Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 5 of 203
Found at i:1360310 original size:50 final size:50
Alignment explanation
Indices: 1360250--1360527 Score: 326
Period size: 50 Copynumber: 5.5 Consensus size: 50
1360240 TCGGTTTACA
1360250 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCAGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCAGTACACG
* * * * * * * * *
1360300 TAGTATCCTGCACATAGTACTACACACGTGATCGA-AACTATCTAGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCCAGTACACG
*
1360351 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCAGTACACG
* * * * * * * * *
1360401 TAGTAGCCTACACATAGTACTACACACGTGATCGA-AACTATCTAGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCCAGTACACG
*
1360452 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCAGTACACG
1360502 TAGTAGCCTGCACATAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
1360528 CGTAACCATC
Statistics
Matches: 183, Mismatches: 39, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
49 2 0.01
50 102 0.56
51 77 0.42
52 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCAGTACACG
Found at i:1360423 original size:101 final size:101
Alignment explanation
Indices: 1360248--1360530 Score: 539
Period size: 101 Copynumber: 2.8 Consensus size: 101
1360238 GTTCGGTTTA
* *
1360248 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCAGTACACGTAGTATCCTGCAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACGTAGTAGCCTGCAC
1360313 ATAGTACTACACACGTGATCGAAACTATCTAGTACG
66 ATAGTACTACACACGTGATCGAAACTATCTAGTACG
*
1360349 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACGTAGTAGCCTACAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACGTAGTAGCCTGCAC
1360414 ATAGTACTACACACGTGATCGAAACTATCTAGTACG
66 ATAGTACTACACACGTGATCGAAACTATCTAGTACG
1360450 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACGTAGTAGCCTGCAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACGTAGTAGCCTGCAC
1360515 ATAGTACTACACACGT
66 ATAGTACTACACACGT
1360531 AACCATCACT
Statistics
Matches: 178, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 178 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCTAGTACG
Found at i:1363101 original size:29 final size:29
Alignment explanation
Indices: 1363064--1363121 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1363054 GGCTACACCA
1363064 TGAATGTTTTCATATCATACGATGCCATG
1 TGAATGTTTTCATATCATACGATGCCATG
1363093 TGAATGTTTTCATATCATACGATGCCATG
1 TGAATGTTTTCATATCATACGATGCCATG
1363122 AGTCTCAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (29 bp):
TGAATGTTTTCATATCATACGATGCCATG
Found at i:1365341 original size:17 final size:17
Alignment explanation
Indices: 1365319--1365359 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1365309 AAACCACAAT
*
1365319 CATTTC-CAAATGTTTCC
1 CATTTCTCAAAT-TTTAC
1365336 CATTTCTCAAATTTTAC
1 CATTTCTCAAATTTTAC
1365353 CATTTCT
1 CATTTCT
1365360 ATCGATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.46
Consensus pattern (17 bp):
CATTTCTCAAATTTTAC
Found at i:1378756 original size:85 final size:85
Alignment explanation
Indices: 1378610--1378788 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
1378600 GGCCGGCCAT
1378610 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1378675 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
1378695 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1378760 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
1378780 GAGCATGGG
1 GAGCATGGG
1378789 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:1379845 original size:18 final size:18
Alignment explanation
Indices: 1379822--1379863 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1379812 AATGAATTGT
1379822 ATTAAATTGCTTGATGTG
1 ATTAAATTGCTTGATGTG
1379840 ATTAAATTGCTTGATGTG
1 ATTAAATTGCTTGATGTG
1379858 ATTAAA
1 ATTAAA
1379864 AATGCATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (18 bp):
ATTAAATTGCTTGATGTG
Found at i:1381055 original size:47 final size:47
Alignment explanation
Indices: 1381002--1381412 Score: 750
Period size: 47 Copynumber: 8.7 Consensus size: 47
1380992 TTAGGATTCT
1381002 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1381049 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1381096 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1381143 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1381190 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1381237 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1381284 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
1381331 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
1381378 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
1381413 TCCCGAAGGG
Statistics
Matches: 354, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 354 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:1388774 original size:19 final size:20
Alignment explanation
Indices: 1388740--1388781 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1388730 TTTCCAACCC
*
1388740 ATCCATCCACTACACACCAT
1 ATCCAACCACTACACACCAT
*
1388760 ATCCAACCA-TACACACTAT
1 ATCCAACCACTACACACCAT
1388779 ATC
1 ATC
1388782 GGAAGGAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.21
Consensus pattern (20 bp):
ATCCAACCACTACACACCAT
Found at i:1403950 original size:23 final size:22
Alignment explanation
Indices: 1403898--1403950 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1403888 TCCACGTCTT
*
1403898 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
1403920 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
1403943 TTTCTTTT
1 TTTCTTTT
1403951 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:1407729 original size:23 final size:22
Alignment explanation
Indices: 1407677--1407729 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1407667 TCCACGTCTT
*
1407677 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
1407699 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
1407722 TTTCTTTT
1 TTTCTTTT
1407730 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:1410950 original size:29 final size:29
Alignment explanation
Indices: 1410895--1410950 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1410885 GTTTGGGTTT
* *
1410895 AATATTACCAAAATACATAATTCAATAAA
1 AATATTACCAAAATACAAAAATCAATAAA
1410924 AATATTACCAAAATACACAAAAT-AATA
1 AATATTACCAAAATACA-AAAATCAATA
1410951 CCGTATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (29 bp):
AATATTACCAAAATACAAAAATCAATAAA
Found at i:1414896 original size:20 final size:20
Alignment explanation
Indices: 1414873--1414940 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1414863 AAATCTAATT
1414873 ATTTACCAATATTTTTAACA
1 ATTTACCAATATTTTTAACA
**
1414893 ATTTACCAATATTGGT--C-
1 ATTTACCAATATTTTTAACA
1414910 --TTACCAATATTTTTAACA
1 ATTTACCAATATTTTTAACA
*
1414928 CTTTACCAATATT
1 ATTTACCAATATT
1414941 ACTAATGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
15 12 0.31
17 1 0.03
18 1 0.03
20 25 0.64
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (20 bp):
ATTTACCAATATTTTTAACA
Found at i:1422934 original size:17 final size:17
Alignment explanation
Indices: 1422912--1422949 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1422902 TTTAGATGAT
1422912 TTTTTTAAAAATATAAA
1 TTTTTTAAAAATATAAA
1422929 TTTTTTAAAAATATAAA
1 TTTTTTAAAAATATAAA
1422946 TTTT
1 TTTT
1422950 AGAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTTAAAAATATAAA
Found at i:1422964 original size:19 final size:19
Alignment explanation
Indices: 1422940--1422976 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1422930 TTTTTAAAAA
1422940 TATAAAT-TTTAGAATTTTT
1 TATAAATATTT-GAATTTTT
1422959 TATAAATATTTGAATTTT
1 TATAAATATTTGAATTTT
1422977 AAAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGAATTTTT
Found at i:1424854 original size:33 final size:33
Alignment explanation
Indices: 1424792--1424854 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1424782 TTCTTTCCTC
1424792 TCTTTTTCTTCTTCTTTTTTTTTTCTTTCCGGT
1 TCTTTTTCTTCTTCTTTTTTTTTTCTTTCCGGT
1424825 TCTTCTTTCTT-TTCTTTTTCTTTTT-TTTCC
1 TCTT-TTTCTTCTTCTTTTT-TTTTTCTTTCC
1424855 AAATTAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (33 bp):
TCTTTTTCTTCTTCTTTTTTTTTTCTTTCCGGT
Found at i:1427754 original size:49 final size:49
Alignment explanation
Indices: 1427682--1427818 Score: 220
Period size: 49 Copynumber: 2.8 Consensus size: 49
1427672 TATTTTCTCG
*
1427682 ATGCCATAGTCCAACTATGGTCTTACACGTAATCACATAACATATACCA
1 ATGCCATAGCCCAACTATGGTCTTACACGTAATCACATAACATATACCA
* * *
1427731 ATGCCATAGCCCAACTATGGTCTTACACTTAATCACATAACATATATCG
1 ATGCCATAGCCCAACTATGGTCTTACACGTAATCACATAACATATACCA
* *
1427780 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATA
1 ATGCCATAGCCCAACTATGGTCTTACACGTAATCACATA
1427819 TCACTGAACG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 81 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.26
Consensus pattern (49 bp):
ATGCCATAGCCCAACTATGGTCTTACACGTAATCACATAACATATACCA
Found at i:1428980 original size:23 final size:23
Alignment explanation
Indices: 1428954--1429049 Score: 111
Period size: 23 Copynumber: 4.2 Consensus size: 23
1428944 AGTGCCACAT
1428954 TGATACGTAGCCGAAGCTACCAC
1 TGATACGTAGCCGAAGCTACCAC
** *
1428977 TGATACGTAGTTGTAGCTACCAC
1 TGATACGTAGCCGAAGCTACCAC
* * * *
1429000 TTAAATGTAGCCGAAGCTACCAT
1 TGATACGTAGCCGAAGCTACCAC
* *
1429023 TGATATGTAGCCGTAGCTACCAC
1 TGATACGTAGCCGAAGCTACCAC
1429046 TGAT
1 TGAT
1429050 CAATAACACT
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (23 bp):
TGATACGTAGCCGAAGCTACCAC
Found at i:1431993 original size:30 final size:30
Alignment explanation
Indices: 1431959--1432020 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1431949 ACTTCATCCC
1431959 TTATTCTTATGTATTATGACATGCTGAACA
1 TTATTCTTATGTATTATGACATGCTGAACA
1431989 TTATTCTTATGTATTATGACATGCTGAACA
1 TTATTCTTATGTATTATGACATGCTGAACA
1432019 TT
1 TT
1432021 TTTCCCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (30 bp):
TTATTCTTATGTATTATGACATGCTGAACA
Found at i:1433207 original size:679 final size:678
Alignment explanation
Indices: 1432313--1433666 Score: 2514
Period size: 679 Copynumber: 2.0 Consensus size: 678
1432303 GGAATCACTT
*
1432313 ACTATGGAGCTTGGTAGCTTGAAAACCCTAACTATGGCTTCCCCCTTGCTATTTTCGTTCATCAT
1 ACTATGGAGCTTGGAAGCTTGAAAACCCTAACTATGGCTTCCCCCTTGCTATTTTCGTTCATCAT
* *
1432378 GGAGAAGATAAGCATATTTTTCCATATTTTCCCTTTTTAATTCTTTTTATTACTAAATTACCAAA
66 GGAGAAGATAAGCACATTTTGCCATATTTTCCCTTTTTAATTCTTTTTATTACTAAATTACCAAA
* *
1432443 TTGCCCCTAACTTAAAAATTTCCTATTTCACTTATCTCATGTCTATTTTTGTCCATAACTTAACC
131 TTACCCCTAACTTAAAAATTTCCTATTTCACTTATCTCATGGCTATTTTTGTCCATAACTTAACC
*
1432508 AATGGTCTAATTACCATATAAAGACCTCCAATTTAAAGTTTCATAACAATTGCAAACCTCTAACA
196 AATGATCTAATTACCATATAAAGACCTCCAATTTAAAGTTTCATAACAATTGCAAACCTCTAACA
1432573 TGTAGAACTCAACTTTTGCACTTTTTACAATTTAGTCCTTTTGACTAAATTAAGTGCCCAAACAT
261 TGTAGAACTCAACTTTTGCACTTTTTACAATTTAGTCCTTTTGACTAAATTAAGTGCCCAAACA-
*
1432638 TGAAA-TTTTTTAACG-ATTTTTCAAAAAATCATTTCGTGAAATCGTAGACCATAAAAATATAAT
325 TCAAATTTTTTTAACGAATTTTTCAAAAAATCATTTCGTGAAATCGTAGACCATAAAAATATAAT
1432701 AAAAATAAATTTTGTCCTCGTCAAATTTGTGGTCCTGAAACCACTATTCTGGCTAGGCCCAAAAT
390 AAAAATAAATTTTGTCCTCGTCAAATTTGTGGTCCTGAAACCACTATTCTGGCTAGGCCCAAAAT
*
1432766 CGAGTTGTTACAACGTTTCTGAGCAAACAGTATCAAAAACGCTTTAAGCAGGATGCTTTTTCAGC
455 CGAGTTGTTACAACGTTTCTGAGCAAACAGTATCAAAAACACTTTAAGCAGGATGC-TTTTCAGC
*
1432831 AAAAGTACTGAAAAAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTTCTGAAAAAATAATT
519 AAAAGTACTGAAAAAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATT
1432896 TCAAGTAGACGTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAA
584 TCAAGTAGACGTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAA
1432961 GTACTGAAAGAAGCTCCCACGTGGACGCTA
649 GTACTGAAAGAAGCTCCCACGTGGACGCTA
1432991 ACTATGGAGCTTGGAAGCTTGAAAACCCTAACTATGGCTTCCCCCTTGCTATTTTCGTTCATCAT
1 ACTATGGAGCTTGGAAGCTTGAAAACCCTAACTATGGCTTCCCCCTTGCTATTTTCGTTCATCAT
*
1433056 GGAGAAGATAAGCACATTTTGCCATCTTTTTCCCTTTTTAATTCTTTTTATTACTAAATTACCAA
66 GGAGAAGATAAGCACATTTTGCCAT-ATTTTCCCTTTTTAATTCTTTTTATTACTAAATTACCAA
1433121 ATTACCCCTAACTTAAAAATTTCCTATTTCACTTATCTCATGGCTATTTTTGTCCATAACTTAAC
130 ATTACCCCTAACTTAAAAATTTCCTATTTCACTTATCTCATGGCTATTTTTGTCCATAACTTAAC
*
1433186 CAATGATCTAATTACCATATAAAGACCTCCAATTTAAAGTTTCATAACAATTGGAAACCTCTAAC
195 CAATGATCTAATTACCATATAAAGACCTCCAATTTAAAGTTTCATAACAATTGCAAACCTCTAAC
1433251 ATGTAGAACTCAACTTTTGCACTTTTTACAATTTAGTCCTTTTGACTAAATTAAGTGCCCAAACA
260 ATGTAGAACTCAACTTTTGCACTTTTTACAATTTAGTCCTTTTGACTAAATTAAGTGCCCAAACA
* *
1433316 TCAAATTTTTTTAACGAATTTTTCAAAAAATTATTTCGTGAAATTGTAGACCATAAAAATATAAT
325 TCAAATTTTTTTAACGAATTTTTCAAAAAATCATTTCGTGAAATCGTAGACCATAAAAATATAAT
*
1433381 AAAAATAAATTTTGTCCTCGTCAAATTTGTGGTCCTGAAACCACTATTCTGGCTAGGCCTAAAAT
390 AAAAATAAATTTTGTCCTCGTCAAATTTGTGGTCCTGAAACCACTATTCTGGCTAGGCCCAAAAT
* * *
1433446 CGAGTTGTTACAACGTTTCTGAGCAAACAGTGTCAAAAACATTTTAAGCAGGATGCTTTTCAGTA
455 CGAGTTGTTACAACGTTTCTGAGCAAACAGTATCAAAAACACTTTAAGCAGGATGCTTTTCAGCA
1433511 AAAGTACTGAAAAAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTT
520 AAAGTACTGAAAAAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTT
1433576 CAAGTAGACGTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAG
585 CAAGTAGACGTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAG
1433641 TACTGAAAGAAGCTCCCACGTGGACG
650 TACTGAAAGAAGCTCCCACGTGGACG
1433667 TGCTTTTGCT
Statistics
Matches: 656, Mismatches: 17, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
678 91 0.14
679 402 0.61
680 163 0.25
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (678 bp):
ACTATGGAGCTTGGAAGCTTGAAAACCCTAACTATGGCTTCCCCCTTGCTATTTTCGTTCATCAT
GGAGAAGATAAGCACATTTTGCCATATTTTCCCTTTTTAATTCTTTTTATTACTAAATTACCAAA
TTACCCCTAACTTAAAAATTTCCTATTTCACTTATCTCATGGCTATTTTTGTCCATAACTTAACC
AATGATCTAATTACCATATAAAGACCTCCAATTTAAAGTTTCATAACAATTGCAAACCTCTAACA
TGTAGAACTCAACTTTTGCACTTTTTACAATTTAGTCCTTTTGACTAAATTAAGTGCCCAAACAT
CAAATTTTTTTAACGAATTTTTCAAAAAATCATTTCGTGAAATCGTAGACCATAAAAATATAATA
AAAATAAATTTTGTCCTCGTCAAATTTGTGGTCCTGAAACCACTATTCTGGCTAGGCCCAAAATC
GAGTTGTTACAACGTTTCTGAGCAAACAGTATCAAAAACACTTTAAGCAGGATGCTTTTCAGCAA
AAGTACTGAAAAAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTC
AAGTAGACGTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGT
ACTGAAAGAAGCTCCCACGTGGACGCTA
Found at i:1433695 original size:126 final size:125
Alignment explanation
Indices: 1433458--1433695 Score: 395
Period size: 126 Copynumber: 1.9 Consensus size: 125
1433448 AGTTGTTACA
* *
1433458 ACGTTTCTGAGCAAACAGTGTCAAAAACATTTTAAGCAGGATGCTTTTCAGTAAAAGTACTGAAA
1 ACGTTTCTGAGCAAACAGTGTCAAAAACACTTTAAGCAGGATGCTTTTCAGCAAAAGTACTGAAA
* *
1433523 AAAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCAAGTAG
66 AAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAG
* *
1433583 ACGTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAA
1 ACGTTTCTGAGCAAACAGTGTCAAAAACACTTTAAGCAGGATGCTTT-TCAGCAAAAGTACTGAA
* *
1433648 AGAAGCTCCCACGTGGACGTGCTTTTGCTACAGTAGCTCCTAAAAAAA
65 AAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAA
1433696 GCTCCTACGT
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
125 45 0.43
126 59 0.57
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (125 bp):
ACGTTTCTGAGCAAACAGTGTCAAAAACACTTTAAGCAGGATGCTTTTCAGCAAAAGTACTGAAA
AAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAG
Found at i:1437372 original size:18 final size:18
Alignment explanation
Indices: 1437346--1437384 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1437336 GACTCGAAAA
* *
1437346 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
1437364 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
1437382 AGG
1 AGG
1437385 GTATGCACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.31, T:0.18
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:1439263 original size:22 final size:21
Alignment explanation
Indices: 1439235--1439287 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
1439225 AAATAGGGAT
1439235 TTGAGAGAAATTTCAAAGGAAA
1 TTGAGAGAAATTT-AAAGGAAA
*
1439257 TTGAGAGCAAATTTAGAGGAAA
1 TTGAGAG-AAATTTAAAGGAAA
*
1439279 TTGAAAGAA
1 TTGAGAGAA
1439288 TATAAGAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 20 0.71
23 6 0.21
ACGTcount: A:0.49, C:0.04, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGAGAGAAATTTAAAGGAAA
Found at i:1443483 original size:22 final size:21
Alignment explanation
Indices: 1443449--1443497 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
1443439 AATTTAAATT
*
1443449 AATATTATATT-AAATTATTGA
1 AATATTAGATTAAAATT-TTGA
1443470 AATATTAGATTTAAAATTTTGA
1 AATATTAGA-TTAAAATTTTGA
1443492 AATATT
1 AATATT
1443498 TCATATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 8 0.32
22 12 0.48
23 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (21 bp):
AATATTAGATTAAAATTTTGA
Found at i:1443509 original size:22 final size:23
Alignment explanation
Indices: 1443455--1443510 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
1443445 AATTAATATT
* *
1443455 ATATTAAATTATTGAAATATTAG
1 ATATAAAATTATTGAAATATTAC
* *
1443478 ATTTAAAATT-TTGAAATATTTC
1 ATATAAAATTATTGAAATATTAC
*
1443500 ATATATAATTA
1 ATATAAAATTA
1443511 ATTTTATAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (23 bp):
ATATAAAATTATTGAAATATTAC
Found at i:1443513 original size:26 final size:26
Alignment explanation
Indices: 1443484--1443539 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1443474 TTAGATTTAA
1443484 AATTTT-GAAAT-ATTTCATATATAATT
1 AATTTTAGAAATAATTT-ATAT-TAATT
*
1443510 AATTTTATAAATAATTTATATTAATT
1 AATTTTAGAAATAATTTATATTAATT
1443536 AATT
1 AATT
1443540 AAAAAGGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 15 0.56
27 8 0.30
28 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
AATTTTAGAAATAATTTATATTAATT
Found at i:1444280 original size:15 final size:16
Alignment explanation
Indices: 1444257--1444306 Score: 66
Period size: 15 Copynumber: 3.0 Consensus size: 16
1444247 TGTATTATAT
1444257 TATTAAATTATTTAAA
1 TATTAAATTATTTAAA
1444273 TA-TAAATTATTATTATAA
1 TATTAAATTA-T-TTA-AA
1444291 TATTAAATTATTTAAA
1 TATTAAATTATTTAAA
1444307 CATCATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 6 0.20
18 5 0.17
19 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTAAATTATTTAAA
Found at i:1444286 original size:18 final size:19
Alignment explanation
Indices: 1444244--1444302 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
1444234 AATTTATATT
*
1444244 TTATGTATTATATTATTAAA
1 TTAT-TATTATAATATTAAA
1444264 TTA-T-TTA-AATA-TAAA
1 TTATTATTATAATATTAAA
1444279 TTATTATTATAATATTAAA
1 TTATTATTATAATATTAAA
1444298 TTATT
1 TTATT
1444303 TAAACATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 6 0.18
18 5 0.15
19 9 0.26
20 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTATTATTATAATATTAAA
Found at i:1444295 original size:34 final size:34
Alignment explanation
Indices: 1444244--1444323 Score: 115
Period size: 34 Copynumber: 2.3 Consensus size: 34
1444234 AATTTATATT
* *
1444244 TTATGTATTATATTATTAAATTATTTAAATATAAA
1 TTAT-TATTATAATATTAAATTATTTAAACATAAA
* *
1444279 TTATTATTATAATATTAAATTATTTAAACATCAT
1 TTATTATTATAATATTAAATTATTTAAACATAAA
1444313 TTATTATTATA
1 TTATTATTATA
1444324 TTTAAACTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 37 0.90
35 4 0.10
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (34 bp):
TTATTATTATAATATTAAATTATTTAAACATAAA
Found at i:1444336 original size:31 final size:33
Alignment explanation
Indices: 1444243--1444337 Score: 113
Period size: 34 Copynumber: 2.8 Consensus size: 33
1444233 TAATTTATAT
*
1444243 TTTATGTATTATATTATTAAATTATTTAAATATAA
1 TTTAT-TATTATA-TATTAAATTATTTAAACATAA
* *
1444278 ATTATTATTATAATATTAAATTATTTAAACATCA
1 TTTATTATTAT-ATATTAAATTATTTAAACATAA
*
1444312 TTTATTATTATAT-TTAAACT-TTTAAA
1 TTTATTATTATATATTAAATTATTTAAA
1444338 ATATTTCATG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
31 6 0.11
32 6 0.11
33 2 0.04
34 35 0.65
35 5 0.09
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (33 bp):
TTTATTATTATATATTAAATTATTTAAACATAA
Found at i:1444411 original size:17 final size:18
Alignment explanation
Indices: 1444379--1444416 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1444369 TTTATTAGTT
*
1444379 ATTTAAAATATATATTTA
1 ATTTAAAATATATATTAA
*
1444397 ATTTATAAT-TATATTAA
1 ATTTAAAATATATATTAA
1444414 ATT
1 ATT
1444417 ATTTGAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAAATATATATTAA
Found at i:1450887 original size:40 final size:39
Alignment explanation
Indices: 1450833--1450955 Score: 108
Period size: 40 Copynumber: 3.1 Consensus size: 39
1450823 CGTTTGGATA
*
1450833 AAAAACGCCACTAAAAAGCAAGCATTAGCGGCGCTTTTAC
1 AAAAACGCCGCTAAAAAGCAAGCATTAGCGGCGCTTTT-C
* * * *
1450873 AAAAACGCCGCT-AAAGGTCGAGCATTAGCGACGCATTTTG
1 AAAAACGCCGCTAAAAAG-CAAGCATTAGCGGCGC-TTTTC
* * * *
1450913 GAAAACCCCGCTAAAAA-TAAGCATTAGCGGTG-TTTTCC
1 AAAAACGCCGCTAAAAAGCAAGCATTAGCGGCGCTTTT-C
1450951 AAAAA
1 AAAAA
1450956 GCGCTGCAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
37 4 0.06
38 4 0.06
39 15 0.23
40 35 0.54
41 7 0.11
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAAGCAAGCATTAGCGGCGCTTTTC
Found at i:1451070 original size:41 final size:41
Alignment explanation
Indices: 1451003--1451145 Score: 187
Period size: 41 Copynumber: 3.5 Consensus size: 41
1450993 AGAGTTTTGA
* * *
1451003 GGGCATTTAGCTGCGTTTTTGGAAAAGCGCCGCTAATGCTT
1 GGGCCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
* * *
1451044 GGGCCTTTAGCGGCGTTTTTGAAAAAGAGCCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
* * *
1451085 GGGCCTTTAGCGGCGATTTTGGAAAAGCACCGCTAATGATC
1 GGGCCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
* *
1451126 GGGCCTTTAGCCGTGTTTTT
1 GGGCCTTTAGCGGCGTTTTT
1451146 AATGCTCGGG
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 87 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTC
Found at i:1451156 original size:27 final size:27
Alignment explanation
Indices: 1451118--1451172 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1451108 AAAGCACCGC
*
1451118 TAATGATCGGGCCTTTAGCCGTGTTTT
1 TAATGATCGGGCCTTTAGCCGCGTTTT
* *
1451145 TAATGCTCGGGCCTTTAGCGGCGTTTT
1 TAATGATCGGGCCTTTAGCCGCGTTTT
1451172 T
1 T
1451173 GAAAAAGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (27 bp):
TAATGATCGGGCCTTTAGCCGCGTTTT
Found at i:1457312 original size:27 final size:26
Alignment explanation
Indices: 1457282--1457338 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
1457272 AATTTCGAGG
*
1457282 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
* *
1457308 ATTTACGTTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
1457335 TTTA
1 TTTA
1457339 TTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:1457463 original size:5 final size:5
Alignment explanation
Indices: 1457453--1457478 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1457443 TAAAATTTTA
1457453 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
1457479 TTTATCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1457925 original size:43 final size:43
Alignment explanation
Indices: 1457534--1457933 Score: 455
Period size: 43 Copynumber: 9.3 Consensus size: 43
1457524 ATGATATGTT
* * * * *
1457534 TTTAGCGGCGCTTT-TGCGAGAAGCGTCGCTAAAGGT-TTGTTC
1 TTTAGCGGCG-TTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * * *
1457576 TATAGCGACGTTTGTGATAAAAAGCGTCGCTAAAAGTCATGTTC
1 TTTAGCGGCGTTTGTGA-GAAAAGCGCCGCTAAAGGTCATGGTC
* *
1457620 TTTAGCGGCGTTTGTGACAAAAGTGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
1457663 TTTAGCGGCATTTGTGAGAAAAGCGCCGTTGAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* ** *
1457706 TTTAGCGGCGTTTGTGGGAAAAGCGCCTTTGAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* *
1457749 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* *
1457792 TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
** * *
1457835 TTTAGCGGTATTTGTGACAAGAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
** * * *
1457878 TTTAGCGGTATTTGTGACAAAAGTGCCGCTAAAGGTCAT-GAC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
1457920 TTTTAGCGGCGTTT
1 -TTTAGCGGCGTTT
1457934 ATTTCTAAAA
Statistics
Matches: 315, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
41 3 0.01
42 12 0.04
43 280 0.89
44 20 0.06
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:1460364 original size:16 final size:17
Alignment explanation
Indices: 1460343--1460380 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1460333 ATAATCTATA
*
1460343 ATATAATAATAG-CCAT
1 ATATAATAATAGTACAT
*
1460359 ATATAATAGTAGTACAT
1 ATATAATAATAGTACAT
1460376 ATATA
1 ATATA
1460381 TATTAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (17 bp):
ATATAATAATAGTACAT
Found at i:1460818 original size:241 final size:230
Alignment explanation
Indices: 1460389--1460872 Score: 589
Period size: 241 Copynumber: 2.0 Consensus size: 230
1460379 TATATTAATT
*
1460389 ATTATATATTATTGTTTATTATATTGATTGAAATATGCTCTAAGTCCCTATACTTTTCGTACATT
1 ATTATATATTATTGTTTATTATATTGATTGAAATATGCTCTAAGTCCCTATACTTTTCGTACATA
* * * *
1460454 TGAAAGTTAGCACTTGTTCAATATTATATTATGCTATATCATACCATATAGTATACAAAATATTA
66 TGAAAGCTAGCACTTGTTCAATATTATATAATGCTATATCATACCATATAATATAAAAAATATTA
*
1460519 ATAGTCATATATGCATCAATAATTAAACATTATAATATCAAGTAATACTATATCTTTTATTATAA
131 ATAGTCATATATGCACCAATAATTAAACATTATAATATCAAGTAATACTATATCTTTTATTATAA
**
1460584 TCTATAATG-TAATAGTTATATATAATAGTAGTAC
196 TCTATAATGATAATAGTTATATATAATAGTACCAC
* * * *
1460618 ATTATATGTTATTGTTTATCATTATATTGGTTGACATATGCTTTAAGTCCCTATAC-TTTCGTAC
1 ATTATATATTATTG-TT-T-ATTATATTGATTGAAATATGCTCTAAGTCCCTATACTTTTCGTAC
* * *
1460682 ATATGAAAGCTAGC-CTT-TCTACTATATTATATAATGTTGTATCATATCACATACTAAATAATA
63 ATATGAAAGCTAGCACTTGT-T-CAATATTATATAATGCTATATCATA-C-CATA-T-AAT-ATA
* * * *
1460745 AATAATATATTAATAGTTTATATGTATGCACCAATGATTGAACATTATAATATCATGTAATACTA
121 AA-AA-ATATTAATAG-TCATA--TATGCACCAATAATTAAACATTATAATATCAAGTAATACTA
* * *
1460810 TATCTTTTATTGTAATCTATATTGTAATAATAGTTATATATATTAGTACCAC
181 TATCTTTTATTATAATCTATAATG--ATAATAGTTATATATAATAGTACCAC
1460862 ATTATATATTA
1 ATTATATATTA
1460873 CAATTAATAA
Statistics
Matches: 214, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
229 14 0.07
230 6 0.03
231 42 0.20
232 34 0.16
233 4 0.02
234 1 0.00
235 2 0.01
236 4 0.02
237 2 0.01
238 10 0.05
239 4 0.02
241 59 0.28
244 32 0.15
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (230 bp):
ATTATATATTATTGTTTATTATATTGATTGAAATATGCTCTAAGTCCCTATACTTTTCGTACATA
TGAAAGCTAGCACTTGTTCAATATTATATAATGCTATATCATACCATATAATATAAAAAATATTA
ATAGTCATATATGCACCAATAATTAAACATTATAATATCAAGTAATACTATATCTTTTATTATAA
TCTATAATGATAATAGTTATATATAATAGTACCAC
Found at i:1460950 original size:26 final size:27
Alignment explanation
Indices: 1460892--1460964 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
1460882 ATATTTTATG
*
1460892 TATTA-GTAATAATTATATATTATATTA
1 TATTATGTAAT-AGTATATATTATATTA
*
1460919 TATTAT-TAATAGTATATATTATGTTA
1 TATTATGTAATAGTATATATTATATTA
*
1460945 GT-TTATGTAGTAG-ATATATT
1 -TATTATGTAATAGTATATATT
1460965 CTAATTTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 25 0.62
27 15 0.38
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (27 bp):
TATTATGTAATAGTATATATTATATTA
Found at i:1467875 original size:27 final size:27
Alignment explanation
Indices: 1467666--1467894 Score: 253
Period size: 27 Copynumber: 8.5 Consensus size: 27
1467656 ATGGAACCAT
* * ** *
1467666 TTCTCTTAGAGTTTGCCATACATATTA
1 TTCTTTTAGAGTTCGCCATATGTACTA
* *
1467693 TTCCTTCAGAGTTCGCCATATGTACTA
1 TTCTTTTAGAGTTCGCCATATGTACTA
*
1467720 TTCTTTTAGAGTTCGCCATACGTACTA
1 TTCTTTTAGAGTTCGCCATATGTACTA
**
1467747 TTCTTTTAGAGTTCGCCATAAATACTA
1 TTCTTTTAGAGTTCGCCATATGTACTA
* **
1467774 TTCTTTTAAAGTTCGCCATACATACTA
1 TTCTTTTAGAGTTCGCCATATGTACTA
1467801 TTCTTTTAGAGTTCGCCATATGTACTA
1 TTCTTTTAGAGTTCGCCATATGTACTA
* *
1467828 TT-TTTCCAGAGTTCTCCATATGTACTA
1 TTCTTT-TAGAGTTCGCCATATGTACTA
* * ** *
1467855 TTATTTTATAGTTCGTTATATGTACCA
1 TTCTTTTAGAGTTCGCCATATGTACTA
*
1467882 TTCTTTCAGAGTT
1 TTCTTTTAGAGTT
1467895 TACCATACCT
Statistics
Matches: 172, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 3 0.02
27 166 0.97
28 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (27 bp):
TTCTTTTAGAGTTCGCCATATGTACTA
Found at i:1468106 original size:27 final size:28
Alignment explanation
Indices: 1468064--1468128 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
1468054 ACAGATCGCT
*
1468064 ACAAAGGC-TTCAATTTTATAAATTGCC
1 ACAAAGGCTTTCAATTTCATAAATTGCC
* *
1468091 ACAAAGGCTTTC-ATTTCATAGATTTCC
1 ACAAAGGCTTTCAATTTCATAAATTGCC
1468118 ACAAAGGCTTT
1 ACAAAGGCTTT
1468129 AACTTTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 31 0.91
28 3 0.09
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (28 bp):
ACAAAGGCTTTCAATTTCATAAATTGCC
Found at i:1473053 original size:41 final size:41
Alignment explanation
Indices: 1473015--1473203 Score: 247
Period size: 41 Copynumber: 4.6 Consensus size: 41
1473005 TTTGAAGTCT
** * *
1473015 AAACAGGGGCATGTGTGTGCAATTCAGGGGTATCGAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTAC
* *
1473056 AAACAGGGGCACATATGTACAATTCAGGGGTACCAAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTAC
* *
1473097 AAACAGGGGCACATATGTACAATTCAGGGGTACCAAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTAC
* *
1473138 AAACAGGGGTACGTATGTGCAA-TCAGGGGTACCGAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTAC
* *
1473178 AAATAGGGGCA-TTCATGTGCAATTCA
1 AAACAGGGGCACAT-ATGTGCAATTCA
1473204 TCAATTTTCT
Statistics
Matches: 133, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 34 0.26
41 98 0.74
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (41 bp):
AAACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTAC
Found at i:1473064 original size:20 final size:19
Alignment explanation
Indices: 1473039--1473186 Score: 93
Period size: 20 Copynumber: 7.3 Consensus size: 19
1473029 GTGTGCAATT
1473039 CAGGGGTATCGAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
* *
1473059 CAGGGGCAC-ATATGTACAATT
1 CAGGGGTACGA-A-GTACAA-A
*
1473080 CAGGGGTACCAAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
* *
1473100 CAGGGGCAC-ATATGTACAATT
1 CAGGGGTACGA-A-GTACAA-A
*
1473121 CAGGGGTACCAAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
* * *
1473141 CAGGGGTACGTATGTGCAAT
1 CAGGGGTACG-AAGTACAAA
1473161 CAGGGGTACCGAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
*
1473181 TAGGGG
1 CAGGGG
1473187 CATTCATGTG
Statistics
Matches: 100, Mismatches: 16, Indels: 24
0.71 0.11 0.17
Matches are distributed among these distances:
18 2 0.02
19 5 0.05
20 59 0.59
21 28 0.28
22 4 0.04
23 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (19 bp):
CAGGGGTACGAAGTACAAA
Found at i:1473085 original size:21 final size:21
Alignment explanation
Indices: 1473059--1473126 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
1473049 GAAGTACAAA
1473059 CAGGGGCACATATGTACAATT
1 CAGGGGCACATATGTACAATT
* * *
1473080 CAGGGGTACCA-AAGTACAA-A
1 CAGGGGCA-CATATGTACAATT
1473100 CAGGGGCACATATGTACAATT
1 CAGGGGCACATATGTACAATT
1473121 CAGGGG
1 CAGGGG
1473127 TACCAAAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 14 0.37
21 20 0.53
22 2 0.05
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (21 bp):
CAGGGGCACATATGTACAATT
Found at i:1473486 original size:95 final size:95
Alignment explanation
Indices: 1473323--1473513 Score: 321
Period size: 95 Copynumber: 2.0 Consensus size: 95
1473313 CAACGAAGTC
1473323 AATTAATCTGAAGCTTTAGCTTTTCCCTGATCTAAATCCGTACAAGGTCTATCTTTATCTAAATA
1 AATTAATCTGAAGCTTTAGCTTTTCCCTGATCTAAATCCGTACAAGGTCTATCTTTATCTAAATA
* *
1473388 GAAAAGTTCAGTCCATTTAATACTTTTATT
66 GAAAAATTCAGTCCATTTAATAATTTTATT
* * *
1473418 AATTAATTTGAAGCTTTAGCTTTT-CCTCGATCTAAATCTGTACGAGGTCTATCTTTATCTAAAT
1 AATTAATCTGAAGCTTTAGCTTTTCCCT-GATCTAAATCCGTACAAGGTCTATCTTTATCTAAAT
1473482 AGAAAAATTCAGTCCATTTAATAATTTTATT
65 AGAAAAATTCAGTCCATTTAATAATTTTATT
1473513 A
1 A
1473514 TTCAACTCAG
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
94 3 0.03
95 87 0.97
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.41
Consensus pattern (95 bp):
AATTAATCTGAAGCTTTAGCTTTTCCCTGATCTAAATCCGTACAAGGTCTATCTTTATCTAAATA
GAAAAATTCAGTCCATTTAATAATTTTATT
Found at i:1474981 original size:33 final size:32
Alignment explanation
Indices: 1474944--1475005 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1474934 GCTTGCATTT
*
1474944 CACATAGTTCGCAATA-AGGCATAGTTTGCAATA
1 CACATAGCTCGCAATAGA-G-ATAGTTTGCAATA
1474977 CACATAGCTCGCAATAGAGATAGTTTGCA
1 CACATAGCTCGCAATAGAGATAGTTTGCA
1475006 TATAATGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 10 0.37
33 16 0.59
34 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (32 bp):
CACATAGCTCGCAATAGAGATAGTTTGCAATA
Found at i:1474990 original size:16 final size:16
Alignment explanation
Indices: 1474944--1474992 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
1474934 GCTTGCATTT
1474944 CACATAGTTCGCAATA
1 CACATAGTTCGCAATA
*
1474960 -AGGCATAGTTTGCAATA
1 CA--CATAGTTCGCAATA
*
1474977 CACATAGCTCGCAATA
1 CACATAGTTCGCAATA
1474993 GAGATAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.04
16 12 0.44
17 13 0.48
18 1 0.04
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (16 bp):
CACATAGTTCGCAATA
Found at i:1477601 original size:31 final size:31
Alignment explanation
Indices: 1477566--1477772 Score: 274
Period size: 31 Copynumber: 6.7 Consensus size: 31
1477556 GTATATGTTT
*
1477566 TATACATTGCCAAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
1477597 TATACATTGCCGAATTTGAATTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
1477628 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
1477659 TATACATTGCCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
** *
1477690 TATACATTATCGAA-TTGATTTGTATGTAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
1477720 TATACATTGCGGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
1477751 TATATATTACCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
1477773 AGCATTGGAT
Statistics
Matches: 153, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
30 32 0.21
31 121 0.79
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:1477782 original size:92 final size:93
Alignment explanation
Indices: 1477566--1477772 Score: 265
Period size: 92 Copynumber: 2.2 Consensus size: 93
1477556 GTATATGTTT
* * * * * *
1477566 TATACATTGCCAAATTTGATTTGTATATAGATATACATTGCCGAATTTGAATTGTTTATAGATAT
1 TATACATTACCGAATTTGATTTGCATATGGATATACATTACCGAATTTGAATTGTATATAGATAT
* *
1477631 ACATTGCCGAATTTGATTTGTATATGGT
66 ACATTGCCGAATTTGATTCGTATATGGA
* * * * *
1477659 TATACATTGCCGAATTTGATTTGTATATGGATATACATTATCGAA-TTGATTTGTATGTAGATAT
1 TATACATTACCGAATTTGATTTGCATATGGATATACATTACCGAATTTGAATTGTATATAGATAT
*
1477723 ACATTGCGGAATTTGATTCGTATATGGA
66 ACATTGCCGAATTTGATTCGTATATGGA
*
1477751 TATATATTACCGAA-TTGATTTG
1 TATACATTACCGAATTTGATTTG
1477773 AGCATTGGAT
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 8 0.08
92 53 0.52
93 41 0.40
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (93 bp):
TATACATTACCGAATTTGATTTGCATATGGATATACATTACCGAATTTGAATTGTATATAGATAT
ACATTGCCGAATTTGATTCGTATATGGA
Found at i:1477952 original size:43 final size:43
Alignment explanation
Indices: 1477887--1478037 Score: 230
Period size: 43 Copynumber: 3.5 Consensus size: 43
1477877 ACTTCTGAGG
*
1477887 TGAGATTTCATGTAAGATCATAGCTGGGCTATTGGCATCGATT
1 TGAGATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATT
* *
1477930 TGAGATTTTATGTAAGACCATAGCTGGGCTATTGGCATCAATT
1 TGAGATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATT
* * *
1477973 TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCAGCGATA
1 TGAGATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATT
*
1478016 CGAGATTTCCATGTAAGACCAT
1 TGAGATTT-CATGTAAGACCAT
1478038 GTCTGGGATG
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 85 0.88
44 12 0.12
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
TGAGATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATT
Found at i:1482815 original size:15 final size:15
Alignment explanation
Indices: 1482792--1482840 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1482782 GGGTGCTGCA
*
1482792 TATTCTTATCATTAT
1 TATTTTTATCATTAT
* *
1482807 TATTTTTATTATTTT
1 TATTTTTATCATTAT
1482822 TATTTTTATTC-TTAT
1 TATTTTTA-TCATTAT
1482837 TATT
1 TATT
1482841 ACTATTATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTTATCATTAT
Found at i:1482883 original size:29 final size:29
Alignment explanation
Indices: 1482803--1482883 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
1482793 ATTCTTATCA
** * *
1482803 TTATTATTTTTATTATTTTTATTTTTATTC
1 TTATTATTACTATTATTCTTA-GTTTATTC
* *
1482833 TTATTATTACTATTATTGTTAGTTTATTG
1 TTATTATTACTATTATTCTTAGTTTATTC
* *
1482862 TTATTTTTACTATTCTTCTTAG
1 TTATTATTACTATTATTCTTAG
1482884 GCTTATTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 25 0.58
30 18 0.42
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (29 bp):
TTATTATTACTATTATTCTTAGTTTATTC
Found at i:1483081 original size:5 final size:5
Alignment explanation
Indices: 1483037--1483069 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1483027 TTATTAGATT
*
1483037 TTTTG TTTTG TTTTG TTTTG TTTTG TTCTG TTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTT
1483070 CATTTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (5 bp):
TTTTG
Found at i:1491599 original size:42 final size:42
Alignment explanation
Indices: 1491553--1491643 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
1491543 GTGTCAATTA
* *
1491553 AGGGTAGACCACACGGGCGTGTGCCCTGAATGTGTTAGGTAC
1 AGGGTAGACCACACGAGCGTGTGCCCTGAATATGTTAGGTAC
* *
1491595 AGGGTAAACCACACGAGCGTGTGCCCTGAATATGTTAGGTGC
1 AGGGTAGACCACACGAGCGTGTGCCCTGAATATGTTAGGTAC
*
1491637 AAGGTAG
1 AGGGTAG
1491644 CCCAAACTCG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (42 bp):
AGGGTAGACCACACGAGCGTGTGCCCTGAATATGTTAGGTAC
Found at i:1505157 original size:39 final size:39
Alignment explanation
Indices: 1504993--1505175 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
1504983 TTGAATGCTG
* * * * * * *
1504993 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
1505033 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
1505073 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
1505113 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
1505152 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
1505176 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:1505195 original size:79 final size:80
Alignment explanation
Indices: 1505029--1505210 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
1505019 GCTAAGTGAA
* * * *
1505029 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
1505093 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
1505109 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
1505173 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
1505188 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
1505211 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:1508333 original size:42 final size:42
Alignment explanation
Indices: 1508232--1508370 Score: 147
Period size: 42 Copynumber: 3.2 Consensus size: 42
1508222 ATGTTTTATT
*
1508232 GTGTAAGACCAC-GTCTGGGACGTTGGCATCG-ATTTGAGATTTAC
1 GTGTAAGACC-CTGTCTGGGACATTGGCATCGTATTT--GATTT-C
* * *
1508276 GTGTAAGACCATGTCTAGGACATTGGCATCGTATATGATTTC
1 GTGTAAGACCCTGTCTGGGACATTGGCATCGTATTTGATTTC
* * *
1508318 GTGTAAGACCCTGTCTGGGGCAGTGGCATCGATATTTGATTAC
1 GTGTAAGACCCTGTCTGGGACATTGGCATCG-TATTTGATTTC
*
1508361 ATGTAAGACC
1 GTGTAAGACC
1508371 ACATCTGGGA
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
42 28 0.35
43 23 0.28
44 27 0.33
45 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCCTGTCTGGGACATTGGCATCGTATTTGATTTC
Found at i:1508388 original size:43 final size:43
Alignment explanation
Indices: 1508232--1508389 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
1508222 ATGTTTTATT
*
1508232 GTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTAC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATT-TGA-TTAC
* * * * *
1508276 GTGTAAGACCATGTCTAGGACATTGGCATCG-TATATGATTTC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTAC
*
1508318 GTGTAAGACC-CTGTCTGGGGCAG-TGGCATCGATATTTGATTAC
1 GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTAC
* * *
1508361 ATGTAAGACCACATCTGGGATGTTGGCAT
1 GTGTAAGACCACGTCTGGGACGTTGGCAT
1508390 TGTACGAGCT
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
42 29 0.32
43 33 0.36
44 30 0.33
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTAC
Found at i:1511895 original size:16 final size:16
Alignment explanation
Indices: 1511876--1511906 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1511866 CATAGTTTGC
1511876 AATACACATAGCTCGT
1 AATACACATAGCTCGT
*
1511892 AATACAGATAGCTCG
1 AATACACATAGCTCG
1511907 CATATAATGG
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:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (16 bp):
AATACACATAGCTCGT
Found at i:1519292 original size:30 final size:30
Alignment explanation
Indices: 1519257--1519319 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
1519247 CACAGAGTCG
*
1519257 TGTAGCTAGGCCGTGTGTGTCACAC-AGCCA
1 TGTAGCTAGGCCGAGTGTGTCACACGA-CCA
1519287 TGTAGCTAGGCCGAGTGTGTCACACGACCA
1 TGTAGCTAGGCCGAGTGTGTCACACGACCA
1519317 TGT
1 TGT
1519320 GACTCCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (30 bp):
TGTAGCTAGGCCGAGTGTGTCACACGACCA
Found at i:1521032 original size:39 final size:40
Alignment explanation
Indices: 1520933--1521076 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
1520923 CGAATGATGT
* * *
1520933 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAA
* * *
1520973 CCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-A
*
1521013 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
*
1521052 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
1521077 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
39 34 0.39
40 43 0.49
41 10 0.11
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
Found at i:1521090 original size:40 final size:39
Alignment explanation
Indices: 1520985--1521083 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
1520975 AGACTAAGAT
** * *
1520985 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGC
1 CCGAAGGCATTTGAACGAGTTACTATA-ACCGGGCTAAGC
** *
1521024 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAG-C
1521064 CCGAAGGCATTTGAACGAGT
1 CCGAAGGCATTTGAACGAGT
1521084 AGCTATATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 33 0.62
40 20 0.38
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAGC
Found at i:1521095 original size:79 final size:80
Alignment explanation
Indices: 1520932--1521082 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 80
1520922 TCGAATGATG
*
1520932 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
**
1520997 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * * *
1521012 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCAGACTAAGAT-CCGAAGGCAT
1521074 TTGAACGAG
64 TTGAACGAG
1521083 TAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 41 0.68
80 18 0.30
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:1534762 original size:10 final size:10
Alignment explanation
Indices: 1534749--1534794 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
1534739 TAAAATAAGG
1534749 TAAAAAGTGT
1 TAAAAAGTGT
*
1534759 TAAAAAGCGT
1 TAAAAAGTGT
*
1534769 AAAAAAGTGT
1 TAAAAAGTGT
*
1534779 TAAACATGTGT
1 TAAA-AAGTGT
1534790 TAAAA
1 TAAAA
1534795 TATGTTAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.26
Consensus pattern (10 bp):
TAAAAAGTGT
Found at i:1534763 original size:20 final size:20
Alignment explanation
Indices: 1534738--1534817 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
1534728 TATTATTTAA
1534738 TTAAAATAAGGTAAAAAGTG
1 TTAAAATAAGGTAAAAAGTG
1534758 TT-AAA-AAGCGTAAAAAAGTG
1 TTAAAATAAG-GT-AAAAAGTG
** *
1534778 TTAAACATGTGTTAAAATA-TG
1 TTAAA-ATAAGGTAAAA-AGTG
*
1534799 TTAACATAAGGTAAAAAGT
1 TTAAAATAAGGTAAAAAGT
1534818 ATTTTCTTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
18 3 0.07
19 6 0.13
20 21 0.46
21 12 0.26
22 3 0.07
23 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.17, T:0.28
Consensus pattern (20 bp):
TTAAAATAAGGTAAAAAGTG
Found at i:1539860 original size:133 final size:130
Alignment explanation
Indices: 1539615--1540060 Score: 399
Period size: 132 Copynumber: 3.4 Consensus size: 130
1539605 ACAGGATGAG
* * * *
1539615 TCAATCATTGTGGTCAAAAAATCAC-T-TGTCACTCTTCCAAAATACAAATACCCTAGCGAAGTT
1 TCAATCGTTGTGGTCAAAACATCACTTCTGTCACTCTCCCAAAATACAAATACCCTAGCGAAG-A
* * * *
1539678 GGT----CGTTGTGGTCAAAACGCCACTTTCATCACTCTATCACTATAAAAATT-TTCTTAGTAG
65 AGTCAACCGTTATGGTCAAAA-GCCACTTTCATCACTCTATCA-AATATAAATTATT-TTAGT-G
1539738 AGAAA
126 AGAAA
* * * *
1539743 TCAATTGTGGTGGTCAAAACATCATTTCTGTCATTCTCCCAAAATACAAATACCCTAGCGAAGAA
1 TCAATCGTTGTGGTCAAAACATCACTTCTGTCACTCTCCCAAAATACAAATACCCTAGCGAAGAA
* * * * *
1539808 GTCAACCATTTTGGTCAAAGAGCCACTTTCATCACTCTTTCAGAATATAAATTCTTTTAATGAAG
66 GTCAACCGTTATGGTCAAA-AGCCACTTTCATCACTCTATCA-AATATAAATTATTTTAGTG-AG
*
1539873 AAT
128 AAA
** * * * * * *
1539876 TTTATCGTTGTGGTC-AAACATCACTTCTGTCACACTCTCAAAATATAAATACCATAGCAAATAA
1 TCAATCGTTGTGGTCAAAACATCACTTCTGTCACTCTCCCAAAATACAAATACCCTAGCGAAGAA
* * ** *
1539940 GTCAACTGTTATGGTCAAAA-CATCACTTTTATGGCTCTCTCAAACTATAAATTATTTT-GATGG
66 GTCAACCGTTATGGTCAAAAGC--CACTTTCATCACTCTATCAAA-TATAAATTATTTTAG-T-G
*
1540003 AGAAG
126 AGAAA
* *
1540008 TCAATCGTTGTGGTCAAAACATCACTTCTGCCACTATCCCAAAATACAAATAC
1 TCAATCGTTGTGGTCAAAACATCACTTCTGTCACTCTCCCAAAATACAAATAC
1540061 TCAATAGAGA
Statistics
Matches: 257, Mismatches: 46, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
128 20 0.08
129 3 0.01
130 34 0.13
131 3 0.01
132 103 0.40
133 91 0.35
134 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.31
Consensus pattern (130 bp):
TCAATCGTTGTGGTCAAAACATCACTTCTGTCACTCTCCCAAAATACAAATACCCTAGCGAAGAA
GTCAACCGTTATGGTCAAAAGCCACTTTCATCACTCTATCAAATATAAATTATTTTAGTGAGAAA
Found at i:1543935 original size:23 final size:23
Alignment explanation
Indices: 1543909--1543990 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
1543899 TTGATCATGG
*
1543909 CACTTCGATGCAATTAACAGAGA
1 CACTTCGATGCAATTAACAGTGA
* * * *
1543932 CACTCCGGTGCAACTGACAGTGA
1 CACTTCGATGCAATTAACAGTGA
*
1543955 CAC-TCTAGTGCAATTGAA-AGTGA
1 CACTTCGA-TGCAATT-AACAGTGA
*
1543978 CACTTCGGTGCAA
1 CACTTCGATGCAA
1543991 ATTAGTAATT
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
22 1 0.02
23 40 0.91
24 3 0.07
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTTCGATGCAATTAACAGTGA
Found at i:1548767 original size:69 final size:67
Alignment explanation
Indices: 1548681--1548812 Score: 192
Period size: 69 Copynumber: 1.9 Consensus size: 67
1548671 TTCAAATAAG
* * * * *
1548681 AAAAGGCAAAACTACGTCGTTTTGATAAATGTTTACCTTTTTAAAGTTAAAAGTCAAAATCATTA
1 AAAAGACAAAACTACGTCATTTTGATAAATGTTTA-CTTATT-AAGTTAAAAGGCAAAACCATTA
1548746 AGTT
64 AGTT
*
1548750 AAAAGACAAAATTACGTCATTTTGATAAATGTTTACTTATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGACAAAACTACGTCATTTTGATAAATGTTTACTTATTAAGTTAAAAGGCAAAACCATTA
1548813 TATTGTCTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 20 0.35
68 5 0.09
69 32 0.56
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (67 bp):
AAAAGACAAAACTACGTCATTTTGATAAATGTTTACTTATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:1556411 original size:242 final size:243
Alignment explanation
Indices: 1555980--1556468 Score: 881
Period size: 242 Copynumber: 2.0 Consensus size: 243
1555970 TCTACGTGCA
* *
1555980 TAAATTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAATCTTCATATTGCAATGGAGAA
1 TAAACTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAAGCTTCATATTGCAATGGAGAA
*
1556045 AGTCAGGAACACAAAATTACATATACATATTCATTTCAATTTAGAAGATTCACACAATGTCAGGC
66 AGTCAGAAACACAAAATTACATATACATATTCATTTCAATTTAGAAGATTCACACAATGTCAGGC
* * *
1556110 TATAAACATGTTAAAACTTTGCAATGCTCCCTCATAATCCTGAACTAGTTCCAGTATTGCTTTCT
131 TATAAAAATGTTAAAACTTTACAATACTCCCTCATAATCCTGAACTAGTTCCAGTATTGCTTTCT
1556175 ATTTGTTTTAATAGCTAGACTCAATCAAATTATGAACAAGTTAATCTT
196 ATTTGTTTTAATAGCTAGACTCAATCAAATTATGAACAAGTTAATCTT
1556223 TAAACTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAAGCTTCATATTGCAATGGAGAA
1 TAAACTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAAGCTTCATATTGCAATGGAGAA
* *
1556288 AGTC-GAAACACGACATTACATATACATATTCATTTCAATTTAGAAGATTCACACAATGTCAGGC
66 AGTCAGAAACACAAAATTACATATACATATTCATTTCAATTTAGAAGATTCACACAATGTCAGGC
*
1556352 TATAAAAATGTTAAAACTTTACAATACTCCCTCATAATCCTGAACTTGTTCCAGTATTGCTTTCT
131 TATAAAAATGTTAAAACTTTACAATACTCCCTCATAATCCTGAACTAGTTCCAGTATTGCTTTCT
*
1556417 ATTTGTTTTAATAGCTAGACTCAATCAAATTATGAACACGTTAATCTT
196 ATTTGTTTTAATAGCTAGACTCAATCAAATTATGAACAAGTTAATCTT
1556465 TAAA
1 TAAA
1556469 TTGCTCCATC
Statistics
Matches: 236, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
242 169 0.72
243 67 0.28
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.31
Consensus pattern (243 bp):
TAAACTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAAGCTTCATATTGCAATGGAGAA
AGTCAGAAACACAAAATTACATATACATATTCATTTCAATTTAGAAGATTCACACAATGTCAGGC
TATAAAAATGTTAAAACTTTACAATACTCCCTCATAATCCTGAACTAGTTCCAGTATTGCTTTCT
ATTTGTTTTAATAGCTAGACTCAATCAAATTATGAACAAGTTAATCTT
Found at i:1565698 original size:171 final size:167
Alignment explanation
Indices: 1565407--1565745 Score: 561
Period size: 171 Copynumber: 2.0 Consensus size: 167
1565397 AGATACTTTC
* *
1565407 AATTGAACTCTAATACTTCTCCTAATAATAAGTAATAAATTAATCTAAATAATTAATTTGACTTC
1 AATTGAACTCTAATACCTCTCCTAATAATAAGTAATAAATTAATATAAATAATTAATTTGACTTC
*
1565472 TAACATAAAACCTTTCACCTAGATAAAATGAAGTATTTCAACTCTTCGCAGAAATCACAAAATAT
66 TAACATAAAACCTTTCACCTAGATAAAATGAAGTATTTCAACTCTTCGCAGAAATCACAAAATAA
* * * *
1565537 GATGTAAACCTCAAATGCATTAGAGAGAGAGGGAGAG
131 GATGTAAACCTCAAACGCATCAGAAAGAGAGAGAGAG
1565574 AATTGAACTCCTAATACCTCTCCTAATAAAATAAGTAATAAATTAATATAAAATAATTAATTTGA
1 AATTGAACT-CTAATACCTCTCCTAAT--AATAAGTAATAAATTAATAT-AAATAATTAATTTGA
* *
1565639 CTTCTAACATAAAACCTTTCACCTAGATGAAATGAAGTATTTCAACTCTTTGCAGAAATCACAAA
62 CTTCTAACATAAAACCTTTCACCTAGATAAAATGAAGTATTTCAACTCTTCGCAGAAATCACAAA
1565704 ATAAGATGTAAACCTCAAACGCATCAGAAAGAGAGAGAGAG
127 ATAAGATGTAAACCTCAAACGCATCAGAAAGAGAGAGAGAG
1565745 A
1 A
1565746 GAGAGACCAG
Statistics
Matches: 159, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
167 9 0.06
168 16 0.10
170 19 0.12
171 115 0.72
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (167 bp):
AATTGAACTCTAATACCTCTCCTAATAATAAGTAATAAATTAATATAAATAATTAATTTGACTTC
TAACATAAAACCTTTCACCTAGATAAAATGAAGTATTTCAACTCTTCGCAGAAATCACAAAATAA
GATGTAAACCTCAAACGCATCAGAAAGAGAGAGAGAG
Found at i:1571150 original size:87 final size:87
Alignment explanation
Indices: 1571004--1571242 Score: 347
Period size: 87 Copynumber: 2.7 Consensus size: 87
1570994 TTGAGTTCTC
* * * * *
1571004 ACTCTTAACGAATTCATATCCC-AGGATTTGGGTGGTCTTATTCAGACGGACTTGATATATTCAC
1 ACTCTTAATGAGTTCATATCCCAAAG-TTTGGGTGGTCCTATTAAGACGGACTTGATATATTCAC
*
1571068 TGACATGTGAGATTGAATTTATT
65 TAACATGTGAGATTGAATTTATT
* * *
1571091 ACTCTTAATTAGTTCATATCCCAAAGTTTGGGTGGTCCTATTGAGACGGACTTGATATATTCACC
1 ACTCTTAATGAGTTCATATCCCAAAGTTTGGGTGGTCCTATTAAGACGGACTTGATATATTCACT
1571156 AACATGTGAGATTGAATTTATT
66 AACATGTGAGATTGAATTTATT
* *
1571178 ACTCTTAATGAGTTCATATCCCAAAGTTTAGGTGGTCCTATTAAGATGGACTTGATGA-ATTCAC
1 ACTCTTAATGAGTTCATATCCCAAAGTTTGGGTGGTCCTATTAAGACGGACTTGAT-ATATTCAC
1571242 T
65 T
1571243 TAATTCAAAT
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
87 134 0.98
88 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (87 bp):
ACTCTTAATGAGTTCATATCCCAAAGTTTGGGTGGTCCTATTAAGACGGACTTGATATATTCACT
AACATGTGAGATTGAATTTATT
Found at i:1577076 original size:17 final size:18
Alignment explanation
Indices: 1577056--1577093 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1577046 TTTTTCAAAA
1577056 GTTAGTTTT-TTTTAATT
1 GTTAGTTTTATTTTAATT
1577073 GTTA-TTTTATTTTAATT
1 GTTAGTTTTATTTTAATT
1577090 -TTAG
1 GTTAG
1577094 AAAACTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (18 bp):
GTTAGTTTTATTTTAATT
Found at i:1585617 original size:100 final size:101
Alignment explanation
Indices: 1585443--1585671 Score: 352
Period size: 100 Copynumber: 2.3 Consensus size: 101
1585433 GGATTGACGA
* *
1585443 ATAAGACCATAATTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAAATGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
1585508 TATGTAAGACCATAATTAGGCTATGGCATTCTGATG
66 TATGTAAGACCATAATTAGGCTATGGCATTCTGATG
* *
1585544 ATAAGACCATAAATGGGTTATGACA-TATGAAGGTAAGACCATGTTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAAATGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
* * * * *
1585608 TATGTAAGACCATAGTTGGGCTATGGTATTTTTATG
66 TATGTAAGACCATAATTAGGCTATGGCATTCTGATG
* *
1585644 ATAAGACCATAACTGGGTTATGGCACTA
1 ATAAGACCATAAATGGGTTATGACACTA
1585672 CGAATATAGA
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
100 91 0.78
101 25 0.22
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (101 bp):
ATAAGACCATAAATGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
TATGTAAGACCATAATTAGGCTATGGCATTCTGATG
Found at i:1587735 original size:29 final size:31
Alignment explanation
Indices: 1587692--1587757 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1587682 CATATTTGAC
* *
1587692 CATGCTTGCTAAAAA-ATTACTCCTTTTGTCA
1 CATGCTTGC-AAAAATATTACTCCATTTGCCA
1587723 CATGCTTGCAAAAATATTACTCCATTTGCCA
1 CATGCTTGCAAAAATATTACTCCATTTGCCA
1587754 CATG
1 CATG
1587758 TATCTATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (31 bp):
CATGCTTGCAAAAATATTACTCCATTTGCCA
Found at i:1588444 original size:27 final size:27
Alignment explanation
Indices: 1588406--1588460 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1588396 TTTTTCATTT
1588406 TGGTACTTAAATT-TTTTTTGTTACAAG
1 TGGTACTTAAATTATTTTTT-TTACAAG
* *
1588433 TGGTATTTAAATTATTTTTTTTCCAAG
1 TGGTACTTAAATTATTTTTTTTACAAG
1588460 T
1 T
1588461 TGATACTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.25, C:0.07, G:0.13, T:0.55
Consensus pattern (27 bp):
TGGTACTTAAATTATTTTTTTTACAAG
Found at i:1593863 original size:29 final size:29
Alignment explanation
Indices: 1593822--1594252 Score: 426
Period size: 29 Copynumber: 15.3 Consensus size: 29
1593812 NNNNNNNTTA
1593822 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
1593851 GGTTAGGGATTTTAATTAAAATAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
1593880 GGTTAGGG-TTTTCATGTAAAATAGGTTAG
1 GGTTAGGGTTTTTAAT-TAAATTAGGTTAG
*
1593909 GGTTAGGGTTTTTAACT-AA--A--TTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* ***
1593932 GGTTAGGGCTTTTAATTAAATTAAAATAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* ***
1593961 GGTAAGGGTTTTTAATTAAATTAAAATAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* **
1593990 GGTAAGGGTTTTTAATTAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* **
1594018 GGTTAGAGTTTTTAATTAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
1594046 GGTTAGAGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
1594075 GGTTAGGGATTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
1594104 GGTTAGAG-TTTTCATGTAAAATAGGTTAG
1 GGTTAGGGTTTTTAAT-TAAATTAGGTTAG
*
1594133 GGTTAGGGTTTTTAACT-AA--A--TTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
****
1594156 GGTTAGGGTTTTTAATTAAATTAAAAAAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
1594185 GGTAAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
1594214 GGTTAGGGATTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1594243 GGTTAGGGTT
1 GGTTAGGGTT
1594253 AGGGTTTTCA
Statistics
Matches: 348, Mismatches: 37, Indels: 34
0.83 0.09 0.08
Matches are distributed among these distances:
23 31 0.09
24 10 0.03
26 4 0.01
28 71 0.20
29 222 0.64
30 10 0.03
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.41
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:1594229 original size:224 final size:224
Alignment explanation
Indices: 1593819--1594233 Score: 740
Period size: 224 Copynumber: 1.9 Consensus size: 224
1593809 NNNNNNNNNN
*
1593819 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGTTAAGGTT
1 TTAGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGTTAAGGTT
*
1593884 AGGGTTTTCATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGGCTTTTAATT
66 AGAGTTTTCATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGGCTTTTAATT
* *
1593949 AAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAA
131 AAATTAAAAAAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGATTTTAATTAAATTAA
1594014 ATTAGGTTAGAGTTTTTAATTAAATTAAA
196 ATTAGGTTAGAGTTTTTAATTAAATTAAA
*
1594043 TTAGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGTTAGGGTT
1 TTAGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGTTAAGGTT
*
1594108 AGAGTTTTCATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGGTTTTTAATT
66 AGAGTTTTCATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGGCTTTTAATT
*** *
1594173 AAATTAAAAAAGGGTAAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAA
131 AAATTAAAAAAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGATTTTAATTAAA
1594234 ATAGGTTAGG
Statistics
Matches: 181, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
224 181 1.00
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.41
Consensus pattern (224 bp):
TTAGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGTTAAGGTT
AGAGTTTTCATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGGCTTTTAATT
AAATTAAAAAAGGGTAAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGATTTTAATTAAATTAA
ATTAGGTTAGAGTTTTTAATTAAATTAAA
Found at i:1594250 original size:35 final size:35
Alignment explanation
Indices: 1594208--1594286 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
1594198 AATTAAATTA
1594208 GGTTAGGGTTAGGGATTTTAAT-TAAAATAGGTTAG
1 GGTTAGGGTTAGGG-TTTTAATGTAAAATAGGTTAG
*
1594243 GGTTAGGGTTAGGGTTTTCATGTAAAATAGGTTAG
1 GGTTAGGGTTAGGGTTTTAATGTAAAATAGGTTAG
1594278 GGTTAGGGT
1 GGTTAGGGT
1594287 GAATGTCTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
34 6 0.14
35 36 0.86
ACGTcount: A:0.27, C:0.01, G:0.35, T:0.37
Consensus pattern (35 bp):
GGTTAGGGTTAGGGTTTTAATGTAAAATAGGTTAG
Found at i:1595958 original size:15 final size:14
Alignment explanation
Indices: 1595930--1595963 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1595920 AATAAATATC
1595930 TAAAAATACATAAA
1 TAAAAATACATAAA
*
1595944 TAAAAATATCTTAAA
1 TAAAAATA-CATAAA
1595959 TAAAA
1 TAAAA
1595964 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAAATACATAAA
Found at i:1596183 original size:22 final size:22
Alignment explanation
Indices: 1596153--1596194 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1596143 ATTTGGAGAT
*
1596153 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
1596175 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
1596195 TTTGAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:1596220 original size:22 final size:22
Alignment explanation
Indices: 1596195--1596265 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
1596185 AATTTGAGAG
* *
1596195 TTTGAGAAAATTTTGGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
1596217 TTTGAGAGAATTTTTGAACGGAA
1 TTTGAGAGAATTTTTGAA-GGAA
1596240 -TTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
*
1596261 ATTGA
1 TTTGA
1596266 TATTGAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.09
22 37 0.82
23 4 0.09
ACGTcount: A:0.38, C:0.01, G:0.27, T:0.34
Consensus pattern (22 bp):
TTTGAGAGAATTTTTGAAGGAA
Found at i:1605633 original size:13 final size:13
Alignment explanation
Indices: 1605615--1605641 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1605605 TATCAAATAT
1605615 TTTCTTATTTTCA
1 TTTCTTATTTTCA
1605628 TTTCTTATTTTCA
1 TTTCTTATTTTCA
1605641 T
1 T
1605642 AAAATTTCAA
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:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCTTATTTTCA
Found at i:1610006 original size:41 final size:41
Alignment explanation
Indices: 1609950--1610029 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
1609940 CCTAATTGGA
1609950 AAAATAATTCCCTTATTCTAATAAACTACAAAAAGATAAGG
1 AAAATAATTCCCTTATTCTAATAAACTACAAAAAGATAAGG
* *
1609991 AAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAA
1 AAAATAATTCCCTTATTCTAATAAACTACAAAAAGATAA
1610030 AATAAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (41 bp):
AAAATAATTCCCTTATTCTAATAAACTACAAAAAGATAAGG
Found at i:1613499 original size:41 final size:41
Alignment explanation
Indices: 1613440--1613521 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1613430 AACTTAATTG
1613440 GGAAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAA
1 GGAAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAA
*
1613481 GGAAAATAATTC-CGTTATTTTAATAAACTACTAAAAGATAA
1 GGAAAATAATTCTC-TTATTCTAATAAACTACTAAAAGATAA
1613522 AATAAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.32
Consensus pattern (41 bp):
GGAAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAA
Found at i:1614816 original size:27 final size:27
Alignment explanation
Indices: 1614769--1614832 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
1614759 AAAACAAATT
* *
1614769 GAAAAAG-AAAATGAGAGTGAGAGTGA
1 GAAAAAGAAAAAAGAAAGTGAGAGTGA
* *
1614795 GAAAAAGAAAAAAGAAATTGAGATTGA
1 GAAAAAGAAAAAAGAAAGTGAGAGTGA
1614822 -AAAAGAGAAAA
1 GAAAA-AGAAAA
1614833 TCAAAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 11 0.34
27 21 0.66
ACGTcount: A:0.62, C:0.00, G:0.27, T:0.11
Consensus pattern (27 bp):
GAAAAAGAAAAAAGAAAGTGAGAGTGA
Found at i:1614845 original size:33 final size:32
Alignment explanation
Indices: 1614770--1614863 Score: 93
Period size: 33 Copynumber: 2.9 Consensus size: 32
1614760 AAACAAATTG
* * ** *
1614770 AAAAAGAAAATGAGAGTGAGAGTGAGAAAAAGA
1 AAAAAGAAATTGAGA-TGAAAAAGAGAAAAACA
*
1614803 AAAAAGAAATTGAGATTGAAAAAGAGAAAATCA
1 AAAAAGAAATTGAGA-TGAAAAAGAGAAAAACA
1614836 AAAAAGAAATTGA-A-GAAAGAAGAGAAAA
1 AAAAAGAAATTGAGATGAAA-AAGAGAAAA
1614864 CGAGTTTGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
30 4 0.08
31 9 0.17
32 1 0.02
33 39 0.74
ACGTcount: A:0.65, C:0.01, G:0.23, T:0.11
Consensus pattern (32 bp):
AAAAAGAAATTGAGATGAAAAAGAGAAAAACA
Found at i:1616798 original size:20 final size:20
Alignment explanation
Indices: 1616773--1616817 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1616763 GTCCTAACCG
1616773 AATTAATTAG-GTCTTAG-TTT
1 AATTAATT-GTGTCTT-GTTTT
1616793 AATTAATTGTGTCTTGTTTT
1 AATTAATTGTGTCTTGTTTT
1616813 AATTA
1 AATTA
1616818 CTTGAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (20 bp):
AATTAATTGTGTCTTGTTTT
Found at i:1619010 original size:21 final size:23
Alignment explanation
Indices: 1618975--1619021 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
1618965 GTGAGCGAGA
* *
1618975 AAAGAACATTGAAAAATAAATTG
1 AAAGAACATTGAAAAAAAAATGG
1618998 AAAGAA-A-TGAAAAAAAAATGG
1 AAAGAACATTGAAAAAAAAATGG
1619019 AAA
1 AAA
1619022 TGAGATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 1 0.05
23 6 0.27
ACGTcount: A:0.68, C:0.02, G:0.15, T:0.15
Consensus pattern (23 bp):
AAAGAACATTGAAAAAAAAATGG
Found at i:1619077 original size:12 final size:12
Alignment explanation
Indices: 1619062--1619134 Score: 53
Period size: 12 Copynumber: 6.1 Consensus size: 12
1619052 GCAAAAAGGG
1619062 ATTGAAAAAGAA
1 ATTGAAAAAGAA
*
1619074 ATTGAAAGAG-A
1 ATTGAAAAAGAA
1619085 A--GAAAAAGAAA
1 ATTGAAAAAG-AA
*
1619096 GAGTGGAAAAAGAA
1 -A-TTGAAAAAGAA
*
1619110 ATTGAAAAAGAG
1 ATTGAAAAAGAA
* *
1619122 TTTGCAAAAGAA
1 ATTGAAAAAGAA
1619134 A
1 A
1619135 CGAGTGAAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 6 0.13
11 3 0.06
12 28 0.60
13 1 0.02
14 2 0.04
15 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (12 bp):
ATTGAAAAAGAA
Found at i:1619095 original size:15 final size:15
Alignment explanation
Indices: 1619077--1619110 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1619067 AAAAGAAATT
1619077 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
1619092 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
1619107 GAAA
1 GAAA
1619111 TTGAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:1623815 original size:20 final size:20
Alignment explanation
Indices: 1623782--1623826 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1623772 TAAATTCATG
1623782 TAATTAAAAAAAGACAC-AAT
1 TAATTAAAAAAAGAC-CTAAT
**
1623802 TAATTAAATTAAGACCTAAT
1 TAATTAAAAAAAGACCTAAT
1623822 TAATT
1 TAATT
1623827 CGGTTGGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (20 bp):
TAATTAAAAAAAGACCTAAT
Found at i:1628152 original size:21 final size:21
Alignment explanation
Indices: 1628128--1628172 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1628118 AAATTCACAT
1628128 ATTTAAAACAAGACAC-AATTA
1 ATTTAAAACAAGAC-CTAATTA
**
1628149 ATTTAAATTAAGACCTAATTA
1 ATTTAAAACAAGACCTAATTA
1628170 ATT
1 ATT
1628173 CGGTTGGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (21 bp):
ATTTAAAACAAGACCTAATTA
Found at i:1631894 original size:36 final size:36
Alignment explanation
Indices: 1631842--1631912 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1631832 CTTACCTTGC
1631842 ATATTTTTCCTCTTCTAGGAATTCTGGGTGGTGCTT
1 ATATTTTTCCTCTTCTAGGAATTCTGGGTGGTGCTT
* * *
1631878 ATATTTTTCCTTTTCTAGGATTTTTGGGTGGTGCT
1 ATATTTTTCCTCTTCTAGGAATTCTGGGTGGTGCT
1631913 CAGCCTTGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.13, C:0.14, G:0.23, T:0.51
Consensus pattern (36 bp):
ATATTTTTCCTCTTCTAGGAATTCTGGGTGGTGCTT
Found at i:1634457 original size:6 final size:6
Alignment explanation
Indices: 1634446--1634476 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1634436 ACCTGCATCC
1634446 TTCACA TTCACA TTCACA TTCACA TTCACA T
1 TTCACA TTCACA TTCACA TTCACA TTCACA T
1634477 AAGAATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (6 bp):
TTCACA
Found at i:1642522 original size:17 final size:17
Alignment explanation
Indices: 1642500--1642532 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1642490 TATATTTTTA
1642500 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
1642517 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
1642533 TATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:1643163 original size:17 final size:18
Alignment explanation
Indices: 1643122--1643163 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1643112 ATAGAAGTTA
1643122 ATAA-ATTTATAAATATT
1 ATAATATTTATAAATATT
*
1643139 ATAGTATTTAT-AATATT
1 ATAATATTTATAAATATT
*
1643156 TTAATATT
1 ATAATATT
1643164 ATTTTATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATAATATTTATAAATATT
Found at i:1646652 original size:20 final size:20
Alignment explanation
Indices: 1646624--1646665 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1646614 ATAAGCTAAT
*
1646624 CCCAGGGAGGATATGCGATC
1 CCCAAGGAGGATATGCGATC
1646644 CCCAAGGAGGATATGCGATC
1 CCCAAGGAGGATATGCGATC
1646664 CC
1 CC
1646666 TTGGCAGTCT
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:0.26, C:0.29, G:0.31, T:0.14
Consensus pattern (20 bp):
CCCAAGGAGGATATGCGATC
Found at i:1646875 original size:110 final size:110
Alignment explanation
Indices: 1646724--1646976 Score: 300
Period size: 110 Copynumber: 2.3 Consensus size: 110
1646714 TGGGGGTTAA
* *
1646724 CCCAATATGGT-TCAGGAAGGATCCACGATCCACAGTCAGAAGAAGAATCATCTATCAATTCAAG
1 CCCAATATGGTCT-AGGAAGGATCCACAATCCATAGTCAGAAGAAGAATCATCTATCAATTCAAG
* * * *
1646788 TGGGATGGTTGA-TTGGGGTTATCCCTAGTGGTGT-GGAATATAGGAT
65 TGGGATGG-TCATTTGGGGTTATCCCCAGT-ATATCGGAATATAGGAT
* * **
1646834 CCCAATATGATCTAGGAAGGATCCACAATCCATAG-CTAGAAGAGGAATCATCTATCGTTTCAAG
1 CCCAATATGGTCTAGGAAGGATCCACAATCCATAGTC-AGAAGAAGAATCATCTATCAATTCAAG
* * *
1646898 TGGGATGGTCATTTGGGGTTATCCCCAGTATATCGGGATGTAGTAT
65 TGGGATGGTCATTTGGGGTTATCCCCAGTATATCGGAATATAGGAT
*
1646944 CCCTATATGGTCTAGTG-AGGATCCACAATCCAT
1 CCCAATATGGTCTAG-GAAGGATCCACAATCCAT
1646977 TGCCCGAATA
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
109 5 0.04
110 116 0.94
111 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (110 bp):
CCCAATATGGTCTAGGAAGGATCCACAATCCATAGTCAGAAGAAGAATCATCTATCAATTCAAGT
GGGATGGTCATTTGGGGTTATCCCCAGTATATCGGAATATAGGAT
Found at i:1648449 original size:4 final size:4
Alignment explanation
Indices: 1648440--1648467 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1648430 GTTCAAAATT
1648440 GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG
1648468 AAATAACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
GATG
Found at i:1652430 original size:29 final size:29
Alignment explanation
Indices: 1652396--1652635 Score: 248
Period size: 29 Copynumber: 8.2 Consensus size: 29
1652386 GTATCGACGC
*
1652396 CCATCGAATATGAAAAGGAATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* **
1652425 TCATCGAATATGAAAAGGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * *
1652454 CCATCGAATATGAAAAAGGATGGCTTCAA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * * * *
1652483 CCATTGATTAGAGAAAAGAGATGGTTTTGA
1 CCATCGAATA-TGAAAAGGGATGGTTTCGA
**
1652513 CCATCGAATATGAAAAGGGATGGGGAT-GA
1 CCATCGAATATGAAAAGGGAT-GGTTTCGA
* **
1652542 CCATCGAATATGGAAAGGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
** *
1652571 CCATCGAATATGAAAAGGGATGGTAACAA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* *
1652600 CCATCGATTAAAGAAAAGGGATGGTTTCGA
1 CCATCGAAT-ATGAAAAGGGATGGTTTCGA
1652630 CCATCG
1 CCATCG
1652636 TTTAGCACAC
Statistics
Matches: 171, Mismatches: 36, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
28 2 0.01
29 123 0.72
30 46 0.27
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGTTTCGA
Found at i:1652602 original size:117 final size:117
Alignment explanation
Indices: 1652396--1652635 Score: 349
Period size: 117 Copynumber: 2.1 Consensus size: 117
1652386 GTATCGACGC
** *
1652396 CCATCGAATATGAAAAGGAATGGTTTCGATCATCGAATATGAAAAGGGATGGTGACGACCATCGA
1 CCATCGAATATGAAAAGGAATGGGATCGACCATCGAATATGAAAAGGGATGGTGACGACCATCGA
* * * *
1652461 ATATGAAAAAGGATGGCTTCAACCATTGATTAGAGAAAAGAGATGGTTTTGA
66 ATATGAAAAAGGATGGCTACAACCATCGATTAAAGAAAAGAGATGGTTTCGA
* *
1652513 CCATCGAATATGAAAAGGGATGGGGAT-GACCATCGAATATGGAAAGGGATGGTGACGACCATCG
1 CCATCGAATATGAAAAGGAAT-GGGATCGACCATCGAATATGAAAAGGGATGGTGACGACCATCG
* *
1652577 AATATGAAAAGGGATGG-TAACAACCATCGATTAAAGAAAAGGGATGGTTTCGA
65 AATATGAAAAAGGATGGCT-ACAACCATCGATTAAAGAAAAGAGATGGTTTCGA
1652630 CCATCG
1 CCATCG
1652636 TTTAGCACAC
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
116 1 0.01
117 106 0.96
118 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (117 bp):
CCATCGAATATGAAAAGGAATGGGATCGACCATCGAATATGAAAAGGGATGGTGACGACCATCGA
ATATGAAAAAGGATGGCTACAACCATCGATTAAAGAAAAGAGATGGTTTCGA
Found at i:1652632 original size:88 final size:88
Alignment explanation
Indices: 1652391--1652635 Score: 255
Period size: 88 Copynumber: 2.8 Consensus size: 88
1652381 ACAAAGTATC
* * *
1652391 GACGCCCATCGAATATGAAAAGGAATGGTTTCGATCATCGAATATGAAAAGGGATGGTGA-CGAC
1 GACGACCATCGAATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGT-ATCGAC
1652455 CATCGAATATGAAAAAGGATGGCT
65 CATCGAATATGAAAAAGGATGGCT
* * * * * * * *
1652479 -TCAACCATTGATTAGAGAAAAGAGATGGTTTTGACCATCGAATATGAAAAGGGATGGGGAT-GA
1 GACGACCATCGAATA-TGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGAT-GGTATCGA
* *
1652542 CCATCGAATATGGAAAGGGATGG-T
64 CCATCGAATATGAAAAAGGATGGCT
** * * * *
1652566 GACGACCATCGAATATGAAAAGGGATGGTAACAACCATCGATTAAAGAAAAGGGATGGTTTCGAC
1 GACGACCATCGAATATGAAAAGGGATGGTTTCGACCATCGAAT-ATGAAAAGGGATGGTATCGAC
1652631 CATCG
65 CATCG
1652636 TTTAGCACAC
Statistics
Matches: 124, Mismatches: 27, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
87 34 0.27
88 88 0.71
89 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (88 bp):
GACGACCATCGAATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGTATCGACC
ATCGAATATGAAAAAGGATGGCT
Found at i:1660562 original size:12 final size:13
Alignment explanation
Indices: 1660538--1660569 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1660528 CATACGTTTC
1660538 AAAAA-AAATAAT
1 AAAAATAAATAAT
1660550 AAAAATAAA-AAT
1 AAAAATAAATAAT
1660562 AAAAATAA
1 AAAAATAA
1660570 TGAACAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAATAAT
Found at i:1669873 original size:85 final size:86
Alignment explanation
Indices: 1669804--1669996 Score: 275
Period size: 85 Copynumber: 2.3 Consensus size: 86
1669794 GGTCACGTTC
* ** * * * *
1669804 TTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA-CTCATG-TTCTTTAGCGGCGCTTTTTCTACG
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT-TTTAGCGGCGCTTTTCCAACA
1669867 AACGCCGCTAAAGAACATGACT
65 AACGCCGCTAAAGAACATGACT
* *
1669889 TTTAGCGGCGC-TTTCCCACAAATGCCGCTAAAGAACATGACTTTTAGCGGTGCTTTTCCAACAA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTTTTCCAACAA
1669953 ACGCCGCTAAAGAACATGACT
66 ACGCCGCTAAAGAACATGACT
1669974 TTTAGCGGCGCTTTTCCCACAAA
1 TTTAGCGGCGCTTTTCCCACAAA
1669997 TGTCGCTATT
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
84 19 0.20
85 65 0.68
86 12 0.12
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (86 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTTTTCCAACAA
ACGCCGCTAAAGAACATGACT
Found at i:1670004 original size:43 final size:43
Alignment explanation
Indices: 1669804--1669996 Score: 266
Period size: 42 Copynumber: 4.5 Consensus size: 43
1669794 GGTCACGTTC
* ** *
1669804 TTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA-CTCATG-TT
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT
* * *
1669845 CTTTAGCGGCGCTTTTTCTACGAACGCCGCTAAAGAACATGACT
1 -TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT
*
1669889 TTTAGCGGCGC-TTTCCCACAAATGCCGCTAAAGAACATGACT
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT
* *
1669931 TTTAGCGGTGCTTTTCCAACAAACGCCGCTAAAGAACATGACT
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT
1669974 TTTAGCGGCGCTTTTCCCACAAA
1 TTTAGCGGCGCTTTTCCCACAAA
1669997 TGTCGCTATT
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
42 68 0.51
43 65 0.49
44 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT
Found at i:1672661 original size:25 final size:25
Alignment explanation
Indices: 1672630--1673304 Score: 490
Period size: 25 Copynumber: 26.9 Consensus size: 25
1672620 TGCTATATTT
*
1672630 TTATGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* *
1672655 TTGTGTATTATGTAAGTTATGT-A-
1 TTATGTATTATGTATGTTATGTAAG
* *
1672678 TTATGTATGTTATGTAAGTTGTGTAAG
1 TTATGTA--TTATGTATGTTATGTAAG
1672705 TTATGTA-TATTGTATGTTATGTAAG
1 TTATGTATTA-TGTATGTTATGTAAG
*
1672730 TTATATATTATGTATGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
1672755 TTATGTA-TATTGTATGTTATGTAAG
1 TTATGTATTA-TGTATGTTATGTAAG
*
1672780 TTATGTATTATGTAAG-TACTGTAAG
1 TTATGTATTATGTATGTTA-TGTAAG
* * *
1672805 TAATGTAAGTTATGTAT-AT-TGTATG
1 TTATGT-A-TTATGTATGTTATGTAAG
* *
1672830 TTATGTAAGTTA--TATATTATGTATG
1 TTATGT-A-TTATGTATGTTATGTAAG
* *
1672855 TTATGTAAGTTATGTAT-AT-TGTATG
1 TTATGT-A-TTATGTATGTTATGTAAG
*
1672880 TTATGGAAGTTATGTA--TTATGTAAG
1 TTAT-GTA-TTATGTATGTTATGTAAG
* * *
1672905 -TACTGTAAGTAAAGTAAGTTATGTAAG
1 TTA-TGT-A-TTATGTATGTTATGTAAG
* * *
1672932 TAATGTACTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* * *
1672957 TAATGTACTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* * *
1672982 TAATGTACTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* * *
1673007 TAATGTACTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* * *
1673032 TAATGTACTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* * *
1673057 TAATGTACTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* * *
1673082 TAATGTACTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* *
1673107 TAATGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* ** * *
1673132 TTGTGGCTTCTGTAAGTTATGT-A-
1 TTATGTATTATGTATGTTATGTAAG
* ** *
1673155 TTATGTGTGTTATGTAAATTGTGTAAG
1 TTA--TGTATTATGTATGTTATGTAAG
1673182 TTATGTA-TATTGTATGTTATGTAAG
1 TTATGTATTA-TGTATGTTATGTAAG
1673207 TTATGTATTATGTA--TTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* * *
1673230 -TACTGTAAGTAAAGTAAGTTATGTAAG
1 TTA-TGT-A-TTATGTATGTTATGTAAG
* *
1673257 TAATGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTATGTTATGTAAG
* * *
1673282 TAATGTATTATGTAAGTTGTGTA
1 TTATGTATTATGTATGTTATGTA
1673305 TAATGTAAGT
Statistics
Matches: 569, Mismatches: 46, Indels: 70
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.00
23 23 0.04
24 16 0.03
25 468 0.82
26 13 0.02
27 45 0.08
28 2 0.00
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (25 bp):
TTATGTATTATGTATGTTATGTAAG
Found at i:1672691 original size:50 final size:51
Alignment explanation
Indices: 1672631--1673403 Score: 510
Period size: 50 Copynumber: 15.5 Consensus size: 51
1672621 GCTATATTTT
*
1672631 TATGTATTATGTAAGTTATGTAAGTTGTGT-A-TTATGTAAGTTATGT-A-T
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGT-AGTTATGTAAGT
*
1672679 TATGTATGTTATGTAAGTTGTGTAAGTTATGT-A--TATTGTATGTTATGTAAGT
1 TATGTA--TTATGTAAGTTATGTAAGTTATGTAAGTTA-TGTA-GTTATGTAAGT
* *
1672731 TATATATTATGTATGTTATGTAAGTTATGT-A--TATTGTATGTTATGTAAGT
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTA-TGTA-GTTATGTAAGT
* *
1672781 TATGTATTATGTAAG-TACTGTAAGTAATGTAAGTTATGTA--TATTGTATGT
1 TATGTATTATGTAAGTTA-TGTAAGTTATGTAAGTTATGTAGTTA-TGTAAGT
* * *
1672831 TATGTAAGTTATAT-A-TTATGTATGTTATGTAAGTTATGTA--TATTGTATGT
1 TATGT-A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAGTTA-TGTAAGT
* * *
1672881 TATGGAAGTTATGT-A-TTATGTAAG-TACTGTAAGTAAAGTAAGTTATGTAAGT
1 TAT-GTA-TTATGTAAGTTATGTAAGTTA-TGTAAGTTATGT-AGTTATGTAAGT
* * * *
1672933 AATGTACTATGTAAGTTATGTAAGTAATGT-A-CTATGTAAGTTATGTAAGT
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGT-AGTTATGTAAGT
* * * *
1672983 AATGTACTATGTAAGTTATGTAAGTAATGT-A-CTATGTAAGTTATGTAAGT
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGT-AGTTATGTAAGT
* * * *
1673033 AATGTACTATGTAAGTTATGTAAGTAATGT-A-CTATGTAAGTTATGTAAGT
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGT-AGTTATGTAAGT
* * *
1673083 AATGTACTATGTAAGTTATGTAAGTAATGT-A-TTATGTAAGTTATGTAAGT
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGT-AGTTATGTAAGT
* ** * ** * *
1673133 TGTGGCTTCTGTAAGTTATGT-A-TTATGTGTGTTATGTAAATTGTGTAAGT
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGT-AGTTATGTAAGT
*
1673183 TATGTA-TATTGTATGTTATGTAAGTTATGT-A-TTATGTA-TTATGTAAG-
1 TATGTATTA-TGTAAGTTATGTAAGTTATGTAAGTTATGTAGTTATGTAAGT
*
1673230 TACTGTA--A-GTAA---A-GTAAGTTATGTAAGTAATGTA-TTATGTAAGT
1 TA-TGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGTAGTTATGTAAGT
* * * *
1673274 TATGTAAGTAATGT-A-TTATGTAAGTTGTGT-A-TAATGTAAGTTA-GGAAGAT
1 TATGT-A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGT-AGTTATGTAAG-T
* * *
1673324 TATGTATTATGTAAGTTATTTAAGTTATGTAGGCTATGTA-TTATGTAAGTTAT
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGTAGTTATGTAAG---T
* *
1673377 TATGTTATTATATAAGTTATGCAAGTT
1 TATG-TATTATGTAAGTTATGTAAGTT
1673404 TATATATAAG
Statistics
Matches: 618, Mismatches: 57, Indels: 94
0.80 0.07 0.12
Matches are distributed among these distances:
41 11 0.02
42 2 0.00
43 18 0.03
44 3 0.00
45 3 0.00
47 5 0.01
48 36 0.06
49 21 0.03
50 426 0.69
51 18 0.03
52 45 0.07
53 11 0.02
54 19 0.03
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (51 bp):
TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGTAGTTATGTAAGT
Found at i:1672775 original size:109 final size:109
Alignment explanation
Indices: 1672630--1673389 Score: 572
Period size: 109 Copynumber: 7.0 Consensus size: 109
1672620 TGCTATATTT
* * *
1672630 TTATGTA--TTATGTAAGTTATGTA-AGTTGTGTATTATGTAAGTTATGTATTATGTATGTTATG
1 TTATGTATGTTATGTAAGTTATGTATA-TTGTATGTTATGTAAGTTATGTATTATGTAAGTTATG
*
1672692 TAAGTTGTGTAAGTTATGTATATTGTATGTTATGTAAGTTATATA
65 TAAGTTATGTAAGTTATGTATATTGTATGTTATGTAAGTTATATA
1672737 TTATGTATGTTATGTAAGTTATGTATATTGTATGTTATGTAAGTTATGTATTATGTAAG-TACTG
1 TTATGTATGTTATGTAAGTTATGTATATTGTATGTTATGTAAGTTATGTATTATGTAAGTTA-TG
*
1672801 TAAGTAATGTAAGTTATGTATATTGTATGTTATGTAAGTTATATA
65 TAAGTTATGTAAGTTATGTATATTGTATGTTATGTAAGTTATATA
*
1672846 TTATGTATGTTATGTAAGTTATGTATATTGTATGTTATGGAAGTTATGTATTATGTAAG-TACTG
1 TTATGTATGTTATGTAAGTTATGTATATTGTATGTTATGTAAGTTATGTATTATGTAAGTTA-TG
* * *
1672910 TAAGTAAAGTAAGTTATGTA-A--GTAATGTACTATGTAAGTTATGTA
65 TAAGTTATGTAAGTTATGTATATTGT-ATGT--TATGTAAGTTATATA
1672955 --A-GTAATGTACTATGTAAGTTATGTA-A--GTAATGTACTATGTAAGTTATGTA--A-GTAAT
1 TTATGT-ATGT--TATGTAAGTTATGTATATTGT-ATGT--TATGTAAGTTATGTATTATGTAA-
* * * *
1673011 GTACTATGTAAGTTATGTAAGTAATGTACTA-TGTAAGTTATGTAAGTAATGTA
59 GT--TATGTAAGTTATGTAAGTTATGTA-TATTGTATGTTATGTAAGTTATATA
* * * * *
1673064 CTATGTAAGTTATGTAAGTAATGTACTA-TGTAAGTTATGTAAGTAATGTATTATGTAAGTTATG
1 TTATGTATGTTATGTAAGTTATGTA-TATTGTATGTTATGTAAGTTATGTATTATGTAAGTTATG
* * * * *
1673128 TAAGTTGTGGCTTCTGTAAGTTATGTAT-TATGTGTGTTATGTAAATTGTGTAA
65 TAA------G-TTATGTAAGTTATGTATAT-TGTATGTTATGTAAGTTATAT-A
* * * *
1673181 GTTATGTAT-AT-TGTATGTTATGTA-AGT-TATGTATTATGT-A-TTATGTAAGTACTGTAAGT
1 -TTATGTATGTTATGTAAGTTATGTATATTGTATG--TTATGTAAGTTATGT-ATTA-TGTAAGT
* * * *
1673240 AAAGTAAGTTATGTAAGTAATGTAT-TATGTAAGTTATGTAAG-----TA
61 TATGTAAGTTATGTAAGTTATGTATAT-TGTATGTTATGTAAGTTATATA
* * * * *
1673284 --ATGTA--TTATGTAAGTTGTGTATAATGTAAGTTA-GGAAGATTATGTATTATGTAAGTTATT
1 TTATGTATGTTATGTAAGTTATGTATATTGTATGTTATGTAAG-TTATGTATTATGTAAGTTATG
* * * *
1673344 TAAGTTATGTAGGCTATGTAT-TATGTAAGTTAT-TATGTTATTATA
65 TAAGTTATGTAAGTTATGTATAT-TGTATGTTATGTAAGTTA-TATA
1673389 T
1 T
1673390 AAGTTATGCA
Statistics
Matches: 541, Mismatches: 54, Indels: 117
0.76 0.08 0.16
Matches are distributed among these distances:
99 5 0.01
100 58 0.11
101 5 0.01
102 9 0.02
103 1 0.00
104 1 0.00
105 2 0.00
106 10 0.02
107 22 0.04
108 4 0.01
109 312 0.58
110 4 0.01
111 15 0.03
112 10 0.02
114 9 0.02
115 7 0.01
116 59 0.11
117 2 0.00
118 6 0.01
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.46
Consensus pattern (109 bp):
TTATGTATGTTATGTAAGTTATGTATATTGTATGTTATGTAAGTTATGTATTATGTAAGTTATGT
AAGTTATGTAAGTTATGTATATTGTATGTTATGTAAGTTATATA
Found at i:1673387 original size:20 final size:19
Alignment explanation
Indices: 1673358--1673396 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1673348 TTATGTAGGC
*
1673358 TATGTATTATGTAAGTTAT
1 TATGTATTATATAAGTTAT
1673377 TATGTTATTATATAAGTTAT
1 TATG-TATTATATAAGTTAT
1673397 GCAAGTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (19 bp):
TATGTATTATATAAGTTAT
Found at i:1673446 original size:16 final size:16
Alignment explanation
Indices: 1673422--1673462 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1673412 AGTTTATATA
*
1673422 TTATATATTATTTAAG
1 TTATATATTATGTAAG
*
1673438 TTATGTATTATGTAAG
1 TTATATATTATGTAAG
1673454 TTTATATAT
1 -TTATATAT
1673463 AAGTTATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (16 bp):
TTATATATTATGTAAG
Found at i:1673474 original size:12 final size:12
Alignment explanation
Indices: 1673399--1673467 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 12
1673389 TAAGTTATGC
1673399 AAGTTTATATAT
1 AAGTTTATATAT
1673411 AAGTTTATATAT
1 AAGTTTATATAT
* * *
1673423 TA-TATATTATTT
1 AAGTTTA-TATAT
*
1673435 AAGTTATGTATTATGT
1 AAG-T-T-TA-TATAT
1673451 AAGTTTATATAT
1 AAGTTTATATAT
1673463 AAGTT
1 AAGTT
1673468 ATGATATGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 3 0.07
12 27 0.60
13 2 0.04
14 2 0.04
15 1 0.02
16 10 0.22
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (12 bp):
AAGTTTATATAT
Found at i:1673550 original size:17 final size:18
Alignment explanation
Indices: 1673514--1673551 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1673504 GATATGATTG
1673514 ATAAATTTTGAAAAAAAT
1 ATAAATTTTGAAAAAAAT
*
1673532 ATAAATTTT-AAAAATAT
1 ATAAATTTTGAAAAAAAT
1673549 ATA
1 ATA
1673552 TATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
ATAAATTTTGAAAAAAAT
Found at i:1673566 original size:15 final size:15
Alignment explanation
Indices: 1673526--1673568 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1673516 AAATTTTGAA
* *
1673526 AAAAATATAAATTTT
1 AAAAATATATATATT
1673541 AAAAATATATATATT
1 AAAAATATATATATT
*
1673556 AAAAATGTATATA
1 AAAAATATATATA
1673569 AATATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AAAAATATATATATT
Found at i:1674103 original size:31 final size:31
Alignment explanation
Indices: 1674061--1674145 Score: 118
Period size: 31 Copynumber: 2.7 Consensus size: 31
1674051 CATGGTTGAT
* *
1674061 TTAGCAGCAAAAAACAATAAAAGGTACCATC
1 TTAGTAGCAAAAACCAATAAAAGGTACCATC
*
1674092 TTAGTAGCAAAAACCAATAGAAGGTACCATC
1 TTAGTAGCAAAAACCAATAAAAGGTACCATC
1674123 TTAGCT-GCAAAAACCAATTAAAA
1 TTAG-TAGCAAAAACCAA-TAAAA
1674146 TCCTTTATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
31 43 0.90
32 5 0.10
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (31 bp):
TTAGTAGCAAAAACCAATAAAAGGTACCATC
Found at i:1674667 original size:32 final size:31
Alignment explanation
Indices: 1674605--1674667 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 31
1674595 CATTAACCAA
* *
1674605 ATACCAAATTAAAACAGTCCCAACTACAAAT
1 ATACCAAATTAAAACAGTCCAAAATACAAAT
*
1674636 ATACCAAATTTAAAAACTGTCCAAAAT-CAAAT
1 ATACCAAA-TT-AAAACAGTCCAAAATACAAAT
1674668 GTAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 8 0.30
32 7 0.26
33 12 0.44
ACGTcount: A:0.52, C:0.22, G:0.03, T:0.22
Consensus pattern (31 bp):
ATACCAAATTAAAACAGTCCAAAATACAAAT
Found at i:1676213 original size:47 final size:47
Alignment explanation
Indices: 1676122--1676213 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 47
1676112 GAAATTTGAT
* * * *
1676122 GTATAGTGCTTGTATTTTTCTTAAAATTTATAGTAGGAACTTAATCC
1 GTATAGTGCTTGTATTTTTCTTAAAATTCAAACTAGAAACTTAATCC
* *
1676169 GTATAGTGTTTGTATTTTTC-TAAAACTTCAAACTAGAAATTTAAT
1 GTATAGTGCTTGTATTTTTCTTAAAA-TTCAAACTAGAAACTTAAT
1676214 TATGTAAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 5 0.13
47 33 0.87
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.45
Consensus pattern (47 bp):
GTATAGTGCTTGTATTTTTCTTAAAATTCAAACTAGAAACTTAATCC
Found at i:1676666 original size:21 final size:22
Alignment explanation
Indices: 1676624--1676671 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1676614 TAACTCTTAC
1676624 ACCATAATCCCTAAACCCCTAA
1 ACCATAATCCCTAAACCCCTAA
* * *
1676646 CCCATATTCCTTAAA-CCCTAA
1 ACCATAATCCCTAAACCCCTAA
1676667 ACCAT
1 ACCAT
1676672 GAAACATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.23
Consensus pattern (22 bp):
ACCATAATCCCTAAACCCCTAA
Found at i:1676700 original size:39 final size:38
Alignment explanation
Indices: 1676657--1676738 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 38
1676647 CCATATTCCT
* *
1676657 TAAACCCTAAACCATGAAACATATATAAACCCTAAACCC
1 TAAACCCTAAACCATAAAACATATATAAACCATAAA-CC
* * *
1676696 TAAACCCTGAATCATAAAACATATATAAACTATAAACC
1 TAAACCCTAAACCATAAAACATATATAAACCATAAACC
1676734 TAAAC
1 TAAAC
1676739 TTCAACCCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
38 7 0.18
39 31 0.82
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (38 bp):
TAAACCCTAAACCATAAAACATATATAAACCATAAACC
Found at i:1677281 original size:101 final size:100
Alignment explanation
Indices: 1677109--1677289 Score: 224
Period size: 101 Copynumber: 1.8 Consensus size: 100
1677099 GTCGCTAATT
* *
1677109 CTTGATTTTTGCGGCATTTTTAGGAATGCGCCACTAATGTCTCTAAATCTGAAAAAGAAAACATC
1 CTTGACTTTTGCGGCATTTTTAGGAATGCGCCACTAATGTCTCTAAAACTGAAAAAGAAAACATC
*
1677174 GTCGTTTGCCTAAAACTATTGTGGCACTTCTAAGG
66 GCCGTTTGCCTAAAACTATTGTGGCACTTCTAAGG
* * * * *
1677209 CTTGACTTTTGCGGCGTTTTTTTGTGAA-GCGCCATTAATGTCTCTAAAACT-CAACAGAAGAAC
1 CTTGACTTTTGCGGC-ATTTTTAG-GAATGCGCCACTAATGTCTCTAAAACTGAAAAAGAA-AAC
*
1677272 GA-CGCCGTTTGCTTAAAA
63 -ATCGCCGTTTGCCTAAAA
1677290 ATTTTTGCGG
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
100 20 0.29
101 44 0.65
102 4 0.06
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (100 bp):
CTTGACTTTTGCGGCATTTTTAGGAATGCGCCACTAATGTCTCTAAAACTGAAAAAGAAAACATC
GCCGTTTGCCTAAAACTATTGTGGCACTTCTAAGG
Found at i:1697241 original size:12 final size:12
Alignment explanation
Indices: 1697224--1697248 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1697214 GCTGTTTGGT
1697224 TTAGGGTGTCAG
1 TTAGGGTGTCAG
1697236 TTAGGGTGTCAG
1 TTAGGGTGTCAG
1697248 T
1 T
1697249 GCAGTGAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.40, T:0.36
Consensus pattern (12 bp):
TTAGGGTGTCAG
Done.