Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009359.1 Hibiscus syriacus cultivar Beakdansim tig00113177_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: 193785
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:3116 original size:15 final size:15
Alignment explanation
Indices: 3096--3131 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3086 ATTATTAGCT
*
3096 TTATAATATATGTTA
1 TTATAATATATATTA
3111 TTATAATATATATTA
1 TTATAATATATATTA
*
3126 TGATAA
1 TTATAA
3132 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:7619 original size:19 final size:20
Alignment explanation
Indices: 7572--7621 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
7562 GAAACCCCTT
**
7572 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
7592 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
7611 TGAAGATACAT
1 TGAAAATACAT
7622 ACTCTTGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:12339 original size:23 final size:22
Alignment explanation
Indices: 12301--12343 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
12291 CAATTCCTTT
12301 ATCTTTTATTTATCTTGTTTTA
1 ATCTTTTATTTATCTTGTTTTA
*
12323 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTATTTATCTTGTTT
12344 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTATTTATCTTGTTTTA
Found at i:14244 original size:22 final size:23
Alignment explanation
Indices: 14219--14261 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
14209 CAATTCCTTT
*
14219 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATTCTTTATATTGTTTTA
*
14241 ATCTTATTTTTTATATTGTTT
1 ATCTTATTCTTTATATTGTTT
14262 CCAGTACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (23 bp):
ATCTTATTCTTTATATTGTTTTA
Found at i:16811 original size:5 final size:5
Alignment explanation
Indices: 16803--16850 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
16793 TGCTTTCTCT
* *
16803 TTTTC TTTTC TTTTC TTTTC --TTC TTTTC TTATTT TTTTC TCTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTT
16851 GTCTTTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
5 29 0.81
6 4 0.11
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:16826 original size:18 final size:18
Alignment explanation
Indices: 16796--16867 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 18
16786 CTTGGCTTGC
16796 TTTCTCTTTTTCTTTTCT
1 TTTCTCTTTTTCTTTTCT
16814 TTTCT-TTTCTTCTTTTCT
1 TTTCTCTTT-TTCTTTTCT
* *
16832 TAT-T-TTTTTCTCTTCT
1 TTTCTCTTTTTCTTTTCT
*
16848 TTTGTCTTTTTC-TTTCT
1 TTTCTCTTTTTCTTTTCT
16865 TTT
1 TTT
16868 TGCACTCCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
16 10 0.21
17 15 0.32
18 22 0.47
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (18 bp):
TTTCTCTTTTTCTTTTCT
Found at i:16867 original size:29 final size:28
Alignment explanation
Indices: 16795--16868 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
16785 CCTTGGCTTG
* *
16795 CTTTCTCTTTTTCTTTTCTTTTCTTTTCT
1 CTTTTTCTTTTT-TTTTCTCTTCTTTTCT
*
16824 -TCTTTTCTTATTTTTTTCTCTTCTTTTGT
1 CT-TTTTCTT-TTTTTTTCTCTTCTTTTCT
*
16853 CTTTTTCTTTCTTTTT
1 CTTTTTCTTTTTTTTT
16869 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 7 0.18
29 27 0.71
30 4 0.11
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.77
Consensus pattern (28 bp):
CTTTTTCTTTTTTTTTCTCTTCTTTTCT
Found at i:17616 original size:19 final size:20
Alignment explanation
Indices: 17575--17625 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
17565 GAAACCCCTT
* *
17575 TGAAAATATATGATTTTTGA
1 TGAAAATACATGATTTTTAA
17595 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
17614 TGAAGATACATG
1 TGAAAATACATG
17626 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:21273 original size:24 final size:24
Alignment explanation
Indices: 21229--21275 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21219 CTTCAAGCGG
**
21229 CATAACTGTTGGAACGTCAAAGGA
1 CATAACTGTTGGAACACCAAAGGA
21253 CATAACT-TGTGGAACACCAAAGG
1 CATAACTGT-TGGAACACCAAAGG
21276 TCACACCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (24 bp):
CATAACTGTTGGAACACCAAAGGA
Found at i:22461 original size:5 final size:5
Alignment explanation
Indices: 22451--22512 Score: 69
Period size: 5 Copynumber: 12.8 Consensus size: 5
22441 TGCTTTCTCT
22451 TTTTC TTTTC TTTT- TTTTC TTTTC TTTTC TTTTC --TTC TTTTC TGATTT-
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T--TTTC
*
22499 TTTTC TCTTC TTTT
1 TTTTC TTTTC TTTT
22513 GTCTTTTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
3 3 0.06
4 7 0.14
5 35 0.71
6 1 0.02
7 3 0.06
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:22469 original size:14 final size:14
Alignment explanation
Indices: 22450--22486 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
22440 TTGCTTTCTC
22450 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
22464 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
22478 TCTTTTCTT
1 T-TTTTCTT
22487 CTTTTCTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTCTTT
Found at i:22517 original size:10 final size:10
Alignment explanation
Indices: 22451--22529 Score: 53
Period size: 9 Copynumber: 8.4 Consensus size: 10
22441 TGCTTTCTCT
*
22451 TTTTCTTTTC
1 TTTTCTCTTC
*
22461 TTTT-TTTTC
1 TTTTCTCTTC
*
22470 TTTTCTTTTC
1 TTTTCTCTTC
22480 -TTT-TCTTC
1 TTTTCTCTTC
* *
22488 TTTTCTGATTT
1 TTTTCT-CTTC
22499 TTTTCTCTTC
1 TTTTCTCTTC
*
22509 TTTTGTC-T-
1 TTTTCTCTTC
22517 TTTTCT-TTC
1 TTTTCTCTTC
22526 TTTT
1 TTTT
22530 TGCACTCCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
8 10 0.18
9 20 0.36
10 18 0.32
11 8 0.14
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (10 bp):
TTTTCTCTTC
Found at i:22530 original size:10 final size:10
Alignment explanation
Indices: 22448--22528 Score: 50
Period size: 11 Copynumber: 8.1 Consensus size: 10
22438 GTTTGCTTTC
22448 TCTTTTTCTTT
1 TCTTTTTC-TT
22459 TCTTTTT-TT
1 TCTTTTTCTT
22468 TC-TTTTCTT
1 TCTTTTTCTT
22477 T-TCTTTTC-T
1 TCT-TTTTCTT
22486 TC-TTTTCTGAT
1 TCTTTTTCT--T
22497 T-TTTTTCTCT
1 TCTTTTTCT-T
22507 TCTTTTGTCTT
1 TCTTTT-TCTT
22518 T-TTCTTTCTT
1 TCTT-TTTCTT
22528 T
1 T
22529 TTGCACTCCA
Statistics
Matches: 58, Mismatches: 1, Indels: 23
0.71 0.01 0.28
Matches are distributed among these distances:
8 9 0.16
9 9 0.16
10 14 0.24
11 23 0.40
12 3 0.05
ACGTcount: A:0.01, C:0.19, G:0.02, T:0.78
Consensus pattern (10 bp):
TCTTTTTCTT
Found at i:22530 original size:18 final size:18
Alignment explanation
Indices: 22439--22531 Score: 56
Period size: 18 Copynumber: 5.2 Consensus size: 18
22429 CTTTTCTTAG
*
22439 TTTG-CTTTCTCTTT-TT
1 TTTGTCTTTTTCTTTCTT
22455 CTTT-TCTTTTT-TTTCTT
1 -TTTGTCTTTTTCTTTCTT
*
22472 TTCT-TTTCTTTTC-TTCTT
1 TT-TGTCT-TTTTCTTTCTT
*
22490 TTCTGATTTTTTTCTCTTC-T
1 TT-TG-TCTTTTTCT-TTCTT
22510 TTTGTCTTTTTCTTTCTT
1 TTTGTCTTTTTCTTTCTT
22528 TTTG
1 TTTG
22532 CACTCCAATT
Statistics
Matches: 63, Mismatches: 3, Indels: 19
0.74 0.04 0.22
Matches are distributed among these distances:
16 5 0.08
17 16 0.25
18 26 0.41
19 7 0.11
20 6 0.10
21 3 0.05
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTGTCTTTTTCTTTCTT
Found at i:23279 original size:19 final size:20
Alignment explanation
Indices: 23238--23288 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
23228 GAAACCCCTT
*
23238 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
23258 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
23277 TGAAGATACATG
1 TGAAAATACATG
23289 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:29881 original size:21 final size:21
Alignment explanation
Indices: 29842--29882 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29832 TAGGAGTCTT
*
29842 TTCTTTCTCTTTTTGTTTTTC
1 TTCTTTCTCTTTTTCTTTTTC
29863 TTCTTTCT-TTTTCTCTTTTT
1 TTCTTTCTCTTTT-TCTTTTT
29883 GTTGCTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (21 bp):
TTCTTTCTCTTTTTCTTTTTC
Found at i:30335 original size:13 final size:13
Alignment explanation
Indices: 30317--30374 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
30307 TAGGCGTGAA
30317 ATGGTGATGGAAG
1 ATGGTGATGGAAG
** *
30330 ATGGTGATGTTAT
1 ATGGTGATGGAAG
* *
30343 A-GGCG-T-GAAA
1 ATGGTGATGGAAG
30353 ATGGTGATGGAAG
1 ATGGTGATGGAAG
30366 ATGGTGATG
1 ATGGTGATG
30375 AACAGATAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 23 0.70
ACGTcount: A:0.29, C:0.02, G:0.41, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:30362 original size:36 final size:35
Alignment explanation
Indices: 30260--30375 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
30250 TTGTAAGGTA
* *
30260 ATGGTGATGATATAGGTGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
*
30295 ATAGTGATGATATAGGCGTGAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
*
30330 ATGGTGATGTTATAGGCGTGAAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATGGAAG
30366 ATGGTGATGA
1 ATGGTGATGA
30376 ACAGATAGTA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 50 0.68
36 24 0.32
ACGTcount: A:0.33, C:0.02, G:0.38, T:0.28
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
Found at i:34051 original size:16 final size:16
Alignment explanation
Indices: 34032--34072 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
34022 AGGATATGGT
34032 AATGAAATAAGAAAAA
1 AATGAAATAAGAAAAA
* * *
34048 AATGAAAGAATAAAGA
1 AATGAAATAAGAAAAA
34064 AATGAAATA
1 AATGAAATA
34073 GTAGGAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (16 bp):
AATGAAATAAGAAAAA
Found at i:34299 original size:6 final size:6
Alignment explanation
Indices: 34281--34322 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
34271 TGTAGGAGTC
*
34281 TTTTCT TTCTCT TTTTCT TTTTCT TCTTTCT TTTTCT CTTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT -TTTT
34323 TGTTGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 22 0.69
7 10 0.31
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:34309 original size:21 final size:21
Alignment explanation
Indices: 34283--34323 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34273 TAGGAGTCTT
34283 TTCTTTCTCTTTT-TCTTTTTC
1 TTCTTTCT-TTTTCTCTTTTTC
34304 TTCTTTCTTTTTCTCTTTTT
1 TTCTTTCTTTTTCTCTTTTT
34324 GTTGTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTCTTTCTTTTTCTCTTTTTC
Found at i:34741 original size:13 final size:12
Alignment explanation
Indices: 34701--34830 Score: 69
Period size: 13 Copynumber: 10.9 Consensus size: 12
34691 TTGTAAGGTA
*
34701 ATGGTGATG-AT
1 ATGGTGATGAAG
34712 ATAGGTG-TGAA-
1 AT-GGTGATGAAG
34723 ATGGTGATAGAAG
1 ATGGTGAT-GAAG
*
34736 ATGGTGATG-AT
1 ATGGTGATGAAG
*
34747 ATAGGCG-TGAA-
1 AT-GGTGATGAAG
34758 ATGGTGATAGAAG
1 ATGGTGAT-GAAG
*
34771 ATGGTAATGGAAG
1 ATGGTGAT-GAAG
**
34784 ATGGTGATG-TT
1 ATGGTGATGAAG
* *
34795 ATAGGCG-TGAAA
1 AT-GGTGATGAAG
34807 ATGGTGATGGAAG
1 ATGGTGAT-GAAG
34820 ATGGTGATGAA
1 ATGGTGATGAA
34831 CAGATAGTAT
Statistics
Matches: 92, Mismatches: 13, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
10 7 0.08
11 22 0.24
12 26 0.28
13 37 0.40
ACGTcount: A:0.34, C:0.02, G:0.38, T:0.27
Consensus pattern (12 bp):
ATGGTGATGAAG
Found at i:34746 original size:35 final size:35
Alignment explanation
Indices: 34701--34775 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
34691 TTGTAAGGTA
*
34701 ATGGTGATGATATAGGTGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
34736 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
34771 ATGGT
1 ATGGT
34776 AATGGAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.33, C:0.01, G:0.37, T:0.28
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
Found at i:34779 original size:19 final size:19
Alignment explanation
Indices: 34722--34780 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
34712 ATAGGTGTGA
34722 AATGGTGATAGAAGATGGT
1 AATGGTGATAGAAGATGGT
* * ** *
34741 GATGAT-ATAGGCG-T-GA
1 AATGGTGATAGAAGATGGT
34757 AATGGTGATAGAAGATGGT
1 AATGGTGATAGAAGATGGT
34776 AATGG
1 AATGG
34781 AAGATGGTGA
Statistics
Matches: 27, Mismatches: 10, Indels: 6
0.63 0.23 0.14
Matches are distributed among these distances:
16 5 0.19
17 6 0.22
18 6 0.22
19 10 0.37
ACGTcount: A:0.36, C:0.02, G:0.37, T:0.25
Consensus pattern (19 bp):
AATGGTGATAGAAGATGGT
Found at i:34798 original size:48 final size:49
Alignment explanation
Indices: 34723--34824 Score: 161
Period size: 48 Copynumber: 2.1 Consensus size: 49
34713 TAGGTGTGAA
*
34723 ATGGTGATAGAAGATGGTGATGATATAGGCGTG-AAATGGTGATAGAAG
1 ATGGTAATAGAAGATGGTGATGATATAGGCGTGAAAATGGTGATAGAAG
* * *
34771 ATGGTAATGGAAGATGGTGATGTTATAGGCGTGAAAATGGTGATGGAAG
1 ATGGTAATAGAAGATGGTGATGATATAGGCGTGAAAATGGTGATAGAAG
34820 ATGGT
1 ATGGT
34825 GATGAACAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 30 0.61
49 19 0.39
ACGTcount: A:0.33, C:0.02, G:0.38, T:0.26
Consensus pattern (49 bp):
ATGGTAATAGAAGATGGTGATGATATAGGCGTGAAAATGGTGATAGAAG
Found at i:34846 original size:49 final size:48
Alignment explanation
Indices: 34746--34846 Score: 132
Period size: 49 Copynumber: 2.1 Consensus size: 48
34736 ATGGTGATGA
* * *
34746 TATAGGCGTGAAATGGTGATAGAAGATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATAGAAGATGGTAATGAAAGATAGTGATCT
* *
34794 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGAACAGATAGT-ATCT
1 TATAGGCGTG-AAATGGTGATAGAAGATGGTAATGAA-AGATAGTGATCT
34843 TATA
1 TATA
34847 AAACTAAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 10 0.22
49 30 0.65
50 6 0.13
ACGTcount: A:0.35, C:0.04, G:0.34, T:0.28
Consensus pattern (48 bp):
TATAGGCGTGAAATGGTGATAGAAGATGGTAATGAAAGATAGTGATCT
Found at i:37550 original size:779 final size:779
Alignment explanation
Indices: 36053--37610 Score: 2674
Period size: 779 Copynumber: 2.0 Consensus size: 779
36043 ATAAAGAAAT
* *
36053 TGATGTGATCCGACTGAGCGTCAAAAATGGACTTGCATCTCCAACCTTTCTCAATATTCAAAGGG
1 TGATGTGATCCGACTCAGCATCAAAAATGGACTTGCATCTCCAACCTTTCTCAATATTCAAAGGG
36118 GGATTTTCTTTAACTTAATCTTTCTTTATACCATAGTTATGATAATAGCTTACATACATTATAAT
66 GGATTTTCTTTAACTTAATCTTTCTTTATACCATAGTTATGATAATAGCTTACATACATTATAAT
* *
36183 TATATTTATGATGATGATATTATGAATGTATGAAGTTATTGTTATGAACCACATATTTATATCTT
131 TATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATTATGAACCACATATTTATATCTT
36248 ATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTTCGGCCACATCATGGGAGCTGAC
196 ATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTTCGGCCACATCATGGGAGCTGAC
* *
36313 TTAAAGCTAGAATTGGAATCAATAAGCTAGGAAATCTTACATAGGATGACTCGGGAGATCATGAA
261 TTAAAGCTAGAATTGAAATCAATAAGCTAGGAAACCTTACATAGGATGACTCGGGAGATCATGAA
*
36378 GAACAAATGGTGAAAAGTTGCTAGTTGACCCCCGAGCTCATAGCTCACTTGAGCTGGACTTTTGA
326 GAACAAATGGTGAAAAGTTGCTAGCTGACCCCCGAGCTCATAGCTCACTTGAGCTGGACTTTTGA
* *
36443 GCTAGCTAGAGACTTCATTTCAGATGGAGAGTTGCACCATCATCTTCACCACATAGAGCACTACA
391 GCTAGCTAGAGACTTCATTTCAGATGGAGAGTTGCACCATCATCTTCACCACACAGACCACTACA
* *
36508 AATATGGTCTAGGTCGAATTTTATGAATTCGTACCTTTCCGCGAAGAGTTGCCATTCCGAGAAGT
456 AATATGGTCTAGGTCAAATTTTATGAATTCGTACCTTTCCGCGAAGAGTTGCCAATCCGAGAAGT
* * ** *
36573 GACTTTTCACAAGGAGTTGTCCTATGACTTGTACACATGTCCTTCATCTATGGCCAGCTCAACTT
521 GACCTTTCACAAGGAGCTGTCCTATGACTCATACACATGTCATTCATCTATGGCCAGCTCAACTT
36638 CAGCTCAAACTCATGGGAAGTAGCTCAAATGATGAAAGGTTGTTTCACACAAATGTGACCTTTCA
586 CAGCTCAAACTCATGGGAAGTAGCTCAAATGATGAAAGGTTGTTTCACACAAATGTGACCTTTCA
* *
36703 TAATTAGTTGCTGCCCCATTGATGCCATGTCACCTAGACACATGTTTGATGCCAAGTCATGCCTA
651 TAATTAGTTGCTGCCCCATTGATGCCAAGTCACCTAGACACATGTTTGATGCCAAGTCACGCCTA
** * * * * *
36768 AGTTTTTGTTCATCTTCACGCCATGGAGGAGTCCACGCCTTAAGCATTCTACACCATCCATGTG
716 AGTTGCTGTTCATCTACACACCATGGAAGAGTCCACGCCTTAAGCATTCAACACCAACCATGTG
* *
36832 TGATGTGATCCGATTCAGCATCAAAAATGGACTTGCATCTCCAACCTTTCTCAATGTTCAAAGGG
1 TGATGTGATCCGACTCAGCATCAAAAATGGACTTGCATCTCCAACCTTTCTCAATATTCAAAGGG
* *
36897 GGATTTTCTTTAACTTAATCTTTCTTTATACCATAGTTATGATAATGGCTTACATACATTATATT
66 GGATTTTCTTTAACTTAATCTTTCTTTATACCATAGTTATGATAATAGCTTACATACATTATAAT
36962 TATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATTATGAACCACATATTTATATCTT
131 TATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATTATGAACCACATATTTATATCTT
* *
37027 ATATTACTTAGCTTATAAATGCTTTCTTTTGTATGTACATGTTCGGCCACATCATGGGAGCTGAT
196 ATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTTCGGCCACATCATGGGAGCTGAC
* * *
37092 TTAAAGCTAGAATT-AAAGTCAATGAGCTAGGAAACCTTACATAGGATGACTTGGGAGATCTTGA
261 TTAAAGCTAGAATTGAAA-TCAATAAGCTAGGAAACCTTACATAGGATGACTCGGGAGATCATGA
*
37156 AGAACAAATGGTGAAAAGTTG-TCAGCTGACCCTCGAGCTCATAGCTCACTTGAGCTGGACTTTT
325 AGAACAAATGGTGAAAAGTTGCT-AGCTGACCCCCGAGCTCATAGCTCACTTGAGCTGGACTTTT
*
37220 GAGCTAGCTAGAGACTTCATTTCAGCTGGAGAGTTGCACCATCATCTTCACCACACAGACCACTA
389 GAGCTAGCTAGAGACTTCATTTCAGATGGAGAGTTGCACCATCATCTTCACCACACAGACCACTA
* *
37285 CAAATATGGTCTAGGTCAAATTTTGTGAATTCGTACCTTTTCGCGAAGAGTTGCCAATCCGAGAA
454 CAAATATGGTCTAGGTCAAATTTTATGAATTCGTACCTTTCCGCGAAGAGTTGCCAATCCGAGAA
* *
37350 GTGGCCTTTCACAAGGAGCTGTCCTATGACTCAT-CTTCATG-CAATTCATCTATGGCCAGCTCA
519 GTGACCTTTCACAAGGAGCTGTCCTATGACTCATAC-ACATGTC-ATTCATCTATGGCCAGCTCA
*
37413 TCTTCAGCTCAAACTCATGGGAAGTAGCTCAAATGATGAAAGGTTGTTTCACACAAATGTGACCT
582 ACTTCAGCTCAAACTCATGGGAAGTAGCTCAAATGATGAAAGGTTGTTTCACACAAATGTGACCT
37478 TTCATAATTAGTTGCTGCCCCATTGATGCCAAGTCACCTAGACACATGTTTGATGCCAAGTCACG
647 TTCATAATTAGTTGCTGCCCCATTGATGCCAAGTCACCTAGACACATGTTTGATGCCAAGTCACG
*
37543 CCTAAGTTGCTGTTCATCTACACACCATGGAAGAGTCCACGCCTTAAGCATTCAACGCCAACCAT
712 CCTAAGTTGCTGTTCATCTACACACCATGGAAGAGTCCACGCCTTAAGCATTCAACACCAACCAT
37608 GTG
777 GTG
37611 AGTGCCACAT
Statistics
Matches: 733, Mismatches: 42, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
778 5 0.01
779 728 0.99
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (779 bp):
TGATGTGATCCGACTCAGCATCAAAAATGGACTTGCATCTCCAACCTTTCTCAATATTCAAAGGG
GGATTTTCTTTAACTTAATCTTTCTTTATACCATAGTTATGATAATAGCTTACATACATTATAAT
TATAGTTATGATGATGATATTATGAATGTATGAAGTTATTATTATGAACCACATATTTATATCTT
ATATTACTTAGCTTATAAATGCTTTCTTTTGTAGGTACATGTTCGGCCACATCATGGGAGCTGAC
TTAAAGCTAGAATTGAAATCAATAAGCTAGGAAACCTTACATAGGATGACTCGGGAGATCATGAA
GAACAAATGGTGAAAAGTTGCTAGCTGACCCCCGAGCTCATAGCTCACTTGAGCTGGACTTTTGA
GCTAGCTAGAGACTTCATTTCAGATGGAGAGTTGCACCATCATCTTCACCACACAGACCACTACA
AATATGGTCTAGGTCAAATTTTATGAATTCGTACCTTTCCGCGAAGAGTTGCCAATCCGAGAAGT
GACCTTTCACAAGGAGCTGTCCTATGACTCATACACATGTCATTCATCTATGGCCAGCTCAACTT
CAGCTCAAACTCATGGGAAGTAGCTCAAATGATGAAAGGTTGTTTCACACAAATGTGACCTTTCA
TAATTAGTTGCTGCCCCATTGATGCCAAGTCACCTAGACACATGTTTGATGCCAAGTCACGCCTA
AGTTGCTGTTCATCTACACACCATGGAAGAGTCCACGCCTTAAGCATTCAACACCAACCATGTG
Found at i:38208 original size:33 final size:33
Alignment explanation
Indices: 38129--38232 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
38119 ATACAATCTG
* *
38129 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
38165 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
38198 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
38231 TC
1 TC
38233 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:42680 original size:33 final size:33
Alignment explanation
Indices: 42601--42704 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
42591 ATACAATCTG
* *
42601 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
42637 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
42670 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
42703 TC
1 TC
42705 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:43565 original size:36 final size:35
Alignment explanation
Indices: 43525--43603 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
43515 ACTATCTATT
* *
43525 CATCACCACCTTCCATCACCATTTTCACGCCTATAA
1 CATCACCACATTCCATCACCA-TATCACGCCTATAA
* * * *
43561 CATCACCATATTCCATTACTATATCACGCCTATAT
1 CATCACCACATTCCATCACCATATCACGCCTATAA
*
43596 TATCACCA
1 CATCACCA
43604 ACTTATAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 19 0.53
36 17 0.47
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.30
Consensus pattern (35 bp):
CATCACCACATTCCATCACCATATCACGCCTATAA
Found at i:44068 original size:14 final size:15
Alignment explanation
Indices: 44045--44088 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
44035 TTTGGAGTGC
44045 AAAAGAAAGAAAATA
1 AAAAGAAAGAAAATA
*
44060 AAAAG-AAGAAAATC
1 AAAAGAAAGAAAATA
44074 AAAAGCAAAAGAAAA
1 AAAAG--AAAGAAAA
44089 GTGAAGCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 13 0.52
15 5 0.20
17 7 0.28
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAGAAAGAAAATA
Found at i:47946 original size:36 final size:35
Alignment explanation
Indices: 47906--47975 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 35
47896 ACTATCTATT
* *
47906 CATCACCACCTTCCATCACCATTTTCACGCCTATAA
1 CATCACCACATTCCATCACCA-TATCACGCCTATAA
* * *
47942 CATCACCATATTCCATTACTATATCACGCCTATA
1 CATCACCACATTCCATCACCATATCACGCCTATA
47976 TTATAACCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.30
Consensus pattern (35 bp):
CATCACCACATTCCATCACCATATCACGCCTATAA
Found at i:51715 original size:23 final size:25
Alignment explanation
Indices: 51689--51743 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
51679 AAATCCAGCA
*
51689 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAACACTCAAAGAGG
* *
51712 AAGAAATTGAAAACACTCAAAGAGG
1 AAGAAAATCAAAACACTCAAAGAGG
51737 AAGAAAA
1 AAGAAAA
51744 AAGAAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 7 0.27
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAACACTCAAAGAGG
Found at i:54525 original size:11 final size:13
Alignment explanation
Indices: 54493--54522 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54483 TGGCCAAAGA
54493 TGAAAAGGTATGT
1 TGAAAAGGTATGT
54506 TGAAAAGGTATG-
1 TGAAAAGGTATGT
54518 TGAAA
1 TGAAA
54523 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:58047 original size:23 final size:23
Alignment explanation
Indices: 58008--58083 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
57998 AAAATCAGTA
*
58008 AAGAAATTG-AAGCACTCAGAAG
1 AAGAAATTGAAAGCACTCAAAAG
58030 AAGAAATTGAAAGCACTCAAAAG
1 AAGAAATTGAAAGCACTCAAAAG
58053 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAATTGAAAGCACTC-AAAA-G
58078 AAGAAA
1 AAGAAA
58084 AAGAAAAGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
22 9 0.18
23 30 0.60
24 4 0.08
25 7 0.14
ACGTcount: A:0.57, C:0.12, G:0.20, T:0.12
Consensus pattern (23 bp):
AAGAAATTGAAAGCACTCAAAAG
Found at i:64659 original size:33 final size:33
Alignment explanation
Indices: 64615--64683 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
64605 CATCACCATA
*
64615 TTCCATCACCATATCA-CGCCAGTAACATCATCC
1 TTCCATCACCATATCATCACCAGTAA-ATCATCC
* * *
64648 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAGTAAATCATCC
64681 TTC
1 TTC
64684 ATTTATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.29, C:0.36, G:0.03, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAGTAAATCATCC
Found at i:70866 original size:2 final size:2
Alignment explanation
Indices: 70854--70890 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
70844 ACATCAAACT
*
70854 TA TA TA GA 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
70891 TATTCCGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:72897 original size:22 final size:20
Alignment explanation
Indices: 72872--72911 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
72862 CATGTTTGTT
72872 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
72894 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
72912 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:73845 original size:177 final size:179
Alignment explanation
Indices: 73544--73901 Score: 654
Period size: 177 Copynumber: 2.0 Consensus size: 179
73534 TCCCAAATAT
73544 CACCTTGTTCGTAGAAAACCTTTCATTTTCCAGCATTGAAACCATCATGTTTCTCTATGAAGAAG
1 CACCTTGTTCGTAGAAAACCTTTCATTTTCCAGCATTGAAACCATCATGTTTCTCTATGAAGAAG
73609 TTTGGTTTCTTGTTTGTTCCTCTTCATTCTTGTCGGGGTTTTGTCTTTGCGCCATGCTTGTACAC
66 TTTGGTTTCTTGTTTGTTCCTCTTCATTCTTGTCGGGGTTTTGTCTTTGCGCCATGCTTGTACAC
73674 TCTTTCTCATATGCAACTGATCTTG-TGCACTTCTTTGGG-GTTAAAGG
131 TCTTTCTCATATGCAACTGATCTTGTTGCACTTCTTTGGGCGTTAAAGG
73721 CACCATTGTTCGTAGAAAACCTTTCATTTTCCAGCATTG-AACCATCATG-TT-TCTATGAAGAA
1 CACC-TTGTTCGTAGAAAACCTTTCATTTTCCAGCATTGAAACCATCATGTTTCTCTATGAAGAA
73783 GTTTGGTTTCTTGTTTTGTTCCTCTTCATTCTTTGTCGGGGTTTTGTCTTTGCGCCATGCTTGTA
65 GTTTGGTTTCTTG-TTTGTTCCTCTTCATTC-TTGTCGGGGTTTTGTCTTTGCGCCATGCTTGTA
73848 CACTCTTTCTCATATGCAACTGATCTTGTTGCACTTCTTTGGGCGTTAAAGG
128 CACTCTTTCTCATATGCAACTGATCTTGTTGCACTTCTTTGGGCGTTAAAGG
73900 CA
1 CA
73902 TCAAGGTCAC
Statistics
Matches: 176, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
175 24 0.14
176 19 0.11
177 75 0.43
178 48 0.27
179 10 0.06
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (179 bp):
CACCTTGTTCGTAGAAAACCTTTCATTTTCCAGCATTGAAACCATCATGTTTCTCTATGAAGAAG
TTTGGTTTCTTGTTTGTTCCTCTTCATTCTTGTCGGGGTTTTGTCTTTGCGCCATGCTTGTACAC
TCTTTCTCATATGCAACTGATCTTGTTGCACTTCTTTGGGCGTTAAAGG
Found at i:77435 original size:20 final size:20
Alignment explanation
Indices: 77410--77449 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
77400 ATATTCTTAT
77410 CATATATATA-TATATAATAA
1 CATATATATACTA-ATAATAA
77430 CATATATATACTAATAATAA
1 CATATATATACTAATAATAA
77450 GTAAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
CATATATATACTAATAATAA
Found at i:77436 original size:16 final size:17
Alignment explanation
Indices: 77415--77446 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
77405 CTTATCATAT
77415 ATATATATA-TAATAAC
1 ATATATATACTAATAAC
77431 ATATATATACTAATAA
1 ATATATATACTAATAA
77447 TAAGTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATATACTAATAAC
Found at i:79577 original size:20 final size:19
Alignment explanation
Indices: 79539--79578 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
79529 TAAGATAATG
* *
79539 TATGAAGCTTATGAGCTAA
1 TATGAAGCATATGAACTAA
79558 TATGAATGCATATGAACTAA
1 TATGAA-GCATATGAACTAA
79578 T
1 T
79579 GAAATGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (19 bp):
TATGAAGCATATGAACTAA
Found at i:84511 original size:33 final size:33
Alignment explanation
Indices: 84469--84537 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
84459 GTTGATGAAT
*
84469 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
84502 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
84535 GAA
1 GAA
84538 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:88977 original size:33 final size:33
Alignment explanation
Indices: 88935--89003 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
88925 GTTGATGAAT
*
88935 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
88968 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
89001 GAA
1 GAA
89004 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:90760 original size:19 final size:20
Alignment explanation
Indices: 90713--90763 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
90703 GAAACCCCTT
**
90713 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
90733 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
90752 TGAAGATACATG
1 TGAAAATACATG
90764 CTCTTCCCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:96666 original size:19 final size:20
Alignment explanation
Indices: 96642--96692 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
96632 CGGCCAAGAG
* *
96642 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
96661 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
96681 CAAGTATTTTCA
1 CATGTATTTTCA
96693 AAGGGGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:99233 original size:13 final size:12
Alignment explanation
Indices: 99211--99284 Score: 85
Period size: 13 Copynumber: 5.7 Consensus size: 12
99201 ATTAGAGTGC
99211 AAAAAGAAAAGA
1 AAAAAGAAAAGA
*
99223 AAATCAGAAAAGA
1 AAA-AAGAAAAGA
99236 AGAAAAGAAAAGA
1 A-AAAAGAAAAGA
99249 AAAATCAGAAAAGA
1 AAAA--AGAAAAGA
99263 AGAAAAGAAAAGA
1 A-AAAAGAAAAGA
99276 AAAAGAGAA
1 AAAA-AGAA
99285 GTTCAAAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
12 9 0.17
13 31 0.57
14 11 0.20
15 3 0.06
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:99252 original size:27 final size:27
Alignment explanation
Indices: 99212--99279 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
99202 TTAGAGTGCA
99212 AAAAGAAAAG-AAAATCAGAAAAGAAG
1 AAAAGAAAAGAAAAATCAGAAAAGAAG
99238 AAAAGAAAAGAAAAATCAGAAAAGAAG
1 AAAAGAAAAGAAAAATCAGAAAAGAAG
99265 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
99280 GAGAAGTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 10 0.24
27 31 0.76
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (27 bp):
AAAAGAAAAGAAAAATCAGAAAAGAAG
Found at i:99299 original size:32 final size:32
Alignment explanation
Indices: 99212--99278 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
99202 TTAGAGTGCA
99212 AAAAGAAAAG-AAAATCAG--AA-AAG--AAG
1 AAAAGAAAAGAAAAATCAGAAAAGAAGAAAAG
99238 AAAAGAAAAGAAAAATCAGAAAAGAAGAAAAG
1 AAAAGAAAAGAAAAATCAGAAAAGAAGAAAAG
99270 AAAAGAAAA
1 AAAAGAAAA
99279 AGAGAAGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 10 0.29
27 8 0.23
29 2 0.06
30 3 0.09
32 12 0.34
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (32 bp):
AAAAGAAAAGAAAAATCAGAAAAGAAGAAAAG
Found at i:99300 original size:6 final size:5
Alignment explanation
Indices: 99212--99278 Score: 54
Period size: 5 Copynumber: 13.8 Consensus size: 5
99202 TTAGAGTGCA
**
99212 AAAAG AAAAG AAAATCAG AAAAG --AAG AAAAG AAAAG AAAA- ATCAG
1 AAAAG AAAAG -AAA--AG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
99257 AAAAG --AAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAA
99279 AGAGAAGTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
3 6 0.12
4 2 0.04
5 34 0.68
6 3 0.06
7 3 0.06
8 2 0.04
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:102470 original size:19 final size:20
Alignment explanation
Indices: 102446--102496 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
102436 CGGCCAAGAG
* *
102446 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
102465 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
102485 CATGTATTTTCA
1 CATGTATTTTCA
102497 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:112413 original size:20 final size:18
Alignment explanation
Indices: 112390--112454 Score: 50
Period size: 19 Copynumber: 3.8 Consensus size: 18
112380 TTTTTTGAAA
*
112390 TTTTGGCTTTTTTGGCTCT
1 TTTTTGCTTTTTTGGC-CT
* *
112409 TTTTTGTTTTTTTTGCC-
1 TTTTTGCTTTTTTGGCCT
112426 TTTTT--TTTTTT-GCCTT
1 TTTTTGCTTTTTTGGCC-T
112442 TTTTTG-TTTTTTG
1 TTTTTGCTTTTTTG
112455 TTTTTTTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 3 0.08
15 6 0.15
16 5 0.13
17 11 0.28
18 1 0.03
19 13 0.33
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.75
Consensus pattern (18 bp):
TTTTTGCTTTTTTGGCCT
Found at i:112434 original size:14 final size:14
Alignment explanation
Indices: 112415--112451 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
112405 CTCTTTTTTG
112415 TTTTTTTTGCCTTT
1 TTTTTTTTGCCTTT
112429 TTTTTTTTGCCTTT
1 TTTTTTTTGCCTTT
112443 TTTTGTTTT
1 TTTT-TTTT
112452 TTGTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (14 bp):
TTTTTTTTGCCTTT
Found at i:120125 original size:19 final size:19
Alignment explanation
Indices: 120101--120142 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
120091 GAAACCCCTT
*
120101 TGAAAA-ACATGATTTTTAA
1 TGAAAATACAT-AATTTTAA
120120 TGAAAATACATAATTTTAA
1 TGAAAATACATAATTTTAA
120139 TGAA
1 TGAA
120143 GATAAATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (19 bp):
TGAAAATACATAATTTTAA
Found at i:126080 original size:17 final size:16
Alignment explanation
Indices: 126058--126092 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
126048 TGTAGGAGTC
126058 TTTTCTTTTCTCTTTTG
1 TTTTCTTTT-TCTTTTG
*
126075 TTTTCTTTTTTTTTTG
1 TTTTCTTTTTCTTTTG
126091 TT
1 TT
126093 GCTTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTG
Found at i:126481 original size:33 final size:33
Alignment explanation
Indices: 126417--126517 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
126407 CTTGTTGATG
* * *
126417 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
126449 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
126482 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
126518 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:130924 original size:33 final size:33
Alignment explanation
Indices: 130860--130960 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
130850 CTTGTTGATG
* * *
130860 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
130892 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
130925 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
130961 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:134178 original size:22 final size:24
Alignment explanation
Indices: 134151--134203 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
134141 AAAATCAGCA
*
134151 AAGAAATTGCAAG-ACT-CAAAAG
1 AAGAAATTGCAAGCACTAAAAAAG
134173 AAGAAAATTGCAAGCACTAAAAAAG
1 AAG-AAATTGCAAGCACTAAAAAAG
134198 AAGAAA
1 AAGAAA
134204 AAAAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 10 0.37
24 6 0.22
25 8 0.30
ACGTcount: A:0.60, C:0.11, G:0.17, T:0.11
Consensus pattern (24 bp):
AAGAAATTGCAAGCACTAAAAAAG
Found at i:134182 original size:23 final size:25
Alignment explanation
Indices: 134154--134204 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
134144 ATCAGCAAAG
*
134154 AAATTGCAAG-ACT-CAAAAGAAGA
1 AAATTGCAAGCACTAAAAAAGAAGA
134177 AAATTGCAAGCACTAAAAAAGAAGA
1 AAATTGCAAGCACTAAAAAAGAAGA
134202 AAA
1 AAA
134205 AAAAGAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 10 0.40
24 3 0.12
25 12 0.48
ACGTcount: A:0.61, C:0.12, G:0.16, T:0.12
Consensus pattern (25 bp):
AAATTGCAAGCACTAAAAAAGAAGA
Found at i:138955 original size:23 final size:25
Alignment explanation
Indices: 138919--138974 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
138909 AAAATTCAGC
138919 AAAGAAAATCAAAGCACTC-AAAAG
1 AAAGAAAATCAAAGCACTCAAAAAG
* *
138943 -AAGAAATTGAAAGCACTCAAAAAG
1 AAAGAAAATCAAAGCACTCAAAAAG
138967 AAAGAAAA
1 AAAGAAAA
138975 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.59
24 5 0.19
25 6 0.22
ACGTcount: A:0.64, C:0.12, G:0.14, T:0.09
Consensus pattern (25 bp):
AAAGAAAATCAAAGCACTCAAAAAG
Found at i:138976 original size:10 final size:10
Alignment explanation
Indices: 138961--138991 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
138951 GAAAGCACTC
138961 AAAAAGAAAG
1 AAAAAGAAAG
138971 AAAAAGAAAAG
1 AAAAAG-AAAG
138982 AAAAAGAAAG
1 AAAAAGAAAG
138992 TTGAAGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:140453 original size:36 final size:36
Alignment explanation
Indices: 140406--140510 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
140396 GATACAATCT
140406 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
140442 GTCCATCACCATCATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
140478 TTCCACCACCA-TATCACGCTTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
140511 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:146135 original size:24 final size:24
Alignment explanation
Indices: 146081--146135 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
146071 AAAAAATCAG
*
146081 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
146104 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
146128 AAAAGAAA
1 AAAAGAAA
146136 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:148914 original size:11 final size:13
Alignment explanation
Indices: 148882--148911 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
148872 TGGCCAAAGA
148882 TGAAAAGGTATGT
1 TGAAAAGGTATGT
148895 TGAAAAGGTATG-
1 TGAAAAGGTATGT
148907 TGAAA
1 TGAAA
148912 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:153780 original size:15 final size:15
Alignment explanation
Indices: 153760--153795 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
153750 ATTATTAGCT
*
153760 TTATAATATATGTTA
1 TTATAATATATATTA
153775 TTATAATATATATTA
1 TTATAATATATATTA
*
153790 TGATAA
1 TTATAA
153796 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:163516 original size:28 final size:28
Alignment explanation
Indices: 163484--163537 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
163474 TGAATTAACT
163484 AAACAAATGATGAACATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
163512 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
163538 TGAATGTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:166297 original size:26 final size:25
Alignment explanation
Indices: 166256--166314 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
166246 CTTTCTTTTC
*
166256 TTTTCTTTTTTTAATTTTCCGAATT
1 TTTTTTTTTTTTAATTTTCCGAATT
*
166281 TGTTTTTTTTTTTAATTTTCGGAATT
1 T-TTTTTTTTTTTAATTTTCCGAATT
166307 TTTTTTTT
1 TTTTTTTT
166315 CAGGATGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.73
Consensus pattern (25 bp):
TTTTTTTTTTTTAATTTTCCGAATT
Found at i:167896 original size:28 final size:28
Alignment explanation
Indices: 167864--167945 Score: 164
Period size: 28 Copynumber: 2.9 Consensus size: 28
167854 TGAATTAACT
167864 AAACAAATGATGAACATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
167892 AAACAAATGATGAACATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
167920 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
167946 AGAATGTGAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:169731 original size:19 final size:21
Alignment explanation
Indices: 169707--169758 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
169697 CGGCCAAGAG
*
169707 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
169726 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
169747 CATGTATTTTCA
1 CATGTATTTTCA
169759 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:170525 original size:21 final size:22
Alignment explanation
Indices: 170468--170526 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
170458 GAGTGCAAAA
*
170468 AGAAAGAAAAAGACAAAAGAAG
1 AGAAAGAAAAAGAGAAAAGAAG
**
170490 AGAAA-AAAATCAGAAAAGAAG
1 AGAAAGAAAAAGAGAAAAGAAG
170511 A-AAAGAAAAAGAGAAA
1 AGAAAGAAAAAGAGAAA
170527 GCAAGCCAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 3 0.10
21 23 0.74
22 5 0.16
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (22 bp):
AGAAAGAAAAAGAGAAAAGAAG
Found at i:173884 original size:33 final size:33
Alignment explanation
Indices: 173842--173910 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
173832 GTTGATGAAT
*
173842 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
173875 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
173908 GAA
1 GAA
173911 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:185238 original size:33 final size:35
Alignment explanation
Indices: 185200--185280 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
185190 ATGGTGATGA
* * *
185200 AATGGTAATGGA-A-GGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGG-TGATGATATAGGCGTGAT
185234 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
185269 AATGGTGATGGA
1 AATGGTGATGGA
185281 CAGATTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
33 9 0.22
34 1 0.03
35 18 0.45
36 12 0.30
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:187654 original size:33 final size:33
Alignment explanation
Indices: 187590--187690 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
187580 CTTGTTGATG
* * *
187590 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
187622 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
187655 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
187691 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:191662 original size:17 final size:16
Alignment explanation
Indices: 191640--191674 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
191630 TTGTAGAGTC
191640 TTTTCTTTTCTCTTTTG
1 TTTTCTTTT-TCTTTTG
*
191657 TTTTCTTTTTTTTTTG
1 TTTTCTTTTTCTTTTG
191673 TT
1 TT
191675 GCTTTGTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTG
Done.