Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 21 of 770
Found at i:5668683 original size:46 final size:46
Alignment explanation
Indices: 5668610--5669108 Score: 669
Period size: 46 Copynumber: 10.8 Consensus size: 46
5668600 TGATGTCATA
* * * * * *
5668610 GTATCTTTCAGCTATGGTTTTACTCATTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATG
** *** *
5668656 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATG
** *** * *
5668703 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATA
1 GTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATG
* *
5668750 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
** *
5668796 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
*
5668842 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCTTG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
* *
5668888 GTATCTTTCAACCATGGTCTTACACATTCCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
5668934 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
* *
5668980 GTATCTTTCAACCATGGTCTTACACATTCCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
5669026 GTATCTTTCAACCATGGTCTTACACA-TTCTATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTC-ATATCAGGTTGCCATG
* *
5669072 GTATCTTTCAACCATAGTCTTACACATTCCATATCAG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5669109 AGAGCACACT
Statistics
Matches: 421, Mismatches: 29, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
45 2 0.00
46 332 0.79
47 87 0.21
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
Found at i:5673653 original size:27 final size:27
Alignment explanation
Indices: 5673623--5673677 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5673613 ATTTTAAAAA
5673623 CCATTTCTTTAACTTTTTTTTCCTTTT
1 CCATTTCTTTAACTTTTTTTTCCTTTT
5673650 CCATTTCTTTAACTTTTTTTTCCTTTT
1 CCATTTCTTTAACTTTTTTTTCCTTTT
5673677 C
1 C
5673678 TTCTTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.65
Consensus pattern (27 bp):
CCATTTCTTTAACTTTTTTTTCCTTTT
Found at i:5673714 original size:30 final size:30
Alignment explanation
Indices: 5673668--5673724 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
5673658 TTAACTTTTT
*
5673668 TTTCCTTTTCTTCTTTTTTCCTTCTTCACC
1 TTTCCTTTTCTTCTTTTTGCCTTCTTCACC
* * *
5673698 TTTCTTTTTTTTCTTTTTGCTTTCTTC
1 TTTCCTTTTCTTCTTTTTGCCTTCTTC
5673725 CGTAAACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70
Consensus pattern (30 bp):
TTTCCTTTTCTTCTTTTTGCCTTCTTCACC
Found at i:5675076 original size:22 final size:22
Alignment explanation
Indices: 5675048--5675089 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5675038 GAGGTAGGAA
5675048 TCTGCATCTGTATCTGATATGT
1 TCTGCATCTGTATCTGATATGT
*
5675070 TCTGCATCTGTATTTGATAT
1 TCTGCATCTGTATCTGATAT
5675090 TCTCTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (22 bp):
TCTGCATCTGTATCTGATATGT
Found at i:5676785 original size:46 final size:46
Alignment explanation
Indices: 5676685--5676786 Score: 134
Period size: 46 Copynumber: 2.2 Consensus size: 46
5676675 CGAGCTTTTA
* * *
5676685 CATATGTTGTGGACTTGAGAATACAAGTATAGGTTCTGAGCTCCAG
1 CATATGTTGCGGACTCGAGAATACAAGTATAGGTTCCGAGCTCCAG
* * *
5676731 CA-AGTGTTGCGGACTCGAGAATACAGGTTTAGGTTCCGAGCTCCTG
1 CATA-TGTTGCGGACTCGAGAATACAAGTATAGGTTCCGAGCTCCAG
5676777 CATATGTTGC
1 CATATGTTGC
5676787 TAACGGGTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
45 1 0.02
46 46 0.96
47 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (46 bp):
CATATGTTGCGGACTCGAGAATACAAGTATAGGTTCCGAGCTCCAG
Found at i:5677296 original size:11 final size:11
Alignment explanation
Indices: 5677280--5677310 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5677270 TAAGGTTTGG
5677280 TTTGAATTGTA
1 TTTGAATTGTA
5677291 TTTGAATTGTA
1 TTTGAATTGTA
5677302 TTTGAATTG
1 TTTGAATTG
5677311 AGTTTATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (11 bp):
TTTGAATTGTA
Found at i:5687890 original size:3 final size:3
Alignment explanation
Indices: 5687877--5687910 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
5687867 TGAACTCCTC
*
5687877 TGA TTA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
5687911 TCTGGTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.38
Consensus pattern (3 bp):
TGA
Found at i:5688032 original size:21 final size:21
Alignment explanation
Indices: 5688007--5688052 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5687997 CTGTGATGGG
5688007 GATGGTGA-GCAGGAAGTGGAT
1 GATGGTGATG-AGGAAGTGGAT
* *
5688028 GATGGTGATGATGAATTGGAT
1 GATGGTGATGAGGAAGTGGAT
5688049 GATG
1 GATG
5688053 AGTTGGTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.28, C:0.02, G:0.43, T:0.26
Consensus pattern (21 bp):
GATGGTGATGAGGAAGTGGAT
Found at i:5690558 original size:13 final size:15
Alignment explanation
Indices: 5690536--5690568 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5690526 TATTTTAATT
5690536 TTTTCTTTTTGT-TA
1 TTTTCTTTTTGTATA
5690550 TTTTC-TTTTGTATA
1 TTTTCTTTTTGTATA
5690564 TTTTC
1 TTTTC
5690569 ATTCTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTTGTATA
Found at i:5691619 original size:125 final size:125
Alignment explanation
Indices: 5691397--5691630 Score: 283
Period size: 125 Copynumber: 1.9 Consensus size: 125
5691387 AAAAAACCTC
* * * * * *
5691397 TTAAAACGAGGCAATATTTTGTATTTAGAAGTTTGAGAGATCGTGCCCAATCGTGTTGGGTTTCG
1 TTAAAACGACGCAATATTTCGTATTTAGAAATTCGAGAAATCGTGCCCAATCGTGCTGGGTTTCG
* ** *
5691462 ATTTTTCATTCGACTAAAATACAGAATATCCTTTTGAAATTTCATCTATGTTTTCTTAAA
66 ATCTACCATTCGACTAAAATACAGAATATCCTTTTAAAATTTCATCTATGTTTTCTTAAA
* * *
5691522 TTAAAATGACGCAATATTTCGTATTTGGAAATTCGATAAATCGTGCCCAATCGTGCTGGGTTTCG
1 TTAAAACGACGCAATATTTCGTATTTAGAAATTCGAGAAATCGTGCCCAATCGTGCTGGGTTTCG
* * * *
5691587 ATCTACCGTTTGGC-CAAATAGCCA-AATATCCTTTTAAAATTTCA
66 ATCTACCATTCGACTAAAATA--CAGAATATCCTTTTAAAATTTCA
5691631 AATGCATGAG
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
124 5 0.06
125 83 0.92
126 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (125 bp):
TTAAAACGACGCAATATTTCGTATTTAGAAATTCGAGAAATCGTGCCCAATCGTGCTGGGTTTCG
ATCTACCATTCGACTAAAATACAGAATATCCTTTTAAAATTTCATCTATGTTTTCTTAAA
Found at i:5697402 original size:232 final size:232
Alignment explanation
Indices: 5696996--5697462 Score: 907
Period size: 232 Copynumber: 2.0 Consensus size: 232
5696986 CTGAGCAGAA
5696996 TAGGATTGTTTCTTTGGGTTTTTTGTCAAGAATACCAGCCAAACAAGATGACAATTAATACGTCA
1 TAGGATTGTTTCTTTGGGTTTTTTGTCAAGAATACCAGCCAAACAAGATGACAATTAATACGTCA
*
5697061 GTGATAAGACCCTGATGAATAATGAGTTATGACACTTTAAGCATAAAAAAATGGCATTTCTCATG
66 GTGATAAGACCCTGATGAATAATGAGTTATGACACTTTAAGCATAAAAAAAGGGCATTTCTCATG
5697126 ACATTTTACATTCATACCAATGTCATTCATAGTACATCTAGTTAAGAGCATTTGATTCATTTTGA
131 ACATTTTACATTCATACCAATGTCATTCATAGTACATCTAGTTAAGAGCATTTGATTCATTTTGA
5697191 TCATAGCATCCTAATTATTTGGCATAAGTATCACATC
196 TCATAGCATCCTAATTATTTGGCATAAGTATCACATC
*
5697228 TAGGATTGTTTTTTTGGGTTTTTTGTCAAGAATACCAGCCAAACAAGATGACAATTAATACGTCA
1 TAGGATTGTTTCTTTGGGTTTTTTGTCAAGAATACCAGCCAAACAAGATGACAATTAATACGTCA
*
5697293 GTGATAAGACCCTGATGAATAATGAGTTATGACACTTTAAGCATAAAAAAGGGGCATTTCTCATG
66 GTGATAAGACCCTGATGAATAATGAGTTATGACACTTTAAGCATAAAAAAAGGGCATTTCTCATG
5697358 ACATTTTACATTCATACCAATGTCATTCATAGTACATCTAGTTAAGAGCATTTGATTCATTTTGA
131 ACATTTTACATTCATACCAATGTCATTCATAGTACATCTAGTTAAGAGCATTTGATTCATTTTGA
5697423 TCATAGCATCCTAATTATTTGGCATAAGTATCACATC
196 TCATAGCATCCTAATTATTTGGCATAAGTATCACATC
5697460 TAG
1 TAG
5697463 CTAGGAGCAT
Statistics
Matches: 232, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
232 232 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (232 bp):
TAGGATTGTTTCTTTGGGTTTTTTGTCAAGAATACCAGCCAAACAAGATGACAATTAATACGTCA
GTGATAAGACCCTGATGAATAATGAGTTATGACACTTTAAGCATAAAAAAAGGGCATTTCTCATG
ACATTTTACATTCATACCAATGTCATTCATAGTACATCTAGTTAAGAGCATTTGATTCATTTTGA
TCATAGCATCCTAATTATTTGGCATAAGTATCACATC
Found at i:5697474 original size:64 final size:64
Alignment explanation
Indices: 5697391--5697514 Score: 194
Period size: 64 Copynumber: 1.9 Consensus size: 64
5697381 CATTCATAGT
* ** *
5697391 ACATCTAGTTAAGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGGCATAAGTATC
1 ACATCTAGCTAAGAGCATTTGATTCATTTCAATCATAGCATCCTAAATATTTGGCATAAGTATC
* *
5697455 ACATCTAGCTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAAATGTTTGGCATAAG
1 ACATCTAGCTAAGAGCATTTGATTCATTTCAATCATAGCATCCTAAATATTTGGCATAAG
5697515 CTTATATACA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (64 bp):
ACATCTAGCTAAGAGCATTTGATTCATTTCAATCATAGCATCCTAAATATTTGGCATAAGTATC
Found at i:5697802 original size:45 final size:46
Alignment explanation
Indices: 5697745--5697841 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 46
5697735 AGTTGCAGGA
* *
5697745 AGCAGA-CTGAAAATTAC-AGATCTTATCTCCATGTATCGGCTATAG
1 AGCAGATCTGAAAATGACGAG-TCTTATCTCCATGTATAGGCTATAG
* *
5697790 AGCAGATC-GAAAATGGCGAGTCTTATCTCCATGTATAGGCTATGG
1 AGCAGATCTGAAAATGACGAGTCTTATCTCCATGTATAGGCTATAG
5697835 AGCAGAT
1 AGCAGAT
5697842 TTTAGCCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 43 0.93
46 3 0.07
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (46 bp):
AGCAGATCTGAAAATGACGAGTCTTATCTCCATGTATAGGCTATAG
Found at i:5697903 original size:133 final size:133
Alignment explanation
Indices: 5697622--5697883 Score: 321
Period size: 133 Copynumber: 2.0 Consensus size: 133
5697612 AACAGGCTTC
* * *
5697622 AAATTATAGATCTTATCTCTATGTATCAGCTATGGAGCAGATCAGAAATGGCGAGTATTATCTCC
1 AAATTACAGATCTTATCTCCATGTATCAGCTATAGAGCAGATCAGAAATGGCGAGTATTATCTCC
* * *** * *
5697687 ATGTATCGGGTATAAAACAAATTTTAACCACTGGTCTTATCCTCCTGAAGTTGCAGGAAGCAGAC
66 ATGTATAGGCTATAAAACAAATTTTAACCACTAACCTTATCCTCCTGAAGTAGCAAGAAGCAGAC
5697752 TGA
131 TGA
* *
5697755 AAATTACAGATCTTATCTCCATGTATCGGCTATAGAGCAGATC-GAAAATGGCGAGTCTTATCTC
1 AAATTACAGATCTTATCTCCATGTATCAGCTATAGAGCAGATCAG-AAATGGCGAGTATTATCTC
** * * * *
5697819 CATGTATAGGCTATGGAGCAGATTTTAGCCACTAACCTTAT-CTCTCTGAGGTAGCAAGAGAGCA
65 CATGTATAGGCTATAAAACAAATTTTAACCACTAACCTTATCCTC-CTGAAGTAGCAAGA-AGCA
5697883 G
128 G
5697884 GTTGAAGATA
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
132 4 0.04
133 99 0.92
134 5 0.05
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (133 bp):
AAATTACAGATCTTATCTCCATGTATCAGCTATAGAGCAGATCAGAAATGGCGAGTATTATCTCC
ATGTATAGGCTATAAAACAAATTTTAACCACTAACCTTATCCTCCTGAAGTAGCAAGAAGCAGAC
TGA
Found at i:5697929 original size:177 final size:176
Alignment explanation
Indices: 5697720--5698595 Score: 1096
Period size: 177 Copynumber: 4.9 Consensus size: 176
5697710 TTAACCACTG
*
5697720 GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
1 GTCTTATCCTCCTGAAGTTGTAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
* *
5697785 TATAGAGCAGATCGAAAATGGCGAGTCTTATCTCCATGTATAGGCTATGGAGCAGATTTTAGCCA
66 TAT-GAGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
*
5697850 CTAACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAA
130 CTGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAA
**
5697897 GTCTTATTTTCCTGAAGTTGTAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
1 GTCTTATCCTCCTGAAGTTGTAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
* * *
5697962 TATGGAGCAGATAAAAAATGGCGAGTCTTATCTCCATGTATCGACTATGGAGTAGATTTTAGCCA
66 TAT-GAGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
** *
5698027 CCAACCTTATCTCTTTGAGGTAGCAAGAGAGCAGGTTGAAGATACAA
130 CTGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAA
* * *
5698074 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAATTACAGATCTTATCTCCATATATCGG
1 GTCTTATCCTCCTGAAGTTGTAGGAAGCAGACTG-AAAATTACAGATCTTATCTCCATGTATCGG
* * * * *
5698139 CTATGGAGCAGATCAGAAATGGTGAATCTTATCTCTATGTATCTGCTATGGAGCAGATTTTAGCC
65 CTAT-GAGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
*
5698204 AAC-GACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
129 -ACTGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAA
* * * *** *
5698252 GCCTTAACCCCCT-AAGCAATAGGGTAA-CAGGCTGAAAATTACAGATCTTATCTCCATGTATCG
1 GTCTTATCCTCCTGAAGTTGTA-GG-AAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCG
* * * * **
5698315 GCTATGAAGTAGATCAAAAATGGCGAGTCTTATCTTCATGTATCGGTTATGAAATAGATTTTAGC
64 GCTATG-AGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
* * **
5698380 CACTGGCATTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGG
128 CACTGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAA
* * * ** * *
5698429 GCCTTAACCCCCT-AAGCAGTAGGGTAA-CAGGCTAAAAATTACAGATCTTATCTCCATGTATCG
1 GTCTTATCCTCCTGAAGTTGTA-GG-AAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCG
* * * * * * *
5698492 GCTATGAAGTAGATTAGAAATGGCAAGTCTTATCTCTATGTCTCGGCTATGGAGCATATTTTAGC
64 GCTATG-AGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
* * * * * *
5698557 CGCGGGCCTTATCTATCTGAGGTAGCAAAATAGCAGGTT
128 CACTGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTT
5698596 AAAAGTATGA
Statistics
Matches: 625, Mismatches: 68, Indels: 12
0.89 0.10 0.02
Matches are distributed among these distances:
176 3 0.00
177 473 0.76
178 145 0.23
179 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (176 bp):
GTCTTATCCTCCTGAAGTTGTAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
TATGAGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAC
TGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAA
Found at i:5698289 original size:355 final size:353
Alignment explanation
Indices: 5697720--5698653 Score: 1193
Period size: 355 Copynumber: 2.6 Consensus size: 353
5697710 TTAACCACTG
5697720 GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTG-AAAATTACAGATCTTATCTCCATGTATCGG
1 GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAAATTACAGATCTTATCTCCATGTATCGG
* * * *
5697784 CTATAGAGCAGATC-GAAAATGGCGAGTCTTATCTCCATGTATAGGCTATGGAGCAGATTTTAGC
66 CTATGGAGCAGATCAG-AAATGG-GAATCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGC
** * * ****
5697848 CACTAACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAAGTCTTATTTTCCTGAA
129 CACGGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGAGCCTTAACCCCCT-AA
** * *
5697913 GTTGTAGG-AAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATAAA
193 GCAGTAGGTAA-CAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGAAGCAGATAAA
* * * *
5697977 AAATGGCGAGTCTTATCTCCATGTATCGACTATGGAGTAGATTTTAGCCACCAACCTTATCTCTT
257 AAATGGCGAGTCTTATCTCCATGTATCGACTATGAAATAGATTTTAGCCACCAACATTATCTCTC
5698042 TGAGGTAGCAAGAGAGCAGGTTGAAGATACAA
322 TGAGGTAGCAAGAGAGCAGGTTGAAGATACAA
* *
5698074 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAAATTACAGATCTTATCTCCATATATCGG
1 GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAAATTACAGATCTTATCTCCATGTATCGG
*
5698139 CTATGGAGCAGATCAGAAATGGTGAATCTTATCTCTATGTATCTGCTATGGAGCAGATTTTAGCC
66 CTATGGAGCAGATCAGAAATGG-GAATCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCC
5698204 AAC-GACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGAGCCTTAACCCCCTAAG
130 -ACGGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGAGCCTTAACCCCCTAAG
* * *
5698268 CAATAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGAAGTAGATCAAA
194 CAGTA-GGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGAAGCAGATAAAA
* ** ***
5698333 AATGGCGAGTCTTATCTTCATGTATCGGTTATGAAATAGATTTTAGCCACTGGCATTATCTCTCT
258 AATGGCGAGTCTTATCTCCATGTATCGACTATGAAATAGATTTTAGCCACCAACATTATCTCTCT
**
5698398 GAGGTAGCAAGAGAGCAGGTTGAAGATACGG
323 GAGGTAGCAAGAGAGCAGGTTGAAGATACAA
* * * ** * *
5698429 GCCTTAACCCCCT-AAGCAGTAGGGTAA-CAGGCT-AAAAATTACAGATCTTATCTCCATGTATC
1 GTCTTATCCTCCTGAAGTTGCA-GG-AAGCAGACTGAAAAATTACAGATCTTATCTCCATGTATC
* * * * * *
5698491 GGCTATGAAGTAGATTAGAAATGGCAAGTCTTATCTCTATGTCTCGGCTATGGAGCATATTTTAG
64 GGCTATGGAGCAGATCAGAAATGGGAA-TCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAG
* * * * * * *
5698556 CCGCGGGCCTTATCTATCTGAGGTAGCAAAATAGCAGGTT-AAAAGTATGAGCCTTAACCCCCTA
128 CCACGGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGA-TACGAGCCTTAACCCCCTA
*
5698620 AGCAGTAAGGTAATAGGCTGGAAAA-TACAGATCT
192 AGCAGT-AGGTAACAGGCT-GAAAATTACAGATCT
5698654 CCCCTAAAAA
Statistics
Matches: 509, Mismatches: 59, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
353 6 0.01
354 201 0.39
355 295 0.58
356 7 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (353 bp):
GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAAATTACAGATCTTATCTCCATGTATCGG
CTATGGAGCAGATCAGAAATGGGAATCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCCA
CGGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGAGCCTTAACCCCCTAAGCA
GTAGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGAAGCAGATAAAAAAT
GGCGAGTCTTATCTCCATGTATCGACTATGAAATAGATTTTAGCCACCAACATTATCTCTCTGAG
GTAGCAAGAGAGCAGGTTGAAGATACAA
Found at i:5698758 original size:84 final size:84
Alignment explanation
Indices: 5698605--5699076 Score: 531
Period size: 84 Copynumber: 5.6 Consensus size: 84
5698595 TAAAAGTATG
* * *
5698605 AGCCTTAACCCCCTAAGCAGTAAGGTAATAGGCTGGAAAATACAGATCTCCCCTAAA-AAGTAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGGAAATACAGATCTCCCCTAAACAA-TAGT
5698669 GGAGCAGATCGAAGATAGCA
65 GGAGCAGATCGAAGATAGCA
* * * * *
5698689 AGCCTTAACCTCCTAAGTAGTAGGGTAGCAGGTTGGGAAATACAGATCTCCCCTAAACAATAGTA
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGGAAATACAGATCTCCCCTAAACAATAGTG
*
5698754 GAGCAGATCGAAGACAGCA
66 GAGCAGATCGAAGATAGCA
* * * * * * *
5698773 AGCCTTAGCCCCCTACGCAGTAGGGTGACAGGTTGGAAAATACAGATTTCCCCTAAACAGTAGTG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGGAAATACAGATCTCCCCTAAACAATAGTG
5698838 GAGCAGATCGAAGATAGCA
66 GAGCAGATCGAAGATAGCA
* * * *
5698857 TGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGGAAATACAGATCTCCCTTAAGCACTAGTG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGGAAATACAGATCTCCCCTAAACAATAGTG
* * **
5698922 AAGCAGATCGAAGATGGTG
66 GAGCAGATCGAAGATAGCA
* * *
5698941 AGCCTTAA-CCCCTAAGCAGTAGGGTAACAGGC--AGAAGATTACAGATCTTATCTGCCTAAGCA
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGGAA-A-TACAGATC---TC-CCCTAAACA
* * * *
5699003 GTAGTGGAGCAGATCAAAGACAGTA
60 ATAGTGGAGCAGATCGAAGATAGCA
* * *
5699028 AGCCTTAACCCCCTAAGTAGTAGGGAAACAGGCT-GAAAATTACAGATCT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGGAAA-TACAGATCT
5699077 TATCTCCTTA
Statistics
Matches: 331, Mismatches: 48, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
81 3 0.01
82 1 0.00
83 32 0.10
84 222 0.67
85 3 0.01
86 2 0.01
87 34 0.10
88 32 0.10
89 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (84 bp):
AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGGAAATACAGATCTCCCCTAAACAATAGTG
GAGCAGATCGAAGATAGCA
Found at i:5699365 original size:29 final size:29
Alignment explanation
Indices: 5699332--5699399 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
5699322 ATCCAATTAG
*
5699332 CACCCTACTAAACCTA-CCACTAACTCCAT
1 CACCCCACTAAACC-ACCCACTAACTCCAT
*
5699361 CACCCCAGTAAACCACCCCACTAACTCCAT
1 CACCCCACTAAACCA-CCCACTAACTCCAT
*
5699391 TACCCCACT
1 CACCCCACT
5699400 TGCCACCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 12 0.36
30 20 0.61
ACGTcount: A:0.32, C:0.49, G:0.01, T:0.18
Consensus pattern (29 bp):
CACCCCACTAAACCACCCACTAACTCCAT
Found at i:5699849 original size:14 final size:14
Alignment explanation
Indices: 5699830--5699862 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5699820 TTATTTTAAT
5699830 TTTTCTTGTTGT-TA
1 TTTTCTT-TTGTATA
5699844 TTTTCTTTTGTATA
1 TTTTCTTTTGTATA
5699858 TTTTC
1 TTTTC
5699863 ATTCTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.73
Consensus pattern (14 bp):
TTTTCTTTTGTATA
Found at i:5700026 original size:21 final size:20
Alignment explanation
Indices: 5699989--5700027 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5699979 TATTTGTATA
5699989 TATATATATATAATGTTTTG
1 TATATATATATAATGTTTTG
* *
5700009 TATATCATTTATACTGTTT
1 TATAT-ATATATAATGTTT
5700028 CGTTACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (20 bp):
TATATATATATAATGTTTTG
Found at i:5703870 original size:19 final size:19
Alignment explanation
Indices: 5703846--5703883 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5703836 GAAATGAATA
*
5703846 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
5703865 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
5703884 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:5704159 original size:2 final size:2
Alignment explanation
Indices: 5704152--5704193 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5704142 GTAGCTAAAT
5704152 TA TA TA 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
5704194 CACATAAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5704797 original size:2 final size:2
Alignment explanation
Indices: 5704790--5704823 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5704780 TTAAATTATG
5704790 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
5704824 ATAAAGAAAA
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):
TA
Found at i:5705107 original size:16 final size:16
Alignment explanation
Indices: 5705086--5705118 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5705076 AGAGGTTAGG
*
5705086 TTTTTTT-TTTTTCAT
1 TTTTTTTATTTTTTAT
5705101 TTTTTTTATTTTTTAT
1 TTTTTTTATTTTTTAT
5705117 TT
1 TT
5705119 ATTATTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTATTTTTTAT
Found at i:5706174 original size:28 final size:28
Alignment explanation
Indices: 5706134--5706190 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
5706124 GCGGGTAGAT
5706134 TACAAATGTACATCTCAAAAATTCTATC
1 TACAAATGTACATCTCAAAAATTCTATC
*
5706162 TACAAATGTACATCTCCAAAATTCTATC
1 TACAAATGTACATCTCAAAAATTCTATC
5706190 T
1 T
5706191 TCAGACTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (28 bp):
TACAAATGTACATCTCAAAAATTCTATC
Found at i:5715714 original size:22 final size:22
Alignment explanation
Indices: 5715689--5715735 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
5715679 AAAACATTAG
5715689 AAACCAGAAATTTTT-GGATAAA
1 AAACCAGAAATTTTTGGGA-AAA
5715711 AAACCAGAAATTTTTGGGAAAA
1 AAACCAGAAATTTTTGGGAAAA
5715733 AAA
1 AAA
5715736 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (22 bp):
AAACCAGAAATTTTTGGGAAAA
Found at i:5724451 original size:46 final size:46
Alignment explanation
Indices: 5724378--5724553 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
5724368 TATTTGGGCA
*
5724378 TCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * * *
5724424 TTCGAACTCGTTGAGTTGAATCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
5724469 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
5724517 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5724554 GCGGGTTATA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.58
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5724533 original size:93 final size:93
Alignment explanation
Indices: 5724374--5724545 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
5724364 GGAATATTTG
* * **
5724374 GGCATCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
5724439 TTGAATCCGAGTTCGTGAGATGTAACTA
66 TTGAATCCGAGTTCGTGAGATGTAACTA
*
5724467 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
5724532 TTGAGTCCGAGTTC
66 TTGAATCCGAGTTC
5724546 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAATCCGAGTTCGTGAGATGTAACTA
Found at i:5727959 original size:17 final size:18
Alignment explanation
Indices: 5727937--5727973 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
5727927 GGAATGAAGT
5727937 TGATAGAAAAAAAAT-TA
1 TGATAGAAAAAAAATCTA
5727954 TGATAGAAAAAAAATCTA
1 TGATAGAAAAAAAATCTA
5727972 TG
1 TG
5727974 TAAGATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.59, C:0.03, G:0.14, T:0.24
Consensus pattern (18 bp):
TGATAGAAAAAAAATCTA
Found at i:5730728 original size:93 final size:93
Alignment explanation
Indices: 5730569--5730740 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
5730559 GGAATATTTG
* *
5730569 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCAAACTCATTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCAAACTCATTGAG
5730634 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
5730662 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCAAACTCATTGAG
*
5730727 TTGAGTCTGAGTTC
66 TTGAGTCCGAGTTC
5730741 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCAAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:5730732 original size:46 final size:46
Alignment explanation
Indices: 5730575--5730748 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
5730565 TTTGGGCATC
* *
5730575 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
1 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCT
* * * * * *
5730621 CAAACTCATTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCAT
1 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC-T
5730667 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCT
1 -CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCT
*
5730714 CGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5730749 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.57
47 25 0.24
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCT
Found at i:5742126 original size:15 final size:15
Alignment explanation
Indices: 5742075--5742126 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
5742065 TATTTATATT
*
5742075 AATATTTTAATAATA
1 AATATATTAATAATA
*
5742090 AATATAAATTACAATTATA
1 AATAT--ATT--AATAATA
5742109 AATATATTAATAATA
1 AATATATTAATAATA
5742124 AAT
1 AAT
5742127 GTTCCATAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 14 0.47
17 5 0.17
19 11 0.37
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:5742526 original size:26 final size:26
Alignment explanation
Indices: 5742466--5742520 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 26
5742456 TACTTATCAC
5742466 ATATTTTAACCTAGTATAAAATATGA
1 ATATTTTAACCTAGTATAAAATATGA
5742492 ATATTTTAA-CTA-TAT-AAATATGA
1 ATATTTTAACCTAGTATAAAATATGA
5742515 ATATTT
1 ATATTT
5742521 GTTTAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.48
24 3 0.10
25 3 0.10
26 9 0.31
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (26 bp):
ATATTTTAACCTAGTATAAAATATGA
Found at i:5744022 original size:3 final size:3
Alignment explanation
Indices: 5744014--5744069 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
5744004 AAAGAAAGCA
* * * * * *
5744014 AAT AAT AAT AAT AAT AAT AAT AAC AAC AAC AAT AAC AAC AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5744062 AAT AAT AA
1 AAT AAT AA
5744070 AGAAGACAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (3 bp):
AAT
Found at i:5746855 original size:19 final size:20
Alignment explanation
Indices: 5746820--5746857 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5746810 CCCTCATTCT
5746820 AAATAAAAATAAAATATTTC
1 AAATAAAAATAAAATATTTC
*
5746840 AAATAAAAA-AATATATTT
1 AAATAAAAATAAAATATTT
5746858 TACTAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAAAAATAAAATATTTC
Found at i:5748685 original size:18 final size:19
Alignment explanation
Indices: 5748663--5748707 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
5748653 GATATATTAA
5748663 AAAATTAAATTAAATTGTT
1 AAAATTAAATTAAATTGTT
*
5748682 -AAATTCAATTAAATTGTT
1 AAAATTAAATTAAATTGTT
5748700 AAAATTAA
1 AAAATTAA
5748708 GTTTAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATTAAATTAAATTGTT
Found at i:5754740 original size:117 final size:117
Alignment explanation
Indices: 5754534--5754763 Score: 397
Period size: 117 Copynumber: 2.0 Consensus size: 117
5754524 CCGAATTGAC
* * *
5754534 AATTGATGGAAATTACCGAAGCAACCTAATCACCCATAATTAGATTTGATTTATTCTTCCTTTTT
1 AATTGATGGAAATTACCAAAGCAAACTAATCACCCATAATCAGATTTGATTTATTCTTCCTTTTT
*
5754599 AATCTTTTAAATTTTAATCTTTTATGTTGTTTTATTTTTATCATTATATGAA
66 AATCTTTTAAATTTTAATCTTTTATGTTGTTTTACTTTTATCATTATATGAA
* *
5754651 AATTGATGGAAATTACCAAAGCAAACTAATCACCCATAATCATATTTGATTTATTCTTCTTTTTT
1 AATTGATGGAAATTACCAAAGCAAACTAATCACCCATAATCAGATTTGATTTATTCTTCCTTTTT
*
5754716 AATCTTTTAAATTTTATTCTTTTATGTTGTTTTACTTTTATCATTATA
66 AATCTTTTAAATTTTAATCTTTTATGTTGTTTTACTTTTATCATTATA
5754764 AAACCCCAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 106 1.00
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (117 bp):
AATTGATGGAAATTACCAAAGCAAACTAATCACCCATAATCAGATTTGATTTATTCTTCCTTTTT
AATCTTTTAAATTTTAATCTTTTATGTTGTTTTACTTTTATCATTATATGAA
Found at i:5767476 original size:43 final size:43
Alignment explanation
Indices: 5767415--5767496 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
5767405 AGAGGACCAG
*
5767415 TTGGAAATAGACATGTTTGGATCATATTGCATATAATTTTCAT
1 TTGGAAATAAACATGTTTGGATCATATTGCATATAATTTTCAT
* *
5767458 TTGGAAATAAACATGTTTGGATTATATTGCATGTAATTT
1 TTGGAAATAAACATGTTTGGATCATATTGCATATAATTT
5767497 ACATACTACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (43 bp):
TTGGAAATAAACATGTTTGGATCATATTGCATATAATTTTCAT
Found at i:5769289 original size:25 final size:25
Alignment explanation
Indices: 5769254--5769324 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
5769244 ACACACCATA
*
5769254 GCTCTCTTGAGCTTTCCGATACTTG
1 GCTCTCATGAGCTTTCCGATACTTG
*
5769279 GCTCTCATGAGC-TTCTCGATATTTG
1 GCTCTCATGAGCTTTC-CGATACTTG
* *
5769304 GCT-TGCAAGAGCTTTCTGATA
1 GCTCT-CATGAGCTTTCCGATA
5769325 TACAGCTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 4 0.10
25 32 0.82
26 3 0.08
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (25 bp):
GCTCTCATGAGCTTTCCGATACTTG
Found at i:5770833 original size:2 final size:2
Alignment explanation
Indices: 5770826--5770860 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5770816 ACGCACATTC
5770826 AT AT AT AT 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 AT AT AT AT A
5770861 CAATTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5777866 original size:35 final size:35
Alignment explanation
Indices: 5777821--5777962 Score: 169
Period size: 35 Copynumber: 4.1 Consensus size: 35
5777811 TACTCTTTGT
* *
5777821 TTGGCGTGTTTCGGTTGGACCAACTCTTATGAGCA
1 TTGGCATGTTTCGGTTGGACTAACTCTTATGAGCA
*
5777856 TTGGCATGTTTTGGTTGGACTAACTCTTATGAGCA
1 TTGGCATGTTTCGGTTGGACTAACTCTTATGAGCA
* * *
5777891 TTGGCGTGTTTCGGTTGGATTAGCTCTTATGAGCA
1 TTGGCATGTTTCGGTTGGACTAACTCTTATGAGCA
* * * * *
5777926 CTGGCATGTTACGATTAGACTAGA-TCTTGTGAGCA
1 TTGGCATGTTTCGGTTGGACTA-ACTCTTATGAGCA
5777961 TT
1 TT
5777963 TGATGTGTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
35 90 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.37
Consensus pattern (35 bp):
TTGGCATGTTTCGGTTGGACTAACTCTTATGAGCA
Found at i:5777947 original size:70 final size:70
Alignment explanation
Indices: 5777821--5777962 Score: 187
Period size: 70 Copynumber: 2.0 Consensus size: 70
5777811 TACTCTTTGT
* ** * *
5777821 TTGGCGTGTTTCGGTTGGACCAACTCTTATGAGCATTGGCATGTTTTGGTTGGACTA-ACTCTTA
1 TTGGCGTGTTTCGGTTGGACCAACTCTTATGAGCACTGGCATGTTACGATTAGACTAGA-TCTTA
5777885 TGAGCA
65 TGAGCA
** * *
5777891 TTGGCGTGTTTCGGTTGGATTAGCTCTTATGAGCACTGGCATGTTACGATTAGACTAGATCTTGT
1 TTGGCGTGTTTCGGTTGGACCAACTCTTATGAGCACTGGCATGTTACGATTAGACTAGATCTTAT
5777956 GAGCA
66 GAGCA
5777961 TT
1 TT
5777963 TGATGTGTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 61 0.98
71 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.37
Consensus pattern (70 bp):
TTGGCGTGTTTCGGTTGGACCAACTCTTATGAGCACTGGCATGTTACGATTAGACTAGATCTTAT
GAGCA
Found at i:5778119 original size:22 final size:22
Alignment explanation
Indices: 5778092--5778138 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
5778082 TGAAAGTATG
5778092 TTTATGTTCATGAAATTGATGA
1 TTTATGTTCATGAAATTGATGA
*
5778114 TTTATGTTCATGAAGTTGATGA
1 TTTATGTTCATGAAATTGATGA
5778136 TTT
1 TTT
5778139 CAAATGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (22 bp):
TTTATGTTCATGAAATTGATGA
Found at i:5783072 original size:28 final size:28
Alignment explanation
Indices: 5783031--5783086 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
5783021 ATTTCGTTGA
*
5783031 ATACTCAATGTCTCACACACTAAGTGCC
1 ATACTCAATATCTCACACACTAAGTGCC
*
5783059 ATACTCGATATCTCACACACTAAGTGCC
1 ATACTCAATATCTCACACACTAAGTGCC
5783087 GTACATAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.25
Consensus pattern (28 bp):
ATACTCAATATCTCACACACTAAGTGCC
Found at i:5783158 original size:40 final size:40
Alignment explanation
Indices: 5783074--5783207 Score: 151
Period size: 40 Copynumber: 3.4 Consensus size: 40
5783064 CGATATCTCA
* * * * * * *
5783074 CACACTAAGTGCCGTACATAGCTAAATCTATCTCAAATCA
1 CACACTAAGTGCCATATATAGCCAAAGCTATGTCGAATCG
* *
5783114 CACACTAAGTGCCATATATAGCCAAAGCTATGTTGAATTG
1 CACACTAAGTGCCATATATAGCCAAAGCTATGTCGAATCG
* * * *
5783154 CACACTAAGTGTCATATATAGTCGAAGCTATGTCGTATCG
1 CACACTAAGTGCCATATATAGCCAAAGCTATGTCGAATCG
5783194 CACACTAAGTGCCA
1 CACACTAAGTGCCA
5783208 CAAATAACCA
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (40 bp):
CACACTAAGTGCCATATATAGCCAAAGCTATGTCGAATCG
Found at i:5783980 original size:10 final size:11
Alignment explanation
Indices: 5783959--5783995 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
5783949 GAGACCTTTA
5783959 TTTTTCTTTTTC
1 TTTTTC-TTTTC
5783971 TTTTTC-TTTC
1 TTTTTCTTTTC
5783981 -TTTTCTTTTC
1 TTTTTCTTTTC
5783991 TTTTT
1 TTTTT
5783996 GGGCCTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.22
10 8 0.35
11 4 0.17
12 6 0.26
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:5784039 original size:3 final size:3
Alignment explanation
Indices: 5784033--5784067 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5784023 TATTATCATC
5784033 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT AC
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT AC
5784068 AATTATTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
ACT
Found at i:5784218 original size:11 final size:12
Alignment explanation
Indices: 5784200--5784228 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
5784190 ACAAGCATTC
5784200 TATTTTCTTTTT
1 TATTTTCTTTTT
5784212 T-TTTTCTTTTT
1 TATTTTCTTTTT
5784223 TATTTT
1 TATTTT
5784229 TGCCATATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (12 bp):
TATTTTCTTTTT
Found at i:5784520 original size:23 final size:22
Alignment explanation
Indices: 5784494--5784564 Score: 58
Period size: 23 Copynumber: 3.3 Consensus size: 22
5784484 CAATTATTTC
*
5784494 AAAATAAATTTTAGATTTTT--
1 AAAAAAAATTTTAGATTTTTAA
* **
5784514 AAGAAAAATAGT-GATTTTTAA
1 AAAAAAAATTTTAGATTTTTAA
*
5784535 AAAAAGAAAATTTAGATTTTTAA
1 AAAAA-AAATTTTAGATTTTTAA
*
5784558 AATAAAA
1 AAAAAAA
5784565 TTCTATTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 7 0.18
20 8 0.21
21 4 0.11
22 6 0.16
23 13 0.34
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (22 bp):
AAAAAAAATTTTAGATTTTTAA
Found at i:5784573 original size:42 final size:42
Alignment explanation
Indices: 5784494--5784575 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
5784484 CAATTATTTC
* * * *
5784494 AAAATAAATTTTAGATTTTTAAGAAAAATAGTGATTTTTAAA
1 AAAAGAAAATTTAGATTTTTAAAAAAAATACTGATTTTTAAA
*
5784536 AAAAGAAAATTTAGATTTTTAAAATAAAATTCT-ATTTTTA
1 AAAAGAAAATTTAGATTTTTAAAA-AAAATACTGATTTTTA
5784576 GTCATTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 28 0.82
43 6 0.18
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.41
Consensus pattern (42 bp):
AAAAGAAAATTTAGATTTTTAAAAAAAATACTGATTTTTAAA
Found at i:5784597 original size:141 final size:144
Alignment explanation
Indices: 5784385--5784695 Score: 424
Period size: 143 Copynumber: 2.2 Consensus size: 144
5784375 TGGGAATTTT
* *
5784385 TTTTTAAAAAAAGAAAAAGTTTAGATTTTTAAAATAAAAATATGATTTTTAGTCATATTAAAGGA
1 TTTTTAAAAAAAG-AAAACTTTAGATTTTTAAAATAAAAATATGATTTTTAGTCATATTAAAGAA
*
5784450 AATTT-AA-TTCTTAAAACAAAGTTTTGATCTTTTTCAATTATTTCAAAATAAA-TTTTAGATTT
65 AATTTAAATTTCTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATAAAGTTTT-GATTT
*
5784512 TTAAGAAAAATAGTGA
129 TTAAGAAAAATAGTAA
* * *
5784528 TTTTTAAAAAAAGAAAA-TTTAGATTTTTAAAATAAAATTCT-ATTTTTAGTCAT-TTTAAGAAA
1 TTTTTAAAAAAAGAAAACTTTAGATTTTTAAAATAAAAATATGATTTTTAGTCATATTAAAG-AA
* *
5784590 AATTTTAAATTTTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTTAAAATAAAGTTTTGATTT
65 AA-TTTAAATTTCTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATAAAGTTTTGATTT
*
5784655 TTAAGAAATATAGTAA
129 TTAAGAAAAATAGTAA
*
5784671 TTTTT--TAAAAGAAAACTTT-GATTTT
1 TTTTTAAAAAAAGAAAACTTTAGATTTT
5784696 GCCAAAAAAA
Statistics
Matches: 152, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
139 5 0.03
140 15 0.10
141 40 0.26
142 9 0.06
143 79 0.52
144 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (144 bp):
TTTTTAAAAAAAGAAAACTTTAGATTTTTAAAATAAAAATATGATTTTTAGTCATATTAAAGAAA
ATTTAAATTTCTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATAAAGTTTTGATTTTT
AAGAAAAATAGTAA
Found at i:5787896 original size:47 final size:47
Alignment explanation
Indices: 5787827--5787963 Score: 238
Period size: 47 Copynumber: 2.9 Consensus size: 47
5787817 TTTTGTTTTA
*
5787827 TTTTAGGTAAAGCGATAGATAACCATTTATATGGCCTATGTATTATG
1 TTTTAGGTAAAACGATAGATAACCATTTATATGGCCTATGTATTATG
* *
5787874 TTTTAGGTAAAACAATAGATAACCATTTATATGGCCTATGTATTCTG
1 TTTTAGGTAAAACGATAGATAACCATTTATATGGCCTATGTATTATG
*
5787921 TTTTAGGTAAAACGATAGATAACCATTTATATGGCCAATGTAT
1 TTTTAGGTAAAACGATAGATAACCATTTATATGGCCTATGTAT
5787964 GCAAAGAGAT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 85 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (47 bp):
TTTTAGGTAAAACGATAGATAACCATTTATATGGCCTATGTATTATG
Found at i:5789316 original size:48 final size:48
Alignment explanation
Indices: 5789243--5789425 Score: 217
Period size: 48 Copynumber: 3.8 Consensus size: 48
5789233 TTCATTAAGG
* *
5789243 GATACTTTGATTTAGCTTCGGGCCATTATATCGGCACTTCGGGTGTGA
1 GATACTTTGATTTAGCTTCGGGCCATGATATCAGCACTTCGGGTGTGA
* * *
5789291 GTTACTTTGATTTGGCTTCGGGCCATGATATCAGCACTTCGAGTGTGA
1 GATACTTTGATTTAGCTTCGGGCCATGATATCAGCACTTCGGGTGTGA
* * * *
5789339 -AT-CTTATTGATTTGGCTTCGGGCCATGATATTAGCACTTCTGGTGCGA
1 GATAC-T-TTGATTTAGCTTCGGGCCATGATATCAGCACTTCGGGTGTGA
* * * *
5789387 GATACATTGAGTTAGCTTTGGGCCATGATATGAGCACTT
1 GATACTTTGATTTAGCTTCGGGCCATGATATCAGCACTT
5789426 AATGTGCGAG
Statistics
Matches: 116, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.01
47 2 0.02
48 110 0.95
49 2 0.02
50 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (48 bp):
GATACTTTGATTTAGCTTCGGGCCATGATATCAGCACTTCGGGTGTGA
Found at i:5789413 original size:96 final size:96
Alignment explanation
Indices: 5789249--5789425 Score: 246
Period size: 96 Copynumber: 1.8 Consensus size: 96
5789239 AAGGGATACT
* * * * * * *
5789249 TTGATTTAGCTTCGGGCCATTATATCGGCACTTCGGGTGTGAGTTACTTTGATTTGGCTTCGGGC
1 TTGATTTAGCTTCGGGCCATGATATCAGCACTTCGGGTGCGAGATACATTGAGTTAGCTTCGGGC
5789314 CATGATATCAGCACTTCGAGTGTGAATCTTA
66 CATGATATCAGCACTTCGAGTGTGAATCTTA
* * * *
5789345 TTGATTTGGCTTCGGGCCATGATATTAGCACTTCTGGTGCGAGATACATTGAGTTAGCTTTGGGC
1 TTGATTTAGCTTCGGGCCATGATATCAGCACTTCGGGTGCGAGATACATTGAGTTAGCTTCGGGC
*
5789410 CATGATATGAGCACTT
66 CATGATATCAGCACTT
5789426 AATGTGCGAG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 69 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (96 bp):
TTGATTTAGCTTCGGGCCATGATATCAGCACTTCGGGTGCGAGATACATTGAGTTAGCTTCGGGC
CATGATATCAGCACTTCGAGTGTGAATCTTA
Found at i:5804737 original size:40 final size:37
Alignment explanation
Indices: 5804636--5804801 Score: 173
Period size: 35 Copynumber: 4.6 Consensus size: 37
5804626 CATGGCAAAG
5804636 TGTGAAATGTAGGTATGG--TATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
* *
5804671 TGTGAAATGTAGGTATGGTAT-T-ATCCATACGGAGC
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
5804706 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-TATC--ATCCATACTGAGT
** * * *
5804746 TAAGAAATGTAGGTATGGCATTTC--CCATACCGAGT
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
***
5804781 TAAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
5804802 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
35 78 0.69
36 2 0.02
37 2 0.02
39 3 0.03
40 28 0.25
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.33
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
Found at i:5804755 original size:75 final size:75
Alignment explanation
Indices: 5804636--5804806 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
5804626 CATGGCAAAG
** *
5804636 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
5804695 CCATACGGAGC
65 CCATACCGAGC
5804706 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
5804771 CATACCGAGT
66 CATACCGAGC
***
5804781 TAAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
5804807 TGAGGAAAGC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:5814613 original size:55 final size:56
Alignment explanation
Indices: 5814493--5814635 Score: 155
Period size: 55 Copynumber: 2.6 Consensus size: 56
5814483 GCGACATGGC
* * * *
5814493 TGTGGTTGAGCCTGTCAAAACAACACGGGCGT-ACGACACGCCTGTGTGGAAGAAT
1 TGTGGTTGAACCTGTCAAAACAACACGGGCGTGACGACACGCCCGTATCGAAGAAT
* * * * * * *
5814548 CGTGGGTGAACCTGTTAAAACAACACGGGCGTGTC-ACACGCCCGTATCTAATACT
1 TGTGGTTGAACCTGTCAAAACAACACGGGCGTGACGACACGCCCGTATCGAAGAAT
**
5814603 TGTGGTTGAACCTGTCAAATGAACACGGGCGTG
1 TGTGGTTGAACCTGTCAAAACAACACGGGCGTG
5814636 GGGCTTTTAT
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
55 70 0.99
56 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (56 bp):
TGTGGTTGAACCTGTCAAAACAACACGGGCGTGACGACACGCCCGTATCGAAGAAT
Found at i:5815330 original size:18 final size:18
Alignment explanation
Indices: 5815309--5815347 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5815299 ATTTCTTCGA
5815309 ATTTGTTTACCTATTATT
1 ATTTGTTTACCTATTATT
*
5815327 ATTTGTTTATCTATTATT
1 ATTTGTTTACCTATTATT
5815345 ATT
1 ATT
5815348 ATTTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (18 bp):
ATTTGTTTACCTATTATT
Found at i:5832046 original size:18 final size:19
Alignment explanation
Indices: 5832012--5832047 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5832002 TGAGAAAAAT
5832012 CTCAAACACACAAATGAAA
1 CTCAAACACACAAATGAAA
*
5832031 CTCAAACAGA-AAATGAA
1 CTCAAACACACAAATGAA
5832048 GAAATAGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.22, G:0.08, T:0.11
Consensus pattern (19 bp):
CTCAAACACACAAATGAAA
Found at i:5842553 original size:24 final size:25
Alignment explanation
Indices: 5842486--5842554 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
5842476 AAGAGCGTCT
*
5842486 CGTTAT-TAGCCCTCTC-GAGCTTCC
1 CGTTATATAGCTCT-TCGGAGCTTCC
* * *
5842510 CGTTATATGGTTCTTGGGAGCTTCC
1 CGTTATATAGCTCTTCGGAGCTTCC
5842535 CGTTA-ATAGCTCTTCGGAGC
1 CGTTATATAGCTCTTCGGAGC
5842555 ATCCTGATTG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
24 19 0.53
25 17 0.47
ACGTcount: A:0.14, C:0.28, G:0.23, T:0.35
Consensus pattern (25 bp):
CGTTATATAGCTCTTCGGAGCTTCC
Found at i:5844178 original size:29 final size:30
Alignment explanation
Indices: 5844123--5844180 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
5844113 TTTACGAGCC
5844123 TAGGGGCTAAATTGTAAATATTTAAAAGTT
1 TAGGGGCTAAATTGTAAATATTTAAAAGTT
*
5844153 TAGGGGTTAAA-TGTAAAT-TTTCAAAAGT
1 TAGGGGCTAAATTGTAAATATTT-AAAAGT
5844181 ATGATTTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 13 0.50
30 10 0.38
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (30 bp):
TAGGGGCTAAATTGTAAATATTTAAAAGTT
Found at i:5844677 original size:43 final size:43
Alignment explanation
Indices: 5844595--5844678 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
5844585 TGAGGTATAT
*
5844595 AGCATCCGAGCTCGTTAAGAGGTCTGAGTTCATTATGGATGCA
1 AGCATCCGAGCTCGTTAAGAGGTCTGAGTTCATGATGGATGCA
* * *
5844638 AGCATCCGAGCTTGTTGAGAGGT-TCGAGTTCATGGTGGATG
1 AGCATCCGAGCTCGTTAAGAGGTCT-GAGTTCATGATGGATG
5844679 TGATTCATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.29
Consensus pattern (43 bp):
AGCATCCGAGCTCGTTAAGAGGTCTGAGTTCATGATGGATGCA
Found at i:5848187 original size:93 final size:93
Alignment explanation
Indices: 5848075--5848245 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5848065 GCCCATAAGT
* *
5848075 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5848140 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
5848168 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5848233 CGAGTTCGGATGC
66 CGAGTTCGGATGC
5848246 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:5848242 original size:46 final size:46
Alignment explanation
Indices: 5848067--5848242 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
5848057 TGTAACCCGC
* * *
5848067 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
5848113 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
5848163 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5848206 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5848243 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:5850649 original size:29 final size:29
Alignment explanation
Indices: 5850610--5850697 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
5850600 CAAAGATAAC
*
5850610 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
5850639 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
5850668 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
5850698 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:5850668 original size:15 final size:15
Alignment explanation
Indices: 5850610--5850688 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
5850600 CAAAGATAAC
*
5850610 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
5850624 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
5850639 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
5850653 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
5850668 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
5850683 AAGAAA
1 AAGAAA
5850689 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:5850697 original size:15 final size:15
Alignment explanation
Indices: 5850621--5850697 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
5850611 AGAAAACCGA
5850621 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
5850636 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
5850650 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
5850664 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
5850680 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
5850695 ATA
1 ATA
5850698 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:5853753 original size:93 final size:93
Alignment explanation
Indices: 5853641--5853811 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5853631 GCCCATAAGT
* *
5853641 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5853706 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
5853734 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5853799 CGAGTTCGGATGC
66 CGAGTTCGGATGC
5853812 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:5853808 original size:46 final size:46
Alignment explanation
Indices: 5853633--5853808 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
5853623 TGTAACCCGC
* * *
5853633 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
5853679 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
5853729 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5853772 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5853809 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:5860937 original size:43 final size:43
Alignment explanation
Indices: 5860855--5860938 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
5860845 GGAGGTATAT
* *
5860855 AGCATCCGAGCTCGTTGAGAGGTCCGAGATTATTATGGATGTA
1 AGCATCCGAGCTCGATGAGAGGTCCGAGATTATGATGGATGTA
* * *
5860898 AGCATCTGAGCTCGATGAGAGGTCTGAG-TTCATGGTGGATG
1 AGCATCCGAGCTCGATGAGAGGTCCGAGATT-ATGATGGATG
5860939 CGATTCATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 33 0.94
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.27
Consensus pattern (43 bp):
AGCATCCGAGCTCGATGAGAGGTCCGAGATTATGATGGATGTA
Found at i:5862746 original size:2 final size:2
Alignment explanation
Indices: 5862739--5862786 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5862729 CTTGTTTCGG
5862739 TA TA TA 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
5862781 TA TA TA
1 TA TA TA
5862787 GTAGACTACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5862906 original size:2 final size:2
Alignment explanation
Indices: 5862899--5862939 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5862889 ATATAGTTTG
5862899 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
5862940 AGGTCTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5865589 original size:39 final size:39
Alignment explanation
Indices: 5865535--5865615 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
5865525 ATATTACTTT
5865535 AAGGGTCTGAGATAGAATTATAAATCTTTGGAGAGGTCA
1 AAGGGTCTGAGATAGAATTATAAATCTTTGGAGAGGTCA
*
5865574 AAGGGTCTGAGATAGAATTATAAATCTTTGGAGGGGTCA
1 AAGGGTCTGAGATAGAATTATAAATCTTTGGAGAGGTCA
5865613 AAG
1 AAG
5865616 CTAAAATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.36, C:0.07, G:0.30, T:0.27
Consensus pattern (39 bp):
AAGGGTCTGAGATAGAATTATAAATCTTTGGAGAGGTCA
Found at i:5868647 original size:30 final size:30
Alignment explanation
Indices: 5868594--5868665 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
5868584 CAGAGACGTA
* * *
5868594 AACGGGGTTACCACGTTCATCAGTCAA-TTG
1 AACGGGGTTGCCACGCTCATCAGT-AAGTGG
* *
5868624 AACGGGGTTGCCATGCTCGTCAGTAAGTGG
1 AACGGGGTTGCCACGCTCATCAGTAAGTGG
*
5868654 AATGGGGTTGCC
1 AACGGGGTTGCC
5868666 GTGCACATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.06
30 33 0.94
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (30 bp):
AACGGGGTTGCCACGCTCATCAGTAAGTGG
Found at i:5891000 original size:27 final size:26
Alignment explanation
Indices: 5890970--5891049 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 26
5890960 TCTAAGTTCA
5890970 TATATTTTTGAAAATTTTTAAGGTTTT
1 TATATTTTTGAAAATTTTTAA-GTTTT
* * *
5890997 TATATTTTT-ATAAATTTCTAAATTTA
1 TATATTTTTGA-AAATTTTTAAGTTTT
*
5891023 TATATATTTG-AAATATTTTAAGTTTT
1 TATATTTTTGAAAAT-TTTTAAGTTTT
5891049 T
1 T
5891050 CTTTATAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
25 4 0.09
26 21 0.49
27 18 0.42
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (26 bp):
TATATTTTTGAAAATTTTTAAGTTTT
Found at i:5891035 original size:53 final size:53
Alignment explanation
Indices: 5890940--5891049 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 53
5890930 AAATCTCAAA
* *
5890940 TTTTATATTTTTATAAATCATCTAAGTTCATATATTTTTGAAA-ATTTTTAAGGT
1 TTTTATATTTTTATAAATCATCTAAATTCATATATATTTGAAATA-TTTTAA-GT
* *
5890994 TTTTATATTTTTATAAAT-TTCTAAATTTATATATATTTGAAATATTTTAAGT
1 TTTTATATTTTTATAAATCATCTAAATTCATATATATTTGAAATATTTTAAGT
5891046 TTTT
1 TTTT
5891050 CTTTATAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
52 6 0.12
53 26 0.51
54 19 0.37
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (53 bp):
TTTTATATTTTTATAAATCATCTAAATTCATATATATTTGAAATATTTTAAGT
Found at i:5899664 original size:20 final size:20
Alignment explanation
Indices: 5899639--5899678 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5899629 TAAGTATGGG
5899639 AAATTAACTTTGTTTTGCTT
1 AAATTAACTTTGTTTTGCTT
5899659 AAATTAACTTTGTTTTGCTT
1 AAATTAACTTTGTTTTGCTT
5899679 TTTATGTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
AAATTAACTTTGTTTTGCTT
Found at i:5906172 original size:27 final size:27
Alignment explanation
Indices: 5906134--5906188 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5906124 CAAAAATCAC
5906134 TAAAAATTTTGGAAATTGAATTAGAGG
1 TAAAAATTTTGGAAATTGAATTAGAGG
5906161 TAAAAATTTTGGAAATTGAATTAGAGG
1 TAAAAATTTTGGAAATTGAATTAGAGG
5906188 T
1 T
5906189 TGAATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.35
Consensus pattern (27 bp):
TAAAAATTTTGGAAATTGAATTAGAGG
Found at i:5907756 original size:84 final size:84
Alignment explanation
Indices: 5907667--5907883 Score: 240
Period size: 92 Copynumber: 2.5 Consensus size: 84
5907657 ATGAAATGTG
*
5907667 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAGACCATGGATGAAAGATACCATGG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAGACCATAGATGAAAGATACCATGG
* *
5907732 CAACATAACGGGAAATGAA
66 CAACATAACAGAAAATGAA
* * *
5907751 TAAGACCATGGTTGAAAGATACCATGGCAAAATGACGAGAAATGAATAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACAT-----GATATG---AAGACCATAGATGAAAGA
* *
5907816 TACCATGGCAACATGACAGAAAATGAG
58 TACCATGGCAACATAACAGAAAATGAA
* * * *
5907843 TAAGACCATAGTTGAAAGACACTATGGCATCATG-T-TGAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAGA
5907884 TAAATAAGAT
Statistics
Matches: 111, Mismatches: 14, Indels: 18
0.78 0.10 0.13
Matches are distributed among these distances:
82 4 0.04
84 32 0.29
85 2 0.02
87 1 0.01
89 5 0.05
92 67 0.60
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (84 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAGACCATAGATGAAAGATACCATGG
CAACATAACAGAAAATGAA
Found at i:5907767 original size:46 final size:46
Alignment explanation
Indices: 5907706--5907876 Score: 234
Period size: 46 Copynumber: 3.7 Consensus size: 46
5907696 ACATGATATG
* * *
5907706 AAGACCATGGATGAAAGATACCATGGCAACATAACGGGAAATGAAT
1 AAGACCATAGTTGAAAGATACCATGGCAACATGACGGGAAATGAAT
* * *
5907752 AAGACCATGGTTGAAAGATACCATGGCAAAATGACGAGAAATGAAT
1 AAGACCATAGTTGAAAGATACCATGGCAACATGACGGGAAATGAAT
* * *
5907798 AAGACCATAGTTGAAAGATACCATGGCAACATGACAGAAAATGAGT
1 AAGACCATAGTTGAAAGATACCATGGCAACATGACGGGAAATGAAT
* * *
5907844 AAGACCATAGTTGAAAGACACTATGGCATCATG
1 AAGACCATAGTTGAAAGATACCATGGCAACATG
5907877 TTGAAGATAA
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 112 1.00
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (46 bp):
AAGACCATAGTTGAAAGATACCATGGCAACATGACGGGAAATGAAT
Found at i:5914452 original size:10 final size:10
Alignment explanation
Indices: 5914439--5914508 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 10
5914429 AAAACGTATT
*
5914439 AAAATTCTAA
1 AAAATTATAA
5914449 AAAATTATAA
1 AAAATTATAA
5914459 AAAA-TA-AA
1 AAAATTATAA
* *
5914467 AAAAATAT-T
1 AAAATTATAA
*
5914476 AAAATTGATAT
1 AAAATT-ATAA
*
5914487 AAACTTAT-A
1 AAAATTATAA
5914496 AAAATTATAA
1 AAAATTATAA
5914506 AAA
1 AAA
5914509 TTAAATAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
8 6 0.12
9 16 0.33
10 21 0.43
11 6 0.12
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:5914519 original size:9 final size:9
Alignment explanation
Indices: 5914424--5914511 Score: 68
Period size: 9 Copynumber: 9.3 Consensus size: 9
5914414 ATTTAATTTT
5914424 TTATAAAAA
1 TTATAAAAA
* *
5914433 CGTATTAAAA
1 -TTATAAAAA
*
5914443 TTCTAAAAAA
1 TTAT-AAAAA
5914453 TTATAAAAA
1 TTATAAAAA
* *
5914462 ATAAAAAAA
1 TTATAAAAA
* *
5914471 ATATTAAAA
1 TTATAAAAA
*
5914480 TTGATATAAAC
1 TT-ATA-AAAA
5914491 TTATAAAAA
1 TTATAAAAA
5914500 TTATAAAAA
1 TTATAAAAA
5914509 TTA
1 TTA
5914512 AATAAATTTG
Statistics
Matches: 61, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
9 37 0.61
10 19 0.31
11 5 0.08
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:5915006 original size:10 final size:9
Alignment explanation
Indices: 5914947--5915005 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
5914937 TTTTTATGAT
5914947 TTTTTA-AA
1 TTTTTACAA
*
5914955 TTTTTATAA
1 TTTTTACAA
*
5914964 CTTTATATC-A
1 -TTTTTA-CAA
5914974 TTTTATA-AA
1 TTTT-TACAA
5914983 TTTTTACAA
1 TTTTTACAA
5914992 TTTTTACAA
1 TTTTTACAA
5915001 TTTTT
1 TTTTT
5915006 TGTTATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 8 0.19
9 26 0.62
10 8 0.19
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTACAA
Found at i:5931687 original size:28 final size:26
Alignment explanation
Indices: 5931646--5931708 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 26
5931636 GAAATACTCT
* *
5931646 TTTCAATATTCAGTATAGTTTTCTTTC
1 TTTCAATTTTCAGTATAG-TTTCATTC
5931673 TATTCAATTTTCAGTATAGTTTCATTC
1 T-TTCAATTTTCAGTATAGTTTCATTC
5931700 TTTCAATTT
1 TTTCAATTT
5931709 ACAACAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 8 0.24
27 9 0.27
28 16 0.48
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.56
Consensus pattern (26 bp):
TTTCAATTTTCAGTATAGTTTCATTC
Found at i:5934674 original size:90 final size:89
Alignment explanation
Indices: 5934507--5934723 Score: 262
Period size: 90 Copynumber: 2.4 Consensus size: 89
5934497 TTAAGGGTGC
* * * *
5934507 AAAAAGCTCTCAAAATTTTTCAAAAAAACAATTAAGCCCTACTTTTTTTTTACACTTATTTTGGT
1 AAAAAGCCCTCAAAACTTTTCAAAAAAACAATTAAGCCCTACTTTTTTTTTACACTCAATTTGGT
* * *
5934572 ATTTGAATTTTCAAAATGCATCAA
66 ATTAGAACTTTCAAAATACATCAA
* * *
5934596 AAAAAGCCCTCAAACCTTTTCAAGAAAAGCAATTAAGCTCCTAC-TTTTTTTTGCACTCAATTTG
1 AAAAAGCCCTCAAAACTTTTCAA-AAAAACAATTAAGC-CCTACTTTTTTTTTACACTCAATTTG
5934660 GTACTTAG-ACTTTCAAAATACATCAA
64 GTA-TTAGAACTTTCAAAATACATCAA
* * *
5934686 AAAGA-CCCT-AAAACATTTAAAAAAAACAATTAAGCCCT
1 AAAAAGCCCTCAAAACTTTTCAAAAAAACAATTAAGCCCT
5934724 TGCTTTTATT
Statistics
Matches: 110, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
86 3 0.03
87 13 0.12
88 9 0.08
89 24 0.22
90 53 0.48
91 8 0.07
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (89 bp):
AAAAAGCCCTCAAAACTTTTCAAAAAAACAATTAAGCCCTACTTTTTTTTTACACTCAATTTGGT
ATTAGAACTTTCAAAATACATCAA
Found at i:5934856 original size:19 final size:20
Alignment explanation
Indices: 5934824--5934895 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 20
5934814 ATTAAAAATT
*
5934824 AAAAA-ATATAAAAATCGTA
1 AAAAATATATAAAAATTGTA
5934843 AAAAATATATAAAAAATTGT-
1 AAAAATATAT-AAAAATTGTA
* *
5934863 AAAATTTTATAAAAATTGTA
1 AAAAATATATAAAAATTGTA
5934883 AAAAAT-TATAAAA
1 AAAAATATATAAAA
5934896 TATAAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 21 0.46
20 17 0.37
21 8 0.17
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAAATATATAAAAATTGTA
Found at i:5934866 original size:29 final size:29
Alignment explanation
Indices: 5934816--5934896 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
5934806 AATCAAATAT
5934816 TAAAAA-T-TAAAAAA-TATAAAAATCGTA
1 TAAAAATTATAAAAAATTAT-AAAATCGTA
* **
5934843 -AAAAATATATAAAAAATTGTAAAATTTTA
1 TAAAAAT-TATAAAAAATTATAAAATCGTA
*
5934872 TAAAAATTGTAAAAAATTATAAAAT
1 TAAAAATTATAAAAAATTATAAAAT
5934897 ATAAATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
26 5 0.11
28 1 0.02
29 30 0.68
30 8 0.18
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (29 bp):
TAAAAATTATAAAAAATTATAAAATCGTA
Found at i:5935167 original size:18 final size:18
Alignment explanation
Indices: 5935144--5935180 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5935134 AAAAAATTCT
*
5935144 AATTTTTAATAAATTTTA
1 AATTTTTAATAAAATTTA
*
5935162 AATTTTTATTAAAATTTA
1 AATTTTTAATAAAATTTA
5935180 A
1 A
5935181 TAATTTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTTTAATAAAATTTA
Found at i:5950226 original size:6 final size:6
Alignment explanation
Indices: 5950217--5950250 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5950207 AAATAAATTA
5950217 TAATGG TAATGG TAATGG TAATGG TAATGG TAAT
1 TAATGG TAATGG TAATGG TAATGG TAATGG TAAT
5950251 TTTAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (6 bp):
TAATGG
Found at i:5954225 original size:53 final size:54
Alignment explanation
Indices: 5954120--5954234 Score: 171
Period size: 53 Copynumber: 2.1 Consensus size: 54
5954110 GCATCGGTGC
*
5954120 AATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTAT-
1 AATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGATATGGCATCGGTATG
* *
5954173 AATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATG
1 AATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGATATGGCATCGGTATG
5954227 ATATGTGA
1 A-ATGTGA
5954235 ACCGTGTAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
52 1 0.02
53 48 0.86
54 1 0.02
55 6 0.11
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (54 bp):
AATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGATATGGCATCGGTATG
Found at i:5961727 original size:53 final size:54
Alignment explanation
Indices: 5961624--5961738 Score: 153
Period size: 53 Copynumber: 2.1 Consensus size: 54
5961614 GCATCGGTGC
* * *
5961624 AATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTAT-
1 AATGTGATAATGTGACTCCGTATAAGACCATAGCTGAGATATAGCATCGGTATG
* *
5961677 AATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGAGATATAGCTTCGGTATG
1 AATGTGATAATGTGACTCCGTATAAGACCATAG-CTGAGATATAGCATCGGTATG
5961731 ATATGTGA
1 A-ATGTGA
5961739 ACCGTGTAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
52 1 0.02
53 46 0.85
54 1 0.02
55 6 0.11
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (54 bp):
AATGTGATAATGTGACTCCGTATAAGACCATAGCTGAGATATAGCATCGGTATG
Found at i:5963359 original size:24 final size:21
Alignment explanation
Indices: 5963319--5963372 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 21
5963309 AATTGATTGT
*
5963319 TTTATAAATGATTTTTACTATTAA
1 TTTATAAATCA-TTTT--TATTAA
5963343 TTTATAAA-CATTATTTATTAA
1 TTTATAAATCATT-TTTATTAA
5963364 TTTATAAAT
1 TTTATAAAT
5963373 GTTAATCTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 14 0.52
22 2 0.07
23 3 0.11
24 8 0.30
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTATAAATCATTTTTATTAA
Found at i:5963829 original size:31 final size:30
Alignment explanation
Indices: 5963765--5963822 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
5963755 TATAGTAATT
* *
5963765 AAGATAAGTTCTCAATTAAATTAATGTAGG
1 AAGATAAGTTCTCAATCAAATTAATATAGG
5963795 AAGATTAAGTTCTCAATCAAATTAATAT
1 AAGA-TAAGTTCTCAATCAAATTAATAT
5963823 GAGAAGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (30 bp):
AAGATAAGTTCTCAATCAAATTAATATAGG
Found at i:5964271 original size:17 final size:18
Alignment explanation
Indices: 5964249--5964285 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5964239 AAAGGGAAAC
*
5964249 AATGTGGAAATGAA-GAT
1 AATGTGGAAACGAATGAT
5964266 AATGTGGAAACGAATGAT
1 AATGTGGAAACGAATGAT
5964284 AA
1 AA
5964286 GAATGATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.03, G:0.27, T:0.22
Consensus pattern (18 bp):
AATGTGGAAACGAATGAT
Found at i:5964728 original size:17 final size:17
Alignment explanation
Indices: 5964688--5964728 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
5964678 ACTTTTCAAA
*
5964688 GAAAAGAGACAATTTAT
1 GAAAAGTGACAATTTAT
5964705 GAAAAGTGACAATTTAT
1 GAAAAGTGACAATTTAT
5964722 GAAAAGT
1 GAAAAGT
5964729 CGTTGGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (17 bp):
GAAAAGTGACAATTTAT
Found at i:5976259 original size:30 final size:31
Alignment explanation
Indices: 5976223--5976291 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
5976213 GGTTTCATTT
* *
5976223 CAGTCACTCAAC-TTTTGAAAAA-TAACAAAA
1 CAGTCACT-AACGTTATAAAAAAGTAACAAAA
*
5976253 CAGTCACTAACGTTATAAAAAAGTGACAAAA
1 CAGTCACTAACGTTATAAAAAAGTAACAAAA
5976284 CAGTCACT
1 CAGTCACT
5976292 GATTAACAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 16 0.47
31 15 0.44
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (31 bp):
CAGTCACTAACGTTATAAAAAAGTAACAAAA
Found at i:5976350 original size:21 final size:20
Alignment explanation
Indices: 5976322--5976366 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
5976312 GTTTCAACAG
*
5976322 AACTGCTGATGTGGCAAGTT
1 AACTGCTGATATGGCAAGTT
*
5976342 AACTAGCTGATATGGCTAGTT
1 AACT-GCTGATATGGCAAGTT
5976363 AACT
1 AACT
5976367 TGCCACGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (20 bp):
AACTGCTGATATGGCAAGTT
Found at i:5980765 original size:30 final size:32
Alignment explanation
Indices: 5980698--5980766 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 32
5980688 ACTATTAATC
* * *
5980698 AGTGACTGTTTTGTCTCTTTTTTATAACGTTA
1 AGTGACTGTTTTGTCTATTTTTCATAAAGTTA
5980730 A-TGACTGTTTTGT-TATTTTTCA-AAAGTTA
1 AGTGACTGTTTTGTCTATTTTTCATAAAGTTA
5980759 AGTGACTG
1 AGTGACTG
5980767 AAATGAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.21
30 13 0.39
31 12 0.36
32 1 0.03
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.49
Consensus pattern (32 bp):
AGTGACTGTTTTGTCTATTTTTCATAAAGTTA
Found at i:5985398 original size:14 final size:14
Alignment explanation
Indices: 5985364--5985399 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5985354 TTAAATACTT
*
5985364 TCTAGTATACAATA
1 TCTAGTGTACAATA
5985378 TCTAGTGTACAATA
1 TCTAGTGTACAATA
5985392 TCTAGTGT
1 TCTAGTGT
5985400 TTGAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (14 bp):
TCTAGTGTACAATA
Found at i:5992374 original size:23 final size:24
Alignment explanation
Indices: 5992348--5992395 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
5992338 TGCGTAGTAT
5992348 AAAAATATA-TACGTAAT-ATAATG
1 AAAAATATATTA-GTAATAATAATG
*
5992371 AAAAGTATATTAGTAATAATAATG
1 AAAAATATATTAGTAATAATAATG
5992395 A
1 A
5992396 TAATGATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.31
Consensus pattern (24 bp):
AAAAATATATTAGTAATAATAATG
Found at i:5992572 original size:3 final size:3
Alignment explanation
Indices: 5992519--5992559 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5992509 AAAAGGATAT
5992519 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5992560 GGGAATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5992582 original size:15 final size:15
Alignment explanation
Indices: 5992548--5992603 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
5992538 TAATAATAAT
*
5992548 AATAATAATAATGGG
1 AATAATAATAGTGGG
5992563 AATAATAATAGT-GG
1 AATAATAATAGTGGG
*
5992577 ATATAAATAATAGTCGTG
1 A-AT-AATAATAGT-GGG
5992595 AA-AATAATA
1 AATAATAATA
5992604 ATAATAGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.09
15 20 0.57
16 9 0.26
17 1 0.03
18 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.16, T:0.29
Consensus pattern (15 bp):
AATAATAATAGTGGG
Found at i:5992613 original size:18 final size:18
Alignment explanation
Indices: 5992521--5992619 Score: 67
Period size: 18 Copynumber: 5.3 Consensus size: 18
5992511 AAGGATATAT
*
5992521 AATAATAATAATAAT-AA
1 AATAATAATAATAGTGAA
*
5992538 TAATAATAATAATAAT-AA
1 -AATAATAATAATAGTGAA
*
5992556 TAATGGGAATAATAATAGTGGA
1 -AAT---AATAATAATAGTGAA
* * *
5992578 TATAAATAATAGTCGTGAA
1 AAT-AATAATAATAGTGAA
*
5992597 AATAATAATAATAGTGAC
1 AATAATAATAATAGTGAA
5992615 AATAA
1 AATAA
5992620 CAGAGATAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
18 38 0.58
19 14 0.21
21 13 0.20
22 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (18 bp):
AATAATAATAATAGTGAA
Found at i:5994808 original size:21 final size:21
Alignment explanation
Indices: 5994782--5994824 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5994772 CACGAAAAAG
5994782 ATTAAGCATCTAAAACCCTTT
1 ATTAAGCATCTAAAACCCTTT
5994803 ATTAAGCATCTAAAACCCTTT
1 ATTAAGCATCTAAAACCCTTT
5994824 A
1 A
5994825 AATCTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (21 bp):
ATTAAGCATCTAAAACCCTTT
Found at i:6005617 original size:20 final size:20
Alignment explanation
Indices: 6005581--6005619 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6005571 ATTTTTTATT
*
6005581 TAAAGTATTAATGAATTTTG
1 TAAAGTATTAATAAATTTTG
6005601 TAAA-TATTGAATAAATTTT
1 TAAAGTATT-AATAAATTTT
6005620 TTATTATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
TAAAGTATTAATAAATTTTG
Found at i:6016491 original size:12 final size:12
Alignment explanation
Indices: 6016474--6016498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6016464 TATATCACCA
6016474 AAATACTCCTAG
1 AAATACTCCTAG
6016486 AAATACTCCTAG
1 AAATACTCCTAG
6016498 A
1 A
6016499 CTAGCTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (12 bp):
AAATACTCCTAG
Found at i:6026828 original size:12 final size:12
Alignment explanation
Indices: 6026811--6026842 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
6026801 TAGTTAGAAA
6026811 AAGAAATTATTG
1 AAGAAATTATTG
6026823 AAGAAATTATTG
1 AAGAAATTATTG
6026835 AAGAAATT
1 AAGAAATT
6026843 GGGTAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (12 bp):
AAGAAATTATTG
Found at i:6035982 original size:29 final size:29
Alignment explanation
Indices: 6035949--6036051 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
6035939 CCTCCGAACT
** * * *
6035949 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
6035978 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
6036007 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
6036036 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
6036052 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:6043485 original size:24 final size:24
Alignment explanation
Indices: 6043419--6043487 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 24
6043409 GGCCGACCCG
6043419 CTTTCCCCTTCCCTTTCCTTTCTCTTT
1 CTTT-CCCTTCCCTTT-CTTT-TCTTT
**
6043446 CTTT--CTTCCCCATCTTTTCTTGT
1 CTTTCCCTTCCCTTTCTTTTCTT-T
6043469 -TTTCCCTTCCCTTTCTTTT
1 CTTTCCCTTCCCTTTCTTTT
6043488 TCCCTTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
22 7 0.20
23 5 0.14
24 19 0.54
27 4 0.11
ACGTcount: A:0.01, C:0.39, G:0.01, T:0.58
Consensus pattern (24 bp):
CTTTCCCTTCCCTTTCTTTTCTTT
Found at i:6044476 original size:24 final size:25
Alignment explanation
Indices: 6044449--6044495 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
6044439 GAGTCCATTT
6044449 ATTTTA-TTATTATTTT-TCTTTTTA
1 ATTTTACTT-TTATTTTGTCTTTTTA
6044473 ATTTTACTTTTATTTTGTCTTTT
1 ATTTTACTTTTATTTTGTCTTTT
6044496 ATTTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (25 bp):
ATTTTACTTTTATTTTGTCTTTTTA
Found at i:6046782 original size:30 final size:30
Alignment explanation
Indices: 6046739--6046802 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
6046729 GAGAAAAATA
6046739 AAAAGTTTTGGGGAATAAAAGTTT-GA-GG
1 AAAAGTTTTGGGGAATAAAAGTTTGGAGGG
* *
6046767 AAAAGTTAATTGGGGAGTAAAATTTTGGAGGG
1 AAAAGTT--TTGGGGAATAAAAGTTTGGAGGG
6046799 AAAA
1 AAAA
6046803 TATTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 7 0.23
30 15 0.50
31 2 0.07
32 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (30 bp):
AAAAGTTTTGGGGAATAAAAGTTTGGAGGG
Found at i:6054631 original size:13 final size:13
Alignment explanation
Indices: 6054613--6054651 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
6054603 TTTTAGTTAC
6054613 TAATAATATATTA
1 TAATAATATATTA
*
6054626 TAATAATTTATTTA
1 TAATAATATA-TTA
6054640 TATATAATATAT
1 TA-ATAATATAT
6054652 AAATATCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 6 0.27
15 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATAATATATTA
Found at i:6060992 original size:207 final size:207
Alignment explanation
Indices: 6060624--6061045 Score: 476
Period size: 207 Copynumber: 2.0 Consensus size: 207
6060614 CAAACCTTGG
* * * * *
6060624 TTTTACAGTTGGGAGCTTTACTCTCGCTAACTATGTTGGAGGTCGCGACTCTTCGTCTACGAACC
1 TTTTACAGTTAGGAGCTTTACTCTCACTAACTATGATGGAGGTCACGACTCTTCGCCTACGAACC
* * * * * * **
6060689 TTAATTTTATAGTTGAGAGCTTTGCTCTCTCTAATTGTGCTAGAGGTCGTGGCTCTTAGCCTACA
66 TTAATTTTACAGCTGAGACCATTGCTCTCGCTAACTGTGCTAGAGGTCGCAGCTCTTAGCCTACA
** * * * *
6060754 AACCTTAATTTTTTAGCTAGGAGCTTTGCTCTCGCTAACTGTGGT-GAAGGTTGC-GACTCTTCG
131 AACCTTAATTTTACAGCTAGGAACATTGCTCTCGCTAACTGTGGTAG-AGGTCGCAG-CCCTTCG
*
6060817 CTTATGAACCTTAA
194 ATTATGAACCTTAA
* * *
6060831 TTTTACAGTTAGGAG-TATTGCTCTCACTAACTATGATGGAGGTCAC-AGCTCTTTGCCTGCGAA
1 TTTTACAGTTAGGAGCT-TTACTCTCACTAACTATGATGGAGGTCACGA-CTCTTCGCCTACGAA
* * * *
6060894 CCTTAATTTTACAGCTGAGACCATTGCTCTCGCTAACTGTGCTGGAGGTCGCAGCTCTTCGCTTG
64 CCTTAATTTTACAGCTGAGACCATTGCTCTCGCTAACTGTGCTAGAGGTCGCAGCTCTTAGCCTA
* * *
6060959 CGAACCTTAATTTTACAG-TTGGAAACATTGCTCTTGCTAACTGTGGTAGAGGTCGCAGCCCTTC
129 CAAACCTTAATTTTACAGCTAGG-AACATTGCTCTCGCTAACTGTGGTAGAGGTCGCAGCCCTTC
* *
6061023 GATTGTGAACCTTAG
193 GATTATGAACCTTAA
6061038 TTTTACAG
1 TTTTACAG
6061046 ACGATAATTT
Statistics
Matches: 178, Mismatches: 32, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
206 5 0.03
207 171 0.96
208 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (207 bp):
TTTTACAGTTAGGAGCTTTACTCTCACTAACTATGATGGAGGTCACGACTCTTCGCCTACGAACC
TTAATTTTACAGCTGAGACCATTGCTCTCGCTAACTGTGCTAGAGGTCGCAGCTCTTAGCCTACA
AACCTTAATTTTACAGCTAGGAACATTGCTCTCGCTAACTGTGGTAGAGGTCGCAGCCCTTCGAT
TATGAACCTTAA
Found at i:6061015 original size:69 final size:69
Alignment explanation
Indices: 6060624--6061045 Score: 345
Period size: 69 Copynumber: 6.1 Consensus size: 69
6060614 CAAACCTTGG
* * * * *
6060624 TTTTACAGTTGGGAGCTTTACTCTCGCTAACTATGTTGGAGGTCGC-GACTCTTCG-TCTACGAA
1 TTTTACAGTTGGAAGCATTGCTCTCGCTAACTGTGCTGGAGGTCGCAG-CTCTTCGCT-TACGAA
6060687 CCTTAA
64 CCTTAA
* * * * * ** * * *
6060693 TTTTATAGTT-GAGAGCTTTGCTCTCTCTAATTGTGCTAGAGGTCGTGGCTCTTAGCCTACAAAC
1 TTTTACAGTTGGA-AGCATTGCTCTCGCTAACTGTGCTGGAGGTCGCAGCTCTTCGCTTACGAAC
6060757 CTTAA
65 CTTAA
** * * * * * *
6060762 TTTTTTAGCTAGG-AGCTTTGCTCTCGCTAACTGTGGTGAAGGTTGC-GACTCTTCGCTTATGAA
1 TTTTACAG-TTGGAAGCATTGCTCTCGCTAACTGTGCTGGAGGTCGCAG-CTCTTCGCTTACGAA
6060825 CCTTAA
64 CCTTAA
* * * * * * * *
6060831 TTTTACAGTTAGG-AGTATTGCTCTCACTAACTATGATGGAGGTCACAGCTCTTTGCCTGCGAAC
1 TTTTACAGTT-GGAAGCATTGCTCTCGCTAACTGTGCTGGAGGTCGCAGCTCTTCGCTTACGAAC
6060895 CTTAA
65 CTTAA
* * *
6060900 TTTTACAGCT-GAGACCATTGCTCTCGCTAACTGTGCTGGAGGTCGCAGCTCTTCGCTTGCGAAC
1 TTTTACAGTTGGA-AGCATTGCTCTCGCTAACTGTGCTGGAGGTCGCAGCTCTTCGCTTACGAAC
6060964 CTTAA
65 CTTAA
* * * * * * **
6060969 TTTTACAGTTGGAAACATTGCTCTTGCTAACTGTGGTAGAGGTCGCAGCCCTTCGATTGTGAACC
1 TTTTACAGTTGGAAGCATTGCTCTCGCTAACTGTGCTGGAGGTCGCAGCTCTTCGCTTACGAACC
*
6061034 TTAG
66 TTAA
6061038 TTTTACAG
1 TTTTACAG
6061046 ACGATAATTT
Statistics
Matches: 284, Mismatches: 58, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
67 1 0.00
68 3 0.01
69 274 0.96
70 5 0.02
71 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (69 bp):
TTTTACAGTTGGAAGCATTGCTCTCGCTAACTGTGCTGGAGGTCGCAGCTCTTCGCTTACGAACC
TTAA
Found at i:6061033 original size:138 final size:137
Alignment explanation
Indices: 6060644--6061045 Score: 400
Period size: 138 Copynumber: 2.9 Consensus size: 137
6060634 GGGAGCTTTA
* * *
6060644 CTCTCGCTAACTATGTTGGAGGTCGCGACTCTTCG-TCTACGAACCTTAATTTTATAGTT-GAGA
1 CTCTCGCTAACTGTGCTGGAGGTCGCGACTCTTCGCT-TACGAACCTTAATTTTACAGTTGGA-A
* * * ** * * **
6060707 GCTTTGCTCTCTCTAATTGTGCTAGAGGTCGTGGCTCTTAGCCTACAAACCTTAATTTTTTAGCT
64 GCATTGCTCT-TCTAACTGTGATAGAGGTCGCAGCTCTTAGCCTGCGAACCTTAATTTTACAGCT
* *
6060772 AGGAGCTTTG
128 AGGACCATTG
* * * *
6060782 CTCTCGCTAACTGTGGTGAAGGTTGCGACTCTTCGCTTATGAACCTTAATTTTACAGTTAGG-AG
1 CTCTCGCTAACTGTGCTGGAGGTCGCGACTCTTCGCTTACGAACCTTAATTTTACAGTT-GGAAG
* * * * * *
6060846 TATTGCTCTCACTAACTATGATGGAGGTCACAGCTCTTTGCCTGCGAACCTTAATTTTACAGCT-
65 CATTGCTCT-TCTAACTGTGATAGAGGTCGCAGCTCTTAGCCTGCGAACCTTAATTTTACAGCTA
6060910 GAGACCATTG
129 G-GACCATTG
* *
6060920 CTCTCGCTAACTGTGCTGGAGGTCGC-AGCTCTTCGCTTGCGAACCTTAATTTTACAGTTGGAAA
1 CTCTCGCTAACTGTGCTGGAGGTCGCGA-CTCTTCGCTTACGAACCTTAATTTTACAGTTGGAAG
* * * ** * *
6060984 CATTGCTCTTGCTAACTGTGGTAGAGGTCGCAGCCCTTCGATTGTGAACCTTAGTTTTACAG
65 CATTGCTCTT-CTAACTGTGATAGAGGTCGCAGCTCTTAGCCTGCGAACCTTAATTTTACAG
6061046 ACGATAATTT
Statistics
Matches: 216, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
137 4 0.02
138 210 0.97
139 1 0.00
140 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (137 bp):
CTCTCGCTAACTGTGCTGGAGGTCGCGACTCTTCGCTTACGAACCTTAATTTTACAGTTGGAAGC
ATTGCTCTTCTAACTGTGATAGAGGTCGCAGCTCTTAGCCTGCGAACCTTAATTTTACAGCTAGG
ACCATTG
Found at i:6069146 original size:28 final size:28
Alignment explanation
Indices: 6069108--6069164 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
6069098 GAGAATCCTT
*
6069108 AAAACATTTCACTACCAATATAAAAATA
1 AAAACATTTCAATACCAATATAAAAATA
*
6069136 AAAACATTTCAATAGCAATATAAAAATA
1 AAAACATTTCAATACCAATATAAAAATA
6069164 A
1 A
6069165 TGATTGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.25
Consensus pattern (28 bp):
AAAACATTTCAATACCAATATAAAAATA
Found at i:6072425 original size:15 final size:16
Alignment explanation
Indices: 6072405--6072444 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
6072395 ATTACCAACA
*
6072405 AATGTAGTAGCAA-TC
1 AATGTAGCAGCAATTC
*
6072420 AATGTAGCAGTAATTC
1 AATGTAGCAGCAATTC
6072436 AATGTAGCA
1 AATGTAGCA
6072445 ATTGGCAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (16 bp):
AATGTAGCAGCAATTC
Found at i:6075890 original size:4 final size:4
Alignment explanation
Indices: 6075883--6075933 Score: 57
Period size: 4 Copynumber: 12.5 Consensus size: 4
6075873 TTTAATCAAT
* * * *
6075883 TTAA TTAA TTAA TTAA TTAA TTAA CTAAA TTAA TTTA TCAA TTAA ATAA
1 TTAA TTAA TTAA TTAA TTAA TTAA -TTAA TTAA TTAA TTAA TTAA TTAA
6075932 TT
1 TT
6075934 TTTCCAACTC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
4 35 0.92
5 3 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:6075904 original size:21 final size:21
Alignment explanation
Indices: 6075874--6075927 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
6075864 TGTTGTTTAT
*
6075874 TTAATCAATTTAA-TTAATTAA
1 TTAATCAA-TTAACTAAATTAA
*
6075895 TTAATTAATTAACTAAATTAA
1 TTAATCAATTAACTAAATTAA
*
6075916 TTTATCAATTAA
1 TTAATCAATTAA
6075928 ATAATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAATCAATTAACTAAATTAA
Found at i:6077894 original size:18 final size:18
Alignment explanation
Indices: 6077871--6077906 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6077861 ATATTGAAAT
*
6077871 TAAATACGTGAAAAACAC
1 TAAATACATGAAAAACAC
*
6077889 TAAATACATTAAAAACAC
1 TAAATACATGAAAAACAC
6077907 ACAATATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (18 bp):
TAAATACATGAAAAACAC
Done.