Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 174 of 226
Found at i:55694459 original size:85 final size:85
Alignment explanation
Indices: 55694317--55694528 Score: 390
Period size: 85 Copynumber: 2.5 Consensus size: 85
55694307 TAACCGTTAC
* *
55694317 ACGGTGGAATCAGCAATTAGCAACCACC-TTATAATCAATGATACGGGGAATCAGCACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
55694381 CCCCTTTCACAGTCAAGGAT
66 CCCCTTTCACAGTCAAGGAT
55694401 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
*
55694466 CCCCTTTCACAGTTAAGGAT
66 CCCCTTTCACAGTCAAGGAT
55694486 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
55694529 GCGAATTCAC
Statistics
Matches: 124, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 27 0.22
85 97 0.78
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (85 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
CCCCTTTCACAGTCAAGGAT
Found at i:55694464 original size:42 final size:43
Alignment explanation
Indices: 55694317--55694528 Score: 267
Period size: 43 Copynumber: 5.0 Consensus size: 43
55694307 TAACCGTTAC
*
55694317 ACGGTGGAATCAGCA-ATTAGCAACCACC-TTATAATCAATGAT
1 ACGGTGGAATCAGCACA-TAGCAACCACCTTTATATTCAATGAT
* * *
55694359 ACGG-GGAATCAGCACATAGCAACC-CCTTTCACAGTCAAGGAT
1 ACGGTGGAATCAGCACATAGCAACCACCTTT-ATATTCAATGAT
*
55694401 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACATAGCAACCACCTTTATATTCAATGAT
* *
55694444 ACGG-GGAATCAGCACATAGCAACC-CCTTTCACAGTT-AAGGAT
1 ACGGTGGAATCAGCACATAGCAACCACCTTT-ATA-TTCAATGAT
*
55694486 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACATAGCAACCACCTTTATATTCAATGAT
55694529 GCGAATTCAC
Statistics
Matches: 147, Mismatches: 13, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
40 2 0.01
41 25 0.17
42 50 0.34
43 60 0.41
44 10 0.07
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (43 bp):
ACGGTGGAATCAGCACATAGCAACCACCTTTATATTCAATGAT
Found at i:55694616 original size:51 final size:50
Alignment explanation
Indices: 55694540--55694728 Score: 220
Period size: 51 Copynumber: 3.7 Consensus size: 50
55694530 CGAATTCACA
* *
55694540 TAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA-TATCCGATACACG
* ** * *
55694591 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGATATCCGATACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCATATCCGATACACG
* * *
55694642 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCAT-TCTGGA-ACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCATATC-CGATACACG
* *
55694692 TAGTAGCCTACACATAGTTCTACACACGTGACCATCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA
55694729 CTTTCACTTT
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 4 0.03
50 35 0.30
51 74 0.64
52 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCATATCCGATACACG
Found at i:55694717 original size:101 final size:102
Alignment explanation
Indices: 55694538--55694722 Score: 286
Period size: 101 Copynumber: 1.8 Consensus size: 102
55694528 TGCGAATTCA
* *
55694538 CATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
55694603 CATAGTACTACACACGTGATCGAAGATATCCGATACG
66 CATAGTACTACACACGTGATCGAAGATATCCGATACG
* *
55694640 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGA-ACACGTAGTAGCCTA
1 CATAGTAGCATGCACATAGTACTACACATGCGACC-ATCACTATC-CGATACACGTAGTAGCCTA
*
55694702 CACATAGTTCTACACACGTGA
64 CACATAGTACTACACACGTGA
55694723 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
101 36 0.47
102 36 0.47
103 4 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (102 bp):
CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGATATCCGATACG
Found at i:55694746 original size:101 final size:102
Alignment explanation
Indices: 55694533--55694722 Score: 260
Period size: 102 Copynumber: 1.9 Consensus size: 102
55694523 AATGATGCGA
* *
55694533 ATTCACATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGC
1 ATTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGC
* * *
55694598 CTGCACATAGTACTACACACGTGATCGAAGATATCCG
66 CTACACATAGTACTACACACGTGATCCAACATATCCG
* * *
55694635 ATACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGA-ACACGTAGTA
1 ATTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATC-CGATACACGTAGTA
*
55694697 GCCTACACATAGTTCTACACACGTGA
64 GCCTACACATAGTACTACACACGTGA
55694723 CCATCACTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
101 36 0.46
102 39 0.49
103 4 0.05
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (102 bp):
ATTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGC
CTACACATAGTACTACACACGTGATCCAACATATCCG
Found at i:55697397 original size:47 final size:48
Alignment explanation
Indices: 55697279--55697405 Score: 150
Period size: 49 Copynumber: 2.6 Consensus size: 48
55697269 GTTTTCACAT
* * *
55697279 TGCCATAGTCCA-ACTATGGTTTTACATGTAATCACATATCACATACCGA
1 TGCCATAGTCCAGA-TATGGTCTTACACGGAATCACATATCACATA-CGA
* * * *
55697328 TGCCATAGCCCAGCTATAGTCTTACACGGAATCACATATCACAT-TGA
1 TGCCATAGTCCAGATATGGTCTTACACGGAATCACATATCACATACGA
*
55697375 TGCCATATTCCAGATATGGTCTTACACGGAA
1 TGCCATAGTCCAGATATGGTCTTACACGGAA
55697406 ATTTCATAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 29 0.44
49 37 0.56
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (48 bp):
TGCCATAGTCCAGATATGGTCTTACACGGAATCACATATCACATACGA
Found at i:55699645 original size:85 final size:85
Alignment explanation
Indices: 55699501--55699712 Score: 372
Period size: 85 Copynumber: 2.5 Consensus size: 85
55699491 TAACCGTTAC
* * *
55699501 ACGGTGGAATCAACAATTAGCAACCACC-TTATAATCAATGATACGGGGAATCAGCACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
55699565 CCCCTTTCACAGTCAAGGAT
66 CCCCTTTCACAGTCAAGGAT
*
55699585 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGTACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
*
55699650 CCCCTTTCACAGTTAAGGAT
66 CCCCTTTCACAGTCAAGGAT
55699670 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
55699713 GCGGATTCAC
Statistics
Matches: 122, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 26 0.21
85 96 0.79
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (85 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
CCCCTTTCACAGTCAAGGAT
Found at i:55699649 original size:42 final size:43
Alignment explanation
Indices: 55699501--55699712 Score: 249
Period size: 43 Copynumber: 5.0 Consensus size: 43
55699491 TAACCGTTAC
* *
55699501 ACGGTGGAATCAACA-ATTAGCAACCACC-TTATAATCAATGAT
1 ACGGTGGAATCAGCACA-TAGCAACCACCTTTATATTCAATGAT
* * *
55699543 ACGG-GGAATCAGCACATAGCAACC-CCTTTCACAGTCAAGGAT
1 ACGGTGGAATCAGCACATAGCAACCACCTTT-ATATTCAATGAT
*
55699585 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACATAGCAACCACCTTTATATTCAATGAT
* * *
55699628 ACGG-GGAATCAGTACATAGCAACC-CCTTTCACAGTT-AAGGAT
1 ACGGTGGAATCAGCACATAGCAACCACCTTT-ATA-TTCAATGAT
*
55699670 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACATAGCAACCACCTTTATATTCAATGAT
55699713 GCGGATTCAC
Statistics
Matches: 144, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
40 2 0.01
41 24 0.17
42 49 0.34
43 59 0.41
44 10 0.07
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (43 bp):
ACGGTGGAATCAGCACATAGCAACCACCTTTATATTCAATGAT
Found at i:55699800 original size:51 final size:50
Alignment explanation
Indices: 55699724--55699912 Score: 220
Period size: 51 Copynumber: 3.7 Consensus size: 50
55699714 CGGATTCACA
* *
55699724 TAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA-TATCCGATACACG
* ** * *
55699775 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGATATCCGATACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCATATCCGATACACG
* * *
55699826 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCAT-TCTGGA-ACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCATATC-CGATACACG
* *
55699876 TAGTAGCCTACACATAGTTCTACACACGTGACCATCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA
55699913 CTTTCACTTT
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 4 0.03
50 35 0.30
51 74 0.64
52 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCATATCCGATACACG
Found at i:55699901 original size:101 final size:102
Alignment explanation
Indices: 55699722--55699906 Score: 286
Period size: 101 Copynumber: 1.8 Consensus size: 102
55699712 TGCGGATTCA
* *
55699722 CATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
55699787 CATAGTACTACACACGTGATCGAAGATATCCGATACG
66 CATAGTACTACACACGTGATCGAAGATATCCGATACG
* *
55699824 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGA-ACACGTAGTAGCCTA
1 CATAGTAGCATGCACATAGTACTACACATGCGACC-ATCACTATC-CGATACACGTAGTAGCCTA
*
55699886 CACATAGTTCTACACACGTGA
64 CACATAGTACTACACACGTGA
55699907 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
101 36 0.47
102 36 0.47
103 4 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (102 bp):
CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGATATCCGATACG
Found at i:55699930 original size:101 final size:102
Alignment explanation
Indices: 55699716--55699906 Score: 262
Period size: 102 Copynumber: 1.9 Consensus size: 102
55699706 CAATGATGCG
* *
55699716 GATTCACATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAG
1 GATTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAG
* * *
55699781 CCTGCACATAGTACTACACACGTGATCGAAGATATCC
66 CCTACACATAGTACTACACACGTGATCCAACATATCC
* * *
55699818 GATACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGA-ACACGTAGT
1 GATTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATC-CGATACACGTAGT
*
55699880 AGCCTACACATAGTTCTACACACGTGA
64 AGCCTACACATAGTACTACACACGTGA
55699907 CCATCACTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
101 36 0.45
102 40 0.50
103 4 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (102 bp):
GATTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAG
CCTACACATAGTACTACACACGTGATCCAACATATCC
Found at i:55704080 original size:15 final size:15
Alignment explanation
Indices: 55704055--55704089 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
55704045 GACTCTATTT
*
55704055 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
55704069 TAATTAATATTAAGA
1 TAATTAATATTAAGA
55704084 TAATTA
1 TAATTA
55704090 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:55706416 original size:19 final size:19
Alignment explanation
Indices: 55706394--55706438 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
55706384 TTTCATTTTC
55706394 TTTTCACTTACTTTTACTAT
1 TTTTCACTTACTTTTAC-AT
*
55706414 TTTTCA-TTTCTTTTACA-
1 TTTTCACTTACTTTTACAT
55706431 TTTTCACT
1 TTTTCACT
55706439 CTTTTCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 9 0.39
20 6 0.26
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTCACTTACTTTTACAT
Found at i:55725364 original size:26 final size:26
Alignment explanation
Indices: 55725328--55725387 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
55725318 ATATTCACAT
* *
55725328 GAGCTATGAAAAGAGTATGCTCAAAC
1 GAGCTGTGAAAAGAGCATGCTCAAAC
* * * *
55725354 GAGCTGTGAAATGGGCCTGCTCACAC
1 GAGCTGTGAAAAGAGCATGCTCAAAC
55725380 GAGCTGTG
1 GAGCTGTG
55725388 GGTTAGAACG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (26 bp):
GAGCTGTGAAAAGAGCATGCTCAAAC
Found at i:55740179 original size:16 final size:17
Alignment explanation
Indices: 55740158--55740193 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
55740148 ATTTTTGGGT
55740158 CCACATGCCCTA-ATGG
1 CCACATGCCCTACATGG
*
55740174 CCACATGTCCTACATGG
1 CCACATGCCCTACATGG
55740191 CCA
1 CCA
55740194 ACCTGTGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.25, C:0.39, G:0.17, T:0.19
Consensus pattern (17 bp):
CCACATGCCCTACATGG
Found at i:55741010 original size:58 final size:59
Alignment explanation
Indices: 55740928--55741041 Score: 169
Period size: 58 Copynumber: 1.9 Consensus size: 59
55740918 TTTAAAAAGG
* *
55740928 AAAAGATAAAAACAACATATATTAAATACTTT-ATTTTATTTATTTTTCAAATAAAACCC
1 AAAAGATAAAAACAACATATATTAAATA-TTTGATTTTATTTATTTTTAAAACAAAACCC
* *
55740987 AAAAGAT-AAAACATCATATATTAATTATTTGATTTTATTTATTTTTAAAACAAAA
1 AAAAGATAAAAACAACATATATTAAATATTTGATTTTATTTATTTTTAAAACAAAA
55741042 TTCATTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 3 0.06
58 40 0.80
59 7 0.14
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (59 bp):
AAAAGATAAAAACAACATATATTAAATATTTGATTTTATTTATTTTTAAAACAAAACCC
Found at i:55746516 original size:131 final size:131
Alignment explanation
Indices: 55746282--55746546 Score: 476
Period size: 131 Copynumber: 2.0 Consensus size: 131
55746272 GGAGGCTACA
* *
55746282 CATCCTCCCCTAGAAACACAGCTGAATCACTATAAAGATAGCTCGGTAATCCACAACAAATGCTG
1 CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCACAACAAATGCTG
*
55746347 GATTCCAATAAGTTTAGTGAATAAACAGTACGTCATCATCTTGTCTTATATCAAACCCATACAAC
66 GATTCCAATAAGTTTAGTGAATAAACAGTAAGTCATCATCTTGTCTTATATCAAACCCATACAAC
55746412 G
131 G
* *
55746413 CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCGCAACAAATGTTG
1 CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCACAACAAATGCTG
*
55746478 GATTCCAATAAGTTTAGTGAATAAACAGTAAGTCATCATCTTGTCTTATATCAAACCCGTACAAC
66 GATTCCAATAAGTTTAGTGAATAAACAGTAAGTCATCATCTTGTCTTATATCAAACCCATACAAC
55746543 G
131 G
55746544 CAT
1 CAT
55746547 GAAATAACTC
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
131 128 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.26
Consensus pattern (131 bp):
CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCACAACAAATGCTG
GATTCCAATAAGTTTAGTGAATAAACAGTAAGTCATCATCTTGTCTTATATCAAACCCATACAAC
G
Found at i:55748718 original size:15 final size:15
Alignment explanation
Indices: 55748700--55748770 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
55748690 TTTATTGTTG
55748700 TTGTTATTATTATTA
1 TTGTTATTATTATTA
55748715 TTGTTATTAGTGATATTA
1 TTGTTATTA-T--TATTA
* * *
55748733 TTGCTACTATT-TGA
1 TTGTTATTATTATTA
* *
55748747 TGTGTTATTAGTATTG
1 T-TGTTATTATTATTA
55748763 TTGTTATT
1 TTGTTATT
55748771 TTTCATTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
14 3 0.07
15 24 0.56
16 3 0.07
17 1 0.02
18 12 0.28
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.59
Consensus pattern (15 bp):
TTGTTATTATTATTA
Found at i:55748721 original size:9 final size:9
Alignment explanation
Indices: 55748658--55748735 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
55748648 AAATTCGCAA
55748658 ATTGTTATT
1 ATTGTTATT
*
55748667 GTTGTTATT
1 ATTGTTATT
55748676 ACTCATGTT-TT
1 A-T--TGTTATT
*
55748687 ATTTTTATT
1 ATTGTTATT
* *
55748696 GTTGTTGTT
1 ATTGTTATT
*
55748705 ATTATTATT
1 ATTGTTATT
55748714 ATTGTTATT
1 ATTGTTATT
* *
55748723 AGTGATATT
1 ATTGTTATT
55748732 ATTG
1 ATTG
55748736 CTACTATTTG
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
8 3 0.06
9 40 0.77
10 2 0.04
11 3 0.06
12 4 0.08
ACGTcount: A:0.21, C:0.03, G:0.14, T:0.63
Consensus pattern (9 bp):
ATTGTTATT
Found at i:55750609 original size:10 final size:10
Alignment explanation
Indices: 55750594--55750618 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55750584 TTGATAATTA
55750594 TTTTTTATAT
1 TTTTTTATAT
55750604 TTTTTTATAT
1 TTTTTTATAT
55750614 TTTTT
1 TTTTT
55750619 AATTGTTACA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:55754972 original size:43 final size:43
Alignment explanation
Indices: 55754924--55755233 Score: 302
Period size: 43 Copynumber: 7.2 Consensus size: 43
55754914 TAGCAATAAT
* *
55754924 CGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA
* * ** * ***
55754967 CGCCGCTAAAGACCATA-ACTTTTAGCAACGTTTTTTATACAAA
1 CGCCGCTAAAGATCA-AGACCTTTAGCGGCGCTTTTCCCACAAA
* * * ** *
55755010 CGCCGCTATAGAACAAGGCCTTTAGCAACGCTTATCCCACAAA
1 CGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA
* * **
55755053 CGCCGCTAAAGATCACA-ACTTTTAACGGCGCTTTTTACACAAA
1 CGCCGCTAAAGATCA-AGACCTTTAGCGGCGCTTTTCCCACAAA
* * *
55755096 CGCCGCTATAGACCAAGACCTTTAGCGGCGCTTTTCCTACAAA
1 CGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA
* * *
55755139 CGCCGCTAAAGATCATGACCTTTAGCGGCACTTTTCCCACGAA
1 CGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA
* * * *
55755182 CACCGCTAAATATC-AGACCTTTAGCGACGCTTTTCACACAAA
1 CGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA
*
55755224 TGCCGCTAAA
1 CGCCGCTAAA
55755234 AACATATCTT
Statistics
Matches: 213, Mismatches: 50, Indels: 9
0.78 0.18 0.03
Matches are distributed among these distances:
42 33 0.15
43 178 0.84
44 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA
Found at i:55755042 original size:86 final size:86
Alignment explanation
Indices: 55754924--55755233 Score: 361
Period size: 86 Copynumber: 3.6 Consensus size: 86
55754914 TAGCAATAAT
*
55754924 CGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATAACTTT
1 CGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCATAACTTT
* *
55754989 TAGCAACGTTTTTTATACAAA
66 TAGCAACGCTTTTTACACAAA
* ** * *
55755010 CGCCGCTATAGAACAAGGCCTTTAGCAACGCTTATCCCACAAACGCCGCTAAAGATCACAACTTT
1 CGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCATAACTTT
* **
55755075 TAACGGCGCTTTTTACACAAA
66 TAGCAACGCTTTTTACACAAA
* * * *
55755096 CGCCGCTATAGACCAAGACCTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGATCATGACCTT
1 CGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCATAACTTT
** * ** *
55755161 TAGCGGCACTTTTCCCACGAA
66 TAGCAACGCTTTTTACACAAA
* * * * * * *
55755182 CACCGCTAAATATC-AGACCTTTAGCGACGCTTTTCACACAAATGCCGCTAAA
1 CGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
55755234 AACATATCTT
Statistics
Matches: 191, Mismatches: 33, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
85 34 0.18
86 157 0.82
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (86 bp):
CGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCATAACTTT
TAGCAACGCTTTTTACACAAA
Found at i:55755161 original size:129 final size:128
Alignment explanation
Indices: 55754926--55755233 Score: 339
Period size: 129 Copynumber: 2.4 Consensus size: 128
55754916 GCAATAATCG
* * * *
55754926 CCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATAACTTTTA
1 CCGCTAAAGATCAA-ACCTTTAGCGGCGCTTTTCACACAAACGCCGCTAAAGACCATAACCTTTA
* * * * * *
55754991 GCAACGTTTTTTATACAAACGCCGCTATAGAACAAGGCCTTTAGCAACGCTTATCCCACAAACG
65 GCAACGCTTTTCATACAAACGCCGCTAAAGAACAAGACCTTTAGCAACACTTATCCCACAAACA
* * * *
55755055 CCGCTAAAGATCACAACTTTTAACGGCGCTTTTTACACAAACGCCGCTATAGACCA-AGACCTTT
1 CCGCTAAAGATCA-AACCTTTAGCGGCGCTTTTCACACAAACGCCGCTAAAGACCATA-ACCTTT
** * * * ** * *
55755119 AGCGGCGCTTTTCCTACAAACGCCGCTAAAGATCATGACCTTTAGCGGCACTTTTCCCACGAACA
64 AGCAACGCTTTTCATACAAACGCCGCTAAAGAACAAGACCTTTAGCAACACTTATCCCACAAACA
* * * *
55755184 CCGCTAAATATCAGACCTTTAGCGACGCTTTTCACACAAATGCCGCTAAA
1 CCGCTAAAGATCAAACCTTTAGCGGCGCTTTTCACACAAACGCCGCTAAA
55755234 AACATATCTT
Statistics
Matches: 146, Mismatches: 31, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
128 31 0.21
129 114 0.78
130 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.24
Consensus pattern (128 bp):
CCGCTAAAGATCAAACCTTTAGCGGCGCTTTTCACACAAACGCCGCTAAAGACCATAACCTTTAG
CAACGCTTTTCATACAAACGCCGCTAAAGAACAAGACCTTTAGCAACACTTATCCCACAAACA
Found at i:55755302 original size:24 final size:23
Alignment explanation
Indices: 55755261--55755314 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
55755251 ATAATTTTTT
*
55755261 TAAATAATATTTATTTTT-ATGA
1 TAAATAATATTTATTTTTAAGGA
*
55755283 TAAATATTATATTATGTTTTAAGGA
1 TAAATAATAT-TTAT-TTTTAAGGA
55755308 TAAATAA
1 TAAATAA
55755315 AAAATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.35
23 4 0.15
24 4 0.15
25 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
TAAATAATATTTATTTTTAAGGA
Found at i:55756997 original size:24 final size:24
Alignment explanation
Indices: 55756964--55757021 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
55756954 TAAGTTTTAC
*
55756964 CATGTTAGTCGTATTCTATACAAG
1 CATGTTAGTCATATTCTATACAAG
*
55756988 TATGTTAGTCATATTCTATACAAG
1 CATGTTAGTCATATTCTATACAAG
55757012 CATGTTAGTC
1 CATGTTAGTC
55757022 TTACATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (24 bp):
CATGTTAGTCATATTCTATACAAG
Found at i:55757580 original size:29 final size:29
Alignment explanation
Indices: 55757538--55757595 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
55757528 CATATTTCCT
55757538 TAAGTTTTTCTTGCGTTCTTCAATAGAAA
1 TAAGTTTTTCTTGCGTTCTTCAATAGAAA
*
55757567 TAAGTTTTTCTTGCGTTCTTCAGTAGAAA
1 TAAGTTTTTCTTGCGTTCTTCAATAGAAA
55757596 CCCTCTGGCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.45
Consensus pattern (29 bp):
TAAGTTTTTCTTGCGTTCTTCAATAGAAA
Found at i:55760233 original size:15 final size:15
Alignment explanation
Indices: 55760212--55760243 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
55760202 TTAAATGGAA
55760212 AATATATA-T-AATT
1 AATATATATTAAATT
55760225 AATATATATTAAATT
1 AATATATATTAAATT
55760240 AATA
1 AATA
55760244 ATAATACGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATATATTAAATT
Found at i:55760930 original size:7 final size:7
Alignment explanation
Indices: 55760918--55760961 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
55760908 ACTAGTTTAT
55760918 CTAAACC
1 CTAAACC
55760925 CTAAACC
1 CTAAACC
*
55760932 ATAAA-C
1 CTAAACC
55760938 CTAAACC
1 CTAAACC
55760945 CTAAAACC
1 CT-AAACC
55760953 CTAAACC
1 CTAAACC
55760960 CT
1 CT
55760962 TAACACATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 5 0.15
7 21 0.64
8 7 0.21
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:55760938 original size:14 final size:14
Alignment explanation
Indices: 55760918--55761110 Score: 68
Period size: 14 Copynumber: 13.4 Consensus size: 14
55760908 ACTAGTTTAT
*
55760918 CTAAACCCTAAACC
1 CTAAACCATAAACC
*
55760932 ATAAACC-TAAACC
1 CTAAACCATAAACC
*
55760945 CTAAAACCCTAAACC
1 CT-AAACCATAAACC
*
55760960 CTTAACACAT-AACC
1 CTAAAC-CATAAACC
**
55760974 TCTAAACTTTAAACC
1 -CTAAACCATAAACC
* *
55760989 C-CAACCTTTAAACC
1 CTAAACC-ATAAACC
* *
55761003 ATAAACCATAAATC
1 CTAAACCATAAACC
* ** *
55761017 ATAGCCCCTAAACC
1 CTAAACCATAAACC
*
55761031 CATAATCCATAAACC
1 C-TAAACCATAAACC
* ** *
55761046 TTAAAATAGTAACTCTC
1 CTAAACCA-TAA-AC-C
** *
55761063 CTAAACTTTAAACT
1 CTAAACCATAAACC
*
55761077 CTAAACCATATACC
1 CTAAACCATAAACC
*
55761091 CTAAACCAAAAACC
1 CTAAACCATAAACC
*
55761105 TTAAAC
1 CTAAAC
55761111 TATAGTGATA
Statistics
Matches: 130, Mismatches: 38, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
13 10 0.08
14 73 0.56
15 37 0.28
16 4 0.03
17 6 0.05
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.22
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:55761546 original size:41 final size:41
Alignment explanation
Indices: 55761417--55761689 Score: 353
Period size: 41 Copynumber: 6.8 Consensus size: 41
55761407 AATTTTTTTT
* *
55761417 GCGGCGCTTTTTCAAAAACGCCGCTAAA---ATAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCT-GAGCATTA
*
55761456 GCGGCGCTTCTTTAAAAACGCCGCTAAAG-CCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
55761496 GCAGCGCTTCTTCAAAAATGCCGCTAAAGCCCTAAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
55761537 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCATGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
55761578 GC-GCGCTTCTTTAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
55761618 GCGGCGCTT-TCCCAAAAACGCCGCTAAAGACAC-GAGCATTA
1 GCGGCGCTTCT-TCAAAAACGCCGCTAAAG-CCCTGAGCATTA
* * *
55761659 GCGGCGCTTTTTAAAAAACGCCACTAAAGCC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
55761690 TCGAAAACTC
Statistics
Matches: 207, Mismatches: 20, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
39 26 0.13
40 74 0.36
41 104 0.50
42 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:55761554 original size:81 final size:80
Alignment explanation
Indices: 55761420--55761689 Score: 352
Period size: 81 Copynumber: 3.4 Consensus size: 80
55761410 TTTTTTTGCG
* * *
55761420 GCGCTTTTTCAAAAACGCCGCTAAA---ATAGAGCATTAGCGGCGCTTCTTTAAAAACGCCGCTA
1 GCGCTTCTTCAAAAACGCCGCTAAAGCCCTA-AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
55761482 AAGCCTGAGCATTAGC
65 AAGCCTGAGCATTAGC
*
55761498 AGCGCTTCTTCAAAAATGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
1 -GCGCTTCTTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
55761563 AAGCCATGAGCATTAGC
65 AAGCC-TGAGCATTAGC
* * *
55761580 GCGCTTCTTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTT-TCCCAAAAACGCCGCTA
1 GCGCTTCTTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCT-TCAAAAACGCCGCTA
55761644 AAGACAC-GAGCATTAGC
65 AAG-C-CTGAGCATTAGC
* * *
55761661 GGCGCTTTTTAAAAAACGCCACTAAAGCC
1 -GCGCTTCTTCAAAAACGCCGCTAAAGCC
55761690 TCGAAAACTC
Statistics
Matches: 172, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
79 23 0.13
80 1 0.01
81 108 0.63
82 39 0.23
83 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (80 bp):
GCGCTTCTTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
AGCCTGAGCATTAGC
Found at i:55761787 original size:39 final size:40
Alignment explanation
Indices: 55761744--55761819 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
55761734 GCGCTTATTG
* *
55761744 GAAAACGCCACTAATGC-TCATTTTTAGCGGCGTTTTCCA
1 GAAAACGCCACTAATACTTCATCTTTAGCGGCGTTTTCCA
** *
55761783 GAAAACGCTGCTAATACTTGATCTTTAGCGGCGTTTT
1 GAAAACGCCACTAATACTTCATCTTTAGCGGCGTTTT
55761820 TTTTAAGCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 14 0.45
40 17 0.55
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
GAAAACGCCACTAATACTTCATCTTTAGCGGCGTTTTCCA
Found at i:55764755 original size:19 final size:19
Alignment explanation
Indices: 55764733--55764797 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
55764723 AGTGTGACAT
55764733 AATTTAATAAAATCTAAAC
1 AATTTAATAAAATCTAAAC
* * *
55764752 AATTTAA-ATAAGTGTAACAT
1 AATTTAATA-AAATCTAA-AC
* *
55764772 AATCTAATAAAACCTAAAC
1 AATTTAATAAAATCTAAAC
55764791 AATTTAA
1 AATTTAA
55764798 ATTGATTAAG
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
20 12 0.35
21 1 0.03
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (19 bp):
AATTTAATAAAATCTAAAC
Found at i:55764763 original size:39 final size:39
Alignment explanation
Indices: 55764720--55764799 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
55764710 CATCCACATC
* * *
55764720 ATAAGTGTGACATAATTTAATAAAATCTAAACAATTTAA
1 ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
55764759 ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
1 ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
55764798 AT
1 AT
55764800 TGATTAAGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (39 bp):
ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
Found at i:55767179 original size:436 final size:435
Alignment explanation
Indices: 55766361--55767230 Score: 1551
Period size: 436 Copynumber: 2.0 Consensus size: 435
55766351 ACTTTTGTAT
* *
55766361 TTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATCCACTCTTTTCCGTGTAT
1 TTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATCCACTCTTCTACGTGTAT
55766426 TTGCTAGTATTGTCTCCTCGCCAGACCTTAGTGTCTGGCTGCAAAGTGTTCCACAGAGGGATGGA
66 TTGCTAGTATTGTCTCCTCGCCAGACCTTAGTGTCTGGCTGCAAAGTGTTCCACAGAGGGATGGA
*
55766491 TCGAATACTTTCTATTTGGTCTTCATAAAAAGATTTCTTAACACATCTTCCTTCCAGGTATTTAA
131 TCGAATACTTTCTATTTGGTCTTCAAAAAAAGATTTCTTAACACATCTTCCTTCCAGGTATTTAA
*
55766556 ATTTGTATTAATTAATTCTTCCACCATGGTATATCTCCTATCAATATTCTAATTTTTTAGTTTTC
196 ATTTGTATTAATTAATTCTTCCACCATGGTATATCTCCTATCAATATTCTAATTTTGTAGTTTTC
*
55766621 CATTCCCAGGATACAGAAGTCATGTATCGTTCCAGATGTTAACAGTCTTTCCGTCGCCTATTCTT
261 CATTCCCAGGATACAGAAGCCATGTATCGTTCCAGATGTTAACAGTCTTTCCGTCGCCTATTCTT
55766686 CAACCAACCCCTGATTCTAATAAGTCCCTTGCACCCTATATACTTCTCCAAGTAAAAGAAGGGTG
326 CAACCAACCCCTGATTCTAATAAGTCCCTTGCACCCTATATACTTCTCCAAGTAAAAGAAGGGTG
*
55766751 AGTTCCTAACTCAGCATTTAAAAAATCACCATGTGGGTAGTAGAC
391 AGTTCCTAACTCAGCATTTAAAAAATCACCACGTGGGTAGTAGAC
*
55766796 TTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCGCTTGTATCCACTCTTCTACGTGTAT
1 TTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATCCACTCTTCTACGTGTAT
*
55766861 TTGCTAGTATTGTCTCCTCGCCAGACCTTAGTGTCTGGCTGCAAAGTTTTCCACAGAGGGATGGA
66 TTGCTAGTATTGTCTCCTCGCCAGACCTTAGTGTCTGGCTGCAAAGTGTTCCACAGAGGGATGGA
* * *
55766926 TCGGATCCTTTCTATTTGGTCTTCAGAAAAAAGATTTCTTAACCCATCTTCCTTCCAGGTATTTA
131 TCGAATACTTTCTATTTGGTCTTCA-AAAAAAGATTTCTTAACACATCTTCCTTCCAGGTATTTA
* *
55766991 AATTTGTATTAATTAATTCTTCTACCATGGTATATCTCCTATCCATATTCTAATTTTGTAGTTTT
195 AATTTGTATTAATTAATTCTTCCACCATGGTATATCTCCTATCAATATTCTAATTTTGTAGTTTT
** *
55767056 CCATTCCCAGGATATTGAAGCCATGTGTCGTTCCAGATGTTAACAGTCTTTCCGTCGCCTATTCT
260 CCATTCCCAGGATACAGAAGCCATGTATCGTTCCAGATGTTAACAGTCTTTCCGTCGCCTATTCT
* * *
55767121 TCAATCAACCCCTGATTCTAATAAGTCCCTTGCACCCTATATAGTTCTCCAGGTAAAAGAAGGGT
325 TCAACCAACCCCTGATTCTAATAAGTCCCTTGCACCCTATATACTTCTCCAAGTAAAAGAAGGGT
*
55767186 GAGTTCCTAACTCAGCATTTAAAAAATCATCACGTGGGTAGTAGA
390 GAGTTCCTAACTCAGCATTTAAAAAATCACCACGTGGGTAGTAGA
55767231 TAGCTTTCAT
Statistics
Matches: 414, Mismatches: 20, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
435 149 0.36
436 265 0.64
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (435 bp):
TTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATCCACTCTTCTACGTGTAT
TTGCTAGTATTGTCTCCTCGCCAGACCTTAGTGTCTGGCTGCAAAGTGTTCCACAGAGGGATGGA
TCGAATACTTTCTATTTGGTCTTCAAAAAAAGATTTCTTAACACATCTTCCTTCCAGGTATTTAA
ATTTGTATTAATTAATTCTTCCACCATGGTATATCTCCTATCAATATTCTAATTTTGTAGTTTTC
CATTCCCAGGATACAGAAGCCATGTATCGTTCCAGATGTTAACAGTCTTTCCGTCGCCTATTCTT
CAACCAACCCCTGATTCTAATAAGTCCCTTGCACCCTATATACTTCTCCAAGTAAAAGAAGGGTG
AGTTCCTAACTCAGCATTTAAAAAATCACCACGTGGGTAGTAGAC
Found at i:55771097 original size:3 final size:3
Alignment explanation
Indices: 55771089--55771125 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
55771079 TTTTTAATCC
55771089 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
55771126 TCTCCTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:55776379 original size:86 final size:87
Alignment explanation
Indices: 55775945--55776472 Score: 745
Period size: 87 Copynumber: 6.1 Consensus size: 87
55775935 ACTTGTAATC
* ** * * *
55775945 TTCGATCTGCTTCACTGTCGACGCAGGAGGGCAAGATCTGCTATCTTTAACCAGTTCCACTGTAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
** *
55776010 CTAATAGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
** * * *
55776032 TTCGATCTGCTTCATTGTTAACACAGGAGGGCAAGATCTGCTATCTCTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
55776097 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
55776119 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
55776184 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
** * ** *
55776206 TTCGATCTTATTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAATTAGCTCCATTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
55776271 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * *
55776293 TTCTATCTGCTTCGCTGTTAATGCAGG-AGGCAAGATCTGCTATCTTTAACCAGCTCCACTGAAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
* * *
55776357 CTGATGAAGGAAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* ** * *
55776379 TTCGATCTGCTTCGCTATTAATACAGGAAGGCAAAATCTGCT-TCTTTAACCAACTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
55776443 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
55776465 TTCGATCT
1 TTCGATCT
55776473 TCACTAATCT
Statistics
Matches: 396, Mismatches: 44, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
86 123 0.31
87 273 0.69
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:55777737 original size:13 final size:13
Alignment explanation
Indices: 55777714--55777739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55777704 CCATTTTACT
55777714 TTTTCATTTTTCA
1 TTTTCATTTTTCA
55777727 TTTTCATTTTTCA
1 TTTTCATTTTTCA
55777740 CCTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:55778171 original size:26 final size:27
Alignment explanation
Indices: 55778122--55778194 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
55778112 TCATATTTTA
*
55778122 TTTTGACTTTGATTGATTTCTCTTTTTTTC
1 TTTTGACTTTGATT--TTTCT-TTTCTTTC
*
55778152 TTTTGACTTTGATTTTTCTTTTCTTTT
1 TTTTGACTTTGATTTTTCTTTTCTTTC
**
55778179 TTTTGTTTTTGATTTT
1 TTTTGACTTTGATTTT
55778195 GATTTTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 20 0.51
28 5 0.13
30 14 0.36
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.73
Consensus pattern (27 bp):
TTTTGACTTTGATTTTTCTTTTCTTTC
Found at i:55778179 original size:30 final size:30
Alignment explanation
Indices: 55778102--55778180 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
55778092 CTCCTTTTTT
*
55778102 TTTTCTCTTTTCATATTTTATTTTGACTTTGA
1 TTTT-TCTTTTC-TTTTTTATTTTGACTTTGA
* *
55778134 TTGATTTC-TCT-TTTTTTCTTTTGACTTTGA
1 TT--TTTCTTTTCTTTTTTATTTTGACTTTGA
55778164 TTTTTCTTTTCTTTTTT
1 TTTTTCTTTTCTTTTTT
55778181 TTGTTTTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
28 4 0.10
29 2 0.05
30 25 0.64
32 4 0.10
33 2 0.05
34 2 0.05
ACGTcount: A:0.10, C:0.13, G:0.06, T:0.71
Consensus pattern (30 bp):
TTTTTCTTTTCTTTTTTATTTTGACTTTGA
Found at i:55778181 original size:33 final size:33
Alignment explanation
Indices: 55778138--55778200 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
55778128 CTTTGATTGA
55778138 TTTCTCTTTTTT-TCTTTTGACTTTGATTTTTCT
1 TTTCTCTTTTTTGT-TTTTGACTTTGATTTTTCT
* *
55778171 TTTCTTTTTTTTGTTTTTGATTTTGATTTT
1 TTTCTCTTTTTTGTTTTTGACTTTGATTTT
55778201 GATTGAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.06, C:0.10, G:0.08, T:0.76
Consensus pattern (33 bp):
TTTCTCTTTTTTGTTTTTGACTTTGATTTTTCT
Found at i:55778212 original size:33 final size:34
Alignment explanation
Indices: 55778117--55778215 Score: 85
Period size: 33 Copynumber: 2.9 Consensus size: 34
55778107 TCTTTTCATA
* * *
55778117 TTTT-ATTTTGACTTTGATTGATTTCTCTTTTTTTC
1 TTTTGATTTTGATTTTGATTGACTT-T-TTTTTGTC
* ** **
55778152 TTTTGACTTTGATTTTTCTTTTCTTTTTTTTGT-
1 TTTTGATTTTGATTTTGATTGACTTTTTTTTGTC
*
55778185 TTTTGATTTTGATTTTGATTGAGTTTTTTTT
1 TTTTGATTTTGATTTTGATTGACTTTTTTTT
55778216 TGAATCTGAA
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
33 25 0.51
34 6 0.12
35 5 0.10
36 13 0.27
ACGTcount: A:0.10, C:0.07, G:0.11, T:0.72
Consensus pattern (34 bp):
TTTTGATTTTGATTTTGATTGACTTTTTTTTGTC
Found at i:55783125 original size:18 final size:18
Alignment explanation
Indices: 55783104--55783150 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
55783094 AAATTAAGCA
55783104 CAAAATTAAAACTACAAC
1 CAAAATTAAAACTACAAC
*
55783122 CAAAATTAAAATTACAAC
1 CAAAATTAAAACTACAAC
55783140 CAAAATTAAAA
1 CAAAATTAAAA
55783151 GAAGAGAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (18 bp):
CAAAATTAAAACTACAAC
Found at i:55785720 original size:18 final size:17
Alignment explanation
Indices: 55785690--55785723 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55785680 ATAATTGTAA
55785690 TTTAAATTATAATTATT
1 TTTAAATTATAATTATT
*
55785707 TTTAAATGTTTAATTAT
1 TTTAAAT-TATAATTAT
55785724 CACAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAAATTATAATTATT
Found at i:55785722 original size:24 final size:24
Alignment explanation
Indices: 55785694--55785767 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
55785684 TTGTAATTTA
55785694 AATTATAATTATTTTTAAATGTTT
1 AATTATAATTATTTTTAAATGTTT
* ** * *
55785718 AATTATCACAATTTCT--A--TTA
1 AATTATAATTATTTTTAAATGTTT
*
55785738 AATTATAATTATTTTTAAATGTAT
1 AATTATAATTATTTTTAAATGTTT
55785762 AATTAT
1 AATTAT
55785768 CACAACCTTT
Statistics
Matches: 35, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
20 14 0.40
22 2 0.06
24 19 0.54
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.53
Consensus pattern (24 bp):
AATTATAATTATTTTTAAATGTTT
Found at i:55789284 original size:63 final size:64
Alignment explanation
Indices: 55789184--55789305 Score: 219
Period size: 63 Copynumber: 1.9 Consensus size: 64
55789174 TACTTCAGGA
55789184 CCAAGATAAAAATTTGTTTTTCCAAGATCTTTCATCTCAAAATCTTTCTTTAAACAATTGTAAG
1 CCAAGATAAAAATTTGTTTTTCCAAGATCTTTCATCTCAAAATCTTTCTTTAAACAATTGTAAG
* *
55789248 CCAAGAT-AAATTTTTTTTTTCCAAGATCTTTCATCTCAAAATCTTTCTTTAAACAATT
1 CCAAGATAAAAATTTGTTTTTCCAAGATCTTTCATCTCAAAATCTTTCTTTAAACAATT
55789306 TATTGTATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 49 0.88
64 7 0.12
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (64 bp):
CCAAGATAAAAATTTGTTTTTCCAAGATCTTTCATCTCAAAATCTTTCTTTAAACAATTGTAAG
Found at i:55795815 original size:40 final size:39
Alignment explanation
Indices: 55795754--55795986 Score: 200
Period size: 40 Copynumber: 5.8 Consensus size: 39
55795744 AGATAATTAT
* *
55795754 CCCTGATTGAACATACGTGCCCCTATTTGTATTTCGGTA
1 CCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTA
* * * * *
55795793 CCATTGATTACACATACATGCCCCTGTTTATACTTCGGTA
1 CC-CTGATTGCACATACGTGCCCCTATTTGTACTTCGGTA
* * *
55795833 TCCCTGATTGCACATATGTGCCCCTATTTATACCTT-GATA
1 -CCCTGATTGCACATACGTGCCCCTATTTGTA-CTTCGGTA
* * **
55795873 CCCCTGATTGCACATACTTGCCCCTGTTTGTACTTTAGTA
1 -CCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTA
* * * *
55795913 TCCTTAATTGCACATATGTGCCCCTGTTTGTACTTCGGTA
1 -CCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTA
** *
55795953 CCCCTGATTGCA-ATTATATGCCCCTATTTATACT
1 -CCCTGATTGCACA-TACGTGCCCCTATTTGTACT
55795987 CTAGTAACCC
Statistics
Matches: 156, Mismatches: 33, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
39 6 0.04
40 145 0.93
41 5 0.03
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.37
Consensus pattern (39 bp):
CCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTA
Found at i:55795840 original size:80 final size:80
Alignment explanation
Indices: 55795751--55795999 Score: 288
Period size: 80 Copynumber: 3.1 Consensus size: 80
55795741 TATAGATAAT
* * * ** *
55795751 TATCCCTGATTGAACATACGTGCCCCTATTTGTATTTCGGTACCATTGATTACACATACATGCCC
1 TATCCCTGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATACATGCCC
*
55795816 CTGTTTATACTTCGG
66 CTGTTTATACTTCAG
* * *
55795831 TATCCCTGATTGCACATATGTGCCCCTATTTATACCTT-GATACCCCTGATTGCACATACTTGCC
1 TATCCCTGATTGCACATATGTGCCCCTATTTGTA-CTTCGGTACCCCTGATTGCACATACATGCC
* *
55795895 CCTGTTTGTACTTTAG
65 CCTGTTTATACTTCAG
* * * *
55795911 TATCCTTAATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTGATTGCA-ATTATATGCC
1 TATCCCTGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACA-TACATGCC
*
55795975 CCTATTTATAC-TCTAG
65 CCTGTTTATACTTC-AG
*
55795991 TAACCCTGA
1 TATCCCTGA
55796000 ATCAAATAGT
Statistics
Matches: 140, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
79 5 0.04
80 133 0.95
81 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (80 bp):
TATCCCTGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATACATGCCC
CTGTTTATACTTCAG
Found at i:55795952 original size:120 final size:120
Alignment explanation
Indices: 55795754--55795985 Score: 317
Period size: 120 Copynumber: 1.9 Consensus size: 120
55795744 AGATAATTAT
* *
55795754 CCCTGATTGAACATACGTGCCCCTATTTGTATTTCGGTACCATTGATTACACATACATGCCCCTG
1 CCCTGATTGAACATACGTGCCCCTATTTGTATTTCAGTACCATTAATTACACATACATGCCCCTG
* *
55795819 TTTATACTTCGGTATCCCTGATTGCACA-TATGTGCCCCTATTTATACCTTGATAC
66 TTTATACTTCGGTACCCCTGATTGCA-ATTATATGCCCCTATTTATACCTTGATAC
* * * * **
55795874 CCCTGATTGCACATACTTGCCCCTGTTTGTACTTT-AGTATCC-TTAATTGCACATATGTGCCCC
1 CCCTGATTGAACATACGTGCCCCTATTTGTA-TTTCAGTA-CCATTAATTACACATACATGCCCC
*
55795937 TGTTTGTACTTCGGTACCCCTGATTGCAATTATATGCCCCTATTTATAC
64 TGTTTATACTTCGGTACCCCTGATTGCAATTATATGCCCCTATTTATAC
55795986 TCTAGTAACC
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
119 1 0.01
120 92 0.94
121 5 0.05
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.37
Consensus pattern (120 bp):
CCCTGATTGAACATACGTGCCCCTATTTGTATTTCAGTACCATTAATTACACATACATGCCCCTG
TTTATACTTCGGTACCCCTGATTGCAATTATATGCCCCTATTTATACCTTGATAC
Found at i:55801924 original size:21 final size:21
Alignment explanation
Indices: 55801898--55801952 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
55801888 TGCAGGGCAG
55801898 ACACGGCCGTGTGGAAGTCTC
1 ACACGGCCGTGTGGAAGTCTC
55801919 ACACGGCCGTGTGGAAGTCTC
1 ACACGGCCGTGTGGAAGTCTC
*
55801940 ACACGCCCGTGTG
1 ACACGGCCGTGTG
55801953 CCGCCGTGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.31, G:0.33, T:0.18
Consensus pattern (21 bp):
ACACGGCCGTGTGGAAGTCTC
Found at i:55808369 original size:24 final size:24
Alignment explanation
Indices: 55808335--55808392 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
55808325 ATTAATTAGT
*
55808335 ATAAAATATT-AATAATTCAATAAA
1 ATAAAA-ATTAAATAATTAAATAAA
*
55808359 TTGAAAAATTAAATAATTAAATAAA
1 AT-AAAAATTAAATAATTAAATAAA
55808384 ATAAAAATT
1 ATAAAAATT
55808393 TAGGAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
ATAAAAATTAAATAATTAAATAAA
Found at i:55809954 original size:16 final size:16
Alignment explanation
Indices: 55809933--55809984 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
55809923 TGGTTCGCTA
*
55809933 TAATGGAATAGAGGTG
1 TAATGGAATAGAGGCG
*
55809949 TAATGGAATAGATGCG
1 TAATGGAATAGAGGCG
*
55809965 TAATAGAATAGAGGCG
1 TAATGGAATAGAGGCG
55809981 TAAT
1 TAAT
55809985 AGGTAATTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.31, T:0.25
Consensus pattern (16 bp):
TAATGGAATAGAGGCG
Found at i:55810051 original size:44 final size:46
Alignment explanation
Indices: 55809970--55810058 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 46
55809960 ATGCGTAATA
* *
55809970 GAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGGAATG
1 GAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTGAATGGAATG
55810016 GAATAGAGGCGTAAT-GGT-ATTCTTCTATTTGGTTGAATGGAAT
1 GAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTGAATGGAAT
55810059 AGAGGTGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 23 0.56
45 3 0.07
46 15 0.37
ACGTcount: A:0.28, C:0.06, G:0.29, T:0.37
Consensus pattern (46 bp):
GAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTGAATGGAATG
Found at i:55810054 original size:39 final size:44
Alignment explanation
Indices: 55809970--55810071 Score: 124
Period size: 39 Copynumber: 2.4 Consensus size: 44
55809960 ATGCGTAATA
* *
55809970 GAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGGAATG
1 GAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTT--ATGGAATG
55810016 GAATAGAGGCGTAAT-GGT-ATTCTTCTATTTGG-T-T-GAATG
1 GAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTATGGAATG
*
55810055 GAATAGAGGTGTAATAG
1 GAATAGAGGCGTAATAG
55810072 CATAAGGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
39 19 0.37
40 2 0.04
43 1 0.02
44 12 0.23
45 3 0.06
46 15 0.29
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.35
Consensus pattern (44 bp):
GAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTATGGAATG
Found at i:55810270 original size:18 final size:17
Alignment explanation
Indices: 55810218--55810270 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
55810208 TTATTATTAA
55810218 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
55810236 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
55810253 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
55810271 CATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55820089 original size:26 final size:24
Alignment explanation
Indices: 55820052--55820101 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
55820042 TGTCGAGCCG
* *
55820052 AATTAATTAAAATGTGATATAAAATT
1 AATTAATCAAAA-GTAAT-TAAAATT
55820078 AATTAATCAAAAGTAATTAAAATT
1 AATTAATCAAAAGTAATTAAAATT
55820102 CAAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 11 0.50
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (24 bp):
AATTAATCAAAAGTAATTAAAATT
Found at i:55820094 original size:14 final size:14
Alignment explanation
Indices: 55820072--55820121 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
55820062 AATGTGATAT
55820072 AAAATTAATTAATC
1 AAAATTAATTAATC
*
55820086 AAAAGTAATTAAAATTC
1 AAAATTAATT--AA-TC
*
55820103 AAAATTAATTAACC
1 AAAATTAATTAATC
55820117 AAAAT
1 AAAAT
55820122 AATCAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 15 0.50
15 2 0.07
16 2 0.07
17 11 0.37
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAATTAATTAATC
Found at i:55820110 original size:31 final size:30
Alignment explanation
Indices: 55820072--55820131 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
55820062 AATGTGATAT
* *
55820072 AAAATTAATTAATCAAAAGTAATTAAAATTC
1 AAAATTAATTAACCAAAA-TAATCAAAATTC
55820103 AAAATTAATTAACCAAAATAATCAAAATT
1 AAAATTAATTAACCAAAATAATCAAAATT
55820132 TATCAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (30 bp):
AAAATTAATTAACCAAAATAATCAAAATTC
Found at i:55822171 original size:39 final size:39
Alignment explanation
Indices: 55822075--55822173 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
55822065 ATTCACTTTT
* * * * *
55822075 AAGCATGTATCACATTACACATATAATCACATAGCATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
55822114 AAGCATATATTACAATACTCATATTATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
55822153 AAGCATATATCACAATACTCA
1 AAGCATATATCACAATACTCA
55822174 AAAACATGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.30
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:55823421 original size:22 final size:22
Alignment explanation
Indices: 55823395--55823446 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
55823385 ACTTTTATTT
*
55823395 AAAACATTGGATTTAATGG-CTA
1 AAAACATTAGATTTAA-GGACTA
*
55823417 AAAAC-TTAGTTTTAAGGACTA
1 AAAACATTAGATTTAAGGACTA
55823438 AACAACATT
1 AA-AACATT
55823447 TAAAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 2 0.08
21 13 0.52
22 8 0.32
23 2 0.08
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (22 bp):
AAAACATTAGATTTAAGGACTA
Found at i:55827998 original size:12 final size:12
Alignment explanation
Indices: 55827981--55828010 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55827971 TCAGGCAGTT
55827981 ACACGGCCTAGC
1 ACACGGCCTAGC
*
55827993 ACACGGCCTTGC
1 ACACGGCCTAGC
55828005 ACACGG
1 ACACGG
55828011 GCGTGTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.27, T:0.10
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:55829098 original size:29 final size:29
Alignment explanation
Indices: 55829065--55829122 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
55829055 TGAGGTGAGC
55829065 TTTATGTTTAAAACATATGAACTTACTAA
1 TTTATGTTTAAAACATATGAACTTACTAA
55829094 TTTATGTTTAAAACATATGAACTTACTAA
1 TTTATGTTTAAAACATATGAACTTACTAA
55829123 GCATATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (29 bp):
TTTATGTTTAAAACATATGAACTTACTAA
Found at i:55831528 original size:298 final size:298
Alignment explanation
Indices: 55830992--55831591 Score: 1191
Period size: 298 Copynumber: 2.0 Consensus size: 298
55830982 ACACCCTATA
*
55830992 GTTGAAATGAACGGAATAAAACATAGTTGGTATTGTGTTTGGTTGTGACTTGAATTAAATTAATT
1 GTTGAAATGAACGGAATAAAACATAGTTGGTATTGTGTTTGGTTGTCACTTGAATTAAATTAATT
55831057 ATAGAATTAATTTAATTTGGTAATCAAATATCGAATACATTATATGTACAAGGTTGTTGTATGCA
66 ATAGAATTAATTTAATTTGGTAATCAAATATCGAATACATTATATGTACAAGGTTGTTGTATGCA
55831122 TAATGAGAACATGAATTTGGTTCGTATATAAATTCATATAAATATATAGTTTACCGAAATCATTA
131 TAATGAGAACATGAATTTGGTTCGTATATAAATTCATATAAATATATAGTTTACCGAAATCATTA
55831187 TTATAATTAATGTAATTATAATTTTTGTTTTAAAACATTGTTATATTTATTTAATTTCTAGAAAC
196 TTATAATTAATGTAATTATAATTTTTGTTTTAAAACATTGTTATATTTATTTAATTTCTAGAAAC
55831252 CCTAAAAATATATATAAAATCTCGTTTTTCTTTGCTTG
261 CCTAAAAATATATATAAAATCTCGTTTTTCTTTGCTTG
55831290 GTTGAAATGAACGGAATAAAACATAGTTGGTATTGTGTTTGGTTGTCACTTGAATTAAATTAATT
1 GTTGAAATGAACGGAATAAAACATAGTTGGTATTGTGTTTGGTTGTCACTTGAATTAAATTAATT
55831355 ATAGAATTAATTTAATTTGGTAATCAAATATCGAATACATTATATGTACAAGGTTGTTGTATGCA
66 ATAGAATTAATTTAATTTGGTAATCAAATATCGAATACATTATATGTACAAGGTTGTTGTATGCA
55831420 TAATGAGAACATGAATTTGGTTCGTATATAAATTCATATAAATATATAGTTTACCGAAATCATTA
131 TAATGAGAACATGAATTTGGTTCGTATATAAATTCATATAAATATATAGTTTACCGAAATCATTA
55831485 TTATAATTAATGTAATTATAATTTTTGTTTTAAAACATTGTTATATTTATTTAATTTCTAGAAAC
196 TTATAATTAATGTAATTATAATTTTTGTTTTAAAACATTGTTATATTTATTTAATTTCTAGAAAC
55831550 CCTAAAAATATATATAAAATCTCGTTTTTCTTTGCTTG
261 CCTAAAAATATATATAAAATCTCGTTTTTCTTTGCTTG
55831588 GTTG
1 GTTG
55831592 GTCTAGCAGC
Statistics
Matches: 301, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
298 301 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (298 bp):
GTTGAAATGAACGGAATAAAACATAGTTGGTATTGTGTTTGGTTGTCACTTGAATTAAATTAATT
ATAGAATTAATTTAATTTGGTAATCAAATATCGAATACATTATATGTACAAGGTTGTTGTATGCA
TAATGAGAACATGAATTTGGTTCGTATATAAATTCATATAAATATATAGTTTACCGAAATCATTA
TTATAATTAATGTAATTATAATTTTTGTTTTAAAACATTGTTATATTTATTTAATTTCTAGAAAC
CCTAAAAATATATATAAAATCTCGTTTTTCTTTGCTTG
Found at i:55840151 original size:48 final size:48
Alignment explanation
Indices: 55840089--55840254 Score: 278
Period size: 48 Copynumber: 3.5 Consensus size: 48
55840079 GATTTCGGTA
* *
55840089 GCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAATATTGGTG
1 GCCTGCACACAGTCCATGCCACCCTTGTATCTTAACAGAATATTGGTG
* *
55840137 GTCTGCACACAGTCCATGCCACCCTTGTATCTTAACAGAAAATTGGTG
1 GCCTGCACACAGTCCATGCCACCCTTGTATCTTAACAGAATATTGGTG
* *
55840185 GCCTGCACACAGTCCTTGCTACCCTTGTATCTTAACAGAATATTGGTG
1 GCCTGCACACAGTCCATGCCACCCTTGTATCTTAACAGAATATTGGTG
55840233 GCCTGCACACAGTCCATGCCAC
1 GCCTGCACACAGTCCATGCCAC
55840255 ATATGCGACC
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 108 1.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
GCCTGCACACAGTCCATGCCACCCTTGTATCTTAACAGAATATTGGTG
Found at i:55845881 original size:3 final size:3
Alignment explanation
Indices: 55845873--55845908 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
55845863 TCTATTTACA
55845873 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55845909 TCTTTAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55846477 original size:40 final size:41
Alignment explanation
Indices: 55846389--55846522 Score: 207
Period size: 41 Copynumber: 3.3 Consensus size: 41
55846379 CGTTTATGAG
*
55846389 AAAGCGCCGCTAATGCTCCGGGTTTTAGCGGCGTTTTTTTA
1 AAAGCGCCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTTA
* *
55846430 AAAGCGCCGCTAATGGTCTGGGTTTTAGCGGC-TTTTTTTC
1 AAAGCGCCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTTA
* *
55846470 AAAGCGCCGCTAATGCTCTAGGTTTTAGCGGCGTTTTTTAA
1 AAAGCGCCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTTA
*
55846511 AAAGTGCCGCTA
1 AAAGCGCCGCTA
55846523 GGTTTTTTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 37 0.44
41 47 0.56
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (41 bp):
AAAGCGCCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTTA
Found at i:55846624 original size:41 final size:41
Alignment explanation
Indices: 55846533--55846624 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
55846523 GGTTTTTTAA
* * * *
55846533 AAAGCGCCGGTAATGGTCTAGGTTTTACCTGTGTTTTTTTT
1 AAAGCGCCGCTAATGGTCTAGGTTTTACCAGCGTTTTTGTT
** * *
55846574 AAAATGCCGCTAATGGTCTTGGTTTTAGCAGCGTTTTTGTT
1 AAAGCGCCGCTAATGGTCTAGGTTTTACCAGCGTTTTTGTT
55846615 AAAGCGCCGC
1 AAAGCGCCGC
55846625 AAAAAACATT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
AAAGCGCCGCTAATGGTCTAGGTTTTACCAGCGTTTTTGTT
Found at i:55846624 original size:104 final size:103
Alignment explanation
Indices: 55846421--55846624 Score: 259
Period size: 104 Copynumber: 2.0 Consensus size: 103
55846411 TTTTAGCGGC
* * * *
55846421 GTTTTTTTAAAAGCGCCGCTAATGGTCTGGGTTTTAGCGGCTTTTTTTCAAAGCGCCGCTAATGC
1 GTTTTTTAAAAAGCGCCGCTAATGGTCTAGGTTTTACCGGCTTTTTTTCAAAACGCCGCTAATGC
* *
55846486 TCTAGGTTTTAGCGGCGTTTTTTAAAAAGTGCCGCTAG
66 TCTAGGTTTTAGCAGCGTTTTTTAAAAAGCGCCGCTAG
* * *
55846524 GTTTTTTAAAAAGCGCCGGTAATGGTCTAGGTTTTACCTGTG-TTTTTTTTAAAATGCCGCTAAT
1 GTTTTTTAAAAAGCGCCGCTAATGGTCTAGGTTTTACC-G-GCTTTTTTTCAAAACGCCGCTAAT
* * *
55846588 GGTCTTGGTTTTAGCAGCGTTTTTGT-TAAAGCGCCGC
64 GCTCTAGGTTTTAGCAGCGTTTTT-TAAAAAGCGCCGC
55846625 AAAAAACATT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
103 34 0.40
104 50 0.58
105 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.39
Consensus pattern (103 bp):
GTTTTTTAAAAAGCGCCGCTAATGGTCTAGGTTTTACCGGCTTTTTTTCAAAACGCCGCTAATGC
TCTAGGTTTTAGCAGCGTTTTTTAAAAAGCGCCGCTAG
Found at i:55847021 original size:14 final size:14
Alignment explanation
Indices: 55847002--55847029 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55846992 ATATGGATTA
55847002 ATTAGGGATTATGG
1 ATTAGGGATTATGG
55847016 ATTAGGGATTATGG
1 ATTAGGGATTATGG
55847030 TTTAATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.36, T:0.36
Consensus pattern (14 bp):
ATTAGGGATTATGG
Found at i:55847378 original size:15 final size:15
Alignment explanation
Indices: 55847358--55847421 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 15
55847348 TGGGATTTAA
*
55847358 GGTTTAGGTGTTAGG
1 GGTTTAGGGGTTAGG
*
55847373 GGTTTAGGGGTTAGA
1 GGTTTAGGGGTTAGG
* *
55847388 CG-TTAGGGGTTAAG
1 GGTTTAGGGGTTAGG
* * *
55847402 AG-TTAGGGATTTGG
1 GGTTTAGGGGTTAGG
55847416 GGTTTA
1 GGTTTA
55847422 CAAATTCAGG
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 21 0.55
15 17 0.45
ACGTcount: A:0.19, C:0.02, G:0.44, T:0.36
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:55847378 original size:22 final size:22
Alignment explanation
Indices: 55847353--55847407 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
55847343 AGGGTTGGGA
* **
55847353 TTTAAGGTTTAGGTGTTAGGGG
1 TTTAAGGGTTAGACGTTAGGGG
*
55847375 TTTAGGGGTTAGACGTTAGGGG
1 TTTAAGGGTTAGACGTTAGGGG
*
55847397 -TTAAGAGTTAG
1 TTTAAGGGTTAG
55847408 GGATTTGGGG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.22, C:0.02, G:0.40, T:0.36
Consensus pattern (22 bp):
TTTAAGGGTTAGACGTTAGGGG
Found at i:55847395 original size:14 final size:14
Alignment explanation
Indices: 55847376--55847409 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
55847366 TGTTAGGGGT
55847376 TTAGGGGTT-AGACG
1 TTAGGGGTTAAGA-G
55847390 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
55847404 TTAGGG
1 TTAGGG
55847410 ATTTGGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.24, C:0.03, G:0.44, T:0.29
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:55847617 original size:305 final size:301
Alignment explanation
Indices: 55847017--55847832 Score: 939
Period size: 305 Copynumber: 2.6 Consensus size: 301
55847007 GGATTATGGA
* * * *
55847017 TTAGGGATTATGGTTTA-ATTAAGGGTTGGGATTTAATGTTTAGGGGCTAGGGGTTTAGGGTTTA
1 TTAGGGATTATGGTTTATATTAAGGGTTGGGATTTAAGGTTTAGGTGTTAGGGGTTTAGGGGTTA
* * **
55847081 AACGTTAGGGGTTAATAGTTAGGGATTTGGGGTTTATGAATTTAGGGGTCGGGTTAGGGTTTTGG
66 GACGTTAGGGGTTAAGAGTTAGGGATTTGGGGTTTACAAATTTAGGGGTCGGGTTAGGGTTTTGG
* *
55847146 GATTAG---ATTATTTTTTATTTATATTTTAAATATGTTATTATATGTGTAATTGTAATTTAATA
131 GTTTAGATTATTATTTTTTATTTATATTTTAAATATGTTA-T-TA--TGTAATTGTAA---AAGA
*
55847208 TAATAATAAAATTGTTTAGAGTTTTAATTAGTTTAGGGTATATGATAAATTTAAAATTTAAGGCC
189 TAATAATAAAAATGTTTAGAGTTTTAATTAGTTTAGGGTATATGATAAATTTAAAATTTAAGGCC
* *
55847273 GGTTTAGGAGTTCATATTTTAAGGTTTAGGTAGTATATATGGAT-T-T
254 GGTTTAGGAGTTCATATTTTAAGGTTTAGGTACTATATATAGATATAT
55847319 TTAGGGATTATGGTTTAATATTTAAGGGTTGGGATTTAAGGTTTAGGTGTTAGGGGTTTAGGGGT
1 TTAGGGATTATGGTTT-ATA-TTAAGGGTTGGGATTTAAGGTTTAGGTGTTAGGGGTTTAGGGGT
*
55847384 TAGACGTTAGGGGTTAAGAGTTAGGGATTTGGGGTTTACAAATTCAGGGGTCGGGTTAGGGTTTT
64 TAGACGTTAGGGGTTAAGAGTTAGGGATTTGGGGTTTACAAATTTAGGGGTCGGGTTAGGGTTTT
* *
55847449 GGGTTTAGATTATTATTTTTTCTTTATATTTTAAATATGTTATTATGTAGTTGTAAAAGATAATA
129 GGGTTTAGATTATTATTTTTTATTTATATTTTAAATATGTTATTATGTAATTGTAAAAGATAATA
* * *
55847514 ATAAAAATGTTTAGGGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAGATTTAAGGCTGGTT
194 ATAAAAATGTTTAGAG-TTTTAATTAGTTTAGGGTATATGATAAATTTAAAATTTAAGGCCGGTT
*
55847579 TAGGAGTTCATATTTTAAGGTTTAGGGAGTACTATATATATATATAT
258 TAGGAGTTCATATTTTAAGGTTTA--G-GTACTATATATAGATATAT
* * * * * *
55847626 ATGGGGATTAATTAGGGATTATAGATT-AGGGATTATGGTTTAATTAAGGGTT-GGCCTGATTTA
1 TTAGGGATT-A-T--GG-TT-TATATTAAGGG--T-TGG--GATTTAAGGTTTAGG--TG--TT-
* * * * **
55847689 AGGTTTAGAGGTTAGGGGTTAGACGTTAGTGGTTAAGAGTTAGGGATTTAGGGTTTAGAGTTTTA
50 AGG----G-GTTTAGGGGTTAGACGTTAGGGGTTAAGAGTTAGGGATTTGGGGTTTACAAATTTA
** * *
55847754 AAGGTCGGGTTAGGGTTTTGGGTTTAGATTAAT-TTTTTTATTTATATTTTAAATATGTTCTTAT
110 GGGGTCGGGTTAGGGTTTTGGGTTTAGATTATTATTTTTTATTTATATTTTAAATATGTTATTAT
55847818 GTAATTGTAAAAGAT
175 GTAATTGTAAAAGAT
55847833 GTATAATCTA
Statistics
Matches: 442, Mismatches: 39, Indels: 45
0.84 0.07 0.09
Matches are distributed among these distances:
301 22 0.05
302 86 0.19
303 1 0.00
304 12 0.03
305 119 0.27
306 3 0.01
307 9 0.02
308 31 0.07
309 1 0.00
310 4 0.01
311 4 0.01
312 5 0.01
313 4 0.01
314 2 0.00
315 9 0.02
316 2 0.00
318 2 0.00
319 3 0.01
323 44 0.10
324 79 0.18
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.43
Consensus pattern (301 bp):
TTAGGGATTATGGTTTATATTAAGGGTTGGGATTTAAGGTTTAGGTGTTAGGGGTTTAGGGGTTA
GACGTTAGGGGTTAAGAGTTAGGGATTTGGGGTTTACAAATTTAGGGGTCGGGTTAGGGTTTTGG
GTTTAGATTATTATTTTTTATTTATATTTTAAATATGTTATTATGTAATTGTAAAAGATAATAAT
AAAAATGTTTAGAGTTTTAATTAGTTTAGGGTATATGATAAATTTAAAATTTAAGGCCGGTTTAG
GAGTTCATATTTTAAGGTTTAGGTACTATATATAGATATAT
Found at i:55847873 original size:2 final size:2
Alignment explanation
Indices: 55847866--55847896 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
55847856 GCCTTAAGAG
*
55847866 AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55847897 ATAGATAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55848179 original size:19 final size:18
Alignment explanation
Indices: 55848146--55848184 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
55848136 AAATTATACG
*
55848146 AAATAAAATTAAAATACAA
1 AAATAAAAATAAAATA-AA
*
55848165 AAATAAAAATGAAATAAA
1 AAATAAAAATAAAATAAA
55848183 AA
1 AA
55848185 CACTAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAAAATAAAATAAA
Found at i:55848256 original size:47 final size:48
Alignment explanation
Indices: 55848179--55848277 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 48
55848169 AAAAATGAAA
* ** * * *
55848179 TAAAAACACTAAATTTTTTAATTTTGTCTAATTTTTATAAATTTTACT
1 TAAAAACACTAAAATTCATAATTTTATCTAATTTTTATAAATATTACC
55848227 TAAAAA-ACTAAAATTCATAATTTTATCTAATTTTTATAAATATTACC
1 TAAAAACACTAAAATTCATAATTTTATCTAATTTTTATAAATATTACC
55848274 TAAA
1 TAAA
55848278 CAAAAGTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
47 39 0.87
48 6 0.13
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.46
Consensus pattern (48 bp):
TAAAAACACTAAAATTCATAATTTTATCTAATTTTTATAAATATTACC
Found at i:55849924 original size:13 final size:13
Alignment explanation
Indices: 55849906--55849930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55849896 TGAATGAACG
55849906 GAATTTTCTGAAT
1 GAATTTTCTGAAT
55849919 GAATTTTCTGAA
1 GAATTTTCTGAA
55849931 GGTAAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
GAATTTTCTGAAT
Found at i:55849980 original size:14 final size:14
Alignment explanation
Indices: 55849961--55849987 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55849951 TAAAAGGTTT
55849961 TTTAGTTAATCATC
1 TTTAGTTAATCATC
55849975 TTTAGTTAATCAT
1 TTTAGTTAATCAT
55849988 GTTGTTGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTAGTTAATCATC
Found at i:55850530 original size:23 final size:24
Alignment explanation
Indices: 55850501--55850585 Score: 99
Period size: 23 Copynumber: 3.7 Consensus size: 24
55850491 ATTATTAATG
55850501 TATAACATATA-TTAATATGTATA
1 TATAACATATATTTAATATGTATA
*
55850524 TATAACATATATTTAA-AT-T-TG
1 TATAACATATATTTAATATGTATA
55850545 TATAACATATACTTTTAATATGTATA
1 TATAACATATA--TTTAATATGTATA
*
55850571 TAT-ACATTTATTTAA
1 TATAACATATATTTAA
55850586 ATTTTATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
21 12 0.23
22 1 0.02
23 23 0.43
24 6 0.11
25 7 0.13
26 4 0.08
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.47
Consensus pattern (24 bp):
TATAACATATATTTAATATGTATA
Found at i:55850548 original size:21 final size:22
Alignment explanation
Indices: 55850501--55850595 Score: 88
Period size: 23 Copynumber: 4.2 Consensus size: 22
55850491 ATTATTAATG
55850501 TATAACATATA-TTAATATGTATA
1 TATAACATATATTTAATAT-T-TA
*
55850524 TATAACATATATTTAA-ATTTG
1 TATAACATATATTTAATATTTA
*
55850545 TATAACATATACTTTTAATATGTA
1 TATAACATATA--TTTAATATTTA
*
55850569 TATATACATTTATTTAA-ATTTTA
1 TATA-ACATATATTTAATA-TTTA
55850592 TATA
1 TATA
55850596 TTTTTTCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
21 12 0.20
22 2 0.03
23 30 0.49
24 11 0.18
25 6 0.10
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (22 bp):
TATAACATATATTTAATATTTA
Found at i:55850571 original size:47 final size:43
Alignment explanation
Indices: 55850499--55850593 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 43
55850489 ATATTATTAA
55850499 TGTATAACATATATTAATATGTATATATAACATATATTTAAATT
1 TGTATAACATATATTAATATGTATATAT-ACATATATTTAAATT
*
55850543 TGTATAACATATACTTTTAATATGTATATATACATTTATTTAAATT
1 TGTATAACATATA---TTAATATGTATATATACATATATTTAAATT
55850589 T-TATA
1 TGTATA
55850594 TATTTTTTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
44 13 0.28
45 4 0.09
46 15 0.32
47 15 0.32
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (43 bp):
TGTATAACATATATTAATATGTATATATACATATATTTAAATT
Found at i:55850740 original size:12 final size:12
Alignment explanation
Indices: 55850723--55850747 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55850713 TACATAATAC
55850723 ATAACTTACATA
1 ATAACTTACATA
55850735 ATAACTTACATA
1 ATAACTTACATA
55850747 A
1 A
55850748 CTCCTATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:55850788 original size:9 final size:9
Alignment explanation
Indices: 55850770--55851007 Score: 140
Period size: 9 Copynumber: 28.3 Consensus size: 9
55850760 CTTATATATA
*
55850770 AACTTGCAT
1 AACTTACAT
55850779 AACTTACAT
1 AACTTACAT
*
55850788 AA-TAACAT
1 AACTTACAT
*
55850796 AAAAACTTAGAT
1 ---AACTTACAT
55850808 AA--TACAT
1 AACTTACAT
* *
55850815 AGCCTACAT
1 AACTTACAT
*
55850824 AACTTAGAT
1 AACTTACAT
55850833 AACTTACAT
1 AACTTACAT
*
55850842 AA--TACAC
1 AACTTACAT
*
55850849 CACTTACAT
1 AACTTACAT
55850858 -A---A-AT
1 AACTTACAT
*
55850862 AACTTGCAT
1 AACTTACAT
55850871 AA--TACAT
1 AACTTACAT
* *
55850878 AGCCTACAT
1 AACTTACAT
55850887 AACTTACAT
1 AACTTACAT
55850896 AACTTACAT
1 AACTTACAT
*
55850905 AA--TACAC
1 AACTTACAT
* *
55850912 CACTTGCAT
1 AACTTACAT
*
55850921 AACTTAAAT
1 AACTTACAT
55850930 AACTTACAT
1 AACTTACAT
55850939 AA--TACAT
1 AACTTACAT
55850946 AACTTACAT
1 AACTTACAT
55850955 AACTTACAT
1 AACTTACAT
55850964 AA--TACAT
1 AACTTACAT
*
55850971 TACTTACAT
1 AACTTACAT
55850980 AACTTAC--
1 AACTTACAT
*
55850987 -ACTATACAC
1 AACT-TACAT
55850996 AACTTACAT
1 AACTTACAT
55851005 AAC
1 AAC
55851008 ATAATTAATA
Statistics
Matches: 175, Mismatches: 29, Indels: 50
0.69 0.11 0.20
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
6 3 0.02
7 36 0.21
8 6 0.03
9 117 0.67
10 3 0.02
11 2 0.01
12 4 0.02
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.29
Consensus pattern (9 bp):
AACTTACAT
Found at i:55850828 original size:54 final size:56
Alignment explanation
Indices: 55850770--55850908 Score: 160
Period size: 63 Copynumber: 2.4 Consensus size: 56
55850760 CTTATATATA
55850770 AACTTGCATAACTTACATAATA-ACATAAA-AACTTAG-ATAATACATAGCCTACAT
1 AACTTGCATAACTTACATAATATACATAAATAACTT-GCATAATACATAGCCTACAT
55850824 AACTTAG-ATAACTTACATAATACACCACTTACATAAATAACTTGCATAATACATAGCCTACAT
1 AACTT-GCATAACTTACATAAT-----A--TACATAAATAACTTGCATAATACATAGCCTACAT
*
55850887 AACTTACATAACTTACATAATA
1 AACTTGCATAACTTACATAATA
55850909 CACCACTTGC
Statistics
Matches: 72, Mismatches: 1, Indels: 20
0.77 0.01 0.22
Matches are distributed among these distances:
54 19 0.26
55 1 0.01
58 1 0.01
59 1 0.01
62 8 0.11
63 42 0.58
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (56 bp):
AACTTGCATAACTTACATAATATACATAAATAACTTGCATAATACATAGCCTACAT
Found at i:55850837 original size:63 final size:63
Alignment explanation
Indices: 55850788--55850965 Score: 225
Period size: 63 Copynumber: 2.8 Consensus size: 63
55850778 TAACTTACAT
*
55850788 AATAACATAAA-AACTTAG-ATAATACATAGCCTACATAACTTAGATAACTTACATAATACACC
1 AATAACATAAATAACTT-GCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
* *
55850850 ACTTACATAAATAACTTGCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
1 AATAACATAAATAACTTGCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
* * * *
55850913 ACTTGCATAACTTAAATAACTTACATAATACATAACTTACATAACTTACATAA
1 A-----ATAACATAAATAACTTGCATAATACATAGCCTACATAACTTACATAA
55850966 TACATTACTT
Statistics
Matches: 100, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
62 10 0.10
63 49 0.49
68 41 0.41
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (63 bp):
AATAACATAAATAACTTGCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
Found at i:55850844 original size:34 final size:33
Alignment explanation
Indices: 55850789--55850965 Score: 175
Period size: 34 Copynumber: 5.4 Consensus size: 33
55850779 AACTTACATA
* *
55850789 ATAACATAAA-AACTTAGATAATACATAGCCTAC
1 ATAACTTAAATAACTTACATAATACATA-CCTAC
*
55850822 ATAACTTAGATAACTTACATAATAC--ACC-AC
1 ATAACTTAAATAACTTACATAATACATACCTAC
* * *
55850852 -TTACATAAATAACTTGCATAATACATAGCCTAC
1 ATAACTTAAATAACTTACATAATACATA-CCTAC
* * * *
55850885 ATAACTTACATAACTTACATAATACACCACTTGC
1 ATAACTTAAATAACTTACATAATACA-TACCTAC
*
55850919 ATAACTTAAATAACTTACATAATACATAACTTAC
1 ATAACTTAAATAACTTACATAATACAT-ACCTAC
*
55850953 ATAACTTACATAA
1 ATAACTTAAATAA
55850966 TACATTACTT
Statistics
Matches: 118, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
29 20 0.17
30 2 0.02
31 3 0.03
32 3 0.03
33 10 0.08
34 79 0.67
35 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (33 bp):
ATAACTTAAATAACTTACATAATACATACCTAC
Found at i:55850910 original size:25 final size:25
Alignment explanation
Indices: 55850799--55851006 Score: 100
Period size: 25 Copynumber: 8.4 Consensus size: 25
55850789 ATAACATAAA
* * *
55850799 AACTTAGATAATACATAGCCTACAT
1 AACTTACATAATACATAACTTACAT
* *
55850824 AACTTAGATAACTTACATAA--TACAC
1 AACTTACATAA--TACATAACTTACAT
* *
55850849 CACTTACAT-A-A-ATAACTTGCAT
1 AACTTACATAATACATAACTTACAT
*
55850871 AA--TACATAGCCTACATAACTTACAT
1 AACTTACATA--ATACATAACTTACAT
** *
55850896 AACTTACATAATACACCACTTGCAT
1 AACTTACATAATACATAACTTACAT
*
55850921 AACTTAAATAACTTACATAA--TACAT
1 AACTTACATAA--TACATAACTTACAT
55850946 AACTTACATAACTTACATAA--TACAT
1 AACTTACATAA--TACATAACTTACAT
* * *
55850971 TACTTACAT-A-ACTTACACTATACAC
1 AACTTACATAATACATA-ACT-TACAT
55850996 AACTTACATAA
1 AACTTACATAA
55851007 CATAATTAAT
Statistics
Matches: 143, Mismatches: 22, Indels: 35
0.71 0.11 0.17
Matches are distributed among these distances:
20 9 0.06
21 5 0.03
22 5 0.03
24 3 0.02
25 103 0.72
26 1 0.01
27 17 0.12
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (25 bp):
AACTTACATAATACATAACTTACAT
Found at i:55851007 original size:25 final size:25
Alignment explanation
Indices: 55850770--55850987 Score: 92
Period size: 25 Copynumber: 8.3 Consensus size: 25
55850760 CTTATATATA
*
55850770 AACTTGCATAACTTACATAATAACAT
1 AACTTACATAACTTACATAAT-ACAT
* *
55850796 AAAAACTTAGATAA--TACATAGCCTACAT
1 ---AACTTACATAACTTACATA--ATACAT
* *
55850824 AACTTAGATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAT
* *
55850849 CACTTACATAAATAACTTGCATAATACAT
1 AACTTAC----ATAACTTACATAATACAT
* *
55850878 AGCCTACATAACTTACATAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
** * *
55850905 AA--TACACCACTTGCATAACTTAAAT
1 AACTTACATAACTTACATAA--TACAT
55850930 AACTTACATAA--TACATAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
*
55850955 AACTTACATAA--TACATTACTTACAT
1 AACTTACATAACTTACA-TA-ATACAT
55850980 AACTTACA
1 AACTTACA
55850988 CTATACACAA
Statistics
Matches: 152, Mismatches: 23, Indels: 32
0.73 0.11 0.15
Matches are distributed among these distances:
25 93 0.61
26 2 0.01
27 23 0.15
28 4 0.03
29 30 0.20
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:55851110 original size:66 final size:62
Alignment explanation
Indices: 55850975--55851134 Score: 171
Period size: 66 Copynumber: 2.5 Consensus size: 62
55850965 ATACATTACT
* **
55850975 TACATAACTTACACTATACACAACTTACATAACATAATTAATATTATACACAACTTACAGCC
1 TACATAACTTACATTATACACAACTTACATAACATAATTAATATTATACACAACTTACAGAA
* * * * *
55851037 TATATAACTTACATTATACACAACTTA-ATTACATAATTTAATTAAAATTTTACATAACTTACAT
1 TACATAACTTACATTATACACAACTTACATAACATAA-TTAA-T---ATTATACACAACTTACAG
55851101 AA
61 AA
*
55851103 TACATAACTTTA-ATAATACACAACTTACATAA
1 TACATAAC-TTACATTATACACAACTTACATAA
55851135 TTACATTATA
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
61 8 0.10
62 29 0.36
63 1 0.01
66 36 0.45
67 6 0.08
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.34
Consensus pattern (62 bp):
TACATAACTTACATTATACACAACTTACATAACATAATTAATATTATACACAACTTACAGAA
Found at i:55851779 original size:18 final size:17
Alignment explanation
Indices: 55851758--55851792 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55851748 TTATTATTAA
*
55851758 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55851776 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55851793 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55851860 original size:159 final size:157
Alignment explanation
Indices: 55851645--55851963 Score: 557
Period size: 159 Copynumber: 2.0 Consensus size: 157
55851635 TAGAATACCC
*
55851645 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
55851710 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
55851775 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
55851802 TTAGCAGAAATTTGTTTTGGTAAATTATTTTATTGTTATTTTTATTTAAATTTTAATAAGATTAT
1 TTAGCAGAAATTTGTTTTGGTAAATGA--TTATTGTTATTGTTATTTAAATTTTAATAAGATTAT
55851867 TAATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAA
64 TAATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAA
55851932 AATATATAATTTAATAAAATTCTTAATAA
129 AATATATAATTTAATAAAATTCTTAATAA
55851961 TTA
1 TTA
55851964 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
157 25 0.16
159 128 0.84
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:55852037 original size:15 final size:16
Alignment explanation
Indices: 55852016--55852058 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
55852006 GTAAAATATA
55852016 AATTAAAATA-ATTAT
1 AATTAAAATATATTAT
*
55852031 TATT-AAATATATTAT
1 AATTAAAATATATTAT
55852046 AATTAAAATATAT
1 AATTAAAATATAT
55852059 AATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 11 0.46
16 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:55852044 original size:120 final size:120
Alignment explanation
Indices: 55851897--55852432 Score: 916
Period size: 120 Copynumber: 4.5 Consensus size: 120
55851887 TTAATCATAT
*
55851897 TTAAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
55851962 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
55852018 TTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
1 TTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
*
55852083 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACAGTAAAATATAAA
66 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
*
55852138 TTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
1 TTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
55852203 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
66 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
*
55852258 TTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
1 TTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
*
55852323 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAA
66 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAAA
* * * * * *
55852377 TTTGAAATAATTAATA-TATCATATATTTTATTTAAAATATATGATTTAATAAAATT
1 -TTAAAATAATTATTATTA-AATATATTATAATTAAAATATATAATTTAATAAAATT
55852433 TAAAATAATT
Statistics
Matches: 400, Mismatches: 12, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
119 9 0.02
120 386 0.96
121 5 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (120 bp):
TTAAAATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
Found at i:55852185 original size:14 final size:15
Alignment explanation
Indices: 55852136--55852187 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
55852126 GTAAAATATA
55852136 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
55852151 TATTAAATATATTAT
1 AATTAAATATATTAT
55852166 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
55852179 AATTTAATA
1 AATTAAATA
55852188 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:55852305 original size:14 final size:15
Alignment explanation
Indices: 55852256--55852307 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
55852246 GTAAAATATA
55852256 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
55852271 TATTAAATATATTAT
1 AATTAAATATATTAT
55852286 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
55852299 AATTTAATA
1 AATTAAATA
55852308 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:55852726 original size:92 final size:92
Alignment explanation
Indices: 55852564--55852737 Score: 246
Period size: 92 Copynumber: 1.9 Consensus size: 92
55852554 NNNNNNNNNN
* * *
55852564 AATAATAATTATTACATATAATTTAATAATTAATATTAAATTTCATAAAATTCTTGATAATAAAT
1 AATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCATAAAATTCTTAATAATAAAT
* *
55852629 TTTCTTATATGAATTTATACAATTTAA
66 GTTCTTATAGGAATTTATACAATTTAA
*
55852656 AATAATTAA-TATTAAATATAATTTAATAGTG-ATA-TATAATTTCATAAAATTCTTAATAATAA
1 AATAA-TAATTATTAAATATAATTTAATAATGAATATTA-AATTTCATAAAATTCTTAATAAT-A
55852718 AATGTTCTTATAGGAATTTA
63 AATGTTCTTATAGGAATTTA
55852738 CTAAAATCAA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
90 2 0.03
91 25 0.34
92 43 0.59
93 3 0.04
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (92 bp):
AATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCATAAAATTCTTAATAATAAAT
GTTCTTATAGGAATTTATACAATTTAA
Found at i:55873794 original size:142 final size:142
Alignment explanation
Indices: 55873539--55873914 Score: 583
Period size: 142 Copynumber: 2.7 Consensus size: 142
55873529 TGTAAGGAAG
* * * *
55873539 CAGATTGAAGCCATAATTCTTACCTCCCTGAGATTACAGC-GAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATTCT
* *
55873603 ATCTCCCTGAGATTATAGTGGAGCGGATTGAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
55873668 AGTAGATCACGT
131 AGTAGATCACGC
*
55873680 CAGATTAAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATTCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATTCT
* * *
55873745 ATCTCCCTAAGATTACAATGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
55873810 AGTAGATCGCGC
131 AGTAGATCACGC
* * * *
55873822 CAGGTTGGAGCAAGAAGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATTCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATTCT
* *
55873887 ATCTCCCTGATATTACAGTGGAGTGGAT
66 ATCTCCCTGAGATTACAGTGGAGCGGAT
55873915 CCAAGCACCA
Statistics
Matches: 213, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
141 36 0.17
142 177 0.83
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATTCT
ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCACGC
Found at i:55874512 original size:20 final size:20
Alignment explanation
Indices: 55874478--55874515 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55874468 AAAAGCCAGC
**
55874478 ATAGAAAAACGGAAGAAATA
1 ATAGAAAAAAAGAAGAAATA
55874498 ATAGAAAAAAAGAAGAAA
1 ATAGAAAAAAAGAAGAAA
55874516 AAACATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (20 bp):
ATAGAAAAAAAGAAGAAATA
Found at i:55876718 original size:32 final size:27
Alignment explanation
Indices: 55876655--55876708 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
55876645 CGTGGATTTG
55876655 TTAAATGCCTATTTAGTATTGAATTGA
1 TTAAATGCCTATTTAGTATTGAATTGA
55876682 TTAAATGCCTATTTAGTATTGAATTGA
1 TTAAATGCCTATTTAGTATTGAATTGA
55876709 AATTCTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (27 bp):
TTAAATGCCTATTTAGTATTGAATTGA
Found at i:55880194 original size:17 final size:17
Alignment explanation
Indices: 55880169--55880205 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
55880159 AATTTAAAAT
*
55880169 AACTATTATTCAAGAAC
1 AACTATTATCCAAGAAC
*
55880186 AACTCTTATCCAAGAAC
1 AACTATTATCCAAGAAC
55880203 AAC
1 AAC
55880206 CATTGTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (17 bp):
AACTATTATCCAAGAAC
Found at i:55880964 original size:26 final size:27
Alignment explanation
Indices: 55880926--55880982 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
55880916 CTTAGTTTTA
*
55880926 TTTAATTTAGGCTATTTTTTA-TATAAT
1 TTTAATTTAGGCT-TTTCTTACTATAAT
55880953 TTTAATTT-GGCTTTTCTTACTATAAT
1 TTTAATTTAGGCTTTTCTTACTATAAT
55880979 TTTA
1 TTTA
55880983 GATTATTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 6 0.21
26 14 0.50
27 8 0.29
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (27 bp):
TTTAATTTAGGCTTTTCTTACTATAAT
Found at i:55891833 original size:19 final size:20
Alignment explanation
Indices: 55891809--55891856 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
55891799 TTTTAATAAT
55891809 AATAAATAGAAAAGAAAT-A
1 AATAAATAGAAAAGAAATCA
*
55891828 AATAAATA-ACAAGAAATCA
1 AATAAATAGAAAAGAAATCA
55891847 AAT-AATAGAA
1 AATAAATAGAA
55891857 GCTGTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (20 bp):
AATAAATAGAAAAGAAATCA
Found at i:55904328 original size:28 final size:28
Alignment explanation
Indices: 55904282--55904355 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
55904272 AAAAACCTGG
* *
55904282 GAAA-GAATGCCTTTCTGGCGAAC-CACT
1 GAAAGGAAAGCCTTTGTGGCGAACTC-CT
*
55904309 GAAAGGAAAGCCTTTGTGGCGAACTCTT
1 GAAAGGAAAGCCTTTGTGGCGAACTCCT
*
55904337 G-AAGGGAAGCCTTTGTGGC
1 GAAAGGAAAGCCTTTGTGGC
55904356 AATATTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 21 0.51
28 19 0.46
29 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (28 bp):
GAAAGGAAAGCCTTTGTGGCGAACTCCT
Found at i:55915391 original size:20 final size:23
Alignment explanation
Indices: 55915360--55915404 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
55915350 TTGTTTGTAC
55915360 TTAAGTACATTTT-GTT-GCATT
1 TTAAGTACATTTTAGTTAGCATT
55915381 TTAAG-ACATTTTAGTTAGCATT
1 TTAAGTACATTTTAGTTAGCATT
55915403 TT
1 TT
55915405 TAATATTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (23 bp):
TTAAGTACATTTTAGTTAGCATT
Found at i:55920973 original size:20 final size:20
Alignment explanation
Indices: 55920948--55920998 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
55920938 GCAGTGTGGC
55920948 TAGGCCGTGTGAGTGTGTCT
1 TAGGCCGTGTGAGTGTGTCT
55920968 TAGGCCGTGTGAGTGTGTCT
1 TAGGCCGTGTGAGTGTGTCT
55920988 TAGGCCGTGTG
1 TAGGCCGTGTG
55920999 GGCATTCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.16, G:0.41, T:0.33
Consensus pattern (20 bp):
TAGGCCGTGTGAGTGTGTCT
Found at i:55922466 original size:24 final size:24
Alignment explanation
Indices: 55922437--55922483 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
55922427 CACAAGCTGT
*
55922437 AAATCGGTAAGCTTATACGAGCTA
1 AAATCGGTAAGCTCATACGAGCTA
55922461 AAATCGGTAAGCTCATACGAGCT
1 AAATCGGTAAGCTCATACGAGCT
55922484 GAGAATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (24 bp):
AAATCGGTAAGCTCATACGAGCTA
Found at i:55926950 original size:18 final size:17
Alignment explanation
Indices: 55926917--55926955 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
55926907 TTTTATAAAT
55926917 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
55926935 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
55926952 TGTG
1 TGTG
55926956 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:55927210 original size:23 final size:23
Alignment explanation
Indices: 55927184--55927276 Score: 168
Period size: 23 Copynumber: 4.0 Consensus size: 23
55927174 GTTATTGATT
*
55927184 AGTGGTAGCTTCGGCTACGTATC
1 AGTGGTAGCTTCGGCTACATATC
55927207 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
*
55927230 AGTGGTAGCTTCGGCTACGTATC
1 AGTGGTAGCTTCGGCTACATATC
55927253 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
55927276 A
1 A
55927277 TTGTGGCACT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATATC
Found at i:55927237 original size:46 final size:46
Alignment explanation
Indices: 55927184--55927276 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
55927174 GTTATTGATT
55927184 AGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATC
55927230 AGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATC
55927276 A
1 A
55927277 TTGTGGCACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (46 bp):
AGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACATATC
Found at i:55935498 original size:66 final size:66
Alignment explanation
Indices: 55935400--55935523 Score: 214
Period size: 66 Copynumber: 1.9 Consensus size: 66
55935390 TGTTAGCAAC
55935400 TTAGGTGGAAGAAACAAGTAAAAATATTGATGG-TTAGAGTTGCAGTAAACAAGTGAATTTAGCT
1 TTAGGTGGAAGAAACAAGTAAAAATATTGATGGTTTA-AGTTGCAGTAAACAAGTGAATTTAGCT
55935464 AG
65 AG
* *
55935466 TTAGGTGGAAGAAATAAGTAAAAATATTGATGGTTTAAGTTGCAGTAAACATGTGAAT
1 TTAGGTGGAAGAAACAAGTAAAAATATTGATGGTTTAAGTTGCAGTAAACAAGTGAAT
55935524 ACAGAAACGC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
66 52 0.95
67 3 0.05
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.29
Consensus pattern (66 bp):
TTAGGTGGAAGAAACAAGTAAAAATATTGATGGTTTAAGTTGCAGTAAACAAGTGAATTTAGCTA
G
Found at i:55937407 original size:14 final size:15
Alignment explanation
Indices: 55937383--55937411 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55937373 AAAAAAGTAG
55937383 TTAAAATATAAAAAT
1 TTAAAATATAAAAAT
55937398 TTAAAA-ATAAAAAT
1 TTAAAATATAAAAAT
55937412 AATGGTCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAATATAAAAAT
Found at i:55940694 original size:13 final size:13
Alignment explanation
Indices: 55940668--55940753 Score: 59
Period size: 13 Copynumber: 6.6 Consensus size: 13
55940658 TCGAACTACC
55940668 TTTAGTTTTA-TTT
1 TTTA-TTTTATTTT
55940681 TTTATTTTATTTT
1 TTTATTTTATTTT
* * *
55940694 TTGAATTTACTTGT
1 TTTATTTTA-TTTT
55940708 TTTATTTTATTTT
1 TTTATTTTATTTT
* **
55940721 ATTA-TGCATTTT
1 TTTATTTTATTTT
* * *
55940733 ATTGTTATATTTT
1 TTTATTTTATTTT
55940746 TTTATTTT
1 TTTATTTT
55940754 TCTCTATTTG
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
12 14 0.25
13 31 0.56
14 10 0.18
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:55940775 original size:19 final size:21
Alignment explanation
Indices: 55940753--55940794 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
55940743 TTTTTTATTT
55940753 TTCTCTAT-TTGTTTTG-TCA
1 TTCTCTATCTTGTTTTGTTCA
* *
55940772 TTCTTTATCTTTTTTTGTTCA
1 TTCTCTATCTTGTTTTGTTCA
55940793 TT
1 TT
55940795 TTCTTATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (21 bp):
TTCTCTATCTTGTTTTGTTCA
Found at i:55943924 original size:22 final size:22
Alignment explanation
Indices: 55943896--55943939 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
55943886 AGTGTGCTAT
55943896 CTAAAGTGTGGGGGATAACATA
1 CTAAAGTGTGGGGGATAACATA
55943918 CTAAAGTGTGGGGGATAACATA
1 CTAAAGTGTGGGGGATAACATA
55943940 GGAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.32, T:0.23
Consensus pattern (22 bp):
CTAAAGTGTGGGGGATAACATA
Found at i:55948218 original size:30 final size:30
Alignment explanation
Indices: 55948184--55948244 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
55948174 CTAATGATTT
55948184 AGTACTGAATTTTGACGAATCTCAATTTCC
1 AGTACTGAATTTTGACGAATCTCAATTTCC
*
55948214 AGTACTGAATTTTGACGAATCTCGATTTCC
1 AGTACTGAATTTTGACGAATCTCAATTTCC
55948244 A
1 A
55948245 ACTAAGTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (30 bp):
AGTACTGAATTTTGACGAATCTCAATTTCC
Found at i:55949297 original size:16 final size:16
Alignment explanation
Indices: 55949276--55949306 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55949266 AAACATCATA
*
55949276 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
55949292 AATTAAATAATTTTC
1 AATTAAATAATTTTC
55949307 TTAACCAAAT
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:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:55961534 original size:19 final size:16
Alignment explanation
Indices: 55961509--55961551 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 16
55961499 ATATTATAAA
55961509 AAAAATTTTAAAGAATAT
1 AAAAATTTTAAA-AAT-T
55961527 ATAAAATTTTAAAAATT
1 A-AAAATTTTAAAAATT
55961544 AAAAATTT
1 AAAAATTT
55961552 CCTAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.29
17 2 0.08
18 4 0.17
19 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AAAAATTTTAAAAATT
Found at i:55962204 original size:24 final size:22
Alignment explanation
Indices: 55962167--55962228 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 22
55962157 ATCCAAAATT
*
55962167 CCTTACAAACCCTAAACAAAAAC
1 CCTTA-AAATCCTAAACAAAAAC
* *
55962190 CCTTAAAGAATCCTAAACCATAAC
1 CCTT-AA-AATCCTAAACAAAAAC
55962214 CCTTAAAATCCTAAA
1 CCTTAAAATCCTAAA
55962229 ACCCTTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 9 0.26
23 7 0.21
24 18 0.53
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (22 bp):
CCTTAAAATCCTAAACAAAAAC
Found at i:55962370 original size:2 final size:2
Alignment explanation
Indices: 55962358--55962401 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
55962348 GTGTTTTCCT
*
55962358 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
55962400 TC
1 TC
55962402 GCAACAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:55963133 original size:2 final size:2
Alignment explanation
Indices: 55963126--55963264 Score: 278
Period size: 2 Copynumber: 69.5 Consensus size: 2
55963116 NNNNNNNNNN
55963126 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
55963168 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
55963210 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
55963252 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
55963265 TTATACACAA
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 137 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.