Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002638.1 Hibiscus syriacus cultivar Beakdansim tig00005382_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: 80253
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1560 original size:206 final size:208
Alignment explanation
Indices: 1203--1605 Score: 555
Period size: 206 Copynumber: 1.9 Consensus size: 208
1193 AAAACTATTA
* * **
1203 TTTTATCAACACAGATTAATTCCATTTACTTATGCACATAGATAATTTTGTAATTTCAACACTCT
1 TTTTATCAACACAGATTAATTCCA-TCACTTATGCACATAGACAATTCAGTAATTTCAACACTCT
* ** *
1268 AAGGACATCTTAGTACTCTAACACACTTATAGTATATCAGACTTATTAAAGCTTAGTAAAATAGT
65 AAGGACATCTTAGTAATCTAACACACACATAGTATATAAGACTTATTAAAGCTTAGTAAAATAGT
* * *
1333 ATTACCTTAATTATCAGTGTTTTAATACCCTTTTTTACACTCTTAGACTTTTGTTATCACTTATT
130 ATTAACTTAATTATCAGTGTTTTAATACCCTTTTTTACACTCTTAGACTTTTCTTATCAATTATT
1398 ATGACTAAGTGCAT
195 ATGACTAAGTGCAT
* *
1412 TTTTATCAACATAGATT-ATTCC-TCACTTATGCACATAAGGACAATTCAGTAATTTCAACCTCT
1 TTTTATCAACACAGATTAATTCCATCACTTATGCACAT-A-GACAATTCAGTAATTTCAA-CACT
* * * * *
1475 CTAAGGACATTTTAGTAATTTGACACTCACA-AGTATATAAG-CTTATTAAAGCTTA-TTAAATA
63 CTAAGGACATCTTAGTAATCTAACACACACATAGTATATAAGACTTATTAAAGCTTAGTAAAATA
* *
1537 GTATTAACTTAATTATCAGTGTTTTAATACCTTTTTTTACACTCTTAGGCTTTTCTTATCAATTA
128 GTATTAACTTAATTATCAGTGTTTTAATACCCTTTTTTACACTCTTAGACTTTTCTTATCAATTA
1602 TTAT
193 TTAT
1606 CATTAAGGGT
Statistics
Matches: 171, Mismatches: 20, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
206 83 0.49
207 15 0.09
208 30 0.18
209 43 0.25
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (208 bp):
TTTTATCAACACAGATTAATTCCATCACTTATGCACATAGACAATTCAGTAATTTCAACACTCTA
AGGACATCTTAGTAATCTAACACACACATAGTATATAAGACTTATTAAAGCTTAGTAAAATAGTA
TTAACTTAATTATCAGTGTTTTAATACCCTTTTTTACACTCTTAGACTTTTCTTATCAATTATTA
TGACTAAGTGCAT
Found at i:3966 original size:18 final size:18
Alignment explanation
Indices: 3921--3964 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
3911 TTGTTTTCAT
3921 TTTTTATTTT--ATTACA
1 TTTTTATTTTAAATTACA
*
3937 TTTTTATTTTAAATTATA
1 TTTTTATTTTAAATTACA
3955 TTTTTCATTT
1 TTTTT-ATTT
3965 AATTTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 10 0.42
18 10 0.42
19 4 0.17
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTATTTTAAATTACA
Found at i:4095 original size:25 final size:22
Alignment explanation
Indices: 4067--4145 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 22
4057 ATCTCAAGTT
4067 ATTTTAATTTAATTCTAATTTTATA
1 ATTTT-ATTT-ATTCT-ATTTTATA
*
4092 ATTTTATTTTATTTTGTATTTTATA
1 ATTTTA-TTTA--TTCTATTTTATA
* *
4117 ATTATTTATTTTTTGTATTTTATA
1 A-T-TTTATTTATTCTATTTTATA
4141 ATTTT
1 ATTTT
4146 TTTTTTAGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
22 3 0.06
23 1 0.02
24 15 0.32
25 17 0.36
26 7 0.15
27 4 0.09
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (22 bp):
ATTTTATTTATTCTATTTTATA
Found at i:4135 original size:24 final size:23
Alignment explanation
Indices: 4084--4151 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 23
4074 TTTAATTCTA
*
4084 ATTTTATAATTTTATTTTATTTTGT
1 ATTTTATAA--TTATTTTTTTTTGT
4109 ATTTTATAATTATTTATTTTTTGT
1 ATTTTATAATTATTT-TTTTTTGT
4133 ATTTTATAATT-TTTTTTTT
1 ATTTTATAATTATTTTTTTT
4152 AGATTATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 5 0.12
23 9 0.22
24 18 0.44
25 9 0.22
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (23 bp):
ATTTTATAATTATTTTTTTTTGT
Found at i:11246 original size:25 final size:25
Alignment explanation
Indices: 11218--11273 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
11208 AAAACAGAAG
11218 ATAAAATTTTAGTTTAGAGAAAGGT
1 ATAAAATTTTAGTTTAGAGAAAGGT
11243 ATAAAATTTTAGTTTAGAGAAAGGT
1 ATAAAATTTTAGTTTAGAGAAAGGT
11268 A-AAAAT
1 ATAAAAT
11274 AAATTAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (25 bp):
ATAAAATTTTAGTTTAGAGAAAGGT
Found at i:12382 original size:21 final size:21
Alignment explanation
Indices: 12356--12402 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
12346 GGCTTTGGAA
*
12356 TTTTCCTGAGATATAACCAGC
1 TTTTCCTGAGATATAACCAAC
* *
12377 TTTTCCTGGGATGTAACCAAC
1 TTTTCCTGAGATATAACCAAC
12398 TTTTC
1 TTTTC
12403 TTGTGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TTTTCCTGAGATATAACCAAC
Found at i:13117 original size:18 final size:19
Alignment explanation
Indices: 13080--13126 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
13070 ACCCCTTTGA
*
13080 AAATACATGATTTTTTATG
1 AAATACATGATTTTTAATG
13099 AAATACATGA-TTTTAATG
1 AAATACATGATTTTTAATG
13117 AAGATACATG
1 AA-ATACATG
13127 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (19 bp):
AAATACATGATTTTTAATG
Found at i:18574 original size:13 final size:12
Alignment explanation
Indices: 18555--18604 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
18545 AATTGTTTTG
18555 AAATAAAAAATA
1 AAATAAAAAATA
18567 AGAAT--AAAATA
1 A-AATAAAAAATA
*
18578 AAATATAAAGATA
1 AAATA-AAAAATA
18591 AAATAAATAAATA
1 AAATAAA-AAATA
18604 A
1 A
18605 TTAAAGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
12 3 0.10
13 18 0.58
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:18576 original size:18 final size:18
Alignment explanation
Indices: 18555--18604 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
18545 AATTGTTTTG
18555 AAATAAAAAAT-AAGAATA
1 AAATAAAAAATAAAG-ATA
*
18573 AAATAAAATATAAAGATA
1 AAATAAAAAATAAAGATA
18591 AAATAAATAAATAA
1 AAATAAA-AAATAA
18605 TTAAAGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAAGATA
Found at i:20100 original size:3 final size:3
Alignment explanation
Indices: 20092--20186 Score: 90
Period size: 3 Copynumber: 32.3 Consensus size: 3
20082 GATATTACTA
* *
20092 TAT TAT TAT TAC TAT TAT TAT ATAT AAT TA- TAT ATAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT
* * * *
20137 TAT TAT TAC TA- TAT TAT TGT TAT TAC TA- TAT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20183 TAT T
1 TAT T
20187 TACAATACTC
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
2 8 0.11
3 62 0.82
4 6 0.08
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:20138 original size:17 final size:16
Alignment explanation
Indices: 20083--20171 Score: 79
Period size: 17 Copynumber: 6.0 Consensus size: 16
20073 GTCTGAGTTG
20083 ATATTACTATATTA-T
1 ATATTACTATATTATT
20098 -TATTAC--TATTATT
1 ATATTACTATATTATT
20111 ATA-TA-TA-ATTA-T
1 ATATTACTATATTATT
*
20123 ATA-TATTATATTATT
1 ATATTACTATATTATT
20138 ATTATTACTATATTATT
1 A-TATTACTATATTATT
*
20155 GTTATTACTATATTATT
1 -ATATTACTATATTATT
20172 GTTATTATTA
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
12 11 0.18
13 9 0.15
14 12 0.19
15 2 0.03
16 2 0.03
17 26 0.42
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (16 bp):
ATATTACTATATTATT
Found at i:20172 original size:17 final size:17
Alignment explanation
Indices: 20129--20186 Score: 93
Period size: 17 Copynumber: 3.5 Consensus size: 17
20119 TTATATATAT
*
20129 TATATTATTATTATTAC
1 TATATTATTGTTATTAC
20146 TATATTATTGTTATTAC
1 TATATTATTGTTATTAC
20163 TATATTATTGTTATTA-
1 TATATTATTGTTATTAC
20179 T-TATTATT
1 TATATTATT
20187 TACAATACTC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
15 7 0.17
16 1 0.03
17 32 0.80
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TATATTATTGTTATTAC
Found at i:21141 original size:11 final size:11
Alignment explanation
Indices: 21125--21156 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
21115 TGTCTTCAAA
21125 TTTTATTTTAC
1 TTTTATTTTAC
21136 TTTTATTTTAC
1 TTTTATTTTAC
21147 TTTTATTTTA
1 TTTTATTTTA
21157 GTCACTGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTTAC
Found at i:21145 original size:16 final size:16
Alignment explanation
Indices: 21124--21156 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21114 TTGTCTTCAA
21124 ATTTTATTTTACTTTT
1 ATTTTATTTTACTTTT
21140 ATTTTACTTTTA-TTTT
1 ATTTTA-TTTTACTTTT
21156 A
1 A
21157 GTCACTGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTATTTTACTTTT
Found at i:22651 original size:46 final size:47
Alignment explanation
Indices: 22561--22653 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 47
22551 GTATTACTAT
* * * *
22561 TTTATTTTCTAAATAAATGCATGCGAACTAGAAATCAAGCGGTTAGG
1 TTTATTTTCCAAACAAATGCATGCGAACTAGAAAGCAAGAGGTTAGG
*
22608 TTTATTTTTCCAAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTTA-TTTTCCAAACAAATGCATGCGAACTAGAAAGCAAGAGGTTAGG
22654 ATATATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
46 20 0.50
47 9 0.22
48 11 0.28
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (47 bp):
TTTATTTTCCAAACAAATGCATGCGAACTAGAAAGCAAGAGGTTAGG
Found at i:23995 original size:21 final size:21
Alignment explanation
Indices: 23969--24018 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
23959 GGTTTTGGAA
23969 TTTTCTTGGGATGCAACCAGC
1 TTTTCTTGGGATGCAACCAGC
* * *
23990 TTTTCTTCGGATGTAACCATC
1 TTTTCTTGGGATGCAACCAGC
24011 TTTTCTTG
1 TTTTCTTG
24019 TGAAATTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (21 bp):
TTTTCTTGGGATGCAACCAGC
Found at i:27475 original size:21 final size:20
Alignment explanation
Indices: 27450--27488 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
27440 CTATTGCCAA
27450 TATTTTTATTTTCTATTTTTC
1 TATTTTTATTTTCT-TTTTTC
*
27471 TATTTTTCTTTTCTTTTT
1 TATTTTTATTTTCTTTTT
27489 GAGCAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (20 bp):
TATTTTTATTTTCTTTTTTC
Found at i:28360 original size:17 final size:17
Alignment explanation
Indices: 28308--28360 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
28298 AATTGTTTTG
28308 AAATAAA-AAATAAGAATA
1 AAATAAATAAAT-A-AATA
*
28326 AAATAAATATAA-AGATA
1 AAATAAATA-AATAAATA
28343 AAATAAATAAATAAATA
1 AAATAAATAAATAAATA
28360 A
1 A
28361 TTAAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.07
17 17 0.57
18 8 0.27
19 1 0.03
20 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (17 bp):
AAATAAATAAATAAATA
Found at i:32241 original size:46 final size:47
Alignment explanation
Indices: 32156--32248 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 47
32146 GTATTATTAT
* *
32156 TTTATTTTCTAAATAAATGCATGCGAACTAGAAACCATGAGGTTAGG
1 TTTATTTTCCAAACAAATGCATGCGAACTAGAAACCATGAGGTTAGG
*
32203 TTTATTTTTCCAAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTTA-TTTTCCAAACAAATGCATGCGAACTAGAAACCATGAGGTTAGG
32249 ATATTGATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 22 0.52
47 9 0.21
48 11 0.26
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (47 bp):
TTTATTTTCCAAACAAATGCATGCGAACTAGAAACCATGAGGTTAGG
Found at i:44490 original size:26 final size:27
Alignment explanation
Indices: 44440--44490 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
44430 TAGTGTTTGG
44440 GGGTATTTTGGTCATTTTAGAGTTTAT
1 GGGTATTTTGGTCATTTTAGAGTTTAT
44467 GGGTATTTTGGTC-TTTTAGAGTTT
1 GGGTATTTTGGTCATTTTAGAGTTT
44491 GAAGGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.16, C:0.04, G:0.27, T:0.53
Consensus pattern (27 bp):
GGGTATTTTGGTCATTTTAGAGTTTAT
Found at i:44497 original size:26 final size:27
Alignment explanation
Indices: 44441--44500 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
44431 AGTGTTTGGG
*
44441 GGTATTTTGGTCATTTTAGAGTTTATG
1 GGTATTTTGGTCATTTTAGAGTTTATA
44468 GGTATTTTGGTC-TTTTAGAGTTTGA-A
1 GGTATTTTGGTCATTTTAGAGTTT-ATA
44494 GGTATTT
1 GGTATTT
44501 CGATTATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.18, C:0.03, G:0.27, T:0.52
Consensus pattern (27 bp):
GGTATTTTGGTCATTTTAGAGTTTATA
Found at i:47890 original size:21 final size:22
Alignment explanation
Indices: 47865--47905 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
47855 CATAAATGAA
*
47865 AATAATTATGGGA-TTAAATTG
1 AATAATAATGGGAGTTAAATTG
*
47886 AATAATAATTGGAGTTAAAT
1 AATAATAATGGGAGTTAAAT
47906 GCCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (22 bp):
AATAATAATGGGAGTTAAATTG
Found at i:53561 original size:57 final size:57
Alignment explanation
Indices: 53492--53602 Score: 204
Period size: 57 Copynumber: 1.9 Consensus size: 57
53482 GGAGAACATG
*
53492 GTCTTAGTACTCTGAATACAATCATGAAGAACCAAGAATCTTTGGTTGATCAGAGTA
1 GTCTGAGTACTCTGAATACAATCATGAAGAACCAAGAATCTTTGGTTGATCAGAGTA
*
53549 GTCTGAGTACTCTGAATATAATCATGAAGAACCAAGAATCTTTGGTTGATCAGA
1 GTCTGAGTACTCTGAATACAATCATGAAGAACCAAGAATCTTTGGTTGATCAGA
53603 TCATTGCCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (57 bp):
GTCTGAGTACTCTGAATACAATCATGAAGAACCAAGAATCTTTGGTTGATCAGAGTA
Found at i:55845 original size:16 final size:16
Alignment explanation
Indices: 55824--55855 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55814 ATTTCAGAGG
55824 ACCGAAATAAAAGGTC
1 ACCGAAATAAAAGGTC
55840 ACCGAAATAAAAGGTC
1 ACCGAAATAAAAGGTC
55856 TAGTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
ACCGAAATAAAAGGTC
Found at i:57083 original size:84 final size:83
Alignment explanation
Indices: 56771--57326 Score: 541
Period size: 84 Copynumber: 6.7 Consensus size: 83
56761 TTTAAGACAA
* * * * *
56771 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCAACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
*
56836 CTCAGCTCCAAGGCGCAT
66 CTCAGCTCCAAGGCACAT
* * * * * * * * *
56854 AATTTGTAGCATAGCTTAAGTCAAGAAAGGCTATCTG---CCAAAG-CCCTCAAGTTCGACTATG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* *
56915 CTCAGCTACGAGGGCACAT
66 CTCAGCT-CCAAGGCACAT
* * * * * * * * *
56934 CATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTCACCAAACACCTTCGCGTTTGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
*
56999 CTCAGCTCCAAGGCATAT
66 CTCAGCTCCAAGGCACAT
*
57017 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
*
57082 GCTCAGCTCCAAGGCGCAT
65 GCTCAGCTCCAAGGCACAT
* * * * *
57101 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT---TCCAAAGACCTTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
** *
57163 CTCAGCTTTGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * * * * * * *
57182 TATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTAGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTAC
57247 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* *** * * *
57266 CATTTGCAGTAGGGCTTAAGTCGAGAAGGGTTATCTTCCAACCGAAGACCTTCAAGTTCGA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGA
57327 TTACACTCGG
Statistics
Matches: 372, Mismatches: 89, Indels: 23
0.77 0.18 0.05
Matches are distributed among these distances:
79 21 0.06
80 69 0.19
81 36 0.10
83 74 0.20
84 144 0.39
85 28 0.08
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:57326 original size:249 final size:247
Alignment explanation
Indices: 56771--57326 Score: 790
Period size: 249 Copynumber: 2.2 Consensus size: 247
56761 TTTAAGACAA
* * ** * *
56771 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCAACTAC
1 CATTTGCAGCAGAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
56835 GCTCAGCTCCAAGGCGCATAATTTGTAGCATAGCTTAAGTCAAGAAAGGCTATCTGCCAAAGCCC
66 GCTCAGCTCCAAGGCGCATAATTTGCAGCATAGCTTAAGTCAAGAAAGGCTATCTGCCAAAGCCC
** * *
56900 TCAAGTTCGACTATGCTCAGCTACGAGGGCACATCATTTACAGCATAACTCAAGGCTATAAGGGT
131 TCAAGTTCGACTACACTCAGCTACGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
* * *
56965 TATCTGTCACCAAACACCTTCGCGTTTGACTACGCTCAGCTCCAAGGCATAT
196 TATCTGTCACCAAACACCTTAGAGTTTGACTACGCTCAGCTCCAAGGCACAT
*
57017 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCAGAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
57082 GCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTCCAAAGACC
66 GCTCAGCTCCAAGGCGCATAATTTGCAGCATAGCTTAAGTCAAGAAAGGCTATCTGCCAAAG-CC
* * * ** *
57147 TTCGAGTTCGATTACACTCAGCTTTGAGGGCACATTATTTACAACATAACTCAAGGCTAGAAGGG
130 CTCAAGTTCGACTACACTCAGCTACGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
*
57212 TTATCTGTCACCAAAAGACCTTAGAGTTTGACTACGCTCAGCTCCAAGGCACAT
195 TTATCTGTCACC-AAACACCTTAGAGTTTGACTACGCTCAGCTCCAAGGCACAT
* ** * * * *
57266 CATTTGCAGTAGGGCTTAAGTCGAGAAGGGTTATCTTCCAACCGAAGACCTTCAAGTTCGA
1 CATTTGCAGCAGAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
57327 TTACACTCGG
Statistics
Matches: 275, Mismatches: 32, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
246 37 0.13
247 79 0.29
248 69 0.25
249 90 0.33
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (247 bp):
CATTTGCAGCAGAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCGCATAATTTGCAGCATAGCTTAAGTCAAGAAAGGCTATCTGCCAAAGCCC
TCAAGTTCGACTACACTCAGCTACGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
TATCTGTCACCAAACACCTTAGAGTTTGACTACGCTCAGCTCCAAGGCACAT
Found at i:58093 original size:37 final size:36
Alignment explanation
Indices: 58024--58178 Score: 147
Period size: 35 Copynumber: 4.3 Consensus size: 36
58014 GTTTTCTAAA
*
58024 AAAAACATTTT-GAAATATATATAATATA--GTTTT
1 AAAAACATTTTAAAAATATATATAATATATGGTTTT
* *
58057 CGAAAACATTTTAAAAATGTATATAATATATGGTTTTT
1 -AAAAACATTTTAAAAATATATATAATATATGG-TTTT
* * *
58095 AAAAAACAGTTTGAAAAATATTTATAATATATAGTTTT
1 -AAAAACA-TTTTAAAAATATATATAATATATGGTTTT
* * * * *
58133 TAAAACATTTTGAAAA-CTATATAGTATATGATTTT
1 AAAAACATTTTAAAAATATATATAATATATGGTTTT
58168 AAAAACATTTT
1 AAAAACATTTT
58179 TTAGAAAGTA
Statistics
Matches: 98, Mismatches: 18, Indels: 9
0.78 0.14 0.07
Matches are distributed among these distances:
34 10 0.10
35 39 0.40
36 7 0.07
37 7 0.07
38 14 0.14
39 21 0.21
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (36 bp):
AAAAACATTTTAAAAATATATATAATATATGGTTTT
Found at i:58199 original size:76 final size:72
Alignment explanation
Indices: 58024--58245 Score: 197
Period size: 76 Copynumber: 3.0 Consensus size: 72
58014 GTTTTCTAAA
* * *
58024 AAAAACATTTTG--AAATA-TATAT-A-ATATAGTTTTCGAAAACATTTTAAAAATGTATATAAT
1 AAAAACAGTTTGAAAAATATTATATAATATATAGTTTT-TAAAACATTTTGAAAA--TATATAAT
*
58084 ATATGGTTTTT
63 ATAT-GATTTT
*
58095 AAAAAACAGTTTGAAAAATATT-TATAATATATAGTTTTTAAAACATTTTGAAAACTATATAGTA
1 -AAAAACAGTTTGAAAAATATTATATAATATATAGTTTTTAAAACATTTTGAAAA-TATATAATA
58159 TATGATTTT
64 TATGATTTT
* * * * *
58168 AAAAACATTTTTTAGAAAGTATGTATATAATATATA-ATTTTAAAATATTATTTGAAAATATATA
1 AAAAACA-GTTTGA-AAAATAT-TATATAATATATAGTTTTTAAAACA-T-TTTGAAAATATATA
*
58232 TTATATGATTTT
61 ATATATGATTTT
58244 AA
1 AA
58246 TTTTTTTAAA
Statistics
Matches: 127, Mismatches: 12, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
72 18 0.14
73 9 0.07
74 25 0.20
75 26 0.20
76 41 0.32
77 8 0.06
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (72 bp):
AAAAACAGTTTGAAAAATATTATATAATATATAGTTTTTAAAACATTTTGAAAATATATAATATA
TGATTTT
Found at i:58279 original size:35 final size:36
Alignment explanation
Indices: 58191--58280 Score: 91
Period size: 35 Copynumber: 2.6 Consensus size: 36
58181 AGAAAGTATG
*
58191 TATATAATATATAATTTTAAAATATTATTTGAAAATA
1 TATATAATATATAATTTT-TAATATTATTTGAAAATA
* *
58228 TATAT--TATATGA-TTTTAAT-TT-TTTTAAACATA
1 TATATAATATATAATTTTTAATATTATTTGAAA-ATA
*
58260 TATATAATATATTATTTTTAA
1 TATATAATATATAATTTTTAA
58281 AATGTTCTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
31 6 0.13
32 10 0.22
33 3 0.07
34 9 0.20
35 12 0.27
37 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (36 bp):
TATATAATATATAATTTTTAATATTATTTGAAAATA
Found at i:59388 original size:26 final size:26
Alignment explanation
Indices: 59354--59420 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
59344 ATGTATTGCA
59354 AAACGACGTAGTTTTGCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
*
59380 AAACAACGTAGTTTTGCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
59406 AAACGACGTAGTTTT
1 AAACGACGTAGTTTT
59421 ATCCCATAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (26 bp):
AAACGACGTAGTTTTGCCACTGCAAG
Found at i:59585 original size:4 final size:4
Alignment explanation
Indices: 59576--59617 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
59566 CACTTTCTGC
* * *
59576 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TTAT ATAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
59618 TTTGTTTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:59738 original size:23 final size:21
Alignment explanation
Indices: 59687--59744 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 21
59677 ATATCTAACC
*
59687 TTTTTAGTTTTTTATTTCATT
1 TTTTTATTTTTTTATTTCATT
59708 TGGATTTTATTTTTTTATTTCCATT
1 T---TTTTATTTTTTTATTT-CATT
59733 ATTTTTATTTTT
1 -TTTTTATTTTT
59745 ATTTTTACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 1 0.03
23 10 0.32
24 15 0.48
25 4 0.13
26 1 0.03
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTTATTTTTTTATTTCATT
Found at i:59852 original size:37 final size:39
Alignment explanation
Indices: 59811--59884 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
59801 TCTTTCGATT
*
59811 TATTTCTTTTA-TCTTCCTT-ATTTTTTATTTTTTTCTC
1 TATTTCTTTAATTCTTCCTTAATTTTTTATTTTTTTCTC
* *
59848 TATTTCTTTAATTTTTCTTTAATTTTTTATTTTTTTC
1 TATTTCTTTAATTCTTCCTTAATTTTTTATTTTTTTC
59885 CTTTTGACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 10 0.31
38 6 0.19
39 16 0.50
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (39 bp):
TATTTCTTTAATTCTTCCTTAATTTTTTATTTTTTTCTC
Found at i:59866 original size:11 final size:11
Alignment explanation
Indices: 59850--59874 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59840 TTTTTCTCTA
59850 TTTCTTTAATT
1 TTTCTTTAATT
59861 TTTCTTTAATT
1 TTTCTTTAATT
59872 TTT
1 TTT
59875 TATTTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTAATT
Found at i:59882 original size:19 final size:18
Alignment explanation
Indices: 59829--59882 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
59819 TTATCTTCCT
59829 TATTTTTTATTTTTTTCTC
1 TATTTTTTA-TTTTTTCTC
* *
59848 TATTTCTTTAATTTTTCTT
1 TATTT-TTTATTTTTTCTC
59867 TAATTTTTTATTTTTT
1 T-ATTTTTTATTTTTT
59883 TCCTTTTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTTTTATTTTTTCTC
Found at i:60416 original size:35 final size:35
Alignment explanation
Indices: 60345--60490 Score: 114
Period size: 35 Copynumber: 4.0 Consensus size: 35
60335 TATAGGTTTT
* *
60345 TTTAAAAAAGCATTTTTGAAAACATATATATTATATAG
1 TTTAAAAAAACA-TTTT-AAAA-ATATATATAATATAG
*
60383 TTTAAAAAAAACATTTT-GAAATATATATAATATAG
1 TTT-AAAAAAACATTTTAAAAATATATATAATATAG
*** *
60418 TTTTCGAAAACATTTTAAAAATGTATATAATATATGG
1 TTTAAAAAAACATTTTAAAAATATATATAATATA--G
** * *
60455 TTTTTTAAAAACAGTTTGAAAAATATTTATAATATA
1 -TTTAAAAAAACA-TTTTAAAAATATATATAATATA
60491 CAGTTTTTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
34 10 0.11
35 32 0.36
36 2 0.02
37 1 0.01
38 17 0.19
39 27 0.30
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (35 bp):
TTTAAAAAAACATTTTAAAAATATATATAATATAG
Found at i:60458 original size:37 final size:36
Alignment explanation
Indices: 60390--60538 Score: 126
Period size: 35 Copynumber: 4.1 Consensus size: 36
60380 TAGTTTAAAA
*
60390 AAAACATTTT-GAAATATATATAATATA--GTTTTCG
1 AAAACATTTTAAAAATATATATAATATATGGTTTT-G
* *
60424 AAAACATTTTAAAAATGTATATAATATATGGTTTTTTA
1 AAAACATTTTAAAAATATATATAATATATGG--TTTTG
* * ** *
60462 AAAACAGTTTGAAAAATATTTATAATATACAGTTTTT
1 AAAACA-TTTTAAAAATATATATAATATATGGTTTTG
* * * *
60499 AAAACATTTTGAAAA-CTATATAGTATATGATTTTG
1 AAAACATTTTAAAAATATATATAATATATGGTTTTG
60534 AAAAC
1 AAAAC
60539 TATATAGTAT
Statistics
Matches: 91, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
34 10 0.11
35 33 0.36
36 7 0.08
37 11 0.12
38 6 0.07
39 24 0.26
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (36 bp):
AAAACATTTTAAAAATATATATAATATATGGTTTTG
Found at i:60477 original size:39 final size:36
Alignment explanation
Indices: 60401--60520 Score: 118
Period size: 37 Copynumber: 3.2 Consensus size: 36
60391 AAACATTTTG
* *
60401 AAATATATATAATAT--AGTTTTCGAAAACATTTTAA
1 AAATATATATAATATACAGTTTT-TAAAACATTTGAA
* **
60436 AAATGTATATAATATATGGTTTTTTAAAAACAGTTTGAA
1 AAATATATATAATATACAG-TTTTT-AAAACA-TTTGAA
*
60475 AAATATTTATAATATACAGTTTTTAAAACATTTTGAA
1 AAATATATATAATATACAGTTTTTAAAACA-TTTGAA
*
60512 AACTATATA
1 AAATATATA
60521 GTATATGATT
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
35 14 0.20
37 20 0.29
38 15 0.22
39 20 0.29
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (36 bp):
AAATATATATAATATACAGTTTTTAAAACATTTGAA
Found at i:60490 original size:74 final size:71
Alignment explanation
Indices: 60389--60532 Score: 173
Period size: 74 Copynumber: 2.0 Consensus size: 71
60379 ATAGTTTAAA
* *
60389 AAAAACATTTTGAAATATATATAATAT-AGTTTTCGAAAACATTTTAAAAATGTATATAATATAT
1 AAAAACAGTTTGAAATATATATAATATAAGTTTT-GAAAACATTTTAAAAA-CTATATAATATAT
*
60453 GGTTTTTT
64 GATTTTTT
* * * *
60461 AAAAACAGTTTGAAAAATATTTATAATATACAGTTTTTAAAACATTTTGAAAACTATATAGTATA
1 AAAAACAGTTTG--AAATATATATAATATA-AGTTTTGAAAACATTTTAAAAACTATATAATATA
60526 TGATTTT
63 TGATTTT
60533 GAAAACTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
72 11 0.18
74 30 0.49
75 14 0.23
76 6 0.10
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (71 bp):
AAAAACAGTTTGAAATATATATAATATAAGTTTTGAAAACATTTTAAAAACTATATAATATATGA
TTTTTT
Found at i:60531 original size:24 final size:24
Alignment explanation
Indices: 60504--60562 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
60494 TTTTTAAAAC
60504 ATTTTGAAAACTATATAGTATATG
1 ATTTTGAAAACTATATAGTATATG
60528 ATTTTGAAAACTATATAGTATATG
1 ATTTTGAAAACTATATAGTATATG
60552 ATTTTGAAAAC
1 ATTTTGAAAAC
60563 ATTTTTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (24 bp):
ATTTTGAAAACTATATAGTATATG
Found at i:60661 original size:33 final size:34
Alignment explanation
Indices: 60581--60661 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 34
60571 AGAAAGTATG
*
60581 TATATA-ATATATAATTTTAAAATATTATTTGAAAA
1 TATATATA-ATATAATTTT-AAATATTATTTAAAAA
* *
60616 TATATATTATATAATTTT-AAT-TTTTTTAAAACA
1 TATATATAATATAATTTTAAATATTATTTAAAA-A
60649 TATATATAATATA
1 TATATATAATATA
60662 TTATTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 8 0.20
33 16 0.40
35 16 0.40
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (34 bp):
TATATATAATATAATTTTAAATATTATTTAAAAA
Found at i:60698 original size:9 final size:8
Alignment explanation
Indices: 60679--60703 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
60669 TAAAATGTTC
60679 TTTTTTAT
1 TTTTTTAT
60687 TTTTTTAT
1 TTTTTTAT
60695 TTTTTTAT
1 TTTTTTAT
60703 T
1 T
60704 ATTTCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTAT
Found at i:61791 original size:26 final size:26
Alignment explanation
Indices: 61730--61796 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
61720 ATGTATTGCA
61730 AAACGACGTAGTTTTGCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
** * *
61756 AAAAAACGTAATTTTGCCACTGCAGG
1 AAACGACGTAGTTTTGCCACTGCAAG
*
61782 AAACGGCGTAGTTTT
1 AAACGACGTAGTTTT
61797 ATCCCATAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (26 bp):
AAACGACGTAGTTTTGCCACTGCAAG
Found at i:61962 original size:4 final size:4
Alignment explanation
Indices: 61953--61998 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
61943 CACTTTCTGC
* * *
61953 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TTAT TTAT ATAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
61999 TTTGTTTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:62824 original size:39 final size:37
Alignment explanation
Indices: 62727--62933 Score: 170
Period size: 37 Copynumber: 5.4 Consensus size: 37
62717 TGCTAATGGT
* *
62727 TTTTGAAATAGATATATATTATATAGGTTTTCTTTAAAAAGCA
1 TTTTGAAA-ATATATATATTATATA-G---T-TTTAAAAAACA
*
62770 TTTTTGAAAACATATATATTATATAGTTTTAAAAAAGCA
1 -TTTTGAAAATATATATATTATATAGTTTTAAAAAA-CA
**
62809 TTTTG-AAATATATATA--ATATAGTTTTCGAAAACA
1 TTTTGAAAATATATATATTATATAGTTTTAAAAAACA
* * * *
62843 TTTTAAAAATGTATATAATATATGGTTTTTAAAAAACA
1 TTTTGAAAATATATATATTATATAG-TTTTAAAAAACA
* * * *
62881 GTTTGAAAAATATTTATAATATATAGTTTT-TAAAACA
1 TTTTG-AAAATATATATATTATATAGTTTTAAAAAACA
62918 TTTTGAAAACTATATA
1 TTTTGAAAA-TATATA
62934 GTATATGATT
Statistics
Matches: 138, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
34 6 0.04
35 24 0.17
36 4 0.03
37 30 0.22
38 30 0.22
39 20 0.14
42 1 0.01
43 15 0.11
44 8 0.06
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (37 bp):
TTTTGAAAATATATATATTATATAGTTTTAAAAAACA
Found at i:62932 original size:74 final size:72
Alignment explanation
Indices: 62771--62950 Score: 195
Period size: 74 Copynumber: 2.5 Consensus size: 72
62761 TAAAAAGCAT
* * *
62771 TTTTGAAAACATATATATTATATAG-TTTTAAAAAAGCATTTTGAAATATATATAATATAGTTTT
1 TTTTGAAAAC-TATATAATATATGGTTTTTAAAAAAGCAGTTTGAAATATATATAATATAGTTTT
62835 CGAAAACA
65 CGAAAACA
* * *
62843 TTTTAAAAATGTATATAATATATGGTTTTTAAAAAA-CAGTTTGAAAAATATTTATAATATATAG
1 TTTTGAAAA-CTATATAATATATGGTTTTTAAAAAAGCAGTTTG--AAATATATAT-A-ATATAG
*
62907 TTTT-TAAAACA
61 TTTTCGAAAACA
* * *
62918 TTTTGAAAACTATATAGTATATGATTTTGAAAA
1 TTTTGAAAACTATATAATATATGGTTTTTAAAA
62951 CATTTTTTTA
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
72 26 0.29
73 10 0.11
74 29 0.32
75 15 0.17
76 10 0.11
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (72 bp):
TTTTGAAAACTATATAATATATGGTTTTTAAAAAAGCAGTTTGAAATATATATAATATAGTTTTC
GAAAACA
Found at i:62951 original size:35 final size:36
Alignment explanation
Indices: 62759--62956 Score: 149
Period size: 35 Copynumber: 5.4 Consensus size: 36
62749 ATAGGTTTTC
* *
62759 TTTAAAAAGCATTTTTGAAAACATATATATTATAT-AGT
1 TTTAAAAAACA-TTTTGAAAAC-TATATAATATATGA-T
62797 TTTAAAAAAGCATTTTGAAATA-TATATAATATA-G-T
1 TTTAAAAAA-CATTTTGAAA-ACTATATAATATATGAT
** * * *
62832 TTTCGAAAACATTTTAAAAATGTATATAATATATGGTT
1 TTTAAAAAACATTTTGAAAA-CTATATAATATAT-GAT
* *
62870 TTTAAAAAACAGTTTGAAAAATATTTATAATATAT-AGT
1 TTTAAAAAACATTTTGAAAACTA--TATAATATATGA-T
* *
62908 TTT-TAAAACATTTTGAAAACTATATAGTATATGAT
1 TTTAAAAAACATTTTGAAAACTATATAATATATGAT
*
62943 TTT-GAAAACATTTT
1 TTTAAAAAACATTTT
62957 TTTAGAAAGT
Statistics
Matches: 132, Mismatches: 16, Indels: 27
0.75 0.09 0.15
Matches are distributed among these distances:
33 1 0.01
34 9 0.07
35 42 0.32
36 1 0.01
37 29 0.22
38 37 0.28
39 13 0.10
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (36 bp):
TTTAAAAAACATTTTGAAAACTATATAATATATGAT
Found at i:64461 original size:34 final size:34
Alignment explanation
Indices: 64404--64496 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 34
64394 AAAAAAGAAT
*
64404 TTTTGAAAACATATATACTATATAGTTAAAAAAAACA
1 TTTTG-AAATATATATA--ATATAGTTAAAAAAAACA
***
64441 TTTTGAAATATATATAATATAGTTTTCAAAAACA
1 TTTTGAAATATATATAATATAGTTAAAAAAAACA
* *
64475 TTTTAAAAATGTATATAATATA
1 TTTT-GAAATATATATAATATA
64497 TGCTTTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
34 19 0.39
35 15 0.31
36 10 0.20
37 5 0.10
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (34 bp):
TTTTGAAATATATATAATATAGTTAAAAAAAACA
Found at i:64490 original size:35 final size:36
Alignment explanation
Indices: 64434--64694 Score: 162
Period size: 35 Copynumber: 7.1 Consensus size: 36
64424 TATAGTTAAA
*
64434 AAAAACATTTT-GAAATATATATAATATA-G-TTTT
1 AAAAACATTTTAAAAATATATATAATATATGATTTT
* *
64467 CAAAAACATTTTAAAAATGTATATAATATATGCTTTTT
1 -AAAAACATTTTAAAAATATATATAATATATG-ATTTT
* *
64505 AAAAAACAATTTGAAAAATATTTATAATATAT-AGTTTT
1 -AAAAAC-ATTTTAAAAATATATATAATATATGA-TTTT
* * * *
64543 TAAAACATTTTGAAAA-CTATATAGTATATGATTTT
1 AAAAACATTTTAAAAATATATATAATATATGATTTT
* * *
64578 GAAAACATTTCTTAGAAAGTATGTATATAATATATAATTTT
1 AAAAACA-TT-TTA-AAA--ATATATATAATATATGATTTT
* *
64619 AAAATAC-TATTTCAAAATATATAT--TATAAGATTTT
1 AAAA-ACAT-TTTAAAAATATATATAATATATGATTTT
**** *
64654 -AATTTTTTTTAAAATATATATATAATATATTATTTT
1 AAAAACATTTTAAAA-ATATATATAATATATGATTTT
*
64690 TAAAA
1 AAAAA
64695 TGTTCTTTTT
Statistics
Matches: 176, Mismatches: 31, Indels: 37
0.72 0.13 0.15
Matches are distributed among these distances:
33 6 0.03
34 22 0.12
35 44 0.25
36 21 0.12
37 16 0.09
38 17 0.10
39 24 0.14
40 4 0.02
41 20 0.11
42 2 0.01
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (36 bp):
AAAAACATTTTAAAAATATATATAATATATGATTTT
Found at i:64508 original size:74 final size:75
Alignment explanation
Indices: 64429--64582 Score: 174
Period size: 74 Copynumber: 2.1 Consensus size: 75
64419 TACTATATAG
* *
64429 TTAAAAAAAACATTTTG-AAATATATAT-A-ATATAGTTTTCAAAAACATTTTAAAAATGTATAT
1 TTAAAAAAAACAATTTGAAAATATATATAATATATAGTTTT-AAAAACATTTTAAAAA-CTATAT
*
64491 AATATATGCTTT
64 AATATATGATTT
* * *
64503 TT--AAAAAACAATTTGAAAAATATTTATAATATATAGTTTTTAAAACATTTTGAAAACTATATA
1 TTAAAAAAAACAATTTG-AAAATATATATAATATATAGTTTTAAAAACATTTTAAAAACTATATA
*
64566 GTATATGATTT
65 ATATATGATTT
*
64577 TGAAAA
1 TTAAAA
64583 CATTTCTTAG
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
72 12 0.18
74 27 0.41
75 15 0.23
76 12 0.18
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (75 bp):
TTAAAAAAAACAATTTGAAAATATATATAATATATAGTTTTAAAAACATTTTAAAAACTATATAA
TATATGATTT
Found at i:64522 original size:39 final size:38
Alignment explanation
Indices: 64389--64565 Score: 140
Period size: 39 Copynumber: 4.8 Consensus size: 38
64379 TATGTAGGTT
*
64389 TTTTTAAAAAAGAATTTTTGAAAACATATATACT-ATATA-G
1 TTTTTAAAAAACAA--TTTGAAAA-ATATATA-TAATATATG
** *
64429 -TTAAAAAAAACATTTTG--AAATATATATAATATA-G
1 TTTTTAAAAAACAATTTGAAAAATATATATAATATATG
* * *
64463 -TTTTCAAAAAC-ATTTTAAAAATGTATATAATATATG
1 TTTTTAAAAAACAATTTGAAAAATATATATAATATATG
*
64499 CTTTTTAAAAAACAATTTGAAAAATATTTATAATATATAG
1 -TTTTTAAAAAACAATTTGAAAAATATATATAATATAT-G
* *
64539 TTTTT--AAAACATTTTGAAAACTATATA
1 TTTTTAAAAAACAATTTGAAAAATATATA
64566 GTATATGATT
Statistics
Matches: 112, Mismatches: 17, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
33 4 0.04
34 21 0.19
35 17 0.15
36 1 0.01
37 23 0.21
38 10 0.09
39 35 0.31
40 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (38 bp):
TTTTTAAAAAACAATTTGAAAAATATATATAATATATG
Found at i:64712 original size:6 final size:6
Alignment explanation
Indices: 64701--64738 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
64691 AAAATGTTCT
* *
64701 TTTTTA TTTTTA TTTTT- TATTTA TTTTTA TTATTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
64739 ATTTTTCAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:64736 original size:16 final size:17
Alignment explanation
Indices: 64703--64744 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
64693 AATGTTCTTT
*
64703 TTTATTTTTATTTTTTA
1 TTTATTTTTATTTATTA
64720 TTTATTTTTA-TTATTA
1 TTTATTTTTATTTATTA
64736 TTTATTTTT
1 TTTATTTTT
64745 CAGGTCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTATTTATTA
Found at i:65701 original size:9 final size:9
Alignment explanation
Indices: 65687--65711 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
65677 TTACAACCCT
65687 CTCTCTCTC
1 CTCTCTCTC
65696 CTCTCTCTC
1 CTCTCTCTC
65705 CTCTCTC
1 CTCTCTC
65712 GTCTTAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (9 bp):
CTCTCTCTC
Found at i:65812 original size:26 final size:26
Alignment explanation
Indices: 65782--65848 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
65772 ATGTATTGCA
* *
65782 AAACGATGTAGTTTTTCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
65808 AAACGACGTAGTTTTGCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
*
65834 AAATGACGTAGTTTT
1 AAACGACGTAGTTTT
65849 ATCCCATAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (26 bp):
AAACGACGTAGTTTTGCCACTGCAAG
Found at i:66014 original size:4 final size:4
Alignment explanation
Indices: 66005--66046 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
65995 CACTTTCTGC
* * *
66005 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TTAT ATAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
66047 TTTTGTTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:66203 original size:17 final size:17
Alignment explanation
Indices: 66178--66214 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
66168 TTATTATTAT
66178 TTTTATTTTTACT-AAA
1 TTTTATTTTTACTAAAA
66194 TTTTATTTTTACTAAAA
1 TTTTATTTTTACTAAAA
66211 TTTT
1 TTTT
66215 TCCCTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTATTTTTACTAAAA
Found at i:66917 original size:39 final size:36
Alignment explanation
Indices: 66833--67061 Score: 182
Period size: 35 Copynumber: 6.1 Consensus size: 36
66823 TGCTAATGGT
66833 TTTTGAAATAGATATATATTATATAGGTTTTTTTAAAAAAGCA
1 TTTTGAAA-A-ATATATATTATATA-G---TTTTAAAAAA-CA
66876 TTTTTGAAAACATATATATTATATAGTTTTAAAAAAACA
1 -TTTTGAAAA-ATATATATTATATAGTTTT-AAAAAACA
* *
66915 TTTTG--AAATATATATAATATAGTTTT-GAAAACA
1 TTTTGAAAAATATATATTATATAGTTTTAAAAAACA
* * *
66948 TTTTAAAAAAGTATATAATATATGGTTTTTAAAAAACA
1 TTTTGAAAAA-TATATATTATATAG-TTTTAAAAAACA
* * *
66986 GTTTGAAAAATATTTATAATATATAGTTTT-TAAAACA
1 TTTTGAAAAATA--TATATTATATAGTTTTAAAAAACA
* * *
67023 TTTTGAAAACTATATAGTATAT-GATTTT-GAAAACA
1 TTTTGAAAAATATATATTATATAG-TTTTAAAAAACA
67058 TTTT
1 TTTT
67062 TTTAGAAAGT
Statistics
Matches: 160, Mismatches: 16, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
33 10 0.06
34 1 0.01
35 44 0.28
36 13 0.08
37 22 0.14
38 23 0.14
39 17 0.11
40 6 0.04
42 1 0.01
43 15 0.09
44 8 0.05
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (36 bp):
TTTTGAAAAATATATATTATATAGTTTTAAAAAACA
Found at i:67037 original size:110 final size:110
Alignment explanation
Indices: 66862--67061 Score: 268
Period size: 110 Copynumber: 1.8 Consensus size: 110
66852 TATATAGGTT
* *
66862 TTTTTAAAAAAGCATTTTTGAAAACATATATATTATATAGTTTTAAAAAAACATTTTGAAATATA
1 TTTTTAAAAAAGCATGTTTGAAAACATATATAATATATAGTTTT-AAAAAACATTTTGAAATATA
66927 TA-TAATAT-AGTTTTGAAAACATTTTAAAAAAGTATATAATATATGG
65 TAGT-ATATGA-TTTTGAAAACATTTTAAAAAAGTATATAATATATGG
*
66973 TTTTTAAAAAA-CA-GTTTGAAAA-ATATTTATAATATATAGTTTT-TAAAACATTTTGAAAACT
1 TTTTTAAAAAAGCATGTTTGAAAACATA--TATAATATATAGTTTTAAAAAACATTTTG-AAA-T
67034 ATATAGTATATGATTTTGAAAACATTTT
62 ATATAGTATATGATTTTGAAAACATTTT
67062 TTTAGAAAGT
Statistics
Matches: 80, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
108 14 0.17
109 11 0.14
110 42 0.52
111 13 0.16
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (110 bp):
TTTTTAAAAAAGCATGTTTGAAAACATATATAATATATAGTTTTAAAAAACATTTTGAAATATAT
AGTATATGATTTTGAAAACATTTTAAAAAAGTATATAATATATGG
Found at i:67085 original size:75 final size:73
Alignment explanation
Indices: 66877--67127 Score: 192
Period size: 75 Copynumber: 3.4 Consensus size: 73
66867 AAAAAAGCAT
* * *
66877 TTTTGAAAACATATATATTATAT-AGTTTTAAAAAAACATTTTG--AAATA--TATATAATATAG
1 TTTTG-AAA-ATATATAATATATGA-TTTTGAAAAAACAGTTTGAAAAATATGTATATAATATAG
*
66937 TTTTGAAAACA
63 TTTTTAAAACA
* * * *
66948 TTTTAAAAAAGTATATAATATATGGTTTTTAAAAAACAGTTTGAAAAATATTTATA-ATATATAG
1 TTTT-GAAAA-TATATAATATATGATTTTGAAAAAACAGTTTGAAAAATATGTATATA-ATATAG
67012 TTTTTAAAACA
63 TTTTTAAAACA
* * *** * *
67023 TTTTGAAAACTATATAGTATATGATTTTGAAAACATTTTTTTAGAAAGTATGTATATAATATA-T
1 TTTTGAAAA-TATATAATATATGATTTTGAAAAAACAGTTTGA-AAAATATGTATATAATATAGT
*
67087 AATTTTAAAATA
64 --TTTTAAAACA
*
67099 TTATTTGAAAATATATATTATATGATTTT
1 -T-TTTGAAAATATATAATATATGATTTT
67128 AATTTTTTTA
Statistics
Matches: 146, Mismatches: 20, Indels: 22
0.78 0.11 0.12
Matches are distributed among these distances:
70 1 0.01
71 34 0.23
73 5 0.03
74 31 0.21
75 39 0.27
76 10 0.07
77 18 0.12
78 8 0.05
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (73 bp):
TTTTGAAAATATATAATATATGATTTTGAAAAAACAGTTTGAAAAATATGTATATAATATAGTTT
TTAAAACA
Found at i:67114 original size:35 final size:36
Alignment explanation
Indices: 66869--67158 Score: 102
Period size: 35 Copynumber: 7.9 Consensus size: 36
66859 GTTTTTTTAA
* *
66869 AAAAGCATT-TTTGAAAACATATATATTATATAGTTTT
1 AAAA-CATTATTTG-AAACATATATAATATATAATTTT
* ** * *
66906 AAAAAAACATTTTGAAATATATATAATATAGT--TTTG
1 AAAACATTA-TTTGAAACATATATAATATA-TAATTTT
* * **
66942 AAAACA-T-TTTAAAAAAGTATATAATATATGGTTTTT
1 AAAACATTATTTGAAACA-TATATAATATAT-AATTTT
** * *
66978 AAAA-AACAGTTTGAAAAATATTTATAATATATAGTTTTT
1 AAAACATTA-TTTGAAACATA--TATAATATATA-ATTTT
* *
67017 AAAACA-T-TTTGAAA-ACTATATAGTATATGATTTT
1 AAAACATTATTTGAAACA-TATATAATATATAATTTT
* *
67051 GAAAACATTTTTTTAGAAAGTATGTATATAATATATAATTTT
1 -AAAACA-TTATTT-GAAA-CA--TATATAATATATAATTTT
* * *
67093 AAAATATTATTTGAAA-ATATATATTATATGATTTT
1 AAAACATTATTTGAAACATATATAATATATAATTTT
* * *
67128 --AA-TTTTTTTAAAACATATATATATATATAAT
1 AAAACATTATTTGAAACATATATA-ATATATAAT
67159 ATATTATTTT
Statistics
Matches: 198, Mismatches: 30, Indels: 53
0.70 0.11 0.19
Matches are distributed among these distances:
32 8 0.04
33 17 0.09
34 22 0.11
35 32 0.16
36 17 0.09
37 31 0.16
38 16 0.08
39 27 0.14
40 6 0.03
41 6 0.03
42 16 0.08
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (36 bp):
AAAACATTATTTGAAACATATATAATATATAATTTT
Found at i:68457 original size:4 final size:4
Alignment explanation
Indices: 68448--68483 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
68438 CACTTTCTAC
* *
68448 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
68484 ATATATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:68466 original size:20 final size:20
Alignment explanation
Indices: 68443--68483 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
68433 TTAGTCACTT
68443 TCTACTTATTTATTTATTTA
1 TCTACTTATTTATTTATTTA
68463 TCTACTTATTTATTTATTTA
1 TCTACTTATTTATTTATTTA
68483 T
1 T
68484 ATATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (20 bp):
TCTACTTATTTATTTATTTA
Found at i:68700 original size:18 final size:19
Alignment explanation
Indices: 68677--68725 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
68667 TTTCTTTTGA
68677 CTTATTTCTTT-TATCTTC
1 CTTATTTCTTTATATCTTC
* *
68695 CTTATTT-TTTATTTTTTC
1 CTTATTTCTTTATATCTTC
68713 CTCTATTTCTTTA
1 CT-TATTTCTTTA
68726 ATTTTAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 3 0.12
18 14 0.54
19 5 0.19
20 4 0.15
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (19 bp):
CTTATTTCTTTATATCTTC
Found at i:68817 original size:3 final size:3
Alignment explanation
Indices: 68809--68835 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
68799 TATTTAGTTA
68809 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
68836 TTCTTGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:69434 original size:26 final size:26
Alignment explanation
Indices: 69394--69460 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
69384 ATGTATTGCA
* *
69394 AAACGACATAGTTTTTCCACTACAAG
1 AAACGACGTAGTTTTGCCACTACAAG
* *
69420 AAACGACGTAATTTTGCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTACAAG
*
69446 AAACGGCGTAGTTTT
1 AAACGACGTAGTTTT
69461 ATCCCATAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (26 bp):
AAACGACGTAGTTTTGCCACTACAAG
Found at i:69626 original size:4 final size:4
Alignment explanation
Indices: 69617--69658 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
69607 CACTTTCTGC
* * *
69617 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TTAT ATAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
69659 TTTGTTTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:69813 original size:6 final size:6
Alignment explanation
Indices: 69772--69798 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
69762 TTTATTTCCA
69772 TTATTT TTATTT TTATTT TTATTT TTA
1 TTATTT TTATTT TTATTT TTATTT TTA
69799 CTAAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:70525 original size:38 final size:38
Alignment explanation
Indices: 70458--70537 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 38
70448 TATAAGTTTT
* *
70458 TTTTATAAAAAGCATTTTTGAAAACATATATATTATATAG
1 TTTTAAAAAAAACATTTTTGAAAACATATATA--ATATAG
*
70498 TTTTAAAAAAAACA-TTTTG-AAATATATATAATATAG
1 TTTTAAAAAAAACATTTTTGAAAACATATATAATATAG
70534 TTTT
1 TTTT
70538 CGAAAACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 10 0.27
38 10 0.27
39 5 0.14
40 12 0.32
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (38 bp):
TTTTAAAAAAAACATTTTTGAAAACATATATAATATAG
Found at i:70628 original size:37 final size:36
Alignment explanation
Indices: 70522--70629 Score: 99
Period size: 37 Copynumber: 2.9 Consensus size: 36
70512 TTTTGAAATA
* * * * *
70522 TATATAATATAGTTTTCGAAAACATTTTATAAATGTT
1 TATAAAATATAGTTTT-TAAAACATTTGAAAAATATT
* *
70559 TATAAAATATGGTTTTTAAAAAATAGTTTGAAAAATATT
1 TATAAAATATAGTTTTT--AAAACA-TTTGAAAAATATT
*
70598 TATAATATATAGTTTTTAAAACATTCTGAAAA
1 TATAAAATATAGTTTTTAAAACATT-TGAAAA
70630 CTATATAGTA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
36 2 0.04
37 25 0.44
38 5 0.09
39 25 0.44
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
TATAAAATATAGTTTTTAAAACATTTGAAAAATATT
Found at i:70789 original size:15 final size:16
Alignment explanation
Indices: 70771--70813 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
70761 TAAAATGTTC
70771 TTTTTTATTTTTA-TA
1 TTTTTTATTTTTATTA
70786 TTTTTTATTTTTATTA
1 TTTTTTATTTTTATTA
* *
70802 TTATTTCTTTTT
1 TTTTTTATTTTT
70814 CAGGTCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTATTTTTATTA
Found at i:71658 original size:13 final size:14
Alignment explanation
Indices: 71634--71663 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
71624 ACGGGAACCA
71634 GGGGATATTTTTAG
1 GGGGATATTTTTAG
71648 GGGGATATTTTTAG
1 GGGGATATTTTTAG
71662 GG
1 GG
71664 CGTTGATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (14 bp):
GGGGATATTTTTAG
Found at i:72050 original size:8 final size:8
Alignment explanation
Indices: 72037--72086 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
72027 CACTTTCTGC
*
72037 TTATTTAT
1 TTATCTAT
*
72045 TTATTTAT
1 TTATCTAT
*
72053 TTATCTAC
1 TTATCTAT
*
72061 TTATCTAC
1 TTATCTAT
72069 TTATCTAT
1 TTATCTAT
*
72077 TTATATAT
1 TTATCTAT
72085 TT
1 TT
72087 GTTGTTTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATCTAT
Found at i:72205 original size:3 final size:3
Alignment explanation
Indices: 72199--72223 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
72189 TTTTATTTCC
72199 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
72224 CTAAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:72819 original size:2 final size:2
Alignment explanation
Indices: 72812--72878 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
72802 TTCGTCCGTA
72812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72854 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
72879 CTAATGGTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72967 original size:42 final size:42
Alignment explanation
Indices: 72886--72986 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
72876 ATACTAATGG
* ** *
72886 TTTTTGAAATAGATATATATTATATAGGTTTTTTTAAAAAGCA
1 TTTTTGAAA-ACATATATATTATATAGGTTTTTAAAAAAAACA
72929 TTTTTGAAAACATATATATTATATA-GTTTTTAAAAAAAAACA
1 TTTTTGAAAACATATATATTATATAGGTTTTT-AAAAAAAACA
*
72971 -TTTTG-AAATATATATA
1 TTTTTGAAAACATATATA
72987 AAATAGTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 10 0.19
41 11 0.21
42 22 0.42
43 9 0.17
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (42 bp):
TTTTTGAAAACATATATATTATATAGGTTTTTAAAAAAAACA
Found at i:73033 original size:37 final size:36
Alignment explanation
Indices: 72965--73118 Score: 129
Period size: 35 Copynumber: 4.3 Consensus size: 36
72955 TTTTTAAAAA
*
72965 AAAACATTTT-GAAATATATATAA-A-ATAGTTTTCG
1 AAAACATTTTAAAAATATATATAATATATAGTTTT-G
* * *
72999 AAAACATTTTAAAAATGTATATAATATATGGTTTTT
1 AAAACATTTTAAAAATATATATAATATATAGTTTTG
* * *
73035 AAAAAACTGTTTGAAAAATATTTATAATATATAGTTTTT
1 AAAACA-T-TTT-AAAAATATATATAATATATAGTTTTG
* * * *
73074 AAAGCATTTTGAAAA-CTATATAGTATAT-GATTTTG
1 AAAACATTTTAAAAATATATATAATATATAG-TTTTG
73109 AAAACATTTT
1 AAAACATTTT
73119 TTTAGAAAGT
Statistics
Matches: 97, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
34 11 0.11
35 34 0.35
36 10 0.10
37 11 0.11
38 4 0.04
39 27 0.28
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (36 bp):
AAAACATTTTAAAAATATATATAATATATAGTTTTG
Found at i:73101 original size:74 final size:71
Alignment explanation
Indices: 72923--73112 Score: 177
Period size: 75 Copynumber: 2.5 Consensus size: 71
72913 GTTTTTTTAA
* *
72923 AAAGCATTTTTGAAAACATATATATTATATAGTTTTTAAAAAAAAACATTTTGAAATATATATAA
1 AAAGCA-TTTTGAAAAC-TATATAATATATGGTTTTT---AAAAAACATTTTGAAATATATATAA
72988 AATAGTTTTCG
61 AATAGTTTTCG
* * * *
72999 AAAACATTTTAAAAATGTATATAATATATGGTTTTTAAAAAAC-TGTTTGAAAAATATTTATAAT
1 AAAGCATTTTGAAAA-CTATATAATATATGGTTTTTAAAAAACAT-TTTG--AAATATATATAA-
*
73063 ATATAGTTTT-T
61 A-ATAGTTTTCG
* * *
73074 AAAGCATTTTGAAAACTATATAGTATATGATTTTGAAAA
1 AAAGCATTTTGAAAACTATATAATATATGGTTTTTAAAA
73113 CATTTTTTTA
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
71 1 0.01
72 11 0.12
74 31 0.33
75 39 0.41
76 13 0.14
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (71 bp):
AAAGCATTTTGAAAACTATATAATATATGGTTTTTAAAAAACATTTTGAAATATATATAAAATAG
TTTTCG
Found at i:73137 original size:42 final size:36
Alignment explanation
Indices: 73090--73186 Score: 97
Period size: 42 Copynumber: 2.5 Consensus size: 36
73080 TTTTGAAAAC
*
73090 TATATAGTATATGATTTTGAAAACATTTTTTTAGAAAGTA
1 TATATA-TATATGATTTT-AAAACATTATTTTA-AAA-TA
* *
73130 TGTATATAATATATAATTTTAAAATATTATTTTAAAATA
1 --TATAT-ATATATGATTTTAAAACATTATTTTAAAATA
73169 TATAT-TATATGATTTTAA
1 TATATATATATGATTTTAA
73187 TTTTTTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
35 12 0.24
37 5 0.10
39 2 0.04
40 3 0.06
41 12 0.24
42 15 0.30
43 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.48
Consensus pattern (36 bp):
TATATATATATGATTTTAAAACATTATTTTAAAATA
Found at i:73161 original size:13 final size:13
Alignment explanation
Indices: 73140--73174 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
73130 TGTATATAAT
*
73140 ATATAATTTTAAA
1 ATATTATTTTAAA
73153 ATATTATTTTAAA
1 ATATTATTTTAAA
73166 ATATATATT
1 ATAT-TATT
73175 ATATGATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTATTTTAAA
Found at i:73242 original size:6 final size:6
Alignment explanation
Indices: 73231--73268 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
73221 AAAATGTTCT
* *
73231 TTTTTA TTTTTA TTTTTA TATTTA TTTTT- TTATTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
73269 CTTTTTCAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:74642 original size:25 final size:27
Alignment explanation
Indices: 74614--74682 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
74604 ATATCTAACC
*
74614 TTTTTAGTTTTTTATTT-CA-T-TTAGA
1 TTTTTATTTTTTTATTTCCATTATTA-A
*
74639 -TTTTATTTTTTTTATTTCCATTATTAT
1 TTTTTA-TTTTTTTATTTCCATTATTAA
74666 TTTTTATTTTTTTATTT
1 TTTTTATTTTTTTATTT
74683 TTACTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 5 0.14
25 10 0.27
26 2 0.05
27 12 0.32
28 8 0.22
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTTATTTTTTTATTTCCATTATTAA
Done.