Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006164.1 Hibiscus syriacus cultivar Beakdansim tig00014642_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: 83421
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Found at i:9447 original size:6 final size:6
Alignment explanation
Indices: 9432--9465 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
9422 TCTATGAACG
9432 AAAA-A AAAATA AAAATA AAAA-A AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
9466 TTAACATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:9454 original size:17 final size:17
Alignment explanation
Indices: 9432--9465 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9422 TCTATGAACG
9432 AAAAAAAAATAAAAATA
1 AAAAAAAAATAAAAATA
9449 AAAAAAAAATAAAAATA
1 AAAAAAAAATAAAAATA
9466 TTAACATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAAAATAAAAATA
Found at i:11740 original size:26 final size:26
Alignment explanation
Indices: 11711--11762 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
11701 AAACCGAGAT
11711 GGTCGAGGCAGCTCCACCGCTGAAAC
1 GGTCGAGGCAGCTCCACCGCTGAAAC
11737 GGTCGAGGCAGCTCCACCGCTGAAAC
1 GGTCGAGGCAGCTCCACCGCTGAAAC
11763 AACCTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.35, G:0.31, T:0.12
Consensus pattern (26 bp):
GGTCGAGGCAGCTCCACCGCTGAAAC
Found at i:15083 original size:13 final size:14
Alignment explanation
Indices: 15060--15088 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
15050 TCAATATTTA
15060 AAATATAAAAAAAT
1 AAATATAAAAAAAT
15074 AAAT-TAAAAAAAT
1 AAATATAAAAAAAT
15087 AA
1 AA
15089 GTAAATGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATATAAAAAAAT
Found at i:16580 original size:15 final size:15
Alignment explanation
Indices: 16560--16588 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16550 GCACACTAAA
16560 TTGCATAAAGCTCAG
1 TTGCATAAAGCTCAG
16575 TTGCATAAAGCTCA
1 TTGCATAAAGCTCA
16589 TTATTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (15 bp):
TTGCATAAAGCTCAG
Found at i:16597 original size:162 final size:161
Alignment explanation
Indices: 16400--16730 Score: 626
Period size: 162 Copynumber: 2.0 Consensus size: 161
16390 AGTCCCTAGA
16400 TGATAAACCTCAGTTGCATAAAGCTCATTATTAATGTTTGAAACTAGTATCAATATGGCATGGTT
1 TGATAAACCTCAGTTGCATAAAGCTCATTATTAATGTTTGAAACTAGTATCAATATGGCATGGTT
*
16465 GCTACTTGTTATTGACAAATAATGCTCAACTGGGCAGTATTTTGGTCAACTAACTCACCCACAAG
66 GCTACTTGTTATTGACAAATAATGCTCAACTGGACAGTATTTTGGTCAACTAACTCACCCACAAG
*
16530 GTAGCAAGTTTCTCTCCAATGCACACTAAAT
131 GTAGCAAATTTCTCTCCAATGCACACTAAAT
*
16561 TGCATAAAGCTCAGTTGCATAAAGCTCATTATTAATGTTTGAAACTAGTATCAATATGGCATGGT
1 TG-ATAAACCTCAGTTGCATAAAGCTCATTATTAATGTTTGAAACTAGTATCAATATGGCATGGT
16626 TGCTACTTGTTATTGACAAATAATGCTCAACTGGACAGTATTTTGGTCAACTAACTCACCCACAA
65 TGCTACTTGTTATTGACAAATAATGCTCAACTGGACAGTATTTTGGTCAACTAACTCACCCACAA
16691 GGTAGCAAATTTCTCTCCAATGCACACTAAAT
130 GGTAGCAAATTTCTCTCCAATGCACACTAAAT
16723 TGATAAAC
1 TGATAAAC
16731 TGCGAGAAAA
Statistics
Matches: 165, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
161 7 0.04
162 158 0.96
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (161 bp):
TGATAAACCTCAGTTGCATAAAGCTCATTATTAATGTTTGAAACTAGTATCAATATGGCATGGTT
GCTACTTGTTATTGACAAATAATGCTCAACTGGACAGTATTTTGGTCAACTAACTCACCCACAAG
GTAGCAAATTTCTCTCCAATGCACACTAAAT
Found at i:19274 original size:3 final size:3
Alignment explanation
Indices: 19266--19321 Score: 58
Period size: 3 Copynumber: 17.0 Consensus size: 3
19256 CTTAAAATTT
*
19266 AGA AGA AGA AGA AGA AGA ACGA AGAA AGAA AGAA ACA AGGA AGA AGA
1 AGA AGA AGA AGA AGA AGA A-GA AG-A AG-A AG-A AGA A-GA AGA AGA
19313 AGA AGA AGA
1 AGA AGA AGA
19322 CCTGGGGGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
3 33 0.69
4 15 0.31
ACGTcount: A:0.66, C:0.04, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19412 original size:68 final size:68
Alignment explanation
Indices: 19295--19425 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 68
19285 CGAAGAAAGA
* *
19295 AAGAAACAAGGAAGAAGAAGAAGAAGACCTGGGGGATGTTGTTTTAACGGATTTAACGTGCCAAG
1 AAGAAACAAAGAAGAAGAAGAAGAAGACCTGGGGGATGTTGTTTTAACGGAATTAACGTGCCAAG
19360 AAG
66 AAG
* * *
19363 AAGAAATAAAGAAGGAAGAAGAAGAAGACC-GGGGGCTTTTGTTTTAACGGAATTAACGTGCCA
1 AAGAAACAAAGAA-GAAGAAGAAGAAGACCTGGGGGATGTTGTTTTAACGGAATTAACGTGCCA
19426 TGTCAGCAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 41 0.72
69 16 0.28
ACGTcount: A:0.41, C:0.11, G:0.30, T:0.18
Consensus pattern (68 bp):
AAGAAACAAAGAAGAAGAAGAAGAAGACCTGGGGGATGTTGTTTTAACGGAATTAACGTGCCAAG
AAG
Found at i:23018 original size:17 final size:17
Alignment explanation
Indices: 22996--23038 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
22986 ATGACAAGCA
*
22996 TATAGTAAGGTTCCCAC
1 TATAGTAAAGTTCCCAC
23013 TATAGTACAAAGTTCCCAC
1 TATAGT--AAAGTTCCCAC
23032 TATAGTA
1 TATAGTA
23039 CAAAGTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 7 0.30
19 16 0.70
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (17 bp):
TATAGTAAAGTTCCCAC
Found at i:23029 original size:19 final size:19
Alignment explanation
Indices: 23005--23044 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
22995 ATATAGTAAG
23005 GTTCCCACTATAGTACAAA
1 GTTCCCACTATAGTACAAA
23024 GTTCCCACTATAGTACAAA
1 GTTCCCACTATAGTACAAA
23043 GT
1 GT
23045 AAATCGCCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (19 bp):
GTTCCCACTATAGTACAAA
Found at i:24850 original size:17 final size:16
Alignment explanation
Indices: 24825--24858 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
24815 ATTAATCAAA
*
24825 ATAATATAAACTAATT
1 ATAATATAAAATAATT
24841 ATAATAATAAAATAATT
1 ATAAT-ATAAAATAATT
24858 A
1 A
24859 GATTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATATAAAATAATT
Found at i:27025 original size:16 final size:16
Alignment explanation
Indices: 27004--27038 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
26994 CTCCCCTATC
*
27004 TTACTTTTATTAGCAA
1 TTACTTTTATTAACAA
27020 TTACTTTTATTAACAA
1 TTACTTTTATTAACAA
27036 TTA
1 TTA
27039 GTTTGCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.51
Consensus pattern (16 bp):
TTACTTTTATTAACAA
Found at i:29422 original size:73 final size:73
Alignment explanation
Indices: 29335--29554 Score: 325
Period size: 73 Copynumber: 3.0 Consensus size: 73
29325 GTTAAGGAAT
* *
29335 CTCCGTAAGTATGCCTATTGGGACCCCTCAGCATCCATTTGTTTGAGCACCCGCCGAGCTTCCTC
1 CTCCGTAAGTATGCCTATTGGGACCTCTCAGCATCCATTTGTTCGAGCACCCGCCGAGCTTCCTC
29400 TTCAGTGG
66 TTCAGTGG
* * * *
29408 CTCCGTAAGTATGCCTATTGGGACCTCTCAGCATCCATTCGATCGAGCACCCACCAAGCTTCCTC
1 CTCCGTAAGTATGCCTATTGGGACCTCTCAGCATCCATTTGTTCGAGCACCCGCCGAGCTTCCTC
*
29473 TTCAGTAG
66 TTCAGTGG
* ** *
29481 CTCCGTAAGTATGCCTATTGGGACCTCTTAGTGTCCATTCT-TTCGAGCACCGGCCGAGCTTCCT
1 CTCCGTAAGTATGCCTATTGGGACCTCTCAGCATCCATT-TGTTCGAGCACCCGCCGAGCTTCCT
29545 CTTCAGTGG
65 CTTCAGTGG
29554 C
1 C
29555 CAGAACAACA
Statistics
Matches: 130, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
73 130 1.00
ACGTcount: A:0.18, C:0.33, G:0.21, T:0.29
Consensus pattern (73 bp):
CTCCGTAAGTATGCCTATTGGGACCTCTCAGCATCCATTTGTTCGAGCACCCGCCGAGCTTCCTC
TTCAGTGG
Found at i:36424 original size:18 final size:18
Alignment explanation
Indices: 36401--36435 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
36391 ACTGAATATT
36401 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
36419 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
36436 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:41534 original size:20 final size:21
Alignment explanation
Indices: 41511--41558 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
41501 AACAACAACG
41511 ATTCTTTTAAC-CACTTGATA
1 ATTCTTTTAACTCACTTGATA
* *
41531 ATTC-TTTAACTTATTTGATA
1 ATTCTTTTAACTCACTTGATA
41551 ATTCTTTT
1 ATTCTTTT
41559 CTTAATAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 15 0.62
21 3 0.12
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTCTTTTAACTCACTTGATA
Found at i:43798 original size:7 final size:7
Alignment explanation
Indices: 43772--43821 Score: 63
Period size: 7 Copynumber: 7.7 Consensus size: 7
43762 TAACAATAAC
43772 AATAAA-
1 AATAAAT
43778 AATAAA-
1 AATAAAT
*
43784 AAT-TAT
1 AATAAAT
43790 AATAAAT
1 AATAAAT
43797 AATAAAT
1 AATAAAT
43804 AATAAAT
1 AATAAAT
43811 AAT-AAT
1 AATAAAT
43817 AATAA
1 AATAA
43822 TAACAAAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 1 0.03
6 18 0.46
7 20 0.51
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:43800 original size:3 final size:3
Alignment explanation
Indices: 43757--43824 Score: 64
Period size: 3 Copynumber: 21.7 Consensus size: 3
43747 TTTTAAAACA
* * * * *
43757 AAT AAT AAC AAT AAC AAT AAA AAT AAA AAT TAT AAT AAAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT
43804 AAT AAAT AAT AAT AAT AAT AA
1 AAT -AAT AAT AAT AAT AAT AA
43825 CAAAAGTATA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
3 43 0.83
4 9 0.17
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:44809 original size:31 final size:30
Alignment explanation
Indices: 44765--44861 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 30
44755 TTAATATACT
* *
44765 AAATAATTGTATAATCTATTAAATATTGTTC
1 AAATAAATATATAATCT-TTAAATATTGTTC
*
44796 AAATAAATATATAATCTTCTAAA-A-GGTT-
1 AAATAAATATATAATCTT-TAAATATTGTTC
* * *
44824 AAATAAAAATATAATATTTTTAAAT-TTATTC
1 AAATAAATATAT-A-ATCTTTAAATATTGTTC
44855 AAATAAA
1 AAATAAA
44862 AATCTAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
28 11 0.21
29 8 0.15
30 8 0.15
31 26 0.49
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (30 bp):
AAATAAATATATAATCTTTAAATATTGTTC
Found at i:48332 original size:24 final size:23
Alignment explanation
Indices: 48298--48342 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
48288 ACAGCCGAGA
*
48298 ATATTAGTTCTCTTATTTTTTTTT
1 ATATTAGTTCT-TTATGTTTTTTT
*
48322 ATATTATTTCTTTATGTTTTT
1 ATATTAGTTCTTTATGTTTTT
48343 CTAGTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (23 bp):
ATATTAGTTCTTTATGTTTTTTT
Found at i:48405 original size:24 final size:25
Alignment explanation
Indices: 48369--48436 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 25
48359 TGAATAAACA
48369 TCTCTG-TCATTGTGACATGA-GTTT
1 TCTCTGCTC-TTGTGACATGACGTTT
*
48393 TCTCTGCTCTTGTGACA-CACGTTT
1 TCTCTGCTCTTGTGACATGACGTTT
* *
48417 CCTCTGCTCTTGTGGCATGA
1 TCTCTGCTCTTGTGACATGA
48437 TCCTCATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 1 0.03
24 33 0.89
25 3 0.08
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41
Consensus pattern (25 bp):
TCTCTGCTCTTGTGACATGACGTTT
Found at i:50877 original size:12 final size:12
Alignment explanation
Indices: 50860--50903 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
50850 AAAAGCACAG
50860 TTTGGGCACTTA
1 TTTGGGCACTTA
50872 TTTGGGCACTTA
1 TTTGGGCACTTA
50884 TTTGGGCACTTA
1 TTTGGGCACTTA
50896 TTTGGGCA
1 TTTGGGCA
50904 TTAATTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (12 bp):
TTTGGGCACTTA
Found at i:59441 original size:64 final size:63
Alignment explanation
Indices: 59333--59557 Score: 224
Period size: 64 Copynumber: 3.5 Consensus size: 63
59323 TAATGAAGGT
* * ** ** * *
59333 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAAGGTATTCGATGTAGTATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGCATTCGATGT-TTATTATTA-TGGG
* *
59397 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGCATTCGATGTTT-ATTATT-ATGGG
* ***
59461 ATGCATCGATGCACTACTTATGCATCGATACA-CGAATTGCATTCGATGTCTTTATT-TTAAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGCATTCGATG--TTTATTATTATGGG
*
59524 AGTGCATCGATGCACTACTAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
59558 ATTCAAACAA
Statistics
Matches: 135, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
63 6 0.04
64 123 0.91
65 3 0.02
66 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGCATTCGATGTTTATTATTATGGG
Found at i:63856 original size:23 final size:26
Alignment explanation
Indices: 63823--63907 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 26
63813 TTGCATAACC
*
63823 CATGTATCTTATTTCAC-T-TCATAT
1 CATGTATCTTATATCACATGTCATAT
63847 CATGT-TCTTATATCACATGTCATAT
1 CATGTATCTTATATCACATGTCATAT
** *
63872 CACATATC--ATATCACATGAACATAT
1 CATGTATCTTATATCACATG-TCATAT
*
63897 -ATATATCTTAT
1 CATGTATCTTAT
63908 GCATGTATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
23 10 0.20
24 22 0.44
25 14 0.28
26 4 0.08
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (26 bp):
CATGTATCTTATATCACATGTCATAT
Found at i:63873 original size:12 final size:12
Alignment explanation
Indices: 63856--63889 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
63846 TCATGTTCTT
63856 ATATCACATGTC
1 ATATCACATGTC
*
63868 ATATCACATATC
1 ATATCACATGTC
63880 ATATCACATG
1 ATATCACATG
63890 AACATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (12 bp):
ATATCACATGTC
Found at i:64300 original size:64 final size:64
Alignment explanation
Indices: 64192--64368 Score: 214
Period size: 64 Copynumber: 2.8 Consensus size: 64
64182 TAATGAAGGT
* * ** ** * * **
64192 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-GTCACTATTAATGGG
* *
64256 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGCATTCGATGTGTCACTATTAATGGG
64320 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
64369 CTTTATTTTA
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
63 3 0.03
64 94 0.97
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:64389 original size:64 final size:63
Alignment explanation
Indices: 64255--64416 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 63
64245 TTATTGTTGG
* * *
64255 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAAAGA
* *
64319 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATTAAAGA
** *
64382 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
64417 ATTCAAACAA
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 4 0.05
64 80 0.92
65 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:71766 original size:2 final size:2
Alignment explanation
Indices: 71759--71789 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
71749 GGTACTTTTC
71759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71790 TGCAAATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72607 original size:21 final size:21
Alignment explanation
Indices: 72583--72641 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
72573 TGATTTATTA
**
72583 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
72604 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
**
72625 TTATGGAGGTCAAGTTT
1 TTATGGATTTCAAGTTT
72642 ATTGGAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.05, G:0.22, T:0.54
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:72897 original size:42 final size:43
Alignment explanation
Indices: 72844--73018 Score: 280
Period size: 43 Copynumber: 4.1 Consensus size: 43
72834 CTTTTGTGGT
*
72844 GTTTGTGGGAAAAACGCCGCTAAATCTCAAGACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* * *
72887 GTTTGT-GGAAAAACGCCGCTAAATATCAACACCTACTGCGAC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
72929 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* * *
72972 GTTTGTTGGAAAAATGCCGCCAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
73015 GTTT
1 GTTT
73019 TTTGTTACCA
Statistics
Matches: 121, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
42 38 0.31
43 83 0.69
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (43 bp):
GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
Found at i:72899 original size:85 final size:86
Alignment explanation
Indices: 72844--73018 Score: 289
Period size: 85 Copynumber: 2.0 Consensus size: 86
72834 CTTTTGTGGT
* *
72844 GTTTGTGGGAAAAACGCCGCTAAATCTCAAGACCTATTGCGGCGTTTG-TGGAAAAACGCCGCTA
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGGAAAAATGCCGCTA
72908 AATATCAACACCTACTGCGAC
66 AATATCAACACCTACTGCGAC
*
72929 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGGAAAAATGCCGCCA
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGGAAAAATGCCGCTA
* * *
72994 AATCTCAACACCTATTGCGGC
66 AATATCAACACCTACTGCGAC
73015 GTTT
1 GTTT
73019 TTTGTTACCA
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 47 0.57
86 36 0.43
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (86 bp):
GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGGAAAAATGCCGCTA
AATATCAACACCTACTGCGAC
Found at i:74403 original size:84 final size:84
Alignment explanation
Indices: 74204--74901 Score: 747
Period size: 84 Copynumber: 8.4 Consensus size: 84
74194 ATTTTATTGA
* * * * * * * * *
74204 CAGATAACTCTTCTTGCCTTGAGCTATGTTGTAAATGATATGCCTTCGAAGCTGAGCATAATCGA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTT-GGAGCTGAGCGTAGTCGA
* *
74269 ACTCGAGGGTC--T--TTGC
65 ACTCGAAGGTCTTTGGTTGG
* * * * *
74285 CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTTGAA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
74350 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGGTTGG
* * *
74369 CAGATAACTCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGA
* *
74433 ACTCAAAGGTCTTTTGTTGG
65 ACTCGAAGGTCTTTGGTTGG
* * * *
74453 CAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
*
74518 CTCGAAGGTCTTTGG-TGA
66 CTCGAAGGTCTTTGGTTGG
* * * * * * * * * * * * *
74536 TAGATAACCCTTCTAGCCTTGAGTTAAGCTGTAAATGATATGCCCTCGAAACTGAGTGTAATCAA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGA
* *
74601 ACTCGAGGGGC--T--TTGG
65 ACTCGAAGGTCTTTGGTTGG
* * * * *
74617 CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTAGAGCTAAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
74682 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGGTTGG
* * * *
74701 CAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAATCGAA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
74766 CTCGAAGGTC-TT--TTGG
66 CTCGAAGGTCTTTGGTTGG
* * * *
74782 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
74847 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGGTTGG
* * * * *
74866 CAGATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
74902 AGTTTCTTCA
Statistics
Matches: 517, Mismatches: 85, Indels: 27
0.82 0.14 0.04
Matches are distributed among these distances:
80 48 0.09
81 142 0.27
82 5 0.01
83 41 0.08
84 279 0.54
85 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTTGG
Found at i:74692 original size:248 final size:247
Alignment explanation
Indices: 74236--74879 Score: 765
Period size: 248 Copynumber: 2.6 Consensus size: 247
74226 GCTATGTTGT
* * * * * *
74236 AAATGATATGCCTTCGAAGCTGAGCATAATCGAACTCGAGGGTC-TTTGCCAGATAGCCCTTCTC
1 AAATGATATGCCTTAG-AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGACAGATAACCCTTCTA
** * * * * ** * ** *
74300 GACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTTGAACTCGAAGGTCTTTGG
65 GACTTAAGCTAAGCTGCAAATGATATGCCTCGAAACTGAGTGTAATCAAACTCGAAGGGC-TT-G
* * * * *
74365 TTGGCAGATAACTCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGT
128 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCGTTGAGCTAAGCGTAGT
* *
74430 CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
193 CGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGC
* * *
74485 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGATAGATAACCCTTCT
1 AAATGATATGCCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTT--TGACAGATAACCCTTCT
* * * * *
74550 AGCCTTGAGTTAAGCTGTAAATGATATGCCCTCGAAACTGAGTGTAATCAAACTCGAGGGGC-T-
64 AGACTTAAGCTAAGCTGCAAATGATATG-CCTCGAAACTGAGTGTAATCAAACTCGAAGGGCTTG
74613 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCC-TTAGAGCTAAGCGTAG
128 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCGTT-GAGCTAAGCGTAG
* * *
74677 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGC
192 TCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGC
* * *
74733 AAATGATATGCCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAGCCCTTCTCG
1 AAATGATATGCCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGACAGATAACCCTTCTAG
* * * * * * *
74798 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGT
66 ACTTAAGCTAAGCTGCAAATGATATGCCTCGAAACTGAGTGTAATCAAACTCGAAGGGC-TT-GT
74863 TGGCAGATAGCCCTTCT
129 TGGCAGATAGCCCTTCT
74880 GGCCTTGAGC
Statistics
Matches: 333, Mismatches: 53, Indels: 18
0.82 0.13 0.04
Matches are distributed among these distances:
245 27 0.08
246 35 0.11
247 3 0.01
248 175 0.53
249 35 0.11
250 1 0.00
251 34 0.10
252 23 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (247 bp):
AAATGATATGCCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGACAGATAACCCTTCTAG
ACTTAAGCTAAGCTGCAAATGATATGCCTCGAAACTGAGTGTAATCAAACTCGAAGGGCTTGTTG
GCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCGTTGAGCTAAGCGTAGTCGA
ACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGC
Found at i:74899 original size:165 final size:165
Alignment explanation
Indices: 74204--74901 Score: 900
Period size: 165 Copynumber: 4.2 Consensus size: 165
74194 ATTTTATTGA
* * * * *
74204 CAGATAACTCTTCTTGCCTTGAGCTATGTTGTAAATGATATGCCTTCGAAGCTGAGCATAATCGA
1 CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATATGCCTTCGAAGCTGAGCGTAATCGA
* * *
74269 ACTCGAGGGTCTTTGCCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGA
66 ACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
* *
74334 GCTGAGCATAGTTGAACTCGAAGGTCTTTGGTTGG
131 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
* * * * * *
74369 CAGATAACTCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-G-AGCTGAGCGTAGTCG
1 CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATATGCC-TTCGAAGCTGAGCGTAATCG
* * * * * * *
74432 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCC
65 AACTCGAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
*
74497 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGA
126 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
* * * * * * * *
74536 TAGATAACCCTTCTAGCCTTGAGTTAAGCTGTAAATGATATGCCCTCGAAACTGAGTGTAATCAA
1 CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATATGCCTTCGAAGCTGAGCGTAATCGA
* * * *
74601 ACTCGAGGGGCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTAGA
66 ACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
*
74666 GCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
131 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
* * *
74701 CAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCTTAG-AGCTGAGCGTAATCGA
1 CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATATGCCTTCGAAGCTGAGCGTAATCGA
74765 ACTCGAAGGTCTTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 ACTCGAAGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
* *
74830 AGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGG
130 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
* * * *
74866 CAGATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAAT
74902 AGTTTCTTCA
Statistics
Matches: 452, Mismatches: 72, Indels: 18
0.83 0.13 0.03
Matches are distributed among these distances:
164 120 0.27
165 195 0.43
166 3 0.01
167 40 0.09
168 94 0.21
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATATGCCTTCGAAGCTGAGCGTAATCGA
ACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
Found at i:78961 original size:17 final size:17
Alignment explanation
Indices: 78935--78967 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
78925 TGCAAACGAT
*
78935 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
78952 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
78968 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:80142 original size:10 final size:9
Alignment explanation
Indices: 80106--80147 Score: 75
Period size: 9 Copynumber: 4.6 Consensus size: 9
80096 GATAAATAAA
80106 AAATAAAAG
1 AAATAAAAG
80115 AAATAAAAG
1 AAATAAAAG
80124 AAATAAAAG
1 AAATAAAAG
80133 AAATTAAAAG
1 AAA-TAAAAG
80143 AAATA
1 AAATA
80148 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 23 0.72
10 9 0.28
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (9 bp):
AAATAAAAG
Found at i:81510 original size:40 final size:39
Alignment explanation
Indices: 81431--81517 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 39
81421 GATTTTAAAA
* *
81431 ATATTA-ATAAGTTTTCCAAAATGTTTTGTTAAAACTAT
1 ATATTATATAAATTTTCCAAAATATTTTGTTAAAACTAT
*
81469 ATATTATATAAATTTTCCAAAAATATTTT-TTAAAAATTAT
1 ATATTATATAAATTTTCC-AAAATATTTTGTT-AAAACTAT
81509 ATATTATAT
1 ATATTATAT
81518 TTTCAAAATG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 6 0.14
39 12 0.28
40 25 0.58
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (39 bp):
ATATTATATAAATTTTCCAAAATATTTTGTTAAAACTAT
Found at i:81599 original size:74 final size:74
Alignment explanation
Indices: 81387--81625 Score: 186
Period size: 74 Copynumber: 3.3 Consensus size: 74
81377 TTTAAAAACA
* * *
81387 TTTT-AAAACCATATATTATAT-AGTTTT-TAAAA-ATGATTTTAAAAA-TAT-TA--ATAAGTT
1 TTTTAAAAACTATATATTATATAAATTTTCCAAAATATG-TTTTAAAAATTATATATTATAAGTT
81444 TTCCAAAATG
65 TTCCAAAATG
* *
81454 TTTTGTTAAAACTATATATTATATAAATTTTCCAAAAATATTTTTTAAAAATTATATATTAT-A-
1 -TTT-TAAAAACTATATATTATATAAATTTTCC-AAAATATGTTTTAAAAATTATATATTATAAG
81517 TTTT-CAAAATG
63 TTTTCCAAAATG
* * *
81528 ATTTCAAAACTATATACTT-TAT-AATTTT-C-AAA-ATGTTTTAAAACTTATATATTGTACATA
1 TTTTAAAAACTATATA-TTATATAAATTTTCCAAAATATGTTTTAAAAATTATATA-T-T--ATA
*
81588 AGTTTTCCAAAACG
61 AGTTTTCCAAAATG
*
81602 TTTTAAAAATCTATATAATATATA
1 TTTTAAAAA-CTATATATTATATA
81626 TTTCAAAAAA
Statistics
Matches: 138, Mismatches: 12, Indels: 34
0.75 0.07 0.18
Matches are distributed among these distances:
67 17 0.12
68 7 0.05
69 2 0.01
70 17 0.12
71 13 0.09
72 16 0.12
73 21 0.15
74 26 0.19
75 16 0.12
76 1 0.01
77 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (74 bp):
TTTTAAAAACTATATATTATATAAATTTTCCAAAATATGTTTTAAAAATTATATATTATAAGTTT
TCCAAAATG
Found at i:81633 original size:34 final size:35
Alignment explanation
Indices: 81397--81633 Score: 116
Period size: 35 Copynumber: 6.6 Consensus size: 35
81387 TTTTAAAACC
* * *
81397 ATATATTATATAGTTTTTAAAAATGATTTTAAAAA-T
1 ATATAATATATA-ATTTTCAAAATG-TTTTAAAAATT
* * *
81433 AT-TAATA-AGT--TTTCCAAAATGTTTTGTTAAAACT
1 ATATAATATA-TAATTTTCAAAATG-TTT-TAAAAATT
* *
81467 ATATATTATATAAATTTTCCAAAAATATTTTTTAAAAATT
1 ATATAATATAT-AATTTT-C--AAA-ATGTTTTAAAAATT
* * *
81507 ATAT-AT-TAT-ATTTTCAAAATGATTTCAAAACT
1 ATATAATATATAATTTTCAAAATGTTTTAAAAATT
* * *
81539 ATATACTTTATAATTTTCAAAATGTTTTAAAACTT
1 ATATAATATATAATTTTCAAAATGTTTTAAAAATT
* * *
81574 ATATATTGTACATAAGTTTTCCAAAACGTTTTAAAAATCT
1 ATATA--ATATATAA-TTTT-CAAAATGTTTTAAAAAT-T
81614 ATATAATATAT-A-TTTCAAAA
1 ATATAATATATAATTTTCAAAA
81634 AATATACTTT
Statistics
Matches: 154, Mismatches: 27, Indels: 42
0.69 0.12 0.19
Matches are distributed among these distances:
32 26 0.17
33 9 0.06
34 12 0.08
35 38 0.25
36 8 0.05
37 6 0.04
38 14 0.09
39 17 0.11
40 16 0.10
41 6 0.04
42 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (35 bp):
ATATAATATATAATTTTCAAAATGTTTTAAAAATT
Found at i:81799 original size:29 final size:28
Alignment explanation
Indices: 81766--81832 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
81756 ATAATTTTAA
81766 AATTTAATAATAAAAAAATACTTTAATAT
1 AATTTAATAAT-AAAAAATACTTTAATAT
* ** *
81795 AATTTAATGATAAAACGTATTTTAATAT
1 AATTTAATAATAAAAAATACTTTAATAT
*
81823 AGTTTAATAA
1 AATTTAATAA
81833 AACTTGATAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (28 bp):
AATTTAATAATAAAAAATACTTTAATAT
Done.