Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 95 of 97
Found at i:37908796 original size:14 final size:14
Alignment explanation
Indices: 37908779--37908810 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
37908769 TCTTAAGAAA
37908779 AAAAAGGAAAAAAG
1 AAAAAGGAAAAAAG
*
37908793 AAAAAGGAAAAAGG
1 AAAAAGGAAAAAAG
37908807 AAAA
1 AAAA
37908811 GAAGGCTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAAGGAAAAAAG
Found at i:37912867 original size:11 final size:11
Alignment explanation
Indices: 37912838--37912867 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
37912828 NNNNNNNNAT
*
37912838 TATATATAATA
1 TATATATTATA
37912849 TATATATTATA
1 TATATATTATA
37912860 TATATATT
1 TATATATT
37912868 TCCTGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATATTATA
Found at i:37914203 original size:4 final size:4
Alignment explanation
Indices: 37914196--37914222 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
37914186 TATATAAAAT
37914196 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
37914223 TCCATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:37916375 original size:86 final size:86
Alignment explanation
Indices: 37916216--37916384 Score: 212
Period size: 86 Copynumber: 2.0 Consensus size: 86
37916206 ATTGTTGATG
* * * **
37916216 CTTCACATGAAATCATAAGCAAAATTTCATTAAAAACAAACCGTCCGAAAACTCAAAACCATTTA
1 CTTCACATGAAATCATAAGCAAAATTTCATTAAAAAAAAACCATCCAAAAACTCAAAACCATCCA
*
37916281 AGACTTTAATCAAATGAGTAA
66 AGACTTTAACCAAATGAGTAA
* * ** **
37916302 CTTCACATGAAATTATAAGCTAAATTTCATTAAAAAAAAACCATCCAAAAACTTGAAATTATCCA
1 CTTCACATGAAATCATAAGCAAAATTTCATTAAAAAAAAACCATCCAAAAACTCAAAACCATCCA
* *
37916367 AGAGTTTAACCTAATGAG
66 AGACTTTAACCAAATGAG
37916385 AATTCGAAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.26
Consensus pattern (86 bp):
CTTCACATGAAATCATAAGCAAAATTTCATTAAAAAAAAACCATCCAAAAACTCAAAACCATCCA
AGACTTTAACCAAATGAGTAA
Found at i:37919743 original size:15 final size:15
Alignment explanation
Indices: 37919719--37919748 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37919709 CCTGCTTCAC
*
37919719 CAACAGCAACAGCAA
1 CAACAACAACAGCAA
37919734 CAACAACAACAGCAA
1 CAACAACAACAGCAA
37919749 GTTGCTCCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.33, G:0.10, T:0.00
Consensus pattern (15 bp):
CAACAACAACAGCAA
Found at i:37929943 original size:22 final size:22
Alignment explanation
Indices: 37929918--37929975 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
37929908 TGTTGGAGTA
37929918 AGGGTTTAAGGGGGAAAGAAAG
1 AGGGTTTAAGGGGGAAAGAAAG
* ** *
37929940 AGGGGTGGAGGGCGAAAGAAAG
1 AGGGTTTAAGGGGGAAAGAAAG
37929962 AGGGTTTAGAGGGG
1 AGGGTTTA-AGGGG
37929976 AGGAAATGGG
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.34, C:0.02, G:0.52, T:0.12
Consensus pattern (22 bp):
AGGGTTTAAGGGGGAAAGAAAG
Found at i:37932746 original size:19 final size:19
Alignment explanation
Indices: 37932697--37932747 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
37932687 ATCATTTAAA
37932697 TTTTGTTTTATAAATAAATT
1 TTTTGTTTT-TAAATAAATT
**
37932717 TCTTTAATTTT-AATAAAATT
1 T-TTTGTTTTTAAAT-AAATT
37932737 TTTTGTTTTTA
1 TTTTGTTTTTA
37932748 TTCTGTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
19 10 0.42
20 8 0.33
21 6 0.25
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTGTTTTTAAATAAATT
Found at i:37933740 original size:23 final size:21
Alignment explanation
Indices: 37933693--37933735 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
37933683 CCCGGAGTTC
*
37933693 CCCCTTCCTTCTTTTTTTTCT
1 CCCCTGCCTTCTTTTTTTTCT
37933714 CCCCTGCCTT-TTTCTTTTTCT
1 CCCCTGCCTTCTTT-TTTTTCT
37933735 C
1 C
37933736 TCCCCCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.58
Consensus pattern (21 bp):
CCCCTGCCTTCTTTTTTTTCT
Found at i:37937889 original size:19 final size:18
Alignment explanation
Indices: 37937865--37937914 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
37937855 TTAGACGAGC
* *
37937865 AATAATTGGTTCGAATTAA
1 AATAATTGATT-GAAATAA
37937884 AATAATTGATTGAAATAA
1 AATAATTGATTGAAATAA
37937902 AATGAATTCGATT
1 AAT-AATT-GATT
37937915 AATTCAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 14 0.52
20 4 0.15
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (18 bp):
AATAATTGATTGAAATAA
Found at i:37946510 original size:21 final size:21
Alignment explanation
Indices: 37946462--37946510 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
37946452 TGAAAGTTTT
*
37946462 ATATTTTTTATTTTGATATGA
1 ATATTTTTAATTTTGATATGA
* ** *
37946483 ATTTTTTTAATTTTTTTATTA
1 ATATTTTTAATTTTGATATGA
37946504 ATATTTT
1 ATATTTT
37946511 GAGAACATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
ATATTTTTAATTTTGATATGA
Found at i:37947933 original size:31 final size:31
Alignment explanation
Indices: 37947898--37947962 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
37947888 TCCCGTAGTC
*
37947898 AAGTCCTTATATCAAAAGAAGAAAGAAGAAG
1 AAGTCCTTAAATCAAAAGAAGAAAGAAGAAG
37947929 AAGTCCTTAAATCAAAAGAAGAAAGAAGAAG
1 AAGTCCTTAAATCAAAAGAAGAAAGAAGAAG
37947960 AAG
1 AAG
37947963 CAGAAGAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.57, C:0.09, G:0.20, T:0.14
Consensus pattern (31 bp):
AAGTCCTTAAATCAAAAGAAGAAAGAAGAAG
Found at i:37948795 original size:32 final size:32
Alignment explanation
Indices: 37948759--37948819 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
37948749 CCATCGCCAA
*
37948759 CCTTTCCCTTTTATTCAATTCCTCTCTTACCC
1 CCTTTCCCTTTTATTCAATTACTCTCTTACCC
*
37948791 CCTTTTCCTTTTATTCAATTACTCTCTTA
1 CCTTTCCCTTTTATTCAATTACTCTCTTA
37948820 GATTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.15, C:0.34, G:0.00, T:0.51
Consensus pattern (32 bp):
CCTTTCCCTTTTATTCAATTACTCTCTTACCC
Found at i:37948889 original size:18 final size:17
Alignment explanation
Indices: 37948868--37948909 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
37948858 CGTAAACATA
37948868 ATAATTATATGAATAAAT
1 ATAATTA-ATGAATAAAT
* *
37948886 ATAATTAATTAATTAAT
1 ATAATTAATGAATAAAT
37948903 AT-ATTAA
1 ATAATTAA
37948910 AATTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 5 0.23
17 10 0.45
18 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATAATTAATGAATAAAT
Found at i:37948889 original size:21 final size:21
Alignment explanation
Indices: 37948860--37948916 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
37948850 ATATATTTCG
*
37948860 TAAACATAATAATTATATGAA
1 TAAATATAATAATTATATGAA
*
37948881 TAAATATAATTAATTA-ATTAA
1 TAAATATAA-TAATTATATGAA
*
37948902 TATAT-TAA-AATTATA
1 TAAATATAATAATTATA
37948917 AAAAAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.16
19 1 0.03
20 3 0.10
21 16 0.52
22 6 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAATATAATAATTATATGAA
Found at i:37953297 original size:6 final size:6
Alignment explanation
Indices: 37953286--37953320 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
37953276 GAGCAACTTG
37953286 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGG
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGG
37953321 GGGAAGGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.69, T:0.14
Consensus pattern (6 bp):
GGAGGT
Found at i:37954764 original size:9 final size:10
Alignment explanation
Indices: 37954743--37954781 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
37954733 ATGTAATGGT
37954743 AAAAATTTAA
1 AAAAATTTAA
37954753 AAAAATTTAA
1 AAAAATTTAA
*
37954763 AATAATATTTTA
1 AA-AA-ATTTAA
37954775 AAAAATT
1 AAAAATT
37954782 ATGAATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 15 0.58
11 4 0.15
12 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:37972392 original size:2 final size:2
Alignment explanation
Indices: 37972385--37972409 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37972375 AATTTCACAA
37972385 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
37972410 TGTTGCAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:37975854 original size:2 final size:2
Alignment explanation
Indices: 37975847--37975970 Score: 147
Period size: 2 Copynumber: 64.5 Consensus size: 2
37975837 GATCTGAATT
37975847 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
37975887 TA TNA T- TA TA TC TA T- TGA -A TT TA -A TA TA TA TA TA TA TA -A
1 TA T-A TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
37975926 TA TA TA TA TA CTA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37975968 TA T
1 TA T
37975971 TGTTTGATTT
Statistics
Matches: 107, Mismatches: 4, Indels: 22
0.80 0.03 0.17
Matches are distributed among these distances:
1 8 0.07
2 95 0.89
3 4 0.04
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:37975934 original size:37 final size:37
Alignment explanation
Indices: 37975848--37975970 Score: 155
Period size: 39 Copynumber: 3.3 Consensus size: 37
37975838 ATCTGAATTT
37975848 ATATATATATA-TATATATATATATATATTATATATATA
1 ATATATATATACTATATATATA-ATATA-TATATATATA
*
37975886 ATATNAT-TATATCTAT-TGAATTTAATATATATATATATA
1 ATAT-ATATATA-CTATAT--ATATAATATATATATATATA
37975925 ATATATATATACTATATATATAATATATATATATAT-
1 ATATATATATACTATATATATAATATATATATATATA
37975961 ATATATATAT
1 ATATATATAT
37975971 TGTTTGATTT
Statistics
Matches: 76, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
36 10 0.13
37 18 0.24
38 14 0.18
39 22 0.29
40 8 0.11
41 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (37 bp):
ATATATATATACTATATATATAATATATATATATATA
Found at i:37975941 original size:61 final size:61
Alignment explanation
Indices: 37975841--37975958 Score: 195
Period size: 61 Copynumber: 1.9 Consensus size: 61
37975831 CAAAATGATC
*
37975841 TGAATTTATATATATATATATATATATATATATATTATATATATAATATNAT-TATATCTAT
1 TGAATTTATATATATATATATATATATATATATACTATATATATAATAT-ATATATATCTAT
37975902 TGAATTTA-ATATATATATATATAATATATATATACTATATATATAATATATATATAT
1 TGAATTTATATATATATATATAT-ATATATATATACTATATATATAATATATATATAT
37975959 ATATATATAT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
60 16 0.30
61 38 0.70
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (61 bp):
TGAATTTATATATATATATATATATATATATATACTATATATATAATATATATATATCTAT
Found at i:37990352 original size:2 final size:2
Alignment explanation
Indices: 37990345--37990369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37990335 TAAAGGAAAA
37990345 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
37990370 AATAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38017354 original size:2 final size:2
Alignment explanation
Indices: 38017347--38017372 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38017337 AGCTCAAGAT
38017347 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
38017373 AACCAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38018695 original size:73 final size:73
Alignment explanation
Indices: 38018601--38018736 Score: 166
Period size: 73 Copynumber: 1.9 Consensus size: 73
38018591 AAGACAAAAC
* * * * *
38018601 AACAGTTTCATTGTTTCTTGTAATAACAT-ATTTCAGATCATTTACCTTTCAACTATAAATTCAA
1 AACAATTTCATTATTTATTGTAAGAACATGA-TTCAGATCATTTACCTTTCAAATATAAATTCAA
38018665 ATGACAAAT
65 ATGACAAAT
* * ** *
38018674 AACAATTTCATTATTTATTGTAAGAATATGATTCAGATGATTTATTTTTTAAATATAAATTCA
1 AACAATTTCATTATTTATTGTAAGAACATGATTCAGATCATTTACCTTTCAAATATAAATTCA
38018737 GAGAAACAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
73 51 0.98
74 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (73 bp):
AACAATTTCATTATTTATTGTAAGAACATGATTCAGATCATTTACCTTTCAAATATAAATTCAAA
TGACAAAT
Found at i:38034464 original size:96 final size:95
Alignment explanation
Indices: 38034165--38034472 Score: 387
Period size: 94 Copynumber: 3.2 Consensus size: 95
38034155 ATGATAAAGT
* * * *
38034165 CAAATTGAATAATTATATTATTATATAATAATGTAAAT-ATTTGATTTTGATTATTAATTTATTA
1 CAAATTGAATAGTTATATTATTATACAATAGTGTAAATGA-TCGATTTTGATTATTAATTTATTA
*
38034229 TTTTTTAAAAAATTATTTTA-CTCGA-TAAGAA
65 TTTTTTAAAAAATTATTTTACCT-AATTAA-AA
* *
38034260 CAAATTGAATAGTTACATTATTATACAATAGTG--AA-GATCGATTTTGATTATTAAATTATTAT
1 CAAATTGAATAGTTATATTATTATACAATAGTGTAAATGATCGATTTTGATTATTAATTTATTA-
* *
38034322 TTTTTTTAAAAAATTGTTTTACCTAATAAAAA
65 -TTTTTTAAAAAATTATTTTACCTAATTAAAA
* *
38034354 CAAATTGAATAGTTATATTATTATGA-AAGAGTGTAAATGATCGATTTTTATTATTAATTTATTA
1 CAAATTGAATAGTTATATTATTAT-ACAATAGTGTAAATGATCGATTTTGATTATTAATTTATTA
38034418 TTTTTTAAAAAACTTATTTTACCTAATTAAAA
65 TTTTTTAAAAAA-TTATTTTACCTAATTAAAA
* *
38034450 CAAATTAAATAGTTATATCATTA
1 CAAATTGAATAGTTATATTATTA
38034473 CAAACAGTAA
Statistics
Matches: 186, Mismatches: 17, Indels: 19
0.84 0.08 0.09
Matches are distributed among these distances:
92 22 0.12
93 3 0.02
94 51 0.27
95 46 0.25
96 40 0.22
97 24 0.13
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (95 bp):
CAAATTGAATAGTTATATTATTATACAATAGTGTAAATGATCGATTTTGATTATTAATTTATTAT
TTTTTAAAAAATTATTTTACCTAATTAAAA
Found at i:38039353 original size:2 final size:2
Alignment explanation
Indices: 38039346--38039372 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38039336 ATTAGAATAC
38039346 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38039373 AATTTCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38042932 original size:18 final size:19
Alignment explanation
Indices: 38042901--38042939 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
38042891 GGTTTTTAAC
38042901 TATTATTTAAATTGAT-AT
1 TATTATTTAAATTGATCAT
**
38042919 TATTATTTTTATTGATCAT
1 TATTATTTAAATTGATCAT
38042938 TA
1 TA
38042940 GAAATGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTATTTAAATTGATCAT
Found at i:38043180 original size:104 final size:104
Alignment explanation
Indices: 38043050--38043289 Score: 295
Period size: 104 Copynumber: 2.3 Consensus size: 104
38043040 AAATTGTTTT
* * *
38043050 TATCAATCATTAAAAATGATATTTTGATTGATTAATAAAAAAATTACTCTTTTTG-CCGTTTATT
1 TATCAATCATTAAAAATGATATTTTGATCGATTAATAAAAAAATTACT-ATTTTGACCGATTATT
* * * *
38043114 -AAAAGTGATGTTTCGATCGATCGTTGGAAAAGTTATTTC
65 GAAAAGTAATATTTCGATCGATCGTTGAAAAAGTTATATC
** * *
38043153 TATCAATCATTAAAAAATGATATTTTGATCGATTGTTAAAAAGATTACTATTTTGATCGATTATT
1 TATCAATCATT-AAAAATGATATTTTGATCGATTAATAAAAAAATTACTATTTTGACCGATTATT
* * *
38043218 GAAATGTAATATTTTGATCGATCTTTGAAAAAGTTATATC
65 GAAAAGTAATATTTCGATCGATCGTTGAAAAAGTTATATC
* * *
38043258 TATTAATCCTTAAAAATTATATTTTGATCGAT
1 TATCAATCATTAAAAATGATATTTTGATCGAT
38043290 CGTTAAAATG
Statistics
Matches: 117, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
103 16 0.14
104 60 0.51
105 41 0.35
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (104 bp):
TATCAATCATTAAAAATGATATTTTGATCGATTAATAAAAAAATTACTATTTTGACCGATTATTG
AAAAGTAATATTTCGATCGATCGTTGAAAAAGTTATATC
Found at i:38043295 original size:25 final size:25
Alignment explanation
Indices: 38043165--38043297 Score: 92
Period size: 26 Copynumber: 5.2 Consensus size: 25
38043155 TCAATCATTA
* *
38043165 AAAAATGATATTTTGATCGATTGTT
1 AAAAATTATATTTTGATCGATCGTT
**
38043190 AAAAAGATTACTATTTTGATCGATTATT
1 -AAAA-ATTA-TATTTTGATCGATCGTT
* *
38043218 -GAAATGTAATATTTTGATCGATCTTT
1 AAAAAT-T-ATATTTTGATCGATCGTT
* ** *
38043244 GAAAAAGTTATA-TCT-ATTAATCCTT
1 -AAAAA-TTATATTTTGATCGATCGTT
38043269 AAAAATTATATTTTGATCGATCGTT
1 AAAAATTATATTTTGATCGATCGTT
38043294 AAAA
1 AAAA
38043298 TGGTTATTAT
Statistics
Matches: 84, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
23 5 0.06
24 7 0.08
25 20 0.24
26 24 0.29
27 7 0.08
28 20 0.24
29 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (25 bp):
AAAAATTATATTTTGATCGATCGTT
Found at i:38044654 original size:57 final size:54
Alignment explanation
Indices: 38044486--38044704 Score: 316
Period size: 54 Copynumber: 4.0 Consensus size: 54
38044476 TGGAACTAAC
* *
38044486 ACCAGTTCCTTCCAGGCACCCGACCCTTTCTCCATGAAAGGTGAAAAAAACAAG
1 ACCAGTTTCTTCCAGGCACCCGACCCTTTATCCATGAAAGGTGAAAAAAACAAG
* * *
38044540 ACCA-TTTCGTTACAGGAACCCAACCCTTTATCCATGAAAGGTGAAAAAAACAAG
1 ACCAGTTTC-TTCCAGGCACCCGACCCTTTATCCATGAAAGGTGAAAAAAACAAG
*
38044594 ACCAGTTTCTTCCAGGCACCCGACCCTTTATCCATGAAATTAGTTGAAAAAAACAAG
1 ACCAGTTTCTTCCAGGCACCCGACCCTTTATCCATG-AA--AGGTGAAAAAAACAAG
*
38044651 ACCAGTTTCTTCC-GGACACCCGACCCTCTATCCATGAAAGGTGAAAAAAACAAG
1 ACCAGTTTCTTCCAGG-CACCCGACCCTTTATCCATGAAAGGTGAAAAAAACAAG
38044705 CGGATAGATC
Statistics
Matches: 148, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
53 3 0.02
54 88 0.59
55 6 0.04
56 4 0.03
57 47 0.32
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (54 bp):
ACCAGTTTCTTCCAGGCACCCGACCCTTTATCCATGAAAGGTGAAAAAAACAAG
Found at i:38044693 original size:111 final size:108
Alignment explanation
Indices: 38044486--38044704 Score: 325
Period size: 111 Copynumber: 2.0 Consensus size: 108
38044476 TGGAACTAAC
*
38044486 ACCAGTTCCTTCCAGGCACCCGACCCTTTCTCCATGAAAGGTGAAAAAAACAAGACCATTTCGTT
1 ACCAGTTCCTTCCAGGCACCCGACCCTTTATCCATGAAAGGTGAAAAAAACAAGACCATTTCGTT
*
38044551 ACAGGAACCCAACCCTTTATCCATGAAAGGTGAAAAAAACAAG
66 ACAGGAACCCAACCCTCTATCCATGAAAGGTGAAAAAAACAAG
* *
38044594 ACCAGTTTCTTCCAGGCACCCGACCCTTTATCCATGAAATTAGTTGAAAAAAACAAGACCAGTTT
1 ACCAGTTCCTTCCAGGCACCCGACCCTTTATCCATG-AA--AGGTGAAAAAAACAAGACCA-TTT
* *
38044659 C-TT-CCGGACACCCGACCCTCTATCCATGAAAGGTGAAAAAAACAAG
62 CGTTACAGGA-ACCCAACCCTCTATCCATGAAAGGTGAAAAAAACAAG
38044705 CGGATAGATC
Statistics
Matches: 100, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
108 34 0.34
109 2 0.02
110 4 0.04
111 56 0.56
112 4 0.04
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (108 bp):
ACCAGTTCCTTCCAGGCACCCGACCCTTTATCCATGAAAGGTGAAAAAAACAAGACCATTTCGTT
ACAGGAACCCAACCCTCTATCCATGAAAGGTGAAAAAAACAAG
Found at i:38046569 original size:27 final size:27
Alignment explanation
Indices: 38046539--38046592 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
38046529 GGAGGGCTGT
38046539 TGCAGAATCCAAGCTTGAATCAATCAA
1 TGCAGAATCCAAGCTTGAATCAATCAA
* *
38046566 TGCAGATTTCAAGCTTGAATCAATCAA
1 TGCAGAATCCAAGCTTGAATCAATCAA
38046593 CACAGCTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (27 bp):
TGCAGAATCCAAGCTTGAATCAATCAA
Found at i:38046660 original size:102 final size:99
Alignment explanation
Indices: 38046467--38046767 Score: 512
Period size: 102 Copynumber: 3.0 Consensus size: 99
38046457 CCGGGGCTGT
* * *
38046467 TGCAGAACCCAAGCTTGAATCAATCAACACAGCTGCAGAATGGGGGTCTGAACCCAACCCTGGGA
1 TGCAGAATCCAAGCTTGAATCAATCAACACAGCTGCAGAATGGGAGTCTCAACCCAACCCTGGGA
38046532 GGGCTGTTGCAGAATCCAAGCTTGAATCAATCAA
66 GGGCTGTTGCAGAATCCAAGCTTGAATCAATCAA
* *
38046566 TGCAGATTTCAAGCTTGAATCAATCAACACAGCTGCAGAATGGGAGTCTCAACGACCCAACCCTG
1 TGCAGAATCCAAGCTTGAATCAATCAACACAGCTGCAGAATGGGAGTCTC-A--ACCCAACCCTG
38046631 GGAGGGCTGTTGCAGAATCCAAGCTTGAATCAATCAA
63 GGAGGGCTGTTGCAGAATCCAAGCTTGAATCAATCAA
*
38046668 TGCAGAATCCAAGCTTGAATCAATCAACACAACTGCAGAATGGGAGTCTCAACCCAACCCTGGGA
1 TGCAGAATCCAAGCTTGAATCAATCAACACAGCTGCAGAATGGGAGTCTCAACCCAACCCTGGGA
*
38046733 GGGCTGTTTCAGAATCCAAGCTTGAATCAATCAA
66 GGGCTGTTGCAGAATCCAAGCTTGAATCAATCAA
38046767 T
1 T
38046768 ACAGCTGCAG
Statistics
Matches: 190, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
99 93 0.49
100 1 0.01
101 1 0.01
102 95 0.50
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (99 bp):
TGCAGAATCCAAGCTTGAATCAATCAACACAGCTGCAGAATGGGAGTCTCAACCCAACCCTGGGA
GGGCTGTTGCAGAATCCAAGCTTGAATCAATCAA
Found at i:38046671 original size:27 final size:27
Alignment explanation
Indices: 38046641--38046694 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
38046631 GGAGGGCTGT
38046641 TGCAGAATCCAAGCTTGAATCAATCAA
1 TGCAGAATCCAAGCTTGAATCAATCAA
38046668 TGCAGAATCCAAGCTTGAATCAATCAA
1 TGCAGAATCCAAGCTTGAATCAATCAA
38046695 CACAACTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (27 bp):
TGCAGAATCCAAGCTTGAATCAATCAA
Found at i:38046787 original size:72 final size:72
Alignment explanation
Indices: 38046670--38046810 Score: 255
Period size: 72 Copynumber: 2.0 Consensus size: 72
38046660 TCAATCAATG
*
38046670 CAGAATCCAAGCTTGAATCAATCAACACAACTGCAGAATGGGAGTCTCAACCCAACCCTGGGAGG
1 CAGAATCCAAGCTTGAATCAATCAACACAACTGCAGAATGGGAGTCTCAACCCAAACCTGGGAGG
38046735 GCTGTTT
66 GCTGTTT
* *
38046742 CAGAATCCAAGCTTGAATCAATCAATACAGCTGCAGAATGGGAGTCTCAACCCAAACCTGGGAGG
1 CAGAATCCAAGCTTGAATCAATCAACACAACTGCAGAATGGGAGTCTCAACCCAAACCTGGGAGG
38046807 GCTG
66 GCTG
38046811 GAGCAGCTCC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (72 bp):
CAGAATCCAAGCTTGAATCAATCAACACAACTGCAGAATGGGAGTCTCAACCCAAACCTGGGAGG
GCTGTTT
Found at i:38052301 original size:45 final size:45
Alignment explanation
Indices: 38052237--38052347 Score: 186
Period size: 45 Copynumber: 2.5 Consensus size: 45
38052227 GTACATGACG
38052237 TGTCACAGGTTTTTGTACATGACGTGTAACAAGCTAACCATGGCT
1 TGTCACAGGTTTTTGTACATGACGTGTAACAAGCTAACCATGGCT
* * * *
38052282 TGTCATAGGCTTTTGTACATGACGTGTTACACGCTAACCATGGCT
1 TGTCACAGGTTTTTGTACATGACGTGTAACAAGCTAACCATGGCT
38052327 TGTCACAGGTTTTTGTACATG
1 TGTCACAGGTTTTTGTACATG
38052348 GCATGTCACA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (45 bp):
TGTCACAGGTTTTTGTACATGACGTGTAACAAGCTAACCATGGCT
Found at i:38052348 original size:69 final size:69
Alignment explanation
Indices: 38052275--38052426 Score: 205
Period size: 69 Copynumber: 2.2 Consensus size: 69
38052265 ACAAGCTAAC
* * * * *
38052275 CATGGCTTGTCATAGGCTTTTGTACATGACGTGTTACACGCTAACCATGGCTTGTCACAGGTTTT
1 CATGGCATGTCACAGACTTTTGTACATGACGTGTAACACGCTAACCATGACTTGTCACAGGTTTT
38052340 TGTA
66 TGTA
* * * *
38052344 CATGGCATGTCACATATTTTTGTACATGATGTGTAACACTCTAACCATGACTTGTCACAGGTTTT
1 CATGGCATGTCACAGACTTTTGTACATGACGTGTAACACGCTAACCATGACTTGTCACAGGTTTT
38052409 TGTA
66 TGTA
* *
38052413 CATGACGTGTCACA
1 CATGGCATGTCACA
38052427 CGCTAATCAT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (69 bp):
CATGGCATGTCACAGACTTTTGTACATGACGTGTAACACGCTAACCATGACTTGTCACAGGTTTT
TGTA
Found at i:38052419 original size:114 final size:113
Alignment explanation
Indices: 38052219--38052536 Score: 474
Period size: 114 Copynumber: 2.8 Consensus size: 113
38052209 GAAGTTTCAT
* * *
38052219 AGGTTTTTGTACATGACGTGTCACAGGTTTTTGTACATGACGTGTAACAAGCTAACCATGGCTTG
1 AGGTTTTTGTACATGGCGTGTCACAGATTTTTGTACATGA-GTGTAACACGCTAACCATGGCTTG
* * *
38052284 TCATAGGCTTTTGTACATGACGTGTTACACGCTAACCATGGCTTGTCAC
65 TCACAGGTTTTTGTACATGACGTGTCACACGCTAACCATGGCTTGTCAC
* * * *
38052333 AGGTTTTTGTACATGGCATGTCACATATTTTTGTACATGATGTGTAACACTCTAACCATGACTTG
1 AGGTTTTTGTACATGGCGTGTCACAGATTTTTGTACATGA-GTGTAACACGCTAACCATGGCTTG
*
38052398 TCACAGGTTTTTGTACATGACGTGTCACACGCTAATCATGGCTTGTCAC
65 TCACAGGTTTTTGTACATGACGTGTCACACGCTAACCATGGCTTGTCAC
* *
38052447 AGATTTTTGTACATAGCGTGTCACAGATTTTTGTACATAGAGTGTAACACGCTAACCATGGCTTG
1 AGGTTTTTGTACATGGCGTGTCACAGATTTTTGTACAT-GAGTGTAACACGCTAACCATGGCTTG
* *
38052512 TCACAGATTTTTGTACATGGCGTGT
65 TCACAGGTTTTTGTACATGACGTGT
38052537 AACATCATAG
Statistics
Matches: 183, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
114 181 0.99
115 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (113 bp):
AGGTTTTTGTACATGGCGTGTCACAGATTTTTGTACATGAGTGTAACACGCTAACCATGGCTTGT
CACAGGTTTTTGTACATGACGTGTCACACGCTAACCATGGCTTGTCAC
Found at i:38052467 original size:45 final size:45
Alignment explanation
Indices: 38052344--38052471 Score: 168
Period size: 45 Copynumber: 2.8 Consensus size: 45
38052334 GGTTTTTGTA
* * * * *
38052344 CATGGCATGTCACATATTTTTGTACATGATGTGTAACACTCTAAC
1 CATGGCTTGTCACAGATTTTTGTACATGACGTGTCACACGCTAAC
* * *
38052389 CATGACTTGTCACAGGTTTTTGTACATGACGTGTCACACGCTAAT
1 CATGGCTTGTCACAGATTTTTGTACATGACGTGTCACACGCTAAC
38052434 CATGGCTTGTCACAGATTTTTGTACAT-AGCGTGTCACA
1 CATGGCTTGTCACAGATTTTTGTACATGA-CGTGTCACA
38052472 GATTTTTGTA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 1 0.01
45 71 0.99
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (45 bp):
CATGGCTTGTCACAGATTTTTGTACATGACGTGTCACACGCTAAC
Found at i:38052469 original size:69 final size:69
Alignment explanation
Indices: 38052396--38052536 Score: 230
Period size: 69 Copynumber: 2.0 Consensus size: 69
38052386 AACCATGACT
* * *
38052396 TGTCACAGGTTTTTGTACAT-GACGTGTCACACGCTAATCATGGCTTGTCACAGATTTTTGTACA
1 TGTCACAGATTTTTGTACATAGA-GTGTAACACGCTAACCATGGCTTGTCACAGATTTTTGTACA
38052460 TAGCG
65 TAGCG
38052465 TGTCACAGATTTTTGTACATAGAGTGTAACACGCTAACCATGGCTTGTCACAGATTTTTGTACAT
1 TGTCACAGATTTTTGTACATAGAGTGTAACACGCTAACCATGGCTTGTCACAGATTTTTGTACAT
*
38052530 GGCG
66 AGCG
38052534 TGT
1 TGT
38052537 AACATCATAG
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 65 0.97
70 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (69 bp):
TGTCACAGATTTTTGTACATAGAGTGTAACACGCTAACCATGGCTTGTCACAGATTTTTGTACAT
AGCG
Found at i:38052485 original size:24 final size:24
Alignment explanation
Indices: 38052441--38052491 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
38052431 AATCATGGCT
*
38052441 TGTCACAGATTTTTGTACATAGCG
1 TGTCACAGATTTTTGTACATAGAG
38052465 TGTCACAGATTTTTGTACATAGAG
1 TGTCACAGATTTTTGTACATAGAG
38052489 TGT
1 TGT
38052492 AACACGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (24 bp):
TGTCACAGATTTTTGTACATAGAG
Found at i:38079310 original size:15 final size:13
Alignment explanation
Indices: 38079266--38079299 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
38079256 GTAATTTTAT
38079266 GAAAAAAAA-AAA
1 GAAAAAAAACAAA
*
38079278 CAAAAAAAACAAA
1 GAAAAAAAACAAA
38079291 GAAAAAAAA
1 GAAAAAAAA
38079300 TTCAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (13 bp):
GAAAAAAAACAAA
Found at i:38088179 original size:3 final size:3
Alignment explanation
Indices: 38088173--38088198 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38088163 AGCTGCGTTA
38088173 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
38088199 CGTGGTGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:38092610 original size:2 final size:2
Alignment explanation
Indices: 38092603--38092633 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38092593 ACAAACATAT
38092603 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
38092634 TAGTTTCTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38098744 original size:3 final size:3
Alignment explanation
Indices: 38098738--38098774 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
38098728 TGAAGAGGAG
*
38098738 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
38098775 GACAGGAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:38110189 original size:15 final size:15
Alignment explanation
Indices: 38110161--38110193 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
38110151 GCATTATATC
38110161 TTTCTCTCTTTTTTT
1 TTTCTCTCTTTTTTT
*
38110176 TTTCT-TCTTCTTTT
1 TTTCTCTCTTTTTTT
38110190 TTTC
1 TTTC
38110194 ACTTAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTCTCTTTTTTT
Found at i:38112381 original size:37 final size:36
Alignment explanation
Indices: 38112264--38112379 Score: 121
Period size: 37 Copynumber: 3.2 Consensus size: 36
38112254 ATTTTTCAAA
** *
38112264 AAAAAATATTAAAAATTTAATTATTACATATCATGCT
1 AAAAAATA-TAATTATTTAATTATTACATATCATGAT
*
38112301 AAAAAATATAATTATTATAAATT-TTACATATTAT-ATT
1 AAAAAATATAATTATT-T-AATTATTACATATCATGA-T
*
38112338 AAAAAATATAATTA-TTAATTATTACGTATCATGAT
1 AAAAAATATAATTATTTAATTATTACATATCATGAT
38112373 GAAAAAA
1 -AAAAAA
38112380 ATTATTACAC
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
34 4 0.06
35 11 0.16
36 14 0.21
37 34 0.51
38 4 0.06
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (36 bp):
AAAAAATATAATTATTTAATTATTACATATCATGAT
Found at i:38113966 original size:4 final size:4
Alignment explanation
Indices: 38113959--38113987 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
38113949 TGGAGTTACA
38113959 ATTT ATTT ATTT ATTT ATTT ATTT -TTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
38113988 AATTAAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:38119235 original size:26 final size:27
Alignment explanation
Indices: 38119206--38119258 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
38119196 AGAAGCTGAA
38119206 TTTTATTGCGTT-TTTT-TTTCACCATC
1 TTTTATTGC-TTGTTTTGTTTCACCATC
*
38119232 TTTTATTGCTTGTTTTGTTTTACCATC
1 TTTTATTGCTTGTTTTGTTTCACCATC
38119259 AGTGTTGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 2 0.08
26 13 0.54
27 9 0.38
ACGTcount: A:0.11, C:0.17, G:0.09, T:0.62
Consensus pattern (27 bp):
TTTTATTGCTTGTTTTGTTTCACCATC
Found at i:38120887 original size:2 final size:2
Alignment explanation
Indices: 38120880--38120905 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38120870 AAGAGAAATA
38120880 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
38120906 GTGGGGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38120981 original size:50 final size:49
Alignment explanation
Indices: 38120895--38120993 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 49
38120885 GAGAGAGAGA
38120895 GAGAGAGAGAGGTGGGGGTGAGCCGTGGGGTTCTCTGAAGGCACCTGCC
1 GAGAGAGAGAGGTGGGGGTGAGCCGTGGGGTTCTCTGAAGGCACCTGCC
38120944 GAGAGAGAGAGGTGGGGGTTGAGCCGTGGGGTTCTCTGAAGGCACCTGCC
1 GAGAGAGAGAGGTGGGGG-TGAGCCGTGGGGTTCTCTGAAGGCACCTGCC
38120994 TTGACGAGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 18 0.37
50 31 0.63
ACGTcount: A:0.18, C:0.18, G:0.46, T:0.17
Consensus pattern (49 bp):
GAGAGAGAGAGGTGGGGGTGAGCCGTGGGGTTCTCTGAAGGCACCTGCC
Found at i:38121403 original size:2 final size:2
Alignment explanation
Indices: 38121396--38121422 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38121386 TTTGCATTCA
38121396 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
38121423 GTGAATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38123018 original size:93 final size:93
Alignment explanation
Indices: 38122845--38123019 Score: 269
Period size: 93 Copynumber: 1.9 Consensus size: 93
38122835 CACGACGGGG
* * * *
38122845 GTGAGATATTTGAACTTGTTTATTGCTAAAGTTTATCCCTACAATTGGTTTTATAAAACTCAACG
1 GTGAGATATTTGAACTTGTGTATTGCCAAAGTTTACCCCTACAATTGGTTTTATAAAACTAAACG
* *
38122910 TCAAGGGTGGCATTTTATTCAAATATTA
66 TCAAGGGCGACATTTTATTCAAATATTA
*
38122938 GTGAGATATTTGAACTTGTGTATTGCCAAAGTTTACCCCTCCAATTGGTTTTATAAAACTAAACG
1 GTGAGATATTTGAACTTGTGTATTGCCAAAGTTTACCCCTACAATTGGTTTTATAAAACTAAACG
* *
38123003 TCGAGGGCGATATTTTA
66 TCAAGGGCGACATTTTA
38123020 CAATCAAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (93 bp):
GTGAGATATTTGAACTTGTGTATTGCCAAAGTTTACCCCTACAATTGGTTTTATAAAACTAAACG
TCAAGGGCGACATTTTATTCAAATATTA
Found at i:38125034 original size:2 final size:2
Alignment explanation
Indices: 38125027--38125060 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38125017 TAAGGGAAAC
38125027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38125061 GATCTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38126000 original size:7 final size:7
Alignment explanation
Indices: 38125988--38126015 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
38125978 AGGTAGAGAG
38125988 AATGGCT
1 AATGGCT
38125995 AATGGCT
1 AATGGCT
38126002 AATGGCT
1 AATGGCT
38126009 AATGGCT
1 AATGGCT
38126016 CCCACATGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
AATGGCT
Found at i:38129633 original size:20 final size:22
Alignment explanation
Indices: 38129600--38129648 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
38129590 TTAATATTAT
38129600 TTTTATTTCAATTTCT-TTTT-A
1 TTTT-TTTCAATTTCTATTTTCA
* *
38129621 TTTTTTTCTATTTGTATTTTCA
1 TTTTTTTCAATTTCTATTTTCA
38129643 TTTTTT
1 TTTTTT
38129649 AATCTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 8 0.33
22 7 0.29
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTTTTCAATTTCTATTTTCA
Found at i:38130449 original size:21 final size:21
Alignment explanation
Indices: 38130425--38130467 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
38130415 CTCCTCCTGA
*
38130425 AACTATTCATACAGGTATTTC
1 AACTATTCATACAAGTATTTC
*
38130446 AACTATTCATACAAGTCTTTC
1 AACTATTCATACAAGTATTTC
38130467 A
1 A
38130468 CTCTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (21 bp):
AACTATTCATACAAGTATTTC
Found at i:38136065 original size:15 final size:15
Alignment explanation
Indices: 38136015--38136071 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
38136005 GAAAATTTTT
* *
38136015 TTTAAAATAATTATAA
1 TTTAAATTAA-TAAAA
*
38136031 TTTATA-TAATAATAA
1 TTTAAATTAATAA-AA
38136046 TTTTAAATTAATAAAA
1 -TTTAAATTAATAAAA
38136062 TTTAAATTAA
1 TTTAAATTAA
38136072 ATTAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 2 0.06
15 15 0.43
16 12 0.34
17 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAATTAATAAAA
Found at i:38141766 original size:15 final size:15
Alignment explanation
Indices: 38141746--38141774 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38141736 AGGGGACCGT
38141746 GGTGGAAGAGGTGGC
1 GGTGGAAGAGGTGGC
38141761 GGTGGAAGAGGTGG
1 GGTGGAAGAGGTGG
38141775 TGGCCGTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.62, T:0.14
Consensus pattern (15 bp):
GGTGGAAGAGGTGGC
Found at i:38141789 original size:18 final size:18
Alignment explanation
Indices: 38141733--38141789 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
38141723 GAGGCTATCA
38141733 AGGAGG-GGACCGTGGTGG
1 AGGAGGTGG-CCGTGGTGG
* * **
38141751 AAGAGGTGGCGGTGGAAG
1 AGGAGGTGGCCGTGGTGG
*
38141769 AGGTGGTGGCCGTGGTGG
1 AGGAGGTGGCCGTGGTGG
38141787 AGG
1 AGG
38141790 CGGCAGAGAT
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
18 27 0.93
19 2 0.07
ACGTcount: A:0.18, C:0.09, G:0.60, T:0.14
Consensus pattern (18 bp):
AGGAGGTGGCCGTGGTGG
Found at i:38155697 original size:45 final size:48
Alignment explanation
Indices: 38155612--38155711 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 48
38155602 TTAGATGTCC
* * * *
38155612 AAAAAAATATTAATAATTATAATTTATTATAAATATTTAAAAACATAG
1 AAAAAAATATTAAAAATTATAATTCATTATAAATAATTAAAAACATAA
* *
38155660 AAAATAATATTAAAAATT-TAATTCATT-T-AATAATTAAAATCATAA
1 AAAAAAATATTAAAAATTATAATTCATTATAAATAATTAAAAACATAA
38155705 AAAAAAA
1 AAAAAAA
38155712 ATTGGGTACA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 20 0.44
46 1 0.02
47 8 0.18
48 16 0.36
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (48 bp):
AAAAAAATATTAAAAATTATAATTCATTATAAATAATTAAAAACATAA
Found at i:38185688 original size:2 final size:2
Alignment explanation
Indices: 38185681--38185707 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38185671 GACGAAAAAT
38185681 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38185708 TTATCCAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38190987 original size:2 final size:2
Alignment explanation
Indices: 38190975--38191034 Score: 65
Period size: 2 Copynumber: 31.5 Consensus size: 2
38190965 GTCAAATCCT
*
38190975 TA TA TA GTA TA TA TA TA TA -A TA TA TA TA TA TT TA -A T- TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
38191014 TA TN TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
38191035 TGTTGTAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
1 4 0.08
2 43 0.88
3 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38190993 original size:13 final size:13
Alignment explanation
Indices: 38190975--38191033 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
38190965 GTCAAATCCT
*
38190975 TATATAGTATATA
1 TATATAATATATA
38190988 TATATAATATATA
1 TATATAATATATA
38191001 TATATTTAAT-TA-A
1 TATA--TAATATATA
*
38191014 TATNTATATATATA
1 TATATA-ATATATA
38191028 TATATA
1 TATATA
38191034 TTGTTGTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 2 0.05
12 2 0.05
13 22 0.58
14 8 0.21
15 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
TATATAATATATA
Found at i:38193529 original size:7 final size:7
Alignment explanation
Indices: 38193517--38193547 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
38193507 GATATTGAGA
38193517 GAGTCTG
1 GAGTCTG
38193524 GAGTCTG
1 GAGTCTG
38193531 GAGTCTG
1 GAGTCTG
38193538 GAGTCTG
1 GAGTCTG
38193545 GAG
1 GAG
38193548 AGCTGGACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.45, T:0.26
Consensus pattern (7 bp):
GAGTCTG
Found at i:38194654 original size:2 final size:2
Alignment explanation
Indices: 38194647--38194673 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38194637 TATTAAGATT
38194647 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38194674 TTATTCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38195139 original size:22 final size:22
Alignment explanation
Indices: 38195088--38195139 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
38195078 AGTCGGCAGC
* *
38195088 GTATAAACTAAGAAAAATTAAT
1 GTATAAATTAAGAAAAAATAAT
*
38195110 GCAT-AATTAAGACAAAAATAAT
1 GTATAAATTAAGA-AAAAATAAT
38195132 -TATAAATT
1 GTATAAATT
38195140 TATATGCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.29
Consensus pattern (22 bp):
GTATAAATTAAGAAAAAATAAT
Found at i:38203733 original size:122 final size:122
Alignment explanation
Indices: 38203485--38203852 Score: 468
Period size: 122 Copynumber: 3.0 Consensus size: 122
38203475 AATAGGTTAC
* * * * *
38203485 TAATTAGGAAGAACCTTGTTTCAACGATCATAAACCTACCCGAGAAAAGGAAAATATGAATTACT
1 TAATTAGGAAGAACTTTGTTTCAATGATCATGAACCTACCAGAGAAAAGGAAAATGTGAATT-CT
* * * * * *
38203550 CTCGTCTTACTATTGTTCTAGAGTAAGAATTATGTTGTCCTCGTTAATGTCATTGTATAT
65 -T-TTCTTAGTACTGTTTTAGAGTAAGAATTATGTTGTCCTTGTTAATGTCATGGTATAT
* *
38203610 TAATTAAGAAGAACTTTGTTTCAATGATCATGAACCTACCAGAGAAAAGGAAAATGTCAATT-TT
1 TAATTAGGAAGAACTTTGTTTCAATGATCATGAACCTACCAGAGAAAAGGAAAATGTGAATTCTT
* *
38203674 ATTCTTAGTACTGTTTTAGAGTGAGAATTGTGTTGTCCTTGTTAATGTCATGGTATAT
66 -TTCTTAGTACTGTTTTAGAGTAAGAATTATGTTGTCCTTGTTAATGTCATGGTATAT
* *
38203732 TAATTAGGAAGAACTTTGTTTCAATGGTCATGAACCTACCGGAGAAAAGGAAAATGTGAATTCTT
1 TAATTAGGAAGAACTTTGTTTCAATGATCATGAACCTACCAGAGAAAAGGAAAATGTGAATTCTT
* * * * *
38203797 TTCGTCTCAGTACTGTATTAGAGAAAGAATTTTGTTGTCATTGTTAATGTCTTGGT
66 TTC-T-T-AGTACTGTTTTAGAGTAAGAATTATGTTGTCCTTGTTAATGTCATGGT
38203853 CTATGCATCT
Statistics
Matches: 213, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
122 111 0.52
123 4 0.02
124 1 0.00
125 97 0.46
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (122 bp):
TAATTAGGAAGAACTTTGTTTCAATGATCATGAACCTACCAGAGAAAAGGAAAATGTGAATTCTT
TTCTTAGTACTGTTTTAGAGTAAGAATTATGTTGTCCTTGTTAATGTCATGGTATAT
Found at i:38223437 original size:106 final size:106
Alignment explanation
Indices: 38223318--38223521 Score: 363
Period size: 106 Copynumber: 1.9 Consensus size: 106
38223308 CCGCCAGTTC
* * *
38223318 TCTCTCTCTTTCTCTCTTCTGTTTCATATTGTAAAGTAAAAGAGAAGAGGGATGCACTGCTAGAC
1 TCTCTCTCTTTCTCTCTTCTGTTTCATATTGTAAAGTAAAAGAGAAGAGGCATGCACTGCTACAA
*
38223383 TCTGTTCATATGCTTTACAAAGATGCTTATATTCCACCAGT
66 TCAGTTCATATGCTTTACAAAGATGCTTATATTCCACCAGT
*
38223424 TCTCTCTCTTTCTCTGTTCTGTTTCATATTGTAAAGTAAAAGAGAAGAGGCATGCACTGCTACAA
1 TCTCTCTCTTTCTCTCTTCTGTTTCATATTGTAAAGTAAAAGAGAAGAGGCATGCACTGCTACAA
38223489 TCAGTTCATATGCTTTACAAAGATGCTTATATT
66 TCAGTTCATATGCTTTACAAAGATGCTTATATT
38223522 GTTGCAAGCT
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 93 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (106 bp):
TCTCTCTCTTTCTCTCTTCTGTTTCATATTGTAAAGTAAAAGAGAAGAGGCATGCACTGCTACAA
TCAGTTCATATGCTTTACAAAGATGCTTATATTCCACCAGT
Found at i:38237235 original size:29 final size:29
Alignment explanation
Indices: 38237193--38237252 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
38237183 TATGCAACAT
38237193 AGATTTTTCTTAGTGATGCTTCCCCCACC
1 AGATTTTTCTTAGTGATGCTTCCCCCACC
*
38237222 AGATTTTTCTTAGTGATGTTTCCCCCACC
1 AGATTTTTCTTAGTGATGCTTCCCCCACC
38237251 AG
1 AG
38237253 TCTTTGCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.38
Consensus pattern (29 bp):
AGATTTTTCTTAGTGATGCTTCCCCCACC
Found at i:38241299 original size:20 final size:20
Alignment explanation
Indices: 38241274--38241313 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38241264 CGCCCCCGTT
38241274 TCTCCATCGAT-CTCATCACA
1 TCTCCATCGATACT-ATCACA
*
38241294 TCTCCATGGATACTATCACA
1 TCTCCATCGATACTATCACA
38241314 GTGGTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.28, C:0.35, G:0.07, T:0.30
Consensus pattern (20 bp):
TCTCCATCGATACTATCACA
Found at i:38242607 original size:15 final size:16
Alignment explanation
Indices: 38242587--38242626 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
38242577 AAACGACAAC
38242587 TTATA-TATATATAAT
1 TTATATTATATATAAT
38242602 TTATATTTATATATAAT
1 TTATA-TTATATATAAT
38242619 TTAT-TTAT
1 TTATATTAT
38242627 TTATCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTATATATAAT
Found at i:38246610 original size:2 final size:2
Alignment explanation
Indices: 38246605--38246629 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38246595 GTTTATCGCC
38246605 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
38246630 TTGAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38258806 original size:79 final size:79
Alignment explanation
Indices: 38258710--38258869 Score: 257
Period size: 79 Copynumber: 2.0 Consensus size: 79
38258700 AGTAGGAAAG
* *
38258710 TTAGTGTTCTCTCTTGACTTGGCCTTTATCTATACAAATTGACAGAGCAAGCTAAATGTCTTCTT
1 TTAGTGTTCTCTCTTGACTTGGCCTTTATATATACAAATTGACAGAGCAAACTAAATGTCTTCTT
*
38258775 AGGTAAGTTCACAT
66 AGGTAAGTTAACAT
* * * *
38258789 TTAGTGTTTTCTCTTGACTTGGCCTTTATATATCCTAATTGACAGAGCAAACTACATGTCTTCTT
1 TTAGTGTTCTCTCTTGACTTGGCCTTTATATATACAAATTGACAGAGCAAACTAAATGTCTTCTT
38258854 AGGTAAGTTAACAT
66 AGGTAAGTTAACAT
38258868 TT
1 TT
38258870 CTGATCCATC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (79 bp):
TTAGTGTTCTCTCTTGACTTGGCCTTTATATATACAAATTGACAGAGCAAACTAAATGTCTTCTT
AGGTAAGTTAACAT
Found at i:38300012 original size:2 final size:2
Alignment explanation
Indices: 38300005--38300036 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
38299995 TCAATAAGAC
*
38300005 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38300037 GGGGGGGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38304065 original size:23 final size:22
Alignment explanation
Indices: 38304039--38304127 Score: 65
Period size: 23 Copynumber: 3.9 Consensus size: 22
38304029 AATAATTAAT
38304039 TTAAATAAAAAATATTAAAAGAA
1 TTAAATAAAAAATATTAAAA-AA
* **
38304062 TTAAATTGAAATAAT-TTTTAAAA
1 TTAAA-T-AAAAAATATTAAAAAA
*
38304085 TTAAA-AAACTTAAATATTAAAAAT
1 TTAAATAAA---AAATATTAAAAAA
*
38304109 TTAAATAAAAAAAATTAAA
1 TTAAATAAAAAATATTAAA
38304128 TTAAAAAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
20 3 0.06
22 9 0.18
23 15 0.29
24 15 0.29
25 9 0.18
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAATAAAAAATATTAAAAAA
Found at i:38304106 original size:15 final size:15
Alignment explanation
Indices: 38304048--38304137 Score: 62
Period size: 14 Copynumber: 5.9 Consensus size: 15
38304038 TTTAAATAAA
38304048 AAATATTAAAAGAATT
1 AAATATTAAAA-AATT
* *
38304064 AAAT-TGAAATAATTTTT
1 AAATATTAAA-AA--ATT
38304081 AAA-ATTAAAAAACTT
1 AAATATTAAAAAA-TT
*
38304096 AAATATTAAAAATTT
1 AAATATTAAAAAATT
*
38304111 AAATA-AAAAAAATT
1 AAATATTAAAAAATT
*
38304125 AAAT-TAAAAAAAT
1 AAATATTAAAAAAT
38304138 ACACATACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
14 19 0.32
15 17 0.28
16 15 0.25
17 9 0.15
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (15 bp):
AAATATTAAAAAATT
Found at i:38304120 original size:14 final size:14
Alignment explanation
Indices: 38304082--38304137 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
38304072 ATAATTTTTA
* *
38304082 AAATTAAAAAACTT
1 AAATAAAAAAATTT
*
38304096 AAATATTAAAAATTT
1 AAATA-AAAAAATTT
*
38304111 AAATAAAAAAAATT
1 AAATAAAAAAATTT
38304125 AAATTAAAAAAAT
1 AAA-TAAAAAAAT
38304138 ACACATACAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 14 0.41
15 20 0.59
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAAAAAAATTT
Found at i:38304480 original size:27 final size:29
Alignment explanation
Indices: 38304426--38304486 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 29
38304416 GACTTCGATC
38304426 GCTGAGCAATAAAAAACGTCCATCTTGATT
1 GCTGAGCAATAAAAAAC-TCCATCTTGATT
*
38304456 GCTGAG-AATAAAAAA-TCCATTTTGATT
1 GCTGAGCAATAAAAAACTCCATCTTGATT
38304483 -CTGA
1 GCTGA
38304487 ATCACTGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 11 0.37
29 9 0.30
30 6 0.20
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (29 bp):
GCTGAGCAATAAAAAACTCCATCTTGATT
Found at i:38309978 original size:25 final size:24
Alignment explanation
Indices: 38309944--38309996 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
38309934 TGATTCCAAC
38309944 TTATAATAAAATATTA-ATATTAAA
1 TTATAATAAAATATTATAT-TTAAA
38309968 TTATAAATAAAATATTATATTTAAA
1 TTAT-AATAAAATATTATATTTAAA
38309993 TTAT
1 TTAT
38309997 CAATTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 4 0.15
25 21 0.78
26 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATAATAAAATATTATATTTAAA
Found at i:38310090 original size:9 final size:10
Alignment explanation
Indices: 38310041--38310088 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
38310031 ATTTAAAAAC
38310041 AAAATAAATTA
1 AAAATAAA-TA
38310052 AAAATAAATA
1 AAAATAAATA
****
38310062 AAAAGCTNTA
1 AAAATAAATA
38310072 AAAATAAATA
1 AAAATAAATA
38310082 AAAATAA
1 AAAATAA
38310089 TATCATTTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.21
Consensus pattern (10 bp):
AAAATAAATA
Found at i:38310128 original size:22 final size:20
Alignment explanation
Indices: 38310095--38310228 Score: 113
Period size: 19 Copynumber: 6.8 Consensus size: 20
38310085 ATAATATCAT
38310095 TTAA-ATTATAAATAAAATA
1 TTAATATTATAAATAAAATA
38310114 TTAATACTT-T--ATAAACAT-
1 TTAATA-TTATAAATAAA-ATA
38310132 TTAA-ATTATAAATAAAATA
1 TTAATATTATAAATAAAATA
* * *
38310151 TTAATATTTTAAAAAGTAAAGA
1 TTAATATTATAAATA--AAATA
*
38310173 TTAA-ATAATAAATAAAATA
1 TTAATATTATAAATAAAATA
38310192 TTAATATT-TAAATGATAAATTA
1 TTAATATTATAAAT-A-AAA-TA
38310214 TTAATATTATAAATA
1 TTAATATTATAAATA
38310229 TATTATCAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 27
0.72 0.06 0.21
Matches are distributed among these distances:
16 2 0.02
17 2 0.02
18 11 0.12
19 28 0.30
20 13 0.14
21 12 0.13
22 19 0.21
23 5 0.05
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (20 bp):
TTAATATTATAAATAAAATA
Found at i:38310177 original size:41 final size:37
Alignment explanation
Indices: 38310092--38310200 Score: 139
Period size: 37 Copynumber: 2.8 Consensus size: 37
38310082 AAAATAATAT
*
38310092 CATTTAAATTATAAATAAAATATTAATACTTTATAAA
1 CATTTAAATTATAAATAAAATATTAATATTTTATAAA
38310129 CATTTAAATTATAAATAAAATATTAATATTTTAAAAAGTAAA
1 CATTTAAATTATAAATAAAATATTAATATTTT----A-TAAA
* *
38310171 GA-TTAAATAATAAATAAAATATTAATATTT
1 CATTTAAATTATAAATAAAATATTAATATTT
38310201 AAATGATAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
37 31 0.48
41 28 0.44
42 5 0.08
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (37 bp):
CATTTAAATTATAAATAAAATATTAATATTTTATAAA
Found at i:38310217 original size:41 final size:40
Alignment explanation
Indices: 38310095--38310228 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 40
38310085 ATAATATCAT
38310095 TTAAATTATAAATAAAATATTAATACTTT--ATA-AACAT-
1 TTAAATTATAAATAAAATATTAATACTTTAAATATAA-ATA
* * *
38310132 TTAAATTATAAATAAAATATTAATATTTTAAAAAGTAAAGA
1 TTAAATTATAAATAAAATATTAATACTTTAAATA-TAAATA
*
38310173 TTAAATAATAAATAAAATATTAATA-TTTAAATGATAAATTA
1 TTAAATTATAAATAAAATATTAATACTTTAAAT-ATAAA-TA
38310214 TTAATATTATAAATA
1 TTAA-ATTATAAATA
38310229 TATTATCAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
37 28 0.34
39 2 0.02
40 11 0.13
41 32 0.39
42 9 0.11
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (40 bp):
TTAAATTATAAATAAAATATTAATACTTTAAATATAAATA
Found at i:38310328 original size:25 final size:25
Alignment explanation
Indices: 38310283--38310345 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
38310273 TTGATCATCA
38310283 TAATATTTAAA-T-TAAATAAAT-T
1 TAATATTTAAATTATAAATAAATAT
38310305 TAATATTTTAAATTATAAATAAATAT
1 TAATA-TTTAAATTATAAATAAATAT
*
38310331 TAATATTGAAATTAT
1 TAATATTTAAATTAT
38310346 CAATTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 5 0.14
23 6 0.17
24 1 0.03
25 18 0.50
26 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TAATATTTAAATTATAAATAAATAT
Found at i:38310367 original size:25 final size:25
Alignment explanation
Indices: 38310339--38310394 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
38310329 ATTAATATTG
38310339 AAATTATCAATTATTAAT-TTTAAA
1 AAATTATCAATTATTAATATTTAAA
*
38310363 TAAATTATCAATTATTAATATTTTAA
1 -AAATTATCAATTATTAATATTTAAA
38310389 AAATTA
1 AAATTA
38310395 AATAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATTATCAATTATTAATATTTAAA
Found at i:38310437 original size:134 final size:138
Alignment explanation
Indices: 38310173--38310451 Score: 408
Period size: 134 Copynumber: 2.0 Consensus size: 138
38310163 AAAGTAAAGA
* *
38310173 TTAAATAATAAATAAAATATTAATATTTAAATGATAAATTATTAATATTATAAATATATTATCAA
1 TTAAATAATAAATAAAATATTAATATTGAAATGATAAATTATTAATATTATAAATAAATTATCAA
* * *
38310238 TTATTAATATTTTCAAATAAAATAAAATAAAATAATTGATCATCATAATATTTAAATTAAATAAA
66 TTATTAATATTTTAAAATAAAATAAAAT-AAATAATTAATCATAATAATATTTAAATTAAATAAA
38310303 T-TTAATATT
130 TGTTAATA-T
* * *
38310312 TTAAATTATAAAT-AAATATTAATATTGAAATTATCAATTATTAAT-TT-TAAATAAATTATCAA
1 TTAAATAATAAATAAAATATTAATATTGAAATGATAAATTATTAATATTATAAATAAATTATCAA
*
38310374 TTATTAATATTTTAAAAATTAAATAAAAT-AA-AATTAATCATAATAATATTTAAATTAAATAAA
66 TTATTAATATTTT-AAAATAAAATAAAATAAATAATTAATCATAATAATATTTAAATTAAATAAA
38310437 TGTTAATAT
130 TGTTAATAT
38310446 TTAAAT
1 TTAAAT
38310452 GATTAATTAT
Statistics
Matches: 129, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
134 38 0.29
135 8 0.06
136 27 0.21
137 15 0.12
138 29 0.22
139 12 0.09
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (138 bp):
TTAAATAATAAATAAAATATTAATATTGAAATGATAAATTATTAATATTATAAATAAATTATCAA
TTATTAATATTTTAAAATAAAATAAAATAAATAATTAATCATAATAATATTTAAATTAAATAAAT
GTTAATAT
Found at i:38310443 original size:23 final size:23
Alignment explanation
Indices: 38310417--38310478 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
38310407 TTAATCATAA
*
38310417 TAATATTTAAATTAAATAAATGT
1 TAATATTTAAATTAAATAAATAT
* * *
38310440 TAATATTTAAA-TGATTAATTAT
1 TAATATTTAAATTAAATAAATAT
*
38310462 TAATATTTTAATTAAAT
1 TAATATTTAAATTAAAT
38310479 TCTAGATTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
TAATATTTAAATTAAATAAATAT
Found at i:38310444 original size:109 final size:114
Alignment explanation
Indices: 38310305--38310518 Score: 298
Period size: 111 Copynumber: 1.9 Consensus size: 114
38310295 TAAATAAATT
*
38310305 TAATATTTTAAATTATAAATAAATATTAATATTGAAATTATCAATTATT-A-ATTTTAAATAAAT
1 TAATATTTTAAATTATAAATAAATATTAATATTGAAATGATCAATTATTAATATTTTAAATAAAT
*
38310368 TATCA-ATTATTAATATTTTAAAAAT-TAAATAAAATAAAATTAATCATAA
66 TAT-AGATTATTAATATTTAAAAAATCT-AATAAAATAAAATTAATCATAA
* * * *
38310417 TAATA-TTTAAA-T-TAAATAAATGTTAATATTTAAATGATTAATTATTAATATTTTAATTAAAT
1 TAATATTTTAAATTATAAATAAATATTAATATTGAAATGATCAATTATTAATATTTTAAATAAAT
*
38310479 TCTAGATTATTAATATTTAAAAAATCTAATAAAATAAAAT
66 TATAGATTATTAATATTTAAAAAATCTAATAAAATAAAAT
38310519 GTCACATAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
109 30 0.33
110 3 0.03
111 52 0.57
112 6 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (114 bp):
TAATATTTTAAATTATAAATAAATATTAATATTGAAATGATCAATTATTAATATTTTAAATAAAT
TATAGATTATTAATATTTAAAAAATCTAATAAAATAAAATTAATCATAA
Found at i:38321064 original size:2 final size:2
Alignment explanation
Indices: 38321059--38321083 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38321049 GGGGATTAAA
38321059 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
38321084 CATTATCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38322046 original size:2 final size:2
Alignment explanation
Indices: 38322041--38322075 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
38322031 GAAAGAGCTG
*
38322041 GA GA GA GA GA GA GA GA GA GC GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
38322076 GATGAAGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38327908 original size:6 final size:6
Alignment explanation
Indices: 38327885--38327931 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
38327875 AAGCCCCCAA
* *
38327885 CACACC CGCACG CACACC CACACC CACACC CACACC CACACC CACAC
1 CACACC CACACC CACACC CACACC CACACC CACACC CACACC CACAC
38327932 GCACCCAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.32, C:0.64, G:0.04, T:0.00
Consensus pattern (6 bp):
CACACC
Found at i:38327908 original size:18 final size:18
Alignment explanation
Indices: 38327885--38327935 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
38327875 AAGCCCCCAA
*
38327885 CACACCCGCACGCACACC
1 CACACCCACACGCACACC
*
38327903 CACACCCACACCCACACC
1 CACACCCACACGCACACC
38327921 CACACCCACACGCAC
1 CACACCCACACGCAC
38327936 CCAAACCTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.63, G:0.06, T:0.00
Consensus pattern (18 bp):
CACACCCACACGCACACC
Found at i:38338327 original size:15 final size:15
Alignment explanation
Indices: 38338283--38338319 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
38338273 TGATTGCAGA
*
38338283 TAATGTAATTATAAG
1 TAATATAATTATAAG
38338298 TAATATAATTATAAG
1 TAATATAATTATAAG
38338313 TAATATA
1 TAATATA
38338320 TTTGTAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (15 bp):
TAATATAATTATAAG
Found at i:38338572 original size:21 final size:23
Alignment explanation
Indices: 38338524--38338573 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
38338514 CATCTGTTAA
38338524 ATATATTTTTAATGTCATATATT
1 ATATATTTTTAATGTCATATATT
38338547 -T-TATTTTT-AT-T-ATAATATT
1 ATATATTTTTAATGTCAT-ATATT
38338566 ATATATTT
1 ATATATTT
38338574 ATTTTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
18 2 0.08
19 6 0.25
20 3 0.12
21 12 0.50
22 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
ATATATTTTTAATGTCATATATT
Found at i:38350809 original size:16 final size:17
Alignment explanation
Indices: 38350788--38350819 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
38350778 TTTCTACCAT
38350788 GAAACTCATAA-AAAAC
1 GAAACTCATAATAAAAC
38350804 GAAACTCATAATAAAA
1 GAAACTCATAATAAAA
38350820 TGTATGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.16, G:0.06, T:0.16
Consensus pattern (17 bp):
GAAACTCATAATAAAAC
Found at i:38351040 original size:20 final size:22
Alignment explanation
Indices: 38350997--38351040 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
38350987 CATGTAATTG
*
38350997 AAATTATTTGTATAATTTTCAC
1 AAATTACTTGTATAATTTTCAC
*
38351019 AAATTACTT-TAT-ATTTTGAC
1 AAATTACTTGTATAATTTTCAC
38351039 AA
1 AA
38351041 CTTCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.48
Consensus pattern (22 bp):
AAATTACTTGTATAATTTTCAC
Found at i:38375026 original size:5 final size:5
Alignment explanation
Indices: 38375016--38375040 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38375006 AATAGAAAGA
38375016 AGAGG AGAGG AGAGG AGAGG AGAGG
1 AGAGG AGAGG AGAGG AGAGG AGAGG
38375041 CCACCAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
AGAGG
Found at i:38375572 original size:14 final size:15
Alignment explanation
Indices: 38375547--38375575 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38375537 TCGAAGGATG
38375547 GCAGGACAGCAGGCA
1 GCAGGACAGCAGGCA
38375562 GCAGG-CAGCAGGCA
1 GCAGGACAGCAGGCA
38375576 TGGTAAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.28, G:0.41, T:0.00
Consensus pattern (15 bp):
GCAGGACAGCAGGCA
Found at i:38404507 original size:12 final size:12
Alignment explanation
Indices: 38404490--38404520 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
38404480 GGAAGAAGAT
38404490 TCCAATTCCAAC
1 TCCAATTCCAAC
*
38404502 TCCAATTCCATC
1 TCCAATTCCAAC
38404514 TCCAATT
1 TCCAATT
38404521 TAATTACCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (12 bp):
TCCAATTCCAAC
Found at i:38405124 original size:2 final size:2
Alignment explanation
Indices: 38405117--38405144 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38405107 CATTCTTATC
38405117 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
38405145 GGTACTAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:38414891 original size:26 final size:26
Alignment explanation
Indices: 38414840--38414892 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
38414830 ACCTCTAATA
* *
38414840 TTCATTATTAATTCCAGGTGTTATTT
1 TTCATTATTAATTCCAGCTGTGATTT
* *
38414866 TTCATTGTTAATTCCATCTGTGATTT
1 TTCATTATTAATTCCAGCTGTGATTT
38414892 T
1 T
38414893 GTCTGCATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (26 bp):
TTCATTATTAATTCCAGCTGTGATTT
Found at i:38417081 original size:26 final size:26
Alignment explanation
Indices: 38416955--38417123 Score: 101
Period size: 27 Copynumber: 6.3 Consensus size: 26
38416945 GCACCGAAGC
** * *
38416955 AGGTGTTCCAAATATGGAAGTGCTCA
1 AGGTGTTCCAAGCATGGAAGCGCCCA
*
38416981 AGGGTGTTCCAA--ATGTGATAGCGCTCA
1 A-GGTGTTCCAAGCATG-GA-AGCGCCCA
* *
38417008 GAAGTGTTCCAAG-AAGAGAAGCGCCCA
1 -AGGTGTTCCAAGCATG-GAAGCGCCCA
* ***
38417035 AGGTGTTCCAAACACAAAAGCGCCCA
1 AGGTGTTCCAAGCATGGAAGCGCCCA
* *
38417061 AGGTGTTCCAAGCATGGAAGCTCTCAA
1 AGGTGTTCCAAGCATGGAAGCGC-CCA
* * * *
38417088 AGGTGTTCCCAGCTTGGAAGTGCTCA
1 AGGTGTTCCAAGCATGGAAGCGCCCA
38417114 AGGGTGTTCC
1 A-GGTGTTCC
38417124 CAGCGTAAGA
Statistics
Matches: 113, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
25 3 0.03
26 42 0.37
27 63 0.56
28 5 0.04
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (26 bp):
AGGTGTTCCAAGCATGGAAGCGCCCA
Found at i:38435319 original size:33 final size:33
Alignment explanation
Indices: 38435282--38435358 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
38435272 CTCCTCCTCC
* * * *
38435282 TCGTCTTCTTCATCTTCATCTTCGTCTTCTTCG
1 TCGTCATCTTCATCTCCATCTTCATCTTCGTCG
38435315 TCGTCATCTTCATCTCCATCTTCATCTTCGTCG
1 TCGTCATCTTCATCTCCATCTTCATCTTCGTCG
*
38435348 TCTTCATCTTC
1 TCGTCATCTTC
38435359 TTCAGCTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.09, C:0.35, G:0.08, T:0.48
Consensus pattern (33 bp):
TCGTCATCTTCATCTCCATCTTCATCTTCGTCG
Found at i:38435322 original size:27 final size:27
Alignment explanation
Indices: 38435291--38435358 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
38435281 CTCGTCTTCT
* *
38435291 TCATCTTCATCTTCGTCTTCTTCGTCG
1 TCATCTTCATCTTCATCTTCATCGTCG
* *
38435318 TCATCTTCATCTCCATCTTCATCTTCG
1 TCATCTTCATCTTCATCTTCATCGTCG
*
38435345 TCGTCTTCATCTTC
1 TCATCTTCATCTTC
38435359 TTCAGCTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.10, C:0.35, G:0.07, T:0.47
Consensus pattern (27 bp):
TCATCTTCATCTTCATCTTCATCGTCG
Found at i:38435358 original size:6 final size:6
Alignment explanation
Indices: 38435288--38435343 Score: 58
Period size: 6 Copynumber: 8.8 Consensus size: 6
38435278 CTCCTCGTCT
* * *
38435288 TCTTCA TCTTCA TCTTCG TCTTCT TCGTCGTCA TCTTCA TCTCCA TCTTCA
1 TCTTCA TCTTCA TCTTCA TCTTCA TC-T--TCA TCTTCA TCTTCA TCTTCA
38435339 TCTTC
1 TCTTC
38435344 GTCGTCTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
6 36 0.86
7 1 0.02
8 1 0.02
9 4 0.10
ACGTcount: A:0.11, C:0.36, G:0.05, T:0.48
Consensus pattern (6 bp):
TCTTCA
Found at i:38436847 original size:14 final size:14
Alignment explanation
Indices: 38436828--38436871 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38436818 CAAATATTAC
38436828 ATATATACATATAT
1 ATATATACATATAT
*
38436842 ATATATATATATAT
1 ATATATACATATAT
** *
38436856 ATGCATGCATATAT
1 ATATATACATATAT
38436870 AT
1 AT
38436872 TATTGCATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:38436871 original size:2 final size:2
Alignment explanation
Indices: 38436828--38436857 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38436818 CAAATATTAC
*
38436828 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38436858 GCATGCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38443114 original size:12 final size:12
Alignment explanation
Indices: 38443097--38443130 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38443087 TACCTTTTAT
38443097 CAATAATAATAA
1 CAATAATAATAA
*
38443109 CAATAATAATAG
1 CAATAATAATAA
*
38443121 TAATAATAAT
1 CAATAATAAT
38443131 GTAAAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (12 bp):
CAATAATAATAA
Found at i:38459619 original size:16 final size:17
Alignment explanation
Indices: 38459598--38459630 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38459588 AAAATCTATG
38459598 ATTATTA-GTTAAATTT
1 ATTATTATGTTAAATTT
*
38459614 ATTATTATGTTTAATTT
1 ATTATTATGTTAAATTT
38459631 GAATTTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
ATTATTATGTTAAATTT
Found at i:38459719 original size:5 final size:5
Alignment explanation
Indices: 38459704--38459741 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
38459694 TGAAAAACAC
* *
38459704 ATGCA ACGCA ATGCA ATGCA ATGCA ATGCA ATGGA ATG
1 ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA ATG
38459742 ATTCCTTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (5 bp):
ATGCA
Found at i:38467822 original size:2 final size:2
Alignment explanation
Indices: 38467811--38467877 Score: 109
Period size: 2 Copynumber: 33.5 Consensus size: 2
38467801 AGCAACTTTT
38467811 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
38467852 TA TA TA TA TA TA TA TA AA TGA TA TA T
1 TA TA TA TA TA TA TA TA TA T-A TA TA T
38467878 TAATGAATTG
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.02
2 58 0.95
3 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:38476100 original size:18 final size:18
Alignment explanation
Indices: 38476077--38476121 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
38476067 CATAAAATAT
38476077 TTAAAAATTTAATTTA-AA
1 TTAAAAATTT-ATTTACAA
38476095 TTAAAAA-TTATTTACAA
1 TTAAAAATTTATTTACAA
38476112 TTAAATAATT
1 TTAAA-AATT
38476122 AAAATTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 9 0.38
18 9 0.38
19 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAAATTTATTTACAA
Found at i:38476122 original size:18 final size:16
Alignment explanation
Indices: 38476077--38476122 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 16
38476067 CATAAAATAT
38476077 TTAAAAATTTAATTTAAA
1 TTAAAAA-TT-ATTTAAA
38476095 TTAAAAATTATTTACAA
1 TTAAAAATTATTTA-AA
38476112 TTAAATAATTA
1 TTAAA-AATTA
38476123 AAATTTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.19
17 9 0.35
18 12 0.46
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAAATTATTTAAA
Found at i:38476594 original size:46 final size:47
Alignment explanation
Indices: 38476505--38476596 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
38476495 ATTTTTAAAC
* * *
38476505 TCTTAGCTAAAGGTGGCCACAAAGTGCAAAAGACCTTCTATTTCCGT
1 TCTTAGCTAAAGGTAGCCACAAACTGCAAAAGACCTTCCATTTCCGT
* * *
38476552 TCTTTGCTGAAGGTAGCCGCAAACTGC-AAAGACCTTCCATTTCCG
1 TCTTAGCTAAAGGTAGCCACAAACTGCAAAAGACCTTCCATTTCCG
38476597 ATCACGATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 17 0.44
47 22 0.56
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (47 bp):
TCTTAGCTAAAGGTAGCCACAAACTGCAAAAGACCTTCCATTTCCGT
Found at i:38482119 original size:2 final size:2
Alignment explanation
Indices: 38482112--38482139 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38482102 TCAGAGATAG
38482112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38482140 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38482641 original size:10 final size:10
Alignment explanation
Indices: 38482628--38482686 Score: 55
Period size: 11 Copynumber: 5.6 Consensus size: 10
38482618 AGAATAGATA
38482628 AAAATAAAAT
1 AAAATAAAAT
*
38482638 AAAATAATTAT
1 AAAATAA-AAT
* * *
38482649 GAAGTGAGAAT
1 AAAAT-AAAAT
38482660 AAAATAAAAT
1 AAAATAAAAT
38482670 AAAAATAAAAT
1 -AAAATAAAAT
38482681 AAAATA
1 AAAATA
38482687 GTTATTACGT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 17 0.45
11 20 0.53
12 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:38482676 original size:6 final size:5
Alignment explanation
Indices: 38482628--38482686 Score: 55
Period size: 5 Copynumber: 11.2 Consensus size: 5
38482618 AGAATAGATA
* * * *
38482628 AAAAT AAAAT AAAAT AATTAT GAAGT GAGAAT AAAAT AAAAT AAAAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT -AAAAT AAAAT AAAAT -AAAAT
38482676 AAAAT AAAAT A
1 AAAAT AAAAT A
38482687 GTTATTACGT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
5 33 0.77
6 10 0.23
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:38482843 original size:26 final size:24
Alignment explanation
Indices: 38482814--38482938 Score: 72
Period size: 26 Copynumber: 4.8 Consensus size: 24
38482804 ATAAAAATAC
38482814 TTTTTATTATAAATATGATTATTTTA
1 TTTTTATT-TAAATAT-ATTATTTTA
* *
38482840 TTTTATTTTTTAAATAATAATATTTTA
1 -TTT-TTATTTAAAT-ATATTATTTTA
* *
38482867 TTTATAATTTAAATATTATTATGATTA
1 TTT-TTATTTAAATA-TATTAT-TTTA
* *
38482894 TTTATT-TTTAAATATTAATAATTTA
1 TTT-TTATTTAAATA-TATTATTTTA
* *
38482919 TAATTTATTTAAAAATATTA
1 T-TTTTATTTAAATATATTA
38482939 AAAACTTATA
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
25 11 0.14
26 38 0.48
27 24 0.30
28 6 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTTATTTAAATATATTATTTTA
Found at i:38482863 original size:27 final size:26
Alignment explanation
Indices: 38482823--38482928 Score: 97
Period size: 26 Copynumber: 3.9 Consensus size: 26
38482813 CTTTTTATTA
* *
38482823 TAAATATGATTATTTTATTTTATTTTT
1 TAAATATTAATATTTTA-TTTATTTTT
* **
38482850 TAAATAATAATATTTTATTTATAATT
1 TAAATATTAATATTTTATTTATTTTT
* *
38482876 TAAATATTATTATGATTATTTA-TTTT
1 TAAATATTAATAT-TTTATTTATTTTT
38482902 TAAATATTAATAATTTATAATTTATTT
1 TAAATATTAAT-ATTT-T-ATTTATTT
38482929 AAAAATATTA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
26 31 0.50
27 24 0.39
28 5 0.08
29 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TAAATATTAATATTTTATTTATTTTT
Found at i:38482934 original size:28 final size:28
Alignment explanation
Indices: 38482893--38482953 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
38482883 TATTATGATT
** * *
38482893 ATTTATTTTTAAATATTAATAATTTATA
1 ATTTATTTAAAAATATTAAAAACTTATA
38482921 ATTTATTTAAAAATATTAAAAACTTATA
1 ATTTATTTAAAAATATTAAAAACTTATA
*
38482949 GTTTA
1 ATTTA
38482954 AATACTAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (28 bp):
ATTTATTTAAAAATATTAAAAACTTATA
Done.