Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001575.1 Hibiscus syriacus cultivar Beakdansim tig00003130_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: 106346
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:3559 original size:31 final size:31
Alignment explanation
Indices: 3475--3580 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
3465 GTCGAGGGTT
*
3475 TACCTATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTAAGGAACATATGGACAGT-A
* ***
3506 TTACCTATG-CCTTTCGAGACATATGGACAGTA
1 -TACCTATGTTCTAAGGA-ACATATGGACAGTA
* *
3538 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTA
*
3569 TACCTAGGTTCT
1 TACCTATGTTCT
3581 TCGGGACCTA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
31 35 0.58
32 24 0.40
33 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:9365 original size:12 final size:12
Alignment explanation
Indices: 9345--9384 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
9335 GTATTACAAC
*
9345 GACCACGACCAT
1 GACCTCGACCAT
*
9357 GACCTCGACCTT
1 GACCTCGACCAT
*
9369 GACCTCGACCAC
1 GACCTCGACCAT
9381 GACC
1 GACC
9385 AAGCCGAGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.25, C:0.45, G:0.17, T:0.12
Consensus pattern (12 bp):
GACCTCGACCAT
Found at i:10150 original size:21 final size:21
Alignment explanation
Indices: 10124--10168 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10114 TGATTCTGGG
* *
10124 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
10145 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
10166 CAA
1 CAA
10169 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:11003 original size:31 final size:31
Alignment explanation
Indices: 10965--11089 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
10955 AGAGTCGAGG
*
10965 GTTTACCTATGTTCTTCGGGACATATGTACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
10996 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
11027 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
11058 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
11089 G
1 G
11090 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:14260 original size:21 final size:21
Alignment explanation
Indices: 14234--14278 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
14224 GATTTCTGGG
* *
14234 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
14255 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
14276 CAA
1 CAA
14279 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:15197 original size:62 final size:62
Alignment explanation
Indices: 15077--15201 Score: 180
Period size: 62 Copynumber: 2.0 Consensus size: 62
15067 AGAGTCGAGG
* * * * * *
15077 GTTTACCTATGTTCTTCGGGACATATGTACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
15139 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAA-CATATGGACT
15201 G
1 G
15202 GTCCTTCGGG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 55 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
Found at i:15201 original size:31 final size:31
Alignment explanation
Indices: 15077--15186 Score: 184
Period size: 31 Copynumber: 3.5 Consensus size: 31
15067 AGAGTCGAGG
*
15077 GTTTACCTATGTTCTTCGGGACATATGTACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
15108 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
15139 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
15170 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
15187 AGAATCTATG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:18639 original size:54 final size:51
Alignment explanation
Indices: 18526--18648 Score: 142
Period size: 54 Copynumber: 2.4 Consensus size: 51
18516 GAGATATGAG
* * * * *
18526 TGGTGAAAGGAGAAGGGAGAAGGATCGAGAGAGTAGGGAGAGAGAACTAGA
1 TGGTGAAAGGAGAAGGGAAAAAGAGCGAGAGAGCAGGGACAGAGAACTAGA
18577 TAGG-GAAAGGAGAAGGGAAAAAGAGCGAGGCAGGAGCAGGGACA-AGAATCTAGA
1 T-GGTGAAAGGAGAAGGGAAAAAGAGCGA-G-A-GAGCAGGGACAGAGAA-CTAGA
18631 TGGTGAAAGGAGAAGGGA
1 TGGTGAAAGGAGAAGGGA
18649 GAAGGTGCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
51 22 0.36
52 3 0.05
53 7 0.11
54 29 0.48
ACGTcount: A:0.42, C:0.06, G:0.44, T:0.08
Consensus pattern (51 bp):
TGGTGAAAGGAGAAGGGAAAAAGAGCGAGAGAGCAGGGACAGAGAACTAGA
Found at i:24692 original size:20 final size:19
Alignment explanation
Indices: 24667--24722 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
24657 AAAGATTTAT
*
24667 TTTTATTTTTATTATTAAAA
1 TTTTATTTATATTATT-AAA
*
24687 TTTTATCTATATTTATTAAA
1 TTTTATTTATA-TTATTAAA
24707 TTTTATTTATATTATT
1 TTTTATTTATATTATT
24723 TTAAATTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 22 0.69
21 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATTTATATTATTAAA
Found at i:26001 original size:180 final size:180
Alignment explanation
Indices: 25699--26063 Score: 730
Period size: 180 Copynumber: 2.0 Consensus size: 180
25689 TTTTTTTAGA
25699 AAAACGTCCCAAAATGTCAGCTATTTCTTTAAAGTAAATACTGTCCAAGATTTTTTATATTCTAA
1 AAAACGTCCCAAAATGTCAGCTATTTCTTTAAAGTAAATACTGTCCAAGATTTTTTATATTCTAA
25764 GAGCTTTATAGTTCTCTTTTCAATTTAATAAATTTTAGTATTTTGTAATAACAAAGTATAACAAC
66 GAGCTTTATAGTTCTCTTTTCAATTTAATAAATTTTAGTATTTTGTAATAACAAAGTATAACAAC
25829 GTTTCCAAAATATGAATTTTGAAACTTTGAGATTTGTAAATGGGGTTATT
131 GTTTCCAAAATATGAATTTTGAAACTTTGAGATTTGTAAATGGGGTTATT
25879 AAAACGTCCCAAAATGTCAGCTATTTCTTTAAAGTAAATACTGTCCAAGATTTTTTATATTCTAA
1 AAAACGTCCCAAAATGTCAGCTATTTCTTTAAAGTAAATACTGTCCAAGATTTTTTATATTCTAA
25944 GAGCTTTATAGTTCTCTTTTCAATTTAATAAATTTTAGTATTTTGTAATAACAAAGTATAACAAC
66 GAGCTTTATAGTTCTCTTTTCAATTTAATAAATTTTAGTATTTTGTAATAACAAAGTATAACAAC
26009 GTTTCCAAAATATGAATTTTGAAACTTTGAGATTTGTAAATGGGGTTATT
131 GTTTCCAAAATATGAATTTTGAAACTTTGAGATTTGTAAATGGGGTTATT
26059 AAAAC
1 AAAAC
26064 ACATTGGGGC
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 185 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (180 bp):
AAAACGTCCCAAAATGTCAGCTATTTCTTTAAAGTAAATACTGTCCAAGATTTTTTATATTCTAA
GAGCTTTATAGTTCTCTTTTCAATTTAATAAATTTTAGTATTTTGTAATAACAAAGTATAACAAC
GTTTCCAAAATATGAATTTTGAAACTTTGAGATTTGTAAATGGGGTTATT
Found at i:34851 original size:4 final size:4
Alignment explanation
Indices: 34842--34868 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
34832 CATACCATGG
34842 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
34869 GGAGAGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:36258 original size:17 final size:18
Alignment explanation
Indices: 36230--36263 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
36220 CCCTACTATT
36230 ATTATGTATTATATTTTC
1 ATTATGTATTATATTTTC
36248 ATTAT-TATTATATTTT
1 ATTATGTATTATATTTT
36264 ATACTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTATGTATTATATTTTC
Found at i:38124 original size:26 final size:26
Alignment explanation
Indices: 38088--38140 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
38078 GAAACAGAAC
*
38088 ACTGCAATGACAACTCAAGGTGAGTT
1 ACTGCAATGACAACTCAAGATGAGTT
38114 ACTGCAATGACAACTCAAGATGAGTT
1 ACTGCAATGACAACTCAAGATGAGTT
38140 A
1 A
38141 ACATCATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (26 bp):
ACTGCAATGACAACTCAAGATGAGTT
Found at i:39675 original size:13 final size:13
Alignment explanation
Indices: 39657--39682 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39647 TCTTCTCGAT
39657 TGTTTTTCAAAGA
1 TGTTTTTCAAAGA
39670 TGTTTTTCAAAGA
1 TGTTTTTCAAAGA
39683 CATCTTGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TGTTTTTCAAAGA
Found at i:42827 original size:30 final size:30
Alignment explanation
Indices: 42793--42855 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
42783 GTCATTTACA
42793 GGTTTGTACTAGTGATTTAAACCATTAACT
1 GGTTTGTACTAGTGATTTAAACCATTAACT
42823 GGTTTGTACTAGTGATTTAAACCATTAACT
1 GGTTTGTACTAGTGATTTAAACCATTAACT
42853 GGT
1 GGT
42856 CTTTGCTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40
Consensus pattern (30 bp):
GGTTTGTACTAGTGATTTAAACCATTAACT
Found at i:43561 original size:16 final size:16
Alignment explanation
Indices: 43526--43566 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
43516 GTTTACTTCA
*
43526 GAATGATT-AAGTGCT
1 GAATGATTCAAATGCT
*
43541 GAATGATTCAAATGTT
1 GAATGATTCAAATGCT
43557 GAATGATTCA
1 GAATGATTCA
43567 GAGGCTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:43579 original size:18 final size:17
Alignment explanation
Indices: 43539--43580 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
43529 TGATTAAGTG
*
43539 CTGAATGATTCAAATGT
1 CTGAATGATTCAAAGGT
*
43556 -TGAATGATTCAGAGGCT
1 CTGAATGATTCAAAGG-T
43573 CTGAATGA
1 CTGAATGA
43581 ATTAGCTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 13 0.62
17 1 0.05
18 7 0.33
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (17 bp):
CTGAATGATTCAAAGGT
Found at i:43698 original size:15 final size:15
Alignment explanation
Indices: 43669--43710 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
43659 CATTGTTTTG
43669 CTGAATCAG-CAGTA
1 CTGAATCAGTCAGTA
43683 CTGAATCAGTCAGTA
1 CTGAATCAGTCAGTA
*
43698 CTGAATCATTCAG
1 CTGAATCAGTCAG
43711 AGGTGCGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (15 bp):
CTGAATCAGTCAGTA
Found at i:47036 original size:22 final size:22
Alignment explanation
Indices: 47011--47053 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
47001 TTCTCGGTGG
47011 AATGCAAC-CTAGCCATTTTATA
1 AATGCAACTC-AGCCATTTTATA
*
47033 AATGTAACTGCAGCCATTTTA
1 AATGCAACT-CAGCCATTTTA
47054 GTCTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 10 0.56
24 1 0.06
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (22 bp):
AATGCAACTCAGCCATTTTATA
Found at i:48704 original size:20 final size:20
Alignment explanation
Indices: 48679--48759 Score: 128
Period size: 20 Copynumber: 4.0 Consensus size: 20
48669 AGTTTCCAAT
48679 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
48699 TTCGCAACAC-ATAAGTCAAA
1 TTCGCAACGCGA-AAGTCAAA
*
48719 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
48739 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
48759 T
1 T
48760 GTTTTTACGC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.02
20 53 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:49165 original size:13 final size:13
Alignment explanation
Indices: 49147--49178 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
49137 AGTATTTGTC
49147 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
49160 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
49173 TTTGTT
1 TTTGTT
49179 GAAGTAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:51240 original size:4 final size:4
Alignment explanation
Indices: 51231--51276 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
51221 TTTTTCGGTA
* * * *
51231 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
51277 TCAGTGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:51467 original size:42 final size:42
Alignment explanation
Indices: 51420--51515 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
51410 GATGCACCTA
* ** * *
51420 TCATCATTCAAGAGGTGCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTC
* *
51462 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCTCTG
1 TCATCATTC-AAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
51504 TCATCGTTCAAG
1 TCATCATTCAAG
51516 TGGTCCCGCC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 2 0.05
42 40 0.91
43 2 0.05
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (42 bp):
TCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:51511 original size:21 final size:21
Alignment explanation
Indices: 51420--51515 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
51410 GATGCACCTA
* **
51420 TCATCATTCAAGAGGTGCCTC
1 TCATCGTTCAAGAGGCCCCTC
51441 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
51462 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * * *
51483 CCACCGTTCAAGAGGCCTCTG
1 TCATCGTTCAAGAGGCCCCTC
51504 TCATCGTTCAAG
1 TCATCGTTCAAG
51516 TGGTCCCGCC
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
20 3 0.05
21 52 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:52200 original size:424 final size:424
Alignment explanation
Indices: 51412--52258 Score: 1462
Period size: 424 Copynumber: 2.0 Consensus size: 424
51402 ATAAGCCCGA
*
51412 TGCACCTATCATCATTCAAGAGGTGCCTCCTATCGTTCAAGAGGCCCCTCTCATCATCGAAGAAG
1 TGCACCTATCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTCTCATCATCGAAGAAG
* * *
51477 CCCCTCCCACCGTTCAAGAGGCCTCTGTCATCGTTCAAGTGGTCCCGCCCGCGGTTCAAGAGCCC
66 CCCCTCCAACCGTTCAAGAGACCTCTGTCATCGTTCAAGTGGTCCCGCCCGCCGTTCAAGAGCCC
* * * *
51542 GATTTACATGGCATCATATGTCGACATATTGATAAACCCCCTCCCGTGCCTGATATGATGGATGC
131 GATTCACATGGCATCATATGTCAACATATTGATAAACCCCCTCCCGTACCCGATATGATGGATGC
* * *
51607 GAGTTGGGTTTCGTATGTGTTACCGGCCAGTACCATTCCTCAGGAGGAGAGGGAAACACTACCGG
196 GAGTTGGCTTTCGCATGTGTTACCGGCCAGTACCATTCCTCAGGAGGAGAGGGAAACACTACCAG
* *
51672 AAACAATTACGGATAATACACTTTGGGCTAAGATCGCAGTTGATTTTTATCTTCATAAGCGGAGC
261 AAACAATTACGGATAATACACTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATAAGCGGAGC
*
51737 AAGGGGTGTTATTCTGACCTATGCCAAATCGACGATGCATATCATTTGTTTATTGATCGGTCTTG
326 AAGGGGTGTTATTCTGACCTAAGCCAAATCGACGATGCATATCATTTGTTTATTGATCGGTCTTG
*
51802 GTGGGGTATTTTATTAGGGGTTGAAGATAATGGT
391 GTGGGATATTTTATTAGGGGTTGAAGATAATGGT
*
51836 TGCACCTATCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCTCTCTCATCATCGAAGAAG
1 TGCACCTATCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTCTCATCATCGAAGAAG
*
51901 CCCCTCCAACCGTTCAAGAGACC-CATGTCATCGTTCAAGTGGTCCCGCCTGCCGTTCAAGAGCC
66 CCCCTCCAACCGTTCAAGAGACCTC-TGTCATCGTTCAAGTGGTCCCGCCCGCCGTTCAAGAGCC
*
51965 CGATTCACATGGCGTCATATGTCAACATATTGATAAACCCCCTCCCGTACCCGATATGATGGATG
130 CGATTCACATGGCATCATATGTCAACATATTGATAAACCCCCTCCCGTACCCGATATGATGGATG
* * *
52030 CGAGTTGGCTTTCGCATGTGTTATCGGCCAGTACCATTCTTCAGGAGGAGAGGGAAATACTACCA
195 CGAGTTGGCTTTCGCATGTGTTACCGGCCAGTACCATTCCTCAGGAGGAGAGGGAAACACTACCA
* *
52095 GAAACAATTACGGATAATACCCTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATGAGCGGAG
260 GAAACAATTACGGATAATACACTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATAAGCGGAG
*
52160 CAAGGGGTGTTATTCTGACCTAAGCCAAATCGACGATGCATATCATTTGTTTTTTGATCGGTCTT
325 CAAGGGGTGTTATTCTGACCTAAGCCAAATCGACGATGCATATCATTTGTTTATTGATCGGTCTT
52225 GGTGGGATATTTTATTAGGGGTTGAAGATAATGG
390 GGTGGGATATTTTATTAGGGGTTGAAGATAATGG
52259 CTATCTTGAA
Statistics
Matches: 398, Mismatches: 24, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
423 1 0.00
424 397 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (424 bp):
TGCACCTATCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTCTCATCATCGAAGAAG
CCCCTCCAACCGTTCAAGAGACCTCTGTCATCGTTCAAGTGGTCCCGCCCGCCGTTCAAGAGCCC
GATTCACATGGCATCATATGTCAACATATTGATAAACCCCCTCCCGTACCCGATATGATGGATGC
GAGTTGGCTTTCGCATGTGTTACCGGCCAGTACCATTCCTCAGGAGGAGAGGGAAACACTACCAG
AAACAATTACGGATAATACACTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATAAGCGGAGC
AAGGGGTGTTATTCTGACCTAAGCCAAATCGACGATGCATATCATTTGTTTATTGATCGGTCTTG
GTGGGATATTTTATTAGGGGTTGAAGATAATGGT
Found at i:53384 original size:14 final size:14
Alignment explanation
Indices: 53365--53400 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
53355 TTTGATTAAT
53365 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
53379 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
53393 TGATTTGT
1 TGATTTGT
53401 TTAATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:53572 original size:20 final size:20
Alignment explanation
Indices: 53549--53645 Score: 89
Period size: 20 Copynumber: 5.2 Consensus size: 20
53539 GATTTTCGGT
53549 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
53569 TTGCGAATTTGACTATCGC-
1 TTGCGAATTTGACTTTCGCG
** *
53588 -AACG--CTT-A-TTTCGCG
1 TTGCGAATTTGACTTTCGCG
* *
53603 TTGCAAATTTGACTTTTGCG
1 TTGCGAATTTGACTTTCGCG
*
53623 TTGCGAATTTAACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
53643 TTG
1 TTG
53646 ATCGCAACAT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
14 5 0.09
15 1 0.02
16 3 0.05
18 4 0.07
19 1 0.02
20 44 0.76
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:53589 original size:54 final size:54
Alignment explanation
Indices: 53530--53641 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
53520 AGGTACAAAT
* *
53530 TCGCAACGCGAT-TTTCG-GTTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
1 TCGCAACGC-ATATTTCGCG-TTGCAAATTTGACTTTCGCGTTGCGAATTTAACTA
* * *
53584 TCGCAACGCTTATTTCGCGTTGCAAATTTGACTTTTGCGTTGCGAATTTAACTT
1 TCGCAACGCATATTTCGCGTTGCAAATTTGACTTTCGCGTTGCGAATTTAACTA
53638 TCGC
1 TCGC
53642 GTTGATCGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
53 1 0.02
54 49 0.96
55 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (54 bp):
TCGCAACGCATATTTCGCGTTGCAAATTTGACTTTCGCGTTGCGAATTTAACTA
Found at i:53858 original size:39 final size:39
Alignment explanation
Indices: 53804--53889 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
53794 TGAAGTTGTA
53804 GATTTTGAATTCCTTTTGC-TTGACACCATAAGAGATTTG
1 GATTTTGAATTCCTTTTGCTTTG-CACCATAAGAGATTTG
* *
53843 GATTTT-AATTTCCTTTTGCTTTGCACCATATGAGCTTTG
1 GATTTTGAA-TTCCTTTTGCTTTGCACCATAAGAGATTTG
53882 GATTTTGA
1 GATTTTGA
53890 TGAGCATCGG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
38 2 0.05
39 36 0.86
40 4 0.10
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.45
Consensus pattern (39 bp):
GATTTTGAATTCCTTTTGCTTTGCACCATAAGAGATTTG
Found at i:54225 original size:18 final size:18
Alignment explanation
Indices: 54202--54238 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54192 CGAAATTTAT
54202 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
54220 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
54238 A
1 A
54239 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:54662 original size:25 final size:25
Alignment explanation
Indices: 54625--54674 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
54615 ATTATTTTTC
*
54625 CAAATAATATACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
*
54650 CAAATAATGTACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
54675 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:54758 original size:20 final size:20
Alignment explanation
Indices: 54735--54776 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
54725 AGATATGTTG
54735 AAGGTAAATTCGCAACGCGA
1 AAGGTAAATTCGCAACGCGA
*
54755 AAGGTAAATTCGTAACGCGA
1 AAGGTAAATTCGCAACGCGA
54775 AA
1 AA
54777 TAAGCGTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (20 bp):
AAGGTAAATTCGCAACGCGA
Found at i:54883 original size:20 final size:20
Alignment explanation
Indices: 54858--54921 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
54848 GTTTGCGATT
*
54858 TCGCGTTACGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* *
54878 TCGCGTTGCGAATTTGTCTT
1 TCGCGTTGCGAATTTGACTA
54898 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
54918 TCGC
1 TCGC
54922 AACGCTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:55261 original size:6 final size:6
Alignment explanation
Indices: 55252--55286 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
55242 TTATGATTGA
**
55252 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
55287 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:55268 original size:18 final size:18
Alignment explanation
Indices: 55245--55285 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
55235 AAGCCGGTTA
55245 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
55263 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
55281 TGATT
1 TGATT
55286 TCCTTTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:57579 original size:24 final size:24
Alignment explanation
Indices: 57545--57612 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
57535 CCATCACATC
57545 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
57569 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
57593 ATCAAATTTCGAATATTGAC
1 ATCAAAATCCGAGTATTGAC
57613 TAGTACTCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:61781 original size:3 final size:3
Alignment explanation
Indices: 61775--61821 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
61765 CATCATCATC
61775 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
61822 GAAAGCTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:66135 original size:60 final size:61
Alignment explanation
Indices: 65998--66135 Score: 142
Period size: 60 Copynumber: 2.3 Consensus size: 61
65988 AGTCTGATTT
* * * * *
65998 TAAATTGGTCTCCAAA-TTTTTAAATGTTTCTATTTCATCCTTAAACTATGACTATCATTC
1 TAAATTGATCCCCAAACTTTTTAAATATTTCAATTTCATCCTTAAACTACGACTATCATTC
** *
66058 TAAATT-AGTCCTTAAACTTTTT-AATATTTCAATTTCAT-CTTCAAACTGCGATCT-TCATTC
1 TAAATTGA-TCCCCAAACTTTTTAAATATTTCAATTTCATCCTT-AAACTACGA-CTATCATTC
66118 TAAATTGATCCCCAAACT
1 TAAATTGATCCCCAAACT
66136 ATACGCATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
59 3 0.05
60 52 0.83
61 8 0.13
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (61 bp):
TAAATTGATCCCCAAACTTTTTAAATATTTCAATTTCATCCTTAAACTACGACTATCATTC
Found at i:71163 original size:17 final size:17
Alignment explanation
Indices: 71136--71174 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
71126 AATTTACAAT
71136 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
71152 TAATTATAAATAATATC
1 TAATTATAAATAATATC
71169 TAATTA
1 TAATTA
71175 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:71303 original size:9 final size:9
Alignment explanation
Indices: 71289--71314 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
71279 TATATTTAAA
71289 GGTTAATTC
1 GGTTAATTC
71298 GGTTAATTC
1 GGTTAATTC
71307 GGTTAATT
1 GGTTAATT
71315 AATCGATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (9 bp):
GGTTAATTC
Found at i:96248 original size:20 final size:21
Alignment explanation
Indices: 96223--96274 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
96213 TTTTCCCAAT
*
96223 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
96243 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
96264 TCGCAATGCGA
1 TCGCAATGCGA
96275 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:96288 original size:20 final size:20
Alignment explanation
Indices: 96263--96376 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
96253 AATTGGGAAA
96263 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
96283 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
96303 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* * *
96323 ATCGCAATGTGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
96344 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
*
96364 TTCGCAATGCGAT
1 ATCGCAATGCGAT
96377 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:96980 original size:19 final size:19
Alignment explanation
Indices: 96933--96974 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
96923 ACGAGAGAAT
*
96933 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
96952 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
96971 CGCA
1 CGCA
96975 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:97016 original size:20 final size:19
Alignment explanation
Indices: 96970--97135 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
96960 GAAACAAAAA
*
96970 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
96989 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
97008 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
97028 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
97044 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
97061 TCGCGTTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
**
97077 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
97094 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
97114 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
97134 TC
1 TC
97136 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 18 0.15
15 1 0.01
16 5 0.04
17 5 0.04
18 1 0.01
19 40 0.34
20 48 0.40
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:97051 original size:39 final size:39
Alignment explanation
Indices: 96975--97051 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
96965 AAAAATCGCA
* **
96975 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
97014 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
97052 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:97060 original size:33 final size:33
Alignment explanation
Indices: 97023--97109 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
97013 GTTGCGATTT
* * *
97023 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTATCGTCGCGATAG
*
97056 TCATTTCGCGTTGCGATTCTATCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTATCGTCGCGATAG
97089 TCATTTCCGCGTTGCGATTCT
1 TCATTT-CGCGTTGCGATTCT
97110 CATTATCTCG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTATCGTCGCGATAG
Found at i:99220 original size:42 final size:42
Alignment explanation
Indices: 99144--99262 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
99134 GACTCGCCTG
* * * * * *
99144 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
*
99186 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * *
99228 TCA-TCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCACTCCCACCGTTCAAGAG
99263 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.06
42 57 0.88
43 4 0.06
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
Found at i:99225 original size:21 final size:21
Alignment explanation
Indices: 99196--99262 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
99186 TCATTCCTCG
*
99196 AGAGTCCACTCCCACCGTTCA
1 AGAGGCCACTCCCACCGTTCA
** * *
99217 AGAGGCCACTGTCATCGTTGA
1 AGAGGCCACTCCCACCGTTCA
*
99238 AGAGGTCC-CTCCCACCATTCA
1 AGAGG-CCACTCCCACCGTTCA
99259 AGAG
1 AGAG
99263 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGGCCACTCCCACCGTTCA
Found at i:100633 original size:14 final size:14
Alignment explanation
Indices: 100614--100649 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
100604 ATTGTTTAAT
100614 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
100628 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
100642 TGATTTGT
1 TGATTTGT
100650 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:100854 original size:33 final size:32
Alignment explanation
Indices: 100812--100938 Score: 157
Period size: 33 Copynumber: 3.9 Consensus size: 32
100802 ATTAAATTCG
*
100812 CGTTGCGATTTTCATTTCGTATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
100845 CGTTGCGATTTTTATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
* *
100878 CATTGCAATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
100911 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
100939 AGTAATTTCC
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
31 3 0.04
33 73 0.92
35 3 0.04
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:100871 original size:19 final size:19
Alignment explanation
Indices: 100808--100938 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
100798 CGAAATTAAA
*
100808 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
100827 TTCGTATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
* *
100843 CTCG--TTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
*
100860 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
100874 TTAGCATTGCAATTTTCAT
1 TTCGCATTGCGATTTTCAT
100893 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
100909 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
100926 TTCGCATTGCGAT
1 TTCGCATTGCGAT
100939 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 23 0.28
16 12 0.15
17 13 0.16
19 34 0.41
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:100902 original size:66 final size:66
Alignment explanation
Indices: 100805--100937 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
100795 ACGCGAAATT
* * * * *
100805 AAATTCGCGTTGCGATTTTCATTTCGTATTGCGATTCCCTCGTTGCGATTTTTATTTCGCATTGC
1 AAATTAGCATTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
100870 G
66 G
*
100871 AAATTAGCATTGCAATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
100936 G
66 G
100937 A
1 A
100938 TAGTAATTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (66 bp):
AAATTAGCATTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:103448 original size:24 final size:24
Alignment explanation
Indices: 103414--103467 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
103404 CTGAAACATC
* *
103414 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
103438 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
103462 ATCAAA
1 ATCAAA
103468 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:104469 original size:20 final size:20
Alignment explanation
Indices: 104444--104501 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
104434 ATTCATTTGA
*
104444 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
104464 CTATCGCAACGAGAAAATGG
1 CTATCGCAACGAGAAAATGG
104484 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
104502 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:104542 original size:19 final size:19
Alignment explanation
Indices: 104520--104573 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
104510 GAAATGAAAA
104520 TCGCATTGCGATTTTCAGT
1 TCGCATTGCGATTTTCAGT
*
104539 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCAGT
104558 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
104574 TCGTTGCGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCAGT
Found at i:104709 original size:14 final size:14
Alignment explanation
Indices: 104690--104726 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
104680 CATCAATTAA
104690 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
104704 ACAAATCATCTTTT
1 ACAAATCAACATTT
104718 ACAAATCAA
1 ACAAATCAA
104727 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Done.