Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, 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: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 3 of 12
Found at i:1574587 original size:3 final size:3
Alignment explanation
Indices: 1574572--1574613 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1574562 AGCGCAAAAG
* **
1574572 GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GGT GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1574614 AGAACAGATC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:1579375 original size:2 final size:2
Alignment explanation
Indices: 1579332--1579365 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1579322 TGTGTGTGTG
1579332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1579366 GCACATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1585325 original size:25 final size:25
Alignment explanation
Indices: 1585291--1585340 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1585281 ATATAAAAAG
*
1585291 GACTCATGTTAAAAGACCCTCCATT
1 GACTCATGTTAAAAGAACCTCCATT
* *
1585316 GACTCTTGTTAAAGGAACCTCCATT
1 GACTCATGTTAAAAGAACCTCCATT
1585341 TAGAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (25 bp):
GACTCATGTTAAAAGAACCTCCATT
Found at i:1595271 original size:31 final size:31
Alignment explanation
Indices: 1595235--1595312 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
1595225 CCCAAGTTGT
1595235 AAAAATTTATAATATATA-TATATATTTTTTAA
1 AAAAATTTATAAT-TATACTAT-TATTTTTTAA
* *
1595267 AAAATATTTATAATTTTACTCTTATTTTTTAA
1 AAAA-ATTTATAATTATACTATTATTTTTTAA
* *
1595299 TAAATTTTATAATT
1 AAAAATTTATAATT
1595313 TCATCTTCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 9 0.22
32 20 0.50
33 11 0.28
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (31 bp):
AAAAATTTATAATTATACTATTATTTTTTAA
Found at i:1604297 original size:25 final size:26
Alignment explanation
Indices: 1604241--1604299 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 26
1604231 ACTTTGTTTG
1604241 GTTCATAAATATTTTTGTTAGCAGTAAAA
1 GTTCATAAATATTTTTGTTAGCAG---AA
*
1604270 GTTCGTAAATATTTTTGTTAGCAG-A
1 GTTCATAAATATTTTTGTTAGCAGAA
1604295 GTTCA
1 GTTCA
1604300 GTTTCCTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 5 0.18
29 23 0.82
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.42
Consensus pattern (26 bp):
GTTCATAAATATTTTTGTTAGCAGAA
Found at i:1631207 original size:35 final size:35
Alignment explanation
Indices: 1631168--1631242 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
1631158 TGCAAAGGAA
*
1631168 ACCCACAGGCTACCATTTGTTCAGTTTGGTCTAGG
1 ACCCACAGGCTACCATTTGGTCAGTTTGGTCTAGG
1631203 ACCCACAGGCTACCATTTGGTCAGTTTGGTCTAGG
1 ACCCACAGGCTACCATTTGGTCAGTTTGGTCTAGG
1631238 ACCCA
1 ACCCA
1631243 ACACTTTCGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (35 bp):
ACCCACAGGCTACCATTTGGTCAGTTTGGTCTAGG
Found at i:1647929 original size:17 final size:17
Alignment explanation
Indices: 1647884--1647931 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1647874 AATTTTATCA
*
1647884 TTATAAATATT-TAATT
1 TTATAAATATTATTATT
*
1647900 TT-T-AATATAATTATT
1 TTATAAATATTATTATT
1647915 TTATAAATATTATTATT
1 TTATAAATATTATTATT
1647932 GTCTTTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.19
15 7 0.27
16 3 0.12
17 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATAAATATTATTATT
Found at i:1673246 original size:93 final size:93
Alignment explanation
Indices: 1673087--1673272 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
1673077 GTTTCCATAA
1673087 TTGGGTTACCCTTTCTGCAGTCCTTCTCTAGACACAAATTGATCAGACCTCAGTCAGACATGGGA
1 TTGGGTTACCCTTTCTGCAGTCCTTCTCTAGACACAAATTGATCAGACCTCAGTCAGACATGGGA
*
1673152 GGGCTATTCAACAGGGAACCTGCAGATC
66 GGGCTATTCAACAAGGAACCTGCAGATC
* * *
1673180 TTGGGTTACCGTTTCTGTAGTCCTTCTCTGGACACAAATTGATCAGACCTCAGTCAGACATGGGA
1 TTGGGTTACCCTTTCTGCAGTCCTTCTCTAGACACAAATTGATCAGACCTCAGTCAGACATGGGA
*
1673245 GGGCTATTCAATAAGGAACCTGCAGATC
66 GGGCTATTCAACAAGGAACCTGCAGATC
1673273 AGTGTTGTAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (93 bp):
TTGGGTTACCCTTTCTGCAGTCCTTCTCTAGACACAAATTGATCAGACCTCAGTCAGACATGGGA
GGGCTATTCAACAAGGAACCTGCAGATC
Found at i:1674870 original size:27 final size:27
Alignment explanation
Indices: 1674830--1675070 Score: 134
Period size: 27 Copynumber: 8.9 Consensus size: 27
1674820 GTGGTTGGAA
**
1674830 CCTTGGA-ACTTTCTGTGCTTGGAACTT
1 CCTTGGACA-TTTCTGTGCTTGGAACGC
* ** *
1674857 CTTTGGATGTTTCTGTACTTGGAACGC
1 CCTTGGACATTTCTGTGCTTGGAACGC
* *
1674884 CCTTGGGCATTTCTGTGCTTGGAACAC
1 CCTTGGACATTTCTGTGCTTGGAACGC
** *
1674911 CCTTAGG-CGCTTCTGTACTTGGAACGC
1 CCTT-GGACATTTCTGTGCTTGGAACGC
* *
1674938 CCTTAGA-AGTTTCTGTGCTTGGAACAC
1 CCTTGGACA-TTTCTGTGCTTGGAACGC
* * *
1674965 CCTTAGG-CACTTCTGTACTTGAAACGC
1 CCTT-GGACATTTCTGTGCTTGGAACGC
* ** ** *
1674992 CCCTGGACGCTTCTACGCTTGGAACTCC
1 CCTTGGACATTTCTGTGCTTGGAAC-GC
* ** * *
1675020 CCTAGG-CGCTTCTGTACTTGGAATGC
1 CCTTGGACATTTCTGTGCTTGGAACGC
*
1675046 CCTT-GAGCGTTTCTGTGCTTGGAAC
1 CCTTGGA-CATTTCTGTGCTTGGAAC
1675071 ACCCCTAGGT
Statistics
Matches: 161, Mismatches: 43, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
25 1 0.01
26 7 0.04
27 144 0.89
28 9 0.06
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (27 bp):
CCTTGGACATTTCTGTGCTTGGAACGC
Found at i:1675086 original size:27 final size:27
Alignment explanation
Indices: 1674867--1675479 Score: 297
Period size: 27 Copynumber: 23.1 Consensus size: 27
1674857 CTTTGGATGT
* * * * **
1674867 TTCTGTACTTGGAACGCCCTTGGGCAT
1 TTCTGTGCTTGGAACACCCCTAGGCGC
*
1674894 TTCTGTGCTTGGAACACCCTTAGGCGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* * * ** *
1674921 TTCTGTACTTGGAACGCCCTTAGAAGT
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* *
1674948 TTCTGTGCTTGGAACACCCTTAGGCAC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* * *
1674975 TTCTGTACTTGAAACGCCCCT-GGACGC
1 TTCTGTGCTTGGAACACCCCTAGG-CGC
** *
1675002 TTCTACGCTTGGAACTCCCCTAGGCGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* ** * *
1675029 TTCTGTACTTGGAA-TGCCCTTGAGCGT
1 TTCTGTGCTTGGAACACCCCTAG-GCGC
*
1675056 TTCTGTGCTTGGAACACCCCTAGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
** ** ** * *
1675083 TTCTGTATTTGGAATGCCTTTGGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
** ** ** * *
1675110 TTCTGCACTTGGAATGCCTTTGGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
** * * *
1675137 TTCTGCACTTGGAACTCCCC-CGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* * * ** * *
1675163 TTCTATACTTGAAATGCCCTTAGGCGT
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* *
1675190 TTCTATGCTTGGAACACCCCTAGACGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* *
1675217 TTCTGTGCTTGAAACACCCCTAGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* * *
1675244 TTCTGTACGTGGAACGCCCCT-GGACGC
1 TTCTGTGCTTGGAACACCCCTAGG-CGC
* ** * **
1675271 TTCTGCGCTTAAAACTCATCT-GG-GC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* * *
1675296 TTCTGTGCTTGAAACA-CCCAAGGACGT
1 TTCTGTGCTTGGAACACCCCTAGG-CGC
1675323 TTCTGTGCTTGGAACACCCCTAGGCGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* * *
1675350 -TCTTGTCCTTGGAACACCCCTGGGTGC
1 TTC-TGTGCTTGGAACACCCCTAGGCGC
** * * *
1675377 TTC--TGC---GAA-TGCCCTGGGTGT
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* *
1675398 TTCTGTACTTGGAACA-CCCTAGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
* * *
1675424 TTCTGTACTTGGAACA-TCCTAAGCGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
*
1675450 TTCTGTGCTTGGAACA-CCTTAGGCGC
1 TTCTGTGCTTGGAACACCCCTAGGCGC
1675476 TTCT
1 TTCT
1675480 ATACTTGAAA
Statistics
Matches: 455, Mismatches: 113, Indels: 37
0.75 0.19 0.06
Matches are distributed among these distances:
21 12 0.03
22 3 0.01
23 2 0.00
24 1 0.00
25 19 0.04
26 91 0.20
27 312 0.69
28 15 0.03
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCTGTGCTTGGAACACCCCTAGGCGC
Found at i:1675329 original size:106 final size:106
Alignment explanation
Indices: 1675190--1675383 Score: 257
Period size: 106 Copynumber: 1.8 Consensus size: 106
1675180 CCTTAGGCGT
* * *
1675190 TTCTATGCTTGGAACACCCCTAGACGCTTCTGTGCTTGAAACACCCCTAGGTGCT-TCTGTACGT
1 TTCTATGCTTGAAACACCCCAAGACGCTTCTGTGCTTGAAACACCCCTAGGCGCTCT-TGTACGT
*
1675254 GGAACGCCCCTGGACGCTTCTGCGCTTAAAACTCATCTGGGC
65 GGAACACCCCTGGACGCTTCTGCGCTTAAAACTCATCTGGGC
* * * * *
1675296 TTCTGTGCTTGAAACA-CCCAAGGACGTTTCTGTGCTTGGAACACCCCTAGGCGCTCTTGTCCTT
1 TTCTATGCTTGAAACACCCCAA-GACGCTTCTGTGCTTGAAACACCCCTAGGCGCTCTTGTACGT
**
1675360 GGAACACCCCTGGGTGCTTCTGCG
65 GGAACACCCCTGGACGCTTCTGCG
1675384 AATGCCCTGG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
105 4 0.05
106 70 0.93
107 1 0.01
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.28
Consensus pattern (106 bp):
TTCTATGCTTGAAACACCCCAAGACGCTTCTGTGCTTGAAACACCCCTAGGCGCTCTTGTACGTG
GAACACCCCTGGACGCTTCTGCGCTTAAAACTCATCTGGGC
Found at i:1701959 original size:22 final size:22
Alignment explanation
Indices: 1701931--1701975 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1701921 GTGGACAATC
*
1701931 TTCTTCTCTTGGAATTGTGATA
1 TTCTTCTCTTGGAATTCTGATA
* *
1701953 TTCTTCTGTTGGAGTTCTGATA
1 TTCTTCTCTTGGAATTCTGATA
1701975 T
1 T
1701976 CTGTCTTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.13, G:0.20, T:0.51
Consensus pattern (22 bp):
TTCTTCTCTTGGAATTCTGATA
Found at i:1706075 original size:66 final size:65
Alignment explanation
Indices: 1705979--1706109 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 65
1705969 CGATTTCGGT
1705979 TAGTTCAATTAGTTATATATTTCGATTCAGTTTCGATTATTTTTAAATTAAGAGTACGATTAGTT
1 TAGTTCAATTAGTTATATATTTCGATTCAGTTTCGATTATTTTTAAA-TAAGAGTACGATTAGTT
1706044 C
65 C
* * *
1706045 TAGTTCGATTAGTTATATATTTCGATTCAGTTTCGATTATTTTTAAATAAGAGTTCGGTTAGTTC
1 TAGTTCAATTAGTTATATATTTCGATTCAGTTTCGATTATTTTTAAATAAGAGTACGATTAGTTC
1706110 GATTATTAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 16 0.26
66 46 0.74
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.47
Consensus pattern (65 bp):
TAGTTCAATTAGTTATATATTTCGATTCAGTTTCGATTATTTTTAAATAAGAGTACGATTAGTTC
Found at i:1706718 original size:5 final size:5
Alignment explanation
Indices: 1706708--1706852 Score: 50
Period size: 5 Copynumber: 27.4 Consensus size: 5
1706698 TAATGTCATA
* *
1706708 TATTT TATTT T-TTAT TATAATT T-TTA TATTT TATTTT TATTT T-TATA
1 TATTT TATTT TATT-T TAT--TT TATTT TATTT TA-TTT TATTT TAT-TT
* * *
1706755 TATTTT TATAT TA-TA TATTT TATTT TATTT TATATAT TATATT AATTT
1 TA-TTT TATTT TATTT TATTT TATTT TATTT TAT-T-T TAT-TT TATTT
* * *
1706803 TAATTT CTGATTCT TATAT TA-TA TATTT TATTT TAATAT T-TTT TATTT
1 T-ATTT -T-ATT-T TATTT TATTT TATTT TATTT T-ATTT TATTT TATTT
1706851 TA
1 TA
1706853 ATTATAATAT
Statistics
Matches: 105, Mismatches: 17, Indels: 36
0.66 0.11 0.23
Matches are distributed among these distances:
4 12 0.11
5 53 0.50
6 24 0.23
7 14 0.13
8 2 0.02
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:1706734 original size:19 final size:19
Alignment explanation
Indices: 1706710--1706860 Score: 84
Period size: 19 Copynumber: 8.0 Consensus size: 19
1706700 ATGTCATATA
*
1706710 TTTTATTTTTTATTATAAT
1 TTTTATATTTTATTATAAT
* *
1706729 TTTTATATTTTATTTTTAT
1 TTTTATATTTTATTATAAT
1706748 TTTTATATATTT-TTAT-A-
1 TTTTATAT-TTTATTATAAT
* *
1706765 TTATATATTTTATT-TTA-
1 TTTTATATTTTATTATAAT
*
1706782 TTTTATATATTA-TATTAA-
1 TTTTATATTTTATTA-TAAT
* *
1706800 TTTTA-ATTTCTGATTCTTAT
1 TTTTATATTT-T-ATTATAAT
* *
1706820 ATTATATATTTTATTTTAAT
1 -TTTTATATTTTATTATAAT
*
1706840 ATTTTTTATTTTAATTATAAT
1 -TTTTATATTTT-ATTATAAT
1706861 ATCACAAAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
16 5 0.05
17 23 0.22
18 9 0.09
19 30 0.29
20 20 0.19
21 12 0.12
22 4 0.04
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (19 bp):
TTTTATATTTTATTATAAT
Found at i:1706771 original size:17 final size:17
Alignment explanation
Indices: 1706689--1706792 Score: 80
Period size: 17 Copynumber: 6.4 Consensus size: 17
1706679 CATTTCTTAA
* *
1706689 ATATATTTTTA-ATGTC
1 ATATATTTTTATATTTT
*
1706705 ATATA-TTTTATTTTTT
1 ATATATTTTTATATTTT
1706721 ATTATAATTTTTATA--TT
1 A-TAT-ATTTTTATATTTT
1706738 -T-TATTTTTAT-TTTT
1 ATATATTTTTATATTTT
*
1706752 ATATATTTTTATATTAT
1 ATATATTTTTATATTTT
*
1706769 ATAT-TTTATTTTATTTT
1 ATATATTT-TTATATTTT
1706786 ATATATT
1 ATATATT
1706793 ATATTAATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
13 8 0.11
14 3 0.04
15 7 0.10
16 20 0.29
17 23 0.33
18 3 0.04
19 6 0.09
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (17 bp):
ATATATTTTTATATTTT
Found at i:1706803 original size:43 final size:42
Alignment explanation
Indices: 1706713--1706854 Score: 116
Period size: 42 Copynumber: 3.4 Consensus size: 42
1706703 TCATATATTT
* *
1706713 TATTTTTTATTATAATTTTTATATTTTATTTTTATTTTTATA
1 TATTTTTTATTATAATATTTATATTTTATTTTTATTTATATA
1706755 TATTTTTATATTAT-ATATTT-TATTTTATTTTATATATTATAT-
1 TATTTTT-TATTATAATATTTATATTTTATTTT-TAT-TTATATA
* * * * *
1706797 TAATTTTAATTTCTGAT-TCTTATATTATATATTTTATTT-TA-A
1 TATTTTTTA-TTATAATAT-TTATATTTTAT-TTTTATTTATATA
*
1706839 TATTTTTTATTTTAAT
1 TATTTTTTATTATAAT
1706855 TATAATATCA
Statistics
Matches: 81, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
41 17 0.21
42 34 0.42
43 17 0.21
44 10 0.12
45 3 0.04
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (42 bp):
TATTTTTTATTATAATATTTATATTTTATTTTTATTTATATA
Found at i:1707015 original size:13 final size:14
Alignment explanation
Indices: 1706990--1707066 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 14
1706980 AAACTGTAAT
1706990 ATAATTATATTATA
1 ATAATTATATTATA
1707004 ATAATT-TATTATA
1 ATAATTATATTATA
*
1707017 A-AATAAATATTATA
1 ATAAT-TATATTATA
1707031 AT-A-TA-ATTA-A
1 ATAATTATATTATA
*
1707041 ATTAAATATATTATA
1 A-TAATTATATTATA
* *
1707056 AAAAATATATT
1 ATAATTATATT
1707067 CTCACCTCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
10 2 0.04
11 5 0.10
12 5 0.10
13 10 0.19
14 28 0.54
15 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATTATATTATA
Found at i:1709275 original size:6 final size:6
Alignment explanation
Indices: 1709261--1709294 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1709251 TTATGAAAAA
*
1709261 TTCATG TTCACG TTCACG TTCACG TTCACG TTCA
1 TTCACG TTCACG TTCACG TTCACG TTCACG TTCA
1709295 GTCAAGTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.15, T:0.38
Consensus pattern (6 bp):
TTCACG
Found at i:1713634 original size:25 final size:26
Alignment explanation
Indices: 1713605--1713653 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1713595 CAATATGTTT
*
1713605 TAAAAATAT-ATAAATAAAAATTTTA
1 TAAAAATATCAAAAATAAAAATTTTA
* *
1713630 TAAAATTATCAAAAATAAAGATTT
1 TAAAAATATCAAAAATAAAAATTT
1713654 CATATTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
TAAAAATATCAAAAATAAAAATTTTA
Found at i:1713708 original size:19 final size:19
Alignment explanation
Indices: 1713686--1713725 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1713676 CTTAATATTT
* *
1713686 TTAAAAAAATTTAAATTAA
1 TTAAAAAAATTAAAATAAA
1713705 TTAAAAAAATTAAAATAAA
1 TTAAAAAAATTAAAATAAA
1713724 TT
1 TT
1713726 TTTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAAAAATTAAAATAAA
Found at i:1717224 original size:21 final size:20
Alignment explanation
Indices: 1717194--1717233 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1717184 GTTTGACCGG
1717194 TAAGCCAAATTTA-AAGAAAT
1 TAAGCCAAA-TTAGAAGAAAT
1717214 TAAGCTCAAATTAGAAGAAA
1 TAAGC-CAAATTAGAAGAAA
1717234 ACACGTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (20 bp):
TAAGCCAAATTAGAAGAAAT
Found at i:1721196 original size:28 final size:28
Alignment explanation
Indices: 1721156--1721211 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1721146 CACCTGTATA
1721156 GGCTTGGGTGTCGACTATAAATGAATCT
1 GGCTTGGGTGTCGACTATAAATGAATCT
*
1721184 GGCTTGGGTGTCGATTATAAATGAATCT
1 GGCTTGGGTGTCGACTATAAATGAATCT
1721212 TACTTGCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.34
Consensus pattern (28 bp):
GGCTTGGGTGTCGACTATAAATGAATCT
Found at i:1722474 original size:20 final size:20
Alignment explanation
Indices: 1722437--1722475 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1722427 TGTTGGGGAG
* *
1722437 AGATTTAAATATTAAAAATT
1 AGATTAAAAAATTAAAAATT
*
1722457 AGATTAAAAAATTCAAAAT
1 AGATTAAAAAATTAAAAAT
1722476 AAGGAAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (20 bp):
AGATTAAAAAATTAAAAATT
Found at i:1724197 original size:16 final size:16
Alignment explanation
Indices: 1724172--1724209 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1724162 GTTTCTTTAC
* *
1724172 CGTTTCTTTTTTGTTT
1 CGTTTTTTTTTTGGTT
1724188 CGTTTTTTTTTTGGTT
1 CGTTTTTTTTTTGGTT
1724204 -GTTTTT
1 CGTTTTT
1724210 CTATGAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (16 bp):
CGTTTTTTTTTTGGTT
Found at i:1736209 original size:26 final size:26
Alignment explanation
Indices: 1736158--1736222 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 26
1736148 TTTATTTTTT
*
1736158 ATTATATTTAATTAAATTAATAATTA
1 ATTATATTTAATTAAATTAAAAATTA
1736184 ATTA-ATTATAATT-AATTAAAATATT-
1 ATTATATT-TAATTAAATTAAAA-ATTA
1736209 ATTAT-TTTATATTA
1 ATTATATTTA-ATTA
1736223 TGTAATATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
24 2 0.06
25 19 0.58
26 12 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTATATTTAATTAAATTAAAAATTA
Found at i:1756545 original size:64 final size:64
Alignment explanation
Indices: 1756345--1756560 Score: 229
Period size: 64 Copynumber: 3.4 Consensus size: 64
1756335 TCAAATAATG
* * * *
1756345 TGATATTCTATATTAATTCTTATA-TATTTAAATTGATAATATATAAATTCAAATTAAGCATAGA
1 TGATATTTTATATTAATTTTTATACT-TTTACATTGATAATATATAAATTCAAATTAAGCATACA
* * * * * * * **
1756409 CGATATTTTA-AGTTAAATTTTATACCTTCACCTTAATAATATATAAATTCAAATTAAGTATATG
1 TGATATTTTATA-TTAATTTTTATACTTTTACATTGATAATATATAAATTCAAATTAAGCATACA
* * *
1756473 TGATATTTTATATTAATTTTTATACTTTTGCATTGATAATATATAAATTTAAATTAAACATACA
1 TGATATTTTATATTAATTTTTATACTTTTACATTGATAATATATAAATTCAAATTAAGCATACA
** *
1756537 TGGCATTTTACATTAATTTTTATA
1 TGATATTTTATATTAATTTTTATA
1756561 AATTTAAGTT
Statistics
Matches: 122, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
63 1 0.01
64 120 0.98
65 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (64 bp):
TGATATTTTATATTAATTTTTATACTTTTACATTGATAATATATAAATTCAAATTAAGCATACA
Found at i:1756573 original size:128 final size:120
Alignment explanation
Indices: 1756299--1756575 Score: 279
Period size: 128 Copynumber: 2.2 Consensus size: 120
1756289 GATATTAGAT
* *
1756299 GTTAATTTTATATATTTATATTAATAATGTATAAATTCAAATAATGTGATATTCTATATTAATTC
1 GTTAATTTTATAAATTTA-ATTAATAATATATAAATTCAAATAATGTGATATTCTATATTAATTC
* * *
1756364 TTATATATTTAAATTGATAATATATAAATTCAAATTAAGCATAGACGATATTTTAA
65 TTATATATTTAAATTGATAATATATAAATTCAAATTAAACATACACGACATTTTAA
** * * *
1756420 GTTAAATTTTATACCTTCACCTTAATAATATATAAATTCAAATTAAGTATATGTGATATTTTATA
1 GTT-AATTTTATAAATTTA-ATTAATAATATATAAATTC--A--AA-TA-ATGTGATATTCTATA
* ** * * *
1756485 TTAATTTTTATACT-TTTGCATTGATAATATATAAATTTAAATTAAACATACATGGCATTTTACA
58 TTAATTCTTATA-TATTTAAATTGATAATATATAAATTCAAATTAAACATACACGACATTTTA-A
1756549 -TTAATTTTTATAAATTTAAGTTAATAA
1 GTTAA-TTTTATAAATTTAA-TTAATAA
1756576 ACAGAAAGAG
Statistics
Matches: 125, Mismatches: 20, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
121 3 0.02
122 29 0.23
124 1 0.01
126 2 0.02
127 4 0.03
128 84 0.67
129 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (120 bp):
GTTAATTTTATAAATTTAATTAATAATATATAAATTCAAATAATGTGATATTCTATATTAATTCT
TATATATTTAAATTGATAATATATAAATTCAAATTAAACATACACGACATTTTAA
Found at i:1758245 original size:69 final size:69
Alignment explanation
Indices: 1758158--1758364 Score: 299
Period size: 69 Copynumber: 3.0 Consensus size: 69
1758148 ATATTATGCA
* *
1758158 GTAGGATGATTTTGAAGCAATATGAGTCCCTCGGGGATACCTCAGTCAGTTCTACCAATCAAGAT
1 GTAGGATGATTCTGAAGCAATTTGAGTCCCTCGGGGATACCTCAGTCAGTTCTACCAATCAAGAT
1758223 CTGT
66 CTGT
* * * * * *
1758227 GTAGGATGATTCTGAAGCAATTTGAGTCTCTGGGGGATACATTAGTCAGTTCTAACTATCAAGAT
1 GTAGGATGATTCTGAAGCAATTTGAGTCCCTCGGGGATACCTCAGTCAGTTCTACCAATCAAGAT
1758292 CTGT
66 CTGT
* * *
1758296 GTAGGATGATTCTGAAG-AAGTTTGAGTCCCTCGGGGATACCTCAGTCAATTCTACCAATCCAGG
1 GTAGGATGATTCTGAAGCAA-TTTGAGTCCCTCGGGGATACCTCAGTCAGTTCTACCAATCAAGA
1758360 TCTGT
65 TCTGT
1758365 TTGTGTGATT
Statistics
Matches: 120, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
68 2 0.02
69 118 0.98
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (69 bp):
GTAGGATGATTCTGAAGCAATTTGAGTCCCTCGGGGATACCTCAGTCAGTTCTACCAATCAAGAT
CTGT
Found at i:1758554 original size:20 final size:20
Alignment explanation
Indices: 1758529--1758568 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1758519 TATGTGTGTG
*
1758529 CATTTTGCATGAGAAAAAGT
1 CATTTTGCAGGAGAAAAAGT
1758549 CATTTTGCAGGAGAAAAAGT
1 CATTTTGCAGGAGAAAAAGT
1758569 TTGGCCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (20 bp):
CATTTTGCAGGAGAAAAAGT
Found at i:1759862 original size:2 final size:2
Alignment explanation
Indices: 1759855--1759892 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1759845 AACAGATTAA
1759855 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
1759893 TCTGTAGTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1779698 original size:46 final size:46
Alignment explanation
Indices: 1779631--1779720 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
1779621 AGGAAGGTAG
* *
1779631 AATGAATATTTTCTGTAGTTATGATTCTCTATCATGTTGTATGTAC
1 AATGAATATTGTCTGTAGTTATGATTCTCTATCATGTTCTATGTAC
* *
1779677 AATGAATATTGTCTGTAGTTATGGTTCTTTATCATGTTCTATGT
1 AATGAATATTGTCTGTAGTTATGATTCTCTATCATGTTCTATGT
1779721 GGTATTATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (46 bp):
AATGAATATTGTCTGTAGTTATGATTCTCTATCATGTTCTATGTAC
Found at i:1782932 original size:2 final size:2
Alignment explanation
Indices: 1782927--1782957 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1782917 TGTATGTGTC
1782927 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 T
1782958 CCGCTCTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1785419 original size:24 final size:23
Alignment explanation
Indices: 1785386--1785435 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
1785376 AAAAGGACAA
* *
1785386 AAAGGAAAGAAAAAGAGAGGTAG
1 AAAGGAAAGAAAAAAACAGGTAG
1785409 AAAGAGAAAGAAAAAAACAGGTAG
1 AAAG-GAAAGAAAAAAACAGGTAG
1785433 AAA
1 AAA
1785436 CAGGCCCGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.66, C:0.02, G:0.28, T:0.04
Consensus pattern (23 bp):
AAAGGAAAGAAAAAAACAGGTAG
Found at i:1788570 original size:61 final size:61
Alignment explanation
Indices: 1788495--1788616 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
1788485 TGCTTTTCTG
*
1788495 TATAATTCTGTCCTGAATTTAGGCCTGCTTCTATATTGCAATTGCATAGCTTACTTCTCTA
1 TATAATTCTGTCCTGAATTTAGGCCTGCTGCTATATTGCAATTGCATAGCTTACTTCTCTA
*
1788556 TATAATTCTGTCCTGAATTTAGGCCTTCTGCTATATTGCAATTGCATAGCTTACTTCTCTA
1 TATAATTCTGTCCTGAATTTAGGCCTGCTGCTATATTGCAATTGCATAGCTTACTTCTCTA
1788617 ATATTTTTTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (61 bp):
TATAATTCTGTCCTGAATTTAGGCCTGCTGCTATATTGCAATTGCATAGCTTACTTCTCTA
Found at i:1790091 original size:27 final size:27
Alignment explanation
Indices: 1790053--1790107 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1790043 GAAAAAGAAC
1790053 GATTGCCCTTTGCTTCTAGTAGATATT
1 GATTGCCCTTTGCTTCTAGTAGATATT
1790080 GATTGCCCTTTGCTTCTAGTAGATATT
1 GATTGCCCTTTGCTTCTAGTAGATATT
1790107 G
1 G
1790108 CGGTCATGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (27 bp):
GATTGCCCTTTGCTTCTAGTAGATATT
Found at i:1790755 original size:21 final size:21
Alignment explanation
Indices: 1790729--1790770 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1790719 GAACATGGCA
*
1790729 TTCTTTAATTGCCTTTGGTTT
1 TTCTTTAATTGCCCTTGGTTT
1790750 TTCTTTAATTGCCCTTGGTTT
1 TTCTTTAATTGCCCTTGGTTT
1790771 CCAGAGGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.17, G:0.14, T:0.60
Consensus pattern (21 bp):
TTCTTTAATTGCCCTTGGTTT
Found at i:1791875 original size:28 final size:28
Alignment explanation
Indices: 1791835--1791891 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1791825 TCTATCCTTC
1791835 AAGATGTATGTAACTTTGTTATAATTTA
1 AAGATGTATGTAACTTTGTTATAATTTA
1791863 AAGATGTATGTAACTTTGTTATAATTTA
1 AAGATGTATGTAACTTTGTTATAATTTA
1791891 A
1 A
1791892 GTGAGACTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.46
Consensus pattern (28 bp):
AAGATGTATGTAACTTTGTTATAATTTA
Found at i:1794212 original size:50 final size:50
Alignment explanation
Indices: 1794152--1794249 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 50
1794142 TGAAACTATA
* * *
1794152 ACCGATAACTGCTAGTTTTGGTTTTGTTTTATTGTGGGTGTCGTGAGATG
1 ACCGATAACTGCTAGTTTAGGTTTTGTTTTATTATGGGTCTCGTGAGATG
*
1794202 ACCGATAACTGCTAGTTTAGGTTTTGTTTTATTATTGGTCTCGTGAGA
1 ACCGATAACTGCTAGTTTAGGTTTTGTTTTATTATGGGTCTCGTGAGA
1794250 ATACCTACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.18, C:0.11, G:0.27, T:0.44
Consensus pattern (50 bp):
ACCGATAACTGCTAGTTTAGGTTTTGTTTTATTATGGGTCTCGTGAGATG
Found at i:1795260 original size:3 final size:3
Alignment explanation
Indices: 1795246--1795293 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
1795236 TCTTATTCTC
* *
1795246 ATG ATG AAG ATG ATG A-A ATG ATG ATG ATG ATG ATG ATG AT- ATG -TG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1795291 ATG
1 ATG
1795294 TCAAATTCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 5 0.13
3 33 0.87
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:1795268 original size:17 final size:17
Alignment explanation
Indices: 1795246--1795278 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1795236 TCTTATTCTC
1795246 ATGATGAAGATGATGAA
1 ATGATGAAGATGATGAA
*
1795263 ATGATGATGATGATGA
1 ATGATGAAGATGATGA
1795279 TGATGATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (17 bp):
ATGATGAAGATGATGAA
Found at i:1799272 original size:2 final size:2
Alignment explanation
Indices: 1799265--1799309 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1799255 ATCATATGAG
1799265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1799307 TA T
1 TA T
1799310 GGAGTATTTG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1805544 original size:6 final size:6
Alignment explanation
Indices: 1805524--1805557 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1805514 AAAAATAATA
*
1805524 TTTAAT TTT-TT TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
1805558 GAATGTGACG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:1807708 original size:2 final size:2
Alignment explanation
Indices: 1807701--1807727 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1807691 TCTTGCTACT
1807701 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 T
1807728 GTTCCACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1809531 original size:2 final size:2
Alignment explanation
Indices: 1809524--1809549 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1809514 GAATTAACTC
1809524 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
1809550 GTATGTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1810874 original size:51 final size:51
Alignment explanation
Indices: 1810714--1811027 Score: 226
Period size: 51 Copynumber: 6.2 Consensus size: 51
1810704 GCGAGGTGCC
* * * ** * *
1810714 AGCAGGGGTGCATGGCACAGGCCCCCGGGCGAGCCAGCCCGGCAGGGA-GCC
1 AGCAGGGGCGCACGGCGCAGGCCCATGGGCGAGCCAGCCCGACA-GGACGCT
* * ** * * *
1810765 AACAAGGGCGCACATCACAGGCCCTTGGGCGAGCC-GTCCCGAC-GGAATGGC-
1 AGCAGGGGCGCACGGCGCAGGCCCATGGGCGAGCCAG-CCCGACAGG-A-CGCT
* ** * * * *
1810816 AGTAGGGGCAAACGGCACAGGCCCCTGGGTGAGCTAGCCCGACAGGACGCT
1 AGCAGGGGCGCACGGCGCAGGCCCATGGGCGAGCCAGCCCGACAGGACGCT
* *
1810867 AGCAGGGGCGCACGGCGCAGGCCCATGGGCGAGCCAGGCCGACAGGATGCT
1 AGCAGGGGCGCACGGCGCAGGCCCATGGGCGAGCCAGCCCGACAGGACGCT
* * * * * *
1810918 GGCAAGGGCGCACGGCGCAGGCCCATGAGCGAGCCAGCCCGACTGGAAGGT
1 AGCAGGGGCGCACGGCGCAGGCCCATGGGCGAGCCAGCCCGACAGGACGCT
* * * * *
1810969 GGCAGGAGCGCAAGGCGCAGGACCC-TGGGCGAGTCAGCCCGACAGAACGCGT
1 AGCAGGGGCGCACGGCGCAGG-CCCATGGGCGAGCCAGCCCGACAGGACGC-T
1811021 -GCAGGGG
1 AGCAGGGG
1811028 TGCCAACCCG
Statistics
Matches: 208, Mismatches: 46, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
49 2 0.01
50 4 0.02
51 193 0.93
52 9 0.04
ACGTcount: A:0.21, C:0.32, G:0.40, T:0.07
Consensus pattern (51 bp):
AGCAGGGGCGCACGGCGCAGGCCCATGGGCGAGCCAGCCCGACAGGACGCT
Found at i:1811530 original size:15 final size:15
Alignment explanation
Indices: 1811510--1811566 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
1811500 TTCCAAATGG
1811510 TTTTGGAGGGAAAAC
1 TTTTGGAGGGAAAAC
*
1811525 TTTTGGAGGGAAATC
1 TTTTGGAGGGAAAAC
*
1811540 CTTTGGAGGGAAAA-
1 TTTTGGAGGGAAAAC
1811554 TTTTGGAGGGAAA
1 TTTTGGAGGGAAA
1811567 TGGGTGGGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 12 0.32
15 26 0.68
ACGTcount: A:0.32, C:0.05, G:0.35, T:0.28
Consensus pattern (15 bp):
TTTTGGAGGGAAAAC
Found at i:1811566 original size:29 final size:30
Alignment explanation
Indices: 1811511--1811567 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
1811501 TCCAAATGGT
1811511 TTTGGAGGGAAAACTTTTGGAGGGAAATCC
1 TTTGGAGGGAAAACTTTTGGAGGGAAATCC
1811541 TTTGGAGGGAAAA-TTTTGGAGGGAAAT
1 TTTGGAGGGAAAACTTTTGGAGGGAAAT
1811568 GGGTGGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.32, C:0.05, G:0.35, T:0.28
Consensus pattern (30 bp):
TTTGGAGGGAAAACTTTTGGAGGGAAATCC
Found at i:1822691 original size:54 final size:54
Alignment explanation
Indices: 1822355--1822718 Score: 254
Period size: 54 Copynumber: 6.7 Consensus size: 54
1822345 CATTAGCATA
* * * *** *
1822355 GGTTGCTTCCCTTCTAGAAA-TTGAATTTCTAGAAATGATCCCATCAGAAACAGA
1 GGTTGATTCCCTTCTAGAAATTTG-ATTTCCAGTAATGATCCCATCAGAAGTGGG
* * * * * **
1822409 AGTTGATTCCCTTCTAGAAATTTGGTTTCCAGCAATAATCCCATCGGAAGCAGG
1 GGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCCATCAGAAGTGGG
* * *
1822463 GGTTGGA-TCCCTTCTAGAAATTTGACTTCCAGTCAA-GATGCCACCAG-A-TGGAG
1 GGTT-GATTCCCTTCTAGAAATTTGATTTCCAGT-AATGATCCCATCAGAAGTGG-G
* * * * * **
1822516 AAGAGCTCGGTTCCCTTCTAGAAATCTGATTTCCAGTAATGATCCTATCAG-GGATGAA
1 --G-G-TTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCCATCAGAAG-TGGG
* * * ** **
1822574 GGTTGATTCCTTTCCAGAAATTTGATTTCCAGTAATGATCCTATCAGGGGTGAC
1 GGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCCATCAGAAGTGGG
* * * *
1822628 AGTTAATTCCCTTCTAGAAATTTGATCTCCAGTAATGATCCCTTCAGAAGTGGG
1 GGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCCATCAGAAGTGGG
* * * *
1822682 GGTTGATTCCCTCCTAGGAATCTGACTTCCAGTAATG
1 GGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATG
1822719 CTTCCCTCAC
Statistics
Matches: 244, Mismatches: 53, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
52 1 0.00
53 2 0.01
54 190 0.78
55 11 0.05
56 5 0.02
57 33 0.14
59 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (54 bp):
GGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCCATCAGAAGTGGG
Found at i:1831392 original size:25 final size:25
Alignment explanation
Indices: 1831363--1831416 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
1831353 TCCAACAAAA
*
1831363 ATTTTGTATTATTAGTAACTAACAT
1 ATTTTGTATTATCAGTAACTAACAT
*
1831388 ATTTTGTATTATCAGTAACTAATAT
1 ATTTTGTATTATCAGTAACTAACAT
1831413 ATTT
1 ATTT
1831417 GTGGAACCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (25 bp):
ATTTTGTATTATCAGTAACTAACAT
Found at i:1839233 original size:20 final size:20
Alignment explanation
Indices: 1839208--1839248 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1839198 TCCAATTTTT
*
1839208 ACTCATCGACATTTATTATC
1 ACTCATCGACATTTATCATC
1839228 ACTCATCGACATTTATCATC
1 ACTCATCGACATTTATCATC
1839248 A
1 A
1839249 AGCATCGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (20 bp):
ACTCATCGACATTTATCATC
Found at i:1839254 original size:20 final size:20
Alignment explanation
Indices: 1839211--1839255 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1839201 AATTTTTACT
* **
1839211 CATCGACATTTATTATCACT
1 CATCGACATTTATCATCAAG
1839231 CATCGACATTTATCATCAAG
1 CATCGACATTTATCATCAAG
1839251 CATCG
1 CATCG
1839256 CAGTGAGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (20 bp):
CATCGACATTTATCATCAAG
Found at i:1839457 original size:3 final size:3
Alignment explanation
Indices: 1839449--1839481 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1839439 AATCCCATAG
1839449 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1839482 ACAACTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1862365 original size:21 final size:20
Alignment explanation
Indices: 1862341--1862386 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
1862331 ACTTGATAAG
1862341 TTAAAATATTTTAAAAAATAT
1 TTAAAATATTTTAAAAAA-AT
*
1862362 TTAAATTATTTTAAAAAAAT
1 TTAAAATATTTTAAAAAAAT
1862382 TTAAA
1 TTAAA
1862387 TTAAGTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAAATATTTTAAAAAAAT
Found at i:1862377 original size:20 final size:21
Alignment explanation
Indices: 1862341--1862389 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
1862331 ACTTGATAAG
* *
1862341 TTAAAATATTTTAAAAAATAT
1 TTAAATTATTTTAAAAAAAAT
1862362 TTAAATTATTTT-AAAAAAAT
1 TTAAATTATTTTAAAAAAAAT
1862382 TTAAATTA
1 TTAAATTA
1862390 AGTATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAATTATTTTAAAAAAAAT
Found at i:1864273 original size:20 final size:22
Alignment explanation
Indices: 1864240--1864288 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
1864230 TAAATTTTTA
*
1864240 AAAAATTATTTAA-TATAAAAT
1 AAAAATTATCTAATTATAAAAT
1864261 AAAAA-TATCTAATTATAAATAAT
1 AAAAATTATCTAATTAT-AA-AAT
1864284 AAAAA
1 AAAAA
1864289 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 8 0.33
22 2 0.08
23 8 0.33
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAATTATCTAATTATAAAAT
Found at i:1866052 original size:2 final size:2
Alignment explanation
Indices: 1866045--1866076 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1866035 GAATAACAAA
1866045 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1866077 AAAGACCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1866448 original size:12 final size:12
Alignment explanation
Indices: 1866431--1866455 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1866421 CTTTCCATCC
1866431 CCAAACAAAATG
1 CCAAACAAAATG
1866443 CCAAACAAAATG
1 CCAAACAAAATG
1866455 C
1 C
1866456 ACGAGCCTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.28, G:0.08, T:0.08
Consensus pattern (12 bp):
CCAAACAAAATG
Found at i:1873213 original size:45 final size:46
Alignment explanation
Indices: 1873118--1873220 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 46
1873108 AAATTGGAGT
* *** *
1873118 AATTTAAAAAAACACTAAATTGATTCAAAAATTGAAATAATTTTTT
1 AATTAAAAAAAACACTAAATTGATTCAAAAATTGAAATAAAGATTA
**
1873164 AATTAAAAAAAAC-CTAAATTGATTC-AATTTTGAATATAAAGATTA
1 AATTAAAAAAAACACTAAATTGATTCAAAAATTGAA-ATAAAGATTA
*
1873209 AATTAAATAAAA
1 AATTAAAAAAAA
1873221 TGTATGAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
44 7 0.15
45 29 0.60
46 12 0.25
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (46 bp):
AATTAAAAAAAACACTAAATTGATTCAAAAATTGAAATAAAGATTA
Found at i:1882223 original size:23 final size:23
Alignment explanation
Indices: 1882193--1882236 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1882183 ATGTTGGGCC
* *
1882193 TTACTAACTAGTCACGCAATAAT
1 TTACTAACAAATCACGCAATAAT
1882216 TTACTAACAAATCACGCAATA
1 TTACTAACAAATCACGCAATA
1882237 CCTAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (23 bp):
TTACTAACAAATCACGCAATAAT
Found at i:1885454 original size:2 final size:2
Alignment explanation
Indices: 1885441--1885483 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1885431 AGTAATGCCT
* *
1885441 TA TA TA TG TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1885483 T
1 T
1885484 GCATCAATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1895198 original size:29 final size:29
Alignment explanation
Indices: 1895168--1895274 Score: 108
Period size: 30 Copynumber: 3.6 Consensus size: 29
1895158 TTAAAAAGAT
* * *
1895168 TTAAACAAATTTTTATACTTTTA-TTACAT
1 TTAAATAAATTTTTATAATTTTATTTA-AG
* * * *
1895197 TTCATTAAGTTTTTATAATTTTATTTTGAG
1 TTAAATAAATTTTTATAATTTTA-TTTAAG
*
1895227 TTAAATAAATTTTTATATTTTTATTTTAAG
1 TTAAATAAATTTTTATAATTTTA-TTTAAG
1895257 TTAAATAAATTTTTATAA
1 TTAAATAAATTTTTATAA
1895275 CTAATGATTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 18 0.29
30 43 0.68
31 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (29 bp):
TTAAATAAATTTTTATAATTTTATTTAAG
Found at i:1895242 original size:30 final size:30
Alignment explanation
Indices: 1895206--1895274 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
1895196 TTTCATTAAG
*
1895206 TTTTTATAATTTTATTTTGAGTTAAATAAA
1 TTTTTATAATTTTATTTTAAGTTAAATAAA
*
1895236 TTTTTATATTTTTATTTTAAGTTAAATAAA
1 TTTTTATAATTTTATTTTAAGTTAAATAAA
1895266 TTTTTATAA
1 TTTTTATAA
1895275 CTAATGATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.59
Consensus pattern (30 bp):
TTTTTATAATTTTATTTTAAGTTAAATAAA
Found at i:1898383 original size:28 final size:28
Alignment explanation
Indices: 1898351--1898405 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1898341 TAGATCACTA
1898351 AATCAACTTGACTATGAAAAAAAAAAAG
1 AATCAACTTGACTATGAAAAAAAAAAAG
1898379 AATCAACTTGACTATGAAAAAAAAAAA
1 AATCAACTTGACTATGAAAAAAAAAAA
1898406 ACACTTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.18
Consensus pattern (28 bp):
AATCAACTTGACTATGAAAAAAAAAAAG
Found at i:1899034 original size:20 final size:20
Alignment explanation
Indices: 1899009--1899054 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1898999 ATTATTACAT
*
1899009 ATTTTACTGTAAATTTAAAG
1 ATTTTACAGTAAATTTAAAG
*
1899029 ATTTTACAGTAAATTTAGAG
1 ATTTTACAGTAAATTTAAAG
1899049 ATTTTA
1 ATTTTA
1899055 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (20 bp):
ATTTTACAGTAAATTTAAAG
Found at i:1899253 original size:15 final size:15
Alignment explanation
Indices: 1899233--1899263 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1899223 GTTATAGATT
1899233 GCAGCCTTTGAACTA
1 GCAGCCTTTGAACTA
1899248 GCAGCCTTTGAACTA
1 GCAGCCTTTGAACTA
1899263 G
1 G
1899264 TGTATGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (15 bp):
GCAGCCTTTGAACTA
Found at i:1908216 original size:22 final size:22
Alignment explanation
Indices: 1908159--1908217 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
1908149 TAGTTTTAGT
* *
1908159 GATTTTTGATCATTGTATAATC
1 GATTTTTAATCATTGTATAATA
*
1908181 GATTTTTGAA-CATTGTATGACTA
1 GATTTTT-AATCATTGTAT-AATA
1908204 G-TTTTTAATCATTG
1 GATTTTTAATCATTG
1908218 CGTTCCTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 2 0.06
22 25 0.81
23 4 0.13
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.49
Consensus pattern (22 bp):
GATTTTTAATCATTGTATAATA
Found at i:1923463 original size:2 final size:2
Alignment explanation
Indices: 1923456--1923490 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1923446 TAGTACACGC
1923456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1923491 GTAGATTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1940321 original size:57 final size:57
Alignment explanation
Indices: 1940220--1940338 Score: 143
Period size: 57 Copynumber: 2.1 Consensus size: 57
1940210 GCCGCCGCCG
* * * * *
1940220 CCACCTCCAGCTCCATTGCAGTCAAATGTAGTGGCGACAGGAGCATC-CCTTCCACCA
1 CCACCTCCAGCTCCACTGCAGTCAAATGTAGTAGCAACAAGAGCA-CAACTTCCACCA
* *
1940277 CCACCTCCAGTTTCACTGCAGTCAAA-GATAGTAGCAACAAGAGCACAACTTCCACCA
1 CCACCTCCAGCTCCACTGCAGTCAAATG-TAGTAGCAACAAGAGCACAACTTCCACCA
1940334 CCACC
1 CCACC
1940339 ACCACCTCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
56 2 0.04
57 51 0.96
ACGTcount: A:0.29, C:0.37, G:0.16, T:0.18
Consensus pattern (57 bp):
CCACCTCCAGCTCCACTGCAGTCAAATGTAGTAGCAACAAGAGCACAACTTCCACCA
Found at i:1943451 original size:2 final size:2
Alignment explanation
Indices: 1943444--1943476 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1943434 AGTAATTTTA
1943444 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1943477 CCCCTTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1947642 original size:18 final size:20
Alignment explanation
Indices: 1947599--1947647 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
1947589 AAGTTATATT
1947599 TTTATTT-TAAATTAAATAA
1 TTTATTTATAAATTAAATAA
*
1947618 ATT-TTTAT-AATT-AATAA
1 TTTATTTATAAATTAAATAA
1947635 TTTATTTAATAAA
1 TTTATTT-ATAAA
1947648 AATATCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 5 0.21
20 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATTTATAAATTAAATAA
Found at i:1949481 original size:2 final size:2
Alignment explanation
Indices: 1949469--1949498 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1949459 GCCTTTATTC
*
1949469 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1949499 AACGTGTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1951941 original size:83 final size:83
Alignment explanation
Indices: 1951802--1951962 Score: 259
Period size: 83 Copynumber: 1.9 Consensus size: 83
1951792 GTAGCTGCCG
* * * *
1951802 ACACTTAAATTTACGCGCTTACCTAACCTTAGCCGTTGAGGCTTTGAATTTCATCCAAAAGGCCA
1 ACACTTAAATTTACACACTTACCTAACATTAGCCATTGAGGCTTTGAATTTCATCCAAAAGGCCA
1951867 ACAAAAGGACTTGGGCCC
66 ACAAAAGGACTTGGGCCC
* * *
1951885 ACACTTAAATTTACACACTTACCTAACATTGGTCATTGAGGCTTTGAATTTCATCCAAAAGGCGA
1 ACACTTAAATTTACACACTTACCTAACATTAGCCATTGAGGCTTTGAATTTCATCCAAAAGGCCA
1951950 ACAAAAGGACTTG
66 ACAAAAGGACTTG
1951963 AGTACTTCGT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (83 bp):
ACACTTAAATTTACACACTTACCTAACATTAGCCATTGAGGCTTTGAATTTCATCCAAAAGGCCA
ACAAAAGGACTTGGGCCC
Found at i:1952153 original size:19 final size:19
Alignment explanation
Indices: 1952093--1952153 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
1952083 AGTATTTAGT
*
1952093 TTATAAATATTTTATTAAAAA
1 TTATATATA-TTTATT-AAAA
1952114 TGTA-ATATTAATTT-TTAAAA
1 T-TATATA-T-ATTTATTAAAA
1952134 TTATATATATTTATTAAAA
1 TTATATATATTTATTAAAA
1952153 T
1 T
1952154 ATAAATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 4 0.12
19 10 0.29
20 8 0.24
21 5 0.15
22 6 0.18
23 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTATATATATTTATTAAAA
Found at i:1952172 original size:41 final size:41
Alignment explanation
Indices: 1952093--1952173 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
1952083 AGTATTTAGT
*
1952093 TTATAAATATTTTATTAAAAATGTAATATTAATTTTTAAAA
1 TTATAAATATTTTATTAAAAATGAAATATTAATTTTTAAAA
*
1952134 TTATATATA-TTTATTAAAATAT-AAAT-TTAATATATTTAAA
1 TTATAAATATTTTATTAAAA-ATGAAATATTAAT-T-TTTAAA
1952174 TTTGTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 5 0.14
40 14 0.40
41 16 0.46
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (41 bp):
TTATAAATATTTTATTAAAAATGAAATATTAATTTTTAAAA
Found at i:1952274 original size:26 final size:26
Alignment explanation
Indices: 1952235--1952314 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
1952225 TATCATATAC
1952235 TTTAT-TTTTA-ATTTTTATTATAAT
1 TTTATATTTTATATTTTTATTATAAT
*
1952259 TTTATATTTTATATTTTTTAATATAAT
1 TTTATATTTTATA-TTTTTATTATAAT
* *
1952286 TTT-TATATTATATATTTTATTTTAAT
1 TTTATATTTTATAT-TTTTATTATAAT
1952312 TTT
1 TTT
1952315 TTTCACCTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.10
25 6 0.12
26 22 0.46
27 15 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTATATTTTATATTTTTATTATAAT
Found at i:1952277 original size:28 final size:28
Alignment explanation
Indices: 1952246--1952303 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
1952236 TTATTTTTAA
* *
1952246 TTTTTATTATAA-TTTTATATTTTATAT
1 TTTTTAATATAATTTTTATATTATATAT
1952273 TTTTTAATATAATTTTTATATTATATAT
1 TTTTTAATATAATTTTTATATTATATAT
1952301 TTT
1 TTT
1952304 ATTTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTTAATATAATTTTTATATTATATAT
Found at i:1952289 original size:14 final size:15
Alignment explanation
Indices: 1952253--1952303 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1952243 TAATTTTTAT
* * *
1952253 TATAATTTTATATTT
1 TATATTTTTATAATA
1952268 TATATTTTT-TAATA
1 TATATTTTTATAATA
*
1952282 TA-ATTTTTATATTA
1 TATATTTTTATAATA
1952296 TATATTTT
1 TATATTTT
1952304 ATTTTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 6 0.20
14 11 0.37
15 13 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATTTTTATAATA
Found at i:1952301 original size:7 final size:7
Alignment explanation
Indices: 1952230--1952305 Score: 54
Period size: 7 Copynumber: 11.4 Consensus size: 7
1952220 TTTAATATCA
*
1952230 TATACTT
1 TATATTT
1952237 TAT-TTT
1 TATATTT
1952243 TA-ATTT
1 TATATTT
*
1952249 T-TATTA
1 TATATTT
1952255 TA-ATTT
1 TATATTT
1952261 TATATTT
1 TATATTT
1952268 TATATTT
1 TATATTT
* * *
1952275 TTTAATA
1 TATATTT
1952282 TA-ATTTT
1 TATA-TTT
*
1952289 TATATTA
1 TATATTT
1952296 TATATTT
1 TATATTT
1952303 TAT
1 TAT
1952306 TTTAATTTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
6 18 0.35
7 33 0.63
8 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (7 bp):
TATATTT
Found at i:1952315 original size:26 final size:26
Alignment explanation
Indices: 1952247--1952401 Score: 111
Period size: 26 Copynumber: 5.8 Consensus size: 26
1952237 TATTTTTAAT
* * *
1952247 TTTTATTATAATTTTATATTTTATATT
1 TTTTATTTTAATTTT-TATATTATATA
* *
1952274 TTTTAATATAATTTTTATATTATATA
1 TTTTATTTTAATTTTTATATTATATA
* *
1952300 TTTTATTTTAATTTTTTTCACCTATATTA
1 TTTTATTTTAATTTTTAT-A-TTATA-TA
* **
1952329 CATAAATTTTAAATTTCTTATA-T-T-TA
1 -TTTTATTTT-AATTT-TTATATTATATA
1952355 TTTTATTATTAATTTTTATATTATATA
1 TTTTATT-TTAATTTTTATATTATATA
*
1952382 TTTTATTTTTATTTTT-TATT
1 TTTTATTTTAATTTTTATATT
1952402 TTAATTATAA
Statistics
Matches: 103, Mismatches: 15, Indels: 22
0.74 0.11 0.16
Matches are distributed among these distances:
24 5 0.05
25 14 0.14
26 37 0.36
27 24 0.23
28 5 0.05
29 3 0.03
30 6 0.06
31 6 0.06
32 3 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTATTTTAATTTTTATATTATATA
Found at i:1952317 original size:14 final size:14
Alignment explanation
Indices: 1952246--1952317 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
1952236 TTATTTTTAA
1952246 TTTTTATTATAATT
1 TTTTTATTATAATT
1952260 TTATATT-TTAT-A-T
1 TT-T-TTATTATAATT
*
1952273 TTTTTAATATAATT
1 TTTTTATTATAATT
*
1952287 TTTATATTAT-A-T
1 TTTTTATTATAATT
* *
1952299 ATTTTATTTTAATT
1 TTTTTATTATAATT
1952313 TTTTT
1 TTTTT
1952318 CACCTATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
11 2 0.05
12 12 0.27
13 6 0.14
14 17 0.39
15 5 0.11
16 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTATTATAATT
Found at i:1952371 original size:13 final size:13
Alignment explanation
Indices: 1952355--1952407 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
1952345 CTTATATTTA
1952355 TTTTATTATTAAT
1 TTTTATTATTAAT
1952368 TTTTA-TATTATAT
1 TTTTATTATTA-AT
* *
1952381 ATTTTATTTTTATT
1 -TTTTATTATTAAT
1952395 TTTTATT-TTAAT
1 TTTTATTATTAAT
1952407 T
1 T
1952408 ATAACATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 10 0.29
13 14 0.41
14 6 0.18
15 4 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTATTATTAAT
Found at i:1952387 original size:24 final size:25
Alignment explanation
Indices: 1952340--1952388 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1952330 ATAAATTTTA
*
1952340 AATTTCTTATATTTATTTTATTATT
1 AATTTCTTATATTTATATTATTATT
1952365 AATTT-TTATATTATATATT-TTATT
1 AATTTCTTATATT-TATATTATTATT
1952389 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
AATTTCTTATATTTATATTATTATT
Found at i:1955374 original size:31 final size:27
Alignment explanation
Indices: 1955321--1955382 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 27
1955311 GAATATTTTA
* *
1955321 TATATTTTTATTATATTTAATAAAATATT
1 TATATTTTTATTAAATTAAAT-AAAT-TT
1955350 TATATTTTTATTTTAAATTAAATAAATTT
1 TATATTTTTA--TTAAATTAAATAAATTT
1955379 TATA
1 TATA
1955383 ATTAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.55
30 4 0.14
31 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATATTTTTATTAAATTAAATAAATTT
Found at i:1955380 original size:29 final size:30
Alignment explanation
Indices: 1955315--1955382 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
1955305 ACGATTGAAT
* *
1955315 ATTTTATATATTTTTATTATATTTAATAAA
1 ATTTTATATATTTTTATTAAATTAAATAAA
*
1955345 ATATTTATAT-TTTTATTTTAAATTAAAT-AA
1 AT-TTTATATATTTT-TATTAAATTAAATAAA
1955375 ATTTTATA
1 ATTTTATA
1955383 ATTAATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 6 0.18
30 10 0.30
31 17 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTTTATATATTTTTATTAAATTAAATAAA
Found at i:1955443 original size:11 final size:11
Alignment explanation
Indices: 1955422--1955454 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
1955412 CTATCATTTT
1955422 ATATT-ATATG
1 ATATTAATATG
1955432 ATATTAATATG
1 ATATTAATATG
1955443 ATATTAATATG
1 ATATTAATATG
1955454 A
1 A
1955455 CATATTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (11 bp):
ATATTAATATG
Found at i:1955584 original size:20 final size:20
Alignment explanation
Indices: 1955555--1955611 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
1955545 ATAAATATAA
1955555 AATT-ATAATAAATATTTTT
1 AATTAATAATAAATATTTTT
* *
1955574 AATTAATAATAATTAATTATT
1 AATTAATAATAAAT-ATTTTT
*
1955595 -ATTAATTATAAA-ATTTT
1 AATTAATAATAAATATTTT
1955612 ATTTAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.13
19 4 0.13
20 18 0.58
21 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTAATAATAAATATTTTT
Found at i:1955613 original size:17 final size:18
Alignment explanation
Indices: 1955588--1955625 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1955578 AATAATAATT
1955588 AATTATTA-TTAATTATAA
1 AATTATTATTTAATT-TAA
1955606 AATT-TTATTTAATTTAA
1 AATTATTATTTAATTTAA
1955623 AAT
1 AAT
1955626 AAAAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTATTATTTAATTTAA
Found at i:1961181 original size:2 final size:2
Alignment explanation
Indices: 1961174--1961205 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1961164 CAACATATCA
1961174 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
1961206 CTATCTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1962537 original size:14 final size:14
Alignment explanation
Indices: 1962495--1962551 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
1962485 TCTAAATATG
*
1962495 ATTTTAAATT-TTA
1 ATTTTAATTTATTA
* * *
1962508 ATTTTTATTAACTA
1 ATTTTAATTTATTA
1962522 ATTTTAATTTATTA
1 ATTTTAATTTATTA
1962536 A-TTTAATTTTATTA
1 ATTTTAA-TTTATTA
1962550 AT
1 AT
1962552 AATATATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
13 12 0.35
14 22 0.65
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTAATTTATTA
Found at i:1963430 original size:19 final size:19
Alignment explanation
Indices: 1963403--1963440 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1963393 CAATTTTACC
*
1963403 CCTATATCAGCAGGTGAAG
1 CCTACATCAGCAGGTGAAG
1963422 CCTACATCAGCAGGTGAAG
1 CCTACATCAGCAGGTGAAG
1963441 AGTACCACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (19 bp):
CCTACATCAGCAGGTGAAG
Found at i:1964811 original size:2 final size:2
Alignment explanation
Indices: 1964804--1964834 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1964794 AAACAAATTA
1964804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1964835 CAGTGAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1984631 original size:2 final size:2
Alignment explanation
Indices: 1984626--1984654 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1984616 AGACACACAC
1984626 AG AG AG AG A- AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1984655 CAAAACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1987781 original size:35 final size:35
Alignment explanation
Indices: 1987734--1987889 Score: 172
Period size: 35 Copynumber: 4.5 Consensus size: 35
1987724 AATGCTCCAC
* *
1987734 TTATTTTTATTATTTTATTTAAAGTAATATTTTAT
1 TTATTTTAATTATTTTATTTAAAATAATATTTTAT
* * * *
1987769 TTATTTTAATTATTTTGTATGAAATAATATTTCAT
1 TTATTTTAATTATTTTATTTAAAATAATATTTTAT
** * *
1987804 TTATTTTAATTATTTTACGTAAAATAACATTTTAC
1 TTATTTTAATTATTTTATTTAAAATAATATTTTAT
* ***
1987839 TTATTTTAATTGTTTTGGATAAAATAATATTTTAT
1 TTATTTTAATTATTTTATTTAAAATAATATTTTAT
1987874 TTA-TTTAATT-TTTTAT
1 TTATTTTAATTATTTTAT
1987890 AATATTATAT
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
33 4 0.04
34 7 0.07
35 89 0.89
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (35 bp):
TTATTTTAATTATTTTATTTAAAATAATATTTTAT
Found at i:1987808 original size:70 final size:70
Alignment explanation
Indices: 1987734--1987888 Score: 206
Period size: 70 Copynumber: 2.2 Consensus size: 70
1987724 AATGCTCCAC
* ** * * * * *
1987734 TTATTTTTATTATTTTATTTAAAGTAATATTTTATTTATTTTAATTATTTTGTATGAAATAATAT
1 TTATTTTAATTATTTTACGTAAAATAACATTTTACTTATTTTAATTATTTTGGATAAAATAATAT
1987799 TTCAT
66 TTCAT
*
1987804 TTATTTTAATTATTTTACGTAAAATAACATTTTACTTATTTTAATTGTTTTGGATAAAATAATAT
1 TTATTTTAATTATTTTACGTAAAATAACATTTTACTTATTTTAATTATTTTGGATAAAATAATAT
*
1987869 TTTAT
66 TTCAT
1987874 TTA-TTTAATT-TTTTA
1 TTATTTTAATTATTTTA
1987889 TAATATTATA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
68 5 0.07
69 7 0.09
70 63 0.84
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.59
Consensus pattern (70 bp):
TTATTTTAATTATTTTACGTAAAATAACATTTTACTTATTTTAATTATTTTGGATAAAATAATAT
TTCAT
Found at i:1987891 original size:26 final size:26
Alignment explanation
Indices: 1987862--1987933 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
1987852 TTTGGATAAA
1987862 ATAATATTTTATTTATTTAATTTTTT
1 ATAATATTTTATTTATTTAATTTTTT
* **
1987888 ATAATATTATATTATAAAATAATTTTTT
1 ATAATATTTTATT-T-ATTTAATTTTTT
* *
1987916 AAAAAATTTATATTTATT
1 ATAATATTT-TATTTATT
1987934 AAAATCAAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
26 12 0.34
27 2 0.06
28 17 0.49
29 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATAATATTTTATTTATTTAATTTTTT
Found at i:1991922 original size:15 final size:15
Alignment explanation
Indices: 1991904--1991941 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1991894 TTCCTCAATC
1991904 TCCTCTTCTTCCTCT
1 TCCTCTTCTTCCTCT
1991919 TCCTCTTCTTCCTCT
1 TCCTCTTCTTCCTCT
1991934 TCCTCTTC
1 TCCTCTTC
1991942 CTCCAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
TCCTCTTCTTCCTCT
Found at i:1992391 original size:27 final size:27
Alignment explanation
Indices: 1992353--1992412 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
1992343 TGAAGAACAA
*
1992353 TAAAAATACAAGTAGAAAAACACTTGC
1 TAAAAGTACAAGTAGAAAAACACTTGC
*
1992380 TAAAAGTACAAGTAGCAAAACACTTGC
1 TAAAAGTACAAGTAGAAAAACACTTGC
1992407 TAAAAG
1 TAAAAG
1992413 CCCCAGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.18
Consensus pattern (27 bp):
TAAAAGTACAAGTAGAAAAACACTTGC
Found at i:1997230 original size:26 final size:27
Alignment explanation
Indices: 1997199--1997254 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1997189 ATAAAAATTT
*
1997199 ATTTAATTTAAA-AT-ATAAATACAAAA
1 ATTTAA-TTAAACATAATAAAAACAAAA
*
1997225 ATTTAATTAAACATAATAAAAATAAAA
1 ATTTAATTAAACATAATAAAAACAAAA
1997252 ATT
1 ATT
1997255 AAATATCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.19
26 8 0.31
27 13 0.50
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (27 bp):
ATTTAATTAAACATAATAAAAACAAAA
Found at i:2006065 original size:21 final size:21
Alignment explanation
Indices: 2006041--2006080 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2006031 TCTTGCAACG
* *
2006041 CAGCCACTGTAGCTGCCCTGC
1 CAGCCACTGCAGCAGCCCTGC
*
2006062 CAGCCTCTGCAGCAGCCCT
1 CAGCCACTGCAGCAGCCCT
2006081 TGCATCATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.45, G:0.23, T:0.17
Consensus pattern (21 bp):
CAGCCACTGCAGCAGCCCTGC
Found at i:2020085 original size:2 final size:2
Alignment explanation
Indices: 2020066--2020112 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
2020056 ATGAAGAAGG
* * *
2020066 TC TC TC TT TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2020108 TC TC T
1 TC TC T
2020113 TCTGGGATGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (2 bp):
TC
Found at i:2022200 original size:20 final size:22
Alignment explanation
Indices: 2022158--2022200 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2022148 AAAATATTTC
*
2022158 ATATAAAAAAGTCAATAATAAA
1 ATATAAAAAAGTCAATAAAAAA
*
2022180 ATATCAAAAAG-C-ATAAAAAA
1 ATATAAAAAAGTCAATAAAAAA
2022200 A
1 A
2022201 GTCTTTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.19
Consensus pattern (22 bp):
ATATAAAAAAGTCAATAAAAAA
Found at i:2030818 original size:2 final size:2
Alignment explanation
Indices: 2030811--2030843 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2030801 TATAGATTTT
*
2030811 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2030844 TCTTTGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2050634 original size:6 final size:5
Alignment explanation
Indices: 2050609--2050642 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
2050599 TTGCGTGAGG
*
2050609 AAAGA AAACA AAAGA AAAGAA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAG-A AAAGA AAAGA AAA
2050643 TGTGAGAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:2050634 original size:11 final size:11
Alignment explanation
Indices: 2050609--2050642 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2050599 TTGCGTGAGG
*
2050609 AAAGAAAA-CA
1 AAAGAAAAGAA
2050619 AAAGAAAAGAA
1 AAAGAAAAGAA
2050630 AAAGAAAAGAA
1 AAAGAAAAGAA
2050641 AA
1 AA
2050643 TGTGAGAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:2052140 original size:16 final size:16
Alignment explanation
Indices: 2052113--2052158 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
2052103 GAATTTATTT
2052113 ATTAAA-TTAATAATA
1 ATTAAATTTAATAATA
2052128 ATTAAATTTAATAA-A
1 ATTAAATTTAATAATA
*
2052143 ATCAAATTTGAATAAT
1 ATTAAATTT-AATAAT
2052159 TCTATTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTAAATTTAATAATA
Found at i:2052151 original size:15 final size:16
Alignment explanation
Indices: 2052119--2052158 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2052109 ATTTATTAAA
*
2052119 TTAATAATAATTAAAT
1 TTAATAATAATCAAAT
2052135 TTAATAA-AATCAAAT
1 TTAATAATAATCAAAT
2052150 TTGAATAAT
1 TT-AATAAT
2052159 TCTATTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
TTAATAATAATCAAAT
Found at i:2070965 original size:14 final size:14
Alignment explanation
Indices: 2070946--2070992 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
2070936 TGTCATTTTG
2070946 ATTAATAATAATTA
1 ATTAATAATAATTA
*
2070960 ATTAATTAT-A-TA
1 ATTAATAATAATTA
2070972 ATT-ATAATAATTA
1 ATTAATAATAATTA
*
2070985 AGTAATAA
1 ATTAATAA
2070993 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
11 4 0.15
12 6 0.22
13 5 0.19
14 12 0.44
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTAATAATAATTA
Found at i:2072967 original size:33 final size:34
Alignment explanation
Indices: 2072930--2073003 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 34
2072920 TTTTAATGTC
*
2072930 ATATATTTTATTTTCATTTC-TTATTATAATCTT
1 ATATATTTTATTTTCATTTCTTTAATATAATCTT
* *
2072963 ATATACTTTATTTTCATTTCTTTAATATAATTTT
1 ATATATTTTATTTTCATTTCTTTAATATAATCTT
*
2072997 TTATATT
1 ATATATT
2073004 ACATATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 19 0.54
34 16 0.46
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (34 bp):
ATATATTTTATTTTCATTTCTTTAATATAATCTT
Found at i:2074419 original size:19 final size:20
Alignment explanation
Indices: 2074395--2074442 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
2074385 TAGATTAATA
2074395 ATTAATAAT-TAATTATATT
1 ATTAATAATATAATTATATT
*
2074414 ATTAATTTAATATGATTATATT
1 ATTAA--TAATATAATTATATT
2074436 -TTAATAA
1 ATTAATAA
2074443 AGTATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 8 0.32
21 8 0.32
22 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTAATAATATAATTATATT
Found at i:2082299 original size:2 final size:2
Alignment explanation
Indices: 2082292--2082324 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2082282 TTCATTTGCT
2082292 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2082325 TCTGATATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2093448 original size:14 final size:14
Alignment explanation
Indices: 2093429--2093456 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2093419 CATGTGCAAG
2093429 CAATTTTTTAATTA
1 CAATTTTTTAATTA
2093443 CAATTTTTTAATTA
1 CAATTTTTTAATTA
2093457 TTTAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
CAATTTTTTAATTA
Found at i:2098548 original size:21 final size:21
Alignment explanation
Indices: 2098524--2098569 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2098514 TATGGAATGC
*
2098524 TTTAATGGTATTACTAATAAT
1 TTTAAGGGTATTACTAATAAT
* * *
2098545 TTTAAGGGTGTTACTAGTTAT
1 TTTAAGGGTATTACTAATAAT
2098566 TTTA
1 TTTA
2098570 GTTCTAGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.50
Consensus pattern (21 bp):
TTTAAGGGTATTACTAATAAT
Found at i:2100140 original size:15 final size:15
Alignment explanation
Indices: 2100120--2100149 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2100110 TCCTCGCAAC
2100120 ATAGAAAGGAAGTGA
1 ATAGAAAGGAAGTGA
2100135 ATAGAAAGGAAGTGA
1 ATAGAAAGGAAGTGA
2100150 TGATTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (15 bp):
ATAGAAAGGAAGTGA
Found at i:2109491 original size:41 final size:41
Alignment explanation
Indices: 2109446--2109524 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
2109436 ACAACATTGG
2109446 AATTAAAAAATCATATTACAAGGAGCACATTGGAATTATAT
1 AATTAAAAAATCATATTACAAGGAGCACATTGGAATTATAT
2109487 AATTAAAAAATCATATTACAAGGAGCACATTGGAATTA
1 AATTAAAAAATCATATTACAAGGAGCACATTGGAATTA
2109525 CCAAGGCTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (41 bp):
AATTAAAAAATCATATTACAAGGAGCACATTGGAATTATAT
Found at i:2112968 original size:135 final size:135
Alignment explanation
Indices: 2112759--2113002 Score: 312
Period size: 135 Copynumber: 1.8 Consensus size: 135
2112749 AAACTTCAAA
* * * * *
2112759 ATCCCGTGGTAATAAATCCCAGACTTATTATCAAACAAATGGGGGTTTTATAGTCCCTAAGGAAA
1 ATCCCGTGGTAATAAATCCCAGAATTATTATCAAACAAATGGGGATTTTACAGCCCCTAAGCAAA
* **
2112824 ATTGGCAACCACTTTCAGCTGC-AGGTGATGCATCTAATGGTGAGCTGAAAAGTGATGAATCGTC
66 ATTGCCAACCACTTTCAGCTGCTA-GCAATGCATCTAATGGTGAGCTGAAAAGTGATGAATCGTC
2112888 AGAATC
130 AGAATC
* * * * * *
2112894 ATCCGGTGGTAATAACTCCCAGAATTATTGTCGAGCAGATGGGGATTTTACAGCCCCTAAGCAAG
1 ATCCCGTGGTAATAAATCCCAGAATTATTATCAAACAAATGGGGATTTTACAGCCCCTAAGCAA-
* *
2112959 AA-TGCCAACCAGTTTCAGCTGCTAGCAATTCATCTAATGGTGAG
65 AATTGCCAACCACTTTCAGCTGCTAGCAATGCATCTAATGGTGAG
2113003 GCCAAAAATG
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
135 88 0.97
136 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (135 bp):
ATCCCGTGGTAATAAATCCCAGAATTATTATCAAACAAATGGGGATTTTACAGCCCCTAAGCAAA
ATTGCCAACCACTTTCAGCTGCTAGCAATGCATCTAATGGTGAGCTGAAAAGTGATGAATCGTCA
GAATC
Found at i:2113015 original size:135 final size:135
Alignment explanation
Indices: 2112759--2113030 Score: 307
Period size: 135 Copynumber: 2.0 Consensus size: 135
2112749 AAACTTCAAA
* * * * *
2112759 ATCCCGTGGTAATAAATCCCAGACTTATTATCAAACAAATGGGGGTTTTATAGTCCCTAAGGAAA
1 ATCCCGTGGTAATAAATCCCAGAATTATTATCAAACAAATGGGGATTTTACAGCCCCTAAGCAAA
* ** * * *
2112824 ATTGGCAACCACTTTCAGCTGCAGGTGATGCATCTAATGGTGAGCTGAAAAGTGATGAATCGTCA
66 ATTGCCAACCACTTTCAGCTGCAGGCAATGCATCTAATGGTGAGCTCAAAAATGATGAACCGTCA
2112889 GAATC
131 GAATC
* * * * * *
2112894 ATCCGGTGGTAATAACTCCCAGAATTATTGTCGAGCAGATGGGGATTTTACAGCCCCTAAGCAAG
1 ATCCCGTGGTAATAAATCCCAGAATTATTATCAAACAAATGGGGATTTTACAGCCCCTAAGCAA-
* * * *
2112959 AA-TGCCAACCAGTTTCAGCTGCTA-GCAATTCATCTAATGGTGAGGC-CAAAAATGATGGACCT
65 AATTGCCAACCACTTTCAGCTGC-AGGCAATGCATCTAATGGTGA-GCTCAAAAATGATGAACCG
2113021 TCAGAATC
128 TCAGAATC
2113029 AT
1 AT
2113031 TCTGTAGTAA
Statistics
Matches: 113, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
135 108 0.96
136 5 0.04
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (135 bp):
ATCCCGTGGTAATAAATCCCAGAATTATTATCAAACAAATGGGGATTTTACAGCCCCTAAGCAAA
ATTGCCAACCACTTTCAGCTGCAGGCAATGCATCTAATGGTGAGCTCAAAAATGATGAACCGTCA
GAATC
Found at i:2113480 original size:23 final size:23
Alignment explanation
Indices: 2113448--2113498 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2113438 TTGTTTTATT
*
2113448 TTATTTCTTTTATCTGAAGATAG
1 TTATTACTTTTATCTGAAGATAG
*
2113471 TTATTACTTTTATCTGAAGATCG
1 TTATTACTTTTATCTGAAGATAG
2113494 TTATT
1 TTATT
2113499 GCAGCTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (23 bp):
TTATTACTTTTATCTGAAGATAG
Found at i:2114596 original size:26 final size:26
Alignment explanation
Indices: 2114560--2114615 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
2114550 TATTACTTGT
2114560 AGATATCATGCAATGTCTTCAATTGC
1 AGATATCATGCAATGTCTTCAATTGC
2114586 AGATATCATGCAATGTCTTCAATTGC
1 AGATATCATGCAATGTCTTCAATTGC
2114612 AGAT
1 AGAT
2114616 GTATGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (26 bp):
AGATATCATGCAATGTCTTCAATTGC
Found at i:2117989 original size:15 final size:17
Alignment explanation
Indices: 2117953--2117986 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
2117943 TCAAATATGG
2117953 AATTTTTTGTTTTAAAT
1 AATTTTTTGTTTTAAAT
2117970 AATTTTTT-TTTTAAAT
1 AATTTTTTGTTTTAAAT
2117986 A
1 A
2117987 TTTGATTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
AATTTTTTGTTTTAAAT
Done.