Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold461
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: 348331
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
File 2 of 2
Found at i:220943 original size:27 final size:28
Alignment explanation
Indices: 220910--220992 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
220900 TCGACTTGTG
*
220910 TGGGCTT-AAAAGGATGCTACTAACTTC
1 TGGGCTTGAAAAGGATGCCACTAACTTC
* * *
220937 TGGGCTTTGAGAAGGATGCCACTGACTTG
1 TGGGC-TTGAAAAGGATGCCACTAACTTC
* *
220966 TGGGCTTTGAGAAGGATGGCACTAACT
1 TGGGC-TTGAAAAGGATGCCACTAACT
220993 GAAAAGATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
27 5 0.10
28 2 0.04
29 41 0.85
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (28 bp):
TGGGCTTGAAAAGGATGCCACTAACTTC
Found at i:220951 original size:29 final size:28
Alignment explanation
Indices: 220919--220992 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 28
220909 GTGGGCTTAA
220919 AAGGATGCTACTAACTTCTGGGCTTTGAG
1 AAGGATGC-ACTAACTTCTGGGCTTTGAG
* *
220948 AAGGATGCCACTGACTTGTGGGCTTTGAG
1 AAGGATG-CACTAACTTCTGGGCTTTGAG
220977 AAGGATGGCACTAACT
1 AAGGAT-GCACTAACT
220993 GAAAAGATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 38 0.95
30 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.27
Consensus pattern (28 bp):
AAGGATGCACTAACTTCTGGGCTTTGAG
Found at i:221032 original size:28 final size:28
Alignment explanation
Indices: 220992--221708 Score: 747
Period size: 28 Copynumber: 25.4 Consensus size: 28
220982 TGGCACTAAC
* * * *
220992 TGAAAAGATGCCATTGACTTGCGAGCTT
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
**
221020 TGAAAAGGTGCCACTGACTTGCAGGCTT
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
221048 TGAGAAAAGGTGCCACTGACTTGTGGGCTT
1 T--GAAAAGGTGCCACTGACTTGTGGGCTT
221078 TG-AAAGGTGCCACT-AGCTTGTGGGCTT
1 TGAAAAGGTGCCACTGA-CTTGTGGGCTT
* *
221105 TGAAAAGGGTTGCCACTAACTTGTGGGCTC
1 TGAAAA-GG-TGCCACTGACTTGTGGGCTT
* *
221135 TGAAAAGATGCCACTGACCTGTGGGC-T
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
* *
221162 CGAAAAGGATGCCACTGACTTGTGGGCAT
1 TGAAAAGG-TGCCACTGACTTGTGGGCTT
* *
221191 TGAAAAGGATGCCACTAACTTATGGGCTT
1 TGAAAAGG-TGCCACTGACTTGTGGGCTT
*
221220 TGAAAAGATGCCACTGACTTGTGGGCTT
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
** *
221248 TG-AAAGGATGCTGCTGACTTGTGGGCTC
1 TGAAAAGG-TGCCACTGACTTGTGGGCTT
* *
221276 T-AAAAGGATGCCACTGATTTATGGGCTT
1 TGAAAAGG-TGCCACTGACTTGTGGGCTT
*
221304 TGAAAGGGTGCCACTGACTTGTGGGCTT
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
* * *
221332 TAAAAAGATGCCACTGACTTGCGGGCTT
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
* * * *
221360 TGAAAAGGCGCCACTGACATGCGAGCTT
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
* *
221388 TGAAAAAGTGCTACTGACTTGTGGGCTT
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
* *
221416 TG-AAAGGTGCCATTGACTTGTGGGCTC
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
* *
221443 T-AAAAGGATGCCACTGACTTATGGGCTC
1 TGAAAAGG-TGCCACTGACTTGTGGGCTT
221471 TG-AAAGGATGCCACTGACTTGTGGGCTT
1 TGAAAAGG-TGCCACTGACTTGTGGGCTT
* * *
221499 TGAAAAGGGATGCCATTGATTTATGGGCTT
1 TGAAAA-GG-TGCCACTGACTTGTGGGCTT
* *
221529 TG-AAAGGATACCACTGACTTATGGGCTT
1 TGAAAAGG-TGCCACTGACTTGTGGGCTT
221557 TG-AAAGGATGCCACTGACTTGTGGGCTT
1 TGAAAAGG-TGCCACTGACTTGTGGGCTT
* * * *
221585 TGAAATGATGCCACTAACTTGCGGGCTT
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
221613 T-AAAAGGATGCCACTGACTTGTGGGCTT
1 TGAAAAGG-TGCCACTGACTTGTGGGCTT
* *
221641 TGAAAGGGTGCCACTAACTTGTGGGCTT
1 TGAAAAGGTGCCACTGACTTGTGGGCTT
* * *
221669 TGAAAAGGGACGCCACTAACTCAG-GGGCTT
1 TGAAAA-GG-TGCCACTGACT-TGTGGGCTT
221699 TGAAAAGGTG
1 TGAAAAGGTG
221709 TCGTATTGAC
Statistics
Matches: 588, Mismatches: 78, Indels: 46
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.00
27 66 0.11
28 367 0.62
29 59 0.10
30 93 0.16
31 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (28 bp):
TGAAAAGGTGCCACTGACTTGTGGGCTT
Found at i:242005 original size:34 final size:32
Alignment explanation
Indices: 241962--242030 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
241952 CGTTACAAGC
241962 CAATGTATCGATACAAT-TTGGTCATGTATCCATA
1 CAATGTATCGATAC-ATCTT-GT-ATGTATCCATA
*
241996 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCCATA
242028 CAA
1 CAA
242031 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 13 0.39
33 4 0.12
34 16 0.48
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCCATA
Found at i:242117 original size:13 final size:13
Alignment explanation
Indices: 242099--242123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242089 TACAGTAGTC
242099 ATGTATCGATACA
1 ATGTATCGATACA
242112 ATGTATCGATAC
1 ATGTATCGATAC
242124 TGTGCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:243891 original size:13 final size:13
Alignment explanation
Indices: 243873--243898 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
243863 TACAGCAAGT
243873 ATGTATCGATACA
1 ATGTATCGATACA
243886 ATGTATCGATACA
1 ATGTATCGATACA
243899 CGAAAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:243896 original size:86 final size:85
Alignment explanation
Indices: 243798--244006 Score: 366
Period size: 86 Copynumber: 2.4 Consensus size: 85
243788 ATACATGTTG
243798 CAATGTATCGATACATGAAAAAGATGTATCGATACATTTCTTGGCAGTAGCCAAACTTGTATCGA
1 CAATGTATCGATACA-GAAAAAGATGTATCGATACATTTCTTGGCAGTAGCCAAACTTGTATCGA
243863 TACAGCAAGTATGTATCGATA
65 TACAGCAAGTATGTATCGATA
243884 CAATGTATCGATACACGAAAAAGATGTATCGATACATTTCTTGGCAGTAGCCAAACTTGTATCGA
1 CAATGTATCGATACA-GAAAAAGATGTATCGATACATTTCTTGGCAGTAGCCAAACTTGTATCGA
243949 TACAGCAAGTATGTATCGATA
65 TACAGCAAGTATGTATCGATA
* *
243970 CAATGTATCGATACACAAAAA-ATTGTATTGATACATT
1 CAATGTATCGATACAGAAAAAGA-TGTATCGATACATT
244007 GGCTTGTAAC
Statistics
Matches: 119, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
84 1 0.01
85 18 0.15
86 100 0.84
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (85 bp):
CAATGTATCGATACAGAAAAAGATGTATCGATACATTTCTTGGCAGTAGCCAAACTTGTATCGAT
ACAGCAAGTATGTATCGATA
Found at i:243977 original size:13 final size:13
Alignment explanation
Indices: 243959--243984 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
243949 TACAGCAAGT
243959 ATGTATCGATACA
1 ATGTATCGATACA
243972 ATGTATCGATACA
1 ATGTATCGATACA
243985 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:250175 original size:13 final size:13
Alignment explanation
Indices: 250157--250182 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
250147 ACATTTTTCT
250157 TTGTATCGATACA
1 TTGTATCGATACA
250170 TTGTATCGATACA
1 TTGTATCGATACA
250183 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:250346 original size:20 final size:20
Alignment explanation
Indices: 250303--250348 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
250293 AAATCTTTTG
250303 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
250324 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
250344 CAAAA
1 CAAAA
250349 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:252718 original size:13 final size:13
Alignment explanation
Indices: 252700--252725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
252690 TACAGCAAGT
252700 ATGTATCGATACA
1 ATGTATCGATACA
252713 ATGTATCGATACA
1 ATGTATCGATACA
252726 CGAAAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:252723 original size:86 final size:85
Alignment explanation
Indices: 252625--252833 Score: 366
Period size: 86 Copynumber: 2.4 Consensus size: 85
252615 ATACATGTTG
*
252625 CAATGTATCGATACATGAAAAAGATGTATCAATACATTTCTTGGCAGTAGCCAAACTTGTATCGA
1 CAATGTATCGATACA-GAAAAAGATGTATCGATACATTTCTTGGCAGTAGCCAAACTTGTATCGA
252690 TACAGCAAGTATGTATCGATA
65 TACAGCAAGTATGTATCGATA
252711 CAATGTATCGATACACGAAAAAGATGTATCGATACATTTCTTGGCAGTAGCCAAACTTGTATCGA
1 CAATGTATCGATACA-GAAAAAGATGTATCGATACATTTCTTGGCAGTAGCCAAACTTGTATCGA
252776 TACAGCAAGTATGTATCGATA
65 TACAGCAAGTATGTATCGATA
*
252797 CAATGTATCGATACACAAAAA-ATTGTATCGATACATT
1 CAATGTATCGATACAGAAAAAGA-TGTATCGATACATT
252834 GGCTTGAAAC
Statistics
Matches: 119, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
84 1 0.01
85 19 0.16
86 99 0.83
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (85 bp):
CAATGTATCGATACAGAAAAAGATGTATCGATACATTTCTTGGCAGTAGCCAAACTTGTATCGAT
ACAGCAAGTATGTATCGATA
Found at i:252804 original size:13 final size:13
Alignment explanation
Indices: 252786--252811 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
252776 TACAGCAAGT
252786 ATGTATCGATACA
1 ATGTATCGATACA
252799 ATGTATCGATACA
1 ATGTATCGATACA
252812 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:254685 original size:13 final size:13
Alignment explanation
Indices: 254667--254691 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
254657 ATAAACCCTT
254667 TGTATCGATACAA
1 TGTATCGATACAA
254680 TGTATCGATACA
1 TGTATCGATACA
254692 GAGAATGCTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:261050 original size:20 final size:20
Alignment explanation
Indices: 261011--261051 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
261001 TTGTGCATTA
*
261011 TGTATCGATACATCTGAAGG
1 TGTATCGATACATCTAAAGG
*
261031 TGTATCGATACATTTAAAGG
1 TGTATCGATACATCTAAAGG
261051 T
1 T
261052 TTTGACCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATCTAAAGG
Found at i:262986 original size:33 final size:33
Alignment explanation
Indices: 262943--263008 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
262933 AAGATGTGTT
* *
262943 TGCCTGGTCTTACCAAGACATGTCCGGATTAGA
1 TGCCTAGTCTTACCAAGACATGTCCAGATTAGA
*
262976 TGCCTAGTCTTACCAAGACATGTCTAGATTAGA
1 TGCCTAGTCTTACCAAGACATGTCCAGATTAGA
263009 CACTACCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (33 bp):
TGCCTAGTCTTACCAAGACATGTCCAGATTAGA
Found at i:266175 original size:1 final size:1
Alignment explanation
Indices: 266169--266238 Score: 77
Period size: 1 Copynumber: 70.0 Consensus size: 1
266159 TTTCTTTTCC
* * * * * * *
266169 AAAAAAAAATAAAAAAAAACAAAAAAAAGAAAAAAGAAAAAAAGAAAAAAAAGAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
266234 AAAAA
1 AAAAA
266239 GAGAAAAGAA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.90, C:0.01, G:0.07, T:0.01
Consensus pattern (1 bp):
A
Found at i:266192 original size:15 final size:14
Alignment explanation
Indices: 266169--266245 Score: 86
Period size: 15 Copynumber: 5.3 Consensus size: 14
266159 TTTCTTTTCC
266169 AAAAAAAAATAAAA-
1 AAAAAAAAA-AAAAG
266183 AAAAACAAAAAAAAG
1 AAAAA-AAAAAAAAG
266198 AAAAAAGAAAAAAAG
1 AAAAAA-AAAAAAAG
266213 AAAAAAAAGAAAAA-
1 AAAAAAAA-AAAAAG
*
266227 AAGAAAAAAAAAGAG
1 AA-AAAAAAAAAAAG
266242 AAAA
1 AAAA
266246 GAAATGAACC
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
14 20 0.36
15 36 0.64
ACGTcount: A:0.88, C:0.01, G:0.09, T:0.01
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:266194 original size:17 final size:17
Alignment explanation
Indices: 266171--266237 Score: 93
Period size: 17 Copynumber: 3.9 Consensus size: 17
266161 TCTTTTCCAA
*
266171 AAAAAAATAAAAAAAA-
1 AAAAAAAGAAAAAAAAG
266187 ACAAAAAA-AAGAAAAAAG
1 A-AAAAAAGAA-AAAAAAG
266205 AAAAAAAGAAAAAAAAG
1 AAAAAAAGAAAAAAAAG
266222 AAAAAAAGAAAAAAAA
1 AAAAAAAGAAAAAAAA
266238 AGAGAAAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.06
17 41 0.87
18 3 0.06
ACGTcount: A:0.90, C:0.01, G:0.07, T:0.01
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Found at i:266245 original size:7 final size:6
Alignment explanation
Indices: 266169--266249 Score: 53
Period size: 6 Copynumber: 13.3 Consensus size: 6
266159 TTTCTTTTCC
* * *
266169 AAAA-A AAAATA AAAAAA AACAAAA AAAAGAA AAAAGA AAAA-A AGAAA-A
1 AAAAGA AAAAGA AAAAGA AA-AAGA AAAAG-A AAAAGA AAAAGA A-AAAGA
*
266217 AAAAGA AAAA-A AGAAAAA AAAAGA GAAAAGA AA
1 AAAAGA AAAAGA A-AAAGA AAAAGA -AAAAGA AA
266250 TGAACCTGCT
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
5 11 0.17
6 34 0.52
7 20 0.31
ACGTcount: A:0.88, C:0.01, G:0.10, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:266245 original size:9 final size:8
Alignment explanation
Indices: 266169--266249 Score: 82
Period size: 7 Copynumber: 10.4 Consensus size: 8
266159 TTTCTTTTCC
266169 AAAAAAA-
1 AAAAAAAG
*
266176 AATAAAA-
1 AAAAAAAG
*
266183 AAAAACA-
1 AAAAAAAG
266190 AAAAAAAG
1 AAAAAAAG
266198 -AAAAAAG
1 AAAAAAAG
266205 AAAAAAAG
1 AAAAAAAG
266213 AAAAAAAAG
1 -AAAAAAAG
266222 AAAAAAAG
1 AAAAAAAG
266230 AAAAAAA-
1 AAAAAAAG
266237 AAGAGAAAAG
1 AA-A-AAAAG
266247 AAA
1 AAA
266250 TGAACCTGCT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
7 26 0.41
8 23 0.36
9 13 0.20
10 2 0.03
ACGTcount: A:0.88, C:0.01, G:0.10, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:266245 original size:17 final size:16
Alignment explanation
Indices: 266169--266249 Score: 80
Period size: 17 Copynumber: 5.2 Consensus size: 16
266159 TTTCTTTTCC
*
266169 AAAAAAAAA-TAAAA-
1 AAAAAAAAAGAAAAAG
*
266183 AAAAACAAA-AAAAAG
1 AAAAAAAAAGAAAAAG
*
266198 AAAAAAGAA-AAAAAG
1 AAAAAAAAAGAAAAAG
*
266213 AAAAAAAAGAAAAAAAG
1 AAAAAAAA-AGAAAAAG
266230 AAAAAAAAAGAGAAAAG
1 AAAAAAAAAGA-AAAAG
266247 AAA
1 AAA
266250 TGAACCTGCT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
14 12 0.21
15 20 0.35
16 3 0.05
17 22 0.39
ACGTcount: A:0.88, C:0.01, G:0.10, T:0.01
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:267352 original size:61 final size:61
Alignment explanation
Indices: 267223--267792 Score: 642
Period size: 61 Copynumber: 9.4 Consensus size: 61
267213 ACCTTTTATC
* * *
267223 CTTT-CAGTCCTCAAAGAGCAGGAC-ACTTTT-CTCTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
267281 CCTTT-TAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTAGTA
1 -CTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * *
267342 CTTTCCAGTCCTTAAAGAGTAGGACGCCCTTTCCTGTTAAAGCCCACATAAGTTAGTGGAA
1 CTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
267403 CTTTCCAGTCCTCAAAGAGCAAGACGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
267464 CTTTCCAATCCTCAAAGAGCAGGACGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
267525 CTTTCCAATCCTCAAAGAGCAGGACGTCTTTTTCTTTTTAAAGCCTACACAAGTTGGTGGCA
1 CTTTCCAGTCCTCAAAGAGCAGGACG-CCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
267587 CCTTT-CAGTCCTCAAAGAAG-AGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 -CTTTCCAGTCCTCAAAG-AGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
267648 CTTTCCATTCCTCAAAGAGCAGGACG-C-TTT-CTTTTCAAAGCCCACACAAATTGGTGACA
1 CTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* * ** ** * * **
267707 CATTT-TAGTCCTCAAAAAGTGGGACG-CTTTCTCCTTACAAAGCCCATATAAGTTAATGGCA
1 C-TTTCCAGTCCTCAAAGAGCAGGACGCCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
267768 CCTTCTAGT-CTCCAAAGAGCAGGAC
1 CTTTCCAGTCCT-CAAAGAGCAGGAC
267793 ACATTTAATT
Statistics
Matches: 440, Mismatches: 56, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
58 5 0.01
59 64 0.15
60 25 0.06
61 288 0.65
62 52 0.12
63 6 0.01
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (61 bp):
CTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:267892 original size:42 final size:42
Alignment explanation
Indices: 267809--267895 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
267799 AATTTCCTTT
* * * * *
267809 TTTTTTCCTTTGTCCTTAGAGAGCAGGACATATTTTATTTCC
1 TTTTTTCCTTTGTCCTCAAAAAGCAAGACATATCTTATTTCC
*
267851 TTTTTTCCTTTGTCCTCAAAAAGCAAGACGTACTCTT-TTTCC
1 TTTTTTCCTTTGTCCTCAAAAAGCAAGACATA-TCTTATTTCC
267893 TTT
1 TTT
267896 GTCCTCAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.47
Consensus pattern (42 bp):
TTTTTTCCTTTGTCCTCAAAAAGCAAGACATATCTTATTTCC
Found at i:268582 original size:47 final size:48
Alignment explanation
Indices: 268507--268635 Score: 145
Period size: 51 Copynumber: 2.6 Consensus size: 48
268497 TCACAATTTA
* *
268507 TATCGATACATCCTTCATTGTATTGATACATCTGGG-TAAACCAGATG
1 TATCGATACATCTTTCATTGTATCGATACATCTGGGTTAAACCAGATG
* *
268554 TATTGATACATCTTTCATTGTATCGATACATTCTGGGTTTTAACCCAGATG
1 TATCGATACATCTTTCATTGTATCGATACA-TCTGGG--TTAAACCAGATG
* * *
268605 TATCAATACAT-TTCTCAATGTATGGATACAT
1 TATCGATACATCTT-TCATTGTATCGATACAT
268636 TCAGGCATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
47 27 0.39
48 6 0.09
50 3 0.04
51 33 0.48
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (48 bp):
TATCGATACATCTTTCATTGTATCGATACATCTGGGTTAAACCAGATG
Found at i:270823 original size:79 final size:79
Alignment explanation
Indices: 270690--271052 Score: 390
Period size: 79 Copynumber: 4.6 Consensus size: 79
270680 TCATTCATGT
* ** * *
270690 TTTTATTTCTAAAGCACTGATTTTTCACAATCGGGGATACTCCAACCTCATTATTTCCGATGGGA
1 TTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCATTATTTCCGAGGGGA
**
270755 TACTCCAACTTCGA
66 TACTCCAACCCCGA
* ** * *
270769 TTTTATTTCTAAAATACCAATTTTCCACAATCAAGGATACTCCAACCTCGTTATTTCTGAGGGGA
1 TTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCATTATTTCCGAGGGGA
* *
270834 TACTTCAACCCCGG
66 TACTCCAACCCCGA
* * * * * *
270848 TTTTATTTCTAAAACATCAATTTTCTATAGTCGGGGATACTCCAACCCCGTTA-TTCCTGAGGGG
1 TTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCATTATTTCC-GAGGGG
270912 ATACTCCAACCCCGA
65 ATACTCCAACCCCGA
* * * * * ** *
270927 TTTTATTTTTAAAATATCGATTTTCTACAATCGGGGATACTCCAATCCT-ATTATTTTTGAGAGG
1 TTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAA-CCTCATTATTTCCGAGGGG
* *
270991 ATACTCCAAACTC-A
65 ATACTCCAACCCCGA
* *
271005 GTTTTATTTCCAAAACACCAATTTTCCACCATCGGGGATACTCCAACC
1 -TTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACC
271053 CTGATTTTAT
Statistics
Matches: 236, Mismatches: 44, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
78 6 0.03
79 226 0.96
80 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (79 bp):
TTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCATTATTTCCGAGGGGA
TACTCCAACCCCGA
Found at i:271049 original size:51 final size:51
Alignment explanation
Indices: 270984--271104 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
270974 CTATTATTTT
* *
270984 TGAGAGGATACTCCAAACTCAG-TTTTATTTCCAAAACACCAATTTTCCACCA
1 TGAG-GGATACTCC-AACCCAGATTTTATTTCCAAAACACCAATTTTCCACAA
* * * *
271036 TCG-GGGATACTCCAACCCTGATTTTATTTCTAGAACATCAATTTTCCACAA
1 T-GAGGGATACTCCAACCCAGATTTTATTTCCAAAACACCAATTTTCCACAA
*
271087 TGAGGGATACTTCAACCC
1 TGAGGGATACTCCAACCC
271105 CATTATTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
50 6 0.10
51 50 0.85
52 2 0.03
53 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.30
Consensus pattern (51 bp):
TGAGGGATACTCCAACCCAGATTTTATTTCCAAAACACCAATTTTCCACAA
Found at i:271062 original size:130 final size:130
Alignment explanation
Indices: 270908--271185 Score: 371
Period size: 130 Copynumber: 2.1 Consensus size: 130
270898 TTATTCCTGA
* * * *
270908 GGGGATACTCCAACCCCGATTTTATTTTTAAAATATCGATTTTCTACAATCG-GGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAAT-GAGGGATACTCCAA
* * * * *
270972 TCCTATTATTTTTGAGAGGATACTCCAAACTCAG-TTTTATTTCCAAAACACCAATTTTCCACCA
65 CCCCATTATTTTCGAGAGGATACTCC-AACCCAGATTTTATTTCCAAAACACCAATTTTCCACAA
271036 TC
129 TC
* * *
271038 GGGGATACTCCAACCCTGATTTTATTTCTAGAACATCAATTTTCCACAATGAGGGATACTTCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATGAGGGATACTCCAAC
* * * *
271103 CCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTGTTTCCAAAACATCAATTTTTCACAATC
66 CCCATTATTTTCGAGAGGATACTCCAACCCAGATTTTATTTCCAAAACACCAATTTTCCACAATC
*
271168 GAGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
271186 TTATTTCTGA
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
129 6 0.05
130 122 0.95
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (130 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATGAGGGATACTCCAAC
CCCATTATTTTCGAGAGGATACTCCAACCCAGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:271123 original size:79 final size:80
Alignment explanation
Indices: 271039--271423 Score: 439
Period size: 79 Copynumber: 4.9 Consensus size: 80
271029 TCCACCATCG
* * * * *
271039 GGGATACTCCAACCCTGATTTTATTTCTAGAACATCAATTTTCCACAAT-GAGGGATACTTCAAC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGGATACTCCAAC
271103 CCCATTATTTTCG-A
66 CCCATTATTTTCGAA
*
271117 GAGGATACTCCAACCCCGATTTTGTTTCCAAAACATCAATTTTTCACAATCGA-GGATACTCCAA
1 G-GGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGGATACTCCAA
*
271181 CCCCGTTA-TTTCTGAA
65 CCCCATTATTTTC-GAA
* *
271197 GGGATACTCCAACCCCGATTTTATTTCTAAAACAT-AGATTTTTCACTATCG-GGGATACTCCAA
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCA-ATTTTTCACAATCGAGGGATACTCCAA
** *
271260 CCCCATTATTCCCGAG
65 CCCCATTATTTTCGAA
* ** * * *
271276 GGGATACTTCAACCTTGA-TTTATTTCCAAAATATCGATTTTTCACAATC-AGAGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGGATACTCCAAC
* *
271339 CCTATTATTTTTGAA
66 CCCATTATTTTCGAA
* * *
271354 GGGATACTCCAACCCCGGTTTTATTTCCAAAACA-CTAA-TTTTCTACCATCGAGAGGATACTCT
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATC-AATTTTTC-ACAATCGAG-GGATACTCC
271417 AACCCCA
63 AACCCCA
271424 ATTTTATTTC
Statistics
Matches: 256, Mismatches: 37, Indels: 25
0.81 0.12 0.08
Matches are distributed among these distances:
78 74 0.29
79 161 0.63
80 8 0.03
81 13 0.05
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (80 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGGATACTCCAAC
CCCATTATTTTCGAA
Found at i:271125 original size:209 final size:209
Alignment explanation
Indices: 270829--271263 Score: 531
Period size: 209 Copynumber: 2.1 Consensus size: 209
270819 TTATTTCTGA
* * * * *
270829 GGGGATACTTCAACCCCGGTTTTATTTCTAAAACATCAATTTTCTATAGTCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAAC
* * ** * *
270894 CCCGTTATTCCTGAGGGGATACTCCAACCCCGATTTTATTTTTAAAATATCGA-TTTTCTACAAT
66 CCCATTATTCCTGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTC-ACAAT
* * * * *
270958 CGGGGATACTCCAATCCTATTATTTTTG-AGAGGATACTCCAAACTCAG-TTTTATTTCCAAAAC
130 CGAGGATACTCCAACCCCATTATTTCTGAAG-GGATACTCC-AACCCAGATTTTATTTCCAAAAC
271021 ACCA-ATTTTCCACCATC
193 A-CAGATTTTCCACCATC
* * *
271038 GGGGATACTCCAACCCTGATTTTATTTCTAGAACATCAATTTTCCACAAT-GAGGGATACTTCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATCG-GGGATACTCCAA
* *
271102 CCCCATTATT-TTCGAGAGGATACTCCAACCCCGATTTTGTTTCCAAAACATCAATTTTTCACAA
65 CCCCATTATTCCT-GAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAA
* * *
271166 TCGAGGATACTCCAACCCCGTTATTTCTGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACA
129 TCGAGGATACTCCAACCCCATTATTTCTGAAGGGATACTCCAACCCAGATTTTATTTCCAAAACA
* * *
271231 TAGATTTTTCACTATC
194 CAGATTTTCCACCATC
271247 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
271264 ATTATTCCCG
Statistics
Matches: 192, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
208 8 0.04
209 177 0.92
210 7 0.04
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (209 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAAC
CCCATTATTCCTGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATC
GAGGATACTCCAACCCCATTATTTCTGAAGGGATACTCCAACCCAGATTTTATTTCCAAAACACA
GATTTTCCACCATC
Found at i:271283 original size:288 final size:288
Alignment explanation
Indices: 270751--271341 Score: 751
Period size: 288 Copynumber: 2.1 Consensus size: 288
270741 TATTTCCGAT
* *
270751 GGGATACTCCAA-CTTCGATTTTATTTCTAAAATACCAATTTTCCACAATCAAGGATACTCCAAC
1 GGGATACTCCAACCCTCGATTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAAC
* * * * * * * *
270815 CTCGTTATTTCTGAGGGGATACTTCAACCCCGGTTTTATTTCTAAAACATCAATTTTCTATAGTC
66 CCCATTATTTCTGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCTACAATC
* * * * *
270880 GGGGATACTCCAACCCCGTTATTCCTGAGGGGATACTCCAACCCCGATTTTATTTTTAAAATATC
131 GAGGATACTCCAACCCCGTTATTCCTGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATA
* * *** *
270945 GATTTTCTACAATCGGGGATACTCCAATCCTATTATTTTTGAGAGGATACTCCAAACTCAGTTTT
196 GATTTTCTACAATCGGGGATACTCCAACCCCATTATTCCCGAGAGGATACTCCAAACT-AGATTT
* *
271010 ATTTCCAAAACACCAATTTTCCACCATCG
260 ATTTCCAAAACACCAATTTTCCACAATCA
* * * * *
271039 GGGATACTCCAACCCT-GATTTTATTTCTAGAACATCAATTTTCCACAATGAGGGATACTTCAAC
1 GGGATACTCCAACCCTCGATTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAAC
*
271103 CCCATTATTT-TCGAGAGGATACTCCAACCCCGATTTTGTTTCCAAAACATCAATTTT-TCACAA
66 CCCATTATTTCT-GAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCT-ACAA
*
271166 TCGAGGATACTCCAACCCCGTTATTTCTGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACA
129 TCGAGGATACTCCAACCCCGTTATTCCTGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACA
* * * * *
271231 TAGATTTT-TCACTATCGGGGATACTCCAACCCCATTATTCCCGAGGGGATACTTCAACCTTGAT
194 TAGATTTTCT-ACAATCGGGGATACTCCAACCCCATTATTCCCGAGAGGATACTCCAAACTAGAT
* * * *
271295 TTATTTCCAAAATATCGATTTTTCACAATCA
258 TTATTTCCAAAACACCAATTTTCCACAATCA
*
271326 GAGATACTCCAACCCT
1 GGGATACTCCAACCCT
271342 ATTATTTTTG
Statistics
Matches: 259, Mismatches: 40, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
287 45 0.17
288 212 0.82
289 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (288 bp):
GGGATACTCCAACCCTCGATTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAAC
CCCATTATTTCTGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCTACAATC
GAGGATACTCCAACCCCGTTATTCCTGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATA
GATTTTCTACAATCGGGGATACTCCAACCCCATTATTCCCGAGAGGATACTCCAAACTAGATTTA
TTTCCAAAACACCAATTTTCCACAATCA
Found at i:271369 original size:157 final size:158
Alignment explanation
Indices: 271039--271423 Score: 492
Period size: 157 Copynumber: 2.4 Consensus size: 158
271029 TCCACCATCG
* * * *
271039 GGGATACTCCAACCCTGATTTTATTTCTAGAACATCAATTTTCCACAAT-GAGGGATACTTCAAC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACAT-AATTTTTCACAATCGAGGGATACTCCAAC
** *
271103 CCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTGTTTCCAAAACATCAATTTTTCACAATC
65 CCCATTATTCCCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATC
*
271168 GAGGATACTCCAACCCCGTTATTTCTGAA
130 GAGGATACTCCAACCCCATTATTTCTGAA
*
271197 GGGATACTCCAACCCCGATTTTATTTCTAAAACATAGATTTTTCACTATCG-GGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATA-ATTTTTCACAATCGAGGGATACTCCAAC
* * ** * *
271261 CCCATTATTCCCGAGGGGATACTTCAACCTTGA-TTTATTTCCAAAATATCGATTTTTCACAATC
65 CCCATTATTCCCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATC
* *
271325 -AGAGATACTCCAACCCTATTATTTTTGAA
130 GAG-GATACTCCAACCCCATTATTTCTGAA
* * * *
271354 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAA-TTTTCTACCATCGAGAGGATACTCTA
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACA-TAATTTTTC-ACAATCGAG-GGATACTCCA
271418 ACCCCA
63 ACCCCA
271424 ATTTTATTTC
Statistics
Matches: 199, Mismatches: 21, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
156 7 0.04
157 91 0.46
158 85 0.43
159 16 0.08
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (158 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAACATAATTTTTCACAATCGAGGGATACTCCAACC
CCATTATTCCCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATCG
AGGATACTCCAACCCCATTATTTCTGAA
Found at i:272734 original size:20 final size:19
Alignment explanation
Indices: 272679--272734 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
272669 AAAACCCTTA
*
272679 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
272699 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
272719 AATGTATCGATACATG
1 AAAGTATCGATACATG
272735 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:272831 original size:21 final size:20
Alignment explanation
Indices: 272785--272837 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
272775 GTAGCCAAAC
**
272785 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
272805 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACAC-AAAAAA
*
272825 TTGTATCAATACA
1 TTGTATCGATACA
272838 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:273906 original size:20 final size:21
Alignment explanation
Indices: 273881--273954 Score: 100
Period size: 20 Copynumber: 3.7 Consensus size: 21
273871 TTTTAACTAG
*
273881 ATGTATCGATACATT-ATTCA
1 ATGTATCGATACATTCATACA
273901 ATGTATCGATACATTCATAC-
1 ATGTATCGATACATTCATACA
* *
273921 ATGTATCGATACATTGA-AAA
1 ATGTATCGATACATTCATACA
273941 ATGTATCGATACAT
1 ATGTATCGATACAT
273955 CTGGGTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.92
21 3 0.06
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTCATACA
Found at i:276965 original size:18 final size:19
Alignment explanation
Indices: 276939--276977 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
276929 AAAAGCACAA
276939 AAGATAAAAAAAAAAACAC
1 AAGATAAAAAAAAAAACAC
* *
276958 AAGA-AAAAAAGAAAAGAC
1 AAGATAAAAAAAAAAACAC
276976 AA
1 AA
276978 AATCAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.79, C:0.08, G:0.10, T:0.03
Consensus pattern (19 bp):
AAGATAAAAAAAAAAACAC
Found at i:277285 original size:11 final size:11
Alignment explanation
Indices: 277269--277295 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
277259 TCTGGTCATA
277269 AAAAAAAAGAT
1 AAAAAAAAGAT
277280 AAAAAAAAGAT
1 AAAAAAAAGAT
277291 AAAAA
1 AAAAA
277296 TTCCACCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAAAAGAT
Found at i:278381 original size:34 final size:33
Alignment explanation
Indices: 278342--278531 Score: 204
Period size: 34 Copynumber: 5.7 Consensus size: 33
278332 TCTCTTTTTT
*
278342 AAGTCCATAACTCTGTGGCAACCTTTTTCTGTTA
1 AAGTCCACAACTCTGTGGC-ACCTTTTTCTGTTA
* ** * *
278376 AAGTCCACAACTCTATGGCACC-TTCCCTTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTTCTGTTA
*
278408 AAGTCCACAACTTTGTGGCAACCTTTTTCTGTTA
1 AAGTCCACAACTCTGTGGC-ACCTTTTTCTGTTA
* ** * * *
278442 AAGTCCATAACTCCATGGCACC-TTTCCTTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTTCTGTTA
* *
278474 AAGTGCACAACCCTGTGGCAACCTTTTTCTGTTA
1 AAGTCCACAACTCTGTGGC-ACCTTTTTCTGTTA
278508 AAGTCCACAACTCTGTGGCACCTT
1 AAGTCCACAACTCTGTGGCACCTT
278532 CCTTTTTTAA
Statistics
Matches: 123, Mismatches: 29, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
32 44 0.36
33 17 0.14
34 62 0.50
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (33 bp):
AAGTCCACAACTCTGTGGCACCTTTTTCTGTTA
Found at i:278443 original size:66 final size:66
Alignment explanation
Indices: 278337--278566 Score: 345
Period size: 66 Copynumber: 3.5 Consensus size: 66
278327 TGGCATCTCT
*
278337 TTTTTAAGTCCATAACTCTGTGGCAACCTTTTTCTGTTAAAGTCCACAACTCTATGGCACCTTCC
1 TTTTTAAGTCCACAACTCTGTGGCAACCTTTTTCTGTTAAAGTCCACAACTCTATGGCACCTTCC
278402 C
66 C
* * * *
278403 TTTTTAAGTCCACAACTTTGTGGCAACCTTTTTCTGTTAAAGTCCATAACTCCATGGCACCTTTC
1 TTTTTAAGTCCACAACTCTGTGGCAACCTTTTTCTGTTAAAGTCCACAACTCTATGGCACCTTCC
278468 C
66 C
* * *
278469 TTTTTAAGTGCACAACCCTGTGGCAACCTTTTTCTGTTAAAGTCCACAACTCTGTGGCACCTTCC
1 TTTTTAAGTCCACAACTCTGTGGCAACCTTTTTCTGTTAAAGTCCACAACTCTATGGCACCTTCC
*
278534 T
66 C
* *
278535 TTTTTAAGTCTACAACT-TCGTGGCACCCTTTT
1 TTTTTAAGTCCACAACTCT-GTGGCAACCTTTT
278567 AAGTCCACAA
Statistics
Matches: 146, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
65 1 0.01
66 145 0.99
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (66 bp):
TTTTTAAGTCCACAACTCTGTGGCAACCTTTTTCTGTTAAAGTCCACAACTCTATGGCACCTTCC
C
Found at i:278576 original size:27 final size:27
Alignment explanation
Indices: 278508--278700 Score: 174
Period size: 27 Copynumber: 7.0 Consensus size: 27
278498 TTTTCTGTTA
*
278508 AAGTCCACAACTCTGTGGCACCTTCCTTTTTT
1 AAGTCCACAACTCCGTGGCA-C--CC--TTTT
* *
278540 AAGTCTACAACTTCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
278567 AAGTCCACAACTCCATGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
278594 TAGTCTACAACTCCTTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * * *
278621 TAGTCCACAACTCCTTGGTACCATTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* ** *
278648 AAAT-CACAACTATGTGGCACCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
278674 AAG-CTCACAACTACGTGGCACCCTTTT
1 AAGTC-CACAACTCCGTGGCACCCTTTT
278701 TAAAGCCCAC
Statistics
Matches: 137, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
26 19 0.14
27 98 0.72
29 2 0.01
31 1 0.01
32 17 0.12
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.33
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:278805 original size:32 final size:32
Alignment explanation
Indices: 278729--278805 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
278719 GGCATCTTTC
* * *
278729 TCTAAAGCCCACACAAATTGATGGCAACCCTT
1 TCTAAAGCCCATACAAATAGATGGCAACCCCT
*
278761 TCTAAAGTCCATACAAAATAG-TGGCAACCCCCT
1 TCTAAAGCCCATAC-AAATAGATGGCAA-CCCCT
278794 T-TAAAGCCCATA
1 TCTAAAGCCCATA
278806 AGTCAGTGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 28 0.74
33 10 0.26
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (32 bp):
TCTAAAGCCCATACAAATAGATGGCAACCCCT
Found at i:278828 original size:28 final size:28
Alignment explanation
Indices: 278796--279301 Score: 217
Period size: 28 Copynumber: 17.3 Consensus size: 28
278786 AACCCCCTTT
*
278796 AAAGCCCATAAGTCAGTGACACCCTTCC
1 AAAGCCCATAAGTCAGTGGCACCCTTCC
* * *
278824 AAAGCCCACAAGTTAGTGGCACCTTTTCC
1 AAAGCCCATAAGTCAGTGGCACC-CTTCC
* *
278853 AAAACCCATAAGTCAGTGGCACCCTTTTC
1 AAAGCCCATAAGTCAGTGGCACCC-TTCC
* ** **
278882 AAAGCCCACACAAGTTGGTGGCATCTTTTTTCC
1 AAAG-CC-CATAAGTCAGTGGCA-C--CCTTCC
* * * **
278915 AAA-CCCTACAAGTCCGTGGCATCCTTGT
1 AAAGCCC-ATAAGTCAGTGGCACCCTTCC
* *
278943 AAAGTCCACACAAGTCAGTGGCAACCCTTTCT
1 AAAG-CC-CATAAGTCAGTGGC-ACCC-TTCC
* ** * *
278975 AAAGTCCACACAAGTTGGTGGTAACCCTCTTC
1 AAAG-CC-CATAAGTCAGTGG-CACCCT-TCC
* ** ** **
279007 AAAGCCCACACAAGTTGGTGGCATCTTTTTTTT
1 AAAG-CC-CATAAGTCAGTGGCA-C--CCTTCC
* *
279040 AAAGCCTA-AGAGTCAGTGGCACCCTTTC
1 AAAGCCCATA-AGTCAGTGGCACCCTTCC
* *
279068 AAAGCCCACAAGTCAGTGCCACCCTTCC
1 AAAGCCCATAAGTCAGTGGCACCCTTCC
* * * *
279096 AAAGCCCATAAATTAGTGGTACCCTTTC
1 AAAGCCCATAAGTCAGTGGCACCCTTCC
* * *
279124 AAAGCCCACAAGTCAGTGGAACCCTTTC
1 AAAGCCCATAAGTCAGTGGCACCCTTCC
*
279152 AAAGCCCATAAGTCAGTGGTAGCCCTT-C
1 AAAGCCCATAAGTCAGTGGCA-CCCTTCC
* * * * * **
279180 AAAGTCCAAAAGTTAGTGGCATCTTTTT
1 AAAGCCCATAAGTCAGTGGCACCCTTCC
* * * **
279208 AAAGCCCACAAGTCAATGGCATCCTTTT
1 AAAGCCCATAAGTCAGTGGCACCCTTCC
* * **
279236 AAAGCCCATAAGTCAATGGCATCCTTTT
1 AAAGCCCATAAGTCAGTGGCACCCTTCC
* * *
279264 AAAGCCCACAAGTTAGTGGCACCCCTTTCT
1 AAAGCCCATAAGTCAGTGGCA-CCC-TTCC
279294 AAAGCCCA
1 AAAGCCCA
279302 CACAAGTCGA
Statistics
Matches: 379, Mismatches: 75, Indels: 46
0.76 0.15 0.09
Matches are distributed among these distances:
27 3 0.01
28 202 0.53
29 38 0.10
30 30 0.08
31 42 0.11
32 51 0.13
33 12 0.03
34 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
AAAGCCCATAAGTCAGTGGCACCCTTCC
Found at i:279014 original size:125 final size:117
Alignment explanation
Indices: 278806--279133 Score: 347
Period size: 125 Copynumber: 2.7 Consensus size: 117
278796 AAAGCCCATA
* * * * * * * *
278806 AGTCAGTGACACCCTTCCAAAGCCCACAAGTTAGTGGC-ACCTTTTCCAAAACCCATAAGTCAGT
1 AGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGT-GCAACC-CTTCCAAAGCCCACAAATTAGT
*
278870 GGCACCCTTTTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTCCAAACCCTACA-
64 GGTACCC-TTTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTCCAAACCCTA-AG
* * * *
278925 AGTCCGTGGCATCCTTGT-AAAGTCCACACAAGTCAGTGGCAACCCTTTCTAAAGTCCACACAAG
1 AGTCAGTGGCACCCTT-TCAAAG-CC-CACAAGTCAGT-GCAACCC-TTCCAAAG-CC-CACAAA
* ** *
278989 TTGGTGGTAACCCTCTTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTTTAAAGCCTAAG
59 TTAGTGGT-ACCCT-TTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTCCAAACCCTAAG
* *
279050 AGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTCCAAAGCCCATAAATTAGTGG
1 AGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGCAACCCTTCCAAAGCCCACAAATTAGTGG
279115 TACCCTTTCAAAGCCCACA
66 TACCCTTTCAAAGCCCACA
279134 AGTCAGTGGA
Statistics
Matches: 176, Mismatches: 22, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
117 13 0.07
118 5 0.03
119 28 0.16
120 4 0.02
121 20 0.11
122 15 0.09
123 13 0.07
124 15 0.09
125 63 0.36
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (117 bp):
AGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGCAACCCTTCCAAAGCCCACAAATTAGTGG
TACCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTCCAAACCCTAAG
Found at i:279114 original size:56 final size:56
Alignment explanation
Indices: 278688--279303 Score: 355
Period size: 56 Copynumber: 10.4 Consensus size: 56
278678 TCACAACTAC
* * * * *
278688 GTGGCACCCTTTTTAAAGCCCACAAGTCAGTGGCATCTTTCTCTAAAGCCCACACAAAT-T
1 GTGGCACCC-TTTCAAAGCCCACAAGTCAGTGGCACCCTT-TC-AAAG-CC-CACAAGTCA
* * *
278748 GATGGCAACCCTTTCTAAAGTCCATACAAAAT-AGTGGCAACCCCCTTT-AAAGCCCATAAGTCA
1 G-TGGC-ACCCTTTC-AAAG-CC-CAC-AAGTCAGTGGC-A--CCCTTTCAAAGCCCACAAGTCA
* * * * * *
278811 GTGACACCCTTCCAAAGCCCACAAGTTAGTGGCACCTTTTCCAAAACCCATAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT-CAAAGCCCACAAGTCA
** ** *
278868 GTGGCACCCTTTTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTCCAAA-CCCTACAAGTCC
1 GTGGCACCC-TTTCAAAG-CC-CACAAGTCAGTGGCA-C-CCTTT-CAAAGCCC-ACAAGTCA
* **
278930 GTGGCATCCTTGT-AAAGTCCACACAAGTCAGTGGCAACCCTTTCTAAAGTCCACACAAGTTG
1 GTGGCACCCTT-TCAAAG-CC-CACAAGTCAGTGGC-ACCCTTTC-AAAG-CC-CACAAGTCA
* ** ** * *
278992 GTGGTAACCCTCTTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTTTAAAGCCTA-AGAGTCA
1 GTGG-CACCCT-TTCAAAG-CC-CACAAGTCAGTGGCA-C--CCTTTCAAAGCCCACA-AGTCA
* * * * *
279055 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTCCAAAGCCCATAAATTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
* * *
279111 GTGGTACCCTTTCAAAGCCCACAAGTCAGTGGAACCCTTTCAAAGCCCATAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
* * * * * * *
279167 GTGGTAGCCC-TTCAAAGTCCAAAAGTTAGTGGCATCTTTTTAAAGCCCACAAGTCA
1 GTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
* * * * * * * *
279223 ATGGCATCCTTTTAAAGCCCATAAGTCAATGGCATCCTTTTAAAGCCCACAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
279279 GTGGCACCCCTTTCTAAAGCCCACA
1 GTGGCA-CCCTTTC-AAAGCCCACA
279304 CAAGTCGATG
Statistics
Matches: 441, Mismatches: 78, Indels: 76
0.74 0.13 0.13
Matches are distributed among these distances:
55 7 0.02
56 154 0.35
57 35 0.08
58 25 0.06
59 17 0.04
60 27 0.06
61 47 0.11
62 59 0.13
63 20 0.05
64 35 0.08
65 8 0.02
66 4 0.01
67 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (56 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
Found at i:279152 original size:84 final size:82
Alignment explanation
Indices: 278790--279303 Score: 316
Period size: 84 Copynumber: 5.9 Consensus size: 82
278780 AGTGGCAACC
* * *
278790 CCCTTT-AAAGCCCATAAGTCAGTGACACCCTTCCAAAGCCCACAAGTTAGTGGCACCTTTTCCA
1 CCCTTTCAAAGCCCATAAGTCAGTGGCACCCTT-CAAAGCCCA-AAATTAGTGGCACCCTTT-CA
* *
278854 AAACCCATAAGTCAGTGGCA
63 AAGCCCACAAGTCAGTGGCA
* ** ** * ** *
278874 CCCTTTTCAAAGCCCACACAAGTTGGTGGCATCTTTTTTCCAAA-CCCTACAAGTCCGTGGCATC
1 CCC-TTTCAAAG-CC-CATAAGTCAGTGGCA-C--CCTT-CAAAGCCC-A-AAATTAGTGGCACC
278938 CTTGT-AAAGTCCACACAAGTCAGTGGCAA
57 CTT-TCAAAG-CC-CACAAGTCAGTGGC-A
* ** * *
278967 CCCTTTCTAAAGTCCACACAAGTTGGTGGTAACCCTCTTCAAAGCCCACACAAGTTGGTGGCATC
1 CCCTTTC-AAAG-CC-CATAAGTCAGTGG-CA-CC-CTTCAAAGCCCA-A-AA-TTAGTGGCA-C
** * *
279032 TTTTTTTTAAAGCCTA-AGAGTCAGTGGCA
56 --CCTTTCAAAGCCCACA-AGTCAGTGGCA
* * *
279061 CCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTCCAAAGCCCATAAATTAGTGGTACCCTTTCAA
1 CCCTTTCAAAGCCCATAAGTCAGTGGCACCCTT-CAAAGCCCA-AAATTAGTGGCACCCTTTCAA
*
279126 AGCCCACAAGTCAGTGGAA
64 AGCCCACAAGTCAGTGGCA
* * * * *
279145 CCCTTTCAAAGCCCATAAGTCAGTGGTAGCCCTTCAAAGTCCAAAAGTTAGTGGCATCTTTTTAA
1 CCCTTTCAAAGCCCATAAGTCAGTGGCA-CCCTTCAAAGCCCAAAA-TTAGTGGCACCCTTTCAA
*
279210 AGCCCACAAGTCAATGGCA
64 AGCCCACAAGTCAGTGGCA
* * * * * *
279229 TCCTTTTAAAGCCCATAAGTCAATGGCATCCTTTTAAAGCCCACAAGTTAGTGGCACCCCTTTCT
1 CCCTTTCAAAGCCCATAAGTCAGTGGCA-CCCTTCAAAGCCCA-AAATTAGTGGCA-CCCTTTC-
279294 AAAGCCCACA
62 AAAGCCCACA
279304 CAAGTCGATG
Statistics
Matches: 342, Mismatches: 58, Indels: 58
0.75 0.13 0.13
Matches are distributed among these distances:
83 3 0.01
84 131 0.38
85 15 0.04
86 15 0.04
87 9 0.03
88 16 0.05
89 13 0.04
90 7 0.02
91 34 0.10
92 27 0.08
93 34 0.10
94 18 0.05
95 11 0.03
96 3 0.01
97 6 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (82 bp):
CCCTTTCAAAGCCCATAAGTCAGTGGCACCCTTCAAAGCCCAAAATTAGTGGCACCCTTTCAAAG
CCCACAAGTCAGTGGCA
Found at i:280698 original size:51 final size:50
Alignment explanation
Indices: 280585--280699 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 50
280575 TGAGTAGTAC
* * *
280585 ATGTATCGATTCATTTTGTTTTTTACCTAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTGTTTTTTACCAAAATGTATCGATACATTTTTCA
* *
280635 ATATATCAATACATTTTGTTTTTTTACCAAAATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTG-TTTTTTACCAAAATGTATCGATACATTTTTCA
*
280686 ATGTATTGATACAT
1 ATGTATCGATACAT
280700 CTAGTTGATT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 15 0.27
51 41 0.73
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (50 bp):
ATGTATCGATACATTTTGTTTTTTACCAAAATGTATCGATACATTTTTCA
Found at i:287171 original size:52 final size:52
Alignment explanation
Indices: 287082--287371 Score: 249
Period size: 52 Copynumber: 5.6 Consensus size: 52
287072 GACAAGAAAG
* * * **
287082 ATAAAGGTGCCAATATGCAGAGTCACA-GCCAATGATATCGAG-CTTAGGAATA
1 ATAAAGATGCCAATATGCTGATTCA-AGGCCAGCGATATCGAGACTTA-GAATA
* * * *
287134 ATAAAGATGCCAATATGTTGATTTAAGGCCAGCGATATCAAG-CTTATGAATGGC
1 ATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGAGACTTA-GAAT--A
* * *
287188 A-AAAG-TTCCAATATGCTGATTCAAGGCCAGCAATATTG-GACTTAGAATA
1 ATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGAGACTTAGAATA
* * * *
287237 ATAAAGATGCTAATATACTGATTCAAGGCCAGCAATATC-AGACTTAAACATGA
1 ATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGAGACTTAGA-AT-A
* * *
287290 CA-AAAG-TGCCAATATGCTGATTTAAGGCCAGTGATATAG-GACTTAAGAATA
1 -ATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGAGACTT-AGAATA
*
287341 ATAAAGATGCCAATATGCTGACTCAAGGCCA
1 ATAAAGATGCCAATATGCTGATTCAAGGCCA
287372 ATAACATTAG
Statistics
Matches: 193, Mismatches: 31, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
49 1 0.01
50 5 0.03
51 46 0.24
52 128 0.66
53 11 0.06
54 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (52 bp):
ATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGAGACTTAGAATA
Found at i:287275 original size:103 final size:103
Alignment explanation
Indices: 287124--287371 Score: 329
Period size: 103 Copynumber: 2.4 Consensus size: 103
287114 TGATATCGAG
* * * * *
287124 CTTAGGAATAATAAAGATGCCAATATGTTGATTTAAGGCCAGCGATATCA-AGCTTATGA-ATGG
1 CTTA-GAATAATAAAGATGCCAATATGCTGATTCAAGGCCAGCAATATCAGA-CTTA-AACATGA
* *
287187 CAAAAGTTCCAATATGCTGATTCAAGGCCAGCAATATTGGA
63 CAAAAGTGCCAATATGCTGATTCAAGGCCAGCAATATAGGA
* *
287228 CTTAGAATAATAAAGATGCTAATATACTGATTCAAGGCCAGCAATATCAGACTTAAACATGACAA
1 CTTAGAATAATAAAGATGCCAATATGCTGATTCAAGGCCAGCAATATCAGACTTAAACATGACAA
* **
287293 AAGTGCCAATATGCTGATTTAAGGCCAGTGATATAGGA
66 AAGTGCCAATATGCTGATTCAAGGCCAGCAATATAGGA
*
287331 CTTAAGAATAATAAAGATGCCAATATGCTGACTCAAGGCCA
1 CTT-AGAATAATAAAGATGCCAATATGCTGATTCAAGGCCA
287372 ATAACATTAG
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
102 1 0.01
103 86 0.68
104 39 0.31
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (103 bp):
CTTAGAATAATAAAGATGCCAATATGCTGATTCAAGGCCAGCAATATCAGACTTAAACATGACAA
AAGTGCCAATATGCTGATTCAAGGCCAGCAATATAGGA
Found at i:287448 original size:32 final size:32
Alignment explanation
Indices: 287395--287737 Score: 180
Period size: 32 Copynumber: 10.7 Consensus size: 32
287385 TGGAAGAGGA
* * *
287395 TGCCTCCAACGTGTGTGGGCTTTTGAGAAGGT
1 TGCCACCAACTTGTGTAGGCTTTTGAGAAGGT
*
287427 TGCCACCAACTTAG-GTAGGC-TTTGAGGAAGAT
1 TGCCACCAACTT-GTGTAGGCTTTTGA-GAAGGT
* * * *
287459 TGACACCAACTTGTGTGGGCTTTGGAAAAAGGT
1 TGCCACCAACTTGTGTAGGCTTTTG-AGAAGGT
* * *
287492 TGCCACCAACTTGTGTGGGC-TTGGAGGAAGAT
1 TGCCACCAACTTGTGTAGGCTTTTGA-GAAGGT
** * * * *
287524 TGCCACTGACTTATGTGGGC-TTTGAAAAAGAT
1 TGCCACCAACTTGTGTAGGCTTTTG-AGAAGGT
* * * * * *
287556 TGCCACTAACTTGTATGGGCTTTGGGGAAGAT
1 TGCCACCAACTTGTGTAGGCTTTTGAGAAGGT
* *
287588 TGCCACCGACTTGTGT-GAGC-TTTGAGGAAGAT
1 TGCCACCAACTTGTGTAG-GCTTTTGA-GAAGGT
* ** * * * * *
287620 TACCACCGGCTTGTATGGGCTTTGGGGAAGAT
1 TGCCACCAACTTGTGTAGGCTTTTGAGAAGGT
* * * *
287652 TGCCACCGACTTGTGTGGGC-TTGGAGGAAGAT
1 TGCCACCAACTTGTGTAGGCTTTTGA-GAAGGT
*
287684 TGCCACCAACTTGTGTGGGC-TTTGAGGAAGGT
1 TGCCACCAACTTGTGTAGGCTTTTGA-GAAGGT
** *
287716 TGCCACTGACTTGTGTGGGCTT
1 TGCCACCAACTTGTGTAGGCTT
287738 AAAAGGATAA
Statistics
Matches: 255, Mismatches: 42, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
31 15 0.06
32 203 0.80
33 36 0.14
34 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (32 bp):
TGCCACCAACTTGTGTAGGCTTTTGAGAAGGT
Found at i:287474 original size:64 final size:62
Alignment explanation
Indices: 287406--287737 Score: 344
Period size: 64 Copynumber: 5.2 Consensus size: 62
287396 GCCTCCAACG
* * *
287406 TGTGTGGGCTTTTGAGAAGGTTGCCACCAACTTAGGTAGGCTTTGAGGAAGATTGACACCAACT
1 TGTGTGGGC-TTTGAGAAGATTGCCACCAACTT-GGTAGGCTTTGAGGAAGATTGCCACCGACT
* * * * *
287470 TGTGTGGGCTTTGGAAAAAGGTTGCCACCAACTTGTGTGGGCTTGGAGGAAGATTGCCACTGACT
1 TGTGTGGGCTTT-G-AGAAGATTGCCACCAACTTG-GTAGGCTTTGAGGAAGATTGCCACCGACT
* * * *
287535 TATGTGGGCTTTGAAAAAGATTGCCACTAACTT-GTATGGGCTTTGGGGAAGATTGCCACCGACT
1 TGTGTGGGCTTTG-AGAAGATTGCCACCAACTTGGTA--GGCTTTGAGGAAGATTGCCACCGACT
* * ** *
287599 TGTGTGAGCTTTGAGGAAGATTACCACCGGCTT-GTATGGGCTTTGGGGAAGATTGCCACCGACT
1 TGTGTGGGCTTTGA-GAAGATTGCCACCAACTTGGTA--GGCTTTGAGGAAGATTGCCACCGACT
* * * *
287663 TGTGTGGGCTTGGAGGAAGATTGCCACCAACTTGTGTGGGCTTTGAGGAAGGTTGCCACTGACT
1 TGTGTGGGCTTTGA-GAAGATTGCCACCAACTTG-GTAGGCTTTGAGGAAGATTGCCACCGACT
287727 TGTGTGGGCTT
1 TGTGTGGGCTT
287738 AAAAGGATAA
Statistics
Matches: 231, Mismatches: 29, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
62 2 0.01
63 4 0.02
64 170 0.74
65 53 0.23
66 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (62 bp):
TGTGTGGGCTTTGAGAAGATTGCCACCAACTTGGTAGGCTTTGAGGAAGATTGCCACCGACT
Found at i:287639 original size:96 final size:97
Alignment explanation
Indices: 287395--287737 Score: 415
Period size: 96 Copynumber: 3.6 Consensus size: 97
287385 TGGAAGAGGA
* * * ** *
287395 TGCCTCCAACGTGTGTGGGCTTTTGA-GAAGGTTGCCACCAACTTAG-GTAGGCTTTGAGGAAGA
1 TGCCACCAACTTGTGTGGGC-TTTGAGGAAGATTGCCACTGACTT-GTGTGGGCTTTGAGGAAGA
* ** *
287458 TTGACACCAACTTGTGTGGGCTTTGGAAAAAGGT
64 TTGCCACCAACTTGTGTGGGCTTTGGAGGAAGAT
* * **
287492 TGCCACCAACTTGTGTGGGCTTGGAGGAAGATTGCCACTGACTTATGTGGGCTTTGAAAAAGATT
1 TGCCACCAACTTGTGTGGGCTTTGAGGAAGATTGCCACTGACTTGTGTGGGCTTTGAGGAAGATT
* *
287557 GCCACTAACTTGTATGGGCTTTGG-GGAAGAT
66 GCCACCAACTTGTGTGGGCTTTGGAGGAAGAT
* * * * * * *
287588 TGCCACCGACTTGTGTGAGCTTTGAGGAAGATTACCACCGGCTTGTATGGGCTTTGGGGAAGATT
1 TGCCACCAACTTGTGTGGGCTTTGAGGAAGATTGCCACTGACTTGTGTGGGCTTTGAGGAAGATT
*
287653 GCCACCGACTTGTGTGGGC-TTGGAGGAAGAT
66 GCCACCAACTTGTGTGGGCTTTGGAGGAAGAT
*
287684 TGCCACCAACTTGTGTGGGCTTTGAGGAAGGTTGCCACTGACTTGTGTGGGCTT
1 TGCCACCAACTTGTGTGGGCTTTGAGGAAGATTGCCACTGACTTGTGTGGGCTT
287738 AAAAGGATAA
Statistics
Matches: 206, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
95 4 0.02
96 132 0.64
97 70 0.34
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (97 bp):
TGCCACCAACTTGTGTGGGCTTTGAGGAAGATTGCCACTGACTTGTGTGGGCTTTGAGGAAGATT
GCCACCAACTTGTGTGGGCTTTGGAGGAAGAT
Found at i:307669 original size:20 final size:21
Alignment explanation
Indices: 307634--307675 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
307624 TATAAAAATA
307634 ATAGTTGAAGTATTTA-TTTT
1 ATAGTTGAAGTATTTAGTTTT
307654 ATAGTGTGAAGT-TTTAGTTTT
1 ATAGT-TGAAGTATTTAGTTTT
307675 A
1 A
307676 ATCAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (21 bp):
ATAGTTGAAGTATTTAGTTTT
Found at i:309998 original size:12 final size:11
Alignment explanation
Indices: 309981--310032 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
309971 TATAAAGGTG
*
309981 GAGAAAATACGA
1 GAGAAAA-AAGA
309993 GAGAAAAAA-A
1 GAGAAAAAAGA
*
310003 GAAAGAAAAAGA
1 GAGA-AAAAAGA
*
310015 AAGAAAAAAGA
1 GAGAAAAAAGA
310026 GAGAAAA
1 GAGAAAA
310033 TAGAAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 4 0.12
11 19 0.58
12 10 0.30
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (11 bp):
GAGAAAAAAGA
Found at i:310011 original size:10 final size:10
Alignment explanation
Indices: 309998--310047 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
309988 TACGAGAGAA
309998 AAAAAGAAAG
1 AAAAAGAAAG
310008 AAAAAGAAAG
1 AAAAAGAAAG
*
310018 AAAAAAGAGAG
1 -AAAAAGAAAG
310029 AAAATAGAAA-
1 AAAA-AGAAAG
310039 AAAAA-AAAG
1 AAAAAGAAAG
310048 CTAAACCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 3 0.09
9 1 0.03
10 18 0.51
11 13 0.37
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:310022 original size:11 final size:11
Alignment explanation
Indices: 309997--310044 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
309987 ATACGAGAGA
309997 AAAAAAGAAAG
1 AAAAAAGAAAG
310008 -AAAAAGAAAG
1 AAAAAAGAAAG
*
310018 AAAAAAGAGAG
1 AAAAAAGAAAG
*
310029 AAAATAGAAA-
1 AAAAAAGAAAG
310039 AAAAAA
1 AAAAAA
310045 AAGCTAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 15 0.47
11 17 0.53
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:310022 original size:22 final size:23
Alignment explanation
Indices: 309982--310047 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 23
309972 ATAAAGGTGG
*
309982 AGAAAATACGAGAGAAAAAAAGAA
1 AGAAAATA-GAAAGAAAAAAAGAA
*
310006 AGAAAA-AGAAAG-AAAAAAGAG
1 AGAAAATAGAAAGAAAAAAAGAA
*
310027 AGAAAATAGAAAAAAAAAAAG
1 AGAAAATAGAAAGAAAAAAAG
310048 CTAAACCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 14 0.38
22 9 0.24
23 8 0.22
24 6 0.16
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.03
Consensus pattern (23 bp):
AGAAAATAGAAAGAAAAAAAGAA
Found at i:310730 original size:34 final size:34
Alignment explanation
Indices: 310658--310723 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
310648 TATATTTTCC
*
310658 ATAGGATTTACTAATTTTTGATGTGTTTAACCAT
1 ATAGGATTTAATAATTTTTGATGTGTTTAACCAT
*
310692 ATAGGATTTAATGATTTTTGATGTGTTTAACC
1 ATAGGATTTAATAATTTTTGATGTGTTTAACC
310724 GAATAGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.47
Consensus pattern (34 bp):
ATAGGATTTAATAATTTTTGATGTGTTTAACCAT
Found at i:313378 original size:18 final size:19
Alignment explanation
Indices: 313348--313395 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
313338 TCACATATAA
313348 TATATGATATAAAAAATTAG
1 TATAT-ATATAAAAAATTAG
*
313368 TATAT-TATAAAAAATTAT
1 TATATATATAAAAAATTAG
313386 TATATATATA
1 TATATATATA
313396 TTTATATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 17 0.65
19 4 0.15
20 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
TATATATATAAAAAATTAG
Found at i:314286 original size:20 final size:20
Alignment explanation
Indices: 314261--314313 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
314251 TCCCGTGTCA
314261 ATGTATCGATACAATTTAGG
1 ATGTATCGATACAATTTAGG
314281 ATGTATCGATACAATTTAGG
1 ATGTATCGATACAATTTAGG
314301 ATGTATCGATACA
1 ATGTATCGATACA
314314 TGCATTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTTAGG
Found at i:314370 original size:13 final size:13
Alignment explanation
Indices: 314352--314379 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
314342 CATTACAAGC
314352 CAATGTATCGATA
1 CAATGTATCGATA
314365 CAATGTATCGATA
1 CAATGTATCGATA
314378 CA
1 CA
314380 TCTTGTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:314486 original size:13 final size:13
Alignment explanation
Indices: 314468--314492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
314458 TACAATAGTC
314468 ATGTATCGATACA
1 ATGTATCGATACA
314481 ATGTATCGATAC
1 ATGTATCGATAC
314493 TGTGCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:316962 original size:13 final size:13
Alignment explanation
Indices: 316944--316981 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
316934 ATAAACCCTT
*
316944 TGTATCGATACAC
1 TGTATCGATACAA
316957 TGTATCGATACAA
1 TGTATCGATACAA
316970 TGTATCGATACA
1 TGTATCGATACA
316982 GAGAATGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:318271 original size:107 final size:107
Alignment explanation
Indices: 318077--318493 Score: 340
Period size: 107 Copynumber: 3.9 Consensus size: 107
318067 AAAAAAAAAT
* * * * * * *
318077 TGGGATTGGAGTATCCC-TTCGAAAATAACGGGGTTGGAGTATCCCCCATTATGAGAAATCAATA
1 TGGGATTGGAGTATCCCGAT-G-AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTA
* * * *
318141 -TTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAA
64 TTTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
* * *
318184 TGGGGTTGGAGTATCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATT
1 TGGGATTGGAGTATCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATT
* *
318249 TTTGGAAATAAAATCGGAGTTGGAGTAT-CCC-C-G-ATTAA
66 TTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
* * * ** *
318287 AGGAAAATTGGCGT-T-TTGA--AAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATT
1 TGG--GATTGGAGTATCCCGATGAAAT--AACGAGG-TTGGAGTATCCCCGATTGT-GAAAAATT
* *
318348 AGTGTTTTAGCG--ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
60 AGTATTTTTG-GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
* * * *
318395 CAGGG-TTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGT
1 -TGGGATTGGAGTAT-CCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAA-AAATTAGT
* * *
318458 GTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCC
63 -ATTTTTGGAAATAAAACCGGAGTTGGAGTATCCCC
318494 GATTATAGAA
Statistics
Matches: 247, Mismatches: 40, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
101 4 0.02
103 14 0.06
104 40 0.16
105 25 0.10
106 48 0.19
107 71 0.29
108 15 0.06
109 28 0.11
110 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (107 bp):
TGGGATTGGAGTATCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATT
TTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
Found at i:318284 original size:52 final size:52
Alignment explanation
Indices: 318215--318551 Score: 203
Period size: 52 Copynumber: 6.4 Consensus size: 52
318205 AAATAACGAG
*
318215 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
318267 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * *
318320 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
318371 GTTGGAGTATCCCC--TCG-GAAATAACAGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTG-AA-AA-A---TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
318426 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
318480 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
*
318531 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
318552 GAGAATTGAT
Statistics
Matches: 216, Mismatches: 43, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
48 1 0.00
49 2 0.01
50 4 0.02
51 39 0.18
52 79 0.37
53 33 0.15
54 28 0.13
55 18 0.08
56 3 0.01
57 8 0.04
58 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:318411 original size:28 final size:27
Alignment explanation
Indices: 318371--318441 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
318361 TAAAACCGGA
**
318371 GTTGGAGTATCCCCTCGGAAATAACAGG
1 GTTGGAGTATCCCCGAGG-AATAACAGG
* * *
318399 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACAGG
318426 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
318442 TTGTGAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACAGG
Found at i:318526 original size:51 final size:53
Alignment explanation
Indices: 318430--318548 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
318420 AACGGGGTTG
* * *
318430 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
318484 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
318535 GAATATCCCCGATT
1 GAGTATCCCCGATT
318549 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:320943 original size:13 final size:13
Alignment explanation
Indices: 320925--320950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
320915 ACAAAGATCC
320925 ATGTATCGATACA
1 ATGTATCGATACA
320938 ATGTATCGATACA
1 ATGTATCGATACA
320951 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:320946 original size:33 final size:33
Alignment explanation
Indices: 320904--320970 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
320894 AAAATTTCCA
***
320904 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
320937 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
320970 A
1 A
320971 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:321015 original size:19 final size:17
Alignment explanation
Indices: 320991--321057 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 17
320981 AGTAGCTAAT
320991 TATGTATCGATACAATACC
1 TATGTATCGATACAA-A-C
321010 TATGTATCGATAC--A-
1 TATGTATCGATACAAAC
321024 T-TGTATCGATACAAAAC
1 TATGTATCGATAC-AAAC
321041 TTATGTATCGATACAAA
1 -TATGTATCGATACAAA
321058 TCATTGAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (17 bp):
TATGTATCGATACAAAC
Found at i:321030 original size:13 final size:13
Alignment explanation
Indices: 321012--321036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
321002 ACAATACCTA
321012 TGTATCGATACAT
1 TGTATCGATACAT
321025 TGTATCGATACA
1 TGTATCGATACA
321037 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:321034 original size:32 final size:32
Alignment explanation
Indices: 320993--321055 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
320983 TAGCTAATTA
*
320993 TGTATCGATACAATACCTATGTATCGATACAT
1 TGTATCGATACAAAACCTATGTATCGATACAT
*
321025 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACCTATGTATCGATACA
321056 AATCATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAAAACCTATGTATCGATACAT
Found at i:321845 original size:55 final size:55
Alignment explanation
Indices: 321761--322290 Score: 668
Period size: 55 Copynumber: 9.4 Consensus size: 55
321751 ATAAACTGTA
* * * *
321761 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
**
321816 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* ** **
321871 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* *
321932 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
321987 TCCTGCTCTTTGAGGATTGGAACATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
** **
322042 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* *
322103 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
322158 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
322213 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTAGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
322268 TCCTGCTCTTTGGGGACTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
322291 GCGGAAGGAG
Statistics
Matches: 418, Mismatches: 42, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
54 2 0.00
55 308 0.74
56 9 0.02
57 2 0.00
60 8 0.02
61 89 0.21
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:321895 original size:26 final size:26
Alignment explanation
Indices: 321807--321896 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
321797 GTGTGGGCTT
* *
321807 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
321833 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
321860 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
321888 TGAAAGGTG
1 TGAAAGGTG
321897 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:321920 original size:29 final size:29
Alignment explanation
Indices: 321833--321921 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
321823 CTTTGAGGAC
321833 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
321862 T-AAGAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGG-CTT
321888 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
321917 TGAAA
1 TGAAA
321922 AGAAAAAGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 8 0.18
28 8 0.18
29 14 0.31
30 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:321974 original size:171 final size:170
Alignment explanation
Indices: 321760--322263 Score: 818
Period size: 171 Copynumber: 2.9 Consensus size: 170
321750 AATAAACTGT
* * * *
321760 ATCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAA-CTCGTGTGGGCTTTGAAAGGCGTCCTGCT
1 ATCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACCT-GTGTGGGCTTTAAAAGGTGTCCTGCT
* * *
321823 CTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGGGGA
64 CTTTGAGGATTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGA
321887 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
127 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
321931 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
*
321996 TTGAGGATTGGAACATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
66 TTGAGGATT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
322061 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
130 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
322102 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
322167 TTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
66 TTGAGGATT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-
* * *
322232 GAAA-ATGCCACCAACTTATGTAGGCTTTGAAA
129 GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
322264 GGTGTCCTGC
Statistics
Matches: 316, Mismatches: 12, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
171 300 0.95
172 16 0.05
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (170 bp):
ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
TTGAGGATTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGA
AAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
Found at i:322164 original size:226 final size:222
Alignment explanation
Indices: 321761--322289 Score: 731
Period size: 226 Copynumber: 2.3 Consensus size: 222
321751 ATAAACTGTA
* * * * *
321761 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* ** *
321825 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTG
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAAGCATCCTGCTCTTTGAGGACTG
** *
321890 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAA
130 AAAAATGCCACCAACCTGTGTGGGCTTTGAAAAG----AGCATCCTGCTCTTTGAGGACTGAAAA
321955 ATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
191 ATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
* *
321987 TCCTGCTCTTTGAGGATTGGAACATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
322052 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---AAG---AAGCATCCTGCTCTTTGAG
** * *
322117 GACTGAAAAATGCCACCAACCTGTGTGGGCTTT-AAAAG-GTGTCCTGCTCTTTGAGGATTGGAA
125 GACTGAAAAATGCCACCAACCTGTGTGGGCTTTGAAAAGAGCATCCTGCTCTTTGAGGACTGAAA
* *
322180 AATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
190 AATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
* *
322213 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTAGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
322278 TGGGGACTGAAA
66 TGAGGACTGAAA
322290 AGCGGAAGGA
Statistics
Matches: 272, Mismatches: 24, Indels: 14
0.88 0.08 0.05
Matches are distributed among these distances:
226 216 0.79
227 3 0.01
229 3 0.01
231 5 0.02
232 45 0.17
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (222 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAAGCATCCTGCTCTTTGAGGACTGA
AAAATGCCACCAACCTGTGTGGGCTTTGAAAAGAGCATCCTGCTCTTTGAGGACTGAAAAATGCC
ACCAACCTGTGTGGGCTTTAAAAGGTG
Found at i:323281 original size:9 final size:8
Alignment explanation
Indices: 323252--323321 Score: 63
Period size: 8 Copynumber: 8.8 Consensus size: 8
323242 CTTAAGTAGG
323252 TTTTTTC-
1 TTTTTTCT
*
323259 TTTTCTCT
1 TTTTTTCT
*
323267 CTTTTTCT
1 TTTTTTCT
*
323275 TTGTTTTGT
1 TT-TTTTCT
*
323284 TTTTTTGT
1 TTTTTTCT
323292 TTTTTTCCT
1 TTTTTT-CT
323301 TTTTTT-T
1 TTTTTTCT
*
323308 TTTTTGCT
1 TTTTTTCT
323316 TTTTTT
1 TTTTTT
323322 TTGAAGAGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
7 12 0.24
8 25 0.49
9 14 0.27
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:323292 original size:13 final size:12
Alignment explanation
Indices: 323268--323323 Score: 60
Period size: 13 Copynumber: 4.6 Consensus size: 12
323258 CTTTTCTCTC
*
323268 TTTTTCTTTGTT
1 TTTTTTTTTGTT
323280 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
**
323293 TTTTTCCTT-TT
1 TTTTTTTTTGTT
323304 TTTTTTTTTGCTT
1 TTTTTTTTTG-TT
323317 TTTTTTT
1 TTTTTTT
323324 GAAGAGAAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 9 0.25
12 7 0.19
13 20 0.56
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:323321 original size:15 final size:15
Alignment explanation
Indices: 323267--323323 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
323257 TCTTTTCTCT
*
323267 CTTTTTCTTTGTTTTG
1 CTTTTT-TTTTTTTTG
* *
323283 TTTTTTTGTTTTTTTC
1 CTTTTTT-TTTTTTTG
323299 CTTTTTTTTTTTTTG
1 CTTTTTTTTTTTTTG
323314 CTTTTTTTTT
1 CTTTTTTTTT
323324 GAAGAGAAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 18 0.51
16 17 0.49
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (15 bp):
CTTTTTTTTTTTTTG
Found at i:338779 original size:19 final size:18
Alignment explanation
Indices: 338750--338801 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
338740 GAGCTATTAA
* *
338750 ATGTA-CGATACATACTT
1 ATGTATCGATACAAACGT
338767 ATGTAATCGATACAAAACGT
1 ATGT-ATCGATAC-AAACGT
338787 ATGTATCGATACAAA
1 ATGTATCGATACAAA
338802 TCGTTGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.13
18 4 0.13
19 14 0.47
20 8 0.27
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (18 bp):
ATGTATCGATACAAACGT
Found at i:339175 original size:56 final size:55
Alignment explanation
Indices: 339043--339348 Score: 344
Period size: 54 Copynumber: 5.6 Consensus size: 55
339033 ATAAACTGTA
* * *
339043 TCCT-CTCTTTGAGGACTGAAAAAT-CCAGCCAACCTGTGTGGGCCTTT-TAAGGT-
1 TCCTGCTCTTTGAGGACTGGAAAATGCCA-CCAACTTGTGTGGG-CTTTGAAAGGTG
* *
339096 TCCTGCTCGTTGAGGAGTGGAAAAGTGCC-CCAACTTGTGTGGGCTTTGAAAAGGTTG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTG-AAAGG-TG
339153 TCCTGCTC-TTGAGGACTGGAAAATGCCACCAACTACTGTG-GGGCTTTGAAAGGT-
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACT--TGTGTGGGCTTTGAAAGGTG
* * * *
339207 TCCTGCTCTTTG-GGACTGAAAAATGCCACCAACCTGGTGTGGGCCTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAA-CTTGTGTGGGCTTTGAAAGGTG
* *
339262 T-CTGCTCTTTGAGGATTGGAAAAATGCCACCAACTTGTGTGGGCGTTGAAAGGTGG
1 TCCTGCTCTTTGAGGACTGG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGT-G
*
339318 TCCTGCTCTATGAGGACTGGAAAATGCCACC
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACC
339349 CCGACTTATG
Statistics
Matches: 218, Mismatches: 17, Indels: 33
0.81 0.06 0.12
Matches are distributed among these distances:
53 11 0.05
54 78 0.36
55 39 0.18
56 54 0.25
57 32 0.15
58 4 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:339258 original size:110 final size:111
Alignment explanation
Indices: 339043--339348 Score: 355
Period size: 110 Copynumber: 2.8 Consensus size: 111
339033 ATAAACTGTA
* *
339043 TCCT-CTCTTTGAGGACTGAAAAAT-CCAGCCAAC-CTGTGTGGGCCTTT-TAAGGTTCCTGCTC
1 TCCTGCTCTTTGAGGACTGGAAAATGCCA-CCAACTCTGTGTGGG-CTTTGAAAGGTTCCTGCTC
* * * * *
339104 GTTGAGGAGTGGAAAAGTGCC-CCAACTTGTGTGGGCTTTGAAAAGGTTG
64 TTTGAGGACT-GAAAAATGCCACCAACTGGTGTGGGCCTTGAAAAGG-TG
339153 TCCTGCTC-TTGAGGACTGGAAAATGCCACCAACTACTGTG-GGGCTTTGAAAGGTTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACT-CTGTGTGGGCTTTGAAAGGTTCCTGCTCT
339216 TTG-GGACTGAAAAATGCCACCAACCTGGTGTGGGCCTT-AAAAGGTG
65 TTGAGGACTGAAAAATGCCACCAA-CTGGTGTGGGCCTTGAAAAGGTG
* *
339262 T-CTGCTCTTTGAGGATTGGAAAAATGCCACCAACT-TGTGTGGGCGTTGAAAGGTGGTCCTGCT
1 TCCTGCTCTTTGAGGACTGG-AAAATGCCACCAACTCTGTGTGGGCTTTGAAAGGT--TCCTGCT
* *
339325 CTATGAGGACTGGAAAATGCCACC
63 CTTTGAGGACTGAAAAATGCCACC
339349 CCGACTTATG
Statistics
Matches: 172, Mismatches: 11, Indels: 24
0.83 0.05 0.12
Matches are distributed among these distances:
108 10 0.06
109 35 0.20
110 57 0.33
111 48 0.28
112 22 0.13
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (111 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCTGTGTGGGCTTTGAAAGGTTCCTGCTCTT
TGAGGACTGAAAAATGCCACCAACTGGTGTGGGCCTTGAAAAGGTG
Found at i:340437 original size:15 final size:15
Alignment explanation
Indices: 340412--340440 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
340402 TTTTGTTCCT
340412 TTTTTTTTTTTTTGC
1 TTTTTTTTTTTTTGC
340427 TTTTTTTTTTTTTG
1 TTTTTTTTTTTTTG
340441 AAGAGAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTTTTTGC
Found at i:340437 original size:16 final size:16
Alignment explanation
Indices: 340395--340439 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
340385 TTTGTGTGTG
* *
340395 TTTTTTGTTTTGTTCC
1 TTTTTTTTTTTTTTCC
*
340411 TTTTTTTTTTTTTTGC
1 TTTTTTTTTTTTTTCC
340427 TTTTTTTTTTTTT
1 TTTTTTTTTTTTT
340440 GAAGAGAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (16 bp):
TTTTTTTTTTTTTTCC
Done.