Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 32 of 362
Found at i:9325906 original size:12 final size:12
Alignment explanation
Indices: 9325889--9325914 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9325879 GTTTTATTCA
9325889 TTTTTTCTTTAT
1 TTTTTTCTTTAT
9325901 TTTTTTCTTTAT
1 TTTTTTCTTTAT
9325913 TT
1 TT
9325915 GATTGGGATA
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:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTTAT
Found at i:9327710 original size:15 final size:15
Alignment explanation
Indices: 9327690--9327719 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9327680 CCACTCGCCC
9327690 AAACTTAAGTAACAA
1 AAACTTAAGTAACAA
9327705 AAACTTAAGTAACAA
1 AAACTTAAGTAACAA
9327720 CACTATCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (15 bp):
AAACTTAAGTAACAA
Found at i:9332335 original size:19 final size:19
Alignment explanation
Indices: 9332298--9332335 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9332288 TTAATTAGGT
*
9332298 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
9332317 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
9332336 AAAAAAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:9332636 original size:33 final size:32
Alignment explanation
Indices: 9332594--9332665 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 32
9332584 AAATGAGTAC
9332594 ATTTATATTATTTA-TATATAATTAGTAAAAAGAT
1 ATTT-TATTATTTATTAT-TAATTAGT-AAAAGAT
9332628 ATTTTATTATTTATTATTAATTAGTAAAAGAT
1 ATTTTATTATTTATTATTAATTAGTAAAAGAT
9332660 -TTTTAT
1 ATTTTAT
9332666 ATGATAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.16
32 7 0.19
33 17 0.46
34 7 0.19
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (32 bp):
ATTTTATTATTTATTATTAATTAGTAAAAGAT
Found at i:9332744 original size:23 final size:23
Alignment explanation
Indices: 9332718--9332761 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9332708 AAAATACAAA
9332718 TGTAAAATATATATGTGTACATT
1 TGTAAAATATATATGTGTACATT
* * *
9332741 TGTAATATTTATATTTGTACA
1 TGTAAAATATATATGTGTACA
9332762 AAAGACCACA
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:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (23 bp):
TGTAAAATATATATGTGTACATT
Found at i:9334732 original size:5 final size:5
Alignment explanation
Indices: 9334722--9334746 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9334712 TATTGGGGTT
9334722 GACAG GACAG GACAG GACAG GACAG
1 GACAG GACAG GACAG GACAG GACAG
9334747 AAGTGAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
GACAG
Found at i:9341505 original size:19 final size:20
Alignment explanation
Indices: 9341460--9341505 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
9341450 AGATGTGTTT
9341460 AATTAGGTTGTAATTAGATGA
1 AATTA-GTTGTAATTAGATGA
*
9341481 ATTTAGTT-TAATTAAGA-GA
1 AATTAGTTGTAATT-AGATGA
9341500 AATTAG
1 AATTAG
9341506 AAAAAAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 12 0.55
20 6 0.27
21 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (20 bp):
AATTAGTTGTAATTAGATGA
Found at i:9341807 original size:33 final size:31
Alignment explanation
Indices: 9341763--9341834 Score: 110
Period size: 33 Copynumber: 2.3 Consensus size: 31
9341753 AAATGAGTAC
9341763 ATTTTTATTATTTA-TATATAATTAGTAAAAAG
1 ATTTTTATTATTTATTAT-TAATTAGT-AAAAG
9341795 ATATTTTATTATTTATTATTAATTAGTAAAAG
1 AT-TTTTATTATTTATTATTAATTAGTAAAAG
9341827 ATTTTTAT
1 ATTTTTAT
9341835 ATGATAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.16
32 9 0.24
33 20 0.53
34 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (31 bp):
ATTTTTATTATTTATTATTAATTAGTAAAAG
Found at i:9347860 original size:27 final size:27
Alignment explanation
Indices: 9347752--9347862 Score: 125
Period size: 28 Copynumber: 4.0 Consensus size: 27
9347742 CACGAAAACT
* * *
9347752 AAGAATAGCCCTTATGGCTAACTCTAGA
1 AAGAATAGCCTTTGTGGCGAACTCT-GA
*
9347780 AAGAATAGCCTTTGTGGTGAACTCTGAA
1 AAGAATAGCCTTTGTGGCGAACTCTG-A
*
9347808 AAGAATAGCCTTTGTGGGGAACTCTGA
1 AAGAATAGCCTTTGTGGCGAACTCTGA
* *
9347835 AAGGAAT-GCCTTTGTGGCAAATTCTGA
1 AA-GAATAGCCTTTGTGGCGAACTCTGA
9347862 A
1 A
9347863 TGGATCGCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
27 22 0.30
28 51 0.70
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (27 bp):
AAGAATAGCCTTTGTGGCGAACTCTGA
Found at i:9348336 original size:19 final size:19
Alignment explanation
Indices: 9348308--9348350 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
9348298 CACGTTTATG
* * *
9348308 TGCCAGGATGCACTTTGTA
1 TGCCAAGATGAACCTTGTA
*
9348327 TGCCAAGATGAACCTTGTG
1 TGCCAAGATGAACCTTGTA
9348346 TGCCA
1 TGCCA
9348351 TATATACGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (19 bp):
TGCCAAGATGAACCTTGTA
Found at i:9349096 original size:14 final size:14
Alignment explanation
Indices: 9349077--9349106 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9349067 TATATAGATA
9349077 GATAGATAGATCTT
1 GATAGATAGATCTT
9349091 GATAGATAGATCTT
1 GATAGATAGATCTT
9349105 GA
1 GA
9349107 ATCATGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (14 bp):
GATAGATAGATCTT
Found at i:9352918 original size:19 final size:19
Alignment explanation
Indices: 9352870--9352924 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
9352860 ATAATCTTCA
9352870 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
9352889 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
9352907 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
9352925 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:9352950 original size:22 final size:22
Alignment explanation
Indices: 9352870--9352947 Score: 80
Period size: 18 Copynumber: 3.8 Consensus size: 22
9352860 ATAATCTTCA
9352870 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
9352889 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
9352907 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
9352929 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
9352948 GATTTAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
18 18 0.35
19 14 0.27
22 8 0.15
23 12 0.23
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:9353237 original size:18 final size:19
Alignment explanation
Indices: 9353214--9353250 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
9353204 TGTTTCCCTG
*
9353214 ATTTTTTTATAT-ATTTTA
1 ATTTTTTTAAATAATTTTA
9353232 ATTTTTTTAAATAATTTTA
1 ATTTTTTTAAATAATTTTA
9353251 GTATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTTTAAATAATTTTA
Found at i:9356756 original size:26 final size:26
Alignment explanation
Indices: 9356725--9356832 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
9356715 ATGAAATGCC
*
9356725 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
9356751 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
9356777 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
9356803 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
9356829 ATCA
1 ATCA
9356833 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:9364336 original size:26 final size:26
Alignment explanation
Indices: 9364300--9364409 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
9364290 TGATACAAAT
9364300 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
9364326 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
9364352 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
9364378 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
9364404 TGATAA
1 TGATAA
9364410 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:9366071 original size:27 final size:27
Alignment explanation
Indices: 9366029--9366141 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
9366019 GAGGAAGCGT
*
9366029 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
9366056 TCTAGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
9366083 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * *
9366111 TCTGGTGGCTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
9366137 TCTGG
1 TCTGG
9366142 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.72
28 16 0.22
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:9366134 original size:54 final size:54
Alignment explanation
Indices: 9366027--9366141 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
9366017 TGGAGGAAGC
9366027 GTTCTGGTGGCTATGCCACAAATATCTGATCTAGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTAGTGGCTCTGCCACATATATCT
* * * * *
9366081 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGGCTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTAGTGGCTCTGCCACATATATCT
9366135 GTTCTGG
1 GTTCTGG
9366142 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTAGTGGCTCTGCCACATATATCT
Found at i:9378284 original size:33 final size:33
Alignment explanation
Indices: 9378212--9378284 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
9378202 CGAGAGGCTA
* * * *
9378212 TGGTCAAGTTAAAGGTGGTAACGGGTTTGGCTG
1 TGGTCAGGTCAAAGGTGGTAACGAGTTTGGCCG
* *
9378245 TGGTCAGGTCAAAGGTGGTGATGAGTTTGGCCG
1 TGGTCAGGTCAAAGGTGGTAACGAGTTTGGCCG
9378278 TGGTCAG
1 TGGTCAG
9378285 AGAGCACCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.19, C:0.11, G:0.41, T:0.29
Consensus pattern (33 bp):
TGGTCAGGTCAAAGGTGGTAACGAGTTTGGCCG
Found at i:9386692 original size:20 final size:20
Alignment explanation
Indices: 9386661--9386713 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
9386651 AAAAAATTAT
9386661 TAAAAATA-TTAAAATTTAA
1 TAAAAATATTTAAAATTTAA
* *
9386680 TAATAATATTTAAAATTTAT
1 TAAAAATATTTAAAATTTAA
9386700 TAAAAAT-TTTAAAA
1 TAAAAATATTTAAAA
9386714 AAAACTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAAATATTTAAAATTTAA
Found at i:9386714 original size:20 final size:19
Alignment explanation
Indices: 9386652--9386713 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
9386642 CATGCGGCAA
* *
9386652 AAAAATTATTAAAAATATT
1 AAAATTTATTAAAAATTTT
* *
9386671 AAAATTTAATAATAATATTT
1 AAAATTTATTAAAAAT-TTT
9386691 AAAATTTATTAAAAATTTT
1 AAAATTTATTAAAAATTTT
9386710 AAAA
1 AAAA
9386714 AAAACTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTTATTAAAAATTTT
Found at i:9386722 original size:20 final size:20
Alignment explanation
Indices: 9386699--9386736 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9386689 TTAAAATTTA
**
9386699 TTAAAAATTTTAAAAAAAAC
1 TTAAAAATCATAAAAAAAAC
9386719 TTAAAAATCATAAAAAAA
1 TTAAAAATCATAAAAAAA
9386737 TATATAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAAAAATCATAAAAAAAAC
Found at i:9387012 original size:36 final size:38
Alignment explanation
Indices: 9386965--9387044 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 38
9386955 TTGTATGATC
* * *
9386965 ATTTTTATAATTTTTTTACGAATTT-T-ATGTTTTTTA
1 ATTTTTATAATTTTATTACGAATTTATAACGTTTTATA
*
9387001 ATTTTTATAATTTTATTACGACTTTATAACGTTTTATA
1 ATTTTTATAATTTTATTACGAATTTATAACGTTTTATA
9387039 ATTTTT
1 ATTTTT
9387045 TTTATATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 23 0.61
37 1 0.03
38 14 0.37
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (38 bp):
ATTTTTATAATTTTATTACGAATTTATAACGTTTTATA
Found at i:9387103 original size:11 final size:12
Alignment explanation
Indices: 9387079--9387114 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
9387069 CTTTCTATGA
9387079 TTTTTATAATTT
1 TTTTTATAATTT
*
9387091 TTTTTCTAATTT
1 TTTTTATAATTT
*
9387103 TTTTTAAAATTT
1 TTTTTATAATTT
9387115 AAGTATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:9390747 original size:16 final size:15
Alignment explanation
Indices: 9390719--9390756 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
9390709 TGAAATTTGG
*
9390719 ATTAAATTCAATAAA
1 ATTAAATTAAATAAA
9390734 ATTATAATTAAAT-AA
1 ATTA-AATTAAATAAA
9390749 ATTAAATT
1 ATTAAATT
9390757 TGATTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 7 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTAAATAAA
Found at i:9419903 original size:16 final size:16
Alignment explanation
Indices: 9419882--9419935 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
9419872 TTTAGTTCAC
*
9419882 TGTAATGGAATAGGGT
1 TGTAATGGAATAGAGT
*
9419898 TGTAATTGAATAGAGT
1 TGTAATGGAATAGAGT
* *
9419914 TGTAATGGAATAAAGC
1 TGTAATGGAATAGAGT
9419930 TGTAAT
1 TGTAAT
9419936 CAGAAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:9422533 original size:19 final size:19
Alignment explanation
Indices: 9422509--9422546 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9422499 GGGCCGATTA
9422509 TTGTCAATGGCCCAACATG
1 TTGTCAATGGCCCAACATG
9422528 TTGTCAATGGCCCAACATG
1 TTGTCAATGGCCCAACATG
9422547 ACATGACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
TTGTCAATGGCCCAACATG
Found at i:9423595 original size:17 final size:19
Alignment explanation
Indices: 9423573--9423615 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
9423563 AATGGTACCG
9423573 ATACTCT-TA-AAGTATCA
1 ATACTCTGTACAAGTATCA
9423590 ATACTCTGGTATCAAGTATCA
1 ATACTCT-GTA-CAAGTATCA
9423611 ATACT
1 ATACT
9423616 TTATTCCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.32
19 2 0.09
21 13 0.59
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (19 bp):
ATACTCTGTACAAGTATCA
Found at i:9432455 original size:8 final size:8
Alignment explanation
Indices: 9432432--9432470 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
9432422 TAAATAAATT
*
9432432 ATTACAAA
1 ATTAAAAA
9432440 ATTAAAAA
1 ATTAAAAA
9432448 TATTAAAAA
1 -ATTAAAAA
9432457 ATTATAAAA
1 ATTA-AAAA
9432466 ATTAA
1 ATTAA
9432471 TTCAACTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 12 0.43
9 16 0.57
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (8 bp):
ATTAAAAA
Found at i:9432457 original size:17 final size:18
Alignment explanation
Indices: 9432425--9432470 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
9432415 TTCAAAGTAA
* *
9432425 ATAAATTATTACAAAATT
1 ATAAAATATTAAAAAATT
9432443 A-AAAATATTAAAAAATT
1 ATAAAATATTAAAAAATT
9432460 ATAAAA-ATTAA
1 ATAAAATATTAA
9432471 TTCAACTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAATATTAAAAAATT
Found at i:9432704 original size:16 final size:17
Alignment explanation
Indices: 9432683--9432722 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
9432673 TAAAATTTTT
9432683 AAAAATA-TGAAAAATA
1 AAAAATATTGAAAAATA
* *
9432699 AAAAATATTTAAAATTA
1 AAAAATATTGAAAAATA
9432716 AAAAATA
1 AAAAATA
9432723 AAAATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAAATATTGAAAAATA
Found at i:9432747 original size:27 final size:24
Alignment explanation
Indices: 9432674--9432748 Score: 71
Period size: 27 Copynumber: 2.9 Consensus size: 24
9432664 TATAACTTTT
* *
9432674 AAAATTTTTAAAAATATGAAAAATAA
1 AAAATATTT-AAAAT-TAAAAAATAA
9432700 AAAATATTTAAAATTAAAAAATAAA
1 AAAATATTTAAAATTAAAAAAT-AA
9432725 AATAATTATTTAAAA-TAATAAAAT
1 AA-AA-TATTTAAAATTAA-AAAAT
9432749 TCTAAAATAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 7 0.16
25 9 0.21
26 13 0.30
27 14 0.33
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (24 bp):
AAAATATTTAAAATTAAAAAATAA
Found at i:9436772 original size:22 final size:22
Alignment explanation
Indices: 9436746--9436790 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9436736 ATTATGTGTA
9436746 TTAATTCATAATATAA-TTAATT
1 TTAATTCA-AATATAATTTAATT
* *
9436768 TTAATTTAAATCTAATTTAATT
1 TTAATTCAAATATAATTTAATT
9436790 T
1 T
9436791 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTCAAATATAATTTAATT
Found at i:9443610 original size:3 final size:3
Alignment explanation
Indices: 9443602--9443634 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
9443592 AAAAAAGTGG
*
9443602 AGA AGA AGA AGA AGA AAA AGA AGA AGA A-A AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
9443635 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9444180 original size:3 final size:3
Alignment explanation
Indices: 9444174--9444207 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
9444164 GAGGAGGAGG
*
9444174 AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
9444208 AAATTACTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9444208 original size:12 final size:12
Alignment explanation
Indices: 9444174--9444210 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
9444164 GAGGAGGAGG
*
9444174 AGAAGAAGAAGA
1 AGAAGAAGAAAA
9444186 AGAAGAAGAAAA
1 AGAAGAAGAAAA
9444198 AGAAGAAGAAAA
1 AGAAGAAGAAAA
9444210 A
1 A
9444211 TTACTAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AGAAGAAGAAAA
Found at i:9445364 original size:3 final size:3
Alignment explanation
Indices: 9445356--9445383 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9445346 TCAGTAACTG
9445356 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
9445384 GTTAAAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:9449581 original size:29 final size:29
Alignment explanation
Indices: 9449542--9449600 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
9449532 AATTTAGCTC
*
9449542 TTTTTTAAAGATT-AATGGTTAAATTTAAT
1 TTTTTTAAAGATTGAA-GGGTAAATTTAAT
9449571 TTTTTTAAAGATTGAAGGGTAAATTTAAT
1 TTTTTTAAAGATTGAAGGGTAAATTTAAT
9449600 T
1 T
9449601 AAAAAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTTTTAAAGATTGAAGGGTAAATTTAAT
Found at i:9450140 original size:21 final size:21
Alignment explanation
Indices: 9450087--9450133 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
9450077 TATGATTGTA
9450087 TGATATAATTCAAATGAAAAG
1 TGATATAATTCAAATGAAAAG
9450108 TGATATAATTCAAATGAAAAG
1 TGATATAATTCAAATGAAAAG
9450129 T-ATAT
1 TGATAT
9450134 GCATTCAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (21 bp):
TGATATAATTCAAATGAAAAG
Found at i:9454503 original size:19 final size:20
Alignment explanation
Indices: 9454472--9454513 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
9454462 ATTTTATTTA
9454472 TTTACCGAATAAACAAGATT
1 TTTACCGAATAAACAAGATT
* *
9454492 TTTACC-AATAAAGAATATT
1 TTTACCGAATAAACAAGATT
9454511 TTT
1 TTT
9454514 TTATATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (20 bp):
TTTACCGAATAAACAAGATT
Found at i:9454514 original size:20 final size:21
Alignment explanation
Indices: 9454466--9454514 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
9454456 CTTTATATTT
9454466 TATTTATTTACCGAATAAACAA
1 TATTT-TTTACCGAATAAACAA
* *
9454488 GA-TTTTTACC-AATAAAGAA
1 TATTTTTTACCGAATAAACAA
9454507 TATTTTTT
1 TATTTTTT
9454515 TATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 9 0.39
20 11 0.48
21 2 0.09
22 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (21 bp):
TATTTTTTACCGAATAAACAA
Found at i:9462013 original size:21 final size:22
Alignment explanation
Indices: 9461989--9462039 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
9461979 TTTTTCTCTC
9461989 TTCTATTAACAAATTTAA-TC-T
1 TTCTATTAA-AAATTTAATTCAT
9462010 TTCTATTAAAAATTTAATTCAT
1 TTCTATTAAAAATTTAATTCAT
9462032 TTCTATTA
1 TTCTATTA
9462040 TTTAACTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.29
21 11 0.39
22 9 0.32
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (22 bp):
TTCTATTAAAAATTTAATTCAT
Found at i:9467900 original size:121 final size:121
Alignment explanation
Indices: 9467686--9467928 Score: 468
Period size: 121 Copynumber: 2.0 Consensus size: 121
9467676 TGTTAGTTAT
*
9467686 TTAAACGCGTAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
1 TTAAACGCATAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
*
9467751 TTGAGGTTTTAAAGTTTCTTTTGTAACTATATTGGTTATTATTTGTCTAAGAATAA
66 TTGAGGTTTTAAAGTTTCTTTCGTAACTATATTGGTTATTATTTGTCTAAGAATAA
9467807 TTAAACGCATAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
1 TTAAACGCATAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
9467872 TTGAGGTTTTAAAGTTTCTTTCGTAACTATATTGGTTATTATTTGTCTAAGAATAA
66 TTGAGGTTTTAAAGTTTCTTTCGTAACTATATTGGTTATTATTTGTCTAAGAATAA
9467928 T
1 T
9467929 GACATGTACA
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 120 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (121 bp):
TTAAACGCATAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
TTGAGGTTTTAAAGTTTCTTTCGTAACTATATTGGTTATTATTTGTCTAAGAATAA
Found at i:9472999 original size:7 final size:7
Alignment explanation
Indices: 9472981--9473012 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
9472971 TTGCAATTCA
9472981 AATTTTT
1 AATTTTT
9472988 -ATTTTT
1 AATTTTT
9472994 -ATTTTT
1 AATTTTT
9473000 AATTTTT
1 AATTTTT
9473007 AATTTT
1 AATTTT
9473013 CTTTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
AATTTTT
Found at i:9473004 original size:13 final size:13
Alignment explanation
Indices: 9472981--9473023 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
9472971 TTGCAATTCA
9472981 AATTTTTATTTTT
1 AATTTTTATTTTT
9472994 -ATTTTTAATTTTT
1 AATTTTT-ATTTTT
9473007 AATTTTCT-TTTTT
1 AATTTT-TATTTTT
9473020 AATT
1 AATT
9473024 CTTCATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.22
13 15 0.56
14 5 0.19
15 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
AATTTTTATTTTT
Found at i:9493752 original size:46 final size:48
Alignment explanation
Indices: 9493695--9493815 Score: 156
Period size: 46 Copynumber: 2.6 Consensus size: 48
9493685 TGATATGTGT
* *
9493695 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGA-CGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATAGACAA
* * * * *
9493741 GCTAGTGTAAGACATGTTTGGGACATGTATCGGCCTTGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATAGACAA
*
9493789 GCTAGTGTAAGACTTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
9493816 ACGTCAGCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 37 0.58
47 1 0.02
48 26 0.41
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATAGACAA
Found at i:9496680 original size:15 final size:15
Alignment explanation
Indices: 9496660--9496691 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
9496650 CAGGGGTCAC
9496660 ACCATATTGAAATCA
1 ACCATATTGAAATCA
9496675 ACCATATTGAAATCA
1 ACCATATTGAAATCA
9496690 AC
1 AC
9496692 TAACCACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (15 bp):
ACCATATTGAAATCA
Found at i:9505513 original size:18 final size:17
Alignment explanation
Indices: 9505492--9505548 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
9505482 TTTTTTTGTT
9505492 TTATTTTATTTTTATTTA
1 TTATTTTATTTTTA-TTA
* *
9505510 TTATTCTTATTTCTATTC
1 TTATT-TTATTTTTATTA
*
9505528 TTA-TTTATTTTTGTTA
1 TTATTTTATTTTTATTA
9505544 -TATTT
1 TTATTT
9505549 AGTTTCATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.06
16 11 0.34
17 1 0.03
18 10 0.31
19 8 0.25
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (17 bp):
TTATTTTATTTTTATTA
Found at i:9505697 original size:3 final size:3
Alignment explanation
Indices: 9505689--9505716 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9505679 TCATTCATTC
9505689 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
9505717 CTTAGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:9507379 original size:26 final size:26
Alignment explanation
Indices: 9507316--9507379 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
9507306 TTTTTAGTTG
*
9507316 TTTTATTTTTATTTTCTTAAACTTAT
1 TTTTATTTTTATCTTCTTAAACTTAT
* * *
9507342 TTCGT-TTCTTATCTT-TTGAACTATAT
1 TT-TTATTTTTATCTTCTTAAACT-TAT
9507368 TTTTATTTTTAT
1 TTTTATTTTTAT
9507380 GGTTGTTTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
25 7 0.24
26 21 0.72
27 1 0.03
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTTATTTTTATCTTCTTAAACTTAT
Found at i:9508011 original size:21 final size:21
Alignment explanation
Indices: 9507970--9508011 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
9507960 TGGTTACGAA
*
9507970 TCTATGAACTTGATTTGTTAT
1 TCTATGAACTTGATTCGTTAT
*
9507991 TCTA-GAACTTGCTTCGATTAT
1 TCTATGAACTTGATTCG-TTAT
9508012 GCATGTCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (21 bp):
TCTATGAACTTGATTCGTTAT
Found at i:9508311 original size:5 final size:5
Alignment explanation
Indices: 9508301--9508328 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
9508291 TTGTTCTAAA
9508301 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
9508329 TAAAAAAAAG
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:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:9508334 original size:15 final size:14
Alignment explanation
Indices: 9508298--9508338 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
9508288 TGATTGTTCT
9508298 AAAAAAAGAAAAGA
1 AAAAAAAGAAAAGA
9508312 AAAGAAAAGAAAAGA
1 AAA-AAAAGAAAAGA
*
9508327 AATAAAA-AAAAG
1 AAAAAAAGAAAAG
9508339 TTACTCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAAGA
Found at i:9510772 original size:70 final size:70
Alignment explanation
Indices: 9510696--9510830 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 70
9510686 TAGTTTATTA
* * * *
9510696 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
9510761 CTTAG
66 CTTAG
*
9510766 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGTTGTCCAAATTAGGACAAAATCATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
9510831 TTATGTGCTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
CTTAG
Found at i:9511663 original size:43 final size:43
Alignment explanation
Indices: 9511599--9511757 Score: 221
Period size: 43 Copynumber: 3.7 Consensus size: 43
9511589 ATTGTTTATC
* * * * *
9511599 GAAATGTTA-CGGGCTTTGGGCCTAGTAGGCTATAATACCGGT
1 GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
9511641 GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
1 GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
* * *
9511684 GAGATAATATCGGGCCTCGGGCCTAGCAGGCTATAATGCCAGT
1 GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
**
9511727 GAAATGATATCGGGCTTCAAGCCTAGCAGGC
1 GAAATGATATCGGGCTTCGGGCCTAGCAGGC
9511758 GAAATGTCGG
Statistics
Matches: 103, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 8 0.08
43 95 0.92
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (43 bp):
GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
Found at i:9517017 original size:23 final size:23
Alignment explanation
Indices: 9516990--9517055 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
9516980 AATGTTAGAT
9516990 ATTAAATATTTTATTTAAGTATA
1 ATTAAATATTTTATTTAAGTATA
* *
9517013 ATTAAATA-TTAATTATAATTATA
1 ATTAAATATTTTATT-TAAGTATA
*
9517036 ATT-ATTATATTT-TTTAAGTA
1 ATTAAATAT-TTTATTTAAGTA
9517056 CGTTCTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
22 13 0.37
23 20 0.57
24 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
ATTAAATATTTTATTTAAGTATA
Found at i:9524964 original size:3 final size:3
Alignment explanation
Indices: 9524956--9525026 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
9524946 CTGCAGACTA
* * * * *
9524956 ATT ATT ATT ATT ACT ATT ATT GTT GTT GTT ATT ATT AGT ATT -TCT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
9525001 ATT ATT GTT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
9525027 AGAAGAGTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 1 0.02
3 56 0.97
4 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:9525383 original size:6 final size:6
Alignment explanation
Indices: 9525374--9525410 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
9525364 AGAGAGAATT
* *
9525374 TTAAAA TTAAAA TTAAAA TTAAAA CTAAAA CTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA T
9525411 CATTAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (6 bp):
TTAAAA
Found at i:9527201 original size:16 final size:16
Alignment explanation
Indices: 9527180--9527211 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9527170 AATTAATTTA
*
9527180 AATTAATTAATTTTCT
1 AATTAAATAATTTTCT
9527196 AATTAAATAATTTTCT
1 AATTAAATAATTTTCT
9527212 CAACCCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAAATAATTTTCT
Found at i:9528173 original size:40 final size:41
Alignment explanation
Indices: 9528113--9528203 Score: 157
Period size: 40 Copynumber: 2.2 Consensus size: 41
9528103 TCATGCGAGT
*
9528113 AGGCCGTGTGTGACACAAGGTCGTGTAACAGCCCGTAT-CC
1 AGGCCGTGTGTGACAAAAGGTCGTGTAACAGCCCGTATCCC
*
9528153 AGGCCGTGTGTGACAAAAGGTCGTGTAATAGCCCGTATCCC
1 AGGCCGTGTGTGACAAAAGGTCGTGTAACAGCCCGTATCCC
9528194 AGGCCGTGTG
1 AGGCCGTGTG
9528204 CATCCAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 36 0.75
41 12 0.25
ACGTcount: A:0.22, C:0.25, G:0.32, T:0.21
Consensus pattern (41 bp):
AGGCCGTGTGTGACAAAAGGTCGTGTAACAGCCCGTATCCC
Found at i:9531747 original size:108 final size:108
Alignment explanation
Indices: 9531618--9531833 Score: 369
Period size: 108 Copynumber: 2.0 Consensus size: 108
9531608 TATACCTAAG
*
9531618 CTTACAATTATCATTCAATAACCAAGCATCAATCAAAGCATATTACATAACATATCATTTTCTCC
1 CTTACAATTATCATTCAATAACCAAGCATCAATCAAAGCATATCACATAACATATCATTTTCTCC
9531683 ACCATTAAACATTAAACATATGATCTAAGCTACCTAGCAAAAT
66 ACCATTAAACATTAAACATATGATCTAAGCTACCTAGCAAAAT
* * *
9531726 CTTACAATTATCATTCCATAACCAAGCATCATTCAAAGCATATCATATAACATATCATTTTCTCC
1 CTTACAATTATCATTCAATAACCAAGCATCAATCAAAGCATATCACATAACATATCATTTTCTCC
* * *
9531791 ACCATTAAACATTAAATATATTATTTAAGCTACCTAGCAAAAT
66 ACCATTAAACATTAAACATATGATCTAAGCTACCTAGCAAAAT
9531834 AATAACATGA
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 101 1.00
ACGTcount: A:0.42, C:0.23, G:0.04, T:0.31
Consensus pattern (108 bp):
CTTACAATTATCATTCAATAACCAAGCATCAATCAAAGCATATCACATAACATATCATTTTCTCC
ACCATTAAACATTAAACATATGATCTAAGCTACCTAGCAAAAT
Found at i:9533191 original size:16 final size:17
Alignment explanation
Indices: 9533170--9533211 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
9533160 CCAAATCCAC
9533170 ATTCAATTTCT-AATTT
1 ATTCAATTTCTCAATTT
* *
9533186 ATTCAATTTTTCATTTT
1 ATTCAATTTCTCAATTT
9533203 ATTCAATTT
1 ATTCAATTT
9533212 AGTCCTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTCAATTTCTCAATTT
Found at i:9534744 original size:30 final size:30
Alignment explanation
Indices: 9534709--9534770 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 30
9534699 ATTATTAATA
9534709 TATTTAATA-T-AATTTATTATTTTAATAAAT
1 TATTTAATATTCAA-TT-TTATTTTAATAAAT
9534739 TATTTAATATTTCAATTTTATTTTAATAAAT
1 TATTTAATA-TTCAATTTTATTTTAATAAAT
9534770 T
1 T
9534771 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 9 0.31
31 15 0.52
32 3 0.10
33 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
TATTTAATATTCAATTTTATTTTAATAAAT
Found at i:9534783 original size:16 final size:16
Alignment explanation
Indices: 9534762--9534795 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
9534752 AATTTTATTT
9534762 TAATAAATTTTAAA-AA
1 TAAT-AATTTTAAATAA
9534778 TAATAATTTTAAATAA
1 TAATAATTTTAAATAA
9534794 TA
1 TA
9534796 TTCTTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:9534788 original size:30 final size:31
Alignment explanation
Indices: 9534725--9534788 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
9534715 ATATAATTTA
* * *
9534725 TTATTTTAATAAATTATTTAATATTTCAATT
1 TTATTTTAATAAATTATTAAAAATATCAATT
9534756 TTATTTTAATAAATT-TTAAAAATAAT-AATT
1 TTATTTTAATAAATTATTAAAAAT-ATCAATT
9534786 TTA
1 TTA
9534789 AATAATATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
TTATTTTAATAAATTATTAAAAATATCAATT
Found at i:9534848 original size:15 final size:15
Alignment explanation
Indices: 9534828--9534884 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
9534818 ATTCAATATT
9534828 AATATTTTAATAATA
1 AATATTTTAATAATA
*
9534843 AATATTTATTATAATTATA
1 AATA--T-TT-TAATAATA
*
9534862 AATATATTAATAATA
1 AATATTTTAATAATA
*
9534877 AATGTTTT
1 AATATTTT
9534885 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 1 0.03
17 2 0.06
18 2 0.06
19 11 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:9534857 original size:19 final size:19
Alignment explanation
Indices: 9534830--9534866 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9534820 TCAATATTAA
*
9534830 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
9534849 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
9534867 ATTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:9535394 original size:101 final size:101
Alignment explanation
Indices: 9535219--9535424 Score: 342
Period size: 101 Copynumber: 2.0 Consensus size: 101
9535209 AGAAAATCTC
* *
9535219 AAATGTATATTTGCTTTATTGAAAACAACTTTTATGAAATATTTGTAAGAAATCTATCAAATGAC
1 AAATGTATATTTCCTTTATTGAAAACAACTTTTATGAAATATTTATAAGAAATCTATCAAATGAC
* *
9535284 AGATAATATTTTACACAAATTCATCCAAACACTAGG
66 AGAAAATATTTTACACAAATTCATCCAAACACTAAG
* *
9535320 AAATGTATGTTTCCTTTATTGAAAACAACTTTTATGAAATATTTATAAGAAATCTGTCAAATGA-
1 AAATGTATATTTCCTTTATTGAAAACAACTTTTATGAAATATTTATAAGAAATCTATCAAATGAC
9535384 AGGAAAATATTTTACACAAATTCATCCAAACACTAAG
66 A-GAAAATATTTTACACAAATTCATCCAAACACTAAG
9535421 AAAT
1 AAAT
9535425 ATTAACTTTT
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 1 0.01
101 97 0.99
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (101 bp):
AAATGTATATTTCCTTTATTGAAAACAACTTTTATGAAATATTTATAAGAAATCTATCAAATGAC
AGAAAATATTTTACACAAATTCATCCAAACACTAAG
Found at i:9536514 original size:33 final size:32
Alignment explanation
Indices: 9536477--9536540 Score: 119
Period size: 33 Copynumber: 2.0 Consensus size: 32
9536467 AGATTAAAAA
9536477 TTTAAAGAGGCCTTATTACATCAAAAATACCCT
1 TTTAAAGAGGCCTTATTACATC-AAAATACCCT
9536510 TTTAAAGAGGCCTTATTACATCAAAATACCC
1 TTTAAAGAGGCCTTATTACATCAAAATACCC
9536541 AAATTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (32 bp):
TTTAAAGAGGCCTTATTACATCAAAATACCCT
Found at i:9536548 original size:33 final size:33
Alignment explanation
Indices: 9536478--9536548 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
9536468 GATTAAAAAT
**
9536478 TTAAAGAGGCCTTATTACATCAAAAATACCCTT
1 TTAAAGAGGCCTTATTACATCAAAAATACCCAA
9536511 TTAAAGAGGCCTTATTACATC-AAAATACCCAAA
1 TTAAAGAGGCCTTATTACATCAAAAATACCC-AA
9536544 TTAAA
1 TTAAA
9536549 TTACTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 9 0.26
33 26 0.74
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (33 bp):
TTAAAGAGGCCTTATTACATCAAAAATACCCAA
Found at i:9546642 original size:138 final size:142
Alignment explanation
Indices: 9546389--9546650 Score: 335
Period size: 138 Copynumber: 1.9 Consensus size: 142
9546379 AGGCTGACGA
*
9546389 CATGTCTCAGACATGGTCTTACACTAGCTCTCACATATCAGTGCTGATGCCATATCCTAGACATG
1 CATGTCTCAGACATGGTCTTACACTAGCTCTCACATATCAGTGCTGATGCCATATCCCAGACATG
* * *
9546454 ATCTTACACTGACACCTCTATACCTGCCGATTCCATGTCCTAGACATGGTCTTACACTGACACAT
66 ATCTTACACTGACACCTCTATA-CTGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACAT
9546519 TTCATAGTCGATG
130 TTCATAGTCGATG
* * *
9546532 CATGTCTCAGACAT-GTCTTACACTGGCT-T-ACATCTCGAG-GCTGATG-CATGTCCCAGACAT
1 CATGTCTCAGACATGGTCTTACACTAGCTCTCACATATC-AGTGCTGATGCCATATCCCAGACAT
*
9546592 G-TCTTACACT-AGCTCTCATCTCA-A-TGCCGATGCCATGTCCCAAACATGGTCTTACACTG
65 GATCTTACACTGA-CAC-C-TCT-ATACTGCCGATGCCATGTCCCAAACATGGTCTTACACTG
9546651 GCTCTCATAA
Statistics
Matches: 106, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
137 1 0.01
138 43 0.41
139 14 0.13
140 17 0.16
141 4 0.04
142 13 0.12
143 14 0.13
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (142 bp):
CATGTCTCAGACATGGTCTTACACTAGCTCTCACATATCAGTGCTGATGCCATATCCCAGACATG
ATCTTACACTGACACCTCTATACTGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACATT
TCATAGTCGATG
Found at i:9546653 original size:94 final size:96
Alignment explanation
Indices: 9546287--9546698 Score: 279
Period size: 94 Copynumber: 4.4 Consensus size: 96
9546277 GGGTATAATA
* *
9546287 CCGATGCTATGTCCCAGACATGGTCTTACACT-G-GCTCATCCATCAA-G-TGATGCCATGTCCC
1 CCGATGC-ATGTCCCAGACATGGTCTTACACTAGCTCTCAT-C-TCAATGCCGATGCCATGTCCC
* *
9546348 AGACATGGTCTTACATTGACTATCAAAAT-TGA-GG
63 AGACATGGTCTTACACTGACTAT--ACATCTGACGG
* * * * * * * *
9546382 CTGACGACATGTCTCAGACATGGTCTTACACTAGCTCTCACATATCAGTGCTGATGCCATATCCT
1 CCGATG-CATGTCCCAGACATGGTCTTACACTAGCTCT--CATCTCAATGCCGATGCCATGTCCC
* * * *
9546447 AGACATGATCTTACACTGAC---ACCTCTATACCTG
63 AGACATGGTCTTACACTGACTATACATCT-GA-CGG
* * * * * * *
9546480 CCGATTCCATGTCCTAGACATGGTCTTACACT-G-ACACATTTC-ATAGTCGATG-CATGTCTCA
1 CCGA-TGCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAAT-GCCGATGCCATGTCCCA
*
9546541 GACAT-GTCTTACACTGGCT-TACATCTCGA-GG
64 GACATGGTCTTACACTGACTATACATCT-GACGG
* *
9546572 CTGATGCATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTCCCAAA
1 CCGATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTCCCAGA
* * * *
9546636 CATGGTCTTACACTGGCTCT-CATAAT-ATGG
66 CATGGTCTTACACTGACTATACAT-CTGACGG
*
9546666 CCGATGCATGCCCCAGACAT-GTCTTACACTAGC
1 CCGATGCATGTCCCAGACATGGTCTTACACTAGC
9546699 ACACAAATAA
Statistics
Matches: 248, Mismatches: 46, Indels: 47
0.73 0.13 0.14
Matches are distributed among these distances:
90 10 0.04
91 15 0.06
92 27 0.11
93 27 0.11
94 68 0.27
95 30 0.12
96 4 0.02
97 6 0.02
98 28 0.11
99 33 0.13
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (96 bp):
CCGATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGACTATACATCTGACGG
Found at i:9546655 original size:48 final size:48
Alignment explanation
Indices: 9546287--9546695 Score: 244
Period size: 46 Copynumber: 8.7 Consensus size: 48
9546277 GGGTATAATA
*
9546287 CCGATGCTATGTCCCAGACATGGTCTTACACTGG--CTCATCCATCAA-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-C-TCAATG
* * * * ** ** *
9546334 -TGATGCCATGTCCCAGACATGGTCTTACATTGACTATCAAAATTGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-ATCTCAATG
* * * * * * *
9546382 CTGACGACATGTCTCAGACATGGTCTTACACTAGCTCTCACATATCAGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT--CATCTCAATG
* * * * * *
9546432 CTGATGCCATATCCTAGACATGATCTTACACTGACAC-C-TCT-ATACCTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCA-A--TG
* * * * *
9546480 CCGATTCCATGTCCTAGACATGGTCTTACACT-G-ACACATTTC-ATAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCAAT-G
* * * *
9546526 TCGATG-CATGTCTCAGACAT-GTCTTACACTGGCT-TACATCTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATCTCAATG
* *
9546572 CTGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCAATG
* *
9546618 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCA--TAATATGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCA-AT-G
*
9546666 CCGATG-CATGCCCCAGACAT-GTCTTACACT
1 CCGATGCCATGTCCCAGACATGGTCTTACACT
9546696 AGCACACAAA
Statistics
Matches: 281, Mismatches: 58, Indels: 47
0.73 0.15 0.12
Matches are distributed among these distances:
44 10 0.04
45 15 0.05
46 99 0.35
47 34 0.12
48 59 0.21
49 31 0.11
50 32 0.11
51 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCAATG
Found at i:9550615 original size:17 final size:17
Alignment explanation
Indices: 9550593--9550631 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
9550583 AGAATTGAGG
9550593 AATTACTTTTGGAAAAC
1 AATTACTTTTGGAAAAC
9550610 AATTACTTTTGGAAAAC
1 AATTACTTTTGGAAAAC
9550627 AATTA
1 AATTA
9550632 AATTAAGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (17 bp):
AATTACTTTTGGAAAAC
Found at i:9551521 original size:19 final size:19
Alignment explanation
Indices: 9551497--9551540 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
9551487 TTTGGCCCAT
9551497 TTTCTCCCTTTTTGGCACG
1 TTTCTCCCTTTTTGGCACG
9551516 TTTCTCCCTTTTTGGCACG
1 TTTCTCCCTTTTTGGCACG
9551535 TTTCTC
1 TTTCTC
9551541 ATTCCTTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.05, C:0.32, G:0.14, T:0.50
Consensus pattern (19 bp):
TTTCTCCCTTTTTGGCACG
Found at i:9551969 original size:20 final size:19
Alignment explanation
Indices: 9551940--9551984 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
9551930 AAATGTGGTG
9551940 TTTTTGAAAAACATTTATC
1 TTTTTGAAAAACATTTATC
9551959 TTTTTGAAAAACATTTATC
1 TTTTTGAAAAACATTTATC
9551978 TTTTTGA
1 TTTTTGA
9551985 CAACCCGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTTTGAAAAACATTTATC
Found at i:9552981 original size:20 final size:19
Alignment explanation
Indices: 9552947--9552987 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
9552937 ATGTTCGTGG
*
9552947 GGCCCACAAGGCCCATTTC
1 GGCCCACAAGGCCCAATTC
*
9552966 GGCCCATCATGGCCCAATTC
1 GGCCCA-CAAGGCCCAATTC
9552986 GG
1 GG
9552988 TCTCAGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.20, C:0.39, G:0.24, T:0.17
Consensus pattern (19 bp):
GGCCCACAAGGCCCAATTC
Found at i:9562863 original size:50 final size:50
Alignment explanation
Indices: 9562788--9562922 Score: 225
Period size: 50 Copynumber: 2.7 Consensus size: 50
9562778 CCAACCAAGT
* * *
9562788 ACACGCCTAGGCGCCAAGTGCCTAGCCCGTAGGCTAACATCCCTCTAGAA
1 ACACGTCTAGGCACCAAGTGCCTAGCCCATAGGCTAACATCCCTCTAGAA
9562838 ACACGTCTAGGCACCAAGTGCCTAGCCCATAGGCTAACATCCCTCTAGAA
1 ACACGTCTAGGCACCAAGTGCCTAGCCCATAGGCTAACATCCCTCTAGAA
* *
9562888 ACACGTCTAGGCACCAAGTGACAAGCCCATAGGCT
1 ACACGTCTAGGCACCAAGTGCCTAGCCCATAGGCT
9562923 TTACATCTGC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 80 1.00
ACGTcount: A:0.29, C:0.34, G:0.21, T:0.16
Consensus pattern (50 bp):
ACACGTCTAGGCACCAAGTGCCTAGCCCATAGGCTAACATCCCTCTAGAA
Found at i:9566998 original size:17 final size:17
Alignment explanation
Indices: 9566963--9567091 Score: 51
Period size: 17 Copynumber: 7.4 Consensus size: 17
9566953 TTTAACAATA
9566963 TATTATTTCA-TAT-TAT
1 TATTATTT-ATTATATAT
9566979 TATTATTTATTATATAT
1 TATTATTTATTATATAT
* *
9566996 TATCT-TTCA-CA-A-AT
1 TAT-TATTTATTATATAT
9567010 TATTATTTTACATTAT-TATT
1 TATTA-TTT--ATTATATA-T
9567030 TATATATTT-TTATTATAT
1 TAT-TATTTATTA-TATAT
*
9567048 TTTTACTTGTATTATATATT
1 TATTA-TT-TATTATATA-T
*
9567068 TATTAATTATT-TATAT
1 TATTATTTATTATATAT
9567084 TATATATT
1 TAT-TATT
9567092 ATTTTTACAT
Statistics
Matches: 86, Mismatches: 8, Indels: 37
0.66 0.06 0.28
Matches are distributed among these distances:
13 1 0.01
14 5 0.06
15 4 0.05
16 16 0.19
17 22 0.26
18 12 0.14
19 9 0.10
20 15 0.17
21 2 0.02
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.62
Consensus pattern (17 bp):
TATTATTTATTATATAT
Found at i:9584302 original size:46 final size:46
Alignment explanation
Indices: 9584235--9584411 Score: 264
Period size: 46 Copynumber: 3.8 Consensus size: 46
9584225 GATATTTGGG
*
9584235 CATCTGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA
1 CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
*
9584281 CATCTGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAA
1 CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** *
9584327 TGTCTGAACCCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
*** * *
9584373 TGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
9584412 GCTGGTTACA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 121 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (46 bp):
CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:9585956 original size:46 final size:46
Alignment explanation
Indices: 9585904--9586122 Score: 248
Period size: 46 Copynumber: 4.7 Consensus size: 46
9585894 TTGGGCATCT
* ** * * *
9585904 GAGCTCGTTGAGTTGAGTCTGATTTTACTTATGGATGCGAATGTCC
1 GAGCTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCC
* * * *
9585950 GAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAAGCTTCC
1 GAGCTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAAC---GC--CC
9585997 GAGCTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCC
1 GAGCTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCC
*
9586043 GAGCTCGTTAAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCC
1 GAGCTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCC
* *
9586089 GAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 GAGCTCGTTGAGTTGAGTCCGAGCTCACTTATGG
9586123 GCGGGTTACA
Statistics
Matches: 148, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
45 3 0.02
46 101 0.68
47 27 0.18
48 4 0.03
50 4 0.03
51 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (46 bp):
GAGCTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCC
Found at i:9585971 original size:20 final size:20
Alignment explanation
Indices: 9585946--9586022 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 20
9585936 GGATGCGAAT
9585946 GTCCGAGCTCGTTGAGTTGA
1 GTCCGAGCTCGTTGAGTTGA
* * *
9585966 GTCCGAGTTCGTGAGATGTAACTAA
1 GTCCGAGCTCGT-TGA-GT---TGA
9585991 GCTTCCGAGCTCGTTGAGTTGA
1 G--TCCGAGCTCGTTGAGTTGA
9586013 GTCCGAGCTC
1 GTCCGAGCTC
9586023 ACTTATGGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
20 20 0.45
21 2 0.05
22 5 0.11
25 5 0.11
26 2 0.05
27 10 0.23
ACGTcount: A:0.18, C:0.22, G:0.31, T:0.29
Consensus pattern (20 bp):
GTCCGAGCTCGTTGAGTTGA
Found at i:9586044 original size:26 final size:26
Alignment explanation
Indices: 9586015--9586094 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
9586005 TGAGTTGAGT
9586015 CCGAGCTCACTTATGGATGCGAACGC
1 CCGAGCTCACTTATGGATGCGAACGC
* * * *
9586041 CCGAGCTC-GTTA-AG-T-TG-A-GT
1 CCGAGCTCACTTATGGATGCGAACGC
9586061 CCGAGCTCACTTATGGATGCGAACGC
1 CCGAGCTCACTTATGGATGCGAACGC
9586087 CCGAGCTC
1 CCGAGCTC
9586095 GTTGAGTTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 9 0.22
21 4 0.10
22 2 0.05
23 2 0.05
24 2 0.05
25 4 0.10
26 17 0.43
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21
Consensus pattern (26 bp):
CCGAGCTCACTTATGGATGCGAACGC
Found at i:9595199 original size:38 final size:39
Alignment explanation
Indices: 9595157--9595244 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 39
9595147 GTCCAACCCA
*
9595157 ACACACCATGT-GAGGATAA-AATCGACCCACCCATCCCT
1 ACACACCATATAGAGGA-AATAATCGACCCACCCATCCCT
* * *
9595195 ACACACCATATACGGGGAAATAATCGTCCCATCCATCCCT
1 ACACACCATATA-GAGGAAATAATCGACCCACCCATCCCT
9595235 ACACACCATA
1 ACACACCATA
9595245 AGGTACCACA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 10 0.23
39 2 0.05
40 31 0.72
ACGTcount: A:0.35, C:0.36, G:0.11, T:0.17
Consensus pattern (39 bp):
ACACACCATATAGAGGAAATAATCGACCCACCCATCCCT
Found at i:9596163 original size:38 final size:38
Alignment explanation
Indices: 9596108--9596183 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
9596098 AAAACTTACC
* * *
9596108 AATGAGGAGAGCGTCAATGAATCGTAGAAGCCCGTTAG
1 AATGAGGAGAACATCAATGAATCGCAGAAGCCCGTTAG
9596146 AATGAGGAGAACATCAATGAATCGCAGAAGCCCGTTAG
1 AATGAGGAGAACATCAATGAATCGCAGAAGCCCGTTAG
9596184 TACGAAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (38 bp):
AATGAGGAGAACATCAATGAATCGCAGAAGCCCGTTAG
Found at i:9599812 original size:26 final size:26
Alignment explanation
Indices: 9599780--9599844 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
9599770 ATAAGAGCCA
* *
9599780 TAATCAGGAAGTTCAC-AAAGAACTTT
1 TAATCAGGAAGCTCACGAAA-AACCTT
*
9599806 TAATCAGGAAGCTCACGAAAAGCCTT
1 TAATCAGGAAGCTCACGAAAAACCTT
9599832 TAATCAGG-AGCTC
1 TAATCAGGAAGCTC
9599845 TGAATAGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.14
26 27 0.77
27 3 0.09
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (26 bp):
TAATCAGGAAGCTCACGAAAAACCTT
Found at i:9599993 original size:65 final size:65
Alignment explanation
Indices: 9599883--9600070 Score: 227
Period size: 65 Copynumber: 2.9 Consensus size: 65
9599873 CTAGCCATAT
*
9599883 CAGGACGCTCACAAAGAGCTGCGTTTGTATCTGCAACATATGCAGGATCACAACCGATCATAAAA
1 CAGGACGCTCACAAAGAGCTGCGTTTGTATCCGCAACATATGCAGGATCACAACCGATCATAAAA
* * * * * * * *
9599948 TAGGATGCTCATAAAGAGCTGTGTTTGTGTCCGCAATATATGCAGGATCACAACTGATCATATAA
1 CAGGACGCTCACAAAGAGCTGCGTTTGTATCCGCAACATATGCAGGATCACAACCGATCATAAAA
* * * * * *
9600013 CAGGACACTCACAAAGAGCTGCGGTAGT-T-CGTAACACATGCAGGATCACTACCGATCA
1 CAGGACGCTCACAAAGAGCTGCGTTTGTATCCGCAACATATGCAGGATCACAACCGATCA
9600071 GAATGTTCGT
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
63 24 0.24
64 1 0.01
65 77 0.75
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (65 bp):
CAGGACGCTCACAAAGAGCTGCGTTTGTATCCGCAACATATGCAGGATCACAACCGATCATAAAA
Found at i:9601048 original size:30 final size:30
Alignment explanation
Indices: 9600989--9601049 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
9600979 TTATTTAATT
9600989 AATTATCATCTTTTATTTTTTTCACTTTCC
1 AATTATCATCTTTTATTTTTTTCACTTTCC
* *
9601019 AATT-TCATCCTTTTCTTTATTTT-ATTTTCC
1 AATTATCAT-CTTTTATTT-TTTTCACTTTCC
9601049 A
1 A
9601050 TGGATGAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.15
30 19 0.70
31 4 0.15
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.61
Consensus pattern (30 bp):
AATTATCATCTTTTATTTTTTTCACTTTCC
Found at i:9602070 original size:17 final size:17
Alignment explanation
Indices: 9602048--9602080 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9602038 ATTTTATAAA
9602048 ATAATATTTTAATTAAG
1 ATAATATTTTAATTAAG
*
9602065 ATAATATTTTATTTAA
1 ATAATATTTTAATTAA
9602081 TAAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
ATAATATTTTAATTAAG
Found at i:9608970 original size:50 final size:50
Alignment explanation
Indices: 9608911--9609009 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
9608901 CAAATATATA
*
9608911 AGAAAACTACAAAACCTATGATAGATACATGTTCAAATCCGACACATCCG
1 AGAAAACTACAAAAACTATGATAGATACATGTTCAAATCCGACACATCCG
9608961 AGAAAACTACAAAAACTATGATAGATACATGTTCAAATCCGACACATCC
1 AGAAAACTACAAAAACTATGATAGATACATGTTCAAATCCGACACATCC
9609010 AAGTTCAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.20
Consensus pattern (50 bp):
AGAAAACTACAAAAACTATGATAGATACATGTTCAAATCCGACACATCCG
Found at i:9619520 original size:31 final size:31
Alignment explanation
Indices: 9619455--9619528 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
9619445 CGTGTTAAAA
* *
9619455 AAATATTATTTATAGTATTCAACAATTATAT
1 AAATATTATTTATAATATTCAACAAATATAT
*
9619486 AAATATTATTT-TAATATATGATACAAATAT-T
1 AAATATTATTTATAATAT-TCA-ACAAATATAT
*
9619517 AAATGTTATTTA
1 AAATATTATTTA
9619529 ATTGTGAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 5 0.14
31 24 0.67
32 7 0.19
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (31 bp):
AAATATTATTTATAATATTCAACAAATATAT
Found at i:9620491 original size:47 final size:47
Alignment explanation
Indices: 9620417--9620511 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 47
9620407 TCATCTTTCA
*
9620417 ATTTGTCAAGGATTATTTATTAGAGGGTTGATTAGAGCTATTAATTG
1 ATTTGTCAAGGATTATTTATTAGAGGGTTGATTAGAGCCATTAATTG
* * *
9620464 ATTTGTTAAGTATTATTTCTT-GAAGGGTTGATTAGAGCCATTAATTG
1 ATTTGTCAAGGATTATTTATTAG-AGGGTTGATTAGAGCCATTAATTG
9620511 A
1 A
9620512 GTTTTTTGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 1 0.02
47 42 0.98
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.43
Consensus pattern (47 bp):
ATTTGTCAAGGATTATTTATTAGAGGGTTGATTAGAGCCATTAATTG
Found at i:9620648 original size:19 final size:19
Alignment explanation
Indices: 9620625--9620673 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
9620615 TTATTTATTT
9620625 AATTTTTTATTA-TT-TTGA
1 AATTTTTTATTAGTTCTT-A
9620643 ATATTTGTTT-TTAGTTCTTA
1 A-ATTT-TTTATTAGTTCTTA
9620663 AATTTTTTATT
1 AATTTTTTATT
9620674 TTAGTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 7 0.27
21 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (19 bp):
AATTTTTTATTAGTTCTTA
Found at i:9623354 original size:15 final size:15
Alignment explanation
Indices: 9623334--9623363 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9623324 CTACTACATA
*
9623334 TATTATTCTCATTAT
1 TATTATTATCATTAT
9623349 TATTATTATCATTAT
1 TATTATTATCATTAT
9623364 AATTTAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATTATCATTAT
Found at i:9623950 original size:129 final size:129
Alignment explanation
Indices: 9623702--9624020 Score: 482
Period size: 129 Copynumber: 2.5 Consensus size: 129
9623692 TAATTATTCG
*
9623702 TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTAGGAATTCGGGGAATCGTGCCCTATC
1 TTTAAAAATTCTTTAAAAC-AAGGCAATGTTCGATGTTTAGGAATTCGAGGAATCGTGCCCTATC
* *
9623767 GTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATAGTCCTTTGGAATTTCACTCATGT
65 GTGCTCGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATAGTCCTTTAGAATTTCACTCATGT
* *
9623832 TTTAAAAATTCTTTAAAACAAAGGCAATGTTTGATGTTTGGGAATTCGAGGAATC-TGCCCTATC
1 TTTAAAAATTCTTTAAAAC-AAGGCAATGTTCGATGTTTAGGAATTCGAGGAATCGTGCCCTATC
* *
9623896 GTGCTCGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATTTCTTTAGAATTTCACTCATGT
65 GTGCTCGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATAGTCCTTTAGAATTTCACTCATGT
* ** * * *
9623961 CTTCTAAATTC--TAAAACAAGGCAATGTTCAATGTCTAGAAATTCGAGGAATCGTGCCCTA
1 TTTAAAAATTCTTTAAAACAAGGCAATGTTCGATGTTTAGGAATTCGAGGAATCGTGCCCTA
9624021 CTGTGCTAGG
Statistics
Matches: 172, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
126 30 0.17
127 13 0.08
129 78 0.45
130 51 0.30
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (129 bp):
TTTAAAAATTCTTTAAAACAAGGCAATGTTCGATGTTTAGGAATTCGAGGAATCGTGCCCTATCG
TGCTCGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATAGTCCTTTAGAATTTCACTCATGT
Found at i:9627615 original size:12 final size:12
Alignment explanation
Indices: 9627598--9627626 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
9627588 ATTCTTTTAT
9627598 TTTTTTTGAATA
1 TTTTTTTGAATA
9627610 TTTTTTTGAATA
1 TTTTTTTGAATA
9627622 TTTTT
1 TTTTT
9627627 CATTCATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTTTTGAATA
Found at i:9630148 original size:13 final size:13
Alignment explanation
Indices: 9630130--9630156 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9630120 TCATATATCA
9630130 TTCATAACACATC
1 TTCATAACACATC
9630143 TTCATAACACATC
1 TTCATAACACATC
9630156 T
1 T
9630157 AGTTAGGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (13 bp):
TTCATAACACATC
Found at i:9630330 original size:32 final size:32
Alignment explanation
Indices: 9630230--9630331 Score: 77
Period size: 32 Copynumber: 3.2 Consensus size: 32
9630220 TAGTTGGGAG
*
9630230 CATTTGATTCATTTCGATCATAGCATCCTAAT
1 CATTTGATTCATTTCGATCATAGCATCTTAAT
* ** * * *
9630262 TATTTGA--CA-TAAGCATCATATC-TAGTTAGGAG
1 CATTTGATTCATTTCG-ATCATAGCAT-CTTA--AT
9630294 CATTTGATTCATTTCGATCATAGCATCTTAAT
1 CATTTGATTCATTTCGATCATAGCATCTTAAT
9630326 CATTTG
1 CATTTG
9630332 GTTTAAGCAT
Statistics
Matches: 49, Mismatches: 13, Indels: 16
0.63 0.17 0.21
Matches are distributed among these distances:
29 3 0.06
30 11 0.22
32 20 0.41
34 12 0.24
35 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (32 bp):
CATTTGATTCATTTCGATCATAGCATCTTAAT
Found at i:9630341 original size:64 final size:64
Alignment explanation
Indices: 9630150--9630331 Score: 310
Period size: 64 Copynumber: 2.8 Consensus size: 64
9630140 ATCTTCATAA
* *
9630150 CACATCTAGTTAGGAGCATTTGATTTATTTCGATCATAGCATCCTAATTATTTGACATAAGTAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
*
9630214 CACATCTAGTTGGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
* * *
9630278 CATATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCTTAATCATTTG
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTG
9630332 GTTTAAGCAT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 111 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:9630548 original size:85 final size:88
Alignment explanation
Indices: 9630404--9630597 Score: 236
Period size: 86 Copynumber: 2.2 Consensus size: 88
9630394 ATCGTTAAAT
* *
9630404 TTACAGATCTTATCTCCCTAAGCAGTACGGAGTAGATCGAAGACAGTAAGCCTTAAA-CCCCTAA
1 TTACAGATCTTATCTCCCTAAGCAGTACGGAGCAGATCAAAGACAGTAAGCCTTAAACCCCCTAA
** *
9630468 GTAGTAGGGTAACAGGTTG-A-A
66 ACAGTAGGGTAACAGGCTGAAGA
* * *
9630489 TTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGGCGGTGAA-CCTT-AACCCCCT
1 TTACAGATCTTATCTCCCTAAGCAGTA-CGGAGCAGATCAAAGACAGT-AAGCCTTAAACCCCCT
9630552 AAACAGTAGGGTAACAGGCTGAAGA
64 AAACAGTAGGGTAACAGGCTGAAGA
** *
9630577 TTGTAGATCTTGTCTCCCTAA
1 TTACAGATCTTATCTCCCTAA
9630598 AGTTACAGTG
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
85 29 0.31
86 42 0.45
87 3 0.03
88 19 0.20
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (88 bp):
TTACAGATCTTATCTCCCTAAGCAGTACGGAGCAGATCAAAGACAGTAAGCCTTAAACCCCCTAA
ACAGTAGGGTAACAGGCTGAAGA
Found at i:9630785 original size:44 final size:44
Alignment explanation
Indices: 9630737--9631345 Score: 165
Period size: 44 Copynumber: 13.8 Consensus size: 44
9630727 AAAGTTTCAG
9630737 TGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
1 TGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
** * * * * ** *
9630781 TGGAGCGGCTCGAAGCCAC-AAT-TCGTATCTCCTTGAAGTTCCAG
1 TGGAGTAGATCGAAGCTACAAATCTC-T-TCTCCCTGAAATGGCAT
* * *
9630825 TGAAGTAGATCGAAGCTACAAATCTCTTCTTCCTGAAATGGCAC
1 TGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
* * * * **
9630869 TGGAG-AGGCTCGAAGCCAC-CAT-TCGTATCT-CCTTAAA--GTTT
1 TGGAGTA-GATCGAAGCTACAAATCTC-T-TCTCCCTGAAATGGCAT
* * * *
9630910 TAGCTGAGTAGATTGAAACTGCAAATCTCTTCTCCCTGAAATGGCAC
1 T-G--GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
* * * * * **
9630957 TAGAG-AGGCTCGAAGCCAC-AAT-TCGTATCTCCTTGAAGTTCCAT
1 TGGAGTA-GATCGAAGCTACAAATCTC-T-TCTCCCTGAAATGGCAT
* * * * * *
9631001 TGGAGTAGATCAAATCTATAAATCTCTTCTCCATGAAATGACAC
1 TGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
* * * * * *** * * ** *
9631045 TGGA-AAGGCTCGAAGCCACCATTCAGATCTCCTTGAAGTTTCAA
1 TGGAGTA-GATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
* *
9631089 CGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAC
1 TGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
* * * ** * * * * *** *
9631133 TAGAGCAGGTTAAAATCAAC-AAT-TCGTATCTCCTTGAAGTTTTAG
1 TGGAGTA-GATCGAAGCTACAAATCTC-T-TCTCCCTGAAATGGCAT
* * * *
9631178 CGGAGTAGATAGAGGCTACAAATCTCTTCTCCCTGAAATGGCGT
1 TGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
* * * * * ** *
9631222 TGGAGTGGTTCGAAGCCAC-AAT-TCGTATCTCCTTGAAGTTTCAG
1 TGGAGTAGATCGAAGCTACAAATCTC-T-TCTCCCTGAAATGGCAT
* ** * * *
9631266 CGGAACAGATCGATGCTACAAATCTTTTCTCCCTGAAATGGCTT
1 TGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
* * * *
9631310 TGGAG-CGATCAAAACTACAAACCT-TATCTCCCTGAA
1 TGGAGTAGATCGAAGCTACAAATCTCT-TCTCCCTGAA
9631346 GTTGTAATGG
Statistics
Matches: 379, Mismatches: 152, Indels: 69
0.63 0.25 0.12
Matches are distributed among these distances:
41 2 0.01
42 10 0.03
43 50 0.13
44 256 0.68
45 50 0.13
46 9 0.02
47 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (44 bp):
TGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCAT
Found at i:9631314 original size:88 final size:88
Alignment explanation
Indices: 9630710--9631307 Score: 775
Period size: 88 Copynumber: 6.8 Consensus size: 88
9630700 GTTAAAATCA
* *
9630710 ACAATTCGTATCTCCTTAAAGTTTCAGTGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* *
9630775 TGGCATTGGAGCGGCTCGAAGCC
66 TGGCACTGGAGAGGCTCGAAGCC
* * * *
9630798 ACAATTCGTATCTCCTTGAAGTTCCAGTGAAGTAGATCGAAGCTACAAATCTCTTCTTCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
9630863 TGGCACTGGAGAGGCTCGAAGCC
66 TGGCACTGGAGAGGCTCGAAGCC
* * * * * * *
9630886 ACCATTCGTATCTCCTTAAAGTTTTAGCTGAGTAGATTGAAACTGCAAATCTCTTCTCCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
*
9630951 TGGCACTAGAGAGGCTCGAAGCC
66 TGGCACTGGAGAGGCTCGAAGCC
* ** * * * *
9630974 ACAATTCGTATCTCCTTGAAGTTCCATTGGAGTAGATCAAATCTATAAATCTCTTCTCCATGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* *
9631039 TGACACTGGAAAGGCTCGAAGCC
66 TGGCACTGGAGAGGCTCGAAGCC
* *
9631062 ACCATTCAG-ATCTCCTTGAAGTTTCAACGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAA
1 ACAATTC-GTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAA
* * ** * *
9631126 ATGGCACTAGAGCAGGTTAAAATCA
65 ATGGCACTGGAG-AGGCTCGAAGCC
* * *
9631151 ACAATTCGTATCTCCTTGAAGTTTTAGCGGAGTAGATAGAGGCTACAAATCTCTTCTCCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
** * *
9631216 TGGCGTTGGAGTGGTTCGAAGCC
66 TGGCACTGGAGAGGCTCGAAGCC
** * *
9631239 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAACAGATCGATGCTACAAATCTTTTCTCCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
9631304 TGGC
66 TGGC
9631308 TTTGGAGCGA
Statistics
Matches: 438, Mismatches: 69, Indels: 6
0.85 0.13 0.01
Matches are distributed among these distances:
88 364 0.83
89 74 0.17
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (88 bp):
ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
TGGCACTGGAGAGGCTCGAAGCC
Found at i:9631701 original size:44 final size:44
Alignment explanation
Indices: 9631563--9632292 Score: 347
Period size: 44 Copynumber: 16.4 Consensus size: 44
9631553 CTTATCCCAT
* * * **
9631563 TGAAGTTACAGTGG-GACAGGTTGAAATTATGAATCTTATCTCCC
1 TGAAGTTGCAGTGGAG-CAGATTGAAGTTACAAATCTTATCTCCC
* * * * *
9631607 TAAAGTTGCAGTGGAGTAGATTAAAG---C---TATAATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCC
* * * *
9631645 TGAAGTTACAGTGGAGCAGGTTGAAGTTACAAGTCTCATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCC
* * * * * * **
9631689 TGAAGTTACAGTGGAGCAAAATGAAGATAGCGAATCTGATCTTTC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTA-CAAATCTTATCTCCC
* * * * * * * *
9631734 TGAAGTTACAGTAGAGTAGATTAAAGCTATAAATCCTATAC-CTC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTAT-CTCCC
* * *
9631778 TGAAGTTGCAGTAGG-TCAGA-TCAAATCTACCATGGTGAATCTTATCTCCC
1 TGAAGTTGCAGT-GGAGCAGATTGAAGT-TA-CA-----AATCTTATCTCCC
* * ** * *
9631828 TGAAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTATCCCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCC
* * * *
9631872 TGAAGTTGCAGTGGGGCAGGTCGAAGTTACAAGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCC
* * * **
9631916 TGAAGTTGCAGTGGAACAGACTGAAGATAGTGAATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTA-CAAATCTTATCTCCC
* * *
9631961 TGAAGTTGAAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCC
* * * *
9632005 TGAAGTTGCAGTAGAGCAGACTGAAGATAGCAAATCTTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTA-CAAATCTTATCTCCC
* * ** * * * * *
9632050 TGAACTTGCAATAAAGCAGATTAAAGCTATAAATCCTATAC-CTC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTAT-CTCCC
* * * * *
9632094 TGAAGTTGCAGTAGG-TCGGA-TCAAATCTACCATGGTGGATCTTATCTCCC
1 TGAAGTTGCAGT-GGAGCAGATTGAAGT-TA-CA-----AATCTTATCTCCC
* * * ** * *
9632144 TGAAGTCGTC-GCGGAGTAGATTGAAGCCACAAACCTTATCCCCC
1 TGAAGTTG-CAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCC
* * * * *
9632188 TAAAGTTGCAGTGGGGCAGGTCGAAGTTACAAGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCC
* * * * *
9632232 TGAAGTTACAGTGGAGCAGACTGAAGATA-ATGAATCTTATTTCCT
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTACA--AATCTTATCTCCC
*
9632277 TGAAGTTGCAATGGAG
1 TGAAGTTGCAGTGGAG
9632293 TGGATAGAAT
Statistics
Matches: 502, Mismatches: 146, Indels: 75
0.69 0.20 0.10
Matches are distributed among these distances:
38 30 0.06
41 1 0.00
43 8 0.02
44 268 0.53
45 135 0.27
49 10 0.02
50 43 0.09
51 7 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (44 bp):
TGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCC
Found at i:9631987 original size:89 final size:89
Alignment explanation
Indices: 9631817--9632053 Score: 332
Period size: 89 Copynumber: 2.7 Consensus size: 89
9631807 CCATGGTGAA
* * * ** * * *
9631817 TCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCA-CAAACCTTATCCCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGA
*
9631881 AGTGGGGCAGGTCGAAGTTACAAG
66 AGTGGAGCAGGTCGAAGTTACAAG
* **
9631905 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGTGAATCTTATCTCCCTGAAGTTGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGA
*
9631970 AGTGGAGCAGGTTGAAGTTACAAG
66 AGTGGAGCAGGTCGAAGTTACAAG
* *
9631994 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATAGCAAATCTTATCTCTCTGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAA
9632054 CTTGCAATAA
Statistics
Matches: 130, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 34 0.26
89 96 0.74
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (89 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGA
AGTGGAGCAGGTCGAAGTTACAAG
Found at i:9632010 original size:227 final size:221
Alignment explanation
Indices: 9631592--9632018 Score: 525
Period size: 227 Copynumber: 1.9 Consensus size: 221
9631582 GTTGAAATTA
* *
9631592 TGAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCTATAATCTCCCTGAAGTTACAGT
1 TGAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCAATAATCCCCCTGAAGTTACAGT
* *
9631657 GGAGCAGGTTGAAGTTACAAGTCTCATCTCCCTGAAGTTACAGTGGAGCAAAATGAAGATAGCGA
66 GGAGCAGGTCGAAGTTACAAGTCTCATCTCCCTGAAGTTACAGTGGAACAAAATGAAGATAGCGA
** * * *
9631722 ATCTGATCTTTCTGAAGTTACAGTAGAGTAGATTAAAGCTATAAATCCTATACCTCTGAAGTTGC
131 ATCTGATCTCCCTGAAGTTACAGTAGAGCAGATTAAAGCTACAAATCCTATACCCCTGAAGTTGC
9631787 AGTAGGTCAGATCAAATCTACCATGG
196 AGTAGGTCAGATCAAATCTACCATGG
* * * *
9631813 TGAATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTATCCCCCTGAAGT
1 TGAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAG---C-AA--TAATCCCCCTGAAGT
* * * * * *
9631878 TGCAGTGGGGCAGGTCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGA
60 TACAGTGGAGCAGGTCGAAGTTACAAGTCTCATCTCCCTGAAGTTACAGTGGAACAAAATGAAGA
* * * * * * * *
9631943 TAGTGAATCTTATCTCCCTGAAGTTGA-AGTGGAGCAGGTTGAAGTTACAAGTCTTAT-CTCCCT
125 TAGCGAATCTGATCTCCCTGAAGTT-ACAGTAGAGCAGATTAAAGCTACAAATCCTATAC-CCCT
9632006 GAAGTTGCAGTAG
188 GAAGTTGCAGTAG
9632019 AGCAGACTGA
Statistics
Matches: 171, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
221 38 0.22
224 1 0.01
225 1 0.01
226 1 0.01
227 129 0.75
228 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (221 bp):
TGAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCAATAATCCCCCTGAAGTTACAGT
GGAGCAGGTCGAAGTTACAAGTCTCATCTCCCTGAAGTTACAGTGGAACAAAATGAAGATAGCGA
ATCTGATCTCCCTGAAGTTACAGTAGAGCAGATTAAAGCTACAAATCCTATACCCCTGAAGTTGC
AGTAGGTCAGATCAAATCTACCATGG
Found at i:9632068 original size:45 final size:45
Alignment explanation
Indices: 9631905--9632069 Score: 165
Period size: 45 Copynumber: 3.7 Consensus size: 45
9631895 AAGTTACAAG
* * **
9631905 TCTTATCTCCCTGAAGTTGCAGTGGAA-CAGACTGAAGATAGTGAA
1 TCTTATCTCCCTGAAGTTGCAAT-AAAGCAGACTGAAGATAGCAAA
** ** * *
9631950 TCTTATCTCCCTGAAGTTG-AAGTGGAGCAGGTTGAAGTTA-CAAG
1 TCTTATCTCCCTGAAGTTGCAA-TAAAGCAGACTGAAGATAGCAAA
* *
9631994 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAATAAAGCAGACTGAAGATAGCAAA
* *
9632039 TCTTATCTCTCTGAACTTGCAATAAAGCAGA
1 TCTTATCTCCCTGAAGTTGCAATAAAGCAGA
9632070 TTAAAGCTAT
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
44 37 0.38
45 61 0.62
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAATAAAGCAGACTGAAGATAGCAAA
Found at i:9632097 original size:89 final size:89
Alignment explanation
Indices: 9631899--9632107 Score: 233
Period size: 89 Copynumber: 2.3 Consensus size: 89
9631889 AGGTCGAAGT
* * * **
9631899 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGTGAATCTTATCTCCCTGA
1 TACAAATCCTATCTCCCTGAAGTTGCAGTAGAACAGACTGAAGATAGCAAATCTTATCTCCCTGA
* ** * * *
9631964 AGTTGAAGTGGAGCAGGTTGAAGT
66 ACTTGAAGTAAAGCAGATTAAAGC
* * * *
9631988 TACAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATAGCAAATCTTATCTCTCTGA
1 TACAAATCCTATCTCCCTGAAGTTGCAGTAGAACAGACTGAAGATAGCAAATCTTATCTCCCTGA
9632053 ACTTGCAA-TAAAGCAGATTAAAGC
66 ACTTG-AAGTAAAGCAGATTAAAGC
* *
9632077 TATAAATCCTATAC-CTCTGAAGTTGCAGTAG
1 TACAAATCCTAT-CTCCCTGAAGTTGCAGTAG
9632108 GTCGGATCAA
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
89 100 0.97
90 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (89 bp):
TACAAATCCTATCTCCCTGAAGTTGCAGTAGAACAGACTGAAGATAGCAAATCTTATCTCCCTGA
ACTTGAAGTAAAGCAGATTAAAGC
Found at i:9632118 original size:316 final size:315
Alignment explanation
Indices: 9631332--9632292 Score: 1131
Period size: 316 Copynumber: 3.1 Consensus size: 315
9631322 AACTACAAAC
* * * *
9631332 CTTATCTCCCTGAAGTTGTAATGGAGCAGGTTGAAGTCACTAGTCTTATCTCCTTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAG
* * * * * *
9631397 TGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTGCAGTGGAA-TAGGTTGAAGCTAT
66 TGGAGCAGACTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGT-AAAGTAGATTAAAGCTAT
* *
9631461 AAATCACAGATCTTATCTCTTAGAAGTTGCAGTAGAGT-AGATCAAA---A-CA-----AATCTT
130 AAATC-C---T-ATACCTC-T-GAAGTTGCAGTAG-GTCAGATCAAATCTACCATGGTGAATCTT
* * ** * * * * ** *
9631516 ATCTCTCTGAAATTACAGT--AG-AG-TTAAAGCTATAAGCCTTATCCCATTGAAGTTACAGTGG
187 ATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTATCCCCCTGAAGTTGCAGTGG
* * * * * * * * *
9631577 GACAGGTTGAAATTATGAA-TCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCTAT--A-
252 GGCAGGTCGAAGTTA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATATGAAT
* * * *
9631638 ---ATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACAAGTCTCATCTCCCTGAAGTTACAG
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAG
* * * * * * *
9631700 TGGAGCAAAATGAAGATAGCGAATCTGATCTTTCTGAAGTTACAGTAGAGTAGATTAAAGCTATA
66 TGGAGCAGACTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAAAGTAGATTAAAGCTATA
9631765 AATCCTATACCTCTGAAGTTGCAGTAGGTCAGATCAAATCTACCATGGTGAATCTTATCTCCCTG
131 AATCCTATACCTCTGAAGTTGCAGTAGGTCAGATCAAATCTACCATGGTGAATCTTATCTCCCTG
9631830 AAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCG
196 AAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCG
*
9631895 AAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGTGAAT
261 AAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-TGAAT
9631951 CTTATCTCCCTGAAGTTG-AAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAA-TGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
* * * *
9632015 GTAGAGCAGACTGAAGATAGCAAATCTTATCTCTCTGAACTTGCAATAAAGCAGATTAAAGCTAT
65 GTGGAGCAGACTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAAAGTAGATTAAAGCTAT
* *
9632080 AAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACCATGGTGGATCTTATCTCCCT
130 AAATCCTATACCTCTGAAGTTGCAGTAGGTCAGATCAAATCTACCATGGTGAATCTTATCTCCCT
* * * *
9632145 GAAGTCGTCGCGGAGTAGATTGAAGCCACAAACCTTATCCCCCTAAAGTTGCAGTGGGGCAGGTC
195 GAAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTC
*
9632210 GAAGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAATGAAT
260 GAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ATGAAT
* *
9632267 CTTATTTCCTTGAAGTTGCAATGGAG
1 CTTATCTCCCTGAAGTTGCAATGGAG
9632293 TGGATAGAAT
Statistics
Matches: 560, Mismatches: 69, Indels: 42
0.83 0.10 0.06
Matches are distributed among these distances:
295 2 0.00
296 21 0.04
297 1 0.00
298 5 0.01
299 2 0.00
300 2 0.00
302 2 0.00
303 108 0.19
305 21 0.04
307 2 0.00
308 4 0.01
309 77 0.14
310 1 0.00
312 1 0.00
315 1 0.00
316 307 0.55
317 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (315 bp):
CTTATCTCCCTGAAGTTGCAATGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAG
TGGAGCAGACTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAAAGTAGATTAAAGCTATA
AATCCTATACCTCTGAAGTTGCAGTAGGTCAGATCAAATCTACCATGGTGAATCTTATCTCCCTG
AAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCG
AAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATATGAAT
Found at i:9634361 original size:130 final size:130
Alignment explanation
Indices: 9634167--9634495 Score: 486
Period size: 130 Copynumber: 2.6 Consensus size: 130
9634157 AAGTTATTCG
*
9634167 TTTAAAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTAGGAATTTGGGGAATCGTGCCCTATC
1 TTTAAAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTAGGAATTCGGGGAATCGTGCCCTATC
* * *
9634232 GTGCTGGATTGGAATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTCACTCCTGT
66 GTGCTGGATTGCAATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGT
* * *
9634297 TTTAAAAATTCTTTAAAACGAAGGCAATGTTTGATGTTTGGGAATTCGGGGAATCGTGCCCTATC
1 TTTAAAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTAGGAATTCGGGGAATCGTGCCCTATC
*
9634362 GTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGT
66 GTGCTGGATTGCAATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGT
* * * * * * *
9634427 CTTCAAAATTC--TAAAAC-AAGGTAATGTTCAATGTCTAGAAATTCGAGGAATCGTGCCCTA-C
1 TTTAAAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTAGGAATTCGGGGAATCGTGCCCTATC
9634488 TGTGCTGG
66 -GTGCTGG
9634496 GTTTCATTTT
Statistics
Matches: 181, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
126 1 0.01
127 43 0.24
128 6 0.03
130 131 0.72
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (130 bp):
TTTAAAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTAGGAATTCGGGGAATCGTGCCCTATC
GTGCTGGATTGCAATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGT
Found at i:9635658 original size:47 final size:47
Alignment explanation
Indices: 9635594--9635694 Score: 148
Period size: 47 Copynumber: 2.1 Consensus size: 47
9635584 GTAATAAATC
* * * **
9635594 GCCACTTAATAATATTGTGGACAAGCCACCACTTTTTTAGATAAACT
1 GCCACTTAAGAAAATTGTGGACAAGCCAACACTTTTGCAGATAAACT
9635641 GCCACTTAAGAAAATTGTGGACAAGCCAACACTTTTGCAGATAAACT
1 GCCACTTAAGAAAATTGTGGACAAGCCAACACTTTTGCAGATAAACT
*
9635688 ACCACTT
1 GCCACTT
9635695 CTTCCTCCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (47 bp):
GCCACTTAAGAAAATTGTGGACAAGCCAACACTTTTGCAGATAAACT
Found at i:9636634 original size:17 final size:17
Alignment explanation
Indices: 9636597--9636633 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
9636587 TCATTCACTT
*
9636597 AAAAGAGAAGAAATGAG
1 AAAAGAGAAGAAATAAG
9636614 AAAAGAGAA-AAATAAG
1 AAAAGAGAAGAAATAAG
9636630 AAAA
1 AAAA
9636634 ATAGAGGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (17 bp):
AAAAGAGAAGAAATAAG
Found at i:9637034 original size:129 final size:129
Alignment explanation
Indices: 9636885--9637144 Score: 493
Period size: 129 Copynumber: 2.0 Consensus size: 129
9636875 GAATGAAAAG
9636885 ATGGAACAAAAGAGTGTTCTTCATCTTGTCTAGGTTCAATAAACATCACATAAGGTAAGGATGAA
1 ATGGAACAAAAGAGTGTTCTTCATCTTGTCTAGGTTCAATAAACATCACATAAGGTAAGGATGAA
9636950 GAGAATGGTATGTTGAGGGGATAAAGAAGCAAAAAGGGGATCATGGGAGTGAAAAAGGGGCTTA
66 GAGAATGGTATGTTGAGGGGATAAAGAAGCAAAAAGGGGATCATGGGAGTGAAAAAGGGGCTTA
*
9637014 ATGGAACAAAAGAGTGTTCTTCATCTTGTCTAGGTTCAATGAACATCACATAAGGTAAGGATGAA
1 ATGGAACAAAAGAGTGTTCTTCATCTTGTCTAGGTTCAATAAACATCACATAAGGTAAGGATGAA
* *
9637079 GAGAATGGTATGTTGAGGGGATAAAGGAGCAAAAAGGGGATCATGGGAGTGAAAAAGGGGTTTA
66 GAGAATGGTATGTTGAGGGGATAAAGAAGCAAAAAGGGGATCATGGGAGTGAAAAAGGGGCTTA
9637143 AT
1 AT
9637145 AAGGGAAGGT
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.38, C:0.09, G:0.30, T:0.23
Consensus pattern (129 bp):
ATGGAACAAAAGAGTGTTCTTCATCTTGTCTAGGTTCAATAAACATCACATAAGGTAAGGATGAA
GAGAATGGTATGTTGAGGGGATAAAGAAGCAAAAAGGGGATCATGGGAGTGAAAAAGGGGCTTA
Found at i:9639756 original size:25 final size:25
Alignment explanation
Indices: 9639722--9639773 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
9639712 GAAATATTAG
9639722 ATAATGTTGCACCAATTCTAAAGAA
1 ATAATGTTGCACCAATTCTAAAGAA
9639747 ATAATGTTGCACCAATTCTAAAGAA
1 ATAATGTTGCACCAATTCTAAAGAA
9639772 AT
1 AT
9639774 CTCAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (25 bp):
ATAATGTTGCACCAATTCTAAAGAA
Found at i:9643259 original size:26 final size:26
Alignment explanation
Indices: 9643212--9643315 Score: 119
Period size: 26 Copynumber: 4.2 Consensus size: 26
9643202 CATCGTATTC
* *
9643212 GCTCTTTC-GAGCT-ATGATCAGTAA
1 GCTCCTTCTGAGCTGATGAACAGTAA
9643236 GCTCCTTCTGAGCTGATGAACAGTAA
1 GCTCCTTCTGAGCTGATGAACAGTAA
*
9643262 GCTCCTTCTGAGCTGATGAACAATAA
1 GCTCCTTCTGAGCTGATGAACAGTAA
* * *
9643288 GCT-CTTTTGAACTGA--AACGGTAA
1 GCTCCTTCTGAGCTGATGAACAGTAA
9643311 GCTCC
1 GCTCC
9643316 GATAAGCTGA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
23 9 0.13
24 8 0.11
25 15 0.21
26 38 0.54
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (26 bp):
GCTCCTTCTGAGCTGATGAACAGTAA
Found at i:9654164 original size:55 final size:55
Alignment explanation
Indices: 9654068--9654180 Score: 129
Period size: 55 Copynumber: 2.1 Consensus size: 55
9654058 CTTCTCCCAT
* ** *
9654068 GCCCGTTTTAATTTAACAGGTTTGCCCACGGTTGCTTGGCACGTACATGTCGCAC
1 GCCCGTGTTAATTTAACAGGTTTGCCCACGGTTGCAAGGCACGGACATGTCGCAC
* * * * *
9654123 GCCCGTGTTAATTTGACAGGTTTGGCCATGGGTT-CAAGGCACGGGCGTGTCGCAC
1 GCCCGTGTTAATTTAACAGGTTTGCCCA-CGGTTGCAAGGCACGGACATGTCGCAC
9654178 GCC
1 GCC
9654181 TGTGCTGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
55 44 0.92
56 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (55 bp):
GCCCGTGTTAATTTAACAGGTTTGCCCACGGTTGCAAGGCACGGACATGTCGCAC
Found at i:9658900 original size:24 final size:24
Alignment explanation
Indices: 9658873--9658919 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
9658863 TTTAGAGAAT
9658873 TTTGTATTTACGTTTTTAGGGTTC
1 TTTGTATTTACGTTTTTAGGGTTC
* *
9658897 TTTGTTTTTAGGTTTTTAGGGTT
1 TTTGTATTTACGTTTTTAGGGTT
9658920 TAGTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.04, G:0.23, T:0.62
Consensus pattern (24 bp):
TTTGTATTTACGTTTTTAGGGTTC
Found at i:9660678 original size:39 final size:40
Alignment explanation
Indices: 9660624--9660715 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 40
9660614 CGTTTGAATG
* *
9660624 AAAAATGCCGCTAAAGAAT-GAGCATTAG-TGGCGC-TTTTT
1 AAAAACGCCGCTAAAG-ATCGAGCATTAGCAGG-GCTTTTTT
* *
9660663 AAAAACGCCTCTAAAGATCGAGTATTAGCAGGGCTTTTTT
1 AAAAACGCCGCTAAAGATCGAGCATTAGCAGGGCTTTTTT
*
9660703 AAAAACGCTGCTA
1 AAAAACGCCGCTA
9660716 TATGTACACC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.05
39 24 0.55
40 18 0.41
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGATCGAGCATTAGCAGGGCTTTTTT
Found at i:9661016 original size:40 final size:38
Alignment explanation
Indices: 9660961--9661103 Score: 133
Period size: 40 Copynumber: 3.6 Consensus size: 38
9660951 TTTTAGTGGC
* * * *
9660961 TTTAGTGGCGCTTTTTAAAAACGCCGCTAAAGATTGAGT
1 TTTAGCGGCGTTTTTTAAAAACGCCGCTAAAG-TAGACT
* *
9661000 ATTAGCGGCGATTTTTTAAGAAACGCCGCTATAAGTACACT
1 TTTAGCGGCG-TTTTTTAA-AAACGCCGCTA-AAGTAGACT
* * * *
9661041 TTTAGCGGCGCTTTTTAAAAAACGCCGCTAATGCTCGATT
1 TTTAGCGGCG-TTTTTTAAAAACGCCGCTAAAG-TAGACT
9661081 TTTAGCGGCGTTTTTTGAAAAAC
1 TTTAGCGGCGTTTTTT-AAAAAC
9661104 ACCACAAAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
39 15 0.18
40 37 0.44
41 30 0.35
42 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (38 bp):
TTTAGCGGCGTTTTTTAAAAACGCCGCTAAAGTAGACT
Found at i:9661027 original size:41 final size:38
Alignment explanation
Indices: 9660962--9661071 Score: 121
Period size: 41 Copynumber: 2.8 Consensus size: 38
9660952 TTTAGTGGCT
* ** *
9660962 TTAGTGGCGCTTTTTAAAAACGCCGCTAAAGATTGAGTA
1 TTAGCGGCGCTTTTTAAAAACGCCGCTAAAG-TACACTA
* *
9661001 TTAGCGGCGATTTTTTAAGAAACGCCGCTATAAGTACACTT
1 TTAGCGGCG-CTTTTTAA-AAACGCCGCTA-AAGTACACTA
9661042 TTAGCGGCGCTTTTTAAAAAACGCCGCTAA
1 TTAGCGGCGCTTTTT-AAAAACGCCGCTAA
9661072 TGCTCGATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
39 9 0.15
40 23 0.38
41 25 0.42
42 3 0.05
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (38 bp):
TTAGCGGCGCTTTTTAAAAACGCCGCTAAAGTACACTA
Found at i:9661340 original size:22 final size:22
Alignment explanation
Indices: 9661315--9661359 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9661305 GAGTTATTAT
* *
9661315 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAAGGG
* *
9661337 TTTAGGGATTATGGTTTAAGGG
1 TTTAAGGATTATGGATTAAGGG
9661359 T
1 T
9661360 GGTTTAATGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (22 bp):
TTTAAGGATTATGGATTAAGGG
Done.