Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008661.1 Hibiscus syriacus cultivar Beakdansim tig00111659_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: 1762280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1530474 original size:30 final size:30
Alignment explanation
Indices: 1530429--1530500 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
1530419 ACTATTTTGT
**
1530429 TGAATCAGGCAGCACTGAATCATTCA-ACAC
1 TGAATCATTCAGCACTGAATCATTCAGA-AC
*
1530459 TGGATCATTCAGCACTGAATCATTCAGAAC
1 TGAATCATTCAGCACTGAATCATTCAGAAC
1530489 TGAATCATTCAG
1 TGAATCATTCAG
1530501 ATATGAGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (30 bp):
TGAATCATTCAGCACTGAATCATTCAGAAC
Found at i:1536255 original size:31 final size:31
Alignment explanation
Indices: 1536217--1536297 Score: 153
Period size: 31 Copynumber: 2.6 Consensus size: 31
1536207 TAATTTTTTT
*
1536217 TTGTTCATGTTCGTTTATTAAGGAATCTAAC
1 TTGTTCATGTTCGTTCATTAAGGAATCTAAC
1536248 TTGTTCATGTTCGTTCATTAAGGAATCTAAC
1 TTGTTCATGTTCGTTCATTAAGGAATCTAAC
1536279 TTGTTCATGTTCGTTCATT
1 TTGTTCATGTTCGTTCATT
1536298 TAATAAATAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (31 bp):
TTGTTCATGTTCGTTCATTAAGGAATCTAAC
Found at i:1536329 original size:16 final size:16
Alignment explanation
Indices: 1536308--1536344 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1536298 TAATAAATAA
1536308 ACGAACACAAACGAAC
1 ACGAACACAAACGAAC
*
1536324 ACGAACATAAACGAAC
1 ACGAACACAAACGAAC
1536340 ACGAA
1 ACGAA
1536345 AACACGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.57, C:0.27, G:0.14, T:0.03
Consensus pattern (16 bp):
ACGAACACAAACGAAC
Found at i:1536353 original size:24 final size:25
Alignment explanation
Indices: 1536304--1536360 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
1536294 CATTTAATAA
1536304 ATAAACGAACACAAACGAACACGAAC
1 ATAAACGAACACAAAC-AACACGAAC
*
1536330 ATAAACGAACACGAA-AACACGAAC
1 ATAAACGAACACAAACAACACGAAC
1536354 ATAAACG
1 ATAAACG
1536361 TTGGAGACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 16 0.53
26 14 0.47
ACGTcount: A:0.58, C:0.25, G:0.12, T:0.05
Consensus pattern (25 bp):
ATAAACGAACACAAACAACACGAAC
Found at i:1537466 original size:14 final size:14
Alignment explanation
Indices: 1537449--1537479 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1537439 AATGAACATA
*
1537449 AACGAACATAACCG
1 AACGAACATAAACG
1537463 AACGAACATAAACG
1 AACGAACATAAACG
1537477 AAC
1 AAC
1537480 ATAACTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.06
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1541281 original size:83 final size:83
Alignment explanation
Indices: 1541137--1541477 Score: 463
Period size: 83 Copynumber: 4.1 Consensus size: 83
1541127 GCTGTAAATT
* * * * * * * *
1541137 TGATTTGCCTCTGAGTTGAATGCAATCAAACTCGAAGGTCTTTGATGACAAATACCCCTTCTCGC
1 TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGACGACAGATAACCCTTCTCGC
1541202 CTTGAGTTACGCTGCAAA
66 CTTGAGTTACGCTGCAAA
1541220 TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGACGACAGATAACCCTTCTCGC
1 TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGACGACAGATAACCCTTCTCGC
*
1541285 CTTGAGTTACGTTGCAAA
66 CTTGAGTTACGCTGCAAA
* *
1541303 TGATATGCCTTTGAGCTAAGTGTAATCAAACTCGAAGGTCTTTGACGACAGATAACCCTTCTCGC
1 TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGACGACAGATAACCCTTCTCGC
*
1541368 CTTGAGTTATGCTGCAAA
66 CTTGAGTTACGCTGCAAA
* * * *
1541386 TGATGTACCATTGAGCTGAGTGTAATCGAACTCGAAGG--TTT-ACTGACAGATAGCCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGAC-GACAGATAACCCTTCTCG
* * **
1541448 CCTTGAGCTATGCTATAAAA
65 CCTTGAGTTACGCT-GCAAA
1541468 TGATGTGCCT
1 TGATGTGCCT
1541478 CGAAAGGTCT
Statistics
Matches: 232, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
80 2 0.01
81 33 0.14
82 11 0.05
83 186 0.80
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (83 bp):
TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGACGACAGATAACCCTTCTCGC
CTTGAGTTACGCTGCAAA
Found at i:1541698 original size:83 final size:84
Alignment explanation
Indices: 1541476--1541945 Score: 483
Period size: 83 Copynumber: 5.7 Consensus size: 84
1541466 AATGATGTGC
* * * * * *
1541476 CTCGAAAGGTCTTTTGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCT
1 CTCG-AAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT
1541541 TTGAGCTGAGTGTAATCGAA
65 TTGAGCTGAGTGTAATCGAA
* * * * * *
1541561 CTCGAAGGTC---T-TTGGCATATAGCCTTTCTTGCCTTAAGTTATGCTACAAATGATGTGCC-T
1 CTCGAAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
* *
1541621 TAAGTTGAGTGTAATCGAA
66 TGAGCTGAGTGTAATCGAA
* *
1541640 CTCGAAGGTCTTTTATTGGCAAAAAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTT
1 CTCGAAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
1541705 TGAGCTGAGTGTAATCGAA
66 TGAGCTGAGTGTAATCGAA
* * * * * * *
1541724 CTCGAAGGTCTTTGA-CGACAAATAACCCTTCTTGCCTTGACTTACGCTGCAAATGATATGCCTT
1 CTCGAAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
* *
1541788 TGAGCTGAGTATAAACGAA
66 TGAGCTGAGTGTAATCGAA
* * * * * * *
1541807 CTCAAAGGTCTTTGA-CGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGTCTT
1 CTCGAAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
*
1541871 TGAGCTAAGTGTAATCGAA
66 TGAGCTGAGTGTAATCGAA
* * * * * * * *
1541890 CTTGAAGG---TTTACTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAAATGAT
1 CTCGAAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTG-CAAATGAT
1541946 ATACCTCGAA
Statistics
Matches: 332, Mismatches: 46, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
79 28 0.08
80 45 0.14
81 32 0.10
82 8 0.02
83 177 0.53
84 38 0.11
85 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (84 bp):
CTCGAAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
TGAGCTGAGTGTAATCGAA
Found at i:1541860 original size:166 final size:166
Alignment explanation
Indices: 1541496--1541927 Score: 536
Period size: 166 Copynumber: 2.6 Consensus size: 166
1541486 CTTTTGTTGG
* * * *
1541496 CAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * * * *
1541561 CTCGAAGGTCTTTG--G-CATATAGCCTTTCTTGCCTTAAGTTATGCTACAAATGATGTGCCTTA
66 CTCGAAGGTCTTTGACGACAAATAGCCCTTCTTGCCTTGACTTACGCTACAAATGATATGCCTTA
* * * * * * *
1541623 AGTTGAGTGTAATCGAACTCGAAGGTCTTTTATTGG
131 AGCTGAGTATAAACGAACTCAAAGGTCTTTGATCGA
* * *
1541659 CAAAAAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* *
1541724 CTCGAAGGTCTTTGACGACAAATAACCCTTCTTGCCTTGACTTACGCTGCAAATGATATGCCTTT
66 CTCGAAGGTCTTTGACGACAAATAGCCCTTCTTGCCTTGACTTACGCTACAAATGATATGCC-TT
*
1541789 GAGCTGAGTATAAACGAACTCAAAGGTCTTTGA-CGA
130 AAGCTGAGTATAAACGAACTCAAAGGTCTTTGATCGA
* * *
1541825 CAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGTCTTTGAGCTAAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * *
1541890 CTTGAAGG--TTT-ACTGACAGATAGCCCTTCTCGCCTTGA
66 CTCGAAGGTCTTTGAC-GACAAATAGCCCTTCTTGCCTTGA
1541928 GCTATGCTGT
Statistics
Matches: 231, Mismatches: 33, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
163 74 0.32
164 24 0.10
165 1 0.00
166 103 0.45
167 29 0.13
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (166 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
CTCGAAGGTCTTTGACGACAAATAGCCCTTCTTGCCTTGACTTACGCTACAAATGATATGCCTTA
AGCTGAGTATAAACGAACTCAAAGGTCTTTGATCGA
Found at i:1542071 original size:80 final size:79
Alignment explanation
Indices: 1541969--1542123 Score: 238
Period size: 80 Copynumber: 1.9 Consensus size: 79
1541959 TCTTTGGTTG
*
1541969 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGAAAATGATATGCCTTTGAGCTGAGTGTAATCGA
1 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGAAAATGATATGCC-TTGAGCTGAGTGTAATCAA
1542034 ACTCGAAGGTCTTTA
65 ACTCGAAGGTCTTTA
* * * * *
1542049 GCAGATAGCCTTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATCAAA
1 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGAAAATGATATGCCTTGAGCTGAGTGTAATCAAA
*
1542114 CTTGAAGGTC
66 CTCGAAGGTC
1542124 ATTTGTTGGC
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
79 28 0.41
80 40 0.59
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.30
Consensus pattern (79 bp):
GCAGATAGCCCTTCTCGACTTAAGCTATGCTGAAAATGATATGCCTTGAGCTGAGTGTAATCAAA
CTCGAAGGTCTTTA
Found at i:1542087 original size:474 final size:474
Alignment explanation
Indices: 1541121--1542229 Score: 1718
Period size: 474 Copynumber: 2.3 Consensus size: 474
1541111 CCTCGGCTTG
* * * * * *
1541121 AGCTATGCTGTAAATTTGATTTGCCTCTGAGTTGAATGCAATCAAACTCGAAGGTCTTTGA-TGA
1 AGCTATGCTGCAAA--TGATGTGCCT-TGAGTTGAGTGTAATCAAACTCGAAGGTCTTTTATTGG
* * * * *
1541185 CAAATACCCCTTCTCGCCTTGAGTTACGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
63 CAAATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* *
1541250 CTCGAAGGTCTTTGACGACAGATAACCCTTCTCGCCTTGAGTTACGTTGCAAATGATATGCCTTT
128 CTCGAAGGTCTTTGACGACAGATAACCCTTCTCGCCTTGACTTACGCTGCAAATGATATGCCTTT
* * *
1541315 GAGCTAAGTGTAATCAAACTCGAAGGTCTTTGACGACAGATAACCCTTCTCGCCTTGAGTTATGC
193 GAGCTAAGTATAAACAAACTCAAAGGTCTTTGACGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
1541380 TGCAAATGATGTACCATTGAGCTGAGTGTAATCGAACTCGAAGGTTTACTGACAGATAGCCCTTC
258 TGCAAATGATGTACCATTGAGCTAAGTGTAATCGAACTCGAAGGTTTACTGACAGATAGCCCTTC
* * *
1541445 TCGCCTTGAGCTATGCTATAAAATGATGTGCCTCGAAAGGTCTTTTGTTGGCAGATAGCCCTTCT
323 TCGCCTTGAGCTATGCTATAAAATGATATACCTCGAAAGGTCTTTGGTTGGCAGATAGCCCTTCT
* * *
1541510 AGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG
388 AGACTTAAGCTATGCTGAAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTA
*
1541575 GCATATAGCCTTTCTTGCCTTA
453 GCAGATAGCCTTTCTTGCCTTA
* * * *
1541597 AGTTATGCTACAAATGATGTGCCTTAAGTTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAA
1 AGCTATGCTGCAAATGATGTGCCTTGAGTTGAGTGTAATCAAACTCGAAGGTCTTTTATTGGCAA
*
1541662 AAAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
66 ATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
1541727 GAAGGTCTTTGACGACAAATAACCCTTCTTGCCTTGACTTACGCTGCAAATGATATGCCTTTGAG
131 GAAGGTCTTTGACGACAGATAACCCTTCTCGCCTTGACTTACGCTGCAAATGATATGCCTTTGAG
* *
1541792 CTGAGTATAAACGAACTCAAAGGTCTTTGACGACAGATAACCCTTCTCGCCTTGAGTTATGCTGC
196 CTAAGTATAAACAAACTCAAAGGTCTTTGACGACAGATAACCCTTCTCGCCTTGAGTTATGCTGC
** * *
1541857 AAATGATGTGTCTTTGAGCTAAGTGTAATCGAACTTGAAGGTTTACTGACAGATAGCCCTTCTCG
261 AAATGATGTACCATTGAGCTAAGTGTAATCGAACTCGAAGGTTTACTGACAGATAGCCCTTCTCG
* *
1541922 CCTTGAGCTATGCTGTAAAATGATATACCTCGAAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGA
326 CCTTGAGCTATGCTATAAAATGATATACCTCGAAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGA
1541987 CTTAAGCTATGCTGAAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTAGCA
391 CTTAAGCTATGCTGAAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTAGCA
1542052 GATAGCCTTTCTTGCCTTA
456 GATAGCCTTTCTTGCCTTA
* * * *
1542071 AGCTATGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATCAAACTTGAAGGTCATTTGTTGGCAA
1 AGCTATGCTGCAAATGATGTGCCTTGAGTTGAGTGTAATCAAACTCGAAGGTCTTTTATTGGCAA
* * * *
1542136 ATAACCCTTCTAGCCTTGAGTTCTGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACAT
66 ATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC-T
* * *
1542201 -GAAGGTCTTCGATGACAGCTAACCCTTCT
130 CGAAGGTCTTTGACGACAGATAACCCTTCT
1542230 AACATTGAGT
Statistics
Matches: 575, Mismatches: 56, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
473 29 0.05
474 534 0.93
475 1 0.00
476 11 0.02
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (474 bp):
AGCTATGCTGCAAATGATGTGCCTTGAGTTGAGTGTAATCAAACTCGAAGGTCTTTTATTGGCAA
ATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTGACGACAGATAACCCTTCTCGCCTTGACTTACGCTGCAAATGATATGCCTTTGAG
CTAAGTATAAACAAACTCAAAGGTCTTTGACGACAGATAACCCTTCTCGCCTTGAGTTATGCTGC
AAATGATGTACCATTGAGCTAAGTGTAATCGAACTCGAAGGTTTACTGACAGATAGCCCTTCTCG
CCTTGAGCTATGCTATAAAATGATATACCTCGAAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGA
CTTAAGCTATGCTGAAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTAGCA
GATAGCCTTTCTTGCCTTA
Found at i:1542224 original size:83 final size:79
Alignment explanation
Indices: 1541969--1542248 Score: 247
Period size: 83 Copynumber: 3.4 Consensus size: 79
1541959 TCTTTGGTTG
* * * * * * * *
1541969 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGAAAATGATATGCCTTTGAGCTGAGTGTAATCGA
1 GCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCC-TTGAGCTGAGTGTAATCGA
*
1542034 ACTCGAAGGTCTTTA-
65 ACT-GAAGGTCTTGAT
* * * * * * *
1542049 GCAGATAGCCTTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATCAAA
1 GCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGAGCTGAGTGTAATCGAA
*
1542114 CTTGAAGGTCATTTGTT
66 C-TGAAGGTC--TTGAT
* * * *
1542131 GGCAAATAACCCTTCTAGCCTTGAGTTCTGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
1 -GCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTT-GAGCTGAGTGTAATCG
1542196 AACATGAAGGTCTTCGAT
64 AAC-TGAAGGTCTT-GAT
* * *
1542214 GACAGCTAACCCTTCTAACATTGAGTTATGTTGCA
1 G-CAGATAACCCTTCTAGCCTTGAGTTATGTTGCA
1542249 TTGGGCACGA
Statistics
Matches: 166, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
79 27 0.16
80 41 0.25
81 2 0.01
82 3 0.02
83 69 0.42
84 24 0.14
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (79 bp):
GCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGAGCTGAGTGTAATCGAA
CTGAAGGTCTTGAT
Found at i:1542564 original size:43 final size:43
Alignment explanation
Indices: 1542499--1542618 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
1542489 ATTGTGTACA
* * * *
1542499 TGGGCACGATATCCTTCATCGTGAAGTTGAAATCGTGGATTTG
1 TGGGCATGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTTG
* * *
1542542 TGGGCATGATACCCTCCGTCGTGGAGTTAAAATTGTGGATTTG
1 TGGGCATGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTTG
1542585 TGGGCATGATATCCTCCGTCGTGGAGTTGAAATC
1 TGGGCATGATATCCTCCGTCGTGGAGTTGAAATC
1542619 TGGCTTGAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (43 bp):
TGGGCATGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTTG
Found at i:1543869 original size:2 final size:2
Alignment explanation
Indices: 1543862--1543888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1543852 TTATTGTATG
1543862 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1543889 TATTTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1547935 original size:12 final size:12
Alignment explanation
Indices: 1547918--1547945 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1547908 TTAATTGCAA
1547918 AAATTAAAATTT
1 AAATTAAAATTT
1547930 AAATTAAAATTT
1 AAATTAAAATTT
1547942 AAAT
1 AAAT
1547946 ATTCAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:1555357 original size:18 final size:18
Alignment explanation
Indices: 1555331--1555373 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1555321 CAACCGGTAC
*
1555331 TGCTTACTTGTTATGCAA
1 TGCTCACTTGTTATGCAA
*
1555349 TGCTCACTTGTTATTCAA
1 TGCTCACTTGTTATGCAA
1555367 TGCTCAC
1 TGCTCAC
1555374 ATAAAGGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (18 bp):
TGCTCACTTGTTATGCAA
Found at i:1556257 original size:16 final size:16
Alignment explanation
Indices: 1556236--1556266 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1556226 TGGTGACATT
1556236 ACAATGAGAAATTTCC
1 ACAATGAGAAATTTCC
1556252 ACAATGAGAAATTTC
1 ACAATGAGAAATTTC
1556267 TTCTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (16 bp):
ACAATGAGAAATTTCC
Found at i:1557925 original size:19 final size:19
Alignment explanation
Indices: 1557862--1557925 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
1557852 TCTTTCCAAA
*
1557862 TAAAATCTCAATTTCCCTCC
1 TAAATTCTCAATTTCCCT-C
* * *
1557882 TAATTTTTCTA-TTCCCTC
1 TAAATTCTCAATTTCCCTC
1557900 TAAATTCTCAATTTCCCTC
1 TAAATTCTCAATTTCCCTC
1557919 TAAATTC
1 TAAATTC
1557926 CCAAATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 9 0.25
19 20 0.56
20 7 0.19
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATTCTCAATTTCCCTC
Found at i:1558156 original size:2 final size:2
Alignment explanation
Indices: 1558131--1558265 Score: 127
Period size: 2 Copynumber: 68.5 Consensus size: 2
1558121 TTATATAGTT
* * *
1558131 TA TA -A TA TA AA TA TA GTT TA TA TA TA AA CT- TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
1558172 TA CA TA CA TA TA TA TA AA CT- TA TA TA T- TA TA TA CA TA CA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
1558213 CA 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
1558255 TA TA TA TA TA T
1 TA TA TA TA TA T
1558266 GAACTAAGGA
Statistics
Matches: 107, Mismatches: 18, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
1 5 0.05
2 101 0.94
3 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1558157 original size:17 final size:18
Alignment explanation
Indices: 1558123--1558158 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1558113 TATAATAATT
1558123 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
1558141 ATATAGTTTAT-ATATAA
1 ATATAGTTTATAATATAA
1558158 A
1 A
1558159 CTTATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:1567863 original size:2 final size:2
Alignment explanation
Indices: 1567856--1567883 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1567846 AGACTAATCC
1567856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1567884 TTGAGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1573499 original size:25 final size:25
Alignment explanation
Indices: 1573471--1573521 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1573461 GTCTTATTTG
*
1573471 AACTTATTAGGGGTCATAAAGAGCC
1 AACTTATTAAGGGTCATAAAGAGCC
1573496 AACTTATTAAGGGTCATAAAGAGCC
1 AACTTATTAAGGGTCATAAAGAGCC
1573521 A
1 A
1573522 CCATATAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (25 bp):
AACTTATTAAGGGTCATAAAGAGCC
Found at i:1579894 original size:19 final size:19
Alignment explanation
Indices: 1579870--1579919 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1579860 CTGACACAAG
1579870 AGTATCGATACCCCCTAGA
1 AGTATCGATACCCCCTAGA
1579889 AGTATCGATACCCCCTAGA
1 AGTATCGATACCCCCTAGA
*
1579908 AATATCGATACC
1 AGTATCGATACC
1579920 AACAACTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AGTATCGATACCCCCTAGA
Found at i:1587771 original size:25 final size:25
Alignment explanation
Indices: 1587729--1587776 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1587719 ACCGAAGTGT
* * *
1587729 TAATACACATAAATTTGTTCCCACC
1 TAATACAAATAAAGTTGTGCCCACC
*
1587754 TAATACAAATAAGGTTGTGCCCA
1 TAATACAAATAAAGTTGTGCCCA
1587777 TGATATGCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (25 bp):
TAATACAAATAAAGTTGTGCCCACC
Found at i:1601019 original size:13 final size:13
Alignment explanation
Indices: 1601003--1601027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1600993 GATTCGATCT
1601003 GATTATCCGATTC
1 GATTATCCGATTC
1601016 GATTATCCGATT
1 GATTATCCGATT
1601028 TCTATACCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
GATTATCCGATTC
Found at i:1610861 original size:3 final size:3
Alignment explanation
Indices: 1610853--1610884 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1610843 TATATGACTA
*
1610853 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1610885 AAAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1612330 original size:3 final size:3
Alignment explanation
Indices: 1612324--1612394 Score: 58
Period size: 3 Copynumber: 23.3 Consensus size: 3
1612314 AAAATTTATT
* * *
1612324 TAA TAA TAA TAA TAA TAA -AA TTA TTA TAG TAA TAA TAA -AA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
1612368 TAA TAA -ATA TAA TAAA TAA TAAA TAA T
1 TAA TAA TA-A TAA T-AA TAA T-AA TAA T
1612395 GAGTAATGGA
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
2 5 0.09
3 42 0.74
4 10 0.18
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1612337 original size:26 final size:26
Alignment explanation
Indices: 1612308--1612394 Score: 88
Period size: 26 Copynumber: 3.2 Consensus size: 26
1612298 TTGGATCTAA
1612308 AATAATAAAATTTATT-TAATAATAAT
1 AATAATAAAA-TTATTATAATAATAAT
*
1612334 AATAATAAAATTATTATAGTAATAAT
1 AATAATAAAATTATTATAATAATAAT
* *
1612360 AA-AATAAATAATAAATATAATAAATAAT
1 AATAAT-AA-AATTATTATAAT-AATAAT
1612388 AAATAAT
1 -AATAAT
1612395 GAGTAATGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
25 8 0.16
26 23 0.45
27 9 0.18
28 6 0.12
29 2 0.04
30 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (26 bp):
AATAATAAAATTATTATAATAATAAT
Found at i:1612374 original size:7 final size:7
Alignment explanation
Indices: 1612354--1612394 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
1612344 TTATTATAGT
1612354 AATAAT-
1 AATAATA
1612360 AA-AATA
1 AATAATA
1612366 AATAATAA
1 AATAAT-A
1612374 ATATAATA
1 A-ATAATA
1612382 AATAATA
1 AATAATA
1612389 AATAAT
1 AATAAT
1612395 GAGTAATGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
5 3 0.10
6 4 0.13
7 15 0.48
8 4 0.13
9 5 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAATA
Found at i:1612381 original size:16 final size:16
Alignment explanation
Indices: 1612353--1612393 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1612343 ATTATTATAG
1612353 TAAT-AATAAAATAAA
1 TAATAAATAAAATAAA
*
1612368 TAATAAATATAATAAA
1 TAATAAATAAAATAAA
1612384 TAATAAATAA
1 TAATAAATAA
1612394 TGAGTAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAATAAATAAAATAAA
Found at i:1612558 original size:17 final size:17
Alignment explanation
Indices: 1612536--1612590 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
1612526 GTTGAATAAG
1612536 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
1612553 TTCTTCTTC-TT-TGAGAC
1 TTCTTC-TCATTATGA-AC
1612570 TAATTCTTCTCATTATGAAC
1 ---TTCTTCTCATTATGAAC
1612590 T
1 T
1612591 ATTCCACTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
16 3 0.10
17 11 0.35
18 2 0.06
19 2 0.06
20 10 0.32
21 3 0.10
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:1612559 original size:20 final size:20
Alignment explanation
Indices: 1612536--1612591 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1612526 GTTGAATAAG
1612536 TTCTTCTCATTATGAAC---
1 TTCTTCTCATTATGAACTAA
1612553 TTCTTCTTC-TT-TGAGACTAA
1 TTCTTC-TCATTATGA-ACTAA
1612573 TTCTTCTCATTATGAACTA
1 TTCTTCTCATTATGAACTA
1612592 TTCCACTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.09
17 10 0.31
18 2 0.06
19 2 0.06
20 12 0.38
21 3 0.09
ACGTcount: A:0.23, C:0.21, G:0.07, T:0.48
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTAA
Found at i:1612942 original size:113 final size:113
Alignment explanation
Indices: 1612738--1613069 Score: 540
Period size: 113 Copynumber: 2.9 Consensus size: 113
1612728 ATAGAATCAT
* *
1612738 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
* * * * *
1612803 ATTATGAACTC-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGA
66 ATTATGAACTCGAC-CTGGCAATGTTGATCCATCGAATGATGAATTCAA
* *
1612851 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCGTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
*
1612916 ATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTTAA
66 ATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAA
* *
1612964 GCCAAAAGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1613029 ATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATG
66 ATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATG
1613070 GATTTGAATC
Statistics
Matches: 204, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 203 1.00
114 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (113 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAA
Found at i:1614981 original size:75 final size:75
Alignment explanation
Indices: 1614805--1614981 Score: 178
Period size: 75 Copynumber: 2.4 Consensus size: 75
1614795 CCAAAATGAT
* * * * * * *
1614805 ATAGGCCTTCAGTATGCCCTAACATTT-GTCGATACAAGCGTTCAAAATGCGCCAACATTCCTCT
1 ATAGGCTTTCAGCATGCCCCAACATTTACT-GATACAAACGTTCAAAATACACCAACATTCCTCT
* *
1614869 TTCTGATTGAT
65 TTCTGATTAAA
* * * *
1614880 ATGGGCTTTCAGCATTCCCCAGCATTTACTGATACAAACGTTCAAAATACATCAACATTCCT-TA
1 ATAGGCTTTCAGCATGCCCCAACATTTACTGATACAAACGTTCAAAATACACCAACATTCCTCT-
1614944 TTCTGATTAAA
65 TTCTGATTAAA
** *
1614955 ATATTCTTTCAGCATGCCTCAACATTT
1 ATAGGCTTTCAGCATGCCCCAACATTT
1614982 GCTTATTGTT
Statistics
Matches: 81, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
74 1 0.01
75 79 0.98
76 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (75 bp):
ATAGGCTTTCAGCATGCCCCAACATTTACTGATACAAACGTTCAAAATACACCAACATTCCTCTT
TCTGATTAAA
Found at i:1618250 original size:8 final size:8
Alignment explanation
Indices: 1618237--1618266 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1618227 TGATTCAATT
1618237 TTTTTTCC
1 TTTTTTCC
1618245 TTTTTTCC
1 TTTTTTCC
*
1618253 TTTTTCCC
1 TTTTTTCC
1618261 TTTTTT
1 TTTTTT
1618267 TGAGTATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCC
Found at i:1620417 original size:19 final size:19
Alignment explanation
Indices: 1620393--1620450 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
1620383 TCGAATGCAT
1620393 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
1620412 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1620431 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1620450 T
1 T
1620451 GATTTAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.21, C:0.40, G:0.16, T:0.24
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1626415 original size:23 final size:22
Alignment explanation
Indices: 1626339--1626419 Score: 76
Period size: 24 Copynumber: 3.6 Consensus size: 22
1626329 CACTTAACAA
*
1626339 TGCATTGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
* *
1626363 TGCATCGATGCATCC--GCATAA
1 TGCATCGATGCATCCTTGAAT-G
*
1626384 TGCACCGATGCATGCCTTGAATG
1 TGCATCGATGCAT-CCTTGAATG
1626407 TGCATCGATGCAT
1 TGCATCGATGCAT
1626420 AAGACCATGC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 3 0.07
21 12 0.26
22 2 0.04
23 14 0.30
24 15 0.33
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:1628981 original size:21 final size:21
Alignment explanation
Indices: 1628957--1628996 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1628947 TTTTCAAAGG
1628957 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
1628978 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
1628997 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:1629046 original size:19 final size:19
Alignment explanation
Indices: 1629022--1629060 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1629012 TCGAATGCAT
1629022 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1629041 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1629060 T
1 T
1629061 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1629085 original size:64 final size:64
Alignment explanation
Indices: 1628957--1629186 Score: 204
Period size: 64 Copynumber: 3.5 Consensus size: 64
1628947 TTTTCAAAGG
* * *
1628957 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGC
1629020 ATT
62 ATT
1629023 CCATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATT
1 -CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCA-T
1629087 T
64 T
* * ** * * *
1629088 GATGCATCGATGCACAATCCATCCATCGATGCAC-CAAGCTATTT--TTCAAACATCGAATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCA-
1629150 TT
63 TT
* * *
1629152 CATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACT
1629187 AGGAGTCCAA
Statistics
Matches: 138, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
63 2 0.01
64 96 0.70
65 17 0.12
66 7 0.05
67 14 0.10
68 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATT
Found at i:1629166 original size:17 final size:19
Alignment explanation
Indices: 1629138--1629186 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1629128 ATTTTTCAAA
1629138 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
1629156 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
1629175 CACCGATGCACT
1 CATCGATGCACT
1629187 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:1631392 original size:43 final size:44
Alignment explanation
Indices: 1631311--1631393 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 44
1631301 TTTTGCATCA
* * *
1631311 AACAAAACTTTTATATGTAGGGGACAACTTTCAGTCCTAATTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAATTTC
* * *
1631355 AACAAAAC-TTTACATATATGGGATAACTTTCCCTCCTAA
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAA
1631394 CTTCTCTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 25 0.76
44 8 0.24
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAATTTC
Found at i:1632713 original size:2 final size:2
Alignment explanation
Indices: 1632706--1632745 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1632696 AAAACATTAA
1632706 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1632746 TAGGAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1633627 original size:2 final size:2
Alignment explanation
Indices: 1633620--1633655 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1633610 TATTATTTAT
1633620 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
1633656 CTTATATGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1633709 original size:14 final size:15
Alignment explanation
Indices: 1633689--1633731 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
1633679 TAATAGTAAT
1633689 AATAAAAAAATAAAC
1 AATAAAAAAATAAAC
*
1633704 -ATAAAAAATTAAAC
1 AATAAAAAAATAAAC
*
1633718 AATAAATAAATAAA
1 AATAAAAAAATAAA
1633732 AGTAAAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAAAAAATAAAC
Found at i:1634330 original size:39 final size:37
Alignment explanation
Indices: 1634248--1634329 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
1634238 TCATTTCTTT
* *
1634248 CTTCTTTCCTTTTCTCTCTAACTGAGAGATTTTCCCC
1 CTTCTCTCCTTTTCTCTCTAACTAAGAGATTTTCCCC
1634285 CTTCTCTCCTTTTCTCTCTAACTAAGAGATTTTCCCC
1 CTTCTCTCCTTTTCTCTCTAACTAAGAGATTTTCCCC
1634322 CTTCTCTC
1 CTTCTCTC
1634330 TAAATACACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.13, C:0.35, G:0.06, T:0.45
Consensus pattern (37 bp):
CTTCTCTCCTTTTCTCTCTAACTAAGAGATTTTCCCC
Found at i:1635153 original size:3 final size:3
Alignment explanation
Indices: 1635147--1635218 Score: 62
Period size: 3 Copynumber: 24.3 Consensus size: 3
1635137 AAAATTTATT
* * *
1635147 TAA TAA TAA TAA TAA TAA TAA -AA TTA TTA TAG TAA TAA TAA -AA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1635192 TAA TAAA TAA -AA TAAA TAA TAAA TAA T
1 TAA T-AA TAA TAA T-AA TAA T-AA TAA T
1635219 GAGTAATGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
2 8 0.14
3 41 0.71
4 9 0.16
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1635182 original size:29 final size:29
Alignment explanation
Indices: 1635130--1635198 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
1635120 TTTGGATCTG
1635130 AAATAATAAAATTTATTTAATAATAATAA
1 AAATAATAAAATTTATTTAATAATAATAA
* *
1635159 TAATAATAAAA-TTATTATAGTAATAATAA
1 AAATAATAAAATTTATT-TAATAATAATAA
1635188 AATATAATAAA
1 AA-ATAATAAA
1635199 TAAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 5 0.14
29 22 0.63
30 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (29 bp):
AAATAATAAAATTTATTTAATAATAATAA
Found at i:1635197 original size:13 final size:13
Alignment explanation
Indices: 1635179--1635214 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1635169 ATTATTATAG
1635179 TAATAATAAAATA
1 TAATAATAAAATA
1635192 TAATAAATAAAATA
1 TAAT-AATAAAATA
1635206 -AATAATAAA
1 TAATAATAAA
1635215 TAATGAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 7 0.32
14 9 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATAATAAAATA
Found at i:1635210 original size:16 final size:14
Alignment explanation
Indices: 1635179--1635217 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
1635169 ATTATTATAG
1635179 TAAT-AATAAAATA
1 TAATAAATAAAATA
1635192 TAATAAATAAAATAAA
1 TAATAAATAAAAT--A
1635208 TAATAAATAA
1 TAATAAATAA
1635218 TGAGTAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
16 11 0.48
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TAATAAATAAAATA
Found at i:1641600 original size:20 final size:20
Alignment explanation
Indices: 1641575--1641616 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1641565 GGAGTCCGAT
1641575 ACTGGGGG-TTCGGTATCGAG
1 ACTGGGGGCTT-GGTATCGAG
1641595 ACTGGGGGCTTGGTATCGAG
1 ACTGGGGGCTTGGTATCGAG
1641615 AC
1 AC
1641617 AATATTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.24
Consensus pattern (20 bp):
ACTGGGGGCTTGGTATCGAG
Found at i:1644079 original size:32 final size:32
Alignment explanation
Indices: 1644034--1644175 Score: 135
Period size: 32 Copynumber: 4.5 Consensus size: 32
1644024 ACTTGTTCAA
* * *
1644034 TTAG-TGATGTGACACATGTCACATCATCATT
1 TTAGATGATATGACACATATCACATCATCACT
* * *
1644065 TTAGATGATATGACACATATCATATTATCATT
1 TTAGATGATATGACACATATCACATCATCACT
* *
1644097 TTAGATGATATGACACATATTACATCGTCACT
1 TTAGATGATATGACACATATCACATCATCACT
* * * *
1644129 TT-GACTAATATGACATATAACATATCATCACT
1 TTAGA-TGATATGACACATATCACATCATCACT
* *
1644161 GTAGATGATGTGACA
1 TTAGATGATATGACA
1644176 ACATGTCATC
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
31 6 0.07
32 82 0.91
33 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TTAGATGATATGACACATATCACATCATCACT
Found at i:1648865 original size:20 final size:20
Alignment explanation
Indices: 1648840--1648877 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1648830 TTTGGTTCAC
*
1648840 GGAATATAAGATTACCAGCG
1 GGAATAAAAGATTACCAGCG
1648860 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
1648878 GGAATAGGAT
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:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGCG
Found at i:1648880 original size:18 final size:19
Alignment explanation
Indices: 1648840--1648883 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1648830 TTTGGTTCAC
*
1648840 GGAATATAAGATTACCAGCG
1 GGAATAAAAGATTACCA-CG
1648860 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCACG
1648878 GGAATA
1 GGAATA
1648884 GGATTACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.18
Consensus pattern (19 bp):
GGAATAAAAGATTACCACG
Found at i:1657575 original size:6 final size:6
Alignment explanation
Indices: 1657556--1657602 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
1657546 AAAAACAATT
* * *
1657556 ATATTA ATAATA ATATTA ATATT- ATAATA ATAATA ATAATTA ATATT
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA AT-ATTA ATATT
1657603 TATAATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 4 0.11
6 26 0.74
7 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
ATATTA
Found at i:1661903 original size:8 final size:7
Alignment explanation
Indices: 1661876--1661900 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1661866 AGTTGTTTAA
1661876 AAAATTT
1 AAAATTT
1661883 AAAATTT
1 AAAATTT
1661890 AAAATTT
1 AAAATTT
1661897 AAAA
1 AAAA
1661901 ATTCTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:1662428 original size:20 final size:21
Alignment explanation
Indices: 1662403--1662447 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1662393 AATTCACAAT
1662403 GCGAATAAGT-AAATCGCAAC
1 GCGAATAAGTAAAATCGCAAC
** *
1662423 GCGAATTGGTAAAATCGCAAT
1 GCGAATAAGTAAAATCGCAAC
1662444 GCGA
1 GCGA
1662448 TACTGACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
GCGAATAAGTAAAATCGCAAC
Found at i:1662461 original size:20 final size:20
Alignment explanation
Indices: 1662437--1662529 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
1662427 ATTGGTAAAA
* *
1662437 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
1662457 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
1662477 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
1662497 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
1662517 TCGCAACGAGATA
1 TCGCAACGCGATA
1662530 ATACAGAATC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1663291 original size:24 final size:24
Alignment explanation
Indices: 1663264--1663309 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1663254 TATTCGAAAT
*
1663264 TTGATCTTGGTCAATACCCGGACA
1 TTGATATTGGTCAATACCCGGACA
*
1663288 TTGATATTGGTCAATACTCGGA
1 TTGATATTGGTCAATACCCGGA
1663310 TTTTGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (24 bp):
TTGATATTGGTCAATACCCGGACA
Found at i:1663315 original size:24 final size:24
Alignment explanation
Indices: 1663263--1663316 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1663253 GTATTCGAAA
*
1663263 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
1663287 ATTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1663311 TTTGAT
1 TTTGAT
1663317 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1664207 original size:117 final size:118
Alignment explanation
Indices: 1663998--1664233 Score: 440
Period size: 117 Copynumber: 2.0 Consensus size: 118
1663988 TCAAGCTTGG
1663998 AGAGCCAAATGTTATGCCTTGGAATTGTGAGGGGGTCGCCAGAAGCATCGTTTGCCCAACTGCCG
1 AGAGCCAAATGTTATGCCTTGGAATTGTGAGGGGGTCGCCAGAAGCATCGTTTGCCCAACTGCCG
*
1664063 GCTTATTGTCACAATTTAAGCTGAAAATCCTGGGTCGGT-AACTCATATCAAA
66 GCTTATTGTCACAATTTAAGCTAAAAATCCTGGGTCGGTAAACTCATATCAAA
1664115 AGAGCCAAATGTTATGCCTTGGAATTGTTGAGGGGGTCGCCAGAAGCATCGTTTG-CCAACTGCC
1 AGAGCCAAATGTTATGCCTTGGAATTG-TGAGGGGGTCGCCAGAAGCATCGTTTGCCCAACTGCC
1664179 GGCTTATTGTCACAATTTAAGCTAAAAATCCTGGGTCGGTAAACTCATATCAAA
65 GGCTTATTGTCACAATTTAAGCTAAAAATCCTGGGTCGGTAAACTCATATCAAA
1664233 A
1 A
1664234 TAGATAGATG
Statistics
Matches: 116, Mismatches: 1, Indels: 3
0.97 0.01 0.03
Matches are distributed among these distances:
117 75 0.65
118 41 0.35
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (118 bp):
AGAGCCAAATGTTATGCCTTGGAATTGTGAGGGGGTCGCCAGAAGCATCGTTTGCCCAACTGCCG
GCTTATTGTCACAATTTAAGCTAAAAATCCTGGGTCGGTAAACTCATATCAAA
Found at i:1664343 original size:12 final size:12
Alignment explanation
Indices: 1664326--1664350 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1664316 ATATAATCCT
1664326 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1664338 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1664350 G
1 G
1664351 TTCTCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1666543 original size:19 final size:19
Alignment explanation
Indices: 1666521--1666651 Score: 103
Period size: 19 Copynumber: 7.7 Consensus size: 19
1666511 GGAAATTACT
1666521 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1666540 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1666554 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1666573 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
1666587 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1666606 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1666620 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1666639 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1666652 TTTAATTTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
14 28 0.33
15 5 0.06
16 4 0.05
17 4 0.05
18 5 0.06
19 40 0.47
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1666563 original size:33 final size:33
Alignment explanation
Indices: 1666521--1666647 Score: 211
Period size: 33 Copynumber: 3.8 Consensus size: 33
1666511 GGAAATTACT
1666521 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1666554 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1666586 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1666620 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1666648 CGAATTTAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
32 1 0.01
33 85 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1666628 original size:66 final size:66
Alignment explanation
Indices: 1666522--1666654 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
1666512 GAAATTACTA
1666522 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1666587 T
66 T
*
1666588 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1666653 T
66 T
1666654 T
1 T
1666655 AATTTCCCGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1666669 original size:19 final size:19
Alignment explanation
Indices: 1666647--1666708 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
1666637 AAATCGCAAC
*
1666647 GCGAATTTAATTTCCCGTT
1 GCGATTTTAATTTCCCGTT
* *
1666666 GCGATTTTCATTTCGCGTT
1 GCGATTTTAATTTCCCGTT
* * *
1666685 GCGATTTTTATTTCGCATT
1 GCGATTTTAATTTCCCGTT
1666704 GCGAT
1 GCGAT
1666709 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (19 bp):
GCGATTTTAATTTCCCGTT
Found at i:1666834 original size:14 final size:14
Alignment explanation
Indices: 1666815--1666848 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1666805 CATCAATTAA
1666815 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1666829 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1666843 ACAAAT
1 ACAAAT
1666849 TAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1669556 original size:14 final size:14
Alignment explanation
Indices: 1669537--1669592 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1669527 GGAAATGACT
1669537 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1669551 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
1669568 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
1669584 ATCGCAACG
1 ATCGCAACG
1669593 CGAAATGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1669570 original size:33 final size:33
Alignment explanation
Indices: 1669513--1669611 Score: 180
Period size: 33 Copynumber: 3.0 Consensus size: 33
1669503 ACGAGATAAT
1669513 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
1669547 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
*
1669580 GAGAATCGCAACGCGAAATGACAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
1669612 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
33 50 0.78
34 14 0.22
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1669575 original size:19 final size:18
Alignment explanation
Indices: 1669488--1669666 Score: 130
Period size: 19 Copynumber: 10.1 Consensus size: 18
1669478 TCTTTTGGTT
*
1669488 GAAATGAAAATCGCAACGA
1 GAAATG-AAATCGCAACGC
1669507 GATAATGAGAATCGCAACGC
1 GA-AATGA-AATCGCAACGC
*
1669527 GGAAATGACTATCGCAA--C
1 -GAAATGA-AATCGCAACGC
*
1669545 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
*
1669561 GAAATGACTATCGCAA--C
1 GAAATGA-AATCGCAACGC
*
1669578 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
1669594 GAAATGACAATCGCAACGC
1 GAAATGA-AATCGCAACGC
1669613 GAAATGAAAATCGCAA--C
1 GAAATG-AAATCGCAACGC
*
1669630 G-AGTG-AATCGCAACGC
1 GAAATGAAATCGCAACGC
*
1669646 GAAATGAAAATCGCAATGC
1 GAAATG-AAATCGCAACGC
1669665 GA
1 GA
1669667 TTTTGGTTTC
Statistics
Matches: 128, Mismatches: 13, Indels: 38
0.72 0.07 0.21
Matches are distributed among these distances:
14 22 0.17
16 15 0.12
17 14 0.11
18 1 0.01
19 47 0.37
20 27 0.21
21 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.12
Consensus pattern (18 bp):
GAAATGAAATCGCAACGC
Found at i:1669615 original size:52 final size:52
Alignment explanation
Indices: 1669550--1669666 Score: 189
Period size: 52 Copynumber: 2.2 Consensus size: 52
1669540 GCAACGAGAG
** *
1669550 AATCGCAACGCGAAATGACTATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
*
1669602 AATCGCAACGCGAAATGAAAATCGCAACGAGTGAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
*
1669654 AATCGCAATGCGA
1 AATCGCAACGCGA
1669667 TTTTGGTTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
Found at i:1669731 original size:20 final size:19
Alignment explanation
Indices: 1669662--1669732 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
1669652 AAAATCGCAA
**
1669662 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1669681 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1669700 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1669720 TGCGATTTTTATT
1 TGCGATTTTTATT
1669733 CTCGAAACTA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1670249 original size:20 final size:20
Alignment explanation
Indices: 1670224--1670275 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1670214 GCTATGTAAA
1670224 TCGCATTGCGATAGTAAGAT
1 TCGCATTGCGATAGTAAGAT
*
1670244 TCGCATTGCAATAGTAAGAT
1 TCGCATTGCGATAGTAAGAT
1670264 TCGCATTGCGAT
1 TCGCATTGCGAT
1670276 TTACGTATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTAAGAT
Found at i:1670285 original size:20 final size:21
Alignment explanation
Indices: 1670262--1670478 Score: 137
Period size: 20 Copynumber: 10.6 Consensus size: 21
1670252 CAATAGTAAG
1670262 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTA
* * *
1670282 ATTCGCAATGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTA
1670303 ATTCGCATTGCGATTTAC-TA
1 ATTCGCATTGCGATTTACGTA
1670323 ATTCG-AGTTGCGATTTACGT-
1 ATTCGCA-TTGCGATTTACGTA
* * *
1670343 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGATTTACGTA
* ** *
1670364 AATCGCAACGCGA-ATACGTA
1 ATTCGCATTGCGATTTACGTA
* * * * *
1670384 AATCGCAATGCGAATTAGGAA
1 ATTCGCATTGCGATTTACGTA
* * *
1670405 AATCGTATTGTGA--TA-GTCA
1 ATTCGCATTGCGATTTACGT-A
* * **
1670424 GTATCGCATTGCGATTTTCCAA
1 AT-TCGCATTGCGATTTACGTA
*
1670446 ATTCGCATTGCGATTTAC-TT
1 ATTCGCATTGCGATTTACGTA
1670466 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1670479 ATTAGGAAAA
Statistics
Matches: 153, Mismatches: 33, Indels: 22
0.74 0.16 0.11
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 88 0.58
21 57 0.37
22 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACGTA
Found at i:1670315 original size:41 final size:40
Alignment explanation
Indices: 1670262--1670355 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 40
1670252 CAATAGTAAG
*
1670262 ATTCGCATTGCGATTTACGT-ATTCGCA-ATGCGATTTTCCT
1 ATTCGCATTGCGATTTAC-TAATTCG-AGATGCGATTTACCT
* *
1670302 AATTCGCATTGCGATTTACTAATTCGAGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACTAATTCGAGATGCGATTTACCT
1670343 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1670356 ATTATGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
40 15 0.31
41 33 0.69
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACTAATTCGAGATGCGATTTACCT
Found at i:1670493 original size:41 final size:40
Alignment explanation
Indices: 1670330--1670493 Score: 123
Period size: 41 Copynumber: 4.0 Consensus size: 40
1670320 CTAATTCGAG
* *
1670330 TTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGCA
1 TTGCGA-TTACTTATTCGCATTGCGAATTAGGAAAATCGCA
** * * * * *
1670371 ACGCGAATACGTAAATCGCAATGCGAATTAGGAAAATCGTA
1 TTGCGATTAC-TTATTCGCATTGCGAATTAGGAAAATCGCA
* * * * *** *
1670412 TTGTGA-TAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATTACTTA-T-TCGCATTGCGAATTAGGAAAATCGCA
1670453 TTGCGATTTACTTATTCGCATTGCGAATTAGGAAAATCGCA
1 TTGCGA-TTACTTATTCGCATTGCGAATTAGGAAAATCGCA
1670494 ACGCGAAATT
Statistics
Matches: 88, Mismatches: 30, Indels: 10
0.69 0.23 0.08
Matches are distributed among these distances:
39 2 0.02
40 5 0.06
41 76 0.86
42 1 0.01
43 4 0.05
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCGATTACTTATTCGCATTGCGAATTAGGAAAATCGCA
Found at i:1670520 original size:21 final size:22
Alignment explanation
Indices: 1670468--1670520 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1670458 ATTTACTTAT
1670468 TCGCATTGCG-AATTAGGAAAA
1 TCGCATTGCGAAATTAGGAAAA
**
1670489 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTAGGAAAA
1670510 TCGCATTGCGA
1 TCGCATTGCGA
1670521 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTAGGAAAA
Found at i:1670559 original size:123 final size:123
Alignment explanation
Indices: 1670307--1670561 Score: 270
Period size: 123 Copynumber: 2.1 Consensus size: 123
1670297 TTCCTAATTC
* * *
1670307 GCATTGCGA-TTTACTAATTCGAGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGCA
1 GCATTGCGATTTTCCAAATTCGAGTTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCGCA
* * * * * **
1670371 ACGCGAATACGTAAATCGCAATGCGAATTAGGAAAATCGTATTGTGATAGTCAGTATC
66 ACGCGAATACGAAAATCGCAATGCGAATTAGCAAAATCGCATTGCGATAGTCAGGAAA
*
1670429 GCATTGCGATTTTCCAAATTCGCA-TTGCGATTTACTTATTCGCATTGCGAATTAGGAAAATCGC
1 GCATTGCGATTTTCCAAATTCG-AGTTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCGC
** * * * *
1670493 AACGCGAAATTGGAAAATCGCATTGCG-A-TAGTCATAATCGCGTTGCGA-A-TCTGGAAA
65 AACGCG-AATACGAAAATCGCAATGCGAATTAG-CAAAATCGCATTGCGATAGTCAGGAAA
1670550 GCGATTTGCGAT
1 GC-A-TTGCGAT
1670562 AATGGAGATC
Statistics
Matches: 110, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
121 6 0.05
122 14 0.13
123 73 0.66
124 17 0.15
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (123 bp):
GCATTGCGATTTTCCAAATTCGAGTTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCGCA
ACGCGAATACGAAAATCGCAATGCGAATTAGCAAAATCGCATTGCGATAGTCAGGAAA
Found at i:1678898 original size:24 final size:24
Alignment explanation
Indices: 1678871--1678937 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
1678861 AGCTCAAAAA
*
1678871 TCGAGATTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
*
1678895 TCGAGCTTCAATCGAGCTGGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
*
1678919 TCGAGCCTCAATCGAGCTC
1 TCGAGCTTCAATCGAGCTC
1678938 TTGGATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.24
Consensus pattern (24 bp):
TCGAGCTTCAATCGAGCTCGAGTC
Found at i:1686653 original size:17 final size:17
Alignment explanation
Indices: 1686617--1686655 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1686607 ATTTTAACAA
**
1686617 AAAATATTATTATTGGG
1 AAAATATTATTATCAGG
*
1686634 AAAATATTATTATCATG
1 AAAATATTATTATCAGG
1686651 AAAAT
1 AAAAT
1686656 CTTTTCCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (17 bp):
AAAATATTATTATCAGG
Found at i:1686809 original size:6 final size:6
Alignment explanation
Indices: 1686793--1686852 Score: 102
Period size: 6 Copynumber: 10.0 Consensus size: 6
1686783 TATGAATAAT
*
1686793 TTTTTA ATTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
1686841 ATTTTA TTTTTA
1 TTTTTA TTTTTA
1686853 AGAAACACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:1690230 original size:19 final size:18
Alignment explanation
Indices: 1690197--1690235 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1690187 AATAAAATTA
*
1690197 TTAGAATGTGCTATTACTC
1 TTAGAATGTGATATTA-TC
*
1690216 TTAGAATGTTATATTATC
1 TTAGAATGTGATATTATC
1690234 TT
1 TT
1690236 GTTTCATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (18 bp):
TTAGAATGTGATATTATC
Found at i:1691054 original size:17 final size:17
Alignment explanation
Indices: 1691032--1691066 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1691022 TGATATTCTA
1691032 AATAATTAT-ATTTTTAC
1 AATAA-TATCATTTTTAC
1691049 AATAATATCATTTTTAC
1 AATAATATCATTTTTAC
1691066 A
1 A
1691067 TCGTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
AATAATATCATTTTTAC
Found at i:1691260 original size:238 final size:243
Alignment explanation
Indices: 1690887--1691364 Score: 657
Period size: 238 Copynumber: 2.0 Consensus size: 243
1690877 TTAGATTTTT
* * * *
1690887 AAATAATTTTCATAAATATCATGTTTATTTATATAAAATATAATATAATAAAAAAAATAATATTG
1 AAATAATTCTAATAAATATCATATTTATTTATATAAAATATAATATAATAAAAAAAATAATAGTG
** * * *
1690952 CAGCCTCGAGTGAACAAAGAAATTAATTTTTCAATATATAAGATCCATTTTTTAATAACTCAAAG
66 -AGCCTCGAAAGAACAAAGAAATTAACTTTTCAATACATAAGATACATTTTTTAATAACTCAAAG
*
1691017 ATAGATGA-TATTCTAAATAATTATA-TTTTTACAATAATATCATTTT-TACATCGTAAAATTAT
130 ATAGAT-ATTATT-TAAATAATTATATTTTTTACAATAATATCATTTTCTACATCATAAAATTAT
* *
1691079 AGATGGTTAATATATTAAATATTAAAAATAT-AAATAATTTTAATTACTCA
193 AAATGATTAATATATTAAATATTAAAAATATAAAATAATTTTAATTACTCA
*
1691129 AAATAATTCTAATAAATATCATATTTATTTATATAAAATATAATATAAT-ATAAAAATAATAGTG
1 AAATAATTCTAATAAATATCATATTTATTTATATAAAATATAATATAATAAAAAAAATAATAGTG
* * * * * * *
1691193 -GGCTCGAAA-AGACAAATATATT-ACTTTTCAATGCCTAAGATATATTTTTTAATTACTCAAAG
66 AGCCTCGAAAGA-ACAAAGAAATTAACTTTTCAATACATAAGATACATTTTTTAATAACTCAAAG
* * *
1691255 ATAGATATTATTTAAATAATTATATTTTTTACAATAATATCATTTTCTGCCTCATAAATTTATAA
130 ATAGATATTATTTAAATAATTATATTTTTTACAATAATATCATTTTCTACATCATAAAATTATAA
1691320 ATGATTAATATATTAAATATTAAAAATATAAAATAATTTTAATTA
195 ATGATTAATATATTAAATATTAAAAATATAAAATAATTTTAATTA
1691365 TTTAAATTTA
Statistics
Matches: 208, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
237 13 0.06
238 65 0.31
239 56 0.27
240 15 0.07
241 13 0.06
242 46 0.22
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (243 bp):
AAATAATTCTAATAAATATCATATTTATTTATATAAAATATAATATAATAAAAAAAATAATAGTG
AGCCTCGAAAGAACAAAGAAATTAACTTTTCAATACATAAGATACATTTTTTAATAACTCAAAGA
TAGATATTATTTAAATAATTATATTTTTTACAATAATATCATTTTCTACATCATAAAATTATAAA
TGATTAATATATTAAATATTAAAAATATAAAATAATTTTAATTACTCA
Found at i:1691279 original size:17 final size:18
Alignment explanation
Indices: 1691259--1691292 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1691249 TCAAAGATAG
1691259 ATATTATTTA-AATAATT
1 ATATTATTTACAATAATT
*
1691276 ATATTTTTTACAATAAT
1 ATATTATTTACAATAAT
1691293 ATCATTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATTTACAATAATT
Found at i:1692081 original size:22 final size:22
Alignment explanation
Indices: 1692041--1692083 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1692031 TTTTATTTTT
*
1692041 TTATTTTTTAATAATAAAAATA
1 TTATTTTTCAATAATAAAAATA
*
1692063 TTATTTTTCAATGAAAAAAAA
1 TTATTTTTCAAT-AATAAAAA
1692084 AACTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
TTATTTTTCAATAATAAAAATA
Found at i:1693700 original size:33 final size:33
Alignment explanation
Indices: 1693655--1693719 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
1693645 CCTTTACAAC
*
1693655 TCCCTAG-TTTTTACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
* *
1693687 TCCCATAGCTTTTACACGGGCTAAGCTAGAACC
1 TCCC-TAGCTTTTA-ACGGGATAAACTAGAACC
1693720 AAAACCCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.15
33 3 0.11
34 4 0.15
35 16 0.59
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (33 bp):
TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
Found at i:1694205 original size:20 final size:20
Alignment explanation
Indices: 1694182--1694220 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1694172 GATGCATCGA
*
1694182 TGCACAGTGTATGGATACAC
1 TGCACAGTGCATGGATACAC
*
1694202 TGCAGAGTGCATGGATACA
1 TGCACAGTGCATGGATACA
1694221 ACACATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (20 bp):
TGCACAGTGCATGGATACAC
Found at i:1694415 original size:21 final size:19
Alignment explanation
Indices: 1694391--1694448 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
1694381 CTGTATAATG
1694391 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
*
1694410 ACAAAATGATATTAATTGTT-
1 A-AAAA-GATATCAATTGTTA
1694430 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
1694449 CCAATTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.34
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:1696017 original size:20 final size:20
Alignment explanation
Indices: 1695963--1696018 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1695953 ATTGAAGTAT
*
1695963 GGAGGCTTGTCGATTGGTAG
1 GGAGGCTTGTCGGTTGGTAG
*
1695983 GGAGGCTTGTTGGTTGGTAG
1 GGAGGCTTGTCGGTTGGTAG
1696003 GGAGGCTTGTCGGTTG
1 GGAGGCTTGTCGGTTG
1696019 AAACGAGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (20 bp):
GGAGGCTTGTCGGTTGGTAG
Found at i:1701110 original size:17 final size:17
Alignment explanation
Indices: 1701090--1701122 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1701080 ATATTTAATT
*
1701090 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
1701107 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
1701123 TATGGTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:1702672 original size:13 final size:13
Alignment explanation
Indices: 1702654--1702705 Score: 77
Period size: 13 Copynumber: 3.8 Consensus size: 13
1702644 AAGAGTTGGG
1702654 AGAAGAAGGATGA
1 AGAAGAAGGATGA
1702667 AGAAGAAGGATGA
1 AGAAGAAGGATGA
*
1702680 AGAAGAAGAGTTTGA
1 AGAAGAAG-G-ATGA
1702695 AGAAGAAGGAT
1 AGAAGAAGGAT
1702706 AAAAAGGCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 22 0.63
14 2 0.06
15 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.37, T:0.12
Consensus pattern (13 bp):
AGAAGAAGGATGA
Found at i:1707836 original size:21 final size:21
Alignment explanation
Indices: 1707787--1707841 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1707777 CCGAAATAAT
* *
1707787 AAAAAATATTATTTTTATTCAA
1 AAAAAATAATA-TTTAATTCAA
* *
1707809 TAAAAATAATATTTAATTGAA
1 AAAAAATAATATTTAATTCAA
1707830 AAAAAATAATAT
1 AAAAAATAATAT
1707842 ATAGAGGGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAAATAATATTTAATTCAA
Found at i:1712414 original size:21 final size:21
Alignment explanation
Indices: 1712381--1712420 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1712371 ACGTTAAAAG
*
1712381 ATTAACATATTAGGTAACGGA
1 ATTAACATATTAGATAACGGA
* *
1712402 ATTAATATTTTAGATAACG
1 ATTAACATATTAGATAACG
1712421 CTTTATCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (21 bp):
ATTAACATATTAGATAACGGA
Found at i:1747205 original size:60 final size:60
Alignment explanation
Indices: 1747140--1747276 Score: 175
Period size: 60 Copynumber: 2.3 Consensus size: 60
1747130 AACATAATGA
* * *
1747140 ATAATCAGGTGACCATTTTGTAACTTTTAATAGTCGAATGACTTAACAAAACAATATTTT
1 ATAATCAGGTGACCATTTTGTAACTTTTAATAGTCGAAGGACTTAACAAAACAACATTCT
** * * *
1747200 ATAATCAAATGATCATTTTGTAACTTTTAATAGTCGAGGGACTTAATAAAACAACATTCT
1 ATAATCAGGTGACCATTTTGTAACTTTTAATAGTCGAAGGACTTAACAAAACAACATTCT
* * *
1747260 ATAGTCGGGAGACCATT
1 ATAATCAGGTGACCATT
1747277 AGTGTAATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (60 bp):
ATAATCAGGTGACCATTTTGTAACTTTTAATAGTCGAAGGACTTAACAAAACAACATTCT
Found at i:1748676 original size:9 final size:9
Alignment explanation
Indices: 1748662--1748686 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1748652 TTAGATTAAA
1748662 TTTAATTTT
1 TTTAATTTT
1748671 TTTAATTTT
1 TTTAATTTT
1748680 TTTAATT
1 TTTAATT
1748687 AAATACCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTAATTTT
Found at i:1753841 original size:25 final size:26
Alignment explanation
Indices: 1753813--1753863 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
1753803 ATCATGTTGC
*
1753813 CATTATTGGGCACTAATAATG-GTGT
1 CATTATTGGGCACCAATAATGCGTGT
*
1753838 CATTATTGTGCACCAATAATGCGTGT
1 CATTATTGGGCACCAATAATGCGTGT
1753864 AAGGGCGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (26 bp):
CATTATTGGGCACCAATAATGCGTGT
Found at i:1754217 original size:116 final size:115
Alignment explanation
Indices: 1754044--1754256 Score: 313
Period size: 116 Copynumber: 1.8 Consensus size: 115
1754034 TGTACATTTT
*
1754044 ATTTTTTTTATTTTAAATATAAATTAATTAGATTATTTAGTTTGATTTTACATATTAAATTGTAT
1 ATTTTTTTTATTTTAAATATAAATTAATTAGACTATTTAGTTTGATTTTACATATTAAATTGTAT
* *
1754109 TTGTGTGGTTTGGTAAGTTTAATTTAAATTTTCGTGTAATATTTTGGGTA
66 TTGAGTAGTTTGGTAAGTTTAATTTAAATTTTCGTGTAATATTTTGGGTA
* * *
1754159 ATTTTTATGTTATTTTAAATA-ATAATT-ATTAGACTATTTATTTTGATTTTAGATATTAAGTTG
1 ATTTTT-T-TTATTTTAAATATA-AATTAATTAGACTATTTAGTTTGATTTTACATATTAAATTG
* *
1754222 TATTTGAGTAGTTTGGTAAGTTTAGTTTAATTTTT
63 TATTTGAGTAGTTTGGTAAGTTTAATTTAAATTTT
1754257 TTTATTGAGT
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
115 6 0.07
116 65 0.75
117 16 0.18
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (115 bp):
ATTTTTTTTATTTTAAATATAAATTAATTAGACTATTTAGTTTGATTTTACATATTAAATTGTAT
TTGAGTAGTTTGGTAAGTTTAATTTAAATTTTCGTGTAATATTTTGGGTA
Found at i:1756604 original size:27 final size:27
Alignment explanation
Indices: 1756572--1756644 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
1756562 ATTAATATCC
1756572 ATCACATTCATTCAAATATTGATATTA
1 ATCACATTCATTCAAATATTGATATTA
* *
1756599 ATCACATTAATTCAACTATTGATATTA
1 ATCACATTCATTCAAATATTGATATTA
*
1756626 ATCACATTCATTAAAATAT
1 ATCACATTCATTCAAATAT
1756645 AGCGTCAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (27 bp):
ATCACATTCATTCAAATATTGATATTA
Found at i:1759579 original size:29 final size:31
Alignment explanation
Indices: 1759536--1759594 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1759526 TTAAAGTTTC
1759536 AAAAATGTAAA-ATATTAACAATATTTTTTT
1 AAAAATGTAAATATATTAACAATATTTTTTT
1759566 AAAAATGTAAATATATTAACAATATTTTT
1 AAAAATGTAAATATATTAACAATATTTTT
1759595 AACATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (31 bp):
AAAAATGTAAATATATTAACAATATTTTTTT
Found at i:1759596 original size:29 final size:29
Alignment explanation
Indices: 1759536--1759594 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
1759526 TTAAAGTTTC
1759536 AAAAATGTAAAATATTAACAATATTTTTTT
1 AAAAATGTAAAATATTAACAATA-TTTTTT
1759566 AAAAATGTAAATATATTAACAATATTTTT
1 AAAAATGTAAA-ATATTAACAATATTTTT
1759595 AACATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (29 bp):
AAAAATGTAAAATATTAACAATATTTTTT
Found at i:1760061 original size:22 final size:21
Alignment explanation
Indices: 1760036--1760087 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 21
1760026 ATGGTGCCAT
1760036 TATTTTTT-GTCATTATAATAAA
1 TATTTTTTCGTCATTATAAT--A
1760058 TATTATTTTTCGTCATTATAATA
1 TA-T-TTTTTCGTCATTATAATA
1760081 TATTTTT
1 TATTTTT
1760088 AACATTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 4 0.15
22 3 0.11
23 4 0.15
24 5 0.19
25 11 0.41
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (21 bp):
TATTTTTTCGTCATTATAATA
Found at i:1760829 original size:39 final size:38
Alignment explanation
Indices: 1760724--1760829 Score: 88
Period size: 38 Copynumber: 2.8 Consensus size: 38
1760714 CCACCCTAGA
* * *
1760724 CTGAAGATGCCAGGTAAGCTTGGAGTCTTCTTATTTGC
1 CTGAAGACGCCAGGTAAGCTTGGAGTCTTCCTAGTTGC
* * ** * * *
1760762 CTGAAGACGTC-GTGCACTCCTGGTGTCTTCCTGGTTGAC
1 CTGAAGACGCCAG-GTAAGCTTGGAGTCTTCCTAGTTG-C
*
1760801 TTGAAGACGCCAGGTAAGCTTGGAGTCTT
1 CTGAAGACGCCAGGTAAGCTTGGAGTCTT
1760830 TGGCTCGGTA
Statistics
Matches: 48, Mismatches: 17, Indels: 5
0.69 0.24 0.07
Matches are distributed among these distances:
37 1 0.02
38 25 0.52
39 21 0.44
40 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (38 bp):
CTGAAGACGCCAGGTAAGCTTGGAGTCTTCCTAGTTGC
Done.