Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 90 of 373
Found at i:28724676 original size:79 final size:80
Alignment explanation
Indices: 28724533--28724716 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 80
28724523 GCTATTCGTT
* * *
28724533 CAAACGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGACAATTGCCTTCGGGACTTAACCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGACAAATGCCTTCGGGACTTAACCCGG
* *
28724597 ATTTAGTAAC-TCGCA
65 ATATAGTAACTTAGCA
* **
28724612 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCG-ACAAATGCCTTCGGGA-CTTAACCC
* *
28724674 GGATATGGTCACTTAGCA
63 GGATATAGTAACTTAGCA
28724692 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
28724717 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
78 21 0.24
79 49 0.55
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCA
Found at i:28727635 original size:26 final size:26
Alignment explanation
Indices: 28727599--28727653 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
28727589 AGTAAACATG
*
28727599 TAATTGTTTTCTATTTAATTGAACGA
1 TAATTGTTTTCTATTTAATTGAAAGA
*
28727625 TAATTGTTTTCTATTTATTTGAAAGA
1 TAATTGTTTTCTATTTAATTGAAAGA
28727651 TAA
1 TAA
28727654 ATAAATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (26 bp):
TAATTGTTTTCTATTTAATTGAAAGA
Found at i:28727688 original size:19 final size:19
Alignment explanation
Indices: 28727664--28727708 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
28727654 ATAAATAAAG
28727664 TTAATTTCACATTTCACTA
1 TTAATTTCACATTTCACTA
28727683 TTAATTTCACATTTCACTA
1 TTAATTTCACATTTCACTA
28727702 TT-ATTTC
1 TTAATTTC
28727709 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAATTTCACATTTCACTA
Found at i:28729369 original size:27 final size:27
Alignment explanation
Indices: 28729337--28729515 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
28729327 ATATTGAGCC
* * **
28729337 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
28729364 CTCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
28729391 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** ** *
28729419 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
28729446 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* * *
28729473 CGCACACTTAGTGCAACATAGTCATAT
1 CGCACACTTAGTGCTACATAATCAAAT
28729500 CGCACACTTAGTGCTA
1 CGCACACTTAGTGCTA
28729516 TACAATTTAA
Statistics
Matches: 129, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:28730079 original size:13 final size:13
Alignment explanation
Indices: 28730061--28730085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28730051 TACTAAATTT
28730061 TCATGGATTCAAG
1 TCATGGATTCAAG
28730074 TCATGGATTCAA
1 TCATGGATTCAA
28730086 TATACCATTA
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:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:28746362 original size:5 final size:5
Alignment explanation
Indices: 28746352--28746379 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28746342 TATTTGACCA
28746352 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
28746380 GATGATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:28752143 original size:46 final size:46
Alignment explanation
Indices: 28752076--28752247 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
28752066 AACCCGCCCC
* * *
28752076 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
*
28752122 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCACATCCA
* * * * *
28752170 TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
*
28752215 TAAGTGAACTCGGACTCAACTCAACAAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
28752248 ATGCTCAACC
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 57 0.55
47 27 0.26
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
Found at i:28752189 original size:93 final size:93
Alignment explanation
Indices: 28752081--28752251 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
28752071 GCCCCTAAGT
* * * *
28752081 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
28752146 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CAAGTTCGGATGCCTAGTTACATTTCAC
* *
28752174 GAACTCGGACTCAACTCAACGAGTTCAGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
28752239 CAAGTTCGGATGC
66 CAAGTTCGGATGC
28752252 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CAAGTTCGGATGCCTAGTTACATTTCAC
Found at i:28752267 original size:46 final size:46
Alignment explanation
Indices: 28752074--28752267 Score: 157
Period size: 46 Copynumber: 4.2 Consensus size: 46
28752064 GTAACCCGCC
* * ** * *
28752074 CCTAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTC-GCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACAT
28752119 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTACAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACAT
* * * * ***
28752169 -TTCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTC-ACAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACAT
*
28752212 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGATGCTCAACCAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAA-CAT
28752260 CCT-AGTGA
1 CCTAAGTGA
28752268 CATGTCACTT
Statistics
Matches: 116, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
43 4 0.03
45 5 0.04
46 66 0.57
47 30 0.26
48 8 0.07
50 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACAT
Found at i:28757273 original size:40 final size:40
Alignment explanation
Indices: 28757179--28757323 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
28757169 TACTCGAATG
*
28757179 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
28757220 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
28757260 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
28757300 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
28757324 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:28765294 original size:40 final size:41
Alignment explanation
Indices: 28765200--28765344 Score: 181
Period size: 40 Copynumber: 3.6 Consensus size: 41
28765190 TACTCGAATG
* *
28765200 ATATCCGGGCTAA-ATCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGACTAAGATCCCGAAGGCATTTGTGCT-AGCGACT
*
28765241 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGACTAAGATCCCGAAGGCATTTGTGCTAGCGACT
* * * *
28765281 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGACTAAGATCCCGAAGGCATTTGTGCTAGCGACT
*
28765321 ATATCCGGATTAAGA-CCCGAAGGC
1 ATATCCGGACTAAGATCCCGAAGGC
28765345 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
39 1 0.01
40 61 0.67
41 27 0.30
42 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (41 bp):
ATATCCGGACTAAGATCCCGAAGGCATTTGTGCTAGCGACT
Found at i:28769960 original size:40 final size:40
Alignment explanation
Indices: 28769736--28769960 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
28769726 AGCTACTGTT
*
28769736 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28769776 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
28769816 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
28769856 CAAATGCCTTC-GGATCTTAGTCCGAATTTAGT-ACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
28769895 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AACTCGCA
28769936 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28769961 CATCATTCGA
Statistics
Matches: 167, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
39 38 0.23
40 116 0.69
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28777738 original size:40 final size:40
Alignment explanation
Indices: 28777701--28777832 Score: 169
Period size: 40 Copynumber: 3.3 Consensus size: 40
28777691 GCTACTCGTT
* *
28777701 CAAATGCCTTCGGGACATAGCCTGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
* *
28777741 CAAATGGCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
28777781 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
28777820 CAAATGCCTTCGG
1 CAAATGCCTTCGG
28777833 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.42
40 46 0.55
41 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:28777818 original size:79 final size:82
Alignment explanation
Indices: 28777701--28777885 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
28777691 GCTACTCGTT
* * * *
28777701 CAAATGCCTTCGGGACATAGCCTGG-TTATAGTAACTCGCACAAATGGCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
28777764 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
28777781 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
28777844 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
28777861 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28777886 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.59
80 34 0.38
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:28780569 original size:22 final size:21
Alignment explanation
Indices: 28780530--28780573 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
28780520 CCCAAAACTA
* *
28780530 ATTACCCTTAACCTATAACCC
1 ATTACACTTAACCCATAACCC
28780551 ATTACACTTAAACCCATAACCC
1 ATTACACTT-AACCCATAACCC
28780573 A
1 A
28780574 ATACCTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (21 bp):
ATTACACTTAACCCATAACCC
Found at i:28781635 original size:3 final size:3
Alignment explanation
Indices: 28781627--28781805 Score: 50
Period size: 3 Copynumber: 60.0 Consensus size: 3
28781617 TTTAATTACT
** * * *
28781627 TTA TTA TTA AAA TTAA TTA TT- TTA GTA TTA TTA TTA TTA GTA GTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
28781672 CTA TTCA TATA CATA TATA TTA TCA TTA TTG TTA CTC TTA CTA TTA TTA
1 TTA TT-A T-TA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
28781721 ATC TTC GTA TTA TTA CTA TTA TT- TCT- TTA TTT TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * *
28781763 TTA -TA TTA -TA TTA -TA TTA TTA GTTT TTA ATA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
28781806 GTTTTAGCTT
Statistics
Matches: 125, Mismatches: 37, Indels: 28
0.66 0.19 0.15
Matches are distributed among these distances:
2 14 0.11
3 97 0.78
4 13 0.10
5 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:28781763 original size:5 final size:5
Alignment explanation
Indices: 28781753--28781781 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28781743 TTCTTTATTT
28781753 TTATA TTATA TTATA TTATA TTATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTAT
28781782 TAGTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:28781811 original size:21 final size:21
Alignment explanation
Indices: 28781770--28781810 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
28781760 ATATTATATT
*
28781770 ATATTATATTATTAGTTTTTA
1 ATATTATAGTATTAGTTTTTA
28781791 ATATTATTAGTATTAGTTTT
1 ATATTA-TAGTATTAGTTTT
28781811 AGCTTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
ATATTATAGTATTAGTTTTTA
Found at i:28781990 original size:38 final size:37
Alignment explanation
Indices: 28781929--28782035 Score: 126
Period size: 37 Copynumber: 2.9 Consensus size: 37
28781919 GTGTACATTC
* *
28781929 TTTTAATAGATATCATGTATATATTTTTATATATTAT-
1 TTTTAATATATATTATGTATATATTTTTA-ATATTATA
*
28781966 TTTTAACTTTATATTATGTATATATTTTTAATATTATA
1 TTTTAA-TATATATTATGTATATATTTTTAATATTATA
* * * *
28782004 TTTTTATATATATTAGGTACATATTTTCAATA
1 TTTTAATATATATTATGTATATATTTTTAATA
28782036 CTATTAATGC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 35 0.58
38 25 0.42
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.57
Consensus pattern (37 bp):
TTTTAATATATATTATGTATATATTTTTAATATTATA
Found at i:28781996 original size:25 final size:24
Alignment explanation
Indices: 28781958--28782014 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
28781948 TATATTTTTA
28781958 TATATTATTTTTAACT-TTATATTATG
1 TATA-TATTTTTAA-TATTATATT-TG
*
28781984 TATATATTTTTAATATTATATTTT
1 TATATATTTTTAATATTATATTTG
28782008 TATATAT
1 TATATAT
28782015 ATTAGGTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 9 0.31
25 16 0.55
26 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TATATATTTTTAATATTATATTTG
Found at i:28782005 original size:14 final size:12
Alignment explanation
Indices: 28781946--28782017 Score: 65
Period size: 13 Copynumber: 5.7 Consensus size: 12
28781936 AGATATCATG
28781946 TATATATTTTTA
1 TATATATTTTTA
28781958 TATATTATTTTTAA
1 TATA-TATTTTT-A
* *
28781972 CTTTATATTATGTA
1 -TATATATT-TTTA
*
28781986 TATAT-TTTTAA
1 TATATATTTTTA
28781997 TATTATATTTTTA
1 TA-TATATTTTTA
28782010 TATATATT
1 TATATATT
28782018 AGGTACATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 4 0.08
12 15 0.31
13 18 0.38
14 6 0.12
15 5 0.10
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (12 bp):
TATATATTTTTA
Found at i:28782209 original size:21 final size:20
Alignment explanation
Indices: 28782176--28782214 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28782166 ATTCATGATT
*
28782176 TTATTTCGTGTTTAATATTA
1 TTATTTCATGTTTAATATTA
28782196 TTATTATCATGTTTAATAT
1 TTATT-TCATGTTTAATAT
28782215 CATGTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (20 bp):
TTATTTCATGTTTAATATTA
Found at i:28785918 original size:22 final size:22
Alignment explanation
Indices: 28785893--28785937 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
28785883 ATTCATGGCT
28785893 AACATTCATTCGTCATTTATTC
1 AACATTCATTCGTCATTTATTC
* *
28785915 AACATTCGTTTGTCATTTATTC
1 AACATTCATTCGTCATTTATTC
28785937 A
1 A
28785938 TTCATCCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (22 bp):
AACATTCATTCGTCATTTATTC
Found at i:28794520 original size:163 final size:162
Alignment explanation
Indices: 28794209--28794539 Score: 450
Period size: 163 Copynumber: 2.0 Consensus size: 162
28794199 GTTTTGGTAC
* * * *
28794209 TCTGATGTTTTAATTTTTGTTTTTTAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGG
1 TCTGTTGTTTAAATTTCTGTTTTTAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGG
* * ** * *
28794274 TCACATGCCGAGGTATTTTCAATTCCTGTTTTTTAAAAGTCAACTCGTATTGCGAGAGGTGAGTT
66 TCACATGCCGAGGAATTTCCAATTCCTGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTT
* * * *
28794339 GAGCTTCAAGTTACACTGAGTTATTTTCAATT
131 GAGCCTCAAGTCACACTGAGGTATTCTCAATT
* *
28794371 TCTGTTGTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGTGTTGAGCCTC-G
1 TCTGTTGTTTAAATTTCTGTTTTT-AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTG
28794435 GTTCACATGCCGAGGAATTTCCAAATT-CTGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGA
65 G-TCACATGCCGAGGAATTTCC-AATTCCTGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGA
* *
28794499 GTTGATCCTCAGGTCACACTGAGGTATTCTCAATT
128 GTTGAGCCTCAAGTCACACTGAGGTATTCTCAATT
*
28794534 TATGTT
1 TCTGTT
28794540 TCAAAAACAT
Statistics
Matches: 147, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
162 23 0.16
163 120 0.82
164 4 0.03
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (162 bp):
TCTGTTGTTTAAATTTCTGTTTTTAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGG
TCACATGCCGAGGAATTTCCAATTCCTGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTT
GAGCCTCAAGTCACACTGAGGTATTCTCAATT
Found at i:28794572 original size:73 final size:72
Alignment explanation
Indices: 28794396--28794764 Score: 330
Period size: 73 Copynumber: 4.9 Consensus size: 72
28794386 TCTGTTTTTC
* * *
28794396 AAAAATCAACTCATATTGCGAGAGGTGTGTTGAGCCTCGGTTCACATGCCGAGGAATTTCCAAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGG-TCACA--CCGAGGTATTT-CAAAT
* *
28794461 TCTGTTTTC-C
62 TATGTTTTCAA
* * *
28794471 AAAAATCAACTCATATTGCGAGAGGTGAGTTGATCCTCAGGTCACACTGAGGTATTCTCAATTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-GGTCACACCGAGGTATT-TCAAATTA
28794536 TG-TTTCAA
64 TGTTTTCAA
* * * ** *
28794544 AAACATTAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCCGAGGTATTTCTAAATTCT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGTCACACCGAGGTATTTC-AAATTAT
28794609 GTTTTCAAACTA
65 GTTTTC--A--A
* *
28794621 TGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTATTC
1 --------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-GGTCACACCGAGGTATT-
*
28794686 TCAATTTATG-TTTCAA
56 TCAAATTATGTTTTCAA
* * **
28794702 AAAAATCAACTCATATTACGAGAGGTGAGTTGAACCTCGGACATGCCGAGGTATTTTCAAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGTCACACCGAGGTA-TTTCAAATT
28794765 CTATTTTTCA
Statistics
Matches: 242, Mismatches: 32, Indels: 43
0.76 0.10 0.14
Matches are distributed among these distances:
71 2 0.01
72 40 0.17
73 92 0.38
74 1 0.00
75 42 0.17
76 2 0.01
77 1 0.00
81 1 0.00
83 1 0.00
85 39 0.16
86 19 0.08
87 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGTCACACCGAGGTATTTCAAATTATG
TTTTCAA
Found at i:28794655 original size:158 final size:157
Alignment explanation
Indices: 28794463--28795018 Score: 740
Period size: 158 Copynumber: 3.5 Consensus size: 157
28794453 TTCCAAATTC
*
28794463 TGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGATCCTCAGGTCACACTGAGGTATTC
1 TGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTATTC
*
28794528 TCAATTTATGTTTCAAAAACATTAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCCGA
66 TCAATTTATGTTTCAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCCGA
**
28794593 GGTA-TTTCTAAATTCTGTTTTCAAACTA
130 GGTATTTTC-AAATTCTGTTTTCAATTTA
28794621 TGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTATTC
1 TGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTATTC
*
28794686 TCAATTTATGTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAACCTCGGACATGCCGA
66 TCAATTTATGTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCCGA
*
28794751 GGTATTTTCAAATTCTATTTTTCAATTTA
130 GGTATTTTCAAATTCT-GTTTTCAATTTA
* *
28794780 TGTTTTCCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCCGAGG
1 TGTTTTCC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCACA--CTGAGG
* * * * **
28794844 TATTTTCAATTTCTGTTCGTC-AAAAATCAACTCATATTGCTAGAAGTGAGTTGAGTCTCGGGCC
61 TATTCTCAATTTATGTT--TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-GG--
* * *
28794908 ACATGCCGAGGTCTTTTCAAATTCTGTTTTTAATTTC
121 ACATGCCGAGGTATTTTCAAATTCTGTTTTCAATTTA
* * * * *
28794945 TGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCACGGGACACGCTGAGGTAT
1 TGTTT-TC-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTAT
*
28795010 TTTCAATTT
64 TCTCAATTT
28795019 CTGCTTTTCA
Statistics
Matches: 357, Mismatches: 25, Indels: 27
0.87 0.06 0.07
Matches are distributed among these distances:
158 132 0.37
159 26 0.07
160 2 0.01
161 42 0.12
163 70 0.20
164 2 0.01
165 55 0.15
166 28 0.08
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (157 bp):
TGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTATTC
TCAATTTATGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCCGAG
GTATTTTCAAATTCTGTTTTCAATTTA
Found at i:28794700 original size:85 final size:82
Alignment explanation
Indices: 28794534--28795152 Score: 302
Period size: 88 Copynumber: 7.5 Consensus size: 82
28794524 ATTCTCAATT
* *
28794534 TATGTTTCAAAAACATTAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCCGAGGTATT
1 TATGTTTCCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCCGAGGTATT
*
28794599 TCTAAA-TTCTGTTTTCAAA
65 TC-AAATTTATG-TTTCAAA
* * ** *
28794618 CTATGTTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACTGAGGTA
1 -TATG-TTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-GGACATGCCGAGGTA
28794683 TTCTC-AATTTATGTTTC--A
63 TT-TCAAATTTATGTTTCAAA
*
28794701 -A-------AAAAATCAACTCATATTACGAGAGGTGAGTTGAACCTCGGACATGCCGAGGTATTT
1 TATGTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCCGAGGTA-TT
* *
28794758 TCAAATTCTATTTTTCAATT
65 TCAAATT-TATGTTTCAA-A
* * *
28794778 TATGTTTTCCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCCGAG
1 TATG-TTTCC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGG---ACATGCCGAG
*
28794843 GTATTTTC-AATTTCTG-TTC---
60 GTA-TTTCAAATTTATGTTTCAAA
* * **
28794862 ---G--T-CAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGTCTCGGGCCACATGCCGAGGTC
1 TATGTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-GG--ACATGCCGAGGT-
* * * *
28794921 TTTTCAAA-TTCTGTTTTTAATT
62 ATTTCAAATTTATG-TTTCAA-A
* * * * * *
28794943 TCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCACGGGACACGCTGAGGT
1 TATG-TT-TC-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-GGACATGCCGAGGT
* *
28795008 ATTTTC-AATTTCTGCTTTTCAATTTC
62 A-TTTCAAATTTATG--TTTCAA---A
* * * *
28795034 TACT-TTTCAAAAAATCAACTCATATTTCGACAGGTGAGTT-AAGCCTCGGGTCACACGCCGAGG
1 TA-TGTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAA-CCTC-GG--ACATGCCGAGG
*
28795097 TATTTC-CA---A--TTTC-AA
61 TATTTCAAATTTATGTTTCAAA
*
28795112 T-T-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 TATGTTTC-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
28795153 GTCCTAGGTC
Statistics
Matches: 430, Mismatches: 51, Indels: 113
0.72 0.09 0.19
Matches are distributed among these distances:
72 13 0.03
73 42 0.10
74 7 0.02
75 55 0.13
76 9 0.02
77 33 0.08
78 4 0.01
81 3 0.01
82 4 0.01
83 1 0.00
84 1 0.00
85 42 0.10
86 25 0.06
87 5 0.01
88 96 0.22
89 15 0.03
90 55 0.13
91 19 0.04
92 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (82 bp):
TATGTTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCCGAGGTATTT
CAAATTTATGTTTCAAA
Found at i:28794894 original size:75 final size:75
Alignment explanation
Indices: 28794790--28794935 Score: 213
Period size: 75 Copynumber: 1.9 Consensus size: 75
28794780 TGTTTTCCAA
* * *
28794790 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCCGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGC-CACACGCCGAGGTATTTTCAAA
28794854 TTCTGTTCGTC
65 TTCTGTTCGTC
* * * *
28794865 AAAAATCAACTCATATTGCTAGAAGTGAGTTGAGTCTCGGGCCACATGCCGAGGTCTTTTCAAAT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCCACACGCCGAGGTATTTTCAAAT
28794930 TCTGTT
66 TCTGTT
28794936 TTTAATTTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
75 60 0.95
76 3 0.05
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCCACACGCCGAGGTATTTTCAAAT
TCTGTTCGTC
Found at i:28795014 original size:88 final size:89
Alignment explanation
Indices: 28794846--28795101 Score: 322
Period size: 88 Copynumber: 2.9 Consensus size: 89
28794836 CGCCGAGGTA
* * * *
28794846 TTTTCAATTTCTGTTCGTC-AAAAATCAACTCATATTGCTAGAAGTGAGTTGAGTCTCGGGCCAC
1 TTTTCAATTTCTGTTTGTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CAC
* *
28794910 ATGCCGAGGTCTTTTCAAATTCTG-
65 ACGCCGAGGTATTTTCAAATTCTGC
* *
28794934 TTTTTAATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCACGGG-AC
1 TTTTCAATTTCTGTTTGTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCAC
* *
28794998 ACGCTGAGGTATTTTCAATTTCTGC
65 ACGCCGAGGTATTTTCAAATTCTGC
* * * *
28795023 TTTTCAATTTCTACTTT-TCAAAAAATCAACTCATATTTCGACAGGTGAGTTAAGCCTCGGGTCA
1 TTTTCAATTTCT-GTTTGTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CA
28795087 CACGCCGAGGTATTT
64 CACGCCGAGGTATTT
28795102 CCAATTTCAA
Statistics
Matches: 145, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
88 77 0.53
89 13 0.09
90 55 0.38
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (89 bp):
TTTTCAATTTCTGTTTGTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACA
CGCCGAGGTATTTTCAAATTCTGC
Found at i:28795028 original size:14 final size:14
Alignment explanation
Indices: 28795009--28795043 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28794999 CGCTGAGGTA
*
28795009 TTTTCAATTTCTGC
1 TTTTCAATTTCTAC
28795023 TTTTCAATTTCTAC
1 TTTTCAATTTCTAC
28795037 TTTTCAA
1 TTTTCAA
28795044 AAAATCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:28795048 original size:253 final size:254
Alignment explanation
Indices: 28794698--28795155 Score: 670
Period size: 253 Copynumber: 1.8 Consensus size: 254
28794688 AATTTATGTT
* *
28794698 TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAACCTCGGACATGCCGAGGTATTTTCAAA
1 TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAACCACGGACACGCCGAGGTATTTTCAAA
* * * * *
28794763 TTCTATTTTTCAATTTATGTTTTCCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
66 TTCTACTTTTCAATTTATCTTTTCCAAAAAAATCAACTCATATTGCGACAGGTGAGTTAAGCCTC
* ** *
28794828 GGCTCACACGCCGAGGTATTTTCAATTTCTGTTCGTC-AAAAATCAACTCATATTGCTAGAAGTG
131 GGCTCACACGCCGAGGTATTTCCAATTTCAATTCGTCAAAAAATCAACTCATATTGCGAGAAGTG
28794892 AGTTGAGTCTCGGGCCACATGCCGAGGTCTTTTCAAATTCTGTTTTTAATTTCTGTTTG
196 AGTTGAGTCTCGGGCCACATGCCGAGGTCTTTTCAAATTCTGTTTTTAATTTCTGTTTG
* * *
28794951 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCACGGGACACGCTGAGGTATTTTCAA
1 TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAACCAC-GGACACGCCGAGGTATTTTCAA
* * * *
28795016 TTTCTGCTTTTCAATTTCTACTTTT-C-AAAAAATCAACTCATATTTCGACAGGTGAGTTAAGCC
65 ATTCTACTTTTCAATTTAT-CTTTTCCAAAAAAATCAACTCATATTGCGACAGGTGAGTTAAGCC
* ** *
28795079 TCGGGTCACACGCCGAGGTATTTCCAATTTCAATTTTTCAAAAAAATCAACTCATATTGCGAGAG
129 TCGGCTCACACGCCGAGGTATTTCCAATTTCAATTCGTC-AAAAAATCAACTCATATTGCGAGAA
28795144 GTGAGTTGAGTC
193 GTGAGTTGAGTC
28795156 CTAGGTCACA
Statistics
Matches: 179, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
253 105 0.59
254 36 0.20
255 38 0.21
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (254 bp):
TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAACCACGGACACGCCGAGGTATTTTCAAA
TTCTACTTTTCAATTTATCTTTTCCAAAAAAATCAACTCATATTGCGACAGGTGAGTTAAGCCTC
GGCTCACACGCCGAGGTATTTCCAATTTCAATTCGTCAAAAAATCAACTCATATTGCGAGAAGTG
AGTTGAGTCTCGGGCCACATGCCGAGGTCTTTTCAAATTCTGTTTTTAATTTCTGTTTG
Found at i:28795770 original size:22 final size:21
Alignment explanation
Indices: 28795730--28795773 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
28795720 CCCAAAACTA
* *
28795730 ATTACCCTTAACCCGTAACCC
1 ATTACACTTAACCCATAACCC
28795751 ATTACACTTAAACCCATAACCC
1 ATTACACTT-AACCCATAACCC
28795773 A
1 A
28795774 ATACCTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.36, C:0.39, G:0.02, T:0.23
Consensus pattern (21 bp):
ATTACACTTAACCCATAACCC
Found at i:28797061 original size:17 final size:18
Alignment explanation
Indices: 28797041--28797076 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28797031 AACATTATTA
28797041 ATTATTATT-TTTTGAAT
1 ATTATTATTATTTTGAAT
*
28797058 ATTATTATTATTTTTAAT
1 ATTATTATTATTTTGAAT
28797076 A
1 A
28797077 CATGCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTATTATTATTTTGAAT
Found at i:28797141 original size:14 final size:12
Alignment explanation
Indices: 28797120--28797153 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
28797110 AGATATCATG
28797120 TATATATTTTTAA
1 TATATATTTTT-A
28797133 TATTATATTTTTA
1 TA-TATATTTTTA
28797146 TATATATT
1 TATATATT
28797154 AGGTACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 5 0.25
14 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATATTTTTA
Found at i:28797337 original size:21 final size:20
Alignment explanation
Indices: 28797304--28797342 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28797294 ATTCATGATT
*
28797304 TTATTTCGTGTTTAATATTA
1 TTATTTCATGTTTAATATTA
28797324 TTATTATCATGTTTAATAT
1 TTATT-TCATGTTTAATAT
28797343 CATGTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (20 bp):
TTATTTCATGTTTAATATTA
Found at i:28801992 original size:23 final size:23
Alignment explanation
Indices: 28801966--28802297 Score: 386
Period size: 23 Copynumber: 14.5 Consensus size: 23
28801956 CAAAGTGCCA
* *
28801966 CACTGTAATATAGCCGAAGCTAT
1 CACTGTAATGTAGCCGAAGCTAC
* *
28801989 CACTGTAACGTAGCCGAAGCTAT
1 CACTGTAATGTAGCCGAAGCTAC
* *
28802012 CACTGTAA-CTAGCCAAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
* *
28802034 CACTGTATTGTAGCCAAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28802057 CACTG-AGATGTAGCTGAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
*
28802080 CACTGTATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28802103 CACTG-AGATGTAGCCAAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
* * *
28802126 CATTGTATTGTAGCTGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
28802149 CACTG-AGATGTAGCCGAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
* *
28802172 CACTATATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28802195 CACTGTATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28802218 CACTGTATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28802241 CACTG-AGATGTAGCCAAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
* * *
28802264 CACTATATTGTAGCTGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28802287 CACTGAAATGT
1 CACTGTAATGT
28802298 TGCCTATATA
Statistics
Matches: 267, Mismatches: 33, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
22 22 0.08
23 241 0.90
24 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGTAATGTAGCCGAAGCTAC
Found at i:28802089 original size:46 final size:46
Alignment explanation
Indices: 28801976--28802297 Score: 452
Period size: 46 Copynumber: 7.0 Consensus size: 46
28801966 CACTGTAATA
* ** * *
28801976 TAGCCGAAGCTATCACTGTAACGTAGCCGAAGCTATCACTGTA-A-C
1 TAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTG-AGATG
* *
28802021 TAGCCAAAGCTACCACTGTATTGTAGCCAAAGCTACCACTGAGATG
1 TAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGAGATG
*
28802067 TAGCTGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGAGATG
1 TAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGAGATG
* * *
28802113 TAGCCAAAGCTACCATTGTATTGTAGCTGAAGCTACCACTGAGATG
1 TAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGAGATG
* *
28802159 TAGCCGAAGCTACCACTATATTGTAGCCGAAGCTACCACTGTA-TTG
1 TAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTG-AGATG
28802205 TAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGAGATG
1 TAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGAGATG
* * * *
28802251 TAGCCAAAGCTACCACTATATTGTAGCTGAAGCTACCACTGAAATG
1 TAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGAGATG
28802297 T
1 T
28802298 TGCCTATATA
Statistics
Matches: 248, Mismatches: 25, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
44 1 0.00
45 37 0.15
46 209 0.84
47 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (46 bp):
TAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGAGATG
Found at i:28803724 original size:18 final size:19
Alignment explanation
Indices: 28803680--28803725 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
28803670 ATATAATAAC
28803680 AAAAAT-TATAAAAGAATA
1 AAAAATATATAAAAGAATA
* * *
28803698 ATAATTATATATAA-AATA
1 AAAAATATATAAAAGAATA
28803716 AAAAATATAT
1 AAAAATATAT
28803726 TGGTTTAGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATATATAAAAGAATA
Found at i:28803836 original size:21 final size:23
Alignment explanation
Indices: 28803778--28803836 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
28803768 AATTTATATT
*
28803778 TATA-ATAAAATAA-TTATATAA
1 TATATATAAAATAAGTTATAGAA
28803799 TATATATAAATATAAGTT-TAGAA
1 TATATATAAA-ATAAGTTATAGAA
28803822 TA-ATATAAAATAAGT
1 TATATATAAAATAAGT
28803837 AATTAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 10 0.29
22 12 0.35
23 10 0.29
24 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (23 bp):
TATATATAAAATAAGTTATAGAA
Found at i:28803977 original size:3 final size:3
Alignment explanation
Indices: 28803969--28804161 Score: 70
Period size: 3 Copynumber: 64.0 Consensus size: 3
28803959 GTTAAAACCT
*
28803969 ATA ATA ATA ATA ATA ATA ATA TATA GATA A-A A-A ATA TATA ATA GT-
1 ATA ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA -ATA ATA ATA
* *
28804014 ATA AAA ATA AT- ATA AT- ATA A-A ATA ATT ATA AT- ATA AT- ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * *
28804055 A-A GTA TATA TGTA AAA ATA ATA TATA ATA TATA AAA ATA ATTA ATAA
1 ATA ATA -ATA -ATA ATA ATA ATA -ATA ATA -ATA ATA ATA A-TA AT-A
* * *
28804102 ATA TATT ATA CA-A GTA AAA AT- ATA ATA ATA ATA TATAA ATA ATA AT-
1 ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA -AT-A ATA ATA ATA
*
28804148 GTA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA
28804162 TTTCGTGAAA
Statistics
Matches: 143, Mismatches: 23, Indels: 48
0.67 0.11 0.22
Matches are distributed among these distances:
2 21 0.15
3 87 0.61
4 34 0.24
5 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28804022 original size:11 final size:11
Alignment explanation
Indices: 28803968--28804145 Score: 53
Period size: 11 Copynumber: 15.2 Consensus size: 11
28803958 AGTTAAAACC
*
28803968 TATAATAATAA
1 TATAAAAATAA
*
28803979 TAATAATAAT-A
1 T-ATAAAAATAA
*
28803990 TATAGATAAAAAA
1 TATA-A-AAATAA
* *
28804003 TAT-ATAATAG
1 TATAAAAATAA
28804013 TATAAAAATAA
1 TATAAAAATAA
28804024 TATAATATAA-AA
1 TATAA-A-AATAA
*
28804036 TAATTATAATATAA
1 T-A-TA-AAAATAA
*
28804050 TATGAAAGTATATA
1 TAT-AAA-AATA-A
*
28804064 TGTAAAAATAA
1 TATAAAAATAA
*
28804075 TAT-ATAAT-A
1 TATAAAAATAA
28804084 TATAAAAATAA
1 TATAAAAATAA
28804095 T-TAATAAATATA
1 TATAA-AAATA-A
*
28804107 TTATACAAGTAAAAA
1 -TATA-AA--AATAA
*
28804122 TATAATAATAA
1 TATAAAAATAA
*
28804133 TATATAAATAA
1 TATAAAAATAA
28804144 TA
1 TA
28804146 ATGTAAAATA
Statistics
Matches: 126, Mismatches: 18, Indels: 46
0.66 0.09 0.24
Matches are distributed among these distances:
9 4 0.03
10 20 0.16
11 40 0.32
12 21 0.17
13 19 0.15
14 16 0.13
15 3 0.02
16 3 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:28804025 original size:14 final size:15
Alignment explanation
Indices: 28803969--28804049 Score: 65
Period size: 16 Copynumber: 4.9 Consensus size: 15
28803959 GTTAAAACCT
28803969 ATAATAATAATAATAATA
1 ATAAT-ATAAT-ATAA-A
*
28803987 AT-ATATAGATAAAAA
1 ATAATATA-ATATAAA
*
28804002 ATATATAATAGTATAAAA
1 ATA-AT-ATAATAT-AAA
28804020 ATAATATAATATAAA
1 ATAATATAATATAAA
28804035 ATAATTATAATATAA
1 ATAA-TATAATATAA
28804050 TATGAAAGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
15 10 0.19
16 22 0.42
17 10 0.19
18 11 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
ATAATATAATATAAA
Found at i:28804117 original size:58 final size:58
Alignment explanation
Indices: 28804020--28804157 Score: 156
Period size: 58 Copynumber: 2.3 Consensus size: 58
28804010 TAGTATAAAA
* * *
28804020 ATAATATAATATAAAATAATTATAATATAATATGAAAGTATATATGTAAAAATAATAT
1 ATAATATAATATAAAATAATTATAATATAATATGAAAGTAAAAATATAAAAATAATAT
* *
28804078 ATAATAT-ATA-AAAATAATTAATAAATATATTAT-ACAAGTAAAAATATAATAATAATAT
1 ATAATATAATATAAAATAATT-AT-AATATAATATGA-AAGTAAAAATATAAAAATAATAT
*
28804136 ATAAATAATAATGTAAAATAAT
1 AT-AAT-ATAATATAAAATAAT
28804158 AATATTTCGT
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
56 9 0.13
57 6 0.09
58 37 0.55
59 3 0.04
60 2 0.03
61 2 0.03
62 8 0.12
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.35
Consensus pattern (58 bp):
ATAATATAATATAAAATAATTATAATATAATATGAAAGTAAAAATATAAAAATAATAT
Found at i:28804158 original size:58 final size:58
Alignment explanation
Indices: 28803998--28804159 Score: 145
Period size: 58 Copynumber: 2.7 Consensus size: 58
28803988 TATATAGATA
* *
28803998 AAAAATAT-ATAATAGTATAAAAATAATATAATATAAAATAATTATAATATAATATGAAAGT
1 AAAAATATAATAATAATATATAAAT-ATATAAT-TAAAATAA-TA-AATATAATATGAAAGT
* * * * * *
28804059 ATATATGTAAAAATAATATAT-AATATATAA-AAATAATTAATAAATATATTAT-ACAAGT
1 AAAAATATAATAATAATATATAAATATATAATTAA-AA-TAATAAATATAATATGA-AAGT
28804117 AAAAATATAATAATAATATATAAATA-ATAATGTAAAATAATAA
1 AAAAATATAATAATAATATATAAATATATAAT-TAAAATAATAA
28804160 TATTTCGTGA
Statistics
Matches: 81, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
57 1 0.01
58 42 0.52
59 10 0.12
60 11 0.14
61 8 0.10
62 9 0.11
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAAATATAATAATAATATATAAATATATAATTAAAATAATAAATATAATATGAAAGT
Found at i:28804204 original size:9 final size:8
Alignment explanation
Indices: 28803972--28804242 Score: 69
Period size: 7 Copynumber: 35.1 Consensus size: 8
28803962 AAAACCTATA
28803972 ATAATAAT
1 ATAATAAT
28803980 AATAATAAT
1 -ATAATAAT
28803989 AT-ATAGAT
1 ATAATA-AT
*
28803997 A-AAAAAT
1 ATAATAAT
28804004 AT-ATAAT
1 ATAATAAT
28804011 AGT-ATAA-
1 A-TAATAAT
28804018 A-AATAAT
1 ATAATAAT
28804025 ATAAT-AT
1 ATAATAAT
*
28804032 AAAATAAT
1 ATAATAAT
28804040 -T-ATAAT
1 ATAATAAT
28804046 ATAAT-AT
1 ATAATAAT
28804053 GA-AAGTATAT
1 -ATAA-TA-AT
28804063 ATGTAA-AA-
1 A--TAATAAT
28804071 ATAAT-AT
1 ATAATAAT
28804078 ATAAT-AT
1 ATAATAAT
28804085 ATAA-AA-
1 ATAATAAT
28804091 ATAATTAAT
1 ATAA-TAAT
28804100 A-AAT-AT
1 ATAATAAT
*
28804106 ATTATACA-
1 ATAATA-AT
*
28804114 AGTAAAAAT
1 A-TAATAAT
28804123 ATAATAAT
1 ATAATAAT
28804131 AATATATAA-
1 -ATA-ATAAT
28804140 ATAATAAT
1 ATAATAAT
*
28804148 GTAA-AAT
1 ATAATAAT
28804155 AATAAT-AT
1 -ATAATAAT
* ** *
28804163 TTCGTGAAA
1 ATAAT-AAT
28804172 AGTAAT-AT
1 A-TAATAAT
28804180 ATAATAA-
1 ATAATAAT
28804187 ATAATAAT
1 ATAATAAT
28804195 ATAGATAAT
1 ATA-ATAAT
28804204 AT-ATAAT
1 ATAATAAT
28804211 GA-AATAAT
1 -ATAATAAT
28804219 -TATATAAT
1 ATA-ATAAT
*
28804227 GT-ATAAT
1 ATAATAAT
*
28804234 ATAAAAAT
1 ATAATAAT
28804242 A
1 A
28804243 AGGTTAAAAA
Statistics
Matches: 197, Mismatches: 20, Indels: 91
0.64 0.06 0.30
Matches are distributed among these distances:
6 20 0.10
7 71 0.36
8 67 0.34
9 28 0.14
10 9 0.05
12 2 0.01
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (8 bp):
ATAATAAT
Found at i:28804225 original size:23 final size:24
Alignment explanation
Indices: 28804175--28804302 Score: 74
Period size: 26 Copynumber: 5.3 Consensus size: 24
28804165 CGTGAAAAGT
28804175 AATATATAATAAATAATAATATAGAT
1 AATATATAATAAATAAT-ATATA-AT
28804201 AATATATAATGAAATAATTATATAAT
1 AATATATAAT-AAATAA-TATATAAT
* **
28804227 GTATAATATAA-AAATAAGGT-TAA-
1 -AAT-ATATAATAAATAATATATAAT
*
28804250 AA-ATAAAATAAATAATA-ATAAT
1 AATATATAATAAATAATATATAAT
* *
28804272 -TTATAT-ATATAATAATAGA-AAT
1 AATATATAATA-AATAATATATAAT
28804294 AAATATATA
1 -AATATATA
28804303 GGGTTAGATT
Statistics
Matches: 79, Mismatches: 10, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
20 5 0.06
21 12 0.15
22 14 0.18
23 1 0.01
24 8 0.10
25 1 0.01
26 18 0.23
27 13 0.16
28 7 0.09
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (24 bp):
AATATATAATAAATAATATATAAT
Found at i:28804236 original size:30 final size:26
Alignment explanation
Indices: 28803971--28804147 Score: 58
Period size: 25 Copynumber: 7.3 Consensus size: 26
28803961 TAAAACCTAT
28803971 AATAATAATAATA-ATAATATATAGATA
1 AATAATAAT-ATAGATAATATATA-ATA
* * *
28803998 AAAAAT-ATATA-ATAGTATA-AAAA
1 AATAATAATATAGATAATATATAATA
*
28804021 TAAT-ATAATATA-A-AATA-ATTAT-
1 -AATAATAATATAGATAATATATAATA
*
28804043 AAT-ATAATAT-GA-AAGTATATATGTA
1 AATAATAATATAGATAA-TATATA-ATA
28804068 AA-AATAATAT--ATAATATATAA-A
1 AATAATAATATAGATAATATATAATA
28804090 AATAATTAATA-A-AT-ATAT-T-ATA
1 AATAA-TAATATAGATAATATATAATA
*
28804112 CAAGTAAAAATATA-ATAATA-ATATATA
1 -AA-TAATAATATAGATAATATATA-ATA
28804139 AATAATAAT
1 AATAATAAT
28804148 GTAAAATAAT
Statistics
Matches: 117, Mismatches: 12, Indels: 44
0.68 0.07 0.25
Matches are distributed among these distances:
21 14 0.12
22 8 0.07
23 22 0.19
24 30 0.26
25 31 0.26
26 4 0.03
27 8 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (26 bp):
AATAATAATATAGATAATATATAATA
Found at i:28808763 original size:51 final size:51
Alignment explanation
Indices: 28808625--28808874 Score: 209
Period size: 52 Copynumber: 4.8 Consensus size: 51
28808615 ATAATGTGTT
* * * **
28808625 TAAAAAAAACATATTTTTTTGAGGGTGGAGGGGGAGAGATGGGTAGCACCAGTA
1 TAAAAAAAA-TTATTTTTTT--TGGTGGAGGGAGAGAGATGGGCGGCACCAGTA
* ** * * *
28808679 TAAAAAATTAGAATTTTTTTTGGTGGAGAGAGAGAGATGGGTGGCACTAGTA
1 TAAAAAA-AATTATTTTTTTTGGTGGAGGGAGAGAGATGGGCGGCACCAGTA
* * * *
28808731 TAAAAAAAATTATTTTTTTTGGTGAAGGGAGAGAGATAGGCGTCTCCAGTA
1 TAAAAAAAATTATTTTTTTTGGTGGAGGGAGAGAGATGGGCGGCACCAGTA
* * * **
28808782 TAAAAAAAATTACTTTTTTTGGGTGGAGGGAGAGAGTTAGGCGGCATTAGTA
1 TAAAAAAAATTA-TTTTTTTTGGTGGAGGGAGAGAGATGGGCGGCACCAGTA
* *
28808834 TAAAAAAGTAA-TATTATTTTAT--TGGAAGGAGAGAGATGGGC
1 TAAAAAA--AATTATT-TTTTTTGGTGGAGGGAGAGAGATGGGC
28808875 AATATCAGTA
Statistics
Matches: 161, Mismatches: 30, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
51 62 0.39
52 75 0.47
53 6 0.04
54 17 0.11
55 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.29
Consensus pattern (51 bp):
TAAAAAAAATTATTTTTTTTGGTGGAGGGAGAGAGATGGGCGGCACCAGTA
Found at i:28808834 original size:52 final size:51
Alignment explanation
Indices: 28808691--28808840 Score: 194
Period size: 51 Copynumber: 2.9 Consensus size: 51
28808681 AAAAATTAGA
* * * *
28808691 ATTTTTTTTGGTGGAGAGAGAGAGATGGGTGGCACTAGTATAAAAAAAATT
1 ATTTTTTTTGGTGGAGGGAGAGAGATAGGCGGCATTAGTATAAAAAAAATT
* * *
28808742 ATTTTTTTTGGTGAAGGGAGAGAGATAGGCGTC-TCCAGTATAAAAAAAATT
1 ATTTTTTTTGGTGGAGGGAGAGAGATAGGCGGCAT-TAGTATAAAAAAAATT
* *
28808793 ACTTTTTTTGGGTGGAGGGAGAGAGTTAGGCGGCATTAGTATAAAAAA
1 A-TTTTTTTTGGTGGAGGGAGAGAGATAGGCGGCATTAGTATAAAAAA
28808841 GTAATATTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
51 44 0.52
52 39 0.46
53 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (51 bp):
ATTTTTTTTGGTGGAGGGAGAGAGATAGGCGGCATTAGTATAAAAAAAATT
Found at i:28808884 original size:103 final size:103
Alignment explanation
Indices: 28808692--28808885 Score: 227
Period size: 103 Copynumber: 1.9 Consensus size: 103
28808682 AAAATTAGAA
* * *
28808692 TTTTTTTTGGTGGAGAGAGAGAGATGGGTGGCACTAGTATAAAAAAAATTATTTTTTTTGGTGAA
1 TTTTTTTGGGTGGAGAGAGAGAGATAGGCGGCACTAGTATAAAAAAAATTATTTTTTTTGGTGAA
* *
28808757 GGGAGAGAGATAGGCGTCTCCAGTATAAAAAAAATTAC
66 GGGAGAGAGATAGGCATATCCAGTATAAAAAAAATTAC
* * *
28808795 TTTTTTTGGGTGGAGGGAGAGAGTTAGGCGGCATTAGTATAAAAAAGTAA-TATTATTTTATT-G
1 TTTTTTTGGGTGGAGAGAGAGAGATAGGCGGCACTAGTATAAAAAA--AATTATT-TTTT-TTGG
*
28808858 -GAA-GGAGAGAGATGGGCAATAT-CAGTAT
62 TGAAGGGAGAGAGATAGGC-ATATCCAGTAT
28808886 TTTCTAGTGC
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
103 59 0.77
104 9 0.12
105 7 0.09
106 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (103 bp):
TTTTTTTGGGTGGAGAGAGAGAGATAGGCGGCACTAGTATAAAAAAAATTATTTTTTTTGGTGAA
GGGAGAGAGATAGGCATATCCAGTATAAAAAAAATTAC
Found at i:28811085 original size:44 final size:44
Alignment explanation
Indices: 28811022--28811109 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
28811012 ACTCGGTCTA
*
28811022 CACTTAACCTTTTCACCTAAAATGAATTTTCTTTATCTAATTAG
1 CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
28811066 CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
1 CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
28811110 TCATCTATGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (44 bp):
CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
Found at i:28817045 original size:39 final size:39
Alignment explanation
Indices: 28816987--28817063 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
28816977 ATGCAGAACA
*
28816987 CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
1 CATATTAATGATGTGCAAACTATGACATAAGTAAAGACT
*
28817026 CATATTAATGATGTTCAAACTATGACATAAGTAAAGAC
1 CATATTAATGATGTGCAAACTATGACATAAGTAAAGAC
28817064 ACAAACTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (39 bp):
CATATTAATGATGTGCAAACTATGACATAAGTAAAGACT
Found at i:28817081 original size:9 final size:9
Alignment explanation
Indices: 28817067--28817092 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28817057 TAAAGACACA
28817067 AACTAAAAT
1 AACTAAAAT
28817076 AACTAAAAT
1 AACTAAAAT
28817085 AACTAAAA
1 AACTAAAA
28817093 ATAAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:28818740 original size:26 final size:27
Alignment explanation
Indices: 28818700--28818769 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
28818690 GCTCTCAATC
* * *
28818700 TCTTTTTGTTCTCTTTCGTTCTCTTTT
1 TCTTTTTATTTTCTTTCATTCTCTTTT
*
28818727 TCTTTTT-TTTTCTTTCATTCTTTTTT
1 TCTTTTTATTTTCTTTCATTCTCTTTT
28818753 TCTTTTTATATTTCTTT
1 TCTTTTTAT-TTTCTTT
28818770 TTCTTTTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.61
27 8 0.21
28 7 0.18
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (27 bp):
TCTTTTTATTTTCTTTCATTCTCTTTT
Found at i:28818766 original size:24 final size:24
Alignment explanation
Indices: 28818721--28818766 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
28818711 TCTTTCGTTC
* *
28818721 TCTTTTTCTTTTTTTTTCTTTCAT
1 TCTTTTTCTTTTTTTATATTTCAT
28818745 TCTTTTT-TTCTTTTTATATTTC
1 TCTTTTTCTT-TTTTTATATTTC
28818767 TTTTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (24 bp):
TCTTTTTCTTTTTTTATATTTCAT
Found at i:28818776 original size:24 final size:23
Alignment explanation
Indices: 28818721--28818778 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 23
28818711 TCTTTCGTTC
28818721 TCTTTTTCTTTTTTTTTCTTTCAT
1 TCTTTTTCTTTTTTTTTCTTT-AT
28818745 TCTTTTTTTCTTTTTATATTTCTTT-T
1 TC--TTTTTCTTTTT-T-TTTCTTTAT
28818771 TCTTTTTC
1 TCTTTTTC
28818779 ACATACTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
24 8 0.27
26 14 0.47
27 1 0.03
28 7 0.23
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (23 bp):
TCTTTTTCTTTTTTTTTCTTTAT
Found at i:28821401 original size:39 final size:39
Alignment explanation
Indices: 28821343--28821419 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
28821333 ATGTAGAACA
28821343 CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
1 CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
*
28821382 CATATTAATGATGTTCAAACTATGACATAATTAAAGAC
1 CATATTAATGATGTGCAAACTATGACATAATTAAAGAC
28821420 ACAAACTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (39 bp):
CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
Found at i:28827169 original size:20 final size:20
Alignment explanation
Indices: 28827144--28827184 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28827134 TTCCTGCATC
28827144 TAACCATTTGATCACTTTCT
1 TAACCATTTGATCACTTTCT
*
28827164 TAACCATTTGATGACTTTCT
1 TAACCATTTGATCACTTTCT
28827184 T
1 T
28827185 TCTCACAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (20 bp):
TAACCATTTGATCACTTTCT
Found at i:28831595 original size:28 final size:29
Alignment explanation
Indices: 28831553--28831667 Score: 128
Period size: 29 Copynumber: 4.0 Consensus size: 29
28831543 TACCTGTATT
* *
28831553 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* * *
28831581 TGGCACATTAGGCCCAAATTACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
28831610 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
28831639 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
28831667 T
1 T
28831668 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
28 26 0.36
29 46 0.63
30 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:28831614 original size:57 final size:58
Alignment explanation
Indices: 28831543--28831654 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 58
28831533 CAATTTCACA
* *
28831543 TACCTGTATTTGGCCCATTAAGCCC-AATCATATTCATATGGCACATTAGGCCCAAAT
1 TACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCACATTAGGCCCAAAT
* * * *
28831600 TACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 TACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCACATTAGGCCCA
28831655 GTCACATTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 23 0.48
58 25 0.52
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (58 bp):
TACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCACATTAGGCCCAAAT
Found at i:28831921 original size:16 final size:16
Alignment explanation
Indices: 28831878--28831924 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
28831868 GTAGCCAAAC
28831878 TTTCGGCTTTTCAGCA
1 TTTCGGCTTTTCAGCA
** *
28831894 TTTCTACTTTTCGGCA
1 TTTCGGCTTTTCAGCA
*
28831910 TTTCGGCATTTCAGC
1 TTTCGGCTTTTCAGC
28831925 TTTTGCCGAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (16 bp):
TTTCGGCTTTTCAGCA
Found at i:28836912 original size:23 final size:23
Alignment explanation
Indices: 28836886--28836936 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
28836876 CAATAGTATT
28836886 CCTATGTTTGGTGTTGTAGAGTA
1 CCTATGTTTGGTGTTGTAGAGTA
28836909 CCTATGTTTGGTGTTGTAGAGTA
1 CCTATGTTTGGTGTTGTAGAGTA
28836932 CCTAT
1 CCTAT
28836937 CCATGCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.43
Consensus pattern (23 bp):
CCTATGTTTGGTGTTGTAGAGTA
Found at i:28838647 original size:30 final size:30
Alignment explanation
Indices: 28838590--28838648 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28838580 TTTTTAGGCC
**
28838590 TAAGGGTAAAATCATAATTTTTGCAAAGTT
1 TAAGGGTAAAATCATAATTTTACCAAAGTT
*
28838620 TAAGGGTAAAA-CGATCATTTTACCAAAGT
1 TAAGGGTAAAATC-ATAATTTTACCAAAGT
28838649 ATGAGTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (30 bp):
TAAGGGTAAAATCATAATTTTACCAAAGTT
Found at i:28842333 original size:68 final size:64
Alignment explanation
Indices: 28842119--28842371 Score: 201
Period size: 68 Copynumber: 3.8 Consensus size: 64
28842109 ATATAGTTCG
* * * *
28842119 GCTCTCTTGTAC-ACATGGTGAACACTCAGTACCACCCATGTGACCTAGCCA-ATTTA-TCTTGT
1 GCTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGCGACCTAGCTACATATATTCTTGT
28842181 A
64 A
* * * ** *
28842182 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCATGCATGCGACCTAGCTACATATA-TCTC
1 GCTCTCTTGTCTACATGGTG---TACA-CTAGTACCACCCATGCGACCTAGCTACATATATTCTT
28842246 GTA
62 GTA
* *
28842249 GCTCTCTTATCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATAATGTCTT
1 GCTCTCTTGTCTACATGGTGTACAC-TAGTACCACCCATGCGACCTAGCTACAT-AT-AT-TCTT
28842314 GTA
62 GTA
* * * ** *
28842317 GCTCTCTTGTAC-ACATGATGTGCACTCAGCACCATACATGTGACCTAGCTACATA
1 GCTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGCGACCTAGCTACATA
28842372 CTATCTGTAC
Statistics
Matches: 151, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
62 1 0.01
63 19 0.13
64 26 0.17
65 2 0.01
66 21 0.14
67 33 0.22
68 48 0.32
69 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.30
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACTAGTACCACCCATGCGACCTAGCTACATATATTCTTGTA
Found at i:28845151 original size:14 final size:12
Alignment explanation
Indices: 28845130--28845163 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
28845120 AGATATCATG
28845130 TATATATTTTTAA
1 TATATATTTTT-A
28845143 TATTATATTTTTA
1 TA-TATATTTTTA
28845156 TATATATT
1 TATATATT
28845164 AGGTACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 5 0.25
14 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATATTTTTA
Found at i:28845346 original size:21 final size:20
Alignment explanation
Indices: 28845313--28845351 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28845303 ATTCATGATT
*
28845313 TTATTTCGTGTTTAATATTA
1 TTATTTCATGTTTAATATTA
28845333 TTATTATCATGTTTAATAT
1 TTATT-TCATGTTTAATAT
28845352 CATGTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (20 bp):
TTATTTCATGTTTAATATTA
Found at i:28850479 original size:40 final size:40
Alignment explanation
Indices: 28850427--28850769 Score: 438
Period size: 40 Copynumber: 8.8 Consensus size: 40
28850417 ATTACCACAA
* * ** *
28850427 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28850467 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28850507 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGG--ATATATCAACTC
* *
28850549 GCACAAATGCCTGCGGGTCTTAGCCC---T-GAT--A-T-
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28850581 --ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28850619 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28850659 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28850699 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
28850739 GCACAATTGCCTTCGGGACTTAGCCCGGATA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
28850770 AAATTCAAAT
Statistics
Matches: 269, Mismatches: 21, Indels: 27
0.85 0.07 0.09
Matches are distributed among these distances:
30 24 0.09
33 2 0.01
34 3 0.01
36 3 0.01
37 2 0.01
39 1 0.00
40 195 0.72
41 4 0.01
42 35 0.13
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:28850587 original size:30 final size:30
Alignment explanation
Indices: 28850551--28850611 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
28850541 ATCAACTCGC
*
28850551 ACAAATGCCTGCGGGTCTTAGCCCTGATAT
1 ACAAATGCCTGCGGGTCTTAGCCCGGATAT
28850581 ACAAATGCCTGCGGGTCTTAGCCCGGATAT
1 ACAAATGCCTGCGGGTCTTAGCCCGGATAT
28850611 A
1 A
28850612 TCAACTCGCA
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:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (30 bp):
ACAAATGCCTGCGGGTCTTAGCCCGGATAT
Found at i:28850617 original size:112 final size:117
Alignment explanation
Indices: 28850472--28850769 Score: 423
Period size: 112 Copynumber: 2.6 Consensus size: 117
28850462 AACTCGCACG
*
28850472 AATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGAT
1 AATGCCTTCGGGTCTTAGCCCGGATATATCAACTAGCACAATTGCCTTCGGGTCTTAGCCCGGAT
28850537 ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCC-T-GAT-A-T-ACA
66 ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGTAGATAACTCACA
* * *
28850584 AATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGG--
1 AATGCCTTCGGGTCTTAGCCCGGATATATCAACTAGCACAATTGCCTTCGGGTCTTAGCCCGGAT
*
28850647 ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACA
66 ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCC-G-TAGAT-AACT--CACA
* *
28850704 AATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTAGCACAATTGCCTTCGGGTCTTAGCCCGGA
28850768 TA
65 TA
28850770 AAATTCAAAT
Statistics
Matches: 164, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
110 38 0.23
112 60 0.37
113 1 0.01
114 2 0.01
116 1 0.01
117 1 0.01
120 56 0.34
121 4 0.02
122 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (117 bp):
AATGCCTTCGGGTCTTAGCCCGGATATATCAACTAGCACAATTGCCTTCGGGTCTTAGCCCGGAT
ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGTAGATAACTCACA
Found at i:28859161 original size:40 final size:40
Alignment explanation
Indices: 28859109--28859421 Score: 509
Period size: 40 Copynumber: 7.8 Consensus size: 40
28859099 ATTACCACAA
* * ** *
28859109 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28859149 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28859189 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGG--ATATATCAACTC
*
28859231 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28859271 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28859311 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28859351 GCACAAATGCCTACGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28859391 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
28859422 AAATTCAAAT
Statistics
Matches: 256, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
40 219 0.86
42 37 0.14
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:28859326 original size:122 final size:120
Alignment explanation
Indices: 28859109--28859421 Score: 509
Period size: 122 Copynumber: 2.6 Consensus size: 120
28859099 ATTACCACAA
* * * ** * *
28859109 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTACGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
* *
28859174 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
66 CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGG--ATATATCAACTC
* *
28859231 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
1 GCACAAATGCCTACGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
28859296 CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
66 CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28859351 GCACAAATGCCTACGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTACGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
28859416 CGGATA
66 CGGATA
28859422 AAATTCAAAT
Statistics
Matches: 179, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
120 81 0.45
122 98 0.55
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (120 bp):
GCACAAATGCCTACGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:28862578 original size:23 final size:23
Alignment explanation
Indices: 28862552--28862815 Score: 309
Period size: 23 Copynumber: 11.5 Consensus size: 23
28862542 CAAAGTGCCA
* *
28862552 CACTGTAATATAGCCGAAGCTAT
1 CACTGTAATGTAGCCGAAGCTAC
* *
28862575 CACTGTAACGTAGCCGAAGCTAT
1 CACTGTAATGTAGCCGAAGCTAC
* *
28862598 CACTGTAACGTAGCCAAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
* **
28862621 CACTGTATTGTAGCAAAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
28862644 CACTG-AGATGTAGCCGAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
* *
28862667 CATTGTATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
28862690 CACTG-AGATGTAGCCGAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
* *
28862713 CACTATATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28862736 CACTGTATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28862759 CACTG-AGATGTAGCCAAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
* * *
28862782 CACTATATTGTAGTCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28862805 CACTGAAATGT
1 CACTGTAATGT
28862816 TGCCTATATA
Statistics
Matches: 209, Mismatches: 26, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
22 3 0.01
23 203 0.97
24 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGTAATGTAGCCGAAGCTAC
Found at i:28864177 original size:7 final size:7
Alignment explanation
Indices: 28864165--28864190 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28864155 AAGTAGTGTT
28864165 TAATATA
1 TAATATA
28864172 TAATATA
1 TAATATA
28864179 TAATATA
1 TAATATA
28864186 TAATA
1 TAATA
28864191 ACAAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATATA
Found at i:28864527 original size:19 final size:18
Alignment explanation
Indices: 28864491--28864538 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
28864481 AACCTTTAAT
28864491 AATAATAT-ATAGATAAA
1 AATAATATAATAGATAAA
28864508 AA-ATATATAATAGTATAAA
1 AATA-ATATAATAG-ATAAA
28864527 AATAATATAATA
1 AATAATATAATA
28864539 CAAAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 6 0.22
18 4 0.15
19 15 0.56
20 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
AATAATATAATAGATAAA
Found at i:28864545 original size:15 final size:16
Alignment explanation
Indices: 28864525--28864554 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28864515 TAATAGTATA
28864525 AAAATAA-TATAATAC
1 AAAATAATTATAATAC
28864540 AAAATAATTATAATA
1 AAAATAATTATAATA
28864555 TAATATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAATTATAATAC
Found at i:28864591 original size:7 final size:7
Alignment explanation
Indices: 28864579--28864748 Score: 86
Period size: 7 Copynumber: 24.1 Consensus size: 7
28864569 ATATGTAAAA
28864579 ATAATAT
1 ATAATAT
28864586 ATAATAT
1 ATAATAT
*
28864593 AT-ATAA
1 ATAATAT
28864599 ATAAT-T
1 ATAATAT
28864605 AATAA-AT
1 -ATAATAT
*
28864612 ATATTAT
1 ATAATAT
*
28864619 ACAAGTA-
1 ATAA-TAT
*
28864626 AAAATAT
1 ATAATAT
28864633 AATAATAT
1 -ATAATAT
28864641 ATAA-AT
1 ATAATAT
*
28864647 AATAATGT
1 -ATAATAT
*
28864655 AAAATA-
1 ATAATAT
28864661 ATAATAT
1 ATAATAT
* * *
28864668 TTCATGAAA
1 ATAAT--AT
*
28864677 AGTAGTAT
1 A-TAATAT
*
28864685 ATAATAA
1 ATAATAT
28864692 ATAATA-
1 ATAATAT
*
28864698 AT-ATAA
1 ATAATAT
28864704 ATAATAT
1 ATAATAT
*
28864711 ATAATAAA
1 ATAAT-AT
28864719 ATAATTAT
1 ATAA-TAT
28864727 ATAATAT
1 ATAATAT
28864734 ATAATAT
1 ATAATAT
28864741 ATAATAT
1 ATAATAT
28864748 A
1 A
28864749 AAAATAAGGT
Statistics
Matches: 123, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
5 3 0.02
6 21 0.17
7 74 0.60
8 21 0.17
9 2 0.02
10 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (7 bp):
ATAATAT
Found at i:28864608 original size:27 final size:25
Alignment explanation
Indices: 28864487--28864815 Score: 99
Period size: 26 Copynumber: 13.6 Consensus size: 25
28864477 TTAAAACCTT
*
28864487 TAATAATAATATATAGATAA-AA-AA
1 TAATAAT-ATATATAAATAATAATAA
*
28864511 TATATAATAGTATAAAAATAAT-ATAA
1 TA-ATAATA-TATATAAATAATAATAA
*
28864537 TACAAAATA-ATTATAATATAAT-ATGAA
1 TA-ATAATATA-TATAA-ATAATAAT-AA
* *
28864564 -AGT-ATATATGTAAA-AATAAT-A
1 TAATAATATATATAAATAATAATAA
28864585 T-ATAATATATATAAATAAT--TAA
1 TAATAATATATATAAATAATAATAA
*
28864607 T-A-AATATATTATACAAGTAAAAAT-A
1 TAATAATATA-TATA-AA-TAATAATAA
*
28864632 TAATAATATATAAATAATAATGTAA-AA
1 TAATAATATATATA-AATAA--TAATAA
* *
28864659 TAATAATATTTCATGAAAAGTAGTATATAA
1 TAATAATATAT-AT--AAA-TAATA-ATAA
28864689 TAAATAATA-ATATAAATAATATATAA
1 T-AATAATATATATAAATAATA-ATAA
*
28864715 TAA-AATA-AT-TATATAAT-AT-A
1 TAATAATATATATAAATAATAATAA
***
28864735 TAAT-ATATAATATAAA-AATAAGGT
1 TAATAATAT-ATATAAATAATAATAA
* * *
28864759 TAAAAATA-AAACAAATAATAATAA
1 TAATAATATATATAAATAATAATAA
*
28864783 T--TTATATATATAAATAAT-AT-A
1 TAATAATATATATAAATAATAATAA
28864804 -AATAA-ATATATA
1 TAATAATATATATA
28864816 GGGTTAGATT
Statistics
Matches: 230, Mismatches: 34, Indels: 85
0.66 0.10 0.24
Matches are distributed among these distances:
20 7 0.03
21 19 0.08
22 32 0.14
23 33 0.14
24 29 0.13
25 30 0.13
26 34 0.15
27 24 0.10
28 3 0.01
29 5 0.02
30 7 0.03
31 7 0.03
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (25 bp):
TAATAATATATATAAATAATAATAA
Found at i:28864650 original size:19 final size:19
Alignment explanation
Indices: 28864487--28864815 Score: 66
Period size: 18 Copynumber: 17.6 Consensus size: 19
28864477 TTAAAACCTT
*
28864487 TAATAATA-ATATATAGATA
1 TAATAATATATAAATA-ATA
* *
28864506 -AAAAATATAT-AATAGTA
1 TAATAATATATAAATAATA
*
28864523 TAAAAATA-ATATAATACA-A
1 TAATAATATATA-AATA-ATA
28864542 -AATAAT-TATAATATAATA
1 TAATAATATATAA-ATAATA
* **
28864560 TGAA-AGTATATATGTAA-A
1 T-AATAATATATAAATAATA
28864578 -AATAATATAT-AATATATA
1 TAATAATATATAAATA-ATA
28864596 TAAATAAT-TAATAAAT-ATA
1 T-AATAATAT-ATAAATAATA
* *
28864615 TTATACA-A-GTAAA-AATA
1 TAATA-ATATATAAATAATA
28864632 TAATAATATATAAATAATA
1 TAATAATATATAAATAATA
*
28864651 -ATGTAA-A-AT-AATAATA
1 TA-ATAATATATAAATAATA
* * * *
28864667 T-TTCATGA-A-AAGTAGTA
1 TAATAAT-ATATAAATAATA
*
28864684 T-ATAATAAAT-AATAATA
1 TAATAATATATAAATAATA
*
28864701 TAAATAATATAT-AATAAAA
1 T-AATAATATATAAATAATA
* *
28864720 TAATTATATAATATATAATA
1 TAATAATAT-ATAAATAATA
*
28864740 T-ATAATATAAAAATAAGGT-
1 TAATAATATATAAATAA--TA
* * *
28864759 TAAAAATAAAACAAATAATAA
1 TAATAAT-ATATAAATAAT-A
28864780 TAATTTATATATATAAATAATA
1 TAA--TA-ATATATAAATAATA
28864802 TAAATAAATATATA
1 T-AAT-AATATATA
28864816 GGGTTAGATT
Statistics
Matches: 226, Mismatches: 38, Indels: 90
0.64 0.11 0.25
Matches are distributed among these distances:
15 2 0.01
16 13 0.06
17 45 0.20
18 52 0.23
19 50 0.22
20 25 0.11
21 22 0.10
22 3 0.01
23 12 0.05
24 2 0.01
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (19 bp):
TAATAATATATAAATAATA
Found at i:28864705 original size:12 final size:12
Alignment explanation
Indices: 28864688--28864811 Score: 68
Period size: 12 Copynumber: 10.6 Consensus size: 12
28864678 GTAGTATATA
28864688 ATAAATAATAAT
1 ATAAATAATAAT
28864700 ATAAATAAT-AT
1 ATAAATAATAAT
*
28864711 ATAATAAAATAAT
1 ATAA-ATAATAAT
*
28864724 -TATATAAT-AT
1 ATAAATAATAAT
28864734 AT-AATATATAAT
1 ATAAATA-ATAAT
28864746 ATAAA-AATAAGGT
1 ATAAATAATAA--T
*
28864759 -TAAA-AATAAA
1 ATAAATAATAAT
*
28864769 ACAAATAAT-A-
1 ATAAATAATAAT
* *
28864779 ATAATTTATATAT
1 ATAAATAATA-AT
*
28864792 ATAAATAATATAA
1 ATAAATAATA-AT
28864805 ATAAATA
1 ATAAATA
28864812 TATAGGGTTA
Statistics
Matches: 87, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
10 11 0.13
11 21 0.24
12 33 0.38
13 22 0.25
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (12 bp):
ATAAATAATAAT
Found at i:28864730 original size:23 final size:25
Alignment explanation
Indices: 28864487--28864815 Score: 63
Period size: 24 Copynumber: 13.0 Consensus size: 25
28864477 TTAAAACCTT
*
28864487 TAATAATAATATATAGATAAAAAATATA
1 TAATAATAATA-AT--ATAAATAATATA
*
28864515 TAATAGTATAA-AA-ATAATATAATACA
1 TAATA--ATAATAATATAA-ATAATATA
* *
28864541 AAATAATTATAATATAATATGAAAGTATA
1 TAATAATAATAATATAA-AT--AA-TATA
* *
28864570 TATGTAAAAATAATAT--ATAATATA
1 TA-ATAATAATAATATAAATAATATA
*
28864594 T-ATAAATAATTA-ATAAAT-ATATTA
1 TAAT-AATAATAATATAAATAATA-TA
* *
28864618 TACA-AGTAAAAATAT-AATAATATA
1 TA-ATAATAATAATATAAATAATATA
* *
28864642 TAAATAATAATGTAAAAT-AATAATATT
1 T-AATAATAA--TAATATAAATAATATA
* *
28864669 TCATGAA-AAGTAGTATATAATAA-ATAA
1 TAAT-AATAA-TAATATA-AATAATAT-A
28864696 TAAT-ATAAATAATATATAATAA-A-A
1 TAATAAT-AATAATATA-AATAATATA
*
28864720 TAATTAT-ATAATATATAATATATAATA
1 TAATAATAATAATATA-AATA-AT-ATA
* *** * * *
28864747 TAAAAATAAGGTTAAAAATAAAACA
1 TAATAATAATAATATAAATAATATA
* *
28864772 -AATAATAATAATTTATAT-ATATA
1 TAATAATAATAATATAAATAATATA
28864795 -AATAAT-ATAA-ATAAAT-ATATA
1 TAATAATAATAATATAAATAATATA
28864816 GGGTTAGATT
Statistics
Matches: 224, Mismatches: 44, Indels: 73
0.66 0.13 0.21
Matches are distributed among these distances:
21 9 0.04
22 7 0.03
23 31 0.14
24 42 0.19
25 28 0.12
26 39 0.17
27 37 0.17
28 12 0.05
29 5 0.02
30 14 0.06
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (25 bp):
TAATAATAATAATATAAATAATATA
Found at i:28864740 original size:30 final size:27
Alignment explanation
Indices: 28864682--28864755 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 27
28864672 TGAAAAGTAG
28864682 TATATAAT-AAATAATAATATAAATAA
1 TATATAATAAAATAATAATATAAATAA
*
28864708 TATATAATAAAATAATTATATAATATATAA
1 TATATAATAAAATAA-TA-AT-ATAAATAA
28864738 TATATAATATAAA-AATAA
1 TATATAATA-AAATAATAA
28864756 GGTTAAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 8 0.19
27 6 0.14
28 3 0.07
29 4 0.10
30 18 0.43
31 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TATATAATAAAATAATAATATAAATAA
Found at i:28864746 original size:49 final size:48
Alignment explanation
Indices: 28864682--28864815 Score: 128
Period size: 49 Copynumber: 2.7 Consensus size: 48
28864672 TGAAAAGTAG
* * *
28864682 TATATAATAAATAATAATATAAATAATATATAATAAAATAATTATATAA
1 TATATAATATATAATAATATAAATAATATATAATAAAACAAATA-ATAA
* *
28864731 TATATAATATATAAT-ATAAAAATAAGGT-TAAAAATAAAACAAATAATAA
1 TATATAATATATAATAATATAAATAA--TAT-ATAATAAAACAAATAATAA
*
28864780 TAATTTATATATATAAATAATATAAATAAATATATA
1 T-ATATA-ATATAT-AATAATATAAAT-AATATATA
28864816 GGGTTAGATT
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
48 9 0.13
49 20 0.29
50 17 0.25
51 6 0.09
52 6 0.09
53 8 0.12
54 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (48 bp):
TATATAATATATAATAATATAAATAATATATAATAAAACAAATAATAA
Found at i:28866863 original size:205 final size:205
Alignment explanation
Indices: 28866350--28867302 Score: 1447
Period size: 205 Copynumber: 4.6 Consensus size: 205
28866340 CTACTTTTTT
* * * *
28866350 GATTTGTTTTCTGACAGTACAGAGATGCCGAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
* *
28866415 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* * * * * *
28866480 CTGCTTCAGTCTAATCATCTGAAGGTTAGATATGCTATGTGTCTGCCCTCCGTCGAATATGGAGA
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAA-GTGGAGA
* ** *
28866545 CGCCAAACTTT
195 TGCCGGACTTC
* * * *
28866556 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAAGCGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
* * * * *
28866621 AAACCAAATCAGCTATGTCTTCGATTTGTTTCTTGTAATCACAAGGATACCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* * *
28866686 GTACTTTAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTTTGCCCTCCGTCGAAGTGGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
28866751 GCCGGACTTC
196 GCCGGACTTC
* * *
28866761 GATTTGTTCTCTGTCAATATAGAGATGCCAAATCATCTTAGATTTGCTTCAACGCAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
28866826 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* * *
28866891 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTTTGCCCTCCGTTGAAGTAGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
28866956 GCCGGACTTC
196 GCCGGACTTC
* *
28866966 GATTTGTTCTCTGACAATACAGAGGTGCCAAATCATCTTAGATTTGCTTCAACGCAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
* * *
28867031 AAGCCAAATCATCTATGTCTTCGATATGCTCCTCGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* **
28867096 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGCGTCTATCCTCCGTCGAAGTGGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
* *
28867161 ACCGGACTTT
196 GCCGGACTTC
* * * * *
28867171 GATTTGTTTTCTGACAATACAGAGATGTCAAATCATTTTAGATTTGCTTTAACATAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
*
28867236 AAGCCAAATCAGCTATGTCTTCAATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
28867301 CT
131 CT
28867303 TGCTTCAGCT
Statistics
Matches: 683, Mismatches: 64, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
205 514 0.75
206 169 0.25
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (205 bp):
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
GCCGGACTTC
Found at i:28875529 original size:40 final size:40
Alignment explanation
Indices: 28875474--28875599 Score: 234
Period size: 40 Copynumber: 3.1 Consensus size: 40
28875464 TTATTTGATG
*
28875474 TGGAATTGTATCCGGGCTTAAAGACCCGCAGACTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
*
28875514 TGGAATCGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
28875554 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
28875594 TGGAAT
1 TGGAAT
28875600 GACATCCGGG
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
Found at i:28875626 original size:39 final size:39
Alignment explanation
Indices: 28875474--28875614 Score: 221
Period size: 40 Copynumber: 3.5 Consensus size: 39
28875464 TTATTTGATG
*
28875474 TGGAATTGTATCCGGGCTTAAAGACCCGCAGACTTCGTGC
1 TGGAA-TGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
28875514 TGGAATCGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAAT-GTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
28875554 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAA-TGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
*
28875594 TGGAATGACATCCGGG-TTAAA
1 TGGAATG-TATCCGGGCTTAAA
28875615 AACCTGTAGG
Statistics
Matches: 96, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
39 8 0.08
40 87 0.91
41 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (39 bp):
TGGAATGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
Found at i:28876446 original size:13 final size:12
Alignment explanation
Indices: 28876427--28876456 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
28876417 TTATATGGAC
28876427 AAAAAAAAAGAA
1 AAAAAAAAAGAA
28876439 AGAAAAAAAAGAA
1 A-AAAAAAAAGAA
28876452 AAAAA
1 AAAAA
28876457 TTTATTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:28879242 original size:46 final size:46
Alignment explanation
Indices: 28879192--28879364 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
28879182 TGGTTGAGCA
28879192 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
28879238 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* * * *
28879283 CATTCGAAATCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * **
28879331 CCCGAGCTCGTTGAGTTGAGTCTAAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28879365 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 56 0.54
47 27 0.26
48 4 0.04
50 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:28879359 original size:93 final size:93
Alignment explanation
Indices: 28879189--28879359 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
28879179 GGATGGTTGA
* *
28879189 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
*
28879254 TGAGTCCGAGTTCCTGAGATGTAACTAG
66 TGAGTCCAAGTTCCTGAGATGTAACTAG
* * * *
28879282 GCATTCGAAATCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
*
28879347 TGAGTCTAAGTTC
66 TGAGTCCAAGTTC
28879360 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (93 bp):
GCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCCTGAGATGTAACTAG
Found at i:28879626 original size:19 final size:20
Alignment explanation
Indices: 28879589--28879626 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28879579 ATAAGGTGGT
28879589 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28879609 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28879627 TTGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28885493 original size:18 final size:19
Alignment explanation
Indices: 28885445--28885503 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
28885435 ACAATATATA
* *
28885445 ATATATAATAACAAAAATT
1 ATATATAAGAATAAAAATT
* *
28885464 -TATAAAAGAATAATAATT
1 ATATATAAGAATAAAAATT
*
28885482 ATATATAA-AATAAAAAAT
1 ATATATAAGAATAAAAATT
28885500 ATAT
1 ATAT
28885504 TGGTTTAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
ATATATAAGAATAAAAATT
Found at i:28885580 original size:21 final size:21
Alignment explanation
Indices: 28885556--28885612 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
28885546 AATTTATATT
*
28885556 TATA-ATAAAATAA-TTATAA
1 TATATATAAAATAAGTTAGAA
28885575 TATATATAAATATAAGTTTAGAA
1 TATATATAAA-ATAAG-TTAGAA
28885598 TA-ATATAAAATAAGT
1 TATATATAAAATAAGT
28885613 AATTAATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 4 0.12
20 6 0.18
21 9 0.27
22 7 0.21
23 7 0.21
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
TATATATAAAATAAGTTAGAA
Found at i:28885795 original size:19 final size:18
Alignment explanation
Indices: 28885748--28885815 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 18
28885738 AAAACCTATA
*
28885748 ATAATAATAATAT-ATAG
1 ATAAAAATAATATAATAG
28885765 ATAAAAAT-ATATAATAG
1 ATAAAAATAATATAATAG
28885782 TATAAAAATAATATAAT--
1 -ATAAAAATAATATAATAG
28885799 AT-AAAATAATTATAATA
1 ATAAAAATAA-TATAATA
28885816 TAATATGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
15 7 0.16
16 12 0.27
17 11 0.24
18 8 0.18
19 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
ATAAAAATAATATAATAG
Found at i:28885807 original size:21 final size:20
Alignment explanation
Indices: 28885747--28885821 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 20
28885737 TAAAACCTAT
28885747 AATAATAATAATATATAGATAAA
1 AATAAT-ATAATATA-A-ATAAA
28885770 AAT-ATATAATAGT--ATAAA
1 AATAATATAATA-TAAATAAA
*
28885788 AATAATATAATATAAAATAAT
1 AATAATATAATAT-AAATAAA
*
28885809 TATAATATAATAT
1 AATAATATAATAT
28885822 GAAAGTATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
18 9 0.20
19 8 0.18
21 22 0.49
22 3 0.07
23 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AATAATATAATATAAATAAA
Found at i:28885852 original size:53 final size:56
Alignment explanation
Indices: 28885747--28885854 Score: 134
Period size: 53 Copynumber: 2.0 Consensus size: 56
28885737 TAAAACCTAT
*
28885747 AATAATAATAATATATAGATAAAAATATATAATAGTATAAAAATAATATAATATAA
1 AATAATAATAATATATAGATAAAAATATATAATAGTAAAAAAATAATATAATATAA
* * * *
28885803 AATAATTATAATATA-ATATGAAAGTATAT-AT-GTAAAAATAAT-ATATAATATA
1 AATAATAATAATATATAGATAAAAATATATAATAGTAAAAA-AATAATATAATATA
28885855 TATAAATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
53 16 0.35
54 5 0.11
55 11 0.24
56 14 0.30
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (56 bp):
AATAATAATAATATATAGATAAAAATATATAATAGTAAAAAAATAATATAATATAA
Found at i:28885928 original size:35 final size:35
Alignment explanation
Indices: 28885745--28886011 Score: 126
Period size: 36 Copynumber: 7.4 Consensus size: 35
28885735 GTTAAAACCT
* *
28885745 ATAATAATAATAATATATAGATAAAAATATATAATA
1 ATAAT-ATAATAATATATAAATAATAATATATAATA
28885781 GTATAA-A-AATAATATAATATAA-AATAAT-TATAAT-
1 --ATAATATAATAATAT-ATA-AATAATAATATATAATA
*
28885815 ATAATATGAAAGTATATATGTAAA-AATAATATATAAT-
1 ATAATAT--AA-TA-ATATATAAATAATAATATATAATA
* * *
28885852 AT-ATATAAATAATTTATAAAT-ATATTATACAAGTA
1 ATAATAT-AATAATATATAAATAATAATATATAA-TA
* * *
28885887 AAAATATAATAATATATAAATAATAATGTAAAATA
1 ATAATATAATAATATATAAATAATAATATATAATA
** * *
28885922 ATAATATTTCGTGAA-A-AGT-AATATATAATAAATAAAA
1 ATAATA--TAAT-AATATA-TAAATA-ATAATATATAATA
* *
28885959 ATAATATAGATAATATATAATAAAATAATTATATAAAA
1 ATAATATA-ATAATATATAA-ATAATAA-TATATAATA
*
28885997 TATAATATAAAAATA
1 -ATAATATAATAATA
28886012 AGGTTAAAAA
Statistics
Matches: 179, Mismatches: 24, Indels: 52
0.70 0.09 0.20
Matches are distributed among these distances:
32 4 0.02
33 17 0.09
34 3 0.02
35 41 0.23
36 43 0.24
37 38 0.21
38 25 0.14
39 8 0.04
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (35 bp):
ATAATATAATAATATATAAATAATAATATATAATA
Found at i:28886006 original size:25 final size:24
Alignment explanation
Indices: 28885744--28886008 Score: 95
Period size: 24 Copynumber: 11.3 Consensus size: 24
28885734 AGTTAAAACC
*
28885744 TATAATAATAATAATATATAGATAAAAA
1 TATAA-AATAAT-ATATATA-AT-ATAA
* * *
28885772 TATATAATAGTATAAAAATAATATAA
1 TATAAAATA--ATATATATAATATAA
28885798 TATAAAAT-A-AT-TATAATATAA
1 TATAAAATAATATATATAATATAA
* *
28885819 TATGAAAGT-ATATATGTAA-A-AA
1 TAT-AAAATAATATATATAATATAA
*
28885841 TA-ATATATAATATATATAA-ATAA
1 TATA-AAATAATATATATAATATAA
* *
28885864 TTTATAAAT-ATATTATACAAGTA-AA
1 TATA-AAATAATA-TATATAA-TATAA
* *
28885889 AATATAATAATATATA-AATAATAA
1 TATAAAATAATATATATAAT-ATAA
* **
28885913 TGTAAAATAATA-ATAT--T-TCG
1 TATAAAATAATATATATAATATAA
*
28885933 TGA-AAAGT-A-ATATATAATA-AA
1 T-ATAAAATAATATATATAATATAA
*
28885954 TA-AAAATAATATAGATAATAT-A
1 TATAAAATAATATATATAATATAA
*
28885976 TAATAAAATAATTATATAAAATATAA
1 T-ATAAAATAA-TATATATAATATAA
28886002 TATAAAA
1 TATAAAA
28886009 ATAAGGTTAA
Statistics
Matches: 178, Mismatches: 31, Indels: 59
0.66 0.12 0.22
Matches are distributed among these distances:
18 1 0.01
19 5 0.03
20 12 0.07
21 17 0.10
22 33 0.19
23 17 0.10
24 40 0.22
25 23 0.13
26 13 0.07
27 6 0.03
28 9 0.05
29 2 0.01
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (24 bp):
TATAAAATAATATATATAATATAA
Found at i:28886012 original size:18 final size:19
Alignment explanation
Indices: 28885754--28886012 Score: 76
Period size: 18 Copynumber: 12.8 Consensus size: 19
28885744 TATAATAATA
*
28885754 ATAATAT-ATAGATAAAA-
1 ATAATATAATAAATAAAAT
*
28885771 AT-ATATAATAGTATAAAA-
1 ATAATATAATA-AATAAAAT
28885789 ATAATATAATATAA-AATAATT
1 ATAATATAATA-AATAA-AA-T
*
28885810 ATAATATAAT--ATGAAAGT
1 ATAATATAATAAAT-AAAAT
* *
28885828 ATATATGTAA-AAATAATAT
1 ATA-ATATAATAAATAAAAT
**
28885847 ATAATATATATAAATAATTT
1 ATAATATA-ATAAATAAAAT
28885867 ATAAATATATTATACAAGTAAAAAT
1 AT-AATATA--ATA-AA-T-AAAAT
28885892 ATAATAATATATAAATAATAAT
1 ATAAT-ATA-ATAAATAA-AAT
* *
28885914 GTAAAATAATAATATTTCGTGAAAAGT
1 ATAATATAATAA-A-----T-AAAA-T
28885941 A-ATATATAATAAATAAAA-
1 ATA-ATATAATAAATAAAAT
*
28885959 ATAATATAGATAATATATAAT
1 ATAATATA-ATAA-ATAAAAT
*
28885980 A-AA-ATAATTATATAAAAT
1 ATAATATAA-TAAATAAAAT
28885998 ATAATATAA-AAATAA
1 ATAATATAATAAATAA
28886013 GGTTAAAAAT
Statistics
Matches: 187, Mismatches: 19, Indels: 71
0.68 0.07 0.26
Matches are distributed among these distances:
16 4 0.02
17 5 0.03
18 38 0.20
19 36 0.19
20 33 0.18
21 24 0.13
22 11 0.06
23 4 0.02
24 8 0.04
25 8 0.04
26 5 0.03
27 11 0.06
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (19 bp):
ATAATATAATAAATAAAAT
Found at i:28886024 original size:99 final size:99
Alignment explanation
Indices: 28885836--28886024 Score: 222
Period size: 99 Copynumber: 1.9 Consensus size: 99
28885826 GTATATATGT
* * * * * *
28885836 AAAAATAATATATAATATATATAAATAATTTATAAATATATTATACAAGTAAAAATATAATAATA
1 AAAAATAATATATAATAAATAAAAATAATATAGAAATATATAATACAAATAAAAATATAATAATA
* *
28885901 TATAAATAATAATGTAAAATAATAATATTTCGTG
66 TATAAAAAATAAGGTAAAATAATAATATTTCGTG
* **
28885935 AAAAGTAATATATAATAAATAAAAATAATATAGATAATATATAATA-AAATAATTATATAA-AAT
1 AAAAATAATATATAATAAATAAAAATAATATAGA-AATATATAATACAAATAAAAATATAATAAT
*
28885998 ATAATATAAAAATAAGGTTAAA-AATAA
65 AT-ATA-AAAAATAAGGTAAAATAATAA
28886025 AACAAATAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
98 5 0.07
99 48 0.64
100 22 0.29
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (99 bp):
AAAAATAATATATAATAAATAAAAATAATATAGAAATATATAATACAAATAAAAATATAATAATA
TATAAAAAATAAGGTAAAATAATAATATTTCGTG
Found at i:28886043 original size:12 final size:12
Alignment explanation
Indices: 28885946--28886043 Score: 55
Period size: 12 Copynumber: 8.2 Consensus size: 12
28885936 AAAGTAATAT
28885946 ATAATAAATAAAA
1 ATAAT-AATAAAA
*
28885959 ATAAT-ATAGATA
1 ATAATAATA-AAA
28885971 ATATATAAT-AAA
1 ATA-ATAATAAAA
28885983 ATAATTATATAAAA
1 ATAA-TA-ATAAAA
28885997 TATAAT-ATAAAA
1 -ATAATAATAAAA
***
28886009 ATAAGGTTAAAA
1 ATAATAATAAAA
*
28886021 AT-A-AA-ACAA
1 ATAATAATAAAA
28886030 ATAATAATAAAA
1 ATAATAATAAAA
28886042 AT
1 AT
28886044 TTATATATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 23
0.68 0.08 0.24
Matches are distributed among these distances:
9 5 0.08
10 1 0.02
11 11 0.17
12 30 0.45
13 9 0.14
14 6 0.09
15 4 0.06
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (12 bp):
ATAATAATAAAA
Found at i:28886073 original size:20 final size:19
Alignment explanation
Indices: 28886028--28886074 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
28886018 AAAATAAAAC
28886028 AAATA-ATAATAAAAATTT
1 AAATATATAATAAAAATTT
*
28886046 ATATATATAATAATAGAA-TT
1 AAATATATAATAA-A-AATTT
28886066 AAATATATA
1 AAATATATA
28886075 GGGTTAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 11 0.46
21 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAATATATAATAAAAATTT
Found at i:28890466 original size:52 final size:51
Alignment explanation
Indices: 28890407--28890608 Score: 246
Period size: 50 Copynumber: 3.9 Consensus size: 51
28890397 TAAAAAACAT
* * *
28890407 ATTTTTTTGAGGGTGGAGGGGGAGAGATGGGTAGCACCAGTAT-AAAAAATTAGA
1 ATTTTTTT--GGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAAATT--A
* * *
28890461 ATTTTTTTGGGTGGAGAGAGAGAGATGGGTGGCACTAGTATAAAAAAATT-
1 ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAAATTA
* * * *
28890511 ATTTTTTTTGGTGAAGGGAGAGAGATAGGTGTCTCCAGTATAAAAAAATTA
1 ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAAATTA
* *
28890562 CTTTTTTTGGGTGGAGGGAGAGAGATAGGCGGCACCAGTATAAAAAA
1 ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAA
28890609 GTAATATTAT
Statistics
Matches: 129, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
50 43 0.33
51 41 0.32
52 29 0.22
53 8 0.06
54 8 0.06
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (51 bp):
ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAAATTA
Found at i:28890558 original size:51 final size:50
Alignment explanation
Indices: 28890397--28890608 Score: 248
Period size: 51 Copynumber: 4.1 Consensus size: 50
28890387 TGATGTGTTT
* * *
28890397 TAAAAAACA-TATTTTTTTGAGGGTGGAGGGGGAGAGATGGGTAGCACCAGTA
1 TAAAAAA-ATTATTTTTTT--GGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
* * *
28890449 T-AAAAAATTAGAATTTTTTTGGGTGGAGAGAGAGAGATGGGTGGCACTAGTA
1 TAAAAAAATT---ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
* * * *
28890501 TAAAAAAATTATTTTTTTTGGTGAAGGGAGAGAGATAGGTGTCTCCAGTA
1 TAAAAAAATTATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
*
28890551 TAAAAAAATTACTTTTTTTGGGTGGAGGGAGAGAGATAGGCGGCACCAGTA
1 TAAAAAAATTA-TTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
28890602 TAAAAAA
1 TAAAAAA
28890609 GTAATATTAT
Statistics
Matches: 138, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
50 45 0.33
51 47 0.34
52 30 0.22
53 8 0.06
54 8 0.06
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (50 bp):
TAAAAAAATTATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
Found at i:28890633 original size:51 final size:47
Alignment explanation
Indices: 28890428--28890638 Score: 165
Period size: 51 Copynumber: 4.1 Consensus size: 47
28890418 GGTGGAGGGG
* *
28890428 GAGAGATGGGTAGCACCAGTAT-AAAAAATTAGAATTTTTTTGGGTGG-AGAGA
1 GAGAGATAGGTGGCACCAGTATAAAAAAATT---ATTTTTTT---TGGAAG-GA
* *
28890480 GAGAGATGGGTGGCACTAGTATAAAAAAATTATTTTTTTTGGTGAAGGGA
1 GAGAGATAGGTGGCACCAGTATAAAAAAATTATTTTTTTT-G-GAA-GGA
* * *
28890530 GAGAGATAGGTGTCTCCAGTATAAAAAAATTACTTTTTTTGGGTGGAGGGA
1 GAGAGATAGGTGGCACCAGTATAAAAAAATTA-TTTTTTT---TGGAAGGA
* *
28890581 GAGAGATAGGCGGCACCAGTATAAAAAAGTAATATTATTTTATTGGAAGGA
1 GAGAGATAGGTGGCACCAGTATAAAAAA--ATTATT-TTTT-TTGGAAGGA
28890632 GAGAGAT
1 GAGAGAT
28890639 GGGCAACATC
Statistics
Matches: 134, Mismatches: 12, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 1 0.01
50 39 0.29
51 50 0.37
52 24 0.18
53 16 0.12
54 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.29, T:0.28
Consensus pattern (47 bp):
GAGAGATAGGTGGCACCAGTATAAAAAAATTATTTTTTTTGGAAGGA
Found at i:28892859 original size:44 final size:44
Alignment explanation
Indices: 28892794--28892881 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
28892784 ACTCGGTCTA
28892794 CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
1 CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
*
28892838 CACTTAACCTTTTCACGTAAAATGAATTTTCTTCATCTAATTAG
1 CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
28892882 TCATCTATGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.41
Consensus pattern (44 bp):
CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
Found at i:28898871 original size:39 final size:40
Alignment explanation
Indices: 28898804--28898880 Score: 122
Period size: 39 Copynumber: 1.9 Consensus size: 40
28898794 TGCAGAACAT
28898804 ATATTAATGATGTGCAAAACTATGACATAAT-TAAAGACTC
1 ATATTAATGATGTGCAAAACTATGACAT-ATGTAAAGACTC
*
28898844 ATATTAATGATGTTC-AAACTATGACATATGTAAAGAC
1 ATATTAATGATGTGCAAAACTATGACATATGTAAAGAC
28898881 AAACTAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 2 0.06
39 19 0.54
40 14 0.40
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (40 bp):
ATATTAATGATGTGCAAAACTATGACATATGTAAAGACTC
Found at i:28898896 original size:9 final size:9
Alignment explanation
Indices: 28898882--28898907 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28898872 TGTAAAGACA
28898882 AACTAAAAT
1 AACTAAAAT
28898891 AACTAAAAT
1 AACTAAAAT
28898900 AACTAAAA
1 AACTAAAA
28898908 ATAAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:28900517 original size:27 final size:27
Alignment explanation
Indices: 28900487--28900547 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
28900477 GCTCTCAATC
*
28900487 TCTTTTTGTTCTCTTTCGTTCTCTTTT
1 TCTTTTTGTTCTCTTTCATTCTCTTTT
* *
28900514 TCTTTTTGTTTTCTTTCATTCTTTTTT
1 TCTTTTTGTTCTCTTTCATTCTCTTTT
28900541 TCTTTTT
1 TCTTTTT
28900548 ATATTTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (27 bp):
TCTTTTTGTTCTCTTTCATTCTCTTTT
Found at i:28902105 original size:37 final size:37
Alignment explanation
Indices: 28902046--28902117 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
28902036 TTTAGCTCGA
*
28902046 ATAATCCCCACACGTAGTCATCGGGTCTTACCCGGGC
1 ATAATCCCCACACGTAGCCATCGGGTCTTACCCGGGC
* *
28902083 ATAATCTCCACATGTAGCCATCGGGTCTTACCCGG
1 ATAATCCCCACACGTAGCCATCGGGTCTTACCCGG
28902118 AATATATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.24
Consensus pattern (37 bp):
ATAATCCCCACACGTAGCCATCGGGTCTTACCCGGGC
Found at i:28902311 original size:48 final size:48
Alignment explanation
Indices: 28902251--28902356 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
28902241 CGGCCACAAT
* *
28902251 ATATACACATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
28902299 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
* *
28902347 ACATATATAT
1 ATATACATAT
28902357 ATATTTATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (48 bp):
ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
Found at i:28905366 original size:24 final size:24
Alignment explanation
Indices: 28905339--28905384 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
28905329 AACTATGAAC
*
28905339 ATTTTCAATCTCTTTTTTTTAATA
1 ATTTTCAATCTCCTTTTTTTAATA
* *
28905363 ATTTTGAATTTCCTTTTTTTAA
1 ATTTTCAATCTCCTTTTTTTAA
28905385 ATACTTACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTTCAATCTCCTTTTTTTAATA
Found at i:28906884 original size:39 final size:39
Alignment explanation
Indices: 28906826--28906902 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
28906816 ATGTAGAACA
28906826 CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
1 CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
*
28906865 CATATTAATGATGTTCAAACTATGACATAATTAAAGAC
1 CATATTAATGATGTGCAAACTATGACATAATTAAAGAC
28906903 ACAAAGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (39 bp):
CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
Found at i:28909586 original size:40 final size:40
Alignment explanation
Indices: 28909531--28909748 Score: 318
Period size: 40 Copynumber: 5.5 Consensus size: 40
28909521 CGGATGATAA
* *
28909531 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
28909571 CCGGGCTAAGCCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28909611 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28909651 CCGGGCTAAGTGCCGAAGGCATTTGTGCGAGTTACTATAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
*
28909692 -CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
28909731 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28909749 TACTTGGTTT
Statistics
Matches: 164, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
39 19 0.12
40 142 0.87
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28923755 original size:24 final size:24
Alignment explanation
Indices: 28923727--28923787 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
28923717 AACCGTATTT
* * *
28923727 GCACACATAGTGCTA-ATTACACTC
1 GCACACATAGTGCCATAGTAAAC-C
28923751 GCACACATAGTGCCATAGTAAACC
1 GCACACATAGTGCCATAGTAAACC
28923775 GCACACATAGTGC
1 GCACACATAGTGC
28923788 ATTGGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAACC
Found at i:28926550 original size:30 final size:30
Alignment explanation
Indices: 28926516--28926576 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
28926506 TCCTTAACTC
28926516 AAACTTTTGCAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
28926546 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
28926576 A
1 A
28926577 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:28939616 original size:49 final size:49
Alignment explanation
Indices: 28939557--28939654 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
28939547 TTCAAGACCA
*
28939557 CAAATCCGATCCGAAAATAAAATTTATTTTTATTTTAATACATGGTCCT
1 CAAATCCGATCCGAAAATAAAATTTATTTTTATTTTAATACAGGGTCCT
*
28939606 CAAATTCGATCCGAAAATAAAATTTATTTTTATTTTAATACAGGGTCCT
1 CAAATCCGATCCGAAAATAAAATTTATTTTTATTTTAATACAGGGTCCT
28939655 TAATATGTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (49 bp):
CAAATCCGATCCGAAAATAAAATTTATTTTTATTTTAATACAGGGTCCT
Found at i:28941041 original size:57 final size:58
Alignment explanation
Indices: 28940915--28941042 Score: 136
Period size: 58 Copynumber: 2.2 Consensus size: 58
28940905 CTTATTATAG
** * * * *
28940915 AAAGGATTTAGTTCGGACGGGTAATCCTAATATAAGTCCTCTCGAGCATATGTTATAG
1 AAAGGATTTAGCCCAGACGGGTAATCCTAATATAAGTCCTCTAGAGCATATGTCATAA
** *
28940973 ATTGGATTTAGCCCAGACGGGTAATCC-AGATCA-AGGTCC-CTAGAGCATATGTCATAA
1 AAAGGATTTAGCCCAGACGGGTAATCCTA-AT-ATAAGTCCTCTAGAGCATATGTCATAA
28941030 AAAGGATTTAGCC
1 AAAGGATTTAGCC
28941043 TGTACTGGTA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
57 27 0.47
58 29 0.51
59 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (58 bp):
AAAGGATTTAGCCCAGACGGGTAATCCTAATATAAGTCCTCTAGAGCATATGTCATAA
Found at i:28944530 original size:27 final size:27
Alignment explanation
Indices: 28944500--28944677 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28944490 ATATTGAGTC
* * * *
28944500 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28944527 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28944554 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28944582 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28944609 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28944636 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28944663 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28944678 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28944639 original size:82 final size:81
Alignment explanation
Indices: 28944521--28944676 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28944511 TGCTATATAA
* *
28944521 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28944586 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28944603 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28944667 CACTTAGTGC
65 CACTTAGTGC
28944677 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28967137 original size:28 final size:26
Alignment explanation
Indices: 28967095--28967164 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 26
28967085 ATATGAATTG
28967095 CACAATTAATAACATGGAGATAGTAA
1 CACAATTAATAACATGGAGATAGTAA
* * *
28967121 CACGATTAAAATAACATGGAGGTAGTCA
1 CACAATT--AATAACATGGAGATAGTAA
28967149 CACAATTAATAACATG
1 CACAATTAATAACATG
28967165 TATTCTGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 15 0.39
28 23 0.61
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (26 bp):
CACAATTAATAACATGGAGATAGTAA
Found at i:28968715 original size:29 final size:29
Alignment explanation
Indices: 28968627--28968718 Score: 114
Period size: 29 Copynumber: 3.2 Consensus size: 29
28968617 TACCTGTATC
* * *
28968627 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* * * *
28968655 TGACCCATCAGGCCCAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
28968684 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
28968713 TGGCCC
1 TGGCCC
28968719 GTTACACCCA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 12 0.23
29 40 0.77
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Done.