Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007751.1 Hibiscus syriacus cultivar Beakdansim tig00110017_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: 1434969
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 4 of 6
Found at i:776460 original size:13 final size:14
Alignment explanation
Indices: 776438--776472 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
776428 TTTTAGTTTT
776438 TTAAAT-TTATTTA
1 TTAAATATTATTTA
776451 TT-AATATTATTTA
1 TTAAATATTATTTA
776464 TTAAATATT
1 TTAAATATT
776473 TAATCAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 11 0.55
14 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAAATATTATTTA
Found at i:777032 original size:23 final size:25
Alignment explanation
Indices: 776989--777037 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
776979 ATACAATTTA
776989 TTATTAATTTTTAAAAATAATTAAT
1 TTATTAATTTTTAAAAATAATTAAT
*
777014 TTATT-ATTTTT-AAATTAATTAAT
1 TTATTAATTTTTAAAAATAATTAAT
777037 T
1 T
777038 AATTTTCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.52
24 6 0.26
25 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTATTAATTTTTAAAAATAATTAAT
Found at i:777957 original size:22 final size:21
Alignment explanation
Indices: 777932--777973 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
777922 ATATTTAGGT
777932 TTGAGTTTAGAGC-GAAAAATAG
1 TTGA-TTT-GAGCTGAAAAATAG
*
777954 TTGATTTGATCTGAAAAATA
1 TTGATTTGAGCTGAAAAATA
777974 ATAAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 11 0.61
22 4 0.22
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (21 bp):
TTGATTTGAGCTGAAAAATAG
Found at i:785156 original size:22 final size:19
Alignment explanation
Indices: 785087--785176 Score: 81
Period size: 19 Copynumber: 4.4 Consensus size: 19
785077 AACTCGATTT
*
785087 TGAAAAATGTGTTGCGAAAG
1 TGAAAAA-GTGTTGCGATAG
* * *
785107 TTAAAATGTGTTGCGAGAG
1 TGAAAAAGTGTTGCGATAG
785126 TTTGAAAAACGTGTTGTTACGATAG
1 --TGAAAAA-GTGTTG---CGATAG
785151 TGAAAAAGTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAG
785170 TGAAAAA
1 TGAAAAA
785177 TCCAAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
19 24 0.41
20 5 0.09
21 5 0.09
22 12 0.21
23 7 0.12
25 5 0.09
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.29
Consensus pattern (19 bp):
TGAAAAAGTGTTGCGATAG
Found at i:785712 original size:61 final size:61
Alignment explanation
Indices: 785632--785777 Score: 229
Period size: 61 Copynumber: 2.4 Consensus size: 61
785622 TTATCGCGTT
785632 GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATTACGATTTTAGAAAATCGCAAC
1 GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATTACGATTTTAGAAAATCGCAAC
* * * * *
785693 GCGATAATCAGAATTGCGTTACGATTTATATATTCGCATTGCGATTTTAGAAAATCGCAAC
1 GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATTACGATTTTAGAAAATCGCAAC
* *
785754 GCGATAGTCAAAATCGCATTGCGA
1 GCGATAGTCAGAATCGCGTTGCGA
785778 ATCTGGAAAC
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 75 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (61 bp):
GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATTACGATTTTAGAAAATCGCAAC
Found at i:785827 original size:19 final size:19
Alignment explanation
Indices: 785803--785839 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
785793 TGCGATACTG
*
785803 GAGATCGCGTTACGATTTA
1 GAGATCGCATTACGATTTA
*
785822 GAGATCGCATTGCGATTT
1 GAGATCGCATTACGATTT
785840 GTTGGTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:799499 original size:61 final size:61
Alignment explanation
Indices: 799419--799573 Score: 158
Period size: 61 Copynumber: 2.6 Consensus size: 61
799409 AAATAAGTTT
* * * *
799419 TTAAACTTTTA-AATATTTTAATTTCATTCTCAAACTACGACT-TTAGTTCTAAATCAG-TCC
1 TTAAAATTTTATAACATTTTAATTTCATTCTCAAACTACGAATCTCA-TTCTAAAT-AGATCC
* * *
799479 TTAAAATTTTTTAACATTTTAATTTCA-TCTTCAAACTATGAATCTCATTCTAAATTGATCC
1 TTAAAATTTTATAACATTTTAATTTCATTC-TCAAACTACGAATCTCATTCTAAATAGATCC
* * *
799540 TTAAAATTTTATATC-TTTTAATTTAATTCCCAAA
1 TTAAAATTTTATAACATTTTAATTTCATTCTCAAA
799574 TTCATCCAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
60 26 0.33
61 51 0.65
62 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.03, T:0.46
Consensus pattern (61 bp):
TTAAAATTTTATAACATTTTAATTTCATTCTCAAACTACGAATCTCATTCTAAATAGATCC
Found at i:802797 original size:20 final size:20
Alignment explanation
Indices: 802772--802823 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
802762 TAATACTGAT
802772 AGTATCGATACTACCTAGTG
1 AGTATCGATACTACCTAGTG
*
802792 AGTATCGATATTACCTAGTG
1 AGTATCGATACTACCTAGTG
802812 AGTATCGATACT
1 AGTATCGATACT
802824 TCCCTTACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTACCTAGTG
Found at i:810320 original size:31 final size:31
Alignment explanation
Indices: 810282--810349 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
810272 ATGGGTTATG
*
810282 TGTATGTATGCCCAATGTATGTTTGAATGTA
1 TGTATGTATGCCCAATGAATGTTTGAATGTA
**
810313 TGTATGTATGCCTGATGAATGTTTGAATGTA
1 TGTATGTATGCCCAATGAATGTTTGAATGTA
810344 TGTATG
1 TGTATG
810350 CCTGATGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (31 bp):
TGTATGTATGCCCAATGAATGTTTGAATGTA
Found at i:810367 original size:54 final size:54
Alignment explanation
Indices: 810305--810424 Score: 204
Period size: 54 Copynumber: 2.2 Consensus size: 54
810295 AATGTATGTT
*
810305 TGAATGTATGTATGTATGCCTGATGAATGTTTGAATGTATGTATGCCTGATGAA
1 TGAATGTATGTATGCATGCCTGATGAATGTTTGAATGTATGTATGCCTGATGAA
* * *
810359 TGTATGTATATATGCATGCCTGATGAATGTTTGAATGTTTGTATGCCTGATGAA
1 TGAATGTATGTATGCATGCCTGATGAATGTTTGAATGTATGTATGCCTGATGAA
810413 TGAATGTATGTA
1 TGAATGTATGTA
810425 CTGATGAACC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (54 bp):
TGAATGTATGTATGCATGCCTGATGAATGTTTGAATGTATGTATGCCTGATGAA
Found at i:810423 original size:27 final size:27
Alignment explanation
Indices: 810308--810424 Score: 162
Period size: 27 Copynumber: 4.3 Consensus size: 27
810298 GTATGTTTGA
810308 ATGTATGTATGTATGCCTGATGAATGT
1 ATGTATGTATGTATGCCTGATGAATGT
* *
810335 TTGAATGTATGTATGCCTGATGAATGT
1 ATGTATGTATGTATGCCTGATGAATGT
* *
810362 ATGTATATATGCATGCCTGATGAATGT
1 ATGTATGTATGTATGCCTGATGAATGT
* * * *
810389 TTGAATGTTTGTATGCCTGATGAATGA
1 ATGTATGTATGTATGCCTGATGAATGT
810416 ATGTATGTA
1 ATGTATGTA
810425 CTGATGAACC
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (27 bp):
ATGTATGTATGTATGCCTGATGAATGT
Found at i:814779 original size:2 final size:2
Alignment explanation
Indices: 814726--814767 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
814716 TTCTATAACC
*
814726 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
814768 CAAAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:816807 original size:2 final size:2
Alignment explanation
Indices: 816800--816844 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
816790 TATTATTTTG
816800 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
816842 TA T
1 TA T
816845 TATTTATCCT
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:819061 original size:23 final size:23
Alignment explanation
Indices: 819035--819086 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
819025 TTGAGTATTG
819035 GTACTTCTTCTCTTAGGGTATCA
1 GTACTTCTTCTCTTAGGGTATCA
819058 GTACTTCTTCTCTTAGGGTATCA
1 GTACTTCTTCTCTTAGGGTATCA
819081 GTACTT
1 GTACTT
819087 TCCAGATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (23 bp):
GTACTTCTTCTCTTAGGGTATCA
Found at i:820291 original size:20 final size:20
Alignment explanation
Indices: 820255--820307 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
820245 TAATACAAAA
* *
820255 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
* *
820275 TTGCAATGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
820295 TCGCAACGCGATT
1 TCGCAACGCGATT
820308 TACATAGTGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:820899 original size:19 final size:19
Alignment explanation
Indices: 820863--820904 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
820853 ACAAGAGAAT
*
820863 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
* *
820882 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAA
820901 CGCA
1 CGCA
820905 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:820922 original size:19 final size:19
Alignment explanation
Indices: 820900--820972 Score: 93
Period size: 19 Copynumber: 4.1 Consensus size: 19
820890 GAAACCAAAA
*
820900 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
820919 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
820933 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
820952 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
820971 TC
1 TC
820973 AACCAAAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 30 0.65
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:822516 original size:63 final size:63
Alignment explanation
Indices: 822412--822541 Score: 251
Period size: 63 Copynumber: 2.1 Consensus size: 63
822402 GTTACGTGAT
*
822412 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGCCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
822475 GAGGCCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGCCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
822538 GAGG
1 GAGG
822542 TGTCTACTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.22
Consensus pattern (63 bp):
GAGGCCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:823190 original size:42 final size:42
Alignment explanation
Indices: 823114--823202 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
823104 GACTCGCCTG
* * *
823114 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
823156 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
823198 TCATC
1 TCATC
823203 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:824588 original size:14 final size:14
Alignment explanation
Indices: 824569--824604 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
824559 ATTGTTTAAT
824569 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
824583 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
824597 TGATTTGT
1 TGATTTGT
824605 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:824748 original size:14 final size:14
Alignment explanation
Indices: 824729--824785 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
824719 GCGAAATGAA
824729 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
824743 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
824762 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
824776 AAACGCAACG
1 AATCGCAACG
824786 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.25, T:0.07
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:824756 original size:33 final size:33
Alignment explanation
Indices: 824711--824800 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
824701 AAAAAGTACT
*
824711 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
824744 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
824777 AACGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
824801 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:824770 original size:19 final size:19
Alignment explanation
Indices: 824711--824771 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
824701 AAAAAGTACT
*
824711 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
824730 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
824744 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
824763 ATCGCAACG
1 ATCGCAACG
824772 AGAGAAACGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:824818 original size:19 final size:19
Alignment explanation
Indices: 824796--824939 Score: 69
Period size: 19 Copynumber: 8.7 Consensus size: 19
824786 CGAAATTAAA
824796 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
824815 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
824830 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
824848 TTCGCATTGCGA-----A-
1 TTCGCGTTGCGATTTTCAT
*
824861 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
824880 TTCGCATT--G---TTC-T
1 TTCGCGTTGCGATTTTCAT
*
824893 AT--CGTTGCG--TTTCAT
1 TTCGCGTTGCGATTTTCAT
824908 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
824927 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
824940 AGTAATTTCC
Statistics
Matches: 91, Mismatches: 15, Indels: 38
0.63 0.10 0.26
Matches are distributed among these distances:
11 3 0.03
13 13 0.14
14 15 0.16
15 2 0.02
16 3 0.03
17 11 0.12
18 1 0.01
19 43 0.47
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:824842 original size:33 final size:32
Alignment explanation
Indices: 824800--824921 Score: 148
Period size: 33 Copynumber: 3.9 Consensus size: 32
824790 ATTAAATTCG
*
824800 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CAT
*
824833 CGTTGCGATTTTCATTTCGCATTGCGAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCAT
824865 CGTTGCGATTTTCATTTCGCATT--G-TTCTAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-AT
*
824895 CGTTGCG--TTTCATTTCGCGTTGCGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATT
824922 TTCATTTCGC
Statistics
Matches: 79, Mismatches: 4, Indels: 14
0.81 0.04 0.14
Matches are distributed among these distances:
28 15 0.19
30 10 0.13
31 2 0.03
32 23 0.29
33 26 0.33
34 3 0.04
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCAT
Found at i:824947 original size:19 final size:19
Alignment explanation
Indices: 824906--824948 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
824896 GTTGCGTTTC
* ** *
824906 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATAGTA
824925 ATTTCGCATTGCGATAGTA
1 ATTTCGCATTGCGATAGTA
824944 ATTTC
1 ATTTC
824949 CGCGTTGATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (19 bp):
ATTTCGCATTGCGATAGTA
Found at i:827212 original size:12 final size:12
Alignment explanation
Indices: 827195--827219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
827185 TTCTTCGGGA
827195 CTTTTTCTTCTT
1 CTTTTTCTTCTT
827207 CTTTTTCTTCTT
1 CTTTTTCTTCTT
827219 C
1 C
827220 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:827428 original size:24 final size:24
Alignment explanation
Indices: 827394--827440 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
827384 CTGAAACATC
*
827394 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
*
827418 ATCAAAGTCCGGGTATTGACCAA
1 ATCAAAATCCGGGTATTGACCAA
827441 GGTCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAT
Found at i:827446 original size:24 final size:24
Alignment explanation
Indices: 827394--827447 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
827384 CTGAAACATC
* *
827394 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
827418 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
*
827442 GTCAAA
1 ATCAAA
827448 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:828520 original size:20 final size:20
Alignment explanation
Indices: 828495--828555 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
828485 GACATTCATT
828495 TGGCTATCGCAACGCGAAAA
1 TGGCTATCGCAACGCGAAAA
828515 TGGCTATCGCAACGCGAAAA
1 TGGCTATCGCAACGCGAAAA
*
828535 TGGCTATCGCAACGAGAAAA
1 TGGCTATCGCAACGCGAAAA
828555 T
1 T
828556 CGCAATGCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (20 bp):
TGGCTATCGCAACGCGAAAA
Found at i:828597 original size:14 final size:14
Alignment explanation
Indices: 828576--828644 Score: 84
Period size: 14 Copynumber: 4.6 Consensus size: 14
828566 AATGAAATCG
828576 CATTGCGATTTTCT
1 CATTGCGATTTTCT
* *
828590 CGTTGCGATTTTCG
1 CATTGCGATTTTCT
828604 CATTGCGATTTTCATTT
1 CATTGCGATTTTC---T
828621 GCATTGCGATTTTCT
1 -CATTGCGATTTTCT
828636 CATTGCGAT
1 CATTGCGAT
828645 AGCCATTTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
14 33 0.70
15 1 0.02
18 13 0.28
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.46
Consensus pattern (14 bp):
CATTGCGATTTTCT
Found at i:828628 original size:32 final size:28
Alignment explanation
Indices: 828573--828644 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 28
828563 CGAAATGAAA
*
828573 TCGCATTGCGATTTTCTCGTTGCGATTT
1 TCGCATTGCGATTTTCTCATTGCGATTT
828601 TCGCATTGCGATTTTCATTTGCATTGCGATTT
1 TCGCATTGCGATTTTC---T-CATTGCGATTT
*
828633 TCTCATTGCGAT
1 TCGCATTGCGAT
828645 AGCCATTTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 16 0.42
31 1 0.03
32 21 0.55
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (28 bp):
TCGCATTGCGATTTTCTCATTGCGATTT
Found at i:828652 original size:32 final size:33
Alignment explanation
Indices: 828592--828663 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
828582 GATTTTCTCG
***
828592 TTGCGATTTTCGCATTGCGATTTTCATTT-GCA
1 TTGCGATTTTCGCATTGCGATAGCCATTTCGCA
* *
828624 TTGCGATTTTCTCATTGCGATAGCCATTTCGCG
1 TTGCGATTTTCGCATTGCGATAGCCATTTCGCA
828657 TTGCGAT
1 TTGCGAT
828664 AGTCTGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 25 0.74
33 9 0.26
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCGCATTGCGATAGCCATTTCGCA
Found at i:828761 original size:14 final size:14
Alignment explanation
Indices: 828742--828778 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
828732 CATCAATTAA
828742 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
828756 ACAAATCATCTTTT
1 ACAAATCAACATTT
828770 ACAAATCAA
1 ACAAATCAA
828779 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:830653 original size:20 final size:19
Alignment explanation
Indices: 830618--830684 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
830608 GAAACTTAAA
830618 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
830637 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
830657 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
830676 ATCGCAACG
1 ATCGCAACG
830685 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:831285 original size:18 final size:18
Alignment explanation
Indices: 831259--831303 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
831249 GTCGATCAGA
*
831259 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
831277 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
831295 TGATGGCTC
1 TGATGGCTC
831304 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:832669 original size:20 final size:20
Alignment explanation
Indices: 832621--832679 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
832611 AATAGTTTCT
** *
832621 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
832641 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
832661 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
832680 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:832964 original size:21 final size:21
Alignment explanation
Indices: 832938--832977 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
832928 GGAGATAGAC
832938 GGATTTCGCCGGAGATGGGGA
1 GGATTTCGCCGGAGATGGGGA
*
832959 GGATTTCGTCGGAGATGGG
1 GGATTTCGCCGGAGATGGG
832978 TGAGAGAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.47, T:0.23
Consensus pattern (21 bp):
GGATTTCGCCGGAGATGGGGA
Found at i:833188 original size:20 final size:20
Alignment explanation
Indices: 833163--833235 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
833153 GATTATGTAT
833163 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
833183 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
833203 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
833223 TATCTCGTTGCGA
1 TATCGCGTTGCGA
833236 TTTTGTATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:833269 original size:20 final size:19
Alignment explanation
Indices: 833143--833277 Score: 90
Period size: 20 Copynumber: 6.7 Consensus size: 19
833133 CGCTTTGAAA
* *
833143 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGA-TA-GTAAT
* *
833164 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGT-AAT
* *
833184 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGT-AAT
*
833204 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAA-T
* * *
833224 ATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA--TAGTAAT
*
833245 ATCGCATTGCGATAGTCAAT
1 ATCGCGTTGCGATAGT-AAT
*
833265 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
833278 TTTCCCAATT
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
19 6 0.06
20 66 0.68
21 22 0.23
22 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATAGTAAT
Found at i:833939 original size:2 final size:2
Alignment explanation
Indices: 833934--833964 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
833924 AAAAAAATTC
833934 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
833965 TGACAATGGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:836223 original size:226 final size:227
Alignment explanation
Indices: 835828--836280 Score: 890
Period size: 226 Copynumber: 2.0 Consensus size: 227
835818 CTGATTTGGA
835828 TGGCAAAGAACAGAATGATGGATATCACACACAGTTCAATGACGAGACACTTTCTCGGGTAGATG
1 TGGCAAAGAACAGAATGATGGATATCACACACAGTTCAATGACGAGACACTTTCTCGGGTAGATG
835893 ATAGAAGTGGTAGAATCCACCAGACTGTTGATGTAGCAGAAGTTATTAGACGTTGGACACATGCA
66 ATAGAAGTGGTAGAATCCACCAGACTGTTGATGTAGCAGAAGTTATTAGACGTTGGACACATGCA
*
835958 CTGCAACGCATTCATAAACAGTCACTTCAGCTGGTATGCCGTTTTATTTTGTTTTTGTTAAGTCA
131 CTGCAACGCATTCATAAACAGTCACTTCAACTGGTATGCCGTTTTATTTTGTTTTTGTTAAGTCA
836023 GCTAGCTTAGTTTGTTTTAATACTTGGCCATC
196 GCTAGCTTAGTTTGTTTTAATACTTGGCCATC
836055 TGGCAAAGAACAGAATGATGGATATCAC-CACAGTTCAATGACGAGACACTTTCTCGGGTAGATG
1 TGGCAAAGAACAGAATGATGGATATCACACACAGTTCAATGACGAGACACTTTCTCGGGTAGATG
836119 ATAGAAGTGGTAGAATCCACCAGACTGTTGATGTAGCAGAAGTTATTAGACGTTGGACACATGCA
66 ATAGAAGTGGTAGAATCCACCAGACTGTTGATGTAGCAGAAGTTATTAGACGTTGGACACATGCA
836184 CTGCAACGCATTCATAAACAGTCACTTCAACTGGTATGCCGTTTTATTTTGTTTTTGTTAAGTCA
131 CTGCAACGCATTCATAAACAGTCACTTCAACTGGTATGCCGTTTTATTTTGTTTTTGTTAAGTCA
836249 GCTAGCTTAGTTTGTTTTAATACTTGGCCATC
196 GCTAGCTTAGTTTGTTTTAATACTTGGCCATC
836281 AGAATTATAC
Statistics
Matches: 225, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
226 197 0.88
227 28 0.12
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (227 bp):
TGGCAAAGAACAGAATGATGGATATCACACACAGTTCAATGACGAGACACTTTCTCGGGTAGATG
ATAGAAGTGGTAGAATCCACCAGACTGTTGATGTAGCAGAAGTTATTAGACGTTGGACACATGCA
CTGCAACGCATTCATAAACAGTCACTTCAACTGGTATGCCGTTTTATTTTGTTTTTGTTAAGTCA
GCTAGCTTAGTTTGTTTTAATACTTGGCCATC
Found at i:842536 original size:22 final size:22
Alignment explanation
Indices: 842510--842556 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
842500 GAGGAAAAAT
842510 AAATAATTA-ATAAAAAATATAA
1 AAAT-ATTATATAAAAAATATAA
* *
842532 AAATATTATTTAAAATATATAA
1 AAATATTATATAAAAAATATAA
842554 AAA
1 AAA
842557 GAAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATTATATAAAAAATATAA
Found at i:844829 original size:20 final size:20
Alignment explanation
Indices: 844793--844830 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
844783 ATCCTATTCC
**
844793 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
844813 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
844831 GTGAATCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:845027 original size:14 final size:15
Alignment explanation
Indices: 845003--845031 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
844993 CACATATAAC
845003 ATTTCTAAAAAATAT
1 ATTTCTAAAAAATAT
845018 ATTT-TAAAAAATAT
1 ATTTCTAAAAAATAT
845032 TTAATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTCTAAAAAATAT
Found at i:848915 original size:59 final size:59
Alignment explanation
Indices: 848793--848938 Score: 152
Period size: 59 Copynumber: 2.4 Consensus size: 59
848783 AATACAATGA
* * * *
848793 ATAGTCGGGTGACCATGTTGTATCTTTTGATAGCCAGAAGACTTAAAAAAGCAACATCTT
1 ATAGTCGGG-GACCATTTTGTAACTTTTAATAGCCAGAAGACTTAAAAAAGCAACATCAT
* * * *
848853 ATAGTCGGGGACCATTTTGTAACTTTTAATAGTCAGATGACTTAATAAAA-TAATATCAT
1 ATAGTCGGGGACCATTTTGTAACTTTTAATAGCCAGAAGACTTAA-AAAAGCAACATCAT
* *
848912 ATAGTTGATGGACCATTTATGT-ACTTT
1 ATAGTCG-GGGACCATTT-TGTAACTTT
848939 ACCCAACTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 43 0.59
60 27 0.37
61 3 0.04
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (59 bp):
ATAGTCGGGGACCATTTTGTAACTTTTAATAGCCAGAAGACTTAAAAAAGCAACATCAT
Found at i:850534 original size:27 final size:27
Alignment explanation
Indices: 850467--850534 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
850457 TAAAAAGCTA
*
850467 TATTTGTAATATTAAAAAATATTTATT
1 TATTTGTAATAATAAAAAATATTTATT
*
850494 TAATTTTTAA-AATAAAAAATATTTATT
1 T-ATTTGTAATAATAAAAAATATTTATT
*
850521 TATTTGAAATAATA
1 TATTTGTAATAATA
850535 TTATTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 6 0.17
27 22 0.63
28 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (27 bp):
TATTTGTAATAATAAAAAATATTTATT
Found at i:850705 original size:23 final size:24
Alignment explanation
Indices: 850659--850710 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
850649 TAATTTAAAA
* *
850659 ATAATAATATTTCAAATAATTAAT
1 ATAATAATATTTCAAAGAAATAAT
*
850683 -TAATATTATTTCAAAGAAATAAT
1 ATAATAATATTTCAAAGAAATAAT
850706 ATAAT
1 ATAAT
850711 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
ATAATAATATTTCAAAGAAATAAT
Found at i:854705 original size:2 final size:2
Alignment explanation
Indices: 854698--854728 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
854688 AATTTGTTGA
854698 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
854729 AAAGAAGGGG
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:861145 original size:24 final size:24
Alignment explanation
Indices: 861113--861163 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
861103 TCCACAAACA
861113 TCAAATAATGTCATGACCGTAACG
1 TCAAATAATGTCATGACCGTAACG
861137 TCAAATAATGTCATGACCGTAACG
1 TCAAATAATGTCATGACCGTAACG
861161 TCA
1 TCA
861164 GTGATGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (24 bp):
TCAAATAATGTCATGACCGTAACG
Found at i:873586 original size:20 final size:20
Alignment explanation
Indices: 873561--873598 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
873551 ATAAATGAGT
873561 TATTATATGGGTGAAAATGA
1 TATTATATGGGTGAAAATGA
* *
873581 TATTATTTTGGTGAAAAT
1 TATTATATGGGTGAAAAT
873599 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (20 bp):
TATTATATGGGTGAAAATGA
Found at i:873604 original size:20 final size:20
Alignment explanation
Indices: 873559--873604 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
873549 TTATAAATGA
873559 GTTATTATATGGGTGAAAAT
1 GTTATTATATGGGTGAAAAT
* * *
873579 GATATTATTTTGGTGAAAAT
1 GTTATTATATGGGTGAAAAT
*
873599 TTTATT
1 GTTATT
873605 TTTATAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (20 bp):
GTTATTATATGGGTGAAAAT
Found at i:880943 original size:23 final size:24
Alignment explanation
Indices: 880912--880957 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
880902 AATAGATGAA
* *
880912 AAATTTATAAAATTTA-AAAAAAC
1 AAATATATAAAATATATAAAAAAC
880935 AAATATATAAAATATATAAAAAA
1 AAATATATAAAATATATAAAAAA
880958 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATATATAAAATATATAAAAAAC
Found at i:881819 original size:15 final size:15
Alignment explanation
Indices: 881799--881837 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
881789 TCGGGCCGGG
881799 TAAATATATATAA-AT
1 TAAATATATA-AATAT
881814 TAAATATATAAATAT
1 TAAATATATAAATAT
*
881829 TATATATAT
1 TAAATATAT
881838 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATATATAAATAT
Found at i:882026 original size:48 final size:48
Alignment explanation
Indices: 881952--882043 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
881942 GATTATTAAA
* * * *
881952 CCCGTCCCCGTCTCCGTTTAAGATAAATGGTTTTTCTCCGTCCCCGTC
1 CCCGTCCCCATCCCCGTTTAAGATAAACGATTTTTCTCCGTCCCCGTC
*
882000 CCCGTCCCCATCCCCGTTT-AGCATAAACGATTTTTTTCCGTCCC
1 CCCGTCCCCATCCCCGTTTAAG-ATAAACGATTTTTCTCCGTCCC
882044 TGTTTAATTC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 2 0.05
48 36 0.95
ACGTcount: A:0.14, C:0.39, G:0.14, T:0.33
Consensus pattern (48 bp):
CCCGTCCCCATCCCCGTTTAAGATAAACGATTTTTCTCCGTCCCCGTC
Found at i:888538 original size:16 final size:16
Alignment explanation
Indices: 888517--888552 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
888507 TAACAATTTT
*
888517 ATTAATAAGGAATGTG
1 ATTAATAAGGAATATG
888533 ATTAATAAGGAATATG
1 ATTAATAAGGAATATG
888549 ATTA
1 ATTA
888553 GTGTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (16 bp):
ATTAATAAGGAATATG
Found at i:888699 original size:61 final size:60
Alignment explanation
Indices: 888619--888737 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 60
888609 CAGAATAAAG
* * * * * *
888619 GTCATAATTTGGGGTTGAAATCAAAATGTTTAAAGGTTTTGAGGATTAATTTGAAATGATA
1 GTCATAATTTAGGGATGAAATCAAAATATTTAAAAGTTTAG-GGATCAATTTGAAATGATA
* **
888680 GTCATAGTTTAGGGATGAAATTGAAATATTTAAAAGTTTAGGGATCAATTTGAAATGA
1 GTCATAATTTAGGGATGAAATCAAAATATTTAAAAGTTTAGGGATCAATTTGAAATGA
888738 GAATCATACT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
60 16 0.33
61 33 0.67
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (60 bp):
GTCATAATTTAGGGATGAAATCAAAATATTTAAAAGTTTAGGGATCAATTTGAAATGATA
Found at i:889901 original size:24 final size:24
Alignment explanation
Indices: 889857--889910 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
889847 CGTTAAAATG
*
889857 ATAAACGAACACACACGAACG-AA
1 ATAAACGAACACACAAGAACGTAA
889880 CATAAACGAACACA-AAGAAACGTAA
1 -ATAAACGAACACACAAG-AACGTAA
889905 ATAAAC
1 ATAAAC
889911 ATAAACGGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 2 0.07
24 23 0.85
25 2 0.07
ACGTcount: A:0.59, C:0.22, G:0.11, T:0.07
Consensus pattern (24 bp):
ATAAACGAACACACAAGAACGTAA
Found at i:892363 original size:42 final size:40
Alignment explanation
Indices: 892300--892932 Score: 412
Period size: 42 Copynumber: 15.1 Consensus size: 40
892290 TTTCCAAATT
*
892300 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
* *
892340 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
* * ** *
892382 TGTTGCGATTGTTGAAGTTCGCGTTGCGATTTATTCCAAGTT--
1 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCG
* *
892424 CGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTC--GTTGCGA--TAGTCCAAGTTCG
* * *
892466 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--
1 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCG
* *
892508 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCG
* **
892552 TGTTGCGATAGTCCAAGTTCGTTGCGATAGTTGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
* * *
892592 CGTTGCGATTTATTCCAAATTCGTTGCGATGGTCCAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
* *
892634 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT--
1 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCG
* * *
892676 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT--
1 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCG
* * *
892718 CGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
* * *
892760 CGTTGCGATTTATTCTAAATTCGTTGCGATAGTCCAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
* *
892802 CGTTGCGATTTATTCCAAATTCGTGTTGCGATAGTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTC--GTTGCGATAGTCCAAGTTCG
* * * *
892844 CGTTGCGATAGTCGAAGTTCGCGTTACGATTTATTCCAAATT--
1 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCG
* *
892886 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCG
892930 CGT
1 CGT
892933 CCAAATATTG
Statistics
Matches: 512, Mismatches: 51, Indels: 56
0.83 0.08 0.09
Matches are distributed among these distances:
40 62 0.12
42 382 0.75
44 68 0.13
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
Found at i:892417 original size:63 final size:62
Alignment explanation
Indices: 892284--892929 Score: 537
Period size: 63 Copynumber: 10.3 Consensus size: 62
892274 ACTATCGCAA
*
892284 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTC-GTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGGTTGCGATAGTTGAAGTTCGCGT
*
892343 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTGTTGCGATTGTTGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG-GTTGCGATAGTTGAAGTTCGCGT
* * *
892406 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGTGTTGCGATTTA-TTCCAAGTT--CG
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG-GTTGCGA--TAGTT-GAAGTTCGCG
892468 T
62 T
* * * * * **
892469 TGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC-GTTGCGATAGTCCAAGTTCGCG
1 TGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCGGTTGCGATAGTTGAAGTTCGCG
892531 T
62 T
892532 TGCGATTTATTCCAAATTCGTGTTGCGATAGTCCAAGTTC-GTTGCGATAGTTGAAGTTCGCGT
1 TGCGATTTATTCCAAATTC--GTTGCGATAGTCCAAGTTCGGTTGCGATAGTTGAAGTTCGCGT
* *
892595 TGCGATTTATTCCAAATTCGTTGCGATGGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG-GTTGCGATAGTTGAAGTTCGCGT
* * * *
892658 TGCGATTTATTCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGCGATTTA-TTCCAAGTT--CG
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG-GTTGCGA--TAGTT-GAAGTTCGCG
892720 T
62 T
* * * * *
892721 TGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTA-TTCTAAATT--CG
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG-GTTGCGA--TAGTT-GAAGTTCGCG
892783 T
62 T
* * * * **
892784 TGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTGTTGCGATAGTCCAAGTT--C
1 TGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCG-GTTGCGATAGTTGAAGTTCGC
892845 GT
61 GT
* * * * * * *
892847 TGCGA--TAGTCGAAGTTCGCGTTACGATTTATTCCAAATTC-GTTGCGATAGTCGAAGTTCGCG
1 TGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCGGTTGCGATAGTTGAAGTTCGCG
892909 T
62 T
*
892910 TGCGATTTATTCCAAGTTCG
1 TGCGATTTATTCCAAATTCG
892930 CGTCCAAATA
Statistics
Matches: 510, Mismatches: 45, Indels: 60
0.83 0.07 0.10
Matches are distributed among these distances:
59 5 0.01
60 2 0.00
61 91 0.18
62 1 0.00
63 344 0.67
64 4 0.01
65 63 0.12
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (62 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGGTTGCGATAGTTGAAGTTCGCGT
Found at i:892435 original size:105 final size:103
Alignment explanation
Indices: 892284--892929 Score: 899
Period size: 105 Copynumber: 6.2 Consensus size: 103
892274 ACTATCGCAA
892284 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCG
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCG
* *
892347 ATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTGT
66 ATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* * * * *
892385 TGCGA-TTGTT-GAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGTGT
1 TGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
892448 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
62 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* * * *
892490 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGT
* * *
892555 TGCGA--TAGTCCAAGTTCGTTGCGATAGTTGAAGTTCGCGT
62 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
*
892595 TGCGATTTATTCCAAATTCGTTGCGATGGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTG
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTG
* *
892660 CGATTTATTCCAAGTTCATTGCGATAGTCGAAGTTCGCGT
64 CGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* * *
892700 TGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTG
1 TGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTG
* *
892765 CGATTTATTCTAAATTCGTTGCGATAGTCCAAGTTCGCGT
64 CGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
*
892805 TGCGATTTATTCCAAATTCGTGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTA
1 TGCGATTTATTCCAAATTC--GTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTG
892870 CGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
64 CGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
*
892910 TGCGATTTATTCCAAGTTCG
1 TGCGATTTATTCCAAATTCG
892930 CGTCCAAATA
Statistics
Matches: 489, Mismatches: 39, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
101 11 0.02
102 2 0.00
103 36 0.07
105 398 0.81
106 4 0.01
107 38 0.08
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (103 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCG
ATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:893171 original size:34 final size:30
Alignment explanation
Indices: 893133--893201 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
893123 TTGATATAAC
893133 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTA
* *
893167 AATTT-ACAATATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTA
893196 AATTTA
1 AATTTA
893202 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 9 0.28
30 12 0.38
31 5 0.16
33 1 0.03
34 5 0.16
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTA
Found at i:893321 original size:21 final size:21
Alignment explanation
Indices: 893292--893357 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
893282 TTCAAGATTG
*
893292 CCCAAGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
893313 CCCAGGGGGTACAGATACCCCC
1 CCCAGGGGGTACAGAT-TCCCC
*
893335 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
893356 CC
1 CC
893358 TGTATAAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 21 0.52
22 19 0.47
ACGTcount: A:0.20, C:0.42, G:0.26, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:893423 original size:20 final size:21
Alignment explanation
Indices: 893383--893426 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
893373 AACAGAATGT
893383 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
893404 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
893425 CC
1 CC
893427 TGTTCAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.45, G:0.27, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:893488 original size:21 final size:21
Alignment explanation
Indices: 893462--893503 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
893452 ATTTGAATAT
*
893462 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
893483 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
893504 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:893566 original size:21 final size:21
Alignment explanation
Indices: 893532--893571 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
893522 TTTGAGTAGA
*
893532 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
893554 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
893572 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:894274 original size:21 final size:20
Alignment explanation
Indices: 894235--894289 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
894225 CGTTGCGATT
*
894235 TTGGACTATCGCA-GCGAAC
1 TTGGACTATCGAACGCGAAC
894254 TTGGACTATCGTAACGCGAAC
1 TTGGACTATCG-AACGCGAAC
*
894275 TTAGACTATCGAACG
1 TTGGACTATCGAACG
894290 AATTTGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 11 0.34
20 5 0.16
21 16 0.50
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
TTGGACTATCGAACGCGAAC
Found at i:894386 original size:19 final size:19
Alignment explanation
Indices: 894359--894401 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
894349 CGATACCGGA
*
894359 GATCACGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
894378 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
894397 GATCG
1 GATCG
894402 TATTGCGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (19 bp):
GATCGCGTTGCGAATTATC
Found at i:894407 original size:19 final size:19
Alignment explanation
Indices: 894366--894409 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
894356 GGAGATCACG
*
894366 TTGCGAATTATCGATCGCG
1 TTGCGAATTATCGATCGCA
*
894385 TTGCGAATTATCGATCGTA
1 TTGCGAATTATCGATCGCA
894404 TTGCGA
1 TTGCGA
894410 TTTAGTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (19 bp):
TTGCGAATTATCGATCGCA
Found at i:900188 original size:19 final size:19
Alignment explanation
Indices: 900143--900189 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
900133 AAACCTTTGA
*
900143 ATAACACGACATCGAATGC
1 ATAACACTACATCGAATGC
900162 ATAACACTACATCGAATGC
1 ATAACACTACATCGAATGC
900181 ATAACACTA
1 ATAACACTA
900190 ACGATTCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.19
Consensus pattern (19 bp):
ATAACACTACATCGAATGC
Found at i:900460 original size:14 final size:14
Alignment explanation
Indices: 900441--900470 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
900431 CTACATTCGA
900441 CTGCTATCGAACCT
1 CTGCTATCGAACCT
900455 CTGCTATCGAACCT
1 CTGCTATCGAACCT
900469 CT
1 CT
900471 CATACCGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (14 bp):
CTGCTATCGAACCT
Found at i:908840 original size:13 final size:13
Alignment explanation
Indices: 908822--908846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
908812 TCTTCGGTGA
908822 TTAATTAATTAAT
1 TTAATTAATTAAT
908835 TTAATTAATTAA
1 TTAATTAATTAA
908847 ACATAAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAATTAATTAAT
Found at i:909126 original size:18 final size:18
Alignment explanation
Indices: 909105--909140 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
909095 TTACTCCATC
909105 ATTAATATTAAAAATATA
1 ATTAATATTAAAAATATA
909123 ATTAATATTAAAAATATA
1 ATTAATATTAAAAATATA
909141 TGTTATCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTAATATTAAAAATATA
Found at i:909821 original size:13 final size:13
Alignment explanation
Indices: 909803--909827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
909793 TATTCGGTGA
909803 TTAATTAATTAAT
1 TTAATTAATTAAT
909816 TTAATTAATTAA
1 TTAATTAATTAA
909828 ACATAAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAATTAATTAAT
Found at i:910147 original size:981 final size:961
Alignment explanation
Indices: 908162--910025 Score: 3077
Period size: 981 Copynumber: 1.9 Consensus size: 961
908152 CATCATTAAT
* * * * **
908162 ATTAAAAATATATGTTATCCGTTGTGTTTATATTTTAAAAATATATATATCTTAAGATAAAATTG
1 ATTAAAAAGATATGTCAGCGGTTGTCCTTATATTTTAAAAATATATATATCTTAAGATAAAATTG
908227 AAAATTATTATAATGTTAAACAAATTAAACTTTTTAATATTTGAAGAGAAACTCCAATTCTTAAT
66 AAAATTATTATAATGTTAAACAAATTAAACTTTTTAATATTTGAAGAGAAACTCCAATTCTTAAT
*
908292 TTTTTTAATTCAATACCTTTATTTCAATCTTTGATCATTTTCGATCACTCATCCATCGTCGTTCA
131 TTTTTTAATTCAATACCTTTATTTCAATCTTCGATCA---TCGATCACTCATCCATCGTCGTTCA
* * * * *
908357 CCCAATTATCTCGTCATCCTTGTTATCATCTCAACTCTGCTAAAATTCTCAACTCTCAAGTTTAA
193 CCCAATAATCTCGTCATCCTTGTCATCATCTCAAATCTGCCAAAATTCTCAACTCTCAAATTTAA
* *
908422 ATCTCTAAAATCCCAAGTACTTAATTCCTAAACCCTACTCAATGATCATTGGTCGCTGATAGATC
258 ATCTCTAAAATCCCAAATACTTAATTCCTAAACCCTAATCAATGATCATTGGTCGCTGATAGATC
908487 TTCGGGCAAAAACAACAACCGCGACTCCTCCACGTTCATTTGTGGCATCGGCGGTGATTGACCGA
323 TTCGGGCAAAAACAACAACCGCGACTCCTCCACGTTCATTTGTGGCATCGGCGGTGATTGACCGA
*
908552 CTAGGTTGGTGGCAGGCGGCAATAATAGAGGATTGAAATTAGGGATTCTAAAACATTTGGGTTTA
388 CTAGGTTGGTGGCAGGCGGCAATAATAAAGGATTGAAATTAGGGATTCTAAAACATTTGGGTTTA
*
908617 TTAAAAATTAAGGTTTTTAATAATAATATTTTAAAGTTCTTTAAAAAAAAATTTAAATACAACAC
453 TTAAAAATTAAGGTTTTTAATAATAATATTTTAAAGTTCTTTAAAAAAAAA-TAAAATACAACAC
*
908682 TTATGAGATAACGAACCTTTTAATGTATATATATATATATTACGATTAAAGCATTAAAAATAACA
517 TTATGAGATAACGAACCTTTTAATATATATATATATATATTACGATTAAAGCATTAAAAATAACA
908747 TTTACAAAAATTGCATTAAAAATTAGCAATAAAATCAACCTTGATATACTTATATTTTATTATGT
582 TTTACAAAAATTGCATTAAAAATTAGCAATAAAATCAACCTTGATATACTTATATTTTATTATGT
*
908812 TCTTCGGTGATTAATTAATTAATTTAATTAATTAAACATAAGATTGTTGACGTTCTTTTTTAATA
647 TATTCGGTGATTAATTAATTAATTTAATTAATTAAACATAAGATTGTTGACGTTCTTTTTTAATA
908877 CTTCTCACCGACGTCTAGGCGTTTGACTCTGCCATGCAATGGCTAGCTGCCACGTCTTCTTTCGA
712 CTTCTCACCGACGTCTAGGCGTTTGACTCTGCCATGCAATGGCTAGCTGCCACGTCTTCTTTCGA
908942 TTGTACTGTTTTCCTTTACTCTACCAGCTTTACCTTGTGATGACGTGTCATGCTTCCATTTGAGA
777 TTGTACTGTTTTCCTTTACTCTACCAGCTTTACCTTGTGATGACGTGTCATGCTTCCATTTGAGA
***
909007 GCGATTGCCGGTTTTTTTTATAACAAAAAAGTTATATTCCGGTAATTCTTCTTTTTATAACCAAG
842 GCGATTGCCGGTTTTTTTTATAACAAAAAAGTTATATTCCGGTAATTC-TCGAATTATAACCAAG
* * * * * * *
909072 TTAGGGCGGAATATTATAAGTATTTACTCCATCATTAATATTAAAAATATAATTAAT
906 TTAAGGCGAAACATTATAAGTATTTA-TCCATCATTAATAGTAAAAATAGAATGAAC
* * * * **
909129 ATTAAAAATATATGTTATCTGTTGTGTTTATATTTTAAAAATATATATATCTTAAGATAAAATTG
1 ATTAAAAAGATATGTCAGCGGTTGTCCTTATATTTTAAAAATATATATATCTTAAGATAAAATTG
909194 AAAATTATTATAATGTTAAACAAATTAAAACTTTTTTAATATTTGAAGAGAAACTCCAAATTCTT
66 AAAATTATTATAATGTTAAACAAATT-AAAC-TTTTTAATATTTGAAGAGAAACTCC-AATTCTT
* *
909259 AAATTTTTTTATTTCAATACCTTTATTTCAATCTTCGATCA-CGATCACTCATCCGTCGTCGTTC
128 -AATTTTTTTAATTCAATACCTTTATTTCAATCTTCGATCATCGATCACTCATCCATCGTCGTTC
909323 ACCCAATAATCACTCGTCATCCTTGTCATCATCTCAAATCTGCCAAAATTCTCAACTCTCAAAAT
192 ACCCAATAAT--CTCGTCATCCTTGTCATCATCTCAAATCTGCCAAAATTCTCAACTCTC-AAAT
*
909388 TTAAATCTCTAAAATCCCAAATACTTAATTCCTAAACTCTAATCAATGATCATTGGTCGCTGATA
254 TTAAATCTCTAAAATCCCAAATACTTAATTCCTAAACCCTAATCAATGATCATTGGTCGCTGATA
909453 GATCTTCGGGCAAAAACAACAACCGCGACTCCTCCACGTTCATTTGTGGCATCGGCGGTGATTGA
319 GATCTTCGGGCAAAAACAACAACCGCGACTCCTCCACGTTCATTTGTGGCATCGGCGGTGATTGA
*
909518 CCGACTAGGTTGGTGGCAGGCGGCGATAATAAAGGATTGAAATTAGGGATTCTAAAACATTTGGG
384 CCGACTAGGTTGGTGGCAGGCGGCAATAATAAAGGATTGAAATTAGGGATTCTAAAACATTTGGG
*
909583 TTTATTAAAAAATTAAGGTTTTTTAATAATAATATTTTAAAGTTATTTTTAAATAATTTAAAA-A
449 TTTATT-AAAAATTAAGG-TTTTTAATAATAATATTTTAAAG-T-TCTTTAAA-AA---AAAATA
909647 AAATACAACACTTATGAGATAACGAACCTTTTAATATATATATATATATATTACGATTAAAGCAT
506 AAATACAACACTTATGAGATAACGAACCTTTTAATATATATATATATATATTACGATTAAAGCA-
909712 TTAAAATAATAACATTTACAAAAATTGCATTATAAAAATTAGCAATAAAATCAACCTTGATATAC
570 TT-AAA-AATAACATTTACAAAAATTGCA-T-TAAAAATTAGCAATAAAATCAACCTTGATATAC
909777 TTATATTTTATTATGTTATTCGGTGATTAATTAATTAATTTAATTAATTAAACATAAGATTGTTG
631 TTATATTTTATTATGTTATTCGGTGATTAATTAATTAATTTAATTAATTAAACATAAGATTGTTG
909842 ACGTTCTTTTTTAATACTTCTCACCGACGTCTAGGCGTTTGACTCTGCCATGCAATGGCTAGCTG
696 ACGTTCTTTTTTAATACTTCTCACCGACGTCTAGGCGTTTGACTCTGCCATGCAATGGCTAGCTG
909907 CCACGTCTTCTTTCGATTGTACTGTTTTCCTTTACTCTACCAGCTTTACCCTTGTTGATGACGTG
761 CCACGTCTTCTTTCGATTGTACTGTTTTCCTTTACTCTACCAGCTTTA-CCTTG-TGATGACGTG
909972 TCATGCTTCCATTTGTTAGAGCGATTGCCGGTTTTATTTTATAAC-AAAAAGTTA
824 TCATGCTTCCATTTG--AGAGCGATTGCCGGTTTT-TTTTATAACAAAAAAGTTA
910026 ATTGCACTGG
Statistics
Matches: 854, Mismatches: 18, Indels: 32
0.94 0.02 0.04
Matches are distributed among these distances:
967 121 0.14
968 4 0.00
969 70 0.08
970 206 0.24
971 49 0.06
972 23 0.03
973 1 0.00
974 7 0.01
975 2 0.00
976 63 0.07
977 2 0.00
978 7 0.01
979 22 0.03
980 1 0.00
981 210 0.25
982 5 0.01
983 25 0.03
985 27 0.03
986 9 0.01
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (961 bp):
ATTAAAAAGATATGTCAGCGGTTGTCCTTATATTTTAAAAATATATATATCTTAAGATAAAATTG
AAAATTATTATAATGTTAAACAAATTAAACTTTTTAATATTTGAAGAGAAACTCCAATTCTTAAT
TTTTTTAATTCAATACCTTTATTTCAATCTTCGATCATCGATCACTCATCCATCGTCGTTCACCC
AATAATCTCGTCATCCTTGTCATCATCTCAAATCTGCCAAAATTCTCAACTCTCAAATTTAAATC
TCTAAAATCCCAAATACTTAATTCCTAAACCCTAATCAATGATCATTGGTCGCTGATAGATCTTC
GGGCAAAAACAACAACCGCGACTCCTCCACGTTCATTTGTGGCATCGGCGGTGATTGACCGACTA
GGTTGGTGGCAGGCGGCAATAATAAAGGATTGAAATTAGGGATTCTAAAACATTTGGGTTTATTA
AAAATTAAGGTTTTTAATAATAATATTTTAAAGTTCTTTAAAAAAAAATAAAATACAACACTTAT
GAGATAACGAACCTTTTAATATATATATATATATATTACGATTAAAGCATTAAAAATAACATTTA
CAAAAATTGCATTAAAAATTAGCAATAAAATCAACCTTGATATACTTATATTTTATTATGTTATT
CGGTGATTAATTAATTAATTTAATTAATTAAACATAAGATTGTTGACGTTCTTTTTTAATACTTC
TCACCGACGTCTAGGCGTTTGACTCTGCCATGCAATGGCTAGCTGCCACGTCTTCTTTCGATTGT
ACTGTTTTCCTTTACTCTACCAGCTTTACCTTGTGATGACGTGTCATGCTTCCATTTGAGAGCGA
TTGCCGGTTTTTTTTATAACAAAAAAGTTATATTCCGGTAATTCTCGAATTATAACCAAGTTAAG
GCGAAACATTATAAGTATTTATCCATCATTAATAGTAAAAATAGAATGAAC
Found at i:924053 original size:4 final size:4
Alignment explanation
Indices: 924021--924060 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
924011 TAATTTGCCC
* * *
924021 TAAA TAAA TCAA TAAA CAAA TATA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
924061 GTTTCTTGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:928121 original size:14 final size:14
Alignment explanation
Indices: 928102--928143 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
928092 CATCCAAACT
928102 CTTTAAATCTTAAA
1 CTTTAAATCTTAAA
928116 CTTTAAATCTTAAA
1 CTTTAAATCTTAAA
*
928130 CCTTAAATCTTAAA
1 CTTTAAATCTTAAA
928144 TCCTAAACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (14 bp):
CTTTAAATCTTAAA
Found at i:928141 original size:7 final size:7
Alignment explanation
Indices: 928104--928150 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
928094 TCCAAACTCT
928104 TTAAATC
1 TTAAATC
928111 TTAAA-C
1 TTAAATC
928117 TTTAAATC
1 -TTAAATC
*
928125 TTAAACC
1 TTAAATC
928132 TTAAATC
1 TTAAATC
928139 TTAAATC
1 TTAAATC
*
928146 CTAAA
1 TTAAA
928151 CCAACGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 1 0.03
7 33 0.94
8 1 0.03
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (7 bp):
TTAAATC
Found at i:929192 original size:16 final size:17
Alignment explanation
Indices: 929142--929193 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
929132 ATAAAAAACA
929142 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
929159 GA-TT-AAA-TTATGAGT
1 AATTTGAAAGTTA-GAGT
929174 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
929190 AATT
1 AATT
929194 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:929523 original size:21 final size:21
Alignment explanation
Indices: 929485--929524 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
929475 ATTGACATGG
*
929485 TCACTTTTATTTCATAAATAT
1 TCACTTTTATGTCATAAATAT
929506 TCACTTTTA-GTCATTAAAT
1 TCACTTTTATGTCA-TAAAT
929525 TTAAAAAATA
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:0.33, C:0.15, G:0.03, T:0.50
Consensus pattern (21 bp):
TCACTTTTATGTCATAAATAT
Found at i:931347 original size:27 final size:27
Alignment explanation
Indices: 931309--931363 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
931299 GTCAAAAAAA
931309 CCATGCCACTTAGCTCTCGCAGTTCAG
1 CCATGCCACTTAGCTCTCGCAGTTCAG
931336 CCATGCCACTTAGCTCTCGCAGTTCAG
1 CCATGCCACTTAGCTCTCGCAGTTCAG
931363 C
1 C
931364 TTTAAATTAA
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:0.38, G:0.18, T:0.25
Consensus pattern (27 bp):
CCATGCCACTTAGCTCTCGCAGTTCAG
Found at i:935064 original size:60 final size:60
Alignment explanation
Indices: 934994--935125 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
934984 AGTATAGGGT
*
934994 AAAA-TATAAAATGA-CTTTCTAACTATA-ATGTATTGTTTTATTAAATCTTTCAACTATTA
1 AAAATTATAAAATGATCTTT-TAACTATAGA-GTATTGTTTTATTAAATCATTCAACTATTA
* * * * *
935053 AAAATTATAAAATGATCTTTTAACTATAGAGTGTTGTTTTGTTGAGTCATTCGACTATTA
1 AAAATTATAAAATGATCTTTTAACTATAGAGTATTGTTTTATTAAATCATTCAACTATTA
*
935113 AAAATTACAAAAT
1 AAAATTATAAAAT
935126 ATCACCTAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 4 0.06
60 54 0.86
61 5 0.08
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (60 bp):
AAAATTATAAAATGATCTTTTAACTATAGAGTATTGTTTTATTAAATCATTCAACTATTA
Found at i:936285 original size:337 final size:335
Alignment explanation
Indices: 935668--936316 Score: 1005
Period size: 337 Copynumber: 1.9 Consensus size: 335
935658 ACTTAGCGTG
* *
935668 TTAGTACCTAAATTTTCAATTTTGGTCAATTTTAATACCTAAACTTTCAAAAAAAATCAAAACTT
1 TTAGTACCTAAATTATCAATTTTGCTCAATTTTAATACCTAAACTTTCAAAAAAAATCAAAACTT
* *
935733 AATGTTAAATTTTGAACAATGATACTAAAATGAAACAACAACTAAACTTTAGATATGATTTTTTA
66 AATGTTAAATTTTGAACAATGATACTAAAATGAAACAAAAACTAAACTTTAGATATGATTTTTAA
* * * *
935798 AAAATTCAAAGTTTTGGTACTAAAAGAGACCAAAATTGAAGTTTGGGTACTAAACACGTAATTTA
131 AAAATTCAAAGTTTAGGTACTAAAAGAGACCAAAATTGAAATTTGAGTACTAAACACATAATTTA
* * *
935863 CCCAAATTTTTAACTATTGTGTTAGCGATCAGATGATTCGATCGTCCAATCATTAAAATTTAAGG
196 CCCAAATTTTTAACTATTGTGTTAGCGATCAGAAGATTCGATCCTCCAATCATTAAAATTCAAGG
*
935928 TTATAAGTTTTGCTTGTACGTATACATACATACAACAAAATTTGGCAAACTTAACACGTTATAAA
261 TTATAAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTTAACACGTTATAAA
935993 CTTAAATCAT
326 CTTAAATCAT
* *
936003 TTAGTACTTAAATTATCAATTTTGCTCTATTTTAATACCTAAACTTTCAAAAAAATATCAAAACT
1 TTAGTACCTAAATTATCAATTTTGCTCAATTTTAATACCTAAACTTTCAAAAAAA-ATCAAAACT
* * * * *
936068 TAATGTTAAATTTTGAACAATGGTACTAAAATGAAATAAAAATTGAACTTTAGATATGGTTTTTA
65 TAATGTTAAATTTTGAACAATGATACTAAAATGAAACAAAAACTAAACTTTAGATATGATTTTTA
* * * * *
936133 AAAACATTCAAAGTTTAGGTACTGAAAGGGATCAAAATTGATAATTTTAGTACTAAACGCATAAT
130 AAAA-ATTCAAAGTTTAGGTACTAAAAGAGACCAAAATTGA-AATTTGAGTACTAAACACATAAT
* *
936198 TTA-CTATAATTTTTAACTATTGTGTTAGCGAT-AGAAGATTCGATCCTCCAGTCATTAAAATTC
193 TTACCCA-AATTTTTAACTATTGTGTTAGCGATCAGAAGATTCGATCCTCCAATCATTAAAATTC
*
936261 GAGGTTATAAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTT
257 AAGGTTATAAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTT
936317 TTCGCCAGAT
Statistics
Matches: 283, Mismatches: 27, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
335 51 0.18
336 71 0.25
337 115 0.41
338 46 0.16
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (335 bp):
TTAGTACCTAAATTATCAATTTTGCTCAATTTTAATACCTAAACTTTCAAAAAAAATCAAAACTT
AATGTTAAATTTTGAACAATGATACTAAAATGAAACAAAAACTAAACTTTAGATATGATTTTTAA
AAAATTCAAAGTTTAGGTACTAAAAGAGACCAAAATTGAAATTTGAGTACTAAACACATAATTTA
CCCAAATTTTTAACTATTGTGTTAGCGATCAGAAGATTCGATCCTCCAATCATTAAAATTCAAGG
TTATAAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTTAACACGTTATAAA
CTTAAATCAT
Found at i:938157 original size:2 final size:2
Alignment explanation
Indices: 938150--938174 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
938140 AACTTGAATA
938150 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
938175 TACCCGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:943305 original size:322 final size:321
Alignment explanation
Indices: 942710--943336 Score: 943
Period size: 322 Copynumber: 2.0 Consensus size: 321
942700 TGTTAGTACC
* *
942710 TAAATTTTCAATTTTGGTCCATTTTAATACCTAAACTTTCAAAAAAAAATCAAAACTTAATGTTA
1 TAAATTATCAATTTTGCTCCATTTTAATACCTAAACTTTCAAAAAAAAATCAAAACTTAATGTTA
* **
942775 AATTTTGAACAATGATACTAAAATGAAACAACAACTAAACTTTAGATATGATTTTTTTAAAATTC
66 AATTTTGAACAATGATACTAAAATGAAACAAAAACTAAACTTTAGATATGATTTTTAAAAAATTC
* * * **
942840 AAAGTTTAGGTACTAAAAGAGACCAAAATTGAAGTTTGGGTACTAAACACGTAATTTACCCAAAT
131 AAAGTTTAGGTACTAAAAGAGAACAAAATTGAAATTTGGATACTAAACAAATAATTTACCCAAAT
* * **
942905 TTTTAACTATTGTGTTAGCGATCTGATGATTCGATCTTCCAGTCATTAAAATTTAAGGTTATAAG
196 TTTTAACTATTGTGTTAGCGATCAGAAGATTCGATCCACCAGTCATTAAAATTTAAGGTTATAAG
*
942970 TTTTGCTTGTACGTATACATACATACAACAAAATTTGGCAAACTTAAACGCATTTAGTATT
261 TTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTTAAACGCATTTAGTATT
* *
943031 TAAATTATCAATTTTGCTCTATTTTAGTACCTAAACTTTC-AAAAAAAATCAAAACTTAATGTTA
1 TAAATTATCAATTTTGCTCCATTTTAATACCTAAACTTTCAAAAAAAAATCAAAACTTAATGTTA
* * * ** *
943095 AATTTTGAACAATGGTACTAAAATGAAATAAAAATTAAACTTTTTATATGGTTTTTAAAAACATT
66 AATTTTGAACAATGATACTAAAATGAAACAAAAACTAAACTTTAGATATGATTTTTAAAAA-ATT
* * * * *
943160 CAAAGTTTAGGTACTGAAAGGGAACAAAATTGATAATTTTGATACTAAA-ATAATAATTTACTCT
130 CAAAGTTTAGGTACTAAAAGAGAACAAAATTGA-AATTTGGATACTAAACA-AATAATTTACCCA
* *
943224 AATTTTTAACTATTGTGTTTGCGATCAGAAGATTCGATCCACCAGTCATTAAAATTTGAGGTTAT
193 AATTTTTAACTATTGTGTTAGCGATCAGAAGATTCGATCCACCAGTCATTAAAATTTAAGGTTAT
943289 AAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTT
258 AAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTT
943337 TTCGCCAGAT
Statistics
Matches: 273, Mismatches: 30, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
320 76 0.28
321 70 0.26
322 127 0.47
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (321 bp):
TAAATTATCAATTTTGCTCCATTTTAATACCTAAACTTTCAAAAAAAAATCAAAACTTAATGTTA
AATTTTGAACAATGATACTAAAATGAAACAAAAACTAAACTTTAGATATGATTTTTAAAAAATTC
AAAGTTTAGGTACTAAAAGAGAACAAAATTGAAATTTGGATACTAAACAAATAATTTACCCAAAT
TTTTAACTATTGTGTTAGCGATCAGAAGATTCGATCCACCAGTCATTAAAATTTAAGGTTATAAG
TTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTTAAACGCATTTAGTATT
Found at i:947337 original size:21 final size:21
Alignment explanation
Indices: 947313--947353 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
947303 AAAGCTCGTT
* *
947313 AAAAGTTGAAAATTTTATTAA
1 AAAACTTGAAAATATTATTAA
*
947334 AAAACTTTAAAATATTATTA
1 AAAACTTGAAAATATTATTA
947354 TATTAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAACTTGAAAATATTATTAA
Found at i:948769 original size:2 final size:2
Alignment explanation
Indices: 948762--948815 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
948752 TAATTTAATG
948762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
948804 AT AT AT AT AT AT
1 AT AT AT AT AT AT
948816 TCACGTATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:949140 original size:23 final size:24
Alignment explanation
Indices: 949097--949176 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 24
949087 CACCGAAGTG
949097 TCACGTAGAATTTGTCCCAAAGGA
1 TCACGTAGAATTTGTCCCAAAGGA
* *
949121 TCACGTAGAA-TTGTCTCAAAGTA
1 TCACGTAGAATTTGTCCCAAAGGA
* ** * *
949144 CCATATAG-ATTTATCCCGAAGGA
1 TCACGTAGAATTTGTCCCAAAGGA
*
949167 TCGCGTAGAA
1 TCACGTAGAA
949177 CCCTCGACTA
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
22 1 0.02
23 29 0.71
24 11 0.27
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (24 bp):
TCACGTAGAATTTGTCCCAAAGGA
Found at i:949273 original size:15 final size:15
Alignment explanation
Indices: 949249--949303 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
949239 CGTAGAGCAC
949249 ATTCACATAAAACAT
1 ATTCACATAAAACAT
* *
949264 TTTCATATAAAACAT
1 ATTCACATAAAACAT
* *
949279 ATTCACGTATAACATT
1 ATTCACATAAAACA-T
*
949295 TTTCACATA
1 ATTCACATA
949304 CCAATAAAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 23 0.74
16 8 0.26
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (15 bp):
ATTCACATAAAACAT
Found at i:952342 original size:97 final size:97
Alignment explanation
Indices: 952179--952369 Score: 296
Period size: 97 Copynumber: 2.0 Consensus size: 97
952169 TTGAGGGAGA
* *
952179 AAAAAAACTCAATCTTTGGCTCATTTTATTACAACAAAACACCTTTTCCCTTGTTTTTTTTATCT
1 AAAAAAACTCAAGCTTTGGCTCATTTTATTACAACAAAACACCTTTGCCCTTGTTTTTTTTATCT
*
952244 GTTTAGAGCCATCTTCAAGCTTGGGTTCTGAG
66 GTTTAGAGCCATCTTCAAGCTAGGGTTCTGAG
* *
952276 AAAAATACTCAAGCTTTGGCTCATTTTATT-CAA-AGAAAGCTCCTTTGCCCTTGTTTTTTTTAT
1 AAAAAAACTCAAGCTTTGGCTCATTTTATTACAACA-AAA-CACCTTTGCCCTTGTTTTTTTTAT
*
952339 CTGTTTTGAGCCATCTTCAAGCTAGGGTTCT
64 CTGTTTAGAGCCATCTTCAAGCTAGGGTTCT
952370 TTTGTTTCTG
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
95 1 0.01
96 6 0.07
97 79 0.92
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (97 bp):
AAAAAAACTCAAGCTTTGGCTCATTTTATTACAACAAAACACCTTTGCCCTTGTTTTTTTTATCT
GTTTAGAGCCATCTTCAAGCTAGGGTTCTGAG
Found at i:953167 original size:13 final size:13
Alignment explanation
Indices: 953149--953173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
953139 CGTATTTAAT
953149 ATTTTAATTATTA
1 ATTTTAATTATTA
953162 ATTTTAATTATT
1 ATTTTAATTATT
953174 TTTTCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTAATTATTA
Found at i:955813 original size:31 final size:31
Alignment explanation
Indices: 955770--955830 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
955760 CCTTCCAAAT
*
955770 GTTACAGAATGATCATTAAATTTATCAAACA
1 GTTACAGAATGATCATTAAACTTATCAAACA
* * *
955801 GTTACAGGATGATCTTTCAACTTATCAAAC
1 GTTACAGAATGATCATTAAACTTATCAAAC
955831 TGATACAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (31 bp):
GTTACAGAATGATCATTAAACTTATCAAACA
Found at i:957510 original size:21 final size:21
Alignment explanation
Indices: 957484--957526 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
957474 TAATCCGGAT
957484 CAGATATTACAGTGGTAAGGG
1 CAGATATTACAGTGGTAAGGG
957505 CAGATATTACAGTGGTAAGGG
1 CAGATATTACAGTGGTAAGGG
957526 C
1 C
957527 GACCCTCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.23
Consensus pattern (21 bp):
CAGATATTACAGTGGTAAGGG
Found at i:978309 original size:58 final size:58
Alignment explanation
Indices: 978219--978328 Score: 220
Period size: 58 Copynumber: 1.9 Consensus size: 58
978209 TATTTATTGA
978219 AACAATACTGGATCAATTGAGAATTACACCTTTTACAATTGAAAATCCGAGTTAGATT
1 AACAATACTGGATCAATTGAGAATTACACCTTTTACAATTGAAAATCCGAGTTAGATT
978277 AACAATACTGGATCAATTGAGAATTACACCTTTTACAATTGAAAATCCGAGT
1 AACAATACTGGATCAATTGAGAATTACACCTTTTACAATTGAAAATCCGAGT
978329 CAAAATCTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (58 bp):
AACAATACTGGATCAATTGAGAATTACACCTTTTACAATTGAAAATCCGAGTTAGATT
Found at i:979024 original size:15 final size:15
Alignment explanation
Indices: 979004--979034 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
978994 TTCGCATCAA
979004 TTTAGCAATCGAAAT
1 TTTAGCAATCGAAAT
979019 TTTAGCAATCGAAAT
1 TTTAGCAATCGAAAT
979034 T
1 T
979035 GTTTAATTGC
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:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (15 bp):
TTTAGCAATCGAAAT
Found at i:981238 original size:58 final size:58
Alignment explanation
Indices: 981165--981337 Score: 195
Period size: 58 Copynumber: 2.9 Consensus size: 58
981155 TAGTCTCTCG
*
981165 ACTATATGACGTTGCTTTGTTGAGTCTTCAAACTATTAAAAGTTACAAAATGATCAATA
1 ACTATATGATGTTGCTTTGTTGAGTC-TCAAACTATTAAAAGTTACAAAATGATCAATA
* * * ** *
981224 AC-ATATGATTTTGCTTTGTTGAGTCTCACAGCTATTAAAAATTACAAAATGATTCTCTG
1 ACTATATGATGTTGCTTTGTTGAGTCTCA-AACTATTAAAAGTTACAAAATGA-TCAATA
* * * ** *
981283 ACTATATGGTGTTGCTTTGTTGTGTCACCGACTATTAAAAGTTATAAAATGATCA
1 ACTATATGATGTTGCTTTGTTGAGTCTCAAACTATTAAAAGTTACAAAATGATCA
981338 CACAATTATT
Statistics
Matches: 94, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
57 3 0.03
58 44 0.47
59 26 0.28
60 21 0.22
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (58 bp):
ACTATATGATGTTGCTTTGTTGAGTCTCAAACTATTAAAAGTTACAAAATGATCAATA
Found at i:983320 original size:8 final size:8
Alignment explanation
Indices: 983307--983340 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
983297 AATTTGTTGA
983307 AAATATAT
1 AAATATAT
983315 AAATATAT
1 AAATATAT
983323 AAATATAT
1 AAATATAT
983331 AAATAT-T
1 AAATATAT
983338 AAA
1 AAA
983341 GATTAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 22 0.85
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATATAT
Found at i:983347 original size:14 final size:16
Alignment explanation
Indices: 983311--983348 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
983301 TGTTGAAAAT
*
983311 ATATAAATATATAAAT
1 ATATAAATATATAAAG
983327 ATATAAATAT-TAAAG
1 ATATAAATATATAAAG
983342 AT-TAAAT
1 ATATAAAT
983349 TTATCTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 6 0.29
16 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATATAAATATATAAAG
Found at i:986777 original size:23 final size:20
Alignment explanation
Indices: 986730--986777 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
986720 TAAGAGTTAG
*
986730 AATATTTATAAAATAATTTA
1 AATATTTATAAAAAAATTTA
*
986750 GATATTATATAAAAAATATTTGA
1 AATATT-TATAAAAAA-ATTT-A
986773 AATAT
1 AATAT
986778 CATAAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 8 0.36
22 4 0.18
23 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
AATATTTATAAAAAAATTTA
Found at i:987100 original size:19 final size:18
Alignment explanation
Indices: 987066--987103 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
987056 ATTCATTAAC
987066 AAATAATTAAAATATATA
1 AAATAATTAAAATATATA
*
987084 AAATAATTATTAATATATA
1 AAATAATTA-AAATATATA
987103 A
1 A
987104 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATAATTAAAATATATA
Found at i:987427 original size:12 final size:12
Alignment explanation
Indices: 987395--987456 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
987385 TGCGGGAAAA
987395 TTAAAA-TTA-T
1 TTAAAATTTATT
*
987405 TT-AAATCTATT
1 TTAAAATTTATT
987416 TTAAAATTTATT
1 TTAAAATTTATT
* **
987428 TTAAAATATAGA
1 TTAAAATTTATT
987440 TT--AATTTATT
1 TTAAAATTTATT
987450 TTAAAAT
1 TTAAAAT
987457 ATAGATTGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
9 3 0.08
10 11 0.28
11 3 0.08
12 22 0.56
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:987445 original size:22 final size:22
Alignment explanation
Indices: 987421--987785 Score: 606
Period size: 22 Copynumber: 16.6 Consensus size: 22
987411 CTATTTTAAA
* *
987421 ATTTATTTTAAAATATAGATTA
1 ATTTATTTTAAAATATGGATTG
*
987443 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
***
987465 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
987487 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
987509 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
987531 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
987553 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
987575 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
987597 ATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGGATTG
987619 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
987641 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
987663 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
987684 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
987707 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
987729 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
987751 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
987773 ATTTATTTTAAAA
1 ATTTATTTTAAAA
987786 AATTTATTAT
Statistics
Matches: 322, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
21 3 0.01
22 316 0.98
23 3 0.01
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:988373 original size:35 final size:34
Alignment explanation
Indices: 988333--988403 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
988323 TTGACATAAC
*
988333 ATATAAAATT-AAGTACTTATTTTGACAAAAAAGTA
1 ATAT-AAATTAAAG-ACTTATTTTGACAAAAAACTA
* *
988368 ATATAATTTAAAGACTTATTTTGACCAAAAACTA
1 ATATAAATTAAAGACTTATTTTGACAAAAAACTA
988402 AT
1 AT
988404 TTAAGGTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 25 0.78
35 7 0.22
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.35
Consensus pattern (34 bp):
ATATAAATTAAAGACTTATTTTGACAAAAAACTA
Found at i:988548 original size:21 final size:19
Alignment explanation
Indices: 988524--988579 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
988514 CCTATAAAGT
988524 ATTACAAATAATTAATAAAA
1 ATTA-AAATAATTAATAAAA
* *
988544 CATTAAATATTATAAATAAAA
1 -ATTAAA-ATAATTAATAAAA
*
988565 ATTAAAAAAATTAAT
1 ATTAAAATAATTAAT
988580 TTTAATATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 6 0.21
20 8 0.28
21 15 0.52
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTAAAATAATTAATAAAA
Found at i:994699 original size:15 final size:15
Alignment explanation
Indices: 994681--994733 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
994671 AAAATAAATT
994681 TTAAATTTAGAGTAA
1 TTAAATTTAGAGTAA
994696 TTAAA-TTAGGAGTAA
1 TTAAATTTA-GAGTAA
*
994711 TTTGAAAGTTA-AGTAA
1 -TT-AAATTTAGAGTAA
994727 TTAAATT
1 TTAAATT
994734 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 7 0.21
15 13 0.39
16 7 0.21
17 3 0.09
18 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (15 bp):
TTAAATTTAGAGTAA
Found at i:995056 original size:2 final size:2
Alignment explanation
Indices: 995049--995078 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
995039 TTTATTAATT
995049 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
995079 GGCAAGTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:996027 original size:20 final size:21
Alignment explanation
Indices: 995988--996028 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
995978 TTCTTTAATA
995988 TATAATATTATGAATATATTT
1 TATAATATTATGAATATATTT
* *
996009 TATAATTTTA-GATTATATTT
1 TATAATATTATGAATATATTT
996029 GATATGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TATAATATTATGAATATATTT
Found at i:996814 original size:14 final size:15
Alignment explanation
Indices: 996776--996816 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
996766 TTATTAATAT
996776 ATTATTAAAATT-AA
1 ATTATTAAAATTAAA
996790 ATTAATT-AAATTAAA
1 ATT-ATTAAAATTAAA
996805 ATT-TTAAAATTA
1 ATTATTAAAATTA
996817 TATTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 14 0.58
15 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTATTAAAATTAAA
Found at i:996874 original size:25 final size:25
Alignment explanation
Indices: 996792--996874 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 25
996782 AAAATTAAAT
996792 TAATTAAATTAAAATTTTAAAATTA
1 TAATTAAATTAAAATTTTAAAATTA
* * *
996817 TATTTAAATAAAAAAATATTCCCAAAATTA
1 TAATTAAAT--TAAAAT-TT--TAAAATTA
*
996847 TAATTAAATTTAAATTTTAAAATTA
1 TAATTAAATTAAAATTTTAAAATTA
996872 TAA
1 TAA
996875 ACTCTCGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
25 18 0.39
27 7 0.15
28 6 0.13
30 15 0.33
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATTAAATTAAAATTTTAAAATTA
Found at i:999880 original size:60 final size:60
Alignment explanation
Indices: 999758--999883 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
999748 AACATAATGA
* * * *
999758 ATAGTCAAATGACCATTTTATAACTTTTAATATTTGAAGGACTTAATAAAACAACATTCT
1 ATAGTCAAATGACCATTTTATAACTTTTAATAGTCGAAGAACTTAATAAAACAACATCCT
* * * * * ** *
999818 ATAGTCATATGATCGTTTTATAACTTTTGATAGTCGAAGAACTTAATGAAGTAGCATCCT
1 ATAGTCAAATGACCATTTTATAACTTTTAATAGTCGAAGAACTTAATAAAACAACATCCT
999878 ATAGTC
1 ATAGTC
999884 GAGGACCGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (60 bp):
ATAGTCAAATGACCATTTTATAACTTTTAATAGTCGAAGAACTTAATAAAACAACATCCT
Found at i:1004301 original size:29 final size:29
Alignment explanation
Indices: 1004264--1004320 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1004254 AACTTTTCTA
* *
1004264 TTTGGTTAAAATAGGAATCTAAAGTATTT
1 TTTGATTAAAATAAGAATCTAAAGTATTT
*
1004293 TTTGATTAAAATAAGTATCTAAAGTATT
1 TTTGATTAAAATAAGAATCTAAAGTATT
1004321 CAACTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTGATTAAAATAAGAATCTAAAGTATTT
Found at i:1005267 original size:20 final size:21
Alignment explanation
Indices: 1005230--1005268 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1005220 TACTTTAGAG
*
1005230 AAATACTAAAACATAATATGA
1 AAATACTAAAACAAAATATGA
*
1005251 AAATA-TAAAATAAAATAT
1 AAATACTAAAACAAAATAT
1005269 TTACAGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (21 bp):
AAATACTAAAACAAAATATGA
Found at i:1009132 original size:20 final size:19
Alignment explanation
Indices: 1009085--1009129 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
1009075 ATAATATTAG
1009085 TTAATGTAAAAAATAAATAT
1 TTAAT-TAAAAAATAAATAT
1009105 TTAAATTAAAAAATATAATAAT
1 TT-AATTAAAAAATA-AAT-AT
1009127 TTA
1 TTA
1009130 TTAGATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 11 0.50
21 7 0.32
22 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TTAATTAAAAAATAAATAT
Found at i:1009681 original size:73 final size:74
Alignment explanation
Indices: 1009604--1010177 Score: 838
Period size: 73 Copynumber: 7.8 Consensus size: 74
1009594 TTAAAAACGA
* * * *
1009604 CTAATAATGTAAACGGT-AAAAAAATAGGTGTTACCTATTACATTAAACTACCTACTGGTTTTTT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
1009668 TAAAGGTTG
66 TAAAGGTTG
* * *
1009677 CTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTATATTAAAATACCTACCGGTTTATT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
* *
1009742 TAAAGATTA
66 TAAAGGTTG
* *
1009751 CTAACAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAATACCTACTGGTTTTT
1 CTAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTT
*
1009816 TTTAAGGTTG
65 TTAAAGGTTG
1009826 CTAATAATGTAAACGGT-AAAAAAATAGGCGCTACCTATTACATTAAAATACCTA-C-GTTTTGT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTT-T
*
1009888 TTAAAGATTG
65 TTAAAGGTTG
* *
1009898 CTAATAATGTAAACGATAAAATAAAATAGGAGCTACCTATTACATTAAAATACCTACCGGTTTTT
1 CTAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTT
*
1009963 TTTAAGGTTG
65 TTAAAGGTTG
* * * *
1009973 TTAATATTGTAAACGGT-AAAAAAATAGACACTACCTATTACATTAAAATACCTACCGGTTTTTT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
*
1010037 TTAAGGTTG
66 TAAAGGTTG
*
1010046 TTAATAATGTAAACGGT-AAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGG-TTTTT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
*
1010109 TGAAGGTTG
66 TAAAGGTTG
* *
1010118 CTAATAATGTAAACGGTAAAAAAAAATAGGTGCTACCTATTACATTAAACTACCTACCGG
1 CTAATAATGTAAACGGT-AAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGG
1010178 ATATATTGAA
Statistics
Matches: 456, Mismatches: 36, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
71 5 0.01
72 54 0.12
73 159 0.35
74 147 0.32
75 86 0.19
76 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (74 bp):
CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
TAAAGGTTG
Found at i:1009946 original size:147 final size:146
Alignment explanation
Indices: 1009604--1010176 Score: 839
Period size: 147 Copynumber: 3.9 Consensus size: 146
1009594 TTAAAAACGA
* * * *
1009604 CTAATAATGTAAACGGTAAAAAAATAGGTGTTACCTATTACATTAAACTACCTACTGGTTTTTTT
1 CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTTT
* * *
1009669 AAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTATATTAAAATACCTACC
66 TAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC
* *
1009734 GGTTTATTTAAAGATTA
131 -GTTTTTTTAAAGATTG
* *
1009751 CTAACAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAATACCTACTGGTTTTT
1 CTAATAATGTAAACGGT-AAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTT
1009816 TTTAAGGTTGCTAATAATGTAAACGGT-AAAAAAATAGGCGCTACCTATTACATTAAAATACCTA
64 TTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTA
1009880 -CGTTTTGTTTAAAGATTG
129 CCGTTTT-TTTAAAGATTG
* *
1009898 CTAATAATGTAAACGATAAAATAAAATAGGAGCTACCTATTACATTAAAATACCTACCGGTTTTT
1 CTAATAATGTAAACGGT-AAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTT
* * * *
1009963 TTTAAGGTTGTTAATATTGTAAACGGT-AAAAAAATAGACACTACCTATTACATTAAAATACCTA
64 TTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTA
* *
1010027 CCGGTTTTTTTTAAGGTTG
129 CC-GTTTTTTTAAAGATTG
*
1010046 TTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGG-TTTTTT
1 CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTTT
* * *
1010110 GAAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGTGCTACCTATTACATTAAACTACCTAC
66 TAAGGTTGCTAATAATGTAAACGGT-AAAAAAAATAGGCGCTACCTATTACATTAAAATACCTAC
1010175 CG
130 CG
1010177 GATATATTGA
Statistics
Matches: 390, Mismatches: 29, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
145 28 0.07
146 42 0.11
147 186 0.48
148 63 0.16
149 71 0.18
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (146 bp):
CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTTT
TAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACC
GTTTTTTTAAAGATTG
Found at i:1010075 original size:220 final size:220
Alignment explanation
Indices: 1009604--1010177 Score: 873
Period size: 220 Copynumber: 2.6 Consensus size: 220
1009594 TTAAAAACGA
* * *
1009604 CTAATAATGTAAACGGTAAAAAAATAGGTGTTACCTATTACATTAAACTACCTACTGGTTTTTTT
1 CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTAC--GTTTTTTT
* * *
1009669 AAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTATATTAAAATACCTACC
64 AAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACC
* *
1009734 GGTTTATTTAAAGATTACTAACAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAA
129 GGTTTATTTAAAGATTACTAACAATGTAAACGGTAAAATAAAATAGACACTACCTATTACATTAA
*
1009799 AATACCTACTGGTTTTTTTTAAGGTTG
194 AATACCTACCGGTTTTTTTTAAGGTTG
1009826 CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACGTTTTGTTTA
1 CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACGTTTT-TTTA
* *
1009891 AAGATTGCTAATAATGTAAACGATAAAATAAAATAGGAGCTACCTATTACATTAAAATACCTACC
65 AAGGTTGCTAATAATGTAAACGGTAAAA-AAAATAGGAGCTACCTATTACATTAAAATACCTACC
* * * ** * *
1009956 GGTTTTTTTTAAGGTTGTTAATATTGTAAACGGT-AAA-AAAATAGACACTACCTATTACATTAA
129 GGTTTATTTAAAGATTACTAACAATGTAAACGGTAAAATAAAATAGACACTACCTATTACATTAA
1010019 AATACCTACCGGTTTTTTTTAAGGTTG
194 AATACCTACCGGTTTTTTTTAAGGTTG
* * *
1010046 TTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTTG
1 CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTA-CGTTTTTTTA
* *
1010111 AAGGTTGCTAATAATGTAAACGGTAAAAAAAAATAGGTGCTACCTATTACATTAAACTACCTACC
65 AAGGTTGCTAATAATGTAAACGGT-AAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACC
1010176 GG
129 GG
1010178 ATATATTGAA
Statistics
Matches: 323, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
220 169 0.52
221 42 0.13
222 112 0.35
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (220 bp):
CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACGTTTTTTTAA
AGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACCGG
TTTATTTAAAGATTACTAACAATGTAAACGGTAAAATAAAATAGACACTACCTATTACATTAAAA
TACCTACCGGTTTTTTTTAAGGTTG
Found at i:1010465 original size:112 final size:113
Alignment explanation
Indices: 1010257--1010486 Score: 363
Period size: 112 Copynumber: 2.0 Consensus size: 113
1010247 TAGCGCCTAT
* *
1010257 AAAGTATCGATACTTTATAAAAATGTATTGATACATAACAATTAATATAACAGGTAAAAACATGA
1 AAAGTATCGATACTTTATAAAAATATATCGATACATAAC-A--AATATAACAGGTAAAAACATGA
* *
1010322 CAAAACCAGTTTTATTATGACAAAGCCGGTAAAGAGCTACCGGATATGTTG
63 CAAAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCGGATATGTTG
*
1010373 AAAGTATCGATACTTTATAAAAATATATCGATACATAAC-AATATAACAGGTAAAAATATGACAA
1 AAAGTATCGATACTTTATAAAAATATATCGATACATAACAAATATAACAGGTAAAAACATGACAA
* *
1010437 AACCAGTTTCATTATGATAAAACTGGTAAAGAGCTACCGGATATGTTG
66 AACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCGGATATGTTG
1010485 AA
1 AA
1010487 GGGTCATCAT
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
112 70 0.65
116 37 0.35
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (113 bp):
AAAGTATCGATACTTTATAAAAATATATCGATACATAACAAATATAACAGGTAAAAACATGACAA
AACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCGGATATGTTG
Found at i:1012066 original size:2 final size:2
Alignment explanation
Indices: 1012059--1012085 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1012049 TAACATCCTC
1012059 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1012086 CTTTTTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1019759 original size:33 final size:33
Alignment explanation
Indices: 1019717--1019795 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
1019707 CATTGGCAGA
*
1019717 CATATATATAGAGAGATGGATCGAACCCATTGG
1 CATATATATAGAGAGATGGACCGAACCCATTGG
1019750 CATATATATAGAGAGATGGACCGAACCCATTGG
1 CATATATATAGAGAGATGGACCGAACCCATTGG
1019783 CATATATATAGAG
1 CATATATATAGAG
1019796 GACGAATCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (33 bp):
CATATATATAGAGAGATGGACCGAACCCATTGG
Found at i:1019759 original size:37 final size:35
Alignment explanation
Indices: 1019704--1019795 Score: 129
Period size: 33 Copynumber: 2.7 Consensus size: 35
1019694 TTCAATCCCT
*
1019704 ACCCATTGGCAGACATATATATAGAGAGATGGATCGA
1 ACCCATTGGCA-A-ATATATATAGAGAGATGGACCGA
1019741 ACCCATTGGC--ATATATATAGAGAGATGGACCGA
1 ACCCATTGGCAAATATATATAGAGAGATGGACCGA
1019774 ACCCATTGGC--ATATATATAGAG
1 ACCCATTGGCAAATATATATAGAG
1019796 GACGAATCAC
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
33 44 0.81
37 10 0.19
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (35 bp):
ACCCATTGGCAAATATATATAGAGAGATGGACCGA
Done.