Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007583.1 Hibiscus syriacus cultivar Beakdansim tig00021682_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: 66845
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2314 original size:123 final size:123
Alignment explanation
Indices: 2095--2339 Score: 445
Period size: 123 Copynumber: 2.0 Consensus size: 123
2085 AAGTCTAGCC
* *
2095 GAAGTTGCTTCTCTACTTTTTCAATTCGATCTGCTCTACTCTTCTGAATGTCAATCTCCAATCCC
1 GAAGTTGCTTATCTACTTTTTCAATTCGATATGCTCTACTCTTCTGAATGTCAATCTCCAATCCC
**
2160 TTTTGATACACTTCATCTTCCAGCTTCTGCAAAGTCATTCTCCATTGTCTCCATTCTT
66 TTTCAATACACTTCATCTTCCAGCTTCTGCAAAGTCATTCTCCATTGTCTCCATTCTT
2218 GAAGTTGCTTATCTACTTTTTCAATTCGATATGCTCTACTCTTCTGAATGTCAATCTCCAATCCC
1 GAAGTTGCTTATCTACTTTTTCAATTCGATATGCTCTACTCTTCTGAATGTCAATCTCCAATCCC
*
2283 TTTCAATACACTTCATCTTCCAGCTTCTGCAAAGTCATTCTCCATTGTCTCCGTTCT
66 TTTCAATACACTTCATCTTCCAGCTTCTGCAAAGTCATTCTCCATTGTCTCCATTCT
2340 GCTTTGAAAT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 117 1.00
ACGTcount: A:0.20, C:0.29, G:0.10, T:0.41
Consensus pattern (123 bp):
GAAGTTGCTTATCTACTTTTTCAATTCGATATGCTCTACTCTTCTGAATGTCAATCTCCAATCCC
TTTCAATACACTTCATCTTCCAGCTTCTGCAAAGTCATTCTCCATTGTCTCCATTCTT
Found at i:4029 original size:45 final size:45
Alignment explanation
Indices: 3894--4044 Score: 239
Period size: 45 Copynumber: 3.3 Consensus size: 45
3884 CCATGCTTTG
* *
3894 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATAC
1 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
3941 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
3986 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
*
4031 GTTTATTCGAAAAA
1 --TTATTCAAAAAA
4045 CAAAAATAAA
Statistics
Matches: 99, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
45 72 0.73
46 9 0.09
47 18 0.18
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
Found at i:8741 original size:24 final size:24
Alignment explanation
Indices: 8709--8759 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
8699 AAATAGTTTG
8709 GGTTTGAGCAACTGCATTGTAAGA
1 GGTTTGAGCAACTGCATTGTAAGA
8733 GGTTTGAGCAACTGCATTGTAAGA
1 GGTTTGAGCAACTGCATTGTAAGA
8757 GGT
1 GGT
8760 GTGCGCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.29
Consensus pattern (24 bp):
GGTTTGAGCAACTGCATTGTAAGA
Found at i:14100 original size:2 final size:2
Alignment explanation
Indices: 14093--14133 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
14083 TAACGAAGAG
14093 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
14134 AGCCCTCTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:15630 original size:130 final size:130
Alignment explanation
Indices: 15489--15736 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
15479 TATTTATATA
*
15489 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
15554 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
15619 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
15684 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
15737 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:15767 original size:130 final size:129
Alignment explanation
Indices: 15503--15767 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
15493 ATTTGGTCCT
* *
15503 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
15568 TGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
15633 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
15698 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
15762 -A
128 CA
15763 AAATT
1 AAATT
15768 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:16095 original size:28 final size:27
Alignment explanation
Indices: 16064--16126 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
16054 AGTTGATACA
*
16064 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
16092 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
16120 ATATTTT
1 ATATTTT
16127 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:16227 original size:16 final size:18
Alignment explanation
Indices: 16206--16239 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
16196 ATTTCTTATT
16206 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
16222 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
16240 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:16386 original size:21 final size:21
Alignment explanation
Indices: 16362--16404 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
16352 TATTACCTTA
16362 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
16383 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
16404 A
1 A
16405 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:16422 original size:35 final size:35
Alignment explanation
Indices: 16373--16458 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
16363 ATTGAAGTAT
** * *
16373 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
16408 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
16443 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
16459 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:16987 original size:17 final size:19
Alignment explanation
Indices: 16953--16990 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
16943 TCACCCAGAA
16953 GAGAGAAGAGTGGGAAGGG
1 GAGAGAAGAGTGGGAAGGG
*
16972 GAGAGAA-AG-GGTAAGGG
1 GAGAGAAGAGTGGGAAGGG
16989 GA
1 GA
16991 AGCAAATTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 2 0.11
19 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.55, T:0.05
Consensus pattern (19 bp):
GAGAGAAGAGTGGGAAGGG
Found at i:20370 original size:30 final size:30
Alignment explanation
Indices: 20334--20394 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
20324 TTAGGAAGCA
**
20334 TTTAGGGA-CTAAAAGGGCAATTTTCAAAAG
1 TTTAGGGATC-AAAAGAACAATTTTCAAAAG
*
20364 TTTAGGGATCAAAAGAATAATTTTCAAAAG
1 TTTAGGGATCAAAAGAACAATTTTCAAAAG
20394 T
1 T
20395 CATGTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.30
Consensus pattern (30 bp):
TTTAGGGATCAAAAGAACAATTTTCAAAAG
Found at i:21548 original size:20 final size:19
Alignment explanation
Indices: 21518--21570 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
21508 GTTGATGGTC
*
21518 AATGCTTGAAATTACTGTTAG
1 AATG-TTGAAATTA-TATTAG
21539 AATGTTGAAATTGATATTAG
1 AATGTTGAAATT-ATATTAG
21559 AATG-TGAAATTA
1 AATGTTGAAATTA
21571 GGTCACTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 17 0.57
21 5 0.17
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (19 bp):
AATGTTGAAATTATATTAG
Found at i:22883 original size:26 final size:26
Alignment explanation
Indices: 22853--22936 Score: 116
Period size: 26 Copynumber: 3.2 Consensus size: 26
22843 GAGTCTTGGT
22853 ATAAATAGCACTTTTGAGTGCGAGTG
1 ATAAATAGCACTTTTGAGTGCGAGTG
* *
22879 ATAAATAGCACTTTCGAGTGAGAGTG
1 ATAAATAGCACTTTTGAGTGCGAGTG
* *
22905 ATAAAT-GACGCTTTTGAGTGCAAGTG
1 ATAAATAG-CACTTTTGAGTGCGAGTG
22931 ATAAAT
1 ATAAAT
22937 GGAACTATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
25 1 0.02
26 50 0.98
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.30
Consensus pattern (26 bp):
ATAAATAGCACTTTTGAGTGCGAGTG
Found at i:30778 original size:84 final size:84
Alignment explanation
Indices: 30674--31552 Score: 1156
Period size: 84 Copynumber: 10.5 Consensus size: 84
30664 TGGTATACCC
* *
30674 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTATTGGCAGATAACCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
*
30739 T-ATAGCAAATGATGTGTCT
66 TGAT-GCAAATGATGTGCCT
* ** *
30758 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGAAGATAACCCTTCTTTCCTTTAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
* *
30823 T-ACCGCAAATGATATGCCT
66 TGA-TGCAAATGATGTGCCT
* * **
30842 TTGAGCTGAGTGTAATTGAACTCGAAGGTATTTTGTTGGCAGATAGTCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
*
30907 TGCTGCAAATGATGTGCCT
66 TGATGCAAATGATGTGCCT
* * * * *
30926 TTGAGCTGAGTCTAATCGAACTTGAAGGTCTTTTGTTGGCATATAGCCCTTCTCGCCTTGAGTTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
30991 T-ACTGCAAATGATGTGCCT
66 TGA-TGCAAATGATGTGCCT
* * *
31010 TTGAGCTCAGTGTAATTGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
*
31075 TGATGCAAATAATGTGCCT
66 TGATGCAAATGATGTGCCT
*
31094 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
*
31159 TGCTGCAAATGATGTGCCT
66 TGATGCAAATGATGTGCCT
* * * * *
31178 TTGAGCTGAGTGTAATTGAACTCAAAGGTCTTTTGTTGGCATATATCTCTTCTCGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
* *
31243 TGTTGCAAATAATGTGCCT
66 TGATGCAAATGATGTGCCT
* * * * * *
31262 TTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAAATAGCCCTTCTTGCCTTGAGTTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
* *
31327 TGCTGCAAATTATGTGCCT
66 TGATGCAAATGATGTGCCT
* * * * *
31346 TTGAGCTGAGTGTAATTGAACTCGAATGTATTTTGTTCGCAGATAACCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
*
31411 T-ACTGCAAATGATGTACCT
66 TGA-TGCAAATGATGTGCCT
* * * * * *
31430 TTGAGCTGAGTGTAATCGAGCTCGAAGGTC-TTGGTTGACAGATAAGCCTTCTCGTCTTGAGTTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
* ** *
31494 TGCTATAAATTTGAAGTGCCT
66 TGATGCAAA--TGATGTGCCT
*
31515 TTGAGCTGAGTGTAATCGAACTCCAAGGTCTTTTGTTG
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
31553 AAGGTGTTTT
Statistics
Matches: 695, Mismatches: 91, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
83 32 0.05
84 620 0.89
85 37 0.05
86 6 0.01
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (84 bp):
TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTA
TGATGCAAATGATGTGCCT
Found at i:32480 original size:95 final size:95
Alignment explanation
Indices: 32307--32545 Score: 322
Period size: 95 Copynumber: 2.5 Consensus size: 95
32297 GGGGAATTTG
* ** *
32307 ACCAATTGCTCTAGAGGGACAACTCAATATCGTTGTA-CATATATTATGATCACCTTTATCAGGC
1 ACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTATATTATAATCACCTTTATCAGGC
32371 TAGCTGAATATTATCCATAAAG-CTGGGGCGTTTA
62 TAGCTGAATATTATCCATAAAGTC-GGGGCGTTTA
** *
32405 ACCAATTGCTCTAGAGGGGTAACTCGAGCTTTATTGTATATTATAATCACCTTTATCAGGCTAGC
1 ACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTATCAGGCTAGC
*
32470 TGAATCTTATCCATAAAGTCGGGGCGTTTA
66 TGAATATTATCCATAAAGTCGGGGCGTTTA
* *
32500 ACCAATTGCTTTAGAGGGACGACTCAAGCTTTATTGTATA-TATAAT
1 ACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
32546 ATTATAATCT
Statistics
Matches: 126, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
94 8 0.06
95 92 0.73
96 3 0.02
98 23 0.18
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (95 bp):
ACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTATCAGGCTAGC
TGAATATTATCCATAAAGTCGGGGCGTTTA
Found at i:36878 original size:21 final size:20
Alignment explanation
Indices: 36792--36949 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
36782 AAATGACCAA
**
36792 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
36811 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
36831 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
36851 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
36872 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
36893 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
36913 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
36934 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
36950 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:36978 original size:20 final size:20
Alignment explanation
Indices: 36917--37145 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
36907 GATTTTCAAG
* ** *
36917 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
36937 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
36957 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
36977 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
36997 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37017 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37037 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37057 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
37077 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
37097 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
37117 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
37137 AATCACAAC
1 AATCGCAAC
37146 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:37863 original size:24 final size:24
Alignment explanation
Indices: 37836--37882 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37826 AAACTTGGTC
37836 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
37860 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
37883 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:39866 original size:53 final size:55
Alignment explanation
Indices: 39803--40096 Score: 341
Period size: 53 Copynumber: 5.5 Consensus size: 55
39793 GCAACGAGAG
*
39803 AATCGCAATGCGAAATGAAAATCCCAA-C-AA-GAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGCAAATGAAAATCGCAATGC-GAAATGAA
*
39856 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA-GC-AAATGAAAATCGCAATGCGAAATGAA
*
39908 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAA-GC-AAATGAAAATCGCAATGCGAAATGAA
*
39961 AATCGCAATGCGAAATGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GC-AAATGAAAATCGCAATGCGAAATGAA
* *
40018 AATCGCAATGCGAAATGAAAATCGCAA-C-GA-GAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGCAAATGAAAATCGCAATGC-GAAATGAA
40071 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
40097 TTGAGATTCT
Statistics
Matches: 222, Mismatches: 7, Indels: 24
0.88 0.03 0.09
Matches are distributed among these distances:
52 60 0.27
53 114 0.51
54 2 0.01
55 3 0.01
56 2 0.01
57 30 0.14
58 11 0.05
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCAAATGAAAATCGCAATGCGAAATGAA
Found at i:39872 original size:19 final size:19
Alignment explanation
Indices: 39803--40096 Score: 376
Period size: 19 Copynumber: 16.4 Consensus size: 19
39793 GCAACGAGAG
39803 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
39822 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
39836 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
39856 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
39875 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
39894 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
39908 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
39928 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
39947 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
39961 AATCGCAATGCGAAATGAG
1 AATCGCAATGCGAAATGAA
39980 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
39999 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
40018 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
40037 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
40051 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
40071 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
40090 AATCGCA
1 AATCGCA
40097 TTGAGATTCT
Statistics
Matches: 244, Mismatches: 8, Indels: 46
0.82 0.03 0.15
Matches are distributed among these distances:
14 40 0.16
15 5 0.02
16 5 0.02
17 9 0.04
18 1 0.00
19 144 0.59
20 40 0.16
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:39896 original size:72 final size:72
Alignment explanation
Indices: 39803--40096 Score: 450
Period size: 72 Copynumber: 4.1 Consensus size: 72
39793 GCAACGAGAG
*
39803 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
39868 AAATGAA
66 AAATGAA
* *
39875 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
39940 AAATGAA
66 AAATGAA
* * * * * *
39947 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAGAATCGCAATGC-GAAATGAAAATCGCAATG
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAGAATCGCAATGCGGAAATGAAAATCGCAATG
40009 CGAAATGAA
64 CGAAATGAA
* *
40018 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
40083 AAATGAA
66 AAATGAA
40090 AATCGCA
1 AATCGCA
40097 TTGAGATTCT
Statistics
Matches: 198, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
69 1 0.01
70 8 0.04
71 52 0.26
72 128 0.65
73 8 0.04
74 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:40116 original size:143 final size:144
Alignment explanation
Indices: 39836--40096 Score: 515
Period size: 143 Copynumber: 1.8 Consensus size: 144
39826 CCAACAAGAA
39836 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
39901 ACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG
66 ACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG
39966 CAATGCGAAATGAG
131 CAATGCGAAATGAG
39980 AATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
40044 ACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
66 ACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
40097 TTGAGATTCT
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
143 106 0.91
144 11 0.09
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (144 bp):
AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
ACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG
CAATGCGAAATGAG
Found at i:40151 original size:19 final size:19
Alignment explanation
Indices: 40111--40198 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
40101 GATTCTCTCG
40111 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
40131 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
40150 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
40164 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
40183 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
40199 AACATAATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 7 0.12
19 25 0.42
20 14 0.24
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:40172 original size:53 final size:52
Alignment explanation
Indices: 40092--40198 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 52
40082 GAAATGAAAA
*
40092 TCGCATTGAGATTCTCTCGTTGCGATTTTCATTTCCGCATTGTGATTTTCATT
1 TCGCATTGAGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
*
40145 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGAGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
40197 TC
1 TC
40199 AACATAATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
52 19 0.37
53 33 0.63
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TCGCATTGAGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:40308 original size:14 final size:14
Alignment explanation
Indices: 40289--40325 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
40279 CATCAATTAC
40289 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
40303 ACAAATCATCTTTT
1 ACAAATCAACTTTT
40317 ACAAATCAA
1 ACAAATCAA
40326 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:41667 original size:20 final size:20
Alignment explanation
Indices: 41636--41718 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
41626 TTTTGGTTGA
41636 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
41656 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
41676 AAATGAAAATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
41696 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
41716 AAT
1 AAT
41719 CGCAACGCGA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 18 0.34
20 20 0.38
21 15 0.28
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:41699 original size:19 final size:19
Alignment explanation
Indices: 41634--41747 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
41624 TCTTTTGGTT
*
41634 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
41653 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
41675 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
41694 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
41711 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
41727 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
41746 GA
1 GA
41748 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 33 0.43
20 12 0.16
21 12 0.16
22 4 0.05
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:41778 original size:14 final size:14
Alignment explanation
Indices: 41759--41815 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
41749 TTTGGTTTCG
41759 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
41773 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
41792 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
41806 CGTTGCGATT
1 CGTTGCGATT
41816 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:41791 original size:33 final size:33
Alignment explanation
Indices: 41743--41822 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
41733 AAAATCGCAA
**
41743 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
41776 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
41809 TGCGATTTTCATTT
1 TGCGATTTTCATTT
41823 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:41828 original size:21 final size:21
Alignment explanation
Indices: 41803--41876 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
41793 GTTGCGATTC
41803 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
41824 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
41845 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
*
41866 TCTCATTGCGA
1 TCTCGTTGCGA
41877 CTCTTCTCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 6 0.14
21 31 0.72
22 6 0.14
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:41998 original size:33 final size:33
Alignment explanation
Indices: 41956--42026 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
41946 AATACTAACT
41956 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
***
41989 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
42022 TGAAA
1 TGAAA
42027 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAACAACGCGAAA
Found at i:42432 original size:20 final size:20
Alignment explanation
Indices: 42406--42558 Score: 182
Period size: 20 Copynumber: 7.6 Consensus size: 20
42396 CTTTAAAAAT
42406 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
42426 TGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
42446 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
42467 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
42487 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
42507 CGCGTTGCGATTTACTGATA
1 CGCGTTGCGATTTACGGATA
* * ** *
42527 CACGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
42547 CGCGTTGCGATT
1 CGCGTTGCGATT
42559 CTGTAAAATC
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
20 98 0.85
21 17 0.15
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:42576 original size:21 final size:20
Alignment explanation
Indices: 42552--42622 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
42542 ATATTCGCGT
42552 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
42573 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
**
42594 TGCGA-TTGTCAAGAATCGCGT
1 TGCGATTTGT-AA-AATCGCAA
42615 TGCGATTT
1 TGCGATTT
42623 TGGAAACTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 29 0.73
22 5 0.12
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:47892 original size:28 final size:27
Alignment explanation
Indices: 47844--47896 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
47834 AAAAATACAA
* **
47844 TTTAAAAAAACCTAATTTTTTCAAATC
1 TTTAAAAAAACCAAAAATTTTCAAATC
47871 TTTAAAAAAACCCAAAAATTTTCAAA
1 TTTAAAAAAA-CCAAAAATTTTCAAA
47897 ACTTCATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (27 bp):
TTTAAAAAAACCAAAAATTTTCAAATC
Found at i:48114 original size:25 final size:24
Alignment explanation
Indices: 48086--48140 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
48076 AAATCCCTTA
* *
48086 GATCGATAGTGGTAATCGGTTGTTT
1 GATCGAT-GTGATAATCGGTCGTTT
*
48111 GATCGGATGTGATAGTCGGTCGTTT
1 GATC-GATGTGATAATCGGTCGTTT
48136 GATCG
1 GATCG
48141 GCCGTGGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 22 0.85
26 3 0.12
ACGTcount: A:0.18, C:0.11, G:0.35, T:0.36
Consensus pattern (24 bp):
GATCGATGTGATAATCGGTCGTTT
Found at i:48151 original size:25 final size:25
Alignment explanation
Indices: 48094--48153 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
48084 TAGATCGATA
* * *
48094 GTGGTAATCGGTTGTTTGATCGGAT
1 GTGGTAGTCGGTCGTTTGATCGGAC
* *
48119 GTGATAGTCGGTCGTTTGATCGGCC
1 GTGGTAGTCGGTCGTTTGATCGGAC
48144 GTGGTAGTCG
1 GTGGTAGTCG
48154 ATCTTTGTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.13, C:0.13, G:0.38, T:0.35
Consensus pattern (25 bp):
GTGGTAGTCGGTCGTTTGATCGGAC
Found at i:50488 original size:218 final size:218
Alignment explanation
Indices: 49798--50735 Score: 1682
Period size: 218 Copynumber: 4.3 Consensus size: 218
49788 GTTGTTAAAA
*
49798 ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATGTATTGTTTTAATGACAAT
1 ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATTTATTGTTTTAATGACAAT
49863 TATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACAATTATGATGGTGTTCTCAC
66 TATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACAATTATGATGGTGTTCTCAC
* *
49928 ATATTTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTCTTTTCTAACAAATTTGAG
131 ATA-TTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTCTTTTCTAATAAACTTGAG
* *
49993 AAAGAATCAAATCTATATTATTGT
195 GAAGAATCAGATCTATATTATTGT
*
50017 ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATTTATTGTTTTAATGACAGT
1 ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATTTATTGTTTTAATGACAAT
* *
50082 TATCTCAAATGT-AGAATATGGGTAAAATTTTATTTATTTAACGAAAATTATGACGGTGTTCTCA
66 TATCTCAAATGTCA-AATATGGGTAAAATTTTATTTATTTAACGACAATTATGATGGTGTTCTCA
50146 CATATTTCTTTTGTTAGGTTTTGAATAG-AATCCAATTAGTTAAACCTCTTTTCTAATAAACTTG
130 CATATTT-TTTTGTTAGGTTTTGAATAGCAA-CCAATTAGTTAAACCTCTTTTCTAATAAACTTG
*
50210 AGGAAGAATCAGATCTATATTATTAT
193 AGGAAGAATCAGATCTATATTATTGT
* *
50236 AACATGAAATAGGCCACCTTGGACCAAACTAGAATTAATATCCTATTTATTGTTTTAATGACAAT
1 ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATTTATTGTTTTAATGACAAT
*
50301 TATCTCAATTGTCAAATATGGGTAAAATTTTATTTATTTAACGACAATTATGATGGTGTTCTCAC
66 TATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACAATTATGATGGTGTTCTCAC
* *
50366 ATATTTTTTTGTTAGGTTTTAAATAGCAACCAATTAGTTAAACCTCTTTTTTAATAAACTTGAGG
131 ATATTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTCTTTTCTAATAAACTTGAGG
50431 AAGAATCAGATCTATATTATTGT
196 AAGAATCAGATCTATATTATTGT
50454 ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATTTATTGTTTTAATGACAAT
1 ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATTTATTGTTTTAATGACAAT
50519 TATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACAATTATGATGGTGTTCTCAC
66 TATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACAATTATGATGGTGTTCTCAC
50584 ATATTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTCTTTTCTAATAAACTTGAGG
131 ATATTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTCTTTTCTAATAAACTTGAGG
* *
50649 AAGAAACATATCTATATTATTGT
196 AAGAATCAGATCTATATTATTGT
50672 ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATTTATTGTTTTAATGACAA
1 ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATTTATTGTTTTAATGACAA
50736 AAATGGCTGT
Statistics
Matches: 689, Mismatches: 25, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
218 357 0.52
219 331 0.48
220 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (218 bp):
ATCATGAAATAGGCCACCTTGGACCAACCTAGAATTAATATCCTATTTATTGTTTTAATGACAAT
TATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACAATTATGATGGTGTTCTCAC
ATATTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTCTTTTCTAATAAACTTGAGG
AAGAATCAGATCTATATTATTGT
Found at i:51331 original size:218 final size:218
Alignment explanation
Indices: 50923--51602 Score: 1270
Period size: 218 Copynumber: 3.1 Consensus size: 218
50913 TGGATGGTCA
*
50923 TTATTGTTTTAATGACAATTATCTCAAATGTCAAATATGAGTAAAATTTTATTTATTTAACGACA
1 TTATTGTTTTAATGACAATTATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACA
*
50988 ATTATGATGGTGTTCTCACATATTTTTTTTGTCAGGTTTTGAATAGCAACCAATTAGTTAAACCT
66 ATTATGATGGTGTTCTCACATA-TTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCT
* * *
51053 CTTTTTTAATAAACTTGAGGAATAATCAGATCTATATTATTGTATCATGAAATTGGCCACCTTGG
130 CTTTTCTAATAAACTTGAGGAAAAATCAGATCTATATTATTGTATCATGAAATAGGCCACCTTGG
51118 ACCAACCTAGAATTAATATCCTAT
195 ACCAACCTAGAATTAATATCCTAT
51142 TTATTGTTTTAATGACAATTATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACA
1 TTATTGTTTTAATGACAATTATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACA
51207 ATTATGATGGTGTTCTCACATATTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTC
66 ATTATGATGGTGTTCTCACATATTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTC
*
51272 TTTTCTAATAAACTTGAGGAAGAATCAGATCTATATTATTGTATCATGAAATAGGCCACCTTGGA
131 TTTTCTAATAAACTTGAGGAAAAATCAGATCTATATTATTGTATCATGAAATAGGCCACCTTGGA
51337 CCAACCTAGAATTAATATCCTAT
196 CCAACCTAGAATTAATATCCTAT
51360 TTATTGTTTTAATGACAATTATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACA
1 TTATTGTTTTAATGACAATTATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACA
*
51425 ATTATGACGGTGTTCTCACATATTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTC
66 ATTATGATGGTGTTCTCACATATTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTC
*
51490 TTTTCTAATAAATTTGAGGAAAAATCAGATCTATATTATTGTATCATGAAATAGGCCACCTTGGA
131 TTTTCTAATAAACTTGAGGAAAAATCAGATCTATATTATTGTATCATGAAATAGGCCACCTTGGA
51555 CCAACCTAGAATTAATATCCTAT
196 CCAACCTAGAATTAATATCCTAT
*
51578 TTATTGTTTTATTGACAATTATCTC
1 TTATTGTTTTAATGACAATTATCTC
51603 TGTCATAACC
Statistics
Matches: 452, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
218 366 0.81
219 86 0.19
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.40
Consensus pattern (218 bp):
TTATTGTTTTAATGACAATTATCTCAAATGTCAAATATGGGTAAAATTTTATTTATTTAACGACA
ATTATGATGGTGTTCTCACATATTTTTTTGTTAGGTTTTGAATAGCAACCAATTAGTTAAACCTC
TTTTCTAATAAACTTGAGGAAAAATCAGATCTATATTATTGTATCATGAAATAGGCCACCTTGGA
CCAACCTAGAATTAATATCCTAT
Found at i:52514 original size:15 final size:16
Alignment explanation
Indices: 52496--52529 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
52486 TATGAACATC
52496 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
52511 AAATAGAATAACAATA
1 AAATAAAATAACAATA
52527 AAA
1 AAA
52530 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:54696 original size:25 final size:25
Alignment explanation
Indices: 54663--54724 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
54653 ACAAAATGTA
*
54663 AATACATATTAAATAATAATAATAAT
1 AATA-ATATTAAATAACAATAATAAT
* * *
54689 AATAATATAAAATGACAATAATAGT
1 AATAATATTAAATAACAATAATAAT
54714 AATAA-ATTAAA
1 AATAATATTAAA
54725 ATAGAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 5 0.16
25 22 0.71
26 4 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (25 bp):
AATAATATTAAATAACAATAATAAT
Done.