Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006099.1 Hibiscus syriacus cultivar Beakdansim tig00014456_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: 120551
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2384 original size:16 final size:16
Alignment explanation
Indices: 2363--2393 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2353 GAACGATCGA
2363 TATCGATGCATCACAG
1 TATCGATGCATCACAG
*
2379 TATCGATTCATCACA
1 TATCGATGCATCACA
2394 AAACATACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (16 bp):
TATCGATGCATCACAG
Found at i:2521 original size:18 final size:18
Alignment explanation
Indices: 2490--2525 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2480 AATTTCTTTA
*
2490 ATATCCCTCTCGTCGTCT
1 ATATCCCTCCCGTCGTCT
*
2508 ATATCTCTCCCGTCGTCT
1 ATATCCCTCCCGTCGTCT
2526 TCATCAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.39, G:0.11, T:0.39
Consensus pattern (18 bp):
ATATCCCTCCCGTCGTCT
Found at i:4136 original size:7 final size:7
Alignment explanation
Indices: 4124--4164 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
4114 AACGCTATAA
4124 TTTTTAT
1 TTTTTAT
4131 TTTTTAT
1 TTTTTAT
4138 TTTTT-T
1 TTTTTAT
4144 TTTTT-T
1 TTTTTAT
4150 TTTTTAT
1 TTTTTAT
4157 TTTTTAT
1 TTTTTAT
4164 T
1 T
4165 ATATTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTAT
Found at i:4145 original size:10 final size:10
Alignment explanation
Indices: 4130--4166 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
4120 ATAATTTTTA
4130 TTTTTTATTT
1 TTTTTTATTT
4140 TTTTTT-TTT
1 TTTTTTATTT
4149 TTTTTTATTT
1 TTTTTTATTT
*
4159 TTTATTAT
1 TTTTTTAT
4167 ATTATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:4152 original size:19 final size:19
Alignment explanation
Indices: 4124--4161 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4114 AACGCTATAA
4124 TTTTTATTTTTTATTTTTT
1 TTTTTATTTTTTATTTTTT
*
4143 TTTTTTTTTTTTATTTTTT
1 TTTTTATTTTTTATTTTTT
4162 ATTATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (19 bp):
TTTTTATTTTTTATTTTTT
Found at i:7688 original size:3 final size:3
Alignment explanation
Indices: 7680--7704 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7670 ACAACTGGCC
7680 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
7705 GATTGAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:15949 original size:15 final size:16
Alignment explanation
Indices: 15929--15959 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15919 GAGAGAAACA
15929 TAAATA-AAGTAATTT
1 TAAATAGAAGTAATTT
15944 TAAATAGAAGTAATTT
1 TAAATAGAAGTAATTT
15960 AAAGAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
TAAATAGAAGTAATTT
Found at i:27269 original size:12 final size:12
Alignment explanation
Indices: 27251--27283 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
27241 TCTATACGGT
27251 ATGAACAGTACC
1 ATGAACAGTACC
*
27263 GTGAACAGTACC
1 ATGAACAGTACC
27275 ATGAACAGT
1 ATGAACAGT
27284 GAAAAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:28170 original size:21 final size:23
Alignment explanation
Indices: 28131--28172 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
28121 GTACCCATGT
*
28131 CATTTCTCTTGTGATCACATATA
1 CATTTCTCTTCTGATCACATATA
28154 CATTT-TCTTCTG-TCACATA
1 CATTTCTCTTCTGATCACATA
28173 CCACATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (23 bp):
CATTTCTCTTCTGATCACATATA
Found at i:28178 original size:22 final size:23
Alignment explanation
Indices: 28131--28178 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
28121 GTACCCATGT
* *
28131 CATTTCTCTTGTGATCACATATA
1 CATTTCTCTTCTGATCACATACA
28154 CATTT-TCTTCTG-TCACATACCA
1 CATTTCTCTTCTGATCACATA-CA
28176 CAT
1 CAT
28179 GTATGTGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.42
Consensus pattern (23 bp):
CATTTCTCTTCTGATCACATACA
Found at i:41220 original size:57 final size:56
Alignment explanation
Indices: 41111--41223 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
41101 TCCAACATCA
* * * * *
41111 TTTCGAACGTGACAATGAGCACTCCCATGATCATCACCATGAAACCAGAAACCATG
1 TTTCAAACATGACAATGAGCACTCCCAAGATCATCACCAAGAAACCAAAAACCATG
41167 TTTCAAACATGACAATGAGCACTCCCAAGTATCATCACCAAGAAACCAAAAACCATG
1 TTTCAAACATGACAATGAGCACTCCCAAG-ATCATCACCAAGAAACCAAAAACCATG
41224 GTTGTGGATA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 26 0.51
57 25 0.49
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (56 bp):
TTTCAAACATGACAATGAGCACTCCCAAGATCATCACCAAGAAACCAAAAACCATG
Found at i:41363 original size:12 final size:12
Alignment explanation
Indices: 41343--41375 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
41333 AGTATTGGTC
*
41343 AGATGTTAATAT
1 AGATCTTAATAT
41355 AGATCTTAATAT
1 AGATCTTAATAT
41367 AGATCTTAA
1 AGATCTTAA
41376 AGTACATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
AGATCTTAATAT
Found at i:41639 original size:132 final size:132
Alignment explanation
Indices: 41415--41654 Score: 408
Period size: 132 Copynumber: 1.8 Consensus size: 132
41405 AATAAAAGTT
* * * * *
41415 TAGAAACATAAATGACAAACGCATAATGTTTTTGTTCTTTGGCACAATATTCTAAAATTTCAGGC
1 TAGAAACATAAATGAAAAACACATAATATTTTTGTTCTTTGGCACAACATTCTAAAATTTCAAGC
* *
41480 AATACTTGTGACATCTTATACTCCAGTATTACAATCATCATTCTCGTAAAACACCATAATTAAAG
66 AATACTTGTGACAACTGATACTCCAGTATTACAATCATCATTCTCGTAAAACACCATAATTAAAG
41545 CC
131 CC
*
41547 TAGAAACATAAATGAAAAACACATAATATTTTTGTTCTTTGGCACAACATTCTCAAATTTCAAGC
1 TAGAAACATAAATGAAAAACACATAATATTTTTGTTCTTTGGCACAACATTCTAAAATTTCAAGC
41612 AATACTTGTGACAACTGATACTCCAGTATTACAATCATCATTC
66 AATACTTGTGACAACTGATACTCCAGTATTACAATCATCATTC
41655 CCTATTTCTT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 100 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (132 bp):
TAGAAACATAAATGAAAAACACATAATATTTTTGTTCTTTGGCACAACATTCTAAAATTTCAAGC
AATACTTGTGACAACTGATACTCCAGTATTACAATCATCATTCTCGTAAAACACCATAATTAAAG
CC
Found at i:43658 original size:36 final size:36
Alignment explanation
Indices: 43609--43688 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
43599 TATATAAAAC
* *
43609 ACATTGAATAGGGGAAAGTAATAAAGCATAAGGAAG
1 ACATTGAACAGGGGAAAGTAATAAAGCACAAGGAAG
*
43645 ACATTGAACAGGGGAAAGTAATAAAGCACAATGAAG
1 ACATTGAACAGGGGAAAGTAATAAAGCACAAGGAAG
43681 ACATTGAA
1 ACATTGAA
43689 TCTCTGAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.50, C:0.09, G:0.25, T:0.16
Consensus pattern (36 bp):
ACATTGAACAGGGGAAAGTAATAAAGCACAAGGAAG
Found at i:45002 original size:15 final size:15
Alignment explanation
Indices: 44982--45018 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
44972 ATTTTTAGCT
*
44982 GGGCGGGCAGATGTG
1 GGGCGGGCAGATGCG
*
44997 GGGCGGGCGGATGCG
1 GGGCGGGCAGATGCG
45012 GGGCGGG
1 GGGCGGG
45019 TAAGGTGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.68, T:0.08
Consensus pattern (15 bp):
GGGCGGGCAGATGCG
Found at i:51895 original size:15 final size:16
Alignment explanation
Indices: 51860--51894 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
51850 ATGTAAACGC
*
51860 AAAATTATATATACTA
1 AAAATAATATATACTA
51876 AAAATAATATATACTA
1 AAAATAATATATACTA
51892 AAA
1 AAA
51895 TCATGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATAATATATACTA
Found at i:52640 original size:172 final size:173
Alignment explanation
Indices: 52353--52701 Score: 691
Period size: 172 Copynumber: 2.0 Consensus size: 173
52343 AATCATTTGA
52353 TTCCCTCCTTTGACCGAAACAAGGCTGTTCACGTATACGAGAGTTGCGAACGACTTCGGGACCCC
1 TTCCCTCCTTTGACCGAAACAAGGCTGTTCACGTATACGAGAGTTGCGAACGACTTCGGGACCCC
52418 ATAAATCGGAAGATCCTTGAGTTCTTGGTTCTTAAGGTTGTAAGAAACAACCAATCCATCAGAGC
66 ATAAATCGGAAGATCCTTGAGTTCTTGGTTCTTAAGGTTGTAAGAAACAACCAATCCATCAGAGC
52483 CTTCCATGAGGATCTCGTCATTTTTCCAAAAAGCCAAAGGCAT
131 CTTCCATGAGGATCTCGTCATTTTTCCAAAAAGCCAAAGGCAT
52526 TTCCCTCCTTTGACCGAAACAAGGCTGTTCACGTATACGAGA-TTGCGAACGACTTCGGGACCCC
1 TTCCCTCCTTTGACCGAAACAAGGCTGTTCACGTATACGAGAGTTGCGAACGACTTCGGGACCCC
52590 ATAAATCGGAAGATCCTTGAGTTCTTGGTTCTTAAGGTTGTAAGAAACAACCAATCCATCAGAGC
66 ATAAATCGGAAGATCCTTGAGTTCTTGGTTCTTAAGGTTGTAAGAAACAACCAATCCATCAGAGC
52655 CTTCCATGAGGATCTCGTCATTTTTCCAAAAAGCCAAAGGCAT
131 CTTCCATGAGGATCTCGTCATTTTTCCAAAAAGCCAAAGGCAT
52698 TTCC
1 TTCC
52702 ACTTTTGTAA
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
172 134 0.76
173 42 0.24
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (173 bp):
TTCCCTCCTTTGACCGAAACAAGGCTGTTCACGTATACGAGAGTTGCGAACGACTTCGGGACCCC
ATAAATCGGAAGATCCTTGAGTTCTTGGTTCTTAAGGTTGTAAGAAACAACCAATCCATCAGAGC
CTTCCATGAGGATCTCGTCATTTTTCCAAAAAGCCAAAGGCAT
Found at i:55519 original size:3 final size:3
Alignment explanation
Indices: 55511--55538 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55501 AGAATGAAAA
55511 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
55539 ATTTGAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:56014 original size:21 final size:21
Alignment explanation
Indices: 55969--56016 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
55959 AATATATGAT
* **
55969 ATTAACGTGACGATTCATATT
1 ATTAATGTGACGATTCATAAA
*
55990 ATTAATGTGACGATTTATAAA
1 ATTAATGTGACGATTCATAAA
56011 ATTAAT
1 ATTAAT
56017 ATAACTATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (21 bp):
ATTAATGTGACGATTCATAAA
Found at i:56752 original size:26 final size:25
Alignment explanation
Indices: 56723--56793 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
56713 TTTTCATCTC
56723 TTAAAATTTTATAAAATTATTTCTTT
1 TTAAAATTTTATAAAATTATTT-TTT
*
56749 TTAAAATTTTATAAAATTAATTTTT
1 TTAAAATTTTATAAAATTATTTTTT
*
56774 TTAAAATTTTATAAATTTAT
1 TTAAAATTTTATAAAATTAT
56794 CGTCTAACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 21 0.50
26 21 0.50
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAAAATTTTATAAAATTATTTTTT
Found at i:56780 original size:25 final size:26
Alignment explanation
Indices: 56723--56788 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
56713 TTTTCATCTC
*
56723 TTAAAATTTTATAAAATTATTTCTTT
1 TTAAAATTTTATAAAATTAATTCTTT
56749 TTAAAATTTTATAAAATTAATT-TTT
1 TTAAAATTTTATAAAATTAATTCTTT
56774 TTAAAATTTTATAAA
1 TTAAAATTTTATAAA
56789 TTTATCGTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 18 0.46
26 21 0.54
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTAAAATTTTATAAAATTAATTCTTT
Found at i:63745 original size:228 final size:226
Alignment explanation
Indices: 63343--63790 Score: 756
Period size: 228 Copynumber: 2.0 Consensus size: 226
63333 GTAAATTATC
* *
63343 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA-CTTTAGT
**
63408 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
65 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
63473 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
130 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
63538 AAACATAAATTACATAACTTTCAAAAAAGTATA
195 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
63571 TATCATTTTTATAAAAGTGTTCATACTTATTTCACTGTTGAAAACATATTTATTAAATTA-TTTG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATT--ATTACTTTA
*
63635 GTTAATATTGTTAAATTTAAATTCTAAATAATA-TTTATAAAATATCAAAACAATCAAATAAAAT
63 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
* *
63699 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
128 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
63764 TGAAACATAAATTACATAACTTTAAAA
193 TGAAACATAAATTACATAACTTTAAAA
63791 GCAGTTTTAA
Statistics
Matches: 208, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
227 4 0.02
228 150 0.72
229 50 0.24
231 4 0.02
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTACTTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:63878 original size:20 final size:19
Alignment explanation
Indices: 63855--63900 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
63845 CGATATACCA
63855 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
63875 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
63895 GGTAAA
1 GGTAAA
63901 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:64045 original size:20 final size:19
Alignment explanation
Indices: 64022--64068 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
64012 CGATATAACA
64022 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
64042 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
64062 GGTAAAA
1 GGTAAAA
64069 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:64070 original size:17 final size:18
Alignment explanation
Indices: 64026--64073 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
64016 ATAACAGGTA
64026 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
64045 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
64065 -AAAATGATA
1 AAAAATGATA
64074 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:66349 original size:21 final size:21
Alignment explanation
Indices: 66302--66366 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
66292 AAGACAATCA
* *
66302 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
66324 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
66344 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
66365 AG
1 AG
66367 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:66442 original size:33 final size:33
Alignment explanation
Indices: 66400--66462 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
66390 AAATAGATGG
*
66400 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
66433 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGG
66463 GTGATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.49, T:0.22
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:68034 original size:19 final size:19
Alignment explanation
Indices: 68010--68058 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
68000 AATGTCGAGT
68010 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
68029 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
68048 TATTTTTGTAT
1 TAATTTTGTAT
68059 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:68751 original size:198 final size:198
Alignment explanation
Indices: 68177--70729 Score: 4915
Period size: 198 Copynumber: 12.9 Consensus size: 198
68167 CAATATGGCC
* *
68177 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
68242 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
68307 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
68372 TGGAA
195 TGG-A
68377 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
68442 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
68507 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
68572 GGAA
196 GG-A
68576 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
68640 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
68705 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
68770 GGA
196 GGA
68773 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
68838 TAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
68902 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
68966 GGA
196 GGA
*
68969 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
69034 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
69099 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
69164 GGAA
196 GG-A
69168 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
69233 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
69298 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
69363 GGAA
196 GG-A
69367 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
69432 C-AAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTATAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
69495 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
69560 GGA
196 GGA
69563 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
69628 TAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
69693 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
69758 GGA
196 GGA
69761 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
69826 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
69891 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
69956 GGAA
196 GG-A
69960 AACAAGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
70024 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
70089 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
70154 GGA
196 GGA
70157 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
70222 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
70287 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
70352 GGA
196 GGA
70355 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
70418 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
70483 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
70548 GGAA
196 GG-A
70552 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
70617 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
70682 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTATGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
70730 AATTTAAATA
Statistics
Matches: 2329, Mismatches: 13, Indels: 23
0.98 0.01 0.01
Matches are distributed among these distances:
196 317 0.14
197 402 0.17
198 976 0.42
199 600 0.26
200 34 0.01
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGA
Found at i:69734 original size:791 final size:794
Alignment explanation
Indices: 68177--70729 Score: 4971
Period size: 791 Copynumber: 3.2 Consensus size: 794
68167 CAATATGGCC
*
68177 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCAATCCCAAAATCATCGAAC
68242 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
68307 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
68372 TGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
195 TGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
68437 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
260 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
68502 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAA
325 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAA
68567 TGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAAT
390 TGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAT
68631 CATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTT
455 CATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTT
68696 TTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCC
520 TTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCC
68761 AGAATGAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
585 AGAATGAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
68826 AATCATCGAACCTAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCG
650 AATCATCGAACCTAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCG
68890 GTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTT
715 GTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTT
68954 CCCAGAATGAATGGA
780 CCCAGAATGAATGGA
68969 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
69034 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
69099 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
69164 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
69229 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
69294 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
69359 GAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
391 GAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
69424 ATCGAACCC-AAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTATAATTATACCGGTTT
456 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTT
69487 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCA
521 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCA
69552 GAATGAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
586 GAATGAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
69617 ATCATCGAACCTAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG
651 ATCATCGAACCTAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG
69682 TTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTC
716 TTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTC
69747 CCAGAATGAATGGA
781 CCAGAATGAATGGA
*
69761 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
69826 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
69891 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
69956 GGAAAACAAGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
70020 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
70085 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
70150 GAATGG-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
391 GAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
*
70214 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
456 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTT
70279 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCA
521 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCA
70344 GAATGAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AA
586 GAATGAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
*
70407 ATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG
651 ATCATCGAACCTAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG
70472 TTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTC
716 TTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTC
70537 CCAGAATGAATGGAA
781 CCAGAATGAATGG-A
*
70552 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
70617 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
70682 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTATGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
70730 AATTTAAATA
Statistics
Matches: 1750, Mismatches: 5, Indels: 13
0.99 0.00 0.01
Matches are distributed among these distances:
790 408 0.23
791 906 0.52
792 436 0.25
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (794 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
GAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTT
TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCA
GAATGAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
ATCATCGAACCTAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG
TTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTC
CCAGAATGAATGGA
Found at i:72205 original size:3 final size:3
Alignment explanation
Indices: 72197--72271 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
72187 TGAAGCTGAC
* * ** * *
72197 GAT GAT GAT GAT GAT GAC GAT GAA GAT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
72245 GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
72272 CCAAACAAGT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.36, C:0.04, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:73811 original size:183 final size:183
Alignment explanation
Indices: 73471--74164 Score: 1241
Period size: 183 Copynumber: 3.8 Consensus size: 183
73461 CAAAGTTTTC
* * * *
73471 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* * *
73536 ACAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
*
73599 TATAACCGGTATAAATATACCGG-TTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
73654 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
73719 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
73784 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
73837 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
73902 AAAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
73967 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
74020 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
74085 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
74150 AACCGGTATAAAAAT
131 AACCGGTATAAAAAT
74165 GTGTCGATAC
Statistics
Matches: 496, Mismatches: 12, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
182 65 0.13
183 428 0.86
185 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:74196 original size:22 final size:23
Alignment explanation
Indices: 74160--74202 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
74150 AACCGGTATA
74160 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATACCTTTTTAT
* *
74183 AAAA-GTGTCTATACTTTTTT
1 AAAATGTGTCGATACCTTTTT
74203 CACTGTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (23 bp):
AAAATGTGTCGATACCTTTTTAT
Found at i:74462 original size:25 final size:25
Alignment explanation
Indices: 74428--74478 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
74418 ACAACAAATC
*
74428 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
74453 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
74478 A
1 A
74479 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:74748 original size:18 final size:18
Alignment explanation
Indices: 74727--74763 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
74717 GTAATTGGAG
74727 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
74745 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
74763 T
1 T
74764 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:74771 original size:24 final size:24
Alignment explanation
Indices: 74719--74765 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
74709 TTTCATATGT
* *
74719 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
74743 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
74766 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:75064 original size:39 final size:39
Alignment explanation
Indices: 75021--75146 Score: 225
Period size: 39 Copynumber: 3.2 Consensus size: 39
75011 TCCGATGCTC
* *
75021 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
75060 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
*
75099 ATCAAAATCCAAATATCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
75138 ATCAAAATC
1 ATCAAAATC
75147 TACAACTTGA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:75580 original size:23 final size:23
Alignment explanation
Indices: 75549--75612 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
75539 ATAGGTAAAC
*
75549 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
75572 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
75595 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
75613 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:75619 original size:23 final size:23
Alignment explanation
Indices: 75549--75621 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
75539 ATAGGTAAAC
* **
75549 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
75572 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
75595 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
75618 ATAT
1 ATAT
75622 TTAGTAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:86543 original size:111 final size:111
Alignment explanation
Indices: 86349--86572 Score: 430
Period size: 111 Copynumber: 2.0 Consensus size: 111
86339 TCCCAGTCTA
86349 GAGCTTCCTCTTCATTTTCTTAGATAGGCATAGATGGTGTTTGTTACGTGCTCATGAAGCTCGGA
1 GAGCTTCCTCTTCATTTTCTTAGATAGGCATAGATGGTGTTTGTTACGTGCTCATGAAGCTCGGA
86414 GGATCTTTCTTCGAGAAAAAGATCCTGGGTTTATCACTGCTTACCT
66 GGATCTTTCTTCGAGAAAAAGATCCTGGGTTTATCACTGCTTACCT
* *
86460 GAGCTTCCTCTTCATTTTCTTAGATGGGCATAGATGGTGTTTGTTACGTGCTCGTGAAGCTCGGA
1 GAGCTTCCTCTTCATTTTCTTAGATAGGCATAGATGGTGTTTGTTACGTGCTCATGAAGCTCGGA
86525 GGATCTTTCTTCGAGAAAAAGATCCTGGGTTTATCACTGCTTACCT
66 GGATCTTTCTTCGAGAAAAAGATCCTGGGTTTATCACTGCTTACCT
86571 GA
1 GA
86573 TGCCCTAATC
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (111 bp):
GAGCTTCCTCTTCATTTTCTTAGATAGGCATAGATGGTGTTTGTTACGTGCTCATGAAGCTCGGA
GGATCTTTCTTCGAGAAAAAGATCCTGGGTTTATCACTGCTTACCT
Found at i:89327 original size:7 final size:7
Alignment explanation
Indices: 89315--89344 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
89305 GTCATTACCT
89315 GTCAATA
1 GTCAATA
89322 GTCAATA
1 GTCAATA
89329 GTCAATA
1 GTCAATA
89336 GTCAATA
1 GTCAATA
89343 GT
1 GT
89345 ACGACTTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (7 bp):
GTCAATA
Found at i:97707 original size:2 final size:2
Alignment explanation
Indices: 97700--97729 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
97690 AATATCAAAT
97700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97730 CTAACAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:104644 original size:33 final size:30
Alignment explanation
Indices: 104601--104676 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
104591 TATTAAGGTA
* * *
104601 TATTTTATTATATTTAGTATTTTTTTAGTAATT
1 TATTTAATTATATTTA--A-TTATTTAATAATT
*
104634 TATTTAATTAT-TTTAATTATTTAATATTT
1 TATTTAATTATATTTAATTATTTAATAATT
104663 TATTTAATTA-ATTT
1 TATTTAATTATATTT
104677 TTTTTGCAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 23 0.61
30 1 0.03
32 4 0.11
33 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (30 bp):
TATTTAATTATATTTAATTATTTAATAATT
Found at i:104663 original size:16 final size:16
Alignment explanation
Indices: 104633--104678 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
104623 TTTTAGTAAT
104633 TTATTTAATTATTTTAA
1 TTATTTAA-TATTTTAA
*
104650 TTATTTAATATTTTAT
1 TTATTTAATATTTTAA
*
104666 TTAATTAAT-TTTT
1 TTATTTAATATTTT
104679 TTTGCAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTAATATTTTAA
Found at i:113204 original size:30 final size:29
Alignment explanation
Indices: 113139--113204 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
113129 TATATTTTGG
* * * *
113139 ACATTTTACTAAAAATATTAAAAATATTG
1 ACATTTTAATAAAAATAATAAAAATAATA
* *
113168 ATATTTTAAATAAAAATAATAAAACTAATA
1 ACATTTT-AATAAAAATAATAAAAATAATA
113198 ACATTTT
1 ACATTTT
113205 TTTAACTATA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (29 bp):
ACATTTTAATAAAAATAATAAAAATAATA
Found at i:113796 original size:22 final size:23
Alignment explanation
Indices: 113757--113812 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
113747 ATCATTTTAA
113757 TAAAATATTAGTTATTAA-ATATT
1 TAAAATA-TAGTTATTAATATATT
* *
113780 TAAAATATATTTATTAATATTTT
1 TAAAATATAGTTATTAATATATT
113803 TAATAATATA
1 TAA-AATATA
113813 ATATCATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.31
23 14 0.48
24 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TAAAATATAGTTATTAATATATT
Found at i:113804 original size:12 final size:12
Alignment explanation
Indices: 113775--113812 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
113765 TAGTTATTAA
113775 ATATTTAA-AAT
1 ATATTTAATAAT
*
113786 ATATTTATTAAT
1 ATATTTAATAAT
*
113798 ATTTTTAATAAT
1 ATATTTAATAAT
113810 ATA
1 ATA
113813 ATATCATATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTAATAAT
Done.