Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 1 of 240
Found at i:2589 original size:2 final size:2
Alignment explanation
Indices: 2582--2628 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2572 AGTATGGTAA
*
2582 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2624 CT CT C
1 CT CT C
2629 CTGGTTAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:3249 original size:20 final size:19
Alignment explanation
Indices: 3212--3251 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3202 TTGGAATATT
* *
3212 AAATATTATAATTTTTTAA
1 AAATATTATAACTATTTAA
3231 AAATATTAATAACTATTTAA
1 AAATATT-ATAACTATTTAA
3251 A
1 A
3252 CACATAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATATTATAACTATTTAA
Found at i:3622 original size:43 final size:44
Alignment explanation
Indices: 3561--3654 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 44
3551 ATCCTAATTG
*
3561 AGAAAATAGTTCTCTTATTCTAATAAACTACTAAAACATAAAA-
1 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAT
* *
3604 AGAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAAT
1 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAT
3648 A-AAAATA
1 AGAAAATA
3655 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (44 bp):
AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAT
Found at i:3701 original size:19 final size:18
Alignment explanation
Indices: 3677--3716 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
3667 GAATAAAAAC
3677 TTATCTATCC-AAATAAGAT
1 TTATCTA-CCTAAATAA-AT
3696 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
3714 TTA
1 TTA
3717 AAATATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:8362 original size:43 final size:44
Alignment explanation
Indices: 8301--8393 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 44
8291 TCCTAATTGG
8301 GAAAATAGTTCCATTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCATTATTCTAATAAACTACTAAAACATAAAATA
* * *
8344 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCATTATTCTAATAAACTACTAAAACATAAAATA
8388 -AAAATA
1 GAAAATA
8394 TTTCTAGGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCATTATTCTAATAAACTACTAAAACATAAAATA
Found at i:10339 original size:17 final size:17
Alignment explanation
Indices: 10317--10351 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
10307 GAGAGTATAA
10317 GTGGTTATAAGAAGGTG
1 GTGGTTATAAGAAGGTG
10334 GTGGTTATAAGAAGGTG
1 GTGGTTATAAGAAGGTG
10351 G
1 G
10352 GGAACTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (17 bp):
GTGGTTATAAGAAGGTG
Found at i:10654 original size:18 final size:18
Alignment explanation
Indices: 10631--10666 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10621 AAAAGCTCAT
* *
10631 CATCAAGTTATTTCAATC
1 CATCAACTTATTGCAATC
10649 CATCAACTTATTGCAATC
1 CATCAACTTATTGCAATC
10667 ACTAAAACAC
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:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (18 bp):
CATCAACTTATTGCAATC
Found at i:12105 original size:118 final size:113
Alignment explanation
Indices: 11890--12112 Score: 320
Period size: 118 Copynumber: 1.9 Consensus size: 113
11880 GCACATTCCA
* *
11890 TATAAATGTTGCTTCTTACATCTGTAAGTGAAATGCGTGTATATATATTCTATTTATATATTTGC
1 TATAAATGTTGCTTCATACATCTCTAAGTGAAATGCGTGTATATATATTCTATTTATATATTTGC
*
11955 ATGCATCCATAAGTGAAATTTGCATGTATATATATTTCTTTCTATCTGT
66 ATGCATCCATAAGTGAAATTTGCATCTATATATA-TTCTTTCTATCTGT
* * * *
12004 TATAAATTTTGCTTCATGCATCTCTAAGTGAAATGTGTGTGTATATATATTCTCTTTTGATATAT
1 TATAAATGTTGCTTCATACATCTCTAAGTGAAA--TGCGTGTATATATATTCT-ATTT-ATATAT
* *
12069 TTGCATGCATCCGTAAGTGGAATTTGCATCTATATATATTCTTT
62 TTGCATGCATCCATAAGTGAAATTTGCATCTATATATATTCTTT
12113 TGGTATATTC
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
114 29 0.30
116 17 0.18
117 9 0.09
118 41 0.43
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.46
Consensus pattern (113 bp):
TATAAATGTTGCTTCATACATCTCTAAGTGAAATGCGTGTATATATATTCTATTTATATATTTGC
ATGCATCCATAAGTGAAATTTGCATCTATATATATTCTTTCTATCTGT
Found at i:13879 original size:21 final size:21
Alignment explanation
Indices: 13834--13879 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
13824 CTACTATGTT
* *
13834 TTTTTTTGCTTGTCATTTGTA
1 TTTTTTTCCTTGTCATTTCTA
* *
13855 TTTTTTTCCTTTTCATTTCTG
1 TTTTTTTCCTTGTCATTTCTA
13876 TTTT
1 TTTT
13880 GGGGTCCCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.13, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTTTTTCCTTGTCATTTCTA
Found at i:15883 original size:5 final size:5
Alignment explanation
Indices: 15873--15907 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
15863 GATTGTTACC
*
15873 TTCTT TTCTT TTCTT TTCTT TTCTAT TTATT TTCT
1 TTCTT TTCTT TTCTT TTCTT TTCT-T TTCTT TTCT
15908 CCTCCCTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:20787 original size:8 final size:8
Alignment explanation
Indices: 20774--20798 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
20764 ACTTGTATAT
20774 ATTATAAA
1 ATTATAAA
20782 ATTATAAA
1 ATTATAAA
20790 ATTATAAA
1 ATTATAAA
20798 A
1 A
20799 CGTCTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTATAAA
Found at i:25097 original size:23 final size:24
Alignment explanation
Indices: 25052--25098 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
25042 CTTTCTCATA
* **
25052 CTTTCAATTCAATCATTTTTCCAC
1 CTTTCAATTCAATAATTAATCCAC
25076 CTTTCAA-TCAATAATTAATCCAC
1 CTTTCAATTCAATAATTAATCCAC
25099 AAATTCACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (24 bp):
CTTTCAATTCAATAATTAATCCAC
Found at i:25248 original size:6 final size:6
Alignment explanation
Indices: 25240--25276 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
25230 TTCCCACTAA
* *
25240 TAATAA TAATAC TAATAC TAATAC TAATAT TAATAC T
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC T
25277 TACCTCACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (6 bp):
TAATAC
Found at i:26185 original size:4 final size:4
Alignment explanation
Indices: 26176--26220 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
26166 AACCCCAAAT
* *
26176 TTTC TTTC TTTC TTTC CTTC TTTT TTTC TTT- TTTC TTTCC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC T
26221 CCCCTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 3 0.09
4 28 0.80
5 4 0.11
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:27411 original size:23 final size:23
Alignment explanation
Indices: 27385--27483 Score: 180
Period size: 23 Copynumber: 4.3 Consensus size: 23
27375 ATAAGTGCCA
27385 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
27408 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
27431 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
27454 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
27477 CACTGAT
1 CACTGAT
27484 CAATAACACT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:27736 original size:18 final size:17
Alignment explanation
Indices: 27710--27748 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
27700 ATTTTCCTTC
* *
27710 CACATTCAATTTTAATT
1 CACATTCAAATATAATT
27727 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
27745 CACA
1 CACA
27749 ATTTATACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.36
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:31968 original size:22 final size:24
Alignment explanation
Indices: 31941--32091 Score: 159
Period size: 25 Copynumber: 6.3 Consensus size: 24
31931 CACTAATGAA
* *
31941 CAGAGAGCACTAAAGTGCT-ATA-
1 CAGAGAGCACCAACGTGCTAATAT
**
31963 CAGAGAGCA-CAGGTGTGCTAA-A-
1 CAGAGAGCACCA-ACGTGCTAATAT
** *
31985 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACCAACGTGCTAATAT
*
32009 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACCAACGTGCTAATA-T
32034 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAAT-AT
32059 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAAT-AT
32084 CAGAGAGC
1 CAGAGAGC
32092 GCACTAAAGT
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
21 1 0.01
22 31 0.28
23 2 0.02
24 19 0.17
25 56 0.51
26 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (24 bp):
CAGAGAGCACCAACGTGCTAATAT
Found at i:32042 original size:25 final size:25
Alignment explanation
Indices: 31985--32091 Score: 171
Period size: 25 Copynumber: 4.3 Consensus size: 25
31975 GTGTGCTAAA
**
31985 CAGAGAGCACTGACGTGCTAA-AAT
1 CAGAGAGCACCAACGTGCTAATAAT
* *
32009 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACCAACGTGCTAATAAT
32034 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
32059 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
32084 CAGAGAGC
1 CAGAGAGC
32092 GCACTAAAGT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
24 18 0.24
25 58 0.76
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.15
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAATAAT
Found at i:33090 original size:5 final size:5
Alignment explanation
Indices: 33082--33149 Score: 54
Period size: 5 Copynumber: 13.8 Consensus size: 5
33072 TATCTATATA
* *
33082 ATAAT ATAAT ATTAT AATAAT ATAAT ATAAT A-ACTT ATTAAT -TAA-
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATA-AT A-TAAT ATAAT
*
33127 ATAAC ATAAT ATAAT AT-AT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAA
33150 CTTAAATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
4 11 0.22
5 34 0.67
6 5 0.10
7 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:33099 original size:16 final size:16
Alignment explanation
Indices: 33078--33114 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
33068 GTTTTATCTA
33078 TATAATAATATAATAT
1 TATAATAATATAATAT
33094 TATAATAATATAATAT
1 TATAATAATATAATAT
*
33110 AATAA
1 TATAA
33115 CTTATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAATAATATAATAT
Found at i:33114 original size:8 final size:8
Alignment explanation
Indices: 33077--33108 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
33067 TGTTTTATCT
33077 ATATAATA
1 ATATAATA
33085 ATATAATA
1 ATATAATA
*
33093 TTATAATA
1 ATATAATA
33101 ATATAATA
1 ATATAATA
33109 TAATAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAATA
Found at i:41540 original size:27 final size:27
Alignment explanation
Indices: 41510--41641 Score: 90
Period size: 27 Copynumber: 4.8 Consensus size: 27
41500 ACAATTGATA
*
41510 AAAACAACT-AAACCCTAAAAATTTAAC
1 AAAACAA-TAAAACCCTAAAAATCTAAC
* **
41537 AAAACAATAAAATCCT-AAAATCTAGT
1 AAAACAATAAAACCCTAAAAATCTAAC
* * *
41563 AAAACAATGAAACCCTAAAAATCCAAAAA
1 AAAACAATAAAACCCTAAAAAT-C-TAAC
* *
41592 AAAACAATGAAAA-CCTAGAAATCTTAC
1 AAAACAAT-AAAACCCTAAAAATCTAAC
* * *
41619 AATAATAACAAAACCTTAAAAAT
1 AA-AACAATAAAACCCTAAAAAT
41642 TCGATAAGAA
Statistics
Matches: 80, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
26 22 0.28
27 25 0.31
28 13 0.16
29 17 0.21
30 3 0.04
ACGTcount: A:0.61, C:0.18, G:0.03, T:0.18
Consensus pattern (27 bp):
AAAACAATAAAACCCTAAAAATCTAAC
Found at i:41592 original size:26 final size:25
Alignment explanation
Indices: 41509--41592 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 25
41499 AACAATTGAT
*
41509 AAAAACAACTAAACCCTAAAAATTTA
1 AAAAACAA-TAAACCCTAAAAATCTA
*
41535 ACAAAACAATAAAATCCT-AAAATCTA
1 A-AAAACAAT-AAACCCTAAAAATCTA
* *
41561 GTAAAACAATGAAACCCTAAAAATCCA
1 -AAAAACAAT-AAACCCTAAAAATCTA
41588 AAAAA
1 AAAAA
41593 AAACAATGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 27 0.57
27 20 0.43
ACGTcount: A:0.62, C:0.19, G:0.02, T:0.17
Consensus pattern (25 bp):
AAAAACAATAAACCCTAAAAATCTA
Found at i:41653 original size:28 final size:28
Alignment explanation
Indices: 41622--41780 Score: 130
Period size: 28 Copynumber: 5.7 Consensus size: 28
41612 ATCTTACAAT
*
41622 AATAACAAAACCTTAAAAATTCGATAAG
1 AATAGCAAAACCTTAAAAATTCGATAAG
*
41650 AATAGCAAAGCCTTAAAAA-TCTGATAAG
1 AATAGCAAAACCTTAAAAATTC-GATAAG
* ** *
41678 AATAGCGAAATCC-TAAAAAGCCGAAAAG
1 AATAGC-AAAACCTTAAAAATTCGATAAG
* ** *
41706 AACAGTGAAACCTTAAAAA-TCCAGTAAG
1 AATAGCAAAACCTTAAAAATTCGA-TAAG
* * *
41734 AATAGCAAAGCCCT-AAAATTCCCATAA-
1 AATAGCAAAACCTTAAAAATT-CGATAAG
41761 AATAGCAAAACCTTAAAAAT
1 AATAGCAAAACCTTAAAAAT
41781 CTAGTTATGT
Statistics
Matches: 104, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
27 24 0.23
28 71 0.68
29 9 0.09
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (28 bp):
AATAGCAAAACCTTAAAAATTCGATAAG
Found at i:41695 original size:56 final size:56
Alignment explanation
Indices: 41635--41782 Score: 144
Period size: 56 Copynumber: 2.6 Consensus size: 56
41625 AACAAAACCT
* *
41635 TAAAAATTCGATAAGAATAGCAAAGCCTTAAAAATCTGA-TAAGAATAGCGAAA-TCC
1 TAAAAATTCGATAAGAATAGCAAA-CCTTAAAAATCTCAGTAAGAATAGC-AAAGCCC
** * * *
41691 TAAAAAGCCGAAAAGAACAGTGAAACCTTAAAAATC-CAGTAAGAATAGCAAAGCCC
1 TAAAAATTCGATAAGAATAG-CAAACCTTAAAAATCTCAGTAAGAATAGCAAAGCCC
*
41747 T-AAAATTCCCATAA-AATAGCAAAACCTTAAAAATCT
1 TAAAAATT-CGATAAGAATAGC-AAACCTTAAAAATCT
41783 AGTTATGTAA
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
55 26 0.36
56 44 0.60
57 3 0.04
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (56 bp):
TAAAAATTCGATAAGAATAGCAAACCTTAAAAATCTCAGTAAGAATAGCAAAGCCC
Found at i:41961 original size:28 final size:27
Alignment explanation
Indices: 41913--42012 Score: 98
Period size: 28 Copynumber: 3.7 Consensus size: 27
41903 TAACGGAACT
41913 CTAAAAATCTAATAATATAACAAAACC
1 CTAAAAATCTAATAATATAACAAAACC
* * *
41940 TTAAAAATCTAGTAGTAATAACAAAACC
1 CTAAAAATCTAATAAT-ATAACAAAACC
* * *
41968 CTAAAAATCCAATAAAATAATGAAAA-C
1 CTAAAAATCTAATAATATAA-CAAAACC
41995 C--AAAATCTAATATATATA
1 CTAAAAATCTAATA-ATATA
42013 TATATATAGT
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
25 10 0.17
26 4 0.07
27 19 0.32
28 26 0.44
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (27 bp):
CTAAAAATCTAATAATATAACAAAACC
Found at i:42062 original size:29 final size:28
Alignment explanation
Indices: 42018--42098 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 28
42008 ATATATATAT
*
42018 ATAGTGAAACCTTAAAAAGTCTAGTAGAA
1 ATAGTGAAACCTTAAAAA-TCTAGTAAAA
*
42047 ATAGTGAAATCC-TAAAAATCTGGTAAAA
1 ATAGTGAAA-CCTTAAAAATCTAGTAAAA
*
42075 AAAGTGAAAACCTTAAAAATCTAG
1 ATAGTG-AAACCTTAAAAATCTAG
42099 ATTGTTTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 15 0.33
29 28 0.62
30 2 0.04
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (28 bp):
ATAGTGAAACCTTAAAAATCTAGTAAAA
Found at i:43382 original size:34 final size:34
Alignment explanation
Indices: 43339--43407 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
43329 TATAGGCAAA
43339 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
1 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
*
43373 ATACAAGAGTAATTGAACTCTAATAAAACTCTTT
1 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
43407 A
1 A
43408 AAATTATCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (34 bp):
ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
Found at i:48935 original size:32 final size:31
Alignment explanation
Indices: 48891--48950 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
48881 TAGGCAACTT
48891 TTTTTGCAGTTTTTTTTGCGATTTTTTTCGC
1 TTTTTGCAGTTTTTTTTGCGATTTTTTTCGC
* *
48922 TTTTTGCGGGTTTTTTTTGCTATTTTTTT
1 TTTTTGC-AGTTTTTTTTGCGATTTTTTT
48951 AACTCGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.05, C:0.10, G:0.17, T:0.68
Consensus pattern (31 bp):
TTTTTGCAGTTTTTTTTGCGATTTTTTTCGC
Found at i:49449 original size:34 final size:34
Alignment explanation
Indices: 49406--49508 Score: 179
Period size: 34 Copynumber: 3.0 Consensus size: 34
49396 TATAGGGAAA
49406 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
1 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
* **
49440 ATACAAGAGTAATTAAACCCTAATAAAACTCGCT
1 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
49474 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
1 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
49508 A
1 A
49509 AAATTATCTA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.27
Consensus pattern (34 bp):
ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
Found at i:52258 original size:23 final size:23
Alignment explanation
Indices: 52224--52275 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
52214 TTATACGAGC
52224 TTACTA-TGTAATATCCC-GAAAA
1 TTACTACTGTAATA-CCCTGAAAA
52246 TTACTACTGTAATACCCTGAAAA
1 TTACTACTGTAATACCCTGAAAA
52269 TTACTAC
1 TTACTAC
52276 AGGAAGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (23 bp):
TTACTACTGTAATACCCTGAAAA
Found at i:56525 original size:47 final size:46
Alignment explanation
Indices: 56438--56526 Score: 142
Period size: 47 Copynumber: 1.9 Consensus size: 46
56428 TTGATGTAAG
** *
56438 TAAAAGCCTGAGTCAAATAGATAAGGAACTGAAAGTTGGTGCATTT
1 TAAAAGCCTGAGTCAAATAGATAAGGAACCAAAAGCTGGTGCATTT
56484 TAAAAGCCTGAGCTCAAATAGATAAGGAACCAAAAGCTGGTGC
1 TAAAAGCCTGAG-TCAAATAGATAAGGAACCAAAAGCTGGTGC
56527 GTTGGGTGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 12 0.31
47 27 0.69
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
TAAAAGCCTGAGTCAAATAGATAAGGAACCAAAAGCTGGTGCATTT
Found at i:57162 original size:6 final size:6
Alignment explanation
Indices: 57150--57184 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
57140 TAGGTTTACT
* *
57150 AAAATG GAAATG GAAATG AAAATG AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT
57185 CGAATCGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:57378 original size:26 final size:26
Alignment explanation
Indices: 57339--57397 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
57329 TATATTCTCG
*
57339 AAATTTTACCAGGGGCAAAATCGTTA
1 AAATTTTACCAGGGGCAAAATCGTCA
* * * *
57365 AAATTTTACTAGGGGTAATATTGTCA
1 AAATTTTACCAGGGGCAAAATCGTCA
57391 AAATTTT
1 AAATTTT
57398 GTTGGGGGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (26 bp):
AAATTTTACCAGGGGCAAAATCGTCA
Found at i:61372 original size:12 final size:12
Alignment explanation
Indices: 61355--61393 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
61345 ATGAGTTATT
61355 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
61367 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
61379 TAAGTGAGTAAG
1 TAAGTAAGCAAG
61391 TAA
1 TAA
61394 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:69540 original size:102 final size:102
Alignment explanation
Indices: 69364--69696 Score: 567
Period size: 102 Copynumber: 3.3 Consensus size: 102
69354 ATTGAATAAA
* *
69364 AAGGGGGTTGCTAAGTGCTGATTCCCCTGAGGGGTTACTAAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
69429 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
* *
69466 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
69531 GGTTGCTAAGTGCTGATTCCACCATATCTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
* *
69568 AAGGGGGCTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
**
69633 GGTTGCTAAGTGCTGAACCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
*
69670 AAAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
69697 GACTCATTGG
Statistics
Matches: 216, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 216 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.30
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
Found at i:81973 original size:30 final size:30
Alignment explanation
Indices: 81926--81983 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
81916 AAAATAATTC
81926 ATATCATAATAAAATTATAAATT-TTTTTGA
1 ATATCATAATAAAATTAT-AATTATTTTTGA
*
81956 ATATC-TAATAATCATTATAATTATTTTT
1 ATATCATAATAA-AATTATAATTATTTTT
81984 AGATGTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (30 bp):
ATATCATAATAAAATTATAATTATTTTTGA
Found at i:93137 original size:13 final size:13
Alignment explanation
Indices: 93121--93173 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
93111 TTTAAACCAA
93121 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
93134 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
93147 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
93160 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
93173 A
1 A
93174 ATGAAGAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:94613 original size:2 final size:2
Alignment explanation
Indices: 94606--94646 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
94596 TAGGTTTCTC
*
94606 TG TG TG TG TG TG TG TC TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
94647 TAGTATCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.02, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:102163 original size:30 final size:30
Alignment explanation
Indices: 102129--102195 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
102119 GTGCTGTTGC
*
102129 TGGGCCTGGTGATTGTATGGGCGCT-GATGA
1 TGGGCCTGGTGAATGTATGGGC-CTCGATGA
* * *
102159 TGGGCCGGGTGAATGTCTGGGCCTCGTTGA
1 TGGGCCTGGTGAATGTATGGGCCTCGATGA
102189 TGGGCCT
1 TGGGCCT
102196 ACGTCGTCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.10, C:0.18, G:0.43, T:0.28
Consensus pattern (30 bp):
TGGGCCTGGTGAATGTATGGGCCTCGATGA
Found at i:104796 original size:220 final size:217
Alignment explanation
Indices: 104416--104849 Score: 701
Period size: 220 Copynumber: 2.0 Consensus size: 217
104406 TTACATTTTT
104416 CTCTCTCTTAGGCAAAGGGTTCTCACGTTTTTCTTTAAAAATTTAAAAAATGTTTGATTTGGAGC
1 CTCTCTCTTAGGCAAAGGGTTCTCACGTTTTTCTTTAAAAATTTAAAAAATGTTTGATTTGGAGC
* *
104481 TTAAATGAAAATTTGTGAAATTTTAAAAGTAATAAAAAATATTTCCATTTAGGACTAGAGATATA
66 TTAAATGAAAACTTGTGAAATTTTAAAAATAATAAAAAATATTTCCATTTAGGACTAGAGATATA
* * *
104546 ATAAACTAAACTAACAATCTGTAGTAAATCTCTCCGTGCATAAAATCGAATAAAAACAAAAACAA
131 ATAAACTAAACTAACAATCCGCAATAAATCTCTCCGTGCATAAAATCGAATAAAAACAAAAACAA
104611 TTTGGTCCTTCCATATGGTTTG
196 TTTGGTCCTTCCATATGGTTTG
** *
104633 CTCTCTCTTAGGCAAAGGGTTCTCACGTTTTT-TTTTTAAA-TTAAAAAATGTTTGATTTGGATC
1 CTCTCTCTTAGGCAAAGGGTTCTCACGTTTTTCTTTAAAAATTTAAAAAATGTTTGATTTGGAGC
104696 TTTTTAAAATGAAAACTTGTGAAATTTTAAAAATAATAAAAAAATATTTCCATTTAGGACTAGAG
66 ---TT-AAATGAAAACTTGTGAAATTTTAAAAATAAT-AAAAAATATTTCCATTTAGGACTAGAG
* * * *
104761 ATATAATGAATTAAACTAACAATCCGCAATAAATCTCTCCGTGCATAATATCGAATCAAAACAAA
126 ATATAATAAACTAAACTAACAATCCGCAATAAATCTCTCCGTGCATAAAATCGAATAAAAACAAA
104826 AACAATTTGGTCCTTCCATATGGT
191 AACAATTTGGTCCTTCCATATGGT
104850 AATGGATTTC
Statistics
Matches: 200, Mismatches: 12, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
215 22 0.11
216 6 0.03
217 32 0.16
218 2 0.01
219 29 0.14
220 109 0.55
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (217 bp):
CTCTCTCTTAGGCAAAGGGTTCTCACGTTTTTCTTTAAAAATTTAAAAAATGTTTGATTTGGAGC
TTAAATGAAAACTTGTGAAATTTTAAAAATAATAAAAAATATTTCCATTTAGGACTAGAGATATA
ATAAACTAAACTAACAATCCGCAATAAATCTCTCCGTGCATAAAATCGAATAAAAACAAAAACAA
TTTGGTCCTTCCATATGGTTTG
Found at i:117411 original size:24 final size:20
Alignment explanation
Indices: 117360--117399 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
117350 CATTTCATTT
117360 ATGCAATTGCTTTATCCATA
1 ATGCAATTGCTTTATCCATA
117380 ATGCAATTGCTTTATCCATA
1 ATGCAATTGCTTTATCCATA
117400 CCATATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (20 bp):
ATGCAATTGCTTTATCCATA
Found at i:117715 original size:4 final size:4
Alignment explanation
Indices: 117706--117762 Score: 60
Period size: 4 Copynumber: 13.8 Consensus size: 4
117696 ACTTTTCTCC
* * * *
117706 TTCT TTCT TTCT TTTT TTCTT TTCT TTCT TTCC TTCT CTGT TTCGT TTCT
1 TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTCT TTCT TTCT TTC-T TTCT
117756 TTCT TTC
1 TTCT TTC
117763 CTTCCTTTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 35 0.81
5 8 0.19
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:117737 original size:25 final size:25
Alignment explanation
Indices: 117697--117771 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
117687 GAAACCTTAA
*
117697 CTTTTCTCCTTCTTTCTTTCTTTTTTT
1 CTTTTCT--TTCTTTCCTTCTTTTTTT
* *
117724 CTTTTCTTTCTTTCCTTCTCTGTTT
1 CTTTTCTTTCTTTCCTTCTTTTTTT
* *
117749 CGTTTCTTTCTTTCCTTCCTTTT
1 CTTTTCTTTCTTTCCTTCTTTTT
117772 CTATTTCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 34 0.83
27 7 0.17
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (25 bp):
CTTTTCTTTCTTTCCTTCTTTTTTT
Found at i:117742 original size:17 final size:17
Alignment explanation
Indices: 117703--117742 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
117693 TTAACTTTTC
117703 TCCTTC-TTTCTTTCTT
1 TCCTTCTTTTCTTTCTT
**
117719 TTTTTCTTTTCTTTCTT
1 TCCTTCTTTTCTTTCTT
117736 TCCTTCT
1 TCCTTCT
117743 CTGTTTCGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TCCTTCTTTTCTTTCTT
Found at i:117758 original size:29 final size:30
Alignment explanation
Indices: 117721--117787 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
117711 TCTTTCTTTT
* *
117721 TTTCTTTTCTTTCTTTCCTTCTCTGTTTC-G
1 TTTC-TTTCTTTCCTTCCTTCTCTATTTCTG
* *
117751 TTTCTTTCTTTCCTTCCTTTTCTATTTCTT
1 TTTCTTTCTTTCCTTCCTTCTCTATTTCTG
117781 TTTCTTT
1 TTTCTTT
117788 TACTTTATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.01, C:0.25, G:0.03, T:0.70
Consensus pattern (30 bp):
TTTCTTTCTTTCCTTCCTTCTCTATTTCTG
Found at i:123000 original size:50 final size:50
Alignment explanation
Indices: 122902--123013 Score: 129
Period size: 50 Copynumber: 2.2 Consensus size: 50
122892 ATACATGTAT
* *
122902 GCTCATACGAGCTATAAACGATAAGCTCCTCTGAGCTGAAATAACAGTAA
1 GCTCATACGAGCTAGAAACGATAAGCTCCTCCGAGCTGAAATAACAGTAA
* * * *
122952 GCTCATATGAGCTGAGAATCGATAAGCT-CTCACGAGCTGCAA-ACCAGTAA
1 GCTCATACGAGCT-AGAAACGATAAGCTCCTC-CGAGCTGAAATAACAGTAA
*
123002 GATCATACGAGC
1 GCTCATACGAGC
123014 CGTGGTGTGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
50 32 0.62
51 20 0.38
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (50 bp):
GCTCATACGAGCTAGAAACGATAAGCTCCTCCGAGCTGAAATAACAGTAA
Found at i:125751 original size:32 final size:32
Alignment explanation
Indices: 125710--125773 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
125700 GTAAAAAATC
*
125710 CTATTTATAGGCTAAATTCGTAGGTCAAATAA
1 CTATTTATAGGCTAAATTCATAGGTCAAATAA
* *
125742 CTATTTATAGGTTAAATTCATAGGTTAAATAA
1 CTATTTATAGGCTAAATTCATAGGTCAAATAA
125774 TAATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (32 bp):
CTATTTATAGGCTAAATTCATAGGTCAAATAA
Found at i:132108 original size:85 final size:87
Alignment explanation
Indices: 131958--132132 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 87
131948 AGGCCTTGTT
* * * **
131958 CTTGGGTAATAATTGCTATGATAAAAGTCAAATGTTTTTTATCTGTAGAAGACTTGTTTAACTGA
1 CTTGAGTAATAATTGCAATGATAAAAGTCAAATGTTCTTTATAGGTAGAAGACTTGTTTAACTGA
132023 GGTTTAAAATGTTAATAAATTG
66 GGTTTAAAATGTTAATAAATTG
* * * * *
132045 CTTGAGTAATAATTGCAATGGT-ATAGT-AAATGTTCTTTATAGGTGGAAGAGTTGTTTAGCTGA
1 CTTGAGTAATAATTGCAATGATAAAAGTCAAATGTTCTTTATAGGTAGAAGACTTGTTTAACTGA
* *
132108 GGTTTAAACTGTTAATAGATTG
66 GGTTTAAAATGTTAATAAATTG
132130 CTT
1 CTT
132133 CACAGTTCAC
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
85 53 0.70
86 4 0.05
87 19 0.25
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (87 bp):
CTTGAGTAATAATTGCAATGATAAAAGTCAAATGTTCTTTATAGGTAGAAGACTTGTTTAACTGA
GGTTTAAAATGTTAATAAATTG
Found at i:145593 original size:118 final size:119
Alignment explanation
Indices: 145384--145624 Score: 475
Period size: 118 Copynumber: 2.0 Consensus size: 119
145374 AAACGGAAAG
145384 AAGTTAGTTTCAGTATGTAAAAGATTTTTTTTTTTATAGTTCTCTTTCCCCCTTTAACTTCACCT
1 AAGTTAGTTTCAGTATGTAAAAGATTTTTTTTTTTATAGTTCTCTTTCCCCCTTTAACTTCACCT
145449 GACTTCCAATGGAACCAGTTGAACCGACAATGGAGATAGGCTTGGGGCCATCCC
66 GACTTCCAATGGAACCAGTTGAACCGACAATGGAGATAGGCTTGGGGCCATCCC
145503 AAGTTAGTTTCAGTATGTAAAAGA-TTTTTTTTTTATAGTTCTCTTTCCCCCTTTAACTTCACCT
1 AAGTTAGTTTCAGTATGTAAAAGATTTTTTTTTTTATAGTTCTCTTTCCCCCTTTAACTTCACCT
145567 GACTTCCAATGGAACCAGTTGAACCGACAATGGAGATAGGCTTGGGGCCATCCC
66 GACTTCCAATGGAACCAGTTGAACCGACAATGGAGATAGGCTTGGGGCCATCCC
145621 AAGT
1 AAGT
145625 CTTGCGTCCA
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 98 0.80
119 24 0.20
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (119 bp):
AAGTTAGTTTCAGTATGTAAAAGATTTTTTTTTTTATAGTTCTCTTTCCCCCTTTAACTTCACCT
GACTTCCAATGGAACCAGTTGAACCGACAATGGAGATAGGCTTGGGGCCATCCC
Found at i:151049 original size:25 final size:24
Alignment explanation
Indices: 151021--151130 Score: 113
Period size: 22 Copynumber: 4.6 Consensus size: 24
151011 TTATTATGCA
*
151021 CTAATGAACAGAGAGCACTAAAGTG
1 CTAAT-AACAGAGAGCACTAATGTG
151046 CT-A-AACAGAGAGCAC-AGATGTG
1 CTAATAACAGAGAGCACTA-ATGTG
* *
151068 CT-A-AACAGAGAGCATTAACGTG
1 CTAATAACAGAGAGCACTAATGTG
*
151090 CTAGTAATCAGAGAGCACTAATGTG
1 CTAATAA-CAGAGAGCACTAATGTG
151115 CTAATAATCAGAGAGC
1 CTAATAA-CAGAGAGC
151131 GCGCTAAAGT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.01
22 36 0.49
23 1 0.01
24 3 0.04
25 32 0.44
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (24 bp):
CTAATAACAGAGAGCACTAATGTG
Found at i:151052 original size:22 final size:22
Alignment explanation
Indices: 151027--151118 Score: 114
Period size: 22 Copynumber: 4.0 Consensus size: 22
151017 TGCACTAATG
*
151027 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAATGTGCTA
151049 AACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-ATGTGCTA
* *
151071 AACAGAGAGCATTAACGTGCTA
1 AACAGAGAGCACTAATGTGCTA
151093 GTAATCAGAGAGCACTAATGTGCTA
1 --AA-CAGAGAGCACTAATGTGCTA
151118 A
1 A
151119 TAATCAGAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
21 1 0.02
22 37 0.62
23 2 0.03
24 2 0.03
25 18 0.30
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (22 bp):
AACAGAGAGCACTAATGTGCTA
Found at i:152122 original size:11 final size:11
Alignment explanation
Indices: 152083--152115 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
152073 TTGTTTTGAT
152083 TAAT-TAAT-A
1 TAATATAATAA
152092 TAATATAATAA
1 TAATATAATAA
152103 TAATATAATAA
1 TAATATAATAA
152114 TA
1 TA
152116 TTTTAATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.18
10 4 0.18
11 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATATAATAA
Found at i:168870 original size:5 final size:5
Alignment explanation
Indices: 168862--168886 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
168852 AAATCATTTT
168862 CTTTC CTTTC CTTTC CTTTC CTTTC
1 CTTTC CTTTC CTTTC CTTTC CTTTC
168887 TATATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTTTC
Found at i:174209 original size:31 final size:31
Alignment explanation
Indices: 174149--174209 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
174139 ATTATACACG
* *
174149 TGAAACTCTAATTGTGGTTTAAATGTATACT
1 TGAAACTCTAATTGTGATTTAAATATATACT
*
174180 TGAAACTCTAATTTTGATTT-AATCATATAC
1 TGAAACTCTAATTGTGATTTAAAT-ATATAC
174210 ATTTAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (31 bp):
TGAAACTCTAATTGTGATTTAAATATATACT
Found at i:176520 original size:51 final size:51
Alignment explanation
Indices: 176444--176548 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
176434 CATGGTCTTG
176444 ATTATTGAATTTTACCATTTTAATGGTGACCTTAATTTTAGCTAAAACCAC
1 ATTATTGAATTTTACCATTTTAATGGTGACCTTAATTTTAGCTAAAACCAC
*
176495 ATTATTGAATTTTATCATTTTAATGGTGACCTTAATTTTAGCTAAAACCAC
1 ATTATTGAATTTTACCATTTTAATGGTGACCTTAATTTTAGCTAAAACCAC
176546 ATT
1 ATT
176549 TAAACCCTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (51 bp):
ATTATTGAATTTTACCATTTTAATGGTGACCTTAATTTTAGCTAAAACCAC
Found at i:182130 original size:4 final size:4
Alignment explanation
Indices: 182121--182149 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
182111 AATGTATGAC
182121 TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA T
182150 CAAGGAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:203997 original size:11 final size:11
Alignment explanation
Indices: 203981--204006 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
203971 GTCACACATG
203981 AAAGTTATTTT
1 AAAGTTATTTT
203992 AAAGTTATTTT
1 AAAGTTATTTT
204003 AAAG
1 AAAG
204007 CAATTATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (11 bp):
AAAGTTATTTT
Found at i:208107 original size:5 final size:5
Alignment explanation
Indices: 208097--208121 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
208087 AAACGCCCAT
208097 CTTGC CTTGC CTTGC CTTGC CTTGC
1 CTTGC CTTGC CTTGC CTTGC CTTGC
208122 TCTAATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.20, T:0.40
Consensus pattern (5 bp):
CTTGC
Found at i:221637 original size:13 final size:13
Alignment explanation
Indices: 221621--221673 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
221611 TTTAAACCAA
221621 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* * *
221634 ACTTCTCCACAGC
1 ACTTTTCAAAAGC
*
221647 ACTTTTCAAAAGA
1 ACTTTTCAAAAGC
221660 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
221673 A
1 A
221674 TTGTCAAACT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:221673 original size:26 final size:26
Alignment explanation
Indices: 221621--221681 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
221611 TTTAAACCAA
* * *
221621 ACTTTTCAAAAGCACTTCTCCACAGC
1 ACTTTTCAAAAGAACTTCTCAAAAGC
*
221647 ACTTTTCAAAAGAACTTTTCAAAAGC
1 ACTTTTCAAAAGAACTTCTCAAAAGC
*
221673 A-TTGTCAAA
1 ACTTTTCAAA
221682 CTAACCCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.30
Consensus pattern (26 bp):
ACTTTTCAAAAGAACTTCTCAAAAGC
Found at i:241889 original size:2 final size:2
Alignment explanation
Indices: 241882--241919 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
241872 ATAGATAGAT
241882 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
241920 GCATATGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:259580 original size:6 final size:6
Alignment explanation
Indices: 259569--259598 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
259559 TTCATCGCTT
259569 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC
259599 ATCAACTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.83, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCCC
Found at i:271891 original size:29 final size:30
Alignment explanation
Indices: 271849--271910 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
271839 TAGGGACCTT
*
271849 ATCAAATTAGTCCCTCTATTATTAAAT-AG
1 ATCAAATTAGTCCCTCTACTATTAAATGAG
* * *
271878 ATCAATTTGGTCCCTGTACTATTAAATGAG
1 ATCAAATTAGTCCCTCTACTATTAAATGAG
271908 ATC
1 ATC
271911 TTTTGGTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (30 bp):
ATCAAATTAGTCCCTCTACTATTAAATGAG
Found at i:275330 original size:9 final size:9
Alignment explanation
Indices: 275316--275340 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
275306 CCAAGCACCA
275316 GGCGGTGGT
1 GGCGGTGGT
275325 GGCGGTGGT
1 GGCGGTGGT
275334 GGCGGTG
1 GGCGGTG
275341 CAACCCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.68, T:0.20
Consensus pattern (9 bp):
GGCGGTGGT
Found at i:285545 original size:23 final size:23
Alignment explanation
Indices: 285505--285567 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
285495 AAATCTAAAA
* *
285505 TTTAATCTTTATATTTTTTAATTT
1 TTTAAT-TTTAAAATTTTTAATTT
285529 TTTAATTTTAAAA-TTTTAATTT
1 TTTAATTTTAAAATTTTTAATTT
285551 TTTATATTTTAAAATTT
1 TTTA-ATTTTAAAATTT
285568 AAATTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 13 0.37
23 14 0.40
24 8 0.23
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAATTTTAAAATTTTTAATTT
Found at i:285548 original size:22 final size:23
Alignment explanation
Indices: 285520--285572 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
285510 TCTTTATATT
285520 TTTTAATTTTTTA-ATTTTAAAA
1 TTTTAATTTTTTATATTTTAAAA
285542 TTTTAATTTTTTATATTTTAAAA
1 TTTTAATTTTTTATATTTTAAAA
*
285565 TTTAAATT
1 TTTTAATT
285573 AAATTTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTAATTTTTTATATTTTAAAA
Found at i:290703 original size:18 final size:18
Alignment explanation
Indices: 290671--290705 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
290661 ATTTTTGACC
*
290671 TTTAAATTTTATTATTTT
1 TTTAAATTCTATTATTTT
*
290689 TTTAAATTCTCTTATTT
1 TTTAAATTCTATTATTT
290706 ATTAATTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTAAATTCTATTATTTT
Found at i:291709 original size:5 final size:5
Alignment explanation
Indices: 291699--291734 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
291689 GTAAGCTAAA
291699 CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC C
1 CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC C
291735 CAATCGCCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.61, G:0.19, T:0.00
Consensus pattern (5 bp):
CGCAC
Found at i:301406 original size:14 final size:14
Alignment explanation
Indices: 301387--301413 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
301377 TATAGATTAA
301387 AAATTTATAAATTC
1 AAATTTATAAATTC
301401 AAATTTATAAATT
1 AAATTTATAAATT
301414 TTTTATTTTG
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:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTATAAATTC
Found at i:307388 original size:67 final size:67
Alignment explanation
Indices: 307275--307407 Score: 257
Period size: 67 Copynumber: 2.0 Consensus size: 67
307265 ACCAAACCGA
307275 TTTGGGGTTTTACTTTACATTGATGAGAAAATACAGTCCATCACCAGTGAATTTTAGCTGTTTTT
1 TTTGGGGTTTTACTTTACATTGATGAGAAAATACAGTCCATCACCAGTGAATTTTAGCTGTTTTT
307340 CT
66 CT
*
307342 TTTGGGGTTTTACTTTACATTGATGAGAAAATACAGTCCATTACCAGTGAATTTTAGCTGTTTTT
1 TTTGGGGTTTTACTTTACATTGATGAGAAAATACAGTCCATCACCAGTGAATTTTAGCTGTTTTT
307407 C
66 C
307408 CATTTCTTTG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (67 bp):
TTTGGGGTTTTACTTTACATTGATGAGAAAATACAGTCCATCACCAGTGAATTTTAGCTGTTTTT
CT
Found at i:310640 original size:145 final size:143
Alignment explanation
Indices: 310379--310662 Score: 505
Period size: 145 Copynumber: 2.0 Consensus size: 143
310369 TGGCCTTGTG
* *
310379 TATTAGGCTTTTCATCTTTATATTCTTGTTTCCAGTTGCTGAGATTGCTCAAAAGTAGGAGATAT
1 TATTAGGATTTTCATATTTATATTCTTGTTTCCAGTTGCTGAGATTGCTCAAAAGTAGGAGATAT
* * *
310444 ATTTCTGTTTCTATTACTTAGTCATTATATATATTGCTTTGATTTCTCTAAACATTTTCGTCCCA
66 ATTTCTGTTTCTATTACCTAGTCATCACATATATTGCTTTGATTTCTCTAAACATTTTCGTCCCA
310509 TTGGTCTTCTGTA
131 TTGGTCTTCTGTA
310522 TATTAGGATTTTCATATTTATATTCTTTGTTTCCAGTTGCTGAGATTGCTCAAAAAGTAGGAGAT
1 TATTAGGATTTTCATATTTATATTC-TTGTTTCCAGTTGCTGAGATTGCTC-AAAAGTAGGAGAT
310587 ATATTTCTGTTTCTATTACCTAGTCATCACATATATTGCTTTGATTTCTCTAAACATTTTCGTCC
64 ATATTTCTGTTTCTATTACCTAGTCATCACATATATTGCTTTGATTTCTCTAAACATTTTCGTCC
310652 CATTGGTCTTC
129 CATTGGTCTTC
310663 CTCTTCTACT
Statistics
Matches: 134, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
143 23 0.17
144 25 0.19
145 86 0.64
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (143 bp):
TATTAGGATTTTCATATTTATATTCTTGTTTCCAGTTGCTGAGATTGCTCAAAAGTAGGAGATAT
ATTTCTGTTTCTATTACCTAGTCATCACATATATTGCTTTGATTTCTCTAAACATTTTCGTCCCA
TTGGTCTTCTGTA
Found at i:328069 original size:4 final size:4
Alignment explanation
Indices: 328062--328087 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
328052 TTCTTCTTCC
328062 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
328088 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:334675 original size:5 final size:5
Alignment explanation
Indices: 334665--334734 Score: 106
Period size: 5 Copynumber: 14.0 Consensus size: 5
334655 TGAGATGGGT
*
334665 GTATA GTATA GTATA GTATA GTATA GTATA GTATA GTATA GTATA GTACA
1 GTATA GTATA GTATA GTATA GTATA GTATA GTATA GTATA GTATA GTATA
*
334715 GCT-TA GTATA GTATG GTATA
1 G-TATA GTATA GTATA GTATA
334735 TCATAGCATA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
4 1 0.02
5 57 0.97
6 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (5 bp):
GTATA
Found at i:335830 original size:13 final size:13
Alignment explanation
Indices: 335812--335859 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
335802 TTCTTCATTC
335812 TTTTGAAAAGTGA
1 TTTTGAAAAGTGA
335825 TTTTGAAAAGT-A
1 TTTTGAAAAGTGA
*
335837 CTTTT-AAGAAGTGC
1 -TTTTGAA-AAGTGA
335851 TTTTGAAAA
1 TTTTGAAAA
335860 TTTTAAGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
12 3 0.10
13 25 0.83
14 2 0.07
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTGA
Found at i:336020 original size:21 final size:20
Alignment explanation
Indices: 335994--336032 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
335984 TTTTAGCAAA
*
335994 AATATTAATATTTTAATATAT
1 AATATTAAT-TTTAAATATAT
336015 AATATTAATTTTAAATAT
1 AATATTAATTTTAAATAT
336033 TTCTAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATTAATTTTAAATATAT
Found at i:336341 original size:16 final size:16
Alignment explanation
Indices: 336320--336353 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
336310 TAAAAGGGAT
336320 AATATTTGAGATATCA
1 AATATTTGAGATATCA
*
336336 AATATTTGAGGTATCA
1 AATATTTGAGATATCA
336352 AA
1 AA
336354 AAGAAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (16 bp):
AATATTTGAGATATCA
Found at i:337883 original size:16 final size:16
Alignment explanation
Indices: 337836--337883 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
337826 TAGAGTTTTG
*
337836 AATTATTTTGAAATTA
1 AATTATTTTGAATTTA
* **
337852 AATCATTTTTTCATTTA
1 AATTA-TTTTGAATTTA
337869 AATTATTTTGAATTT
1 AATTATTTTGAATTT
337884 GAACACCTTC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (16 bp):
AATTATTTTGAATTTA
Found at i:346016 original size:30 final size:30
Alignment explanation
Indices: 345982--346069 Score: 140
Period size: 30 Copynumber: 2.9 Consensus size: 30
345972 AAATTGACCA
* *
345982 TTCTCCATCAAACTCTCTGCACAAATAAAT
1 TTCTCCATCAAACTCTCTGCACAAACAAAC
*
346012 TTCTCCATCTAACTCTCTGCACAAACAAAC
1 TTCTCCATCAAACTCTCTGCACAAACAAAC
*
346042 TTCTCCATCAAACTCTCTGCCCAAACAA
1 TTCTCCATCAAACTCTCTGCACAAACAA
346070 CACATGAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.34, C:0.35, G:0.03, T:0.27
Consensus pattern (30 bp):
TTCTCCATCAAACTCTCTGCACAAACAAAC
Found at i:346277 original size:11 final size:11
Alignment explanation
Indices: 346261--346301 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
346251 CATGCATCTT
346261 TTCCACTCACA
1 TTCCACTCACA
346272 TTCCACTC-CA
1 TTCCACTCACA
346282 TTCTCACTCACA
1 TTC-CACTCACA
*
346294 TCCCACTC
1 TTCCACTC
346302 TGCATTCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 5 0.19
11 18 0.67
12 4 0.15
ACGTcount: A:0.22, C:0.49, G:0.00, T:0.29
Consensus pattern (11 bp):
TTCCACTCACA
Found at i:348929 original size:11 final size:11
Alignment explanation
Indices: 348915--348954 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 11
348905 ACTTTTTTAA
348915 TTTTAAAATAT
1 TTTTAAAATAT
348926 TTTTAAAATATAT
1 TTTT-AAA-ATAT
348939 TTTTAAAAT-T
1 TTTTAAAATAT
348949 TTTTAA
1 TTTTAA
348955 TTTTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 7 0.26
11 6 0.22
12 6 0.22
13 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:348942 original size:30 final size:30
Alignment explanation
Indices: 348883--348995 Score: 94
Period size: 30 Copynumber: 3.8 Consensus size: 30
348873 TATTTTTTAA
* *
348883 AATTTTAAAATATTTTTTACATACTTTTTT
1 AATTTTAAAATATTTTTAAAATACTTTTTT
348913 AATTTTAAAATATTTTTAAAATA-TATTTTT
1 AATTTTAAAATATTTTTAAAATACT-TTTTT
* *
348943 AAAATTTT---TTAATTTTAAAATACTTTTTTT
1 --AATTTTAAAATATTTTTAAAATAC-TTTTTT
348973 AATTTTTTAAAA-A-TTTTAAAATA
1 AA--TTTTAAAATATTTTTAAAATA
348996 AAAATGGGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
28 2 0.03
29 13 0.19
30 35 0.51
31 11 0.16
32 7 0.10
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
AATTTTAAAATATTTTTAAAATACTTTTTT
Found at i:348951 original size:40 final size:42
Alignment explanation
Indices: 348885--348970 Score: 133
Period size: 40 Copynumber: 2.1 Consensus size: 42
348875 TTTTTTAAAA
*
348885 TTTTAAAATATTTTTTACATACTTTTTTAATTTTAAAATA-T
1 TTTTAAAATATTTTTTACATAATTTTTTAATTTTAAAATACT
348926 TTTTAAAATATATTTTTA-A-AATTTTTTAATTTTAAAATACT
1 TTTTAAAATAT-TTTTTACATAATTTTTTAATTTTAAAATACT
348967 TTTT
1 TTTT
348971 TTAATTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
40 19 0.45
41 17 0.40
42 6 0.14
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (42 bp):
TTTTAAAATATTTTTTACATAATTTTTTAATTTTAAAATACT
Found at i:348978 original size:28 final size:29
Alignment explanation
Indices: 348926--348982 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
348916 TTTAAAATAT
348926 TTTTAAAATATATTTTTAAAATTTTTTAA
1 TTTTAAAATATATTTTTAAAATTTTTTAA
*
348955 TTTTAAAATACT-TTTTT-TAATTTTTTAA
1 TTTTAAAATA-TATTTTTAAAATTTTTTAA
348983 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 10 0.38
29 15 0.58
30 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTAAAATATATTTTTAAAATTTTTTAA
Found at i:350585 original size:3 final size:3
Alignment explanation
Indices: 350577--350628 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
350567 CAATTTTATG
* *
350577 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTG TTA TATA TATA TCT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA TTA
350624 TTA TT
1 TTA TT
350629 CTCATTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 1 0.02
3 33 0.79
4 8 0.19
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:350728 original size:12 final size:12
Alignment explanation
Indices: 350713--350737 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
350703 TATATTTGCT
350713 TATATATGTATA
1 TATATATGTATA
350725 TATATATGTATA
1 TATATATGTATA
350737 T
1 T
350738 GTATTTGTTT
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATATATGTATA
Found at i:352891 original size:19 final size:20
Alignment explanation
Indices: 352851--352894 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
352841 GTCTCTTTAG
* *
352851 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
352870 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
352889 GCATTA
1 GCATTA
352895 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:355455 original size:7 final size:8
Alignment explanation
Indices: 355434--355463 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
355424 TCTCATGAAT
355434 TCAAAAAA
1 TCAAAAAA
355442 TCAAAAAA
1 TCAAAAAA
355450 TCAAAAAAA
1 TC-AAAAAA
355459 TCAAA
1 TCAAA
355464 GTCAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (8 bp):
TCAAAAAA
Found at i:357832 original size:88 final size:88
Alignment explanation
Indices: 357615--358391 Score: 1038
Period size: 88 Copynumber: 8.9 Consensus size: 88
357605 ATGAAGTTAC
* * * *
357615 AGATCTTGCCTTCCTGCATTGATAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
*
357680 T-AGTGGAGCTGGTT-AA-AGAAA
66 TGA-TGGAGCTGGTTGAAGACAAA
* *
357701 AGATCTTGCTTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
*
357766 TGATAGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
357789 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
357854 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
357877 AGATCTTGCTTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGCTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
*
357942 TGATAGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
357965 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
358030 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
358053 AGATCTTGCTTTTCTGCATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
*
358118 TGATAGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
358141 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
* **
358206 T-AGTGGAGCTGGTTAAAGA-AGC
66 TGA-TGGAGCTGGTTGAAGACAAA
* * * ** *
358228 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCATCCATCGATT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGGTT
* * * **
358291 G-CAGTGGAGCTAGTTAAAGA-AGC
65 GTGA-TGGAGCTGGTTGAAGACAAA
* * * * **
358314 AGATCTTGCCTTCCTGCATTAACAGCAAAACAGATC-AA-AAACAAAGCCTTGCCTCCATCGGTT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGGTT
*
358377 G-CATTGGAGCTGGTT
65 GTGA-TGGAGCTGGTT
358392 AAAGGTTACA
Statistics
Matches: 631, Mismatches: 53, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
85 8 0.01
86 172 0.27
87 40 0.06
88 411 0.65
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:357964 original size:41 final size:41
Alignment explanation
Indices: 357831--357964 Score: 94
Period size: 43 Copynumber: 3.1 Consensus size: 41
357821 GATCGAAGAC
* *
357831 ACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAG
1 ACAAACCTTGCCTCTTTCGGCTGTGATAGAGCTGGTTGAAG
* * * * * *
357872 ACAAAAGATCTTG-CT-TTTCTGCAT-TGACAGCGAAGCAGATCGAAG
1 AC--AA-ACCTTGCCTCTTTCGGC-TGTGATA--G-AGCTGGTTGAAG
357917 ACACAAACCTTGCCTCTTTCGGCTGTGATAGAGCTGGTTGAAG
1 --ACAAACCTTGCCTCTTTCGGCTGTGATAGAGCTGGTTGAAG
357960 ACAAA
1 ACAAA
357965 AGATCTTGCC
Statistics
Matches: 67, Mismatches: 14, Indels: 24
0.64 0.13 0.23
Matches are distributed among these distances:
41 7 0.10
42 8 0.12
43 14 0.21
44 12 0.18
45 14 0.21
46 10 0.15
47 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (41 bp):
ACAAACCTTGCCTCTTTCGGCTGTGATAGAGCTGGTTGAAG
Found at i:358434 original size:86 final size:84
Alignment explanation
Indices: 358141--358438 Score: 226
Period size: 86 Copynumber: 3.4 Consensus size: 84
358131 TGAAGACAAA
* * * * * * *
358141 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAA-CCTTGCCTCTC-TCGGT
1 AGATCTTGCCTCCCTGCAGT-A-AGCGAAGCAGATC-AA-AAACAAAGCCTTGCATC-CATCGAT
* *
358204 TGTAGTGGAGCTGGTTAAAGAAGC
61 TGCAGTGGAGCTAGTTAAAGAAGC
* * * *
358228 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCATCCATCGATTGC
1 AGATCTTGCCTCCCTGCAGT-A-AGCGAAGCAGATCAAAAACAAAGCCTTGCATCCATCGATTGC
358293 AGTGGAGCTAGTTAAAGAAGC
64 AGTGGAGCTAGTTAAAGAAGC
* * * * * *
358314 AGATCTTGCCTTCCTGCATTAACAGCAAAACAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGC
1 AGATCTTGCCTCCCTGCAGT-A-AGCGAAGCAGATCAAAAACAAAGCCTTGCATCCATCGATTGC
* * *
358379 ATTGGAGCTGGTTAAAGGTTA-C
64 AGTGGAGCTAGTTAAA-G-AAGC
* * *
358401 AGATTTTGTCTCCCTAAGCCGT-AGCGAAGCAGATCAAA
1 AGATCTTGCCTCCCT--GCAGTAAGCGAAGCAGATCAAA
358439 GACAGCAAAT
Statistics
Matches: 179, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
85 7 0.04
86 122 0.68
87 46 0.26
88 1 0.01
89 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (84 bp):
AGATCTTGCCTCCCTGCAGTAAGCGAAGCAGATCAAAAACAAAGCCTTGCATCCATCGATTGCAG
TGGAGCTAGTTAAAGAAGC
Found at i:360240 original size:14 final size:14
Alignment explanation
Indices: 360223--360249 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
360213 TATATTTGCT
360223 TATATATGTATATA
1 TATATATGTATATA
360237 TATATATGTATAT
1 TATATATGTATAT
360250 GTATTTGTTT
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TATATATGTATATA
Found at i:362898 original size:22 final size:22
Alignment explanation
Indices: 362873--362921 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
362863 ATGCCAATTA
362873 GAGTGAGAATAGAGTGGAATGT
1 GAGTGAGAATAGAGTGGAATGT
*
362895 GAGTGAGAATGGAGTGGAATGT
1 GAGTGAGAATAGAGTGGAATGT
362917 GAGTG
1 GAGTG
362922 GAAAAGGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.45, T:0.22
Consensus pattern (22 bp):
GAGTGAGAATAGAGTGGAATGT
Found at i:363152 original size:30 final size:30
Alignment explanation
Indices: 363116--363203 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
363106 TTTTCATGTG
* *
363116 TTGTTTGGGCAGAGAGTTTGATGGAGAAGT
1 TTGTTTGTGCAGAGAGTTTGATGGAGAAAT
* *
363146 TTGTTTGTGCAGAGAATTAGATGGAGAAAT
1 TTGTTTGTGCAGAGAGTTTGATGGAGAAAT
* *
363176 TTATTTGTGCAGAGAGTTTGACGGAGAA
1 TTGTTTGTGCAGAGAGTTTGATGGAGAA
363204 TGGTCAATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.05, G:0.34, T:0.33
Consensus pattern (30 bp):
TTGTTTGTGCAGAGAGTTTGATGGAGAAAT
Found at i:365242 original size:71 final size:72
Alignment explanation
Indices: 365151--365290 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 72
365141 CCCCAAAAAG
* * * *
365151 AATCATTAATTCGCAAGTTGAAGAAAGACAAAGTGAATGGTAATTAATTAATATA-AAAGGGGGT
1 AATCATTAATTCACAAGTTGAAGAAAGACAAAGTAAACGGTAATTAATTAATATAGAAAGGAGGT
365215 TAAGGCA
66 TAAGGCA
* * *
365222 AATCATTAATTCATAGGTTGAAGAAAGACAAAGTAAACGGTATTTAATTAATATAGAAAGGAGGT
1 AATCATTAATTCACAAGTTGAAGAAAGACAAAGTAAACGGTAATTAATTAATATAGAAAGGAGGT
365287 TAAG
66 TAAG
365291 ACGAACATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
71 49 0.80
72 12 0.20
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.26
Consensus pattern (72 bp):
AATCATTAATTCACAAGTTGAAGAAAGACAAAGTAAACGGTAATTAATTAATATAGAAAGGAGGT
TAAGGCA
Found at i:371429 original size:13 final size:13
Alignment explanation
Indices: 371411--371436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
371401 TGATTGAGCC
371411 ATTAATATTGCCT
1 ATTAATATTGCCT
371424 ATTAATATTGCCT
1 ATTAATATTGCCT
371437 TTGCTATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTAATATTGCCT
Found at i:377156 original size:5 final size:5
Alignment explanation
Indices: 377146--377179 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
377136 CAAATTAGGT
*
377146 TTTTC TTTTC TTTTC TTCTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
377180 TTAATTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:406355 original size:40 final size:40
Alignment explanation
Indices: 406282--406401 Score: 95
Period size: 40 Copynumber: 3.0 Consensus size: 40
406272 AAATTGTTCA
* *
406282 TCCACGTCAGCAAATCGCGTCCT--CGTAGG-CGCGATTTGTG
1 TCCACGTAAGCAAATCGCG--CTGACGT-GGACGCGATTTCTG
*
406322 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATGTCCTG
1 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGAT-TTCTG
* * **
406363 -ACATGTACCCTAACATCGCGCTGACGTGGACGCGATTTC
1 TCCACGTAAGC-AA-ATCGCGCTGACGTGGACGCGATTTC
406402 GCGAAAAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 33 0.50
41 7 0.11
42 22 0.33
ACGTcount: A:0.21, C:0.30, G:0.27, T:0.23
Consensus pattern (40 bp):
TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATTTCTG
Found at i:408689 original size:30 final size:29
Alignment explanation
Indices: 408655--408711 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
408645 GGGTAAAACC
* *
408655 GAATTAATTCGTTTAATCGGTCGGTTAACT
1 GAATTAATTCGGTCAAT-GGTCGGTTAACT
408685 GAATTAATTCGGTCAATGGTCGGTTAA
1 GAATTAATTCGGTCAATGGTCGGTTAA
408712 TAATTTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (29 bp):
GAATTAATTCGGTCAATGGTCGGTTAACT
Found at i:410306 original size:31 final size:31
Alignment explanation
Indices: 410248--410336 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 31
410238 AGCAACTCAA
* *
410248 TGACTTAAATAAAAA-ATACAAATAGTTTAG
1 TGACTTAAATAAAAACATTCGAATAGTTTAG
*** * *
410278 TTTTTTAAATAAAAACTTTTGAATAGTTTAG
1 TGACTTAAATAAAAACATTCGAATAGTTTAG
*
410309 TGACTTAAATGAAAACATTCGAATAGTT
1 TGACTTAAATAAAAACATTCGAATAGTT
410337 CAATGATCAT
Statistics
Matches: 45, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
30 12 0.27
31 33 0.73
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (31 bp):
TGACTTAAATAAAAACATTCGAATAGTTTAG
Found at i:430419 original size:28 final size:28
Alignment explanation
Indices: 430384--430439 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
430374 ATTTCATTAG
430384 ACAAGTAGATGAA-TTTCTCCATTTGTTT
1 ACAAGTAGAT-AAGTTTCTCCATTTGTTT
* *
430412 ACAAGTAGATAAGTTTTTTCATTTGTTT
1 ACAAGTAGATAAGTTTCTCCATTTGTTT
430440 CACGAATCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (28 bp):
ACAAGTAGATAAGTTTCTCCATTTGTTT
Found at i:430735 original size:13 final size:13
Alignment explanation
Indices: 430698--430737 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
430688 AGTTCTTCAT
430698 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
430711 TGCTATGGAAAAG
1 TGCTTTTGAAAAG
*
430724 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
430737 T
1 T
430738 TTGGTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:432860 original size:31 final size:31
Alignment explanation
Indices: 432799--432863 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
432789 TTTAACAGCC
* *
432799 CAATGATTTAAATAAAAACTATCGACTAGTT
1 CAATGACTTAAATAAAAACTATAGACTAGTT
* *
432830 CAATGACTTAAATGAAAACTTTTAGA-TAGTT
1 CAATGACTTAAATAAAAAC-TATAGACTAGTT
432861 CAA
1 CAA
432864 AAATCATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (31 bp):
CAATGACTTAAATAAAAACTATAGACTAGTT
Found at i:437773 original size:20 final size:20
Alignment explanation
Indices: 437735--437774 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
437725 TAATATTTTG
*
437735 TTAACTAATAATTATAATTT
1 TTAACTAATAATTACAATTT
437755 TTAACTAAATAATT-CAATTT
1 TTAACT-AATAATTACAATTT
437775 AAAGGGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAACTAATAATTACAATTT
Found at i:462440 original size:36 final size:37
Alignment explanation
Indices: 462371--462440 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
462361 ATATTTTTAT
* *
462371 ATTTGTATATATTTTTAAAAATTTGTGATTTTAATTA
1 ATTTGTATAGATTTTTAAAAATTTGTGAGTTTAATTA
*
462408 ATTT-TATAGATTTTTAAATAATTT-TTAGTTTAA
1 ATTTGTATAGATTTTTAAA-AATTTGTGAGTTTAA
462441 GATTTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 20 0.69
37 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (37 bp):
ATTTGTATAGATTTTTAAAAATTTGTGAGTTTAATTA
Found at i:462448 original size:25 final size:24
Alignment explanation
Indices: 462410--462457 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
462400 TTTAATTAAT
462410 TTTATAGATTTTTAAATAATTTTTAG
1 TTTATAGATTTTT-AA-AATTTTTAG
462436 TTTA-AGATTTTTAAAATTTTTA
1 TTTATAGATTTTTAAAATTTTTA
462458 AAATTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.36
24 2 0.09
25 8 0.36
26 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (24 bp):
TTTATAGATTTTTAAAATTTTTAG
Found at i:470788 original size:18 final size:19
Alignment explanation
Indices: 470746--470788 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
470736 TATCAATTTC
* *
470746 ACATTTTATCTTTAAGATA
1 ACATTTTATCTTAAAAATA
470765 AC-TTTTAT-TTAAAAATA
1 ACATTTTATCTTAAAAATA
470782 ACATTTT
1 ACATTTT
470789 TTATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 10 0.48
19 2 0.10
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (19 bp):
ACATTTTATCTTAAAAATA
Found at i:476157 original size:25 final size:25
Alignment explanation
Indices: 476112--476174 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
476102 TAAGCATGTA
*
476112 TGTACATAT-TA-AATATAAAAACG
1 TGTACATATATATATTATAAAAACG
* *
476135 TGTACATATATATATTATGAAAATG
1 TGTACATATATATATTATAAAAACG
* *
476160 TATATATATATATAT
1 TGTACATATATATAT
476175 AGATATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 9 0.27
24 2 0.06
25 22 0.67
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (25 bp):
TGTACATATATATATTATAAAAACG
Found at i:476263 original size:3 final size:3
Alignment explanation
Indices: 476224--476333 Score: 86
Period size: 3 Copynumber: 36.7 Consensus size: 3
476214 ATGTATTAGT
* * *
476224 ATA ATA GTA ATAA ATA AAA AGA A-A ATA A-A ACTA ATA ATA ATTA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A-TA ATA ATA A-TA ATA
* **
476270 ATA GTA ATA ATA ATA ATA ACC ATA ATA ATA ATA AGCTA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA ATA ATA ATA
476316 AT- ATA ATA AT- ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
476334 GAGCAAATAA
Statistics
Matches: 87, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
2 10 0.11
3 66 0.76
4 8 0.09
5 3 0.03
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:481206 original size:123 final size:123
Alignment explanation
Indices: 480977--481323 Score: 606
Period size: 123 Copynumber: 2.8 Consensus size: 123
480967 TTATTTCGAG
* * *
480977 TTGATGTTTCTG-GTCAAATAATATAAAATCGCCTCTACCAGTATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCCTCTACCAGAATGCTATTTGAGAAGAAATTGT
* * * * *
481041 GAAATCGCACCCGCGTGAACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAAGTCATGTAAGAAATAATTTTT
481100 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGAATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGAATGCTATTTGAGAAGAAATTGTG
481165 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAAGTCATGTAAGAAATAATTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAAGTCATGTAAGAAATAATTTTT
481223 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGAATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGAATGCTATTTGAGAAGAAATTGTG
481288 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTA
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTA
481324 GCAAGTTTGG
Statistics
Matches: 215, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
123 214 1.00
124 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGAATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAAGTCATGTAAGAAATAATTTTT
Found at i:483321 original size:51 final size:50
Alignment explanation
Indices: 483250--483364 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 50
483240 TTTAAAAAAT
* *
483250 GAAATTAAGGAGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGATG
1 GAAATTGA-GAGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
* *
483301 GGAATTGAGAGAAACTTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGAAA-TTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
483352 GAAATTTAGAGAA
1 GAAATTGAGAGAA
483365 TTTTGGAAGG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 6 0.11
51 51 0.89
ACGTcount: A:0.43, C:0.01, G:0.27, T:0.30
Consensus pattern (50 bp):
GAAATTGAGAGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:483362 original size:22 final size:22
Alignment explanation
Indices: 483334--483384 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
483324 AAATATGGGT
483334 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
483356 TTTAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
483378 TTGAGAG
1 TTGAGAG
483385 GATTAGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:486472 original size:19 final size:19
Alignment explanation
Indices: 486438--486474 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
486428 ATTATTTAAT
**
486438 TAAAAAATTATTAAAAATG
1 TAAAAAATTAAAAAAAATG
486457 TAAAAAATTAAAAAAAAT
1 TAAAAAATTAAAAAAAAT
486475 TCAAACCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
TAAAAAATTAAAAAAAATG
Found at i:510785 original size:34 final size:34
Alignment explanation
Indices: 510746--510822 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
510736 AATTTAATCC
* * *
510746 TCTCTCAAATTTCCTCT-TAATTTCTTCTAAATTT
1 TCTCTCAAATTTCCTCTCAAATTCCTTC-AAAATT
*
510780 TCTCTC-AATTTGCTCTCAAATTCCTTCAAAATT
1 TCTCTCAAATTTCCTCTCAAATTCCTTCAAAATT
510813 TCTCTCAAAT
1 TCTCTCAAAT
510823 CCATATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 20 0.54
34 17 0.46
ACGTcount: A:0.26, C:0.26, G:0.01, T:0.47
Consensus pattern (34 bp):
TCTCTCAAATTTCCTCTCAAATTCCTTCAAAATT
Found at i:510822 original size:11 final size:11
Alignment explanation
Indices: 510746--510822 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
510736 AATTTAATCC
510746 TCTCTCAAATT
1 TCTCTCAAATT
*
510757 TC-CTCTTAATT
1 TCTCTC-AAATT
510768 TCT-TCTAAATTT
1 TCTCTC-AAA-TT
510780 TCTCTC-AATT
1 TCTCTCAAATT
510790 TGCTCTCAAATT
1 T-CTCTCAAATT
*
510802 CCT-TCAAAATT
1 TCTCTC-AAATT
510813 TCTCTCAAAT
1 TCTCTCAAAT
510823 CCATATTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
10 8 0.15
11 33 0.61
12 11 0.20
13 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.01, T:0.47
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:510847 original size:51 final size:51
Alignment explanation
Indices: 510784--510881 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
510774 AAATTTTCTC
510784 TCAATTTGCTCTCAA-ATTC-CTTCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGCTCTCAAGATTCTCTT--AAATTTCTCTCAAATCCATATTTATTT
* * * *
510835 TCAATTTTCTCTCAAGTTTCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAGATTCTCTTAAATTTCTCTCAAATCCATATTT
510882 TTAAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 35 0.85
52 3 0.07
53 3 0.07
ACGTcount: A:0.27, C:0.23, G:0.02, T:0.48
Consensus pattern (51 bp):
TCAATTTGCTCTCAAGATTCTCTTAAATTTCTCTCAAATCCATATTTATTT
Found at i:517941 original size:22 final size:21
Alignment explanation
Indices: 517917--517974 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
517907 AATATTTCTA
517917 AAAATGTAAAAATAAAATTTT
1 AAAATGTAAAAATAAAATTTT
* *
517938 AAAATATATAAATACAAATTTT
1 AAAATGTAAAAATA-AAATTTT
*
517960 AAAATGTCAAAATAA
1 AAAATGTAAAAATAA
517975 TATGTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAATGTAAAAATAAAATTTT
Found at i:517949 original size:23 final size:23
Alignment explanation
Indices: 517894--517964 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 23
517884 AAAAATATAT
*
517894 TATATAACATATAAATATTTCTAAAA
1 TATATAA-AAATAAA-ATTT-TAAAA
*
517920 -ATGTAAAAATAAAATTTTAAAA
1 TATATAAAAATAAAATTTTAAAA
517942 TATAT--AAATACAAATTTTAAAA
1 TATATAAAAATA-AAATTTTAAAA
517964 T
1 T
517965 GTCAAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 5 0.12
22 17 0.43
23 7 0.17
24 6 0.15
25 5 0.12
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (23 bp):
TATATAAAAATAAAATTTTAAAA
Found at i:518403 original size:28 final size:30
Alignment explanation
Indices: 518371--518427 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
518361 ATTTATAAAA
**
518371 TTTTAAATTAGTAA-TAAT-AAAATTATAC
1 TTTTAAATTAAAAATTAATAAAAATTATAC
*
518399 TTTTAATTTAAAAATTAATAAAAATTATA
1 TTTTAAATTAAAAATTAATAAAAATTATA
518428 AAAATATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 4 0.17
30 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (30 bp):
TTTTAAATTAAAAATTAATAAAAATTATAC
Found at i:523004 original size:28 final size:28
Alignment explanation
Indices: 522948--523004 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
522938 ACACACAGAC
** *
522948 ACACATTCTTACATACATACGTACTTAT
1 ACACATTCTTACATACATACAAACATAT
*
522976 ACACATTCTTACCTACATACAAACATAT
1 ACACATTCTTACATACATACAAACATAT
523004 A
1 A
523005 TGTATATGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.32
Consensus pattern (28 bp):
ACACATTCTTACATACATACAAACATAT
Done.