATTTTTATATATTAAAATATTATA
Found at i:2601060 original size:21 final size:22
Alignment explanation
Indices: 2601007--2601088 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 22
2600997 TATGTATTTA
**
2601007 TATTTATATTTTTTGATATATAAAA
1 TATTTATA-TTTTT-ATATA-AATT
2601032 TA-TTATATTTTTATATAAATT
1 TATTTATATTTTTATATAAATT
*
2601053 T-TTTATA-TATTA-AT-AATT
1 TATTTATATTTTTATATAAATT
2601071 TATTT-TATTTTATATATA
1 TATTTATATTTT-TATATA
2601089 TATATATATG
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
18 7 0.15
19 7 0.15
20 6 0.13
21 10 0.21
22 5 0.11
23 5 0.11
24 5 0.11
25 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (22 bp):
TATTTATATTTTTATATAAATT
Found at i:2601088 original size:27 final size:30
Alignment explanation
Indices: 2601050--2601121 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 30
2601040 TTTTATATAA
* *
2601050 ATTTTTTATATATTA-ATA-ATTTATTT-T
1 ATTTTATATATATTATATATATGTATTTGT
2601077 ATTTTATATATA-TATATATATGTATTTGT
1 ATTTTATATATATTATATATATGTATTTGT
* *
2601106 ATTATGTATATATTAT
1 ATTTTATATATATTAT
2601122 TTTTAAGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.05
27 14 0.38
28 7 0.19
29 11 0.30
30 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (30 bp):
ATTTTATATATATTATATATATGTATTTGT
Found at i:2601108 original size:29 final size:26
Alignment explanation
Indices: 2601053--2601118 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 26
2601043 TATATAAATT
*
2601053 TTTTATATAT-TAATAATTTATTTTA
1 TTTTATATATATAATAATGTATTTTA
2601078 TTTTATATATATATATATATGTATTTGTA
1 TTTTATATATATA-ATA-ATGTATTT-TA
* *
2601107 TTATGTATATAT
1 TTTTATATATAT
2601119 TATTTTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.29
26 2 0.06
27 3 0.09
28 7 0.21
29 12 0.35
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.61
Consensus pattern (26 bp):
TTTTATATATATAATAATGTATTTTA
Found at i:2602417 original size:13 final size:14
Alignment explanation
Indices: 2602381--2602419 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
2602371 TATAAGAATA
2602381 TTAATATATATGAT
1 TTAATATATATGAT
*
2602395 TTAAAAATATAT-AT
1 TT-AATATATATGAT
2602409 TTAATATATAT
1 TTAATATATAT
2602420 TAAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 8 0.36
14 6 0.27
15 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TTAATATATATGAT
Found at i:2602439 original size:24 final size:24
Alignment explanation
Indices: 2602365--2602445 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
2602355 TCTTTTAGTG
*
2602365 TATATATA-TAAGAATATT-AATA
1 TATATATATTAAAAATATTAAATA
* *
2602387 TATATGAT-TTAAAAATA-TATATT
1 TATAT-ATATTAAAAATATTAAATA
*
2602410 TAATATATATTAAAAATATTAAAAA
1 T-ATATATATTAAAAATATTAAATA
*
2602435 TATATAAATTA
1 TATATATATTA
2602446 TTTAAAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
22 6 0.13
23 14 0.30
24 22 0.48
25 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TATATATATTAAAAATATTAAATA
Found at i:2602468 original size:20 final size:20
Alignment explanation
Indices: 2602445--2602491 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2602435 TATATAAATT
2602445 ATTTAAAAAATAAAATAATA
1 ATTTAAAAAATAAAATAATA
* * *
2602465 ATTTTAAAAGTAAAATGATA
1 ATTTAAAAAATAAAATAATA
*
2602485 AATTAAA
1 ATTTAAA
2602492 TATTTATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
ATTTAAAAAATAAAATAATA
Found at i:2602791 original size:22 final size:24
Alignment explanation
Indices: 2602761--2602809 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
2602751 TTAATATAAA
*
2602761 TATATTTAAAAATTTATATTTA-G
1 TATATTTAAAAATATATATTTATG
*
2602784 TATA-TTAATAATATATATTTATG
1 TATATTTAAAAATATATATTTATG
2602807 TAT
1 TAT
2602810 CGTTAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TATATTTAAAAATATATATTTATG
Found at i:2606240 original size:17 final size:18
Alignment explanation
Indices: 2606210--2606248 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2606200 TGGAGCCATT
*
2606210 TAAATTCAATTTTAAAAA
1 TAAATTCAAGTTTAAAAA
2606228 TAAA-TCAAGTTTAAAAA
1 TAAATTCAAGTTTAAAAA
2606245 TAAA
1 TAAA
2606249 AAGTAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (18 bp):
TAAATTCAAGTTTAAAAA
Found at i:2607041 original size:18 final size:17
Alignment explanation
Indices: 2606995--2607041 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
2606985 AAATTGAAGC
2606995 ATATTA-TATAATATTT
1 ATATTATTATAATATTT
2607011 ATATTATTAATAATATTT
1 ATATTATT-ATAATATTT
2607029 -TAATTTATTATAA
1 AT-A-TTATTATAA
2607042 ATAAAGTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.22
17 2 0.07
18 14 0.52
19 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTATTATAATATTT
Found at i:2608197 original size:54 final size:52
Alignment explanation
Indices: 2608088--2608205 Score: 134
Period size: 54 Copynumber: 2.2 Consensus size: 52
2608078 ATCGTAAATA
* *
2608088 ATTTAATTA-TTTAATATATAAATTATTTTAAATAATTATCATGAATCATCT
1 ATTTAATTATTTTAATATATAAATTATTTTAAATAATTATAATAAATCATCT
* * *
2608139 ATTTAATTATTTTAA-ATTTAATTTAAATTTTAACATGATTATAATAAATCATAC-
1 ATTTAATTATTTTAATATATAAATT--ATTTTAA-ATAATTATAATAAATCAT-CT
2608193 ATTTAATTATTTT
1 ATTTAATTATTTT
2608206 TAGATTTGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
51 16 0.28
52 5 0.09
53 7 0.12
54 28 0.49
55 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (52 bp):
ATTTAATTATTTTAATATATAAATTATTTTAAATAATTATAATAAATCATCT
Found at i:2608347 original size:21 final size:20
Alignment explanation
Indices: 2608310--2608349 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2608300 TTCGAAGGTA
2608310 ATTTTTTTAATTATTTTTAC
1 ATTTTTTTAATTATTTTTAC
* *
2608330 ATTTTATTTATTTGTTTTTA
1 ATTTT-TTTAATTATTTTTA
2608350 TTTATATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (20 bp):
ATTTTTTTAATTATTTTTAC
Found at i:2610965 original size:25 final size:21
Alignment explanation
Indices: 2610909--2610955 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2610899 TGGACATGTT
2610909 AAAAATGCATGAAACATAATA
1 AAAAATGCATGAAACATAATA
2610930 AAAAATGCATGAAACATAATA
1 AAAAATGCATGAAACATAATA
2610951 AAAAA
1 AAAAA
2610956 AAAATGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (21 bp):
AAAAATGCATGAAACATAATA
Found at i:2611924 original size:20 final size:20
Alignment explanation
Indices: 2611877--2611951 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
2611867 AAAAAGACAT
*
2611877 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2611896 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2611917 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
2611937 AATGTATCGATACAT
1 AATGTATCGATACAT
2611952 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2611945 original size:40 final size:39
Alignment explanation
Indices: 2611874--2611951 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2611864 GGTAAAAAGA
* *
2611874 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
2611913 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
2611952 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:2612345 original size:16 final size:17
Alignment explanation
Indices: 2612324--2612361 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2612314 TTTAAATAAT
2612324 AAATTTAT-TATTTTGA
1 AAATTTATGTATTTTGA
* *
2612340 AAATTTATGTCTTTTTA
1 AAATTTATGTATTTTGA
2612357 AAATT
1 AAATT
2612362 AAGTAATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
AAATTTATGTATTTTGA
Found at i:2612920 original size:19 final size:21
Alignment explanation
Indices: 2612893--2612946 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2612883 TTACAAAGTA
2612893 AATTATATATATATATATTAC
1 AATTATATATATATATATTAC
2612914 AATTATATATATATATATTAC
1 AATTATATATATATATATTAC
2612935 AATTATATATAT
1 AATTATATATAT
2612947 TTCTACCGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTATATATATATATATTAC
Found at i:2612933 original size:15 final size:15
Alignment explanation
Indices: 2612894--2612946 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
2612884 TACAAAGTAA
2612894 ATTATATATATATAT
1 ATTATATATATATAT
*
2612909 ATTACA-AT-TATAT
1 ATTATATATATATAT
*
2612922 A-TATATATAT-TACA
1 ATTATATATATATA-T
2612936 ATTATATATAT
1 ATTATATATAT
2612947 TTCTACCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 3 0.10
13 10 0.32
14 4 0.13
15 14 0.45
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATATATATATAT
Found at i:2614198 original size:31 final size:28
Alignment explanation
Indices: 2614163--2614222 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 28
2614153 AGGACTTTAG
*
2614163 ATTAAAATGTATATATATATATAATAATTAA
1 ATTAAAAT-T-TATAT-TAAATAATAATTAA
*
2614194 ATTAAAATTTATGTTAAATAATAATTAA
1 ATTAAAATTTATATTAAATAATAATTAA
2614222 A
1 A
2614223 AAATTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 14 0.52
29 4 0.15
30 1 0.04
31 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (28 bp):
ATTAAAATTTATATTAAATAATAATTAA
Found at i:2614344 original size:17 final size:16
Alignment explanation
Indices: 2614324--2614374 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 16
2614314 AAAGTAAAGG
2614324 TATTAAAAATTATACTA
1 TATTAAAAATTATA-TA
*
2614341 TATTAAACAATAAAATATA
1 TATTAAA-AAT--TATATA
2614360 TATTAAAAATTATAT
1 TATTAAAAATTATAT
2614375 TTGGATTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 6 0.21
19 9 0.31
20 3 0.10
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (16 bp):
TATTAAAAATTATATA
Found at i:2618147 original size:1 final size:1
Alignment explanation
Indices: 2618143--2618168 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2618133 ATTTTTTTGC
2618143 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2618169 CCGAGACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2627903 original size:6 final size:6
Alignment explanation
Indices: 2627892--2627927 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
2627882 ATATTTAAAA
2627892 ATTTAT ATTTAT ATTTAT ATTTAT ATTTATT ATTTA
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTA-T ATTTA
2627928 AAATAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTAT
Found at i:2628730 original size:35 final size:38
Alignment explanation
Indices: 2628675--2628749 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 38
2628665 TTTTATTATA
* *
2628675 TTATATAAAAATTTATTTAATTAAT-ATTTATAAATAT
1 TTATATAAAAATTTACTTAATTAATAATTTAAAAATAT
*
2628712 TTAT-TAAAAA-TTACTTAATTATTAATTTAAAAATAT
1 TTATATAAAAATTTACTTAATTAATAATTTAAAAATAT
2628748 TT
1 TT
2628750 TTTTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 11 0.32
36 19 0.56
37 4 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (38 bp):
TTATATAAAAATTTACTTAATTAATAATTTAAAAATAT
Found at i:2628742 original size:23 final size:23
Alignment explanation
Indices: 2628715--2628783 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
2628705 TAAATATTTA
2628715 TTAAAAATTACTTAATTATTAAT
1 TTAAAAATTACTTAATTATTAAT
* ** *
2628738 TTAAAAA-TATTTTTTTATATATT
1 TTAAAAATTACTTAATTAT-TAAT
*
2628761 TTAAATATTACTTAA--ATTAAT
1 TTAAAAATTACTTAATTATTAAT
2628782 TT
1 TT
2628784 TATTAAATAT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
21 5 0.14
22 10 0.29
23 16 0.46
24 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAAAATTACTTAATTATTAAT
Found at i:2628743 original size:22 final size:22
Alignment explanation
Indices: 2628709--2628783 Score: 55
Period size: 22 Copynumber: 3.4 Consensus size: 22
2628699 TATTTATAAA
* *
2628709 TATTTATTAAAAATTACTTAAT
1 TATTAATTTAAAATTACTTAAT
* * **
2628731 TATTAATTTAAAAATATTTTTT
1 TATTAATTTAAAATTACTTAAT
*
2628753 TATATATTTTAAATATTACTTAA-
1 TAT-TAATTTAAA-ATTACTTAAT
2628776 -ATTAATTT
1 TATTAATTT
2628784 TATTAAATAT
Statistics
Matches: 39, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
21 5 0.13
22 21 0.54
23 8 0.21
24 5 0.13
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTAATTTAAAATTACTTAAT
Found at i:2628749 original size:46 final size:44
Alignment explanation
Indices: 2628683--2628783 Score: 105
Period size: 46 Copynumber: 2.2 Consensus size: 44
2628673 TATTATATAA
* *
2628683 AAATTTATTTAATTAATATTTATAAATAT-TTATTAAAAATTACTT
1 AAATTAATTTAA-AAATATTTATAAATATATT-TTAAAAATTACTT
* ** *
2628728 AATTATTAATTTAAAAATATTTTTTTATATATTTTAAATATTACTT
1 AA--ATTAATTTAAAAATATTTATAAATATATTTTAAAAATTACTT
2628774 AAATTAATTT
1 AAATTAATTT
2628784 TATTAAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
44 8 0.17
45 2 0.04
46 26 0.55
47 11 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (44 bp):
AAATTAATTTAAAAATATTTATAAATATATTTTAAAAATTACTT
Found at i:2629852 original size:14 final size:14
Alignment explanation
Indices: 2629820--2629861 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2629810 TCATAAAATT
*
2629820 AGAATAA-AATTAA
1 AGAATAATAATTTA
2629833 AG-ATAATAATTTA
1 AGAATAATAATTTA
2629846 AGAATAACTAATTTA
1 AGAATAA-TAATTTA
2629861 A
1 A
2629862 ATATATTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 4 0.16
13 9 0.36
14 4 0.16
15 8 0.32
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (14 bp):
AGAATAATAATTTA
Found at i:2630191 original size:2 final size:2
Alignment explanation
Indices: 2630184--2630213 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2630174 AAAGCAGCAG
2630184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2630214 AATACAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2631267 original size:3 final size:3
Alignment explanation
Indices: 2631259--2631286 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2631249 ACCTTTTTCA
2631259 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2631287 CATATGTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2632668 original size:23 final size:23
Alignment explanation
Indices: 2632642--2632687 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2632632 TGAATCTATA
*
2632642 TATTATTAATAAATTAAATAATT
1 TATTATTAATAAATTAAAAAATT
* *
2632665 TATTTTTATTAAATTAAAAAATT
1 TATTATTAATAAATTAAAAAATT
2632688 ATTTATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTATTAATAAATTAAAAAATT
Found at i:2632696 original size:22 final size:23
Alignment explanation
Indices: 2632651--2632696 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2632641 ATATTATTAA
* *
2632651 TAAATTAAATAATTTATTTTTAT
1 TAAATTAAATAAATTATTTATAT
2632674 TAAATTAAA-AAATTATTTATAT
1 TAAATTAAATAAATTATTTATAT
2632696 T
1 T
2632697 TTATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTAAATAAATTATTTATAT
Found at i:2636148 original size:2 final size:2
Alignment explanation
Indices: 2636137--2636176 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2636127 AAGCAAAACC
2636137 TA TA -A TA TA 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 TA TA TA TA TA T
2636177 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2637438 original size:4 final size:4
Alignment explanation
Indices: 2637423--2637476 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
2637413 GAAGATGACA
* * * *
2637423 ATAT ACAT ATAT ATAT ATAT ATAT ATAT ATAC ATAC ATAT ACAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
2637471 ATAT AT
1 ATAT AT
2637477 GCCTCTTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:2637438 original size:6 final size:6
Alignment explanation
Indices: 2637423--2637476 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
2637413 GAAGATGACA
* * * *
2637423 ATATAC ATATAT ATATAT ATATAT ATATAT ACATAC ATATAC ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
2637471 ATATAT
1 ATATAT
2637477 GCCTCTTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:2637442 original size:10 final size:10
Alignment explanation
Indices: 2637423--2637476 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
2637413 GAAGATGACA
*
2637423 ATATACATAT
1 ATATATATAT
2637433 ATATATATAT
1 ATATATATAT
2637443 ATATATATAT
1 ATATATATAT
* *
2637453 ACATACATAT
1 ATATATATAT
*
2637463 ACATATATAT
1 ATATATATAT
2637473 ATAT
1 ATAT
2637477 GCCTCTTTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATAT
Found at i:2637812 original size:2 final size:2
Alignment explanation
Indices: 2637805--2637830 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2637795 AAGCACTAGT
2637805 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2637831 AAAGAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2641490 original size:20 final size:20
Alignment explanation
Indices: 2641465--2641502 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2641455 CGATTTATAT
*
2641465 AAAATTTTAATTTTTTTAAA
1 AAAATTTCAATTTTTTTAAA
*
2641485 AAAATTTCATTTTTTTTA
1 AAAATTTCAATTTTTTTA
2641503 TTTTTTAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
AAAATTTCAATTTTTTTAAA
Found at i:2641517 original size:21 final size:22
Alignment explanation
Indices: 2641493--2641545 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
2641483 AAAAAATTTC
*
2641493 ATTTTTTTTATTTTT-TAATCA
1 ATTTTTTTTATTTTTATAATAA
* *
2641514 ATTTCTTGTATTTTTATAATAA
1 ATTTTTTTTATTTTTATAATAA
2641536 ATTTTGTTTT
1 ATTTT-TTTT
2641546 CATAATATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 13 0.52
22 9 0.36
23 3 0.12
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (22 bp):
ATTTTTTTTATTTTTATAATAA
Found at i:2642760 original size:22 final size:22
Alignment explanation
Indices: 2642724--2642788 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
2642714 ATTTATTAAA
*
2642724 AATAAAA-AATTAAATTAAATT
1 AATAAAATATTTAAATTAAATT
* ** *
2642745 CATAAGTTATTTAAATTAAAAT
1 AATAAAATATTTAAATTAAATT
*
2642767 AATAAAATATTTAAATTTAATT
1 AATAAAATATTTAAATTAAATT
2642789 TGCTCAATAA
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AATAAAATATTTAAATTAAATT
Found at i:2647881 original size:17 final size:17
Alignment explanation
Indices: 2647861--2647893 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2647851 TAAGACACTT
2647861 TTAATCATTAAATCAAA
1 TTAATCATTAAATCAAA
*
2647878 TTAATTATTAAATCAA
1 TTAATCATTAAATCAA
2647894 GAGATTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAATCATTAAATCAAA
Found at i:2649179 original size:17 final size:16
Alignment explanation
Indices: 2649157--2649211 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 16
2649147 TATTTAATAT
2649157 ATTTTATATTTATATTA
1 ATTTTATA-TTATATTA
2649174 ATTTTA-A-TATATTA
1 ATTTTATATTATATTA
*
2649188 ATAATTTATATTATATAA
1 AT--TTTATATTATATTA
2649206 ATTTTA
1 ATTTTA
2649212 AAAATATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 9 0.27
16 9 0.27
17 7 0.21
18 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTATATTATATTA
Found at i:2649183 original size:27 final size:27
Alignment explanation
Indices: 2649149--2649200 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
2649139 CATAATCTTA
*
2649149 TTTAATATATT-TTATATTTATATTAAT
1 TTTAATATATTAATA-ATTTATATTAAT
2649176 TTTAATATATTAATAATTTATATTA
1 TTTAATATATTAATAATTTATATTA
2649201 TATAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTAATATATTAATAATTTATATTAAT
Found at i:2658742 original size:20 final size:20
Alignment explanation
Indices: 2658717--2658767 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2658707 TTTTACCCAG
*
2658717 ATGTATTGATATATTATTCA
1 ATGTATCGATATATTATTCA
*
2658737 ATGTATCAATATATTATTCA
1 ATGTATCGATATATTATTCA
2658757 ATGTATCGATA
1 ATGTATCGATA
2658768 CATGCAAGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (20 bp):
ATGTATCGATATATTATTCA
Found at i:2665725 original size:22 final size:22
Alignment explanation
Indices: 2665684--2665728 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
2665674 ATGAAAAAGT
2665684 AAAAAAAAAAAAACAAAAAAAC
1 AAAAAAAAAAAAACAAAAAAAC
*
2665706 AAAAAAAAACATACACAAAAAAA
1 AAAAAAAAA-A-AAACAAAAAAA
2665729 GTACAAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAAAACAAAAAAAC
Found at i:2666976 original size:34 final size:33
Alignment explanation
Indices: 2666930--2667030 Score: 125
Period size: 33 Copynumber: 3.0 Consensus size: 33
2666920 TTCAAATCTC
* *
2666930 TTTTCTCAAAGTCCACAACTCAGTGGTATCTTT
1 TTTTCTCAAAGTCCACGACTCAGTGGCATCTTT
*
2666963 TTTTCTCCAAAGTCCACGACTTAGTGGCATC-TT
1 TTTTCT-CAAAGTCCACGACTCAGTGGCATCTTT
*
2666996 TTTTCTTCAATA-TCCACGACTCAGTAGCATCTTT
1 TTTTC-TCAA-AGTCCACGACTCAGTGGCATCTTT
2667030 T
1 T
2667031 CCAAAAGTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
33 33 0.56
34 26 0.44
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.40
Consensus pattern (33 bp):
TTTTCTCAAAGTCCACGACTCAGTGGCATCTTT
Found at i:2667044 original size:30 final size:32
Alignment explanation
Indices: 2666925--2667047 Score: 110
Period size: 33 Copynumber: 3.8 Consensus size: 32
2666915 AATTCTTCAA
* * *
2666925 ATCTCTTTTCTC-AAAGTCCACAACTCAGTGGT
1 ATCT-TTTTCTCAAAAGTCCACGACTCAGTAGC
* * *
2666957 ATCTTTTTTTCTCCAAAGTCCACGACTTAGTGGC
1 ATC--TTTTTCTCAAAAGTCCACGACTCAGTAGC
*
2666991 ATCTTTTTTCTTCAATA-TCCACGACTCAGTAGC
1 ATC-TTTTTC-TCAAAAGTCCACGACTCAGTAGC
2667024 ATC-TTTTC-CAAAAGTCCACGACTC
1 ATCTTTTTCTCAAAAGTCCACGACTC
2667048 TGTGACATCC
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.05
30 10 0.13
31 5 0.06
32 3 0.04
33 31 0.40
34 25 0.32
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.36
Consensus pattern (32 bp):
ATCTTTTTCTCAAAAGTCCACGACTCAGTAGC
Found at i:2667074 original size:27 final size:26
Alignment explanation
Indices: 2667035--2667087 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
2667025 TCTTTTCCAA
*
2667035 AAGTCCACGACTCTGTGACATCCTTTT
1 AAGTCCACAACTCTGTGACA-CCTTTT
*
2667062 AAGTCCACAACTCTGTGGCACCTTTT
1 AAGTCCACAACTCTGTGACACCTTTT
2667088 TCTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (26 bp):
AAGTCCACAACTCTGTGACACCTTTT
Found at i:2667165 original size:61 final size:61
Alignment explanation
Indices: 2667055--2667574 Score: 384
Period size: 61 Copynumber: 8.4 Consensus size: 61
2667045 CTCTGTGACA
* * *
2667055 TCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTTAAAGCCCACAACTTCGTGGCACTCT
1 TCCTTTTAAGTCCACAACTCCGTGGCACC-----C-TTTT-AAGTCCACAACTCCGTGGCACTCT
2667120 TTT
59 TTT
* *
2667123 TCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACTCTTTT
1 TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACTCTTTT
* * * *
2667184 CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCTACAATTACGTGGCA-------
1 TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACTCTTTT
* * *
2667238 TCCTTTTATGCCCACAACTCCGTGGCATTCTTTTTCCTTTTAAGTCTACAACTCCGTGGCA--C-
1 TCCTTTTAAGTCCACAACTCCGTGGCA--C-----CCTTTTAAGTCCACAACTCCGTGGCACTCT
2667300 ---
59 TTT
* * * *
2667300 -CCTTTTAAGTTCACAACTCCGTGGCGCCTTGTTCCTTTTAAGTCCACAACTCTGT-GC-CAC--
1 TCCTTTTAAGTCCACAACTCCGTGGC-AC-----CCTTTTAAGTCCACAACTCCGTGGCACTCTT
2667360 --
60 TT
**
2667360 -CCTTTTAAGTCCACAACTCAATGGCACCTTTTTCTTTTTAAAG-CCTACAACTCCGTGGCACTC
1 TCCTTTTAAGTCCACAACTCCGTGGCACC-----C-TTTT-AAGTCC-ACAACTCCGTGGCACTC
2667423 TTTT
58 TTTT
* * * *
2667427 TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACGCCGTGACATTCTTTT
1 TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACTCTTTT
* * **
2667488 TCCTTTTAAGTCCACAACTCCGTGGTACCTTTTTAAGTCCACAACTCCGTGGCAC-CTTGC
1 TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACTCTTTT
*
2667548 TCCTTTTAAGTCCACAACTTCGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
2667575 TCTTTCTCCT
Statistics
Matches: 381, Mismatches: 44, Indels: 62
0.78 0.09 0.13
Matches are distributed among these distances:
54 25 0.07
56 1 0.00
59 4 0.01
60 82 0.22
61 200 0.52
62 12 0.03
63 4 0.01
68 53 0.14
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (61 bp):
TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACTCTTTT
Found at i:2667277 original size:88 final size:88
Alignment explanation
Indices: 2667124--2667324 Score: 296
Period size: 88 Copynumber: 2.3 Consensus size: 88
2667114 CACTCTTTTT
* *
2667124 CCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACTCTTTTCCCTT
1 CCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTCCCTT
2667189 TTAAGTCCACAACTCCGTGGCAC
66 TTAAGTCCACAACTCCGTGGCAC
* * * * *
2667212 CCTTTTAAGTCTACAA-TTACGTGGCATCCTTTTATGCCCACAACTCCGTGGCATTCTTTTTCCT
1 CCTTTTAAGTCCACAACTT-CGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTCCCT
*
2667276 TTTAAGTCTACAACTCCGTGGCAC
65 TTTAAGTCCACAACTCCGTGGCAC
* *
2667300 CCTTTTAAGTTCACAACTCCGTGGC
1 CCTTTTAAGTCCACAACTTCGTGGC
2667325 GCCTTGTTCC
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
87 2 0.02
88 97 0.97
89 1 0.01
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (88 bp):
CCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTCCCTT
TTAAGTCCACAACTCCGTGGCAC
Found at i:2667361 original size:60 final size:61
Alignment explanation
Indices: 2667212--2667458 Score: 212
Period size: 60 Copynumber: 4.0 Consensus size: 61
2667202 TCCGTGGCAC
* * * * * * * ** *
2667212 CCTTTTAAGTCTACAATTACGTGGCATCCTTTTATGCCCACAACTCCGTGGCATTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGCCACCCTTTTAAGTCCACAACTCCGTGGCAGCCTTGTT
* * *
2667273 CCTTTTAAGTCTACAACTCCGTGGCACCCTTTTAAGTTCACAACTCCGTGGC-GCCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGCCACCCTTTTAAGTCCACAACTCCGTGGCAGCCTTGTT
* ** *
2667333 CCTTTTAAGTCCACAACTCTGTGCCACCCTTTTAAGTCCACAACTCAATGGCA-CCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGCCACCCTTTTAAGTCCACAACTCCGTGGCAGCCTTGTT
* * *
2667393 CTTTTTAAAG-CCTACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCC
1 CCTTTT-AAGTCC-ACAACTCCGT-GC-CAC-----CCTTTTAAGTCCACAACTCCGTGGCAGCC
2667457 TT
57 TT
2667459 TTAAGCCCAC
Statistics
Matches: 154, Mismatches: 21, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
60 64 0.42
61 58 0.38
62 2 0.01
63 2 0.01
68 24 0.16
69 4 0.03
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (61 bp):
CCTTTTAAGTCCACAACTCCGTGCCACCCTTTTAAGTCCACAACTCCGTGGCAGCCTTGTT
Found at i:2667606 original size:33 final size:33
Alignment explanation
Indices: 2667055--2667607 Score: 359
Period size: 27 Copynumber: 17.8 Consensus size: 33
2667045 CTCTGTGACA
* * *
2667055 TCCTTTTAAGTCCACAACTCTGTGGCACCTTTT
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
* * * *
2667088 TCTTTTTAAAGCCCACAACTTCGTGGCACTCTTTT
1 TCCTTTT-AAGTCCACAACTCCGTGGCA-TCTTTC
*
2667123 TCCTTTTAAGTCCACAACTTCGTGGCA-----C
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
*
2667151 -CCTTTTAAGTCCACAACTCTGTGGCACTCTTT-
1 TCCTTTTAAGTCCACAACTCCGTGGCA-TCTTTC
2667183 TCCCTTTTAAGTCCACAACTCCGTGGCA-----C
1 T-CCTTTTAAGTCCACAACTCCGTGGCATCTTTC
* * *
2667212 -CCTTTTAAGTCTACAATTACGTGGCA------
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
* * *
2667238 TCCTTTTATGCCCACAACTCCGTGGCATTCTTTT
1 TCCTTTTAAGTCCACAACTCCGTGGCA-TCTTTC
*
2667272 TCCTTTTAAGTCTACAACTCCGTGGCA-----C
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
* **
2667300 -CCTTTTAAGTTCACAACTCCGTGGCGCCTTGT-
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTT-TC
* *
2667332 TCCTTTTAAGTCCACAACTCTGT-GC--C--AC
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
** * *
2667360 -CCTTTTAAGTCCACAACTCAATGGCACCTTTT
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
* *
2667392 TCTTTTTAAAG-CCTACAACTCCGTGGCACTCTTTT
1 TCCTTTT-AAGTCC-ACAACTCCGTGGCA-TCTTTC
2667427 TCCTTTTAAGTCCACAACTCCGTGGCA-----C
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
* * * *
2667455 -CCTTTTAAGCCCACAACGCCGTGACATTCTTTT
1 TCCTTTTAAGTCCACAACTCCGTGGCA-TCTTTC
*
2667488 TCCTTTTAAGTCCACAACTCCGTGGTA-C---C
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
* *
2667517 T--TTTTAAGTCCACAACTCCGTGGCACCTTGC
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
*
2667548 TCCTTTTAAGTCCACAACTTCGTGGCATCTTTC
1 TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
* * *
2667581 TCCTTTTAAGCCCACAAGTCAGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
2667608 CCCTTTTCAA
Statistics
Matches: 414, Mismatches: 56, Indels: 100
0.73 0.10 0.18
Matches are distributed among these distances:
27 157 0.38
28 3 0.01
29 1 0.00
30 2 0.00
31 2 0.00
32 3 0.01
33 83 0.20
34 139 0.34
35 24 0.06
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (33 bp):
TCCTTTTAAGTCCACAACTCCGTGGCATCTTTC
Found at i:2667683 original size:29 final size:29
Alignment explanation
Indices: 2667588--2667683 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 29
2667578 TTCTCCTTTT
*
2667588 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAA
2667618 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* **
2667646 AAGCACACAAGTTGGT-GCAATCCTTTCAA
1 AAGCCCACAAGTCAGTGGCAA-CCTTTCAA
2667675 AAGCCCACA
1 AAGCCCACA
2667684 CAAGTTAGTG
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.07
28 20 0.34
29 13 0.22
30 22 0.37
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.18
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:2667866 original size:39 final size:39
Alignment explanation
Indices: 2667823--2668057 Score: 218
Period size: 39 Copynumber: 5.6 Consensus size: 39
2667813 AATGTTGCAA
2667823 GCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTG
* * * *
2667862 GCCTTGAATTAGCACATTGGCACCTTGTCTCTAAGACCAATGTCGTTG
1 GCCTTGAATCAGCACATTGGCA---------TAAGCCCAATATCGCTG
2667910 GCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTG
* * * *
2667949 GCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTTGCTG
1 GCCTTGAATCAGCACATTGGCA---------TAAGCCCAATATCGCTG
*
2667997 GCCTTGAATCAGCACATTGGCATAAGCCCAATATCACTG
1 GCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTG
*
2668036 GCCTTGAATCAGCATATTGGCA
1 GCCTTGAATCAGCACATTGGCA
2668058 CCTTGTCTCT
Statistics
Matches: 160, Mismatches: 18, Indels: 36
0.75 0.08 0.17
Matches are distributed among these distances:
39 90 0.56
48 70 0.44
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (39 bp):
GCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTG
Found at i:2667921 original size:87 final size:87
Alignment explanation
Indices: 2667754--2668109 Score: 552
Period size: 87 Copynumber: 4.0 Consensus size: 87
2667744 TCTTTATCTT
* * * *
2667754 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTCTAAAACCAATGTT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTCTAAGACCAATGTC
*
2667819 GCAAGCCTTGAATCAGCACATTGGCA
62 GCTAGCCTTGAATCAGCACATTGGCA
* * * *
2667845 TAAGCCCAATATCGCTGGCCTTGAATTAGCACATTGGCACCTTGTCTCTAAGACCAATGTCGTTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
2667910 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* *
2667932 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTTGCTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
2667997 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
*
2668019 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
2668084 G-CTTGGAATCAGCACATTGGCA
66 GCCTT-GAATCAGCACATTGGCA
2668106 TAAG
1 TAAG
2668110 TCCACAACTT
Statistics
Matches: 248, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
86 3 0.01
87 205 0.83
90 3 0.01
91 37 0.15
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (87 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
GCCTTGAATCAGCACATTGGCA
Found at i:2667924 original size:48 final size:48
Alignment explanation
Indices: 2667845--2668105 Score: 263
Period size: 48 Copynumber: 5.8 Consensus size: 48
2667835 CACATTGGCA
* *
2667845 TAAGCCCAATATCGCTGGCCTTGAATTAGCACATTGGCACCTTGTCTC
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
* *
2667893 TAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCA---------
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
* *
2667932 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTC
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
* *
2667980 TAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGGCA---------
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
* * *
2668019 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTC
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
* *
2668067 TAAGACCAATGTCGCTAG-CTTGGAATCAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTT-GAATCAGCACATTGGCA
2668106 TAAGTCCACA
Statistics
Matches: 172, Mismatches: 22, Indels: 38
0.74 0.09 0.16
Matches are distributed among these distances:
39 69 0.40
47 3 0.02
48 100 0.58
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (48 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
Found at i:2668149 original size:34 final size:33
Alignment explanation
Indices: 2668106--2668626 Score: 381
Period size: 27 Copynumber: 16.9 Consensus size: 33
2668096 CACATTGGCA
*
2668106 TAAGTCCACAACTTCGTGGCACTCTTTTTCCTTT
1 TAAGTCCACAACTCCGTGGCAC-CTTTTTCCTTT
**
2668140 TAAGTCCACAACTTTGTGGCA-C-----CCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* *
2668167 TAAGTCCACAACTCTGTGGCACTCTTTTCCCTTT
1 TAAGTCCACAACTCCGTGGCAC-CTTTTTCCTTT
*
2668201 TAAGTCCACAACTCTGTGGCA-C-----CCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* *
2668228 TAAGTCTACAATTCCGTGGCA------TCCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* * *
2668255 TATGCCCACAACTCCGTGGCATTCTTTTTCCTTT
1 TAAGTCCACAACTCCGTGGCA-CCTTTTTCCTTT
*
2668289 TAAGTCTACAACTCCGTGGCA-C-----CCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* *
2668316 TAAGTCCACAACTCCGTGGCGCCTTATTCCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* *
2668349 TAAGTCCACAACTCTGTGCCA-C-----CCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* * *
2668376 TAAGTCCACAACTCCATGGCATCTTTTTCTTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
2668409 TAAAG-CCTACAACTCCGTGGCACTCTTTTTCCTTT
1 T-AAGTCC-ACAACTCCGTGGCAC-CTTTTTCCTTT
2668444 TAAGTCCACAACTCCGTGGCA-C-----CCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* * * *
2668471 TAAGCCCACAACGCCGTGACATTCTTTTTCCTTT
1 TAAGTCCACAACTCCGTGGCA-CCTTTTTCCTTT
2668505 TAAGTCCACAACTCCGTGGCACC----T--TTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* *
2668532 TAAGTCCACAACTCCGTGGCGCCTTGTTCCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* * * *
2668565 TAAGTCCACAACTTCATGGCATCTTTCTCCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
* * * *
2668598 TAAGCCCACAAGTCAGTGGCACCCTTTTC
1 TAAGTCCACAACTCCGTGGCACCTTTTTC
2668627 AAAAGCCCAC
Statistics
Matches: 397, Mismatches: 46, Indels: 89
0.75 0.09 0.17
Matches are distributed among these distances:
27 165 0.42
28 2 0.01
29 3 0.01
31 1 0.00
32 5 0.01
33 82 0.21
34 126 0.32
35 13 0.03
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (33 bp):
TAAGTCCACAACTCCGTGGCACCTTTTTCCTTT
Found at i:2668201 original size:61 final size:60
Alignment explanation
Indices: 2668106--2668577 Score: 354
Period size: 61 Copynumber: 7.8 Consensus size: 60
2668096 CACATTGGCA
* * **
2668106 TAAGTCCACAACTTCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTTGTGGCACCCTTT
1 TAAGTCCACAACTCCGTGGCAC-CTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
* *
2668167 TAAGTCCACAACTCTGTGGCACTCTTTTCCCTTTTAAGTCCACAACTCTGTGGCACCCTTT
1 TAAGTCCACAACTCCGTGGCAC-CTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
* * * *
2668228 TAAGTCTACAATTCCGTGGCA-----T-CCTTTTATGCCCACAACTCCGTGGCATTCTTTTTCCT
1 TAAGTCCACAACTCCGTGGCACCTTTTCCCTTTTAAGTCCACAACTCCGTGGCA--C-----CCT
2668287 TT
59 TT
* *
2668289 TAAGTCTACAACTCCGTGGCA------CCCTTTTAAGTCCACAACTCCGTGGCGCCTTATTCCTT
1 TAAGTCCACAACTCCGTGGCACCTTTTCCCTTTTAAGTCCACAACTCCGT-G-G-C--A-CCCTT
2668348 T
60 T
* * * *
2668349 TAAGTCCACAACTCTGT-G--CC---ACCCTTTTAAGTCCACAACTCCATGGCATCTTTTTCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTTCCCTTTTAAGTCCACAACTCCGTGGCA-C-----CCTT
2668408 T
60 T
*
2668409 TAAAG-CCTACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
1 T-AAGTCC-ACAACTCCGTGGCAC-CTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
* * * * * *
2668471 TAAGCCCACAACGCCGTGACATTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
1 TAAGTCCACAACTCCGTGGCA-CCTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
*
2668532 TAAGTCCACAACTCCGTGGCGCCTTGTT-CCTTTTAAGTCCACAACT
1 TAAGTCCACAACTCCGTGGCACCTT-TTCCCTTTTAAGTCCACAACT
2668578 TCATGGCATC
Statistics
Matches: 345, Mismatches: 33, Indels: 67
0.78 0.07 0.15
Matches are distributed among these distances:
54 23 0.07
55 3 0.01
56 1 0.00
57 1 0.00
58 1 0.00
59 2 0.01
60 70 0.20
61 203 0.59
62 9 0.03
63 1 0.00
64 2 0.01
65 2 0.01
66 1 0.00
67 1 0.00
68 25 0.07
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (60 bp):
TAAGTCCACAACTCCGTGGCACCTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
Done.