Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 203 of 221
Found at i:59645438 original size:98 final size:97
Alignment explanation
Indices: 59645323--59645527 Score: 313
Period size: 98 Copynumber: 2.1 Consensus size: 97
59645313 TTTTTTAGTT
* * * *
59645323 TATATATGTAATTATTATATTTATGATTTATATATTTATTACCTTATATATA-TATGTACGTATA
1 TATATATATAATCATTATATTTATGATCTATATATTTATTAACTTATATATAGTATGTA--TATA
59645387 TATTATACTTTCTATACATATTTTATAATTTCTA
64 TATTATACTTTCTATACATATTTTATAATTTCTA
*
59645421 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATGTATGTATATAT
1 TATATATATAATCATTATATTTATGATCTATATATTTATTAACTTATATATA-GTATGTATATAT
*
59645486 ATTATACTTTCTATCCATATTTTATAATTTCTA
65 ATTATACTTTCTATACATATTTTATAATTTCTA
*
59645519 TATGTATAT
1 TATATATAT
59645528 TTTTCTTTAT
Statistics
Matches: 98, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
98 92 0.94
100 6 0.06
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (97 bp):
TATATATATAATCATTATATTTATGATCTATATATTTATTAACTTATATATAGTATGTATATATA
TTATACTTTCTATACATATTTTATAATTTCTA
Found at i:59645472 original size:46 final size:46
Alignment explanation
Indices: 59645323--59645473 Score: 121
Period size: 46 Copynumber: 3.2 Consensus size: 46
59645313 TTTTTTAGTT
* * * *
59645323 TATATATGTAATTATTATATTTATGATTTATATATTTATTACCTTA
1 TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTA
* *
59645369 TATATATATGTACGTATATATTATACTTTCT-ATAC-ATAT-TTTA-TAATTTCTA
1 TATATATA--TA---AT-TATTAT-CTTTATGAT-CTATATATTTATTAA-CT-TA
*
59645421 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTA
1 TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTA
59645467 TATATAT
1 TATATAT
59645474 GTATGTATAT
Statistics
Matches: 82, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
45 6 0.07
46 27 0.33
47 7 0.09
48 5 0.06
50 4 0.05
51 7 0.09
52 22 0.27
53 4 0.05
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (46 bp):
TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTA
Found at i:59645510 original size:20 final size:20
Alignment explanation
Indices: 59645482--59645519 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59645472 ATGTATGTAT
*
59645482 ATATATTATACTTTCTATCC
1 ATATATTATAATTTCTATCC
*
59645502 ATATTTTATAATTTCTAT
1 ATATATTATAATTTCTAT
59645520 ATGTATATTT
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:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTATAATTTCTATCC
Found at i:59652525 original size:44 final size:44
Alignment explanation
Indices: 59652477--59652790 Score: 121
Period size: 44 Copynumber: 7.1 Consensus size: 44
59652467 CCTGGACAAC
*
59652477 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAGT
** * * * * * * *
59652521 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTATGGTTA-T
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCTA-AG-CAGT
* * * ** **
59652566 AGTGGAGTACATTGAAGCTAGT-A-AT-TCTA-CTTCCCTGGGCAAC
1 AGTGGAATAGATTGAAGAT-GTCAGATCT-TATC-TCCCTAAGCAGT
* *
59652609 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGAAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAGT
** * * * * * * *
59652653 AGTGGAGCAGATCGAATATGGCGGATTTTACCTCCCT--GTAGTT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAG-T
* * * * **
59652696 ACAGTGGAGTATATTG--GA-GCCAGTAAT-TCTA-CTTCCCTAGGCAAC
1 --AGTGGAATAGATTGAAGATGTCAG--ATCT-TATC-TCCCTAAGCAGT
*
59652741 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAGT
59652785 AGTGGA
1 AGTGGA
59652791 GAAGATCGAA
Statistics
Matches: 192, Mismatches: 54, Indels: 48
0.65 0.18 0.16
Matches are distributed among these distances:
42 8 0.04
43 37 0.19
44 106 0.55
45 34 0.18
46 7 0.04
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAGT
Found at i:59652535 original size:132 final size:131
Alignment explanation
Indices: 59652368--59652906 Score: 798
Period size: 132 Copynumber: 4.1 Consensus size: 131
59652358 GGTTAAAACC
* * *
59652368 GATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTATCTCCTTGAGGTTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTA
*
59652433 TAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTT
66 CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGG-CAACAGTGGAATAGATTGAAGATTT
59652498 CA
130 CA
*
59652500 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCT-ATGGTT
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGA-GGTT
* *
59652564 ATAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATT
65 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGCAACAGTGGAATAGATTGAAGATT
59652629 TCA
129 TCA
* * *
59652632 GATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCGAATATGGCGGATTTTACCTCCCTGTA-GTT
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTG-AGGTT
* *
59652696 ACAGTGGAGTATATTGGAGCCAGTAATTCTACTTCCCTAGGCAACAGTGGAATAGATTGAAGATT
65 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGCAACAGTGGAATAGATTGAAGATT
59652761 TCA
129 TCA
* * * *
59652764 GATCTTATCTCCCTAAGCAGTAGTGGAGAAGATCGAATATGGTAGATTTTACCTCCCTGTGGTTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTA
* * *
59652829 CAGTGGAGTACATTGAAGCCAGTAATCCTA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 CAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGG-CAACAGTGGAATAGATTGAAGATT
*
59652893 GTAA
129 -TCA
59652897 G-TCTTATCTC
1 GATCTTATCTC
59652907 TCTGCAGTTG
Statistics
Matches: 376, Mismatches: 23, Indels: 16
0.91 0.06 0.04
Matches are distributed among these distances:
131 4 0.01
132 366 0.97
133 5 0.01
134 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (131 bp):
GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTA
CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGCAACAGTGGAATAGATTGAAGATTTC
A
Found at i:59653162 original size:19 final size:19
Alignment explanation
Indices: 59653138--59653269 Score: 194
Period size: 19 Copynumber: 6.8 Consensus size: 19
59653128 AATTTTTGAG
59653138 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
59653157 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
*
59653176 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
59653195 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
59653216 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
59653235 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
59653254 GATCA-GCAATCTTAGA
1 GAT-ATGCAATCTTAGA
59653270 AGATGTGATT
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
19 83 0.81
20 1 0.01
21 18 0.18
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:59653232 original size:59 final size:59
Alignment explanation
Indices: 59653139--59653269 Score: 221
Period size: 59 Copynumber: 2.3 Consensus size: 59
59653129 ATTTTTGAGG
59653139 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
* *
59653198 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATATAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
*
59653257 -CA-GCAATCTTAGA
1 ATATGCAATCTTAGA
59653270 AGATGTGATT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
57 11 0.16
58 1 0.01
59 57 0.83
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (59 bp):
ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
Found at i:59653898 original size:16 final size:17
Alignment explanation
Indices: 59653879--59653921 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
59653869 TTTTTATGAT
59653879 TTATATATTTAT-TACC
1 TTATATATTTATGTACC
* *
59653895 TTATATATATATGTACG
1 TTATATATTTATGTACC
59653912 TATATATATT
1 T-TATATATT
59653922 ATACTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 4 0.18
18 7 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (17 bp):
TTATATATTTATGTACC
Found at i:59653933 original size:18 final size:18
Alignment explanation
Indices: 59653912--59654046 Score: 57
Period size: 18 Copynumber: 7.3 Consensus size: 18
59653902 TATATGTACG
* *
59653912 TATATATATTATACTTTT
1 TATATATATTATAATTTC
*
59653930 TATACATATTTTATAATTTC
1 TAT--ATATATTATAATTTC
* *
59653950 TATATATATAATCATTATC
1 TATATATATTATAATT-TC
59653969 T-T-TATGATCTAT-ATATT-
1 TATATAT-AT-TATAAT-TTC
* *
59653986 TAT-TA-ACTTATATATATG
1 TATATATA-TTATA-ATTTC
*
59654004 TATATATATTATACTTTC
1 TATATATATTATAATTTC
*
59654022 TATCCATATTTTATAATTTC
1 TAT--ATATATTATAATTTC
59654042 TATAT
1 TATAT
59654047 GTATATTTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 30
0.67 0.10 0.23
Matches are distributed among these distances:
16 4 0.04
17 6 0.07
18 34 0.38
19 13 0.15
20 32 0.36
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.55
Consensus pattern (18 bp):
TATATATATTATAATTTC
Found at i:59653938 original size:20 final size:20
Alignment explanation
Indices: 59653915--59653959 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
59653905 ATGTACGTAT
* *
59653915 ATATATTATACTTTTTATAC
1 ATATATTATAATTTCTATAC
* *
59653935 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
59653955 ATATA
1 ATATA
59653960 ATCATTATCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:59653954 original size:48 final size:46
Alignment explanation
Indices: 59653902--59654049 Score: 137
Period size: 46 Copynumber: 3.2 Consensus size: 46
59653892 ACCTTATATA
59653902 TATATGTACGTATATATATTATACTTTTTATACATATTTTATAATTTC
1 TATATGTA-GTATATATATTATACTTTTTAT-CATATTTTATAATTTC
* * *
59653950 TATA--TA-TATA-ATCATTAT-CTTTATGATCTATATATTTATTAACTTA
1 TATATGTAGTATATAT-ATTATACTTT-TTATC-ATAT-TTTA-TAATTTC
* *
59653996 TATATAT-GTATATATATTATACTTTCTATCCATATTTTATAATTTC
1 TATATGTAGTATATATATTATACTTTTTAT-CATATTTTATAATTTC
59654042 TATATGTA
1 TATATGTA
59654050 TATTTTTCTT
Statistics
Matches: 80, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
43 7 0.09
44 16 0.20
45 4 0.05
46 22 0.28
47 4 0.05
48 20 0.25
49 7 0.09
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (46 bp):
TATATGTAGTATATATATTATACTTTTTATCATATTTTATAATTTC
Found at i:59654035 original size:20 final size:20
Alignment explanation
Indices: 59654007--59654044 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59653997 ATATATGTAT
*
59654007 ATATATTATACTTTCTATCC
1 ATATATTATAATTTCTATCC
*
59654027 ATATTTTATAATTTCTAT
1 ATATATTATAATTTCTAT
59654045 ATGTATATTT
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:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTATAATTTCTATCC
Found at i:59654048 original size:44 final size:44
Alignment explanation
Indices: 59653911--59654052 Score: 162
Period size: 44 Copynumber: 3.1 Consensus size: 44
59653901 ATATATGTAC
* *
59653911 GTATATATATTATACTTTTTATACATATTTTATAATTTCTATAT
1 GTATATATATTATACTTTATATCCATATTTTATAATTTCTATAT
* * *
59653955 ATATA-ATCATTAT-CTTTATGATCTATATATTTATTAACTTATATATAT
1 GTATATAT-ATTATACTTTAT-ATCCATAT-TTTA-TAA-TT-TCTATAT
*
59654003 GTATATATATTATACTTTCTATCCATATTTTATAATTTCTATAT
1 GTATATATATTATACTTTATATCCATATTTTATAATTTCTATAT
59654047 GTATAT
1 GTATAT
59654053 TTTTCTTTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
43 7 0.09
44 27 0.33
45 6 0.07
46 6 0.07
47 6 0.07
48 22 0.27
49 7 0.09
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (44 bp):
GTATATATATTATACTTTATATCCATATTTTATAATTTCTATAT
Found at i:59654052 original size:98 final size:96
Alignment explanation
Indices: 59653852--59654051 Score: 282
Period size: 92 Copynumber: 2.1 Consensus size: 96
59653842 TTTTTTAGTT
* * * * *
59653852 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATA-GTA-GTATAT
*
59653917 ATATTATACTTTTTATACATATTTTATAATTTC
64 ATATTATACTTTCTATACATATTTTATAATTTC
59653950 TATATATATAATCATTATCTTTATGATCTATATATTTATTAAC-T-TATATATA-T-GTATATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATAGTAGTATATAT
*
59654011 ATTATACTTTCTATCCATATTTTATAATTTC
66 ATTATACTTTCTATACATATTTTATAATTTC
*
59654042 TATATGTATA
1 TATATATATA
59654052 TTTTTCTTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
92 46 0.49
94 1 0.01
96 8 0.09
97 1 0.01
98 38 0.40
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (96 bp):
TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATAGTAGTATATAT
ATTATACTTTCTATACATATTTTATAATTTC
Found at i:59654104 original size:20 final size:20
Alignment explanation
Indices: 59654081--59654121 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
59654071 ATGTATTATA
59654081 TATATAAATTTTATATTTTT
1 TATATAAATTTTATATTTTT
59654101 TATATAAATTTTATATTTTT
1 TATATAAATTTTATATTTTT
59654121 T
1 T
59654122 TTCCATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATATAAATTTTATATTTTT
Found at i:59659210 original size:29 final size:29
Alignment explanation
Indices: 59659147--59659213 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
59659137 GTTTGACCTT
*
59659147 ATTTGATTCATTTTAATAGTACAAGGACTA
1 ATTTGA-TCAATTTAATAGTACAAGGACTA
* *
59659177 A-TTGATCAATTTAATAGTAGAGGGACTA
1 ATTTGATCAATTTAATAGTACAAGGACTA
59659205 ATTTGATCA
1 ATTTGATCA
59659214 TGTATCTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 21 0.64
29 11 0.33
30 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (29 bp):
ATTTGATCAATTTAATAGTACAAGGACTA
Found at i:59665663 original size:32 final size:31
Alignment explanation
Indices: 59665619--59665679 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
59665609 AGTTCAAAAA
* * *
59665619 TTTTTTTACCAACTTTTATGAGACCTAAATT
1 TTTTTTTACCAACTTGTAAGAAACCTAAATT
*
59665650 TTTTTTTCTCCAACTTGTAAGAAACCTAAA
1 TTTTTTT-ACCAACTTGTAAGAAACCTAAA
59665680 ACCCTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (31 bp):
TTTTTTTACCAACTTGTAAGAAACCTAAATT
Found at i:59669818 original size:25 final size:25
Alignment explanation
Indices: 59669784--59669831 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
59669774 TTCAATGGGC
*
59669784 CTGCTAAACACAGTCTGCACAAAGT
1 CTGCCAAACACAGTCTGCACAAAGT
59669809 CTGCCAAACACAGTCTGCACAAA
1 CTGCCAAACACAGTCTGCACAAA
59669832 TGTCAACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.17
Consensus pattern (25 bp):
CTGCCAAACACAGTCTGCACAAAGT
Found at i:59672666 original size:10 final size:11
Alignment explanation
Indices: 59672639--59672663 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59672629 TAATGAAAAA
59672639 AAAAGAATGTT
1 AAAAGAATGTT
59672650 AAAAGAATGTT
1 AAAAGAATGTT
59672661 AAA
1 AAA
59672664 GAAAAAAAAT
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:0.00, G:0.16, T:0.24
Consensus pattern (11 bp):
AAAAGAATGTT
Found at i:59673782 original size:22 final size:22
Alignment explanation
Indices: 59673757--59673812 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
59673747 AAGCTCACTC
59673757 ATATTATTTTTTAAAAATATTT
1 ATATTATTTTTTAAAAATATTT
* * **
59673779 ATATTATATTATATTAATATTT
1 ATATTATTTTTTAAAAATATTT
*
59673801 A-ATAATTTTTTA
1 ATATTATTTTTTA
59673813 TTTATTAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATTATTTTTTAAAAATATTT
Found at i:59673793 original size:32 final size:30
Alignment explanation
Indices: 59673757--59673828 Score: 74
Period size: 32 Copynumber: 2.4 Consensus size: 30
59673747 AAGCTCACTC
59673757 ATATTATTTTTTAAAAATATTTATATTATATT
1 ATATTATTTTTTAAAAAT-TTTATATT-TATT
* * * *
59673789 ATATTAATATTTAATAATTTTTTATTTATT
1 ATATTATTTTTTAAAAATTTTATATTTATT
*
59673819 AAATT-TTTTT
1 ATATTATTTTT
59673829 ATATAGTCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 3 0.09
30 8 0.24
31 7 0.21
32 15 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
ATATTATTTTTTAAAAATTTTATATTTATT
Found at i:59675453 original size:30 final size:30
Alignment explanation
Indices: 59675417--59675503 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 30
59675407 CGGACCTATT
59675417 TTTTTTTCAATTCGGTACTTAAACTTGACA-
1 TTTTTTTCAATT-GGTACTTAAACTTGACAG
* *
59675447 TTTTTTTCTAATTTGGTACCTAAACTTGATAG
1 TTTTTTTC-AA-TTGGTACTTAAACTTGACAG
*
59675479 TTTTCTT-AAGTTGGTACTTAAACTT
1 TTTTTTTCAA-TTGGTACTTAAACTT
59675504 TTGGGAATCC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 24 0.49
31 17 0.35
32 8 0.16
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (30 bp):
TTTTTTTCAATTGGTACTTAAACTTGACAG
Found at i:59679580 original size:33 final size:35
Alignment explanation
Indices: 59679515--59679580 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
59679505 ATGTGAAATT
* * *
59679515 ATATATTTGTTTTATAATTTTGTAATATTATAATA
1 ATATATTTGTTTTAAAAATTTGTAATACTATAATA
*
59679550 ATAT-TTTGTTTTAAAAATTT-TATTACTATAA
1 ATATATTTGTTTTAAAAATTTGTAATACTATAA
59679581 CTTAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 9 0.33
34 14 0.52
35 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (35 bp):
ATATATTTGTTTTAAAAATTTGTAATACTATAATA
Found at i:59682597 original size:40 final size:40
Alignment explanation
Indices: 59682526--59682602 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
59682516 TCCACAGCAT
* *
59682526 CTCTATACTTATGCTTAGCTAAAAATGTATGTTTGTACAC
1 CTCTATACTTATGCTTAGCTAAAAATATATGTATGTACAC
*
59682566 CTCTGTACTTATGCTTAGCTAAAGAA-ATATGTATGTA
1 CTCTATACTTATGCTTAGCTAAA-AATATATGTATGTA
59682603 TTGTATGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (40 bp):
CTCTATACTTATGCTTAGCTAAAAATATATGTATGTACAC
Found at i:59689159 original size:24 final size:24
Alignment explanation
Indices: 59689132--59689188 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
59689122 AAACCTAATT
59689132 CTAATCAAA-GTCAAATATATTATG
1 CTAAT-AAATGTCAAATATATTATG
* * *
59689156 CTAATAAATGTTAAATTTATTATA
1 CTAATAAATGTCAAATATATTATG
*
59689180 CTCATAAAT
1 CTAATAAAT
59689189 ACTAAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.39
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATG
Found at i:59689194 original size:24 final size:24
Alignment explanation
Indices: 59689144--59689197 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
59689134 AATCAAAGTC
* **
59689144 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
* *
59689168 AAATTTATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
59689192 AAATAT
1 AAATAT
59689198 TCTAGAAAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:59693593 original size:24 final size:24
Alignment explanation
Indices: 59693566--59693617 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
59693556 AATCAAAGTC
* *
59693566 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
59693590 AAATATGTTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
59693614 AAAT
1 AAAT
59693618 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:59703162 original size:118 final size:118
Alignment explanation
Indices: 59702945--59703182 Score: 440
Period size: 118 Copynumber: 2.0 Consensus size: 118
59702935 CAACACTCTT
59702945 AGGCACAAGCTTAAACTTTTCATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
1 AGGCACAAGCTTAAACTTTTCATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
* *
59703010 CAAAATATGATGCTTTTAAGCACGAGCATGATTTGTTCGCCCCAAAATGCAAA
66 CAAAATATGATGCTTCTAAGCACGAGCATAATTTGTTCGCCCCAAAATGCAAA
59703063 AGGCACAAGCTTAAACTTTTCATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
1 AGGCACAAGCTTAAACTTTTCATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
* *
59703128 CAAAATATGATGCTTCTAAGCATGAGGATAATTTGTTCGCCCCAAAATGCAAA
66 CAAAATATGATGCTTCTAAGCACGAGCATAATTTGTTCGCCCCAAAATGCAAA
59703181 AG
1 AG
59703183 TGCATGAGCG
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (118 bp):
AGGCACAAGCTTAAACTTTTCATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTAATC
CAAAATATGATGCTTCTAAGCACGAGCATAATTTGTTCGCCCCAAAATGCAAA
Found at i:59703164 original size:41 final size:41
Alignment explanation
Indices: 59703084--59703164 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
59703074 TAAACTTTTC
* * **
59703084 ATCCAAAGTATGATGCTTCTAAGTATAAGTTTAAATTGTTA
1 ATCCAAAATATGATGCTTCTAAGCATAAGGATAAATTGTTA
* *
59703125 ATCCAAAATATGATGCTTCTAAGCATGAGGATAATTTGTT
1 ATCCAAAATATGATGCTTCTAAGCATAAGGATAAATTGTT
59703165 CGCCCCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (41 bp):
ATCCAAAATATGATGCTTCTAAGCATAAGGATAAATTGTTA
Found at i:59704572 original size:17 final size:17
Alignment explanation
Indices: 59704550--59704582 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
59704540 TCCTAGATTT
59704550 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
59704567 TGATACCCATATCTTT
1 TGATACCCATATCTTT
59704583 GACTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:59707348 original size:17 final size:17
Alignment explanation
Indices: 59707326--59707358 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
59707316 TCCCAGATTT
59707326 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
59707343 TGATACCCATATCTTT
1 TGATACCCATATCTTT
59707359 GACTATCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:59725384 original size:11 final size:11
Alignment explanation
Indices: 59725370--59725405 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
59725360 ATATTCAAAT
*
59725370 AATAATAATAA
1 AATAATAGTAA
59725381 AATAATAGTAA
1 AATAATAGTAA
*
59725392 TATAATAGTAA
1 AATAATAGTAA
59725403 AAT
1 AAT
59725406 GGTAGCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (11 bp):
AATAATAGTAA
Found at i:59725512 original size:20 final size:20
Alignment explanation
Indices: 59725487--59725536 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
59725477 TGGCTTAAAA
59725487 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
59725507 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
59725524 GTGGTAGTGGATT
1 TTGGTAGTGGATT
59725537 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:59730151 original size:20 final size:20
Alignment explanation
Indices: 59730126--59730175 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
59730116 TGGCTTAAAA
59730126 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
59730146 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
59730163 GTGGTAGTGGATT
1 TTGGTAGTGGATT
59730176 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:59744149 original size:43 final size:43
Alignment explanation
Indices: 59744092--59744237 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
59744082 GTTTATATAG
** *
59744092 AGAAGCGCTGCTAAAGATCATGTTCTTTAATGGCGTTTTTAGT
1 AGAAGCGCCACTAAAGATCATGTTCTTTAGTGGCGTTTTTAGT
* * * ***
59744135 AGAAGTGCCACTAAAGATCATTTTATTTAGCAACGTTTTTACG-
1 AGAAGCGCCACTAAAGATCATGTTCTTTAGTGGCGTTTTTA-GT
* ** * *
59744178 AGACGCGCTGCTAAAAATCATGTTCTATAGTGGCGTTTTTAGT
1 AGAAGCGCCACTAAAGATCATGTTCTTTAGTGGCGTTTTTAGT
* *
59744221 AGAAGCGTCGCTAAAGA
1 AGAAGCGCCACTAAAGA
59744238 CCATATCAAA
Statistics
Matches: 77, Mismatches: 24, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
42 1 0.01
43 75 0.97
44 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (43 bp):
AGAAGCGCCACTAAAGATCATGTTCTTTAGTGGCGTTTTTAGT
Found at i:59747341 original size:23 final size:23
Alignment explanation
Indices: 59747283--59747350 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
59747273 TGTGTATCCT
* * *
59747283 TTCATATTCAAGCCTCTTAACTT
1 TTCATATTCAAGTCTCTTCACTA
*
59747306 TTCATCTTCAAGTCTCTTCACTA
1 TTCATATTCAAGTCTCTTCACTA
*
59747329 TTCATATTCAAGTTTCTTCACT
1 TTCATATTCAAGTCTCTTCACT
59747351 CTTCTAACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.24, C:0.26, G:0.04, T:0.46
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTA
Found at i:59748491 original size:19 final size:19
Alignment explanation
Indices: 59748467--59748504 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
59748457 AATCGATGCG
59748467 GCTGTACCATGCTCTGGGT
1 GCTGTACCATGCTCTGGGT
59748486 GCTGTACCATGCTCTGGGT
1 GCTGTACCATGCTCTGGGT
59748505 TATTGCTTCA
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:0.11, C:0.26, G:0.32, T:0.32
Consensus pattern (19 bp):
GCTGTACCATGCTCTGGGT
Found at i:59751842 original size:23 final size:23
Alignment explanation
Indices: 59751781--59751845 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
59751771 GTATCCTTTA
* * *
59751781 ATATTCAAGCCTCTTAACTTTTC
1 ATATTCAAGTCTCTTCACTATTC
*
59751804 ATCTTCAAGTCTCTTCACTATTC
1 ATATTCAAGTCTCTTCACTATTC
59751827 ATATTCAAGTCTCTTCACT
1 ATATTCAAGTCTCTTCACT
59751846 CTTCTAACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.25, C:0.28, G:0.05, T:0.43
Consensus pattern (23 bp):
ATATTCAAGTCTCTTCACTATTC
Found at i:59754004 original size:24 final size:24
Alignment explanation
Indices: 59753977--59754033 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
59753967 TCGTATGAGT
*
59753977 TTCCTGTTAATGACTCCCCGAAGC
1 TTCCCGTTAATGACTCCCCGAAGC
* *
59754001 TTCCCGTTAATGGCTCCCCGGAGC
1 TTCCCGTTAATGACTCCCCGAAGC
59754025 TTCCCGTTA
1 TTCCCGTTA
59754034 TATGGCTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.35, G:0.19, T:0.30
Consensus pattern (24 bp):
TTCCCGTTAATGACTCCCCGAAGC
Found at i:59754074 original size:25 final size:25
Alignment explanation
Indices: 59753998--59754067 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
59753988 GACTCCCCGA
****
59753998 AGCTTCCCGTTA-ATGGCTCCCCGG
1 AGCTTCCCGTTATATGGCTCAAAAG
59754022 AGCTTCCCGTTATATGGCTCAAAAG
1 AGCTTCCCGTTATATGGCTCAAAAG
*
59754047 AGCTTCCTGTT-TATGTGCTCA
1 AGCTTCCCGTTATATG-GCTCA
59754068 TATGAGCATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 16 0.41
25 23 0.59
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCAAAAG
Found at i:59754202 original size:21 final size:22
Alignment explanation
Indices: 59754178--59754222 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
59754168 GTTCATATAT
59754178 GTTTATGTACAT-GAAATTAAA
1 GTTTATGTACATGGAAATTAAA
*
59754199 GTTTATGTACATGGAAGTTAAA
1 GTTTATGTACATGGAAATTAAA
59754221 GT
1 GT
59754223 GAACCATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (22 bp):
GTTTATGTACATGGAAATTAAA
Found at i:59770990 original size:79 final size:79
Alignment explanation
Indices: 59770859--59771021 Score: 308
Period size: 79 Copynumber: 2.1 Consensus size: 79
59770849 AGTTATTCAA
*
59770859 TTCATGTAAATATCAATAACAAAGATGAGCTCATCAAATACCAAGTTCCATGCATTTCATGTATT
1 TTCATGTAAATATCAATAACAAAGATAAGCTCATCAAATACCAAGTTCCATGCATTTCATGTATT
*
59770924 TTTTAGATATTGAT
66 TTTCAGATATTGAT
59770938 TTCATGTAAATATCAATAACAAAGATAAGCTCATCAAATACCAAGTTCCATGCATTTCATGTATT
1 TTCATGTAAATATCAATAACAAAGATAAGCTCATCAAATACCAAGTTCCATGCATTTCATGTATT
59771003 TTTCAGATATTGAT
66 TTTCAGATATTGAT
59771017 TTCAT
1 TTCAT
59771022 TTTGATTTTC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (79 bp):
TTCATGTAAATATCAATAACAAAGATAAGCTCATCAAATACCAAGTTCCATGCATTTCATGTATT
TTTCAGATATTGAT
Found at i:59774767 original size:18 final size:18
Alignment explanation
Indices: 59774739--59774793 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
59774729 GATGTAAAAA
59774739 ATTTT-TATTTTTATTA-
1 ATTTTATATTTTTATTAG
59774755 A-TTTATATATTTTA-TAG
1 ATTTTATAT-TTTTATTAG
* *
59774772 ATTTTAAATTTTTATTAT
1 ATTTTATATTTTTATTAG
59774790 ATTT
1 ATTT
59774794 GTCGCATCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 3 0.09
16 6 0.19
17 11 0.34
18 12 0.38
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTATATTTTTATTAG
Found at i:59785901 original size:14 final size:14
Alignment explanation
Indices: 59785882--59785913 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
59785872 TCAAATCACC
59785882 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
59785896 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
59785910 GGGC
1 GGGC
59785914 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:59791027 original size:14 final size:14
Alignment explanation
Indices: 59791008--59791039 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
59790998 TCAAATCACC
59791008 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
59791022 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
59791036 GGGC
1 GGGC
59791040 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:59801582 original size:23 final size:25
Alignment explanation
Indices: 59801552--59801602 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
59801542 AGAATTTTTT
*
59801552 TTATATTA-TAAA-GTTAAAAAAAA
1 TTATATTACTAAATCTTAAAAAAAA
59801575 TTATATTATCTAAATCTTAAAAAAAA
1 TTATATTA-CTAAATCTTAAAAAAAA
59801601 TT
1 TT
59801603 CTGAAGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
25 4 0.17
26 12 0.50
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (25 bp):
TTATATTACTAAATCTTAAAAAAAA
Found at i:59805482 original size:31 final size:32
Alignment explanation
Indices: 59805436--59805504 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
59805426 GGATAAATTT
* *
59805436 TTAAAAAAATTAATAATTT-ATATGTAATAAA
1 TTAATAAAATAAATAATTTAATATGTAATAAA
* *
59805467 TTAATAAAATAAATAATTTAAATATTTAATACA
1 TTAATAAAATAAATAATTT-AATATGTAATAAA
59805500 TTAAT
1 TTAAT
59805505 GGTAATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 17 0.53
33 15 0.47
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
TTAATAAAATAAATAATTTAATATGTAATAAA
Found at i:59818757 original size:48 final size:48
Alignment explanation
Indices: 59818686--59818779 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
59818676 CAGAGGATAG
59818686 CTGAGATTCCTTCTCCGACTAACGAC-TCTTCAAGGACAGCATATGGAA
1 CTGAGATTCCTTCTCCGACTAACG-CTTCTTCAAGGACAGCATATGGAA
*
59818734 CTGAGATTCCTTCTCCGGCTAACGCTTCTTCAAGGACAGCATATGG
1 CTGAGATTCCTTCTCCGACTAACGCTTCTTCAAGGACAGCATATGG
59818780 TTTCAGCTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 1 0.02
48 43 0.98
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (48 bp):
CTGAGATTCCTTCTCCGACTAACGCTTCTTCAAGGACAGCATATGGAA
Found at i:59819595 original size:24 final size:24
Alignment explanation
Indices: 59819548--59819595 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
59819538 GATGACTGTG
* *
59819548 ATTAAACCTTAACTGCCAACTACA
1 ATTAAACATTAACAGCCAACTACA
59819572 ATTAAACATTAACCAGCCAA-TACA
1 ATTAAACATTAA-CAGCCAACTACA
59819596 TGGACCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.46, C:0.27, G:0.04, T:0.23
Consensus pattern (24 bp):
ATTAAACATTAACAGCCAACTACA
Found at i:59823413 original size:25 final size:25
Alignment explanation
Indices: 59823371--59823418 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
59823361 GCTGGTGGTG
*
59823371 CAGCATGCTGGCTCACTTCATCATA
1 CAGCATGCTAGCTCACTTCATCATA
59823396 CAGCATGCTAGC-CAACTTCATCA
1 CAGCATGCTAGCTC-ACTTCATCA
59823419 CTCCTCCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (25 bp):
CAGCATGCTAGCTCACTTCATCATA
Found at i:59825469 original size:13 final size:13
Alignment explanation
Indices: 59825451--59825475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59825441 TAATTTATAT
59825451 GTGTGAAAATTTC
1 GTGTGAAAATTTC
59825464 GTGTGAAAATTT
1 GTGTGAAAATTT
59825476 TATCGTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:59827409 original size:41 final size:41
Alignment explanation
Indices: 59827258--59827400 Score: 205
Period size: 41 Copynumber: 3.5 Consensus size: 41
59827248 GTGAAATTGT
* * * *
59827258 TCAGGCTATATGTCTAGCAGGCTAAGTGCCGGTGAACCGAA
1 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGAACTGAA
*
59827299 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGAACTGAA
59827340 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGAACTGAA
1 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGAACTGAA
* * * *
59827381 TTAGACTTTAAACCTAGCAG
1 TCAGGCTATAAGCCTAGCAG
59827401 ATGAAGTGCT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (41 bp):
TCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGAACTGAA
Found at i:59827415 original size:41 final size:41
Alignment explanation
Indices: 59827271--59827416 Score: 159
Period size: 41 Copynumber: 3.6 Consensus size: 41
59827261 GGCTATATGT
* * * * *
59827271 CTAGCAGGCTAAGTGCCGGTGAACCGAATCAGGCTATAAGC
1 CTAGCAGGATAAGTGCCAGTGAACTGAATCAGACTATAAAC
* * * *
59827312 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGATAAGTGCCAGTGAACTGAATCAGACTATAAAC
* * *
59827353 CTAGCAGGCTAAGTGCCAGTGAACTGAATTAGACTTTAAAC
1 CTAGCAGGATAAGTGCCAGTGAACTGAATCAGACTATAAAC
*
59827394 CTAGCA-GATGAAGTGCTAGTGAA
1 CTAGCAGGAT-AAGTGCCAGTGAA
59827417 TCTGTTTAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 2 0.02
41 94 0.98
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.21
Consensus pattern (41 bp):
CTAGCAGGATAAGTGCCAGTGAACTGAATCAGACTATAAAC
Found at i:59827416 original size:82 final size:82
Alignment explanation
Indices: 59827258--59827416 Score: 203
Period size: 82 Copynumber: 1.9 Consensus size: 82
59827248 GTGAAATTGT
* * * * * *
59827258 TCAGGCTATATGTCTAGCAGGCTAAGTGCCGGTGAACCGAATCAGGCTATAAGCCTAGCAGGCTA
1 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGAACCGAATCAGACTATAAACCTAGCAGGATA
*
59827323 AGTGCCGGTGAACTGAA
66 AGTGCCAGTGAACTGAA
* * *
59827340 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGAACTGAATTAGACTTTAAACCTAGCA-GATG
1 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGAACCGAATCAGACTATAAACCTAGCAGGAT-
*
59827404 AAGTGCTAGTGAA
65 AAGTGCCAGTGAA
59827417 TCTGTTTAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
81 2 0.03
82 63 0.97
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (82 bp):
TCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGAACCGAATCAGACTATAAACCTAGCAGGATA
AGTGCCAGTGAACTGAA
Found at i:59836051 original size:25 final size:25
Alignment explanation
Indices: 59836007--59836056 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
59835997 TGGCTGGTGG
* **
59836007 TGCAGCATGCTGGCTCACTTCATCA
1 TGCAGCATGCTAGCGAACTTCATCA
*
59836032 TGCAGCATGCTAGCGAACTTTATCA
1 TGCAGCATGCTAGCGAACTTCATCA
59836057 GGATCCCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (25 bp):
TGCAGCATGCTAGCGAACTTCATCA
Found at i:59837934 original size:22 final size:22
Alignment explanation
Indices: 59837882--59837934 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
59837872 CTTTATCTGT
**
59837882 GGTTTTTTATCCTCTTCGGAGA
1 GGTTTTTCCTCCTCTTCGGAGA
59837904 GGTTTTTCCTCCTCTTCGGAGA
1 GGTTTTTCCTCCTCTTCGGAGA
59837926 GGTTTTTCC
1 GGTTTTTCC
59837935 ATGTAAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (22 bp):
GGTTTTTCCTCCTCTTCGGAGA
Found at i:59839955 original size:11 final size:11
Alignment explanation
Indices: 59839941--59839985 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
59839931 AGATAAATAT
59839941 TATTTTATTAA
1 TATTTTATTAA
*
59839952 TATTTTCTTGAAA
1 TATTTTATT--AA
*
59839965 TATTTTACTAA
1 TATTTTATTAA
59839976 TATTTTATTA
1 TATTTTATTA
59839986 TAAATAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 19 0.68
13 9 0.32
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:59841744 original size:26 final size:26
Alignment explanation
Indices: 59841559--59841746 Score: 135
Period size: 26 Copynumber: 7.5 Consensus size: 26
59841549 CCGGAGCTCT
* **
59841559 TGATTAAAGGCTCTTCATGAGCTTCC
1 TGATTAATGGCTCTTTGTGAGCTTCC
** * *
59841585 TGATTAAAAGTTCTTTGTGAACTTCC
1 TGATTAATGGCTCTTTGTGAGCTTCC
* *
59841611 TAATT-ATGGCTCTTT-TAAGCTTCC
1 TGATTAATGGCTCTTTGTGAGCTTCC
* ** * *
59841635 TG-TTATATAGC-C-CAGATAAGCTTCT
1 TGATTA-ATGGCTCTTTG-TGAGCTTCC
59841660 TGA-T-A-GGCTCTTTGTGAGCTT-C
1 TGATTAATGGCTCTTTGTGAGCTTCC
59841682 TCGATTAATGGCTCTTTGTGAGCTTCC
1 T-GATTAATGGCTCTTTGTGAGCTTCC
*
59841709 CGATTAATGGCTCTTTGTGAGCTTCC
1 TGATTAATGGCTCTTTGTGAGCTTCC
59841735 TG-TTATATGGCT
1 TGATTA-ATGGCT
59841747 TGAGAAATGA
Statistics
Matches: 126, Mismatches: 23, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
22 3 0.02
23 12 0.10
24 11 0.09
25 26 0.21
26 73 0.58
27 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (26 bp):
TGATTAATGGCTCTTTGTGAGCTTCC
Found at i:59849878 original size:13 final size:15
Alignment explanation
Indices: 59849849--59849877 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59849839 TTTAGTAGTC
59849849 ATATAATTTAAAAAA
1 ATATAATTTAAAAAA
59849864 ATATAA-TTAAAAAA
1 ATATAATTTAAAAAA
59849878 TTATCAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATATAATTTAAAAAA
Found at i:59853397 original size:5 final size:5
Alignment explanation
Indices: 59853387--59853425 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
59853377 CTTTTGGTTC
59853387 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
59853426 ATTAAAAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:59867835 original size:132 final size:132
Alignment explanation
Indices: 59867598--59867861 Score: 501
Period size: 132 Copynumber: 2.0 Consensus size: 132
59867588 GAGTTGACGG
*
59867598 AATTTTAGCAAATAAACACTGGATTCTGCGTATTGTGGATTATTCTCAACATACCTACAAGGGAA
1 AATTTTAGCAAATAAACACTGGATTCTGCATATTGTGGATTATTCTCAACATACCTACAAGGGAA
* *
59867663 ATTTTTTATTAAAATATTTTGATGATATGTGCTCATATGGACAGTTATTACACGATTGTCAAACA
66 AATTTTGATTAAAATATTTTGATGATATGTGCTCATATGGACAGTTATTACACGATTGTCAAACA
59867728 GT
131 GT
59867730 AATTTTAGCAAATAAACACTGGATTCTGCATATTGTGGATTATTCTCAACATACCTACAAGGGAA
1 AATTTTAGCAAATAAACACTGGATTCTGCATATTGTGGATTATTCTCAACATACCTACAAGGGAA
59867795 AATTTTGATTAAAATATTTTGATGATATGTGCTCATATGGACAGTTATTACACGATTGTCAAACA
66 AATTTTGATTAAAATATTTTGATGATATGTGCTCATATGGACAGTTATTACACGATTGTCAAACA
59867860 GT
131 GT
59867862 TTGCACATGC
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 129 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (132 bp):
AATTTTAGCAAATAAACACTGGATTCTGCATATTGTGGATTATTCTCAACATACCTACAAGGGAA
AATTTTGATTAAAATATTTTGATGATATGTGCTCATATGGACAGTTATTACACGATTGTCAAACA
GT
Found at i:59872779 original size:31 final size:31
Alignment explanation
Indices: 59872741--59872811 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
59872731 TTGAAGGAGG
59872741 AAAATAAAAATAGAAATTGAGATTAAAAATA
1 AAAATAAAAATAGAAATTGAGATTAAAAATA
59872772 AAAATAAAAATAGAAATTGAGATTAAAAATA
1 AAAATAAAAATAGAAATTGAGATTAAAAATA
59872803 AAAATAAAA
1 AAAATAAAA
59872812 TTCGTACCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.21
Consensus pattern (31 bp):
AAAATAAAAATAGAAATTGAGATTAAAAATA
Found at i:59872812 original size:5 final size:6
Alignment explanation
Indices: 59872741--59872811 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
59872731 TTGAAGGAGG
* * * * * *
59872741 AAAATA AAAATA GAAATTG AGATTA AAAATA AAAATA AAAATA GAAATTG
1 AAAATA AAAATA -AAAATA AAAATA AAAATA AAAATA AAAATA -AAAATA
* *
59872791 AGATTA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAA
59872812 TTCGTACCTT
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
6 43 0.84
7 8 0.16
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:59874887 original size:19 final size:18
Alignment explanation
Indices: 59874847--59874887 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
59874837 AAATCTCTAA
59874847 AATAATAACAAAATTAAC
1 AATAATAACAAAATTAAC
59874865 AATAA-AACAAAAGTTATAC
1 AATAATAACAAAA-TTA-AC
59874884 AATA
1 AATA
59874888 CCAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAATAACAAAATTAAC
Found at i:59879659 original size:15 final size:15
Alignment explanation
Indices: 59879639--59879667 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59879629 TTAAAGAAAA
59879639 ATGAATATTGTAAAG
1 ATGAATATTGTAAAG
59879654 ATGAATATTGTAAA
1 ATGAATATTGTAAA
59879668 AATATTGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (15 bp):
ATGAATATTGTAAAG
Found at i:59882045 original size:20 final size:20
Alignment explanation
Indices: 59882008--59882045 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
59881998 TTTATTTTTA
*
59882008 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
59882028 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
59882046 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:59883053 original size:11 final size:11
Alignment explanation
Indices: 59883039--59883093 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
59883029 TTAAATATGG
59883039 ATTTGAGAGAA
1 ATTTGAGAGAA
*
59883050 ATTTG-GAAGGA
1 ATTTGAG-AGAA
59883061 ATTTGAGAGTAA
1 ATTTGAGAG-AA
59883073 A-TTGAGAGGAA
1 ATTTGAGA-GAA
59883084 ATTTGAGAGA
1 ATTTGAGAGA
59883094 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 1 0.03
11 26 0.70
12 10 0.27
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:59883086 original size:23 final size:22
Alignment explanation
Indices: 59883039--59883093 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
59883029 TTAAATATGG
59883039 ATTTGAGAGAAATTTGGAAGGA
1 ATTTGAGAGAAATTTGGAAGGA
59883061 ATTTGAGAGTAAA-TT-GAGAGGAA
1 ATTTGAGAG-AAATTTGGA-AGG-A
59883084 ATTTGAGAGA
1 ATTTGAGAGA
59883094 GGATTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.07
22 15 0.50
23 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (22 bp):
ATTTGAGAGAAATTTGGAAGGA
Found at i:59884527 original size:28 final size:27
Alignment explanation
Indices: 59884486--59884538 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
59884476 AGGGAAGCAG
**
59884486 AAAACTAAACCCTAAACTATGAAGAAT
1 AAAACTAAACCCTAAAAGATGAAGAAT
59884513 AAAACATAAACCCTAAAAGATGAAGA
1 AAAAC-TAAACCCTAAAAGATGAAGA
59884539 GAAAACGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.58, C:0.17, G:0.09, T:0.15
Consensus pattern (27 bp):
AAAACTAAACCCTAAAAGATGAAGAAT
Found at i:59884601 original size:47 final size:47
Alignment explanation
Indices: 59884548--59884645 Score: 169
Period size: 47 Copynumber: 2.1 Consensus size: 47
59884538 AGAAAACGAG
* * *
59884548 AAAACTAGGCTAAAGTCTCGTGTCTCGTGTGTTTTCTCTCTGAAGCC
1 AAAACTAAGCTAAAGTCTCATGTCTCGTGTGTCTTCTCTCTGAAGCC
59884595 AAAACTAAGCTAAAGTCTCATGTCTCGTGTGTCTTCTCTCTGAAGCC
1 AAAACTAAGCTAAAGTCTCATGTCTCGTGTGTCTTCTCTCTGAAGCC
59884642 AAAA
1 AAAA
59884646 ATTTGGCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (47 bp):
AAAACTAAGCTAAAGTCTCATGTCTCGTGTGTCTTCTCTCTGAAGCC
Found at i:59885226 original size:26 final size:23
Alignment explanation
Indices: 59885195--59885278 Score: 96
Period size: 27 Copynumber: 3.3 Consensus size: 23
59885185 CCCATTTTTT
*
59885195 AATAAACATAAAAAATTTATTTTAAA
1 AATAAAAATAAAAAA--TATTTT-AA
59885221 AATAAAAATAAAAAATATTTTAA
1 AATAAAAATAAAAAATATTTTAA
59885244 AATAAAAATATTTTAAAAATATTTTAA
1 AATAAAAATA----AAAAATATTTTAA
59885271 AATAAAAA
1 AATAAAAA
59885279 ATATATATTT
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
23 12 0.23
24 6 0.11
26 14 0.26
27 21 0.40
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAAAAATAAAAAATATTTTAA
Found at i:59885245 original size:11 final size:11
Alignment explanation
Indices: 59885246--59885272 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
59885236 TATTTTAAAA
59885246 TAAAAATATTT
1 TAAAAATATTT
59885257 TAAAAATATTT
1 TAAAAATATTT
59885268 TAAAA
1 TAAAA
59885273 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:59885262 original size:17 final size:17
Alignment explanation
Indices: 59885223--59885264 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
59885213 ATTTTAAAAA
59885223 TAAAAATAAAAAATATTT
1 TAAAAAT-AAAAATATTT
59885241 T-AAAATAAAAATATTT
1 TAAAAATAAAAATATTT
59885257 TAAAAATA
1 TAAAAATA
59885265 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.48
17 11 0.48
18 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAATAAAAATATTT
Found at i:59886159 original size:26 final size:26
Alignment explanation
Indices: 59886110--59886169 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
59886100 TTAAAAAAAA
* *
59886110 TTTAAAATATTTTTTATTTTTTTATT
1 TTTAAAATATTTTTTATATGTTTATT
59886136 TTTAAAATAATTTTTTA-ATGTTTATT
1 TTTAAAAT-ATTTTTTATATGTTTATT
*
59886162 TTAAAAAT
1 TTTAAAAT
59886170 GGGCCGGGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTAAAATATTTTTTATATGTTTATT
Found at i:59886404 original size:29 final size:28
Alignment explanation
Indices: 59886367--59886421 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
59886357 TACTCACAAA
*
59886367 TTTAAAATTTAAT-TCTTATATTTTTATT
1 TTTAAAATTTAATAT-TTAAATTTTTATT
59886395 TTTAAGAATTTAATATTTAAATTTTTA
1 TTTAA-AATTTAATATTTAAATTTTTA
59886422 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 18 0.75
30 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTAAAATTTAATATTTAAATTTTTATT
Found at i:59886411 original size:23 final size:23
Alignment explanation
Indices: 59886392--59886436 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
59886382 TTATATTTTT
*
59886392 ATTTTTAAGAATTTAATATTTAA
1 ATTTTTAAAAATTTAATATTTAA
*
59886415 ATTTTTAAAAA-TTAAAATTTAA
1 ATTTTTAAAAATTTAATATTTAA
59886437 GTTAAATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTTTAAAAATTTAATATTTAA
Found at i:59900780 original size:42 final size:41
Alignment explanation
Indices: 59900704--59900806 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 41
59900694 AGTTCCGGTT
* *
59900704 TTTTTTGGTTTCAGACCATTTCAGGTTAGAATCAGTTT-CA
1 TTTTTTGGATTCAGACCGTTTCAGGTTAGAATCAGTTTCCA
*
59900744 GGTTTTTTGGATTCAGACCGTTT-TGGATTA-ATATCAGTTTCCA
1 --TTTTTTGGATTCAGACCGTTTCAGG-TTAGA-ATCAGTTTCCA
59900787 TTTTTTGGATTC-GAACCGTT
1 TTTTTTGGATTCAG-ACCGTT
59900807 CGAGCGCGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
40 1 0.02
41 21 0.39
42 30 0.56
43 2 0.04
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (41 bp):
TTTTTTGGATTCAGACCGTTTCAGGTTAGAATCAGTTTCCA
Found at i:59905267 original size:42 final size:42
Alignment explanation
Indices: 59905220--59905345 Score: 139
Period size: 42 Copynumber: 3.0 Consensus size: 42
59905210 ATTGTAAACA
* *
59905220 GAAGCTCATAGGAGCTAGACGGAAACCCATAAGGGTTAATCT
1 GAAGCTCAAAAGAGCTAGACGGAAACCCATAAGGGTTAATCT
* * * *
59905262 GAAGCTTAAAAGAGCTCA-ACGGAAACCCATTAGGATTAAACT
1 GAAGCTCAAAAGAGCT-AGACGGAAACCCATAAGGGTTAATCT
* * *
59905304 GAAGCTCAAAAGAGCT-GAACTGCAACCCAGAAGGGTTAATCT
1 GAAGCTCAAAAGAGCTAG-ACGGAAACCCATAAGGGTTAATCT
59905346 AAAACTCATA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 67 0.99
43 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (42 bp):
GAAGCTCAAAAGAGCTAGACGGAAACCCATAAGGGTTAATCT
Found at i:59924677 original size:27 final size:28
Alignment explanation
Indices: 59924611--59924677 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
59924601 AACCTTTTCT
59924611 TTTATAATTAATATATTTATATAATTATG
1 TTTA-AATTAATATATTTATATAATTATG
*
59924640 ATTAAAGTTAAT-TATTATAATATAA-TA-G
1 TTTAAA-TTAATATATT-T-ATATAATTATG
59924668 TTTAAATTAA
1 TTTAAATTAA
59924678 AATAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
27 4 0.12
28 12 0.36
29 11 0.33
30 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
TTTAAATTAATATATTTATATAATTATG
Found at i:59932565 original size:19 final size:20
Alignment explanation
Indices: 59932537--59932575 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
59932527 AATTGAGTGC
59932537 ATTTTGTTTA-ATTAATTTTT
1 ATTTTGTTTATA-TAATTTTT
59932557 ATTTT-TTTATATAATTTTT
1 ATTTTGTTTATATAATTTTT
59932576 TACTAATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
ATTTTGTTTATATAATTTTT
Found at i:59946945 original size:23 final size:22
Alignment explanation
Indices: 59946894--59946945 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
59946884 CCTCGTCTTT
*
59946894 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
59946916 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
59946939 TTCTTTT
1 TTCTTTT
59946946 TCAGTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:59950757 original size:23 final size:22
Alignment explanation
Indices: 59950706--59950757 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
59950696 CCTCGTCTTT
*
59950706 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
59950728 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
59950751 TTCTTTT
1 TTCTTTT
59950758 TCAGTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:59953352 original size:36 final size:36
Alignment explanation
Indices: 59953305--59953377 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
59953295 GTATCACTAA
59953305 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
59953341 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
59953377 C
1 C
59953378 TAAAGCTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:59959530 original size:17 final size:17
Alignment explanation
Indices: 59959508--59959597 Score: 83
Period size: 19 Copynumber: 5.0 Consensus size: 17
59959498 ACACAATAAT
59959508 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
59959525 AATTTTTTTGAAAACACGGA
1 AA--TTTTTGAAAACAC-GA
*
59959545 ATTTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
* *
59959562 AA-ATTTGTCAAACACGGGA
1 AATTTTTG-AAAACAC--GA
*
59959581 ATTTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
59959598 TTACATCAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.07
17 13 0.22
18 13 0.22
19 22 0.37
20 7 0.12
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
AATTTTTGAAAACACGA
Found at i:59959548 original size:36 final size:36
Alignment explanation
Indices: 59959510--59959597 Score: 124
Period size: 36 Copynumber: 2.4 Consensus size: 36
59959500 ACAATAATAA
* *
59959510 TTTTTGAAAACACGAAATTTTTTTGAAAACAC-GGAAT
1 TTTTTGAAAACACGAAA-ATTTGT-AAAACACGGGAAT
*
59959547 TTTTTGAAAACACGAAAATTTGTCAAACACGGGAAT
1 TTTTTGAAAACACGAAAATTTGTAAAACACGGGAAT
59959583 TTTTTGAAAACACGA
1 TTTTTGAAAACACGA
59959598 TTACATCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
35 6 0.13
36 24 0.51
37 17 0.36
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (36 bp):
TTTTTGAAAACACGAAAATTTGTAAAACACGGGAAT
Found at i:59959549 original size:18 final size:18
Alignment explanation
Indices: 59959510--59959597 Score: 106
Period size: 18 Copynumber: 4.8 Consensus size: 18
59959500 ACAATAATAA
59959510 TTTTTGAAAACACGAAATT
1 TTTTTGAAAACACGAAA-T
*
59959529 TTTTTGAAAACACGGAAT
1 TTTTTGAAAACACGAAAT
*
59959547 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAT
* * *
59959565 TTTGT-CAAACACGGGAAT
1 TTTTTGAAAACAC-GAAAT
59959583 TTTTTGAAAACACGA
1 TTTTTGAAAACACGA
59959598 TTACATCAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
17 6 0.11
18 29 0.51
19 22 0.39
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAT
Found at i:59959656 original size:17 final size:17
Alignment explanation
Indices: 59959628--59959686 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
59959618 ACGAGAATTT
59959628 TTTTTTGAAAACACGAAA
1 TTTTTT-AAAACACGAAA
* *
59959646 TTTTTTCAAACACGGGAA
1 TTTTTTAAAACAC-GAAA
*
59959664 -TTTTGAAAACACGAAAA
1 TTTTTTAAAACACG-AAA
59959681 TTTTTT
1 TTTTTT
59959687 TATTCACGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 1 0.03
17 18 0.56
18 13 0.41
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (17 bp):
TTTTTTAAAACACGAAA
Found at i:59959819 original size:18 final size:17
Alignment explanation
Indices: 59959778--59959826 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
59959768 TATTATTATT
59959778 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAGAA
*
59959795 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACACGAGAA
59959812 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
59959827 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (17 bp):
ATTTTGAAACACGAGAA
Found at i:59960377 original size:43 final size:42
Alignment explanation
Indices: 59960330--59960412 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
59960320 TGCCAGGAAG
* * *
59960330 TGGGCCGAATCTGCTGGCCTGCTGGGCACT-GGTCTGCTGCTAT
1 TGGGCCGAAGCTGCTGGACTGCT--GCACTGGGCCTGCTGCTAT
*
59960373 TGGGCTGAAGCTGCTGGACTGCTGCACTGGGCCTGCTGCT
1 TGGGCCGAAGCTGCTGGACTGCTGCACTGGGCCTGCTGCT
59960413 GGACTGCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 5 0.14
42 10 0.29
43 20 0.57
ACGTcount: A:0.10, C:0.28, G:0.36, T:0.27
Consensus pattern (42 bp):
TGGGCCGAAGCTGCTGGACTGCTGCACTGGGCCTGCTGCTAT
Found at i:59960446 original size:23 final size:24
Alignment explanation
Indices: 59960416--59960482 Score: 86
Period size: 23 Copynumber: 2.8 Consensus size: 24
59960406 TGCTGCTGGA
59960416 CTGCTTCTTTCTTCTTCTTTTT-T-
1 CTGCTTCTTTCTTCTT-TTTTTCTG
59960439 CTGCTTCTTTCTTTCTTTTTTTCTG
1 CTGCTTCTTTC-TTCTTTTTTTCTG
*
59960464 CTGCTTCTTT-TTCTATTTT
1 CTGCTTCTTTCTTCTTTTTT
59960483 GTTTTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 24 0.60
24 6 0.15
25 10 0.25
ACGTcount: A:0.01, C:0.24, G:0.06, T:0.69
Consensus pattern (24 bp):
CTGCTTCTTTCTTCTTTTTTTCTG
Found at i:59960482 original size:22 final size:22
Alignment explanation
Indices: 59960416--59960482 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
59960406 TGCTGCTGGA
* *
59960416 CTGCTTCTTTCTTCTTCTTTTTT
1 CTGCTGCTTTCTTTTTC-TTTTT
*
59960439 CTGCTTCTTTCTTTCTT-TTTTT
1 CTGCTGCTTTCTTT-TTCTTTTT
59960461 CTGCTGC-TTCTTTTTCTATTTT
1 CTGCTGCTTTCTTTTTCT-TTTT
59960483 GTTTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 2 0.05
21 7 0.18
22 15 0.38
23 13 0.33
24 2 0.05
ACGTcount: A:0.01, C:0.24, G:0.06, T:0.69
Consensus pattern (22 bp):
CTGCTGCTTTCTTTTTCTTTTT
Found at i:59960611 original size:22 final size:21
Alignment explanation
Indices: 59960568--59960643 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 21
59960558 CGATATATTA
* *
59960568 TTTTTTATT-TTTCTTTCCGT
1 TTTTTTCTTCTTTCTTTCTGT
59960588 TTTTTTCTTCTTTCTTCTCTG-
1 TTTTTTCTTCTTTCTT-TCTGT
*
59960609 TTTCTTCTTTCTTTC-TTCT-T
1 TTTTTTC-TTCTTTCTTTCTGT
59960629 TTTTTT-TTCTTTCTT
1 TTTTTTCTTCTTTCTT
59960644 CTCCGTTCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
18 7 0.15
19 1 0.02
20 16 0.34
21 13 0.28
22 10 0.21
ACGTcount: A:0.01, C:0.20, G:0.03, T:0.76
Consensus pattern (21 bp):
TTTTTTCTTCTTTCTTTCTGT
Found at i:59960637 original size:18 final size:19
Alignment explanation
Indices: 59960569--59960645 Score: 72
Period size: 18 Copynumber: 4.1 Consensus size: 19
59960559 GATATATTAT
59960569 TTTTTATTTTTCTTTC--C
1 TTTTTATTTTTCTTTCTTC
*
59960586 GTTTTT-TTCTTCTTTCTTC
1 -TTTTTATTTTTCTTTCTTC
*
59960605 TCTGTTTCTTCTTTCTTTCTTC
1 T-T-TTTATT-TTTCTTTCTTC
59960627 TTTTT-TTTTTCTTTCTTC
1 TTTTTATTTTTCTTTCTTC
59960645 T
1 T
59960646 CCGTTCAGCC
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
17 9 0.18
18 18 0.35
19 4 0.08
20 6 0.12
21 3 0.06
22 11 0.22
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTTATTTTTCTTTCTTC
Found at i:59960761 original size:19 final size:20
Alignment explanation
Indices: 59960730--59960794 Score: 80
Period size: 20 Copynumber: 3.1 Consensus size: 20
59960720 CTCTTCTCTC
59960730 TTTCTTCTTTGCTTGTTTTT
1 TTTCTTCTTTGCTTGTTTTT
59960750 TTTCTT-TTTGCTTGTTGTTT
1 TTTCTTCTTTGCTTGTT-TTT
59960770 TTT-TTCTTTGACTTTGCTTTTT
1 TTTCTTCTTTG-C-TTG-TTTTT
59960792 TTT
1 TTT
59960795 TATTGGCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
19 12 0.30
20 16 0.40
21 1 0.03
22 9 0.22
23 2 0.05
ACGTcount: A:0.02, C:0.12, G:0.11, T:0.75
Consensus pattern (20 bp):
TTTCTTCTTTGCTTGTTTTT
Found at i:59960792 original size:22 final size:23
Alignment explanation
Indices: 59960736--59960795 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
59960726 TCTCTTTCTT
59960736 CTTTGCTTGTTTTTTTTCTTTTTG
1 CTTTGCTTGTTTTTTTTC-TTTTG
59960760 C-TTG-TTGTTTTTTTTC-TTTG
1 CTTTGCTTGTTTTTTTTCTTTTG
59960780 ACTTTGCTT-TTTTTTT
1 -CTTTGCTTGTTTTTTT
59960796 ATTGGCTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 4 0.12
21 1 0.03
22 22 0.67
23 5 0.15
24 1 0.03
ACGTcount: A:0.02, C:0.12, G:0.12, T:0.75
Consensus pattern (23 bp):
CTTTGCTTGTTTTTTTTCTTTTG
Found at i:59960804 original size:20 final size:19
Alignment explanation
Indices: 59960767--59960808 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
59960757 TTGCTTGTTG
59960767 TTTTTTTTCTTTGACTTTGC
1 TTTTTTTTCTTTGACTTT-C
*
59960787 TTTTTTTT-TATTGGCTTTC
1 TTTTTTTTCT-TTGACTTTC
59960806 TTT
1 TTT
59960809 GTCTTTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.05, C:0.12, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTTTTTTCTTTGACTTTC
Found at i:59960914 original size:10 final size:11
Alignment explanation
Indices: 59960888--59960913 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59960878 TTGCTGCTGT
59960888 TTTTTGCTTGA
1 TTTTTGCTTGA
59960899 TTTTTGCTTGA
1 TTTTTGCTTGA
59960910 TTTT
1 TTTT
59960914 GTTGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.15, T:0.69
Consensus pattern (11 bp):
TTTTTGCTTGA
Found at i:59961218 original size:30 final size:29
Alignment explanation
Indices: 59961184--59961256 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 29
59961174 GTAATTTCTT
*
59961184 GAAAGTTTAGGGGTTGAAGTAAAATTTTGA
1 GAAAGTTTAGGGGTTGAAATAAAATTTT-A
** **
59961214 GAAAGTTTAAAGGTTGAAATGTAATTTTA
1 GAAAGTTTAGGGGTTGAAATAAAATTTTA
59961243 GAAAAGTTT-GGGGT
1 G-AAAGTTTAGGGGT
59961257 CAAAAATGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (29 bp):
GAAAGTTTAGGGGTTGAAATAAAATTTTA
Found at i:59961287 original size:31 final size:30
Alignment explanation
Indices: 59961230--59961327 Score: 128
Period size: 30 Copynumber: 3.3 Consensus size: 30
59961220 TTAAAGGTTG
* *
59961230 AAATGT-AATTTTAGAAAAGT-TTGGGGTCAA
1 AAATGTAAATTTCA-AAAAGTATAGGGGTC-A
59961260 AAATGTAAATTTCAAAAAGTATAGGGGTCA
1 AAATGTAAATTTCAAAAAGTATAGGGGTCA
* *
59961290 AAATGTAAATTTCAAAAAGTATATGGGTGA
1 AAATGTAAATTTCAAAAAGTATAGGGGTCA
59961320 AAATGTAA
1 AAATGTAA
59961328 TTTTTTTAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
30 49 0.79
31 13 0.21
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (30 bp):
AAATGTAAATTTCAAAAAGTATAGGGGTCA
Found at i:59961635 original size:75 final size:75
Alignment explanation
Indices: 59961495--59962352 Score: 1273
Period size: 75 Copynumber: 11.3 Consensus size: 75
59961485 ACAGAAATTG
* * * * **
59961495 AAAATACCTCGGCGGGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTAAAAAA
* *
59961560 ACAGAAATTTAAA-A
63 AAAGACA--TAAATA
* * * * **
59961574 GAAATACATCGGCATGGTCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTT-AAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
59961637 GACATAAATTA
66 GACATAAA-TA
59961648 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTT--AAAAAA
59961713 AGAAGACATAAATTA
63 A-AAGACATAAA-TA
59961728 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
59961793 GACATAAATTA
66 GACATAAA-TA
59961804 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTAAAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
59961868 GACATAAATTA
66 GACATAAA-TA
59961879 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTT-AAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
59961942 GACATAAATTA
66 GACATAAA-TA
* * **
59961953 AAAATACCTCAGCGTGACCCGAGGCTCAACTTACCTCTGTATTGTGAGTTGATTTTTTTTAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA--TTTTAAAAAAA
59962018 AAGACATAAATTA
64 AAGACATAAA-TA
*
59962031 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGA-TTTAAAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
59962095 GACATAAATTA
66 GACATAAA-TA
59962106 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTAAAAAAAA
59962171 AGACATAAATTA
65 AGACATAAA-TA
59962183 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTAAAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
59962247 GACATAAATTA
66 GACATAAA-TA
* *
59962258 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTAAAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
59962323 GACATAAATTA
66 GACATAAA-TA
59962334 AAAATACCTCAGCGTGACC
1 AAAATACCTCAGCGTGACC
59962353 TAGAGGTGTG
Statistics
Matches: 738, Mismatches: 26, Indels: 33
0.93 0.03 0.04
Matches are distributed among these distances:
72 4 0.01
74 125 0.17
75 227 0.31
76 121 0.16
77 108 0.15
78 67 0.09
79 21 0.03
80 65 0.09
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (75 bp):
AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAA
GACATAAATA
Found at i:59962072 original size:152 final size:152
Alignment explanation
Indices: 59961481--59962352 Score: 1402
Period size: 152 Copynumber: 5.7 Consensus size: 152
59961471 TTTTTACTTG
* * * * * *
59961481 AAAA-ACAGAAATTGAAAATACCTCGGCGGGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGA
1 AAAAGACATAAATTAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGA
* ** * * * * **
59961545 GTTGATTTTTGAAAAACAGAA-ATTTAAA--AGAAATACATCGGCATGGTCCGAGGCTCAACTCA
63 GTTGATTTTT-AAAAA-AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCA
59961607 CCTCTGTATTATGAGTTGATTT-AAAA
126 CCTCTGTATTATGAGTTGATTTAAAAA
59961633 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
59961698 GATTTTTAAAAAAAAAGAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
66 GATTTTT--AAAAAAA-AAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
59961763 TCTGTATTATGAGTTGATTTTAAAAA
128 TCTGTATTATGAGTTGA-TTTAAAAA
59961789 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
59961854 GA--TTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
66 GATTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
59961917 GTATTATGAGTTGATTT-AAAA
131 GTATTATGAGTTGATTTAAAAA
* *
59961938 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTTACCTCTGTATTGTGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
** *
59962003 GATTTTTTTTAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATC
66 GA-TTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTC
59962068 TGTATTATGAGTTGATTTAAAAA
130 TGTATTATGAGTTGATTTAAAAA
59962091 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
59962156 GATTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
66 GATTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
59962221 GTATTATGAGTTGATTTAAAAA
131 GTATTATGAGTTGATTTAAAAA
*
59962243 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
59962308 GATTTTT-AAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACC
66 GATTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACC
59962353 TAGAGGTGTG
Statistics
Matches: 681, Mismatches: 27, Indels: 25
0.93 0.04 0.03
Matches are distributed among these distances:
149 69 0.10
150 21 0.03
151 134 0.20
152 244 0.36
153 89 0.13
154 50 0.07
155 3 0.00
156 71 0.10
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (152 bp):
AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
GATTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
GTATTATGAGTTGATTTAAAAA
Found at i:59962080 original size:227 final size:227
Alignment explanation
Indices: 59961481--59962352 Score: 1371
Period size: 227 Copynumber: 3.8 Consensus size: 227
59961471 TTTTTACTTG
* * * * * *
59961481 AAAA-ACAGAAATTGAAAATACCTCGGCGGGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGA
1 AAAAGACATAAATTAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGA
** * * * * * * **
59961545 GTTGATTTTTGAAAAACAGAAATTTAAA--AGAAATACATCGGCATGGTCCGAGGCTCAACTCAC
63 GTTGATTTTAAAAAAAAAGACA--TAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCAC
*
59961608 CTCTGTATTATGAGTTGATTT-AAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGG
126 ATCTGTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGG
59961672 CTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAA
191 CTCAACTCACCTCTGTATTATGAGTTGA-TTTT--AAAAA
59961712 AAGAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
1 AA-AAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
*
59961777 TGATTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
65 TGATTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATCT
59961842 GTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCA
130 GTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCA
59961907 ACTCACCTCTGTATTATGAGTTGA-TTT-AAAA
195 ACTCACCTCTGTATTATGAGTTGATTTTAAAAA
* *
59961938 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTTACCTCTGTATTGTGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
**
59962003 GATTTTTTTTAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATC
66 GA--TTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATC
59962068 TGTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTC
129 TGTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTC
59962133 AACTCACCTCTGTATTATGAGTTGATTTTTAAAAA
194 AACTCACCTCTGTATTATGAGTTGA-TTTTAAAAA
59962168 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
59962233 GA-TTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATCTG
66 GATTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATCTG
*
59962297 TATTATGAGTTGATTTTTAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACC
131 TATTATGAGTTGA-TTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACC
59962353 TAGAGGTGTG
Statistics
Matches: 604, Mismatches: 26, Indels: 25
0.92 0.04 0.04
Matches are distributed among these distances:
225 63 0.10
226 6 0.01
227 221 0.37
228 45 0.07
229 6 0.01
230 144 0.24
231 97 0.16
232 2 0.00
233 20 0.03
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (227 bp):
AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
GATTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATCTG
TATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAA
CTCACCTCTGTATTATGAGTTGATTTTAAAAA
Found at i:59963426 original size:9 final size:9
Alignment explanation
Indices: 59963414--59963439 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
59963404 ATCATCATCC
59963414 TCATCGTCG
1 TCATCGTCG
59963423 TCATCGTCG
1 TCATCGTCG
59963432 TCATCGTC
1 TCATCGTC
59963440 CTTTTTGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.19, T:0.35
Consensus pattern (9 bp):
TCATCGTCG
Found at i:59965892 original size:16 final size:16
Alignment explanation
Indices: 59965871--59965907 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
59965861 GAACTCTTTA
*
59965871 ATTAACTTGCTGTTAT
1 ATTAACTTACTGTTAT
59965887 ATTAACTTACTGTTAT
1 ATTAACTTACTGTTAT
59965903 ATTAA
1 ATTAA
59965908 TTTGTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (16 bp):
ATTAACTTACTGTTAT
Found at i:59965915 original size:13 final size:15
Alignment explanation
Indices: 59965871--59965916 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
59965861 GAACTCTTTA
*
59965871 ATTAACTTGCTGTTAT
1 ATTAACTT-ATGTTAT
59965887 ATTAACTTACTGTTAT
1 ATTAACTTA-TGTTAT
59965903 ATTAA-TT-TGTTAT
1 ATTAACTTATGTTAT
59965916 A
1 A
59965917 AATATATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.25
15 2 0.07
16 19 0.68
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (15 bp):
ATTAACTTATGTTAT
Found at i:59968425 original size:81 final size:76
Alignment explanation
Indices: 59968166--59968537 Score: 595
Period size: 78 Copynumber: 4.8 Consensus size: 76
59968156 GCCCATGAAC
59968166 ACCTCTAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACA
1 ACCTC-AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACA
59968231 TAAATTAAAAAT
65 TAAATTAAAAAT
*
59968243 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAAATAC
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT--AAAAAAAAGAC
*
59968308 ATGAATTAAAAAT
64 ATAAATTAAAAAT
59968321 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATCTTTTTTTTAAAAAAAA
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-----TTTTTAAAAAAAA
59968386 GACATAAATTAAAAAT
61 GACATAAATTAAAAAT
**
59968402 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTT-AAAAAAAGACCG
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACAT
59968465 AAATTAAAAAT
66 AAATTAAAAAT
*
59968476 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATATTTGAAAAAAAA
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGAT-TTTTAAAAAAAA
59968538 CAAAAAGTGA
Statistics
Matches: 277, Mismatches: 7, Indels: 21
0.91 0.02 0.07
Matches are distributed among these distances:
74 54 0.19
75 18 0.06
76 47 0.17
77 8 0.03
78 76 0.27
81 69 0.25
83 5 0.02
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (76 bp):
ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACAT
AAATTAAAAAT
Found at i:59968543 original size:159 final size:153
Alignment explanation
Indices: 59968166--59968537 Score: 599
Period size: 159 Copynumber: 2.4 Consensus size: 153
59968156 GCCCATGAAC
59968166 ACCTCTAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACA
1 ACCTC-AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACA
59968231 TAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTA
65 TAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTA
59968296 AAAAAAAAATACATGAATTAAAAAT
130 AAAAAAAAATACA-GAATTAAAAAT
59968321 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATCTTTTTTTTAAAAAAAA
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-----TTTTTAAAAAAAA
59968386 GACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-T
61 GACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
* *
59968450 TTT---AAAAAAAGACCGAAATTAAAAAT
126 TTTAAAAAAAAAATACAG-AATTAAAAAT
*
59968476 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATATTTGAAAAAAAA
1 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGAT-TTTTAAAAAAAA
59968538 CAAAAAGTGA
Statistics
Matches: 206, Mismatches: 3, Indels: 19
0.90 0.01 0.08
Matches are distributed among these distances:
151 1 0.00
152 11 0.05
154 43 0.21
155 57 0.28
156 14 0.07
158 4 0.02
159 76 0.37
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (153 bp):
ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACAT
AAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAA
AAAAAAAATACAGAATTAAAAAT
Found at i:59969427 original size:17 final size:16
Alignment explanation
Indices: 59969407--59969474 Score: 52
Period size: 17 Copynumber: 4.3 Consensus size: 16
59969397 TCATCTTGAT
59969407 TTTTTCTTCTTCTTTTA
1 TTTTTCTT-TTCTTTTA
* *
59969424 TTTTTCTGTTTTTTTTC
1 TTTTTCT-TTTCTTTTA
*
59969441 TTTTTCTTAT-TTTT-
1 TTTTTCTTTTCTTTTA
* *
59969455 TTGTTGTTTT-TTTTA
1 TTTTTCTTTTCTTTTA
59969470 TTTTT
1 TTTTT
59969475 TTAGGCATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
14 11 0.26
15 8 0.19
16 2 0.05
17 20 0.48
18 1 0.02
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTA
Found at i:59969447 original size:28 final size:29
Alignment explanation
Indices: 59969406--59969474 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
59969396 TTCATCTTGA
*
59969406 TTTTTTCTTCTTCTT-TTATTTTT-CTGTT
1 TTTTTTCTTTTTCTTATT-TTTTTGCTGTT
*
59969434 TTTTTTCTTTTTCTTATTTTTTTGTTGTT
1 TTTTTTCTTTTTCTTATTTTTTTGCTGTT
*
59969463 TTTTTTATTTTT
1 TTTTTTCTTTTT
59969475 TTAGGCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.53
29 17 0.47
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (29 bp):
TTTTTTCTTTTTCTTATTTTTTTGCTGTT
Found at i:59969464 original size:20 final size:19
Alignment explanation
Indices: 59969432--59969476 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
59969422 TATTTTTCTG
59969432 TTTTTTTTCTTTTTCTTAT
1 TTTTTTTTCTTTTTCTTAT
* *
59969451 TTTTTTGTTGTTTTTTTTAT
1 TTTTTT-TTCTTTTTCTTAT
59969471 TTTTTT
1 TTTTTT
59969477 AGGCATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.04, C:0.04, G:0.04, T:0.87
Consensus pattern (19 bp):
TTTTTTTTCTTTTTCTTAT
Found at i:59975065 original size:18 final size:18
Alignment explanation
Indices: 59975013--59975147 Score: 125
Period size: 18 Copynumber: 7.4 Consensus size: 18
59975003 TTTTGTTTTT
*
59975013 AAACACGAGAA-TTTTGA
1 AAACACGAAAATTTTTGA
**
59975030 AACACAATAATAATTTTTGA
1 AA-ACACGAA-AATTTTTGA
*
59975050 AAACACGAAGATTTTTG-
1 AAACACGAAAATTTTTGA
59975067 AAACACGAAAATTTTTTGA
1 AAACACGAAAA-TTTTTGA
*
59975086 AAACAC-AGAATTTTTTGA
1 AAACACGA-AAATTTTTGA
* *
59975104 AAACACGAAAATTTGT-C
1 AAACACGAAAATTTTTGA
*
59975121 AAACACGAGAATTTTTTGA
1 AAACACGA-AAATTTTTGA
59975140 AAACACGA
1 AAACACGA
59975148 TAACATAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
17 20 0.21
18 43 0.45
19 24 0.25
20 8 0.08
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (18 bp):
AAACACGAAAATTTTTGA
Found at i:59975080 original size:54 final size:51
Alignment explanation
Indices: 59975008--59975145 Score: 152
Period size: 54 Copynumber: 2.5 Consensus size: 51
59974998 TTTTTTTTTG
* *
59975008 TTTTTAAACACGAGAATTTTG-AAACACAATAATAATTTTTGAAAACACGAAGA
1 TTTTTAAACACGAGAATTTTGAAAACAC-AGAAT--TTTTTGAAAACACGAAAA
*
59975061 TTTTTGAAACACGAAAATTTTTTGAAAACACAGAATTTTTTGAAAACACGAAAA
1 TTTTT-AAACACGAGAA--TTTTGAAAACACAGAATTTTTTGAAAACACGAAAA
*
59975115 TTTGTCAAACACGAGAATTTTTTGAAAACAC
1 TTT-TTAAACACGAGAA--TTTTGAAAACAC
59975146 GATAACATAA
Statistics
Matches: 75, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
53 5 0.07
54 54 0.72
55 1 0.01
56 9 0.12
57 6 0.08
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (51 bp):
TTTTTAAACACGAGAATTTTGAAAACACAGAATTTTTTGAAAACACGAAAA
Found at i:59975215 original size:17 final size:17
Alignment explanation
Indices: 59975192--59975282 Score: 78
Period size: 17 Copynumber: 5.2 Consensus size: 17
59975182 TTAAAACACG
59975192 AAAACACGAAATTTTTT
1 AAAACACGAAATTTTTT
* *
59975209 CAAACACGAGAA-TTTTG
1 AAAACACGA-AATTTTTT
59975226 AAAACACGAAATTTTTTT
1 AAAACACGAAA-TTTTTT
* **
59975244 TATTCACGAGAA-TTTTT
1 AAAACACGA-AATTTTTT
*
59975261 GAAACACGGAAATTTTTT
1 AAAACAC-GAAATTTTTT
59975279 AAAA
1 AAAA
59975283 AAAAAGAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
16 2 0.04
17 31 0.54
18 22 0.39
19 2 0.04
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (17 bp):
AAAACACGAAATTTTTT
Found at i:59975252 original size:35 final size:36
Alignment explanation
Indices: 59975191--59975278 Score: 119
Period size: 35 Copynumber: 2.5 Consensus size: 36
59975181 TTTAAAACAC
59975191 GAAAACACGAAA-TTTTTTCAAACACGAGAA-TTTT
1 GAAAACACGAAATTTTTTTCAAACACGAGAATTTTT
* **
59975225 GAAAACACGAAATTTTTTTTATTCACGAGAATTTTT
1 GAAAACACGAAATTTTTTTCAAACACGAGAATTTTT
59975261 G-AAACACGGAAATTTTTT
1 GAAAACAC-GAAATTTTTT
59975279 AAAAAAAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
34 12 0.25
35 21 0.44
36 15 0.31
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (36 bp):
GAAAACACGAAATTTTTTTCAAACACGAGAATTTTT
Found at i:59975357 original size:17 final size:17
Alignment explanation
Indices: 59975335--59975383 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
59975325 TATTATTATT
*
59975335 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAAAA
*
59975352 ATTTTGAAGACA-TAAAA
1 ATTTTGAA-ACACGAAAA
59975369 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
59975384 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (17 bp):
ATTTTGAAACACGAAAA
Found at i:59975774 original size:14 final size:13
Alignment explanation
Indices: 59975755--59975788 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
59975745 TACAATATTT
59975755 AAATAAATGGACTA
1 AAATAAATGGA-TA
59975769 AAATAAATGGATA
1 AAATAAATGGATA
59975782 AAA-AAAT
1 AAATAAAT
59975789 TACCCAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 5 0.25
14 11 0.55
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.21
Consensus pattern (13 bp):
AAATAAATGGATA
Found at i:59975997 original size:23 final size:24
Alignment explanation
Indices: 59975967--59976033 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 24
59975957 TGTTGCTGGA
59975967 CTGCTTCTTTCTTCTTCTTTTT-T-
1 CTGCTTCTTTCTTCTT-TTTTTCTG
*
59975990 CTGCTTCTTCCTTTCTTTTTTTCTG
1 CTGCTTCTTTC-TTCTTTTTTTCTG
*
59976015 CTGCTTCTTT-TTCTATTTT
1 CTGCTTCTTTCTTCTTTTTT
59976034 GTTTTTTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 23 0.61
24 6 0.16
25 9 0.24
ACGTcount: A:0.01, C:0.25, G:0.06, T:0.67
Consensus pattern (24 bp):
CTGCTTCTTTCTTCTTTTTTTCTG
Found at i:59976033 original size:22 final size:21
Alignment explanation
Indices: 59975975--59976033 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
59975965 GACTGCTTCT
* *
59975975 TTCTTCTTCTTTTTTCTGCTTC
1 TTCTTTTTC-TTTTTCTGCTGC
59975997 TTCCTTTCTT-TTTTTCTGCTGC
1 TT-CTTT-TTCTTTTTCTGCTGC
59976019 TTCTTTTTCTATTTT
1 TTCTTTTTCT-TTTT
59976034 GTTTTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 5 0.16
22 19 0.61
23 3 0.10
24 2 0.06
ACGTcount: A:0.02, C:0.24, G:0.05, T:0.69
Consensus pattern (21 bp):
TTCTTTTTCTTTTTCTGCTGC
Found at i:59976163 original size:11 final size:11
Alignment explanation
Indices: 59976147--59976189 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
59976137 CTTTTTCTTC
59976147 TTTCTTCTTTG
1 TTTCTTCTTTG
59976158 TTTCTTCTTTG
1 TTTCTTCTTTG
*
59976169 TTTCTTCTTTT
1 TTTCTTCTTTG
*
59976180 TTTTTTCTTT
1 TTTCTTCTTT
59976190 CTTCTCCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTCTTCTTTG
Found at i:59976192 original size:18 final size:19
Alignment explanation
Indices: 59976138--59976194 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
59976128 TCTTTCCCCC
*
59976138 TTTTTCTTCTTTCTTCTTTG
1 TTTTTTTTCTTTCTTC-TTG
*
59976158 TTTCTTCTTTGTTTCTTCTT-
1 TTT-TT-TTTCTTTCTTCTTG
59976178 TTTTTTTTCTTTCTTCT
1 TTTTTTTTCTTTCTTCT
59976195 CCGTTCAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 11 0.34
19 2 0.06
20 6 0.19
21 4 0.12
22 9 0.28
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTTTTTTCTTTCTTCTTG
Done.