Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008604.1 Hibiscus syriacus cultivar Beakdansim tig00111560_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: 305402
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3262 original size:31 final size:31
Alignment explanation
Indices: 3203--3262 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3193 AATTAAAAAA
* * *
3203 TTAAAAAATATAACAATAGATACTTAAAATT
1 TTAAAAAATATAACAATAAAAACCTAAAATT
3234 TTAAAAAATATAACAATAAAAACCTAAAA
1 TTAAAAAATATAACAATAAAAACCTAAAA
3263 GTATAACGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (31 bp):
TTAAAAAATATAACAATAAAAACCTAAAATT
Found at i:5539 original size:30 final size:30
Alignment explanation
Indices: 5503--5622 Score: 170
Period size: 30 Copynumber: 4.0 Consensus size: 30
5493 ATTCTACATT
*
5503 GGATAAATTCCCCGTTCTAACATCTGCATG
1 GGATAAACTCCCCGTTCTAACATCTGCATG
* * *
5533 GGATAAACTCCCCGTTCTGACATCTGCTTA
1 GGATAAACTCCCCGTTCTAACATCTGCATG
*
5563 AGATAAACTCCCCGTTCTAACATCTGCATG
1 GGATAAACTCCCCGTTCTAACATCTGCATG
*
5593 GGATAAA-TCCCCCGTTCTGACATCTGCATG
1 GGATAAACT-CCCCGTTCTAACATCTGCATG
5623 AGATTATATC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 1 0.01
30 78 0.99
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (30 bp):
GGATAAACTCCCCGTTCTAACATCTGCATG
Found at i:5576 original size:60 final size:60
Alignment explanation
Indices: 5504--5619 Score: 207
Period size: 60 Copynumber: 1.9 Consensus size: 60
5494 TTCTACATTG
*
5504 GATAAATTCCCCGTTCTAACATCTGCATGGGATAAA-CTCCCCGTTCTGACATCTGCTTAA
1 GATAAACTCCCCGTTCTAACATCTGCATGGGATAAATC-CCCCGTTCTGACATCTGCTTAA
5564 GATAAACTCCCCGTTCTAACATCTGCATGGGATAAATCCCCCGTTCTGACATCTGC
1 GATAAACTCCCCGTTCTAACATCTGCATGGGATAAATCCCCCGTTCTGACATCTGC
5620 ATGAGATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
60 53 0.98
61 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (60 bp):
GATAAACTCCCCGTTCTAACATCTGCATGGGATAAATCCCCCGTTCTGACATCTGCTTAA
Found at i:5643 original size:30 final size:30
Alignment explanation
Indices: 5504--5647 Score: 116
Period size: 30 Copynumber: 4.8 Consensus size: 30
5494 TTCTACATTG
* * * *
5504 GATAAATTCCCCGTTCTAACATCTGCATGG
1 GATAAATCCCCCGTCCTGACATCTGCATGA
* * *
5534 GATAAA-CTCCCCGTTCTGACATCTGCTTAA
1 GATAAATC-CCCCGTCCTGACATCTGCATGA
* * *
5564 GATAAA-CTCCCCGTTCTAACATCTGCATGG
1 GATAAATC-CCCCGTCCTGACATCTGCATGA
*
5594 GATAAATCCCCCGTTCTGACATCTGCATGA
1 GATAAATCCCCCGTCCTGACATCTGCATGA
* *
5624 GATTATAT-CTCCGTCCTGAC-TCTG
1 GA-TAAATCCCCCGTCCTGACATCTG
5648 TTTGGGATGC
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.04
30 88 0.91
31 5 0.05
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (30 bp):
GATAAATCCCCCGTCCTGACATCTGCATGA
Found at i:6257 original size:23 final size:23
Alignment explanation
Indices: 6213--6257 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6203 TTATTTGGAT
*
6213 TTTAAAATATTAATGGGTTTAAG
1 TTTAAAATATTAATAGGTTTAAG
*
6236 TTTAAAA-ATTATTAGGTATTAA
1 TTTAAAATATTAATAGGT-TTAA
6258 TATTTCGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (23 bp):
TTTAAAATATTAATAGGTTTAAG
Found at i:7202 original size:20 final size:20
Alignment explanation
Indices: 7179--7250 Score: 135
Period size: 20 Copynumber: 3.6 Consensus size: 20
7169 AACGCGATCC
7179 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
7199 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
7219 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
7239 CCAAAATCGCAA
1 CCAGAATCGCAA
7251 CGCGATTCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:7210 original size:40 final size:40
Alignment explanation
Indices: 7161--7256 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
7151 ACGCGAAATA
7161 AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC
1 AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC
* ** **
7201 AGAATCGCAAATC-AGTTTCCAGAATCGCAAATCAGTTTCC
1 AAAATCGCAACGCGA-TCCCCAGAATCGCAAATCAGTTTCC
7241 AAAATCGCAACGCGAT
1 AAAATCGCAACGCGAT
7257 TCTTGAAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.02
40 44 0.96
41 1 0.02
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (40 bp):
AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC
Found at i:7332 original size:20 final size:20
Alignment explanation
Indices: 7307--7500 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
7297 GATTTTCCAT
* *
7307 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
7327 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
7347 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
7367 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
7387 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
7407 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
7427 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
7447 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
7468 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
7488 AATCGCAACGCGA
1 AATCGCAACGCGA
7501 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:7352 original size:40 final size:39
Alignment explanation
Indices: 7303--7500 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
7293 TTGCGATTTT
* ** *
7303 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
7341 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
7382 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
7422 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
7461 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
7501 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:7390 original size:60 final size:60
Alignment explanation
Indices: 7307--7499 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
7297 GATTTTCCAT
* ** * *
7307 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
7367 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
7427 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
7488 AATCGCAACGCG
1 AATCGCAACGCG
7500 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:7921 original size:33 final size:33
Alignment explanation
Indices: 7882--7952 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
7872 TTCACTTAGA
*
7882 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
7915 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
7948 TTTCA
1 TTTCA
7953 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:8092 original size:14 final size:14
Alignment explanation
Indices: 8073--8127 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
8063 AGAATGACTG
8073 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
8087 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
8106 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
8120 TCGCAACG
1 TCGCAACG
8128 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:8110 original size:33 final size:33
Alignment explanation
Indices: 8073--8143 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
8063 AGAATGACTG
**
8073 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
8106 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
8139 TCGCA
1 TCGCA
8144 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:8180 original size:14 final size:14
Alignment explanation
Indices: 8161--8264 Score: 109
Period size: 14 Copynumber: 6.7 Consensus size: 14
8151 TTTCATTTCG
8161 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
8175 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
8189 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
8208 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
8222 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
8239 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
8255 CGTTGCGATT
1 CGTTGCGATT
8265 TTCATTTCAA
Statistics
Matches: 78, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
14 42 0.54
15 1 0.01
16 8 0.10
17 8 0.10
18 1 0.01
19 18 0.23
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:8212 original size:33 final size:33
Alignment explanation
Indices: 8175--8272 Score: 178
Period size: 33 Copynumber: 3.0 Consensus size: 33
8165 GCGATTCTCT
8175 CGTTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 CGTTGCGATTCTCTCGTTGCGATTTTCATTTCG
* *
8208 CGTTGCGATTCTCTCGTTGCGATTGTCATCTCG
1 CGTTGCGATTCTCTCGTTGCGATTTTCATTTCG
8241 CGTTGCGATTCTCTCGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCTCGTTGCGATTTTCATTTC
8273 AACCAAAAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTCTCTCGTTGCGATTTTCATTTCG
Found at i:8259 original size:47 final size:46
Alignment explanation
Indices: 8154--8264 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 46
8144 TTGCGATTTT
* *
8154 CATTTCGCGTTGCGATTCTCTCGTTGCGATTCTCTCGTTGCGATTTT
1 CATTTCGCGTTGCGATTCTCTCGTTGCGATTCTCTCGTCGCGA-TTG
*
8201 CATTTCGCGTTGCGATTCTCTCGTTGCGATTGTCATC-TCGCG-TTG
1 CATTTCGCGTTGCGATTCTCTCGTTGCGATTCTC-TCGTCGCGATTG
*
8246 CGATTCTCTCGTTGCGATT
1 C-ATT-TCGCGTTGCGATT
8265 TTCATTTCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
45 3 0.05
46 3 0.05
47 49 0.86
48 2 0.04
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (46 bp):
CATTTCGCGTTGCGATTCTCTCGTTGCGATTCTCTCGTCGCGATTG
Found at i:9405 original size:19 final size:19
Alignment explanation
Indices: 9381--9509 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
9371 AGACGTCAAA
9381 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
9400 TGCGA--TTC-TTT--CGT
1 TGCGATTTTCATTTCGCGT
*
9414 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
9433 TGCGA--TTC-TGT--CGT
1 TGCGATTTTCATTTCGCGT
*
9447 TGCGATTTTAATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
9466 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
9485 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
9505 TGCGA
1 TGCGA
9510 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 15 0.17
16 10 0.11
17 11 0.12
19 41 0.46
20 12 0.13
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:9416 original size:14 final size:14
Alignment explanation
Indices: 9397--9453 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
9387 TTTCATTTCG
9397 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
9411 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
9428 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
9444 CGTTGCGATT
1 CGTTGCGATT
9454 TTAATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:9423 original size:33 final size:33
Alignment explanation
Indices: 9381--9472 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
9371 AGACGTCAAA
*
9381 TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
9414 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
9447 TGCGATTTTAATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
9473 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:11441 original size:14 final size:14
Alignment explanation
Indices: 11422--11457 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11412 ATTGTTTAAT
11422 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
11436 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
11450 TGATTTGT
1 TGATTTGT
11458 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:11580 original size:19 final size:19
Alignment explanation
Indices: 11564--11664 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
11554 AAAAATGACT
11564 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
11583 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
11602 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
11616 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
11634 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
11654 ATCGCAATGCG
1 ATCGCAATGCG
11665 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.16
19 34 0.47
20 12 0.16
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:11711 original size:52 final size:52
Alignment explanation
Indices: 11655--11927 Score: 183
Period size: 52 Copynumber: 5.2 Consensus size: 52
11645 GAAATGAAAA
*
11655 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* * *
11707 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* * *
11759 TCGCATTGCGA--TT-CTTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTAATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATT
** * * * *
11811 TCGCATTGCGATTCTGTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATT
1 TCGCATTGCGATT-T-TAATTTCGCA-TTGCGATTATCTCGTTGCGATTTTCATT
** * * * *
11863 TCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATT
1 TCGCATTGCGATT-T-TAATTTCGCA-TTGCGATTATCTCGTTGCGATTTTCATT
11915 TCGCATTGCGATT
1 TCGCATTGCGATT
11928 CTCTCGTTGC
Statistics
Matches: 193, Mismatches: 15, Indels: 26
0.82 0.06 0.11
Matches are distributed among these distances:
47 6 0.03
49 7 0.04
50 7 0.04
52 156 0.81
53 3 0.02
54 2 0.01
55 1 0.01
56 3 0.02
57 4 0.02
58 1 0.01
59 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:11713 original size:33 final size:33
Alignment explanation
Indices: 11671--11994 Score: 181
Period size: 33 Copynumber: 9.5 Consensus size: 33
11661 TGCGTTTATA
11671 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
11704 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
11740 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
11773 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
11808 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
11841 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
11881 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
11912 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
11945 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
11979 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
11995 GTATTTTTCG
Statistics
Matches: 247, Mismatches: 21, Indels: 46
0.79 0.07 0.15
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 133 0.54
34 29 0.12
35 18 0.07
36 19 0.08
37 2 0.01
38 20 0.08
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:11770 original size:85 final size:83
Alignment explanation
Indices: 11671--11908 Score: 343
Period size: 85 Copynumber: 2.8 Consensus size: 83
11661 TGCGTTTATA
11671 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
11736 ATTCTTTCGTTGCGATTTTC
64 ATTCTGTCGTTGCGATTTTC
*
11756 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCG
1 ATTTCGCATTGCGA-T-TTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
11821 ATTCTGTCGTTGCGATTTTC
64 ATTCTGTCGTTGCGATTTTC
* * * * *
11841 ATTTCGCATTGCGATTTTCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGC
11905 GATT
63 GATT
11909 TTCATTTCGC
Statistics
Matches: 140, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
83 11 0.08
84 5 0.04
85 121 0.86
86 2 0.01
87 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (83 bp):
ATTTCGCATTGCGATTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
TCTGTCGTTGCGATTTTC
Found at i:11928 original size:52 final size:52
Alignment explanation
Indices: 11693--11966 Score: 423
Period size: 52 Copynumber: 5.2 Consensus size: 52
11683 GATTATCTCG
*
11693 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
*
11745 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
* *
11797 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
11849 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
11901 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
11954 TTGCGATTTTCAT
1 TTGCGATTTTCAT
11967 GTTGGGATTT
Statistics
Matches: 212, Mismatches: 4, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
47 6 0.03
49 8 0.04
50 8 0.04
52 173 0.82
53 17 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:14284 original size:12 final size:12
Alignment explanation
Indices: 14267--14291 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14257 TCTTCGGGGA
14267 CTTTTTCTTCTT
1 CTTTTTCTTCTT
14279 CTTTTTCTTCTT
1 CTTTTTCTTCTT
14291 C
1 C
14292 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:14497 original size:24 final size:24
Alignment explanation
Indices: 14463--14509 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
14453 CTGAAACATC
14463 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
14487 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
14510 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:15221 original size:20 final size:20
Alignment explanation
Indices: 15193--15561 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
15183 AAATTTCAGT
* * * *
15193 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
15213 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
15233 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
15253 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
15273 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
15293 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
15313 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
15333 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
15353 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
15373 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
15393 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
15413 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
15433 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
15453 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
15473 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
15493 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
15513 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
15533 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
15553 GTTGCGATT
1 GTTGCGATT
15562 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:22656 original size:22 final size:23
Alignment explanation
Indices: 22621--22665 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
22611 AATTTGGTGA
** *
22621 TTTTAAAATTTATTTTTA-ATTT
1 TTTTAAAAAATATTATTATATTT
22643 TTTTAAAAAATATTATTATATTT
1 TTTTAAAAAATATTATTATATTT
22666 AAAAACATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAAAAAATATTATTATATTT
Found at i:24382 original size:22 final size:22
Alignment explanation
Indices: 24357--24398 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
24347 TAATAGCTAA
*
24357 ATTGATGTGAAAATACGATAGG
1 ATTGATGCGAAAATACGATAGG
24379 ATTGATGCGAAAATACGATA
1 ATTGATGCGAAAATACGATA
24399 TGGACGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (22 bp):
ATTGATGCGAAAATACGATAGG
Found at i:31040 original size:23 final size:23
Alignment explanation
Indices: 31014--31065 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
31004 ATTTTTAGTA
*
31014 TTTAAATTATC-ACTTTTTATTTT
1 TTTAAA-TATCAAATTTTTATTTT
31037 TTT-AATATCTAAATTTTTATTTT
1 TTTAAATATC-AAATTTTTATTTT
31060 TTTAAA
1 TTTAAA
31066 ATAATGTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.16
22 2 0.08
23 17 0.68
24 2 0.08
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTAAATATCAAATTTTTATTTT
Found at i:32847 original size:14 final size:16
Alignment explanation
Indices: 32828--32864 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
32818 AATAAATATA
32828 TAATAAAA-ATA-ATT
1 TAATAAAATATACATT
32842 TAATAAAATATACATT
1 TAATAAAATATACATT
32858 TCAATAA
1 T-AATAA
32865 TTTTTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 3 0.15
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAAAATATACATT
Found at i:65993 original size:28 final size:28
Alignment explanation
Indices: 65956--66016 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
65946 TATTACAAAT
*
65956 ATATAGATTATTTTATAAATATTTT-TAG
1 ATATAGATTATTTTAT-AATATTTTCGAG
*
65984 ATATATATTATTTTATAATATTTTCGAG
1 ATATAGATTATTTTATAATATTTTCGAG
66012 ATATA
1 ATATA
66017 CCTCATTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (28 bp):
ATATAGATTATTTTATAATATTTTCGAG
Found at i:77000 original size:2 final size:2
Alignment explanation
Indices: 76993--77027 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
76983 TGATGAATAA
76993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
77028 CCTTCGATAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:78398 original size:21 final size:21
Alignment explanation
Indices: 78374--78423 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
78364 TATCAATATC
78374 ATAGACTGCCATGTAAGCACT
1 ATAGACTGCCATGTAAGCACT
78395 ATAGACTGCCATGTAAGCACT
1 ATAGACTGCCATGTAAGCACT
78416 ATAGACTG
1 ATAGACTG
78424 TCACATCAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
ATAGACTGCCATGTAAGCACT
Found at i:79209 original size:3 final size:3
Alignment explanation
Indices: 79201--79257 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
79191 TGATTGCTCC
79201 AAT AAT AAT AAT AAT AAT AAT 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
79249 AAT AAT AAT
1 AAT AAT AAT
79258 TCATTCTCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:84561 original size:22 final size:22
Alignment explanation
Indices: 84533--84575 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
84523 AACGGTCAAC
84533 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
84555 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
84576 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:87181 original size:22 final size:24
Alignment explanation
Indices: 87149--87200 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
87139 TTGTTCCTCG
* *
87149 GATT-TTTTCTCTTCATTCT-CAT
1 GATTCTTTTCTCATCAATCTCCAT
87171 G-TTCTTTTCTCATCAATCTCCAT
1 GATTCTTTTCTCATCAATCTCCAT
87194 GATTCTT
1 GATTCTT
87201 GCTGATATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 14 0.56
23 4 0.16
24 5 0.20
ACGTcount: A:0.15, C:0.25, G:0.06, T:0.54
Consensus pattern (24 bp):
GATTCTTTTCTCATCAATCTCCAT
Found at i:99131 original size:13 final size:13
Alignment explanation
Indices: 99094--99131 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
99084 AAATAAAATA
* *
99094 TTTTTAAGTTTTT
1 TTTTTAAATTATT
99107 TTTTTAAA-TATT
1 TTTTTAAATTATT
99119 TTTTTAAATTATT
1 TTTTTAAATTATT
99132 AGATTATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTTTAAATTATT
Found at i:99847 original size:15 final size:15
Alignment explanation
Indices: 99827--99857 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
99817 GGATTTAGTA
99827 TGTGTTAGAAAAGGG
1 TGTGTTAGAAAAGGG
99842 TGTGTTAGAAAAGGG
1 TGTGTTAGAAAAGGG
99857 T
1 T
99858 ACGAGTCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (15 bp):
TGTGTTAGAAAAGGG
Found at i:102064 original size:18 final size:18
Alignment explanation
Indices: 102038--102074 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
102028 TTGGGGTGAA
102038 TGTTATATACCAATCTTT
1 TGTTATATACCAATCTTT
*
102056 TGTTTTATACCAATCTTT
1 TGTTATATACCAATCTTT
102074 T
1 T
102075 AAAGTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.54
Consensus pattern (18 bp):
TGTTATATACCAATCTTT
Found at i:103798 original size:22 final size:22
Alignment explanation
Indices: 103773--103816 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
103763 TCGTCACTGT
*
103773 TGGTTTTAGTTCTTATATTAAA
1 TGGTTTTAGTTCCTATATTAAA
103795 TGGTTTTAGTTCCTATATTAAA
1 TGGTTTTAGTTCCTATATTAAA
103817 AAAACTAGAA
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:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (22 bp):
TGGTTTTAGTTCCTATATTAAA
Found at i:107197 original size:41 final size:41
Alignment explanation
Indices: 107152--107347 Score: 356
Period size: 41 Copynumber: 4.8 Consensus size: 41
107142 ACAACTGTAG
107152 ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCA
107193 ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCA
* *
107234 ACTATCGTAACGCGAAATGGAAAATCGCAATGTGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCA
*
107275 ACTATCGTAACGCGAAATGGAAAATCGCAACGTGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCA
*
107316 ACTATCGCAACGTGAAATGGAAAATCGCAACG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG
107348 CGAATTTGCG
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 150 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCA
Found at i:108539 original size:13 final size:14
Alignment explanation
Indices: 108516--108545 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
108506 TTCCCATTAC
108516 AGACGTGCATATGA
1 AGACGTGCATATGA
108530 AGAC-TGCATATGA
1 AGACGTGCATATGA
108543 AGA
1 AGA
108546 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:110879 original size:150 final size:149
Alignment explanation
Indices: 110682--110997 Score: 562
Period size: 150 Copynumber: 2.1 Consensus size: 149
110672 TATAAATGCA
*
110682 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAA-TGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
110746 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTTCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTC-TTTCAAGACTTCACACATGT
* *
110811 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
110832 CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
1 CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
110897 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
110962 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
*
110981 CCGAAGGACCGCGTAGA
1 CCGAATGACCGCGTAGA
110998 CCCTCTACCC
Statistics
Matches: 160, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
149 56 0.35
150 104 0.65
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:111519 original size:19 final size:20
Alignment explanation
Indices: 111482--111519 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
111472 TTTTTATACA
*
111482 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
111502 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
111520 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:117823 original size:150 final size:149
Alignment explanation
Indices: 117626--117941 Score: 562
Period size: 150 Copynumber: 2.1 Consensus size: 149
117616 TATAAATGCA
*
117626 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
117690 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTTCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTC-TTTCAAGACTTCACACATGT
* * *
117755 TCCACATAATATATATATATC
129 TCCAAAGAATATACATATATC
117776 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
117841 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
117906 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
117925 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
117942 CCCTCTACCC
Statistics
Matches: 160, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
149 55 0.34
150 105 0.66
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:118455 original size:20 final size:20
Alignment explanation
Indices: 118427--118467 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
118417 TTTATACATG
*
118427 GGGGAATCGGTTCCCCCCTA
1 GGGGAATCGATTCCCCCCTA
* *
118447 GGGGTATCGATTCCCCTCTA
1 GGGGAATCGATTCCCCCCTA
118467 G
1 G
118468 CATTCTGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (20 bp):
GGGGAATCGATTCCCCCCTA
Found at i:125925 original size:33 final size:33
Alignment explanation
Indices: 125888--125951 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
125878 ATTTTTTCCC
125888 TATAATATGTAAGAGATCAATGTTATTTTTCTT
1 TATAATATGTAAGAGATCAATGTTATTTTTCTT
125921 TATAATATGTAAGAGATCAATGTTATTTTTC
1 TATAATATGTAAGAGATCAATGTTATTTTTC
125952 CTTCTTTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (33 bp):
TATAATATGTAAGAGATCAATGTTATTTTTCTT
Found at i:128689 original size:28 final size:29
Alignment explanation
Indices: 128658--128714 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
128648 AATAGTAGGG
128658 TGACCA-TTTATAACTTTTAATAGTCAGA
1 TGACCATTTTATAACTTTTAATAGTCAGA
128686 TGACCATTTTATAACTTTTAATAGTCAGA
1 TGACCATTTTATAACTTTTAATAGTCAGA
128715 AGACTCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (29 bp):
TGACCATTTTATAACTTTTAATAGTCAGA
Found at i:130766 original size:2 final size:2
Alignment explanation
Indices: 130759--130783 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
130749 TGTTTGATTC
130759 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 A
130784 AAACACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:131618 original size:21 final size:21
Alignment explanation
Indices: 131568--131618 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
131558 CCCTAACTTA
*
131568 AAACCCTAAACCTTAAAACAT
1 AAACCCTAAACCATAAAACAT
* *
131589 AATCTCTAAACCAT-AAACATT
1 AAACCCTAAACCATAAAACA-T
131610 AAACCCTAA
1 AAACCCTAA
131619 CTTAAGATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCCTAAACCATAAAACAT
Found at i:131919 original size:14 final size:14
Alignment explanation
Indices: 131900--131928 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
131890 AACCATTGAC
131900 TTGATATGCCTCTA
1 TTGATATGCCTCTA
131914 TTGATATGCCTCTA
1 TTGATATGCCTCTA
131928 T
1 T
131929 AGGGTAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (14 bp):
TTGATATGCCTCTA
Found at i:132010 original size:13 final size:13
Alignment explanation
Indices: 131992--132016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
131982 TAAATAATAT
131992 TATTTTTAATAAA
1 TATTTTTAATAAA
132005 TATTTTTAATAA
1 TATTTTTAATAA
132017 TGTTAATTGA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTTTAATAAA
Found at i:135833 original size:24 final size:22
Alignment explanation
Indices: 135806--135856 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
135796 AAAAATAAGT
135806 TAAATGATAGAGAAAAACATTTCA
1 TAAATGATAG-G-AAAACATTTCA
* * *
135830 TAAAGGATAGGAAAGCCTTTCA
1 TAAATGATAGGAAAACATTTCA
135852 TAAAT
1 TAAAT
135857 ATAATATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 13 0.57
23 1 0.04
24 9 0.39
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (22 bp):
TAAATGATAGGAAAACATTTCA
Found at i:141477 original size:15 final size:16
Alignment explanation
Indices: 141452--141484 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
141442 ACATGATTGA
*
141452 GGGACTAAAATCGAAC
1 GGGACTAAAATCAAAC
141468 GGGA-TAAAATCAAAC
1 GGGACTAAAATCAAAC
141483 GG
1 GG
141485 ATTGATAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.15, G:0.27, T:0.12
Consensus pattern (16 bp):
GGGACTAAAATCAAAC
Found at i:141510 original size:31 final size:31
Alignment explanation
Indices: 141468--141535 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
141458 AAAATCGAAC
**
141468 GGGA-TAAAATCAAACGGATTGATAACGTTA
1 GGGACTAAAATCAAACGGATCAATAACGTTA
* * *
141498 TGGACTAAAATCAGACGGATCAATAATGTTA
1 GGGACTAAAATCAAACGGATCAATAACGTTA
141529 GGGACTA
1 GGGACTA
141536 TTCCCCCATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (31 bp):
GGGACTAAAATCAAACGGATCAATAACGTTA
Found at i:147130 original size:15 final size:16
Alignment explanation
Indices: 147098--147130 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
147088 AAAATATTTC
147098 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
147114 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
147129 TT
1 TT
147131 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:147907 original size:16 final size:17
Alignment explanation
Indices: 147880--147914 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
147870 TATCGCCGAC
147880 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
147897 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
147913 CG
1 CG
147915 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:150553 original size:16 final size:16
Alignment explanation
Indices: 150534--150583 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 16
150524 AAACATTTTT
150534 TATTAAAATAATAAAA
1 TATTAAAATAATAAAA
150550 TATTAAAATACAT--AA
1 TATTAAAATA-ATAAAA
*
150565 TATT-CAATAA-AAAA
1 TATTAAAATAATAAAA
150579 TATTA
1 TATTA
150584 TAATTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
13 1 0.03
14 10 0.34
15 6 0.21
16 10 0.34
17 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
TATTAAAATAATAAAA
Found at i:150947 original size:31 final size:31
Alignment explanation
Indices: 150900--150958 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
150890 AATTATAAAA
150900 TTTACTAATAAAAATAATCA-TTAAATTTAT
1 TTTACTAATAAAAATAATCATTTAAATTTAT
* *
150930 TTTACTATTATAAAATAATTATTTAAATT
1 TTTACTAATA-AAAATAATCATTTAAATT
150959 ATTGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 9 0.36
32 7 0.28
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTACTAATAAAAATAATCATTTAAATTTAT
Found at i:152972 original size:18 final size:18
Alignment explanation
Indices: 152949--153015 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
152939 TGTGTAAAAC
152949 TATAATATAATAAAATTA
1 TATAATATAATAAAATTA
* *
152967 TATAATATATTTAAATTA
1 TATAATATAATAAAATTA
* *
152985 TATAATATATTTAAATTA
1 TATAATATAATAAAATTA
153003 T-TAA-A-AATAAAAT
1 TATAATATAATAAAAT
153016 GATAAAAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
15 6 0.13
16 1 0.02
17 3 0.07
18 35 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATAATATAATAAAATTA
Found at i:158634 original size:15 final size:15
Alignment explanation
Indices: 158616--158731 Score: 52
Period size: 15 Copynumber: 7.5 Consensus size: 15
158606 TGCAAGTGCC
158616 GCTCATGTAAATGCA
1 GCTCATGTAAATGCA
* ** *
158631 GCTCTTGCGACTGCA
1 GCTCATGTAAATGCA
* *
158646 GTTCAAGTAAATGCA
1 GCTCATGTAAATGCA
* ** *
158661 GCTCCTGCGACTGCA
1 GCTCATGTAAATGCA
* * *
158676 GTTCTTGTAAGTGCA
1 GCTCATGTAAATGCA
158691 GCAGTTCATGTAAATGCA
1 GC---TCATGTAAATGCA
* * * *
158709 GCTCGTGTGACTGCT
1 GCTCATGTAAATGCA
158724 GCTCATGT
1 GCTCATGT
158732 TCAAGCTGCT
Statistics
Matches: 69, Mismatches: 29, Indels: 6
0.66 0.28 0.06
Matches are distributed among these distances:
15 56 0.81
18 13 0.19
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.29
Consensus pattern (15 bp):
GCTCATGTAAATGCA
Found at i:158691 original size:30 final size:30
Alignment explanation
Indices: 158618--158692 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
158608 CAAGTGCCGC
*
158618 TCATGTAAATGCAGCTCTTGCGACTGCAGT
1 TCATGTAAATGCAGCTCCTGCGACTGCAGT
*
158648 TCAAGTAAATGCAGCTCCTGCGACTGCAGT
1 TCATGTAAATGCAGCTCCTGCGACTGCAGT
* *
158678 TCTTGTAAGTGCAGC
1 TCATGTAAATGCAGC
158693 AGTTCATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (30 bp):
TCATGTAAATGCAGCTCCTGCGACTGCAGT
Found at i:158696 original size:18 final size:18
Alignment explanation
Indices: 158673--158710 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
158663 TCCTGCGACT
* *
158673 GCAGTTCTTGTAAGTGCA
1 GCAGTTCATGTAAATGCA
158691 GCAGTTCATGTAAATGCA
1 GCAGTTCATGTAAATGCA
158709 GC
1 GC
158711 TCGTGTGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (18 bp):
GCAGTTCATGTAAATGCA
Found at i:158802 original size:63 final size:63
Alignment explanation
Indices: 158702--158872 Score: 218
Period size: 63 Copynumber: 2.7 Consensus size: 63
158692 CAGTTCATGT
* * * *
158702 AAATGCAGCTCGTGTGACTGCTGCTCATGTTCAAGCTGCTGCACAATCTCGAAATGGCGATGC
1 AAATGCAGCTCGTGCGACTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCGAAATGGCGATGC
158765 AAATGCAGCTCGTGCGACTGCTGTTCGTGTTTC-AGCTGCTGCACAATCCCGAAATGGCGATGC
1 AAATGCAGCTCGTGCGACTGCTGTTCGTG-TTCAAGCTGCTGCACAATCCCGAAATGGCGATGC
* * * * *
158828 AAGTGCGGCTCATCATGCGACTACTGTTCGTGTTCGAGCTGCTGC
1 AAATGCAG--C-TCGTGCGACTGCTGTTCGTGTTCAAGCTGCTGC
158873 GTGATCCCAA
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
63 61 0.64
64 3 0.03
65 4 0.04
66 27 0.28
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.26
Consensus pattern (63 bp):
AAATGCAGCTCGTGCGACTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCGAAATGGCGATGC
Found at i:163450 original size:14 final size:12
Alignment explanation
Indices: 163414--163445 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
163404 ATATTTTAAA
163414 TTTTTTATATAT
1 TTTTTTATATAT
163426 TTTTTTATATAT
1 TTTTTTATATAT
163438 TTTTTTAT
1 TTTTTTAT
163446 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTATATAT
Found at i:164504 original size:20 final size:21
Alignment explanation
Indices: 164479--164523 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
164469 ATCTCCGGTA
* *
164479 TCGCAAATC-ATTTTCCAGAT
1 TCGCAAAGCGATTTTCCAAAT
*
164499 TCGCAACGCGATTTTCCAAAT
1 TCGCAAAGCGATTTTCCAAAT
164520 TCGC
1 TCGC
164524 GTTACGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (21 bp):
TCGCAAAGCGATTTTCCAAAT
Found at i:165630 original size:14 final size:14
Alignment explanation
Indices: 165611--165647 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
165601 CATCAATTAA
165611 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
165625 ACAAATCATCTTTT
1 ACAAATCAACATTT
165639 ACAAATCAA
1 ACAAATCAA
165648 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:167108 original size:42 final size:41
Alignment explanation
Indices: 167001--167112 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 41
166991 TCTAGAGTGT
* * *
167001 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* ** *
167043 TGGGATGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 TGGGA-GGGCCTCTTGAACGATGACAGGGGCCTCTTGAACG--A
167087 TGGGA-GGCCTCTTGAACGATGACAGG
1 TGGGAGGGCCTCTTGAACGATGACAGG
167113 TGAGTCGGGC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
42 48 0.86
43 3 0.05
44 5 0.09
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
TGGGAGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:167618 original size:20 final size:20
Alignment explanation
Indices: 167595--167661 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
167585 AACTTAAAAG
*
167595 CGCAACGCGAAAATGACTAT
1 CGCAATGCGAAAATGACTAT
167615 CGCAATGCGAAAATGACTAT
1 CGCAATGCGAAAATGACTAT
**
167635 CGCAATGCGAATTTGACTAT
1 CGCAATGCGAAAATGACTAT
167655 CGCAATG
1 CGCAATG
167662 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (20 bp):
CGCAATGCGAAAATGACTAT
Found at i:167716 original size:19 final size:19
Alignment explanation
Indices: 167694--167756 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
167684 AAATCGCAAC
*
167694 GCGATTATAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
167713 GCGATTTTGGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
167732 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
167751 GTGATT
1 GCGATT
167757 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.11, C:0.16, G:0.27, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:167770 original size:33 final size:33
Alignment explanation
Indices: 167728--167790 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
167718 TTTGGTTTCG
*
167728 CGTTGCGATTTTCATTTCGCGTTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
167761 CGTTGCGATTTTCATTTCTCGTTGCGATTC
1 CGTTGCGATTTTCATTTCGCGTTGCGATTC
167791 ATTTCGCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:167782 original size:19 final size:19
Alignment explanation
Indices: 167704--167829 Score: 113
Period size: 19 Copynumber: 6.9 Consensus size: 19
167694 GCGATTATAG
**
167704 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGATTTTCA
167723 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
167742 TTTCGCGTTGTGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
167758 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
167775 TTTCTCGTTGCGA--TTCA
1 TTTCGCGTTGCGATTTTCA
**
167792 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
167811 TTTTTCACGTTGCGATTTT
1 --TTTCGCGTTGCGATTTT
167830 AAGTTTCGTG
Statistics
Matches: 88, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.10
16 3 0.03
17 19 0.22
19 43 0.49
21 14 0.16
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:168039 original size:94 final size:94
Alignment explanation
Indices: 167893--168272 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
167883 ATGGATTGCA
* *
167893 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
167957 TTAGCAGAATTGGCAGCAACTGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
167986 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAATACATAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
168051 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
168080 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
168145 TTAGCAGAATTGGTAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
168174 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATATTAACTTCACAATGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * * *
168238 TTTAGCAGTATTGGCAGGAACTGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
168268 TTACT
1 TTACT
168273 AAGCAATCTA
Statistics
Matches: 268, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
93 23 0.09
94 245 0.91
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:175167 original size:21 final size:21
Alignment explanation
Indices: 175141--175180 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
175131 CCCCCTTTGA
*
175141 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
175162 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
175181 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:179591 original size:20 final size:20
Alignment explanation
Indices: 179566--179647 Score: 96
Period size: 20 Copynumber: 4.2 Consensus size: 20
179556 TTTTGGTTGA
179566 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
179586 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
** *
179605 AAATGACTATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
*
179625 AATTAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
179645 AAT
1 AAT
179648 CGCAATGCGA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.31
20 36 0.69
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:179608 original size:40 final size:39
Alignment explanation
Indices: 179564--179640 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
179554 TCTTTTGGTT
179564 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAACGAGA-AATGAAAATCGCAACGCG
** * *
179604 GAAATGACTATCGCAACGCGAAATTAAAATCGCAACG
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACG
179641 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 15 0.45
40 18 0.55
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGCG
Found at i:179675 original size:19 final size:19
Alignment explanation
Indices: 179653--179759 Score: 71
Period size: 19 Copynumber: 5.7 Consensus size: 19
179643 AGAATCGCAA
**
179653 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
179672 TGCGATTTTCATTTTGCGT
1 TGCGATTTTCATTTCGCGT
*
179691 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
* *
179705 TGCGATTTTAATTTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGT
** *
179726 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
179746 TGCGATTTTCATTT
1 TGCGATTTTCATTT
179760 TCATGTTTCG
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
14 9 0.13
16 2 0.03
17 3 0.04
19 24 0.35
20 13 0.19
21 17 0.25
ACGTcount: A:0.11, C:0.18, G:0.21, T:0.50
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:179739 original size:21 final size:21
Alignment explanation
Indices: 179696--179751 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
179686 TGCGTTGCGA
**
179696 TTCTCTCGTTGCGATTTTAAT
1 TTCTCTCGTTGCGATAGTAAT
*
179717 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATAGTAAT
179738 TT-TCGT-GTTGCGAT
1 TTCTC-TCGTTGCGAT
179752 TTTCATTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATAGTAAT
Found at i:179772 original size:20 final size:20
Alignment explanation
Indices: 179703--179774 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
179693 CGATTCTCTC
*
179703 GTTGCGATTTTAATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
179723 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
179744 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
*
179764 GTTTCGATTTT
1 GTTGCGATTTT
179775 ATGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.14, C:0.15, G:0.18, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:180311 original size:20 final size:20
Alignment explanation
Indices: 180286--180458 Score: 195
Period size: 20 Copynumber: 8.6 Consensus size: 20
180276 CTTTAAAAAT
*
180286 CGCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
180306 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
180326 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
180347 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
** *
180367 CTTGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
180387 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
180407 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
180427 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
180448 CTCGTTGCGAT
1 CGCGTTGCGAT
180459 AGTCAGAATC
Statistics
Matches: 125, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
20 89 0.71
21 36 0.29
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:180374 original size:40 final size:41
Alignment explanation
Indices: 180288--180458 Score: 265
Period size: 40 Copynumber: 4.2 Consensus size: 41
180278 TTAAAAATCG
* *
180288 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
180329 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
180369 TGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
180409 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
180450 CGTTGCGAT
1 CGTTGCGAT
180459 AGTCAGAATC
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 74 0.62
41 45 0.38
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:180442 original size:81 final size:80
Alignment explanation
Indices: 180288--180499 Score: 266
Period size: 81 Copynumber: 2.6 Consensus size: 80
180278 TTAAAAATCG
* * *
180288 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCATT
* *
180353 GCGATTTACGTATTCT
65 GCGATTTACGGATACT
* *
180369 TGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTG
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTG
180434 CGATTTTACGGATACT
66 CGA-TTTACGGATACT
* ** * *
180450 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCGCGTTGCGATT
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACGTATTCTCGTTGCGATT
180500 CTGGAAAATC
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
80 39 0.34
81 75 0.65
82 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (80 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTG
CGATTTACGGATACT
Found at i:184083 original size:89 final size:89
Alignment explanation
Indices: 183927--184104 Score: 302
Period size: 89 Copynumber: 2.0 Consensus size: 89
183917 ATTCTAATAA
* * **
183927 ACATTTGGAATTCTTCCAAGTTACACACATGTTTGTATTAGTATATGTATAATTATACAGATGGA
1 ACATTTAGAATTCTTCCAAGTTACACACATGTTCGTATTAGTATATGTATAATTATACAGAAAGA
*
183992 TAGAGAAGATTACAGAAATTAGGG
66 TAGAGAAGATTAAAGAAATTAGGG
184016 ACATTTAGAATTCTTCCAAGTTACACACATGTTCGTATTAGTATATGTATAATTATACAGAAAGA
1 ACATTTAGAATTCTTCCAAGTTACACACATGTTCGTATTAGTATATGTATAATTATACAGAAAGA
*
184081 TAGAGAAGATTAAAGATATTAGGG
66 TAGAGAAGATTAAAGAAATTAGGG
184105 TAAATTATGT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (89 bp):
ACATTTAGAATTCTTCCAAGTTACACACATGTTCGTATTAGTATATGTATAATTATACAGAAAGA
TAGAGAAGATTAAAGAAATTAGGG
Found at i:193411 original size:49 final size:49
Alignment explanation
Indices: 193338--193435 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
193328 AATTGTTGAA
193338 GCAACTCCTATATTGAGTTAGTGGATGCTTGTGATATTCATGCAAGGTG
1 GCAACTCCTATATTGAGTTAGTGGATGCTTGTGATATTCATGCAAGGTG
*
193387 GCAACTCCTATATTGAGTTGGTGGATGCTTGTGATATTCATGCAAGGTG
1 GCAACTCCTATATTGAGTTAGTGGATGCTTGTGATATTCATGCAAGGTG
193436 TTCGAAGCAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (49 bp):
GCAACTCCTATATTGAGTTAGTGGATGCTTGTGATATTCATGCAAGGTG
Found at i:194437 original size:31 final size:31
Alignment explanation
Indices: 194394--194452 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
194384 CGAATTGAGT
* *
194394 ATTAAAATTGAACAAATTGATAATATTATGG
1 ATTAAAAGTGAACAAATCGATAATATTATGG
*
194425 ATTAAAAGTGAACGAATCGATAATATTA
1 ATTAAAAGTGAACAAATCGATAATATTA
194453 GGGAGGAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (31 bp):
ATTAAAAGTGAACAAATCGATAATATTATGG
Found at i:195798 original size:60 final size:60
Alignment explanation
Indices: 195686--195798 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 60
195676 TATATGTTAC
* * * * *
195686 TATTTTATTAAGTTATTTGATTATTAAAAGTTACAAAACGGTCCTCTAACTATAGAATGT
1 TATTTTATTAAATCATTTGACTATTAAAAGTTACAAAACGATCATCTAACTATAGAATGT
* * * * *
195746 TATTTTGTTAAATCATTTGACTATTAAAAGTTACACAATGATTATCTGACTAT
1 TATTTTATTAAATCATTTGACTATTAAAAGTTACAAAACGATCATCTAACTAT
195799 TTATTAGATT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (60 bp):
TATTTTATTAAATCATTTGACTATTAAAAGTTACAAAACGATCATCTAACTATAGAATGT
Found at i:204521 original size:60 final size:59
Alignment explanation
Indices: 204389--204521 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 59
204379 TCAGGTGACT
* * * *
204389 ATTTTATAACTTTTAATAGTTGAGGGACTCAATAAAGTAAACTCTATAGTTAGAGGATC
1 ATTTTATAACTTTTAATAGTTGAAGGACTCAATAAAATAAACTCTATAATCAGAGGATC
* * *
204448 ATTTTTATAACTTTTAATAGTTGAAGGACTTAATAAAATAGTA-TCTTATAATCGGAGGATC
1 A-TTTTATAACTTTTAATAGTTGAAGGACTCAATAAAATA-AACTC-TATAATCAGAGGATC
204509 ATTTGTAT-ACTTT
1 ATTT-TATAACTTT
204522 ACCCTAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 1 0.02
60 45 0.71
61 17 0.27
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (59 bp):
ATTTTATAACTTTTAATAGTTGAAGGACTCAATAAAATAAACTCTATAATCAGAGGATC
Found at i:215588 original size:21 final size:21
Alignment explanation
Indices: 215564--215605 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
215554 TACGCGTGAC
*
215564 CTGCTTCAACGCTGTTGTTGA
1 CTGCTTCAACGCTGTTATTGA
* *
215585 CTGCTTCTACTCTGTTATTGA
1 CTGCTTCAACGCTGTTATTGA
215606 AGTTGGTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (21 bp):
CTGCTTCAACGCTGTTATTGA
Found at i:218935 original size:23 final size:25
Alignment explanation
Indices: 218890--218935 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
218880 GACGTGGCAT
218890 AAATAATAAATATTAATTTTAAATA
1 AAATAATAAATATTAATTTTAAATA
*
218915 AAATAAT-AAT-TTGATTTTAAA
1 AAATAATAAATATTAATTTTAAA
218936 AGTAGAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AAATAATAAATATTAATTTTAAATA
Found at i:242314 original size:15 final size:15
Alignment explanation
Indices: 242289--242326 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
242279 GGACAACCGG
242289 TATTG-TTCCATACC
1 TATTGTTTCCATACC
242303 TATTGTTTCCATACC
1 TATTGTTTCCATACC
*
242318 TTTTGTTTC
1 TATTGTTTC
242327 TTTATTCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.53
Consensus pattern (15 bp):
TATTGTTTCCATACC
Found at i:243331 original size:72 final size:73
Alignment explanation
Indices: 243241--243379 Score: 271
Period size: 72 Copynumber: 1.9 Consensus size: 73
243231 TGGCATGTGC
243241 ATCTGTCAGTCTATCTCATTTAAATGCAATCTGAAGGTTGGATTTACTGCTT-CCGATGTGCCTC
1 ATCTGTCAGTCTATCTCATTTAAATGCAATCTGAAGGTTGGATTTACTGCTTCCCGATGTGCCTC
243305 AACTGTTT
66 AACTGTTT
243313 ATCTGTCAGTCTATCTCATTTAAATGCAATCTGAAGGTTGGATTTACTGCTTCCCGATGTGCCTC
1 ATCTGTCAGTCTATCTCATTTAAATGCAATCTGAAGGTTGGATTTACTGCTTCCCGATGTGCCTC
243378 AA
66 AA
243380 TACTGTTGGA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 52 0.79
73 14 0.21
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (73 bp):
ATCTGTCAGTCTATCTCATTTAAATGCAATCTGAAGGTTGGATTTACTGCTTCCCGATGTGCCTC
AACTGTTT
Found at i:247160 original size:2 final size:2
Alignment explanation
Indices: 247153--247220 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
247143 TATGAACAGC
*
247153 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
247195 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
247221 GATGTTAACT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:253488 original size:19 final size:19
Alignment explanation
Indices: 253461--253498 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
253451 TTATCCTCAA
*
253461 AATTCTACCTCTATTTTTT
1 AATTCTACCTATATTTTTT
*
253480 AATTTTACCTATATTTTTT
1 AATTCTACCTATATTTTTT
253499 GTTATTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTCTACCTATATTTTTT
Found at i:257683 original size:29 final size:29
Alignment explanation
Indices: 257605--257675 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
257595 ACTAAAGTTA
*
257605 TTGGTCAAAATAGGTTCCTAACTTACTTT
1 TTGGTCAAAACAGGTTCCTAACTTACTTT
257634 TTGGTCAAAACAGGTTCCTAACTTACTTT
1 TTGGTCAAAACAGGTTCCTAACTTACTTT
257663 TTGGTCAAAACAG
1 TTGGTCAAAACAG
257676 ATACCTAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (29 bp):
TTGGTCAAAACAGGTTCCTAACTTACTTT
Found at i:263138 original size:25 final size:25
Alignment explanation
Indices: 263065--263127 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
263055 TTGAATGAAA
**
263065 AAAATTAAAAAATAAAGATTAATAATAG
1 AAAA-TAAAAAATAATTATT-A-AATAG
*
263093 AAAATAAAAAATATTTATTAAATAG
1 AAAATAAAAAATAATTATTAAATAG
263118 AAAATAAAAA
1 AAAATAAAAA
263128 GTTAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.47
26 1 0.03
27 12 0.38
28 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (25 bp):
AAAATAAAAAATAATTATTAAATAG
Found at i:272457 original size:22 final size:22
Alignment explanation
Indices: 272398--272467 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
272388 ATTTAACACA
*
272398 TTTT-GTACCTAAACTATAAGT
1 TTTTAGTACCTAAACTTTAAGT
272419 TTTTAGTACCTAAACTTTAAGT
1 TTTTAGTACCTAAACTTTAAGT
*
272441 TTTTAGTACCTAAACTTTCAATT
1 TTTTAGTACCTAAACTTT-AAGT
272464 TTTT
1 TTTT
272468 CAAAACTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.09
22 34 0.76
23 7 0.16
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (22 bp):
TTTTAGTACCTAAACTTTAAGT
Found at i:284657 original size:38 final size:38
Alignment explanation
Indices: 284604--284682 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
284594 GTTCATAAAC
* *
284604 TTCTTCCTGGTATTATCCTATGTTGCCTAATTATTCTT
1 TTCTTCCTGGGATTATCCTATCTTGCCTAATTATTCTT
*
284642 TTCTTCCTGGGATTATCCTATCTTGCCTAATTATTTTT
1 TTCTTCCTGGGATTATCCTATCTTGCCTAATTATTCTT
284680 TTC
1 TTC
284683 ATTGTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.15, C:0.22, G:0.10, T:0.53
Consensus pattern (38 bp):
TTCTTCCTGGGATTATCCTATCTTGCCTAATTATTCTT
Found at i:288923 original size:21 final size:21
Alignment explanation
Indices: 288899--288938 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
288889 GGTTATGGAG
*
288899 TTATGATTTAGGGTTTAAGAT
1 TTATAATTTAGGGTTTAAGAT
*
288920 TTATAATTTAGTGTTTAAG
1 TTATAATTTAGGGTTTAAG
288939 TTAGGGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (21 bp):
TTATAATTTAGGGTTTAAGAT
Found at i:290186 original size:21 final size:21
Alignment explanation
Indices: 290160--290203 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
290150 CCATTTGTTT
290160 TTTTATTTATTACTATAATTA
1 TTTTATTTATTACTATAATTA
* *
290181 TTTTATTTATTATTATTATTA
1 TTTTATTTATTACTATAATTA
290202 TT
1 TT
290204 ATTAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATTTATTACTATAATTA
Found at i:290193 original size:24 final size:24
Alignment explanation
Indices: 290157--290206 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
290147 TATCCATTTG
290157 TTTTTTTATTTATTACTATAATTA
1 TTTTTTTATTTATTACTATAATTA
* *
290181 TTTTATTTA-TTATTATTATTATTA
1 TTTT-TTTATTTATTACTATAATTA
290205 TT
1 TT
290207 AAATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTTATTTATTACTATAATTA
Found at i:290195 original size:3 final size:3
Alignment explanation
Indices: 290166--290207 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
290156 GTTTTTTTAT
* *
290166 TTA TTA CTA TAA TTA TT- TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
290208 AATAATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:290862 original size:16 final size:16
Alignment explanation
Indices: 290841--290877 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
290831 CACACGTTGT
290841 TGAAGAACCAAAACGG
1 TGAAGAACCAAAACGG
290857 TGAAGAACCAAAACGG
1 TGAAGAACCAAAACGG
290873 TGAAG
1 TGAAG
290878 GTAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.27, T:0.08
Consensus pattern (16 bp):
TGAAGAACCAAAACGG
Found at i:291972 original size:139 final size:140
Alignment explanation
Indices: 291815--292193 Score: 626
Period size: 140 Copynumber: 2.7 Consensus size: 140
291805 TAATCATATT
* *
291815 TTAATA-TTATTTATTTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCATCTAGAAGTTC-TTT
1 TTAATATTTATTTA-TTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAG-TCATTT
291878 TCTGATATTCTTAAATAAATAAATATACTATTTTTATAAA-TATATATTAATTTTTTATTTTTAG
64 TCTGATATTCTTAAATAAATAAATATACTATTTTTATAAATTATATATTAATTTTTTATTTTTAG
291942 AAAAATGTTTTA
129 AAAAATGTTTTA
* * *
291954 TTAATATTTATTTATTTTTTAATATTAAGAAATGTGCTGTCTTAAAGTACCTAGAAGTCATGTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTC
292019 TGATATTCTTAAATAAATAAATATACTATTTTTATAAATTATATATTAATTTTTTATTTTTAGAA
66 TGATATTCTTAAATAAATAAATATACTATTTTTATAAATTATATATTAATTTTTTATTTTTAGAA
292084 AAATGTTTTA
131 AAATGTTTTA
*
292094 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCATTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTC
* *
292159 TGATATTC-TAAGTAAATAAATAT-C-ATATTTATAAA
66 TGATATTCTTAAATAAATAAATATACTATTTTTATAAA
292194 AATAAAAATA
Statistics
Matches: 227, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
137 10 0.04
138 3 0.01
139 101 0.44
140 113 0.50
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (140 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTC
TGATATTCTTAAATAAATAAATATACTATTTTTATAAATTATATATTAATTTTTTATTTTTAGAA
AAATGTTTTA
Found at i:291985 original size:41 final size:40
Alignment explanation
Indices: 291909--291985 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
291899 AATATACTAT
* *
291909 TTTTATAAATATATATTAATTTTTTATTTTTAGAAAAATG
1 TTTTATAAATATATATTAATTTTTTATATTAAGAAAAATG
* * *
291949 TTTTATTAATATTTATTTATTTTTTAATATTAAGAAA
1 TTTTATAAATATATATTAATTTTTT-ATATTAAGAAA
291986 TGTGCTGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 22 0.71
41 9 0.29
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (40 bp):
TTTTATAAATATATATTAATTTTTTATATTAAGAAAAATG
Found at i:292125 original size:41 final size:41
Alignment explanation
Indices: 292048--292125 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
292038 AATATACTAT
* *
292048 TTTTATAAATTATATATTAATTTTTTATTTTTAGAAAAATG
1 TTTTATAAATTATATATTAATTTTTTATATTAAGAAAAATG
* * *
292089 TTTTATTAA-TATTTATTTATTTTTTAATATTAAGAAA
1 TTTTATAAATTATATATTAATTTTTT-ATATTAAGAAA
292126 TGGGCTGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 14 0.45
41 17 0.55
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (41 bp):
TTTTATAAATTATATATTAATTTTTTATATTAAGAAAAATG
Found at i:298927 original size:18 final size:18
Alignment explanation
Indices: 298887--298928 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
298877 GCACCACTAA
298887 CGCCGCCGCGGCACACAC
1 CGCCGCCGCGGCACACAC
*
298905 GGCCGCCGC-GCACACCAC
1 CGCCGCCGCGGCACA-CAC
298923 CGCCGC
1 CGCCGC
298929 ACCGACCGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.14, C:0.57, G:0.29, T:0.00
Consensus pattern (18 bp):
CGCCGCCGCGGCACACAC
Done.