Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 172 of 352
Found at i:56269670 original size:49 final size:49
Alignment explanation
Indices: 56269617--56269732 Score: 164
Period size: 49 Copynumber: 2.4 Consensus size: 49
56269607 TTCGATGTCG
*
56269617 TGTCCCAAACAGGTCTTACACTAACT-TCCATATATCGAG-GCCGATGCCA
1 TGTCCCAGACAGGTCTTACACTAACTCT-CATATATCG-GTGCCGATGCCA
* * *
56269666 TGTCCCAGACAGGTCTTACACTAGCTCTCATCTATCGGTGTCGATGCCA
1 TGTCCCAGACAGGTCTTACACTAACTCTCATATATCGGTGCCGATGCCA
56269715 TGTCCCAGACAGGTCTTA
1 TGTCCCAGACAGGTCTTA
56269733 TACTGACACA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
48 1 0.02
49 59 0.97
50 1 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (49 bp):
TGTCCCAGACAGGTCTTACACTAACTCTCATATATCGGTGCCGATGCCA
Found at i:56271309 original size:19 final size:21
Alignment explanation
Indices: 56271287--56271336 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
56271277 TAAGCTTTGG
56271287 AGCTTCTGTTCAAC-CTT-CA
1 AGCTTCTGTTCAACTCTTACA
* *
56271306 AGCTTCTGTTCAGCTCTTACG
1 AGCTTCTGTTCAACTCTTACA
56271327 AGCTTCTGTT
1 AGCTTCTGTT
56271337 GGTGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 13 0.48
20 3 0.11
21 11 0.41
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (21 bp):
AGCTTCTGTTCAACTCTTACA
Found at i:56271330 original size:40 final size:40
Alignment explanation
Indices: 56271229--56271336 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 40
56271219 GTATTTTATT
* * *
56271229 TTCTGTTCAGCTTTTATGAGCTTCTATTCAACTCTTATGAGT
1 TTCTGTTCAGC-TTTACGAGCTTCTGTTCAACTCTTA-GAGC
* * *
56271271 TTTTGTTAAGCTTT-GGAGCTTCTGTTCAAC-CTTCA-AGC
1 TTCTGTTCAGCTTTACGAGCTTCTGTTCAACTCTT-AGAGC
56271309 TTCTGTTCAGCTCTTACGAGCTTCTGTT
1 TTCTGTTCAGCT-TTACGAGCTTCTGTT
56271337 GGTGTATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
38 12 0.22
39 5 0.09
40 26 0.47
41 3 0.05
42 9 0.16
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (40 bp):
TTCTGTTCAGCTTTACGAGCTTCTGTTCAACTCTTAGAGC
Found at i:56271332 original size:21 final size:21
Alignment explanation
Indices: 56271229--56271336 Score: 89
Period size: 21 Copynumber: 5.3 Consensus size: 21
56271219 GTATTTTATT
* *
56271229 TTCTGTTCAGCTTTTATGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * *
56271250 TTCTATTCAACTCTTATGAGT
1 TTCTGTTCAGCTCTTACGAGC
* * *
56271271 TTTTGTTAAGCT-TT-GGAGC
1 TTCTGTTCAGCTCTTACGAGC
* *
56271290 TTCTGTTCAAC-CTT-CAAGC
1 TTCTGTTCAGCTCTTACGAGC
56271309 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
56271330 TTCTGTT
1 TTCTGTT
56271337 GGTGTATTTA
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
19 26 0.39
20 5 0.07
21 36 0.54
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:56278711 original size:17 final size:17
Alignment explanation
Indices: 56278689--56278727 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
56278679 TTATTTATTC
56278689 TATTGTTGGAATT-TAA
1 TATTGTTGGAATTATAA
56278705 GTATTGTTGGAATTATAA
1 -TATTGTTGGAATTATAA
56278723 TATTG
1 TATTG
56278728 AATTGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAATTATAA
Found at i:56278890 original size:21 final size:21
Alignment explanation
Indices: 56278864--56278910 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
56278854 CATGTTTTAC
*
56278864 TTTCTGTTCAAATCTTATGAG
1 TTTCTGTTCAAATCTTACGAG
* **
56278885 TTTCTGTTTAGCTCTTACGAG
1 TTTCTGTTCAAATCTTACGAG
56278906 TTTCT
1 TTTCT
56278911 ATACTTTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (21 bp):
TTTCTGTTCAAATCTTACGAG
Found at i:56283045 original size:40 final size:40
Alignment explanation
Indices: 56282982--56283272 Score: 455
Period size: 40 Copynumber: 7.3 Consensus size: 40
56282972 ATTCGGATTG
56282982 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
56283021 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
56283061 ATAACCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
56283101 ATAACCGGGCCAAGTCCCGAAGGCGA-TTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGC-ATTTGTGCGAGTTACT
* *
56283141 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
56283181 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
56283221 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
*
56283261 ATATCC-GGCTAA
1 ATAACCGGGCTAA
56283273 ACCCCGACGG
Statistics
Matches: 239, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
39 22 0.09
40 216 0.90
41 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:56285573 original size:22 final size:23
Alignment explanation
Indices: 56285548--56285590 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
56285538 AAAGCCGAGG
56285548 AGCTCAGTAT-GGAG-AAAAGAAA
1 AGCTCA-TATGGGAGCAAAAGAAA
*
56285570 AGCTGATATGGGAGCAAAAGA
1 AGCTCATATGGGAGCAAAAGA
56285591 GTTTCGTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 9 0.50
23 6 0.33
ACGTcount: A:0.47, C:0.09, G:0.30, T:0.14
Consensus pattern (23 bp):
AGCTCATATGGGAGCAAAAGAAA
Found at i:56291247 original size:40 final size:40
Alignment explanation
Indices: 56291182--56291481 Score: 428
Period size: 40 Copynumber: 7.6 Consensus size: 40
56291172 ATTCGGATTG
56291182 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
56291221 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
56291261 ATAACTGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
56291301 ATAACCTGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
56291341 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
56291381 ATAACCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
56291420 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* **
56291460 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
56291482 TACTTGGTTT
Statistics
Matches: 240, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
39 68 0.28
40 172 0.72
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:56293347 original size:16 final size:16
Alignment explanation
Indices: 56293326--56293358 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
56293316 GTATGGGGAT
56293326 TTACTTTTAGTAATGA
1 TTACTTTTAGTAATGA
56293342 TTACTTTTAGTAATGA
1 TTACTTTTAGTAATGA
56293358 T
1 T
56293359 GGTTGATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (16 bp):
TTACTTTTAGTAATGA
Found at i:56295816 original size:20 final size:20
Alignment explanation
Indices: 56295771--56295816 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
56295761 GACAATGTTC
*
56295771 AAGTTGTGAAAGACTATTGT
1 AAGTTGTGAAAGACTATGGT
* *
56295791 ATGTTGTGAAAGATTATGGT
1 AAGTTGTGAAAGACTATGGT
56295811 AAGTTG
1 AAGTTG
56295817 CAAGTTGGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (20 bp):
AAGTTGTGAAAGACTATGGT
Found at i:56301740 original size:46 final size:46
Alignment explanation
Indices: 56301651--56301770 Score: 145
Period size: 46 Copynumber: 2.6 Consensus size: 46
56301641 TATGTGTGCT
*
56301651 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATCATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATCACGAGAGCC
* * *
56301697 AGTGTAAGACATGTCTGGGACATGCATCGG-CA-TTGAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAT--CACGAGAGCC
* * *
56301743 ACTGTAATACATGTCTGGGACATACATC
1 AGTGTAAGACATGTCTGGGACATGCATC
56301771 AGCCTCGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 1 0.02
45 2 0.03
46 62 0.95
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATCACGAGAGCC
Found at i:56301899 original size:49 final size:49
Alignment explanation
Indices: 56301793--56302008 Score: 189
Period size: 48 Copynumber: 4.6 Consensus size: 49
56301783 TACAAGCTAG
* * * * *
56301793 TGTAAGACCTGTCTGGGACATGGCATCAAC-TTG-T-TATG--TGTCAA
1 TGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAAAGGCAA
* * *
56301837 TGTAAGACATGTCTAGGACATGGCATCGACATCGATAGATGAGAGGCAA
1 TGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAAAGGCAA
* * * *
56301886 TGTAAGACCTGTCTGGGACATGGCATCG-CCTCGTTATATGAAAGTCAA
1 TGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAAAGGCAA
* * ** *
56301934 TGTAAGACCTATCTGGGACATGGCATCGAC-TTGAT-G-TGTTAGGCAG
1 TGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAAAGGCAA
* *
56301980 TGTAAGACCATGTCTGGGATATGGAATCG
1 TGTAAGACC-TGTCTGGGACATGGCATCG
56302009 GCGTCTTATC
Statistics
Matches: 140, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
44 27 0.19
45 2 0.01
46 16 0.11
47 19 0.14
48 45 0.32
49 31 0.22
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (49 bp):
TGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAAAGGCAA
Found at i:56301904 original size:93 final size:93
Alignment explanation
Indices: 56301793--56302003 Score: 248
Period size: 97 Copynumber: 2.2 Consensus size: 93
56301783 TACAAGCTAG
* * *
56301793 TGTAAGACCTGTCTGGGACATGGCATCAACTTG-T-TATG-TGTCAATGTAAGACATGTCTAGGA
1 TGTAAGACCTGTCTGGGACATGGCATCAACTCGTTATATGAAGTCAATGTAAGACATATCTAGGA
56301855 CATGGCATCGACATCGATAGATGAGAGGCAA
66 CATGGCATCGAC-TCGAT-G-TGAGAGGCAA
** * *
56301886 TGTAAGACCTGTCTGGGACATGGCATCGCCTCGTTATATGAAAGTCAATGTAAGACCTATCTGGG
1 TGTAAGACCTGTCTGGGACATGGCATCAACTCGTTATATG-AAGTCAATGTAAGACATATCTAGG
* ** *
56301951 ACATGGCATCGACTTGATGTGTTAGGCAG
65 ACATGGCATCGACTCGATGTGAGAGGCAA
*
56301980 TGTAAGACCATGTCTGGGATATGG
1 TGTAAGACC-TGTCTGGGACATGG
56302004 AATCGGCGTC
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
93 30 0.30
94 17 0.17
95 18 0.18
96 4 0.04
97 32 0.32
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (93 bp):
TGTAAGACCTGTCTGGGACATGGCATCAACTCGTTATATGAAGTCAATGTAAGACATATCTAGGA
CATGGCATCGACTCGATGTGAGAGGCAA
Found at i:56301905 original size:141 final size:138
Alignment explanation
Indices: 56301699--56301966 Score: 328
Period size: 141 Copynumber: 1.9 Consensus size: 138
56301689 TGAGAGCCAG
* * * * *
56301699 TGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAGAGCTACTGTAATACATGTCTGGGAC
1 TGTAAGACATGTCTAGGACATGCATCGACATCGAGACGAGAGCTAATGTAAGACATGTCTGGGAC
* *
56301764 AT-ACATCAGCCTCGAAATAT-ACAAG-CTAGTGTAAGACCTGTCTGGGACATGGCATCAACTTG
66 ATGACATC-GCCTCGAAATATGA-AAGTC-AATGTAAGACCTATCTGGGACATGGCATCAACTTG
56301826 TTATGTGTCAA
128 TTATGTGTCAA
* *
56301837 TGTAAGACATGTCTAGGACATGGCATCGACATCGATAGATGAGAGGC-AATGTAAGACCTGTCTG
1 TGTAAGACATGTCTAGGACAT-GCATCGACATCG--AGACGAGA-GCTAATGTAAGACATGTCTG
* ** *
56301901 GGACATGGCATCGCCTCGTTATATGAAAGTCAATGTAAGACCTATCTGGGACATGGCATCGACTT
62 GGACATGACATCGCCTCGAAATATGAAAGTCAATGTAAGACCTATCTGGGACATGGCATCAACTT
56301966 G
127 G
56301967 ATGTGTTAGG
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
138 20 0.18
139 10 0.09
141 72 0.65
142 8 0.07
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (138 bp):
TGTAAGACATGTCTAGGACATGCATCGACATCGAGACGAGAGCTAATGTAAGACATGTCTGGGAC
ATGACATCGCCTCGAAATATGAAAGTCAATGTAAGACCTATCTGGGACATGGCATCAACTTGTTA
TGTGTCAA
Found at i:56309493 original size:49 final size:49
Alignment explanation
Indices: 56309436--56309660 Score: 290
Period size: 49 Copynumber: 4.6 Consensus size: 49
56309426 ATACGCATAA
*
56309436 TAGCCTGCACTTAGTACTACACATGTGACCAACAATCCAGTACACGTAG
1 TAGCCTGCACTTAGTACTACACACGTGACCAACAATCCAGTACACGTAG
*
56309485 TAGCCTGCACTTAGTACTACACACGTGACCAACAATCCAGTACACATAG
1 TAGCCTGCACTTAGTACTACACACGTGACCAACAATCCAGTACACGTAG
* * * * *
56309534 TAGCCTACACTTAGTACTACGCACGTGACCTCACCAT-CTGATACACGTAG
1 TAGCCTGCACTTAGTACTACACACGTGACC-AACAATCCAG-TACACGTAG
* * * * ***
56309584 TAGCCTGCACTTAGTACTACACATGCGACTTAACAGTATGGTACACGTAG
1 TAGCCTGCACTTAGTACTACACACGTGAC-CAACAATCCAGTACACGTAG
56309634 TAGCCTGCACTTAGTACTACACACGTG
1 TAGCCTGCACTTAGTACTACACACGTG
56309661 TATTCACAAT
Statistics
Matches: 152, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
49 77 0.51
50 74 0.49
51 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
TAGCCTGCACTTAGTACTACACACGTGACCAACAATCCAGTACACGTAG
Found at i:56309549 original size:23 final size:23
Alignment explanation
Indices: 56309474--56309550 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 23
56309464 CCAACAATCC
* *
56309474 AGTACACGTAGTAGCCTGCACTT
1 AGTACACATAGTAGCCTACACTT
* * * *
56309497 AGTACTACACACGT-GACCAACAATCC
1 AGTAC-ACATA-GTAG-CCTACACT-T
56309523 AGTACACATAGTAGCCTACACTT
1 AGTACACATAGTAGCCTACACTT
56309546 AGTAC
1 AGTAC
56309551 TACGCACGTG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
23 10 0.26
24 12 0.31
25 12 0.31
26 5 0.13
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.22
Consensus pattern (23 bp):
AGTACACATAGTAGCCTACACTT
Found at i:56310957 original size:43 final size:43
Alignment explanation
Indices: 56310896--56311021 Score: 191
Period size: 44 Copynumber: 2.9 Consensus size: 43
56310886 CTCGTACAAC
* * *
56310896 GCCAACGTCCTAGACGTGGTCTTACATGTAATCACATATCGAT
1 GCCAACATCCCAGACGTGGTCTTACACGTAATCACATATCGAT
* *
56310939 GCCAACATCCCAGACGTGGCCTTACACGTAAATCACAAATCGAT
1 GCCAACATCCCAGACGTGGTCTTACACGT-AATCACATATCGAT
56310983 GCCAACATCCCAGACGTGGTCTTACACG-AATCACATATC
1 GCCAACATCCCAGACGTGGTCTTACACGTAATCACATATC
56311022 AGAATCCTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
42 10 0.13
43 25 0.33
44 40 0.53
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
GCCAACATCCCAGACGTGGTCTTACACGTAATCACATATCGAT
Found at i:56314814 original size:44 final size:44
Alignment explanation
Indices: 56314617--56314826 Score: 229
Period size: 44 Copynumber: 4.9 Consensus size: 44
56314607 TTTTATCAAA
* *
56314617 TCACCGGCATT-TAGCCTGCTAGGTTTTAAA--CCCGA-ATTCA-T
1 TCACCGGCATTATAGCCTGCTAGG-CTCAAAGGCCCGATA-TCATT
* * * * *
56314658 CCACCGGCATT-TCGTCTGCTAGGCTCAAA-GCCTGTTATCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGATATCATT
*
56314700 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCG-ATA-TCATT
*
56314745 TCACCGGCATTATAACCTGCTAGGCTCAAAGGCCCGATATCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGATATCATT
**
56314789 TCACTAGCATTATAGCCTGCTAGGCTCAAAGGCCCGAT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAT
56314827 TAGTACCGTA
Statistics
Matches: 143, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
40 4 0.03
41 26 0.18
42 12 0.08
43 17 0.12
44 44 0.31
45 39 0.27
46 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (44 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGATATCATT
Found at i:56320089 original size:47 final size:47
Alignment explanation
Indices: 56319970--56320141 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 47
56319960 GGGATATTTG
**
56319970 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACAGATGGATACGA
* * * *
56320017 -GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACAGATGGATACGA
* **
56320063 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT--GAA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACAGATGGATACG-A
* *
56320109 CGC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCAC
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
56320142 TTATGGGCGG
Statistics
Matches: 107, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
44 30 0.28
46 42 0.39
47 35 0.33
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (47 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACAGATGGATACGA
Found at i:56320131 original size:44 final size:44
Alignment explanation
Indices: 56319975--56320147 Score: 193
Period size: 44 Copynumber: 3.8 Consensus size: 44
56319965 ATTTGGGCAT
* *
56319975 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAGCGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT--GAACGC
*** * *** *
56320021 CCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGAACGC
*
56320066 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAACGC
*
56320112 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56320148 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
44 36 0.34
45 1 0.01
46 36 0.34
47 32 0.30
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (44 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAACGC
Found at i:56324146 original size:49 final size:49
Alignment explanation
Indices: 56324089--56324360 Score: 305
Period size: 49 Copynumber: 5.5 Consensus size: 49
56324079 ATACGCATAA
56324089 TAGCCTGCACTTAGTACTACACATGTGACCAACAATCCAGTACACGTAG
1 TAGCCTGCACTTAGTACTACACATGTGACCAACAATCCAGTACACGTAG
* *
56324138 TAGCCTGCACTTAGTACTACACATGTGACCAACAATCCAATACACATAG
1 TAGCCTGCACTTAGTACTACACATGTGACCAACAATCCAGTACACGTAG
* * * * *
56324187 TAGCCTGCACTTAGTACTACGCACGTGACCTCACCAT-CTGATACACGTAG
1 TAGCCTGCACTTAGTACTACACATGTGACC-AACAATCCAG-TACACGTAG
* * ** ** *
56324237 TAGCCTGCACTTAGTACTACACACGTGATCGAAGTC-ATTGAGTAGGCATAG
1 TAGCCTGCACTTAGTACTACACATGTGA-CCAA--CAATCCAGTACACGTAG
* * ***
56324288 TAGCCTGCACTTAGTACTACACATGTGACTTAACAGTATGGTACACGTAG
1 TAGCCTGCACTTAGTACTACACATGTGAC-CAACAATCCAGTACACGTAG
56324338 TAGCCTGCACTTAGTACTACACA
1 TAGCCTGCACTTAGTACTACACA
56324361 CGTGTATTCA
Statistics
Matches: 189, Mismatches: 26, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
49 77 0.41
50 72 0.38
51 38 0.20
52 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGCCTGCACTTAGTACTACACATGTGACCAACAATCCAGTACACGTAG
Found at i:56324333 original size:101 final size:98
Alignment explanation
Indices: 56324079--56324364 Score: 360
Period size: 101 Copynumber: 2.9 Consensus size: 98
56324069 AAGCTATCTG
* **
56324079 ATACGCATAATAGCCTGCACTTAGTACTACACATGTGAC-CAACAATCCAGTACACGTAGTAGCC
1 ATACGCATAGTAGCCTGCACTTAGTACTACACATGTGACTCAAC-ATCTGGTACACGTAGTAGCC
*
56324143 TGCACTTAGTACTACACATGTGACCAACAATCCA
65 TGCACTTAGTACTACACACGTGACCAACAATCCA
* * * * *
56324177 ATACACATAGTAGCCTGCACTTAGTACTACGCACGTGACCTCACCATCTGATACACGTAGTAGCC
1 ATACGCATAGTAGCCTGCACTTAGTACTACACATGTGA-CTCAACATCTGGTACACGTAGTAGCC
* **
56324242 TGCACTTAGTACTACACACGTGATCGAAGTC-ATTGA
65 TGCACTTAGTACTACACACGTGA-CCAA--CAATCCA
* * * *
56324278 GTAGGCATAGTAGCCTGCACTTAGTACTACACATGTGACTTAACAGTATGGTACACGTAGTAGCC
1 ATACGCATAGTAGCCTGCACTTAGTACTACACATGTGACTCAACA-TCTGGTACACGTAGTAGCC
56324343 TGCACTTAGTACTACACACGTG
65 TGCACTTAGTACTACACACGTG
56324365 TATTCACAAT
Statistics
Matches: 161, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
98 34 0.21
99 40 0.25
100 11 0.07
101 75 0.47
102 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (98 bp):
ATACGCATAGTAGCCTGCACTTAGTACTACACATGTGACTCAACATCTGGTACACGTAGTAGCCT
GCACTTAGTACTACACACGTGACCAACAATCCA
Found at i:56325753 original size:44 final size:43
Alignment explanation
Indices: 56325605--56325771 Score: 139
Period size: 42 Copynumber: 3.9 Consensus size: 43
56325595 CTCGTACAAC
*
56325605 GCCAACATCCCAGACGTGGTCTTACATGTAATCACATATCGAT
1 GCCAACATCCCAGACGTGGTCTTACACGTAATCACATATCGAT
* * * *
56325648 GCC-ACTGTCCTAGACAG-GG-CTTACAC-AAACTCATATAT-GAT
1 GCCAAC-ATCCCAGAC-GTGGTCTTACACGTAA-TCACATATCGAT
*** ** * * *
56325689 GTTGATGTCCCAAACATGGTCTTACACGTAATTCACAAATCGAT
1 GCCAACATCCCAGACGTGGTCTTACACGTAA-TCACATATCGAT
56325733 GCCAACATCCCAGACGTGGTCTTACACG-AATCACATATC
1 GCCAACATCCCAGACGTGGTCTTACACGTAATCACATATC
56325772 AGAATCCTAT
Statistics
Matches: 93, Mismatches: 23, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
41 15 0.16
42 31 0.33
43 22 0.24
44 25 0.27
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (43 bp):
GCCAACATCCCAGACGTGGTCTTACACGTAATCACATATCGAT
Found at i:56331565 original size:29 final size:28
Alignment explanation
Indices: 56331518--56331616 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 28
56331508 CATGAGATTG
** *
56331518 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCAAGTTT-AATTACATA
* *
56331547 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTTAATTACATA
** * **
56331575 GCACTAAGTGTGTGAGTTTGATTATGTAA
1 GCACTAAGTGTGCAAGTTTAATTACAT-A
56331604 GCACTAAGTGTGC
1 GCACTAAGTGTGC
56331617 GGACTTACTA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
28 30 0.50
29 30 0.50
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTTAATTACATA
Found at i:56331584 original size:28 final size:28
Alignment explanation
Indices: 56331544--56331616 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
56331534 TTTAAATTGC
56331544 ATAGCACTAAGTGTGCAAGTTTGATTAT
1 ATAGCACTAAGTGTGCAAGTTTGATTAT
**
56331572 ATAGCACTAAGTGTGTGAGTTTGATTAT
1 ATAGCACTAAGTGTGCAAGTTTGATTAT
*
56331600 GTAAGCACTAAGTGTGC
1 AT-AGCACTAAGTGTGC
56331617 GGACTTACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 27 0.68
29 13 0.32
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (28 bp):
ATAGCACTAAGTGTGCAAGTTTGATTAT
Found at i:56340865 original size:43 final size:42
Alignment explanation
Indices: 56340776--56340884 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 42
56340766 TAAGATTACG
* *
56340776 TGTAAGACCATA-TCTGGGATATGGCATCGATATGAGACTTCG
1 TGTAAGACCATAGT-TGGGATATGGCATCGATATGAGACTCCA
* * *
56340818 TGTAAGACCATAGTTGGGCTATTGGCGTCGATATGAG-GTCCCA
1 TGTAAGACCATAGTTGGGATA-TGGCATCGATATGAGACT-CCA
*
56340861 TGTAAGACCATAGCTGGGATATGG
1 TGTAAGACCATAGTTGGGATATGG
56340885 AATTGGTATG
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
42 22 0.39
43 35 0.61
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATAGTTGGGATATGGCATCGATATGAGACTCCA
Found at i:56340998 original size:20 final size:20
Alignment explanation
Indices: 56340970--56341016 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
56340960 TAGCAATGTT
56340970 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
56340990 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
56341010 TAAGTTG
1 TAAGTTG
56341017 CAAGTTGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:56341880 original size:13 final size:13
Alignment explanation
Indices: 56341862--56341891 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56341852 GACACAGCCA
56341862 TGTGTCTCGGCCG
1 TGTGTCTCGGCCG
*
56341875 TGTGTCTGGGCCG
1 TGTGTCTCGGCCG
56341888 TGTG
1 TGTG
56341892 AAGGACACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.43, T:0.33
Consensus pattern (13 bp):
TGTGTCTCGGCCG
Found at i:56344892 original size:21 final size:22
Alignment explanation
Indices: 56344867--56344917 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
56344857 CCTATAGCAT
**
56344867 GGGCGTGTCCC-AGGGTCACAC
1 GGGCGTGTCCCTAGGACCACAC
* *
56344888 GGGCGTGCCCCTTGGACCACAC
1 GGGCGTGTCCCTAGGACCACAC
56344910 GGGCGTGT
1 GGGCGTGT
56344918 GAGCCCTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.12, C:0.33, G:0.39, T:0.16
Consensus pattern (22 bp):
GGGCGTGTCCCTAGGACCACAC
Found at i:56345519 original size:30 final size:30
Alignment explanation
Indices: 56345483--56345541 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
56345473 TGCAGATAAG
*
56345483 GATTTGGATAATGAGAAGGGTAAGGAAAAA
1 GATTTGGATAATGAGAAAGGTAAGGAAAAA
56345513 GATTTGGATAATGAGAAAGGTAAGGAAAA
1 GATTTGGATAATGAGAAAGGTAAGGAAAA
56345542 TGAATATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.20
Consensus pattern (30 bp):
GATTTGGATAATGAGAAAGGTAAGGAAAAA
Found at i:56346436 original size:20 final size:18
Alignment explanation
Indices: 56346383--56346437 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
56346373 TTTTAAAAAT
*
56346383 AATATATTTTTATTTATA
1 AATATATTTTTATTTTTA
*
56346401 AA-ATATTTATAATTTTTA
1 AATATATTT-TTATTTTTA
56346419 ATATATATTTTTAGTTTTT
1 A-ATATATTTTTA-TTTTT
56346438 TTATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 6 0.20
18 10 0.33
19 3 0.10
20 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
AATATATTTTTATTTTTA
Found at i:56347457 original size:10 final size:11
Alignment explanation
Indices: 56347426--56347458 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
56347416 CGGCCCGCCC
56347426 ATATTAATTTT
1 ATATTAATTTT
*
56347437 ATATTATTTTT
1 ATATTAATTTT
56347448 ATA-TAATTTT
1 ATATTAATTTT
56347458 A
1 A
56347459 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:56347468 original size:16 final size:18
Alignment explanation
Indices: 56347447--56347482 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
56347437 ATATTATTTT
56347447 TATATAAT-T-TTAAAAA
1 TATATAATATATTAAAAA
56347463 TATATAATATATTAAAAA
1 TATATAATATATTAAAAA
56347481 TA
1 TA
56347483 CTAACAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 1 0.06
18 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATATAATATATTAAAAA
Found at i:56347624 original size:30 final size:29
Alignment explanation
Indices: 56347581--56347641 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
56347571 CTTAACAAGA
*
56347581 AAATGTCTCTAAAATAATAATAAAATTAAC
1 AAATGTATCTAAAATAATAA-AAAATTAAC
*
56347611 AAATGTATTTAAAATAATAAAAAATTAAC
1 AAATGTATCTAAAATAATAAAAAATTAAC
56347640 AA
1 AA
56347642 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (29 bp):
AAATGTATCTAAAATAATAAAAAATTAAC
Found at i:56354483 original size:42 final size:43
Alignment explanation
Indices: 56354395--56354501 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 43
56354385 TAAGATTACG
* *
56354395 TGTAAGACCATA-TCTGGGATATGGCATCGATATGAGACTTCG
1 TGTAAGACCATAGTCTGGGATATGGCATCGATATGAGACTCCA
* * *
56354437 TGTAAGACCATAGT-TGGGCTATTGGCGTCGATATGAG-GTCCA
1 TGTAAGACCATAGTCTGGGATA-TGGCATCGATATGAGACTCCA
56354479 TGTAAGACCATAG-C-GGGATATGG
1 TGTAAGACCATAGTCTGGGATATGG
56354502 AATTGGTATG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
40 3 0.05
41 5 0.09
42 33 0.59
43 15 0.27
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (43 bp):
TGTAAGACCATAGTCTGGGATATGGCATCGATATGAGACTCCA
Found at i:56354615 original size:20 final size:20
Alignment explanation
Indices: 56354587--56354633 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
56354577 TAGCAATGTT
56354587 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
56354607 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
56354627 TAAGTTG
1 TAAGTTG
56354634 CAAGTGGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:56355484 original size:13 final size:13
Alignment explanation
Indices: 56355466--56355495 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56355456 AGACACGCCA
56355466 TGTGTCTCGGCCG
1 TGTGTCTCGGCCG
*
56355479 TGTGTCTGGGCCG
1 TGTGTCTCGGCCG
56355492 TGTG
1 TGTG
56355496 AAGACACAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.43, T:0.33
Consensus pattern (13 bp):
TGTGTCTCGGCCG
Found at i:56358452 original size:21 final size:22
Alignment explanation
Indices: 56358426--56358475 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
56358416 CCTATAGCAT
**
56358426 GGGCGTGTCCC-AGGGTCACAC
1 GGGCGTGTCCCTAGGACCACAC
*
56358447 GGGCGTG-CCCTTGGACCACAC
1 GGGCGTGTCCCTAGGACCACAC
56358468 GGGCGTGT
1 GGGCGTGT
56358476 GAGCCCTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.12, C:0.32, G:0.40, T:0.16
Consensus pattern (22 bp):
GGGCGTGTCCCTAGGACCACAC
Found at i:56359085 original size:29 final size:29
Alignment explanation
Indices: 56359035--56359091 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
56359025 TGCAGATAAG
56359035 GATTTGGATAATGAGAAGGGTAAGGAAAA
1 GATTTGGATAATGAGAAGGGTAAGGAAAA
56359064 GATTTGGATAATAGAGAA-GGTAAGGAAA
1 GATTTGGATAAT-GAGAAGGGTAAGGAAA
56359092 TGAATATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.21
Consensus pattern (29 bp):
GATTTGGATAATGAGAAGGGTAAGGAAAA
Found at i:56368168 original size:43 final size:42
Alignment explanation
Indices: 56368079--56368187 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 42
56368069 TAAGATTACG
* *
56368079 TGTAAGACCATA-TCTGGGATATGGCATCGATATGAGACTTCG
1 TGTAAGACCATAGT-TGGGATATGGCATCGATATGAGACTCCA
* * *
56368121 TGTAAGACCATAGTTGGGCTATTGGCGTCGATATGAG-GTCCCA
1 TGTAAGACCATAGTTGGGATA-TGGCATCGATATGAGACT-CCA
*
56368164 TGTAAGACCATAGCTGGGATATGG
1 TGTAAGACCATAGTTGGGATATGG
56368188 AATTGGTATG
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
42 22 0.39
43 35 0.61
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATAGTTGGGATATGGCATCGATATGAGACTCCA
Found at i:56368301 original size:20 final size:20
Alignment explanation
Indices: 56368273--56368319 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
56368263 TAGCAATGTT
56368273 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
56368293 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
56368313 TAAGTTG
1 TAAGTTG
56368320 CAAGTTGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:56369186 original size:13 final size:13
Alignment explanation
Indices: 56369168--56369197 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56369158 GACACAGCCA
56369168 TGTGTCTCGGCCG
1 TGTGTCTCGGCCG
*
56369181 TGTGTCTGGGCCG
1 TGTGTCTCGGCCG
56369194 TGTG
1 TGTG
56369198 AAGGACACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.43, T:0.33
Consensus pattern (13 bp):
TGTGTCTCGGCCG
Found at i:56376415 original size:39 final size:39
Alignment explanation
Indices: 56376359--56376435 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
56376349 CCTCTGACAT
*
56376359 ATTTCTGGGAACCTTCCACTAAAGTATGGCTCCAATCTC
1 ATTTCTAGGAACCTTCCACTAAAGTATGGCTCCAATCTC
* * *
56376398 ATTTCTAGGAACTTTCCACTGAAGTATGGCTTCAATCT
1 ATTTCTAGGAACCTTCCACTAAAGTATGGCTCCAATCT
56376436 TCTTCGGATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (39 bp):
ATTTCTAGGAACCTTCCACTAAAGTATGGCTCCAATCTC
Found at i:56378239 original size:94 final size:94
Alignment explanation
Indices: 56378078--56378356 Score: 522
Period size: 94 Copynumber: 3.0 Consensus size: 94
56378068 AGTCAAGATT
56378078 TCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGC
1 TCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGC
56378143 AATTTACTTAATTCAAATAGCATATAAAA
66 AATTTACTTAATTCAAATAGCATATAAAA
*
56378172 TCTGCACACAAAGTGACATTTAATTTCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGC
1 TCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGC
56378237 AATTTACTTAATTCAAATAGCATATAAAA
66 AATTTACTTAATTCAAATAGCATATAAAA
* *
56378266 TCTACACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATATGGC
1 TCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGC
*
56378331 AACTTACTTAATTCAAATAGCATATA
66 AATTTACTTAATTCAAATAGCATATA
56378357 CGGTCACATT
Statistics
Matches: 180, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 180 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (94 bp):
TCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGC
AATTTACTTAATTCAAATAGCATATAAAA
Found at i:56385842 original size:24 final size:25
Alignment explanation
Indices: 56385814--56385877 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
56385804 TCAACCAAAT
* * *
56385814 TCGCACACATAGTGCTA-ATTAAGC
1 TCGCACACATAGTGCCATACTAAAC
56385838 TCGCACACATAGTGCCATACTAAAC
1 TCGCACACATAGTGCCATACTAAAC
56385863 -CGCACACATAGTGCC
1 TCGCACACATAGTGCC
56385878 TGAAATTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (25 bp):
TCGCACACATAGTGCCATACTAAAC
Found at i:56386019 original size:94 final size:94
Alignment explanation
Indices: 56385906--56386187 Score: 503
Period size: 94 Copynumber: 3.0 Consensus size: 94
56385896 ATCGACATTC
*
56385906 AAATCTGCACACATAGTGACATTTAATTCCGCACACATTATGCCAATGTTAACTCATTATAATAA
1 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATTATGCCAATGTTAACTCATTATAATAA
56385971 GGCAATTTACTTAATTCAAATAGCATATA
66 GGCAATTTACTTAATTCAAATAGCATATA
*
56386000 AAATCTGCACACAGAGTGACATTTAATTCCGCACACA-TAGTGCCAATGTTAACTCATTATAATA
1 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATTA-TGCCAATGTTAACTCATTATAATA
56386064 AGGCAATTTACTTAATTCAAATAGCATATA
65 AGGCAATTTACTTAATTCAAATAGCATATA
* *
56386094 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATTGTGCCAATGTTAACTCATTATAATAT
1 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATTATGCCAATGTTAACTCATTATAATAA
*
56386159 GGCAACTTACTTAATTCAAATAGCATATA
66 GGCAATTTACTTAATTCAAATAGCATATA
56386188 TGGTCACATT
Statistics
Matches: 181, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
93 2 0.01
94 178 0.98
95 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (94 bp):
AAATCTGCACACAAAGTGACATTTAATTCCGCACACATTATGCCAATGTTAACTCATTATAATAA
GGCAATTTACTTAATTCAAATAGCATATA
Found at i:56387404 original size:17 final size:17
Alignment explanation
Indices: 56387379--56387413 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
56387369 TTTCTCTCCC
*
56387379 TTTCTTATTAATTCCTT
1 TTTCCTATTAATTCCTT
56387396 TTTCCTATTAATTCCTT
1 TTTCCTATTAATTCCTT
56387413 T
1 T
56387414 CTTTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTCCTATTAATTCCTT
Found at i:56389264 original size:16 final size:17
Alignment explanation
Indices: 56389239--56389283 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
56389229 TATTTAAGAA
56389239 ATAATAAATAATAAA-T
1 ATAATAAATAATAAAGT
*
56389255 ATAATTAATAATAAAGT
1 ATAATAAATAATAAAGT
*
56389272 AAAATAAATAAT
1 ATAATAAATAAT
56389284 GAATGAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAATAAATAATAAAGT
Found at i:56389294 original size:20 final size:18
Alignment explanation
Indices: 56389237--56389295 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 18
56389227 ATTATTTAAG
56389237 AAATAATAAATAATAAATAT
1 AAATAAT-AATAATAAA-AT
*
56389257 AATTAATAATAAAGTAAAAT
1 AAATAATAAT-AA-TAAAAT
56389277 AAATAATGAATGAATAAAA
1 AAATAAT-AAT-AATAAAA
56389296 GAAAACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 21 0.64
21 9 0.27
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAATAATAATAATAAAAT
Found at i:56391400 original size:16 final size:16
Alignment explanation
Indices: 56391379--56391414 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
56391369 AAACCCTAAT
56391379 TTTCCCTTTCTT-TTTC
1 TTTCCCTTT-TTCTTTC
56391395 TTTCCCTTTTTCTTTC
1 TTTCCCTTTTTCTTTC
56391411 TTTC
1 TTTC
56391415 TTTCCCTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTCCCTTTTTCTTTC
Found at i:56392801 original size:13 final size:14
Alignment explanation
Indices: 56392775--56392807 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
56392765 ATAAAATATA
56392775 AATTTATATTTAAT
1 AATTTATATTTAAT
56392789 AATTTAT-TTTAAT
1 AATTTATATTTAAT
56392802 ATATTT
1 A-ATTT
56392808 CATTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTATATTTAAT
Found at i:56409449 original size:15 final size:15
Alignment explanation
Indices: 56409431--56409495 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
56409421 TTATCTTGGG
56409431 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
56409446 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
* *
56409461 TTTC-TCAATCTTGGA
1 TTTCTTTATTC-TGGA
*
56409476 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
56409490 TTTCTT
1 TTTCTT
56409496 GTTATCTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
14 12 0.29
15 25 0.61
16 4 0.10
ACGTcount: A:0.11, C:0.15, G:0.14, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:56409461 original size:30 final size:31
Alignment explanation
Indices: 56409427--56409495 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
56409417 TATCTTATCT
* *
56409427 TGGGTTTCTTTATTC-TGGATTTCTTTATTC
1 TGGGTTTCTTCAATCTTGGATTTCTTTATTC
56409457 TGGGTTTC-TCAATCTTGGATTTCTTTATTC
1 TGGGTTTCTTCAATCTTGGATTTCTTTATTC
*
56409487 -GGTTTTCTT
1 TGGGTTTCTT
56409496 GTTATCTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.10, C:0.14, G:0.17, T:0.58
Consensus pattern (31 bp):
TGGGTTTCTTCAATCTTGGATTTCTTTATTC
Found at i:56413880 original size:42 final size:42
Alignment explanation
Indices: 56413833--56413974 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 42
56413823 AGGGTTGAAT
*
56413833 AGAAGCTCGTAAGAGCTGAACGAAAACTCATATGAGTTAAAC
1 AGAAGCTCATAAGAGCTGAACGAAAACTCATATGAGTTAAAC
* * * *
56413875 GGAAGCTCATAAGAACTGAA-TAGAAACTCATAAGAGGTT-AAC
1 AGAAGCTCATAAGAGCTGAACGA-AAACTCATATGA-GTTAAAC
* * *
56413917 AGAA-CTTAAAAGAGCTGAACGGAAACTCATATGAGTTAAAC
1 AGAAGCTCATAAGAGCTGAACGAAAACTCATATGAGTTAAAC
*
56413958 AGAAGCTCGTAAGAGCT
1 AGAAGCTCATAAGAGCT
56413975 AATATCTCAA
Statistics
Matches: 80, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
40 3 0.04
41 31 0.39
42 43 0.54
43 3 0.04
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (42 bp):
AGAAGCTCATAAGAGCTGAACGAAAACTCATATGAGTTAAAC
Found at i:56413920 original size:21 final size:21
Alignment explanation
Indices: 56413809--56413972 Score: 68
Period size: 21 Copynumber: 7.9 Consensus size: 21
56413799 ATGAAGGCTA
*
56413809 AACAGAAACCCATAAG-GGTT
1 AACAGAAACTCATAAGAGGTT
* * * * *
56413829 GAATAGAAGCTCGTAAGAGCTG
1 -AACAGAAACTCATAAGAGGTT
*
56413851 AAC-GAAAACTCATATGA-GTT
1 AACAG-AAACTCATAAGAGGTT
* * ** *
56413871 AAACGGAAGCTCATAAGAACTG
1 -AACAGAAACTCATAAGAGGTT
*
56413893 AATAGAAACTCATAAGAGGTT
1 AACAGAAACTCATAAGAGGTT
* * * *
56413914 AACAG-AACTTAAAAGAGCTG
1 AACAGAAACTCATAAGAGGTT
* *
56413934 AACGGAAACTCATATGA-GTT
1 AACAGAAACTCATAAGAGGTT
* *
56413954 AAACAGAAGCTCGTAAGAG
1 -AACAGAAACTCATAAGAG
56413973 CTAATATCTC
Statistics
Matches: 98, Mismatches: 37, Indels: 15
0.65 0.25 0.10
Matches are distributed among these distances:
20 18 0.18
21 76 0.78
22 4 0.04
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGGTT
Found at i:56420242 original size:18 final size:18
Alignment explanation
Indices: 56420219--56420254 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
56420209 GCAAAGGCAG
56420219 ATTCCATCTATAGATACT
1 ATTCCATCTATAGATACT
56420237 ATTCCATCTATAGATACT
1 ATTCCATCTATAGATACT
56420255 GTTGAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (18 bp):
ATTCCATCTATAGATACT
Found at i:56423558 original size:4 final size:4
Alignment explanation
Indices: 56423549--56423703 Score: 75
Period size: 4 Copynumber: 39.5 Consensus size: 4
56423539 GGATACTTTA
* * * *
56423549 TCTC TCTC TCTC TCTC TCTC TCCC TCTC CCTC TCTC TCCC TCCC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
* * * * * * * * * * *
56423597 TCTC TCCC TCCC TCCC TATC ACTC CCCC TCCC CCTC -CCC TC-C CCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
* * * * * *
56423643 TCCC TCTC TCTC TCTC TCTC TC-C CCATC TCTA TTTC TCCC TCCC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TC-TC TCTC TCTC TCTC TCTC TCTC
*
56423691 CCTC -CTC TCTC TC
1 TCTC TCTC TCTC TC
56423704 CCCTCCCCTC
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
3 9 0.08
4 105 0.91
5 2 0.02
ACGTcount: A:0.03, C:0.61, G:0.00, T:0.37
Consensus pattern (4 bp):
TCTC
Found at i:56423570 original size:16 final size:16
Alignment explanation
Indices: 56423549--56423771 Score: 127
Period size: 16 Copynumber: 14.7 Consensus size: 16
56423539 GGATACTTTA
*
56423549 TCTCTCTCTCTCTCTC
1 TCTCTCCCTCTCTCTC
*
56423565 TCTCTCCCTCTCCCTC
1 TCTCTCCCTCTCTCTC
*
56423581 TCTCTCCCTCCCTCTC
1 TCTCTCCCTCTCTCTC
* *
56423597 TCTCTCCCTCCCTCCCTA
1 TCTCTCCCT--CTCTCTC
* *
56423615 TCACTCCC-C-CTCCC
1 TCTCTCCCTCTCTCTC
* *
56423629 CCTC-CCCTC-CCCTC
1 TCTCTCCCTCTCTCTC
* *
56423643 TCCCTCTCTCTCTCTC
1 TCTCTCCCTCTCTCTC
*
56423659 TCTCTCCC-CATCTCTA
1 TCTCTCCCTC-TCTCTC
*
56423675 TTTCTCCCTC-C-CTC
1 TCTCTCCCTCTCTCTC
*
56423689 TCCCT-CCTCTCTCTC
1 TCTCTCCCTCTCTCTC
*
56423704 -CCCTCCC-CTC-C-C
1 TCTCTCCCTCTCTCTC
*
56423716 -CTCTCCCTCTCTCCC
1 TCTCTCCCTCTCTCTC
56423731 TCTCTCCC-C-CTC-C
1 TCTCTCCCTCTCTCTC
* *
56423744 TCCCTCCCTCTCTCCCC
1 TCTCTCCCTCTCT-CTC
*
56423761 TCCCTCCCTCT
1 TCTCTCCCTCT
56423772 TCCCCCTCCC
Statistics
Matches: 161, Mismatches: 28, Indels: 35
0.72 0.12 0.16
Matches are distributed among these distances:
12 7 0.04
13 19 0.12
14 28 0.17
15 16 0.10
16 67 0.42
17 13 0.08
18 11 0.07
ACGTcount: A:0.02, C:0.64, G:0.00, T:0.35
Consensus pattern (16 bp):
TCTCTCCCTCTCTCTC
Found at i:56423637 original size:11 final size:12
Alignment explanation
Indices: 56423621--56423793 Score: 64
Period size: 11 Copynumber: 14.2 Consensus size: 12
56423611 CCTATCACTC
56423621 CCCCTCCCC-CT
1 CCCCTCCCCTCT
56423632 CCCCTCCCCTCT
1 CCCCTCCCCTCT
*
56423644 -CCCT-CTCTCT
1 CCCCTCCCCTCT
* *
56423654 -CTCT-CTCTCT
1 CCCCTCCCCTCT
** *
56423664 CCCCATCTCTATTT
1 CCCC-TC-CCCTCT
56423678 CTCCCT-CCCTCT
1 C-CCCTCCCCTCT
56423690 -CCCTCCTCTCTCT
1 CCCCTCC-C-CTCT
56423703 CCCCTCCCCTC-
1 CCCCTCCCCTCT
56423714 CCCTCTCCCTCTCT
1 CCC-CTCCC-CTCT
*
56423728 CCCTCTCTCCCCCT
1 CCC-CTC-CCCTCT
56423742 CCTCCCTCCCTCTCT
1 -C-CCCTCCC-CTCT
56423757 CCCCT-CCCTC-
1 CCCCTCCCCTCT
*
56423767 CCTCTTCCCC-CT
1 CC-CCTCCCCTCT
56423779 CCCC-CTCCCTCT
1 CCCCTC-CCCTCT
56423791 CCC
1 CCC
56423794 TCTGTTAACC
Statistics
Matches: 128, Mismatches: 12, Indels: 43
0.70 0.07 0.23
Matches are distributed among these distances:
10 21 0.16
11 29 0.23
12 27 0.21
13 12 0.09
14 25 0.20
15 12 0.09
16 2 0.02
ACGTcount: A:0.01, C:0.68, G:0.00, T:0.31
Consensus pattern (12 bp):
CCCCTCCCCTCT
Found at i:56423725 original size:6 final size:6
Alignment explanation
Indices: 56423549--56423796 Score: 129
Period size: 6 Copynumber: 40.5 Consensus size: 6
56423539 GGATACTTTA
* * * * *
56423549 TCTCTC TCTCTC TCTCTC TCTCCC TCTCCC TCTCTCTC CCTCCC TCTCTC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTC-C-C TCTCCC TCTCCC
* * * *
56423599 TCTCCC TCCCTCCC TATCAC TCCCCC TCCCCC TC-CCC TC-CCC TCTCCC
1 TCTCCC T--CTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC
* ** * *
56423647 TCTCTCTC TCTCTC TCTCCCC ATCTCTA TTTCTCC -CTCCC TCTCCC TCCTCTC
1 TCTC-C-C TCTCCC TCT-CCC -TCTCCC TCTC-CC TCTCCC TCTCCC T-CTCCC
* *
56423700 TCTCCC -CTCCC -CTCCCC TCTCCC TCTCTCC -CTCTC TCCCCC TCCTCCC
1 TCTCCC TCTCCC TCT-CCC TCTCCC TCTC-CC TCTCCC TCTCCC T-CTCCC
* *
56423748 TC-CCTC TCTCCC -CT-CC -CTCCC TCTTCCC CCTCCC CCTCCC TCTCCC
1 TCTCC-C TCTCCC TCTCCC TCTCCC TC-TCCC TCTCCC TCTCCC TCTCCC
56423794 TCT
1 TCT
56423797 GTTAACCCGT
Statistics
Matches: 194, Mismatches: 26, Indels: 44
0.73 0.10 0.17
Matches are distributed among these distances:
4 4 0.02
5 26 0.13
6 119 0.61
7 27 0.14
8 18 0.09
ACGTcount: A:0.02, C:0.65, G:0.00, T:0.34
Consensus pattern (6 bp):
TCTCCC
Found at i:56423789 original size:4 final size:4
Alignment explanation
Indices: 56423678--56423770 Score: 66
Period size: 4 Copynumber: 22.8 Consensus size: 4
56423668 ATCTCTATTT
* * *
56423678 CTCC CTCC CT-- CTCC CTCC TCTCT CTCCC CTCCC CTCC C-CT CTCC CTCT
1 CTCC CTCC CTCC CTCC CTCC -CTCC CT-CC CT-CC CTCC CTCC CTCC CTCC
* * *
56423726 CTCC CTCT CTCC CCCTC CTCC CTCC CTCT CTCCC CTCC CTCC CTC
1 CTCC CTCC CTCC CTC-C CTCC CTCC CTCC CT-CC CTCC CTCC CTC
56423771 TTCCCCCTCC
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
2 2 0.03
3 2 0.03
4 49 0.70
5 17 0.24
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (4 bp):
CTCC
Found at i:56423794 original size:10 final size:10
Alignment explanation
Indices: 56423552--56423795 Score: 142
Period size: 10 Copynumber: 24.9 Consensus size: 10
56423542 TACTTTATCT
* *
56423552 CTCTCTCTCT
1 CTCTCCCTCC
*
56423562 CTCTCTCTCC
1 CTCTCCCTCC
*
56423572 CTCTCCCTCT
1 CTCTCCCTCC
56423582 CTCTCCCTCC
1 CTCTCCCTCC
*
56423592 CTCTCTCTCTC
1 CTCTCCCTC-C
56423603 C-CTCCCTCC
1 CTCTCCCTCC
* *
56423612 CTATCACTCC
1 CTCTCCCTCC
*
56423622 CCCT-CC-CC
1 CTCTCCCTCC
56423630 CTC-CCCTCCC
1 CTCTCCCT-CC
*
56423640 CTCTCCCTCT
1 CTCTCCCTCC
* *
56423650 CTCTCTCTCT
1 CTCTCCCTCC
56423660 CTCTCCCCATCTC
1 CTCT-CCC-TC-C
*
56423673 TATTTCTCCCTCC
1 ---CTCTCCCTCC
56423686 CTCTCCCT-C
1 CTCTCCCTCC
*
56423695 CTCTCTCTCC
1 CTCTCCCTCC
56423705 C-CTCCCCTCC
1 CTCT-CCCTCC
56423715 C-CT--CTCC
1 CTCTCCCTCC
56423722 CTCT--CTCC
1 CTCTCCCTCC
56423730 CTCTCTCC-CC
1 CTCTC-CCTCC
56423740 CTCCTCCCTCC
1 CT-CTCCCTCC
56423751 CTCT--CTCC
1 CTCTCCCTCC
56423759 C-CTCCCTCC
1 CTCTCCCTCC
*
56423768 CTCTTCC-CC
1 CTCTCCCTCC
*
56423777 CTCCCCCTCC
1 CTCTCCCTCC
56423787 CTCTCCCTC
1 CTCTCCCTC
56423796 TGTTAACCCG
Statistics
Matches: 186, Mismatches: 24, Indels: 48
0.72 0.09 0.19
Matches are distributed among these distances:
7 7 0.04
8 21 0.11
9 25 0.13
10 106 0.57
11 16 0.09
12 2 0.01
13 1 0.01
14 2 0.01
15 3 0.02
16 3 0.02
ACGTcount: A:0.02, C:0.65, G:0.00, T:0.33
Consensus pattern (10 bp):
CTCTCCCTCC
Found at i:56424048 original size:2 final size:2
Alignment explanation
Indices: 56424041--56424230 Score: 52
Period size: 2 Copynumber: 100.0 Consensus size: 2
56424031 CTTTGGCCCT
* *
56424041 TC TC TC TC TC TC GTC TC GT- TC TC GC -C TC CC TC TC TC -C TC TC
1 TC TC TC TC TC TC -TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
56424082 TC -C TC TC -C TC TGC -C TC -C TA TC GTC -C TC TC TC CC GTC AC
1 TC TC TC TC TC TC T-C TC TC TC TC TC -TC TC TC TC TC TC -TC TC
* *
56424120 -C TC TC TC TC CC TC -C TC GTC AC -C TC TC TC TC TC -C TC TC -C
1 TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * *
56424158 CC TC TC CC TC TC CC TC CC TC TC T- TC -C CC TC TC TC CC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
56424198 TC -C CC CC TC TC TC CC CC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
56424231 ATACATAAAA
Statistics
Matches: 142, Mismatches: 24, Indels: 44
0.68 0.11 0.21
Matches are distributed among these distances:
1 16 0.11
2 117 0.82
3 9 0.06
ACGTcount: A:0.02, C:0.58, G:0.04, T:0.36
Consensus pattern (2 bp):
TC
Found at i:56424198 original size:75 final size:72
Alignment explanation
Indices: 56424065--56424230 Score: 167
Period size: 75 Copynumber: 2.2 Consensus size: 72
56424055 CTCGTTCTCG
* * * * *
56424065 CCTCCCTCTCTCCTCTCTCCTCTCCTCTGCCTCCTATCGTCCTCTCTCCCGTCACCTCTCTCTCC
1 CCTCTCTCTCTCCTCTCCCCTCTCCTCTCCCTCCTATCGTCCCCTCTCCCG-CACCTCTC-CCCC
56424130 CTC-CTCGTCA
64 CTCTCTC--CA
* *
56424140 CCTCTCTCTCTCCTCTCCCCTCTCCCTCTCCCTCCCTCTCTTCCCCTCTCTCC-C-CCTCTCCCC
1 CCTCTCTCTCTCCTCTCCCCTCT-CCTCTCCCT-CCTATCGTCCCCTCTC-CCGCACCTCTCCCC
*
56424203 CCTCTCTCCC
63 CCTCTCTCCA
56424213 CCTCTCTCTCTCTCTCTC
1 CCTCTCTCTCTC-CTCTC
56424231 ATACATAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
73 13 0.17
74 11 0.14
75 30 0.38
76 9 0.12
77 13 0.17
78 2 0.03
ACGTcount: A:0.02, C:0.61, G:0.02, T:0.35
Consensus pattern (72 bp):
CCTCTCTCTCTCCTCTCCCCTCTCCTCTCCCTCCTATCGTCCCCTCTCCCGCACCTCTCCCCCCT
CTCTCCA
Found at i:56424258 original size:36 final size:36
Alignment explanation
Indices: 56424215--56424334 Score: 179
Period size: 36 Copynumber: 3.3 Consensus size: 36
56424205 TCTCTCCCCC
56424215 TCTCTCTCTCTCTCTCATACATAAAATAGCGAGAAG
1 TCTCTCTCTCTCTCTCATACATAAAATAGCGAGAAG
56424251 TCTCTCTCTCTCTCTCATACATAAAATAGCGAG-AG
1 TCTCTCTCTCTCTCTCATACATAAAATAGCGAGAAG
* * *
56424286 TCTCTCTCTCTCTTCCTCCCTCCCTAAAATAGCGAGAAG
1 TCTCTCTCTCTC-T-CT-CATACATAAAATAGCGAGAAG
56424325 TCTCTCTCTC
1 TCTCTCTCTC
56424335 ACAACTCTCT
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 14 0.18
36 34 0.44
37 2 0.03
38 15 0.19
39 12 0.16
ACGTcount: A:0.24, C:0.33, G:0.10, T:0.33
Consensus pattern (36 bp):
TCTCTCTCTCTCTCTCATACATAAAATAGCGAGAAG
Found at i:56424332 original size:2 final size:2
Alignment explanation
Indices: 56424325--56425512 Score: 587
Period size: 2 Copynumber: 614.0 Consensus size: 2
56424315 TAGCGAGAAG
* * *
56424325 TC TC TC TC TC AC AAC TC TC T- TC TC T- TC TC TC T- TC GC TC TC
1 TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
56424365 TC TC -C TC TC TC CC TC TC TC CC TC -C CC T- TC CC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
56424404 T- TC TC TC TC CC TC CC TC CC TT TC TC CC TC TC TC TC -C TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
56424444 TC -C TC CC TC TC TC -C CC TC CC TC -C TC T- TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
56424482 TC -C TC TC GC -C TC CC TC TC TC CC TC CC TC -C TT TC -C CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
56424520 TC TC TC CC TC TC TC TC TC TC TC TAC TC -C CC TC CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC
* *
56424562 TC TC TC TC TG TC TC -C GTC TC TC TC TC T- TC TC TC ATC TC CC TC
1 TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC -TC TC TC TC
* * * * * * * *
56424604 CC TC TC CC TC CC TC TC TC -C CC CC TC -C TC CC TC TC CC TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * *
56424644 TC CC TC -C CC TC -C GC CC TC CC TC CC TC -C TC -C TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* ** * *
56424682 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC ATAC ATAA AA TA GC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -T-C -T-C TC TC TC
** ** ** * * *
56424726 GA GA AG TC TC TC CC TC TC CC TC TC TC TC TC TC TC ATAC AT- TA
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -T-C -TC TC
** * * ** ** ** *
56424768 AA TA GC GA GA AG TC TC TC TC TC AC TC TC TC TC TC TC T- TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * *
56424809 TC TC TC TC TC TC CC TC TC CC TC CC TC CC TC CC TC CC TC TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
56424851 TC CC TC -C TC -C TC TC -C ATC TC TC CC TC CC TC CC TC TT TC CC
1 TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
56424891 TC -C TC -C ATC CC TC CC TC CC CC TC TC TC TC CC TC TC -C TC -C
1 TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
56424930 CC TC TC TC TC TC TC TC TC CC TC -C ATC TC TC TC TC TC CC TC -C
1 TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC
* * *
56424971 CC TC CC TC TC TC TC TC TC TC TC TC TC -C T- TC TC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
56425011 TC -C TC -C TC TC TC TC CC TC -C T- TC CC TC TC TC CC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
56425049 CC TC -C TT TC CC TC TC TC TC TC TC TC CC TC -C TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
56425089 GC TC TC TC CC TT TC TC TC TC CC TC TC TC TC TC TC TT TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
56425131 TC CC TC CC TC TC TC TC TC TC CC TC TC TC TC TC CC CC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
56425173 TC TC CC TC CC TC TC TC TC TC -C CC TC CC TC TC TC CC TC -C TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
56425213 CC TC CC TC CC TC -C TC CC TC TC T- TC TC TC TC TC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
56425253 TC TC TC CC TC TC TC TC TC TC AC TC -C TC CC TC CC TC -C CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
56425293 TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC AC TC TGC -C TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC
* * *
56425335 TC TC CC TC TC TC TC TC TC TC TC TC TC AC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
56425377 -C TC TC TC CC TC TC -C T- TC TC CC TC TC TC TC CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
56425416 CC TT TC CC TC TC CC TC TC TC CC TC TC CC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
56425458 TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
56425499 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
56425513 ATACATACAA
Statistics
Matches: 883, Mismatches: 236, Indels: 134
0.70 0.19 0.11
Matches are distributed among these distances:
1 55 0.06
2 808 0.92
3 13 0.01
4 7 0.01
ACGTcount: A:0.03, C:0.57, G:0.01, T:0.39
Consensus pattern (2 bp):
TC
Found at i:56425581 original size:19 final size:19
Alignment explanation
Indices: 56425557--56425614 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 19
56425547 AAGAAATTAG
*
56425557 TAATATATATAAATATTTT
1 TAATATATATTAATATTTT
56425576 TAATATAT-TTAA-A-TTT
1 TAATATATATTAATATTTT
56425592 TAATATATATTAATAATTTT
1 TAATATATATTAAT-ATTTT
56425612 TAA
1 TAA
56425615 GAAATTAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 11 0.32
17 5 0.15
18 3 0.09
19 9 0.26
20 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATATATATTAATATTTT
Found at i:56425606 original size:10 final size:9
Alignment explanation
Indices: 56425557--56425610 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
56425547 AAGAAATTAG
56425557 TAATATATAT
1 TAATATAT-T
* *
56425567 AAATATTTT
1 TAATATATT
56425576 TAATATATT
1 TAATATATT
56425585 TAA-AT-TT
1 TAATATATT
56425592 TAATATATAT
1 TAATATAT-T
56425602 TAATA-ATT
1 TAATATATT
56425610 T
1 T
56425611 TTAAGAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 5 0.14
8 6 0.16
9 14 0.38
10 12 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TAATATATT
Found at i:56425968 original size:20 final size:20
Alignment explanation
Indices: 56425925--56425968 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
56425915 AAAAAATGAT
* *
56425925 TAAAGATTGTAAAATTTATT
1 TAAAAATTGTAAAATTTATA
56425945 TAAAAATTGTGAAAA-TTATA
1 TAAAAATTGT-AAAATTTATA
56425965 TAAA
1 TAAA
56425969 TTGAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (20 bp):
TAAAAATTGTAAAATTTATA
Found at i:56426448 original size:21 final size:22
Alignment explanation
Indices: 56426422--56426480 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
56426412 GTTTTAAGAA
*
56426422 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
56426443 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
56426465 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
56426481 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:56426495 original size:26 final size:24
Alignment explanation
Indices: 56426451--56426500 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
56426441 ATTTGTTTTA
*
56426451 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
56426475 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
56426501 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:56426936 original size:10 final size:9
Alignment explanation
Indices: 56426847--56426938 Score: 51
Period size: 9 Copynumber: 9.9 Consensus size: 9
56426837 GAGTTTTCAC
*
56426847 AAATTTTTT
1 AAATTTTTA
56426856 AAATTTTTA
1 AAATTTTTA
* *
56426865 ATATTTTTCT
1 AAATTTTT-A
*
56426875 ACA-TTTTA
1 AAATTTTTA
**
56426883 AAAAATTTA
1 AAATTTTTA
*
56426892 CAATTTTTA
1 AAATTTTTA
* *
56426901 TAGTTTTTA
1 AAATTTTTA
*
56426910 ACAATTTATTT
1 A-AATTT-TTA
56426921 AAATTTTTA
1 AAATTTTTA
56426930 AAGATTTTT
1 AA-ATTTTT
56426939 TACAACTTTT
Statistics
Matches: 62, Mismatches: 16, Indels: 9
0.71 0.18 0.10
Matches are distributed among these distances:
8 2 0.03
9 40 0.65
10 17 0.27
11 3 0.05
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (9 bp):
AAATTTTTA
Found at i:56426936 original size:20 final size:19
Alignment explanation
Indices: 56426891--56426940 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
56426881 TAAAAAATTT
*
56426891 ACAA-TTTTTATAGTTTTTA
1 ACAATTTTTTA-AATTTTTA
56426910 ACAATTTATTTAAATTTTTA
1 ACAATTT-TTTAAATTTTTA
56426930 A-AGATTTTTTA
1 ACA-ATTTTTTA
56426941 CAACTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 9 0.33
20 14 0.52
21 4 0.15
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (19 bp):
ACAATTTTTTAAATTTTTA
Found at i:56426938 original size:30 final size:30
Alignment explanation
Indices: 56426887--56426953 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
56426877 ATTTTAAAAA
*
56426887 ATTTACAATTTTTATAGTTTTTAACAA-TTT
1 ATTTA-AATTTTTAAAGTTTTTAACAACTTT
*
56426917 ATTTAAATTTTTAAAGATTTTTTACAACTTT
1 ATTTAAATTTTTAAAG-TTTTTAACAACTTT
*
56426948 TTTTAA
1 ATTTAA
56426954 TAATTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 10 0.31
30 14 0.44
31 8 0.25
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (30 bp):
ATTTAAATTTTTAAAGTTTTTAACAACTTT
Found at i:56426988 original size:28 final size:29
Alignment explanation
Indices: 56426945--56427027 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 29
56426935 TTTTTACAAC
*
56426945 TTTTTTTAATAA--TTTAAATAATTTTTA
1 TTTTTTTGATAATTTTTAAATAATTTTTA
*
56426972 TTATTTTT-AT-ATTTTTAAATACATTTTAA
1 TT-TTTTTGATAATTTTTAAATA-ATTTTTA
*
56427001 TTTTTTTGTTAATTTTT-AATAATTTTT
1 TTTTTTTGATAATTTTTAAATAATTTTT
56427028 CCAATTTGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 23 0.49
29 13 0.28
30 6 0.13
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (29 bp):
TTTTTTTGATAATTTTTAAATAATTTTTA
Found at i:56429895 original size:25 final size:24
Alignment explanation
Indices: 56429867--56429915 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
56429857 TTTTACGTAA
* *
56429867 TATAAATTATTAACATGTTTAATAT
1 TATAAAATAATAACAT-TTTAATAT
*
56429892 TATAAAATAATAATATTTTAATAT
1 TATAAAATAATAACATTTTAATAT
56429916 AATTATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TATAAAATAATAACATTTTAATAT
Found at i:56431733 original size:20 final size:21
Alignment explanation
Indices: 56431708--56431748 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56431698 ATGAATTCTT
56431708 TAAATTA-TT-TTCATTTAAAA
1 TAAATTAGTTATT-ATTTAAAA
56431728 TAAATTAGTTATTATTTAAAA
1 TAAATTAGTTATTATTTAAAA
56431749 ATGAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 10 0.53
22 2 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAATTAGTTATTATTTAAAA
Found at i:56435545 original size:22 final size:22
Alignment explanation
Indices: 56435517--56435579 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
56435507 AGGAATATGC
56435517 ATCTGTATCTTATTTGTTCTAT
1 ATCTGTATCTTATTTGTTCTAT
* *
56435539 ATCTGTACCTTATATT-CTCTAT
1 ATCTGTATCTTAT-TTGTTCTAT
* *
56435561 TTCTGTTTCTGTATTTGTT
1 ATCTGTATCT-TATTTGTT
56435580 TTTGAGAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.59
Consensus pattern (22 bp):
ATCTGTATCTTATTTGTTCTAT
Found at i:56441238 original size:26 final size:26
Alignment explanation
Indices: 56441209--56441261 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
56441199 GATTCCTGTA
56441209 CTTTATTTTT-TTCTTTTACATTATTT
1 CTTTATTTTTCTTCTTTT-CATTATTT
*
56441235 CTTTATTTTTCTTCTTTTCCTTATTT
1 CTTTATTTTTCTTCTTTTCATTATTT
56441261 C
1 C
56441262 ATTTTCCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (26 bp):
CTTTATTTTTCTTCTTTTCATTATTT
Found at i:56442613 original size:22 final size:21
Alignment explanation
Indices: 56442573--56442613 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
56442563 GGGGTAAGAA
*
56442573 TCTAATTTGTATCTAATATGT
1 TCTAATTTGTACCTAATATGT
*
56442594 TCTATATTTGTACCTGATAT
1 TCTA-ATTTGTACCTAATAT
56442614 TCTCTGTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
TCTAATTTGTACCTAATATGT
Found at i:56457032 original size:17 final size:18
Alignment explanation
Indices: 56457008--56457056 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
56456998 ATTGATAAGC
56457008 ATATAATATATATACACA
1 ATATAATATATATACACA
*
56457026 A-ATAATATATACACACA
1 ATATAATATATATACACA
56457043 ATTATAATA-ATATA
1 A-TATAATATATATA
56457057 AAAATCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.59
18 5 0.19
19 6 0.22
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAATATATATACACA
Found at i:56457887 original size:22 final size:22
Alignment explanation
Indices: 56457853--56457894 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
56457843 ATAAAATTAA
56457853 AAAAAGAAAAATGAATCAATCC
1 AAAAAGAAAAATGAATCAATCC
* *
56457875 AAAAATAATAATGAATCAAT
1 AAAAAGAAAAATGAATCAAT
56457895 TCATTCTCAA
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:0.64, C:0.10, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAAAGAAAAATGAATCAATCC
Found at i:56458685 original size:18 final size:18
Alignment explanation
Indices: 56458655--56458690 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
56458645 ATATTTGTAC
56458655 ATATTATTTAAATTTTAT
1 ATATTATTTAAATTTTAT
56458673 ATATT-TTTAAAATTTTAT
1 ATATTATTT-AAATTTTAT
56458691 TTTCTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTATTTAAATTTTAT
Found at i:56459140 original size:18 final size:17
Alignment explanation
Indices: 56459117--56459161 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
56459107 TAAAAAATAT
56459117 TATTAAAAATTATAAAAA
1 TATTAAAAATT-TAAAAA
*
56459135 TATTAAAAAATTTAAAAG
1 TATT-AAAAATTTAAAAA
*
56459153 TAATAAAAA
1 TATTAAAAA
56459162 GACCATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 12 0.50
19 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
TATTAAAAATTTAAAAA
Found at i:56459962 original size:18 final size:18
Alignment explanation
Indices: 56459907--56459962 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
56459897 ACTTTTCAAC
56459907 TTTTAAATAGTTTTGATTAAT
1 TTTTAAATA--TTT-ATTAAT
* *
56459928 TTTTAATTTTTTATTAAT
1 TTTTAAATATTTATTAAT
56459946 TTTTAGAATATTT-TTAA
1 TTTTA-AATATTTATTAA
56459963 ATGTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 15 0.50
19 8 0.27
21 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTAAATATTTATTAAT
Found at i:56467808 original size:44 final size:45
Alignment explanation
Indices: 56467757--56467849 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 45
56467747 TACAACATCT
*
56467757 ATTCCATTCAACCGAACACAA-GAATT-CT-ATTACAGCTCTATTCC
1 ATTCCATTCAACC-AA-ACAATAAATTACTGATTACAGCTCTATTCC
56467801 ATTCCATTCAACCAAACAATTAAATTACTGATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACAA-TAAATTACTGATTACAGCTCTATTCC
56467847 ATT
1 ATT
56467850 ACAGTTCTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
42 4 0.09
43 2 0.05
44 17 0.39
45 2 0.05
46 19 0.43
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (45 bp):
ATTCCATTCAACCAAACAATAAATTACTGATTACAGCTCTATTCC
Found at i:56467852 original size:16 final size:16
Alignment explanation
Indices: 56467831--56467885 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
56467821 TAAATTACTG
56467831 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* **
56467847 ATTACAGTTCTATTTA
1 ATTACAGCTCTATTCC
56467863 ATTACAGCAT-TATTCC
1 ATTACAGC-TCTATTCC
56467879 ATTACAG
1 ATTACAG
56467886 TGAATCAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 31 0.97
17 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:56468762 original size:20 final size:20
Alignment explanation
Indices: 56468737--56468776 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
56468727 TAAGGTTTTT
56468737 CTTGAGCTAGAGAGAGAAAG
1 CTTGAGCTAGAGAGAGAAAG
* * *
56468757 CTTGAGTTAGTGTGAGAAAG
1 CTTGAGCTAGAGAGAGAAAG
56468777 TGAAAAACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (20 bp):
CTTGAGCTAGAGAGAGAAAG
Found at i:56469074 original size:24 final size:26
Alignment explanation
Indices: 56469047--56469096 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
56469037 AATAAGTTAT
*
56469047 TTTTATACA-ATA-ATTATTTTTAAA
1 TTTTAGACATATATATTATTTTTAAA
*
56469071 TTTTAGACATATATTTTATTTTTAAA
1 TTTTAGACATATATATTATTTTTAAA
56469097 ATATAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 3 0.14
26 11 0.50
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTAGACATATATATTATTTTTAAA
Found at i:56469212 original size:20 final size:20
Alignment explanation
Indices: 56469187--56469258 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
56469177 TAACTTACTA
56469187 AATATTTAATTACATTATAT
1 AATATTTAATTACATTATAT
* *
56469207 AATATTTATTATAAATTATTTAT
1 AATATTTAAT-TACATTA--TAT
*
56469230 ACTAATTTCAATTACATTATAT
1 AAT-ATTT-AATTACATTATAT
*
56469252 AGTATTT
1 AATATTT
56469259 GATAATTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
20 9 0.22
21 10 0.24
22 5 0.12
23 5 0.12
24 10 0.24
25 2 0.05
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (20 bp):
AATATTTAATTACATTATAT
Found at i:56477908 original size:20 final size:20
Alignment explanation
Indices: 56477883--56477947 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
56477873 TCTTGAAGAA
56477883 GTGCTCATGTTAGCACTACG
1 GTGCTCATGTTAGCACTACG
* * **
56477903 GTGCTCCTGATAGTGCTACG
1 GTGCTCATGTTAGCACTACG
* *
56477923 ATGCTCTTGTTAGCACTACG
1 GTGCTCATGTTAGCACTACG
56477943 GTGCT
1 GTGCT
56477948 TCTAATAGCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (20 bp):
GTGCTCATGTTAGCACTACG
Found at i:56477956 original size:20 final size:20
Alignment explanation
Indices: 56477893--56477957 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
56477883 GTGCTCATGT
*
56477893 TAGCACTACGGTGCTCCTGA
1 TAGCACTACGGTGCTTCTGA
** * *
56477913 TAGTGCTACGATGC-TCTTGT
1 TAGCACTACGGTGCTTC-TGA
*
56477933 TAGCACTACGGTGCTTCTAA
1 TAGCACTACGGTGCTTCTGA
56477953 TAGCA
1 TAGCA
56477958 TATGTATGCT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 1 0.03
20 30 0.91
21 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.31
Consensus pattern (20 bp):
TAGCACTACGGTGCTTCTGA
Found at i:56477967 original size:40 final size:39
Alignment explanation
Indices: 56477884--56477982 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
56477874 CTTGAAGAAG
* *
56477884 TGCTCATGTTAGCACTACGGTGCTCCTGATAGTGCTACGA
1 TGCTCTTGTTAGCACTACGGTGCTCCTAATAG-GCTACGA
* *
56477924 TGCTCTTGTTAGCACTACGGTGCTTCTAATA-GCATATGTA
1 TGCTCTTGTTAGCACTACGGTGCTCCTAATAGGC-TACG-A
* *
56477964 TGCTCTTGTTTGCATTACG
1 TGCTCTTGTTAGCACTACG
56477983 ATTCCCTTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
38 2 0.04
39 3 0.06
40 46 0.90
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (39 bp):
TGCTCTTGTTAGCACTACGGTGCTCCTAATAGGCTACGA
Found at i:56478680 original size:28 final size:28
Alignment explanation
Indices: 56478646--56478702 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
56478636 TGTGTATAAC
56478646 ACTTATTCATGATCATAAGATGGTATGT
1 ACTTATTCATGATCATAAGATGGTATGT
56478674 ACTTATTCATGATCATAAGATGGTATGT
1 ACTTATTCATGATCATAAGATGGTATGT
56478702 A
1 A
56478703 TATAAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (28 bp):
ACTTATTCATGATCATAAGATGGTATGT
Found at i:56480594 original size:22 final size:22
Alignment explanation
Indices: 56480566--56480631 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
56480556 CTCCAATTAC
56480566 TAGCACATTAGTGCTCTCTGTT
1 TAGCACATTAGTGCTCTCTGTT
* * *
56480588 TAGCACATTCGTGTTCTCTGTA
1 TAGCACATTAGTGCTCTCTGTT
56480610 TAGCAC-TTCAGTGCTCTCTGTT
1 TAGCACATT-AGTGCTCTCTGTT
56480632 CATTAGTGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 2 0.05
22 35 0.95
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCTGTT
Found at i:56486089 original size:23 final size:23
Alignment explanation
Indices: 56486039--56486089 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
56486029 GGAGAGTATT
*
56486039 TTATATTTAAGATTTATTTAATA
1 TTATATTTAAGATTTATTAAATA
* *
56486062 TTATATTTGATATTTA-TAAATA
1 TTATATTTAAGATTTATTAAATA
56486084 TATATA
1 T-TATA
56486090 AAATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTATATTTAAGATTTATTAAATA
Found at i:56490181 original size:18 final size:18
Alignment explanation
Indices: 56490158--56490200 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
56490148 GAATAGGTTT
56490158 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
56490176 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
56490194 TTAATTA
1 TTAATTA
56490201 CACTTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:56495407 original size:6 final size:6
Alignment explanation
Indices: 56495396--56495454 Score: 66
Period size: 6 Copynumber: 9.7 Consensus size: 6
56495386 AAGAAGTCTA
* * *
56495396 AAAAAT AAAAAT AAACAG AAAAAT AAAAAT -AGAAT AAAATAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT
56495444 GAAAAAT AAAA
1 -AAAAAT AAAA
56495455 GAAAATAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
5 4 0.09
6 28 0.64
7 12 0.27
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:56495439 original size:18 final size:17
Alignment explanation
Indices: 56495394--56495469 Score: 66
Period size: 18 Copynumber: 4.3 Consensus size: 17
56495384 TAAAGAAGTC
56495394 TAAAAAATAAAAATAAA
1 TAAAAAATAAAAATAAA
*
56495411 CAGAAAAATAAAAATAGAA
1 TA-AAAAATAAAAATA-AA
*
56495430 TAAAATATAAAAATGAAA
1 TAAAAAATAAAAAT-AAA
*
56495448 -AATAAAA-GAAAATAAA
1 TAA-AAAATAAAAATAAA
56495464 TTAAAA
1 -TAAAA
56495470 TAGACTCAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
16 3 0.06
17 10 0.21
18 31 0.65
19 4 0.08
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.17
Consensus pattern (17 bp):
TAAAAAATAAAAATAAA
Found at i:56495459 original size:25 final size:23
Alignment explanation
Indices: 56495396--56495461 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
56495386 AAGAAGTCTA
*
56495396 AAAAATAAAAATAAACAGAAAAAT
1 AAAAATAAAAA-AAATAGAAAAAT
* *
56495420 AAAAATAGAATAAAATATAAAAAT
1 AAAAATA-AAAAAAATAGAAAAAT
56495444 GAAAAATAAAAGAAAATA
1 -AAAAATAAAA-AAAATA
56495462 AATTAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 19 0.54
25 16 0.46
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (23 bp):
AAAAATAAAAAAAATAGAAAAAT
Found at i:56497118 original size:15 final size:15
Alignment explanation
Indices: 56497074--56497119 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
56497064 AATTACAATA
*
56497074 AATAAATAATTGAACT
1 AATAAATAATT-AATT
56497090 AA-AAATAATT-ATT
1 AATAAATAATTAATT
*
56497103 AATAAAGAATTAATT
1 AATAAATAATTAATT
56497118 AA
1 AA
56497120 AGAAAAAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 13 0.50
16 2 0.08
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
AATAAATAATTAATT
Found at i:56497126 original size:32 final size:31
Alignment explanation
Indices: 56497045--56497126 Score: 74
Period size: 32 Copynumber: 2.5 Consensus size: 31
56497035 ATAAAAGAAA
* *
56497045 AATTGATTAAAAAAATAATAATTACAATAAAT
1 AATTAATTAAAAAAA-AATAATTACAATAAAG
* ** *
56497077 AAATAATTGAACTAAAAATAATTATTAATAAAG
1 AATTAATT-AAAAAAAAATAATTA-CAATAAAG
*
56497110 AATTAATTAAAGAAAAA
1 AATTAATTAAAAAAAAA
56497127 GGTAGAGTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
32 21 0.54
33 18 0.46
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (31 bp):
AATTAATTAAAAAAAAATAATTACAATAAAG
Found at i:56504547 original size:47 final size:47
Alignment explanation
Indices: 56504426--56504601 Score: 237
Period size: 47 Copynumber: 3.7 Consensus size: 47
56504416 GATATGTGAG
* * * * *
56504426 AGCTAGTGTAAGACCATGTCTGGGACATGGCGTTGGCCTCGATTTTGA-T
1 AGCTAGTGTAAGACCATGTCTGGGACATGGC-ATCGACTTGA--TGGATT
*
56504475 AGTTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATT
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATT
*
56504522 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATG
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATT
* *
56504569 AGCCAGTGTAAGACCATGTTTGGGACATGGCAT
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCAT
56504602 TGGCATTGTA
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
46 3 0.03
47 77 0.66
48 6 0.05
49 30 0.26
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATT
Found at i:56506582 original size:15 final size:15
Alignment explanation
Indices: 56506549--56506603 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
56506539 GGTATCGTGA
*
56506549 TTGGATTTTCTTGT-T
1 TTGGA-TTTCTTATAT
56506564 TTGGATTTCTT-TAT
1 TTGGATTTCTTATAT
56506578 GTTGGATTT-TTATAT
1 -TTGGATTTCTTATAT
56506593 TCTGGATTTCT
1 T-TGGATTTCT
56506604 CTGTTATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.03
14 10 0.29
15 23 0.66
16 1 0.03
ACGTcount: A:0.13, C:0.07, G:0.18, T:0.62
Consensus pattern (15 bp):
TTGGATTTCTTATAT
Found at i:56509259 original size:46 final size:45
Alignment explanation
Indices: 56509149--56509270 Score: 133
Period size: 46 Copynumber: 2.6 Consensus size: 45
56509139 TGTGTGTGCT
56509149 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAAATGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-G-CACATTATGAAATGCC
* * * *
56509196 AGTGAAAGTCATATCTGGGACATACATCG-ACATTGA-GACGAGA-GCC
1 AGTGTAAGACATGTCTGGGACATGCATCGCACATT-ATGA--A-ATGCC
56509242 AGTGTAAGACATGTCTGGGACATGCATCG
1 AGTGTAAGACATGTCTGGGACATGCATCG
56509271 GCTCTGAGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
44 7 0.11
45 1 0.02
46 30 0.48
47 25 0.40
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCACATTATGAAATGCC
Found at i:56509279 original size:46 final size:45
Alignment explanation
Indices: 56509149--56509310 Score: 125
Period size: 46 Copynumber: 3.5 Consensus size: 45
56509139 TGTGTGTGCT
* * *
56509149 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGA-A-ATGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCTC-TGA-GAGAGA-GCC
* * * * *
56509196 AGTGAAAGTCATATCTGGGACATACATCGACAT-TGAGACGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-TCTGAGA-GAGAGCC
* * *
56509242 AGTGTAAGACATGTCTGGGACATGCATCGGCTCTGAGA-TGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTCTGAGAGAGAGCC
*
56509286 AGTGTAAGACCATGTCTAGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
56509311 GTATCGGCAC
Statistics
Matches: 93, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
44 14 0.15
45 17 0.18
46 37 0.40
47 25 0.27
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTCTGAGAGAGAGCC
Found at i:56509405 original size:49 final size:51
Alignment explanation
Indices: 56509235--56509411 Score: 144
Period size: 49 Copynumber: 3.7 Consensus size: 51
56509225 ACATTGAGAC
* * * * *
56509235 GAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GC-ATCGGCTCTGAGATGT
1 GAGAGTCAGTGTAAGACCATGTATGGGACATGGCTATCGGCACAGATATGT
* *
56509283 ----GTCAGTGTAAGACCATGTCTAGGACATGG-TATCGGCACAGATATGT
1 GAGAGTCAGTGTAAGACCATGTATGGGACATGGCTATCGGCACAGATATGT
* * * *
56509329 GAGAG-CTAGTATAAGACCATGTTTGGGACATGGCT-TCGGCCTCA-AT-TTT
1 GAGAGTC-AGTGTAAGACCATGTATGGGACATGGCTATCGG-CACAGATATGT
*
56509378 GATAGTCAGTGTAAGACCATGTATGGGACATGGC
1 GAGAGTCAGTGTAAGACCATGTATGGGACATGGC
56509412 ACTGACTTGA
Statistics
Matches: 105, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
44 11 0.10
45 13 0.12
46 14 0.13
49 32 0.30
50 31 0.30
51 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (51 bp):
GAGAGTCAGTGTAAGACCATGTATGGGACATGGCTATCGGCACAGATATGT
Found at i:56513177 original size:79 final size:81
Alignment explanation
Indices: 56513037--56513221 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
56513027 TTGAATGATG
*
56513037 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
56513101 TGTGCGAGACACTA-A
66 TGTGCGAGACACTATA
* * * * **
56513116 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATTCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
**
56513178 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGACACTATA
* *
56513196 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
56513222 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGACACTATA
Found at i:56513228 original size:40 final size:40
Alignment explanation
Indices: 56513037--56513221 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
56513027 TTGAATGATG
* * * *
56513037 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* ** *
56513077 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGACACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
56513117 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
56513156 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
56513197 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
56513222 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 33 0.27
40 81 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:56518591 original size:46 final size:45
Alignment explanation
Indices: 56518498--56518791 Score: 226
Period size: 46 Copynumber: 6.4 Consensus size: 45
56518488 GTGCGCCAGA
* *
56518498 GTAAGACATGTCTGGGACATGCATCGGCCACATTGCGA--A-AGCAAGT
1 GTAAGACATGTCTGGGACATGCATCGG---C-TTGAGATGAGAGCTAGT
* *
56518544 GTAGGACATGTCTGGGACATGCATCAGCTTTGAGATGAGAGCTAGT
1 GTAAGACATGTCTGGGACATGCATCGGC-TTGAGATGAGAGCTAGT
* * *
56518590 GTAAGACATGTCTGGAACATGCATTGGCCTTGAGAT-ATGTGTTCTAGT
1 GTAAGACATGTCTGGGACATGCATCGG-CTTGAGATGA-GAG--CTAGT
* *** * *
56518638 GTAAGACATGTCTGGGACATGCATCAGCCACATCATGAAAGCTAGT
1 GTAAGACATGTCTGGGACATGCATCGGCTTGA-GATGAGAGCTAGT
* * *
56518684 GTAAGACCATGTCTGGGACATGGCATCGGCTTGATATGTG-TC-AGT
1 GTAAGA-CATGTCTGGGACAT-GCATCGGCTTGAGATGAGAGCTAGT
* * * *
56518729 GTAAGACATGTCTAGGACATGGCATCGGCTTGATATGTG-TC-AGT
1 GTAAGACATGTCTGGGACAT-GCATCGGCTTGAGATGAGAGCTAGT
*
56518773 GTAAGACCTGTCTGGGACA
1 GTAAGACATGTCTGGGACA
56518792 CGACATGGAC
Statistics
Matches: 207, Mismatches: 30, Indels: 24
0.79 0.11 0.09
Matches are distributed among these distances:
43 6 0.03
44 54 0.26
45 11 0.05
46 75 0.36
47 20 0.10
48 40 0.19
49 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (45 bp):
GTAAGACATGTCTGGGACATGCATCGGCTTGAGATGAGAGCTAGT
Found at i:56518658 original size:94 final size:92
Alignment explanation
Indices: 56518541--56518759 Score: 266
Period size: 94 Copynumber: 2.4 Consensus size: 92
56518531 TGCGAAAGCA
* ** * *
56518541 AGTGTAGGACATGTCTGGGACATGCATCAGCTTTGA-GATGAGAGCTAGTGTAAGA-CATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCTTACATCATGAAAGCTAGTGTAAGACCATGTCTG
*
56518604 GAACAT-GCATTGGCCTTGAGATATGTGTTC
66 GAACATGGCATCGG-CTT--GATATGTG-TC
*
56518634 TAGTGTAAGACATGTCTGGGACATGCATCAGC-CACATCATGAAAGCTAGTGTAAGACCATGTCT
1 -AGTGTAAGACATGTCTGGGACATGCATCAGCTTACATCATGAAAGCTAGTGTAAGACCATGTCT
*
56518698 GGGACATGGCATCGGCTTGATATGTGTC
65 GGAACATGGCATCGGCTTGATATGTGTC
* *
56518726 AGTGTAAGACATGTCTAGGACATGGCATCGGCTT
1 AGTGTAAGACATGTCTGGGACAT-GCATCAGCTT
56518760 GATATGTGTC
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
91 22 0.20
92 9 0.08
93 9 0.08
94 47 0.43
95 16 0.15
96 6 0.06
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCTTACATCATGAAAGCTAGTGTAAGACCATGTCTG
GAACATGGCATCGGCTTGATATGTGTC
Found at i:56518750 original size:44 final size:44
Alignment explanation
Indices: 56518541--56518791 Score: 247
Period size: 44 Copynumber: 5.5 Consensus size: 44
56518531 TGCGAAAGCA
* * * * *
56518541 AGTGTAGGACATGTCTGGGACATGCATCAGCTTTGAGATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-TTGATATGTG-TCT
* *
56518587 AGTGTAAGACATGTCTGGAACATGCATTGGCCTTGAGATATGTGTTCT
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTT--GATATGTG-TCT
* *** *
56518635 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATCATGAAAG-CT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTTGAT-ATG--TGTCT
56518681 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATGTGTC-
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTTGATATGTGTCT
*
56518726 AGTGTAAGACATGTCTAGGACATGGCATCGGCTTGATATGTGTC-
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCTTGATATGTGTCT
*
56518770 AGTGTAAGACCTGTCTGGGACA
1 AGTGTAAGACATGTCTGGGACA
56518792 CGACATGGAC
Statistics
Matches: 173, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
44 54 0.31
45 12 0.07
46 43 0.25
47 19 0.11
48 45 0.26
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTTGATATGTGTCT
Found at i:56529729 original size:49 final size:50
Alignment explanation
Indices: 56529572--56529741 Score: 261
Period size: 52 Copynumber: 3.4 Consensus size: 50
56529562 CGATGACTTG
* * *
56529572 CACATAGTACCACCCTTGTAGTCAAAGCTACCTTCTTCACAAAGTGGCCTT
1 CACATAGTACCACACTTGT-GTCCAAGCTATCTTCTTCACAAAGTGGCCTT
*
56529623 CACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCACAAAGTGGCCTT
1 CACATAGTACCACACTTGTGTCC-AAGCTATC-TTCTTCACAAAGTGGCCTT
*
56529675 CACATAGTACCACACTTGTGTCCAAGCTATC-TCTTCTCAAAGTGGCCTT
1 CACATAGTACCACACTTGTGTCCAAGCTATCTTCTTCACAAAGTGGCCTT
56529724 CACATAGTACCACACTTG
1 CACATAGTACCACACTTG
56529742 AGTCACTAGT
Statistics
Matches: 111, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
49 35 0.32
50 2 0.02
51 33 0.30
52 41 0.37
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.28
Consensus pattern (50 bp):
CACATAGTACCACACTTGTGTCCAAGCTATCTTCTTCACAAAGTGGCCTT
Found at i:56533222 original size:45 final size:45
Alignment explanation
Indices: 56533115--56533215 Score: 143
Period size: 45 Copynumber: 2.2 Consensus size: 45
56533105 TCTGAGCTCG
* *
56533115 TTGAGTTGGTCCAAGTTCGTGATATATGTGAGAAGTCTGAAGTTG
1 TTGAGTTGGTCCAAGTTCGTGATATATGTGAGAAGTCCGAAGTTA
*
56533160 TTGAGTTGGTCCAAGTTCGTGATATATGTGAAGCA-TCCG-AGCTTA
1 TTGAGTTGGTCCAAGTTCGTGATATATGTG-AGAAGTCCGAAG-TTA
56533205 TTGAGTTGGTC
1 TTGAGTTGGTC
56533216 TGAGTTCATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 2 0.04
45 46 0.90
46 3 0.06
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.36
Consensus pattern (45 bp):
TTGAGTTGGTCCAAGTTCGTGATATATGTGAGAAGTCCGAAGTTA
Found at i:56533253 original size:44 final size:47
Alignment explanation
Indices: 56533191--56533328 Score: 156
Period size: 44 Copynumber: 2.9 Consensus size: 47
56533181 ATATATGTGA
**
56533191 AGCATCCGAGCTTATTGAGTTGGTCTGAGTTCATTATGGAT-A-C-G
1 AGCATCCGAGCTCGTTGAGTTGGTCTGAGTTCATTATGGATGAGCAG
* * *
56533235 AGCATCTGAGCTCGTTGAGTTGGTCCGAGTTTATTATGGATGTGATGCATG
1 AGCATCCGAGCTCGTTGAGTTGGTCTGAGTTCATTATGGA--TGA-GCA-G
*
56533286 TGACATCCGAGCTCGTTGAGTTGGTCTGAGTTCATTATGGATG
1 AG-CATCCGAGCTCGTTGAGTTGGTCTGAGTTCATTATGGATG
56533329 TATACATGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
44 35 0.45
46 1 0.01
47 1 0.01
49 1 0.01
50 2 0.03
51 2 0.03
52 35 0.45
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (47 bp):
AGCATCCGAGCTCGTTGAGTTGGTCTGAGTTCATTATGGATGAGCAG
Found at i:56533304 original size:52 final size:51
Alignment explanation
Indices: 56533237--56533337 Score: 157
Period size: 52 Copynumber: 2.0 Consensus size: 51
56533227 TGGATACGAG
* * *
56533237 CATCTGAGCTCGTTGAGTTGGTCCGAGTTTATTATGGATGTGATGCATGTGA
1 CATCCGAGCTCGTTGAGTTGGTCCGAGTTCATTATGGATGT-ATACATGTGA
*
56533289 CATCCGAGCTCGTTGAGTTGGTCTGAGTTCATTATGGATGTATACATGT
1 CATCCGAGCTCGTTGAGTTGGTCCGAGTTCATTATGGATGTATACATGT
56533338 TATGAGGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 7 0.16
52 38 0.84
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.37
Consensus pattern (51 bp):
CATCCGAGCTCGTTGAGTTGGTCCGAGTTCATTATGGATGTATACATGTGA
Found at i:56536007 original size:17 final size:17
Alignment explanation
Indices: 56535966--56535998 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56535956 GACATACTTA
56535966 AATACATATAACTCGTC
1 AATACATATAACTCGTC
*
56535983 TATACATATAACTCGT
1 AATACATATAACTCGT
56535999 GAATGCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (17 bp):
AATACATATAACTCGTC
Found at i:56537134 original size:19 final size:18
Alignment explanation
Indices: 56537106--56537142 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
56537096 GGCTAGACAT
56537106 AAAAAGATCATTGTAATC
1 AAAAAGATCATTGTAATC
56537124 AAAATAGATCATTGTAATC
1 AAAA-AGATCATTGTAATC
56537143 TATTCCACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (18 bp):
AAAAAGATCATTGTAATC
Found at i:56539427 original size:55 final size:53
Alignment explanation
Indices: 56539366--56539620 Score: 209
Period size: 55 Copynumber: 4.8 Consensus size: 53
56539356 ATTAGGGTTT
* *
56539366 AAGGATACCATGTAGGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAA-GTTTCTAAGGC
* * * * * * **
56539421 AAGGATACCATGTAAGACCATGTCAATACATGGCATTGATTAGTTACTATAACGTA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTT--TCTAA-GGC
* * * *
56539477 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTC-TAAGGC
* * *
56539529 AAGGATACCATGTAAGACCATGTCGAGACATGGCAA-TGGTAAGTTT-GAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAGTTTCTAAGGC
* * * *
56539578 AAGGATACCACGTAAGACCATGACAAGTCATGGAAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAG
56539621 GTACTCGTGT
Statistics
Matches: 162, Mismatches: 30, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
48 2 0.01
49 36 0.22
52 8 0.05
53 36 0.22
54 10 0.06
55 65 0.40
56 5 0.03
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTCTAAGGC
Done.