Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 88 of 126
Found at i:26788133 original size:43 final size:43
Alignment explanation
Indices: 26788085--26788168 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
26788075 ACCCCAAAAC
** *
26788085 GACTCCAAGCCAATGCGCTTTTTGAATTGAAATCAAGTTAAAT
1 GACTCCAAGCCAACACACTTTTTGAATTGAAATCAAGTTAAAT
* *
26788128 GACTCCAAGCCAACACACTTTTTGAATTTAAATCGAGTTAA
1 GACTCCAAGCCAACACACTTTTTGAATTGAAATCAAGTTAA
26788169 CTTTAAGAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (43 bp):
GACTCCAAGCCAACACACTTTTTGAATTGAAATCAAGTTAAAT
Found at i:26803278 original size:43 final size:43
Alignment explanation
Indices: 26803224--26803348 Score: 150
Period size: 43 Copynumber: 3.0 Consensus size: 43
26803214 TCCCGAGGTG
26803224 TGATTTCGTGTAAGACCATGTCTAGGACATTGGCATCGATATGA
1 TGATTTCGTGTAAGACCATGTCTAGGACATTGGCATCGATAT-A
*
26803268 -GATTACGTGTAAGACCATGTCT-GCGACATTGGCATC-ATATA
1 TGATTTCGTGTAAGACCATGTCTAG-GACATTGGCATCGATATA
* * * * *
26803309 TGATTTCGTATAA-ACCCTATCTAGGATAGTGGCATCGATA
1 TGATTTCGTGTAAGACCATGTCTAGGACATTGGCATCGATA
26803349 CGCGATAACA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
41 18 0.26
42 19 0.27
43 33 0.47
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCATGTCTAGGACATTGGCATCGATATA
Found at i:26811576 original size:40 final size:40
Alignment explanation
Indices: 26811493--26811755 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
26811483 TTGAATGCTG
* * * * * *
26811493 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
26811533 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
26811573 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
26811613 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
26811653 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
26811693 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
26811732 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
26811756 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:26811775 original size:79 final size:80
Alignment explanation
Indices: 26811532--26811790 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
26811522 AAGTGAATAT
* * * * * *
26811532 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
26811596 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
26811612 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
26811677 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
26811692 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
26811756 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
26811771 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
26811791 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:26819529 original size:40 final size:40
Alignment explanation
Indices: 26819446--26819708 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
26819436 TTGAATGCTG
* * * * * *
26819446 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
26819486 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
26819526 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
26819566 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
26819606 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
26819646 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
26819685 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
26819709 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:26819728 original size:79 final size:80
Alignment explanation
Indices: 26819485--26819743 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
26819475 AAGTGAATAT
* * * * * *
26819485 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
26819549 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
26819565 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
26819630 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
26819645 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
26819709 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
26819724 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
26819744 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:26821948 original size:43 final size:44
Alignment explanation
Indices: 26821895--26821981 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
26821885 CCCGAGGTGT
* * *
26821895 GATTTCGTGTAAGACCGTGTCTGAGACATTGGCATCG-ATATGA
1 GATTACGTGTAAGACCATGTCTGAGACATTGACATCGTATATGA
* *
26821938 GATTACGTGTAAGACCATGTTTGCGACATTGACATCGTATATGA
1 GATTACGTGTAAGACCATGTCTGAGACATTGACATCGTATATGA
26821982 TTTCATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 32 0.84
44 6 0.16
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
GATTACGTGTAAGACCATGTCTGAGACATTGACATCGTATATGA
Found at i:26834076 original size:7 final size:8
Alignment explanation
Indices: 26834060--26834088 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
26834050 CTAATGTTAT
26834060 AAAAGAAA
1 AAAAGAAA
26834068 AAAAGAAA
1 AAAAGAAA
26834076 AAAAGAAA
1 AAAAGAAA
26834084 AAAAG
1 AAAAG
26834089 TACAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:26852643 original size:534 final size:534
Alignment explanation
Indices: 26851619--26852683 Score: 1697
Period size: 534 Copynumber: 2.0 Consensus size: 534
26851609 TTCTACTATA
* *
26851619 TGGAAGTACAATGAATGCTTTGTTAAATGTTATCTTATTAAATCTTATTTTTATTGTTTAATCTT
1 TGGAAGTACAATGAATGCTCTGTTAAATGTTATCTTATAAAATCTTATTTTTATTGTTTAATCTT
* *
26851684 GGGGGTTCGAATGTTCTAAACACGGAAGTGTTATTGCAGTCACTAACACTGGAAGGTGCAGTGAC
66 GGGGGTTCGAATCTTCTAAACACGGAAGTGTTATTGCAGTCACTAACACTAGAAGGTGCAGTGAC
* * *
26851749 AGTTTGAGCTAATAAGCATTTCAGTGGAAGTTGAGTAAGGACTAAAGGAATTTAGTCCACTTCTT
131 AGTTTGAGCTAATAAGAATTTCAGTAGAAGTTAAGTAAGGACTAAAGGAATTTAGTCCACTTCTT
* * *
26851814 CTTAATAGTGTCACATTTCCATCATCGAAAGGTAAGGTTAGTGTGCATGGCTAAGTCCCAGATTA
196 CTTAATAGTGTCACATTGCCATCATCGAAAGGTAAGGTTAATATGCATGGCTAAGTCCCAGATTA
* **
26851879 AATAAAAGAGTGGAATTTGGTAAGATATACATTAAATTTTATTACTTCGACAATCACCTATCTTT
261 AACAAAAGAGTGGAATTTGGTAAGATATACATTAAATTTTATTACGCCGACAATCACCTATCTTT
* *
26851944 TATACCTTGTGAGTACTTAGTATATTGCTTAAGATTCATGTTGGGGATCCCAATTTATCCATAGC
326 TATACCTTGTGAGTACTTAGTATACTGCTTAAGATTCATGTTGGGGATCCCAATTTATCCATAAC
*
26852009 ATACTTTATCTTATTATTGTCAAGTTATTTCTTCGACAACTATACTCAAAATTTATCTTGTTTCT
391 ATACTTTATCTTATTATTGTCAAGTTATTTCTTCGACAACTATACTCAAAATTTATCTTATTTCT
*
26852074 ATCTAGTTATTGCACCAACATTAATAGAAAAAAGACAACCATCCCTATAGGATCGATATCTAATA
456 ATCTAGTTATTGCACCAACATTAATAGAAAAAAGACAACCATCCCTATAGGATCGATATCTAACA
26852139 GACTCACATCTGTT
521 GACTCACATCTGTT
* *
26852153 TGGAAGTATAATGAATGCTCTGTTAAATGTTATCTTCTAAAATCTTATTTTTATTGTTTAATCTT
1 TGGAAGTACAATGAATGCTCTGTTAAATGTTATCTTATAAAATCTTATTTTTATTGTTTAATCTT
* * *
26852218 GGTGGTTTGAATCTTCTAAACACGGAAGTGTTATTGTAGTCACTAACACTAGAAGGTGCAGTGAC
66 GGGGGTTCGAATCTTCTAAACACGGAAGTGTTATTGCAGTCACTAACACTAGAAGGTGCAGTGAC
* * * *
26852283 AGTTTGATCTAATAAGAATTTCGGTAGAAGTTAAGTAAGGACTACAGGAATTTAGTCCACTTGTT
131 AGTTTGAGCTAATAAGAATTTCAGTAGAAGTTAAGTAAGGACTAAAGGAATTTAGTCCACTTCTT
* *
26852348 CTTAATAGTGTCATATTGCCATCATCCG-AAGGTAAGGTTAATATGCATGGTTAAGTCCCAGATT
196 CTTAATAGTGTCACATTGCCATCAT-CGAAAGGTAAGGTTAATATGCATGGCTAAGTCCCAGATT
* *
26852412 AAACAAAAGAGTGGCATTTGGTAAGATATACATTAAATTTTATTGCGCCGACAATCACCTATCTT
260 AAACAAAAGAGTGGAATTTGGTAAGATATACATTAAATTTTATTACGCCGACAATCACCTATCTT
26852477 TTATACCTTGTGAGTACTTAGTATACTG-TTGAAGATTCATGTTGGGGATCCCAATTTATCCATA
325 TTATACCTTGTGAGTACTTAGTATACTGCTT-AAGATTCATGTTGGGGATCCCAATTTATCCATA
* *
26852541 ACATACTTTATCTTATTATTTTCAAGTTATTGT-TTCGACAACTATACTCACAATTTATCTTATT
389 ACATACTTTATCTTATTATTGTCAAGTTATT-TCTTCGACAACTATACTCAAAATTTATCTTATT
* * * * * * * *
26852605 TCTATCTAGTTATAT-CACCGACATTAGTAGACAAAAGACAACCATGCTTGTGGGATCGATATTT
453 TCTATCTAGTTAT-TGCACCAACATTAATAGAAAAAAGACAACCATCCCTATAGGATCGATATCT
*
26852669 GACAGACTCACATCT
517 AACAGACTCACATCT
26852684 ATCTATTATA
Statistics
Matches: 486, Mismatches: 41, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
533 2 0.00
534 480 0.99
535 4 0.01
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (534 bp):
TGGAAGTACAATGAATGCTCTGTTAAATGTTATCTTATAAAATCTTATTTTTATTGTTTAATCTT
GGGGGTTCGAATCTTCTAAACACGGAAGTGTTATTGCAGTCACTAACACTAGAAGGTGCAGTGAC
AGTTTGAGCTAATAAGAATTTCAGTAGAAGTTAAGTAAGGACTAAAGGAATTTAGTCCACTTCTT
CTTAATAGTGTCACATTGCCATCATCGAAAGGTAAGGTTAATATGCATGGCTAAGTCCCAGATTA
AACAAAAGAGTGGAATTTGGTAAGATATACATTAAATTTTATTACGCCGACAATCACCTATCTTT
TATACCTTGTGAGTACTTAGTATACTGCTTAAGATTCATGTTGGGGATCCCAATTTATCCATAAC
ATACTTTATCTTATTATTGTCAAGTTATTTCTTCGACAACTATACTCAAAATTTATCTTATTTCT
ATCTAGTTATTGCACCAACATTAATAGAAAAAAGACAACCATCCCTATAGGATCGATATCTAACA
GACTCACATCTGTT
Found at i:26854071 original size:25 final size:25
Alignment explanation
Indices: 26854034--26854089 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 25
26854024 CTATACATGA
26854034 ATGCTCATACGAGTTGT-GAATCAGT
1 ATGCTCATACGAGTTGTAG-ATCAGT
26854059 ATGCTCACT-CGAGTTGTAGATCAGT
1 ATGCTCA-TACGAGTTGTAGATCAGT
26854084 ATGCTC
1 ATGCTC
26854090 TCATGAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 27 0.93
26 2 0.07
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (25 bp):
ATGCTCATACGAGTTGTAGATCAGT
Found at i:26854106 original size:25 final size:25
Alignment explanation
Indices: 26854052--26854125 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 25
26854042 ACGAGTTGTG
* *
26854052 AATCAGTATGCTCACTCGAGTTGTA
1 AATCAGTATGCTCACTCGAGCTATA
* *
26854077 GATCAGTATGCTCTCAT-GAGCTATA
1 AATCAGTATGCTCAC-TCGAGCTATA
* * *
26854102 AATCAGAATGCACACACGAGCTAT
1 AATCAGTATGCTCACTCGAGCTAT
26854126 GAGTCAGAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
25 37 0.97
26 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (25 bp):
AATCAGTATGCTCACTCGAGCTATA
Found at i:26857931 original size:48 final size:49
Alignment explanation
Indices: 26857835--26857945 Score: 152
Period size: 48 Copynumber: 2.3 Consensus size: 49
26857825 ACTGAATCAC
* ** *
26857835 TTTAATATTAAATTAATATGATACTTATCAAGAAAAATATTAAATTAAA
1 TTTAATATTAAATTAACAAAATACTTATCAAGAAAAATATCAAATTAAA
* * *
26857884 TTTAATATTAAATTAACAAAATAC-TATCAATATAAGTATCAAATTAAA
1 TTTAATATTAAATTAACAAAATACTTATCAAGAAAAATATCAAATTAAA
26857932 TTTAATATTAAATT
1 TTTAATATTAAATT
26857946 TATTACAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 34 0.62
49 21 0.38
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (49 bp):
TTTAATATTAAATTAACAAAATACTTATCAAGAAAAATATCAAATTAAA
Found at i:26858340 original size:13 final size:13
Alignment explanation
Indices: 26858319--26858351 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
26858309 TTAAATTTAA
26858319 TTAATTTGATGAAT
1 TTAA-TTGATGAAT
26858333 TTAATTGATGAAT
1 TTAATTGATGAAT
26858346 TTAATT
1 TTAATT
26858352 TAGTTAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (13 bp):
TTAATTGATGAAT
Found at i:26863556 original size:14 final size:16
Alignment explanation
Indices: 26863526--26863557 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26863516 CTTATTTTAA
26863526 TTTTTATATAAATAAT
1 TTTTTATATAAATAAT
26863542 TTTTTAT-TAAA-AAT
1 TTTTTATATAAATAAT
26863556 TT
1 TT
26863558 GATTTTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 4 0.25
16 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTATATAAATAAT
Found at i:26863646 original size:19 final size:19
Alignment explanation
Indices: 26863624--26863673 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
26863614 ATTAAATTCC
26863624 ATTTAAT-TATCTTTTAAAA
1 ATTTAATATAT-TTTTAAAA
*
26863643 ATTTTCATATATTTTTAAAA
1 A-TTTAATATATTTTTAAAA
*
26863663 ATATAA-ATATT
1 ATTTAATATATT
26863674 ATAATAGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 5 0.19
19 4 0.15
20 14 0.54
21 3 0.12
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTAATATATTTTTAAAA
Found at i:26871808 original size:30 final size:30
Alignment explanation
Indices: 26871774--26871836 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
26871764 ACTTATTTTA
*
26871774 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
*
26871804 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
26871834 TTG
1 TTG
26871837 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:26871985 original size:12 final size:12
Alignment explanation
Indices: 26871962--26871995 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
26871952 TATAATTTTT
26871962 AAAATT-ATATA
1 AAAATTAATATA
26871973 AAAATTAATATA
1 AAAATTAATATA
26871985 AAAATTAATAT
1 AAAATTAATAT
26871996 GGGTAAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:26878628 original size:32 final size:32
Alignment explanation
Indices: 26878592--26878656 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
26878582 AAGCTCAAAG
26878592 TAAGTGGGCTCGACAATGGACAAAAATCAGTC
1 TAAGTGGGCTCGACAATGGACAAAAATCAGTC
26878624 TAAGTGGGCTCGACAATGGACAAAAATCAGTC
1 TAAGTGGGCTCGACAATGGACAAAAATCAGTC
26878656 T
1 T
26878657 TAAGGAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (32 bp):
TAAGTGGGCTCGACAATGGACAAAAATCAGTC
Found at i:26879561 original size:73 final size:74
Alignment explanation
Indices: 26879427--26879577 Score: 216
Period size: 73 Copynumber: 2.1 Consensus size: 74
26879417 CCCAGCCCTC
* * *
26879427 GTGTCTTTCAAAATCTTAAAAAATTAAGCTCTAGGACTCACATAGACTAGGACACTCCCTTGTGT
1 GTGTCTTTCAAAATCTTAAAAAATTAAGCTCCAGGACTCACATAGACTAGGACACGCCCTTGTAT
*
26879492 CCTTGCCGT
66 CCTGGCCGT
* * *
26879501 GTGTCTTTCAAAATCTT-AAAAATTAAGCTCCAGGACTCACATGGCCTAAGG-CACGGCCTTGTA
1 GTGTCTTTCAAAATCTTAAAAAATTAAGCTCCAGGACTCACATAGACT-AGGACACGCCCTTGTA
26879564 TCCTGGCCGT
65 TCCTGGCCGT
26879574 GTGT
1 GTGT
26879578 AATCATTCTT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 49 0.71
74 20 0.29
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (74 bp):
GTGTCTTTCAAAATCTTAAAAAATTAAGCTCCAGGACTCACATAGACTAGGACACGCCCTTGTAT
CCTGGCCGT
Found at i:26884126 original size:10 final size:10
Alignment explanation
Indices: 26884111--26884141 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
26884101 ATAAAATCCA
26884111 TTTTTAATAT
1 TTTTTAATAT
26884121 TTTTTAATAT
1 TTTTTAATAT
26884131 TTTTTATATAT
1 TTTTTA-ATAT
26884142 ATTCGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:26886270 original size:18 final size:18
Alignment explanation
Indices: 26886247--26886286 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
26886237 TTAAACCCTT
*
26886247 AAAAACCCTAACCCTAAC
1 AAAAACCCTAAACCTAAC
26886265 AAAAACCCTAAACCTAAC
1 AAAAACCCTAAACCTAAC
26886283 AAAA
1 AAAA
26886287 TTAAAAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.57, C:0.33, G:0.00, T:0.10
Consensus pattern (18 bp):
AAAAACCCTAAACCTAAC
Found at i:26888135 original size:18 final size:18
Alignment explanation
Indices: 26888112--26888146 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
26888102 CCCAGCCGTC
26888112 TTCTCATTTCTTTCTCAT
1 TTCTCATTTCTTTCTCAT
26888130 TTCTCATTTCTTTCTCA
1 TTCTCATTTCTTTCTCA
26888147 CGTCTGAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
TTCTCATTTCTTTCTCAT
Found at i:26890735 original size:120 final size:120
Alignment explanation
Indices: 26890581--26890847 Score: 489
Period size: 120 Copynumber: 2.2 Consensus size: 120
26890571 AAAAATTGAT
26890581 TATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATT
1 TATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATT
* *
26890646 CATATAAGAATATTTAATATTATGAATTTTATTAAATCATATATTTTAATTAAAA
66 CATATAAGAATATTGAATATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
26890701 TATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATT
1 TATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATT
* *
26890766 CATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAA
66 CATATAAGAATATTGAATATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
26890821 TATATTTAATAATAATTATGTTTAAAT
1 TATATTTAATAATAATTATG-TTAAAT
26890848 ATGATTAAAT
Statistics
Matches: 142, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
120 136 0.96
121 6 0.04
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
TATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATT
CATATAAGAATATTGAATATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
Found at i:26890819 original size:18 final size:17
Alignment explanation
Indices: 26890791--26890825 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
26890781 ATTATTAAGA
*
26890791 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
26890808 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
26890826 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:26891134 original size:16 final size:16
Alignment explanation
Indices: 26891113--26891164 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
26891103 TTTGGTTCGC
26891113 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
26891129 TGTATTGGATTATAGG
1 TGTATTGGATTAGAGG
* *
26891145 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
26891161 TGTA
1 TGTA
26891165 ATAGCAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:26891211 original size:45 final size:44
Alignment explanation
Indices: 26891145--26891239 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
26891135 GGATTATAGG
* *
26891145 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
26891190 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
26891234 TGTAAT
1 TGTAAT
26891240 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:26891422 original size:18 final size:17
Alignment explanation
Indices: 26891401--26891435 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
26891391 TTATTATTTA
*
26891401 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
26891419 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
26891436 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:26891429 original size:28 final size:27
Alignment explanation
Indices: 26891359--26891431 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
26891349 TTTATTATCA
*
26891359 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
26891387 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
26891414 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
26891432 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:26891569 original size:18 final size:17
Alignment explanation
Indices: 26891548--26891582 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
26891538 TTATTATTAA
*
26891548 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
26891566 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
26891583 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:26891594 original size:147 final size:149
Alignment explanation
Indices: 26891320--26891594 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
26891310 ATGATTATTG
*
26891320 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
26891385 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
26891450 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
*
26891469 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
26891532 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
26891595 ATATTCTTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 95 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:26891626 original size:54 final size:54
Alignment explanation
Indices: 26891568--26891746 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 54
26891558 ATTAAAATAT
*
26891568 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
** * * * * *
26891622 ATAATATATGATACTGTAAAATAT-AAAATAACATAATTATTATTAAATAT-AATATAATTAAAA
1 ATAAT-T-T-A-A---TAAAAT-TCTTAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA
*
26891685 TAT
53 -AC
*
26891688 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
26891742 ATAAT
1 ATAAT
26891747 ATATGATACT
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 4 0.04
57 7 0.08
58 5 0.05
59 11 0.12
61 11 0.12
62 5 0.05
63 7 0.08
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:26891689 original size:18 final size:17
Alignment explanation
Indices: 26891668--26891702 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
26891658 TTATTATTAA
26891668 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
26891686 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
26891703 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:26891817 original size:18 final size:17
Alignment explanation
Indices: 26891778--26891809 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
26891768 TTTTAAATAA
26891778 TTAATATTAAATATATT
1 TTAATATTAAATATATT
26891795 TTAAT-TTAAATATAT
1 TTAATATTAAATATAT
26891810 GATTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATTAAATATATT
Found at i:26891834 original size:120 final size:120
Alignment explanation
Indices: 26891531--26891823 Score: 482
Period size: 120 Copynumber: 2.4 Consensus size: 120
26891521 ATCATATTTA
26891531 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
26891596 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAAAT
* *
26891651 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
26891716 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATA-AAATTTT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAA--AT
* * *
26891772 AA-ATAATTAATATTAAATATATTTTAATTTAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
26891824 TAAAATAATT
Statistics
Matches: 161, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
119 3 0.02
120 155 0.96
121 3 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAAAT
Found at i:26891934 original size:91 final size:91
Alignment explanation
Indices: 26891839--26892046 Score: 258
Period size: 91 Copynumber: 2.3 Consensus size: 91
26891829 TAATTATAAC
* * * *
26891839 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
26891903 TAATATAAAATTTCATAAAATTCTTGA
65 TAATATAAAATTTCATAAAATTCTTAA
* * *
26891930 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* * * *
26891995 GATATATAATTTCATGAAATTGTTAA
66 AATATAAAATTTCATAAAATTCTTAA
*
26892021 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
26892047 CTAAAATCAA
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
91 79 0.77
92 22 0.22
93 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATAAAATTTCATAAAATTCTTAA
Found at i:26892575 original size:12 final size:12
Alignment explanation
Indices: 26892560--26892589 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
26892550 AATACAAACA
26892560 ACAGAAGCTGCT
1 ACAGAAGCTGCT
26892572 ACAGAAGCTGCT
1 ACAGAAGCTGCT
*
26892584 AAAGAA
1 ACAGAA
26892590 ATTAACCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (12 bp):
ACAGAAGCTGCT
Found at i:26892868 original size:14 final size:14
Alignment explanation
Indices: 26892849--26892879 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
26892839 AAAATATTAA
26892849 CAACAAATAGTTCC
1 CAACAAATAGTTCC
26892863 CAACAAATAGTTCC
1 CAACAAATAGTTCC
26892877 CAA
1 CAA
26892880 TTGCCAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (14 bp):
CAACAAATAGTTCC
Found at i:26895857 original size:20 final size:21
Alignment explanation
Indices: 26895832--26895885 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
26895822 TAAAAATAGT
*
26895832 TGACTTGA-TGGTTGAATCAA
1 TGACTTGACTGGTTGAACCAA
*
26895852 TGACTTGACT-GATGAACCAA
1 TGACTTGACTGGTTGAACCAA
26895872 TGACTTGACTGGTT
1 TGACTTGACTGGTT
26895886 CGACTACCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (21 bp):
TGACTTGACTGGTTGAACCAA
Found at i:26898204 original size:3 final size:3
Alignment explanation
Indices: 26898196--26898225 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
26898186 TCATTCTTGC
26898196 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
26898226 AGAAGTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:26898630 original size:31 final size:31
Alignment explanation
Indices: 26898592--26898692 Score: 166
Period size: 31 Copynumber: 3.3 Consensus size: 31
26898582 TTGATATTTC
26898592 CAAGTTTAGGCCTCAATTTGGGAGCAATTGT
1 CAAGTTTAGGCCTCAATTTGGGAGCAATTGT
26898623 CAAGTTTAGGCCTCAATTTGGGAGCAATTGT
1 CAAGTTTAGGCCTCAATTTGGGAGCAATTGT
* * * *
26898654 CAAGTTCAGGCCTCAATGTGGGAACAATTCT
1 CAAGTTTAGGCCTCAATTTGGGAGCAATTGT
26898685 CAAGTTTA
1 CAAGTTTA
26898693 AGGGCTAACT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (31 bp):
CAAGTTTAGGCCTCAATTTGGGAGCAATTGT
Found at i:26898790 original size:58 final size:58
Alignment explanation
Indices: 26898667--26898792 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 58
26898657 GTTCAGGCCT
* ** * * *
26898667 CAATGTGGGAACAATTCTCAAGTTTAAGGGCTAACTTGAACAAAAAGAGCTCTAGCCC
1 CAATGTGGGAACAATTATCAAGTACAAGGACTAACTTGAACAAAAAAAGCTCTAGACC
* * * * *
26898725 CAGTGTGGGAATAATTATCAAGTACAAGGACTAATTTGGACAAAAAAAG-TTTAGAACC
1 CAATGTGGGAACAATTATCAAGTACAAGGACTAACTTGAACAAAAAAAGCTCTAG-ACC
26898783 CAATGTGGGA
1 CAATGTGGGA
26898793 GTTATTTCCA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 51 0.93
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (58 bp):
CAATGTGGGAACAATTATCAAGTACAAGGACTAACTTGAACAAAAAAAGCTCTAGACC
Found at i:26899490 original size:13 final size:13
Alignment explanation
Indices: 26899472--26899499 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
26899462 AGTAATCTTC
26899472 TTTTCTATGTAAG
1 TTTTCTATGTAAG
26899485 TTTTCTATGTAAG
1 TTTTCTATGTAAG
26899498 TT
1 TT
26899500 CAAGTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (13 bp):
TTTTCTATGTAAG
Found at i:26899537 original size:3 final size:3
Alignment explanation
Indices: 26899529--26899564 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
26899519 TCTTGCTTAT
* *
26899529 TTA TTA TTA ATA CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
26899565 AGAAGTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:26901482 original size:15 final size:16
Alignment explanation
Indices: 26901462--26901494 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26901452 TATTTCACTA
*
26901462 TTATGT-TTTTTTATT
1 TTATGTGTTTTATATT
26901477 TTATGTGTTTTATATT
1 TTATGTGTTTTATATT
26901493 TT
1 TT
26901495 GCATGTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (16 bp):
TTATGTGTTTTATATT
Found at i:26902681 original size:18 final size:18
Alignment explanation
Indices: 26902658--26902692 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
26902648 TTTTGATCAA
26902658 GTAAAATTAAATTAATCG
1 GTAAAATTAAATTAATCG
26902676 GTAAAATTAAATTAATC
1 GTAAAATTAAATTAATC
26902693 AAATCAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (18 bp):
GTAAAATTAAATTAATCG
Found at i:26903171 original size:37 final size:36
Alignment explanation
Indices: 26903120--26903227 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 36
26903110 GTTCCAAAAA
*
26903120 TAATATTATTTTAATAGTTTAATATTACATTTAAT-T
1 TAATATTATCTTAATAGTTTAATATTA-ATTTAATAT
*
26903156 TAATACTTATCTTAATAGTATT-TTATTAATTTAATAT
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTAATAT
*
26903193 TAAAGTGATTATCTTAATA-TTAAAT-TTAATTTAAT
1 T-AA-T-ATTATCTTAATAGTTTAATATTAATTTAAT
26903228 GTTTATCTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
36 12 0.20
37 30 0.49
38 6 0.10
39 12 0.20
40 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (36 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATAT
Found at i:26911924 original size:19 final size:19
Alignment explanation
Indices: 26911900--26911938 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
26911890 AATTACAAGA
26911900 ATGTCACCTAACTCTTAAT
1 ATGTCACCTAACTCTTAAT
26911919 ATGTCACCTAACTCTTAAT
1 ATGTCACCTAACTCTTAAT
26911938 A
1 A
26911939 CCAATTCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (19 bp):
ATGTCACCTAACTCTTAAT
Found at i:26914180 original size:31 final size:31
Alignment explanation
Indices: 26914142--26914211 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
26914132 TTAATATTTC
* *
26914142 CAAGTTTAGGCCCCAATTTGGGAGCAATTGT
1 CAAGTTTAGGCCCCAATGTGGGAACAATTGT
*
26914173 CAAGTTTAGGCCTCAATGTGGGAACAATTGT
1 CAAGTTTAGGCCCCAATGTGGGAACAATTGT
26914204 CAAGTTTA
1 CAAGTTTA
26914212 AGGACTAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (31 bp):
CAAGTTTAGGCCCCAATGTGGGAACAATTGT
Found at i:26917960 original size:17 final size:18
Alignment explanation
Indices: 26917938--26917973 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
26917928 CCAAAATTTT
26917938 ATTTTAATGTT-TTATAC
1 ATTTTAATGTTATTATAC
*
26917955 ATTTTAATTTTATTATAC
1 ATTTTAATGTTATTATAC
26917973 A
1 A
26917974 CATTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTTAATGTTATTATAC
Found at i:26918508 original size:70 final size:71
Alignment explanation
Indices: 26918384--26918535 Score: 252
Period size: 70 Copynumber: 2.2 Consensus size: 71
26918374 TTGTAGTGCA
* *
26918384 TTTAATATTGTTAATGTGATGCATTTATATGTTTAAATTTCTTTTTACTCGCAATGTAATTAAAT
1 TTTAATATTGTTAATGTGATGCATTTATATGTTTAAATTTCTTTTTAATCGCAATGTAATTAAAA
26918449 TTTTAT
66 TTTTAT
* * *
26918455 TTTTATATTGTTAATGTGATGTATTTATGT-TTTAAATTTCTTTTTAATCGCAATGTAATTAAAA
1 TTTAATATTGTTAATGTGATGCATTTATATGTTTAAATTTCTTTTTAATCGCAATGTAATTAAAA
26918519 TTTTAT
66 TTTTAT
26918525 TTTAATATTGT
1 TTTAATATTGT
26918536 ATATATTTCT
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
70 48 0.64
71 27 0.36
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (71 bp):
TTTAATATTGTTAATGTGATGCATTTATATGTTTAAATTTCTTTTTAATCGCAATGTAATTAAAA
TTTTAT
Found at i:26918523 original size:35 final size:35
Alignment explanation
Indices: 26918415--26918523 Score: 96
Period size: 35 Copynumber: 3.1 Consensus size: 35
26918405 CATTTATATG
* *
26918415 TTTAAATTTCTTTTTACTCGCAATGTAATTAAATT
1 TTTAAATTTCTTTTTAATCGCAATGTAATTAAAAT
** * ** * **
26918450 TTTATTTTTATATTGTTAAT-GTGATGT-ATTTATGT
1 TTTAAATTTCT-TT-TTAATCGCAATGTAATTAAAAT
26918485 TTTAAATTTCTTTTTAATCGCAATGTAATTAAAAT
1 TTTAAATTTCTTTTTAATCGCAATGTAATTAAAAT
26918520 TTTA
1 TTTA
26918524 TTTTAATATT
Statistics
Matches: 53, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
33 5 0.09
34 7 0.13
35 30 0.57
36 7 0.13
37 4 0.08
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.55
Consensus pattern (35 bp):
TTTAAATTTCTTTTTAATCGCAATGTAATTAAAAT
Found at i:26931849 original size:11 final size:11
Alignment explanation
Indices: 26931833--26931857 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
26931823 ATTGGATATC
26931833 AAAATTCAATT
1 AAAATTCAATT
26931844 AAAATTCAATT
1 AAAATTCAATT
26931855 AAA
1 AAA
26931858 CAAACATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATTCAATT
Found at i:26934868 original size:26 final size:27
Alignment explanation
Indices: 26934814--26934920 Score: 117
Period size: 27 Copynumber: 4.0 Consensus size: 27
26934804 TAAGCGATCT
* *
26934814 TTTTAGAATTTGCCATAAAGGCTATTC
1 TTTTAGAGTTTGCCACAAAGGCTATTC
* *
26934841 TTTCAGAGTTTGCCACAAATG-TATTC
1 TTTTAGAGTTTGCCACAAAGGCTATTC
* * *
26934867 TTTTATAGTTCGCCACAAAGGCTGTTC
1 TTTTAGAGTTTGCCACAAAGGCTATTC
** *
26934894 TTTTAGAGTTCACCATAAAGGCTATTC
1 TTTTAGAGTTTGCCACAAAGGCTATTC
26934921 CTTGTTGTCG
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
26 22 0.33
27 44 0.67
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (27 bp):
TTTTAGAGTTTGCCACAAAGGCTATTC
Found at i:26935780 original size:12 final size:12
Alignment explanation
Indices: 26935763--26935788 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
26935753 GGAAAAAAAG
26935763 GAGAAAGAGGAA
1 GAGAAAGAGGAA
26935775 GAGAAAGAGGAA
1 GAGAAAGAGGAA
26935787 GA
1 GA
26935789 AGAAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
GAGAAAGAGGAA
Found at i:26935788 original size:18 final size:18
Alignment explanation
Indices: 26935743--26935801 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
26935733 CCACTTAAGG
26935743 AAGAGGAAGAGGAA-AAA
1 AAGAGGAAGAGGAAGAAA
* *
26935760 AAGGAGAAAGAGGAAGAGA
1 AA-GAGGAAGAGGAAGAAA
*
26935779 AAGAGGAAGAAGAAGAAA
1 AAGAGGAAGAGGAAGAAA
26935797 GAAGA
1 -AAGA
26935802 ACCCCTTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 2 0.06
18 24 0.71
19 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (18 bp):
AAGAGGAAGAGGAAGAAA
Found at i:26959042 original size:17 final size:18
Alignment explanation
Indices: 26959010--26959055 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
26959000 ATATATTTAT
*
26959010 TAACATT-TTTT-GTATA
1 TAACATTATTTTACTATA
26959026 T-ACATTATTTTACTATA
1 TAACATTATTTTACTATA
*
26959043 TAATATTATTTTA
1 TAACATTATTTTA
26959056 AGTGTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 5 0.20
17 5 0.20
18 10 0.40
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (18 bp):
TAACATTATTTTACTATA
Found at i:26960969 original size:31 final size:30
Alignment explanation
Indices: 26960933--26960990 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
26960923 TTATAAAAAA
26960933 AATTAT-AGCAAATTATTTAAAAATTATTGAG
1 AATTATAAG-AAATTA-TTAAAAATTATTGAG
*
26960964 AATTATAAGAAATTATTAATAATTATT
1 AATTATAAGAAATTATTAAAAATTATT
26960991 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 12 0.48
32 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (30 bp):
AATTATAAGAAATTATTAAAAATTATTGAG
Found at i:26961277 original size:21 final size:21
Alignment explanation
Indices: 26961239--26961282 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
26961229 TGAATGTTGA
* *
26961239 TTTCAATAAATTTTAAATATT
1 TTTCAATAAATCTAAAATATT
*
26961260 TTTCAATAAATCTAAAATCTT
1 TTTCAATAAATCTAAAATATT
26961281 TT
1 TT
26961283 AAATAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTCAATAAATCTAAAATATT
Found at i:26961282 original size:20 final size:21
Alignment explanation
Indices: 26961239--26961288 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
26961229 TGAATGTTGA
*
26961239 TTTCAATAAATTTTAAATATT
1 TTTCAATAAATTCTAAATATT
26961260 TTTCAATAAA-TCTAAA-ATCT
1 TTTCAATAAATTCTAAATAT-T
*
26961280 TTTAAATAA
1 TTTCAATAA
26961289 TTTTCTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 10 0.38
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTCAATAAATTCTAAATATT
Found at i:26962977 original size:12 final size:12
Alignment explanation
Indices: 26962960--26962987 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
26962950 ATATGAAGAC
26962960 ATTAAAAATCAG
1 ATTAAAAATCAG
26962972 ATTAAAAATCAG
1 ATTAAAAATCAG
26962984 ATTA
1 ATTA
26962988 TCACATACCA
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:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (12 bp):
ATTAAAAATCAG
Found at i:26968208 original size:94 final size:93
Alignment explanation
Indices: 26968109--26969539 Score: 1462
Period size: 94 Copynumber: 15.3 Consensus size: 93
26968099 TCATTTCAAC
* * * * *
26968109 CCACTGTAACTTCAAGGGTATAGGATTTGTAGCTTCGTCTTGCTCCACTGCAACTTTAGGGAAAT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
* * * *
26968174 AAGATTCGCTATTGTAGTTTCATTATGA
66 AAGATTCGCTATGGTAGCTTCAATCTGA
* * * * * *
26968202 CACACTGCATCTTCAGGGGTATAGGATTTCTAACTTTATCTTGCTCCACTACAACTTCAGGAAGA
1 C-CACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
* * * *
26968267 TAAGATTCGCTATGGTAACTTTATTCTGG
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* * * ** * *
26968296 CCTACTACATCCTCAGGGACATAGGATTTGTAGCTTCATCTTGCTCCATTGCAACTTCAAGGAGA
1 CC-ACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
* *
26968361 TAAGATTTGCTATGGTAGCTTC-ATTTCGA
65 TAAGATTCGCTATGGTAGCTTCAATCT-GA
* * * * * * * * * ** * *
26968390 CCTATTTCATCTTCAGGGGCATAGAATTTGTAGCTTTATTTTGTTTCACTATAATTTTAGGGAGA
1 CC-ACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
* ***
26968455 TAAGATTCACTATGGTAGCTTCAATAAAA
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* * * *
26968484 CCTACTGCAACTTCAGGGGTATATGATTTGTAGCTTCATCTTACTCCACTACAACTTCAAGGAGA
1 CC-ACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
* *
26968549 TAAGATTTGCTATGGTAGCTTCATTCTGA
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* * * *
26968578 CCCATTGTAACTTCAGGGGTATAGGATTTGTAGCTTCA-CTTTGCTCCACTGTAACTTTAGGGAG
1 -CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATC-TTGCTCCACTGCAACTTCAGGGAG
* * *
26968642 ATAAGATTTGCTATGGTAGCTTCATTCCGA
64 ATAAGATTCGCTATGGTAGCTTCAATCTGA
* * * * * *
26968672 CCACTGCAACTCCAGGGGTATAGGATTTATAGCTTCATCTTACTCTACTGTAACGTCAGGGAGAT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
26968737 AAGATTCGCTATGGTAGCTTCAATCTGA
66 AAGATTCGCTATGGTAGCTTCAATCTGA
* * * * *
26968765 CCTACTGTAACTTCAGAGGTATAAGATTTGTAGCTTCATCTTGCTTCACTTCAACTTCAGGGAGA
1 CC-ACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
*
26968830 TAAGATTCGCTATTGTAGCTTCAATCTGA
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* * * * *
26968859 TCCACTGCAACTTCAGGGGTACAAGATTTGTAGCTCCATCTTTCTCCACTGCAACTTCAAGGAGA
1 -CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
* *
26968924 TAAAATTTAG-T-TGGTAGCTTCAATCTGA
65 TAAGA-TTCGCTATGGTAGCTTCAATCTGA
* * * * * *
26968952 CCTGCTGCAACTTCAAGGGTATATGATTTGTAGCTTTATCTTGCTCCACTACAACTTTAGGGAGA
1 CC-ACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
26969017 T-AGATTCGCTATGGTA--TTC---C-GA
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* * * * * *
26969039 CCCATTGCATCTTCAAGGGTATATGATTTGTAGCTTCATCTTACTCCACTGTAACTTCAGGGAGA
1 -CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
* * *
26969104 TAGGATTCGCTATGGTAGCTTTAATTTGA
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* * * * * *
26969133 CCCACTGTAACTTTAGGGGTATAAGATTTGTATCTTCATCTTGCTCCACTGCAAATTTAGGGAGA
1 -CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
*
26969198 TAAGATTCACTATGGTAGCTTCAATCTGA
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* * * * * *
26969227 CCCACTGCAACTTCAGGGGTACAGGATTTATGGCTTCATCTTACTCCACTGCAACTTCAGGAAGG
1 -CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
26969292 TAAGATTCGCTATGGTAGCTTCAATCTGA
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* * * * * * ** **
26969321 CCCACTACAACTTCAGAGGTATAAGATTTGTAGCTTCATGTTACTCCATTAAAACTTCAAAGAGA
1 -CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
* *** *
26969386 TAATATTTATTATTGTAGCTTCAATCTGA
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* * * * * *
26969415 CCCACTACAATTTCAGGGGTATAGGATTTCTAGCTTTATCTTGCTCCACTGTAGCTTCAGGGAGA
1 -CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
* *
26969480 TAAGATTTGCTATGGTAGCTTCAATCCGA
65 TAAGATTCGCTATGGTAGCTTCAATCTGA
* *
26969509 CATACTGCAACTTCAAGGGTATAGGATTTGT
1 C-CACTGCAACTTCAGGGGTATAGGATTTGT
26969540 TATTTCATTG
Statistics
Matches: 1105, Mismatches: 211, Indels: 43
0.81 0.16 0.03
Matches are distributed among these distances:
87 57 0.05
88 17 0.02
90 2 0.00
91 6 0.01
92 5 0.00
93 162 0.15
94 847 0.77
95 9 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (93 bp):
CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
AAGATTCGCTATGGTAGCTTCAATCTGA
Found at i:26968539 original size:44 final size:44
Alignment explanation
Indices: 26968487--26969488 Score: 380
Period size: 44 Copynumber: 21.6 Consensus size: 44
26968477 AATAAAACCT
*
26968487 ACTGCAACTTCAGGGGTATATGATTTGTAGCTTCATCTTACTCC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
* * *
26968531 ACTACAACTTCAAGGAG-ATAAGATTTGCTATGGTAGCTTCATTCTGAC-CC
1 ACTGCAACTTC-AGGGGTATAAGA--T--T-T-GTAGCTTCA-TCTTACTCC
* * * *
26968581 ATTGTAACTTCAGGGGTATAGGATTTGTAGCTTCA-CTTTGCTCC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATC-TTACTCC
* * * * * * *
26968625 ACTGTAACTTTAGGGAG-ATAAGATTTGCTATGGTAGCTTCATTCCGACC
1 ACTGCAACTTCAGGG-GTATAAGATTTG-TA-GCT-TCATC-TTAC-TCC
* * * *
26968674 ACTGCAACTCCAGGGGTATAGGATTTATAGCTTCATCTTACTCT
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
* * * *
26968718 ACTGTAACGTCAGGGAG-ATAAGATTCGCTATGGTAGCTTCAATCTGAC-CT
1 ACTGCAACTTCAGGG-GTATAAGA-T---T-T-GTAGCTTC-ATCTTACTCC
* * * *
26968768 ACTGTAACTTCAGAGGTATAAGATTTGTAGCTTCATCTTGCTTC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
* *
26968812 ACTTCAACTTCAGGGAG-ATAAGATTCGCTATTGTAGCTTCAATCTGA-TCC
1 ACTGCAACTTCAGGG-GTATAAGA-----T-TTGTAGCTTC-ATCTTACTCC
* * *
26968862 ACTGCAACTTCAGGGGTACAAGATTTGTAGCTCCATCTTTCTCC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
* * * *
26968906 ACTGCAACTTCAAGGAG-ATAAAATTTAGTTGGTAGCTTCAATCTGAC-CT
1 ACTGCAACTTC-AGGGGTATAAGA--T--TT-GTAGCTTC-ATCTTACTCC
* * * * *
26968955 GCTGCAACTTCAAGGGTATATGATTTGTAGCTTTATCTTGCTCC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
* * * * **
26968999 ACTACAACTTTAGGGAG-AT-AGATTCGCTATG-GT-ATTCCGAC-CC
1 ACTGCAACTTCAGGG-GTATAAGATTTG-TA-GCTTCA-TCTTACTCC
* * * *
26969042 ATTGCATCTTCAAGGGTATATGATTTGTAGCTTCATCTTACTCC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
* * *
26969086 ACTGTAACTTCAGGGAG-ATAGGATTCGCTATGGTAGCTTTAAT-TTGAC-CC
1 ACTGCAACTTCAGGG-GTATAAGA-T---T-T-GTAGC-TTCATCTT-ACTCC
* * * *
26969136 ACTGTAACTTTAGGGGTATAAGATTTGTATCTTCATCTTGCTCC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
* * *
26969180 ACTGCAAATTTAGGGAG-ATAAGATTCACTATGGTAGCTTCAATCTGAC-CC
1 ACTGCAACTTCAGGG-GTATAAGA-T---T-T-GTAGCTTC-ATCTTACTCC
* * * *
26969230 ACTGCAACTTCAGGGGTACAGGATTTATGGCTTCATCTTACTCC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
*
26969274 ACTGCAACTTCAGGAAGG--TAAGATTCGCTATGGTAGCTTCAATCTGAC-CC
1 ACTGCAACTTCAGG--GGTATAAGA-T---T-T-GTAGCTTC-ATCTTACTCC
* * *
26969324 ACTACAACTTCAGAGGTATAAGATTTGTAGCTTCATGTTACTCC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
* ** * * ** *
26969368 ATTAAAACTTCAAAGAGATAATATTTATTATTGTAGCTTCAATCTGAC-CC
1 ACTGCAACTTC--AGGGGT-ATA-AGA-T-TTGTAGCTTC-ATCTTACTCC
* * * * * *
26969418 ACTACAATTTCAGGGGTATAGGATTTCTAGCTTTATCTTGCTCC
1 ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
* *
26969462 ACTGTAGCTTCAGGGAG-ATAAGATTTG
1 ACTGCAACTTCAGGG-GTATAAGATTTG
26969489 CTATGGTAGC
Statistics
Matches: 713, Mismatches: 146, Indels: 198
0.67 0.14 0.19
Matches are distributed among these distances:
42 3 0.00
43 64 0.09
44 270 0.38
45 34 0.05
46 20 0.03
47 10 0.01
48 25 0.04
49 63 0.09
50 187 0.26
51 37 0.05
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
ACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTACTCC
Found at i:26976232 original size:16 final size:15
Alignment explanation
Indices: 26976211--26976243 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
26976201 TAGTGAATAC
26976211 AATAACAAGAAATAAT
1 AATAACAAG-AATAAT
26976227 AATAACAAGAATAAT
1 AATAACAAGAATAAT
26976242 AA
1 AA
26976244 AAATATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (15 bp):
AATAACAAGAATAAT
Found at i:26976608 original size:11 final size:12
Alignment explanation
Indices: 26976580--26976607 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
26976570 TTGCAAAAAA
26976580 AAAAAGAATAAG
1 AAAAAGAATAAG
26976592 AAAAAGAATAAG
1 AAAAAGAATAAG
26976604 AAAA
1 AAAA
26976608 GGGAAATAAA
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:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAAGAATAAG
Found at i:26988008 original size:123 final size:123
Alignment explanation
Indices: 26987789--26988033 Score: 312
Period size: 123 Copynumber: 2.0 Consensus size: 123
26987779 AAACTCGCCG
* ** *
26987789 CTCCAGCACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAAAGATTGGCCGGTTTAAGATCG
1 CTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAAAGATTGGCCGACTTAAGATCA
* * * * * *
26987854 CAACCTCCAAAGCAGCTAGTAGACTTATGTTCTCAACTGACATTATAAGATCTCATAT
66 CAACATCCAAAGCAGCTAGCAGACCTATGTTCCCAACTAACATTATAAGACCTCATAT
* * * * * *
26987912 CTCCAACACAGCTAGC-AGACTTACGCTCTCAATTGATGTCATGAAGGTTTGCCGACTTAAGATC
1 CTCCAACACAGCTAGCGA-ACCTACGCTCCCAACTGATGTCATAAAGATTGGCCGACTTAAGATC
* *
26987976 ACAACATCCAAAGTAGCTAGCAGACCTATGTTCCCAGCTAACATTATAAGACCTCATA
65 ACAACATCCAAAGCAGCTAGCAGACCTATGTTCCCAACTAACATTATAAGACCTCATA
26988034 GAGTTAAGCT
Statistics
Matches: 103, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
122 1 0.01
123 102 0.99
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (123 bp):
CTCCAACACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAAAGATTGGCCGACTTAAGATCA
CAACATCCAAAGCAGCTAGCAGACCTATGTTCCCAACTAACATTATAAGACCTCATAT
Found at i:26992147 original size:20 final size:20
Alignment explanation
Indices: 26992121--26992174 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
26992111 CTCTCGAAAC
*
26992121 AAAAATTACAAAATAATTT-T
1 AAAAATTTCAAAAT-ATTTAT
*
26992141 CAAAATTTCAAAATATTTAT
1 AAAAATTTCAAAATATTTAT
26992161 AAAAATTTCAAAAT
1 AAAAATTTCAAAAT
26992175 TTATATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTTCAAAATATTTAT
Found at i:26992202 original size:18 final size:19
Alignment explanation
Indices: 26992179--26992225 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
26992169 CAAAATTTAT
*
26992179 ATTTTAAAAAAA-TATAAA
1 ATTTTAAAAAAACTAAAAA
26992197 ATTTTAAAAAAATCTAAAAA
1 ATTTTAAAAAAA-CTAAAAA
26992217 ATTTTAAAA
1 ATTTTAAAA
26992226 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTTTAAAAAAACTAAAAA
Found at i:26992207 original size:10 final size:10
Alignment explanation
Indices: 26992194--26992243 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
26992184 AAAAAAATAT
26992194 AAAATTTTAA
1 AAAATTTTAA
* *
26992204 AAAAATCTAA
1 AAAATTTTAA
26992214 AAAATTTT--
1 AAAATTTTAA
26992222 AAAATTTTAA
1 AAAATTTTAA
**
26992232 AATTTTTTAA
1 AAAATTTTAA
26992242 AA
1 AA
26992244 TAATAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
8 8 0.25
10 24 0.75
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:26995050 original size:41 final size:41
Alignment explanation
Indices: 26995005--26995112 Score: 144
Period size: 41 Copynumber: 2.6 Consensus size: 41
26994995 GTGATAATCG
* * *
26995005 GGCTTTATACTTAGCAGGCTTTATGCTAGTGAATTATATCA
1 GGCTTTACACCTAGCAGGCTTTATGCTAGTGAACTATATCA
* *
26995046 GGCTTTACGCCTAGCAGGCTTTATGCTGGTGAACTATATCA
1 GGCTTTACACCTAGCAGGCTTTATGCTAGTGAACTATATCA
* * *
26995087 GGCTTTACGCCTAGCAAGCTTAATGC
1 GGCTTTACACCTAGCAGGCTTTATGC
26995113 CGATGTACCA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (41 bp):
GGCTTTACACCTAGCAGGCTTTATGCTAGTGAACTATATCA
Found at i:27002856 original size:41 final size:41
Alignment explanation
Indices: 27002811--27002911 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
27002801 GATAATCGGA
* *
27002811 CTTTATGCCTATCACGCTTTGTG-CTGGTGAATTATATCAGG
1 CTTTATGCCTAGCACGCTTTATGTC-GGTGAATTATATCAGG
* *
27002852 CTTTATGCCTAGCAGGCTTTATGTCGGTGAATTATATCAGT
1 CTTTATGCCTAGCACGCTTTATGTCGGTGAATTATATCAGG
* *
27002893 CTTTACGCCTAGCAAGCTT
1 CTTTATGCCTAGCACGCTT
27002912 ACTGCCAGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 52 0.98
42 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
CTTTATGCCTAGCACGCTTTATGTCGGTGAATTATATCAGG
Found at i:27006365 original size:94 final size:93
Alignment explanation
Indices: 27006277--27006576 Score: 384
Period size: 94 Copynumber: 3.2 Consensus size: 93
27006267 CCACTGTAAT
* * *
27006277 TTCAGGGATATAGGATTTGTAGTTTCATCTTGCTCCACTGCATCTTCAGGGAGATAAGATTCACC
1 TTCAGGG-TATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCACT
*
27006342 ATGGTAGCTTTAATTTGACCCACTACAAC
65 ATGGTAGCTTCAATTTGACCCACTACAAC
* * * * *
27006371 TTTAGGGGTATAGGATTTGTAGCTTCATCTCGCTCCACTACAACTCCAGGGAGATAAGAGTCACT
1 TTCA-GGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCACT
* * * * *
27006436 ATGGTTGCTTCAATCTGACCGATTGCAAC
65 ATGGTAGCTTCAATTTGACCCACTACAAC
* * * *
27006465 TTCACGGTATAGGATTTGTAGCTTCATCTTGCACCATTGCAACTTCAGGGAGATAAGATTCGCTA
1 TTCAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTA
** *
27006530 TTTTAGCTTCAATTCGACCCACTACAAC
66 TGGTAGCTTCAATTTGACCCACTACAAC
27006558 TTCAGAGGTATAGGATTTG
1 TTCAG-GGTATAGGATTTG
27006577 AGGTTTCACT
Statistics
Matches: 172, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
93 77 0.45
94 92 0.53
95 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (93 bp):
TTCAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTA
TGGTAGCTTCAATTTGACCCACTACAAC
Found at i:27015013 original size:24 final size:24
Alignment explanation
Indices: 27014954--27015003 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
27014944 GAAATTAAAC
**
27014954 ATAAAATATTAAATAACATAAAGG
1 ATAAAATAAAAAATAACATAAAGG
27014978 ATAAAATAAAAAATAACATAAAGG
1 ATAAAATAAAAAATAACATAAAGG
27015002 AT
1 AT
27015004 CGAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.22
Consensus pattern (24 bp):
ATAAAATAAAAAATAACATAAAGG
Found at i:27019868 original size:40 final size:40
Alignment explanation
Indices: 27019824--27019935 Score: 170
Period size: 40 Copynumber: 2.8 Consensus size: 40
27019814 TTTGTCTAGC
* *
27019824 GTGTTTCGATTAGATTAGCTCTTATGAGCTTCTATCTGGA
1 GTGTTTCGGTTGGATTAGCTCTTATGAGCTTCTATCTGGA
* * * *
27019864 GTGTTTCGGGTGGATTAGCTCTTATGAGCTTCTTTTTGGT
1 GTGTTTCGGTTGGATTAGCTCTTATGAGCTTCTATCTGGA
27019904 GTGTTTCGGTTGGATTAGCTCTTATGAGCTTC
1 GTGTTTCGGTTGGATTAGCTCTTATGAGCTTC
27019936 GTTCTAGTGT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.14, C:0.14, G:0.27, T:0.45
Consensus pattern (40 bp):
GTGTTTCGGTTGGATTAGCTCTTATGAGCTTCTATCTGGA
Found at i:27019946 original size:40 final size:39
Alignment explanation
Indices: 27019818--27019954 Score: 168
Period size: 40 Copynumber: 3.5 Consensus size: 39
27019808 ACACTCTTTG
* * *
27019818 TCTAGCGTGTTTCGATTAGATTAGCTCTTATGAGCTTCT
1 TCTAGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTCT
* * *
27019857 ATCTGGAGTGTTTCGGGTGGATTAGCTCTTATGAGCTTCTT
1 -TCTAGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTC-T
* *
27019898 TTTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTCGT
1 TCTAGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTC-T
27019938 TCTAGTGTG-TTCGGTTG
1 TCTAGTGTGTTTCGGTTG
27019955 ATCTGACGAT
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 8 0.09
40 76 0.89
41 1 0.01
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.45
Consensus pattern (39 bp):
TCTAGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTCT
Found at i:27021663 original size:43 final size:43
Alignment explanation
Indices: 27021573--27021666 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
27021563 TGTGTTTTCG
* * * * *
27021573 TGTAAGACAATGTCTGGTACATTGGCATTGACTTGTGTTTACG
1 TGTAAGACAATGTCTGGGACAGTGGCATCGACTTGTGATTACA
*
27021616 TGTAAGACACTGTCTGGGACAGTGGCATCGA-TATGTGATTACA
1 TGTAAGACAATGTCTGGGACAGTGGCATCGACT-TGTGATTACA
27021659 TGTAAGAC
1 TGTAAGAC
27021667 CACATCTGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 43 0.98
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTAAGACAATGTCTGGGACAGTGGCATCGACTTGTGATTACA
Found at i:27033182 original size:73 final size:72
Alignment explanation
Indices: 27033099--27033246 Score: 183
Period size: 72 Copynumber: 2.0 Consensus size: 72
27033089 TACCTTCCCA
* * *
27033099 AAAAAATTTACTTCCCCCCAAA-TCCCCAAAACTTTTTTCCTTTTACTTT-TCCCAAGACATTTA
1 AAAAAATTTACTT-CACCAAAACT-CCCAAAACTTTTTTCCTTTTACTTTCTCCCAAAACATTTA
27033162 CTTCTCCCTC
64 CTT-TCCCTC
* * **
27033172 AAAAATTTTACTTCACCAAAACTCCCAAAATTTTTTTCCTTTTGTTTTCTCCCAAAACATTTACT
1 AAAAAATTTACTTCACCAAAACTCCCAAAACTTTTTTCCTTTTACTTTCTCCCAAAACATTTACT
*
27033237 TTTCCTC
66 TTCCCTC
27033244 AAA
1 AAA
27033247 TCATCAAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
72 36 0.55
73 29 0.45
ACGTcount: A:0.30, C:0.30, G:0.01, T:0.39
Consensus pattern (72 bp):
AAAAAATTTACTTCACCAAAACTCCCAAAACTTTTTTCCTTTTACTTTCTCCCAAAACATTTACT
TTCCCTC
Found at i:27034093 original size:12 final size:13
Alignment explanation
Indices: 27034062--27034100 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
27034052 AATTTAGTAT
* *
27034062 TATTTTTGAGAAA
1 TATTTTTAAAAAA
27034075 TATTTTTAAAAAA
1 TATTTTTAAAAAA
27034088 TA-TTTTAAAAAA
1 TATTTTTAAAAAA
27034100 T
1 T
27034101 TGATTTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (13 bp):
TATTTTTAAAAAA
Found at i:27040501 original size:15 final size:14
Alignment explanation
Indices: 27040467--27040507 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
27040457 TTGACAACAA
* *
27040467 TTATTTTTCAGTAT
1 TTATTTTTTAATAT
27040481 TTATTTTTTAATAT
1 TTATTTTTTAATAT
27040495 TTAATTTTTTAAT
1 TT-ATTTTTTAAT
27040508 TTATCAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (14 bp):
TTATTTTTTAATAT
Found at i:27048048 original size:5 final size:5
Alignment explanation
Indices: 27048038--27048069 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
27048028 AAAATTGCAT
27048038 AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
27048070 GATATAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:27060706 original size:26 final size:25
Alignment explanation
Indices: 27060677--27060755 Score: 110
Period size: 26 Copynumber: 3.2 Consensus size: 25
27060667 GGACTCACCA
27060677 CAGCTCGTATGAGCTTACCGTTATAT
1 CAGCTCGTATGAGCTTACCGTT-TAT
*
27060703 CAGCTCTTATGAGCTTACCG-TT-T
1 CAGCTCGTATGAGCTTACCGTTTAT
27060726 CAGCTCG-ATAGAGCTTACCGTTTAT
1 CAGCTCGTAT-GAGCTTACCGTTTAT
27060751 CAGCT
1 CAGCT
27060756 TGGAATGAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.04
23 17 0.35
24 3 0.06
25 7 0.15
26 19 0.40
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACCGTTTAT
Found at i:27060739 original size:23 final size:23
Alignment explanation
Indices: 27060677--27060748 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 23
27060667 GGACTCACCA
27060677 CAGCTCGTATGAGCTTACCGTTATAT
1 CAGCTCGTATGAGCTTACCG-T-T-T
*
27060703 CAGCTCTTATGAGCTTACCGTTT
1 CAGCTCGTATGAGCTTACCGTTT
27060726 CAGCTCG-ATAGAGCTTACCGTTT
1 CAGCTCGTAT-GAGCTTACCGTTT
27060749 ATCAGCTTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
22 2 0.05
23 20 0.47
24 1 0.02
25 1 0.02
26 19 0.44
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (23 bp):
CAGCTCGTATGAGCTTACCGTTT
Found at i:27060977 original size:20 final size:20
Alignment explanation
Indices: 27060924--27060978 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
27060914 GTAGTTATAT
* *
27060924 GGATGAATTACTGTTGATAT
1 GGATAAATTACTGTTGATAC
* *
27060944 GTATAAGTTACTGTTGATAC
1 GGATAAATTACTGTTGATAC
*
27060964 GGATAAATTTCTGTT
1 GGATAAATTACTGTT
27060979 ATTACTGATG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (20 bp):
GGATAAATTACTGTTGATAC
Found at i:27061046 original size:25 final size:25
Alignment explanation
Indices: 27061018--27061071 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
27061008 AGAAACGAAC
* **
27061018 TGATATAAAAGTTAGATGATTTACA
1 TGATATAAAAGTTACATGAAATACA
* *
27061043 TGATTTATAAGTTACATGAAATACA
1 TGATATAAAAGTTACATGAAATACA
27061068 TGAT
1 TGAT
27061072 TTACATGGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.37
Consensus pattern (25 bp):
TGATATAAAAGTTACATGAAATACA
Found at i:27067160 original size:7 final size:7
Alignment explanation
Indices: 27067150--27067183 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
27067140 GTCCAAAAGT
27067150 CCACAAA
1 CCACAAA
27067157 CCACAAA
1 CCACAAA
27067164 CCACAAA
1 CCACAAA
*
27067171 CCAGAAA
1 CCACAAA
27067178 CC-CAAA
1 CCACAAA
27067184 ATTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 3 0.12
7 22 0.88
ACGTcount: A:0.56, C:0.41, G:0.03, T:0.00
Consensus pattern (7 bp):
CCACAAA
Found at i:27070800 original size:23 final size:23
Alignment explanation
Indices: 27070773--27070826 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
27070763 CGGTGGTGCG
*
27070773 ATGGTGGAGGATG-AAGGTTGGTC
1 ATGGTGGAGGA-GCAAGGTTGATC
27070796 ATGGTGGAGGAGCAAGGTTGATC
1 ATGGTGGAGGAGCAAGGTTGATC
27070819 ATGGTGGA
1 ATGGTGGA
27070827 AGAGGTGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.24, C:0.06, G:0.46, T:0.24
Consensus pattern (23 bp):
ATGGTGGAGGAGCAAGGTTGATC
Found at i:27072767 original size:23 final size:23
Alignment explanation
Indices: 27072724--27072767 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
27072714 TACATTTAAA
* *
27072724 TAAAGATAATAAAAATCAAATTG
1 TAAACATAATAAAAATAAAATTG
*
27072747 TAAACATAATAAACATAAAAT
1 TAAACATAATAAAAATAAAAT
27072768 AATTATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (23 bp):
TAAACATAATAAAAATAAAATTG
Found at i:27079575 original size:33 final size:33
Alignment explanation
Indices: 27079511--27079575 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
27079501 TATTTATGGC
* *
27079511 TTAAATTGAAAATGATTTTTATATAGGGGGAGT
1 TTAAATTGAAAATGACTTTTATATAGAGGGAGT
27079544 TTAAATTGAAAATGACTTTTAT-TAAGAGGGAG
1 TTAAATTGAAAATGACTTTTATAT-AGAGGGAG
27079576 CAACCTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (33 bp):
TTAAATTGAAAATGACTTTTATATAGAGGGAGT
Found at i:27079922 original size:20 final size:20
Alignment explanation
Indices: 27079899--27079937 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27079889 TATCGGTACT
*
27079899 TTTCTTAAGGTATCGATATA
1 TTTCCTAAGGTATCGATATA
*
27079919 TTTCCTAAGGTATTGATAT
1 TTTCCTAAGGTATCGATAT
27079938 TTCATACTCT
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:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTCCTAAGGTATCGATATA
Found at i:27082064 original size:17 final size:19
Alignment explanation
Indices: 27082042--27082076 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
27082032 TCAGAGGGAC
27082042 GAAGTA-AAGA-AGAAAAA
1 GAAGTACAAGATAGAAAAA
27082059 GAAGTACAAGATAGAAAA
1 GAAGTACAAGATAGAAAA
27082077 CTTAGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.66, C:0.03, G:0.23, T:0.09
Consensus pattern (19 bp):
GAAGTACAAGATAGAAAAA
Found at i:27082344 original size:20 final size:20
Alignment explanation
Indices: 27082319--27082360 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
27082309 CAAGTTTTGC
27082319 AACTAGTAGCTCTAGTAATA
1 AACTAGTAGCTCTAGTAATA
27082339 AACTAGTAGCTCTAGTAATA
1 AACTAGTAGCTCTAGTAATA
27082359 AA
1 AA
27082361 GTGGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
AACTAGTAGCTCTAGTAATA
Found at i:27085415 original size:22 final size:22
Alignment explanation
Indices: 27085373--27085415 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
27085363 CATACTCAGT
* *
27085373 CATACTCTAATATTTCAATACG
1 CATACACTAATATATCAATACG
27085395 CATACACTAATA-ATCACATAC
1 CATACACTAATATATCA-ATAC
27085416 TATACTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (22 bp):
CATACACTAATATATCAATACG
Found at i:27087849 original size:75 final size:76
Alignment explanation
Indices: 27087726--27087869 Score: 263
Period size: 75 Copynumber: 1.9 Consensus size: 76
27087716 AGTGTTGAAA
*
27087726 AATTGCCAAGGAGAGTTCAATTATTGTCTTGCAAATTTGTATCACAAATACTT-AAAAAGTTAGA
1 AATTGCCAAGGAGAGTTCAATTATAGTCTTGCAAATTTGTATCACAAATACTTAAAAAAGTTAGA
27087790 ATTTGTATCAT
66 ATTTGTATCAT
*
27087801 AATTGCGAAGGAGAGTTCAATTATAGTCTTGCAAATTTGTATCACAAATACTTAAAAAAGTTAGA
1 AATTGCCAAGGAGAGTTCAATTATAGTCTTGCAAATTTGTATCACAAATACTTAAAAAAGTTAGA
27087866 ATTT
66 ATTT
27087870 ATTCGAGTTC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
75 51 0.77
76 15 0.23
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (76 bp):
AATTGCCAAGGAGAGTTCAATTATAGTCTTGCAAATTTGTATCACAAATACTTAAAAAAGTTAGA
ATTTGTATCAT
Found at i:27096184 original size:52 final size:50
Alignment explanation
Indices: 27096119--27096232 Score: 122
Period size: 50 Copynumber: 2.2 Consensus size: 50
27096109 GAGCAAATTA
* * * *
27096119 GTTACTTAATGCATG-ACTTAATTTAATGATGCAGACTTAAACTAGCATGGGG
1 GTTACATAATGCATGTA-ATAATTT-ATGATGCAAACTT-AACTAACATGGGG
* * *
27096171 GTTACATAGTGCATGTAATAATTTATGATGCAAACTTAACTAACATGAGA
1 GTTACATAATGCATGTAATAATTTATGATGCAAACTTAACTAACATGGGG
*
27096221 GTTCCATAATGC
1 GTTACATAATGC
27096233 CTGACTTCAT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
50 20 0.38
51 12 0.23
52 19 0.37
53 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (50 bp):
GTTACATAATGCATGTAATAATTTATGATGCAAACTTAACTAACATGGGG
Found at i:27098979 original size:9 final size:9
Alignment explanation
Indices: 27098962--27098998 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
27098952 TATAGTTTGA
27098962 TATTCGAAT
1 TATTCGAAT
*
27098971 TATTTGAAT
1 TATTCGAAT
*
27098980 TATTCGAGT
1 TATTCGAAT
27098989 TATTCGAAT
1 TATTCGAAT
27098998 T
1 T
27098999 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:27102047 original size:452 final size:453
Alignment explanation
Indices: 27101202--27102097 Score: 1474
Period size: 452 Copynumber: 2.0 Consensus size: 453
27101192 CAATTTTATG
* * *
27101202 GGACCAACTTCAGGGGCTTGTGGTCGAAGTTGGAGCAACTTTTTGAGGCTGAAAGAGTATTGGAT
1 GGACCAACTTCAGGAGCTTGTGGTCAAAGTTGGAGCAACTTTTTGAGGCTAAAAGAGTATTGGAT
* * * *
27101267 CATGTCAAAGTAAGAGCTGTCATGCTTCACTTAGAAGGTAAGGCTCTAGATTGGCACAATTTTTT
66 CATGTCAAAGTAAGAACTGTCATGCTTCACTCAGAAGGTAACGCTCTAGATTGGCACAATATTTT
* * * *
27101332 TTACTCAAAGGTAAGGTGGCCATCATGTACTTACTTGAGATTTATATGCATGAGGCCTGAAGGAG
131 TTACTCAAAGGTAAGGTGGCCATCATATACTTACCTGAGATGTATATGCATGAAGCCTGAAGGAG
* * *
27101397 AGATTCGGGTCCAGTTCGTTTTGGACCCCATGGCCGAGTTGGTTTCACTTAAGCAACAAGGTATT
196 AGATTCGGGTCCAATTCGTTTTGGACCCCATGGCCGAGTTGGTTTCACTTAAACAACAAGGTAGT
*
27101462 GTTGATTAGTACCATGATGCCTTTGTAAGCTTGTTAAACCAATTACATTTGCCTGAAAGTTATGC
261 GTTGATCAGTACCATGATGCCTTTGTAAGCTTGTTAAACCAATTACATTTGCCTGAAAGTTATGC
27101527 TCTTAGCATATTTGTCAGTAACCTATAGTGAAAAGTAGGCCAATATTTGCAACTCTTCAAGCCCA
326 TCTTAGCATATTTGTCAGTAACCTATAGTGAAAAGTAGGCCAATATTTGCAACTCTTCAAGCCCA
*
27101592 AGTCATTAGTAGAGGGCTTTCTCGTTTCTCAACAAGTGGAGAATATTATGCTACGATTTGATA
391 AGTCATTAGTAGAGGGCTTTCTCGTTGCTCAACAAGTGGAGAATATTATGCTACGATTTGATA
*
27101655 GGACCAACTTCAGGAG-TTGGTGGTCAAAGTTGGAGCAA-TTTTTAGAGGCTAAAAGAGTCTTGG
1 GGACCAACTTCAGGAGCTT-GTGGTCAAAGTTGGAGCAACTTTTT-GAGGCTAAAAGAGTATTGG
*
27101718 ATCATGTCAAAGTAAGAATTGTCATGCTTCACTCAGAAGGTAACGCTCTAGATTGGCACAA-ATT
64 ATCATGTCAAAGTAAGAACTGTCATGCTTCACTCAGAAGGTAACGCTCTAGATTGGCACAATATT
* * * *
27101782 TTTTGCTTAAAGGTAAGGTGGCCTTCATATACTTACCTGGGATGTATATGCATGAAGCCTGAAGG
129 TTTTACTCAAAGGTAAGGTGGCCATCATATACTTACCTGAGATGTATATGCATGAAGCCTGAAGG
* *
27101847 AGAGATTCGGGTCCAATTTGTTTTGGACCCCATGGCCGAGTTGGTTTCACTTAAACAACAGGGTA
194 AGAGATTCGGGTCCAATTCGTTTTGGACCCCATGGCCGAGTTGGTTTCACTTAAACAACAAGGTA
* *
27101912 GTGTTGATCAGTACCATGATGCCTTTGTAAGCTTGTTGAACCAATTACATTTGCTTGAAAGTTAT
259 GTGTTGATCAGTACCATGATGCCTTTGTAAGCTTGTTAAACCAATTACATTTGCCTGAAAGTTAT
* * *
27101977 GCTCTTAGCATATTTGTCAGTAACCTGTAGTGAGAAGTAGGCTAATATTTGCAACTCTTCAAGCC
324 GCTCTTAGCATATTTGTCAGTAACCTATAGTGAAAAGTAGGCCAATATTTGCAACTCTTCAAGCC
* *
27102042 CAAGTCATTAGTAGAGGGCTTTCTTGTTGCTCAACATGTGGAGAATATTATGCTAC
389 CAAGTCATTAGTAGAGGGCTTTCTCGTTGCTCAACAAGTGGAGAATATTATGCTAC
27102098 ATAACCATCA
Statistics
Matches: 410, Mismatches: 31, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
452 303 0.74
453 107 0.26
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (453 bp):
GGACCAACTTCAGGAGCTTGTGGTCAAAGTTGGAGCAACTTTTTGAGGCTAAAAGAGTATTGGAT
CATGTCAAAGTAAGAACTGTCATGCTTCACTCAGAAGGTAACGCTCTAGATTGGCACAATATTTT
TTACTCAAAGGTAAGGTGGCCATCATATACTTACCTGAGATGTATATGCATGAAGCCTGAAGGAG
AGATTCGGGTCCAATTCGTTTTGGACCCCATGGCCGAGTTGGTTTCACTTAAACAACAAGGTAGT
GTTGATCAGTACCATGATGCCTTTGTAAGCTTGTTAAACCAATTACATTTGCCTGAAAGTTATGC
TCTTAGCATATTTGTCAGTAACCTATAGTGAAAAGTAGGCCAATATTTGCAACTCTTCAAGCCCA
AGTCATTAGTAGAGGGCTTTCTCGTTGCTCAACAAGTGGAGAATATTATGCTACGATTTGATA
Found at i:27106249 original size:16 final size:17
Alignment explanation
Indices: 27106216--27106249 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27106206 TGGAGTAAAT
*
27106216 AAGAAGATGGAGTGGGG
1 AAGAAGATGGAATGGGG
27106233 AAGAAGAT-GAATGGGG
1 AAGAAGATGGAATGGGG
27106249 A
1 A
27106250 CAGAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.47, T:0.12
Consensus pattern (17 bp):
AAGAAGATGGAATGGGG
Found at i:27106493 original size:26 final size:26
Alignment explanation
Indices: 27106463--27106512 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
27106453 ATAGAAGGAT
27106463 AGTTTAG-TA-CAAAATTAGAAAAAAAA
1 AGTTTAGATACCAAAA-T-GAAAAAAAA
27106489 AGTTTAGATACCAAAATGAAAAAA
1 AGTTTAGATACCAAAATGAAAAAA
27106513 CGAGTATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 14 0.64
27 3 0.14
28 5 0.23
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (26 bp):
AGTTTAGATACCAAAATGAAAAAAAA
Found at i:27107491 original size:16 final size:16
Alignment explanation
Indices: 27107458--27107504 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
27107448 AAAAACAAAA
*
27107458 TTATATAAAAA-TATAT
1 TTATAAAAAAATTA-AT
27107474 TTATAAAAAAATTAAT
1 TTATAAAAAAATTAAT
27107490 TT-TAAAATAAATTAA
1 TTATAAAA-AAATTAA
27107505 GTTTTGATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 5 0.18
16 21 0.75
17 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTATAAAAAAATTAAT
Found at i:27108221 original size:17 final size:17
Alignment explanation
Indices: 27108199--27108232 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27108189 TCATAGACAT
27108199 TTGTGTGTAGGCCGTGA
1 TTGTGTGTAGGCCGTGA
*
27108216 TTGTGTGTAGGCTGTGA
1 TTGTGTGTAGGCCGTGA
27108233 CATTTTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.41, T:0.38
Consensus pattern (17 bp):
TTGTGTGTAGGCCGTGA
Found at i:27110115 original size:43 final size:43
Alignment explanation
Indices: 27110021--27110198 Score: 157
Period size: 43 Copynumber: 4.2 Consensus size: 43
27110011 CGTTTATGTG
* * * *
27110021 AACCTTTAGCAGCGCTATAGCCACAAATGCCGCTAAAG-ATCGT
1 AACCTTTAGCGGCGCTTTAGCCACAAACGCCGCTAAAGAAT-AT
* * *
27110064 GACATTTAGCGGCGCTTTAGCCGCAAACGCCGCTAAAGAATAT
1 AACCTTTAGCGGCGCTTTAGCCACAAACGCCGCTAAAGAATAT
* * ** * *
27110107 AACCTTTAGCGACGCTTTTGTTAAAAACGCCGCTAAAGAACA-
1 AACCTTTAGCGGCGCTTTAGCCACAAACGCCGCTAAAGAATAT
* * * *
27110149 AACCTTTAGCGGCGCTTCT-GGCAAAAACACCGCTAAA-AACAT
1 AACCTTTAGCGGCGCTT-TAGCCACAAACGCCGCTAAAGAATAT
27110191 AACCTTTA
1 AACCTTTA
27110199 AAAAATTATT
Statistics
Matches: 112, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.04
42 39 0.35
43 67 0.60
44 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (43 bp):
AACCTTTAGCGGCGCTTTAGCCACAAACGCCGCTAAAGAATAT
Found at i:27110175 original size:42 final size:43
Alignment explanation
Indices: 27110088--27110198 Score: 154
Period size: 42 Copynumber: 2.6 Consensus size: 43
27110078 CTTTAGCCGC
* * **
27110088 AAACGCCGCTAAAGAATATAACCTTTAGCGACGCTTTTGTTAA
1 AAACGCCGCTAAAGAACATAACCTTTAGCGACGCTTCTGGCAA
*
27110131 AAACGCCGCTAAAGAACA-AACCTTTAGCGGCGCTTCTGGCAA
1 AAACGCCGCTAAAGAACATAACCTTTAGCGACGCTTCTGGCAA
*
27110173 AAACACCGCTAAA-AACATAACCTTTA
1 AAACGCCGCTAAAGAACATAACCTTTA
27110199 AAAAATTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 4 0.07
42 40 0.66
43 17 0.28
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATAACCTTTAGCGACGCTTCTGGCAA
Found at i:27111547 original size:20 final size:20
Alignment explanation
Indices: 27111482--27111548 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
27111472 GTAAAAAATA
* * *
27111482 ATAAATTAAATAAATAATAC
1 ATAATTTAAAAAAATAACAC
*
27111502 ATGAAATTAAAAAAATAACAC
1 AT-AATTTAAAAAAATAACAC
*
27111523 TTAATTTAAAGAAAATAA-AC
1 ATAATTTAAA-AAAATAACAC
27111543 ATAATT
1 ATAATT
27111549 ATCTAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.28
Consensus pattern (20 bp):
ATAATTTAAAAAAATAACAC
Found at i:27115134 original size:14 final size:15
Alignment explanation
Indices: 27115115--27115147 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
27115105 CTTAAACCAG
27115115 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
27115129 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
27115144 AATC
1 AATC
27115148 TATAAACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:27115838 original size:41 final size:41
Alignment explanation
Indices: 27115479--27115835 Score: 450
Period size: 41 Copynumber: 8.7 Consensus size: 41
27115469 TGTTTTCGCA
* * *
27115479 GCGCTTTTTCAAAAACGCCACTAAAAGCTCAAGCATTAGCG
1 GCGCTTTTTCAAAAACGCCGCTAAAAGCCCGAGCATTAGCG
* * *
27115520 GCGCTTTTTTACAAACGTCGCTAAAAGCCCGAGCATTAGCG
1 GCGCTTTTTCAAAAACGCCGCTAAAAGCCCGAGCATTAGCG
* *
27115561 GCGCTTTCTCAAAAATGCCGCTAAAAGCCCGAGCATTAGCG
1 GCGCTTTTTCAAAAACGCCGCTAAAAGCCCGAGCATTAGCG
* * *
27115602 GCGCTTTCTCAAAAACACCACTAAAAGCCCGAGCATTAGCG
1 GCGCTTTTTCAAAAACGCCGCTAAAAGCCCGAGCATTAGCG
*
27115643 GCGCTTTCTCAAAAACGCCGCTAAAAGCCCGAGCATTAGCG
1 GCGCTTTTTCAAAAACGCCGCTAAAAGCCCGAGCATTAGCG
* * **
27115684 GCGCTTTCTCAAAAACACCGCTAAAAGCCTAAGCATTAGCG
1 GCGCTTTTTCAAAAACGCCGCTAAAAGCCCGAGCATTAGCG
* * *
27115725 GCGCTTTTTTAAAAACGTCGCT-AAAGCTCTGAGCATTAGCG
1 GCGCTTTTTCAAAAACGCCGCTAAAAGC-CCGAGCATTAGCG
* *
27115766 GCGCTTTTTTAAAAACGCCACT-AAAGCCCTGAGCATTAGCG
1 GCGCTTTTTCAAAAACGCCGCTAAAAGCCC-GAGCATTAGCG
* * * *
27115807 GCACTTTTTTAGAAACGCCACT-AAAGCCC
1 GCGCTTTTTCAAAAACGCCGCTAAAAGCCC
27115836 TGAAAGTTCA
Statistics
Matches: 285, Mismatches: 29, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
40 6 0.02
41 279 0.98
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (41 bp):
GCGCTTTTTCAAAAACGCCGCTAAAAGCCCGAGCATTAGCG
Found at i:27126932 original size:79 final size:81
Alignment explanation
Indices: 27126823--27127005 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
27126813 TACTCGTTCA
* *
27126823 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
27126886 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
27126903 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
27126966 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
27126982 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
27127006 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:27127005 original size:40 final size:40
Alignment explanation
Indices: 27126802--27127005 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
27126792 CGGAATTTAA
** *
27126802 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
27126842 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
27126882 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
27126921 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
27126961 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
27127001 CCGGA
1 CCGGA
27127006 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:27132981 original size:10 final size:10
Alignment explanation
Indices: 27132946--27132984 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
27132936 CTTATGGTTA
27132946 ATTAATTAAAG
1 ATTAATT-AAG
*
27132957 TTTAATTAA-
1 ATTAATTAAG
27132966 ATTAATTAAG
1 ATTAATTAAG
27132976 ATTAATTAA
1 ATTAATTAA
27132985 AAATTAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 11 0.44
11 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (10 bp):
ATTAATTAAG
Found at i:27132985 original size:19 final size:20
Alignment explanation
Indices: 27132945--27132985 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
27132935 ACTTATGGTT
*
27132945 AATTAATTAAAGTTTAATTA
1 AATTAATTAAAGATTAATTA
27132965 AATTAATT-AAGATTAATTA
1 AATTAATTAAAGATTAATTA
27132984 AA
1 AA
27132986 AATTAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
AATTAATTAAAGATTAATTA
Found at i:27133778 original size:62 final size:62
Alignment explanation
Indices: 27133703--27133822 Score: 215
Period size: 62 Copynumber: 1.9 Consensus size: 62
27133693 TAAATTATTT
27133703 TTTGAATTATATTTGTTTCAATTTTATGTTTATATTTAAGTGAG-TTTATGGAAATTGAATAA
1 TTTGAATTATATTTGTTTCAATTTTATGTTTATATTTAAGTG-GCTTTATGGAAATTGAATAA
*
27133765 TTTGAATTGTATTTGTTTCAATTTTATGTTTATATTTAAGTGGCTTTATGGAAATTGA
1 TTTGAATTATATTTGTTTCAATTTTATGTTTATATTTAAGTGGCTTTATGGAAATTGA
27133823 CTTATTTAGC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 1 0.02
62 55 0.98
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (62 bp):
TTTGAATTATATTTGTTTCAATTTTATGTTTATATTTAAGTGGCTTTATGGAAATTGAATAA
Found at i:27140213 original size:26 final size:27
Alignment explanation
Indices: 27140161--27140213 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
27140151 ACCATAGCAC
* *
27140161 AAATCAGTCATTTACCCTCGAGGGGCA
1 AAATCAGTCATTTACCCTCCAGAGGCA
27140188 AAAT-AGTCATTTACCCTCCAGAGGCA
1 AAATCAGTCATTTACCCTCCAGAGGCA
27140214 TTAGGGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (27 bp):
AAATCAGTCATTTACCCTCCAGAGGCA
Found at i:27150943 original size:44 final size:46
Alignment explanation
Indices: 27150893--27150985 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
27150883 TTACACCTCT
* *
27150893 ATTCCATTCAACCAAACACAAGAA-TACC-ATTATGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
27150937 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
27150983 ATT
1 ATT
27150986 ACGCATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 4 0.09
46 18 0.40
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:27150988 original size:16 final size:16
Alignment explanation
Indices: 27150967--27151019 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
27150957 AGAATTACCT
27150967 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
* *
27150983 ATTACGCATATATTCC
1 ATTACGCCTCTATTCC
*
27150999 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
27151015 ATTAC
1 ATTAC
27151020 AGCGAACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.26, C:0.32, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:27152074 original size:22 final size:21
Alignment explanation
Indices: 27152043--27152083 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
27152033 TTGATGTCGT
27152043 AACTTAAGGGTTCCTCGTCCC
1 AACTTAAGGGTTCCTCGTCCC
27152064 AACTTCAAGGGTTCCTCGTC
1 AACTT-AAGGGTTCCTCGTC
27152084 ACAATGCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.29
Consensus pattern (21 bp):
AACTTAAGGGTTCCTCGTCCC
Found at i:27159013 original size:14 final size:15
Alignment explanation
Indices: 27158994--27159031 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
27158984 TCGATTTTTC
27158994 TTTATAAAAATCATT
1 TTTATAAAAATCATT
*
27159009 TTATAAAAAAATCATT
1 TT-TATAAAAATCATT
27159025 TTTATAA
1 TTTATAA
27159032 GTATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTATAAAAATCATT
Found at i:27159020 original size:16 final size:17
Alignment explanation
Indices: 27158999--27159031 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
27158989 TTTTCTTTAT
27158999 AAAAATCA-TTTTATAA
1 AAAAATCATTTTTATAA
27159015 AAAAATCATTTTTATAA
1 AAAAATCATTTTTATAA
27159032 GTATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAATCATTTTTATAA
Found at i:27161369 original size:9 final size:9
Alignment explanation
Indices: 27161355--27161382 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
27161345 ACATGGAACC
27161355 TAAGGAGCT
1 TAAGGAGCT
27161364 TAAGGAGCT
1 TAAGGAGCT
27161373 TAAGGAGCT
1 TAAGGAGCT
27161382 T
1 T
27161383 CAAGCCTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.25
Consensus pattern (9 bp):
TAAGGAGCT
Found at i:27165798 original size:34 final size:33
Alignment explanation
Indices: 27165733--27165800 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
27165723 TCTTATAGGC
* *
27165733 ATGTTTTTCTTAAATTATTTTAAAAAAATTAATT
1 ATGTTTTTATTAAATTA-TTAAAAAAAATTAATT
27165767 ATGTTTTTATTAAATTA-TAAACAAAATATTAATT
1 ATGTTTTTATTAAATTATTAAA-AAAA-ATTAATT
27165801 CGAAAATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 3 0.10
33 4 0.13
34 23 0.77
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (33 bp):
ATGTTTTTATTAAATTATTAAAAAAAATTAATT
Found at i:27167598 original size:21 final size:21
Alignment explanation
Indices: 27167558--27167598 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27167548 TGAGTCAAAA
* * *
27167558 ATTTTCAAATATGTTTTAATC
1 ATTTTCAAACAAGTTATAATC
27167579 ATTTTCAAACAAGTTATAAT
1 ATTTTCAAACAAGTTATAAT
27167599 TGCTCCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTTTCAAACAAGTTATAATC
Found at i:27170469 original size:33 final size:33
Alignment explanation
Indices: 27170403--27170465 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
27170393 ATCTTTATGC
* *
27170403 CTTAAATTGAAAATTATTTTTATATAAGGGGAG
1 CTTAAATTGAAAATGAATTTTATATAAGGGGAG
27170436 CTTAAATTGAAAATGAATTTTAT-TAAGGGG
1 CTTAAATTGAAAATGAATTTTATATAAGGGG
27170466 GAGCAATCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (33 bp):
CTTAAATTGAAAATGAATTTTATATAAGGGGAG
Found at i:27175674 original size:19 final size:19
Alignment explanation
Indices: 27175606--27175766 Score: 73
Period size: 19 Copynumber: 8.3 Consensus size: 19
27175596 GTATTTTATA
27175606 ATTAAAATTATAAAAAAATT
1 ATTAAAATTATAAAAAAA-T
* * ***
27175626 ATACAAAATCATAAAGTTTAT
1 AT-TAAAATTATAAA-AAAAT
* *
27175647 ATAAAAATTATAAAGAAAT
1 ATTAAAATTATAAAAAAAT
*
27175666 TTTAAAATTATAAAAAAAT
1 ATTAAAATTATAAAAAAAT
* **
27175685 ATT-AAAGT-GCAAAAAAT
1 ATTAAAATTATAAAAAAAT
27175702 ATATAGAAATTTATAAAAAAATT
1 AT-TA-AAA-TTATAAAAAAA-T
* *
27175725 ATTATAA--ATGAAAAAA-
1 ATTAAAATTATAAAAAAAT
*
27175741 ATTATAAACTATAAAAATAAT
1 ATTA-AAATTATAAAAA-AAT
27175762 -TTAAA
1 ATTAAA
27175767 TTTGCTAAAA
Statistics
Matches: 104, Mismatches: 24, Indels: 27
0.67 0.15 0.17
Matches are distributed among these distances:
16 4 0.04
17 11 0.11
18 13 0.12
19 28 0.27
20 20 0.19
21 16 0.15
22 9 0.09
23 3 0.03
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (19 bp):
ATTAAAATTATAAAAAAAT
Done.