Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010301.1 Kokia drynarioides strain JFW-HI SEQ_125158, 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: 64724
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:105 original size:2 final size:2
Alignment explanation
Indices: 98--124 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
88 TTATTAACTA
98 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 A
125 AAGAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:597 original size:17 final size:18
Alignment explanation
Indices: 575--608 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
565 TAAATGAGTT
575 AATTAGGAT-TAAATTGA
1 AATTAGGATATAAATTGA
*
592 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
609 GATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGA
Found at i:930 original size:18 final size:18
Alignment explanation
Indices: 907--943 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
897 TTTGTGATCA
907 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
925 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
943 A
1 A
944 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:4190 original size:23 final size:24
Alignment explanation
Indices: 4156--4221 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
4146 TAATAAAAAG
4156 TAATTTTAAATTAATTAAATA-AT
1 TAATTTTAAATTAATTAAATATAT
*
4179 TAATTTTTAATT--TTAAAAATATAT
1 TAATTTTAAATTAATT--AAATATAT
4203 TAACTTTTAAATTAATTAA
1 TAA-TTTTAAATTAATTAA
4222 GTCCTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
21 2 0.06
23 16 0.46
24 5 0.14
25 10 0.29
27 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATTTTAAATTAATTAAATATAT
Found at i:4194 original size:25 final size:25
Alignment explanation
Indices: 4159--4221 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
4149 TAAAAAGTAA
*
4159 TTTTAAATTAATTAAATA-ATTAAT
1 TTTTAAATTAATTAAATATATTAAC
*
4183 TTTTAATTTTAA--AAATATATTAAC
1 TTTTAA-ATTAATTAAATATATTAAC
4207 TTTTAAATTAATTAA
1 TTTTAAATTAATTAA
4222 GTCCTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 9 0.28
24 17 0.53
25 6 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTAAATTAATTAAATATATTAAC
Found at i:5543 original size:6 final size:7
Alignment explanation
Indices: 5522--5546 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5512 ATTAAGGATG
5522 AAATAAA
1 AAATAAA
5529 AAATAAA
1 AAATAAA
5536 AAATAAA
1 AAATAAA
5543 AAAT
1 AAAT
5547 TACATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:10420 original size:13 final size:13
Alignment explanation
Indices: 10402--10426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10392 GCAATGAAAA
10402 TAAAATTAAAAGG
1 TAAAATTAAAAGG
10415 TAAAATTAAAAG
1 TAAAATTAAAAG
10427 AAAATAAAAA
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:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
TAAAATTAAAAGG
Found at i:11304 original size:18 final size:17
Alignment explanation
Indices: 11283--11329 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
11273 TTATAATTTG
11283 TTTAAAATTTATCAAAA
1 TTTAAAATTTATCAAAA
*
11300 CTTTATAATGTT-TCAAAA
1 -TTTAAAAT-TTATCAAAA
*
11318 TTTAAAAATTAT
1 TTTAAAATTTAT
11330 AATATGTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 2 0.08
17 7 0.29
18 13 0.54
19 2 0.08
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAAATTTATCAAAA
Found at i:11560 original size:17 final size:18
Alignment explanation
Indices: 11515--11562 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
11505 TGGTATCTAC
*
11515 AAAATATTGTTTAAAAATT
1 AAAATATT-TTTTAAAATT
*
11534 AAAA-ACTTTTTAAAA-T
1 AAAATATTTTTTAAAATT
11550 AAAATATTTTTTA
1 AAAATATTTTTTA
11563 TAAAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 5 0.20
17 14 0.56
18 2 0.08
19 4 0.16
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATATTTTTTAAAATT
Found at i:11568 original size:19 final size:19
Alignment explanation
Indices: 11515--11570 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
11505 TGGTATCTAC
*
11515 AAAATATTGTTTA-AAAATT
1 AAAATATTTTTTATAAAA-T
*
11534 AAAA-A-CTTTT-TAAAAT
1 AAAATATTTTTTATAAAAT
11550 AAAATATTTTTTATAAAAT
1 AAAATATTTTTTATAAAAT
11569 AA
1 AA
11571 TATAGATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 5 0.17
17 8 0.27
18 5 0.17
19 12 0.40
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATATTTTTTATAAAAT
Found at i:12908 original size:90 final size:89
Alignment explanation
Indices: 12751--12922 Score: 247
Period size: 90 Copynumber: 1.9 Consensus size: 89
12741 AAAGTTCAAA
* *
12751 GGTCAAATTTGAATTTTAGAAAATTTAGGGGTCAAATTGGAATTTTTGGAAAGTTTAATGGTCAA
1 GGTCAAATTTGAATTTTAGAAAATTTAGGGGTCAAATTGGAATTTTTGGAAAATTTAAGGGTCAA
*
12816 ATTCAAATTTTTGGAAAGTTTAGG
66 ATTCAAATTTTTAGAAAGTTTAGG
* * *
12840 GGTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAAATTGGAA-TTTTGAGAAAATTTGAGGGTT
1 GGTCAAATTTGAA-TTTTAGAAAATTTAGGGGTCAAATTGGAATTTTTG-GAAAATTTAAGGGTC
**
12904 AAATTTGAATTTTTAGAAA
64 AAATTCAAATTTTTAGAAA
12923 AATTAAGGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
89 18 0.25
90 55 0.75
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.38
Consensus pattern (89 bp):
GGTCAAATTTGAATTTTAGAAAATTTAGGGGTCAAATTGGAATTTTTGGAAAATTTAAGGGTCAA
ATTCAAATTTTTAGAAAGTTTAGG
Found at i:12932 original size:30 final size:30
Alignment explanation
Indices: 12721--12932 Score: 221
Period size: 30 Copynumber: 7.1 Consensus size: 30
12711 ATTAAAACTA
* * *
12721 GGTCAAATTTGAAATTTTA-AAAAGTTCAAA
1 GGTCAAATTTGAATTTTTAGAAAA-TTTAAG
*
12751 GGTCAAATTTGAA-TTTTAGAAAATTTAGG
1 GGTCAAATTTGAATTTTTAGAAAATTTAAG
* * * *
12780 GGTCAAATTGGAATTTTTGGAAAGTTTAAT
1 GGTCAAATTTGAATTTTTAGAAAATTTAAG
** * * *
12810 GGTCAAATTCAAATTTTTGGAAAGTTTAGG
1 GGTCAAATTTGAATTTTTAGAAAATTTAAG
* *
12840 GGTCAAATTTGAATTTTTGGAAAATTTAGG
1 GGTCAAATTTGAATTTTTAGAAAATTTAAG
* * *
12870 GGTCAAATTGGAATTTTGAGAAAATTTGAG
1 GGTCAAATTTGAATTTTTAGAAAATTTAAG
* *
12900 GGTTAAATTTGAATTTTTAGAAAAATTAAG
1 GGTCAAATTTGAATTTTTAGAAAATTTAAG
12930 GGT
1 GGT
12933 AAAAACATGA
Statistics
Matches: 155, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
29 20 0.13
30 135 0.87
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (30 bp):
GGTCAAATTTGAATTTTTAGAAAATTTAAG
Found at i:14662 original size:40 final size:40
Alignment explanation
Indices: 14599--15267 Score: 405
Period size: 40 Copynumber: 16.9 Consensus size: 40
14589 TATAGCTTTA
* * *
14599 GGGGTAAAAGATTTG-ATTG-CTTCAATTTGCCCCATGGTT
1 GGGGTAAAAGA-TCGAATTGTCTTCAATCTGCCCCATGGTC
* * * *
14638 GGGGTCAGAGATCGAATTGTCTTCAATTTGCCCTC-TGGTT
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCC-CATGGTC
* ** *
14678 AGGGTAAAAGATTTAATTG-CTTCAATCTGCCCCGTGGTC
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCATGGTC
* * * *
14717 GGGGTAAAAGATTGGA-TGTCTTCAATCTGCCTCATAGTC
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCATGGTC
* * * * ** *
14756 GGGGTAAGAGATCGGATGGTCTTCAATATGCCCTC-TAATT
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCC-CATGGTC
** * * * *
14796 AAGGTAAAAGATTGGATTG-CTTCAATCTGCCCTATGGCC
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCATGGTC
* * * * *
14835 GGGGTAAAAGATTGGATGGTATTCAATTTGCCCCATGGTC
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCATGGTC
* * * ** *
14875 GGGGTAAAAGATGGGATGGTCTTCTGTTTGCCCCATGGTC
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCATGGTC
* * * * * *
14915 GAGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TGATT
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCC-CATGGTC
** * *
14955 AAGGTAAAAGATTGAATTG-CTTCAATCTGCCCTATGGTC
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCATGGTC
* * * * ** *
14994 GAGGTAAAAGATTGGATTGTCTTCAATTTTTCTCATGGTC
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCATGGTC
* * * * *
15034 GAGGTAAAAGAT-TAGATGGTCTTCCATTTGCCCCATGGTC
1 GGGGTAAAAGATCGA-ATTGTCTTCAATCTGCCCCATGGTC
* * * * * *
15074 GGGGTAAAATATTGGATGGTCTTCAATCTGCCCTC-TAGTT
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCC-CATGGTC
* ** * *
15114 AGGGTAAAAGATTTAATTG-CTTCAATCTGACCCATAGTC
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCATGGTC
* * *
15153 GAGGTAAAAGA-CTAGATGGTCTTCAATCTGCCCCATGGTC
1 GGGGTAAAAGATCGA-ATTGTCTTCAATCTGCCCCATGGTC
* * * *
15193 GGGGTAAAAAATCGGATGGTCTTCAATCTGCCCTC-TGGTT
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCC-CATGGTC
* * * * *
15233 AGGGTAAAAAATTGGATTG-CTTTAATCTGCCCCAT
1 GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCAT
15268 AGTTAAGGTA
Statistics
Matches: 507, Mismatches: 102, Indels: 42
0.78 0.16 0.06
Matches are distributed among these distances:
38 9 0.02
39 176 0.35
40 316 0.62
41 6 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (40 bp):
GGGGTAAAAGATCGAATTGTCTTCAATCTGCCCCATGGTC
Found at i:14697 original size:79 final size:78
Alignment explanation
Indices: 14600--15267 Score: 268
Period size: 79 Copynumber: 8.4 Consensus size: 78
14590 ATAGCTTTAG
* * * * *
14600 GGGTAAAAGATTTGATTGCTTCAATTTGCCCCATGGTTGGGGTCAGAGATCGAATTGTCTTCAAT
1 GGGTAAAAGATTTAATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGAA-TGTCTTCAAT
*
14665 TTGCCCTCTGGTTA
65 CTGCCCTCTGGTTA
* * *
14679 GGGTAAAAGATTTAATTGCTTCAATCTGCCCCGTGGTCGGGGTAAAAGATTGGATGTCTTCAATC
1 GGGTAAAAGATTTAATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGAATGTCTTCAATC
* **
14744 TG-CCTCATAGTCG
66 TGCCCTC-TGGTTA
* *** * * ** *** * *
14757 GGGTAAGAGATCGGATGGTCTTCAATATGCCCTC-TAATTAAGGTAAAAGATTGGAT-TGCTTCA
1 GGGTAAAAGATTTAATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAAAGATCGAATGT-CTTCA
* ***
14820 ATCTGCCCTATGGCCG
63 ATCTGCCCTCTGGTTA
** * * * * * **
14836 GGGTAAAAGATTGGATGGTATTCAATTTGCCCCATGGTCGGGGTAAAAGATGGGATGGTCTTCTG
1 GGGTAAAAGATTTAATTG-CTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGAAT-GTCTTCAA
* *
14901 TTTGCCC-CATGG-TC
64 TCTGCCCTC-TGGTTA
** * * *** *
14915 GAGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TGATTAAGGTAAAAGATTGAAT-TGCTTC
1 G-GGTAAAAGATTTAATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAAAGATCGAATGT-CTTC
* *
14978 AATCTGCCCTATGG-TC
62 AATCTGCCCTCTGGTTA
** * ** * * *
14994 GAGGTAAAAGATTGGATTGTCTTCAATTTTTCTCATGGTCGAGGTAAAAGAT-TAGATGGTCTTC
1 G-GGTAAAAGATTTAATTG-CTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGA-AT-GTCTTC
* * **
15058 CATTTGCCC-CATGGTCG
62 AATCTGCCCTC-TGGTTA
* ** * * ** **
15075 GGGTAAAATATTGGATGGTCTTCAATCTGCCCTC-TAGTTAGGGTAAAAGATTTAAT-TGCTTCA
1 GGGTAAAAGATTTAATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAAAGATCGAATGT-CTTCA
* * *
15138 ATCTGACCC-ATAG-TC
63 ATCTG-CCCTCTGGTTA
* * * *
15153 GAGGTAAAAGA-CTAGATGGTCTTCAATCTGCCCCATGGTCGGGGTAAAAAATCGGATGGTCTTC
1 G-GGTAAAAGATTTA-ATTG-CTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGAAT-GTCTTC
15217 AATCTGCCCTCTGGTTA
62 AATCTGCCCTCTGGTTA
* ** *
15234 GGGTAAAAAATTGGATTGCTTTAATCTGCCCCAT
1 GGGTAAAAGATTTAATTGCTTCAATCTGCCCCAT
15268 AGTTAAGGTA
Statistics
Matches: 454, Mismatches: 104, Indels: 62
0.73 0.17 0.10
Matches are distributed among these distances:
77 4 0.01
78 36 0.08
79 262 0.58
80 142 0.31
81 10 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (78 bp):
GGGTAAAAGATTTAATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGAATGTCTTCAATC
TGCCCTCTGGTTA
Found at i:14926 original size:119 final size:120
Alignment explanation
Indices: 14599--15283 Score: 615
Period size: 119 Copynumber: 5.8 Consensus size: 120
14589 TATAGCTTTA
* * * * * * *
14599 GGGGTAAAAGATTTGATTG-CTTCAATTTGCCCCATGGTTGGGGTCAGAGATCGAATTGTCTTCA
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGGATTGTCTTCA
* * *
14663 ATTTGCCCTC-TGGT-TAGGGTAAAAGATTTA-ATTG-CTTCAATCTGCCCCGTGGTC
66 ATTTGCCC-CATGGTCGA-GGTAAAAGA-TTAGATGGTCTTCAATCTGCCCCATGGTC
* * * *
14717 GGGGTAAAAGATTGGAT-GTCTTCAATCTGCCTCATAGTCGGGGTAAGAGATCGGATGGTCTTCA
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGGATTGTCTTCA
* ** ** * * * *
14781 ATATGCCCTC-TAATTAAGGTAAAAGATTGGATTG-CTTCAATCTGCCCTATGGCC
66 ATTTGCCC-CATGGTCGAGGTAAAAGATTAGATGGTCTTCAATCTGCCCCATGGTC
* * * * *
14835 GGGGTAAAAGATTGGATGGTATTCAATTTGCCCCATGGTCGGGGTAAAAGATGGGATGGTCTTCT
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGGATTGTCTTCA
* * * *
14900 GTTTGCCCCATGGTCGAGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TGATT
66 ATTTGCCCCATGGTCGAGGTAAAAGATTAGATGGTCTTCAATCTGCCC-CATGGTC
** * * * * *
14955 AAGGTAAAAGATTGAATTG-CTTCAATCTGCCCTATGGTCGAGGTAAAAGATTGGATTGTCTTCA
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGGATTGTCTTCA
** * * *
15019 ATTTTTCTCATGGTCGAGGTAAAAGATTAGATGGTCTTCCATTTGCCCCATGGTC
66 ATTTGCCCCATGGTCGAGGTAAAAGATTAGATGGTCTTCAATCTGCCCCATGGTC
* * ** ***
15074 GGGGTAAAATATTGGATGGTCTTCAATCTGCCCTC-TAGTTAGGGTAAAAGATTTAATTG-CTTC
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCC-CATGGTCGGGGTAAAAGATCGGATTGTCTTC
* * * *
15137 AATCTGACCCATAGTCGAGGTAAAAGACTAGATGGTCTTCAATCTGCCCCATGGTC
65 AATTTGCCCCATGGTCGAGGTAAAAGATTAGATGGTCTTCAATCTGCCCCATGGTC
* * ** * * *
15193 GGGGTAAAAAATCGGATGGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAAATTGGATTG-CTTT
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCC-CATGGTCGGGGTAAAAGATCGGATTGTCTTC
* * **
15256 AATCTGCCCCATAGTTAAGGTAAAAGAT
65 AATTTGCCCCATGGTCGAGGTAAAAGAT
15284 AGGATTGTAA
Statistics
Matches: 472, Mismatches: 85, Indels: 19
0.82 0.15 0.03
Matches are distributed among these distances:
117 3 0.01
118 114 0.24
119 294 0.62
120 61 0.13
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (120 bp):
GGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCGGATTGTCTTCA
ATTTGCCCCATGGTCGAGGTAAAAGATTAGATGGTCTTCAATCTGCCCCATGGTC
Found at i:14956 original size:159 final size:159
Alignment explanation
Indices: 14646--15283 Score: 736
Period size: 159 Copynumber: 4.0 Consensus size: 159
14636 TTGGGGTCAG
* * * * ** *
14646 AGATCGAATTGTCTTCAATTTGCCCTCTGGT-TAGGGTAAAAGATTTAATTG-CTTCAATCTGCC
1 AGATTGAATTG-CTTCAATCTGCCCTATGGTCGA-GGTAAAAGATTGGATGGTCTTCAATCTGCC
* * * * * *
14709 CCGTGGTCGGGGTAAAAGATTGGAT-GTCTTCAATCTGCCTCATAGTCGGGGTAAGAGATCGGAT
64 CCATGGTCGGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCGAGGTAAAAGATTGGAT
* *
14773 GGTCTTCAATATGCCCTCTAATTAAGGTAAA
129 GGTCTTCAATCTGCCCTCTAGTTAAGGTAAA
* * * * *
14804 AGATTGGATTGCTTCAATCTGCCCTATGGCCGGGGTAAAAGATTGGATGGTATTCAATTTGCCCC
1 AGATTGAATTGCTTCAATCTGCCCTATGGTCGAGGTAAAAGATTGGATGGTCTTCAATCTGCCCC
* ** *
14869 ATGGTCGGGGTAAAAGATGGGATGGTCTTCTGTTTGCCCCATGGTCGAGGTAAAAGATTGGATGG
66 ATGGTCGGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCGAGGTAAAAGATTGGATGG
14934 TCTTCAATCTGCCCTCT-GATTAAGGTAAA
131 TCTTCAATCTGCCCTCTAG-TTAAGGTAAA
* * ** *
14963 AGATTGAATTGCTTCAATCTGCCCTATGGTCGAGGTAAAAGATTGGATTGTCTTCAATTTTTCTC
1 AGATTGAATTGCTTCAATCTGCCCTATGGTCGAGGTAAAAGATTGGATGGTCTTCAATCTGCCCC
* * * * * *
15028 ATGGTCGAGGTAAAAGATTAGATGGTCTTCCATTTGCCCCATGGTCGGGGTAAAATATTGGATGG
66 ATGGTCGGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCGAGGTAAAAGATTGGATGG
*
15093 TCTTCAATCTGCCCTCTAGTTAGGGTAAA
131 TCTTCAATCTGCCCTCTAGTTAAGGTAAA
* * * *
15122 AGATTTAATTGCTTCAATCTGACCC-ATAGTCGAGGTAAAAGACTAGATGGTCTTCAATCTGCCC
1 AGATTGAATTGCTTCAATCTG-CCCTATGGTCGAGGTAAAAGATTGGATGGTCTTCAATCTGCCC
* * * *
15186 CATGGTCGGGGTAAAAAATCGGATGGTCTTCAATCTGCCCTC-TGGT-TAGGGTAAAAAATTGGA
65 CATGGTCGGGGTAAAAGATTGGATGGTCTTCAATCTGCCC-CATGGTCGA-GGTAAAAGATTGGA
* *
15249 TTG-CTTTAATCTGCCC-CATAGTTAAGGTAAA
128 TGGTCTTCAATCTGCCCTC-TAGTTAAGGTAAA
15280 AGAT
1 AGAT
15284 AGGATTGTAA
Statistics
Matches: 410, Mismatches: 61, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
157 31 0.08
158 70 0.17
159 304 0.74
160 5 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (159 bp):
AGATTGAATTGCTTCAATCTGCCCTATGGTCGAGGTAAAAGATTGGATGGTCTTCAATCTGCCCC
ATGGTCGGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCGAGGTAAAAGATTGGATGG
TCTTCAATCTGCCCTCTAGTTAAGGTAAA
Found at i:15441 original size:48 final size:50
Alignment explanation
Indices: 15339--15443 Score: 124
Period size: 48 Copynumber: 2.1 Consensus size: 50
15329 GTCCTTACGA
** *
15339 CTTCAATTTGCTTCTCTACAACTTTAGGTGAATGAGATTCGCCATTACGG
1 CTTCAATTTGCCCCTCTACAACTTTAGGTGAATGAGATTCGCCATTACAG
* * * * *
15389 CTTCAATTTGCCCCTCTACAGC-TTA-GTGTATGAGATTTGCTATTGCAG
1 CTTCAATTTGCCCCTCTACAACTTTAGGTGAATGAGATTCGCCATTACAG
15437 CTTCAAT
1 CTTCAAT
15444 CCGTTCCTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 25 0.53
49 3 0.06
50 19 0.40
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (50 bp):
CTTCAATTTGCCCCTCTACAACTTTAGGTGAATGAGATTCGCCATTACAG
Found at i:27091 original size:30 final size:30
Alignment explanation
Indices: 27057--27291 Score: 142
Period size: 29 Copynumber: 8.0 Consensus size: 30
27047 AAACCGAGTC
* *
27057 AAATTTGAAATTTTAGAAAGTTCAAGGGTT
1 AAATTTGAAATTTTAGAAAATTCGAGGGTT
* * *
27087 AAATTTG-AATTTTAAAAAATTTGAGGGTC
1 AAATTTGAAATTTTAGAAAATTCGAGGGTT
* * * * *** *
27116 AAA-TTGGAATTTTTGTAAAGTT-TAATATC
1 AAATTTGAAATTTTAG-AAAATTCGAGGGTT
* * * *
27145 AAATTTGAATTTTTGGAAAATT-TAGGGTC
1 AAATTTGAAATTTTAGAAAATTCGAGGGTT
* *
27174 AAATTTG-ACTTTTGGAAAATTCGAGGGTT
1 AAATTTGAAATTTTAGAAAATTCGAGGGTT
* * *
27203 AAA-TTCAAATTTTTAGAAAATT-TAGGGGT
1 AAATTTGAAA-TTTTAGAAAATTCGAGGGTT
* * * * *
27232 CAATTTTAAATTTTTGAAAAGTTTGATGGTT
1 AAATTTGAAATTTTAGAAAA-TTCGAGGGTT
*
27263 AAATTTGAATTTTTAGAAAATTCGAGGGT
1 AAATTTGAAATTTTAGAAAATTCGAGGGT
27292 AAACACATAA
Statistics
Matches: 157, Mismatches: 39, Indels: 18
0.73 0.18 0.08
Matches are distributed among these distances:
28 18 0.11
29 73 0.46
30 46 0.29
31 20 0.13
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (30 bp):
AAATTTGAAATTTTAGAAAATTCGAGGGTT
Found at i:27113 original size:29 final size:30
Alignment explanation
Indices: 27054--27291 Score: 193
Period size: 30 Copynumber: 8.1 Consensus size: 30
27044 TTAAAACCGA
* * **
27054 GTCAAATTTGAAATTTTAGAAAGTTCAAGG
1 GTCAAATTTGAATTTTTAGAAAATTTGAGG
* *
27084 GTTAAATTTGAA-TTTTAAAAAATTTGAGG
1 GTCAAATTTGAATTTTTAGAAAATTTGAGG
* * **
27113 GTCAAATTGGAATTTTT-GTAAAGTTT-AAT
1 GTCAAATTTGAATTTTTAG-AAAATTTGAGG
* *
27142 ATCAAATTTGAATTTTTGGAAAATTT-AGG
1 GTCAAATTTGAATTTTTAGAAAATTTGAGG
* * *
27171 GTCAAATTTG-ACTTTTGGAAAATTCGAGG
1 GTCAAATTTGAATTTTTAGAAAATTTGAGG
* **
27200 GTTAAATTCAAATTTTTAGAAAATTT-AGGG
1 GTCAAATTTGAATTTTTAGAAAATTTGA-GG
* * *
27230 GTCAATTTTAAATTTTT-GAAAAGTTTGATG
1 GTCAAATTTGAATTTTTAGAAAA-TTTGAGG
* *
27260 GTTAAATTTGAATTTTTAGAAAATTCGAGG
1 GTCAAATTTGAATTTTTAGAAAATTTGAGG
27290 GT
1 GT
27292 AAACACATAA
Statistics
Matches: 165, Mismatches: 34, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
28 13 0.08
29 71 0.43
30 75 0.45
31 6 0.04
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (30 bp):
GTCAAATTTGAATTTTTAGAAAATTTGAGG
Found at i:27207 original size:58 final size:59
Alignment explanation
Indices: 27054--27284 Score: 218
Period size: 58 Copynumber: 3.9 Consensus size: 59
27044 TTAAAACCGA
* * * *
27054 GTCAAATTTGAAATTTTAGAAAGTTCAAGGGTTAAATTTGAA-TTTTAAAAAATTTGAGG
1 GTCAAATTTGAAATTTTGGAAAATTCGAGGGTTAAATTTGAATTTTTAGAAAATTT-AGG
* * * * * *** * *
27113 GTCAAATTGGAATTTTTGTAAAGTT-TAATATCAAATTTGAATTTTTGGAAAATTTAGG
1 GTCAAATTTGAAATTTTGGAAAATTCGAGGGTTAAATTTGAATTTTTAGAAAATTTAGG
* **
27171 GTCAAATTTG-ACTTTTGGAAAATTCGAGGGTTAAATTCAAATTTTTAGAAAATTTAGGG
1 GTCAAATTTGAAATTTTGGAAAATTCGAGGGTTAAATTTGAATTTTTAGAAAATTTA-GG
* * * *
27230 GTC-AATTTTAAATTTTTGAAAAGTTTGATGGTTAAATTTGAATTTTTAGAAAATT
1 GTCAAATTTGAAATTTTGGAAAA-TTCGAGGGTTAAATTTGAATTTTTAGAAAATT
27285 CGAGGGTAAA
Statistics
Matches: 137, Mismatches: 30, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
57 11 0.08
58 51 0.37
59 47 0.34
60 28 0.20
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (59 bp):
GTCAAATTTGAAATTTTGGAAAATTCGAGGGTTAAATTTGAATTTTTAGAAAATTTAGG
Found at i:28461 original size:20 final size:19
Alignment explanation
Indices: 28432--28510 Score: 85
Period size: 20 Copynumber: 4.2 Consensus size: 19
28422 AAAATTATAA
*
28432 AAAAAATTAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
28451 CAAAAATTTAAAATATTTAT
1 -AAAAATTTAAAATATTTAT
28471 AAAAATTT-AAA-ATTTAT
1 AAAAATTTAAAATATTTAT
28488 AAAAATTCTAAAA-ATTATAT
1 AAAAATT-TAAAATATT-TAT
28508 AAA
1 AAA
28511 GAAAGTTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
17 13 0.24
18 4 0.07
19 18 0.33
20 19 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:28478 original size:10 final size:10
Alignment explanation
Indices: 28421--28510 Score: 59
Period size: 9 Copynumber: 9.3 Consensus size: 10
28411 CTCTCTCAAC
*
28421 AAAAATTATAA
1 AAAAATT-TAT
*
28432 AAAAAATTA-
1 AAAAATTTAT
28441 AAATAATTT-T
1 AAA-AATTTAT
28451 CAAAAATTTA-
1 -AAAAATTTAT
*
28461 AAATATTTAT
1 AAAAATTTAT
28471 AAAAA-TT-T
1 AAAAATTTAT
28479 -AAAATTTAT
1 AAAAATTTAT
*
28488 AAAAA-TTCT
1 AAAAATTTAT
28497 AAAAATTATAT
1 AAAAATT-TAT
28508 AAA
1 AAA
28511 GAAAGTTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
7 4 0.06
8 3 0.05
9 22 0.35
10 20 0.32
11 14 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:28482 original size:26 final size:26
Alignment explanation
Indices: 28453--28503 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
28443 ATAATTTTCA
*
28453 AAAATTTA-AAATATTTATAAAAATTT
1 AAAATTTATAAA-AATTATAAAAATTT
*
28479 AAAATTTATAAAAATTCTAAAAATT
1 AAAATTTATAAAAATTATAAAAATT
28504 ATATAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AAAATTTATAAAAATTATAAAAATTT
Found at i:28520 original size:39 final size:36
Alignment explanation
Indices: 28421--28532 Score: 113
Period size: 39 Copynumber: 3.0 Consensus size: 36
28411 CTCTCTCAAC
28421 AAAAATTATA-AAAAAAATTAAAATAATTTTCAAAAATTT
1 AAAAATTATATAAAAAAATT--AA-AATTTT-AAAAATTT
*
28460 AAAATATT-TAT-AAAAATTTAAAATTTATAAAAATTCT
1 AAAA-ATTATATAAAAAAATTAAAATTT-TAAAAATT-T
*
28497 AAAAATTATATAAAGAAAGTTAAAATTTTAAAAATT
1 AAAAATTATATAAA-AAAATTAAAATTTTAAAAATT
28533 GTTATTTTAT
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
36 15 0.23
37 11 0.17
38 10 0.16
39 25 0.39
40 3 0.05
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (36 bp):
AAAAATTATATAAAAAAATTAAAATTTTAAAAATTT
Found at i:28532 original size:9 final size:9
Alignment explanation
Indices: 28445--28532 Score: 58
Period size: 9 Copynumber: 9.4 Consensus size: 9
28435 AAATTAAAAT
28445 AATTTTCAAA
1 AATTTT-AAA
28455 AA-TTTAAA
1 AATTTTAAA
28463 ATATTTATAAA
1 A-ATTT-TAAA
28474 AA-TTT-AA
1 AATTTTAAA
28481 AATTTATAAA
1 AATTT-TAAA
*
28491 AATTCTAAA
1 AATTTTAAA
28500 AATTATATAAA
1 AATT-T-TAAA
**
28511 GAAAGTT-AA
1 -AATTTTAAA
28520 AATTTTAAA
1 AATTTTAAA
28529 AATT
1 AATT
28533 GTTATTTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
7 4 0.06
8 11 0.18
9 23 0.37
10 12 0.19
11 10 0.16
12 2 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (9 bp):
AATTTTAAA
Found at i:28536 original size:18 final size:16
Alignment explanation
Indices: 28445--28532 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 16
28435 AAATTAAAAT
28445 AATTTTCAAAAATTTAAA
1 AATTTT-AAAAATTT-AA
28463 ATATTTATAAAAATTTAA
1 A-ATTT-TAAAAATTTAA
28481 AATTTATAAAAATTCTAAA
1 AATTT-TAAAAATT-T-AA
*
28500 AATTATATAAAGAAAGTTAA
1 AATT-T-T-AA-AAATTTAA
28520 AATTTTAAAAATT
1 AATTTTAAAAATT
28533 GTTATTTTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
16 4 0.07
17 15 0.25
18 6 0.10
19 19 0.31
20 10 0.16
21 3 0.05
22 4 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AATTTTAAAAATTTAA
Found at i:37042 original size:120 final size:120
Alignment explanation
Indices: 36829--37066 Score: 296
Period size: 120 Copynumber: 2.0 Consensus size: 120
36819 TTCCACAAAC
* * *
36829 TATAATCCAAAATTTCATCCTCATGTCTGTATCAACTCTATTACCAATATACGATGCTGCTCACA
1 TATAATCCAAAATTTCATCCTCATATATGTATCAACTCTATTACCAATATACGATACTGCTCACA
* * ** * * *
36894 CGAGTTGTTGAGGACTCGCAACAAATGCGGTACCCCAACCATCTATACGGTATGA
66 CGAGCTATCAAGGACTCACAACAAATGCGGTACCCCAACCATCGATACAGTATGA
* * * * * *
36949 TATAATCCATAATTTCATTCTCATATATGTATCATCTCTATTACTAGTATACGATATTGCTCACA
1 TATAATCCAAAATTTCATCCTCATATATGTATCAACTCTATTACCAATATACGATACTGCTCACA
* * * *
37014 TGAGCTATCAAGGACTCACAACATATGCGGTACCTCAGCCATCGATACAGTAT
66 CGAGCTATCAAGGACTCACAACAAATGCGGTACCCCAACCATCGATACAGTAT
37067 CTGTGCATAT
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
120 98 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (120 bp):
TATAATCCAAAATTTCATCCTCATATATGTATCAACTCTATTACCAATATACGATACTGCTCACA
CGAGCTATCAAGGACTCACAACAAATGCGGTACCCCAACCATCGATACAGTATGA
Found at i:40588 original size:20 final size:20
Alignment explanation
Indices: 40544--40582 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40534 TTGTGTCGTT
*
40544 CACTTGACAAATTGTCTACG
1 CACTTGACAAATCGTCTACG
*
40564 CACTTGATAAATCGTCTAC
1 CACTTGACAAATCGTCTAC
40583 CTACTTCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
CACTTGACAAATCGTCTACG
Found at i:43759 original size:21 final size:21
Alignment explanation
Indices: 43730--43769 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43720 AGATTCTAGG
*
43730 TTTTGGATTCAAGGTTCAAGA
1 TTTTAGATTCAAGGTTCAAGA
*
43751 TTTTAGATTCAGGGTTCAA
1 TTTTAGATTCAAGGTTCAA
43770 AGTAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (21 bp):
TTTTAGATTCAAGGTTCAAGA
Found at i:44448 original size:31 final size:32
Alignment explanation
Indices: 44412--44480 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
44402 TTTTGAGTCC
44412 AATTTGGTACT-CAAACTTGACAC-TTTTTCAT
1 AATTTGGTA-TACAAACTTGACACTTTTTTCAT
* *
44443 AATTTGGTATATAAACTTGACACTTTTTTCTT
1 AATTTGGTATACAAACTTGACACTTTTTTCAT
44475 AATTTG
1 AATTTG
44481 ATACCTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 1 0.03
31 20 0.59
32 13 0.38
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.46
Consensus pattern (32 bp):
AATTTGGTATACAAACTTGACACTTTTTTCAT
Found at i:44735 original size:59 final size:60
Alignment explanation
Indices: 44628--44799 Score: 206
Period size: 59 Copynumber: 2.9 Consensus size: 60
44618 AATATTTAAT
* * * * * *
44628 AAATTTAGGTACCAAATTGGATCTAAAAAAAAGCTTAGGTGCCAAATTAGTAAAAG-A-TGTC
1 AAATTCAGATACCAAATTGG--GTAAAAAAAAGTTTAGGTACCAAATTA-AAAAAGAAGTGTC
*
44689 AAATTCAGATACCAAATTGGGTAAAAAAAAGTTTAGGTACTAAATTAAAAAAGAAGTGTC
1 AAATTCAGATACCAAATTGGGTAAAAAAAAGTTTAGGTACCAAATTAAAAAAGAAGTGTC
* * *
44749 AAGTTCAGATATCAAATTGGGT-AAAAAAAGTTTAAGTACCAAATTAAAAAA
1 AAATTCAGATACCAAATTGGGTAAAAAAAAGTTTAGGTACCAAATTAAAAAA
44800 AAAATCAAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
58 5 0.05
59 51 0.52
60 24 0.24
61 18 0.18
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (60 bp):
AAATTCAGATACCAAATTGGGTAAAAAAAAGTTTAGGTACCAAATTAAAAAAGAAGTGTC
Found at i:46022 original size:14 final size:14
Alignment explanation
Indices: 45994--46039 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
45984 TTAAATTTTA
45994 AAAAATATAAGAATT
1 AAAAATATAA-AATT
*
46009 AAAAATATCAAATT
1 AAAAATATAAAATT
46023 -AAAATATAAAAATT
1 AAAAATAT-AAAATT
46037 AAA
1 AAA
46040 GACAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.26
14 9 0.33
15 11 0.41
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (14 bp):
AAAAATATAAAATT
Found at i:46028 original size:13 final size:13
Alignment explanation
Indices: 45995--46039 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
45985 TAAATTTTAA
45995 AAAATATAAGAATT
1 AAAATATAA-AATT
*
46009 AAAAATATCAAATT
1 -AAAATATAAAATT
46023 AAAATATAAAAATT
1 AAAATAT-AAAATT
46037 AAA
1 AAA
46040 GACAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 7 0.26
14 12 0.44
15 8 0.30
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (13 bp):
AAAATATAAAATT
Found at i:49974 original size:16 final size:17
Alignment explanation
Indices: 49950--49996 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
49940 TATAAATTAC
49950 ATAAGATATAAAAATAAT
1 ATAA-ATATAAAAATAAT
*
49968 AT-AATAT-AAAATATT
1 ATAAATATAAAAATAAT
*
49983 ATAAACATAAAAAT
1 ATAAATATAAAAAT
49997 GAGCTAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 6 0.24
18 2 0.08
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
ATAAATATAAAAATAAT
Found at i:52264 original size:119 final size:119
Alignment explanation
Indices: 52053--52294 Score: 466
Period size: 119 Copynumber: 2.0 Consensus size: 119
52043 AAAAAATCGA
* *
52053 TACATTTTTATTTGGTATCGATCTTCTAGTTTTACATCCCAACGACTCTATTAATTACCACAACA
1 TACATTTTTATTTGGTATCGATCTTCTAGTTTTACATCCCAACAACTCTATTAATTACCAAAACA
52118 ACCTCAACGATTGGAAATCAATTAGGGAGTATAAATACCAACTTCCAAAGACCC
66 ACCTCAACGATTGGAAATCAATTAGGGAGTATAAATACCAACTTCCAAAGACCC
52172 TACATTTTTATTTGGTATCGATCTTCTAGTTTTACATCCCAACAACTCTATTAATTACCAAAACA
1 TACATTTTTATTTGGTATCGATCTTCTAGTTTTACATCCCAACAACTCTATTAATTACCAAAACA
52237 ACCTCAACGATTGGAAATCAATTAGGGAGTATAAATACCAACTTCCAAAGACCC
66 ACCTCAACGATTGGAAATCAATTAGGGAGTATAAATACCAACTTCCAAAGACCC
52291 TACA
1 TACA
52295 ACAACAAGAA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 121 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (119 bp):
TACATTTTTATTTGGTATCGATCTTCTAGTTTTACATCCCAACAACTCTATTAATTACCAAAACA
ACCTCAACGATTGGAAATCAATTAGGGAGTATAAATACCAACTTCCAAAGACCC
Found at i:55534 original size:19 final size:21
Alignment explanation
Indices: 55510--55549 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
55500 GTAATAGAAA
55510 ATAATATT-AAATA-AAATAT
1 ATAATATTAAAATATAAATAT
55529 ATAATATTAAAATATAAATAT
1 ATAATATTAAAATATAAATAT
55550 TTTTTGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATATTAAAATATAAATAT
Found at i:55539 original size:15 final size:14
Alignment explanation
Indices: 55521--55550 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
55511 TAATATTAAA
55521 TAAAATATATAATAT
1 TAAAATATA-AATAT
55536 TAAAATATAAATAT
1 TAAAATATAAATAT
55550 T
1 T
55551 TTTTGGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAATATAAATAT
Found at i:55918 original size:61 final size:61
Alignment explanation
Indices: 55790--55918 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 61
55780 GCATAATAAC
* ** *
55790 AAATTTAGCTCTTCAATGTTTGCAAACTCTATCATTTAGTCTTAAATCTAAAAAATTGAAT
1 AAATTTAGCTCTTCAATCTTTGCAAACTCTATCATTTAGTCTTAAATCTAAAAAATAAAAA
* * * * * *
55851 AAATTTAGCTC-TCAA-CTTTGCATATTTTATCAATTTAGTCTTGATTCTTAAAAATAAAAA
1 AAATTTAGCTCTTCAATCTTTGCAAACTCTATC-ATTTAGTCTTAAATCTAAAAAATAAAAA
55911 AATATTTA
1 AA-ATTTA
55919 AAAGTTCATT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 12 0.21
60 28 0.50
61 16 0.29
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (61 bp):
AAATTTAGCTCTTCAATCTTTGCAAACTCTATCATTTAGTCTTAAATCTAAAAAATAAAAA
Found at i:57989 original size:6 final size:6
Alignment explanation
Indices: 57978--58022 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
57968 TGATCAAAAT
* * *
57978 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
58023 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:61909 original size:19 final size:21
Alignment explanation
Indices: 61885--61924 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
61875 GTAATAGAAA
61885 ATAATATT-AAATA-AAATAT
1 ATAATATTAAAATATAAATAT
61904 ATAATATTAAAATATAAATAT
1 ATAATATTAAAATATAAATAT
61925 TTTTTGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATATTAAAATATAAATAT
Found at i:61914 original size:15 final size:14
Alignment explanation
Indices: 61896--61925 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
61886 TAATATTAAA
61896 TAAAATATATAATAT
1 TAAAATATA-AATAT
61911 TAAAATATAAATAT
1 TAAAATATAAATAT
61925 T
1 T
61926 TTTTGGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAATATAAATAT
Found at i:62293 original size:61 final size:61
Alignment explanation
Indices: 62165--62293 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 61
62155 GCATAATAAC
* ** *
62165 AAATTTAGCTCTTCAATGTTTGCAAACTCTATCATTTAGTCTTAAATCTAAAAAATTGAAT
1 AAATTTAGCTCTTCAATCTTTGCAAACTCTATCATTTAGTCTTAAATCTAAAAAATAAAAA
* * * * * *
62226 AAATTTAGCTC-TCAA-CTTTGCATATTTTATCAATTTAGTCTTGATTCTTAAAAATAAAAA
1 AAATTTAGCTCTTCAATCTTTGCAAACTCTATC-ATTTAGTCTTAAATCTAAAAAATAAAAA
62286 AATATTTA
1 AA-ATTTA
62294 AAAGTTCATT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 12 0.21
60 28 0.50
61 16 0.29
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (61 bp):
AAATTTAGCTCTTCAATCTTTGCAAACTCTATCATTTAGTCTTAAATCTAAAAAATAAAAA
Found at i:64364 original size:6 final size:6
Alignment explanation
Indices: 64353--64397 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
64343 TGATCAAAAT
* * *
64353 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
64398 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Done.