Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009432.1 Hibiscus syriacus cultivar Beakdansim tig00113421_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: 327225
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
File 1 of 2
Found at i:3438 original size:21 final size:21
Alignment explanation
Indices: 3410--3484 Score: 134
Period size: 21 Copynumber: 3.6 Consensus size: 21
3400 TCATAAGCGA
3410 ATGG-ACAACCACTCACCTAG
1 ATGGTACAACCACTCACCTAG
3430 ATGGTACAACCACTCACCTAG
1 ATGGTACAACCACTCACCTAG
3451 ATGGTACAACCACTCACCTAG
1 ATGGTACAACCACTCACCTAG
*
3472 ATGGTGCAACCAC
1 ATGGTACAACCAC
3485 ATGATTCAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 4 0.08
21 49 0.92
ACGTcount: A:0.33, C:0.33, G:0.16, T:0.17
Consensus pattern (21 bp):
ATGGTACAACCACTCACCTAG
Found at i:7357 original size:20 final size:20
Alignment explanation
Indices: 7332--7370 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
7322 TCCTTCTCTG
7332 CATCCAAATAAATTCATCAA
1 CATCCAAATAAATTCATCAA
7352 CATCCAAATAAATTCATCA
1 CATCCAAATAAATTCATCA
7371 TATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (20 bp):
CATCCAAATAAATTCATCAA
Found at i:7381 original size:19 final size:20
Alignment explanation
Indices: 7337--7381 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
7327 CTCTGCATCC
**
7337 AAATAAATTCATCAACATCC
1 AAATAAATTCATCAACATAA
*
7357 AAATAAATTCATC-ATATAA
1 AAATAAATTCATCAACATAA
7376 AAATAA
1 AAATAA
7382 CATATTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAAATTCATCAACATAA
Found at i:8154 original size:20 final size:20
Alignment explanation
Indices: 8126--8185 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
8116 TGACGATGAA
8126 GAATGGGGGAAATGAGGAAC
1 GAATGGGGGAAATGAGGAAC
* * * * *
8146 GAATTGGGG-ATTTAGAAATT
1 GAATGGGGGAAATGAGGAA-C
8166 GAATGGGGGAAATGAGGAAC
1 GAATGGGGGAAATGAGGAAC
8186 AAATTAGGGA
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
19 6 0.21
20 16 0.57
21 6 0.21
ACGTcount: A:0.38, C:0.03, G:0.40, T:0.18
Consensus pattern (20 bp):
GAATGGGGGAAATGAGGAAC
Found at i:8171 original size:40 final size:40
Alignment explanation
Indices: 8126--8206 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
8116 TGACGATGAA
* *
8126 GAATGGGGGAAATGAGGAACGAATTGGGGATTTAGAAATT
1 GAATGGGGGAAATGAGGAACAAATTAGGGATTTAGAAATT
8166 GAATGGGGGAAATGAGGAACAAATTAGGGATTTAGAAATT
1 GAATGGGGGAAATGAGGAACAAATTAGGGATTTAGAAATT
8206 G
1 G
8207 TTACCTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.02, G:0.36, T:0.22
Consensus pattern (40 bp):
GAATGGGGGAAATGAGGAACAAATTAGGGATTTAGAAATT
Found at i:16778 original size:24 final size:24
Alignment explanation
Indices: 16738--16783 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
16728 TCTATTGAAG
*
16738 TATCAACCAAGTCTATTATTAAAC
1 TATCAACCAAGTATATTATTAAAC
*
16762 TATCAACCATA-TATATTGTTAA
1 TATCAACCA-AGTATATTATTAA
16784 TAGCATGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.37
Consensus pattern (24 bp):
TATCAACCAAGTATATTATTAAAC
Found at i:17557 original size:20 final size:21
Alignment explanation
Indices: 17532--17583 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
17522 TTTTCCCAAT
*
17532 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
17552 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
17573 TCGCAATGCGA
1 TCGCAATGCGA
17584 TACTTACTAT
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:17662 original size:20 final size:20
Alignment explanation
Indices: 17614--17666 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
17604 TAATACAAAA
* *
17614 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
17634 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
17654 TCGCAACGCGATT
1 TCGCAACGCGATT
17667 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:18243 original size:19 final size:19
Alignment explanation
Indices: 18183--18263 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
18173 TTCGAGAGTG
18183 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
18203 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
18219 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
18236 AAAATCGCAACACGAAACC
1 AAAATCGCAACGCGAAATA
18255 AAAATCGCA
1 AAAATCGCA
18264 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 7 0.15
16 5 0.10
17 4 0.08
18 1 0.02
19 23 0.48
20 8 0.17
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:18281 original size:19 final size:19
Alignment explanation
Indices: 18259--18443 Score: 147
Period size: 19 Copynumber: 10.1 Consensus size: 19
18249 GAAACCAAAA
*
18259 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18278 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
18297 TTGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
18316 TCGCAGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
**
18336 TCGCGTTGCGATAGTC---
1 TCGCGTTGCGATTTTCATT
* **
18352 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
18369 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
18383 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
18402 TCCACGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
18422 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
18442 TC
1 TC
18444 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 21 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 57 0.42
20 49 0.36
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:18336 original size:39 final size:38
Alignment explanation
Indices: 18259--18443 Score: 147
Period size: 33 Copynumber: 5.1 Consensus size: 38
18249 GAAACCAAAA
*
18259 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
18297 TTGCGTTGCGATTTTTATTTCGCAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
** * **
18336 TCGCGTTGCGATAGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
18369 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
18402 TCCACGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
18442 TC
1 TC
18444 AACCAAAAGA
Statistics
Matches: 120, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
31 3 0.03
33 38 0.32
34 9 0.08
35 1 0.01
36 3 0.03
38 20 0.17
39 28 0.23
40 18 0.15
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:18420 original size:20 final size:20
Alignment explanation
Indices: 18386--18443 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
18376 GCGATTCTCT
**
18386 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATTCTCATTTCCA
*
18406 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCA
*
18426 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
18444 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCA
Found at i:20493 original size:42 final size:42
Alignment explanation
Indices: 20433--20525 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
20423 GCCCGACTCG
* * *
20433 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
20475 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
20517 ACTGTCATC
1 CCTATCATC
20526 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:21946 original size:14 final size:14
Alignment explanation
Indices: 21912--21948 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
21902 GATTGTTTAA
21912 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
21926 GTAATTTGTAAAAG
1 TTGATTTGTAAAAG
21940 TTGATTTGT
1 TTGATTTGT
21949 TTAATTGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:22149 original size:19 final size:19
Alignment explanation
Indices: 22127--22277 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
22117 CGAAATTAAA
22127 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22146 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
22161 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
22179 TTCGCATTGTGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
22193 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22212 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
22227 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * ** *
22245 TTTGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
22264 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
22278 GGACATTAAG
Statistics
Matches: 91, Mismatches: 25, Indels: 31
0.62 0.17 0.21
Matches are distributed among these distances:
14 27 0.30
16 6 0.07
17 6 0.07
19 43 0.47
20 9 0.10
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:22173 original size:33 final size:32
Alignment explanation
Indices: 22131--22257 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
22121 ATTAAATTCG
22131 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
22164 CGTTGCGATTTTCATTTCGCATTGTGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
22197 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
22230 CGTTGCGATTTTCATTTTGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
22258 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:22220 original size:66 final size:66
Alignment explanation
Indices: 22124--22253 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
22114 ACGCGAAATT
*
22124 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
22189 G
66 G
* *
22190 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
22254 CGATAGTAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
G
Found at i:24566 original size:12 final size:12
Alignment explanation
Indices: 24549--24573 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24539 TCTTCGGGGA
24549 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24561 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24573 C
1 C
24574 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:24782 original size:24 final size:24
Alignment explanation
Indices: 24748--24801 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
24738 CTGAAACATC
*
24748 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
*
24772 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
24796 ATCAAA
1 ATCAAA
24802 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAT
Found at i:24815 original size:24 final size:24
Alignment explanation
Indices: 24764--24815 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
24754 ATCCGTGTAT
** *
24764 TGACCAATATCAAAGTCCGGGTAT
1 TGACCAATATCAAAGTCCGAATAC
* *
24788 TGACCAATATCAAATTTCGAATAC
1 TGACCAATATCAAAGTCCGAATAC
24812 TGAC
1 TGAC
24816 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (24 bp):
TGACCAATATCAAAGTCCGAATAC
Found at i:25886 original size:20 final size:20
Alignment explanation
Indices: 25861--25918 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
25851 ATTCATTTGA
25861 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
25881 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
25901 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
25919 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:25978 original size:19 final size:19
Alignment explanation
Indices: 25937--26004 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
25927 GAAATGAAAA
25937 TCGCATTGCGATTTTC--T
1 TCGCATTGCGATTTTCATT
25954 T-G--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
25970 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
25989 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
26005 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 2 0.04
19 30 0.65
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:28081 original size:19 final size:19
Alignment explanation
Indices: 28001--28118 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
27991 TAGTTTACTT
* *
28001 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
28021 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
28040 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
* *
28060 TCGCAATGCGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
28079 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
28093 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
28111 TCGCAACG
1 TCGCAACG
28119 ACAAAATCGC
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.15
19 24 0.30
20 29 0.36
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:28094 original size:14 final size:14
Alignment explanation
Indices: 28075--28132 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
28065 ATGCGAAATT
28075 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
28089 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
28105 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
28121 AAAATCGCAACG
1 AAAATCGCAACG
28133 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:28104 original size:33 final size:32
Alignment explanation
Indices: 28059--28148 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
28049 GGAAATGGCT
*
28059 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAACGCGAAA-TAAAATCGCAACGACAAA
*
28092 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATAAAATCGCAACGACAAA
*
28124 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAACGCGAAATA-AAATCGCA
28149 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 31 0.60
33 21 0.40
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATAAAATCGCAACGACAAA
Found at i:28166 original size:19 final size:19
Alignment explanation
Indices: 28144--28225 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
28134 GAAACACAAA
28144 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
28163 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
28181 TCACATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
28197 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
28214 TCGCATTGCGAT
1 TCGCATTGCGAT
28226 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 3 0.06
17 4 0.08
18 19 0.37
19 17 0.33
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:28241 original size:39 final size:35
Alignment explanation
Indices: 28144--28245 Score: 95
Period size: 33 Copynumber: 2.8 Consensus size: 35
28134 GAAACACAAA
28144 TCGCATTGCGATTTTCATTTCGCGTTGCGA-TTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTTCATT
*
28181 TCACATTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGATTTTCATT
28214 TCGCATTGCGATAGCCATTTCCGCGTTGCGAT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGAT
28246 AGTCATTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
31 1 0.02
32 11 0.20
33 18 0.33
34 1 0.02
37 10 0.19
38 3 0.06
39 9 0.17
40 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (35 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTTCATT
Found at i:28244 original size:20 final size:19
Alignment explanation
Indices: 28210--28264 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
28200 TTGCGATTTT
*
28210 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
28229 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
28249 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
28265 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:28766 original size:18 final size:18
Alignment explanation
Indices: 28740--28784 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
28730 GTCGATCAGA
*
28740 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
28758 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
28776 TGATGGCTC
1 TGATGGCTC
28785 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:30128 original size:20 final size:20
Alignment explanation
Indices: 30103--30156 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
30093 AATAGTTTCT
30103 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
30123 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
30143 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
30157 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:30415 original size:22 final size:22
Alignment explanation
Indices: 30390--30433 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30380 GATTTAGATA
30390 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
30412 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
30434 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:30646 original size:20 final size:20
Alignment explanation
Indices: 30621--30734 Score: 129
Period size: 20 Copynumber: 5.7 Consensus size: 20
30611 GATTATGTAT
30621 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
30641 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
30661 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
30681 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
30702 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
30722 TATCGCATTGCGA
1 TATCGCGTTGCGA
30735 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 67 0.84
21 13 0.16
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:30753 original size:21 final size:21
Alignment explanation
Indices: 30724--30816 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
30714 ATAGTCAGTA
30724 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
30745 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
30765 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
30786 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
30806 TCGCATTGCGA
1 TCGCATTGCGA
30817 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:30754 original size:41 final size:41
Alignment explanation
Indices: 30601--30797 Score: 143
Period size: 41 Copynumber: 4.8 Consensus size: 41
30591 CGCTTTGAAA
* ** * *
30601 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* *** * * *
30642 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* * ** * *
30682 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* *
30723 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT--TTACTT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGATAGTCA-GT
30763 ATTCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 A-TCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
30798 TTACTTATTC
Statistics
Matches: 128, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 2 0.02
40 35 0.27
41 89 0.70
42 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
Found at i:30798 original size:41 final size:41
Alignment explanation
Indices: 30724--30816 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
30714 ATAGTCAGTA
30724 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
30765 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
30806 TCGCATTGCGA
1 TCGCATTGCGA
30817 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:31665 original size:3 final size:3
Alignment explanation
Indices: 31659--31718 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
31649 AAAGGTTTAA
*
31659 AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31707 AAT AAT AAT AAT
1 AAT AAT AAT AAT
31719 GAAAACTATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:33815 original size:111 final size:106
Alignment explanation
Indices: 33591--33872 Score: 343
Period size: 111 Copynumber: 2.6 Consensus size: 106
33581 TTGAAATCCA
* * *
33591 AGCTTGTGTTGTTTCGAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGCTTTGAAACTGGGA
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGACTTTGAAACTGGAA
*
33655 AATTGTTTGTTGACAGCCAACCGCCTCTTCGCTGTGAAGTTG
65 AATTGTTTGTTGACAACCAACCGCCTCTTCGCTGTGAAGTTG
* * *
33697 AGCTTGTGTTGTCTCGAGTCTAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAA-TT
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACT-T---TGAAACTG
* * *
33761 GAAAAGTTTGTTTGTTGACAATCAATCGCCTCTTCGTTGTGAAGTTG
62 GAAAA--TTGTTTGTTGACAACCAACCGCCTCTTCGCTGTGAAGTTG
* * * * *
33808 AGGTTGTGTTGTCTTGAGTCCAATATCATTCGCTGTGAAGTTGAACTTGGCTTTGAAACTAGGAA
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTTTGAAACT-GGAA
33873 GCCCCTTCAT
Statistics
Matches: 149, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
106 46 0.31
107 7 0.05
108 1 0.01
109 8 0.05
110 6 0.04
111 81 0.54
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (106 bp):
AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTTTGAAACTGGAAA
ATTGTTTGTTGACAACCAACCGCCTCTTCGCTGTGAAGTTG
Found at i:37991 original size:2 final size:2
Alignment explanation
Indices: 37986--38072 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
37976 TAACATGGAG
37986 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
38028 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
38070 AT A
1 AT A
38073 AGAATGTCAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39222 original size:3 final size:3
Alignment explanation
Indices: 39179--39204 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39169 TGGGTCCTAA
39179 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
39205 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39438 original size:43 final size:41
Alignment explanation
Indices: 39391--39576 Score: 162
Period size: 43 Copynumber: 4.3 Consensus size: 41
39381 ATAAAAATTT
** * *
39391 AGATTAGAAAAATTAGGAACCTCAATTTTAAAGGTAGAAAGTG
1 AGATTA-AAAAATTAGGGGCCTCAATTGTAAATGTA-AAAGTG
* * *
39434 AGATTAAAAAAATTAGGGGTCTAAATTATATAA-GTCAAAAGT-
1 AGATT-AAAAAATTAGGGGCCTCAATTGTA-AATGT-AAAAGTG
39476 AGGATTTAAAAAATTAGGGG-CTCAATTGTAAATGTAAAAGGTG
1 A-GA-TTAAAAAATTAGGGGCCTCAATTGTAAATGTAAAA-GTG
* * *
39519 AGAATAAAAAATTAGGGGCCTCCATTGTAAATGTAGAAAGTC
1 AGATTAAAAAATTAGGGGCCTCAATTGTAAATGTA-AAAGTG
39561 AGATTGAGAAAAATTA
1 AGATT-A-AAAAATTA
39577 AGAGCACAAT
Statistics
Matches: 120, Mismatches: 11, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
41 20 0.17
42 36 0.30
43 50 0.42
44 14 0.12
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.26
Consensus pattern (41 bp):
AGATTAAAAAATTAGGGGCCTCAATTGTAAATGTAAAAGTG
Found at i:39573 original size:85 final size:84
Alignment explanation
Indices: 39390--39596 Score: 199
Period size: 85 Copynumber: 2.4 Consensus size: 84
39380 GATAAAAATT
* * * * *
39390 TAGATTAGAAAAATTAGGAACCTCAATTTTAAAGGTAGAAAGTGAGATTAAAAAAATTAGGGGTC
1 TAGATTAGAAAAATTAGG-AGCTCAATTATAAATGTAGAAAGTGAGAATAAAAAAATTAGGGGCC
39455 TAAATTATATAAGTCAAAAG
65 TAAATTATATAAGTCAAAAG
* *
39475 TAGGATTTA-AAAAATTAGGGGCTCAATTGTAAATGTA-AAAGGTGAGAAT-AAAAAATTAGGGG
1 TA-GA-TTAGAAAAATTAGGAGCTCAATTATAAATGTAGAAA-GTGAGAATAAAAAAATTAGGGG
** *
39537 CCTCCATTGTA-AATGT-AGAAAG
63 CCTAAATTATATAA-GTCA-AAAG
* *
39559 TCAGATTGAGAAAAATTAAGAGCACAATTATAAATGTA
1 T-AGATT-AGAAAAATTAGGAGCTCAATTATAAATGTA
39597 TAAATAGGAT
Statistics
Matches: 101, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
83 5 0.05
84 33 0.33
85 48 0.48
86 12 0.12
87 3 0.03
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (84 bp):
TAGATTAGAAAAATTAGGAGCTCAATTATAAATGTAGAAAGTGAGAATAAAAAAATTAGGGGCCT
AAATTATATAAGTCAAAAG
Found at i:39615 original size:42 final size:45
Alignment explanation
Indices: 39546--39664 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 45
39536 GCCTCCATTG
* *
39546 TAAATGT-AGAAAGTCA-GATTGAGAAAAATTAAGAGC-ACAATTA
1 TAAATGTAAAAAAGT-AGGATTGAAAAAAATTAAGAGCAACAATTA
* *
39589 TAAATGT-ATAAA-TAGGATTGAAAAAAATTAAGATCAACAATTA
1 TAAATGTAAAAAAGTAGGATTGAAAAAAATTAAGAGCAACAATTA
*
39632 TAAATGTAAAAAAGTGGGATTGAAAAAAATTAA
1 TAAATGTAAAAAAGTAGGATTGAAAAAAATTAA
39665 AGCCTTAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
41 1 0.01
42 19 0.28
43 25 0.37
44 4 0.06
45 18 0.27
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (45 bp):
TAAATGTAAAAAAGTAGGATTGAAAAAAATTAAGAGCAACAATTA
Found at i:39750 original size:23 final size:25
Alignment explanation
Indices: 39724--39769 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
39714 ACTGTAAAGA
39724 TAAAA-ATAAAATT-TAAAAAAAAT
1 TAAAAGATAAAATTATAAAAAAAAT
**
39747 TAAAAGATTGAATTATAAAAAAA
1 TAAAAGATAAAATTATAAAAAAA
39770 TAAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 6 0.32
25 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (25 bp):
TAAAAGATAAAATTATAAAAAAAAT
Found at i:40993 original size:20 final size:20
Alignment explanation
Indices: 40964--41009 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
40954 TATAATGCTC
*
40964 CATGCATATTCGACCACACA
1 CATGCCTATTCGACCACACA
* *
40984 CATGCCTATTCGGCCAGACA
1 CATGCCTATTCGACCACACA
41004 CATGCC
1 CATGCC
41010 ATGCACATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.37, G:0.15, T:0.20
Consensus pattern (20 bp):
CATGCCTATTCGACCACACA
Found at i:41905 original size:21 final size:22
Alignment explanation
Indices: 41881--41921 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41871 GCAAAAAAAA
*
41881 AAGACAAAAAG-AAGAAAAATT
1 AAGAAAAAAAGAAAGAAAAATT
41902 AAGAAAAAAAGAAAGAAAAA
1 AAGAAAAAAAGAAAGAAAAA
41922 GAATTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (22 bp):
AAGAAAAAAAGAAAGAAAAATT
Found at i:41924 original size:18 final size:19
Alignment explanation
Indices: 41876--41921 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
41866 GGAGTGCAAA
*
41876 AAAAAAAGACAAAAAGAAG
1 AAAAAAAGAAAAAAAGAAG
41895 AAAAATTAAGAAAAAAAGAAAG
1 AAAAA--AAGAAAAAAAG-AAG
41917 AAAAA
1 AAAAA
41922 GAATTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAGAAG
Found at i:42152 original size:17 final size:18
Alignment explanation
Indices: 42130--42164 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
42120 ACCTTTAAAT
42130 CATTTCTTCTA-TCTTTC
1 CATTTCTTCTATTCTTTC
42147 CATTTCTTCTATTCTTTC
1 CATTTCTTCTATTCTTTC
42165 TACCCTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
CATTTCTTCTATTCTTTC
Found at i:44866 original size:15 final size:16
Alignment explanation
Indices: 44826--44868 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
44816 AATATTTTAA
*
44826 TATAGTTATTTTCATC
1 TATAGTTATTATCATC
44842 TATA-TATATTAT-ATC
1 TATAGT-TATTATCATC
44857 TATAGTTATTAT
1 TATAGTTATTAT
44869 GATGATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (16 bp):
TATAGTTATTATCATC
Found at i:47275 original size:21 final size:21
Alignment explanation
Indices: 47251--47323 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
47241 TTTACCTCAA
*
47251 GGCCTAAGTAATAAGTCATAG
1 GGCCTAAATAATAAGTCATAG
* * * *
47272 GGCCTAATTAAATAATTTCAAATT
1 GGCCTAAAT-AATAA-GTCATA-G
*
47296 CGCCTAAATAATAAGTCATAG
1 GGCCTAAATAATAAGTCATAG
47317 GGCCTAA
1 GGCCTAA
47324 TTCAATCATT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
21 14 0.36
22 9 0.23
23 9 0.23
24 7 0.18
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
GGCCTAAATAATAAGTCATAG
Found at i:47316 original size:45 final size:45
Alignment explanation
Indices: 47252--47341 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
47242 TTACCTCAAG
*
47252 GCCTAAGTAATAAGTCATAGGGCCTAATTAAATAATTTCAAATTC
1 GCCTAAATAATAAGTCATAGGGCCTAATTAAATAATTTCAAATTC
* *
47297 GCCTAAATAATAAGTCATAGGGCCTAATTCAATCATTTCAAATTC
1 GCCTAAATAATAAGTCATAGGGCCTAATTAAATAATTTCAAATTC
47342 TTTTAACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (45 bp):
GCCTAAATAATAAGTCATAGGGCCTAATTAAATAATTTCAAATTC
Found at i:48297 original size:19 final size:19
Alignment explanation
Indices: 48270--48310 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
48260 TAGCTTTTGA
*
48270 ACTTCTAAATGGTATAATT
1 ACTTCTAAATGGTATAACT
*
48289 ACTTTTAAATGGTATAACT
1 ACTTCTAAATGGTATAACT
48308 ACT
1 ACT
48311 CTCTTGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (19 bp):
ACTTCTAAATGGTATAACT
Found at i:50542 original size:54 final size:54
Alignment explanation
Indices: 50384--50803 Score: 499
Period size: 54 Copynumber: 7.7 Consensus size: 54
50374 AATATTATAG
* * * * * *
50384 CTCATTATAAATTCCGTGGGTTTGCACACATGGCG-CTGATACGATCATTCACAAA
1 CTCATTATGAATTACGTGGG-TTGCACACATAGTGTC-GATACGGTAATTCACAAA
* * * *
50439 CACATTGTGAATTACGTGGGTTTGCACACATAGTGCCAATACGGTAATTCACAAA
1 CTCATTATGAATTACGTGGG-TTGCACACATAGTGTCGATACGGTAATTCACAAA
** ** *
50494 CTCATTATGAATTATATGGGTTGCACACATAGTGTCGATACAATAATTCGCAAA
1 CTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACAAA
* *
50548 CTCATTATGAATTACATGGGTTGC-CAACATAGTGTCGATACGGTAATTCATAAA
1 CTCATTATGAATTACGTGGGTTGCAC-ACATAGTGTCGATACGGTAATTCACAAA
* * *
50602 CTCATTTTGAATTACGTGGGTTGCACACATATTG-CTGATACGGTATTTCACAAA
1 CTCATTATGAATTACGTGGGTTGCACACATAGTGTC-GATACGGTAATTCACAAA
* * * *
50656 CGCATTATGAATTACGTGGGTTGTACACATAAT-TCCA-ACATGGTAATTCACAAA
1 CTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATAC--GGTAATTCACAAA
*
50710 CTCATTATGAATTACGTGGGTTGCACACATAATGTCGATACGGTAATTCACAAA
1 CTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACAAA
* *
50764 CTCAGTATGAATTACGTAGGTTGCACACATAGTGTCGATA
1 CTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATA
50804 GTACACATAG
Statistics
Matches: 316, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.01
53 3 0.01
54 244 0.77
55 64 0.20
56 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (54 bp):
CTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACAAA
Found at i:57032 original size:2 final size:2
Alignment explanation
Indices: 57025--57074 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
57015 GAGCATCGTC
57025 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
57067 AT AT AT AT
1 AT AT AT AT
57075 TACATGCCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57504 original size:54 final size:54
Alignment explanation
Indices: 57298--57764 Score: 589
Period size: 54 Copynumber: 8.7 Consensus size: 54
57288 TAAATATTAC
* * * * * *
57298 AACTCATTATAAATTCCATGGGTTTGCACACATATTGCCTATACAGTAATTCACA
1 AACTCATTATGAATTACGTGGG-TTGCACACATAGTGCCGATACGGTAATTCACA
* * * *
57353 AACTCATTATGAATTACGTGGGTTTTCACACATAGTGTCGATACGGTATTTTACA
1 AACTCATTATGAATTACGTGGG-TTGCACACATAGTGCCGATACGGTAATTCACA
* **
57408 AACTCATTATGAATT--GTGAGTTGCACACATAGTGTTGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
** * * *
57460 AACTCATTATGAATTATATAGGTTGCACACATAGTACCGATACGGTTATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * *
57514 AACTCATTATGAATTACGTGGGTTGTACACATAGTGCTGATACGATAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* *
57568 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCTGATACAGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * * *
57622 AACTCATTATGAATTACGTGGGTTGCACACATAATGCCGACACGATAATTCATA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * *
57676 AACTCATTATGAATTATGTGGGTTGCACACATAATGCCGACAC-GTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * * *
57729 AACGCATTATGTATTACGTAGGTTGTACACATAGTG
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTG
57765 TTGATAGTAC
Statistics
Matches: 362, Mismatches: 48, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
52 43 0.12
53 42 0.12
54 217 0.60
55 60 0.17
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (54 bp):
AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
Found at i:62315 original size:17 final size:17
Alignment explanation
Indices: 62293--62331 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
62283 TGAATCAAAT
62293 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
62310 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
62327 -AATTA
1 TAATTA
62332 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:62750 original size:29 final size:28
Alignment explanation
Indices: 62717--62801 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 28
62707 AAATTTTTTC
62717 TAGTGACTAAAATGTAAGTTTTTAAAGTT
1 TAGTGACTAAAATGTAA-TTTTTAAAGTT
* * * **
62746 TAGTGGCTAAAGTATAAACTTTAAAAAGTT
1 TAGTGACTAAAATGT-AA-TTTTTAAAGTT
*
62776 TAGGGACTAAAATTGTAATTTTTAAA
1 TAGTGACTAAAA-TGTAATTTTTAAA
62802 AGATATATTT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
29 18 0.43
30 22 0.52
31 2 0.05
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (28 bp):
TAGTGACTAAAATGTAATTTTTAAAGTT
Found at i:69860 original size:24 final size:24
Alignment explanation
Indices: 69828--69877 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
69818 ATTGGTATGG
69828 AAATTGTGTTAAAAACAATAAAGC
1 AAATTGTGTTAAAAACAATAAAGC
69852 AAATTGTGTTAAAAACAATAAAGC
1 AAATTGTGTTAAAAACAATAAAGC
69876 AA
1 AA
69878 TAAAGTTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAATTGTGTTAAAAACAATAAAGC
Found at i:73813 original size:15 final size:15
Alignment explanation
Indices: 73793--73821 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
73783 TTTTTATCTT
73793 TTAAAATTATTTTTC
1 TTAAAATTATTTTTC
73808 TTAAAATTATTTTT
1 TTAAAATTATTTTT
73822 AGTTACTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAAAATTATTTTTC
Found at i:79810 original size:21 final size:22
Alignment explanation
Indices: 79768--79811 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
79758 GGATGAATAT
**
79768 TCTAGATCATTTTGGGGATGAA
1 TCTAGATCATTTTGAAGATGAA
*
79790 TCTAGAT-ATTTTGAAGCTGAA
1 TCTAGATCATTTTGAAGATGAA
79811 T
1 T
79812 ATGACCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (22 bp):
TCTAGATCATTTTGAAGATGAA
Found at i:80600 original size:18 final size:18
Alignment explanation
Indices: 80558--80603 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
80548 TAGTTTGATT
*
80558 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
80576 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
80594 AATGAACTAA
1 AATGAACTAA
80604 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:82884 original size:42 final size:41
Alignment explanation
Indices: 82837--82939 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 41
82827 AATTGGTAAG
* *
82837 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAA
1 TCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGA-TAAA
* * * *
82879 TCCTTCGGATCATCTGTAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGATAAA
* *
82920 TCCTTCAGGTCATCCGTAAG
1 TCCTTCGGGTCATCAGTAAG
82940 ACCTTCGAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 20 0.38
42 32 0.62
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (41 bp):
TCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGATAAA
Found at i:83091 original size:258 final size:257
Alignment explanation
Indices: 82575--83774 Score: 1696
Period size: 258 Copynumber: 4.7 Consensus size: 257
82565 TTCTTACTTA
* * * * *
82575 GTAAGTCCTTCAGACCACCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGATCATCTGTA
* * * * * * * *
82640 AGTCTTTCGAGCAAGATGATAATTTCTTTAGGACATCCATAAGACCTTCGGGTAAGATGTTTT-G
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCA
* * * *
82704 CATGAATTTAAAAAAATAAGAAAGTGATTTCCAAAGTTTCTCATTTAGTTTTTTCAGAAAATAAA
131 CATGAATTTTAAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATAAA
* *
82769 TTTTTTGAAAAGTAAGAAAGCAATTTCCAATGTTTCTTCCCCAGTAAACTATTTCCCAAATTG
196 -TTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTG
82832 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGATCATCTGTA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGATCATCTGTA
* *
82897 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGTCATCCGTAAGACCTTCGAATAGGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCA
* *
82962 CATGAATTTTAAAAAATGAGAAAGAGATTTTCAAAGTTTCTAATTTAGTATTTTCAGAAAATAAA
131 CATGAATTTTAAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATAAA
* * * *
83027 GTTTTTGAAAAATAAGAAAGCAATTTCCCAAGTTTCTTACCTAG-ATAATTATTTCCCAAATTG
196 -TTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCCAGTA-AACTATTTCCCAAATTG
*
83090 GTAAGTCCTTCGGGCCATCAGTAAGTGTTTCAAGCATGATGATTAAATCCTTCAGG-TCATCTGT
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTC-GGATCATCTGT
* * * * *
83154 AAGTGTTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCCGTAAGACCTTCGAGTAGGATATTTTC
65 AAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTC
* *
83219 ACATGAATTTTAAAAAATAAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGA
130 ACATGAATTTTAAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAAT-A
* ** *
83284 AACTTTTGAAAAGTAAGAAAGCGGTTTCCAAAGTTTCGTACCCAGTAAACTATTTCCCAAATTG
194 AATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTG
* * * *
83348 GTAAGTCCTTCGGGCCATCAGTAAGTCTTT-GAGCATGATAATTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGATCATCTGTA
* * ** * * *
83412 A-T-TTTTGTAGCAAGATGATAAGTACTTTGGGCCATCCGTAAGACCTTAGGGTAAGATGTTTTC
66 AGTCTTTCG-AGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTC
* *
83475 ACATGAATTTTAAAAAATGAGAAAGCA-ATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATA
130 ACATGAATTTTAAAAAATGAGAAAG-AGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAAT-
* * *
83539 AAATTTTTGAAAAGTAAGAATGCTATTTTCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTG
193 AAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTG
* * *
83604 GTAAGTCCTTCGGGTCATCGGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGATCATCTGTA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGATCATCTGTA
*
83669 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCAGTAAGACCTTC-AGGTAGGATGTTTTC
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGA-GTAGGATGTTTTC
* * * *
83733 ACATGAAATTTAGAAAATGAGAAAGATATTTTCAAAGTTTCT
130 ACATGAATTTTAAAAAATGAGAAAGAGATTTCCAAAGTTTCT
83775 TACCTAGTAA
Statistics
Matches: 841, Mismatches: 89, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
255 4 0.00
256 195 0.23
257 176 0.21
258 456 0.54
259 10 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (257 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGATCATCTGTA
AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCA
CATGAATTTTAAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATAAA
TTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTG
Found at i:83156 original size:42 final size:41
Alignment explanation
Indices: 83095--83197 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
83085 AATTGGTAAG
* *
83095 TCCTTCGGGCCATCAGTAAGTGTTTCAAGCATGATGATTAAA
1 TCCTTCAGGCCATCAGTAAGTGTTTCAAGCAAGATG-TTAAA
* * * *
83137 TCCTTCAGGTCATCTGTAAGTGTTTCGAGCAAGATGTTAAG
1 TCCTTCAGGCCATCAGTAAGTGTTTCAAGCAAGATGTTAAA
* * *
83178 TCCCTCGGGCCATCCGTAAG
1 TCCTTCAGGCCATCAGTAAG
83198 ACCTTCGAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 20 0.39
42 31 0.61
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (41 bp):
TCCTTCAGGCCATCAGTAAGTGTTTCAAGCAAGATGTTAAA
Found at i:83613 original size:514 final size:516
Alignment explanation
Indices: 82575--83774 Score: 1725
Period size: 514 Copynumber: 2.3 Consensus size: 516
82565 TTCTTACTTA
* * * *
82575 GTAAGTCCTTCAGACCACCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC-GGCTCATCTGT
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGG-TCATCTGT
* * * * * * *
82639 AAGTCTTTCGAGCAAGATGATAATTTCTTTAGGACATCCATAAGACCTTCGGGTAAGATGTTTT-
65 AAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTC
* * * *
82703 GCATGAATTTAAAAAAATAAGAAAGTGATTTCCAAAGTTTCTCATTTAGTTTTTTCAGAAAATAA
130 ACATGAATTTTAAAAAATAAGAAAGAGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATAA
* * * *
82768 ATTTTTTGAAAAGTAAGAAAGCAATTTCCAATGTTTCTTCCCCAGTAAACTATTTCCCAAATTGG
195 ATCTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCGTACCCAGTAAACTATTTCCCAAATTGG
* *
82833 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGATCATCTGTAA
260 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATAATTAAATCCTTCGGATCATCTATAA
* * * *
82898 GTCTTTCGAGCAAGATGATAAGTCCTTCAGGTCATCCGTAAGACCTTCGAATAGGATGTTTTCAC
325 GTCTTTCGAGCAAGATGATAAGTACTTCAGGCCATCCGTAAGACCTTAGAATAAGATGTTTTCAC
* * * *
82963 ATGAATTTTAAAAAATGAGAAAGAGATTTTCAAAGTTTCTAATTTAGTATTTTCAGAAAATAAAG
390 ATGAATTTTAAAAAATGAGAAAGAGATTTCCAAAGTTTCTAATATAGTATTTTCAAAAAATAAAA
* * *
83028 TTTTTGAAAAATAAGAAAGCAATTTCCCAAGTTTCTTACCTAGATAATTATTTCCCAAATTG
455 TTTTTGAAAAATAAGAAAGCAATTTCCAAAGTTTCTTACCCAGATAACTATTTCCCAAATTG
*
83090 GTAAGTCCTTCGGGCCATCAGTAAGTGTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTGTA
* * * * *
83155 AGTGTTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCCGTAAGACCTTCGAGTAGGATATTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCA
*
83220 CATGAATTTTAAAAAATAAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAA
131 CATGAATTTTAAAAAATAAGAAAGAGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAAT-AA
**
83285 A-CTTTTGAAAAGTAAGAAAGCGGTTTCCAAAGTTTCGTACCCAGTAAACTATTTCCCAAATTGG
195 ATCTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCGTACCCAGTAAACTATTTCCCAAATTGG
* *
83349 TAAGTCCTTCGGGCCATCAGTAAGTCTTT-GAGCATGATAATTAAATCCTTCGGGTCATCTATAA
260 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATAATTAAATCCTTCGGATCATCTATAA
* ** **
83413 -T-TTTTGTAGCAAGATGATAAGTACTTTGGGCCATCCGTAAGACCTTAGGGTAAGATGTTTTCA
325 GTCTTTCG-AGCAAGATGATAAGTACTTCAGGCCATCCGTAAGACCTTAGAATAAGATGTTTTCA
*
83476 CATGAATTTTAAAAAATGAGAAAGCA-ATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATAA
389 CATGAATTTTAAAAAATGAGAAAG-AGATTTCCAAAGTTTCTAATATAGTATTTTCAAAAAATAA
* * * *
83540 AATTTTTGAAAAGTAAGAATGCTATTTTCAAAGTTTCTTACCCAG-TAAACTATTTCCCAAATTG
453 AATTTTTGAAAAATAAGAAAGCAATTTCCAAAGTTTCTTACCCAGAT-AACTATTTCCCAAATTG
* * *
83604 GTAAGTCCTTCGGGTCATCGGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGATCATCTGTA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTGTA
*
83669 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCAGTAAGACCTTC-AGGTAGGATGTTTTC
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGA-GTAGGATGTTTTC
* * * * *
83733 ACATGAAATTTAGAAAATGAGAAAGATATTTTCAAAGTTTCT
130 ACATGAATTTTAAAAAATAAGAAAGAGATTTCCAAAGTTTCT
83775 TACCTAGTAA
Statistics
Matches: 610, Mismatches: 68, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
513 6 0.01
514 314 0.51
515 140 0.23
516 147 0.24
517 3 0.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (516 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTGTA
AGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCA
CATGAATTTTAAAAAATAAGAAAGAGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATAAA
TCTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCGTACCCAGTAAACTATTTCCCAAATTGGT
AAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATAATTAAATCCTTCGGATCATCTATAAG
TCTTTCGAGCAAGATGATAAGTACTTCAGGCCATCCGTAAGACCTTAGAATAAGATGTTTTCACA
TGAATTTTAAAAAATGAGAAAGAGATTTCCAAAGTTTCTAATATAGTATTTTCAAAAAATAAAAT
TTTTGAAAAATAAGAAAGCAATTTCCAAAGTTTCTTACCCAGATAACTATTTCCCAAATTG
Found at i:83670 original size:42 final size:41
Alignment explanation
Indices: 83609--83699 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 41
83599 AATTGGTAAG
* * *
83609 TCCTTCGGGTCATCGGTAAGTCTTTCAAGCATGATGATTAAA
1 TCCTTCAGATCATCGGTAAGTCTTTCAAGCAAGATGA-TAAA
* * *
83651 TCCTTCAGATCATCTGTAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCAGATCATCGGTAAGTCTTTCAAGCAAGATGATAAA
83692 TCCTTCAG
1 TCCTTCAG
83700 GCCATCAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 11 0.26
42 32 0.74
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (41 bp):
TCCTTCAGATCATCGGTAAGTCTTTCAAGCAAGATGATAAA
Found at i:83900 original size:195 final size:196
Alignment explanation
Indices: 83562--83969 Score: 581
Period size: 195 Copynumber: 2.1 Consensus size: 196
83552 GTAAGAATGC
* * * *
83562 TATTTTCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGTCATCGGTA
1 TATTTTCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCCTTCAGGCCATCAGTA
83627 AGTCTTTCAAGCATGATGATTAAATCCTTCAGATCATCTGTAAGTCTTTCGAGCAAGATGATAAG
66 AGTCTTTCAAGCATGATGATTAAATCCTTCAGATCATCTGTAAGTCTTTCGAGCAAGATGATAAG
* * *
83692 TCCTTCAGGCCATCAGTAAGACCTTCAGGTAGGATGTTTTCACATGAAATTTAGAAAATGAGAAA
131 TCCTTCAGGCCATCAGTAAGACCTTCAGGTAGGATATTATCACATGAAATTTAAAAAATGAGAAA
83757 G
196 G
*
83758 ATATTTTCAAAGTTTCTTACCTAGTAAA-TATTTCCCAAAATT-ATAAGTCCTTCAGGCCATCAG
1 -TATTTTCAAAGTTTCTTACCCAGTAAACTATTTCCC-AAATTGATAAGTCCTTCAGGCCATCAG
* * * * * *
83821 TATGTCTTTCGAGCAT-ATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGTTA
64 TAAGTCTTTCAAGCATGATGATTAAATCCTTCAGATCATCTGTAAGTCTTTCGAGCAAGATGATA
* * * *
83885 AGTTCC-TCGGGCCATCCGTAAGACCTTCGGGTAGGATATTATCATATGAAATTTAAAAAATGAG
129 AG-TCCTTCAGGCCATCAGTAAGACCTTCAGGTAGGATATTATCACATGAAATTTAAAAAATGAG
83949 AAAG
193 AAAG
*
83953 TGATTTCCAAAGTTTCT
1 T-ATTTTCAAAGTTTCT
83970 CATTTAGTAT
Statistics
Matches: 189, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
194 1 0.01
195 115 0.61
196 42 0.22
197 31 0.16
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (196 bp):
TATTTTCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCCTTCAGGCCATCAGTA
AGTCTTTCAAGCATGATGATTAAATCCTTCAGATCATCTGTAAGTCTTTCGAGCAAGATGATAAG
TCCTTCAGGCCATCAGTAAGACCTTCAGGTAGGATATTATCACATGAAATTTAAAAAATGAGAAA
G
Found at i:84159 original size:454 final size:453
Alignment explanation
Indices: 83299--84228 Score: 1248
Period size: 454 Copynumber: 2.1 Consensus size: 453
83289 TTGAAAAGTA
* * * * *
83299 AGAAAGCGGTTTCCAAAGTTTCGTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCC
1 AGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCCTTCAGGCC
83364 ATCAGTAAGTCTTTGAGCATGATAATTAAATCCTTCGGGTCATCTATAATTTTTGTAGCAAGATG
66 ATCAGTAAGTCTTTGAGCATGATAATTAAATCCTTCGGGTCATCTATAATTTTTGTAGCAAGATG
* * * * *
83429 ATAAGTACTTTGGGCCATCCGTAAGACCTTAGGGTAAGATGTTTTCACATGAATTTTAAAAAATG
131 ATAAGTACCTCGGGCCATCCGTAAGACCTTAGGGTAAGATATTATCACATGAAATTTAAAAAATG
*
83494 AGAAAGCAATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATAAAATTTTTGAAAAGTAAGAA
196 AGAAAGCAATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATAAAATTTGTGAAAAGTAAGAA
* * * **
83559 TGCTATTTTCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGTCATCG
261 AGCTATTTCCAAAGTTTCATACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGACCATCG
* * * *
83624 GTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGATCATCTGTAAGTCTTTCGAGCAAGATGAT
326 GTAAGTCCTTCAAGCATGAGGATTAAATCCTTAAGATAATCTGTAAGTCTTTCGAGCAAGATGAT
*
83689 AAGTCCTTCAGGCCATC-AGTAAGACCTTCAGGTAGGATGTTTTCACATGAAATTT-AGAAAATG
391 AAGTCCCTCAGGCCATCTA-TAAGACCTTCAGGTAGGATGTTTTCACAT-AAATTTGAGAAAATG
* * *
83752 AGAAAGATATTTTCAAAGTTTCTTACCTAGTAAA-TATTTCCCAAAATT-ATAAGTCCTTCAGGC
1 AGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCC-AAATTGATAAGTCCTTCAGGC
* * *
83815 CATCAGTATGTCTTTCGAGCAT-ATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTTG-AGCAA
65 CATCAGTAAGTCTTT-GAGCATGATAATTAAATCCTTCGGGTCATCTATAA-T-TTTTGTAGCAA
* * * * *
83878 GATGTTAAGTTCCTCGGGCCATCCGTAAGACCTTCGGGTAGGATATTATCATATGAAATTTAAAA
127 GATGATAAGTACCTCGGGCCATCCGTAAGACCTTAGGGTAAGATATTATCACATGAAATTTAAAA
** * * * *
83943 AATGAGAAAGTGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAATTTGTGAAAAAGT
192 AATGAGAAAGCAATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATAAAATTTGTG-AAAAGT
** **
84008 AAGAAAG-TGATTTCCCCAGTTTCATACCCAGTAAACTATTTTTCAAATTGGTAAGTCCTTCGGA
256 AAGAAAGCT-ATTTCCAAAGTTTCATACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGA
* * *
84072 CCAT-GAGTAAGTCCTTCGAGCATGAGGATTAAATCTTTTAAG-TAATCTGTAATTCTTTCGAGC
320 CCATCG-GTAAGTCCTTCAAGCATGAGGATTAAATC-CTTAAGATAATCTGTAAGTCTTTCGAGC
* * * * *
84135 AAGATGTTACGTCCCTCGGGCCATCTATAAGACCTTCGGGTAGGTTGTTTTCACATAAATTTGAG
383 AAGATGATAAGTCCCTCAGGCCATCTATAAGACCTTCAGGTAGGATGTTTTCACATAAATTTGAG
84200 AAAATG
448 AAAATG
*
84206 AGAAAGCGATTTCCAAAGTTTCT
1 AGAAAGAGATTTCCAAAGTTTCT
84229 CATTTAGTAT
Statistics
Matches: 414, Mismatches: 53, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
452 61 0.15
453 159 0.38
454 189 0.46
455 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (453 bp):
AGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCCTTCAGGCC
ATCAGTAAGTCTTTGAGCATGATAATTAAATCCTTCGGGTCATCTATAATTTTTGTAGCAAGATG
ATAAGTACCTCGGGCCATCCGTAAGACCTTAGGGTAAGATATTATCACATGAAATTTAAAAAATG
AGAAAGCAATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATAAAATTTGTGAAAAGTAAGAA
AGCTATTTCCAAAGTTTCATACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGACCATCG
GTAAGTCCTTCAAGCATGAGGATTAAATCCTTAAGATAATCTGTAAGTCTTTCGAGCAAGATGAT
AAGTCCCTCAGGCCATCTATAAGACCTTCAGGTAGGATGTTTTCACATAAATTTGAGAAAATG
Found at i:84415 original size:258 final size:257
Alignment explanation
Indices: 83735--84575 Score: 996
Period size: 258 Copynumber: 3.3 Consensus size: 257
83725 ATGTTTTCAC
* * * * *
83735 ATGAAA-TTTAGAAAA-TGAGAAAGATATTTTCAAAGTTTCTTACCTAGTAAA-TATTTCCCAAA
1 ATGAAATTTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCC-AA
* * * *
83797 ATT-ATAAGTCCTTCAGGCCATCAG-TATGTCTTTCGAGCAT-ATGATTAAATCCTTCGGGTCAT
65 ATTGGTAAGTCCTTCGGGCCATCAGTTA-GTCTTTCGAGCATGATGATTAAATCCTTCAGGTCAA
* * ** *
83859 CTGTAAGTCTTTTGAGCAAGATGTTAAGTTCCTCGGGCCATCCGTAAGACCTTCGGGTAGGATAT
129 CTGTAAGTCTTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCTATAAGACCTTCGGGTAGGATGT
* * * *
83924 TATCATATGAAATTTAAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAA
194 TTTCACAT-AAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAA
* * ** * **
83989 ATGAAATTTGTGAAAAAGTAAGAAAGTGATTTCCCCAGTTTCATACCCAGTAAACTATTTTTCAA
1 ATGAAATTTTTG-AAAAGTAAGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAA
* * * * * * * *
84054 ATTGGTAAGTCCTTCGGACCATGAGTAAGTCCTTCGAGCATGAGGATTAAATCTTTTAAGT-AAT
65 ATTGGTAAGTCCTTCGGGCCATCAGTTAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCAA-
* * *
84118 CTGTAATTCTTTCGAGCAAGATGTTACGTCCCTCGGGCCATCTATAAGACCTTCGGGTAGGTTGT
129 CTGTAAGTCTTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCTATAAGACCTTCGGGTAGGATGT
*
84183 TTTCACATAAATTTGAGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTGGAAA
194 TTTCACATAAATTTGA-AAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAA
*
84248 ATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAA
1 ATGAAATTTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAA
* * * * *
84313 TTGGTAAGTTCTTTGGGTCATTAGTTAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCAACT
66 TTGGTAAGTCCTTCGGGCCATCAGTTAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCAACT
* * * * * *
84378 ATAAGTCTTTCGAGTAAGATGTTAAGTCCCACGGGCCATCTATAAGAACTTCGGGCAGGACGTTT
131 GTAAGTCTTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCTATAAGACCTTCGGGTAGGATGTTT
* * * * *
84443 CCACATGATTTTCGAAAAATGAGAAAGCGATTTCCATAGTTTCTCATTTA-AATCTTTTATGAAA
196 TCACATAAATTT-GAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTAT-TTTTA-GAAA
* * * *** *
84507 ATGAAATTTTTCAAAACTAAGAAAGAGATTTACAAAGTTTCTTATATAGTAAACTATTTCCAAAA
1 ATGAAATTTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAA
84572 TTGG
66 TTGG
84576 ATTATCAAAT
Statistics
Matches: 495, Mismatches: 79, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
254 6 0.01
255 3 0.01
256 4 0.01
257 35 0.07
258 243 0.49
259 204 0.41
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (257 bp):
ATGAAATTTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAA
TTGGTAAGTCCTTCGGGCCATCAGTTAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCAACT
GTAAGTCTTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCTATAAGACCTTCGGGTAGGATGTTT
TCACATAAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAA
Found at i:84486 original size:712 final size:711
Alignment explanation
Indices: 83028--84486 Score: 2027
Period size: 712 Copynumber: 2.0 Consensus size: 711
83018 GAAAATAAAG
* * * *
83028 TTTTTGAAAAATAAGAAAGCAATTTCCCAAGTTTCTTACCTAGATAATTATTTCCCAAATTGGTA
1 TTTTAGAAAAATGAGAAAGCAATTT-CCAAGTTTCTTACCTAGATAAATATTTCCCAAATTGATA
* *
83093 AGTCCTTCGGGCCATCAGTAAGTGTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGT
65 AGTCCTTCAGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGT
* *
83158 GTTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCCGTAAGACCTTCGAGTAGGATATTTTCACAT
130 CTTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCCGTAAGACCTTCGAGTAGGATATTATCACAT
*
83223 GAATTTTAAAAAATAAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAACT
195 GAAATTTAAAAAATAAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAACT
* *
83288 TTTGAAAAGTAAGAAAGCGGTTTCCAAAGTTTCGTACCCAGTAAACTATTTCCCAAATTGGTAAG
260 TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCATACCCAGTAAACTATTTCCCAAATTGGTAAG
* * * ** *
83353 TCCTTCGGGCCATCAGTAAGTCTTTGAGCATGATAATTAAATCCTTCGGGTCATCTATAATTTTT
325 TCCTTCGGACCATCAGTAAGTCTTCGAGCATGAGAATTAAATCCTTCAAGTAATCTATAATTTTT
* * * *
83418 GTAGCAAGATGATAAGTACTTTGGGCCATCCGTAAGACCTTAGGGTAAGATGTTTTCACATGAAT
390 GTAGCAAGATGATAAGTACCTCGGGCCATCCATAAGACCTTAGGGTAAGATGTTTTCACATAAAT
*
83483 TTTAAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATAAAATTTTTG
455 TTGAAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATAAAATTTTTG
* * *
83548 AAAAGTAAGAATGCTATTTTCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCT
520 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCT
* * *
83613 TCGGGTCATCGGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGATCATCTGTAAGTCTTTCG
585 TCGGGTCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGATCAACTATAAGTCTTTCG
** * * * *
83678 AGCAAGATGATAAGTCCTTCAGGCCATCAGTAAGACCTTCAGGTAGGATGTTTTCACATGAA
650 AGCAAGATGATAAGTCCCACAGGCCATCAGTAAGAACTTCAGGCAGGACGTTTCCACATGAA
* *
83740 ATTTAG-AAAATGAGAAAG-ATATTTTCAAAGTTTCTTACCTAG-TAAATATTTCCCAAAATT-A
1 TTTTAGAAAAATGAGAAAGCA-A-TTTCCAAGTTTCTTACCTAGATAAATATTTCCC-AAATTGA
* * *
83801 TAAGTCCTTCAGGCCATCAGTATGTCTTTCGAGCAT-ATGATTAAATCCTTCGGGTCATCTGTAA
63 TAAGTCCTTCAGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTGTAA
* * * *
83865 GTCTTTTGAGCAAGATGTTAAGTTCCTCGGGCCATCCGTAAGACCTTCGGGTAGGATATTATCAT
128 GTCTTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCCGTAAGACCTTCGAGTAGGATATTATCAC
* * *
83930 ATGAAATTTAAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAA
193 ATGAAATTTAAAAAATAAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAA
* ** **
83995 -TTTGTGAAAAAGTAAGAAAGTGATTTCCCCAGTTTCATACCCAGTAAACTATTTTTCAAATTGG
258 CTTT-TG-AAAAGTAAGAAAGCGATTTCCAAAGTTTCATACCCAGTAAACTATTTCCCAAATTGG
* * * * *
84059 TAAGTCCTTCGGACCATGAGTAAGTCCTTCGAGCATGAGGATTAAATCTTTTAAGTAATCTGTAA
321 TAAGTCCTTCGGACCATCAGTAAGT-CTTCGAGCATGAGAATTAAATCCTTCAAGTAATCTATAA
* * * * * * *
84124 TTCTTTCG-AGCAAGATGTTACGTCCCTCGGGCCATCTATAAGACCTTCGGGTAGGTTGTTTTCA
385 TT-TTT-GTAGCAAGATGATAAGTACCTCGGGCCATCCATAAGACCTTAGGGTAAGATGTTTTCA
* * * *** *
84188 CATAAATTTGAGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTGGAAAATGAA
448 CATAAATTTGAAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATAAA
84253 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGT
513 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGT
* * * * *
84318 AAGTTCTTTGGGTCATTAGTTAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCAACTATAAG
578 AAGTCCTTCGGGTCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGATCAACTATAAG
* * * *
84383 TCTTTCGAGTAAGATGTTAAGTCCCACGGGCCATCTA-TAAGAACTTCGGGCAGGACGTTTCCAC
643 TCTTTCGAGCAAGATGATAAGTCCCACAGGCCATC-AGTAAGAACTTCAGGCAGGACGTTTCCAC
84447 ATG-A
707 ATGAA
* *
84451 TTTTCGAAAAATGAGAAAGCGATTTCCATAGTTTCT
1 TTTTAGAAAAATGAGAAAGCAATTTCCA-AGTTTCT
84487 CATTTAAATC
Statistics
Matches: 652, Mismatches: 83, Indels: 24
0.86 0.11 0.03
Matches are distributed among these distances:
708 3 0.00
709 149 0.23
710 117 0.18
711 75 0.12
712 306 0.47
713 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (711 bp):
TTTTAGAAAAATGAGAAAGCAATTTCCAAGTTTCTTACCTAGATAAATATTTCCCAAATTGATAA
GTCCTTCAGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTC
TTTCGAGCAAGATGTTAAGTCCCTCGGGCCATCCGTAAGACCTTCGAGTAGGATATTATCACATG
AAATTTAAAAAATAAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAACTT
TTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCATACCCAGTAAACTATTTCCCAAATTGGTAAGT
CCTTCGGACCATCAGTAAGTCTTCGAGCATGAGAATTAAATCCTTCAAGTAATCTATAATTTTTG
TAGCAAGATGATAAGTACCTCGGGCCATCCATAAGACCTTAGGGTAAGATGTTTTCACATAAATT
TGAAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATATAGTATTTTCAAAAAATAAAATTTTTGA
AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTT
CGGGTCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGATCAACTATAAGTCTTTCGA
GCAAGATGATAAGTCCCACAGGCCATCAGTAAGAACTTCAGGCAGGACGTTTCCACATGAA
Found at i:94316 original size:49 final size:51
Alignment explanation
Indices: 94204--94323 Score: 144
Period size: 49 Copynumber: 2.5 Consensus size: 51
94194 ACCTTTTATC
94204 CCATAAGCTCATAAGCTTA----TTTTTTCCAAAATACTTACCATTTAAATT
1 CCATAAGCTCATAAGCTTATTTGTTTTTTCCAAAATACTTACCATTT-AATT
* * * *
94252 CCATAAGCTCGTAAGCTTATTTGTTTTTTTCAATATACTTGCCA-TT-ATT
1 CCATAAGCTCATAAGCTTATTTGTTTTTTCCAAAATACTTACCATTTAATT
*
94301 CCGTAAGCTCATAAGCTTATTTG
1 CCATAAGCTCATAAGCTTATTTG
94324 CATGGTTACC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
48 18 0.29
49 24 0.39
51 2 0.03
52 18 0.29
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (51 bp):
CCATAAGCTCATAAGCTTATTTGTTTTTTCCAAAATACTTACCATTTAATT
Found at i:101267 original size:46 final size:48
Alignment explanation
Indices: 101145--101273 Score: 140
Period size: 46 Copynumber: 2.8 Consensus size: 48
101135 ATATAAATTT
* * *
101145 CTTACC-TTTTATCCCATAATCTCATAAGCTTA-TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
* ** *
101191 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
* *
101240 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
101274 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
46 29 0.41
47 3 0.04
48 21 0.30
49 17 0.24
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (48 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
Found at i:104197 original size:2 final size:2
Alignment explanation
Indices: 104190--104215 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
104180 TCCTCATTTG
104190 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
104216 GGATTTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119380 original size:18 final size:17
Alignment explanation
Indices: 119351--119412 Score: 53
Period size: 19 Copynumber: 3.7 Consensus size: 17
119341 ATGTTATAAA
119351 ATTTATATTTTTAAGTTAT
1 ATTTA-ATTTTT-AGTTAT
119370 ATTTAA--TTT--TTAT
1 ATTTAATTTTTAGTTAT
119383 A-TTAATTTTTATGTTAT
1 ATTTAATTTTTA-GTTAT
119400 ATTTAATATTTTA
1 ATTTAAT-TTTTA
119413 TTTTTAAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
12 4 0.11
13 5 0.14
14 3 0.08
16 3 0.08
17 5 0.14
18 6 0.17
19 10 0.28
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTAATTTTTAGTTAT
Found at i:119389 original size:12 final size:13
Alignment explanation
Indices: 119366--119394 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
119356 TATTTTTAAG
119366 TTATATTTAATTT
1 TTATATTTAATTT
119379 TTATA-TTAATTT
1 TTATATTTAATTT
119391 TTAT
1 TTAT
119395 GTTATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATATTTAATTT
Found at i:122569 original size:20 final size:20
Alignment explanation
Indices: 122542--122602 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
122532 GATTAGGACA
*
122542 ATTATTTGAATTGAACCGAT
1 ATTATTTGAATTGTACCGAT
*
122562 -TCTATTTGAATTGTATCGAT
1 AT-TATTTGAATTGTACCGAT
122582 ATTATTTGAATTGTACCGAT
1 ATTATTTGAATTGTACCGAT
122602 A
1 A
122603 CTGCTCGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
21 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (20 bp):
ATTATTTGAATTGTACCGAT
Found at i:129723 original size:23 final size:23
Alignment explanation
Indices: 129670--129723 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
129660 TCGAGGATTT
*
129670 TATGTGGTCCTTCGGGACAAAAC
1 TATGTGGTCCTTCAGGACAAAAC
* **
129693 TATATGGTCCTTCAGGACAATCC
1 TATGTGGTCCTTCAGGACAAAAC
129716 TATGTGGT
1 TATGTGGT
129724 ATTTTGGGAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (23 bp):
TATGTGGTCCTTCAGGACAAAAC
Found at i:139326 original size:13 final size:13
Alignment explanation
Indices: 139310--139335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
139300 TTTTCCGTTA
139310 AATTTTTATTTTT
1 AATTTTTATTTTT
139323 AATTTTTATTTTT
1 AATTTTTATTTTT
139336 GTTCGACCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
AATTTTTATTTTT
Found at i:139379 original size:14 final size:14
Alignment explanation
Indices: 139356--139391 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
139346 GCGTGTTTAA
*
139356 TTTATTTTTTTCTT
1 TTTATTTTTTTATT
*
139370 TTTCTTTTTTTATT
1 TTTATTTTTTTATT
139384 TTTATTTT
1 TTTATTTT
139392 GCAGAAACTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTATTTTTTTATT
Found at i:145740 original size:23 final size:23
Alignment explanation
Indices: 145687--145748 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
145677 AACATTTTAT
* * *
145687 GTGGCACTTCAGTGCATTTCTAG
1 GTGGCACTTCGGTGCAGTTCTAC
* * *
145710 GCGACACTTCGGTGTAGTTCTAC
1 GTGGCACTTCGGTGCAGTTCTAC
*
145733 GTGGCACTTTGGTGCA
1 GTGGCACTTCGGTGCA
145749 TTTATACGAG
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.29, T:0.32
Consensus pattern (23 bp):
GTGGCACTTCGGTGCAGTTCTAC
Found at i:152758 original size:23 final size:23
Alignment explanation
Indices: 152703--152760 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
152693 TTCTATACGA
*
152703 CACTTTGGTGCAATTCTACGTGT
1 CACTTTGGTGCAATTCTACGTGC
*
152726 CA-TTTCGGTGCAATTCTACTTGC
1 CACTTT-GGTGCAATTCTACGTGC
152749 CACTTTGGTGCA
1 CACTTTGGTGCA
152761 TTTATACGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 3 0.10
23 25 0.81
24 3 0.10
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (23 bp):
CACTTTGGTGCAATTCTACGTGC
Found at i:159032 original size:19 final size:19
Alignment explanation
Indices: 159008--159055 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
158998 AAGTTTGAAA
*
159008 TTAGGATTATCTCTTGTTT
1 TTAGGATTATCTCTTATTT
*
159027 TTAGGAATTATCTTTTATTT
1 TTAGG-ATTATCTCTTATTT
159047 TTAGGATTA
1 TTAGGATTA
159056 AGTTTGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.56
Consensus pattern (19 bp):
TTAGGATTATCTCTTATTT
Found at i:163049 original size:6 final size:6
Alignment explanation
Indices: 163002--163049 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
162992 TTCGTAATAA
* * * *
163002 AAAAAG AAAAATG AAAAAG AGAAAG AGAAAG AGAAAG GAAAAG AAAAA
1 AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
163050 AACCAAATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:167691 original size:23 final size:24
Alignment explanation
Indices: 167634--167704 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 24
167624 ATTTTTTAAA
* *
167634 ATATATATTATAAAAGTAGTATATT
1 ATATA-ATTTTAAAAATAGTATATT
*
167659 ATATATTTTTAAAAATA-TATATT
1 ATATAATTTTAAAAATAGTATATT
* *
167682 ATATAATTTTGACAATAGTATAT
1 ATATAATTTTAAAAATAGTATAT
167705 AGTTTTGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 20 0.51
24 14 0.36
25 5 0.13
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (24 bp):
ATATAATTTTAAAAATAGTATATT
Found at i:167782 original size:48 final size:48
Alignment explanation
Indices: 167673--167782 Score: 109
Period size: 49 Copynumber: 2.3 Consensus size: 48
167663 ATTTTTAAAA
* * ** *
167673 ATATATATTATATAATTTTGACAATAGTATATAGTTTTGAAAGTATATT
1 ATATATA-CATATAATTTTGAAAATAGTATATAGTTTAAAAAATATATT
*
167722 ATATATATATATAATATTTGAAAATA-TATATTAGTTTAAAAAATAGTA-T
1 ATATATACATATAAT-TTTGAAAATAGTATA-TAGTTTAAAAAATA-TATT
167771 ATA-ATACATATA
1 ATATATACATATA
167783 TAACTTTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
48 20 0.38
49 31 0.58
50 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (48 bp):
ATATATACATATAATTTTGAAAATAGTATATAGTTTAAAAAATATATT
Found at i:168631 original size:15 final size:15
Alignment explanation
Indices: 168611--168640 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
168601 CTTAAAACCC
168611 TTTTTTTACTCTATG
1 TTTTTTTACTCTATG
*
168626 TTTTTTTACTTTATG
1 TTTTTTTACTCTATG
168641 ACAACTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTTTTTACTCTATG
Found at i:172615 original size:12 final size:13
Alignment explanation
Indices: 172598--172626 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
172588 CTTAATTCCA
172598 AAAATTAAAA-TT
1 AAAATTAAAATTT
172610 AAAATTAAAATTT
1 AAAATTAAAATTT
172623 AAAA
1 AAAA
172627 ACTCGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:174141 original size:16 final size:16
Alignment explanation
Indices: 174120--174153 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
174110 ATAAATAAAT
174120 AAATAAAGGAAAATAA
1 AAATAAAGGAAAATAA
174136 AAATAAAGGAAAATAA
1 AAATAAAGGAAAATAA
174152 AA
1 AA
174154 TACAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAATAAAGGAAAATAA
Found at i:174300 original size:70 final size:69
Alignment explanation
Indices: 174184--174357 Score: 201
Period size: 70 Copynumber: 2.5 Consensus size: 69
174174 AAAATTATTT
* * * *
174184 TTTTAAAAATATTATATGCTATATGTTTTCAAACTTACTTTCAAAACTATA-TACTATTTATTTT
1 TTTTAAAAATACTATAT--TATATGTTTTCAAAATTACTTTAAAAACTATAGTAC-ATGT-TTTT
* *
174248 CAAAACCG
62 CAAAAACA
174256 TTTTAAAAATTA-TATATTATATGTTTTCAAAATTACTTTAAAAACTATATGGTACATGTTTTTC
1 TTTTAAAAA-TACTATATTATATGTTTTCAAAATTACTTTAAAAACTATA--GTACATGTTTTTC
174320 AAAAACA
63 AAAAACA
*
174327 TTTTAAAAAAACTATA-TATATGTTTTCAAAA
1 TTTTAAAAATACTATATTATATGTTTTCAAAA
174358 GTTATATTTG
Statistics
Matches: 91, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
70 46 0.51
71 23 0.25
72 17 0.19
73 5 0.05
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (69 bp):
TTTTAAAAATACTATATTATATGTTTTCAAAATTACTTTAAAAACTATAGTACATGTTTTTCAAA
AACA
Found at i:174315 original size:35 final size:35
Alignment explanation
Indices: 174196--174357 Score: 130
Period size: 35 Copynumber: 4.6 Consensus size: 35
174186 TTAAAAATAT
* * *
174196 TATATGCTATATGTTTTCAAACTTACTTTCAAAAC
1 TATATACTATATGTTTTCAAAATTACTTTAAAAAC
* * **** *
174231 TATATACTATTTATTTTCAAAACCGTTTTAAAAAT
1 TATATACTATATGTTTTCAAAATTACTTTAAAAAC
*
174266 TATATATTATATGTTTTCAAAATTACTTTAAAAAC
1 TATATACTATATGTTTTCAAAATTACTTTAAAAAC
** * ** *
174301 TATATGGTACATGTTTTTCAAAAACATTTTAAAAA-
1 TATATACTATATG-TTTTCAAAATTACTTTAAAAAC
*
174336 AACTATA-TATATGTTTTCAAAA
1 TA-TATACTATATGTTTTCAAAA
174358 GTTATATTTG
Statistics
Matches: 98, Mismatches: 27, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
34 9 0.09
35 68 0.69
36 21 0.21
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (35 bp):
TATATACTATATGTTTTCAAAATTACTTTAAAAAC
Found at i:178311 original size:23 final size:23
Alignment explanation
Indices: 178281--178357 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
178271 GAGTCGAGGG
178281 TTCTACGTGGTCCTTAAGGACAA
1 TTCTACGTGGTCCTTAAGGACAA
178304 TTCTACGTGGTCCTTAAGGACAA
1 TTCTACGTGGTCCTTAAGGACAA
* * **
178327 TACTATGTGGTCCTTTGGGACATA
1 TTCTACGTGGTCCTTAAGGACA-A
178351 TTCTACG
1 TTCTACG
178358 CAGTCCTTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 41 0.87
24 6 0.13
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTAAGGACAA
Found at i:178365 original size:47 final size:47
Alignment explanation
Indices: 178287--178401 Score: 126
Period size: 47 Copynumber: 2.5 Consensus size: 47
178277 AGGGTTCTAC
** **
178287 GTGGTCCTTAAGGACA-ATTCTACGTGGTCCTTAAGGACAATACTAT
1 GTGGTCCTTTGGGACATATTCTACGCAGTCCTTAAGGACAATACTAT
** * *
178333 GTGGTCCTTTGGGACATATTCTACGCAGTCCTTCGGGACATTTCTAT
1 GTGGTCCTTTGGGACATATTCTACGCAGTCCTTAAGGACAATACTAT
* *
178380 GTTGTCCTTTGGTACAT-TTCTA
1 GTGGTCCTTTGGGACATATTCTA
178402 TGTGGCACTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 19 0.33
47 39 0.67
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (47 bp):
GTGGTCCTTTGGGACATATTCTACGCAGTCCTTAAGGACAATACTAT
Found at i:178386 original size:23 final size:23
Alignment explanation
Indices: 178329--178404 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
178319 AAGGACAATA
*
178329 CTATGTGGTCCTTTGGGACATATT
1 CTATGTAGTCCTTTGGGACAT-TT
* * *
178353 CTACGCAGTCCTTCGGGACATTT
1 CTATGTAGTCCTTTGGGACATTT
* *
178376 CTATGTTGTCCTTTGGTACATTT
1 CTATGTAGTCCTTTGGGACATTT
178399 CTATGT
1 CTATGT
178405 GGCACTTTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 26 0.60
24 17 0.40
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (23 bp):
CTATGTAGTCCTTTGGGACATTT
Found at i:178412 original size:23 final size:23
Alignment explanation
Indices: 178370--178455 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
178360 GTCCTTCGGG
*
178370 ACATTTCTATGTTGTC-CTTTGGT
1 ACATTTCTATG-TGGCACTTTGGT
*
178393 ACATTTCTATGTGGCACTTTGAT
1 ACATTTCTATGTGGCACTTTGGT
* * * *
178416 GCATATTCTACGTGACACTTCGGT
1 ACAT-TTCTATGTGGCACTTTGGT
* *
178440 GCAATTCTATGTGGCA
1 ACATTTCTATGTGGCA
178456 GTTTTGACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
22 3 0.06
23 30 0.59
24 18 0.35
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (23 bp):
ACATTTCTATGTGGCACTTTGGT
Found at i:178434 original size:24 final size:23
Alignment explanation
Indices: 178397--178448 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
178387 TTTGGTACAT
* * *
178397 TTCTATGTGGCACTTTGATGCATA
1 TTCTACGTGACACTTCGATGCA-A
*
178421 TTCTACGTGACACTTCGGTGCAA
1 TTCTACGTGACACTTCGATGCAA
178444 TTCTA
1 TTCTA
178449 TGTGGCAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (23 bp):
TTCTACGTGACACTTCGATGCAA
Found at i:181624 original size:21 final size:21
Alignment explanation
Indices: 181600--181640 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
181590 CTAGTCGTCC
* *
181600 ACCGTCCGTCGCTTGTCATCT
1 ACCGTCCGCCGCTTGCCATCT
*
181621 ACCGTTCGCCGCTTGCCATC
1 ACCGTCCGCCGCTTGCCATC
181641 CGCCGTTCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.41, G:0.20, T:0.29
Consensus pattern (21 bp):
ACCGTCCGCCGCTTGCCATCT
Found at i:190303 original size:40 final size:39
Alignment explanation
Indices: 190252--190392 Score: 156
Period size: 40 Copynumber: 3.5 Consensus size: 39
190242 TCTTACCTTT
* * * * *
190252 GGTATCGATACTACAAGAACAATATCAGTATTATTTATGT
1 GGTATCAATACTATAAGAATAATATTAGTATT-TTTATGC
*
190292 GGTATCAATACTATAAGAATAATATTTGTATTTTTCATGC
1 GGTATCAATACTATAAGAATAATATTAGTATTTTT-ATGC
* * * *
190332 AGTATCGATACTATAAGAATAATATTACTATTGTTCATGC
1 GGTATCAATACTATAAGAATAATATTAGTATT-TTTATGC
*
190372 GGTATCAATTCTATAAGAATA
1 GGTATCAATACTATAAGAATA
190393 TTATCGATAC
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
39 3 0.04
40 80 0.94
41 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (39 bp):
GGTATCAATACTATAAGAATAATATTAGTATTTTTATGC
Found at i:191279 original size:19 final size:19
Alignment explanation
Indices: 191258--191320 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
191248 ATATGCGGTT
* *
191258 TCGAAACTTTGAGAAAGTT
1 TCGAAACTTTGTGAAAGTA
191277 TCGAAACTTTGTGAAAGTA
1 TCGAAACTTTGTGAAAGTA
191296 TCGAAACTTTGTGAAAGTA
1 TCGAAACTTTGTGAAAGTA
191315 TCGAAA
1 TCGAAA
191321 TTTTTAAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (19 bp):
TCGAAACTTTGTGAAAGTA
Found at i:195131 original size:19 final size:18
Alignment explanation
Indices: 195107--195152 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
195097 CTTTTTCATG
195107 TCTTTTTTC-TCTTCTTCTC
1 TCTTTTTTCTTCTT-TT-TC
*
195126 TCTTTTTTCTTCTTTTTT
1 TCTTTTTTCTTCTTTTTC
195144 TCTTTTTTC
1 TCTTTTTTC
195153 GAACAACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 10 0.40
19 11 0.44
20 4 0.16
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (18 bp):
TCTTTTTTCTTCTTTTTC
Found at i:203680 original size:18 final size:19
Alignment explanation
Indices: 203648--203694 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
203638 GTAATGAGAT
*
203648 ATTTAAAT-GATAAAAGCA
1 ATTTAAATAAATAAAAGCA
203666 A-TTAAATAAATAAAAGCA
1 ATTTAAATAAATAAAAGCA
203684 ATTTAAATAAA
1 ATTTAAATAAA
203695 AATAAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 9 0.35
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (19 bp):
ATTTAAATAAATAAAAGCA
Found at i:213897 original size:24 final size:23
Alignment explanation
Indices: 213846--213898 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
213836 CTACAAAAAC
213846 ATTA-TATTATATTTATTTATTT
1 ATTATTATTATATTTATTTATTT
213868 ATTTATTATTAT-TATTATTTATTTT
1 A-TTATTATTATAT-TTATTTA-TTT
213893 ATTATT
1 ATTATT
213899 TTTGTAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 1 0.04
23 4 0.15
24 18 0.67
25 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTATTATTATATTTATTTATTT
Found at i:213990 original size:33 final size:33
Alignment explanation
Indices: 213948--214020 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
213938 TTCAAAGAAT
213948 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACGTATTTGAGTCCTATTGAAACACTA
213981 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACGTATTTGAGTCCTATTGAAACACTA
214014 AAACCAA
1 AAACCAA
214021 AACATTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (33 bp):
AAACCAACGTATTTGAGTCCTATTGAAACACTA
Found at i:214442 original size:34 final size:36
Alignment explanation
Indices: 214360--214442 Score: 84
Period size: 38 Copynumber: 2.3 Consensus size: 36
214350 TCTCCTAATT
*
214360 TTAATATTTTTATTTCTTTTTACATTGTTATATATA
1 TTAATATTTTTATTTCTTTTTACATTATTATATATA
*
214396 TATATATTTTTTTCATTT-TTTATTA-A-TATTAT-TATA
1 T-TA-ATATTTTT-ATTTCTTT-TTACATTATTATATATA
214432 TTAATATTTTT
1 TTAATATTTTT
214443 TATTATTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
34 7 0.17
35 2 0.05
36 6 0.15
37 7 0.17
38 11 0.28
39 7 0.17
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (36 bp):
TTAATATTTTTATTTCTTTTTACATTATTATATATA
Found at i:216601 original size:18 final size:17
Alignment explanation
Indices: 216547--216595 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
216537 TTGGACCCTT
* *
216547 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
216565 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
216583 AGTGCATTCGATG
1 AGTGCA-TCGATG
216596 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:216702 original size:65 final size:65
Alignment explanation
Indices: 216568--216726 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
216558 GCACTAAGAG
* * * *
216568 TGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATATCCAGAGTGTATCGATACATGGCTGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATATCCACAGTGCATCGATACATGGCTGA
* *
216632 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-TA
1 TGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATATCCACAGTGCATCGATACATGGCT-
*
216695 TA
64 GA
*
216697 TGCATCGATGCATGAAATGCATTCGATGTT
1 TGCATCGATGCATCAAATGCATTCGATGTT
216727 CAATTTAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.33
65 53 0.63
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATATCCACAGTGCATCGATACATGGCTGA
Found at i:216766 original size:65 final size:64
Alignment explanation
Indices: 216567--216776 Score: 182
Period size: 65 Copynumber: 3.2 Consensus size: 64
216557 TGCACTAAGA
* * * **
216567 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATATC-CAGAGTGTATCGATACATG-GC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTCAG-G-GCATCGATGCATGATA
216629 TG
63 TG
* *
216631 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGGGCATCGATGCATGATAT
216696 -
64 G
* * **
216696 ATGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGGGCATCGATGCATAGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GGGCATCGATGCAT-GAT
216759 -TG
62 ATG
*
216761 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
216777 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 47 0.39
65 60 0.50
66 5 0.04
67 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGGGCATCGATGCATGATATG
Found at i:223210 original size:21 final size:21
Alignment explanation
Indices: 223186--223235 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
223176 GAAGCTTTAA
223186 GATCATCAATTTTATTTTGAT
1 GATCATCAATTTTATTTTGAT
*
223207 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTTATTTTGAT
223228 GATCATCA
1 GATCATCA
223236 TTGACCTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (21 bp):
GATCATCAATTTTATTTTGAT
Found at i:223227 original size:18 final size:20
Alignment explanation
Indices: 223180--223235 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
223170 TCAAAAGAAG
*
223180 CTTTAAGATCATCAATTTTA
1 CTTTATGATCATCAATTTTA
*
223200 TTTTGATGATCATCAATTTT-
1 CTTT-ATGATCATCAATTTTA
223220 CTTTTGATGATCATCA
1 C-TTT-ATGATCATCA
223236 TTGACCTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (20 bp):
CTTTATGATCATCAATTTTA
Found at i:223244 original size:21 final size:21
Alignment explanation
Indices: 223186--223244 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
223176 GAAGCTTTAA
***
223186 GATCATCAATTTTATTTTGAT
1 GATCATCAATTACCTTTTGAT
**
223207 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTACCTTTTGAT
223228 GATCATC-ATTGACCTTT
1 GATCATCAATT-ACCTTT
223245 GAAAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.09
21 31 0.91
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49
Consensus pattern (21 bp):
GATCATCAATTACCTTTTGAT
Found at i:228813 original size:110 final size:110
Alignment explanation
Indices: 228644--229163 Score: 717
Period size: 110 Copynumber: 4.8 Consensus size: 110
228634 AGAGAAGGGG
* * * *
228644 TGACTGCCAACAAACAAATTTTTAGTTTCATTCAGAGTCAATTTTAACTTCACAGCGAAGGATAT
1 TGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATAT
*
228709 TGGACTCGATACAACACAAGCTCAACTTCACAACGAAGGGGCGAC
66 TGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGAC
* *
228754 TGACTGTTAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATAT
1 TGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATAT
228819 TGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGAC
66 TGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGAC
* * * * * **
228864 TGACTGTCAACAAACAGCTTTTTAATTTCATTCAAAGTCAATTTTAACTTCACAATGAAGGATAT
1 TGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATAT
* * * *
228929 TAGACTCGAGACAATACAAGCTCAACTTCACAGCGAAGGGGTGAC
66 TGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGAC
* * * * * *
228974 TGACTGTCAAAAAAATAACTTATCAGTTTCATTCAGATTCAATTTCAAATTCACAGTGAAGGATA
1 TGACTGTC-AACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
*
229039 TTGGACTCGAGACAACACAAGCTCAACTTCACTA-GAAGGGGCGAC
65 TTGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGAC
* * * *
229084 TGGCTGTCAACAAATAACTTTCCAG--T--TTCAGAGTCAATTTCAACTTCACGGCGAAGGATAT
1 TGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATAT
* *
229145 TGGCCTCGAAACAACACAA
66 TGGACTCGAGACAACACAA
229164 ATATTTGGAT
Statistics
Matches: 365, Mismatches: 44, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
105 48 0.13
107 1 0.00
109 14 0.04
110 227 0.62
111 75 0.21
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (110 bp):
TGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATAT
TGGACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGAC
Found at i:229400 original size:84 final size:83
Alignment explanation
Indices: 229270--229853 Score: 509
Period size: 84 Copynumber: 7.0 Consensus size: 83
229260 AATCGTGCCC
* * * *
229270 ACCAAAGGCCTTCGCGTTTGACTACGCTCAGCTCCAAGACATATCATTTGCAGCATAACTTAAGT
1 ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
229335 CGAGAAGGGTTATCTACCA
66 CGAGAAGGGTTATCT-CCA
* * * * *
229354 ACCAAAGACCTTCGAGATCGACTACGCTCAGCTCCAAGGTACATCATTTGTAGCATTAGCTTAAG
1 ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCA-TAACTTAAG
*
229419 TCGAGAAGGGCTATCT---
65 TCGAGAAGGGTTATCTCCA
* * * * * * * *
229435 TCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAG
1 ACCAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
* * ***
229500 GCTAGAAGGGTTATCTGTG
65 TCGAGAAGGGTTATCTCCA
* * *
229519 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAG
1 ACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
229584 TC-ATGAAGGGTTATCTGCCA
65 TCGA-GAAGGGTTATCT-CCA
* * * *
229604 ACCAAAGACCTTCGAGTTTGACTATGCTCAGCTCAAAGGTACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
229669 CGAGAAGAGCTATCT---
66 CGAGAAGGGTTATCTCCA
* * * ** * * * * * *
229684 ACCAAAGACCCTCGAATTTGATTACAATCAGCTTCAAGGGCACATTATTTACGGTATAACTCAAG
1 ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAG
* * *
229749 GCTAGAAGGGTTATCTGTCA
65 TCGAGAAGGGTTATCT-CCA
* * * ** * * *
229769 A-CAAAGACCTTCGAGTTCGACTCCACTCAATTCAAAGGCACCATCATTTGCAGCATAGCTCAAG
1 ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTTAAG
* * *
229833 GCAAGAAGGGCTATCTGCCA
65 TCGAGAAGGGTTATCT-CCA
229853 A
1 A
229854 AGACCTTTGA
Statistics
Matches: 398, Mismatches: 87, Indels: 30
0.77 0.17 0.06
Matches are distributed among these distances:
80 29 0.07
81 78 0.20
82 18 0.05
83 5 0.01
84 215 0.54
85 53 0.13
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (83 bp):
ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
CGAGAAGGGTTATCTCCA
Found at i:229817 original size:249 final size:249
Alignment explanation
Indices: 229273--229853 Score: 797
Period size: 249 Copynumber: 2.3 Consensus size: 249
229263 CGTGCCCACC
* * * * * * * *
229273 AAAGGCCTTCGCGTTTGACTACGCTCAGCTCCAAGACATATCATTTGCAGCATAACTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACACTCAACTCAAAGGCACATCATTTGCAGCATAACTTAAGTC-A
* *
229338 GAAGGGTTATCTACCAACCAAAGACCTTCGAGATCGACTACGCTCAGCTCCAAGGTACATCATTT
65 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGATCGACTACGCTCAGCTCAAAGGTACATCATTT
* * * * *
229403 GTAGCATTAGCTTAAGTCGAGAAGGGCTATCTTCCAAAGACCCTCGAGTTTGATTACACTCAGCT
130 GCAGCATTAGCTTAAGTCGAGAAGAGCTATCTACCAAAGACCCTCGAATTTGATTACAATCAGCT
* * *
229468 TCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
195 TCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACA
* * * * *
229523 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTCAT
1 AAAGACCTTCGAGTTCGACTACACTCAACTCAAAGGCACATCATTTGCAGCATAACTTAAGTCA-
* * *
229588 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTATGCTCAGCTCAAAGGTACATCATTT
65 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGATCGACTACGCTCAGCTCAAAGGTACATCATTT
229653 GCAGCA-TAGCTTAAGTCGAGAAGAGCTATCTACCAAAGACCCTCGAATTTGATTACAATCAGCT
130 GCAGCATTAGCTTAAGTCGAGAAGAGCTATCTACCAAAGACCCTCGAATTTGATTACAATCAGCT
* * *
229717 TCAAGGGCACATTATTTACGGTATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-
195 TCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACA
* * * * *
229771 AAAGACCTTCGAGTTCGACTCCACTCAATTCAAAGGCACCATCATTTGCAGCATAGCTCAAGGCA
1 AAAGACCTTCGAGTTCGACTACACTCAACTCAAAGGCA-CATCATTTGCAGCATAACTTAAGTC-
*
229836 AGAAGGGCTATCTGCCAA
64 AGAAGGGTTATCTGCCAA
229854 AGACCTTTGA
Statistics
Matches: 296, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
248 33 0.11
249 139 0.47
250 124 0.42
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (249 bp):
AAAGACCTTCGAGTTCGACTACACTCAACTCAAAGGCACATCATTTGCAGCATAACTTAAGTCAG
AAGGGTTATCTGCCAACCAAAGACCTTCGAGATCGACTACGCTCAGCTCAAAGGTACATCATTTG
CAGCATTAGCTTAAGTCGAGAAGAGCTATCTACCAAAGACCCTCGAATTTGATTACAATCAGCTT
CAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACA
Found at i:230249 original size:17 final size:18
Alignment explanation
Indices: 230214--230272 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
230204 ACAAAAACAT
230214 TTTATTATATTATATTTA
1 TTTATTATATTATATTTA
230232 TTTATT-TATTAT-TATTA
1 TTTATTATATTATAT-TTA
230249 -TTATTAATATT-T-TTTA
1 TTTATT-ATATTATATTTA
230265 TTTTATTA
1 -TTTATTA
230273 CTTTTGCAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 9 0.25
17 12 0.33
18 15 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTATATTATATTTA
Found at i:230366 original size:33 final size:33
Alignment explanation
Indices: 230324--230391 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
230314 TTCAGAAAAT
*
230324 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACGTATTTGAGTCCTATTAAAACACTA
230357 AAACCAACGTATTTGAGTCCTATTAAAACACTA
1 AAACCAACGTATTTGAGTCCTATTAAAACACTA
230390 AA
1 AA
230392 CCCGAAGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (33 bp):
AAACCAACGTATTTGAGTCCTATTAAAACACTA
Found at i:230746 original size:35 final size:36
Alignment explanation
Indices: 230679--230747 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
230669 TGACTTATTC
*
230679 TTTTTATTTCATTTTTTATTTATTTACTTTATATATA
1 TTTTTATTTCATTTTTTATTAATTTAC-TTATATATA
230716 TTTTT-TTTCATTTTTTATTAATATTA-TTATAT
1 TTTTTATTTCATTTTTTATTAAT-TTACTTATAT
230748 TAATGTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 6 0.20
36 16 0.53
37 8 0.27
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (36 bp):
TTTTTATTTCATTTTTTATTAATTTACTTATATATA
Found at i:230757 original size:35 final size:36
Alignment explanation
Indices: 230685--230758 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
230675 ATTCTTTTTA
* *
230685 TTTCATTTTTTATTTATTTACTTTATATATATTTTT
1 TTTCATTTTTTATTAATTTACTTTATATATATGTTT
230721 TTTCATTTTTTATTAATATTA--TTATAT-TAATGTTT
1 TTTCATTTTTTATTAAT-TTACTTTATATAT-ATGTTT
230756 TTT
1 TTT
230759 ATTATTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 1 0.03
35 14 0.41
36 16 0.47
37 3 0.09
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.70
Consensus pattern (36 bp):
TTTCATTTTTTATTAATTTACTTTATATATATGTTT
Found at i:234690 original size:17 final size:18
Alignment explanation
Indices: 234655--234713 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
234645 ACAAAAACAT
234655 TTTATTATATTATATTTA
1 TTTATTATATTATATTTA
234673 TTTATT-TATTAT-TATTA
1 TTTATTATATTATAT-TTA
234690 -TTATTAATATT-T-TTTA
1 TTTATT-ATATTATATTTA
234706 TTTTATTA
1 -TTTATTA
234714 CTTTTGCAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 9 0.25
17 12 0.33
18 15 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTATATTATATTTA
Found at i:234807 original size:33 final size:33
Alignment explanation
Indices: 234765--234835 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
234755 TTCAGAAAAT
*
234765 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACGTATTTGAGTCCTATTAAAACACTA
234798 AAACCAACGTATTTGAGTCCTATTAAAACACTA
1 AAACCAACGTATTTGAGTCCTATTAAAACACTA
234831 AAACC
1 AAACC
234836 GAAGCATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (33 bp):
AAACCAACGTATTTGAGTCCTATTAAAACACTA
Found at i:241209 original size:13 final size:13
Alignment explanation
Indices: 241191--241218 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
241181 GCCCATGTAA
241191 CTTAATGTGAGAG
1 CTTAATGTGAGAG
241204 CTTAATGTGAGAG
1 CTTAATGTGAGAG
241217 CT
1 CT
241219 GTAGGTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (13 bp):
CTTAATGTGAGAG
Found at i:241280 original size:18 final size:18
Alignment explanation
Indices: 241257--241361 Score: 183
Period size: 18 Copynumber: 5.8 Consensus size: 18
241247 AGGGATTATC
241257 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
241275 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
241293 AGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGGGACAT
241311 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
241329 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
**
241347 AGTTTTCCTTCGGGA
1 AGTGGTCCTTCGGGA
241362 GAAATATTCA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 83 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:244055 original size:20 final size:20
Alignment explanation
Indices: 244030--244087 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
244020 TAATTCAATC
244030 AGTATCGATACCAAAGGGGG
1 AGTATCGATACCAAAGGGGG
** *
244050 AGTATCGATACTGAAGAGGG
1 AGTATCGATACCAAAGGGGG
244070 AGTATCGATACCGAAAGG
1 AGTATCGATACC-AAAGG
244088 AAGGAATCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.36, C:0.14, G:0.33, T:0.17
Consensus pattern (20 bp):
AGTATCGATACCAAAGGGGG
Done.