Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008129.1 Hibiscus syriacus cultivar Beakdansim tig00110684_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: 2577775
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:2144660 original size:10 final size:10
Alignment explanation
Indices: 2144626--2144671 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
2144616 CTTTTTTGGC
2144626 TTTTTTTTGT
1 TTTTTTTTGT
* *
2144636 GTTTTTTTGG
1 TTTTTTTTGT
*
2144646 CTTTTTTTGT
1 TTTTTTTTGT
*
2144656 TTTTTTTTAT
1 TTTTTTTTGT
2144666 TTTTTT
1 TTTTTT
2144672 GAAAAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:2144663 original size:21 final size:21
Alignment explanation
Indices: 2144617--2144663 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
2144607 AAATTTTGGC
2144617 TTTTTTGGCTTTTTTTTGTGT
1 TTTTTTGGCTTTTTTTTGTGT
*
2144638 TTTTTTGGC-TTTTTTTGTTT
1 TTTTTTGGCTTTTTTTTGTGT
2144658 TTTTTT
1 TTTTTT
2144664 ATTTTTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.81
Consensus pattern (21 bp):
TTTTTTGGCTTTTTTTTGTGT
Found at i:2144668 original size:18 final size:20
Alignment explanation
Indices: 2144617--2144672 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2144607 AAATTTTGGC
*
2144617 TTTTTTGGCTTTTTTTTGTGT
1 TTTTTTGG-ATTTTTTTGTGT
*
2144638 TTTTTTGGCTTTTTTTGT-T
1 TTTTTTGGATTTTTTTGTGT
*
2144657 TTTTTT-TATTTTTTTG
1 TTTTTTGGATTTTTTTG
2144673 AAAAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.25
19 7 0.22
20 9 0.28
21 8 0.25
ACGTcount: A:0.02, C:0.04, G:0.14, T:0.80
Consensus pattern (20 bp):
TTTTTTGGATTTTTTTGTGT
Found at i:2153351 original size:35 final size:36
Alignment explanation
Indices: 2153293--2153361 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
2153283 AGATACAATC
2153293 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 TTCCATCACCATTATCACGCCTATATCATCACCATA
*
2153329 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 TTCCATCACCATTATCACGCCTATATCATCACCA
2153362 ACTTCTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.66
36 11 0.34
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.30
Consensus pattern (36 bp):
TTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:2158810 original size:15 final size:15
Alignment explanation
Indices: 2158790--2158836 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2158780 TACCTTGATA
2158790 TCATTTCTTTCCATT
1 TCATTTCTTTCCATT
*
2158805 TCATTTCTTATCAATT
1 TCATTTCTT-TCCATT
2158821 TCCATTTCTTT-CATT
1 T-CATTTCTTTCCATT
2158836 T
1 T
2158837 TTTATTTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 13 0.46
16 7 0.25
17 8 0.29
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (15 bp):
TCATTTCTTTCCATT
Found at i:2159681 original size:19 final size:20
Alignment explanation
Indices: 2159653--2159691 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2159643 GAATAATAAT
2159653 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
2159673 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
2159692 GGGATGGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:2162638 original size:24 final size:24
Alignment explanation
Indices: 2162603--2162678 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
2162593 ACTTGAAGCC
2162603 TCAA-TGATCACAACTTGTGGAACT
1 TCAAGTGA-CACAACTTGTGGAACT
* * *
2162627 TCAAGTGACACATCTTTTTGAACT
1 TCAAGTGACACAACTTGTGGAACT
* * * *
2162651 TCTAGAGACATAA-TTGTTGGAACC
1 TCAAGTGACACAACTTG-TGGAACT
2162675 TCAA
1 TCAA
2162679 AGGACATGTC
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
23 2 0.05
24 34 0.87
25 3 0.08
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (24 bp):
TCAAGTGACACAACTTGTGGAACT
Found at i:2166845 original size:14 final size:15
Alignment explanation
Indices: 2166811--2166857 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2166801 AATTTGGAGT
2166811 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
2166826 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
2166840 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
2166857 G
1 G
2166858 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:2175144 original size:26 final size:26
Alignment explanation
Indices: 2175110--2175173 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
2175100 CTTGGCTTGC
2175110 TTTC-TCTTTT-TGAACTTCTTTTTCT
1 TTTCTTCTTTTCTGAA-TTCTTTTTCT
*
2175135 TTTCTTCTTTTCTGAATTTTTTTTCT
1 TTTCTTCTTTTCTGAATTCTTTTTCT
2175161 TTT-TGTCTTTTCT
1 TTTCT-TCTTTTCT
2175174 TTTCTTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 5 0.14
26 26 0.74
27 4 0.11
ACGTcount: A:0.06, C:0.17, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTCTTCTTTTCTGAATTCTTTTTCT
Found at i:2175473 original size:19 final size:20
Alignment explanation
Indices: 2175445--2175484 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2175435 GAATAATAAT
2175445 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
2175465 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
2175484 A
1 A
2175485 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:2179136 original size:23 final size:23
Alignment explanation
Indices: 2179077--2179125 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
2179067 TTCATTCAAA
*
2179077 GGACATGTCCTTATGAGGACCAAT
1 GGACATGACC-TATGAGGACCAAT
*
2179101 GGACGTGACCTATGAGGACTCAAT
1 GGACATGACCTATGAGGAC-CAAT
2179125 G
1 G
2179126 ATCATGCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (23 bp):
GGACATGACCTATGAGGACCAAT
Found at i:2179991 original size:19 final size:20
Alignment explanation
Indices: 2179944--2179994 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2179934 AAAACCCCTT
**
2179944 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2179964 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2179983 TGAAGATACATG
1 TGAAAATACATG
2179995 CTCTTGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2181967 original size:24 final size:24
Alignment explanation
Indices: 2181940--2181999 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
2181930 GTTGGTTCTT
2181940 CAAAAGACATGTCTTGTGGATCAC
1 CAAAAGACATGTCTTGTGGATCAC
* * * * * **
2181964 CAAAGGTCATGACTTTTGGTTCTT
1 CAAAAGACATGTCTTGTGGATCAC
2181988 CAAAAGACATGT
1 CAAAAGACATGT
2182000 TTCTTGAATC
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (24 bp):
CAAAAGACATGTCTTGTGGATCAC
Found at i:2183935 original size:19 final size:20
Alignment explanation
Indices: 2183888--2183938 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2183878 AAAACCCCTT
**
2183888 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2183908 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2183927 TGAAGATACATG
1 TGAAAATACATG
2183939 CTCTTGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2186534 original size:19 final size:20
Alignment explanation
Indices: 2186487--2186537 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2186477 AAAACCCCTT
**
2186487 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2186507 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2186526 TGAAGATACATG
1 TGAAAATACATG
2186538 CTCTTGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2190804 original size:15 final size:15
Alignment explanation
Indices: 2190783--2190829 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
2190773 ACCTTGATAT
2190783 CATTTCTTTCTATTT-
1 CATTTCTTTC-ATTTC
*
2190798 TATTTCTTATCAATTTC
1 CATTTCTT-TC-ATTTC
2190815 CATTTCTTTCATTTC
1 CATTTCTTTCATTTC
2190830 TTATTTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 12 0.44
16 8 0.30
17 7 0.26
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (15 bp):
CATTTCTTTCATTTC
Found at i:2191286 original size:13 final size:15
Alignment explanation
Indices: 2191266--2191305 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 15
2191256 GAAATATGAA
2191266 ATAAGAAATGGAA-G
1 ATAAGAAATGGAATG
2191280 A-AAGAAATGGAATG
1 ATAAGAAATGGAATG
2191294 ATAAGAAA-GGAA
1 ATAAGAAATGGAA
2191306 ATGGAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
14 7 0.29
15 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (15 bp):
ATAAGAAATGGAATG
Found at i:2193905 original size:24 final size:24
Alignment explanation
Indices: 2193858--2193909 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2193848 TCAAAATATC
*
2193858 AAGAGACATGTCTTGTGAATCACA
1 AAGAGACATGTCTTGTGAACCACA
2193882 AAGAGACATGTCTTGT-AGACCACA
1 AAGAGACATGTCTTGTGA-ACCACA
2193906 AAGA
1 AAGA
2193910 CTCACGCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (24 bp):
AAGAGACATGTCTTGTGAACCACA
Found at i:2202000 original size:11 final size:10
Alignment explanation
Indices: 2201989--2202037 Score: 57
Period size: 9 Copynumber: 5.0 Consensus size: 10
2201979 TTTTGAATTC
2201989 TTTTTCTTTT
1 TTTTTCTTTT
*
2201999 CTTTTCTTCTT
1 TTTTTCTT-TT
*
2202010 TTTGTCTTTT
1 TTTTTCTTTT
2202020 TTTTT-TTTT
1 TTTTTCTTTT
2202029 TTTTT-TTTT
1 TTTTTCTTTT
2202038 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 13 0.38
10 13 0.38
11 8 0.24
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:2217212 original size:15 final size:16
Alignment explanation
Indices: 2217166--2217212 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
2217156 ACCTTGATAT
*
2217166 CATTTCTTTCCATTT-
1 CATTTCTTTCAATTTC
2217181 CATTTCTTATCAATTTC
1 CATTTCTT-TCAATTTC
2217198 CATTTCTTT-AATTTC
1 CATTTCTTTCAATTTC
2217213 TTAATTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 14 0.48
16 7 0.24
17 8 0.28
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.57
Consensus pattern (16 bp):
CATTTCTTTCAATTTC
Found at i:2217430 original size:18 final size:19
Alignment explanation
Indices: 2217403--2217445 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2217393 GTGCTGCAAC
*
2217403 AAAAAGCAAAAGAA-AGAAG
1 AAAAAGCAAAA-AAGAAAAG
2217422 AAAAA-CAAAAAAGAAAAG
1 AAAAAGCAAAAAAGAAAAG
2217440 AAAAAG
1 AAAAAG
2217446 ACTCTTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.10
18 14 0.67
19 5 0.24
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAGCAAAAAAGAAAAG
Found at i:2220915 original size:16 final size:16
Alignment explanation
Indices: 2220894--2220926 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2220884 TAGTTAGCTC
2220894 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
2220910 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
2220926 A
1 A
2220927 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:2224520 original size:16 final size:16
Alignment explanation
Indices: 2224499--2224531 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2224489 TAGTTAGCTC
2224499 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
2224515 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
2224531 A
1 A
2224532 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:2226439 original size:24 final size:25
Alignment explanation
Indices: 2226404--2226458 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
2226394 ACTTGGAGCC
*
2226404 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
2226428 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
2226452 TCAAGTG
1 TCAAGTG
2226459 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:2226560 original size:30 final size:31
Alignment explanation
Indices: 2226526--2226583 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
2226516 TTGGTTCTTC
* *
2226526 AAAAGACATGTTTC-TTGAATTTTCTACTTG
1 AAAAGACATGTCTCTTTGAATATTCTACTTG
*
2226556 AAAAGATATGTCTCTTTGAATATTCTAC
1 AAAAGACATGTCTCTTTGAATATTCTAC
2226584 AAGGAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (31 bp):
AAAAGACATGTCTCTTTGAATATTCTACTTG
Found at i:2227822 original size:36 final size:37
Alignment explanation
Indices: 2227744--2227829 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 37
2227734 TTTAGTGCTG
* * *
2227744 GATTTTTCTTTCTTTTGAGTTCTTCACTTTCTTTTCT
1 GATTTTTCTTTTTTTTGACTTCTGCACTTTCTTTTCT
2227781 GATTTTTCTTTTTCTTTGACTT-TGCAC-TTCTTTT-T
1 GATTTTTCTTTTT-TTTGACTTCTGCACTTTCTTTTCT
2227816 GTATTTTTCTTTTT
1 G-ATTTTTCTTTTT
2227830 GTTGTTGATG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
35 2 0.05
36 19 0.43
37 16 0.36
38 7 0.16
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.67
Consensus pattern (37 bp):
GATTTTTCTTTTTTTTGACTTCTGCACTTTCTTTTCT
Found at i:2231531 original size:21 final size:21
Alignment explanation
Indices: 2231505--2231544 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2231495 CCAGAATCCC
*
2231505 TGGGGGGTATCGATTCCCCTG
1 TGGGGGGAATCGATTCCCCTG
*
2231526 TGGGGGGAATCGGTTCCCC
1 TGGGGGGAATCGATTCCCC
2231545 ATCAAAGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGGGGGAATCGATTCCCCTG
Found at i:2231577 original size:23 final size:23
Alignment explanation
Indices: 2231527--2231576 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2231517 ATTCCCCTGT
2231527 GGGGGGAATCGGTTCCCCATCAA
1 GGGGGGAATCGGTTCCCCATCAA
*
2231550 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCATCAA
2231571 GGGGGG
1 GGGGGG
2231577 GTCGATTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCATCAA
Found at i:2237379 original size:20 final size:19
Alignment explanation
Indices: 2237350--2237401 Score: 86
Period size: 20 Copynumber: 2.7 Consensus size: 19
2237340 CGTTATACAA
2237350 GGGGGGAATCGGTACCCCT
1 GGGGGGAATCGGTACCCCT
2237369 GGGGGGAAATCGGTACCCCT
1 GGGGGG-AATCGGTACCCCT
*
2237389 GGGGGTAATCGGT
1 GGGGGGAATCGGT
2237402 TCCCTCCGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.17, C:0.21, G:0.44, T:0.17
Consensus pattern (19 bp):
GGGGGGAATCGGTACCCCT
Found at i:2240037 original size:11 final size:11
Alignment explanation
Indices: 2240021--2240045 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2240011 TTTAATATTC
2240021 ATTAAAGGTAA
1 ATTAAAGGTAA
2240032 ATTAAAGGTAA
1 ATTAAAGGTAA
2240043 ATT
1 ATT
2240046 TAGCATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (11 bp):
ATTAAAGGTAA
Found at i:2248622 original size:19 final size:19
Alignment explanation
Indices: 2248598--2248640 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2248588 ACATTCTTAT
2248598 TACTTTATAATAATTCATA
1 TACTTTATAATAATTCATA
2248617 TACTTTATAATAATTCATA
1 TACTTTATAATAATTCATA
2248636 TACTT
1 TACTT
2248641 AGCTTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
TACTTTATAATAATTCATA
Found at i:2256978 original size:23 final size:23
Alignment explanation
Indices: 2256926--2256972 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2256916 TAAGTTAAGT
2256926 ATATGAAATATATATATATGTATA
1 ATAT-AAATATATATATATGTATA
*
2256950 ATATAAATGTATACTATA-GTATA
1 ATATAAATATATA-TATATGTATA
2256973 TAATAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (23 bp):
ATATAAATATATATATATGTATA
Found at i:2256987 original size:25 final size:26
Alignment explanation
Indices: 2256941--2257012 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 26
2256931 AAATATATAT
*
2256941 ATATGTATAAT-ATAAATGTATA-CT-
1 ATATATATAATAATAAAT-TATATCTC
*
2256965 ATAGTATATAATAATAACTTATATCTC
1 ATA-TATATAATAATAAATTATATCTC
*
2256992 ATATAT-TAATGAATAAGTTAT
1 ATATATATAAT-AATAAATTAT
2257013 CATCATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (26 bp):
ATATATATAATAATAAATTATATCTC
Found at i:2257843 original size:33 final size:33
Alignment explanation
Indices: 2257779--2257879 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
2257769 CTTGTTGATG
* * *
2257779 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
2257811 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
2257844 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
2257880 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:2261338 original size:16 final size:16
Alignment explanation
Indices: 2261305--2261346 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
2261295 TGTAGGAGTC
2261305 TTTTCTTTTCTCTTTTG
1 TTTTCTTTT-TCTTTTG
*
2261322 TTTTCTTTTTTTTTTG
1 TTTTCTTTTTCTTTTG
2261338 -TTTCTTTTT
1 TTTTCTTTTT
2261347 GTTGTAGCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 9 0.38
16 6 0.25
17 9 0.38
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTG
Found at i:2261749 original size:33 final size:33
Alignment explanation
Indices: 2261685--2261785 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
2261675 CTTGTTGATG
* * *
2261685 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
2261717 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
2261750 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
2261786 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:2269430 original size:10 final size:9
Alignment explanation
Indices: 2269416--2269465 Score: 59
Period size: 8 Copynumber: 5.6 Consensus size: 9
2269406 TTTTGAATTC
2269416 TTTTTCTTT
1 TTTTTCTTT
2269425 TCTTTTCTCTT
1 T-TTTTCT-TT
*
2269436 TTTGTCTTT
1 TTTTTCTTT
2269445 TTTTT-TTT
1 TTTTTCTTT
2269453 TTTTT-TTT
1 TTTTTCTTT
2269461 TTTTT
1 TTTTT
2269466 TTGCACTCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
8 16 0.43
9 7 0.19
10 11 0.30
11 3 0.08
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2269446 original size:1 final size:1
Alignment explanation
Indices: 2269442--2269467 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2269432 TCTTTTTGTC
2269442 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
2269468 GCACTCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2282959 original size:11 final size:13
Alignment explanation
Indices: 2282928--2282956 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2282918 GGCCAAAGAT
2282928 GAAAAGGTATGTA
1 GAAAAGGTATGTA
2282941 GAAAAGGTATGT-
1 GAAAAGGTATGTA
2282953 GAAA
1 GAAA
2282957 GGTGTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (13 bp):
GAAAAGGTATGTA
Found at i:2291194 original size:19 final size:21
Alignment explanation
Indices: 2291151--2291202 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
2291141 GAAACCCCTT
2291151 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
2291172 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
2291191 TGAAGATACATG
1 TGAAAATACATG
2291203 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:2295339 original size:19 final size:21
Alignment explanation
Indices: 2295296--2295347 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
2295286 GAAACCCCTT
2295296 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
2295317 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
2295336 TGAAGATACATG
1 TGAAAATACATG
2295348 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:2299255 original size:26 final size:26
Alignment explanation
Indices: 2299221--2299283 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
2299211 TGGAGGATGT
2299221 TGATGGTGATGAAGTTGAAATGGAGA
1 TGATGGTGATGAAGTTGAAATGGAGA
2299247 TGATGGTGATGAAGTTGAAATGGAGA
1 TGATGGTGATGAAGTTGAAATGGAGA
*
2299273 TGGTGGTGATG
1 TGATGGTGATG
2299284 TTGTATCTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.30, C:0.00, G:0.41, T:0.29
Consensus pattern (26 bp):
TGATGGTGATGAAGTTGAAATGGAGA
Found at i:2313112 original size:18 final size:18
Alignment explanation
Indices: 2313074--2313113 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2313064 TGAATGAGTC
*
2313074 TTTTCTTTTTCTTTTTGT
1 TTTTCTTTTTCTTTCTGT
2313092 TTTTCTTCTTTCTTTCT-T
1 TTTTCTT-TTTCTTTCTGT
2313110 TTTT
1 TTTT
2313114 GTTGCAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTCTTTCTGT
Found at i:2313320 original size:11 final size:11
Alignment explanation
Indices: 2313293--2313326 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2313283 GAAATGGATT
*
2313293 AATGAAATAAGA
1 AATGAAATGA-A
2313305 AATGAAATGAA
1 AATGAAATGAA
2313316 AATGAAATGAA
1 AATGAAATGAA
2313327 TGAATAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (11 bp):
AATGAAATGAA
Found at i:2313324 original size:16 final size:16
Alignment explanation
Indices: 2313293--2313330 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2313283 GAAATGGATT
2313293 AATGAAATAAGAAATG
1 AATGAAATAAGAAATG
*
2313309 AAATGAAA-ATGAAATG
1 -AATGAAATAAGAAATG
2313325 AATGAA
1 AATGAA
2313331 TAGAGATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 7 0.35
17 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.18, T:0.18
Consensus pattern (16 bp):
AATGAAATAAGAAATG
Found at i:2322144 original size:5 final size:5
Alignment explanation
Indices: 2322134--2322201 Score: 50
Period size: 5 Copynumber: 12.8 Consensus size: 5
2322124 GAACTTCTCT
* *
2322134 TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TGATTTT TTTTC TTCTTT
1 TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC T--TTTC TTTTC TT-TTC
2322183 TTTTC TTTT- TATTTC TTTT
1 TTTTC TTTTC T-TTTC TTTT
2322202 TGCACTCCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
4 1 0.02
5 38 0.73
6 9 0.17
7 4 0.08
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:2322184 original size:13 final size:13
Alignment explanation
Indices: 2322136--2322186 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
2322126 ACTTCTCTTT
*
2322136 TTCTTTTCTTTTC
1 TTCTTTTTTTTTC
*
2322149 TTCTTTTCTTCTT-
1 TTCTTTT-TTTTTC
2322162 TTCTGATTTTTTTTC
1 TTCT--TTTTTTTTC
2322177 TTCTTTTTTT
1 TTCTTTTTTT
2322187 CTTTTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 17 0.55
14 7 0.23
15 7 0.23
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:2322188 original size:8 final size:8
Alignment explanation
Indices: 2322128--2322202 Score: 53
Period size: 8 Copynumber: 9.0 Consensus size: 8
2322118 TTTTTTGAAC
*
2322128 TTCTCTTT
1 TTCTTTTT
2322136 TTCTTTTCTT
1 TTC-TTT-TT
*
2322146 TTCTTCTT
1 TTCTTTTT
*
2322154 TTCTTCTT
1 TTCTTTTT
**
2322162 TTCTGATT
1 TTCTTTTT
*
2322170 TT-TTTTC
1 TTCTTTTT
2322177 TTCTTTTT
1 TTCTTTTT
2322185 TTCTTTTTAT
1 TTC-TTTT-T
2322195 TTCTTTTT
1 TTCTTTTT
2322203 GCACTCCAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
7 4 0.07
8 29 0.54
9 12 0.22
10 9 0.17
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.79
Consensus pattern (8 bp):
TTCTTTTT
Found at i:2322201 original size:28 final size:27
Alignment explanation
Indices: 2322131--2322202 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
2322121 TTTGAACTTC
* *
2322131 TCTTTTTCTTTTCTTTTCTTCTTTTCT
1 TCTTTTTATTTTTTTTTCTTCTTTTCT
*
2322158 TCTTTTCTGA-TTTTTTTTCTTCTTTTTT
1 TCTTTT-T-ATTTTTTTTTCTTCTTTTCT
*
2322186 TCTTTTTATTTCTTTTT
1 TCTTTTTATTTTTTTTT
2322203 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 1 0.03
27 14 0.37
28 23 0.61
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.79
Consensus pattern (27 bp):
TCTTTTTATTTTTTTTTCTTCTTTTCT
Found at i:2324104 original size:17 final size:16
Alignment explanation
Indices: 2324082--2324129 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
2324072 AAATTGGAGT
2324082 ACAAAAAGAAAGAAAAG
1 ACAAAAAG-AAGAAAAG
*
2324099 ACAAAAAGAAGAAAAA
1 ACAAAAAGAAGAAAAG
*
2324115 AAAGAAAAGAAGAAA
1 ACA-AAAAGAAGAAA
2324130 GGAAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (16 bp):
ACAAAAAGAAGAAAAG
Found at i:2324112 original size:20 final size:20
Alignment explanation
Indices: 2324087--2324128 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2324077 GGAGTACAAA
*
2324087 AAGAAAGAAAAGACAAA-AAG
1 AAGAAAAAAAAGA-AAAGAAG
2324107 AAGAAAAAAAAGAAAAGAAG
1 AAGAAAAAAAAGAAAAGAAG
2324127 AA
1 AA
2324129 AGGAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (20 bp):
AAGAAAAAAAAGAAAAGAAG
Found at i:2328534 original size:18 final size:17
Alignment explanation
Indices: 2328500--2328533 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2328490 AGTGCTTCAA
2328500 CTTTCTTTCTGTCTTTT
1 CTTTCTTTCTGTCTTTT
2328517 CTTTGCTTTCT-TCTTTT
1 CTTT-CTTTCTGTCTTTT
2328534 TGAGTGCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.24, G:0.06, T:0.71
Consensus pattern (17 bp):
CTTTCTTTCTGTCTTTT
Found at i:2328701 original size:28 final size:28
Alignment explanation
Indices: 2328661--2328721 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
2328651 TGATTACCGC
2328661 TTGATGCAAGGCACTTGTACCTTATCAA
1 TTGATGCAAGGCACTTGTACCTTATCAA
2328689 TTGATGCAAGGCACTTGTACCTTATCAA
1 TTGATGCAAGGCACTTGTACCTTATCAA
2328717 TTGAT
1 TTGAT
2328722 TATGGATCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (28 bp):
TTGATGCAAGGCACTTGTACCTTATCAA
Found at i:2331793 original size:21 final size:21
Alignment explanation
Indices: 2331769--2331813 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2331759 GTATGTCATT
2331769 CTTTGCTGGTCATTCTTTCTC
1 CTTTGCTGGTCATTCTTTCTC
*
2331790 CTTTGCTGGTCGTTCTTTCTC
1 CTTTGCTGGTCATTCTTTCTC
2331811 CTT
1 CTT
2331814 GTCAGGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.29, G:0.16, T:0.53
Consensus pattern (21 bp):
CTTTGCTGGTCATTCTTTCTC
Found at i:2337935 original size:8 final size:8
Alignment explanation
Indices: 2337922--2337966 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
2337912 ATCTTTTTCT
2337922 TTTTCTTC
1 TTTTCTTC
2337930 TTTTCTTC
1 TTTTCTTC
2337938 TTTTCTTC
1 TTTTCTTC
2337946 TTTT-TGTC
1 TTTTCT-TC
2337954 TTTTCTTTC
1 TTTTC-TTC
2337963 TTTT
1 TTTT
2337967 TGCACTCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 26 0.76
9 6 0.18
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTTC
Found at i:2337968 original size:17 final size:16
Alignment explanation
Indices: 2337913--2337968 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
2337903 CTTTTTGAAA
*
2337913 TCTTTTTCT-TTTTCT
1 TCTTTTTGTCTTTTCT
2337928 TCTTTTCT-TCTTTTCT
1 TCTTTT-TGTCTTTTCT
2337944 TCTTTTTGTCTTTTCTT
1 TCTTTTTGTCTTTTC-T
2337961 TCTTTTTG
1 TCTTTTTG
2337969 CACTCCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.22
16 20 0.54
17 9 0.24
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.77
Consensus pattern (16 bp):
TCTTTTTGTCTTTTCT
Found at i:2340809 original size:21 final size:21
Alignment explanation
Indices: 2340785--2340824 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2340775 TTTTTTGAAA
2340785 TTTTGGCTT-TTTTTTTTTGCC
1 TTTT-GCTTGTTTTTTTTTGCC
*
2340806 TTTTTCTTGTTTTTTTTTG
1 TTTTGCTTGTTTTTTTTTG
2340825 TTTTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (21 bp):
TTTTGCTTGTTTTTTTTTGCC
Found at i:2340825 original size:10 final size:10
Alignment explanation
Indices: 2340794--2340833 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
2340784 ATTTTGGCTT
2340794 TTTTTTTTTG
1 TTTTTTTTTG
* *
2340804 CCTTTTTCTTG
1 -TTTTTTTTTG
2340815 TTTTTTTTTG
1 TTTTTTTTTG
2340825 TTTTTTTTT
1 TTTTTTTTT
2340834 AAAAATAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:2351172 original size:24 final size:24
Alignment explanation
Indices: 2351145--2351199 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2351135 CCTCAATGAT
*
2351145 CACAACTTGTGGCACTTCAAGTGG
1 CACAACTTGTGGAACTTCAAGTGG
* * *
2351169 CACATCTTTTTGAACTTCAAGTGG
1 CACAACTTGTGGAACTTCAAGTGG
*
2351193 CATAACT
1 CACAACT
2351200 GTTGGAATGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (24 bp):
CACAACTTGTGGAACTTCAAGTGG
Found at i:2354562 original size:19 final size:21
Alignment explanation
Indices: 2354519--2354570 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
2354509 GAAACCCCTT
2354519 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
2354540 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
2354559 TGAAGATACATG
1 TGAAAATACATG
2354571 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:2356581 original size:24 final size:24
Alignment explanation
Indices: 2356531--2356580 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2356521 AACACAACTC
* *
2356531 TTGGCACTTCAAATGACATTTCTT
1 TTGGAACTTCAAATGACATATCTT
*
2356555 TTGGAACTTCAAATGGCATCATCTT
1 TTGGAACTTCAAATGACAT-ATCTT
2356580 T
1 T
2356581 GAAACATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (24 bp):
TTGGAACTTCAAATGACATATCTT
Found at i:2357892 original size:8 final size:8
Alignment explanation
Indices: 2357879--2357903 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2357869 ACTTTTTCTT
2357879 TTCTTTTC
1 TTCTTTTC
2357887 TTCTTTTC
1 TTCTTTTC
2357895 TTCTTTTC
1 TTCTTTTC
2357903 T
1 T
2357904 AATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:2358674 original size:19 final size:21
Alignment explanation
Indices: 2358631--2358682 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
2358621 GAAACCCCTT
*
2358631 TGAAAATACATAACTTTTAAA
1 TGAAAATACATGACTTTTAAA
2358652 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
2358671 TGAAGATACATG
1 TGAAAATACATG
2358683 CTCTTGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:2364653 original size:24 final size:25
Alignment explanation
Indices: 2364607--2364653 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
2364597 CACCATGATC
* * *
2364607 TGCATTTTCTTCAGTTTCTTCATCT
1 TGCATTGTCTTCAGGTTCCTCATCT
2364632 TGCATTGT-TTCAGGTTCCTCAT
1 TGCATTGTCTTCAGGTTCCTCAT
2364654 AAAAAATAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.51
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCATCT
Found at i:2367165 original size:19 final size:19
Alignment explanation
Indices: 2367141--2367210 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
2367131 CGGCCAAGAG
2367141 CATGTATCTTCATTTAAAT
1 CATGTATCTTCATTTAAAT
2367160 CATGTATCTTCATTTAAAT
1 CATGTATCTTCATTTAAAT
* **
2367179 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCAT-TTAAAT
*
2367199 CATGTATTTTCA
1 CATGTATCTTCA
2367211 AAGGGGTTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 31 0.66
20 16 0.34
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.46
Consensus pattern (19 bp):
CATGTATCTTCATTTAAAT
Found at i:2367596 original size:36 final size:36
Alignment explanation
Indices: 2367549--2367653 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
2367539 GATACAATCT
2367549 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
2367585 GTCCATCACCATTATCACTCCTATATCATCACTATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
2367621 TTCCATCATCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
2367654 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 19 0.31
36 43 0.69
ACGTcount: A:0.30, C:0.34, G:0.04, T:0.31
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:2372447 original size:24 final size:24
Alignment explanation
Indices: 2372420--2372479 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
2372410 GTTGGTTCTT
2372420 CAAAAGACATGTCTTGTGGATCAC
1 CAAAAGACATGTCTTGTGGATCAC
* * * * * **
2372444 CAAAGGTCATGACTTTTGGTTCTT
1 CAAAAGACATGTCTTGTGGATCAC
2372468 CAAAAGACATGT
1 CAAAAGACATGT
2372480 TTCTTGAATC
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (24 bp):
CAAAAGACATGTCTTGTGGATCAC
Found at i:2373694 original size:27 final size:28
Alignment explanation
Indices: 2373651--2373708 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
2373641 CTTTCTTTTT
*
2373651 TTTCTTTGCTTTTGAGTGC-TGAATTTC
1 TTTCTTTGCTTTTGAGTGCTTCAATTTC
2373678 TTTCTTT-CTTTTGGAGTGCTTCAATTTC
1 TTTCTTTGCTTTT-GAGTGCTTCAATTTC
2373706 TTT
1 TTT
2373709 TCTGATTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 5 0.18
27 13 0.46
28 10 0.36
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.59
Consensus pattern (28 bp):
TTTCTTTGCTTTTGAGTGCTTCAATTTC
Found at i:2374416 original size:19 final size:20
Alignment explanation
Indices: 2374369--2374419 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2374359 AAAACCCCTT
**
2374369 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2374389 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2374408 TGAAGATACATG
1 TGAAAATACATG
2374420 CTCTTGGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2379301 original size:14 final size:13
Alignment explanation
Indices: 2379284--2379333 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
2379274 GTGCAAAAAG
2379284 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
2379298 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
2379311 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
2379322 AAAGAAAAAGAA
1 AAAGAAAAAGAA
2379334 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:2379330 original size:19 final size:18
Alignment explanation
Indices: 2379278--2379333 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
2379268 ATTGGAGTGC
2379278 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
2379295 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
2379314 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
2379333 A
1 A
2379334 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:2379331 original size:11 final size:11
Alignment explanation
Indices: 2379278--2379333 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
2379268 ATTGGAGTGC
2379278 AAAAAG-AAAG
1 AAAAAGAAAAG
2379288 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
2379302 AAGAAGAAAAG
1 AAAAAGAAAAG
2379313 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
2379326 AAAAAGAA
1 AAAAAGAA
2379334 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:2394198 original size:11 final size:11
Alignment explanation
Indices: 2394176--2394212 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
2394166 CTTGATTTCT
2394176 TTCACTTTGCAC
1 TTCAC-TTGCAC
2394188 TTCACTTGCAC
1 TTCACTTGCAC
2394199 TTCACTTGCAC
1 TTCACTTGCAC
2394210 TTC
1 TTC
2394213 TTTTTGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.16, C:0.35, G:0.08, T:0.41
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:2401928 original size:18 final size:18
Alignment explanation
Indices: 2401885--2401929 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
2401875 ATTGGAGTGT
2401885 AAAAAG-AAAGAAGAAAA
1 AAAAAGAAAAGAAGAAAA
* *
2401902 AAATCAGAAAAGTAGAAAA
1 AAA-AAGAAAAGAAGAAAA
2401921 AAAAAGAAA
1 AAAAAGAAA
2401930 TTCAAAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 7 0.30
19 13 0.57
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAGAAGAAAA
Found at i:2404366 original size:22 final size:22
Alignment explanation
Indices: 2404338--2404412 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
2404328 CTATTGAAAA
2404338 CCAAAGGGAAATGATTTTTCAT
1 CCAAAGGGAAATGATTTTTCAT
** *** *
2404360 CCAAAGGG-TGTGACTTATGAAAA
1 CCAAAGGGAAATGA-TT-TTTCAT
2404383 CCAAAGGGAAATGATTTTTCAT
1 CCAAAGGGAAATGATTTTTCAT
2404405 CCAAAGGG
1 CCAAAGGG
2404413 TGTGACTTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 3 0.08
22 20 0.53
23 12 0.32
24 3 0.08
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (22 bp):
CCAAAGGGAAATGATTTTTCAT
Found at i:2404383 original size:45 final size:45
Alignment explanation
Indices: 2404332--2404424 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
2404322 TCATGGCTAT
2404332 TGAAAACCAAAGGGAAATGATTTTTCATCCAAAGGGTGTGACTTA
1 TGAAAACCAAAGGGAAATGATTTTTCATCCAAAGGGTGTGACTTA
2404377 TGAAAACCAAAGGGAAATGATTTTTCATCCAAAGGGTGTGACTTA
1 TGAAAACCAAAGGGAAATGATTTTTCATCCAAAGGGTGTGACTTA
2404422 TGA
1 TGA
2404425 GGGCATCACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (45 bp):
TGAAAACCAAAGGGAAATGATTTTTCATCCAAAGGGTGTGACTTA
Found at i:2404847 original size:2 final size:2
Alignment explanation
Indices: 2404840--2404904 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2404830 TTCTAACTCT
2404840 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2404882 AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC A
2404905 TATATATATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2406181 original size:12 final size:12
Alignment explanation
Indices: 2406155--2406191 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2406145 ATTGCCATTT
2406155 CATCATCAA--C
1 CATCATCAATTC
2406165 CATCATCAATTC
1 CATCATCAATTC
2406177 CATCATCAATTC
1 CATCATCAATTC
2406189 CAT
1 CAT
2406192 AATTCTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (12 bp):
CATCATCAATTC
Found at i:2412367 original size:10 final size:10
Alignment explanation
Indices: 2412352--2412399 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
2412342 TATTTTTTTC
2412352 AAAAAAAC-A
1 AAAAAAACAA
2412361 AAAAAAACGAA
1 AAAAAAAC-AA
*
2412372 AAAAAAGCAA
1 AAAAAAACAA
*
2412382 AAAAAAGGCAA
1 AAAAAA-ACAA
2412393 AAAAAAA
1 AAAAAAA
2412400 AAGCCAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.24
10 8 0.24
11 18 0.53
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:2412387 original size:14 final size:14
Alignment explanation
Indices: 2412380--2412410 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2412370 AAAAAAAAGC
*
2412380 AAAAAAAAGGCAAA
1 AAAAAAAAGCCAAA
2412394 AAAAAAAAGCCAAA
1 AAAAAAAAGCCAAA
2412408 AAA
1 AAA
2412411 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGCCAAA
Found at i:2412410 original size:11 final size:10
Alignment explanation
Indices: 2412352--2412398 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
2412342 TATTTTTTTC
2412352 AAAAAAA-CA
1 AAAAAAAGCA
2412361 AAAAAAA-CGA
1 AAAAAAAGC-A
2412371 AAAAAAAGCA
1 AAAAAAAGCA
2412381 AAAAAAAGGCA
1 AAAAAAA-GCA
2412392 AAAAAAA
1 AAAAAAA
2412399 AAAGCCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCA
Found at i:2412411 original size:23 final size:24
Alignment explanation
Indices: 2412370--2412417 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2412360 AAAAAAAACG
*
2412370 AAAAAAAAGCAAAAAAAAGGCAAA
1 AAAAAAAAGCAAAAAAAAGCCAAA
*
2412394 AAAAAAAAGC-CAAAAAAGCCAAA
1 AAAAAAAAGCAAAAAAAAGCCAAA
2412417 A
1 A
2412418 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.77, C:0.12, G:0.10, T:0.00
Consensus pattern (24 bp):
AAAAAAAAGCAAAAAAAAGCCAAA
Found at i:2417220 original size:195 final size:195
Alignment explanation
Indices: 2416888--2417281 Score: 761
Period size: 195 Copynumber: 2.0 Consensus size: 195
2416878 TCAATTTCTA
*
2416888 ACATTAACAAGGATTTGCCTAGTGTATTTTCATCTTTGTTACAAGATTTTTGAGAAGTGTTAGGT
1 ACATTAACAAGGATTTGCCTAGTGTATTTTCATCTTTGTTACAAGATTTTCGAGAAGTGTTAGGT
*
2416953 GATCCACCTAACGAATTAACACCAAAAAGAGGAAAACAACACCAAACCAATCTAATTCAAGGTTC
66 GATCCACCTAACGAATTAACACCAAAAAGAGGAAAACAACACCAAACCAATCTAACTCAAGGTTC
2417018 CATCATACCTCGTCAAACATACAATATCGAAGAAACCAAAGAGTTAGATTTGTTACGAAAAGGCT
131 CATCATACCTCGTCAAACATACAATATCGAAGAAACCAAAGAGTTAGATTTGTTACGAAAAGGCT
2417083 ACATTAACAAGGATTTGCCTAGTGTATTTTCATCTTTGTTACAAGATTTTCGAGAAGTGTTAGGT
1 ACATTAACAAGGATTTGCCTAGTGTATTTTCATCTTTGTTACAAGATTTTCGAGAAGTGTTAGGT
2417148 GATCCACCTAACGAATTAACACCAAAAAGAGGAAAACAACACCAAACCAATCTAACTCAAGGTTC
66 GATCCACCTAACGAATTAACACCAAAAAGAGGAAAACAACACCAAACCAATCTAACTCAAGGTTC
*
2417213 CATCATACCTCTTCAAACATACAATATCGAAGAAACCAAAGAGTTAGATTTGTTACGAAAAGGCT
131 CATCATACCTCGTCAAACATACAATATCGAAGAAACCAAAGAGTTAGATTTGTTACGAAAAGGCT
2417278 ACAT
1 ACAT
2417282 CCATAAAAGC
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
195 196 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (195 bp):
ACATTAACAAGGATTTGCCTAGTGTATTTTCATCTTTGTTACAAGATTTTCGAGAAGTGTTAGGT
GATCCACCTAACGAATTAACACCAAAAAGAGGAAAACAACACCAAACCAATCTAACTCAAGGTTC
CATCATACCTCGTCAAACATACAATATCGAAGAAACCAAAGAGTTAGATTTGTTACGAAAAGGCT
Found at i:2421727 original size:7 final size:7
Alignment explanation
Indices: 2421712--2421769 Score: 55
Period size: 7 Copynumber: 7.7 Consensus size: 7
2421702 TATTTTTTTC
2421712 AAAAA-A
1 AAAAACA
2421718 AAAAACA
1 AAAAACA
2421725 AAAAACA
1 AAAAACA
2421732 AAAAAGGCAA
1 AAAAA--C-A
*
2421742 AAAAAAA
1 AAAAACA
2421749 AAAAAGCCA
1 AAAAA--CA
2421758 AAAAACA
1 AAAAACA
2421765 AAAAA
1 AAAAA
2421770 AAAGAGCCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
6 5 0.11
7 26 0.59
9 7 0.16
10 6 0.14
ACGTcount: A:0.84, C:0.10, G:0.05, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:2421736 original size:16 final size:16
Alignment explanation
Indices: 2421715--2421771 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
2421705 TTTTTTCAAA
2421715 AAAAAAAACAAAAAAC
1 AAAAAAAACAAAAAAC
**
2421731 AAAAAAGGCAAAAAA-
1 AAAAAAAACAAAAAAC
2421746 AAAAAAAAGCCAAAAAAC
1 AAAAAAAA--CAAAAAAC
2421764 AAAAAAAA
1 AAAAAAAA
2421772 AGAGCCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.18
16 13 0.38
17 7 0.21
18 8 0.24
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAC
Found at i:2421790 original size:21 final size:21
Alignment explanation
Indices: 2421743--2421783 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2421733 AAAAGGCAAA
2421743 AAAAAAAAAAAGCCAAAAAAC
1 AAAAAAAAAAAGCCAAAAAAC
*
2421764 AAAAAAAAAGAGCCAAAAAA
1 AAAAAAAAAAAGCCAAAAAA
2421784 GCCAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAGCCAAAAAAC
Found at i:2426258 original size:16 final size:16
Alignment explanation
Indices: 2426233--2426269 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2426223 TGGCATTTCA
2426233 TTTGTAATATAAAC-C
1 TTTGTAATATAAACTC
2426248 TTTGATAATATAAACTC
1 TTTG-TAATATAAACTC
2426265 TTTGT
1 TTTGT
2426270 GAGATTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 11 0.55
17 5 0.25
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (16 bp):
TTTGTAATATAAACTC
Found at i:2431587 original size:11 final size:11
Alignment explanation
Indices: 2431571--2431596 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2431561 TTTTTTGAAA
2431571 TTTTGCCTTTT
1 TTTTGCCTTTT
2431582 TTTTGCCTTTT
1 TTTTGCCTTTT
2431593 TTTT
1 TTTT
2431597 TGTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTGCCTTTT
Found at i:2431614 original size:12 final size:11
Alignment explanation
Indices: 2431578--2431615 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
2431568 AAATTTTGCC
*
2431578 TTTTTTTTGCCT
1 TTTTTTTTG-TT
2431590 TTTTTTTTGTT
1 TTTTTTTTGTT
2431601 TTTTTTTTGTT
1 TTTTTTTTGTT
2431612 TTTT
1 TTTT
2431616 GAAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:2433806 original size:35 final size:37
Alignment explanation
Indices: 2433737--2433816 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
2433727 ATACTATTTC
* * *
2433737 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCATCCATTATCACACCTATAT
*
2433774 CATCACCATAGTCCATCAT-CA-TATCACACCTATAT
1 CATCACCATAATCCATCATCCATTATCACACCTATAT
2433809 CATCACCA
1 CATCACCA
2433817 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 2 0.05
37 16 0.41
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCATCCATTATCACACCTATAT
Found at i:2433810 original size:11 final size:12
Alignment explanation
Indices: 2433767--2433815 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
2433757 CATTATCACG
2433767 CCTATATCATCA
1 CCTATATCATCA
2433779 CC-ATAGTCCATCA
1 CCTATA-T-CATCA
*
2433792 TC-ATATCA-CA
1 CCTATATCATCA
2433802 CCTATATCATCA
1 CCTATATCATCA
2433814 CC
1 CC
2433816 AAATTCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 3 0.10
11 11 0.35
12 8 0.26
13 9 0.29
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.29
Consensus pattern (12 bp):
CCTATATCATCA
Found at i:2437751 original size:35 final size:37
Alignment explanation
Indices: 2437682--2437761 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
2437672 ATACTATTTC
* * *
2437682 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCATCCATTATCACACCTATAT
*
2437719 CATCACCATAGTCCATCAT-CA-TATCACACCTATAT
1 CATCACCATAATCCATCATCCATTATCACACCTATAT
2437754 CATCACCA
1 CATCACCA
2437762 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 2 0.05
37 16 0.41
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCATCCATTATCACACCTATAT
Found at i:2437755 original size:11 final size:12
Alignment explanation
Indices: 2437712--2437760 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
2437702 CATTATCACG
2437712 CCTATATCATCA
1 CCTATATCATCA
2437724 CC-ATAGTCCATCA
1 CCTATA-T-CATCA
*
2437737 TC-ATATCA-CA
1 CCTATATCATCA
2437747 CCTATATCATCA
1 CCTATATCATCA
2437759 CC
1 CC
2437761 AAATTCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 3 0.10
11 11 0.35
12 8 0.26
13 9 0.29
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.29
Consensus pattern (12 bp):
CCTATATCATCA
Found at i:2440643 original size:23 final size:25
Alignment explanation
Indices: 2440612--2440657 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
2440602 TAGCTGTTGG
2440612 AGAACTAAA-AGATGTGACTTTTAA
1 AGAACTAAATAGATGTGACTTTTAA
* *
2440636 AGAA-TAAATAGTTGTTACTTTT
1 AGAACTAAATAGATGTGACTTTT
2440658 GGTGATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (25 bp):
AGAACTAAATAGATGTGACTTTTAA
Found at i:2447025 original size:17 final size:19
Alignment explanation
Indices: 2446995--2447041 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2446985 TAACCAAAGC
*
2446995 AAAAAGAAAGAAG-AAGAA
1 AAAAACAAAGAAGAAAGAA
2447013 AAAAACAAA-AAGAAAGAA
1 AAAAACAAAGAAGAAAGAA
2447031 AAAAA-AAAGAA
1 AAAAACAAAGAA
2447042 TCAAAAGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAACAAAGAAGAAAGAA
Found at i:2447047 original size:15 final size:16
Alignment explanation
Indices: 2446994--2447057 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 16
2446984 GTAACCAAAG
*
2446994 CAAAAAGAAAGAAGAAGA
1 CAAAAACAAA-AAGAA-A
*
2447012 AAAAAACAAAAAGAAA
1 CAAAAACAAAAAGAAA
* *
2447028 GAAAAA-AAAAAGAAT
1 CAAAAACAAAAAGAAA
*
2447043 CAAAAGC-AAAAGAAA
1 CAAAAACAAAAAGAAA
2447058 AAGTGAAGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 19 0.50
16 6 0.16
17 5 0.13
18 8 0.21
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (16 bp):
CAAAAACAAAAAGAAA
Found at i:2447048 original size:24 final size:23
Alignment explanation
Indices: 2446994--2447047 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 23
2446984 GTAACCAAAG
*
2446994 CAAAAAGAAAGAAGAAGAAAAAAA
1 CAAAAAGAAAGAA-AAAAAAAAAA
2447018 CAAAAAGAAAGAAAAAAAAAAGAA
1 CAAAAAGAAAGAAAAAAAAAA-AA
2447042 TCAAAA
1 -CAAAA
2447048 GCAAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.26
24 15 0.56
25 5 0.19
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.02
Consensus pattern (23 bp):
CAAAAAGAAAGAAAAAAAAAAAA
Found at i:2449445 original size:15 final size:15
Alignment explanation
Indices: 2449434--2449462 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2449424 ACTCAAAAAG
2449434 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
2449449 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
2449463 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:2453921 original size:24 final size:24
Alignment explanation
Indices: 2453910--2453956 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2453900 TTTCAAAGAT
2453910 AATGTCGTTTGAAGTTCCAAGAGA
1 AATGTCGTTTGAAGTTCCAAGAGA
** *
2453934 AATGTCACTTGAAGTGCCAAGAG
1 AATGTCGTTTGAAGTTCCAAGAG
2453957 TTGTGTCTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (24 bp):
AATGTCGTTTGAAGTTCCAAGAGA
Found at i:2455901 original size:26 final size:25
Alignment explanation
Indices: 2455872--2455938 Score: 86
Period size: 24 Copynumber: 2.7 Consensus size: 25
2455862 GTGCTACAAC
2455872 AAAAAGCAACAAGAAAGAAGAAGAA-A
1 AAAAAGCAA-AAGAAA-AAGAAGAATA
*
2455898 AAAAAG-AAAAGAAAAAGAAGAATC
1 AAAAAGCAAAAGAAAAAGAAGAATA
2455922 AAAAAGC-AAAGAAAAAG
1 AAAAAGCAAAAGAAAAAG
2455939 TGAAGCAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
23 8 0.21
24 22 0.58
25 2 0.05
26 6 0.16
ACGTcount: A:0.75, C:0.06, G:0.18, T:0.01
Consensus pattern (25 bp):
AAAAAGCAAAAGAAAAAGAAGAATA
Found at i:2455911 original size:14 final size:15
Alignment explanation
Indices: 2455885--2455919 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2455875 AAGCAACAAG
2455885 AAAGAAGAAGAAAAA
1 AAAGAAGAAGAAAAA
2455900 AAAGAA-AAGAAAAA
1 AAAGAAGAAGAAAAA
*
2455914 GAAGAA
1 AAAGAA
2455920 TCAAAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAGAAAAA
Found at i:2455955 original size:24 final size:24
Alignment explanation
Indices: 2455871--2455948 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
2455861 AGTGCTACAA
2455871 CAAAAAGCAACAAGAAAGAAGAAGAA-
1 CAAAAAGC-A-AAGAAA-AAGAAGAAG
* * *
2455897 AAAAAAGAAAAGAAAAAGAAGAAT
1 CAAAAAGCAAAGAAAAAGAAGAAG
*
2455921 CAAAAAGCAAAGAAAAAG-TGAAG
1 CAAAAAGCAAAGAAAAAGAAGAAG
2455944 CAAAA
1 CAAAA
2455949 TTGCAAATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
23 16 0.36
24 22 0.49
25 1 0.02
26 6 0.13
ACGTcount: A:0.72, C:0.08, G:0.18, T:0.03
Consensus pattern (24 bp):
CAAAAAGCAAAGAAAAAGAAGAAG
Found at i:2457000 original size:19 final size:20
Alignment explanation
Indices: 2456950--2457000 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2456940 GAAACCCCTT
**
2456950 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
*
2456970 TGAAAATGCATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2456989 TGAAGATACATG
1 TGAAAATACATG
2457001 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2459896 original size:15 final size:16
Alignment explanation
Indices: 2459845--2459897 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
2459835 AGAAAGTGAA
2459845 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
2459862 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
2459879 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
2459894 ATAA
1 ATAA
2459898 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:2460117 original size:24 final size:23
Alignment explanation
Indices: 2460085--2460129 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
2460075 GTTGTAGGAG
2460085 TCTTTTCTT-TCTCTTTTTGTTTT
1 TCTTTTCTTCT-TCTTTTTGTTTT
2460108 TCTTCTTCTTCTTCTTTTTGTT
1 TCTT-TTCTTCTTCTTTTTGTT
2460130 GCTTTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 4 0.20
24 15 0.75
25 1 0.05
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (23 bp):
TCTTTTCTTCTTCTTTTTGTTTT
Found at i:2460932 original size:19 final size:20
Alignment explanation
Indices: 2460885--2460935 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2460875 GAAACCCCTT
**
2460885 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2460905 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2460924 TGAAGATACATG
1 TGAAAATACATG
2460936 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2465552 original size:16 final size:16
Alignment explanation
Indices: 2465523--2465556 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2465513 GTAATGAAAC
2465523 AAGAAGAAAAAAATGA
1 AAGAAGAAAAAAATGA
* *
2465539 AAGAATAAAGAAATGA
1 AAGAAGAAAAAAATGA
2465555 AA
1 AA
2465557 TAGTAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (16 bp):
AAGAAGAAAAAAATGA
Found at i:2469685 original size:29 final size:28
Alignment explanation
Indices: 2469632--2469686 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
2469622 TGTAGGAGTC
*
2469632 TCTTCTTTCTCTTTTTTTTTGTTTTTCT
1 TCTTCTTTCTCTTTTTTGTTGTTTTTCT
2469660 TCTTCTTT-TCTCTTTTTGTTGCTTTTT
1 TCTTCTTTCTCT-TTTTTGTTG-TTTTT
2469687 TGCAGCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 3 0.12
28 16 0.67
29 5 0.21
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.76
Consensus pattern (28 bp):
TCTTCTTTCTCTTTTTTGTTGTTTTTCT
Found at i:2475197 original size:24 final size:24
Alignment explanation
Indices: 2475165--2475211 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2475155 GATGTAGGAG
2475165 TCTTTTTCTT-TT-CTCTTTTGTTT
1 TCTTTTTCTTGTTGCT-TTTTGTTT
2475188 TCTTCTTTCTTGTTGCTTTTTGTT
1 TCTT-TTTCTTGTTGCTTTTTGTT
2475212 GTAGCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (24 bp):
TCTTTTTCTTGTTGCTTTTTGTTT
Found at i:2485719 original size:36 final size:36
Alignment explanation
Indices: 2485656--2485750 Score: 156
Period size: 36 Copynumber: 2.7 Consensus size: 36
2485646 TGGTGATAAT
*
2485656 ATAGGCGTGATAA-GGTGATGGAATATGGTGACGAC
1 ATAGGCGTGATAATGGTGATGGACTATGGTGACGAC
* *
2485691 ATAGGCGTGATAATGGTGATGGACTATGGTGATGAT
1 ATAGGCGTGATAATGGTGATGGACTATGGTGACGAC
2485727 ATAGGCGTGATAATGGTGATGGAC
1 ATAGGCGTGATAATGGTGATGGAC
2485751 AGATTGTATC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 13 0.23
36 43 0.77
ACGTcount: A:0.29, C:0.07, G:0.37, T:0.26
Consensus pattern (36 bp):
ATAGGCGTGATAATGGTGATGGACTATGGTGACGAC
Found at i:2486134 original size:19 final size:20
Alignment explanation
Indices: 2486087--2486137 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2486077 GAAACCCCTT
**
2486087 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2486107 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2486126 TGAAGATACATG
1 TGAAAATACATG
2486138 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2487133 original size:18 final size:18
Alignment explanation
Indices: 2487107--2487144 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2487097 TGCTCATAAT
*
2487107 AGTATATAAGCATAAA-TA
1 AGTAAATAAG-ATAAAGTA
2487125 AGTAAATAAGATAAAGTA
1 AGTAAATAAGATAAAGTA
2487143 AG
1 AG
2487145 GAGGAACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.58, C:0.03, G:0.16, T:0.24
Consensus pattern (18 bp):
AGTAAATAAGATAAAGTA
Found at i:2487627 original size:24 final size:24
Alignment explanation
Indices: 2487600--2487675 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
2487590 AGTCATGACC
2487600 TTTGGTGATCCACACGACATGTCT
1 TTTGGTGATCCACACGACATGTCT
* * * * * *
2487624 TTTGGGGAACCA-ATAGTCATGACC
1 TTTGGTGATCCACA-CGACATGTCT
2487648 TTTGGTGATCCACACGACATGTCT
1 TTTGGTGATCCACACGACATGTCT
2487672 TTTG
1 TTTG
2487676 AAGATCCAAC
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (24 bp):
TTTGGTGATCCACACGACATGTCT
Found at i:2487643 original size:48 final size:48
Alignment explanation
Indices: 2487580--2487675 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2487570 ACAAGTCTTT
2487580 GGGAACCAATAGTCATGACCTTTGGTGATCCACACGACATGTCTTTTG
1 GGGAACCAATAGTCATGACCTTTGGTGATCCACACGACATGTCTTTTG
2487628 GGGAACCAATAGTCATGACCTTTGGTGATCCACACGACATGTCTTTTG
1 GGGAACCAATAGTCATGACCTTTGGTGATCCACACGACATGTCTTTTG
2487676 AAGATCCAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (48 bp):
GGGAACCAATAGTCATGACCTTTGGTGATCCACACGACATGTCTTTTG
Found at i:2489766 original size:35 final size:37
Alignment explanation
Indices: 2489697--2489776 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
2489687 ATACTATTTC
* *
2489697 CATCACAATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
2489734 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
2489769 CATCACCA
1 CATCACCA
2489777 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:2490252 original size:14 final size:15
Alignment explanation
Indices: 2490218--2490264 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2490208 AATTTGGAGT
2490218 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
2490233 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
2490247 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
2490264 G
1 G
2490265 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:2495436 original size:35 final size:37
Alignment explanation
Indices: 2495366--2495445 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
2495356 ATATTATTTC
*
2495366 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
2495403 CATCACCATAGTCCATC-ACCA-TATCACGGCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
2495438 CATCACCA
1 CATCACCA
2495446 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:2496367 original size:90 final size:89
Alignment explanation
Indices: 2496248--2496427 Score: 243
Period size: 90 Copynumber: 2.0 Consensus size: 89
2496238 GGGAAATGAT
* * *
2496248 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGTGCCTAAATAAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTATTCATCTTGGCGCCTAAATAAACCACATGC-AGGCACATG
* *
2496313 GGGTTGTTCACATGCAAAACACATG
65 GGGCTGGTCACATGCAAAACACATG
* * * *
2496338 GCTTGGCCGAATAGGGAGAGAACTATTCATCTTGGCGCCTAATTGATCCTCATGCAGGCACATGG
1 GCTTGGCCGAATAGGGAGAGAACTATTCATCTTGGCGCCTAAATAAACCACATGCAGGCACATGG
* **
2496403 GGCTGGTCATATGCAAGGCACATG
66 GGCTGGTCACATGCAAAACACATG
2496427 G
1 G
2496428 GTGTTCTAGG
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 30 0.38
90 48 0.62
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (89 bp):
GCTTGGCCGAATAGGGAGAGAACTATTCATCTTGGCGCCTAAATAAACCACATGCAGGCACATGG
GGCTGGTCACATGCAAAACACATG
Found at i:2501837 original size:12 final size:13
Alignment explanation
Indices: 2501820--2501849 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2501810 CTAAAACACC
2501820 TTTCA-CATACCT
1 TTTCACCATACCT
2501832 TTTCACCATACCT
1 TTTCACCATACCT
2501845 TTTCA
1 TTTCA
2501850 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCACCATACCT
Found at i:2507788 original size:18 final size:18
Alignment explanation
Indices: 2507765--2507817 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2507755 TGATATTTTT
*
2507765 TAAAAAAAACAAAAAAGG
1 TAAAAAAAGCAAAAAAGG
*
2507783 TAAAAAAAGGCAAAAAAAG
1 TAAAAAAA-GCAAAAAAGG
*
2507802 -AAAGAAAGCAAAAAAG
1 TAAAAAAAGCAAAAAAG
2507818 CCAAAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 8 0.27
18 14 0.47
19 8 0.27
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.04
Consensus pattern (18 bp):
TAAAAAAAGCAAAAAAGG
Done.