Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 173 of 316
Found at i:55471629 original size:33 final size:33
Alignment explanation
Indices: 55471582--55471679 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 33
55471572 CTGACTGCAT
* *
55471582 ACTGTACTAATTCTGTAATGGGCTTAGGCCC-C
1 ACTGTACTAATTCTGAAATGGGCTCAGGCCCAC
*
55471614 ACTGATACTATTTCTGAAATGGGCTCAGGCCCAC
1 ACTG-TACTAATTCTGAAATGGGCTCAGGCCCAC
** * *
55471648 ACTGTTTTTGATTCTGAAATGGGCTAAGGCCC
1 ACTG-TACTAATTCTGAAATGGGCTCAGGCCC
55471680 TAACCGAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 4 0.07
33 24 0.44
34 27 0.49
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (33 bp):
ACTGTACTAATTCTGAAATGGGCTCAGGCCCAC
Found at i:55478197 original size:16 final size:17
Alignment explanation
Indices: 55478171--55478209 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
55478161 AATGAGCAAG
*
55478171 GAAAGAAAGAAGGAAAAA
1 GAAA-AAAGAAAGAAAAA
55478189 -AAAAAAGAAAGAAAAA
1 GAAAAAAGAAAGAAAAA
55478205 GAAAA
1 GAAAA
55478210 GGGAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAAGAAAAA
Found at i:55485628 original size:11 final size:11
Alignment explanation
Indices: 55485591--55485629 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
55485581 GAATGAGCAG
55485591 GGAAAGAAATAA
1 GGAAAGAAA-AA
55485603 GGAAA-AAAAA
1 GGAAAGAAAAA
*
55485613 AGAAAGAAAAA
1 GGAAAGAAAAA
55485624 GGAAAG
1 GGAAAG
55485630 GGAAAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 6 0.25
11 13 0.54
12 5 0.21
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (11 bp):
GGAAAGAAAAA
Found at i:55486433 original size:6 final size:6
Alignment explanation
Indices: 55486422--55486451 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
55486412 GTACCAGTAT
*
55486422 TGTTAC TGTTAC TGTTAC TGTTAG TGTTAC
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC
55486452 CCTTACGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (6 bp):
TGTTAC
Found at i:55492083 original size:23 final size:23
Alignment explanation
Indices: 55492056--55492103 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
55492046 ATACTTTATC
55492056 ATACATTCACCAA-GCAATAACAT
1 ATACA-TCACCAAGGCAATAACAT
* *
55492079 ATACATCATCAAGGCACTAACAT
1 ATACATCACCAAGGCAATAACAT
55492102 AT
1 AT
55492104 GCATGCATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (23 bp):
ATACATCACCAAGGCAATAACAT
Found at i:55495979 original size:131 final size:129
Alignment explanation
Indices: 55495553--55496034 Score: 384
Period size: 130 Copynumber: 3.7 Consensus size: 129
55495543 TTGCCTCACC
* * ** * **
55495553 TTAGAAAATACGAGTGAAATTCCGAA-GAGATATTCGATTATTTTGAACAAAC-AGGAAATTGCA
1 TTAGAAAACATGAGTGAAATTTTGAAGGA-ATATTCGATTGTTTTGAACAAACGA-GAAATCACA
*** * * ** * * * ** *
55495616 ACCCAGCACGATAGGGTACTATTCCCTGAATTGCCAAACATCAAATATCACCTTCATTTTAAAGG
64 ACCCAGCGTAATAGGGCACGATT-CC-GAATTATCAAACACCGAGTATTGCCTTCATTTCAAA-G
55495681 GTTT
126 GTTT
* * *
55495685 TTAGAAAACGTGAGTGAAATTTTGAAGGAATCTTCGATTGTTTTGAAAAAACGAGAAATCACAAC
1 TTAGAAAACATGAGTGAAATTTTGAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAAC
* * ** * * **
55495750 CTAACGTGTTAGGGCACGATTCCGAATTATCAAACACCGAGTATTGTCTTCTTTTTGGAAGGTTT
66 CCAGCGTAATAGGGCACGATTCCGAATTATCAAACACCGAGTATTGCCTTC-ATTTCAAAGGTTT
* *** * *
55495815 TTA-ATAAACACGAGTGAAAACCTAAAGGAATATTCAATTGTTTTGAACAAACGAGAAATCACAA
1 TTAGA-AAACATGAGTGAAATTTTGAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAA
* * *
55495879 CCCAGC-TCAATAGGGCATGGTTCTCGAATTATCAAACACCGAGTATTGCCTTCAGTTCAAAGGA
65 CCCAGCGT-AATAGGGCACGATTC-CGAATTATCAAACACCGAGTATTGCCTTCATTTCAAAGG-
55495943 TTT
127 TTT
* * * * **
55495946 TTAGAAGACATGAGTGAAATTTTGAAGGGATATTTGATTATTTT-AAGCAAACGAGAAATTGCAA
1 TTAGAAAACATGAGTGAAATTTTGAAGGAATATTCGATTGTTTTGAA-CAAACGAGAAATCACAA
55496010 CCCAGCACGT--TAGGGCACGATTCCG
65 CCCAG--CGTAATAGGGCACGATTCCG
55496035 TGAATTACCA
Statistics
Matches: 276, Mismatches: 62, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
129 2 0.01
130 103 0.37
131 101 0.37
132 65 0.24
133 4 0.01
134 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (129 bp):
TTAGAAAACATGAGTGAAATTTTGAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAAC
CCAGCGTAATAGGGCACGATTCCGAATTATCAAACACCGAGTATTGCCTTCATTTCAAAGGTTT
Found at i:55496072 original size:131 final size:131
Alignment explanation
Indices: 55495553--55496079 Score: 442
Period size: 131 Copynumber: 4.0 Consensus size: 131
55495543 TTGCCTCACC
* * * **
55495553 TTAGAAAATACGAGTGAAATTCCGAA-GAGATATTCGATTATTTTGAACAAAC-AGGAAATTGCA
1 TTAGAAAACATGAGTGAAATTCTGAAGGA-ATATTCGATTATTTTGAACAAACGA-GAAATCACA
* * * * * * * *
55495616 ACCCAGCACGATAGGGTACTATTCCCTGAATTGCCAAACATCAAATATCACCTTCATTTTAAAGG
64 ACCCAGCACGATAGGGCACGATT-CCTGAATTACCAAACACCGAGTATCGCCTTCAGTTTAAAGG
*
55495681 GTTT
128 ATTT
* * * * *
55495685 TTAGAAAACGTGAGTGAAATTTTGAAGGAATCTTCGATTGTTTTGAAAAAACGAGAAATCACAAC
1 TTAGAAAACATGAGTGAAATTCTGAAGGAATATTCGATTATTTTGAACAAACGAGAAATCACAAC
* * ** * * * * ** *
55495750 CTAACGTGTTAGGGCACGATTCC-GAATTATCAAACACCGAGTATTGTCTTCTTTTTGGAAGG-T
66 CCAGCACGATAGGGCACGATTCCTGAATTACCAAACACCGAGTATCGCCTTCAGTTT-AAAGGAT
55495813 TT
130 TT
* ** * * *
55495815 TTA-ATAAACACGAGTGAAAACCTAAAGGAATATTCAATTGTTTTGAACAAACGAGAAATCACAA
1 TTAGA-AAACATGAGTGAAATTCTGAAGGAATATTCGATTATTTTGAACAAACGAGAAATCACAA
* * * * * * *
55495879 CCCAGCTCAATAGGGCATGGTT-CTCGAATTATCAAACACCGAGTATTGCCTTCAGTTCAAAGGA
65 CCCAGCACGATAGGGCACGATTCCT-GAATTACCAAACACCGAGTATCGCCTTCAGTTTAAAGGA
55495943 TTT
129 TTT
* * * * **
55495946 TTAGAAGACATGAGTGAAATTTTGAAGGGATATTTGATTATTTT-AAGCAAACGAGAAATTGCAA
1 TTAGAAAACATGAGTGAAATTCTGAAGGAATATTCGATTATTTTGAA-CAAACGAGAAATCACAA
* * *
55496010 CCCAGCACGTTAGGGCACGATTCCGTGAATTACCAAATATCGCA-TATCGCCTTC-GTTTAAAGG
65 CCCAGCACGATAGGGCACGATTCC-TGAATTACCAAACACCG-AGTATCGCCTTCAGTTTAAAGG
55496073 ATTT
128 ATTT
55496077 TTA
1 TTA
55496080 ATAATTGTGA
Statistics
Matches: 312, Mismatches: 71, Indels: 25
0.76 0.17 0.06
Matches are distributed among these distances:
129 2 0.01
130 100 0.32
131 117 0.38
132 88 0.28
133 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (131 bp):
TTAGAAAACATGAGTGAAATTCTGAAGGAATATTCGATTATTTTGAACAAACGAGAAATCACAAC
CCAGCACGATAGGGCACGATTCCTGAATTACCAAACACCGAGTATCGCCTTCAGTTTAAAGGATT
T
Found at i:55496428 original size:21 final size:23
Alignment explanation
Indices: 55496378--55496428 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 23
55496368 ATGATAATGT
* *
55496378 ACATAGCATGATATAGAATAACC
1 ACATAGCAAGATATAGAATAACA
55496401 A-AT-GCAAGATATA-AA-AACA
1 ACATAGCAAGATATAGAATAACA
55496420 ACATAGCAA
1 ACATAGCAA
55496429 TTAGAAGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 13 0.54
22 2 0.08
23 1 0.04
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.18
Consensus pattern (23 bp):
ACATAGCAAGATATAGAATAACA
Found at i:55504745 original size:27 final size:27
Alignment explanation
Indices: 55504715--55504811 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 27
55504705 TAGGGCAAAT
*
55504715 CAGTCATATTACCTTACAAGGGTATTA
1 CAGTCATTTTACCTTACAAGGGTATTA
*
55504742 CAGTCATTTTACCATACAAGGGTATTA
1 CAGTCATTTTACCTTACAAGGGTATTA
* *** *
55504769 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCTTACAAGGGTATTA
55504796 CAGTCATTTTACCTTA
1 CAGTCATTTTACCTTA
55504812 TGGGGGCATT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (27 bp):
CAGTCATTTTACCTTACAAGGGTATTA
Found at i:55504813 original size:27 final size:27
Alignment explanation
Indices: 55504734--55504957 Score: 288
Period size: 27 Copynumber: 8.3 Consensus size: 27
55504724 TACCTTACAA
* * ***
55504734 GGGTATTACAGTCATTTTACCATACAA
1 GGGTATTTCAGTCATTTTACCCTATGG
*
55504761 GGGTATTACAGTCATTTTACCCTATGG
1 GGGTATTTCAGTCATTTTACCCTATGG
*
55504788 GGGTATTTCAGTCATTTTACCTTATGG
1 GGGTATTTCAGTCATTTTACCCTATGG
* **
55504815 GGGCATTTTGGTCATTTTACCCTATGG
1 GGGTATTTCAGTCATTTTACCCTATGG
* * *
55504842 AGATATTTCAGTCATTTTACCCTTTGG
1 GGGTATTTCAGTCATTTTACCCTATGG
*
55504869 GGGTATTTCAGTTATTTTACCCTATAGG
1 GGGTATTTCAGTCATTTTACCCTAT-GG
55504897 GGG-ATTTCAGTCATTTTACCCTATGG
1 GGGTATTTCAGTCATTTTACCCTATGG
* *
55504923 GGGTATTTCGGTCATTTTACCCTATGA
1 GGGTATTTCAGTCATTTTACCCTATGG
55504950 GGGTATTT
1 GGGTATTT
55504958 GGGCCCAACA
Statistics
Matches: 172, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 5 0.03
27 162 0.94
28 5 0.03
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTCAGTCATTTTACCCTATGG
Found at i:55507376 original size:19 final size:19
Alignment explanation
Indices: 55507352--55507391 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
55507342 ATGTAATTTG
55507352 TTAAGAAT-AAATTTTCTAA
1 TTAAGAATAAAATTTT-TAA
*
55507371 TTAAGATTAAAATTTTTAA
1 TTAAGAATAAAATTTTTAA
55507390 TT
1 TT
55507392 TTCATTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAAGAATAAAATTTTTAA
Found at i:55515535 original size:54 final size:54
Alignment explanation
Indices: 55515441--55515612 Score: 231
Period size: 54 Copynumber: 3.2 Consensus size: 54
55515431 TGTACCTAGA
* * *
55515441 CCCCATATATGGTAAAATGACTCTTTTGCCCCTATATGGTAAAATGACTGTTTTG
1 CCCC-TATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
* * *
55515496 CCCCTATGTTGTAAAATGA-TGATTTTGCCCTTATGTGGTAAAATGACTATTTTG
1 CCCCTATGTGGTAAAATGACT-ATTTTGCCCTTATATGGTAAAATGACTGTTTTG
* * *
55515550 CCCCTATGTGGTGAAATGACTATTTTGCCCTTATATGGTAAGATGACTGCTTTG
1 CCCCTATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
55515604 -CCCTATGTG
1 CCCCTATGTG
55515613 ATATATATAT
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 10 0.10
54 88 0.85
55 5 0.05
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (54 bp):
CCCCTATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
Found at i:55515604 original size:81 final size:80
Alignment explanation
Indices: 55515450--55515612 Score: 220
Period size: 81 Copynumber: 2.0 Consensus size: 80
55515440 ACCCCATATA
* * * *
55515450 TGGTAAAATGACTCTTTTGCCCCTATATGGTAAAATGACTGTTTTGCCCCTATGTTGTAAAATGA
1 TGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGA
*
55515515 TGATTTTGCCCTTATG
66 TGACTTTGCCC-TATG
* * * *
55515531 TGGTAAAATGACTATTTTGCCCCTATGTGGTGAAATGACTATTTTGCCCTTATATGGTAAGATGA
1 TGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGA
55515596 CTG-CTTTGCCCTATG
66 -TGACTTTGCCCTATG
55515611 TG
1 TG
55515613 ATATATATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
80 6 0.08
81 64 0.89
82 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (80 bp):
TGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGACTATTTTGCCCCTATATGGTAAAATGA
TGACTTTGCCCTATG
Found at i:55515607 original size:27 final size:27
Alignment explanation
Indices: 55515441--55515606 Score: 199
Period size: 27 Copynumber: 6.1 Consensus size: 27
55515431 TGTACCTAGA
*
55515441 CCCCATATATGGTAAAATGACTCTTTTG
1 CCCC-TATATGGTAAAATGACTGTTTTG
55515469 CCCCTATATGGTAAAATGACTGTTTTG
1 CCCCTATATGGTAAAATGACTGTTTTG
* *
55515496 CCCCTATGTTGTAAAATGA-TGATTTTG
1 CCCCTATATGGTAAAATGACTG-TTTTG
* * *
55515523 CCCTTATGTGGTAAAATGACTATTTTG
1 CCCCTATATGGTAAAATGACTGTTTTG
* * *
55515550 CCCCTATGTGGTGAAATGACTATTTTG
1 CCCCTATATGGTAAAATGACTGTTTTG
* * *
55515577 CCCTTATATGGTAAGATGACTGCTTTG
1 CCCCTATATGGTAAAATGACTGTTTTG
55515604 CCC
1 CCC
55515607 TATGTGATAT
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
26 2 0.02
27 115 0.94
28 5 0.04
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (27 bp):
CCCCTATATGGTAAAATGACTGTTTTG
Found at i:55519305 original size:26 final size:27
Alignment explanation
Indices: 55519272--55519418 Score: 143
Period size: 27 Copynumber: 5.5 Consensus size: 27
55519262 ATACCCCATG
* * *
55519272 TGTGGTAAAGTTACT-TTTTTCCCCTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
* * * *
55519298 TGTGGTAAAATAACTATTTTTCCCTTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
*
55519325 TGTGGTAAAATGACTGTTTTGCCCTTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
*
55519352 TATGGTAAAATGACTGTTTTGCCCCTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
* * * * *
55519379 TATGGTAAAAAGACTATTTTTCCCGTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
* *
55519406 TATGGTAAGATGA
1 TGTGGTAAAATGA
55519419 TTGTGTAACA
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
26 13 0.12
27 93 0.88
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (27 bp):
TGTGGTAAAATGACTGTTTTGCCCCTA
Found at i:55519362 original size:54 final size:53
Alignment explanation
Indices: 55519272--55519413 Score: 158
Period size: 54 Copynumber: 2.6 Consensus size: 53
55519262 ATACCCCATG
* * * * *
55519272 TGTGGTAAAGTTACTTTTTTCCCCTATGTGGTAAAATAACTATTTTTCCCTTA
1 TGTGGTAAAATGACTTTTTTCCCCTATATGGTAAAATAACTATTTTGCCCCTA
* * * *
55519325 TGTGGTAAAATGACTGTTTTGCCCTTATATGGTAAAATGACTGTTTTGCCCCTA
1 TGTGGTAAAATGACT-TTTTTCCCCTATATGGTAAAATAACTATTTTGCCCCTA
* * *
55519379 TATGGTAAAAAGACTATTTTTCCCGTATATGGTAA
1 TGTGGTAAAATGACT-TTTTTCCCCTATATGGTAA
55519414 GATGATTGTG
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 13 0.18
54 61 0.82
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (53 bp):
TGTGGTAAAATGACTTTTTTCCCCTATATGGTAAAATAACTATTTTGCCCCTA
Found at i:55527194 original size:30 final size:30
Alignment explanation
Indices: 55527136--55527194 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
55527126 ATTTTCAGGC
* **
55527136 CTAGGGGTAAAATGGTCATTTTGTCAAAGT
1 CTAGGGGCAAAATGGTCATTTTACCAAAGT
55527166 CTAGGGGCAAAATGGTCATTTTACCAAAG
1 CTAGGGGCAAAATGGTCATTTTACCAAAG
55527195 ATATAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (30 bp):
CTAGGGGCAAAATGGTCATTTTACCAAAGT
Found at i:55527595 original size:47 final size:44
Alignment explanation
Indices: 55527530--55527701 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 44
55527520 GGATTATTGT
55527530 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATT-ATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGG---CATTGATGA
*
55527576 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGGGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATT--GATGA
* * * *
55527624 GTGCTAGTGTAAGACATGTCTGGCACATGCATCGACCTTGA-GA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGATGA
* **
55527667 CGTAAGCCAGTGTAAGACATGTCTCAGACATGCAT
1 -G--AGCTAGTGTAAGACATGTCTGGGACATGCAT
55527702 TACGAAATGT
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
45 4 0.04
46 48 0.45
47 27 0.25
48 23 0.21
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGATGA
Found at i:55531525 original size:696 final size:690
Alignment explanation
Indices: 55530126--55532816 Score: 3273
Period size: 696 Copynumber: 4.0 Consensus size: 690
55530116 GGGTGTTACA
* * *
55530126 AAATTGC-GCTCACATTGGTCTGGACCTTTCAAAGTTGTCGAAGTATTTCCTCATGGTGCAGTCA
1 AAATTGCAG-TCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTTCTTCATGGTGCAGTCA
* * * *
55530190 CAATCAGAGATTTACATGATGGACACTAGTTCAAAGTGAATGGACAATGGTTGAAGCA-CTTTAT
65 CAATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACACCATT-T
* *
55530254 TGGGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTAGTCTAAAAATTTTAATTTTTATTGA
129 TGGGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTGGTC-AAAATTTTTAATTTTTATTGA
* * *
55530319 ATTTATCATCATGTGATTTTATTTTA-TTT-TATTG-TTTTTGTTCAAGTTTGTTTTAC-TTCTT
193 ATTTATCATTATGTGATTTTATTTTATTTTGTTTTGTTTTTTGTTCAAGTTTGTTTTACTTTTTT
* * * *
55530380 TTTTTTCCAGAATAATTTGGTACCATTGTCGATGCACTTGGGCTTTATTGTCAACGCAGTTCCTA
258 TTTTTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGTTCGTA
* * * *
55530445 CTATTGTATTGTCACTTATGACTCATCAAGAAAGAGGGCATATAAAAAATTTCAGATCTCATCAT
323 CTATTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCCATCGT
* * *
55530510 TTGATCAAAAGTTACCTAGCCGTCTGATCTGTCTCAGCGGGCGCAATTCTCATTGGACATATTTA
388 TTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACATATTTA
* * *
55530575 TTCCTGCCAGCTTTATATCCCTTCACAAAACTCACGCCTTTCCATCTTCTTCCGTTACTGGAAAG
453 TTCCTGCCAACTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTGGAAAG
* * * * *
55530640 AAAAGGTTGTTGGATATCACTGAACTAGAGGAGATTAGACGAAATGCCTATGTAAACT-CTACAA
518 AAAAGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATG-AAAATGCTACAA
* * * * * *
55530704 TTTACAAGGAAAAGACCAGACAATGGCAGGATAGAAGTATTTTGTAGCAAAAATTTATCGCGGGT
582 TTTACAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGCAACAATTTATCGCGGGT
* * *
55530769 CAACAAGTTTTATTATTCAATTCTAGACTGAATTTGTACTCAAGT
647 CAACAAGTTTTATTATTCAATTCTAGACTGAAATTGCAC-CCAGT
* * *
55530814 AAATTGTACTCACATTGGTTTGGACCTTTCGAAGTTGTC-AAGATATTTCTTCATGGTG-AGTTA
1 AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAG-TATTTCTTCATGGTGCAGTCA
* * * *
55530877 GAATTAGAGATTTACATGATTGACACCAGTTCAAAGTGAATGGATAACGGTTGAAACACCATTTT
65 CAATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACACCATTTT
* *
55530942 GGGAATATTAATCAAAAGCAGGCAA-AGACAATTAAATTGGTCAAAATTTTTTAATTTTTATTGA
130 GGGAATATTAATCAAAAGCAAG-AAGAGACCATTAAATTGGTCAAAA-TTTTTAATTTTTATTGA
* *
55531006 ATTTATGATTATGTGATTTTATTTTATTTTGTTTTGTTTTTTGTTCAAGTTTGTTTTTCTTCTTC
193 ATTTATCATTATGTGATTTTATTTTATTTTGTTTTGTTTTTTGTTCAAGTTTG--TTT-TACTT-
*
55531071 TTTCTTTTTTTTTAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGT
254 TTT-TTTTTTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGT
* * * * *
55531136 TCGTACTATTGTACTGTAACTTATGAATCATCAAGAATGAGGGCATATTAGAAATTTTAGATCCC
318 TCGTACTATTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCC
* * * * * *
55531201 ATCGTTTGATCAAAATTGACCTATCCATCTGATTTGTCTGAGCGGGCGTAATTGTCATTCGACAT
383 ATCGTTTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACAT
* *
55531266 ATTTATT-CTCGTCAATTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACT
448 ATTTATTCCT-GCCAACTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACT
* *
55531330 GGAAAGAAAAGGCTGTTGGATATCACTGAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGA
512 GGAAAGAAAAGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGC
* * *
55531395 TGCAATTTACAAGGAAAAGACCAAACAATGGCATGATAGAATTATTTTGCAGCAACAATTTATCA
577 TACAATTTACAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGCAACAATTTATCG
* *
55531460 CAGGTCAACAAGTTTTATTATTCAATTC-ACAACTGAAATTGCACCCAGGT
642 CGGGTCAACAAGTTTTATTATTCAATTCTA-GACTGAAATTGCACCCA-GT
55531510 AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTTCCTT-ATGGTGCAGTCA
1 AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTT-CTTCATGGTGCAGTCA
* **
55531574 CAATCAGAGATTTACGTGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACATTATTTT
65 CAATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACACCATTTT
* * * ** *
55531639 GGGAATATTAATCAAAAGCAGGTAGAGACCATTAAATTTGTTGAAATTTTTAATTTTTATTAAAT
130 GGGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTGGTCAAAATTTTTAATTTTTATTGAAT
* * * * *
55531704 TTTTAATTATGTGATTTTATTTTATTTTATTTTGTTTTGTTTTCGTTCAAGTTTGTTTAAC-TTG
195 TTATCATTATGTGATTTTATTTTATTTTGTTTTG--TT-TTTT-GTTCAAGTTTGTTTTACTTTT
*
55531768 TTTTTTTTTCAGAATAAGTAGGTACCATTGT-------C----G----A---T----GCAGTTCG
256 TTTTTTTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGTTCG
** * * *
55531811 TACTATTGTACTACCACTTATGACTCGTCAAGAATTAGGGCATATAAAAAATTTTAGATCCCA-C
321 TACTATTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCCATC
* * *
55531875 AGTTTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGACACAATTCTCATTGGACATAT
386 -GTTTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACATAT
* *
55531940 TTATTCCTGCCAACTTTATATCCCTTCACAAAAGTCATGCCTTTCCATCTTCTT-CGTTACTGGA
450 TTATTCCTGCCAACTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTGGA
* * * * *
55532004 AAGAAAAGGTTGTTGGATATCACTAAACTAGAGGAGATTAGGCGAAATGCATATAAAAATGCTGC
515 AAGAAAAGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGCTAC
** * * * *
55532069 AATTTACAAGGAAAAGACCAAATGATAGCATGACAGAATTATTTTCCAGCGACAATTTATCGTGG
580 AATTTACAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGCAACAATTTATCGCGG
* *
55532134 GTCAACAAGTTTTATTATTCAATTCTAGACTAAAATTGCATCCAG-
645 GTCAACAAGTTTTATTATTCAATTCTAGACTGAAATTGCACCCAGT
* * *
55532179 -----GCAGTCACATCGGTTTGGACCTTTCGAAGTTGTCAAAGTATTT-TCTCATGGTGTAGTCA
1 AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTTCT-TCATGGTGCAGTCA
* ** *
55532238 CAATCAGAGATTTACATGATGGACATCAGTTCAAAGTGAATGGA-AAGCGAATGAAACACTATTT
65 CAATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAA-CGGTTGAAACACCATTT
*
55532302 TGGGAATATTAATCAAAAGAAAGAAGAGACCATTAAATTGGTCAAAA-----AA---TTA--GAA
129 TGGGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTGGTCAAAATTTTTAATTTTTATTGAA
* * * * * ** *
55532357 ATTACCATTATGTGATGTT-TTTTGTTTT-TTTTATTCAAATTGTTTC-ACTTCT-TTTTA--TT
194 TTTATCATTATGTGATTTTATTTTATTTTGTTTTGTT--TTTTG-TTCAAGTT-TGTTTTACTTT
* * * * * *
55532416 TTTATTTTTGCTGAATAATTAGGAACCATTGTCGACTCACTTGGGCTTTATTGTCAACGCAATTC
255 TTTTTTTTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGTTC
* ** * * *
55532481 GTACTATTGTACT-TCCCTTATGACTCATTGAGAATGAGGGCA-ATTAGAAATTTCAGATCCCAC
320 GTACTATTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCCAT
* *
55532544 CGTTTGATCAAAAGTGACCTAGCTGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCAACATAT
385 CGTTTGATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACATAT
** *
55532609 TTATTCCCACCAGCTTTATATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTG
450 TTATTCCTGCCAAC-TT-TATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTG
* * *
55532674 GAAAGAAAAGGCTATTAGATATCACTAAACTAGAGAAGATTAGGTGAAATGCCTATGAAAATGCT
513 GAAAGAAAAGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGCT
* * * * *
55532739 ACAATTTACAAGG-AAAGACAAAACGATGGCATGACAGAATTATTTTGTA-CTGATAATTTATCG
578 ACAATTTACAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGC-AACAATTTATCG
*
55532802 GGGGTCAACAAGTTT
642 CGGGTCAACAAGTTT
55532817 GTGGGTGCAA
Statistics
Matches: 1742, Mismatches: 199, Indels: 141
0.84 0.10 0.07
Matches are distributed among these distances:
649 28 0.02
650 10 0.01
651 6 0.00
652 4 0.00
653 8 0.00
654 16 0.01
656 4 0.00
659 2 0.00
660 1 0.00
662 1 0.00
663 3 0.00
664 150 0.09
667 1 0.00
669 87 0.05
670 28 0.02
671 276 0.16
672 244 0.14
673 2 0.00
676 1 0.00
679 1 0.00
683 1 0.00
686 4 0.00
687 137 0.08
688 56 0.03
689 4 0.00
690 16 0.01
692 3 0.00
693 2 0.00
694 29 0.02
695 13 0.01
696 476 0.27
697 108 0.06
698 5 0.00
699 4 0.00
700 11 0.01
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (690 bp):
AAATTGCAGTCACATTGGTTTGGACCTTTCGAAGTTGTCGAAGTATTTCTTCATGGTGCAGTCAC
AATCAGAGATTTACATGATGGACACCAGTTCAAAGTGAATGGACAACGGTTGAAACACCATTTTG
GGAATATTAATCAAAAGCAAGAAGAGACCATTAAATTGGTCAAAATTTTTAATTTTTATTGAATT
TATCATTATGTGATTTTATTTTATTTTGTTTTGTTTTTTGTTCAAGTTTGTTTTACTTTTTTTTT
TTTTCAGAATAATTAGGTACCATTGTCGACGCACTTGGGCTTTATTGTCAACGCAGTTCGTACTA
TTGTACTGTCACTTATGACTCATCAAGAATGAGGGCATATAAAAAATTTCAGATCCCATCGTTTG
ATCAAAAGTGACCTAGCCGTCTGATCTGTCTGAGCGGGCGCAATTCTCATTCGACATATTTATTC
CTGCCAACTTTATATCCCTTCACAAAAGTCACGCCTTTCCATCTTCTTCCGCTACTGGAAAGAAA
AGGCTGTTGGATATCACTAAACTAGAGAAGATTAGGCGAAATGCCTATGAAAATGCTACAATTTA
CAAGGAAAAGACCAAACAATGGCATGACAGAATTATTTTGCAGCAACAATTTATCGCGGGTCAAC
AAGTTTTATTATTCAATTCTAGACTGAAATTGCACCCAGT
Found at i:55537199 original size:55 final size:54
Alignment explanation
Indices: 55537061--55537267 Score: 256
Period size: 53 Copynumber: 3.8 Consensus size: 54
55537051 TTCCTTTTTA
* *
55537061 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
55537114 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * *
55537168 TAGTTTACCAGTGCCATGCCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAG
1 -AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* *
55537223 AACTTACCAATGCCATGCCTT-AGCATGGTCTTACTTGGTATCCTT
1 AACTTACCATTGCCATGCCTTGA-CATGGTCTTACATGGTATCCTT
55537268 AAACCCTAAT
Statistics
Matches: 129, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
53 47 0.36
54 38 0.29
55 44 0.34
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (54 bp):
AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:55545303 original size:47 final size:47
Alignment explanation
Indices: 55545246--55545502 Score: 347
Period size: 47 Copynumber: 5.4 Consensus size: 47
55545236 ATTGATGTAC
* * *
55545246 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
55545293 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
55545342 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
55545389 ACA-TGCATATGTGAGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
55545436 AAGTGTATATATGTGATAAGACCGAATGGCCAATGTGATGGATGTGG
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
55545483 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
55545503 TCCCGAAGGG
Statistics
Matches: 191, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
46 1 0.01
47 149 0.78
49 40 0.21
50 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.27
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:55545380 original size:22 final size:22
Alignment explanation
Indices: 55545353--55545427 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
55545343 CATGTGTATG
55545353 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
55545375 TGTGATGAATG-TGAACAT-G-CATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
55545398 TGTGAGATAAGGCCGAATGGCCAA
1 TGT--GATAAGGCCGAATGGCCAA
55545422 TGTGAT
1 TGTGAT
55545428 GAATGTGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.30
23 11 0.28
24 11 0.28
25 6 0.15
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:55547994 original size:38 final size:38
Alignment explanation
Indices: 55547930--55548004 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
55547920 AATCCGAGTT
*
55547930 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
55547968 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
55548005 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:55548126 original size:40 final size:40
Alignment explanation
Indices: 55548058--55548338 Score: 393
Period size: 40 Copynumber: 7.0 Consensus size: 40
55548048 AGGTCTCGAC
* *
55548058 GATG-ATCCGAGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
55548097 GATGTACCCGGGCTAAGTCCCGAAAAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
55548137 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
55548177 GATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
55548217 GATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * ** *
55548257 GATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * * *
55548297 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
55548337 GA
1 GA
55548339 CGTGTATTCG
Statistics
Matches: 215, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
39 4 0.02
40 211 0.98
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:55565881 original size:27 final size:26
Alignment explanation
Indices: 55565837--55565888 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
55565827 CTCGTTGCAA
*
55565837 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
55565864 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
55565889 GCAGCCTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:55565967 original size:27 final size:26
Alignment explanation
Indices: 55565927--55565986 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
55565917 CCACATATAT
*
55565927 ATATCTATTCTGGTGACCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
55565953 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
55565980 ATATCTG
1 ATATCTG
55565987 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:55571787 original size:33 final size:31
Alignment explanation
Indices: 55571706--55571793 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 31
55571696 AATTGCATTA
* * *
55571706 CACTGTACTAATACTGTATTGGGCTTAGGCC
1 CACTGTACTGATACTGTATAGGGCTAAGGCC
*
55571737 CAC---ACTGTTACTGTATAGGGCTAAGGCC
1 CACTGTACTGATACTGTATAGGGCTAAGGCC
55571765 CTGACTGTACTGATACTGTATAGGGCTAA
1 C--ACTGTACTGATACTGTATAGGGCTAA
55571794 AGCCTATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
28 22 0.47
30 2 0.04
31 3 0.06
33 20 0.43
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (31 bp):
CACTGTACTGATACTGTATAGGGCTAAGGCC
Found at i:55600232 original size:14 final size:14
Alignment explanation
Indices: 55600209--55600239 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55600199 GTTTTGTTGT
55600209 TTCGACTTTCTTTC
1 TTCGACTTTCTTTC
*
55600223 TTCGATTTTCTTTC
1 TTCGACTTTCTTTC
55600237 TTC
1 TTC
55600240 CTCAACTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.26, G:0.06, T:0.61
Consensus pattern (14 bp):
TTCGACTTTCTTTC
Found at i:55607355 original size:27 final size:26
Alignment explanation
Indices: 55607318--55607432 Score: 97
Period size: 27 Copynumber: 4.3 Consensus size: 26
55607308 AGCATGACTG
* *
55607318 CCAGAACAGATATTGTGATAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
* *
55607344 CCAGATACAGATAATGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* *
55607371 CCAGAATAGATATTTGTGGC-GTAGCCA
1 CCAGAACAGATA-TTGTGACAG-AGCCA
* * *
55607398 CTAGAAACAGATATTTGTGGCATAGCCA
1 CCAG-AACAGATA-TTGTGACAGAGCCA
55607426 CCAGAAC
1 CCAGAAC
55607433 GCTTCCTCCA
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
26 12 0.16
27 39 0.53
28 23 0.31
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:55607417 original size:28 final size:28
Alignment explanation
Indices: 55607342--55607431 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 28
55607332 GTGATAGAGT
* * *
55607342 CACCAGATACAGATA-ATGTGGCAGAGC
1 CACCAGAAACAGATATTTGTGGCATAGC
* *
55607369 CACCAG-AATAGATATTTGTGGCGTAGC
1 CACCAGAAACAGATATTTGTGGCATAGC
*
55607396 CACTAGAAACAGATATTTGTGGCATAGC
1 CACCAGAAACAGATATTTGTGGCATAGC
55607424 CACCAGAA
1 CACCAGAA
55607432 CGCTTCCTCC
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 6 0.12
27 20 0.38
28 26 0.50
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (28 bp):
CACCAGAAACAGATATTTGTGGCATAGC
Found at i:55610221 original size:15 final size:14
Alignment explanation
Indices: 55610203--55610293 Score: 74
Period size: 15 Copynumber: 5.9 Consensus size: 14
55610193 AGATTGAAAA
55610203 ATAATATATAAATAG
1 ATAATATA-AAATAG
55610218 ATAATATAAAAATAG
1 ATAATAT-AAAATAG
*
55610233 ATAATATAATAATAA
1 ATAATATAA-AATAG
* *
55610248 ATAATAGAATAATTG
1 ATAATATAA-AATAG
*
55610263 ATAGAATAATAAAATAA
1 AT--AAT-ATAAAATAG
55610280 ATAATATAGAAATA
1 ATAATATA-AAATA
55610294 TAGATTTATA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
14 5 0.08
15 46 0.73
16 1 0.02
17 8 0.13
18 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
ATAATATAAAATAG
Found at i:55610226 original size:20 final size:20
Alignment explanation
Indices: 55610203--55610342 Score: 67
Period size: 20 Copynumber: 7.5 Consensus size: 20
55610193 AGATTGAAAA
55610203 ATAATATATAAATAGAT-A-
1 ATAATATATAAATAGATAAT
55610221 AT-ATA-A-AAATAGATAAT
1 ATAATATATAAATAGATAAT
55610238 ATAATA-ATAAATA-ATAGA-
1 ATAATATATAAATAGATA-AT
*
55610256 ATAAT-TGATAGAATA-ATAAA
1 ATAATAT-ATA-AATAGATAAT
*
55610276 ATAA-ATA-ATATAGA-AAT
1 ATAATATATAAATAGATAAT
* *
55610293 ATAGATTTATAAATCGA-AAT
1 ATA-ATATATAAATAGATAAT
* *
55610313 ATATTAATATAAATATAATAAT
1 ATAAT-ATATAAATA-GATAAT
55610335 ATAA-ATAT
1 ATAATATAT
55610343 TATTAATTAC
Statistics
Matches: 95, Mismatches: 10, Indels: 32
0.69 0.07 0.23
Matches are distributed among these distances:
15 8 0.08
16 2 0.02
17 13 0.14
18 17 0.18
19 14 0.15
20 34 0.36
21 1 0.01
22 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.33
Consensus pattern (20 bp):
ATAATATATAAATAGATAAT
Found at i:55610237 original size:30 final size:30
Alignment explanation
Indices: 55610203--55610298 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 30
55610193 AGATTGAAAA
*
55610203 ATAATATATAAATAGATAATATAAAAATAG
1 ATAATATATAAATAAATAATATAAAAATAG
* * *
55610233 ATAATATA-ATAATAAATAATAGAATAATTG
1 ATAATATATA-AATAAATAATATAAAAATAG
55610263 ATAGA-ATAATAAAATAAATAATATAGAAATATAG
1 ATA-ATAT-AT-AAATAAATAATATA-AAA-ATAG
55610297 AT
1 AT
55610299 TTATAAATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
29 1 0.02
30 29 0.56
31 2 0.04
32 12 0.23
33 3 0.06
34 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (30 bp):
ATAATATATAAATAAATAATATAAAAATAG
Found at i:55610258 original size:12 final size:11
Alignment explanation
Indices: 55610201--55610285 Score: 54
Period size: 12 Copynumber: 7.7 Consensus size: 11
55610191 ATAGATTGAA
*
55610201 AAATAATATAT
1 AAATAATAAAT
55610212 AAATAGATAATAT
1 AAATA-ATAA-AT
*
55610225 AAA-AATAGAT
1 AAATAATAAAT
55610235 AATATAAT-AAT
1 AA-ATAATAAAT
55610246 AAATAATAGAAT
1 AAATAATA-AAT
* *
55610258 AATTGATAGAAT
1 AAATAATA-AAT
55610270 -AAT-A-AAAT
1 AAATAATAAAT
55610278 AAATAATA
1 AAATAATA
55610286 TAGAAATATA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
8 3 0.05
9 4 0.07
10 11 0.19
11 16 0.27
12 20 0.34
13 5 0.08
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:55610328 original size:14 final size:14
Alignment explanation
Indices: 55610309--55610349 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
55610299 TTATAAATCG
55610309 AAATATATTAATAT
1 AAATATATTAATAT
*
55610323 AAATATAATAATAT
1 AAATATATTAATAT
55610337 AAATATTATTAAT
1 AAATA-TATTAAT
55610350 TACTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATTAATAT
Found at i:55621316 original size:27 final size:26
Alignment explanation
Indices: 55621247--55621361 Score: 97
Period size: 27 Copynumber: 4.3 Consensus size: 26
55621237 AGCATGGCTG
** *
55621247 CCAGAACAGATATTGTGATAGAGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
* *
55621273 CCAGATATAGATATTGTAGCAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
55621300 CCAGAACAGATATTTGTGGC-GTAGCCA
1 CCAGAACAGATA-TTGTGGCAG-AGCCA
* * *
55621327 CCAAAAACAGATGTTTGTGGCATAGCCA
1 CC-AGAACAGAT-ATTGTGGCAGAGCCA
*
55621355 CTAGAAC
1 CCAGAAC
55621362 GCTTCCTCCA
Statistics
Matches: 71, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
26 12 0.17
27 38 0.54
28 21 0.30
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:55621343 original size:28 final size:27
Alignment explanation
Indices: 55621281--55621355 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 27
55621271 CACCAGATAT
* * *
55621281 AGATA-TTGTAGCAGAGCCACCAGAAC
1 AGATATTTGTGGCATAGCCACCAAAAC
*
55621307 AGATATTTGTGGCGTAGCCACCAAAAAC
1 AGATATTTGTGGCATAGCCACC-AAAAC
*
55621335 AGATGTTTGTGGCATAGCCAC
1 AGATATTTGTGGCATAGCCAC
55621356 TAGAACGCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.12
27 13 0.32
28 23 0.56
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (27 bp):
AGATATTTGTGGCATAGCCACCAAAAC
Found at i:55621680 original size:21 final size:22
Alignment explanation
Indices: 55621649--55621689 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
55621639 GAATGTGTTG
*
55621649 TGATGTATGTGGAAATGAAATA
1 TGATGTATGTGCAAATGAAATA
*
55621671 TGAT-TATGTGCCAATGAAA
1 TGATGTATGTGCAAATGAAA
55621690 CATAAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (22 bp):
TGATGTATGTGCAAATGAAATA
Found at i:55638679 original size:42 final size:43
Alignment explanation
Indices: 55638620--55638733 Score: 131
Period size: 53 Copynumber: 2.4 Consensus size: 43
55638610 AATACTCAAT
55638620 ATCTCGCACACTAAGTGCCGAAGC-ATAGCTGAAGCTATTATA
1 ATCTCGCACACTAAGTGCCGAAGCTATAGCTGAAGCTATTATA
55638662 ATCTCGCACACTAAGTGCCTTTCATAGCCGAAGCTATAGCTGAAGCTATTATA
1 ATCTCGCACACTAA--G-------T-GCCGAAGCTATAGCTGAAGCTATTATA
55638715 ATCTCGCACACTAAGTGCC
1 ATCTCGCACACTAAGTGCC
55638734 TTTCATAGCC
Statistics
Matches: 61, Mismatches: 0, Indels: 21
0.74 0.00 0.26
Matches are distributed among these distances:
42 14 0.23
43 3 0.05
44 2 0.03
51 2 0.03
52 8 0.13
53 32 0.52
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
ATCTCGCACACTAAGTGCCGAAGCTATAGCTGAAGCTATTATA
Found at i:55638715 original size:53 final size:53
Alignment explanation
Indices: 55638636--55638751 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
55638626 CACACTAAGT
55638636 GCCGAAGC-ATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
1 GCCGAAGCTATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
55638688 GCCGAAGCTATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
1 GCCGAAGCTATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
55638741 GCCGAAGCTAT
1 GCCGAAGCTAT
55638752 CTCAGTCTCA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 8 0.13
53 55 0.87
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (53 bp):
GCCGAAGCTATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCCTTTCATA
Found at i:55640663 original size:23 final size:25
Alignment explanation
Indices: 55640637--55640691 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
55640627 ACCATAAATA
55640637 ATAT-TAAAT-AAATTTTTACACAT
1 ATATATAAATGAAATTTTTACACAT
**
55640660 ATATATTCATGAAATTTTTACACAT
1 ATATATAAATGAAATTTTTACACAT
55640685 ATATATA
1 ATATATA
55640692 TTTACATGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 4 0.15
24 3 0.11
25 20 0.74
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (25 bp):
ATATATAAATGAAATTTTTACACAT
Found at i:55642068 original size:42 final size:42
Alignment explanation
Indices: 55641947--55642134 Score: 146
Period size: 42 Copynumber: 4.4 Consensus size: 42
55641937 TGATTTCTGA
* * * * * *
55641947 TATTTGATTTCATGTAAGACTATGTCTGGGACGTTGGCATC-
1 TATTTGATTACGTGTAAGGCTTTGTCTGGGACATCGGCATCG
* * * * * *
55641988 AATTTGAGATTATGTGTAAGACTATGTCCGGGACATCGGCATTG
1 TATTT--GATTACGTGTAAGGCTTTGTCTGGGACATCGGCATCG
*
55642032 TATTTGATTACGTGTAAGGCTTTGTCTGGGAGATCGGCATCG
1 TATTTGATTACGTGTAAGGCTTTGTCTGGGACATCGGCATCG
* * * * *
55642074 TATTTGATTTCGTGTTAGGCCTTGTCTAGGATAGT-GGCATCG
1 TATTTGATTACGTGTAAGGCTTTGTCTGGGACA-TCGGCATCG
* *
55642116 ATATTTAATTACATGTAAG
1 -TATTTGATTACGTGTAAG
55642135 ACCACGTCTG
Statistics
Matches: 118, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
41 4 0.03
42 66 0.56
43 44 0.37
44 4 0.03
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.37
Consensus pattern (42 bp):
TATTTGATTACGTGTAAGGCTTTGTCTGGGACATCGGCATCG
Found at i:55643875 original size:29 final size:28
Alignment explanation
Indices: 55643834--55643979 Score: 145
Period size: 29 Copynumber: 5.1 Consensus size: 28
55643824 GTGAGCATGA
55643834 ATAT-AATGTGATTTGGGCCAGATGGGCC
1 ATATAAATGTGA-TTGGGCCAGATGGGCC
* *
55643862 ATATAAATGAGATTGGGTCTA-ATGGGCC
1 ATATAAATGTGATTGGG-CCAGATGGGCC
*
55643890 ATATAAATGTGAATTGGGCCTGATGGGCC
1 ATATAAATGTG-ATTGGGCCAGATGGGCC
* * * * *
55643919 AAATGAACGTGAATTGGCCCGGATGGGCC
1 ATATAAATGTG-ATTGGGCCAGATGGGCC
*
55643948 ATATAAATGAGATTGGGCCTAG-TGGGCC
1 ATATAAATGTGATTGGGCC-AGATGGGCC
55643976 ATAT
1 ATAT
55643980 GCATGTATGT
Statistics
Matches: 97, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
28 44 0.45
29 53 0.55
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCAGATGGGCC
Found at i:55651586 original size:29 final size:29
Alignment explanation
Indices: 55651501--55651647 Score: 128
Period size: 29 Copynumber: 5.2 Consensus size: 29
55651491 GTGAGCATGA
*
55651501 ATATG-ATGTGATTTGGG-CTGGATGGGCC
1 ATATGAATGTGAATTGGGCCT-GATGGGCC
* * * **
55651529 ATATAAATGAG-ATTGGGCCTAATAAGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
55651557 ATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
*
55651586 ATA-GAAACGTGAATT-GGCCTGAATGGGCC
1 ATATG-AATGTGAATTGGGCCTG-ATGGGCC
* *
55651615 ATATAAATGAG-ATTGGGCCT-AGTGGGCC
1 ATATGAATGTGAATTGGGCCTGA-TGGGCC
55651643 ATATG
1 ATATG
55651648 CAGGTATGTA
Statistics
Matches: 95, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
27 1 0.01
28 43 0.45
29 51 0.54
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTGATGGGCC
Found at i:55651588 original size:57 final size:57
Alignment explanation
Indices: 55651501--55651646 Score: 151
Period size: 57 Copynumber: 2.6 Consensus size: 57
55651491 GTGAGCATGA
*
55651501 ATATG-ATGTGATTTGGG-CTGGATGGGCCATATAAA-TGAGATTGGGCCT-AATAAGCC
1 ATATGAATGTGAATTGGGCCT-GATGGGCCATATAAACTGA-ATT-GGCCTGAATAAGCC
* **
55651557 ATATGAATGTGAATTGGGCCTGATGGGCCATAGAAACGTGAATTGGCCTGAATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCCATATAAAC-TGAATTGGCCTGAATAAGCC
* *
55651615 ATATAAATGAG-ATTGGGCCT-AGTGGGCCATAT
1 ATATGAATGTGAATTGGGCCTGA-TGGGCCATAT
55651647 GCAGGTATGT
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
56 6 0.08
57 48 0.62
58 20 0.26
59 3 0.04
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.27
Consensus pattern (57 bp):
ATATGAATGTGAATTGGGCCTGATGGGCCATATAAACTGAATTGGCCTGAATAAGCC
Found at i:55655479 original size:18 final size:19
Alignment explanation
Indices: 55655456--55655498 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
55655446 TGTGAGTTGG
*
55655456 CCGTGTGGG-TTCACATGC
1 CCGTGTGGGATGCACATGC
*
55655474 CCGTGTGGGATGGACATGC
1 CCGTGTGGGATGCACATGC
55655493 CCGTGT
1 CCGTGT
55655499 CTTCAGCCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.12, C:0.26, G:0.37, T:0.26
Consensus pattern (19 bp):
CCGTGTGGGATGCACATGC
Found at i:55657516 original size:46 final size:45
Alignment explanation
Indices: 55657411--55657533 Score: 162
Period size: 46 Copynumber: 2.7 Consensus size: 45
55657401 ATATTCGTAC
*
55657411 CGATGCATGTCCCAGACATGTCTTACACTAGC-ACATCTCGTAGCT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTACATCTC-TAGCT
* * *
55657456 -GATGTATTTCCCAGACATGTCTTACACTGGCTTACATCT-TAAGGT
1 CGATGCATGTCCCAGACATGTCTTACACTGGC-TACATCTCT-AGCT
55657501 CGATGCATGTCCCAGACATGTCTTACACTGGCT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCT
55657534 CACGTAACAG
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
44 29 0.43
45 4 0.06
46 35 0.51
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTACATCTCTAGCT
Found at i:55660712 original size:16 final size:16
Alignment explanation
Indices: 55660691--55660727 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
55660681 ATGAATCTCC
*
55660691 ATTATCAATGCACATG
1 ATTATCAATCCACATG
*
55660707 ATTATCAATCCAGATG
1 ATTATCAATCCACATG
55660723 ATTAT
1 ATTAT
55660728 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (16 bp):
ATTATCAATCCACATG
Found at i:55663536 original size:14 final size:14
Alignment explanation
Indices: 55663517--55663549 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
55663507 ATTTATGCGA
55663517 TTAATTCCTTTTAT
1 TTAATTCCTTTTAT
55663531 TTAATTCCTTTTAT
1 TTAATTCCTTTTAT
55663545 TTAAT
1 TTAAT
55663550 CGGACACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (14 bp):
TTAATTCCTTTTAT
Found at i:55673355 original size:30 final size:30
Alignment explanation
Indices: 55673260--55673356 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
55673250 AGCTCACTCC
** * *
55673260 TAGCTCATTTTCAACTCGCGAGCTAAACCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * * *
55673290 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
55673320 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
55673350 TAGCTCA
1 TAGCTCA
55673357 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:55675750 original size:16 final size:16
Alignment explanation
Indices: 55675731--55675772 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
55675721 AAGAGAAAAC
55675731 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
* *
55675747 AAAGAAAACAAAATAA
1 AAAGAAAAGAAAAGAA
55675763 AAAGAAAAGA
1 AAAGAAAAGA
55675773 GCGGCAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:55675896 original size:30 final size:30
Alignment explanation
Indices: 55675854--55675934 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
55675844 TTGGAAAACA
*
55675854 AAAAAG-GAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAG-AATGAAAAAGAAAATGAGAGTG
* ***
55675884 AAAAAGAGAATGAAGAAGAGTTTGAGAGTG
1 AAAAAGAGAATGAAAAAGAAAATGAGAGTG
55675914 AAAAAGA-AGATGAAAAAGAAA
1 AAAAAGAGA-ATGAAAAAGAAA
55675935 TTGAAACAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (30 bp):
AAAAAGAGAATGAAAAAGAAAATGAGAGTG
Found at i:55683892 original size:21 final size:21
Alignment explanation
Indices: 55683868--55683921 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
55683858 AAAACAGGGC
55683868 ACACGCCCGTGTGGAAGGGTA
1 ACACGCCCGTGTGGAAGGGTA
*
55683889 ACACGCCCGTGTTGAAGGGTA
1 ACACGCCCGTGTGGAAGGGTA
* *
55683910 ACATGCTCGTGT
1 ACACGCCCGTGT
55683922 CCCACATCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.20
Consensus pattern (21 bp):
ACACGCCCGTGTGGAAGGGTA
Found at i:55685222 original size:26 final size:26
Alignment explanation
Indices: 55685193--55685266 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
55685183 AATGCTTGGA
55685193 TATTATATAAATTGTATATACGTGAC
1 TATTATATAAATTGTATATACGTGAC
*
55685219 TATTGT-T--A-TGT-T-TGAC--GA-
1 TATTATATAAATTGTATAT-ACGTGAC
55685237 TATTATATAAATTGTATATACGTGAC
1 TATTATATAAATTGTATATACGTGAC
55685263 TATT
1 TATT
55685267 GTTATGTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 5 0.14
19 3 0.08
20 1 0.03
21 4 0.11
22 6 0.17
23 4 0.11
24 1 0.03
25 3 0.08
26 9 0.25
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (26 bp):
TATTATATAAATTGTATATACGTGAC
Found at i:55685240 original size:44 final size:44
Alignment explanation
Indices: 55685191--55685280 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
55685181 TTAATGCTTG
*
55685191 GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTGAC
1 GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTAAC
55685235 GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTAAC
1 GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTAAC
55685279 GA
1 GA
55685281 CATATCGACT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (44 bp):
GATATTATATAAATTGTATATACGTGACTATTGTTATGTTTAAC
Found at i:55685433 original size:28 final size:28
Alignment explanation
Indices: 55685402--55685458 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
55685392 AATGTGAAAA
* * *
55685402 ATATTAAGAATGGTACTTGGTGTGCGAG
1 ATATTAAGAATGGCACTTAGTGTACGAG
* *
55685430 ATATTGAGTATGGCACTTAGTGTACGAG
1 ATATTAAGAATGGCACTTAGTGTACGAG
55685458 A
1 A
55685459 CATCGAAGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (28 bp):
ATATTAAGAATGGCACTTAGTGTACGAG
Found at i:55688964 original size:28 final size:30
Alignment explanation
Indices: 55688933--55688993 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
55688923 AAAGTGATTT
*
55688933 TTGACAAAAATGTCAATT-A-GGGATTAAA
1 TTGACAAAAATGTAAATTGAGGGGATTAAA
* * *
55688961 TTGAGAAAAGTGTAAATTGAGGGGGTTAAA
1 TTGACAAAAATGTAAATTGAGGGGATTAAA
55688991 TTG
1 TTG
55688994 TGAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 15 0.56
29 1 0.04
30 11 0.41
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.30
Consensus pattern (30 bp):
TTGACAAAAATGTAAATTGAGGGGATTAAA
Found at i:55689630 original size:43 final size:43
Alignment explanation
Indices: 55689472--55689638 Score: 142
Period size: 43 Copynumber: 3.9 Consensus size: 43
55689462 GGTTATTGAG
* * *
55689472 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-T
1 ATGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGAT
* * * *
55689514 ATTGAGATTACGTGTAAGACCATGTCTGGGACATTGGCATC-ATT
1 A-TGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGA-T
* * * * * * * *
55689558 ATTTAATTTCGTATAAGTCCCTATTTGGGACAATGGCATCGAT
1 ATGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGAT
* *
55689601 ATGTGATAACATGTAAGACCATATCTGGGA-TATGGCAT
1 ATGTGATTACATGTAAGACCATATCTGGGACAATGGCAT
55689639 TGTATGAACT
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
42 8 0.08
43 87 0.89
44 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGAT
Found at i:55692176 original size:79 final size:80
Alignment explanation
Indices: 55692008--55692189 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 80
55691998 GCTACTCGTT
* * *
55692008 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
* *
55692073 ATTTAGTAACTCGCAC
65 ATATAGTAACTAGCAC
* **
55692089 CAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCA
1 CAAAGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCA
* *
55692151 GATATGGTCACTTAGCA-
64 GATATAGTAAC-TAGCAC
55692168 CAAAGCCTTCGGGACTTAGCCC
1 CAAAGCCTTCGGGACTTAGCCC
55692190 AGACATCATT
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
78 4 0.05
79 58 0.67
80 21 0.24
81 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGA
TATAGTAACTAGCAC
Found at i:55692192 original size:40 final size:40
Alignment explanation
Indices: 55691989--55692189 Score: 223
Period size: 40 Copynumber: 5.0 Consensus size: 40
55691979 CAGAATTTAA
** *
55691989 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55692029 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55692069 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
55692108 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
55692148 CCAGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
55692188 CC
1 CC
55692190 AGACATCATT
Statistics
Matches: 137, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 90 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:55693352 original size:56 final size:56
Alignment explanation
Indices: 55693285--55693460 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
55693275 TATTAGTTTA
*
55693285 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
55693341 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
55693397 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
55693453 TTGCCCAT
1 TTGCCCAT
55693461 CATCCCTTGT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:55694673 original size:17 final size:17
Alignment explanation
Indices: 55694633--55694676 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
55694623 AAATAAACAT
*
55694633 AAAAATAAACACCTAAA
1 AAAAATAAACAACTAAA
55694650 AAGAAATAAA-AACTAAA
1 AA-AAATAAACAACTAAA
55694667 GAAAAATAAA
1 -AAAAATAAA
55694677 TTCCCCCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.75, C:0.09, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAATAAACAACTAAA
Found at i:55697104 original size:19 final size:20
Alignment explanation
Indices: 55697067--55697104 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
55697057 ATAAGGTGGT
55697067 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
55697087 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
55697105 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:55705363 original size:29 final size:29
Alignment explanation
Indices: 55705303--55705494 Score: 228
Period size: 29 Copynumber: 6.6 Consensus size: 29
55705293 GATAGTCAAA
*
55705303 ACCATCCCTTTTTCATATTCGATAGT-TGTC
1 ACCATCCC-TTTTCATATTTGATAGTCT-TC
*
55705333 ACCATCCCTTTTCATATTTGATGGTCTTC
1 ACCATCCCTTTTCATATTTGATAGTCTTC
* * **
55705362 ACCATCCATTTTCATATTTGATGGTC-GA
1 ACCATCCCTTTTCATATTTGATAGTCTTC
* * *
55705390 AACATCCCTTTTCATATTCGACAGT-TGTC
1 ACCATCCCTTTTCATATTTGATAGTCT-TC
* *
55705419 ACCATCCCTTTTCATATTTGATGGTCATC
1 ACCATCCCTTTTCATATTTGATAGTCTTC
*
55705448 ACCATCCCTTTTCATATTTGATAGTCGTC
1 ACCATCCCTTTTCATATTTGATAGTCTTC
55705477 ACCATCCCTTTTCATATT
1 ACCATCCCTTTTCATATT
55705495 GATTGGCGTC
Statistics
Matches: 139, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
28 20 0.14
29 110 0.79
30 9 0.06
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTTGATAGTCTTC
Found at i:55705460 original size:86 final size:87
Alignment explanation
Indices: 55705292--55705494 Score: 311
Period size: 86 Copynumber: 2.3 Consensus size: 87
55705282 GTGTGCTAAA
* *
55705292 TGATAGTC-AAAACCATCCCTTTTTCATATTCGATAGTTGTCACCATCCCTTTTCATATTTGATG
1 TGATAGTCGTAAA-CATCCC-TTTTCATATTCGACAGTTGTCACCATCCCTTTTCATATTTGATG
*
55705356 GTCTTCACCATCCATTTTCATATT
64 GTCATCACCATCCATTTTCATATT
*
55705380 TGATGGTCG-AAACATCCCTTTTCATATTCGACAGTTGTCACCATCCCTTTTCATATTTGATGGT
1 TGATAGTCGTAAACATCCCTTTTCATATTCGACAGTTGTCACCATCCCTTTTCATATTTGATGGT
*
55705444 CATCACCATCCCTTTTCATATT
66 CATCACCATCCATTTTCATATT
* *
55705466 TGATAGTCGTCACCATCCCTTTTCATATT
1 TGATAGTCGTAAACATCCCTTTTCATATT
55705495 GATTGGCGTC
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
86 73 0.69
87 23 0.22
88 10 0.09
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.41
Consensus pattern (87 bp):
TGATAGTCGTAAACATCCCTTTTCATATTCGACAGTTGTCACCATCCCTTTTCATATTTGATGGT
CATCACCATCCATTTTCATATT
Found at i:55707861 original size:37 final size:37
Alignment explanation
Indices: 55707811--55707886 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
55707801 ATGAAAGCCT
55707811 TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
1 TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
55707848 TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
1 TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
55707885 TA
1 TA
55707887 AACTTAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (37 bp):
TATAGAACAAATCTTACAACAACTTCTTTTTATCTGG
Found at i:55711979 original size:51 final size:51
Alignment explanation
Indices: 55711919--55712021 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
55711909 CTTGACATCT
** * *
55711919 TGTAATAGCCTGTTTTCAGTGAAATT-GAAACAGTGGTTCTGGGACCACAAA
1 TGTAATAGCCCATTTTCAGTCAAATTAG-AACAGTGGTTCTGAGACCACAAA
* * *
55711970 TGTAATAGCCCATTTTTAGTCAAATTAGAATAGTGGTTTTGAGACCACAAA
1 TGTAATAGCCCATTTTCAGTCAAATTAGAACAGTGGTTCTGAGACCACAAA
55712021 T
1 T
55712022 TCGACGTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (51 bp):
TGTAATAGCCCATTTTCAGTCAAATTAGAACAGTGGTTCTGAGACCACAAA
Found at i:55714812 original size:21 final size:20
Alignment explanation
Indices: 55714783--55714822 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55714773 CTTTGAAACA
* *
55714783 GGGCACACGTCTGTGTGGAT
1 GGGCACACGCCCGTGTGGAT
55714803 GGGCAACACGCCCGTGTGGA
1 GGGC-ACACGCCCGTGTGGA
55714823 ACTTGAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.17, C:0.25, G:0.40, T:0.17
Consensus pattern (20 bp):
GGGCACACGCCCGTGTGGAT
Found at i:55720263 original size:40 final size:40
Alignment explanation
Indices: 55720139--55720323 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 40
55720129 TATTCGAATG
* *
55720139 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
55720180 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
** * *
55720220 ATATTTGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
55720260 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
55720300 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
55720324 CTTGTGCAAG
Statistics
Matches: 117, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 87 0.74
41 29 0.25
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:55720314 original size:80 final size:78
Alignment explanation
Indices: 55720141--55720359 Score: 210
Period size: 80 Copynumber: 2.7 Consensus size: 78
55720131 TTCGAATGAT
* * * *
55720141 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGAT-CCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGC-TTTGTGCTA-G-GATTATATCCGGGCTAAG-TCCCGAAGGCA
* * *
55720205 TTCGTGCGAGTTGCTAT
62 TTCATGCGAGTTGCCAC
**
55720222 ATTTGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAG-GATTATATCCGGGCTAAGTCCCGAAGGCATT
* *
55720287 TATGCTAG-TGACCAC
64 CATGCGAGTTG-CCAC
* * * *
55720302 ATCCGGGCTAAGACCCGAAGGCCTTGTGCAAGTAGTTATATCC-GGCTAAATCCCGAAG
1 ATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGGA-TTATATCCGGGCTAAGTCCCGAAG
55720360 ATTTCTTGAG
Statistics
Matches: 116, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
78 15 0.13
79 19 0.16
80 54 0.47
81 28 0.24
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (78 bp):
ATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGGATTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCGAGTTGCCAC
Found at i:55737308 original size:40 final size:40
Alignment explanation
Indices: 55737207--55737391 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 40
55737197 TATTCGAATG
* *
55737207 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * * *
55737248 GTAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* * *
55737288 ATATCCGGGCTAAGACCCGAAGGCATTTGTGATAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
55737328 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
55737368 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
55737392 CTTGTGCAAG
Statistics
Matches: 117, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 88 0.75
41 28 0.24
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:55741537 original size:41 final size:41
Alignment explanation
Indices: 55741466--55741598 Score: 164
Period size: 41 Copynumber: 3.2 Consensus size: 41
55741456 TTGATATCAC
* *
55741466 GCACACTAAGTGCCAATACATAGCGGAAGCTAT-TATAATCTT
1 GCACACTAAGTGCC-ATACATAGCCGAAGCTATCT-CAATCTT
* **
55741508 GCACACTAAGTGCCTTACATAGCCGAAGCTATCTCGGTCTT
1 GCACACTAAGTGCCATACATAGCCGAAGCTATCTCAATCTT
*
55741549 GCACACTAAGTGCCATATATAGCCGAAGCTATCTCGAA--TT
1 GCACACTAAGTGCCATACATAGCCGAAGCTATCTC-AATCTT
55741589 GCACACTAAG
1 GCACACTAAG
55741599 GCCTATTCTG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
40 12 0.15
41 53 0.66
42 15 0.19
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (41 bp):
GCACACTAAGTGCCATACATAGCCGAAGCTATCTCAATCTT
Found at i:55743493 original size:56 final size:56
Alignment explanation
Indices: 55743422--55743568 Score: 179
Period size: 56 Copynumber: 2.6 Consensus size: 56
55743412 ACTTGGAAGT
* * **
55743422 ATATGTGATTCTGATATATGTGTACGAGTAAGACCACTTTTTATACGTTGGCATTG
1 ATATATGATTCTGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCA
* * *
55743478 ATATATGACTT-TGATATATATGTTCGAGTAAGACAACGTTTTATACGTTGGCATCA
1 ATATATGA-TTCTGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCA
* * * *
55743534 ATATGTGATTCCGATATGTGTTTACGAGTAAGACC
1 ATATATGATTCTGATATATGTGTACGAGTAAGACC
55743569 CTATCTGGGA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
55 2 0.03
56 71 0.95
57 2 0.03
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.37
Consensus pattern (56 bp):
ATATATGATTCTGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCA
Found at i:55747926 original size:50 final size:51
Alignment explanation
Indices: 55747850--55747958 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 51
55747840 CCTTGTAGTA
* *
55747850 AAAGCTACCTTCTTCACAAAGTGGCCTTCACATAGTA-CACACT-TGCGACC
1 AAAGCTATCTTCTTCACAAAGTGGCCTGCACATAGTATCACA-TATGCGACC
* * * *
55747900 AAAGCTATCTT-TTACACATAGTGGCCTGCACTTAGTATCACATATGTGATC
1 AAAGCTATCTTCTT-CACAAAGTGGCCTGCACATAGTATCACATATGCGACC
55747951 AAAGCTAT
1 AAAGCTAT
55747959 TGGGTATGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 2 0.04
50 31 0.62
51 17 0.34
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (51 bp):
AAAGCTATCTTCTTCACAAAGTGGCCTGCACATAGTATCACATATGCGACC
Found at i:55750057 original size:413 final size:412
Alignment explanation
Indices: 55749291--55750117 Score: 1537
Period size: 413 Copynumber: 2.0 Consensus size: 412
55749281 TCCTTTTAGC
*
55749291 TAAATTGAGTGCCCAAATGTCAAAATTTTTGAACGCAATTTTCATGAAATTATTCTGTGAAATTG
1 TAAATTGAGTGCCCAAATGTCAAAATTTTCGAACGCAATTTTCATGAAATTATTCTGTGAAATTG
*
55749356 TAGACCATAAAATGTAATAAAAATAAAATTTTTCTCATCGGATTTGTGGTCCCGAAACCACTATT
66 TAAACCATAAAATGTAATAAAAATAAAATTTTTCTCATCGGATTTGTGGTCCCGAAACCACTATT
* * *
55749421 CTGACTACGCCCAAAATCGGGATGTTACATTTCTCCCGCTTTAGGGATTTTCGTCCCCGGAAGTC
131 CTGACTACGCCCAAAATCGGGATGTTACATTACTCCCGCTTTAGGGATTTTCGTCCCCGAAAATC
*
55749486 TTACCACAAAAGTGGTTTTGGTTTTTCACTTATTTTCCTCAATCCTATAGTCGATGTCAATGAAC
196 TTACCACAAAAGTAGTTTTGGTTTTTCACTTATTTTCCTCAATCCTATAGTCGATGTCAATGAAC
* *
55749551 TTTCACTCAAGCTAAGCTTTTACTACCTATCTCTTAAATTCCAGATACAAGAGTCATGAGTGGTT
261 TTTCACTCAAGCTAAGCTTTTACTACCTATCTCTTAAATTCCAGATACAAAAGTCATGAATGGTT
55749616 TTCGCTTTGTAACATTTTCACTGAAACTTAATCTTGATCAGAAAGTTCATGTACTCAAAAGTCCA
326 TTCGCTTTGTAACATTTTCACTGAAACTTAATCTTGATCAGAAAGTTCATGTACTCAAAAGTCCA
55749681 ATCCATTCTATCATGATACATA
391 ATCCATTCTATCATGATACATA
55749703 TAAATTGAGTGCCCAAATGTCAAAATTTTCGAACGCAATTTTCATGAAATTATTCTGTGAAATTG
1 TAAATTGAGTGCCCAAATGTCAAAATTTTCGAACGCAATTTTCATGAAATTATTCTGTGAAATTG
*
55749768 TAAACCATAAAAATGTAATAAAAATAAAATTTTTCTCATCGGATTTGTGGTCCCGAAACCACTGT
66 TAAACCAT-AAAATGTAATAAAAATAAAATTTTTCTCATCGGATTTGTGGTCCCGAAACCACTAT
*
55749833 TCTGACTAGGCCCAAAATCGGGATGTTACATTACTCCCGCTTTAGGGATTTTCGTCCCCGAAAAT
130 TCTGACTACGCCCAAAATCGGGATGTTACATTACTCCCGCTTTAGGGATTTTCGTCCCCGAAAAT
*
55749898 CTTACCAGAAAAGTAGTTTTGGTTTTTCACTTATTTTCCTCAATCCTATAGTCGATGTCAATGAA
195 CTTACCACAAAAGTAGTTTTGGTTTTTCACTTATTTTCCTCAATCCTATAGTCGATGTCAATGAA
55749963 CTTTCACTCAAGCTAAGCTTTTACTACCTATCTCTTAAATTCCAGATACAAAAGTCATGAATGGT
260 CTTTCACTCAAGCTAAGCTTTTACTACCTATCTCTTAAATTCCAGATACAAAAGTCATGAATGGT
55750028 TTTCGCTTTGTAACATTTTCACTGAAACTTAATCTTGATCAGAAAGTTCATGTACTCAAAAGTCC
325 TTTCGCTTTGTAACATTTTCACTGAAACTTAATCTTGATCAGAAAGTTCATGTACTCAAAAGTCC
*
55750093 AATCCATTCTATCATGTTACATA
390 AATCCATTCTATCATGATACATA
55750116 TA
1 TA
55750118 CATTCATACT
Statistics
Matches: 402, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
412 71 0.18
413 331 0.82
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (412 bp):
TAAATTGAGTGCCCAAATGTCAAAATTTTCGAACGCAATTTTCATGAAATTATTCTGTGAAATTG
TAAACCATAAAATGTAATAAAAATAAAATTTTTCTCATCGGATTTGTGGTCCCGAAACCACTATT
CTGACTACGCCCAAAATCGGGATGTTACATTACTCCCGCTTTAGGGATTTTCGTCCCCGAAAATC
TTACCACAAAAGTAGTTTTGGTTTTTCACTTATTTTCCTCAATCCTATAGTCGATGTCAATGAAC
TTTCACTCAAGCTAAGCTTTTACTACCTATCTCTTAAATTCCAGATACAAAAGTCATGAATGGTT
TTCGCTTTGTAACATTTTCACTGAAACTTAATCTTGATCAGAAAGTTCATGTACTCAAAAGTCCA
ATCCATTCTATCATGATACATA
Found at i:55754624 original size:51 final size:51
Alignment explanation
Indices: 55754514--55754624 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 51
55754504 CCCTTGTAGT
* * *
55754514 CAAAGCTACCTTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGAC
1 CAAAGCTATCTTCTTCACAAAGTGGCCTGCACATAGTACCACACATGTGAC
* * * *
55754565 CAAAGCTATCTT-TTACACATAGTGGTCTGCACTTAGTACCACACATGTGAT
1 CAAAGCTATCTTCTT-CACAAAGTGGCCTGCACATAGTACCACACATGTGAC
*
55754616 CGAAGCTAT
1 CAAAGCTAT
55754625 TGGGTACATA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 2 0.04
51 49 0.96
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (51 bp):
CAAAGCTATCTTCTTCACAAAGTGGCCTGCACATAGTACCACACATGTGAC
Found at i:55754638 original size:51 final size:51
Alignment explanation
Indices: 55754547--55754766 Score: 176
Period size: 51 Copynumber: 4.3 Consensus size: 51
55754537 GGCCTTCACA
* ** *
55754547 TAGTACCACACTTGTGACCAAAGCTATCTTTTACACATAGT-GGTCTGCACT
1 TAGTACCACACATGTGACCAAAGCTATCTGGTACACATAGTAGCT-TGCACT
* * *
55754598 TAGTACCACACATGTGATCGAAGCTAT-TGGGTACATATAGTAGCTTGCACT
1 TAGTACCACACATGTGACCAAAGCTATCT-GGTACACATAGTAGCTTGCACT
* * * * *
55754649 TAGTACTACACATGCGACCTAATC-ATCTGGTACACGTAGTAGCTTGCACT
1 TAGTACCACACATGTGACCAAAGCTATCTGGTACACATAGTAGCTTGCACT
* * * * * * *** * *
55754699 TAGTACTACACACGTAACCTAAAACCATTTTAAACACATAGTAGCCTGCACA
1 TAGTACCACACATGTGACC-AAAGCTATCTGGTACACATAGTAGCTTGCACT
*
55754751 TAGTACTACACATGTG
1 TAGTACCACACATGTG
55754767 TTTTCACAAC
Statistics
Matches: 136, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
50 39 0.29
51 62 0.46
52 35 0.26
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (51 bp):
TAGTACCACACATGTGACCAAAGCTATCTGGTACACATAGTAGCTTGCACT
Found at i:55763318 original size:39 final size:39
Alignment explanation
Indices: 55763268--55763354 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
55763258 AACTTAATGT
* * * *
55763268 CTAGCAGGCCTCGTGCTGGTGATAAATTTAGGTTTATAC
1 CTAGCAGGCCTCGTACCGGTGATAAACTCAGGTTTATAC
*
55763307 CTAGCAGGCCTCGTACCGGTGATAAGCTCAGGTTTATAC
1 CTAGCAGGCCTCGTACCGGTGATAAACTCAGGTTTATAC
55763346 CTAGCAGGC
1 CTAGCAGGC
55763355 TAATTGCCGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (39 bp):
CTAGCAGGCCTCGTACCGGTGATAAACTCAGGTTTATAC
Found at i:55765634 original size:40 final size:40
Alignment explanation
Indices: 55765557--55765778 Score: 279
Period size: 40 Copynumber: 5.6 Consensus size: 40
55765547 AAACCAAGTA
* * * *
55765557 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCACTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
55765596 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
55765636 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
55765676 CCTTCGGGACTTAGCCTGGTTATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * * * * * *
55765716 CCTTCGGGGCTTAGCCCGG-AATTAGTCATTAGCACAATTT
1 CCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATG
*
55765756 CCTTCGGGACTTAGCCCAGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
55765779 CATCCGAATA
Statistics
Matches: 163, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
39 15 0.09
40 147 0.90
41 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:55793126 original size:9 final size:9
Alignment explanation
Indices: 55793112--55793137 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55793102 CTCCCTAATT
55793112 CACAAAATA
1 CACAAAATA
55793121 CACAAAATA
1 CACAAAATA
55793130 CACAAAAT
1 CACAAAAT
55793138 TTGCCTGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.23, G:0.00, T:0.12
Consensus pattern (9 bp):
CACAAAATA
Found at i:55798811 original size:43 final size:42
Alignment explanation
Indices: 55798733--55798854 Score: 106
Period size: 43 Copynumber: 2.9 Consensus size: 42
55798723 AGTTCGTACA
* * * *
55798733 ATGCCAACTTTCCAGACATGGTCTTACATGTAATCAAATATCG
1 ATGCCAACTATCCAGACAGGGTCTTACACGAAATCAAATA-CG
* *
55798776 ATGCC-ACTATCCTAGACAGGGTCTTAGACGAAATCAAGTACG
1 ATGCCAACTATCC-AGACAGGGTCTTACACGAAATCAAATACG
* *
55798818 ATGCTAACGT-CCCAGAC-GTGGTCTTACACGTAAATCA
1 ATGCCAAC-TATCCAGACAG-GGTCTTACACG-AAATCA
55798855 TAAGTCGATG
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 1 0.02
42 26 0.40
43 37 0.57
44 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAACTATCCAGACAGGGTCTTACACGAAATCAAATACG
Found at i:55798841 original size:42 final size:43
Alignment explanation
Indices: 55798744--55798887 Score: 136
Period size: 44 Copynumber: 3.3 Consensus size: 43
55798734 TGCCAACTTT
* * * *
55798744 CCAGACATGGTCTTACATGT-AATCAAATATCGATGC-CACTATC
1 CCAGACGTGGTCTTACACGTAAATCAAA-GTCGATGCTAAC-ATC
* * *
55798787 CTAGACAG-GGTCTTAGACG-AAATC-AAGTACGATGCTAACGTC
1 CCAGAC-GTGGTCTTACACGTAAATCAAAGT-CGATGCTAACATC
55798829 CCAGACGTGGTCTTACACGTAAATCATAAGTCGATGCTAACATC
1 CCAGACGTGGTCTTACACGTAAATCA-AAGTCGATGCTAACATC
*
55798873 CCAGATGTGGTCTTA
1 CCAGACGTGGTCTTA
55798888 TAAGTCGATG
Statistics
Matches: 82, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
41 2 0.02
42 25 0.30
43 25 0.30
44 26 0.32
45 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
CCAGACGTGGTCTTACACGTAAATCAAAGTCGATGCTAACATC
Found at i:55798866 original size:44 final size:42
Alignment explanation
Indices: 55798744--55798927 Score: 140
Period size: 33 Copynumber: 4.5 Consensus size: 42
55798734 TGCCAACTTT
* * * * *
55798744 CCAGACATGGTCTTACATGTAATCAAATATCGATGC-CACTATC
1 CCAGACGTGGTCTTACACGAAATCAAGTA-CGATGCTAAC-ATC
* * *
55798787 CTAGACAG-GGTCTTAGACGAAATCAAGTACGATGCTAACGTC
1 CCAGAC-GTGGTCTTACACGAAATCAAGTACGATGCTAACATC
55798829 CCAGACGTGGTCTTACACGTAAATCATAAGT-CGATGCTAACATC
1 CCAGACGTGGTCTTACACG-AAATC--AAGTACGATGCTAACATC
*
55798873 CCAGATGTGGTCTT-------AT-AAGT-CGATGCTAACATC
1 CCAGACGTGGTCTTACACGAAATCAAGTACGATGCTAACATC
*
55798906 CCAGATGTGGTCTTACACGAAA
1 CCAGACGTGGTCTTACACGAAA
55798928 ACACATATCG
Statistics
Matches: 116, Mismatches: 12, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
33 31 0.27
36 2 0.02
40 1 0.01
41 1 0.01
42 23 0.20
43 29 0.25
44 25 0.22
45 4 0.03
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (42 bp):
CCAGACGTGGTCTTACACGAAATCAAGTACGATGCTAACATC
Found at i:55801210 original size:46 final size:43
Alignment explanation
Indices: 55801020--55801202 Score: 131
Period size: 45 Copynumber: 4.0 Consensus size: 43
55801010 AACCCGCCCC
* * * *
55801020 TAAGTGAACTCGGACTCAACTCAATGAGCTCAGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G-GTTCTCAACCA
* *
55801065 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-TTCTC-A---ACCA
* * *
55801111 TCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATT-TGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGG---TTCT-CAACCA
55801158 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGTTGCTCAACCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGTT-CTCAACCA
55801202 T
1 T
55801203 CCTAGTGACA
Statistics
Matches: 111, Mismatches: 12, Indels: 31
0.72 0.08 0.20
Matches are distributed among these distances:
43 4 0.04
44 10 0.09
45 31 0.28
46 30 0.27
47 30 0.27
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGTTCTCAACCA
Found at i:55801648 original size:30 final size:30
Alignment explanation
Indices: 55801614--55801673 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
55801604 ATTTGATACG
55801614 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
55801644 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
55801674 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:55808369 original size:19 final size:20
Alignment explanation
Indices: 55808345--55808382 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
55808335 GGTACCACCA
55808345 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
55808364 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
55808383 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:55808727 original size:93 final size:93
Alignment explanation
Indices: 55808612--55808781 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
55808602 GCCCCTAAGT
* *
55808612 GAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAATGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAATGAACTCAGACTCAACTCA
55808676 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
55808705 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCAA
55808770 CGAGTTCGGATG
66 CGAGTTCGGATG
55808782 GTCAACCATC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 69 0.97
94 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:55808778 original size:46 final size:47
Alignment explanation
Indices: 55808607--55808779 Score: 203
Period size: 46 Copynumber: 3.7 Consensus size: 47
55808597 AACCCGCCCC
* * *
55808607 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
* * *
55808653 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-ATTTGCATCCA
* *
55808701 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
*
55808746 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55808780 TGGTCAACCA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 57 0.53
47 31 0.29
48 3 0.03
49 2 0.02
50 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
Found at i:55816235 original size:10 final size:10
Alignment explanation
Indices: 55816222--55816246 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55816212 TGGGTTGTTC
55816222 TGGGCCGAAA
1 TGGGCCGAAA
55816232 TGGGCCGAAA
1 TGGGCCGAAA
55816242 TGGGC
1 TGGGC
55816247 TGTATGGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.20, G:0.44, T:0.12
Consensus pattern (10 bp):
TGGGCCGAAA
Found at i:55816604 original size:16 final size:16
Alignment explanation
Indices: 55816585--55816615 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55816575 ACTGATTTTG
*
55816585 TACATGACATTCTGCA
1 TACATGACATACTGCA
55816601 TACATGACATACTGC
1 TACATGACATACTGC
55816616 TTGGGATTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (16 bp):
TACATGACATACTGCA
Found at i:55818641 original size:83 final size:83
Alignment explanation
Indices: 55818502--55818668 Score: 316
Period size: 83 Copynumber: 2.0 Consensus size: 83
55818492 AGCATCCTGT
*
55818502 AGCTCGGACCTGATGATCGGGTTGGACGATGGGTGTTACAAAAAGTAAGTATGATTTTATGAAAC
1 AGCTCGGACCTGATGATCGGGTTGGACAATGGGTGTTACAAAAAGTAAGTATGATTTTATGAAAC
55818567 ATGGTTTGTAATATCTGG
66 ATGGTTTGTAATATCTGG
*
55818585 AGCTCGGACCTGATGATTGGGTTGGACAATGGGTGTTACAAAAAGTAAGTATGATTTTATGAAAC
1 AGCTCGGACCTGATGATCGGGTTGGACAATGGGTGTTACAAAAAGTAAGTATGATTTTATGAAAC
55818650 ATGGTTTGTAATATCTGG
66 ATGGTTTGTAATATCTGG
55818668 A
1 A
55818669 TGGATTAAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32
Consensus pattern (83 bp):
AGCTCGGACCTGATGATCGGGTTGGACAATGGGTGTTACAAAAAGTAAGTATGATTTTATGAAAC
ATGGTTTGTAATATCTGG
Found at i:55828283 original size:20 final size:20
Alignment explanation
Indices: 55828235--55828283 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
55828225 CCATGTTTCC
* *
55828235 ATTAAAAAACGTTCTTAATA
1 ATTAAAAACCCTTCTTAATA
55828255 ATTAAAAACCCTTCTTAATA
1 ATTAAAAACCCTTCTTAATA
55828275 ATTAAAAAC
1 ATTAAAAAC
55828284 TTATACCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTAAAAACCCTTCTTAATA
Found at i:55828845 original size:6 final size:6
Alignment explanation
Indices: 55828824--55828926 Score: 93
Period size: 6 Copynumber: 16.8 Consensus size: 6
55828814 TATTAGAACA
* * * *
55828824 AGAATC AAAATG AGAATC AGAATC AAAATC A-AGTGAC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * *
55828873 AGAATC AGAATC AGAATC AAAATC AGTATC AGGTAA-C AGAATC AAAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
55828922 AGAAT
1 AGAAT
55828927 GTGAATGCAA
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
5 4 0.05
6 66 0.85
7 5 0.06
8 3 0.04
ACGTcount: A:0.52, C:0.15, G:0.16, T:0.17
Consensus pattern (6 bp):
AGAATC
Found at i:55828872 original size:43 final size:43
Alignment explanation
Indices: 55828824--55828926 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 43
55828814 TATTAGAACA
*
55828824 AGAATCAAAATGAGAATCAGAATCAAAATCAAGTGA-CA-G-AATC
1 AGAATCAAAATCAGAATCAGAATCAAAATC-AGT-ATCAGGTAA-C
*
55828867 AGAATCAGAATCAGAATCAGAATCAAAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAAAATCAGTATCAGGTAAC
55828910 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
55828927 GTGAATGCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
41 1 0.02
42 5 0.09
43 46 0.85
44 2 0.04
ACGTcount: A:0.52, C:0.15, G:0.16, T:0.17
Consensus pattern (43 bp):
AGAATCAAAATCAGAATCAGAATCAAAATCAGTATCAGGTAAC
Found at i:55829091 original size:27 final size:26
Alignment explanation
Indices: 55829043--55829102 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
55829033 GCGAGGCTGC
*
55829043 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
55829070 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
55829096 CAGATAT
1 CAGATAT
55829103 ATATATGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55829189 original size:27 final size:26
Alignment explanation
Indices: 55829142--55829192 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
55829132 CGAGGCTGCC
*
55829142 AGATATTGTGACGAAGTCACCAGAAT
1 AGATATTGTGACGAAGCCACCAGAAT
* *
55829168 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
55829193 TTGCAGCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAT
Found at i:55829501 original size:27 final size:27
Alignment explanation
Indices: 55829437--55829577 Score: 194
Period size: 27 Copynumber: 5.3 Consensus size: 27
55829427 AGGGTAAAAT
* * * *
55829437 GGTAATTTTACCCCACAAGGGTA-TCC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
55829463 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
55829490 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
55829517 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
55829544 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
55829571 GGTAATT
1 GGTAATT
55829578 TTGTAAATCA
Statistics
Matches: 102, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 19 0.19
27 83 0.81
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:55829592 original size:27 final size:27
Alignment explanation
Indices: 55829562--55829738 Score: 139
Period size: 27 Copynumber: 6.6 Consensus size: 27
55829552 TACCCTACAG
* *
55829562 GGGTATTTCGGTAATTTTGTAAATCAA
1 GGGTATTTCGGTAATTTTGCAAATCGA
*** *
55829589 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTATTTCGGTAATTTTGCAAATCGA
* * *
55829616 GGGTACTTT-GGTAATTTTACAAGTTGA
1 GGGTA-TTTCGGTAATTTTGCAAATCGA
* *
55829643 GGGTATTTCAGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTGCAAATCGA
*
55829670 GGGTATTTCAGTAATTTTGCAAA-CTGA
1 GGGTATTTCGGTAATTTTGCAAATC-GA
* * * *
55829697 --GTATTTCAGTCATTTTACAAAT-TA
1 GGGTATTTCGGTAATTTTGCAAATCGA
*
55829721 GGGGTATTTTGGTAATTT
1 -GGGTATTTCGGTAATTT
55829739 GGTAAACTAA
Statistics
Matches: 122, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
24 1 0.01
25 19 0.16
26 4 0.03
27 98 0.80
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTGCAAATCGA
Found at i:55829601 original size:54 final size:54
Alignment explanation
Indices: 55829491--55829604 Score: 133
Period size: 54 Copynumber: 2.1 Consensus size: 54
55829481 GGGTATTTCA
* ** ***
55829491 GTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACAATACAAGGGTAAAACG
*
55829545 GTAATTCTACCCTACAGGGGTATTTCGGTAATTTTGTA-AAT-CAAGGGTAAAACG
1 GTAATTCTACCCTACAGGGGTATTTCGGT-A-TTTCTACAATACAAGGGTAAAACG
55829599 GTAATT
1 GTAATT
55829605 TTGTAAATCG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
54 44 0.86
55 2 0.04
56 5 0.10
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (54 bp):
GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACAATACAAGGGTAAAACG
Found at i:55829601 original size:81 final size:79
Alignment explanation
Indices: 55829425--55829606 Score: 186
Period size: 81 Copynumber: 2.3 Consensus size: 79
55829415 TTTAACATCC
* *
55829425 TAAGGGTAAAATGGTAATTTTACCCCACAAGGGTATCCGGTAATTCTACCCTATAGGGGTATTTC
1 TAAGGGTAAAACGGT-ATTTTACCCCACAAGGGTATCCGGTAATTCTACCCTACAGGGGTATTTC
**
55829490 AGTAATTCTACCCTA
65 AGTAATTCTACCAAA
* *** * *
55829505 TAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
1 TAAGGGTAAAACGGTATTT-TACCCCACAAGGGTA-TCCGGTAATTCTACCCTACAGGGGTATTT
* ***
55829570 CGGTAATT-TTGTAAA
64 CAGTAATTCTACCAAA
55829585 TCAAGGGTAAAACGGTAATTTT
1 T-AAGGGTAAAACGGT-ATTTT
55829607 GTAAATCGAG
Statistics
Matches: 80, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
79 4 0.05
80 27 0.34
81 45 0.56
82 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (79 bp):
TAAGGGTAAAACGGTATTTTACCCCACAAGGGTATCCGGTAATTCTACCCTACAGGGGTATTTCA
GTAATTCTACCAAA
Found at i:55829746 original size:52 final size:52
Alignment explanation
Indices: 55829645--55829746 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
55829635 CAAGTTGAGG
* *
55829645 GTATTTCAGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTGCAAACTGA
1 GTATTTCAGTAATTTTACAAATAGAGGGTATTTCAGTAATTTGGCAAACTGA
* ** *
55829697 GTATTTCAGTCATTTTACAAATTAG-GGGTATTTTGGTAATTTGGTAAACT
1 GTATTTCAGTAATTTTACAAA-TAGAGGGTATTTCAGTAATTTGGCAAACT
55829747 AAATTATTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 41 0.95
53 2 0.05
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (52 bp):
GTATTTCAGTAATTTTACAAATAGAGGGTATTTCAGTAATTTGGCAAACTGA
Found at i:55831754 original size:38 final size:38
Alignment explanation
Indices: 55831711--55831786 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
55831701 TTCATCCTTT
*
55831711 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGACCGAAAATTCTAAGGAAGGAGGAA
55831749 TTCATTTCTTTTGACCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGACCGAAAATTCTAAGGAAGGAGGAA
55831787 GGAGTTCTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGACCGAAAATTCTAAGGAAGGAGGAA
Found at i:55832329 original size:40 final size:40
Alignment explanation
Indices: 55832235--55832379 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
55832225 TACTCGAATG
*
55832235 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
55832276 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
55832316 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
55832356 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
55832380 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:55844330 original size:16 final size:16
Alignment explanation
Indices: 55844309--55844341 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55844299 AGACGTGGTC
55844309 TTACACGCAGAACAGA
1 TTACACGCAGAACAGA
55844325 TTACACGCAGAACAGA
1 TTACACGCAGAACAGA
55844341 T
1 T
55844342 ATCGAAAATC
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:0.42, C:0.24, G:0.18, T:0.15
Consensus pattern (16 bp):
TTACACGCAGAACAGA
Found at i:55846217 original size:27 final size:27
Alignment explanation
Indices: 55846186--55846313 Score: 186
Period size: 27 Copynumber: 4.8 Consensus size: 27
55846176 CAGTAACGCA
* *
55846186 GCAAAGCTACCAATATCAGTATATGTG
1 GCAAAGCCACCAATAGCAGTATATGTG
* * **
55846213 GCAAAGACACCAGTAATAGTATATGTG
1 GCAAAGCCACCAATAGCAGTATATGTG
55846240 GCAAAGCCACCAATAGCAGTATATGTG
1 GCAAAGCCACCAATAGCAGTATATGTG
55846267 GCAAAGCCACCAATAGCAGTATATGTG
1 GCAAAGCCACCAATAGCAGTATATGTG
*
55846294 GCAAAGCCACCAGTA-CAGTA
1 GCAAAGCCACCAATAGCAGTA
55846314 CACTTCCTCC
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 5 0.05
27 86 0.95
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (27 bp):
GCAAAGCCACCAATAGCAGTATATGTG
Found at i:55846450 original size:26 final size:27
Alignment explanation
Indices: 55846414--55846467 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
55846404 ATCATAGCAC
*
55846414 AAAACAGTCA-TTTACCCTCGAGGGGT
1 AAAACAGTCATTTTACCCTAGAGGGGT
* *
55846440 AAAATAGTCATTTTACCCTATAGGGGT
1 AAAACAGTCATTTTACCCTAGAGGGGT
55846467 A
1 A
55846468 TTTTGCTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (27 bp):
AAAACAGTCATTTTACCCTAGAGGGGT
Found at i:55849996 original size:27 final size:26
Alignment explanation
Indices: 55849942--55850052 Score: 132
Period size: 27 Copynumber: 4.2 Consensus size: 26
55849932 AGCATGGCTG
* * * *
55849942 CCAGAACAGATAATGTGACAGTGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
55849968 CCAGAACAGATAGTTGTGGCAGAGCCA
1 CCAGAACAGATA-TTGTGGCAGAGCCA
*
55849995 CCAGAACAGATATATGTGGCAGTGCCA
1 CCAGAACAGATAT-TGTGGCAGAGCCA
* *
55850022 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGAT-ATTGTGGCAGAGCCA
55850049 CCAG
1 CCAG
55850053 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.18
27 59 0.80
28 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:55850026 original size:54 final size:53
Alignment explanation
Indices: 55849942--55850052 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 53
55849932 AGCATGGCTG
* *
55849942 CCAGAACAGATAATGTGACAGTGTCACCAGAACAGATAGTTGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGTGCCACCAGAACAGATAATTGTGGCAGAGCCA
* * *
55849995 CCAGAACAGATATATGTGGCAGTGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGTGCCACCAGAACAGATAATTGTGGCAGAGCCA
55850049 CCAG
1 CCAG
55850053 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
53 12 0.23
54 40 0.77
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (53 bp):
CCAGAACAGATAATGTGACAGTGCCACCAGAACAGATAATTGTGGCAGAGCCA
Found at i:55861211 original size:47 final size:47
Alignment explanation
Indices: 55861160--55861721 Score: 901
Period size: 47 Copynumber: 11.7 Consensus size: 47
55861150 TTAGGATTCT
* * *
55861160 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
55861207 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
55861254 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
55861301 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
55861350 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
55861397 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
55861446 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
55861495 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGACG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
55861544 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
55861591 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
* * * * *
55861640 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
55861687 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
55861722 TCCCGAAGGG
Statistics
Matches: 491, Mismatches: 17, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
46 1 0.00
47 253 0.52
49 237 0.48
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:55861235 original size:25 final size:25
Alignment explanation
Indices: 55861207--55861285 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
55861197 CTAATGGCCG
55861207 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
55861232 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
55861254 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
55861279 ATGTGAT
1 ATGTGAT
55861286 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:55861346 original size:49 final size:49
Alignment explanation
Indices: 55861181--55861721 Score: 908
Period size: 49 Copynumber: 11.3 Consensus size: 49
55861171 GTGAACATGC
*
55861181 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
55861228 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
55861275 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
55861324 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
55861371 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
55861420 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
55861469 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
55861518 ATATATGTGATAAGGCCTAATGGACGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
55861565 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
55861614 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * * *
55861661 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
55861710 A-A-ATGTGATAAG
1 ATATATGTGATAAG
55861722 TCCCGAAGGG
Statistics
Matches: 472, Mismatches: 14, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
47 232 0.49
48 1 0.00
49 239 0.51
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (49 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:55861375 original size:96 final size:96
Alignment explanation
Indices: 55861160--55861721 Score: 954
Period size: 96 Copynumber: 5.9 Consensus size: 96
55861150 TTAGGATTCT
* * *
55861160 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
55861224 GTG--TATATATGTGATAAGGCCTAATGGCCG
65 GTGTATATATATGTGATAAGGCCTAATGGCCG
55861254 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
55861319 TGTATATATATGTGATAAGGCCTAATGGCCG
66 TGTATATATATGTGATAAGGCCTAATGGCCG
*
55861350 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
55861415 TGTATATATATGTGATAAGGCCTAATGGCCG
66 TGTATATATATGTGATAAGGCCTAATGGCCG
55861446 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
55861511 AGTGTATATATATGTGATAAGGCCTAATGGACG
64 AGTGTATATATATGTGATAAGGCCTAATGGCCG
55861544 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
55861609 TGTATATATATGTGATAAGGCCTAATGGCCG
66 TGTATATATATGTGATAAGGCCTAATGGCCG
* * * * * * *
55861640 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
55861705 TGTATA-A-ATGTGATAAG
66 TGTATATATATGTGATAAG
55861722 TCCCGAAGGG
Statistics
Matches: 449, Mismatches: 14, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
93 1 0.00
94 72 0.16
95 1 0.00
96 281 0.63
98 94 0.21
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATATGTGATAAGGCCTAATGGCCG
Found at i:55861898 original size:37 final size:37
Alignment explanation
Indices: 55861840--55861918 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
55861830 CCGAGCTCTA
* * * *
55861840 AAGACCCGATGACTACTTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
55861877 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
55861914 AAGAC
1 AAGAC
55861919 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:55863616 original size:42 final size:43
Alignment explanation
Indices: 55863516--55863665 Score: 135
Period size: 43 Copynumber: 3.5 Consensus size: 43
55863506 AATGCCGACA
* * *
55863516 TCCCAGACATGGTCTTACATGTAATCAAACATCGATGCCACTG
1 TCCCAGACATGGTCTTACACGAAATCAAACATCGATGCCAATG
* * **
55863559 TCCCAGACA-GCGTCTTACACGAAATCAGATAT-GATGTTAATG
1 TCCCAGACATG-GTCTTACACGAAATCAAACATCGATGCCAATG
* * *
55863601 TCCCAGACATGGTCTTACACGCAAAACAAA-AGTTGATACCAATG
1 TCCCAGACATGGTCTTACACG-AAATCAAACA-TCGATGCCAATG
** *
55863645 TCATAGACGTGGTCTTACACG
1 TCCCAGACATGGTCTTACACG
55863666 CAGAACAGAT
Statistics
Matches: 87, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 28 0.32
43 34 0.39
44 25 0.29
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAAATCAAACATCGATGCCAATG
Found at i:55866086 original size:48 final size:46
Alignment explanation
Indices: 55865952--55866157 Score: 172
Period size: 48 Copynumber: 4.5 Consensus size: 46
55865942 TACTTGGAAA
* * * * * *
55865952 CTCGCACACTTAGTGCCAA-ATA--AATAGCAGAAGCTATATCAAT
1 CTCGCACACTAAGTGCCAATATATTTATAGCTGAAGTTATCTCAGT
* * * * * *
55865995 CTTGCACACTAAGTGCCAATATGTATGTATAGCCGGAGCTATCTCAAT
1 CTCGCACACTAAGTGCCAATA--TATTTATAGCTGAAGTTATCTCAGT
* * *
55866043 CACGCACACTAAGTGCCAATATATGTATATAACTGAAGTTATCT-GGT
1 CTCGCACACTAAGTGCCAATATAT-T-TATAGCTGAAGTTATCTCAGT
* *
55866090 CTCGCACACTTAGTGCCAATATA-TT-TAGCTAAAGTTATCTCAGT
1 CTCGCACACTAAGTGCCAATATATTTATAGCTGAAGTTATCTCAGT
*
55866134 CTCGCACACTTAGTGCCAATATAT
1 CTCGCACACTAAGTGCCAATATAT
55866158 AACCGAATCG
Statistics
Matches: 134, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
43 30 0.22
44 27 0.20
45 1 0.01
46 5 0.04
47 22 0.16
48 49 0.37
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (46 bp):
CTCGCACACTAAGTGCCAATATATTTATAGCTGAAGTTATCTCAGT
Found at i:55866112 original size:47 final size:45
Alignment explanation
Indices: 55866034--55866157 Score: 153
Period size: 44 Copynumber: 2.7 Consensus size: 45
55866024 TAGCCGGAGC
* * * *
55866034 TATCTCAATCACGCACACTAAGTGCCAATATATGTATATAACTGAAGT
1 TATCTCAGTCTCGCACACTTAGTGCCAATATAT-T-T-TAACTAAAGT
* *
55866082 TATCT-GGTCTCGCACACTTAGTGCCAATATA-TTTAGCTAAAGT
1 TATCTCAGTCTCGCACACTTAGTGCCAATATATTTTAACTAAAGT
55866125 TATCTCAGTCTCGCACACTTAGTGCCAATATAT
1 TATCTCAGTCTCGCACACTTAGTGCCAATATAT
55866158 AACCGAATCG
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
43 13 0.19
44 26 0.39
45 1 0.01
47 22 0.33
48 5 0.07
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (45 bp):
TATCTCAGTCTCGCACACTTAGTGCCAATATATTTTAACTAAAGT
Found at i:55871357 original size:48 final size:47
Alignment explanation
Indices: 55871297--55871516 Score: 207
Period size: 46 Copynumber: 4.7 Consensus size: 47
55871287 ACAACAAGCT
* * *
55871297 GATGCCATGTCCC-GAACAGGTCTTACTCTAGCGTGTATATCTCAAGGCT
1 GATG-CATGTCCCAG-ACATGTCTTACACTAGC-TGTATATCTCAAGGCC
* * * ** *
55871346 GATGCATGTCCCAGACAAGTTTTACACTAGCTCT-CGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTGTATATCTCAAGGCC
* * *
55871392 AATGCATGTCCTAGACATGTCTTACACTAGCCTGTATATCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAG-CTGTATATCTCAAGGCC
* * *
55871440 GATGCATGTCCCAGACATGTCTTACACTGGCTCGCATAATGT---GGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCT-GTAT-ATCTCAAGGCC
*
55871486 GATGCATGTCCTAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
55871517 ACAAATATCA
Statistics
Matches: 142, Mismatches: 24, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
46 67 0.47
47 7 0.05
48 60 0.42
49 8 0.06
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (47 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTGTATATCTCAAGGCC
Found at i:55871422 original size:94 final size:93
Alignment explanation
Indices: 55871316--55871516 Score: 264
Period size: 94 Copynumber: 2.1 Consensus size: 93
55871306 TCCCGAACAG
* * * * *
55871316 GTCTTACTCTAGCGTGTATATCTCAAGGCTGATGCATGTCCCAGACAAGTTTTACACTAGCTCTC
1 GTCTTACACTAGCCTGTATATCTCAAGGCCGATGCATGTCCCAGACAAGTCTTACACT-G-GCTC
55871381 GTC-TCAA-T-GCCAATGCATGTCCTAGACAT
64 G-CAT-AAGTGGCCAATGCATGTCCTAGACAT
* *
55871410 GTCTTACACTAGCCTGTATATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCGC
1 GTCTTACACTAGCCTGTATATCTCAAGGCCGATGCATGTCCCAGACAAGTCTTACACTGGCTCGC
*
55871475 ATAATGTGGCCGATGCATGTCCTAGACAT
66 ATAA-GTGGCCAATGCATGTCCTAGACAT
55871504 GTCTTACACTAGC
1 GTCTTACACTAGC
55871517 ACAAATATCA
Statistics
Matches: 95, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
91 3 0.03
92 5 0.05
93 2 0.02
94 85 0.89
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (93 bp):
GTCTTACACTAGCCTGTATATCTCAAGGCCGATGCATGTCCCAGACAAGTCTTACACTGGCTCGC
ATAAGTGGCCAATGCATGTCCTAGACAT
Found at i:55877702 original size:64 final size:64
Alignment explanation
Indices: 55877621--55877802 Score: 156
Period size: 67 Copynumber: 2.8 Consensus size: 64
55877611 AGACATTATG
* ** *
55877621 ATGTAGCTAGGTGGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAACTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAACTACAAGATAA
* * * * * *
55877685 ATGTAGCTAGGTCGCATGCGTGGCTTC-AGGTGAAGGACACCATGTAGACAAGAGAGCTACAAGA
1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATGTAGACAAGAGAACTACAAGA
55877749 TAA
62 TAA
* * * *
55877752 AT-TGGCTAGGTCACATGGGTGGTACTGAT-TGTTCACCATGT-GTACAAGAGA
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG-ACAAGAGA
55877803 GTCGAACACT
Statistics
Matches: 93, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
62 1 0.01
63 17 0.18
64 20 0.22
65 7 0.08
66 17 0.18
67 31 0.33
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAACTACAAGATAA
Found at i:55891602 original size:37 final size:37
Alignment explanation
Indices: 55891552--55891630 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
55891542 TTATTACGAA
* *
55891552 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
55891589 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
55891626 GTCTT
1 GTCTT
55891631 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Done.