Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003416.1 Hibiscus syriacus cultivar Beakdansim tig00007194_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: 63971
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:5015 original size:2 final size:2
Alignment explanation
Indices: 5008--5039 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4998 TCTTTAAAAC
5008 AT AT AT AT -T 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 AT AT AT AT A
5040 CCCCCATCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5226 original size:24 final size:24
Alignment explanation
Indices: 5199--5304 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
5189 AAACGGAGAT
*
5199 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
5223 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * * *
5247 GTTAGGAATCATATCAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
5271 ATCAGATGTCAAAAC-GAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
5294 ATCAGAAATCA
1 ATCAGAAATCA
5305 GATAAAATTC
Statistics
Matches: 60, Mismatches: 22, Indels: 1
0.72 0.27 0.01
Matches are distributed among these distances:
23 15 0.25
24 45 0.75
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:9745 original size:17 final size:17
Alignment explanation
Indices: 9672--9747 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
9662 ACAACATAAA
* *
9672 AAAAGGAGTTGTAACCT
1 AAAATGAGTTGCAACCT
* * * *
9689 ATAATGTGGTGCAAACT
1 AAAATGAGTTGCAACCT
* * *
9706 AAAATGAGATACAGCCAT
1 AAAATGAGTTGCAACC-T
9724 AAAATGAGTTGCAACCT
1 AAAATGAGTTGCAACCT
9741 AAAATGA
1 AAAATGA
9748 CAATCATAAA
Statistics
Matches: 43, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
17 29 0.67
18 14 0.33
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (17 bp):
AAAATGAGTTGCAACCT
Found at i:10236 original size:37 final size:37
Alignment explanation
Indices: 10186--10260 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
10176 TAAATATAAA
10186 TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
1 TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
10223 TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
1 TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
10260 T
1 T
10261 ATTATCTGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (37 bp):
TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
Found at i:10514 original size:3 final size:3
Alignment explanation
Indices: 10508--10539 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
10498 AAATAATAAC
10508 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
10540 TGTATTAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12260 original size:26 final size:27
Alignment explanation
Indices: 12226--12286 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
12216 GGTTTATAAC
*
12226 TATTTAT-CA-ATAATCATTTATTATAT
1 TATTTATACAGATAAT-ATTTATAATAT
12252 TATTTATCACATGATAATATTTATAATAT
1 TATTTAT-ACA-GATAATATTTATAATAT
12281 TATTTA
1 TATTTA
12287 GCTATAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.23
28 2 0.07
29 16 0.53
30 5 0.17
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (27 bp):
TATTTATACAGATAATATTTATAATAT
Found at i:19434 original size:21 final size:21
Alignment explanation
Indices: 19408--19459 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
19398 GAAGTAAGTA
19408 TCGATACTCATTTAAAGGGAG
1 TCGATACTCATTTAAAGGGAG
*
19429 TCGATACTCATTTAATGGGAG
1 TCGATACTCATTTAAAGGGAG
19450 TCGATACTCA
1 TCGATACTCA
19460 GGGTCTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (21 bp):
TCGATACTCATTTAAAGGGAG
Found at i:23183 original size:5 final size:6
Alignment explanation
Indices: 23170--23206 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
23160 CGTTTCTTAA
23170 TTTATT TTTA-T TTTATT TTTA-T TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
23207 CTTGAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:23186 original size:11 final size:11
Alignment explanation
Indices: 23150--23205 Score: 76
Period size: 11 Copynumber: 4.9 Consensus size: 11
23140 AGCTAACCCC
*
23150 TTTTTATTTTCG
1 TTTTTATTTT-A
*
23162 TTTCTTAATTTA
1 TTT-TTATTTTA
23174 TTTTTATTTTA
1 TTTTTATTTTA
23185 TTTTTATTTTA
1 TTTTTATTTTA
23196 TTTTTATTTT
1 TTTTTATTTT
23206 TCTTGAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 28 0.70
12 6 0.15
13 6 0.15
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:23192 original size:17 final size:17
Alignment explanation
Indices: 23170--23206 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
23160 CGTTTCTTAA
23170 TTTATTTTTATTTTATT
1 TTTATTTTTATTTTATT
23187 TTTA-TTTTATTTTTATT
1 TTTATTTTTA-TTTTATT
23204 TTT
1 TTT
23207 CTTGAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTATTTTTATTTTATT
Found at i:23215 original size:22 final size:21
Alignment explanation
Indices: 23162--23216 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
23152 TTTATTTTCG
23162 TTTCTTAA-TTTATTTTTATT
1 TTTCTTAATTTTATTTTTATT
* *
23182 TTATTTTTATTTTATTTTTATT
1 TT-TCTTAATTTTATTTTTATT
23204 TTTCTTGAATTTT
1 TTTCTT-AATTTT
23217 CAAGTACCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 7 0.25
22 19 0.68
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTCTTAATTTTATTTTTATT
Found at i:27248 original size:18 final size:18
Alignment explanation
Indices: 27209--27254 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
27199 AAATTCTAGG
27209 GTTTTA-TTTTATTTCAA
1 GTTTTATTTTTATTTCAA
*
27226 CTTTTATTTTTACTTT-AA
1 GTTTTATTTTTA-TTTCAA
27244 GTTTTTATTTT
1 G-TTTTATTTT
27255 CTTTTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.21
18 7 0.29
19 12 0.50
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (18 bp):
GTTTTATTTTTATTTCAA
Found at i:28937 original size:20 final size:20
Alignment explanation
Indices: 28894--28961 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
28884 CATGATGAAG
28894 GTATCGATACTGTA-CCA-GTA
1 GTATCGATACTG-ACCCATG-A
*
28914 GTATCGATACTGACCCATGG
1 GTATCGATACTGACCCATGA
*
28934 GTATC-ATACTCACCC-TGA
1 GTATCGATACTGACCCATGA
28952 GTATCGATAC
1 GTATCGATAC
28962 CAAATATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.17
19 14 0.33
20 20 0.48
21 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (20 bp):
GTATCGATACTGACCCATGA
Found at i:28948 original size:19 final size:19
Alignment explanation
Indices: 28913--28961 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
28903 CTGTACCAGT
*
28913 AGTATCGATACTGACCCATG
1 AGTATCGATACTCACCC-TG
*
28933 GGTATC-ATACTCACCCTG
1 AGTATCGATACTCACCCTG
28951 AGTATCGATAC
1 AGTATCGATAC
28962 CAAATATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 7 0.28
19 13 0.52
20 5 0.20
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (19 bp):
AGTATCGATACTCACCCTG
Found at i:30302 original size:39 final size:39
Alignment explanation
Indices: 30245--30334 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 39
30235 AGGACCTGTA
* *
30245 GTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGCG
1 GTAAGGACTTACCCTGAGCACAAAGCCGAGGAACATGCG
* *
30284 GTAAGGACTTACCTTGAGCACAAAGCTGAGGAACATGCG
1 GTAAGGACTTACCCTGAGCACAAAGCCGAGGAACATGCG
* *
30323 GGACGGACTTAC
1 GTAAGGACTTAC
30335 AAGTCATAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.16
Consensus pattern (39 bp):
GTAAGGACTTACCCTGAGCACAAAGCCGAGGAACATGCG
Found at i:37033 original size:39 final size:39
Alignment explanation
Indices: 36975--37070 Score: 138
Period size: 39 Copynumber: 2.5 Consensus size: 39
36965 GTCATAAGGA
* *
36975 CCTGCGGTAAGGACATACCCTGAGCACAAAGCCAAAGAG
1 CCTGCGGTAAGGACTTACCCTGAGCAAAAAGCCAAAGAG
* * * *
37014 CCTGCGATTAGGACTTACCCTGAGCAAAAAGCCGAGGAG
1 CCTGCGGTAAGGACTTACCCTGAGCAAAAAGCCAAAGAG
37053 CCTGCGGTAAGGACTTAC
1 CCTGCGGTAAGGACTTAC
37071 AAGTCATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.15
Consensus pattern (39 bp):
CCTGCGGTAAGGACTTACCCTGAGCAAAAAGCCAAAGAG
Found at i:39585 original size:17 final size:17
Alignment explanation
Indices: 39563--39598 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
39553 TGCTTGAGTA
39563 AAGAGAATGAGAAGAAG
1 AAGAGAATGAGAAGAAG
39580 AAGAGAATGAGAAGAAG
1 AAGAGAATGAGAAGAAG
39597 AA
1 AA
39599 AAGTGAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (17 bp):
AAGAGAATGAGAAGAAG
Found at i:39612 original size:17 final size:19
Alignment explanation
Indices: 39563--39613 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 19
39553 TGCTTGAGTA
39563 AAGAGAAT--GAGAAGAAG
1 AAGAGAATGAGAGAAGAAG
39580 AAGAGAATGAGAAGAAGAA-
1 AAGAGAATGAG-AGAAGAAG
*
39599 AAGTGAA-GAGAGAAG
1 AAGAGAATGAGAGAAG
39614 TGAAGAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 13 0.43
18 3 0.10
19 7 0.23
20 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.06
Consensus pattern (19 bp):
AAGAGAATGAGAGAAGAAG
Found at i:39614 original size:12 final size:13
Alignment explanation
Indices: 39576--39625 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
39566 AGAATGAGAA
*
39576 GAAGAAGAGAATGA
1 GAAGAAGAGAA-GT
*
39590 GAAGAAGAAAAGT
1 GAAGAAGAGAAGT
39603 GAAG-AGAGAAGT
1 GAAGAAGAGAAGT
39615 GAAG-AGAGAAG
1 GAAGAAGAGAAG
39626 ATAAGAGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 18 0.55
13 5 0.15
14 10 0.30
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.06
Consensus pattern (13 bp):
GAAGAAGAGAAGT
Found at i:39625 original size:43 final size:42
Alignment explanation
Indices: 39564--39647 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 42
39554 GCTTGAGTAA
39564 AGAGAATGAGAAGAAGAAGAGAATGA-GAAGAAGAAAAGTGAAG
1 AGAGAATGAGAAGAAGAAGAGAA-GAGGAAGAAGAAAA-TGAAG
* * *
39607 AGAGAA-GTGAAGAGAGAAGATAAGAGGAAGAAGGAAATGAA
1 AGAGAATGAGAAGA-AGAAGAGAAGAGGAAGAAGAAAATGAA
39648 CCCTTTTTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 12 0.33
43 24 0.67
ACGTcount: A:0.57, C:0.00, G:0.36, T:0.07
Consensus pattern (42 bp):
AGAGAATGAGAAGAAGAAGAGAAGAGGAAGAAGAAAATGAAG
Found at i:39631 original size:12 final size:13
Alignment explanation
Indices: 39571--39637 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 13
39561 TAAAGAGAAT
*
39571 GAGAAGAAGAAGA
1 GAGAAGATGAAGA
*
39584 GA-ATGA-GAAGA
1 GAGAAGATGAAGA
*
39595 -AGAAAAGTGAAGA
1 GAGAAGA-TGAAGA
39608 GAGAAG-TGAAGA
1 GAGAAGATGAAGA
39620 GAGAAGAT-AAGA
1 GAGAAGATGAAGA
39632 G-GAAGA
1 GAGAAGA
39638 AGGAAATGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
10 1 0.02
11 12 0.27
12 20 0.44
13 8 0.18
14 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.06
Consensus pattern (13 bp):
GAGAAGATGAAGA
Found at i:41945 original size:2 final size:2
Alignment explanation
Indices: 41938--41965 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41928 TCTTTTTACA
41938 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
41966 TATTAGATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46506 original size:5 final size:5
Alignment explanation
Indices: 46496--46524 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
46486 ATCAATAGCA
46496 TGCAT TGCAT TGCAT TGCAT TGCAT TGCA
1 TGCAT TGCAT TGCAT TGCAT TGCAT TGCA
46525 ACCTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (5 bp):
TGCAT
Found at i:46994 original size:63 final size:63
Alignment explanation
Indices: 46869--47003 Score: 164
Period size: 63 Copynumber: 2.1 Consensus size: 63
46859 TTTTTCAACC
* * ***
46869 TGGAGTCTAGCTTCAATTTTTTTTATTTCTAGTCGATCATAAAAATTTTAAGCTCGTGAGCTT
1 TGGAGTCAAGCTTCAATTTTTTTTATTTCTAGTCGATCATAAAAATTTTAAACTCACAAGCTT
* * * *
46932 TGGAGTCAAGTTTTAATTTTTTTTATTTCTAGTCGAGT-TTAACAATTTTAAACTCACAAGCTT
1 TGGAGTCAAGCTTCAATTTTTTTTATTTCTAGTCGA-TCATAAAAATTTTAAACTCACAAGCTT
*
46995 TCGAGTCAA
1 TGGAGTCAA
47004 CTCGAGCTCA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
63 60 0.98
64 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (63 bp):
TGGAGTCAAGCTTCAATTTTTTTTATTTCTAGTCGATCATAAAAATTTTAAACTCACAAGCTT
Found at i:51783 original size:29 final size:28
Alignment explanation
Indices: 51751--51837 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
51741 TCTTTTTCAT
51751 TAAATACTTAAAGCATTTTTTTGTCAAAA
1 TAAATACTTAAAG-ATTTTTTTGTCAAAA
*
51780 TAAATA-TATAAAG-TTATTTTTAGTCACAA
1 TAAATACT-TAAAGATT-TTTTT-GTCAAAA
* *
51809 T-AATACATAAAG-TATTTTATGTCAAAA
1 TAAATACTTAAAGAT-TTTTTTGTCAAAA
51836 TA
1 TA
51838 GATGTCTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
27 9 0.19
28 20 0.42
29 19 0.40
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (28 bp):
TAAATACTTAAAGATTTTTTTGTCAAAA
Found at i:51813 original size:28 final size:28
Alignment explanation
Indices: 51751--51837 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 28
51741 TCTTTTTCAT
* * *
51751 TAAATACTTAAAGCATTTTTTTGTCAAAA
1 TAAATACATAAAGTA-TTTTTAGTCAAAA
* *
51780 TAAATATATAAAGTTATTTTTAGTCACAA
1 TAAATACATAAAG-TATTTTTAGTCAAAA
51809 T-AATACATAAAGTA-TTTTATGTCAAAA
1 TAAATACATAAAGTATTTTTA-GTCAAAA
51836 TA
1 TA
51838 GATGTCTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
26 5 0.10
27 9 0.19
28 10 0.21
29 23 0.48
30 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (28 bp):
TAAATACATAAAGTATTTTTAGTCAAAA
Found at i:52035 original size:30 final size:30
Alignment explanation
Indices: 51928--52042 Score: 117
Period size: 30 Copynumber: 3.8 Consensus size: 30
51918 TTAGATAAAA
* *
51928 AAAATAAAATACTTTAGGTACTTATTTTGATC
1 AAAA-AAAATAATTTAAGTACTTATTTTGA-C
** * *
51960 -AAAAAAAT-ATTTTTGCTGCATATTTTGAC
1 AAAAAAAATAATTTAAG-TACTTATTTTGAC
*
51989 AAAAAACATAACTTTAAGTACTTATTTTGAC
1 AAAAAAAATAA-TTTAAGTACTTATTTTGAC
52020 AAAAAAAATAATTTAAGTACTTA
1 AAAAAAAATAATTTAAGTACTTA
52043 AGTAAAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
29 5 0.07
30 34 0.50
31 25 0.37
32 4 0.06
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (30 bp):
AAAAAAAATAATTTAAGTACTTATTTTGAC
Found at i:52112 original size:3 final size:3
Alignment explanation
Indices: 52104--52155 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
52094 ATAACCCTAT
52104 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52152 TTA T
1 TTA T
52156 AACGGCTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54258 original size:9 final size:9
Alignment explanation
Indices: 54217--54277 Score: 61
Period size: 9 Copynumber: 6.6 Consensus size: 9
54207 CTACAAAAAA
54217 TTTTATTAT
1 TTTTATTAT
*
54226 ATTATATTCAT
1 -TTTTATT-AT
54237 TTATTATTAT
1 TT-TTATTAT
*
54247 TTTTAATAT
1 TTTTATTAT
*
54256 TTTTTTTA-
1 TTTTATTAT
54264 TTTTATTAT
1 TTTTATTAT
54273 TTTTA
1 TTTTA
54278 CAGGCCCCAC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
8 7 0.17
9 17 0.40
10 12 0.29
11 6 0.14
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATTAT
Found at i:54375 original size:32 final size:33
Alignment explanation
Indices: 54327--54407 Score: 121
Period size: 32 Copynumber: 2.5 Consensus size: 33
54317 GAAAATAAAT
54327 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
*
54360 CAACGTA-TTGAGTCCTATTGAAATACTAAAAC
1 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
*
54392 CGAA-GCATTTGAGTCC
1 C-AACGTATTTGAGTCC
54408 AAGTAGGACT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 27 0.61
33 17 0.39
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTGAAACACTAAAAC
Found at i:54934 original size:7 final size:7
Alignment explanation
Indices: 54922--54982 Score: 83
Period size: 7 Copynumber: 8.9 Consensus size: 7
54912 ATGATAATAC
54922 ATTATTT
1 ATTATTT
54929 ATTATTT
1 ATTATTT
54936 ATT-TATT
1 ATTAT-TT
54943 ATTATTT
1 ATTATTT
54950 ATTTATTT
1 A-TTATTT
54958 ATTATTT
1 ATTATTT
54965 A-T-TTT
1 ATTATTT
54970 ATTATTT
1 ATTATTT
54977 ATTATT
1 ATTATT
54983 CATTTTTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.08
6 3 0.06
7 34 0.69
8 8 0.16
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTATTT
Found at i:54937 original size:4 final size:4
Alignment explanation
Indices: 54923--54979 Score: 70
Period size: 4 Copynumber: 15.2 Consensus size: 4
54913 TGATAATACA
54923 TTAT TTA- TTAT TTAT TTA- TTA- TTAT TTAT TTAT TTA- TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
54967 TT-T ATTAT TTAT T
1 TTAT -TTAT TTAT T
54980 ATTCATTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
3 13 0.27
4 34 0.71
5 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:54939 original size:11 final size:11
Alignment explanation
Indices: 54923--54979 Score: 77
Period size: 11 Copynumber: 5.5 Consensus size: 11
54913 TGATAATACA
54923 TTATTTATTAT
1 TTATTTATTAT
54934 TTATTTATTA-
1 TTATTTATTAT
54944 TTA--T-TTAT
1 TTATTTATTAT
54952 TTATTTATTAT
1 TTATTTATTAT
54963 TTATTTTATTAT
1 TTA-TTTATTAT
54975 TTATT
1 TTATT
54980 ATTCATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
10 4 0.10
11 19 0.46
12 11 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:54987 original size:11 final size:10
Alignment explanation
Indices: 54922--54987 Score: 77
Period size: 10 Copynumber: 6.7 Consensus size: 10
54912 ATGATAATAC
54922 ATTATTTATT
1 ATTATTTATT
54932 ATTTATTTATT
1 A-TTATTTATT
54943 ATTATTTA-T
1 ATTATTTATT
54952 -TTATTTATT
1 ATTATTTATT
54961 ATT-TATT-TT
1 ATTAT-TTATT
54970 ATTATTTATT
1 ATTATTTATT
54980 ATTCATTT
1 ATT-ATTT
54988 TTTTCTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.14
9 10 0.20
10 18 0.37
11 14 0.29
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTATTTATT
Found at i:54988 original size:19 final size:19
Alignment explanation
Indices: 54930--54988 Score: 86
Period size: 19 Copynumber: 3.1 Consensus size: 19
54920 ACATTATTTA
54930 TTATTTATTTATTATTA-T
1 TTATTTATTTATTATTATT
54948 TTATTTATTTATTATTTATT
1 TTATTTATTTATTA-TTATT
54968 TTA-TTATTTATTATTCATT
1 TTATTTATTTATTATT-ATT
54987 TT
1 TT
54989 TTTCTTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 16 0.42
19 18 0.47
20 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTTATTTATTATTATT
Found at i:57523 original size:110 final size:106
Alignment explanation
Indices: 57333--57538 Score: 259
Period size: 110 Copynumber: 1.9 Consensus size: 106
57323 GATGGTGGTT
* * *
57333 GCTCAACTTCACAACGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTTATTTAGAGTAAATT
1 GCTCAACTTCACAACGAAGGGGCGACTGTCAACAAACAACTTTGCAGTTTCATTCAGAGTAAATT
*
57398 TCAACTTCACAGCGAAAGATATTGGACTCGAGACAATACAA
66 TCAACTTCACAGCGAAAGAGATTGGACTCGAGACAATACAA
* * * * *
57439 GCTCAACTTTACAGCGAATGGGCGACTGATTATCAATAAACAACTTTGCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAACGAAGGGGCGACTG----TCAACAAACAACTTTGCAGTTTCATTCAGAGTA
* * * *
57504 AATTTTAACTTCGCGGCGAAGGAGATTGGACTCGA
62 AATTTCAACTTCACAGCGAAAGAGATTGGACTCGA
57539 AACGACATAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
106 25 0.30
110 58 0.70
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (106 bp):
GCTCAACTTCACAACGAAGGGGCGACTGTCAACAAACAACTTTGCAGTTTCATTCAGAGTAAATT
TCAACTTCACAGCGAAAGAGATTGGACTCGAGACAATACAA
Found at i:58234 original size:111 final size:111
Alignment explanation
Indices: 57861--58393 Score: 715
Period size: 111 Copynumber: 4.9 Consensus size: 111
57851 GCTTCCCAGT
* * *
57861 TTCATAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
* * ** * *
57926 CAACGAAGGGGCGACTGGTTGTCAATAAACAACTTC-CCAG--T--
66 CAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGTTTCA
* * *
57967 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGATAGCACAAGCTCAACTTCA
1 TTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
*
58032 CAGCGAAGGGGCAGCTGACTGTCAACAAACAAC-TCTTCAGTTTCA
66 CAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGTTTCA
* * * *
58077 TTCAGAG-TCAATTTCAACTACACAGCGAAGAATATTGAACTCAAGACATCACAAGCTCAACTTC
1 TTCAGAGCT-AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTC
*
58141 ACAGTGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGTTTCA
65 ACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGTTTCA
*
58188 TTCAGAGCTAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
* * * * * * *
58253 CAGCGAAGGGTCGACTGACTATCAACAAACAACTTATTTAGCTCCA
66 CAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGTTTCA
* *
58299 TTCAGAG-TCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
1 TTCAGAGCT-AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTC
* *
58363 ACAGAGAA-GGGCGGCTGACTATCAACAAACA
65 ACAGCGAAGGGGCGGCTGACTGTCAACAAACA
58394 TTTCCTAGCT
Statistics
Matches: 380, Mismatches: 38, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
105 2 0.01
106 91 0.24
108 1 0.00
110 111 0.29
111 174 0.46
112 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (111 bp):
TTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
CAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGTTTCA
Found at i:58250 original size:221 final size:217
Alignment explanation
Indices: 57869--58425 Score: 746
Period size: 221 Copynumber: 2.6 Consensus size: 217
57859 GTTTCATAGC
*
57869 CAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACA-ACGAA
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGA-GAA
* ** *
57933 GGGGCGACTGGTTGTCAATAAACAACTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGG
65 GGGGCGGCTGACTGTCAACAAACAACTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGG
* * * *
57998 ATATTGGACTCAAGATAGCACAAGCTCAACTTCACAGCGAAGGGGC-AGCTGACTGTCAACAAAC
130 ACATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGA-CTGACTATCAACAAAC
* * *
58062 AAC-TCTTCAGTTTCATTCAGAGT
194 AACTTATTCAGCTCCATTCAGAGT
* * * * *
58085 CAATTTCAACTACACAGCGAAGAATATTGAACTCAAGACATCACAAGCTCAACTTCACAGTGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGAGAAG
* *
58150 GGGCGGCTGACTGTCAACAAACAACTTCTTCAGTTTCATTCAGAGCTAATTTCAACTTCACAGCG
66 GGGCGGCTGACTGTCAACAAACAACTTC-CCAG--T--TTCAGAGCCAATTTCAACTTCACAGCG
*
58215 AAGGACATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGTCGACTGACTATCAACA
126 AAGGACATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTATCAACA
*
58280 AACAACTTATTTAGCTCCATTCAGAGT
191 AACAACTTATTCAGCTCCATTCAGAGT
* *
58307 CAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGAGAA-
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGAGAAG
* * * * * **
58371 GGGCGGCTGACTATCAACAAAC-ATTTCCTAGCTCCAGATTCAATTTCAACTTCAC
66 GGGCGGCTGACTGTCAACAAACAACTTCCCAGTTTCAGAGCCAATTTCAACTTCAC
58426 GACGGAGGAT
Statistics
Matches: 296, Mismatches: 37, Indels: 17
0.85 0.11 0.05
Matches are distributed among these distances:
215 19 0.06
216 82 0.28
217 3 0.01
219 3 0.01
220 4 0.01
221 111 0.38
222 74 0.25
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (217 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGAGAAG
GGGCGGCTGACTGTCAACAAACAACTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
CATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTATCAACAAACAA
CTTATTCAGCTCCATTCAGAGT
Found at i:59015 original size:37 final size:36
Alignment explanation
Indices: 58957--59038 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 36
58947 AGTCATCTCT
58957 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
*
58993 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCC
59030 CTTGAAACA
1 CTTGAAACA
59039 CCAATCTTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 11 0.25
37 33 0.75
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
Found at i:59092 original size:64 final size:67
Alignment explanation
Indices: 58987--59135 Score: 189
Period size: 67 Copynumber: 2.2 Consensus size: 67
58977 TCTTGAGACA
* * * * *
58987 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAC-CAATCTTTGAA
1 GTTTCTCTTGAAACAAAGATTTG-CTCTCTGGAGACAGTTTCTCTTGAAACACAAAACCTTTGAA
59051 -TAT
65 GT-T
59054 GTTTCTCTTGAAACAAA-ATTTG-TCTCTGGAGACAGTTTCTCTTGAAACACAAAAAACCTTTGA
1 GTTTCTCTTGAAACAAAGATTTGCTCTCTGGAGACAGTTTCTCTTGAAACAC--AAAACCTTTGA
59117 AGTT
64 AGTT
59121 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
59136 CAAAAAACCT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
64 27 0.37
66 4 0.05
67 41 0.56
68 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (67 bp):
GTTTCTCTTGAAACAAAGATTTGCTCTCTGGAGACAGTTTCTCTTGAAACACAAAACCTTTGAAG
TT
Found at i:59130 original size:33 final size:32
Alignment explanation
Indices: 59088--59207 Score: 147
Period size: 33 Copynumber: 3.8 Consensus size: 32
59078 TCTGGAGACA
* *
59088 GTTTCTCTTGAAACACAAAAAACCTTTGAAGTT
1 GTTTCTCTTGAAACA-AAAAAACCTTTGAAATC
*
59121 GTTTCTCTTGAAACACAAAAAACCTTTAAAATC
1 GTTTCTCTTGAAACA-AAAAAACCTTTGAAATC
*
59154 GTTTCTCTTG--A-AAAAAAACCTTTGAAAAC
1 GTTTCTCTTGAAACAAAAAAACCTTTGAAATC
* *
59183 ATTTCTCTTGAAACAAAAAGACCTT
1 GTTTCTCTTGAAACAAAAAAACCTT
59208 CGAGTTCGAC
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
29 24 0.31
30 1 0.01
31 2 0.03
32 10 0.13
33 40 0.52
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (32 bp):
GTTTCTCTTGAAACAAAAAAACCTTTGAAATC
Found at i:59171 original size:29 final size:29
Alignment explanation
Indices: 59104--59201 Score: 99
Period size: 29 Copynumber: 3.2 Consensus size: 29
59094 CTTGAAACAC
* * *
59104 AAAAAACCTTTGAAGTTGTTTCTCTTGAAACA
1 AAAAAACCTTTAAAATCGTTTCTCTTG--A-A
59136 CAAAAAACCTTTAAAATCGTTTCTCTTGAA
1 -AAAAAACCTTTAAAATCGTTTCTCTTGAA
*
59166 AAAAAACCTTTGAAAA-CATTTCTCTTGAA
1 AAAAAACCTTT-AAAATCGTTTCTCTTGAA
59195 ACAAAAA
1 A-AAAAA
59202 GACCTTCGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
29 24 0.41
30 10 0.17
31 1 0.02
33 24 0.41
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (29 bp):
AAAAAACCTTTAAAATCGTTTCTCTTGAA
Found at i:59352 original size:83 final size:83
Alignment explanation
Indices: 59199--59466 Score: 374
Period size: 83 Copynumber: 3.2 Consensus size: 83
59189 CTTGAAACAA
* *
59199 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTACAGCATAACTCAAGGCTA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGACTA
*
59264 GAAGGGTTATATGCCAAC
66 GAAGGGTTATCTGCCAAC
* * * * * ** * * *
59282 AAAGACCTTCGAGTTCAACCATGCTCAGCTCAAAGGCACATCATTTGCAGCATGGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGACTA
* *
59347 TAAGGGTTATCTGCTAAC
66 GAAGGGTTATCTGCCAAC
*
59365 AAAGAACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTACAGCATAACTCAAGACT
1 AAAG-ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGACT
*
59430 AGAAGGGTTATCTGTCAAC
65 AGAAGGGTTATCTGCCAAC
59449 AAAGACCTTCGAGTTCGA
1 AAAGACCTTCGAGTTCGA
59467 TTCCATTCAG
Statistics
Matches: 156, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
83 87 0.56
84 69 0.44
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGACTA
GAAGGGTTATCTGCCAAC
Found at i:59831 original size:22 final size:20
Alignment explanation
Indices: 59806--59853 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
59796 TCTACAAAAA
59806 TATTTATTATATATTTAATTAT
1 TATTTATTAT-TATTTAATT-T
*
59828 TA-TTATTATTATTTTATTT
1 TATTTATTATTATTTAATTT
59847 T-TTTATT
1 TATTTATT
59854 TTTACAGGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.29
20 8 0.33
21 7 0.29
22 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTATTATTATTTAATTT
Found at i:59989 original size:32 final size:33
Alignment explanation
Indices: 59901--60020 Score: 181
Period size: 33 Copynumber: 3.7 Consensus size: 33
59891 ATTCAGAAAA
*
59901 TAAAATCAACGTATTTGAGTCCTATTGAAACAC
1 TAAAACCAACGTATTTGAGTCCTATTGAAACAC
59934 TAAAACCAACGTATTTGAGTCCTATTGAAACAC
1 TAAAACCAACGTATTTGAGTCCTATTGAAACAC
*
59967 TAAAACCAACGTA-TTGAGTCCTATTAAAACAC
1 TAAAACCAACGTATTTGAGTCCTATTGAAACAC
* *
59999 TAAAATCGAA-GCATTTGAGTCC
1 TAAAA-CCAACGTATTTGAGTCC
60021 AAGTAGGACT
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
32 25 0.31
33 56 0.69
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (33 bp):
TAAAACCAACGTATTTGAGTCCTATTGAAACAC
Found at i:60564 original size:7 final size:7
Alignment explanation
Indices: 60552--60615 Score: 66
Period size: 7 Copynumber: 9.6 Consensus size: 7
60542 TGATAATACA
60552 TATTTAT
1 TATTTAT
60559 TATTTATT
1 TATTTA-T
60567 TATTTAT
1 TATTTAT
60574 T-TATTAT
1 TAT-TTAT
60581 TATTTA-
1 TATTTAT
60587 T-TTTAT
1 TATTTAT
*
60593 T-TTTTT
1 TATTTAT
60599 TA-TTAT
1 TATTTAT
60605 TATTTAT
1 TATTTAT
60612 TATT
1 TATT
60616 CATTTTTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 4 0.08
6 13 0.27
7 24 0.49
8 8 0.16
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TATTTAT
Found at i:60565 original size:4 final size:4
Alignment explanation
Indices: 60552--60612 Score: 60
Period size: 4 Copynumber: 16.0 Consensus size: 4
60542 TGATAATACA
60552 TATT TA-T TATT TATT TATT TATT TA-T TA-T TATT TATTT TATT T-TT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TA-TT TATT TATT
*
60597 TTTAT TA-T TATT TATT
1 TAT-T TATT TATT TATT
60613 ATTCATTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
3 15 0.30
4 29 0.58
5 6 0.12
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:60572 original size:15 final size:14
Alignment explanation
Indices: 60552--60620 Score: 76
Period size: 12 Copynumber: 5.1 Consensus size: 14
60542 TGATAATACA
60552 TATTTATTATTTATT
1 TATTTATTA-TTATT
60567 TATTTATTTATTA-T
1 TATTTA-TTATTATT
60581 TATTTATT-TTATT
1 TATTTATTATTATT
60594 T-TTT-TTATTA-T
1 TATTTATTATTATT
60605 TATTTATTATTCATT
1 TATTTATTATT-ATT
60620 T
1 T
60621 TTTCTTTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
11 4 0.09
12 12 0.26
13 9 0.19
14 8 0.17
15 11 0.23
16 3 0.06
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTATTATTATT
Found at i:60605 original size:31 final size:32
Alignment explanation
Indices: 60554--60634 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 32
60544 ATAATACATA
*
60554 TTTATTATTTATTTATTTATT-TATTATTATTTAT
1 TTTATT-TTT-TTTATTTATTAT-TTATTATTCAT
60588 TTTATTTTTTTTA-TTATTATTTATTATTCAT
1 TTTATTTTTTTTATTTATTATTTATTATTCAT
* *
60619 TTT-TTCTTTTTGTTTA
1 TTTATTTTTTTTATTTA
60635 GCATTCAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 7 0.17
31 21 0.50
32 5 0.12
33 3 0.07
34 6 0.14
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.75
Consensus pattern (32 bp):
TTTATTTTTTTTATTTATTATTTATTATTCAT
Done.