Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006821.1 Hibiscus syriacus cultivar Beakdansim tig00017332_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: 135836
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5618 original size:37 final size:37
Alignment explanation
Indices: 5570--5642 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
5560 TTCTTTGAAC
5570 ATATATTGTAATATACTTACCCGAATTAATAAAAAAT
1 ATATATTGTAATATACTTACCCGAATTAATAAAAAAT
*
5607 ATATATTGTAATATACTTACTCGAATTAATAAAAAA
1 ATATATTGTAATATACTTACCCGAATTAATAAAAAA
5643 ATTAGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (37 bp):
ATATATTGTAATATACTTACCCGAATTAATAAAAAAT
Found at i:6839 original size:2 final size:2
Alignment explanation
Indices: 6832--6857 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6822 GCTGCAAAAT
6832 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
6858 GTTATCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19136 original size:26 final size:26
Alignment explanation
Indices: 19100--19168 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
19090 AGTTACGCTA
19100 GAAATGAGAAGAGAGAAGCGAAAAAG
1 GAAATGAGAAGAGAGAAGCGAAAAAG
19126 GAAATGAGAAGAGAGAAGCGAAAAAG
1 GAAATGAGAAGAGAGAAGCGAAAAAG
19152 GAAATGAGAAGAGAGAA
1 GAAATGAGAAGAGAGAA
19169 AAGGAATTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.58, C:0.03, G:0.35, T:0.04
Consensus pattern (26 bp):
GAAATGAGAAGAGAGAAGCGAAAAAG
Found at i:21115 original size:2 final size:2
Alignment explanation
Indices: 21110--21154 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
21100 GCATAAATGA
21110 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
21152 AT A
1 AT A
21155 CATGCATATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23223 original size:3 final size:3
Alignment explanation
Indices: 23215--23247 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
23205 AACTTGTAAT
23215 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23248 GATTAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30079 original size:31 final size:32
Alignment explanation
Indices: 30044--30105 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
30034 ATGATAATTC
* *
30044 AATTTTTTTTAATAATTTTATAG-AATATTTT
1 AATTTTTTTTAATAATTATAAAGTAATATTTT
*
30075 AATTTTTTTTATTAATTATAAAGTAATATTT
1 AATTTTTTTTAATAATTATAAAGTAATATTT
30106 GTTTTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (32 bp):
AATTTTTTTTAATAATTATAAAGTAATATTTT
Found at i:30536 original size:19 final size:19
Alignment explanation
Indices: 30512--30550 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
30502 AAATAGGGGC
*
30512 CCTCCCTTGACGTTATCAT
1 CCTCCCTTGACCTTATCAT
30531 CCTCCCTTGACCTTATCAT
1 CCTCCCTTGACCTTATCAT
30550 C
1 C
30551 TTCATCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.41, G:0.08, T:0.36
Consensus pattern (19 bp):
CCTCCCTTGACCTTATCAT
Found at i:32641 original size:3 final size:3
Alignment explanation
Indices: 32635--32662 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
32625 ATTAATAATA
32635 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
32663 TTAATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:32724 original size:33 final size:36
Alignment explanation
Indices: 32658--32729 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
32648 ATTATTATTA
*
32658 TTATTTTAATAAATAAATAGTATAATTTATAATAATT
1 TTATTTTAATAAATAAATAG-ATAATCTATAATAATT
*
32695 TTATTTTAATAAAT-AATA-ATAATCT-TAATATTT
1 TTATTTTAATAAATAAATAGATAATCTATAATAATT
32728 TT
1 TT
32730 TTATTTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 9 0.27
34 6 0.18
36 4 0.12
37 14 0.42
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (36 bp):
TTATTTTAATAAATAAATAGATAATCTATAATAATT
Found at i:34281 original size:20 final size:21
Alignment explanation
Indices: 34256--34307 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
34246 TTTTCCCAAT
*
34256 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
34276 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
34297 TCGCAATGCGA
1 TCGCAATGCGA
34308 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:34321 original size:20 final size:20
Alignment explanation
Indices: 34296--34430 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
34286 AATTGGGAAA
34296 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
34316 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* * *
34336 ATTGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
34357 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
34377 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
34397 TTCGCAAAGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
34417 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
34431 TTTTAAAGCG
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.69
21 23 0.25
22 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:34358 original size:61 final size:61
Alignment explanation
Indices: 34293--34430 Score: 188
Period size: 61 Copynumber: 2.3 Consensus size: 61
34283 GCGAATTGGG
* * *
34293 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATT-GCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACT-TTCGCAAAGCGATAATAC
* * * *
34354 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAAAGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTTTCGCAAAGCGATAATAC
*
34415 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
34431 TTTTAAAGCG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
60 2 0.03
61 64 0.97
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTTTCGCAAAGCGATAATAC
Found at i:34626 original size:22 final size:22
Alignment explanation
Indices: 34598--34641 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
34588 CACTCTCTCA
34598 CCCATCTCCGAAGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
**
34620 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
34642 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGAAGAAATCCGTC
Found at i:34958 original size:20 final size:20
Alignment explanation
Indices: 34904--34962 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
34894 GCGATTCTCT
**
34904 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
34924 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
34944 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
34963 AGAAACTATT
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:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:35153 original size:25 final size:24
Alignment explanation
Indices: 35099--35153 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
35089 TGTTTATTAT
* *
35099 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
35123 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
35149 TGTTT
1 TGTTT
35154 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:36303 original size:18 final size:18
Alignment explanation
Indices: 36282--36326 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
36272 TCCACTTCGG
*
36282 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
36300 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
36318 GAGCCATCA
1 GAGCCATCA
36327 TCTGATCGAC
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:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:36832 original size:20 final size:20
Alignment explanation
Indices: 36807--36852 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
36797 TAGTTTACTT
*
36807 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
36827 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
36847 TCGCAA
1 TCGCAA
36853 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:36861 original size:19 final size:20
Alignment explanation
Indices: 36818--36862 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
36808 CGCAACATGA
36818 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
36838 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
36857 AAATGA
1 AAATGA
36863 AAATCGTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:36868 original size:19 final size:19
Alignment explanation
Indices: 36846--36942 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
36836 GGAAATGGCT
36846 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
36865 ATCGTAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
36879 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
36898 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
36912 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
36931 GTCGCAATGCGA
1 ATCGCAATGCGA
36943 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.49
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:36888 original size:33 final size:33
Alignment explanation
Indices: 36846--36937 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
36836 GGAAATGGCT
*
36846 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
36879 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
36912 ATCGCAATGCGAAATGAAAGTCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
36938 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:36914 original size:14 final size:14
Alignment explanation
Indices: 36862--36918 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
36852 ATGCGAAATG
*
36862 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
36876 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
36895 AAAATCGCAACGAC
1 AAAATCGCAACGAC
36909 AAAATCGCAA
1 AAAATCGCAA
36919 TGCGAAATGA
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:0.51, C:0.21, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:37003 original size:33 final size:33
Alignment explanation
Indices: 36956--37046 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
36946 GTGTTTCGCA
*
36956 TTGCGA-TTTCATTTCACATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
36988 TTGCGATTTTCATTTCGCATTGGGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
37021 TTGCGATTTGCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
37047 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 6 0.11
33 48 0.89
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:37045 original size:19 final size:19
Alignment explanation
Indices: 36932--37088 Score: 88
Period size: 19 Copynumber: 8.7 Consensus size: 19
36922 GAAATGAAAG
* **
36932 TCGCAATGCGATTTGTGTT
1 TCGCATTGCGATTTGCATT
36951 TCGCATTGCGATTT-CATT
1 TCGCATTGCGATTTGCATT
* *
36969 TCACATTGCGATTT---TG
1 TCGCATTGCGATTTGCATT
*
36985 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTGCATT
* *
37002 TCGCATTGGGATTT---TG
1 TCGCATTGCGATTTGCATT
37018 TCG--TTGCGATTTGCATT
1 TCGCATTGCGATTTGCATT
*
37035 TCGCATTGCGA-TAGCCATT
1 TCGCATTGCGATTTG-CATT
* *
37054 TCCGCGTTGCGA-TAGTCATTT
1 T-CGCATTGCGATTTG-CA-TT
37075 TCGCATTGCGATTT
1 TCGCATTGCGATTT
37089 TAAGTTTCGT
Statistics
Matches: 108, Mismatches: 16, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
14 17 0.16
16 7 0.06
17 8 0.07
18 17 0.16
19 32 0.30
20 23 0.21
21 4 0.04
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTGCATT
Found at i:37065 original size:20 final size:19
Alignment explanation
Indices: 37031--37086 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
37021 TTGCGATTTG
37031 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
37050 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
37070 CATTTTCGCATTGCGAT
1 CA-TTTCGCATTGCGAT
37087 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:37445 original size:19 final size:19
Alignment explanation
Indices: 37421--37474 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
37411 ATCGCAACGA
37421 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
* *
37440 GAAAATCGCAACGAGAAAT
1 GAAAATCGCAATGCGAAAT
37459 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
37475 TTTTCATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:37507 original size:33 final size:34
Alignment explanation
Indices: 37464--37598 Score: 103
Period size: 40 Copynumber: 3.8 Consensus size: 34
37454 GAAATGAAAA
* ***
37464 TCGCAATGCGATTTTCATA-TTGCGATTTTCA-TT
1 TCGCATTGCGATTTTC-TAGTTGCGATAGCCATTT
37497 TCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
1 TCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
* *
37531 TCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCATTT
1 TCGCATTGCGA-TTTTC---T--AGTTGCGATAGCCATTT
* * **
37571 TCGCGTTGCGATTTCCCCGTTGCGATAG
1 TCGCATTGCGATTTTCTAGTTGCGATAG
37599 TCAAATGAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
32 2 0.02
33 24 0.29
34 21 0.25
35 5 0.06
38 1 0.01
39 4 0.05
40 27 0.32
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (34 bp):
TCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
Found at i:37532 original size:20 final size:20
Alignment explanation
Indices: 37507--37582 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
37497 TCGCATTGCG
*
37507 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
37527 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
37548 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
37567 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
37583 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:37821 original size:20 final size:20
Alignment explanation
Indices: 37796--37845 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
37786 TTGAAGATGA
37796 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
37816 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
37836 TTGCGATTTT
1 TTGCGATTTT
37846 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:38715 original size:24 final size:24
Alignment explanation
Indices: 38688--38742 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
38678 GTATTCGAAA
*
38688 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATATTGGTCAATACTCGGAC
*
38712 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCGGAC
38736 TTTGATA
1 TTTGATA
38743 ATTTTTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Found at i:41253 original size:19 final size:19
Alignment explanation
Indices: 41231--41328 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
41221 GGAAATTACT
41231 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
41250 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
41264 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
41283 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
41297 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
41316 ATCGCAACGCGAA
1 ATCGCAATGCGAA
41329 TTTAATTTCT
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:41273 original size:33 final size:33
Alignment explanation
Indices: 41231--41324 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
41221 GGAAATTACT
41231 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
41264 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
41297 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
41325 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:41346 original size:19 final size:19
Alignment explanation
Indices: 41324--41365 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41314 AAATCGCAAC
*
41324 GCGAATTTAATTTCTCGTT
1 GCGAATTTAATTTCACGTT
* *
41343 GCGATTTTCATTTCACGTT
1 GCGAATTTAATTTCACGTT
41362 GCGA
1 GCGA
41366 TTCTCTCGTT
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:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (19 bp):
GCGAATTTAATTTCACGTT
Found at i:41366 original size:19 final size:19
Alignment explanation
Indices: 41333--41399 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
41323 CGCGAATTTA
41333 ATTTCTCGTTGCGATTTTC
1 ATTTCTCGTTGCGATTTTC
*
41352 ATTTCACGTTGCGA--TTC
1 ATTTCTCGTTGCGATTTTC
41369 ---TCTCGTTGCGATTTTC
1 ATTTCTCGTTGCGATTTTC
* *
41385 ATTTCGCATTGCGAT
1 ATTTCTCGTTGCGAT
41400 AGTACTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 23 0.59
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
ATTTCTCGTTGCGATTTTC
Found at i:41375 original size:33 final size:33
Alignment explanation
Indices: 41336--41399 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
41326 GAATTTAATT
*
41336 TCTCGTTGCGATTTTCATTTCACGTTGCGATTC
1 TCTCGTTGCGATTTTCATTTCACATTGCGATTC
*
41369 TCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCTCGTTGCGATTTTCATTTCACATTGCGAT
41400 AGTACTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
TCTCGTTGCGATTTTCATTTCACATTGCGATTC
Found at i:42972 original size:42 final size:42
Alignment explanation
Indices: 42926--43005 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
42916 CGATGACAGT
* * *
42926 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
42968 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
43006 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:43404 original size:91 final size:90
Alignment explanation
Indices: 43227--43411 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 90
43217 ATTTCAAACT
* *
43227 TTCAACTAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
43292 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGAAGCAACCGAATAAATTTAC
43320 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
43384 GTATTGGAAGCAACTGAATAAATTTAC
64 GAATTGGAAGCAACCGAATAAATTTAC
43411 T
1 T
43412 AAACAATCTA
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 40 0.47
93 18 0.21
95 27 0.32
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGAAGCAACCGAATAAATTTAC
Found at i:45119 original size:14 final size:14
Alignment explanation
Indices: 45100--45188 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
45090 GAAAATGACT
45100 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
45114 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
45131 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
* *
45147 ATTGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
45166 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
45180 ATCACAACG
1 ATCGCAACG
45189 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 24 0.41
15 1 0.02
16 8 0.14
17 8 0.14
18 1 0.02
19 16 0.28
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:45134 original size:33 final size:33
Alignment explanation
Indices: 45079--45205 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
45069 TTGAAATGAA
**
45079 AATCGCAACGCGAAAATGACTATCGCAACGAGAG
1 AATCGCAACGCG-AAATGAAAATCGCAACGAGAG
**
45113 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
45146 AATTGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
45179 AATCACAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
45206 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 76 0.86
34 12 0.14
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:45239 original size:19 final size:19
Alignment explanation
Indices: 45206--45272 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
45196 AAAATCGCAA
**
45206 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
45225 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
* **
45244 TGCAATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
45264 TGCGATTTT
1 TGCGATTTT
45273 CATTCTCGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:45844 original size:20 final size:20
Alignment explanation
Indices: 45792--45863 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
45782 GCTATGTAAA
* *
45792 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
45812 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
45832 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
45853 TCGCATTGCGA
1 TCGCATTGCGA
45864 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 3 0.07
20 30 0.65
21 13 0.28
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:45877 original size:21 final size:21
Alignment explanation
Indices: 45853--46028 Score: 69
Period size: 21 Copynumber: 8.5 Consensus size: 21
45843 TTTTCCTAAT
45853 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTATGAAAA
** * * *
45874 TCGCAACGCTAA-TACGTAAA
1 TCGCATTGCGAATTATGAAAA
* *
45894 TCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGAATTATGAAAA
* * **
45915 TTGCATTGCG-A-TAGTCAGTA
1 TCGCATTGCGAATTA-TGAAAA
* * *
45935 TCGCATTGC-AATTTTCCAAAT
1 TCGCATTGCGAATTAT-GAAAA
* * *
45956 TCGCATTGCGATTTACT--TAT
1 TCGCATTGCGAATTA-TGAAAA
**
45976 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATTATGAAAA
** *
45997 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCG-AATTATGAAAA
46018 TCGCATTGCGA
1 TCGCATTGCGA
46029 TAGTCATAAT
Statistics
Matches: 113, Mismatches: 32, Indels: 21
0.68 0.19 0.13
Matches are distributed among these distances:
19 2 0.02
20 45 0.40
21 58 0.51
22 7 0.06
23 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGAATTATGAAAA
Found at i:46001 original size:41 final size:40
Alignment explanation
Indices: 45789--46001 Score: 119
Period size: 41 Copynumber: 5.2 Consensus size: 40
45779 GGCGCTATGT
* * *
45789 AAATCGCATTGCGA-TAGTAAGATTCGCATTGCGATTTACG-
1 AAATCGCATTGCGATTACT-A-ATTCGCATTGCGAATTAGGA
* * * *
45829 TATTCGCATTGCGATTTTCCTAATTCGCATTGCGAATTATGA
1 AAATCGCATTGCGA--TTACTAATTCGCATTGCGAATTAGGA
** * * * *
45871 AAATCGCAACGCTAATACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCATTGCGATTAC-TAATTCGCATTGCGAATTAGGA
* * * ***
45912 AAATTGCATTGCGA-TAGTCAGTATCGCATTGC-AATTTTCCA
1 AAATCGCATTGCGATTACT-AAT-TCGCATTGCGAA-TTAGGA
* * *
45953 AATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGA
1 AAATCGCATTGCGA-TTACTAATTCGCATTGCGAATTAGGA
45994 AAATCGCA
1 AAATCGCA
46002 ACGCGAAATT
Statistics
Matches: 126, Mismatches: 36, Indels: 21
0.69 0.20 0.11
Matches are distributed among these distances:
39 1 0.01
40 19 0.15
41 88 0.70
42 13 0.10
43 5 0.04
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (40 bp):
AAATCGCATTGCGATTACTAATTCGCATTGCGAATTAGGA
Found at i:46828 original size:3 final size:3
Alignment explanation
Indices: 46820--46898 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
46810 TGGCACTTAA
46820 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
46868 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
46899 GACTCCGAAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:55770 original size:2 final size:2
Alignment explanation
Indices: 55763--55803 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
55753 AAGAAGTGAA
* *
55763 AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG AG TG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
55804 AAAGTGTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.49, T:0.05
Consensus pattern (2 bp):
AG
Found at i:68469 original size:44 final size:48
Alignment explanation
Indices: 68360--68478 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 48
68350 TAAATATATA
* * *
68360 ATTTTTTATTAAAATAAATATTTAAGTTATTATTCATAAATATTTTAATT
1 ATTTTTTATTAAAATAAATATTT-ACTTATTATTCATAAATATATT-ATC
* * *
68410 ATTTCTTTATCAAAATAAATATTTACTTTTTA-T-ATAAGT-TATT-TC
1 ATTT-TTTATTAAAATAAATATTTACTTATTATTCATAAATATATTATC
68455 ATTTTTTATTAAAATAAATATTTA
1 ATTTTTTATTAAAATAAATATTTA
68479 AATTTATGTG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
44 19 0.31
45 5 0.08
47 3 0.05
48 5 0.08
49 1 0.02
50 10 0.16
51 18 0.30
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (48 bp):
ATTTTTTATTAAAATAAATATTTACTTATTATTCATAAATATATTATC
Found at i:68905 original size:31 final size:31
Alignment explanation
Indices: 68832--68910 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
68822 TGTAAATCAG
* *
68832 TCGAGTCGATTTAAAAATTTTGAAATAGAGC
1 TCGACTCGATTTGAAAATTTTGAAATAGAGC
* * *
68863 TCGATTTGATTTGAAAATTTTGAAATAGAGT
1 TCGACTCGATTTGAAAATTTTGAAATAGAGC
68894 TCGACTCGATTTGAAAA
1 TCGACTCGATTTGAAAA
68911 CTCACGAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (31 bp):
TCGACTCGATTTGAAAATTTTGAAATAGAGC
Found at i:70188 original size:14 final size:14
Alignment explanation
Indices: 70169--70206 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
70159 CCTTCATTCT
*
70169 CATTTTCCTTCTCC
1 CATTTTCCTCCTCC
70183 CATTTTCCTCCTCC
1 CATTTTCCTCCTCC
70197 CATTTTCCTC
1 CATTTTCCTC
70207 TTCAAGTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.45, G:0.00, T:0.47
Consensus pattern (14 bp):
CATTTTCCTCCTCC
Found at i:70886 original size:20 final size:20
Alignment explanation
Indices: 70861--70953 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
70851 ATGCTCATAC
*
70861 GGGTATCGATACTGCAGGTA
1 GGGTATCGATACTGCAAGTA
70881 GGGTATCGATACTGCAAGTA
1 GGGTATCGATACTGCAAGTA
70901 GGGTATCGATACTGCAAGTA
1 GGGTATCGATACTGCAAGTA
70921 GGGTATCGATACTGCAAGTA
1 GGGTATCGATACTGCAAGTA
*
70941 GGGTATCAATACT
1 GGGTATCGATACT
70954 ACTCACTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACTGCAAGTA
Found at i:73899 original size:34 final size:34
Alignment explanation
Indices: 73861--73931 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
73851 ATTGACCTGC
73861 TATGCAAAACATAAACATATAATCATATTTATAT
1 TATGCAAAACATAAACATATAATCATATTTATAT
73895 TATGCAAAACATAAACATATAATCATATTTATAT
1 TATGCAAAACATAAACATATAATCATATTTATAT
73929 TAT
1 TAT
73932 ATGGTATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (34 bp):
TATGCAAAACATAAACATATAATCATATTTATAT
Found at i:76120 original size:26 final size:26
Alignment explanation
Indices: 76086--76149 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
76076 AAAGCTGCAC
76086 CACTTTCGGTGCCTAATAATCCAATG
1 CACTTTCGGTGCCTAATAATCCAATG
76112 CACTTTCGGTGCCTAATAATCCAATG
1 CACTTTCGGTGCCTAATAATCCAATG
76138 CACTTTCGGTGC
1 CACTTTCGGTGC
76150 ATTTGTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.31
Consensus pattern (26 bp):
CACTTTCGGTGCCTAATAATCCAATG
Found at i:81845 original size:116 final size:117
Alignment explanation
Indices: 81603--81880 Score: 398
Period size: 116 Copynumber: 2.3 Consensus size: 117
81593 CAAGCCCAAC
* * *
81603 TCACTACACCACCAGCTTTTTTAGTTGGATGATGATGCTAAGTAGAAGAATATGAACAAAGTTAG
1 TCACTATACCACCAGCTGTCTTAGTTGGATGATGATGCTAAGTAGAAGAATATGAACAAAGTTAG
81668 AACTTATAATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCACCTGCA
66 -----A-AATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCACCTGCA
* * *
81726 TCACTATACCATCAGCTGTCTTAATTGGATGATGATGCTCAGTAGAAGAATATGAACAAAGTTAG
1 TCACTATACCACCAGCTGTCTTAGTTGGATGATGATGCTAAGTAGAAGAATATGAACAAAGTTAG
81791 -AATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCACCCT-CA
66 AAATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCA-CCTGCA
*
81842 TCACTATACCACCAGCTGAATCTTAGCTGGATGATGATG
1 TCACTATACCACCAGCTG--TCTTAGTTGGATGATGATG
81881 ATCTTCCTTT
Statistics
Matches: 143, Mismatches: 9, Indels: 11
0.88 0.06 0.07
Matches are distributed among these distances:
116 64 0.45
117 3 0.02
118 17 0.12
123 59 0.41
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (117 bp):
TCACTATACCACCAGCTGTCTTAGTTGGATGATGATGCTAAGTAGAAGAATATGAACAAAGTTAG
AAATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCACCTGCA
Found at i:83911 original size:103 final size:103
Alignment explanation
Indices: 83732--83925 Score: 370
Period size: 103 Copynumber: 1.9 Consensus size: 103
83722 GAACCTAAAA
* *
83732 ACAATTGCGACAGTTAGATTAAAAACCTCGCGTTGTGTTTTGTACATGTGCTGCTTGAATGCCGC
1 ACAATTGCGACAGTTAGATTAAAAACCTCGCCTTGTGTTTTGTACATGCGCTGCTTGAATGCCGC
83797 TGCTTTTGGTTCGGTATCTGTCATCCCATACCCGAATG
66 TGCTTTTGGTTCGGTATCTGTCATCCCATACCCGAATG
83835 ACAATTGCGACAGTTAGATTAAAAACCTCGCCTTGTGTTTTGTACATGCGCTGCTTGAATGCCGC
1 ACAATTGCGACAGTTAGATTAAAAACCTCGCCTTGTGTTTTGTACATGCGCTGCTTGAATGCCGC
83900 TGCTTTTGGTTCGGTATCTGTCATCC
66 TGCTTTTGGTTCGGTATCTGTCATCC
83926 AATCCAAGTG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 89 1.00
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (103 bp):
ACAATTGCGACAGTTAGATTAAAAACCTCGCCTTGTGTTTTGTACATGCGCTGCTTGAATGCCGC
TGCTTTTGGTTCGGTATCTGTCATCCCATACCCGAATG
Found at i:84501 original size:3 final size:3
Alignment explanation
Indices: 84493--84543 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
84483 CTTTTTTGTA
** *
84493 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
84539 TAT TA
1 TAT TA
84544 ATATATTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:88396 original size:31 final size:32
Alignment explanation
Indices: 88360--88421 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
88350 ATTTTACATG
88360 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
88391 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
88422 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:90879 original size:26 final size:25
Alignment explanation
Indices: 90850--90927 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
90840 AATTTTTGAC
90850 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
90876 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
* *
90896 ATTCCCTCTCTTTGAGACTTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
90922 ATTCTT
1 ATTCTT
90928 TCCACCTTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 13
0.66 0.12 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.13
26 13 0.33
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:91561 original size:18 final size:17
Alignment explanation
Indices: 91517--91563 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
91507 GAGTGCAAAG
*
91517 ATCAAACCAAAGAAAAA
1 ATCAAAGCAAAGAAAAA
91534 A-CAAAGAGCAAAGAGAAAA
1 ATC-AA-AGCAAAGA-AAAA
91553 ATCAAAGCAAA
1 ATCAAAGCAAA
91564 AAATCAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 13 0.52
19 7 0.28
20 1 0.04
ACGTcount: A:0.68, C:0.15, G:0.13, T:0.04
Consensus pattern (17 bp):
ATCAAAGCAAAGAAAAA
Found at i:91565 original size:13 final size:12
Alignment explanation
Indices: 91542--91590 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
91532 AAACAAAGAG
91542 CAAAGAGAAAAAT
1 CAAAGA-AAAAAT
91555 CAAAGCAAAAAAT
1 CAAAG-AAAAAAT
*
91568 CAAAG-AAAAAG
1 CAAAGAAAAAAT
91579 CAAAGAACAAAA
1 CAAAGAA-AAAA
91591 GAAGACAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.31
12 1 0.03
13 20 0.62
14 1 0.03
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.04
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:92787 original size:4 final size:4
Alignment explanation
Indices: 92778--92807 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
92768 AGAAAAGTAT
92778 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
92808 CCATGATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:93415 original size:105 final size:101
Alignment explanation
Indices: 93274--93511 Score: 264
Period size: 105 Copynumber: 2.3 Consensus size: 101
93264 TGAGAATTTT
* * * *
93274 AAAACAAATTGTGTTTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
** *
93338 TAAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTT-GA-AATCGTTTC--TCA
* * * *
93379 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGGATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
93444 TTAAACAAAGTTGATCTCACTTGAAATCGTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAAATCGTTTCTCA
* *
93480 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
93512 TCTAAAAACA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
100 2 0.02
101 29 0.25
102 6 0.05
103 2 0.02
104 3 0.03
105 71 0.62
106 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (101 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TAAAACAAAATTAATCTCACTTGAAATCGTTTCTCA
Found at i:93502 original size:35 final size:36
Alignment explanation
Indices: 93458--93538 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
93448 ACAAAGTTGA
*
93458 TCTCACTTGAAATC-GTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAAA-CAATTTCTCTAAAAACAAACTTTG
* * *
93493 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
*
93529 TCTCATTTGA
1 TCTCACTTGA
93539 GACTATATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.03
35 16 0.42
36 21 0.55
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (36 bp):
TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
Found at i:93529 original size:36 final size:36
Alignment explanation
Indices: 93473--93576 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
93463 CTTGAAATCG
*
93473 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
93508 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
93544 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
93577 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 22 0.38
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:93846 original size:28 final size:28
Alignment explanation
Indices: 93818--94009 Score: 260
Period size: 28 Copynumber: 6.8 Consensus size: 28
93808 AAGACAATTT
* *
93818 CTTTTGAAAAAAATCTTTGGGTTTGTTT
1 CTTTTGAAAAAAATCTTTGAGTTTGTTC
*
93846 CTCTTGAAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAATCTTTGAGTTTGTTC
*
93874 CTCTTGAAAAAAAATCTTTGAGTTTGTTC
1 CTTTTG-AAAAAAATCTTTGAGTTTGTTC
* *
93903 CTCTTGAAAAAAATCTTTGAGTTTGCTC
1 CTTTTGAAAAAAATCTTTGAGTTTGTTC
*
93931 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTGAA-AAAAATCTTTGAGTTTGTTC
*
93960 CTTTTGAATAAAAATCTTTGAG-TTGTTT
1 CTTTTGAA-AAAAATCTTTGAGTTTGTTC
* *
93988 CTTTTGTAAAATATCTTTGAGT
1 CTTTTGAAAAAAATCTTTGAGT
94010 CTATTTATTT
Statistics
Matches: 150, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
27 12 0.08
28 71 0.47
29 67 0.45
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (28 bp):
CTTTTGAAAAAAATCTTTGAGTTTGTTC
Found at i:93908 original size:57 final size:57
Alignment explanation
Indices: 93818--94009 Score: 264
Period size: 57 Copynumber: 3.4 Consensus size: 57
93808 AAGACAATTT
* *
93818 CTTTTG-AAAAAAATCTTTGGGTTTGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTC
* *
93874 CTCTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAATCTTTGAGTTTGCTC
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTC
* * * *
93931 CTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAAATCTTTGAG-TTGTTT
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTGAA-AAAAATCTTTGAGTTTGTTC
* *
93988 CTTTTG-TAAAATATCTTTGAGT
1 CTTTTGAAAAAAAATCTTTGAGT
94010 CTATTTATTT
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
56 17 0.14
57 90 0.75
58 13 0.11
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (57 bp):
CTTTTGAAAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTC
Found at i:94098 original size:52 final size:53
Alignment explanation
Indices: 94020--94123 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
94010 CTATTTATTT
94020 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
94072 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
94124 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 36 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:94147 original size:27 final size:27
Alignment explanation
Indices: 94110--94166 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
94100 AATTTTGTGA
*
94110 AAAAAATCTTTGAGATT-GTTTCTTTTG
1 AAAAAATCTTTGAG-TTGGTTTCTTTGG
94137 AAAAAATCTTTGAGTTGGTTTCTTTGG
1 AAAAAATCTTTGAGTTGGTTTCTTTGG
94164 AAA
1 AAA
94167 TAAAATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.44
Consensus pattern (27 bp):
AAAAAATCTTTGAGTTGGTTTCTTTGG
Found at i:94197 original size:37 final size:37
Alignment explanation
Indices: 94155--94275 Score: 112
Period size: 37 Copynumber: 3.5 Consensus size: 37
94145 TTTGAGTTGG
*
94155 TTTCTTTGGAAATAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* * * * **
94192 TTTCTTTTGAAACAAAA------ATCT-TTGAGTTTG
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
94222 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* *
94259 TTTCTTTTGAAAAAAAA
1 TTTCTTTGGAAACAAAA
94276 AAATCTTTGA
Statistics
Matches: 62, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
30 21 0.34
31 3 0.05
36 3 0.05
37 35 0.56
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (37 bp):
TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:94216 original size:67 final size:68
Alignment explanation
Indices: 94137--94285 Score: 255
Period size: 67 Copynumber: 2.2 Consensus size: 68
94127 GTTTCTTTTG
*
94137 AAAAAATCTTTGAGTTGGTTTCTTTGGAAATAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG-
1 AAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
94201 AAA
66 AAA
* *
94204 CAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG-
94269 AAAA
65 AAAA
94273 AAAAAATCTTTGA
1 AAAAAATCTTTGA
94286 ATCTGTTTCT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
67 61 0.80
69 15 0.20
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (68 bp):
AAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
AAA
Found at i:94619 original size:63 final size:62
Alignment explanation
Indices: 94517--94639 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 62
94507 GATGTAATCC
* * *
94517 ATCTTTGAGTCTGTTTCTTTTAAAACAAAATTTTATCTCTTAACGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTTATCTCTCAA-GACAACTTCTTTTGAAAAA
* * *
94580 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAA
1 ATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAA
94640 CCACCCACAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 16 0.30
63 38 0.70
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (62 bp):
ATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAAAA
Found at i:94860 original size:36 final size:36
Alignment explanation
Indices: 94787--94861 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
94777 AACAAACATC
*
94787 TTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCA
1 TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
* *
94823 TTTGAGA-CAGTTTTCCTTTAAAC-AATCTTTGAGTCA
1 TTTGAGATCA-TTTCCCTTTAAACGAAT-TTTGACTCA
94859 TTT
1 TTT
94862 CCTTTGAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (36 bp):
TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
Found at i:94878 original size:63 final size:63
Alignment explanation
Indices: 94780--94899 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
94770 GAAACAAAAC
*
94780 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTT-GAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTAGAGACAGTTTTCCTTT
*
94842 AAACAATCTTTGAG-TCATTT-CCTTTGAAACAAAATTTTGTCTCTTTTAAGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCCTTT-AAAC-AAATTTTGTCTCATTT-AGAGACAGTT
94900 GCTTTTGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
61 5 0.10
62 14 0.27
63 23 0.45
65 9 0.18
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (63 bp):
AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTAGAGACAGTTTTCCTTT
Found at i:95047 original size:46 final size:45
Alignment explanation
Indices: 94979--95394 Score: 249
Period size: 46 Copynumber: 9.7 Consensus size: 45
94969 ACCATAACTT
* * * *
94979 TTAGATGGCCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC
*
95024 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT-ACC
1 -TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
** *
95069 -CCGA---CCAGATCTCTTCATCACGTATGAGCCGTG---TCACC
1 TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
* ** * * * * *
95107 CTAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGCTATCACC
1 TTAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC
*
95152 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT-ACC
1 -TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
** * *
95197 -CCGA---ACAGATCTCTTCATCACGTATGAGCCGTG---TCACC
1 TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
* ** * * * *
95235 CTAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC
*
95280 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC
1 -TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTA-TCACC
* * * *
95326 --CGA---CCAGATCTCTTCATCACGTAGGAGCCGTGTCA--ACC
1 TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
* **
95364 ATAGATAACCA-AACTCTTCATCACGTATGAG
1 TTAGATGGCCAGAACTCTTCATCACGTATGAG
95395 TAGTGGCGTC
Statistics
Matches: 292, Mismatches: 48, Indels: 64
0.72 0.12 0.16
Matches are distributed among these distances:
37 2 0.01
38 8 0.03
39 4 0.01
40 87 0.30
41 2 0.01
42 63 0.22
43 9 0.03
45 16 0.05
46 96 0.33
47 5 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (45 bp):
TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
Found at i:95088 original size:40 final size:40
Alignment explanation
Indices: 95033--95394 Score: 229
Period size: 40 Copynumber: 8.6 Consensus size: 40
95023 CTTTAGATGG
*
95033 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCCGA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCAGA
*
95073 CCAGATCTCTTCATCACGTATGAGCCGTGTC--ACCCTAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCC-AG---A
* * * * *
95115 CCAG-CCGTCCTCATCACGTAGGAACCGTG-CTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTC-AT-ACC--CAGA
*
95158 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCCGA
1 ---CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCAGA
* *
95201 ACAGATCTCTTCATCACGTATGAGCCGTGTC--ACCCTAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCC-AG---A
* * * * * *
95243 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCAT-ACC--CAGA
* *
95286 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 ---CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCAGA
* * *
95329 CCAGATCTCTTCATCACGTAGGAGCCGTGTCA-ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACC-CAG---A
95372 CCA-AACTCTTCATCACGTATGAG
1 CCAGAACTCTTCATCACGTATGAG
95395 TAGTGGCGTC
Statistics
Matches: 250, Mismatches: 38, Indels: 66
0.71 0.11 0.19
Matches are distributed among these distances:
38 8 0.03
39 4 0.02
40 90 0.36
41 3 0.01
42 66 0.26
43 10 0.04
45 11 0.04
46 55 0.22
47 3 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCAGA
Found at i:95390 original size:128 final size:128
Alignment explanation
Indices: 94987--95374 Score: 722
Period size: 128 Copynumber: 3.0 Consensus size: 128
94977 TTTTAGATGG
94987 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
95052 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
66 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
*
95115 CCAGCCGTCCTCATCACGTAGGAACCGTGCTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
*
95180 ATGAGCCGTGTCATACCCCGAACAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
66 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
95243 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
* * *
95308 ATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
66 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACCCTAGATAA
95372 CCA
1 CCA
95375 AACTCTTCAT
Statistics
Matches: 252, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
128 239 0.95
129 13 0.05
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (128 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
Found at i:95565 original size:3 final size:3
Alignment explanation
Indices: 95557--95607 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
95547 CTTTTTTGTA
** *
95557 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
95603 TAT TA
1 TAT TA
95608 ATATATTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:99013 original size:3 final size:3
Alignment explanation
Indices: 99007--99145 Score: 95
Period size: 3 Copynumber: 43.7 Consensus size: 3
98997 TCACATATAG
*
99007 TAT TATT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TCAT GT-T TAAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TAT T-AT
* * *
99055 TAT TAT CCA- TGT TAT GTAT TAT TAT TAT TAT TAT CACT TAT TATT TATT
1 TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TA-T
* * *
99104 TAG TAT TA- TATT TAT TAT TAT ATAT TAT AAT AAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
99146 AGAACATTGA
Statistics
Matches: 111, Mismatches: 12, Indels: 26
0.74 0.08 0.17
Matches are distributed among these distances:
2 3 0.03
3 82 0.74
4 25 0.23
5 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:99076 original size:16 final size:16
Alignment explanation
Indices: 99034--99076 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
99024 ATTATTATTA
*
99034 TTATTATTATTCATGT
1 TTATTATTATCCATGT
99050 TTAATTATTATCCATG-
1 TT-ATTATTATCCATGT
99066 TTATGTATTAT
1 TTAT-TATTAT
99077 TATTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 10 0.42
17 12 0.50
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (16 bp):
TTATTATTATCCATGT
Found at i:99120 original size:45 final size:44
Alignment explanation
Indices: 98991--99144 Score: 115
Period size: 45 Copynumber: 3.4 Consensus size: 44
98981 TACTAAGTAT
*
98991 TTATTATCACATA-TAGTATTATTTACTATTAT-TATTATTATTATTA
1 TTATTATCACTTATTA-T-TTATTTA-TATTATAT-TTATTATTATTA
* *
99037 TTATTATTCA-TGT-TTAATTA-TTATCCATGT-TATGTATTATTATTA
1 TTATTA-TCACT-TATTATTTATTTAT--AT-TATATTTATTATTATTA
99082 TTATTATCACTTATTATTTATTTAGTATTATATTTATTATTATATA
1 TTATTATCACTTATTATTTATTTA-TATTATATTTATTATTAT-TA
* *
99128 TTATAAT-AATTATTATT
1 TTATTATCACTTATTATT
99145 AAGAACATTG
Statistics
Matches: 88, Mismatches: 7, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
43 1 0.01
44 8 0.09
45 53 0.60
46 19 0.22
47 7 0.08
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.58
Consensus pattern (44 bp):
TTATTATCACTTATTATTTATTTATATTATATTTATTATTATTA
Found at i:108339 original size:15 final size:16
Alignment explanation
Indices: 108315--108348 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
108305 ATTTTAGCCA
*
108315 TATTATGTATTAAT-T
1 TATTAAGTATTAATAT
108330 TATTAAGTATTAATAT
1 TATTAAGTATTAATAT
108346 TAT
1 TAT
108349 GCATACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TATTAAGTATTAATAT
Found at i:110906 original size:28 final size:27
Alignment explanation
Indices: 110857--110911 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
110847 CGATATACTT
*
110857 AATATATTATATAAAAATAAGATAATAG
1 AATATATTATAGAAAAATAAGA-AATAG
*
110885 AATATTTTATAGAAAAGA-AAGAAATAG
1 AATATATTATAGAAAA-ATAAGAAATAG
110912 GTACAAGGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 18 0.75
29 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (27 bp):
AATATATTATAGAAAAATAAGAAATAG
Found at i:122073 original size:17 final size:17
Alignment explanation
Indices: 122044--122079 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
122034 GTCTTACAAA
122044 ACGTATTTATGGACATC
1 ACGTATTTATGGACATC
122061 ACGT-TTTATTGGACATC
1 ACGTATTTA-TGGACATC
122078 AC
1 AC
122080 ATGGTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (17 bp):
ACGTATTTATGGACATC
Found at i:124884 original size:30 final size:32
Alignment explanation
Indices: 124808--124885 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 32
124798 TAATACTATG
124808 CTCATAATAACAAATAATGAAAAAACTTAGAT
1 CTCATAATAACAAATAATGAAAAAACTTAGAT
* * * * *
124840 TTC-TAGTAAAAAATACTGAAAAAA-TTGGA-
1 CTCATAATAACAAATAATGAAAAAACTTAGAT
124869 CTCATAATAACAAATAA
1 CTCATAATAACAAATAA
124886 ATATTAAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
29 2 0.06
30 14 0.39
31 18 0.50
32 2 0.06
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.26
Consensus pattern (32 bp):
CTCATAATAACAAATAATGAAAAAACTTAGAT
Found at i:125097 original size:31 final size:30
Alignment explanation
Indices: 125058--125146 Score: 90
Period size: 32 Copynumber: 2.9 Consensus size: 30
125048 GAGTAGGTCC
125058 TAAT-ATAAATATTTAAAAAAATTGAGCCCA
1 TAATAATAAATA-TTAAAAAAATTGAGCCCA
* * **
125088 TAATAATAAATATTAAGAAAAATTTAAACCTT
1 TAATAATAAATATTAA-AAAAA-TTGAGCCCA
*
125120 TAATAACAAATATTAAAAATAATTGAG
1 TAATAATAAATATTAAAAA-AATTGAG
125147 TTCTATAACT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
30 8 0.17
31 18 0.38
32 22 0.46
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (30 bp):
TAATAATAAATATTAAAAAAATTGAGCCCA
Found at i:127447 original size:35 final size:35
Alignment explanation
Indices: 127408--127480 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
127398 GGTTGATTAA
127408 CTATGGGGGCGGAGTGGGGTTTCTTCAATGTAAAT
1 CTATGGGGGCGGAGTGGGGTTTCTTCAATGTAAAT
127443 CTATGGGGGCGGAGTGGGGTTTCTTCAATGTAAAT
1 CTATGGGGGCGGAGTGGGGTTTCTTCAATGTAAAT
127478 CTA
1 CTA
127481 ATTGATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.21, C:0.12, G:0.36, T:0.32
Consensus pattern (35 bp):
CTATGGGGGCGGAGTGGGGTTTCTTCAATGTAAAT
Found at i:128989 original size:52 final size:52
Alignment explanation
Indices: 128911--129017 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
128901 TCGTCGGGTG
128911 ATCATTCTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
1 ATCATTCTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
*
128963 ATCATTTTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
1 ATCATTCTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
129015 ATC
1 ATC
129018 GAAAGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (52 bp):
ATCATTCTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
Found at i:129966 original size:20 final size:19
Alignment explanation
Indices: 129927--129968 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
129917 TTAACTATAA
*
129927 ATAAAATTTAAATTGATAT
1 ATAAAATTTAAATAGATAT
*
129946 ATAAAATATTAAATAGGTAT
1 ATAAAAT-TTAAATAGATAT
129966 ATA
1 ATA
129969 TCTGCAGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (19 bp):
ATAAAATTTAAATAGATAT
Found at i:131758 original size:12 final size:12
Alignment explanation
Indices: 131741--131766 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
131731 AGAAATGTAA
131741 GTCAACACTGGG
1 GTCAACACTGGG
131753 GTCAACACTGGG
1 GTCAACACTGGG
131765 GT
1 GT
131767 TTCATGTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (12 bp):
GTCAACACTGGG
Done.