Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_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: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1459515 original size:3 final size:3
Alignment explanation
Indices: 1459495--1459587 Score: 87
Period size: 3 Copynumber: 31.0 Consensus size: 3
1459485 TGAAGCTGAC
* * * * * ** *
1459495 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * *
1459543 GAC GAC GAT GAT GAT GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1459588 CCAAACAAGT
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.35, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:1459587 original size:12 final size:12
Alignment explanation
Indices: 1459483--1459583 Score: 94
Period size: 12 Copynumber: 8.4 Consensus size: 12
1459473 GGTCGCAGAA
*
1459483 GATGAAGCTGAC
1 GATGAAGATGAC
1459495 GATGAAGATGAC
1 GATGAAGATGAC
*
1459507 GATGATGATGAC
1 GATGAAGATGAC
* *
1459519 GATGAAGCTGGC
1 GATGAAGATGAC
*
1459531 GATGAAGATGAT
1 GATGAAGATGAC
* * *
1459543 GACGACGATGAT
1 GATGAAGATGAC
* *
1459555 GATGATGATGAT
1 GATGAAGATGAC
* *
1459567 GATGATGATGAA
1 GATGAAGATGAC
1459579 GATGA
1 GATGA
1459584 TGATCCAAAC
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 76 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1459587 original size:18 final size:18
Alignment explanation
Indices: 1459480--1459583 Score: 100
Period size: 18 Copynumber: 5.8 Consensus size: 18
1459470 AGCGGTCGCA
*
1459480 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
1459498 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
1459516 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* *
1459534 GAAGATGATGACGACGAT
1 GAAGATGAAGATGACGAT
* * *
1459552 GATGATGATGATGATGAT
1 GAAGATGAAGATGACGAT
*
1459570 GATGATGAAGATGA
1 GAAGATGAAGATGA
1459584 TGATCCAAAC
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:1461361 original size:183 final size:182
Alignment explanation
Indices: 1461051--1461536 Score: 846
Period size: 183 Copynumber: 2.7 Consensus size: 182
1461041 TTCAACATAT
* *
1461051 TATAAATATACCGGTTTTTTGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
* * *
1461116 TCGGTACTTTATATCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTATCGACATTT
*
1461181 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
1461234 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
*
1461299 TCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTATCGACATTT
*
1461364 ACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
* *
1461417 TATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
*
1461482 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTTGATACCATTTAAAAAAGT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGT
1461537 GTCGGTAATT
Statistics
Matches: 289, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
183 285 0.99
184 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (182 bp):
TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTATCGACATTTA
CACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
Found at i:1464040 original size:25 final size:25
Alignment explanation
Indices: 1464006--1464070 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1463996 TTATCATTAA
1464006 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
1464031 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
1464056 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
1464071 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:1464430 original size:20 final size:22
Alignment explanation
Indices: 1464405--1464480 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
1464395 ACTTTCAATA
*
1464405 TAATAGGTA-AAC-ATATGATG
1 TAATAGGTAGAACTATATAATG
*
1464425 TAATAGGTAGCACTTATATAATG
1 TAATAGGTAGAAC-TATATAATG
**
1464448 TAATAGGTATCG-TTTATATAATG
1 TAATAGGTA--GAACTATATAATG
1464471 TAATAGGTAG
1 TAATAGGTAG
1464481 TGGTTATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.19
21 3 0.06
23 34 0.72
25 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (22 bp):
TAATAGGTAGAACTATATAATG
Found at i:1464448 original size:23 final size:23
Alignment explanation
Indices: 1464417--1464480 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1464407 ATAGGTAAAC
*
1464417 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCACTT
* **
1464440 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCACTT
1464463 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
1464481 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCACTT
Found at i:1464487 original size:23 final size:23
Alignment explanation
Indices: 1464417--1464489 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1464407 ATAGGTAAAC
* **
1464417 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGTGCTT
*
1464440 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
1464463 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
1464486 ATAT
1 ATAT
1464490 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:1464934 original size:18 final size:18
Alignment explanation
Indices: 1464913--1464949 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1464903 GTAATTGGAG
1464913 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1464931 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1464949 T
1 T
1464950 ATATTTCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1465258 original size:34 final size:34
Alignment explanation
Indices: 1465220--1465285 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1465210 AAATCCAAAG
*
1465220 CTCATATGGTGCCAAGCAAAAGGAAATCAAAAAT
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
1465254 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
1465286 TCTACAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (34 bp):
CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
Found at i:1465692 original size:22 final size:22
Alignment explanation
Indices: 1465644--1465692 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1465634 AAATTACATA
*
1465644 ACTTTTAAAAAAAAGTATCGAT
1 ACTTTTAAAAAAAAGTATCGAC
* * * *
1465666 TCTTTTTATAAAAAGTATGGAC
1 ACTTTTAAAAAAAAGTATCGAC
1465688 ACTTT
1 ACTTT
1465693 CAATATAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ACTTTTAAAAAAAAGTATCGAC
Found at i:1465741 original size:23 final size:23
Alignment explanation
Indices: 1465710--1465782 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1465700 ATAGGTAAAC
*
1465710 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1465733 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1465756 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1465779 ATAT
1 ATAT
1465783 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1465987 original size:30 final size:29
Alignment explanation
Indices: 1465928--1465994 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1465918 GTTACGATAT
* *
1465928 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
1465958 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
1465988 ATTTTTT
1 ATATTTT
1465995 GTGCAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:1470879 original size:28 final size:28
Alignment explanation
Indices: 1470844--1470920 Score: 145
Period size: 28 Copynumber: 2.8 Consensus size: 28
1470834 GTTTATAATC
1470844 ATTTTATCACATCAAATATTGGTTCATT
1 ATTTTATCACATCAAATATTGGTTCATT
*
1470872 ATTTTATCATATCAAATATTGGTTCATT
1 ATTTTATCACATCAAATATTGGTTCATT
1470900 ATTTTATCACATCAAATATTG
1 ATTTTATCACATCAAATATTG
1470921 ATTCTTCATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (28 bp):
ATTTTATCACATCAAATATTGGTTCATT
Found at i:1482881 original size:87 final size:86
Alignment explanation
Indices: 1482738--1482930 Score: 271
Period size: 87 Copynumber: 2.2 Consensus size: 86
1482728 TAATATTATT
* * * * *
1482738 TTTTATTCATTCTTACGAATGAAACCAAGCGACGGCGCGACATTGTAACTGCGTAAAAGCAAAAA
1 TTTTATTCATTCTTATGAATAAAACCAAGCGACGACACGACATTGTAACTACGTAAAAGCAAAAA
1482803 CTCAAATCACATTTTATTTTTA
66 -TCAAATCACATTTTATTTTTA
* *
1482825 TTTTATTCATTCTTATGAATAAAACCAAGCGA-TACTACGACATTGTAACTATGTAAAAGCAAAA
1 TTTTATTCATTCTTATGAATAAAACCAAGCGACGAC-ACGACATTGTAACTACGTAAAAGCAAAA
**
1482889 ATCCGATCACATTTTATTTTTA
65 ATCAAATCACATTTTATTTTTA
*
1482911 TTTTATTCGTTCTTATGAAT
1 TTTTATTCATTCTTATGAAT
1482931 CCTGCTCCAA
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
86 39 0.41
87 56 0.59
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (86 bp):
TTTTATTCATTCTTATGAATAAAACCAAGCGACGACACGACATTGTAACTACGTAAAAGCAAAAA
TCAAATCACATTTTATTTTTA
Found at i:1486010 original size:18 final size:18
Alignment explanation
Indices: 1485987--1486036 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
1485977 AGTAAATATT
1485987 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1486005 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
1486023 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
1486037 GCTAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1486642 original size:19 final size:19
Alignment explanation
Indices: 1486576--1486672 Score: 90
Period size: 19 Copynumber: 4.8 Consensus size: 19
1486566 TTATTTAAAG
*
1486576 TAGGTATCGATA-CCCTCT
1 TAGGTATCGATACCCCCCT
1486594 ATAGGGTATCGATACATCCCTCAACT
1 -TA-GGTATCGATAC--CCC-C--CT
*
1486620 TAGGTATCGGTACCCCCCT
1 TAGGTATCGATACCCCCCT
*
1486639 TAGGTATCGATA-CCCCTT
1 TAGGTATCGATACCCCCCT
1486657 TAGGTATCGATACCCC
1 TAGGTATCGATACCCC
1486673 AATTGTATTC
Statistics
Matches: 66, Mismatches: 4, Indels: 16
0.77 0.05 0.19
Matches are distributed among these distances:
18 17 0.26
19 18 0.27
20 10 0.15
21 1 0.02
22 3 0.05
23 3 0.05
24 10 0.15
25 2 0.03
26 2 0.03
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.29
Consensus pattern (19 bp):
TAGGTATCGATACCCCCCT
Found at i:1486659 original size:18 final size:18
Alignment explanation
Indices: 1486576--1486672 Score: 86
Period size: 18 Copynumber: 4.9 Consensus size: 18
1486566 TTATTTAAAG
*
1486576 TAGGTATCGATACCCTCTA
1 TAGGTATCGATACCC-CTT
1486595 TAGGGTATCGATACATCCCTCAACT
1 TA-GGTATCGATAC--CCCT----T
* *
1486620 TAGGTATCGGTACCCCCCT
1 TAGGTATCGATA-CCCCTT
1486639 TAGGTATCGATACCCCTT
1 TAGGTATCGATACCCCTT
1486657 TAGGTATCGATACCCC
1 TAGGTATCGATACCCC
1486673 AATTGTATTC
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
18 21 0.32
19 14 0.22
20 11 0.17
21 2 0.03
22 2 0.03
23 3 0.05
24 9 0.14
25 3 0.05
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.29
Consensus pattern (18 bp):
TAGGTATCGATACCCCTT
Found at i:1492272 original size:23 final size:23
Alignment explanation
Indices: 1492246--1492314 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1492236 CACCACAGCT
* *
1492246 CGTATAATTGCACCGAAGTGTCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1492269 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1492292 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1492315 TATAATAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1492501 original size:103 final size:99
Alignment explanation
Indices: 1492330--1492543 Score: 356
Period size: 103 Copynumber: 2.1 Consensus size: 99
1492320 TAATGTCCAT
* *
1492330 AAGGACCACATATAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1492395 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACAC-TGTTCCAAAG-ATAC--ATATGTCCCG
* *
1492433 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1492498 GACTTCACACTGTTCCAAAGATACATATGTCCCG
66 GACTTCACACTGTTCCAAAGATACATATGTCCCG
1492532 AAGGACCACATA
1 AAGGACCACATA
1492544 GACCCTCGGC
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
99 22 0.21
101 4 0.04
102 10 0.09
103 71 0.66
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (99 bp):
AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACTGTTCCAAAGATACATATGTCCCG
Found at i:1492575 original size:33 final size:33
Alignment explanation
Indices: 1492533--1492599 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1492523 TATGTCCCGA
1492533 AGGACCACATAGACCCTCGGCTCTTGGCATGCC
1 AGGACCACATAGACCCTCGGCTCTTGGCATGCC
1492566 AGGACCACATAGACCCTCGGCTCTTGGCATGCC
1 AGGACCACATAGACCCTCGGCTCTTGGCATGCC
1492599 A
1 A
1492600 ACTATACCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (33 bp):
AGGACCACATAGACCCTCGGCTCTTGGCATGCC
Found at i:1496687 original size:13 final size:13
Alignment explanation
Indices: 1496669--1496707 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1496659 AATGACGTTC
1496669 AATGCGCGTCATA
1 AATGCGCGTCATA
*
1496682 AATGCGCATCATA
1 AATGCGCGTCATA
1496695 AATGCGCGTCATA
1 AATGCGCGTCATA
1496708 GATTTATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:1498353 original size:24 final size:25
Alignment explanation
Indices: 1498306--1498353 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1498296 GGATTATGTA
* *
1498306 TGATTTGTTTTTTTATTATTAGATC
1 TGATTTCTTATTTTATTATTAGATC
1498331 TGATTTCTTATTTT-TTATTAGAT
1 TGATTTCTTATTTTATTATTAGAT
1498354 TTGGTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.21, C:0.04, G:0.10, T:0.65
Consensus pattern (25 bp):
TGATTTCTTATTTTATTATTAGATC
Found at i:1498598 original size:3 final size:3
Alignment explanation
Indices: 1498592--1498639 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
1498582 GTAGTAGTAG
1498592 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
1498638 TA
1 TA
1498640 TAGCACGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1500189 original size:399 final size:399
Alignment explanation
Indices: 1499451--1500249 Score: 1562
Period size: 399 Copynumber: 2.0 Consensus size: 399
1499441 TTGCTTACAC
1499451 TTTTATTGGGGGGGGGGGGCGACTCACCTAACGGTTTAATATACTTCTTTAGAAATCCAAGTCAT
1 TTTTATTGGGGGGGGGGGGCGACTCACCTAACGGTTTAATATACTTCTTTAGAAATCCAAGTCAT
1499516 CACCAAAACGTTGGTGAGCAAGGACTTTTAAATATTATTTTCGATAATATATTAATTATAAAAGA
66 CACCAAAACGTTGGTGAGCAAGGACTTTTAAATATTATTTTCGATAATATATTAATTATAAAAGA
1499581 AGTTGTTTACAAATGTCCATAGATGCCTATACCCTTAATAGGTCAATTCATTTTTTGTGTGAAAT
131 AGTTGTTTACAAATGTCCATAGATGCCTATACCCTTAATAGGTCAATTCATTTTTTGTGTGAAAT
1499646 ATACATATTGATTTTTCATTCAATTAAATATCGAGAGAATGTCAACCTCAGTCATGATAGCTTAG
196 ATACATATTGATTTTTCATTCAATTAAATATCGAGAGAATGTCAACCTCAGTCATGATAGCTTAG
* *
1499711 TGTACACAAGGTTGGTATTCTTGAACCCGCTTTATCGAATATACCTAATATTACATTCTACGAAG
261 TGTACACAAGGCTGGTATTCTTGAACCCGCTTTATCGAATATACCTAAGATTACATTCTACGAAG
1499776 TAGGTTTTGCAGTATCCAGAAAATGGCCAATCTCAGACGGATCATGTTTGAGGATGTCGACGACA
326 TAGGTTTTGCAGTATCCAGAAAATGGCCAATCTCAGACGGATCATGTTTGAGGATGTCGACGACA
1499841 CATAAAGAG
391 CATAAAGAG
1499850 TTTTATTGGGGGGGGGGGGCGACTCACCTAACGGTTTAATATACTTCTTTAGAAATCCAAGTCAT
1 TTTTATTGGGGGGGGGGGGCGACTCACCTAACGGTTTAATATACTTCTTTAGAAATCCAAGTCAT
1499915 CACCAAAACGTTGGTGAGCAAGGACTTTTAAATATTATTTTCGATAATATATTAATTATAAAAGA
66 CACCAAAACGTTGGTGAGCAAGGACTTTTAAATATTATTTTCGATAATATATTAATTATAAAAGA
1499980 AGTTGTTTACAAATGTCCATAGATGCCTATACCCTTAATAGGTCAATTCATTTTTTGTGTGAAAT
131 AGTTGTTTACAAATGTCCATAGATGCCTATACCCTTAATAGGTCAATTCATTTTTTGTGTGAAAT
1500045 ATACATATTGATTTTTCATTCAATTAAATATCGAGAGAATGTCAACCTCAGTCATGATAGCTTAG
196 ATACATATTGATTTTTCATTCAATTAAATATCGAGAGAATGTCAACCTCAGTCATGATAGCTTAG
* *
1500110 TGTACACAAGGCTGGTATTCTTGAACCCGCTTTATCGAGTATACCTAAGATTGCATTCTACGAAG
261 TGTACACAAGGCTGGTATTCTTGAACCCGCTTTATCGAATATACCTAAGATTACATTCTACGAAG
1500175 TAGGTTTTGCAGTATCCAGAAAATGGCCAATCTCAGACGGATCATGTTTGAGGATGTCGACGACA
326 TAGGTTTTGCAGTATCCAGAAAATGGCCAATCTCAGACGGATCATGTTTGAGGATGTCGACGACA
1500240 CATAAAGAG
391 CATAAAGAG
1500249 T
1 T
1500250 CTCATTCGAT
Statistics
Matches: 396, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
399 396 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (399 bp):
TTTTATTGGGGGGGGGGGGCGACTCACCTAACGGTTTAATATACTTCTTTAGAAATCCAAGTCAT
CACCAAAACGTTGGTGAGCAAGGACTTTTAAATATTATTTTCGATAATATATTAATTATAAAAGA
AGTTGTTTACAAATGTCCATAGATGCCTATACCCTTAATAGGTCAATTCATTTTTTGTGTGAAAT
ATACATATTGATTTTTCATTCAATTAAATATCGAGAGAATGTCAACCTCAGTCATGATAGCTTAG
TGTACACAAGGCTGGTATTCTTGAACCCGCTTTATCGAATATACCTAAGATTACATTCTACGAAG
TAGGTTTTGCAGTATCCAGAAAATGGCCAATCTCAGACGGATCATGTTTGAGGATGTCGACGACA
CATAAAGAG
Found at i:1504376 original size:20 final size:20
Alignment explanation
Indices: 1504353--1504400 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1504343 ACACATAAGT
*
1504353 CAAATTCGCAACGCGATTTA
1 CAAATTCGAAACGCGATTTA
* * *
1504373 CAAATTCAAAATGCGATTTC
1 CAAATTCGAAACGCGATTTA
1504393 CAAATTCG
1 CAAATTCG
1504401 TAACACTGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (20 bp):
CAAATTCGAAACGCGATTTA
Found at i:1504447 original size:20 final size:20
Alignment explanation
Indices: 1504418--1504465 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1504408 GAATTTCAAT
1504418 TTCACAACTCGA-TTTCTGAA
1 TTCACAACTCGATTTTC-GAA
*
1504438 TTCGCAACTCGATTTTCGAA
1 TTCACAACTCGATTTTCGAA
1504458 TTCACAAC
1 TTCACAAC
1504466 ACGAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (20 bp):
TTCACAACTCGATTTTCGAA
Found at i:1504923 original size:18 final size:18
Alignment explanation
Indices: 1504890--1504925 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1504880 AAGCAAAAGG
**
1504890 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
1504908 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1504926 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1505323 original size:64 final size:64
Alignment explanation
Indices: 1505244--1505392 Score: 255
Period size: 64 Copynumber: 2.3 Consensus size: 64
1505234 AATTTAAAAC
1505244 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACA-CATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTT-CATCATCAATTA
***
1505308 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCATCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTCATCATCAATTA
1505372 AACAAATCAACTTTTACAAAT
1 AACAAATCAACTTTTACAAAT
1505393 ATATCAATTT
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
63 2 0.02
64 79 0.98
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTCATCATCAATTA
Found at i:1506765 original size:21 final size:21
Alignment explanation
Indices: 1506736--1506806 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
1506726 GTGAATCGAG
*
1506736 CTCTCGAACGGTTGGAGGGAC
1 CTCTTGAACGGTTGGAGGGAC
* * *
1506757 CTCTTGAAC-GATGACAGGGGC
1 CTCTTGAACGGTTG-GAGGGAC
* *
1506778 CTCTTGAACGGTAGGAGGGTC
1 CTCTTGAACGGTTGGAGGGAC
1506799 CTCTTGAA
1 CTCTTGAA
1506807 TGATGATAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 3 0.08
21 35 0.88
22 2 0.05
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTTGGAGGGAC
Found at i:1506802 original size:42 final size:41
Alignment explanation
Indices: 1506736--1506856 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 41
1506726 GTGAATCGAG
* * * *
1506736 CTCTCGAACGGTTGGAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTAGGAGGG-CCTCTTGAATGATGACAAGGGC
*
1506778 CTCTTGAACGGTAGGAGGGTCCTCTTGAATGATGATAAGGGC
1 CTCTTGAACGGTAGGAGGG-CCTCTTGAATGATGACAAGGGC
* **
1506820 CTCTTGAACGATAATAGAGGCCTCTTGAATGATGACA
1 CTCTTGAACGGTAGGAG-GGCCTCTTGAATGATGACA
1506857 TGTGAATTGG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 66 0.97
43 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTAGGAGGGCCTCTTGAATGATGACAAGGGC
Found at i:1506822 original size:21 final size:21
Alignment explanation
Indices: 1506751--1506854 Score: 95
Period size: 21 Copynumber: 4.9 Consensus size: 21
1506741 GAACGGTTGG
*
1506751 AGGGACCTCTTGAACGATGACA
1 AGGG-CCTCTTGAACGATGATA
* * **
1506773 GGGGCCTCTTGAACGGT-AGG
1 AGGGCCTCTTGAACGATGATA
*
1506793 AGGGTCCTCTTGAATGATGATA
1 AGGG-CCTCTTGAACGATGATA
*
1506815 AGGGCCTCTTGAACGATAAT-
1 AGGGCCTCTTGAACGATGATA
*
1506835 AGAGGCCTCTTGAATGATGA
1 AG-GGCCTCTTGAACGATGA
1506855 CATGTGAATT
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.09
21 52 0.79
22 8 0.12
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (21 bp):
AGGGCCTCTTGAACGATGATA
Found at i:1507253 original size:21 final size:21
Alignment explanation
Indices: 1507229--1507278 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1507219 ACCATTATCT
* *
1507229 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
* **
1507250 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
1507271 TCACGTAA
1 TCACGTAA
1507279 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:1508977 original size:20 final size:20
Alignment explanation
Indices: 1508954--1509019 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 20
1508944 TCTGAAACTT
1508954 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
*
1508974 AAAATCACAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
* * *
1508993 AAAATCGTAATGCGAAACT-
1 AAAATCGCAACGCGAAAATG
1509012 AAAATCGC
1 AAAATCGC
1509020 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.50, C:0.20, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1508993 original size:19 final size:20
Alignment explanation
Indices: 1508954--1508998 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1508944 TCTGAAACTT
*
1508954 AAAATCGCAACGCGAAAATG
1 AAAATCACAACGCGAAAATG
1508974 AAAATCACAACGCG-AAATG
1 AAAATCACAACGCGAAAATG
1508993 AAAATC
1 AAAATC
1508999 GTAATGCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.53, C:0.20, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCACAACGCGAAAATG
Found at i:1509415 original size:22 final size:22
Alignment explanation
Indices: 1509390--1509463 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 22
1509380 GAGATAGACA
* *
1509390 GATTTCGCCAGATATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
*
1509412 GATTTCGTCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
*
1509434 GATTTCGTCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
*
1509456 GATGTCGC
1 GATTTCGC
1509464 TGTAGAGAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACG
Found at i:1509655 original size:20 final size:20
Alignment explanation
Indices: 1509632--1509681 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1509622 TGACTTATGT
*
1509632 GTTGCGAATTACAGATTCGC
1 GTTGCGAATTACAGATTCAC
*
1509652 GTTGCGATTTACAGATTCAC
1 GTTGCGAATTACAGATTCAC
*
1509672 ATTGCGAATT
1 GTTGCGAATT
1509682 TGGAAACTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTACAGATTCAC
Found at i:1513528 original size:2 final size:2
Alignment explanation
Indices: 1513521--1513555 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1513511 ACTCATGCAT
1513521 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1513556 ACTTAAGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1516460 original size:2 final size:2
Alignment explanation
Indices: 1516453--1516525 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1516443 TAACTACGTT
1516453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1516495 TA TA 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 TA TA T
1516526 TATCAATAGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1521720 original size:14 final size:14
Alignment explanation
Indices: 1521703--1521731 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1521693 GAACATAAGT
1521703 GAACATAAACGAAC
1 GAACATAAACGAAC
1521717 GAACATAAACGAAC
1 GAACATAAACGAAC
1521731 G
1 G
1521732 TTCACGAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.21, G:0.17, T:0.07
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:1521730 original size:24 final size:24
Alignment explanation
Indices: 1521684--1521730 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1521674 AAGTTAAACG
* **
1521684 TAAATGAACGAACATAAGTGAACA
1 TAAACGAACGAACATAAACGAACA
1521708 TAAACGAACGAACATAAACGAAC
1 TAAACGAACGAACATAAACGAAC
1521731 GTTCACGAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.55, C:0.17, G:0.15, T:0.13
Consensus pattern (24 bp):
TAAACGAACGAACATAAACGAACA
Found at i:1523901 original size:21 final size:21
Alignment explanation
Indices: 1523854--1523906 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1523844 AGCTAAAGTT
* * *
1523854 ACTGTAGTAGTGCATCGGTAT
1 ACTGTAGCAGTGCATCAGTAC
*
1523875 ATTGTAGCAGTGCATCAGTAC
1 ACTGTAGCAGTGCATCAGTAC
*
1523896 ACTGTACCAGT
1 ACTGTAGCAGT
1523907 ACATAGGTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCAGTAC
Found at i:1524784 original size:20 final size:20
Alignment explanation
Indices: 1524759--1524804 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1524749 ATAGGATTTA
1524759 TGCATCGATGCATGGTGTGG
1 TGCATCGATGCATGGTGTGG
1524779 TGCATCGATGCATGGTGTGG
1 TGCATCGATGCATGGTGTGG
1524799 TGCATC
1 TGCATC
1524805 AATGTATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.37, T:0.30
Consensus pattern (20 bp):
TGCATCGATGCATGGTGTGG
Found at i:1525202 original size:31 final size:30
Alignment explanation
Indices: 1525153--1525212 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1525143 TTATATAAGC
*
1525153 TATGTGATACAATGATGGAACATGATATGTT
1 TATGTGATACAAGGATGGAA-ATGATATGTT
*
1525184 TATGTGATA-AAGGTATGGAAATTATATGT
1 TATGTGATACAAGG-ATGGAAATGATATGT
1525213 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATACAAGGATGGAAATGATATGTT
Found at i:1525490 original size:23 final size:23
Alignment explanation
Indices: 1525435--1525495 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1525425 CAATCTTATA
* *
1525435 TGGCACTACGGTACAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * *
1525458 CGGTATTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1525481 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1525496 TTTATACGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1532121 original size:31 final size:30
Alignment explanation
Indices: 1532072--1532131 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1532062 TTATATAAGC
*
1532072 TATGTGATACAATGATGGAACATGATATGTT
1 TATGTGATACAAGGATGGAA-ATGATATGTT
*
1532103 TATGTGATA-AAGGTATGGAAATTATATGT
1 TATGTGATACAAGG-ATGGAAATGATATGT
1532132 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATACAAGGATGGAAATGATATGTT
Found at i:1532406 original size:23 final size:23
Alignment explanation
Indices: 1532354--1532414 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1532344 CAATCTTATA
* * *
1532354 TGGCACTACAGTGCAATTTTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1532377 CGACACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1532400 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1532415 TTTATACAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1534086 original size:23 final size:23
Alignment explanation
Indices: 1534055--1534115 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1534045 CACCACAGCT
* *
1534055 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTACCA
* * *
1534078 CTTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGAAGTACCA
1534101 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
1534116 TAGTTCTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTACCA
Found at i:1547203 original size:15 final size:15
Alignment explanation
Indices: 1547183--1547211 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1547173 ACATTCTTGC
1547183 AATAATATCCCACAA
1 AATAATATCCCACAA
1547198 AATAATATCCCACA
1 AATAATATCCCACA
1547212 GTTATCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAATATCCCACAA
Found at i:1549506 original size:8 final size:7
Alignment explanation
Indices: 1549488--1549525 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1549478 TTTAATTGCG
1549488 AAAAATT
1 AAAAATT
1549495 AAAAATT
1 AAAAATT
1549502 AAAAA-T
1 AAAAATT
1549508 -AAAATT
1 AAAAATT
*
1549514 AAAATTT
1 AAAAATT
1549521 AAAAA
1 AAAAA
1549526 CCCAATTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.15
6 2 0.07
7 21 0.78
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:1549513 original size:19 final size:19
Alignment explanation
Indices: 1549489--1549525 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1549479 TTAATTGCGA
1549489 AAAATTAAAAATTAAAAAT
1 AAAATTAAAAATTAAAAAT
*
1549508 AAAATTAAAATTTAAAAA
1 AAAATTAAAAATTAAAAA
1549526 CCCAATTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATTAAAAATTAAAAAT
Found at i:1549664 original size:24 final size:25
Alignment explanation
Indices: 1549615--1549722 Score: 64
Period size: 24 Copynumber: 4.3 Consensus size: 25
1549605 TTAATAATAC
** *
1549615 ATAAATATTAAATAAATTAAAGAAA
1 ATAAATAAAAAATAAAGTAAAGAAA
*
1549640 A-ACATAAAAAATAAAGTAATA-AAA
1 ATAAATAAAAAATAAAGTAA-AGAAA
* *
1549664 ATAAATAAAAAAGACAA-AAAATGAAAA
1 ATAAATAAAAAATA-AAGTAAA-G-AAA
*
1549691 ATGAAAAAAAAAATAAA-TCAAAGAAA
1 AT-AAATAAAAAATAAAGT-AAAGAAA
1549717 A-AAATA
1 ATAAATA
1549723 TTAAAAAAAG
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
24 23 0.36
25 14 0.22
26 6 0.09
27 8 0.12
28 13 0.20
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.17
Consensus pattern (25 bp):
ATAAATAAAAAATAAAGTAAAGAAA
Found at i:1549690 original size:16 final size:16
Alignment explanation
Indices: 1549645--1549731 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
1549635 AGAAAAACAT
* *
1549645 AAAAAATAAAGTAATAA
1 AAAAAATAAA-AAATGA
1549662 AAATAAATAAAAAA-GA
1 AAA-AAATAAAAAATGA
*
1549678 CAAAAAATGAAAAATGA
1 -AAAAAATAAAAAATGA
*
1549695 AAAAAA-AAATAAATCA
1 AAAAAATAAA-AAATGA
* * *
1549711 AAGAAA-AAAATATTA
1 AAAAAATAAAAAATGA
1549726 AAAAAA
1 AAAAAA
1549732 GTTAATCTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
15 11 0.19
16 29 0.51
17 10 0.18
18 7 0.12
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (16 bp):
AAAAAATAAAAAATGA
Found at i:1549986 original size:24 final size:23
Alignment explanation
Indices: 1549959--1550013 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1549949 ATACAGGTAT
* *
1549959 AATATAAT-ATTAAATAAGTAATAA
1 AATATAATAAATAAAAAAG-AAT-A
*
1549983 AATAAAATAAATAAAAAAGAATA
1 AATATAATAAATAAAAAAGAATA
1550006 AATATAAT
1 AATATAAT
1550014 GATAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 8 0.31
24 10 0.38
25 8 0.31
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
AATATAATAAATAAAAAAGAATA
Found at i:1550012 original size:25 final size:25
Alignment explanation
Indices: 1549969--1550033 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
1549959 AATATAATAT
*
1549969 TAAATAAGTAATAAAATAA-AATAAA
1 TAAAAAAG-AATAAAATAATAATAAA
*
1549994 TAAAAAAGAATAAATATAATGATAAA
1 TAAAAAAGAATAAA-ATAATAATAAA
*
1550020 GAAAAAA-AATAAAA
1 TAAAAAAGAATAAAA
1550034 GAAATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 7 0.20
25 17 0.49
26 11 0.31
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (25 bp):
TAAAAAAGAATAAAATAATAATAAA
Found at i:1550071 original size:13 final size:12
Alignment explanation
Indices: 1550054--1550153 Score: 68
Period size: 13 Copynumber: 8.4 Consensus size: 12
1550044 TATATACGTT
1550054 AATAAT-AAAT-
1 AATAATAAAATA
1550064 AATAATAAAA-A
1 AATAATAAAATA
*
1550075 AATTA-AAAATA
1 AATAATAAAATA
* *
1550086 TATATATATAATA
1 AATA-ATAAAATA
1550099 ACAT-AT-AAATA
1 A-ATAATAAAATA
1550110 AAGTAATAAAATA
1 AA-TAATAAAATA
1550123 AATAAATAAAATA
1 AAT-AATAAAATA
* *
1550136 AACAAATAAAAGA
1 AA-TAATAAAATA
1550149 AATAA
1 AATAA
1550154 AATTAGAGGT
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
10 11 0.16
11 16 0.23
12 8 0.11
13 33 0.47
14 2 0.03
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:1550121 original size:44 final size:47
Alignment explanation
Indices: 1550022--1550132 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 47
1550012 ATGATAAAGA
* * *
1550022 AAAAAAATAAAAGAAATATATATATATACGTTAATAATAAATAATAAT
1 AAAAAAAT-AAATAAATATATATATATACATAAATAATAAATAATAAT
*
1550070 AAAAAAATTAA-AAATATATATATATA-ATAACAT-ATAAATAAAGTAAT
1 AAAAAAATAAATAAATATATATATATACATAA-ATAATAAAT-AA-TAAT
1550117 AAAATAAATAAATAAA
1 AAAA-AAATAAATAAA
1550133 ATAAACAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
45 8 0.15
46 19 0.35
47 10 0.19
48 14 0.26
49 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (47 bp):
AAAAAAATAAATAAATATATATATATACATAAATAATAAATAATAAT
Found at i:1550125 original size:17 final size:17
Alignment explanation
Indices: 1550103--1550156 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1550093 ATAATAACAT
1550103 ATAAATAAAGTAATAAA
1 ATAAATAAAGTAATAAA
*
1550120 ATAAATAAA-TAAAATAA
1 ATAAATAAAGTAATA-AA
* *
1550137 ACAAATAAAAGAAATAAA
1 ATAAAT-AAAGTAATAAA
1550155 AT
1 AT
1550157 TAGAGGTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 4 0.14
17 16 0.55
18 6 0.21
19 3 0.10
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (17 bp):
ATAAATAAAGTAATAAA
Found at i:1566711 original size:8 final size:8
Alignment explanation
Indices: 1566698--1566738 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1566688 CTCATTTTCA
1566698 GAGAATTT
1 GAGAATTT
1566706 GAGAATTT
1 GAGAATTT
*
1566714 -AGAGTTT
1 GAGAATTT
*
1566721 GGGAATTT
1 GAGAATTT
1566729 GAGAATTT
1 GAGAATTT
1566737 GA
1 GA
1566739 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1567176 original size:128 final size:128
Alignment explanation
Indices: 1566809--1567549 Score: 1203
Period size: 128 Copynumber: 5.9 Consensus size: 128
1566799 TAATCGGAGT
1566809 ACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1566873 CATTG-CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1566935 ACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCTATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1566999 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1567062 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
* *
1567127 CATTGCCCTATTATGTCACTCATGTCCCTCGAGGACACTAGATATATCAGTACCTATTATTTT
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
1567190 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTCGTTAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
* *
1567255 CATTGCCCTATTATGTCACTTATGTCTCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
1567318 TC-AGGGGATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1567382 TCATTGCCCTATTATGTCACTC-TGTCCCTCGGGG--A-TAGATATATCAGTA-CTATTATTT-
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
1567440 -C---TCA-GTGAAGGCGCGTT-CCGGGTGCGCGCCTTCCATTATTTCGTCAGA-AATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1567498 CATTGCCCTATTATGTCA-TCATGTCCCTCGGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTC-GGGGACACTAGATATATCAGTA
1567550 AATCAGGTAA
Statistics
Matches: 582, Mismatches: 25, Indels: 23
0.92 0.04 0.04
Matches are distributed among these distances:
114 2 0.00
115 36 0.06
116 34 0.06
117 12 0.02
118 2 0.00
119 14 0.02
121 1 0.00
123 9 0.02
124 14 0.02
125 1 0.00
126 68 0.12
127 94 0.16
128 295 0.51
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:1567986 original size:34 final size:34
Alignment explanation
Indices: 1567948--1568047 Score: 121
Period size: 33 Copynumber: 3.0 Consensus size: 34
1567938 AAATTTAATG
*
1567948 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* * * * *
1567982 TTAAA-TTTGAATAATGTTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* *
1568015 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
1568048 AATATTTATC
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 27 0.51
34 26 0.49
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:1568655 original size:21 final size:21
Alignment explanation
Indices: 1568567--1568660 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
1568557 TATGGTATAA
* *
1568567 AACCCTGCGGGTTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1568588 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1568609 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1568630 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1568651 AACCCTGCGG
1 AACCCTGCGG
1568661 AGATGGCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 3 0.04
21 62 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.26, G:0.35, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1568690 original size:21 final size:21
Alignment explanation
Indices: 1568664--1568711 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1568654 CCTGCGGAGA
*
1568664 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1568685 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1568706 GGGCAT
1 TGGCAT
1568712 GTACCCCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1570209 original size:29 final size:30
Alignment explanation
Indices: 1570139--1570226 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 30
1570129 CAACATCCTA
*
1570139 AATAATATACATTATAAAAAAAAAATATAAATT
1 AATAATA-ACA-T-TAAAATAAAAATATAAATT
* * *
1570172 CATAATAACTTTAAAATAAAAATA-AATTT
1 AATAATAACATTAAAATAAAAATATAAATT
* *
1570201 AATATTAACATTAATTATAAAAATAT
1 AATAATAACATTAA-AATAAAAATAT
1570227 TACCATATCG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 15 0.33
30 21 0.47
31 1 0.02
32 2 0.04
33 6 0.13
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (30 bp):
AATAATAACATTAAAATAAAAATATAAATT
Found at i:1570365 original size:15 final size:16
Alignment explanation
Indices: 1570345--1570417 Score: 55
Period size: 15 Copynumber: 4.8 Consensus size: 16
1570335 ATAATTCTAA
1570345 ATAAATAATAATT-AT
1 ATAAATAATAATTAAT
* *
1570360 ATAAATATTATTTTAAT
1 ATAAATAATA-ATTAAT
* * *
1570377 AAAAATAAT-ATTTAC
1 ATAAATAATAATTAAT
1570392 ATAAAT-AT-ATTAAT
1 ATAAATAATAATTAAT
*
1570406 ATAAAAAATAAT
1 ATAAATAATAAT
1570418 AACTATTTAA
Statistics
Matches: 43, Mismatches: 11, Indels: 7
0.70 0.18 0.11
Matches are distributed among these distances:
14 11 0.26
15 19 0.44
16 4 0.09
17 9 0.21
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAATAATAATTAAT
Found at i:1570413 original size:32 final size:32
Alignment explanation
Indices: 1570342--1570419 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
1570332 TTAATAATTC
* *
1570342 TAAATAAATAATAATTATATAAATATTATTTTA
1 TAAA-AAATAATAATTACATAAATATTATTATA
*
1570375 -ATAAAAATAATATTTACATAAATA-TATTAATA
1 TA-AAAAATAATAATTACATAAATATTATT-ATA
1570407 TAAAAAATAATAA
1 TAAAAAATAATAA
1570420 CTATTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
31 4 0.11
32 31 0.82
33 3 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTATA
Found at i:1571713 original size:17 final size:17
Alignment explanation
Indices: 1571672--1571716 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1571662 TCCTACTTGA
1571672 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
1571689 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
1571706 TTAAATATTTA
1 TTAAATATTTA
1571717 TTTTTCAATT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:1571855 original size:21 final size:22
Alignment explanation
Indices: 1571831--1571871 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1571821 ATTTAAATCG
*
1571831 TAAACTAATGC-TTTATTAATA
1 TAAACTAATACTTTTATTAATA
1571852 TAAACTAATACTTTTATTAA
1 TAAACTAATACTTTTATTAA
1571872 AAATGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAACTAATACTTTTATTAATA
Found at i:1574702 original size:22 final size:21
Alignment explanation
Indices: 1574639--1574725 Score: 61
Period size: 22 Copynumber: 4.0 Consensus size: 21
1574629 ATAAAAATAA
*
1574639 TTAAATAAATATTTAT-ATATT
1 TTAAA-AATTATTTATAATATT
* *
1574660 TATGAAAATTATATTAAAATATT
1 T-TAAAAATTAT-TTATAATATT
*
1574683 TTAAAAATGTATTTATAATACT
1 TTAAAAAT-TATTTATAATATT
* * *
1574705 ATAAAAATAAATTA-AATATT
1 TTAAAAATTATTTATAATATT
1574725 T
1 T
1574726 ATTTATTTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
20 5 0.10
21 10 0.20
22 27 0.53
23 9 0.18
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAAAAATTATTTATAATATT
Found at i:1574753 original size:21 final size:22
Alignment explanation
Indices: 1574718--1574770 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1574708 AAAATAAATT
*
1574718 AAATATTTATTTATTT-TTTAAA
1 AAATA-TTATATATTTATTTAAA
1574740 AAATATTATATATTTATTTAAA
1 AAATATTATATATTTATTTAAA
1574762 ATAATATTA
1 A-AATATTA
1574771 ATTAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 9 0.32
22 12 0.43
23 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATATTATATATTTATTTAAA
Found at i:1574779 original size:23 final size:22
Alignment explanation
Indices: 1574719--1574791 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
1574709 AAATAAATTA
* *
1574719 AATATTTATTTATTTTTTAAAA-
1 AATA-TTATTAATTATTTAAAAT
*
1574741 AATATTATATATTTATTTAAAAT
1 AATATTAT-TAATTATTTAAAAT
*
1574764 AATATTAATTAATTATTTGAAAT
1 AATATT-ATTAATTATTTAAAAT
1574787 AATAT
1 AATAT
1574792 ATTTTTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.09
22 14 0.33
23 23 0.53
24 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
AATATTATTAATTATTTAAAAT
Found at i:1575009 original size:22 final size:23
Alignment explanation
Indices: 1574956--1575020 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
1574946 ATTTTTAAAA
*
1574956 ATAAATAAATATTTTTATAATATT
1 ATAAATATA-ATTTTTATAATATT
*
1574980 ATAAATATACTTTTTATAATTATT
1 ATAAATATAATTTTTATAA-TATT
*
1575004 -T-CATATAATTTTTATAA
1 ATAAATATAATTTTTATAA
1575021 AAAATTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.39
23 10 0.28
24 12 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAAATATAATTTTTATAATATT
Found at i:1576278 original size:5 final size:5
Alignment explanation
Indices: 1576268--1576295 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1576258 TACAGTGATG
1576268 GGGTA GGGTA GGGTA GGGTA GGGTA GGG
1 GGGTA GGGTA GGGTA GGGTA GGGTA GGG
1576296 CAGGCAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.64, T:0.18
Consensus pattern (5 bp):
GGGTA
Found at i:1581560 original size:23 final size:23
Alignment explanation
Indices: 1581533--1581585 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1581523 ATTTTATTTA
1581533 TTTTTA-CAAGAGAAACAACACTT
1 TTTTTATCAAGAGAAACAACA-TT
***
1581556 TTTTTATTGGGAGAAACAACATT
1 TTTTTATCAAGAGAAACAACATT
1581579 TTTTTAT
1 TTTTTAT
1581586 AAATGTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (23 bp):
TTTTTATCAAGAGAAACAACATT
Found at i:1588166 original size:94 final size:95
Alignment explanation
Indices: 1588005--1588194 Score: 373
Period size: 94 Copynumber: 2.0 Consensus size: 95
1587995 ATGGTGTGAA
1588005 GATATGATTGTTCTAATCAAATCTTCAAGTGGGAGATTGTTGAAAAGTCAAGTAAAGTGGCCAAA
1 GATATGATTGTTCTAATCAAATCTTCAAGTGGGAGATTGTTGAAAAGTCAAGTAAAGTGGCCAAA
1588070 CATATTGAAAAAAATC-AGCAAAAATTTCG
66 CATATTGAAAAAAATCAAGCAAAAATTTCG
1588099 GATATGATTGTTCTAATCAAATCTTCAAGTGGGAGATTGTTGAAAAGTCAAGTAAAGTGGCCAAA
1 GATATGATTGTTCTAATCAAATCTTCAAGTGGGAGATTGTTGAAAAGTCAAGTAAAGTGGCCAAA
1588164 CATATTGAAAAAAATCAAGCAAAAATTTCG
66 CATATTGAAAAAAATCAAGCAAAAATTTCG
1588194 G
1 G
1588195 TGCACATGCT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 81 0.85
95 14 0.15
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (95 bp):
GATATGATTGTTCTAATCAAATCTTCAAGTGGGAGATTGTTGAAAAGTCAAGTAAAGTGGCCAAA
CATATTGAAAAAAATCAAGCAAAAATTTCG
Found at i:1597584 original size:18 final size:18
Alignment explanation
Indices: 1597544--1597595 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1597534 ATGTTTAGAC
1597544 TTTTGTAAAAAATATTTTA
1 TTTT-TAAAAAATATTTTA
1597563 -TTTTAAAAAATATTTTA
1 TTTTTAAAAAATATTTTA
*
1597580 TTTTTAAAAAAAATTT
1 TTTTTAAAAAATATTT
1597596 AAACATCACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTTTAAAAAATATTTTA
Found at i:1601061 original size:3 final size:3
Alignment explanation
Indices: 1601028--1601076 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
1601018 AACCCGATGA
* *
1601028 AAT AA- AAT AA- AAT AAA AAT AA- GAT GAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
1601071 AAT AAT
1 AAT AAT
1601077 GCTAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 5 0.13
3 31 0.82
4 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1602289 original size:6 final size:6
Alignment explanation
Indices: 1602273--1602329 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
1602263 ACCCTGCAAC
* *
1602273 AAAAT- AAAATA AAAATA AAAAT- AAAATA AGTAATA ATAATA ATAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA A-AAATA AAAATA A-AAATA
1602321 ATAAATA AA
1 A-AAATA AA
1602330 TAACAAAAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
5 10 0.22
6 19 0.41
7 17 0.37
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
AAAATA
Found at i:1602311 original size:3 final size:3
Alignment explanation
Indices: 1602275--1602324 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
1602265 CCTGCAACAA
* *
1602275 AAT AA- AAT AAA AAT AAA AAT AA- AAT AAGT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT -AAT
1602320 AAT AA
1 AAT AA
1602325 ATAAATAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 4 0.10
3 29 0.74
4 6 0.15
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:1602320 original size:7 final size:7
Alignment explanation
Indices: 1602280--1602328 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
1602270 AACAAAATAA
1602280 AATAAA-
1 AATAAAT
1602286 AATAAA-
1 AATAAAT
1602292 AATAAAAT
1 AAT-AAAT
1602300 AAGT-AAT
1 AA-TAAAT
1602307 AAT-AAT
1 AATAAAT
1602313 AATAAAT
1 AATAAAT
1602320 AATAAAT
1 AATAAAT
1602327 AA
1 AA
1602329 ATAACAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 16 0.41
7 20 0.51
8 2 0.05
9 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:1602343 original size:25 final size:25
Alignment explanation
Indices: 1602315--1602363 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1602305 ATAATAATAA
*
1602315 TAAATAATAAATAAA-TAACAAAAGG
1 TAAATAAAAAATAAACTAA-AAAAGG
1602340 TAAATAAAAAATAAACTAAAAAAG
1 TAAATAAAAAATAAACTAAAAAAG
1602364 CAGTTTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.18
Consensus pattern (25 bp):
TAAATAAAAAATAAACTAAAAAAGG
Found at i:1602354 original size:11 final size:11
Alignment explanation
Indices: 1602273--1602362 Score: 65
Period size: 12 Copynumber: 7.4 Consensus size: 11
1602263 ACCCTGCAAC
1602273 AAAATAAAATAA
1 AAAAT-AAATAA
*
1602285 AAATAAAAATAA
1 AAA-ATAAATAA
1602297 AATAAGT-AATAA
1 AA-AA-TAAATAA
1602309 TAATAATAAATAA
1 -AA-AATAAATAA
*
1602322 TAAATAAATAA
1 AAAATAAATAA
1602333 CAAAAGGTAAATAA
1 -AAAA--TAAATAA
1602347 AAAATAAACTAA
1 AAAATAAA-TAA
1602359 AAAA
1 AAAA
1602363 GCAGTTTCCA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
11 13 0.20
12 29 0.45
13 16 0.25
14 7 0.11
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:1602470 original size:28 final size:29
Alignment explanation
Indices: 1602428--1602483 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
1602418 ATTATATGTT
*
1602428 TTTTTAAAAACGTTTTCAAAATTATATAG
1 TTTTTAAAAACGTTTTCAAAACTATATAG
* *
1602457 TTTTT-AAAATGTTTTTAAAACTATATA
1 TTTTTAAAAACGTTTTCAAAACTATATA
1602484 TTATAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (29 bp):
TTTTTAAAAACGTTTTCAAAACTATATAG
Found at i:1602559 original size:30 final size:28
Alignment explanation
Indices: 1602521--1602586 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
1602511 CTATATAATA
*
1602521 TATATATATTCTTCAAAATATTTTTTAAAAAC
1 TATATATA-TCTTC-AAA-A-TGTTTAAAAAC
*
1602553 TATATATATTTTCAAAATGTTTAAAAAC
1 TATATATATCTTCAAAATGTTTAAAAAC
1602581 TATATA
1 TATATA
1602587 ATATATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 16 0.50
29 1 0.03
30 3 0.09
31 4 0.12
32 8 0.25
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (28 bp):
TATATATATCTTCAAAATGTTTAAAAAC
Found at i:1602585 original size:62 final size:62
Alignment explanation
Indices: 1602518--1602649 Score: 167
Period size: 64 Copynumber: 2.1 Consensus size: 62
1602508 AAACTATATA
* *
1602518 ATATATATATATTCTTCAAAATATTTTTTAAAAACTATATATATTTTCAAAAT-GTTTAAAAACT
1 ATATATATATA-TCTTCAAAAAATGTTTTAAAAA-T-TATATATTTTCAAAATAGTTTAAAAACT
* * * *
1602582 ATATAATATATATTTTTAAAAAATGTTTTAAAAATTATTTATTTTCAAAATATTTTAAAAACT
1 ATAT-ATATATATCTTCAAAAAATGTTTTAAAAATTATATATTTTCAAAATAGTTTAAAAACT
1602645 ATATA
1 ATATA
1602650 ATGTATAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
62 16 0.27
63 15 0.25
64 22 0.37
65 7 0.12
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (62 bp):
ATATATATATATCTTCAAAAAATGTTTTAAAAATTATATATTTTCAAAATAGTTTAAAAACT
Found at i:1602598 original size:103 final size:99
Alignment explanation
Indices: 1602372--1602603 Score: 247
Period size: 103 Copynumber: 2.3 Consensus size: 99
1602362 AGCAGTTTCC
* * * * *
1602372 AAAAATCTATATAATATATATTTTTAAAAATATTTTAAAATTATATATTATATGTTTTTTTAAAA
1 AAAAA-CTATATAATATATATTTTTAAAAATATTTAAAAACTATATATTATATATTTCTTCAAAA
* *
1602437 ACGTTTTCAAAATTATATAGTTTTTAAAATGTTTT
65 ACGTTTTAAAAATTATATAGTTTTCAAAATGTTTT
* * *
1602472 TAAAACTATATATTATA-AGTTTTT-GAAATGATTTAAAAACTATATAATATATATATATTCTTC
1 AAAAACTATATAATATATA-TTTTTAAAAAT-ATTTAAAAACTATAT-AT-TATATAT-TTCTTC
**
1602535 AAAATATTTTTTAAAAACTATATATA-TTTTCAAAATG-TTT
61 AAAA-ACGTTTTAAAAA-T-TATATAGTTTTCAAAATGTTTT
1602575 AAAAACTATATAATATATATTTTTAAAAA
1 AAAAACTATATAATATATATTTTTAAAAA
1602604 ATGTTTTAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
98 5 0.05
99 29 0.27
100 6 0.06
101 6 0.06
102 8 0.07
103 32 0.30
104 15 0.14
105 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (99 bp):
AAAAACTATATAATATATATTTTTAAAAATATTTAAAAACTATATATTATATATTTCTTCAAAAA
CGTTTTAAAAATTATATAGTTTTCAAAATGTTTT
Found at i:1602646 original size:63 final size:67
Alignment explanation
Indices: 1602497--1602689 Score: 218
Period size: 63 Copynumber: 2.9 Consensus size: 67
1602487 TAAGTTTTTG
* *
1602497 AAATGATTTAAAAACTATATAATATATATATATTCTTCAAAATATTTTTTAAAAACTATATATAT
1 AAATG-TTTAAAAACTATAT-A-ATATATATATTCTTCAAAAAATGTTTTAAAAACTATATATAT
1602562 TTTCA
63 TTTCA
*
1602567 AAATGTTTAAAAACTATATAATATATAT-TT-TT-AAAAAATGTTTTAAAAA-T-TATTTATTTT
1 AAATGTTTAAAAACTATATAATATATATATTCTTCAAAAAATGTTTTAAAAACTATATATATTTT
1602627 CA
66 CA
* * * * * *
1602629 AAATATTTTAAAAACTATATAATGTATAAATGTTTTC-AAACATGTTTTCAAAACTATATAT
1 AAAT-GTTTAAAAACTATATAATATATATAT-TCTTCAAAAAATGTTTTAAAAACTATATAT
1602690 TATATATAAG
Statistics
Matches: 107, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
62 15 0.14
63 22 0.21
64 16 0.15
65 3 0.03
66 18 0.17
67 9 0.08
68 5 0.05
69 14 0.13
70 5 0.05
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (67 bp):
AAATGTTTAAAAACTATATAATATATATATTCTTCAAAAAATGTTTTAAAAACTATATATATTTT
CA
Found at i:1602703 original size:39 final size:38
Alignment explanation
Indices: 1602623--1602735 Score: 124
Period size: 39 Copynumber: 2.9 Consensus size: 38
1602613 AAATTATTTA
* *
1602623 TTTTCAAAATATTTTAAAAACTATATAATGTATA-AATG
1 TTTTCAAAATATTTT-AAAACTATATATTATATATAATG
*
1602661 TTTTCAAACATGTTTTCAAAACTATATATTATATATAA-G
1 TTTTCAAA-ATATTTT-AAAACTATATATTATATATAATG
*
1602700 TTTT-AAAATATTTTTAAACTATAATATATATATATA
1 TTTTCAAAATATTTTAAAACTAT-ATAT-TATATATA
1602736 TATATATATA
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
36 7 0.11
37 10 0.15
38 19 0.29
39 27 0.42
40 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (38 bp):
TTTTCAAAATATTTTAAAACTATATATTATATATAATG
Found at i:1602730 original size:2 final size:2
Alignment explanation
Indices: 1602719--1602755 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1602709 ATTTTTAAAC
1602719 TA TA -A 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
1602756 AATGAGACGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1603243 original size:84 final size:83
Alignment explanation
Indices: 1603082--1604069 Score: 1088
Period size: 84 Copynumber: 12.0 Consensus size: 83
1603072 TGGTTGATAG
* * * * * * *
1603082 GCCTTCGAGCTGAGTGTAATCAAACTCGAGGGTC-TT--TGGCAGATAGCCCTTCTCGAGTTAAG
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAG
* *
1603144 CTATGTTGCAAATGATGT
66 TTATGCTGCAAATGATGT
* * * ** * * *
1603162 TCCTTGGAGCTGAACGTAGTCGAACTCGAATGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAA
*
1603227 GTTATGCTGTAAATGATGT
65 GTTATGCTGCAAATGATGT
* * * * * ** *
1603246 GCCCTCGAAACTGAGTGTAATCGAACTCGGGGGTC-TT--TGGCAGATAGCCCTTCTCGACTTAA
1 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAA
*
1603308 GCTATGCTGCAAATGATGT
65 GTTATGCTGCAAATGATGT
* * ** * * *
1603327 GTCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTATTGGCAGACAACCTTTCTAGACTTA
1 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTA
* * *
1603391 AGTTGTACTGCAAATGATAT
64 AGTTATGCTGCAAATGATGT
1603411 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAA
* * *
1603476 GTTGTACTGCAAATGATAT
65 GTTATGCTGCAAATGATGT
* *
1603495 GCCTTGGAGCTGAGCG-AGGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAATTA
1 GCCTTGGAGCTGAGCGTA-GTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTA
*
1603559 AGTTATGCTGCAAATGATAT
64 AGTTATGCTGCAAATGATGT
* *
1603579 GCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAA
*
1603644 GTTATGCTGCAAATGATAT
65 GTTATGCTGCAAATGATGT
* * * * * *
1603663 GCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAG
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAG
**
1603728 TTATGCTATAAATGATGT
66 TTATGCTGCAAATGATGT
* * * * * * *
1603746 CCCATCGAAGCTGAGTGTAATCGAACTCGAAGGTC-TT--TGGCAGATAGCCCTTCTCGATTTAA
1 GCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAA
*
1603808 GCTATGCTGCAAATGATGT
65 GTTATGCTGCAAATGATGT
*
1603827 GCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC-TT--TGGCAGATAACCCTTCTCGACTTAAG
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAG
*
1603889 CTATGCTGCAAATGATGT
66 TTATGCTGCAAATGATGT
* * * ** *
1603907 GCCTCGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTATTGGCAGATAACCCTTCTCGACGTAA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAA
*
1603972 GTTATGCTGCAAATGATAT
65 GTTATGCTGCAAATGATGT
* * * * *
1603991 GCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGTTGGCATATAACCCTTCTAGTA-TTAA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCG-ACTTAA
1604055 GTTATGCTGCAAATG
65 GTTATGCTGCAAATG
1604070 TTGTCTAAGA
Statistics
Matches: 775, Mismatches: 114, Indels: 35
0.84 0.12 0.04
Matches are distributed among these distances:
80 151 0.19
81 75 0.10
82 6 0.01
83 88 0.11
84 430 0.55
85 25 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (83 bp):
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAG
TTATGCTGCAAATGATGT
Found at i:1606237 original size:97 final size:97
Alignment explanation
Indices: 1606071--1606264 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
1606061 CCGTGATATT
1606071 CACAATGTGCATTCTCATCATACCACTTGGGGTATGGGGCTTCATGGGTTATACCGGATATGGTG
1 CACAATGTGCATTCTCATCATACCACTTGGGGTATGGGGCTTCATGGGTTATACCGGATATGGTG
1606136 ACACTACATGGGTGTCAAGAAGTTGCTGGTAA
66 ACACTACATGGGTGTCAAGAAGTTGCTGGTAA
1606168 CACAATGTGCATTCTCATCATACCACTTGGGGTATGGGGCTTCATGGGTTATACCGGATATGGTG
1 CACAATGTGCATTCTCATCATACCACTTGGGGTATGGGGCTTCATGGGTTATACCGGATATGGTG
1606233 ACACTACATGGGTGTCAAGAAGTTGCTGGTAA
66 ACACTACATGGGTGTCAAGAAGTTGCTGGTAA
1606265 AGCTCCTTAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (97 bp):
CACAATGTGCATTCTCATCATACCACTTGGGGTATGGGGCTTCATGGGTTATACCGGATATGGTG
ACACTACATGGGTGTCAAGAAGTTGCTGGTAA
Found at i:1610735 original size:12 final size:11
Alignment explanation
Indices: 1610655--1610738 Score: 55
Period size: 12 Copynumber: 6.9 Consensus size: 11
1610645 CCCTGTAACA
1610655 AAATAAAAAAAT
1 AAAT-AAAAAAT
1610667 AAA-AATAAAAT
1 AAATAA-AAAAT
*
1610678 AAGTAATAATAAT
1 AAATAA-AA-AAT
1610691 -AATAAAATAAAT
1 AAAT-AAA-AAAT
1610703 AAATAACAAAAGGT
1 AAATAA-AAAA--T
1610717 AAATAAAAAAT
1 AAATAAAAAAT
1610728 AAACTAAAAAA
1 AAA-TAAAAAA
1610739 ACAGTTTCCA
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
10 2 0.03
11 11 0.18
12 26 0.43
13 14 0.23
14 7 0.12
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:1610831 original size:37 final size:37
Alignment explanation
Indices: 1610735--1610831 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 37
1610725 AATAAACTAA
* * *
1610735 AAAAACAGTTTCCAAAAATCTATATAATATATATTTTT
1 AAAAAC-GTTTTCAAAATTATATATAATATATATTTTT
** * * *
1610773 AAAAATATTTT-AAAATTATATATTATATGTTTTTTT
1 AAAAACGTTTTCAAAATTATATATAATATATATTTTT
1610809 AAAAACGTTTTCAAAATTATATA
1 AAAAACGTTTTCAAAATTATATA
1610832 GCTTTTAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
36 29 0.60
37 14 0.29
38 5 0.10
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAAACGTTTTCAAAATTATATATAATATATATTTTT
Found at i:1610840 original size:29 final size:29
Alignment explanation
Indices: 1610805--1610860 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1610795 TTATATGTTT
*
1610805 TTTTAAAAACGTTTTCAAAATTATATAGC
1 TTTTAAAAACGTTTTCAAAACTATATAGC
* *
1610834 TTTTAAAAATGTTTTTAAAACTATATA
1 TTTTAAAAACGTTTTCAAAACTATATA
1610861 TTATAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (29 bp):
TTTTAAAAACGTTTTCAAAACTATATAGC
Found at i:1611017 original size:63 final size:67
Alignment explanation
Indices: 1610880--1611066 Score: 194
Period size: 63 Copynumber: 2.8 Consensus size: 67
1610870 TTTGAAATGA
* *
1610880 TTTAAAAACTATATAATATATATATGTTCTTCAAAATATTTTTTTAAAAACTATATATATTTTCA
1 TTTAAAAACTATAT-A-ATATATATGTTCTTCAAAATAATGTTTTAAAAACTATATATATTTTCA
1610945 AAAT
64 AAAT
* *
1610949 GTTAAAAACTATATAATATATAT-TT-TT-AAAA-AATGTTTTAAAAA-T-TATTTATTTTCAAA
1 TTTAAAAACTATATAATATATATGTTCTTCAAAATAATGTTTTAAAAACTATATATATTTTC-AA
1611008 ATAT
65 A-AT
* * *
1611012 TTTAAAAACTATATAATGTATAAATGTT-TTC-AAA-CATGTTTTTAAAACTATATAT
1 TTTAAAAACTATATAA--TATATATGTTCTTCAAAATAATGTTTTAAAAACTATATAT
1611067 TATATATAGG
Statistics
Matches: 101, Mismatches: 9, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
61 10 0.10
62 4 0.04
63 28 0.28
64 4 0.04
65 8 0.08
66 20 0.20
67 9 0.09
68 5 0.05
69 13 0.13
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (67 bp):
TTTAAAAACTATATAATATATATGTTCTTCAAAATAATGTTTTAAAAACTATATATATTTTCAAA
AT
Found at i:1611062 original size:39 final size:38
Alignment explanation
Indices: 1611000--1611111 Score: 127
Period size: 39 Copynumber: 2.9 Consensus size: 38
1610990 AAATTATTTA
* * *
1611000 TTTTCAAAATATTTTAAAAACTATATAATGTATAAATG
1 TTTTCAAAATATTTTTAAAACTATATAATATATAAAGG
* * *
1611038 TTTTCAAACATGTTTTTAAAACTATATATTATATATAGG
1 TTTTCAAA-ATATTTTTAAAACTATATAATATATAAAGG
*
1611077 TTTTAAAAATATTTTT-AAACTATAATATATATATA
1 TTTTCAAAATATTTTTAAAACTAT-ATA-ATATATA
1611112 TATATATATA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
37 7 0.11
38 18 0.29
39 37 0.60
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTTCAAAATATTTTTAAAACTATATAATATATAAAGG
Found at i:1611108 original size:2 final size:2
Alignment explanation
Indices: 1611097--1611139 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1611087 ATTTTTAAAC
* *
1611097 TA TA -A TA TA TA TA TA TA TA TA TA TA TC TA TA TC 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
1611138 TA
1 TA
1611140 AATGAGACGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1611241 original size:25 final size:25
Alignment explanation
Indices: 1611204--1611259 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
1611194 TCACCAATTT
1611204 GGTTGGGTCGAAGAAAAAGAAGAAG
1 GGTTGGGTCGAAGAAAAAGAAGAAG
*
1611229 GGTTGGGTTGAAGAAAAAGAAGAAG
1 GGTTGGGTCGAAGAAAAAGAAGAAG
*
1611254 AGTTGG
1 GGTTGG
1611260 TCAAAATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.41, T:0.16
Consensus pattern (25 bp):
GGTTGGGTCGAAGAAAAAGAAGAAG
Found at i:1615511 original size:45 final size:45
Alignment explanation
Indices: 1615447--1615533 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
1615437 TAAAAGTATG
*
1615447 TAAGATTAAGAATGTCTAAACACTTTATATTTATTTATTTATTTT
1 TAAGATTAAGAATGTCTAAACACTTGATATTTATTTATTTATTTT
1615492 TAAGATTAAGAATGTCTAAACACTTGATATTTATTTATTTAT
1 TAAGATTAAGAATGTCTAAACACTTGATATTTATTTATTTAT
1615534 GATGGAATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (45 bp):
TAAGATTAAGAATGTCTAAACACTTGATATTTATTTATTTATTTT
Found at i:1615655 original size:63 final size:60
Alignment explanation
Indices: 1615569--1615685 Score: 180
Period size: 63 Copynumber: 1.9 Consensus size: 60
1615559 AAATATTATA
* **
1615569 TCATTTAAAATGTCTTACGAATGTAAAATGTCTCACTTTTTAATCAAAATAAATCACTAGGT
1 TCATTTAAAATGTCTTACAAATGTAAAATG--AAACTTTTTAATCAAAATAAATCACTAGGT
1615631 TCATTTCAAAATGTCTTACAAATGTAAAATGAAACTTTTTAATCAAAATAAATCA
1 TCATTT-AAAATGTCTTACAAATGTAAAATGAAACTTTTTAATCAAAATAAATCA
1615686 GTCAAATCTA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
61 22 0.43
62 6 0.12
63 23 0.45
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.36
Consensus pattern (60 bp):
TCATTTAAAATGTCTTACAAATGTAAAATGAAACTTTTTAATCAAAATAAATCACTAGGT
Found at i:1619066 original size:23 final size:23
Alignment explanation
Indices: 1619028--1619078 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1619018 TAAGCAACCA
*
1619028 AAAGGCAGAGAAAAATGTATCAC
1 AAAGGCAAAGAAAAATGTATCAC
* * *
1619051 AAAGGCAAAGATAAATGTGTCAT
1 AAAGGCAAAGAAAAATGTATCAC
1619074 AAAGG
1 AAAGG
1619079 TAGAGAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.24, T:0.16
Consensus pattern (23 bp):
AAAGGCAAAGAAAAATGTATCAC
Found at i:1623759 original size:147 final size:147
Alignment explanation
Indices: 1623409--1623702 Score: 516
Period size: 147 Copynumber: 2.0 Consensus size: 147
1623399 GCTTTCTTTG
* *
1623409 TCTAACAAATTGATCACCGATGTACTCATTCTTAAACTCTTCTGAAACAATATCTACATCTCTTG
1 TCTAACAAATTGATCACCGATGAACTCATTCTTAAACTCTTCAGAAACAATATCTACATCTCTTG
1623474 ATCCATTTTAGATACTTCTATTTTGCAATTTACATAATTTTTAACAGAACTTTCAGTCCAATCCA
66 ATCCATTTTAGATACTTCTATTTTGCAATTTACATAATTTTTAACAGAACTTTCAGTCCAATCCA
***
1623539 ACACTTTCATATCTTTG
131 ACACTTTCATATCTAAC
* *
1623556 TCTAACAAATTGATCACCGATGTACTCATTCTTAAACTCTTCTGAAACAATATCTACATCTCTTG
1 TCTAACAAATTGATCACCGATGAACTCATTCTTAAACTCTTCAGAAACAATATCTACATCTCTTG
1623621 ATCCATTTTAGATACTTCTTATTTTGCAATTTACATAATTTTTAACAGAACTTTCAGTCCAATCC
66 ATCCATTTTAGATACTTC-TATTTTGCAATTTACATAATTTTTAACAGAACTTTCAGTCCAATCC
1623686 AACACTTTCATATCTAA
130 AACACTTTCATATCTAA
1623703 ACTTAACTTC
Statistics
Matches: 144, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
147 83 0.58
148 61 0.42
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.39
Consensus pattern (147 bp):
TCTAACAAATTGATCACCGATGAACTCATTCTTAAACTCTTCAGAAACAATATCTACATCTCTTG
ATCCATTTTAGATACTTCTATTTTGCAATTTACATAATTTTTAACAGAACTTTCAGTCCAATCCA
ACACTTTCATATCTAAC
Found at i:1624613 original size:17 final size:17
Alignment explanation
Indices: 1624591--1624625 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1624581 TTGGTTTAAG
1624591 CCTAGAACCGGCTAAAC
1 CCTAGAACCGGCTAAAC
*
1624608 CCTAGAATCGGCTAAAC
1 CCTAGAACCGGCTAAAC
1624625 C
1 C
1624626 TTAGCTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.14
Consensus pattern (17 bp):
CCTAGAACCGGCTAAAC
Found at i:1641821 original size:42 final size:42
Alignment explanation
Indices: 1641762--1641880 Score: 222
Period size: 41 Copynumber: 2.9 Consensus size: 42
1641752 ATTTTGACCT
1641762 TAATTATTAAAGTGTAAAATAACTTAACACCCCCCACGATTA
1 TAATTATTAAAGTGTAAAATAACTTAACACCCCCCACGATTA
1641804 TAATTATTAAAGTGTAAAATAACTTAACA-CCCCCACGATTA
1 TAATTATTAAAGTGTAAAATAACTTAACACCCCCCACGATTA
*
1641845 TAATTATTAAAGTTTAAAATAACTTAACACCCCCCA
1 TAATTATTAAAGTGTAAAATAACTTAACACCCCCCA
1641881 ATGGAAGAGA
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
41 40 0.53
42 35 0.47
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (42 bp):
TAATTATTAAAGTGTAAAATAACTTAACACCCCCCACGATTA
Found at i:1643172 original size:14 final size:14
Alignment explanation
Indices: 1643153--1643179 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1643143 CAAAGTGTAG
1643153 ATTTATTCTAATTT
1 ATTTATTCTAATTT
1643167 ATTTATTCTAATT
1 ATTTATTCTAATT
1643180 CTAAATTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTATTCTAATTT
Found at i:1653068 original size:33 final size:33
Alignment explanation
Indices: 1653022--1653085 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1653012 TTTGTGTTTC
*
1653022 AAGAGAAACTGTCTCAAGAGAGACAAAATTTTT
1 AAGAGAAAATGTCTCAAGAGAGACAAAATTTTT
1653055 AAGAGAAAATGTCTCAAGAGAGACAAAATTT
1 AAGAGAAAATGTCTCAAGAGAGACAAAATTT
1653086 GTTTTAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.22
Consensus pattern (33 bp):
AAGAGAAAATGTCTCAAGAGAGACAAAATTTTT
Found at i:1653098 original size:36 final size:36
Alignment explanation
Indices: 1653016--1653608 Score: 266
Period size: 36 Copynumber: 17.4 Consensus size: 36
1653006 AAAGATTTTG
*
1653016 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1653050 T-TTTTAAGAGAAAATGTCTCAAGAGAGACAAAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1653085 TGTTTTAAAAGAAACCGTCTCAAG-GAAGACGAAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAG-AGACAAAATT
* * *
1653121 TGTTTCAAG-GAAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTTAAGAG-AAACTG-TCTCAAGAGAGACAAAATT
* * *
1653150 TGTTTCAAGGGAAACTGTCTCAAGAGAGA-GAAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1653185 T-TTTAAAGAGAAAATGTCTTAAGAGAGACAAAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * **
1653220 TGTTTTAAAAGAAACTGTTTTAAGGGAGATGAAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
* ** *
1653256 TGTTTCAAG-GAAAACAAAT-TC-A-A-AG----ATTT
1 TGTTTTAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* * * *
1653285 TGTTTCAAGGGAAGCTGTCTCAAGGGAGACAAAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1653321 TGTTTCAAG-GAAAACAGAT-TC-A-A-AG-----ATT
1 TGTTTTAAGAG-AAACTG-TCTCAAGAGAGACAAAATT
* *
1653349 TTTTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATT
1 TGTTTT-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1653386 TGTTTTAAGAGAAAATGTCTCAAGAGTGACAAAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1653422 TGTTTGAAG-GAAAATAGAT-TC-A-A-AG----ATTT
1 TGTTTTAAGAGAAACT-G-TCTCAAGAGAGACAAAATT
* * * * *
1653451 TGTTTCAAGGGAAATTGTCTGAAGATAGACAAAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
1653487 TGATTCAAGGGAAACTGTCTCAAGAGAGATAAAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
1653523 TGTTTCAAGAGAAATTGTCTAAAAAGAGACAAAACTT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * **
1653560 AGTTTCAAAAGAAACTGTCTCAAGGGAGACGCAATT
1 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1653596 TGTTTCAAG-GAAA
1 TGTTTTAAGAGAAA
1653609 AATTCAAAGA
Statistics
Matches: 432, Mismatches: 74, Indels: 105
0.71 0.12 0.17
Matches are distributed among these distances:
28 11 0.03
29 59 0.14
30 12 0.03
31 3 0.01
32 8 0.02
33 37 0.09
34 25 0.06
35 29 0.07
36 208 0.48
37 40 0.09
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1653169 original size:101 final size:101
Alignment explanation
Indices: 1653059--1653536 Score: 458
Period size: 101 Copynumber: 4.7 Consensus size: 101
1653049 ATTTTTAAGA
* * * *
1653059 GAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACCGTCTCAAG-GAAGACGAAATTTG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAG-AGACAAAATTTG
1653123 TTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGG
65 TTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGG
* * * *
1653160 GAAACTGTCTCAAGAGAGA-GAAATTT-TTTAAAGAGAAAATGTCTTAAGAGAGACAAAATTTGT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * * *
1653223 TTTAA-AAGAAACTGTTTTAAGGGAGATGAAATTTGTTTCAAGG
66 TTCAAGGA-AAACAGATTCAA---AGAT----TTTGTTTCAAGG
* ** * * * * *
1653266 AAAACAAAT-TC-A-A-AG----ATTTTGTTTCAAGGGAAGCTGTCTCAAGGGAGACAAAATTTG
1 GAAAC-TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
1653323 TTTCAAGGAAAACAGATTCAAAGATTTTTTTTCAAGA
65 TTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGG
* * *
1653360 GAAACCGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGTGACAAAATTTGT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
1653425 TTGAAGGAAAATAGATTCAAAGATTTTGTTTCAAGG
66 TTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGG
* * * * * * *
1653461 GAAATTGTCTGAAGATAGACAAAATTTGATTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
1653526 TTCAAGAGAAA
66 TTCAAG-GAAA
1653537 TTGTCTAAAA
Statistics
Matches: 301, Mismatches: 55, Indels: 41
0.76 0.14 0.10
Matches are distributed among these distances:
93 1 0.00
94 16 0.05
95 1 0.00
96 1 0.00
97 2 0.01
98 5 0.02
99 42 0.14
100 11 0.04
101 190 0.63
102 9 0.03
103 2 0.01
104 1 0.00
105 1 0.00
106 18 0.06
107 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.28
Consensus pattern (101 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
TTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGG
Found at i:1653170 original size:65 final size:65
Alignment explanation
Indices: 1652911--1653400 Score: 297
Period size: 65 Copynumber: 7.3 Consensus size: 65
1652901 AAAGAGACAT
* * * *
1652911 AATTCGTTTCAAGGGAAAC-GATCTCAAAGATATTTGTTGGTTCATGAGAAACAGTCTCAAGGTA
1 AATTTGTTTCAAGGAAAACAGAT-TCAAAGAT-TTTG-T--TTCAAGAGAAACTGTCTCAAGG-A
*
1652975 A-ACAA
60 AGACGA
* * * *
1652980 AATTTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA-GAGAG
1 AA-TTTGTTTCAAGGAAAACAGATTCAAAGA-TTT-TGTTTCAAGAGAAACTGTCTCAAGGA-AG
1653044 AC-A
62 ACGA
* * * * * *
1653047 AAATT-TTT-AAGAGAAAA-TG-TCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACCGTCTCAA
1 AATTTGTTTCAAG-GAAAACAGAT-TC-A-A-AG----ATTTTGTTTCAAGAGAAACTGTCTCAA
1653108 GGAAGACGA
57 GGAAGACGA
*
1653117 AATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAA-GAGAGA-G
1 AATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGGA-AGACG
1653180 A
65 A
* ** * * * *
1653181 AATTT-TTTAAAGAGAAAATGTCTTAAGAGAGACAAA-A-TTTGTTTTAAAAGAAACTGTTTTAA
1 AATTTGTTTCAAG-GAAAA---C-----AGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAA
* *
1653243 GGGAGATGA
57 GGAAGACGA
* * * * *
1653252 AATTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAGCTGTCTCAAGGGAGACAA
1 AATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGGAAGACGA
* * *
1653317 AATTTGTTTCAAGGAAAACAGATTCAAAGATTTTTTTTCAAGAGAAACCGTCTCAA-GAGAGACA
1 AATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGGA-AGACG
1653381 A
65 A
*
1653382 AATTTGTTTTAAGAGAAAA
1 AATTTGTTTCAAG-GAAAA
1653401 TGTCTCAAGA
Statistics
Matches: 334, Mismatches: 49, Indels: 79
0.72 0.11 0.17
Matches are distributed among these distances:
63 13 0.04
64 21 0.06
65 128 0.38
66 9 0.03
67 8 0.02
68 21 0.06
69 28 0.08
70 57 0.17
71 29 0.09
72 19 0.06
73 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (65 bp):
AATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGGAAGACGA
Found at i:1653220 original size:135 final size:134
Alignment explanation
Indices: 1652957--1653321 Score: 525
Period size: 135 Copynumber: 2.7 Consensus size: 134
1652947 TTGGTTCATG
* * * *
1652957 AGAAACAGTCTCAAGGTAA-ACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTT
1 AGAAACAGTCTCAAGG-AAGACGAAA-TTTGTTTCAAGGAAAACAAATTCAAAGA-TTT-TGTTT
*
1653021 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTT
62 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTT
1653086 GTTTTAAA
127 GTTTTAAA
* *
1653094 AGAAACCGTCTCAAGGAAGACGAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAG
1 AGAAACAGTCTCAAGGAAGACGAAATTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAG
* * *
1653159 GGAAACTGTCTCAAGAGAGAGAAATTTTTTAAAGAGAAAATGTCTTAAGAGAGACAAAATTTGTT
66 GGAAACTGTCTCAAGAGAGACAAAATTTTT-AAGAGAAAATGTCTCAAGAGAGACAAAATTTGTT
1653224 TTAAA
130 TTAAA
* * * * *
1653229 AGAAACTGTTTTAAGGGAGATGAAATTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAG
1 AGAAACAGTCTCAAGGAAGACGAAATTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAG
* *
1653294 GGAAGCTGTCTCAAGGGAGACAAAATTT
66 GGAAACTGTCTCAAGAGAGACAAAATTT
1653322 GTTTCAAGGA
Statistics
Matches: 206, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
134 36 0.17
135 124 0.60
136 26 0.13
137 20 0.10
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (134 bp):
AGAAACAGTCTCAAGGAAGACGAAATTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTT
TAAA
Found at i:1653384 original size:166 final size:169
Alignment explanation
Indices: 1653148--1653658 Score: 568
Period size: 166 Copynumber: 3.0 Consensus size: 169
1653138 ATTCAAAGAT
* * * * * * *
1653148 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAGAAATTTTTTAAAGAGAAAATGTCTTAAGAGAGA
1 TTTGATTCAAGGAAAACAGTCTCAAGAGAGA-TATTTTTTTCAAGAGAAAATGTCTAAAGAGAGA
* * *
1653213 CAAAATTTGTTTTAAAAGAAACTGTTTTAAGGGAGATGAAATTTGTTTCAAGGAAAACAAATTCA
65 CAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAA-AAATTCA
** *
1653278 AAGATTTTGTTTCAAGGGAAGCTGTCTCAAGGGAGACAAAA
129 AAGATTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
* ** *
1653319 TTTGTTTCAAGGAAAACAGAT-TC-A-A-AGAT-TTTTTTTCAAGAGAAACCGTCTCAAGAGAGA
1 TTTGATTCAAGGAAAACAG-TCTCAAGAGAGATATTTTTTTCAAGAGAAAATGTCTAAAGAGAGA
* * * * * * *
1653379 CAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGTGACAAAATTTGTTTGAAGGAAAATAGATTCA
65 CAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAA-AAATTCA
* *
1653444 AAGATTTTGTTTCAAGGGAAATTGTCTGAAGATAGACAAAA
129 AAGATTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
* * * * *
1653485 TTTGATTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAGAAATTGTCTAAAAAGA
1 TTTGATTCAAGGAAAACAGTCTCAAGAGAGAT---ATTTTTTTCAAGAGAAAATGTCTAAAGAGA
* * *
1653550 GACAAAACTTAGTTTCAAAAGAAACTGTCTCAAGGGAGACGCAATTTGTTTCAAGG--AAAAATT
63 GACAAAA-TTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAAAAATT
* * *
1653613 CAAAGATTTTTTTTCAATGGAAATTGTCTCAAGAGACACAAAA
127 CAAAGATTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1653656 TTT
1 TTT
1653659 TATTTTGAGT
Statistics
Matches: 283, Mismatches: 47, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
165 1 0.00
166 134 0.47
167 1 0.00
168 4 0.01
169 5 0.02
170 1 0.00
171 64 0.23
172 3 0.01
173 31 0.11
174 39 0.14
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.30
Consensus pattern (169 bp):
TTTGATTCAAGGAAAACAGTCTCAAGAGAGATATTTTTTTCAAGAGAAAATGTCTAAAGAGAGAC
AAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAAAAATTCAAA
GATTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
Found at i:1653601 original size:73 final size:71
Alignment explanation
Indices: 1653449--1653608 Score: 194
Period size: 73 Copynumber: 2.2 Consensus size: 71
1653439 ATTCAAAGAT
* * * * **
1653449 TTTGTTTCAAGGGAAATTGTCTGAAGATAGACAAAATTTGATTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAA-GGAAATTGTCTAAAAAGAGACAAAATTAGATTCAAAAGAAACTGTCTCAAGAGA
*
1653514 GATAAAA
65 GACAAAA
* *
1653521 TTTGTTTCAAGAGAAATTGTCTAAAAAGAGACAAAACTTAGTTTCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAG-GAAATTGTCTAAAAAGAGACAAAA-TTAGATTCAAAAGAAACTGTCTCAAGAG
**
1653586 AGACGCAA
64 AGACAAAA
1653594 TTTGTTTCAAGGAAA
1 TTTGTTTCAAGGAAA
1653609 AATTCAAAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
71 1 0.01
72 35 0.47
73 39 0.52
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.28
Consensus pattern (71 bp):
TTTGTTTCAAGGAAATTGTCTAAAAAGAGACAAAATTAGATTCAAAAGAAACTGTCTCAAGAGAG
ACAAAA
Found at i:1658197 original size:162 final size:163
Alignment explanation
Indices: 1657930--1658254 Score: 643
Period size: 162 Copynumber: 2.0 Consensus size: 163
1657920 CAGTCAGTTC
1657930 TTCCAAGATAGACTTTCATTATGCTTAATGTAGACCCGATTCATTCTGAGTCCTTTATAACGCAG
1 TTCCAAGATAGACTTTCATTATGCTTAATGTAGACCCGATTCATTCTGAGTCCTTTATAACGCAG
1657995 CAGAGTGATATACCCTTCAATTGTGGGCACTGCATCTTCTAAATTGAATGTGACACATAGTTGCC
66 CAGAGTGATATACCCTTCAATTGTGGGCACTGCATCTTCTAAATTGAATGTGACACATAGTTGCC
1658060 TTGTAAACTGTCCTATGTA-TTTCATCTCTTGT
131 TTGTAAACTGTCCTATGTATTTTCATCTCTTGT
1658092 TTCCAAGATAGACTTTCATTATGCTTAATGTAGACCCGATTCATTCTGAGTCCTTTATAACGCAG
1 TTCCAAGATAGACTTTCATTATGCTTAATGTAGACCCGATTCATTCTGAGTCCTTTATAACGCAG
1658157 CAGAGTGATATACCCTTCAATTGTGGGCACTGCATCTTCTAAATTGAATGTGACACATAGTTGCC
66 CAGAGTGATATACCCTTCAATTGTGGGCACTGCATCTTCTAAATTGAATGTGACACATAGTTGCC
1658222 TTGTAAACTGTCCTATGTATTTTCATCTCTTGT
131 TTGTAAACTGTCCTATGTATTTTCATCTCTTGT
1658255 ATTACAACCC
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 149 0.92
163 13 0.08
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (163 bp):
TTCCAAGATAGACTTTCATTATGCTTAATGTAGACCCGATTCATTCTGAGTCCTTTATAACGCAG
CAGAGTGATATACCCTTCAATTGTGGGCACTGCATCTTCTAAATTGAATGTGACACATAGTTGCC
TTGTAAACTGTCCTATGTATTTTCATCTCTTGT
Found at i:1658425 original size:26 final size:24
Alignment explanation
Indices: 1658377--1658425 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
1658367 AAAAGTTAGC
*
1658377 AAAATAAAAATGATAAAATAAAAT
1 AAAATAAAAATGATAAAAGAAAAT
*
1658401 AAAATAAATAAATGATGAAAGAAAA
1 AAAAT-AA-AAATGATAAAAGAAAA
1658426 AATGAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 2 0.10
26 14 0.67
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (24 bp):
AAAATAAAAATGATAAAAGAAAAT
Found at i:1660905 original size:18 final size:18
Alignment explanation
Indices: 1660862--1660899 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1660852 AAGATATAAC
* *
1660862 ATAGTACATATATATTAT
1 ATAGTATATATATACTAT
1660880 ATAGTATATATATACTAT
1 ATAGTATATATATACTAT
1660898 AT
1 AT
1660900 GTTATAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
ATAGTATATATATACTAT
Found at i:1664462 original size:21 final size:21
Alignment explanation
Indices: 1664437--1664480 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1664427 AATTTAGTTA
1664437 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1664458 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1664479 AT
1 AT
1664481 ATTATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1664487 original size:5 final size:5
Alignment explanation
Indices: 1664477--1664537 Score: 67
Period size: 5 Copynumber: 12.6 Consensus size: 5
1664467 TTAGTTTAAG
*
1664477 TTATA TTATA TTATA TTATA TTA-A TT-TG TTAGT- TTA-A GTTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA TTATA -TTATA TTATA
1664525 TTATA TTATA TTA
1 TTATA TTATA TTA
1664538 ATTTGTTAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
4 5 0.10
5 42 0.86
6 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:1664505 original size:38 final size:38
Alignment explanation
Indices: 1664457--1664558 Score: 195
Period size: 38 Copynumber: 2.7 Consensus size: 38
1664447 TAGTATAAAT
*
1664457 TATTAGTTTGTTAGTTTAAGTTATATTATATTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTATATTATATTA
1664495 TATTAATTTGTTAGTTTAAGTTATATTATATTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTATATTATATTA
1664533 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
1664559 ATTAGATTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (38 bp):
TATTAATTTGTTAGTTTAAGTTATATTATATTATATTA
Found at i:1664519 original size:33 final size:34
Alignment explanation
Indices: 1664457--1664570 Score: 129
Period size: 38 Copynumber: 3.1 Consensus size: 34
1664447 TAGTATAAAT
*
1664457 TATTAGTTTGTTAGTTTAAGTTATATTATATTATATTA
1 TATTAATTTGTTAGTTTAAG---T-TTATATTATATTA
1664495 TATTAATTTGTTAGTTTAAGTTATATTATATTATATTA
1 TATTAATTTGTTAGTTTAAG---T-TTATATTATATTA
*
1664533 TATTAATTTGTTAGTTTAAGTTATATATTAGATTA
1 TATTAATTTGTTAGTTTAAGTT-TATATTATATTA
1664568 TAT
1 TAT
1664571 AAAAAATTAG
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
34 1 0.01
35 15 0.21
38 57 0.78
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (34 bp):
TATTAATTTGTTAGTTTAAGTTTATATTATATTA
Found at i:1664642 original size:45 final size:49
Alignment explanation
Indices: 1664534--1664642 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 49
1664524 ATTATATTAT
*
1664534 ATTAATTTGTTAGTTTAAGTTATATATTAGATTATATAAAAAATTAGTAA
1 ATTAATTTGTTAGTTTAAGTTATATA-TAGATTATATAAAAAAATAGTAA
* * * *
1664584 ATTAGTTTCTTAGTTTAAGTTAT-TA-A-ATGTA-A-AAAAAAATATTTA
1 ATTAATTTGTTAGTTTAAGTTATATATAGAT-TATATAAAAAAATAGTAA
1664629 ATTAATTTGTTAGT
1 ATTAATTTGTTAGT
1664643 GTGTTTAAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
45 22 0.43
46 3 0.06
47 3 0.06
49 2 0.04
50 21 0.41
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (49 bp):
ATTAATTTGTTAGTTTAAGTTATATATAGATTATATAAAAAAATAGTAA
Done.