Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold426
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: 634051
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 4 of 6
Found at i:303133 original size:22 final size:20
Alignment explanation
Indices: 303066--303123 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
303056 TATTAATGAG
* *
303066 AAAAATAGTATAAACATGTC-
1 AAAAATA-TATAAAAATATCA
* *
303086 ATAAATATATAAATATATCA
1 AAAAATATATAAAAATATCA
303106 AAAAATATATAAAAATAT
1 AAAAATATATAAAAATAT
303124 GAGTAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 10 0.31
20 22 0.69
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAATATATAAAAATATCA
Found at i:303574 original size:21 final size:21
Alignment explanation
Indices: 303550--303602 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
303540 CCACAAATTT
303550 TTTTCTCTTTTTTTCTTTTCC
1 TTTTCTCTTTTTTTCTTTTCC
* *
303571 TTTTC-CTTATTTATCTTTTGC
1 TTTTCTCTT-TTTTTCTTTTCC
303592 TTTT-T-TTTTTT
1 TTTTCTCTTTTTT
303603 AGGTTTTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 5 0.19
21 19 0.70
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCTCTTTTTTTCTTTTCC
Found at i:304857 original size:15 final size:15
Alignment explanation
Indices: 304837--304868 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
304827 TATCTATATG
304837 TTTTTAAAAAATAAT
1 TTTTTAAAAAATAAT
*
304852 TTTTTAAAACATAAT
1 TTTTTAAAAAATAAT
304867 TT
1 TT
304869 CTTTTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTTAAAAAATAAT
Found at i:308074 original size:18 final size:19
Alignment explanation
Indices: 308039--308076 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
308029 AAAAAGTTTT
308039 TAAAAATATAATTAATTTA
1 TAAAAATATAATTAATTTA
308058 TAAAAATATAATT-ATTTA
1 TAAAAATATAATTAATTTA
308076 T
1 T
308077 TTAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAAATATAATTAATTTA
Found at i:309122 original size:15 final size:15
Alignment explanation
Indices: 309084--309130 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
309074 TGATTCGATC
*
309084 TTAATTTAATATCTT
1 TTAATTTATTATCTT
* *
309099 TT-TTTTATTATGTT
1 TTAATTTATTATCTT
*
309113 TTAATTTATTATTTT
1 TTAATTTATTATCTT
309128 TTA
1 TTA
309131 TTATGTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (15 bp):
TTAATTTATTATCTT
Found at i:309133 original size:25 final size:26
Alignment explanation
Indices: 309099--309172 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 26
309089 TTAATATCTT
*
309099 TTTTTTATTATGTTTTAATTTATTA-
1 TTTTTTATTATGTTTTAAATTATTAG
*
309124 TTTTTTATTATG-TATAAATTATTAG
1 TTTTTTATTATGTTTTAAATTATTAG
* *
309149 TTATTTTTTTATATTTTAAGATTA
1 TT-TTTTATTATGTTTTAA-ATTA
309173 ATAAAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 10 0.25
25 14 0.35
26 8 0.20
27 4 0.10
28 4 0.10
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.66
Consensus pattern (26 bp):
TTTTTTATTATGTTTTAAATTATTAG
Found at i:309379 original size:16 final size:18
Alignment explanation
Indices: 309343--309379 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
309333 TATAATTTAT
*
309343 AAATTTAGTACAAAATTA
1 AAATTTAGTACAAAATAA
309361 AAATTTA-T-CAAAATAA
1 AAATTTAGTACAAAATAA
309377 AAA
1 AAA
309380 ATATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (18 bp):
AAATTTAGTACAAAATAA
Found at i:309984 original size:2 final size:2
Alignment explanation
Indices: 309977--310005 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
309967 GTCATTATTT
309977 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
310006 TACTGTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:312690 original size:8 final size:9
Alignment explanation
Indices: 312656--312696 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 9
312646 TAATATTAAT
312656 TAAAAAATA
1 TAAAAAATA
312665 TAAAAATATA
1 TAAAAA-ATA
312675 TAATAAAA-A
1 TAA-AAAATA
312684 TAAAAAA-A
1 TAAAAAATA
312692 TAAAA
1 TAAAA
312697 TTAGATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 10 0.33
9 10 0.33
10 7 0.23
11 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
TAAAAAATA
Found at i:318351 original size:3 final size:3
Alignment explanation
Indices: 318343--318370 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
318333 TTAAAATAAA
318343 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
318371 AATCTAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:318817 original size:2 final size:2
Alignment explanation
Indices: 318810--318854 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
318800 CAATTTAGTC
* *
318810 AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT TT 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
318852 AT A
1 AT A
318855 GATAAGGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:319058 original size:2 final size:2
Alignment explanation
Indices: 318989--319040 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
318979 TAGCAAAATC
* * * *
318989 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AC GT GT 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
319031 AT AT AT AT AT
1 AT AT AT AT AT
319041 GAGAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:321476 original size:39 final size:39
Alignment explanation
Indices: 321433--321511 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
321423 TAAAATGTAC
321433 GATTCATTAAAAATTATTGCATAACTACAGTACCATCAG
1 GATTCATTAAAAATTATTGCATAACTACAGTACCATCAG
321472 GATTCATTAAAAATTATTGCATAACTACAGTACCATCAG
1 GATTCATTAAAAATTATTGCATAACTACAGTACCATCAG
321511 G
1 G
321512 TTTTGAGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (39 bp):
GATTCATTAAAAATTATTGCATAACTACAGTACCATCAG
Found at i:324512 original size:30 final size:29
Alignment explanation
Indices: 324481--324557 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
324471 TTTATTTTTA
324481 AAATATAATAAAAATATAAAAAATTATTT
1 AAATATAATAAAAATATAAAAAATTATTT
* * *
324510 -AA-ATAATAATAATAATAATAACTTATTT
1 AAATATAATAAAAAT-ATAAAAAATTATTT
*
324538 AAATGTAATAAAAAATATAA
1 AAATATAAT-AAAAATATAA
324558 GATCTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 10 0.26
28 14 0.36
29 2 0.05
30 8 0.21
31 5 0.13
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
AAATATAATAAAAATATAAAAAATTATTT
Found at i:324565 original size:30 final size:28
Alignment explanation
Indices: 324481--324567 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 28
324471 TTTATTTTTA
*
324481 AAATATAATAAAAATATAAAAAATTATTT
1 AAAT-TAATAAAAATATAAAAACTTATTT
* *
324510 AAA-TAATAATAATAATAATAACTTATTT
1 AAATTAATAAAAAT-ATAAAAACTTATTT
* *
324538 AAATGTAATAAAAAATATAAGATCTTATTT
1 AAAT-TAAT-AAAAATATAAAAACTTATTT
324568 CAAAAAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
27 9 0.19
28 15 0.31
29 3 0.06
30 16 0.33
31 5 0.10
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
AAATTAATAAAAATATAAAAACTTATTT
Found at i:324846 original size:8 final size:7
Alignment explanation
Indices: 324825--324849 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
324815 TTAAAATAAT
324825 ATTAAAA
1 ATTAAAA
324832 ATTAAAA
1 ATTAAAA
324839 ATTAAAA
1 ATTAAAA
324846 ATTA
1 ATTA
324850 TTATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATTAAAA
Found at i:325903 original size:20 final size:19
Alignment explanation
Indices: 325880--325917 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
325870 TTTAATATGA
*
325880 TTAAATTTTATTTTTAAAAT
1 TTAAA-TTTAATTTTAAAAT
325900 TTAAATTTAATTTTAAAA
1 TTAAATTTAATTTTAAAA
325918 AAATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAAATTTAATTTTAAAAT
Found at i:325918 original size:20 final size:20
Alignment explanation
Indices: 325880--325918 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
325870 TTTAATATGA
* *
325880 TTAAATTTTATTTTTAAAAT
1 TTAAATTTAATTTTAAAAAT
325900 TTAAATTTAATTTTAAAAA
1 TTAAATTTAATTTTAAAAA
325919 AATAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAATTTAATTTTAAAAAT
Found at i:325924 original size:20 final size:20
Alignment explanation
Indices: 325881--325924 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
325871 TTAATATGAT
* * **
325881 TAAATTTTATTTTTAAAATT
1 TAAATTTAATTTTAAAAAAA
325901 TAAATTTAATTTTAAAAAAA
1 TAAATTTAATTTTAAAAAAA
325921 TAAA
1 TAAA
325925 ATAAAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAATTTAATTTTAAAAAAA
Found at i:326059 original size:18 final size:19
Alignment explanation
Indices: 326017--326060 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
326007 TTAAAGTTCA
**
326017 AATTAAAAATTTTAATATT
1 AATTAAAAATTAAAATATT
*
326036 ATTTAAAAATTAAAAT-TT
1 AATTAAAAATTAAAATATT
326054 AATTAAA
1 AATTAAA
326061 TTCATAAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTAAAAATTAAAATATT
Found at i:326942 original size:159 final size:159
Alignment explanation
Indices: 326653--326946 Score: 437
Period size: 159 Copynumber: 1.8 Consensus size: 159
326643 TTCCAGGTTT
* * * *
326653 CCTCAGAGTTCCAATCGATTTTCCTATCAAATGGCCAGAAAAGTGGCTCATCAGCACTGAAATCT
1 CCTCAGAATTCCAATCAATTTTCCTATCAAATAGCCAGAAAAGTGGCTCATCACCACTGAAATCT
* * * * *
326718 GCCATAGTTTCTGCTTGAGAAGTCTGATCTAATGACAAATTGGATTCTGGAGTTTCATCCTTCCT
66 GCCATAGTTTCGGCTTCAGAAGTCTGATCTAAGGACAAATTAGAGTCTGGAGTTTCATCCTTCCT
326783 GTTAAGAGTTGTGTGGATGCTTGATTTAG
131 GTTAAGAGTTGTGTGGATGCTTGATTTAG
*
326812 CCTCAGAATTCCAATCAATTTTCCTCTCAAATAGCCAGAAAAGTGGCTCATCACCACTGAAATCT
1 CCTCAGAATTCCAATCAATTTTCCTATCAAATAGCCAGAAAAGTGGCTCATCACCACTGAAATCT
** * * *
326877 GCCATTTTTTCGGCTTCAGAAGTCTGATTTAAGGACAGATTAGAGTCTGGCA-TTTCATCTTTCC
66 GCCATAGTTTCGGCTTCAGAAGTCTGATCTAAGGACAAATTAGAGTCTGG-AGTTTCATCCTTCC
326941 TGTTAA
130 TGTTAA
326947 TGGTAGTACA
Statistics
Matches: 119, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
159 118 0.99
160 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (159 bp):
CCTCAGAATTCCAATCAATTTTCCTATCAAATAGCCAGAAAAGTGGCTCATCACCACTGAAATCT
GCCATAGTTTCGGCTTCAGAAGTCTGATCTAAGGACAAATTAGAGTCTGGAGTTTCATCCTTCCT
GTTAAGAGTTGTGTGGATGCTTGATTTAG
Found at i:326968 original size:159 final size:159
Alignment explanation
Indices: 326653--326981 Score: 428
Period size: 159 Copynumber: 2.1 Consensus size: 159
326643 TTCCAGGTTT
* * * *
326653 CCTCAGAGTTCCAATCGATTTTCCTATCAAATGGCCAGAAAAGTGGCTCATCAGCACTGAAATCT
1 CCTCAGAATTCCAATCAATTTTCCTATCAAATAGCCAGAAAAGTGGCTCATCACCACTGAAATCT
* * * * *
326718 GCCATAGTTTCTGCTTGAGAAGTCTGATCTAATGACAAATTGGATTCTGGAGTTTCATCCTTCCT
66 GCCATAGTTTCGGCTTCAGAAGTCTGATCTAAGGACAAATTAGAGTCTGGAGTTTCATCCTTCCT
* *** *
326783 GTTAAGAGTTGTGTGGATGCTTGATTTAG
131 GTTAAGAGTAGTACAGATGCTAGATTTAG
*
326812 CCTCAGAATTCCAATCAATTTTCCTCTCAAATAGCCAGAAAAGTGGCTCATCACCACTGAAATCT
1 CCTCAGAATTCCAATCAATTTTCCTATCAAATAGCCAGAAAAGTGGCTCATCACCACTGAAATCT
** * * *
326877 GCCATTTTTTCGGCTTCAGAAGTCTGATTTAAGGACAGATTAGAGTCTGGCA-TTTCATCTTTCC
66 GCCATAGTTTCGGCTTCAGAAGTCTGATCTAAGGACAAATTAGAGTCTGG-AGTTTCATCCTTCC
*
326941 TGTTAATG-GTAGTACAGTTGCTAGATTTAG
130 TGTTAA-GAGTAGTACAGATGCTAGATTTAG
*
326971 CTTCAGAATTC
1 CCTCAGAATTC
326982 TGATCATCAG
Statistics
Matches: 146, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
159 144 0.99
160 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (159 bp):
CCTCAGAATTCCAATCAATTTTCCTATCAAATAGCCAGAAAAGTGGCTCATCACCACTGAAATCT
GCCATAGTTTCGGCTTCAGAAGTCTGATCTAAGGACAAATTAGAGTCTGGAGTTTCATCCTTCCT
GTTAAGAGTAGTACAGATGCTAGATTTAG
Found at i:335017 original size:29 final size:30
Alignment explanation
Indices: 334966--335023 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
334956 AATCCATCTA
*
334966 TTATTTTTAATATTAAAGTTTTAATTTTTT
1 TTATTTTTAATATTAAAGTTTTAACTTTTT
*
334996 TTATTTTTAA-ATT-TAGATTTTAACTTTT
1 TTATTTTTAATATTAAAG-TTTTAACTTTT
335024 GATTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 13 0.52
30 10 0.40
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (30 bp):
TTATTTTTAATATTAAAGTTTTAACTTTTT
Found at i:335132 original size:23 final size:24
Alignment explanation
Indices: 335089--335144 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
335079 TTATCTGAAA
335089 TAAATT-AAATAATAAATTTTATT
1 TAAATTAAAATAATAAATTTTATT
335112 TAAATATAAAAT-ATAAA-TTTATT
1 TAAAT-TAAAATAATAAATTTTATT
*
335135 TGAATTAAAA
1 TAAATTAAAA
335145 AAATTAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 15 0.50
24 6 0.20
25 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TAAATTAAAATAATAAATTTTATT
Found at i:335146 original size:24 final size:25
Alignment explanation
Indices: 335075--335146 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 25
335065 ATTTATATTA
*
335075 AAATTTATCTGAAATAAATTAAATAAT
1 AAATTTATTTGAAATAAA--AAATAAT
*
335102 AAATTTTATTT-AAATATAAAAT-AT
1 AAA-TTTATTTGAAATAAAAAATAAT
*
335126 AAATTTATTTGAATTAAAAAA
1 AAATTTATTTGAAATAAAAAA
335147 ATTAAAGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 7 0.18
24 13 0.33
25 4 0.10
27 9 0.23
28 6 0.15
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (25 bp):
AAATTTATTTGAAATAAAAAATAAT
Found at i:336026 original size:16 final size:16
Alignment explanation
Indices: 336007--336091 Score: 86
Period size: 16 Copynumber: 5.4 Consensus size: 16
335997 TGAACTCGAA
*
336007 TTATTTTAAATTTAAT
1 TTATTTTAAATTTAAG
*
336023 TTA-TTTAAATTTTAAA
1 TTATTTTAAA-TTTAAG
*
336039 TTATTTTGAATTTAAG
1 TTATTTTAAATTTAAG
*
336055 TTATTTAAAATTTGAA-
1 TTATTTTAAATTT-AAG
*
336071 TTATTTTGAA-TTAAG
1 TTATTTTAAATTTAAG
336086 TTATTT
1 TTATTT
336092 CAGATTTGAG
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.03
15 14 0.24
16 35 0.60
17 7 0.12
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TTATTTTAAATTTAAG
Found at i:336051 original size:32 final size:32
Alignment explanation
Indices: 336005--336091 Score: 131
Period size: 32 Copynumber: 2.8 Consensus size: 32
335995 TTTGAACTCG
* * *
336005 AATTATTTTAAATTTAATTTATTTAAATTTTA
1 AATTATTTTGAATTTAAGTTATTTAAAATTTA
*
336037 AATTATTTTGAATTTAAGTTATTTAAAATTTG
1 AATTATTTTGAATTTAAGTTATTTAAAATTTA
336069 AATTATTTTGAA-TTAAGTTATTT
1 AATTATTTTGAATTTAAGTTATTT
336092 CAGATTTGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 11 0.22
32 40 0.78
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (32 bp):
AATTATTTTGAATTTAAGTTATTTAAAATTTA
Found at i:336826 original size:28 final size:26
Alignment explanation
Indices: 336794--336845 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
336784 AATTAAAATT
336794 TAAAAACTTATTTAAGATAATAAAAACA
1 TAAAAACTTATTTAA-A-AATAAAAACA
336822 TAAAAACTTATTTAAAAATAAAAA
1 TAAAAACTTATTTAAAAATAAAAA
336846 AAATTAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 8 0.33
27 1 0.04
28 15 0.62
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (26 bp):
TAAAAACTTATTTAAAAATAAAAACA
Found at i:336846 original size:28 final size:27
Alignment explanation
Indices: 336794--336857 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
336784 AATTAAAATT
*
336794 TAAAAACTTATTTAAGATAATAAAAACA
1 TAAAAACTTATTTAAAATAATAAAAA-A
336822 TAAAAACTTATTTAAAAATAA-AAAAAA
1 TAAAAACTTATTT-AAAATAATAAAAAA
*
336849 TTAAAACTT
1 TAAAAACTT
336858 TTTTTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 9 0.27
28 18 0.55
29 6 0.18
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (27 bp):
TAAAAACTTATTTAAAATAATAAAAAA
Found at i:338123 original size:30 final size:30
Alignment explanation
Indices: 338087--338177 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
338077 TTATTGTTAG
338087 ACATTTAGCAACGAATTAATTAAACATCAA
1 ACATTTAGCAACGAATTAATTAAACATCAA
338117 ACATTTAGCAACGAATTAATTAAACATCAA
1 ACATTTAGCAACGAATTAATTAAACATCAA
* * *
338147 ACATTCAGCAACGAATTAATTAGAGATCAA
1 ACATTTAGCAACGAATTAATTAAACATCAA
338177 A
1 A
338178 GATTGGTCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.25
Consensus pattern (30 bp):
ACATTTAGCAACGAATTAATTAAACATCAA
Found at i:338272 original size:18 final size:18
Alignment explanation
Indices: 338254--338291 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
338244 TTAATTAATT
338254 TTTTATA-TTT-TTATAA
1 TTTTATATTTTATTATAA
338270 TTTTATATTTTATTAT-A
1 TTTTATATTTTATTATAA
338287 TTTTA
1 TTTTA
338292 ATAAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATATTTTATTATAA
Found at i:339081 original size:3 final size:3
Alignment explanation
Indices: 339073--339130 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
339063 TGGAAATGTA
339073 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
339121 ATT ATT ATT A
1 ATT ATT ATT A
339131 ATTTGCTGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:339729 original size:8 final size:8
Alignment explanation
Indices: 339716--339748 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
339706 TATTAAATAT
339716 TATTTATA
1 TATTTATA
339724 TATTTATA
1 TATTTATA
339732 T-TTTATA
1 TATTTATA
*
339739 TATTTTTA
1 TATTTATA
339747 TA
1 TA
339749 ATTAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTTATA
Found at i:346146 original size:23 final size:23
Alignment explanation
Indices: 346118--346161 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
346108 GAAGGAAGAG
346118 ATATTTTCTGCTTTAATAGCTAT
1 ATATTTTCTGCTTTAATAGCTAT
*
346141 ATATTTTCTGTTTTAATAGCT
1 ATATTTTCTGCTTTAATAGCT
346162 GTAAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (23 bp):
ATATTTTCTGCTTTAATAGCTAT
Found at i:351044 original size:23 final size:23
Alignment explanation
Indices: 351018--351064 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
351008 GAAGGAAGAG
351018 ATATTTTCTGTTTTAATAGCTGT
1 ATATTTTCTGTTTTAATAGCTGT
351041 ATATTTTCTGTTTTAATAGCTGT
1 ATATTTTCTGTTTTAATAGCTGT
351064 A
1 A
351065 AATATTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (23 bp):
ATATTTTCTGTTTTAATAGCTGT
Found at i:355314 original size:12 final size:12
Alignment explanation
Indices: 355297--355321 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
355287 AAAAACTAGG
355297 ACTTAAAAAAGA
1 ACTTAAAAAAGA
355309 ACTTAAAAAAGA
1 ACTTAAAAAAGA
355321 A
1 A
355322 GACATGGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (12 bp):
ACTTAAAAAAGA
Found at i:356960 original size:20 final size:19
Alignment explanation
Indices: 356931--356972 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
356921 TAAATTTAAA
356931 TAATAAAAAATATATAAATT
1 TAATAAAAAATATAT-AATT
* *
356951 TAATATAAAATTTATAATT
1 TAATAAAAAATATATAATT
356970 TAA
1 TAA
356973 AATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAAAAAATATATAATT
Found at i:356963 original size:12 final size:12
Alignment explanation
Indices: 356939--356990 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
356929 AATAATAAAA
356939 AATATATAAATTT
1 AATATA-AAATTT
356952 AATATAAAATTTAT
1 AATATAAAA-TT-T
*
356966 AATTTAAAATTT
1 AATATAAAATTT
* *
356978 AATTTAAATTTT
1 AATATAAAATTT
356990 A
1 A
356991 TTAAATTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 16 0.46
13 10 0.29
14 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATATAAAATTT
Found at i:357112 original size:26 final size:26
Alignment explanation
Indices: 357056--357118 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
357046 TTAATAAAAA
*
357056 TAAATTTAATT-TTTATGTTAAGTTT
1 TAAATTTAATTATTTATGTTAAATTT
357081 TAAATTTAATTATTTATGTTTAAATTT
1 TAAATTTAATTATTTATG-TTAAATTT
*
357108 T-AATTCAATTA
1 TAAATTTAATTA
357119 AGATTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 11 0.32
26 15 0.44
27 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (26 bp):
TAAATTTAATTATTTATGTTAAATTT
Found at i:357522 original size:21 final size:20
Alignment explanation
Indices: 357488--357533 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
357478 ACACATGCCC
* * *
357488 AAAAATATAAAATATTTTTA
1 AAAAATAAAAAATAATATTA
357508 AAAAATAAAATAATAATATTA
1 AAAAATAAAA-AATAATATTA
357529 AAAAA
1 AAAAA
357534 GTAAGTGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATAAAAAATAATATTA
Found at i:358078 original size:21 final size:24
Alignment explanation
Indices: 358040--358084 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
358030 TTGATATATA
358040 TTTTTAAATATAATTTTTTTATTT
1 TTTTTAAATATAATTTTTTTATTT
358064 TTTTTAAAT-T-A-TTTTTTATTT
1 TTTTTAAATATAATTTTTTTATTT
358085 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 1 0.05
24 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTAAATATAATTTTTTTATTT
Found at i:358291 original size:25 final size:25
Alignment explanation
Indices: 358262--358309 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
358252 AGTAATTTTA
* * *
358262 TATTATGATTAAATAATTATAAAAT
1 TATTATAATAAAAAAATTATAAAAT
358287 TATTATAATAAAAAAATTATAAA
1 TATTATAATAAAAAAATTATAAA
358310 TCAAATGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TATTATAATAAAAAAATTATAAAAT
Found at i:358441 original size:8 final size:8
Alignment explanation
Indices: 358430--358535 Score: 67
Period size: 8 Copynumber: 12.6 Consensus size: 8
358420 TTAATTATTA
358430 TAAAATAT
1 TAAAATAT
358438 TAAAATAT
1 TAAAATAT
358446 TAAAATAT
1 TAAAATAT
358454 ATAATTTAATA-
1 -TAA---AATAT
* *
358465 AAAAATAA
1 TAAAATAT
358473 TATAAATA-
1 TA-AAATAT
*
358481 TAATATAT
1 TAAAATAT
*
358489 ATAAATTAT
1 -TAAAATAT
358498 T-AAATAT
1 TAAAATAT
358505 TAAAATCA-
1 TAAAAT-AT
358513 TATAAATAT
1 TA-AAATAT
358522 TAAAATAAT
1 TAAAAT-AT
358531 TAAAA
1 TAAAA
358536 CACCAACTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
7 14 0.18
8 31 0.39
9 28 0.35
10 2 0.03
12 4 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (8 bp):
TAAAATAT
Found at i:358521 original size:35 final size:34
Alignment explanation
Indices: 358426--358534 Score: 100
Period size: 35 Copynumber: 3.3 Consensus size: 34
358416 AATTTTAATT
*
358426 ATTATAAAATATTAAAATAT-TAAA-ATATATAA
1 ATTATTAAATATTAAAATATATAAATATATATAA
* * * * * *
358458 TTTAATAAAAAATAATATAAATATAATATATATAA
1 ATTATTAAATATTAAAATATATA-AATATATATAA
358493 ATTATTAAATATTAAAATCATATAAATAT-TA-AA
1 ATTATTAAATATTAAAAT-ATATAAATATATATAA
*
358526 ATAATTAAA
1 ATTATTAAA
358535 ACACCAACTA
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
32 13 0.22
33 12 0.20
34 4 0.07
35 26 0.44
36 4 0.07
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
ATTATTAAATATTAAAATATATAAATATATATAA
Found at i:358857 original size:18 final size:21
Alignment explanation
Indices: 358827--358884 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
358817 AATAAATTTA
358827 ATAATATTAAAAATATATAAA-
1 ATAATA-TAAAAATATATAAAT
358848 ATAAT-TAAAATATAATATAAAT
1 ATAATATAAAA-AT-ATATAAAT
358870 ATAATAT-AAAATATA
1 ATAATATAAAAATATA
358885 AATATTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.15
20 5 0.15
21 14 0.42
22 8 0.24
23 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAATATAAAAATATATAAAT
Found at i:358860 original size:16 final size:16
Alignment explanation
Indices: 358841--358882 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
358831 TATTAAAAAT
*
358841 ATATAAAATAATTAAA
1 ATATAAAATAAATAAA
* *
358857 ATATAATATAAATATA
1 ATATAAAATAAATAAA
358873 ATATAAAATA
1 ATATAAAATA
358883 TAAATATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAAATAAATAAA
Found at i:358862 original size:11 final size:11
Alignment explanation
Indices: 358848--358885 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
358838 AATATATAAA
358848 ATAATTAAAAT
1 ATAATTAAAAT
358859 ATAA-TATAAAT
1 ATAATTA-AAAT
358870 ATAATATAAAAT
1 ATAAT-TAAAAT
358882 ATAA
1 ATAA
358886 ATATTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 12 0.50
12 8 0.33
13 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAATTAAAAT
Found at i:358877 original size:32 final size:32
Alignment explanation
Indices: 358827--358921 Score: 90
Period size: 32 Copynumber: 3.0 Consensus size: 32
358817 AATAAATTTA
*
358827 ATAATATTAAAAAT-ATATAAAATAATTAAAAT
1 ATAATA-TAAATATAATATAAAATAATTAAAAT
358859 ATAATATAAATATAATATAAAAT-A-TAAATATT
1 ATAATATAAATATAATATAAAATAATTAAA-A-T
* * **
358891 TTAACATTTATATAATATAAAA-AATTAAAAT
1 ATAATATAAATATAATATAAAATAATTAAAAT
358922 TTTAAAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
30 4 0.08
31 9 0.17
32 36 0.68
33 4 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (32 bp):
ATAATATAAATATAATATAAAATAATTAAAAT
Found at i:358924 original size:32 final size:32
Alignment explanation
Indices: 358841--358945 Score: 106
Period size: 32 Copynumber: 3.2 Consensus size: 32
358831 TATTAAAAAT
* * **
358841 ATATAAAATAATTAAAA-TATAATATAAATATA
1 ATATAAAA-AATTAAAATTTTAAAATTTATATA
* *
358873 ATATAAAATA-TAAATATTTTAACATTTATATA
1 ATATAAAAAATTAAA-ATTTTAAAATTTATATA
358905 ATATAAAAAATTAAAATTTTAAAATTTTATATAA
1 ATATAAAAAATTAAAATTTTAAAA-TTTATAT-A
358939 ATATAAA
1 ATATAAA
358946 TTATTTTAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
30 4 0.07
31 2 0.03
32 36 0.59
33 11 0.18
34 8 0.13
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
ATATAAAAAATTAAAATTTTAAAATTTATATA
Found at i:359632 original size:22 final size:23
Alignment explanation
Indices: 359592--359634 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
359582 AGAAATTCTT
359592 TAAATAAAATTGATTTTTAATTA
1 TAAATAAAATTGATTTTTAATTA
*
359615 TAAATTAAATT-ATTTTTAAT
1 TAAATAAAATTGATTTTTAAT
359635 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TAAATAAAATTGATTTTTAATTA
Found at i:359641 original size:22 final size:23
Alignment explanation
Indices: 359593--359642 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
359583 GAAATTCTTT
* * *
359593 AAATAAAATTGATTTTTAATTAT
1 AAATTAAATTGATTTTTAATAAA
359616 AAATTAAATT-ATTTTTAATAAA
1 AAATTAAATTGATTTTTAATAAA
359638 AAATT
1 AAATT
359643 TACAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTAAATTGATTTTTAATAAA
Found at i:359731 original size:3 final size:3
Alignment explanation
Indices: 359723--359750 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
359713 ATACTTATAT
359723 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
359751 AGATATACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:360169 original size:11 final size:11
Alignment explanation
Indices: 360141--360191 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
360131 TTTGATATAT
*
360141 ATAATATGAAAT
1 ATAATAT-AAAA
360153 ATAATATAAAA
1 ATAATATAAAA
360164 ATAATAT--AA
1 ATAATATAAAA
360173 AT-ATATAAAA
1 ATAATATAAAA
*
360183 ATTATATAA
1 ATAATATAA
360192 TATAAATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
8 4 0.11
9 4 0.11
10 4 0.11
11 16 0.46
12 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:360178 original size:8 final size:8
Alignment explanation
Indices: 360151--360242 Score: 50
Period size: 8 Copynumber: 11.6 Consensus size: 8
360141 ATAATATGAA
360151 ATAT-AAT
1 ATATAAAT
*
360158 ATAAAAAT
1 ATATAAAT
360166 AATATAAAT
1 -ATATAAAT
*
360175 ATATAAAA
1 ATATAAAT
*
360183 AT-TATAT
1 ATATAAAT
360190 AATATAAAT
1 -ATATAAAT
*
360199 -TATTAAT
1 ATATAAAT
360206 ATTATAAA-
1 A-TATAAAT
*
360214 AT-TTAAT
1 ATATAAAT
*
360221 AATATATAT
1 -ATATAAAT
*
360230 ATATATAT
1 ATATAAAT
360238 ATATA
1 ATATA
360243 TGATATGAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
6 3 0.05
7 13 0.20
8 30 0.46
9 19 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:360193 original size:18 final size:18
Alignment explanation
Indices: 360156--360228 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 18
360146 ATGAAATATA
*
360156 ATATAAAAATAATATAAAT
1 ATATAAAAATTATAT-AAT
360175 ATATAAAAATTATAT-A-
1 ATATAAAAATTATATAAT
360191 ATAT--AAATTAT-TAAT
1 ATATAAAAATTATATAAT
*
360206 ATTATAAAATTTA-ATAAT
1 A-TATAAAAATTATATAAT
360224 ATATA
1 ATATA
360229 TATATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 1 0.02
16 7 0.15
17 5 0.11
18 10 0.22
19 14 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAAAAATTATATAAT
Found at i:360736 original size:3 final size:3
Alignment explanation
Indices: 360730--360769 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
360720 GAAATAGCAA
*
360730 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
360770 GATAAGAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:367772 original size:12 final size:13
Alignment explanation
Indices: 367755--367791 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
367745 TTAAGTCTCC
367755 GGTGCTGGTG-CT
1 GGTGCTGGTGCCT
367767 GGTGCTGGTGCCT
1 GGTGCTGGTGCCT
*
367780 -GTGCTGGCGCCT
1 GGTGCTGGTGCCT
367792 TCAACAGCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 21 0.91
13 2 0.09
ACGTcount: A:0.00, C:0.24, G:0.46, T:0.30
Consensus pattern (13 bp):
GGTGCTGGTGCCT
Found at i:372167 original size:33 final size:31
Alignment explanation
Indices: 372128--372211 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 31
372118 TTCTCTTTAA
* *
372128 ATTATATCAAATAATATTAAATAATATAAATAT
1 ATTATATAAAATAATATTAAAAAAT-TAAA-AT
* * * *
372161 ATTATATTATATTATATAAAAAAATTAAAAT
1 ATTATATAAAATAATATTAAAAAATTAAAAT
*
372192 AATATATAAAATAATATTAA
1 ATTATATAAAATAATATTAA
372212 TATATGAATA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
31 17 0.41
32 4 0.10
33 20 0.49
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
ATTATATAAAATAATATTAAAAAATTAAAAT
Found at i:372187 original size:23 final size:23
Alignment explanation
Indices: 372136--372187 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
372126 AAATTATATC
* *
372136 AAATAATATTAAATAATATAAAT
1 AAATTATATTAAATAATATAAAA
* * *
372159 ATATTATATTATATTATATAAAA
1 AAATTATATTAAATAATATAAAA
372182 AAATTA
1 AAATTA
372188 AAATAATATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTATATTAAATAATATAAAA
Found at i:372210 original size:23 final size:23
Alignment explanation
Indices: 372130--372211 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 23
372120 CTCTTTAAAT
*
372130 TATATCAAATAATATT-AAATAA
1 TATATAAAATAATATTAAAATAA
* * ** *
372152 TATA-AATATATTA-TATTATAT
1 TATATAAAATAATATTAAAATAA
372173 TATATAAAA-AA-ATTAAAATAA
1 TATATAAAATAATATTAAAATAA
372194 TATATAAAATAATATTAA
1 TATATAAAATAATATTAA
372212 TATATGAATA
Statistics
Matches: 44, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
20 2 0.05
21 28 0.64
22 9 0.20
23 5 0.11
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (23 bp):
TATATAAAATAATATTAAAATAA
Found at i:372297 original size:22 final size:21
Alignment explanation
Indices: 372266--372310 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
372256 TTAAATTTTT
* *
372266 TAAATTTAAAATATTTAAAATA
1 TAAATATAAAATA-ATAAAATA
372288 TAAATATAAAATAATAAAATA
1 TAAATATAAAATAATAAAATA
372309 TA
1 TA
372311 TGAGTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATAAAATAATAAAATA
Found at i:373657 original size:22 final size:21
Alignment explanation
Indices: 373621--373683 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
373611 GATAGTAGGT
*
373621 ATTTTATATATTAAATATATA
1 ATTTTATATAATAAATATATA
*
373642 ATTTTATTATAATAAATATTTA
1 ATTTTA-TATAATAAATATATA
* *
373664 AATTAATA-AATAAATATATA
1 ATTTTATATAATAAATATATA
373684 GAAGGTTTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 11 0.31
21 8 0.22
22 17 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTTATATAATAAATATATA
Found at i:373745 original size:2 final size:2
Alignment explanation
Indices: 373738--373767 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
373728 CCAATGAAAT
373738 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
373768 GGACTTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:374012 original size:16 final size:15
Alignment explanation
Indices: 373991--374022 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
373981 TTATTTAGAT
373991 AAATATAAAAATAATA
1 AAATATAAAAA-AATA
374007 AAATATAAAAAAATA
1 AAATATAAAAAAATA
374022 A
1 A
374023 TCATAGGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATATAAAAAAATA
Found at i:374637 original size:3 final size:3
Alignment explanation
Indices: 374629--374653 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
374619 TCGAAGCTTT
374629 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
374654 AGTATGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:374856 original size:5 final size:5
Alignment explanation
Indices: 374843--374970 Score: 67
Period size: 5 Copynumber: 26.2 Consensus size: 5
374833 TCTTGGTATG
* * *
374843 TATAA TATAT TATAT T-T-G TATAT TATAAT T-TA- TATAAT TTTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT TAT-AT TATAT TATAT
* * *
374891 TA-AT AAT-T TATAT TATA- TAAAT TTTAT TATAT TATA- TAT-T TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* *
374936 TATTTT TATAA TATATT ATATAT TATAT TAATAT T
1 TA-TAT TATAT TATA-T -TATAT TATAT T-ATAT T
374971 TAATGATATA
Statistics
Matches: 93, Mismatches: 15, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
3 2 0.02
4 19 0.20
5 53 0.57
6 15 0.16
7 4 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:374880 original size:9 final size:9
Alignment explanation
Indices: 374866--374947 Score: 52
Period size: 9 Copynumber: 9.7 Consensus size: 9
374856 ATTTGTATAT
374866 TATAATTTA
1 TATAATTTA
374875 TATAATTT-
1 TATAATTTA
*
374883 TATTATATTA
1 TATAAT-TTA
374893 -ATAATTTA
1 TATAATTTA
*
374901 TAT--TATA
1 TATAATTTA
374908 TA-AATTT-
1 TATAATTTA
*
374915 TATTATATTA
1 TATAAT-TTA
374925 TAT-ATTTA
1 TATAATTTA
* *
374933 TATTATTTT
1 TATAATTTA
374942 TATAAT
1 TATAAT
374948 ATATTATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
7 7 0.12
8 18 0.32
9 29 0.51
10 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATAATTTA
Found at i:374880 original size:32 final size:33
Alignment explanation
Indices: 374843--374981 Score: 114
Period size: 31 Copynumber: 4.3 Consensus size: 33
374833 TCTTGGTATG
*
374843 TATAATATATTATATTTGTATATTATA-ATTTA
1 TATAATATATTATATTTATATATTATATATTTA
* *
374875 TATAATTTTATTATATTAATA-ATT-TATA-TTA
1 TATAA-TATATTATATTTATATATTATATATTTA
* *
374906 TATAA-ATTTTATTATATTATATATTTATATTATTTT
1 TATAATATATTA-TAT-TTATATA-TTATA-TATTTA
*
374942 TATAATATATTATATAT-TATATTA-ATATTTA
1 TATAATATATTATATTTATATATTATATATTTA
*
374973 -ATGATATAT
1 TATAATATAT
374982 AAAATATTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 22
0.72 0.09 0.18
Matches are distributed among these distances:
29 4 0.05
30 11 0.13
31 19 0.22
32 11 0.13
33 17 0.20
34 6 0.07
35 3 0.03
36 10 0.12
37 5 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (33 bp):
TATAATATATTATATTTATATATTATATATTTA
Found at i:374947 original size:50 final size:50
Alignment explanation
Indices: 374863--374957 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
374853 TATATTTGTA
374863 TATTATAATTTATATAATTTTATTATATTAATAATTTATATTATATAAATTT
1 TATTATAATTTATATAATTTTATTATATTAATAA--TATATTATATAAATTT
* *
374915 TATTAT-A-TTATAT-ATTTATATTATTTTTATAATATATTATATA
1 TATTATAATTTATATAATTT-TATTATATTAATAATATATTATATA
374958 TTATATTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
48 11 0.28
49 4 0.10
50 18 0.45
51 1 0.03
52 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (50 bp):
TATTATAATTTATATAATTTTATTATATTAATAATATATTATATAAATTT
Found at i:374982 original size:27 final size:27
Alignment explanation
Indices: 374913--374979 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
374903 TTATATAAAT
* * *
374913 TTTATTATATTATATATTTATATTATTT
1 TTTAATATATTATATA-TTATATTAATA
374941 TTATAATATATTATATATTATATTAATA
1 TT-TAATATATTATATATTATATTAATA
374969 TTTAATGATAT
1 TTTAAT-ATAT
374980 ATAAAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.12
28 17 0.50
29 13 0.38
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTAATATATTATATATTATATTAATA
Found at i:374984 original size:73 final size:70
Alignment explanation
Indices: 374848--374980 Score: 175
Period size: 70 Copynumber: 1.9 Consensus size: 70
374838 GTATGTATAA
374848 TATATTATATTTGTATATTATAATTTATATAATTTTATTATATTAATAATTTATATTATATAAAT
1 TATATTATATTTGTATATTATAATTTATATAATTTTATTATATTAATAATTTATATTATATAAAT
374913 TTTAT
66 TTTAT
* *
374918 TATATTATATATT-TATATTAT-TTTTATAATATATTATATATTATATTAAT-ATTTA-ATGATA
1 TATATTATAT-TTGTATATTATAATTTAT-ATA-ATT-T-TATTATATTAATAATTTATATTATA
374979 TA
61 TA
374981 TAAAATATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
69 5 0.09
70 21 0.38
71 12 0.21
72 6 0.11
73 12 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (70 bp):
TATATTATATTTGTATATTATAATTTATATAATTTTATTATATTAATAATTTATATTATATAAAT
TTTAT
Found at i:375433 original size:11 final size:11
Alignment explanation
Indices: 375417--375441 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
375407 TACAATATTT
375417 TATAATATAAA
1 TATAATATAAA
375428 TATAATATAAA
1 TATAATATAAA
375439 TAT
1 TAT
375442 TTTAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATAATATAAA
Found at i:380502 original size:12 final size:12
Alignment explanation
Indices: 380460--380502 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
380450 ATTTAAATTT
380460 AAATTTAATTAA
1 AAATTTAATTAA
*
380472 AAATTTATATT-T
1 AAATTTA-ATTAA
*
380484 AATTTTAATTAA
1 AAATTTAATTAA
380496 AAATTTA
1 AAATTTA
380503 TTTTATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 3 0.12
12 19 0.76
13 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATTTAATTAA
Found at i:380503 original size:24 final size:24
Alignment explanation
Indices: 380450--380507 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
380440 TTAGGTTTTT
*
380450 ATTTAAATTTAAATTTAATTAAAA
1 ATTTATATTTAAATTTAATTAAAA
*
380474 ATTTATATTTAATTTTAATTAAAA
1 ATTTATATTTAAATTTAATTAAAA
380498 ATTTAT-TTTA
1 ATTTATATTTA
380508 TTATTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTATATTTAAATTTAATTAAAA
Found at i:380515 original size:19 final size:23
Alignment explanation
Indices: 380450--380518 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
380440 TTAGGTTTTT
*
380450 ATTTAAATTTAAATTTAATTAAAA
1 ATTTATATTT-AATTTAATTAAAA
380474 ATTTATATTTAATTTTAATTAAAA
1 ATTTATATTTAA-TTTAATTAAAA
380498 ATTTAT-TTT-A-TT-ATTAAAA
1 ATTTATATTTAATTTAATTAAAA
380517 AT
1 AT
380519 ATTAAATAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
19 9 0.21
20 2 0.05
22 1 0.02
23 5 0.12
24 26 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTATATTTAATTTAATTAAAA
Found at i:380872 original size:183 final size:183
Alignment explanation
Indices: 380516--380872 Score: 522
Period size: 183 Copynumber: 2.0 Consensus size: 183
380506 TATTATTAAA
* *
380516 AATATTAAATAACAAATTATATCAATAATTATATATTTTTTAATAATTAAATTTAAATAAAAATA
1 AATATTAAATAAAAAATTATATCAATAATTATATATGTTTTAATAATTAAATTTAAATAAAAATA
* * * * *
380581 TTTTTATTAATTAAATAATAAAAATTAAAATTAAAATAATATGAAATACAAAAATTCAAGTCTAA
66 TTTTTATTAATTAAATAATAAAAATTAAAATTAAAATAATATAAAATAAAAAAACTCAAATCCAA
* * * *
380646 ACTTATTTTAATTCGAAATAAAAAGATTATCAAACCTTAAATTACATGCAAAT
131 ACTCATTTTAATTCGAAACAAAAAGACTATCAAACCCTAAATTACATGCAAAT
* *
380699 AATATTAAATATAAAAAATTATATCAATAATTTTATGTGTTTTAATAATTAAATTTAAATAAAAA
1 AATATT-AA-ATAAAAAATTATATCAATAATTATATATGTTTTAATAATTAAATTTAAATAAAAA
*
380764 TA-TTTTATTAATTAAATAATTAAAATT-AAATTAAAATAATATAAAATAAAAAAACTCAAATCC
64 TATTTTTATTAATTAAATAATAAAAATTAAAATTAAAATAATATAAAATAAAAAAACTCAAATCC
* *
380827 AAACTCATTTTAATTTGAGACAAAGAA-ACTATCAAACCCTAAATTA
129 AAACTCATTTTAATTCGAAACAAA-AAGACTATCAAACCCTAAATTA
380873 TATACTAAAA
Statistics
Matches: 155, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
183 74 0.48
184 28 0.18
185 53 0.34
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (183 bp):
AATATTAAATAAAAAATTATATCAATAATTATATATGTTTTAATAATTAAATTTAAATAAAAATA
TTTTTATTAATTAAATAATAAAAATTAAAATTAAAATAATATAAAATAAAAAAACTCAAATCCAA
ACTCATTTTAATTCGAAACAAAAAGACTATCAAACCCTAAATTACATGCAAAT
Found at i:380947 original size:184 final size:185
Alignment explanation
Indices: 380557--380953 Score: 414
Period size: 183 Copynumber: 2.1 Consensus size: 185
380547 TATATTTTTT
380557 AATAATTAAATTTAAATAAAAATATTTTTATTAATTAAATAATAAAAATTAAAATTAAAATAATA
1 AATAATT--ATTTAAATAAAAATA-TTTTATTAATTAAATAATAAAAATTAAAATTAAAATAATA
* * * * * * * * *
380622 TGAAATACAAAAATTCAAGTCTAAACTTATTTTAATTCGAAATAAAAAGATTATCAAACCTTAAA
63 TAAAATAAAAAAACTCAAATCCAAACTCATTTTAATTCGAAACAAAAAGACTATCAAACCCTAAA
* * **** ***
380687 TTACATGCAAATAATATTAAATATAAAAAATTATATCAATAATTTTATGTGTTTTAATA
128 TTACATACAAATAATATTAAATAT-AAAAATTATATCAATAATTTAAAAAATAAAAATA
* *
380746 ATTAA--ATTTAAATAAAAATATTTTATTAATTAAATAATTAAAATT-AAATTAAAATAATATAA
1 AATAATTATTTAAATAAAAATATTTTATTAATTAAATAATAAAAATTAAAATTAAAATAATATAA
* *
380808 AATAAAAAAACTCAAATCCAAACTCATTTTAATTTGAGACAAAGAA-ACTATCAAACCCTAAATT
66 AATAAAAAAACTCAAATCCAAACTCATTTTAATTCGAAACAAA-AAGACTATCAAACCCTAAATT
* * * *
380872 ATATACTAAA-AAT-TTCAAAT-T-TAACTTGATATTAATTAATTTAAAAAATAAAAATA
130 ACATAC-AAATAATATT-AAATATAAAAATT-ATATCAA-TAATTTAAAAAATAAAAATA
380928 AATAATTATTTAAATAAAAATCATTT
1 AATAATTATTTAAATAAAAAT-ATTT
380954 AATACTCTAA
Statistics
Matches: 173, Mismatches: 27, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
180 4 0.02
181 6 0.03
182 19 0.11
183 78 0.45
184 43 0.25
185 19 0.11
189 4 0.02
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (185 bp):
AATAATTATTTAAATAAAAATATTTTATTAATTAAATAATAAAAATTAAAATTAAAATAATATAA
AATAAAAAAACTCAAATCCAAACTCATTTTAATTCGAAACAAAAAGACTATCAAACCCTAAATTA
CATACAAATAATATTAAATATAAAAATTATATCAATAATTTAAAAAATAAAAATA
Found at i:380955 original size:15 final size:16
Alignment explanation
Indices: 380923--380955 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
380913 TAAAAAATAA
*
380923 AAATAAATAATTATTT
1 AAATAAATAATCATTT
380939 AAATAAA-AATCATTT
1 AAATAAATAATCATTT
380954 AA
1 AA
380956 TACTCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAAATAATCATTT
Found at i:381405 original size:35 final size:33
Alignment explanation
Indices: 381357--381422 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 33
381347 AAGTGATATT
381357 AATTTAATTAAAAA-ATTATTAAAAATTTAAATG
1 AATTTAATTAAAAATA-TATTAAAAATTTAAATG
* *
381390 AATTATAAGTTAAAAATATATTTAAATTTTAAA
1 AATT-TAA-TTAAAAATATATTAAAAATTTAAA
381423 ATATTTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 4 0.14
34 3 0.11
35 20 0.71
36 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (33 bp):
AATTTAATTAAAAATATATTAAAAATTTAAATG
Found at i:381473 original size:26 final size:26
Alignment explanation
Indices: 381405--381473 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
381395 TAAGTTAAAA
*
381405 ATATATTTAAAT-TTTAAAATATTTT
1 ATATATTTAAATATTTATAATATTTT
* * *
381430 ATGTATTTAAAAAATTATAAT-TTTAT
1 ATATATTTAAATATTTATAATATTT-T
*
381456 TTATATTTAAATATTTAT
1 ATATATTTAAATATTTAT
381474 TGAATATAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
25 13 0.38
26 21 0.62
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
ATATATTTAAATATTTATAATATTTT
Found at i:381744 original size:18 final size:18
Alignment explanation
Indices: 381723--381757 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
381713 TAAATATAGA
* *
381723 TATATGTTTAATATATTT
1 TATATATTTAAAATATTT
381741 TATATATTTAAAATATT
1 TATATATTTAAAATATT
381758 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATATATTTAAAATATTT
Found at i:383575 original size:23 final size:22
Alignment explanation
Indices: 383524--383575 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
383514 AATTTTTATT
* *
383524 ATAA-TATTTATATTTTATAAC
1 ATAATTATTTATATTTTACAAA
383545 ATAATTATTTATATTTTACAATA
1 ATAATTATTTATATTTTACAA-A
383568 ATAATTAT
1 ATAATTAT
383576 AATTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 4 0.15
22 15 0.56
23 8 0.30
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATTATTTATATTTTACAAA
Found at i:383684 original size:15 final size:16
Alignment explanation
Indices: 383657--383714 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 16
383647 CAATATTAAC
383657 AAAATAT-TTAAA-TA
1 AAAATATATTAAATTA
383671 AAAATATATTAAATTA
1 AAAATATATTAAATTA
** *
383687 TGAA-AGATTAAATTAA
1 AAAATATATTAAATT-A
383703 AAAATATATTAA
1 AAAATATATTAA
383715 TAAAATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 7 0.21
15 14 0.41
16 7 0.21
17 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AAAATATATTAAATTA
Found at i:383718 original size:20 final size:21
Alignment explanation
Indices: 383695--383749 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
383685 TATGAAAGAT
*
383695 TAAATTAAAAAAT-ATATTAA
1 TAAATTAAAAAATAATATAAA
* *
383715 TAAAATAAAACATAATATAAA
1 TAAATTAAAAAATAATATAAA
*
383736 AAAATATAAAAAAT
1 TAAAT-TAAAAAAT
383750 TTAAATTACT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 11 0.41
21 9 0.33
22 7 0.26
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAATTAAAAAATAATATAAA
Found at i:383783 original size:18 final size:16
Alignment explanation
Indices: 383759--383803 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
383749 TTTAAATTAC
383759 TTATTTATAAATAAAGA
1 TTATTTATAAAT-AAGA
383776 TGTATTTAAATAAATAAGA
1 T-TATTT--ATAAATAAGA
383795 TTATTTATA
1 TTATTTATA
383804 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.12
17 1 0.04
18 10 0.40
19 5 0.20
20 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (16 bp):
TTATTTATAAATAAGA
Found at i:383790 original size:20 final size:18
Alignment explanation
Indices: 383765--383801 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
383755 TTACTTATTT
383765 ATAAATAAAGATGTATTTAA
1 ATAAAT-AAGAT-TATTTAA
383785 ATAAATAAGATTATTTA
1 ATAAATAAGATTATTTA
383802 TATTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (18 bp):
ATAAATAAGATTATTTAA
Found at i:384384 original size:24 final size:24
Alignment explanation
Indices: 384342--384409 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
384332 TGAATCATAA
*
384342 AAAATTATTGAAATAATATCAAAATT
1 AAAATT-TTAAAAT-ATATCAAAATT
* *
384368 TAAATTTTAAAATATATTAAAATT
1 AAAATTTTAAAATATATCAAAATT
384392 AAAATTTTAAAATATATC
1 AAAATTTTAAAATATATC
384410 TTGATATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 26 0.70
25 6 0.16
26 5 0.14
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (24 bp):
AAAATTTTAAAATATATCAAAATT
Found at i:384747 original size:21 final size:21
Alignment explanation
Indices: 384721--384761 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
384711 AATATAAAAA
384721 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
384742 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
384762 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:384811 original size:19 final size:17
Alignment explanation
Indices: 384749--384818 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 17
384739 TATATATTTT
384749 ATAA-TTAAATTTAAATAA
1 ATAATTTAAA-TTAAAT-A
*
384767 AAAATTTATTAA-TAAATA
1 ATAATTTA--AATTAAATA
384785 ATAATTTAAATTAAATTA
1 ATAATTTAAATTAAA-TA
384803 ATCAATTTAAATTAAA
1 AT-AATTTAAATTAAA
384819 AAAATTCATC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
16 2 0.05
17 4 0.09
18 15 0.34
19 21 0.48
21 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATTTAAATTAAATA
Found at i:385289 original size:20 final size:20
Alignment explanation
Indices: 385247--385289 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
385237 TTTGTAGATT
* *
385247 AAATTATTTTTAAAAATTTA
1 AAATTATATTTAAAAATTAA
*
385267 AAATTATATTTAATAATTAA
1 AAATTATATTTAAAAATTAA
385287 AAA
1 AAA
385290 AATATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTATATTTAAAAATTAA
Found at i:385301 original size:14 final size:14
Alignment explanation
Indices: 385279--385308 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
385269 ATTATATTTA
*
385279 ATAATTAAAAAAAT
1 ATAAATAAAAAAAT
385293 ATAAATAAAAAAAT
1 ATAAATAAAAAAAT
385307 AT
1 AT
385309 TAAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAATAAAAAAAT
Found at i:386310 original size:26 final size:26
Alignment explanation
Indices: 386227--386312 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 26
386217 ATTCATGTTC
* *
386227 AAATTTAATTTTAAAT-TATAATTTTT
1 AAATTTAATTATAAATATA-AATTATT
386253 AAATATTAATTATAAATATAAATTATT
1 AAAT-TTAATTATAAATATAAATTATT
386280 AAAATTTAATT-T-AATAATAAATTAATT
1 -AAATTTAATTATAAAT-ATAAATT-ATT
386307 AAATTT
1 AAATTT
386313 TTAAATTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
25 3 0.06
26 18 0.34
27 26 0.49
28 6 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AAATTTAATTATAAATATAAATTATT
Found at i:387073 original size:92 final size:92
Alignment explanation
Indices: 386916--387103 Score: 376
Period size: 92 Copynumber: 2.0 Consensus size: 92
386906 GATTGGGGCA
386916 GTTTCTGTCTCTTCTTATCACTTCTACTGGCTTCTCTTCCTCGGAACTCGCTAAGAAAGGTTACT
1 GTTTCTGTCTCTTCTTATCACTTCTACTGGCTTCTCTTCCTCGGAACTCGCTAAGAAAGGTTACT
386981 TTTGTTTTTATTTGTAATTTTTTGGGT
66 TTTGTTTTTATTTGTAATTTTTTGGGT
387008 GTTTCTGTCTCTTCTTATCACTTCTACTGGCTTCTCTTCCTCGGAACTCGCTAAGAAAGGTTACT
1 GTTTCTGTCTCTTCTTATCACTTCTACTGGCTTCTCTTCCTCGGAACTCGCTAAGAAAGGTTACT
387073 TTTGTTTTTATTTGTAATTTTTTGGGT
66 TTTGTTTTTATTTGTAATTTTTTGGGT
387100 GTTT
1 GTTT
387104 TTCCTCTATG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 96 1.00
ACGTcount: A:0.15, C:0.19, G:0.16, T:0.49
Consensus pattern (92 bp):
GTTTCTGTCTCTTCTTATCACTTCTACTGGCTTCTCTTCCTCGGAACTCGCTAAGAAAGGTTACT
TTTGTTTTTATTTGTAATTTTTTGGGT
Found at i:397008 original size:28 final size:28
Alignment explanation
Indices: 396923--397008 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
396913 ATATGATATA
396923 TTTATTATCATAA-ATATTTTAA-TATATT
1 TTTA-TATCATAATATATTTTAATTA-ATT
* * * * *
396951 TATATAT-ATATTATAATTGT-CTTATTT
1 TTTATATCATAATAT-ATTTTAATTAATT
396978 TTTATATCATAATATATTTTAATTAATT
1 TTTATATCATAATATATTTTAATTAATT
397006 TTT
1 TTT
397009 TTTGATTATA
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
26 3 0.07
27 17 0.40
28 23 0.53
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (28 bp):
TTTATATCATAATATATTTTAATTAATT
Found at i:399456 original size:3 final size:3
Alignment explanation
Indices: 399448--399492 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
399438 TATAGCCATG
399448 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
399493 AAGATTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:399608 original size:18 final size:18
Alignment explanation
Indices: 399572--399607 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
399562 ATTATTATTT
*
399572 ATTTGAATATCATTAAAA
1 ATTTGAATATAATTAAAA
399590 ATTTGAA-ATAATTAAAA
1 ATTTGAATATAATTAAAA
399607 A
1 A
399608 AAGAGATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.36
Consensus pattern (18 bp):
ATTTGAATATAATTAAAA
Found at i:402440 original size:4 final size:4
Alignment explanation
Indices: 402431--402475 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
402421 ATTAAATATT
*
402431 AATA AATA AATA AATA AATA ATATA ATTA AATAA AATA AA-A AATA
1 AATA AATA AATA AATA AATA A-ATA AATA AAT-A AATA AATA AATA
402476 TAATTGCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 3 0.08
4 25 0.69
5 8 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:402453 original size:25 final size:25
Alignment explanation
Indices: 402425--402475 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
402415 TTTCGAATTA
402425 AATATTAA-TAAAT-AAATAAATAAAT
1 AATA-TAATTAAATAAAATAAA-AAAT
402450 AATATAATTAAATAAAATAAAAAAT
1 AATATAATTAAATAAAATAAAAAAT
402475 A
1 A
402476 TAATTGCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 3 0.12
25 14 0.58
26 7 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
AATATAATTAAATAAAATAAAAAAT
Found at i:403465 original size:9 final size:9
Alignment explanation
Indices: 403436--403467 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
403426 AATTAAAAAT
403436 AAAAT-TAA
1 AAAATATAA
403444 AAAA-ATAA
1 AAAATATAA
403452 AAAATATAA
1 AAAATATAA
403461 AAAATAT
1 AAAATAT
403468 TTTACCAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 11 0.50
9 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAATATAA
Found at i:405277 original size:33 final size:33
Alignment explanation
Indices: 405033--405284 Score: 192
Period size: 33 Copynumber: 7.7 Consensus size: 33
405023 CTGGGAGGAG
*
405033 CATATGGATTAGCA-TTCGGCTGTGCGGGTTGGC
1 CATATGGATTAGCACTT-GGCTGTGCAGGTTGGC
* * * *
405066 CATACGGATTAGCATTTGTCTGTGCAGGTTGGT
1 CATATGGATTAGCACTTGGCTGTGCAGGTTGGC
* * * **
405099 CGTATGGATTAGCATTTGACTGTGGGGGTTGGC
1 CATATGGATTAGCACTTGGCTGTGCAGGTTGGC
*
405132 CATAGGGATTAGCA-TGTGGCTGTGTC-GGTT-GC
1 CATATGGATTAGCACT-TGGCTGTG-CAGGTTGGC
* * * * *
405164 TATAAGGATTAACACTTGAC--TGCACGGATTGCC
1 CATATGGATTAGCACTTGGCTGTGCA-GG-TTGGC
* * * * * * *
405197 CATACGCATTAGAACTTGGCTATCCGGGTTGGT
1 CATATGGATTAGCACTTGGCTGTGCAGGTTGGC
*
405230 CATATGGGTTAGCACTTGGCTGTGCAGGTTGGC
1 CATATGGATTAGCACTTGGCTGTGCAGGTTGGC
*
405263 CATATGGATTAGCACCTGGCTG
1 CATATGGATTAGCACTTGGCTG
405285 CGTGAATGGA
Statistics
Matches: 170, Mismatches: 39, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
29 1 0.01
30 2 0.01
31 2 0.01
32 19 0.11
33 140 0.82
34 4 0.02
35 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (33 bp):
CATATGGATTAGCACTTGGCTGTGCAGGTTGGC
Found at i:406272 original size:29 final size:29
Alignment explanation
Indices: 406239--406303 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
406229 ATACGAGATA
406239 AATATAATAAAAAAAT-TAAAATATAATATG
1 AATATAA-AAAAAAATAT-AAATATAATATG
*
406269 -ATATGAAAAAATAATATAAATATAATATG
1 AATAT-AAAAAAAAATATAAATATAATATG
406298 AATATA
1 AATATA
406304 TTAATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (29 bp):
AATATAAAAAAAAATATAAATATAATATG
Found at i:406296 original size:24 final size:25
Alignment explanation
Indices: 406236--406299 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
406226 TAGATACGAG
406236 ATAAATATAATA--AAAAAATTAAA
1 ATAAATATAATATGAAAAAATTAAA
* *
406259 ATATAATATGATATGAAAAAA-TAAT
1 ATA-AATATAATATGAAAAAATTAAA
406284 ATAAATATAATATGAA
1 ATAAATATAATATGAA
406300 TATATTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 3 0.09
24 20 0.57
25 6 0.17
26 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (25 bp):
ATAAATATAATATGAAAAAATTAAA
Found at i:406352 original size:32 final size:33
Alignment explanation
Indices: 406288--406365 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 33
406278 AATAATATAA
* * *
406288 ATATAATATGAATATATTAATATTTTAAAATTT
1 ATATAATATAAATATAATAATATATTAAAATTT
*
406321 ATATAATATAAAT-TAATATTATATTAAAATTT
1 ATATAATATAAATATAATAATATATTAAAATTT
406353 ATATAAATATAAA
1 ATAT-AATATAAA
406366 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 20 0.50
33 20 0.50
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
ATATAATATAAATATAATAATATATTAAAATTT
Found at i:406356 original size:17 final size:17
Alignment explanation
Indices: 406312--406367 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
406302 TATTAATATT
406312 TTAAAATTTATATAATA
1 TTAAAATTTATATAATA
* *
406329 -T-AAATTAATATTATA
1 TTAAAATTTATATAATA
406344 TTAAAATTTATATAA-A
1 TTAAAATTTATATAATA
406360 TATAAAAT
1 T-TAAAAT
406368 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 12 0.38
16 4 0.12
17 16 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAAATTTATATAATA
Found at i:406374 original size:27 final size:28
Alignment explanation
Indices: 406305--406375 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 28
406295 ATGAATATAT
406305 TAATATTTTAAAATTTATATAATATAAA
1 TAATATTTTAAAATTTATATAATATAAA
406333 TTAATATTATATTAAAATTTATATAA-ATATAA
1 -TAATA-T-T-TTAAAATTTATATAATATA-AA
406365 -AATATTTTAAA
1 TAATATTTTAAA
406376 TATAATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
27 5 0.13
28 1 0.03
29 6 0.16
30 5 0.13
31 4 0.11
32 17 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATATTTTAAAATTTATATAATATAAA
Found at i:410177 original size:27 final size:27
Alignment explanation
Indices: 410138--410205 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
410128 AACATGCCAC
* *
410138 CATTTTTGACAAATAAAAAGAAACTA-
1 CATTTTTGACAAACAAAAAGAAACCAT
* *
410164 CTATTTTTGACAAACATAAAGTAACCAT
1 C-ATTTTTGACAAACAAAAAGAAACCAT
410192 CATTTTTGACAAAC
1 CATTTTTGACAAAC
410206 TAAGGGTGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 34 0.94
28 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (27 bp):
CATTTTTGACAAACAAAAAGAAACCAT
Found at i:412136 original size:21 final size:22
Alignment explanation
Indices: 412098--412143 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
412088 ATCTGTTGAA
**
412098 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGTTGCGGAGTACT
412119 ACTCCACCTGTTGCGGAGTACT
1 ACTCCACCTGTTGCGGAGTACT
412141 ACT
1 ACT
412144 TGTCTGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGTTGCGGAGTACT
Found at i:413969 original size:27 final size:25
Alignment explanation
Indices: 413909--413982 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
413899 AAACAACATG
413909 CCACTATTTTTGACAAATAAAAAAA
1 CCACTATTTTTGACAAATAAAAAAA
413934 CCA-TCATTTTTGACAAATATAAAATAA
1 CCACT-ATTTTTGACAAATA-AAAA-AA
* * *
413961 TCACTATTTTTAATAAATAAAA
1 CCACTATTTTTGACAAATAAAA
413983 GATGATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 1 0.02
25 17 0.40
26 7 0.17
27 16 0.38
28 1 0.02
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.34
Consensus pattern (25 bp):
CCACTATTTTTGACAAATAAAAAAA
Found at i:415706 original size:21 final size:21
Alignment explanation
Indices: 415680--415723 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
415670 AATAAAAATT
*
415680 TATATAAAT-TATATTATAAAA
1 TATATAAATAT-TAATATAAAA
415701 TATATAAATATTAATATAAAA
1 TATATAAATATTAATATAAAA
415722 TA
1 TA
415724 ATTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATATAAATATTAATATAAAA
Found at i:416316 original size:15 final size:16
Alignment explanation
Indices: 416296--416349 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 16
416286 GATTGGTTTA
416296 ATTAAAAAAT-TAAAT
1 ATTAAAAAATATAAAT
416311 ATTAAAAAATAATAAAT
1 ATTAAAAAAT-ATAAAT
416328 ATAATAAAAAATCAATAAAT
1 AT--TAAAAAAT--ATAAAT
416348 AT
1 AT
416350 ATGTATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 10 0.29
17 7 0.21
19 8 0.24
20 9 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAAATATAAAT
Found at i:416344 original size:20 final size:19
Alignment explanation
Indices: 416298--416350 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
416288 TTGGTTTAAT
416298 TAAAAAAT--TAAATAT--
1 TAAAAAATAATAAATATAA
416313 TAAAAAATAATAAATATAA
1 TAAAAAATAATAAATATAA
416332 TAAAAAATCAATAAATATA
1 TAAAAAAT-AATAAATATA
416351 TGTATTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.24
17 7 0.21
19 8 0.24
20 10 0.30
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAATAATAAATATAA
Found at i:420453 original size:2 final size:2
Alignment explanation
Indices: 420446--420478 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
420436 ACAAGTAAAG
420446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
420479 GGAAGAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:421685 original size:33 final size:33
Alignment explanation
Indices: 421589--421855 Score: 158
Period size: 33 Copynumber: 8.1 Consensus size: 33
421579 TGACAGGAGA
* *
421589 ATATGAATTAGCATTTGGCTGTGCGGGTTGACC
1 ATATGGATTAGCATTTGGCTGTGCGGGTTGGCC
* * * **
421622 ATACGGATCAGCATTTGGCAGTGTAGGTTGGCC
1 ATATGGATTAGCATTTGGCTGTGCGGGTTGGCC
* * *
421655 GTATGGATTAGCATTTGGCTGTGGGGGTTGGCT
1 ATATGGATTAGCATTTGGCTGTGCGGGTTGGCC
* * * *
421688 ATA-GAGATTAGGATGTGGCTGTGCCGGTTGGCT
1 ATATG-GATTAGCATTTGGCTGTGCGGGTTGGCC
* * * ** * *
421721 ATAAGGATTAACACTTGGCTGCACGGATTGCCC
1 ATATGGATTAGCATTTGGCTGTGCGGGTTGGCC
* ** * * * * * * * **
421754 GTATACATCAGAACTTGGCTCTCCGGGGTCGTA
1 ATATGGATTAGCATTTGGCTGTGCGGGTTGGCC
* * * *
421787 ATATGGGTTAGCACTCGGCTGTGCAGGTTGGCC
1 ATATGGATTAGCATTTGGCTGTGCGGGTTGGCC
* * *
421820 ATATGGATTAGCATTTGGCTGCGAGGGTTGACC
1 ATATGGATTAGCATTTGGCTGTGCGGGTTGGCC
421853 ATA
1 ATA
421856 GATACATGGC
Statistics
Matches: 166, Mismatches: 66, Indels: 4
0.70 0.28 0.02
Matches are distributed among these distances:
32 1 0.01
33 164 0.99
34 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (33 bp):
ATATGGATTAGCATTTGGCTGTGCGGGTTGGCC
Found at i:422307 original size:23 final size:22
Alignment explanation
Indices: 422256--422308 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
422246 TATTATAAAA
*
422256 ATTTATTTTTATATAAATATTT
1 ATTTATTTTTATATAAATATAT
*
422278 ATATATTTTTATAATAAA-ATAAT
1 ATTTATTTTTAT-ATAAATAT-AT
422301 ATTTATTT
1 ATTTATTT
422309 ATTTATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTATTTTTATATAAATATAT
Found at i:423232 original size:7 final size:7
Alignment explanation
Indices: 423199--423225 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
423189 TAACATTAAT
423199 TTAAAAA
1 TTAAAAA
423206 TTAAAAA
1 TTAAAAA
423213 TTAAAAA
1 TTAAAAA
423220 TTAAAA
1 TTAAAA
423226 TAAAAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:424559 original size:15 final size:15
Alignment explanation
Indices: 424539--424568 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
424529 ACAACTTTAC
*
424539 CTTTAAGCATAAAGA
1 CTTTAAGCACAAAGA
424554 CTTTAAGCACAAAGA
1 CTTTAAGCACAAAGA
424569 GGATGATTTT
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:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (15 bp):
CTTTAAGCACAAAGA
Found at i:427286 original size:26 final size:28
Alignment explanation
Indices: 427250--427305 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
427240 TTTTGATCGA
427250 AATTATTATTT-ATTTAA-TAAAATAAT
1 AATTATTATTTAATTTAATTAAAATAAT
* *
427276 AATTTTTATTTAAATTTAATTATAATAAT
1 AATTATTATTT-AATTTAATTAAAATAAT
427305 A
1 A
427306 TATAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.40
28 6 0.24
29 9 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTATTATTTAATTTAATTAAAATAAT
Found at i:427325 original size:37 final size:33
Alignment explanation
Indices: 427256--427330 Score: 80
Period size: 36 Copynumber: 2.2 Consensus size: 33
427246 TCGAAATTAT
*
427256 TATTTATTTAATAAAATAATAATTTTTATTTAA
1 TATTTATTTAATAAAATAAAAATTTTTATTTAA
*
427289 -ATTTAATTATAATAATATATAAAAATTATTTTTTTAA
1 TATTT-ATT-TAATAA-A-ATAAAAATT-TTTATTTAA
427326 TATTT
1 TATTT
427331 TTAACAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
32 4 0.12
33 3 0.09
34 6 0.18
35 1 0.03
36 8 0.24
37 8 0.24
38 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TATTTATTTAATAAAATAAAAATTTTTATTTAA
Found at i:429787 original size:2 final size:2
Alignment explanation
Indices: 429782--429807 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
429772 ATACATACGT
429782 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
429808 AAAGCCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:435571 original size:50 final size:50
Alignment explanation
Indices: 435493--435751 Score: 380
Period size: 50 Copynumber: 5.2 Consensus size: 50
435483 AGTTGTTATC
* * *
435493 ATTGTTGACTA-TCATTCACCAACTTTTGACAATAGAGAGAGGTGACCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
** *
435543 ATTGTTGATGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGTCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
435593 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
435643 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
435693 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGATGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
435743 ATTGTTGAC
1 ATTGTTGAC
435752 TCTAAGTATA
Statistics
Matches: 190, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
49 1 0.01
50 187 0.98
51 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Done.