Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 11 of 213
Found at i:3177517 original size:17 final size:17
Alignment explanation
Indices: 3177495--3177530 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3177485 ATAACTCTTA
3177495 TTTTATTGTTAATTTTG
1 TTTTATTGTTAATTTTG
3177512 TTTTATTGTTAATTTTG
1 TTTTATTGTTAATTTTG
3177529 TT
1 TT
3177531 AGTATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (17 bp):
TTTTATTGTTAATTTTG
Found at i:3180064 original size:18 final size:18
Alignment explanation
Indices: 3180043--3180104 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
3180033 ATATATAGAT
3180043 ATATATAATAAGATATAA
1 ATATATAATAAGATATAA
*
3180061 ATATATAATAAGATGATAT
1 ATATATAATAAGAT-ATAA
*
3180080 ATATA-AAT-AGTTAT-A
1 ATATATAATAAGATATAA
3180095 ATA-ATAATAA
1 ATATATAATAA
3180105 TAATAATAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 3 0.08
17 3 0.08
18 17 0.45
19 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
ATATATAATAAGATATAA
Found at i:3180095 original size:35 final size:33
Alignment explanation
Indices: 3180040--3180104 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
3180030 GAGATATATA
3180040 GATATATATAATAAGATATAAATATATAATAAGAT
1 GATATATATAATAAGATAT-AATA-ATAATAAGAT
*
3180075 GATATATATAA-ATAGTTATAATAATAATAA
1 GATATATATAATA-AGATATAATAATAATAA
3180105 TAATAATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 5 0.18
35 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (33 bp):
GATATATATAATAAGATATAATAATAATAAGAT
Found at i:3181869 original size:44 final size:46
Alignment explanation
Indices: 3181816--3181938 Score: 144
Period size: 46 Copynumber: 2.7 Consensus size: 46
3181806 CATTTATTTT
* * *
3181816 AATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T--ACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAT-GCTTC
* *
3181860 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATGCTTC
* * *
3181906 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGA
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGA
3181939 CCTGGTGCGA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 31 0.46
45 1 0.01
46 33 0.49
47 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (46 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATGCTTC
Found at i:3182292 original size:43 final size:42
Alignment explanation
Indices: 3182159--3182720 Score: 123
Period size: 43 Copynumber: 13.1 Consensus size: 42
3182149 CCGATGGAGA
3182159 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAACGCAGGAAGG
1 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAA-GCAGGAAGG
* * * * * * *
3182202 CAA-GATCTGCTATCTTC-AACTAGCTCCATTG--CAGCCAATGAAGG
1 CAAGGCTTTG-T-T-TTCGATCT-GCTTCGTTGTTAAG-C-AGGAAGG
3182246 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAATGCAGGAAGG
1 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAA-GCAGGAAGG
* * * * * * ** * * *
3182289 CAA-GATATGCTATCTTTGACCAGCTCCACTG-CAACCAATGAAGG
1 CAAGGCTTTG-T-T-TTCGATCTGCTTCGTTGTTAAGC-AGGAAGG
3182333 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAATGCAGGAAGG
1 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAA-GCAGGAAGG
* * * * * ** * *
3182376 CAA-GATCTGCTTCTT-TAACTAGCTCCACTG-TAACCAATGAAGG
1 CAAGGCTTTG-TT-TTCGATCT-GCTTCGTTGTTAAGC-AGGAAGG
** *
3182419 CAACACTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
1 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAA-GCAGGAAGG
* * ** * * * ** * * *
3182462 CAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAACCAATGAAGG
1 CAAGGCTTTG-TT-TTCGATCTGCTTCGTTGTTAAGC-AGGAAGG
* *
3182505 CATGGCTTTGTTTT-GATCTGCTTCGCTGTTAACGCAGGAAGG
1 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAA-GCAGGAAGG
* * ** * * * ** * * *
3182547 CAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAACCAATGAAGG
1 CAAGGCTTTG-TT-TTCGATCTGCTTCGTTGTTAAGC-AGGAAGG
*
3182590 CAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGG
1 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAA-GCAGGAAGG
* * * * * * ** * * *
3182633 CAAGATCTTT-CTTT-AACCAGCTCCACTG-CAACCAATGAAGG
1 CAAG-GCTTTGTTTTCGATCTGCTTCGTTGTTAAGC-AGGAAGG
*
3182674 CAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
1 CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAA-GCAGGAAGG
3182717 CAAG
1 CAAG
3182721 ATCTGCTTCT
Statistics
Matches: 355, Mismatches: 119, Indels: 90
0.63 0.21 0.16
Matches are distributed among these distances:
40 5 0.01
41 28 0.08
42 92 0.26
43 124 0.35
44 76 0.21
45 30 0.08
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (42 bp):
CAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAAGCAGGAAGG
Found at i:3182450 original size:86 final size:86
Alignment explanation
Indices: 3182138--3182731 Score: 969
Period size: 86 Copynumber: 6.9 Consensus size: 86
3182128 CTTCAATCTA
* * * *
3182138 CTCCACTGCAACCGATGGAGACAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAACGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
* *
3182203 AAGATCTGCTATCTTCAACTAG
66 AAGATCTGCT-TCTTTAACCAG
* * * *
3182225 CTCCATTGCAGCCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAATGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
* *
3182290 AAGATATGCTATCTTTGACCAG
66 AAGATCTGCT-TCTTTAACCAG
* *
3182312 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAATGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
*
3182377 AAGATCTGCTTCTTTAACTAG
66 AAGATCTGCTTCTTTAACCAG
* **
3182398 CTCCACTGTAACCAATGAAGGCAACACTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
3182463 AAGATCTGCTTCTTTAACCAG
66 AAGATCTGCTTCTTTAACCAG
*
3182484 CTCCACTGCAACCAATGAAGGCATGGCTTTGTTTT-GATCTGCTTCGCTGTTAACGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
3182548 AAGATCTGCTTCTTTAACCAG
66 AAGATCTGCTTCTTTAACCAG
*
3182569 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
3182634 AAGATCT--TTCTTTAACCAG
66 AAGATCTGCTTCTTTAACCAG
3182653 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
3182718 AAGATCTGCTTCTT
66 AAGATCTGCTTCTT
3182732 CACTGATCTG
Statistics
Matches: 476, Mismatches: 28, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
84 83 0.17
85 84 0.18
86 160 0.34
87 149 0.31
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (86 bp):
CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
AAGATCTGCTTCTTTAACCAG
Found at i:3182576 original size:171 final size:172
Alignment explanation
Indices: 3182138--3182731 Score: 987
Period size: 171 Copynumber: 3.5 Consensus size: 172
3182128 CTTCAATCTA
* * * *
3182138 CTCCACTGCAACCGATGGAGACAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAACGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
* * *
3182203 AAGATCTGCTATCTTCAACTAGCTCCATTGCAGCCAATGAAGGCAAGGCTTTGTTTTCGATCTGC
66 AAGATCTGCT-TCTTTAACTAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGC
* * *
3182268 TTCGTTGTTAATGCAGGAAGGCAAGATATGCTATCTTTGACCAG
130 TTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACCAG
* *
3182312 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAATGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
* **
3182377 AAGATCTGCTTCTTTAACTAGCTCCACTGTAACCAATGAAGGCAACACTTTGTTTTCGATCTGCT
66 AAGATCTGCTTCTTTAACTAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCT
*
3182442 TCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAG
131 TCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAG
*
3182484 CTCCACTGCAACCAATGAAGGCATGGCTTTGTTTT-GATCTGCTTCGCTGTTAACGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
*
3182548 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCT
66 AAGATCTGCTTCTTTAACTAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCT
3182613 TCGCTGTTAATGCAGGAAGGCAAGATCT--TTCTTTAACCAG
131 TCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAG
3182653 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
1 CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
3182718 AAGATCTGCTTCTT
66 AAGATCTGCTTCTT
3182732 CACTGATCTG
Statistics
Matches: 396, Mismatches: 23, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
169 46 0.12
170 43 0.11
171 115 0.29
172 44 0.11
173 77 0.19
174 71 0.18
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (172 bp):
CTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGC
AAGATCTGCTTCTTTAACTAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCT
TCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAG
Found at i:3191119 original size:10 final size:10
Alignment explanation
Indices: 3191090--3191122 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3191080 CATTCGTAAA
*
3191090 ATATATATAT
1 ATATATATAG
3191100 ATATATATAG
1 ATATATATAG
3191110 ATATATATAG
1 ATATATATAG
3191120 ATA
1 ATA
3191123 CTTTTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (10 bp):
ATATATATAG
Found at i:3191212 original size:3 final size:3
Alignment explanation
Indices: 3191204--3191284 Score: 71
Period size: 3 Copynumber: 27.3 Consensus size: 3
3191194 ATGCACTTAT
*
3191204 ATA ATA ATA ATG ATA AT- ATA ATA GGA-A AT- ATA GA-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA -ATA ATA ATA ATA
* * *
3191248 ATA ATA ATA ACA TTA ATA ATA ATA ATA ATA CTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3191285 AATTGCTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
2 6 0.10
3 54 0.86
4 2 0.03
5 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3198065 original size:3 final size:3
Alignment explanation
Indices: 3198057--3198081 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3198047 AAAGGGTATA
3198057 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
3198082 TTACAAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3199509 original size:26 final size:25
Alignment explanation
Indices: 3199428--3199509 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 25
3199418 GATGAACACG
*
3199428 TGTGTAGTACTATGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTAC-A
* * *
3199454 CGTGTA-TCAATAAAT-AATGG-TACA
1 TGTGTAGT-ACTAAGTGAA-GGCTACA
3199478 TGTGTAGTACTAAGTGAAGGCTACAA
1 TGTGTAGTACTAAGTGAAGGCTAC-A
3199504 TGTGTA
1 TGTGTA
3199510 CCGAGAAGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
24 13 0.30
25 12 0.28
26 18 0.42
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (25 bp):
TGTGTAGTACTAAGTGAAGGCTACA
Found at i:3199546 original size:51 final size:51
Alignment explanation
Indices: 3199424--3199867 Score: 352
Period size: 51 Copynumber: 8.8 Consensus size: 51
3199414 TATCGATGAA
* * * * * *
3199424 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCAATAA-ATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAAGCT-TTGGT
* * *
3199475 -ACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAAGCTTTGGT
* * * * * *
3199525 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAA-ATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAAGCT-TTGGT
* * * * *
3199576 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAAGCTTTGGT
* * * *
3199627 CACGTGTGCAGTACTATGTGAAGGCTACT-TCGTGAACCGTA-AAAC-TTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTAT-GTGTACCG-AGAAGCTTTGGT
* * * *
3199677 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACC-AGAATG-ATAGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAA-GCTTTGGT
* * * * ***
3199727 CGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCG-GATAGCTTCAAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGA-AGCTTTGGT
* * * *
3199778 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-AGATAG-TGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGA-AGCT-TTGGT
* * * *
3199829 CACCTGTGTAGTACTATGTGCATGCTACTATGTGAACCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCG
3199868 GTATCATTGA
Statistics
Matches: 313, Mismatches: 64, Indels: 31
0.77 0.16 0.08
Matches are distributed among these distances:
48 1 0.00
49 2 0.01
50 119 0.38
51 189 0.60
52 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAAGCTTTGGT
Found at i:3199609 original size:26 final size:26
Alignment explanation
Indices: 3199529--3199611 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
3199519 TTTGGTCACG
**
3199529 TGTGTAGTACTGTGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* * *
3199555 CGTGTA-T-CGATAAATGATGG-TCAC-A
1 TGTGTAGTAC--TAAGTGAAGGCT-ACTA
3199580 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
3199606 TGTGTA
1 TGTGTA
3199612 CTGAAAAGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:3199630 original size:102 final size:102
Alignment explanation
Indices: 3199424--3199714 Score: 399
Period size: 101 Copynumber: 2.9 Consensus size: 102
3199414 TATCGATGAA
*
3199424 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCAATAAATAATGGT-ACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
* * *
3199488 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAT
* *
3199525 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
*
3199590 TAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTGAT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAT
* * * * * * *
3199627 CACGTGTGCAGTACTATGTGAAGGCTACTTCGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCACATGTGTAGTA
* * *
3199690 CTATGTGTAGGCTACTACGTGTACC
65 CTAAGTGAAGGCTACTATGTGTACC
3199715 AGAATGATAG
Statistics
Matches: 168, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
101 88 0.52
102 80 0.48
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAT
Found at i:3199780 original size:101 final size:102
Alignment explanation
Indices: 3199675--3199860 Score: 304
Period size: 101 Copynumber: 1.8 Consensus size: 102
3199665 GTAAAACTTG
* *
3199675 ATCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAG
1 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAG
3199738 TACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCA
65 TACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCA
* *
3199776 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAGTGATGGTCACCTGTGTAGT
1 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGT
*
3199841 ACTATGTGCATGCTACTATG
66 ACTATGTGCAGGCTACTATG
3199861 TGAACCGGTA
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
101 41 0.53
102 33 0.42
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (102 bp):
ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGT
ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCA
Found at i:3199780 original size:151 final size:152
Alignment explanation
Indices: 3199478--3199811 Score: 413
Period size: 151 Copynumber: 2.2 Consensus size: 152
3199468 TAATGGTACA
* * * * * * * *
3199478 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCACGTGTGTAGTACTGT
1 TGTGCAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGATCACGTGTGTAGTACTAT
*
3199542 GTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTAT
64 GTGAAGGCTACTACGTGTATCCATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTAT
* * **
3199607 GTGTACTGAAAAGCTTTGATCACG
129 GCGTACCGAAAAGCTTCAATCACG
*
3199631 TGTGCAGTACTATGTGAAGGCTACTTCGTGAACCGTAAAACTTGATCACGTGTGTAGTACTATGT
1 TGTGCAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACGTGTGTAGTACTATGT
* * * * *
3199696 GTAGGCTACTACGTGTA-CCA-GAATGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATG
66 GAAGGCTACTACGTGTATCCATAAATGAT-GGTCACATGTGTAGTACTAAGTGAAGGCTACTATG
* *
3199759 CGTACCGGATAGCTTCAATCACG
130 CGTACCGAAAAGCTTCAATCACG
* *
3199782 TGTGTAGTACTATGTGCAGGCTACTACGTG
1 TGTGCAGTACTATGTGAAGGCTACTACGTG
3199812 TATCAGATAG
Statistics
Matches: 155, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
150 6 0.04
151 78 0.50
152 38 0.25
153 32 0.21
154 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (152 bp):
TGTGCAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACGTGTGTAGTACTATGT
GAAGGCTACTACGTGTATCCATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGC
GTACCGAAAAGCTTCAATCACG
Found at i:3205054 original size:18 final size:18
Alignment explanation
Indices: 3204980--3205055 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 18
3204970 AACTATAAAA
* *
3204980 ATATAAAAGATATATATGT
1 ATATAAAAG-TATGTATAT
* * * *
3204999 GTATAAAATTATGGAAAT
1 ATATAAAAGTATGTATAT
**
3205017 ATATAAAAACATG--TAT
1 ATATAAAAGTATGTATAT
3205033 ATATAAAAGTATGTATAT
1 ATATAAAAGTATGTATAT
3205051 ATATA
1 ATATA
3205056 TGTATACTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
16 13 0.30
18 23 0.53
19 7 0.16
ACGTcount: A:0.53, C:0.01, G:0.11, T:0.36
Consensus pattern (18 bp):
ATATAAAAGTATGTATAT
Found at i:3205060 original size:16 final size:16
Alignment explanation
Indices: 3205015--3205053 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3205005 AATTATGGAA
**
3205015 ATATATAAAAACATGT
1 ATATATAAAAGTATGT
3205031 ATATATAAAAGTATGT
1 ATATATAAAAGTATGT
3205047 ATATATA
1 ATATATA
3205054 TATGTATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (16 bp):
ATATATAAAAGTATGT
Found at i:3205246 original size:16 final size:16
Alignment explanation
Indices: 3205227--3205259 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3205217 GTGAGAAAAA
3205227 ATATAAATATACATAT
1 ATATAAATATACATAT
*
3205243 ATATAAATATATATAT
1 ATATAAATATACATAT
3205259 A
1 A
3205260 AAATGAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAATATACATAT
Found at i:3205314 original size:12 final size:12
Alignment explanation
Indices: 3205297--3205321 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3205287 AAATAAAAAA
3205297 ATATATATACGT
1 ATATATATACGT
3205309 ATATATATACGT
1 ATATATATACGT
3205321 A
1 A
3205322 AGCAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATATATATACGT
Found at i:3205450 original size:3 final size:3
Alignment explanation
Indices: 3205390--3205438 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
3205380 AAGTGTAAAT
* *
3205390 ATA ATG ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3205438 A
1 A
3205439 ACAAAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3208188 original size:22 final size:24
Alignment explanation
Indices: 3208162--3208205 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3208152 GAAAAATATT
3208162 AAATAT-ATA-TATTTTATTTTTA
1 AAATATAATAGTATTTTATTTTTA
*
3208184 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTATTTTATTTT
3208206 AATTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 3 0.16
24 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
AAATATAATAGTATTTTATTTTTA
Found at i:3208414 original size:16 final size:16
Alignment explanation
Indices: 3208393--3208434 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3208383 AATAATTTGA
*
3208393 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
3208409 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
3208425 TAGTTTTAAT
1 TAATTTTAAT
3208435 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:3208418 original size:22 final size:22
Alignment explanation
Indices: 3208408--3208462 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3208398 TTACTAACAA
* * *
3208408 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
3208430 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
3208452 TTAATTTTAAT
1 TTAATTTTAAT
3208463 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:3212814 original size:14 final size:14
Alignment explanation
Indices: 3212795--3212827 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3212785 AGCAGAGTTC
*
3212795 AACTAACCGAATTT
1 AACTAACCAAATTT
3212809 AACTAACCAAATTT
1 AACTAACCAAATTT
3212823 AACTA
1 AACTA
3212828 CTACCTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.27
Consensus pattern (14 bp):
AACTAACCAAATTT
Found at i:3216027 original size:18 final size:18
Alignment explanation
Indices: 3216006--3216056 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3215996 TTTTCTTCTC
*
3216006 CTCATTATTATTCT-CATT
1 CTCATTATTATTATAC-TT
*
3216024 CTCATCATTATTATACTT
1 CTCATTATTATTATACTT
*
3216042 CTTATTATTATTATA
1 CTCATTATTATTATA
3216057 GTAGAGAGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (18 bp):
CTCATTATTATTATACTT
Found at i:3217056 original size:87 final size:87
Alignment explanation
Indices: 3216910--3217080 Score: 229
Period size: 87 Copynumber: 2.0 Consensus size: 87
3216900 TTCTACTCAA
* * * * **
3216910 TACTGCAGATTGCGATATGTGATGTTTTGCTTTGGACTCTGTCTTAACGGAATTGGTATGCGTAT
1 TACTGCAGAATGCGATATATGATGTTTTGCTTTGGACTCTGCCTTAACGGAATAGGTATGCAAAT
3216975 GGTCTCACTTT-TATATATATCG
66 GGTCTCA-TTTCTATATATATCG
* * *
3216997 TACTGCGGAATGCGATATATGATGTTTTG-TTTGGAACTCTGCCTTTACGGAGTAGGTATGCAAA
1 TACTGCAGAATGCGATATATGATGTTTTGCTTTGG-ACTCTGCCTTAACGGAATAGGTATGCAAA
3217061 TGGTCTCATTTCTATATATA
65 TGGTCTCATTTCTATATATA
3217081 CCGAAGCATA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
86 8 0.11
87 65 0.89
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (87 bp):
TACTGCAGAATGCGATATATGATGTTTTGCTTTGGACTCTGCCTTAACGGAATAGGTATGCAAAT
GGTCTCATTTCTATATATATCG
Found at i:3219234 original size:13 final size:13
Alignment explanation
Indices: 3219216--3219240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3219206 GACTCATTTG
3219216 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
3219229 TCTTTTTTTTTT
1 TCTTTTTTTTTT
3219241 CTTAAGAAGA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:3219982 original size:4 final size:4
Alignment explanation
Indices: 3219973--3220010 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
3219963 TTTTTATGTA
*
3219973 TTAT TTAT TTATT TTAT TTAT TTAT TTAC TTA- TTAT TT
1 TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT TTAT TT
3220011 CCTTTACTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.77
5 4 0.13
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:3219985 original size:21 final size:22
Alignment explanation
Indices: 3219961--3220006 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3219951 GATTTTTTAA
*
3219961 TATTTTTATGTA-TTATTTATT
1 TATTTTTATGTATTTATTTACT
*
3219982 TA-TTTTATTTATTTATTTACT
1 TATTTTTATGTATTTATTTACT
3220003 TATT
1 TATT
3220007 ATTTCCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 8 0.38
21 12 0.57
22 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
TATTTTTATGTATTTATTTACT
Found at i:3219989 original size:13 final size:13
Alignment explanation
Indices: 3219973--3219999 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3219963 TTTTTATGTA
3219973 TTATTTATTTATT
1 TTATTTATTTATT
3219986 TTATTTATTTATT
1 TTATTTATTTATT
3219999 T
1 T
3220000 ACTTATTATT
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTATTTATTTATT
Found at i:3220005 original size:16 final size:16
Alignment explanation
Indices: 3219973--3220023 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3219963 TTTTTATGTA
*
3219973 TTATTTATTTATTTTAT
1 TTATTTATTTA-CTTAT
3219990 TTATTTATTTACTTA-
1 TTATTTATTTACTTAT
*
3220005 TTATTTCCTTTACTT-T
1 TTATTT-ATTTACTTAT
3220021 TTA
1 TTA
3220024 AATATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 6 0.20
16 13 0.43
17 11 0.37
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTATTTACTTAT
Found at i:3225077 original size:46 final size:46
Alignment explanation
Indices: 3225010--3225109 Score: 191
Period size: 46 Copynumber: 2.2 Consensus size: 46
3225000 AATTGCAAGC
3225010 ATTGTGTAGGTAAAGGACATTTTTCTCACTAAGTTCTTATGACCTT
1 ATTGTGTAGGTAAAGGACATTTTTCTCACTAAGTTCTTATGACCTT
3225056 ATTGTGTAGGTAAAGGACATTTTTCTCACTAAGTTCTTATGACCTT
1 ATTGTGTAGGTAAAGGACATTTTTCTCACTAAGTTCTTATGACCTT
3225102 ACTTGTGT
1 A-TTGTGT
3225110 GTAATATGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 47 0.89
47 6 0.11
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (46 bp):
ATTGTGTAGGTAAAGGACATTTTTCTCACTAAGTTCTTATGACCTT
Found at i:3227585 original size:31 final size:29
Alignment explanation
Indices: 3227515--3227588 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
3227505 GCCTTAGGTT
*
3227515 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTGAAATGTA
* ***
3227544 ACGTTTTAGTCACTTATGTTATCGTGTTGTA
1 ACATTTTAGTCACTTATGTT-T-GAAATGTA
3227575 ACATTTTAGTCACT
1 ACATTTTAGTCACT
3227589 GATAGACCTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 1 0.03
31 17 0.46
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATGTA
Found at i:3227926 original size:9 final size:9
Alignment explanation
Indices: 3227912--3227939 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3227902 CTTTGTTACA
3227912 ACAATTAAT
1 ACAATTAAT
3227921 ACAATTAAT
1 ACAATTAAT
3227930 ACAATTAAT
1 ACAATTAAT
3227939 A
1 A
3227940 TTTGATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:3228013 original size:59 final size:58
Alignment explanation
Indices: 3227921--3228054 Score: 250
Period size: 59 Copynumber: 2.3 Consensus size: 58
3227911 AACAATTAAT
3227921 ACAATTAATACAATTAATATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
1 ACAATTAATACAATTAATATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
*
3227979 ACAATTAATACAATTACTAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
1 ACAATTAATACAATTAAT-ATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
3228038 ACAATTAATACAATTAA
1 ACAATTAATACAATTAA
3228055 CAATTAATAA
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 17 0.23
59 56 0.77
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (58 bp):
ACAATTAATACAATTAATATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
Found at i:3228091 original size:16 final size:16
Alignment explanation
Indices: 3228070--3228111 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3228060 AATAATTTGA
*
3228070 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
3228086 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
3228102 TAGTTTTAAT
1 TAATTTTAAT
3228112 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:3228095 original size:22 final size:22
Alignment explanation
Indices: 3228085--3228139 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3228075 TTACTAACAA
* * *
3228085 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
3228107 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
3228129 TTAATTTTAAT
1 TTAATTTTAAT
3228140 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:3228126 original size:29 final size:29
Alignment explanation
Indices: 3228093--3228152 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
3228083 AATTAATTTT
*
3228093 AATAACAATTAGTTTTAATTTT-ATTAAAA
1 AATAA-AATTAATTTTAATTTTAATTAAAA
**
3228122 AATAATTTTAATTTTAATTTTAATTAAAA
1 AATAAAATTAATTTTAATTTTAATTAAAA
3228151 AA
1 AA
3228153 GGGCCGGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (29 bp):
AATAAAATTAATTTTAATTTTAATTAAAA
Found at i:3228871 original size:31 final size:29
Alignment explanation
Indices: 3228833--3228909 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
3228823 CTAACGGCTC
* *
3228833 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
3228864 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
3228893 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
3228910 TTGAGCCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:3229708 original size:3 final size:3
Alignment explanation
Indices: 3229700--3229734 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3229690 ATCACATGTT
3229700 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3229735 TGGATGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3229813 original size:73 final size:73
Alignment explanation
Indices: 3229735--3229920 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
3229725 TATTATTATT
*
3229735 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
3229800 ATTTTAAG
66 ATTTTAAG
3229808 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
3229873 ATTTTAAG
66 ATTTTAAG
3229881 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
3229921 GTCAAGTTGT
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:3234144 original size:3 final size:3
Alignment explanation
Indices: 3234136--3234167 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3234126 ATCACATGTT
3234136 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3234168 TGGATGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3234287 original size:73 final size:73
Alignment explanation
Indices: 3234168--3234426 Score: 500
Period size: 73 Copynumber: 3.5 Consensus size: 73
3234158 TATTATTATT
*
3234168 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
3234233 ATTTTAAG
66 ATTTTAAG
3234241 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
3234306 ATTTTAAG
66 ATTTTAAG
*
3234314 TGGATGTAATGATGAAACTTAGTTGTATTCCAACCAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
3234379 ATTTTAAG
66 ATTTTAAG
3234387 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
3234427 GTCAAGTTGT
Statistics
Matches: 183, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 183 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:3242032 original size:19 final size:19
Alignment explanation
Indices: 3242008--3242047 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3241998 CTTTTGGGTT
3242008 AGTAAATTAGGTAGTTCTA
1 AGTAAATTAGGTAGTTCTA
3242027 AGTAAATTAGGTAGTTCTA
1 AGTAAATTAGGTAGTTCTA
3242046 AG
1 AG
3242048 GCGAAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.35
Consensus pattern (19 bp):
AGTAAATTAGGTAGTTCTA
Found at i:3243573 original size:7 final size:7
Alignment explanation
Indices: 3243561--3243605 Score: 72
Period size: 7 Copynumber: 6.1 Consensus size: 7
3243551 CTTTTTAAAA
3243561 TATATTT
1 TATATTT
3243568 TATATTT
1 TATATTT
3243575 TATATTT
1 TATATTT
3243582 TATATTT
1 TATATTT
3243589 TATATTT
1 TATATTT
3243596 AATATATTT
1 --TATATTT
3243605 T
1 T
3243606 TTAGTATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 29 0.81
9 7 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:3244112 original size:18 final size:18
Alignment explanation
Indices: 3244081--3244115 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3244071 TGGTGAGGAA
*
3244081 AAGCAACCTGAAGATGCC
1 AAGCAACCTCAAGATGCC
*
3244099 AAGCAGCCTCAAGATGC
1 AAGCAACCTCAAGATGC
3244116 TACTAAAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.29, G:0.23, T:0.11
Consensus pattern (18 bp):
AAGCAACCTCAAGATGCC
Found at i:3251439 original size:18 final size:18
Alignment explanation
Indices: 3251416--3251472 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
3251406 CCCAACTACT
*
3251416 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
3251434 GTATACATGAATAGTGCC
1 GTATACGTGAATAGTACC
*
3251452 GTATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
3251470 GTA
1 GTA
3251473 AACGGTCGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:3254174 original size:24 final size:24
Alignment explanation
Indices: 3254140--3254191 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3254130 TTTCTAGAAG
* **
3254140 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGACCATAATAT
*
3254164 ATTTAGCATTTATTACCATAATAT
1 ATTTAGCATTTATGACCATAATAT
3254188 ATTT
1 ATTT
3254192 GACTTTGATT
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:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGACCATAATAT
Found at i:3258631 original size:24 final size:24
Alignment explanation
Indices: 3258569--3258620 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3258559 TTTCTAGAAG
* * *
3258569 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
3258593 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
3258617 ATTT
1 ATTT
3258621 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:3271637 original size:24 final size:24
Alignment explanation
Indices: 3271603--3271654 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3271593 TTTCTAGAAG
* **
3271603 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGACCATAATAT
*
3271627 ATTTAGCATTTATTACCATAATAT
1 ATTTAGCATTTATGACCATAATAT
3271651 ATTT
1 ATTT
3271655 GACTTTGATT
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:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGACCATAATAT
Found at i:3276095 original size:24 final size:24
Alignment explanation
Indices: 3276033--3276084 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3276023 TTTCTAGAAG
* * *
3276033 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
3276057 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
3276081 ATTT
1 ATTT
3276085 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:3284069 original size:16 final size:16
Alignment explanation
Indices: 3284036--3284069 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3284026 TACCTGTGTT
* *
3284036 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
3284052 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
3284068 AA
1 AA
3284070 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:3288848 original size:16 final size:16
Alignment explanation
Indices: 3288815--3288848 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3288805 GGAGATTGTT
* *
3288815 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
3288831 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
3288847 AA
1 AA
3288849 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:3299058 original size:21 final size:21
Alignment explanation
Indices: 3299020--3299064 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3299010 TTATGTTAGA
* * *
3299020 AGATAAGTATATGTTTAAAAT
1 AGATAAGCATAGGGTTAAAAT
*
3299041 AGATAAGCATAGGGTTAAGAT
1 AGATAAGCATAGGGTTAAAAT
3299062 AGA
1 AGA
3299065 GTTTGTCACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (21 bp):
AGATAAGCATAGGGTTAAAAT
Found at i:3300774 original size:34 final size:37
Alignment explanation
Indices: 3300736--3300803 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
3300726 AATAATTTAT
3300736 TTTATG-T-ATATTTTAATATATTT-AT-ATATTCATG
1 TTTATGTTAATATTTTAATAT-TTTCATAATATTCATG
*
3300770 TTTATGTTAATTTTTTAATATTTTCATAATATTC
1 TTTATGTTAATATTTTAATATTTTCATAATATTC
3300804 GTATTATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 6 0.21
35 4 0.14
36 13 0.45
37 6 0.21
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (37 bp):
TTTATGTTAATATTTTAATATTTTCATAATATTCATG
Found at i:3300779 original size:28 final size:24
Alignment explanation
Indices: 3300725--3300780 Score: 58
Period size: 28 Copynumber: 2.2 Consensus size: 24
3300715 TTTTATGCGA
*
3300725 TAATAATTTATTTTATGTATATTT
1 TAATAATTTATTTTATGTATATGT
*
3300749 TAATATATTTATATATTCATGTTTATGT
1 TAATA-ATTTAT-T-TT-ATGTATATGT
3300777 TAAT
1 TAAT
3300781 TTTTTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 5 0.19
25 6 0.23
26 1 0.04
27 2 0.08
28 12 0.46
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (24 bp):
TAATAATTTATTTTATGTATATGT
Found at i:3301811 original size:10 final size:8
Alignment explanation
Indices: 3301788--3301847 Score: 57
Period size: 8 Copynumber: 7.1 Consensus size: 8
3301778 AGCTTTTACT
3301788 AATTTTTA
1 AATTTTTA
3301796 AATTTTTA
1 AATTTTTA
3301804 ATAGTTTTTA
1 A-A-TTTTTA
** *
3301814 TTTTTTTTT
1 -AATTTTTA
3301823 AATTTTTA
1 AATTTTTA
3301831 AATTTTTA
1 AATTTTTA
*
3301839 AATATTTA
1 AATTTTTA
3301847 A
1 A
3301848 GAAGGACCCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 30 0.71
9 6 0.14
10 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (8 bp):
AATTTTTA
Found at i:3304980 original size:21 final size:21
Alignment explanation
Indices: 3304954--3304994 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3304944 AGATGAGCAA
* *
3304954 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3304975 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3304995 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3308964 original size:21 final size:20
Alignment explanation
Indices: 3308935--3308977 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3308925 TGTTTTATAA
*
3308935 TTATAAAAAATTTT-AATTAT
1 TTATTAAAAATTTTCAA-TAT
3308955 TTATTAAAAATTTTCAATAT
1 TTATTAAAAATTTTCAATAT
3308975 TTA
1 TTA
3308978 GTATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTAAAAATTTTCAATAT
Found at i:3309657 original size:19 final size:18
Alignment explanation
Indices: 3309610--3309657 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
3309600 TTTTTTATAA
*
3309610 TTAAAAATATTTTTTACTT
1 TTAAAAA-ATTTTTTAATT
* *
3309629 TTTAATAATTTTTTAAATT
1 TTAAAAAATTTTTT-AATT
3309648 TTAAAAAATT
1 TTAAAAAATT
3309658 AATTAATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAAAAAATTTTTTAATT
Found at i:3311498 original size:20 final size:20
Alignment explanation
Indices: 3311473--3311512 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3311463 TCAATACATG
3311473 CTCTTGGGTTTTAGAAACCT
1 CTCTTGGGTTTTAGAAACCT
3311493 CTCTTGGGTTTTAGAAACCT
1 CTCTTGGGTTTTAGAAACCT
3311513 TAGATCCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
CTCTTGGGTTTTAGAAACCT
Found at i:3323833 original size:15 final size:15
Alignment explanation
Indices: 3323813--3323843 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3323803 AATCAACCAG
3323813 CTTTTAGTTGAAAAA
1 CTTTTAGTTGAAAAA
3323828 CTTTTAGTTGAAAAA
1 CTTTTAGTTGAAAAA
3323843 C
1 C
3323844 ATGCTGCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (15 bp):
CTTTTAGTTGAAAAA
Found at i:3325246 original size:22 final size:21
Alignment explanation
Indices: 3325221--3325262 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3325211 AGTAAGAATT
3325221 AAAAAAAAGGTGAAACAGAAAA
1 AAAAAAAAGGTGAAA-AGAAAA
* *
3325243 AAAAAGAAGTTGAAAAGAAA
1 AAAAAAAAGGTGAAAAGAAA
3325263 CAGTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.07
Consensus pattern (21 bp):
AAAAAAAAGGTGAAAAGAAAA
Found at i:3339208 original size:19 final size:19
Alignment explanation
Indices: 3339184--3339226 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3339174 ACACGGCCGT
*
3339184 GTGCCCCGGCTATGTGGAA
1 GTGCCCCGACTATGTGGAA
*
3339203 GTGCCCCGACTGTGTGGAA
1 GTGCCCCGACTATGTGGAA
3339222 GTGCC
1 GTGCC
3339227 TAGGCCGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (19 bp):
GTGCCCCGACTATGTGGAA
Found at i:3339271 original size:21 final size:20
Alignment explanation
Indices: 3339245--3339300 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
3339235 GTGGGGGTCT
3339245 ACACACCCGTGTGAAGGCCAC
1 ACACACCCGTGTGAAGG-CAC
* *
3339266 ACACACCCGTGTGGACGGGAC
1 ACACACCCGTGT-GAAGGCAC
*
3339287 ACACGCCCGTGTGA
1 ACACACCCGTGTGA
3339301 GCAGCCCGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.06
21 25 0.81
22 4 0.13
ACGTcount: A:0.25, C:0.36, G:0.29, T:0.11
Consensus pattern (20 bp):
ACACACCCGTGTGAAGGCAC
Found at i:3354443 original size:22 final size:22
Alignment explanation
Indices: 3354418--3354461 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3354408 TACACCAAAA
*
3354418 TAGGCTTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGGCGCTTTTT
3354440 TAGGCCTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGGCGCTTTTT
3354462 AGCGCCACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.43
Consensus pattern (22 bp):
TAGGCCTTTAGCGGCGCTTTTT
Found at i:3354648 original size:42 final size:43
Alignment explanation
Indices: 3354533--3354694 Score: 236
Period size: 43 Copynumber: 3.8 Consensus size: 43
3354523 ACGTCGCTAA
*
3354533 CTTTTGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGTT
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGTT
* *
3354576 CTTTAGCGGCGCTTTTCCCACAATCGCCGCTAAAGACCATGTT
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGTT
* **
3354619 CTTTAGCGGCGCTT-TCCCACAAATGCCGCTAAAGACCATAAT
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGTT
* * *
3354661 CTTTAGCGACGCTTCTCGCAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAA
3354695 AACATATCAT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 37 0.35
43 70 0.65
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.25
Consensus pattern (43 bp):
CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGTT
Found at i:3354691 original size:85 final size:86
Alignment explanation
Indices: 3354533--3354694 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 86
3354523 ACGTCGCTAA
* ** * * *
3354533 CTTTTGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCACA
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATAATCTTTAGCGACGCTTCTCCCAAA
*
3354598 ATCGCCGCTAAAGACCATGTT
66 AACGCCGCTAAAGACCATGTT
* *
3354619 CTTTAGCGGCGCTT-TCCCACAAATGCCGCTAAAGACCATAATCTTTAGCGACGCTTCTCGCAAA
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATAATCTTTAGCGACGCTTCTCCCAAA
3354683 AACGCCGCTAAA
66 AACGCCGCTAAA
3354695 AACATATCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 54 0.81
86 13 0.19
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.25
Consensus pattern (86 bp):
CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATAATCTTTAGCGACGCTTCTCCCAAA
AACGCCGCTAAAGACCATGTT
Found at i:3355638 original size:15 final size:17
Alignment explanation
Indices: 3355620--3355657 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
3355610 GGATAAGGAA
3355620 AAAAATTAT-AAAT-AT
1 AAAAATTATAAAATAAT
*
3355635 AAAAATTCTAAAATAAT
1 AAAAATTATAAAATAAT
3355652 AAAAAT
1 AAAAAT
3355658 AAACAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 4 0.20
17 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATTATAAAATAAT
Found at i:3358870 original size:4 final size:4
Alignment explanation
Indices: 3358861--3358885 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3358851 TTATTTTGCT
3358861 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
3358886 CAATATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3359064 original size:50 final size:50
Alignment explanation
Indices: 3359008--3359106 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
3358998 CACCAATTAA
* * *
3359008 TCCTAAACCTTAAATCGTAAAATAGAAACTCTAAACCCCTAACCCCTATC
1 TCCTAAACCCTAAATCATAAAATAAAAACTCTAAACCCCTAACCCCTATC
3359058 TCCTAAACCCTAAATCATAAAATAAAAACTCTAAACCCCTAACCCCTAT
1 TCCTAAACCCTAAATCATAAAATAAAAACTCTAAACCCCTAACCCCTAT
3359107 TTTACTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.42, C:0.32, G:0.02, T:0.23
Consensus pattern (50 bp):
TCCTAAACCCTAAATCATAAAATAAAAACTCTAAACCCCTAACCCCTATC
Found at i:3359234 original size:21 final size:21
Alignment explanation
Indices: 3359187--3359254 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3359177 CCCCGAATAT
* * *
3359187 CTAAACCCTAAATCACTAACTC
1 CTAACCCCTAACT-ACTAACCC
* *
3359209 TTAACCTCTAACATA-TAACCC
1 CTAACCCCTAAC-TACTAACCC
*
3359230 CTAACCCCTGACTACTAACCC
1 CTAACCCCTAACTACTAACCC
3359251 CTAA
1 CTAA
3359255 ACCTTATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
20 2 0.06
21 24 0.67
22 9 0.25
23 1 0.03
ACGTcount: A:0.37, C:0.38, G:0.01, T:0.24
Consensus pattern (21 bp):
CTAACCCCTAACTACTAACCC
Found at i:3359330 original size:17 final size:17
Alignment explanation
Indices: 3359297--3359330 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3359287 TTTGTTATGC
* *
3359297 TAATTTTTTTTATAAAT
1 TAATTTTTTATAAAAAT
3359314 TAATTTTTTATAAAAAT
1 TAATTTTTTATAAAAAT
3359331 AAAAAAACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTTTTTATAAAAAT
Found at i:3359990 original size:15 final size:15
Alignment explanation
Indices: 3359970--3360001 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3359960 CATAAACGCT
3359970 AATCCATAATCCCTA
1 AATCCATAATCCCTA
*
3359985 AATCCATACTCCCTA
1 AATCCATAATCCCTA
3360000 AA
1 AA
3360002 CCTTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (15 bp):
AATCCATAATCCCTA
Found at i:3360227 original size:23 final size:23
Alignment explanation
Indices: 3360191--3360242 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
3360181 AACTTTTAAC
*
3360191 CCTTAACACGTCTAACCCCTAAA
1 CCTTAACACCTCTAACCCCTAAA
3360214 GCCTTAAC-CCTCTAACCCCTAAA
1 -CCTTAACACCTCTAACCCCTAAA
3360237 CCTTAA
1 CCTTAA
3360243 ATCCCAACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 6 0.22
23 14 0.52
24 7 0.26
ACGTcount: A:0.33, C:0.40, G:0.04, T:0.23
Consensus pattern (23 bp):
CCTTAACACCTCTAACCCCTAAA
Found at i:3360626 original size:41 final size:41
Alignment explanation
Indices: 3360571--3360766 Score: 311
Period size: 41 Copynumber: 4.8 Consensus size: 41
3360561 ATAAAATGCT
*
3360571 TTTAGCGGCGCTTCTTAAAAAACGCCCCTAAAGACCAGAGC
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
*
3360612 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGA
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
*
3360653 TTTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGC
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
* * * * *
3360694 ATTAGTGGCGCTTCATCAAAAACGCCGCTAAAGACTAGAGC
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
*
3360735 ATTAGCGGCGCTTCTTAAAAAACGCCGCTAAA
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAA
3360767 TCCTTAAAAA
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 144 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.20
Consensus pattern (41 bp):
TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
Found at i:3360941 original size:40 final size:40
Alignment explanation
Indices: 3360818--3360943 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 40
3360808 TTTGCAGCGC
* * * * *
3360818 TTTTTGTAAAACGCCGCTAATG-CTCATTTTTAGTGGCG-
1 TTTTTATAAAGCGCCGCTAATGATTGATTTTTAGCGGCGT
* * *
3360856 TTTTTAGAAAAGCGCCGCTAAT-ACTCGATCTTTAGCGGCGT
1 TTTTTA-TAAAGCGCCGCTAATGA-TTGATTTTTAGCGGCGT
*
3360897 TTTTTATATAGCGCCGCTAATGATTGATTTTTAGCGGCGT
1 TTTTTATAAAGCGCCGCTAATGATTGATTTTTAGCGGCGT
3360937 TTTTTAT
1 TTTTTAT
3360944 TCAAACGCCA
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
38 5 0.07
39 13 0.18
40 46 0.65
41 7 0.10
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (40 bp):
TTTTTATAAAGCGCCGCTAATGATTGATTTTTAGCGGCGT
Found at i:3364954 original size:23 final size:22
Alignment explanation
Indices: 3364900--3364964 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
3364890 TTATACGTTA
3364900 AAATAAA-TTTAAAATAAATAAT
1 AAATAAAGTTT-AAATAAATAAT
*
3364922 ATATAAAGTTTGAAATAAATCAA-
1 AAATAAAGTTT-AAATAAAT-AAT
*
3364945 AAATAGAGTTTAAA-AAATAA
1 AAATAAAGTTTAAATAAATAA
3364965 ACACTACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 2 0.05
21 4 0.11
22 9 0.24
23 20 0.54
24 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (22 bp):
AAATAAAGTTTAAATAAATAAT
Found at i:3365470 original size:23 final size:23
Alignment explanation
Indices: 3365417--3365472 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3365407 TAGCATAACA
*
3365417 AATAATACATGATGAAATTAAAT
1 AATAATATATGATGAAATTAAAT
*
3365440 AATAATATATGAT-AAATTCAA-
1 AATAATATATGATGAAATTAAAT
*
3365461 ACTAATATATGA
1 AATAATATATGA
3365473 AGAACCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 11 0.37
22 7 0.23
23 12 0.40
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (23 bp):
AATAATATATGATGAAATTAAAT
Found at i:3365540 original size:23 final size:23
Alignment explanation
Indices: 3365524--3365597 Score: 80
Period size: 24 Copynumber: 3.3 Consensus size: 23
3365514 AATGAAAATT
3365524 TTAAAATAATAAAAATGATAAAC
1 TTAAAATAATAAAAATGATAAAC
* **
3365547 TTACAATAATAATGCATGATAAAC
1 TTAAAATAATAA-AAATGATAAAC
* *
3365571 TTAAAATAAT--ACATGAAAAAC
1 TTAAAATAATAAAAATGATAAAC
3365592 TTAAAA
1 TTAAAA
3365598 AAAACAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
21 15 0.34
23 11 0.25
24 18 0.41
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (23 bp):
TTAAAATAATAAAAATGATAAAC
Found at i:3365580 original size:21 final size:21
Alignment explanation
Indices: 3365524--3365597 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
3365514 AATGAAAATT
*
3365524 TTAAAATAATAAAAATGATAAAC
1 TTAAAATAAT--ACATGATAAAC
*
3365547 TTACAATAATAATGCATGATAAAC
1 TT--AA-AATAATACATGATAAAC
*
3365571 TTAAAATAATACATGAAAAAC
1 TTAAAATAATACATGATAAAC
3365592 TTAAAA
1 TTAAAA
3365598 AAAACAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 21 0.48
22 2 0.05
23 2 0.05
24 11 0.25
25 2 0.05
26 6 0.14
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (21 bp):
TTAAAATAATACATGATAAAC
Found at i:3365600 original size:24 final size:24
Alignment explanation
Indices: 3365515--3365600 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 24
3365505 AATAATGTTA
** * *
3365515 ATGAAAATTTTAAAATAATAA-AA
1 ATGAAAAACTTAAAAAAATAATAC
* * * *
3365538 ATGATAAACTTACAATAATAATGC
1 ATGAAAAACTTAAAAAAATAATAC
*
3365562 ATGATAAACTT---AAAATAATAC
1 ATGAAAAACTTAAAAAAATAATAC
3365583 ATGAAAAACTTAAAAAAA
1 ATGAAAAACTTAAAAAAA
3365601 ACAAATACAT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
21 18 0.36
23 17 0.34
24 15 0.30
ACGTcount: A:0.60, C:0.07, G:0.06, T:0.27
Consensus pattern (24 bp):
ATGAAAAACTTAAAAAAATAATAC
Found at i:3365719 original size:19 final size:18
Alignment explanation
Indices: 3365676--3365712 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3365666 ATTGATGATG
3365676 AGTTTAAAAATAATATTA
1 AGTTTAAAAATAATATTA
*
3365694 AGCTTAAAAATTAATATTA
1 AGTTTAAAAA-TAATATTA
3365713 TATTTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
AGTTTAAAAATAATATTA
Found at i:3370344 original size:11 final size:10
Alignment explanation
Indices: 3370323--3370347 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3370313 CAGCCGACCC
3370323 AAAATAAAAA
1 AAAATAAAAA
3370333 AAAATAAAAA
1 AAAATAAAAA
3370343 AAAAT
1 AAAAT
3370348 CATACCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:3376998 original size:44 final size:44
Alignment explanation
Indices: 3376950--3377156 Score: 143
Period size: 44 Copynumber: 4.7 Consensus size: 44
3376940 AAAATCGGCC
* * *
3376950 ATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTA
1 ATCTTCAATCTACTCCACTGCTGCTCAGGGAGATAAGATCTGTA
* * * *
3376994 ATCTTCAATCTATTCCACTGTTGCCCAGGGAGAT-AGA-AT-TA
1 ATCTTCAATCTACTCCACTGCTGCTCAGGGAGATAAGATCTGTA
* * ** * * * **
3377035 CTAGCTTCAATGTACTCCACTGCAACCTCAAGGAGGTAAAATCCACT-
1 --ATCTTCAATCTACTCCACTGC-TGCTCAGGGAGATAAGAT-CTGTA
* * ** *
3377082 ATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTA
1 ATCTTCAATCTACTCCACTGCTGCTCAGGGAGATAAGATCTGTA
* *
3377126 ATCTTCAATCTATTCCACTGCTGCCCAGGGA
1 ATCTTCAATCTACTCCACTGCTGCTCAGGGA
3377157 AGTAGAATTA
Statistics
Matches: 115, Mismatches: 40, Indels: 16
0.67 0.23 0.09
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 22 0.19
44 72 0.63
45 17 0.15
48 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTGCTGCTCAGGGAGATAAGATCTGTA
Found at i:3377056 original size:43 final size:44
Alignment explanation
Indices: 3376996--3377189 Score: 128
Period size: 44 Copynumber: 4.4 Consensus size: 44
3376986 GATCTGTAAT
*
3376996 CTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAAT-TACTAG
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGAATCTACTAG
* *** * * * * *
3377039 CTTCAATGTACTCCACTGCAACCTCAAGGAGGTAAAATCCACTAT
1 CTTCAATCTACTCCACTGTTGCC-CAGGGAGATAGAATCTACTAG
* * * ** * *
3377084 CTTCGATCTGCTCCACTATTGCTTAGGGAGATA-AGATCT-GTAAT
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGA-ATCTACT-AG
* * *
3377128 CTTCAATCTATTCCACTGCTGCCCAGGGA-AGTAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGA-TAGAATCTACTAG
*
3377171 CTTCAATGTACTCCACTGT
1 CTTCAATCTACTCCACTGT
3377190 AACCACAGGG
Statistics
Matches: 108, Mismatches: 36, Indels: 14
0.68 0.23 0.09
Matches are distributed among these distances:
43 38 0.35
44 50 0.46
45 20 0.19
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGAATCTACTAG
Found at i:3377929 original size:133 final size:133
Alignment explanation
Indices: 3376890--3377919 Score: 1324
Period size: 133 Copynumber: 7.8 Consensus size: 133
3376880 GCAACTTCAA
* * *
3376890 GGAGATAGGAA-TACTGGCTTCAATGTACTCCATTGTAACCTCAGGGAGGTAAAATCGGCCATCT
1 GGAGATA-GAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCT
* * * ** ** * *
3376954 TCGATCTACTCCACT-AC--TGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
65 TCGATCTGCTCCACTGTCTATGC--AGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCT
3377016 GCCCAG
128 GCCCAG
* * * * ** *
3377022 GGAGATAGAATTACTAGCTTCAATGTACTCCACTGCAACCTCAAGGAGGTAAAATCCACTATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
* * ** ** *
3377087 CGATCTGCTCCAC--TAT-TGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTG
66 CGATCTGCTCCACTGTCTATGC--AGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCTG
3377149 CCCAG
129 CCCAG
3377154 GGA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCT
1 GGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCT
* * * * ** * * * * * *
3377218 TTGATCTGCCCCACT-ACTGTTTAGGGAGACAATATATGAAATCTTCAATCTATTCCACTGCTGC
65 TCGATCTGCTCCACTGTCTATGCAGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCTGC
3377282 CCAG
130 CCAG
* *
3377286 GGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCGTCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
* *
3377351 CGATCTTCTTCACTGTCTATGCAGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCTGCC
66 CGATCTGCTCCACTGTCTATGCAGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCTGCC
*
3377416 CGG
131 CAG
** *
3377419 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAATGAGGTAAAATCTGCCGTCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
* * * *
3377484 CGATCTTCTTCGCTGTCTATGCAGGAAGGCAAGATCTAAAATCTTTAGTCTATTCCACTGCTGCC
66 CGATCTGCTCCACTGTCTATGCAGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCTGCC
3377549 CAG
131 CAG
* * *
3377552 AGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGAAGGTAAAATCTACCATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
* * * *
3377617 CGACCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTAAAATCTTCAGTCTATTCTACTGCTGCC
66 CGATCTGCTCCACTGTCTATGCAGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCTGCC
3377682 CAG
131 CAG
* *
3377685 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCTGCCGTCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
* * *
3377750 CGACCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCTGCC
66 CGATCTGCTCCACTGTCTATGCAGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCTGCC
3377815 CAG
131 CAG
* * * *
3377818 GGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCATAGGGAGGTAAAAT-TCACCACCT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCT
*
3377882 TTGATCTGCTCCACTGTCTATGCAGGAAGGCAAGATCT
65 TCGATCTGCTCCACTGTCTATGCAGGAAGGCAAGATCT
3377920 GCTATCTTCA
Statistics
Matches: 813, Mismatches: 77, Indels: 15
0.90 0.09 0.02
Matches are distributed among these distances:
131 4 0.00
132 297 0.37
133 511 0.63
134 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (133 bp):
GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
CGATCTGCTCCACTGTCTATGCAGGAAGGCAAGATCTAAAATCTTCAGTCTATTCCACTGCTGCC
CAG
Found at i:3391663 original size:29 final size:30
Alignment explanation
Indices: 3391631--3391689 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3391621 TATGGTTTAA
*
3391631 TATGTAACTGTATACATGAACT-TTGATTT
1 TATGTAACTGTATACATGAAATATTGATTT
* * *
3391660 TATGTAATTTTATATATGAAATATTGATTT
1 TATGTAACTGTATACATGAAATATTGATTT
3391690 GATCCAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (30 bp):
TATGTAACTGTATACATGAAATATTGATTT
Found at i:3392605 original size:15 final size:14
Alignment explanation
Indices: 3392585--3392618 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3392575 TATAAATATA
3392585 AAAATTAATGAATTT
1 AAAATTAA-GAATTT
*
3392600 AAAATTTAGAATTT
1 AAAATTAAGAATTT
3392614 AAAAT
1 AAAAT
3392619 GATAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (14 bp):
AAAATTAAGAATTT
Found at i:3394736 original size:18 final size:18
Alignment explanation
Indices: 3394711--3394755 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
3394701 AAATTCTATT
3394711 TAAAAAAATTAAAA-ATCTA
1 TAAAAAAA-TAAAATA-CTA
*
3394730 TAAAAAAATAAATTACTA
1 TAAAAAAATAAAATACTA
3394748 TAAAAAAA
1 TAAAAAAA
3394756 AAGATAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAAAAATAAAATACTA
Found at i:3396193 original size:21 final size:20
Alignment explanation
Indices: 3396132--3396200 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
3396122 AGGATTAACT
3396132 CTAAACCCCTAA-CCTCTAAATC
1 CTAAACCCC-AACCCT-TAAA-C
*
3396154 CTAAA-CCCGACCC-TAAAC
1 CTAAACCCCAACCCTTAAAC
3396172 CTTAAACCCCAACCCTTAAAC
1 C-TAAACCCCAACCCTTAAAC
3396193 CGTAAACC
1 C-TAAACC
3396201 ATAAAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.05
19 8 0.20
20 8 0.20
21 17 0.43
22 5 0.12
ACGTcount: A:0.38, C:0.42, G:0.03, T:0.17
Consensus pattern (20 bp):
CTAAACCCCAACCCTTAAAC
Found at i:3397014 original size:40 final size:41
Alignment explanation
Indices: 3396964--3397064 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
3396954 TTTGCGGCCC
* * *
3396964 TTTTAAAAAAACGCCGCTAAA-AATAGAGCATTAGCGGTGCT
1 TTTTCAAAAAACGCCGCTAAAGAACAGAGCATTAGCGGTG-A
* *
3397005 TTTTC-AAAAACGCCGCTAAAGACCCGAGCATTAGCGGTGA
1 TTTTCAAAAAACGCCGCTAAAGAACAGAGCATTAGCGGTGA
3397045 TTTTCAAAAAACGCCGCTAA
1 TTTTCAAAAAACGCCGCTAA
3397065 CGCCCCGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
40 20 0.38
41 33 0.62
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (41 bp):
TTTTCAAAAAACGCCGCTAAAGAACAGAGCATTAGCGGTGA
Found at i:3397146 original size:39 final size:40
Alignment explanation
Indices: 3397122--3397196 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 40
3397112 GCGCTTTCTG
*
3397122 AAAAACGCCGCTAATGC-TAATTTTTAGCGTCGTTTACCA
1 AAAAACGCCGCTAATGCTTAATTTTTAGCGGCGTTTACCA
*
3397161 AAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTT
1 AAAAACGCCGCTAATGCTTAATTTTTAGCGGCGTTT
3397197 TTTATCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
39 17 0.52
40 16 0.48
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (40 bp):
AAAAACGCCGCTAATGCTTAATTTTTAGCGGCGTTTACCA
Found at i:3397901 original size:42 final size:39
Alignment explanation
Indices: 3397849--3397932 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 39
3397839 AAAAAATAAA
3397849 AAATATTAAAAATATTTTAATTAATATTTCATAATTAAATTT
1 AAATATTAAAAATATTTT-ATTAATATTT-A-AATTAAATTT
* * *
3397891 AAATTTTAAAAATATTTTTTTACTATTTAAATTAAATTT
1 AAATATTAAAAATATTTTATTAATATTTAAATTAAATTT
3397930 AAA
1 AAA
3397933 CCAAATCGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 13 0.33
40 1 0.03
41 8 0.21
42 17 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (39 bp):
AAATATTAAAAATATTTTATTAATATTTAAATTAAATTT
Found at i:3410025 original size:63 final size:63
Alignment explanation
Indices: 3409923--3410050 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 63
3409913 ACACACATTC
* *
3409923 CACATAACCGTGCTGGGCTTGTTTTATCTGTAAGTAAATTTTGAACAACGCTAGTAAGCTTAT
1 CACATAACCGTGCTGGGCTTGTTTTATCTATAAGCAAATTTTGAACAACGCTAGTAAGCTTAT
* * *
3409986 CACATAATCGTGCTGGGCTTGTTTTATCTATAAGCAAATTTTGAGCAACGTTAGTAAGCTTAT
1 CACATAACCGTGCTGGGCTTGTTTTATCTATAAGCAAATTTTGAACAACGCTAGTAAGCTTAT
3410049 CA
1 CA
3410051 ATTTTGTCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (63 bp):
CACATAACCGTGCTGGGCTTGTTTTATCTATAAGCAAATTTTGAACAACGCTAGTAAGCTTAT
Found at i:3411248 original size:17 final size:18
Alignment explanation
Indices: 3411219--3411261 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3411209 ATAAATAAAC
3411219 AATTAAA-TAAATTAG-A
1 AATTAAATTAAATTAGAA
3411235 AATTAAATTAAATTAGAA
1 AATTAAATTAAATTAGAA
3411253 AATTAAATT
1 AATTAAATT
3411262 CGAATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 7 0.28
17 8 0.32
18 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
AATTAAATTAAATTAGAA
Found at i:3413635 original size:40 final size:39
Alignment explanation
Indices: 3413546--3413655 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 39
3413536 GTTTGGACAA
* *
3413546 AAAACGCCGTTAAAAATCGAGCATTAGCGGCGCTTTACAT
1 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTACAG
* * * *
3413586 AAAATGCCGCTAGAGATTGAGCATTAGCGGCGC-TTCCAGG
1 AAAACGCCGCTA-AAAATGAGCATTAGCGGCGCTTTACA-G
*
3413626 AAAGCGCCGCTAAAAATGAGCATTAGCGGC
1 AAAACGCCGCTAAAAATGAGCATTAGCGGC
3413656 ATTTCTTAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
39 20 0.34
40 35 0.60
41 3 0.05
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTACAG
Found at i:3413680 original size:39 final size:39
Alignment explanation
Indices: 3413545--3413681 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 39
3413535 CGTTTGGACA
* * *
3413545 AAAAACGCCGTTAAAAATCGAGCATTAGCGGCGCTTTACA-
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCAC-TTCCAG
* * * * *
3413585 TAAAATGCCGCTAGAGATTGAGCATTAGCGGCGCTTCCAG
1 AAAAACGCCGCTA-AAAATGAGCATTAGCGGCACTTCCAG
* * * *
3413625 GAAAGCGCCGCTAAAAATGAGCATTAGCGGCATTTCTTAG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCACTTC-CAG
*
3413665 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
3413682 CCTAAGCCCA
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
39 23 0.30
40 51 0.66
41 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCACTTCCAG
Found at i:3414021 original size:14 final size:15
Alignment explanation
Indices: 3413991--3414023 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3413981 AAGGTTTATA
3413991 GATTATGGAATTAGG
1 GATTATGGAATTAGG
3414006 GATTATGGAA-TAGG
1 GATTATGGAATTAGG
3414020 GATT
1 GATT
3414024 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:3414148 original size:7 final size:7
Alignment explanation
Indices: 3414138--3414176 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
3414128 TGGGTTAGTA
3414138 GTTAGGG
1 GTTAGGG
*
3414145 GTTAAGG
1 GTTAGGG
*
3414152 GTTTGGG
1 GTTAGGG
3414159 GTTAGGG
1 GTTAGGG
*
3414166 GTTAGAG
1 GTTAGGG
3414173 GTTA
1 GTTA
3414177 AGAGTTAGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.49, T:0.33
Consensus pattern (7 bp):
GTTAGGG
Found at i:3414159 original size:14 final size:14
Alignment explanation
Indices: 3414138--3414184 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3414128 TGGGTTAGTA
3414138 GTTAGGGGTTAAGG
1 GTTAGGGGTTAAGG
* *
3414152 GTTTGGGGTTAGGG
1 GTTAGGGGTTAAGG
* *
3414166 GTTAGAGGTTAAGA
1 GTTAGGGGTTAAGG
3414180 GTTAG
1 GTTAG
3414185 TGATTTAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (14 bp):
GTTAGGGGTTAAGG
Found at i:3414183 original size:21 final size:21
Alignment explanation
Indices: 3414129--3414184 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
3414119 TAATATTTAT
3414129 GGGTT-AGTAGTTAGGGGTTAA
1 GGGTTAAG-AGTTAGGGGTTAA
** *
3414150 GGGTTTGGGGTTAGGGGTT-A
1 GGGTTAAGAGTTAGGGGTTAA
3414170 GAGGTTAAGAGTTAG
1 G-GGTTAAGAGTTAG
3414185 TGATTTAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.32
Consensus pattern (21 bp):
GGGTTAAGAGTTAGGGGTTAA
Found at i:3414319 original size:14 final size:14
Alignment explanation
Indices: 3414300--3414333 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3414290 AGGGGTTAGG
3414300 GGTTTAGGATTTAA
1 GGTTTAGGATTTAA
* *
3414314 GGTTTATGATTTAG
1 GGTTTAGGATTTAA
3414328 GGTTTA
1 GGTTTA
3414334 AGAGATAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
GGTTTAGGATTTAA
Found at i:3414462 original size:129 final size:128
Alignment explanation
Indices: 3414212--3414463 Score: 276
Period size: 129 Copynumber: 1.9 Consensus size: 128
3414202 ATTCGGGGTC
* * *
3414212 GGGTTAGGGTTTAAGGTTTAGATTAATTAGTATTTTTTTAATTTATATATTAATTAAGTTCTTAT
1 GGGTTAGGGTTTAAGGCTTAGATTAATTAGTAGTTTTTTAATTTATATATTAAATAAGTTCTTAT
* ** ** ****
3414277 ATAATTGTAAAAGAGGGGTTAGGGGTTTAGGATTTAAGGTTTATGATTTAGGGTTTAAGAGATAG
66 ATAATTGTAAAAGAGAGAATAGAAGTTTA-GATTTAAAAAGTATGATTTA-GGTTTAAGAGATAG
* *
3414342 GGGTTAGGGTTTAAGGCTTAGATTAATTGGT-GTTTTTTAATTTATATATTAAATAATTTCTTAT
1 GGGTTAGGGTTTAAGGCTTAGATTAATTAGTAGTTTTTTAATTTATATATTAAATAAGTTCTTAT
* * *
3414406 ATAATTGTAAAAGAGATAATATTAATTTTA-ATTTATTAAAAGTATGATTATA-GTTTAA
66 ATAATTGTAAAAGAGAGAATA-GAAGTTTAGATTTA--AAAAGTATGATT-TAGGTTTAA
3414464 ATTATTTAAG
Statistics
Matches: 101, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
128 5 0.05
129 53 0.52
130 41 0.41
131 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (128 bp):
GGGTTAGGGTTTAAGGCTTAGATTAATTAGTAGTTTTTTAATTTATATATTAAATAAGTTCTTAT
ATAATTGTAAAAGAGAGAATAGAAGTTTAGATTTAAAAAGTATGATTTAGGTTTAAGAGATAG
Found at i:3421220 original size:28 final size:28
Alignment explanation
Indices: 3421188--3421242 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3421178 TTGACTATTG
3421188 TGGTCAGCAAATGCATTCACATTCTTTT
1 TGGTCAGCAAATGCATTCACATTCTTTT
3421216 TGGTCAGCAAATGCATTCACATTCTTT
1 TGGTCAGCAAATGCATTCACATTCTTT
3421243 CTCCTTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (28 bp):
TGGTCAGCAAATGCATTCACATTCTTTT
Found at i:3427027 original size:17 final size:17
Alignment explanation
Indices: 3427005--3427038 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3426995 TACATAAAAC
*
3427005 AAAAGAAAGAATAGAAA
1 AAAAGAAAGAAAAGAAA
3427022 AAAAGAAAGAAAAGAAA
1 AAAAGAAAGAAAAGAAA
3427039 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAAAGAAAAGAAA
Found at i:3427034 original size:9 final size:9
Alignment explanation
Indices: 3427005--3427038 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3426995 TACATAAAAC
3427005 AAAAGAAAG
1 AAAAGAAAG
*
3427014 AATAGAAA-
1 AAAAGAAAG
3427022 AAAAGAAAG
1 AAAAGAAAG
3427031 AAAAGAAA
1 AAAAGAAA
3427039 CAGAATAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:3427530 original size:44 final size:45
Alignment explanation
Indices: 3427435--3427549 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 45
3427425 ACAGGACAGA
* * *
3427435 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGACATTGGAG
* *
3427481 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGACATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGACATTGGAG
* **
3427525 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
3427550 GTCAAAGACA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
44 34 0.57
46 26 0.43
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGACATTGGAG
Found at i:3429286 original size:26 final size:27
Alignment explanation
Indices: 3429232--3429288 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
3429222 AATTTTAAAA
* *
3429232 TATTTTTAAAATACTTTTTTTAATTTT
1 TATTTTTAAAATACATTTTTTAATGTT
**
3429259 TATTTTTAAAATA-ATTTTTTGGTGTT
1 TATTTTTAAAATACATTTTTTAATGTT
3429285 TATT
1 TATT
3429289 AAAAAATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTTTTAAAATACATTTTTTAATGTT
Found at i:3431573 original size:3 final size:3
Alignment explanation
Indices: 3431537--3431561 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3431527 ACTTATATAT
3431537 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3431562 GGCAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3432242 original size:18 final size:18
Alignment explanation
Indices: 3432210--3432244 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3432200 GTTGAACTAT
3432210 ATTTTATAATTTTTAATA
1 ATTTTATAATTTTTAATA
3432228 ATTTT-TAATTATTTAAT
1 ATTTTATAATT-TTTAAT
3432245 TTGAACCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTATAATTTTTAATA
Found at i:3432761 original size:2 final size:2
Alignment explanation
Indices: 3432756--3432784 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3432746 AAAAAAAAAG
3432756 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3432785 TTTTCGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3435052 original size:16 final size:17
Alignment explanation
Indices: 3435014--3435052 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3435004 ATAACTAATG
* *
3435014 TAAAGTAATATATAAGG
1 TAAAATAATATATAAGC
3435031 TAAAATAATATA-AAGC
1 TAAAATAATATATAAGC
3435047 TAAAAT
1 TAAAAT
3435053 GAAGTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (17 bp):
TAAAATAATATATAAGC
Found at i:3441819 original size:3 final size:3
Alignment explanation
Indices: 3441813--3441844 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3441803 TATTATTTTT
3441813 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3441845 TAGAAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3444948 original size:21 final size:22
Alignment explanation
Indices: 3444904--3444950 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3444894 TAATAATGAT
*
3444904 TTTTTAAAATATATACATTTAA
1 TTTTTAAAATATATACATTAAA
3444926 TTTTTAAATATATATA-A-TAAA
1 TTTTTAAA-ATATATACATTAAA
3444947 TTTT
1 TTTT
3444951 CTAACTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 9 0.39
23 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTAAAATATATACATTAAA
Found at i:3447193 original size:18 final size:18
Alignment explanation
Indices: 3447167--3447227 Score: 86
Period size: 18 Copynumber: 3.2 Consensus size: 18
3447157 TAAATTTGTA
3447167 TCAGATTTAGACCTATCT
1 TCAGATTTAGACCTATCT
*
3447185 TCAGGTTTAGTAGACCTATCT
1 TCA-GATT--TAGACCTATCT
3447206 TCAGATTTAGACCTATCT
1 TCAGATTTAGACCTATCT
3447224 TCAG
1 TCAG
3447228 GATTAGGACC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 18 0.47
19 3 0.08
20 3 0.08
21 14 0.37
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (18 bp):
TCAGATTTAGACCTATCT
Found at i:3447200 original size:21 final size:21
Alignment explanation
Indices: 3447174--3447233 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 21
3447164 GTATCAGATT
*
3447174 TAGACCTATCTTCAGGTTTAG
1 TAGACCTATCTTCAGGATTAG
3447195 TAGACCTATCTTCA-GATT--
1 TAGACCTATCTTCAGGATTAG
3447213 TAGACCTATCTTCAGGATTAG
1 TAGACCTATCTTCAGGATTAG
3447234 GACCTTGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 14 0.40
19 4 0.11
20 3 0.09
21 14 0.40
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (21 bp):
TAGACCTATCTTCAGGATTAG
Found at i:3447819 original size:3 final size:3
Alignment explanation
Indices: 3447811--3447855 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3447801 TTTTACAGTC
3447811 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3447856 GTTATTAGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:3448526 original size:24 final size:24
Alignment explanation
Indices: 3448499--3448574 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 24
3448489 AATCAAAGTC
3448499 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
3448523 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
3448547 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
3448571 AAAT
1 AAAT
3448575 TTTCTAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Done.