Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005171.1 Hibiscus syriacus cultivar Beakdansim tig00011669_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: 61850
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3740 original size:19 final size:19
Alignment explanation
Indices: 3713--3781 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
3703 AAAATCGAAA
*
3713 TCGGTTTTTTCGGTTCGGT
1 TCGGATTTTTCGGTTCGGT
**
3732 TCGGATTTTTC--AACGGT
1 TCGGATTTTTCGGTTCGGT
* *
3749 TCGAATTTTTCGGTTCAGT
1 TCGGATTTTTCGGTTCGGT
3768 TC-GATTTTTCGGTT
1 TCGGATTTTTCGGTT
3782 TTTCAATGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
17 14 0.35
18 11 0.28
19 15 0.38
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.49
Consensus pattern (19 bp):
TCGGATTTTTCGGTTCGGT
Found at i:5521 original size:22 final size:22
Alignment explanation
Indices: 5477--5541 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
5467 ATATGAAATT
*
5477 TGTCCCGAAGGACCTCATGTATA
1 TGTCCCGAAAGACCT-ATGTATA
*
5500 TGTCCCGAATGACCTATGTATA
1 TGTCCCGAAAGACCTATGTATA
5522 TGTCCCGAAAGACCTATGTA
1 TGTCCCGAAAGACCTATGTA
5542 ACCCTCGGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 26 0.65
23 14 0.35
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (22 bp):
TGTCCCGAAAGACCTATGTATA
Found at i:6984 original size:19 final size:19
Alignment explanation
Indices: 6960--7011 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
6950 CATGCTTGTA
*
6960 GTATCGATACCCTTCCACG
1 GTATCGATACCCATCCACG
6979 GTATCGATACCCATCCACG
1 GTATCGATACCCATCCACG
6998 GTATCGATACCCAT
1 GTATCGATACCCAT
7012 TTTCGATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (19 bp):
GTATCGATACCCATCCACG
Found at i:9391 original size:29 final size:29
Alignment explanation
Indices: 9304--9693 Score: 132
Period size: 30 Copynumber: 13.0 Consensus size: 29
9294 ATTAAAAGTA
* *
9304 TTTATTTTTATTTTAAATTATTAAAT-CTAT
1 TTTATTTTTATTTTAACTTA--AAATATTAT
* * * *
9334 TTTATTATTGTCTTAATCTAAAAATATATTAT
1 TTTATTTTTATTTTAA-CT-TAAA-ATATTAT
9366 TTTATTTTTATTTTAACTTAAAATA-TAT
1 TTTATTTTTATTTTAACTTAAAATATTAT
* * **
9394 TTTAATCTTATCATAACTTAAAA-ATATAT
1 TTTATTTTTATTTTAACTTAAAATAT-TAT
*
9423 TTTATTTTTATCTTAACTTTTAAAA-ATATAT
1 TTTATTTTTATTTTAAC--TTAAAATAT-TAT
* * *
9454 CTTATTTTTATTTGAACTTATTACATA-TAT
1 TTTATTTTTATTTTAACTTA--AAATATTAT
* * ** *
9484 TATATTCTTAACTTAAGTTATTAAATA-TAT
1 TTTATTTTTATTTTAACTTA--AAATATTAT
* * ** * *
9514 TTTA-GTCTACCTTAAATTATTAAATA-TAA
1 TTTATTTTTATTTTAACTTA--AAATATTAT
* ** * *
9543 TTCATCCTTATTTTAACATAAAGTATATAT
1 TTTATTTTTATTTTAACTTAAAATAT-TAT
* * *
9573 TTTATTCTTATTTTTAACTTAACATGTATAT
1 TTTATTTTTA-TTTTAACTTAAAATAT-TAT
* *
9604 TTTATTTATATTTTAATTTAAAAATATTTAT
1 TTTATTTTTATTTTAACTT-AAAATA-TTAT
** * * * *
9635 GCTAATTTTGTTTTGATTTAAAA-ATATAT
1 TTTATTTTTATTTTAACTTAAAATAT-TAT
* *
9664 TTTATTTTTATCTTAATTTTAAAATATTAT
1 TTTATTTTTATTTTAA-CTTAAAATATTAT
9694 AAGAATAAAA
Statistics
Matches: 271, Mismatches: 69, Indels: 40
0.71 0.18 0.11
Matches are distributed among these distances:
27 1 0.00
28 27 0.10
29 59 0.22
30 86 0.32
31 79 0.29
32 19 0.07
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTATTTTTATTTTAACTTAAAATATTAT
Found at i:9493 original size:36 final size:32
Alignment explanation
Indices: 9352--9472 Score: 107
Period size: 31 Copynumber: 4.0 Consensus size: 32
9342 TGTCTTAATC
* *
9352 TAAAAATATATTATTTTATTTTTATTTTAAC--T
1 TAAAAATATA-T-TCTTATTTTTATCTTAACTTT
* * *
9384 T-AAAATATATT-TTAATCTTATCATAAC--T
1 TAAAAATATATTCTTATTTTTATCTTAACTTT
9412 TAAAAATATATT-TTATTTTTATCTTAACTTT
1 TAAAAATATATTCTTATTTTTATCTTAACTTT
9443 TAAAAATATA-TCTTATTTTTAT-TTGAACTT
1 TAAAAATATATTCTTATTTTTATCTT-AACTT
9473 ATTACATATA
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
28 14 0.18
29 24 0.31
30 4 0.05
31 34 0.44
32 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.55
Consensus pattern (32 bp):
TAAAAATATATTCTTATTTTTATCTTAACTTT
Found at i:9505 original size:30 final size:29
Alignment explanation
Indices: 9471--9541 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
9461 TTATTTGAAC
* * *
9471 TTATTACATATATTATATTCTTAACTTAAG
1 TTATTAAATATATTATAGTC-TAACTTAAA
* *
9501 TTATTAAATATATTTTAGTCTACCTTAAA
1 TTATTAAATATATTATAGTCTAACTTAAA
9530 TTATTAAATATA
1 TTATTAAATATA
9542 ATTCATCCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 19 0.53
30 17 0.47
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATTAAATATATTATAGTCTAACTTAAA
Found at i:9771 original size:30 final size:28
Alignment explanation
Indices: 9731--9840 Score: 107
Period size: 29 Copynumber: 3.7 Consensus size: 28
9721 AGGTAACAAC
9731 AAAT-TATTTTTTAAGTTAATAAAAAATTA
1 AAATATATTTTTTAAGTTAA-AAAAAA-TA
*
9760 AAATGTATTTTTTAAGTTAAAATAAGAATA
1 AAATATATTTTTTAAGTTAAAA-AA-AATA
*
9790 AAATATA-TTTCTAAGTTAAGATAAAAATA
1 AAATATATTTTTTAAGTTAA-A-AAAAATA
*
9819 AAATATACATTTTTAATGTTAA
1 AAATATA-TTTTTTAA-GTTAA
9841 GATGTTAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
29 28 0.40
30 28 0.40
31 9 0.13
32 5 0.07
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (28 bp):
AAATATATTTTTTAAGTTAAAAAAAATA
Found at i:9863 original size:18 final size:18
Alignment explanation
Indices: 9830--9876 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
9820 AATATACATT
*
9830 TTTAATGTTAAGATGTTAA
1 TTTAAT-TTAAGATGTGAA
*
9849 TTTAATTTAATATGTGAA
1 TTTAATTTAAGATGTGAA
*
9867 TTTAAGTTAA
1 TTTAATTTAA
9877 AATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (18 bp):
TTTAATTTAAGATGTGAA
Found at i:10705 original size:69 final size:69
Alignment explanation
Indices: 10594--10728 Score: 261
Period size: 69 Copynumber: 2.0 Consensus size: 69
10584 TTGTTGTTAT
10594 TGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
1 TGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
10659 AAGC
66 AAGC
*
10663 TGTCGGAACCGTCTTTCGGTTGGGCTCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
1 TGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
10728 A
66 A
10729 CCGACCACTT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (69 bp):
TGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATGAATTGGAGTCGCC
AAGC
Found at i:11123 original size:25 final size:26
Alignment explanation
Indices: 11052--11124 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
11042 TGAAAGAAAG
*
11052 AAATAATAAAATAATAATAAAAGGTTA
1 AAATAA-AAAATAATAATAAAAAGTTA
* *
11079 AATTAAAAAA-AATATTTAAAAAG-TA
1 AAATAAAAAATAATA-ATAAAAAGTTA
11104 AAATAAAAAATAA-AGATAAAA
1 AAATAAAAAATAATA-ATAAAA
11125 CTTAGGATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 21 0.55
26 12 0.32
27 5 0.13
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (26 bp):
AAATAAAAAATAATAATAAAAAGTTA
Found at i:12386 original size:9 final size:9
Alignment explanation
Indices: 12359--12414 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
12349 AAAAAAAAGT
12359 AAAATAA-A
1 AAAATAATA
*
12367 ATAAGTAATA
1 A-AAATAATA
12377 AAAATAATA
1 AAAATAATA
*
12386 ATAATAATA
1 AAAATAATA
*
12395 ATAATAATA
1 AAAATAATA
*
12404 AATATAA-A
1 AAAATAATA
12412 AAA
1 AAA
12415 CTATATAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 4 0.10
9 34 0.85
10 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (9 bp):
AAAATAATA
Found at i:12387 original size:3 final size:3
Alignment explanation
Indices: 12361--12404 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
12351 AAAAAAGTAA
*
12361 AAT AA- AAT AAGT AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12405 ATATAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:12510 original size:30 final size:30
Alignment explanation
Indices: 12464--12552 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
12454 CTATATATTA
*
12464 TATATAAATTTCCAAAAATATTTTTAAAAAC
1 TATAT-AATTTTCAAAAATATTTTTAAAAAC
* * *
12495 TATATAATTTTCAAAAATGTCTTTAAGAAC
1 TATATAATTTTCAAAAATATTTTTAAAAAC
*
12525 CATATAATTTTCAAAAATA-TTTTAAAAA
1 TATATAATTTTCAAAAATATTTTTAAAAA
12553 TCATATATTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 7 0.14
30 38 0.76
31 5 0.10
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.39
Consensus pattern (30 bp):
TATATAATTTTCAAAAATATTTTTAAAAAC
Found at i:12630 original size:38 final size:37
Alignment explanation
Indices: 12526--12720 Score: 182
Period size: 38 Copynumber: 5.1 Consensus size: 37
12516 TTTAAGAACC
*
12526 ATATA-ATTTTCAAAAATATTTTAAAAA-TCATATATT
1 ATATATATTTTCAAAAATGTTTTAAAAACT-ATATATT
* *
12562 ATATATGTTTTC-AAAATGTTTTTTCAAAAAATTATATATTCT
1 ATATATATTTTCAAAAATG--TTTT--AAAAACTATATA-T-T
* *
12604 ATATTTATTTTC-AAAATGTTTTAAAAACTATATAAT
1 ATATATATTTTCAAAAATGTTTTAAAAACTATATATT
* *
12640 ATATATATTTTTCAAAAATGTCTTGAAAACTATATATT
1 ATATATA-TTTTCAAAAATGTTTTAAAAACTATATATT
* * * *
12678 ATATTTATTTTCAAAAACGTTTTAAAAAACCATATAAT
1 ATATATATTTTCAAAAATGTTTT-AAAAACTATATATT
12716 ATATA
1 ATATA
12721 AATGTTTTCA
Statistics
Matches: 131, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
36 17 0.13
37 24 0.18
38 57 0.44
40 14 0.11
41 2 0.02
42 17 0.13
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
ATATATATTTTCAAAAATGTTTTAAAAACTATATATT
Found at i:12713 original size:76 final size:77
Alignment explanation
Indices: 12589--12733 Score: 215
Period size: 76 Copynumber: 1.9 Consensus size: 77
12579 GTTTTTTCAA
* * * *
12589 AAAATTATATATTCTATATTTATTTTCAAAATGTTTTAAAAACTATATAATATATATAT-TTTTC
1 AAAACTATATATTCTATATTTATTTTCAAAACGTTTTAAAAACCATATAATATATAAATGTTTTC
12653 AAAAATGTCTTG
66 AAAAATGTCTTG
12665 AAAACTATATA-T-TATATTTATTTTCAAAAACGTTTTAAAAAACCATATAATATATAAATGTTT
1 AAAACTATATATTCTATATTTATTTTC-AAAACGTTTT-AAAAACCATATAATATATAAATGTTT
12728 TCAAAA
64 TCAAAA
12734 TGAAAATGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
74 13 0.21
75 10 0.16
76 30 0.48
77 9 0.15
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (77 bp):
AAAACTATATATTCTATATTTATTTTCAAAACGTTTTAAAAACCATATAATATATAAATGTTTTC
AAAAATGTCTTG
Found at i:13546 original size:165 final size:165
Alignment explanation
Indices: 13293--14303 Score: 1780
Period size: 165 Copynumber: 6.1 Consensus size: 165
13283 AGTTTTATTG
* * * * * * * * * *
13293 ACAGATAACCCTTCTTGCATTGAGCTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGTGTAAT
** *
13357 CGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
64 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* *
13422 GGAACTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTC
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
13459 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
13524 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
13589 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
13624 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
13689 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
13754 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
13789 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
13854 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
13919 AGCTGAGCGTAGTCGAACTCGAAGGTC--TTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
13952 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
14017 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
14082 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
14117 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
14182 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
*
14247 AGCTGAGCGTAGTCGAACTCGAAGGTC--TTGGTG
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* * *
14280 GCAGATAGCCCTTCTGGCCTTGAG
1 ACAGATAACCCTTCTAGCCTTGAG
14304 CTAAGCTACA
Statistics
Matches: 820, Mismatches: 22, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
163 188 0.23
164 6 0.01
165 595 0.73
166 31 0.04
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (165 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
Found at i:14128 original size:328 final size:328
Alignment explanation
Indices: 13293--14303 Score: 1799
Period size: 328 Copynumber: 3.1 Consensus size: 328
13283 AGTTTTATTG
* * * * * * * * * *
13293 ACAGATAACCCTTCTTGCATTGAGCTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGTGTAAT
** *
13357 CGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
64 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* *
13422 GGAACTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
13487 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCT
194 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCT
*
13552 TCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
259 TCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-
13617 TTTGGTC
323 -TTGGTC
13624 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
13689 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
13754 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
13819 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
196 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
13884 TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTG
261 TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTG
13949 GTC
326 GTC
13952 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
14017 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
14082 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
14147 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
196 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
14212 TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTG
261 TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTG
*
14277 GTG
326 GTC
* * *
14280 GCAGATAGCCCTTCTGGCCTTGAG
1 ACAGATAACCCTTCTAGCCTTGAG
14304 CTAAGCTACA
Statistics
Matches: 659, Mismatches: 20, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
328 354 0.54
329 6 0.01
330 268 0.41
331 31 0.05
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (328 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTG
GTC
Found at i:17701 original size:18 final size:19
Alignment explanation
Indices: 17660--17704 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
17650 AGTTAATGTG
17660 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
17679 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
17697 AATGCAAA
1 AATGCAAA
17705 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:19173 original size:69 final size:69
Alignment explanation
Indices: 19062--19209 Score: 296
Period size: 69 Copynumber: 2.1 Consensus size: 69
19052 TGTCCCCAGC
19062 GGAGTCGCCAAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
1 GGAGTCGCCAAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
19127 AATT
66 AATT
19131 GGAGTCGCCAAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
1 GGAGTCGCCAAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
19196 AATT
66 AATT
19200 GGAGTCGCCA
1 GGAGTCGCCA
19210 CCGACCACTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 79 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (69 bp):
GGAGTCGCCAAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
AATT
Found at i:19604 original size:25 final size:26
Alignment explanation
Indices: 19533--19605 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
19523 TGAAAGAAAG
*
19533 AAATAATAAAATAATAATAAAAGGTTA
1 AAATAA-AAAATAATAATAAAAAGTTA
* *
19560 AATTAAAAAA-AATATTTAAAAAG-TA
1 AAATAAAAAATAATA-ATAAAAAGTTA
19585 AAATAAAAAATAA-AGATAAAA
1 AAATAAAAAATAATA-ATAAAA
19606 CTTAGGATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 21 0.55
26 12 0.32
27 5 0.13
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (26 bp):
AAATAAAAAATAATAATAAAAAGTTA
Found at i:20863 original size:16 final size:16
Alignment explanation
Indices: 20838--20885 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
20828 AAAAAAAAAG
20838 TAAAATAAAATAAGTAA
1 TAAAATAAAATAA-TAA
*
20855 TAAAAAAAAATAATAA
1 TAAAATAAAATAATAA
20871 TAATAATAAATATAA
1 TAA-AATAAA-ATAA
20886 AAAACTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 6 0.22
17 17 0.63
18 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
TAAAATAAAATAATAA
Found at i:20866 original size:22 final size:22
Alignment explanation
Indices: 20839--20880 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
20829 AAAAAAAAGT
20839 AAAATAA-AATAAGTAATAAAAA
1 AAAATAATAATAA-TAATAAAAA
20861 AAAATAATAATAATAATAAA
1 AAAATAATAATAATAATAAA
20881 TATAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATAATAATAATAATAAAAA
Found at i:20872 original size:28 final size:28
Alignment explanation
Indices: 20828--20889 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
20818 TTGGACCTGG
*
20828 AAAAAAAAAGTAAAATAA-AATAAGTAAT
1 AAAAAAAAAGTAAAATAATAATAAAT-AT
20856 AAAAAAAAA-TAATAATAATAATAAATAT
1 AAAAAAAAAGTAA-AATAATAATAAATAT
20884 AAAAAA
1 AAAAAA
20890 CTATATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 3 0.10
28 22 0.71
29 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (28 bp):
AAAAAAAAAGTAAAATAATAATAAATAT
Found at i:20875 original size:26 final size:24
Alignment explanation
Indices: 20841--20889 Score: 55
Period size: 25 Copynumber: 2.0 Consensus size: 24
20831 AAAAAAGTAA
20841 AATAAAATAAGTAATAAAAAAAAAT
1 AATAAAATAAGTAAT-AAAAAAAAT
*
20866 AATAATAATAA-TAAATATAAAAAA
1 AATAA-AATAAGT-AATAAAAAAAA
20890 CTATATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (24 bp):
AATAAAATAAGTAATAAAAAAAAT
Found at i:20985 original size:30 final size:30
Alignment explanation
Indices: 20939--21027 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
20929 CTATATATTA
*
20939 TATATAAATTTCCAAAAATATTTTTAAAAAC
1 TATAT-AATTTTCAAAAATATTTTTAAAAAC
* * *
20970 TATATAATTTTCAAAAATGTCTTTAAGAAC
1 TATATAATTTTCAAAAATATTTTTAAAAAC
*
21000 CATATAATTTTCAAAAATA-TTTTAAAAA
1 TATATAATTTTCAAAAATATTTTTAAAAA
21028 TCATATATTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 7 0.14
30 38 0.76
31 5 0.10
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.39
Consensus pattern (30 bp):
TATATAATTTTCAAAAATATTTTTAAAAAC
Found at i:21124 original size:38 final size:38
Alignment explanation
Indices: 21001--21204 Score: 181
Period size: 37 Copynumber: 5.4 Consensus size: 38
20991 TTTAAGAACC
* *
21001 ATATA-ATTTTCAAAAATATTTTAAAAA-T-CATATAT
1 ATATATATTTTCAAAAATGTTTTAAAAACTATATATAT
* * *
21036 -TATATGTTTTC-AAAATGTTTTTTCAAAAAAT-TATATTT
1 ATATATATTTTCAAAAATG--TTTT-AAAAACTATATATAT
*
21074 ATATTTATTTTC-AAAATGTTTTAAAAACTATATAATAT
1 ATATATATTTTCAAAAATGTTTTAAAAACTATAT-ATAT
* *
21112 ATATATATTTTCAAAAATGTCTTGAAAACTATATAT-T
1 ATATATATTTTCAAAAATGTTTTAAAAACTATATATAT
* * *
21149 ATATTTATTTTCAAAAACGTTTTAAAAACCCATATAATAT
1 ATATATATTTTCAAAAATGTTTTAAAAA-CTATAT-ATAT
* *
21189 ATAAATGTTTTCAAAA
1 ATATATATTTTCAAAA
21205 TGAAAATGTT
Statistics
Matches: 138, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
34 9 0.07
35 5 0.04
36 10 0.07
37 37 0.27
38 27 0.20
39 36 0.26
40 14 0.10
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (38 bp):
ATATATATTTTCAAAAATGTTTTAAAAACTATATATAT
Found at i:21163 original size:75 final size:76
Alignment explanation
Indices: 21062--21204 Score: 218
Period size: 77 Copynumber: 1.9 Consensus size: 76
21052 GTTTTTTCAA
* * * *
21062 AAAATTATATTTATATTTATTTTC-AAAATGTTTTAAAAA-CTATATAATATATATATATTTTCA
1 AAAACTATATTTATATTTATTTTCAAAAACGTTTTAAAAACCCATATAATATATAAATATTTTCA
21125 AAAATGTCTTG
66 AAAATGTCTTG
*
21136 AAAACTATATATTATATTTATTTTCAAAAACGTTTTAAAAACCCATATAATATATAAATGTTTTC
1 AAAACTATAT-TTATATTTATTTTCAAAAACGTTTTAAAAACCCATATAATATATAAATATTTTC
21201 AAAA
65 AAAA
21205 TGAAAATGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
74 9 0.15
75 14 0.23
76 14 0.23
77 24 0.39
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (76 bp):
AAAACTATATTTATATTTATTTTCAAAAACGTTTTAAAAACCCATATAATATATAAATATTTTCA
AAAATGTCTTG
Found at i:23744 original size:31 final size:31
Alignment explanation
Indices: 23685--23754 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
23675 GAAAAGTAAT
*
23685 ATTTT-GTCACTTACATTATCAGTTTATAAC
1 ATTTTGGTCACTTACATTATCAGTATATAAC
* *
23715 TTTTTGGTCACTTACGTTATC-GATATATAAC
1 ATTTTGGTCACTTACATTATCAG-TATATAAC
*
23746 AATTTGGTC
1 ATTTTGGTC
23755 CCTGAGATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTTTGGTCACTTACATTATCAGTATATAAC
Found at i:23879 original size:31 final size:31
Alignment explanation
Indices: 23831--23912 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
23821 TGACCCACAC
*
23831 TAGATAAAAT-ACTAATTTAACCCTT-AAATT
1 TAGATAAAATAAC-AATTTAACCCTTAAAATA
* *
23861 TAAGATAAATTAACAATTTAACTCTTAAAATA
1 T-AGATAAAATAACAATTTAACCCTTAAAATA
*
23893 TAGATAAAATATCAATTTAA
1 TAGATAAAATAACAATTTAA
23913 GCTAAGAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.02
31 36 0.82
32 7 0.16
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (31 bp):
TAGATAAAATAACAATTTAACCCTTAAAATA
Found at i:25898 original size:41 final size:41
Alignment explanation
Indices: 25772--25930 Score: 142
Period size: 41 Copynumber: 3.8 Consensus size: 41
25762 AGTGGTAAAT
* * *
25772 TAGTGGCGTTTATACCACAAACGCCGCAATAG-ATTACACATA
1 TAGTGGCGTTTTTA-GACAAACGCCGCAATAGTATTACTCA-A
*** * * *
25814 TAGTGGCGTTCTTTTCCTCAAATGCCGTAATAGTGA-TAATCAA
1 TAGTGGCG-T-TTTTAGACAAACGCCGCAATAGT-ATTACTCAA
*
25857 TAGTTGCGTTTTTAGACAAACGCCGCAATAGTATTACTCAA
1 TAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTACTCAA
* *
25898 TAGTGGCATTTTTAGACAAAACGCCACAATAGT
1 TAGTGGCGTTTTTAGAC-AAACGCCGCAATAGT
25931 GGTAAATAAG
Statistics
Matches: 94, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
40 1 0.01
41 39 0.41
42 23 0.24
43 23 0.24
44 7 0.07
45 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (41 bp):
TAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTACTCAA
Found at i:28253 original size:21 final size:21
Alignment explanation
Indices: 28227--28268 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28217 AGGTATTGCC
28227 AAAAGAACCGGATGAGATACT
1 AAAAGAACCGGATGAGATACT
28248 AAAAGAACCGGATGAGATACT
1 AAAAGAACCGGATGAGATACT
28269 GGCTTCGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (21 bp):
AAAAGAACCGGATGAGATACT
Found at i:29009 original size:54 final size:54
Alignment explanation
Indices: 28941--29061 Score: 172
Period size: 54 Copynumber: 2.2 Consensus size: 54
28931 CATCATTGCC
* *
28941 ACCATAAGATGTGATACTCGGTATCGGTTCAAAATCACTAGTGAATGATTTCTT-
1 ACCATAAGAAGTGATACTCGGTATCGGTTCAAAATCACCAGTGAATGATTT-TTG
* * *
28995 ACCATAAGAAGTGATGCTCGGTATGGGTTCAAAATCACCGGTGAATGATTTTTG
1 ACCATAAGAAGTGATACTCGGTATCGGTTCAAAATCACCAGTGAATGATTTTTG
*
29049 GCCATAAGAAGTG
1 ACCATAAGAAGTG
29062 CTCAGTCTCG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 2 0.03
54 58 0.97
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (54 bp):
ACCATAAGAAGTGATACTCGGTATCGGTTCAAAATCACCAGTGAATGATTTTTG
Found at i:29219 original size:54 final size:54
Alignment explanation
Indices: 29128--29234 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
29118 ATCATCGCCT
* * * *
29128 CCATAAGAAGTGGTGCTTGGTCTCGGTTTGAAATCACTAGTGAATGATTTCTTA
1 CCATAAGAAGTGATGCTCGGTCTCAGTTTCAAATCACTAGTGAATGATTTCTTA
* * *
29182 CCATAAGATGTGATGCTCGGTCTCAG-TTCAAATTCACTAGTTAATGTTTTCTT
1 CCATAAGAAGTGATGCTCGGTCTCAGTTTCAAA-TCACTAGTGAATGATTTCTT
29235 CACTCCTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 5 0.11
54 40 0.89
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (54 bp):
CCATAAGAAGTGATGCTCGGTCTCAGTTTCAAATCACTAGTGAATGATTTCTTA
Found at i:29457 original size:135 final size:134
Alignment explanation
Indices: 28995--29484 Score: 610
Period size: 135 Copynumber: 3.6 Consensus size: 134
28985 ATGATTTCTT
* * * * ** * *
28995 ACCATAAGAAGTGATGCTCGGTATGGGTTCAAAATCACCGGTGAATGATTTTTGGCCATAAGAA-
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
* * * * *
29059 -G-TGCTCAGTCTCGGTTCAAAATTGCTAGGAAAAGTTTTCTTCACTCCTTTAAGATCAACATCA
66 TGATGCTCGGTCTCGGTTCAAATTTACTA-GTAATGTTTTCTTCACTCCTTTAAGATCAACATCA
29122 TCGCC
130 TCGCC
* ** * *
29127 TCCATAAGAAGTGGTGCTTGGTCTCGGTTTGAAATCACTAGTGAATGATTTCTTACCATAAGATG
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
* *
29192 TGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACATC
66 TGATGCTCGGTCTCGGTTCAAATTTACTAG-TAATGTTTTCTTCACTCC-TTTAAGATCAACATC
*
29257 ATTGCC
129 ATCGCC
* * *
29263 ACCATAAGAAGTGGTGCTTGGTCTCGGCTCAAAATCAATAGTGAATGATTTTTGACCATAA-AAC
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAA-
*
29327 GTGATGCTCGGTCTCGGTTCAAATTTACTAGTAATTGATTTCTTCACTCCTTTAAGATCAACATC
65 GTGATGCTCGGTCTCGGTTCAAATTTACTAGTAA-TGTTTTCTTCACTCCTTTAAGATCAACATC
29392 ATCGCC
129 ATCGCC
* * * * * * *
29398 GCCATAAGATGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGGCCATAAGAAG
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
*
29463 TGGTGCTCGGTCTCGGTTCAAA
66 TGATGCTCGGTCTCGGTTCAAA
29485 ATAGCTCTCC
Statistics
Matches: 306, Mismatches: 44, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
132 51 0.17
134 2 0.01
135 134 0.44
136 119 0.39
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (134 bp):
ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
TGATGCTCGGTCTCGGTTCAAATTTACTAGTAATGTTTTCTTCACTCCTTTAAGATCAACATCAT
CGCC
Found at i:29475 original size:271 final size:268
Alignment explanation
Indices: 28995--29484 Score: 694
Period size: 271 Copynumber: 1.8 Consensus size: 268
28985 ATGATTTCTT
* * * * *
28995 ACCATAAGAAGTGATGCTCGGTATGGGTTCAAAATCACCGGTGAATGATTTTTGGCCATAAGAAG
1 ACCATAAGAAGTGATGCTCGGTATCGGCTCAAAATCAACAGTGAATGATTTTTGACCATAAGAAG
* *
29060 TGCTCAGTCTCGGTTCAAAATTGCTAGGAAAAGTTTTCTTCACTCCTTTAAGATCAACATCATCG
66 TGCTCAGTCTCGGTTCAAAATTACTAGGAAAAGATTTCTTCACTCCTTTAAGATCAACATCATCG
* * * * * *
29125 CCTCCATAAGAAGTGGTGCTTGGTCTCGGTTTGAAATCACTAGTGAATGATTTCTTACCATAAGA
131 CCGCCATAAGAAGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGACCATAAGA
*
29190 TGTGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACA
196 AGTGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACA
29255 TCATTGCC
261 TCATTGCC
* * * *
29263 ACCATAAGAAGTGGTGCTTGGTCTCGGCTCAAAATCAATAGTGAATGATTTTTGACCATAA-AAC
1 ACCATAAGAAGTGATGCTCGGTATCGGCTCAAAATCAACAGTGAATGATTTTTGACCATAAGAA-
* * * **
29327 GTGATGCTCGGTCTCGGTTCAAATTTACTAGTAATTGATTTCTTCACTCCTTTAAGATCAACATC
65 --G-TGCTCAGTCTCGGTTCAAAATTACTAGGAAAAGATTTCTTCACTCCTTTAAGATCAACATC
* *
29392 ATCGCCGCCATAAGATGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGGCCAT
127 ATCGCCGCCATAAGAAGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGACCAT
* *
29457 AAGAAGTGGTGCTCGGTCTCGGTTCAAA
192 AAGAAGTGATGCTCGGTCTCAGTTCAAA
29485 ATAGCTCTCC
Statistics
Matches: 191, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
267 2 0.01
268 52 0.27
270 1 0.01
271 136 0.71
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (268 bp):
ACCATAAGAAGTGATGCTCGGTATCGGCTCAAAATCAACAGTGAATGATTTTTGACCATAAGAAG
TGCTCAGTCTCGGTTCAAAATTACTAGGAAAAGATTTCTTCACTCCTTTAAGATCAACATCATCG
CCGCCATAAGAAGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGACCATAAGA
AGTGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACA
TCATTGCC
Found at i:30148 original size:17 final size:17
Alignment explanation
Indices: 30128--30171 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
30118 AAATGTATAT
* *
30128 AATATATTATTTTTTAA
1 AATATATTATTTCTGAA
*
30145 AATATATAATTTCTGAA
1 AATATATTATTTCTGAA
30162 AATATATTAT
1 AATATATTAT
30172 ATAGTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AATATATTATTTCTGAA
Found at i:32028 original size:23 final size:23
Alignment explanation
Indices: 31975--32030 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
31965 ATGAGGATCG
* *
31975 TGTCACAAGAGTAGAGGAATCGCA
1 TGTCACAAGAGCAGAGAAATC-CA
*
31999 TGCCACAAGAGCAGAGAAAAT-CA
1 TGTCACAAGAGCAGAG-AAATCCA
32022 TGTCACAAG
1 TGTCACAAG
32031 GATAGAGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 10 0.37
24 14 0.52
25 3 0.11
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (23 bp):
TGTCACAAGAGCAGAGAAATCCA
Found at i:32757 original size:24 final size:22
Alignment explanation
Indices: 32730--32778 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
32720 TTAACTTTAG
32730 CAATTAA-GCCAACCTTTTCATCTT
1 CAATTAATG-CAACC-TTT-ATCTT
32754 CAA-TAATGCAACCTTTATCTT
1 CAATTAATGCAACCTTTATCTT
32775 CAAT
1 CAAT
32779 AGAGGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
21 8 0.35
22 3 0.13
23 8 0.35
24 4 0.17
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (22 bp):
CAATTAATGCAACCTTTATCTT
Found at i:36300 original size:21 final size:21
Alignment explanation
Indices: 36274--36315 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
36264 AGGTATTGCC
36274 AAAAGAACCGGATGAGATACT
1 AAAAGAACCGGATGAGATACT
36295 AAAAGAACCGGATGAGATACT
1 AAAAGAACCGGATGAGATACT
36316 GGCTTCGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (21 bp):
AAAAGAACCGGATGAGATACT
Found at i:37055 original size:54 final size:54
Alignment explanation
Indices: 36987--37107 Score: 172
Period size: 54 Copynumber: 2.2 Consensus size: 54
36977 CATCATTGCC
* *
36987 ACCATAAGATGTGATACTCGGTATCGGTTCAAAATCACTAGTGAATGATTTCTT-
1 ACCATAAGAAGTGATACTCGGTATCGGTTCAAAATCACCAGTGAATGATTT-TTG
* * *
37041 ACCATAAGAAGTGATGCTCGGTATGGGTTCAAAATCACCGGTGAATGATTTTTG
1 ACCATAAGAAGTGATACTCGGTATCGGTTCAAAATCACCAGTGAATGATTTTTG
*
37095 GCCATAAGAAGTG
1 ACCATAAGAAGTG
37108 CTCAGTCTCG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 2 0.03
54 58 0.97
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (54 bp):
ACCATAAGAAGTGATACTCGGTATCGGTTCAAAATCACCAGTGAATGATTTTTG
Found at i:37265 original size:54 final size:54
Alignment explanation
Indices: 37174--37280 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
37164 ATCATCGCCT
* * * *
37174 CCATAAGAAGTGGTGCTTGGTCTCGGTTTGAAATCACTAGTGAATGATTTCTTA
1 CCATAAGAAGTGATGCTCGGTCTCAGTTTCAAATCACTAGTGAATGATTTCTTA
* * *
37228 CCATAAGATGTGATGCTCGGTCTCAG-TTCAAATTCACTAGTTAATGTTTTCTT
1 CCATAAGAAGTGATGCTCGGTCTCAGTTTCAAA-TCACTAGTGAATGATTTCTT
37281 CACTCCTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 5 0.11
54 40 0.89
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (54 bp):
CCATAAGAAGTGATGCTCGGTCTCAGTTTCAAATCACTAGTGAATGATTTCTTA
Found at i:37503 original size:135 final size:134
Alignment explanation
Indices: 37041--37530 Score: 610
Period size: 135 Copynumber: 3.6 Consensus size: 134
37031 ATGATTTCTT
* * * * ** * *
37041 ACCATAAGAAGTGATGCTCGGTATGGGTTCAAAATCACCGGTGAATGATTTTTGGCCATAAGAA-
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
* * * * *
37105 -G-TGCTCAGTCTCGGTTCAAAATTGCTAGGAAAAGTTTTCTTCACTCCTTTAAGATCAACATCA
66 TGATGCTCGGTCTCGGTTCAAATTTACTA-GTAATGTTTTCTTCACTCCTTTAAGATCAACATCA
37168 TCGCC
130 TCGCC
* ** * *
37173 TCCATAAGAAGTGGTGCTTGGTCTCGGTTTGAAATCACTAGTGAATGATTTCTTACCATAAGATG
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
* *
37238 TGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACATC
66 TGATGCTCGGTCTCGGTTCAAATTTACTAG-TAATGTTTTCTTCACTCC-TTTAAGATCAACATC
*
37303 ATTGCC
129 ATCGCC
* * *
37309 ACCATAAGAAGTGGTGCTTGGTCTCGGCTCAAAATCAATAGTGAATGATTTTTGACCATAA-AAC
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAA-
*
37373 GTGATGCTCGGTCTCGGTTCAAATTTACTAGTAATTGATTTCTTCACTCCTTTAAGATCAACATC
65 GTGATGCTCGGTCTCGGTTCAAATTTACTAGTAA-TGTTTTCTTCACTCCTTTAAGATCAACATC
37438 ATCGCC
129 ATCGCC
* * * * * * *
37444 GCCATAAGATGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGGCCATAAGAAG
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
*
37509 TGGTGCTCGGTCTCGGTTCAAA
66 TGATGCTCGGTCTCGGTTCAAA
37531 AATAGCTCTC
Statistics
Matches: 306, Mismatches: 44, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
132 51 0.17
134 2 0.01
135 134 0.44
136 119 0.39
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (134 bp):
ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
TGATGCTCGGTCTCGGTTCAAATTTACTAGTAATGTTTTCTTCACTCCTTTAAGATCAACATCAT
CGCC
Found at i:37521 original size:271 final size:268
Alignment explanation
Indices: 37041--37530 Score: 694
Period size: 271 Copynumber: 1.8 Consensus size: 268
37031 ATGATTTCTT
* * * * *
37041 ACCATAAGAAGTGATGCTCGGTATGGGTTCAAAATCACCGGTGAATGATTTTTGGCCATAAGAAG
1 ACCATAAGAAGTGATGCTCGGTATCGGCTCAAAATCAACAGTGAATGATTTTTGACCATAAGAAG
* *
37106 TGCTCAGTCTCGGTTCAAAATTGCTAGGAAAAGTTTTCTTCACTCCTTTAAGATCAACATCATCG
66 TGCTCAGTCTCGGTTCAAAATTACTAGGAAAAGATTTCTTCACTCCTTTAAGATCAACATCATCG
* * * * * *
37171 CCTCCATAAGAAGTGGTGCTTGGTCTCGGTTTGAAATCACTAGTGAATGATTTCTTACCATAAGA
131 CCGCCATAAGAAGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGACCATAAGA
*
37236 TGTGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACA
196 AGTGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACA
37301 TCATTGCC
261 TCATTGCC
* * * *
37309 ACCATAAGAAGTGGTGCTTGGTCTCGGCTCAAAATCAATAGTGAATGATTTTTGACCATAA-AAC
1 ACCATAAGAAGTGATGCTCGGTATCGGCTCAAAATCAACAGTGAATGATTTTTGACCATAAGAA-
* * * **
37373 GTGATGCTCGGTCTCGGTTCAAATTTACTAGTAATTGATTTCTTCACTCCTTTAAGATCAACATC
65 --G-TGCTCAGTCTCGGTTCAAAATTACTAGGAAAAGATTTCTTCACTCCTTTAAGATCAACATC
* *
37438 ATCGCCGCCATAAGATGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGGCCAT
127 ATCGCCGCCATAAGAAGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGACCAT
* *
37503 AAGAAGTGGTGCTCGGTCTCGGTTCAAA
192 AAGAAGTGATGCTCGGTCTCAGTTCAAA
37531 AATAGCTCTC
Statistics
Matches: 191, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
267 2 0.01
268 52 0.27
270 1 0.01
271 136 0.71
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (268 bp):
ACCATAAGAAGTGATGCTCGGTATCGGCTCAAAATCAACAGTGAATGATTTTTGACCATAAGAAG
TGCTCAGTCTCGGTTCAAAATTACTAGGAAAAGATTTCTTCACTCCTTTAAGATCAACATCATCG
CCGCCATAAGAAGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGACCATAAGA
AGTGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACA
TCATTGCC
Found at i:44271 original size:10 final size:10
Alignment explanation
Indices: 44256--44304 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
44246 ATATCAATTT
*
44256 AAAATATAAC
1 AAAATATAAA
44266 AAAATATAAA
1 AAAATATAAA
*
44276 AAAATAAAAA
1 AAAATATAAA
44286 TAAAATA-AAA
1 -AAAATATAAA
44296 AAAATATAA
1 AAAATATAA
44305 TTATAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 6 0.17
10 23 0.66
11 6 0.17
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATATAAA
Found at i:44287 original size:16 final size:15
Alignment explanation
Indices: 44266--44304 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
44256 AAAATATAAC
44266 AAAATATAAAAAAATA
1 AAAATATAAAAAAA-A
*
44282 AAAATA-AAATAAAA
1 AAAATATAAAAAAAA
44296 AAAATATAA
1 AAAATATAA
44305 TTATAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATATAAAAAAAA
Found at i:44290 original size:14 final size:14
Alignment explanation
Indices: 44255--44301 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
44245 TATATCAATT
44255 TAAAATATAACAAAATA
1 TAAAATA-AA-AAAA-A
44272 TAAAA-AAATAAAAA
1 TAAAATAAA-AAAAA
44286 TAAAATAAAAAAAA
1 TAAAATAAAAAAAA
44300 TA
1 TA
44302 TAATTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 13 0.46
15 9 0.32
16 1 0.04
17 5 0.18
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAAATAAAAAAAA
Found at i:44312 original size:20 final size:20
Alignment explanation
Indices: 44266--44316 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
44256 AAAATATAAC
44266 AAAATATAAAAAAATAAAAAT
1 AAAATA-AAAAAAATAAAAAT
* *
44287 AAAATAAAAAAAATATAATT
1 AAAATAAAAAAAATAAAAAT
*
44307 ATAATAAAAA
1 AAAATAAAAA
44317 CATATTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAATAAAAAAAATAAAAAT
Found at i:44315 original size:19 final size:19
Alignment explanation
Indices: 44256--44321 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
44246 ATATCAATTT
44256 AAAATATAACA-AAATATAAA
1 AAAATATAA-ATAAA-ATAAA
*
44276 AAAATAAAAATAAAATAAAA
1 AAAATATAAATAAAAT-AAA
* *
44296 AAAATATAATTATAATAAA
1 AAAATATAAATAAAATAAA
*
44315 AACATAT
1 AAAATAT
44322 TTTATATAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.31
20 27 0.69
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATATAAATAAAATAAA
Found at i:44727 original size:14 final size:14
Alignment explanation
Indices: 44710--44743 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
44700 TAGTAATTTA
*
44710 ATTTTTATTTTAAT
1 ATTTTTACTTTAAT
44724 ATTTTTACTTTAAT
1 ATTTTTACTTTAAT
44738 -TTTTTA
1 ATTTTTA
44744 AAAATATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTTACTTTAAT
Found at i:45173 original size:23 final size:22
Alignment explanation
Indices: 45142--45188 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
45132 AAATATTTGT
45142 TATGGATTTA-ATAATTTAAATAA
1 TATGGATTTATAT-ATTT-AATAA
*
45165 TATGTATTTATATATTTAATAA
1 TATGGATTTATATATTTAATAA
45187 TA
1 TA
45189 AATAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 13 0.59
24 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (22 bp):
TATGGATTTATATATTTAATAA
Found at i:53236 original size:23 final size:24
Alignment explanation
Indices: 53205--53257 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
53195 TTTGAGACAA
*
53205 ACTTCGGTGCAAACCTATGTGG-C
1 ACTTTGGTGCAAACCTATGTGGTC
53228 ACTTTGGTGCAAACCTATGTGGTC
1 ACTTTGGTGCAAACCTATGTGGTC
53252 A-TTTGG
1 ACTTTGG
53258 GATAATTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (24 bp):
ACTTTGGTGCAAACCTATGTGGTC
Found at i:59501 original size:16 final size:16
Alignment explanation
Indices: 59482--59512 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59472 TATAAAATAC
*
59482 TAAAATATTAATTTAT
1 TAAAAAATTAATTTAT
59498 TAAAAAATTAATTTA
1 TAAAAAATTAATTTA
59513 ATTAGTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAAAATTAATTTAT
Done.