Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 190 of 205
Found at i:56437822 original size:41 final size:41
Alignment explanation
Indices: 56437787--56437945 Score: 221
Period size: 41 Copynumber: 3.9 Consensus size: 41
56437777 GTGAAATTGT
**
56437787 TCAGACTATACGTCTTGCAGGCTAAGTGCCGGTGAATTGAA
1 TCAGACTATACGTCCAGCAGGCTAAGTGCCGGTGAATTGAA
* *
56437828 TCGGACTATACGTCCAGCAAGCTAAGTGCCGGTGAATTGAA
1 TCAGACTATACGTCCAGCAGGCTAAGTGCCGGTGAATTGAA
* * *
56437869 TCAGATTATATGTCCAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATACGTCCAGCAGGCTAAGTGCCGGTGAATTGAA
* *
56437910 TCAGGCTATA-GGCCTAGCAGGCTAAGTGCCGGTGAA
1 TCAGACTATACGTCC-AGCAGGCTAAGTGCCGGTGAA
56437946 CGAAATTAGA
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 3 0.03
41 102 0.97
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
TCAGACTATACGTCCAGCAGGCTAAGTGCCGGTGAATTGAA
Found at i:56437960 original size:41 final size:41
Alignment explanation
Indices: 56437787--56437988 Score: 180
Period size: 41 Copynumber: 4.9 Consensus size: 41
56437777 GTGAAATTGT
* * * *
56437787 TCAGACTATACGTCTTGCAGGCTAAGTGCCGGTGAATTGAA
1 TCAGACTATAGGCCTAGCAGGCTAAGTGCCGGTGAATCGAA
* * * *
56437828 TCGGACTATACGTCC-AGCAAGCTAAGTGCCGGTGAATTGAA
1 TCAGACTATA-GGCCTAGCAGGCTAAGTGCCGGTGAATCGAA
* *
56437869 TCAGATTATATGTCC-AGCAGGCTAAGTGCCGGTGAA-CTGAA
1 TCAGACTATA-GGCCTAGCAGGCTAAGTGCCGGTGAATC-GAA
*
56437910 TCAGGCTATAGGCCTAGCAGGCTAAGTGCCGGTGAA-CGAAA
1 TCAGACTATAGGCCTAGCAGGCTAAGTGCCGGTGAATCG-AA
* * * * *
56437951 TTAGACTATAAGTCTATCAGG-TGAAGTGCCAGTGAATC
1 TCAGACTATAGGCCTAGCAGGCT-AAGTGCCGGTGAATC
56437989 TGTTTAAATT
Statistics
Matches: 135, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
40 5 0.04
41 128 0.95
42 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (41 bp):
TCAGACTATAGGCCTAGCAGGCTAAGTGCCGGTGAATCGAA
Found at i:56437978 original size:82 final size:82
Alignment explanation
Indices: 56437787--56437986 Score: 221
Period size: 82 Copynumber: 2.4 Consensus size: 82
56437777 GTGAAATTGT
* * *
56437787 TCAGACTATACGTCT-TGCAGGCTAAGTGCCGGTGAATTGAATCGGACTATACGTCCAGCAAGCT
1 TCAGACTATAAGTCTAT-CAGGCTAAGTGCCGGTGAACTGAATCGGACTATACGGCCAGCAAGCT
*
56437851 AAGTGCCGGTGAATTGAA
65 AAGTGCCGGTGAATCGAA
* * * * *
56437869 TCAGATTATATGTCCAGCAGGCTAAGTGCCGGTGAACTGAATCAGG-CTATA-GGCCTAGCAGGC
1 TCAGACTATAAGTCTATCAGGCTAAGTGCCGGTGAACTGAATC-GGACTATACGGCC-AGCAAGC
56437932 TAAGTGCCGGTGAA-CGAAA
64 TAAGTGCCGGTGAATCG-AA
* *
56437951 TTAGACTATAAGTCTATCAGG-TGAAGTGCCAGTGAA
1 TCAGACTATAAGTCTATCAGGCT-AAGTGCCGGTGAA
56437987 TCTGTTTAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
81 5 0.05
82 92 0.93
83 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (82 bp):
TCAGACTATAAGTCTATCAGGCTAAGTGCCGGTGAACTGAATCGGACTATACGGCCAGCAAGCTA
AGTGCCGGTGAATCGAA
Found at i:56438244 original size:37 final size:37
Alignment explanation
Indices: 56438174--56438293 Score: 143
Period size: 37 Copynumber: 3.5 Consensus size: 37
56438164 TTTAAATGTG
*
56438174 TATATGTATGCATTTGGCATAGGTGGATAT-A---TA
1 TATATGTATGCATTCGGCATAGGTGGATATAAGTGTA
56438207 T-T-TGTATGCATTCGGCATAGGTGGATATAAGTGTA
1 TATATGTATGCATTCGGCATAGGTGGATATAAGTGTA
* *
56438242 TATATGTCTGCATTCGGCATAGGTGGGTATAAGTG-A
1 TATATGTATGCATTCGGCATAGGTGGATATAAGTGTA
56438278 -ATATG--TGCATTCGGCA
1 TATATGTATGCATTCGGCA
56438294 CTTATAGTTG
Statistics
Matches: 78, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
31 25 0.32
32 2 0.03
33 12 0.15
35 8 0.10
36 2 0.03
37 29 0.37
ACGTcount: A:0.27, C:0.10, G:0.28, T:0.36
Consensus pattern (37 bp):
TATATGTATGCATTCGGCATAGGTGGATATAAGTGTA
Found at i:56440391 original size:6 final size:6
Alignment explanation
Indices: 56440380--56440413 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
56440370 TGCAGTAATC
*
56440380 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTT ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTT
56440414 AATGAAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
ATTTTA
Found at i:56441120 original size:20 final size:20
Alignment explanation
Indices: 56441095--56441134 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56441085 TGTTGCACTG
56441095 CTTTACTATTATGCACAGGT
1 CTTTACTATTATGCACAGGT
56441115 CTTTACTATTATGCACAGGT
1 CTTTACTATTATGCACAGGT
56441135 TCTTCTGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (20 bp):
CTTTACTATTATGCACAGGT
Found at i:56452368 original size:21 final size:20
Alignment explanation
Indices: 56452344--56452386 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
56452334 TAACTAGTTT
56452344 AATTGAAAAGAT-TATTAAAAA
1 AATTGAAAA-ATATA-TAAAAA
*
56452365 AATTTAAAAATATATAAAAA
1 AATTGAAAAATATATAAAAA
56452385 AA
1 AA
56452387 CAGAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AATTGAAAAATATATAAAAA
Found at i:56461739 original size:19 final size:19
Alignment explanation
Indices: 56461717--56461767 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
56461707 GGGTCTTTTT
*
56461717 ATGAAATTTAATGCATATG-
1 ATGAAATGTAATGC-TATGA
56461736 ATGAAATGTAATGCTATGA
1 ATGAAATGTAATGCTATGA
56461755 ATGAAATG-AATGC
1 ATGAAATGTAATGC
56461768 AAAAAGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.30
19 21 0.70
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (19 bp):
ATGAAATGTAATGCTATGA
Found at i:56463579 original size:9 final size:8
Alignment explanation
Indices: 56463544--56463590 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 8
56463534 TAAAATGATA
56463544 AATAATA-
1 AATAATAT
*
56463551 AATAATAG
1 AATAATAT
*
56463559 AATACTAT
1 AATAATAT
56463567 AATAATGAT
1 AATAAT-AT
56463576 AATAATATT
1 AATAATA-T
56463585 AATAAT
1 AATAAT
56463591 GTAAAATAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 7 0.21
8 12 0.35
9 15 0.44
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (8 bp):
AATAATAT
Found at i:56474930 original size:3 final size:3
Alignment explanation
Indices: 56474924--56474976 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
56474914 TGACGACGAC
56474924 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
56474972 GAT GA
1 GAT GA
56474977 ATGACTGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:56484505 original size:2 final size:2
Alignment explanation
Indices: 56484498--56484541 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
56484488 GTACATGTTA
* * * *
56484498 AG AG AG AG AG AG AG AG GG AG GG AG GG AG GG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56484540 AG
1 AG
56484542 CAAATTTTCT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56488758 original size:112 final size:112
Alignment explanation
Indices: 56488561--56488790 Score: 451
Period size: 112 Copynumber: 2.1 Consensus size: 112
56488551 TATCAACAGC
56488561 AAGAACTTGAATCTAGCCCAGTACAAAGGTTTGCAGCCATTATTAAGGGGAAAAAAGATAAAAGG
1 AAGAACTTGAATCTAGCCCAGTACAAAGGTTTGCAGCCATTATTAAGGGGAAAAAAGATAAAAGG
56488626 GGAAAAGACTTAAATGCAAGATGTAGTTTCCACAGTTTTCAGTATGA
66 GGAAAAGACTTAAATGCAAGATGTAGTTTCCACAGTTTTCAGTATGA
56488673 AAGAACTTGAATCTAGCCCAGTACAAAGGTTTGCAGCCATTATTAAGGGGAAAAAAGATAAAAGG
1 AAGAACTTGAATCTAGCCCAGTACAAAGGTTTGCAGCCATTATTAAGGGGAAAAAAGATAAAAGG
56488738 GGAAAAGACTTAAATGCAAGATGTAGTTTCCACAGTTTTCAGTATGA
66 GGAAAAGACTTAAATGCAAGATGTAGTTTCCACAGTTTTCAGTATGA
*
56488785 AGGAAC
1 AAGAAC
56488791 AACTAACTAG
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 117 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (112 bp):
AAGAACTTGAATCTAGCCCAGTACAAAGGTTTGCAGCCATTATTAAGGGGAAAAAAGATAAAAGG
GGAAAAGACTTAAATGCAAGATGTAGTTTCCACAGTTTTCAGTATGA
Found at i:56491978 original size:4 final size:4
Alignment explanation
Indices: 56491969--56491995 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
56491959 CTTGGGGTTG
56491969 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
56491996 ATATTTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:56495567 original size:152 final size:153
Alignment explanation
Indices: 56495287--56495595 Score: 575
Period size: 152 Copynumber: 2.0 Consensus size: 153
56495277 CAAGTCCGGG
56495287 TAACGAAGTTCATCATTACCAACCAATTCTCGCTATCAAGTTAAATACTTGAGGTTTAAGGTTTA
1 TAACGAAGTTCATCATT---AACCAATTCTCGCTATCAAGTTAAATACTTGAGGTTTAAGGTTTA
*
56495352 AAGAAATGGTAGAATTTCATGAAAACTGATGAATGCCAGGGAGATAACTGAGAATCTGTGAGTTT
63 AAGAAATGGTAGAATTTCATGAAAACTGATAAATGCCAGGGAGATAACTGAGAATCTGTGAGTTT
56495417 TAATAACTAGTGACTAGAATGTTGTT
128 TAATAACTAGTGACTAGAATGTTGTT
56495443 TAACGAAGTTCATCATT-ACCAATTCTCGCTATCAAGTTAAATACTTGAGGTTTAAGGTTTAAAG
1 TAACGAAGTTCATCATTAACCAATTCTCGCTATCAAGTTAAATACTTGAGGTTTAAGGTTTAAAG
56495507 AAATGGTAGAATTTCATGAAAACTGATAAATGCCAGGGAGATAACTGAGAATCTGTGAGTTTTAA
66 AAATGGTAGAATTTCATGAAAACTGATAAATGCCAGGGAGATAACTGAGAATCTGTGAGTTTTAA
56495572 TAACTAGTGACTAGAATGTTGTT
131 TAACTAGTGACTAGAATGTTGTT
56495595 T
1 T
56495596 TGCAGGTTAC
Statistics
Matches: 152, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
152 135 0.89
156 17 0.11
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (153 bp):
TAACGAAGTTCATCATTAACCAATTCTCGCTATCAAGTTAAATACTTGAGGTTTAAGGTTTAAAG
AAATGGTAGAATTTCATGAAAACTGATAAATGCCAGGGAGATAACTGAGAATCTGTGAGTTTTAA
TAACTAGTGACTAGAATGTTGTT
Found at i:56495836 original size:26 final size:26
Alignment explanation
Indices: 56495790--56495840 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
56495780 TAGAAGTACA
*
56495790 TAATTTTAGTTGCTTATTCTACAAGT
1 TAATTTTAGTTGCTTAGTCTACAAGT
*
56495816 TAATTTTAGCTT-TTTAGTCTACAAG
1 TAATTTTAG-TTGCTTAGTCTACAAG
56495841 AATAAAGCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (26 bp):
TAATTTTAGTTGCTTAGTCTACAAGT
Found at i:56501054 original size:102 final size:102
Alignment explanation
Indices: 56500878--56501067 Score: 254
Period size: 102 Copynumber: 1.9 Consensus size: 102
56500868 CTGGTTTCAC
* * * * * * * *
56500878 TATCATCTAATTTCTTTAAATTATTAAACTAGAATTCTTTTCATTTTCAAAGAGATACAGAAGCA
1 TATCATCTAATTCCTTAAAATCATTAAACTAAAAATCTTTCCATTGTCAAAGAGATAAAGAAGCA
*
56500943 TAAATACGGCTAAATGGCAAGAACACGACCGCTAGTT
66 TAAATACGGCTAAATGACAAGAACACGACCGCTAGTT
* * * **
56500980 TATCATCTAATTCCTTAAAATCATTAAGCTAAAAATCTTTCCATTGTCAATGAGATAAAGATGTT
1 TATCATCTAATTCCTTAAAATCATTAAACTAAAAATCTTTCCATTGTCAAAGAGATAAAGAAGCA
56501045 TAAATACGGCTAAATGACAAGAA
66 TAAATACGGCTAAATGACAAGAA
56501068 TGTTCATGTA
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
102 74 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (102 bp):
TATCATCTAATTCCTTAAAATCATTAAACTAAAAATCTTTCCATTGTCAAAGAGATAAAGAAGCA
TAAATACGGCTAAATGACAAGAACACGACCGCTAGTT
Found at i:56507627 original size:16 final size:16
Alignment explanation
Indices: 56507606--56507643 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
56507596 TTTGGTTCGC
56507606 TGTAATGGAATAGAA-G
1 TGTAATGGAATA-AAGG
56507622 TGTAATGGAATAAAGG
1 TGTAATGGAATAAAGG
56507638 TGTAAT
1 TGTAAT
56507644 AGGTAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAAAGG
Found at i:56507707 original size:44 final size:46
Alignment explanation
Indices: 56507625--56507717 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
56507615 ATAGAAGTGT
*
56507625 AATGGAATAAAGGTGTAATAGGTAATTCTTCTGTTTGGTTGAATGG
1 AATGGAATAAAGGCGTAATAGGTAATTCTTCTGTTTGGTTGAATGG
* *
56507671 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAAAGGCGTAATAGGTAATTCTTCTGTTTGGTTGAATGG
56507715 AAT
1 AAT
56507718 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 24 0.55
45 3 0.07
46 17 0.39
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGGAATAAAGGCGTAATAGGTAATTCTTCTGTTTGGTTGAATGG
Found at i:56507713 original size:39 final size:44
Alignment explanation
Indices: 56507625--56507730 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 44
56507615 ATAGAAGTGT
*
56507625 AATGGAATAAAGGTGTAATAGGTAATTCTTCTGTTTGGTTGAATGG
1 AATGGAATAGAGGTGTAATAGGTAATTCTTCTGTTTGGTT--ATGG
* *
56507671 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGTGTAATAGGTAATTCTTCTGTTTGGTTATGG
56507710 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGTGTAATAG
56507731 CATAAGAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 19 0.35
40 2 0.04
43 1 0.02
44 13 0.24
45 3 0.05
46 17 0.31
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGTGTAATAGGTAATTCTTCTGTTTGGTTATGG
Found at i:56507889 original size:18 final size:17
Alignment explanation
Indices: 56507866--56507902 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
56507856 AATTATTATT
56507866 AAATATAT-A-TTAATTA
1 AAATATATAATTTAA-TA
56507882 AAATATATAATTTAATA
1 AAATATATAATTTAATA
56507899 AAAT
1 AAAT
56507903 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATAATTTAATA
Found at i:56507896 original size:14 final size:15
Alignment explanation
Indices: 56507859--56507898 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
56507849 TTAACATAAT
56507859 TATT-ATTAAATATA
1 TATTAATTAAATATA
56507873 TATTAATTAAA-ATA
1 TATTAATTAAATATA
*
56507887 TA-TAATTTAATA
1 TATTAATTAAATA
56507899 AAATTCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 10 0.43
15 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAATTAAATATA
Found at i:56507914 original size:15 final size:17
Alignment explanation
Indices: 56507894--56507928 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
56507884 ATATATAATT
56507894 TAATAAA-ATTCTTA-A
1 TAATAAATATTCTTATA
56507909 TAATAAATATTCTTATA
1 TAATAAATATTCTTATA
56507926 TAA
1 TAA
56507929 ATTTACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 7 0.39
17 4 0.22
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATAAATATTCTTATA
Found at i:56507948 original size:61 final size:61
Alignment explanation
Indices: 56507883--56508190 Score: 260
Period size: 61 Copynumber: 5.1 Consensus size: 61
56507873 TATTAATTAA
*
56507883 AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATAAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATAAATTTATTAAAATCAT
** * * * * * * * *
56507944 AATATATGGTACT-ATAAAA-T-ATAAT-TTGAAATAATTATTAT-TAAATATATTTTAAGT-AA
1 AATATATAAT-TTAATAAAATTCTTAATAAT-AAAT-ATTCTTATATAAATTTA-TTAAAATCAT
*
56508003 AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTATTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATAAATTTATTAAAATCAT
* * * * * * ** * *
56508064 AATATATGATACT-ATAAAA-T-ATAAT-TTGAAATAATTATTAT-TAAATATATTTTAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAAT-AAAT-ATTCTTATATAAATTTATTAAAATCAT
* *
56508123 AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATAAATTTATTAAAATCAT
56508184 AATATAT
1 AATATAT
56508191 GATACTATAA
Statistics
Matches: 184, Mismatches: 45, Indels: 36
0.69 0.17 0.14
Matches are distributed among these distances:
58 4 0.02
59 65 0.35
60 41 0.22
61 70 0.38
62 4 0.02
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATAAATTTATTAAAATCAT
Found at i:56507992 original size:120 final size:120
Alignment explanation
Indices: 56507854--56508205 Score: 659
Period size: 120 Copynumber: 2.9 Consensus size: 120
56507844 ATATTTTAAC
*
56507854 ATAATTATTATTAAATATATATTAATTAAAATATATAATTTAATAAAATTCTTAATAATAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATAAATAT
* *
56507919 TCTTATATAAATTTACTAAAATCATAATATATGGTACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
*
56507974 ATAATTATTATTAAATATATTTTAAGTAAAATATATAATTTAATAAAATTCTTAATAATAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATAAATAT
*
56508039 TCTTATATGAATTTATTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
56508094 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATAAATAT
56508159 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATAT
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATAT
56508206 TTTTAATTAA
Statistics
Matches: 225, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 225 1.00
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATAAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:56508015 original size:18 final size:17
Alignment explanation
Indices: 56507988--56508022 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56507978 TTATTATTAA
*
56507988 ATATATTTTAAGTAAAAT
1 ATATAATTTAA-TAAAAT
56508006 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56508023 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56508034 original size:15 final size:16
Alignment explanation
Indices: 56508014--56508043 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56508004 ATATATAATT
56508014 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
56508029 TAATAAATATTCTTA
1 TAATAAATATTCTTA
56508044 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:56508129 original size:18 final size:17
Alignment explanation
Indices: 56508108--56508142 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56508098 TTATTATTAA
*
56508108 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56508126 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56508143 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56508140 original size:59 final size:59
Alignment explanation
Indices: 56507854--56508142 Score: 225
Period size: 59 Copynumber: 4.8 Consensus size: 59
56507844 ATATTTTAAC
* * *
56507854 ATAATTATTATTAAATATATATTAATTAAAATATATAATTTAATAAAAT-T--CTTAATA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATATAATTTGA-A
* * * * * *
56507911 ATAAATATTCTTATATA-AATTT-ACTAAAATCATAATATATGGTACTATAAAATATAATTTGAA
1 ATAATTATTATTAAATATATTTTAATTAAAAT-AT-ATA-AT-TTA--ATAAAATATAATTTGAA
* * *
56507974 ATAATTATTATTAAATATATTTTAAGTAAAATATATAATTTAATAAAATTCTTAATAAT-AA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAA-T-ATAAT-TTGAA
* * * ** * * * *
56508035 AT-ATTCTTATATGAATTTATTAAAATCATAATATATGATACT-ATAAAATATAATTTGAA
1 ATAATTATTAT-TAAATATATTTTAATTAAAATATATAAT-TTAATAAAATATAATTTGAA
56508094 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAAT
56508143 TCTTAATAAT
Statistics
Matches: 175, Mismatches: 38, Indels: 36
0.70 0.15 0.14
Matches are distributed among these distances:
55 7 0.04
56 5 0.03
57 17 0.10
58 4 0.02
59 44 0.25
60 16 0.09
61 43 0.25
62 5 0.03
63 18 0.10
64 9 0.05
65 7 0.04
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (59 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATATAATTTGAA
Found at i:56508154 original size:15 final size:16
Alignment explanation
Indices: 56508134--56508163 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56508124 ATATATAATT
56508134 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
56508149 TAATAAATATTCTTA
1 TAATAAATATTCTTA
56508164 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:56509333 original size:13 final size:13
Alignment explanation
Indices: 56509315--56509339 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56509305 GCTGTCTCAG
56509315 TTTTTGTGCCCAC
1 TTTTTGTGCCCAC
56509328 TTTTTGTGCCCA
1 TTTTTGTGCCCA
56509340 ACCTAGCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.28, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTTGTGCCCAC
Found at i:56512622 original size:16 final size:16
Alignment explanation
Indices: 56512598--56512651 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
56512588 TGGTTCGCTA
*
56512598 TAATGGAATAGAGGCG
1 TAATAGAATAGAGGCG
*
56512614 TAATAGAATAGAGGCT
1 TAATAGAATAGAGGCG
* *
56512630 TAATGGAATAGAGACG
1 TAATAGAATAGAGGCG
56512646 TAATAG
1 TAATAG
56512652 CAATTCAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.30, T:0.22
Consensus pattern (16 bp):
TAATAGAATAGAGGCG
Found at i:56512693 original size:45 final size:44
Alignment explanation
Indices: 56512630--56512717 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
56512620 AATAGAGGCT
*
56512630 TAATGGAATAGAGACGTAATAGCAATTCAAT-TGTTTGGTTGAATG
1 TAATAGAATAGAGACGTAATAG-AATTC-ATGTGTTTGGTTGAATG
* * * *
56512675 TAATAGAATAGGGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 TAATAGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAAT
56512718 TGAATGGAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.03
44 17 0.46
45 19 0.51
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (44 bp):
TAATAGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAATG
Found at i:56512874 original size:35 final size:35
Alignment explanation
Indices: 56512809--56512897 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 35
56512799 ATTGTTTTGT
56512809 TATAAA-ATTTTAATAAGATTATTAAAATAATATAA
1 TATAAATATTTTAATAAGATTATTAAAATAAT-TAA
* * * *
56512844 TATAAATATTTTAATCATATT-TTAACATAATTAT
1 TATAAATATTTTAATAAGATTATTAAAATAATTAA
56512878 TATTAAATATAATTTAATAA
1 TA-TAAATAT--TTTAATAA
56512898 AAAATATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
34 4 0.09
35 22 0.49
36 12 0.27
37 7 0.16
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (35 bp):
TATAAATATTTTAATAAGATTATTAAAATAATTAA
Found at i:56515930 original size:14 final size:14
Alignment explanation
Indices: 56515911--56515937 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56515901 AGCAGAAATC
56515911 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
56515925 TGGAGAAAAGAAA
1 TGGAGAAAAGAAA
56515938 GAAATGTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.30, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:56520959 original size:15 final size:15
Alignment explanation
Indices: 56520939--56520974 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
56520929 TAACCGAATT
56520939 GGTGACCTGATTAAG
1 GGTGACCTGATTAAG
56520954 GGTGACCTGATTAAG
1 GGTGACCTGATTAAG
56520969 GGTGAC
1 GGTGAC
56520975 ACCAACTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.36, T:0.25
Consensus pattern (15 bp):
GGTGACCTGATTAAG
Found at i:56524110 original size:67 final size:67
Alignment explanation
Indices: 56523999--56524125 Score: 227
Period size: 67 Copynumber: 1.9 Consensus size: 67
56523989 AGGAACATCC
* *
56523999 AAATACATACCTAGATCCCTTACCTTTGTAAATCTAAGATTGTTACATAAATTAGTTGATAACAC
1 AAATACATACCTAGATCCCTTACCTTTGTAAATCCAAGACTGTTACATAAATTAGTTGATAACAC
56524064 CT
66 CT
*
56524066 AAATACATACCTAGATCCCTTGCCTTTGTAAATCCAAGACTGTTACATAAATTAGTTGAT
1 AAATACATACCTAGATCCCTTACCTTTGTAAATCCAAGACTGTTACATAAATTAGTTGAT
56524126 TCTTCCTATG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (67 bp):
AAATACATACCTAGATCCCTTACCTTTGTAAATCCAAGACTGTTACATAAATTAGTTGATAACAC
CT
Found at i:56524818 original size:14 final size:15
Alignment explanation
Indices: 56524792--56524821 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56524782 AAACACGGTC
56524792 CATAAAAACCCATAT
1 CATAAAAACCCATAT
56524807 CATAAAAA-CCATAT
1 CATAAAAACCCATAT
56524821 C
1 C
56524822 CAAAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAAAAACCCATAT
Found at i:56524827 original size:14 final size:16
Alignment explanation
Indices: 56524790--56524827 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
56524780 TGAAACACGG
56524790 TCCATAAAAACCCATA
1 TCCATAAAAACCCATA
56524806 T-CATAAAAA-CCATA
1 TCCATAAAAACCCATA
56524820 TCCA-AAAA
1 TCCATAAAA
56524828 CAAAGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 10 0.48
15 10 0.48
16 1 0.05
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.18
Consensus pattern (16 bp):
TCCATAAAAACCCATA
Found at i:56527933 original size:22 final size:22
Alignment explanation
Indices: 56527874--56527930 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
56527864 ATCTTCAAGT
56527874 ATATGCAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
56527893 ATATGCAATCTTAGAAGATATG
1 ATATGCAATCTTAGAAGATATG
* *
56527915 ATTTTGTAATCTTAGA
1 A-TATGCAATCTTAGA
56527931 GATTTAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 12 0.38
22 8 0.25
23 12 0.38
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
ATATGCAATCTTAGAAGATATG
Found at i:56528231 original size:155 final size:155
Alignment explanation
Indices: 56527949--56528259 Score: 622
Period size: 155 Copynumber: 2.0 Consensus size: 155
56527939 TTGTAGATAC
56527949 CATTTAATCTTAGCCGTTGATGTATTGATCTGTACCATTGGATTTGGGGAGGCTCAACTATAAAT
1 CATTTAATCTTAGCCGTTGATGTATTGATCTGTACCATTGGATTTGGGGAGGCTCAACTATAAAT
56528014 AGAGGCCTCTCCCTTCATTGTAAAATACTTAAGTTGGGAGCAATAATAATTCTTAAGAGCATTCA
66 AGAGGCCTCTCCCTTCATTGTAAAATACTTAAGTTGGGAGCAATAATAATTCTTAAGAGCATTCA
56528079 CTCAAATTTCTCCCTCTCTTGCGTT
131 CTCAAATTTCTCCCTCTCTTGCGTT
56528104 CATTTAATCTTAGCCGTTGATGTATTGATCTGTACCATTGGATTTGGGGAGGCTCAACTATAAAT
1 CATTTAATCTTAGCCGTTGATGTATTGATCTGTACCATTGGATTTGGGGAGGCTCAACTATAAAT
56528169 AGAGGCCTCTCCCTTCATTGTAAAATACTTAAGTTGGGAGCAATAATAATTCTTAAGAGCATTCA
66 AGAGGCCTCTCCCTTCATTGTAAAATACTTAAGTTGGGAGCAATAATAATTCTTAAGAGCATTCA
56528234 CTCAAATTTCTCCCTCTCTTGCGTT
131 CTCAAATTTCTCCCTCTCTTGCGTT
56528259 C
1 C
56528260 TTATTTTCTG
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 156 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (155 bp):
CATTTAATCTTAGCCGTTGATGTATTGATCTGTACCATTGGATTTGGGGAGGCTCAACTATAAAT
AGAGGCCTCTCCCTTCATTGTAAAATACTTAAGTTGGGAGCAATAATAATTCTTAAGAGCATTCA
CTCAAATTTCTCCCTCTCTTGCGTT
Found at i:56544001 original size:4 final size:4
Alignment explanation
Indices: 56543987--56544017 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
56543977 ATCTTTTCAT
*
56543987 GTTA ATTA GTTA GTTA GTTA GTTA GTTA GTT
1 GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTT
56544018 GATAAGTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
GTTA
Found at i:56546068 original size:13 final size:13
Alignment explanation
Indices: 56546047--56546086 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
56546037 AGTTCTTCTT
56546047 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
56546060 TGCTGTTGAAAAG
1 TGCTTTTGAAAAG
56546073 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
56546086 T
1 T
56546087 TTGGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:56549028 original size:23 final size:23
Alignment explanation
Indices: 56548998--56549046 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
56548988 TTTAAAATTT
56548998 AAAAAATTAAAAAAATATTTTTA
1 AAAAAATTAAAAAAATATTTTTA
56549021 AAAAAATTAAAAAAATATTTTTA
1 AAAAAATTAAAAAAATATTTTTA
56549044 AAA
1 AAA
56549047 GTATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAAATTAAAAAAATATTTTTA
Found at i:56549055 original size:23 final size:23
Alignment explanation
Indices: 56548998--56549055 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
56548988 TTTAAAATTT
*
56548998 AAAAAATTAAAAAAATATTTTTA
1 AAAAAATAAAAAAAATATTTTTA
*
56549021 AAAAAATTAAAAAAATATTTTTA
1 AAAAAATAAAAAAAATATTTTTA
**
56549044 AAAGTATAAAAA
1 AAAAAATAAAAA
56549056 TTAGTTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAAAATAAAAAAAATATTTTTA
Found at i:56554108 original size:60 final size:60
Alignment explanation
Indices: 56553987--56554109 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 60
56553977 GCTTGAGTTC
* * * *
56553987 TTTTTATCCAAGTTAAGTCTTAAACTTGGCAATTGTTCCCACATTGAGATCTAAAACTTT
1 TTTTTATCCAAGTTAAGTCTGAAACTTGACAAATGTTCCCACATTGAGACCTAAAACTTT
** **
56554047 TTTTTATCCAAGTTAAGTCCTGAAA-TTGACAAATGTTCCCATGTTGAG-CCTTCAACTTT
1 TTTTTATCCAAGTTAAGT-CTGAAACTTGACAAATGTTCCCACATTGAGACCTAAAACTTT
56554106 TTTT
1 TTTT
56554110 ATTATTATCT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 12 0.22
60 37 0.69
61 5 0.09
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (60 bp):
TTTTTATCCAAGTTAAGTCTGAAACTTGACAAATGTTCCCACATTGAGACCTAAAACTTT
Found at i:56555839 original size:4 final size:4
Alignment explanation
Indices: 56555830--56555856 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
56555820 TAACCTTTTG
56555830 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
56555857 TAAATTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:56563662 original size:26 final size:28
Alignment explanation
Indices: 56563633--56563694 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
56563623 GAACTTATTT
56563633 AATT-ATT-TTTAATAATATATG-GACTA
1 AATTGATTATTTAATAATATA-GAGACTA
56563659 AATTGATTCATTTAATAATATAGAGACTA
1 AATTGATT-ATTTAATAATATAGAGACTA
*
56563688 ATTTGAT
1 AATTGAT
56563695 CCAGTCTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 4 0.13
27 3 0.10
28 1 0.03
29 23 0.74
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.44
Consensus pattern (28 bp):
AATTGATTATTTAATAATATAGAGACTA
Found at i:56565320 original size:18 final size:18
Alignment explanation
Indices: 56565297--56565334 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
56565287 TCCAAGACCG
56565297 GCGGTTTGCGAGACTTAA
1 GCGGTTTGCGAGACTTAA
*
56565315 GCGGTTTGTGAGACTTAA
1 GCGGTTTGCGAGACTTAA
56565333 GC
1 GC
56565335 TCTAGCCCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (18 bp):
GCGGTTTGCGAGACTTAA
Found at i:56576178 original size:64 final size:64
Alignment explanation
Indices: 56576063--56576192 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 64
56576053 CGAGCATCCC
* * * * *
56576063 GATCGGTAGTAATCCTGCATGTGTTGCGTACATACCGCAACTATTTGTGAGCGTCCTGTTATAT
1 GATCGATAGTAATCCTACATGTGTTGCGGACATACCACAACTATTTATGAGCGTCCTGTTATAT
* ** * *
56576127 GATCGATAGTGATCCTACATGTGTTGCGGACATACCACAGTTCTTTATGAGCTTCCTGTTATAT
1 GATCGATAGTAATCCTACATGTGTTGCGGACATACCACAACTATTTATGAGCGTCCTGTTATAT
56576191 GA
1 GA
56576193 CTCTCTAGAG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (64 bp):
GATCGATAGTAATCCTACATGTGTTGCGGACATACCACAACTATTTATGAGCGTCCTGTTATAT
Found at i:56576409 original size:23 final size:24
Alignment explanation
Indices: 56576375--56576448 Score: 75
Period size: 23 Copynumber: 3.1 Consensus size: 24
56576365 AGCTCAAATA
56576375 AGCTTC-CTGATA-GACTCTTTGTG
1 AGCTTCTCTGATATG-CTCTTTGTG
*
56576398 AGCTTCTC-GATATGCTTTTTGTG
1 AGCTTCTCTGATATGCTCTTTGTG
56576421 AGCTTCT-TGATTAATGGCTCTTTGTG
1 AGCTTCTCTGA-T-AT-GCTCTTTGTG
56576447 AG
1 AG
56576449 TTTCCTGTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
23 27 0.63
24 3 0.07
25 2 0.05
26 11 0.26
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (24 bp):
AGCTTCTCTGATATGCTCTTTGTG
Found at i:56576463 original size:26 final size:27
Alignment explanation
Indices: 56576407--56576466 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
56576397 GAGCTTCTCG
* *
56576407 ATAT-GCTTTTTGTGAGCTTCTTGATT
1 ATATGGCTCTTTGTGAGCTTCCTGATT
*
56576433 A-ATGGCTCTTTGTGAGTTTCCTG-TT
1 ATATGGCTCTTTGTGAGCTTCCTGATT
56576458 ATATGGCTC
1 ATATGGCTC
56576467 GAGAGAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (27 bp):
ATATGGCTCTTTGTGAGCTTCCTGATT
Found at i:56580546 original size:13 final size:13
Alignment explanation
Indices: 56580528--56580552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56580518 TAAAAGTTTG
56580528 AGGGAGAGTAAAT
1 AGGGAGAGTAAAT
56580541 AGGGAGAGTAAA
1 AGGGAGAGTAAA
56580553 ATTTTGGAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.40, T:0.12
Consensus pattern (13 bp):
AGGGAGAGTAAAT
Found at i:56580904 original size:9 final size:9
Alignment explanation
Indices: 56580890--56580926 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
56580880 TATAGTTTGA
56580890 TATTCGAAT
1 TATTCGAAT
56580899 TATTCGAAT
1 TATTCGAAT
*
56580908 TATTCGAGT
1 TATTCGAAT
56580917 TATTCGAAT
1 TATTCGAAT
56580926 T
1 T
56580927 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:56581062 original size:16 final size:16
Alignment explanation
Indices: 56581041--56581072 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56581031 CCCCTACGCT
56581041 AAACAGCTGTCGTGCC
1 AAACAGCTGTCGTGCC
*
56581057 AAACAGTTGTCGTGCC
1 AAACAGCTGTCGTGCC
56581073 CACAATGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (16 bp):
AAACAGCTGTCGTGCC
Found at i:56586619 original size:24 final size:23
Alignment explanation
Indices: 56586586--56586633 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
56586576 AGATTGAAAG
* *
56586586 CCAAAACGTGTTAGGTTAGCAGA
1 CCAAAACGTGCTAGGGTAGCAGA
*
56586609 CCAAAGACGTGCTAGGGTAGTAGA
1 CCAAA-ACGTGCTAGGGTAGCAGA
56586633 C
1 C
56586634 TTTTAGGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (23 bp):
CCAAAACGTGCTAGGGTAGCAGA
Found at i:56588853 original size:22 final size:21
Alignment explanation
Indices: 56588815--56588874 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
56588805 TAATATTATA
*
56588815 TTTATATTTTAAGTTTATTTC
1 TTTATATTTTAAATTTATTTC
56588836 TTTATATTTTAAAATTTATTTC
1 TTTATATTTT-AAATTTATTTC
56588858 TTT-TAGTATTTAAATTT
1 TTTATA-T-TTTAAATTT
56588875 CATGAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 12 0.34
22 20 0.57
23 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTATATTTTAAATTTATTTC
Found at i:56594378 original size:29 final size:29
Alignment explanation
Indices: 56594345--56594403 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
56594335 TTCGATCTCT
*
56594345 ATATTTTTAAAATATTTTTAATTAGTTCA
1 ATATTTTTAAAATATTATTAATTAGTTCA
*
56594374 ATATTTTTATAATATTATTAATTAGTTCA
1 ATATTTTTAAAATATTATTAATTAGTTCA
56594403 A
1 A
56594404 ATGGTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
ATATTTTTAAAATATTATTAATTAGTTCA
Found at i:56596644 original size:31 final size:28
Alignment explanation
Indices: 56596589--56596688 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 28
56596579 GGTTTAGGGA
* *
56596589 TTTTAAA-AATTAAATCAAGATTTAGCATTT
1 TTTTAAATAATTAAAT-TAGTTTTAG--TTT
***
56596619 TTTTAAATAATTAAATTAGGTTTTAGGGGG
1 TTTTAAATAATTAAATTA-GTTTTA-GTTT
56596649 TTTTAAATAAATTAAATTAGTGTTTAGTTT
1 TTTTAAAT-AATTAAATTAGT-TTTAGTTT
56596679 TTTTAAATAA
1 TTTTAAATAA
56596689 CTTTGTGTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
29 2 0.04
30 27 0.47
31 27 0.47
32 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (28 bp):
TTTTAAATAATTAAATTAGTTTTAGTTT
Found at i:56596683 original size:30 final size:31
Alignment explanation
Indices: 56596616--56596688 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
56596606 AGATTTAGCA
56596616 TTTTTTTAAAT-AATTAAATTAGGTTTTAGG
1 TTTTTTTAAATAAATTAAATTAGGTTTTAGG
***
56596646 GGGTTTTAAATAAATTAAATTA-GTGTTTA-G
1 TTTTTTTAAATAAATTAAATTAGGT-TTTAGG
56596676 TTTTTTTAAATAA
1 TTTTTTTAAATAA
56596689 CTTTGTGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.51
Consensus pattern (31 bp):
TTTTTTTAAATAAATTAAATTAGGTTTTAGG
Found at i:56596901 original size:126 final size:126
Alignment explanation
Indices: 56596740--56597010 Score: 470
Period size: 126 Copynumber: 2.2 Consensus size: 126
56596730 AATAAGGATT
* *
56596740 TTTTTCTACAGTAATTCTTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
* * *
56596805 ACGCTTCAAGCACGATGCACTGTCAGCAAAATTGATGAAAAAGGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCACGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
*
56596866 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
* *
56596931 ACGCTTTAAGCAGGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCACGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
56596992 TTTTTCTACAGTAGTTCCT
1 TTTTTCTACAGTAGTTCCT
56597011 ATTTGGCCTT
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 136 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCACGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
Found at i:56600446 original size:18 final size:18
Alignment explanation
Indices: 56600420--56600462 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
56600410 GACTGGGAAA
* *
56600420 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
56600438 AGGATACATATCAGGGCT
1 AGGATACATATAAGGGCT
56600456 AGGATAC
1 AGGATAC
56600463 GCATTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:56601184 original size:7 final size:7
Alignment explanation
Indices: 56601174--56601198 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56601164 AGATATACAT
56601174 AATACTA
1 AATACTA
56601181 AATACTA
1 AATACTA
56601188 AATACTA
1 AATACTA
56601195 AATA
1 AATA
56601199 TGAAACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:56602076 original size:10 final size:10
Alignment explanation
Indices: 56602063--56602090 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
56602053 AAAATTATAA
56602063 AATTAAAATT
1 AATTAAAATT
56602073 AATTAAAATT
1 AATTAAAATT
56602083 AATTAAAA
1 AATTAAAA
56602091 GAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATTAAAATT
Found at i:56602309 original size:30 final size:30
Alignment explanation
Indices: 56602275--56602339 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
56602265 ATTAATTAAA
56602275 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
1 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
* *
56602305 GAGAGCTTTGATAAATTTAGGGAGAAATTT
1 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
56602335 GAGAG
1 GAGAG
56602340 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.29
Consensus pattern (30 bp):
GAGAGCTTTGAAAAATTTAAGGAGAAATTT
Found at i:56604897 original size:22 final size:23
Alignment explanation
Indices: 56604854--56604898 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
56604844 TTTCAATAAA
*
56604854 TAAAAAAATAAAATTATTAATAT
1 TAAAAAAATAAAATTATAAATAT
* *
56604877 TAAAACAATATAA-TATAAATAT
1 TAAAAAAATAAAATTATAAATAT
56604899 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAAAAATAAAATTATAAATAT
Found at i:56605858 original size:8 final size:8
Alignment explanation
Indices: 56605841--56605871 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
56605831 CCTTTTACTA
*
56605841 TATATTTG
1 TATATATG
56605849 TATATATG
1 TATATATG
56605857 TATATATG
1 TATATATG
56605865 TATATAT
1 TATATAT
56605872 AGCAAACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (8 bp):
TATATATG
Found at i:56610712 original size:41 final size:41
Alignment explanation
Indices: 56610660--56610741 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
56610650 ATATTTTATT
* * *
56610660 TTATGTTTTAGTAGTTTATTAGAATAAGTGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
56610701 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
56610742 CAATTAGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
Found at i:56622580 original size:3 final size:3
Alignment explanation
Indices: 56622572--56622628 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
56622562 GGACTCGTAT
* *
56622572 TCA TCA TCA TCA TCA TCA T-A ACAA TAA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA TCA TCA TCA
56622617 TCA TCA TCA TCA
1 TCA TCA TCA TCA
56622629 AAAGAAGTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 1 0.02
3 46 0.96
4 1 0.02
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:56623817 original size:10 final size:10
Alignment explanation
Indices: 56623802--56623838 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
56623792 TTTTTTAAAA
*
56623802 ATTAAAAATC
1 ATTAAAAATT
56623812 ATT-AAAATT
1 ATTAAAAATT
56623821 ATTAAAAATT
1 ATTAAAAATT
56623831 A-TAAAAAT
1 ATTAAAAAT
56623839 ATTTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 15 0.60
10 10 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:56623837 original size:19 final size:19
Alignment explanation
Indices: 56623802--56623838 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56623792 TTTTTTAAAA
*
56623802 ATTAAAAATCATTAAAATT
1 ATTAAAAATCATAAAAATT
*
56623821 ATTAAAAATTATAAAAAT
1 ATTAAAAATCATAAAAAT
56623839 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAAAATCATAAAAATT
Found at i:56623858 original size:48 final size:48
Alignment explanation
Indices: 56623765--56623856 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
56623755 TTTTAAAATT
* *
56623765 TTAAAATTTTTAAAAATATAAGAACTATTTTTTAAAAATTAAAAATCA
1 TTAAAATTATTAAAAATATAAGAAATATTTTTTAAAAATTAAAAATCA
*
56623813 TTAAAATTATTAAAAATTATAA-AAATATTTTTT-AAATTTAAAAA
1 TTAAAATTATTAAAAA-TATAAGAAATATTTTTTAAAAATTAAAAA
56623857 ATTAAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 10 0.25
48 25 0.62
49 5 0.12
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (48 bp):
TTAAAATTATTAAAAATATAAGAAATATTTTTTAAAAATTAAAAATCA
Found at i:56627650 original size:30 final size:32
Alignment explanation
Indices: 56627616--56627674 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
56627606 TAAATTAATG
*
56627616 AAATATGTTG-ATTTTTTTTA-ATATTTAAGT
1 AAATAGGTTGTATTTTTTTTATATATTTAAGT
*
56627646 AAATAGGTTGTCTTTTTTTTATATATTTA
1 AAATAGGTTGTATTTTTTTTATATATTTA
56627675 TCGGTTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 9 0.36
32 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (32 bp):
AAATAGGTTGTATTTTTTTTATATATTTAAGT
Found at i:56631162 original size:50 final size:50
Alignment explanation
Indices: 56631091--56631275 Score: 361
Period size: 50 Copynumber: 3.7 Consensus size: 50
56631081 ACATGCCAAA
56631091 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
56631141 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
56631191 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
*
56631241 GCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56631276 TTACCCAAAT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 134 1.00
ACGTcount: A:0.17, C:0.33, G:0.24, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
Found at i:56631391 original size:13 final size:13
Alignment explanation
Indices: 56631370--56631401 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56631360 GCTTGGATCA
*
56631370 TCATCAAATAAAT
1 TCATAAAATAAAT
56631383 TCATAAAATAAAT
1 TCATAAAATAAAT
56631396 TCATAA
1 TCATAA
56631402 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:56640163 original size:16 final size:16
Alignment explanation
Indices: 56640142--56640172 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56640132 CAAAATTCTT
56640142 GGACAATCTTCTCATG
1 GGACAATCTTCTCATG
*
56640158 GGACAATCTTTTCAT
1 GGACAATCTTCTCAT
56640173 TCCATATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (16 bp):
GGACAATCTTCTCATG
Found at i:56640806 original size:31 final size:31
Alignment explanation
Indices: 56640768--56640831 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
56640758 GCCAAACAAT
56640768 TTAGTGTAATTACTACTACCATACGCAAATA
1 TTAGTGTAATTACTACTACCATACGCAAATA
* *
56640799 TTAGTGTAATTACTACTAGCATATGCAAATA
1 TTAGTGTAATTACTACTACCATACGCAAATA
56640830 TT
1 TT
56640832 GCTCTGGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (31 bp):
TTAGTGTAATTACTACTACCATACGCAAATA
Found at i:56647400 original size:11 final size:11
Alignment explanation
Indices: 56647384--56647424 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
56647374 ATTTTCTCAT
56647384 AAAAAATTATA
1 AAAAAATTATA
56647395 AAAAAA-TA-A
1 AAAAAATTATA
56647404 AATAAAATTATA
1 AA-AAAATTATA
*
56647416 AAAATATTA
1 AAAAAATTA
56647425 AAATTGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 3 0.12
10 6 0.23
11 14 0.54
12 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:56647412 original size:21 final size:22
Alignment explanation
Indices: 56647386--56647428 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
56647376 TTTCTCATAA
56647386 AAAATTATAAAAA-AATAAAAT
1 AAAATTATAAAAATAATAAAAT
*
56647407 AAAATTATAAAAATATTAAAAT
1 AAAATTATAAAAATAATAAAAT
56647429 TGATATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATTATAAAAATAATAAAAT
Found at i:56647427 original size:28 final size:28
Alignment explanation
Indices: 56647396--56647520 Score: 81
Period size: 27 Copynumber: 4.2 Consensus size: 28
56647386 AAAATTATAA
56647396 AAAAATAAAATAAAATTATAAAAATATT
1 AAAAATAAAATAAAATTATAAAAATATT
* * * *
56647424 AAAATTGATATAAAATTATTAAAATTATT
1 AAAAATAAAATAAAATTA-TAAAAATATT
*
56647453 AAAATTATAAATTATTATAATTATTATAAAAATATA
1 AAAA--ATAAA--A-TA-AA--ATTATAAAAATATT
** * *
56647489 AAAAATCTAAT-AAATTATAAAATTAAT
1 AAAAATAAAATAAAATTATAAAAATATT
56647516 AAAAA
1 AAAAA
56647521 ATTATTTAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
27 16 0.22
28 15 0.20
29 15 0.20
31 3 0.04
32 1 0.01
33 1 0.01
34 5 0.07
35 2 0.03
36 12 0.16
37 4 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (28 bp):
AAAAATAAAATAAAATTATAAAAATATT
Found at i:56647435 original size:20 final size:20
Alignment explanation
Indices: 56647412--56647449 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
56647402 AAAATAAAAT
56647412 TATAAAAATATTAAAATTGA
1 TATAAAAATATTAAAATTGA
*
56647432 TATAAAATTATTAAAATT
1 TATAAAAATATTAAAATT
56647450 ATTAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
TATAAAAATATTAAAATTGA
Found at i:56647522 original size:19 final size:19
Alignment explanation
Indices: 56647382--56647525 Score: 56
Period size: 19 Copynumber: 7.6 Consensus size: 19
56647372 ATATTTTCTC
*
56647382 ATAAAAAATTATAAAA-AA
1 ATAAAAAATTATAAAATTA
*
56647400 ATAAAATAAAATTATAAAAAT-
1 AT--AA-AAAATTATAAAATTA
* *
56647421 ATTAAAATTGATATAAAATT-
1 ATAAAAAAT--TATAAAATTA
*
56647441 AT-TAAAATTATTAAAATT-
1 ATAAAAAATTA-TAAAATTA
**
56647459 ATAAATTATTAT--AATTA
1 ATAAAAAATTATAAAATTA
*
56647476 TTATAAAAA-TATAAAA--A
1 ATA-AAAAATTATAAAATTA
*
56647493 ATCTAATAAATTATAAAATTA
1 A--TAAAAAATTATAAAATTA
56647514 ATAAAAAATTAT
1 ATAAAAAATTAT
56647526 TTAAAATATT
Statistics
Matches: 94, Mismatches: 15, Indels: 33
0.66 0.11 0.23
Matches are distributed among these distances:
16 4 0.04
17 8 0.09
18 23 0.24
19 31 0.33
20 12 0.13
21 16 0.17
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (19 bp):
ATAAAAAATTATAAAATTA
Found at i:56648053 original size:9 final size:9
Alignment explanation
Indices: 56648041--56648231 Score: 64
Period size: 9 Copynumber: 20.0 Consensus size: 9
56648031 TTTTATGATT
56648041 TTTTTATAA
1 TTTTTATAA
56648050 TTTTTATAA
1 TTTTTATAA
**
56648059 GTTCATATCAA
1 -TTTTTAT-AA
* *
56648070 TTTTAATAC
1 TTTTTATAA
* *
56648079 TATTTATGA
1 TTTTTATAA
*
56648088 TTTTAATAGAA
1 TTTT--TATAA
* *
56648099 TTTTAATATG
1 TTTTTATA-A
56648109 TTTTTATAAA
1 TTTTTAT-AA
*
56648119 TTTTTAAATA
1 TTTTTATA-A
*
56648129 TGTTTTATTA
1 T-TTTTATAA
*
56648139 CTTTTATAAA
1 TTTTTAT-AA
*
56648149 TTTTATAGAA
1 TTTT-TATAA
*
56648159 TTTTTAT-G
1 TTTTTATAA
56648167 TTTTTGATAA
1 TTTTT-ATAA
*
56648177 TATTTATAA
1 TTTTTATAA
*
56648186 GTTTATATCAA
1 -TTTTTAT-AA
*
56648197 TTTTCAT-A
1 TTTTTATAA
56648205 TATTTT-TAA
1 T-TTTTATAA
* *
56648214 TATTTATAT
1 TTTTTATAA
56648223 TTTTTATAA
1 TTTTTATAA
56648232 ATATTTTCTG
Statistics
Matches: 127, Mismatches: 38, Indels: 34
0.64 0.19 0.17
Matches are distributed among these distances:
8 11 0.09
9 49 0.39
10 48 0.38
11 19 0.15
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:56648108 original size:22 final size:22
Alignment explanation
Indices: 56648083--56648135 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
56648073 TAATACTATT
56648083 TATGATTTTAATAGAA-TTTT-AA
1 TATG-TTTTAATA-AATTTTTAAA
*
56648105 TATGTTTTTATAAATTTTTAAA
1 TATGTTTTAATAAATTTTTAAA
56648127 TATGTTTTA
1 TATGTTTTA
56648136 TTACTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 11 0.41
22 14 0.52
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (22 bp):
TATGTTTTAATAAATTTTTAAA
Found at i:56648122 original size:20 final size:19
Alignment explanation
Indices: 56648083--56648233 Score: 73
Period size: 20 Copynumber: 7.8 Consensus size: 19
56648073 TAATACTATT
*
56648083 TATGATTTTAATAGAATTTTAA
1 TATG-TTTTTATA-AATTTT-A
56648105 TATGTTTTTATAAATTTTTAAA
1 TATGTTTTTATAAA-TTTT--A
* *
56648127 TATG-TTTTATTACTTTTA
1 TATGTTTTTATAAATTTTA
**
56648145 TA-AATTTTATAGAATTTT-
1 TATGTTTTTATA-AATTTTA
56648163 TATGTTTTTGAT-AATATTTA
1 TATGTTTTT-ATAAAT-TTTA
* * *
56648183 TAAGTTTATATCAATTTTCA
1 TATGTTTTTATAAATTTT-A
* *
56648203 TATATTTTTA-ATA-TTTA
1 TATGTTTTTATAAATTTTA
56648220 TAT-TTTTTATAAAT
1 TATGTTTTTATAAAT
56648234 ATTTTCTGTT
Statistics
Matches: 101, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
16 6 0.06
17 6 0.06
18 17 0.17
19 18 0.18
20 26 0.26
21 18 0.18
22 10 0.10
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
TATGTTTTTATAAATTTTA
Found at i:56648199 original size:38 final size:37
Alignment explanation
Indices: 56648152--56648256 Score: 88
Period size: 38 Copynumber: 2.8 Consensus size: 37
56648142 TTATAAATTT
56648152 TATAGAATTTTTATGTTTTTGATAATATTTATAAGTTTA
1 TATA-AATTTTTATGTTTTTGATAATATTTAT-AGTTTA
* * * * *
56648191 TATCAATTTTCATATATTTT--TAATATTTATATTTTT
1 TATAAATTTTTATGT-TTTTGATAATATTTATAGTTTA
* * *
56648227 TATAAATATTTTCTGTTATTGATATTATTT
1 TATAAAT-TTTTATGTTTTTGATAATATTT
56648257 TTATGGGAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
36 13 0.25
37 15 0.29
38 16 0.31
39 7 0.14
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (37 bp):
TATAAATTTTTATGTTTTTGATAATATTTATAGTTTA
Found at i:56651620 original size:93 final size:94
Alignment explanation
Indices: 56651461--56651773 Score: 517
Period size: 93 Copynumber: 3.3 Consensus size: 94
56651451 ATCAGGTATA
56651461 TTGATCT-ATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
1 TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
56651525 ACACTATCGGGTATGTAATATTATCTTAT
66 ACACTATCGGGTATGTAATATTATCTTAT
56651554 TTGATCT-ATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
1 TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
*
56651618 ACACTATTGGGTATGTAATATTATCTTAT
66 ACACTATCGGGTATGTAATATTATCTTAT
*
56651647 TTGAT-TCATTTAGTTGGAGGGTAAAATTTTACTATTTGATTGATGGAATGTAAGATTATTTATT
1 TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAA-A--A-TTATT
*
56651711 TAGTACACCATCGGGTATGTAATATTATCTTAT
62 TAGTACACTATCGGGTATGTAATATTATCTTAT
* *
56651744 TTG-TTTCATTTAGCTGGAGGGTAAAATTTT
1 TTGATCTCATTTAGTTGGAGGGTAAAATTTT
56651774 TGATAAAATG
Statistics
Matches: 209, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
92 1 0.00
93 142 0.68
94 1 0.00
96 2 0.01
97 63 0.30
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (94 bp):
TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
ACACTATCGGGTATGTAATATTATCTTAT
Found at i:56666423 original size:113 final size:112
Alignment explanation
Indices: 56666262--56666806 Score: 442
Period size: 114 Copynumber: 4.8 Consensus size: 112
56666252 AAATCTCAAG
* * *
56666262 ACCAACACGCAGCGTTCTGGTGTTGATGTATATTGGC-ATTAGTGGCGCTTACGAACAAACGCCG
1 ACCAAAACGCAGCGTT-TGGTCTTGATGTATATT-GCAATTAGTGGCGCTTATGAA-AAACGCC-
* * * *
56666326 GC-AATGTATAGTATTAGCGGCGCTTAGTGGAAGTGCTGCAAAAGATGTTA
62 GCTAAAGTATAGTATTAGCGGCGCTTAGTGGAAGCGCCGCAAAAGATCTTA
* * * *
56666376 GCCAAAACGCAGAGTTTGGTCTTGATGTATATTTCAATTAGTGGCGCTTATAAATAAAACGCCGC
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTAT-GA-AAAACGCCGC
* ** * * * *
56666441 TAATGTATAGTATTAGCGGCGCAGAGCCT-TAAACGCCGCAAGACATCTTA
64 TAAAGTATAGTATTAGCGGCGCTTAG--TGGAAGCGCCGCAAAAGATCTTA
* * ** * * * *
56666491 ATCAAAACGCAGCGTGTTGGTCTTGATGTATAATATAATTAGTGGCGTTTAAGGAAAACACCAGC
1 ACCAAAACGCAGCGT-TTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATGAAAAACGCC-GC
* * * * * *
56666556 -AAAGGATAGT-TATAGCAGCGTTTGGTGGTAAGCGCCTCAAAATATCTTA
64 TAAAGTATAGTAT-TAGCGGCGCTTAGTGG-AAGCGCCGCAAAAGATCTTA
* * *
56666605 ACCAAAACGCAGAGTTTGGTCTTGAGGTGTATTAG-AATTAGTGGCGCTTGATGAAAAACGCCGC
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATT-GCAATTAGTGGCGCTT-ATGAAAAACGCCGC
*
56666669 TAAAGTATA-TCATTAGCGGCG-TTTGTGGAACGCGCCGC-AAAGTATCTTA
64 TAAAGTATAGT-ATTAGCGGCGCTTAGTGGAA-GCGCCGCAAAAG-ATCTTA
* * * * ** * *
56666718 ACCAAAACACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTGGCGCAAATGGGAAAACGCCAC
1 ACCAAAACGCAGCGTTT-GGTCTTGATGTATATTGCAATTAGTGGCGCTTAT-GAAAAACGCCGC
* *
56666783 TGAAGCATAGTATTAGCGGCGCTT
64 TAAAGTATAGTATTAGCGGCGCTT
56666807 TTACCGAAAC
Statistics
Matches: 342, Mismatches: 66, Indels: 45
0.75 0.15 0.10
Matches are distributed among these distances:
112 7 0.02
113 100 0.29
114 170 0.50
115 33 0.10
116 32 0.09
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (112 bp):
ACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATGAAAAACGCCGCTA
AAGTATAGTATTAGCGGCGCTTAGTGGAAGCGCCGCAAAAGATCTTA
Found at i:56666930 original size:18 final size:18
Alignment explanation
Indices: 56666909--56666944 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
56666899 TCATTTTATA
56666909 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
56666927 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
56666945 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:56667299 original size:29 final size:29
Alignment explanation
Indices: 56667266--56667322 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
56667256 AAGGGTTGTA
*
56667266 ATTTAGGGGTTATAGATTAAGAGTCAGGG
1 ATTTAAGGGTTATAGATTAAGAGTCAGGG
* * * *
56667295 ATTTAAGGTTTATGGATTCAGTGTCAGG
1 ATTTAAGGGTTATAGATTAAGAGTCAGG
56667323 TTAGGCTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.28, C:0.05, G:0.32, T:0.35
Consensus pattern (29 bp):
ATTTAAGGGTTATAGATTAAGAGTCAGGG
Found at i:56667900 original size:7 final size:7
Alignment explanation
Indices: 56667890--56667950 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
56667880 GACTTTTACT
56667890 GTTTGGG
1 GTTTGGG
**
56667897 GTTTTAAG
1 G-TTTGGG
*
56667905 GTTTAGG
1 GTTTGGG
*
56667912 GTTTAGG
1 GTTTGGG
56667919 GTTTGGG
1 GTTTGGG
56667926 GTTTGGG
1 GTTTGGG
56667933 GTTTGGG
1 GTTTGGG
*
56667940 GTTTGAG
1 GTTTGGG
56667947 GTTT
1 GTTT
56667951 AAGGTTTACA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
7 43 0.90
8 5 0.10
ACGTcount: A:0.08, C:0.00, G:0.46, T:0.46
Consensus pattern (7 bp):
GTTTGGG
Found at i:56667955 original size:7 final size:7
Alignment explanation
Indices: 56667899--56667958 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
56667889 TGTTTGGGGT
*
56667899 TTTAAGG
1 TTTAGGG
56667906 TTTAGGG
1 TTTAGGG
56667913 TTTAGGG
1 TTTAGGG
*
56667920 TTTGGGG
1 TTTAGGG
*
56667927 TTTGGGG
1 TTTAGGG
*
56667934 TTTGGGG
1 TTTAGGG
56667941 TTT-GAGG
1 TTTAG-GG
*
56667948 TTTAAGG
1 TTTAGGG
56667955 TTTA
1 TTTA
56667959 CAAATTATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
6 1 0.02
7 47 0.98
ACGTcount: A:0.13, C:0.00, G:0.42, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:56668536 original size:74 final size:74
Alignment explanation
Indices: 56668458--56668685 Score: 211
Period size: 74 Copynumber: 3.1 Consensus size: 74
56668448 TGAAATGTTG
56668458 TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
1 TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
56668523 GAAACGGCT
66 GAAACGGCT
* * * * ** * * *
56668532 TCGTTTTGAGT-TATAG--TTAGTGGCGCTTTCCATAAAACGCCGCAAAATT--TTAATTA-TGT
1 TCGTTTT-TGTCTATTGTATTAGTGGCGTTTTTC-GGAAACGCCACAACATTGGGTAA--ACTG-
*** *
56668591 TTATTGAAATGTTG-T
61 TTGGGGAAACG--GCT
56668606 T-GTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
1 TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
*
56668670 GAAACGACT
66 GAAACGGCT
56668679 TCGTTTT
1 TCGTTTT
56668686 GAGTAATAGT
Statistics
Matches: 112, Mismatches: 27, Indels: 30
0.66 0.16 0.18
Matches are distributed among these distances:
71 3 0.03
72 17 0.15
73 32 0.29
74 39 0.35
75 18 0.16
76 3 0.03
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (74 bp):
TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
GAAACGGCT
Found at i:56668561 original size:147 final size:147
Alignment explanation
Indices: 56668401--56668727 Score: 591
Period size: 147 Copynumber: 2.2 Consensus size: 147
56668391 TACGTTGCTA
*
56668401 TTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
1 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
*
56668466 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
66 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
*
56668531 TTCGTTTTGAGTTATAG
131 TTCGTTTTGAGTAATAG
*
56668548 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTTT
1 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
56668613 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
66 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
56668678 TTCGTTTTGAGTAATAG
131 TTCGTTTTGAGTAATAG
* * *
56668695 TTAGTGGCGCTTTACTTGAAACGCCGCAAAATT
1 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATT
56668728 GTTCAAACAT
Statistics
Matches: 173, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 173 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (147 bp):
TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
TTCGTTTTGAGTAATAG
Found at i:56668611 original size:73 final size:74
Alignment explanation
Indices: 56668400--56668631 Score: 183
Period size: 73 Copynumber: 3.1 Consensus size: 74
56668390 TTACGTTGCT
* *
56668400 ATTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTT
1 ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
* *
56668465 TGTCTATTG
66 AGTCTATAG
* * ** * * * *** *
56668474 TATTAGTGGCGTTTTTC-GGAAACGCCACAACATTGGGTAA--ACTG-TTGGGGAAACG--GCTT
1 -ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATT--TTAATTA-TGTTTATTGAAATGTTG-TT
56668533 CGTTTTGAGT-TATAG
61 -GTTTT-AGTCTATAG
56668548 -TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
1 ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
* *
56668612 TGTCTATTG
66 AGTCTATAG
56668621 TATTAGTGGCG
1 -ATTAGTGGCG
56668632 TTTTTCGGAA
Statistics
Matches: 114, Mismatches: 28, Indels: 30
0.66 0.16 0.17
Matches are distributed among these distances:
71 3 0.03
72 18 0.16
73 31 0.27
74 31 0.27
75 28 0.25
76 3 0.03
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.41
Consensus pattern (74 bp):
ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
AGTCTATAG
Found at i:56668718 original size:73 final size:71
Alignment explanation
Indices: 56668476--56668728 Score: 181
Period size: 73 Copynumber: 3.5 Consensus size: 71
56668466 GTCTATTGTA
* * * *
56668476 TTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGCTTCGTTTTGA
1 TTAGTGGCGCTTTACTGAAACGCCACAAAATTGGGTAAACTGTTGGGGAAAC-GCTTCGTTTTGA
56668541 GTTATAG
65 GTTATAG
* * * * *** * * *
56668548 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATT--TTAATTA-TGTTTATTGAAATGTTGTTGTT
1 TTAGTGGCGCTTTAC-TGAAACGCCACAAAATTGGGTAA--ACTG-TTGGGGAAACGCT-TCGTT
* *
56668610 TT-TGTCTATTG
61 TTGAGT-TATAG
* * * *
56668621 TATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGACTTCGTTTT
1 --TTAGTGGCGCTTTACTGAAACGCCACAAAATTGGGTAAACTGTTGGGGAAACG-CTTCGTTTT
*
56668686 GAGTAATAG
63 GAGTTATAG
*
56668695 TTAGTGGCGCTTTACTTGAAACGCCGCAAAATTG
1 TTAGTGGCGCTTTAC-TGAAACGCCACAAAATTG
56668729 TTCAAACATT
Statistics
Matches: 131, Mismatches: 36, Indels: 27
0.68 0.19 0.14
Matches are distributed among these distances:
71 3 0.02
72 32 0.24
73 45 0.34
74 30 0.23
75 18 0.14
76 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (71 bp):
TTAGTGGCGCTTTACTGAAACGCCACAAAATTGGGTAAACTGTTGGGGAAACGCTTCGTTTTGAG
TTATAG
Found at i:56668745 original size:147 final size:146
Alignment explanation
Indices: 56668401--56668781 Score: 543
Period size: 147 Copynumber: 2.6 Consensus size: 146
56668391 TACGTTGCTA
* * **
56668401 TTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAATGTTGTCGTTTTT
*
56668466 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
65 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
*
56668531 TTCGTTTTGAGTTATAG
130 TTCGTTTTGAGTAATAG
* ** *
56668548 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAATGTTGTCGTTTTT
56668613 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
65 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
56668678 TTCGTTTTGAGTAATAG
130 TTCGTTTTGAGTAATAG
* * * * *
56668695 TTAGTGGCGCTTTACTTGAAACGCCGCAAAATTGTTCAA-ACATTTGTTGAAACGTTGCCG-TTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATT-TT-AATACATTTATTGAAATGTTGTCGTTTT
* *
56668758 TGT-AAATGTTATTAGTGGCGTTTT
64 TGTCTATTG-TATTAGTGGCGTTTT
56668782 ACCGAAAATG
Statistics
Matches: 216, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
145 3 0.01
146 21 0.10
147 188 0.87
148 2 0.01
149 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (146 bp):
TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAATACATTTATTGAAATGTTGTCGTTTTTG
TCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGACT
TCGTTTTGAGTAATAG
Found at i:56668814 original size:147 final size:146
Alignment explanation
Indices: 56668401--56668853 Score: 482
Period size: 147 Copynumber: 3.1 Consensus size: 146
56668391 TACGTTGCTA
* * ** * *
56668401 TTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAACGTTGCCGTTTTT
** * * *
56668466 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
65 GTAAATTGTATTAGTGGCGTTTTCCGAAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
56668531 TTCGTTTTGAGTTATAG
130 TTCGTTTTGAGTTATAG
* ** * **
56668548 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAACGTTGCCGTTTTT
** * *
56668613 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
65 GTAAATTGTATTAGTGGCGTTTTCCGAAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
*
56668678 TTCGTTTTGAGTAATAG
130 TTCGTTTTGAGTTATAG
* * *
56668695 TTAGTGGCGCTTTACTTGAAACGCCGCAAAATTGTTCAA-ACATTTGTTGAAACGTTGCCG-TTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATT-TT-AATACATTTATTGAAACGTTGCCGTTTT
* ***** * ** *
56668758 TGTAAA-TGTTATTAGTGGCGTTTTACCGAAAATGCCATGGGTTTGAGGT-AAGTGTTGATGAAG
64 TGTAAATTG-TATTAGTGGCGTTTT-CCGAAAACGCCACAACATTG-GGTAAACTGTTGGGGAAA
**
56668821 CGACCGCGTTTTGAGTTATAG
126 CGACTTCGTTTTGAGTTATAG
56668842 TTAGTGGCGCTT
1 TTAGTGGCGCTT
56668854 AGTTTAAAAC
Statistics
Matches: 271, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
145 2 0.01
146 22 0.08
147 240 0.89
148 5 0.02
149 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (146 bp):
TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAATACATTTATTGAAACGTTGCCGTTTTTG
TAAATTGTATTAGTGGCGTTTTCCGAAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGACT
TCGTTTTGAGTTATAG
Found at i:56670289 original size:10 final size:10
Alignment explanation
Indices: 56670274--56670312 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
56670264 GTTATGGGTA
*
56670274 AATTTTAAAT
1 AATTTTATAT
56670284 AATTTTATAT
1 AATTTTATAT
*
56670294 AATTTTATTT
1 AATTTTATAT
56670304 AATTTTATA
1 AATTTTATA
56670313 ATTATTCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AATTTTATAT
Found at i:56673637 original size:7 final size:7
Alignment explanation
Indices: 56673620--56673652 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
56673610 AGAGAAAGAA
56673620 AAAAAAT
1 AAAAAAT
56673627 -AAAAAT
1 AAAAAAT
56673633 AAAAAAT
1 AAAAAAT
56673640 AAAAAAT
1 AAAAAAT
56673647 AAAAAA
1 AAAAAA
56673653 ACGAATAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:56673638 original size:14 final size:15
Alignment explanation
Indices: 56673619--56673653 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
56673609 CAGAGAAAGA
56673619 AAAAAAAT-AAAAAT
1 AAAAAAATAAAAAAT
56673633 -AAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
56673647 AAAAAAA
1 AAAAAAA
56673654 CGAATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 6 0.32
15 6 0.32
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:56675373 original size:7 final size:7
Alignment explanation
Indices: 56675356--56675388 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
56675346 AGAGAAAGAA
56675356 AAAAAAT
1 AAAAAAT
56675363 -AAAAAT
1 AAAAAAT
56675369 AAAAAAT
1 AAAAAAT
56675376 AAAAAAT
1 AAAAAAT
56675383 AAAAAA
1 AAAAAA
56675389 ACGAATAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:56675374 original size:14 final size:15
Alignment explanation
Indices: 56675355--56675389 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
56675345 CAGAGAAAGA
56675355 AAAAAAAT-AAAAAT
1 AAAAAAATAAAAAAT
56675369 -AAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
56675383 AAAAAAA
1 AAAAAAA
56675390 CGAATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 6 0.32
15 6 0.32
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:56679304 original size:21 final size:21
Alignment explanation
Indices: 56679278--56679327 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
56679268 CTACAACTTA
*
56679278 AAGCAGAGGCGGCAGCAAGGG
1 AAGCAGAGGCGGCAGCAAGAG
* * *
56679299 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
56679320 AAGCAGAG
1 AAGCAGAG
56679328 CAGGCCAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:56679719 original size:42 final size:41
Alignment explanation
Indices: 56679609--56679724 Score: 115
Period size: 41 Copynumber: 2.8 Consensus size: 41
56679599 GTTTTTGTAT
* * * *
56679609 AAAAGCGCCGCTAAAGAACATGTTCTTTAGTGGGGTTTAAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAA
* *****
56679650 AAAAACGCCACTATTTTTCATGTTCTTTAGCGGCGCTTAAGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAA-A
* *
56679692 ATAAACGCCGCTAAAGAACATGATCTTTAGCGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGG
56679725 TGTTTTTTTC
Statistics
Matches: 56, Mismatches: 18, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
41 30 0.54
42 26 0.46
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAA
Found at i:56679744 original size:42 final size:42
Alignment explanation
Indices: 56679697--56679794 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
56679687 TAAGAATAAA
*
56679697 CGCCGCTAAAGAACATGATCTTTAGCGGTGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * *
56679739 TGCCGCTAAAGTACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
56679781 CGCCGCTAAAGAAC
1 CGCCGCTAAAGAAC
56679795 TCAAAGCGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:56680754 original size:14 final size:15
Alignment explanation
Indices: 56680715--56680756 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56680705 TTTTAACATA
*
56680715 ATTATTATTAAATAT
1 ATTATAATTAAATAT
56680730 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
56680744 A-TATAATTTAATA
1 ATTATAATTAAATA
56680757 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:56680867 original size:18 final size:17
Alignment explanation
Indices: 56680846--56680880 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56680836 TTATTATTAA
*
56680846 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56680864 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56680881 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56680985 original size:16 final size:16
Alignment explanation
Indices: 56680941--56680987 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
56680931 TACTATAAAA
*
56680941 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
56680957 TATTATT-AAATATAT
1 TATAATTAAAATATAT
56680972 TATAATTAAAATATAT
1 TATAATTAAAATATAT
56680988 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:56681130 original size:120 final size:120
Alignment explanation
Indices: 56680706--56681121 Score: 787
Period size: 120 Copynumber: 3.5 Consensus size: 120
56680696 TTAATCATAT
56680706 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
56680771 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
*
56680826 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
56680891 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
56680946 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
56681011 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
* * * *
56681066 TTTAACATAATTAATATTAAATATATTTTAATTAAAATACATGATTTAATAAAATT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
56681122 TAAAATAATT
Statistics
Matches: 290, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 290 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
Found at i:56681200 original size:71 final size:71
Alignment explanation
Indices: 56681125--56681302 Score: 184
Period size: 71 Copynumber: 2.5 Consensus size: 71
56681115 TAAAATTTAA
* * *
56681125 AATAAT-TATAA-CTAATAAATTTTCTT-AT-ATGAATTTGTATAATTTAAAATAATTATTATTA
1 AATAATATATAATCTAATAAA-ATTCTTGATAATAAATTT-TAT--TTTAAAATAATTAATATTA
56681186 AATATAATTT
62 AATATAATTT
* * * *
56681196 AATAATATATAATTTCATAAAATTCTTGATAATAAATTTTCTTTTAGAATAATTAATATTAAATA
1 AATAATATATAATCTAATAAAATTCTTGATAATAAATTTTATTTTAAAATAATTAATATTAAATA
56681261 TAATTT
66 TAATTT
* *
56681267 AATAATGATATATAATTTCATAAAATTCTTGATAAT
1 AAT-A--ATATATAATCTAATAAAATTCTTGATAAT
56681303 TTAATCATGA
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
71 36 0.39
72 11 0.12
73 10 0.11
74 36 0.39
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (71 bp):
AATAATATATAATCTAATAAAATTCTTGATAATAAATTTTATTTTAAAATAATTAATATTAAATA
TAATTT
Found at i:56681205 original size:15 final size:15
Alignment explanation
Indices: 56681162--56681215 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
56681152 TATGAATTTG
56681162 TATAATTTAA-AATA
1 TATAATTTAATAATA
* *
56681176 -ATTA-TTATTAA-A
1 TATAATTTAATAATA
56681188 TATAATTTAATAATA
1 TATAATTTAATAATA
*
56681203 TATAATTTCATAA
1 TATAATTTAATAA
56681216 AATTCTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.13
13 8 0.26
14 6 0.19
15 13 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATTTAATAATA
Found at i:56681284 original size:74 final size:71
Alignment explanation
Indices: 56681167--56681302 Score: 227
Period size: 71 Copynumber: 1.9 Consensus size: 71
56681157 ATTTGTATAA
*
56681167 TTTAAAATAATTATTATTAAATATAATTTAATAATATATAATTTCATAAAATTCTTGATAATAAA
1 TTTAAAATAATTAATATTAAATATAATTTAATAATATATAATTTCATAAAATTCTTGATAATAAA
56681232 TTTTCT
66 TTTTCT
*
56681238 TTTAGAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTGATAAT
1 TTTAAAATAATTAATATTAAATATAATTTAAT-A--ATATATAATTTCATAAAATTCTTGATAAT
56681303 TTAATCATGA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
71 30 0.50
72 1 0.02
74 29 0.48
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (71 bp):
TTTAAAATAATTAATATTAAATATAATTTAATAATATATAATTTCATAAAATTCTTGATAATAAA
TTTTCT
Found at i:56688657 original size:6 final size:6
Alignment explanation
Indices: 56688634--56688669 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
56688624 ATATACATAG
* *
56688634 TCAGAT TTAGAA TCAGAT TCAGAT TCAGAT TCAGAT
1 TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT
56688670 AACAGAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (6 bp):
TCAGAT
Found at i:56689203 original size:32 final size:32
Alignment explanation
Indices: 56689128--56689209 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
56689118 GGGCCCAGAT
* * *
56689128 ACCCGTGTGGCCCATACACCCAGATTGGCCTT
1 ACCCGTGTGGCCCACACGCCCAGATTGGCCTA
* * *
56689160 ACCCATATGGCCCACACGCCCAGTTTGGCC-A
1 ACCCGTGTGGCCCACACGCCCAGATTGGCCTA
56689191 AGCCCGTGTGGCCCACACG
1 A-CCCGTGTGGCCCACACG
56689210 TCCACACCCA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 1 0.02
32 40 0.98
ACGTcount: A:0.20, C:0.40, G:0.23, T:0.17
Consensus pattern (32 bp):
ACCCGTGTGGCCCACACGCCCAGATTGGCCTA
Found at i:56690258 original size:29 final size:32
Alignment explanation
Indices: 56690225--56690283 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
56690215 TGCATCTTGT
56690225 AAAAA-TTGAAAAA-ATA-AAATAAAAAAAGA
1 AAAAATTTGAAAAATATATAAATAAAAAAAGA
* *
56690254 AAAAATTTTAAAAATATATAACTAAAAAAA
1 AAAAATTTGAAAAATATATAAATAAAAAAA
56690284 TTAATGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 7 0.28
31 3 0.12
32 10 0.40
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (32 bp):
AAAAATTTGAAAAATATATAAATAAAAAAAGA
Found at i:56696408 original size:46 final size:46
Alignment explanation
Indices: 56696336--56696446 Score: 147
Period size: 46 Copynumber: 2.4 Consensus size: 46
56696326 GTAAAAGTAT
* *
56696336 ATTT-ATAATATTTT-ATAAATATCGTAAATAACAGATA-TCAACTTG
1 ATTTAATAAT-TTTTAATGAATATCGTAAAAAACAGATACT-AACTTG
* *
56696381 ATTTAATACTTTTTAATGAATATCGTAAAAAACAGATACTAGCTTG
1 ATTTAATAATTTTTAATGAATATCGTAAAAAACAGATACTAACTTG
56696427 ATTTAATAATTTTTAATGAA
1 ATTTAATAATTTTTAATGAA
56696447 AATATTAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
45 8 0.14
46 49 0.84
47 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (46 bp):
ATTTAATAATTTTTAATGAATATCGTAAAAAACAGATACTAACTTG
Found at i:56700277 original size:115 final size:115
Alignment explanation
Indices: 56700073--56700405 Score: 377
Period size: 115 Copynumber: 2.9 Consensus size: 115
56700063 ACGGATAGTG
* *
56700073 AAAGCGCCGCAAAATAT-TTGAACCAAAACGCATCGTTTTGGTATTGATGTATACTAGAATTAGT
1 AAAGCGCCGCAAAATATCTT-AACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGT
* * *
56700137 GGCGTTTACGGTAAAACGCCGCTAAACCATAGTATTAGCAGCGATT-CTTTG-
65 GGCGCTTACGGGAAAACGCCGCTAAACCATAGTATTAGCAGCCATTAC--TGA
** * * *
56700188 CTAGCGCCGCAAAATATCCTAACTAAAACGCAGCGTTTTGGTCTTGATGTATACTAAAATTAGTG
1 AAAGCGCCGCAAAATATCTTAACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTG
* ** * *
56700253 GCGCTTACGGGAAACCGCCGCTAAAGAATAGTATTAGCGGCCCTTACTGA
66 GCGCTTACGGGAAAACGCCGCTAAACCATAGTATTAGCAGCCATTACTGA
* * ***
56700303 AAAGCGCCACAAAATATCTTAACCT-AAACGCATAGTTTTAACCTTGATGTATACTAGAATTAGT
1 AAAGCGCCGCAAAATATCTTAA-CTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGT
** ** *
56700367 GGCGCTTACTAGAAAACGCCATTAAATCATAGTATTAGC
65 GGCGCTTACGGGAAAACGCCGCTAAACCATAGTATTAGC
56700406 GGCGCTTTTT
Statistics
Matches: 182, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
114 2 0.01
115 176 0.97
116 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (115 bp):
AAAGCGCCGCAAAATATCTTAACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTG
GCGCTTACGGGAAAACGCCGCTAAACCATAGTATTAGCAGCCATTACTGA
Found at i:56700669 original size:84 final size:84
Alignment explanation
Indices: 56700508--56700670 Score: 231
Period size: 84 Copynumber: 1.9 Consensus size: 84
56700498 GGTGAAGCGC
* * **
56700508 CGCAAAATATCTGAACCAAAACGCATCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTTA
1 CGCAAAATACCTGAACCAAAACGCAGCGTTTTGGTCTCGATGTATACTAAAATTAGTGGCGCTTA
*
56700573 CGTTGAAACGCCGCCAAAA
66 CGGTGAAACGCCGCCAAAA
*
56700592 CGCAAAATACCTTAACCAAAACGCAGCGTTTTGGTCGT-GATGTATACTAAAATTAGTGGCGCTT
1 CGCAAAATACCTGAACCAAAACGCAGCGTTTTGGTC-TCGATGTATACTAAAATTAGTGGCGCTT
*
56700656 AGGGT-AAACCGCCGC
65 ACGGTGAAA-CGCCGC
56700671 GAAAGCATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
83 3 0.04
84 66 0.94
85 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (84 bp):
CGCAAAATACCTGAACCAAAACGCAGCGTTTTGGTCTCGATGTATACTAAAATTAGTGGCGCTTA
CGGTGAAACGCCGCCAAAA
Found at i:56701751 original size:114 final size:115
Alignment explanation
Indices: 56701491--56701811 Score: 314
Period size: 114 Copynumber: 2.8 Consensus size: 115
56701481 AGCAAAACAG
* * * *
56701491 TGTCG-TTTTGTCTGAT-TTTTTAGTGGCGTTT-TGACTAAAACGCCGCAAAAGGAGT-TATATT
1 TGTCGTTTTTATCT-ATGTTTTTAGTGGCGTTTGT-ACCAAAACACCGCAAAAGGA-TATGTATT
** * * * * ** *
56701552 AGTGGCGTTTTACAAAAAAACGCCACAATT-TTGTTTTTAGTC-ACTGTTAAGCGT
63 AGTGGCGTTTTA-TTATAAACGCCGCAATTATT-TTATTAGGCTTTTG-TAAACGT
* * * * * *
56701606 TGTCGTTTTTATGTATGTTTTTAGTGGCGTTTTTACTAAACCACCGCAAAATGATTTGTATTAGT
1 TGTCGTTTTTATCTATGTTTTTAGTGGCGTTTGTACCAAAACACCGCAAAAGGATATGTATTAGT
* *
56701671 GGCGTTTTTTTGT-AACGCCGCAATTATTTTATTAGGCTTTTGTAAACGT
66 GGCGTTTTATTATAAACGCCGCAATTATTTTATTAGGCTTTTGTAAACGT
* ** *
56701720 TGTCGTTTTTATCTATGTTTTTAGTGGCGTTTGTACCAAAACGCCGGTAAAGGATATGTTTTAGT
1 TGTCGTTTTTATCTATGTTTTTAGTGGCGTTTGTACCAAAACACCGCAAAAGGATATGTATTAGT
56701785 GGCGTTTTATTATAAACGCCGCAATTA
66 GGCGTTTTATTATAAACGCCGCAATTA
56701812 AGTTTTAAGT
Statistics
Matches: 170, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
114 90 0.53
115 25 0.15
116 54 0.32
117 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (115 bp):
TGTCGTTTTTATCTATGTTTTTAGTGGCGTTTGTACCAAAACACCGCAAAAGGATATGTATTAGT
GGCGTTTTATTATAAACGCCGCAATTATTTTATTAGGCTTTTGTAAACGT
Found at i:56702046 original size:40 final size:40
Alignment explanation
Indices: 56701991--56702067 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
56701981 TCCCTAATTT
* *
56701991 CCCATTTCCTATTCCCCCAACTTCCCCGATTTCATTTTCC
1 CCCAATTCCTATTCCCCCAACTTCCCCGATTTAATTTTCC
* *
56702031 CCCAATTCCTTTTCCCCCAATTTCCCCGATTTAATTT
1 CCCAATTCCTATTCCCCCAACTTCCCCGATTTAATTT
56702068 CCCTAAATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.17, C:0.42, G:0.03, T:0.39
Consensus pattern (40 bp):
CCCAATTCCTATTCCCCCAACTTCCCCGATTTAATTTTCC
Done.