Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007816.1 Hibiscus syriacus cultivar Beakdansim tig00110151_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3994936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1835216 original size:99 final size:99
Alignment explanation
Indices: 1835042--1835266 Score: 256
Period size: 99 Copynumber: 2.3 Consensus size: 99
1835032 GCTCACCCAT
* * * * * *
1835042 ATTGAATAGATCTAGCCGCTTTTGGGTGAATTGAAGATGCCAATGTTCCTTCTCTCTGAGGACGT
1 ATTGAAGAGATCTAACCACTTTCGGGTAAATTGAAGATGCCAATGTTCCTTCTCTCTCAGGACGT
* *
1835107 CTGGTCAATC-TGCGAAATGACACTACTCATCTGC
66 CTGGTAAATCTTG-GAAATGACACTACTCATCCGC
* * * *
1835141 ATTGAAGAGATCTAACCACTTTCGGTTAAATTGAAGATGGCATTGTTTCTTCTCTCTCAGGACGT
1 ATTGAAGAGATCTAACCACTTTCGGGTAAATTGAAGATGCCAATGTTCCTTCTCTCTCAGGACGT
* * *
1835206 C-GAGTAAATCTTGGAAATGTCACTGCTCATCCGT
66 CTG-GTAAATCTTGGAAATGACACTACTCATCCGC
* * *
1835240 ATTGAAGATATCTATCCTCTTTCGGGT
1 ATTGAAGAGATCTAACCACTTTCGGGT
1835267 GATGACACTG
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
98 1 0.01
99 102 0.97
100 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (99 bp):
ATTGAAGAGATCTAACCACTTTCGGGTAAATTGAAGATGCCAATGTTCCTTCTCTCTCAGGACGT
CTGGTAAATCTTGGAAATGACACTACTCATCCGC
Found at i:1835360 original size:53 final size:53
Alignment explanation
Indices: 1835266--1835366 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
1835256 CTCTTTCGGG
** *
1835266 TGATGACACTGTTCCTTCTCTCTGAGGATGTCAAGTCAATCTGGAGATAATTT
1 TGATGACACTGTTCCTTCTCTCTGAGGAAATCAAGTAAATCTGGAGATAATTT
* **
1835319 TGATGACATTGTTCCTTCTCTCTGAGGAAATCGGGTAAATCTGGAGAT
1 TGATGACACTGTTCCTTCTCTCTGAGGAAATCAAGTAAATCTGGAGAT
1835367 GAAACTGCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (53 bp):
TGATGACACTGTTCCTTCTCTCTGAGGAAATCAAGTAAATCTGGAGATAATTT
Found at i:1842004 original size:18 final size:18
Alignment explanation
Indices: 1841983--1842028 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1841973 GAAGTTGTTC
*
1841983 GAAAGAAAAAGAGAGAGA-
1 GAAAGAAAAA-AGAGACAT
1842001 GAAA-AAAAAAGAGACAT
1 GAAAGAAAAAAGAGACAT
1842018 GAAAGAAAAAA
1 GAAAGAAAAAA
1842029 TGGAAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 9 0.36
18 10 0.40
ACGTcount: A:0.72, C:0.02, G:0.24, T:0.02
Consensus pattern (18 bp):
GAAAGAAAAAAGAGACAT
Found at i:1849287 original size:27 final size:27
Alignment explanation
Indices: 1849256--1849321 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
1849246 AGATGTCAAA
*
1849256 AATCTATAATTCCTGAAGAATTAAAAT
1 AATCTATAATTCCTGAAGAATTAAAAG
* *
1849283 AATCTATATTTCCTTAAGAATTAAAAG
1 AATCTATAATTCCTGAAGAATTAAAAG
1849310 AATCTATAATTC
1 AATCTATAATTC
1849322 AATCGATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (27 bp):
AATCTATAATTCCTGAAGAATTAAAAG
Found at i:1857705 original size:41 final size:41
Alignment explanation
Indices: 1857625--1857705 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
1857615 TCACAATTCA
*
1857625 ATTCAATTCAATTCAATCATGACAACATGCAATAGTTCACC
1 ATTCAATTCAATTCAATCATGACAACATGCAATACTTCACC
* * * * *
1857666 ATTCGATTTAATTCAATCATGGCACCATGTAATACTTCAC
1 ATTCAATTCAATTCAATCATGACAACATGCAATACTTCAC
1857706 TAGTCAAATT
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:0.23, G:0.09, T:0.32
Consensus pattern (41 bp):
ATTCAATTCAATTCAATCATGACAACATGCAATACTTCACC
Found at i:1857772 original size:41 final size:41
Alignment explanation
Indices: 1857654--1857991 Score: 408
Period size: 41 Copynumber: 8.3 Consensus size: 41
1857644 TGACAACATG
* * * * * * * *
1857654 CAATAGTTCACCATTCGATTTAATTCAATCATGGCACCATG
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* * * * * * *
1857695 TAATACTTCACTAGTCAAATTGATTCGGTCAAGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* * *
1857736 CAATAATTTACCATTCATCTTGATTCAATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* * *
1857777 CAATAATTCACCAATCAACTTGATTCGATCATTGTATCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* *
1857818 C-ATTATTCACCATTTAACTTGATTCGATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
*
1857858 CAATAATTCACCATTCAACTTGATTCAATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* * *
1857899 TAATAATTAACCATTCAACTTCATTCGATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
**
1857940 CAATAATTCACCATTCAACTTGATTAAATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
1857981 CAATAATTCAC
1 CAATAATTCAC
1857992 AAACCAATTC
Statistics
Matches: 250, Mismatches: 46, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
40 35 0.14
41 215 0.86
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (41 bp):
CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
Found at i:1858113 original size:41 final size:41
Alignment explanation
Indices: 1858052--1858346 Score: 364
Period size: 41 Copynumber: 7.2 Consensus size: 41
1858042 ATGCAATAGC
* *
1858052 TAATTTACCAATT-AACTTGATTCGATCATGGTAGCATACAT
1 TAATTCACC-ATTCAACTTGATTCGATCATGGTAGCATACAA
* * * *
1858093 TAATTCA-CTTCTCAAGTTGATTTGATCATGTTAGCATACAA
1 TAATTCACCAT-TCAACTTGATTCGATCATGGTAGCATACAA
* *
1858134 TAATTCACCATTCAACTTGATTTGATCATGGTAGAATACAA
1 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
* *
1858175 TAATTCACCAATT-AACTTGAAGT-GATCATGGTAGCATACAT
1 TAATTCACC-ATTCAACTTG-ATTCGATCATGGTAGCATACAA
* *
1858216 TAATTCACCATTCGACTTGATTCAATCATGGTAGCATACAA
1 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
1858257 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
1 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
* * * * * *
1858298 TAATTCACCATTGAACATGATTTGATCATGGTGGAAAACAA
1 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
1858339 TAATTCAC
1 TAATTCAC
1858347 AAACCAATTG
Statistics
Matches: 222, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.00
40 7 0.03
41 207 0.93
42 7 0.03
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (41 bp):
TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
Found at i:1858387 original size:123 final size:123
Alignment explanation
Indices: 1858127--1858375 Score: 306
Period size: 123 Copynumber: 2.0 Consensus size: 123
1858117 ATCATGTTAG
* *
1858127 CATACAATAATTCACCATTCAACTTGATTTGATCATGGTAGAATACAATAATTCACCAATTAACT
1 CATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGAATACAATAATTCACCAATTAACA
* * * ** * * * * *
1858192 TGAAGTGATCATGGTAGCATACATTAATTCACCATTCGACTTGATTCAATCATGGTAG
66 TGAAGTGATCATGGTAGAAAACAATAATTCACCAAACCAATTGATTCAATCATAGAAA
*
1858250 CATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCACC-ATTGAAC
1 CATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGAATACAATAATTCACCAATT-AAC
** *
1858314 ATGATTTGATCATGGTGGAAAACAATAATTCA-CAAACCAATTGAATT-AAGTCATAGAAA
65 ATGAAGTGATCATGGTAGAAAACAATAATTCACCAAACCAATTG-ATTCAA-TCATAGAAA
1858373 CAT
1 CAT
1858376 GTATTAATTC
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
122 12 0.11
123 95 0.89
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (123 bp):
CATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGAATACAATAATTCACCAATTAACA
TGAAGTGATCATGGTAGAAAACAATAATTCACCAAACCAATTGATTCAATCATAGAAA
Found at i:1866463 original size:41 final size:41
Alignment explanation
Indices: 1866371--1866727 Score: 315
Period size: 41 Copynumber: 8.7 Consensus size: 41
1866361 TCACAATTCA
* * * * **
1866371 ATTCAATCATGACAACATACAATAGTTCACCATTCGA-TCCA
1 ATTCAATCATGGCAGCATACAATAATTCACCATTCAACT-TG
* * * * * *
1866412 ATTAAATCATGGCAGTATGCAATACTTCGCCATTCAAGTTG
1 ATTCAATCATGGCAGCATACAATAATTCACCATTCAACTTG
* * *
1866453 ATTCAGTCATGGTAGCATACAATAATTCACCATTTAACTTG
1 ATTCAATCATGGCAGCATACAATAATTCACCATTCAACTTG
* * * * *
1866494 ATTTAATCATGGTAACATACAATAATTCAACAATCAACTTG
1 ATTCAATCATGGCAGCATACAATAATTCACCATTCAACTTG
* * * *
1866535 ATTCGATCATGGTAGCATACATTAATTCACTATTCAACTTG
1 ATTCAATCATGGCAGCATACAATAATTCACCATTCAACTTG
* *
1866576 ATTCGATCATGGTAGCATACAATAA-TCAACCATTCAACTTG
1 ATTCAATCATGGCAGCATACAATAATTC-ACCATTCAACTTG
* * * *
1866617 GTTCGATCATGGTAGCATACAATAATTCACCATTCAGCTTG
1 ATTCAATCATGGCAGCATACAATAATTCACCATTCAACTTG
* * * * *
1866658 ATTCGATCATGGTATC-TGACAATCATTAACCATTCAACTTG
1 ATTCAATCATGGCAGCAT-ACAATAATTCACCATTCAACTTG
** * *
1866699 ATTTGATCATGGTAGTATACAATAATTCA
1 ATTCAATCATGGCAGCATACAATAATTCA
1866728 AAAACCAATT
Statistics
Matches: 265, Mismatches: 46, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
40 3 0.01
41 258 0.97
42 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.32
Consensus pattern (41 bp):
ATTCAATCATGGCAGCATACAATAATTCACCATTCAACTTG
Found at i:1866502 original size:82 final size:82
Alignment explanation
Indices: 1866416--1866727 Score: 362
Period size: 82 Copynumber: 3.8 Consensus size: 82
1866406 GATCCAATTA
* * * * *
1866416 AATCATGGCAGTATGCAATACTTCGCCATTCAAGTTGATTC-AGTCATGGTAGCATACAATAATT
1 AATCATGGTAGCATACAATACTTCACCATTCAACTTGATTCGA-TCATGGTAGCATACAATAATT
* *
1866480 CACCATTTAACTTGATTT
65 CACCATTCAACTTGATTC
* * * * *
1866498 AATCATGGTAACATACAATAATTCAACAATCAACTTGATTCGATCATGGTAGCATACATTAATTC
1 AATCATGGTAGCATACAATACTTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAATTC
*
1866563 ACTATTCAACTTGATTC
66 ACCATTCAACTTGATTC
* * *
1866580 GATCATGGTAGCATACAATA-ATCAACCATTCAACTTGGTTCGATCATGGTAGCATACAATAATT
1 AATCATGGTAGCATACAATACTTC-ACCATTCAACTTGATTCGATCATGGTAGCATACAATAATT
*
1866644 CACCATTCAGCTTGATTC
65 CACCATTCAACTTGATTC
* * * * *
1866662 GATCATGGTATC-TGACAAT-CATTAACCATTCAACTTGATTTGATCATGGTAGTATACAATAAT
1 AATCATGGTAGCAT-ACAATAC-TTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAAT
1866725 TCA
64 TCA
1866728 AAAACCAATT
Statistics
Matches: 197, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
81 3 0.02
82 192 0.97
83 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (82 bp):
AATCATGGTAGCATACAATACTTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAATTC
ACCATTCAACTTGATTC
Found at i:1866546 original size:123 final size:123
Alignment explanation
Indices: 1866417--1866727 Score: 378
Period size: 123 Copynumber: 2.5 Consensus size: 123
1866407 ATCCAATTAA
* * *
1866417 ATCATGGCAGTATGCAATACTTCGCCATTCAAGTTGATTC-AGTCATGGTAGCATACAATAATTC
1 ATCATGGTAGTATGCAATACTTCACCATTCAACTTGATTCGA-TCATGGTAGCATACAATAATTC
* *
1866481 ACCATTTAACTTGATTTAATCATGGTAACATACAATAATTCAACAATCAACTTGATTCG
65 ACCATTCAACTTGATTCAATCATGGTAACATACAATAATTCAACAATCAACTTGATTCG
* * * * *
1866540 ATCATGGTAGCATACATTAATTCACTATTCAACTTGATTCGATCATGGTAGCATACAATAA-TCA
1 ATCATGGTAGTATGCAATACTTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAATTC-
* * * * * *
1866604 ACCATTCAACTTGGTTCGATCATGGTAGCATACAATAATTCACCATTCAGCTTGATTCG
65 ACCATTCAACTTGATTCAATCATGGTAACATACAATAATTCAACAATCAACTTGATTCG
* * * *
1866663 ATCATGGTA-TCTGACAAT-CATTAACCATTCAACTTGATTTGATCATGGTAGTATACAATAATT
1 ATCATGGTAGTATG-CAATAC-TTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAATT
1866726 CA
64 CA
1866728 AAAACCAATT
Statistics
Matches: 158, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
122 3 0.02
123 152 0.96
124 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (123 bp):
ATCATGGTAGTATGCAATACTTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCA
CCATTCAACTTGATTCAATCATGGTAACATACAATAATTCAACAATCAACTTGATTCG
Found at i:1876030 original size:51 final size:51
Alignment explanation
Indices: 1875933--1876158 Score: 277
Period size: 50 Copynumber: 4.6 Consensus size: 51
1875923 TTCTTTCAAG
*
1875933 AAAAAA-TGTAGCGCTTAACACATACTTA-ACTGGTGTAAGTAAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTATACTGGTGTAAGTAAATAAAAT
* * * * *
1875982 AAACAAGTCTAGCACTTAACACATACTTATACGGGTGTAAGTGAATAAAAC
1 AAAAAAGTGTAGCACTTAACACATACTTATACTGGTGTAAGTAAATAAAAT
* * * * * *
1876033 AAAAAAGTGTAGCACTTAGCACCTAC-TAAACTAGTGTAAGTGAATAACAT
1 AAAAAAGTGTAGCACTTAACACATACTTATACTGGTGTAAGTAAATAAAAT
* *
1876083 AAAAAAGTGTAGCACTTAACACATATTTATAATGGTGTAAGTAAAT-AAAT
1 AAAAAAGTGTAGCACTTAACACATACTTATACTGGTGTAAGTAAATAAAAT
1876133 ---AAAGTGTAGCACTTAACACATACTTA
1 AAAAAAGTGTAGCACTTAACACATACTTA
1876159 CACCAATGTA
Statistics
Matches: 150, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
47 25 0.17
49 5 0.03
50 65 0.43
51 55 0.37
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (51 bp):
AAAAAAGTGTAGCACTTAACACATACTTATACTGGTGTAAGTAAATAAAAT
Found at i:1876113 original size:101 final size:100
Alignment explanation
Indices: 1875933--1876156 Score: 283
Period size: 101 Copynumber: 2.3 Consensus size: 100
1875923 TTCTTTCAAG
* * * *
1875933 AAAAAATGTAGCGCTTAACACATACTTAACTGGTGTAAGTAAATAAAATAAACAAGTCTAGCACT
1 AAAAAATGTAGCACTTAACACATACTAAACTAGTGTAAGTAAATAAAATAAAAAAGTCTAGCACT
* *
1875998 TAACACATACTTATACGGGTGTAAGTGAATAAAAC
66 TAACACATACTTATAAGGGTGTAAGTAAATAAAAC
* * * * *
1876033 AAAAAAGTGTAGCACTTAGCACCTACTAAACTAGTGTAAGTGAATAACATAAAAAAGTGTAGCAC
1 AAAAAA-TGTAGCACTTAACACATACTAAACTAGTGTAAGTAAATAAAATAAAAAAGTCTAGCAC
* *
1876098 TTAACACATATTTATAATGGTGTAAGTAAAT--AA-
65 TTAACACATACTTATAAGGGTGTAAGTAAATAAAAC
* *
1876131 ATAAAGTGTAGCACTTAACACATACT
1 AAAAAATGTAGCACTTAACACATACT
1876157 TACACCAATG
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
97 18 0.17
98 4 0.04
99 2 0.02
100 6 0.06
101 76 0.72
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (100 bp):
AAAAAATGTAGCACTTAACACATACTAAACTAGTGTAAGTAAATAAAATAAAAAAGTCTAGCACT
TAACACATACTTATAAGGGTGTAAGTAAATAAAAC
Found at i:1891423 original size:22 final size:22
Alignment explanation
Indices: 1891393--1891474 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
1891383 TCATTTCACA
1891393 AAAGTGCCTTAGCACTGGTACT
1 AAAGTGCCTTAGCACTGGTACT
* * * *
1891415 ATAGTGCCTTGGCACT-GAATCG
1 AAAGTGCCTTAGCACTGGTA-CT
* * *
1891437 AAAGTGCATTTGCACTGATACT
1 AAAGTGCCTTAGCACTGGTACT
1891459 AAAGTGCCTTAGCACT
1 AAAGTGCCTTAGCACT
1891475 CGTGGCGTAT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
21 2 0.04
22 43 0.93
23 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (22 bp):
AAAGTGCCTTAGCACTGGTACT
Found at i:1892720 original size:21 final size:21
Alignment explanation
Indices: 1892674--1892749 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
1892664 TGTCACCCTG
*
1892674 AGTATTGATACT--GCAAGGGT
1 AGTATTGATACTCCGC-ATGGT
* *
1892694 AATATTGATACTCCGCTTGGT
1 AGTATTGATACTCCGCATGGT
* * *
1892715 AGTATTGATACTTCTCATGGC
1 AGTATTGATACTCCGCATGGT
1892736 AGTATTGATACTCC
1 AGTATTGATACTCC
1892750 TAGTCAAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 11 0.24
21 32 0.71
22 2 0.04
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (21 bp):
AGTATTGATACTCCGCATGGT
Found at i:1896435 original size:28 final size:28
Alignment explanation
Indices: 1896399--1896466 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1896389 CCAAATTTTC
1896399 TAGGATTTGGAGATTAT-AGTATAATTTA
1 TAGGATTTGGAGATTATGA-TATAATTTA
* * * *
1896427 TAGGTTTTGAAGTTTATGATGTAATTTA
1 TAGGATTTGGAGATTATGATATAATTTA
*
1896455 TAGGGTTTGGAG
1 TAGGATTTGGAG
1896467 TAAATTACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (28 bp):
TAGGATTTGGAGATTATGATATAATTTA
Found at i:1896703 original size:27 final size:28
Alignment explanation
Indices: 1896667--1896736 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
1896657 GAACAAACAA
*
1896667 TTATAGGATTTGGAGATTATGATATAAT
1 TTATAGGATTTGGAGATTATAATATAAT
* * *
1896695 TTATA-GATTTTGAAATTATAATGTAAT
1 TTATAGGATTTGGAGATTATAATATAAT
*
1896722 TTATAGGGTTTGGAG
1 TTATAGGATTTGGAG
1896737 TAAATTACAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.44
Consensus pattern (28 bp):
TTATAGGATTTGGAGATTATAATATAAT
Found at i:1896840 original size:279 final size:280
Alignment explanation
Indices: 1895821--1896908 Score: 1090
Period size: 279 Copynumber: 3.9 Consensus size: 280
1895811 GAAACGTTAA
* * * * * *
1895821 TGAATAAAAATTTATAGGATTTGGAGATTCTGATATAATTCAGT-GGGTTTGAAGTTTATGATGC
1 TGAACAAAAA-TTATAGGATTTGGAGATTATGATATAATTTA-TAGGTTTTGAAGTTTATAATGT
* ** * * * * **
1895885 AATTTATAGCGTTTCAAATAAATTACAAAAAATAGAGATAAATA-AGGGTAAATTTTTTATAAAA
64 AATTTATAGGGTTTGGAGTAAATTACAAAAAATA-AAATAAATATA-AGTCAATTTCATATAAAA
* * * * * * *
1895949 ATATAATTGTAATGATTAAATTAAATAAACATGAAATTATAAAGTGAAGTTTAAATAAATTAAAT
127 ATATAATTTTAAGGACTAAATTAAATAAACATGAAATTAAAAACTTAAATTTAAATAAATTAAAT
* * * * *** *
1896014 AACATGCATGAATAAAATAGAAATAATTGTAAAATATAATGTTGAAATTAATATCAACTTTGAC-
192 AACATGCATGGATCAAATAGAAACAATTGTAAAATGTAAAAATGAAATTAATATCAA-ATTGACT
* *
1896078 ----TGTATTCATTT-AGAAATTCGG
256 AAATTGCATTCATTTGACAAATT-GG
* * *
1896099 TGAACAAAAATTTATAGGATTTGTAGATTATGATATAATTTATAGGGTTTTCAAGTTTACAATGT
1 TGAACAAAAA-TTATAGGATTTGGAGATTATGATATAATTTATA-GGTTTTGAAGTTTATAATGT
* ** * ** * *
1896164 AATTTATAGGATTTATAGTAAATTACAAAAAAAAAGAAATAAATATGGGCCAATTTCAAATAAAA
64 AATTTATAGGGTTTGGAGTAAATTAC-AAAAAATA-AAATAAATATAAGTCAATTTCATATAAAA
** *
1896229 ATATAATTTTAAAAACTAAATTAAATAAACATGAAATTAATAAACTAAAATTTAAA-AGAATTAA
127 ATATAATTTTAAGGACTAAATTAAATAAACATGAAATTAA-AAACTTAAATTTAAATA-AATTAA
* * * * * *
1896293 ATAACCTGCATGGATTAAATAGAACCAATTATAAAATGTAAAGAA-AAAACTAATATCAAATATG
190 ATAACATGCATGGATCAAATAGAAACAATTGTAAAATGTAAA-AATGAAATTAATATCAAAT-TG
* *
1896357 CCTAAATTGCATTCATTTGACAAGTTGG
253 ACTAAATTGCATTCATTTGACAAATTGG
** * *
1896385 TGAACCAAATTTTCTAGGATTTGGAGATTAT-AGTATAATTTATAGGTTTTGAAGTTTATGATGT
1 TGAA-CAAAAATTATAGGATTTGGAGATTATGA-TATAATTTATAGGTTTTGAAGTTTATAATGT
* ** *
1896449 AATTTATAGGGTTTGGAGTAAATTAC-------AAAA-AAATATGAGTCAATTTCGGATTAAAAT
64 AATTTATAGGGTTTGGAGTAAATTACAAAAAATAAAATAAATATAAGTCAATTTCATATAAAAAT
* * * *
1896506 ATAATTTTAAGGACTAAATTAAATAAACATGAAACTATAAA-TTAAAATCTAAATAAATCAAATA
129 ATAATTTTAAGGACTAAATTAAATAAACATGAAATTAAAAACTT-AAATTTAAATAAATTAAATA
* * * * * *
1896570 ACATACATCGATCAAATATAGATAATTGT-AAATGTAAAAATGAAGTTAATATCAAATTGATCTA
193 ACATGCATGGATCAAATAGAAACAATTGTAAAATGTAAAAATGAAATTAATATCAAATTGA-CTA
*
1896634 AATTGCATTCATTTGA-AAATTTG
257 AATTGCATTCATTTGACAAATTGG
* *
1896657 -GAACAAACAATTATAGGATTTGGAGATTATGATATAATTTATAGATTTTGAA-ATTATAATGTA
1 TGAACAAA-AATTATAGGATTTGGAGATTATGATATAATTTATAGGTTTTGAAGTTTATAATGTA
*
1896720 ATTTATAGGGTTTGGAGTAAATTACAAAACATAACAATAAATATAAGTCAATTTCATATAAAAAT
65 ATTTATAGGGTTTGGAGTAAATTACAAAAAATAA-AATAAATATAAGTCAATTTCATATAAAAAT
* * *
1896785 ATAATCTTAAGGATTAAATTAAATAGACATGAAATTAAAAACTTAAATTTAAATAAATTAAATAA
129 ATAATTTTAAGGACTAAATTAAATAAACATGAAATTAAAAACTTAAATTTAAATAAATTAAATAA
** *
1896850 CATTTATGGATCAAATAGAAACAATTGTAAAATGTAAAGATGAAATTAATATCAAATTG
194 CATGCATGGATCAAATAGAAACAATTGTAAAATGTAAAAATGAAATTAATATCAAATTG
1896909 GATGTAAAGA
Statistics
Matches: 668, Mismatches: 109, Indels: 64
0.79 0.13 0.08
Matches are distributed among these distances:
270 38 0.06
271 41 0.06
272 10 0.01
273 42 0.06
274 39 0.06
275 57 0.09
276 3 0.00
277 4 0.01
278 40 0.06
279 136 0.20
280 96 0.14
281 67 0.10
285 41 0.06
286 45 0.07
287 9 0.01
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (280 bp):
TGAACAAAAATTATAGGATTTGGAGATTATGATATAATTTATAGGTTTTGAAGTTTATAATGTAA
TTTATAGGGTTTGGAGTAAATTACAAAAAATAAAATAAATATAAGTCAATTTCATATAAAAATAT
AATTTTAAGGACTAAATTAAATAAACATGAAATTAAAAACTTAAATTTAAATAAATTAAATAACA
TGCATGGATCAAATAGAAACAATTGTAAAATGTAAAAATGAAATTAATATCAAATTGACTAAATT
GCATTCATTTGACAAATTGG
Found at i:1896927 original size:28 final size:29
Alignment explanation
Indices: 1896881--1896943 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 29
1896871 CAATTGTAAA
*
1896881 ATGTAAAGATGAAATTAATATCAAATTGG
1 ATGTAAAGATGAAATTAATATCAAATTAG
1896910 ATGTAAAGA-GAAATTAATATCAAATTAG
1 ATGTAAAGATGAAATTAATATCAAATTAG
1896938 AT-TAAA
1 ATGTAAA
1896944 TTACATTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
27 4 0.12
28 20 0.61
29 9 0.27
ACGTcount: A:0.52, C:0.03, G:0.14, T:0.30
Consensus pattern (29 bp):
ATGTAAAGATGAAATTAATATCAAATTAG
Found at i:1899270 original size:17 final size:16
Alignment explanation
Indices: 1899207--1899270 Score: 83
Period size: 16 Copynumber: 3.9 Consensus size: 16
1899197 ATCAATATTT
*
1899207 CTTAATATCGATACTC
1 CTTAGTATCGATACTC
1899223 CTTAGTATCGATACTC
1 CTTAGTATCGATACTC
1899239 CTTAGTATCGAATACTC
1 CTTAGTATCG-ATACTC
* *
1899256 CATGAGTATTGATAC
1 C-TTAGTATCGATAC
1899271 CAAAATAGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
16 25 0.58
17 11 0.26
18 7 0.16
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (16 bp):
CTTAGTATCGATACTC
Found at i:1899270 original size:34 final size:32
Alignment explanation
Indices: 1899207--1899270 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
1899197 ATCAATATTT
*
1899207 CTTAATATCGATACTCCTTAGTATCGATACTC
1 CTTAATATCGATACTCCTGAGTATCGATACTC
* *
1899239 CTTAGTATCGAATACTCCATGAGTATTGATAC
1 CTTAATATCG-ATACTCC-TGAGTATCGATAC
1899271 CAAAATAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 9 0.33
33 7 0.26
34 11 0.41
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (32 bp):
CTTAATATCGATACTCCTGAGTATCGATACTC
Found at i:1905548 original size:59 final size:59
Alignment explanation
Indices: 1905436--1905550 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
1905426 TCCAACAGCT
* * ** **
1905436 TCATATTCGGGATCGTACTAAAGGATAACTAGTGTATATGGTGGGCATGACCTTATATA
1 TCATATTCAGGATCGTACTAAAAGATAACTAGTACATATGGTGGGCACAACCTTATATA
* * * *
1905495 TCATTTTCAGGATTGTACTAAAAGATACCTAGTACATATGGTGGGTACAACCTTAT
1 TCATATTCAGGATCGTACTAAAAGATAACTAGTACATATGGTGGGCACAACCTTAT
1905551 GTGTCGTATT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (59 bp):
TCATATTCAGGATCGTACTAAAAGATAACTAGTACATATGGTGGGCACAACCTTATATA
Found at i:1906983 original size:406 final size:407
Alignment explanation
Indices: 1906231--1907048 Score: 1413
Period size: 406 Copynumber: 2.0 Consensus size: 407
1906221 ATTATTTTAT
*
1906231 AATAAATGTTAAAATTTGGAAACTTGTAAAGGAAATAAATATTACGAATTTGGGTTAAGAAACAT
1 AATAAATGTTAAAATTTGGAAACTTGTAAAGGAAATAAATATTACCAATTTGGGTTAAGAAACAT
* ** * *
1906296 TTTGAATATTTGATGTGATATCTTTGAATCGTAATAGTACACGTATATGGGTTAAGGGTGTTACA
66 TTTGAATATTTGATGTGATATCTTTGAATCGTAATAGTACACATATACAGGTTAAGGATATTACA
* *
1906361 TTTATTGGTATAAAAGCTGCAGGTTTAGCCGATTCTTGGACTAAATCGAGCTTGTTTTGAGTTAA
131 TTTATTGGTATAAAAGCTACAGGTTTAGCCGATTCTTGGACTAAATCGAGCTTGTTCTGAGTTAA
* *
1906426 AAAGTGTATACATGCCACTAGGATGTCATTGTTACTAATATGGTGTTTTTAAAGTCGATTGATGC
196 AAAGTGTATACATGCCACTAGGATGTCATTGTTACTAATATAGTGTTTGTAAAGTCGATTGATGC
** *
1906491 CACTCCTTACTCATGAAGGTGAATAAATATATGGTATGTATAAGATGTGTGTAATTGAGGTTTTG
261 CACTCCTTACTCATGAAGGTGAATAAATATATGGTATGTATAAGATGTGTGTAATCAAGGTTTTA
* *
1906556 AAGTAAATGACCAAGTAGGAGGTTT-AAATAAAGCTAAAACTGATAGTAATGTTGTTATCCTTCA
326 AAGTAAATGACCAAGTAGGAGGTTTAAAAAAAAGCTAAAACTGATAGTAATGTTGTTATCCTCCA
1906620 GTCTCATGTTTAGTCTA
391 GTCTCATGTTTAGTCTA
*
1906637 AATAAATGTTAAAATTTGGAAACTTGTAAAGGAAATAAATATTACCAATTTGGGTTAAGAAACGT
1 AATAAATGTTAAAATTTGGAAACTTGTAAAGGAAATAAATATTACCAATTTGGGTTAAGAAACAT
*
1906702 TTTGAATATTTGATGTGATATCTTTTAATCGTAATAGTACACATATACAGGTTAAGGATATTACA
66 TTTGAATATTTGATGTGATATCTTTGAATCGTAATAGTACACATATACAGGTTAAGGATATTACA
* *
1906767 TTTATTGGTATAAAAGTTACAGGTTTAGCCGATTCTTGGACTAAATGGAGCTTGTTCTGAGTTAA
131 TTTATTGGTATAAAAGCTACAGGTTTAGCCGATTCTTGGACTAAATCGAGCTTGTTCTGAGTTAA
* * *
1906832 AAAGTGTATACATGCCACTAGGATGTCTTTGTTACTGATCTAGTGTTTGTAAAGTCGATTGATGC
196 AAAGTGTATACATGCCACTAGGATGTCATTGTTACTAATATAGTGTTTGTAAAGTCGATTGATGC
* *
1906897 TACTCCTTACTCATGAAGGTGAATAAATATATGGTATGTATATGATGTGTGTAATCAAGGTTTTA
261 CACTCCTTACTCATGAAGGTGAATAAATATATGGTATGTATAAGATGTGTGTAATCAAGGTTTTA
1906962 AAGTAAATGACCAAGTAGGAGGTTTAAAAAAAAGCTAAAACTGATAGTAATGTTGTTATCCTCCA
326 AAGTAAATGACCAAGTAGGAGGTTTAAAAAAAAGCTAAAACTGATAGTAATGTTGTTATCCTCCA
1907027 GTCTCATGTTTAGTCTA
391 GTCTCATGTTTAGTCTA
1907044 AATAA
1 AATAA
1907049 GATGATGCAG
Statistics
Matches: 387, Mismatches: 24, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
406 328 0.85
407 59 0.15
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (407 bp):
AATAAATGTTAAAATTTGGAAACTTGTAAAGGAAATAAATATTACCAATTTGGGTTAAGAAACAT
TTTGAATATTTGATGTGATATCTTTGAATCGTAATAGTACACATATACAGGTTAAGGATATTACA
TTTATTGGTATAAAAGCTACAGGTTTAGCCGATTCTTGGACTAAATCGAGCTTGTTCTGAGTTAA
AAAGTGTATACATGCCACTAGGATGTCATTGTTACTAATATAGTGTTTGTAAAGTCGATTGATGC
CACTCCTTACTCATGAAGGTGAATAAATATATGGTATGTATAAGATGTGTGTAATCAAGGTTTTA
AAGTAAATGACCAAGTAGGAGGTTTAAAAAAAAGCTAAAACTGATAGTAATGTTGTTATCCTCCA
GTCTCATGTTTAGTCTA
Found at i:1909640 original size:29 final size:30
Alignment explanation
Indices: 1909603--1909668 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
1909593 AAAGTTTCGG
1909603 AAAAGTTT-AGAGACT-AAAG-GTAATTTTTC
1 AAAAGTTTAAG-GACTAAAAGTGTAA-TTTTC
*
1909632 AAAAGTTTAAGGACTAAAAGTTTAATTTTC
1 AAAAGTTTAAGGACTAAAAGTGTAATTTTC
1909662 AAAAGTT
1 AAAAGTT
1909669 AAGTGTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 12 0.36
30 18 0.55
31 3 0.09
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (30 bp):
AAAAGTTTAAGGACTAAAAGTGTAATTTTC
Found at i:1910803 original size:19 final size:20
Alignment explanation
Indices: 1910755--1910804 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1910745 TTGTTGTACT
1910755 TGTTGGAAATTAATATTAGAG
1 TGTT-GAAATTAATATTAGAG
*
1910776 TGTTGAAATTGATATTATGA-
1 TGTTGAAATTAATATTA-GAG
1910796 TG-TGAAATT
1 TGTTGAAATT
1910805 CGACCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 7 0.26
20 14 0.52
21 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (20 bp):
TGTTGAAATTAATATTAGAG
Found at i:1912551 original size:68 final size:68
Alignment explanation
Indices: 1912442--1912578 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
1912432 GTGGTTTTAT
1912442 ATTTGTTTTATAAGAATTAAATAAACATGATTAATAAAAAATAAATATTTTTAATGGAAATTGTA
1 ATTTGTTTTATAAGAATTAAATAAACATGATTAATAAAAAATAAATATTTTTAATGGAAATTGTA
1912507 AAA
66 AAA
1912510 ATTTGTTTTATAAGAATTAAATAAACATGATTAATAAAAAATAAATATTTTTAATGGAAATTGTA
1 ATTTGTTTTATAAGAATTAAATAAACATGATTAATAAAAAATAAATATTTTTAATGGAAATTGTA
1912575 AAA
66 AAA
1912578 A
1 A
1912579 ATAAAAATTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (68 bp):
ATTTGTTTTATAAGAATTAAATAAACATGATTAATAAAAAATAAATATTTTTAATGGAAATTGTA
AAA
Found at i:1912744 original size:13 final size:13
Alignment explanation
Indices: 1912726--1912755 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1912716 GAATCGGACT
1912726 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
1912739 TTTTAATTTTTAA
1 TTTTAAATTTTAA
1912752 TTTT
1 TTTT
1912756 CGTAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1919919 original size:53 final size:52
Alignment explanation
Indices: 1919842--1919949 Score: 148
Period size: 56 Copynumber: 2.0 Consensus size: 52
1919832 GTGGCCAAGT
1919842 ATCCAAGTGGTGGCCACATAGTGTCAGTTCC-AA-AAGAAAGAAAGGTTTGC
1 ATCCAAGTGGTGGCCACATAGTGTCAGTTCCGAAGAAGAAAGAAAGGTTTGC
* *
1919892 ATCCAGAGTGGGTGGCCAACATAGTGTCAGTTCCGAAGGAAGACAGGAAGGTTTGC
1 ATCCA-AGT-GGTGGCC-ACATAGTGTCAGTTCCGAA-GAAGAAAGAAAGGTTTGC
1919948 AT
1 AT
1919950 GTGCATCGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
50 5 0.10
51 3 0.06
52 7 0.14
53 16 0.32
54 2 0.04
56 17 0.34
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.21
Consensus pattern (52 bp):
ATCCAAGTGGTGGCCACATAGTGTCAGTTCCGAAGAAGAAAGAAAGGTTTGC
Found at i:1920787 original size:50 final size:51
Alignment explanation
Indices: 1920722--1920823 Score: 197
Period size: 50 Copynumber: 2.0 Consensus size: 51
1920712 ATGGGGTATG
1920722 TCCTGGGTCAACATGACGAGTCCGGGAAGAAGGAAAGATCCATATACTATT
1 TCCTGGGTCAACATGACGAGTCCGGGAAGAAGGAAAGATCCATATACTATT
1920773 TCCT-GGTCAACATGACGAGTCCGGGAAGAAGGAAAGATCCATATACTATT
1 TCCTGGGTCAACATGACGAGTCCGGGAAGAAGGAAAGATCCATATACTATT
1920823 T
1 T
1920824 AAGCAAGAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 47 0.92
51 4 0.08
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (51 bp):
TCCTGGGTCAACATGACGAGTCCGGGAAGAAGGAAAGATCCATATACTATT
Found at i:1922133 original size:59 final size:59
Alignment explanation
Indices: 1922066--1922184 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
1922056 AGCCTTTCTC
1922066 TATGTGGGGCATGGATGTTATCGGGCAATTCCATCTAAAGGCTTCGAATGGTCACCTTT
1 TATGTGGGGCATGGATGTTATCGGGCAATTCCATCTAAAGGCTTCGAATGGTCACCTTT
1922125 TATGTGGGGCATGGATGTTATCGGGCAATTCCATCTAAAGGCTTCGAATGGTCACCTTT
1 TATGTGGGGCATGGATGTTATCGGGCAATTCCATCTAAAGGCTTCGAATGGTCACCTTT
1922184 T
1 T
1922185 CATTCTCGTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (59 bp):
TATGTGGGGCATGGATGTTATCGGGCAATTCCATCTAAAGGCTTCGAATGGTCACCTTT
Found at i:1923051 original size:19 final size:17
Alignment explanation
Indices: 1923008--1923059 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
1922998 CCTAAGTCGG
* *
1923008 AAAAAAGGAAAAACAGCA
1 AAAAAAAGAAAAAAAG-A
1923026 AAAAAAAGAAGAAAAAGA
1 AAAAAAAGAA-AAAAAGA
1923044 AAATAAAAGAAAAAAA
1 AAA-AAAAGAAAAAAA
1923060 TGTTTAGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAGA
Found at i:1923133 original size:16 final size:17
Alignment explanation
Indices: 1923108--1923139 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1923098 AAAAATGGAA
1923108 AAAAATAGAAAAAGAAC
1 AAAAATAGAAAAAGAAC
1923125 AAAAA-AGAAAAAGAA
1 AAAAATAGAAAAAGAA
1923140 AAATAAGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAATAGAAAAAGAAC
Found at i:1924171 original size:43 final size:43
Alignment explanation
Indices: 1924123--1924244 Score: 181
Period size: 43 Copynumber: 2.8 Consensus size: 43
1924113 ACGAAGGGGC
*
1924123 CATCCACGATTTCAACTCTACGACAGAGGATATCGTACCCACA
1 CATCCACGATTTCAACTCTACGACGGAGGATATCGTACCCACA
* * *
1924166 CATCCACTATTTCAACTCTACGACGGAGTATATCATACCCACA
1 CATCCACGATTTCAACTCTACGACGGAGGATATCGTACCCACA
* * *
1924209 CATCCACGATTTTAACTCCACGATGGAGGATATCGT
1 CATCCACGATTTCAACTCTACGACGGAGGATATCGT
1924245 GCCATTTGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (43 bp):
CATCCACGATTTCAACTCTACGACGGAGGATATCGTACCCACA
Found at i:1924445 original size:85 final size:85
Alignment explanation
Indices: 1924298--1924457 Score: 284
Period size: 85 Copynumber: 1.9 Consensus size: 85
1924288 CAACAAACAA
* * *
1924298 CTTCCCAATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGT
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
1924363 TCAACTTCACGACGAAGGGG
66 TCAACTTCACGACGAAGGGG
*
1924383 CTTCCCAATTTCAGATCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
1924448 TCAACTTCAC
66 TCAACTTCAC
1924458 AGTGAAAGGG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (85 bp):
CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
TCAACTTCACGACGAAGGGG
Found at i:1924456 original size:43 final size:43
Alignment explanation
Indices: 1924322--1924458 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 43
1924312 AGCCAATTTT
*
1924322 AACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGTTC
1 AACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTC
* *** * ** *
1924365 AACTTCACGACGAAGGGGCTT---CCCAATTTCAGATC-CAATTTC
1 AACTTCACAACGAAGGATATTGGACTCAA-GACA-A-CACAAGTTC
*
1924407 AACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTC
1 AACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTC
1924450 AACTTCACA
1 AACTTCACA
1924459 GTGAAAGGGG
Statistics
Matches: 69, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
40 4 0.06
41 2 0.03
42 24 0.35
43 33 0.48
44 2 0.03
45 4 0.06
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.20
Consensus pattern (43 bp):
AACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTC
Found at i:1924797 original size:94 final size:94
Alignment explanation
Indices: 1924675--1924847 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 94
1924665 ATTTCAGAGC
* * * *
1924675 CAATTTCAACTTCCCAGCGAAGGATATTGGACCCAAGATAACACAAGCTTAACTCCACAAAAAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTCCACAAAAAAG
1924740 GGACGACTGATTGTTAACCAACAACTTTT
66 GGACGACTGATTGTTAACCAACAACTTTT
* * * * **
1924769 CAATTTCGACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTCCACAAAAAAG
*
1924834 GGGCGACTGATTGT
66 GGACGACTGATTGT
1924848 CAACAAATAA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
94 68 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (94 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTCCACAAAAAAG
GGACGACTGATTGTTAACCAACAACTTTT
Found at i:1925196 original size:152 final size:144
Alignment explanation
Indices: 1924904--1925200 Score: 481
Period size: 152 Copynumber: 2.0 Consensus size: 144
1924894 ATATTGGACT
1924904 CGAAGCAACAACTTACTTGAATTTCACACTTCACGACGATATCCAATTCCAGGCTCAACTTCACG
1 CGAAGCAACAACTTACTTGAATTTCACACTTCACGACGATATCCAATTCCAGGCTCAACTTCACG
1924969 ACGAAGGCCACCCGCGGTTTCAACTTCACACGACGAATGGATCGTGCACACAGCAGCATCCATCT
66 ACGAAGGCCACCCGCGGTTTCAACTT-ACACGACGAATGGATCGTGCACACAGCAGCATCCATCT
1925034 CTAGATTGGATTTCA
130 CTAGATTGGATTTCA
1925049 CGAAGCAATACAACTTACTTGAATTTCA-ACTTCACGACGAAGGATATCCAATTCCAGGCTCAAC
1 CGAAGC-A-ACAACTTACTTGAATTTCACACTTCACGAC----GATATCCAATTCCAGGCTCAAC
1925113 TTCACGACGAAGGAGCCACCCGCGGTTTCAACTT-CACGACGAATGGAATCGTGCACACAAGCAG
60 TTCACGACGAA-G-GCCACCCGCGGTTTCAACTTACACGACGAATGG-ATCGTGCACAC-AGCAG
1925177 CATCCATCTCTAGATTGGATTTCA
121 CATCCATCTCTAGATTGGATTTCA
1925201 GCTTCACGAC
Statistics
Matches: 142, Mismatches: 0, Indels: 13
0.92 0.00 0.08
Matches are distributed among these distances:
145 6 0.04
146 11 0.08
147 19 0.13
150 45 0.32
151 12 0.08
152 49 0.35
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.23
Consensus pattern (144 bp):
CGAAGCAACAACTTACTTGAATTTCACACTTCACGACGATATCCAATTCCAGGCTCAACTTCACG
ACGAAGGCCACCCGCGGTTTCAACTTACACGACGAATGGATCGTGCACACAGCAGCATCCATCTC
TAGATTGGATTTCA
Found at i:1925689 original size:83 final size:84
Alignment explanation
Indices: 1925525--1925682 Score: 194
Period size: 83 Copynumber: 1.9 Consensus size: 84
1925515 GATATCGTGT
* * * * *
1925525 TCATTTGCAACATAGCTCAAGGCAAGAAGAATTATTTTCCAACCAAAGACCTTTGAGTTCGACTA
1 TCATTTGCAACATAGATCAAGGCAAAAAGAACTATCTGCCAACCAAAGACCTTTGAGTTCGACTA
* *
1925590 CGCTCAGCTCCAAGGCACA
66 CACTCAACTCCAAGGCACA
* * *
1925609 TCATTTGCGACATAGATCAAGGCAAAAAG-GCTATCTGCCAACCAAAGACCTATT-AGTTCGATT
1 TCATTTGCAACATAGATCAAGGCAAAAAGAACTATCTGCCAACCAAAGACCT-TTGAGTTCGACT
*
1925672 ACATTCAACTC
65 ACACTCAACTC
1925683 AGAGGCAACT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
83 34 0.55
84 28 0.45
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (84 bp):
TCATTTGCAACATAGATCAAGGCAAAAAGAACTATCTGCCAACCAAAGACCTTTGAGTTCGACTA
CACTCAACTCCAAGGCACA
Found at i:1925996 original size:3 final size:3
Alignment explanation
Indices: 1925990--1926030 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
1925980 TATTATACTA
*
1925990 TAT TAT TAT TAT TTT TAT TAT TAT TAT TATT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
1926031 TATATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:1926007 original size:9 final size:9
Alignment explanation
Indices: 1925990--1926041 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
1925980 TATTATACTA
*
1925990 TATTATTAT
1 TATTTTTAT
1925999 TATTTTTAT
1 TATTTTTAT
*
1926008 TATTATTAT
1 TATTTTTAT
1926017 TATTTATTAT
1 TATTT-TTAT
*
1926027 TATTTATAT
1 TATTTTTAT
1926036 T-TTTTT
1 TATTTTT
1926042 GTAGGCTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
8 4 0.11
9 24 0.65
10 9 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTTTAT
Found at i:1926023 original size:28 final size:28
Alignment explanation
Indices: 1925979--1926036 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1925969 TAAAAACATT
*
1925979 TTATTATACTATATTATTATTATTTTTA
1 TTATTATACTATATTATTATTATTTATA
*
1926007 TTATTATTATTAT-TTATTATTATTTATA
1 TTATTA-TACTATATTATTATTATTTATA
1926035 TT
1 TT
1926037 TTTTTGTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TTATTATACTATATTATTATTATTTATA
Found at i:1931551 original size:54 final size:54
Alignment explanation
Indices: 1931460--1931963 Score: 641
Period size: 54 Copynumber: 9.3 Consensus size: 54
1931450 TTTTTAACAT
* **
1931460 ATAGTGTCGATACGGTAATTCACAAAC-CAATTGTGAATTACGTATGTTGCACAC
1 ATAGTGTCGATACGGTAATTCACAAACTC-ATTATGAATTACGTGGGTTGCACAC
* * * * *
1931514 ATAGTGTCGATACAGCAATTCATAAACTCATTATGAATTACTTAGGTTGCACAC
1 ATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
* ** * * *
1931568 ATAGTGCCGATACAATAATTCATAAACTCATTATGAATTACTTAGGTTGCACAC
1 ATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
** * * * * * *
1931622 ATAGTACCGATGCGGTAATTCGCAAAGTAATTATGAATTACTTAGGTTGCACAC
1 ATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
*
1931676 ATAGTATCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
1 ATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
* * *
1931730 ATATTGTTGATACGGTAATTCACAAACTCATTATGAATTACGTGGGATGCACAC
1 ATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
* * * *
1931784 ATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTATGTGGGTTACACAC
1 ATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
* * * *
1931838 ATAGTGCCAATATGGTAATTCACAAACTCCTTATGAATTACGTGGGTTGCACAC
1 ATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
* * * *
1931892 TTAGTGGCGGTACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCAGAC
1 ATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
*
1931946 ATAGTGTCAATACGGTAA
1 ATAGTGTCGATACGGTAA
1931964 ATATAACATA
Statistics
Matches: 399, Mismatches: 50, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
54 398 1.00
55 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (54 bp):
ATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACAC
Found at i:1932027 original size:15 final size:15
Alignment explanation
Indices: 1932003--1932039 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1931993 CTATGACTTT
*
1932003 CATAACATATAAGTA
1 CATAATATATAAGTA
1932018 CATAATATATAAGTA
1 CATAATATATAAGTA
1932033 CATAATA
1 CATAATA
1932040 AATGCACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (15 bp):
CATAATATATAAGTA
Found at i:1934316 original size:17 final size:18
Alignment explanation
Indices: 1934296--1934341 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
1934286 TTTAAGCTTT
1934296 TAGTTCATTTAGGGAA-G
1 TAGTTCATTTAGGGAATG
* * *
1934313 TAGTTCAATTA-TGAATT
1 TAGTTCATTTAGGGAATG
1934330 TAGTTCATTTAG
1 TAGTTCATTTAG
1934342 TAAGTTACGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (18 bp):
TAGTTCATTTAGGGAATG
Found at i:1934403 original size:17 final size:17
Alignment explanation
Indices: 1934383--1934428 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1934373 TTAATAAAGT
1934383 TAGTTCATTAATTTAAC
1 TAGTTCATTAATTTAAC
* *
1934400 TAGTTCAATCATTTAAC
1 TAGTTCATTAATTTAAC
*
1934417 TACTTCATTAAT
1 TAGTTCATTAAT
1934429 ATATCTAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (17 bp):
TAGTTCATTAATTTAAC
Found at i:1935123 original size:21 final size:22
Alignment explanation
Indices: 1935099--1935139 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1935089 GAAAAACAAA
1935099 ACATTTA-A-ATGTAATTCATGT
1 ACATTTACATATGT-ATTCATGT
1935120 ACATTTACATATGTATTCAT
1 ACATTTACATATGTATTCAT
1935140 TCACCTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (22 bp):
ACATTTACATATGTATTCATGT
Found at i:1936153 original size:195 final size:195
Alignment explanation
Indices: 1935821--1936212 Score: 748
Period size: 195 Copynumber: 2.0 Consensus size: 195
1935811 GCCTTTAGGA
1935821 ACATAATATTATATTAACTTAATTCATATATGGAACTTGACGTTGGATTTTCTGCTTAGAGAAGT
1 ACATAATATTATATTAACTTAATTCATATATGGAACTTGACGTTGGATTTTCTGCTTAGAGAAGT
*
1935886 ACGATTATAATCTAAGGGCATATATTGACCTGACATCCTATAACAGTTGACTGAACAGTCTAACC
66 ACGATTATAATCTAAGGGCATATATTGACCTGACATCCTACAACAGTTGACTGAACAGTCTAACC
1935951 AAAAGGAAAATATCAACCTAAGCTATGATACCACTAAATGTAACTCCCTCAGACCGATACAAGTG
131 AAAAGGAAAATATCAACCTAAGCTATGATACCACTAAATGTAACTCCCTCAGACCGATACAAGTG
* *
1936016 ACATAATATTATATTAACTTAATTCATATATGGGACTTGATGTTGGATTTTCTGCTTAGAGAAGT
1 ACATAATATTATATTAACTTAATTCATATATGGAACTTGACGTTGGATTTTCTGCTTAGAGAAGT
*
1936081 ACGATTATAATCTAAGGGCATATATTGACCTGACGTCCTACAACAGTTGACTGAACAGTCTAACC
66 ACGATTATAATCTAAGGGCATATATTGACCTGACATCCTACAACAGTTGACTGAACAGTCTAACC
1936146 AAAAGGAAAATATCAACCTAAGCTATGATACCACTAAATGTAACTCCCTCAGACCGATACAAGTG
131 AAAAGGAAAATATCAACCTAAGCTATGATACCACTAAATGTAACTCCCTCAGACCGATACAAGTG
1936211 AC
1 AC
1936213 TCGATCTGAT
Statistics
Matches: 193, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
195 193 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (195 bp):
ACATAATATTATATTAACTTAATTCATATATGGAACTTGACGTTGGATTTTCTGCTTAGAGAAGT
ACGATTATAATCTAAGGGCATATATTGACCTGACATCCTACAACAGTTGACTGAACAGTCTAACC
AAAAGGAAAATATCAACCTAAGCTATGATACCACTAAATGTAACTCCCTCAGACCGATACAAGTG
Found at i:1941303 original size:133 final size:133
Alignment explanation
Indices: 1941062--1941319 Score: 435
Period size: 133 Copynumber: 1.9 Consensus size: 133
1941052 ACCAAAATAG
* **
1941062 ATATCAGTCAGTAAACTCGATCGACTGGTCAATAACATTCAAGCGAATAACCTTATTTCCTTCTC
1 ATATCAGTCAGCAAACTCGATCGAAAGGTCAATAACATTCAAGCGAATAACCTTATTTCCTTCTC
*
1941127 TGACAATGAAATCATGCCCGGGGTAGAGGTAGAGATAAGGTATTGTACATCACAACCCACCGAAA
66 TGACAATGAAATCATGCCCGGGGTAGAGGTAGAGATAAAGTATTGTACATCACAACCCACCGAAA
1941192 GAT
131 GAT
* * * * *
1941195 ATATCATTCAGCAAACTTGATCGAAAGGTCAATAATATTCAAGCGGATAACCTTATTTCCTTTTC
1 ATATCAGTCAGCAAACTCGATCGAAAGGTCAATAACATTCAAGCGAATAACCTTATTTCCTTCTC
1941260 TGACAATGAAATCATGCCCGGGGTAGAGGTAGAGATAAAGTATTGTACATCACAACCCAC
66 TGACAATGAAATCATGCCCGGGGTAGAGGTAGAGATAAAGTATTGTACATCACAACCCAC
1941320 TGTAAGGGGA
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
133 116 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (133 bp):
ATATCAGTCAGCAAACTCGATCGAAAGGTCAATAACATTCAAGCGAATAACCTTATTTCCTTCTC
TGACAATGAAATCATGCCCGGGGTAGAGGTAGAGATAAAGTATTGTACATCACAACCCACCGAAA
GAT
Found at i:1941984 original size:23 final size:23
Alignment explanation
Indices: 1941920--1941985 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
1941910 CATATATTTT
*
1941920 TCCCGAAGGACCGTGTAGAATTC
1 TCCCGAAGGACCGCGTAGAATTC
* * * * *
1941943 TCCTGAATGACCACATAGAATTG
1 TCCCGAAGGACCGCGTAGAATTC
*
1941966 TCCCGAAGGACTGCGTAGAA
1 TCCCGAAGGACCGCGTAGAA
1941986 CCCTCGACTC
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (23 bp):
TCCCGAAGGACCGCGTAGAATTC
Found at i:1953152 original size:24 final size:25
Alignment explanation
Indices: 1953125--1953171 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1953115 AAAACCAACA
1953125 AAGAAAAGTCAAACACTC-CAAAAG
1 AAGAAAAGTCAAACACTCACAAAAG
* *
1953149 AAGAAAAGTTAAGCACTCACAAA
1 AAGAAAAGTCAAACACTCACAAA
1953172 GGAGAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.57, C:0.19, G:0.13, T:0.11
Consensus pattern (25 bp):
AAGAAAAGTCAAACACTCACAAAAG
Found at i:1958191 original size:3 final size:3
Alignment explanation
Indices: 1958183--1958210 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1958173 TCAATTTAAT
1958183 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1958211 ATATCTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1961547 original size:45 final size:45
Alignment explanation
Indices: 1961494--1961707 Score: 299
Period size: 45 Copynumber: 4.8 Consensus size: 45
1961484 AACAAATAAA
*
1961494 CAAAATAATAATGGATATGGGTGCATTATAGGCATGAACGGATG-
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGC
* *
1961538 CAAACATAATAATGCATATGGGGGCATTATAGGCATAAACGGATGC
1 CAAA-ATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGC
* *
1961584 CGAAATAATAATGCATATGGGTGCATTATAGGCATGAATGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGC
* * **
1961629 TAAAATAATAATTCATAT-GGTGCATTATAGGCATGGAA-AAATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCAT-GAACGGATGC
*
1961673 CAAAATAATAATGCATATAGGTGCATTATAGGCAT
1 CAAAATAATAATGCATATGGGTGCATTATAGGCAT
1961708 AAAAGAATGC
Statistics
Matches: 152, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
44 40 0.26
45 109 0.72
46 3 0.02
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGC
Found at i:1964712 original size:21 final size:21
Alignment explanation
Indices: 1964686--1964729 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1964676 AAAAACTCAT
1964686 GTTGTTTACTATCGGAGGTTA
1 GTTGTTTACTATCGGAGGTTA
1964707 GTTGTTTACTATCGGAGGTTA
1 GTTGTTTACTATCGGAGGTTA
1964728 GT
1 GT
1964730 AAAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.30, T:0.43
Consensus pattern (21 bp):
GTTGTTTACTATCGGAGGTTA
Found at i:1966816 original size:45 final size:45
Alignment explanation
Indices: 1966764--1966981 Score: 346
Period size: 45 Copynumber: 4.8 Consensus size: 45
1966754 ATGAATGAAC
* * *
1966764 AAATAATAATGCATATGGGTGCATTACAGGCATGAACGAATGCCA
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCA
* * *
1966809 AAGTAATAATGCATATGGGTGCATTATAGCCATGAACGGATGCCA
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCA
**
1966854 AAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATTTCA
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCA
* *
1966899 AAATAATAATGAATATGGGTGCATTATAGGAATGAAAGGATGCCA
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCA
1966944 AAATAATAATGCATATGGGTGCATTATAGGCATGAAAG
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAAAG
1966982 AATGTCATAA
Statistics
Matches: 158, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 158 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.25
Consensus pattern (45 bp):
AAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCA
Found at i:1967066 original size:49 final size:47
Alignment explanation
Indices: 1966963--1967087 Score: 135
Period size: 49 Copynumber: 2.6 Consensus size: 47
1966953 TGCATATGGG
* * *
1966963 TGCATTATAGGCATGAAAGAATGTCATAACTAAAAATGCATGAAATGA
1 TGCATTA-AGGCATGAAAGGATGCCATAACTAAAAAAGCATGAAATGA
* * *
1967011 TACATTAAGGCATAAAAGGATGCCATAATTAAAAAAAAGCATGAACAT-A
1 TGCATTAAGGCATGAAAGGATGCCATAACT--AAAAAAGCATGAA-ATGA
* *
1967060 TGCATTAAGGCATGATAGGATACCATAA
1 TGCATTAAGGCATGAAAGGATGCCATAA
1967088 ATGAAATTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
47 19 0.30
48 6 0.09
49 37 0.58
50 2 0.03
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (47 bp):
TGCATTAAGGCATGAAAGGATGCCATAACTAAAAAAGCATGAAATGA
Found at i:1969483 original size:2 final size:2
Alignment explanation
Indices: 1969476--1969520 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1969466 TGTCAGAAAG
1969476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1969518 AT A
1 AT A
1969521 ACTTTTATGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1971698 original size:19 final size:21
Alignment explanation
Indices: 1971674--1971728 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
1971664 TGCATAAATG
1971674 GTATCGGTACCATG-AT-GGA
1 GTATCGGTACCATGTATAGGA
*
1971693 GTATCGGTACCATAGTATAGTA
1 GTATCGGTACCAT-GTATAGGA
*
1971715 GTATCGATACCATG
1 GTATCGGTACCATG
1971729 GTAGTGGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 13 0.42
20 1 0.03
21 3 0.10
22 14 0.45
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (21 bp):
GTATCGGTACCATGTATAGGA
Found at i:1972204 original size:45 final size:45
Alignment explanation
Indices: 1972154--1972369 Score: 342
Period size: 45 Copynumber: 4.8 Consensus size: 45
1972144 ATGAATGAAT
1972154 AAATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGCCA
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGCCA
* * * *
1972199 AAATAATAATGCATATGAGTGCAATATTGGCATGAATGGATGCCA
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGCCA
* * *
1972244 AAATAATAATACATATGTGTGCATTATAGGCTTGAACGGATGCCA
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGCCA
* *
1972289 AAATAATAATGCATATGGGTGCATTATAGGCATTAAAGGATGCCA
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGCCA
*
1972334 AAATAATAATGCATATGGGTACATTATAGGCATGAA
1 AAATAATAATGCATATGGGTGCATTATAGGCATGAA
1972370 AGAATTACAT
Statistics
Matches: 154, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 154 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.27
Consensus pattern (45 bp):
AAATAATAATGCATATGGGTGCATTATAGGCATGAACGGATGCCA
Found at i:1976670 original size:2 final size:2
Alignment explanation
Indices: 1976663--1976695 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1976653 TCTATTAATT
1976663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1976696 TTATTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1977049 original size:12 final size:11
Alignment explanation
Indices: 1977024--1977097 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
1977014 ACGACTTAAG
1977024 ATAATAATAAA
1 ATAATAATAAA
1977035 ATAATAATGAAA
1 ATAATAAT-AAA
1977047 ATAATAATTTAAA
1 ATAATAA--TAAA
*
1977060 CATATATCA-AAA
1 -ATA-ATAATAAA
1977072 ATAATAATAAA
1 ATAATAATAAA
* *
1977083 ACAA-AACAAA
1 ATAATAATAAA
1977093 ATAAT
1 ATAAT
1977098 CAAAATCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
10 11 0.22
11 17 0.33
12 13 0.25
13 3 0.06
14 4 0.08
15 3 0.06
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:1977152 original size:17 final size:17
Alignment explanation
Indices: 1977117--1977164 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
1977107 AATAAAAGAA
*
1977117 ATTAAAA-GCAATA-AT
1 ATTAAAATGCAAAATAT
1977132 ATTAAAATGCAAAATAT
1 ATTAAAATGCAAAATAT
*
1977149 ATT-AAATGAAAAATAT
1 ATTAAAATGCAAAATAT
1977165 CAAACTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 17 0.59
17 5 0.17
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29
Consensus pattern (17 bp):
ATTAAAATGCAAAATAT
Found at i:1977615 original size:29 final size:27
Alignment explanation
Indices: 1977582--1977670 Score: 128
Period size: 27 Copynumber: 3.3 Consensus size: 27
1977572 CCTCTTTTCC
*
1977582 TTCTCTCTCTAAACTTGAGAA-GACATT
1 TTCTCTCTCTAAAATTGAGAAGGA-ATT
1977609 TTCTCTCTCTAAAATTGAGAAGGAATT
1 TTCTCTCTCTAAAATTGAGAAGGAATT
*
1977636 TTCTCTCTCT-AAATGAGAGAAGGAATT
1 TTCTCTCTCTAAAAT-TGAGAAGGAATT
1977663 TTCTCTCT
1 TTCTCTCT
1977671 GTCTTCTCTC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
26 4 0.07
27 52 0.90
28 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (27 bp):
TTCTCTCTCTAAAATTGAGAAGGAATT
Found at i:1978444 original size:3 final size:3
Alignment explanation
Indices: 1978438--1978505 Score: 75
Period size: 3 Copynumber: 22.0 Consensus size: 3
1978428 ATTATTTATT
* *
1978438 TAA TAA TAA T-A TGAT TAT TAA TAA TAA TATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
1978484 TATA TAA TAA TAA TAA AAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA
1978506 ATGGATGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
2 2 0.04
3 48 0.84
4 7 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1978480 original size:19 final size:19
Alignment explanation
Indices: 1978438--1978504 Score: 93
Period size: 19 Copynumber: 3.6 Consensus size: 19
1978428 ATTATTTATT
*
1978438 TAATAATAATATGAT--TAT
1 TAATAATAATAT-ATAATAA
1978456 TAATAATAATATATAATAA
1 TAATAATAATATATAATAA
1978475 TAATAATAATATATAATAA
1 TAATAATAATATATAATAA
*
1978494 TAATAAAAATA
1 TAATAATAATA
1978505 AATGGATGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
17 2 0.04
18 12 0.27
19 31 0.69
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (19 bp):
TAATAATAATATATAATAA
Found at i:1980171 original size:22 final size:22
Alignment explanation
Indices: 1980146--1980187 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1980136 CAATTCATTT
1980146 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
1980168 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
1980188 CCAGCACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:1985436 original size:22 final size:22
Alignment explanation
Indices: 1985408--1985461 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1985398 AATAAAGCTT
1985408 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1985430 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1985452 TCATCTTTGA
1 TCATCTTTGA
1985462 GGAATGTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1993242 original size:13 final size:14
Alignment explanation
Indices: 1993226--1993279 Score: 78
Period size: 13 Copynumber: 4.0 Consensus size: 14
1993216 AGTAAACAAC
1993226 AAATGCAAAATG-A
1 AAATGCAAAATGCA
1993239 AAATGCAAAGATGCA
1 AAATGCAAA-ATGCA
1993254 AAATGC-AAATGCA
1 AAATGCAAAATGCA
1993267 AAATGC-AAATGCA
1 AAATGCAAAATGCA
1993280 TGTATGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
13 27 0.69
14 5 0.13
15 7 0.18
ACGTcount: A:0.56, C:0.13, G:0.17, T:0.15
Consensus pattern (14 bp):
AAATGCAAAATGCA
Found at i:1993254 original size:21 final size:20
Alignment explanation
Indices: 1993226--1993275 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 20
1993216 AGTAAACAAC
1993226 AAATGCAAAATGAAAATGCA
1 AAATGCAAAATGAAAATGCA
*
1993246 AAGATGCAAAATGCAAATGCA
1 AA-ATGCAAAATGAAAATGCA
1993267 AAATGCAAA
1 AAATGCAAA
1993276 TGCATGTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (20 bp):
AAATGCAAAATGAAAATGCA
Found at i:1993261 original size:7 final size:7
Alignment explanation
Indices: 1993226--1993279 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 7
1993216 AGTAAACAAC
1993226 AAATGCA
1 AAATGCA
1993233 AAATG-A
1 AAATGCA
1993239 AAATGCA
1 AAATGCA
1993246 AAGATGCA
1 AA-ATGCA
1993254 AAATGC-
1 AAATGCA
1993260 AAATGCA
1 AAATGCA
1993267 AAATGC-
1 AAATGCA
1993273 AAATGCA
1 AAATGCA
1993280 TGTATGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
6 18 0.42
7 18 0.42
8 7 0.16
ACGTcount: A:0.56, C:0.13, G:0.17, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:1995608 original size:3 final size:3
Alignment explanation
Indices: 1995600--1995679 Score: 50
Period size: 3 Copynumber: 28.7 Consensus size: 3
1995590 ACGACATAAG
* *
1995600 ATA ATA ATA A-A ATA ATA ATA AAA ATA ATA AT- TTA A-A CATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA
* *
1995644 A-A A-A ATA ATA ATA A-A ACA A-A ACA A-A ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1995680 CAAAATAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
2 14 0.22
3 46 0.72
4 4 0.06
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:1995614 original size:11 final size:11
Alignment explanation
Indices: 1995595--1995678 Score: 82
Period size: 11 Copynumber: 7.4 Consensus size: 11
1995585 TTTATACGAC
*
1995595 ATAAGATAATA
1 ATAAAATAATA
1995606 ATAAAATAATA
1 ATAAAATAATA
1995617 ATAAAAATAATA
1 AT-AAAATAATA
1995629 ATTTAAACATATATA
1 A--TAAA-ATA-ATA
1995644 A-AAAATAATA
1 ATAAAATAATA
*
1995654 ATAAAACAA-A
1 ATAAAATAATA
*
1995664 ACAAAATAATA
1 ATAAAATAATA
1995675 ATAA
1 ATAA
1995679 TCAAAATAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
10 12 0.20
11 25 0.41
12 13 0.21
13 3 0.05
14 4 0.07
15 4 0.07
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:1995694 original size:24 final size:21
Alignment explanation
Indices: 1995600--1995678 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 21
1995590 ACGACATAAG
1995600 ATAATAATAAAATAATAATAAAA
1 ATAATAATAAAATAA-AA-AAAA
*
1995623 ATAATAATTTAAACATATATAAAAA
1 ATAATAA--TAAA-ATA-AAAAAAA
* *
1995648 ATAATAATAAAACAAAACAAA
1 ATAATAATAAAATAAAAAAAA
1995669 ATAATAATAA
1 ATAATAATAA
1995679 TCAAAATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 11 0.23
25 15 0.31
26 4 0.08
27 1 0.02
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (21 bp):
ATAATAATAAAATAAAAAAAA
Found at i:1995736 original size:15 final size:17
Alignment explanation
Indices: 1995693--1995730 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1995683 AATAAAAGAA
*
1995693 ATTAAAA-GCAATA-AT
1 ATTAAAATGCAAAATAT
1995708 ATTAAAATGCAAAATAT
1 ATTAAAATGCAAAATAT
1995725 ATTAAA
1 ATTAAA
1995731 TGAAAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 5 0.25
17 8 0.40
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (17 bp):
ATTAAAATGCAAAATAT
Found at i:1997074 original size:3 final size:3
Alignment explanation
Indices: 1997068--1997149 Score: 112
Period size: 3 Copynumber: 27.0 Consensus size: 3
1997058 ATTATTTATT
* *
1997068 TAA TAA TAA TAA TAT TAA TAA TAA TAA TATA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
1997114 TAT TAA TAA TAA TAA TATA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
1997150 ATGCATGAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.03
3 62 0.89
4 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1997110 original size:34 final size:34
Alignment explanation
Indices: 1997067--1997148 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
1997057 TATTATTTAT
1997067 TTAATAATAATAATATTAATAATAATAATATATA
1 TTAATAATAATAATATTAATAATAATAATATATA
1997101 TTAATAATAATAATATTAATAATAATAATATATA
1 TTAATAATAATAATATTAATAATAATAATATATA
*
1997135 ATAATAATAA-AATA
1 TTAATAATAATAATA
1997149 AATGCATGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 4 0.09
34 43 0.91
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
TTAATAATAATAATATTAATAATAATAATATATA
Found at i:2001353 original size:3 final size:3
Alignment explanation
Indices: 2001345--2001374 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2001335 ATGTAAAATA
2001345 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2001375 GTGGGATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2001368 original size:17 final size:16
Alignment explanation
Indices: 2001341--2001374 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
2001331 TGGGATGTAA
2001341 AATAAATAATAATAAT
1 AATAAATAATAATAAT
2001357 AATAATATAATAATAAT
1 AATAA-ATAATAATAAT
2001374 A
1 A
2001375 GTGGGATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAATAATAATAAT
Found at i:2001958 original size:2 final size:2
Alignment explanation
Indices: 2001951--2001985 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2001941 AATGGATTGT
2001951 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2001986 GTATGTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2002313 original size:2 final size:2
Alignment explanation
Indices: 2002306--2002332 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2002296 GTTTCAATTA
2002306 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2002333 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2002452 original size:14 final size:14
Alignment explanation
Indices: 2002435--2002462 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2002425 AAAATATTTT
2002435 AAATAATATATTAA
1 AAATAATATATTAA
2002449 AAATAATATATTAA
1 AAATAATATATTAA
2002463 TATTAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATAATATATTAA
Found at i:2004904 original size:23 final size:23
Alignment explanation
Indices: 2004870--2004939 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
2004860 GAGTCAAGGG
* *
2004870 TTCTACGCGGTCCTTTGGAACAA
1 TTCTACGCGGTCCTTCGGGACAA
* * *
2004893 TTCTACGTGGTCATTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAA
2004916 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
2004939 T
1 T
2004940 ACTATATGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:2004939 original size:46 final size:46
Alignment explanation
Indices: 2004870--2004966 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
2004860 GAGTCAAGGG
* * * *
2004870 TTCTACGCGGTCCTTTGGAACAATTCTACGTGGTCATTCGGGACAT
1 TTCTACGCGGTCCTTCGGAACAATACTACATGGTCATTCAGGACAT
* * * *
2004916 TTCTACGCGGTCCTTCGGGACAATACTATATGGTCCTTCATGACAT
1 TTCTACGCGGTCCTTCGGAACAATACTACATGGTCATTCAGGACAT
2004962 TTCTA
1 TTCTA
2004967 TGTGGCACTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCGGAACAATACTACATGGTCATTCAGGACAT
Found at i:2005146 original size:18 final size:17
Alignment explanation
Indices: 2005095--2005154 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
2005085 TATAATGAAC
*
2005095 TGTGATAATGATAATAA
1 TGTGATAATGATAATGA
*
2005112 TAGTGACAATGATAATGA
1 T-GTGATAATGATAATGA
2005130 TGTTGATAATGATAATGA
1 TG-TGATAATGATAATGA
2005148 TGATGAT
1 TG-TGAT
2005155 GCAGATGAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 2 0.05
18 35 0.95
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.35
Consensus pattern (17 bp):
TGTGATAATGATAATGA
Found at i:2005155 original size:6 final size:6
Alignment explanation
Indices: 2005097--2005154 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
2005087 TAATGAACTG
* * * **
2005097 TGATAA TGATAA TAATAG TGACAA TGATAA TGATGT TGATAA TGATAA
1 TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA
*
2005145 TGATGA TGAT
1 TGATAA TGAT
2005155 GCAGATGAGG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (6 bp):
TGATAA
Found at i:2009431 original size:23 final size:23
Alignment explanation
Indices: 2009400--2009501 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 23
2009390 AGGGTTCTAC
* *
2009400 GGTCATTCGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTATGT
* * * **
2009423 GGTCTTTCGGGACATTTCTGTAC
1 GGTCCTTCGGGACAATTCTATGT
* *
2009446 GGTCCTTCGGGATAATACTATGT
1 GGTCCTTCGGGACAATTCTATGT
* *
2009469 GGTCCTTCGAGACATTTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
2009492 GG-CACTTCGG
1 GGTC-CTTCGG
2009502 TGCAATTTAT
Statistics
Matches: 60, Mismatches: 18, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
22 1 0.02
23 59 0.98
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTATGT
Found at i:2009471 original size:46 final size:46
Alignment explanation
Indices: 2009397--2009487 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
2009387 TCGAGGGTTC
* * *
2009397 TACGGTCATTCGGGACAATTCTACGTGGTCTTTCGGGACATTTCTG
1 TACGGTCATTCGGGACAATACTACGTGGTCCTTCGAGACATTTCTG
* * *
2009443 TACGGTCCTTCGGGATAATACTATGTGGTCCTTCGAGACATTTCT
1 TACGGTCATTCGGGACAATACTACGTGGTCCTTCGAGACATTTCT
2009488 ATGTGGCACT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (46 bp):
TACGGTCATTCGGGACAATACTACGTGGTCCTTCGAGACATTTCTG
Found at i:2009630 original size:6 final size:6
Alignment explanation
Indices: 2009621--2009672 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
2009611 AAATGAACAG
* * * * **
2009621 TGATAA TGATAA TGACAG TGACAA AGATAA TGATGT TGATAA TGATAA
1 TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA
2009669 TGAT
1 TGAT
2009673 GATAATGCTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (6 bp):
TGATAA
Found at i:2009640 original size:18 final size:18
Alignment explanation
Indices: 2009612--2009671 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
2009602 GAAAAAATAA
2009612 AATGAACAGTGATAATGAT
1 AATG-ACAGTGATAATGAT
* *
2009631 AATGACAGTGACAAAGAT
1 AATGACAGTGATAATGAT
*
2009649 AATGA-TGTTGATAATGAT
1 AATGACAG-TGATAATGAT
2009667 AATGA
1 AATGA
2009672 TGATAATGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 1 0.03
18 30 0.86
19 4 0.11
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.27
Consensus pattern (18 bp):
AATGACAGTGATAATGAT
Found at i:2009707 original size:2 final size:2
Alignment explanation
Indices: 2009702--2009741 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2009692 TATATATATA
2009702 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2009742 CACTTATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2016176 original size:42 final size:41
Alignment explanation
Indices: 2016095--2016195 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
2016085 AGGTCTTATG
* * *
2016095 GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCAAAAGACTTACA
* * * *
2016136 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCAAAAGACTTACA
2016178 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
2016196 TAAGTTGTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCAAAAGACTTACA
Found at i:2016353 original size:216 final size:215
Alignment explanation
Indices: 2015639--2017700 Score: 3184
Period size: 216 Copynumber: 9.6 Consensus size: 215
2015629 TCTTGGTGAA
* * ** * * * * * * *
2015639 AAAACATCCTGCCCGAAGATCCCATGGATGACCCGAATGATTTATCATCTTGCTCGAGAGACTCA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
* ** * * * *
2015704 CAAATGATTCGAAGGATTTAAACATCATGCTAGAAAGACTTGCTAATGGCCCGAAGGACTTACTA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-TA
* * * * * * *
2015769 AG-TGTGAAATTGTGGAAATCGCATTCTTAGTTTCCAAAAATTTCATCATCTTCAAACATCATTT
130 AGTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
* * ** **
2015833 TCTCATTTTCATTTTCAAATG
195 TTTCATTTCCAAATTCATGTG
* *
2015854 AAAACAACCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTGTCATCTTGCTCAAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
* * * *
2015919 CATATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTTCTGATGGCCCAAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* * * * * * * *
2015984 ATTATGAAATTTTGAAAAATTGTATTCTTCGTTTTAAAAAAATCCATCATCTTAAAATATCA-TT
131 GTTGTGAAATTTTG-AAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
*
2016048 TTTCATTTTCAAATTCATGTG
195 TTTCATTTCCAAATTCATGTG
2016069 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
2016134 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* *
2016199 GTTGTGAAATATTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTTTTAAAACATCATTTT
131 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTT
2016264 TTTCATTTCCAAATTCATGTG
195 TTTCATTTCCAAATTCATGTG
* *
2016285 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGGTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
* *
2016350 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACATATTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* *
2016415 ATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
131 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTT
2016480 TTTCATTTCCAAATTCATGTG
195 TTTCATTTCCAAATTCATGTG
* * * *
2016501 AAAACATCTTACCCGAAGGTCTTATTGATGGCCCGAAAGACTTATCATCTTGCTAAAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
*
2016566 CAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
*
2016631 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTTTTAAAACATCATTTT
131 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA--TT
*
2016696 TTTTCATTTTCAAATTCATGTG
194 TTTTCATTTCCAAATTCATGTG
* *
2016718 AAAACATCCTACCCGAAGGTCTTATTGATGGCCCGAAGGACTTATCATCTTGCTAAAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
* * *
2016783 CAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGACATATTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* *
2016848 ATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
131 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
2016913 TTCCATTTCCAAATTCATGTG
196 TT-CATTTCCAAATTCATGTG
*
2016934 AAAACATCCTACCCGAAGGTCTTAT-GATGGCCCGAAGGACTTATCATCTTGCTAAAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
2016998 CAGATGACCCGAA-GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
2017062 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCAT-TT-TTAAAACATCATTTT
131 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
2017125 TTCATTTCCAAATTCATGTG
196 TTCATTTCCAAATTCATGTG
* * *
2017145 AAAACATCCTACCCGAAGGTCTTATTGATGGCCCGAATGACTTATCATCTTGCTAAAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
* *
2017210 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGCAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
2017275 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
131 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
*
2017340 TTCATTTCCCAATTCATGTG
196 TTCATTTCCAAATTCATGTG
* * * * * *
2017360 AAAACATCCTACCCGAAGTTATTATTGATGGCCCGAATGACTTATCATCTTGCTCTAAAGTCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
*
2017425 CAAATGACCCGAAGGA-TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* * *
2017489 ATTGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAGCATCATTTT
131 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
2017554 TTCATTTCCAAATTCATGTG
196 TTCATTTCCAAATTCATGTG
* *
2017574 AAAACATCCTACCCGAAGGTCTTATGAATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
* * * * *
2017639 CAGGTTACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTAATGATGGCCCGAAGGGCTTA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
2017701 CTGATGGGTT
Statistics
Matches: 1718, Mismatches: 118, Indels: 22
0.92 0.06 0.01
Matches are distributed among these distances:
211 43 0.03
212 68 0.04
213 97 0.06
214 336 0.20
215 478 0.28
216 488 0.28
217 208 0.12
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (215 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
TTCATTTCCAAATTCATGTG
Found at i:2016619 original size:42 final size:41
Alignment explanation
Indices: 2016521--2016627 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
2016511 ACCCGAAGGT
* * * *
2016521 CTTATTGATGGCCCGAAAGACTTATCATCTTGCTAAAAAGG
1 CTTACTGATGGCCCGAAAGACTTAGCATCATGCTAAAAAGA
* * * **
2016562 CTTACAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGA
1 CTTACTGATGGCCCGAAAGACTT-AGCATCATGCTAAAAAGA
*
2016604 CTTACTGATGGCCCGAAGGACTTA
1 CTTACTGATGGCCCGAAAGACTTA
2016628 TAAGTTGTGA
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 20 0.38
42 32 0.62
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (41 bp):
CTTACTGATGGCCCGAAAGACTTAGCATCATGCTAAAAAGA
Found at i:2017286 original size:427 final size:427
Alignment explanation
Indices: 2015639--2017700 Score: 3182
Period size: 427 Copynumber: 4.8 Consensus size: 427
2015629 TCTTGGTGAA
* * ** * * * * * * *
2015639 AAAACATCCTGCCCGAAGATCCCATGGATGACCCGAATGATTTATCATCTTGCTCGAGAGACTCA
1 AAAACATCCTACCCGAAGGTCTTAT-GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
* ** * * * *
2015704 CAAATGATTCGAAGGATTTAAACATCATGCTAGAAAGACTTGCTAATGGCCCGAAGGACTTACTA
65 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-TA
* * * * * * *
2015769 AG-TGTGAAATTGTGGAAATCGCATTCTTAGTTTCCAAAAATTTCATCATCTTCAAACATCATTT
129 AGTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCAT--TTTTAAAACATCATTT
* * ** ** * * *
2015833 TCTCATTTTCATTTTCAAATGAAAACAACCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTG
192 TTTCATTTCCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATTGATGGCCCGAAGGACTTA
* *
2015898 TCATCTTGCTCAAAAGGCTTACATATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTT-TC
257 TCATCTTGCTCAAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAT-
* * * * *
2015962 TGATGGCCCAAAGGACTTATAAATTATGAAATTTTGAAAAATTGTATTCTTCGTTTTAAAAAAAT
321 TGATGGCCCGAAGGACTTATAAATTGTGAAATTTTG-AAAATTGCATTCTTCGTTTTCAAAAATT
* * *
2016027 CCATCATCTTAAAATATCA-TTTTTCATTTTCAAATTCATGTG
385 CCATCTTCTTAAAACATCATTTTTTCATTTCCAAATTCATGTG
2016069 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTAT-GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
2016134 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
65 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
*
2016199 GTTGTGAAATATTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTTTTAAAACATCATTTT
130 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCA--TTTTTAAAACATCA-TTT
*
2016264 TTTCATTTCCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTA
192 TTTCATTTCCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATTGATGGCCCGAAGGACTTA
* * *
2016329 TCATCTTGCTCTAAAGGGTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACATATT
257 TCATCTTGCTCAAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATT
2016394 GATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCC
322 GATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCC
2016459 ATCTTCTTAAAACATCATTTTTTTCATTTCCAAATTCATGTG
387 ATCTTCTTAAAACATCA-TTTTTTCATTTCCAAATTCATGTG
* * *
2016501 AAAACATCTTACCCGAAGGTCTTATTGATGGCCCGAAAGACTTATCATCTTGCTAAAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTA-TGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
*
2016566 CAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
65 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
2016631 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTTTTAAAACATCATTTT
130 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCA--TTTTTAAAACATCA--TT
*
2016696 TTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATTGATGGCCCGAAGGACTT
191 TTTTCATTTCCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATTGATGGCCCGAAGGACTT
* * *
2016761 ATCATCTTGCTAAAAAGGCTTACAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGACATAT
256 ATCATCTTGCTCAAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAT
2016826 TGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTC
321 TGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTC
2016891 CATCTTCTTAAAACATCATTTTTTCCATTTCCAAATTCATGTG
386 CATCTTCTTAAAACATCATTTTTT-CATTTCCAAATTCATGTG
*
2016934 AAAACATCCTACCCGAAGGTCTTATGATGGCCCGAAGGACTTATCATCTTGCTAAAAAGGCTTAC
1 AAAACATCCTACCCGAAGGTCTTATGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTAC
2016999 AGATGACCCGAA-GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAG
66 AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAG
2017063 TTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATTTTTAAAACATCATTTTTTC
131 TTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATTTTTAAAACATCATTTTTTC
*
2017128 ATTTCCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATTGATGGCCCGAATGACTTATCAT
196 ATTTCCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATTGATGGCCCGAAGGACTTATCAT
*
2017193 CTTGCTAAAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATG
261 CTTGCTCAAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATG
* * *
2017258 GCCCGCAGGACTTATAAGTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCT
326 GCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCT
*
2017323 TCTTAAAACATCATTTTTTCATTTCCCAATTCATGTG
391 TCTTAAAACATCATTTTTTCATTTCCAAATTCATGTG
* * * * *
2017360 AAAACATCCTACCCGAAGTTATTATTGATGGCCCGAATGACTTATCATCTTGCTCTAAAGTCTTA
1 AAAACATCCTACCCGAAGGTCTTA-TGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTA
*
2017425 CAAATGACCCGAAGGA-TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
65 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* * *
2017489 ATTGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAGCATCATTTT
130 GTTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCAT-TT-TTAAAACATCATTTT
2017554 TTCATTTCCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTA-TGAATGGCCCGAAGGACTTA
193 TTCATTTCCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATTG-ATGGCCCGAAGGACTTA
* * * * *
2017618 TCATCTTGCTCTAAAGGCTTACAGGTTACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTAAT
257 TCATCTTGCTCAAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATT
*
2017683 GATGGCCCGAAGGGCTTA
322 GATGGCCCGAAGGACTTA
2017701 CTGATGGGTT
Statistics
Matches: 1530, Mismatches: 87, Indels: 31
0.93 0.05 0.02
Matches are distributed among these distances:
426 39 0.03
427 354 0.23
428 6 0.00
429 167 0.11
430 199 0.13
431 247 0.16
432 266 0.17
433 252 0.16
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (427 bp):
AAAACATCCTACCCGAAGGTCTTATGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTAC
AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAG
TTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATTTTTAAAACATCATTTTTTC
ATTTCCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATTGATGGCCCGAAGGACTTATCAT
CTTGCTCAAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATG
GCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCT
TCTTAAAACATCATTTTTTCATTTCCAAATTCATGTG
Found at i:2017843 original size:37 final size:37
Alignment explanation
Indices: 2017744--2017849 Score: 110
Period size: 37 Copynumber: 2.9 Consensus size: 37
2017734 CTCAAGGTGG
** * **
2017744 TGCTTCACTGC-TCTTCAGTGAAGGTTTAAGA-TGGTT
1 TGCTTCACT-CTTCTTTGGTGAAGGCTTAAGATTAATT
2017780 TGCTTCACTCTTCTTTGGTGAAGGCTTAAGATTAATT
1 TGCTTCACTCTTCTTTGGTGAAGGCTTAAGATTAATT
* *
2017817 TGCTTCACTCCTT-TTTTGTGATGGCTTAAGATT
1 TGCTTCACT-CTTCTTTGGTGAAGGCTTAAGATT
2017850 GACTTAGTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
35 1 0.02
36 26 0.43
37 30 0.50
38 3 0.05
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (37 bp):
TGCTTCACTCTTCTTTGGTGAAGGCTTAAGATTAATT
Found at i:2028813 original size:65 final size:65
Alignment explanation
Indices: 2028737--2028860 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 65
2028727 CTGTAAGTTC
* *
2028737 ACATTAAAAATGACTAATAATTGACTATCTTTAATTAAAAGAACTACTACCAAAATATATGCAAA
1 ACATTAAAAATGACTAATAATTGACAATCTTTAATTAAAAGAAATACTACCAAAATATATGCAAA
* * *
2028802 ACATTAAAAATGACTAATAATTGGCAATCTTTAATTACAAGAAATACTTCCAAAATATA
1 ACATTAAAAATGACTAATAATTGACAATCTTTAATTAAAAGAAATACTACCAAAATATA
2028861 CGTAAAACGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (65 bp):
ACATTAAAAATGACTAATAATTGACAATCTTTAATTAAAAGAAATACTACCAAAATATATGCAAA
Found at i:2035342 original size:90 final size:90
Alignment explanation
Indices: 2035189--2035361 Score: 319
Period size: 90 Copynumber: 1.9 Consensus size: 90
2035179 CCTAACACAC
2035189 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
2035254 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTTAATAAT
* *
2035279 CCTTTTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
2035344 ATTTAATTAATTGAAATT
66 ATTTAATTAATTGAAATT
2035362 AAGTATTCGG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTTAATAAT
Found at i:2038983 original size:74 final size:73
Alignment explanation
Indices: 2038862--2038999 Score: 197
Period size: 74 Copynumber: 1.9 Consensus size: 73
2038852 TAAATGACTA
* *
2038862 GGGGTATCGGTACATCTAAGGGGTATCGATACCCATAGGGCATTATGTTTTTCTCAGAGCCAAAT
1 GGGGTATCGGTACACCTAAGGGGTATCGATACCCATAGGGCAATATGTTTTTCTCAGAGCCAAAT
2038927 TTTGCATT
66 TTTGCATT
* * * *
2038935 GGGGTATCGGTAC-CCTATGAGGGGTATCGGTACCCTTTGGGCAATATGTTTTTCTCGGAGCCAA
1 GGGGTATCGGTACACCTA--AGGGGTATCGATACCCATAGGGCAATATGTTTTTCTCAGAGCCAA
2038999 A
64 A
2039000 ATTAACATAG
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
72 3 0.05
73 13 0.23
74 41 0.72
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (73 bp):
GGGGTATCGGTACACCTAAGGGGTATCGATACCCATAGGGCAATATGTTTTTCTCAGAGCCAAAT
TTTGCATT
Found at i:2043997 original size:21 final size:21
Alignment explanation
Indices: 2043971--2044012 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2043961 CCAGAATGGG
*
2043971 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
2043992 GGGAATTGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2044013 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:2044178 original size:34 final size:34
Alignment explanation
Indices: 2044140--2044206 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
2044130 AATATATACC
*
2044140 CGGGGAATCGATA-CCCTTGGGGGGAATCAGTTCT
1 CGGGGAATCGATACCCCCT-GGGGGAATCAGTTCT
*
2044174 CGGGGAATCGATACCCCCTGGGGGAATCTGTTC
1 CGGGGAATCGATACCCCCTGGGGGAATCAGTTC
2044207 CCCCTGGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.22
Consensus pattern (34 bp):
CGGGGAATCGATACCCCCTGGGGGAATCAGTTCT
Found at i:2044199 original size:19 final size:19
Alignment explanation
Indices: 2044175--2044233 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 19
2044165 ATCAGTTCTC
2044175 GGGGAATC-GATACCCCCTG
1 GGGGAATCTG-TACCCCCTG
*
2044194 GGGGAATCTGTTCCCCCTGGGG
1 GGGGAATCTGTACCCCCT---G
2044216 GGGGAATCTGTACCCCCT
1 GGGGAATCTGTACCCCCT
2044234 AGACAATCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 15 0.44
20 1 0.03
22 18 0.53
ACGTcount: A:0.15, C:0.31, G:0.34, T:0.20
Consensus pattern (19 bp):
GGGGAATCTGTACCCCCTG
Found at i:2047738 original size:15 final size:15
Alignment explanation
Indices: 2047710--2047773 Score: 58
Period size: 15 Copynumber: 4.0 Consensus size: 15
2047700 AACCATGCAG
2047710 GGGGAATCTG-TACCC
1 GGGGAATC-GATACCC
2047725 GGGGAATCGATACCTC
1 GGGGAATCGATACC-C
* *
2047741 TGGGGGGAATCTATTCCC
1 ---GGGGAATCGATACCC
2047759 GGGGAATCGATACCC
1 GGGGAATCGATACCC
2047774 CCTGGGGGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 1 0.03
15 25 0.62
16 1 0.03
18 1 0.03
19 12 0.30
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (15 bp):
GGGGAATCGATACCC
Found at i:2047793 original size:35 final size:34
Alignment explanation
Indices: 2047709--2047793 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
2047699 AAACCATGCA
* *
2047709 GGGGGAATCTGTACCCGGGGAATCGATACCTCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
*
2047743 GGGGGAATCTATTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCTG
*
2047778 GGGGGAATTTGTTCCC
1 GGGGGAATCTGTTCCC
2047794 CCTGGGGGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 26 0.58
35 19 0.42
ACGTcount: A:0.19, C:0.25, G:0.34, T:0.22
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:2047809 original size:24 final size:24
Alignment explanation
Indices: 2047777--2047822 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2047767 GATACCCCCT
* *
2047777 GGGGGGAATTTGTTCCCCCTGGGG
1 GGGGGGAATCTGTACCCCCTGGGG
2047801 GGGGGGAATCTGTACCCCCTGG
1 GGGGGGAATCTGTACCCCCTGG
2047823 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (24 bp):
GGGGGGAATCTGTACCCCCTGGGG
Found at i:2049439 original size:23 final size:23
Alignment explanation
Indices: 2049413--2049460 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2049403 ACCTTTTCGG
*
2049413 TGAAATGAATTAACTATTTTTCA
1 TGAAAAGAATTAACTATTTTTCA
* *
2049436 TGAAAAGACTTAATTATTTTTCA
1 TGAAAAGAATTAACTATTTTTCA
2049459 TG
1 TG
2049461 GATAGATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (23 bp):
TGAAAAGAATTAACTATTTTTCA
Found at i:2049830 original size:37 final size:37
Alignment explanation
Indices: 2049778--2049881 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
2049768 CTTTTCGTCA
*
2049778 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
* *
2049815 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
** * *
2049852 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
2049882 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
Found at i:2050585 original size:21 final size:21
Alignment explanation
Indices: 2050551--2050607 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2050541 CTATTTAGTA
*
2050551 TTTTATTATATTATACATACAT
1 TTTTA-TATTTTATACATACAT
* **
2050573 TTTTATATTTTATATATATTT
1 TTTTATATTTTATACATACAT
*
2050594 TTTTATTTTTTATA
1 TTTTATATTTTATA
2050608 TACTATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATATTTTATACATACAT
Found at i:2050601 original size:19 final size:19
Alignment explanation
Indices: 2050556--2050609 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
2050546 TAGTATTTTA
* * *
2050556 TTATATTATACATACATTT
1 TTATATTTTATATATATTT
2050575 TTATATTTTATATATATTT
1 TTATATTTTATATATATTT
* *
2050594 TTTTATTTTTTATATA
1 TTATATTTTATATATA
2050610 CTATTTATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATATTTTATATATATTT
Found at i:2050608 original size:21 final size:22
Alignment explanation
Indices: 2050572--2050615 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2050562 TATACATACA
2050572 TTTTTATATTTTATATA-TATT
1 TTTTTATATTTTATATACTATT
*
2050593 TTTTTATTTTTTATATACTATT
1 TTTTTATATTTTATATACTATT
2050615 T
1 T
2050616 ATTCATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTATATTTTATATACTATT
Found at i:2050737 original size:20 final size:19
Alignment explanation
Indices: 2050710--2050765 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2050700 TTTTATCTTC
2050710 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
2050729 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
2050749 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
2050766 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:2055065 original size:15 final size:14
Alignment explanation
Indices: 2055045--2055094 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2055035 AAAGGTCAAA
2055045 AACAAAAAGAAAAG
1 AACAAAAAGAAAAG
*
2055059 AAGCAAAAAGAAGA-
1 AA-CAAAAAGAAAAG
2055073 AACAAAAA-AGAAAG
1 AACAAAAAGA-AAAG
2055087 AACAAAAA
1 AACAAAAA
2055095 TCAAAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 1 0.03
13 8 0.26
14 12 0.39
15 10 0.32
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (14 bp):
AACAAAAAGAAAAG
Found at i:2056805 original size:106 final size:106
Alignment explanation
Indices: 2056681--2057616 Score: 1246
Period size: 106 Copynumber: 9.0 Consensus size: 106
2056671 GTGCCACTTG
* * * * *
2056681 AGACAACATAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAAATT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
2056746 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
2056787 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
2056852 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
2056893 AGACAACGA-AAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCCAATT
1 AGACAAC-ACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATT
*
2056957 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
65 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * *
2056999 AGACAACGCTAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* **
2057064 CAGAGCCAATTTTAACTTCACAGTGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* ** * *
2057105 AGACAACGCAAGTTCAACTTCATAACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* ** * * *
2057170 CGGAGATAATTTCAACTTCACAGCGAATGATATTGGACTCT
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
** * *
2057211 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAACAAACAACTTCTC-ATTT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
2057275 ---AGCCAATTTCAACTTCAGAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
2057313 AG--------A---C--CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
** * *
2057365 CAGAGCCAATTTCAACTTCACACAAAAAGGA-ATTGTACTCG
66 CAGAGCCAATTTCAACTTCACA-ACGAAGGATATTGGACTCC
* * * *
2057406 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCTACAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * * *
2057471 CGGAGCCAATTTCAACTTCGCAACAAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * *
2057512 AGACAACACAAGTTCAACTTCGCGACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTC
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
2057577 CAGAGCCAATTTCAACTTCACGAC-AGAGGATATTGGACTC
66 CAGAGCCAATTTCAACTTCACAACGA-AGGATATTGGACTC
2057617 AGAACAATGC
Statistics
Matches: 741, Mismatches: 67, Indels: 44
0.87 0.08 0.05
Matches are distributed among these distances:
89 41 0.06
90 4 0.01
91 1 0.00
93 28 0.04
94 7 0.01
101 1 0.00
102 34 0.05
104 1 0.00
105 12 0.02
106 611 0.82
107 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
Found at i:2058708 original size:14 final size:14
Alignment explanation
Indices: 2058668--2058717 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
2058658 TTTATTATTA
2058668 TTTTTTTTATCTATG
1 TTTTTTTTA-CTATG
2058683 TTTACTTATTTACTATG
1 TTT--TT-TTTACTATG
*
2058700 TTTTTTTTACTATA
1 TTTTTTTTACTATG
2058714 TTTT
1 TTTT
2058718 CCTAACGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 12 0.39
15 5 0.16
17 10 0.32
18 4 0.13
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.70
Consensus pattern (14 bp):
TTTTTTTTACTATG
Found at i:2058901 original size:22 final size:22
Alignment explanation
Indices: 2058817--2058902 Score: 77
Period size: 22 Copynumber: 3.8 Consensus size: 22
2058807 ATTTTTCATT
*
2058817 TATTTATTATTATTATTACTATTTA
1 TATTT-TTATTATT-TTA-TATATA
* *
2058842 GTA-TTTTATTATATTATACATA
1 -TATTTTTATTATTTTATATATA
*
2058864 CATTTTTA-TATTTTTATATATA
1 TATTTTTATTA-TTTTATATATA
2058886 TATTTTTATTATTTTAT
1 TATTTTTATTATTTTAT
2058903 TTACTATTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 3 0.06
22 31 0.62
23 5 0.10
24 7 0.14
25 2 0.04
26 2 0.04
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (22 bp):
TATTTTTATTATTTTATATATA
Found at i:2058929 original size:15 final size:15
Alignment explanation
Indices: 2058880--2058930 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2058870 TATATTTTTA
* *
2058880 TATATATATTTTTAT
1 TATATTTATTTTCAT
*
2058895 TAT-TTTATTTACTAT
1 TATATTTATTTTC-AT
2058910 T-TATTTATTTTCAT
1 TATATTTATTTTCAT
2058924 TATATTT
1 TATATTT
2058931 TAGTTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (15 bp):
TATATTTATTTTCAT
Found at i:2058932 original size:20 final size:20
Alignment explanation
Indices: 2058867--2058932 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
2058857 ATACATACAT
2058867 TTTTATATT-TTTATATATATA
1 TTTTATATTATTT-TAT-TATA
2058888 TTTT-TATTATTTTATT-TA
1 TTTTATATTATTTTATTATA
2058906 CTATTTAT-TTATTTTCATTATA
1 -T-TTTATATTATTTT-ATTATA
2058928 TTTTA
1 TTTTA
2058933 GTTTCTTTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 21 0.54
21 12 0.31
22 2 0.05
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATATTATTTTATTATA
Found at i:2059053 original size:21 final size:20
Alignment explanation
Indices: 2059016--2059069 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
2059006 TTATCTTATT
*
2059016 ATTTTATTTTATTCAATTTC
1 ATTTTATTTTATCCAATTTC
* *
2059036 ATTTTTTTTTCATCCAATTTT
1 ATTTTATTTT-ATCCAATTTC
2059057 ATTTTATTATTAT
1 ATTTTATT-TTAT
2059070 GTTTCATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 9 0.32
21 17 0.61
22 2 0.07
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTATTTTATCCAATTTC
Found at i:2059271 original size:70 final size:72
Alignment explanation
Indices: 2059170--2059313 Score: 274
Period size: 70 Copynumber: 2.0 Consensus size: 72
2059160 TAAACTCATT
2059170 AAGGGTAAGTAATTCGGATCAAATTTTACTTTTAAATTTAACTTGCAATTTTCTTAATCAAAGAC
1 AAGGGTAAGTAATTCGGATCAAATTTTACTTTTAAATTTAACTTGCAATTTTCTTAATCAAAGAC
2059235 AACTGGA
66 AACTGGA
2059242 AAGGGTAAGT-ATTCGGATC-AATTTTACTTTTAAATTTAACTTGCAATTTTCTTAATCAAAGAC
1 AAGGGTAAGTAATTCGGATCAAATTTTACTTTTAAATTTAACTTGCAATTTTCTTAATCAAAGAC
2059305 AACTGGA
66 AACTGGA
2059312 AA
1 AA
2059314 TTACGTAGTA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
70 53 0.74
71 9 0.12
72 10 0.14
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (72 bp):
AAGGGTAAGTAATTCGGATCAAATTTTACTTTTAAATTTAACTTGCAATTTTCTTAATCAAAGAC
AACTGGA
Found at i:2064743 original size:22 final size:23
Alignment explanation
Indices: 2064718--2064763 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2064708 TAAAATTTTG
2064718 TTTCAA-TTTAAAAACATTTACA
1 TTTCAACTTTAAAAACATTTACA
*
2064740 TTTCAACTTTAAAATCATTTACA
1 TTTCAACTTTAAAAACATTTACA
2064763 T
1 T
2064764 AAACACATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTCAACTTTAAAAACATTTACA
Found at i:2070381 original size:15 final size:16
Alignment explanation
Indices: 2070361--2070390 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2070351 TATCAACTAT
2070361 ATGCTCAT-CTCCATC
1 ATGCTCATCCTCCATC
2070376 ATGCTCATCCTCCAT
1 ATGCTCATCCTCCAT
2070391 GTGCTCTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.40, G:0.07, T:0.33
Consensus pattern (16 bp):
ATGCTCATCCTCCATC
Found at i:2072247 original size:21 final size:21
Alignment explanation
Indices: 2072223--2072272 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2072213 TCATCGAGAA
2072223 ATCAATCCTTTTGGTAAAGGG
1 ATCAATCCTTTTGGTAAAGGG
* *
2072244 ATCAATCATTTTTGTAAAGGG
1 ATCAATCCTTTTGGTAAAGGG
*
2072265 ATCGATCC
1 ATCAATCC
2072273 CAAACTCACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (21 bp):
ATCAATCCTTTTGGTAAAGGG
Done.