Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005474.1 Hibiscus syriacus cultivar Beakdansim tig00012548_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: 81635
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:3423 original size:14 final size:13
Alignment explanation
Indices: 3390--3429 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
3380 ACATAGATAC
*
3390 TATTTTATTAAAT
1 TATTTTGTTAAAT
*
3403 AATTTTGTTAATAT
1 TATTTTGTTAA-AT
3417 TATTTTGTTAAAT
1 TATTTTGTTAAAT
3430 GATTCAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (13 bp):
TATTTTGTTAAAT
Found at i:10867 original size:329 final size:329
Alignment explanation
Indices: 10269--10923 Score: 1247
Period size: 329 Copynumber: 2.0 Consensus size: 329
10259 TCAACTATAT
10269 GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGGGTAATGTAGTAATAGA
1 GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGGGTAATGTAGTAATAGA
* *
10334 CAACGGTATCTGAGTAAACCCCTAAAAGATTAAAGTAATCTTCGAGTGAGAAGTACCTAATAATT
66 CAACGGTATCTGAGTAAACCCCCAAAAGATTAAAGTAATCTTCGAGTGAGAACTACCTAATAATT
10399 TCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAATGCCCTAATCCAGTTA
131 TCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAATGCCCTAATCCAGTTA
10464 GACCCAAAGTTCCATGGATTACAATGTTACACAGGATTACCGAAATAGTGACCCAAAAGTTTCTT
196 GACCCAAAGTTCCATGGATTACAATGTTACACAGGATTACCGAAATAGTGACCCAAAAGTTTCTT
*
10529 TTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAACACTTAATAATAA
261 TTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAAAACTTAATAATAA
10594 TCTA
326 TCTA
10598 GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGGGTAATGTAGTAATAGA
1 GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGGGTAATGTAGTAATAGA
* *
10663 CAACGGTATCTGAGTAAACCCCCAAAAGATTAAAGTAATCTTTGAGTGGGAACTACCTAATAATT
66 CAACGGTATCTGAGTAAACCCCCAAAAGATTAAAGTAATCTTCGAGTGAGAACTACCTAATAATT
10728 TCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAATGCCCTAATCCAGTTA
131 TCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAATGCCCTAATCCAGTTA
* *
10793 GACTCAAAGTTCCATGGATTACAATGTTACACAGGATTACCGAAATAGTGACCCAAAATTTTCTT
196 GACCCAAAGTTCCATGGATTACAATGTTACACAGGATTACCGAAATAGTGACCCAAAAGTTTCTT
10858 TTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAAAACTTAATAATAA
261 TTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAAAACTTAATAATAA
10923 T
326 T
10924 ATAGGCTTAC
Statistics
Matches: 319, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
329 319 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (329 bp):
GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGGGTAATGTAGTAATAGA
CAACGGTATCTGAGTAAACCCCCAAAAGATTAAAGTAATCTTCGAGTGAGAACTACCTAATAATT
TCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAATGCCCTAATCCAGTTA
GACCCAAAGTTCCATGGATTACAATGTTACACAGGATTACCGAAATAGTGACCCAAAAGTTTCTT
TTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAAAACTTAATAATAA
TCTA
Found at i:14839 original size:18 final size:20
Alignment explanation
Indices: 14816--14861 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
14806 AATTTGGTAC
*
14816 CGATACTC-ATGG-GAGTAT
1 CGATACTCAAGGGAGAGTAT
14834 CGATAC-CAAGGGTAGAGTAT
1 CGATACTCAAGGG-AGAGTAT
14854 CGATACTC
1 CGATACTC
14862 CCCATAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 9 0.39
20 12 0.52
21 1 0.04
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (20 bp):
CGATACTCAAGGGAGAGTAT
Found at i:16305 original size:5 final size:5
Alignment explanation
Indices: 16295--16376 Score: 164
Period size: 5 Copynumber: 16.4 Consensus size: 5
16285 GAGTCAGGTC
16295 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA
16345 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TG
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TG
16377 CCCGTGAACT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 77 1.00
ACGTcount: A:0.20, C:0.00, G:0.21, T:0.60
Consensus pattern (5 bp):
TGTTA
Found at i:16552 original size:17 final size:18
Alignment explanation
Indices: 16530--16564 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16520 TCAAGGATAA
16530 CTTAAAC-AAATTAATAT
1 CTTAAACTAAATTAATAT
*
16547 CTTAAACTTAATTAATAT
1 CTTAAACTAAATTAATAT
16565 TTTTTAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
CTTAAACTAAATTAATAT
Found at i:16813 original size:12 final size:12
Alignment explanation
Indices: 16791--16816 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16781 TCACCACCAC
16791 CACCATCACCCT
1 CACCATCACCCT
16803 CACCATCACCCT
1 CACCATCACCCT
16815 CA
1 CA
16817 TCTGCATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.58, G:0.00, T:0.15
Consensus pattern (12 bp):
CACCATCACCCT
Found at i:16818 original size:21 final size:22
Alignment explanation
Indices: 16772--16818 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
16762 CTCATCAACA
16772 TCATCACCATCACCACCACCAC
1 TCATCACCATCACCACCACCAC
* *
16794 -CATCACCCTCACCATCACC-C
1 TCATCACCATCACCACCACCAC
16814 TCATC
1 TCATC
16819 TGCATATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.28, C:0.55, G:0.00, T:0.17
Consensus pattern (22 bp):
TCATCACCATCACCACCACCAC
Found at i:21223 original size:33 final size:33
Alignment explanation
Indices: 21186--21251 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
21176 CATCTTAAGA
* *
21186 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACATCAACTTCTTTCACCACT
*
21219 TCACCCCTCAACACATCTACTTCTTTCACCACT
1 TCACCCCTCAACACATCAACTTCTTTCACCACT
21252 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACATCAACTTCTTTCACCACT
Found at i:21310 original size:21 final size:21
Alignment explanation
Indices: 21285--21349 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
21275 CCCCTTATGC
* *
21285 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
21306 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
21327 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
21348 CT
1 CT
21350 TGATTGTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.15, C:0.32, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:23629 original size:20 final size:19
Alignment explanation
Indices: 23584--23629 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
23574 CCGGTAGCGC
23584 TTTT-CCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
23602 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
23623 TTTTACC
1 TTTTACC
23630 TATTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 1 0.04
20 17 0.74
21 3 0.13
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:24948 original size:2 final size:2
Alignment explanation
Indices: 24941--24996 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
24931 TTTTAACAAA
24941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
24983 AA AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT
24997 TATCTATCCA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25211 original size:15 final size:13
Alignment explanation
Indices: 25178--25216 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
25168 ATGAGATTCC
25178 TTAAAAATATTTT
1 TTAAAAATATTTT
*
25191 TAAAAAATATATATT
1 TTAAAAATAT-T-TT
25206 TTAAAAATATT
1 TTAAAAATATT
25217 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAAAATATTTT
Found at i:26585 original size:35 final size:35
Alignment explanation
Indices: 26538--26609 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
26528 ATATAACATA
* *
26538 AACATTCTAATATGCCTATATAAATTAACTTCATT
1 AACATTCTAATATGCCTATATAAACTAACTCCATT
*
26573 AACATTAC-AATATGCTTATATAAACTAACTCCATT
1 AACATT-CTAATATGCCTATATAAACTAACTCCATT
26608 AA
1 AA
26610 GCTCTTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (35 bp):
AACATTCTAATATGCCTATATAAACTAACTCCATT
Found at i:27049 original size:43 final size:43
Alignment explanation
Indices: 26988--27069 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
26978 TTTTCTCGAA
* *
26988 CCACATGATTCTCACATTAAAGTATACGTAGGAGGTATGTGTT
1 CCACATGATTCTCACATTAAAGTAGACGTAAGAGGTATGTGTT
27031 CCACATGATTCTCACATTAAAGTAGACGTAAGAGGTATG
1 CCACATGATTCTCACATTAAAGTAGACGTAAGAGGTATG
27070 AATTTTACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (43 bp):
CCACATGATTCTCACATTAAAGTAGACGTAAGAGGTATGTGTT
Found at i:27099 original size:16 final size:16
Alignment explanation
Indices: 27078--27112 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27068 TGAATTTTAC
*
27078 TCTCTTATTTTATTCA
1 TCTCTTATTTTACTCA
27094 TCTCTTATTTTACTCA
1 TCTCTTATTTTACTCA
27110 TCT
1 TCT
27113 ACAAAATCAT
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:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (16 bp):
TCTCTTATTTTACTCA
Found at i:27243 original size:25 final size:26
Alignment explanation
Indices: 27205--27253 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
27195 AATAATTACT
* * *
27205 TAAAATA-TTTTTTTATTTAAATATA
1 TAAAATACTATTTTGATTAAAATATA
27230 TAAAATACTATTTTGATTAAAATA
1 TAAAATACTATTTTGATTAAAATA
27254 AATATATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TAAAATACTATTTTGATTAAAATATA
Found at i:28182 original size:15 final size:16
Alignment explanation
Indices: 28162--28194 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28152 ATATTATCTT
28162 AATTTTATATTTT-TA
1 AATTTTATATTTTATA
*
28177 AATTTTTTATTTTATA
1 AATTTTATATTTTATA
28193 AA
1 AA
28195 AAGTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATTTTATATTTTATA
Found at i:33147 original size:265 final size:262
Alignment explanation
Indices: 32665--33148 Score: 641
Period size: 265 Copynumber: 1.8 Consensus size: 262
32655 AATATTTTAA
*
32665 GTTGCGCCTAATGTTATCAAAGTTTAAGCTGACGGAACGTTGGATTTTCTCACGATAAGAAAATA
1 GTTGCGCCTAATGTTATCAAAGTTTAAGCTGACGGAACGTTGGATTTTCTCAC-ATAAAAAAATA
* * * *
32730 AGTTAAAAGCTAAAAATGTTATTAATATATATAAGAAATACAATTGCGCCCAATAATATTATAAT
65 AGTTAAAAGCTAAAAATATTATGAATATAAATAAGAAATACAATTGCGCCCAATAATATCATAAT
* * * *
32795 TAGCTAAGAAATAGATTATGATATGTAATATTACTATTTTTATTAATAAAATAGGTTGCGCATAA
130 TAGCTAAGAAACAGATTATGATATGTAATATTAATAATTTTATTAATAAAATAGGTTGCGCACAA
*
32860 GGATGTCATGGTTCACTAAGAAAGCATGTTGTAATATGGAATCTTAATATTTTTAATAATAAAAA
195 GAATGTCATGGTTCACTAAGAAAGCATGTTGTAATATGGAATCTTAATATTTTTAATAATAAAAA
32925 TAG
260 TAG
* * * * *
32928 GTTGCGCCTAAAATGTTATCAGAGTTTAAGCTGATGGAGCTTTGGATTTTCCTGTA-ATAAAAAA
1 GTTGCGCCT--AATGTTATCAAAGTTTAAGCTGACGGAACGTTGGATTTT-CT-CACATAAAAAA
* * * ** *
32992 ATAAGTTAAAAGTTCAAAATATTATGAATATAAATAAGAAATACAATTGTGTTCAATAATGTCAT
62 ATAAGTTAAAAGCTAAAAATATTATGAATATAAATAAGAAATACAATTGCGCCCAATAATATCAT
* * * * *
33057 AGTTCA-CTAAGAAGCAGATTGTGATATGTAATGTTAATAATTTTATTAATAAAATAGGTTGTGT
127 AATT-AGCTAAGAAACAGATTATGATATGTAATATTAATAATTTTATTAATAAAATAGGTTGCG-
*
33121 C-CAAGAATGTTATGGTTCACTAAGAAAG
190 CACAAGAATGTCATGGTTCACTAAGAAAG
33149 TAAGTTGTGA
Statistics
Matches: 188, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
263 9 0.05
265 174 0.93
266 4 0.02
267 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (262 bp):
GTTGCGCCTAATGTTATCAAAGTTTAAGCTGACGGAACGTTGGATTTTCTCACATAAAAAAATAA
GTTAAAAGCTAAAAATATTATGAATATAAATAAGAAATACAATTGCGCCCAATAATATCATAATT
AGCTAAGAAACAGATTATGATATGTAATATTAATAATTTTATTAATAAAATAGGTTGCGCACAAG
AATGTCATGGTTCACTAAGAAAGCATGTTGTAATATGGAATCTTAATATTTTTAATAATAAAAAT
AG
Found at i:33437 original size:73 final size:73
Alignment explanation
Indices: 33330--33532 Score: 223
Period size: 73 Copynumber: 2.8 Consensus size: 73
33320 TTATTATAGG
** *
33330 TACTTTTAAATATAAAAAAAAGTTGA-AGATAAGATCAAAATTTAAAATATCGATACTCATGCGG
1 TACTTTTAAATA-ATGAAAAAGTTGATAGA-AAGATCAAAATTTAAAATATCGATACTCATGCGA
33394 TAATAATCAA
64 TAATAATCAA
* *
33404 TACTTTTAAA-AATTGAAAAAGTTGATAGAAAGATCAAAATTTAAAATATCGATATTTATGCGAT
1 TACTTTTAAATAA-TGAAAAAGTTGATAGAAAGATCAAAATTTAAAATATCGATACTCATGCGAT
* * *
33468 GATGATCGA
65 AATAATCAA
* * * * *
33477 TACTTTTAAATAATGAATAAGTTAAT-GAATATGATCGATAGTTAAAATATCGATAC
1 TACTTTTAAATAATGAAAAAGTTGATAGAA-A-GATCAAAATTTAAAATATCGATAC
33533 ATATGTTATG
Statistics
Matches: 110, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
72 4 0.04
73 71 0.65
74 35 0.32
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.33
Consensus pattern (73 bp):
TACTTTTAAATAATGAAAAAGTTGATAGAAAGATCAAAATTTAAAATATCGATACTCATGCGATA
ATAATCAA
Found at i:33554 original size:74 final size:73
Alignment explanation
Indices: 33346--33557 Score: 189
Period size: 73 Copynumber: 2.9 Consensus size: 73
33336 TAAATATAAA
* * * * **
33346 AAAAAGTTGA-AGATAAGATCAAAATTTAAAATATCGATAC-TCATGCGGTAATAATCAATACTT
1 AAAAAGTTAATAGA-AAGATCAAAAGTTAAAATATCGATACAT-ATGCGATGAGGATCAATACTT
33409 TTAAAAATTG
64 TTAAAAATTG
* * ** * *
33419 AAAAAGTTGATAGAAAGATCAAAATTTAAAATATCGATATTTATGCGATGATGATCGATACTTTT
1 AAAAAGTTAATAGAAAGATCAAAAGTTAAAATATCGATACATATGCGATGAGGATCAATACTTTT
33484 AAATAA-TG
66 AAA-AATTG
* * * ** *
33492 AATAAGTTAAT-GAATATGATCGATAGTTAAAATATCGATACATATGTTATGAGGTTCAATACTT
1 AAAAAGTTAATAGAA-A-GATCAAAAGTTAAAATATCGATACATATGCGATGAGGATCAATACTT
33556 TT
64 TT
33558 TTTATTTATA
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
72 3 0.03
73 69 0.59
74 45 0.38
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (73 bp):
AAAAAGTTAATAGAAAGATCAAAAGTTAAAATATCGATACATATGCGATGAGGATCAATACTTTT
AAAAATTG
Found at i:33582 original size:42 final size:41
Alignment explanation
Indices: 33523--33608 Score: 145
Period size: 42 Copynumber: 2.1 Consensus size: 41
33513 GATAGTTAAA
33523 ATATCGATACATATGTTATGAGGTTCAATACTTTTTTTATTT
1 ATATCGATACATATGTTATGAGGTTCAATAC-TTTTTTATTT
**
33565 ATATCGATACATATGTTATGAGGTTTGATACTTTTTTATTT
1 ATATCGATACATATGTTATGAGGTTCAATACTTTTTTATTT
33606 ATA
1 ATA
33609 CAAATACTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 13 0.31
42 29 0.69
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (41 bp):
ATATCGATACATATGTTATGAGGTTCAATACTTTTTTATTT
Found at i:33621 original size:41 final size:42
Alignment explanation
Indices: 33523--33624 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 42
33513 GATAGTTAAA
*
33523 ATATCGATACATATGTTATGAGGTTCAATACTTTTTTTATTT
1 ATATCAATACATATGTTATGAGGTTCAATACTTTTTTTATTT
* **
33565 ATATCGATACATATGTTATGAGGTTTGATAC-TTTTTTATTT
1 ATATCAATACATATGTTATGAGGTTCAATACTTTTTTTATTT
*
33606 ATA-CAAATACTTATGTTAT
1 ATATC-AATACATATGTTAT
33625 TGTATTTGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
40 1 0.02
41 25 0.45
42 29 0.53
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (42 bp):
ATATCAATACATATGTTATGAGGTTCAATACTTTTTTTATTT
Found at i:33961 original size:23 final size:23
Alignment explanation
Indices: 33931--33979 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
33921 ATCTAATACG
*
33931 TTATCATGAGCACATGTTTTGTC
1 TTATCATGAGCACATGTTTTATC
33954 TTATCATGAGCACATGTTTTATC
1 TTATCATGAGCACATGTTTTATC
33977 TTA
1 TTA
33980 CTTTTGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.45
Consensus pattern (23 bp):
TTATCATGAGCACATGTTTTATC
Found at i:34090 original size:99 final size:100
Alignment explanation
Indices: 33965--34319 Score: 441
Period size: 99 Copynumber: 3.6 Consensus size: 100
33955 TATCATGAGC
* * * *
33965 ACATGTTTTATCTTACTTTTGTATAATATAAATGGTTTAATACTTATAACTTAAACAATTGACAT
1 ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACAT
* * *
34030 AAAAAATG-CGCTACCTACTATGTTATCATGTGAA
66 AAAAAATGACGCTACCTACTACGTTATCACGAGAA
* * *
34064 TA-ATATTTTGTCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGGTTGACA
1 -ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACA
* *
34128 TAAAAAA-GACGCCACCTACTACGTTTTCACGAGAA
65 TAAAAAATGACGCTACCTACTACGTTATCACGAGAA
* * * * *
34163 ACATGTTTTGTCTTACTTTTACATAATATAAATAGTTTTATACTTATAACTCAAATGATTGACAT
1 ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACAT
* * *
34228 AAAAAAATGTC-CTACCTACTACATTATTACGAGAA
66 -AAAAAATGACGCTACCTACTACGTTATCACGAGAA
* * *
34263 ATATGTTTTATCTTACTTTTGCATCATATAAA-CGATTTCATACTTATAACTTAAACG
1 ACATGTTTTATCTTACTTTTGCATAATATAAATAG-TTTCATACTTATAACTTAAACG
34320 GTTGTCATTT
Statistics
Matches: 219, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
98 2 0.01
99 141 0.64
100 74 0.34
101 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (100 bp):
ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACAT
AAAAAATGACGCTACCTACTACGTTATCACGAGAA
Found at i:34314 original size:199 final size:198
Alignment explanation
Indices: 33965--34323 Score: 508
Period size: 199 Copynumber: 1.8 Consensus size: 198
33955 TATCATGAGC
** * *
33965 ACATGTTTTATCTTACTTTTGTATAATATAAATGGTTTAATACTTATAACTTAAACAATTGACAT
1 ACATGTTTTATCTTACTTTTACATAATATAAATAGTTTAATACTTATAACTCAAACAATTGACAT
** * * *
34030 AAAAAATGCGCTACCTACTATGTTATCATGTGAATAATATTTTGTCTTACTTTTGCATAATATAA
66 AAAAAATGCGCTACCTACTACATTATCACGAGAATAATATTTTATCTTACTTTTGCATAATATAA
*
34095 ATAGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAGACGCCACCTACTACGTTTTCACGA
131 AGAGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAGACGCCACCTACTACGTTTTCACGA
34160 GAA
196 GAA
* * **
34163 ACATGTTTTGTCTTACTTTTACATAATATAAATAGTTTTATACTTATAACTCAAATGATTGACAT
1 ACATGTTTTATCTTACTTTTACATAATATAAATAGTTTAATACTTATAACTCAAACAATTGACAT
* * *
34228 AAAAAAATGTC-CTACCTACTACATTATTACGAGAA-ATATGTTTTATCTTACTTTTGCATCATA
66 -AAAAAATG-CGCTACCTACTACATTATCACGAGAATA-ATATTTTATCTTACTTTTGCATAATA
34291 TAAACGA-TTTCATACTTATAACTTAAACGGTTG
128 TAAA-GAGTTTCATACTTATAACTTAAACGGTTG
34324 TCATTTAAAA
Statistics
Matches: 140, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
198 58 0.41
199 80 0.57
200 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (198 bp):
ACATGTTTTATCTTACTTTTACATAATATAAATAGTTTAATACTTATAACTCAAACAATTGACAT
AAAAAATGCGCTACCTACTACATTATCACGAGAATAATATTTTATCTTACTTTTGCATAATATAA
AGAGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAGACGCCACCTACTACGTTTTCACGA
GAA
Found at i:34582 original size:132 final size:135
Alignment explanation
Indices: 34436--34709 Score: 362
Period size: 132 Copynumber: 2.1 Consensus size: 135
34426 ATATTTGTGG
* * * * *
34436 AAAAGTATTGATACTCTGCAGCCTGCTCATTTTTCATGTTTTTTCTTTAAATTCGAAAGTATCAA
1 AAAAGTATCGATACTCTGCAGCATGCTCATTTTCCATG-TTTTACTTTAAATTCGAAAATATCAA
** *
34501 TA-C-TTTGAAAAAATATCCGTACTTTCGAA-TT-AAAAAACAT-AGAAATGGTATTTTAACTTT
65 TACCTTTTG-AAAAATATCAATACTTTCGAATTTAAAAAAACATGAGAAATGATATTTTAACTTT
34561 -AGAATTT
129 CA-AATTT
* ** *
34568 AAAAGTATCGATACTTTGCAGCATTTTCATTTTCCATGTTTTACTTTAAATTCGAAAATATCGAT
1 AAAAGTATCGATACTCTGCAGCATGCTCATTTTCCATGTTTTACTTTAAATTCGAAAATATCAAT
*
34633 ACCTTTTGAAAAATATCAATACTTTTGAATTTAAAAAAACATGAGAAATGATATTTTAACTTTCA
66 ACCTTTTGAAAAATATCAATACTTTCGAATTTAAAAAAACATGAGAAATGATATTTTAACTTTCA
34698 AATTT
131 AATTT
34703 AAAAGTA
1 AAAAGTA
34710 AAGATACTTT
Statistics
Matches: 123, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
131 25 0.20
132 51 0.41
133 6 0.05
134 9 0.07
135 31 0.25
136 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (135 bp):
AAAAGTATCGATACTCTGCAGCATGCTCATTTTCCATGTTTTACTTTAAATTCGAAAATATCAAT
ACCTTTTGAAAAATATCAATACTTTCGAATTTAAAAAAACATGAGAAATGATATTTTAACTTTCA
AATTT
Found at i:34657 original size:19 final size:20
Alignment explanation
Indices: 34622--34661 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
34612 TTTAAATTCG
*
34622 AAAATATCGATACCTTTTGA
1 AAAATATCAATACCTTTTGA
34642 AAAATATCAATA-CTTTTGA
1 AAAATATCAATACCTTTTGA
34661 A
1 A
34662 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAATATCAATACCTTTTGA
Found at i:35147 original size:75 final size:76
Alignment explanation
Indices: 34818--35188 Score: 374
Period size: 77 Copynumber: 4.9 Consensus size: 76
34808 TTTTCCAATT
* ** * *
34818 TTTTA-TAATAGAAAA-ATTAACATTCCAGATTACAATTTACTTTCTTATTGAACCATAACATTC
1 TTTTATTAATA-AAAATATTAACATTCCAGATCACAACCTA-TTTCTTAGTGAACCATGACATT-
* * *
34881 TTGTGCGAAACCTA
63 TTTTGCGTAACCCA
* * * *
34895 TTTTATTAATAAAAATATTAACATTCTAGATCACAACATATTTCTTAGTGAACCATGA-AATTAT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATGACATTTTT
*
34959 TGGGTGAAACCCA
66 TGCGT--AACCCA
* * *
34972 TTTTATTAATAAAAATATTAGCATTCCATATCACAACCTATTTCTTAGTGAACCGTGACATTCTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATGACATT-TT
** * *
35037 ACGCGCAATCCA
65 TTGCGTAACCCA
* ** *
35049 TTTTATTAATAAAAATATTAACATCCCAGATCGTAACCTATCTCTTAGTGAACCATGACATTTTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATGACATTTTT
*
35114 TGCGTAA-GCA
66 TGCGTAACCCA
* * * * *
35124 TTTTATTAATAAAAATATTAACATTTCATAT-ATAAACCTGTTTCTTAGTTAACCATGACATTTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCA-CAACCTATTTCTTAGTGAACCATGACATTTT
35188 T
65 T
35189 AGGCCCAACT
Statistics
Matches: 244, Mismatches: 43, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
75 62 0.25
76 9 0.04
77 143 0.59
78 27 0.11
79 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (76 bp):
TTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATGACATTTTT
TGCGTAACCCA
Found at i:39307 original size:40 final size:40
Alignment explanation
Indices: 39251--39386 Score: 202
Period size: 40 Copynumber: 3.4 Consensus size: 40
39241 GCGATTTTCC
* *
39251 GACTATTGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATAT
*
39291 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATAT
* *
39331 GTA-AATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGAATATGTAAATCGCAATGCGAATAT
*
39371 TACTATCGCAATGCGA
1 GACTATCGCAATGCGA
39387 TTCTGACTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 84 0.98
41 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATAT
Found at i:39401 original size:20 final size:20
Alignment explanation
Indices: 39258--39386 Score: 181
Period size: 20 Copynumber: 6.5 Consensus size: 20
39248 TCCGACTATT
39258 GCAATGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
* *
39278 GCAATGCGAGTATG-ACTATC
1 GCAATGCGAATATGTA-AATC
*
39298 GCAACGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
39318 GCAATGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
39338 GCAATGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
* *
39358 GCAATGCGATTAT-TACTATC
1 GCAATGCGAATATGTA-AATC
39378 GCAATGCGA
1 GCAATGCGA
39387 TTCTGACTAT
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
19 3 0.03
20 94 0.96
21 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (20 bp):
GCAATGCGAATATGTAAATC
Found at i:39406 original size:20 final size:20
Alignment explanation
Indices: 39251--39408 Score: 126
Period size: 20 Copynumber: 7.9 Consensus size: 20
39241 GCGATTTTCC
* *
39251 GACTATTGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
39271 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGATTAT
* *
39291 GACTATCGCAACGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
39311 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGATTAT
* *
39331 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGATTAT
*
39351 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
39371 TACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
*
39391 GACTATCGCAACGCGATT
1 GACTATCGCAATGCGATT
39409 TTCAAAGTGC
Statistics
Matches: 120, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 116 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:40255 original size:24 final size:24
Alignment explanation
Indices: 40204--40257 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
40194 GTATTCGAAA
*
40204 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
40228 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
40252 TTTGAT
1 TTTGAT
40258 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:40473 original size:14 final size:14
Alignment explanation
Indices: 40444--40480 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
40434 AGAAAAAGAA
40444 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
40459 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
40473 GAAGAAAA
1 GAAGAAAA
40481 TGCCACTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:40867 original size:82 final size:82
Alignment explanation
Indices: 40730--40893 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
40720 TGTACGTGGC
40730 GTATGATTGCAAAGAGGATAAAAGATTGCGAAATGTTTCAAGTTAGGACTTTTATTGATAAACAT
1 GTATGATTGCAAAGAGGATAAAAGATTGCGAAATGTTTCAAGTTAGGACTTTTATTGATAAACAT
40795 ACATGTTCAAGAACCCA
66 ACATGTTCAAGAACCCA
40812 GTATGATTGCAAAGAGGATAAAAGATTGCGAAATGTTTCAAGTTAGGACTTTTATTGATAAACAT
1 GTATGATTGCAAAGAGGATAAAAGATTGCGAAATGTTTCAAGTTAGGACTTTTATTGATAAACAT
40877 ACATGTTCAAGAACCCA
66 ACATGTTCAAGAACCCA
40894 AGTTTTTCCT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (82 bp):
GTATGATTGCAAAGAGGATAAAAGATTGCGAAATGTTTCAAGTTAGGACTTTTATTGATAAACAT
ACATGTTCAAGAACCCA
Found at i:42825 original size:20 final size:20
Alignment explanation
Indices: 42800--43149 Score: 214
Period size: 20 Copynumber: 18.7 Consensus size: 20
42790 CACATTCATT
*
42800 TGACTATCGCAACGTGAATA
1 TGACTATCGCAACGCGAATA
42820 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
42840 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
42860 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
** *
42877 T-A--ATCGCAATACGAAAA
1 TGACTATCGCAACGCGAATA
*
42894 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
42911 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
42928 TGACTATCGCAATG-GGATA
1 TGACTATCGCAACGCGAATA
* *
42947 --A-T-T-GCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* * *
42962 TGACTATTGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
42982 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
*
43002 TGACTATCACAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
43022 TGACTATAGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
43042 TAAC-CT-GCATAATCGCGAATT
1 TGACTATCGC--AA-CGCGAATA
*
43063 TGACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
43080 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
*
43096 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
43116 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
43136 TGACTATCGCAACG
1 TGACTATCGCAACG
43150 AGAAAATCGC
Statistics
Matches: 265, Mismatches: 35, Indels: 60
0.74 0.10 0.17
Matches are distributed among these distances:
14 28 0.11
15 6 0.02
16 8 0.03
17 13 0.05
18 7 0.03
19 20 0.08
20 167 0.63
21 13 0.05
22 1 0.00
23 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:42937 original size:54 final size:54
Alignment explanation
Indices: 42801--43015 Score: 136
Period size: 54 Copynumber: 4.0 Consensus size: 54
42791 ACATTCATTT
* * * * * *
42801 GACTATCGCAACGTGAATATGACTATCGCAACGCGAATATGACTATCGCAACGT
1 GACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGG
* * * *** *
42855 GAAT-TTG-AATATCGCAACGGGA-TAATCGCAATACGAAAATGACTATCGCAACGG
1 GACTATCGCAAT-GCG-AAAATGACT-ATCGCAATGCGAAAATGACTATCGCAACGG
* * * ***
42909 GA-TAATCGCAATGCGAAAATGACTATCGCAATGGGATAATTG-CAAT-GCGAAAAT
1 GACT-ATCGCAATGCGAAAATGACTATCGCAATGCGA-AAATGACTATCGC-AACGG
* * *
42963 GACTATTGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAACG
1 GACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACG
43016 CGAATATGAC
Statistics
Matches: 117, Mismatches: 32, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
52 2 0.02
53 11 0.09
54 90 0.77
55 11 0.09
56 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (54 bp):
GACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGG
Found at i:42975 original size:34 final size:34
Alignment explanation
Indices: 42864--42973 Score: 184
Period size: 34 Copynumber: 3.2 Consensus size: 34
42854 TGAATTTGAA
*
42864 TATCGCAACGGGATAATCGCAATACGAAAATGAC
1 TATCGCAACGGGATAATCGCAATGCGAAAATGAC
42898 TATCGCAACGGGATAATCGCAATGCGAAAATGAC
1 TATCGCAACGGGATAATCGCAATGCGAAAATGAC
* *
42932 TATCGCAATGGGATAATTGCAATGCGAAAATGAC
1 TATCGCAACGGGATAATCGCAATGCGAAAATGAC
*
42966 TATTGCAA
1 TATCGCAA
42974 TGCGAAAATG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 72 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (34 bp):
TATCGCAACGGGATAATCGCAATGCGAAAATGAC
Found at i:43103 original size:33 final size:33
Alignment explanation
Indices: 43055--43182 Score: 121
Period size: 33 Copynumber: 3.6 Consensus size: 33
43045 CCTGCATAAT
43055 CGCGAATTTGACTATCGCAACGAGATAATCGCAA
1 CGCGAA-TTGACTATCGCAACGAGATAATCGCAA
* *
43089 CGCGAAATGACTATCGCAACGCGAATTTGATTATCGCAA
1 CGCGAATTGACTATCGCAA--CG-A---GATAATCGCAA
* *
43128 CGGGAATTTGACTATCGCAACGAGAAAATCGCAA
1 CGCGAA-TTGACTATCGCAACGAGATAATCGCAA
* * *
43162 AGTGTATTGACTATCGCAACG
1 CGCGAATTGACTATCGCAACG
43183 CGAATATGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
33 27 0.35
34 18 0.23
35 2 0.03
36 1 0.01
37 1 0.01
38 2 0.03
39 15 0.19
40 12 0.15
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (33 bp):
CGCGAATTGACTATCGCAACGAGATAATCGCAA
Found at i:43151 original size:73 final size:75
Alignment explanation
Indices: 43011--43192 Score: 221
Period size: 73 Copynumber: 2.5 Consensus size: 75
43001 ATGACTATCA
*
43011 CAACGCGAATATGACTATAGCAACGCGAATTT-A-ACCTGCATAATCGCGAATTTGACTATCGCA
1 CAACGCGAA-ATGACTATCGCAACGCGAATTTGATACCTGCA-AATCGCGAATTTGACTATCGCA
*
43074 ACGAGATAATCG
64 ACGAGAAAATCG
* *
43086 CAACGCGAAATGACTATCGCAACGCGAATTTGATTATC-GC-AA-CGGGAATTTGACTATCGCAA
1 CAACGCGAAATGACTATCGCAACGCGAATTTGA-TACCTGCAAATCGCGAATTTGACTATCGCAA
43148 CGAGAAAATCG
65 CGAGAAAATCG
* * * * *
43159 CAAAGTGTATTGACTATCGCAACGCGAATATGAT
1 CAACGCGAAATGACTATCGCAACGCGAATTTGAT
43193 GTAGATTGAA
Statistics
Matches: 95, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
72 1 0.01
73 57 0.60
74 23 0.24
75 10 0.11
76 2 0.02
77 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (75 bp):
CAACGCGAAATGACTATCGCAACGCGAATTTGATACCTGCAAATCGCGAATTTGACTATCGCAAC
GAGAAAATCG
Found at i:43324 original size:36 final size:34
Alignment explanation
Indices: 43283--43362 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
43273 TCAACTTTTA
43283 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
43319 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
43349 ATCAATTAAACAAA
1 ATCAATTAAACAAA
43363 TCAACTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:43333 original size:30 final size:30
Alignment explanation
Indices: 43298--43363 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
43288 TTAAACAAGC
43298 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
43328 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
43358 ACAAAT
1 ACAAAT
43364 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:44854 original size:42 final size:42
Alignment explanation
Indices: 44747--44854 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
44737 TCTAGAATGT
* * *
44747 TGGGAG-GGACCTCTTCAACGATGATAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGATAGGGGCCTCTTGAACGA
* * **
44789 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
44831 TAGGG-GAGGCCTCTTGAACGATGA
1 T-GGGAGAGGCCTCTTGAACGATGA
44855 CAGGTGAGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 49 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:45459 original size:20 final size:20
Alignment explanation
Indices: 45434--45500 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
45424 CGATTCTTTT
*
45434 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
* *
45454 GTTGCGATAGTCATTTTCAC
1 GTTGCGATAGTCAATTTCGC
45474 GTTGCGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
45494 GTTGCGA
1 GTTGCGA
45501 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.07
20 38 0.93
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:45671 original size:18 final size:18
Alignment explanation
Indices: 45648--45697 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
45638 TTTACTAAGC
45648 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
45666 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
45684 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
45698 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:47475 original size:20 final size:20
Alignment explanation
Indices: 47432--47519 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
47422 GAAACTTAAA
* **
47432 ATCGCAACACGAAAATAAAA
1 ATCGCAACACGAAAATGACT
47452 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* ** *
47472 ATCGCAACGCGAATTTGATT
1 ATCGCAACACGAAAATGACT
* **
47492 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
47512 ATCGCAAC
1 ATCGCAAC
47520 GCGAGAATCG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:47520 original size:20 final size:20
Alignment explanation
Indices: 47452--47523 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
47442 GAAAATAAAA
* **
47452 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
*
47472 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
47492 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
47512 ATCGCAACGCGA
1 ATCGCAACGCGA
47524 GAATCGTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:47973 original size:22 final size:22
Alignment explanation
Indices: 47941--47997 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
47931 GATGGAGATA
*
47941 GACGAATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
47963 GACTGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
47985 GACGGATGTCGCC
1 GACGGATTTCGCC
47998 TTAGAGAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:48194 original size:20 final size:20
Alignment explanation
Indices: 48162--48234 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
48152 GCGCTTTGAA
*
48162 AATCGTATTGCGACAGTCAG
1 AATCGCATTGCGACAGTCAG
* * *
48182 AATTGCGTTGCGATAGTCAG
1 AATCGCATTGCGACAGTCAG
* * *
48202 AATCGCATTGCGATAGTAAT
1 AATCGCATTGCGACAGTCAG
*
48222 AATCACATTGCGA
1 AATCGCATTGCGA
48235 TTTACATATT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (20 bp):
AATCGCATTGCGACAGTCAG
Found at i:48252 original size:20 final size:20
Alignment explanation
Indices: 48204--48295 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
48194 ATAGTCAGAA
* *
48204 TCGCATTGCGATAGTA-ATAA
1 TCGCATTGCGAT-TTACATAT
*
48224 TCACATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* * *
48244 TCGCGTTGCGA-TAACCATAC
1 TCGCATTGCGATTTA-CATAT
48264 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
48284 TCGCATTGCGAT
1 TCGCATTGCGAT
48296 AGTCGGAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.07
20 53 0.90
21 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:48253 original size:40 final size:40
Alignment explanation
Indices: 48204--48298 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
48194 ATAGTCAGAA
48204 TCGCATTGCGATAGTAATAATCACATTGCGATTTACATAT
1 TCGCATTGCGATAGTAATAATCACATTGCGATTTACATAT
* *** * *
48244 TCGCGTTGCGATAACCATACTCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTAATAATCACATTGCGATTTACATAT
48284 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
48299 CGGAAAATCG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTAATAATCACATTGCGATTTACATAT
Found at i:49833 original size:29 final size:29
Alignment explanation
Indices: 49800--49859 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
49790 GTTTAAATCT
49800 TACATTTTTTAATTGAATAAACT-TGATTG
1 TACATTTTTTAATTGAATAAACTGT-ATTG
49829 TACATTTTTTAATTGAATAAACTGTATTG
1 TACATTTTTTAATTGAATAAACTGTATTG
49858 TA
1 TA
49860 AAAGTTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (29 bp):
TACATTTTTTAATTGAATAAACTGTATTG
Found at i:57090 original size:6 final size:6
Alignment explanation
Indices: 57079--57206 Score: 186
Period size: 6 Copynumber: 21.2 Consensus size: 6
57069 ATAGGTACTG
57079 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC
* *
57127 AAATTC AAATTC AAATTC AAATTC AAATTC AAATCC AAATCC AAA-TC
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC
* * *
57174 CAATTCC AAATCC AAATCC AAATTTC AAATTC A
1 AAATT-C AAATTC AAATTC AAA-TTC AAATTC A
57207 TGTTTCTAAG
Statistics
Matches: 113, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
5 3 0.03
6 101 0.89
7 9 0.08
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTC
Found at i:61173 original size:21 final size:22
Alignment explanation
Indices: 61132--61174 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
61122 CATTATTTTA
* *
61132 TTGTTGTATGTTGATGACATGC
1 TTGTTGTAGGTTCATGACATGC
61154 TTGTTGTAGGTTCA-GACATGC
1 TTGTTGTAGGTTCATGACATGC
61175 AAGAGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.42
Consensus pattern (22 bp):
TTGTTGTAGGTTCATGACATGC
Found at i:65033 original size:25 final size:26
Alignment explanation
Indices: 64974--65033 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
64964 TTTTATAAAC
* *
64974 TTATTTCTTTTCTTTTCTTTTCAAGTT
1 TTATTT-TTTTATTTTATTTTCAAGTT
65001 TT-TCTTTTTTATTTTATTTT-AAGTT
1 TTAT-TTTTTTATTTTATTTTCAAGTT
65026 TTATTTTT
1 TTATTTTT
65034 CAACATGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 11 0.38
26 14 0.48
27 4 0.14
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.75
Consensus pattern (26 bp):
TTATTTTTTTATTTTATTTTCAAGTT
Found at i:71187 original size:30 final size:30
Alignment explanation
Indices: 71135--71197 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
71125 ATAAATAACA
* *
71135 TGAAAGAAGCTATATGTCTATATGTATATG
1 TGAAAGAAGCTATATGTCTATATGAACATG
71165 TGAAAGAAGCTATGA-G-CTTATATGAACATG
1 TGAAAGAAGCTAT-ATGTC-TATATGAACATG
71195 TGA
1 TGA
71198 TATGAAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 27 0.93
31 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (30 bp):
TGAAAGAAGCTATATGTCTATATGAACATG
Found at i:71322 original size:18 final size:18
Alignment explanation
Indices: 71299--71368 Score: 122
Period size: 18 Copynumber: 3.9 Consensus size: 18
71289 GGGTCTACGC
71299 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
71317 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
71335 GGTCCTTCAGGACATAGT
1 GGTCCTTCGGGACATAGT
*
71353 GGTCTTTCGGGACATA
1 GGTCCTTCGGGACATA
71369 TGTGTTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:72239 original size:20 final size:20
Alignment explanation
Indices: 72214--72255 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
72204 TCATATTCGG
72214 GTCGAATACGGGTTGGGGGT
1 GTCGAATACGGGTTGGGGGT
72234 GTCGAATACGGGTTGGGGGT
1 GTCGAATACGGGTTGGGGGT
72254 GT
1 GT
72256 TACATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.10, G:0.50, T:0.26
Consensus pattern (20 bp):
GTCGAATACGGGTTGGGGGT
Found at i:74255 original size:15 final size:15
Alignment explanation
Indices: 74235--74264 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
74225 CAAAACAAAG
74235 GTTAGTTTCTGGTTA
1 GTTAGTTTCTGGTTA
*
74250 GTTAGTTTCTTGTTA
1 GTTAGTTTCTGGTTA
74265 AATTTAAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.07, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTAGTTTCTGGTTA
Found at i:75514 original size:30 final size:30
Alignment explanation
Indices: 75464--75524 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
75454 AATTACATGA
* *
75464 AAAGAAGCTATATGTCTATATGTATATGTG
1 AAAGAAGCTATATGTCTATATGAACATGTG
75494 AAAGAAGCTATGA-G-CTTATATGAACATGTG
1 AAAGAAGCTAT-ATGTC-TATATGAACATGTG
75524 A
1 A
75525 TATGAAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 1 0.04
30 25 0.93
31 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31
Consensus pattern (30 bp):
AAAGAAGCTATATGTCTATATGAACATGTG
Found at i:75649 original size:18 final size:18
Alignment explanation
Indices: 75626--75677 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
75616 GGGTCTATGC
75626 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
75644 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
75662 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
75678 TGTGTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.27
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:79828 original size:24 final size:24
Alignment explanation
Indices: 79800--79873 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
79790 AGCAACCGTC
79800 TTTTCTAGAACAACATACCTCATT
1 TTTTCTAGAACAACATACCTCATT
*
79824 TTTTCTAGAAC-A-ATA-ATC-TT
1 TTTTCTAGAACAACATACCTCATT
* * *
79844 CTTTTCCATAACAACATCCCTCATT
1 -TTTTCTAGAACAACATACCTCATT
79869 TTTTC
1 TTTTC
79874 CAAAACAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 2 0.05
21 11 0.28
22 4 0.10
23 3 0.08
24 18 0.45
25 2 0.05
ACGTcount: A:0.30, C:0.26, G:0.03, T:0.42
Consensus pattern (24 bp):
TTTTCTAGAACAACATACCTCATT
Found at i:79893 original size:45 final size:45
Alignment explanation
Indices: 79799--79916 Score: 128
Period size: 45 Copynumber: 2.6 Consensus size: 45
79789 TAGCAACCGT
* * * * * **
79799 CTTTTCTAGAACAACATACCTCATTTTTTCTAGAACAATAATCTT
1 CTTTTCTATAACAACATCCCTCATTTTTTCCAAAACAATAACCCA
* *
79844 CTTTTCCATAACAACATCCCTCATTTTTTCCAAAACAATAGCCCA
1 CTTTTCTATAACAACATCCCTCATTTTTTCCAAAACAATAACCCA
* * *
79889 CTTTTCTATAATAGCAACCCTCATTTTT
1 CTTTTCTATAACAACATCCCTCATTTTT
79917 CCTAGACTAG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.38
Consensus pattern (45 bp):
CTTTTCTATAACAACATCCCTCATTTTTTCCAAAACAATAACCCA
Done.