Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009364.1 Hibiscus syriacus cultivar Beakdansim tig00113188_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: 150245
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6536 original size:42 final size:41
Alignment explanation
Indices: 6489--6585 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
6479 ACAATTTAAG
* * *
6489 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
* * *
6531 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
* *
6572 TCATTCGTGCCATC
1 TCCTTCGGGCCATC
6586 CATAAGACCT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 13 0.28
42 33 0.72
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:6862 original size:42 final size:42
Alignment explanation
Indices: 6803--6904 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
6793 ATCAGTAATT
6803 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
* * *
6845 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
*
6887 GCCATCAGTAAGTTTTTC
1 GCCATCAGTAAGTCTTTC
6905 AGGTAAAATG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
Found at i:6916 original size:42 final size:42
Alignment explanation
Indices: 6803--6946 Score: 150
Period size: 42 Copynumber: 3.5 Consensus size: 42
6793 ATCAGTAATT
** * * *
6803 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
1 GCCATCAGTAAGTCTTTCGAGCAAAATGATTAAATCCTTCGG
**
6845 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCAAAATGATTAAATCCTTCGG
* *
6887 GCCATCAGTAAGTTTTTC-AGGTAAAATGA-TAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGA-GCAAAATGATTAAATCCTTCGG
* *
6928 GTCATCCA-TAAGTCCTTCG
1 GCCAT-CAGTAAGTCTTTCG
6947 GGTAGGATGT
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
41 25 0.28
42 64 0.72
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCAAAATGATTAAATCCTTCGG
Found at i:10686 original size:25 final size:23
Alignment explanation
Indices: 10648--10704 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
10638 AATTGAATTT
* *
10648 AAAATT-CAATTAATGAGAATTTCC
1 AAAATTACCATTAATGA-AACTT-C
*
10672 AAAATTACCATTAATGAAACTTG
1 AAAATTACCATTAATGAAACTTC
10695 AAAATTACCA
1 AAAATTACCA
10705 AATGTCATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.34
24 10 0.34
25 9 0.31
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (23 bp):
AAAATTACCATTAATGAAACTTC
Found at i:11154 original size:16 final size:16
Alignment explanation
Indices: 11135--11170 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11125 TGACATCAGG
*
11135 TTCAGTTCGGGTTAAT
1 TTCAGTTCGGATTAAT
*
11151 TTCAGTTCGGATTGAT
1 TTCAGTTCGGATTAAT
11167 TTCA
1 TTCA
11171 TTTCAGGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (16 bp):
TTCAGTTCGGATTAAT
Found at i:11849 original size:27 final size:26
Alignment explanation
Indices: 11778--11878 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 26
11768 TTCTCTATTC
11778 TCTCTAAA-TTTCTAAATTTCCCTCTAT
1 TCTC-AAATTTTC-AAATTTCCCTCTAT
* ** *
11805 TCCCAAATATCCCCAATTTCCCTCTAT
1 TCTCAAAT-TTTCAAATTTCCCTCTAT
*
11832 TCTCAAAATTTTCAAATTTCACTCTAAAT
1 TCTC-AAATTTTCAAATTTCCCTCT--AT
11861 TCTC-AATTTTCCAAATTT
1 TCTCAAATTTT-CAAATTT
11879 TTTCAATTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
26 3 0.05
27 37 0.63
28 13 0.22
29 6 0.10
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.43
Consensus pattern (26 bp):
TCTCAAATTTTCAAATTTCCCTCTAT
Found at i:11894 original size:37 final size:38
Alignment explanation
Indices: 11840--11941 Score: 136
Period size: 37 Copynumber: 2.7 Consensus size: 38
11830 ATTCTCAAAA
* *
11840 TTTTCAAATTTCACTCTAAATTCTCAATTTTCC-AAATT
1 TTTTC-AATTTCCCTCTAAATTCTCAATTTCCCAAAATT
*
11878 TTTTCAATTTCCCTCTAAATTCCCAATTTCCCAAAATT
1 TTTTCAATTTCCCTCTAAATTCTCAATTTCCCAAAATT
*
11916 TCTT-AATTTCCCCTCTAAATTCTCAA
1 TTTTCAATTT-CCCTCTAAATTCTCAA
11942 ATAAAATCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 29 0.51
38 28 0.49
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (38 bp):
TTTTCAATTTCCCTCTAAATTCTCAATTTCCCAAAATT
Found at i:12220 original size:13 final size:13
Alignment explanation
Indices: 12197--12240 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
12187 TGAAATTAAT
*
12197 TTAATGATTATAA
1 TTAAGGATTATAA
12210 TTAA-GATTTATAA
1 TTAAGGA-TTATAA
12223 TATAAGGATTATAA
1 T-TAAGGATTATAA
12237 TTAA
1 TTAA
12241 TATACAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 10 0.36
15 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (13 bp):
TTAAGGATTATAA
Found at i:12391 original size:16 final size:16
Alignment explanation
Indices: 12370--12422 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
12360 TATAACTTAT
12370 AAGTCAGGTAAATATC
1 AAGTCAGGTAAATATC
*
12386 AAGTCAGATAAATATC
1 AAGTCAGGTAAATATC
* *
12402 ATA-TCAGGTCAATAAC
1 A-AGTCAGGTAAATATC
12418 AAGTC
1 AAGTC
12423 GAATTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 29 0.94
17 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (16 bp):
AAGTCAGGTAAATATC
Found at i:13865 original size:12 final size:12
Alignment explanation
Indices: 13840--13909 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
13830 ACGAATATAT
* *
13840 CAGAAATCAAAA
1 CAGAATTCAGAA
13852 CAGAATTCAGAA
1 CAGAATTCAGAA
13864 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
13876 CAGAATCCATAT
1 CAGAATTCAGAA
*
13888 CAGAAATCAGAA
1 CAGAATTCAGAA
*
13900 CATAATTCAG
1 CAGAATTCAG
13910 GTCATTTATC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:13867 original size:24 final size:24
Alignment explanation
Indices: 13840--13909 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
13830 ACGAATATAT
*
13840 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * *
13864 CAGATATCAGAACAGAATCCATAT
1 CAGAAATCAGAACAGAATTCAGAA
*
13888 CAGAAATCAGAACATAATTCAG
1 CAGAAATCAGAACAGAATTCAG
13910 GTCATTTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:15117 original size:43 final size:43
Alignment explanation
Indices: 15051--15134 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
15041 GATCCACGGT
* *
15051 ATTTAAATCTTTTTCCTCTATCCGGTCTTATTATTTAATTCCA
1 ATTTAAATCTTTTTCCTCCATCCGATCTTATTATTTAATTCCA
*
15094 ATTTATATCTTTTTCCTCCATCCGATCTTATTATTTAATTC
1 ATTTAAATCTTTTTCCTCCATCCGATCTTATTATTTAATTC
15135 AATCTCATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.52
Consensus pattern (43 bp):
ATTTAAATCTTTTTCCTCCATCCGATCTTATTATTTAATTCCA
Found at i:15584 original size:63 final size:63
Alignment explanation
Indices: 15485--15607 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
15475 TGCTTTCTTG
15485 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
15548 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
15608 CCTAGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:16549 original size:16 final size:17
Alignment explanation
Indices: 16518--16555 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
16508 GGTCAACAAT
16518 GGTCAACGCCGGTCAACG
1 GGTCAACG-CGGTCAACG
*
16536 GGTCAACG-GGTCAACT
1 GGTCAACGCGGTCAACG
16552 GGTC
1 GGTC
16556 GGATAAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.16
Consensus pattern (17 bp):
GGTCAACGCGGTCAACG
Found at i:18669 original size:12 final size:12
Alignment explanation
Indices: 18644--18713 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
18634 ACGAAGATAT
* *
18644 CAGAAATCAAAA
1 CAGAATTCAGAA
18656 CAGAATTCAGAA
1 CAGAATTCAGAA
*
18668 CAG-ATATCAAAA
1 CAGAAT-TCAGAA
* * *
18680 CAGAATCCATAT
1 CAGAATTCAGAA
*
18692 CAGAAATCAGAA
1 CAGAATTCAGAA
*
18704 CATAATTCAG
1 CAGAATTCAG
18714 GTCATTTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:18671 original size:24 final size:24
Alignment explanation
Indices: 18644--18713 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
18634 ACGAAGATAT
18644 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAAAACAGAATTCAGAA
* * * *
18668 CAGATATCAAAACAGAATCCATAT
1 CAGAAATCAAAACAGAATTCAGAA
* *
18692 CAGAAATCAGAACATAATTCAG
1 CAGAAATCAAAACAGAATTCAG
18714 GTCATTTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATTCAGAA
Found at i:18748 original size:24 final size:24
Alignment explanation
Indices: 18643--18750 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
18633 AACGAAGATA
*
18643 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * * *
18666 AACAGATATCAAAACAGAATCCATA-
1 -TCAGAAATCAGAACAGAATTCA-AG
* *
18691 TCAGAAATCAGAACATAATTCAGG
1 TCAGAAATCAGAACAGAATTCAAG
***
18715 TCATTTATCAGAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
*
18739 TCGGAAATCAGA
1 TCAGAAATCAGA
18751 TAAAATATTT
Statistics
Matches: 63, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
24 62 0.98
26 1 0.02
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:20361 original size:63 final size:63
Alignment explanation
Indices: 20289--20411 Score: 228
Period size: 63 Copynumber: 2.0 Consensus size: 63
20279 TGCTTTCTTG
20289 AACACTCTCTGATCTTAAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTAAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
* *
20352 AACACTCTCTGATCTTGAAACGGTTCTCTTAACATACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTAAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
20412 CCTAGGATTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.35
Consensus pattern (63 bp):
AACACTCTCTGATCTTAAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:21369 original size:18 final size:18
Alignment explanation
Indices: 21346--21384 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
21336 AACGGGTCAA
21346 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
21364 CGGGTCGGGTCAACTGGT
1 CGGGTCGGGTCAACAGGT
21382 CGG
1 CGG
21385 ATAAACGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:21373 original size:31 final size:31
Alignment explanation
Indices: 21338--21405 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
21328 CGCCGGTCAA
* *
21338 CGGGTCAACGGGTCGGGTCAACAGGTCGGGT
1 CGGGTCAACGGGTCGGATAAACAGGTCGGGT
* *
21369 CGGGTCAACTGGTCGGATAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGATAAACAGGTCGGGT
21400 CGGGTC
1 CGGGTC
21406 GGGTTATGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGATAAACAGGTCGGGT
Found at i:21384 original size:13 final size:13
Alignment explanation
Indices: 21338--21369 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
21328 CGCCGGTCAA
*
21338 CGGGTCAACGGGT
1 CGGGTCAACAGGT
21351 CGGGTCAACAGGT
1 CGGGTCAACAGGT
21364 CGGGTC
1 CGGGTC
21370 GGGTCAACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACAGGT
Found at i:26267 original size:29 final size:31
Alignment explanation
Indices: 26199--26264 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
26189 TGTTCAAAGT
* *
26199 TTGGCCACCAACCAAGATGGAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCC-A-AAC
26232 TTGGCCACCAACCAAGATGAAATTTCC-AAC
1 TTGGCCACCAACCAAGATGAAATTTCCAAAC
26262 TTG
1 TTG
26265 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCCAAAC
Found at i:27960 original size:23 final size:23
Alignment explanation
Indices: 27934--28000 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
27924 CCACATCTCA
*
27934 TATAATTACACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
*
27957 TATAATTGCACCGGAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* *
27980 TAGAATTGCACCGTAGTGCCA
1 TATAATTGCACCGAAGTGCCA
28001 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:28187 original size:103 final size:103
Alignment explanation
Indices: 28016--28231 Score: 387
Period size: 103 Copynumber: 2.1 Consensus size: 103
28006 TAATGTCCAT
* * * *
28016 AAGGACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACACATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
28081 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
28119 AAGGACCACACATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACACATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
28184 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
28222 AAGGACCACA
1 AAGGACCACA
28232 TAGACCCTCG
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACACATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:41814 original size:131 final size:133
Alignment explanation
Indices: 41564--41820 Score: 358
Period size: 131 Copynumber: 1.9 Consensus size: 133
41554 ATCATCAAAT
* * * * *
41564 TCACCATCAATTGGAGTCCACAGCCTGCAGAAAAAGGACAGTGTGATTCATAATAATTTCTTTGA
1 TCACCATCAATTGGAGTCCAAAGCCAGCAGAAAAAGGACAGTGTGACTCATAATAATTGCTTTAA
41629 GAAAAAAACATCACCATTAAGAAGTATGGTTTATGACTAGTGTTAAAACAGAGAACTTCTACATC
66 GAAAAAAACATCACCATTAAGAAGTATGGTTTATGACTAGTGTTAAAACAGAGAACTTCTACATC
41694 AAC
131 AAC
* *
41697 TCACCGTCAATTGGAGTCCAAAGCCAGCAGAAAAAGGATAG-GTGACTCATAATAATTGC-TTAA
1 TCACCATCAATTGGAGTCCAAAGCCAGCAGAAAAAGGACAGTGTGACTCATAATAATTGCTTTAA
* ** * * * *
41760 GAGAAAGGCATCATCATTGAGAAGCT-TGGTTTATGACTATTGTTAAAACTGAGAACTTCTA
66 GAAAAAAACATCACCATTAAGAAG-TATGGTTTATGACTAGTGTTAAAACAGAGAACTTCTA
41821 AGTTCTTATA
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
131 55 0.50
132 17 0.16
133 37 0.34
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (133 bp):
TCACCATCAATTGGAGTCCAAAGCCAGCAGAAAAAGGACAGTGTGACTCATAATAATTGCTTTAA
GAAAAAAACATCACCATTAAGAAGTATGGTTTATGACTAGTGTTAAAACAGAGAACTTCTACATC
AAC
Found at i:41916 original size:2 final size:2
Alignment explanation
Indices: 41909--41939 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41899 TTTTCTACCT
41909 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41940 TTCATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47901 original size:166 final size:166
Alignment explanation
Indices: 47614--47948 Score: 503
Period size: 166 Copynumber: 2.0 Consensus size: 166
47604 GTGATAGTAT
* *
47614 ATGTCCAATGTGTGGAATGGAAGAAGAGATGGTCGTTCATGTCTTGAGAGACTGCGCATATGCTC
1 ATGTCCAATGTGTGGAATGGAAGAAGAGACGATCGTTCATGTCTTGAGAGACTGCGCATATGCTC
* ** * *
47679 AGGAAACGTTTGTTTGTGTTGGAGTACAAGGTGGGTTTTTCTGGTCAACTTTGTATCTCCATTAG
66 AGGAAACGTTTATTTGTGCCGGAGCACAAGGTGGGTTTTTCTAGTCAACTTTGTATCTCCATTAG
* * * *
47744 ATTGGCTCA-ATTTGGCAATCTCTGTCATGAAGGTTG
131 ATTGGCT-AGATCTGGCAATCTATGCCATGAAGATTG
*
47780 ATGTCCAATGTGTGGAATGGAAGAAGAGACGATCGTTCATGTCTTGAGAGACTGTGCATATGCTC
1 ATGTCCAATGTGTGGAATGGAAGAAGAGACGATCGTTCATGTCTTGAGAGACTGCGCATATGCTC
*
47845 AGGAAACTTTTATTTGTGCCGGAGCACAAGGTGGGTTTTGTCTAGTCAAC-TTGTATCTCCATTA
66 AGGAAACGTTTATTTGTGCCGGAGCACAAGGTGGGTTTT-TCTAGTCAACTTTGTATCTCCATTA
* *
47909 GATTTGCTAGATCTGGTAATCTATGCCATGAAGATTG
130 GATTGGCTAGATCTGGCAATCTATGCCATGAAGATTG
47946 ATG
1 ATG
47949 ATCTAGCTTG
Statistics
Matches: 152, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
165 1 0.01
166 142 0.93
167 9 0.06
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (166 bp):
ATGTCCAATGTGTGGAATGGAAGAAGAGACGATCGTTCATGTCTTGAGAGACTGCGCATATGCTC
AGGAAACGTTTATTTGTGCCGGAGCACAAGGTGGGTTTTTCTAGTCAACTTTGTATCTCCATTAG
ATTGGCTAGATCTGGCAATCTATGCCATGAAGATTG
Found at i:53958 original size:2 final size:2
Alignment explanation
Indices: 53951--53984 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
53941 CTTTTAATGT
53951 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
53985 CATTATTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64970 original size:7 final size:7
Alignment explanation
Indices: 64952--64984 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
64942 AAGAAGATAA
64952 CATTTG-
1 CATTTGC
64958 CATTTGC
1 CATTTGC
64965 CATTTGC
1 CATTTGC
64972 CATTTGC
1 CATTTGC
64979 CATTTG
1 CATTTG
64985 ACACAAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.45
Consensus pattern (7 bp):
CATTTGC
Found at i:68626 original size:36 final size:37
Alignment explanation
Indices: 68558--68871 Score: 240
Period size: 37 Copynumber: 8.6 Consensus size: 37
68548 TTTTATAGCA
** *
68558 ATATAATATA-A-TTTTTGAAAATGTTTTTAAAATAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
* * * * *
68593 ATGTACTCTATAG-TTTCGAAAACATTTCGAAAATAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
* * * *
68629 ATATAGTATATAGTTTTTTAAAAAATTTTGAAAACAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
*
68666 ATATAATGTATAGTTTTTGAAAATGCA-TTTGAAAATAT
1 ATATAATATATAGTTTTTGAAAA--CATTTTGAAAATAT
*
68704 ATATAATATATAG-TTTTGAAATCATTTTGAAAATAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
* *
68740 -TTTAATATATAGTTTTTAAAAAAACATTTTTGAAAA-ATT
1 ATATAATATATAGTTTTT--GAAAACA-TTTTGAAAATA-T
* ** *
68779 ATATAATATATAG-TTTTAAAAACATATTTTTAAATCT
1 ATATAATATATAGTTTTTGAAAACAT-TTTGAAAATAT
* * *
68816 -TAT-ATA-ATA-TTTTT-AAATCATTTTTAAAAAAACT
1 ATATAATATATAGTTTTTGAAAACA-TTTTGAAAATA-T
*
68850 ATATAATATATAGTTTTGGAAA
1 ATATAATATATAGTTTTTGAAA
68872 TTTTTTAAGA
Statistics
Matches: 221, Mismatches: 36, Indels: 40
0.74 0.12 0.13
Matches are distributed among these distances:
33 11 0.05
34 9 0.04
35 26 0.12
36 51 0.23
37 63 0.29
38 32 0.14
39 18 0.08
40 11 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
Found at i:68646 original size:73 final size:74
Alignment explanation
Indices: 68558--68795 Score: 211
Period size: 75 Copynumber: 3.2 Consensus size: 74
68548 TTTTATAGCA
** * * * *
68558 ATATAATATA-A-TTTTTGAAAATGTTTTTAAAATATATGTACTCTATAG-TTTCGAAAA-CATT
1 ATATAATATATAGTTTTTGAAAAAATTTTGAAAACATATATAATCTATAGTTTTCGAAAAGCATT
68619 TCGAAAATAT
66 T-GAAAATAT
* * * *
68629 ATATAGTATATAGTTTTTTAAAAAATTTTGAAAACATATATAATGTATAGTTTTTGAAAATGCAT
1 ATATAATATATAGTTTTTGAAAAAATTTTGAAAACATATATAATCTATAGTTTTCGAAAA-GCAT
68694 TTGAAAATAT
65 TTGAAAATAT
** * * * ** *
68704 ATATAATATATAG-TTTTGAAATCATTTTGAAAATAT-TTTAATATATAGTTTTTAAAAAAACAT
1 ATATAATATATAGTTTTTGAAAAAATTTTGAAAACATATATAATCTATAG-TTTTCGAAAAGCA-
68767 TTTTGAAAA-ATT
64 -TTTGAAAATA-T
68779 ATATAATATATAGTTTT
1 ATATAATATATAGTTTT
68796 AAAAACATAT
Statistics
Matches: 137, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
71 9 0.07
72 1 0.01
73 41 0.30
74 36 0.26
75 42 0.31
76 8 0.06
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (74 bp):
ATATAATATATAGTTTTTGAAAAAATTTTGAAAACATATATAATCTATAGTTTTCGAAAAGCATT
TGAAAATAT
Found at i:68772 original size:75 final size:75
Alignment explanation
Indices: 68611--68938 Score: 270
Period size: 75 Copynumber: 4.5 Consensus size: 75
68601 TATAGTTTCG
* * * * * *
68611 AAAACA-TTTCGAAAATATATATAGTATATAGTTTTTTAAAAAATTTTGAAAACATATATAATGT
1 AAAACATTTTTGAAAATATATATAATATATAG-TTTTGAAAACATTTTGAAAATAT-TATAATAT
*
68675 ATAGTTTTTGAA
64 ATAGTTTTTAAA
** * *
68687 AATGCA--TTTGAAAATATATATAATATATAGTTTTGAAATCATTTTGAAAATATTTTAATATAT
1 AAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATATTATAATATAT
68750 AGTTTTTAAA
66 AGTTTTTAAA
* ** *
68760 AAAACATTTTTGAAAA-ATTATATAATATATAGTTTTAAAAACATATTTTTAAATCTTAT-ATA-
1 AAAACATTTTTGAAAATA-TATATAATATATAGTTTTGAAAACAT-TTTGAAAATATTATAATAT
68822 ATA-TTTTT---
64 ATAGTTTTTAAA
* * * * * * *
68830 AAATCATTTTTAAAAAAACTATATAATATATAGTTTTGGAAA-TTTTTTAAGA-A-TATAATATA
1 AAAACATTTTTGAAAATA-TATATAATATATAGTTTTGAAAACATTTTGAAAATATTATAATATA
*
68892 TAGTTTTAAAAA
65 TAGTTTT-TAAA
* *
68904 AAATATATTTTTG-AAATATATATATTATATAGTTT
1 AAA-ACATTTTTGAAAATATATATAATATATAGTTT
68939 ATATTATATT
Statistics
Matches: 205, Mismatches: 34, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
67 3 0.01
68 3 0.01
69 9 0.04
70 19 0.09
71 22 0.11
73 42 0.20
74 30 0.15
75 63 0.31
76 14 0.07
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (75 bp):
AAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATATTATAATATAT
AGTTTTTAAA
Found at i:68800 original size:38 final size:36
Alignment explanation
Indices: 68601--68903 Score: 170
Period size: 37 Copynumber: 8.4 Consensus size: 36
68591 ATATGTACTC
** * *
68601 TATAGTTTCGAAAACATTTCG-AAAATATATATAGTA
1 TATAGTTTTAAAAACATTTTGAAAAAT-TATATAATA
*
68637 TATAGTTTTTTAAAAA-ATTTTGAAAACA-TATATAATG
1 TATAG--TTTTAAAAACATTTTGAAAA-ATTATATAATA
*
68674 TATAGTTTTTGAAAATGCA-TTTG-AAAATATATATAATA
1 TATAG-TTTT-AAAA-ACATTTTGAAAAAT-TATATAATA
* *
68712 TATAGTTTTGAAATCATTTTGAAAATATT-T-TAATA
1 TATAGTTTTAAAAACATTTTGAAAA-ATTATATAATA
68747 TATAGTTTTTAAAAAAACATTTTTGAAAAATTATATAATA
1 TATAG-TTTT--AAAAACA-TTTTGAAAAATTATATAATA
**
68787 TATAGTTTTAAAAACATATTT-TTAAATCT-TAT-ATA
1 TATAGTTTTAAAAACAT-TTTGAAAAAT-TATATAATA
* * * *
68822 -ATA-TTTTTAAATCATTTTTAAAAAAACTATATAATA
1 TATAGTTTTAAAAACA-TTTT-GAAAAATTATATAATA
** ** *
68858 TATAGTTTT-GGAA-ATTTTTTAAGA--ATATAATA
1 TATAGTTTTAAAAACATTTTGAAAAATTATATAATA
68890 TATAGTTTTAAAAA
1 TATAGTTTTAAAAA
68904 AAATATATTT
Statistics
Matches: 213, Mismatches: 26, Indels: 59
0.71 0.09 0.20
Matches are distributed among these distances:
32 17 0.08
33 14 0.07
34 8 0.04
35 25 0.12
36 35 0.16
37 47 0.22
38 41 0.19
39 16 0.08
40 10 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
TATAGTTTTAAAAACATTTTGAAAAATTATATAATA
Found at i:71365 original size:5 final size:5
Alignment explanation
Indices: 71355--71408 Score: 92
Period size: 5 Copynumber: 10.8 Consensus size: 5
71345 CACTAACTCT
71355 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT- TTTTCA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A
71405 TTTT
1 TTTT
71409 GTTCTCATCA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.09
5 39 0.83
6 4 0.09
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:72067 original size:19 final size:19
Alignment explanation
Indices: 72033--72077 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
72023 ATTTAGACAT
72033 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
72051 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
72070 TTTGCATT
1 TTTGCATT
72078 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:75341 original size:165 final size:164
Alignment explanation
Indices: 75066--77019 Score: 2847
Period size: 165 Copynumber: 11.9 Consensus size: 164
75056 TTTTTTAACA
* * ***
75066 ATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
** *
75131 TCAGCTTCGAGGGCACATCATTTACAATATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAG
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTACC-AAAG
75196 ACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCAC
130 ACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCAC
* * * * *
75231 ATCATTTGCAGCATAGCTTACGTCGAGAAGGGCTATCTGCCAAAGA-CCTTCGAGTTCGACTACG
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTT-AAGTTCGATTACA
* * * * * * *
75295 CTCAGCTCCGAGGGCATATCATTTGCAGCACAACAT-AAGTCTAGAAGGGTTGTCTGTAAACCAA
65 CTCAGCTTCGAGGGCACATCATTTACAGCATAAC-TCAAGGCTAGAAGGGTTATCTGT-TACCAA
* *
75359 AGACCTTTGAGTTCGACTACACTCGGCT-CAACGGCAC
128 AGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCAC
* * ***
75396 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * **
75461 TCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TTACCAAAG
*
75526 ACCTTTGAGTTCGACTATGCTCAGCTCCAAGGCAC
130 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * ** *
75561 ATCATTTCCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATCACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * * * * *
75626 TCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAG
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TTACCAAAG
75691 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
130 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
75726 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * * *
75791 TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTTAGCAAAGA
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAGA
75856 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
131 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
75890 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * *
75955 TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGA
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAGA
76020 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
131 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * * ***
76054 ATCATTTACAGAATAACTTAAGTCGAGAAGGGCTATTTGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * **
76119 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTG-GAGAAGGGTTATCTGCCAACCAAA
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAG-GCTAGAAGGGTTATCTG-TTACCAAA
76183 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
129 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * *** *
76219 ATCATTTCCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATCACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * * * * * *
76284 TCAACTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAG
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TTACCAAAG
76349 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
130 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
76384 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTTAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * * *
76449 TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGTTAGCAAAGA
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAGA
76514 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
131 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
76548 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * *
76613 TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGA
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAGA
76678 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
131 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
76712 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * * *
76777 TCAACTTCAAGGGCATAGCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGA
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAGA
76842 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
131 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* *
76876 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCAATTACTC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * ** *
76941 TCAGCTTGGAGGGCACATCATTCACAATATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAG
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-TACCAAAG
*
77006 ACCTTCGAGTTCGA
130 ACCTTTGAGTTCGA
77020 TTATATTCAA
Statistics
Matches: 1656, Mismatches: 122, Indels: 22
0.92 0.07 0.01
Matches are distributed among these distances:
164 790 0.48
165 857 0.52
166 9 0.01
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (164 bp):
ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAGA
CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
Found at i:76324 original size:658 final size:658
Alignment explanation
Indices: 75066--77019 Score: 3166
Period size: 658 Copynumber: 3.0 Consensus size: 658
75056 TTTTTTAACA
* * ***
75066 ATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
* * * ** * *
75131 TCAGCTTCGAGGGCACATCATTTACAATATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAG
66 TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGC-AAAG
* *
75196 ACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTACGTCGAGAA
130 ACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGAATAGCTTAAGTCGAGAA
* * * * * * *
75260 GGGCTATCTGCCAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCGAGGGCATATCATTTGCAGC
194 GGGCTATCTGCCAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAGCATTTACAGC
* * * * * * *
75324 ACAACAT-AAGTCTAGAAGGGTTGTCTGTAAACCAAAGACCTTTGAGTTCGACTACACTCGGCT-
258 ATAAC-TCAAGGCTAGAAGGGTTATCTGT-TAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
*
75387 CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCCCGAGTT
321 CAA-GGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCCCGAGTT
*
75452 CGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGC
385 CGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTGGAGAAGGGTTATCTGC
*
75517 CAACCAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTCCAGCATAGCTTAA
450 CAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTCCAGCATAGCTTAA
75582 GTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATCACACTCAGCTTCGAGGGCACATCAT
515 GTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATCACACTCAGCTTCGAGGGCACATCAT
75647 TTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCT
580 TTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCT
75712 CAGCTCCAAGGCAC
645 CAGCTCCAAGGCAC
75726 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
*
75791 TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTTAGCAAAGA
66 TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGA
75856 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGG
131 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGG
75921 GCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAGCATTTACAGCATA
196 GCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAGCATTTACAGCATA
75986 ACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
261 ACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* * *
76051 CACATCATTTACAGAATAACTTAAGTCGAGAAGGGCTATTTGCCAAAGACCCCCGAGTTCGATTA
326 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCCCGAGTTCGATTA
*
76116 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTGGAGAAGGGTTATCTGCCAACCA
391 CACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTGGAGAAGGGTTATCTGCCAACCA
76181 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTCCAGCATAGCTTAAGTCGAG
456 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTCCAGCATAGCTTAAGTCGAG
* *
76246 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATCACACTCAACTTCGAGGGCACATCATTTGCAG
521 AAGGGCTATCTGCCAAAGACCCCCAAGTTCGATCACACTCAGCTTCGAGGGCACATCATTTGCAG
76311 TATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTC
586 TATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTC
76376 CAAGGCAC
651 CAAGGCAC
*
76384 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTTAGTTCGATTACAC
1 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
*
76449 TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGTTAGCAAAGA
66 TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGA
76514 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGG
131 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGG
76579 GCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAGCATTTACAGCATA
196 GCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAGCATTTACAGCATA
76644 ACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
261 ACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* ***
76709 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTA
326 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCCCGAGTTCGATTA
* * * * * * ** *
76774 CACTCAACTTCAAGGGCATAGCATTTACAGCATAACTCAAG-GCTAGAAGGGTTATCTG-TTAGC
391 CACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTG-GAGAAGGGTTATCTGCCAACC
* *
76837 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGA
455 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTCCAGCATAGCTTAAGTCGA
** * * * * **
76902 GAAGGGCTATCTGCCAAAGACCCTTAAGTTCAATTACTCTCAGCTTGGAGGGCACATCATTCACA
520 GAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATCACACTCAGCTTCGAGGGCACATCATTTGCA
* * * * * *
76967 ATATAACTCAAGGCTAGAAGGGTTATCTG-TCAACCAAAGACCTTCGAGTTCGA
585 GTATAACTTAAGTCAAGAAGGGTTATCTGCT-AACAAAAGACCTTTGAGTTCGA
77020 TTATATTCAA
Statistics
Matches: 1213, Mismatches: 75, Indels: 15
0.93 0.06 0.01
Matches are distributed among these distances:
656 1 0.00
657 166 0.14
658 787 0.65
659 140 0.12
660 119 0.10
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (658 bp):
ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
TCAGCTTCAAGGGCATAGCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGA
CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGG
GCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAGCATTTACAGCATA
ACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCCCGAGTTCGATTA
CACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTGGAGAAGGGTTATCTGCCAACCA
AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTCCAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCCCAAGTTCGATCACACTCAGCTTCGAGGGCACATCATTTGCAG
TATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTC
CAAGGCAC
Found at i:77720 original size:37 final size:37
Alignment explanation
Indices: 77610--77922 Score: 229
Period size: 37 Copynumber: 8.6 Consensus size: 37
77600 TTTTATAGCA
** *
77610 ATATAATATA-A-TTTTTGAAAATGTTTTTAAAATAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
* * * * *
77645 ATGTACTCTATAG-TTTCGAAAACATTTCGAAAATAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
* * * *
77681 ATATAGTATATAGTTTTTTAAAAAATTTTGAAAACAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
*
77718 ATATAATGTATAGTTTTTGAAAATGCA-TTTGAAAATAT
1 ATATAATATATAGTTTTTGAAAA--CATTTTGAAAATAT
*
77756 ATATAATATATAG-TTTTGAAATCATTTTGAAAATAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
* * * *
77792 -TTTAATATATAGTTTTTAAAAAAAAAATTTGAAAA-ATT
1 ATATAATATATAGTTTTT--GAAAACATTTTGAAAATA-T
* ** *
77830 ATATAATATATAG-TTTTAAAAACATATTTTTAAATCT
1 ATATAATATATAGTTTTTGAAAACAT-TTTGAAAATAT
* * *
77867 -TAT-ATA-ATA-TTTTT-AAATCATTTTTAAAAAAACT
1 ATATAATATATAGTTTTTGAAAACA-TTTTGAAAATA-T
*
77901 ATATAATATATAGTTTTGGAAA
1 ATATAATATATAGTTTTTGAAA
77923 TTTTTTAAGA
Statistics
Matches: 217, Mismatches: 40, Indels: 38
0.74 0.14 0.13
Matches are distributed among these distances:
33 11 0.05
34 9 0.04
35 26 0.12
36 56 0.26
37 57 0.26
38 43 0.20
39 15 0.07
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (37 bp):
ATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
Found at i:77835 original size:74 final size:74
Alignment explanation
Indices: 77663--77988 Score: 221
Period size: 74 Copynumber: 4.4 Consensus size: 74
77653 TATAGTTTCG
* * * *
77663 AAAACATTTCGAAAATATATATAGTATATAGTTTTTTAAAAAATTTTGAAAACATATATAATGTA
1 AAAAAATTT-GAAAATATATATAATATATAG-TTTTGAAAAAATTTTGAAAACATATATAATATA
*
77728 TAGTTTTTGAA
64 TAGTTTTTAAA
*** ** * *
77739 AATGCATTTGAAAATATATATAATATATAGTTTTGAAATCATTTTGAAAATAT-TTTAATATATA
1 AAAAAATTTGAAAATATATATAATATATAGTTTTGAAAAAATTTTGAAAACATATATAATATATA
77803 GTTTTTAAAA
66 GTTTTT-AAA
* * *
77813 AAAAAATTTGAAAA-ATTATATAATATATAGTTTTAAAAACATATTTTTAAATC-T-TAT-ATA-
1 AAAAAATTTGAAAATA-TATATAATATATAGTTTTGAAAA-A-ATTTTGAAAACATATATAATAT
77873 ATA-TTTTT-AA
63 ATAGTTTTTAAA
** ** * * * ** *
77883 ATCATTTTTAAAAAAACTATATAATATATAGTTTTG--GAAATTTT-TTAAGA-ATATAATATAT
1 AAAAAATTTGAAAATA-TATATAATATATAGTTTTGAAAAAATTTTGAAAACATATATAATATAT
77944 AG-TTTTAAA
65 AGTTTTTAAA
*
77953 AAAATATATTTTTG-AAATATATATATTATATAGTTT
1 AAAA-A-A--TTTGAAAATATATATAATATATAGTTT
77989 ATATTATATT
Statistics
Matches: 196, Mismatches: 39, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
66 1 0.01
67 8 0.04
68 4 0.02
69 8 0.04
70 15 0.08
71 19 0.10
72 21 0.11
73 23 0.12
74 59 0.30
75 23 0.12
76 15 0.08
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (74 bp):
AAAAAATTTGAAAATATATATAATATATAGTTTTGAAAAAATTTTGAAAACATATATAATATATA
GTTTTTAAA
Found at i:77870 original size:38 final size:38
Alignment explanation
Indices: 77634--77988 Score: 157
Period size: 38 Copynumber: 9.7 Consensus size: 38
77624 TTGAAAATGT
* * * **
77634 TTTTAAAATA-TATGTACTCTATAGTTTCGAAAACAT-
1 TTTTAAAATATTATATAATATATAGTTTTAAAAACATA
** *
77670 TTCGAAAATA-TATATAGTATATAGTTTTTTAAAAA-AT-
1 TTTTAAAATATTATATAATATATAG--TTTTAAAAACATA
* * * **
77707 TTTGAAAACA-TATATAATGTATAGTTTTTGAAA-ATGCA
1 TTTTAAAATATTATATAATATATAGTTTTAAAAACAT--A
* * *
77745 TTTGAAAATA-TATATAATATATAGTTTTGAAATCAT-
1 TTTTAAAATATTATATAATATATAGTTTTAAAAACATA
* * *
77781 TTTGAAAATATT-T-TAATATATAGTTTTTAAAAAAAAAA
1 TTTTAAAATATTATATAATATATAG-TTTT-AAAAACATA
*
77819 TTTGAAAA-ATTATATAATATATAGTTTTAAAAACATA
1 TTTTAAAATATTATATAATATATAGTTTTAAAAACATA
* * *
77856 TTTTTAAATCTTATAT-A-ATAT--TTTT-AAATCAT-
1 TTTTAAAATATTATATAATATATAGTTTTAAAAACATA
* * **
77888 TTTTAAAAAAACTATATAATATATAGTTTT-GGAA-AT-
1 TTTT-AAAATATTATATAATATATAGTTTTAAAAACATA
* * *
77924 TTTT-TAAGA--ATATAATATATAGTTTTAAAAAAATATA
1 TTTTAAAATATTATATAATATATAGTTTT--AAAAACATA
* *
77961 TTTTTGAAATA-TATATATTATATAGTTT
1 -TTTTAAAATATTATATAATATATAGTTT
77989 ATATTATATT
Statistics
Matches: 251, Mismatches: 42, Indels: 48
0.74 0.12 0.14
Matches are distributed among these distances:
32 21 0.08
33 14 0.06
34 8 0.03
35 25 0.10
36 46 0.18
37 49 0.20
38 58 0.23
39 15 0.06
40 15 0.06
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (38 bp):
TTTTAAAATATTATATAATATATAGTTTTAAAAACATA
Found at i:77978 original size:17 final size:16
Alignment explanation
Indices: 77937--77979 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
77927 TTAAGAATAT
*
77937 AATATATAGTTTTAAA
1 AATATATATTTTTAAA
*
77953 AAAATATATTTTTGAAA
1 AATATATATTTTT-AAA
*
77970 TATATATATT
1 AATATATATT
77980 ATATAGTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
AATATATATTTTTAAA
Found at i:78042 original size:10 final size:10
Alignment explanation
Indices: 78027--78068 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
78017 TTATTATTAT
*
78027 TTTCATTTCA
1 TTTCATTTAA
*
78037 TTTCATTTTA
1 TTTCATTTAA
78047 -TTCATTTAA
1 TTTCATTTAA
*
78056 TTTAATTTAA
1 TTTCATTTAA
78066 TTT
1 TTT
78069 AATTGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTCATTTAA
Found at i:80241 original size:13 final size:16
Alignment explanation
Indices: 80202--80232 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
80192 TATTTTTTCA
*
80202 AATAATCATAATAAAC
1 AATAATTATAATAAAC
80218 AATAATTATAATAAA
1 AATAATTATAATAAA
80233 AAAATATAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATTATAATAAAC
Found at i:82420 original size:23 final size:24
Alignment explanation
Indices: 82357--82423 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
82347 TTAATAAAAA
*
82357 TATTTATGTCTTTGTGAT-ATG-T
1 TATTTATGTCTTTGTGATCACGTT
*
82379 TA-TT-TGTCTTTATGA-CACGTT
1 TATTTATGTCTTTGTGATCACGTT
82400 TATTTATGTCTTTGT-ATCACGTT
1 TATTTATGTCTTTGTGATCACGTT
82423 T
1 T
82424 TTCTCTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 12 0.32
21 5 0.14
22 5 0.14
23 15 0.41
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.57
Consensus pattern (24 bp):
TATTTATGTCTTTGTGATCACGTT
Found at i:84898 original size:38 final size:38
Alignment explanation
Indices: 84847--84923 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
84837 TACTCATGCT
* *
84847 TAAATTTATCAGATTTCCACTATATTGGTTGATTTTAC
1 TAAATTTATCAGATTTACACTATATTGGGTGATTTTAC
84885 TAAATTTATCAGATTTACACTATATTGGGTGATTTTAC
1 TAAATTTATCAGATTTACACTATATTGGGTGATTTTAC
84923 T
1 T
84924 TCTTGTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (38 bp):
TAAATTTATCAGATTTACACTATATTGGGTGATTTTAC
Found at i:95301 original size:34 final size:33
Alignment explanation
Indices: 95247--95314 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
95237 CTTGTGGGTA
95247 TACCGTACGCGTCACCTTTAGTAAGGAAAATCT
1 TACCGTACGCGTCACCTTTAGTAAGGAAAATCT
* *
95280 TACCGTACCGTGTTACCTTTAGTAAGGAAAATCT
1 TACCGTA-CGCGTCACCTTTAGTAAGGAAAATCT
95314 T
1 T
95315 CTAGGTACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (33 bp):
TACCGTACGCGTCACCTTTAGTAAGGAAAATCT
Found at i:102001 original size:3 final size:3
Alignment explanation
Indices: 101995--102028 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
101985 ATTTCTTTTT
* *
101995 TTA TTA TTA TTG TTA TTG TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
102029 CTTTTTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:104954 original size:132 final size:128
Alignment explanation
Indices: 104553--104956 Score: 436
Period size: 132 Copynumber: 3.1 Consensus size: 128
104543 CCAAATAAAA
* * *
104553 CGGTTGGGCCCTTTTTTATGTATTTTTTAAAAATTAAAAACAATTTTTATATAAAAAAATTAAAC
1 CGGTTGGGCCCTTTTTTGTGTATCTTTT--AAATTAAAAACAGTTTTTATATAAAAAAATTAAAC
* * * * *
104618 CCCCAAGCAATTGGGTCTATAGCTCAGCGATGGTACTGCAGATCAAGAGTTCAACTGTTCGAACC
64 CCTCAAGCAATTGGGTCTATAGCTCAGTGGTAGTACTGCAGATCAAGAGTTCAACGGTTCGAACC
* ** * *
104683 CGGTTGGGCCATTTTTTGCCTATCTTTTAAATGAAAAACAGTTTTTATAT--AAAAATTAGACCC
1 CGGTTGGGCCCTTTTTTGTGTATCTTTTAAATTAAAAACAGTTTTTATATAAAAAAATTAAACCC
* * * ** *
104746 TCTAGCAATTGGGTTTATAACCCTGTGGTGGATACTTAACTGCAGATCAAGAGTTCAACGGTTCG
66 TCAAGCAATTGGGTCTAT-A-GCT-CAGTGG-TA-GT-ACTGCAGATCAAGAGTTCAACGGTTCG
104811 AACC
125 AACC
* * *
104815 TGGTTGGGCCCTTTATCGTGTATCTTTTAAATTAAAAACAGTTTTTATATAATAAAAAAATTAAA
1 CGGTTGGGCCCTTTTTTGTGTATCTTTTAAATTAAAAACAG-TTTT-TAT-ATAAAAAAATTAAA
* * * *
104880 CCCTCAATCAATTGGGTCTATAGCTCAGTGGTAGTACTGCAGTTCAAG-TTGTCACCGGTTCGAA
63 CCCTCAAGCAATTGGGTCTATAGCTCAGTGGTAGTACTGCAGATCAAGAGT-TCAACGGTTCGAA
104944 CC
127 CC
104946 CGGTTTGGGCC
1 CGG-TTGGGCC
104957 GGGTTTTTTT
Statistics
Matches: 223, Mismatches: 38, Indels: 24
0.78 0.13 0.08
Matches are distributed among these distances:
126 27 0.12
127 1 0.00
128 22 0.10
129 2 0.01
130 25 0.11
131 29 0.13
132 72 0.32
133 6 0.03
134 7 0.03
135 4 0.02
136 1 0.00
137 27 0.12
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (128 bp):
CGGTTGGGCCCTTTTTTGTGTATCTTTTAAATTAAAAACAGTTTTTATATAAAAAAATTAAACCC
TCAAGCAATTGGGTCTATAGCTCAGTGGTAGTACTGCAGATCAAGAGTTCAACGGTTCGAACC
Found at i:112735 original size:2 final size:2
Alignment explanation
Indices: 112728--112759 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
112718 TAAAAAGTAA
112728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112760 AATTTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115867 original size:16 final size:16
Alignment explanation
Indices: 115831--115869 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
115821 TCGGATTCAT
115831 TTAAAAAATAAATTTA
1 TTAAAAAATAAATTTA
*
115847 ATAAAATAATAAA-TTA
1 TTAAAA-AATAAATTTA
115863 TTAAAAA
1 TTAAAAA
115870 TATTACGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.65
17 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAAAATAAATTTA
Found at i:135886 original size:21 final size:21
Alignment explanation
Indices: 135840--135879 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
135830 AAATTATATT
*
135840 AATTAATTATAATTTAATTCA
1 AATTAATTATAATTTAATCCA
135861 AATTAA-TA-AATTTAATCCA
1 AATTAATTATAATTTAATCCA
135880 CCAATTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTAATTATAATTTAATCCA
Found at i:137108 original size:25 final size:25
Alignment explanation
Indices: 137078--137127 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
137068 CTCTTTGAGA
137078 GAGTGTTCTCAATAATTTGAGGTAT
1 GAGTGTTCTCAATAATTTGAGGTAT
137103 GAGTGTTCTCAATAATTTGAGGTAT
1 GAGTGTTCTCAATAATTTGAGGTAT
137128 AATTCTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (25 bp):
GAGTGTTCTCAATAATTTGAGGTAT
Found at i:139989 original size:24 final size:26
Alignment explanation
Indices: 139944--139995 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
139934 CGTTCGTGAA
*
139944 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
139970 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
139994 CG
1 CG
139996 AACAGAGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:140264 original size:10 final size:10
Alignment explanation
Indices: 140249--140290 Score: 57
Period size: 10 Copynumber: 3.9 Consensus size: 10
140239 TTTTTTTTTA
140249 TTCGTTTATG
1 TTCGTTTATG
140259 TTCGTTTATTGTG
1 TTCGTTTA---TG
140272 TTCGTTTATG
1 TTCGTTTATG
140282 TTCGTTTAT
1 TTCGTTTAT
140291 TATTTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 19 0.66
13 10 0.34
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.62
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:140293 original size:13 final size:13
Alignment explanation
Indices: 140254--140293 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
140244 TTTTATTCGT
140254 TTATGTTCGTTTA
1 TTATGTTCGTTTA
*
140267 TTGTGTTCG--T-
1 TTATGTTCGTTTA
140277 TTATGTTCGTTTA
1 TTATGTTCGTTTA
140290 TTAT
1 TTAT
140294 TTAAATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 8 0.36
11 1 0.05
12 1 0.05
13 12 0.55
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.62
Consensus pattern (13 bp):
TTATGTTCGTTTA
Found at i:140334 original size:21 final size:21
Alignment explanation
Indices: 140308--140355 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
140298 ATGAACGAAC
*
140308 ATGAACAAGCTATATTCTTTA
1 ATGAACAAGCTATATTCCTTA
*
140329 ATGAACAAGTTATATTCCTTA
1 ATGAACAAGCTATATTCCTTA
140350 ATGAAC
1 ATGAAC
140356 GAACATGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (21 bp):
ATGAACAAGCTATATTCCTTA
Found at i:144079 original size:28 final size:28
Alignment explanation
Indices: 144048--144128 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 28
144038 TTTAAGTACT
*
144048 TAAAGTTTTTTTTATCAAAATAAATATC
1 TAAAGTTTTTTTTGTCAAAATAAATATC
**
144076 TAAAGTTATCTTTTTGGTCAAAATAGGTATC
1 TAAAGTT-T-TTTTT-GTCAAAATAAATATC
* *
144107 TAAAGTATTTTATGTCAAAATA
1 TAAAGTTTTTTTTGTCAAAATA
144129 GGTACTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 16 0.36
29 5 0.11
30 6 0.13
31 18 0.40
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (28 bp):
TAAAGTTTTTTTTGTCAAAATAAATATC
Found at i:144138 original size:28 final size:28
Alignment explanation
Indices: 144048--144132 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 28
144038 TTTAAGTACT
* * **
144048 TAAAGTTTTTTTTATCAAAATAAATATC
1 TAAAGTATTTTTTGTCAAAATAGGTATC
144076 TAAAGTTATCTTTTTGGTCAAAATAGGTATC
1 TAAAG-TAT-TTTTT-GTCAAAATAGGTATC
*
144107 TAAAGTATTTTATGTCAAAATAGGTA
1 TAAAGTATTTTTTGTCAAAATAGGTA
144133 CTTAAACTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 18 0.37
29 6 0.12
30 8 0.16
31 17 0.35
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (28 bp):
TAAAGTATTTTTTGTCAAAATAGGTATC
Found at i:144310 original size:31 final size:29
Alignment explanation
Indices: 144229--144330 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 29
144219 AAAAATGAAT
* *
144229 ACTTTATGTACCTATTTTGACC-AAAAAT-
1 ACTTTA-GTACTTATTTAGACCAAAAAATA
* * *
144257 AGTTTAGATACCTATTTTGACCAAAAATATA
1 ACTTTAG-TACTTATTTAGACCAAAAA-ATA
* *
144288 ACTTTGGGTACTTATTTAGACCAAAAAATT
1 ACTTT-AGTACTTATTTAGACCAAAAAATA
144318 ACTTTAGTACTTA
1 ACTTTAGTACTTA
144331 AATGAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.02
28 19 0.31
29 11 0.18
30 9 0.15
31 21 0.34
32 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (29 bp):
ACTTTAGTACTTATTTAGACCAAAAAATA
Done.