Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001918.1 Hibiscus syriacus cultivar Beakdansim tig00003881_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: 57243
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:168 original size:18 final size:18
Alignment explanation
Indices: 125--159 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
115 TTTGCCAACC
125 ACGACCA-TTGTGCTGAT
1 ACGACCATTTGTGCTGAT
142 ACGACCATTTGTGCTGAT
1 ACGACCATTTGTGCTGAT
160 GTCGCCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (18 bp):
ACGACCATTTGTGCTGAT
Found at i:5033 original size:13 final size:14
Alignment explanation
Indices: 5015--5046 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
5005 TTAGTGAGGC
5015 ATAATAATAATA-T
1 ATAATAATAATACT
5028 ATAATAATAATACT
1 ATAATAATAATACT
5042 ATAAT
1 ATAAT
5047 GAAATGGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATAATAATACT
Found at i:5259 original size:23 final size:22
Alignment explanation
Indices: 5233--5309 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
5223 CATCACAGCT
*
5233 CGTATAAATGCACCGAAATGCCA
1 CGTA-AAATGCACCGAAGTGCCA
* *
5256 CGTAAAATTGCACCGAAGTGTCG
1 CGTAAAA-TGCACCGAAGTGCCA
*
5279 CGTAGAAATGCACTGAAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
*
5302 TGTAAAAT
1 CGTAAAAT
5310 TGTCCATAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 7 0.16
23 35 0.78
24 3 0.07
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (22 bp):
CGTAAAATGCACCGAAGTGCCA
Found at i:5418 original size:20 final size:20
Alignment explanation
Indices: 5390--5428 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5380 CAAAGGACCC
*
5390 CATAAATGTTCCAAAGGATA
1 CATAAATGTCCCAAAGGATA
* *
5410 CATATATGTCCCGAAGGAT
1 CATAAATGTCCCAAAGGAT
5429 CACGTAGACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
CATAAATGTCCCAAAGGATA
Found at i:6062 original size:36 final size:36
Alignment explanation
Indices: 6015--6084 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
6005 ATTTCAAAAA
6015 ATGGTATCGATACCTA-CCTTTCTGGTATCGATACTC
1 ATGGTATCGATA-CTACCCTTTCTGGTATCGATACTC
*
6051 ATGGTATCGATACTACCCTTTTTGGTATCGATAC
1 ATGGTATCGATACTACCCTTTCTGGTATCGATAC
6085 CCTATGGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 3 0.09
36 29 0.91
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (36 bp):
ATGGTATCGATACTACCCTTTCTGGTATCGATACTC
Found at i:8404 original size:14 final size:14
Alignment explanation
Indices: 8385--8411 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8375 CACTAACTTT
8385 TTTATTTTATTTTA
1 TTTATTTTATTTTA
8399 TTTATTTTATTTT
1 TTTATTTTATTTT
8412 TATATTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:8423 original size:26 final size:25
Alignment explanation
Indices: 8383--8431 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
8373 ACCACTAACT
8383 TTTTTATTTTATTTT-ATTTATTTTA
1 TTTTTATTTTATTTTCA-TTATTTTA
*
8408 TTTTTATATTTGTTTTCATTATTT
1 TTTTTAT-TTTATTTTCATTATTT
8432 GATTCGACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (25 bp):
TTTTTATTTTATTTTCATTATTTTA
Found at i:8472 original size:122 final size:123
Alignment explanation
Indices: 8316--8631 Score: 469
Period size: 122 Copynumber: 2.6 Consensus size: 123
8306 TATTACTCGG
* *
8316 CCTTGTGGTGACCAGATCAGGGGTAAGATCCACATTATTATGGTTCGAACTCTCCTAACCACTAA
1 CCTTGTGGTGACCCGATCAGGGGTAAGATCCACATTATTATGGTTCGAACTCTGCTAACCACTAA
*
8381 CTTTTTTATTTTATTTTATTTATTTTA-TTTTTATATTTGTTTT-CATTATTTGATTCGA
66 CTTTTTTATTTTA-TTTATTTATTTTATTTTTTATATTT-TTTTGCATTATTCGATTCGA
* *
8439 CCTTGTGGTGACCCGATC-CGGGTAAGATCCACATTATTATGGTTC-AGACTCTGCTAACCCCTA
1 CCTTGTGGTGACCCGATCAGGGGTAAGATCCACATTATTATGGTTCGA-ACTCTGCTAACCACTA
8502 ACTTTTTTATTTTATTTATTTATTTTATTTTTTTATATTTTTTTGCATTATTCGATTCGA
65 ACTTTTTTATTTTATTTATTTATTTTA-TTTTTTATATTTTTTTGCATTATTCGATTCGA
* * * * * *
8562 CCTTATGGTAACCCGATCTGGGGTAAGATCCACATTATTATGGTCCGGACTCTGCTAACCGCTAA
1 CCTTGTGGTGACCCGATCAGGGGTAAGATCCACATTATTATGGTTCGAACTCTGCTAACCACTAA
8627 CTTTT
66 CTTTT
8632 CTAATTTACT
Statistics
Matches: 176, Mismatches: 11, Indels: 11
0.89 0.06 0.06
Matches are distributed among these distances:
121 14 0.08
122 58 0.33
123 58 0.33
124 46 0.26
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (123 bp):
CCTTGTGGTGACCCGATCAGGGGTAAGATCCACATTATTATGGTTCGAACTCTGCTAACCACTAA
CTTTTTTATTTTATTTATTTATTTTATTTTTTATATTTTTTTGCATTATTCGATTCGA
Found at i:8542 original size:9 final size:8
Alignment explanation
Indices: 8504--8544 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 8
8494 AACCCCTAAC
8504 TTTTTTAT
1 TTTTTTAT
8512 TTTATTTAT
1 TTT-TTTAT
8521 TTATTTTAT
1 TT-TTTTAT
8530 TTTTTTAT
1 TTTTTTAT
8538 ATTTTTT
1 -TTTTTT
8545 TGCATTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 9 0.30
9 20 0.67
10 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTAT
Found at i:8545 original size:13 final size:13
Alignment explanation
Indices: 8504--8537 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
8494 AACCCCTAAC
8504 TTTTTTATTTTAT
1 TTTTTTATTTTAT
*
8517 TTATTTATTTTAT
1 TTTTTTATTTTAT
8530 TTTTTTAT
1 TTTTTTAT
8538 ATTTTTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTATTTTAT
Found at i:8665 original size:124 final size:119
Alignment explanation
Indices: 8316--8667 Score: 418
Period size: 124 Copynumber: 2.8 Consensus size: 119
8306 TATTACTCGG
* * *
8316 CCTTGTGGTGACCAGATCAGGGGTAAGATCCACATTATTATGGTTCGAACTCTCCTAACCACTAA
1 CCTTGTGGTGACCCGATC-GGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACCACTAA
* * *
8381 CTTTTTTATTTTATTTTATTTATTTTATTTTTATATTTGTTTTCATTATTTGATTCGA
65 CTTTTTTATTTTATATTATTTATTTTA-TTTTAT-TTT-TTTGCATTATTCGATTCGA
* * *
8439 CCTTGTGGTGACCCGATCCGGGTAAGATCCACATTATTATGGTTCAGACTCTGCTAACCCCTAAC
1 CCTTGTGGTGACCCGATCGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACCACTAAC
8504 TTTTTTATTTTAT-TTATTTATTTTATTTTTTTATATTTTTTTGCATTATTCGATTCGA
66 TTTTTTATTTTATATTATTTATTTTA----TTT-TATTTTTTTGCATTATTCGATTCGA
* * * *
8562 CCTTATGGTAACCCGATCTGGGGTAAGATCCACATTATTATGGTCCGGACTCTGCTAACCGCTAA
1 CCTTGTGGTGACCCGATC-GGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACCACTAA
* * **
8627 CTTTTCTAATTTACTAACATTCTAACTTTTATTTTATTTTT
65 CTTTTTTATTTTA-TATTATT-T-A-TTTTATTTTATTTTT
8668 CATACTAACA
Statistics
Matches: 201, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
121 12 0.06
122 55 0.27
123 50 0.25
124 67 0.33
125 7 0.03
126 3 0.01
127 1 0.00
128 1 0.00
129 5 0.02
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (119 bp):
CCTTGTGGTGACCCGATCGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACCACTAAC
TTTTTTATTTTATATTATTTATTTTATTTTATTTTTTTGCATTATTCGATTCGA
Found at i:8737 original size:74 final size:75
Alignment explanation
Indices: 8632--8797 Score: 246
Period size: 74 Copynumber: 2.2 Consensus size: 75
8622 GCTAACTTTT
* *
8632 CTAATTTACTAACATTCTAACTTTTATTTTATTTTTCATACTAACATTA-TAAC-TTTTTATTTT
1 CTAACTTACTAACATTCTAACTTTTATTTTATTGTTCATACTAACA-TACTAACTTTTTTATTTT
8695 TATTGTTCTTA
65 TATTGTTCTTA
* **
8706 CTAACTTACTAATATTCTAACTTTTATTTTATTGTTCATACTAACATACTGTCTTTTTTTATTTT
1 CTAACTTACTAACATTCTAACTTTTATTTTATTGTTCATACTAACATACTAAC-TTTTTTATTTT
8771 TATTGTTCTTA
65 TATTGTTCTTA
*
8782 CTAACTTACGAACATT
1 CTAACTTACTAACATT
8798 TTATTTTTGT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
73 2 0.02
74 45 0.55
76 35 0.43
ACGTcount: A:0.28, C:0.15, G:0.03, T:0.54
Consensus pattern (75 bp):
CTAACTTACTAACATTCTAACTTTTATTTTATTGTTCATACTAACATACTAACTTTTTTATTTTT
ATTGTTCTTA
Found at i:8748 original size:40 final size:42
Alignment explanation
Indices: 8668--8755 Score: 126
Period size: 40 Copynumber: 2.1 Consensus size: 42
8658 TTTTATTTTT
*
8668 CATACTAACATTATAACTTTTTATTTTTATTGTTCTTACTAA
1 CATACTAACATTATAACTTTTTATTTTTATTGTTCATACTAA
* * *
8710 CTTACTAATATTCTAAC-TTTTA-TTTTATTGTTCATACTAA
1 CATACTAACATTATAACTTTTTATTTTTATTGTTCATACTAA
8750 CATACT
1 CATACT
8756 GTCTTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 22 0.54
41 5 0.12
42 14 0.34
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (42 bp):
CATACTAACATTATAACTTTTTATTTTTATTGTTCATACTAA
Found at i:10516 original size:2 final size:2
Alignment explanation
Indices: 10509--10542 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10499 ATTAAAGTAA
10509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10543 GGTTTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10663 original size:2 final size:2
Alignment explanation
Indices: 10656--10683 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10646 CAAATATTTC
10656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10684 TAATGTGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11813 original size:15 final size:16
Alignment explanation
Indices: 11784--11815 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
11774 GGGGCGGGCT
11784 GAGGCATCTGGTAGTG
1 GAGGCATCTGGTAGTG
11800 GAGGCATC-GGTAGTG
1 GAGGCATCTGGTAGTG
11815 G
1 G
11816 CGGCTGGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.19, C:0.12, G:0.47, T:0.22
Consensus pattern (16 bp):
GAGGCATCTGGTAGTG
Found at i:13051 original size:41 final size:42
Alignment explanation
Indices: 13001--13102 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
12991 GCCCGAAGTT
* * * * *
13001 CTTATAGATGGCCCAAAGGACTT-ATCATCTTGCTCGAAAGG
1 CTTAAAGATGACCCAAAGGACTTAAGCATCATGCTCGAAAGA
* *
13042 CTTAAAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTAAAGATGACCCAAAGGACTTAAGCATCATGCTCGAAAGA
**
13084 CTTACGGATGACCCGAAAG
1 CTTAAAGATGACCC-AAAG
13103 ATTTACAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
41 19 0.39
42 27 0.55
43 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (42 bp):
CTTAAAGATGACCCAAAGGACTTAAGCATCATGCTCGAAAGA
Found at i:13082 original size:42 final size:42
Alignment explanation
Indices: 13026--13107 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
13016 AAGGACTTAT
* * *
13026 CATCTTGCTCGAAAGGCTTAAAGATGACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTAAAGATGACCCGAAAGATTTAAG
**
13068 CATCATGCTCGAAAGACTTACGGATGACCCGAAAGATTTA
1 CATCATGCTCGAAAGACTTAAAGATGACCCGAAAGATTTA
13108 CAAATCAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTAAAGATGACCCGAAAGATTTAAG
Found at i:13337 original size:262 final size:263
Alignment explanation
Indices: 12453--13638 Score: 1690
Period size: 263 Copynumber: 4.5 Consensus size: 263
12443 CAATGGAAAT
* * * * *
12453 TTTGAAAACATTCTACCTGAAGGTCTTATGAATGGCCCGAAGGACTTATCATCTTGCTCGAAAGG
1 TTTGAAAACATCCTGCCCGAAGGTCTTATG-ATGGCCAGAAGGTCTTATCATCTTGCTCGAAAGG
* * * * *
12518 ATTATAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTGCATAT-ATCCCGAAGGACT
65 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGATGA-CCCGAAGGATT
* * * **
12582 TACGAATCAATAAACCCTCGAAAGCTTAGTTTCTTAGTTATCAAGGAATCCCTTTGTTATCCTTA
129 TACAAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTTTGTTAGGCTTA
* *
12647 GCTTCCTTTAACAACTCTTTTGATATAATTAGTG-AACCCCTCAAAATTAGGCTTAGTTTCTAAA
194 GCTTCCTTTAACAACTCTTTTGAGATAATTAG-GAAACCCCTTAAAATTAGGCTTAGTTTCTAAA
12711 ATCTCA
258 ATCTCA
* * * * *
12717 TTTGGAAATATCCTGCCTGAAGGTCTTATGGTAGGCCCA-AAGGTCTTATCATCTTGTTCGAAAG
1 TTTGAAAACATCCTGCCCGAAGGTCTTATGAT-GG-CCAGAAGGTCTTATCATCTTGCTCGAAAG
* * * *
12781 GCTTACAGATGACCTGAAGGATTTAAGCATCATGGTCGAAAGACTTACGGATGACCCGAAGGATT
64 GCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATT
*
12846 TAAAAATCAAG-AACCCTCGAAAGCTTAGTTTCTTAGTTATCAAGGAA-CCCTTTGTTAGG-TTA
129 TACAAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTTTGTTAGGCTTA
12908 GCTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAA
194 GCTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAA
12973 TCTCA
259 TCTCA
* *
12978 TTTGAAAACAT-CTGCCCGAAGTTCTTATAGATGGCCCA-AAGGACTTATCATCTTGCTCGAAAG
1 TTTGAAAACATCCTGCCCGAAGGTCTTAT-GATGG-CCAGAAGGTCTTATCATCTTGCTCGAAAG
* * *
13041 GCTTAAAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACGGATGACCCGAAAGATT
64 GCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATT
* *
13106 TACAAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTAGTTAGGCTTA
129 TACAAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTTTGTTAGGCTTA
*
13171 GCTTCCTTTAACAACTC-TTTGAGATCATTAGGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAA
194 GCTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAA
13235 TCTCA
259 TCTCA
*
13240 TTTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCAGAAGGTCTTATCATCTTGCTCAAAAGG
1 TTTGAAAACATCCTGCCCGAAGGTCTTAT-GATGGCCAGAAGGTCTTATCATCTTGCTCGAAAGG
* * * * * * *
13305 CTTATAGATGA-CCGAAGGAATTAAACATCATGCTCGAAAGACTTAAATATGGCCCGAATGACTT
65 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTT
** * * * *
13369 ATGAATCAAGAAACCCTCGAAATCTTAGTTTCTTAGTTGTCAATGAACCTCTTTGTTAGGCTTAG
130 ACAAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTTTGTTAGGCTTAG
* *
13434 CTTCCTTTAACAACTCTTTTGAGATAATTAGGAAATCTCTTAAAATTAGGCTTAGTTTCTAAAAT
195 CTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAAT
13499 CTCA
260 CTCA
* * **
13503 TTTGAAAACATTCTACCCGAAGGTCTTATGGATGGCTTGAAGGTCTTATCATCTTGCTCGAAAGG
1 TTTGAAAACATCCTGCCCGAAGGTCTTAT-GATGGCCAGAAGGTCTTATCATCTTGCTCGAAAGG
* * * *
13568 CTTATAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGACTCGAATGATTT
65 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTT
13633 ACAAAT
130 ACAAAT
13639 TCGGGAAATA
Statistics
Matches: 835, Mismatches: 75, Indels: 24
0.89 0.08 0.03
Matches are distributed among these distances:
260 116 0.14
261 115 0.14
262 206 0.25
263 232 0.28
264 163 0.20
265 3 0.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (263 bp):
TTTGAAAACATCCTGCCCGAAGGTCTTATGATGGCCAGAAGGTCTTATCATCTTGCTCGAAAGGC
TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
CAAATCAAGAAACCCTCGAAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTTTGTTAGGCTTAGC
TTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAATC
TCA
Found at i:13608 original size:42 final size:42
Alignment explanation
Indices: 13552--13633 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
13542 AAGGTCTTAT
* *
13552 CATCTTGCTCGAAAGGCTTA-TAGATGACCCGAAGGATTTAAA
1 CATCATGCTCGAAAGACTTACT-GATGACCCGAAGGATTTAAA
* *
13594 CATCATGCTCGAAAGACTTACTGATGACTCGAATGATTTA
1 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTA
13634 CAAATTCGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAAA
Found at i:17158 original size:29 final size:29
Alignment explanation
Indices: 17124--17181 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
17114 TCTCGACATG
17124 ATATGGTCCAAATAGCCTTGTTCGAGATC
1 ATATGGTCCAAATAGCCTTGTTCGAGATC
17153 ATATGGTCCAAATAGCCTTGTTCGAGATC
1 ATATGGTCCAAATAGCCTTGTTCGAGATC
17182 TAATTAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (29 bp):
ATATGGTCCAAATAGCCTTGTTCGAGATC
Found at i:18862 original size:21 final size:22
Alignment explanation
Indices: 18838--18883 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
18828 AAAATATAAC
18838 AATTGATATTTT-A-TATTTTTA
1 AATTGA-ATTTTAATTATTTTTA
*
18859 AATTTAATTTTAATTATTTTTA
1 AATTGAATTTTAATTATTTTTA
18881 AAT
1 AAT
18884 ATTTATTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 6 0.27
22 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
AATTGAATTTTAATTATTTTTA
Found at i:23947 original size:85 final size:85
Alignment explanation
Indices: 23833--24000 Score: 196
Period size: 85 Copynumber: 2.0 Consensus size: 85
23823 GGTGACACGC
* * * * * * *
23833 ATTTATGACTCACATTTATGACGCGCATTG-AGCGTTATTGAAGCCCCCGTCA-TAAATGAAGAT
1 ATTTATGACACACATGTATGACGCACATTGCA-CGTCATTGAAGCACACGTCATTAAA-AAAGAT
*
23896 GACACACATTTGTGTGTCATAA
64 GACACACATTCGTGTGTCATAA
* * * *
23918 ATTTATGACACGCATGTATGACTCACATTGCATGTCATTGAAGCACACGTCATTAAAAAAGATGG
1 ATTTATGACACACATGTATGACGCACATTGCACGTCATTGAAGCACACGTCATTAAAAAAGATGA
23983 CACACATTCGTGTGTCAT
66 CACACATTCGTGTGTCAT
24001 GATTGTATTT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 64 0.93
86 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (85 bp):
ATTTATGACACACATGTATGACGCACATTGCACGTCATTGAAGCACACGTCATTAAAAAAGATGA
CACACATTCGTGTGTCATAA
Found at i:24025 original size:2 final size:2
Alignment explanation
Indices: 24018--24046 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24008 TTTCGTAAAT
24018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24047 GTAGATTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32758 original size:5 final size:5
Alignment explanation
Indices: 32748--32826 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
32738 AACGGTCAAC
* *
32748 GGTCG GGTCG GGTCG GGTCAAC GGTC- GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
32796 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
32827 TGACCGGTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.06
5 46 0.74
7 12 0.19
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:32769 original size:22 final size:22
Alignment explanation
Indices: 32741--32826 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
32731 AACGGTCAAC
32741 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
32763 GGTCAACGGTC-GGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
32784 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
32806 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
32827 TGACCGGTCA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
21 21 0.33
22 42 0.67
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:32773 original size:17 final size:18
Alignment explanation
Indices: 32753--32826 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 18
32743 TCAACGGTCG
32753 GGTCGGGTCGGGTCAACGGTC
1 GGTCGGGTCGGGTCAA--G-C
32774 GGTCGGGTCGGGTCAACGGTC
1 GGTCGGGTCGGGTCAA--G-C
32795 GGGTCGGGTCGGGTCAA-C
1 -GGTCGGGTCGGGTCAAGC
32813 GGTCGGGTCGGGTC
1 GGTCGGGTCGGGTC
32827 TGACCGGTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.27
18 1 0.02
21 21 0.40
22 16 0.31
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCGGGTCAAGC
Found at i:32790 original size:43 final size:44
Alignment explanation
Indices: 32741--32826 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 44
32731 AACGGTCAAC
32741 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTC-GGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCGGGTCG
32784 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCGGGTC
32827 TGACCGGTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 33 0.79
44 9 0.21
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (44 bp):
GGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCGGGTCG
Found at i:32841 original size:9 final size:9
Alignment explanation
Indices: 32829--32920 Score: 78
Period size: 9 Copynumber: 9.7 Consensus size: 9
32819 GTCGGGTCTG
32829 ACCGGTCAA
1 ACCGGTCAA
*
32838 ACCGGTTCAG
1 ACCGG-TCAA
32848 ACCGGTCAA
1 ACCGGTCAA
*
32857 ACCGGTTCGA
1 ACCGG-TCAA
*
32867 ACCGGTTGAA
1 ACCGG-TCAA
32877 ACCGGTCAA
1 ACCGGTCAA
32886 ACC-GTCAGA
1 ACCGGTCA-A
*
32895 ACCGGTTGAAA
1 ACCGG-T-CAA
*
32906 ACCGGTTAA
1 ACCGGTCAA
32915 ACCGGT
1 ACCGGT
32921 TTCCAGCAGC
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
8 4 0.06
9 31 0.45
10 26 0.38
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:32850 original size:19 final size:19
Alignment explanation
Indices: 32828--32921 Score: 86
Period size: 19 Copynumber: 4.9 Consensus size: 19
32818 GGTCGGGTCT
32828 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
32847 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
*
32865 GAACCGGTTGAAACCGG-TCA
1 G-ACCGG-TCAAACCGGTTCA
* *
32885 AACC-GTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
32905 AACCGGTTAAACCGGTT
1 GACCGGTCAAACCGGTT
32922 TCCAGCAGCC
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
17 2 0.03
18 8 0.13
19 29 0.46
20 21 0.33
21 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:32907 original size:29 final size:28
Alignment explanation
Indices: 32837--32918 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 28
32827 TGACCGGTCA
* *
32837 AACCGGTTCAGACCGGTCAAACCGGTTCG
1 AACCGGTTGAAACCGGTCAAACC-GTTCG
32866 AACCGGTTGAAACCGGTCAAACCG-TCAG
1 AACCGGTTGAAACCGGTCAAACCGTTC-G
*
32894 AACCGGTTGAAAACCGGTTAAACCG
1 AACCGGTTG-AAACCGGTCAAACCG
32919 GTTTCCAGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
27 2 0.04
28 11 0.23
29 35 0.73
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (28 bp):
AACCGGTTGAAACCGGTCAAACCGTTCG
Found at i:39725 original size:5 final size:5
Alignment explanation
Indices: 39715--39793 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
39705 CAACGTCAAC
* *
39715 GGTCG GGTC- GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
39763 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
39794 TGACCGGTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
4 4 0.07
5 45 0.74
7 12 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:39791 original size:22 final size:22
Alignment explanation
Indices: 39709--39793 Score: 163
Period size: 22 Copynumber: 3.9 Consensus size: 22
39699 AACGGTCAAC
39709 GTCAACGGTCGGGTC-GGTCGG
1 GTCAACGGTCGGGTCGGGTCGG
39730 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCGGGTCGG
39752 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCGGGTCGG
39774 GTCAACGGTCGGGTCGGGTC
1 GTCAACGGTCGGGTCGGGTC
39794 TGACCGGTCA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 15 0.24
22 48 0.76
ACGTcount: A:0.09, C:0.24, G:0.48, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCGGGTCGGGTCGG
Found at i:39808 original size:9 final size:9
Alignment explanation
Indices: 39796--39887 Score: 85
Period size: 9 Copynumber: 9.7 Consensus size: 9
39786 GTCGGGTCTG
39796 ACCGGTCAA
1 ACCGGTCAA
*
39805 ACCGGTTCAG
1 ACCGG-TCAA
39815 ACCGGTCAA
1 ACCGGTCAA
*
39824 ACCGGTTCGA
1 ACCGG-TCAA
* *
39834 ACCGTTGAA
1 ACCGGTCAA
39843 ACCGGTCAA
1 ACCGGTCAA
39852 ACCGGTCAGA
1 ACCGGTCA-A
*
39862 ACCGGTTGAAA
1 ACCGG-T-CAA
*
39873 ACCGGTTAA
1 ACCGGTCAA
39882 ACCGGT
1 ACCGGT
39888 TTCCAGCAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
9 38 0.56
10 22 0.32
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:39817 original size:19 final size:19
Alignment explanation
Indices: 39795--39888 Score: 93
Period size: 19 Copynumber: 4.9 Consensus size: 19
39785 GGTCGGGTCT
39795 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
39814 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
* *
39832 GAACCGTTGAAACCGG-TCA
1 G-ACCGGTCAAACCGGTTCA
* *
39851 AACCGGTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
39872 AACCGGTTAAACCGGTT
1 GACCGGTCAAACCGGTT
39889 TCCAGCAGCC
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.14
19 36 0.57
20 9 0.14
21 9 0.14
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:39821 original size:28 final size:28
Alignment explanation
Indices: 39796--39887 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 28
39786 GTCGGGTCTG
*
39796 ACCGGTCAAACCGGTTCAGACCGGTCAA
1 ACCGGTCAAACCGGTTCAAACCGGTCAA
* *
39824 ACCGGTTCGAACC-GTTGAAACCGGTCAA
1 ACCGG-TCAAACCGGTTCAAACCGGTCAA
* *
39852 ACCGGTCAGAACCGGTTGAAAACCGGTTAA
1 ACCGGTCA-AACCGGTT-CAAACCGGTCAA
39882 ACCGGT
1 ACCGGT
39888 TTCCAGCAGC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 2 0.04
28 27 0.50
29 9 0.17
30 16 0.30
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTCAAACCGGTCAA
Found at i:43937 original size:55 final size:55
Alignment explanation
Indices: 43872--43977 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 55
43862 TCAAACAATT
* * *
43872 CATGAAGAAAGACATCGGATGAATGAGGAAATTTGAAACTGATTGAAGACTGATC
1 CATGAAGAAAGACATCCGATGAATGAAGAAATTTGAAACTGATCGAAGACTGATC
* **
43927 CATGAAGAAAGACATCCGATGAATGAAGAAGTTTGAAGTTGATCGAAGACT
1 CATGAAGAAAGACATCCGATGAATGAAGAAATTTGAAACTGATCGAAGACT
43978 TCTTTCAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (55 bp):
CATGAAGAAAGACATCCGATGAATGAAGAAATTTGAAACTGATCGAAGACTGATC
Found at i:48625 original size:11 final size:10
Alignment explanation
Indices: 48600--48686 Score: 58
Period size: 10 Copynumber: 8.9 Consensus size: 10
48590 TTTTGCTTGA
*
48600 AGAAGAAAAG
1 AGAAAAAAAG
48610 AGAAAAAAAGG
1 AGAAAAAAA-G
48621 AGAAAAATGAA-
1 AGAAAAA--AAG
*
48632 A-AAAAAAAT
1 AGAAAAAAAG
* *
48641 TG-AAAAATG
1 AGAAAAAAAG
48650 A-AAAAAAA-
1 AGAAAAAAAG
*
48658 AGGAAAAAAG
1 AGAAAAAAAG
*
48668 AAAAAAAAAG
1 AGAAAAAAAG
48678 AGAAAAAAA
1 AGAAAAAAA
48687 TAGGTCTAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
8 3 0.05
9 16 0.27
10 29 0.49
11 9 0.15
13 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:48626 original size:18 final size:18
Alignment explanation
Indices: 48603--48683 Score: 60
Period size: 18 Copynumber: 4.3 Consensus size: 18
48593 TGCTTGAAGA
*
48603 AGAAAAGAGAAAAAAAGG
1 AGAAAAGAGAAAAAAAAG
*
48621 AGAAAA-ATGAAAAAAAAA
1 AGAAAAGA-GAAAAAAAAG
48639 ATTGAAAA-ATGAAAAAAAA-
1 A--GAAAAGA-GAAAAAAAAG
*
48658 AGGAAAAAAGAAAAAAAAAG
1 A-GAAAAGAG-AAAAAAAAG
48678 AGAAAA
1 AGAAAA
48684 AAATAGGTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
17 1 0.02
18 21 0.39
19 15 0.28
20 17 0.31
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (18 bp):
AGAAAAGAGAAAAAAAAG
Found at i:48634 original size:19 final size:19
Alignment explanation
Indices: 48612--48684 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
48602 AAGAAAAGAG
48612 AAAAAAAGGAGAAAAATGA
1 AAAAAAAGGAGAAAAATGA
*
48631 AAAAAAA-AATTGAAAAATGAA
1 AAAAAAAGGA--GAAAAATG-A
48652 AAAAAAAGGA-AAAAA-GA
1 AAAAAAAGGAGAAAAATGA
*
48669 AAAAAAAAGAGAAAAA
1 AAAAAAAGGAGAAAAA
48685 AATAGGTCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
17 10 0.22
18 7 0.15
19 12 0.26
20 8 0.17
21 8 0.17
22 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAAAAAGGAGAAAAATGA
Found at i:48637 original size:20 final size:20
Alignment explanation
Indices: 48612--48684 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
48602 AAGAAAAGAG
48612 AAAAAAAGGAGAAAAATGAA
1 AAAAAAAGGAGAAAAATGAA
***
48632 AAAAAAAATTGAAAAATGAA
1 AAAAAAAGGAGAAAAATGAA
48652 AAAAAAAGGA-AAAAA-GAA
1 AAAAAAAGGAGAAAAATGAA
48670 AAAAAAA-GAGAAAAA
1 AAAAAAAGGAGAAAAA
48685 AATAGGTCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
17 2 0.04
18 15 0.33
19 5 0.11
20 24 0.52
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAAAGGAGAAAAATGAA
Found at i:48684 original size:18 final size:19
Alignment explanation
Indices: 48612--48684 Score: 96
Period size: 18 Copynumber: 3.8 Consensus size: 19
48602 AAGAAAAGAG
*
48612 AAAAAAAGGAGAAAAATGA
1 AAAAAAAAGAGAAAAATGA
48631 AAAAAAAA-ATTGAAAAATGA
1 AAAAAAAAGA--GAAAAATGA
*
48651 AAAAAAAAG-GAAAAAAGA
1 AAAAAAAAGAGAAAAATGA
48669 AAAAAAAAGAGAAAAA
1 AAAAAAAAGAGAAAAA
48685 AATAGGTCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
18 18 0.38
19 13 0.27
20 17 0.35
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAAAAAAGAGAAAAATGA
Found at i:48685 original size:19 final size:19
Alignment explanation
Indices: 48600--48685 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 19
48590 TTTTGCTTGA
*
48600 AGAAGAAAAGAGAAAAAAAGG
1 AGAA-AAAAGA-AAAAAAAAG
*
48621 AGAAAAATGAAAAAAAAA-
1 AGAAAAAAGAAAAAAAAAG
*
48639 ATTGAAAAATGAAAAAAAAAG
1 A--GAAAAAAGAAAAAAAAAG
48660 -GAAAAAAGAAAAAAAAAG
1 AGAAAAAAGAAAAAAAAAG
48678 AGAAAAAA
1 AGAAAAAA
48686 ATAGGTCTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
18 18 0.31
19 14 0.24
20 22 0.38
21 4 0.07
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AGAAAAAAGAAAAAAAAAG
Found at i:53265 original size:18 final size:18
Alignment explanation
Indices: 53244--53284 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
53234 TTTTTTGAAA
*
53244 TTTTGGCTTTTTTGTTTT
1 TTTTGGCCTTTTTGTTTT
**
53262 TTTTTTCCTTTTTGTTTT
1 TTTTGGCCTTTTTGTTTT
53280 TTTTG
1 TTTTG
53285 AAAAAAATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.80
Consensus pattern (18 bp):
TTTTGGCCTTTTTGTTTT
Found at i:55757 original size:37 final size:37
Alignment explanation
Indices: 55713--55837 Score: 187
Period size: 37 Copynumber: 3.4 Consensus size: 37
55703 CGAAGAAGTG
*
55713 AATCCATCATAAGCCTTCACCGAAGAGTAGTGAAGAA
1 AATCCATCATAAGCCTTCACCGAAGAGTAGTGAAGCA
* * *
55750 AATCCATCCTAAGCCTTCATCGAAGGGTAGTGAAGCA
1 AATCCATCATAAGCCTTCACCGAAGAGTAGTGAAGCA
* *
55787 AATCCATCTTAAGCCTTCACCTAAGAGTAGTGAAGCA
1 AATCCATCATAAGCCTTCACCGAAGAGTAGTGAAGCA
55824 AATCCATCAGTAAG
1 AATCCATCA-TAAG
55838 TCTTTCGAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
37 74 0.95
38 4 0.05
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (37 bp):
AATCCATCATAAGCCTTCACCGAAGAGTAGTGAAGCA
Found at i:56034 original size:42 final size:42
Alignment explanation
Indices: 55957--56039 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
55947 ATCAATAAGT
* *
55957 GCCACCAGTAAGTCTTTCGAGCATGATTATGAAATCCTTCGA
1 GCCACCAGTAAGTCTTTCGAACATGATGATGAAATCCTTCGA
* * *
55999 GCCATCAGTAAGTCTTTCGAACGTGATGATTAAATCCTTCG
1 GCCACCAGTAAGTCTTTCGAACATGATGATGAAATCCTTCG
56040 GGTAATTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (42 bp):
GCCACCAGTAAGTCTTTCGAACATGATGATGAAATCCTTCGA
Found at i:57061 original size:55 final size:54
Alignment explanation
Indices: 56520--57216 Score: 702
Period size: 53 Copynumber: 13.2 Consensus size: 54
56510 GAAGCAAATC
* * * **
56520 CAGAAGATTGTTCGAGTTCCTACACCCTAAAGAAAGAGGAAGTGAA-AAGTA-G
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* *
56572 C---A-TTTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTA-G
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* * * *
56621 CAGAAGATTGATCGAGTTCCTACTGGCCTAAAGAAAGAGGGAGCAAACCCGTAGA
1 CAGAAGATTGTTCGAGTTCCTACT-CCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* * * * * *
56676 TAGAAGATTATTCAAGATCCTACT-CCTAAAGAAAGAGGGAGC-AA--CGACAGA
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCG-TAGG
* *
56727 CA-AAGATTGTTCGAGTTCCTACTCCTTAAAG-AAGAGGGGAGCGAACTCGTAGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGA-GGGAGCGAACCCGTAGG
* * * * * *
56780 CAGAAGATTGTTTGAATTCCTACTTCCTAAAGAAAGAGGGAACGAACCTGTAAG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* * *
56834 CA-AATATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAA----TATG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* *
56883 CAGAAGATTGATCGAGTTCCTACTCCCTGAAAGAAAGAGGGAGCGAACCC-TTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAGG
* * * * *
56937 CAGAATATTGTTTGAGTTTCTACTCCCTGAAGAAA-A-GGAGCGAACACGTAGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* ** * *
56989 CAGAAGATTGTTTGAGTTCCTACTCCCTGAAAGAAAGAGGGAATGAACCCATGGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAGG
* * * * *
57044 CAGAAGAATATTCGAGTTCCTACTCCCTGAAAGAAAGAGGGAACGAACCCATTGG
1 CAGAAGATTGTTCGAGTTCCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAGG
* * * *
57099 CAGAAGATTGTTCAAGTT-CTACTCCCTAAAGAAAGAGGAAGTGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* * * *
57152 CAGAAGATTATTCGAGTT-CTACTCCCTGAAGCAAGAGGGAGCGAACCCGTATG
1 CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
57205 CAGAAGATTGTT
1 CAGAAGATTGTT
57217 TGAGGACGAG
Statistics
Matches: 540, Mismatches: 81, Indels: 47
0.81 0.12 0.07
Matches are distributed among these distances:
48 37 0.07
49 11 0.02
50 47 0.09
51 43 0.08
52 36 0.07
53 164 0.30
54 103 0.19
55 99 0.18
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (54 bp):
CAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
Done.