Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000265.1 Hibiscus syriacus cultivar Beakdansim tig00000488_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: 159973
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:6857 original size:4 final size:4
Alignment explanation
Indices: 6848--6874 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6838 ACTGTTCAAC
6848 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
6875 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:7221 original size:21 final size:21
Alignment explanation
Indices: 7188--7242 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
7178 TTCCAACTTT
*
7188 TTTTATGTCTTAA-AGATATTTA
1 TTTTAT-TTTTAAGAGATA-TTA
*
7210 TGTTT-TTTTTAAGTGATATTA
1 T-TTTATTTTTAAGAGATATTA
7231 TTTTATTTTTAA
1 TTTTATTTTTAA
7243 TGTTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 6 0.21
23 3 0.11
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTATTTTTAAGAGATATTA
Found at i:7228 original size:22 final size:21
Alignment explanation
Indices: 7202--7242 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
7192 ATGTCTTAAA
7202 GATATTTATGTTT-TTTTTAAGT
1 GATA-TTAT-TTTATTTTTAAGT
7224 GATATTATTTTATTTTTAA
1 GATATTATTTTATTTTTAA
7243 TGTTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 11 0.61
22 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (21 bp):
GATATTATTTTATTTTTAAGT
Found at i:10712 original size:26 final size:25
Alignment explanation
Indices: 10630--10712 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
10620 TTATATTTTG
*
10630 TTATAGTTTAAATTGATATAATTCA
1 TTATAGTTTAAATTGATATGATTCA
* * * * *
10655 TACATAGTAATAAATT-TTTTGAATTTA
1 T-TATAGT-TTAAATTGATATG-ATTCA
10682 TTATAGTTTAAATTGATATGATTCA
1 TTATAGTTTAAATTGATATGATTCA
10707 TGTATA
1 T-TATA
10713 AAAGTGTAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 9
0.68 0.18 0.15
Matches are distributed among these distances:
25 12 0.29
26 19 0.45
27 11 0.26
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.48
Consensus pattern (25 bp):
TTATAGTTTAAATTGATATGATTCA
Found at i:13774 original size:15 final size:16
Alignment explanation
Indices: 13756--13793 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
13746 TTTTAATATA
13756 AAATATTATT-TAAAT
1 AAATATTATTATAAAT
*
13771 AAATATTATTATTAAT
1 AAATATTATTATAAAT
13787 -AATATTA
1 AAATATTA
13794 AAAAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTATTATAAAT
Found at i:13783 original size:18 final size:17
Alignment explanation
Indices: 13747--13780 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
13737 ATTAAATAAT
13747 TTTAATATAAAATATTA
1 TTTAATATAAAATATTA
13764 TTTAA-AT-AAATATTA
1 TTTAATATAAAATATTA
13779 TT
1 TT
13781 ATTAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 2 0.12
17 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATATAAAATATTA
Found at i:14921 original size:30 final size:30
Alignment explanation
Indices: 14887--14950 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
14877 TTAATTTAAA
* * *
14887 AATAGTTTATCGTTGTTATTGATGAAAACC
1 AATAGGTTATAGTTATTATTGATGAAAACC
* *
14917 AATAGGTTGTAGTTATTGTTGATGAAAACC
1 AATAGGTTATAGTTATTATTGATGAAAACC
14947 AATA
1 AATA
14951 AGTTGTAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (30 bp):
AATAGGTTATAGTTATTATTGATGAAAACC
Found at i:14931 original size:27 final size:28
Alignment explanation
Indices: 14901--14957 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
14891 GTTTATCGTT
*
14901 GTTA-TTGATGAAAACCAATAGGTTGTA
1 GTTATTTGATGAAAACCAATAAGTTGTA
14928 GTTATTGTTGATGAAAACCAATAAGTTGTA
1 GTTA-T-TTGATGAAAACCAATAAGTTGTA
14958 ATAACTATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
30 22 0.85
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (28 bp):
GTTATTTGATGAAAACCAATAAGTTGTA
Found at i:25405 original size:24 final size:23
Alignment explanation
Indices: 25378--25465 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 23
25368 ATTTCCGACT
25378 TGAATTCTGTTCTGATACATGAC
1 TGAATTCTGTTCTGATACATGAC
*
25401 GTGAATTCTGTTCTGATTTC-TGATC
1 -TGAATTCTGTTCTGA-TACATGA-C
* * *
25426 TGGATTCTGTTCTGATATATGTTC
1 TGAATTCTGTTCTGATACATG-AC
*
25450 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
25466 TTCTGATATC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.02
24 49 0.92
25 3 0.06
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACATGAC
Found at i:25427 original size:12 final size:12
Alignment explanation
Indices: 25406--25470 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
25396 ATGACGTGAA
25406 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
25418 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
25430 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* * *
25442 ATATGTTCTGAA
1 TTCTGTTCTGAT
*
25454 TTCTGTTTTGAT
1 TTCTGTTCTGAT
25466 TTCTG
1 TTCTG
25471 ATATCTCCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:25469 original size:48 final size:49
Alignment explanation
Indices: 25364--25472 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 49
25354 AAATATTTTA
*
25364 TTTGATTTCCGA-CTTGAATTCTGTTCTGATACATGACGTGAATTCTGT
1 TTTGATTTCTGATCTTGAATTCTGTTCTGATACATGACGTGAATTCTGT
* * * *
25412 TCTGATTTCTGATC-TGGATTCTGTTCTGATATATGTTC-TGAATTCTGT
1 TTTGATTTCTGATCTTGAATTCTGTTCTGATACATG-ACGTGAATTCTGT
25460 TTTGATTTCTGAT
1 TTTGATTTCTGAT
25473 ATCTCCGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 51 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.49
Consensus pattern (49 bp):
TTTGATTTCTGATCTTGAATTCTGTTCTGATACATGACGTGAATTCTGT
Found at i:26597 original size:19 final size:19
Alignment explanation
Indices: 26573--26612 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
26563 GATATTTTAG
26573 GACATCTTCAGTGTAAATT
1 GACATCTTCAGTGTAAATT
26592 GACATCTTCAGTGTAAATT
1 GACATCTTCAGTGTAAATT
26611 GA
1 GA
26613 AGACACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (19 bp):
GACATCTTCAGTGTAAATT
Found at i:27379 original size:10 final size:9
Alignment explanation
Indices: 27364--27397 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
27354 AACGCTGGAA
27364 ACCGGTTTTG
1 ACCGG-TTTG
*
27374 ACCGGTTTA
1 ACCGGTTTG
27383 ACCGGTTTG
1 ACCGGTTTG
27392 ACCGGT
1 ACCGGT
27398 CACGACCCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:27456 original size:13 final size:13
Alignment explanation
Indices: 27410--27456 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
27400 CGACCCGTTT
*
27410 ACCCGTTTACCCG
1 ACCCGTTGACCCG
27423 ACCCGTTGACCCG
1 ACCCGTTGACCCG
27436 ACCC---GACCCG
1 ACCCGTTGACCCG
27446 ACCCGTTGACC
1 ACCCGTTGACC
27457 GTTGACCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.17, C:0.49, G:0.19, T:0.15
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:27525 original size:29 final size:29
Alignment explanation
Indices: 27465--27539 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
27455 CCGTTGACCA
*** *
27465 GTGCTATTATGGGAATTAATTCGGTTTTG
1 GTGCTATTATGGGAATTAATTCGAAATGG
*
27494 GTGCTATTCTGGGAATTAATTCGAAATGG
1 GTGCTATTATGGGAATTAATTCGAAATGG
* *
27523 GTGCTATTTTGGTAATT
1 GTGCTATTATGGGAATT
27540 TTTTAAAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.43
Consensus pattern (29 bp):
GTGCTATTATGGGAATTAATTCGAAATGG
Found at i:35508 original size:3 final size:3
Alignment explanation
Indices: 35500--35541 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
35490 TTAGCTTCCG
35500 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35542 GATATAATGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36570 original size:18 final size:18
Alignment explanation
Indices: 36544--36579 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36534 TCGAAAGGAC
*
36544 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
36562 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
36580 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:37744 original size:24 final size:24
Alignment explanation
Indices: 37717--37811 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
37707 ATTTCCGACT
** *
37717 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
37741 TGAAATT-TGTTCTGATTTCTGATC
1 TG-AATTCTGTTCTGATATCTGATC
* *
37765 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
37789 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
37812 ATCTTCGTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
23 3 0.05
24 51 0.88
25 4 0.07
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:37766 original size:12 final size:12
Alignment explanation
Indices: 37748--37809 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
37738 ACCTGAAATT
37748 TGTTCTGATTTC
1 TGTTCTGATTTC
*
37760 TGATCTGGA-TTC
1 TGTTCT-GATTTC
*
37772 TGTTCTGATATC
1 TGTTCTGATTTC
*
37784 TGTTCTGAATTC
1 TGTTCTGATTTC
*
37796 TGTTTTGATTTC
1 TGTTCTGATTTC
37808 TG
1 TG
37810 ATATCTTCGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.13, C:0.15, G:0.19, T:0.53
Consensus pattern (12 bp):
TGTTCTGATTTC
Found at i:37792 original size:48 final size:49
Alignment explanation
Indices: 37703--37811 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 49
37693 AAATATTTTA
*
37703 TCTGATTTCCGA-CTTGAATTCTGTTCTGATAAATGACCTGAAATT-TGT
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATAAATGACCTG-AATTCTGT
* ** **
37751 TCTGATTTCTGATC-TGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
*
37799 TTTGATTTCTGAT
1 TCTGATTTCTGAT
37812 ATCTTCGTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 4 0.08
48 47 0.90
49 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:40196 original size:3 final size:3
Alignment explanation
Indices: 40188--40235 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
40178 TTAGCTTCCG
40188 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40236 GATATAATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41269 original size:18 final size:18
Alignment explanation
Indices: 41243--41278 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41233 TCGAAAGGAC
*
41243 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
41261 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
41279 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:42446 original size:24 final size:24
Alignment explanation
Indices: 42419--42513 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
42409 ATTTTCGACT
** *
42419 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
42443 TGAAATT-TGTTCTGATTTCTGATC
1 TG-AATTCTGTTCTGATATCTGATC
* *
42467 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
42491 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
42514 ATCTTCGTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
23 3 0.05
24 51 0.88
25 4 0.07
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:42468 original size:12 final size:12
Alignment explanation
Indices: 42450--42511 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
42440 ACCTGAAATT
42450 TGTTCTGATTTC
1 TGTTCTGATTTC
*
42462 TGATCTGGA-TTC
1 TGTTCT-GATTTC
*
42474 TGTTCTGATATC
1 TGTTCTGATTTC
*
42486 TGTTCTGAATTC
1 TGTTCTGATTTC
*
42498 TGTTTTGATTTC
1 TGTTCTGATTTC
42510 TG
1 TG
42512 ATATCTTCGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.13, C:0.15, G:0.19, T:0.53
Consensus pattern (12 bp):
TGTTCTGATTTC
Found at i:42494 original size:48 final size:48
Alignment explanation
Indices: 42422--42513 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
42412 TTCGACTTGA
42422 ATTCTGTTCTGATAAATGACCTGAAATT-TGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATAAATGACCTG-AATTCTGTTCTGATTTCTGATCTGG
** ** *
42470 ATTCTGTTCTGATATCTGTTCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGAT
42514 ATCTTCGTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 4 0.11
48 34 0.89
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:42678 original size:2 final size:2
Alignment explanation
Indices: 42671--42695 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42661 TGGGATGGGG
42671 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 T
42696 GTTTTAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44912 original size:3 final size:3
Alignment explanation
Indices: 44904--44981 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
44894 TTAGCTTCCG
44904 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44952 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44982 GATATAATGG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:46016 original size:18 final size:18
Alignment explanation
Indices: 45990--46025 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45980 TCGAAAGGAC
*
45990 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
46008 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
46026 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:47225 original size:24 final size:25
Alignment explanation
Indices: 47153--47261 Score: 93
Period size: 24 Copynumber: 4.5 Consensus size: 25
47143 AAATATTTTA
* *
47153 TCTGATTTCCGACT-TGAATTCTGT
1 TCTGATTTCTGATTCTGAATTCTGT
*** *
47177 TCTGATAAATGA-CCTGAAATT-TGT
1 TCTGATTTCTGATTCTG-AATTCTGT
*
47201 TCTGATTTCTGATT-TGGATTCTGT
1 TCTGATTTCTGATTCTGAATTCTGT
*
47225 TCTGATATCTG-TTCTGAATTCTGT
1 TCTGATTTCTGATTCTGAATTCTGT
*
47249 TTTGATTTCTGAT
1 TCTGATTTCTGAT
47262 ATCTTCGTTA
Statistics
Matches: 65, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
23 5 0.08
24 55 0.85
25 5 0.08
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (25 bp):
TCTGATTTCTGATTCTGAATTCTGT
Found at i:47242 original size:48 final size:48
Alignment explanation
Indices: 47153--47261 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
47143 AAATATTTTA
* *
47153 TCTGATTTCCGACTTGAATTCTGTTCTGATAAATGACCTGAAATT-TGT
1 TCTGATTTCTGATTTGAATTCTGTTCTGATAAATGACCTG-AATTCTGT
* ** **
47201 TCTGATTTCTGATTTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
*
47249 TTTGATTTCTGAT
1 TCTGATTTCTGAT
47262 ATCTTCGTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 4 0.08
48 48 0.92
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:48228 original size:11 final size:11
Alignment explanation
Indices: 48189--48237 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
48179 GAACGCTGGA
48189 AACCGGTTTTG
1 AACCGGTTTTG
48200 -ACCGG-TTT-
1 AACCGGTTTTG
*
48208 AACTGGTTTTG
1 AACCGGTTTTG
48219 AACCGGTTTTG
1 AACCGGTTTTG
48230 -ACCGGTTT
1 AACCGGTTT
48238 GACCGGTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 7 0.21
10 16 0.48
11 10 0.30
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:48240 original size:9 final size:10
Alignment explanation
Indices: 48190--48244 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
48180 AACGCTGGAA
48190 ACCGGTTTTG
1 ACCGGTTTTG
*
48200 ACCGG-TTTA
1 ACCGGTTTTG
*
48209 ACTGGTTTTG
1 ACCGGTTTTG
48219 AACCGGTTTTG
1 -ACCGGTTTTG
48230 ACCGG-TTTG
1 ACCGGTTTTG
48239 ACCGGT
1 ACCGGT
48245 CACGACCCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 16 0.42
10 13 0.34
11 9 0.24
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:48303 original size:13 final size:13
Alignment explanation
Indices: 48257--48303 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
48247 CGACCCGTTT
*
48257 ACCCGTTTACCCG
1 ACCCGTTGACCCG
48270 ACCCGTTGACCCG
1 ACCCGTTGACCCG
48283 ACCC---GACCCG
1 ACCCGTTGACCCG
48293 ACCCGTTGACC
1 ACCCGTTGACC
48304 GTTGACCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.17, C:0.49, G:0.19, T:0.15
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:51441 original size:36 final size:36
Alignment explanation
Indices: 51383--51533 Score: 236
Period size: 36 Copynumber: 4.2 Consensus size: 36
51373 ATTACATCCG
51383 CTTTAGC-TTAGGTAAAAGCTTAAACGTAATATGAA
1 CTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGAA
*
51418 CTTTAGCTTTAGGTGAAAA-CTTAAACGGAATATGAA
1 CTTTAGCTTTAGGT-AAAAGCTTAAACGTAATATGAA
*
51454 CTTTAGCTTTAGGTAAAAGCTTAAATGTAATATGAA
1 CTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGAA
*
51490 CTTTAGCTTTATGTAAAAGCTTAAACGTAATATGAA
1 CTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGAA
*
51526 -TCTAGCTT
1 CTTTAGCTT
51534 CTTATAATAT
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
35 18 0.17
36 85 0.79
37 4 0.04
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (36 bp):
CTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGAA
Found at i:54886 original size:15 final size:16
Alignment explanation
Indices: 54868--54897 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54858 TTAATTTCAA
54868 AATTTTAT-AAAATAC
1 AATTTTATCAAAATAC
54883 AATTTTATCAAAATA
1 AATTTTATCAAAATA
54898 ACTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTTATCAAAATAC
Found at i:60047 original size:35 final size:35
Alignment explanation
Indices: 60007--60139 Score: 176
Period size: 35 Copynumber: 3.8 Consensus size: 35
59997 AGATGAACAT
* *
60007 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCATTCAC
* * * * *
60042 TTGAATCAAAAGTGCCGATGCTTCTTTTCATTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCATTC-AC
* *
60078 TTGAATCGAAAGTGTTGATGCTTTCTTCCATTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCATTCAC
60113 TTGAATCGAAAGTGTCGATGCTTCCTT
1 TTGAATCGAAAGTGTCGATGCTTCCTT
60140 TCGTCCTTCT
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
35 53 0.65
36 28 0.35
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCATTCAC
Found at i:60125 original size:71 final size:71
Alignment explanation
Indices: 60007--60150 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
59997 AGATGAACAT
* *
60007 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCACTTGAATCAAAAGTGCCGATGCTTCTTTTCA
1 TTGAATCGAAAGTGTTGATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCCTTTCA
*
60072 TTCTTC
66 TCCTTC
* * * *
60078 TTGAATCGAAAGTGTTGATGCTTTCTTCCATTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGTTGATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCCTTTCA
60143 TCCTTC
66 TCCTTC
60149 TT
1 TT
60151 ATTCACCTTC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.40
Consensus pattern (71 bp):
TTGAATCGAAAGTGTTGATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCCTTTCA
TCCTTC
Found at i:61125 original size:14 final size:14
Alignment explanation
Indices: 61106--61132 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
61096 AGATACCAGA
61106 AGAAGAAGAAGAAC
1 AGAAGAAGAAGAAC
61120 AGAAGAAGAAGAA
1 AGAAGAAGAAGAA
61133 GTAGAAGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.30, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAGAAC
Found at i:64888 original size:14 final size:14
Alignment explanation
Indices: 64869--64896 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64859 ACTTTGCACT
64869 ATGGTATCGATACC
1 ATGGTATCGATACC
64883 ATGGTATCGATACC
1 ATGGTATCGATACC
64897 CTTTCATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
ATGGTATCGATACC
Found at i:68230 original size:21 final size:21
Alignment explanation
Indices: 68204--68252 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
68194 GGTTACCGCA
68204 ATTGCGGCCATAGCGAGCGCT
1 ATTGCGGCCATAGCGAGCGCT
* * *
68225 ATTGCGACCATAGCGGGCTCT
1 ATTGCGGCCATAGCGAGCGCT
68246 ATTGCGG
1 ATTGCGG
68253 GTATATCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.27, G:0.33, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCATAGCGAGCGCT
Found at i:71542 original size:3 final size:3
Alignment explanation
Indices: 71527--71566 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
71517 CTTTTCCCCT
*
71527 TTC TTC CTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
71567 CAGCACAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:80135 original size:30 final size:30
Alignment explanation
Indices: 80086--80165 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
80076 CTTTTAAAAC
80086 TTGCAATACAG-TCCCCCAACATTTAGTTCAT
1 TTGCAATA-AGAT-CCCCAACATTTAGTTCAT
* * *
80117 TTGCAATATGGTCCCCAACATTTAGTTCGT
1 TTGCAATAAGATCCCCAACATTTAGTTCAT
*
80147 TTGTAATAAGATCCCCAAC
1 TTGCAATAAGATCCCCAAC
80166 GTAACTGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 34 0.79
31 9 0.21
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (30 bp):
TTGCAATAAGATCCCCAACATTTAGTTCAT
Found at i:82127 original size:50 final size:50
Alignment explanation
Indices: 82049--82151 Score: 156
Period size: 50 Copynumber: 2.1 Consensus size: 50
82039 ACAATGTTCA
*
82049 TTTTTCAAAGAATTGCAAATGTAGATTTAGTTTTAATTTCAATTTCACAT
1 TTTTTAAAAGAATTGCAAATGTAGATTTAGTTTTAATTTCAATTTCACAT
*
82099 TTTTTAAAAGAATTGCGAATATG-A-ATTTAGTTTTAATTTTAATTTCACAT
1 TTTTTAAAAGAATTGC-AA-ATGTAGATTTAGTTTTAATTTCAATTTCACAT
82149 TTT
1 TTT
82152 AAAAAATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
50 43 0.88
51 3 0.06
52 3 0.06
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.49
Consensus pattern (50 bp):
TTTTTAAAAGAATTGCAAATGTAGATTTAGTTTTAATTTCAATTTCACAT
Found at i:82996 original size:20 final size:21
Alignment explanation
Indices: 82971--83022 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
82961 TTTTCCCAAT
*
82971 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
82991 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
83012 TCGCAATGCGA
1 TCGCAATGCGA
83023 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:83036 original size:20 final size:20
Alignment explanation
Indices: 83011--83118 Score: 101
Period size: 20 Copynumber: 5.3 Consensus size: 20
83001 AATTGGGAAA
83011 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
83031 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
83051 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
83072 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* ** *
83092 TTCGCAACACGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
83112 TTCGCAA
1 ATCGCAA
83119 CGTGATTTAC
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 57 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:83125 original size:20 final size:20
Alignment explanation
Indices: 83073--83125 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
83063 TAATACAAAA
*
83073 TCGCAACGAGATACTGACTT
1 TCGCAACGAGATTCTGACTT
83093 TCGCAAC-ACGATTCTGACTT
1 TCGCAACGA-GATTCTGACTT
*
83113 TCGCAACGTGATT
1 TCGCAACGAGATT
83126 TACATAATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:83660 original size:20 final size:20
Alignment explanation
Indices: 83606--83664 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
83596 GCGATTCTCT
**
83606 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
83626 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
83646 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
83665 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:85004 original size:18 final size:18
Alignment explanation
Indices: 84983--85027 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
84973 TCCAGTTCGG
84983 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
85001 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
85019 GAGCCATCA
1 GAGCCATCA
85028 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:85544 original size:99 final size:99
Alignment explanation
Indices: 85393--85586 Score: 379
Period size: 99 Copynumber: 2.0 Consensus size: 99
85383 ATTCGGTTGC
*
85393 TGCCAATACTGCTAAACTGTTTTTGTTAGTATTTGTTTTTGGTTTTGTTTTTGTCTTTTGGTTGA
1 TGCCAATACTGCTAAACTGTTTTTGTTAGTATTTGTTTTTGGTTTTGTTTTTGTCTTTTGATTGA
85458 AGTAATGCAATCCATTCAAGTTTCAATTTGTTTT
66 AGTAATGCAATCCATTCAAGTTTCAATTTGTTTT
85492 TGCCAATACTGCTAAACTGTTTTTGTTAGTATTTGTTTTTGGTTTTGTTTTTGTCTTTTGATTGA
1 TGCCAATACTGCTAAACTGTTTTTGTTAGTATTTGTTTTTGGTTTTGTTTTTGTCTTTTGATTGA
85557 AGTAATGCAATCCATTCAAGTTTCAATTTG
66 AGTAATGCAATCCATTCAAGTTTCAATTTG
85587 CAGAAGAAGA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (99 bp):
TGCCAATACTGCTAAACTGTTTTTGTTAGTATTTGTTTTTGGTTTTGTTTTTGTCTTTTGATTGA
AGTAATGCAATCCATTCAAGTTTCAATTTGTTTT
Found at i:85662 original size:19 final size:20
Alignment explanation
Indices: 85608--85663 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
85598 TAGTTTACTT
* *
85608 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
85628 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* *
85648 TCGTAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
85664 AAATTGCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:85686 original size:14 final size:14
Alignment explanation
Indices: 85663--85720 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
85653 ATGCGAAATG
*
85663 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
85677 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
85693 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
85709 AAAATCGCAACG
1 AAAATCGCAACG
85721 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:85710 original size:32 final size:33
Alignment explanation
Indices: 85647--85737 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
85637 GGAAATGGCT
* *
85647 ATCGTAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
85680 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
85712 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
85738 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:85731 original size:19 final size:19
Alignment explanation
Indices: 85677--85742 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
85667 TTGCAACGAC
85677 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
85696 -AAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
*
85709 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
85728 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
85743 TTTGTGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
14 10 0.26
16 4 0.11
18 10 0.26
19 14 0.37
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:85773 original size:14 final size:14
Alignment explanation
Indices: 85754--85843 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
85744 TTGTGTTTCG
85754 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
85768 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
85784 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
85800 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
85816 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
85832 CGTTGCGATTTT
1 CGTTGCGATTTT
85844 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.47
16 16 0.25
18 18 0.28
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:85792 original size:32 final size:32
Alignment explanation
Indices: 85749--85859 Score: 204
Period size: 32 Copynumber: 3.4 Consensus size: 32
85739 GCGATTTGTG
*
85749 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
85781 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
85813 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGA-TTTCA
85846 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
85860 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 58 0.75
33 19 0.25
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.47
Consensus pattern (32 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
Found at i:85878 original size:20 final size:19
Alignment explanation
Indices: 85844--85899 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
85834 TTGCGATTTT
85844 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
85863 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
85883 CATTTTCGCATTGCGAT
1 CA-TTTCGCATTGCGAT
85900 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:87788 original size:14 final size:14
Alignment explanation
Indices: 87769--87802 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
87759 TGTTTAATTA
87769 ATTTGTAAAAGATG
1 ATTTGTAAAAGATG
* *
87783 ATTTGTAAATGTTG
1 ATTTGTAAAAGATG
87797 ATTTGT
1 ATTTGT
87803 TTAATTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGATG
Found at i:87963 original size:19 final size:18
Alignment explanation
Indices: 87938--87987 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
87928 TATCGTAACT
87938 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCGAA
87956 ATGAAAATCGCAA--CG-A
1 A-GAAAATCGCAATGCGAA
87972 A-AAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
87988 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 10 0.36
16 4 0.14
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.50, C:0.18, G:0.20, T:0.12
Consensus pattern (18 bp):
AGAAAATCGCAATGCGAA
Found at i:88044 original size:34 final size:34
Alignment explanation
Indices: 87994--88097 Score: 91
Period size: 40 Copynumber: 2.9 Consensus size: 34
87984 GCGATTTTCA
**
87994 TTTCGCATTGTAATTTTCTAGTTGCGATAGCCAT
1 TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
* *
88028 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCATTGCGA-TTTTC---T--AGTTGCGATAGCCAT
* **
88068 TTTCGCATTGCGATTTCCCCGTTGCGATAG
1 TTTCGCATTGCGATTTTCTAGTTGCGATAG
88098 TCAAATGAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
34 19 0.35
35 5 0.09
38 1 0.02
39 4 0.07
40 26 0.47
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.41
Consensus pattern (34 bp):
TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
Found at i:88071 original size:20 final size:20
Alignment explanation
Indices: 88015--88081 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
88005 AATTTTCTAG
*
88015 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCA
*** *
88035 TTGCGATTTTTCA-TTTCGAA
1 TTGCGA-TAGCCATTTTCGCA
88055 TTGCGATAGCCATTTTCGCA
1 TTGCGATAGCCATTTTCGCA
88075 TTGCGAT
1 TTGCGAT
88082 TTCCCCGTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 3 0.08
20 30 0.83
21 3 0.08
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCA
Found at i:88638 original size:12 final size:12
Alignment explanation
Indices: 88619--88652 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
88609 CTCTCCGGCG
88619 ACATCCGTTCCT
1 ACATCCGTTCCT
*
88631 ATATCCGTTCCT
1 ACATCCGTTCCT
88643 ACATCC-TTCC
1 ACATCCGTTCC
88653 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:89258 original size:24 final size:24
Alignment explanation
Indices: 89207--89260 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
89197 GTATTCGAAA
* *
89207 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
89231 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
89255 TTTGAT
1 TTTGAT
89261 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:89452 original size:12 final size:12
Alignment explanation
Indices: 89435--89459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89425 ATATAATCCT
89435 GAAGAAGAAAAA
1 GAAGAAGAAAAA
89447 GAAGAAGAAAAA
1 GAAGAAGAAAAA
89459 G
1 G
89460 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:91772 original size:19 final size:18
Alignment explanation
Indices: 91750--91880 Score: 79
Period size: 19 Copynumber: 7.7 Consensus size: 18
91740 GGAAATTACT
91750 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
91769 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
91783 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
91802 ATCGCAA-CG--CT-AAT
1 ATCGCAAGCGAAATGAAA
*
91816 TTCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
91835 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
91849 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
91868 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
91881 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 12, Indels: 32
0.66 0.09 0.25
Matches are distributed among these distances:
14 25 0.30
15 5 0.06
16 6 0.07
17 6 0.07
18 5 0.06
19 37 0.44
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:91792 original size:33 final size:33
Alignment explanation
Indices: 91750--91876 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
91740 GGAAATTACT
91750 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
91783 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
91815 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
91849 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
91877 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:91861 original size:66 final size:66
Alignment explanation
Indices: 91751--91883 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
91741 GAAATTACTA
* *
91751 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGAAT
91816 T
66 T
*
91817 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGAAT
91882 T
66 T
91883 T
1 T
91884 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:91898 original size:19 final size:19
Alignment explanation
Indices: 91876--91917 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
91866 AAATCGCAAC
91876 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
91895 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
91914 GCGA
1 GCGA
91918 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:91918 original size:19 final size:19
Alignment explanation
Indices: 91885--91951 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
91875 CGCGAATTTA
91885 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
91904 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
91921 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
91937 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
91952 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:92077 original size:14 final size:14
Alignment explanation
Indices: 92058--92094 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
92048 CATCAATTAA
92058 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
92072 ACAAATCACCTTTT
1 ACAAATCAACTTTT
92086 ACAAATCAA
1 ACAAATCAA
92095 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:93495 original size:21 final size:21
Alignment explanation
Indices: 93465--93630 Score: 77
Period size: 21 Copynumber: 7.9 Consensus size: 21
93455 TGAATGGTGG
*
93465 GAGGGACCTCTTCAACGATGA
1 GAGGGGCCTCTTCAACGATGA
* * * * *
93486 TAGTGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTCAACGATGA
* * *
93507 GAGGGGACTC-TCGAGGAATGA
1 GAGGGGCCTCTTCAACG-ATGA
*
93528 TAGGGGCCTCTTCAACGAT-A
1 GAGGGGCCTCTTCAACGATGA
* * * **
93548 GGAGTGGACTCTTGAGGGATGA
1 -GAGGGGCCTCTTCAACGATGA
* * * *
93570 CAGTGGCCTCTTCAACGGTGG
1 GAGGGGCCTCTTCAACGATGA
* * *
93591 GAGGGGACTC-TCGAGGAATGA
1 GAGGGGCCTCTTCAACG-ATGA
*
93612 TAGGGGCCTCTTCAACGAT
1 GAGGGGCCTCTTCAACGAT
93631 AGGAGTGGAC
Statistics
Matches: 97, Mismatches: 42, Indels: 12
0.64 0.28 0.08
Matches are distributed among these distances:
20 8 0.08
21 80 0.82
22 9 0.09
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
GAGGGGCCTCTTCAACGATGA
Found at i:93510 original size:42 final size:41
Alignment explanation
Indices: 93451--93653 Score: 176
Period size: 42 Copynumber: 4.8 Consensus size: 41
93441 GTGAATCGGG
* * *
93451 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGATAGTGGC
1 CTCTTCAACGGTGGGAGGGA-CTCTTCAAGGATGATAGTGGC
* * *
93493 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTCAACGGTGGGA-GGGACTCTTCAAGG-ATGATAGTGGC
* * * * *
93535 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTCAACGGTGGGAG-GGACTCTTCAAGGATGATAGTGGC
* *
93577 CTCTTCAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTCAACGGTGGGA-GGGACTCTTCAAGG-ATGATAGTGGC
* * * *
93619 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTCAACGGTGGGAG-GGACTCTTCAAGGATGA
93654 CAGGCGAGTC
Statistics
Matches: 129, Mismatches: 24, Indels: 16
0.76 0.14 0.09
Matches are distributed among these distances:
41 9 0.07
42 109 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTCAACGGTGGGAGGGACTCTTCAAGGATGATAGTGGC
Found at i:93592 original size:84 final size:84
Alignment explanation
Indices: 93481--93656 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
93471 CCTCTTCAAC
* *
93481 GATGATAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTCAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
93546 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
93565 GATGACAGTGGCCTCTTCAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTCAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
93630 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
93649 GATGACAG
1 GATGACAG
93657 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTCAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:94044 original size:91 final size:90
Alignment explanation
Indices: 93875--94059 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
93865 ATTTCAAACT
*
93875 TTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATAAACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
93940 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
93968 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
94032 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
94059 T
1 T
94060 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 43 0.49
93 19 0.22
95 26 0.30
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:95810 original size:19 final size:19
Alignment explanation
Indices: 95746--95858 Score: 101
Period size: 19 Copynumber: 6.1 Consensus size: 19
95736 TCTTTTGGTT
* *
95746 GAAATGAAAATCGCAACGA
1 GAAATGACAATCGCAACGC
*
95765 GATAATGAGAATCGCAACGC
1 GA-AATGACAATCGCAACGC
*
95785 GGAAATGACTATCGCAACGC
1 -GAAATGACAATCGCAACGC
*
95805 GAAATGACTATCGCAA--C
1 GAAATGACAATCGCAACGC
*
95822 G--A-GAGAATCGCAACGC
1 GAAATGACAATCGCAACGC
* *
95838 GAAATGAAAATCGCAATGC
1 GAAATGACAATCGCAACGC
95857 GA
1 GA
95859 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 32 0.41
20 30 0.38
21 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGACAATCGCAACGC
Found at i:95876 original size:19 final size:19
Alignment explanation
Indices: 95854--95901 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
95844 AAAATCGCAA
*
95854 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
95873 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
95893 TGCGATTTT
1 TGCGATTTT
95902 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:96444 original size:20 final size:20
Alignment explanation
Indices: 96419--96471 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
96409 GCGCTATGTA
96419 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
96439 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
96459 TATCTCGTTGCGA
1 AATCGCGTTGCGA
96472 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:96505 original size:20 final size:20
Alignment explanation
Indices: 96480--96533 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
96470 GATTTTGTAT
96480 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
96500 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
96520 TATCGCATTGCGAT
1 TATCGCATTGCGAT
96534 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:96518 original size:61 final size:61
Alignment explanation
Indices: 96420--96536 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
96410 CGCTATGTAA
* * * * *
96420 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
96481 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
96537 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:96552 original size:61 final size:61
Alignment explanation
Indices: 96420--96554 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
96410 CGCTATGTAA
* * * * * ** *
96420 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
96481 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
96543 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
96555 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:101980 original size:17 final size:18
Alignment explanation
Indices: 101947--101980 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
101937 GCTTTAACCA
*
101947 AAGTTTATTTATTTTTTG
1 AAGTTTATTTATATTTTG
101965 AAGTTTA-TTATATTTT
1 AAGTTTATTTATATTTT
101981 CATATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
AAGTTTATTTATATTTTG
Found at i:102044 original size:18 final size:18
Alignment explanation
Indices: 102012--102059 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
102002 ACATTAAAAA
102012 AATAATTAAGATAA-TATT
1 AATAATTAA-ATAATTATT
102030 AATAATTAAATTAATTTATT
1 AATAATTAAA-TAA-TTATT
*
102050 AATATTTAAA
1 AATAATTAAA
102060 CTTATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
20 13 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AATAATTAAATAATTATT
Found at i:103595 original size:16 final size:15
Alignment explanation
Indices: 103571--103601 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
103561 AAATTAATAT
103571 TAAAATTTAAAGATA
1 TAAAATTTAAAGATA
103586 TAAAAGTTTAAAGATA
1 TAAAA-TTTAAAGATA
103602 AATTTACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (15 bp):
TAAAATTTAAAGATA
Found at i:112670 original size:20 final size:20
Alignment explanation
Indices: 112641--112683 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
112631 ATTCCACCAC
*
112641 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCATAA
* *
112661 ATGCATCTATATGGTCATAA
1 ATGCAACTATATGCTCATAA
112681 ATG
1 ATG
112684 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCATAA
Found at i:116844 original size:17 final size:17
Alignment explanation
Indices: 116822--116859 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
116812 CTTAACACAC
* *
116822 AATATTATTTTTTTATT
1 AATATTAATTTTTTATA
116839 AATATTAATTTTTTATA
1 AATATTAATTTTTTATA
116856 AATA
1 AATA
116860 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATATTAATTTTTTATA
Found at i:127740 original size:26 final size:24
Alignment explanation
Indices: 127690--127740 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
127680 AAGTCAAATT
**
127690 TATTTTCAAATTTCACTTATCAAC
1 TATTTTCAAATTTCACTTAGAAAC
*
127714 TATTTTCCAAGATTTCATTTAGAAAC
1 TATTTT-CAA-ATTTCACTTAGAAAC
127740 T
1 T
127741 CCTTCTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 13 0.59
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (24 bp):
TATTTTCAAATTTCACTTAGAAAC
Found at i:129536 original size:14 final size:14
Alignment explanation
Indices: 129517--129547 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
129507 TTTATAAATA
129517 AATTTTAATTTTAT
1 AATTTTAATTTTAT
*
129531 AATTTTATTTTTAT
1 AATTTTAATTTTAT
129545 AAT
1 AAT
129548 AATTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
AATTTTAATTTTAT
Found at i:135601 original size:20 final size:20
Alignment explanation
Indices: 135578--135627 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
135568 GTTCTTACAG
135578 TATCAATACTATATGAACAA
1 TATCAATACTATATGAACAA
135598 TATCAATACTATATGAACAA
1 TATCAATACTATATGAACAA
*
135618 TATCGATACT
1 TATCAATACT
135628 GTTCATATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (20 bp):
TATCAATACTATATGAACAA
Found at i:137386 original size:33 final size:33
Alignment explanation
Indices: 137335--137408 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
137325 GTTTGGCAAG
* * *
137335 TTGGAAATTTTATATTGGTTGATAGTCAACTTA
1 TTGGAAAATTCATATTGGTTGATAGCCAACTTA
* * *
137368 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATATTGGTTGATAGCCAACTTA
137401 TTGGAAAA
1 TTGGAAAA
137409 AGCTTTGGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (33 bp):
TTGGAAAATTCATATTGGTTGATAGCCAACTTA
Found at i:137423 original size:31 final size:33
Alignment explanation
Indices: 137361--137433 Score: 105
Period size: 31 Copynumber: 2.3 Consensus size: 33
137351 GGTTGATAGT
** *
137361 CAACTTATTGGAAAATTCATCTTGGTTGGTGGC
1 CAACTTATTGGAAAAAGCATCTTGGTAGGTGGC
137394 CAACTTATTGGAAAAAGC-T-TTGGTAGGTGGC
1 CAACTTATTGGAAAAAGCATCTTGGTAGGTGGC
137425 CAACTTATT
1 CAACTTATT
137434 TTTCATCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 20 0.54
32 1 0.03
33 16 0.43
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (33 bp):
CAACTTATTGGAAAAAGCATCTTGGTAGGTGGC
Found at i:141428 original size:33 final size:32
Alignment explanation
Indices: 141380--141478 Score: 119
Period size: 33 Copynumber: 3.1 Consensus size: 32
141370 GTTTTGCAAG
* *
141380 TTGGAAATTTTATCTTGATTGGTGGCCAACTTA
1 TTGGAAA-ATTATCTTGGTTGGTGGCCAACTTA
**
141413 TTGGAAAATTCATCTTGGTTGGTGGTTAACTTA
1 TTGGAAAATT-ATCTTGGTTGGTGGCCAACTTA
* *
141446 TTGGAAAAATAT-TTGGTAGGTGGCCAACTTA
1 TTGGAAAATTATCTTGGTTGGTGGCCAACTTA
141477 TT
1 TT
141479 TTTCATCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
31 18 0.32
32 4 0.07
33 35 0.61
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.40
Consensus pattern (32 bp):
TTGGAAAATTATCTTGGTTGGTGGCCAACTTA
Found at i:144508 original size:16 final size:16
Alignment explanation
Indices: 144487--144524 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
144477 CATAGAAACA
144487 TTATTATAATGTATTT
1 TTATTATAATGTATTT
*
144503 TTATTATATTGTATTT
1 TTATTATAATGTATTT
144519 TTATTA
1 TTATTA
144525 ATACAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (16 bp):
TTATTATAATGTATTT
Found at i:150889 original size:19 final size:20
Alignment explanation
Indices: 150867--150905 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
150857 ATTAAATTTT
150867 TAAAACTTTT-AAAAATAAA
1 TAAAACTTTTAAAAAATAAA
*
150886 TAAAATTTTTAAAAAATAAA
1 TAAAACTTTTAAAAAATAAA
150906 AATTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAACTTTTAAAAAATAAA
Found at i:150904 original size:16 final size:17
Alignment explanation
Indices: 150883--150920 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
150873 TTTTAAAAAT
* *
150883 AAATAAAATTTTTA-AA
1 AAATAAAAATTTAATAA
150899 AAATAAAAATTTAATAA
1 AAATAAAAATTTAATAA
150916 AAATA
1 AAATA
150921 TATAAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAAAAATTTAATAA
Found at i:150917 original size:17 final size:16
Alignment explanation
Indices: 150878--150920 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
150868 AAAACTTTTA
*
150878 AAAATAAATAAAATTTT
1 AAAA-AAATAAAAATTT
*
150895 TAAAAAATAAAAATTT
1 AAAAAAATAAAAATTT
150911 AATAAAAATA
1 AA-AAAAATA
150921 TATAAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAAAATAAAAATTT
Found at i:153623 original size:3 final size:3
Alignment explanation
Indices: 153615--153688 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
153605 CTGTAATATG
* *
153615 TAA TAA TAA TATT TAT TAA TAA TAA TAA -AA -AA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
153659 TAA TAA TAA CAA TTA TAA TAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
153689 AACGGGCAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 4 0.07
3 55 0.90
4 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:154360 original size:4 final size:4
Alignment explanation
Indices: 154351--154397 Score: 87
Period size: 4 Copynumber: 12.0 Consensus size: 4
154341 ATGATGAATA
154351 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
154398 GACACACATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.07
4 39 0.93
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:154892 original size:2 final size:2
Alignment explanation
Indices: 154885--154913 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
154875 GAATGCATAC
154885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
154914 ATACAAGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:158417 original size:20 final size:20
Alignment explanation
Indices: 158392--158433 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
158382 ATGATTATTA
158392 ATCAAAACTGAATGTTAGGC
1 ATCAAAACTGAATGTTAGGC
158412 ATCAAAACTGAATGTTAGGC
1 ATCAAAACTGAATGTTAGGC
158432 AT
1 AT
158434 GGTTTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCAAAACTGAATGTTAGGC
Found at i:158897 original size:14 final size:13
Alignment explanation
Indices: 158880--158937 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
158870 TTTACCATAT
158880 TTAATTTAAAATAA
1 TTAATTTAAAA-AA
*
158894 TTAA-TTAATAAA
1 TTAATTTAAAAAA
* *
158906 TTAAATATCAAAAA
1 TT-AATTTAAAAAA
*
158920 TTAAATTAAAAAA
1 TTAATTTAAAAAA
158933 TTAAT
1 TTAAT
158938 ATCATGAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
12 4 0.12
13 19 0.56
14 11 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAATTTAAAAAA
Found at i:158938 original size:26 final size:26
Alignment explanation
Indices: 158892--158941 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
158882 AATTTAAAAT
*
158892 AATTAATTAATAAATTAAATATCAAA
1 AATTAATTAAAAAATTAAATATCAAA
158918 AATTAAATTAAAAAATT-AATATCA
1 AATT-AATTAAAAAATTAAATATCA
158942 TGAAAAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (26 bp):
AATTAATTAAAAAATTAAATATCAAA
Done.