Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008437.1 Hibiscus syriacus cultivar Beakdansim tig00111236_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: 223559
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:3056 original size:18 final size:18
Alignment explanation
Indices: 3035--3083 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
3025 CCAAATTGTC
*
3035 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
* * *
3053 TATTACACAATTGTAAAA
1 TATTATATATTTGTAAAA
3071 TATTTATATATTT
1 TA-TTATATATTT
3084 TCTTTAAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:3994 original size:22 final size:23
Alignment explanation
Indices: 3954--3998 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3944 GTATTTAATA
*
3954 TTTTAAAATGACTTGAAAAAATT
1 TTTTAAAATGAATTGAAAAAATT
*
3977 TTTTATAATGAATT-AAAAAATT
1 TTTTAAAATGAATTGAAAAAATT
3999 ACATTACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (23 bp):
TTTTAAAATGAATTGAAAAAATT
Found at i:6088 original size:16 final size:16
Alignment explanation
Indices: 6067--6104 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6057 TAAAAAACTA
6067 ATATTTT-ATAAATATT
1 ATATTTTAATAAA-ATT
*
6083 ATATTTTAATTAAATT
1 ATATTTTAATAAAATT
6099 ATATTT
1 ATATTT
6105 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTAATAAAATT
Found at i:6643 original size:21 final size:20
Alignment explanation
Indices: 6609--6651 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
6599 GATTGATATC
*
6609 ATTGAATAGTTAAAAAATTG
1 ATTGAATAATTAAAAAATTG
*
6629 ATTGATATAATTAAAAGATTG
1 ATTGA-ATAATTAAAAAATTG
6650 AT
1 AT
6652 GCTCATATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (20 bp):
ATTGAATAATTAAAAAATTG
Found at i:7410 original size:27 final size:27
Alignment explanation
Indices: 7372--7424 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
7362 TATATAACGA
7372 TATTTTTAAACGCCGCTAAAACAATTG
1 TATTTTTAAACGCCGCTAAAACAATTG
7399 TATTTTTAAACGCCGCTAAAACAATT
1 TATTTTTAAACGCCGCTAAAACAATT
7425 TTGCGCCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (27 bp):
TATTTTTAAACGCCGCTAAAACAATTG
Found at i:11919 original size:14 final size:14
Alignment explanation
Indices: 11883--11925 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
11873 TTTTATATTT
11883 TAATAATAAAA-AA
1 TAATAATAAAATAA
**
11896 TACACCATAAAATAA
1 TA-ATAATAAAATAA
11911 TAATAATAAAATAA
1 TAATAATAAAATAA
11925 T
1 T
11926 TTGTAGTGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 2 0.08
14 18 0.75
15 4 0.17
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (14 bp):
TAATAATAAAATAA
Found at i:12650 original size:24 final size:23
Alignment explanation
Indices: 12603--12650 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
12593 TGGTTCGAAC
*
12603 AAAGGAAAAGAAAATGAAAGAAA
1 AAAGAAAAAGAAAATGAAAGAAA
12626 AAAGAAAAAGGAAAATG--AGAAA
1 AAAGAAAAA-GAAAATGAAAGAAA
12648 AAA
1 AAA
12651 CTTTTATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 8 0.35
24 7 0.30
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (23 bp):
AAAGAAAAAGAAAATGAAAGAAA
Found at i:13498 original size:15 final size:15
Alignment explanation
Indices: 13478--13511 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13468 GTGATGACAA
13478 AATAATAATAAAGAT
1 AATAATAATAAAGAT
**
13493 AATAATTTTAAAGAT
1 AATAATAATAAAGAT
13508 AATA
1 AATA
13512 CAAACTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
AATAATAATAAAGAT
Found at i:14896 original size:19 final size:19
Alignment explanation
Indices: 14846--14902 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
14836 TCATATTCTT
14846 TACATATATA-TATATATA
1 TACATATATATTATATATA
* * *
14864 TA-ACTATGTGTTATATATG
1 TACA-TATATATTATATATA
14883 TACATATATATTATAT-TA
1 TACATATATATTATATATA
14901 TA
1 TA
14903 TGAAATATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
17 1 0.03
18 9 0.30
19 19 0.63
20 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
TACATATATATTATATATA
Found at i:16761 original size:2 final size:2
Alignment explanation
Indices: 16754--16790 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16744 TTTGAAGAAA
16754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16791 AGTTATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18192 original size:2 final size:2
Alignment explanation
Indices: 18180--18209 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
18170 TGATACGATA
18180 AT AT GAT 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
18210 CACAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23558 original size:54 final size:54
Alignment explanation
Indices: 23465--23797 Score: 218
Period size: 54 Copynumber: 6.3 Consensus size: 54
23455 GGTAAGTGAG
* * * *
23465 ACTTGAAAATCTTCAG-ACAACAGGTTCGCTCCCTATTCCTTCATGGAGTAGA-A
1 ACTTGAAAATCTTCTGCA-AACGGGTTCGCTCCCTCTTCCTTCAGGGAGTAGAGA
* * ** *
23518 ACTCAT-ACAATCTTTTGCCTACGGGTTCGCTCCCTCTTCCTTCAGGGAGTATAGA
1 ACT--TGAAAATCTTCTGCAAACGGGTTCGCTCCCTCTTCCTTCAGGGAGTAGAGA
* * *
23573 ACTTGAAAATCTTCTGCAAACGGGTTCTCTCCCTCTTTCTTCAGGGAGTATAGA
1 ACTTGAAAATCTTCTGCAAACGGGTTCGCTCCCTCTTCCTTCAGGGAGTAGAGA
* * ** ** * *
23627 ACTCGAAAATCTTTTAAAGAACATG-TCTGCTCCCTATTCCTTCA--GAGTATAGA
1 ACTTGAAAATCTTCTGCA-AACGGGTTC-GCTCCCTCTTCCTTCAGGGAGTAGAGA
* * * * * * * *
23680 ACTCGAACATC-TCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGA
1 ACTTGAAAATCTTCTGCAAACGGGTTCGCTCCCTCTTCCTTCAGGGAGTAGAGA
* * * * * * *
23733 ACTCGAACATC-T-T-CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGA
1 ACTTGAAAATCTTCTGCAAACGGGTTCGCTCCCTCTTCCTTCAGGGAGTAGAGA
* *
23784 ACTCGAACATCTTC
1 ACTTGAAAATCTTC
23798 AACTGGGTTC
Statistics
Matches: 234, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
51 65 0.28
52 7 0.03
53 44 0.19
54 96 0.41
55 22 0.09
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (54 bp):
ACTTGAAAATCTTCTGCAAACGGGTTCGCTCCCTCTTCCTTCAGGGAGTAGAGA
Found at i:23751 original size:51 final size:51
Alignment explanation
Indices: 23538--23954 Score: 393
Period size: 51 Copynumber: 8.0 Consensus size: 51
23528 TCTTTTGCCT
* * * * * *
23538 ACGGGTTCGCTCCCTCTTCCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATC-T-T-CAA
* * * * * *
23592 ACGGGTTCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATC-TTCAA
** * *
23644 A-GAACATGTCTGCTCC--CTATTCCTTCA-GAGTATAGAACTCGAACATCTCTTCAA
1 ACG--GGT-TC-GCTCCTTCT-TTCTTTAAGGAGTATAGAACTCGAACA--TCTTCAA
23698 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
23749 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-A
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
*
23799 ACTGGGTTCGCTCCCTTC-TT-TTTAAGGAGTATAGAACTCGAACATCTTC-G
1 AC-GGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* * * *
23849 ACTGGGTTCGCTCCATT-TTTCTTCAAGGGAGTATGGAACTTAGACATATCTTCAA
1 AC-GGGTTCGCTCC-TTCTTTCTTTAA-GGAGTATAGAAC-TCGA-ACATCTTCAA
* * *
23904 ACGGATTCGCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
23955 CAATCGTGTC
Statistics
Matches: 314, Mismatches: 28, Indels: 45
0.81 0.07 0.12
Matches are distributed among these distances:
49 2 0.01
50 48 0.15
51 87 0.28
52 30 0.10
53 57 0.18
54 81 0.26
55 9 0.03
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (51 bp):
ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
Found at i:23926 original size:155 final size:153
Alignment explanation
Indices: 23671--23955 Score: 423
Period size: 155 Copynumber: 1.8 Consensus size: 153
23661 TATTCCTTCA
*
23671 GAGTATAGAACTCGAACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACT
1 GAGTATAGAACTCGAACA-CTCTTCAAACGGGTTCGCTCCTTCTTTCTTCAAGGAGTATAGAACT
* * *
23736 CGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAC
65 AGAACATCTTCAAACGGATTCGCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAACATCTTCAAC
23801 TGGGTTCGCTCCCTTCTTTTTAAG
130 TGGGTTCGCTCCCTTCTTTTTAAG
* *
23825 GAGTATAGAACTCGAACA-TCTTC-GACTGGGTTCGCTCCATT-TTTCTTCAAGGGAGTATGGAA
1 GAGTATAGAACTCGAACACTCTTCAAAC-GGGTTCGCTCC-TTCTTTCTTCAA-GGAGTATAGAA
* *
23887 CTTAGACATATCTTCAAACGGATTCGCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCTT
63 C-TAGA-ACATCTTCAAACGGATTCGCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAACATCTT
23952 CAAC
126 CAAC
23956 AATCGTGTCT
Statistics
Matches: 118, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
151 2 0.02
152 24 0.20
153 13 0.11
154 21 0.18
155 58 0.49
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (153 bp):
GAGTATAGAACTCGAACACTCTTCAAACGGGTTCGCTCCTTCTTTCTTCAAGGAGTATAGAACTA
GAACATCTTCAAACGGATTCGCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAACATCTTCAACT
GGGTTCGCTCCCTTCTTTTTAAG
Found at i:24091 original size:52 final size:55
Alignment explanation
Indices: 23939--24174 Score: 288
Period size: 52 Copynumber: 4.4 Consensus size: 55
23929 GGAGAATAGA
* * * *
23939 ACTCGAA-TATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAG
1 ACTCGAACAATCTTCAACAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* * * * *
23993 ACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* *
24048 AC-C-CACAATCTTCATCAATTGCGTCTGC-CCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* * *
24100 AC-C-CACAATCTTCATC-ATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAG
1 ACTCGAACAATCTTCAACAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
*
24152 ACTCGAACAATCTTCAATAATTG
1 ACTCGAACAATCTTCAACAATTG
24175 TTGGGAAATC
Statistics
Matches: 161, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
51 11 0.07
52 64 0.40
53 21 0.13
54 18 0.11
55 47 0.29
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
Found at i:25119 original size:14 final size:14
Alignment explanation
Indices: 25090--25136 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
25080 TGAACCCTTC
*
25090 TTTTTT-TTTTCCA
1 TTTTTTATTTTTCA
25103 TTTTTTCATTTTT-A
1 TTTTTT-ATTTTTCA
25117 TTTTTTATTTTTCA
1 TTTTTTATTTTTCA
25131 TTTTTT
1 TTTTTT
25137 TTATTTTCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 12 0.40
14 14 0.47
15 4 0.13
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTATTTTTCA
Found at i:35128 original size:16 final size:16
Alignment explanation
Indices: 35107--35144 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
35097 AACCTTATTC
35107 ACATGATATCTACCCA
1 ACATGATATCTACCCA
35123 ACATGATATCTACCCA
1 ACATGATATCTACCCA
35139 ATCATG
1 A-CATG
35145 CTTTAGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:41156 original size:25 final size:25
Alignment explanation
Indices: 41128--41216 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
41118 TAATGATTAG
41128 TAATAATGAAGTTATTATTAATATT
1 TAATAATGAAGTTATTATTAATATT
* *
41153 TAATGATTTGATAGGAATTATTTAGTAATGATT
1 TAAT-A-ATGA-A-G--TTA-TTATTAAT-ATT
*
41186 AATAATAATGAAATTATTATTAATATT
1 --TAATAATGAAGTTATTATTAATATT
41213 TAAT
1 TAAT
41217 CATTTGATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
25 8 0.16
26 1 0.02
27 6 0.12
28 8 0.16
29 4 0.08
31 3 0.06
32 8 0.16
33 6 0.12
34 1 0.02
35 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (25 bp):
TAATAATGAAGTTATTATTAATATT
Found at i:41163 original size:49 final size:49
Alignment explanation
Indices: 41008--41262 Score: 225
Period size: 49 Copynumber: 5.0 Consensus size: 49
40998 TTTGATTTAG
* * ** *
41008 TAATGATTTGATAATCATGATT--TAATAATGATTTTA-TATTTAAAATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAGTTATTA-TTAATATT
* * *
41055 ATAATAATTAT-TTAGTAATGATTAGTAATAATG-ATTTATTATTAATATT
1 -TAATGATT-TGATAGTAATGATTAGTAATAATGAAGTTATTATTAATATT
*
41104 TAATGTTTTGATAGTAATGATTAGTAATAATGAAGTTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAGTTATTATTAATATT
* *
41153 TAATGATTTGATAGGAATTATTTAGTAATGATTAATAATAATGAAATTATTATTAATATT
1 TAATGA-TT--T--G----A--TAGTAATGATTAGTAATAATGAAGTTATTATTAATATT
*
41213 TAATCATTTGATAGTAATGATTAGTAATAATGAAGTTA-TATTAATGATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAGTTATTATTAAT-ATT
41262 T
1 T
41263 TATACTTATG
Statistics
Matches: 173, Mismatches: 16, Indels: 35
0.77 0.07 0.16
Matches are distributed among these distances:
47 1 0.01
48 50 0.29
49 61 0.35
50 12 0.07
51 1 0.01
52 1 0.01
54 1 0.01
55 1 0.01
57 1 0.01
58 1 0.01
59 2 0.01
60 41 0.24
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (49 bp):
TAATGATTTGATAGTAATGATTAGTAATAATGAAGTTATTATTAATATT
Found at i:41182 original size:60 final size:59
Alignment explanation
Indices: 41115--41240 Score: 198
Period size: 60 Copynumber: 2.1 Consensus size: 59
41105 AATGTTTTGA
* * * *
41115 TAGTAATGATTAGTAATAATGAAGTTATTATTAATATTTAATGATTTGATAGGAATTATT
1 TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATCATTTGATAGGAATGA-T
*
41175 TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATCATTTGATAGTAATGAT
1 TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATCATTTGATAGGAATGAT
41234 TAGTAAT
1 TAGTAAT
41241 AATGAAGTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
59 8 0.13
60 53 0.87
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (59 bp):
TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATCATTTGATAGGAATGAT
Found at i:41228 original size:109 final size:108
Alignment explanation
Indices: 41060--41262 Score: 345
Period size: 109 Copynumber: 1.9 Consensus size: 108
41050 AAATTATAAT
* * **
41060 AATTATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAATGTTTTGATAGTAATGAT
1 AATTATTTAGTAATGATTAATAATAATGAATTATTATTAATATTTAATCATTTGATAGTAATGAT
41125 TAGTAATAATGAAGTTATTATTAAT-ATTTAATGATTTGATAGG
66 TAGTAATAATGAAGTTA-TATTAATGATTTAATGATTTGATAGG
41168 AATTATTTAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATCATTTGATAGTAATGA
1 AATTATTTAGTAATGATTAATAATAATG-AATTATTATTAATATTTAATCATTTGATAGTAATGA
41233 TTAGTAATAATGAAGTTATATTAATGATTT
65 TTAGTAATAATGAAGTTATATTAATGATTT
41263 TATACTTATG
Statistics
Matches: 89, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
108 34 0.38
109 55 0.62
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (108 bp):
AATTATTTAGTAATGATTAATAATAATGAATTATTATTAATATTTAATCATTTGATAGTAATGAT
TAGTAATAATGAAGTTATATTAATGATTTAATGATTTGATAGG
Found at i:41706 original size:13 final size:14
Alignment explanation
Indices: 41672--41826 Score: 58
Period size: 13 Copynumber: 10.9 Consensus size: 14
41662 AAAAATATAG
*
41672 TAATGA-TTAATAA
1 TAATGATTTAATAT
*
41685 TAATGATTTATTAT
1 TAATGATTTAATAT
41699 TAAT-ATTTAATAT
1 TAATGATTTAATAT
*
41712 T--TGATATTAAAAATTTAG
1 TAATGAT-TT---AA--TAT
* *
41730 TAATGA-TTAGTAA
1 TAATGATTTAATAT
*
41743 TAATGATTTATTAT
1 TAATGATTTAATAT
41757 TAAT-ATTTAAATATT
1 TAATGATTT-AATA-T
*
41772 TAAT-ATTAATAATTTAG
1 TAATGATT--TAA--TAT
*
41789 TAATGA-TTAATAA
1 TAATGATTTAATAT
*
41802 TAATGATTTATTAT
1 TAATGATTTAATAT
41816 TAAT-ATTTAAT
1 TAATGATTTAAT
41827 GTTTTGATAT
Statistics
Matches: 109, Mismatches: 14, Indels: 38
0.68 0.09 0.24
Matches are distributed among these distances:
11 1 0.01
12 2 0.02
13 43 0.39
14 30 0.28
15 12 0.11
16 4 0.04
17 6 0.06
18 8 0.07
20 3 0.03
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (14 bp):
TAATGATTTAATAT
Found at i:41709 original size:59 final size:59
Alignment explanation
Indices: 41546--41891 Score: 434
Period size: 59 Copynumber: 5.8 Consensus size: 59
41536 ATATGATTTG
* * * * *
41546 ATTTAGTAATGATTTGATAATTATGATTTAATAATGATTTTATATTTAA-AA-TT-ATAATAATA
1 ATTTAGTAATGA-TTAATAATAATGATTT-AT--T-A-TTAATATTTAATAATTTGATATTAAAA
*
41608 ATTTAGTAATGATTAATAATAAT-ATTTATTATTAATATTTAATAATTTGATACTAAAA
1 ATTTAGTAATGATTAATAATAATGATTTATTATTAATATTTAATAATTTGATATTAAAA
*
41666 ATATAGTAATGATTAATAATAATGATTTATTATTAATATTTAAT-ATTTGATATTAAAA
1 ATTTAGTAATGATTAATAATAATGATTTATTATTAATATTTAATAATTTGATATTAAAA
* * *
41724 ATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAA-ATATTTAATATTAATA
1 ATTTAGTAATGATTAATAATAATGATTTATTATTAATATTTAATA-ATTTGATATTAAAA
** *
41783 ATTTAGTAATGATTAATAATAATGATTTATTATTAATATTTAATGTTTTGATATTAATA
1 ATTTAGTAATGATTAATAATAATGATTTATTATTAATATTTAATAATTTGATATTAAAA
* * *
41842 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATCATTT
1 ATTTAGTAATGATTAATAATAATG-ATTTATTATTAATATTTAATAATTT
41892 TGAAATTATT
Statistics
Matches: 257, Mismatches: 19, Indels: 18
0.87 0.06 0.06
Matches are distributed among these distances:
55 10 0.04
56 3 0.01
57 3 0.01
58 83 0.32
59 111 0.43
60 26 0.10
61 9 0.04
62 12 0.05
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (59 bp):
ATTTAGTAATGATTAATAATAATGATTTATTATTAATATTTAATAATTTGATATTAAAA
Found at i:41798 original size:24 final size:23
Alignment explanation
Indices: 41742--41812 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 23
41732 ATGATTAGTA
*
41742 ATAATGATTTATTATTAATATTT
1 ATAATGATTTAATATTAATATTT
41765 A-AAT-ATTTAATATTAATAATTT
1 ATAATGATTTAATATTAAT-ATTT
*
41787 AGTAATGA-TTAATAATAATGATTT
1 A-TAATGATTTAATATTAAT-ATTT
41811 AT
1 AT
41813 TATTAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 12 0.29
22 8 0.20
23 2 0.05
24 18 0.44
25 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (23 bp):
ATAATGATTTAATATTAATATTT
Found at i:44222 original size:4 final size:4
Alignment explanation
Indices: 44213--44242 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
44203 ATCTAATATA
*
44213 AACT AACT AACG AACT AACT AACT AACT AA
1 AACT AACT AACT AACT AACT AACT AACT AA
44243 TTTACAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.53, C:0.23, G:0.03, T:0.20
Consensus pattern (4 bp):
AACT
Found at i:44385 original size:30 final size:30
Alignment explanation
Indices: 44351--44437 Score: 140
Period size: 30 Copynumber: 2.9 Consensus size: 30
44341 TTCCCTTAAA
44351 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
44381 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* *
44411 AAACTAATAAACGATT-TTTAATTATAA
1 CAACTAATAAACTATTCTTTAA-TATAA
44438 TTTACTACTA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 5 0.09
30 49 0.91
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:44403 original size:15 final size:16
Alignment explanation
Indices: 44355--44409 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
44345 CTTAAACAAC
44355 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
44370 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
44385 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
44400 TAATATAACT
1 TAATATAACT
44410 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:44791 original size:30 final size:28
Alignment explanation
Indices: 44739--44798 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
44729 TTTAAATAAT
*
44739 TATTCTTTTATATAACTTAAACTAATAAAC
1 TATTCTTTTATATAACTAAAACT--TAAAC
*
44769 TATTTTTTTATTATAA-TAAAACTTAAAC
1 TATTCTTTTA-TATAACTAAAACTTAAAC
44797 TA
1 TA
44799 CTAATTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.26
30 15 0.56
31 5 0.19
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (28 bp):
TATTCTTTTATATAACTAAAACTTAAAC
Found at i:45079 original size:351 final size:341
Alignment explanation
Indices: 44393--45040 Score: 754
Period size: 355 Copynumber: 1.8 Consensus size: 341
44383 ACTAATAAAC
44393 TATTCTTTAATATAACTTAAACTAATAAACGATTTTTAATTATAATTTACTACTAAAAACCTAAT
1 TATTCTTTAATATAACTTAAACTAATAAACGATTTTTAATTATAATTTACTACTAAAAACCTAAT
*
44458 TAACTAAATTTTTTATATAATATAAATTCAACAAATAATATGGAGACTTAACTATTTAACTAACA
66 TAACTAAATTTTTTATATAATATAAATTCAACAAAAAATAT-GAGACTTAACTATTTAACTAACA
44523 CAAACAAATTACATATTTTTTTATATATAACTAACGACTAACAAACTAACTAATTATTTTTATTA
130 CAAACAAATTACATATTTTTTTATATATAACTAACGACTAACAAACTAACTAATTATTTTTATTA
* * *
44588 ATATATAACTATCAAACATACTAATTAAATAATTTTTTTATTTCTATATGATATAACTTAAACTA
195 ATATATAACTATCAAACAAACTAATTAAATAATTTTTTTATTTATATATGATAGAACTTAAACTA
* ***** ** * **
44653 ACAAACTAATTAACTAATTTTTTGTTTTACCCTAAACCCTAAACCAACAAACTAATAATTTATAA
260 ACAAAATAATTAACTAACAAACTGAATTACACTAAA--C-AAACCAAC-AACTAATAACCTATAA
*
44718 TAATAAACTAATTTAAATAAT
321 CAATAAACTAATTTAAATAAT
* * *
44739 TATTCTTTTATATAACTTAAACTAATAAACTATTTTTTTATTATAATAAAACTTAAACTACTAAT
1 TATTCTTTAATATAACTTAAACTAATAAACGA-TTTTTAATTATAAT-----TT--ACTACTAA-
* * *
44804 TAA-CTAATTAACT-AATTTTTTATATAATATAAATTCAACAAACAAATAT-A-ACTTAATTTTT
57 AAACCTAATTAACTAAATTTTTTATATAATATAAATTCAACAAA-AAATATGAGACTTAACTATT
* *
44865 TAACTAACTACAAACTAATTA-AT-TATTTTTTATATATAACTAACGACTAACAAACAAACTAAT
121 TAACTAAC-ACAAACAAATTACATAT-TTTTTTATATATAACTAACGACT----AACAAACTAAC
* * *
44928 TAATTATTATTTTTTAATTTATAACTATCAAACAAACTAATTAAA-AATTTTTTTATTTATGTAT
180 TAATTATT-TTTATTAATATATAACTATCAAACAAACTAATTAAATAATTTTTTTATTTATATAT
44992 GATAGAACTTAAACTAACAATAATATAACTTAAACTAACAAACT-AATTA
244 GATAGAACTTAAACTAAC-A-AA-ATAA-TT-AACTAACAAACTGAATTA
45041 AGTAAAAAAT
Statistics
Matches: 257, Mismatches: 23, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
346 30 0.12
347 13 0.05
350 1 0.00
351 42 0.16
352 14 0.05
353 29 0.11
354 23 0.09
355 54 0.21
356 34 0.13
357 2 0.01
358 3 0.01
359 5 0.02
360 7 0.03
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (341 bp):
TATTCTTTAATATAACTTAAACTAATAAACGATTTTTAATTATAATTTACTACTAAAAACCTAAT
TAACTAAATTTTTTATATAATATAAATTCAACAAAAAATATGAGACTTAACTATTTAACTAACAC
AAACAAATTACATATTTTTTTATATATAACTAACGACTAACAAACTAACTAATTATTTTTATTAA
TATATAACTATCAAACAAACTAATTAAATAATTTTTTTATTTATATATGATAGAACTTAAACTAA
CAAAATAATTAACTAACAAACTGAATTACACTAAACAAACCAACAACTAATAACCTATAACAATA
AACTAATTTAAATAAT
Found at i:46032 original size:2 final size:2
Alignment explanation
Indices: 46025--46059 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
46015 ATGTATTGAA
46025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46060 AAAGAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46151 original size:14 final size:14
Alignment explanation
Indices: 46115--46141 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46105 TAATATAATT
46115 AATATTTTATTTTA
1 AATATTTTATTTTA
46129 AATATTTTATTTT
1 AATATTTTATTTT
46142 TACATTTTTA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTATTTTA
Found at i:46324 original size:30 final size:27
Alignment explanation
Indices: 46290--46344 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 27
46280 TATATTATTC
46290 AAAAATTATAAAAAAGGGAAGATTTCATAA
1 AAAAATT-T-AAAAA-GGAAGATTTCATAA
*
46320 AAAAATTTAAAAATGAAGATTTCAT
1 AAAAATTTAAAAAGGAAGATTTCAT
46345 GATTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 11 0.46
28 5 0.21
29 1 0.04
30 7 0.29
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.27
Consensus pattern (27 bp):
AAAAATTTAAAAAGGAAGATTTCATAA
Found at i:46356 original size:28 final size:29
Alignment explanation
Indices: 46325--46383 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
46315 CATAAAAAAA
* *
46325 TTTAAAAA-TGAAGATTTCATGATTTTTT
1 TTTAAAAACTGAAGATATAATGATTTTTT
*
46353 TTTAAAAACTTGAGGATATAATGATTTTTT
1 TTTAAAAAC-TGAAGATATAATGATTTTTT
46383 T
1 T
46384 GAAAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.31
30 18 0.69
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTAAAAACTGAAGATATAATGATTTTTT
Found at i:47211 original size:23 final size:25
Alignment explanation
Indices: 47184--47236 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
47174 CACAAAAGGA
*
47184 AAAAAAAACAAAAG-TCAAAG-TTTG
1 AAAAAAGA-AAAAGTTCAAAGATTTG
*
47208 AAAAAAGAAAAAGTTGAAAGATTTG
1 AAAAAAGAAAAAGTTCAAAGATTTG
47233 AAAA
1 AAAA
47237 TTTTGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.20
24 12 0.48
25 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.15, T:0.17
Consensus pattern (25 bp):
AAAAAAGAAAAAGTTCAAAGATTTG
Found at i:47416 original size:17 final size:19
Alignment explanation
Indices: 47396--47442 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
47386 CGAAAAGAAG
47396 AAAAAAAATAAAA-A-AAT
1 AAAAAAAATAAAAGATAAT
*
47413 AAAAACAAAAAAAAGATAAT
1 AAAAA-AAATAAAAGATAAT
*
47433 AACAAAAATA
1 AAAAAAAATA
47443 TATATAAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.21
18 7 0.29
19 5 0.21
20 7 0.29
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.11
Consensus pattern (19 bp):
AAAAAAAATAAAAGATAAT
Found at i:47552 original size:11 final size:11
Alignment explanation
Indices: 47505--47605 Score: 61
Period size: 10 Copynumber: 9.4 Consensus size: 11
47495 ACACACGTAT
*
47505 AAATAAAATATT
1 AAATAAAA-ATA
47517 AAATAAAAATA
1 AAATAAAAATA
*** *
47528 AAA-GGGAATT
1 AAATAAAAATA
47538 AAATAAAAATA
1 AAATAAAAATA
47549 AAATAAATAAT-
1 AAATAAA-AATA
47560 AAAT-AAAA-A
1 AAATAAAAATA
*
47569 AATTAAAAA-A
1 AAATAAAAATA
*
47579 AAAGACGAAAATA
1 AAATA--AAAATA
47592 AAAT-AAAATA
1 AAATAAAAATA
47602 AAAT
1 AAAT
47606 TATCAGTAAC
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
9 5 0.07
10 26 0.38
11 19 0.28
12 15 0.22
13 4 0.06
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:48717 original size:2 final size:2
Alignment explanation
Indices: 48710--48761 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
48700 GTAAATGATA
48710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
48752 AC AT -T AT AT A
1 AT AT AT AT AT A
48762 ATTATAAGAC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50511 original size:20 final size:19
Alignment explanation
Indices: 50469--50511 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
50459 TATCAATACC
* *
50469 ATATCAAGTAGGGGTATTA
1 ATATCAAGTAAGGGTATCA
*
50488 ATATCTAAGTAAGGGTATCG
1 ATATC-AAGTAAGGGTATCA
50508 ATAT
1 ATAT
50512 TGGTTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (19 bp):
ATATCAAGTAAGGGTATCA
Found at i:51961 original size:13 final size:13
Alignment explanation
Indices: 51945--51969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51935 TTGCACATGG
51945 TATTTCAAACATA
1 TATTTCAAACATA
51958 TATTTCAAACAT
1 TATTTCAAACAT
51970 GTATATAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTTCAAACATA
Found at i:52445 original size:13 final size:13
Alignment explanation
Indices: 52427--52451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52417 TTGACTTTTT
52427 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
52440 GGTCAAAGTCAA
1 GGTCAAAGTCAA
52452 TAGTCAATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:54955 original size:13 final size:13
Alignment explanation
Indices: 54937--54962 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54927 TTTGACTTTT
54937 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
54950 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
54963 AATCAATAGT
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:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
TGGTCAAAGTCAA
Found at i:54963 original size:19 final size:19
Alignment explanation
Indices: 54939--54975 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54929 TGACTTTTTG
* *
54939 GTCAAAGTCAATGGTCAAA
1 GTCAAAATCAATAGTCAAA
54958 GTCAAAATCAATAGTCAA
1 GTCAAAATCAATAGTCAA
54976 TGAACATGTC
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:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (19 bp):
GTCAAAATCAATAGTCAAA
Found at i:61386 original size:20 final size:21
Alignment explanation
Indices: 61361--61411 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
61351 TCAGATGATC
*
61361 AGTATCGATATTGAT-TGAAG
1 AGTATCGATACTGATGTGAAG
*
61381 AGTATCGATACTGATGTGGAG
1 AGTATCGATACTGATGTGAAG
61402 -GTATCGATAC
1 AGTATCGATAC
61412 CATAATCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTGATGTGAAG
Found at i:62110 original size:23 final size:23
Alignment explanation
Indices: 62066--62132 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
62056 GTCGAGGGTT
62066 CTATGTGGTC-CTTCGG-GACAAAA
1 CTATGTGG-CACTTCGGTG-CAAAA
62089 CTATGTGGCACTTCGGTGC-AAA
1 CTATGTGGCACTTCGGTGCAAAA
* * *
62111 TTATGTGGCATTTCAGTGCAAA
1 CTATGTGGCACTTCGGTGCAAA
62133 TTATGTGAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 20 0.53
23 17 0.45
24 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (23 bp):
CTATGTGGCACTTCGGTGCAAAA
Found at i:62118 original size:22 final size:22
Alignment explanation
Indices: 62090--62139 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
62080 GGGACAAAAC
*
62090 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCAGTGCAAAT
*
62112 TATGTGGCATTTCAGTGCAAAT
1 TATGTGGCACTTCAGTGCAAAT
62134 TATGTG
1 TATGTG
62140 AGCAGTGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (22 bp):
TATGTGGCACTTCAGTGCAAAT
Found at i:75087 original size:16 final size:15
Alignment explanation
Indices: 75066--75095 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
75056 CTGCCTAAAC
75066 TAAAATTTGATAATGA
1 TAAAATTTG-TAATGA
75082 TAAAATTTGTAATG
1 TAAAATTTGTAATG
75096 CTTATGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (15 bp):
TAAAATTTGTAATGA
Found at i:77985 original size:18 final size:19
Alignment explanation
Indices: 77944--77985 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
77934 TCCCCTTTGA
*
77944 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCCT
77963 AGGGGAACCGATACCCCCT
1 AGGGGAACCGATACCCCCT
77982 -GGGG
1 AGGGG
77986 TTCTGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.12
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:79996 original size:2 final size:2
Alignment explanation
Indices: 79989--80022 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
79979 GGATGTTTGA
79989 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80023 TTGGTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83776 original size:116 final size:116
Alignment explanation
Indices: 83552--84018 Score: 503
Period size: 116 Copynumber: 4.0 Consensus size: 116
83542 ATAGACCAAA
* * * * *
83552 CATTTGCAATGGAAGGGTTCATAATGAGAAGAACTCGTCCGATGAGAGAGAAAAAGTTCCTAATG
1 CATTTCCAATAGAAGGGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCCTAATG
*
83617 AGAAGAACTTGTTCAACCTTGGTTCATCCATCATACA-AA-GAGGTGGATTAG
66 AGAAGAACTTGTTCAACCTTGGTTCATCCAT--TACAGAAGGAGGTGGATCAG
* * * * * * *
83668 TATTTCCAGTGGAAGAGTTTATAATGAGAAAAACTCGTCTAATGAGGGAGAAGAAGTTCCTAATG
1 CATTTCCAATAGAAGGGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCCTAATG
* * *
83733 AGAAGAACTTGTTCAACCTTGATTCATCCATTACAGAAGGAGGTCGA-CCG
66 AGAAGAACTTGTTCAACCTTGGTTCATCCATTACAGAAGGAGGTGGATCAG
* * *
83783 ACATTTCCAATAGCAGGGTTAATAATAAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCCTAAT
1 -CATTTCCAATAGAAGGGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCCTAAT
* * * * * * *
83848 GAGAAGAACTTGATCAACATTGGCTT-GTTCATCACAGAAGGAGGTGGACCAA
65 GAGAAGAACTTGTTCAACCTTGG-TTCATCCATTACAGAAGGAGGTGGATCAG
* * * * *
83900 CGTGTCCAATAAAAGGGTTCATAATGAGAAGAACTCGTCCGATGAGGGACAAGAAGTTCCTAATG
1 CATTTCCAATAGAAGGGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCCTAATG
* * * * * * * * *
83965 AAAACAACTTG-TCAATCTTGGCTCGTCTATTACATAAGGAGTTGGATCAT
66 AGAAGAACTTGTTCAACCTTGGTTCATCCATTACAGAAGGAGGTGGATCAG
84015 CATT
1 CATT
84019 ACATTTTTCT
Statistics
Matches: 291, Mismatches: 54, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
114 5 0.02
115 32 0.11
116 251 0.86
117 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (116 bp):
CATTTCCAATAGAAGGGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTCCTAATG
AGAAGAACTTGTTCAACCTTGGTTCATCCATTACAGAAGGAGGTGGATCAG
Found at i:84218 original size:36 final size:36
Alignment explanation
Indices: 84111--84311 Score: 231
Period size: 36 Copynumber: 5.6 Consensus size: 36
84101 ATCATTTCAA
* * *
84111 AGATTTTATCTTACTTGAGATTGTCTTTCTTAAAAC
1 AGATTTTATCTCACTTGAGATTATTTTTCTTAAAAC
* * *
84147 ATATTTCATCTCACATGAGATTATTTTTTCTTAAAAC
1 AGATTTTATCTCACTTGAGATTA-TTTTTCTTAAAAC
* *
84184 GGATTTTATCTCACTTGAGATTATTTTTCTTAAAAA
1 AGATTTTATCTCACTTGAGATTATTTTTCTTAAAAC
* *
84220 AGATTTTATCTCACTTGAGATTGTTTTCCTTAAAAC
1 AGATTTTATCTCACTTGAGATTATTTTTCTTAAAAC
* * * * **
84256 AGATTTTATCTCACTTGAAATTGTGTCTCTCGAAAC
1 AGATTTTATCTCACTTGAGATTATTTTTCTTAAAAC
* *
84292 AAATTTTATCCCACTTGAGA
1 AGATTTTATCTCACTTGAGA
84312 CAATTTTCCT
Statistics
Matches: 140, Mismatches: 24, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
36 109 0.78
37 31 0.22
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (36 bp):
AGATTTTATCTCACTTGAGATTATTTTTCTTAAAAC
Found at i:84231 original size:73 final size:72
Alignment explanation
Indices: 84111--84273 Score: 227
Period size: 73 Copynumber: 2.2 Consensus size: 72
84101 ATCATTTCAA
* * * * * *
84111 AGATTTTATCTTACTTGAGATTGTCTTTCTTAAAACATATTTCATCTCACATGAGATTATTTTTT
1 AGATTTTATCTCACTTGAGATTATCTTTCTTAAAAAAGATTTCATCTCACATGAGATT-GTTTTC
84176 CTTAAAAC
65 CTTAAAAC
* * * *
84184 GGATTTTATCTCACTTGAGATTATTTTTCTTAAAAAAGATTTTATCTCACTTGAGATTGTTTTCC
1 AGATTTTATCTCACTTGAGATTATCTTTCTTAAAAAAGATTTCATCTCACATGAGATTGTTTTCC
84249 TTAAAAC
66 TTAAAAC
84256 AGATTTTATCTCACTTGA
1 AGATTTTATCTCACTTGA
84274 AATTGTGTCT
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 29 0.37
73 50 0.63
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (72 bp):
AGATTTTATCTCACTTGAGATTATCTTTCTTAAAAAAGATTTCATCTCACATGAGATTGTTTTCC
TTAAAAC
Found at i:99188 original size:18 final size:17
Alignment explanation
Indices: 99165--99211 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
99155 TGTTTCTGAG
99165 GGAATTGGAATCTGTAAA
1 GGAATTGGAATCTGT-AA
* *
99183 GGAATTGAAATCTGTCA
1 GGAATTGGAATCTGTAA
*
99200 GGAATTAGAATC
1 GGAATTGGAATC
99212 CAATTCCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:99963 original size:245 final size:239
Alignment explanation
Indices: 99573--100160 Score: 835
Period size: 243 Copynumber: 2.4 Consensus size: 239
99563 CCTCCATCTG
* *
99573 AGACCCGACTCAACCAAAATAAAGTTTCACCCGACCCGTCCCGAATATATGAATTAGAAACCCGA
1 AGACCCGACCCGACCAAAATAAAGTTTCACCCGA-----CCCGAATATATGAATTAGAAA--C--
* **
99638 CCAGACCCGAAATAATAAAAAAAAAAAATTTATTCAATAAAAACAGACTTAATTGAAAAAAAATT
57 CC-GACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGACTTAATTGAAAAAAAATT
* *
99703 ATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAATTTATATATTTTTTGGG
121 ATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAACTTATATA-TTTTCGGG
*
99768 TC-GG-GTATTTTTCACCCTAAACCTGAACCCGACCCGAATATCACACTTAAAAAAA
185 TCGGGTGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACAC-T-AAAAAA
*
99823 ACTGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACTCGACCC
1 A--GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCC
*
99888 GAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAATGGCTTAATTGAAAAAAAATTATATA
64 GAAATAATAAAAAAAA-TATTTTTATTCAATAAAAAC-A-GACTTAATTGAAAAAAAATTATATA
99953 TAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAACTTATATATTTTCGGGTCGGGT
126 TAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAACTTATATATTTTCGGGTCGGG-
* *
100018 CATGTATTTTTCACCCTAAACCCGAACTCGACCCGAATATCACACTCAAAAA
190 --TGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTAAAAAA
100070 A-A-CCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGA
1 AGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGA
*
100133 AATAAT-AAAAATATATTTTTATTCAATA
66 AATAATAAAAAAAATATTTTTATTCAATA
100161 TATGAATAAG
Statistics
Matches: 314, Mismatches: 14, Indels: 29
0.88 0.04 0.08
Matches are distributed among these distances:
241 15 0.05
242 27 0.09
243 84 0.27
244 11 0.04
245 77 0.25
247 27 0.09
248 1 0.00
249 40 0.13
250 1 0.00
252 31 0.10
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (239 bp):
AGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGA
AATAATAAAAAAAATATTTTTATTCAATAAAAACAGACTTAATTGAAAAAAAATTATATATAGAG
GGGTATTATTGTAATTATTCCTAAATATATAAGGTAAACTTATATATTTTCGGGTCGGGTGTATT
TTTCACCCTAAACCCGAACCCGACCCGAATATCACACTAAAAAA
Found at i:107188 original size:26 final size:26
Alignment explanation
Indices: 107159--107219 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
107149 TTCGTTTGCA
*
107159 ATTTTTTTTGAAATTTTGGC-TTTTTT
1 ATTTTTTTT-AAATTTTGCCTTTTTTT
* *
107185 ATTTTTTTTTATTTTTGCCTTTTTTT
1 ATTTTTTTTAAATTTTGCCTTTTTTT
*
107211 GTTTTTTTT
1 ATTTTTTTT
107220 TTTGTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.10, C:0.05, G:0.08, T:0.77
Consensus pattern (26 bp):
ATTTTTTTTAAATTTTGCCTTTTTTT
Found at i:114626 original size:33 final size:33
Alignment explanation
Indices: 114589--114669 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
114579 AGTCCTACTT
* *
114589 GGACTCAAATGC-TTCAGTTTTAGTGTTTTAATA
1 GGACTCAAATACGTT-AGTTTTAGTGTTTCAATA
*
114622 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTTAGTTTTAGTGTTTCAATA
114655 GGACTCAAATACGTT
1 GGACTCAAATACGTT
114670 GATTTATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 42 0.95
34 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (33 bp):
GGACTCAAATACGTTAGTTTTAGTGTTTCAATA
Found at i:114670 original size:33 final size:33
Alignment explanation
Indices: 114605--114670 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
114595 AAATGCTTCA
*
114605 GTTTTAGTGTTTTAATAGGACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
114638 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
114671 ATTTATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (33 bp):
GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
Found at i:114741 original size:4 final size:4
Alignment explanation
Indices: 114724--114781 Score: 56
Period size: 4 Copynumber: 15.8 Consensus size: 4
114714 GGCCTGCAAA
*
114724 AAAT AAAA AAAT AAAT -AAT -AAT -AAT -AAT -AAT -AAT AAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
114767 AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAA
114782 ATATAATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 18 0.36
4 29 0.58
5 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:114741 original size:12 final size:12
Alignment explanation
Indices: 114724--114782 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
114714 GGCCTGCAAA
114724 AAATAAAAAAAT
1 AAATAAAAAAAT
*
114736 AAATAATAATAAT
1 AAATAA-AAAAAT
*
114749 AATAATAATAAAAT
1 -A-AATAAAAAAAT
*
114763 AAATAAATAAAT
1 AAATAAAAAAAT
114775 AAATAAAA
1 AAATAAAA
114783 TATAATATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 22 0.58
13 6 0.16
14 5 0.13
15 5 0.13
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:114743 original size:3 final size:3
Alignment explanation
Indices: 114737--114799 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
114727 TAAAAAAATA
114737 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAAT AAAT AAAT AAAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT -AAT AAT AAT
114784 -AT AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT A
114800 TTTTTGTAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 10 0.19
3 29 0.54
4 15 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:114778 original size:39 final size:36
Alignment explanation
Indices: 114724--114799 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 36
114714 GGCCTGCAAA
114724 AAATAAAAAAATAAATAATAATAATAATAATAATAAAAT
1 AAATAAAAAAATAAATAA-AAT-ATAAT-ATAATAAAAT
* *
114763 AAATAAATAAATAAATAAAATATAATATAATATAAT
1 AAATAAAAAAATAAATAAAATATAATATAATAAAAT
114799 A
1 A
114800 TTTTTGTAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 10 0.29
37 5 0.14
38 3 0.09
39 17 0.49
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (36 bp):
AAATAAAAAAATAAATAAAATATAATATAATAAAAT
Found at i:114800 original size:5 final size:5
Alignment explanation
Indices: 114741--114800 Score: 56
Period size: 5 Copynumber: 12.4 Consensus size: 5
114731 AAAATAAATA
* *
114741 ATAAT AATAAT AATAAT AAAAT A-AAT A-AAT A-AAT A-AAT AAAAT ATAAT
1 ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
114789 ATAAT ATAAT AT
1 ATAAT ATAAT AT
114801 TTTTGTAGAC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
4 16 0.31
5 24 0.47
6 11 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (5 bp):
ATAAT
Found at i:115332 original size:83 final size:83
Alignment explanation
Indices: 115157--115401 Score: 321
Period size: 83 Copynumber: 2.9 Consensus size: 83
115147 TCGAAGGTAT
* * ** * * * *
115157 TTGGCATATAGCCCTTCTTGCCTTGAGTTATGCTACAAATGATGGTGCCTTTGACCTGAGTGGAG
1 TTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGAT-GTGCCTTGGAGCTGAGCGTAG
* *
115222 TCAAACTCGGAGGTCCTTG
65 TCGAACTCGAAGGTCCTTG
*
115241 TTGACAGATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
115306 CGAACTCGAAGGTCTTTG
66 CGAACTCGAAGGTCCTTG
* * *
115324 TTGGCAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGT-CTCTTGAAGCTGAGCGTAG
1 TTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC-CTTGGAGCTGAGCGTAG
*
115388 TAGAACTCGAAGGT
65 TCGAACTCGAAGGT
115402 TTGATGTTTC
Statistics
Matches: 143, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
82 1 0.01
83 104 0.73
84 38 0.27
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (83 bp):
TTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCCTTG
Found at i:115467 original size:30 final size:30
Alignment explanation
Indices: 115408--115469 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
115398 AGGTTTGATG
*
115408 TTTCAAGAGAAAAATTTTCAAAGGTTTTTT
1 TTTCAAGAGAAAAATTTTCAAAGGGTTTTT
* *
115438 TTTCAAGAGAAACAA-TTTCGAGGGGTTTTT
1 TTTCAAGAGAAA-AATTTTCAAAGGGTTTTT
115468 TT
1 TT
115470 GTGTTTCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (30 bp):
TTTCAAGAGAAAAATTTTCAAAGGGTTTTT
Found at i:115537 original size:31 final size:32
Alignment explanation
Indices: 115500--115562 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
115490 TCAAGATGGA
115500 AAAAATTT-GTT-TCAAAAGAAACTGTCTCAAG
1 AAAAATTTAGTTCT-AAAAGAAACTGTCTCAAG
115531 AAAAATTTAGTTCTAAAAGAAACTGTCTCAAG
1 AAAAATTTAGTTCTAAAAGAAACTGTCTCAAG
115563 GGAGACGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 8 0.27
32 21 0.70
33 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.29
Consensus pattern (32 bp):
AAAAATTTAGTTCTAAAAGAAACTGTCTCAAG
Found at i:115688 original size:37 final size:36
Alignment explanation
Indices: 115600--115709 Score: 184
Period size: 36 Copynumber: 3.0 Consensus size: 36
115590 ATATTCAAAG
115600 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
115636 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* *
115672 TATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGGCAA
1 -ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
115709 A
1 A
115710 ACTTGGAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 36 0.52
37 33 0.48
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (36 bp):
ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:116975 original size:33 final size:32
Alignment explanation
Indices: 116881--116975 Score: 111
Period size: 32 Copynumber: 2.9 Consensus size: 32
116871 ATTCCCAAAG
* * *
116881 ATGCCCCAATATTCGATGTTGAATCTAAAAAA
1 ATGCCCCAAAATTTGATGTTGAATCTCAAAAA
*
116913 ATG-CCCAAAATTTTGATGTTAAATCTCAAAAA
1 ATGCCCCAAAA-TTTGATGTTGAATCTCAAAAA
**
116945 ATGCCCCAGCATTTGATGTTGAATCTTCAAA
1 ATGCCCCAAAATTTGATGTTGAATC-TCAAA
116976 GATGCCCTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
31 6 0.11
32 37 0.70
33 10 0.19
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.31
Consensus pattern (32 bp):
ATGCCCCAAAATTTGATGTTGAATCTCAAAAA
Found at i:116981 original size:32 final size:32
Alignment explanation
Indices: 116876--116982 Score: 101
Period size: 32 Copynumber: 3.3 Consensus size: 32
116866 ATTGAATTCC
* * * *
116876 CAAAGATGCCCCAATATTCGATGTTGAATCTA
1 CAAAAATGCCCCAAAATTTGATGTTGAATCTT
* *
116908 AAAAAATG-CCCAAAATTTTGATGTTAAATC-T
1 CAAAAATGCCCCAAAA-TTTGATGTTGAATCTT
**
116939 CAAAAAATGCCCCAGCATTTGATGTTGAATCTT
1 C-AAAAATGCCCCAAAATTTGATGTTGAATCTT
*
116972 CAAAGATGCCC
1 CAAAAATGCCC
116983 TCATTGTTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
31 6 0.10
32 47 0.78
33 7 0.12
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (32 bp):
CAAAAATGCCCCAAAATTTGATGTTGAATCTT
Found at i:121570 original size:31 final size:31
Alignment explanation
Indices: 121532--121592 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
121522 TGCTTTAGTT
*
121532 TTAGTGTTTCAATAATACTCAAATACGTTGG
1 TTAGTGTTTCAATAAGACTCAAATACGTTGG
*
121563 TTAGTGTTTCAATAGGACTCAAATACGTTG
1 TTAGTGTTTCAATAAGACTCAAATACGTTG
121593 ATTTATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (31 bp):
TTAGTGTTTCAATAAGACTCAAATACGTTGG
Found at i:125466 original size:250 final size:256
Alignment explanation
Indices: 124937--125477 Score: 783
Period size: 250 Copynumber: 2.1 Consensus size: 256
124927 ACACGACACA
*
124937 AAATAATAAAAAAAATTATTTTTATTCAATAAAAAAATTGACTTAATTGAAAAAAATTATATATA
1 AAATAAT-AAAAAAA-TATTTTTATTCAATAAAAAAAGTGACTTAATTGAAAAAAATTATATATA
* *
125002 TAGGGGTATTATTGTAATTATTCTTAAATATATAAGGTAAAATTATATATTTTTTCGGGTCGGTC
64 TAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGG--
* * * *
125067 CGGTTTTTTTCACCCTAAACCCAAACCCGACTCGACCCGAATATCACAGTTAAAAAAACGACTCG
127 CGGTATTTTTCACCCT-AA-CCAAACCCAACCCGACCCGAATATCACACTTAAAAAAACGACTCG
* * * *
125132 ACCCGAACAAAATAAAGTTTCACCCGATCCGACCCCAATATATGAATTAGAAATCTGACCCGACC
190 ACCCGAACAAAATAAAGTTTCACCCGACCCGACCCCAATATATGAATTAGAAACCCGAACCGACC
125197 CG
255 CG
* *
125199 AAATAATAAACAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA-TATATA-A-A
1 AAATAATAAAAAAATATTTTTATTCAATAAAAAAAGTGACTTAATTGAAAAAAATTATATATATA
*
125261 GGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAATTTATATATATTTTCGGGTC-G-GGT
66 GGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGCGGT
* * *
125324 ATTTTTCACCCT-A-TAAACTCAACCCGACCCGAATATCACACTTAAAAAAACCGA-TCCGATCC
131 ATTTTTCACCCTAACCAAACCCAACCCGACCCGAATATCACACTTAAAAAAA-CGACT-CGACCC
* *
125386 GACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAACCGACCCG
194 GAACAAAATAAAGTTTCACCCGACCCGACCCCAATATATGAATTAGAAACCCGAACCGACCCG
125449 AAATAATAAAAAAATATTTTTATTCAATA
1 AAATAATAAAAAAATATTTTTATTCAATA
125478 TATAAATAAG
Statistics
Matches: 257, Mismatches: 20, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
249 33 0.13
250 93 0.36
251 1 0.00
253 14 0.05
256 1 0.00
257 57 0.22
258 1 0.00
259 6 0.02
260 38 0.15
261 6 0.02
262 7 0.03
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.29
Consensus pattern (256 bp):
AAATAATAAAAAAATATTTTTATTCAATAAAAAAAGTGACTTAATTGAAAAAAATTATATATATA
GGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGCGGT
ATTTTTCACCCTAACCAAACCCAACCCGACCCGAATATCACACTTAAAAAAACGACTCGACCCGA
ACAAAATAAAGTTTCACCCGACCCGACCCCAATATATGAATTAGAAACCCGAACCGACCCG
Found at i:134472 original size:17 final size:17
Alignment explanation
Indices: 134450--134484 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
134440 GCATCAAATA
134450 CATCAGCCAAGGTTTGT
1 CATCAGCCAAGGTTTGT
134467 CATCAGCCAAGGTTTGT
1 CATCAGCCAAGGTTTGT
134484 C
1 C
134485 TTGTCTGCTT
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:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (17 bp):
CATCAGCCAAGGTTTGT
Found at i:139809 original size:21 final size:23
Alignment explanation
Indices: 139761--139811 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
139751 ATTCCCTTGT
139761 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
139784 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
139805 GGGGGGA
1 GGGGGGA
139812 TCGATTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:142186 original size:3 final size:3
Alignment explanation
Indices: 142178--142219 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
142168 TTCGTTTTAT
* *
142178 TTA TTA TTA TTA TTA ATA TTA GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
142220 AATAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:143543 original size:22 final size:21
Alignment explanation
Indices: 143513--143566 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
143503 TATTCTATTG
143513 TTATATATTTAAATTAATAATAA
1 TTAT-TATTTAAATT-ATAATAA
* *
143536 TTATTATTTTAATTATATTAA
1 TTATTATTTAAATTATAATAA
143557 TATATTATTT
1 T-TATTATTT
143567 GATTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.25
22 17 0.61
23 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTATTTAAATTATAATAA
Found at i:143867 original size:140 final size:140
Alignment explanation
Indices: 143592--143859 Score: 305
Period size: 140 Copynumber: 1.9 Consensus size: 140
143582 AAATTTATAA
* * * *
143592 TAATGTTTATTTATTTTTTAATATCAAAGAAAAAGATAGTCTTAAAGCAACTAGATGTCTGTTTT
1 TAATATTTATTTATTTTTTAATATCAAAGAAAAAGATAGTCTTAAAACAACTAGAAGTCTCTTTT
* * * * *** *
143657 CTGATAATTTTAAATAAATAAATATTTTACTTTTATAAATTGTATATATTAATCTATTTTTTTAG
66 ATGATAATTTTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAAAATTATAG
143722 ATAAATGTTT
131 ATAAATGTTT
** * *
143732 TAATATTTATTTATTTTTTAATATCAAAGGAAGGAGCT-GTCTTAAAACACCTAGAAGT-TCTTT
1 TAATATTTATTTATTTTTTAATATCAAA-GAAAAAGATAGTCTTAAAACAACTAGAAGTCTCTTT
*
143795 TATGAT-ATTTCTAAATAAATAAATATCTTA-TTTATATAAATTAATAAAT-TTACT-TAAAATT
65 TATGATAATTT-TAAATAAATAAATATCTTACTTT-TATAAATT-ATAAATATTAATCTAAAATT
143856 ATAG
127 ATAG
143860 TAATAAATTT
Statistics
Matches: 107, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
138 14 0.13
139 39 0.36
140 48 0.45
141 6 0.06
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.46
Consensus pattern (140 bp):
TAATATTTATTTATTTTTTAATATCAAAGAAAAAGATAGTCTTAAAACAACTAGAAGTCTCTTTT
ATGATAATTTTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAAAATTATAG
ATAAATGTTT
Found at i:145391 original size:21 final size:21
Alignment explanation
Indices: 145367--145419 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
145357 GCGTTTGTTT
*
145367 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTTCATATTTT-AAAAA
145388 TCATTTTT-ATATTTTAAAAA
1 TCATTTTTCATATTTTAAAAA
*
145408 TAATTTTTCATA
1 TCATTTTTCATA
145420 ATCCGAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATTTTTCATATTTTAAAAA
Found at i:150185 original size:11 final size:11
Alignment explanation
Indices: 150137--150178 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
150127 ATGTCAATTT
150137 AAATATAATAA
1 AAATATAATAA
150148 AAATATAA-AA
1 AAATATAATAA
150158 GAAATATAATAA
1 -AAATATAATAA
150170 AAATATAAT
1 AAATATAAT
150179 TACAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.07
11 25 0.86
12 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
AAATATAATAA
Found at i:150358 original size:2 final size:2
Alignment explanation
Indices: 150351--150387 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
150341 AGTAAATCTA
*
150351 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
150388 ACTTCTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:150879 original size:26 final size:26
Alignment explanation
Indices: 150842--150892 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
150832 CCTACAAACC
150842 AGTTTATCCAC-TAAATAAATTAAATG
1 AGTTTATCCACTTAAA-AAATTAAATG
*
150868 AGTTTA-CACACTTAAAACATTAAAT
1 AGTTTATC-CACTTAAAAAATTAAAT
150893 AAGATCCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 1 0.05
26 17 0.77
27 4 0.18
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (26 bp):
AGTTTATCCACTTAAAAAATTAAATG
Found at i:151851 original size:161 final size:162
Alignment explanation
Indices: 151552--151940 Score: 398
Period size: 161 Copynumber: 2.4 Consensus size: 162
151542 AAAAGAATGA
* ** * *
151552 TTTCCTACCAATTAGTGTTGTGATCATAAATTAAAGAAAAAGTTGTGACCATAAATCAAAGTTAG
1 TTTCCTACTAATTAAAGTTGAG-TCATAAATTAAAGAAAAA-TTGTGACCATAAATTAAAGTTAG
*
151617 GAACAAATTTTCTTTGGTTTTATGATTCACATTGACAATGGTAAGAATTATATTCATTTATATAT
64 GAACAAATTTTCTTTGGTTTTATGATTCACATTAACAATGGTAAGAATTATATTCATTTATATAT
151682 CATTTCACATCAATAATAATAAGTGAAAGATGT-AT
129 CATTTCACATCAATAATAATAAGTGAAAG--GTCAT
* * *
151717 TTT-CT-GTCAATTAAAGTTG-GTCATAAATTAAA-AAAAATTATGACCATAAATTAAAGTTATG
1 TTTCCTACT-AATTAAAGTTGAGTCATAAATTAAAGAAAAATTGTGACCATAAATTAAAGTTAGG
*** * * * *
151778 AGTGAATTTT-TTT-GTAACTTTGTGATTCACATTAATAGTGGTAA-TATTATATTCACTTTATA
65 AACAAATTTTCTTTGGT---TTTATGATTCACATTAACAATGGTAAGAATTATATTCA-TTTATA
* ** ** ** * *
151840 TTTCATTTCACATTGATGGTGGTAGGTGAAAGGTCCT
126 TATCATTTCACATCAATAATAATAAGTGAAAGGTCAT
*
151877 TTTCCTACTAATTAAAGTTGTAGTCATAAATTAAAGAAAAATTGGGACCATAAATTAAAGTTAG
1 TTTCCTACTAATTAAAGTTG-AGTCATAAATTAAAGAAAAATTGTGACCATAAATTAAAGTTAG
151941 CAAATGCAAC
Statistics
Matches: 185, Mismatches: 28, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
158 2 0.01
159 5 0.03
160 42 0.23
161 70 0.38
162 13 0.07
163 14 0.08
164 36 0.19
165 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (162 bp):
TTTCCTACTAATTAAAGTTGAGTCATAAATTAAAGAAAAATTGTGACCATAAATTAAAGTTAGGA
ACAAATTTTCTTTGGTTTTATGATTCACATTAACAATGGTAAGAATTATATTCATTTATATATCA
TTTCACATCAATAATAATAAGTGAAAGGTCAT
Found at i:152515 original size:384 final size:384
Alignment explanation
Indices: 151756--152555 Score: 1530
Period size: 385 Copynumber: 2.1 Consensus size: 384
151746 AAAAAAAATT
*
151756 ATGACCATAAATTAAAGTTATGAGTGAATTTTTTTGTAACTTTGTGATTCACATTAATAGTGGTA
1 ATGACCATAAATTAAAGTTATGAGTGAATTTTTTTGTAACTTTGTGATTCACATTAATAGTGATA
* *
151821 ATATTATATTCACTTTATATTTCATTTCACATTGATGGTGGTAGGTGAAAGGTCCTTTTCCTACT
66 AGATTATATTCACTTTATATTTCATTTCACATTGATGGTGGTAGGTGAAAGGTCATTTTCCTACT
151886 AATTAAAGTTGTAGTCATAAATTAAAGAAAAATTGGGACCATAAATTAAAGTTAGCAAATGCAAC
131 AATTAAAGTTGTAGTCATAAATTAAAGAAAAATTGGGACCATAAATTAAAGTTAGCAAATGCAAC
*
151951 AGGAATGATTGAACATTCATTGTTAAATGATTGCTAGTATTTAGAACAAATACTACTTTCTAATC
196 AGGAATGATTGAACATTCATTGTTAAATGATTGATAGTATTTAGAACAAATACTACTTTCTAATC
152016 AACTTAGCATAATAAAAAAAATTAAGAGTGAATTTCCTTTAACTTTATGATTTACATTAATAGTG
261 AACTTAGCATAATAAAAAAAATTAAGAGTGAATTTCCTTTAACTTTATGATTTACATTAATAGTG
152081 GTAAGAATTGTATTCACTTCATATATCATTTCACATTAATAGTAATAGGTGAAAGATCG
326 GTAAGAATTGTATTCACTTCATATATCATTTCACATTAATAGTAATAGGTGAAAGATCG
152140 ATGACCATAAATTAAAGTTATGAGTGAATATTTTTTGTAACTTTGTGATTCACATTAATAGTGAT
1 ATGACCATAAATTAAAGTTATGAGTGAAT-TTTTTTGTAACTTTGTGATTCACATTAATAGTGAT
152205 AAGATTATATTCACTTTATATTTCATTTCACATTGATGGTGGTAGGTGAAAGGTCATTTTCCTAC
65 AAGATTATATTCACTTTATATTTCATTTCACATTGATGGTGGTAGGTGAAAGGTCATTTTCCTAC
152270 TAATTAAAGTTGTAGTCATAAATTAAAGAAAAATTGGGACCATAAATTAAAGTTAGCAAATGCAA
130 TAATTAAAGTTGTAGTCATAAATTAAAGAAAAATTGGGACCATAAATTAAAGTTAGCAAATGCAA
*
152335 CAGGGATGATTGAACATTCATTGTTAAATGATTGATAGTATTTAGAACAAATACTACTTTCTAAT
195 CAGGAATGATTGAACATTCATTGTTAAATGATTGATAGTATTTAGAACAAATACTACTTTCTAAT
*
152400 CAACTTAGCATAAT-AAAAAAATTAGGAGTGAATTTCCTTTAACTTTATGATTTACATTAATAGT
260 CAACTTAGCATAATAAAAAAAATTAAGAGTGAATTTCCTTTAACTTTATGATTTACATTAATAGT
152464 GGTAAGAATTGTATTCACTTCATATATCATTTCACATTAATAGTAATAGGTGAAAGATCG
325 GGTAAGAATTGTATTCACTTCATATATCATTTCACATTAATAGTAATAGGTGAAAGATCG
152524 ATGACCATAAATTAAAGTTATGAGTGAATTTT
1 ATGACCATAAATTAAAGTTATGAGTGAATTTT
152556 GTAACACCTA
Statistics
Matches: 409, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
383 3 0.01
384 167 0.41
385 239 0.58
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (384 bp):
ATGACCATAAATTAAAGTTATGAGTGAATTTTTTTGTAACTTTGTGATTCACATTAATAGTGATA
AGATTATATTCACTTTATATTTCATTTCACATTGATGGTGGTAGGTGAAAGGTCATTTTCCTACT
AATTAAAGTTGTAGTCATAAATTAAAGAAAAATTGGGACCATAAATTAAAGTTAGCAAATGCAAC
AGGAATGATTGAACATTCATTGTTAAATGATTGATAGTATTTAGAACAAATACTACTTTCTAATC
AACTTAGCATAATAAAAAAAATTAAGAGTGAATTTCCTTTAACTTTATGATTTACATTAATAGTG
GTAAGAATTGTATTCACTTCATATATCATTTCACATTAATAGTAATAGGTGAAAGATCG
Found at i:153405 original size:25 final size:25
Alignment explanation
Indices: 153336--153408 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
153326 TATCAATACT
153336 TCCTAAATCTAACACTGAAAAAATA
1 TCCTAAATCTAACACTGAAAAAATA
* * * * *
153361 TCTTAAGTCCAACGCTGAAAAAATG
1 TCCTAAATCTAACACTGAAAAAATA
* *
153386 TCCTAAATCTGACACCGAAAAAA
1 TCCTAAATCTAACACTGAAAAAA
153409 GGGTATCGAT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.22
Consensus pattern (25 bp):
TCCTAAATCTAACACTGAAAAAATA
Found at i:156938 original size:44 final size:44
Alignment explanation
Indices: 156860--156946 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
156850 ATAGTGATAA
* * *
156860 GAATTTTATTCACTTTATATATCATTTTAAATTAATGCCGGTAG
1 GAATTGTATTCACTTTATATATCATCTCAAATTAATGCCGGTAG
* * *
156904 GAATTGTATTCACTTTGTATATCATCTCACATTAATGGCGGTA
1 GAATTGTATTCACTTTATATATCATCTCAAATTAATGCCGGTA
156947 CGTGTAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (44 bp):
GAATTGTATTCACTTTATATATCATCTCAAATTAATGCCGGTAG
Found at i:157014 original size:24 final size:25
Alignment explanation
Indices: 156987--157045 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
156977 AGTTGTGTTC
*
156987 ATAAATTAAAGAAA-AATTATGACT
1 ATAAATTAAAGAAACAATTATAACT
157011 ATAAATTAAAGAAACAATTATAACT
1 ATAAATTAAAGAAACAATTATAACT
157036 ATAAATTAAA
1 ATAAATTAAA
157046 ATTATGAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (25 bp):
ATAAATTAAAGAAACAATTATAACT
Found at i:157933 original size:43 final size:44
Alignment explanation
Indices: 157864--157961 Score: 144
Period size: 43 Copynumber: 2.2 Consensus size: 44
157854 AACTTTATGA
* * *
157864 TTCATATTAATGGTGATAAAAATTGTATTCACTTCATATATCAT
1 TTCAAATTAATGATGATAAAAATTGTATTCACTTCACATATCAT
*
157908 TTCAAATTAATGATG-TAACAATTGTATTCACTTCACATATCAT
1 TTCAAATTAATGATGATAAAAATTGTATTCACTTCACATATCAT
*
157951 TTCACATTAAT
1 TTCAAATTAAT
157962 AATGGTAGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 36 0.73
44 13 0.27
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (44 bp):
TTCAAATTAATGATGATAAAAATTGTATTCACTTCACATATCAT
Found at i:158249 original size:44 final size:44
Alignment explanation
Indices: 158200--158284 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
158190 GGTTATAAGG
* *
158200 ATTGTATTCACTTCATATATCATTTCAAATTAATACTGGTAACA
1 ATTGTATTCACTTCACATATCATTTCAAATTAATAATGGTAACA
**
158244 ATTGTATTCACTTCACATATCATTTCATGTTAATAATGGTA
1 ATTGTATTCACTTCACATATCATTTCAAATTAATAATGGTA
158285 GGTCGAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (44 bp):
ATTGTATTCACTTCACATATCATTTCAAATTAATAATGGTAACA
Found at i:159693 original size:44 final size:44
Alignment explanation
Indices: 159625--159709 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
159615 TATTATTCAC
*
159625 ATTAATAGTGATAAGAATTTTATTCACTACATATATCATTTTAA
1 ATTAATAGTGATAAGAATTGTATTCACTACATATATCATTTTAA
* * * *
159669 ATTAATGGTGGTAAGAATTGTATTCACTTCATATATTATTT
1 ATTAATAGTGATAAGAATTGTATTCACTACATATATCATTT
159710 CACTTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (44 bp):
ATTAATAGTGATAAGAATTGTATTCACTACATATATCATTTTAA
Found at i:160103 original size:12 final size:12
Alignment explanation
Indices: 160086--160116 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
160076 TCCTTCTCAT
160086 TTTCATTCCTAA
1 TTTCATTCCTAA
160098 TTTCATTCCTAA
1 TTTCATTCCTAA
160110 TTTCATT
1 TTTCATT
160117 AACCGTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTCATTCCTAA
Found at i:163576 original size:44 final size:44
Alignment explanation
Indices: 163508--163678 Score: 229
Period size: 44 Copynumber: 3.9 Consensus size: 44
163498 TTAGTGGTGA
*
163508 TAATAATTGTATTCATTTCATATATCGTTTCAAATTAATGATGG
1 TAATAATTGTATTCATTTCATATATCATTTCAAATTAATGATGG
* * * *
163552 TAACAATTGTATTCACTTTC-TATATCATTTCATATTAATGGTGA
1 TAATAATTGTATTCA-TTTCATATATCATTTCAAATTAATGATGG
* * *
163596 TAATAATTGTATTTATTTCAAATATCGTTTCAAATTAATGATGG
1 TAATAATTGTATTCATTTCATATATCATTTCAAATTAATGATGG
*
163640 TAATAATTGTATTCACTTT-ATATATCATTTCACATTAAT
1 TAATAATTGTATTCA-TTTCATATATCATTTCAAATTAAT
163679 AGTGATAGGT
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
43 4 0.04
44 97 0.90
45 7 0.06
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.46
Consensus pattern (44 bp):
TAATAATTGTATTCATTTCATATATCATTTCAAATTAATGATGG
Found at i:163600 original size:88 final size:88
Alignment explanation
Indices: 163492--163685 Score: 325
Period size: 88 Copynumber: 2.2 Consensus size: 88
163482 AACTTTATGA
* *
163492 TTCATATTAGTGGTGATAATAATTGTATTCATTTCATATATCGTTTCAAATTAATGATGGTAACA
1 TTCATATTAATGGTGATAATAATTGTATTCATTTCAAATATCGTTTCAAATTAATGATGGTAACA
*
163557 ATTGTATTCACTTTCTATATCAT
66 ATTGTATTCACTTTATATATCAT
* *
163580 TTCATATTAATGGTGATAATAATTGTATTTATTTCAAATATCGTTTCAAATTAATGATGGTAATA
1 TTCATATTAATGGTGATAATAATTGTATTCATTTCAAATATCGTTTCAAATTAATGATGGTAACA
163645 ATTGTATTCACTTTATATATCAT
66 ATTGTATTCACTTTATATATCAT
* *
163668 TTCACATTAATAGTGATA
1 TTCATATTAATGGTGATA
163686 GGTGAAAGGT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 99 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (88 bp):
TTCATATTAATGGTGATAATAATTGTATTCATTTCAAATATCGTTTCAAATTAATGATGGTAACA
ATTGTATTCACTTTATATATCAT
Found at i:164017 original size:164 final size:162
Alignment explanation
Indices: 163624--164166 Score: 642
Period size: 164 Copynumber: 3.4 Consensus size: 162
163614 CAAATATCGT
* * * * *
163624 TTCAAATTAATGATGGTAATAATTGTATTCACTTTATATATCATTTCACATTAATAGTGATAGGT
1 TTCACATTAATGGTGATAAGAATTGTATTCACTTCATATATCATTTCACATTAATAGTGATAGGT
* * *
163689 GAAAGGTTGA-TTTCCTACCAATTAAAGTTGTGGTCATAAATTAAAGAAATAA-TTATGACCATA
66 GTAATG-TCACTTTCCTACCAATTAAAGTTGT-GTCATAAATTAAA-AAA-AAGTTATGACCATA
* *
163752 AATTAAAGTTATGAGTG-ATTTTTTTAAGTTTATAA
127 AATTAAAGTTATGAGTGAATTTTTTTAACTTTATGA
* * * * *
163787 TTTC-CTTTAATAGTAATAAGTATTGTATTCACTTCATATATCATTTCACATTAATTA-TGGTAG
1 -TTCACATTAATGGTGATAAGAATTGTATTCACTTCATATATCATTTCACATTAA-TAGTGATAG
*
163850 GTGTAATGTCACTTTCCTATCAATTAAAGTTGTGAT-AGTAAATTAAAAAAAAGTTATGACCATA
64 GTGTAATGTCACTTTCCTACCAATTAAAGTTGTG-TCA-TAAATTAAAAAAAAGTTATGACCATA
163914 AATTAAAGTTATGAGTGAATTTTATTTAACTTTATGA
127 AATTAAAGTTATGAGTGAATTTT-TTTAACTTTATGA
* * **
163951 TTCACATTAATGGTGATGAGAATTATATTCACTTCATATATCATTTCACATTAACGGTGATAGGT
1 TTCACATTAATGGTGATAAGAATTGTATTCACTTCATATATCATTTCACATTAATAGTGATAGGT
* * *
164016 GTAATGTCACTTTCCTGCC-ATTAAAGTTGTTGTCATAAATTTAAAAAAAAGTTATAAACATAAA
66 GTAATGTCACTTTCCTACCAATTAAAGTTG-TGTCATAAA-TTAAAAAAAAGTTATGACCATAAA
* *
164080 TTAAAATTATGGGTGAA---TTTT--CTTTATGA
129 TTAAAGTTATGAGTGAATTTTTTTAACTTTATGA
* * * *
164109 TTCACATTAATGATGTTAAGAATTGTATTCATTTCATATATCATTTCAAATTAATAGT
1 TTCACATTAATGGTGATAAGAATTGTATTCACTTCATATATCATTTCACATTAATAGT
164167 TGTAATCAGT
Statistics
Matches: 328, Mismatches: 39, Indels: 30
0.83 0.10 0.08
Matches are distributed among these distances:
158 58 0.18
160 3 0.01
161 3 0.01
162 35 0.11
163 105 0.32
164 124 0.38
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (162 bp):
TTCACATTAATGGTGATAAGAATTGTATTCACTTCATATATCATTTCACATTAATAGTGATAGGT
GTAATGTCACTTTCCTACCAATTAAAGTTGTGTCATAAATTAAAAAAAAGTTATGACCATAAATT
AAAGTTATGAGTGAATTTTTTTAACTTTATGA
Found at i:166014 original size:2 final size:2
Alignment explanation
Indices: 166007--166052 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
165997 TGTACTTATA
166007 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
166049 TG TG
1 TG TG
166053 GTTTCTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:168330 original size:12 final size:12
Alignment explanation
Indices: 168313--168350 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
168303 TCAACACCGT
*
168313 TTTGCATTTACA
1 TTTGCATTCACA
168325 TTTGCACTTCACA
1 TTTGCA-TTCACA
168338 TTTGCATTCACA
1 TTTGCATTCACA
168350 T
1 T
168351 CCTTACATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.45
Consensus pattern (12 bp):
TTTGCATTCACA
Found at i:173364 original size:12 final size:12
Alignment explanation
Indices: 173347--173371 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
173337 GACCCAACTC
173347 GACCCGTTGACT
1 GACCCGTTGACT
173359 GACCCGTTGACT
1 GACCCGTTGACT
173371 G
1 G
173372 TTGACCGGAT
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:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (12 bp):
GACCCGTTGACT
Found at i:173516 original size:29 final size:29
Alignment explanation
Indices: 173385--173568 Score: 103
Period size: 29 Copynumber: 6.4 Consensus size: 29
173375 ACCGGATGAC
* * * *
173385 ATTTTGGTAATTATTTTGGAAATG-GTGCT
1 ATTTTCGTAATTATTTT-AAAAAGAGTGAT
* * * * *
173414 ATTCTGGTAATTATTTTGAAAAGGGTGTT
1 ATTTTCGTAATTATTTTAAAAAGAGTGAT
* * *
173443 ATTTTTC-TAATTTTTTTTAAAA-AGTGAC
1 A-TTTTCGTAATTATTTTAAAAAGAGTGAT
* *
173471 AATTTCGTAAACT-TTTTAAAAAGAGTGAT
1 ATTTTCGT-AATTATTTTAAAAAGAGTGAT
* * *
173500 ATTTTAGTAATTATTTTGAAAATGA-TGCT
1 ATTTTCGTAATTATTTT-AAAAAGAGTGAT
*
173529 ATTTT-GATAATTAATTTTAAAAAG-GTGTT
1 ATTTTCG-TAATT-ATTTTAAAAAGAGTGAT
173558 ATTTTCGTAAT
1 ATTTTCGTAAT
173569 GTTAAAAAAA
Statistics
Matches: 123, Mismatches: 21, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
27 4 0.03
28 22 0.18
29 82 0.67
30 15 0.12
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (29 bp):
ATTTTCGTAATTATTTTAAAAAGAGTGAT
Found at i:173582 original size:25 final size:25
Alignment explanation
Indices: 173540--173588 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
173530 TTTTGATAAT
* ** *
173540 TAATTTTAAAAAGGTGTTATTTTCG
1 TAATGTTAAAAAAATGTTAATTTCG
173565 TAATGTTAAAAAAATGTTAATTTC
1 TAATGTTAAAAAAATGTTAATTTC
173589 TTAAAACGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (25 bp):
TAATGTTAAAAAAATGTTAATTTCG
Found at i:174287 original size:24 final size:24
Alignment explanation
Indices: 174251--174302 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
174241 ATTTTTGACG
* *
174251 TGGATTTTGATATGGTACTCGACC
1 TGGATTTTGATATGATACTCGACA
* *
174275 TGGATTTTTATATGATACTTGACA
1 TGGATTTTGATATGATACTCGACA
174299 TGGA
1 TGGA
174303 ATCTGATCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (24 bp):
TGGATTTTGATATGATACTCGACA
Found at i:180560 original size:13 final size:13
Alignment explanation
Indices: 180542--180567 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
180532 TTGACCGATT
180542 TTGACCCGACCCG
1 TTGACCCGACCCG
180555 TTGACCCGACCCG
1 TTGACCCGACCCG
180568 ACCCGTTGAC
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:0.15, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:180617 original size:16 final size:17
Alignment explanation
Indices: 180596--180633 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
180586 TGACCGTTGA
180596 TATTTT-GAAAAGGTGC
1 TATTTTGGAAAAGGTGC
*
180612 TATTTTGGGAAATGGTGC
1 TATTTT-GGAAAAGGTGC
180630 TATT
1 TATT
180634 CTGGTGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (17 bp):
TATTTTGGAAAAGGTGC
Found at i:182625 original size:2 final size:2
Alignment explanation
Indices: 182574--182609 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
182564 TTTATTTTTA
* *
182574 AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
182610 TTTGACTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:183732 original size:44 final size:43
Alignment explanation
Indices: 183677--183764 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 43
183667 AATTTTATGA
* * *
183677 TTCACATTAATGTTGATAAGAATTGTATTCATTTCATATAACAT
1 TTCAAATTAATGATGATAAGAATTGTATTCACTTCATAT-ACAT
* *
183721 TTCAAATTAATGATGATGATAATTGTATTCACTTCATATACAT
1 TTCAAATTAATGATGATAAGAATTGTATTCACTTCATATACAT
183764 T
1 T
183765 AATGGTGGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 5 0.13
44 34 0.87
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (43 bp):
TTCAAATTAATGATGATAAGAATTGTATTCACTTCATATACAT
Found at i:183897 original size:201 final size:205
Alignment explanation
Indices: 183447--183916 Score: 528
Period size: 201 Copynumber: 2.3 Consensus size: 205
183437 GTTGATAAGA
* * * * *
183447 GAATTTTCTCTAACTTTATGATTCATATTAATGATAATATGAATTGTATT-ATTTTCATGTATCA
1 GAATTTTCTCTAACTTTATGATTCACATTAATGATGATAAGAATTGTATTCA-TTTCATATAACA
* *
183511 TTTCATATTAATGATGGTAGCAATTATATTCACTTCATATATCATTTCACATCAAAAGTGGTAAG
65 TTTCAAATTAATGATGATAGCAATTATATTCACTTCATATATCATTTCACAT---AAGTGGTAAG
* * * *
183576 TTAAATGTTAATTTCTTACTCATTAAAGTTGTGGGCATAAATTAAAGAAAAAATTATGATCATAA
127 TT-AATGTTAATTTCCTACTAATTAAAGTTGTGGGCATAAACTAAAGAAAAAATTATGACCATAA
*
183641 ATTAAAAATATGAGT
191 ATTAAAAATAGGAGT
* * *
183656 GAATTTTCTTTAATTTTATGATTCACATTAATGTTGATAAGAATTGTATTCATTTCATATAACAT
1 GAATTTTCTCTAACTTTATGATTCACATTAATGATGATAAGAATTGTATTCATTTCATATAACAT
* * * **
183721 TTCAAATTAATGATGAT-GATAATTGTATTCACTTCATATA-CA-TT-A-AT-GGTGGTTGGTGT
66 TTCAAATTAATGATGATAG-CAATTATATTCACTTCATATATCATTTCACATAAGTGGTAAGT-T
** * *
183780 -ATGGTTGTTTTCCTACTAATTAAAGTAT-TGGTCATAAACTAAAGAAAAAGTTATGACCATAAA
129 AAT-GTTAATTTCCTACTAATTAAAGT-TGTGGGCATAAACTAAAGAAAAAATTATGACCATAAA
* *
183843 TTAACATTAGGAGT
192 TTAAAAATAGGAGT
* * *
183857 GAATTTCCTCTAACTTTATGATTCACATTAGTGATGATAAGAATTGTATTCACTT-ATATA
1 GAATTTTCTCTAACTTTATGATTCACATTAATGATGATAAGAATTGTATTCATTTCATATA
183917 TTATTTCACA
Statistics
Matches: 224, Mismatches: 32, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
200 7 0.03
201 117 0.52
202 2 0.01
205 2 0.01
206 1 0.00
207 2 0.01
208 3 0.01
209 89 0.40
210 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (205 bp):
GAATTTTCTCTAACTTTATGATTCACATTAATGATGATAAGAATTGTATTCATTTCATATAACAT
TTCAAATTAATGATGATAGCAATTATATTCACTTCATATATCATTTCACATAAGTGGTAAGTTAA
TGTTAATTTCCTACTAATTAAAGTTGTGGGCATAAACTAAAGAAAAAATTATGACCATAAATTAA
AAATAGGAGT
Found at i:189146 original size:2 final size:2
Alignment explanation
Indices: 189139--189167 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
189129 ATTATATCGT
189139 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
189168 TAATGATTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:190579 original size:21 final size:21
Alignment explanation
Indices: 190541--190581 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
190531 CTAGAAATGC
*
190541 TTTCTGTTATATGTTATATGA
1 TTTCTGTTAAATGTTATATGA
190562 TTTCTGTTAAAATG-TATATG
1 TTTCTGTT-AAATGTTATATG
190582 TACTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (21 bp):
TTTCTGTTAAATGTTATATGA
Found at i:191482 original size:30 final size:30
Alignment explanation
Indices: 191418--191482 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
191408 GTGGTAGTTG
* *
191418 TGAAAGTTGTGCTGTAGAAATGGATAATGT
1 TGAAAGTGGTGCTGTAGAAATGGATAATGA
* **
191448 TGAAAGTGGTGGTGTAGAAATGGATGCTGA
1 TGAAAGTGGTGCTGTAGAAATGGATAATGA
191478 TGAAA
1 TGAAA
191483 TGGGTAATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (30 bp):
TGAAAGTGGTGCTGTAGAAATGGATAATGA
Found at i:193358 original size:10 final size:10
Alignment explanation
Indices: 193345--193380 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
193335 TAAGATGTGT
193345 TGTTGAAATA
1 TGTTGAAATA
*
193355 TGTTGAGATA
1 TGTTGAAATA
*
193365 TGTTGAAGTA
1 TGTTGAAATA
193375 TGTTGA
1 TGTTGA
193381 GACCATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.42
Consensus pattern (10 bp):
TGTTGAAATA
Found at i:193370 original size:20 final size:20
Alignment explanation
Indices: 193345--193382 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
193335 TAAGATGTGT
193345 TGTTGAAATATGTTGAGATA
1 TGTTGAAATATGTTGAGATA
*
193365 TGTTGAAGTATGTTGAGA
1 TGTTGAAATATGTTGAGA
193383 CCATTTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (20 bp):
TGTTGAAATATGTTGAGATA
Found at i:193390 original size:20 final size:20
Alignment explanation
Indices: 193347--193410 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
193337 AGATGTGTTG
* *
193347 TTGAAATATGTTGAGA-TAT
1 TTGAAGTATGTTGAGACCAT
193366 GTTGAAGTATGTTGAGACCAT
1 -TTGAAGTATGTTGAGACCAT
193387 TTG-AG-ATG-TGTAGACCAT
1 TTGAAGTATGTTG-AGACCAT
193405 TATGAA
1 T-TGAA
193411 TGCTGAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 2 0.05
18 11 0.29
19 4 0.11
20 19 0.50
21 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGAAGTATGTTGAGACCAT
Found at i:195792 original size:7 final size:7
Alignment explanation
Indices: 195780--195809 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
195770 CAAACAATCC
195780 TCTCATT
1 TCTCATT
195787 TCTCATT
1 TCTCATT
195794 TCTCATT
1 TCTCATT
*
195801 TCTCCTT
1 TCTCATT
195808 TC
1 TC
195810 CCTTTCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (7 bp):
TCTCATT
Found at i:196528 original size:16 final size:16
Alignment explanation
Indices: 196486--196528 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
196476 TTAGGGTTTG
196486 ATTAAAAATATTTTTA
1 ATTAAAAATATTTTTA
*
196502 ATATTAAAATATTTTT-
1 AT-TAAAAATATTTTTA
196518 ATTAAATAATA
1 ATTAAA-AATA
196529 AGTGATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.13
16 8 0.35
17 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAAAATATTTTTA
Found at i:198445 original size:2 final size:2
Alignment explanation
Indices: 198438--198470 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
198428 AAACCAAACT
198438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
198471 TAAGTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:200020 original size:13 final size:13
Alignment explanation
Indices: 199992--200030 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
199982 TGGGCAAGGT
*
199992 TTTGAAAA-ACTA
1 TTTGAAAATAATA
200004 TTTGAAAATAATA
1 TTTGAAAATAATA
*
200017 TTTGTAAATAATA
1 TTTGAAAATAATA
200030 T
1 T
200031 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:202442 original size:13 final size:13
Alignment explanation
Indices: 202424--202448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
202414 TTATCATCGA
202424 AAACAACATGTAT
1 AAACAACATGTAT
202437 AAACAACATGTA
1 AAACAACATGTA
202449 AATACTCGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (13 bp):
AAACAACATGTAT
Found at i:204176 original size:22 final size:21
Alignment explanation
Indices: 204134--204173 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
204124 GAGTTTATTT
*
204134 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
204155 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
204174 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:206239 original size:45 final size:46
Alignment explanation
Indices: 206151--206241 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
206141 TTGAAAAATC
* * *
206151 CTGAGTGTATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
206197 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
206242 TTCGATGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:206606 original size:31 final size:31
Alignment explanation
Indices: 206578--206636 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
206568 TCAAAGTGTT
* *
206578 CAAAACTTATTAAAACGATAACGTAAGTGAC
1 CAAAACTTAATAAAACAATAACGTAAGTGAC
* *
206609 CAAAACTTAATAAACCAATAATGTAAGT
1 CAAAACTTAATAAAACAATAACGTAAGT
206637 ATTGTAGCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (31 bp):
CAAAACTTAATAAAACAATAACGTAAGTGAC
Found at i:207758 original size:22 final size:23
Alignment explanation
Indices: 207714--207758 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
207704 TTTTTTGCTA
*
207714 TATGTTGCCTTGTTTTTTCTTGT
1 TATGTTGCCTTGTTTTTGCTTGT
*
207737 TATGTTG-CTTGTTTTTGGTTGT
1 TATGTTGCCTTGTTTTTGCTTGT
207759 GTTGCACGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.04, C:0.09, G:0.22, T:0.64
Consensus pattern (23 bp):
TATGTTGCCTTGTTTTTGCTTGT
Found at i:208500 original size:39 final size:40
Alignment explanation
Indices: 208435--208579 Score: 116
Period size: 39 Copynumber: 3.8 Consensus size: 40
208425 AATAAATAAA
* *
208435 AATATA-AAAATA-ATAATAATACTATATAATACACATACC
1 AATATATAAAATATATAATAATAATATATAATACATATA-C
208474 AATATATAAAATATA-AAT-ATAATATATAAATACATATA-
1 AATATATAAAATATATAATAATAATATAT-AATACATATAC
208512 AATATACT---ATACTATAATAATAATA-ATAATA-ATATAC
1 AATATA-TAAAATA-TATAATAATAATATATAATACATATAC
*
208549 TAA-ATATAATATATTACTAAT-ATAATATATA
1 -AATATATAAAATA-TA-TAATAATAATATATA
208580 CAATATAGAT
Statistics
Matches: 89, Mismatches: 3, Indels: 27
0.75 0.03 0.23
Matches are distributed among these distances:
36 9 0.10
37 9 0.10
38 13 0.15
39 32 0.36
40 25 0.28
41 1 0.01
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (40 bp):
AATATATAAAATATATAATAATAATATATAATACATATAC
Found at i:208513 original size:30 final size:31
Alignment explanation
Indices: 208477--208604 Score: 106
Period size: 30 Copynumber: 4.2 Consensus size: 31
208467 ACATACCAAT
208477 ATATAAAATA-TA-AATATAATATATAAATA
1 ATATAAAATACTACAATATAATATATAAATA
* *
208506 CATATAAATATACTATACTATAATA-AT-AATA
1 -ATATAAA-ATACTACAATATAATATATAAATA
* * *
208537 ATAATAATATACTA-AATATAATATATTACTA
1 AT-ATAAAATACTACAATATAATATATAAATA
* *
208568 ATATAATATA-TACAATATAGATATATACTATA
1 ATATAAAATACTACAATATA-ATATATA-AATA
208600 ATATA
1 ATATA
208605 TGATATATAA
Statistics
Matches: 82, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
29 10 0.12
30 31 0.38
31 22 0.27
32 11 0.13
33 8 0.10
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (31 bp):
ATATAAAATACTACAATATAATATATAAATA
Found at i:208537 original size:25 final size:25
Alignment explanation
Indices: 208478--208602 Score: 83
Period size: 25 Copynumber: 5.3 Consensus size: 25
208468 CATACCAATA
208478 TATAA-AAT-ATAAATATAATATA-
1 TATAATAATAATAAATATAATATAC
*
208500 TA-AATACAT-ATAAATATACTATAC
1 TATAATA-ATAATAAATATAATATAC
208524 TATAATAATAAT-AATAATAATATAC
1 TATAATAATAATAAAT-ATAATATAC
* *
208549 TA-AAT-ATAATATATTACTAATATAA
1 TATAATAATAATA-AATA-TAATATAC
* * *
208574 TAT-AT-ACAATATAGAT-ATATAC
1 TATAATAATAATAAATATAATATAC
208596 TATAATA
1 TATAATA
208603 TATGATATAT
Statistics
Matches: 82, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
21 2 0.02
22 11 0.13
23 23 0.28
24 12 0.15
25 34 0.41
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.37
Consensus pattern (25 bp):
TATAATAATAATAAATATAATATAC
Found at i:208554 original size:12 final size:11
Alignment explanation
Indices: 208474--208639 Score: 50
Period size: 11 Copynumber: 15.0 Consensus size: 11
208464 TACACATACC
208474 AATATAT-AA-
1 AATATATAAAT
208483 AATATA-AATAT
1 AATATATAA-AT
208494 AATATATAAAT
1 AATATATAAAT
208505 ACATATA-AATAT
1 A-ATATATAA-AT
*
208517 ACTATACTATAAT
1 AATATA-TA-AAT
208530 AATA-AT-AAT
1 AATATATAAAT
*
208539 AATA-ATATACT
1 AATATATA-AAT
208550 AA-ATAT-AAT
1 AATATATAAAT
208559 -ATATTACTAATAT
1 AATA-TA-TAA-AT
208572 AATATATACAAT
1 AATATATA-AAT
* *
208584 -ATAGATATAT
1 AATATATAAAT
* *
208594 ACTATAATATAT
1 AATAT-ATAAAT
* *
208606 GATATATAACT
1 AATATATAAAT
*
208617 AATA-ATATAT
1 AATATATAAAT
208627 ATATATATTAAAT
1 A-ATATA-TAAAT
208640 TTGTCCGAAC
Statistics
Matches: 117, Mismatches: 16, Indels: 44
0.66 0.09 0.25
Matches are distributed among these distances:
8 1 0.01
9 19 0.16
10 11 0.09
11 41 0.35
12 26 0.22
13 15 0.13
14 4 0.03
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (11 bp):
AATATATAAAT
Done.