Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_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: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 19
Found at i:1769287 original size:28 final size:29
Alignment explanation
Indices: 1769255--1769312 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1769245 AAAAAATCGG
*
1769255 TTAATCGGGTTCAGTTAATAA-TTTCAAA
1 TTAATCAGGTTCAGTTAATAATTTTCAAA
* **
1769283 TTAATTAGGTTTGGTTAATAATTTTCAAA
1 TTAATCAGGTTCAGTTAATAATTTTCAAA
1769312 T
1 T
1769313 AAATTTTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAATCAGGTTCAGTTAATAATTTTCAAA
Found at i:1769443 original size:67 final size:68
Alignment explanation
Indices: 1769326--1769466 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 68
1769316 TTTTGGTTCG
* * *** *
1769326 ATTAACCGAACCGAATTAACCGATTTTTTTCTTTAACTGTTAATCGAACCAAAATTTATTTGAAA
1 ATTAACCAAACCGAATTAACCGAATTTTTTCTTTAAAAATTAATCAAACCAAAATTTATTTGAAA
1769391 ATT
66 ATT
* *
1769394 ATTAACCAAACCTAATTAACC-AATTTTTTCTTTAAAAATTAATTAAACCAAAATTTATTTGAAA
1 ATTAACCAAACCGAATTAACCGAATTTTTTCTTTAAAAATTAATCAAACCAAAATTTATTTGAAA
1769458 ATT
66 ATT
1769461 ATTAAC
1 ATTAAC
1769467 TGCACCGAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 46 0.71
68 19 0.29
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (68 bp):
ATTAACCAAACCGAATTAACCGAATTTTTTCTTTAAAAATTAATCAAACCAAAATTTATTTGAAA
ATT
Found at i:1770059 original size:30 final size:29
Alignment explanation
Indices: 1770019--1770075 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
1770009 TAATGGTCGA
*
1770019 TGATTTGATTGAATTAATTAAATAATTCAG
1 TGATCTGATTGAATTAATTAAA-AATTCAG
*
1770049 TGATCTGATTGATTTAATTAAAAATTC
1 TGATCTGATTGAATTAATTAAAAATTC
1770076 GATGATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (29 bp):
TGATCTGATTGAATTAATTAAAAATTCAG
Found at i:1770092 original size:29 final size:30
Alignment explanation
Indices: 1770019--1770092 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
1770009 TAATGGTCGA
*
1770019 TGATTTGATTGAA-TTAATTAAATAATTCAG
1 TGATCTGATT-AATTTAATTAAATAATTCAG
*
1770049 TGATCTGATTGATTTAATTAAA-AATTC-G
1 TGATCTGATTAATTTAATTAAATAATTCAG
1770077 ATGATCAT-ATTAATTT
1 -TGATC-TGATTAATTT
1770093 TTGACCATAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 1 0.03
29 18 0.47
30 19 0.50
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (30 bp):
TGATCTGATTAATTTAATTAAATAATTCAG
Found at i:1772734 original size:139 final size:137
Alignment explanation
Indices: 1772445--1772695 Score: 324
Period size: 139 Copynumber: 1.8 Consensus size: 137
1772435 ATCATTCACC
* * * * *
1772445 TTAGGTTTAATTTCACCTTAGTCCTTTAATTTAGGGAGAATTTTTAATTTGGTCATCATTTTTGC
1 TTAGGTTTAATTTCACATTAATCCTTCAATTTAGGGAGAATTCTTAATTTGGTCATCACTTTTGC
* * * *
1772510 TCGAGGTTTCATTTTAATTATTCGAATCAATAAGTGGTTAAAATTGACTAGGTTAGTTAATAGAA
66 TCGAGGTTCCATTTTAATTATTCGAATCAATAAATGATTAAAAATGACTAGG-T-GTTAATAGAA
*
1772575 GACTCCATA
129 GACTACATA
* *
1772584 TTAGGTTTAATTTCACATTCAATCCTTCAATTTA-GGAGAGTTCTTAATTTGGTCATCGCTTTTG
1 TTAGGTTTAATTTCACATT-AATCCTTCAATTTAGGGAGAATTCTTAATTTGGTCATCACTTTTG
* * * *
1772648 CTCGAGGTTCCATTTTAATTATTTGATTCAGTAAATTATTAAAAATGA
65 CTCGAGGTTCCATTTTAATTATTCGAATCAATAAATGATTAAAAATGA
1772696 TTTGGGTTAA
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
139 84 0.88
140 12 0.12
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (137 bp):
TTAGGTTTAATTTCACATTAATCCTTCAATTTAGGGAGAATTCTTAATTTGGTCATCACTTTTGC
TCGAGGTTCCATTTTAATTATTCGAATCAATAAATGATTAAAAATGACTAGGTGTTAATAGAAGA
CTACATA
Found at i:1779362 original size:5 final size:5
Alignment explanation
Indices: 1779352--1779383 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1779342 AATGATTATC
1779352 TTTTA TTTTA TTTTA --TTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1779384 TATATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.12
5 22 0.88
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1779389 original size:13 final size:13
Alignment explanation
Indices: 1779354--1779381 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1779344 TGATTATCTT
1779354 TTATTTTATTTTA
1 TTATTTTATTTTA
1779367 TTATTTTATTTTA
1 TTATTTTATTTTA
1779380 TT
1 TT
1779382 TTTATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:1779389 original size:18 final size:17
Alignment explanation
Indices: 1779347--1779389 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
1779337 ACACGAATGA
*
1779347 TTATCTTTTATTTTATT
1 TTATATTTTATTTTATT
1779364 TTATTATTTTATTTTATTT
1 TTA-TATTTTATTTTA-TT
1779383 TTATATT
1 TTATATT
1779390 AAATATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 15 0.65
19 5 0.22
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATATTTTATTTTATT
Found at i:1779724 original size:11 final size:12
Alignment explanation
Indices: 1779690--1779721 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
1779680 ATATCACTTT
1779690 TTATCTTTTAAAA
1 TTAT-TTTTAAAA
1779703 TTATTTTTAAAA
1 TTATTTTTAAAA
1779715 TTATTTT
1 TTATTTT
1779722 AAATTTAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:1784745 original size:78 final size:78
Alignment explanation
Indices: 1784639--1784791 Score: 179
Period size: 77 Copynumber: 2.0 Consensus size: 78
1784629 ATATAGTAAG
**
1784639 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAAT-TGATATTT-ATTTCAGAA-TAA
1 TAAACATTAAAAGAATGTAATTAAGATTACAACTC-TTTAATAT-ATATTTAATTT--GAATTAA
1784701 TTAAATAAGATTTTAAA
62 TTAAATAAGATTTTAAA
* * * *
1784718 TAAACATT-AAAGATTTTAATTAAGATTATAAGTCTTTAATATATATTTAATTTGAATTAATTAA
1 TAAACATTAAAAGAATGTAATTAAGATTACAACTCTTTAATATATATTTAATTTGAATTAATTAA
*
1784782 ATAAGTTTTT
66 ATAAGATTTT
1784792 TTAATTTGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
76 3 0.05
77 28 0.44
78 25 0.39
79 8 0.12
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTAAGATTACAACTCTTTAATATATATTTAATTTGAATTAATTAA
ATAAGATTTTAAA
Found at i:1790709 original size:4 final size:4
Alignment explanation
Indices: 1790700--1790758 Score: 52
Period size: 4 Copynumber: 15.2 Consensus size: 4
1790690 ACTTTGCCTG
* * *
1790700 AAGA AAGA AAAA AAGA AAGA AAAA AAGA AAGA AA-A AAGGA AA-A TA-A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA-GA AAGA AAGA
*
1790746 AAGA AAAA AAGA A
1 AAGA AAGA AAGA A
1790759 GAAGAAGAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 7 0.16
4 34 0.77
5 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:1790716 original size:8 final size:8
Alignment explanation
Indices: 1790703--1790804 Score: 71
Period size: 8 Copynumber: 12.1 Consensus size: 8
1790693 TTGCCTGAAG
1790703 AAAGAAAA
1 AAAGAAAA
1790711 AAAGAAAGA
1 AAAGAAA-A
*
1790720 AAA-AAAG
1 AAAGAAAA
1790727 AAAGAAAA
1 AAAGAAAA
*
1790735 AAGGAAAATA
1 AAAG-AAA-A
1790745 AAAGAAAA
1 AAAGAAAA
1790753 AAAGAAGAA
1 AAAGAA-AA
*
1790762 GAAGAAATA
1 AAAGAAA-A
*
1790771 AATGAAAA
1 AAAGAAAA
*
1790779 AAGGTAAAA
1 AAAG-AAAA
* *
1790788 AAATAAAT
1 AAAGAAAA
*
1790796 AAATAAAA
1 AAAGAAAA
1790804 A
1 A
1790805 TGAGGGTTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
7 3 0.04
8 39 0.52
9 29 0.39
10 4 0.05
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (8 bp):
AAAGAAAA
Found at i:1790717 original size:12 final size:12
Alignment explanation
Indices: 1790700--1790761 Score: 76
Period size: 11 Copynumber: 5.4 Consensus size: 12
1790690 ACTTTGCCTG
1790700 AAGAAAGAAAAA
1 AAGAAAGAAAAA
1790712 AAGAAAGAAAAA
1 AAGAAAGAAAAA
1790724 AAGAAAG-AAAA
1 AAGAAAGAAAAA
* *
1790735 AAGGAA-AATAA
1 AAGAAAGAAAAA
*
1790746 AAGAAA-AAAAG
1 AAGAAAGAAAAA
1790757 AAGAA
1 AAGAA
1790762 GAAGAAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
11 25 0.57
12 19 0.43
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (12 bp):
AAGAAAGAAAAA
Found at i:1790778 original size:44 final size:43
Alignment explanation
Indices: 1790703--1790787 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
1790693 TTGCCTGAAG
1790703 AAAGAAAAAAAGAAAGAAAAAAAGAAAGAAAAAAGG-AAAATA
1 AAAGAAAAAAAGAAAGAAAAAAAGAAAGAAAAAAGGTAAAATA
*
1790745 AAAGAAAAAAAG-AAGAAGAAGAAATAAATGAAAAAAGGTAAAA
1 AAAGAAAAAAAGAAAGAA-AA-AAAGAAA-GAAAAAAGGTAAAA
1790788 AAATAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
41 5 0.13
42 14 0.37
43 6 0.16
44 9 0.24
45 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.05
Consensus pattern (43 bp):
AAAGAAAAAAAGAAAGAAAAAAAGAAAGAAAAAAGGTAAAATA
Found at i:1790799 original size:26 final size:26
Alignment explanation
Indices: 1790703--1790804 Score: 81
Period size: 26 Copynumber: 4.0 Consensus size: 26
1790693 TTGCCTGAAG
*
1790703 AAAGAA-AAAAAGAAAGAAA--AAAA
1 AAAGAAGAAAAAGAAATAAATGAAAA
* *
1790726 GAAAGAA-AAAAGGAAAATAAAAGAAAA
1 -AAAGAAGAAAAAG-AAATAAATGAAAA
*
1790753 AAAGAAGAAGAAGAAATAAATGAAAA
1 AAAGAAGAAAAAGAAATAAATGAAAA
* *
1790779 AAGGTAA-AAAAATAAATAAAT-AAAA
1 AAAG-AAGAAAAAGAAATAAATGAAAA
1790804 A
1 A
1790805 TGAGGGTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
24 11 0.17
25 11 0.17
26 33 0.51
27 10 0.15
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (26 bp):
AAAGAAGAAAAAGAAATAAATGAAAA
Found at i:1794818 original size:7 final size:7
Alignment explanation
Indices: 1794806--1794883 Score: 52
Period size: 7 Copynumber: 10.3 Consensus size: 7
1794796 TTGCCTGAAT
1794806 AAAGAAA
1 AAAGAAA
1794813 AAAGAAA
1 AAAGAAA
1794820 AATA-AAA
1 AA-AGAAA
1794827 GAAA-AATA
1 -AAAGAA-A
1794835 AAAGAAAA
1 AAAG-AAA
1794843 AAAGAAGA
1 AAAGAA-A
*
1794851 AGAAAAAA
1 A-AAGAAA
1794859 TAAATGAAA
1 -AAA-GAAA
*
1794868 AAGGAAA
1 AAAGAAA
1794875 AAAGAAA
1 AAAGAAA
1794882 AA
1 AA
1794884 TAAATAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
7 32 0.55
8 16 0.28
9 10 0.17
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (7 bp):
AAAGAAA
Found at i:1794829 original size:18 final size:18
Alignment explanation
Indices: 1794806--1794876 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
1794796 TTGCCTGAAT
1794806 AAAGAAAAAAGAAAAATA
1 AAAGAAAAAAGAAAAATA
*
1794824 AAAGAAAAATA-AAAGAAAA
1 AAAGAAAAA-AGAAA-AATA
*
1794843 AAAG-AAGAAGAAAAAATA
1 AAAGAAAAAAG-AAAAATA
* *
1794861 AATGAAAAAGGAAAAA
1 AAAGAAAAAAGAAAAA
1794877 AGAAAAATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
17 1 0.02
18 26 0.62
19 15 0.36
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAATA
Found at i:1794850 original size:11 final size:10
Alignment explanation
Indices: 1794810--1794877 Score: 64
Period size: 11 Copynumber: 6.3 Consensus size: 10
1794800 CTGAATAAAG
1794810 AAAAAAGAAA
1 AAAAAAGAAA
1794820 AATAAAAGAAA
1 AA-AAAAGAAA
1794831 AATAAAAGAAA
1 AA-AAAAGAAA
*
1794842 AAAAGAAGAAG
1 AAAA-AAGAAA
*
1794853 AAAAAATAAA
1 AAAAAAGAAA
*
1794863 TGAAAAAGGAAA
1 --AAAAAAGAAA
1794875 AAA
1 AAA
1794878 GAAAAATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 11 0.22
11 30 0.61
12 8 0.16
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1794888 original size:25 final size:24
Alignment explanation
Indices: 1794817--1794893 Score: 86
Period size: 26 Copynumber: 3.1 Consensus size: 24
1794807 AAGAAAAAAG
* *
1794817 AAAAATAAAAGAAAAATAAAAGAA
1 AAAAAGAAAAGAAAAATAAATGAA
1794841 AAAAAGAAGAAGAAAAAATAAATGAA
1 AAAAAGAA-AAG-AAAAATAAATGAA
1794867 AAAGGAA-AAAAGAAAAATAAAT-AA
1 AAA--AAGAAAAGAAAAATAAATGAA
1794891 AAA
1 AAA
1794894 TGAGGGTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
24 12 0.26
25 13 0.28
26 18 0.38
27 2 0.04
28 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (24 bp):
AAAAAGAAAAGAAAAATAAATGAA
Found at i:1794894 original size:6 final size:6
Alignment explanation
Indices: 1794806--1794883 Score: 52
Period size: 6 Copynumber: 12.5 Consensus size: 6
1794796 TTGCCTGAAT
* * * *
1794806 AAAGAAA AAAGAA AAA-TA AAAGAA AAATAA AAGAAAA AAAGAA GAAGAA
1 AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAGAA
*
1794855 AAA-ATA AATGAA AAAGGAAA AAAGAA AAA
1 AAAGA-A AAAGAA AAA-G-AA AAAGAA AAA
1794884 TAAATAAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
5 5 0.09
6 34 0.61
7 12 0.21
8 5 0.09
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:1798670 original size:5 final size:5
Alignment explanation
Indices: 1798660--1798693 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1798650 AATGATTATC
* *
1798660 TTTTA TTTTA TTATC TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1798694 TATATTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:1798674 original size:15 final size:15
Alignment explanation
Indices: 1798654--1798686 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1798644 TACTCGAATG
1798654 ATTATCTTTTATTTT
1 ATTATCTTTTATTTT
1798669 ATTATCTTTTATTTT
1 ATTATCTTTTATTTT
1798684 ATT
1 ATT
1798687 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTATCTTTTATTTT
Found at i:1798693 original size:15 final size:15
Alignment explanation
Indices: 1798654--1798693 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1798644 TACTCGAATG
*
1798654 ATTATCTTTTATTTT
1 ATTATATTTTATTTT
*
1798669 ATTATCTTTTATTTT
1 ATTATATTTTATTTT
*
1798684 ATTTTATTTT
1 ATTATATTTT
1798694 TATATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTATATTTTATTTT
Found at i:1803749 original size:45 final size:45
Alignment explanation
Indices: 1803626--1803751 Score: 119
Period size: 45 Copynumber: 2.7 Consensus size: 45
1803616 ATAATGCATC
* * * *
1803626 ATTATACATTTTCATTTATGGTAACCGTTCATGCCTTTTTATATACT
1 ATTATACA-TTTCATTTATGG-CATCTTTCATGCCTTTTTATACACT
* ** * *
1803673 ATTATATATTTTGTTTACGACATCATTTCATGCC-TTTTATACACT
1 ATTATACATTTCATTTATGGCATC-TTTCATGCCTTTTTATACACT
*
1803718 GTTATACATTTCATTTATGGCATCTTATCATGCC
1 ATTATACATTTCATTTATGGCATCTT-TCATGCC
1803752 AATAATGCAC
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
44 2 0.03
45 37 0.60
46 16 0.26
47 7 0.11
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (45 bp):
ATTATACATTTCATTTATGGCATCTTTCATGCCTTTTTATACACT
Found at i:1803851 original size:79 final size:79
Alignment explanation
Indices: 1803720--1804176 Score: 792
Period size: 79 Copynumber: 5.8 Consensus size: 79
1803710 TATACACTGT
* *
1803720 TATACATTTCATTTATGGCAT-CTTATCATGCCAATAATGCACCCATATGCATTATTCTATTATG
1 TATACATTTCATCTATGGCATCCTT-TCATGCCAATAATGCACCCATATGCATTATTCTTTTATG
1803784 CTGACAATGTACCCA
65 CTGACAATGTACCCA
*
1803799 TATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGC
1 TATACATTTCATCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGC
1803864 TGACAATGTACCCA
66 TGACAATGTACCCA
* *
1803878 TATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACACATATGCATTATTCTTTTATG-
1 TATACATTTCATCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGC
1803942 TCGACAATGTACCCA
66 T-GACAATGTACCCA
1803957 TATACATTTCATCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGC
1 TATACATTTCATCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGC
*
1804022 TGACAATGTACACA
66 TGACAATGTACCCA
* *
1804036 TATACATTTCAGCTATGTCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGC
1 TATACATTTCATCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGC
*
1804101 TGACAAAGTACCCA
66 TGACAATGTACCCA
*
1804115 TATACATTTCATCTATGGCATCCTTTCATGCCAATAATGCACCCATATGTATTATTCTTTTA
1 TATACATTTCATCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTA
1804177 CTCAACGGTA
Statistics
Matches: 360, Mismatches: 15, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
78 1 0.00
79 355 0.99
80 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (79 bp):
TATACATTTCATCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGC
TGACAATGTACCCA
Found at i:1804286 original size:68 final size:68
Alignment explanation
Indices: 1804201--1804382 Score: 274
Period size: 68 Copynumber: 2.7 Consensus size: 68
1804191 ATCGCTTATA
* * *
1804201 TAACTAGCATAATTGACACCTTTATGTCAAATACACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
1 TAACTGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGACACTTAGCCTTTC
*
1804266 ATT
66 ATC
* * *
1804269 TAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGACTCAAAGACACTTAGTCTTTC
1 TAACTGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGACACTTAGCCTTTC
1804334 ATC
66 ATC
* * *
1804337 TAACTGGCATAATTGACACCTTTATGTTATATGCACAATTAGGCCT
1 TAACTGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCT
1804383 TAAATCTTTT
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 102 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (68 bp):
TAACTGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGACACTTAGCCTTTC
ATC
Found at i:1804798 original size:58 final size:59
Alignment explanation
Indices: 1804732--1804892 Score: 218
Period size: 58 Copynumber: 2.8 Consensus size: 59
1804722 TTTTCCATAC
* * * * * *
1804732 GGAAATTCATACACTTAGGATAAATTTCTTATCATTTTAGCACACAAGGTGCCC-ATCT
1 GGAAATTCATACACTTAGTATGAATTCCTTAACATTTTAGCACACAAAGTGCCCTATAT
** **
1804790 GGAAATTCATACACTTAGTATGAATTCCTTCCCAGGTTAGCACACAAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTAACATTTTAGCACACAAAGTGCCCTATAT
1804849 GGAAATTCATACACTTAGTATGAATTCCTTAACATTTT-GCACAC
1 GGAAATTCATACACTTAGTATGAATTCCTTAACATTTTAGCACAC
1804893 TTAGTGCCAT
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 52 0.58
59 37 0.42
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTCCTTAACATTTTAGCACACAAAGTGCCCTATAT
Found at i:1805354 original size:95 final size:95
Alignment explanation
Indices: 1805215--1805440 Score: 237
Period size: 95 Copynumber: 2.4 Consensus size: 95
1805205 TCTAGCTCCA
* *** * * *
1805215 TAGTATCGATACTAC-TATCATGGTATTGATACTTTTATGTTATGGTA-TCGATAC-CACCTTTT
1 TAGTATCGATACT-CTTACCATGGTATTGATACTACCATGATATGGTACT-AATACTC-CCTTCT
* * *
1805277 GGTATCAATAACAATTTTAGGTTCTATG-TTGCT
63 GGTATCAATAACAATTTTAGATTCGATGATT-CC
*
1805310 TAGTATCGATACTCTTACCATGGTATCGATACTACCATGATATGGTACTAATACTCCCTTCTGGT
1 TAGTATCGATACTCTTACCATGGTATTGATACTACCATGATATGGTACTAATACTCCCTTCTGGT
* * *
1805375 ATCGATACCAATTTTTGATTCGATGATTCC
66 ATCAATAACAATTTTAGATTCGATGATTCC
*
1805405 TGGTATCGATAC-CTTTACCATGGTATTGATACTACC
1 TAGTATCGATACTC-TTACCATGGTATTGATACTACC
1805441 TCTTCGGTAT
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
94 2 0.02
95 104 0.95
96 4 0.04
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (95 bp):
TAGTATCGATACTCTTACCATGGTATTGATACTACCATGATATGGTACTAATACTCCCTTCTGGT
ATCAATAACAATTTTAGATTCGATGATTCC
Found at i:1807079 original size:32 final size:32
Alignment explanation
Indices: 1807032--1807102 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
1807022 AAAACCTAAA
* *
1807032 GGAGTATCTTGGGGCC-AGAAAGCCTACCCAAG
1 GGAGTACCTTAGGGCCTA-AAAGCCTACCCAAG
* *
1807064 GGAGTACCTTAGGGCCTAAGAGCCTACTCAAG
1 GGAGTACCTTAGGGCCTAAAAGCCTACCCAAG
1807096 GGAGTAC
1 GGAGTAC
1807103 ACCTTGGGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.31, T:0.17
Consensus pattern (32 bp):
GGAGTACCTTAGGGCCTAAAAGCCTACCCAAG
Found at i:1808613 original size:20 final size:20
Alignment explanation
Indices: 1808588--1808625 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1808578 ATTATGAACC
1808588 GATTTACAGGTCTTCCAACT
1 GATTTACAGGTCTTCCAACT
*
1808608 GATTTATAGGTCTTCCAA
1 GATTTACAGGTCTTCCAA
1808626 ATATGTCAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (20 bp):
GATTTACAGGTCTTCCAACT
Found at i:1811354 original size:2 final size:2
Alignment explanation
Indices: 1811347--1811371 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1811337 AATGTTAACA
1811347 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 A
1811372 ATTCCTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1812340 original size:32 final size:32
Alignment explanation
Indices: 1812297--1812412 Score: 108
Period size: 32 Copynumber: 3.6 Consensus size: 32
1812287 ATAGGCCATT
* * * *
1812297 GGGCGTAAGAGCCAACCTAAAGGAGTATCTTG
1 GGGCCTAAGAGCCTACCCAAAGGAGTATCTTA
* *
1812329 GGGCCTGAGAGCCTACCCAAGGGAGTA-CATTA
1 GGGCCTAAGAGCCTACCCAAAGGAGTATC-TTA
* * *
1812361 GGGCCTAAGAGCCTACCCAATGGAGTATATTT
1 GGGCCTAAGAGCCTACCCAAAGGAGTATCTTA
* **
1812393 GGGCCTTAGAGTATACCCAA
1 GGGCCTAAGAGCCTACCCAA
1812413 GGAAATGACT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
31 1 0.01
32 68 0.99
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.20
Consensus pattern (32 bp):
GGGCCTAAGAGCCTACCCAAAGGAGTATCTTA
Found at i:1812410 original size:64 final size:63
Alignment explanation
Indices: 1812293--1812414 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 63
1812283 TACCATAGGC
* * * *
1812293 CATTGGGCGTAAGAGCCAACCTAAAGGAGTATCTTGGGGCCTGAGAGCCTACCCAAGGGAGTA
1 CATTGGGCCTAAGAGCCAACCCAAAGGAGTATATTGGGGCCTGAGAGCATACCCAAGGGAGTA
* * * * *
1812356 CATTAGGGCCTAAGAGCCTACCCAATGGAGTATATTTGGGCCTTAGAGTATACCCAAGG
1 CATT-GGGCCTAAGAGCCAACCCAAAGGAGTATATTGGGGCCTGAGAGCATACCCAAGG
1812415 AAATGACTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
63 4 0.08
64 45 0.92
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (63 bp):
CATTGGGCCTAAGAGCCAACCCAAAGGAGTATATTGGGGCCTGAGAGCATACCCAAGGGAGTA
Found at i:1813889 original size:20 final size:20
Alignment explanation
Indices: 1813864--1813905 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1813854 GATGATTATG
*
1813864 AACCGATTTTCAGGTATTCC
1 AACCGATTTACAGGTATTCC
*
1813884 AACCGATTTACAGGTCTTCC
1 AACCGATTTACAGGTATTCC
1813904 AA
1 AA
1813906 ACAAGTCAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (20 bp):
AACCGATTTACAGGTATTCC
Found at i:1815960 original size:31 final size:30
Alignment explanation
Indices: 1815922--1815983 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
1815912 TGTAGGAAGT
1815922 ATTCTATAATCCTTAGAAAAATTT-GGGGACC
1 ATTCTATAAT-CTTAG-AAAATTTAGGGGACC
* *
1815953 ATTCTATAATTTTTGAAAATTTAGGGGACC
1 ATTCTATAATCTTAGAAAATTTAGGGGACC
1815983 A
1 A
1815984 AATTGGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.25
30 11 0.39
31 10 0.36
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (30 bp):
ATTCTATAATCTTAGAAAATTTAGGGGACC
Found at i:1825753 original size:28 final size:28
Alignment explanation
Indices: 1825713--1825771 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
1825703 CAAGGAATAC
*
1825713 TACTTTTCCTTATGTAGGTCTGGCAGAG
1 TACTTTTCCTTATGTAGATCTGGCAGAG
1825741 TACTTTTCCTTATGTAGATCTGGCAGAG
1 TACTTTTCCTTATGTAGATCTGGCAGAG
1825769 TAC
1 TAC
1825772 CTCTGAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (28 bp):
TACTTTTCCTTATGTAGATCTGGCAGAG
Found at i:1826937 original size:21 final size:21
Alignment explanation
Indices: 1826911--1826966 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
1826901 TTTATGTTTA
* *
1826911 CATTTGCATTTTTACATCATG
1 CATTTGCATTTTTACATAATC
1826932 CATTTGCATTTTTACATAATC
1 CATTTGCATTTTTACATAATC
*
1826953 CATTTTCACTTTTT
1 CATTTGCA-TTTTT
1826967 TTGTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (21 bp):
CATTTGCATTTTTACATAATC
Found at i:1828426 original size:16 final size:16
Alignment explanation
Indices: 1828407--1828441 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1828397 CTATTATTAT
1828407 TTTAAATTATT-TATTC
1 TTTAAATT-TTCTATTC
1828423 TTTAAATTTTCTATTC
1 TTTAAATTTTCTATTC
1828439 TTT
1 TTT
1828442 CATTCATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAAATTTTCTATTC
Found at i:1830062 original size:6 final size:6
Alignment explanation
Indices: 1830051--1830187 Score: 59
Period size: 6 Copynumber: 21.5 Consensus size: 6
1830041 ACACTTGAAC
* * *
1830051 AAAAAG AAAAAGAG AGAAAAG AAAAAT AAAAAT AAAAAT AAAAAG AAAGAAAG
1 AAAAAG -AAAA-AG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AA-AAAG
*
1830104 AAAGAAAG AAAGAG AAAAA- ATAAAA- ATAAAAG ATAAAAG ATAAAA-
1 -AA-AAAG AAAAAG AAAAAG A-AAAAG A-AAAAG A-AAAAG A-AAAAG
* * *
1830149 AAGAAAT AAAAA- AATAAA- AAAAAG GAAAAG AAAGAG AAA
1 AA-AAAG AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG AAA
1830188 GAAATAAAAA
Statistics
Matches: 113, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
5 7 0.06
6 62 0.55
7 27 0.24
8 17 0.15
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:1830101 original size:4 final size:4
Alignment explanation
Indices: 1830092--1830116 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1830082 ATAAAAATAA
1830092 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
1830117 GAAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1830169 original size:47 final size:47
Alignment explanation
Indices: 1830072--1830171 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 47
1830062 GAGAGAAAAG
* *
1830072 AAAAATAAAAATAAAAATAAAAAGAAAGAAAGAAAGAAAGAAAGAGA
1 AAAAATAAAAATAAAAATAAAAAGAAAAAAAGAAAGAAAAAAAGAGA
* * *
1830119 AAAAATAAAAATAAAAGAT-AAAAGATAAAAAAGAAATAAAAAAATAAA
1 AAAAATAAAAATAAAA-ATAAAAAGA-AAAAAAGAAAGAAAAAAAGAGA
1830167 AAAAA
1 AAAAA
1830172 GGAAAAGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 22 0.48
48 24 0.52
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.09
Consensus pattern (47 bp):
AAAAATAAAAATAAAAATAAAAAGAAAAAAAGAAAGAAAAAAAGAGA
Found at i:1830625 original size:116 final size:116
Alignment explanation
Indices: 1830363--1830626 Score: 275
Period size: 117 Copynumber: 2.3 Consensus size: 116
1830353 TTTGGGAATG
* * * * *
1830363 AGCTTCACATCTGCAAACATTCTGACAACATTTTAAGTCTTTTAGACAAAAGCTTACATTCACGC
1 AGCTTCACATCTAC-AACATTCTGAAAACATATTAAGTCTTTTAGACAAAAGCTTACATTAACAC
* * * * *
1830428 TCAGGGGACTATACCTAGTTTATTTTCTTAGAGAGCATGATACTTTTAGATA
65 TCAGGGGACCATACATAGTTGATTGTCTTAGAGAGCATGATACTTTTAGAGA
* * * * *
1830480 AGTTTCACATCTACAAGCATTCTGGAAACATATTAAGTCTTTTGGACAAAAGCTTACTTTAATAC
1 AGCTTCACATCTACAA-CATTCTGAAAACATATTAAGTCTTTTAGACAAAAGCTTACATTAACAC
* *
1830545 TTC-GGGG-CCATACATAGTTGATTGGT-TTAGAGAGCTTGATA-TTTTGAGAGG
65 -TCAGGGGACCATACATAGTTGATT-GTCTTAGAGAGCATGATACTTTT-AGAGA
* *
1830596 GGCTTCACATCTACAGACATTTTGAAAACAT
1 AGCTTCACATCTACA-ACATTCTGAAAACAT
1830627 TTGAGATCTT
Statistics
Matches: 121, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
115 4 0.03
116 57 0.47
117 58 0.48
118 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (116 bp):
AGCTTCACATCTACAACATTCTGAAAACATATTAAGTCTTTTAGACAAAAGCTTACATTAACACT
CAGGGGACCATACATAGTTGATTGTCTTAGAGAGCATGATACTTTTAGAGA
Found at i:1833128 original size:32 final size:32
Alignment explanation
Indices: 1833087--1833151 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 32
1833077 AATTAAGCAA
1833087 TAGAAATCAAAGAGCTTTTGGCA-TGTATTTTT
1 TAGAAATCAAAGAGCTTTTGGCAGT-TATTTTT
1833119 TAGAAATCAAAGAGCTTTTGGCAGTTATTTTT
1 TAGAAATCAAAGAGCTTTTGGCAGTTATTTTT
1833151 T
1 T
1833152 CTCGTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (32 bp):
TAGAAATCAAAGAGCTTTTGGCAGTTATTTTT
Found at i:1834938 original size:138 final size:138
Alignment explanation
Indices: 1834693--1834945 Score: 328
Period size: 138 Copynumber: 1.8 Consensus size: 138
1834683 GATCATTCAC
* * * * * *
1834693 CTTAGGTTTAATTTCGCCTTAGTCCTTTAATTTAGGGGGAATTTTTAATTTGGTCATCACTTTTG
1 CTTAGGTTTAATTTCACCTTAGTCCTTCAATTTAGGGAGAATTCTTAATTTGGTCATCACTTATA
* * * *
1834758 CTCGAGGTTTCATTTTAATTATTCGAATCAATAAGTGGTTAAAATTGATTAGGTTAGTTAATAGA
66 CTCGAGGTTCCATTTTAATTATTCGAATCAATAAATGATTAAAAATGATTAGGTTAGTTAATAGA
1834823 GCCTCCAT
131 GCCTCCAT
* * * *
1834831 CTTAGGTTTAATTTCACATTTAGTCCTTCAATTTA-GGAGAGTTCTTAATTTGGTCCTCGCTTAT
1 CTTAGGTTTAATTTCAC-CTTAGTCCTTCAATTTAGGGAGAATTCTTAATTTGGTCATCACTTAT
** * *
1834895 ACTCGAGGTTCCATTTTAATTATTCGGTTTAATAAATTATTAAAAATGATT
65 ACTCGAGGTTCCATTTTAATTATTCGAATCAATAAATGATTAAAAATGATT
1834946 TGGGTTAATA
Statistics
Matches: 96, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
138 81 0.84
139 15 0.16
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (138 bp):
CTTAGGTTTAATTTCACCTTAGTCCTTCAATTTAGGGAGAATTCTTAATTTGGTCATCACTTATA
CTCGAGGTTCCATTTTAATTATTCGAATCAATAAATGATTAAAAATGATTAGGTTAGTTAATAGA
GCCTCCAT
Found at i:1836927 original size:74 final size:77
Alignment explanation
Indices: 1836839--1837052 Score: 298
Period size: 76 Copynumber: 2.9 Consensus size: 77
1836829 TAAAACATCT
* * *
1836839 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT-AAACACTA-ATAATAT-T
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACCTAAAACA-AAGATAAAATAT
* *
1836900 TAAAATAATATTC
65 AAAAATAATATCC
1836913 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1836977 AAAATAATATCC
66 AAAATAATATCC
* * *
1836989 TAAAACTTAATTAAAATA-TTAAAACCTATTTAAACTAAAATACCTAAAA-AAGGATAAAATATA
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1837052 A
66 A
1837053 TGTTAAAAAT
Statistics
Matches: 127, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
73 5 0.04
74 39 0.31
75 25 0.20
76 58 0.46
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (77 bp):
TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
AAAATAATATCC
Found at i:1843954 original size:73 final size:76
Alignment explanation
Indices: 1843868--1844081 Score: 319
Period size: 76 Copynumber: 2.9 Consensus size: 76
1843858 TAAAACATCT
* * * *
1843868 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAA-ATA-ATAATAT-TT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
*
1843929 AAAATAATATTC
65 AAAATAATATCC
1843941 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1844006 AAATAATATCC
66 AAATAATATCC
* * *
1844017 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGGTAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1844082 TGTTTAAAAT
Statistics
Matches: 129, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
72 5 0.04
73 42 0.33
74 2 0.02
75 6 0.05
76 74 0.57
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (76 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATCC
Found at i:1843979 original size:24 final size:24
Alignment explanation
Indices: 1843952--1844066 Score: 72
Period size: 25 Copynumber: 4.6 Consensus size: 24
1843942 AAATCCTAAT
1843952 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
** ** *
1843976 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATA-CTAAAACCTATTTAAAC
* * * *
1844001 TATAAA-AATAATATCCTAAAACTT-AAT
1 TA-AAATACTAA-AACCT---ATTTAAAC
1844028 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
1844052 TAAAATACCTAAAAC
1 TAAAATA-CTAAAAC
1844067 AAAGGTAAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
23 3 0.05
24 19 0.29
25 24 0.36
26 10 0.15
27 8 0.12
28 2 0.03
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.26
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Found at i:1846192 original size:19 final size:19
Alignment explanation
Indices: 1846168--1846212 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1846158 TGTTATTTCA
1846168 GCCCTCAGCAAAACTAGTT
1 GCCCTCAGCAAAACTAGTT
1846187 GCCCTCAGCAAAACTAGTT
1 GCCCTCAGCAAAACTAGTT
1846206 GCCCTCA
1 GCCCTCA
1846213 ACATGTTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.20
Consensus pattern (19 bp):
GCCCTCAGCAAAACTAGTT
Found at i:1852666 original size:42 final size:41
Alignment explanation
Indices: 1852565--1852726 Score: 200
Period size: 42 Copynumber: 3.8 Consensus size: 41
1852555 CTATACACCA
* *
1852565 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCTAGG-AAACT
*
1852609 GTAAGGTTTATCCTTGCACACAGCAAAGGGACCTAGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTAGGAAACT
*
1852651 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTAGGAAACT
* *
1852693 GTAAGGCTTACCTTCGTACACAACAAAGGGACCT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCT
1852727 GATAATACTT
Statistics
Matches: 107, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
41 4 0.04
42 71 0.66
43 18 0.17
44 14 0.13
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTAGGAAACT
Found at i:1853688 original size:29 final size:29
Alignment explanation
Indices: 1853656--1853811 Score: 163
Period size: 29 Copynumber: 5.4 Consensus size: 29
1853646 AATTTTACAG
* *
1853656 AAATAGCACCCTTTTCAAATTAATTACTA
1 AAATAACACCCTTTTCGAATTAATTACTA
* * *
1853685 AAATACCA-CATATTTTGAATTAATTACTA
1 AAATAACACCCT-TTTCGAATTAATTACTA
* *
1853714 AAATATCACCCATTTT-GAATTAATTACTG
1 AAATAACACCC-TTTTCGAATTAATTACTA
* * *
1853743 AAATAACACCCATTTCAAATTAATTATTA
1 AAATAACACCCTTTTCGAATTAATTACTA
* * *
1853772 AAATAGCACCCATTTCGAATTAATTAATA
1 AAATAACACCCTTTTCGAATTAATTACTA
1853801 AAATAACACCC
1 AAATAACACCC
1853812 GGTCAACGGT
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.05
29 97 0.91
30 4 0.04
31 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (29 bp):
AAATAACACCCTTTTCGAATTAATTACTA
Found at i:1853803 original size:87 final size:87
Alignment explanation
Indices: 1853650--1853811 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 87
1853640 GTCGACAATT
* * * * *
1853650 TTACAGAAATAGCACCCTTTTCAAATTAATTACTAAAATACCACATATTTTGAATTAATTACTAA
1 TTACAGAAATAACACCCATTTCAAATTAATTACTAAAATACCACACATTTCGAATTAATTAATAA
*
1853715 AATATCACCCATTTTGAATTAA
66 AATAACACCCATTTTGAATTAA
* * * *
1853737 TTACTGAAATAACACCCATTTCAAATTAATTATTAAAATAGCACCCATTTCGAATTAATTAATAA
1 TTACAGAAATAACACCCATTTCAAATTAATTACTAAAATACCACACATTTCGAATTAATTAATAA
1853802 AATAACACCC
66 AATAACACCC
1853812 GGTCAACGGT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (87 bp):
TTACAGAAATAACACCCATTTCAAATTAATTACTAAAATACCACACATTTCGAATTAATTAATAA
AATAACACCCATTTTGAATTAA
Found at i:1853810 original size:58 final size:58
Alignment explanation
Indices: 1853656--1853811 Score: 204
Period size: 58 Copynumber: 2.7 Consensus size: 58
1853646 AATTTTACAG
* * * ** **
1853656 AAATAGCACCCTTTTCAAATTAATTACTAAAATACCACATATTTTGAATTAATTACTA
1 AAATAGCACCCATTTCGAATTAATTACTAAAATAACACCCATTTCAAATTAATTACTA
* * * *
1853714 AAATATCACCCATTTTGAATTAATTACTGAAATAACACCCATTTCAAATTAATTATTA
1 AAATAGCACCCATTTCGAATTAATTACTAAAATAACACCCATTTCAAATTAATTACTA
*
1853772 AAATAGCACCCATTTCGAATTAATTAATAAAATAACACCC
1 AAATAGCACCCATTTCGAATTAATTACTAAAATAACACCC
1853812 GGTCAACGGT
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (58 bp):
AAATAGCACCCATTTCGAATTAATTACTAAAATAACACCCATTTCAAATTAATTACTA
Found at i:1853823 original size:7 final size:7
Alignment explanation
Indices: 1853811--1853836 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1853801 AAATAACACC
1853811 CGGTCAA
1 CGGTCAA
1853818 CGGTCAA
1 CGGTCAA
1853825 CGGTCAA
1 CGGTCAA
1853832 CGGTC
1 CGGTC
1853837 GGGTCGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:1855924 original size:21 final size:20
Alignment explanation
Indices: 1855894--1855932 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1855884 CATCAAGGTC
1855894 TTTGTAGAGGCCATGAAATAT
1 TTTGTAGAGGCCAT-AAATAT
*
1855915 TTTGTCGAGGCCATAAAT
1 TTTGTAGAGGCCATAAAT
1855933 TCCTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (20 bp):
TTTGTAGAGGCCATAAATAT
Found at i:1860680 original size:19 final size:19
Alignment explanation
Indices: 1860620--1860681 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
1860610 ATTTATAACT
1860620 TATATATTAACATAATTTCAA
1 TATATATTAACATAA-TT-AA
*
1860641 TAT-TATAAATTCAT-ATT--
1 TATATATTAA--CATAATTAA
1860658 TATATATTAACATAATTAA
1 TATATATTAACATAATTAA
1860677 TATAT
1 TATAT
1860682 TTATAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
16 3 0.09
17 6 0.18
18 5 0.15
19 5 0.15
20 7 0.21
21 4 0.12
22 3 0.09
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATATTAACATAATTAA
Found at i:1861500 original size:3 final size:3
Alignment explanation
Indices: 1861492--1861534 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1861482 TATGATGTGG
1861492 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1861535 TAATATGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1863570 original size:2 final size:2
Alignment explanation
Indices: 1863563--1863619 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1863553 ATGGTTGTTC
1863563 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
1863605 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1863620 AAAACAATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1865272 original size:35 final size:36
Alignment explanation
Indices: 1865216--1865287 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 36
1865206 CATCACCATT
* *
1865216 GGTGGTGGTCGGAGAGGGGAAGA-ACGCCGATTTAC
1 GGTGGGGGTCGGAGAGGGGAAGAGACACCGATTTAC
* *
1865251 GGTGGGGGTC-GACGAGTGGAAGAGGCACCGATTTAC
1 GGTGGGGGTCGGA-GAGGGGAAGAGACACCGATTTAC
1865287 G
1 G
1865288 ACGGGCGAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 2 0.06
35 18 0.58
36 11 0.35
ACGTcount: A:0.22, C:0.15, G:0.46, T:0.17
Consensus pattern (36 bp):
GGTGGGGGTCGGAGAGGGGAAGAGACACCGATTTAC
Found at i:1865603 original size:28 final size:28
Alignment explanation
Indices: 1865563--1865624 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1865553 TTTATGTTAC
* *
1865563 TTTACTTTAATTTGGT-ATTGTATTTTAT
1 TTTATTTTAATTTGGTCATTGT-TTTTAA
1865591 TTTATTTTAATTTGGTCATTGTTTTTAA
1 TTTATTTTAATTTGGTCATTGTTTTTAA
1865619 TTTATT
1 TTTATT
1865625 ATTTTTCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.66
Consensus pattern (28 bp):
TTTATTTTAATTTGGTCATTGTTTTTAA
Found at i:1871506 original size:16 final size:18
Alignment explanation
Indices: 1871485--1871530 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1871475 TATGGAATTG
1871485 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
1871501 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1871519 GATTCCAATTCC
1 GATTCCAATTCC
1871531 CTCATAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.43
17 1 0.04
18 15 0.54
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1872053 original size:28 final size:30
Alignment explanation
Indices: 1871985--1872053 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 30
1871975 AAATTTTTAT
* *
1871985 TATTTACATTTTTGGCTTTTAAATTTCTGT
1 TATTTACATTTCTGGCTTTTAAATTTCTGA
1872015 TATTTTA-ATTTCT-GC-TTTAAATTAT-TGA
1 TA-TTTACATTTCTGGCTTTTAAATT-TCTGA
1872043 TATTTACATTT
1 TATTTACATTT
1872054 TAGTCCATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 4 0.12
28 16 0.47
29 3 0.09
30 7 0.21
31 4 0.12
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.59
Consensus pattern (30 bp):
TATTTACATTTCTGGCTTTTAAATTTCTGA
Found at i:1872640 original size:139 final size:137
Alignment explanation
Indices: 1872309--1873081 Score: 726
Period size: 138 Copynumber: 5.6 Consensus size: 137
1872299 CCTTGGCAAA
* * *
1872309 AGGTCCCATTTTAATTATTTG-ATCCAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGAC
1 AGGTTCCATTTTAATTATTCGAAT-CAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCC
* * * * **
1872373 TCTATTTTAGCCTTAATTTTATACTTAGTCCTTTAATTTAAGGGATTTTTTAATTTGGTCTTCGT
65 TCTATTTTAGGCTTAATTTCATACTTAGTCCTTTAATTT-AGGAATTTTTTAATTTGGTCCTCAC
**
1872438 TTTTTCTCG
129 TTTTAATCG
* * * * * *
1872447 ATGTTCTATTTTAATTATTCAAATAAAAAATTGATTAAAATTGACTAAGTTAATAATTAGAGCCT
1 AGGTTCCATTTTAATTATTCGAATCAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCT
*
1872512 CTATTTTAGGCTTAATTTCATACTTAGTCATTTAATTTAGGAATTCTTTTTAATTTGGTCCTCAC
66 CTATTTTAGGCTTAATTTCATACTTAGTCCTTTAATTTAGGAA-T-TTTTTAATTTGGTCCTCAC
1872577 TTTTAATCG
129 TTTTAATCG
** * *
1872586 AGGTTTTATTTTAATTATTCGAATCAATGATTGATTGAAATTGACTAGGTTAATAATTAGAGCCT
1 AGGTTCCATTTTAATTATTCGAATCAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCT
*
1872651 CTATTTTAGGCTTAATTTCATACTTAGTCCTTTAA-TTAGGGGAA-TTTTAAATTTGGTCCTCAC
66 CTATTTTAGGCTTAATTTCATACTTAGTCCTTTAATTTA--GGAATTTTTTAATTTGGTCCTCAC
* **
1872714 TTATGCTCG
129 TTTTAATCG
* * ** * * *
1872723 AGGTTACATTTTAATTATTTGAA-CAAATAATTGGCTAAAACTGAGTAGTTTAATAATTAGAGCC
1 AGGTTCCATTTTAATTATTCGAATC-AATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCC
* * * *
1872787 TC-AGCTTTAGGCTTAATTTAATAATTAGTCCTTTAATTTAGGGGAA-TTTTTAATTTGATCCT-
65 TCTA-TTTTAGGCTTAATTTCATACTTAGTCCTTTAATTTA--GGAATTTTTTAATTTGGTCCTC
* **
1872849 AGTTTTTGTTCG
127 A-CTTTTAATCG
* * * * * * *
1872861 AGGTTCCATTTTAATAATTCGATTCAATATTTGGTTAAAACAT-ATTAGGTTAATATTTAGAGCC
1 AGGTTCCATTTTAATTATTCGAATCAATAATTGATTAAAA-TTGACTAGGTTAATAATTAGAGCC
* * * * *
1872925 TCCACTTTAGGCTTAATTCCATAAC-TAGTCCTTTAATATAGGATAATTTTTT-ATTTAGTCCTC
65 TCTATTTTAGGCTTAATTTCAT-ACTTAGTCCTTTAATTTAGG--AATTTTTTAATTTGGTCCTC
*
1872988 CCTTTTATGATCG
127 ACTTTTA--ATCG
* * * ** * *
1873001 AGATTCCATTTTGATTATTC-AACTCAATAATTTATTAAAAACGATTTGGATTAAT-ATTAGAGC
1 AGGTTCCATTTTAATTATTCGAA-TCAATAATTGATTAAAATTGACTAGG-TTAATAATTAGAGC
*
1873064 CTAC-ATTTTAGGTTTAAT
64 CT-CTATTTTAGGCTTAAT
1873082 CTTTTAGGTT
Statistics
Matches: 531, Mismatches: 81, Indels: 44
0.81 0.12 0.07
Matches are distributed among these distances:
136 4 0.01
137 112 0.21
138 218 0.41
139 127 0.24
140 64 0.12
141 6 0.01
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (137 bp):
AGGTTCCATTTTAATTATTCGAATCAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCT
CTATTTTAGGCTTAATTTCATACTTAGTCCTTTAATTTAGGAATTTTTTAATTTGGTCCTCACTT
TTAATCG
Found at i:1874915 original size:137 final size:136
Alignment explanation
Indices: 1874453--1875220 Score: 701
Period size: 138 Copynumber: 5.5 Consensus size: 136
1874443 CAAAAGGTCC
* * *
1874453 CATTTTAATTATTTGATCCAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGACTCTATTT
1 CATTTTAATTATTCGA-ACAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTATTT
* * * * * ** *
1874518 TAGGCTTAATTTTATACTTAGTACTTTAATTTAAGGGATTTTTTAATTTGGTCTTCGTTTTTTCT
65 TAGGCTTAATTTCATACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCACTTTTGCT
*
1874583 CGATGTT
130 CGAGGTT
* * * *
1874590 CTATTTTAATTATTCAAATAAAAAATTGATTAAAATTGACTAAGTTAATAATTAGAGCCTCTATT
1 C-ATTTTAATTATTCGAA-CAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTATT
*
1874655 TTAGGCTTAATTTTCATACTTAGTCATTTAATTTA--GGAATTCTTTTTAATTTGGTCCTCACTT
64 TTAGGCTTAA-TTTCATACTTAGTCCTTTAATTTAGGGGAA---TTTTTAATTTGGTCCTCACTT
**
1874718 TTAATCGAGGTTT
125 TTGCTCGAGG-TT
* * *
1874731 TATTTTAATTATTCGAATCAATGATTGATTGAAATTGACTAGGTTAATAATTAGAGCCTCTATTT
1 CATTTTAATTATTCGAA-CAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTATTT
* *
1874796 TAGGCTTAATTTCATACTTAGTCCTTTAA-TTAGGGGAATTTTAAATTTGGTCCTCACTTATGCT
65 TAGGCTTAATTTCATACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCACTTTTGCT
1874860 CGAGGTT
130 CGAGGTT
* ** * * * *
1874867 ACATTTTAATTATTTGAACAAATAATTGGCTAAAACTGAGTAGTTTAATAATTAGAGCCTC-AGC
1 -CATTTTAATTATTCGAAC-AATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTA-T
* * * *
1874931 TTTAGGCTTAATTTAATAATTAGTCCTTTAATTTAGGGGAATTTTTAATTTGATCCT-AGTTTTT
63 TTTAGGCTTAATTTCATACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCA-CTTTT
*
1874995 GTTCGAGGTT
127 GCTCGAGGTT
* * * * * * * * *
1875005 CCATTTTAATAATTCGATTCAATATTTGGTTAAAACAT-ATTAGGTTAATATTTAGAGCCTCCAC
1 -CATTTTAATTATTCGA-ACAATAATTGATTAAAA-TTGACTAGGTTAATAATTAGAGCCTCTAT
* * ** * * *
1875069 TTTAGGCTTAATTCCATAAC-TAGTCCTTTAATATAGGATAATTTTTTATTTAGTCCTCCCTTTT
63 TTTAGGCTTAATTTCAT-ACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCAC-TTT
* *
1875133 ATGATCGAGATT
126 -TGCTCGAGGTT
* * ** * *
1875145 CCATTTTGATTATTC-AACTCAATAATTTATTAAAAACGATTTGGATTAAT-ATTAGAGCCTAC-
1 -CATTTTAATTATTCGAA--CAATAATTGATTAAAATTGACTAGG-TTAATAATTAGAGCCT-CT
*
1875207 ATTTTAGGTTTAAT
61 ATTTTAGGCTTAAT
1875221 CTTTTAGGTT
Statistics
Matches: 525, Mismatches: 80, Indels: 49
0.80 0.12 0.07
Matches are distributed among these distances:
136 4 0.01
137 110 0.21
138 197 0.38
139 49 0.09
140 157 0.30
141 8 0.02
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (136 bp):
CATTTTAATTATTCGAACAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTATTTT
AGGCTTAATTTCATACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCACTTTTGCTC
GAGGTT
Found at i:1877058 original size:137 final size:136
Alignment explanation
Indices: 1876596--1877363 Score: 701
Period size: 138 Copynumber: 5.5 Consensus size: 136
1876586 CAAAAGGTCC
* * *
1876596 CATTTTAATTATTTGATCCAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGACTCTATTT
1 CATTTTAATTATTCGA-ACAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTATTT
* * * * * ** *
1876661 TAGGCTTAATTTTATACTTAGTACTTTAATTTAAGGGATTTTTTAATTTGGTCTTCGTTTTTTCT
65 TAGGCTTAATTTCATACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCACTTTTGCT
*
1876726 CGATGTT
130 CGAGGTT
* * * *
1876733 CTATTTTAATTATTCAAATAAAAAATTGATTAAAATTGACTAAGTTAATAATTAGAGCCTCTATT
1 C-ATTTTAATTATTCGAA-CAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTATT
*
1876798 TTAGGCTTAATTTTCATACTTAGTCATTTAATTTA--GGAATTCTTTTTAATTTGGTCCTCACTT
64 TTAGGCTTAA-TTTCATACTTAGTCCTTTAATTTAGGGGAA---TTTTTAATTTGGTCCTCACTT
**
1876861 TTAATCGAGGTTT
125 TTGCTCGAGG-TT
* * *
1876874 TATTTTAATTATTCGAATCAATGATTGATTGAAATTGACTAGGTTAATAATTAGAGCCTCTATTT
1 CATTTTAATTATTCGAA-CAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTATTT
* *
1876939 TAGGCTTAATTTCATACTTAGTCCTTTAA-TTAGGGGAATTTTAAATTTGGTCCTCACTTATGCT
65 TAGGCTTAATTTCATACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCACTTTTGCT
1877003 CGAGGTT
130 CGAGGTT
* ** * * * *
1877010 ACATTTTAATTATTTGAACAAATAATTGGCTAAAACTGAGTAGTTTAATAATTAGAGCCTC-AGC
1 -CATTTTAATTATTCGAAC-AATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTA-T
* * * *
1877074 TTTAGGCTTAATTTAATAATTAGTCCTTTAATTTAGGGGAATTTTTAATTTGATCCT-AGTTTTT
63 TTTAGGCTTAATTTCATACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCA-CTTTT
*
1877138 GTTCGAGGTT
127 GCTCGAGGTT
* * * * * * * * *
1877148 CCATTTTAATAATTCGATTCAATATTTGGTTAAAACAT-ATTAGGTTAATATTTAGAGCCTCCAC
1 -CATTTTAATTATTCGA-ACAATAATTGATTAAAA-TTGACTAGGTTAATAATTAGAGCCTCTAT
* * ** * * *
1877212 TTTAGGCTTAATTCCATAAC-TAGTCCTTTAATATAGGATAATTTTTTATTTAGTCCTCCCTTTT
63 TTTAGGCTTAATTTCAT-ACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCAC-TTT
* *
1877276 ATGATCGAGATT
126 -TGCTCGAGGTT
* * ** * *
1877288 CCATTTTGATTATTC-AACTCAATAATTTATTAAAAACGATTTGGATTAAT-ATTAGAGCCTAC-
1 -CATTTTAATTATTCGAA--CAATAATTGATTAAAATTGACTAGG-TTAATAATTAGAGCCT-CT
*
1877350 ATTTTAGGTTTAAT
61 ATTTTAGGCTTAAT
1877364 CTTTTAGGTT
Statistics
Matches: 525, Mismatches: 80, Indels: 49
0.80 0.12 0.07
Matches are distributed among these distances:
136 4 0.01
137 110 0.21
138 197 0.38
139 49 0.09
140 157 0.30
141 8 0.02
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (136 bp):
CATTTTAATTATTCGAACAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTATTTT
AGGCTTAATTTCATACTTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCACTTTTGCTC
GAGGTT
Found at i:1877197 original size:415 final size:414
Alignment explanation
Indices: 1876596--1877363 Score: 924
Period size: 415 Copynumber: 1.9 Consensus size: 414
1876586 CAAAAGGTCC
* * * * *
1876596 CATTTTAATTATTTGATCCAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGACTCTATTT
1 CATTTTAATTATTTGAACAAATAATTGACTAAAACTGACTAGGTTAATAATTAGAGACTCTACTT
* * * * * *
1876661 TAGGCTTAATTTTATACTTAGTACTTTAATTTAAGGGATTTTTTAATTTGGTCTTCGTTTTTTCT
66 TAGGCTTAATTTAATAATTAGTACTTTAATTTAAGGGAATTTTTAATTTGATCCTAGTTTTTTCT
* * * *
1876726 CGATGTTCTATTTTAATTATTCAAATAAAAAATTGATTAAAATTGACTAAGTTAATAATTAGAGC
131 CGAGGTTCCATTTTAATAATTCAAATAAAAAATTGATTAAAAATGACTAAGTTAATAATTAGAGC
* * * * * *
1876791 CTCTATTTTAGGCTTAATTTTCAT-ACTTAGTCATTTAATTTAGGA-ATTCTTTTTAATTTGGTC
196 CTCCACTTTAGGCTTAA-TTCCATAAC-TAGTCATTTAATATAGGATAAT-TTTTT-ATTTAGTC
* ** * * **
1876854 CTCACTTTTA-ATCGAGGTTTTATTTTAATTATTCGAA-TCAATGATTGATTGAAATTGACTAGG
257 CTCACTTTTAGATCGAGATTCCATTTTAATTATTC-AACTCAATAATTGATTAAAAACGACTAGG
1876917 -TTAATAATTAGAGCCT-CTATTTTAGGCTTAATTTCATACTTAGTCCTTTAATTAGGGGAATTT
321 ATTAAT-ATTAGAGCCTAC-ATTTTAGGCTTAATTTCATACTTAGTCCTTTAATTAGGGGAATTT
1876980 TAAATTTGGTCCTCACTTATGCTCGAGGTTA
384 TAAATTTGGTCCTCACTTATGCTCGAGGTTA
* * * *
1877011 CATTTTAATTATTTGAACAAATAATTGGCTAAAACTGAGTAGTTTAATAATTAGAGCCTC-AGCT
1 CATTTTAATTATTTGAACAAATAATTGACTAAAACTGACTAGGTTAATAATTAGAGACTCTA-CT
* *
1877075 TTAGGCTTAATTTAATAATTAGTCCTTTAATTTAGGGGAATTTTTAATTTGATCCTAGTTTTTGT
65 TTAGGCTTAATTTAATAATTAGTACTTTAATTTAAGGGAATTTTTAATTTGATCCTAGTTTTT-T
* * * * * * * * *
1877140 -TCGAGGTTCCATTTTAATAATTCGATTCAATATTTGGTTAAAACAT-ATTAGGTTAATATTTAG
129 CTCGAGGTTCCATTTTAATAATTCAAATAAAAAATTGATTAAAA-ATGACTAAGTTAATAATTAG
*
1877203 AGCCTCCACTTTAGGCTTAATTCCATAACTAGTCCTTTAATATAGGATAATTTTTTATTTAGTCC
193 AGCCTCCACTTTAGGCTTAATTCCATAACTAGTCATTTAATATAGGATAATTTTTTATTTAGTCC
* * * * *
1877268 TCCCTTTTATGATCGAGATTCCATTTTGATTATTCAACTCAATAATTTATTAAAAACGATTTGGA
258 TCACTTTTA-GATCGAGATTCCATTTTAATTATTCAACTCAATAATTGATTAAAAACGACTAGGA
*
1877333 TTAATATTAGAGCCTACATTTTAGGTTTAAT
322 TTAATATTAGAGCCTACATTTTAGGCTTAAT
1877364 CTTTTAGGTT
Statistics
Matches: 293, Mismatches: 50, Indels: 20
0.81 0.14 0.06
Matches are distributed among these distances:
413 16 0.05
414 29 0.10
415 240 0.82
416 8 0.03
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (414 bp):
CATTTTAATTATTTGAACAAATAATTGACTAAAACTGACTAGGTTAATAATTAGAGACTCTACTT
TAGGCTTAATTTAATAATTAGTACTTTAATTTAAGGGAATTTTTAATTTGATCCTAGTTTTTTCT
CGAGGTTCCATTTTAATAATTCAAATAAAAAATTGATTAAAAATGACTAAGTTAATAATTAGAGC
CTCCACTTTAGGCTTAATTCCATAACTAGTCATTTAATATAGGATAATTTTTTATTTAGTCCTCA
CTTTTAGATCGAGATTCCATTTTAATTATTCAACTCAATAATTGATTAAAAACGACTAGGATTAA
TATTAGAGCCTACATTTTAGGCTTAATTTCATACTTAGTCCTTTAATTAGGGGAATTTTAAATTT
GGTCCTCACTTATGCTCGAGGTTA
Found at i:1881284 original size:22 final size:23
Alignment explanation
Indices: 1881237--1881298 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1881227 CGATTCCCCT
1881237 AGGGGGAATCGGTTCCCATTCAA
1 AGGGGGAATCGGTTCCCATTCAA
*
1881260 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCATTCAA
* *
1881282 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
1881299 TCTGCCCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCATTCAA
Found at i:1891947 original size:16 final size:16
Alignment explanation
Indices: 1891926--1891964 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
1891916 GAATCAAATT
1891926 CATGCATTAAAGGCTA
1 CATGCATTAAAGGCTA
1891942 CATGCATTAAAGGCTA
1 CATGCATTAAAGGCTA
1891958 CATGCAT
1 CATGCAT
1891965 AGGAAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (16 bp):
CATGCATTAAAGGCTA
Found at i:1892084 original size:20 final size:19
Alignment explanation
Indices: 1892061--1892133 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
1892051 ATTTAAGGAG
1892061 AGTTTTGAAACTTTGATGAA
1 AGTTTTGAAACTTTGA-GAA
* *
1892081 AGTTGTGAAACACTTGAGAA
1 AGTTTTGAAAC-TTTGAGAA
* *
1892101 AGTATTGAAACTATTGACAA
1 AGTTTTGAAACT-TTGAGAA
*
1892121 AGTTTCGAAACTT
1 AGTTTTGAAACTT
1892134 CTAAATATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.02
20 38 0.88
21 4 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (19 bp):
AGTTTTGAAACTTTGAGAA
Found at i:1892510 original size:9 final size:9
Alignment explanation
Indices: 1892496--1892801 Score: 175
Period size: 9 Copynumber: 32.9 Consensus size: 9
1892486 AAAGGTAATA
1892496 AAAATAAAT
1 AAAATAAAT
*
1892505 AAAATAAAG
1 AAAATAAAT
*
1892514 AAAA-CAA-
1 AAAATAAAT
1892521 AAAA-AAAT
1 AAAATAAAT
* *
1892529 GAAATAAAG
1 AAAATAAAT
1892538 AAAA-AACA-
1 AAAATAA-AT
*
1892546 AAGATAAAGT
1 AAAATAAA-T
1892556 AAAGATAAA-
1 AAA-ATAAAT
* *
1892565 AAGAGTAAAC
1 AA-AATAAAT
*
1892575 AAAATAAAC
1 AAAATAAAT
*
1892584 AAAATAAAG
1 AAAATAAAT
*
1892593 ATAAAGAAAT
1 A-AAATAAAT
1892603 AAAATAAAT
1 AAAATAAAT
1892612 AAAATAAAAT
1 AAAAT-AAAT
1892622 AAAATAAAT
1 AAAATAAAT
1892631 AAAATAAAAT
1 AAAAT-AAAT
1892641 AAAAATAAAT
1 -AAAATAAAT
1892651 AAAATAAA-
1 AAAATAAAT
1892659 ATAAATAAAAT
1 A-AAAT-AAAT
1892670 AAAATAAAAT
1 AAAAT-AAAT
1892680 AAAATAAAT
1 AAAATAAAT
1892689 AAAA-AATAT
1 AAAATAA-AT
1892698 ATACAATAAAT
1 A-A-AATAAAT
* *
1892709 AAATAAAAAC
1 AAA-ATAAAT
1892719 AAGAATAAAAT
1 AA-AAT-AAAT
*
1892730 AAAA-AGAT
1 AAAATAAAT
*
1892738 ATAAAGAAAT
1 A-AAATAAAT
1892748 AAAATAAAT
1 AAAATAAAT
*** *
1892757 ACCGTAAAG
1 AAAATAAAT
1892766 ATAAATAAAAT
1 A-AAAT-AAAT
1892777 AAAAATAAA-
1 -AAAATAAAT
*
1892786 GAAA-AAAT
1 AAAATAAAT
1892794 AAAATAAA
1 AAAATAAA
1892802 AGAAAGAAAG
Statistics
Matches: 236, Mismatches: 31, Indels: 60
0.72 0.09 0.18
Matches are distributed among these distances:
7 9 0.04
8 24 0.10
9 106 0.45
10 65 0.28
11 29 0.12
12 3 0.01
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1892511 original size:5 final size:5
Alignment explanation
Indices: 1892496--1892802 Score: 177
Period size: 5 Copynumber: 62.8 Consensus size: 5
1892486 AAAGGTAATA
* * * * * *
1892496 AAAAT -AAAT AAAAT -AAAG AAAAC AAAAA AAAAT GAAAT AAAGAA AAAAC
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT
* * * * *
1892545 AAAGAT AAAGT AAAGAT AAAA- AGAGT -AAAC AAAAT -AAAC AAAAT AAAGAT
1 AAA-AT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT
*
1892595 -AAA- GAAAT AAAAT -AAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1892641 AAAA- ATAAAT AAAAT AAAAT -AAAT AAAAT AAAAT AAAAT AAAAT -AAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
1892689 AAAA- AATATAT ACAAT -AAAT -AAAT AAAAAC AAGAAT AAAAT -AAA-
1 AAAAT AA-A-AT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAAT
* * ***
1892733 AAGAT ATAAA- GAAAT AAAAT -AAAT ACCGT AAAGAT -AAAT AAAAT AAAAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT -AAAAT
*
1892783 AAAGAA AAAAT AAAAT AAAA
1 AAA-AT AAAAT AAAAT AAAA
1892803 GAAAGAAAGA
Statistics
Matches: 234, Mismatches: 36, Indels: 64
0.70 0.11 0.19
Matches are distributed among these distances:
4 57 0.24
5 140 0.60
6 36 0.15
7 1 0.00
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1892522 original size:24 final size:23
Alignment explanation
Indices: 1892495--1892806 Score: 143
Period size: 24 Copynumber: 13.0 Consensus size: 23
1892485 AAAAGGTAAT
1892495 AAAAATAAATAAAATAAAGAAAA
1 AAAAATAAATAAAATAAAGAAAA
* *
1892518 CAAAAAAAAATGAAATAAAGAAAA
1 -AAAAATAAATAAAATAAAGAAAA
* * *
1892542 AACAA-AGATAAAGTAAAGATAAA
1 AAAAATAAATAAAATAAAGA-AAA
* * * *
1892565 AAGAGTAAACAAAATAAACAAAATAA
1 AAAAATAAATAAAAT-AA-AGAA-AA
* *
1892591 AGATAAAGAAATAAAATAAATAAAA
1 A-A-AAATAAATAAAATAAAGAAAA
* *
1892616 TAAAATAAA-ATAAATAAAATAAAA
1 AAAAATAAATA-AAAT-AAAGAAAA
1892640 TAAAAATAAATAAAATAAA-ATAAA
1 -AAAAATAAATAAAATAAAGA-AAA
* *
1892664 TAAAATAAAATAAAATAAAATAAATA
1 AAAAAT-AAATAAAAT-AAAGAAA-A
* * *
1892690 AAAAATATATACAATAAATAAATA
1 AAAAATAAATAAAATAAAGAAA-A
*
1892714 AAAACA-AGAATAAAATAAA-AAGAT
1 AAAA-ATA-AATAAAATAAAGAA-AA
* * * ***
1892738 ATAAAGAAATAAAATAAATACCGT
1 AAAAATAAATAAAATAAAGA-AAA
*
1892762 AAAGATAAATAAAATAAA-AATAA
1 AAAAATAAATAAAATAAAGAA-AA
*
1892785 AGAAA-AAATAAAATAAAAGAAA
1 AAAAATAAATAAAAT-AAAGAAA
1892807 GAAAGAAAGA
Statistics
Matches: 225, Mismatches: 38, Indels: 51
0.72 0.12 0.16
Matches are distributed among these distances:
22 21 0.09
23 46 0.20
24 90 0.40
25 40 0.18
26 16 0.07
27 3 0.01
28 9 0.04
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAAATAAATAAAATAAAGAAAA
Found at i:1892604 original size:14 final size:13
Alignment explanation
Indices: 1892575--1892802 Score: 157
Period size: 14 Copynumber: 16.7 Consensus size: 13
1892565 AAGAGTAAAC
1892575 AAAATAAACAAAAT
1 AAAATAAA-AAAAT
*
1892589 AAAGATAAAGAAAT
1 AAA-ATAAAAAAAT
1892603 AAAATAAATAAAAT
1 AAAATAAA-AAAAT
1892617 AAAATAAAATAAAT
1 AAAATAAAA-AAAT
*
1892631 AAAAT-AAAATA-
1 AAAATAAAAAAAT
1892642 AAAATAAATAAAAT
1 AAAATAAA-AAAAT
1892656 AAAATAAATAAAAT
1 AAAATAAA-AAAAT
1892670 AAAATAAAATAAA-
1 AAAATAAAA-AAAT
1892683 ATAAATAAAAAATAT
1 A-AAATAAAAAA-AT
*
1892698 ATACAATAAATAAAT
1 A-A-AATAAAAAAAT
* *
1892713 AAAA-ACAAGAAT
1 AAAATAAAAAAAT
*
1892725 AAAATAAAAAGAT
1 AAAATAAAAAAAT
*
1892738 ATAAAGAAATAAAAT
1 A-AAATAAA-AAAAT
1892753 AAATACCGTAAAGATAAAT
1 AAA-A---TAAA-A-AAAT
1892772 AAAAT--AAAAAT
1 AAAATAAAAAAAT
*
1892783 -AAA-GAAAAAAT
1 AAAATAAAAAAAT
1892794 AAAATAAAA
1 AAAATAAAA
1892803 GAAAGAAAGA
Statistics
Matches: 175, Mismatches: 16, Indels: 47
0.74 0.07 0.20
Matches are distributed among these distances:
10 3 0.02
11 15 0.09
12 17 0.10
13 28 0.16
14 74 0.42
15 18 0.10
16 8 0.05
18 5 0.03
19 7 0.04
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:1892784 original size:11 final size:11
Alignment explanation
Indices: 1892768--1892802 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1892758 CCGTAAAGAT
1892768 AAATAAAATAA
1 AAATAAAATAA
1892779 AAATAAAGA-AA
1 AAATAAA-ATAA
1892790 AAATAAAATAA
1 AAATAAAATAA
1892801 AA
1 AA
1892803 GAAAGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.05
11 20 0.91
12 1 0.05
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:1892794 original size:17 final size:17
Alignment explanation
Indices: 1892772--1892806 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1892762 AAAGATAAAT
1892772 AAAATAAAA-ATAAAGAA
1 AAAATAAAATA-AAAGAA
1892789 AAAATAAAATAAAAGAA
1 AAAATAAAATAAAAGAA
1892806 A
1 A
1892807 GAAAGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAATAAAATAAAAGAA
Found at i:1892905 original size:19 final size:20
Alignment explanation
Indices: 1892878--1892923 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1892868 AAAACATTAG
*
1892878 ATAAAAAATAACAAAAAATA
1 ATAATAAATAACAAAAAATA
* *
1892898 A-AATAAATAATAAATAATA
1 ATAATAAATAACAAAAAATA
1892917 ATAATAA
1 ATAATAA
1892924 TAATAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
ATAATAAATAACAAAAAATA
Found at i:1892909 original size:12 final size:12
Alignment explanation
Indices: 1892894--1892950 Score: 57
Period size: 11 Copynumber: 4.7 Consensus size: 12
1892884 AATAACAAAA
1892894 AATAAAATAAAT
1 AATAAAATAAAT
1892906 AAT-AAAT-AAT
1 AATAAAATAAAT
1892916 AATAATAATAATAAT
1 AATAA-AAT-A-AAT
1892931 AATAAAAATAAA-
1 AAT-AAAATAAAT
1892943 AATAAAAT
1 AATAAAAT
1892951 GACTAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
10 6 0.15
11 10 0.26
12 9 0.23
13 2 0.05
14 1 0.03
15 9 0.23
16 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:1892916 original size:3 final size:3
Alignment explanation
Indices: 1892894--1892947 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
1892884 AATAACAAAA
*
1892894 AAT AA- AAT AAAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAA AAT
1 AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1892940 AAA AAT AA
1 AAT AAT AA
1892948 AATGACTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1893993 original size:18 final size:17
Alignment explanation
Indices: 1893970--1894026 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
1893960 AAATAGTATA
1893970 AATATATTATATAATTAT
1 AATATATTATATAA-TAT
*
1893988 AATATATAATATAATAT
1 AATATATTATATAATAT
* *
1894005 GTATATATTATGTAATAT
1 -AATATATTATATAATAT
1894023 AATA
1 AATA
1894027 CTATAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 6 0.18
18 27 0.82
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
AATATATTATATAATAT
Found at i:1894767 original size:85 final size:85
Alignment explanation
Indices: 1894613--1894931 Score: 279
Period size: 85 Copynumber: 3.8 Consensus size: 85
1894603 ATGTGTCATC
* * * * ** *
1894613 GAGCTGAATGGAATC-ACACTCGACA-GTTTTTGTTGACAGATAG-CTTTTCTCATCTTAAGCTA
1 GAGCTGAATGTAATCGA-ACTCGA-AGGTCTTAGTTGACAGATAGAC-CTTCTCCCCTTGAGCTA
* *
1894675 TGTTGTAAATTTAATATGCCTTT
63 TGCTGTAAATTTAATGTGCCTTT
* * ** * *
1894698 GAGTTGAATGTAATCGAACTTGAATTTATTTAG-TGATAGATAGACCTTCTCCCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGT-CTTAGTTGACAGATAGACCTTCTCCCCTTGAGCTATG
*
1894762 CTGTAAATTTGATGTGCCTTT
65 CTGTAAATTTAATGTGCCTTT
* * * * *
1894783 GAGCTGAATGTAATCGACCTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTAAGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTAGTTGACAGATAGACCTTCTCCCCTTGAGCTATGC
*
1894848 TGTAAATTTTATGTGCCTTT
66 TGTAAATTTAATGTGCCTTT
* * * * * * * **
1894868 GACCTGAATATAATCAAACACAAAGGTCTTTGTTGACAAATA-ACCCTTCTTGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTAGTTGACAGATAGA-CCTTCTCCCCTTGAGCTATG
1894932 TTATAATACG
Statistics
Matches: 192, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
84 4 0.02
85 182 0.95
86 6 0.03
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTAGTTGACAGATAGACCTTCTCCCCTTGAGCTATGC
TGTAAATTTAATGTGCCTTT
Found at i:1901825 original size:5 final size:5
Alignment explanation
Indices: 1901810--1902057 Score: 87
Period size: 5 Copynumber: 50.6 Consensus size: 5
1901800 AAAGGGAATG
* * * *
1901810 AAAAT -AAAT AAAAT -AAAG AAAAT AAAAA ACAAAT AAAAA ACAAAT GAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT A-AAAT AAAAT
* * * *
1901860 -AAAG AAAAT GAAAT AAAGAA AAAAT AAAGAT AAAGAA AAAAT AAAGAT
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AAA-AT AAA-AT AAAAT AAA-AT
* * * * *
1901908 AAAGAA AAAAC AAAGAT AAAA- AGAGT -AAAC AAAAT -AAAT AAAAT AAAA-
1 AAA-AT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * * *
1901956 GAAAT AAAA- ATAA- AAAAT AAAA- GAAAT AATAAT AAAAT -ATAT ACAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT
* * * *
1902003 -AAAT -AAA- AAAAT AAAGT AAAGAT -AAAG AAAAT AAAA- AAAACA AAAAA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAA-T AAAAT
1902050 AAAAT AAA
1 AAAAT AAA
1902058 GAAAGAAAAT
Statistics
Matches: 181, Mismatches: 39, Indels: 46
0.68 0.15 0.17
Matches are distributed among these distances:
4 46 0.25
5 90 0.50
6 45 0.25
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:1901886 original size:11 final size:11
Alignment explanation
Indices: 1901819--1902080 Score: 77
Period size: 11 Copynumber: 23.5 Consensus size: 11
1901809 GAAAATAAAT
1901819 AAAATAAAGAA
1 AAAATAAAGAA
* *
1901830 AATAAAAAACAA
1 AA-AATAAAGAA
*
1901842 ATAAA-AAACAA
1 A-AAATAAAGAA
1901853 ATGAAATAAAGAAA
1 A--AAATAAAG-AA
1901867 ATGAAATAAAGAA
1 A--AAATAAAGAA
1901880 AAAATAAAGATA
1 AAAATAAAGA-A
1901892 AAGAA-AAA-ATA
1 AA-AATAAAGA-A
*
1901903 AAGATAAAGAA
1 AAAATAAAGAA
*
1901914 AAAACAAAGATA
1 AAAATAAAGA-A
* *
1901926 AAAAGAGTAA-AC
1 AAAATA--AAGAA
*
1901938 AAAATAAATAA
1 AAAATAAAGAA
*
1901949 AATA-AAAGAA
1 AAAATAAAGAA
* *
1901959 ATAA-AAATAA
1 AAAATAAAGAA
1901969 AAAATAAAAGAA
1 AAAAT-AAAGAA
* *
1901981 ATAAT-AATAA
1 AAAATAAAGAA
* * *
1901991 AATATATACAA
1 AAAATAAAGAA
*
1902002 TAAAT--A-AA
1 AAAATAAAGAA
*
1902010 AAAATAAAGTA
1 AAAATAAAGAA
*
1902021 AAGATAAAG--
1 AAAATAAAGAA
1902030 AAAATAAA-AA
1 AAAATAAAGAA
1902040 AAACA-AAA-AA
1 AAA-ATAAAGAA
1902050 AAAATAAAGAAA
1 AAAATAAAG-AA
*
1902062 GAAAATAATAGTA
1 -AAAATAA-AGAA
1902075 AAAATA
1 AAAATA
1902081 TATATATAAT
Statistics
Matches: 193, Mismatches: 31, Indels: 53
0.70 0.11 0.19
Matches are distributed among these distances:
8 6 0.03
9 9 0.05
10 40 0.21
11 55 0.28
12 48 0.25
13 18 0.09
14 17 0.09
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (11 bp):
AAAATAAAGAA
Found at i:1901894 original size:17 final size:17
Alignment explanation
Indices: 1901819--1901927 Score: 108
Period size: 17 Copynumber: 6.8 Consensus size: 17
1901809 GAAAATAAAT
*
1901819 AAAATAAAGA-AAATAA
1 AAAATAAAGATAAAGAA
*
1901835 AAAA-CAA-ATAAA-AA
1 AAAATAAAGATAAAGAA
*
1901849 ACAAATGAA-ATAAAG--
1 A-AAATAAAGATAAAGAA
*
1901864 AAAATGAA-ATAAAGAA
1 AAAATAAAGATAAAGAA
1901880 AAAATAAAGATAAAGAA
1 AAAATAAAGATAAAGAA
1901897 AAAATAAAGATAAAGAA
1 AAAATAAAGATAAAGAA
*
1901914 AAAACAAAGATAAA
1 AAAATAAAGATAAA
1901928 AAGAGTAAAC
Statistics
Matches: 82, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
14 17 0.21
15 9 0.11
16 18 0.22
17 38 0.46
ACGTcount: A:0.77, C:0.03, G:0.09, T:0.11
Consensus pattern (17 bp):
AAAATAAAGATAAAGAA
Found at i:1901910 original size:34 final size:33
Alignment explanation
Indices: 1901819--1902061 Score: 117
Period size: 34 Copynumber: 7.5 Consensus size: 33
1901809 GAAAATAAAT
* *
1901819 AAAATAAAGA-AAATAAAAAA-CAAATAAA-AA
1 AAAATAAAGATAAAGAAAAAATAAAATAAAGAA
* *
1901849 ACAAATGAA-ATAAAG--AAAATGAAATAAAGAA
1 A-AAATAAAGATAAAGAAAAAATAAAATAAAGAA
1901880 AAAATAAAGATAAAGAAAAAATAAAGATAAAGAA
1 AAAATAAAGATAAAGAAAAAATAAA-ATAAAGAA
* * *
1901914 AAAACAAAGATAAA-AAGAGTAAACAAAATAAATAA
1 AAAATAAAGATAAAGAA-A--AAATAAAATAAAGAA
*
1901949 AATA-AAAGA-AATA-AAAATAA-AAAATAAAAGAA
1 AAAATAAAGATAA-AGAAAA-AATAAAAT-AAAGAA
* * * * *
1901981 ATAATAATA-A-AATATATACAAT-AAATAAAAAA
1 AAAATAA-AGATAA-AGAAAAAATAAAATAAAGAA
* *
1902013 ATAAAGTAAAGATAAAG--AAAATAAAAAAAACAA
1 A-AAA-TAAAGATAAAGAAAAAATAAAATAAAGAA
1902046 AAAA-AAA-ATAAAGAAA
1 AAAATAAAGATAAAGAAA
1902062 GAAAATAATA
Statistics
Matches: 168, Mismatches: 20, Indels: 49
0.71 0.08 0.21
Matches are distributed among these distances:
29 10 0.06
30 18 0.11
31 25 0.15
32 22 0.13
33 37 0.22
34 38 0.23
35 12 0.07
36 6 0.04
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.13
Consensus pattern (33 bp):
AAAATAAAGATAAAGAAAAAATAAAATAAAGAA
Found at i:1902067 original size:101 final size:97
Alignment explanation
Indices: 1901810--1902078 Score: 223
Period size: 101 Copynumber: 2.7 Consensus size: 97
1901800 AAAGGGAATG
*
1901810 AAAATAAATAAA-ATAAAGAAAATAAAAAACAAATAAAAAACAAATGAAATAAAGAAAATGAAAT
1 AAAATAAATAAAGATAAAGAAAATAAAAAA-AAA-AAAAAA-AAAT-AAAGAAAGAAAAT-AAAT
*
1901874 AAAGAAAAAATAAAGATAAAGAAAAAATAAAGATAAA
61 AAAAAAAAAATAAAGATAAAGAAAAAATAAAGATAAA
* * * * * * *
1901911 GAAA-AAACAAAGATAAA-AAGAGT-AAACAAAATAAATAAAATAAAAGAAATAAAAATAAA-AA
1 AAAATAAATAAAGATAAAGAA-AATAAAAAAAAAAAAAAAAAAT-AAAGAAA-GAAAATAAATAA
1901972 ATAAAAGAAATAATA-ATAAA-ATATATACAAT-AA-ATAAA
63 A-AAAA-AAATAA-AGATAAAGA-A-A-A-AATAAAGATAAA
1902010 AAAATAAAGTAAAGATAAAGAAAATAAAAAAAACAAAAAAAAAATAAAGAAAGAAAATAATAGTA
1 AAAATAAA-TAAAGATAAAGAAAATAAAAAAAA-AAAAAAAAAATAAAGAAAGAAAATAA-A-TA
1902075 AAAA
62 AAAA
1902079 TATATATATA
Statistics
Matches: 133, Mismatches: 17, Indels: 34
0.72 0.09 0.18
Matches are distributed among these distances:
96 3 0.02
97 17 0.13
98 21 0.16
99 13 0.10
100 18 0.14
101 31 0.23
102 16 0.12
103 11 0.08
104 3 0.02
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (97 bp):
AAAATAAATAAAGATAAAGAAAATAAAAAAAAAAAAAAAAAATAAAGAAAGAAAATAAATAAAAA
AAAAATAAAGATAAAGAAAAAATAAAGATAAA
Found at i:1902086 original size:88 final size:85
Alignment explanation
Indices: 1901934--1902166 Score: 205
Period size: 88 Copynumber: 2.7 Consensus size: 85
1901924 TAAAAAGAGT
*
1901934 AAACA-AA-ATAAATAAAATAAAAGAAATAAAAATAAAAAAT--AAAAGAAATAATA-ATAAA-A
1 AAACATAAGATAAA-AAAATAAAA-AAA-AAAAA-AAAAAATAAAAAAGAAATAATATAAAAATA
1901993 TATATACAAT-AAATAAAAAAATA
62 TATATACAATAAAATAAAAAAATA
**
1902016 AAGTA-AAGATAAAGAAAATAAAAAAAACAAAAAAAAAATAAAGAAAGAAAATAATAGTAAAAAT
1 AAACATAAGATAAA-AAAATAAAAAAAA-AAAAAAAAAATAAA-AAAG-AAATAATA-TAAAAAT
* ** *
1902080 ATATATATAATAAAATGTATAAATA
61 ATATATACAATAAAATAAAAAAATA
* * * *
1902105 AAACATTAGAT-AAAAAATAAAAAAGAAATAAAAAAATAAAAAAAGAAATAATAATAATAATA
1 AAACATAAGATAAAAAAATAAAAAAAAAAAAAAAAAAT-AAAAAAGAAATAAT-ATAAAAATA
1902167 ATAAAAGGAC
Statistics
Matches: 124, Mismatches: 14, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
81 8 0.06
82 12 0.10
83 15 0.12
84 4 0.03
85 8 0.06
86 14 0.11
87 19 0.15
88 25 0.20
89 15 0.12
90 4 0.03
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (85 bp):
AAACATAAGATAAAAAAATAAAAAAAAAAAAAAAAAATAAAAAAGAAATAATATAAAAATATATA
TACAATAAAATAAAAAAATA
Found at i:1902139 original size:20 final size:20
Alignment explanation
Indices: 1902116--1902155 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1902106 AACATTAGAT
1902116 AAAAAAT-AAAAAAGAAATA
1 AAAAAATAAAAAAAGAAATA
1902135 AAAAAATAAAAAAAGAAATA
1 AAAAAATAAAAAAAGAAATA
1902155 A
1 A
1902156 TAATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAAAATAAAAAAAGAAATA
Found at i:1902181 original size:78 final size:79
Alignment explanation
Indices: 1902037--1902181 Score: 174
Period size: 79 Copynumber: 1.8 Consensus size: 79
1902027 AAGAAAATAA
* *
1902037 AAAAAACAAAAAAAAAATAAAGAAAGAAAATAATAGTAAAAATATATATATAATAAAATGTATAA
1 AAAAAACAAAAAAAAAATAAAAAAAGAAAATAATAGTAAAAATATATATATAATAAAATGGATAA
1902102 ATAAAACATTAGAT
66 ATAAAACATTAGAT
* * *
1902116 AAAAAATAAAAAAGAAATAAAAAAATAAAA-AA-AG-AAATAATA-ATAATAATAATAAAA-GGA
1 AAAAAACAAAAAAAAAATAAAAAAAGAAAATAATAGTAAA-AATATAT-AT-ATAATAAAATGGA
1902176 CTAAAT
63 -TAAAT
1902182 TTAAAGAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
76 5 0.09
77 10 0.18
78 16 0.28
79 26 0.46
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.19
Consensus pattern (79 bp):
AAAAAACAAAAAAAAAATAAAAAAAGAAAATAATAGTAAAAATATATATATAATAAAATGGATAA
ATAAAACATTAGAT
Found at i:1903161 original size:18 final size:17
Alignment explanation
Indices: 1903138--1903194 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 17
1903128 AAATAGAAGC
1903138 AATATATTATATAATTAT
1 AATATATTATATAA-TAT
*
1903156 AATATATGATATAATAT
1 AATATATTATATAATAT
*
1903173 GTATATATTATATAATAT
1 -AATATATTATATAATAT
1903191 AATA
1 AATA
1903195 ATATAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 6 0.18
18 28 0.82
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
AATATATTATATAATAT
Found at i:1903898 original size:85 final size:85
Alignment explanation
Indices: 1903829--1904100 Score: 375
Period size: 85 Copynumber: 3.2 Consensus size: 85
1903819 CTTTTCTCAG
* * *
1903829 CTTAAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTTATCAAACTCGAAGGTCTTTAG
1 CTTAAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTT-G
1903894 -TGACAGATAGCCCTTCTCGC
65 CTGACAGATAGCCCTTCTCGC
* * *
1903914 CTTAAGCTATACTGTAAATTTGATGTGCCTTAGAGCTGAATGTAATCGAACTCAAAGGTCTTTGC
1 CTTAAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGC
* *
1903979 TGATAGATAGCCCTTCTCAC
66 TGACAGATAGCCCTTCTCGC
* * * * * * *
1903999 CTTGAGCTAAGCTATAAATTTGATGTTCCTTTGAGATGAATATAATCGAACTCGAAGGTCTTTGT
1 CTTAAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGC
1904064 TGACAGATAGCCCTTCTCGC
66 TGACAGATAGCCCTTCTCGC
* *
1904084 CTTGAGCTATGTTGTAA
1 CTTAAGCTATGCTGTAA
1904101 TAGGGTGAGA
Statistics
Matches: 163, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
84 1 0.01
85 162 0.99
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (85 bp):
CTTAAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGC
TGACAGATAGCCCTTCTCGC
Found at i:1910559 original size:5 final size:5
Alignment explanation
Indices: 1910546--1910826 Score: 83
Period size: 5 Copynumber: 56.6 Consensus size: 5
1910536 GAAGGCAATG
* * * * * *
1910546 AAATT AAATA AAAT- AAAGA AAATA AAACAA AAAAA CAAATG AAAT- AAAGA
1 AAATA AAATA AAATA AAATA AAATA AAA-TA AAATA -AAATA AAATA AAATA
* * * * *
1910596 AAATAA AAAGA TAAAGA AAATA AAA-G AAATA AAAGTA AAATG TAA-A
1 AAAT-A AAATA -AAATA AAATA AAATA AAATA AAA-TA AAATA AAATA
* * * *
1910642 AAAT- AAATA AAATA ATAATA AAAT- ATATA CAAT- AAAT- AAATA GATACA
1 AAATA AAATA AAATA A-AATA AAATA AAATA AAATA AAATA AAATA -AAATA
* **
1910690 AGAATA AAATAA AAATA AAAT- AAA-G AAATA AAAT- AAAT- AAATA TAAAGG
1 A-AATA AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAATA -AAATA
** * *
1910739 AAATA AAA-A AATATA AAGGA AATATAA AAATA AAGTA AAGAT- AAAGA
1 AAATA AAATA AA-ATA AAATA AA-AT-A AAATA AAATA AA-ATA AAATA
* * *
1910786 AAATA AAA-A TAAATA AAA-A TAATT GAA-A AAATA AAATA AAA
1 AAATA AAATA -AAATA AAATA AAATA AAATA AAATA AAATA AAA
1910827 CAATTAAAGA
Statistics
Matches: 204, Mismatches: 42, Indels: 60
0.67 0.14 0.20
Matches are distributed among these distances:
4 49 0.24
5 105 0.51
6 47 0.23
7 3 0.01
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1910616 original size:26 final size:25
Alignment explanation
Indices: 1910558--1910629 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
1910548 ATTAAATAAA
*
1910558 ATAAAGAAAATAAAACAA-AAAAAC
1 ATAAAGAAAATAAAAAAATAAAAAC
* *
1910582 A-AATG-AAATAAAGAAAATAAAAAG
1 ATAAAGAAAATAAA-AAAATAAAAAC
1910606 ATAAAGAAAATAAAAGAAATAAAA
1 ATAAAGAAAATAAAA-AAATAAAA
1910630 GTAAAATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 7 0.18
23 6 0.15
24 7 0.18
25 4 0.10
26 15 0.38
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (25 bp):
ATAAAGAAAATAAAAAAATAAAAAC
Found at i:1910654 original size:29 final size:29
Alignment explanation
Indices: 1910555--1910681 Score: 88
Period size: 29 Copynumber: 4.4 Consensus size: 29
1910545 GAAATTAAAT
* *
1910555 AAAATAAAGAAAATAA-AACAAAA-A-AA
1 AAAATAAATAAAATAATAATAAAATATAA
* *
1910581 CAAATGAAATAAAGAAAATAA-AAAGATA-AA
1 AAAAT-AAATAAA-ATAATAATAAA-ATATAA
*
1910611 GAAAATAAA-AGAAATAA-AAGTAAAATGTAA
1 -AAAATAAATA-AAATAATAA-TAAAATATAA
*
1910641 AAAATAAATAAAATAATAATAAAATATAT
1 AAAATAAATAAAATAATAATAAAATATAA
*
1910670 ACAATAAATAAA
1 AAAATAAATAAA
1910682 TAGATACAAG
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.05
27 6 0.08
28 8 0.10
29 42 0.52
30 16 0.20
31 4 0.05
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (29 bp):
AAAATAAATAAAATAATAATAAAATATAA
Found at i:1910682 original size:17 final size:17
Alignment explanation
Indices: 1910638--1910802 Score: 74
Period size: 19 Copynumber: 9.5 Consensus size: 17
1910628 AAGTAAAATG
*
1910638 TAAA-AAATAAATAAAA
1 TAAATAAATATATAAAA
*
1910654 TAATAATAAAATATATACAA
1 T-A-AAT-AAATATATAAAA
* *
1910674 TAAATAAATAGATACAA
1 TAAATAAATATATAAAA
*
1910691 -GAATAAA-ATA-AAAA
1 TAAATAAATATATAAAA
* *
1910705 TAAAATAAAGAAATAAAA
1 T-AAATAAATATATAAAA
*
1910723 TAAATAAATATAAAGGAAA
1 TAAATAAATATATA--AAA
* *
1910742 TAAAAAAATATAAAGGAAA
1 TAAATAAATATATA--AAA
*
1910761 TATAA-AAATAAAGTAAAGA
1 TA-AATAAATATA-TAAA-A
*
1910780 TAAAGAAA-ATA-AAAA
1 TAAATAAATATATAAAA
1910795 TAAATAAA
1 TAAATAAA
1910803 AATAATTGAA
Statistics
Matches: 119, Mismatches: 16, Indels: 29
0.73 0.10 0.18
Matches are distributed among these distances:
14 3 0.03
15 10 0.08
16 16 0.13
17 24 0.20
18 16 0.13
19 36 0.30
20 14 0.12
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.20
Consensus pattern (17 bp):
TAAATAAATATATAAAA
Found at i:1910803 original size:9 final size:9
Alignment explanation
Indices: 1910546--1910825 Score: 122
Period size: 9 Copynumber: 31.3 Consensus size: 9
1910536 GAAGGCAATG
*
1910546 AAATTAAAT
1 AAATAAAAT
1910555 AAAATAAAGA-
1 -AAATAAA-AT
*
1910565 AAATAAAAC
1 AAATAAAAT
*
1910574 AAA-AAAAC
1 AAATAAAAT
*
1910582 AAATGAAAT
1 AAATAAAAT
*
1910591 AAAGAAAAT
1 AAATAAAAT
*
1910600 AAA-AAGAT
1 AAATAAAAT
*
1910608 AAAGAAAAT
1 AAATAAAAT
1910617 AAA-AGAAAT
1 AAATA-AAAT
1910626 AAAAGTAAAAT
1 -AAA-TAAAAT
*
1910637 GTAA-AAAAT
1 -AAATAAAAT
1910646 AAATAAAAT
1 AAATAAAAT
1910655 AATAATAAAAT
1 -A-AATAAAAT
* *
1910666 ATATACAAT
1 AAATAAAAT
1910675 AAAT-AAAT
1 AAATAAAAT
* *
1910683 AGATACAA-
1 AAATAAAAT
*
1910691 GAATAAAAT
1 AAATAAAAT
*
1910700 AAA-AATA-
1 AAATAAAAT
*
1910707 AAAT-AAAG
1 AAATAAAAT
1910715 AAATAAAAT
1 AAATAAAAT
1910724 AAATAAATAT
1 AAATAAA-AT
**
1910734 AAAGGAAAT
1 AAATAAAAT
*
1910743 AAAAAAATAT
1 AAATAAA-AT
**
1910753 AAAGGAAAT
1 AAATAAAAT
*
1910762 ATA-AAAAT
1 AAATAAAAT
1910770 AAAGTAAAGAT
1 AAA-TAAA-AT
*
1910781 AAAGAAAAT
1 AAATAAAAT
1910790 --A-AAAAT
1 AAATAAAAT
1910796 AAATAAAAAT
1 AAAT-AAAAT
* *
1910806 AATTGAAA-
1 AAATAAAAT
1910814 AAATAAAAT
1 AAATAAAAT
1910823 AAA
1 AAA
1910826 ACAATTAAAG
Statistics
Matches: 207, Mismatches: 37, Indels: 53
0.70 0.12 0.18
Matches are distributed among these distances:
6 5 0.02
7 6 0.03
8 50 0.24
9 86 0.42
10 39 0.19
11 20 0.10
12 1 0.00
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1910815 original size:47 final size:44
Alignment explanation
Indices: 1910695--1910825 Score: 133
Period size: 47 Copynumber: 2.8 Consensus size: 44
1910685 ATACAAGAAT
*
1910695 AAAATAAAAATAAAATAAAGAAA-T-AAAATAAATAAATATAAAG
1 AAAATAAAAAT-AAATAAAGAAATTAAAAATAAATAAAGATAAAG
*
1910738 GAAATAAAAA-AATATAAAGGAAATATAAAAATAAAGTAAAGATAAAG
1 AAAATAAAAATAA-ATAAA-GAAAT-TAAAAATAAA-TAAAGATAAAG
*
1910785 AAAATAAAAATAAATAAAAATAATTGAAAAAATAAAATAAA
1 AAAATAAAAATAAATAAAGA-AATT--AAAAAT-AAATAAA
1910826 ACAATTAAAG
Statistics
Matches: 73, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
41 2 0.03
42 5 0.07
43 13 0.18
45 1 0.01
46 10 0.14
47 27 0.37
48 12 0.16
49 3 0.04
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (44 bp):
AAAATAAAAATAAATAAAGAAATTAAAAATAAATAAAGATAAAG
Found at i:1910839 original size:23 final size:23
Alignment explanation
Indices: 1910790--1910842 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
1910780 TAAAGAAAAT
* *
1910790 AAAAAT-AAATAAAAATAATTGA
1 AAAAATAAAATAAAAACAATTAA
1910812 AAAAATAAAAT-AAAACAATTAA
1 AAAAATAAAATAAAAACAATTAA
1910834 AGAAAATAA
1 A-AAAATAA
1910843 TAGTAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAAATAAAATAAAAACAATTAA
Found at i:1910948 original size:29 final size:30
Alignment explanation
Indices: 1910880--1910951 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
1910870 AATAAAATGT
* *
1910880 ATAAATAAAACAT-TAGATTAAAAAATAATA
1 ATAAATAAAA-ATAAAGATTAAAAAATAACA
* *
1910910 AAAAAT-AAAATAAAGATTAAAATA-AACA
1 ATAAATAAAAATAAAGATTAAAAAATAACA
1910938 ATAAATAAAAATAA
1 ATAAATAAAAATAA
1910952 TAAAAGGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 10 0.29
29 20 0.57
30 5 0.14
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (30 bp):
ATAAATAAAAATAAAGATTAAAAAATAACA
Found at i:1919324 original size:26 final size:26
Alignment explanation
Indices: 1919288--1919339 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1919278 AGATTTGTAA
1919288 GTGAAGGGAGAATATGGTGTCATGTG
1 GTGAAGGGAGAATATGGTGTCATGTG
1919314 GTGAAGGGAGAATATGGTGTCATGTG
1 GTGAAGGGAGAATATGGTGTCATGTG
1919340 ATGTTTGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.42, T:0.27
Consensus pattern (26 bp):
GTGAAGGGAGAATATGGTGTCATGTG
Found at i:1919564 original size:18 final size:18
Alignment explanation
Indices: 1919541--1919576 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1919531 TTGCGGAGGA
1919541 GAACATCAGAGAATTTAT
1 GAACATCAGAGAATTTAT
1919559 GAACATCAGAGAATTTAT
1 GAACATCAGAGAATTTAT
1919577 AGTCCACCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
GAACATCAGAGAATTTAT
Found at i:1920552 original size:44 final size:43
Alignment explanation
Indices: 1920390--1920570 Score: 290
Period size: 43 Copynumber: 4.2 Consensus size: 43
1920380 TTCTATTTAG
* *
1920390 AAATAAAAAGGATAAGATTTATAGTTAATATAAACTACAAAGTC
1 AAATAATAA-GATAAGAGTTATAGTTAATATAAACTACAAAGTC
* *
1920434 AAATAATAAGATGAGAGTTAAAGTTAATATAAACTACAAAGTC
1 AAATAATAAGATAAGAGTTATAGTTAATATAAACTACAAAGTC
*
1920477 AAATAATAAGATAAGAGTTATAGTTAATCTAAACTACAAAGTC
1 AAATAATAAGATAAGAGTTATAGTTAATATAAACTACAAAGTC
*
1920520 AAATAATAAGATAAAGAGTTATAGTTAATCTAAACTACAAAGTC
1 AAATAATAAGAT-AAGAGTTATAGTTAATATAAACTACAAAGTC
1920564 AAATAAT
1 AAATAAT
1920571 CAATTGCTAT
Statistics
Matches: 129, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
43 83 0.64
44 46 0.36
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.27
Consensus pattern (43 bp):
AAATAATAAGATAAGAGTTATAGTTAATATAAACTACAAAGTC
Found at i:1923619 original size:19 final size:19
Alignment explanation
Indices: 1923581--1923619 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1923571 CAAAAGTCAC
* * *
1923581 AAAAATTATTTGATTTTTT
1 AAAAATAATTTGAGTGTTT
1923600 AAAAATAATTTGAGTGTTT
1 AAAAATAATTTGAGTGTTT
1923619 A
1 A
1923620 TAAGGTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
AAAAATAATTTGAGTGTTT
Found at i:1926123 original size:2 final size:2
Alignment explanation
Indices: 1926116--1926156 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1926106 CAAGTTTCAT
1926116 TA TA TA 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 TA TA TA T
1926157 TATTACTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1926514 original size:2 final size:2
Alignment explanation
Indices: 1926507--1926565 Score: 63
Period size: 2 Copynumber: 31.0 Consensus size: 2
1926497 TTATTATTAT
* *
1926507 TA TA TA TA TA TA TA TA TA -A TA CA TA TA TGA T- TA TA -A TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
1926547 -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1926566 AAAGAGCTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
1 4 0.08
2 42 0.88
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1928936 original size:8 final size:8
Alignment explanation
Indices: 1928923--1928949 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1928913 TGAAATATCT
1928923 TATATGTA
1 TATATGTA
1928931 TATATGTA
1 TATATGTA
1928939 TATATGTA
1 TATATGTA
1928947 TAT
1 TAT
1928950 TTTCTAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (8 bp):
TATATGTA
Found at i:1929129 original size:12 final size:12
Alignment explanation
Indices: 1929112--1929205 Score: 98
Period size: 12 Copynumber: 7.8 Consensus size: 12
1929102 TTTTATTTCC
*
1929112 ATGTATATATAT
1 ATGTATATGTAT
1929124 ATGTATATGTAT
1 ATGTATATGTAT
*
1929136 ATGTTTATGTAT
1 ATGTATATGTAT
*
1929148 ATGTATATGTGT
1 ATGTATATGTAT
* *
1929160 ATGTGTATGTGT
1 ATGTATATGTAT
* *
1929172 ATGTGTATGTGT
1 ATGTATATGTAT
* *
1929184 ATGTGTATGTGT
1 ATGTATATGTAT
*
1929196 ATGTGTATGT
1 ATGTATATGT
1929206 GTGCGTGTGC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 77 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (12 bp):
ATGTATATGTAT
Found at i:1929130 original size:6 final size:6
Alignment explanation
Indices: 1929123--1929207 Score: 125
Period size: 6 Copynumber: 14.2 Consensus size: 6
1929113 TGTATATATA
* * * * *
1929123 TATGTA TATGTA TATGTT TATGTA TATGTA TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1929171 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG T
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG T
1929208 GCGTGTGCGT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 76 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (6 bp):
TATGTG
Found at i:1929135 original size:18 final size:18
Alignment explanation
Indices: 1929112--1929205 Score: 98
Period size: 18 Copynumber: 5.2 Consensus size: 18
1929102 TTTTATTTCC
*
1929112 ATGTATATATATATGTAT
1 ATGTATATGTATATGTAT
*
1929130 ATGTATATGTTTATGTAT
1 ATGTATATGTATATGTAT
* *
1929148 ATGTATATGTGTATGTGT
1 ATGTATATGTATATGTAT
* * *
1929166 ATGTGTATGTGTATGTGT
1 ATGTATATGTATATGTAT
* * *
1929184 ATGTGTATGTGTATGTGT
1 ATGTATATGTATATGTAT
1929202 ATGT
1 ATGT
1929206 GTGCGTGTGC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 71 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (18 bp):
ATGTATATGTATATGTAT
Found at i:1929213 original size:6 final size:6
Alignment explanation
Indices: 1929204--1929345 Score: 248
Period size: 6 Copynumber: 23.7 Consensus size: 6
1929194 GTATGTGTAT
* * *
1929204 GTGTGC GTGTGC GTGTGC GTGTGC GTGAGC GTGTGC GTTTGC GTTTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
*
1929252 GTTTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
1929300 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGT
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGT
1929346 ATATGTATAT
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 132 1.00
ACGTcount: A:0.01, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
GTGTGC
Found at i:1929616 original size:6 final size:6
Alignment explanation
Indices: 1929347--1929913 Score: 553
Period size: 6 Copynumber: 94.8 Consensus size: 6
1929337 TGTGCGTGTA
* * * * * * * *
1929347 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
1929395 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
1929443 TATGTA TATGTA TATGTA TATGTA TATGTC TATGTA TATGTC TATGTC
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
*
1929491 TATGTC TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1929539 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * *
1929587 TATGTG TATGTG TATGTG TATGTG TATGTG TACGTG TACGTG TACGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
1929635 TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
1929683 TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
1929731 TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
1929779 TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * *
1929827 TACGTG TACGTG TACGTG TATGTG TATGTG --TGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1929873 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGT
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGT
1929914 ATTTTTTTAA
Statistics
Matches: 553, Mismatches: 6, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
4 4 0.01
6 549 0.99
ACGTcount: A:0.20, C:0.07, G:0.29, T:0.43
Consensus pattern (6 bp):
TATGTG
Found at i:1934086 original size:12 final size:12
Alignment explanation
Indices: 1934034--1934086 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
1934024 TACATACATA
1934034 TATTATCATT-T
1 TATTATCATTAT
* *
1934045 CATTATCCTTAT
1 TATTATCATTAT
1934057 TATTAGTCTCATTAT
1 TATTA---TCATTAT
1934072 TATTATCATTAT
1 TATTATCATTAT
1934084 TAT
1 TAT
1934087 CATTTGAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
11 8 0.24
12 15 0.44
15 11 0.32
ACGTcount: A:0.28, C:0.13, G:0.02, T:0.57
Consensus pattern (12 bp):
TATTATCATTAT
Found at i:1940677 original size:19 final size:19
Alignment explanation
Indices: 1940655--1940698 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1940645 TTTGCATCTC
*
1940655 CATTTTACTTTTTACATTA
1 CATTTTACTTTTCACATTA
* *
1940674 CA-TTTACTTTTCGCATTG
1 CATTTTACTTTTCACATTA
1940692 CATTTTA
1 CATTTTA
1940699 TTTATTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (19 bp):
CATTTTACTTTTCACATTA
Found at i:1949211 original size:2 final size:2
Alignment explanation
Indices: 1949206--1949250 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1949196 TTGTTTTTTC
1949206 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
1949248 AT A
1 AT A
1949251 CTAATACAAT
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:1949550 original size:17 final size:17
Alignment explanation
Indices: 1949505--1949551 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1949495 ATATTATTAT
* *
1949505 TATATATATGTAATATG
1 TATATATATATAATATA
1949522 TATATGAT-TATAATATA
1 TATAT-ATATATAATATA
1949539 TATATATATATAA
1 TATATATATATAA
1949552 GAACTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TATATATATATAATATA
Found at i:1955029 original size:7 final size:6
Alignment explanation
Indices: 1955001--1955030 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1954991 TAAAACCTTG
1955001 TGCATT TGCATT TGCATT TGCATTT TGCAT
1 TGCATT TGCATT TGCATT TGCA-TT TGCAT
1955031 ATCATGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
TGCATT
Found at i:1958604 original size:109 final size:107
Alignment explanation
Indices: 1958412--1958655 Score: 344
Period size: 109 Copynumber: 2.2 Consensus size: 107
1958402 TTAGGATATG
1958412 TTGGGGCACGACTGAACCCACATCATTCAGACCAAGGAGACATGAAGAATGAGCCTTACAATTTG
1 TTGGGGCACGACTGAACCCACATCATTCAGACCAAGGAGACATGAAGAATGAGCCTTACAATTTG
* * *
1958477 AGTTAATGGGGCAATTTGAAGGCTCATCCCAGTAGAAGATAACA
66 AGGTAATGGGGCAATTTGAAGGCCCATACCAGTAGAAGAT-A-A
* * * * *
1958521 TTGGGGCACGATTGAACCCACATCTTTTAGACTAAGGAGGCATGAAGAATGAGCCTTACAATTTG
1 TTGGGGCACGACTGAACCCACATCATTCAGACCAAGGAGACATGAAGAATGAGCCTTACAATTTG
* * * *
1958586 AGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAA
66 AGGTAATGGGGCAATTTGAAGGCCCATACCAGTAGAAGATAA
1958628 TGTGGAGGCACGACTGAACCCACATCAT
1 T-TGG-GGCACGACTGAACCCACATCAT
1958656 GTTGAGATGA
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
107 2 0.02
108 4 0.03
109 113 0.95
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (107 bp):
TTGGGGCACGACTGAACCCACATCATTCAGACCAAGGAGACATGAAGAATGAGCCTTACAATTTG
AGGTAATGGGGCAATTTGAAGGCCCATACCAGTAGAAGATAA
Found at i:1959028 original size:80 final size:80
Alignment explanation
Indices: 1958892--1959051 Score: 275
Period size: 80 Copynumber: 2.0 Consensus size: 80
1958882 GAGTGAAAAC
* *
1958892 GGTGAAACAATGACAGTGGGGTTTACTGTATATGATCATTTTGTCAATCATCAGTTGCATTACCC
1 GGTGAAACAATGACAGTGGGGTTTACTGTATATGATCATTTTATCAATCATCAGTTGCATTAACC
1958957 TAGTGATTTCCACTG
66 TAGTGATTTCCACTG
* *
1958972 GGTGAAACAATGACAGTGGGGTTTACTGTATATGATCATTTTATCAATCATTAGTTGCATTAATC
1 GGTGAAACAATGACAGTGGGGTTTACTGTATATGATCATTTTATCAATCATCAGTTGCATTAACC
*
1959037 TGGTGATTTCCACTG
66 TAGTGATTTCCACTG
1959052 AGTTTTAGTA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (80 bp):
GGTGAAACAATGACAGTGGGGTTTACTGTATATGATCATTTTATCAATCATCAGTTGCATTAACC
TAGTGATTTCCACTG
Found at i:1960614 original size:214 final size:214
Alignment explanation
Indices: 1960007--1960950 Score: 1380
Period size: 215 Copynumber: 4.4 Consensus size: 214
1959997 CCGAAAATTT
*
1960007 TAAGT-CTTCCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTATA
1 TAAGTCCTT-CGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
* *
1960071 AGCCTTTAGAGCAAGATGATAAGTCTTTAGGGCCATCCATAAGACCTTCGAGTAGAATATTTTCA
65 AGCCTTTAGAGCAAGATGATAAGTCTTCA-GGCCATCCATAAGACCTTCGAGTAGGATATTTTCA
* * *
1960136 AATGAATTTGAAAATGAGAAAATAATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCTA
129 CATGAATTTGAAAATGAGAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCGA
*
1960201 TTTTCAAAATTT--CACTTAG
194 TTTCCAAAATTTCACACTTAG
* *
1960220 TAAGTCCTTCGGGCTATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTATAA
1 TAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
* ** * * *
1960285 GACTTTAGAGCAAGATGATAAGTCCTTCAGGCTGTTCATAAGACCTTCGGGTAGGATGTTTTCAC
66 GCCTTTAGAGCAAGATGATAAGT-CTTCAGGCCATCCATAAGACCTTCGAGTAGGATATTTTCAC
* *
1960350 ATGAATTTGAAAATGAGAAAATGATGTTTTAAGATGATGAAACTTTTGAAAACTAAGAAGGCGAT
130 ATGAATTTGAAAATGAGAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCGAT
*
1960415 TTCCAATAATTT-GCACTATA-
195 TTCCAA-AATTTCACACT-TAG
* * * * *
1960435 TAAGTCCTTCGGACCATCATTAAGTCTTTCAAGCACGATGATTAAATCCTTTGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
* *
1960500 GCCTTTTA-AGTAAGATGATAAGTTCTTCAGGCCATCCATAA-ACCTTCGGGTAGGATATTTTCA
66 GCC-TTTAGAGCAAGATGATAAG-TCTTCAGGCCATCCATAAGACCTTCGAGTAGGATATTTTCA
* * *
1960563 CATGAATTTGAAAATGAGAAAATGATGTTTCAAGAAGATGAAATTTTTGAAAACTAAGAATGTGA
129 CATGAATTTGAAAATGAGAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCGA
1960628 TTTCCAAAATTTCACACTTAG
194 TTTCCAAAATTTCACACTTAG
* * * * *
1960649 TAAGTCCTTCGAGCCATCATTAAGTCTTTCGAGTATGATGTTTAAATCCTTCGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
* *
1960714 GCCTTTAGAGTAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGTAGGATATTTTCAC
66 GCCTTTAGAGCAAGATGATAAGTC-TTCAGGCCATCCATAAGACCTTCGAGTAGGATATTTTCAC
*
1960779 ATGAATTTGAAAATGAGAAAATGATGTTTTAAGATGATGAAATTTTTGAAAACTAAGAAGGCGAT
130 ATGAATTTGAAAATGAGAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCGAT
*
1960844 TTCTAAAATTTCACACTTAG
195 TTCCAAAATTTCACACTTAG
* * * **
1960864 TAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATAAGTAA
1 TAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
*
1960929 GCCTTTTGAGCAAGATGATAAG
66 GCCTTTAGAGCAAGATGATAAG
1960951 ACCTTTGGGT
Statistics
Matches: 662, Mismatches: 57, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
213 190 0.29
214 194 0.29
215 271 0.41
216 7 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (214 bp):
TAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
GCCTTTAGAGCAAGATGATAAGTCTTCAGGCCATCCATAAGACCTTCGAGTAGGATATTTTCACA
TGAATTTGAAAATGAGAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCGATT
TCCAAAATTTCACACTTAG
Found at i:1960828 original size:429 final size:428
Alignment explanation
Indices: 1960007--1960950 Score: 1407
Period size: 429 Copynumber: 2.2 Consensus size: 428
1959997 CCGAAAATTT
*
1960007 TAAGT-CTTCCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTATA
1 TAAGTCCTT-CGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
*
1960071 AGCC-TTTAGAGCAAGATGATAAGTCTTTAGGGCCATCCATAAGACCTTCGAGTAGAATATTTTC
65 AGCCTTTTA-AGCAAGATGATAAGTCTTCAGGGCCATCCATAAGACCTTCGAGTAGAATATTTTC
*
1960135 AAATGAATTTGAAAATGAGAAAATAATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCT
129 AAATGAATTTGAAAATGAGAAAATAATGTTTCAAGAAGATGAAATTTTTGAAAACTAAGAAGGCT
* * *
1960200 ATTTTCAAAATTTCACTTAGTAAGTCCTTCGGGCTATCAATAAGTCTTTCAAGCATGATGCTTAA
194 ATTTCCAAAATTTCACTTAGTAAGTCCTTCGAGCCATCAATAAGTCTTTCAAGCATGATGCTTAA
* ** *
1960265 ATCCTTCGGGTCATCTATAAGACTTTAGAGCAAGATGATAAGTCCTTCAGGCTGTTCATAAGACC
259 ATCCTTCGGGTCATCTATAAGACTTTAGAGCAAGATGATAAGTCATTCAGGCCATCCATAAGACC
* *
1960330 TTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAGAAAATGATGTTTTAAGATGATGAAACTT
324 TTCGAGTAGGATATTTTCACATGAATTTGAAAATGAGAAAATGATGTTTTAAGATGATGAAACTT
*
1960395 TTGAAAACTAAGAAGGCGATTTCCAATAATTT-GCACTATA-
389 TTGAAAACTAAGAAGGCGATTTCCAA-AATTTCACACT-TAG
* * * * *
1960435 TAAGTCCTTCGGACCATCATTAAGTCTTTCAAGCACGATGATTAAATCCTTTGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
* * *
1960500 GCCTTTTAAGTAAGATGATAAGTTCTTCA-GGCCATCCATAA-ACCTTCGGGTAGGATATTTTCA
66 GCCTTTTAAGCAAGATGATAAG-TCTTCAGGGCCATCCATAAGACCTTCGAGTAGAATATTTTCA
* * *
1960563 CATGAATTTGAAAATGAGAAAATGATGTTTCAAGAAGATGAAATTTTTGAAAACTAAGAATG-TG
130 AATGAATTTGAAAATGAGAAAATAATGTTTCAAGAAGATGAAATTTTTGAAAACTAAGAAGGCT-
* * * *
1960627 ATTTCCAAAATTTCACACTTAGTAAGTCCTTCGAGCCATCATTAAGTCTTTCGAGTATGATGTTT
194 ATTTCCAAAATTT--CACTTAGTAAGTCCTTCGAGCCATCAATAAGTCTTTCAAGCATGATGCTT
* * * *
1960692 AAATCCTTCGGGTCATCTGTAAGCCTTTAGAGTAAGATGATAAGTCATTCGGGCCATCCATAAGA
257 AAATCCTTCGGGTCATCTATAAGACTTTAGAGCAAGATGATAAGTCATTCAGGCCATCCATAAGA
*
1960757 CCTTCGAGTAGGATATTTTCACATGAATTTGAAAATGAGAAAATGATGTTTTAAGATGATGAAAT
322 CCTTCGAGTAGGATATTTTCACATGAATTTGAAAATGAGAAAATGATGTTTTAAGATGATGAAAC
*
1960822 TTTTGAAAACTAAGAAGGCGATTTCTAAAATTTCACACTTAG
387 TTTTGAAAACTAAGAAGGCGATTTCCAAAATTTCACACTTAG
* * * **
1960864 TAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATAAGTAA
1 TAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
*
1960929 GCCTTTTGAGCAAGATGATAAG
66 GCCTTTTAAGCAAGATGATAAG
1960951 ACCTTTGGGT
Statistics
Matches: 463, Mismatches: 45, Indels: 15
0.89 0.09 0.03
Matches are distributed among these distances:
426 1 0.00
427 90 0.19
428 90 0.19
429 282 0.61
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (428 bp):
TAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAA
GCCTTTTAAGCAAGATGATAAGTCTTCAGGGCCATCCATAAGACCTTCGAGTAGAATATTTTCAA
ATGAATTTGAAAATGAGAAAATAATGTTTCAAGAAGATGAAATTTTTGAAAACTAAGAAGGCTAT
TTCCAAAATTTCACTTAGTAAGTCCTTCGAGCCATCAATAAGTCTTTCAAGCATGATGCTTAAAT
CCTTCGGGTCATCTATAAGACTTTAGAGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTT
CGAGTAGGATATTTTCACATGAATTTGAAAATGAGAAAATGATGTTTTAAGATGATGAAACTTTT
GAAAACTAAGAAGGCGATTTCCAAAATTTCACACTTAG
Found at i:1961075 original size:22 final size:21
Alignment explanation
Indices: 1961044--1961117 Score: 53
Period size: 22 Copynumber: 3.5 Consensus size: 21
1961034 GGCCATCAGT
*
1961044 AAGTCTTTCGAGCTTGATGATG
1 AAGTCCTTCGAGC-TGATGATG
* *
1961066 AAGTCCTTCGGGCT-ATCA-G
1 AAGTCCTTCGAGCTGATGATG
* *
1961085 TAAGTCTTTCGAGCATGATGATT
1 -AAGTCCTTCGAGC-TGATGATG
*
1961108 AAATCCTTCG
1 AAGTCCTTCG
1961118 GGTAACTTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.36
21 2 0.05
22 22 0.56
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (21 bp):
AAGTCCTTCGAGCTGATGATG
Found at i:1961085 original size:42 final size:42
Alignment explanation
Indices: 1961038--1961119 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
1961028 TAAGAAGGCC
* *
1961038 ATCAGTAAGTCTTTCGAGCTTGATGATGAAGTCCTTCGGGCT
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCT
*
1961080 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
1961120 TAACTTGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (42 bp):
ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCT
Done.