Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 98 of 228
Found at i:28508925 original size:101 final size:101
Alignment explanation
Indices: 28508810--28509043 Score: 251
Period size: 101 Copynumber: 2.3 Consensus size: 101
28508800 ATAGCTTCAA
* * *
28508810 TCACGTGTGTAGTACTATGTGCAGGCTACTA-CGTATATCGGATGAAAAT-GGTCATGTGTGTAG
1 TCACATGTGTAGTACTATGTGCAGGCTACTAGCGTA-AT-GGAT-AAAATCGATCACGTGTGTAG
* * * *
28508873 TATTATGTGTAGGCTACTACGTGTACCGGAATG-ATA-GG
63 TACTATGTGCAGGCTACTACGTGTACCAG-ATGAAAATGG
* * * * ***
28508911 TCGCATGTGCAGTACTATGTGTAGGCTACTATGCGTACTGGATAGCTTCGATCACGTGTGTAGTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTA-GCGTAATGGATAAAATCGATCACGTGTGTAGTA
*
28508976 CTATGTGCAGGCTACTACGTGTATCAGATGAAAATGG
65 CTATGTGCAGGCTACTACGTGTACCAGATGAAAATGG
*
28509013 TTACATGTGTAGTACTATGTGCAGGCTACTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTA
28509044 TGTGAACCGA
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
100 5 0.05
101 70 0.64
102 30 0.28
103 4 0.04
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTAGCGTAATGGATAAAATCGATCACGTGTGTAGTAC
TATGTGCAGGCTACTACGTGTACCAGATGAAAATGG
Found at i:28508983 original size:152 final size:152
Alignment explanation
Indices: 28508707--28509052 Score: 539
Period size: 152 Copynumber: 2.3 Consensus size: 152
28508697 GAAGTTGCTA
* * * *
28508707 GGTCACGTTTGTAGTACTATGCGCAGGCTACTACGTGTACTGGAATGATAGGTCGCATGTATAGT
1 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTACAGT
28508772 ACTATGTGCAGGCTACTATGCGTACTGAATAGCTTCAATCACGTGTGTAGTACTATGTGCAGGCT
66 ACTATGTGCAGGCTACTATGCGTACTGAATAGCTTCAATCACGTGTGTAGTACTATGTGCAGGCT
*
28508837 ACTACGTATATCGGATGAAAAT
131 ACTACGTATATCAGATGAAAAT
* * * *
28508859 GGTCATGTGTGTAGTATTATGTGTAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGCAGT
1 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTACAGT
* * *
28508924 ACTATGTGTAGGCTACTATGCGTACTGGATAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCT
66 ACTATGTGCAGGCTACTATGCGTACTGAATAGCTTCAATCACGTGTGTAGTACTATGTGCAGGCT
*
28508989 ACTACGTGTATCAGATGAAAAT
131 ACTACGTATATCAGATGAAAAT
* * * *
28509011 GGTTACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
28509053 AGTATCATTT
Statistics
Matches: 174, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
152 174 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (152 bp):
GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTACAGT
ACTATGTGCAGGCTACTATGCGTACTGAATAGCTTCAATCACGTGTGTAGTACTATGTGCAGGCT
ACTACGTATATCAGATGAAAAT
Found at i:28509047 original size:26 final size:26
Alignment explanation
Indices: 28508967--28509047 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
28508957 TTCGATCACG
28508967 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *** *
28508993 CGTGTA-T-CAGATGAAAATGGTTAC-A
1 TGTGTAGTAC-TATGTGCA-GGCTACTA
28509018 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
28509044 TGTG
1 TGTG
28509048 AACCGAGTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
24 1 0.03
25 16 0.42
26 20 0.53
27 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:28511197 original size:29 final size:29
Alignment explanation
Indices: 28511155--28511220 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
28511145 ATCGCTATCC
*
28511155 ATAATGGAAAAGAACATTTGCCCATTTAT
1 ATAACGGAAAAGAACATTTGCCCATTTAT
28511184 ATAACGGAAAAGAACATTTGCCCATTTAT
1 ATAACGGAAAAGAACATTTGCCCATTTAT
28511213 ATAACGGA
1 ATAACGGA
28511221 TCGTATGGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (29 bp):
ATAACGGAAAAGAACATTTGCCCATTTAT
Found at i:28512141 original size:19 final size:19
Alignment explanation
Indices: 28512113--28512149 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28512103 AATTGAATTA
28512113 ATTTTTATAATTT-TTTTT
1 ATTTTTATAATTTATTTTT
28512131 ATTTTTGATAATTTATTTT
1 ATTTTT-ATAATTTATTTT
28512150 CTATGAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (19 bp):
ATTTTTATAATTTATTTTT
Found at i:28512403 original size:10 final size:11
Alignment explanation
Indices: 28512375--28512405 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
28512365 ATTTTTGTTT
28512375 ATATTTTTAAA
1 ATATTTTTAAA
28512386 ATATTTTTAAA
1 ATATTTTTAAA
28512397 ATATTTTTA
1 ATATTTTTA
28512406 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:28512414 original size:24 final size:24
Alignment explanation
Indices: 28512387--28512441 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
28512377 ATTTTTAAAA
**
28512387 TATTTTTAAAATATTT-TTATTTTT
1 TATTTTTAAAAT-TTTAAAATTTTT
28512411 TATTTTTAAAATTTTAAAATTTTT
1 TATTTTTAAAATTTTAAAATTTTT
28512435 TATTTTT
1 TATTTTT
28512442 TTCCAAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTTTTAAAATTTTAAAATTTTT
Found at i:28512438 original size:31 final size:32
Alignment explanation
Indices: 28512356--28512442 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
28512346 AGATAACATT
* *
28512356 AAATTTT-AAA-TTTTT-GTTTATATTTTTAA
1 AAATTTTAAAATTTTTTATTTTTTATTTTTAA
28512385 AATATTTTTAAAATATTTTTATTTTTTATTTTT-A
1 AA-A-TTTTAAAAT-TTTTTATTTTTTATTTTTAA
28512419 AAATTTTAAAATTTTTTATTTTTT
1 AAATTTTAAAATTTTTTATTTTTT
28512443 TCCAAAAGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
29 2 0.04
30 1 0.02
31 16 0.32
32 12 0.24
33 1 0.02
34 8 0.16
35 10 0.20
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (32 bp):
AAATTTTAAAATTTTTTATTTTTTATTTTTAA
Found at i:28512482 original size:22 final size:23
Alignment explanation
Indices: 28512456--28512499 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28512446 AAAAGTTTTA
28512456 TTTAAAAAAATAT-ATTTTTAAT
1 TTTAAAAAAATATAATTTTTAAT
**
28512478 TTTAAAAAGTTATAATTTTTAA
1 TTTAAAAAAATATAATTTTTAA
28512500 AATTTTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAAAAAAATATAATTTTTAAT
Found at i:28515837 original size:121 final size:122
Alignment explanation
Indices: 28515550--28515842 Score: 518
Period size: 122 Copynumber: 2.4 Consensus size: 122
28515540 CAAACTTTAG
*
28515550 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
*
28515615 TTATATATTATGATTTTAGTAAATTAATATAAGAATATATTTAATATTAAAAATTTT
66 TTATATATTATGATTTTAGTAAATTAATATAAGAATATATCTAATATTAAAAATTTT
*
28515672 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTCTAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
* *
28515737 TTATATATTATGATTTTAGTAATTTAATATTAAG-A-ATATCTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATTAATA-TAAGAATATATCTAATATTAAAAATTTT
28515793 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
28515843 ATATGATTAA
Statistics
Matches: 165, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
121 69 0.42
122 92 0.56
123 4 0.02
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (122 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
TTATATATTATGATTTTAGTAAATTAATATAAGAATATATCTAATATTAAAAATTTT
Found at i:28515915 original size:121 final size:115
Alignment explanation
Indices: 28515550--28515901 Score: 361
Period size: 122 Copynumber: 2.9 Consensus size: 115
28515540 CAAACTTTAG
* *
28515550 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA-TATA-TTT-TAGAA
* * * *
28515615 TTATATATTATGATTTTAGTAAATTAATATAAGAATATATTTAA-TATTAAAAATTTT
63 TTATATATTATGATTTTAGT-AATTTAT-TAA-AAT-TA-ATAACAATAAAAAATTTT
*
28515672 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTCTAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA-TATA-TTT-TAGAA
* * * * *
28515737 TTATATATTATGATTTTAGTAATTTAATATTAA-GAATATCTAATATTAAGAATTTT
63 TTATATATTATGATTTTAGTAATTTATTA-AAATTAATAAC-AATA--AAAAATTTT
*
28515793 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA-ATATGATTA-AATT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATATAT-TTTAGAATT
* * *
28515856 ATTTATTACTGATATTAATAATCTTATTAAAATTTAATAACAATAA
65 ATATATTA-TGATTTTAGTAAT-TTATTAAAA-TTAATAACAATAA
28515902 CAATAATTAT
Statistics
Matches: 200, Mismatches: 20, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
117 13 0.06
118 17 0.09
119 15 0.08
120 9 0.05
121 63 0.31
122 83 0.41
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (115 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATATATTTTAGAATTA
TATATTATGATTTTAGTAATTTATTAAAATTAATAACAATAAAAAATTTT
Found at i:28516113 original size:20 final size:20
Alignment explanation
Indices: 28516088--28516129 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
28516078 TTATGCCTCT
28516088 ATTTCAATACAGCGAAGCAA
1 ATTTCAATACAGCGAAGCAA
*
28516108 ATTTCAATACAGCTAAGCAA
1 ATTTCAATACAGCGAAGCAA
28516128 AT
1 AT
28516130 GTGCCATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (20 bp):
ATTTCAATACAGCGAAGCAA
Found at i:28523820 original size:22 final size:22
Alignment explanation
Indices: 28523792--28523841 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
28523782 ACAAATCCTA
28523792 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
*
28523814 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCCAAAATCC
28523836 TCTCAA
1 TCTCAA
28523842 ACTCTCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:28523849 original size:30 final size:30
Alignment explanation
Indices: 28523813--28523869 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
28523803 TTCCAAAATC
*
28523813 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTTCCTTCCAAAATCCTCTCAAA
28523843 CTCTCAATTTCCTTCCAAAATCCTCTC
1 CTCTCAATTTCCTTCCAAAATCCTCTC
28523870 GATTTCCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (30 bp):
CTCTCAATTTCCTTCCAAAATCCTCTCAAA
Found at i:28523868 original size:22 final size:22
Alignment explanation
Indices: 28523843--28523893 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
28523833 TTCTCTCAAA
28523843 CTCTCAATTTCCTTCC-AAAAT
1 CTCTCAATTTCCTTCCAAAAAT
*
28523864 CCTCTCGATTTCCTTCCAAAAAT
1 -CTCTCAATTTCCTTCCAAAAAT
28523887 CTCTCAA
1 CTCTCAA
28523894 ATCCATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.27, C:0.35, G:0.02, T:0.35
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAAAT
Found at i:28523875 original size:52 final size:52
Alignment explanation
Indices: 28523792--28523894 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
28523782 ACAAATCCTA
*
28523792 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAATTCTCTCAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAAC
*
28523844 TCTCAATTTCCTTCCAAAATCCTCTCGATTTCCTTCCAAAAATCTCTCAAA
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAA
28523895 TCCATATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.29, C:0.34, G:0.01, T:0.36
Consensus pattern (52 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAAC
Found at i:28523962 original size:31 final size:31
Alignment explanation
Indices: 28523927--28523993 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
28523917 CCTCAATTTC
28523927 ATTTTTTTAAAATAATTTTAAATTTTTTAAT
1 ATTTTTTTAAAATAATTTTAAATTTTTTAAT
*
28523958 ATTTTTTTAAAATAATTTTAAATTTTTTTAT
1 ATTTTTTTAAAATAATTTTAAATTTTTTAAT
28523989 ATTTT
1 ATTTT
28523994 CATCAATGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (31 bp):
ATTTTTTTAAAATAATTTTAAATTTTTTAAT
Found at i:28526339 original size:30 final size:30
Alignment explanation
Indices: 28526305--28526754 Score: 658
Period size: 30 Copynumber: 14.8 Consensus size: 30
28526295 TAATAAAAAT
*
28526305 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
28526335 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
28526364 CCTAATTTAATTAAAAACCCTAAACCTTAACCCTAT
1 CCTAATTTAATTAAAAACCCT--A----AACCCTAA
*
28526400 CCTAATTTAATTAAAAACCATAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
28526430 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
28526459 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
28526489 CCTAATTTAATTAAAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
28526519 CCTAATTTAATTAAAAACCCTAAACCGTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
* *
28526549 CTTAATTTAAGTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
* *
28526578 CTTAATTTAATTAAAAATCCTAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCT--A----AACCCTAA
28526614 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
28526644 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
28526673 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
28526702 CCTAATTTAATTAATAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
28526732 CTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
28526755 CCATTAACAA
Statistics
Matches: 386, Mismatches: 18, Indels: 32
0.89 0.04 0.07
Matches are distributed among these distances:
29 140 0.36
30 190 0.49
34 2 0.01
36 54 0.14
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.28
Consensus pattern (30 bp):
CCTAATTTAATTAAAAACCCTAAACCCTAA
Found at i:28526395 original size:59 final size:59
Alignment explanation
Indices: 28526305--28526756 Score: 647
Period size: 59 Copynumber: 7.4 Consensus size: 59
28526295 TAATAAAAAT
*
28526305 CCTAATTTAATTAAAAACCCTAAACACTAACCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
* *
28526364 CCTAATTTAATTAAAAACCCTAAACCTTAACCCTATCCTAATTTAATTAAAAACCATAAACCCTA
1 CCTAATTTAATTAAAAA--C----CC-TAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTA
28526429 A
59 A
28526430 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
* *
28526489 CCTAATTTAATTAAAAACCTTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCGTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
* * * *
28526549 CTTAATTTAAGTAAAAACCCTAACCCTAACTTAATTTAATTAAAAATCCTAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT--A----AACCCTAA
28526614 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
*
28526673 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAATAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
*
28526732 CTTAATTTAATTAAAAACCCTAACC
1 CCTAATTTAATTAAAAACCCTAACC
28526757 ATTAACAAAA
Statistics
Matches: 357, Mismatches: 19, Indels: 34
0.87 0.05 0.08
Matches are distributed among these distances:
58 28 0.08
59 162 0.45
60 57 0.16
61 2 0.01
64 1 0.00
65 54 0.15
66 53 0.15
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (59 bp):
CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
Found at i:28526430 original size:95 final size:94
Alignment explanation
Indices: 28526303--28526756 Score: 593
Period size: 95 Copynumber: 4.9 Consensus size: 94
28526293 TGTAATAAAA
* *
28526303 ATCCTAATTTAATTAAAAACCCTAAACACTAACCTAATTTAATTAAAAACCCT-AACCCTAACCT
1 ATCCTAATTTAATTAAAAACCATAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCT
28526367 AATTTAATTAAAAACCCTAAACCTTAACCCT
66 AATTTAATTAAAAACCCT-AACC-TAACCCT
28526398 ATCCTAATTTAATTAAAAACCATAAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAACCT
1 ATCCTAATTTAATTAAAAACCATAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCT
28526462 AATTTAATTAAAAACCCT-A---AACCCT
66 AATTTAATTAAAAACCCTAACCTAACCCT
* * * *
28526487 AACCTAATTTAATTAAAAACCTTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCGTAACTT
1 ATCCTAATTTAATTAAAAACCATAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCT
*
28526552 AATTTAAGTAAAAACCCTAACCCTAA--C-
66 AATTTAATTAAAAACCCTAA-CCTAACCCT
*
28526579 -T--TAATTTAATTAAAAATCCTAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCC
1 ATCCTAATTTAATTAAAAA-CC-ATA----AACCCTAACCTAATTTAATTAAAAACCCTAAACCC
28526641 TAACCTAATTTAATTAAAAA--C---CCTAACCCT
60 TAACCTAATTTAATTAAAAACCCTAACCTAACCCT
* * * *
28526671 AACCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAATAACCCTAAACCCTAACTT
1 ATCCTAATTTAATTAAAAACCATAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCT
28526735 AATTTAATTAAAAACCCTAACC
66 AATTTAATTAAAAACCCTAACC
28526757 ATTAACAAAA
Statistics
Matches: 318, Mismatches: 18, Indels: 48
0.83 0.05 0.12
Matches are distributed among these distances:
88 53 0.17
89 77 0.24
90 29 0.09
91 3 0.01
93 5 0.02
94 2 0.01
95 149 0.47
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (94 bp):
ATCCTAATTTAATTAAAAACCATAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCT
AATTTAATTAAAAACCCTAACCTAACCCT
Found at i:28526636 original size:23 final size:24
Alignment explanation
Indices: 28526606--28526756 Score: 88
Period size: 29 Copynumber: 5.4 Consensus size: 24
28526596 CCTAAACCCT
28526606 AACCCTAACCTAATTTAATTAAAAACCCTA
1 AACCCTAACCTAATTTAATT--AAA----A
28526636 AACCCTAACCTAATTTAATTAAAAA
1 AACCCTAACCTAATTTAATT-AAAA
28526661 CCCTAACCCTAACCTAATTTAATTAAAAA
1 ----AACCCTAACCTAATTTAATT-AAAA
28526690 CCCTAACCCTAACCTAATTTAATTAATAACCCTA
1 ----AACCCTAACCTAATTTAATT-A-AA----A
*
28526724 AACCCTAACTTAATTTAATT-AAA
1 AACCCTAACCTAATTTAATTAAAA
28526747 AACCCTAACC
1 AACCCTAACC
28526757 ATTAACAAAA
Statistics
Matches: 110, Mismatches: 2, Indels: 25
0.80 0.01 0.18
Matches are distributed among these distances:
23 10 0.09
25 1 0.01
27 2 0.02
29 55 0.50
30 41 0.37
34 1 0.01
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (24 bp):
AACCCTAACCTAATTTAATTAAAA
Found at i:28534963 original size:15 final size:15
Alignment explanation
Indices: 28534943--28534974 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28534933 AAAAGAAAAT
28534943 TATCATTAATCAAAG
1 TATCATTAATCAAAG
28534958 TATCATTAATCAAAG
1 TATCATTAATCAAAG
28534973 TA
1 TA
28534975 GCTCTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (15 bp):
TATCATTAATCAAAG
Found at i:28537431 original size:22 final size:22
Alignment explanation
Indices: 28537403--28537448 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
28537393 TTTTCTGAGC
* *
28537403 TTTCAGGGTTTTAGCGGCATTT
1 TTTCAGGGCTTTACCGGCATTT
*
28537425 TTTCAGGGCTTTACCGGCGTTT
1 TTTCAGGGCTTTACCGGCATTT
28537447 TT
1 TT
28537449 GGGAAAGCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.46
Consensus pattern (22 bp):
TTTCAGGGCTTTACCGGCATTT
Found at i:28537491 original size:41 final size:41
Alignment explanation
Indices: 28537427--28537613 Score: 270
Period size: 41 Copynumber: 4.6 Consensus size: 41
28537417 CGGCATTTTT
* *
28537427 TCAGGGCTTTACCGGCGTTTTTGGGAAAGCGCCGCTAATGA
1 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGA
* * *
28537468 TTAGGCCTTTAGCGGCGTGTTTGGAAAAGCGCCGCTAATGA
1 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGA
28537509 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGA
1 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGA
* * *
28537550 TCAGAGATTTAGCGGCGTTTTT-GAGTAAGCGCCGCTAAT-A
1 TCAGGGCTTTAGCGGCGTTTTTGGA-AAAGCGCCGCTAATGA
28537590 CTCAGGGCTTTAGCGGCGTTTTTG
1 -TCAGGGCTTTAGCGGCGTTTTTG
28537614 AAGTAGAGCC
Statistics
Matches: 130, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 3 0.02
41 127 0.98
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (41 bp):
TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGA
Found at i:28537676 original size:81 final size:82
Alignment explanation
Indices: 28537427--28537682 Score: 266
Period size: 82 Copynumber: 3.1 Consensus size: 82
28537417 CGGCATTTTT
* * * * * * *
28537427 TCAGGGCTTTACCGGCGTTTTTGGGAAAGCGCCGCTAATGATTAG-GCCTTTAGCGGCGTGTTTG
1 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGAGCCGCTAATGATCAGAG-ATTTAGCGGCGTTTTTA
* *
28537491 GAAAAGCGCCGCTAATGA
65 AAAAAGCGCCGCTAATGC
* *
28537509 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGATCAGAGATTTAGCGGCGTTTTTGA
1 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGAGCCGCTAATGATCAGAGATTTAGCGGCGTTTTTAA
** *
28537574 GTAAGCGCCGCTAATAC
66 AAAAGCGCCGCTAATGC
* ** * ** *
28537591 TCAGGGCTTTAGCGGCGTTTTT-GAAGTAGAGCCGCTAATTCTC-TATTTTTAGTGGCGTTTTTA
1 TCAGGGCTTTAGCGGCGTTTTTGGAA-AAGAGCCGCTAATGATCAGAGATTTAGCGGCGTTTTTA
*
28537654 AAAAAGCGCTGCTAATGC
65 AAAAAGCGCCGCTAATGC
*
28537672 TCAGGGATTTA
1 TCAGGGCTTTA
28537683 ATATAATCTA
Statistics
Matches: 148, Mismatches: 24, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
81 42 0.28
82 105 0.71
83 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (82 bp):
TCAGGGCTTTAGCGGCGTTTTTGGAAAAGAGCCGCTAATGATCAGAGATTTAGCGGCGTTTTTAA
AAAAGCGCCGCTAATGC
Found at i:28538666 original size:7 final size:7
Alignment explanation
Indices: 28538656--28538693 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
28538646 TATGGTTTAA
28538656 GGGTTAG
1 GGGTTAG
28538663 GGGTTAG
1 GGGTTAG
28538670 GGGTTAG
1 GGGTTAG
*
28538677 GGGATAG
1 GGGTTAG
28538684 GGGTTTAG
1 GGG-TTAG
28538692 GG
1 GG
28538694 TTTATGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 23 0.82
8 5 0.18
ACGTcount: A:0.16, C:0.00, G:0.58, T:0.26
Consensus pattern (7 bp):
GGGTTAG
Found at i:28539525 original size:14 final size:15
Alignment explanation
Indices: 28539497--28539531 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
28539487 AATCAATTGT
28539497 AAAGATGAGGGGGGG
1 AAAGATGAGGGGGGG
28539512 AAAGATGA-GGGGGG
1 AAAGATGAGGGGGGG
28539526 AAAGAT
1 AAAGAT
28539532 ATTTCAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.51, T:0.09
Consensus pattern (15 bp):
AAAGATGAGGGGGGG
Found at i:28540789 original size:32 final size:33
Alignment explanation
Indices: 28540753--28540817 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
28540743 CTGGAATTTG
*
28540753 TTTATTTGTAATTTGTTAT-TTTTCTGTGTTTT
1 TTTATTTGTAATTTGTTATGTTTTCTGGGTTTT
28540785 TTTATTTGTAATTTGTTATGTTTTCTGGGTTTT
1 TTTATTTGTAATTTGTTATGTTTTCTGGGTTTT
28540818 GCTTATAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.69
Consensus pattern (33 bp):
TTTATTTGTAATTTGTTATGTTTTCTGGGTTTT
Found at i:28542047 original size:5 final size:5
Alignment explanation
Indices: 28542039--28542065 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28542029 ATATTTTACC
28542039 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
28542066 AACAAGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:28543071 original size:43 final size:43
Alignment explanation
Indices: 28542927--28543071 Score: 191
Period size: 43 Copynumber: 3.4 Consensus size: 43
28542917 CGGAAAAAAT
* * * *
28542927 GCCGCTAAAGGCCAGGACCTTTAGCGGCGCTTTTCTCACAAAT
1 GCCGCTAAAGACCAGAACCTTTAGCGGCGCTTTTCCCACAAAC
* * * *
28542970 GTCGCTAAAGATCAGGACCTTTAGCGGCGCTTTTTCCACAAAC
1 GCCGCTAAAGACCAGAACCTTTAGCGGCGCTTTTCCCACAAAC
* *
28543013 ACCGCTGAAGACCAGAACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCAGAACCTTTAGCGGCGCTTTTCCCACAAAC
*
28543056 GCCACTAAAGACCAGA
1 GCCGCTAAAGACCAGA
28543072 CTCCCCAAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 87 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (43 bp):
GCCGCTAAAGACCAGAACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:28543917 original size:39 final size:40
Alignment explanation
Indices: 28543830--28543930 Score: 118
Period size: 39 Copynumber: 2.6 Consensus size: 40
28543820 CGTTTGGATA
* * *
28543830 AAAAAT-GCCACTAAAAATAAGCATTAGCGGCGCTTTTTG
1 AAAAATCGCCGCTAAAAATAAGCATTACCGGCGCTTTTTC
* *
28543869 GAAAA-CGCCGCTAAAGATAAGCATTACCGGCG-TTTTTC
1 AAAAATCGCCGCTAAAAATAAGCATTACCGGCGCTTTTTC
*
28543907 AAAAATCGCCGCAAAAAACTAAGC
1 AAAAATCGCCGCTAAAAA-TAAGC
28543931 CAAACGACGT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
38 9 0.18
39 37 0.73
40 5 0.10
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.21
Consensus pattern (40 bp):
AAAAATCGCCGCTAAAAATAAGCATTACCGGCGCTTTTTC
Found at i:28544016 original size:41 final size:41
Alignment explanation
Indices: 28543959--28544201 Score: 378
Period size: 41 Copynumber: 5.9 Consensus size: 41
28543949 GAGTTTTTGA
* *
28543959 GGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATTCTCG
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
*
28544000 GGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCG
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* * * *
28544041 GGCTTTTAGCGGCGTTTGTGAAGAAGCGCCACTAATGCTCG
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* *
28544082 GGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATACTCG
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* * *
28544123 GGCCTTTAGCGGTGTTTTTTAAAAAGCGCCGCTAATGCTTG
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
28544164 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
28544202 CCGCTTTTGA
Statistics
Matches: 183, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 183 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (41 bp):
GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
Found at i:28544583 original size:14 final size:14
Alignment explanation
Indices: 28544566--28544602 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
28544556 GGGTTTAATA
28544566 TATATGGTTTAGGG
1 TATATGGTTTAGGG
*
28544580 TATATGATTTAGGG
1 TATATGGTTTAGGG
28544594 TATATGGTT
1 TATATGGTT
28544603 AATTTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:28544679 original size:14 final size:14
Alignment explanation
Indices: 28544660--28544691 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
28544650 AGATTATGGA
28544660 ATTAGGGATTCTGG
1 ATTAGGGATTCTGG
28544674 ATTAGGGATTCTGG
1 ATTAGGGATTCTGG
28544688 ATTA
1 ATTA
28544692 AGGGTTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (14 bp):
ATTAGGGATTCTGG
Found at i:28544924 original size:7 final size:7
Alignment explanation
Indices: 28544901--28544945 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
28544891 TAAATAAGAT
28544901 TTAGGGG
1 TTAGGGG
**
28544908 TTAGTAG
1 TTAGGGG
28544915 TTAGGGG
1 TTAGGGG
28544922 TTAGGGG
1 TTAGGGG
*
28544929 TTAAGGG
1 TTAGGGG
28544936 TTAGGGG
1 TTAGGGG
28544943 TTA
1 TTA
28544946 AAGGTTAGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:28544946 original size:14 final size:14
Alignment explanation
Indices: 28544914--28544953 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
28544904 GGGGTTAGTA
*
28544914 GTTAGGGGTTAGGG
1 GTTAAGGGTTAGGG
28544928 GTTAAGGGTTAGGG
1 GTTAAGGGTTAGGG
*
28544942 GTTAAAGGTTAG
1 GTTAAGGGTTAG
28544954 AGATTAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.47, T:0.30
Consensus pattern (14 bp):
GTTAAGGGTTAGGG
Found at i:28545462 original size:13 final size:13
Alignment explanation
Indices: 28545444--28545470 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28545434 ATAAATAAAT
28545444 AAATTAATGTAAC
1 AAATTAATGTAAC
28545457 AAATTAATGTAAC
1 AAATTAATGTAAC
28545470 A
1 A
28545471 GATTGACAAT
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:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
AAATTAATGTAAC
Found at i:28549228 original size:43 final size:43
Alignment explanation
Indices: 28549168--28549258 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
28549158 CTTTGAGTTC
* * * *
28549168 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
28549210 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
28549253 ATTACC
1 ATTACC
28549259 TTGCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:28549606 original size:43 final size:42
Alignment explanation
Indices: 28549532--28549757 Score: 235
Period size: 42 Copynumber: 5.3 Consensus size: 42
28549522 AAGATATATT
* ** *
28549532 TTTAGCGGCGGTTGTGTTAAAAGCGCTGCTAAAGGTCTAT-TC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGTC
* * * *
28549574 TATAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGCT-TAATATT
1 TTTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCT--TGTC
**
28549618 TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG-TC
*
28549661 TTTAGCGGCGTTTGTGGG-GAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTT-GTC
* *
28549703 TTTAGCGGCGTTTGTGGG-AAAGAGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TTGTC
*
28549745 TTTAGCAGCGTTT
1 TTTAGCGGCGTTT
28549758 ATTTATAAAA
Statistics
Matches: 157, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
42 86 0.55
43 54 0.34
44 17 0.11
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTC
Found at i:28549624 original size:86 final size:84
Alignment explanation
Indices: 28549527--28549693 Score: 237
Period size: 86 Copynumber: 2.0 Consensus size: 84
28549517 TTTAAAAGAT
** *
28549527 ATATTTTTAGCGGCGGTTGTGTTAAAAGCGCTGCTAAAGGTC-TATTCTATAGCGGCGTTTGTGG
1 ATATTTTTAGCGGCGGTTGTGAAAAAAGCGCCGCTAAAGGTCTTA-TCTATAGCGGCGTTTGTGG
28549591 GAAAAAGCGCCGCTAAAGCTTA
65 G--AAAGCGCCGCTAAAGCTTA
* *
28549613 ATATTTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTTTAGCGGCGTTTGTGG
1 ATATTTTTAGCGGCGGTTGTGAAAAAAGCGCCGCTAAAGGTCTT-ATCTATAGCGGCGTTTGTGG
*
28549678 GGAAGCGCCGCTAAAG
65 GAAAGCGCCGCTAAAG
28549694 GTCTTGGTCT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
85 14 0.19
86 38 0.52
87 20 0.27
88 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (84 bp):
ATATTTTTAGCGGCGGTTGTGAAAAAAGCGCCGCTAAAGGTCTTATCTATAGCGGCGTTTGTGGG
AAAGCGCCGCTAAAGCTTA
Found at i:28552859 original size:95 final size:95
Alignment explanation
Indices: 28552693--28552871 Score: 223
Period size: 95 Copynumber: 1.9 Consensus size: 95
28552683 GTTCACCAGG
* * * * **
28552693 AAACATGAGGTTATATTGTGTAAGACCATAACTCGACTATGGCAGCTTATGGAGTCTGTCGGAAC
1 AAACATGAGGTTATATTATGTAAGACCATAACTCGACTATGACAACATATGGAACCTGTCGGAAC
* *
28552758 ATTAAACATAAGGTAGTCCGCTTGGACGTT
66 AATAAACATAAGATAGTCCGCTTGGACGTT
* * * * * *
28552788 AAACATGGGGTTATATTATGTAAGACCATAGCTTGGCTATGACAACATATGGAACCTGTTGGGAC
1 AAACATGAGGTTATATTATGTAAGACCATAACTCGACTATGACAACATATGGAACCTGTCGGAAC
*
28552853 AATAAACATGAGATAGTCC
66 AATAAACATAAGATAGTCC
28552872 ACTGAGATAA
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
95 69 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (95 bp):
AAACATGAGGTTATATTATGTAAGACCATAACTCGACTATGACAACATATGGAACCTGTCGGAAC
AATAAACATAAGATAGTCCGCTTGGACGTT
Found at i:28555137 original size:51 final size:51
Alignment explanation
Indices: 28555014--28555144 Score: 146
Period size: 50 Copynumber: 2.6 Consensus size: 51
28555004 GAAAGTGATG
* *
28555014 GTCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGGAATGATAGTTC
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATC-G-ATGATAGTTC
* * *
28555067 G-CA--TGTATAGTACTATGTGCAGGCTACTATGCGTA-C-CTGATAGTTTC
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCGATGATAG-TTC
28555114 GATCACGTGTGTAGTACTATGTGCAGGCTAC
1 G-TCACGTGTGTAGTACTATGTGCAGGCTAC
28555145 GTGTATCGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
46 6 0.09
47 4 0.06
49 3 0.04
50 28 0.42
51 23 0.34
52 2 0.03
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (51 bp):
GTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCGATGATAGTTC
Found at i:28556833 original size:23 final size:23
Alignment explanation
Indices: 28556803--28556848 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
28556793 TAGTTTCTCG
*
28556803 AAAAAAAAATTCAAAAAAAAATT
1 AAAAAAAAATTAAAAAAAAAATT
28556826 AAAAAAAAATTAAAAAAAAAATT
1 AAAAAAAAATTAAAAAAAAAATT
28556849 TTGGTTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (23 bp):
AAAAAAAAATTAAAAAAAAAATT
Found at i:28556848 original size:12 final size:11
Alignment explanation
Indices: 28556803--28556845 Score: 77
Period size: 11 Copynumber: 3.8 Consensus size: 11
28556793 TAGTTTCTCG
28556803 AAAAAAAAATT
1 AAAAAAAAATT
28556814 CAAAAAAAAATT
1 -AAAAAAAAATT
28556826 AAAAAAAAATT
1 AAAAAAAAATT
28556837 AAAAAAAAA
1 AAAAAAAAA
28556846 ATTTTGGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:28556911 original size:15 final size:14
Alignment explanation
Indices: 28556886--28556940 Score: 92
Period size: 14 Copynumber: 3.9 Consensus size: 14
28556876 GGATATCAAG
*
28556886 TTGTGAAAAAAAAT
1 TTGTGAAAAAAAAA
*
28556900 TTTTGAAAAAAAAA
1 TTGTGAAAAAAAAA
28556914 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
28556928 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
28556941 GAGAGCTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:28561123 original size:45 final size:45
Alignment explanation
Indices: 28561054--28561142 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
28561044 TGTGTACTGA
* *
28561054 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
*
28561099 ACATTATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
28561143 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:28566217 original size:65 final size:65
Alignment explanation
Indices: 28566113--28566259 Score: 242
Period size: 65 Copynumber: 2.3 Consensus size: 65
28566103 GATACACGGA
* *
28566113 TCTCCAACACACCAAATGACTCATAGAGTCAAACATATCCC-AAAGTTGAAGCATAGAGCTAACA
1 TCTCCAACACACCAAATGACTCATAGAGTCAAACATATCCCAAAAG-TGAAGCATAAAACTAACA
28566177 C
65 C
* *
28566178 TCTCCAACACACTAAATGACTCATAGAGTCGAACATATCCCAAAAGTGAAGCATAAAACTAACAC
1 TCTCCAACACACCAAATGACTCATAGAGTCAAACATATCCCAAAAGTGAAGCATAAAACTAACAC
28566243 TCTCCAACACACCAAAT
1 TCTCCAACACACCAAAT
28566260 ATGTCCCATT
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
65 72 0.95
66 4 0.05
ACGTcount: A:0.43, C:0.29, G:0.10, T:0.18
Consensus pattern (65 bp):
TCTCCAACACACCAAATGACTCATAGAGTCAAACATATCCCAAAAGTGAAGCATAAAACTAACAC
Found at i:28568485 original size:4 final size:4
Alignment explanation
Indices: 28568476--28568508 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
28568466 TCTAACATTC
28568476 ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA A
1 ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA A
28568509 TAAAGGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:28570627 original size:22 final size:22
Alignment explanation
Indices: 28570579--28570627 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
28570569 AAAGAGATGA
*
28570579 TTTTTATAGAGAAAAAATTAGT
1 TTTTTACAGAGAAAAAATTAGT
* *
28570601 GTTTTACAG-GAAAAACTTGAGT
1 TTTTTACAGAGAAAAAATT-AGT
28570623 TTTTT
1 TTTTT
28570628 TTATAAAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (22 bp):
TTTTTACAGAGAAAAAATTAGT
Found at i:28572316 original size:27 final size:27
Alignment explanation
Indices: 28572278--28572335 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
28572268 CATTTTGAGC
*
28572278 TTCTCTAACTCCAATCTCAGCTTCTCA
1 TTCTCTAACTCCAATCTCAGCCTCTCA
28572305 TTCTCTAACTCCAATCTCAGCCTCTCA
1 TTCTCTAACTCCAATCTCAGCCTCTCA
28572332 TTCT
1 TTCT
28572336 GGTGCAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.38, G:0.03, T:0.38
Consensus pattern (27 bp):
TTCTCTAACTCCAATCTCAGCCTCTCA
Found at i:28574070 original size:3 final size:3
Alignment explanation
Indices: 28574062--28574096 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28574052 GTTGGTAGTT
28574062 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28574097 TAAAATAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28578703 original size:28 final size:28
Alignment explanation
Indices: 28578681--28578775 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 28
28578671 AAATTTTAAT
*
28578681 AAAATATTAAAATATTAAAAATTAGAAA
1 AAAATATAAAAATATTAAAAATTAGAAA
** *
28578709 AAAATATAAAAATCGTAAAAA-TATAAA
1 AAAATATAAAAATATTAAAAATTAGAAA
* * * *
28578736 AAATTGT-AAAATTTTATAAAGATT-GTAA
1 AAAATATAAAAATATTA-AAA-ATTAGAAA
28578764 AAAATATAAAAA
1 AAAATATAAAAA
28578776 ATAGAAGTAT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
26 7 0.14
27 13 0.25
28 26 0.51
29 5 0.10
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.28
Consensus pattern (28 bp):
AAAATATAAAAATATTAAAAATTAGAAA
Found at i:28578711 original size:19 final size:19
Alignment explanation
Indices: 28578689--28578740 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
28578679 ATAAAATATT
28578689 AAAATATTAAAAATTAGAA
1 AAAATATTAAAAATTAGAA
* *
28578708 AAAA-ATATAAAAA-TCGTA
1 AAAATAT-TAAAAATTAGAA
*
28578726 AAAATATAAAAAATT
1 AAAATATTAAAAATT
28578741 GTAAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAATATTAAAAATTAGAA
Found at i:28578739 original size:37 final size:38
Alignment explanation
Indices: 28578689--28578781 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 38
28578679 ATAAAATATT
*
28578689 AAAATATTAAAAATTAGAAAAAAATATAAAAATCGT-A
1 AAAATATAAAAAATTAGAAAAAAATATAAAAATCGTAA
*** * *
28578726 AAAATATAAAAAATT-GTAAAATTTTATAAAGATTGTAA
1 AAAATATAAAAAATTAG-AAAAAAATATAAAAATCGTAA
28578764 AAAATATAAAAAA-TAGAA
1 AAAATATAAAAAATTAGAA
28578782 GTATAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 1 0.02
37 31 0.66
38 15 0.32
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (38 bp):
AAAATATAAAAAATTAGAAAAAAATATAAAAATCGTAA
Found at i:28578799 original size:53 final size:54
Alignment explanation
Indices: 28578707--28578809 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 54
28578697 AAAAATTAGA
* *
28578707 AAAAAATATAAAAATCGTAAAAATATAAAAAATTGTAAAATTTTATAAAGATTGT
1 AAAAAATATAAAAA-CATAAAAATATAAAAAATTATAAAATTTTATAAAGATTGT
* *
28578762 AAAAAATATAAAAA-ATAGAAGTATAAAAAATTATAAAATTTTATAAAG
1 AAAAAATATAAAAACATAAAAATATAAAAAATTATAAAATTTTATAAAG
28578810 TCATAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 30 0.68
55 14 0.32
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (54 bp):
AAAAAATATAAAAACATAAAAATATAAAAAATTATAAAATTTTATAAAGATTGT
Found at i:28579103 original size:26 final size:27
Alignment explanation
Indices: 28579047--28579108 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
28579037 TTTGATGCAT
**
28579047 TTTTTATTTTTATAAAATTTTACAATT
1 TTTTTATTTTTATAAAATTTTACAAAG
** *
28579074 TTTTTATTTTT-TATGATTTTATAAAG
1 TTTTTATTTTTATAAAATTTTACAAAG
28579100 TTTTT-TTTT
1 TTTTTATTTT
28579109 CTAATTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 4 0.13
26 15 0.50
27 11 0.37
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTTTATTTTTATAAAATTTTACAAAG
Found at i:28579143 original size:28 final size:28
Alignment explanation
Indices: 28579112--28579166 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
28579102 TTTTTTTCTA
*
28579112 ATTTTTAGTAAATTTTAA-ATATTTTTAC
1 ATTTTTAGTAAAATTTAATA-ATTTTTAC
*
28579140 ATTTTTATTAAAATTTAATAATTTTTA
1 ATTTTTAGTAAAATTTAATAATTTTTA
28579167 TAAAACTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTTAGTAAAATTTAATAATTTTTAC
Found at i:28594103 original size:21 final size:21
Alignment explanation
Indices: 28594055--28594105 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
28594045 CACCTAAAAT
* *
28594055 AAATAAAAAATAAATTATTAA
1 AAATAAAAAATAAATAAATAA
**
28594076 AGTTAAAAAATAAATAAATAA
1 AAATAAAAAATAAATAAATAA
28594097 AAATAAAAA
1 AAATAAAAA
28594106 CCACACTGTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
AAATAAAAAATAAATAAATAA
Found at i:28595135 original size:25 final size:24
Alignment explanation
Indices: 28595090--28595136 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
28595080 TGGGTTAATA
* * *
28595090 GGGAGTGATTTTAGGAGATAATGG
1 GGGAGAGATTTTAGAAAATAATGG
28595114 GGGAGAGATTATTAGAAAATAAT
1 GGGAGAGATT-TTAGAAAATAAT
28595137 CTGATTATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (24 bp):
GGGAGAGATTTTAGAAAATAATGG
Found at i:28598020 original size:7 final size:7
Alignment explanation
Indices: 28598010--28598041 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
28598000 GAGGGATGAT
28598010 GGATCAG
1 GGATCAG
28598017 GGATCAG
1 GGATCAG
28598024 GGATCAG
1 GGATCAG
28598031 GGATCAG
1 GGATCAG
28598038 GGAT
1 GGAT
28598042 GTATGGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.44, T:0.16
Consensus pattern (7 bp):
GGATCAG
Found at i:28598027 original size:21 final size:21
Alignment explanation
Indices: 28598001--28598041 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28597991 ATGAATGTTG
* *
28598001 AGGGATGATGGATCAGGGATC
1 AGGGATCAGGGATCAGGGATC
28598022 AGGGATCAGGGATCAGGGAT
1 AGGGATCAGGGATCAGGGAT
28598042 GTATGGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.44, T:0.17
Consensus pattern (21 bp):
AGGGATCAGGGATCAGGGATC
Found at i:28601771 original size:21 final size:21
Alignment explanation
Indices: 28601747--28601788 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28601737 GATGTGACTT
28601747 GAAAGGAAG-AAAATAACAAAA
1 GAAA-GAAGAAAAATAACAAAA
* *
28601768 GAAATAAGAAAAATAAGAAAA
1 GAAAGAAGAAAAATAACAAAA
28601789 CTAAACAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (21 bp):
GAAAGAAGAAAAATAACAAAA
Found at i:28604536 original size:12 final size:14
Alignment explanation
Indices: 28604506--28604537 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28604496 AAAAAAAGGA
28604506 AAAAATTAGAATGT
1 AAAAATTAGAATGT
28604520 AAAAATTA-AAT-T
1 AAAAATTAGAATGT
28604532 AAAAAT
1 AAAAAT
28604538 AAAAGTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATGT
Found at i:28605363 original size:31 final size:31
Alignment explanation
Indices: 28605314--28605375 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
28605304 AAAAAACGCC
* * *
28605314 GCTAAAGATCGAGTATTAGGGGCGCTTTTTG
1 GCTAAAAATCGAGCATTAGCGGCGCTTTTTG
* *
28605345 GCTAAAAATTGAGCATTAGCGGCGTTTTTTG
1 GCTAAAAATCGAGCATTAGCGGCGCTTTTTG
28605376 AAACTTAGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (31 bp):
GCTAAAAATCGAGCATTAGCGGCGCTTTTTG
Found at i:28605502 original size:41 final size:41
Alignment explanation
Indices: 28605413--28605512 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 41
28605403 TAAGGTTTCG
* * * *
28605413 GGGCTTTAGTGGC-TTTTTTAAGAAGCATCGCTAATGCATG
1 GGGCTTTAGCGGCGTTTTTTAAAAAGCATCGCTAAAGCATA
* * * **
28605453 GGGATTTAGCGGCGTTTTTTAAAAAGCGTCGGTAAAGGTTA
1 GGGCTTTAGCGGCGTTTTTTAAAAAGCATCGCTAAAGCATA
28605494 GGGCTTTAGCGGCGTTTTT
1 GGGCTTTAGCGGCGTTTTT
28605513 AAGGAAGCGC
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
40 11 0.22
41 38 0.78
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTTAAAAAGCATCGCTAAAGCATA
Found at i:28605972 original size:7 final size:7
Alignment explanation
Indices: 28605927--28606022 Score: 70
Period size: 7 Copynumber: 13.7 Consensus size: 7
28605917 AGTTACTATT
28605927 TTTA-GG
1 TTTATGG
*
28605933 TTTATAG
1 TTTATGG
*
28605940 ATTATGAG
1 TTTATG-G
*
28605948 TTTAGGG
1 TTTATGG
* *
28605955 ATTATGA
1 TTTATGG
28605962 TTTATGG
1 TTTATGG
28605969 TTTATGG
1 TTTATGG
28605976 TTTATGG
1 TTTATGG
*
28605983 TTTAAGG
1 TTTATGG
28605990 TTTA-GAG
1 TTTATG-G
* *
28605997 GTTACGG
1 TTTATGG
*
28606004 TTTATGA
1 TTTATGG
*
28606011 TTTAAGG
1 TTTATGG
28606018 TTTAT
1 TTTAT
28606023 AGATTAAGGG
Statistics
Matches: 68, Mismatches: 18, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
6 5 0.07
7 57 0.84
8 6 0.09
ACGTcount: A:0.24, C:0.01, G:0.26, T:0.49
Consensus pattern (7 bp):
TTTATGG
Found at i:28606029 original size:14 final size:14
Alignment explanation
Indices: 28605863--28606031 Score: 92
Period size: 14 Copynumber: 11.9 Consensus size: 14
28605853 TTAATTATCA
*
28605863 TTATAGTTTATGGT
1 TTATAGTTTAAGGT
28605877 TTATAG-TTAAGGGT
1 TTATAGTTTAA-GGT
* *
28605891 ATATAGTTTAGGGT
1 TTATAGTTTAAGGT
*
28605905 TTAAAGTTTAAGAG-
1 TTATAGTTTAAG-GT
* *
28605919 TTACTATTTTTAGGT
1 TTA-TAGTTTAAGGT
* *
28605934 TTATAGATTATGAGT
1 TTATAGTTTAAG-GT
** * * *
28605949 TTAGGGATTATGAT
1 TTATAGTTTAAGGT
* *
28605963 TTATGGTTTATGGT
1 TTATAGTTTAAGGT
*
28605977 TTATGGTTTAAGGT
1 TTATAGTTTAAGGT
* * *
28605991 TTAGAGGTTACGGT
1 TTATAGTTTAAGGT
28606005 TTAT-GATTTAAGGT
1 TTATAG-TTTAAGGT
*
28606019 TTATAGATTAAGG
1 TTATAGTTTAAGG
28606032 GTTGGGGTTT
Statistics
Matches: 119, Mismatches: 28, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
13 4 0.03
14 89 0.75
15 26 0.22
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (14 bp):
TTATAGTTTAAGGT
Found at i:28606042 original size:21 final size:21
Alignment explanation
Indices: 28606016--28606075 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
28606006 TATGATTTAA
28606016 GGTTTATAGATTAAGGGTT-GG
1 GGTTTA-AGATTAAGGGTTAGG
* * *
28606037 GGTTTAGGGTTAGGGGTTAGG
1 GGTTTAAGATTAAGGGTTAGG
28606058 GG-TTAAGAGTTAAGGGTT
1 GGTTTAAGA-TTAAGGGTT
28606076 TAAGGTTTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (21 bp):
GGTTTAAGATTAAGGGTTAGG
Found at i:28606207 original size:16 final size:16
Alignment explanation
Indices: 28606188--28606242 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
28606178 ATAGTTTAAA
*
28606188 TTATTTATAAATAATT
1 TTATATATAAATAATT
28606204 TTATAT-TAAATAA-T
1 TTATATATAAATAATT
28606218 TTATATATTAAATAATT
1 TTATATA-TAAATAATT
*
28606235 TAATATAT
1 TTATATAT
28606243 TAACATAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 7 0.21
15 7 0.21
16 13 0.38
17 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATATAAATAATT
Found at i:28606215 original size:15 final size:16
Alignment explanation
Indices: 28606195--28606251 Score: 89
Period size: 16 Copynumber: 3.5 Consensus size: 16
28606185 AAATTATTTA
28606195 TAAATAATTT-TATAT
1 TAAATAATTTATATAT
28606210 TAAATAATTTATATAT
1 TAAATAATTTATATAT
28606226 TAAATAATTTAATATAT
1 TAAATAATTT-ATATAT
28606243 TAACATAAT
1 TAA-ATAAT
28606252 GATTATAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.26
16 15 0.38
17 9 0.23
18 5 0.13
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATAATTTATATAT
Found at i:28606258 original size:17 final size:15
Alignment explanation
Indices: 28606195--28606258 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 15
28606185 AAATTATTTA
*
28606195 TAAATAATTTTATAT
1 TAAATAATATTATAT
*
28606210 TAAATAATTTATATAT
1 TAAATAATAT-TATAT
*
28606226 TAAATAATTTAATATAT
1 TAAATAA--TATTATAT
28606243 TAACATAATGATTATA
1 TAA-ATAAT-ATTATA
28606259 GTGTTTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.24
16 13 0.32
17 13 0.32
18 5 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TAAATAATATTATAT
Found at i:28606455 original size:502 final size:480
Alignment explanation
Indices: 28605770--28606677 Score: 1207
Period size: 502 Copynumber: 1.8 Consensus size: 480
28605760 GTTTTTTAGG
*
28605770 TACATGACTGATTTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAAAGATAGTAT
1 TACATGACTGATTTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAAAGATAATAT
*
28605835 TAATTTTAAAATATTGAATTAATTATCATTATAGTTTATGGTTTATAGTTAAGGGTATATAGTTT
66 TAATTTTAAAATATTGAATTAATTATCATTATAGTTTATGGTTTATAGTTAAGGGTATATAGTGT
* * *
28605900 AGGGTTTAAAGTTTAAGAGTTACTATTTTTAGGTTTATAGATTATGAGTTTAGGGATTA-TGATT
131 AAGGTTTAAAGTTTAAGAGTTACTATTTTAAGGTTTATAGATTATGAGTTTAGGGATTACAG-TT
* * * *
28605964 TATGGTTT-ATGGTTTATGGTTTAAGGTTTAGAGGTTA-CGGTTTATGATTT-AAGGTTTATAGA
195 TATGGTTTAAGGGTTGA-GATTTAAGGTTTAGAGGTTAGCGGTTTAAGATTTCAAGG-TTAT-G-
* * *
28606026 TTAAGGGTTGGGGTTTAGGGTTAGGGGTTAGGGGTTAAGAGTTAAGGGTTTAAGGTTTAGATTAA
256 TT-----TTAGGATTTA----T--GAGTTAGGGG---AGAG---A-GGTTTAAGGTTTAGATTAA
* *
28606091 TTAGTGTTTTTTAATTTATATATTAAATAATTTATTATATAGTTGTAAAAGAGATAATATTAAAT
303 TTAGTGTTTATTAATTTATATATTAAATAATTTATTATATAATTGTAAAAGAGATAATATTAAAT
*
28606156 TTAAAATATTAAAAATATGATTATAGTTTAAATTATTTATAAATAATTTTATATTAAATAATTTA
368 TTAAAATATTAAAAATATAATTATAGTTTAAATTATTTATAAATAATTTTATATTAAATAATTTA
28606221 TATATTAAATAATTTAATATATTAACATAATGATTATAGTGTTTTTAA
433 TATATTAAATAATTTAATATATTAACATAATGATTATAGTGTTTTTAA
*
28606269 TACATGACTGATTGTTTTTTAATTTATATATTAAATTATTTCTTATATAATCGTAAAAGAGATAA
1 TACATGACTGA-T-TTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAA-AGATAA
* * *
28606334 TATTAATTTTAAAATATTGAATTAATTATGATTATAGTTT-TGGGTTTATAGTTTAGGGTATATG
63 TATTAATTTTAAAATATTGAATTAATTATCATTATAGTTTAT-GGTTTATAGTTAAGGGTATATA
* *
28606398 GTGTAAGGTTT-AAGCTTTAAGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATTAC
127 GTGTAAGGTTTAAAG-TTTAAGAGTTACTATTTTAAGGTTTATAGATTATGAGTTTAGGGATTAC
* * *
28606462 AGTTTATTGTTTAAGGGTTGAGATTTAAGGTTTAGGGGTTAGGGGTTTAAGATTTCAAGGTTATG
191 AGTTTATGGTTTAAGGGTTGAGATTTAAGGTTTAGAGGTTAGCGGTTTAAGATTTCAAGGTTATG
* * * *
28606527 TTTTATGATTTATGATTTAGGGGATAGAGGTTTAGGGTTTAGATTAATTAGTGTTTATTAATTTA
256 TTTTAGGATTTATGAGTTAGGGGAGAGAGGTTTAAGGTTTAGATTAATTAGTGTTTATTAATTTA
* * * * * * *
28606592 TCTATTAAATATTTTCTTATATAATTGTGAAAGAGATAATATTAATTTTAATATATTAAAATTAT
321 TATATTAAATAATTTATTATATAATTGTAAAAGAGATAATATTAAATTTAAAATATTAAAAATAT
28606657 AATTATAGTTTAAATTATTTA
386 AATTATAGTTTAAATTATTTA
28606678 AGAGATAATC
Statistics
Matches: 365, Mismatches: 35, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
483 112 0.31
484 1 0.00
487 3 0.01
490 8 0.02
492 1 0.00
496 7 0.02
499 11 0.03
500 1 0.00
501 49 0.13
502 146 0.40
503 22 0.06
504 4 0.01
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.46
Consensus pattern (480 bp):
TACATGACTGATTTTTTTAATTTATATATTAAATAATTTCTTATATAATCGTAAAAAGATAATAT
TAATTTTAAAATATTGAATTAATTATCATTATAGTTTATGGTTTATAGTTAAGGGTATATAGTGT
AAGGTTTAAAGTTTAAGAGTTACTATTTTAAGGTTTATAGATTATGAGTTTAGGGATTACAGTTT
ATGGTTTAAGGGTTGAGATTTAAGGTTTAGAGGTTAGCGGTTTAAGATTTCAAGGTTATGTTTTA
GGATTTATGAGTTAGGGGAGAGAGGTTTAAGGTTTAGATTAATTAGTGTTTATTAATTTATATAT
TAAATAATTTATTATATAATTGTAAAAGAGATAATATTAAATTTAAAATATTAAAAATATAATTA
TAGTTTAAATTATTTATAAATAATTTTATATTAAATAATTTATATATTAAATAATTTAATATATT
AACATAATGATTATAGTGTTTTTAA
Found at i:28610050 original size:27 final size:27
Alignment explanation
Indices: 28610012--28610072 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
28610002 GGAAGGACCA
28610012 AACGCGCAAATTCCCTTTTAGGGCCAG
1 AACGCGCAAATTCCCTTTTAGGGCCAG
28610039 AACGCGCAAATTCCCTTTTAGGGCCAG
1 AACGCGCAAATTCCCTTTTAGGGCCAG
28610066 AACGCGC
1 AACGCGC
28610073 GGACCCTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (27 bp):
AACGCGCAAATTCCCTTTTAGGGCCAG
Found at i:28612139 original size:22 final size:22
Alignment explanation
Indices: 28612092--28612140 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
28612082 AAATAGCTTA
* *
28612092 TTTTTACAGATAAAAATCTAGG
1 TTTTTACAGAGAAAAATATAGG
28612114 TTTTTACAG-GAAAAATAT-GAG
1 TTTTTACAGAGAAAAATATAG-G
28612135 TTTTTA
1 TTTTTA
28612141 TAGGGAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.58
22 9 0.38
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (22 bp):
TTTTTACAGAGAAAAATATAGG
Found at i:28613570 original size:21 final size:21
Alignment explanation
Indices: 28613554--28613624 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
28613544 CCAAAAATTT
28613554 ATTTTAAAAATTAAAAAAAAG
1 ATTTTAAAAATTAAAAAAAAG
** *
28613575 ATTTTAAAAATATTTAAAAAAT
1 ATTTTAAAAAT-TAAAAAAAAG
*
28613597 ACTTT-AAAATTAAAAAAAA-
1 ATTTTAAAAATTAAAAAAAAG
28613616 A-TTTAAAAA
1 ATTTTAAAAA
28613625 GTATTTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.07
19 5 0.12
20 7 0.17
21 16 0.38
22 11 0.26
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (21 bp):
ATTTTAAAAATTAAAAAAAAG
Found at i:28613583 original size:10 final size:10
Alignment explanation
Indices: 28613577--28613704 Score: 72
Period size: 11 Copynumber: 13.0 Consensus size: 10
28613567 AAAAAAAGAT
28613577 TTTAAAAATA
1 TTTAAAAATA
28613587 TTTAAAAAATA
1 TTT-AAAAATA
28613598 CTTT-AAAAT-
1 -TTTAAAAATA
** *
28613607 TAAAAAAAAA
1 TTTAAAAATA
28613617 TTTAAAAAGTA
1 TTTAAAAA-TA
*
28613628 TTTTAAAATA
1 TTTAAAAATA
*
28613638 TTT-TAAA-A
1 TTTAAAAATA
*
28613646 TTAAAAAATAA
1 TTTAAAAAT-A
**
28613657 TAAAAAAATA
1 TTTAAAAATA
28613667 TTTTAAAAATA
1 -TTTAAAAATA
*
28613678 TTT-TAAA-A
1 TTTAAAAATA
*
28613686 -TTAAAAAAA
1 TTTAAAAATA
28613695 TTTAAAAATA
1 TTTAAAAATA
28613705 AATATATTTA
Statistics
Matches: 90, Mismatches: 16, Indels: 24
0.69 0.12 0.18
Matches are distributed among these distances:
7 2 0.02
8 8 0.09
9 14 0.16
10 31 0.34
11 32 0.36
12 3 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:28613620 original size:30 final size:30
Alignment explanation
Indices: 28613580--28613636 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
28613570 AAAAGATTTT
*
28613580 AAAAATATTTAAAAAATACTTTAAAATTAA
1 AAAAAAATTTAAAAAATACTTTAAAATTAA
* *
28613610 AAAAAAATTTAAAAAGTATTTTAAAAT
1 AAAAAAATTTAAAAAATACTTTAAAAT
28613637 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAAAAATTTAAAAAATACTTTAAAATTAA
Found at i:28613623 original size:40 final size:39
Alignment explanation
Indices: 28613553--28613704 Score: 191
Period size: 40 Copynumber: 3.8 Consensus size: 39
28613543 ACCAAAAATT
28613553 TATTTTAAAAATTAAAAAAAAGATTTTAAAAATATTTAAAAAA
1 TATTTT-AAAATTAAAAAAAA-A-TTTAAAAATATTT-AAAAA
* *
28613596 TACTTTAAAATTAAAAAAAAATTTAAAAAGTATTTTAAAA
1 TATTTTAAAATTAAAAAAAAATTTAAAAA-TATTTAAAAA
* **
28613636 TATTTTAAAATTAAAAAATAATAAAAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAAAAAATTTAAAAATA-TTTAAAAA
28613676 TATTTTAAAATT--AAAAAAATTTAAAAATA
1 TATTTTAAAATTAAAAAAAAATTTAAAAATA
28613705 AATATATTTA
Statistics
Matches: 97, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
38 14 0.14
39 2 0.02
40 56 0.58
41 6 0.06
42 14 0.14
43 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAAAATTTAAAAATATTTAAAAA
Found at i:28613691 original size:17 final size:17
Alignment explanation
Indices: 28613669--28613713 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
28613659 AAAAAATATT
28613669 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
28613686 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
28613702 ATAAATATATTT
1 TTAAAAATATTT
28613714 ATTATATCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:28615736 original size:10 final size:10
Alignment explanation
Indices: 28615721--28615748 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
28615711 CAATTGCTAC
28615721 ATTTTAAATA
1 ATTTTAAATA
28615731 ATTTTAAATA
1 ATTTTAAATA
28615741 ATTTTAAA
1 ATTTTAAA
28615749 AGCAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTTTAAATA
Found at i:28617334 original size:20 final size:20
Alignment explanation
Indices: 28617294--28617334 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28617284 AAACAATCAC
*
28617294 AAAAAGTATCGATGCCCTTT
1 AAAAAGTATCGATACCCTTT
* *
28617314 AAAAAGTATTGATACCTTTT
1 AAAAAGTATCGATACCCTTT
28617334 A
1 A
28617335 CCAGGTGTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (20 bp):
AAAAAGTATCGATACCCTTT
Found at i:28618735 original size:12 final size:11
Alignment explanation
Indices: 28618718--28618789 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 11
28618708 GATAAGAAGA
28618718 AATAATGAAAAT
1 AATAAT-AAAAT
28618730 AATAATAACAAT
1 AATAATAA-AAT
*
28618742 AATAGTACAAAT
1 AATAATA-AAAT
* *
28618754 AATAATAGGATT
1 AATAATA-AAAT
*
28618766 AATAA-ATAAT
1 AATAATAAAAT
*
28618776 AATAATAAATT
1 AATAATAAAAT
28618787 AAT
1 AAT
28618790 TAGTAAAAGC
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
10 7 0.15
11 9 0.19
12 31 0.65
13 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:28619035 original size:19 final size:21
Alignment explanation
Indices: 28618997--28619035 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
28618987 CTTTTTTTAA
*
28618997 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
28619018 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
28619036 ACAGTAAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:28619253 original size:19 final size:19
Alignment explanation
Indices: 28619229--28619303 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
28619219 AATCACATCT
28619229 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
28619248 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
28619269 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
28619288 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
28619304 CTCGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:28619266 original size:21 final size:21
Alignment explanation
Indices: 28619240--28619302 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
28619230 CTAAGATTAC
28619240 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
28619261 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
28619280 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
28619301 AT
1 AT
28619303 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:28619313 original size:17 final size:18
Alignment explanation
Indices: 28619232--28619313 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 18
28619222 CACATCTTCT
* *
28619232 AAGATTACATATCATATCT
1 AAGATTGCATATCA-ATCG
*
28619251 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCA-ATCG
*
28619272 AAGATTGCATATCATATCT
1 AAGATTGCATATCA-ATCG
*
28619291 AAGATTGCATATC-CTCG
1 AAGATTGCATATCAATCG
28619308 AAGATT
1 AAGATT
28619314 ATGTTTCCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.14
19 31 0.53
21 19 0.33
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
AAGATTGCATATCAATCG
Found at i:28623504 original size:43 final size:43
Alignment explanation
Indices: 28623456--28623681 Score: 305
Period size: 43 Copynumber: 5.3 Consensus size: 43
28623446 TTTTAGAAAT
* *
28623456 AAACGCCGCTATAGATCATAACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATAACTTTTAGCGGCGCTTTTTCCAC
28623499 AAACGCCGCTATAGCA-CA-AGACTTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAG-ATCATA-ACTTTTAGCGGCGCTTTTTCCAC
* *
28623542 AAACGCCGCTATAAATCATGACTTTTAGCGGCGCTTTCTTCC-C
1 AAACGCCGCTATAGATCATAACTTTTAGCGGCGCTTT-TTCCAC
* * * *
28623585 AAACGCCGCTATAGATCATGACTTTTAGCGACGCTTCTCCCAC
1 AAACGCCGCTATAGATCATAACTTTTAGCGGCGCTTTTTCCAC
* * *
28623628 AAACGCCGCTATAGATCATTACTTTTAGCGACGCTTTTTTCAC
1 AAACGCCGCTATAGATCATAACTTTTAGCGGCGCTTTTTCCAC
28623671 AAACGCCGCTA
1 AAACGCCGCTA
28623682 AAAGTGCCAT
Statistics
Matches: 165, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
42 5 0.03
43 155 0.94
44 5 0.03
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATAACTTTTAGCGGCGCTTTTTCCAC
Found at i:28628170 original size:24 final size:23
Alignment explanation
Indices: 28628143--28628197 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
28628133 TATATGAAAT
28628143 TATTTAATATATAAATTAAAAACA
1 TATTTAATATATAAATTAAAAA-A
*
28628167 TATTTAAAATATAAATTAAAAAA
1 TATTTAATATATAAATTAAAAAA
*
28628190 TAATTAAT
1 TATTTAAT
28628198 CTAAACCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TATTTAATATATAAATTAAAAAA
Found at i:28628353 original size:15 final size:15
Alignment explanation
Indices: 28628317--28628357 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
28628307 AAATCTCAAC
28628317 CCTTAAA-CCATAAT
1 CCTTAAATCCATAAT
*
28628331 CCCT-AATCCATAAT
1 CCTTAAATCCATAAT
28628345 CCTTAAATCCATA
1 CCTTAAATCCATA
28628358 CTCCCTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 8 0.35
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (15 bp):
CCTTAAATCCATAAT
Found at i:28628370 original size:22 final size:22
Alignment explanation
Indices: 28628296--28628373 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
28628286 ACCACTAACC
28628296 CCCTAAACCTTAAATCTCA-AC-
1 CCCTAAACCTTAAATC-CATACT
* * * *
28628317 CCTTAAACCAT-AATCCCTAAT
1 CCCTAAACCTTAAATCCATACT
* *
28628338 CCATAATCCTTAAATCCATACT
1 CCCTAAACCTTAAATCCATACT
28628360 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
28628374 ACAGTAACTC
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 17 0.40
22 20 0.47
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (22 bp):
CCCTAAACCTTAAATCCATACT
Found at i:28628800 original size:41 final size:41
Alignment explanation
Indices: 28628730--28628866 Score: 179
Period size: 41 Copynumber: 3.3 Consensus size: 41
28628720 GGCGTTTAAT
*
28628730 CAAAAACGCCGCTAAAGCCCCTA--CAATTAGCGGCGCTTTTC
1 CAAAAACGCCGCTAAAGACCC-AGGC-ATTAGCGGCGCTTTTC
*
28628771 CAAAAACGCCGCTAAAGACCCGGGCATTAGCGGCGCTTTTC
1 CAAAAACGCCGCTAAAGACCCAGGCATTAGCGGCGCTTTTC
* * * *
28628812 CAAAAACGCCGCAAAACACCTAGGCATTAGCGGCGTTTTTC
1 CAAAAACGCCGCTAAAGACCCAGGCATTAGCGGCGCTTTTC
*
28628853 CAAAAACGCTGCTA
1 CAAAAACGCCGCTA
28628867 TTGCTTGATT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 84 0.99
42 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (41 bp):
CAAAAACGCCGCTAAAGACCCAGGCATTAGCGGCGCTTTTC
Found at i:28629746 original size:39 final size:39
Alignment explanation
Indices: 28629650--28629748 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
28629640 ATTCACTTTT
* * * *
28629650 AAGCCTATATCACATTACACATATAAGTACATAACGTTC
1 AAGCATATATCACAATACTCATATAAGTACATAACATTC
* * *
28629689 AAGCACATATCGCAATACTCATATAA-TCACATAATATTC
1 AAGCATATATCACAATACTCATATAAGT-ACATAACATTC
*
28629728 AAGCATATAACACAATACTCA
1 AAGCATATATCACAATACTCA
28629749 AAAACATGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
38 1 0.02
39 48 0.98
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.26
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAAGTACATAACATTC
Found at i:28642897 original size:6 final size:6
Alignment explanation
Indices: 28642886--28642933 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
28642876 AATTTAGCCA
**
28642886 TTTAAT TTTAAT TTTAAT TTTAA- --TAAT TTTGTT TTTAAT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
28642931 TTT
1 TTT
28642934 CTTTTATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.09
6 32 0.91
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:28642914 original size:21 final size:21
Alignment explanation
Indices: 28642888--28642930 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
28642878 TTTAGCCATT
28642888 TAATTTTAATTTTAATTTTAA
1 TAATTTTAATTTTAATTTTAA
**
28642909 TAATTTTGTTTTTAATTTTAA
1 TAATTTTAATTTTAATTTTAA
28642930 T
1 T
28642931 TTTCTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TAATTTTAATTTTAATTTTAA
Found at i:28644611 original size:16 final size:16
Alignment explanation
Indices: 28644587--28644623 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
28644577 AAAAGATCCA
*
28644587 ATAAGTTTAATGTCTT
1 ATAAATTTAATGTCTT
28644603 ATAAATTTAATGTCTT
1 ATAAATTTAATGTCTT
28644619 ATAAA
1 ATAAA
28644624 ATGTTCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (16 bp):
ATAAATTTAATGTCTT
Found at i:28652155 original size:17 final size:16
Alignment explanation
Indices: 28652125--28652215 Score: 85
Period size: 16 Copynumber: 5.5 Consensus size: 16
28652115 ATTATTTAGA
*
28652125 TTTTATTTAGTTTTAT
1 TTTTATTTATTTTTAT
*
28652141 GTTTTATTTATTTTTCT
1 -TTTTATTTATTTTTAT
* *
28652158 TTTTCTTTTTTTTCTAT
1 TTTTATTTATTTT-TAT
28652175 TTTTACTTTTATTTTTAT
1 TTTTA--TTTATTTTTAT
* *
28652193 TATTAGTTATTTTTA-
1 TTTTATTTATTTTTAT
28652208 TTTTATTT
1 TTTTATTT
28652216 TTAGACTTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
15 6 0.10
16 20 0.33
17 20 0.33
18 7 0.12
19 7 0.12
ACGTcount: A:0.15, C:0.04, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATTTATTTTTAT
Found at i:28652192 original size:6 final size:6
Alignment explanation
Indices: 28652130--28652218 Score: 64
Period size: 6 Copynumber: 15.7 Consensus size: 6
28652120 TTAGATTTTA
* * * *
28652130 TTTAGT TTTATGT TTTA-- TTTATT TTTCTT TTTCTT TTT-TT TCTATT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* * *
28652176 TTTACT TTTATT TTTATT ATTA-- GTTATT TTTA-T TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
28652219 GACTTATATG
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
4 7 0.10
5 9 0.13
6 46 0.69
7 5 0.07
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:28655139 original size:20 final size:20
Alignment explanation
Indices: 28655114--28655158 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28655104 TATAATACAT
28655114 AAAAAA-TACTAAAAACATTA
1 AAAAAATTACTAAAAA-ATTA
* *
28655134 AAAAAATTCCTAACAAATTA
1 AAAAAATTACTAAAAAATTA
28655154 AAAAA
1 AAAAA
28655159 CAAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAAATTACTAAAAAATTA
Found at i:28661952 original size:16 final size:16
Alignment explanation
Indices: 28661928--28661958 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28661918 TCATAAACTT
28661928 TTTAATATTTATTTTA
1 TTTAATATTTATTTTA
*
28661944 TTTATTATTTATTTT
1 TTTAATATTTATTTT
28661959 TAAATTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTAATATTTATTTTA
Found at i:28662053 original size:19 final size:20
Alignment explanation
Indices: 28662012--28662057 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
28662002 CGTTAGCATC
*
28662012 ATTAAAATTTTAATAATTTA
1 ATTAAAATTTTAATAATTAA
28662032 ATTAAAA-TTTAA-AATTAAA
1 ATTAAAATTTTAATAATT-AA
28662051 ATTAAAA
1 ATTAAAA
28662058 GTATTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.54
20 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTAAAATTTTAATAATTAA
Found at i:28662924 original size:23 final size:23
Alignment explanation
Indices: 28662898--28662942 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
28662888 ACCGCAATAA
28662898 ATACATAACAAAAATATTAACCT
1 ATACATAACAAAAATATTAACCT
28662921 ATACATAACAAAAATATTAACC
1 ATACATAACAAAAATATTAACC
28662943 CTCTCTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (23 bp):
ATACATAACAAAAATATTAACCT
Found at i:28667667 original size:14 final size:14
Alignment explanation
Indices: 28667648--28667687 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
28667638 TAAAATAGAA
28667648 ATAATATAAATATT
1 ATAATATAAATATT
28667662 ATAATATAAATATT
1 ATAATATAAATATT
*
28667676 ATAATACAAATA
1 ATAATATAAATA
28667688 ATATTGTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATAAATATT
Found at i:28668658 original size:25 final size:25
Alignment explanation
Indices: 28668630--28668710 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
28668620 ACCAAATGGT
28668630 ATATTAAGCCTATTAAAATTACTAA
1 ATATTAAGCCTATTAAAATTACTAA
* * **
28668655 ATATTAAG-TTGTTACCAAA-TGGT--
1 ATATTAAGCCTATTA--AAATTACTAA
28668678 ATATTAAGCCTATTAAAATTACTAA
1 ATATTAAGCCTATTAAAATTACTAA
28668703 ATATTAAG
1 ATATTAAG
28668711 TTGTTAAGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
22 3 0.07
23 10 0.24
24 8 0.19
25 18 0.43
26 3 0.07
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (25 bp):
ATATTAAGCCTATTAAAATTACTAA
Found at i:28668690 original size:48 final size:48
Alignment explanation
Indices: 28668619--28668716 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
28668609 CAAACTTGGG
28668619 TACCAAATGGTATATTAAGCCTATTAAAATTACTAAATATTAAGTTGT
1 TACCAAATGGTATATTAAGCCTATTAAAATTACTAAATATTAAGTTGT
28668667 TACCAAATGGTATATTAAGCCTATTAAAATTACTAAATATTAAGTTGT
1 TACCAAATGGTATATTAAGCCTATTAAAATTACTAAATATTAAGTTGT
28668715 TA
1 TA
28668717 AGCTTAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (48 bp):
TACCAAATGGTATATTAAGCCTATTAAAATTACTAAATATTAAGTTGT
Found at i:28669254 original size:20 final size:19
Alignment explanation
Indices: 28669229--28669276 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
28669219 AAAACATAAA
28669229 ATTTTAAAAACTATAATTTT
1 ATTTTAAAAACTATAA-TTT
* *
28669249 ATTTTAAAAATTTTAATTT
1 ATTTTAAAAACTATAATTT
28669268 -TTTTAAAAA
1 ATTTTAAAAA
28669277 AAATTATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
19 3 0.12
20 14 0.54
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTAAAAACTATAATTT
Found at i:28669575 original size:15 final size:17
Alignment explanation
Indices: 28669548--28669582 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
28669538 TAAAGCAAAT
28669548 AAATTATTAAAA-TAAA
1 AAATTATTAAAATTAAA
28669564 AAATTA-TAAAATTAAA
1 AAATTATTAAAATTAAA
28669580 AAA
1 AAA
28669583 ATGGGTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATTATTAAAATTAAA
Found at i:28674181 original size:13 final size:13
Alignment explanation
Indices: 28674163--28674196 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28674153 TCAGTCAATT
28674163 TTTTTTCATTTAA
1 TTTTTTCATTTAA
*
28674176 TTTTTTGATTTAA
1 TTTTTTCATTTAA
28674189 TTCTTTTC
1 TT-TTTTC
28674197 CTTTTCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTTTTCATTTAA
Found at i:28675208 original size:24 final size:22
Alignment explanation
Indices: 28675154--28675218 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 22
28675144 ACATATAAGT
*
28675154 CTAAAAATTAAAATAAAAACAA
1 CTAAAAAATAAAATAAAAACAA
*
28675176 CTAACAAATAAAATAAAAGTACAA
1 CTAAAAAATAAAATAAAA--ACAA
28675200 CTAAAAAATAAAAATAAAA
1 CTAAAAAAT-AAAATAAAA
28675219 TAACTAGAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.43
24 12 0.32
25 9 0.24
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (22 bp):
CTAAAAAATAAAATAAAAACAA
Found at i:28675239 original size:28 final size:29
Alignment explanation
Indices: 28675174--28675239 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
28675164 AAATAAAAAC
*
28675174 AACTAACAAATAAAATAAAAGTACAACTAAA
1 AACTAA-AAATAAAAT-AAACTACAACTAAA
* * *
28675205 AAATAAAAATAAAAT-AACTAGAACTGAA
1 AACTAAAAATAAAATAAACTACAACTAAA
28675233 AACTAAA
1 AACTAAA
28675240 GAAGATTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 16 0.53
30 9 0.30
31 5 0.17
ACGTcount: A:0.68, C:0.11, G:0.05, T:0.17
Consensus pattern (29 bp):
AACTAAAAATAAAATAAACTACAACTAAA
Found at i:28678025 original size:3 final size:3
Alignment explanation
Indices: 28678017--28678096 Score: 56
Period size: 3 Copynumber: 26.7 Consensus size: 3
28678007 TATTTTTAAC
* * * *
28678017 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATCT -TC ACT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
* * * *
28678062 AGT A-T ATTT ATT AAT ATT ATT GTT ATT ATT GTT AT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT AT
28678097 GTTTTTATTT
Statistics
Matches: 58, Mismatches: 15, Indels: 8
0.72 0.19 0.10
Matches are distributed among these distances:
2 2 0.03
3 54 0.93
4 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:28682080 original size:18 final size:17
Alignment explanation
Indices: 28682059--28682125 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
28682049 GCTTTAATTT
28682059 TTTTATTTATTTGTTTAC
1 TTTTATTTATTTGTTT-C
28682077 TTTTATTTA-TTGATTTC
1 TTTTATTTATTTG-TTTC
*
28682094 TTTT-TATTATATGTTTGCC
1 TTTTAT-TTATTTGTTT--C
28682113 ATTTTATTTATTT
1 -TTTTATTTATTT
28682126 ATCTTTTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
16 1 0.03
17 14 0.35
18 14 0.35
19 1 0.03
20 9 0.22
21 1 0.03
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (17 bp):
TTTTATTTATTTGTTTC
Found at i:28682085 original size:22 final size:21
Alignment explanation
Indices: 28682051--28682092 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
28682041 ATTTAAGTGC
*
28682051 TTTAATTTTTTTATTTATTTG
1 TTTAATTTTTTTATTGATTTG
*
28682072 TTTACTTTTATTTATTGATTT
1 TTTAATTTT-TTTATTGATTT
28682093 CTTTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTAATTTTTTTATTGATTTG
Found at i:28688465 original size:15 final size:15
Alignment explanation
Indices: 28688430--28688480 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
28688420 TATTTAGCTA
**
28688430 ATTATTTTTAACGTT
1 ATTATTTTTAATATT
28688445 ATTATTTTTAATATT
1 ATTATTTTTAATATT
* * *
28688460 ACTATTATTATTATT
1 ATTATTTTTAATATT
28688475 ATTATT
1 ATTATT
28688481 ATTATCATCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (15 bp):
ATTATTTTTAATATT
Found at i:28688468 original size:3 final size:3
Alignment explanation
Indices: 28688443--28688539 Score: 63
Period size: 3 Copynumber: 32.3 Consensus size: 3
28688433 ATTTTTAACG
* * * *
28688443 TTA TTA TTT TTA ATA TTA CTA TTA TTA TTA TTA TTA TTA TTA TCA TCT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * * * *
28688491 TCA CTA TTG TTA TTA GTA -TA TTTA TTA ATA TTA TTG TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
28688536 TTA T
1 TTA T
28688540 GTTTTTATTT
Statistics
Matches: 69, Mismatches: 21, Indels: 8
0.70 0.21 0.08
Matches are distributed among these distances:
2 2 0.03
3 65 0.94
4 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:28688937 original size:18 final size:17
Alignment explanation
Indices: 28688914--28688979 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 17
28688904 TTAATTTTTA
28688914 TTTATTTATTTGTTTACT
1 TTTATTTATTTGTTT-CT
28688932 TTTATTTA-TTGATTTCT
1 TTTATTTATTTG-TTTCT
*
28688949 TTT-TATTATATGTTTGCCAT
1 TTTAT-TTATTTGTTT--C-T
28688969 TTTATTTATTT
1 TTTATTTATTT
28688980 ATCTTTTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
16 1 0.03
17 14 0.36
18 13 0.33
19 1 0.03
20 9 0.23
21 1 0.03
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (17 bp):
TTTATTTATTTGTTTCT
Found at i:28689931 original size:30 final size:30
Alignment explanation
Indices: 28689897--28689997 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
28689887 CTAAAATCAT
* *
28689897 TAATACTAATAATGAACAGAATAAG-AATAC
1 TAATACTAATAATAAACAAAAT-AGTAATAC
*
28689927 TAATATTAATAATAAACAAAATAGTAATAC
1 TAATACTAATAATAAACAAAATAGTAATAC
* *
28689957 TAATACTACA-AATAAA-AAAAGTAATAATAT
1 TAATACTA-ATAATAAACAAAA-TAGTAATAC
*
28689987 TAATAGTAATA
1 TAATACTAATA
28689998 GTAATAGTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 7 0.12
30 52 0.87
31 1 0.02
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (30 bp):
TAATACTAATAATAAACAAAATAGTAATAC
Found at i:28689996 original size:6 final size:6
Alignment explanation
Indices: 28689981--28690010 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28689971 AAAAAAGTAA
*
28689981 TAATAT TAATAG TAATAG TAATAG TAATAG
1 TAATAG TAATAG TAATAG TAATAG TAATAG
28690011 AAACTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
TAATAG
Found at i:28696781 original size:43 final size:43
Alignment explanation
Indices: 28696688--28696952 Score: 277
Period size: 43 Copynumber: 6.2 Consensus size: 43
28696678 ATGCCGTTAT
** * **
28696688 AGAACATGACCTTTAGCAACGCTTTTAT-AAAAAAACCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACTCCGCTAA
* *
28696730 AGAGCATGACCTTTAGCGGCG-TTTTACCCACAAACTCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTA-TCACAAACTCCGCTAA
* *
28696773 AGAACATGATCTTTAGTGGCGCTTTTATCACAAA-TGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACT-CCGCTAA
* *
28696816 AGAACATGACCTTTAGCAGCGCTTTTATCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACTCCGCTAA
* * * *
28696859 AGAGCATGACCTTTAGCGGTGCTTTTATCACAAACGCCGCTAT
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACTCCGCTAA
* ** ** *
28696902 AGAGA-ATGACTTTTAGCAACTTTTTTTTCACAAACTCCGCTAA
1 AGA-ACATGACCTTTAGCGGCGCTTTTATCACAAACTCCGCTAA
*
28696945 ATAACATG
1 AGAACATG
28696953 TTCTTTCGCG
Statistics
Matches: 186, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
41 5 0.03
42 20 0.11
43 156 0.84
44 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGGCGCTTTTATCACAAACTCCGCTAA
Found at i:28696933 original size:129 final size:128
Alignment explanation
Indices: 28696676--28696952 Score: 328
Period size: 129 Copynumber: 2.2 Consensus size: 128
28696666 CATGTGAAAA
* *
28696676 AAATGCCGTTATAGAACATGACCTTTAGCAACGCTTTTATAAAAAAACCGCTAAAGAGCATGACC
1 AAATGCCGCTAAAGAACATGACCTTTAGCAACGCTTTTATAAAAAAACCGCTAAAGAGCATGACC
* ***
28696741 TTTAGCGGCGTTTTACCCACAAACTCCGCTAAAGAACATGATCTTTAGTGGCGCTTTTATCAC
66 TTTAGCGGCGTTTTACCCACAAACGCCGCTAAAGAACATGATCTTTAGCAACGCTTTTATCAC
* * **
28696804 AAATGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTATCACAAACGCCGCTAAAGAGCATGAC
1 AAATGCCGCTAAAGAACATGACCTTTAGCAACGCTTTTAT-AAAAAAACCGCTAAAGAGCATGAC
* * * ** *
28696869 CTTTAGCGGTGCTTTTA-TCACAAACGCCGCTATAGAGA-ATGA-CTTTTAGCAACTTTTTTTTC
65 CTTTAGCGGCG-TTTTACCCACAAACGCCGCTAAAGA-ACATGATC-TTTAGCAACGCTTTTATC
28696931 AC
127 AC
*
28696933 AAACT-CCGCTAAATAACATG
1 AAA-TGCCGCTAAAGAACATG
28696953 TTCTTTCGCG
Statistics
Matches: 127, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
128 38 0.30
129 82 0.65
130 7 0.06
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (128 bp):
AAATGCCGCTAAAGAACATGACCTTTAGCAACGCTTTTATAAAAAAACCGCTAAAGAGCATGACC
TTTAGCGGCGTTTTACCCACAAACGCCGCTAAAGAACATGATCTTTAGCAACGCTTTTATCAC
Found at i:28702834 original size:9 final size:9
Alignment explanation
Indices: 28702820--28703050 Score: 90
Period size: 9 Copynumber: 24.0 Consensus size: 9
28702810 TAAGTATAAT
28702820 TAAGTTATG
1 TAAGTTATG
28702829 TAAGTTATG
1 TAAGTTATG
*
28702838 TGAGTTATG
1 TAAGTTATG
28702847 TAAGTTATG
1 TAAGTTATG
* *
28702856 ATATGATATATA
1 -TAAG-T-TATG
28702868 TAAGTTATTATG
1 TAAG---TTATG
*
28702880 TATGTTATG
1 TAAGTTATG
*
28702889 TGAGTTATG
1 TAAGTTATG
28702898 TAAGTTATG
1 TAAGTTATG
* *
28702907 ATATGATATATA
1 -TAAG-T-TATG
28702919 TAAGTTAT-
1 TAAGTTATG
*
28702927 TAAGTTAAG
1 TAAGTTATG
* *
28702936 ATCCAAAGTTTTTTTT
1 -T---AAG---TTATG
* *
28702952 TAA-TTCTT
1 TAAGTTATG
28702960 TAAAGTTATG
1 T-AAGTTATG
28702970 TAAGTTATG
1 TAAGTTATG
*
28702979 TAAGTTTTG
1 TAAGTTATG
* * **
28702988 ATATGATACA
1 -TAAGTTATG
*
28702998 T-ATTTATG
1 TAAGTTATG
28703006 TAAGTTATG
1 TAAGTTATG
*
28703015 TAAATTATG
1 TAAGTTATG
*
28703024 CAAGTTATG
1 TAAGTTATG
28703033 TAAGTTATG
1 TAAGTTATG
*
28703042 TTAGTTATG
1 TAAGTTATG
28703051 ATATATATTT
Statistics
Matches: 165, Mismatches: 37, Indels: 40
0.68 0.15 0.17
Matches are distributed among these distances:
8 15 0.09
9 104 0.63
10 16 0.10
11 8 0.05
12 14 0.08
13 5 0.03
15 1 0.01
16 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Done.