Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 6 of 91
Found at i:1796643 original size:28 final size:27
Alignment explanation
Indices: 1796594--1796648 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
1796584 ATGTAAACTG
1796594 TAGTTCTTGATTTAGTTGCTTTTTTCT
1 TAGTTCTTGATTTAGTTGCTTTTTTCT
*
1796621 TAGTTCTTTGATTTTGCTT-CTTTTTTCT
1 TAGTTC-TTGATTTAG-TTGCTTTTTTCT
1796649 GCTTACCAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 17 0.68
29 2 0.08
ACGTcount: A:0.09, C:0.13, G:0.13, T:0.65
Consensus pattern (27 bp):
TAGTTCTTGATTTAGTTGCTTTTTTCT
Found at i:1799955 original size:96 final size:96
Alignment explanation
Indices: 1799787--1799977 Score: 346
Period size: 96 Copynumber: 2.0 Consensus size: 96
1799777 TAAACAAAGT
*
1799787 AACAACCAAACAAATCCTAAATTGTTAGCACTCTATGTCTTGGTTTCCGAAACTTATGCTCTATG
1 AACAACCAAACAAATCCTAAATTGTTAGCACTCTATGTCTTGATTTCCGAAACTTATGCTCTATG
1799852 TTCTTATGAAATTTTCCTGTTCCACTTGGGA
66 TTCTTATGAAATTTTCCTGTTCCACTTGGGA
* *
1799883 AACAACCAAACAAATCCTAAATTGTTAGCACTCTATGTCTTGATTTCTGAAACTTATGCTTTATG
1 AACAACCAAACAAATCCTAAATTGTTAGCACTCTATGTCTTGATTTCCGAAACTTATGCTCTATG
*
1799948 TTTTTATGAAATTTTCCTGTTCCACTTGGG
66 TTCTTATGAAATTTTCCTGTTCCACTTGGG
1799978 TCTTGAATGA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (96 bp):
AACAACCAAACAAATCCTAAATTGTTAGCACTCTATGTCTTGATTTCCGAAACTTATGCTCTATG
TTCTTATGAAATTTTCCTGTTCCACTTGGGA
Found at i:1803620 original size:11 final size:11
Alignment explanation
Indices: 1803586--1803632 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
1803576 TATTTTATAT
*
1803586 AAAAAATTA-A
1 AAAAAATAATA
1803596 AAAAAATCAATA
1 AAAAAAT-AATA
*
1803608 AAAAAATAGTA
1 AAAAAATAATA
1803619 AAAAAATAA-A
1 AAAAAATAATA
1803629 AAAA
1 AAAA
1803633 TACGTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 12 0.38
11 12 0.38
12 8 0.25
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:1804450 original size:25 final size:24
Alignment explanation
Indices: 1804422--1804470 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1804412 AAAATAAAGA
1804422 TAAAAAAATCTTAAATCAATTAAAT
1 TAAAAAAATCTTAAAT-AATTAAAT
* *
1804447 TAAAAATATCTTAAATACTTAAAT
1 TAAAAAAATCTTAAATAATTAAAT
1804471 ATAAGCAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
TAAAAAAATCTTAAATAATTAAAT
Found at i:1814520 original size:27 final size:27
Alignment explanation
Indices: 1814490--1814545 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1814480 AAGGAAGTCA
1814490 GGTGCAGTTACCTTTGTCTCTTTCTCT
1 GGTGCAGTTACCTTTGTCTCTTTCTCT
1814517 GGTGCAGTTACCTTTGTCTCTTTCTCT
1 GGTGCAGTTACCTTTGTCTCTTTCTCT
1814544 GG
1 GG
1814546 CTTCTGATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.07, C:0.25, G:0.21, T:0.46
Consensus pattern (27 bp):
GGTGCAGTTACCTTTGTCTCTTTCTCT
Found at i:1816046 original size:4 final size:4
Alignment explanation
Indices: 1816033--1816063 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1816023 AGCAAAATTT
1816033 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1816064 ACGTAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:1834293 original size:87 final size:85
Alignment explanation
Indices: 1834147--1834412 Score: 379
Period size: 87 Copynumber: 3.1 Consensus size: 85
1834137 GCCTTCCATA
* * * *
1834147 ATAAAACATTATTTCTGTTTTTTTAAACAAAAGTAAAACATGTTTGATAATATTTTTATATAAAA
1 ATAAAACATTATTTCTGTTTTTTTAAATAAAAATAAAACACGTTTGATAATATTCTTATA-AAAA
*
1834212 TATTGTTAACAATAAAAATAAC
65 -ATTGTTAACAATAAAAATGAC
* *
1834234 ATAAAACATTATTTCTGTTTTTTTAAATAAAAATAAAACACATTTGACAATATTCTTATACAATA
1 ATAAAACATTATTTCTGTTTTTTTAAATAAAAATAAAACACGTTTGATAATATTCTTATA-AA-A
1834299 AATTGTTAACAATAAAAATGAC
64 AATTGTTAACAATAAAAATGAC
* * *
1834321 ATAAAGCATTATTTTTGTTTTTTTAAAATTAAAATAAAACACGTTTGATAATATTCTTATAAAAA
1 ATAAAACATTATTTCTGTTTTTTT-AAATAAAAATAAAACACGTTTGATAATATTCTTAT-AAAA
*
1834386 AATTGTTAACAATAAAGATGAC
64 AATTGTTAACAATAAAAATGAC
1834408 ATAAA
1 ATAAA
1834413 CTATTGTTTA
Statistics
Matches: 162, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
87 125 0.77
88 36 0.22
89 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (85 bp):
ATAAAACATTATTTCTGTTTTTTTAAATAAAAATAAAACACGTTTGATAATATTCTTATAAAAAA
TTGTTAACAATAAAAATGAC
Found at i:1834630 original size:28 final size:28
Alignment explanation
Indices: 1834581--1834634 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1834571 AAACCTAGCA
*
1834581 AATGTGAACATAACTATTATAACTCAAT
1 AATGTGAACATAACTATCATAACTCAAT
**
1834609 AATGTGAACATAGTTATCATAACTCA
1 AATGTGAACATAACTATCATAACTCA
1834635 CGGAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.31
Consensus pattern (28 bp):
AATGTGAACATAACTATCATAACTCAAT
Found at i:1838644 original size:18 final size:18
Alignment explanation
Indices: 1838603--1838645 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1838593 ATTTCCAATG
*
1838603 CACTTGCAAGAGTATGGGC
1 CACTT-CAAGAGTATGAGC
* *
1838622 TACTTCAAGAGTTTGAGC
1 CACTTCAAGAGTATGAGC
1838640 CACTTC
1 CACTTC
1838646 TAACTTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (18 bp):
CACTTCAAGAGTATGAGC
Found at i:1839751 original size:53 final size:53
Alignment explanation
Indices: 1839692--1839802 Score: 150
Period size: 53 Copynumber: 2.1 Consensus size: 53
1839682 AAAAATAGAA
* * *
1839692 TAAAAATTAACAGAACAAAATATGTAAGACATTTTAGGTATTGTTTGATAAAC
1 TAAAAATTAACAGAACAAAATATGTAAGACATTATAGGTATCGTTTAATAAAC
* * * * *
1839745 TAAAAATTAACTGCACAGAATTTTTAAGACATTATAGGTATCGTTTAATAAAC
1 TAAAAATTAACAGAACAAAATATGTAAGACATTATAGGTATCGTTTAATAAAC
1839798 TAAAA
1 TAAAA
1839803 TTGTTTAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (53 bp):
TAAAAATTAACAGAACAAAATATGTAAGACATTATAGGTATCGTTTAATAAAC
Found at i:1840278 original size:69 final size:69
Alignment explanation
Indices: 1840167--1840307 Score: 228
Period size: 69 Copynumber: 2.0 Consensus size: 69
1840157 CATTATCATA
* **
1840167 CAATACGCGATACATATCATACGATACTAATAGAAAACGTTACATGTCTATAACTGTATAGCATT
1 CAATACGCAATACATATCATACGATACTAATAGAAAACGTTACATGTCTATAACTACATAGCATT
1840232 TGAT
66 TGAT
* * *
1840236 CAATACGCAATACATATCATATGATACTAATAGAAAACGTTACGTGTCTATAACTACATCGCATT
1 CAATACGCAATACATATCATACGATACTAATAGAAAACGTTACATGTCTATAACTACATAGCATT
1840301 TGAT
66 TGAT
1840305 CAA
1 CAA
1840308 GTGTTGAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (69 bp):
CAATACGCAATACATATCATACGATACTAATAGAAAACGTTACATGTCTATAACTACATAGCATT
TGAT
Found at i:1840666 original size:23 final size:23
Alignment explanation
Indices: 1840627--1840680 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
1840617 ATGTTGAAAG
* *
1840627 TTTAAATT-AAAACAATAATCTT
1 TTTAATTTAAAAAAAATAATCTT
1840649 TTTAATTTAAAAAAAATAATCTT
1 TTTAATTTAAAAAAAATAATCTT
1840672 TTTAATTTA
1 TTTAATTTA
1840681 CGTCCTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 7 0.24
23 22 0.76
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAATTTAAAAAAAATAATCTT
Found at i:1848900 original size:12 final size:12
Alignment explanation
Indices: 1848883--1848907 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1848873 TTTCTATAAT
1848883 ACAAGAAGAAGA
1 ACAAGAAGAAGA
1848895 ACAAGAAGAAGA
1 ACAAGAAGAAGA
1848907 A
1 A
1848908 GAGTGCTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (12 bp):
ACAAGAAGAAGA
Found at i:1853998 original size:22 final size:21
Alignment explanation
Indices: 1853956--1854000 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
1853946 ATTAAAAATA
1853956 AAAAAAATTTATTTGAATTAAT
1 AAAAAAATTTATTT-AATTAAT
1853978 AAAAAAATTATAATTT-ATTAAT
1 AAAAAAATT-T-ATTTAATTAAT
1854000 A
1 A
1854001 TTTTTATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 16 0.76
23 1 0.05
24 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAAAATTTATTTAATTAAT
Found at i:1857311 original size:17 final size:16
Alignment explanation
Indices: 1857289--1857341 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
1857279 TAGTAATATT
1857289 TATGTATAAATTAATTA
1 TATGTATAAATTAA-TA
*
1857306 TATGTATATA-TAATA
1 TATGTATAAATTAATA
*
1857321 TATTTATACAATTATATA
1 TATGTATA-AATTA-ATA
1857339 TAT
1 TAT
1857342 ATTCACAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 9 0.30
16 4 0.13
17 11 0.37
18 6 0.20
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (16 bp):
TATGTATAAATTAATA
Found at i:1871485 original size:17 final size:18
Alignment explanation
Indices: 1871461--1871513 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
1871451 TATTTATTAA
1871461 TTTAAAAAAAATATTTTG
1 TTTAAAAAAAATATTTTG
1871479 TTTAAAAAAAATATTTTG
1 TTTAAAAAAAATATTTTG
*
1871497 TTTAAAAAAATTATTTT
1 TTTAAAAAAAATATTTT
1871514 TTACTAGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
TTTAAAAAAAATATTTTG
Found at i:1871790 original size:23 final size:20
Alignment explanation
Indices: 1871754--1871804 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
1871744 GATCGGTGCT
1871754 TTTTTTAAAAAATATAATAATA
1 TTTTTTAAAAAATA-AA-AATA
*
1871776 TTTTTTAAATTAATAAAAATA
1 TTTTTTAAA-AAATAAAAATA
*
1871797 TATTTTAA
1 TTTTTTAA
1871805 TCTTTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTTTAAAAAATAAAAATA
Found at i:1878036 original size:17 final size:20
Alignment explanation
Indices: 1877998--1878037 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1877988 TAAATTTTAT
1877998 ATTTTTTATTAAATTAAATA
1 ATTTTTTATTAAATTAAATA
1878018 ATTTTTTA-T-AATT-AATA
1 ATTTTTTATTAAATTAAATA
1878035 ATT
1 ATT
1878038 AATTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 1 0.05
20 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTTATTAAATTAAATA
Found at i:1878057 original size:25 final size:25
Alignment explanation
Indices: 1878009--1878057 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1877999 TTTTTTATTA
*
1878009 AATTAAATAATTTTTTATAATTAAT
1 AATTAAATAATTTATTATAATTAAT
*
1878034 AATTAATTAA-TTATTATAAGTTAA
1 AATTAAATAATTTATTATAA-TTAA
1878058 AATGACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
AATTAAATAATTTATTATAATTAAT
Found at i:1892197 original size:21 final size:22
Alignment explanation
Indices: 1892158--1892200 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1892148 AAAATATATA
* *
1892158 TAAAAATAAGAGTATTGGACAT
1 TAAAAATAAAAGTAATGGACAT
1892180 TAAAAATAAAAG-AATGGACAT
1 TAAAAATAAAAGTAATGGACAT
1892201 AATTTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.23
Consensus pattern (22 bp):
TAAAAATAAAAGTAATGGACAT
Found at i:1893680 original size:24 final size:23
Alignment explanation
Indices: 1893653--1893701 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1893643 TATGTATGGT
*
1893653 GTATTAAGATATATACTATGTATA
1 GTATTAAGATAT-TACTATATATA
*
1893677 GTATTAATATATTACTATATATA
1 GTATTAAGATATTACTATATATA
1893700 GT
1 GT
1893702 TAATAGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (23 bp):
GTATTAAGATATTACTATATATA
Found at i:1893704 original size:21 final size:20
Alignment explanation
Indices: 1893661--1893720 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 20
1893651 GTGTATTAAG
*
1893661 ATATATACTATGTATAGTATTA
1 ATATATACTATATATAG--TTA
1893683 ATATATTACTATATATAGTTA
1 ATATA-TACTATATATAGTTA
*
1893704 ATAGATACT-TATATAGT
1 ATATATACTATATATAGT
1893721 ATATAAGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 8 0.23
20 4 0.11
21 7 0.20
22 5 0.14
23 11 0.31
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (20 bp):
ATATATACTATATATAGTTA
Found at i:1894694 original size:13 final size:13
Alignment explanation
Indices: 1894676--1894700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1894666 GGGAGAGAGA
1894676 TACAAAAAAAAAT
1 TACAAAAAAAAAT
1894689 TACAAAAAAAAA
1 TACAAAAAAAAA
1894701 GAAACCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (13 bp):
TACAAAAAAAAAT
Found at i:1894985 original size:17 final size:17
Alignment explanation
Indices: 1894953--1895027 Score: 84
Period size: 15 Copynumber: 4.4 Consensus size: 17
1894943 TGGGAGAGAG
1894953 AAGAAGAAAGAAAAAGAAA
1 AAGAA-AAA-AAAAAGAAA
1894972 AAGAAAAAAAAAAG--A
1 AAGAAAAAAAAAAGAAA
*
1894987 AAGAAAAAAAAGA-AAA
1 AAGAAAAAAAAAAGAAA
*
1895003 AAGGAAAAAAAAAGAAAA
1 AAGAAAAAAAAAAG-AAA
1895021 AAGAAAA
1 AAGAAAA
1895028 GGATTTGGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
15 13 0.27
16 12 0.25
17 6 0.12
18 12 0.25
19 5 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:1894994 original size:27 final size:27
Alignment explanation
Indices: 1894956--1895027 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 27
1894946 GAGAGAGAAG
1894956 AAGAAAGAAAAAGAAAAAGAAAA-AAAA
1 AAGAAAGAAAAAGAAAAA-AAAAGAAAA
1894983 AAGAAAGAAAAA-AAAGAAAAAAGGAAAA
1 AAGAAAGAAAAAGAAA-AAAAAA-GAAAA
1895011 AA-AAAGAAAAAAGAAAA
1 AAGAAAG-AAAAAGAAAA
1895028 GGATTTGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
26 7 0.17
27 18 0.45
28 12 0.30
29 3 0.08
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (27 bp):
AAGAAAGAAAAAGAAAAAAAAAGAAAA
Found at i:1895004 original size:31 final size:30
Alignment explanation
Indices: 1894956--1895028 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
1894946 GAGAGAGAAG
1894956 AAGAAAGAAAAAGAAAAAGAAAAAAAAAAGA
1 AAGAAA-AAAAAGAAAAAGAAAAAAAAAAGA
*
1894987 AAGAAAAAAAAGAAAAAAGGAAAAAAAAAGA
1 AAGAAAAAAAAG-AAAAAGAAAAAAAAAAGA
*
1895018 AA-AAAGAAAAG
1 AAGAAAAAAAAG
1895029 GATTTGGGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 14 0.36
31 25 0.64
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (30 bp):
AAGAAAAAAAAGAAAAAGAAAAAAAAAAGA
Found at i:1895296 original size:7 final size:7
Alignment explanation
Indices: 1895284--1895423 Score: 52
Period size: 7 Copynumber: 18.6 Consensus size: 7
1895274 TTAGTGTTAG
1895284 AAAATAA
1 AAAATAA
*
1895291 AAAATAG
1 AAAATAA
*
1895298 AAAGT-A
1 AAAATAA
1895304 AAAATAA
1 AAAATAA
1895311 AAAATAA
1 AAAATAA
1895318 TAATAATAA
1 -AA-AATAA
1895327 ATAAATGATA
1 A-AAAT-A-A
* *
1895337 ATATTAA
1 AAAATAA
*
1895344 AAAAT-C
1 AAAATAA
*
1895350 ATAATACA
1 AAAATA-A
*
1895358 AATATAA
1 AAAATAA
1895365 AAATTATAA
1 AAA--ATAA
*
1895374 AAAGT-A
1 AAAATAA
1895380 AAAATAA
1 AAAATAA
**
1895387 ATTATGAA
1 AAAAT-AA
1895395 GAAGAATAA
1 -AA-AATAA
1895404 AGAAATAA
1 A-AAATAA
1895412 AAAATAA
1 AAAATAA
1895419 GAAAA
1 -AAAA
1895424 AATATAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 31
0.66 0.14 0.21
Matches are distributed among these distances:
6 13 0.13
7 36 0.37
8 24 0.25
9 20 0.21
10 4 0.04
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (7 bp):
AAAATAA
Found at i:1895329 original size:33 final size:33
Alignment explanation
Indices: 1895286--1895366 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
1895276 AGTGTTAGAA
1895286 AATAAAAAATAGAAAG-TAAAAATAAAAAATAAT
1 AATAAAAAATA-AAAGATAAAAATAAAAAATAAT
* * * * *
1895319 AATAATAAATAAATGATAATATTAAAAAATCAT
1 AATAAAAAATAAAAGATAAAAATAAAAAATAAT
*
1895352 AATACAAATATAAAA
1 AATA-AAAAATAAAA
1895367 ATTATAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
32 3 0.08
33 28 0.74
34 7 0.18
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (33 bp):
AATAAAAAATAAAAGATAAAAATAAAAAATAAT
Found at i:1895348 original size:20 final size:20
Alignment explanation
Indices: 1895284--1895348 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
1895274 TTAGTGTTAG
1895284 AAAATAAAAAATAGA-AAGT-A
1 AAAATAAAAAATA-ATAA-TAA
1895304 AAAATAAAAAATAATAATAA
1 AAAATAAAAAATAATAATAA
* ** *
1895324 TAAATAAATGATAATATTAA
1 AAAATAAAAAATAATAATAA
1895344 AAAAT
1 AAAAT
1895349 CATAATACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 2 0.05
20 36 0.95
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAATAAAAAATAATAATAA
Found at i:1895701 original size:19 final size:18
Alignment explanation
Indices: 1895672--1895718 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
1895662 AATAATATAT
*
1895672 AATAAATAAAAAATAACAA
1 AATAAA-AAAAAATAAAAA
*
1895691 AATAACAAAAAACTAAAAA
1 AATAA-AAAAAAATAAAAA
1895710 AATAAAAAA
1 AATAAAAAA
1895719 GCAAATACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 20 0.80
20 1 0.04
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (18 bp):
AATAAAAAAAAATAAAAA
Found at i:1901120 original size:13 final size:13
Alignment explanation
Indices: 1901102--1901126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1901092 GGGAGAGAGA
1901102 TACAAAAAAAAAT
1 TACAAAAAAAAAT
1901115 TACAAAAAAAAA
1 TACAAAAAAAAA
1901127 GAAACCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (13 bp):
TACAAAAAAAAAT
Found at i:1901394 original size:6 final size:6
Alignment explanation
Indices: 1901379--1901451 Score: 92
Period size: 6 Copynumber: 11.5 Consensus size: 6
1901369 TGGGAGAGAG
*
1901379 AAGAAGA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA GAAAAAA AAGAAAA
1 AAGAA-A AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA -AAGAAA AAG-AAA
*
1901430 AAGGAAA AATAAA AAGAAA AAG
1 AA-GAAA AAGAAA AAGAAA AAG
1901452 GCAAAGGATT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
6 38 0.64
7 20 0.34
8 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (6 bp):
AAGAAA
Found at i:1901414 original size:28 final size:27
Alignment explanation
Indices: 1901377--1901451 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
1901367 GTTGGGAGAG
*
1901377 AGAAGAAGAAAGAAAAAGAAA-AAGAAAA
1 AGAAAAAGAAAGAAAAA-AAAGAA-AAAA
1901405 AGAAAAAGAAAGAAAAAAAAGAAAAAA
1 AGAAAAAGAAAGAAAAAAAAGAAAAAA
* * *
1901432 GGAAAAATAAA-AAGAAAAAG
1 AGAAAAAGAAAGAAAAAAAAG
1901452 GCAAAGGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.19
27 16 0.38
28 18 0.43
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (27 bp):
AGAAAAAGAAAGAAAAAAAAGAAAAAA
Found at i:1901757 original size:16 final size:16
Alignment explanation
Indices: 1901736--1901785 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1901726 GGAAAGTAAA
1901736 AATAAATAATAATAAT
1 AATAAATAATAATAAT
*
1901752 AATAAATAAATGATAAT
1 AATAAAT-AATAATAAT
* * *
1901769 ATTAAAAAATTATAAT
1 AATAAATAATAATAAT
1901785 A
1 A
1901786 CAAATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
AATAAATAATAATAAT
Found at i:1901758 original size:20 final size:19
Alignment explanation
Indices: 1901739--1901866 Score: 74
Period size: 20 Copynumber: 6.8 Consensus size: 19
1901729 AAGTAAAAAT
*
1901739 AAATAATAATAATAATAAA
1 AAATTATAATAATAATAAA
*
1901758 TAAATGATAAT-AT--TAAA
1 -AAATTATAATAATAATAAA
1901775 AAATTATAATACA-AATATAA
1 AAATTATAATA-ATAATA-AA
*
1901795 AAATTATAAAAAGTAA-AAA
1 AAATTATAATAA-TAATAAA
* *
1901814 TAAATTATGAAGAAGAATAAA
1 -AAATTAT-AATAATAATAAA
* *
1901835 GAAA-TA-AAAAATAAGAAA
1 -AAATTATAATAATAATAAA
1901853 AAA-TATAATAATAA
1 AAATTATAATAATAA
1901867 AAAGAAGTAG
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
16 9 0.10
17 9 0.10
18 17 0.20
19 7 0.08
20 33 0.38
21 12 0.14
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (19 bp):
AAATTATAATAATAATAAA
Found at i:1902087 original size:16 final size:19
Alignment explanation
Indices: 1902056--1902092 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1902046 TTGTTTAAAA
1902056 AAATATAAAATGAATA-AT
1 AAATATAAAATGAATATAT
1902074 AAATA-AAAAT-AATATAT
1 AAATATAAAATGAATATAT
1902091 AA
1 AA
1902093 TAATATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 9 0.50
18 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AAATATAAAATGAATATAT
Found at i:1902123 original size:19 final size:18
Alignment explanation
Indices: 1902101--1902140 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1902091 AATAATATGT
*
1902101 AAAAAATAACAAAATAACA
1 AAAAAATAAAAAAATAA-A
*
1902120 AAAAACTAAAAAAATAAA
1 AAAAAATAAAAAAATAAA
1902138 AAA
1 AAA
1902141 GGAAATACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.10
Consensus pattern (18 bp):
AAAAAATAAAAAAATAAA
Found at i:1910724 original size:59 final size:60
Alignment explanation
Indices: 1910627--1911109 Score: 634
Period size: 59 Copynumber: 8.1 Consensus size: 60
1910617 CAATTAAGTT
* * * * *
1910627 GAACCTGTTTTAAGATAGGTCGACCCTAGATCAAGTTTAGGAATTTCAA-TATTTGAATC
1 GAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATC
* * * * * * * *
1910686 GAACTTGTTTTGAGATAGGTCAAGCCTATATTAAGTTTAGAAATTTCAA-TTTTTGATTC
1 GAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATC
* *
1910745 GAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATC
1 GAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATC
* * * * *
1910805 GAACTTATTTTAAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAA-TTTTTGATTC
1 GAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATC
* *
1910864 AAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATC
1 GAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATC
* * * *
1910924 AAACTTGTTTTAAGATAGGTCGGGCCTAGATTAAGTCTAGGAATTTC-ATTTTTTGAATC
1 GAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATC
* * * *
1910983 GAACATG-TTTAAGATAGGTCGAGCCTAGATCAATTATAGGAATGTCAATTTTTTAAATC
1 GAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATC
* * *
1911042 GAACCTGTTTTAAGATGGGTCGAGCCTAGATCAAGTCTAAGAATTTCAATTTTTTAAATC
1 GAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATC
1911102 GAACTTGT
1 GAACTTGT
1911110 CGCGAGATAG
Statistics
Matches: 368, Mismatches: 52, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
58 34 0.09
59 176 0.48
60 158 0.43
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (60 bp):
GAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATC
Found at i:1910856 original size:119 final size:119
Alignment explanation
Indices: 1910627--1911095 Score: 701
Period size: 119 Copynumber: 4.0 Consensus size: 119
1910617 CAATTAAGTT
* * * * *
1910627 GAACCTGTTTTAAGATAGGTCGACCCTAGATCAAGTTTAGGAATTTCAA-TATTTGAATCGAACT
1 GAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAACT
* * * *
1910691 TGTTTTGAGATAGGTCAAGCCTATATTAAGTTTAGAAATTTCAATTTTTGATTC
66 TGTTTTAAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTTTTGATTC
1910745 GAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAACT
1 GAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAACT
*
1910810 TATTTTAAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTTTTGATTC
66 TGTTTTAAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTTTTGATTC
* * *
1910864 AAACTTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCAAACT
1 GAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAACT
* * * *
1910929 TGTTTTAAGATAGGTCGGGCCTAGATTAAGTCTAGGAATTTCATTTTTTGAATC
66 TGTTTTAAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTTTTGATTC
* * * *
1910983 GAACATG-TTTAAGATAGGTCGAGCCTAGATCAATTATAGGAATGTCAATTTTTTAAATCGAACC
1 GAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAACT
* *
1911047 TGTTTTAAGATGGGTCGAGCCTAGATCAAGTCTA-AGAATTTCAATTTTT
66 TGTTTTAAGATAGGTCGAGCCTAGATTAAGTCTAGA-AATTTCAATTTTT
1911096 TAAATCGAAC
Statistics
Matches: 320, Mismatches: 29, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
118 142 0.44
119 178 0.56
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (119 bp):
GAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAACT
TGTTTTAAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTTTTGATTC
Found at i:1910977 original size:178 final size:177
Alignment explanation
Indices: 1910634--1911109 Score: 641
Period size: 178 Copynumber: 2.7 Consensus size: 177
1910624 GTTGAACCTG
* * * *
1910634 TTTTAAGATAGGTCGACCCTAGATCAAGTTTAGGAATTTCAATATTTGAATCGAACTTGTTTTGA
1 TTTTAAGATAGGTCGAGCCTAGATCAAGTATAGGAATTTCAATTTTTGAATCGAACTTGTTTTAA
* * * * * * * *
1910699 GATAGGTCAAGCCTATATTAAGTTTAGAAATTTCAA-TTTTTGATTCGAACCTGTTTTAAGATAG
66 GATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATCGAACTTGTTTTAAGATAG
1910763 GTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAACTTA
131 GTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAAC--A
* * * * *
1910812 TTTTAAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTTTTGATTCAAACTTGTTTTAA
1 TTTTAAGATAGGTCGAGCCTAGATCAAGTATAGGAATTTCAATTTTTGAATCGAACTTGTTTTAA
* *
1910877 GATAGGTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCAAACTTGTTTTAAGATAG
66 GATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATCGAACTTGTTTTAAGATAG
* * * *
1910942 GTCGGGCCTAGATTAAGTCTAGGAATTTC-ATTTTTTGAATCGAACA
131 GTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAACA
* * * *
1910988 TGTTTAAGATAGGTCGAGCCTAGATCAATTATAGGAATGTCAATTTTTTAAATCGAACCTGTTTT
1 T-TTTAAGATAGGTCGAGCCTAGATCAAGTATAGGAATTTCAA-TTTTTGAATCGAACTTGTTTT
* *
1911053 AAGATGGGTCGAGCCTAGATCAAGTCTAAGAATTTCAATTTTTTAAATCGAACTTGT
64 AAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATCGAACTTGT
1911110 CGCGAGATAG
Statistics
Matches: 260, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
176 2 0.01
177 36 0.14
178 172 0.66
179 50 0.19
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (177 bp):
TTTTAAGATAGGTCGAGCCTAGATCAAGTATAGGAATTTCAATTTTTGAATCGAACTTGTTTTAA
GATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTTAAATCGAACTTGTTTTAAGATAG
GTCGAGCCTAGATCAAGTCTAGGAATGTCAATTTTTTAAATCGAACA
Found at i:1911939 original size:13 final size:12
Alignment explanation
Indices: 1911924--1912006 Score: 91
Period size: 12 Copynumber: 6.8 Consensus size: 12
1911914 AGAGAAGAGG
1911924 AAAGAAAAAGAA
1 AAAGAAAAAGAA
1911936 GAAAGAAAAA-AA
1 -AAAGAAAAAGAA
1911948 AAAGAAAAAGAAA
1 AAAGAAAAAG-AA
*
1911961 GAAAGAAAAGGAA
1 -AAAGAAAAAGAA
1911974 AAA-AAAAAGATA
1 AAAGAAAAAGA-A
1911986 AAA-AAAAAGAA
1 AAAGAAAAAGAA
*
1911997 AAAGGAAAAG
1 AAAGAAAAAG
1912007 GATTTGGGTC
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
11 19 0.31
12 21 0.34
13 13 0.21
14 9 0.15
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (12 bp):
AAAGAAAAAGAA
Found at i:1911958 original size:30 final size:30
Alignment explanation
Indices: 1911925--1912005 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 30
1911915 GAGAAGAGGA
1911925 AAGAAAAAGAAGAAAGAAAAAAAAAAGA-AA
1 AAGAAAAAGAA-AAAGAAAAAAAAAAGATAA
*
1911955 AAGAAAGAAAGAAAAGGAAAAAAAAAAGATAA
1 AAG-AA-AAAGAAAAAGAAAAAAAAAAGATAA
*
1911987 AA-AAAAAGAAAAAGGAAAA
1 AAGAAAAAGAAAAAGAAAAA
1912006 GGATTTGGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
29 13 0.29
30 5 0.11
31 17 0.38
32 10 0.22
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (30 bp):
AAGAAAAAGAAAAAGAAAAAAAAAAGATAA
Found at i:1911960 original size:21 final size:21
Alignment explanation
Indices: 1911934--1912000 Score: 84
Period size: 21 Copynumber: 3.1 Consensus size: 21
1911924 AAAGAAAAAG
1911934 AAGAAAGAAAAAAAAAAGAAA
1 AAGAAAGAAAAAAAAAAGAAA
*
1911955 AAGAAAGAAAGAAAAGGAA-AAA
1 AAGAAAGAAA-AAAA-AAAGAAA
1911977 AA-AAAGATAAAAAAAAAGAAA
1 AAGAAAGA-AAAAAAAAAGAAA
1911998 AAG
1 AAG
1912001 GAAAAGGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 2 0.05
21 24 0.62
22 11 0.28
23 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (21 bp):
AAGAAAGAAAAAAAAAAGAAA
Found at i:1912434 original size:19 final size:17
Alignment explanation
Indices: 1912381--1912448 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 17
1912371 GAAGAAGAAT
*
1912381 AAAGAAATAAAAAATAA
1 AAAGAAATAAATAATAA
1912398 GAAA-AAATATAATAATAA
1 -AAAGAAATA-AATAATAA
1912416 AAAGAAATAGAAGTAATAA
1 AAAGAAATA-AA-TAATAA
1912435 ATAA-ATAATAAATA
1 A-AAGA-AATAAATA
1912449 TACATTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
17 8 0.19
18 19 0.44
19 10 0.23
20 6 0.14
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (17 bp):
AAAGAAATAAATAATAA
Found at i:1912625 original size:13 final size:13
Alignment explanation
Indices: 1912604--1912689 Score: 55
Period size: 12 Copynumber: 7.3 Consensus size: 13
1912594 ATTGTTTTAA
1912604 AAAAT-ATAAAAT
1 AAAATAATAAAAT
1912616 AAAATAAT-AAAT
1 AAAATAATAAAAT
*
1912628 -AAA-AATAATAT
1 AAAATAATAAAAT
* *
1912639 ATAATAAT-ATAT
1 AAAATAATAAAAT
*
1912651 AATA-AATAAAA-
1 AAAATAATAAAAT
*
1912662 AAAATAACAAAAT
1 AAAATAATAAAAT
*
1912675 AACA-AA-AAAAT
1 AAAATAATAAAAT
1912686 AAAA
1 AAAA
1912690 AAGCAAATAC
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
10 3 0.05
11 20 0.34
12 27 0.47
13 8 0.14
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:1912631 original size:17 final size:17
Alignment explanation
Indices: 1912609--1912689 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
1912599 TTTAAAAAAT
1912609 ATAAAATAAAATAATAA
1 ATAAAATAAAATAATAA
1912626 ATAAAAATAATATATAATAA
1 AT-AAAATAA-A-ATAATAA
*
1912646 TATATAAT-AAATAA-AA
1 -ATAAAATAAAATAATAA
* * *
1912662 AAAATAACAAAATAACAA
1 ATAA-AATAAAATAATAA
1912680 A-AAAATAAAA
1 ATAAAATAAAA
1912690 AAGCAAATAC
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
15 2 0.04
16 10 0.19
17 14 0.27
18 11 0.21
19 2 0.04
20 11 0.21
21 2 0.04
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
ATAAAATAAAATAATAA
Found at i:1912637 original size:28 final size:28
Alignment explanation
Indices: 1912602--1912691 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
1912592 TAATTGTTTT
1912602 AAAAAATATAAAATAA-AATAATAAATA
1 AAAAAATATAAAATAACAATAATAAATA
* *
1912629 AAAATAATATATAATAATATATAATAAATAA
1 AAAA-AATATAAAATAACA-ATAATAAAT-A
*
1912660 AAAAAATAACAAAATAACAA-AA-AAATA
1 AAAAAAT-ATAAAATAACAATAATAAATA
1912687 AAAAA
1 AAAAA
1912692 GCAAATACCA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 10 0.19
28 15 0.28
29 3 0.06
30 13 0.24
31 13 0.24
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (28 bp):
AAAAAATATAAAATAACAATAATAAATA
Found at i:1912665 original size:33 final size:30
Alignment explanation
Indices: 1912607--1912690 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
1912597 GTTTTAAAAA
1912607 ATATAAAATAAAATAATAAATAAAAATAAT
1 ATATAAAATAAAATAATAAATAAAAATAAT
* *
1912637 ATATAATAAT-ATATAATAAATAAAAAAAAT
1 ATATAA-AATAAAATAATAAATAAAAATAAT
*
1912667 A-ACAAAATAACAA-AA-AAATAAAAA
1 ATATAAAATAA-AATAATAAATAAAAA
1912691 AGCAAATACC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
28 12 0.26
29 6 0.13
30 26 0.55
31 3 0.06
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (30 bp):
ATATAAAATAAAATAATAAATAAAAATAAT
Found at i:1914338 original size:72 final size:73
Alignment explanation
Indices: 1914244--1914388 Score: 206
Period size: 74 Copynumber: 2.0 Consensus size: 73
1914234 CTTCCTATAT
* *
1914244 TTCTTCAAGTACTTCTTATTTTC-TTCTCTCCTAAGTGTCTTCCATTACCACTGCTTT-TCCCCA
1 TTCTTCAAGTACTTCTTATTTTCATTCCCTCATAAGTGTCTTCCATTACCACTGCTTTCT-CCCA
1914307 TGTTGATAC
65 TGTTGATAC
* *
1914316 TTCTTCAAGTA-TTACTTCTTTTCATTTCCCTCATAAGTGTCTTCCATTACCACTGCTTTCTCCT
1 TTCTTCAAGTACTT-CTTATTTTCA-TTCCCTCATAAGTGTCTTCCATTACCACTGCTTTCTCCC
1914380 ATGTTGATA
64 ATGTTGATA
1914389 ACTCCAAAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
71 2 0.03
72 19 0.29
74 43 0.66
75 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.08, T:0.46
Consensus pattern (73 bp):
TTCTTCAAGTACTTCTTATTTTCATTCCCTCATAAGTGTCTTCCATTACCACTGCTTTCTCCCAT
GTTGATAC
Found at i:1918103 original size:20 final size:20
Alignment explanation
Indices: 1918078--1918118 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1918068 ATTCTAGTAT
*
1918078 TATATAATAGTACATTGTTA
1 TATATAATAGTAAATTGTTA
1918098 TATATAATAGTAAATTGTTA
1 TATATAATAGTAAATTGTTA
1918118 T
1 T
1918119 TGACTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (20 bp):
TATATAATAGTAAATTGTTA
Found at i:1918186 original size:7 final size:7
Alignment explanation
Indices: 1918142--1918172 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1918132 TATTGATAAG
*
1918142 TATACTA
1 TATAATA
1918149 TATAATA
1 TATAATA
1918156 TATAATA
1 TATAATA
1918163 TATAATA
1 TATAATA
1918170 TAT
1 TAT
1918173 GGTTATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (7 bp):
TATAATA
Found at i:1918199 original size:15 final size:18
Alignment explanation
Indices: 1918178--1918217 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
1918168 TATATGGTTA
1918178 TATATTA-TAATAT-AGT
1 TATATTATTAATATAAGT
1918194 TA-ATTATTAATATAAGT
1 TATATTATTAATATAAGT
1918211 TATATTA
1 TATATTA
1918218 CTATAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.19
16 8 0.38
17 5 0.24
18 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TATATTATTAATATAAGT
Found at i:1918243 original size:34 final size:31
Alignment explanation
Indices: 1918137--1918246 Score: 96
Period size: 34 Copynumber: 3.3 Consensus size: 31
1918127 TAATATATTG
1918137 ATAAG-TATACTATATAATATATAATATATAAT
1 ATAAGTTATA-TATATAATATATAATA-ATAAT
* *
1918169 ATATGGTTATATATTATAATATAGTTAATTATTAAT
1 ATA-AGTTATATA-TATAATATA--TAA-TAATAAT
*
1918205 ATAAGTTATATTACTATAAGATACTAATAATAAT
1 ATAAGTTATA-TA-TATAATATA-TAATAATAAT
1918239 ATAAGTTA
1 ATAAGTTA
1918247 CTTTAGTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
32 3 0.05
33 3 0.05
34 27 0.42
35 9 0.14
36 20 0.31
37 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (31 bp):
ATAAGTTATATATATAATATATAATAATAAT
Found at i:1918273 original size:20 final size:19
Alignment explanation
Indices: 1918219--1918275 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
1918209 GTTATATTAC
*
1918219 TATAAG-ATACTAATAATAA
1 TATAAGTATACT-ATAGTAA
*
1918238 TATAAGT-TACTTTAGTAA
1 TATAAGTATACTATAGTAA
1918256 TATAAGCTATACTATAGTAA
1 TATAAG-TATACTATAGTAA
1918276 CATTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 11 0.34
19 11 0.34
20 10 0.31
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (19 bp):
TATAAGTATACTATAGTAA
Found at i:1918449 original size:16 final size:16
Alignment explanation
Indices: 1918437--1918467 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1918427 ATAATATATT
1918437 AATAACTTAATATAAA
1 AATAACTTAATATAAA
*
1918453 AATAAGTTAATATAA
1 AATAACTTAATATAA
1918468 TAAGTTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
AATAACTTAATATAAA
Found at i:1919059 original size:50 final size:50
Alignment explanation
Indices: 1918989--1919093 Score: 138
Period size: 50 Copynumber: 2.1 Consensus size: 50
1918979 GGATGTTGTC
* * * * *
1918989 TTTTACTAATGTGGTTTTCATGCGTGGGAATGGGTTTTGTGGTTTAGGGT
1 TTTTGCTAATGTGGTCTTCATGCGTGAGAAGGGGTTTTGTGGTTTAGGAT
* * *
1919039 TTTTGCTAGTGTGGTCTTCATGTGTTAGAAGGGGTTTTGTGGTTTAGGAT
1 TTTTGCTAATGTGGTCTTCATGCGTGAGAAGGGGTTTTGTGGTTTAGGAT
1919089 TTTTG
1 TTTTG
1919094 TTTGTTGTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.13, C:0.06, G:0.33, T:0.48
Consensus pattern (50 bp):
TTTTGCTAATGTGGTCTTCATGCGTGAGAAGGGGTTTTGTGGTTTAGGAT
Found at i:1923180 original size:34 final size:33
Alignment explanation
Indices: 1923122--1923198 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 33
1923112 TTCAATATTT
* *
1923122 CAACAA-TTTTGTATTCAATTTTCAACAACTTA
1 CAACAACTTTTGCATCCAATTTTCAACAACTTA
*
1923154 CAACAACTTTTGCATCCAATATTTCAACAATTTA
1 CAACAACTTTTGCATCCAAT-TTTCAACAACTTA
*
1923188 TAACAACTTTT
1 CAACAACTTTT
1923199 ATCAAACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 6 0.15
33 11 0.28
34 22 0.56
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.39
Consensus pattern (33 bp):
CAACAACTTTTGCATCCAATTTTCAACAACTTA
Found at i:1924493 original size:2 final size:2
Alignment explanation
Indices: 1924486--1924544 Score: 75
Period size: 2 Copynumber: 29.5 Consensus size: 2
1924476 ATTTTGTAAT
* * *
1924486 TA TA TA TA TA TA TA TA TA TNG TA TA TT TG TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
1924528 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1924545 CTAAAAAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1924901 original size:25 final size:26
Alignment explanation
Indices: 1924873--1924922 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1924863 ACAATATTTT
*
1924873 TTTTTTC-AAAATATCATGTAATAAA
1 TTTTTTCGAAAATAGCATGTAATAAA
* *
1924898 TTTTTTCGAACATGGCATGTAATAA
1 TTTTTTCGAAAATAGCATGTAATAA
1924923 CAATATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (26 bp):
TTTTTTCGAAAATAGCATGTAATAAA
Found at i:1931150 original size:15 final size:14
Alignment explanation
Indices: 1931127--1931164 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
1931117 TGTTTGTATA
1931127 TTTTTATATAAATT
1 TTTTTATATAAATT
1931141 TTTTTCATATAAATT
1 TTTTT-ATATAAATT
*
1931156 GTTTTATAT
1 TTTTTATAT
1931165 TGTCTTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (14 bp):
TTTTTATATAAATT
Found at i:1933909 original size:2 final size:2
Alignment explanation
Indices: 1933902--1933929 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1933892 ATCAATGGAG
1933902 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
1933930 CATCCACCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1946668 original size:18 final size:19
Alignment explanation
Indices: 1946647--1946691 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1946637 TTTTCTTTCA
1946647 ATTTATTTTA-TTATTTAT
1 ATTTATTTTATTTATTTAT
*
1946665 ATTTA-TTTATTTATTTCT
1 ATTTATTTTATTTATTTAT
1946683 ATTCTATTT
1 ATT-TATTT
1946692 ACTCATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 2 0.09
20 2 0.09
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTATTTTATTTATTTAT
Found at i:1946674 original size:14 final size:13
Alignment explanation
Indices: 1946647--1946692 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
1946637 TTTTCTTTCA
1946647 ATTTATTTTA-TT
1 ATTTATTTTATTT
1946659 ATTTATATTTATTT
1 ATTTAT-TTTATTT
1946673 ATTTATTTCTATTCT
1 ATTTATTT-TATT-T
1946688 ATTTA
1 ATTTA
1946693 CTCATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.20
13 6 0.20
14 12 0.40
15 6 0.20
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTATTTTATTT
Found at i:1946692 original size:41 final size:39
Alignment explanation
Indices: 1946612--1946692 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 39
1946602 GCGTGACTCA
* *
1946612 ATTTTAATATATATATATTTTGTTTTTTTCTTTCAATTT
1 ATTTTAATATATATATATTTTATTTATTTCTTTCAATTT
* * * *
1946651 ATTTTATTATTTATATTTATTTATTTATTTCTATTCTATTT
1 ATTTTAATATATATATAT-TTTATTTATTTCT-TTCAATTT
1946692 A
1 A
1946693 CTCATATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 15 0.44
40 11 0.32
41 8 0.24
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (39 bp):
ATTTTAATATATATATATTTTATTTATTTCTTTCAATTT
Found at i:1948724 original size:27 final size:27
Alignment explanation
Indices: 1948682--1948742 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
1948672 AGCACCAGCT
*
1948682 CAGCAGCGGCCAACACAATATCCC-CCA
1 CAGCAGCAGCCAACACAATA-CCCTCCA
*
1948709 CAGCAGCAGCCGACACAATACCCTCCA
1 CAGCAGCAGCCAACACAATACCCTCCA
*
1948736 CCGCAGC
1 CAGCAGC
1948743 CTAACCAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.31, C:0.46, G:0.16, T:0.07
Consensus pattern (27 bp):
CAGCAGCAGCCAACACAATACCCTCCA
Found at i:1950109 original size:2 final size:2
Alignment explanation
Indices: 1950102--1950142 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1950092 TGATATGTCA
*
1950102 AT AT AT AT AT AT AT AT AT GT 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 AT AT AT AT AT AT AT A
1950143 GTGTTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1952466 original size:16 final size:19
Alignment explanation
Indices: 1952433--1952468 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 19
1952423 ACTTATTTAA
1952433 ATTATAAATATTATATTTT
1 ATTATAAATATTATATTTT
1952452 ATTA-AAAT-TTA-ATTTT
1 ATTATAAATATTATATTTT
1952468 A
1 A
1952469 AAATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATAAATATTATATTTT
Found at i:1953285 original size:18 final size:18
Alignment explanation
Indices: 1953262--1953311 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
1953252 TTTTCTATCA
1953262 ATTTATTT-TATTATTTAT
1 ATTTATTTAT-TTATTTAT
1953280 ATTTATTTATTTATTTAT
1 ATTTATTTATTTATTTAT
1953298 -TTCTATTCTATTTA
1 ATT-TATT-TATTTA
1953312 CTCATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.07
18 20 0.69
19 7 0.24
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTATTTATTTATTTAT
Found at i:1953287 original size:22 final size:23
Alignment explanation
Indices: 1953262--1953311 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
1953252 TTTTCTATCA
1953262 ATTTATTT-TATTATTTATATT-T
1 ATTTATTTAT-TTATTTATATTCT
*
1953284 ATTTATTTATTTATTTCTATTCT
1 ATTTATTTATTTATTTATATTCT
1953307 ATTTA
1 ATTTA
1953312 CTCATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTATTTATTTATTTATATTCT
Found at i:1953289 original size:14 final size:12
Alignment explanation
Indices: 1953262--1953295 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
1953252 TTTTCTATCA
1953262 ATTTATTTTATT
1 ATTTATTTTATT
1953274 ATTTATATTTATTT
1 ATTTAT-TTTA-TT
1953288 ATTTATTT
1 ATTTATTT
1953296 ATTTCTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 6 0.30
14 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTATTTTATT
Found at i:1956877 original size:48 final size:48
Alignment explanation
Indices: 1956820--1956929 Score: 157
Period size: 48 Copynumber: 2.3 Consensus size: 48
1956810 TCAGTTCCAG
* ***
1956820 CCACAGCAGCAGCCACCACCGGCTCAGCAGCAGCCAGTGCAATACCCC
1 CCACAGCAGCAGCCACCACCAGCTCAGCAGCAGCCAACACAATACCCC
* * *
1956868 CCACCGCAGCAGCCAGCACCAGCTCAGCAGCAGCCAACACAATATCCC
1 CCACAGCAGCAGCCACCACCAGCTCAGCAGCAGCCAACACAATACCCC
1956916 CCACAGCAGCAGCC
1 CCACAGCAGCAGCC
1956930 GACACAATAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.29, C:0.46, G:0.19, T:0.05
Consensus pattern (48 bp):
CCACAGCAGCAGCCACCACCAGCTCAGCAGCAGCCAACACAATACCCC
Found at i:1956934 original size:27 final size:27
Alignment explanation
Indices: 1956892--1956952 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
1956882 AGCACCAGCT
1956892 CAGCAGCAGCCAACACAATATCCC-CCA
1 CAGCAGCAGCCAACACAATA-CCCTCCA
*
1956919 CAGCAGCAGCCGACACAATACCCTCCA
1 CAGCAGCAGCCAACACAATACCCTCCA
*
1956946 CCGCAGC
1 CAGCAGC
1956953 CTAACCAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.33, C:0.46, G:0.15, T:0.07
Consensus pattern (27 bp):
CAGCAGCAGCCAACACAATACCCTCCA
Found at i:1967018 original size:5 final size:5
Alignment explanation
Indices: 1966989--1967039 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
1966979 AGAGAGAAGG
* *
1966989 AAGAGA AAG-A AAG-A AAGAA ATGAA AAGAA AAGAA AAGAA AGGAA AAGAA
1 AAGA-A AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
1967038 AA
1 AA
1967040 TAACAAGCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
4 8 0.20
5 29 0.73
6 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:1967107 original size:25 final size:25
Alignment explanation
Indices: 1967048--1967109 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
1967038 AATAACAAGC
*
1967048 AAGAA-AAATGGGCATGGTCCAATA
1 AAGAAGAAATGGGCATGGCCCAATA
1967072 AAGGAAG-AATGGGCATGGCCCAATTA
1 AA-GAAGAAATGGGCATGGCCCAA-TA
1967098 AA-AAGAAATGGG
1 AAGAAGAAATGGG
1967110 AGAAGTCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 5 0.15
25 24 0.73
26 4 0.12
ACGTcount: A:0.45, C:0.11, G:0.29, T:0.15
Consensus pattern (25 bp):
AAGAAGAAATGGGCATGGCCCAATA
Found at i:1969150 original size:22 final size:22
Alignment explanation
Indices: 1969125--1969190 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1969115 TTCAGCTGGT
1969125 ATCAGAGCTTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
1969147 ATCAGAGCTTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
* * *
1969169 ATTAAAGCTTTTGGGTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
1969191 TTGTTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.41
Consensus pattern (22 bp):
ATCAGAGCTTTTGGTTTTAAAG
Found at i:1971494 original size:7 final size:7
Alignment explanation
Indices: 1971482--1971506 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1971472 AGGTAGAATG
1971482 GAAATTT
1 GAAATTT
1971489 GAAATTT
1 GAAATTT
1971496 GAAATTT
1 GAAATTT
1971503 GAAA
1 GAAA
1971507 ATGCTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (7 bp):
GAAATTT
Found at i:1972665 original size:19 final size:20
Alignment explanation
Indices: 1972638--1972683 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1972628 AGGAGACAAG
*
1972638 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
1972657 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
1972676 ATAATATT
1 ATAATATT
1972684 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:1973923 original size:25 final size:25
Alignment explanation
Indices: 1973864--1973925 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1973854 AATAACAAAC
* *
1973864 AAGAA-AAATGGACATGGTCCAATA
1 AAGAAGAAATGGGCATGGCCCAATA
1973888 AAGGAAG-AATGGGCATGGCCCAATTA
1 AA-GAAGAAATGGGCATGGCCCAA-TA
1973914 AA-AAGAAATGGG
1 AAGAAGAAATGGG
1973926 AGAAGTCCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
24 5 0.16
25 23 0.72
26 4 0.12
ACGTcount: A:0.47, C:0.11, G:0.27, T:0.15
Consensus pattern (25 bp):
AAGAAGAAATGGGCATGGCCCAATA
Found at i:1978111 original size:32 final size:32
Alignment explanation
Indices: 1978075--1978138 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1978065 TTACAGTTTT
* *
1978075 TTTTTGTTTTTAACCTTCAAATTACATCATTA
1 TTTTTGTTTTCAACATTCAAATTACATCATTA
1978107 TTTTTGTTTTCAACATTCAAATTACATCATTA
1 TTTTTGTTTTCAACATTCAAATTACATCATTA
1978139 ATTGTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.52
Consensus pattern (32 bp):
TTTTTGTTTTCAACATTCAAATTACATCATTA
Found at i:1979847 original size:74 final size:73
Alignment explanation
Indices: 1979738--1979910 Score: 235
Period size: 74 Copynumber: 2.4 Consensus size: 73
1979728 TTAGTTGACC
* *
1979738 AAGAAGGATGGTTAGTCGACTAAGAGCTTATTGCTAGAAATCTGGATTACA-AGACATAAAG-AA
1 AAGAAGCATTGTTAGTCGACTAAGAGCTTATTGCTAGAAA-CTGGATT-CAGAGACA-AAAGCAA
1979801 CTTAATCAACT
63 CTTAATCAACT
* *
1979812 AAGAAGCATTGTTAGTCGACTAAGAGCTTATTGCTAGAAACTGGATTCAGAGACAAAGGCGACTT
1 AAGAAGCATTGTTAGTCGACTAAGAGCTTATTGCTAGAAACTGGATTCAGAGACAAAAGCAACTT
*
1979877 AATCGACT
66 AATCAACT
* *
1979885 AAGATGTA-TGTTAGTCGACTAAGAGC
1 AAGAAGCATTGTTAGTCGACTAAGAGC
1979911 ACACTGTCAG
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
72 23 0.26
73 29 0.32
74 38 0.42
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (73 bp):
AAGAAGCATTGTTAGTCGACTAAGAGCTTATTGCTAGAAACTGGATTCAGAGACAAAAGCAACTT
AATCAACT
Found at i:1980701 original size:19 final size:20
Alignment explanation
Indices: 1980674--1980719 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1980664 AGGAGACAAG
*
1980674 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
1980693 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
1980712 ATAATATT
1 ATAATATT
1980720 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:1981166 original size:20 final size:20
Alignment explanation
Indices: 1981121--1981158 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1981111 TTTTGGCCCC
1981121 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
1981141 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
1981159 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:1982422 original size:13 final size:13
Alignment explanation
Indices: 1982404--1982428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1982394 AGGGAAATTG
1982404 TGATTTTATAAAA
1 TGATTTTATAAAA
1982417 TGATTTTATAAA
1 TGATTTTATAAA
1982429 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:1984206 original size:20 final size:20
Alignment explanation
Indices: 1984181--1984225 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1984171 GTATAAGCTT
1984181 TGGATAGAACCTTTAGTTTC
1 TGGATAGAACCTTTAGTTTC
1984201 TGGATAGAACCTTTAGTTTC
1 TGGATAGAACCTTTAGTTTC
1984221 TGGAT
1 TGGAT
1984226 GAAAATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.40
Consensus pattern (20 bp):
TGGATAGAACCTTTAGTTTC
Found at i:1987285 original size:14 final size:14
Alignment explanation
Indices: 1987266--1987298 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1987256 CAGGATTGTT
*
1987266 AGAAAAATAGTATA
1 AGAAAAATAGTACA
1987280 AGAAAAATAGTACA
1 AGAAAAATAGTACA
1987294 AGAAA
1 AGAAA
1987299 CTACTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.15, T:0.15
Consensus pattern (14 bp):
AGAAAAATAGTACA
Found at i:1988651 original size:26 final size:26
Alignment explanation
Indices: 1988600--1988652 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
1988590 CATGACTCAA
*
1988600 TTTTAATATATATTTTTTGTTTTTTC
1 TTTTAATATATATTTTTTATTTTTTC
1988626 TTTTAAT-T-TATTTTATTATTTATTTC
1 TTTTAATATATATTTT-TTATTT-TTTC
1988652 T
1 T
1988653 ATTCTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 6 0.25
26 12 0.50
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTAATATATATTTTTTATTTTTTC
Found at i:1989688 original size:245 final size:245
Alignment explanation
Indices: 1989242--1989732 Score: 905
Period size: 245 Copynumber: 2.0 Consensus size: 245
1989232 TTATTATAAC
*
1989242 CTATTATATCTTAACAGTTCAATCTAATAGCCTATAATAACATATTATATCTCAATAGTTAAATT
1 CTATTATATCTTAACAGTTCAATCTAATAACCTATAATAACATATTATATCTCAATAGTTAAATT
1989307 ATAAAACTTAATATATTAATTAGTAATTTAAGAGGTAAATAGAAAAAAAAAAAAAGAGCTAAAAC
66 ATAAAACTTAATATATTAATTAGTAATTTAAGAGGTAAATAGAAAAAAAAAAAAAGAGCTAAAAC
1989372 ACACAAGGTAAAGAGACAATTCATTTAAATTTGAAAAATTATTTTCTCTTCCACTCTTGTGCGCA
131 ACACAAGGTAAAGAGACAATTCATTTAAATTTGAAAAATTATTTTCTCTTCCACTCTTGTGCGCA
1989437 AAGAGTGAGAAAGACTCTTTTAATGGTTTCATTTAGTCATATATAGATGA
196 AAGAGTGAGAAAGACTCTTTTAATGGTTTCATTTAGTCATATATAGATGA
* * * *
1989487 CNTATTATGTCTTAACAGTTTAA-CTTAATAACTTATTATAACATATTATATCTCAATAGTTAAA
1 C-TATTATATCTTAACAGTTCAATC-TAATAACCTATAATAACATATTATATCTCAATAGTTAAA
1989551 TTATAAAACTTAATATATTAATTAGTAATTTAAGAGGTAAATAG-AAAAAAAAAAAAGAGCTAAA
64 TTATAAAACTTAATATATTAATTAGTAATTTAAGAGGTAAATAGAAAAAAAAAAAAAGAGCTAAA
1989615 ACACACAAGGTAAAGAGACAATTCATTTAAATTTGAAAAATTATTTTCTCTTCCACTCTTGTGCG
129 ACACACAAGGTAAAGAGACAATTCATTTAAATTTGAAAAATTATTTTCTCTTCCACTCTTGTGCG
1989680 CAAAGAGTGAGAAAGACTCTTTTAATGGTTTCATTTAGTCATATATAGATGA
194 CAAAGAGTGAGAAAGACTCTTTTAATGGTTTCATTTAGTCATATATAGATGA
1989732 C
1 C
1989733 ACCATCATTA
Statistics
Matches: 239, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
245 140 0.59
246 99 0.41
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (245 bp):
CTATTATATCTTAACAGTTCAATCTAATAACCTATAATAACATATTATATCTCAATAGTTAAATT
ATAAAACTTAATATATTAATTAGTAATTTAAGAGGTAAATAGAAAAAAAAAAAAAGAGCTAAAAC
ACACAAGGTAAAGAGACAATTCATTTAAATTTGAAAAATTATTTTCTCTTCCACTCTTGTGCGCA
AAGAGTGAGAAAGACTCTTTTAATGGTTTCATTTAGTCATATATAGATGA
Found at i:1990694 original size:48 final size:48
Alignment explanation
Indices: 1990637--1990746 Score: 157
Period size: 48 Copynumber: 2.3 Consensus size: 48
1990627 TCAGTTCCAG
* ***
1990637 CCACAGCAGCAGCCACCACCGGCTCAGCAGCAGCCAGTGCAATACCCC
1 CCACAGCAGCAGCCACCACCAGCTCAGCAGCAGCCAACACAATACCCC
* * *
1990685 CCACCGCAGCAGCCAGCACCAGCTCAGCAGCAGCCAACACAATATCCC
1 CCACAGCAGCAGCCACCACCAGCTCAGCAGCAGCCAACACAATACCCC
1990733 CCACAGCAGCAGCC
1 CCACAGCAGCAGCC
1990747 GACACAATAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.29, C:0.46, G:0.19, T:0.05
Consensus pattern (48 bp):
CCACAGCAGCAGCCACCACCAGCTCAGCAGCAGCCAACACAATACCCC
Found at i:1990751 original size:27 final size:27
Alignment explanation
Indices: 1990709--1990769 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
1990699 AGCACCAGCT
1990709 CAGCAGCAGCCAACACAATATCCC-CCA
1 CAGCAGCAGCCAACACAATA-CCCTCCA
*
1990736 CAGCAGCAGCCGACACAATACCCTCCA
1 CAGCAGCAGCCAACACAATACCCTCCA
*
1990763 CCGCAGC
1 CAGCAGC
1990770 CTAACCAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.33, C:0.46, G:0.15, T:0.07
Consensus pattern (27 bp):
CAGCAGCAGCCAACACAATACCCTCCA
Found at i:1996750 original size:14 final size:14
Alignment explanation
Indices: 1996731--1996758 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1996721 ACATTATCAC
1996731 ATCTTCCAAATCTT
1 ATCTTCCAAATCTT
1996745 ATCTTCCAAATCTT
1 ATCTTCCAAATCTT
1996759 TTCCCCATGT
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:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
ATCTTCCAAATCTT
Found at i:2008333 original size:32 final size:32
Alignment explanation
Indices: 2008291--2008354 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
2008281 ACAGTTTTTT
* *
2008291 TTTTTTTTTTTAACCTTCAAATTACATCATTA
1 TTTTTGTTTTTAACATTCAAATTACATCATTA
*
2008323 TTTTTGTTTTTAACATTCCAATTACATCATTA
1 TTTTTGTTTTTAACATTCAAATTACATCATTA
2008355 ATTGTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.55
Consensus pattern (32 bp):
TTTTTGTTTTTAACATTCAAATTACATCATTA
Found at i:2011344 original size:23 final size:22
Alignment explanation
Indices: 2011312--2011371 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
2011302 AAATATTATA
*
2011312 CGTAAGAAAAATTTAAAAACAAC
1 CGTAAAAAAAATTT-AAAACAAC
** *
2011335 CGTAAAAAAAAATTTTTAACACC
1 CGT-AAAAAAAATTTAAAACAAC
*
2011358 CATAAAAAAAATTT
1 CGTAAAAAAAATTT
2011372 TTAGATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 11 0.35
23 10 0.32
24 10 0.32
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.23
Consensus pattern (22 bp):
CGTAAAAAAAATTTAAAACAAC
Found at i:2034812 original size:3 final size:3
Alignment explanation
Indices: 2034804--2034829 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2034794 AAGATATCAA
2034804 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2034830 AACAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2043126 original size:131 final size:131
Alignment explanation
Indices: 2042878--2043118 Score: 391
Period size: 131 Copynumber: 1.8 Consensus size: 131
2042868 TTATTGAGAT
*
2042878 GAATCTACATTATTGAGTCCTCCATTATTTTGAAAAACTGTCTTGTGTTCTTTTCCTTTTGCTTT
1 GAATCTACATTATTGAGTCCTCCATTATTTTGAAAAACTGTCTTGTCTTCTTTTCCTTTTGCTTT
*
2042943 TGCTGAGACTTGCTTGTCTTCTTTTTCTTTTGAAAAGCTGGCTGTCATCTTTTCCGTTTGCTTTT
66 TGCTGAGACTGGCTTGTCTTCTTTTTCTTTTGAAAAGCTGGCTGTCATCTTTTCCGTTTGCTTTT
2043008 G
131 G
*
2043009 GAATCTACATTATTGAGTCCTCCATTATTTTGAAAGACTAG-CTTGTCTTCTTTTCCTTTTGCTT
1 GAATCTACATTATTGAGTCCTCCATTATTTTGAAAAACT-GTCTTGTCTTCTTTTCCTTTTGCTT
2043073 TTGCTGAGACTGGCTTTAGT-TT-TTTTTCTTTTG-AAAGACTGGCTGT
65 TTGCTGAGACTGGC-TT-GTCTTCTTTTTCTTTTGAAAAG-CTGGCTGT
2043119 TGTCTTTTTT
Statistics
Matches: 103, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
130 4 0.04
131 92 0.89
132 5 0.05
133 2 0.02
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.49
Consensus pattern (131 bp):
GAATCTACATTATTGAGTCCTCCATTATTTTGAAAAACTGTCTTGTCTTCTTTTCCTTTTGCTTT
TGCTGAGACTGGCTTGTCTTCTTTTTCTTTTGAAAAGCTGGCTGTCATCTTTTCCGTTTGCTTTT
G
Found at i:2043150 original size:69 final size:69
Alignment explanation
Indices: 2043036--2043230 Score: 214
Period size: 69 Copynumber: 3.0 Consensus size: 69
2043026 TCCTCCATTA
* * *
2043036 TTTTGAAAGACTAGC--TTGTC--TTCTTTTCCTTTTGCTTTTGCTGAGACTGGCTTTAGT-TT-
1 TTTTGAAAGACTGGCTGTTGTCTTTTTTTTTCCTTTTGCTTTTGCTGAGACTAGC-TT-GTCTTC
2043095 TTTTTC
64 TTTTTC
* * *
2043101 TTTTGAAAGACTGGCTGTTGTCTTTTTTTTTTCTTTTGTTTTTGTTGAGACTAGCTTGTCTTCTT
1 TTTTGAAAGACTGGCTGTTGTCTTTTTTTTTCCTTTTGCTTTTGCTGAGACTAGCTTGTCTTCTT
2043166 TTTC
66 TTTC
* * *
2043170 TTTTGAAAGACTGGC---TGTC--GTTTTTTCCGTTTGCTTTTGCTGAGACTAGCTTGCCTTCTT
1 TTTTGAAAGACTGGCTGTTGTCTTTTTTTTTCCTTTTGCTTTTGCTGAGACTAGCTTGTCTTCTT
2043230 T
66 T
2043231 GACTGGTTTA
Statistics
Matches: 112, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
64 36 0.32
65 14 0.12
66 4 0.04
67 7 0.06
68 4 0.04
69 47 0.42
ACGTcount: A:0.11, C:0.16, G:0.18, T:0.54
Consensus pattern (69 bp):
TTTTGAAAGACTGGCTGTTGTCTTTTTTTTTCCTTTTGCTTTTGCTGAGACTAGCTTGTCTTCTT
TTTC
Found at i:2043598 original size:16 final size:16
Alignment explanation
Indices: 2043577--2043614 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
2043567 TTGGTTTTGA
2043577 AAGTGCAGATAATTGT
1 AAGTGCAGATAATTGT
*
2043593 AAGTGCAGATAATTTT
1 AAGTGCAGATAATTGT
2043609 AAGTGC
1 AAGTGC
2043615 TCCATTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.32
Consensus pattern (16 bp):
AAGTGCAGATAATTGT
Found at i:2046943 original size:21 final size:23
Alignment explanation
Indices: 2046904--2046946 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2046894 CTTGATTTGC
*
2046904 TATTGCAGGTTTTTCAATTTTTT
1 TATTGCAGGTTTTTAAATTTTTT
2046927 TATTG-AGG-TTTTAAATTTTT
1 TATTGCAGGTTTTTAAATTTTT
2046947 CAAGGTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.21, C:0.05, G:0.14, T:0.60
Consensus pattern (23 bp):
TATTGCAGGTTTTTAAATTTTTT
Found at i:2047823 original size:17 final size:16
Alignment explanation
Indices: 2047792--2047836 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
2047782 GAGAAATGAG
*
2047792 AGAAAGAGAAGGAAAA
1 AGAAAGAAAAGGAAAA
2047808 AGAAAGAAAGAGGAAAA
1 AGAAAGAAA-AGGAAAA
*
2047825 AAAAAGGAAAAG
1 AGAAA-GAAAAG
2047837 CTAGCGGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
17 13 0.52
18 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAGGAAAA
Found at i:2047918 original size:4 final size:4
Alignment explanation
Indices: 2047909--2047971 Score: 59
Period size: 4 Copynumber: 17.5 Consensus size: 4
2047899 CGGCTAGGAG
*
2047909 AGAA AGAA AGAA AGAA AG-- AGAA AGAA AG-A AGAA AGAG A-AA AG-A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
2047952 A-AA AGAA AGAG AG-A AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AG
2047972 GGGGAACGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
2 2 0.04
3 11 0.23
4 35 0.73
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2047941 original size:79 final size:78
Alignment explanation
Indices: 2047846--2048051 Score: 281
Period size: 79 Copynumber: 2.6 Consensus size: 78
2047836 GCTAGCGGGG
* *
2047846 GAAAGAAA-AGAGAAGAAAGAGAAAGAAAGAAGAAAGAGAAAAGAAGGGGGGAGCGGCTAGGAGA
1 GAAAGAAAGAAAGAAGAAAGAGAAAGAAA-AAGAAAGAGAAAAGAAGGGGGGAACGGCTAGGAGA
2047910 GAAAGAAAGAAAGA
65 GAAAGAAAGAAAGA
* * *
2047924 -AAGAGAAAGAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAAGGGGGAACGGCTGGGAG
1 GAA-AGAAAGAAAGAAGAAAGAG-AAAGAAAAAGAAAGAGAAAAGAAGGGGGGAACGGCTAGGAG
2047988 AGAAAGAAAGAAAGA
64 AGAAAGAAAGAAAGA
* * *
2048003 GAAAGAAAGAAAGAGAGAAAGAAAAAGAAACAAAAAAGAGAAAAAAAGG
1 GAAAGAAAGAAAGA-AGAAAGAGAAAGAAA-AAGAAAGAGAAAAGAAGG
2048052 AGAAAGGTTC
Statistics
Matches: 112, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
77 2 0.02
78 5 0.04
79 75 0.67
80 30 0.27
ACGTcount: A:0.63, C:0.02, G:0.33, T:0.01
Consensus pattern (78 bp):
GAAAGAAAGAAAGAAGAAAGAGAAAGAAAAAGAAAGAGAAAAGAAGGGGGGAACGGCTAGGAGAG
AAAGAAAGAAAGA
Found at i:2047942 original size:17 final size:17
Alignment explanation
Indices: 2047907--2047971 Score: 96
Period size: 17 Copynumber: 3.7 Consensus size: 17
2047897 AGCGGCTAGG
2047907 AGAGAAAGAAAGAAAGAA
1 AGAGAAAGAAAG-AAGAA
2047925 AGAGAAAGAAAGAAGAA
1 AGAGAAAGAAAGAAGAA
2047942 AGAGAAAAGAAA-AAGAA
1 AGAG-AAAGAAAGAAGAA
2047959 AGAGAGAAGAAAG
1 AGAGA-AAGAAAG
2047972 GGGGAACGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.02
17 24 0.55
18 19 0.43
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AGAGAAAGAAAGAAGAA
Found at i:2047958 original size:28 final size:29
Alignment explanation
Indices: 2047909--2047971 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
2047899 CGGCTAGGAG
*
2047909 AGAAAGAAAGAAAGAAAGAGAAAGAAAGA
1 AGAAAGAAAGAAAGAAAAAGAAAGAAAGA
* *
2047938 AGAAAGAGA-AAAGAAAAAGAAAGAGAGA
1 AGAAAGAAAGAAAGAAAAAGAAAGAAAGA
2047966 AGAAAG
1 AGAAAG
2047972 GGGGAACGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 23 0.74
29 8 0.26
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (29 bp):
AGAAAGAAAGAAAGAAAAAGAAAGAAAGA
Found at i:2047997 original size:4 final size:4
Alignment explanation
Indices: 2047988--2048026 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
2047978 CGGCTGGGAG
*
2047988 AGAA AGAA AGAA AG-- AGAA AGAA AGAA AGAG AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
2048027 AAGAAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
4 29 0.94
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2048054 original size:11 final size:11
Alignment explanation
Indices: 2048006--2048056 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2047996 AGAAAGAGAA
*
2048006 AGAAAGAAAGAG
1 AGAAA-AAAAAG
2048018 AGAAAGAAAAAG
1 AGAAA-AAAAAG
2048030 A-AACAAAAAAG
1 AGAA-AAAAAAG
*
2048041 AGAAAAAAAGG
1 AGAAAAAAAAG
2048052 AGAAA
1 AGAAA
2048057 GGTTCAAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 20 0.57
12 15 0.43
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:2057518 original size:60 final size:60
Alignment explanation
Indices: 2057405--2058323 Score: 884
Period size: 60 Copynumber: 15.5 Consensus size: 60
2057395 TTGGTGAATT
* * * * *
2057405 AAATCAAACCTATTTTAAGATAGGTCGAGCCTAGATCGAGTCTAGAAATTTCAATTTTCA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * * *
2057465 AAATTGAACCTGTTTTAAGATAAGTCGAGCCTAGATCAAGTTTAGGAACTTCAATTTTTA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * *
2057525 AAATCGAA-CTGTTTTAAGATAGGTCGAGTCTAGATCAAGTTTAGGAACTTCAATTTTTA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * * * * *
2057584 AAATCGAACCTGTTTTAAGATAGGTCGAGCCCAAATCAAGTCTAAGAATTTTAATCTTCA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * *
2057644 AAATCGAACCTGTTTTAAGATAGGTCAAGCCTAGATCGAGTCTAGGAATTTCAATTTTCA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * * * * *
2057704 AAATTGAACTTGTTTTAAGATAGGTCAAGCCTAGATCAAGTTTAGAAACTTCAATTTTTA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * *
2057764 AAATCAAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTTTAGGAACTTCAATTTTTA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* ** * * *
2057824 AAATCGAACCTGTTTTAAGATAGGTCGAGCCCAGATCAAGTCTAAAAATTTTAATCTTAA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * *
2057884 AAATCGAACCTATTTTAAGATAGGTCGAGCCTAAATCAAGTCTAGGAATTTCAATTTTGTTT
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAA-TTT-TTA
* * * * *
2057946 AAATCGAACCTGTTGTGAA-ATAGGTCGAGCCTAGATTAAGTTTAGGAGTTTTAATTTTT-
1 AAATCGAACCTGTT-TTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * * * * *
2058005 AAATCGAACCTGTTTGTGAGATAAGTCGAGCCTATATTAAGTCTAGAAATTTTAATTTTT-
1 AAATCGAACCTGTTT-TAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * * * * ** *
2058065 AAA---AACCTGTTGTGAGATATGTCGAGCCTAAATTAAGTCTAAAAATTTTAA-TTTT-
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
* * * * * * * * *
2058120 AAATTGAACCCGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAAGAATTTCAATTTTGTTT
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAA-TTT-TTA
* * * * *
2058182 AAATCAAACCTGTTGTGAGATAGGTCGGGCCTAGATTAAGTCTA-G-A----AA-TTTT-
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
** * * * * * *
2058234 -AATCGAATTTGTTCTAATATGGGTCAAGCCTAGATCAAGTCTAGAAATTTCAATTTTGTTT
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAA-TTT-TTA
* * * *
2058295 AAATCGAACTTATTTTGAGATAAGTCGAG
1 AAATCGAACCTGTTTTAAGATAGGTCGAG
2058324 TCTAAATCGA
Statistics
Matches: 729, Mismatches: 106, Indels: 46
0.83 0.12 0.05
Matches are distributed among these distances:
51 33 0.05
53 3 0.00
54 2 0.00
55 7 0.01
56 38 0.05
57 10 0.01
58 44 0.06
59 74 0.10
60 405 0.56
61 8 0.01
62 102 0.14
63 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (60 bp):
AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATTTCAATTTTTA
Found at i:2058860 original size:17 final size:16
Alignment explanation
Indices: 2058826--2058864 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2058816 GAGAAAGGAG
* *
2058826 AGAAAGAGAAGGAGAA
1 AGAAAGAAAAGGAAAA
2058842 AGAAAGAAAGAGGAAAA
1 AGAAAGAAA-AGGAAAA
2058859 AGAAAG
1 AGAAAG
2058865 GAGAAGCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAGGAAAA
Found at i:2058908 original size:24 final size:22
Alignment explanation
Indices: 2058881--2058941 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 22
2058871 CCAGCGGGGG
2058881 AAAGAAAGGAGAAGAAAGAGAAAA
1 AAAGAAAGGAGAAGAAA-A-AAAA
*
2058905 AAAG-AA-GA-AAGAGAAAAGAA
1 AAAGAAAGGAGAAGA-AAAAAAA
2058925 AAAGAAAGAGAGAAGAA
1 AAAGAAAG-GAGAAGAA
2058942 GGGGGGAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
20 7 0.23
21 7 0.23
22 4 0.13
23 5 0.16
24 8 0.26
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAGAAAGGAGAAGAAAAAAAA
Found at i:2058912 original size:17 final size:18
Alignment explanation
Indices: 2058890--2059013 Score: 103
Period size: 17 Copynumber: 6.6 Consensus size: 18
2058880 GAAAGAAAGG
2058890 AGAAGAAAGAGAAAA-AA
1 AGAAGAAAGAGAAAAGAA
2058907 AGAAGAAAGAGAAAAGAA
1 AGAAGAAAGAGAAAAGAA
*
2058925 A-AAGAAAGAGAGAAGAA
1 AGAAGAAAGAGAAAAGAA
* *
2058942 GGGGGGAACGGCTAAGAGAGAAAGAA
1 ----AGAA--G-AAAGAGA-AAAGAA
2058968 AGAAAGAAAGAG-AAAGAA
1 AG-AAGAAAGAGAAAAGAA
*
2058986 GGAAGAAAGAGAAAAGAA
1 AGAAGAAAGAGAAAAGAA
2059004 A-AAGAAAGAG
1 AGAAGAAAGAG
2059014 TGAAGAAAGG
Statistics
Matches: 87, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
17 48 0.55
18 16 0.18
20 5 0.06
21 1 0.01
22 3 0.03
23 2 0.02
24 1 0.01
25 6 0.07
26 5 0.06
ACGTcount: A:0.65, C:0.02, G:0.32, T:0.01
Consensus pattern (18 bp):
AGAAGAAAGAGAAAAGAA
Found at i:2058930 original size:28 final size:27
Alignment explanation
Indices: 2058882--2058941 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
2058872 CAGCGGGGGA
* *
2058882 AAGAAAGGAGAAGAAAGAGAAAAAAAG
1 AAGAAAGGAAAAGAAAAAGAAAAAAAG
* *
2058909 AAGAAAGAGAAAAGAAAAAGAAAGAGAG
1 AAGAAAG-GAAAAGAAAAAGAAAAAAAG
2058937 AAGAA
1 AAGAA
2058942 GGGGGGAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (27 bp):
AAGAAAGGAAAAGAAAAAGAAAAAAAG
Found at i:2058978 original size:79 final size:79
Alignment explanation
Indices: 2058880--2059067 Score: 268
Period size: 79 Copynumber: 2.3 Consensus size: 79
2058870 GCCAGCGGGG
*
2058880 GAAAGAAAGGAGAAGAAAGAGAAAAAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAGGG
1 GAAAGAAA-GA-AAGAAAGAGAAAAAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAAGG
*
2058945 GGGAACGGCTAAGAGA
64 GGGAACGACTAAGAGA
* * *
2058961 GAAAGAAAGAAAGAAAGAGAAAGAAGGAAGAAAGAGAAAAGAAAAAGAAAGAGTGAAGAAAGGGG
1 GAAAGAAAGAAAGAAAGAGAAAAAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAAGGGG
*
2059026 GAACGACTAGGAGA
66 GAACGACTAAGAGA
* *
2059040 GAAAGAATAAGAAAAAAAAAGAAAAAAA
1 GAAAG-A-AAGAAAGAAAGAGAAAAAAA
2059068 AATTCAAACA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 68 0.72
80 3 0.03
81 24 0.25
ACGTcount: A:0.64, C:0.02, G:0.31, T:0.02
Consensus pattern (79 bp):
GAAAGAAAGAAAGAAAGAGAAAAAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAAGGGG
GAACGACTAAGAGA
Found at i:2059009 original size:28 final size:29
Alignment explanation
Indices: 2058960--2059022 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
2058950 CGGCTAAGAG
*
2058960 AGAAAGAAAGAAAGAAAGAGAAAGAAG-GA
1 AGAAAGAAAGAAAGAAAAAGAAAG-AGTGA
*
2058989 AGAAAGAGA-AAAGAAAAAGAAAGAGTGA
1 AGAAAGAAAGAAAGAAAAAGAAAGAGTGA
2059017 AGAAAG
1 AGAAAG
2059023 GGGGAACGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 2 0.06
28 21 0.68
29 8 0.26
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (29 bp):
AGAAAGAAAGAAAGAAAAAGAAAGAGTGA
Found at i:2064956 original size:45 final size:45
Alignment explanation
Indices: 2064867--2064974 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
2064857 TAATAAAATC
* * *
2064867 ACACGCCATGTACAAAAATATGTTACATGCCATGATTAGTTTGTT
1 ACACGCCATGTACAAAAATATGTGACATCCCATGATTAGGTTGTT
*
2064912 ACACGTCATGTACAAAAATATGTGACA-CCCTAT-AGTTAGGTTGTT
1 ACACGCCATGTACAAAAATATGTGACATCCC-ATGA-TTAGGTTGTT
* *
2064957 ACATGCCATGCACAAAAA
1 ACACGCCATGTACAAAAA
2064975 CATGCTACAC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 3 0.06
45 51 0.94
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (45 bp):
ACACGCCATGTACAAAAATATGTGACATCCCATGATTAGGTTGTT
Found at i:2064996 original size:69 final size:68
Alignment explanation
Indices: 2064911--2065248 Score: 226
Period size: 69 Copynumber: 5.0 Consensus size: 68
2064901 ATTAGTTTGT
* * * *
2064911 TACACGTCATGTACAAAAATATGTGACAC-CCTATAGTTAGGTTGTTACATGCCATGCACAAAAA
1 TACACGTCATGAACAAAAACATGTGACACATCT-TAGTTAGGTTGTTACACGCCATG-ACAAAAA
2064975 CATGC
64 CATGC
* * ** ***
2064980 TACACGTCATGAACAAAAACATGTGACACATCTTGGTTAGGTTGCTACACGCCATG--ATTAGGT
1 TACACGTCATGAACAAAAACATGTGACACATCTTAGTTAGGTTGTTACACGCCATGACAAAAACA
2065043 TGC
66 TGC
* * * * * *
2065046 TACACG-CTATGTACAAAAACATGTAATA-ACTCATGGTTAGGTTGTTACACCCCATGTACAAAA
1 TACACGTC-ATGAACAAAAACATGTGACACA-TCTTAGTTAGGTTGTTACACGCCATG-ACAAAA
* *
2065109 ATATGT
63 ACATGC
* * * * * ******
2065115 TACACGTCATGAATAAAAATATGTGACACGTCTTAGTTAGATTGTTACACGTCATG--ATTCGGT
1 TACACGTCATGAACAAAAACATGTGACACATCTTAGTTAGGTTGTTACACGCCATGACAAAAACA
*
2065178 TGT
66 TGC
* * * *
2065181 TACACGCCATGTACAAAAACATGTG--ACATGCTATGGTTAGGTTGTTGCACGCCATGTACAAAA
1 TACACGTCATGAACAAAAACATGTGACACAT-CT-TAGTTAGGTTGTTACACGCCATG-ACAAAA
2065244 ACATG
63 ACATG
2065249 TGACATACCA
Statistics
Matches: 201, Mismatches: 55, Indels: 26
0.71 0.20 0.09
Matches are distributed among these distances:
64 3 0.01
65 4 0.02
66 95 0.47
69 96 0.48
70 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (68 bp):
TACACGTCATGAACAAAAACATGTGACACATCTTAGTTAGGTTGTTACACGCCATGACAAAAACA
TGC
Found at i:2065115 original size:24 final size:24
Alignment explanation
Indices: 2065088--2065143 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2065078 ATGGTTAGGT
*
2065088 TGTTACACCCCATGTACAAAAATA
1 TGTTACACCCCATGAACAAAAATA
** *
2065112 TGTTACACGTCATGAATAAAAATA
1 TGTTACACCCCATGAACAAAAATA
*
2065136 TGTGACAC
1 TGTTACAC
2065144 GTCTTAGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (24 bp):
TGTTACACCCCATGAACAAAAATA
Found at i:2065125 original size:45 final size:45
Alignment explanation
Indices: 2065025--2065280 Score: 175
Period size: 45 Copynumber: 5.7 Consensus size: 45
2065015 GTTAGGTTGC
* * *
2065025 TACACGCCATGATTAGGTTGCTACACGCTATGTACAAAAACATGT
1 TACACGTCATGATTAGGTTGTTACACGCCATGTACAAAAACATGT
* * *
2065070 AATA-AC-TCATGGTTAGGTTGTTACACCCCATGTACAAAAATATGT
1 --TACACGTCATGATTAGGTTGTTACACGCCATGTACAAAAACATGT
* ** * * *** * *
2065115 TACACGTCATGAATAAAAATATGTGACACGTC-T-TAGTTAGA-TTGT
1 TACACGTCATG-AT-TAGGT-TGTTACACGCCATGTACAAAAACATGT
*
2065160 TACACGTCATGATTCGGTTGTTACACGCCATGTACAAAAACATGT
1 TACACGTCATGATTAGGTTGTTACACGCCATGTACAAAAACATGT
* * * *
2065205 GACATG-CTATGGTTAGGTTGTTGCACGCCATGTACAAAAACATGT
1 TACACGTC-ATGATTAGGTTGTTACACGCCATGTACAAAAACATGT
* ***
2065250 GACATACCAT-AGTTAGGTTGTTACACGCCAT
1 TACACGTCATGA-TTAGGTTGTTACACGCCAT
2065281 ATTGAAAAAA
Statistics
Matches: 161, Mismatches: 37, Indels: 24
0.73 0.17 0.11
Matches are distributed among these distances:
42 9 0.06
43 4 0.02
44 9 0.06
45 118 0.73
46 8 0.05
47 5 0.03
48 8 0.05
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (45 bp):
TACACGTCATGATTAGGTTGTTACACGCCATGTACAAAAACATGT
Found at i:2065139 original size:135 final size:134
Alignment explanation
Indices: 2064890--2065249 Score: 445
Period size: 135 Copynumber: 2.7 Consensus size: 134
2064880 AAAAATATGT
* * * * * * *
2064890 TACATGCCATGATTAGTTTGTTACACG-TCATGTACAAAAATATGTGACACCCTATAGTTAGGTT
1 TACACGCCATGATTAGGTTGTTACACGCT-ATGTACAAAAACATGTAATACTC-ATGGTTAGGTT
* * * *
2064954 GTTACATGCCATGCACAAAAACATGCTACACGTCATGAACAAAAACATGTGACACATCTTGGTTA
64 GTTACACGCCATGTACAAAAACATGTTACACGTCATGAACAAAAACATGTGACACATCTTAGTTA
*
2065019 GGTTGC
129 GATTGC
*
2065025 TACACGCCATGATTAGGTTGCTACACGCTATGTACAAAAACATGTAATAACTCATGGTTAGGTTG
1 TACACGCCATGATTAGGTTGTTACACGCTATGTACAAAAACATGTAAT-ACTCATGGTTAGGTTG
* * * * *
2065090 TTACACCCCATGTACAAAAATATGTTACACGTCATGAATAAAAATATGTGACACGTCTTAGTTAG
65 TTACACGCCATGTACAAAAACATGTTACACGTCATGAACAAAAACATGTGACACATCTTAGTTAG
*
2065155 ATTGT
130 ATTGC
* * * *
2065160 TACACGTCATGATTCGGTTGTTACACGCCATGTACAAAAACATGTGACATGCT-ATGGTTAGGTT
1 TACACGCCATGATTAGGTTGTTACACGCTATGTACAAAAACATGT-A-ATACTCATGGTTAGGTT
*
2065224 GTTGCACGCCATGTACAAAAACATGT
64 GTTACACGCCATGTACAAAAACATGT
2065250 GACATACCAT
Statistics
Matches: 194, Mismatches: 27, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
135 185 0.95
136 7 0.04
137 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (134 bp):
TACACGCCATGATTAGGTTGTTACACGCTATGTACAAAAACATGTAATACTCATGGTTAGGTTGT
TACACGCCATGTACAAAAACATGTTACACGTCATGAACAAAAACATGTGACACATCTTAGTTAGA
TTGC
Found at i:2065205 original size:66 final size:65
Alignment explanation
Indices: 2064887--2065236 Score: 236
Period size: 66 Copynumber: 5.2 Consensus size: 65
2064877 TACAAAAATA
* * * * * * * *
2064887 TGTTACATGCCATGATTAGTTTGTTACACGTCATGTACAAAAATATGTGACACCCTATAGTTAGG
1 TGTTACACGCCATGATTCGGTTGTTACACGCCATGAACAAAAACATGTGACACTCT-TGGTTAGG
2064952 T
65 T
* ****** * *
2064953 TGTTACATGCCATGCACAAAAACATGCTACACGTCATGAACAAAAACATGTGACACATCTTGGTT
1 TGTTACACGCCATG---ATTCGGTTGTTACACGCCATGAACAAAAACATGTGACAC-TCTTGGTT
2065018 AGGT
62 AGGT
* * * * * * * *
2065022 TGCTACACGCCATGATTAGGTTGCTACACGCTATGTACAAAAACATGTAATAACTCATGGTTAGG
1 TGTTACACGCCATGATTCGGTTGTTACACGCCATGAACAAAAACATGTGA-CACTCTTGGTTAGG
2065087 T
65 T
* * ** * * * *
2065088 TGTTACACCCCATG-TACAAAAATATGTTACACGTCATGAATAAAAATATGTGACACGTCTTAGT
1 TGTTACACGCCATGATTC---GGT-TGTTACACGCCATGAACAAAAACATGTGACAC-TCTTGGT
*
2065152 TAGAT
61 TAGGT
* *
2065157 TGTTACACGTCATGATTCGGTTGTTACACGCCATGTACAAAAACATGTGACA-TGCTATGGTTAG
1 TGTTACACGCCATGATTCGGTTGTTACACGCCATGAACAAAAACATGTGACACT-CT-TGGTTAG
2065221 GT
64 GT
*
2065223 TGTTGCACGCCATG
1 TGTTACACGCCATG
2065237 TACAAAAACA
Statistics
Matches: 218, Mismatches: 53, Indels: 26
0.73 0.18 0.09
Matches are distributed among these distances:
64 1 0.00
65 3 0.01
66 110 0.50
67 3 0.01
68 3 0.01
69 94 0.43
70 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (65 bp):
TGTTACACGCCATGATTCGGTTGTTACACGCCATGAACAAAAACATGTGACACTCTTGGTTAGGT
Found at i:2065289 original size:45 final size:45
Alignment explanation
Indices: 2065175--2065280 Score: 176
Period size: 45 Copynumber: 2.4 Consensus size: 45
2065165 GTCATGATTC
* * *
2065175 GGTTGTTACACGCCATGTACAAAAACATGTGACATGCTATGGTTA
1 GGTTGTTACACGCCATGTACAAAAACATGTGACATACCATAGTTA
*
2065220 GGTTGTTGCACGCCATGTACAAAAACATGTGACATACCATAGTTA
1 GGTTGTTACACGCCATGTACAAAAACATGTGACATACCATAGTTA
2065265 GGTTGTTACACGCCAT
1 GGTTGTTACACGCCAT
2065281 ATTGAAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (45 bp):
GGTTGTTACACGCCATGTACAAAAACATGTGACATACCATAGTTA
Found at i:2065302 original size:31 final size:31
Alignment explanation
Indices: 2065266--2065349 Score: 109
Period size: 29 Copynumber: 2.8 Consensus size: 31
2065256 CCATAGTTAG
2065266 GTTGTTACACGCCATATTGAAAAAAAATATT
1 GTTGTTACACGCCATATTGAAAAAAAATATT
* *
2065297 GTTGTTACACGCCAT-GTG-GAAAAAATATT
1 GTTGTTACACGCCATATTGAAAAAAAATATT
** *
2065326 GTTGTTACATACCATATTCAAAAA
1 GTTGTTACACGCCATATTGAAAAA
2065350 CATTTTATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 23 0.52
30 3 0.07
31 18 0.41
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (31 bp):
GTTGTTACACGCCATATTGAAAAAAAATATT
Found at i:2070368 original size:21 final size:20
Alignment explanation
Indices: 2070352--2070390 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2070342 CCTCAAATCT
2070352 TACTCCAATTAAGTCAAATTA
1 TACTCCAA-TAAGTCAAATTA
2070373 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
2070391 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Done.