Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 4 of 27
Found at i:471335 original size:20 final size:20
Alignment explanation
Indices: 471310--471363 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
471300 AAAAACTAAG
* *
471310 AATGTATTGATACAATGAAA
1 AATGTATCGATACAATAAAA
* *
471330 AATGTATCAATATAATAAAA
1 AATGTATCGATACAATAAAA
471350 AATGTATCGATACA
1 AATGTATCGATACA
471364 TTTTCTTTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACAATAAAA
Found at i:475643 original size:27 final size:27
Alignment explanation
Indices: 475613--475676 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
475603 ATAAATTAAC
*
475613 ACCATACACATTATAAAAATCACAAAA
1 ACCATACACATCATAAAAATCACAAAA
475640 ACCATACACATCATAAAAATCACAAAA
1 ACCATACACATCATAAAAATCACAAAA
475667 ACCATACACA
1 ACCATACACA
475677 AAATCATAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.16
Consensus pattern (27 bp):
ACCATACACATCATAAAAATCACAAAA
Found at i:475679 original size:21 final size:24
Alignment explanation
Indices: 475627--475692 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 24
475617 TACACATTAT
475627 AAAAATCACAAAAACCATACACATC
1 AAAAATCACAAAAACCATA-ACATC
475652 ATAAAAATCACAAAAACCAT-ACA-C
1 --AAAAATCACAAAAACCATAACATC
* *
475676 -AAAATCATAACAACCAT
1 AAAAATCACAAAAACCAT
475693 TCAACCAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 15 0.41
24 1 0.03
25 3 0.08
27 18 0.49
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.14
Consensus pattern (24 bp):
AAAAATCACAAAAACCATAACATC
Found at i:477663 original size:21 final size:21
Alignment explanation
Indices: 477639--477713 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
477629 TTTTTGCCAA
*
477639 AATGTATTGATACATGCCCTT
1 AATGTATCGATACATGCCCTT
* *
477660 AATGTATCAATACATGCACTT
1 AATGTATCGATACATGCCCTT
* *
477681 GATGTAT--ACACATGCCCTT
1 AATGTATCGATACATGCCCTT
*
477700 GATGTATCGATACA
1 AATGTATCGATACA
477714 AGGCCCCAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 17 0.38
21 28 0.62
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (21 bp):
AATGTATCGATACATGCCCTT
Found at i:477778 original size:20 final size:20
Alignment explanation
Indices: 477750--477913 Score: 163
Period size: 20 Copynumber: 7.8 Consensus size: 20
477740 TTTTCACATT
477750 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
477770 TTGTCTCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
477790 TTGTATCGATACATTCTGGGTTTACCCA
1 TTGTATCGATACA-T-T--G-TT---CA
*
477818 GATGTATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
*
477839 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
477859 TTGTATCGATACATTGCTT-A
1 TTGTATCGATACATTG-TTCA
477879 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
477899 ATGTATCGATACATT
1 TTGTATCGATACATT
477914 CAGGCATTTT
Statistics
Matches: 123, Mismatches: 8, Indels: 26
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.02
20 94 0.76
21 5 0.04
22 1 0.01
23 2 0.02
24 1 0.01
25 2 0.02
27 1 0.01
28 3 0.02
29 12 0.10
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:480278 original size:53 final size:51
Alignment explanation
Indices: 480202--480334 Score: 178
Period size: 53 Copynumber: 2.6 Consensus size: 51
480192 AAATTTCTAG
* *
480202 ATTTTTCAT-CTCGGGGATACTCCAATCCCAGTTTCATTTCCAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACCCCAGTTTCATTTCCAAAACATCA
* * * *
480252 ATTTTTCTTAATCAAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCA
1 ATTTTTCATAATC--GGGGATACTCCAACCCCAGTTTCATTTCCAAAACATCA
*
480305 ATTTTTCATAGTCGGGGATACTCCAACCCC
1 ATTTTTCATAATCGGGGATACTCCAACCCC
480335 GTTATTTCTG
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
50 8 0.11
51 19 0.26
53 45 0.62
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAACCCCAGTTTCATTTCCAAAACATCA
Found at i:480399 original size:79 final size:79
Alignment explanation
Indices: 480266--480442 Score: 284
Period size: 79 Copynumber: 2.2 Consensus size: 79
480256 TTCTTAATCA
* *
480266 AGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAGTCGGGGATACTCCAA
1 AGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAA
480331 CCCCGTTA-TTTCTG
66 CCCCGTTATTTTC-G
* * *
480345 AGGGGATACTCCAATCCTGATTTTATTTCTAAATCATCAATTTTTCATAATCGGGGATACTCCAA
1 AGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAA
480410 CCCCGTTATTTTCG
66 CCCCGTTATTTTCG
*
480424 AGGGGATACTCTAACCCCG
1 AGGGGATACTCCAACCCCG
480443 TTATTATCTC
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 85 0.96
80 4 0.04
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (79 bp):
AGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAA
CCCCGTTATTTTCG
Found at i:486797 original size:60 final size:60
Alignment explanation
Indices: 486606--487202 Score: 402
Period size: 60 Copynumber: 9.9 Consensus size: 60
486596 TAGCCTTTCC
* * * * *
486606 AGTCCTCAAAGAGCAGGACATCTTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGAC-GC--CTTTTCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * *
486669 AGTCCTCAAAGAGCAGGATGCCTTTTTTCTTTTTAAAGTCCACACAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACGCC--TTTTCTCTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * * **
486732 AGTCCTCAAGGAGCAGGACGCCTTCTC-CTTCAAAGCCCACACGAGTTGGTGGCACCCTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * *
486792 AGTCCTCAAAGAGCAGGACGTCTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACG-C-CTTTTCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * *
486854 ACTCCTCAAAGAGCAGTATGCCTTTTC-CTTTCAAAGCTCACACAAGTTGGTGGCACCTCCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTC-TTCAAAGCCCACACAAGTTGGTGGCACCT-TT
* * * * ** *** * * * * ** *
486915 AGTCCTCAAAAAGCAGGATGCATTTTATTCCCCCTTGTCCTCAAAGAGTAGGACGCA-CTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTT-CTCTTCAAAGCCCACACA-AGTTGGTGGCACCTTT
* ** * ** *
486976 A-T--T------TC----CTTCTTTTCCCTTTTGAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTC-TTCAAAGCCCACACAAGTTGGTGGCAC-CTT-T
* * * **
487026 AGTCCTTAAAGAGCAAGACGCCTTTTC-CTTTCAAAGCCTACACAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTC-TTCAAAGCCCACACAAGTTGGTGGCACCTT-T
*
487087 AGTCCTCAAAGAGCAGGATGCCTTTTC-CTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTC-TTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * *
487147 AGTCCTTAAAGAGCAGGATGCCTTTTCCCTTTAAAGCCCACACAAGTTGGTGGCAC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTCAAAGCCCACACAAGTTGGTGGCAC
487203 ATTTTACAAT
Statistics
Matches: 420, Mismatches: 85, Indels: 61
0.74 0.15 0.11
Matches are distributed among these distances:
47 9 0.02
48 10 0.02
49 2 0.00
50 1 0.00
51 1 0.00
52 1 0.00
53 1 0.00
58 1 0.00
59 1 0.00
60 132 0.31
61 89 0.21
62 89 0.21
63 83 0.20
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:486877 original size:122 final size:123
Alignment explanation
Indices: 486641--486932 Score: 435
Period size: 123 Copynumber: 2.4 Consensus size: 123
486631 TTTTCTTTTT
** *
486641 AAAGCCCACACGAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCCTTTTTTCTTTTTAAA
1 AAAGCCCACACGAGTTGGTGGCACCTCCAGTCCTCAAAGAGCAGGACGCCTTTTTTCTTTTTAAA
* * *
486706 GTCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAGGAGCAGGACGCCTTCTCC-TTC
66 GCCCACACAAGTTGGTGGCACCCTTTACTCCTCAAAGAGCAGGACGCCTTCTCCTTTC
*
486763 AAAGCCCACACGAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACGTCTTTTTTCTTTTTAA
1 AAAGCCCACACGAGTTGGTGGCA-CCTCCAGTCCTCAAAGAGCAGGACGCCTTTTTTCTTTTTAA
* * *
486828 AGCCCACACAAGTTGGTGGCA-CCTTTACTCCTCAAAGAGCAGTATGCCTTTTCCTTTC
65 AGCCCACACAAGTTGGTGGCACCCTTTACTCCTCAAAGAGCAGGACGCCTTCTCCTTTC
* * *
486886 AAAGCTCACACAAGTTGGTGGCACCTCCTAGTCCTCAAAAAGCAGGA
1 AAAGCCCACACGAGTTGGTGGCACCTCC-AGTCCTCAAAGAGCAGGA
486933 TGCATTTTAT
Statistics
Matches: 154, Mismatches: 13, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
122 56 0.36
123 98 0.64
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (123 bp):
AAAGCCCACACGAGTTGGTGGCACCTCCAGTCCTCAAAGAGCAGGACGCCTTTTTTCTTTTTAAA
GCCCACACAAGTTGGTGGCACCCTTTACTCCTCAAAGAGCAGGACGCCTTCTCCTTTC
Found at i:487111 original size:61 final size:61
Alignment explanation
Indices: 486997--487201 Score: 324
Period size: 61 Copynumber: 3.4 Consensus size: 61
486987 TTCCCTTTTG
* *
486997 AAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAAGACGCCTTTTCCTTTCA
1 AAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTTAAAGAGCAGGATGCCTTTTCCTTTCA
* *
487059 AAGCCTACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCA
1 AAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTTAAAGAGCAGGATGCCTTTTCCTTTCA
**
487120 AAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTTAAAGAGCAGGATGCCTTTTCCCTTT-A
1 AAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTTAAAGAGCAGGATGCCTTTT-CCTTTCA
487180 AAGCCCACACAAGTTGGTGGCA
1 AAGCCCACACAAGTTGGTGGCA
487202 CATTTTACAA
Statistics
Matches: 134, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
60 49 0.37
61 64 0.48
62 21 0.16
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (61 bp):
AAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTTAAAGAGCAGGATGCCTTTTCCTTTCA
Found at i:489742 original size:79 final size:78
Alignment explanation
Indices: 489576--489753 Score: 266
Period size: 79 Copynumber: 2.3 Consensus size: 78
489566 TTTTTCTTAA
** * *
489576 TCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTAATAGTCGGGGATCCTCC
1 TCGAGGGGATACTCCAACCCCAATTTTATTTCTAAAACATCAATTTTAATAATCGGGGATACTCC
489641 AACCCCGTTATTT
66 AACCCCGTTATTT
* * * *
489654 TCGAGGGGATACTCCAATCCCAATTTTATTTTTAAATCATCAATTTTTCATAATCGGGGATACTC
1 TCGAGGGGATACTCCAACCCCAATTTTATTTCTAAAACATCAA-TTTTAATAATCGGGGATACTC
489719 CAACCCCGTTATTT
65 CAACCCCGTTATTT
*
489733 TCGAGGGGATACTCTAACCCC
1 TCGAGGGGATACTCCAACCCC
489754 GTTATTATCT
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 38 0.43
79 51 0.57
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (78 bp):
TCGAGGGGATACTCCAACCCCAATTTTATTTCTAAAACATCAATTTTAATAATCGGGGATACTCC
AACCCCGTTATTT
Found at i:491672 original size:78 final size:77
Alignment explanation
Indices: 491474--491677 Score: 207
Period size: 77 Copynumber: 2.6 Consensus size: 77
491464 TACATGACCT
* * * *
491474 TAAAGACTTGGTTTTAAGGTACTATTTCCTAAATGACTT-TAATGGACATTTATTGATAAAGAAG
1 TAAAGACTCGATTTTAAGGTACTATTACCTAAATGA-TTCTAATGGACATGTATTGATAAAGAAG
** *
491538 TTCCTTTATGACC
65 TTCCCGTATAACC
* * * * * *** *
491551 TTAGGAGTCGATTTTAAGGTACTATAACCTATATGGCCCTAATGGACATGTATTGATGTAA-AAG
1 TAAAGACTCGATTTTAAGGTACTATTACCTAAATGATTCTAATGGACATGTATTGAT-AAAGAAG
491615 TTCCCGTATAACCC
65 TTCCCGTATAA-CC
491629 TAAAGACTCGATTTTAAGGTGA-TATTACCTAAATGATTCTAATGGACAT
1 TAAAGACTCGATTTTAAGGT-ACTATTACCTAAATGATTCTAATGGACAT
491678 ATATCAACAT
Statistics
Matches: 99, Mismatches: 24, Indels: 7
0.76 0.18 0.05
Matches are distributed among these distances:
77 55 0.56
78 43 0.43
79 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (77 bp):
TAAAGACTCGATTTTAAGGTACTATTACCTAAATGATTCTAATGGACATGTATTGATAAAGAAGT
TCCCGTATAACC
Found at i:492428 original size:58 final size:56
Alignment explanation
Indices: 492334--492464 Score: 165
Period size: 58 Copynumber: 2.3 Consensus size: 56
492324 GTCAAAGTGA
* * * *
492334 CCCTAGATTATGTAAAATAATCTAAATGGTCCTAAAATGCATGAAAATTACTAAATAGT
1 CCCTAGATTACGT-AAATAATCTAAAAGGCCCTAAAATGCAT-AAAATTAATAAAT-GT
*
492393 CCCTAGATTACGTAAATAA-CTTAAAAGGCCCTAAAATGCATAGAATTAATAAATGT
1 CCCTAGATTACGTAAATAATC-TAAAAGGCCCTAAAATGCATAAAATTAATAAATGT
*
492449 CCCTAGATTACATAAA
1 CCCTAGATTACGTAAA
492465 ATATTTTAGG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
56 17 0.26
57 12 0.18
58 24 0.37
59 12 0.18
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.28
Consensus pattern (56 bp):
CCCTAGATTACGTAAATAATCTAAAAGGCCCTAAAATGCATAAAATTAATAAATGT
Found at i:492462 original size:28 final size:27
Alignment explanation
Indices: 492378--492464 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 27
492368 AAATGCATGA
* *
492378 AAATTACTAAATAGTCCCTAGATTACGT
1 AAATTAATAAAT-GTCCCTAGATTACAT
* * * * *
492406 AAA-TAACTTAAAAGGCCCTAAAATGCAT
1 AAATTAA--TAAATGTCCCTAGATTACAT
492434 AGAATTAATAAATGTCCCTAGATTACAT
1 A-AATTAATAAATGTCCCTAGATTACAT
492462 AAA
1 AAA
492465 ATATTTTAGG
Statistics
Matches: 43, Mismatches: 12, Indels: 9
0.67 0.19 0.14
Matches are distributed among these distances:
27 4 0.09
28 30 0.70
29 6 0.14
30 3 0.07
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (27 bp):
AAATTAATAAATGTCCCTAGATTACAT
Found at i:492930 original size:18 final size:19
Alignment explanation
Indices: 492895--492941 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
492885 ATAAAACTTT
492895 AAACAAAAATCATCCAAAA
1 AAACAAAAATCATCCAAAA
492914 AAACAAAAATCAT-CAAAA
1 AAACAAAAATCATCCAAAA
*
492932 AAACCAAAAT
1 AAACAAAAAT
492942 AAAATATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.70, C:0.19, G:0.00, T:0.11
Consensus pattern (19 bp):
AAACAAAAATCATCCAAAA
Found at i:494698 original size:19 final size:18
Alignment explanation
Indices: 494671--494713 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
494661 TTCCCCCTCA
* *
494671 TTTCATTTTGTTGCATTTT
1 TTTCTTTTTCTTGC-TTTT
*
494690 TTTCTTTTTCTTTCTTTT
1 TTTCTTTTTCTTGCTTTT
494708 TTTCTT
1 TTTCTT
494714 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTCTTTTTCTTGCTTTT
Found at i:494707 original size:15 final size:13
Alignment explanation
Indices: 494686--494725 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
494676 TTTTGTTGCA
494686 TTTTTTTCTTTTTC
1 TTTTTTT-TTTTTC
494700 TTTCTTTTTTTCTTC
1 TTT-TTTTTTT-TTC
494715 TTTTTTTTTTT
1 TTTTTTTTTTT
494726 CTCAATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.04
14 13 0.54
15 10 0.42
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:494707 original size:18 final size:17
Alignment explanation
Indices: 494686--494725 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
494676 TTTTGTTGCA
494686 TTTTTTTCTT-TTTCTTT
1 TTTTTTTCTTCTTT-TTT
494703 CTTTTTTTCTTCTTTTTT
1 -TTTTTTTCTTCTTTTTT
494721 TTTTT
1 TTTTT
494726 CTCAATTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 13 0.62
19 3 0.14
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTCTTCTTTTTT
Found at i:494708 original size:11 final size:10
Alignment explanation
Indices: 494686--494723 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
494676 TTTTGTTGCA
494686 TTTTTTTCTT
1 TTTTTTTCTT
*
494696 TTTCTTTCTT
1 TTTTTTTCTT
494706 TTTTTCTTCTT
1 TTTTT-TTCTT
494717 TTTTTTT
1 TTTTTTT
494724 TTCTCAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:494709 original size:12 final size:12
Alignment explanation
Indices: 494694--494727 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
494684 CATTTTTTTC
494694 TTTTTCTTTCTT
1 TTTTTCTTTCTT
494706 TTTTTC-TTCTT
1 TTTTTCTTTCTT
*
494717 TTTTTTTTTCT
1 TTTTTCTTTCT
494728 CAATTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:494726 original size:15 final size:15
Alignment explanation
Indices: 494686--494727 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
494676 TTTTGTTGCA
*
494686 TTTTTTTCTTT-TTC
1 TTTTTTTTTTTCTTC
*
494700 TTTCTTTTTTTCTTC
1 TTTTTTTTTTTCTTC
494715 TTTTTTTTTTTCT
1 TTTTTTTTTTTCT
494728 CAATTACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTCTTC
Found at i:496540 original size:22 final size:22
Alignment explanation
Indices: 496515--496563 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
496505 ATATTAAGTT
**
496515 TTTTAAAATATAATTTTTTATA
1 TTTTAAAATATAATTTTAAATA
496537 TTTTAAAATATAATTTTAAATA
1 TTTTAAAATATAATTTTAAATA
496559 TTTTA
1 TTTTA
496564 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATATAATTTTAAATA
Found at i:500032 original size:13 final size:13
Alignment explanation
Indices: 500014--500040 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
500004 ACACTGTTTT
500014 TTGTATCGATACA
1 TTGTATCGATACA
500027 TTGTATCGATACA
1 TTGTATCGATACA
500040 T
1 T
500041 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:504843 original size:13 final size:13
Alignment explanation
Indices: 504825--504849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
504815 CAAAGATCAG
504825 TGTATCGATACAA
1 TGTATCGATACAA
504838 TGTATCGATACA
1 TGTATCGATACA
504850 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:504929 original size:13 final size:13
Alignment explanation
Indices: 504911--504967 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
504901 ACAAAACTTA
504911 TGTATCGATACAT
1 TGTATCGATACAT
504924 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
504942 ATGTATCGATACAT
1 -TGTATCGATACAT
504956 TGTATCGATACA
1 TGTATCGATACA
504968 ACACTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:504935 original size:32 final size:32
Alignment explanation
Indices: 504890--504986 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
504880 AGTAGCTTAT
* *
504890 ATTGTATCAATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
504922 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
504954 ATTGTATCGATACAACACTTTTGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
504986 A
1 A
504987 ACACTTTATG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:504948 original size:19 final size:19
Alignment explanation
Indices: 504892--505007 Score: 112
Period size: 19 Copynumber: 6.7 Consensus size: 19
504882 TAGCTTATAT
* *
504892 TGTATCAATACAAAACTTA
1 TGTATCGATACAACACTTA
504911 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
504924 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
504943 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
504956 TGTATCGATACAACACTTT
1 TGTATCGATACAACACTTA
504975 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
504995 TGTATCGATACAA
1 TGTATCGATACAA
505008 ATCGTTGAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 25
0.74 0.03 0.23
Matches are distributed among these distances:
13 18 0.22
14 2 0.02
16 11 0.14
18 2 0.02
19 33 0.41
20 15 0.19
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:505881 original size:14 final size:14
Alignment explanation
Indices: 505862--505890 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
505852 TATTATTAAA
505862 ATTTTTTTAAAAAT
1 ATTTTTTTAAAAAT
505876 ATTTTTTTAAAAAT
1 ATTTTTTTAAAAAT
505890 A
1 A
505891 AAATAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTTTTAAAAAT
Found at i:506752 original size:18 final size:18
Alignment explanation
Indices: 506729--506765 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
506719 TCACAATATT
506729 AAATAAAAT-TATATATAA
1 AAATAAAATATA-ATATAA
506747 AAATAAAATATAATATAA
1 AAATAAAATATAATATAA
506765 A
1 A
506766 TATGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATAAAATATAATATAA
Found at i:506784 original size:38 final size:39
Alignment explanation
Indices: 506732--506806 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 39
506722 CAATATTAAA
506732 TAAAATTATATATAAAAATAAAATA-TAATATAAATATGT
1 TAAAATTATATAT-AAAATAAAATATTAATATAAATATGT
* *
506771 TAAAATT-TATATAATATAAAATATTAATATATATAT
1 TAAAATTATATATAAAATAAAATATTAATATAAATAT
506807 ATATATATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 10 0.30
38 16 0.48
39 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (39 bp):
TAAAATTATATATAAAATAAAATATTAATATAAATATGT
Found at i:507948 original size:16 final size:16
Alignment explanation
Indices: 507929--508010 Score: 58
Period size: 16 Copynumber: 4.8 Consensus size: 16
507919 CATAAATCTG
507929 AAATAATTCAAATTTA
1 AAATAATTCAAATTTA
* *
507945 AAATAATTAAAACTT-
1 AAATAATTCAAATTTA
* *
507960 AATTAATTCGAATATTAA
1 AAATAATTC-AA-ATTTA
507978 AATTGATTAATTCAAATTTA
1 AA---A-TAATTCAAATTTA
*
507998 AAATAACTCAAAT
1 AAATAATTCAAAT
508011 AGAAATAATT
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
15 7 0.14
16 24 0.48
17 3 0.06
18 2 0.04
20 6 0.12
21 2 0.04
22 6 0.12
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (16 bp):
AAATAATTCAAATTTA
Found at i:507989 original size:22 final size:22
Alignment explanation
Indices: 507945--508001 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
507935 TTCAAATTTA
507945 AAATAATTAAAACTTAATTAATTC
1 AAAT-ATTAAAA-TTAATTAATTC
* *
507969 GAATATTAAAATTGATTAATTC
1 AAATATTAAAATTAATTAATTC
507991 AAAT-TTAAAAT
1 AAATATTAAAAT
508002 AACTCAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.23
22 13 0.43
23 7 0.23
24 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (22 bp):
AAATATTAAAATTAATTAATTC
Found at i:508534 original size:13 final size:13
Alignment explanation
Indices: 508448--508531 Score: 53
Period size: 13 Copynumber: 5.9 Consensus size: 13
508438 TTGTATAGAT
508448 TAATTTTATTAAA
1 TAATTTTATTAAA
* *
508461 TTATATTATTAAA
1 TAATTTTATTAAA
*
508474 -ATTTTTATTATTAA
1 TAATTTTATTA--AA
*
508488 TAAATTAAGTTATTATAT
1 T-AATT---TTATTA-AA
508506 TAATTTTATTAAA
1 TAATTTTATTAAA
508519 TAATTTTAATTAA
1 TAATTTT-ATTAA
508532 TAACAAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
12 7 0.13
13 19 0.35
14 13 0.24
16 3 0.05
17 4 0.07
18 3 0.05
19 6 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (13 bp):
TAATTTTATTAAA
Found at i:509363 original size:18 final size:18
Alignment explanation
Indices: 509337--509373 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
509327 AAAAATTGAT
509337 TAAAATTTTATATATAAA
1 TAAAATTTTATATATAAA
* *
509355 TAAATTTTTTTATATAAA
1 TAAAATTTTATATATAAA
509373 T
1 T
509374 TAATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAAATTTTATATATAAA
Found at i:509412 original size:24 final size:24
Alignment explanation
Indices: 509342--509419 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 24
509332 TTGATTAAAA
*
509342 TTTTAT-ATATAAATAA-AT-TTT
1 TTTTATAATATTAATAATATATTT
*
509363 TTTATATAA-ATTAAT-ATA-A-TA
1 TTT-TATAATATTAATAATATATTT
*
509384 ATTTATAATATTAATAATATATTT
1 TTTTATAATATTAATAATATATTT
*
509408 TTTTAAAATATT
1 TTTTATAATATT
509420 TATTTTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
20 5 0.12
21 13 0.30
22 12 0.28
23 2 0.05
24 11 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTATAATATTAATAATATATTT
Found at i:509915 original size:29 final size:29
Alignment explanation
Indices: 509865--509956 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
509855 GCAATATTTA
509865 AAATAAA-AAATATTATATAAATGTTAGAT
1 AAATAAATAAATATTATATAAAT-TTAGAT
* **
509894 AAATAAATAAATATTTTA-AAATTTATTT
1 AAATAAATAAATATTATATAAATTTAGAT
* * *
509922 AATATAAATAATTAATATATTAAAATTTATAT
1 AA-ATAAATAAATATTATA-T-AAATTTAGAT
509954 AAA
1 AAA
509957 ATATTTTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 6 0.12
29 24 0.47
30 9 0.18
31 1 0.02
32 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
AAATAAATAAATATTATATAAATTTAGAT
Found at i:509953 original size:14 final size:15
Alignment explanation
Indices: 509918--509971 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
509908 TTTAAAATTT
509918 ATTTA-ATATAAATA
1 ATTTATATATAAATA
* *
509932 ATTAATATATTAA-A
1 ATTTATATATAAATA
509946 ATTTATATA-AAATA
1 ATTTATATATAAATA
* *
509960 TTTTAAATATAA
1 ATTTATATATAA
509972 TTATAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
13 2 0.06
14 21 0.68
15 8 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTATATATAAATA
Found at i:511083 original size:2 final size:2
Alignment explanation
Indices: 511076--511100 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
511066 CTTCGGATGT
511076 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
511101 TCTACTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:514065 original size:35 final size:35
Alignment explanation
Indices: 514017--514089 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
514007 ATTAATTATT
* * *
514017 TTTATATCAATATAAATTATTTCTCCTCATATATA
1 TTTATACCAATATAAATTATTCCTCCTCATAAATA
*
514052 TTTATACCGATATAAATTATTCCTCCTCATAAATA
1 TTTATACCAATATAAATTATTCCTCCTCATAAATA
514087 TTT
1 TTT
514090 TTAAATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.01, T:0.47
Consensus pattern (35 bp):
TTTATACCAATATAAATTATTCCTCCTCATAAATA
Found at i:515176 original size:2 final size:2
Alignment explanation
Indices: 515169--515197 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
515159 TATTAGAAGA
515169 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 A
515198 CTCTCGACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:515285 original size:54 final size:54
Alignment explanation
Indices: 515203--515307 Score: 201
Period size: 54 Copynumber: 1.9 Consensus size: 54
515193 ATATACTCTC
515203 GACTGAAATTTTGCATTTTCTGAAAATTAAGATAAGCCAATGAGATAAATGCAT
1 GACTGAAATTTTGCATTTTCTGAAAATTAAGATAAGCCAATGAGATAAATGCAT
*
515257 GACTGAAATTTTGCATTTTCTGAAAATTAAGATAAGCCCATGAGATAAATG
1 GACTGAAATTTTGCATTTTCTGAAAATTAAGATAAGCCAATGAGATAAATG
515308 TATATATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (54 bp):
GACTGAAATTTTGCATTTTCTGAAAATTAAGATAAGCCAATGAGATAAATGCAT
Found at i:515852 original size:22 final size:20
Alignment explanation
Indices: 515799--515860 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
515789 TATATGAAAT
* *
515799 TAAATTTTAAT-TTTTTTTG
1 TAAATATTAATATTTTTTTA
515818 TAAATATTAATATTTTTTTA
1 TAAATATTAATATTTTTTTA
*
515838 TAAATATTATTATATTTTATTA
1 TAAATATTA--ATATTTTTTTA
515860 T
1 T
515861 TTATTTACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.27
20 16 0.43
22 11 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TAAATATTAATATTTTTTTA
Found at i:515883 original size:11 final size:11
Alignment explanation
Indices: 515853--515895 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
515843 ATTATTATAT
*
515853 TTTATTATTTA
1 TTTAATATTTA
*
515864 TTT-ACATTTA
1 TTTAATATTTA
515874 TTTAATATTTA
1 TTTAATATTTA
515885 TTTAAT-TTTA
1 TTTAATATTTA
515895 T
1 T
515896 ATTATAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 13 0.46
11 15 0.54
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTAATATTTA
Found at i:515895 original size:21 final size:21
Alignment explanation
Indices: 515853--515892 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
515843 ATTATTATAT
*
515853 TTTATTATTTATTTACATTTA
1 TTTAATATTTATTTACATTTA
515874 TTTAATATTTATTTA-ATTT
1 TTTAATATTTATTTACATTT
515893 TATATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTAATATTTATTTACATTTA
Found at i:516991 original size:2 final size:2
Alignment explanation
Indices: 516945--516978 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
516935 CTAGATATTA
516945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
516979 GCGTGGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:517805 original size:20 final size:19
Alignment explanation
Indices: 517777--517820 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
517767 AAGAATATTT
*
517777 TTAAAAATTATTATGTAAAA
1 TTAAAAATTACTAT-TAAAA
*
517797 TTAAGAATTACTATTAAAA
1 TTAAAAATTACTATTAAAA
517816 -TAAAA
1 TTAAAA
517821 CTATTCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
20 12 0.57
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
TTAAAAATTACTATTAAAA
Found at i:518919 original size:17 final size:17
Alignment explanation
Indices: 518897--518931 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
518887 AATATTCACA
518897 TATTTATTATTATAATT
1 TATTTATTATTATAATT
* *
518914 TATTTATTTTTTTAATT
1 TATTTATTATTATAATT
518931 T
1 T
518932 TAAAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTATTATTATAATT
Found at i:519648 original size:30 final size:30
Alignment explanation
Indices: 519586--519669 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
519576 ACGACAGATA
519586 AAATTTTAAAATATA-T-TTTATATTAATATT
1 AAATTTTAAAATATATTATTTA-ATT-ATATT
*
519616 AAATTTTAAAATATATTATTTAATTATTTT
1 AAATTTTAAAATATATTATTTAATTATATT
*
519646 AAA---TAAAATATTTTATATTAATTA
1 AAATTTTAAAATATATTAT-TTAATTA
519670 AATTTTTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
27 12 0.24
28 7 0.14
30 22 0.45
31 4 0.08
32 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
AAATTTTAAAATATATTATTTAATTATATT
Found at i:519675 original size:30 final size:29
Alignment explanation
Indices: 519586--519675 Score: 86
Period size: 28 Copynumber: 3.2 Consensus size: 29
519576 ACGACAGATA
*
519586 AAATTTTAA-AATATATTTTATATTAATATT
1 AAATTTTAATAAAATATTTTATATT-A-ATT
*
519616 AAA-TTT--TAAAATATATTAT-TTAATT
1 AAATTTTAATAAAATATTTTATATTAATT
519641 --ATTTTAAATAAAATATTTTATATTAATT
1 AAATTTT-AATAAAATATTTTATATTAATT
519669 AAATTTT
1 AAATTTT
519676 TATTAATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 3 0.06
26 1 0.02
27 14 0.29
28 16 0.33
29 3 0.06
30 8 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
AAATTTTAATAAAATATTTTATATTAATT
Found at i:519681 original size:15 final size:16
Alignment explanation
Indices: 519655--519688 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
519645 TAAATAAAAT
*
519655 ATTTTATATTAATTAA
1 ATTTTATATTAATAAA
519671 ATTTT-TATTAATAAA
1 ATTTTATATTAATAAA
519686 ATT
1 ATT
519689 ATTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTATATTAATAAA
Found at i:520288 original size:8 final size:8
Alignment explanation
Indices: 520275--520309 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
520265 GCGTGAACCA
520275 AAAAAGCG
1 AAAAAGCG
520283 AAAAA--G
1 AAAAAGCG
520289 AAAAAGCG
1 AAAAAGCG
520297 AAAAAGCG
1 AAAAAGCG
520305 AAAAA
1 AAAAA
520310 CAATTTGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
8 19 0.76
ACGTcount: A:0.71, C:0.09, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAGCG
Found at i:520294 original size:14 final size:14
Alignment explanation
Indices: 520275--520302 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
520265 GCGTGAACCA
520275 AAAAAGCGAAAAAG
1 AAAAAGCGAAAAAG
520289 AAAAAGCGAAAAAG
1 AAAAAGCGAAAAAG
520303 CGAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAGCGAAAAAG
Found at i:531551 original size:52 final size:52
Alignment explanation
Indices: 531481--531601 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
531471 GAAAATTTAT
*
531481 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
531533 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
531585 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
531602 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:531614 original size:52 final size:51
Alignment explanation
Indices: 531481--531621 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
531471 GAAAATTTAT
531481 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
531533 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
531585 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
531622 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:531628 original size:13 final size:13
Alignment explanation
Indices: 531610--531634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
531600 CAAAGATCAG
531610 TGTATCGATACAA
1 TGTATCGATACAA
531623 TGTATCGATACA
1 TGTATCGATACA
531635 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:531718 original size:13 final size:13
Alignment explanation
Indices: 531700--531724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
531690 CAAAAAAATA
531700 TGTATCGATACAT
1 TGTATCGATACAT
531713 TGTATCGATACA
1 TGTATCGATACA
531725 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:531720 original size:33 final size:33
Alignment explanation
Indices: 531678--531744 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
531668 AGTAGCTTAA
531678 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
531711 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
531744 A
1 A
531745 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:547071 original size:13 final size:13
Alignment explanation
Indices: 547053--547079 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
547043 ACATAATGCT
547053 TTGTATCGATACA
1 TTGTATCGATACA
547066 TTGTATCGATACA
1 TTGTATCGATACA
547079 T
1 T
547080 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:547109 original size:20 final size:19
Alignment explanation
Indices: 547063--547119 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
547053 TTGTATCGAT
*
547063 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
547082 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
547101 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
547120 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:547173 original size:20 final size:20
Alignment explanation
Indices: 547148--547201 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
547138 CTACCATTGT
* ** *
547148 TTGTATTGATACATGGCACA
1 TTGTATCGATACATAACAAA
*
547168 TTGTATCAATACATAACAAA
1 TTGTATCGATACATAACAAA
547188 TTGTATCGATACAT
1 TTGTATCGATACAT
547202 TGTATCAAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATAACAAA
Found at i:552182 original size:52 final size:52
Alignment explanation
Indices: 552034--552162 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
552024 CGAAATATGA
552034 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
552086 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
552138 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
552163 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:552189 original size:13 final size:13
Alignment explanation
Indices: 552171--552195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
552161 CAAAGATCAG
552171 TGTATCGATACAA
1 TGTATCGATACAA
552184 TGTATCGATACA
1 TGTATCGATACA
552196 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:552274 original size:32 final size:32
Alignment explanation
Indices: 552233--552333 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
552223 GGCAGTAGCT
* *
552233 TACATTGTATCGATATAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
552265 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
552297 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
552330 TACA
1 TACA
552334 GATCGTTGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 51 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:552275 original size:13 final size:13
Alignment explanation
Indices: 552257--552313 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
552247 ATAAAACTTA
552257 TGTATCGATACAT
1 TGTATCGATACAT
552270 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
552288 ATGTATCGATACAT
1 -TGTATCGATACAT
552302 TGTATCGATACA
1 TGTATCGATACA
552314 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:552294 original size:19 final size:19
Alignment explanation
Indices: 552238--552333 Score: 81
Period size: 19 Copynumber: 5.6 Consensus size: 19
552228 TAGCTTACAT
* *
552238 TGTATCGATATAAAACTTA
1 TGTATCGATACAACACTTA
552257 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
552270 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
552289 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
552302 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
552322 TGTATCGATACA
1 TGTATCGATACA
552334 GATCGTTGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 25
0.71 0.01 0.28
Matches are distributed among these distances:
13 18 0.29
14 2 0.03
16 11 0.17
18 1 0.02
19 19 0.30
20 12 0.19
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:557054 original size:13 final size:13
Alignment explanation
Indices: 557032--557068 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
557022 CTGTTCTTTA
557032 TATCGATACATTG
1 TATCGATACATTG
* *
557045 TATTGATACAATG
1 TATCGATACATTG
557058 TATCGATACAT
1 TATCGATACAT
557069 GGGTTACTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:559428 original size:19 final size:19
Alignment explanation
Indices: 559404--559451 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
559394 CTTCTAAGTG
559404 ATTTTCAATATCTATAAAT
1 ATTTTCAATATCTATAAAT
* *
559423 ATTTTCGAGTTATGTATAAAT
1 ATTTTC-A-ATATCTATAAAT
*
559444 GTTTTCAA
1 ATTTTCAA
559452 GCTTTAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
19 6 0.26
20 2 0.09
21 15 0.65
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (19 bp):
ATTTTCAATATCTATAAAT
Found at i:559617 original size:13 final size:13
Alignment explanation
Indices: 559599--559625 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
559589 ACATAATGCT
559599 TTGTATCGATACA
1 TTGTATCGATACA
559612 TTGTATCGATACA
1 TTGTATCGATACA
559625 T
1 T
559626 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:559655 original size:20 final size:19
Alignment explanation
Indices: 559609--559665 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
559599 TTGTATCGAT
*
559609 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
559628 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
559647 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
559666 AAACTAGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:559739 original size:33 final size:33
Alignment explanation
Indices: 559695--559759 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
559685 TACCACTGCT
* *
559695 TGTATCGATACATG-GGATATTGTATCTATACAA
1 TGTATCAATACATGAGGA-ATTGTATCGATACAA
*
559728 TGTATCAATACATGATGAATTGTATCGATACA
1 TGTATCAATACATGAGGAATTGTATCGATACA
559760 TTGCTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCAATACATGAGGAATTGTATCGATACAA
Found at i:564453 original size:19 final size:18
Alignment explanation
Indices: 564424--564492 Score: 78
Period size: 19 Copynumber: 4.1 Consensus size: 18
564414 TTGAATTTCA
564424 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
564441 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
564460 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
564473 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
564492 A
1 A
564493 ATGTATCGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.25
15 2 0.05
17 6 0.14
18 1 0.02
19 24 0.55
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:564467 original size:13 final size:13
Alignment explanation
Indices: 564449--564506 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
564439 ACATAAGTGT
564449 TGTATCGATACAA
1 TGTATCGATACAA
564462 TGTATCGATACATAA
1 TGTATCGATAC--AA
564477 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
564494 TGTATCGCTACAA
1 TGTATCGATACAA
564507 AGTTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:564471 original size:32 final size:32
Alignment explanation
Indices: 564430--564509 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
564420 TTCAATAATT
564430 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
564462 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
564494 TGTATCGCTACA-AAGT
1 TGTATCGATACATAAGT
564510 TACTGCCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 4 0.09
32 42 0.91
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:564562 original size:13 final size:13
Alignment explanation
Indices: 564544--564569 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
564534 CATTTTTCAA
564544 TGTATCGATACAT
1 TGTATCGATACAT
564557 TGTATCGATACAT
1 TGTATCGATACAT
564570 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:568189 original size:19 final size:19
Alignment explanation
Indices: 568165--568212 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
568155 CTTCTAAGTG
568165 ATTTTCAATATCTATAAAT
1 ATTTTCAATATCTATAAAT
* *
568184 ATTTTCGAGTTATGTATAAAT
1 ATTTTC-A-ATATCTATAAAT
*
568205 GTTTTCAA
1 ATTTTCAA
568213 GCTTTAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
19 6 0.26
20 2 0.09
21 15 0.65
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (19 bp):
ATTTTCAATATCTATAAAT
Found at i:568378 original size:13 final size:13
Alignment explanation
Indices: 568360--568386 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
568350 ACATAATGCT
568360 TTGTATCGATACA
1 TTGTATCGATACA
568373 TTGTATCGATACA
1 TTGTATCGATACA
568386 T
1 T
568387 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:568416 original size:20 final size:19
Alignment explanation
Indices: 568370--568426 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
568360 TTGTATCGAT
*
568370 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
568389 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
568408 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
568427 AAACTAGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:568500 original size:33 final size:33
Alignment explanation
Indices: 568456--568520 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
568446 TACCACTGCT
* *
568456 TGTATCGATACATG-GGATATTGTATCTATACAA
1 TGTATCAATACATGAGGA-ATTGTATCGATACAA
*
568489 TGTATCAATACATGATGAATTGTATCGATACA
1 TGTATCAATACATGAGGAATTGTATCGATACA
568521 TTGCTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCAATACATGAGGAATTGTATCGATACAA
Found at i:573214 original size:19 final size:18
Alignment explanation
Indices: 573185--573253 Score: 78
Period size: 19 Copynumber: 4.1 Consensus size: 18
573175 TTGAATTTCA
573185 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
573202 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
573221 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
573234 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
573253 A
1 A
573254 ATGTATCGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.25
15 2 0.05
17 6 0.14
18 1 0.02
19 24 0.55
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:573228 original size:13 final size:13
Alignment explanation
Indices: 573210--573267 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
573200 ACATAAGTGT
573210 TGTATCGATACAA
1 TGTATCGATACAA
573223 TGTATCGATACATAA
1 TGTATCGATAC--AA
573238 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
573255 TGTATCGCTACAA
1 TGTATCGATACAA
573268 AGTTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:573232 original size:32 final size:32
Alignment explanation
Indices: 573191--573270 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
573181 TTCAATAATT
573191 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
573223 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
573255 TGTATCGCTACA-AAGT
1 TGTATCGATACATAAGT
573271 TACTGCCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 4 0.09
32 42 0.91
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:573323 original size:13 final size:13
Alignment explanation
Indices: 573305--573330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
573295 CATTTTTCAA
573305 TGTATCGATACAT
1 TGTATCGATACAT
573318 TGTATCGATACAT
1 TGTATCGATACAT
573331 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:575780 original size:50 final size:52
Alignment explanation
Indices: 575688--575820 Score: 171
Period size: 51 Copynumber: 2.6 Consensus size: 52
575678 TTAAGTTTCT
* * *
575688 CAATTTTTCATAATCGGGGGTACTCCAACCCCGGTTTTATTT-CTAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * * * *
575739 TAATTTTCCACAATCGGGGATAC-CCCACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
*
575790 CATTTTTTCATAATCGGGGATACTCCAACCC
1 CAATTTTTCATAATCGGGGATACTCCAACCC
575821 TTTTAATCAT
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
50 15 0.23
51 46 0.70
52 5 0.08
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (52 bp):
CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
Found at i:575832 original size:27 final size:27
Alignment explanation
Indices: 575802--575876 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 27
575792 TTTTTTCATA
575802 ATCGGGGATACTCCAACCCTT-TTAATC
1 ATCGGGGATACTCCAACCCTTATT-ATC
*
575829 ATCGGGGATACTCCAACCACGTTATTTTC
1 ATCGGGGATACTCCAACC-C-TTATTATC
*
575858 A-AGGGGATACTCCAACCCT
1 ATCGGGGATACTCCAACCCT
575877 GGCTTTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
26 1 0.02
27 19 0.44
28 16 0.37
29 5 0.12
30 2 0.05
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCTTATTATC
Found at i:576258 original size:28 final size:28
Alignment explanation
Indices: 576226--576298 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
576216 TTATCACAAT
576226 CAGGGATACTCCAACCCCGTTATTTTCG
1 CAGGGATACTCCAACCCCGTTATTTTCG
* *
576254 CAGGGATACTCGAACCCCGTTATTTTTG
1 CAGGGATACTCCAACCCCGTTATTTTCG
576282 -AGGGGATACTCCAACCC
1 CA-GGGATACTCCAACCC
576299 TGATTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (28 bp):
CAGGGATACTCCAACCCCGTTATTTTCG
Found at i:576271 original size:79 final size:79
Alignment explanation
Indices: 575829--576272 Score: 692
Period size: 79 Copynumber: 5.6 Consensus size: 79
575819 CCTTTTAATC
* * * *
575829 ATCGGGGATACTCCAACCACGTTATTTTCAAGGGGATACTCCAACCCTGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
*
575894 ATTGATTTCTCATA
66 ATTGATTTCTCACA
** *
575908 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTAGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
575973 ATTGATTTCTCACA
66 ATTGATTTCTCACA
* *
575987 ATCGGGGATACTCCGACCCCGTTATTTCCGAGGGGATACTCCAACCTCGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
576052 ATTGATTTCTCACA
66 ATTGATTTCTCACA
* * *
576066 ATCGGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCTAACCCCGGTTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
576131 ATTGATTTCTCACA
66 ATTGATTTCTCACA
* * *
576145 ATCGGGGATATTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
*
576210 ATTGATTTATCACA
66 ATTGATTTCTCACA
* * *
576224 ATCAGGGATACTCCAACCCCGTTATTTTCGCA-GGGATACTCGAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTCCG-AGGGGATACTCCAACCCCG
576273 TTATTTTTGA
Statistics
Matches: 338, Mismatches: 26, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
79 337 1.00
80 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
ATTGATTTCTCACA
Found at i:576338 original size:107 final size:107
Alignment explanation
Indices: 576149--576379 Score: 270
Period size: 107 Copynumber: 2.2 Consensus size: 107
576139 CTCACAATCG
* * * ***
576149 GGGATATTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAATATTG
1 GGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTCCTAAAACACCA
576214 ATTTATCACAATCAGGGATACTCCAACCCCGTTATTTTCGCA
66 ATTTATCACAATCAGGGATACTCCAACCCCGTTATTTTCGCA
* * * *
576256 GGGATACTCGAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATT-TTCAAAACACC
1 GGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTCCT-AAAACACC
* * * * **
576320 AATTT-TCTATAATTAGGGATACTCCAACCCTGTTA-CTTCTAA
65 AATTTATC-ACAATCAGGGATACTCCAACCCCGTTATTTTCGCA
576362 GGGGATACTCCAACCCCG
1 -GGGATACTCCAACCCCG
576380 ATTTTATTTC
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
106 7 0.07
107 97 0.93
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (107 bp):
GGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTCCTAAAACACCA
ATTTATCACAATCAGGGATACTCCAACCCCGTTATTTTCGCA
Found at i:576430 original size:79 final size:79
Alignment explanation
Indices: 576254--576431 Score: 239
Period size: 79 Copynumber: 2.3 Consensus size: 79
576244 GTTATTTTCG
* * * * * * *
576254 CAGGGATACTCGAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTTCAAAACAC
1 CAGGGATACTCCAACCCTGTTACTTCTAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC
*
576319 CAATTTTCTATAAT
66 CAATTTTCCATAAT
* *
576333 TAGGGATACTCCAACCCTGTTACTTCTAAGGGGATACTCCAACCCCGATTTTATTTCCAGAACAC
1 CAGGGATACTCCAACCCTGTTACTTCTAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC
*
576398 CGATTTTCCATAAT
66 CAATTTTCCATAAT
* *
576412 CAGGGGTACTCCAGCCCTGT
1 CAGGGATACTCCAACCCTGT
576432 CGTCATCCCA
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 85 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (79 bp):
CAGGGATACTCCAACCCTGTTACTTCTAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC
CAATTTTCCATAAT
Found at i:581390 original size:52 final size:52
Alignment explanation
Indices: 581312--581440 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
581302 CGAAATATGA
**
581312 AAATTTGCCGGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
581364 AAATTTGCTTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
581416 AAATTTGCTTGCATGTATCGATACA
1 AAATTTGCTTGCATGTATCGATACA
581441 ATGTATCGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:581446 original size:13 final size:13
Alignment explanation
Indices: 581428--581453 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
581418 ATTTGCTTGC
581428 ATGTATCGATACA
1 ATGTATCGATACA
581441 ATGTATCGATACA
1 ATGTATCGATACA
581454 TTTGAGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:581516 original size:13 final size:13
Alignment explanation
Indices: 581498--581549 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
581488 AGCTTCGTAG
581498 CGATACATTGTAT
1 CGATACATTGTAT
581511 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
581530 CGATACATTGTAT
1 CGATACATTGTAT
581543 CGATACA
1 CGATACA
581550 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:581530 original size:19 final size:18
Alignment explanation
Indices: 581506--581569 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
581496 AGCGATACAT
581506 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
581525 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
581538 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
581557 TGTATCGATACAA
1 TGTATCGATACAA
581570 TTACGGTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:581539 original size:32 final size:32
Alignment explanation
Indices: 581498--581568 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
581488 AGCTTCGTAG
581498 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
581530 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
581562 CGATACA
1 CGATACA
581569 ATTACGGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:587071 original size:52 final size:50
Alignment explanation
Indices: 587002--587132 Score: 140
Period size: 50 Copynumber: 2.6 Consensus size: 50
586992 AAATAACGAG
** *
587002 GTTGGAGTATCTTCGATTGTGAAAAATTGGTGTTTTTGGAAA-TAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGG-G-TTTT-GAAAGTAAAATCGGA
* * *
587054 GTTGGAGTATCCCCGATTAAAGGAAAATT-GGTTTTGAAAGTAAAATCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGGTTTTGAAAGTAAAATCGGA
* *
587104 GTTGGAATATCCCCGATTATGAACAATTG
1 GTTGGAGTATCCCCGATTATGAAAAATTG
587133 AGAAACTTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
49 11 0.17
50 30 0.45
51 1 0.02
52 17 0.26
53 7 0.11
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGGTTTTGAAAGTAAAATCGGA
Found at i:589511 original size:13 final size:13
Alignment explanation
Indices: 589493--589518 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
589483 ACAAAGATCG
589493 ATGTATCGATACA
1 ATGTATCGATACA
589506 ATGTATCGATACA
1 ATGTATCGATACA
589519 CTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:589529 original size:21 final size:21
Alignment explanation
Indices: 589505--589546 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
589495 GTATCGATAC
589505 AATGTATCGATACACTTCCTT
1 AATGTATCGATACACTTCCTT
*
589526 AATGTATCGATACATTTCCTT
1 AATGTATCGATACACTTCCTT
589547 GGTAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACACTTCCTT
Found at i:589732 original size:13 final size:13
Alignment explanation
Indices: 589714--589750 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
589704 ATGTTTTTTT
589714 TTTATTTTATTTA
1 TTTATTTTATTTA
589727 TTTATTTTA-TTA
1 TTTATTTTATTTA
589739 -TTATTTT-TTTA
1 TTTATTTTATTTA
589750 T
1 T
589751 CCTTTTTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.45
12 3 0.14
13 9 0.41
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:589742 original size:19 final size:18
Alignment explanation
Indices: 589713--589750 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
589703 AATGTTTTTT
589713 TTTTATTTTATTTATTTA
1 TTTTATTTTATTTATTTA
*
589731 TTTTATTATTATTTTTTTA
1 TTTTATT-TTATTTATTTA
589750 T
1 T
589751 CCTTTTTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTATTTTATTTATTTA
Found at i:590539 original size:61 final size:62
Alignment explanation
Indices: 590447--590617 Score: 159
Period size: 61 Copynumber: 2.8 Consensus size: 62
590437 AAGTGCATCC
* *
590447 TGCTCTTTGAGGACTAAAAAGTGCGACCAACTCATGTGGGCTTTGAAAAG-GAAAGGCGTCT
1 TGCTCTTTAAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGAGAAAGGCGTCT
** * * * * * *
590508 TGCTCTTTAAGGACTGGAAGGTGCCATCAACTCGTGTGGGCTTTGCAAAGAGAAA-GCATCC
1 TGCTCTTTAAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGAGAAAGGCGTCT
* * * * ** *
590569 TGCTTTTTGAGAACTAGAAAA-TGCCACAAACTTGTGCGGGCTTTGAAAA
1 TGCTCTTTAAGGACTA-AAAAGTGCCACCAACTCATGTGGGCTTTGAAAA
590618 ACGTCCTGCT
Statistics
Matches: 87, Mismatches: 21, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
61 81 0.93
62 6 0.07
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (62 bp):
TGCTCTTTAAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGAGAAAGGCGTCT
Found at i:590650 original size:55 final size:55
Alignment explanation
Indices: 590566--590710 Score: 175
Period size: 55 Copynumber: 2.6 Consensus size: 55
590556 AGAGAAAGCA
* * * **
590566 TCCTGCTTTTTGAGAACTAGAAAATGCCACAAACTTGTGCGGGCTTTGAAAA-ACG
1 TCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTACGCGGGCTTT-AAAAGACG
* * * *
590621 TCCTGCTCTTTGAGGGCTGGAAAATGCCACCAACTTACGTGGGCTTTAAAAGGCG
1 TCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTACGCGGGCTTTAAAAGACG
* *
590676 TCCTACTTTTTGAAGACTGGAAAATGCCACCAACT
1 TCCTGCTTTTTGAGGACTGGAAAATGCCACCAACT
590711 AATTGAACTT
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 4 0.05
55 72 0.95
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (55 bp):
TCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTACGCGGGCTTTAAAAGACG
Found at i:590935 original size:120 final size:116
Alignment explanation
Indices: 590755--590970 Score: 256
Period size: 120 Copynumber: 1.8 Consensus size: 116
590745 GTGTCCCACC
* * * *
590755 TTTTGAGGACAAAGGAAAAGAGAATGAAATAGGTCTTGCTCCTTGAGGACAAAAGGAAGAGAAGA
1 TTTTGAGGACAAAGGAAAAGAGAACGAAATACGTCCTGCTCCTTGAGGACAAAA-GAA-AGAGGA
590820 AAAGGAAAGTG-TCCTGCTTCTTGAGGA-TAAAGTGAAAAAGAGTACGTCCCAT
64 AAA-GAAAGTGATCCTGCTTCTTGAGGACTAAAGTGAAAAAGAGTACGTCCCAT
* * * **
590872 TTTTCGAGGACAAGGGAAAAAGGGAAACGAAATACGTCCTGCTCTTTGAGGATGAAAGAAAGAGG
1 TTTT-GAGGACAAAGG-AAAAGAG-AACGAAATACGTCCTGCTCCTTGAGGACAAAAGAAAGAGG
* *
590937 AAAATAAAGTGCATCCTGCTTTTTGAGGACTAAA
63 AAAAGAAAGTG-ATCCTGCTTCTTGAGGACTAAA
590971 AAGTGCCACC
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
117 10 0.12
118 18 0.22
119 24 0.29
120 30 0.37
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.21
Consensus pattern (116 bp):
TTTTGAGGACAAAGGAAAAGAGAACGAAATACGTCCTGCTCCTTGAGGACAAAAGAAAGAGGAAA
AGAAAGTGATCCTGCTTCTTGAGGACTAAAGTGAAAAAGAGTACGTCCCAT
Found at i:591038 original size:61 final size:56
Alignment explanation
Indices: 590942--591363 Score: 318
Period size: 55 Copynumber: 7.4 Consensus size: 56
590932 AGAGGAAAAT
* * * *
590942 AAAGTGCATCCTGCTTTTTGAGGACT-AAAAAGTGCCACCAGCTCATGTGGGCTTTGAAAAGG
1 AAAG-GCATCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTCGTGTGGGCTTT----A-G
* ** *
591004 AAAGGCTTCCTGCTCTTTGAGGACTGGAAGGTGCCATCAACTCGTGTGGGCTTTGCAAAG
1 AAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTT----AG
* * * * * * *
591064 AGAAAGCATCCTGATTTTTGAGAACTAGAAAATGCCACCAACTTGTGCGGGCTTT-G
1 A-AAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTAG
* * * * **
591120 AAAAGCGTCATGCTCTTTGAGGATTGGAAAATGCCACCAACTTATGTGGGCTTTA-
1 AAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTAG
* * *
591175 AAAGGCATCCTACTTTTTGAGGATTGGAAAATGCCACCAACTCGTGTGGGCTTT-G
1 AAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTAG
* * * *
591230 AAAGGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTA-
1 AAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTAG
** * * * *** *
591285 AAAGGTGTCCTACTCTTTGAGGACT-GAAAGGTGCCGCTGTCTTGTGTGGGCTTT-G
1 AAAGGCATCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTCGTGTGGGCTTTAG
* **
591340 AAAAGCGCCCTGCTCTTTGAGGAC
1 AAAGGCATCCTGCTCTTTGAGGAC
591364 AAAAAGGGGA
Statistics
Matches: 299, Mismatches: 54, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
54 3 0.01
55 201 0.67
56 2 0.01
60 2 0.01
61 85 0.28
62 6 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (56 bp):
AAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTAG
Found at i:591151 original size:55 final size:55
Alignment explanation
Indices: 591011--591363 Score: 343
Period size: 55 Copynumber: 6.3 Consensus size: 55
591001 AGGAAAGGCT
** * * *
591011 TCCTGCTCTTTGAGGACTGGAAGGTGCCATCAACTCGTGTGGGCTTTGCAAAGAGAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAAGCG
* * * * *
591072 TCCTGATTTTTGAGAACTAGAAAATGCCACCAACTTGTGCGGGCTTTGAAAAGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGCG
* * * *
591127 TCATGCTCTTTGAGGATTGGAAAATGCCACCAACTTATGTGGGCTTT-AAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAA-GCG
* * * * *
591182 TCCTACTTTTTGAGGATTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGCG
* * *
591237 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAA-GCG
* * * ***
591292 TCCTACTCTTTGAGGACT-GAAAGGTGCCGCTGTCTTGTGTGGGCTTTGAAAAGCG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGCG
*
591347 CCCTGCTCTTTGAGGAC
1 TCCTGCTCTTTGAGGAC
591364 AAAAAGGGGA
Statistics
Matches: 244, Mismatches: 43, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
54 10 0.04
55 187 0.77
56 9 0.04
61 38 0.16
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGCG
Found at i:591163 original size:506 final size:506
Alignment explanation
Indices: 590211--591216 Score: 1807
Period size: 506 Copynumber: 2.0 Consensus size: 506
590201 ACTTGTGTAG
590211 ACTTTAGGAGGGGAAAGAAATGGAAGGGGTGTCCCACCTTTTGAGGACAAAGGAAAAGAGAATGA
1 ACTTTAGGAGGGGAAAGAAATGGAAGGGGTGTCCCACCTTTTGAGGACAAAGGAAAAGAGAATGA
590276 AATAGGTCTTGCTCCTTGAGGACAAAAGGAAGAGAAGAAAAAGAAAGTGTCCTGCTTCTTAAGGA
66 AATAGGTCTTGCTCCTTGAGGACAAAAGGAAGAGAAGAAAAAGAAAGTGTCCTGCTTCTTAAGGA
* *
590341 TAAAGTGAAAAAGAGTACGTCCCATTTTTTGAGGACAAGGGAAAAAAGGAAACGAAATACGTCTT
131 TAAAGTGAAAAAGAGTACGTCCCATTTTTCGAGGACAAGGGAAAAAAGGAAACGAAATACGTCCT
590406 GCTCTTTGAGGATGAAAGAAAGAGGAAAATAAAGTGCATCCTGCTCTTTGAGGACTAAAAAGTGC
196 GCTCTTTGAGGATGAAAGAAAGAGGAAAATAAAGTGCATCCTGCTCTTTGAGGACTAAAAAGTGC
* *
590471 GACCAACTCATGTGGGCTTTGAAAAGGAAAGGCGTCTTGCTCTTTAAGGACTGGAAGGTGCCATC
261 CACCAACTCATGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTAAGGACTGGAAGGTGCCATC
*
590536 AACTCGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTTTTTGAGAACTAGAAAATGCCACAAACT
326 AACTCGTGTGGGCTTTGCAAAGAGAAAGCATCCTGATTTTTGAGAACTAGAAAATGCCACAAACT
* *
590601 TGTGCGGGCTTTGAAAAACGTCCTGCTCTTTGAGGGCTGGAAAATGCCACCAACTTACGTGGGCT
391 TGTGCGGGCTTTGAAAAACGTCATGCTCTTTGAGGACTGGAAAATGCCACCAACTTACGTGGGCT
*
590666 TTAAAAGGCGTCCTACTTTTTGAAGACTGGAAAATGCCACCAACTAATTGA
456 TTAAAAGGCATCCTACTTTTTGAAGACTGGAAAATGCCACCAACTAATTGA
590717 ACTTTAGGAGGGGAAAGAAATGGCAA-GGGTGTCCCACCTTTTGAGGACAAAGGAAAAGAGAATG
1 ACTTTAGGAGGGGAAAGAAATGG-AAGGGGTGTCCCACCTTTTGAGGACAAAGGAAAAGAGAATG
* *
590781 AAATAGGTCTTGCTCCTTGAGGACAAAAGGAAGAGAAGAAAAGGAAAGTGTCCTGCTTCTTGAGG
65 AAATAGGTCTTGCTCCTTGAGGACAAAAGGAAGAGAAGAAAAAGAAAGTGTCCTGCTTCTTAAGG
*
590846 ATAAAGTGAAAAAGAGTACGTCCCATTTTTCGAGGACAAGGGAAAAAGGGAAACGAAATACGTCC
130 ATAAAGTGAAAAAGAGTACGTCCCATTTTTCGAGGACAAGGGAAAAAAGGAAACGAAATACGTCC
*
590911 TGCTCTTTGAGGATGAAAGAAAGAGGAAAATAAAGTGCATCCTGCTTTTTGAGGACTAAAAAGTG
195 TGCTCTTTGAGGATGAAAGAAAGAGGAAAATAAAGTGCATCCTGCTCTTTGAGGACTAAAAAGTG
* * *
590976 CCACCAGCTCATGTGGGCTTTGAAAAGGAAAGGCTTCCTGCTCTTTGAGGACTGGAAGGTGCCAT
260 CCACCAACTCATGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTAAGGACTGGAAGGTGCCAT
*
591041 CAACTCGTGTGGGCTTTGCAAAGAGAAAGCATCCTGATTTTTGAGAACTAGAAAATGCCACCAAC
325 CAACTCGTGTGGGCTTTGCAAAGAGAAAGCATCCTGATTTTTGAGAACTAGAAAATGCCACAAAC
* * *
591106 TTGTGCGGGCTTTGAAAAGCGTCATGCTCTTTGAGGATTGGAAAATGCCACCAACTTATGTGGGC
390 TTGTGCGGGCTTTGAAAAACGTCATGCTCTTTGAGGACTGGAAAATGCCACCAACTTACGTGGGC
* *
591171 TTTAAAAGGCATCCTACTTTTTGAGGATTGGAAAATGCCACCAACT
455 TTTAAAAGGCATCCTACTTTTTGAAGACTGGAAAATGCCACCAACT
591217 CGTGTGGGCT
Statistics
Matches: 478, Mismatches: 21, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
506 476 1.00
507 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (506 bp):
ACTTTAGGAGGGGAAAGAAATGGAAGGGGTGTCCCACCTTTTGAGGACAAAGGAAAAGAGAATGA
AATAGGTCTTGCTCCTTGAGGACAAAAGGAAGAGAAGAAAAAGAAAGTGTCCTGCTTCTTAAGGA
TAAAGTGAAAAAGAGTACGTCCCATTTTTCGAGGACAAGGGAAAAAAGGAAACGAAATACGTCCT
GCTCTTTGAGGATGAAAGAAAGAGGAAAATAAAGTGCATCCTGCTCTTTGAGGACTAAAAAGTGC
CACCAACTCATGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTAAGGACTGGAAGGTGCCATC
AACTCGTGTGGGCTTTGCAAAGAGAAAGCATCCTGATTTTTGAGAACTAGAAAATGCCACAAACT
TGTGCGGGCTTTGAAAAACGTCATGCTCTTTGAGGACTGGAAAATGCCACCAACTTACGTGGGCT
TTAAAAGGCATCCTACTTTTTGAAGACTGGAAAATGCCACCAACTAATTGA
Found at i:591228 original size:110 final size:110
Alignment explanation
Indices: 590942--591363 Score: 418
Period size: 110 Copynumber: 3.7 Consensus size: 110
590932 AGAGGAAAAT
* * * * *
590942 AAAGTGCATCCTGCTTTTTGAGGACTAAAAAGTGCCACCAGCTCATGTGGGCTTTGAAAAGGAAA
1 AAAGAGCATCCTACTTTTTGAGGACTGAAAA-TGCCACCAACTCGTGTGGGCTTTG---A--AAA
* * * *
591007 GGCTTCCTGCTCTTTGAGGACTGGAAGGTGCCATCAACTCGTGTGGGCTTTGCA
60 -GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT--A
* * *
591061 AAGAGAAAGCATCCTGA-TTTTTGAGAACTAGAAAATGCCACCAACTTGTGCGGGCTTTGAAAAG
1 AA-AG--AGCATCCT-ACTTTTTGAGGACT-GAAAATGCCACCAACTCGTGTGGGCTTTGAAAAG
* * * *
591125 CGTCATGCTCTTTGAGGATTGGAAAATGCCACCAACTTATGTGGGCTTTA
61 CGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTA
* *
591175 AAAG-GCATCCTACTTTTTGAGGATTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTC
1 AAAGAGCATCCTACTTTTTGAGGACT-GAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGCGTC
*
591239 CTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTA
65 CTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTA
** * * * *** * *
591285 AAAG-GTGTCCTACTCTTTGAGGACTGAAAGGTGCCGCTGTCTTGTGTGGGCTTTGAAAAGCGCC
1 AAAGAGCATCCTACTTTTTGAGGACTGAAA-ATGCCACCAACTCGTGTGGGCTTTGAAAAGCGTC
591349 CTGCTCTTTGAGGAC
65 CTGCTCTTTGAGGAC
591364 AAAAAGGGGA
Statistics
Matches: 257, Mismatches: 39, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
109 5 0.02
110 155 0.60
113 2 0.01
114 3 0.01
116 42 0.16
117 3 0.01
119 3 0.01
120 2 0.01
122 38 0.15
123 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (110 bp):
AAAGAGCATCCTACTTTTTGAGGACTGAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGCGTCC
TGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTA
Found at i:591475 original size:55 final size:55
Alignment explanation
Indices: 591386--591793 Score: 559
Period size: 55 Copynumber: 7.3 Consensus size: 55
591376 GGAGAGAGCA
* *
591386 TCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAAGTG
1 TCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCG
* *
591441 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCG
* * *
591496 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCG
* *
591551 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCG
*
591606 TCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---A--AAAA-GCG
* * *
591667 TCCCGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAAGCG
* * * *
591723 TCCTGCTCATTGAGGACT-GAAAGGTGCCCCCAACTTGTGTGGGCTTTGAAAAGCG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAAGCG
*
591778 CCCTGCTCTTTGAGGA
1 TCCTGCTCTTTGAGGA
591794 AAAAAAGGCG
Statistics
Matches: 319, Mismatches: 25, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
54 2 0.01
55 242 0.76
56 19 0.06
57 3 0.01
58 1 0.00
59 1 0.00
60 4 0.01
61 24 0.08
62 23 0.07
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCG
Found at i:591507 original size:149 final size:154
Alignment explanation
Indices: 591064--591652 Score: 535
Period size: 165 Copynumber: 3.7 Consensus size: 154
591054 CTTTGCAAAG
* * * * * * * * *
591064 AGAAA-GCATCCTGATTTTTGAGAACTAGAAAATGCCACCAACTTGTGCGGGCTTTGAAAAGCGT
1 AGAAAGGCATCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGTGT
* * * * * ** *
591128 CATGCTCTTTGAGGATTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAGGCATCCTACTTTTT
66 CCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCGCCCTACTCTTT
* * *
591193 GAGGATTGGAAAATGCCACCAACTCGTGTGGGCTT
131 GAGGA-CGAAAAAGGCCA-CAA------T-GG--T
* * *
591228 TGAAAGGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGT
1 AGAAAGGCATCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGTGT
* * *** * *
591293 CCTACTCTTTGAGGACT-GAAAGGTGCCGCTGTCTTGTGTGGGCTTTGAAAAGCGCCCTGCTCTT
66 CCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAAGCGCCCTACTCTT
**
591357 TGAGGAC-AAAAAGGGGA-AA-GG-
130 TGAGGACGAAAAAGGCCACAATGGT
* *
591378 AGAGA-GCATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGTGT
1 AGAAAGGCATCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGTGT
* *
591442 CCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGTGTCCTACTCTTT
66 CCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCGCCCTACTCTTT
* *
591507 GAGGACTGGAAAATGCCACCAACTTGTGTGGGCTT
131 GAGGAC-GAAAAAGGCCA-CAA------T-GG--T
* * *
591542 TGAAAGGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGCGT
1 AGAAAGGCATCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGTGT
* *
591607 CCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT
66 CCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT
591653 GAAAGGAAAA
Statistics
Matches: 349, Mismatches: 57, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
149 113 0.32
150 7 0.02
151 6 0.02
153 4 0.01
161 4 0.01
163 6 0.02
164 11 0.03
165 198 0.57
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (154 bp):
AGAAAGGCATCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGTGT
CCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCGCCCTACTCTTT
GAGGACGAAAAAGGCCACAATGGT
Found at i:591519 original size:28 final size:28
Alignment explanation
Indices: 591433--591519 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 28
591423 TGTGGGCTTT
591433 AAAAAGTGTCCTACTCTTTGAGGACTGG
1 AAAAAGTGTCCTACTCTTTGAGGACTGG
* *** * * * * **
591461 AAAATGCCACCAACT-TGTGTGGGCTTT
1 AAAAAGTGTCCTACTCTTTGAGGACTGG
591488 AAAAAGTGTCCTACTCTTTGAGGACTGG
1 AAAAAGTGTCCTACTCTTTGAGGACTGG
591516 AAAA
1 AAAA
591520 TGCCACCAAC
Statistics
Matches: 38, Mismatches: 20, Indels: 2
0.63 0.33 0.03
Matches are distributed among these distances:
27 17 0.45
28 21 0.55
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (28 bp):
AAAAAGTGTCCTACTCTTTGAGGACTGG
Found at i:591645 original size:314 final size:314
Alignment explanation
Indices: 591063--591656 Score: 920
Period size: 314 Copynumber: 1.9 Consensus size: 314
591053 GCTTTGCAAA
* *
591063 GAGAAAGCATCCTGATTTTTGAGAACTAGAAAATGCCACCAACTTGTGCGGGCTTTGAAAAGCGT
1 GAGAAAGCATCCTGATCTTTGAGAACTAGAAAATGCCACCAACTTGTGCGGGCTTTAAAAAGCGT
* * * *
591128 CATGCTCTTTGAGGATTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAGGCATCCTACTTTTT
66 CATACTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAAGCATCCTACTCTTT
*
591193 GAGGATTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGGG
131 GAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGGG
* * * * *
591258 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTACTCTTTGAGGACTGAAAGGTGCCGCT
196 AAGTGCCACCAACTTGTGTGGGCTTTAAAAAGCGTCCTACTCTTTGAGGACTGAAAGATGCCACC
**
591323 GTCTTGTGTGGGCTTTGAAAAGCGCCCTGCTCTTTGAGGACAAAAAGGGGAAAG
261 AACTTGTGTGGGCTTTGAAAAGCGCCCTGCTCTTTGAGGACAAAAAGGGGAAAG
* * * * * * *
591377 GAGAGAGCATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGTGT
1 GAGAAAGCATCCTGATCTTTGAGAACTAGAAAATGCCACCAACTTGTGCGGGCTTTAAAAAGCGT
* * **
591442 CCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGTGTCCTACTCTTT
66 CATACTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAAGCATCCTACTCTTT
*
591507 GAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGGG
131 GAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGGG
* *
591572 AAGTGCCACCAACTTGTGTGGGCTTTAAAAAGCGTCCTGCTTTTTGAGGACTGGAAA-ATGCCAC
196 AAGTGCCACCAACTTGTGTGGGCTTTAAAAAGCGTCCTACTCTTTGAGGACT-GAAAGATGCCAC
591636 CAACTTGTGTGGGCTTTGAAA
260 CAACTTGTGTGGGCTTTGAAA
591657 GGAAAAGGCG
Statistics
Matches: 251, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
314 247 0.98
315 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (314 bp):
GAGAAAGCATCCTGATCTTTGAGAACTAGAAAATGCCACCAACTTGTGCGGGCTTTAAAAAGCGT
CATACTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAAGCATCCTACTCTTT
GAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGGG
AAGTGCCACCAACTTGTGTGGGCTTTAAAAAGCGTCCTACTCTTTGAGGACTGAAAGATGCCACC
AACTTGTGTGGGCTTTGAAAAGCGCCCTGCTCTTTGAGGACAAAAAGGGGAAAG
Found at i:591878 original size:55 final size:54
Alignment explanation
Indices: 591813--592059 Score: 305
Period size: 55 Copynumber: 4.4 Consensus size: 54
591803 GAAAGGAGAG
* *
591813 AGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGCAGGCTTTAAAA
1 AGCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTAGGCTTTAAAA
* *
591868 AGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA
1 AGCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTAGGCTTT------AAAA
* *
591929 AGCGTCCCGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
1 AGCGTCCTGCTCTTTGAGGACT-G-AAAGTGCCACCAACTTGTGTAGGCTTTAAAA
* * *
591985 GGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCCCCAACTTGTGTAGGCTTTGAAA
1 AGCGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTAGGCTTTAAAA
*
592040 AGCGCCCTGCTCTTTGAGGA
1 AGCGTCCTGCTCTTTGAGGA
592060 AAAAAAGGCA
Statistics
Matches: 169, Mismatches: 15, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
54 3 0.02
55 90 0.53
56 24 0.14
61 26 0.15
62 26 0.15
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (54 bp):
AGCGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTAGGCTTTAAAA
Found at i:592022 original size:117 final size:116
Alignment explanation
Indices: 591803--592039 Score: 359
Period size: 117 Copynumber: 2.0 Consensus size: 116
591793 AAAAAAAGGC
* * * *
591803 GAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGCAGGCTTTAAAA
1 GAAAGGAAAAAGCGTCCCGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGCAGGCTTTAAAA
*
591868 AGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT
66 AGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTAGGCTTT
**
591919 GAAAGGAAAAAGCGTCCCGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAA
1 GAAAGGAAAAAGCGTCCCGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGCAGGCTTTAAA
* * *
591984 AGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCCCCAACTTGTGTAGGCTTT
65 AAGCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTAGGCTTT
592036 GAAA
1 GAAA
592040 AGCGCCCTGC
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
116 35 0.32
117 74 0.68
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (116 bp):
GAAAGGAAAAAGCGTCCCGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGCAGGCTTTAAAA
AGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTAGGCTTT
Found at i:592022 original size:266 final size:266
Alignment explanation
Indices: 591548--592252 Score: 1320
Period size: 266 Copynumber: 2.7 Consensus size: 266
591538 GCTTTGAAAG
* *
591548 GCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGCGTCCTGCT
1 GCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGCGGGCTTTAAAAAGCGTCCTGCT
*
591613 TTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCCGCTCTTT
66 CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCCGCTCTTT
591678 GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCATTGAGGACTGA
131 GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCATTGAGGACTGA
* *
591743 AAGGTGCCCCCAACTTGTGTGGGCTTTGAAAAGCGCCCTGCTCTTTGAGGAAAAAAAGGCGAAAG
196 AAGGTGCCCCCAACTTGTGTAGGCTTTGAAAAGCGCCCTGCTCTTTGAGGAAAAAAAGGCAAAAG
591808 GAGAGA
261 GAGAGA
*
591814 GCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGCAGGCTTTAAAAAGCGTCCTGCT
1 GCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGCGGGCTTTAAAAAGCGTCCTGCT
*
591879 CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAAGCGTCCCGCTCTTT
66 CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCCGCTCTTT
*
591944 GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTGA
131 GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCATTGAGGACTGA
592009 AAGGTGCCCCCAACTTGTGTAGGCTTTGAAAAGCGCCCTGCTCTTTGAGGAAAAAAAGGCAAAAG
196 AAGGTGCCCCCAACTTGTGTAGGCTTTGAAAAGCGCCCTGCTCTTTGAGGAAAAAAAGGCAAAAG
592074 GAGAGA
261 GAGAGA
*
592080 GCTTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGCGGGCTTTAAAAAGCGTCCTGCT
1 GCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGCGGGCTTTAAAAAGCGTCCTGCT
*
592145 CTTTGAGGGCTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCCGCTCTTT
66 CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCCGCTCTTT
592210 GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
131 GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
592253 AAAAGGCATC
Statistics
Matches: 427, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
266 427 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (266 bp):
GCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGCGGGCTTTAAAAAGCGTCCTGCT
CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCCGCTCTTT
GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCATTGAGGACTGA
AAGGTGCCCCCAACTTGTGTAGGCTTTGAAAAGCGCCCTGCTCTTTGAGGAAAAAAAGGCAAAAG
GAGAGA
Found at i:592245 original size:62 final size:61
Alignment explanation
Indices: 592083--592285 Score: 278
Period size: 62 Copynumber: 3.4 Consensus size: 61
592073 GGAGAGAGCT
* *
592083 TCCTGCTCTTTGAGGACTAG-GAAGTGCCACCAACTTGTGCGGGCTTT--A--AAAA-GCG
1 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCG
* *
592138 TCCTGCTCTTTGAGGGCTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGAAAAGGCG
* *
592199 TCCCGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGAAAAGGCG
592261 TCCTGCTCTTTGAGGACT-GAAAAGT
1 TCCTGCTCTTTGAGGACTAGAAAAGT
592286 AGAAGGAGAA
Statistics
Matches: 130, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
55 40 0.31
56 2 0.02
58 1 0.01
60 4 0.03
61 31 0.24
62 52 0.40
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCG
Found at i:593271 original size:1 final size:1
Alignment explanation
Indices: 593251--593327 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
593241 CTTTTCTCTC
* * * * * * ** *
593251 TTTTTTCTTTGTTTTGTTTTTTTTGTTTTTTTGTTTTTTTTTTGTTTTTTTTTTTGCTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
593316 TTGTTTTTTTTT
1 TTTTTTTTTTTT
593328 AGAAGAGAAG
Statistics
Matches: 57, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (1 bp):
T
Found at i:593274 original size:18 final size:18
Alignment explanation
Indices: 593251--593326 Score: 88
Period size: 16 Copynumber: 4.3 Consensus size: 18
593241 CTTTTCTCTC
593251 TTTTTTCTTTGTTTTGTT
1 TTTTTTCTTTGTTTTGTT
*
593269 TTTTTTGTTT-TTTTG-T
1 TTTTTTCTTTGTTTTGTT
593285 TTTTTT-TTTGTTTT-TT
1 TTTTTTCTTTGTTTTGTT
*
593301 TTTTTGCTTTTGTTTTTGTT
1 TTTTTTC-TTTG-TTTTGTT
593321 TTTTTT
1 TTTTTT
593327 TAGAAGAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
15 3 0.06
16 17 0.35
17 5 0.10
18 13 0.27
19 4 0.08
20 7 0.14
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.87
Consensus pattern (18 bp):
TTTTTTCTTTGTTTTGTT
Found at i:593288 original size:33 final size:34
Alignment explanation
Indices: 593251--593324 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
593241 CTTTTCTCTC
593251 TTTTTTCTTTGTTTTGTTTTTTT-TGTT-TTTTTG
1 TTTTTTCTTTGTTTT-TTTTTTTCTGTTGTTTTTG
* *
593284 TTTTTTTTTTGTTTTTTTTTTTGCTTTTGTTTTTG
1 TTTTTTCTTTGTTTTTTTTTTT-CTGTTGTTTTTG
593319 TTTTTT
1 TTTTTT
593325 TTTAGAAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 7 0.19
33 14 0.39
34 3 0.08
35 12 0.33
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (34 bp):
TTTTTTCTTTGTTTTTTTTTTTCTGTTGTTTTTG
Found at i:593289 original size:24 final size:22
Alignment explanation
Indices: 593251--593327 Score: 93
Period size: 23 Copynumber: 3.5 Consensus size: 22
593241 CTTTTCTCTC
*
593251 TTTTTTCTTTG-TTTTGTTTTT
1 TTTTTTTTTTGCTTTTGTTTTT
* *
593272 TTTGTTTTTTTGTTTTTTTTTTGT
1 TTT-TTTTTTTGCTTTTGTTTT-T
593296 TTTTTTTTTTGCTTTTGTTTTT
1 TTTTTTTTTTGCTTTTGTTTTT
*
593318 GTTTTTTTTT
1 TTTTTTTTTT
593328 AGAAGAGAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.06
22 17 0.35
23 24 0.50
24 4 0.08
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (22 bp):
TTTTTTTTTTGCTTTTGTTTTT
Found at i:593325 original size:33 final size:33
Alignment explanation
Indices: 593251--593327 Score: 102
Period size: 35 Copynumber: 2.3 Consensus size: 33
593241 CTTTTCTCTC
*
593251 TTTTTTCTTTGTTTTGTTTTTTTTGTTTTTTTG
1 TTTTTTTTTTGTTTTGTTTTTTTTGTTTTTTTG
*
593284 TTTTTTTTTTGTTTT-TTTTTTTGCTTTTGTTTTTG
1 TTTTTTTTTTGTTTTGTTTTTTT--TGTT-TTTTTG
593319 TTTTTTTTT
1 TTTTTTTTT
593328 AGAAGAGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 7 0.18
33 14 0.36
34 3 0.08
35 15 0.38
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (33 bp):
TTTTTTTTTTGTTTTGTTTTTTTTGTTTTTTTG
Found at i:595298 original size:47 final size:47
Alignment explanation
Indices: 595229--595322 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
595219 CTATCGCTCT
*
595229 ACCTTTTATAGCTTTTTAGCTCACGTACACAATGTCGTATTCTGACA
1 ACCTTTTATAGCTTTCTAGCTCACGTACACAATGTCGTATTCTGACA
*
595276 ACCTTTTATAGCTTTCTAGCTCAGGTACACAATGTCGTATTCTGACA
1 ACCTTTTATAGCTTTCTAGCTCACGTACACAATGTCGTATTCTGACA
595323 GCAAGATTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (47 bp):
ACCTTTTATAGCTTTCTAGCTCACGTACACAATGTCGTATTCTGACA
Found at i:605878 original size:79 final size:79
Alignment explanation
Indices: 605747--605927 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 79
605737 TTTTGGAGAT
* * * *
605747 AATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTACGAAATAAAATCGGGATTGG
1 AATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTACGAAATAAAACCGGGATTGG
*
605812 TGTATCCCCTCAGA
66 AGTATCCCCTCAGA
* ** * *
605826 AATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTTGGAAATAAAGCCGGGGTTG
1 AATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGA-TTACGAAATAAAACCGGGATTG
*
605890 GAGTATCCCCTCGGA
65 GAGTATCCCCTCAGA
**
605905 GGTAACGGGGTTGGAGTATCCCC
1 AATAACGGGGTTGGAGTATCCCC
605928 GATGAAAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 1 0.01
79 87 0.99
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
AATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTACGAAATAAAACCGGGATTGG
AGTATCCCCTCAGA
Done.