Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001352.1 Hibiscus syriacus cultivar Beakdansim tig00002633_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: 96953
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3006 original size:3 final size:3
Alignment explanation
Indices: 3000--3036 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2990 ATAATTTATT
*
3000 TAA TAA TAA TAA TAA TAA CAA TAA -AA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3037 AAAATGGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:3012 original size:9 final size:8
Alignment explanation
Indices: 3000--3041 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
2990 ATAATTTATT
3000 TAATAATAA
1 TAATAA-AA
3009 TAATAATAA
1 TAATAA-AA
*
3018 CAATAAAA
1 TAATAAAA
3026 TAATAAAA
1 TAATAAAA
3034 TAA-AAAA
1 TAATAAAA
3041 T
1 T
3042 GGGCAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 5 0.16
8 12 0.39
9 14 0.45
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (8 bp):
TAATAAAA
Found at i:3427 original size:136 final size:137
Alignment explanation
Indices: 3273--3628 Score: 408
Period size: 136 Copynumber: 2.6 Consensus size: 137
3263 AATCTAGCAA
*
3273 AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCTCTTCAGATGAGTTCTTCTCATTATAA
1 AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCTCTTCAGATGAGTTCTTCTCATTATGA
* * * * *
3338 ACTCCT-TCTGGAAATGCTGAT-CCTCAAAAGAGGGT-GTCGT-TGATTCAACTTCATATGTGAT
66 ACT-CTATCTGGAAATGTTGATCCCTCAAAAGAGGGTCGTC-TCTAATTCAACTCCATAAGTGAC
*
3399 GAATTAAGGC
129 GAA-CAAGGC
*
3409 AAGGTTGAACAA-ATTTT-TCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTC-T-CTCTTCAGATGAGTTCTTCTCATTAT
* * * * * * *
3472 GAACTTTCTCTCG-AATGTTGATCCCTCGAATGAGGTTCTTCTCTAATTCAACTCCATAAGTGAC
64 GAACTCTATCTGGAAATGTTGATCCCTCAAAAGAGGGTCGTCTCTAATTCAACTCCATAAGTGAC
* **
3536 GAACCAGTT
129 GAACAAGGC
* *
3545 AAGGTCGAACAAGTTCTTCTC--TATGAACTTCTTCT-TCCTTCAGATGAGTTCTTCTCATTATG
1 AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCT-CTTCAGATGAGTTCTTCTCATTATG
3607 AACTCTATCTGGAAATGTTGAT
65 AACTCTATCTGGAAATGTTGAT
3629 GCTAATATAT
Statistics
Matches: 187, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
133 1 0.01
134 51 0.27
135 24 0.13
136 84 0.45
137 25 0.13
138 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (137 bp):
AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCTCTTCAGATGAGTTCTTCTCATTATGA
ACTCTATCTGGAAATGTTGATCCCTCAAAAGAGGGTCGTCTCTAATTCAACTCCATAAGTGACGA
ACAAGGC
Found at i:3762 original size:122 final size:119
Alignment explanation
Indices: 3545--3985 Score: 603
Period size: 119 Copynumber: 3.7 Consensus size: 119
3535 CGAACCAGTT
*
3545 AAGGTCGAACAAGTTCTTCTC--TATGAACTTCTTCTTCCTTCAGATGAGTTCTTCTCATTATGA
1 AAGGTTGAACAAGTT-TTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTC-TCTCATTATGA
* * * * * *
3608 ACTCTATCTGGAAATGTTGATGCTAATATATCTCATTCTGTGATAGAGTCAAGTAA
64 ACTCTACCTGGAAATGTTGATGCTGATCTATCTCATTCTATGATAGAGTCGAGCAA
*
3664 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT-TCTTATAT
1 AAGGTTGAACAAGTT-TTCTCATTATGAACTTCTTCTT-C-CTTCAGATGAGTTCTCTCAT-TAT
* *
3728 GAACTCTACCTGGAAATGTTGATACTGATCTATCTCATTCTATGATAGAGTTGAGCAA
62 GAACTCTACCTGGAAATGTTGATGCTGATCTATCTCATTCTATGATAGAGTCGAGCAA
* *
3786 AAGGTTGAACAAGTTTTCTCATTATGAACTTCTTCTTTCTTCATATGAGTTCTCTCATTATGAAC
1 AAGGTTGAACAAGTTTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTCTCATTATGAAC
* *
3851 TATACCT-GACAATGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCGAGCAA
66 TCTACCTGGA-AATGTTGATGCTGATCTATCTCATTCTATGATAGAGTCGAGCAA
3905 AAGGTTGAACAAGTTTTCTCATTATGAAC-T-TTCTTCCTTCTAGATGAG-T-TCTCATTATGAA
1 AAGGTTGAACAAGTTTTCTCATTATGAACTTCTTCTTCCTTC-AGATGAGTTCTCTCATTATGAA
*
3966 CTCT-CTTTGGAAATGTTGAT
65 CTCTAC-CTGGAAATGTTGAT
3986 CAATCGAGTG
Statistics
Matches: 291, Mismatches: 21, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
115 1 0.00
116 25 0.09
117 12 0.04
118 9 0.03
119 117 0.40
120 3 0.01
121 40 0.14
122 70 0.24
123 14 0.05
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (119 bp):
AAGGTTGAACAAGTTTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTCTCATTATGAAC
TCTACCTGGAAATGTTGATGCTGATCTATCTCATTCTATGATAGAGTCGAGCAA
Found at i:7105 original size:31 final size:32
Alignment explanation
Indices: 7054--7114 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
7044 GAAACAATGT
*
7054 TATATGCATATGAGAAAAAGATA-TATGTGAAC
1 TATATGCAAATGAGAAAAAGA-ACTATGTGAAC
*
7086 TATATG-AAATGAGATAAAGAACTATGTGA
1 TATATGCAAATGAGAAAAAGAACTATGTGA
7115 TGTGATCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.04
31 19 0.73
32 6 0.23
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.28
Consensus pattern (32 bp):
TATATGCAAATGAGAAAAAGAACTATGTGAAC
Found at i:7359 original size:21 final size:21
Alignment explanation
Indices: 7335--7390 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
7325 GGGTCTACGC
* *
7335 GGTCCTTCAGGACATCTAAGT
1 GGTCATTCGGGACATCTAAGT
7356 GGTCATTCGGGACATCTAAGT
1 GGTCATTCGGGACATCTAAGT
7377 GGTCATTCGGGACA
1 GGTCATTCGGGACA
7391 AATTCTACGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (21 bp):
GGTCATTCGGGACATCTAAGT
Found at i:10884 original size:17 final size:18
Alignment explanation
Indices: 10834--10884 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
10824 TAAATTTATG
*
10834 AAATAATATAATGAATGT
1 AAATAATATAAAGAATGT
*
10852 AAATAATGTAAA-AATGT
1 AAATAATATAAAGAATGT
*
10869 AAA-AGTATAAAGAATG
1 AAATAATATAAAGAATG
10885 AGTGCCATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 6 0.21
17 12 0.43
18 10 0.36
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (18 bp):
AAATAATATAAAGAATGT
Found at i:22367 original size:35 final size:33
Alignment explanation
Indices: 22316--22388 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 33
22306 TCTGAGTTGA
22316 TATTATTATTACTATTATATATAAATA-TATATA
1 TATTATTATTACTATTATATATAAATATTAT-TA
* *
22349 TATTATGCTATTATTATTATATATTAATATTATTA
1 TATTAT--TATTACTATTATATATAAATATTATTA
22384 TATTA
1 TATTA
22389 CAAATTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 6 0.17
35 26 0.74
36 3 0.09
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (33 bp):
TATTATTATTACTATTATATATAAATATTATTA
Found at i:22379 original size:19 final size:20
Alignment explanation
Indices: 22315--22384 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
22305 ATCTGAGTTG
*
22315 ATATTATTATTA-CTATTAT
1 ATATTATTATTATATATTAT
* *
22334 ATATAAATATATATATATTAT
1 ATATTATTAT-TATATATTAT
*
22355 GCTATTATTATTATATATTA-
1 -ATATTATTATTATATATTAT
22375 ATATTATTAT
1 ATATTATTAT
22385 ATTACAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 17 0.41
20 2 0.05
21 15 0.37
22 7 0.17
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (20 bp):
ATATTATTATTATATATTAT
Found at i:22381 original size:16 final size:16
Alignment explanation
Indices: 22328--22386 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
22318 TTATTATTAC
*
22328 TATTATATATAAATA-
1 TATTATATATTAATAT
*
22343 TATATATATTATGCTATTAT
1 TAT-TATA-TAT--TAATAT
22363 TATTATATATTAATAT
1 TATTATATATTAATAT
22379 TATTATAT
1 TATTATAT
22387 TACAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.08
16 17 0.47
17 3 0.08
18 3 0.08
19 7 0.19
20 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TATTATATATTAATAT
Found at i:23729 original size:8 final size:8
Alignment explanation
Indices: 23705--23747 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
23695 CCGTTTACCC
*
23705 GACCCGAT
1 GACCCGTT
*
23713 GAACCGTT
1 GACCCGTT
23721 GACCCGTT
1 GACCCGTT
23729 GA-CCGTT
1 GACCCGTT
23736 GACCCGTT
1 GACCCGTT
23744 GACC
1 GACC
23748 GGTGTTGACC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
7 7 0.23
8 24 0.77
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:23735 original size:15 final size:15
Alignment explanation
Indices: 23705--23748 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
23695 CCGTTTACCC
*
23705 GACCCGATGAACCGTT
1 GACCCGTTG-ACCGTT
23721 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
23736 GACCCGTTGACCG
1 GACCCGTTGACCG
23749 GTGTTGACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.20
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:25918 original size:24 final size:24
Alignment explanation
Indices: 25891--25954 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
25881 ATTTATGATT
25891 TGAATTATGTTATGATACCTGACA
1 TGAATTATGTTATGATACCTGACA
* * * * *
25915 TGAATTCTGATCTGATACTTGACC
1 TGAATTATGTTATGATACCTGACA
* *
25939 TGAACTATGTTTTGAT
1 TGAATTATGTTATGAT
25955 TTTTGATATA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (24 bp):
TGAATTATGTTATGATACCTGACA
Found at i:26135 original size:57 final size:57
Alignment explanation
Indices: 26057--26220 Score: 238
Period size: 57 Copynumber: 2.9 Consensus size: 57
26047 TGACGGGGAA
26057 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGAAGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGAAGTT
* * **
26114 GAATACTTGCAGGTTCCTCGGCTTTGTGTTGAGAGCCTTACTGTTCATGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGAAGTT
* * * * * *
26171 GATTACTTGCAGGTTTCTTGGCTTTATGCTTAGGGCCTTACTGTTCGTGA
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGA
26221 TGGGGGTTGT
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 95 1.00
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.37
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGAAGTT
Found at i:27642 original size:17 final size:17
Alignment explanation
Indices: 27620--27657 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
27610 ATCCCTAATA
*
27620 TTTAATATCTTTTATT-T
1 TTTAATA-CTATTATTAT
27637 TTTAATACTATTATTAT
1 TTTAATACTATTATTAT
27654 TTTA
1 TTTA
27658 TTTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAATACTATTATTAT
Found at i:28530 original size:60 final size:60
Alignment explanation
Indices: 28420--28532 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
28410 TATAGGATAC
* * * *
28420 TACTTTGTTGAGTCCTCTAACTATTAAAAGTTAGAAAATTGTCTGCCAACTATAAAAAGT
1 TACTTTGTTGAGTCCTCTAACTATTAAAAATTACAAAATGGTCTACCAACTATAAAAAGT
* *
28480 TACTTTGTTTAGTCC-CTCGACTATTAAAAATTACAAAATGGTC-ACACAACTAT
1 TACTTTGTTGAGTCCTCT-AACTATTAAAAATTACAAAATGGTCTAC-CAACTAT
28533 TCATTATGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.07
60 42 0.93
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (60 bp):
TACTTTGTTGAGTCCTCTAACTATTAAAAATTACAAAATGGTCTACCAACTATAAAAAGT
Found at i:30268 original size:154 final size:155
Alignment explanation
Indices: 29929--30277 Score: 337
Period size: 158 Copynumber: 2.2 Consensus size: 155
29919 TGTCTCTAGC
* * * * *
29929 GAGACAAAATTTGTTTTGGGAGAAATAATCTCAAAGGCTTATATTTCAAAAGAAAATGTCTCAAG
1 GAGACGAAATTTGTTTTGAGAGAAACAATCTAAAAGGCTTATATTTCAAAAGAAAATGTCTCAAA
* * * * *
29994 CGAGACGAAATTTGTTTCAAGGAAACAATCTCAAGTGAGATCAATTTTTTTCAGGTGCAAAAATT
66 AGAGACGAAATTTGTTTCAAAGAAACAACCTCAAGCGAGATCAATTTTATT---GTGCAAAAATT
** * ** *
30059 TCAAAATTGGTGGAAAATTGTCTCAAGC
128 TCAAAATTGACGAAAAATCATCTCAAGA
* * * * * * *
30087 GAGACGAAATTTGTTTCGAGATG-AACAATC-AAAAGGATTTGTGTTTTAAGAGAAATTGTCTCA
1 GAGACGAAATTTGTTTTGAGA-GAAACAATCTAAAAGG-CTTATATTTCAAAAGAAAATGTCTCA
* * *
30150 AAAGATACGAAATTTGTTTTGAAAGAAACAACCTCAAGCGAGATCAATTTTATT-T-CAAAATTT
64 AAAGAGACGAAATTTG-TTTCAAAGAAACAACCTCAAGCGAGATCAATTTTATTGTGCAAAAATT
* *
30213 TCAAAATTTACGAAAAATCATCTTAAGA
128 TCAAAATTGACGAAAAATCATCTCAAGA
* *
30241 GAGTCGAAATTTGTTTTGTGAGAAACAATCTCAAAAG
1 GAGACGAAATTTGTTTTGAGAGAAACAATCT-AAAAG
30278 ATTATAGACT
Statistics
Matches: 154, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
153 1 0.01
154 52 0.34
155 1 0.01
156 5 0.03
157 5 0.03
158 57 0.37
159 33 0.21
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (155 bp):
GAGACGAAATTTGTTTTGAGAGAAACAATCTAAAAGGCTTATATTTCAAAAGAAAATGTCTCAAA
AGAGACGAAATTTGTTTCAAAGAAACAACCTCAAGCGAGATCAATTTTATTGTGCAAAAATTTCA
AAATTGACGAAAAATCATCTCAAGA
Found at i:30821 original size:24 final size:24
Alignment explanation
Indices: 30789--30835 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
30779 CTTGCCCCAG
30789 CAAATTTTGTCCCTGATGAATTTA
1 CAAATTTTGTCCCTGATGAATTTA
30813 CAAATTTTGTCCCTGATGAATTT
1 CAAATTTTGTCCCTGATGAATTT
30836 GGCTTCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (24 bp):
CAAATTTTGTCCCTGATGAATTTA
Found at i:36428 original size:2 final size:2
Alignment explanation
Indices: 36421--36484 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
36411 CTTATACATT
36421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36462 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
36485 TATTTATTGT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37797 original size:21 final size:21
Alignment explanation
Indices: 37768--37820 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
37758 ATTCTGACTA
37768 TCGCATTGCGATTTACCAAAT
1 TCGCATTGCGATTTACCAAAT
* * *
37789 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCAAAT
*
37810 TCGCAATGCGA
1 TCGCATTGCGA
37821 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTACCAAAT
Found at i:37835 original size:20 final size:20
Alignment explanation
Indices: 37810--37891 Score: 121
Period size: 20 Copynumber: 4.1 Consensus size: 20
37800 TTTTCCTAAT
37810 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
37830 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
37850 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
37870 TCGCAATGCAAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
37890 TC
1 TC
37892 ACAACGAGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 1 0.02
20 55 0.98
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:41279 original size:20 final size:20
Alignment explanation
Indices: 41242--41330 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
41232 TAACGCGGAA
41242 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* *
41262 ATCGTAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
41282 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
41302 ATCGCAACGCGGAAATAACT
1 ATCGCAACGCGGAAATGACT
*
41322 ATCTCAACG
1 ATCGCAACG
41331 AGAGAATCGC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 55 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:41363 original size:33 final size:34
Alignment explanation
Indices: 41326--41397 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
41316 ATAACTATCT
*
41326 CAACGAGAGAATCGCAATGC-GAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCAAAAATGAAAATCG
* *
41359 CAACGAGTGAATCGCAATGCAAAAATGAAAATGG
1 CAACGAGAGAATCGCAATGCAAAAATGAAAATCG
41393 CAACG
1 CAACG
41398 CGAAATTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 19 0.54
34 16 0.46
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (34 bp):
CAACGAGAGAATCGCAATGCAAAAATGAAAATCG
Found at i:41451 original size:33 final size:33
Alignment explanation
Indices: 41414--41495 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
41404 TAGTTTCACA
41414 TTGCGATTTTCATTTTCGCA-TACGATTCACTCG
1 TTGCGATTTTCA-TTTCGCATTACGATTCACTCG
* *
41447 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTACGATTCACTCG
**
41480 TTGCGATAGTCATTTC
1 TTGCGATTTTCATTTC
41496 CGCGTTGCGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 7 0.16
33 37 0.84
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTACGATTCACTCG
Found at i:41471 original size:19 final size:19
Alignment explanation
Indices: 41407--41473 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 19
41397 GCGAAATTAG
*
41407 TTTCACATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
41426 TTTTCGCA-TACGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
41443 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
41459 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
41474 CTCTCGTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 13
0.67 0.09 0.24
Matches are distributed among these distances:
14 4 0.11
15 3 0.08
16 4 0.11
17 7 0.19
19 12 0.33
20 6 0.17
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:41627 original size:14 final size:14
Alignment explanation
Indices: 41608--41644 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
41598 CATCAATTAA
41608 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
41622 ACAAATCATCTTTT
1 ACAAATCAACATTT
41636 ACAAATCAA
1 ACAAATCAA
41645 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:43031 original size:21 final size:21
Alignment explanation
Indices: 43007--43066 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
42997 TTGGGAGGGA
* *
43007 CCTCTTCAACGATGACAGTGG
1 CCTCTTGAACGATGACAGAGG
**
43028 CCTCTTGAACGAT-AGGGGAGG
1 CCTCTTGAACGATGA-CAGAGG
43049 CCTCTTGAACGATGACAG
1 CCTCTTGAACGATGACAG
43067 GTGAGTCGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGAGG
Found at i:43570 original size:20 final size:20
Alignment explanation
Indices: 43547--43595 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
43537 GAAACTTAAA
43547 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
43567 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
43587 ATCGCAACG
1 ATCGCAACG
43596 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:43774 original size:54 final size:54
Alignment explanation
Indices: 43706--43810 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
43696 GCGATTTTCA
* *
43706 TTTCGTATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
**
43760 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGT
43811 AAACTATTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (54 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
Found at i:43806 original size:20 final size:20
Alignment explanation
Indices: 43727--43810 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
43717 GATTCTTTCG
**
43727 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
43747 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
43767 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
43781 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
43801 TTGCGATAGT
1 TTGCGATAGT
43811 AAACTATTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.13
16 6 0.11
18 6 0.11
20 35 0.65
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:45658 original size:20 final size:20
Alignment explanation
Indices: 45600--45667 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
45590 GAAACTTTAA
**
45600 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
45620 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
45640 ATGGCAACACGAATTTGACT
1 ATCGCAACACGAAAATGACT
45660 ATCGCAAC
1 ATCGCAAC
45668 GCAAGAATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:45738 original size:20 final size:20
Alignment explanation
Indices: 45713--45759 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
45703 GATTCTCTCG
45713 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
45733 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
45753 TTGCGAT
1 TTGCGAT
45760 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:46637 original size:2 final size:2
Alignment explanation
Indices: 46632--46664 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
46622 TAATTTTTTG
46632 AT AT AT AT 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 AT AT AT AT A
46665 CCTTTGTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46764 original size:6 final size:6
Alignment explanation
Indices: 46747--46786 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
46737 TTATTTTTTC
*
46747 TCATTT TAATTT TCATTT TCATTT TCATTT T--TTT TCATTT
1 TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT
46787 ATCTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.13
6 26 0.87
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.70
Consensus pattern (6 bp):
TCATTT
Found at i:46770 original size:18 final size:16
Alignment explanation
Indices: 46728--46786 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
46718 ATTTCCTTTG
46728 TTTTTTT-A-TTT-AT
1 TTTTTTTCATTTTAAT
*
46741 TTTTTCTCATTTTAAT
1 TTTTTTTCATTTTAAT
*
46757 TTTCATTTTCATTTTCAT
1 TTT--TTTTCATTTTAAT
46775 TTTTTTTCATTT
1 TTTTTTTCATTT
46787 ATCTTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 6 0.16
14 1 0.03
15 3 0.08
16 14 0.37
18 14 0.37
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTCATTTTAAT
Found at i:46802 original size:9 final size:9
Alignment explanation
Indices: 46731--47041 Score: 88
Period size: 9 Copynumber: 32.4 Consensus size: 9
46721 TCCTTTGTTT
46731 TTTTATTTA
1 TTTTATTTA
46740 TTTT-TTCTCA
1 TTTTATT-T-A
46750 TTTTAATTTTCA
1 TTTT-A-TTT-A
46762 TTTTCATTTTCA
1 TTTT-A-TTT-A
*
46774 TTTTTTTTCA
1 TTTTATTT-A
46784 -TTTATCTTA
1 TTTTAT-TTA
46793 TTTTATTTA
1 TTTTATTTA
*
46802 TATTATATGTA
1 T-TT-TATTTA
*
46813 TTATTTTTTA
1 TT-TTATTTA
46823 CTATTT-TTTA
1 -T-TTTATTTA
46833 CTATTT-TTTA
1 -T-TTTATTTA
46843 TTTTA-TTA
1 TTTTATTTA
46851 TTTTTATTTA
1 -TTTTATTTA
*
46861 TTTT-TTTC
1 TTTTATTTA
* *
46869 TTAT-TTTC
1 TTTTATTTA
46877 TTATT-TTTA
1 TT-TTATTTA
46886 TCTTTATTTCA
1 T-TTTATTT-A
*
46897 TTTGTTTTTA
1 TTT-TATTTA
*
46907 TTTGTTTTTA
1 TTT-TATTTA
*
46917 TTGTATTTA
1 TTTTATTTA
*
46926 TCTTATTTA
1 TTTTATTTA
46935 TATTTATTTTA
1 T-TTTA-TTTA
46946 TTTTTATCTT-
1 -TTTTAT-TTA
46956 TTTTATCTTA
1 TTTTAT-TTA
*
46966 TCATT-TTTA
1 T-TTTATTTA
* *
46975 TTTCATTTGT
1 TTTTATTT-A
*
46985 TTTTTTTTA
1 TTTTATTTA
*
46994 TTTTCTTTA
1 TTTTATTTA
*
47003 TTTTAATT-
1 TTTTATTTA
*
47011 TTTTA-TCA
1 TTTTATTTA
*
47019 TCTTATTTA
1 TTTTATTTA
*
47028 TTTTTATTTC
1 -TTTTATTTA
47038 TTTT
1 TTTT
47042 TTATCTAACA
Statistics
Matches: 240, Mismatches: 31, Indels: 62
0.72 0.09 0.19
Matches are distributed among these distances:
7 1 0.00
8 30 0.12
9 80 0.33
10 79 0.33
11 28 0.12
12 20 0.08
13 2 0.01
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTATTTA
Found at i:46850 original size:35 final size:37
Alignment explanation
Indices: 46811--46883 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 37
46801 ATATTATATG
46811 TATTATTTTT-TACTATTTTTTAC-TATTTT-TTATTT
1 TATTATTTTTAT-CTATTTTTTACTTATTTTCTTATTT
* *
46846 TATTATTTTTATTTATTTTTTTCTTATTTTCTTATTT
1 TATTATTTTTATCTATTTTTTACTTATTTTCTTATTT
46883 T
1 T
46884 TATCTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 19 0.58
36 7 0.21
37 7 0.21
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (37 bp):
TATTATTTTTATCTATTTTTTACTTATTTTCTTATTT
Found at i:46852 original size:15 final size:14
Alignment explanation
Indices: 46836--47036 Score: 129
Period size: 15 Copynumber: 13.7 Consensus size: 14
46826 TTTTTTACTA
46836 TTTTTTATTTTATT
1 TTTTTTATTTTATT
*
46850 ATTTTTA-TTTATTT
1 TTTTTTATTTTA-TT
*
46864 TTTTCTTATTTTCTT
1 TTTT-TTATTTTATT
*
46879 ATTTTTATCTTTATT
1 TTTTTTAT-TTTATT
*
46894 TCATTTGT-TTTTATT
1 T--TTTTTATTTTATT
*
46909 TGTTTTTATTGTATT
1 T-TTTTTATTTTATT
* *
46924 TATCTTATTTATATT
1 TTTTTTATTT-TATT
* *
46939 TATTTTATTTTTATC
1 TTTTTTA-TTTTATT
* *
46954 TTTTTTATCTTATC
1 TTTTTTATTTTATT
* *
46968 ATTTTTATTTCATT
1 TTTTTTATTTTATT
46982 TGTTTTT-TTTTATT
1 T-TTTTTATTTTATT
*
46996 TTCTTTATTTTAATT
1 TTTTTTATTTT-ATT
* *
47011 TTTTATCATCTTATT
1 TTTT-TTATTTTATT
47026 TATTTTTATTT
1 T-TTTTTATTT
47037 CTTTTTTATC
Statistics
Matches: 144, Mismatches: 29, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
13 8 0.06
14 52 0.36
15 65 0.45
16 15 0.10
17 4 0.03
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTTTATTTTATT
Found at i:46861 original size:10 final size:10
Alignment explanation
Indices: 46784--47042 Score: 80
Period size: 10 Copynumber: 25.3 Consensus size: 10
46774 TTTTTTTTCA
46784 TTTATCTTA-T
1 TTTAT-TTATT
46794 TTTATTTATAT
1 TTTATTTAT-T
* *
46805 TATATGTATT
1 TTTATTTATT
*
46815 ATTT-TTTACTA
1 -TTTATTTA-TT
*
46826 TTT-TTTACTA
1 TTTATTTA-TT
46836 TTT-TTTA-T
1 TTTATTTATT
46844 TTTA-TTATT
1 TTTATTTATT
46853 TTTATTTATT
1 TTTATTTATT
*
46863 TTTTTCTTA-T
1 TTTAT-TTATT
*
46873 TTT-CTTATT
1 TTTATTTATT
46882 TTTATCTT-TAT
1 TTTAT-TTAT-T
* *
46893 TTCATTTGTT
1 TTTATTTATT
*
46903 TTTATTTGTT
1 TTTATTTATT
46913 TTTATTGTATTT
1 TTTATT-TA-TT
*
46925 ATCTTATTTATA
1 -T-TTATTTATT
46937 TTTATTTTATT
1 TTTA-TTTATT
46948 TTTATCTT-TT
1 TTTAT-TTATT
*
46958 TTATCTTATCATT
1 TT-TATT-T-ATT
46971 TTTATTTCATT
1 TTTATTT-ATT
*
46982 TGT-TTT-TT
1 TTTATTTATT
*
46990 TTTATTT-TC
1 TTTATTTATT
*
46999 TTTATTT-TAA
1 TTTATTTAT-T
47009 TTT-TTTATCAT
1 TTTATTTAT--T
*
47020 CTTATTTATT
1 TTTATTTATT
*
47030 TTTATTTCTT
1 TTTATTTATT
47040 TTT
1 TTT
47043 TATCTAACAC
Statistics
Matches: 197, Mismatches: 24, Indels: 56
0.71 0.09 0.20
Matches are distributed among these distances:
8 13 0.07
9 27 0.14
10 86 0.44
11 48 0.24
12 11 0.06
13 7 0.04
14 5 0.03
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTATTTATT
Found at i:46877 original size:8 final size:7
Alignment explanation
Indices: 46834--46884 Score: 52
Period size: 8 Copynumber: 7.0 Consensus size: 7
46824 TATTTTTTAC
46834 TATTTTT
1 TATTTTT
46841 TATTTTAT
1 TATTTT-T
46849 TA-TTTT
1 TATTTTT
46855 TATTTATT
1 TATTT-TT
46863 T-TTTTCT
1 TATTTT-T
46870 TATTTTCT
1 TATTTT-T
46878 TATTTTT
1 TATTTTT
46885 ATCTTTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 4 0.10
7 17 0.44
8 18 0.46
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (7 bp):
TATTTTT
Found at i:46892 original size:35 final size:36
Alignment explanation
Indices: 46824--47045 Score: 110
Period size: 35 Copynumber: 6.1 Consensus size: 36
46814 TATTTTTTAC
* *
46824 TATTTTTTAC-TATTTTTTATTTTATTATTTTTATT
1 TATTTTTTTCTTATTTTTTATTTTATTATCTTTATT
46859 TATTTTTTTCTTATTTTCTTA-TTT-TTATCTTTATT
1 TATTTTTTTCTTATTTT-TTATTTTATTATCTTTATT
* *
46894 TCATTTGTTTT-TATTTGTTTTTATTGTATTTATC-TTATT
1 T-ATTT-TTTTCT-TAT-TTTTTATTTTA-TTATCTTTATT
* *
46933 TATATTTATT-TTA-TTTTTATCTTTTTTATC-TTATCAT
1 TAT-TTTTTTCTTATTTTTTAT-TTTATTATCTTTAT--T
* *
46970 T-TTTATTTCATT-TGTTTTT-TTTTATTTTCTTTATTT
1 TATTTTTTTC-TTAT-TTTTTATTTTATTATCTTTA-TT
* * *
47006 TAATTTTTTATCATCTTATTTATTTTTATT-TCTTT-TT
1 T-ATTTTTT-TCTTATTTTTTA-TTTTATTATCTTTATT
47043 TAT
1 TAT
47046 CTAACACATT
Statistics
Matches: 147, Mismatches: 15, Indels: 49
0.70 0.07 0.23
Matches are distributed among these distances:
35 40 0.27
36 28 0.19
37 24 0.16
38 27 0.18
39 16 0.11
40 12 0.08
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (36 bp):
TATTTTTTTCTTATTTTTTATTTTATTATCTTTATT
Found at i:46905 original size:74 final size:80
Alignment explanation
Indices: 46827--46988 Score: 178
Period size: 83 Copynumber: 2.1 Consensus size: 80
46817 TTTTTACTAT
*
46827 TTTTTACTAT-TTTTTA-T-TTTA-TTATTTTTATTTATTTT-TTTCTTAT-TTTCTTAT-TT-T
1 TTTTTA-TATGTTTTTATTATTTACTTATTTATATTTATTTTATTT-TTATCTTTCTTATCTTAT
*
46884 TATCTTTATTTCATTTG
64 CATCTTTATTTCATTTG
* *
46901 TTTTTATTTGTTTTTATTGTATTTATCTTATTTATATTTATTTTATTTTTATCTTTTTTATCTTA
1 TTTTTATATGTTTTTA-T-TATTTA-CTTATTTATATTTATTTTATTTTTATCTTTCTTATCTTA
*
46966 TCATTTTTATTTCATTTG
63 TCATCTTTATTTCATTTG
46984 TTTTT
1 TTTTT
46989 TTTTATTTTC
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
73 2 0.03
74 12 0.17
77 1 0.01
78 4 0.06
80 20 0.28
81 10 0.14
82 2 0.03
83 21 0.29
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (80 bp):
TTTTTATATGTTTTTATTATTTACTTATTTATATTTATTTTATTTTTATCTTTCTTATCTTATCA
TCTTTATTTCATTTG
Found at i:47386 original size:3 final size:3
Alignment explanation
Indices: 47378--47440 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
47368 TTCCGAAATA
*
47378 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
47426 TAT TA- TATT TAT TAT
1 TAT TAT TA-T TAT TAT
47441 CTTAAGTAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.93
4 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:48556 original size:15 final size:15
Alignment explanation
Indices: 48538--48568 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
48528 AAATTCTAAA
48538 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
48553 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
48568 T
1 T
48569 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:56050 original size:21 final size:20
Alignment explanation
Indices: 55964--56121 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
55954 AAATGACCAA
**
55964 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
55983 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
56003 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
56023 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
56044 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
56065 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
56085 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
56106 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
56122 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:56114 original size:20 final size:20
Alignment explanation
Indices: 56089--56399 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
56079 GATTTTCAAT
* *
56089 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
56109 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
56129 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
56149 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
56169 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
56189 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
56209 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
56229 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
56250 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
56270 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
56290 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
56310 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
56330 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
56350 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
56370 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
56390 AATCGCAACG
1 AATCGCAACG
56400 ATAATCCGTA
Statistics
Matches: 244, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.01
20 224 0.92
21 16 0.07
22 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:56134 original size:40 final size:40
Alignment explanation
Indices: 56089--56478 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
56079 GATTTTCAAT
* ** * * *
56089 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
56129 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
56169 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
56209 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
56250 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
56290 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
56330 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
56370 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
56410 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
56450 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
56479 ACTGAAATTT
Statistics
Matches: 312, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.01
40 272 0.87
41 34 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:56406 original size:20 final size:19
Alignment explanation
Indices: 56127--56478 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
56117 CGCGAACACA
56127 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
56147 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
56167 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
56187 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
56207 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
56227 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
56247 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
56268 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
56288 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
56308 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
56328 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
56348 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
56368 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
56388 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
56408 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
56428 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
56448 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
56468 TAAATCACAAC
1 TAAATCGCAAC
56479 ACTGAAATTT
Statistics
Matches: 290, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 270 0.93
21 16 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:57193 original size:24 final size:24
Alignment explanation
Indices: 57154--57200 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
57144 AAATTTGGTC
57154 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
57178 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
57201 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):
TTGGTCAATATCCGGACTTTGATA
Found at i:57392 original size:12 final size:12
Alignment explanation
Indices: 57375--57399 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57365 ATATAATCCT
57375 GAAGAAGAAAAA
1 GAAGAAGAAAAA
57387 GAAGAAGAAAAA
1 GAAGAAGAAAAA
57399 G
1 G
57400 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:59700 original size:19 final size:19
Alignment explanation
Indices: 59678--60074 Score: 476
Period size: 19 Copynumber: 22.4 Consensus size: 19
59668 CGGAAAATAC
*
59678 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59697 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
59711 AATTGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
59731 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
59745 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59764 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
*
59783 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
59797 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59816 CATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59835 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
59854 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59873 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59892 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
*
59906 AATCGCAATGCGGAATGAA
1 AATCGCAATGCGAAATGAA
59925 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59944 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
59958 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59977 CATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59996 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
60015 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
60029 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
60048 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
60067 AATCGCAA
1 AATCGCAA
60075 CGAGATAATC
Statistics
Matches: 327, Mismatches: 20, Indels: 62
0.80 0.05 0.15
Matches are distributed among these distances:
14 56 0.17
15 3 0.01
16 18 0.06
17 18 0.06
18 4 0.01
19 216 0.66
20 12 0.04
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:59728 original size:34 final size:33
Alignment explanation
Indices: 59678--60051 Score: 210
Period size: 33 Copynumber: 10.7 Consensus size: 33
59668 CGGAAAATAC
*
59678 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAA
* * *
59711 AATTGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCCCAACGAGAA
* *
59745 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* * * * *
59783 AATCGCAACGAGAGAATCG-CAATGCGAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACGA-GAA
* * *
59816 CATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
59854 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
59892 AATCGCAA--CGAAA-G--AATCGCAATGCGGAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C-G-A-GAA
* *
59925 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
* *
59958 AATCGCAATGCGAAATGAACATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
59996 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
60028 GAATCGCAATGCGAAATGAAAATC
1 -AATCGCAATGCGAAATGAAAATC
60052 GCAATGCGAA
Statistics
Matches: 285, Mismatches: 28, Indels: 56
0.77 0.08 0.15
Matches are distributed among these distances:
31 1 0.00
32 10 0.04
33 115 0.40
34 31 0.11
35 12 0.04
36 9 0.03
37 2 0.01
38 96 0.34
39 8 0.03
40 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAA
Found at i:59793 original size:52 final size:52
Alignment explanation
Indices: 59706--60055 Score: 494
Period size: 52 Copynumber: 6.6 Consensus size: 52
59696 AAATCCCAAC
*
59706 ATGAAAATTGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
59759 ATGAAAATCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
59811 ATGAACATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
* *
59868 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGGA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
59920 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
59972 ATGAACATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
60027 A-G--AATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
60056 TGCGAAATGA
Statistics
Matches: 275, Mismatches: 12, Indels: 21
0.89 0.04 0.07
Matches are distributed among these distances:
52 185 0.67
53 16 0.06
54 7 0.03
55 10 0.04
56 2 0.01
57 55 0.20
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:59830 original size:71 final size:72
Alignment explanation
Indices: 59678--60096 Score: 447
Period size: 71 Copynumber: 6.0 Consensus size: 72
59668 CGGAAAATAC
* * *
59678 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATTGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-G-AATGAAAATCGCA
*
59738 A--CGAGA-G
63 ATGCGAAATG
* *
59745 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATAAAAATCGCAA-CG-A-GAGAATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATG
59807 CGAAATG
66 CGAAATG
*
59814 AACATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGC
1 -A-ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGC
59879 AATGCGAAATG
62 AATGCGAAATG
*
59890 AAAATCGCAA--CGAAA-G--AATCGCAATGCGGAATGAAAATCGCAATGCGAAATGAAAATCGC
1 --AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGC
*
59950 AA--CGAGA-G
62 AATGCGAAATG
*
59958 AATCGCAATGCGAAATGAACATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAA
60023 --CGAAA-G
64 TGCGAAATG
*
60029 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GATAATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATG
60091 CGAAAT
66 CGAAAT
60097 TATAAACGCA
Statistics
Matches: 311, Mismatches: 17, Indels: 46
0.83 0.05 0.12
Matches are distributed among these distances:
66 28 0.09
67 27 0.09
68 15 0.05
69 10 0.03
70 2 0.01
71 181 0.58
72 11 0.04
73 3 0.01
74 5 0.02
75 1 0.00
76 26 0.08
77 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATG
CGAAATG
Found at i:60056 original size:52 final size:52
Alignment explanation
Indices: 59710--60096 Score: 424
Period size: 52 Copynumber: 7.3 Consensus size: 52
59700 CCCAACATGA
* *
59710 AAATTGCAATGCGGAAATGAAAATCGCAACG--AGAGAATCGCAATGCGAAATG
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAATG
* *
59762 AAAATCGCAATGCGAAATAAAAATCGCAACG--AGAGAATCGCAATGCGAAATG
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAATG
*
59814 AACATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATG
1 AA-ATCGCAATGCGAAATGAAAATCGCAA--CGAAA-GAAAATCGCAA-GCGAAATG
*
59871 AAAATCGCAATGCGAAATGAAAATCGCAACGAAAG--AATCGCAATGCGGAATG
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAATG
*
59923 AAAATCGCAATGCGAAATGAAAATCGCAACG--AGAGAATCGCAATGCGAAATG
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAATG
59975 AACATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G
1 AA-ATCGCAATGCGAAATGAAAATCGCAA--CGAAA-GAAAATCGCAAGCGAAATG
*
60029 -AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT-
1 AAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-GAAAATCGCAAGCGAAATG
60081 -AATCGCAATGCGAAAT
1 AAATCGCAATGCGAAAT
60097 TATAAACGCA
Statistics
Matches: 309, Mismatches: 9, Indels: 33
0.88 0.03 0.09
Matches are distributed among these distances:
50 2 0.01
51 4 0.01
52 217 0.70
53 12 0.04
54 6 0.02
55 10 0.03
56 2 0.01
57 54 0.17
58 2 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAAGCGAAATG
Found at i:60193 original size:19 final size:19
Alignment explanation
Indices: 60103--60185 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
60093 AAATTATAAA
60103 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
60122 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
60142 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
60158 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
60175 CGCATTGCGAT
1 CGCATTGCGAT
60186 AGTCATTTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:60310 original size:14 final size:14
Alignment explanation
Indices: 60291--60327 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
60281 CATCAATTAC
60291 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
60305 ACAAATCATCTTTT
1 ACAAATCAACTTTT
60319 ACAAATCAA
1 ACAAATCAA
60328 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:62299 original size:14 final size:14
Alignment explanation
Indices: 62280--62336 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
62270 GCGAAATGAA
*
62280 AATCGCAACGACAG
1 AATCGCAACGAAAG
62294 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
62311 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
62327 AATCGCAACG
1 AATCGCAACG
62337 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:62307 original size:33 final size:33
Alignment explanation
Indices: 62261--62353 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
62251 GCGAAACCAA
*
62261 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
62294 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
62327 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
62354 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:62318 original size:19 final size:19
Alignment explanation
Indices: 62224--62358 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
62214 TAGTTTACTT
* *
62224 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
62244 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
62263 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
62282 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
62296 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
62315 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
62329 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
62348 TCGCAATGCGA
1 TCGCAACGCGA
62359 TTTTGGTTTT
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:62376 original size:19 final size:19
Alignment explanation
Indices: 62354--62482 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
62344 AAAATCGCAA
*
62354 TGCGATTTTGGTTTTGCGT
1 TGCGATTTTGGTTTCGCGT
*
62373 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
62387 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
62406 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
62420 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
62439 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
62458 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
62478 TGCGA
1 TGCGA
62483 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:62396 original size:33 final size:33
Alignment explanation
Indices: 62354--62445 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
62344 AAAATCGCAA
*
62354 TGCGATTTTGGTTTTGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
62387 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
62420 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
62446 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:62696 original size:92 final size:92
Alignment explanation
Indices: 62526--62996 Score: 915
Period size: 92 Copynumber: 5.1 Consensus size: 92
62516 TTGAATGGAT
62526 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
62591 AGTTTAGCAGAATTGGCAGCAACCGAAC
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
62619 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
62684 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
62711 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
62776 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
62803 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
62868 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
62895 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
*
62960 AGTTTAGCAGAATTGGCAGCAACCGAAT
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
62988 AAATTTACT
1 AAATTTACT
62997 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 276 0.73
93 100 0.27
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (92 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:64739 original size:33 final size:33
Alignment explanation
Indices: 64694--64807 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
64684 TCTTTTGGTT
64694 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
64727 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
64760 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
64792 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
64808 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.41
33 45 0.59
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:64740 original size:19 final size:18
Alignment explanation
Indices: 64701--64812 Score: 95
Period size: 14 Copynumber: 6.8 Consensus size: 18
64691 GTTGAAATGA
64701 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
64716 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
64733 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
64749 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
64766 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
64781 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
64798 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
64813 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 18 0.23
17 8 0.10
18 8 0.10
19 20 0.25
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:64843 original size:14 final size:14
Alignment explanation
Indices: 64824--64878 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
64814 TTTGGTTTCG
64824 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
64838 CGTTGCGATTTTCATCT
1 CGTTGCGA--TTC-TCT
64855 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
64871 CGTTGCGA
1 CGTTGCGA
64879 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.44
16 6 0.17
17 6 0.17
19 8 0.22
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:65041 original size:33 final size:33
Alignment explanation
Indices: 64999--65069 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
64989 AATACTAACT
*
64999 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
65032 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
65065 TGAAA
1 TGAAA
65070 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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:65303 original size:22 final size:22
Alignment explanation
Indices: 65251--65305 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
65241 TGGTTGTGAG
**
65251 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
65273 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
65295 GGATTTCTTCG
1 GGATTTCTTCG
65306 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:65476 original size:20 final size:20
Alignment explanation
Indices: 65451--65643 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
65441 CTTTAAATAT
65451 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
65471 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
65493 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
65512 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
65532 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
65552 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
65572 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
65592 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
65612 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
65632 CGCGTTGCGATT
1 CGCGTTGCGATT
65644 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:65638 original size:60 final size:60
Alignment explanation
Indices: 65451--65643 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
65441 CTTTAAATAT
**
65451 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
65512 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
65572 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
65632 CGCGTTGCGATT
1 CGCGTTGCGATT
65644 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:67207 original size:24 final size:24
Alignment explanation
Indices: 67180--67250 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
67170 ACGAACGACC
* *
67180 ATAAATGAACATAAATGATTGAAT
1 ATAAACGAACATAAATGAATGAAT
* * *
67204 ATAAACGAATATAAATAAACGAAT
1 ATAAACGAACATAAATGAATGAAT
* *
67228 ATAAACAAACATAAATGACTGAA
1 ATAAACGAACATAAATGAATGAA
67251 CATATTACCG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (24 bp):
ATAAACGAACATAAATGAATGAAT
Found at i:67221 original size:14 final size:14
Alignment explanation
Indices: 67204--67237 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
67194 ATGATTGAAT
67204 ATAAACGAATATAA
1 ATAAACGAATATAA
67218 ATAAACGAATATAA
1 ATAAACGAATATAA
*
67232 ACAAAC
1 ATAAAC
67238 ATAAATGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (14 bp):
ATAAACGAATATAA
Found at i:71722 original size:19 final size:19
Alignment explanation
Indices: 71698--71734 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
71688 ATGACCAATA
*
71698 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
71717 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
71735 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:71843 original size:20 final size:20
Alignment explanation
Indices: 71820--71908 Score: 108
Period size: 20 Copynumber: 4.4 Consensus size: 20
71810 GAATATGTAA
71820 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
71840 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* *
71860 AATCGTAACTCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
71881 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
71901 GTCGCAAC
1 ATCGCAAC
71909 ACTGAATTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 40 0.70
21 13 0.23
22 2 0.04
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:72780 original size:24 final size:24
Alignment explanation
Indices: 72723--72782 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
72713 TAGTCAGTAT
72723 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * * *
72747 CCGGACTTTGATCTTTGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
72771 TCGAATTTTGAT
1 TCGAAATTTGAT
72783 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:75038 original size:18 final size:18
Alignment explanation
Indices: 75015--75049 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
75005 AGCAAAAGGC
75015 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
75033 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
75050 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:75359 original size:140 final size:140
Alignment explanation
Indices: 75107--75389 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
75097 GTAAACGTTG
* *
75107 TATTATGTGAATTTTATGTGTAAATTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGAATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTACTAGTAACTTGAGT
*
75172 TTGAACATTACTATGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTACTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
75237 CGAATTTGAC
131 CGAATTTGAC
*
75247 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTACTAGTAACTTGAGT
1 TATTATGTGAATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTACTAGTAACTTGAGT
**
75312 TTGAACATTGTTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTACTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
75377 CGAATTTGAC
131 CGAATTTGAC
75387 TAT
1 TAT
75390 CGCAACGTGA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTGAATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTACTAGTAACTTGAGT
TTGAACATTACTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:75385 original size:20 final size:20
Alignment explanation
Indices: 75360--75485 Score: 122
Period size: 20 Copynumber: 6.7 Consensus size: 20
75350 TTACACATTC
*
75360 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
75380 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
75400 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
75420 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
75440 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
75454 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
75474 A-TTGACTTTCGC
1 ATTTGACTATCGC
75486 GTTGCGATTT
Statistics
Matches: 87, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
14 10 0.11
16 1 0.01
18 1 0.01
19 9 0.10
20 66 0.76
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:75415 original size:40 final size:40
Alignment explanation
Indices: 75360--75436 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
75350 TTACACATTC
75360 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGTGA
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGTGA
* *
75400 ATTTGATTATCGCAACGGGAATTTGACTATCGCAACG
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACG
75437 AGAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (40 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGTGA
Found at i:75504 original size:20 final size:20
Alignment explanation
Indices: 75475--75532 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
75465 GCAACGCGAA
75475 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
*
75495 TT-AGCTTTCGCATTGCGATT
1 TTGA-CTTTCGCGTTGCGATT
*
75515 TTGACTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
75533 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:75693 original size:13 final size:13
Alignment explanation
Indices: 75646--75697 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
75636 TTTACACATT
75646 AATTAAACAAATC
1 AATTAAACAAATC
** *
75659 AACTTTTACAAATAAG
1 AA-TTAAACAAAT--C
75675 AATTAAACAAATC
1 AATTAAACAAATC
75688 AATTAAACAA
1 AATTAAACAA
75698 GCAAAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
13 12 0.40
14 8 0.27
15 8 0.27
16 2 0.07
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.25
Consensus pattern (13 bp):
AATTAAACAAATC
Found at i:77109 original size:21 final size:21
Alignment explanation
Indices: 77085--77187 Score: 82
Period size: 21 Copynumber: 4.9 Consensus size: 21
77075 GTGGGAGAGA
*
77085 CCTCTTCAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
* **
77106 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* ** *
77127 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGGGG
* * *
77148 TCTCTTGAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-CAGGGG
*
77169 CCTCTTTAACGATGACAGG
1 CCTCTTGAACGATGACAGG
77188 TGAGTCGGGC
Statistics
Matches: 61, Mismatches: 19, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
20 1 0.02
21 59 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:77132 original size:42 final size:42
Alignment explanation
Indices: 77065--77187 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
77055 GTGAATCGGG
* *
77065 CTCTTGAATGGTGGGA-GAGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAGGGGC
* ** * *
77107 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGT
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
* * * * *
77149 CTCTTGAACGATAGGAGAGGCCTCTTTAACGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGG
77188 TGAGTCGGGC
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
42 62 0.95
43 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
Found at i:77688 original size:20 final size:20
Alignment explanation
Indices: 77663--77706 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
77653 AATAGTTTCT
77663 GAAACTTAAAATCACAACAC
1 GAAACTTAAAATCACAACAC
* *
77683 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCACAACAC
77703 GAAA
1 GAAA
77707 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.23, G:0.11, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCACAACAC
Found at i:77716 original size:20 final size:20
Alignment explanation
Indices: 77693--77740 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
77683 GAAACTTAAA
77693 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
77713 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
77733 ATCGCAAC
1 ATCGCAAC
77741 AAGATAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:77808 original size:19 final size:19
Alignment explanation
Indices: 77746--77808 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
77736 GCAACAAGAT
*
77746 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
*
77765 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACTAA
77784 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
77803 ATTCGC
1 AATCGC
77809 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.46, C:0.25, G:0.16, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:77833 original size:20 final size:20
Alignment explanation
Indices: 77804--77841 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
77794 CGAAACTAAA
*
77804 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
77824 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATTTTCA
77842 CGTTGCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:77880 original size:33 final size:34
Alignment explanation
Indices: 77808--77873 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
77798 ACTAAATTCG
* *
77808 CGTTGCGATTTTCATTTTCGCATTGCGATTTTCA
1 CGTTGCAATTTTCATTTTCGCATTGCGATTATCA
*
77842 CGTTGCAATTTTTA-TTTCGCATTGCGATTATC
1 CGTTGCAATTTTCATTTTCGCATTGCGATTATC
77874 TTGTTGCGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.47
Consensus pattern (34 bp):
CGTTGCAATTTTCATTTTCGCATTGCGATTATCA
Found at i:77901 original size:20 final size:20
Alignment explanation
Indices: 77876--77923 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
77866 CGATTATCTT
77876 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
77896 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
77916 GTTGCGAT
1 GTTGCGAT
77924 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:77933 original size:20 final size:20
Alignment explanation
Indices: 77876--77942 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
77866 CGATTATCTT
*
77876 GTTGCGATAGTCAA-ATTCGC
1 GTTGCGATAGT-AAGTTTCGC
* *
77896 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTAAGTTTCGC
** *
77916 GTTGCGATTTTAAGTTTCGT
1 GTTGCGATAGTAAGTTTCGC
77936 GTTGCGA
1 GTTGCGA
77943 CTATTCTTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGTAAGTTTCGC
Found at i:79876 original size:21 final size:21
Alignment explanation
Indices: 79836--79892 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
79826 TCTGTAACTT
79836 AAAATCGCAACACG-AAAATG
1 AAAATCGCAACACGAAAAATG
79856 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACACGAAAAATG
** *
79877 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
79893 TTTGACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACACGAAAAATG
Found at i:79953 original size:20 final size:19
Alignment explanation
Indices: 79836--79957 Score: 67
Period size: 20 Copynumber: 6.4 Consensus size: 19
79826 TCTGTAACTT
*
79836 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
*
79856 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
79877 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
**
79897 ACTATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
79911 ATAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
79930 AAAAATCGCAACGTGAAACT-
1 -AAAATCGCAACGCGAAA-TG
79950 AAAATCGC
1 AAAATCGC
79958 GTTGCGATTT
Statistics
Matches: 84, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.11
16 2 0.02
18 3 0.04
19 11 0.13
20 41 0.49
21 18 0.21
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:80360 original size:22 final size:22
Alignment explanation
Indices: 80334--80384 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
80324 GATAGAGATA
80334 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
80356 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
80378 GACGGAT
1 GACGGAT
80385 GTATGAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:80590 original size:20 final size:20
Alignment explanation
Indices: 80531--80612 Score: 94
Period size: 20 Copynumber: 4.0 Consensus size: 20
80521 TCGTAACGCA
80531 ATAGTCAGAATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
** *
80551 ATTATGT-ATTATCACGTTGCG
1 A-TA-GTCAGAATCGCGTTGCG
*
80572 ATAGTCAGAATCGCGTTGCT
1 ATAGTCAGAATCGCGTTGCG
*
80592 ATAGTCAAAATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
80612 A
1 A
80613 ATCTGGAAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.04
20 32 0.64
21 14 0.28
22 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (20 bp):
ATAGTCAGAATCGCGTTGCG
Found at i:81905 original size:34 final size:34
Alignment explanation
Indices: 81862--81993 Score: 110
Period size: 34 Copynumber: 3.7 Consensus size: 34
81852 GAATGAATTG
81862 TAGTTACGACCCCTCATTAGTAAGTAGCAACTGA
1 TAGTTACGACCCCTCATTAGTAAGTAGCAACTGA
* * *
81896 TAGTCACGA--CC-CATTAGAAAAGAGGTAAGGAA-TGAA
1 TAGTTACGACCCCTCATTAG--TA-A-GT-AGCAACTG-A
*
81932 TTGTAGTTACGACCCCTCAATAGTAAGTAGCAACTGA
1 ---TAGTTACGACCCCTCATTAGTAAGTAGCAACTGA
*
81969 TAGTTACAACCCCTCATTAGTAAGT
1 TAGTTACGACCCCTCATTAGTAAGT
81994 TCAAAATCAA
Statistics
Matches: 76, Mismatches: 9, Indels: 26
0.68 0.08 0.23
Matches are distributed among these distances:
31 6 0.08
32 2 0.03
33 1 0.01
34 32 0.42
35 4 0.05
36 5 0.07
37 5 0.07
38 4 0.05
39 9 0.12
40 1 0.01
41 2 0.03
42 5 0.07
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (34 bp):
TAGTTACGACCCCTCATTAGTAAGTAGCAACTGA
Found at i:81956 original size:73 final size:73
Alignment explanation
Indices: 81836--81972 Score: 265
Period size: 73 Copynumber: 1.9 Consensus size: 73
81826 GAATAGAGTG
*
81836 TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCATTAGTAAGTAGCAACTGATAGTC
1 TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCAATAGTAAGTAGCAACTGATAGTC
81901 ACGACCCA
66 ACGACCCA
81909 TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCAATAGTAAGTAGCAACTGATAGT
1 TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCAATAGTAAGTAGCAACTGATAGT
81973 TACAACCCCT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (73 bp):
TTAGAAAAGAGGTAAGGAATGAATTGTAGTTACGACCCCTCAATAGTAAGTAGCAACTGATAGTC
ACGACCCA
Found at i:84735 original size:21 final size:22
Alignment explanation
Indices: 84711--84752 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
84701 TAGCATTTTT
84711 ATATTT-AATT-TTTTATATTTC
1 ATATTTAAATTATTTT-TATTTC
84732 ATATTTAAATTATTTTTATTT
1 ATATTTAAATTATTTTTATTT
84753 TTTCCCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
ATATTTAAATTATTTTTATTTC
Found at i:88096 original size:17 final size:16
Alignment explanation
Indices: 88070--88101 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
88060 ATATATTTGT
88070 AAATTTTAATTAATTA
1 AAATTTTAATTAATTA
88086 AAATATTTAATTAATT
1 AAAT-TTTAATTAATT
88102 TCAAAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTTAATTAATTA
Found at i:91163 original size:14 final size:14
Alignment explanation
Indices: 91144--91176 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
91134 CTTTCGAACA
91144 TCTTTTT-TTCTTTT
1 TCTTTTTCTT-TTTT
91158 TCTTTTTCTTTTTT
1 TCTTTTTCTTTTTT
91172 TCTTT
1 TCTTT
91177 CATTCAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Done.