Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_pilon, whole genome shotgun sequence
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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2730015 original size:54 final size:53
Alignment explanation
Indices: 2729945--2730112 Score: 185
Period size: 54 Copynumber: 3.3 Consensus size: 53
2729935 ATCGACACTC
2729945 CTTTTCAGTATCGATACCATTTCTATATTCTGTAATCCATGGTATCGATACCTTT
1 CTTTT-AGTATCGATACCATTTCTATATT-TGTAATCCATGGTATCGATACCTTT
* * **
2730000 CTTTTAGTATCGATA-C--TTCTATA----T-AT-TATGGTACCGATA-CTCC
1 CTTTTAGTATCGATACCATTTCTATATTTGTAATCCATGGTATCGATACCTTT
*
2730043 CTTTCAGTATCGATACCATTTCTATATTTTGTAATCCATGGTATCGATACCTTT
1 CTTTTAGTATCGATACCATTTCTATA-TTTGTAATCCATGGTATCGATACCTTT
*
2730097 CTCTTAGTATCGATAC
1 CTTTTAGTATCGATAC
2730113 ATCTATATAT
Statistics
Matches: 91, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
43 16 0.18
44 12 0.13
45 2 0.02
46 8 0.09
51 8 0.09
52 2 0.02
53 12 0.13
54 26 0.29
55 5 0.05
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.43
Consensus pattern (53 bp):
CTTTTAGTATCGATACCATTTCTATATTTGTAATCCATGGTATCGATACCTTT
Found at i:2730055 original size:97 final size:97
Alignment explanation
Indices: 2729911--2730209 Score: 449
Period size: 97 Copynumber: 3.1 Consensus size: 97
2729901 CTCTACCATG
* * * * *
2729911 GTATCGATA-TT-TTTATACTATGGTATCGACACTCCTTTTCAGTATCGATACCATTTCTATATT
1 GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
*
2729974 CTGTAATCCATGGTATCGATACCTTTCTTTTA
66 CTGTAATCCATGGTATCGATACCTTTCTCTTA
2730006 GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
1 GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
*
2730071 TTGTAATCCATGGTATCGATACCTTTCTCTTA
66 CTGTAATCCATGGTATCGATACCTTTCTCTTA
* * * * *
2730103 GTATCGATACATCTATATATTATGGAACCGATACTCCCTTTCAATATCGATGCCATTTCTACATT
1 GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
* *
2730168 CTGGAATCCCTGGTATCGATACCTTTCTCTTA
66 CTGTAATCCATGGTATCGATACCTTTCTCTTA
*
2730200 ATATCGATAC
1 GTATCGATAC
2730210 ATACAGAAAT
Statistics
Matches: 186, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
95 9 0.05
96 2 0.01
97 175 0.94
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (97 bp):
GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
CTGTAATCCATGGTATCGATACCTTTCTCTTA
Found at i:2742174 original size:46 final size:46
Alignment explanation
Indices: 2742121--2742211 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
2742111 ATTATACTTT
* **
2742121 ATTTTCATATATAGCATCATTTCATGCTTATAATGCACCGTTATGC
1 ATTTTCATATATAGCATCATTTCACGCCAATAATGCACCGTTATGC
* * * * *
2742167 ATTTTCATTTATGGTATCCTTTTACGCCAATAATGCACCGTTATG
1 ATTTTCATATATAGCATCATTTCACGCCAATAATGCACCGTTATG
2742212 AAATTCATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (46 bp):
ATTTTCATATATAGCATCATTTCACGCCAATAATGCACCGTTATGC
Found at i:2742245 original size:45 final size:46
Alignment explanation
Indices: 2742150--2742248 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 46
2742140 TTTCATGCTT
** * * *
2742150 ATAATGCACCGTTATGCATTTTCATTTATGGTATCCTTTTACGCCA
1 ATAATGCACCGTTATGCAAATTCATTTATGGCATCCTTTCACACCA
* *
2742196 ATAATGCACCGTTATG-AAATTCATTTATGGCATCCTTTCATACCG
1 ATAATGCACCGTTATGCAAATTCATTTATGGCATCCTTTCACACCA
2742241 ATAATGCA
1 ATAATGCA
2742249 TCTAATTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 30 0.65
46 16 0.35
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (46 bp):
ATAATGCACCGTTATGCAAATTCATTTATGGCATCCTTTCACACCA
Found at i:2742294 original size:45 final size:45
Alignment explanation
Indices: 2742256--2742412 Score: 201
Period size: 45 Copynumber: 3.5 Consensus size: 45
2742246 GCATCTAATT
* *
2742256 TATGGTATCATTTCAAGCCTATAATGCACCGTTATGCATTACATA
1 TATGGTATCCTTTCATGCCTATAATGCACCGTTATGCATTACATA
* * * *
2742301 CAT-GTCATCCTTTCATGACTATAACGCACCG-TACTGAATTACATA
1 TATGGT-ATCCTTTCATGCCTATAATGCACCGTTA-TGCATTACATA
* *
2742346 TATGGAATCCTTTCATGCCTATAATGTACCGTTATGCATTACATA
1 TATGGTATCCTTTCATGCCTATAATGCACCGTTATGCATTACATA
*
2742391 TATGGCATCCTTTCATGCCTAT
1 TATGGTATCCTTTCATGCCTAT
2742413 TCCTACTATA
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
44 4 0.04
45 88 0.93
46 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (45 bp):
TATGGTATCCTTTCATGCCTATAATGCACCGTTATGCATTACATA
Found at i:2742310 original size:80 final size:83
Alignment explanation
Indices: 2742173--2742407 Score: 237
Period size: 80 Copynumber: 2.8 Consensus size: 83
2742163 ATGCATTTTC
* * * * *
2742173 ATTTATGGTATCCTTTTACGCCAATAATGCACCGTTATGAAATT-CATTTATGGCATCCTTTCAT
1 ATTTATGGTATCCTTTCAAGCCTATAATGCACCGTTATG-CATTACATATATGGCATCCTTTCAT
*
2742237 -ACCGATAATGCA-T-CT-A
65 GA-CGATAACGCACTACTGA
* * *
2742253 ATTTATGGTATCATTTCAAGCCTATAATGCACCGTTATGCATTACATACATGTCATCCTTTCATG
1 ATTTATGGTATCCTTTCAAGCCTATAATGCACCGTTATGCATTACATATATGGCATCCTTTCATG
*
2742318 ACTATAACGCACCGTACTGA
66 ACGATAACGCA-C-TACTGA
* * *
2742338 ATTACATATATGGAATCCTTTCATGCCTATAATGTACCGTTATGCATTACATATATGGCATCCTT
1 A-T---T-TATGGTATCCTTTCAAGCCTATAATGCACCGTTATGCATTACATATATGGCATCCTT
2742403 TCATG
61 TCATG
2742408 CCTATTCCTA
Statistics
Matches: 127, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
79 3 0.02
80 60 0.47
81 1 0.01
83 1 0.01
84 2 0.02
85 2 0.02
86 1 0.01
89 1 0.01
90 56 0.44
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (83 bp):
ATTTATGGTATCCTTTCAAGCCTATAATGCACCGTTATGCATTACATATATGGCATCCTTTCATG
ACGATAACGCACTACTGA
Found at i:2742370 original size:125 final size:126
Alignment explanation
Indices: 2742136--2742371 Score: 291
Period size: 125 Copynumber: 1.9 Consensus size: 126
2742126 CATATATAGC
* * * ** * * *
2742136 ATCATTTCATGCTTATAATGCACCGTTATGCATTTTCATTTATGGTATCCTTTTACGCCAATAAT
1 ATCATTTCAAGCCTATAATGCACCGTTATGCATTTACATACATGGTATCCTTTCACGACAATAAC
* *
2742201 GCACCGTTATGAAATTCATTTATGGCATCCTTTCATACCGATAATGCATCTAATTTATGGT
66 GCACCGTTATGAAATTCATATATGGAATCCTTTCATACCGATAATGCATCTAATTTATGGT
* *
2742262 ATCATTTCAAGCCTATAATGCACCGTTATGCA-TTACATACAT-GTCATCCTTTCATGACTATAA
1 ATCATTTCAAGCCTATAATGCACCGTTATGCATTTACATACATGGT-ATCCTTTCACGACAATAA
* *
2742325 CGCACCG-TACTG-AATTACATATATGGAATCCTTTCATGCCTATAATG
65 CGCACCGTTA-TGAAATT-CATATATGGAATCCTTTCATACCGATAATG
2742372 TACCGTTATG
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
124 8 0.09
125 55 0.59
126 30 0.32
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (126 bp):
ATCATTTCAAGCCTATAATGCACCGTTATGCATTTACATACATGGTATCCTTTCACGACAATAAC
GCACCGTTATGAAATTCATATATGGAATCCTTTCATACCGATAATGCATCTAATTTATGGT
Found at i:2743019 original size:97 final size:97
Alignment explanation
Indices: 2742846--2743118 Score: 384
Period size: 97 Copynumber: 2.8 Consensus size: 97
2742836 TATGGTACTA
** *
2742846 ATACTCCCTTTCAGTATCGATACCATTTCTACCCTCTGTAATCCATGGTATCGATATCTTTCTCT
1 ATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGTAATCCATGGTATCGATACCTTTCTCT
*
2742911 TAGTATTGATACTTCTATATATTATGATACCG
66 TAATATTGATACTTCTATATATTATGATACCG
* * * *
2742943 ATACTCCCTTTCAGTATCGATACGATTTCTAAATTCTATAATGCATGGTATCGATACCTTTCTCT
1 ATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGTAATCCATGGTATCGATACCTTTCTCT
* * *
2743008 TACTATCGATACTTCTATATATTATGGTACCG
66 TAATATTGATACTTCTATATATTATGATACCG
* * * * * * *
2743040 ATACTCCCTTTTAGTATCTATACCATTTCTACATTCTGGAATCCCTGGTATCAATACATTTCTGT
1 ATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGTAATCCATGGTATCGATACCTTTCTCT
2743105 TAATATTGATACTT
66 TAATATTGATACTT
2743119 ACAACAATAT
Statistics
Matches: 153, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
97 153 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (97 bp):
ATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGTAATCCATGGTATCGATACCTTTCTCT
TAATATTGATACTTCTATATATTATGATACCG
Found at i:2750352 original size:29 final size:29
Alignment explanation
Indices: 2750316--2750395 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 29
2750306 AAAACATGAT
*
2750316 AAGATATAATCCCATGCAGAATCAGAATG
1 AAGATATAATCCCATGCAAAATCAGAATG
* * * *
2750345 AATATATAATACAATGCAAAATCAGGATG
1 AAGATATAATCCCATGCAAAATCAGAATG
** *
2750374 GGGATATAATCCCATTCAAAAT
1 AAGATATAATCCCATGCAAAAT
2750396 TAGGACATGA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (29 bp):
AAGATATAATCCCATGCAAAATCAGAATG
Found at i:2750448 original size:29 final size:28
Alignment explanation
Indices: 2750304--2750455 Score: 81
Period size: 29 Copynumber: 5.3 Consensus size: 28
2750294 GGATCCTACA
* *
2750304 CAAAAACATGATAAGATATAATCCCATG
1 CAAAATCATGATAAGATTTAATCCCATG
* * * * *
2750332 CAGAATCA-GAATGAATATATAATACAATG
1 CAAAATCATG-AT-AAGATTTAATCCCATG
* ** * *
2750361 CAAAATCAGGATGGGGATATAATCCCATT
1 CAAAATCATGAT-AAGATTTAATCCCATG
* * * * **
2750390 CAAAATTAGGACATGATTTAATCCTGTG
1 CAAAATCATGATAAGATTTAATCCCATG
*
2750418 CAGAATCATGATAAGAATTTAATCCCATG
1 CAAAATCATGATAAG-ATTTAATCCCATG
*
2750447 CATAATCAT
1 CAAAATCAT
2750456 AAATGCATTA
Statistics
Matches: 92, Mismatches: 28, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
27 1 0.01
28 28 0.30
29 62 0.67
30 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.26
Consensus pattern (28 bp):
CAAAATCATGATAAGATTTAATCCCATG
Found at i:2750514 original size:2 final size:2
Alignment explanation
Indices: 2750507--2750532 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2750497 CATAAATAAG
2750507 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
2750533 TCAATTACGA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2750918 original size:13 final size:13
Alignment explanation
Indices: 2750900--2750925 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2750890 TTGAAAACAA
2750900 AAACGAACTAAAG
1 AAACGAACTAAAG
2750913 AAACGAACTAAAG
1 AAACGAACTAAAG
2750926 TCATTGTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (13 bp):
AAACGAACTAAAG
Found at i:2755401 original size:77 final size:77
Alignment explanation
Indices: 2755234--2755387 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 77
2755224 TTGGATATAC
2755234 CCATCATCTTGATGACATGAGCTCCTACAAGAGTTCACTCTTCCATTTTGCATTGAAATAGAGCT
1 CCATCATCTTGATGACATGAGCTCCTACAAGAGTTCACTCTTCCATTTTGCATTGAAATAGAGCT
2755299 TTAGAGGTCTCA
66 TTAGAGGTCTCA
*
2755311 CCATCATCTTGATGACATGAGCTCCTACAGGAGTTCACTCTTCCATTTTGCATTGAAATAGAGCT
1 CCATCATCTTGATGACATGAGCTCCTACAAGAGTTCACTCTTCCATTTTGCATTGAAATAGAGCT
2755376 TTAGAGGTCTCA
66 TTAGAGGTCTCA
2755388 TATCTCTCTT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (77 bp):
CCATCATCTTGATGACATGAGCTCCTACAAGAGTTCACTCTTCCATTTTGCATTGAAATAGAGCT
TTAGAGGTCTCA
Found at i:2759216 original size:2 final size:2
Alignment explanation
Indices: 2759204--2759250 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2759194 CTATAAAGGC
*
2759204 TA TA CA 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
2759246 TA TA T
1 TA TA T
2759251 GTTTCTGACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2761790 original size:81 final size:81
Alignment explanation
Indices: 2761703--2762113 Score: 536
Period size: 81 Copynumber: 5.1 Consensus size: 81
2761693 AACATATAAA
* * * * * *
2761703 CTTTTACCCAAATGCATATAACCTTTCATCTAACTTGCATGATTGACACCTTCCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCA
2761768 CAACTAGGCCATTAAT
66 CAACTAGGCCATTAAT
* *
2761784 ATTTTACTCAAAGGTATTTAATCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCA
*
2761849 CAACTAGACCATTAAT
66 CAACTAGGCCATTAAT
* * * *
2761865 CTTTTACTTAAAGATATTTAACCTTTCATCTAA-TTGGCATAATTGACACCTTTTTGTCAAATAC
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTT-GCATAATTGACACCTTTCTGTCAAATGC
2761929 ACAACTAGGCCATTAAT
65 ACAACTAGGCCATTAAT
* * * * * * *
2761946 CGTTTACTAAAAAGTATTTAACCTTTCATCTAACTGGTATAATTGACACTTTTATGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCA
* *
2762011 CAGCTAGGCCCTTAAT
66 CAACTAGGCCATTAAT
* ** * *
2762027 CTTTTACTCAAAGGTATTTAAGCTTTCATCTAACGGGCATAATTGACACCTTTGTATCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCA
* * *
2762092 CATCTAGACCAGTAAT
66 CAACTAGGCCATTAAT
2762108 CTTTTA
1 CTTTTA
2762114 TTTTGGAATA
Statistics
Matches: 288, Mismatches: 40, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
80 2 0.01
81 285 0.99
82 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (81 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCA
CAACTAGGCCATTAAT
Found at i:2762327 original size:55 final size:55
Alignment explanation
Indices: 2762262--2762370 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
2762252 CATATTACTA
*
2762262 ATACCAAAATTCATAAACTTATTATGAATTTATTATTTTTACACACAAAGTGCCC
1 ATACCAAAATTCATAAACTTATTATGAATTTATTAGTTTTACACACAAAGTGCCC
* * * *
2762317 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATAGTGCC
1 ATACCAAAATTCATAAACTTATTATGAATTTATTAGTTTTACACACAAAGTGCC
2762371 ATTTGGTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (55 bp):
ATACCAAAATTCATAAACTTATTATGAATTTATTAGTTTTACACACAAAGTGCCC
Found at i:2768146 original size:49 final size:49
Alignment explanation
Indices: 2768069--2768421 Score: 339
Period size: 49 Copynumber: 7.1 Consensus size: 49
2768059 TGCCTAACGA
*
2768069 TGCATTTTTGGGCAGAAAGGTACCACTAATGCAAGTTAGATGAAAAATGG
1 TGCATTTTT-GGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
* * *** * *
2768119 TGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAAATGCCTAACGA
1 TGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
* * ** *
2768168 TGCCTTTTTGAGCATAAAGGTGTGACTAATGCAAGTTAGCTGAAAAATGG
1 TGCATTTTTG-GCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
** * * * *** * *
2768218 TGCATTTTTGGCAGAAATATGCAACTAATGAAAGTTAAATGCCTAACGA
1 TGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
* * * *
2768267 TGCATTTTTGGGCAGAAAGGTGTCACTAATGCAAGCTAGATGAAATATTG
1 TGCATTTTT-GGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
** * *** * *
2768317 AACATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAACGA
1 TGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
*
2768366 TGCAATTTTGGGCA-AAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
1 TGC-ATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
2768415 TGCATTT
1 TGCATTT
2768422 CAAAAAAAAG
Statistics
Matches: 233, Mismatches: 67, Indels: 8
0.76 0.22 0.03
Matches are distributed among these distances:
48 4 0.02
49 139 0.60
50 90 0.39
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (49 bp):
TGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
Found at i:2768167 original size:99 final size:98
Alignment explanation
Indices: 2768051--2768421 Score: 555
Period size: 99 Copynumber: 3.8 Consensus size: 98
2768041 TCTAATACGA
*
2768051 AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTACCACTAATGCAAGTTAGATGAAAAA
1 AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAA
2768116 TGGTGCATTTTTGGCAGAAAGGTGTCACTAATGC
66 TGGTGCATTTTTGGCAGAAAGGTG-CACTAATGC
* * * ** *
2768150 AAGTTAAATGCCTAACGATGCCTTTTTGAGCATAAAGGTGTGACTAATGCAAGTTAGCTGAAAAA
1 AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAA
** *
2768215 TGGTGCATTTTTGGCAGAAATATGCAACTAATGA
66 TGGTGCATTTTTGGCAGAAAGGTGC-ACTAATGC
* * *
2768249 AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTGTCACTAATGCAAGCTAGATGAAATA
1 AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAA
* **
2768314 TTGAACATTTTTGGCAGAAAGGTGCCACTAATGC
66 TGGTGCATTTTTGGCAGAAAGGTG-CACTAATGC
*
2768348 AAGTTAAATGCCTAACGATGCAATTTTGGGCA-AAAGGTGCCACTAATGCAAGTTAGATGAAAAA
1 AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAA
2768412 TGGTGCATTT
66 TGGTGCATTT
2768422 CAAAAAAAAG
Statistics
Matches: 240, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
98 37 0.15
99 202 0.84
100 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (98 bp):
AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAA
TGGTGCATTTTTGGCAGAAAGGTGCACTAATGC
Found at i:2776492 original size:45 final size:45
Alignment explanation
Indices: 2776437--2776555 Score: 193
Period size: 45 Copynumber: 2.6 Consensus size: 45
2776427 TTGTGTTATT
* *
2776437 GTAGTAGTACATTTGTTGTACTATGGCACTAGGTGTGTAAAGATG
1 GTAGTAGTACATTTGTTGTACTATGGCACTAGGTGTGCAAAGATA
* *
2776482 GTAGTAGTACATTTGTTGTTCTATGGCACTATGTGTGCAAAGATA
1 GTAGTAGTACATTTGTTGTACTATGGCACTAGGTGTGCAAAGATA
*
2776527 GAAGTAGTACATTTGTTGTACTATGGCAC
1 GTAGTAGTACATTTGTTGTACTATGGCAC
2776556 AAATGTACTA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.36
Consensus pattern (45 bp):
GTAGTAGTACATTTGTTGTACTATGGCACTAGGTGTGCAAAGATA
Found at i:2781860 original size:45 final size:45
Alignment explanation
Indices: 2781636--2781853 Score: 258
Period size: 45 Copynumber: 4.8 Consensus size: 45
2781626 TCTTTATTGG
* * *
2781636 AGTAGTGCATTTGTTGTACTATGGCACTAAGTGTGCAAATATAGT
1 AGTAGTACATTTGTTGTACTATGGCACTATGTGTGCAAAGATAGT
* *
2781681 AGTAGTACATTTGTTGTACTATGGCACTATGCGTGCAAAGAAAGT
1 AGTAGTACATTTGTTGTACTATGGCACTATGTGTGCAAAGATAGT
* * * * **
2781726 AGTATTACATTTGTTTTATTATTGCACTATGCATGCAAAGATAGT
1 AGTAGTACATTTGTTGTACTATGGCACTATGTGTGCAAAGATAGT
* * ** *
2781771 AGTACTACATTTGTTGTACTATGGTACTATGTGTTTAAAGATGGT
1 AGTAGTACATTTGTTGTACTATGGCACTATGTGTGCAAAGATAGT
* *
2781816 AGTAGTACATTTTTTGTACTATAGG-ACTGTGTGTGCAA
1 AGTAGTACATTTGTTGTACTAT-GGCACTATGTGTGCAA
2781854 GGATGGTGTT
Statistics
Matches: 146, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
45 144 0.99
46 2 0.01
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (45 bp):
AGTAGTACATTTGTTGTACTATGGCACTATGTGTGCAAAGATAGT
Found at i:2786138 original size:20 final size:20
Alignment explanation
Indices: 2786100--2786138 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2786090 GACGGCTAGA
**
2786100 AACATTCAAAAACTCATTCC
1 AACATTCAAAAACAAATTCC
*
2786120 AACATTTAAAAACAAATTC
1 AACATTCAAAAACAAATTC
2786139 AAGACACTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (20 bp):
AACATTCAAAAACAAATTCC
Found at i:2786774 original size:85 final size:85
Alignment explanation
Indices: 2786645--2786866 Score: 191
Period size: 85 Copynumber: 2.6 Consensus size: 85
2786635 TGCTTTTTTA
* * * * *
2786645 TTTCTCTAAAGGATG-TAAAATCAGAGAATGGTCTTCCTCATTTCTCTAAAGGGA-GAAAAGTCA
1 TTTCTATAAAGGAAGCT-AAATCAGA-AATGATCTTTCTCCTTTCTCTAAAGGGATGAAAAGTCA
2786708 TAATCAAGGGTTGATCTACTCC
64 TAATCAAGGGTTGATCTACTCC
* * * **
2786730 TTTCTATAAAGGAAGCTAAATTGAGAAATGATCTTTCTCCTTTCTTTGAA-GGATGCCAAGTCAT
1 TTTCTATAAAGGAAGCTAAA-TCAGAAATGATCTTTCTCCTTTCTCTAAAGGGATGAAAAGTCAT
* * * *
2786794 GATCAATGGTTGTTCTGCTCC
65 AATCAAGGGTTGATCTACTCC
* * * * * *
2786815 TTTTTTTGAAGGACGCCAAATCAGGAAATGATCTCGT-TCCTTTCTCTAAAGG
1 TTTCTATAAAGGAAGCTAAATCA-GAAATGATCT-TTCTCCTTTCTCTAAAGG
2786867 ATTCCAAGTC
Statistics
Matches: 108, Mismatches: 23, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
84 5 0.05
85 96 0.89
86 7 0.06
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (85 bp):
TTTCTATAAAGGAAGCTAAATCAGAAATGATCTTTCTCCTTTCTCTAAAGGGATGAAAAGTCATA
ATCAAGGGTTGATCTACTCC
Found at i:2786867 original size:85 final size:83
Alignment explanation
Indices: 2786753--2786925 Score: 206
Period size: 85 Copynumber: 2.1 Consensus size: 83
2786743 AGCTAAATTG
* * * * *
2786753 AGAAATGATCTTTCTCCTTTCTTTGAAGGATGCCAAGTCATGATCAATGGTTGTTCTGCTCCTTT
1 AGAAATGATCTGTCTCCTTTCTCTAAAGGATGCCAAGTCATGATCAATGATTGCTCTG-T--TTT
2786818 T-TTTGAAGGACGCCAAATCA
63 TCTTTGAAGGACGCCAAATCA
* * *
2786838 GGAAATGATCTCGT-TCCTTTCTCTAAAGGATTCCAAGTCGTGATCAATGATTGCTCTGTTTTTC
1 AGAAATGATCT-GTCTCCTTTCTCTAAAGGATGCCAAGTCATGATCAATGATTGCTCTGTTTTTC
* *
2786902 TTTTAAGGATGCCAAATCA
65 TTTGAAGGACGCCAAATCA
2786921 AGAAA
1 AGAAA
2786926 AAAAATCTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
82 4 0.05
83 21 0.28
84 1 0.01
85 48 0.64
86 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (83 bp):
AGAAATGATCTGTCTCCTTTCTCTAAAGGATGCCAAGTCATGATCAATGATTGCTCTGTTTTTCT
TTGAAGGACGCCAAATCA
Found at i:2788807 original size:195 final size:195
Alignment explanation
Indices: 2788468--2788854 Score: 472
Period size: 195 Copynumber: 2.0 Consensus size: 195
2788458 AGGAATAAAA
* *
2788468 GGTATTTTGGGATGGCTTCTTGGGTCAAGATTTAGCACCTCTAATTCTTTTATGTTCCTCGCTCT
1 GGTATTTTGGGATGGCTTCTTGGGTCAAGATTTAGCACCTCTAATTCTTTGATGTTCATCGCTCT
* * * * * * *
2788533 AACATGTTCATCTTCTAGAAATGTCCACTGGTTCTAAGCTCTCACAAATGCTTATTGGATGTACG
66 AACATGTTCATCTTCTAGAAATATCCACTAGTTCTAAACTCTCACAAATGCGTATTGAATATAAG
* * * *
2788598 ACACTTTTTCAAGAGATTTATAAGCCCACCTCTTGTGAAACAGTTGCACAATTTTAACATTTGAG
131 ACACTTTGTCAAGAGATTTATAAGCCCACCTCTTGTAAAACAGTTGCAAAACTTTAACATTTGAG
* * *
2788663 GGTATTTTGGGTTGGCTTCTCT-GGTTAAGATTTAGCACAC-CTAGTTCTTTGATGTTCATCGCT
1 GGTATTTTGGGATGGCTTCT-TGGGTCAAGATTTAGCAC-CTCTAATTCTTTGATGTTCATCGCT
* * * * *** *
2788726 GTAGCATGTTCATCTTCTATAAATATCCATTAGTTCTAAACTCTCGTGAATGCGTCTTGAATATA
64 CTAACATGTTCATCTTCTAGAAATATCCACTAGTTCTAAACTCTCACAAATGCGTATTGAATATA
* * * * * *
2788791 AGACTCTTTGTCAAGAGTTTTATAAGCTCGCCTCTTGTAAAATAGTTGCAAAACTTTCACATTT
129 AGACACTTTGTCAAGAGATTTATAAGCCCACCTCTTGTAAAACAGTTGCAAAACTTTAACATTT
2788855 AACCCGCCTT
Statistics
Matches: 160, Mismatches: 30, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
195 158 0.99
196 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (195 bp):
GGTATTTTGGGATGGCTTCTTGGGTCAAGATTTAGCACCTCTAATTCTTTGATGTTCATCGCTCT
AACATGTTCATCTTCTAGAAATATCCACTAGTTCTAAACTCTCACAAATGCGTATTGAATATAAG
ACACTTTGTCAAGAGATTTATAAGCCCACCTCTTGTAAAACAGTTGCAAAACTTTAACATTTGAG
Found at i:2790743 original size:121 final size:121
Alignment explanation
Indices: 2790596--2790841 Score: 492
Period size: 121 Copynumber: 2.0 Consensus size: 121
2790586 ATTTTAATCC
2790596 TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
1 TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
2790661 TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
66 TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
2790717 TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
1 TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
2790782 TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
66 TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
2790838 TATT
1 TATT
2790842 CTTTTGTTTT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 125 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (121 bp):
TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
Found at i:2797754 original size:136 final size:136
Alignment explanation
Indices: 2797463--2797959 Score: 721
Period size: 136 Copynumber: 3.7 Consensus size: 136
2797453 TTTAACATTT
*
2797463 CCTATCACTCGATTCACGGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
1 CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
* * * * * * * *
2797528 GGAGAGTTC---ATGGGAATAACTCATCCAACAGAGGGAGAAGAAGTTTATAATGAAAAGAGATT
66 TGAGAGTTCATAATGAGAAGAACTCATTCAATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
*
2797590 GTTTGA
131 GTTCGA
* * *
2797596 CCTATCACTTGATTTACAGCATTTCGAATCAGTGATGCCTCACTTGAGGGATTGACATTTCCAAT
1 CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
* *
2797661 TGAAAGTTCATAATGAGAAGAACTCATTCGATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
66 TGAGAGTTCATAATGAGAAGAACTCATTCAATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
*
2797726 GTTCAA
131 GTTCGA
* * * *
2797732 CCTATCACTTGATTCACGGCATTTCGAATCAGTGACGTCTCGCTTGAGGGATTGACATTTCCAAT
1 CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
* * *
2797797 TGAGAGTTCATAGTGAGAAGAACTCATTCAATAGAGGGAGAAGAAGATCATAATGAGAAGAGCTT
66 TGAGAGTTCATAATGAGAAGAACTCATTCAATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
2797862 GTTCGA
131 GTTCGA
* * * * *
2797868 CCTATCACTCGATTCACAACATTTTGAATCTGTGATGCCTCGCTTGAGTGATGGACATTTCCAAT
1 CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
2797933 TGAGAGTTCATAATGAGAAGAACTCAT
66 TGAGAGTTCATAATGAGAAGAACTCAT
2797960 CCTAAAGGAG
Statistics
Matches: 324, Mismatches: 37, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
133 68 0.21
136 256 0.79
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (136 bp):
CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
TGAGAGTTCATAATGAGAAGAACTCATTCAATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
GTTCGA
Found at i:2798910 original size:22 final size:24
Alignment explanation
Indices: 2798872--2798922 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
2798862 TCTGGGTCTT
2798872 GGTC-TGC-TGGATCTTGT-ATTG
1 GGTCTTGCTTGGATCTTGTAATTG
*
2798893 GG-CTTGCTTGGATGTTGTAATTG
1 GGTCTTGCTTGGATCTTGTAATTG
2798916 GGTCTTG
1 GGTCTTG
2798923 GGAGAGACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 5 0.20
22 9 0.36
23 6 0.24
24 4 0.16
ACGTcount: A:0.10, C:0.12, G:0.35, T:0.43
Consensus pattern (24 bp):
GGTCTTGCTTGGATCTTGTAATTG
Found at i:2798973 original size:3 final size:3
Alignment explanation
Indices: 2798965--2799008 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
2798955 GTAACACACT
* *
2798965 TAA TAA TAA TAA TAA TAA TAT TAA T-A TAA T-A TAA TAA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2799009 TTTTAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2805096 original size:49 final size:47
Alignment explanation
Indices: 2805032--2805172 Score: 133
Period size: 47 Copynumber: 2.9 Consensus size: 47
2805022 CGCATTTAAC
* * **
2805032 TTTCATTAGTGGTACCTTTTATGTCGAAATGCACCATTATGCATTACTT
1 TTTCATTAGTAGTACC-TTTATGT-AAAAAACACCATTATGCATTACTT
2805081 TTTCATTAGTAGTACCTTTATGTAAAAAACACCATTATGCATTTAAC--
1 TTTCATTAGTAGTACCTTTATGTAAAAAACACCATTATGCA-TT-ACTT
* * * * *
2805128 TTGCATTAGTGGCACCTTTCTGCTAAAAATGCACCATTATGCATT
1 TTTCATTAGTAGTACCTTTATG-TAAAAA-ACACCATTATGCATT
2805173 TCACTTGCAT
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
47 33 0.42
48 17 0.22
49 29 0.37
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (47 bp):
TTTCATTAGTAGTACCTTTATGTAAAAAACACCATTATGCATTACTT
Found at i:2805179 original size:49 final size:49
Alignment explanation
Indices: 2805023--2805329 Score: 351
Period size: 49 Copynumber: 6.3 Consensus size: 49
2805013 TGAAATGCAC
* * **
2805023 GCATTTAACTTTCATTAGTGGTACCTTTTATG-TCGAAATGCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACC-TTTATGCTAAAAATGCACCATTAT
* * * *
2805072 GCA-TT-ACTTTTTCATTAGTAGTACCTTTATG-TAAAAA-ACACCATTAT
1 GCATTTAAC--TTGCATTAGTGGCACCTTTATGCTAAAAATGCACCATTAT
*
2805119 GCATTTAACTTGCATTAGTGGCACCTTTCTGCTAAAAATGCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACCTTTATGCTAAAAATGCACCATTAT
* *
2805168 GCATTTCACTTGCATTAGTGGCACCTTTCTGC-AAAATATGCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACCTTTATGCTAAAA-ATGCACCATTAT
* * * * *
2805217 GAATTTAACTTGCATTGGTGACACCTTTCTGCCAAAAATGCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACCTTTATGCTAAAAATGCACCATTAT
* *
2805266 GCATTCAACTTGCATTAGTGGCAGCTTTATGC-AAAAA-GCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACCTTTATGCTAAAAATGCACCATTAT
*
2805313 GCAGTTAACTTGCATTA
1 GCATTTAACTTGCATTA
2805330 TAGAGTAGTT
Statistics
Matches: 228, Mismatches: 22, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
47 57 0.25
48 29 0.13
49 138 0.61
50 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (49 bp):
GCATTTAACTTGCATTAGTGGCACCTTTATGCTAAAAATGCACCATTAT
Found at i:2805245 original size:98 final size:96
Alignment explanation
Indices: 2805023--2805329 Score: 375
Period size: 96 Copynumber: 3.2 Consensus size: 96
2805013 TGAAATGCAC
* ** * * * * ** *
2805023 GCATTTAACTTTCATTAGTGGTACCTTTTATGTC-GAAATGCACCATTATGCATTACTTTTTCAT
1 GCATTTAACTTGCATTAGTGACACC-TTTCTGCCAAAAATGCACCATTATGCATTTCACTTGCAT
* * * *
2805087 TAGTAGTACCTTTATGTAAAAAACACCATTAT
65 TAGTGGCACCTTTATGCAAAAAGCACCATTAT
* *
2805119 GCATTTAACTTGCATTAGTGGCACCTTTCTGCTAAAAATGCACCATTATGCATTTCACTTGCATT
1 GCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATTATGCATTTCACTTGCATT
*
2805184 AGTGGCACCTTTCTGCAAAATATGCACCATTAT
66 AGTGGCACCTTTATGCAAAA-A-GCACCATTAT
* *
2805217 GAATTTAACTTGCATTGGTGACACCTTTCTGCCAAAAATGCACCATTATGCA-TTCAACTTGCAT
1 GCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATTATGCATTTC-ACTTGCAT
*
2805281 TAGTGGCAGCTTTATGCAAAAAGCACCATTAT
65 TAGTGGCACCTTTATGCAAAAAGCACCATTAT
*
2805313 GCAGTTAACTTGCATTA
1 GCATTTAACTTGCATTA
2805330 TAGAGTAGTT
Statistics
Matches: 183, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
95 5 0.03
96 89 0.49
97 5 0.03
98 84 0.46
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (96 bp):
GCATTTAACTTGCATTAGTGACACCTTTCTGCCAAAAATGCACCATTATGCATTTCACTTGCATT
AGTGGCACCTTTATGCAAAAAGCACCATTAT
Found at i:2805675 original size:17 final size:17
Alignment explanation
Indices: 2805634--2805680 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
2805624 ATTTTCAATT
*
2805634 TTTCATAAAATTCATCC
1 TTTCTTAAAATTCATCC
2805651 TTTCTTAAAATTCATCC
1 TTTCTTAAAATTCATCC
2805668 TATT-TTAAAATTC
1 T-TTCTTAAAATTC
2805681 TAGGCTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTCTTAAAATTCATCC
Found at i:2806067 original size:16 final size:15
Alignment explanation
Indices: 2806042--2806071 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2806032 ATCCAATAAC
2806042 TCAACTCTTCATTTT
1 TCAACTCTTCATTTT
2806057 TCAATCTCTTCATTT
1 TCAA-CTCTTCATTT
2806072 CTACTTATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (15 bp):
TCAACTCTTCATTTT
Found at i:2806965 original size:32 final size:32
Alignment explanation
Indices: 2806922--2806982 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2806912 TTTAAATAGA
2806922 TTTAGTATTTTA-ATTAAGTTTTAGGATATTATT
1 TTTAGTATTTTATATT-AGTTTTAGG-TATTATT
*
2806955 TTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTAGTATTTTATATTAGTTTTAGGTATT
2806983 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 4 0.15
32 15 0.58
33 7 0.27
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.62
Consensus pattern (32 bp):
TTTAGTATTTTATATTAGTTTTAGGTATTATT
Found at i:2807704 original size:4 final size:4
Alignment explanation
Indices: 2807655--2807687 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
2807645 CTCCATCTCT
2807655 TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
2807688 ATTGTTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2813583 original size:12 final size:13
Alignment explanation
Indices: 2813544--2813589 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
2813534 ACCCAATTCG
*
2813544 TTATATTTTTGTT
1 TTATATTTTCGTT
*
2813557 TT-TATTTTCATT
1 TTATATTTTCGTT
2813569 TTAT-TTTTCGTT
1 TTATATTTTCGTT
*
2813581 TTATGTTTT
1 TTATATTTT
2813590 TAGCGAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 21 0.75
13 7 0.25
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (13 bp):
TTATATTTTCGTT
Found at i:2815488 original size:31 final size:31
Alignment explanation
Indices: 2815446--2815505 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
2815436 TTTAAATAGG
2815446 TTTTAGTATTTA-ATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTATATT-AGTTTTA-GATATTAT
2815478 TTTTA-TATTTATATTAGTTTTAGATATT
1 TTTTAGTATTTATATTAGTTTTAGATATT
2815506 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 6 0.22
31 13 0.48
32 8 0.30
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (31 bp):
TTTTAGTATTTATATTAGTTTTAGATATTAT
Found at i:2815611 original size:62 final size:62
Alignment explanation
Indices: 2815486--2815604 Score: 177
Period size: 62 Copynumber: 1.9 Consensus size: 62
2815476 ATTTTTATAT
2815486 TTATATTAGTTTTAGATATTTTAAATTAAATAGGTTTTAGTATTTTATTAGGATTTAGAATA
1 TTATATTAGTTTTAGATATTTTAAATTAAATAGGTTTTAGTATTTTATTAGGATTTAGAATA
* * ** *
2815548 TTATATTATTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTATTAGGATTTA
1 TTATATTAGTTTTAGATATTTTAAATTAAATAGGTTTT-AGTATTTTATTAGGATTTA
2815605 AGATATTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 5 0.10
62 46 0.90
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (62 bp):
TTATATTAGTTTTAGATATTTTAAATTAAATAGGTTTTAGTATTTTATTAGGATTTAGAATA
Found at i:2816197 original size:15 final size:15
Alignment explanation
Indices: 2816179--2816209 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2816169 TCTCAATCTC
*
2816179 TTTTATTTTTTTATT
1 TTTTATTTATTTATT
2816194 TTTTATTTATTTATT
1 TTTTATTTATTTATT
2816209 T
1 T
2816210 AATTGTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTATTTATTTATT
Found at i:2818959 original size:49 final size:48
Alignment explanation
Indices: 2818895--2819216 Score: 380
Period size: 48 Copynumber: 6.6 Consensus size: 48
2818885 TTTTATGCTG
* * *
2818895 AATGCACCGTTATGCATTTAACTTTCATTAGTGGTACCTTTTATGCTC-A
1 AATGCACCATTATGCATTTAACTTGCATTAGTGGCACC-TTTATGC-CAA
* * * * * *
2818944 AATACACCGTTATGCA-TTAAATTTCATTAGCGGTACCTTTATGCCAAA
1 AATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTATGCC-AA
* * *
2818992 AATACACCATTATGCATTTAA-TTGCATTAGTGACACCTTTATACCAAA
1 AATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTATGCC-AA
*
2819040 AATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
1 AATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTATGCCAA
* * *
2819088 AAGTGCACCATTATGCATTTAACTTGCATTATTGGAACCTTTCTGCCAA
1 AA-TGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTATGCCAA
* * * *
2819137 AATGCACCATTATGAATTTAACTTGCATTAGTGGCACCTATCTGCAAAAA
1 AATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTATGC--CAA
2819187 AATGCACCATTATGCATTTAACTTGCATTA
1 AATGCACCATTATGCATTTAACTTGCATTA
2819217 TAGAGCAGTT
Statistics
Matches: 245, Mismatches: 21, Indels: 13
0.88 0.08 0.05
Matches are distributed among these distances:
46 1 0.00
47 7 0.03
48 120 0.49
49 86 0.35
50 31 0.13
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (48 bp):
AATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTATGCCAA
Found at i:2819079 original size:97 final size:96
Alignment explanation
Indices: 2818895--2819216 Score: 398
Period size: 97 Copynumber: 3.3 Consensus size: 96
2818885 TTTTATGCTG
* * * * *
2818895 AATGCACCGTTATGCATTTAACTTTCATTAGTGGTACCTTTTATGCTC-AAATACACCGTTATGC
1 AATGCACCATTATGCATTTAACTTGCATTAGT-GAACC-TTTATGC-CAAAATGCACCATTATGC
* * * * *
2818959 A-TTAAATTTCATTAGCGGTACCTTTATGCCAAA
63 ATTTAACTTGCATTAGTGGCACCTTTCTGCCAAA
* *
2818992 AATACACCATTATGCATTTAA-TTGCATTAGTGACACCTTTATACCAAAAATGCACCATTATGCA
1 AATGCACCATTATGCATTTAACTTGCATTAGTGA-ACCTTTATGCC-AAAATGCACCATTATGCA
2819056 TTTAACTTGCATTAGTGGCACCTTTCTGCCAAA
64 TTTAACTTGCATTAGTGGCACCTTTCTGCCAAA
* * * *
2819089 AGTGCACCATTATGCATTTAACTTGCATTATTGGAACCTTTCTGCCAAAATGCACCATTATGAAT
1 AATGCACCATTATGCATTTAACTTGCATTAGT-GAACCTTTATGCCAAAATGCACCATTATGCAT
* *
2819154 TTAACTTGCATTAGTGGCACCTATCTGCAAAAA
65 TTAACTTGCATTAGTGGCACCTTTCTGC-CAAA
2819187 AATGCACCATTATGCATTTAACTTGCATTA
1 AATGCACCATTATGCATTTAACTTGCATTA
2819217 TAGAGCAGTT
Statistics
Matches: 197, Mismatches: 21, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
94 1 0.01
95 7 0.04
96 27 0.14
97 110 0.56
98 50 0.25
99 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (96 bp):
AATGCACCATTATGCATTTAACTTGCATTAGTGAACCTTTATGCCAAAATGCACCATTATGCATT
TAACTTGCATTAGTGGCACCTTTCTGCCAAA
Found at i:2822030 original size:33 final size:38
Alignment explanation
Indices: 2821991--2822089 Score: 100
Period size: 40 Copynumber: 2.6 Consensus size: 38
2821981 ACAAAATACA
*
2821991 ACATTCCC-A-GTAATC-ATATTC-C-CTGGTAATCTT
1 ACATTCCCAACGTAATCTACATTCTCACTGGTAATCTT
2822024 ACATTCCCAACGGTAATCTTACATTCTCACTGGTAATCTT
1 ACATTCCCAAC-GTAATC-TACATTCTCACTGGTAATCTT
* *
2822064 ACATTCCTACAGGTAATCTTACATTC
1 ACATTCCCA-ACGTAATC-TACATTC
2822090 CTTGAACCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
33 8 0.15
34 1 0.02
36 6 0.11
38 5 0.09
39 1 0.02
40 33 0.60
41 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.35
Consensus pattern (38 bp):
ACATTCCCAACGTAATCTACATTCTCACTGGTAATCTT
Found at i:2822040 original size:20 final size:20
Alignment explanation
Indices: 2822015--2822090 Score: 109
Period size: 20 Copynumber: 3.8 Consensus size: 20
2822005 CATATTCCCT
2822015 GGTAATCTTACATTCCCA-A
1 GGTAATCTTACATTCCCACA
* *
2822034 CGGTAATCTTACATTCTCACT
1 -GGTAATCTTACATTCCCACA
*
2822055 GGTAATCTTACATTCCTACA
1 GGTAATCTTACATTCCCACA
2822075 GGTAATCTTACATTCC
1 GGTAATCTTACATTCC
2822091 TTGAACCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (20 bp):
GGTAATCTTACATTCCCACA
Found at i:2822058 original size:40 final size:40
Alignment explanation
Indices: 2822013--2822089 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
2822003 ATCATATTCC
2822013 CTGGTAATCTTACATTCCCAAC-GGTAATCTTACATTCTCA
1 CTGGTAATCTTACATT-CCAACAGGTAATCTTACATTCTCA
*
2822053 CTGGTAATCTTACATTCCTACAGGTAATCTTACATTC
1 CTGGTAATCTTACATTCCAACAGGTAATCTTACATTC
2822090 CTTGAACCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.36
Consensus pattern (40 bp):
CTGGTAATCTTACATTCCAACAGGTAATCTTACATTCTCA
Found at i:2822512 original size:11 final size:11
Alignment explanation
Indices: 2822483--2822516 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2822473 AATATATTTA
*
2822483 AAAAGTAAAAT
1 AAAATTAAAAT
2822494 ACAAATTAAAAT
1 A-AAATTAAAAT
2822506 AAAATTAAAAT
1 AAAATTAAAAT
2822517 GAATATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:2825790 original size:40 final size:40
Alignment explanation
Indices: 2825697--2825819 Score: 162
Period size: 40 Copynumber: 3.1 Consensus size: 40
2825687 TATCGATTAA
*
2825697 GCACTTTGGTGCATATGGTA-GGCACGACCTTATGTGT-AT
1 GCACTTCGGTGCATATGG-AGGGCACGACCTTATGTGTAAT
* * * *
2825736 GCACTTCAGAGCATATAGAGGGCATGACCTTATGTGTAAT
1 GCACTTCGGTGCATATGGAGGGCACGACCTTATGTGTAAT
*
2825776 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAA-
1 GCACTTCGGTGCATATGGAGGGCACGACCTTATGTGTAAT
2825815 GCACT
1 GCACT
2825820 ATTGCATTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 35 0.49
40 36 0.50
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
GCACTTCGGTGCATATGGAGGGCACGACCTTATGTGTAAT
Found at i:2834348 original size:35 final size:36
Alignment explanation
Indices: 2834309--2834408 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 36
2834299 GATTTTTAAA
2834309 TTCTCTCATCT-CTATT-TTGATTTTAATTATCAAGT
1 TTCTCTC-TCTCCTATTCTTGATTTTAATTATCAAGT
* *
2834344 TTCTCTTCTCTCCTCTTCTTGTTTTTAATTATCAAGT
1 TTCTC-TCTCTCCTATTCTTGATTTTAATTATCAAGT
* * *
2834381 TTCTCTTCTCTCATCTTCTTGTTTTTAA
1 TTCTC-TCTCTCCTATTCTTGATTTTAA
2834409 AGCTTGATCA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
35 8 0.14
36 6 0.10
37 45 0.76
ACGTcount: A:0.16, C:0.22, G:0.05, T:0.57
Consensus pattern (36 bp):
TTCTCTCTCTCCTATTCTTGATTTTAATTATCAAGT
Found at i:2834372 original size:37 final size:37
Alignment explanation
Indices: 2834329--2834408 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
2834319 TCTATTTTGA
*
2834329 TTTTAATTATCAAGTTTCTCTTCTCTCCTCTTCTTGT
1 TTTTAATTATCAAGTTTCTCTTCTCTCATCTTCTTGT
2834366 TTTTAATTATCAAGTTTCTCTTCTCTCATCTTCTTGT
1 TTTTAATTATCAAGTTTCTCTTCTCTCATCTTCTTGT
2834403 TTTTAA
1 TTTTAA
2834409 AGCTTGATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.57
Consensus pattern (37 bp):
TTTTAATTATCAAGTTTCTCTTCTCTCATCTTCTTGT
Found at i:2845798 original size:21 final size:21
Alignment explanation
Indices: 2845772--2845823 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
2845762 CTCTTGCTAG
2845772 GTATCGATACACATTGAATGT
1 GTATCGATACACATTGAATGT
* *
2845793 GTATCGATATACCTTGAATGT
1 GTATCGATACACATTGAATGT
2845814 GTATCGATAC
1 GTATCGATAC
2845824 CCCTAGATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (21 bp):
GTATCGATACACATTGAATGT
Found at i:2850792 original size:24 final size:24
Alignment explanation
Indices: 2850762--2850811 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
2850752 TCTATTGATT
2850762 ATATATGTTGATTTGTAGAATATG
1 ATATATGTTGATTTGTAGAATATG
*
2850786 ATATATGTTGATTTTTAGAATATG
1 ATATATGTTGATTTGTAGAATATG
2850810 AT
1 AT
2850812 GTTAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (24 bp):
ATATATGTTGATTTGTAGAATATG
Found at i:2851165 original size:21 final size:20
Alignment explanation
Indices: 2851141--2851180 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2851131 GTTCCCTTCG
*
2851141 CAAAATGGATCGATCTTTTTT
1 CAAAA-GGATCGATCCTTTTT
*
2851162 CAAAAGGATTGATCCTTTT
1 CAAAAGGATCGATCCTTTT
2851181 AGGCCAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
CAAAAGGATCGATCCTTTTT
Found at i:2851175 original size:20 final size:22
Alignment explanation
Indices: 2851141--2851180 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2851131 GTTCCCTTCG
2851141 CAAAATGGATCGAT-CTTTTTT
1 CAAAATGGATCGATCCTTTTTT
*
2851162 CAAAA-GGATTGATCCTTTT
1 CAAAATGGATCGATCCTTTT
2851181 AGGCCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (22 bp):
CAAAATGGATCGATCCTTTTTT
Found at i:2853554 original size:14 final size:13
Alignment explanation
Indices: 2853535--2853584 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
2853525 AGTTCAAAAG
2853535 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
2853549 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
2853562 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
2853573 AAAGAAAAAGAA
1 AAAGAAAAAGAA
2853585 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:2853581 original size:19 final size:18
Alignment explanation
Indices: 2853530--2853584 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 18
2853520 AAAGAAGTTC
2853530 AAAAG-AAAGAAAAAGACA
1 AAAAGAAAAGAAAAAGA-A
2853548 AAAAGAAGAAG-AAAAGAA
1 AAAAGAA-AAGAAAAAGAA
2853566 GAAAAGAAAAGAAAAAGAA
1 -AAAAGAAAAGAAAAAGAA
2853585 TTCAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 9 0.27
19 21 0.64
20 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAGAA
Found at i:2853591 original size:29 final size:32
Alignment explanation
Indices: 2853512--2853597 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 32
2853502 ATTTGGCGTG
2853512 CAAAGGAAAAAGAAGTTCAAAAGAAAGAAAAAGA
1 CAAA-GAAAAAGAA-TTCAAAAGAAAGAAAAAGA
* *
2853546 CAAA-AAGAAGAA--GAAAAG-AAG-AAAAGA
1 CAAAGAAAAAGAATTCAAAAGAAAGAAAAAGA
2853573 -AAAGAAAAAGAATTCAAAAAGAAAG
1 CAAAGAAAAAGAATTC-AAAAGAAAG
2853598 CAAAGCCAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
26 3 0.07
27 13 0.30
28 3 0.07
29 5 0.12
30 5 0.12
31 3 0.07
32 7 0.16
34 4 0.09
ACGTcount: A:0.71, C:0.05, G:0.20, T:0.05
Consensus pattern (32 bp):
CAAAGAAAAAGAATTCAAAAGAAAGAAAAAGA
Found at i:2853597 original size:21 final size:19
Alignment explanation
Indices: 2853530--2853597 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
2853520 AAAGAAGTTC
2853530 AAAAGAAAGAAAAAG-ACA
1 AAAAGAAAGAAAAAGAACA
*
2853548 AAAAG-AAGAAGAAAAGAA-G
1 AAAAGAAAG-A-AAAAGAACA
2853567 AAAAGAAAAGAAAAAGAATTCA
1 AAAAG-AAAGAAAAAGAA--CA
2853589 AAAAGAAAG
1 AAAAGAAAG
2853598 CAAAGCCAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
17 3 0.08
18 6 0.15
19 17 0.43
20 2 0.05
21 7 0.17
22 5 0.12
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (19 bp):
AAAAGAAAGAAAAAGAACA
Found at i:2859679 original size:21 final size:20
Alignment explanation
Indices: 2859619--2859686 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
2859609 TGTGTTTGTA
*
2859619 ATCGATCCCTTTACAAAGTGG
1 ATCGATCCCTTTACAAA-AGG
** *
2859640 ATCGATCCCTCAAGGAAAAGG
1 ATCGATCCCTTTA-CAAAAGG
*
2859661 CTCGATCCCTTTACCAAAAGG
1 ATCGATCCCTTTA-CAAAAGG
2859682 ATCGA
1 ATCGA
2859687 AACCTCGATG
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 33 0.92
22 3 0.08
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGATCCCTTTACAAAAGG
Found at i:2859684 original size:42 final size:42
Alignment explanation
Indices: 2859620--2859713 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
2859610 GTGTTTGTAA
* **
2859620 TCGATCCCTTTACAAAGTGGATCGATCCCTCAAGGAAAAGGC
1 TCGATCCCTTTACAAAGAGGATCGAAACCTCAAGGAAAAGGC
* * *
2859662 TCGATCCCTTTACCAAA-AGGATCGAAACCTCGATGAAAAGGT
1 TCGATCCCTTTA-CAAAGAGGATCGAAACCTCAAGGAAAAGGC
2859704 TCGATCCCTT
1 TCGATCCCTT
2859714 CCCTTAAAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 41 0.91
43 4 0.09
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
TCGATCCCTTTACAAAGAGGATCGAAACCTCAAGGAAAAGGC
Found at i:2865617 original size:16 final size:17
Alignment explanation
Indices: 2865596--2865640 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
2865586 AGCAAAATGA
*
2865596 AATGG-ATGTTGGTGTG
1 AATGGAATGATGGTGTG
2865612 AATGGAATGATGGTGT-
1 AATGGAATGATGGTGTG
*
2865628 AATAGAAT-ATGGT
1 AATGGAATGATGGT
2865641 AGGAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 5 0.19
16 12 0.46
17 9 0.35
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (17 bp):
AATGGAATGATGGTGTG
Found at i:2867716 original size:18 final size:17
Alignment explanation
Indices: 2867672--2867718 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
2867662 AGGATAAATA
2867672 AAACAAATTAATAATTT
1 AAACAAATTAATAATTT
*
2867689 AAACTTAATTAATAATTT
1 AAAC-AAATTAATAATTT
2867707 AAACAAAATTAA
1 AAAC-AAATTAA
2867719 AAAAATTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
AAACAAATTAATAATTT
Found at i:2867949 original size:30 final size:30
Alignment explanation
Indices: 2867909--2867968 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2867899 TATTCATCGG
*
2867909 CATCAACATCACTATCACCCTCATCAACAT
1 CATCAACATCACTATCACCCTAATCAACAT
* *
2867939 CATCACCATCACTATCACCCTAATCTACAT
1 CATCAACATCACTATCACCCTAATCAACAT
2867969 GTCTAGTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (30 bp):
CATCAACATCACTATCACCCTAATCAACAT
Found at i:2884817 original size:55 final size:55
Alignment explanation
Indices: 2884733--2885129 Score: 555
Period size: 55 Copynumber: 7.2 Consensus size: 55
2884723 ATATATCAGT
*
2884733 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGGTGAATAACCGTACAGGC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
*
2884788 ACTATGTGTGCAAATCCACGGAATTCATCAAGAGTTGATGAATAACCGTACAGGC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* *
2884843 ACTATGTGTGAAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATGC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* * * * *
2884898 ACTATGTGTTCAAATCAACGGAATTCATCATGAGTTGATGAATAACCATACATGT
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* * *
2884953 ATTATGTGTGCAAATCCACGGAATTCATCATGATTTGATGAATAACCGTGCAGGC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* ** * * *
2885008 ACTATGTGTTCAAATCCACATAATTCATCATGAGTTGATGAATAATCATACAGAC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* ** * *
2885063 ACTATGGGTGCAAATCCACATAATTTATCATGAGTTGATGAACT-ACCGTATAGGC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAACCGTACAGGC
2885118 ACTACT-TGTGCA
1 ACTA-TGTGTGCA
2885130 TCTTAATAAA
Statistics
Matches: 305, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
55 303 0.99
56 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (55 bp):
ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
Found at i:2891733 original size:23 final size:22
Alignment explanation
Indices: 2891705--2891747 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2891695 AAAAATAGTC
2891705 TTTTTAAAAAAAATAATTTTATT
1 TTTTTAAAAAAAAT-ATTTTATT
* *
2891728 TTTTTAGAAAATATATTTTA
1 TTTTTAAAAAAAATATTTTA
2891748 AGAAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTAAAAAAAATATTTTATT
Found at i:2907580 original size:20 final size:20
Alignment explanation
Indices: 2907555--2907592 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2907545 TTGGAATTGA
*
2907555 ATGTTAGAATGTTAATTTTG
1 ATGTTAGAAGGTTAATTTTG
2907575 ATGTTAGAAGGTTAATTT
1 ATGTTAGAAGGTTAATTT
2907593 GGATCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (20 bp):
ATGTTAGAAGGTTAATTTTG
Found at i:2908552 original size:24 final size:24
Alignment explanation
Indices: 2908525--2908578 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2908515 TCGATCTTGC
*
2908525 ATTAGTGAATTGGTGCACTCATGT
1 ATTAGTGAATTGGTGCACTCACGT
* * *
2908549 ATTAGTGCATTTGTGCACTCCCGT
1 ATTAGTGAATTGGTGCACTCACGT
2908573 ATTAGT
1 ATTAGT
2908579 AGCACTATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (24 bp):
ATTAGTGAATTGGTGCACTCACGT
Found at i:2908598 original size:24 final size:24
Alignment explanation
Indices: 2908540--2908604 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
2908530 TGAATTGGTG
*
2908540 CACTCATGTATTAGT-GCATTTGT
1 CACTCATGTATTAGTAGCATATGT
**
2908563 GCACTCCCGTATTAGTAGCACTATGT
1 -CACTCATGTATTAGTAGCA-TATGT
2908589 -ACTCATGTATTTAGTA
1 CACTCATGTA-TTAGTA
2908605 CATTTGTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
24 20 0.61
25 9 0.27
26 4 0.12
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (24 bp):
CACTCATGTATTAGTAGCATATGT
Found at i:2912119 original size:55 final size:56
Alignment explanation
Indices: 2912059--2912170 Score: 140
Period size: 55 Copynumber: 2.0 Consensus size: 56
2912049 ATCCCAAACA
* * *
2912059 AAAATTGAACG-GGCATATAATCCCATA-CGAAACAGATTGA-GAATAAATCTCATAC
1 AAAATTGAACGAGGAATA-AATCCCATATAGAAA-AGATCGAGGAATAAATCTCATAC
* *
2912114 AAAATTGATCGAGGAATAAATCCCATATAGAGAAGATCGAGGAATAAATCTCATAC
1 AAAATTGAACGAGGAATAAATCCCATATAGAAAAGATCGAGGAATAAATCTCATAC
2912170 A
1 A
2912171 TAACAGATCG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
55 25 0.51
56 24 0.49
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.21
Consensus pattern (56 bp):
AAAATTGAACGAGGAATAAATCCCATATAGAAAAGATCGAGGAATAAATCTCATAC
Found at i:2912178 original size:28 final size:28
Alignment explanation
Indices: 2912077--2912180 Score: 104
Period size: 28 Copynumber: 3.8 Consensus size: 28
2912067 ACGGGCATAT
* * *
2912077 AATCCCATACGAAACAGATTGA-GAATA
1 AATCTCATACAAAACAGATCGAGGAATA
**
2912104 AATCTCATACAAAATTGATCGAGGAATA
1 AATCTCATACAAAACAGATCGAGGAATA
* * *
2912132 AATCCCATATAGAGA-AGATCGAGGAATA
1 AATCTCATACA-AAACAGATCGAGGAATA
*
2912160 AATCTCATACATAACAGATCG
1 AATCTCATACAAAACAGATCG
2912181 GAACTATGCC
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
27 18 0.30
28 41 0.67
29 2 0.03
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.21
Consensus pattern (28 bp):
AATCTCATACAAAACAGATCGAGGAATA
Found at i:2914537 original size:17 final size:17
Alignment explanation
Indices: 2914517--2914554 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2914507 CGATTAATAC
2914517 ACTAGTTTAATGAATGA
1 ACTAGTTTAATGAATGA
* *
2914534 ACTAGTTTGATTAATGA
1 ACTAGTTTAATGAATGA
2914551 ACTA
1 ACTA
2914555 ACTTTATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (17 bp):
ACTAGTTTAATGAATGA
Found at i:2930325 original size:21 final size:22
Alignment explanation
Indices: 2930290--2930330 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2930280 AAAGTGACTA
*
2930290 AACATTTTTAAATCATTTACTC
1 AACATTTTCAAATCATTTACTC
2930312 AACA-TTTCAAATCATTTAC
1 AACATTTTCAAATCATTTAC
2930331 ACAAAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (22 bp):
AACATTTTCAAATCATTTACTC
Found at i:2930598 original size:70 final size:70
Alignment explanation
Indices: 2930485--2930624 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
2930475 CCCCTAAGAC
2930485 TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
1 TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
2930550 TTTGA
66 TTTGA
2930555 TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
1 TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
2930620 TTTGA
66 TTTGA
2930625 AAGTTGAGCT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (70 bp):
TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
TTTGA
Found at i:2932941 original size:19 final size:21
Alignment explanation
Indices: 2932906--2932945 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
2932896 AGGGCCCGAG
2932906 TGGTAACTTTCCCCAAAAATA
1 TGGTAACTTTCCCCAAAAATA
2932927 TGGTAA-TTT-CCCAAAAATA
1 TGGTAACTTTCCCCAAAAATA
2932946 AATTTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (21 bp):
TGGTAACTTTCCCCAAAAATA
Found at i:2934033 original size:20 final size:20
Alignment explanation
Indices: 2933988--2934034 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2933978 ATTTTGCTGG
* *
2933988 AATTTAATGTTAAAGTGTTT
1 AATTTGATGTTAAAGTGTGT
2934008 AATTTGATGTTAGAA-TGTGT
1 AATTTGATGTTA-AAGTGTGT
2934028 AATTTGA
1 AATTTGA
2934035 CTATTTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (20 bp):
AATTTGATGTTAAAGTGTGT
Found at i:2935728 original size:24 final size:25
Alignment explanation
Indices: 2935681--2935729 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2935671 CGTGAACCAC
* *
2935681 CTAGCTCGCTAGCTCCTTTCAGCTT
1 CTAGCTCGCCAGCTCCTTGCAGCTT
*
2935706 CTAGCTCGCCA-CTCCTTGGAGCTT
1 CTAGCTCGCCAGCTCCTTGCAGCTT
2935730 TATCAATGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.12, C:0.37, G:0.18, T:0.33
Consensus pattern (25 bp):
CTAGCTCGCCAGCTCCTTGCAGCTT
Found at i:2944615 original size:25 final size:24
Alignment explanation
Indices: 2944586--2944663 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
2944576 ACCTTTGTGT
* *
2944586 ACTCCAGTATTAGTGCATTTTTTGC
1 ACTCCAGTATTAGTGC-CTTGTTGC
* *
2944611 ACTCCTGTTTTAGTGCCTTGTTGC
1 ACTCCAGTATTAGTGCCTTGTTGC
** * * *
2944635 ACTCCAACAATAGTGCATTGGTGC
1 ACTCCAGTATTAGTGCCTTGTTGC
2944659 ACTCC
1 ACTCC
2944664 TATATTATTA
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 28 0.67
25 14 0.33
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (24 bp):
ACTCCAGTATTAGTGCCTTGTTGC
Found at i:2944756 original size:24 final size:24
Alignment explanation
Indices: 2944712--2944760 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2944702 TGTGCACTAT
*
2944712 TGTGTTAGTATCTTTGAGTACTCC
1 TGTGTTAGTATCTTCGAGTACTCC
*
2944736 TGTGTTAGTA-CATTCGTGTACTCC
1 TGTGTTAGTATC-TTCGAGTACTCC
2944760 T
1 T
2944761 CGTACTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.45
Consensus pattern (24 bp):
TGTGTTAGTATCTTCGAGTACTCC
Found at i:2947777 original size:18 final size:19
Alignment explanation
Indices: 2947737--2947778 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2947727 ATGGAAATAT
*
2947737 GCAACAACATTACCAACCA
1 GCAACAACAATACCAACCA
*
2947756 -CAACAACAATA-CAATCA
1 GCAACAACAATACCAACCA
2947773 GCAACA
1 GCAACA
2947779 GATGATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.52, C:0.33, G:0.05, T:0.10
Consensus pattern (19 bp):
GCAACAACAATACCAACCA
Found at i:2959552 original size:85 final size:85
Alignment explanation
Indices: 2959446--2959658 Score: 268
Period size: 85 Copynumber: 2.5 Consensus size: 85
2959436 ATGACGTGTT
* *
2959446 CTTCAATGACACGCAATGTAAGTCATACATGCATGTCATAAATTTATGACACACAAATGTATGTC
1 CTTCAATGACACTCAATGTAAGTCATACATGCATGTCATAAATTTATGACACACAAATATATGTC
* *
2959511 AAGTAGATTTAAGATGGGGG
66 AACTAGATTTAAGATCGGGG
* * *
2959531 CTTCAATGACATTCAATGTAAGTCATACATGCGAT-TCATATATTTATGACACACAAATATGTGT
1 CTTCAATGACACTCAATGTAAGTCATACATGC-ATGTCATAAATTTATGACACACAAATATATGT
* ** *
2959595 CATCTTTATTTATGATCGGGG
65 CAACTAGATTTAAGATCGGGG
* * *
2959616 CTTCAATGACGCTCAATG-AACGTCATAAATGCACGTCATAAAT
1 CTTCAATGACACTCAATGTAA-GTCATACATGCATGTCATAAAT
2959659 GTGTGTCATA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
84 3 0.03
85 104 0.95
86 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (85 bp):
CTTCAATGACACTCAATGTAAGTCATACATGCATGTCATAAATTTATGACACACAAATATATGTC
AACTAGATTTAAGATCGGGG
Found at i:2959651 original size:13 final size:13
Alignment explanation
Indices: 2959630--2959681 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
2959620 AATGACGCTC
*
2959630 AATGAACGTCATA
1 AATGCACGTCATA
2959643 AATGCACGTCATA
1 AATGCACGTCATA
***
2959656 AATGTGTGTCATA
1 AATGCACGTCATA
*
2959669 AATGCGCGTCATA
1 AATGCACGTCATA
2959682 GATTTATGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (13 bp):
AATGCACGTCATA
Found at i:2959659 original size:26 final size:26
Alignment explanation
Indices: 2959630--2959681 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2959620 AATGACGCTC
2959630 AATGAACGTCATAAATGCACGTCATA
1 AATGAACGTCATAAATGCACGTCATA
*** *
2959656 AATGTGTGTCATAAATGCGCGTCATA
1 AATGAACGTCATAAATGCACGTCATA
2959682 GATTTATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (26 bp):
AATGAACGTCATAAATGCACGTCATA
Found at i:2975109 original size:47 final size:49
Alignment explanation
Indices: 2974981--2975110 Score: 128
Period size: 47 Copynumber: 2.7 Consensus size: 49
2974971 ATATAAATTT
* *
2974981 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA--TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
** *
2975027 CTTACCATTTAAATTCCATAAGCT-AGTAAGCTTATTTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCA-TAAGCTTATTTTTTTACCAAAATA
* **
2975077 CTTGCCA-TT-ATTCTGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
2975111 GTATGGTTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
46 6 0.09
47 25 0.36
48 20 0.29
49 2 0.03
50 17 0.24
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (49 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
Found at i:2977743 original size:36 final size:36
Alignment explanation
Indices: 2977696--2977764 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
2977686 CTTCAATCTG
*
2977696 ATTTAAAAATATCTATACATTTTCATATCATCCCAA
1 ATTTAAAAATATCTACACATTTTCATATCATCCCAA
2977732 ATTTAAAAATATCTACACATTTTCATATCATCC
1 ATTTAAAAATATCTACACATTTTCATATCATCC
2977765 TCTCTATCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (36 bp):
ATTTAAAAATATCTACACATTTTCATATCATCCCAA
Found at i:2979153 original size:17 final size:17
Alignment explanation
Indices: 2979126--2979171 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
2979116 TTTTCATCTC
*
2979126 TCATTTTTTTCTCTTTT
1 TCATTTTTTTCTCGTTT
2979143 TC-TTTTCTTTCTCGTTT
1 TCATTTT-TTTCTCGTTT
2979160 TCATTTTTTTCT
1 TCATTTTTTTCT
2979172 TCTTCGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.15
17 18 0.69
18 4 0.15
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (17 bp):
TCATTTTTTTCTCGTTT
Found at i:2979169 original size:27 final size:27
Alignment explanation
Indices: 2979139--2979193 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
2979129 TTTTTTTCTC
*
2979139 TTTTTCTT-TTC-TTTCTCGTTTTCATT
1 TTTTTCTTCTTCGTTT-TCATTTTCATT
2979165 TTTTTCTTCTTCGTTTTCATTTTCATT
1 TTTTTCTTCTTCGTTTTCATTTTCATT
2979192 TT
1 TT
2979194 CTATATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.31
27 15 0.58
28 3 0.12
ACGTcount: A:0.05, C:0.18, G:0.04, T:0.73
Consensus pattern (27 bp):
TTTTTCTTCTTCGTTTTCATTTTCATT
Found at i:2979174 original size:20 final size:22
Alignment explanation
Indices: 2979145--2979187 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2979135 TCTCTTTTTC
2979145 TTTTCTTTC-TCGTTTTCATTT
1 TTTTCTTTCTTCGTTTTCATTT
2979166 TTTTC-TTCTTCGTTTTCATTT
1 TTTTCTTTCTTCGTTTTCATTT
2979187 T
1 T
2979188 CATTTTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.72
Consensus pattern (22 bp):
TTTTCTTTCTTCGTTTTCATTT
Found at i:2979195 original size:21 final size:20
Alignment explanation
Indices: 2979150--2979195 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2979140 TTTTCTTTTC
*
2979150 TTTC-TCGTTTTCATTTTTT
1 TTTCTTCGTTTTCATTTTAT
2979169 TCTTCTTCGTTTTCATTTTCAT
1 T-TTCTTCGTTTTCATTTT-AT
2979191 TTTCT
1 TTTCT
2979196 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 3 0.13
21 17 0.74
22 2 0.09
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTCTTCGTTTTCATTTTAT
Found at i:2979219 original size:17 final size:17
Alignment explanation
Indices: 2979129--2979229 Score: 55
Period size: 17 Copynumber: 5.8 Consensus size: 17
2979119 TCATCTCTCA
2979129 TTTTTTTC-TCTTTTTCT
1 TTTTTTTCTTCTTTTT-T
* **
2979146 TTTCTTTC-TCGTTTTCA
1 TTTTTTTCTTC-TTTTTT
*
2979163 TTTTTTTCTTCTTCGTTT
1 TTTTTTTCTTCTT-TTTT
** *
2979181 TCATTTTCATT-TTCTATAT
1 TTTTTTTC-TTCTT-T-TTT
2979200 TTTTTTTCTTCTTTTTT
1 TTTTTTTCTTCTTTTTT
*
2979217 TTTTCTTCTTCTT
1 TTTTTTTCTTCTT
2979230 ATAATATTTT
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
17 32 0.51
18 19 0.30
19 12 0.19
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTTTCTTCTTTTTT
Found at i:2979221 original size:33 final size:32
Alignment explanation
Indices: 2979112--2979221 Score: 89
Period size: 34 Copynumber: 3.3 Consensus size: 32
2979102 AAGTGAAATA
* * *
2979112 TTTTTTTTCA-TCTCTCATTTTTTTCTCTTTTT
1 TTTTTTTTCATTTTCT-ATTTTTTTTTCTTCTT
*
2979144 CTTTTCTTTCTCGTTTTC-ATTTTTTTCTTCTTCGTT
1 -TTTT-TTT-TCATTTTCTATTTTTTT-TTCTTC-TT
**
2979180 TTCATTTTCATTTTCTATATTTTTTTTCTTCTT
1 TTTTTTTTCATTTTCTAT-TTTTTTTTCTTCTT
2979213 TTTTTTTTC
1 TTTTTTTTC
2979222 TTCTTCTTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
33 20 0.33
34 22 0.36
35 14 0.23
36 5 0.08
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.74
Consensus pattern (32 bp):
TTTTTTTTCATTTTCTATTTTTTTTTCTTCTT
Found at i:2979223 original size:14 final size:14
Alignment explanation
Indices: 2979199--2979226 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2979189 ATTTTCTATA
2979199 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
2979213 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
2979227 CTTATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:2980323 original size:6 final size:6
Alignment explanation
Indices: 2980312--2980336 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2980302 ACACTTGTAT
2980312 CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC C
2980337 TATGTGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:2993341 original size:99 final size:99
Alignment explanation
Indices: 2993170--2993354 Score: 370
Period size: 99 Copynumber: 1.9 Consensus size: 99
2993160 TCATCTAACA
2993170 TAGGGGTATTTTGGTAACTTACACATAAAATGACATTTCAGTAAATTTACCCCTCTCAAAGGTAT
1 TAGGGGTATTTTGGTAACTTACACATAAAATGACATTTCAGTAAATTTACCCCTCTCAAAGGTAT
2993235 TTTAGTTTTGGGCAAACTATATGGGAATTCATCT
66 TTTAGTTTTGGGCAAACTATATGGGAATTCATCT
2993269 TAGGGGTATTTTGGTAACTTACACATAAAATGACATTTCAGTAAATTTACCCCTCTCAAAGGTAT
1 TAGGGGTATTTTGGTAACTTACACATAAAATGACATTTCAGTAAATTTACCCCTCTCAAAGGTAT
2993334 TTTAGTTTTGGGCAAACTATA
66 TTTAGTTTTGGGCAAACTATA
2993355 CGGGCGGTCC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 86 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (99 bp):
TAGGGGTATTTTGGTAACTTACACATAAAATGACATTTCAGTAAATTTACCCCTCTCAAAGGTAT
TTTAGTTTTGGGCAAACTATATGGGAATTCATCT
Found at i:2997498 original size:37 final size:37
Alignment explanation
Indices: 2997404--2997507 Score: 113
Period size: 37 Copynumber: 2.8 Consensus size: 37
2997394 CATTTTCGTC
2997404 CTACTAGGATTCAAACTT-CTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAA-TTCCTAAAAATAGGATAAAATT
* * * * *
2997441 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAATTCCTAAAAATAGGATAAAATT
* * *
2997478 CTACTAAGATTTAAATTCCT-AAGATAGGAT
1 CTACTAGGATTCAAATTCCTAAAAATAGGAT
2997508 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
36 10 0.18
37 45 0.82
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAATTCCTAAAAATAGGATAAAATT
Found at i:2997916 original size:56 final size:55
Alignment explanation
Indices: 2997848--2997972 Score: 130
Period size: 56 Copynumber: 2.3 Consensus size: 55
2997838 ATTAGTCCCT
* * * *
2997848 TTATTTAT-TATATGGATAT-TT-TATTCATTTATTTTTATTATTAATGTTATTATTA
1 TTATATATATATATAGATATATTATATTCATTTATTTTT-TTACT-ATATT-TTATTA
* * *
2997903 TTATATGTATATATATATATAATTATTTTCATTTATTTTTTTACTATATTTTATTA
1 TTATATATATATATAGATAT-ATTATATTCATTTATTTTTTTACTATATTTTATTA
2997959 TTATATATATATAT
1 TTATATATATATAT
2997973 TTCTTTAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
55 6 0.10
56 28 0.48
57 4 0.07
58 6 0.10
59 14 0.24
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (55 bp):
TTATATATATATATAGATATATTATATTCATTTATTTTTTTACTATATTTTATTA
Found at i:2998484 original size:21 final size:22
Alignment explanation
Indices: 2998460--2998500 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2998450 TATATAATTA
* *
2998460 TTATTTTAC-TATTTTTTTTTC
1 TTATCTTACTTATTTATTTTTC
2998481 TTATCTTACTTATTTATTTT
1 TTATCTTACTTATTTATTTT
2998501 ATTTTTCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (22 bp):
TTATCTTACTTATTTATTTTTC
Found at i:3004245 original size:183 final size:183
Alignment explanation
Indices: 3003931--3004467 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
3003921 ATTAAATCCG
* *
3003931 TAAAGATGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAAATCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
**
3003996 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCAATGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
3004061 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
*
3004114 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTTGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
3004179 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
3004244 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTATCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
3004297 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * * *
3004362 ATAGATTACATTCAAAAC-ATGATATTTCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTC-AAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
3004426 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
3004468 TAAACCTGAT
Statistics
Matches: 338, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 334 0.99
184 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
Found at i:3005620 original size:36 final size:34
Alignment explanation
Indices: 3005580--3005693 Score: 93
Period size: 36 Copynumber: 3.2 Consensus size: 34
3005570 CACTCAAATT
3005580 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * * ** *
3005616 TGTTTTTCTCGAAAAAAGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAAACA-ATTTGTCTCACTTGAGAC
*
3005652 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
3005688 CGTTTT
1 TGTTTT
3005694 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
35 4 0.07
36 49 0.83
37 6 0.10
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:3005656 original size:72 final size:75
Alignment explanation
Indices: 3005564--3005739 Score: 209
Period size: 72 Copynumber: 2.4 Consensus size: 75
3005554 ATGCAGATGA
* * * *
3005564 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
3005626 GAAA-AAAG-AT
64 GAAAGAAAGCAT
*
3005636 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
*
3005701 AAGAAGGCAT
66 AAGAAAGCAT
** *
3005711 TTCATTTCACTCAAGGCTGTTTTTTTTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
3005740 GAAGATTTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 50 0.56
73 8 0.09
74 3 0.03
75 4 0.04
76 23 0.26
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAAGCAT
Found at i:3005798 original size:39 final size:39
Alignment explanation
Indices: 3005739--3005905 Score: 113
Period size: 39 Copynumber: 4.0 Consensus size: 39
3005729 GTTTTTTTTA
* ** *
3005739 AGAAGATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAAATTTTATCTCCCTTGAGACAGTTTCCCTCGAAAC
* *
3005778 AGAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAAAC
1 AGAAAATTTTATCTCCCTTGAGACAGTTTCCCTCG-AAAC
* *
3005818 ATTCCCTTGAAATTAATTTTTTCTCTCC-TGAGATAGTTTCCCTCGAAAC
1 A-------G-AA--AATTTTATCTC-CCTTGAGACAGTTTCCCTCGAAAC
* * *
3005867 AGAAAATTTTTTCT-CCTTGAGACAGTTTCTCTTGAAAC
1 AGAAAATTTTATCTCCCTTGAGACAGTTTCCCTCGAAAC
3005905 A
1 A
3005906 TAAACATTGA
Statistics
Matches: 102, Mismatches: 13, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
37 2 0.02
38 19 0.19
39 39 0.38
40 5 0.05
41 2 0.02
42 1 0.01
47 1 0.01
48 2 0.02
49 5 0.05
50 24 0.24
51 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (39 bp):
AGAAAATTTTATCTCCCTTGAGACAGTTTCCCTCGAAAC
Found at i:3005888 original size:38 final size:39
Alignment explanation
Indices: 3005832--3005905 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
3005822 CCTTGAAATT
*
3005832 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
1 AATTTTTTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
* * *
3005871 AATTTTTTCTC-CTTGAGACAGTTTCTCTTGAAACA
1 AATTTTTTCTCTCCTGAGACAGTTTCCCTCGAAACA
3005906 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 20 0.65
39 11 0.35
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (39 bp):
AATTTTTTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
Found at i:3006021 original size:104 final size:104
Alignment explanation
Indices: 3005810--3006125 Score: 498
Period size: 104 Copynumber: 3.1 Consensus size: 104
3005800 ACAGTTTCTC
* *
3005810 TTGAAAACA-TTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
*
3005874 TTTTTCT-CCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
3005912 TTGAAAACATTTCCCTTAAAATGATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
*
3005977 TTTGTCTCCCTTGACACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
3006016 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
**
3006078 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
3006117 TTGAAAACA
1 TTGAAAACA
3006126 ATTTAACGAA
Statistics
Matches: 198, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
101 48 0.24
102 9 0.05
103 58 0.29
104 83 0.42
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:3006072 original size:36 final size:36
Alignment explanation
Indices: 3006025--3006100 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
3006015 ATTGAAAACA
* * *
3006025 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
3006061 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
3006097 TTTC
1 TTTC
3006101 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:3006500 original size:105 final size:105
Alignment explanation
Indices: 3006300--3006928 Score: 914
Period size: 105 Copynumber: 6.0 Consensus size: 105
3006290 ATATCGTGAC
* * * * *
3006300 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
3006365 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
3006406 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTTCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
3006471 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
3006511 ACTTCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
3006576 ATCTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
3006616 ACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAATAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
3006681 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
3006721 ACTCCAGATAACGCAAGTTCAACTCCACGACGAAGGGATCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
3006782 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
3006821 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAA-TT-TC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
** * *
3006884 GGTTCCAGAGCCAATTTCAACTTCACGAC-AGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGA-AGGATATTGG
3006925 ACTC
1 ACTC
3006929 GGAACAATGC
Statistics
Matches: 480, Mismatches: 38, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
100 80 0.17
101 3 0.01
102 7 0.01
103 3 0.01
104 38 0.08
105 302 0.63
106 47 0.10
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:3007523 original size:37 final size:37
Alignment explanation
Indices: 3007470--3007574 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
3007460 CATTTTCGTC
3007470 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3007507 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3007544 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3007575 CCACAAACAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:3007970 original size:18 final size:17
Alignment explanation
Indices: 3007931--3007973 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3007921 ATTATATGAA
3007931 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
3007947 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
3007965 TATTATTAT
1 TATTATTAT
3007974 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:3008280 original size:21 final size:21
Alignment explanation
Indices: 3008227--3008281 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3008217 CTTTATATAT
* * *
3008227 TTATATTATTTTTTATTATTT
1 TTATATTATTATTCATTATTA
* * *
3008248 TTGTTTTTTTATTCATTATTA
1 TTATATTATTATTCATTATTA
3008269 TTATATTATTATT
1 TTATATTATTATT
3008282 TAAAAAAACC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTATATTATTATTCATTATTA
Found at i:3008456 original size:36 final size:38
Alignment explanation
Indices: 3008407--3008482 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
3008397 ATTGGGAGGG
*
3008407 TAGCTTTTCTA-TTT-TTAAGTA-TTTGATGTATATATA
1 TAGCTTTTCTATTTTATTAA-TACTTTGATATATATATA
3008443 TAGCTTATT-TATTTTATTAATACTTTGATATATATATA
1 TAGCTT-TTCTATTTTATTAATACTTTGATATATATATA
3008481 TA
1 TA
3008483 TTTATATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 8 0.23
37 7 0.20
38 20 0.57
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (38 bp):
TAGCTTTTCTATTTTATTAATACTTTGATATATATATA
Found at i:3008573 original size:22 final size:22
Alignment explanation
Indices: 3008531--3008573 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
3008521 AATTAGTATT
* *
3008531 TTACTATTTGTTTTTTCTTATC
1 TTACTATTTATTTTATCTTATC
3008553 TTACTTATTTATTTTAT-TTAT
1 TTAC-TATTTATTTTATCTTAT
3008574 TTTATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (22 bp):
TTACTATTTATTTTATCTTATC
Found at i:3011424 original size:16 final size:16
Alignment explanation
Indices: 3011403--3011457 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
3011393 GGAATTACCC
3011403 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
3011419 GACCTGTTTTCAATCT
1 GACCTGTTTTCAACCT
* *
3011435 GACCAGTTTTTAACCT
1 GACCTGTTTTCAACCT
*
3011451 GGCCTGT
1 GACCTGT
3011458 AAATGATCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:3011624 original size:29 final size:28
Alignment explanation
Indices: 3011591--3011658 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
3011581 TTAAATGTTA
**
3011591 TAATAAAATATTTATTATGAT-AATTATAT
1 TAATAAAATACCTATTAT-ATAAATTAT-T
3011620 TAATAAATATACCTATTATATAAAATTATT
1 TAATAAA-ATACCTATTATAT-AAATTATT
3011650 TAATAAAAT
1 TAATAAAAT
3011659 TAATAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 11 0.32
30 17 0.50
31 6 0.18
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (28 bp):
TAATAAAATACCTATTATATAAATTATT
Found at i:3011736 original size:14 final size:14
Alignment explanation
Indices: 3011714--3011760 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
3011704 TGCAAAGGAA
*
3011714 AATTAATATAGTTT
1 AATTTATATAGTTT
3011728 AATTTATATA----
1 AATTTATATAGTTT
3011738 AA-TTATATAGTTT
1 AATTTATATAGTTT
3011751 AATTTATATA
1 AATTTATATA
3011761 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:3011747 original size:23 final size:24
Alignment explanation
Indices: 3011713--3011762 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
3011703 ATGCAAAGGA
3011713 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
3011737 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
3011760 AAA
1 AAA
3011763 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:3012273 original size:19 final size:20
Alignment explanation
Indices: 3012233--3012277 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
3012223 AAATTTTCTA
3012233 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
*
3012253 TTCCCTCTAAA-TTCTCAAT
1 TTCCCTCTAAATTTCCCAAT
3012272 TTCCCT
1 TTCCCT
3012278 ATATTCTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.22, C:0.36, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCCCTCTAAATTTCCCAAT
Found at i:3012389 original size:2 final size:2
Alignment explanation
Indices: 3012382--3012424 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
3012372 ACTTTGAATA
*
3012382 AT AT AT AT AT AT AT AC AT A- AT AT A- 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 AT AT AT AT
3012422 AT A
1 AT A
3012425 ATTAAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3012408 original size:24 final size:24
Alignment explanation
Indices: 3012379--3012434 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
3012369 CTCACTTTGA
3012379 ATAATATATATATATATACATAAT
1 ATAATATATATATATATACATAAT
*
3012403 ATAATATATATATATATATATAAT
1 ATAATATATATATATATACATAAT
3012427 -TAA-ATATA
1 ATAATATATA
3012435 AGTGACTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 5 0.16
23 3 0.10
24 23 0.74
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATATATATATATATACATAAT
Found at i:3012869 original size:2 final size:2
Alignment explanation
Indices: 3012862--3012897 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3012852 TACGTTTAAT
3012862 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3012898 TATTCAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3013028 original size:19 final size:19
Alignment explanation
Indices: 3013006--3013049 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3012996 TTGAGAATAT
* *
3013006 AGGGAAATTGGGAATTTAG
1 AGGGAAATTAGGAAATTAG
3013025 AGGGAAATTAGGAAATTAG
1 AGGGAAATTAGGAAATTAG
3013044 AGGGAA
1 AGGGAA
3013050 TAGAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.20
Consensus pattern (19 bp):
AGGGAAATTAGGAAATTAG
Found at i:3013063 original size:46 final size:47
Alignment explanation
Indices: 3012965--3013065 Score: 127
Period size: 46 Copynumber: 2.2 Consensus size: 47
3012955 TATTGATTTT
* **
3012965 ATTTGGGAATTTAGAGGGAAATTAAGAAATTTTGAGAATATAGGGAA
1 ATTTGGGAATTTAGAGGGAAATTAAGAAATTTAGAGAATATAGAAAA
* *
3013012 A-TTGGGAATTTAGAGGGAAATTAGGAAA-TTAGAGGGA-ATAGAAAA
1 ATTTGGGAATTTAGAGGGAAATTAAGAAATTTAGA-GAATATAGAAAA
3013057 ATTTGGGAA
1 ATTTGGGAA
3013066 GTTGGCGCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 11 0.23
46 35 0.74
47 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.27
Consensus pattern (47 bp):
ATTTGGGAATTTAGAGGGAAATTAAGAAATTTAGAGAATATAGAAAA
Found at i:3013302 original size:21 final size:21
Alignment explanation
Indices: 3013278--3013388 Score: 104
Period size: 21 Copynumber: 5.3 Consensus size: 21
3013268 TATAATTTAT
*
3013278 ATAAACCTTAAATCCTAAATC
1 ATAAACCTTAAACCCTAAATC
3013299 ATAAACCTTAAACCCTAAATC
1 ATAAACCTTAAACCCTAAATC
*
3013320 ATAAA-CTCTAAACAAC-AAATC
1 ATAAACCT-TAAAC-CCTAAATC
* *
3013341 CTAAATCC-TAAACACTAAATC
1 ATAAA-CCTTAAACCCTAAATC
* *
3013362 TTAAACC-TAAACCCTATATC
1 ATAAACCTTAAACCCTAAATC
*
3013382 CTAAACC
1 ATAAACC
3013389 CTAATGTATG
Statistics
Matches: 78, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
20 23 0.29
21 53 0.68
22 1 0.01
23 1 0.01
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (21 bp):
ATAAACCTTAAACCCTAAATC
Found at i:3013303 original size:14 final size:13
Alignment explanation
Indices: 3013279--3013392 Score: 63
Period size: 14 Copynumber: 8.2 Consensus size: 13
3013269 ATAATTTATA
3013279 TAAACCTTAAATCC
1 TAAACC-TAAATCC
*
3013293 TAAATCATAAA-CC
1 TAAA-CCTAAATCC
*
3013306 TTAAACCCTAAATCA
1 -TAAA-CCTAAATCC
3013321 TAAACTCTAAA-CAAC
1 TAAAC-CTAAATC--C
3013336 -AAATCCTAAATCC
1 TAAA-CCTAAATCC
*
3013349 TAAACACTAAATCT
1 TAAAC-CTAAATCC
*
3013363 TAAACCTAAACCC
1 TAAACCTAAATCC
* *
3013376 TATATCCTAAACCC
1 TA-AACCTAAATCC
3013390 TAA
1 TAA
3013393 TGTATGTATA
Statistics
Matches: 80, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
13 15 0.19
14 61 0.76
15 4 0.05
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAACCTAAATCC
Found at i:3013346 original size:7 final size:7
Alignment explanation
Indices: 3013336--3013392 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
3013326 TCTAAACAAC
3013336 AAATCCT
1 AAATCCT
3013343 AAATCCT
1 AAATCCT
3013350 AAA-CACT
1 AAATC-CT
*
3013357 AAATCTT
1 AAATCCT
3013364 AAA-CCT
1 AAATCCT
*
3013370 AAACCCT
1 AAATCCT
*
3013377 ATATCCT
1 AAATCCT
*
3013384 AAACCCT
1 AAATCCT
3013391 AA
1 AA
3013393 TGTATGTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
6 6 0.15
7 34 0.83
8 1 0.02
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (7 bp):
AAATCCT
Done.