Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003811.1 Hibiscus syriacus cultivar Beakdansim tig00008170_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: 112437
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2238 original size:21 final size:22
Alignment explanation
Indices: 2212--2262 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
2202 ATTTAAAAAA
*
2212 TTAAAAAAT-T-ATTATTATTTT
1 TTAAAAAATCTCAATATT-TTTT
2233 TTAAAAAATCTCAATATTTTTT
1 TTAAAAAATCTCAATATTTTTT
2255 TTAAAAAA
1 TTAAAAAA
2263 AATCCAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.33
22 13 0.48
23 5 0.19
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAAAAATCTCAATATTTTTT
Found at i:2527 original size:23 final size:23
Alignment explanation
Indices: 2501--2552 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
2491 GATGACTCAA
*
2501 GCAATTAACATGAGTGAATTAAT
1 GCAATTAACATGAGTGAATTAAC
* * * *
2524 GCAACTGATATGAGTGAGTTAAC
1 GCAATTAACATGAGTGAATTAAC
2547 GCAATT
1 GCAATT
2553 GTTAATTGCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (23 bp):
GCAATTAACATGAGTGAATTAAC
Found at i:3969 original size:31 final size:30
Alignment explanation
Indices: 3910--3998 Score: 94
Period size: 30 Copynumber: 2.9 Consensus size: 30
3900 GATTTAGTTA
* *
3910 GTGACCAAATTATAAGATTTTAAAAGTTT-G
1 GTGACCAAAATATAA-ATTTAAAAAGTTTAG
3940 GTGACCAAAATATAAATATTGAAAAAGTTTAG
1 GTGACCAAAATATAAAT-TT-AAAAAGTTTAG
3972 G-GACCAAAATGAT-AATTTCAAAAAGTT
1 GTGACCAAAAT-ATAAATTT-AAAAAGTT
3999 ACAATTGGTC
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
29 2 0.04
30 26 0.50
31 20 0.38
32 4 0.08
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (30 bp):
GTGACCAAAATATAAATTTAAAAAGTTTAG
Found at i:8547 original size:21 final size:21
Alignment explanation
Indices: 8500--8547 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
8490 TTCATGGTAC
*
8500 TATTCATCACTTTCATGTCAT
1 TATTCATCACTTTCACGTCAT
* *
8521 TGTTCATTACTATTCACGT-AT
1 TATTCATCACT-TTCACGTCAT
8542 TATTCA
1 TATTCA
8548 CACCGTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (21 bp):
TATTCATCACTTTCACGTCAT
Found at i:13712 original size:202 final size:202
Alignment explanation
Indices: 13470--13885 Score: 715
Period size: 202 Copynumber: 2.0 Consensus size: 202
13460 TATAAGCTAT
* *
13470 ATGATACGATCTATGTGAATACATACACATGTGATATATGTTATATGATATGAACCTATGTGATA
1 ATGATATGATCTATGTGAATACATACACATGTGATATATGTTATATGATATAAACCTATGTGATA
13535 TGGGTTATATGACAAGAATATTATACAAGGATCTATGAGATCATACAAGAATGATATACAAGCTA
66 TGGGTTATATGACAAGAATATTATACAAGGATCTATGAGATCATACAAGAATGATATACAAGCTA
* *
13600 CATGAGAACACGTTATGAGATTACATGTTTATATGATACAAGTGGTGTGAACTGTTATAAATGAT
131 CAAGAGAACAAGTTATGAGATTACATGTTTATATGATACAAGTGGTGTGAACTGTTATAAATGAT
13665 AATGCCC
196 AATGCCC
* * * * *
13672 ATGATATGATCTATGTGATTACATGCATATGTGTTATATGTTGTATGATATAAACCTATGTGATA
1 ATGATATGATCTATGTGAATACATACACATGTGATATATGTTATATGATATAAACCTATGTGATA
13737 TGGGTTATATGACAAGAATATTATACAAGGATCTATGAGATCATACAAGAATGATATACAAGCTA
66 TGGGTTATATGACAAGAATATTATACAAGGATCTATGAGATCATACAAGAATGATATACAAGCTA
* *
13802 TAAGAGAACAAGTTATGAGATTACATGTTTATATGATACAAGTGGTGTGAATTGTTATAAATGAT
131 CAAGAGAACAAGTTATGAGATTACATGTTTATATGATACAAGTGGTGTGAACTGTTATAAATGAT
13867 AATGCCC
196 AATGCCC
13874 ATGTTATATGAT
1 ATG--ATATGAT
13886 ATGAGAGCTA
Statistics
Matches: 201, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
202 194 0.97
204 7 0.03
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (202 bp):
ATGATATGATCTATGTGAATACATACACATGTGATATATGTTATATGATATAAACCTATGTGATA
TGGGTTATATGACAAGAATATTATACAAGGATCTATGAGATCATACAAGAATGATATACAAGCTA
CAAGAGAACAAGTTATGAGATTACATGTTTATATGATACAAGTGGTGTGAACTGTTATAAATGAT
AATGCCC
Found at i:14789 original size:17 final size:17
Alignment explanation
Indices: 14767--14820 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
14757 AAAAAATATA
*
14767 ATTTAAGTAATTATCTT
1 ATTTAAATAATTATCTT
14784 ATTTAAATAATTATCTT
1 ATTTAAATAATTATCTT
14801 ATTTAAATAATTATCTT
1 ATTTAAATAATTATCTT
14818 ATT
1 ATT
14821 AGAGACATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTTAAATAATTATCTT
Found at i:19389 original size:13 final size:13
Alignment explanation
Indices: 19371--19395 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19361 CACACATCAT
19371 CTAACAACTTCAG
1 CTAACAACTTCAG
19384 CTAACAACTTCA
1 CTAACAACTTCA
19396 TCATTCAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.04, T:0.24
Consensus pattern (13 bp):
CTAACAACTTCAG
Found at i:28102 original size:35 final size:36
Alignment explanation
Indices: 28055--28161 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
28045 AATGTTGATA
28055 ATGCTCAAATTAGGTTATCCCACTAGTATTAG-AAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATT-GCAAAT
28091 ATGCT-AAATTAGGTTATCCCACTAGTATTGCAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTGCAAAT
*
28126 ATGCTCAAATTAGGTTATCCCACTAGTATTGTAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTGCAAAT
28162 GACGATTTTG
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
34 1 0.01
35 33 0.49
36 34 0.50
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (36 bp):
ATGCTCAAATTAGGTTATCCCACTAGTATTGCAAAT
Found at i:31259 original size:29 final size:31
Alignment explanation
Indices: 31227--31293 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 31
31217 GACTTAATTT
*
31227 TTAATTTGACTTC-TAAACTTTA-A-AAAATA
1 TTAATTTGAC-CCATAAACTTTACATAAAATA
*
31256 TTAATTTGACCCATAAATTTTACATAAAATA
1 TTAATTTGACCCATAAACTTTACATAAAATA
31287 TTAATTT
1 TTAATTT
31294 AATCTCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 1 0.03
29 18 0.55
30 1 0.03
31 13 0.39
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (31 bp):
TTAATTTGACCCATAAACTTTACATAAAATA
Found at i:31304 original size:31 final size:28
Alignment explanation
Indices: 31227--31304 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 28
31217 GACTTAATTT
* *
31227 TTAATTTGACTTCTAAACTTTAAAAAATA
1 TTAATTTAAC-TCTAAATTTTAAAAAATA
* *
31256 TTAATTTGACCCATAAATTTTACATAAAATA
1 TTAATTTAACTC-TAAATTTTA-A-AAAATA
31287 TTAATTTAATCTCTAAAT
1 TTAATTTAA-CTCTAAAT
31305 CTGATCAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 18 0.44
30 1 0.02
31 19 0.46
32 2 0.05
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.42
Consensus pattern (28 bp):
TTAATTTAACTCTAAATTTTAAAAAATA
Found at i:33418 original size:21 final size:21
Alignment explanation
Indices: 33377--33419 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33367 AATAAAATTT
**
33377 ATTACAATTTAATACAATAAA
1 ATTACAATAAAATACAATAAA
*
33398 ATTACAATAAAAT-CAATTAA
1 ATTACAATAAAATACAATAAA
33418 AT
1 AT
33420 AAATTTATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTACAATAAAATACAATAAA
Found at i:33508 original size:7 final size:7
Alignment explanation
Indices: 33498--33542 Score: 51
Period size: 6 Copynumber: 6.9 Consensus size: 7
33488 ATATATTGAT
*
33498 ATATACC
1 ATATATC
33505 ATATATC
1 ATATATC
*
33512 ATATTTC
1 ATATATC
33519 ATAT-TC
1 ATATATC
33525 ATATA-C
1 ATATATC
33531 ATATA-C
1 ATATATC
33537 ATATAT
1 ATATAT
33543 TACTTATGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 18 0.53
7 16 0.47
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATATC
Found at i:33758 original size:19 final size:19
Alignment explanation
Indices: 33734--33774 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
33724 ACCTCATTGA
* *
33734 TCGCCAAGTGTTCCATAGG
1 TCGCCAAGTGCTCCATAAG
33753 TCGCCAAGTGCTCCATAAG
1 TCGCCAAGTGCTCCATAAG
33772 TCG
1 TCG
33775 TCGTGTGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (19 bp):
TCGCCAAGTGCTCCATAAG
Found at i:34254 original size:17 final size:17
Alignment explanation
Indices: 34234--34268 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34224 TCCTTGTCAC
*
34234 TTATATATATATATATA
1 TTATATATATATACATA
*
34251 TTATTTATATATACATA
1 TTATATATATATACATA
34268 T
1 T
34269 ATTTATAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATATATATATACATA
Found at i:34301 original size:32 final size:32
Alignment explanation
Indices: 34265--34332 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
34255 TTATATATAC
* * * *
34265 ATATATTTATAAGTGTGTGTATATATATAA-GT
1 ATATACTTATAA-TGTATGCATAAATATAATGT
34297 ATATACTTATAATGTATGCATAAATATAATGT
1 ATATACTTATAATGTATGCATAAATATAATGT
34329 ATAT
1 ATAT
34333 TATATATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (32 bp):
ATATACTTATAATGTATGCATAAATATAATGT
Found at i:34386 original size:20 final size:21
Alignment explanation
Indices: 34328--34402 Score: 84
Period size: 20 Copynumber: 3.6 Consensus size: 21
34318 AAATATAATG
*
34328 TATATTATATATACATGCATCA
1 TATA-TATATATACATTCATCA
34350 TAT-TAT-TATAACATTCATCA
1 TATATATATAT-ACATTCATCA
*
34370 TATATATATATAC-TTCATAA
1 TATATATATATACATTCATCA
*
34390 TATATATTTATAC
1 TATATATATATAC
34403 TTATACTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.06
20 33 0.70
21 5 0.11
22 6 0.13
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.45
Consensus pattern (21 bp):
TATATATATATACATTCATCA
Found at i:34962 original size:2 final size:2
Alignment explanation
Indices: 34955--34986 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
34945 GACTCATAAT
34955 TA TA TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34987 ATTTATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:35424 original size:24 final size:24
Alignment explanation
Indices: 35379--35424 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
35369 CTCAATCTGT
* *
35379 ATCCGATTTAACCTGACCCGATAG
1 ATCCGATTAAACCTGACACGATAG
35403 ATCCGACTTAAACCTGA-ACGAT
1 ATCCGA-TTAAACCTGACACGAT
35425 TATCTGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCCGATTAAACCTGACACGATAG
Found at i:42137 original size:14 final size:14
Alignment explanation
Indices: 42118--42183 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
42108 AAGTCAACAG
42118 GTTGACTCAGACGA
1 GTTGACTCAGACGA
*
42132 GTTGACTCAGTCCGA
1 GTTGACTCAG-ACGA
* * *
42147 GATGACTCAAACAA
1 GTTGACTCAGACGA
*
42161 GTTGACTCGGACCGA
1 GTTGACTCAGA-CGA
*
42176 GCTGACTC
1 GTTGACTC
42184 GGTGACTAGA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
14 20 0.50
15 20 0.50
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:42163 original size:29 final size:29
Alignment explanation
Indices: 42120--42183 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
42110 GTCAACAGGT
* * *
42120 TGACTCAGACGAGTTGACTCAGTCCGAGA
1 TGACTCAAACAAGTTGACTCAGACCGAGA
* *
42149 TGACTCAAACAAGTTGACTCGGACCGAGC
1 TGACTCAAACAAGTTGACTCAGACCGAGA
42178 TGACTC
1 TGACTC
42184 GGTGACTAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (29 bp):
TGACTCAAACAAGTTGACTCAGACCGAGA
Found at i:43331 original size:23 final size:23
Alignment explanation
Indices: 43301--43349 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
43291 TATTTATATC
43301 CGTGAACATGTTCGTTTAACGTT
1 CGTGAACATGTTCGTTTAACGTT
*
43324 CGTGAACATGTTCGTTTAACTTT
1 CGTGAACATGTTCGTTTAACGTT
43347 CGT
1 CGT
43350 TTATATCTCT
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:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (23 bp):
CGTGAACATGTTCGTTTAACGTT
Found at i:45815 original size:16 final size:15
Alignment explanation
Indices: 45760--45827 Score: 100
Period size: 15 Copynumber: 4.5 Consensus size: 15
45750 TGAGACATTA
*
45760 CCCGCCCCGCATCCT
1 CCCGCCCCGCATCCG
45775 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
* *
45790 TCCGCCCTGCATCCG
1 CCCGCCCCGCATCCG
45805 CCCGCCCCTGCATCCG
1 CCCGCCCC-GCATCCG
45821 CCCGCCC
1 CCCGCCC
45828 AGCTAAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
15 33 0.70
16 14 0.30
ACGTcount: A:0.06, C:0.65, G:0.18, T:0.12
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:49041 original size:22 final size:21
Alignment explanation
Indices: 49015--49068 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
49005 CTACTAAAAA
*
49015 TTAATTAACA-AAATTAACATTT
1 TTAA-TAACATAAAATAACA-TT
*
49037 TTAATAAAATAAAATAACATT
1 TTAATAACATAAAATAACATT
49058 TTAAATAACAT
1 TT-AATAACAT
49069 TTTACTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
TTAATAACATAAAATAACATT
Found at i:49065 original size:12 final size:12
Alignment explanation
Indices: 49048--49086 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
49038 TAATAAAATA
49048 AAATAACATTTT
1 AAATAACATTTT
49060 AAATAACATTTT
1 AAATAACATTTT
** *
49072 ACTTAAAATTTT
1 AAATAACATTTT
49084 AAA
1 AAA
49087 AAATATTAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (12 bp):
AAATAACATTTT
Found at i:52440 original size:21 final size:22
Alignment explanation
Indices: 52399--52445 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
52389 TAATTTTACC
52399 TTTTATTATTTTGTCATTATTA
1 TTTTATTATTTTGTCATTATTA
52421 TTTTATTATCTTT-T-ATTATTA
1 TTTTATTAT-TTTGTCATTATTA
52442 TTTT
1 TTTT
52446 CCATTTCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.46
22 10 0.42
23 3 0.12
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTATTATTTTGTCATTATTA
Found at i:52524 original size:2 final size:2
Alignment explanation
Indices: 52517--52549 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52507 ATATTTATGT
52517 TA TA 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 TA TA T
52550 GTATTTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52737 original size:19 final size:19
Alignment explanation
Indices: 52715--52755 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
52705 TACTATTTTC
52715 ATTTTATTCTTTTATTCTT
1 ATTTTATTCTTTTATTCTT
* * *
52734 ATTTTGTTTTTTTATTTTT
1 ATTTTATTCTTTTATTCTT
52753 ATT
1 ATT
52756 CACTTATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (19 bp):
ATTTTATTCTTTTATTCTT
Found at i:56136 original size:24 final size:25
Alignment explanation
Indices: 56084--56141 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
56074 GCATTTCTTG
*
56084 CATTTTATA-TTTCATGTTTGTTTT
1 CATTTTATATTTTCATGTTTGTTTA
*
56108 TATTTTATATTTTCCATG-TT-TTTA
1 CATTTTATATTTT-CATGTTTGTTTA
56132 CA-TTTATATT
1 CATTTTATATT
56142 AACTAACAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 8 0.28
24 12 0.41
25 5 0.17
26 4 0.14
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.66
Consensus pattern (25 bp):
CATTTTATATTTTCATGTTTGTTTA
Found at i:56413 original size:14 final size:15
Alignment explanation
Indices: 56394--56422 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56384 TTTACAACAA
56394 CGGAGAA-GTGCATC
1 CGGAGAAGGTGCATC
56408 CGGAGAAGGTGCATC
1 CGGAGAAGGTGCATC
56423 TGAGGGGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.21, G:0.38, T:0.14
Consensus pattern (15 bp):
CGGAGAAGGTGCATC
Found at i:56636 original size:21 final size:21
Alignment explanation
Indices: 56607--56647 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
56597 CGAGGAGGAT
56607 AAGACAAGGAAGATAGAAGAA
1 AAGACAAGGAAGATAGAAGAA
* * *
56628 AAGATAAGGATGTTAGAAGA
1 AAGACAAGGAAGATAGAAGA
56648 CCAAATGAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.02, G:0.29, T:0.12
Consensus pattern (21 bp):
AAGACAAGGAAGATAGAAGAA
Found at i:60013 original size:15 final size:15
Alignment explanation
Indices: 59993--60023 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
59983 AAGCAAGACA
59993 AAACCTAATAGTCTT
1 AAACCTAATAGTCTT
60008 AAACCTAATAGTCTT
1 AAACCTAATAGTCTT
60023 A
1 A
60024 CTTCAGGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (15 bp):
AAACCTAATAGTCTT
Found at i:60499 original size:21 final size:22
Alignment explanation
Indices: 60475--60516 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
60465 ATGTGGGGAA
* *
60475 CCTTCTG-CTACAAGATGATGC
1 CCTTCTGACTAAAAAATGATGC
60496 CCTTCTGACTAAAAAATGATG
1 CCTTCTGACTAAAAAATGATG
60517 GGGGCAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (22 bp):
CCTTCTGACTAAAAAATGATGC
Found at i:64798 original size:106 final size:106
Alignment explanation
Indices: 64430--64798 Score: 562
Period size: 106 Copynumber: 3.5 Consensus size: 106
64420 ACGAAGGGGC
* * * *
64430 TTCCCAATTTCATAACCAATTTCAACTTCACAGCGAAGGATATTGGTCCCAAGACAACACAAGTT
1 TTCCCAATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
* * *
64495 CAACTTCACAACGAAGGGGCGACTGGTTGTCAACAAATAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
* *
64536 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTC-AGGACAACACAAGT
1 TTCCCAATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA-GACAACACAAGT
64600 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
65 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
* *
64642 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAATACAAGTT
1 TTCCCAATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
*
64707 CAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
* * * *
64748 TTCCCAGTTCCAGAACCAATTTCAACTTCAC-GACGGAGGATATTAGACTCG
1 TTCCCAATTTCAGAACCAATTTCAACTTCACAG-CGAAGGATATTGGACTCG
64799 GAACAATACA
Statistics
Matches: 244, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
105 2 0.01
106 241 0.99
107 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
TTCCCAATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
Found at i:65485 original size:26 final size:26
Alignment explanation
Indices: 65456--65516 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
65446 TCCAGGAACC
65456 CTAGCGCCGCATGCCCCTTCCTCGTT
1 CTAGCGCCGCATGCCCCTTCCTCGTT
65482 CTAGCGCCGCATGCCCCTTCCTCGTT
1 CTAGCGCCGCATGCCCCTTCCTCGTT
65508 CTAGCGCCG
1 CTAGCGCCG
65517 TTTCCACTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.08, C:0.46, G:0.21, T:0.25
Consensus pattern (26 bp):
CTAGCGCCGCATGCCCCTTCCTCGTT
Found at i:66490 original size:12 final size:13
Alignment explanation
Indices: 66473--66505 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
66463 TTTCCATTTC
66473 TTGTTATTCTTA-
1 TTGTTATTCTTAT
66485 TTGTTATTCTTAT
1 TTGTTATTCTTAT
66498 TTGTTATT
1 TTGTTATT
66506 ATTTTCTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.70
Consensus pattern (13 bp):
TTGTTATTCTTAT
Found at i:66545 original size:2 final size:2
Alignment explanation
Indices: 66538--66568 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
66528 ATATTTATGT
66538 TA 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 TA T
66569 GTATTTAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66657 original size:2 final size:2
Alignment explanation
Indices: 66650--66681 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
66640 GTTTTATTTA
66650 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
66682 TTTATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67459 original size:21 final size:22
Alignment explanation
Indices: 67418--67464 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
67408 TAATTTTACC
67418 TTTTATTATTTTGTCATTATTA
1 TTTTATTATTTTGTCATTATTA
67440 TTTTATTATCTTT-T-ATTATTA
1 TTTTATTAT-TTTGTCATTATTA
67461 TTTT
1 TTTT
67465 CCATTTCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.46
22 10 0.42
23 3 0.12
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTATTATTTTGTCATTATTA
Found at i:67684 original size:55 final size:52
Alignment explanation
Indices: 67625--67735 Score: 118
Period size: 53 Copynumber: 2.1 Consensus size: 52
67615 TTATTTTTCC
* *
67625 ATTTCCCTTATTTGTTTTATT-T-AATATATATATATATATATATATATTATTTATT
1 ATTT-CCTTA-TT-TTTTATTATCAATAT-TATATACATATATATATAT-ATTTACT
* * *
67680 ATTTCTTTATTTTTTATTATCGATATTATTTACATATATATATATATTTACT
1 ATTTCCTTATTTTTTATTATCAATATTATATACATATATATATATATTTACT
67732 ATTT
1 ATTT
67736 TCATTTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
52 17 0.35
53 20 0.41
54 8 0.16
55 4 0.08
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (52 bp):
ATTTCCTTATTTTTTATTATCAATATTATATACATATATATATATATTTACT
Found at i:68018 original size:21 final size:20
Alignment explanation
Indices: 67932--68088 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
67922 AAATGACCAA
**
67932 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
67951 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
67971 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
67991 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
68012 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
68032 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
68052 ACAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
68073 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
68089 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:68041 original size:41 final size:41
Alignment explanation
Indices: 67991--68088 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
67981 AATCAGTTTC
* *
67991 CAAAATCGCAACGCGATTCTT-GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGATT-TTACAAAATCGCAACGCGAATA-T
* **
68032 CAAATTCGCATTGCGATTTTACAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTTACAAAATCGCAACGCGAATAT
*
68073 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
68089 ACACATAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 41 0.89
42 3 0.07
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (41 bp):
CAAAATCGCAACGCGATTTTACAAAATCGCAACGCGAATAT
Found at i:68098 original size:20 final size:20
Alignment explanation
Indices: 68075--68248 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
68065 GCGAATATGA
68075 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
68095 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
68115 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
68135 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
68155 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
68175 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
68195 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
68215 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
68236 AAATCGCAACGCG
1 AAATCGCAACGCG
68249 ATATTTAAAG
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 107 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:68102 original size:61 final size:61
Alignment explanation
Indices: 67931--68107 Score: 182
Period size: 61 Copynumber: 2.9 Consensus size: 61
67921 AAAATGACCA
* * * *
67931 ACAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCAGAATCGCAAAT-C-AGTTT
1 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGC-AATGCGAGTTT
* * * * ** * * *
67990 CCAAAATCGCAACGCGATTCTTGAAAATCGCAATGCGATAGTCAAATTCGCATTGCGATTTT
1 ACAAAATCGCAACGCGAAT-ATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTT
68052 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAATGCG
1 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACA-AAATCGCAATGCG
68108 TATCCGTAAA
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
59 16 0.17
60 5 0.05
61 51 0.55
62 21 0.23
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (61 bp):
ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTT
Found at i:68119 original size:40 final size:39
Alignment explanation
Indices: 68055--68249 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
68045 CGATTTTACA
* ** *
68055 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
68095 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
68135 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * ** *
68175 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
68215 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
68250 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:68140 original size:60 final size:60
Alignment explanation
Indices: 68055--68248 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
68045 CGATTTTACA
* ** * *
68055 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
68115 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
68175 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
68236 AAATCGCAACGCG
1 AAATCGCAACGCG
68249 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:68670 original size:33 final size:33
Alignment explanation
Indices: 68631--68701 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
68621 TTCACTTAGA
68631 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
68664 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
68697 TTTCA
1 TTTCA
68702 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:68838 original size:41 final size:41
Alignment explanation
Indices: 68780--68857 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
68770 TTGCAGAAGA
*
68780 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
68821 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
68858 CGCAAAGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:68854 original size:21 final size:21
Alignment explanation
Indices: 68781--68856 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
68771 TGCAGAAGAG
*
68781 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
68802 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
68822 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
68843 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
68857 TCGCAAAGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:68860 original size:14 final size:14
Alignment explanation
Indices: 68841--68897 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
68831 GAGAAATGAA
68841 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
68855 AATCGCAAAGCGATATGAA
1 AATCGC-AA-CG--A-GAG
68874 AATCGCAACGAGAG
1 AATCGCAACGAGAG
68888 AATCGCAACG
1 AATCGCAACG
68898 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 8 0.22
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:68874 original size:33 final size:33
Alignment explanation
Indices: 68836--68900 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
68826 AACGAGAGAA
68836 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
*
68869 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGA
68901 AACCAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
Found at i:68909 original size:33 final size:33
Alignment explanation
Indices: 68839--68913 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
68829 GAGAGAAATG
* **
68839 AAAATCGCAACGAGAGAATCGCAAAGCGATATG
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
*
68872 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
68905 AAAATCGCA
1 AAAATCGCA
68914 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
Found at i:68931 original size:19 final size:19
Alignment explanation
Indices: 68909--69006 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
68899 GAAACCAAAA
*
68909 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
68928 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
68942 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
68961 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
68975 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
68994 TCGCGTTGCGATT
1 TCGCGTTGCGATT
69007 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
16 6 0.09
17 6 0.09
19 32 0.50
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:68950 original size:14 final size:14
Alignment explanation
Indices: 68931--69020 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
68921 TTTCATTTCG
68931 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
68945 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
68964 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
68978 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
68997 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
69011 CGTTGCGATT
1 CGTTGCGATT
69021 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:68956 original size:33 final size:33
Alignment explanation
Indices: 68914--69028 Score: 230
Period size: 33 Copynumber: 3.5 Consensus size: 33
68904 CAAAATCGCA
68914 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
68947 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
68980 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
69013 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
69029 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:70882 original size:93 final size:92
Alignment explanation
Indices: 70723--70912 Score: 353
Period size: 93 Copynumber: 2.1 Consensus size: 92
70713 TAGATTGCTT
70723 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
70788 TTTGTCTTTGTTTTATCTTTTGGTTGAA
66 TTTGTCTTTGTTTTATCTTTTGGTTG-A
*
70816 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
70881 TTTGTCTTTGTTTTGTCTTTTGGTTGA
66 TTTGTCTTTGTTTTATCTTTTGGTTGA
70908 AGTAA
1 AGTAA
70913 TGCAATCCAT
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 6 0.06
93 89 0.94
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (92 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTATCTTTTGGTTGA
Found at i:72529 original size:14 final size:14
Alignment explanation
Indices: 72510--72545 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
72500 ATTGTTTAAT
72510 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
72524 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
72538 TGATTTGT
1 TGATTTGT
72546 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:72668 original size:19 final size:19
Alignment explanation
Indices: 72652--72749 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
72642 AAAAATGACT
72652 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
72671 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
72690 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
72704 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
72723 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
72743 ATCGCAA
1 ATCGCAA
72750 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:72781 original size:53 final size:53
Alignment explanation
Indices: 72652--72767 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
72642 AAAAATGACT
72652 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
72704 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
72757 ATCGCAATGCG
1 ATCGCAATGCG
72768 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:72820 original size:19 final size:19
Alignment explanation
Indices: 72796--73031 Score: 278
Period size: 19 Copynumber: 13.4 Consensus size: 19
72786 GATTCTCTCG
72796 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
72815 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
72834 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
72853 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
72867 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
72886 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
72905 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
72919 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
72938 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
72957 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
72971 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
72991 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
73005 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
73024 TTGCGATT
1 TTGCGATT
73032 GTAATTTCCG
Statistics
Matches: 188, Mismatches: 8, Indels: 42
0.79 0.03 0.18
Matches are distributed among these distances:
14 29 0.15
16 23 0.12
17 20 0.11
18 3 0.02
19 101 0.54
20 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:72831 original size:52 final size:52
Alignment explanation
Indices: 72815--73003 Score: 369
Period size: 52 Copynumber: 3.6 Consensus size: 52
72805 TCATTTCGCA
72815 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
72867 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
72919 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
72971 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCAT
73004 GTTGGGATTT
Statistics
Matches: 136, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 119 0.88
53 17 0.12
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:72849 original size:71 final size:71
Alignment explanation
Indices: 72774--73031 Score: 327
Period size: 71 Copynumber: 3.7 Consensus size: 71
72764 TGCGTTTATA
72774 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
72839 ATTTTC
66 ATTTTC
72845 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
72910 ATTCTCTC
66 ATT-T-TC
* * * * * *
72918 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
72975 GATTTTC
65 GATTTTC
* * *
72982 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
73032 GTAATTTCCG
Statistics
Matches: 164, Mismatches: 13, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
64 4 0.02
65 6 0.04
66 12 0.07
67 25 0.15
68 4 0.02
69 3 0.02
71 96 0.59
72 5 0.03
73 9 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (71 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTTTC
Found at i:73377 original size:20 final size:20
Alignment explanation
Indices: 73355--73505 Score: 153
Period size: 20 Copynumber: 7.5 Consensus size: 20
73345 CACAGATTCT
*
73355 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
73375 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
73395 CGTTGCGATATACGGAAACG
1 CGTTGCGATTTACGGATACG
**
73415 CGTTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
* *
73435 CGTTGCGATTTACAGATACA
1 CGTTGCGATTTACGGATACG
* *
73455 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
73475 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
73495 CGTTGCGATTT
1 CGTTGCGATTT
73506 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
19 2 0.02
20 107 0.97
21 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:73522 original size:21 final size:20
Alignment explanation
Indices: 73472--73569 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
73462 ATTTATGTGT
* * * *
73472 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
73492 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
73513 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
73533 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
73554 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
73570 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:73545 original size:61 final size:60
Alignment explanation
Indices: 73472--73628 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
73462 ATTTATGTGT
*
73472 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
73533 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
73594 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
73629 TTGGTAATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:73564 original size:41 final size:41
Alignment explanation
Indices: 73472--73628 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
73462 ATTTATGTGT
* * *
73472 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
73513 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
73554 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
73594 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
73629 TTGGTAATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:79752 original size:2 final size:2
Alignment explanation
Indices: 79739--79790 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
79729 TTAATAAAAT
*
79739 TA TA TT TA TA TA 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 TA TA TA TA TA TA
79781 TA TA TA TA TA
1 TA TA TA TA TA
79791 AAGATTTTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:85150 original size:256 final size:254
Alignment explanation
Indices: 84655--85238 Score: 779
Period size: 256 Copynumber: 2.3 Consensus size: 254
84645 CTTATTCATA
84655 TATTGAATAAAAATATTTTTTTATTATTTCGTGTCGGGTC-A----GATTTTTAATTCATATATT
1 TATTGAATAAAAATATTTTTTTATTATTTCG-GTCGGGTCGAGTTGGATTTTTAATTCATATATT
*
84715 CGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGAGTATAGTCAGTTTTTTAAGTGTGATATTCGG
65 CGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGAGTAGAGTCAGTTTTTTAAGTGTGATATTCGG
* *
84780 GTCGGGTCGAGTTTGGATTTAAGGTGAAAAATATCCGACCCGAAAATATATATAATTTTACCTTA
130 GT---GTC--G--TGGATTTAAGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTA
*
84845 TATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGT-A-TGTT
188 TATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCACTATT
84908 TT
253 TT
84910 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGAGTTGGATTTTTAATTCATATATT
1 TATTGAATAAAAATATTTTTTTATTATTTC-GGTCGGGTCGAGTTGGATTTTTAATTCATATATT
* * * *
84975 CGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTC
65 CGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGAGTAGAGTCAG--TTTTTTAAGTGTGATATTC
85040 GGGT-TC-TGG-TTT-AGGCTGAAAAATACCCGACCCGACCCAAAAAATATATAATTTTACCTTA
128 GGGTGTCGTGGATTTAAGG-TGAAAAATACCCGACCCG----AAAAAATATATAATTTTACCTTA
85101 TATATTTAGAAATAATTACAATAATACCCCTCTATATAT-ATATTTTTTTCAATTAAGTCACTAT
188 TATATTTAGAAATAATTACAATAATACCCCTCTATATATAAT-TTTTTTTCAATTAAGTCACTAT
85165 TTT
252 TTT
* * *
85168 TATTGAATAAAAATAATTTTATTATTATTT--AT--GGTCGAGTTAGG-TTTCTAATTCATATAT
1 TATTGAATAAAAAT-ATTTTTTTATTATTTCGGTCGGGTCGAGTT-GGATTTTTAATTCATATAT
85228 TCGGGTCGGGT
64 TCGGGTCGGGT
85239 GGACCAAAAA
Statistics
Matches: 300, Mismatches: 11, Indels: 37
0.86 0.03 0.11
Matches are distributed among these distances:
251 3 0.01
252 20 0.07
253 3 0.01
254 35 0.12
255 42 0.14
256 80 0.27
257 1 0.00
258 21 0.07
259 14 0.05
260 58 0.19
262 23 0.08
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (254 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGTCGGGTCGAGTTGGATTTTTAATTCATATATTC
GGGTCGGGTCGGGTGAAACTTTATTTTGGTCGAGTAGAGTCAGTTTTTTAAGTGTGATATTCGGG
TGTCGTGGATTTAAGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTA
GAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCACTATTTT
Found at i:85597 original size:18 final size:18
Alignment explanation
Indices: 85570--85621 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
85560 ATTCTTGACC
*
85570 GATTCTAATTCCTTCACA
1 GATTCCAATTCCTTCACA
85588 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
85606 GATTCCAATTCCTTCA
1 GATTCCAATTCCTTCA
85622 TAAACATTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.27, C:0.31, G:0.06, T:0.37
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:85616 original size:36 final size:35
Alignment explanation
Indices: 85553--85621 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
85543 TATGGAATCG
* * * *
85553 GATTTCAATTCTTGACCGATTCTAATTCCTTCACA
1 GATTCCAATTCTTCACAGATTCCAATTCCTTCACA
85588 GATTCCAATTCCTTCACAGATTCCAATTCCTTCA
1 GATTCCAATT-CTTCACAGATTCCAATTCCTTCA
85622 TAAACATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 9 0.31
36 20 0.69
ACGTcount: A:0.26, C:0.29, G:0.07, T:0.38
Consensus pattern (35 bp):
GATTCCAATTCTTCACAGATTCCAATTCCTTCACA
Found at i:90243 original size:16 final size:17
Alignment explanation
Indices: 90205--90243 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
90195 TTTAAGATAA
* *
90205 AAAATGAAATAACAAAG
1 AAAATTAAATAACAAAC
90222 AAAATTAAATAAC-AAC
1 AAAATTAAATAACAAAC
90238 AAAATT
1 AAAATT
90244 TAATCAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.69, C:0.08, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAATTAAATAACAAAC
Found at i:91874 original size:3 final size:3
Alignment explanation
Indices: 91861--91905 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
91851 CTCGTGTTTG
91861 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
91906 GTCGTAGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:94321 original size:54 final size:54
Alignment explanation
Indices: 94228--94548 Score: 292
Period size: 54 Copynumber: 5.8 Consensus size: 54
94218 TCAAACTTGG
*
94228 CTTCTTTAAAAATTCATTT-ACAATTATCATCAAGAAACCCCTAAAAATTAGGCTTAT
1 CTTCTTTCAAAATTCATTTGA-AA--A-CATCAAGAAACCCCTAAAAATTAGGCTTAT
* * ** * *
94285 CATT-TTT-ACAAATTAAGTTGAAGGCATCAAGAAACCCCTGAAAATCAGGCTTAT
1 C-TTCTTTCA-AAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAT
* * * * * *
94339 CTTCTTTCCAAATTCATTTGAAAACTTCAAGAAACCCCTGAAAATCATGCTTAC
1 CTTCTTTCAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAT
* * ***
94393 CTTCTTTCAAAATTCATTGGAAAACATCGAGAAATTTCTAAAAATTAGGCTTAGT
1 CTTCTTTCAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTA-T
* *
94448 -TTCTTTCAAAATTCATTTGAAGACATCAAGAAACCCCTAAAAATTAGACTTAGT
1 CTTCTTTCAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTA-T
* * **
94502 -TTATTTCAAAAATCATTTGAAGAAATCATCAAGAAACTTCTAAAAAT
1 CTTCTTTCAAAATTCATTTG-A-AAA-CATCAAGAAACCCCTAAAAAT
94549 CGGACTTAGC
Statistics
Matches: 218, Mismatches: 37, Indels: 18
0.80 0.14 0.07
Matches are distributed among these distances:
53 2 0.01
54 177 0.81
55 1 0.00
56 3 0.01
57 32 0.15
58 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
CTTCTTTCAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAT
Found at i:97081 original size:23 final size:23
Alignment explanation
Indices: 97027--97082 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
97017 TCATATATGG
* *
97027 CACTACGGTGCAATTCTACGCGG
1 CACTTCGGTGCAATTCTACGCGA
* *
97050 CA-TTACGGTGCAATTCTATGTGA
1 CACTT-CGGTGCAATTCTACGCGA
97073 CACTTCGGTG
1 CACTTCGGTG
97083 TATTTATACG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 1 0.04
23 24 0.89
24 2 0.07
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGA
Found at i:97207 original size:2 final size:2
Alignment explanation
Indices: 97200--97243 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
97190 AACGTATGCA
97200 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
97242 AT
1 AT
97244 GATGTGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97536 original size:2 final size:2
Alignment explanation
Indices: 97531--97555 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
97521 TATATATATA
97531 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
97556 ATTATGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:98072 original size:52 final size:54
Alignment explanation
Indices: 97984--98085 Score: 138
Period size: 52 Copynumber: 1.9 Consensus size: 54
97974 AATAATTTGA
97984 AGAAATCATCAAGAAACTTCCAAAAATCAGACTTAGCTCCTTT-AAAAATTAGTT
1 AGAAATCATCAAGAAAC-TCCAAAAATCAGACTTAGCTCCTTTGAAAAATTAGTT
* * *
98038 AGAAA-CATCAAGAAAC-CCTTAAAATGAGGCTTAGCTCCTTTGAAAAAT
1 AGAAATCATCAAGAAACTCC-AAAAATCAGACTTAGCTCCTTTGAAAAAT
98086 CATTTGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
51 2 0.05
52 19 0.44
53 17 0.40
54 5 0.12
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (54 bp):
AGAAATCATCAAGAAACTCCAAAAATCAGACTTAGCTCCTTTGAAAAATTAGTT
Found at i:99479 original size:28 final size:28
Alignment explanation
Indices: 99447--99536 Score: 146
Period size: 28 Copynumber: 3.2 Consensus size: 28
99437 TTAGGCTGAC
*
99447 TTGGGAAGGTAGA-GTGTTTCAGGTTAAT
1 TTGGGGAGGT-GATGTGTTTCAGGTTAAT
*
99475 TTGGGGATGTGATGTGTTTCAGGTTAAT
1 TTGGGGAGGTGATGTGTTTCAGGTTAAT
99503 TTGGGGAGGTGATGTGTTTCAGGTTAAT
1 TTGGGGAGGTGATGTGTTTCAGGTTAAT
99531 TTGGGG
1 TTGGGG
99537 GAGGGGAAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 2 0.03
28 56 0.97
ACGTcount: A:0.19, C:0.03, G:0.39, T:0.39
Consensus pattern (28 bp):
TTGGGGAGGTGATGTGTTTCAGGTTAAT
Found at i:107136 original size:49 final size:49
Alignment explanation
Indices: 107079--107251 Score: 301
Period size: 49 Copynumber: 3.5 Consensus size: 49
107069 CGAGGTTGCT
*
107079 AAAGTTAAATGCATAACGGTGCATTTCGGTATAAAAGGTGCCACTAATG
1 AAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATG
**
107128 AAAGTTAAATGCATAATAGTGCATTTCGGCATAAAAGGTGCCACTAATG
1 AAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATG
*
107177 AAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATG
1 AAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATG
*
107226 AAAGTTAAATGCATAATGGTGCATTT
1 AAAGTTAAATGCATAACGGTGCATTT
107252 TTGGCAAAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 117 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (49 bp):
AAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATG
Found at i:109099 original size:20 final size:19
Alignment explanation
Indices: 109063--109113 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
109053 AAATGATTTG
*
109063 ATTTTGAAAGAAAAAAAATTA
1 ATTTTG-AA-AAAAAAAATGA
* *
109084 TTTTTGAAAAACAAAATGA
1 ATTTTGAAAAAAAAAATGA
109103 ATTTTGAAAAA
1 ATTTTGAAAAA
109114 TGATTTAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 19 0.73
20 2 0.08
21 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (19 bp):
ATTTTGAAAAAAAAAATGA
Found at i:111725 original size:23 final size:23
Alignment explanation
Indices: 111687--111752 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
111677 CACCACAGCT
*
111687 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
111710 TGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
111733 CGTAGAAATGCACCGTAGTG
1 CGTAGAAATGCACCGAAGTG
111753 TCATATATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Done.