Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004464.1 Hibiscus syriacus cultivar Beakdansim tig00009840_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: 466920
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:2123 original size:13 final size:13
Alignment explanation
Indices: 2105--2129 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2095 TTCCAACCTG
2105 ACCCGACCCGTTT
1 ACCCGACCCGTTT
2118 ACCCGACCCGTT
1 ACCCGACCCGTT
2130 GACCGATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:4623 original size:12 final size:12
Alignment explanation
Indices: 4603--4669 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 12
4593 GATACATAAC
*
4603 CTGAATTCTGTT
1 CTGATTTCTGTT
* *
4615 ATGATTTCTGAT
1 CTGATTTCTGTT
4627 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
*
4639 CTGATATCTGTT
1 CTGATTTCTGTT
*
4651 CTGAATTCTGTT
1 CTGATTTCTGTT
*
4663 TTGATTT
1 CTGATTT
4670 ATGATATCTC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.52
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:4634 original size:24 final size:24
Alignment explanation
Indices: 4603--4674 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
4593 GATACATAAC
4603 CTGAATTCTGTTATGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * * *
4627 CTGGATTCTGTTCTGATATCTGTT
1 CTGAATTCTGTTATGATTTCTGAT
* *
4651 CTGAATTCTGTTTTGATTTATGAT
1 CTGAATTCTGTTATGATTTCTGAT
4675 ATCTCCGTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:4835 original size:2 final size:2
Alignment explanation
Indices: 4828--4864 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4818 GTTGGATGGG
4828 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4865 GTTTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6784 original size:18 final size:18
Alignment explanation
Indices: 6761--6795 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6751 CGGTTCCAAC
*
6761 CCGACCTGACCCGTTGAT
1 CCGACCCGACCCGTTGAT
6779 CCGACCCGACCCGTTGA
1 CCGACCCGACCCGTTGA
6796 CCGTTGACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAT
Found at i:8197 original size:24 final size:24
Alignment explanation
Indices: 8170--8288 Score: 107
Period size: 24 Copynumber: 5.0 Consensus size: 24
8160 AAACATAAAT
*
8170 CAGGTCAAGTATCATATCA-AACTC
1 CAGGTCAAGTATCAGATCAGAA-TC
*
8194 CAGGTCAAGAATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
8218 AAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* ** *
8242 TATATC-AGATATCAGATCATAATC
1 CAGGTCAAG-TATCAGATCAGAATC
* * *
8266 CATGTCAAATATCATATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
8289 TCAAACCGAA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
23 2 0.03
24 73 0.94
25 3 0.04
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:8226 original size:48 final size:48
Alignment explanation
Indices: 8173--8288 Score: 128
Period size: 48 Copynumber: 2.4 Consensus size: 48
8163 CATAAATCAG
*
8173 GTCAAGTATCATATCA-AACTCCAGGTCAAGA-ATCAGATCAGAATCAAA
1 GTCAAGTATCATATCAGAA-TCCAGATC-AGATATCAGATCAGAATCAAA
* * * * * *
8221 GTCAAGTATCAGATCAGAATCTATATCAGATATCAGATCATAATCCAT
1 GTCAAGTATCATATCAGAATCCAGATCAGATATCAGATCAGAATCAAA
*
8269 GTCAAATATCATATCAGAAT
1 GTCAAGTATCATATCAGAAT
8289 TCAAACCGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 3 0.05
48 52 0.91
49 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCAGATCAGATATCAGATCAGAATCAAA
Found at i:8260 original size:12 final size:11
Alignment explanation
Indices: 8201--8265 Score: 58
Period size: 12 Copynumber: 5.5 Consensus size: 11
8191 CTCCAGGTCA
8201 AGAATCAGATC
1 AGAATCAGATC
*
8212 AGAATCAAAGTC
1 AGAATCAGA-TC
*
8224 AAGTATCAGATC
1 -AGAATCAGATC
*
8236 AGAATCTATATC
1 AGAATC-AGATC
8248 AGATATCAGATC
1 AGA-ATCAGATC
*
8260 ATAATC
1 AGAATC
8266 CATGTCAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 16 0.37
12 17 0.40
13 10 0.23
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (11 bp):
AGAATCAGATC
Found at i:11663 original size:36 final size:37
Alignment explanation
Indices: 11616--11689 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
11606 AGTTCTGGAA
11616 TTAAGTAAT-AAAAGAATCATCCATGGATATGTAGAT
1 TTAAGTAATAAAAAGAATCATCCATGGATATGTAGAT
*
11652 TTAAGTGATAAAAAGAATCATCCATGGATATGTAGAT
1 TTAAGTAATAAAAAGAATCATCCATGGATATGTAGAT
11689 T
1 T
11690 ATAATTTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 8 0.22
37 28 0.78
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (37 bp):
TTAAGTAATAAAAAGAATCATCCATGGATATGTAGAT
Found at i:13525 original size:12 final size:12
Alignment explanation
Indices: 13464--13544 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
13454 ATTTCCGACT
13464 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
13476 TG-ATACATGACC
1 TGAATTC-TGTTC
*
13488 TGAATTATGTTC
1 TGAATTCTGTTC
* * *
13500 CGATTTCTGATC
1 TGAATTCTGTTC
*
13512 TGGATTCTGTTC
1 TGAATTCTGTTC
*
13524 TGAATTCTGTTT
1 TGAATTCTGTTC
*
13536 TGATTTCTG
1 TGAATTCTG
13545 ATATCTCTGT
Statistics
Matches: 49, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
11 3 0.06
12 44 0.90
13 2 0.04
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.47
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:13712 original size:2 final size:2
Alignment explanation
Indices: 13705--13739 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13695 GGAATGGGGG
13705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13740 GTTTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15246 original size:13 final size:13
Alignment explanation
Indices: 15228--15257 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15218 TATTACCTTT
15228 AACCCTAAATCAA
1 AACCCTAAATCAA
*
15241 AACCCTAATTCAA
1 AACCCTAAATCAA
15254 AACC
1 AACC
15258 AAGTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (13 bp):
AACCCTAAATCAA
Found at i:16340 original size:17 final size:18
Alignment explanation
Indices: 16317--16361 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
16307 GAAGTTATAT
16317 TTTTCTTTCATCTCTATC
1 TTTTCTTTCATCTCTATC
* *
16335 -TTTCTTTC-TTTCTTTC
1 TTTTCTTTCATCTCTATC
16351 TTTTCTTTCAT
1 TTTTCTTTCAT
16362 TATTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 6 0.26
17 16 0.70
18 1 0.04
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTCTTTCATCTCTATC
Found at i:16355 original size:13 final size:13
Alignment explanation
Indices: 16318--16371 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
16308 AAGTTATATT
* *
16318 TTTCTTTCATCTC
1 TTTCTTTCTTTTC
*
16331 TATCTTTC-TTTC
1 TTTCTTTCTTTTC
16343 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
* *
16356 TTTCATTATTTTC
1 TTTCTTTCTTTTC
16369 TTT
1 TTT
16372 TCACAATGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Found at i:16967 original size:18 final size:18
Alignment explanation
Indices: 16939--16987 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
16929 TGAGGCTATA
16939 TCATCTTTATTTAATTCTTC
1 TCAT-TTTATTT-ATTCTTC
*
16959 T-ATTTTATTTATTTTTC
1 TCATTTTATTTATTCTTC
16976 TCATTATTATTT
1 TCATT-TTATTT
16988 TTATTCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.27
18 10 0.38
19 8 0.31
20 1 0.04
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.67
Consensus pattern (18 bp):
TCATTTTATTTATTCTTC
Found at i:29380 original size:3 final size:3
Alignment explanation
Indices: 29374--29419 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
29364 AGAAGAAGAA
* *
29374 GAG GAG GAG GAG GAA GAG GAA GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
29420 GTGTTGACGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:29389 original size:21 final size:21
Alignment explanation
Indices: 29365--29408 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
29355 AGAAGAAGAA
29365 GAAGAAGAAGAGGAGGAGGAG
1 GAAGAAGAAGAGGAGGAGGAG
*
29386 GAAGAGGAAGAGGAGGAGGAG
1 GAAGAAGAAGAGGAGGAGGAG
29407 GA
1 GA
29409 GGAGGAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (21 bp):
GAAGAAGAAGAGGAGGAGGAG
Found at i:33904 original size:21 final size:20
Alignment explanation
Indices: 33880--33953 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 20
33870 TCCAGCAAAG
33880 GATCGATCCCTCGAGATAAAA
1 GATCGATCCCTCGAGA-AAAA
*
33901 GATCGATCCCTTGGAGAAAAA
1 GATCGATCCC-TCGAGAAAAA
*
33922 GATCAATCCCTCGA-AAGAAA
1 GATCGATCCCTCGAGAA-AAA
*
33942 TGATTGATCCCT
1 -GATCGATCCCT
33954 TATCTGTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.04
20 6 0.13
21 32 0.71
22 5 0.11
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
GATCGATCCCTCGAGAAAAA
Found at i:35071 original size:45 final size:44
Alignment explanation
Indices: 34970--35074 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
34960 TGCAAGGTGC
* *
34970 CGATGTTGTGTGACCCGGACCTAGCCTAAGGTATTGGGAGGTGT
1 CGATGTTGTGTGACCCGGACCTAGCCTAAGATATTGGGAGATGT
* * * *
35014 CGATGCTATGTGACCTGGACCTCA-CCTGAGATACTTGGGAGATGAT
1 CGATGTTGTGTGACCCGGACCT-AGCCTAAGATA-TTGGGAGATG-T
35060 -GATGTTGTGTGACCC
1 CGATGTTGTGTGACCC
35075 AGGTCTACCC
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
44 26 0.53
45 22 0.45
46 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.28
Consensus pattern (44 bp):
CGATGTTGTGTGACCCGGACCTAGCCTAAGATATTGGGAGATGT
Found at i:39150 original size:4 final size:4
Alignment explanation
Indices: 39141--39165 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39131 ACAAATTTAG
39141 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
39166 GATAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:43227 original size:12 final size:12
Alignment explanation
Indices: 43212--43236 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43202 GTCACTGCAA
43212 TGTTATAATGAG
1 TGTTATAATGAG
43224 TGTTATAATGAG
1 TGTTATAATGAG
43236 T
1 T
43237 TTGACAAATT
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:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TGTTATAATGAG
Found at i:43290 original size:31 final size:30
Alignment explanation
Indices: 43242--43326 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 30
43232 TGAGTTTGAC
* *
43242 AAATTTAGTGATCATTTTGTAAATGTTTGATA
1 AAATTTAATGATCATTTTGTAAA--TTAGATA
*
43274 AAATTTAATGAT-ATTTTATAGCAATTAGATA
1 AAATTTAATGATCATTTTGTA--AATTAGATA
43305 AAATTTAATGATCATTTTGTAA
1 AAATTTAATGATCATTTTGTAA
43327 CTTCTAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 1 0.02
31 25 0.54
32 18 0.39
33 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.45
Consensus pattern (30 bp):
AAATTTAATGATCATTTTGTAAATTAGATA
Found at i:53089 original size:40 final size:40
Alignment explanation
Indices: 53038--53113 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
53028 TCGAGAGCTA
53038 CTTAAGCGATATCAAAATGCTTACCACTTGAACCAATCCT
1 CTTAAGCGATATCAAAATGCTTACCACTTGAACCAATCCT
* * * *
53078 CTTAAGTGATATCAAGATTCTTATCACTTGAACCAA
1 CTTAAGCGATATCAAAATGCTTACCACTTGAACCAA
53114 CCCTGTTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.30
Consensus pattern (40 bp):
CTTAAGCGATATCAAAATGCTTACCACTTGAACCAATCCT
Found at i:54828 original size:23 final size:23
Alignment explanation
Indices: 54798--54853 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
54788 GCATTTGAAT
54798 CAATCCTGCAAATAGGGTATGAC
1 CAATCCTGCAAATAGGGTATGAC
54821 CAATCCTGCAAATAGGGTATGAC
1 CAATCCTGCAAATAGGGTATGAC
54844 CAATCCTGCA
1 CAATCCTGCA
54854 GACTTTTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (23 bp):
CAATCCTGCAAATAGGGTATGAC
Found at i:59233 original size:27 final size:26
Alignment explanation
Indices: 59179--59243 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
59169 AAGATTATAA
**
59179 AAATATTATAATTAATATTTTATTTT
1 AAATATTATAATTAATATTTTAAATT
* *
59205 AAATATTTTATATTTATATTTTAAATT
1 AAATATTATA-ATTAATATTTTAAATT
59232 -AAT-TTATAATTA
1 AAATATTATAATTA
59244 TACGTTGAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 3 0.09
25 4 0.12
26 12 0.38
27 13 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AAATATTATAATTAATATTTTAAATT
Found at i:59244 original size:23 final size:22
Alignment explanation
Indices: 59186--59245 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
59176 TAAAAATATT
* *
59186 ATAATTAAT-ATTTTATTTTAA
1 ATAATTTATAATTATATTTTAA
* *
59207 ATATTTTATATTTATATTTTAA
1 ATAATTTATAATTATATTTTAA
59229 ATTAATTTATAATTATA
1 A-TAATTTATAATTATA
59246 CGTTGAGTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 7 0.23
22 11 0.35
23 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATAATTTATAATTATATTTTAA
Found at i:65725 original size:29 final size:29
Alignment explanation
Indices: 65683--65743 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
65673 TAAAATTGAA
*
65683 GTAAGTCGTTTCTCCTATCTCAATGGTGG
1 GTAAGCCGTTTCTCCTATCTCAATGGTGG
65712 GTAAGCCGTTTCTCCTATCTCAATGGTGG
1 GTAAGCCGTTTCTCCTATCTCAATGGTGG
65741 GTA
1 GTA
65744 TGGACGGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (29 bp):
GTAAGCCGTTTCTCCTATCTCAATGGTGG
Found at i:75350 original size:2 final size:2
Alignment explanation
Indices: 75343--75392 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
75333 AAACTTCAAA
75343 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
75385 AT AT AT AT
1 AT AT AT AT
75393 TGCAGACTGT
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:79290 original size:2 final size:2
Alignment explanation
Indices: 79283--79337 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
79273 AGTAAGTTGG
79283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
79325 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
79338 TATCTTAGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:81017 original size:19 final size:20
Alignment explanation
Indices: 80995--81032 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
80985 ATCTAACAAA
*
80995 CTAACAAA-TTAATAACTGC
1 CTAACAAACTAAATAACTGC
81014 CTAACAAACTAAATAACTG
1 CTAACAAACTAAATAACTG
81033 AAATCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (20 bp):
CTAACAAACTAAATAACTGC
Found at i:85538 original size:19 final size:20
Alignment explanation
Indices: 85516--85553 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
85506 ATCTAACAAA
*
85516 CTAACAAA-TTAATAACTGC
1 CTAACAAACTAAATAACTGC
85535 CTAACAAACTAAATAACTG
1 CTAACAAACTAAATAACTG
85554 AAATCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (20 bp):
CTAACAAACTAAATAACTGC
Found at i:86533 original size:33 final size:33
Alignment explanation
Indices: 86491--86556 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
86481 TAAGTTATAG
*
86491 TATAAAAAGATAGTCTACACATGGATTGTTGAA
1 TATAAAAAGAAAGTCTACACATGGATTGTTGAA
86524 TATAAAAAGAAAGTCTACACATGGATTGTTGAA
1 TATAAAAAGAAAGTCTACACATGGATTGTTGAA
86557 ACTTTGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (33 bp):
TATAAAAAGAAAGTCTACACATGGATTGTTGAA
Found at i:88990 original size:33 final size:34
Alignment explanation
Indices: 88953--89024 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
88943 TTTCTTCTCC
*
88953 TTTTACAAT-TATTT-CCAATAATGCAATGGGGTT
1 TTTTAC-ATCTATTTCCCAATAATGCAATGGAGTT
*
88986 TTTTACATCTATTTCCCAATAATGCAATGGATTT
1 TTTTACATCTATTTCCCAATAATGCAATGGAGTT
89020 TTTTA
1 TTTTA
89025 ATCATACTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 2 0.06
33 11 0.31
34 22 0.63
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (34 bp):
TTTTACATCTATTTCCCAATAATGCAATGGAGTT
Found at i:91251 original size:69 final size:69
Alignment explanation
Indices: 91140--91269 Score: 260
Period size: 69 Copynumber: 1.9 Consensus size: 69
91130 TAAAGGGAAG
91140 TCATATATAAAACAAAGGAATCCACCCATCTTTTGTTATTCCTCAAGATATAGGAAACTTCCCAA
1 TCATATATAAAACAAAGGAATCCACCCATCTTTTGTTATTCCTCAAGATATAGGAAACTTCCCAA
91205 CGCA
66 CGCA
91209 TCATATATAAAACAAAGGAATCCACCCATCTTTTGTTATTCCTCAAGATATAGGAAACTTC
1 TCATATATAAAACAAAGGAATCCACCCATCTTTTGTTATTCCTCAAGATATAGGAAACTTC
91270 TAACATCGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (69 bp):
TCATATATAAAACAAAGGAATCCACCCATCTTTTGTTATTCCTCAAGATATAGGAAACTTCCCAA
CGCA
Found at i:99859 original size:19 final size:19
Alignment explanation
Indices: 99837--99875 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
99827 CTTTATTCAT
* *
99837 ATAATTTTATTTTATGAAA
1 ATAATTATATTTTAAGAAA
*
99856 ATAATTATGTTTTAAGAAA
1 ATAATTATATTTTAAGAAA
99875 A
1 A
99876 AGAAATATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
ATAATTATATTTTAAGAAA
Found at i:105945 original size:228 final size:227
Alignment explanation
Indices: 105544--105991 Score: 792
Period size: 228 Copynumber: 2.0 Consensus size: 227
105534 GTAAATTATC
* * *
105544 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
105609 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
105674 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
105738 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
105771 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
105836 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
*
105900 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
105965 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
105992 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
227 38 0.18
228 146 0.69
229 27 0.13
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:106080 original size:20 final size:19
Alignment explanation
Indices: 106057--106102 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
106047 CGATATACCA
106057 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
106077 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
106097 GGTAAA
1 GGTAAA
106103 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:106247 original size:20 final size:19
Alignment explanation
Indices: 106224--106270 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
106214 CGATATAACA
106224 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
106244 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
106264 GGTAAAA
1 GGTAAAA
106271 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:106272 original size:17 final size:19
Alignment explanation
Indices: 106233--106275 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
106223 AGGTAAAAAT
106233 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
106253 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
106270 ATGATA
1 ATGATA
106276 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:108355 original size:9 final size:9
Alignment explanation
Indices: 108343--108373 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
108333 AGGATGTAGA
108343 GGAGGCAGT
1 GGAGGCAGT
108352 GGAGGCAGT
1 GGAGGCAGT
*
108361 GGAGGCAGA
1 GGAGGCAGT
108370 GGAG
1 GGAG
108374 AAGAAAGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.58, T:0.06
Consensus pattern (9 bp):
GGAGGCAGT
Found at i:108559 original size:21 final size:21
Alignment explanation
Indices: 108512--108576 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
108502 AAGACAATCA
* *
108512 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
108534 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
108554 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
108575 AG
1 AG
108577 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:108652 original size:33 final size:33
Alignment explanation
Indices: 108610--108675 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
108600 AAATAGATGG
* *
108610 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAAGGGTGA
* *
108643 AGTGGTGAAAGAAGTTGGGGTGTTAAAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAAGGGTGA
108676 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAAGGGTGA
Found at i:110491 original size:19 final size:19
Alignment explanation
Indices: 110467--110515 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
110457 AATGTCGAGT
110467 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
110486 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
110505 TATTTTTGTAT
1 TAATTTTGTAT
110516 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:111170 original size:198 final size:198
Alignment explanation
Indices: 110634--111998 Score: 2653
Period size: 198 Copynumber: 6.9 Consensus size: 198
110624 CAATATGGCC
* *
110634 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
110699 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
110764 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
110829 GGAA
196 GG-A
110833 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
110898 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
110963 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
111028 GGA
196 GGA
111031 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
111096 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111161 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
111226 GGA
196 GGA
111229 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
111292 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACAGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111357 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
111422 GGA
196 GGA
111425 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
111490 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111555 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
111620 GGA
196 GGA
111623 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
111688 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111753 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
111818 GGA
196 GGA
111821 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
111886 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111951 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
111999 AATTTAAATA
Statistics
Matches: 1158, Mismatches: 6, Indels: 5
0.99 0.01 0.00
Matches are distributed among these distances:
196 179 0.15
197 30 0.03
198 754 0.65
199 195 0.17
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGA
Found at i:111472 original size:394 final size:396
Alignment explanation
Indices: 110634--111998 Score: 2662
Period size: 394 Copynumber: 3.4 Consensus size: 396
110624 CAATATGGCC
* *
110634 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
110699 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
110764 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
110829 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GG-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
110894 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
260 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATG
110959 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
325 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
111024 GAATGGA
390 GAATGGA
111031 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
111096 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111161 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
111226 GGAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGA
196 GGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
*
111289 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACAGGTACAATTACACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGA
111354 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
326 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
111419 AATGGA
391 AATGGA
111425 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
111490 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111555 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
111620 GGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
196 GGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
111685 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGA
111750 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
326 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
111815 AATGGA
391 AATGGA
111821 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
111886 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111951 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
111999 AATTTAAATA
Statistics
Matches: 959, Mismatches: 7, Indels: 5
0.99 0.01 0.01
Matches are distributed among these distances:
394 376 0.39
395 30 0.03
396 358 0.37
397 195 0.20
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (396 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGA
GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
AATGGA
Found at i:111811 original size:592 final size:595
Alignment explanation
Indices: 110634--111998 Score: 2655
Period size: 592 Copynumber: 2.3 Consensus size: 595
110624 CAATATGGCC
* *
110634 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
110699 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
110764 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
110829 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
110894 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATG
110959 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
111024 GAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
391 GAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
*
111089 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
456 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTT
111154 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAG
521 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAG
111219 AATGAATGGA
586 AATGAATGGA
111229 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
111292 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACAGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111357 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
111422 GG-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
111486 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATG
111551 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
111616 GAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
391 GAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
111681 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTT
456 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTT
111746 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAG
521 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAG
111811 AATGAATGGA
586 AATGAATGGA
111821 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
111886 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
111951 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
111999 AATTTAAATA
Statistics
Matches: 760, Mismatches: 8, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
592 430 0.57
593 158 0.21
594 138 0.18
595 34 0.04
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (595 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
GAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTT
ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAG
AATGAATGGA
Found at i:113443 original size:3 final size:3
Alignment explanation
Indices: 113435--113506 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
113425 TCTTTTAACA
* * * ** * *
113435 GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
113483 GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
113507 CCAAACAAGT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:115014 original size:183 final size:183
Alignment explanation
Indices: 114706--115399 Score: 1239
Period size: 183 Copynumber: 3.8 Consensus size: 183
114696 CAAAGTTTTC
* * * *
114706 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
114771 AAAAAAGTGTCG--ATTGAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAAT
66 AAAAAAGTGTCGACATT--AACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAAT
* *
114834 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
129 ATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
114889 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
114954 AAAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTAACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
115019 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
*
115072 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
115137 AAAAAAGTGTCGACATTAACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTAACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
115202 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
*
115255 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
115320 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTAACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
115385 AAACGGTATAAAAAT
131 AACCGGTATAAAAAT
115400 GTGTCGATAC
Statistics
Matches: 495, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
183 492 0.99
185 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTAACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
Found at i:115428 original size:22 final size:23
Alignment explanation
Indices: 115395--115437 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
115385 AAACGGTATA
115395 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATACCTTTTTAT
*
115418 AAAA-GTGTCGATACTTTTTT
1 AAAATGTGTCGATACCTTTTT
115438 CACTGTGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (23 bp):
AAAATGTGTCGATACCTTTTTAT
Found at i:118593 original size:23 final size:23
Alignment explanation
Indices: 118562--118624 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
118552 ATAGGTAAAC
*
118562 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTACCCCTT
* **
118585 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTACCCCTT
118608 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
118625 GTGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTACCCCTT
Found at i:118632 original size:23 final size:23
Alignment explanation
Indices: 118562--118634 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
118552 ATAGGTAAAC
* * **
118562 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
118585 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
118608 ATATAATGTAATAGGTAGT-GGTT
1 ATATAATGTAATAGGTA-TCGGTT
118631 ATAT
1 ATAT
118635 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:119024 original size:23 final size:23
Alignment explanation
Indices: 118993--119056 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
118983 ATAGGTAAAC
*
118993 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
119016 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
119039 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
119057 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:119063 original size:23 final size:23
Alignment explanation
Indices: 118993--119065 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
118983 ATAGGTAAAC
* **
118993 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
119016 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
119039 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
119062 ATAT
1 ATAT
119066 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:119364 original size:25 final size:25
Alignment explanation
Indices: 119330--119380 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
119320 ACAACAAATC
*
119330 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
119355 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
119380 A
1 A
119381 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:119650 original size:18 final size:18
Alignment explanation
Indices: 119629--119665 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
119619 GTAATTGGAG
119629 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
119647 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
119665 T
1 T
119666 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:119673 original size:24 final size:24
Alignment explanation
Indices: 119621--119667 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
119611 TTTCATATGT
* *
119621 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
119645 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
119668 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:119966 original size:39 final size:39
Alignment explanation
Indices: 119923--120048 Score: 216
Period size: 39 Copynumber: 3.2 Consensus size: 39
119913 TCCGATGCTC
* * *
119923 ATCAAAATGCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
*
119962 ATCAAAATCCAAATCTTATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
120001 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
120040 ATCAAAATC
1 ATCAAAATC
120049 TACAACTTGA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:120483 original size:23 final size:23
Alignment explanation
Indices: 120452--120515 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
120442 ATAGGTAAAC
*
120452 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
120475 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
120498 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
120516 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:120522 original size:23 final size:23
Alignment explanation
Indices: 120452--120524 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
120442 ATAGGTAAAC
* **
120452 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
120475 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
120498 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
120521 ATAT
1 ATAT
120525 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:122347 original size:2 final size:2
Alignment explanation
Indices: 122340--122368 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
122330 TTGATAGCAA
122340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
122369 GCAAACATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:124592 original size:41 final size:40
Alignment explanation
Indices: 124547--124656 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 40
124537 ATTCACGTTG
* *
124547 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTC
*
124588 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-GAAATCGCGTTGCGATTTTC
124629 CATTTCGCGTTGCGATAGTTGAAATCGC
1 CATTTCGCGTTGCGATAGTTGAAATCGC
124657 AACGCGATCT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 7 0.11
41 56 0.88
42 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
Found at i:124643 original size:20 final size:20
Alignment explanation
Indices: 124572--124644 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
124562 TAGTTGAAAA
*
124572 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
124592 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGAT-TTTCCATT
124613 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
124633 TCGCGTTGCGAT
1 TCGCGTTGCGAT
124645 AGTTGAAATC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:124656 original size:20 final size:21
Alignment explanation
Indices: 124551--124656 Score: 67
Period size: 20 Copynumber: 5.2 Consensus size: 21
124541 ACGTTGCATT
*
124551 TCGCATTGCGATAGTT-GAAAA
1 TCGCGTTGCGATAGTTCG-AAA
** * **
124572 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
* *
124592 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTCGAAA
* * **
124613 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
124633 TCGCGTTGCGATAGTT-GAAA
1 TCGCGTTGCGATAGTTCGAAA
124653 TCGC
1 TCGC
124657 AACGCGATCT
Statistics
Matches: 61, Mismatches: 21, Indels: 7
0.69 0.24 0.08
Matches are distributed among these distances:
20 34 0.56
21 27 0.44
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCGAAA
Found at i:124861 original size:6 final size:6
Alignment explanation
Indices: 124850--124886 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
124840 GACACGTATT
124850 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
124887 GACGAGACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:124893 original size:5 final size:5
Alignment explanation
Indices: 124883--124930 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
124873 GACCACGACC
124883 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
124931 GCGGCGGCGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.40, C:0.21, G:0.40, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:125428 original size:6 final size:6
Alignment explanation
Indices: 125412--125443 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
125402 TCTCGTCTCG
125412 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
125444 AATGGTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:125449 original size:6 final size:6
Alignment explanation
Indices: 125440--125470 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
125430 GTCGTGGTCG
125440 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
125471 ACGTGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:125613 original size:20 final size:20
Alignment explanation
Indices: 125588--125758 Score: 166
Period size: 20 Copynumber: 8.4 Consensus size: 20
125578 ACTGTAGACT
*
125588 ATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
125608 ATCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG--GAAA
*
125629 ATCGCAACGCAAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
125649 ATCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG--GAAA
125670 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
125690 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
125711 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
125731 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
125751 ATCGCAAC
1 ATCGCAAC
125759 ACGATTTTCA
Statistics
Matches: 119, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
19 5 0.04
20 68 0.57
21 40 0.34
22 6 0.05
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:125623 original size:41 final size:41
Alignment explanation
Indices: 125544--125742 Score: 296
Period size: 41 Copynumber: 4.9 Consensus size: 41
125534 CTTTTTTTTA
* *
125544 ACTATCGCAA--CGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGACTGTAG
*
125585 ACTATCGCAACGCGAAACGGAAAATCGCAACGCGACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAG
*
125626 ACTATCGCAACGCAAAATGGAAAATCGCAACGCGACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAG
* *
125667 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA-
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-AG
125708 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
125743 AATGGAAAAT
Statistics
Matches: 147, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
41 128 0.87
42 15 0.10
43 4 0.03
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAG
Found at i:125694 original size:61 final size:61
Alignment explanation
Indices: 125560--125787 Score: 176
Period size: 61 Copynumber: 3.7 Consensus size: 61
125550 GCAACGAATT
* * * * *
125560 TGGAAAATCGCAACG-ACAACTGTAGACTATCGCAACGCGAAACGGAAAATCGCAACGCG-AC
1 TGGAAAATCGCAACGCA-AAATGCA-ACAATCGCAACGCGAAATGGAAAATCGCAACGCGAAA
** * * **
125621 TGTAGACTATCGCAACGCAAAATGGAA-AATCGCAACGCG-ACTGTAGACTATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCAAAATGCAACAATCGCAACGCGAAATG--GAAAATCGCAACGCGAAA
* ** * *
125684 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAAAATGCAACAATCGCAACGCGAAATGGAAAATCGCAACGCGAAA
* * ** * *
125745 TGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATG
1 TGGAAAATCGCAACGCAAAATGCAACAATCGCAACGCGAAATG
125788 CAACGCGAAT
Statistics
Matches: 137, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
60 2 0.01
61 87 0.64
62 25 0.18
63 22 0.16
64 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (61 bp):
TGGAAAATCGCAACGCAAAATGCAACAATCGCAACGCGAAATGGAAAATCGCAACGCGAAA
Found at i:125818 original size:61 final size:61
Alignment explanation
Indices: 125670--125787 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 61
125660 ACTGTAGACT
*
125670 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATGGAAA
125731 ATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATG
125788 CAACGCGAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (61 bp):
ATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:126728 original size:21 final size:20
Alignment explanation
Indices: 126686--126733 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
126676 GACCCCGATG
* *
126686 TTTTTTATTATATTTTTCTT
1 TTTTTTATTATATCTTTATT
*
126706 TTTTTATATTGTATCTTTATT
1 TTTTT-TATTATATCTTTATT
126727 TTCTTTT
1 TT-TTTT
126734 GTTTTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 15 0.65
22 3 0.13
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTATTATATCTTTATT
Found at i:132120 original size:16 final size:16
Alignment explanation
Indices: 132099--132138 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
132089 AAATTTTTTT
*
132099 ACTATTCATGAAATTC
1 ACTATTCACGAAATTC
132115 ACTATTCACGAAATTC
1 ACTATTCACGAAATTC
132131 ACTATTCA
1 ACTATTCA
132139 AGTGAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (16 bp):
ACTATTCACGAAATTC
Found at i:132682 original size:41 final size:41
Alignment explanation
Indices: 132592--132683 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
132582 TATCAACCGA
* *
132592 CTGCCATCTAGAATGTCATGCAAAATTTCAACAATTGCTAG
1 CTGCCATCTAGAATGCCATGCAAAATTTCAACAATTGATAG
** *
132633 CTATCATCTAGAATGCCATGCAAAATTTCAACAATTGATGG
1 CTGCCATCTAGAATGCCATGCAAAATTTCAACAATTGATAG
132674 CTGCCATCTA
1 CTGCCATCTA
132684 CTGCCATCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (41 bp):
CTGCCATCTAGAATGCCATGCAAAATTTCAACAATTGATAG
Found at i:136075 original size:13 final size:12
Alignment explanation
Indices: 136058--136098 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
136048 TGAAATATAG
136058 ATTTGATTTAGT
1 ATTTGATTTAGT
136070 GATTTGA-TTA-T
1 -ATTTGATTTAGT
136081 ATATTGATTTAGT
1 AT-TTGATTTAGT
136094 ATTTG
1 ATTTG
136099 TAAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.08
11 5 0.20
12 9 0.36
13 9 0.36
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (12 bp):
ATTTGATTTAGT
Found at i:136220 original size:21 final size:21
Alignment explanation
Indices: 136178--136220 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
136168 TATTTTGATA
*
136178 TTATGTTTGATATTTATAAAT
1 TTATGTTTGATATATATAAAT
*
136199 TTATGTTT-AGTATATATTAAT
1 TTATGTTTGA-TATATATAAAT
136220 T
1 T
136221 AATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (21 bp):
TTATGTTTGATATATATAAAT
Found at i:141338 original size:3 final size:3
Alignment explanation
Indices: 141330--141398 Score: 120
Period size: 3 Copynumber: 23.0 Consensus size: 3
141320 TAATATAAAT
*
141330 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
141378 TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
141399 GGATAATTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:141724 original size:113 final size:113
Alignment explanation
Indices: 141526--142287 Score: 1168
Period size: 113 Copynumber: 6.7 Consensus size: 113
141516 TCTTGATGAG
141526 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTC
* * *
141589 TGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 TGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
141639 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
141704 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* *
141752 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * * *
141817 GCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
141865 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
141930 GAAAAGCTGATCCATCAAATGACGGATTCAAGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
141978 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
142043 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* *
142091 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * * *
142156 GCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
142204 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
142269 GAAAAGAATGATCCATCAA
66 GAAAAG-ATGATCCATCAA
142288 GTGGATTTGA
Statistics
Matches: 588, Mismatches: 58, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
112 1 0.00
113 575 0.98
114 12 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:142033 original size:339 final size:339
Alignment explanation
Indices: 141524--142287 Score: 1424
Period size: 339 Copynumber: 2.3 Consensus size: 339
141514 GCTCTTGATG
141524 AGTTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC
1 AGTTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-C
* * * *
141588 -CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTAT
64 TCTGGAAAAGATGATCCATCAAATGACGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTAT
141652 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTC
129 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTC
141717 ACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTC
194 ACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTC
141782 TTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTA
259 TTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTA
141847 AACAAAAAGTTGAACA
324 AACAAAAAGTTGAACA
141863 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
141928 TGGAAAAGCTGATCCATCAAATGACGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGA
66 TGGAAAAGATGATCCATCAAATGACGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
141993 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTCAC
131 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTCAC
142058 CAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTT
196 CAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTT
142123 CAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
261 CAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
142188 CAAAAAGTTGAACA
326 CAAAAAGTTGAACA
142202 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
142267 TGGAAAAGAATGATCCATCAA
66 TGGAAAAG-ATGATCCATCAA
142288 GTGGATTTGA
Statistics
Matches: 415, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
338 1 0.00
339 402 0.97
340 12 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (339 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGATGATCCATCAAATGACGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTCAC
CAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTT
CAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
CAAAAAGTTGAACA
Found at i:143156 original size:82 final size:82
Alignment explanation
Indices: 142820--143184 Score: 563
Period size: 83 Copynumber: 4.4 Consensus size: 82
142810 TTTACTATGA
* *
142820 GCAAATTCATCTTCCAAATTCAATGATTGTTCT-ATCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGCT-AAACCAGATCAGATAACTCAAAGAACAC
142884 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
* * * *
142902 GCAAATTCATCTTCCAAATTCAATGCTTGGTTCT-ATATAATCAGATCAAATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTGCTA-AACCAGATCAGATAACTCAAAGAACA
142966 CTTCCAGAAGATGCTATTG
64 CTTCCAGAAGATGCTATTG
* *
142985 GCAAATTCATCTTCCAAATTCAATGCTTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTGCTAAACCAGATCAGATAACTCAAAGAACAC
143050 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
* *
143068 GCAAATTCATCTTCCAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACT
143133 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* **
143150 GTAAATTCATCTTCCATTTTCAATGATTGTTCTGC
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGC
143185 GATATCACAG
Statistics
Matches: 266, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
82 112 0.42
83 152 0.57
84 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (82 bp):
GCAAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTG
Found at i:144311 original size:12 final size:12
Alignment explanation
Indices: 144288--144371 Score: 90
Period size: 12 Copynumber: 7.2 Consensus size: 12
144278 CCTTGACCCC
144288 CTTTTC-TTTTT
1 CTTTTCTTTTTT
*
144299 CTTCTCTTTTTT
1 CTTTTCTTTTTT
144311 CTATTTTCTATTTTT
1 C--TTTTCT-TTTTT
144326 -TTTTCTTTTTT
1 CTTTTCTTTTTT
144337 CTTTTC---TTT
1 CTTTTCTTTTTT
144346 CTTTTC-TTTTT
1 CTTTTCTTTTTT
144357 CTTTTCTTTTTT
1 CTTTTCTTTTTT
144369 CTT
1 CTT
144372 CAAGCATAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
9 9 0.14
11 19 0.30
12 25 0.40
14 5 0.08
15 5 0.08
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTCTTTTTT
Found at i:144332 original size:26 final size:26
Alignment explanation
Indices: 144289--144361 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
144279 CTTGACCCCC
* *
144289 TTTTCTTTTTCTTCTCTTTTTTC-TA
1 TTTTCTTTTTTTTTTCTTTTTTCTTA
*
144314 TTTTCTATTTTTTTTTCTTTTTTCTTT
1 TTTTCT-TTTTTTTTTCTTTTTTCTTA
*
144341 TCTTTCTTTTCTTTTTCTTTT
1 T-TTTCTTTTTTTTTTCTTTT
144362 CTTTTTTCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.15
26 15 0.37
27 15 0.37
28 5 0.12
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTCTTTTTTTTTTCTTTTTTCTTA
Found at i:144334 original size:5 final size:5
Alignment explanation
Indices: 144333--144366 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
144323 TTTTTTTCTT
144333 TTTTC TTTTC -TTTC TTTTC TTTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTT
144367 TTCTTCAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:144339 original size:7 final size:7
Alignment explanation
Indices: 144303--144371 Score: 61
Period size: 7 Copynumber: 9.6 Consensus size: 7
144293 CTTTTTCTTC
144303 TCTTTTT
1 TCTTTTT
*
144310 TCTATTT
1 TCTTTTT
*
144317 TC-TATT
1 TCTTTTT
144323 T-TTTTT
1 TCTTTTT
144329 TCTTTTT
1 TCTTTTT
144336 TCTTTTCTT
1 TC-TTT-TT
144345 TCTTTTCT
1 TCTTTT-T
*
144353 TTTTCTTT
1 TCTT-TTT
144361 TCTTTTT
1 TCTTTTT
144368 TCTT
1 TCTT
144372 CAAGCATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
6 7 0.14
7 23 0.46
8 14 0.28
9 6 0.12
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (7 bp):
TCTTTTT
Found at i:144367 original size:32 final size:33
Alignment explanation
Indices: 144289--144371 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 33
144279 CTTGACCCCC
* *
144289 TTTTCTTTT-TCTTCTCTTTTTTCTATTTTCTA
1 TTTTCTTTTCTTTTTTCTTTTTTCTATTTTCTA
* *
144321 TTTTTTTTTCTTTTTTCTTTTCTT-TCTTTTCT-
1 TTTTCTTTTCTTTTTTCTTTT-TTCTATTTTCTA
144353 TTTTCTTTTCTTTTTTCTT
1 TTTTCTTTTCTTTTTTCTT
144372 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
32 26 0.59
33 16 0.36
34 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (33 bp):
TTTTCTTTTCTTTTTTCTTTTTTCTATTTTCTA
Found at i:149050 original size:17 final size:17
Alignment explanation
Indices: 149010--149051 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
149000 ATACTTGCAA
*
149010 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATC
149028 ATAAAAATAATAAATA-C
1 ATAAAAAT-ATAAATATC
149045 ATAAAAA
1 ATAAAAA
149052 ATTTGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATATAAATATC
Found at i:151229 original size:3 final size:3
Alignment explanation
Indices: 151212--151309 Score: 135
Period size: 3 Copynumber: 32.7 Consensus size: 3
151202 TTAATATATT
*
151212 TAA T-A TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** *
151257 TAA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
151305 TAA TA
1 TAA TA
151310 TGGATAAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
2 2 0.02
3 78 0.94
4 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:167622 original size:11 final size:11
Alignment explanation
Indices: 167606--167650 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
167596 TCCAACTTAG
167606 AGAAAAAAAGA
1 AGAAAAAAAGA
167617 AGAAAAAAAGA
1 AGAAAAAAAGA
*
167628 TTGAAGAAAAAAGA
1 -AG-A-AAAAAAGA
167642 AGAAAAAAA
1 AGAAAAAAA
167651 CGCTCTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 17 0.59
12 2 0.07
13 2 0.07
14 8 0.28
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:168383 original size:2 final size:2
Alignment explanation
Indices: 168378--168420 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
168368 GATAATTTTC
168378 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
168420 A
1 A
168421 ACATTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:174309 original size:19 final size:20
Alignment explanation
Indices: 174269--174339 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 20
174259 CTTTTTGATA
*
174269 TTATATA-ATATA-CTTATA
1 TTATATACATATATCTTATT
*
174287 TTATATA-ATATATTTTATT
1 TTATATACATATATCTTATT
*
174306 TTAT-TACATATATCGTATT
1 TTATATACATATATCTTATT
* *
174325 TACATATATATATAT
1 T-TATATACATATAT
174340 TTGTTTTGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.33
19 19 0.44
20 2 0.05
21 8 0.19
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (20 bp):
TTATATACATATATCTTATT
Found at i:175560 original size:18 final size:18
Alignment explanation
Indices: 175530--175585 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
175520 TTTTACCATT
*
175530 TTATTTTTATTATTATTA
1 TTATTTATATTATTATTA
* **
175548 TTCTTTATATTATCCTTA
1 TTATTTATATTATTATTA
* *
175566 TTATTTCTATTATTACTA
1 TTATTTATATTATTATTA
175584 TT
1 TT
175586 TTTTTTACTT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTTATATTATTATTA
Found at i:175614 original size:2 final size:2
Alignment explanation
Indices: 175607--175640 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
175597 TTTATGTATG
175607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
175641 CGTTTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:175751 original size:2 final size:2
Alignment explanation
Indices: 175744--175791 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
175734 TGTTTAACTA
175744 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
175786 AT AT AT
1 AT AT AT
175792 TTACATGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176106 original size:13 final size:13
Alignment explanation
Indices: 176090--176160 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
176080 TTCTAATTTG
176090 TTTATTTGTTTAT
1 TTTATTTGTTTAT
176103 TTTATTTGTTTAT
1 TTTATTTGTTTAT
* *
176116 TATCTTAT-TTTAT
1 TTTATT-TGTTTAT
*
176129 TTT-TTTGTTTGT
1 TTTATTTGTTTAT
*
176141 TTTATCTTTTTTA-
1 TTTAT-TTGTTTAT
176154 TTTATTT
1 TTTATTT
176161 TTTTTAAGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
11 1 0.02
12 11 0.23
13 30 0.62
14 6 0.12
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTATTTGTTTAT
Found at i:176109 original size:21 final size:21
Alignment explanation
Indices: 176085--176160 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
176075 GGTTTTTCTA
176085 ATTTGTTTATTTGTTTATTTT
1 ATTTGTTTATTTGTTTATTTT
*
176106 ATTTGTTTATTAT-CTTATTTT
1 ATTTGTTTATT-TGTTTATTTT
* *
176127 ATTTTTTTGTTTGTTTTATCTTT
1 ATTTGTTTATTTG-TTTAT-TTT
*
176150 -TTTATTTATTT
1 ATTTGTTTATTT
176161 TTTTTAAGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.02
21 27 0.60
22 14 0.31
23 3 0.07
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (21 bp):
ATTTGTTTATTTGTTTATTTT
Found at i:176129 original size:26 final size:27
Alignment explanation
Indices: 176086--176160 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 27
176076 GTTTTTCTAA
*
176086 TTTGT-TTAT-TTGTTTATTTTATTTG
1 TTTGTATTATCTTTTTTATTTTATTTG
176111 -TT-TATTATCTTATTTTATTTT-TTTG
1 TTTGTATTATCTT-TTTTATTTTATTTG
*
176136 TTTGTTTTATCTTTTTTA-TTTATTT
1 TTTGTATTATCTTTTTTATTTTATTT
176161 TTTTTAAGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
23 1 0.02
24 6 0.14
25 9 0.21
26 18 0.43
27 8 0.19
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (27 bp):
TTTGTATTATCTTTTTTATTTTATTTG
Found at i:186703 original size:73 final size:73
Alignment explanation
Indices: 186563--186705 Score: 180
Period size: 73 Copynumber: 2.0 Consensus size: 73
186553 AGTACTTCGC
* * * * *
186563 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAACAAAAGACAAAAGAAAAGAG
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAAACAAAAGAAAAAAGAAAAAAG
186628 AAGAACGT
66 AAGAACGT
* * * * *
186636 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAA-AGAGGAAAAAAGAATAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAAACAAAAGAAAAAAGAA-AAAA
186700 GAAGAA
65 GAAGAA
186706 AAATAAGGTG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 11 0.19
73 48 0.81
ACGTcount: A:0.54, C:0.11, G:0.24, T:0.10
Consensus pattern (73 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAAACAAAAGAAAAAAGAAAAAAG
AAGAACGT
Found at i:187432 original size:72 final size:72
Alignment explanation
Indices: 187300--187437 Score: 172
Period size: 72 Copynumber: 1.9 Consensus size: 72
187290 AGTACTTCGC
* * * * *
187300 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAACAAAAGACAAAAGAAAAGAGA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAACAAAAGAAAAAAGAAAAAAGA
187365 AGAACGT
66 AGAACGT
* * *
187372 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTG-AGAAAAGAA-AAAAGAAAAAGAGGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAACAAAAGAAAAA-A-GAAAAAA
187435 GAA
64 GAA
187438 TAAAAGAAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
70 9 0.16
71 8 0.14
72 39 0.70
ACGTcount: A:0.54, C:0.12, G:0.25, T:0.10
Consensus pattern (72 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAACAAAAGAAAAAAGAAAAAAGA
AGAACGT
Found at i:187433 original size:16 final size:18
Alignment explanation
Indices: 187410--187451 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
187400 AAATTGAGAA
187410 AAGAAAAAAG-A-AAAAG
1 AAGAAAAAAGAATAAAAG
*
187426 AGGAAAAAAGAATAAAAG
1 AAGAAAAAAGAATAAAAG
187444 AAGAAAAA
1 AAGAAAAA
187452 TAAGGTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 1 0.05
18 12 0.55
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAGAATAAAAG
Found at i:187442 original size:8 final size:7
Alignment explanation
Indices: 187408--187450 Score: 50
Period size: 7 Copynumber: 5.6 Consensus size: 7
187398 CTAAATTGAG
187408 AAAAGAA
1 AAAAGAA
187415 AAAAGAA
1 AAAAGAA
187422 AAAGAGGAA
1 AAA-A-GAA
187431 AAAAGAA
1 AAAAGAA
187438 TAAAAGAA
1 -AAAAGAA
187446 GAAAA
1 -AAAA
187451 ATAAGGTGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
7 13 0.41
8 13 0.41
9 6 0.19
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:188393 original size:105 final size:105
Alignment explanation
Indices: 188206--189075 Score: 1422
Period size: 105 Copynumber: 8.4 Consensus size: 105
188196 AGGTTTTACC
* * *
188206 CAGAGTCAATTTCAACTTCACAATGAAGGATACTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
188271 ACGAAGGGACCGTTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
188311 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
188376 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
188416 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
188481 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
188521 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
188586 ATGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATA
66 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
188626 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
188691 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
**
188731 CAGAGCCAATTTCAACTTCACAATAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
188796 ACGAGGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
* * *
188836 CAGAGCTAATCTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** *
188901 ACGAAGGGACCGCTGGTTGTCAATAAACAATT-TCC---T
66 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
188937 -------AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* ** * *
188995 ACGAAGGGACCGTTGGTTGTCAATAAACAATTT-TCCAGCTC
66 ACGAAGGGACCGCTGGTTGTCACCAAAC-ATTTCTCCA-ATT
* * * *
189036 CAGAACCAATTTCAACTTCACAGCGGAGGATGTTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
189076 GGAACGATAC
Statistics
Matches: 725, Mismatches: 28, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
94 83 0.11
95 6 0.01
101 1 0.00
104 3 0.00
105 602 0.83
106 30 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
Found at i:188895 original size:43 final size:42
Alignment explanation
Indices: 188847--189001 Score: 114
Period size: 43 Copynumber: 3.4 Consensus size: 42
188837 AGAGCTAATC
188847 TCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGT
1 TCAACTTCACAACGAAGGATATT-GACTCCAGACAACGCAAGT
* * * *** * *
188890 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC-CTAATT
1 TCAACTTCACAACGAA-GGA----T-ATTGACTCCAGACAA---CGC-AAGT
188941 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
1 TCAACTTCACAACGAAGGATATT-GACTCCAGACAACGCAAGT
*
188984 TCAACTTCACGACGAAGG
1 TCAACTTCACAACGAAGG
189002 GACCGTTGGT
Statistics
Matches: 83, Mismatches: 17, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
43 36 0.43
44 4 0.05
45 2 0.02
46 8 0.10
48 8 0.10
49 2 0.02
50 4 0.05
51 19 0.23
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.21
Consensus pattern (42 bp):
TCAACTTCACAACGAAGGATATTGACTCCAGACAACGCAAGT
Found at i:189002 original size:94 final size:94
Alignment explanation
Indices: 188841--189027 Score: 347
Period size: 94 Copynumber: 2.0 Consensus size: 94
188831 CAATTCAGAG
188841 CTAATCTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CTAATCTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
188906 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
* *
188935 CTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CTAATCTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
189000 GGGACCGTTGGTTGTCAATAAACAATTT
66 GGGACCGCTGGTTGTCAATAAACAATTT
189028 TCCAGCTCCA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (94 bp):
CTAATCTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTC
Found at i:189509 original size:19 final size:20
Alignment explanation
Indices: 189469--189539 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 20
189459 CTTTTTGATA
*
189469 TTATATA-ATATA-CTTATA
1 TTATATACATATATCTTATT
*
189487 TTATATA-ATATATTTTATT
1 TTATATACATATATCTTATT
*
189506 TTAT-TACATATATCGTATT
1 TTATATACATATATCTTATT
* *
189525 TACATATATATATAT
1 T-TATATACATATAT
189540 TTGTTTTGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.33
19 19 0.44
20 2 0.05
21 8 0.19
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (20 bp):
TTATATACATATATCTTATT
Found at i:190655 original size:2 final size:2
Alignment explanation
Indices: 190650--190714 Score: 61
Period size: 2 Copynumber: 35.5 Consensus size: 2
190640 TACGTTTTAT
*
190650 TA TA TA TA TA TA TA TA TA TA TA T- TA T- TG T- TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
190687 T- TA TA TG TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
190715 CTACTTATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
1 6 0.11
2 47 0.89
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (2 bp):
TA
Found at i:190760 original size:9 final size:9
Alignment explanation
Indices: 190748--190816 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
190738 TTTACCATTT
190748 TTATTTTTA
1 TTATTTTTA
*
190757 TTATTATTA
1 TTATTTTTA
* *
190766 TTCTTTATA
1 TTATTTTTA
**
190775 TTATCCTTA
1 TTATTTTTA
*
190784 TTATTTCTA
1 TTATTTTTA
**
190793 TTATTACTA
1 TTATTTTTA
190802 TT-TTTTTA
1 TTATTTTTA
190810 CTTATTT
1 -TTATTT
190817 ATGTATGTAT
Statistics
Matches: 44, Mismatches: 14, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
8 4 0.09
9 37 0.84
10 3 0.07
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (9 bp):
TTATTTTTA
Found at i:190778 original size:18 final size:18
Alignment explanation
Indices: 190748--190803 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
190738 TTTACCATTT
*
190748 TTATTTTTATTATTATTA
1 TTATTTATATTATTATTA
* **
190766 TTCTTTATATTATCCTTA
1 TTATTTATATTATTATTA
* *
190784 TTATTTCTATTATTACTA
1 TTATTTATATTATTATTA
190802 TT
1 TT
190804 TTTTTACTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTTATATTATTATTA
Found at i:190831 original size:2 final size:2
Alignment explanation
Indices: 190824--190849 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
190814 TTTATGTATG
190824 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
190850 CGTTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:190964 original size:2 final size:2
Alignment explanation
Indices: 190957--190999 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
190947 TAACTAATAG
190957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
190999 T
1 T
191000 TACATGTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:191320 original size:13 final size:13
Alignment explanation
Indices: 191304--191379 Score: 68
Period size: 13 Copynumber: 5.9 Consensus size: 13
191294 TTCTAATTTG
191304 TTTATTTGTTTAT
1 TTTATTTGTTTAT
191317 TTTATTTGTTTAT
1 TTTATTTGTTTAT
* *
191330 TATCTTAT-TTTAT
1 TTTATT-TGTTTAT
*
191343 TTT-TTTGTTTGT
1 TTTATTTGTTTAT
*
191355 TTTATCTTTTTTA-
1 TTTAT-TTGTTTAT
*
191368 TTTATTTTTTTA
1 TTTATTTGTTTA
191380 AGTCATTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
11 1 0.02
12 16 0.30
13 30 0.57
14 6 0.11
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (13 bp):
TTTATTTGTTTAT
Found at i:191323 original size:21 final size:21
Alignment explanation
Indices: 191299--191379 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
191289 GGTTTTTCTA
191299 ATTTGTTTATTTGTTTATTTT
1 ATTTGTTTATTTGTTTATTTT
*
191320 ATTTGTTTATTAT-CTTATTTT
1 ATTTGTTTATT-TGTTTATTTT
* *
191341 ATTTTTTTGTTTGTTTTATCTTT
1 ATTTGTTTATTTG-TTTAT-TTT
* *
191364 -TTTATTTATTTTTTTA
1 ATTTGTTTATTTGTTTA
191380 AGTCATTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 1 0.02
21 31 0.63
22 14 0.29
23 3 0.06
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (21 bp):
ATTTGTTTATTTGTTTATTTT
Found at i:192276 original size:42 final size:42
Alignment explanation
Indices: 192214--192330 Score: 191
Period size: 42 Copynumber: 2.8 Consensus size: 42
192204 CCCCGAATTA
*
192214 CCGTGTTTGTTTCACATAATTCGTTTTCCGGAAAATG-TTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTT
192255 CCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTT
1 CC-GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTT
* *
192298 CCGTGTTTGTTTCACGTAATTGGTTTTTCGGAA
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
192331 CGTAATTCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
41 2 0.03
42 63 0.89
43 6 0.08
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTT
Found at i:192542 original size:15 final size:15
Alignment explanation
Indices: 192522--192580 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
192512 TTATTTATTA
192522 ATATTTATAATAATT
1 ATATTTATAATAATT
*
192537 ATATTTTTAAT-ATT
1 ATATTTATAATAATT
**
192551 ATATAAAATAATCAATT
1 ATAT-TTATAAT-AATT
192568 ATA-TTATAATAAT
1 ATATTTATAATAAT
192581 ATAAGATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
14 10 0.29
15 19 0.54
17 6 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTTATAATAATT
Found at i:193040 original size:15 final size:15
Alignment explanation
Indices: 193020--193070 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
193010 CATTTTTCAG
193020 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
**
193035 AATTCATTTTCCAGT
1 AATTCAAATTCCAGT
193050 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
193065 AATTCA
1 AATTCA
193071 TTTTCAGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:193056 original size:30 final size:29
Alignment explanation
Indices: 193007--193075 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 29
192997 CAGAAATGTG
*
193007 ATTCATTTTTCAGAATTCAAATTCCAGTA
1 ATTCATTTTCCAGAATTCAAATTCCAGTA
193036 ATTCATTTTCCAGTAATTCAAATTCCAGTA
1 ATTCATTTTCCAG-AATTCAAATTCCAGTA
193066 ATTCATTTTC
1 ATTCATTTTC
193076 AGGAAAACCA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 12 0.32
30 26 0.68
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (29 bp):
ATTCATTTTCCAGAATTCAAATTCCAGTA
Found at i:202130 original size:16 final size:17
Alignment explanation
Indices: 202109--202146 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
202099 ACACAAACAT
202109 TCAAACCCTCTCAAA-C
1 TCAAACCCTCTCAAAGC
202125 TCAAACCCTCTCAAAGC
1 TCAAACCCTCTCAAAGC
202142 TCAAA
1 TCAAA
202147 TTCTATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.39, C:0.39, G:0.03, T:0.18
Consensus pattern (17 bp):
TCAAACCCTCTCAAAGC
Found at i:202304 original size:37 final size:37
Alignment explanation
Indices: 202263--202373 Score: 161
Period size: 37 Copynumber: 3.0 Consensus size: 37
202253 AACATAACAT
* * *
202263 TAGAGTTCTATTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
* *
202300 TAGAGTTTTACTATGATTTAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
202337 TAGAATTTTACTATGATTCAAACTCCT-AAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
202373 T
1 T
202374 CCATAAGCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
36 9 0.14
37 57 0.86
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:203083 original size:33 final size:33
Alignment explanation
Indices: 203004--203085 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 33
202994 TATATACATA
*
203004 TATTTTATTTATTATTCTTATACCCTTCTATTTT
1 TATTTTATTTATTACTCTTATA-CCTTCTATTTT
* *
203038 TATTTTCTTTTATTACTCTT-TA-CTTACTGTTTT
1 TATTTT-ATTTATTACTCTTATACCTT-CTATTTT
203071 TATTATTATTTATTA
1 TATT-TTATTTATTA
203086 TTATTATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
32 3 0.07
33 17 0.41
34 10 0.24
35 11 0.27
ACGTcount: A:0.21, C:0.12, G:0.01, T:0.66
Consensus pattern (33 bp):
TATTTTATTTATTACTCTTATACCTTCTATTTT
Found at i:203091 original size:16 final size:17
Alignment explanation
Indices: 203070--203101 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
203060 CTTACTGTTT
203070 TTATTATTATT-TATTA
1 TTATTATTATTCTATTA
203086 TTATTATTATTCTATT
1 TTATTATTATTCTATT
203102 CTATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTATTATTCTATTA
Found at i:203222 original size:27 final size:27
Alignment explanation
Indices: 203169--203224 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
203159 ATTCCTTATC
*
203169 TTTATTTTTTATCTTCTTTATATTTGT
1 TTTATTTTTTATCTTCTTTATACTTGT
203196 TTTATTTTTTAT-TT-TTTATTTACTTGT
1 TTTATTTTTTATCTTCTTTA--TACTTGT
203223 TT
1 TT
203225 ATTATGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 4 0.15
26 2 0.08
27 20 0.77
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (27 bp):
TTTATTTTTTATCTTCTTTATACTTGT
Done.