Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold367
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: 914901
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 5
Found at i:180812 original size:13 final size:13
Alignment explanation
Indices: 180794--180820 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
180784 TACAATGAAC
180794 ATGTATCGATACA
1 ATGTATCGATACA
180807 ATGTATCGATACA
1 ATGTATCGATACA
180820 A
1 A
180821 AGCATAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:180868 original size:20 final size:20
Alignment explanation
Indices: 180829--180868 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
180819 AAAGCATAAA
**
180829 GTATCGATACATCTGGGGGT
1 GTATCGATACATCTACGGGT
*
180849 GTATCGATACATTTACGGGT
1 GTATCGATACATCTACGGGT
180869 TTTGACCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (20 bp):
GTATCGATACATCTACGGGT
Found at i:183302 original size:13 final size:13
Alignment explanation
Indices: 183284--183309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
183274 ATTTTTTTTG
183284 TGTATCGATACAT
1 TGTATCGATACAT
183297 TGTATCGATACAT
1 TGTATCGATACAT
183310 ATTTTGTGTA
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):
TGTATCGATACAT
Found at i:183432 original size:20 final size:20
Alignment explanation
Indices: 183379--183434 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
183369 ACATCTTTTT
*
183379 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
183399 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
183418 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
183435 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:184227 original size:22 final size:22
Alignment explanation
Indices: 184202--184243 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
184192 AGATAAACAT
184202 ATTTCTCCCCTTTTATCAAAGC
1 ATTTCTCCCCTTTTATCAAAGC
* *
184224 ATTTCTCCCTTTTTGTCAAA
1 ATTTCTCCCCTTTTATCAAA
184244 TCAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTTCTCCCCTTTTATCAAAGC
Found at i:188665 original size:120 final size:120
Alignment explanation
Indices: 188452--188691 Score: 462
Period size: 120 Copynumber: 2.0 Consensus size: 120
188442 AAAAATACCT
* *
188452 TCATCACTTTTAGCTTCGAATTTACCAAGATTGTCTTTTCCATTATTTAAAATAAAACATTTGCA
1 TCATCACTTTTAGCATCGAATTTACCAAGATTGTCTTTTCCATTATTTAAAACAAAACATTTGCA
188517 TCCAAAAGGATGAAAATAACTTATGTTAGGCCTTTTTCCTTTGTAAAGCTCATAA
66 TCCAAAAGGATGAAAATAACTTATGTTAGGCCTTTTTCCTTTGTAAAGCTCATAA
188572 TCATCACTTTTAGCATCGAATTTACCAAGATTGTCTTTTCCATTATTTAAAACAAAACATTTGCA
1 TCATCACTTTTAGCATCGAATTTACCAAGATTGTCTTTTCCATTATTTAAAACAAAACATTTGCA
188637 TCCAAAAGGATGAAAATAACTTATGTTAGGCCTTTTTCCTTTGTAAAGCTCATAA
66 TCCAAAAGGATGAAAATAACTTATGTTAGGCCTTTTTCCTTTGTAAAGCTCATAA
188692 GAAGTTTTCT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 118 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (120 bp):
TCATCACTTTTAGCATCGAATTTACCAAGATTGTCTTTTCCATTATTTAAAACAAAACATTTGCA
TCCAAAAGGATGAAAATAACTTATGTTAGGCCTTTTTCCTTTGTAAAGCTCATAA
Found at i:191127 original size:19 final size:20
Alignment explanation
Indices: 191083--191132 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
191073 ACGCCCAGAT
* *
191083 GTATCAATACATATTGCTTT
1 GTATCGATACATATTGCTTA
*
191103 GTATCGATACATGTT-CTTA
1 GTATCGATACATATTGCTTA
191122 GTATCGATACA
1 GTATCGATACA
191133 CACTAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
GTATCGATACATATTGCTTA
Found at i:201320 original size:17 final size:18
Alignment explanation
Indices: 201298--201336 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
201288 CCACCTTTTT
* *
201298 AAAAAAATAAAA-AAATA
1 AAAAAAACAAAACAAAGA
201315 AAAAAAACAAAACAAAGA
1 AAAAAAACAAAACAAAGA
201333 AAAA
1 AAAA
201337 TGAGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.87, C:0.05, G:0.03, T:0.05
Consensus pattern (18 bp):
AAAAAAACAAAACAAAGA
Found at i:202491 original size:55 final size:54
Alignment explanation
Indices: 202421--202796 Score: 239
Period size: 61 Copynumber: 6.4 Consensus size: 54
202411 CTCTTTTCAC
* * * * * *
202421 CCTTTAGTCCTCAAAGAGCAGGACGTCTTTCAAAGCCTATACCAGTTGATGGCA
1 CCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGATGGCA
** * *
202475 TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGCTGGTGGCA
1 CCTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGATGGCA
* * *
202530 CCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGCTGATGGCA
* * * * *
202590 CTTTCCAGTCCTCAAAGAGCGGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTT-CAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGCTGATGGCA
* * * *
202651 CCTTCAGTCCTCAAAGAGTAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGCTGATGGCA
* * ** *
202711 CTTTTCTAGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACACAAATTGGTGGCA
1 C-CTTC-AGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGCTGATGGCA
*
202773 CCTTTCAGTCCTTAAAGAGCAGGA
1 CC-TTCAGTCCTCAAAGAGCAGGA
202797 TGCTTTCTCC
Statistics
Matches: 276, Mismatches: 29, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
54 25 0.09
55 47 0.17
56 1 0.00
60 67 0.24
61 76 0.28
62 55 0.20
65 3 0.01
66 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (54 bp):
CCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGATGGCA
Found at i:202506 original size:27 final size:27
Alignment explanation
Indices: 202476--202559 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
202466 TTGATGGCAT
202476 TTTCCAGTCCTCAAAGAGCAGGATGCC
1 TTTCCAGTCCTCAAAGAGCAGGATGCC
* * * * *
202503 TTTCAAAGCCCACACA-AGCTGG-TGGCAC
1 TTTC-CAGTCCTCAAAGAGCAGGAT-GC-C
*
202531 CTT-CAGTCCTCAAAGAGCAGGATGCC
1 TTTCCAGTCCTCAAAGAGCAGGATGCC
202557 TTT
1 TTT
202560 TCCTTTTAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 11
0.63 0.19 0.17
Matches are distributed among these distances:
26 11 0.28
27 18 0.45
28 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGATGCC
Found at i:202625 original size:61 final size:61
Alignment explanation
Indices: 202477--202991 Score: 595
Period size: 61 Copynumber: 8.6 Consensus size: 61
202467 TGATGGCATT
* *
202477 TTCCAGTCCTCAAAGAGCAGGATGCC-TTT-C----AAAGCCCACACAAGCTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
202532 TT-CAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
202592 TTCCAGTCCTCAAAGAGCGGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* ** *
202653 TT-CAGTCCTCAAAGAGTAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-C
* * *
202714 TTCTAGTCCTCAAAGAGCAGGACGCATTTTCCTTTTAAAGCCCACACAAATTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
202775 TTTCAGTCCTTAAAGAGCAGGATG-CTTTCTCCTTTTAAAGACCACAAAAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * * *
202836 TTCCAATCCTCAAAAAGCAAGATG-C-TTTCTCTTTGCAAAGCCCACACACGTAGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTC-CTTT-TAAAGCCCACACAAGTTGGTGGCACC
* * * * * *
202897 TTCCAGTCCTCAAAAAGCAAGATGCCTTTT-CTTTTCAAAGCCCACACGAGTTGGTAGCACT
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACC
** *
202958 TTTTAGTCCTCAAAGAGCAGGACGCATTTTCCTT
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
202992 CTCTCCTTTA
Statistics
Matches: 395, Mismatches: 49, Indels: 25
0.84 0.10 0.05
Matches are distributed among these distances:
54 23 0.06
55 5 0.01
56 1 0.00
59 2 0.01
60 86 0.22
61 219 0.55
62 56 0.14
63 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (61 bp):
TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:203215 original size:41 final size:41
Alignment explanation
Indices: 202963--203317 Score: 215
Period size: 41 Copynumber: 8.5 Consensus size: 41
202953 GCACTTTTTA
* *
202963 GTCCTCAAAGAGCAGGACGCA--T--TTTCCTTCTCTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTAATTTCCTT-TTTCCTTT
* * *
203001 ATTCTCAAAGAGCAGGACATA-TTACATTTCCTTTTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACACATTTA-ATTTCC--TTTTT-CC-TTT
* * * * * *
203046 GTCCTCAAAGAGCGGGACGCCTTT-TTTTCTTTTTTCTTTT
1 GTCCTCAAAGAGCAGGACACATTTAATTTCCTTTTTCCTTT
* * * *
203086 GTCCTCAAAGAGCAAGACACACTTCATTTTCTTCTTTTCCCTTCT
1 GTCCTCAAAGAGCAGGACACA-TTTAATTTC--CTTTTTCCTT-T
* *
203131 AGTTCTCAAAGAGCAGGACGCACTTT-ATTCTCCTTTTTCCTTT
1 -GTCCTCAAAGAGCAGGACACA-TTTAATT-TCCTTTTTCCTTT
*
203174 GTCCTCAAAAAGCAGGACACATTTAATTTCCTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTAATTTCCTTTTTCCTTT
* * ** * *
203215 GTCTTCAAAGGGCAGGATGCATTTTATTTCCTTTTTGCCTTA
1 GTCCTCAAAGAGCAGGACACATTTAATTTCCTTTTT-CCTTT
* * * * * *
203257 GTCC-CCAAGAAGTAGGACCCATTTCA-TTCTCATTTTCCTTA
1 GTCCTCAAAG-AGCAGGACACATTTAATTTC-CTTTTTCCTTT
* *
203298 ATCCTCAAAAAGCAGGACAC
1 GTCCTCAAAGAGCAGGACAC
203318 CTCCTTCCTT
Statistics
Matches: 245, Mismatches: 51, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
38 17 0.07
39 1 0.00
40 20 0.08
41 72 0.29
42 62 0.25
43 3 0.01
44 24 0.10
45 21 0.09
46 25 0.10
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (41 bp):
GTCCTCAAAGAGCAGGACACATTTAATTTCCTTTTTCCTTT
Found at i:203293 original size:83 final size:83
Alignment explanation
Indices: 203136--203315 Score: 202
Period size: 83 Copynumber: 2.2 Consensus size: 83
203126 CTTCTAGTTC
* *
203136 TCAAAGAGCAGGACGCACTTTATTCTCCTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTAAT
1 TCAAAGAGCAGGACGCACTTTATTCTCCTTTTTCCTTAGTCCCCAAAAAGCAGGACACATTTAAT
*
203201 TTCCTTTTTCCTTTGTCT
66 TTCCATTTTCCTTTGTCT
* * * * * * *
203219 TCAAAGGGCAGGATGCATTTTATT-TCCTTTTTGCCTTAGTCCCCAAGAAGTAGGACCCATTTCA
1 TCAAAGAGCAGGACGCACTTTATTCTCCTTTTT-CCTTAGTCCCCAAAAAGCAGGACACATTTAA
** *
203283 -TTCTCATTTTCCTTAATCC
65 TTTC-CATTTTCCTTTGTCT
*
203302 TCAAAAAGCAGGAC
1 TCAAAGAGCAGGAC
203316 ACCTCCTTCC
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
82 11 0.14
83 68 0.86
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (83 bp):
TCAAAGAGCAGGACGCACTTTATTCTCCTTTTTCCTTAGTCCCCAAAAAGCAGGACACATTTAAT
TTCCATTTTCCTTTGTCT
Found at i:203974 original size:49 final size:49
Alignment explanation
Indices: 203842--203974 Score: 221
Period size: 49 Copynumber: 2.7 Consensus size: 49
203832 TTTCACAATT
* * *
203842 TGTATCGATACATTGTTCATTATATCGATGCATTATGGGTTTACCCAGA
1 TGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTACCCAGA
203891 TGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTACCCAGA
1 TGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTACCCAGA
* *
203940 TGTATCGATACATTTTTCAATGTATCGATACATTC
1 TGTATCGATACATTGTTCATTGTATCGATACATTC
203975 AGGCATTTTG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 79 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (49 bp):
TGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTACCCAGA
Found at i:206624 original size:51 final size:51
Alignment explanation
Indices: 206359--206624 Score: 172
Period size: 51 Copynumber: 5.3 Consensus size: 51
206349 TCATTTCTGA
* * * *
206359 GGGGATACTCCAACCCTGGTTTTATTTCTAAAACACCAATTT-TCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTCT-CACAATC
* * * * *
206410 GGGGATAATCCAACTCCGATTTTATTT-TCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACATCGATTTCTCACAATC
* * * * ** ** *
206461 GAGGATACTCCAACCTC-ATTAT-TTTATCCAACCCCGTTATTTCT---GA--
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCG--ATTTCTCACAATC
** * ** * *
206507 GGAAATACTCCAAACCCGGCTTTATTTCTAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTCTCACAATC
* * *
206558 GGGGATACTCCAACCCCGATTTTATTTCTAAAGCATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTCTCACAATC
*
206609 GGGGATACTCTAACCC
1 GGGGATACTCCAACCC
206625 TGTTATTTTC
Statistics
Matches: 161, Mismatches: 42, Indels: 24
0.71 0.19 0.11
Matches are distributed among these distances:
46 18 0.11
47 2 0.01
48 8 0.05
49 9 0.06
50 6 0.04
51 117 0.73
52 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTCTCACAATC
Found at i:206633 original size:148 final size:148
Alignment explanation
Indices: 206340--206623 Score: 367
Period size: 148 Copynumber: 1.9 Consensus size: 148
206330 CGATGAAACA
* ** *
206340 CCAACCTCGTCATTTCTGAGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACCAATTTTCCA
1 CCAACCCCGTCATTTCTGAGGAAATACTCCAACCCTGGCTTTATTTCTAAAACACCAATTTTCCA
*
206405 CAATCGGGGATAATCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATACT
66 CAATCGGGGATAATCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATACT
206470 CCAACCTCATTATTTTAT
131 CCAACCTCATTATTTTAT
* * ***
206488 CCAACCCCGTTATTTCTGAGGAAATACTCCAAACCC-GGCTTTATTTCTAAAATATTGA-TTTCT
1 CCAACCCCGTCATTTCTGAGGAAATACTCC-AACCCTGGCTTTATTTCTAAAACACCAATTTTC-
* * * * * *
206551 CACAATCGGGGATACTCCAACCCCGATTTTA-TTTCTAAAGCATCGATTTTTCATAATCGGGGAT
64 CACAATCGGGGATAATCCAACCCCGATTTTATTTTC-AAAACACCAATTTTTCACAATCGAGGAT
*
206615 ACTCTAACC
128 ACTCCAACC
206624 CTGTTATTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
147 8 0.07
148 103 0.89
149 5 0.04
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (148 bp):
CCAACCCCGTCATTTCTGAGGAAATACTCCAACCCTGGCTTTATTTCTAAAACACCAATTTTCCA
CAATCGGGGATAATCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATACT
CCAACCTCATTATTTTAT
Found at i:206716 original size:78 final size:78
Alignment explanation
Indices: 206558--206774 Score: 294
Period size: 78 Copynumber: 2.8 Consensus size: 78
206548 TCTCACAATC
* *
206558 GGGGATACTCCAACCCCGATTTTATTTCTAAAGCA-TCGATTTT-TCATAATCGGGGATACTCTA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACT-G-TTTTCT-ATAATCGGGGATACTCCA
*
206621 ACCCTGTTATTTTCGA
63 ACCCTGTTATTTCCGA
*
206637 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTGTTTTCTATAATCAGGGATACTCCAACC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTGTTTTCTATAATCGGGGATACTCCAACC
206702 CTGTTATTTCCGA
66 CTGTTATTTCCGA
* * * ** *
206715 GGGGATACTCCAACCCCGATTTTACTTCCAGAACACCAATTTTCCATAATCGGGGATACT
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACA-CTGTTTTCTATAATCGGGGATACT
206775 TCAGCCCCGT
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
78 67 0.54
79 56 0.45
80 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTGTTTTCTATAATCGGGGATACTCCAACC
CTGTTATTTCCGA
Found at i:213008 original size:34 final size:35
Alignment explanation
Indices: 212944--213010 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
212934 ATCATTACTC
212944 TTCATTCTTCATCAAAATCTTCATCAAAAACTAGTT
1 TTCATTC-TCATCAAAATCTTCATCAAAAACTAGTT
*
212980 TTCATTC-CATC-AAATCTTTCATCCAAAACTA
1 TTCATTCTCATCAAAATC-TTCATCAAAAACTA
213011 CCAAAAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 5 0.17
34 17 0.59
36 7 0.24
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.37
Consensus pattern (35 bp):
TTCATTCTCATCAAAATCTTCATCAAAAACTAGTT
Found at i:215342 original size:20 final size:22
Alignment explanation
Indices: 215301--215345 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
215291 GTTAAGTATA
215301 AATGTTTTTCAAGCATAAAAAT
1 AATGTTTTTCAAGCATAAAAAT
*
215323 AATG-TTTTCAAGTA-AAAAAT
1 AATGTTTTTCAAGCATAAAAAT
215343 AAT
1 AAT
215346 TCAAAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 9 0.41
22 4 0.18
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.36
Consensus pattern (22 bp):
AATGTTTTTCAAGCATAAAAAT
Found at i:223881 original size:22 final size:21
Alignment explanation
Indices: 223851--223904 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
223841 TATTTCATGT
223851 AAAT-ATTATTAAATAATTATC-
1 AAATAATTATTAAAT--TTATCA
*
223872 AAATAATTATTTAATTTATCA
1 AAATAATTATTAAATTTATCA
223893 GAAATAATTATT
1 -AAATAATTATT
223905 CGACCCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 4 0.14
22 20 0.69
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
AAATAATTATTAAATTTATCA
Found at i:227938 original size:7 final size:7
Alignment explanation
Indices: 227929--227963 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
227919 GCACCTGCAC
*
227929 GTGCCAC
1 GTGCCAA
227936 GTGTCCAA
1 GTG-CCAA
227944 GTGCCAA
1 GTGCCAA
227951 GTGCCAA
1 GTGCCAA
227958 GTGCCA
1 GTGCCA
227964 TATAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.23, C:0.31, G:0.29, T:0.17
Consensus pattern (7 bp):
GTGCCAA
Found at i:238675 original size:2 final size:2
Alignment explanation
Indices: 238668--238698 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
238658 CACAAGAAAA
238668 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
238699 AACTGAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:241722 original size:17 final size:16
Alignment explanation
Indices: 241702--241733 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
241692 AAGAAGGAAA
241702 AAATGAATGTAACAAAC
1 AAATGAAT-TAACAAAC
241719 AAATGAATTAACAAA
1 AAATGAATTAACAAA
241734 AAAAACACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (16 bp):
AAATGAATTAACAAAC
Found at i:249656 original size:2 final size:2
Alignment explanation
Indices: 249651--249676 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
249641 TGTGTGTGTG
249651 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
249677 GGTTATTTTG
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:251381 original size:13 final size:13
Alignment explanation
Indices: 251363--251387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
251353 ATTCAAATAT
251363 TTTTTAAAAGTAC
1 TTTTTAAAAGTAC
251376 TTTTTAAAAGTA
1 TTTTTAAAAGTA
251388 AAATAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAGTAC
Found at i:253220 original size:14 final size:14
Alignment explanation
Indices: 253189--253269 Score: 69
Period size: 14 Copynumber: 5.8 Consensus size: 14
253179 AAATTTGTCT
*
253189 ATATTTTTTAA-AA
1 ATATTTTTTAATTA
253202 TATATTTTTTAATTA
1 -ATATTTTTTAATTA
**
253217 ATATTTAATAATTTA
1 ATATTTTTTAA-TTA
253232 ATATTTTTT-ATTA
1 ATATTTTTTAATTA
**
253245 A-ATTTTTTTGTTA
1 ATATTTTTTAATTA
253258 ATATTATTTTAA
1 ATATT-TTTTAA
253270 AAGTGCATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
12 7 0.13
13 8 0.15
14 24 0.44
15 15 0.28
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (14 bp):
ATATTTTTTAATTA
Found at i:253510 original size:18 final size:20
Alignment explanation
Indices: 253478--253516 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
253468 TTCTTCGATT
253478 TTTTTTAAATATTAAATAAA
1 TTTTTTAAATATTAAATAAA
253498 TTTTTT-AAT-TTAAATAAA
1 TTTTTTAAATATTAAATAAA
253516 T
1 T
253517 AGCTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTTAAATATTAAATAAA
Found at i:254531 original size:37 final size:37
Alignment explanation
Indices: 254402--254583 Score: 152
Period size: 37 Copynumber: 4.8 Consensus size: 37
254392 ATAAGTTAGC
* * *
254402 ACAAAAATTACTATTTTAATCCGGTGGCAC-GGTTCGAA
1 ACAAAAACTACTATTTTTA-CCGGTGGCACAGG-TCGGA
* * *
254440 ACAAAAACTACTATTCTTACCGATGGCACATGTTGGTTGGA
1 ACAAAAACTACTATTTTTACCGGTGGCACA----GGTCGGA
* * *
254481 ACAAAAACAACTATTTTTACCAGTAGCACAGGTCGGA
1 ACAAAAACTACTATTTTTACCGGTGGCACAGGTCGGA
* * *
254518 ACAAAAACTACTATTTTTACCGGTGGCACAGATTGAA
1 ACAAAAACTACTATTTTTACCGGTGGCACAGGTCGGA
* * *
254555 ATAAAAA-TCACTATTCTTACCGATGGCAC
1 ACAAAAACT-ACTATTTTTACCGGTGGCAC
254584 GGTTGAAACC
Statistics
Matches: 117, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
36 1 0.01
37 70 0.60
38 16 0.14
41 28 0.24
42 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (37 bp):
ACAAAAACTACTATTTTTACCGGTGGCACAGGTCGGA
Found at i:257033 original size:21 final size:21
Alignment explanation
Indices: 257009--257050 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
256999 AAAATATTTT
257009 TATTTAAAT-TTAATTATAAAA
1 TATTTAAATATT-ATTATAAAA
257030 TATTTAAATATTATTATAAAA
1 TATTTAAATATTATTATAAAA
257051 ATAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTTAAATATTATTATAAAA
Found at i:257063 original size:24 final size:24
Alignment explanation
Indices: 257031--257079 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
257021 ATTATAAAAT
257031 ATTTAAATATTATTATAAA-AATAA
1 ATTTAAATATT-TTATAAATAATAA
* *
257055 ATTTTAATATTTTTTAAATAATAA
1 ATTTAAATATTTTATAAATAATAA
257079 A
1 A
257080 ATAAATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTAAATATTTTATAAATAATAA
Found at i:264869 original size:2 final size:2
Alignment explanation
Indices: 264851--264883 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
264841 TTCAAAAACT
*
264851 TA TA T- TA TA TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
264884 GAATGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:265302 original size:18 final size:20
Alignment explanation
Indices: 265280--265327 Score: 82
Period size: 18 Copynumber: 2.5 Consensus size: 20
265270 TAAAAATTAG
265280 AAATATAATTCAATT-AAAT
1 AAATATAATTCAATTAAAAT
265299 -AATATAATTCAATTAAAAT
1 AAATATAATTCAATTAAAAT
265318 AAATATAATT
1 AAATATAATT
265328 ATTTAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.52
19 4 0.15
20 9 0.33
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATAATTCAATTAAAAT
Found at i:270520 original size:2 final size:2
Alignment explanation
Indices: 270513--270537 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
270503 ACACTAGGCA
270513 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
270538 GTATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:271036 original size:16 final size:16
Alignment explanation
Indices: 271003--271038 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
270993 TCAAATTTAT
*
271003 ATTTAAAATAATTAAA
1 ATTTAAAATAATCAAA
*
271019 ATTTAAAATAATCGAA
1 ATTTAAAATAATCAAA
271035 ATTT
1 ATTT
271039 GATACAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTTAAAATAATCAAA
Found at i:275021 original size:2 final size:2
Alignment explanation
Indices: 275014--275041 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
275004 TGGTTCACGA
275014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
275042 TTTAATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:275445 original size:14 final size:15
Alignment explanation
Indices: 275419--275447 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
275409 ATATATTTGA
275419 TTTAATGATATAATT
1 TTTAATGATATAATT
275434 TTTAAT-ATATAATT
1 TTTAATGATATAATT
275448 AATAAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTAATGATATAATT
Found at i:277144 original size:13 final size:13
Alignment explanation
Indices: 277109--277159 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
277099 TATATTCTAT
277109 ATAATATA-AATAA
1 ATAATATATAA-AA
*
277122 CATAATATATAAAT
1 -ATAATATATAAAA
*
277136 ATAAAATATAAAA
1 ATAATATATAAAA
277149 ATAATATATAA
1 ATAATATATAA
277160 TTAAAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 21 0.66
14 9 0.28
15 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATATATAAAA
Found at i:277154 original size:18 final size:17
Alignment explanation
Indices: 277133--277167 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
277123 ATAATATATA
277133 AATATAAAATATAAAAAT
1 AATATAAAAT-TAAAAAT
*
277151 AATATATAATTAAAAAT
1 AATATAAAATTAAAAAT
277168 TAAGTTGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATATAAAATTAAAAAT
Found at i:286937 original size:53 final size:53
Alignment explanation
Indices: 286879--286988 Score: 220
Period size: 53 Copynumber: 2.1 Consensus size: 53
286869 CTTCTTTTAT
286879 TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTGCCCTTGTTGCATTGGTA
1 TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTGCCCTTGTTGCATTGGTA
286932 TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTGCCCTTGTTGCATTGGTA
1 TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTGCCCTTGTTGCATTGGTA
286985 TCTT
1 TCTT
286989 TTCCTTTCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43
Consensus pattern (53 bp):
TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTGCCCTTGTTGCATTGGTA
Found at i:289914 original size:18 final size:18
Alignment explanation
Indices: 289891--289927 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
289881 ATGAAAATAA
* *
289891 TAAAATTTAATATTAAAT
1 TAAAATATAATAATAAAT
289909 TAAAATATAATAATAAAT
1 TAAAATATAATAATAAAT
289927 T
1 T
289928 TATTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATATAATAATAAAT
Found at i:289921 original size:31 final size:31
Alignment explanation
Indices: 289886--289963 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
289876 ATTCAATGAA
289886 AATAATAAAATTTAATATTAA-ATTAAAATAT
1 AATAAT-AAATTTAATATTAATATTAAAATAT
* * * *
289917 AATAATAAATTTATTTTTAATCTTAAAGTAT
1 AATAATAAATTTAATATTAATATTAAAATAT
289948 AATAA-AAATATTAATA
1 AATAATAAAT-TTAATA
289964 AAATAAAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 16 0.41
31 23 0.59
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
AATAATAAATTTAATATTAATATTAAAATAT
Found at i:294828 original size:14 final size:16
Alignment explanation
Indices: 294802--294834 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
294792 AAAGGAAGTG
294802 AAAAAATTGAATA-AT
1 AAAAAATTGAATATAT
294817 AAAAAATT-AATATAT
1 AAAAAATTGAATATAT
294832 AAA
1 AAA
294835 TACACATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAAAATTGAATATAT
Found at i:322683 original size:20 final size:20
Alignment explanation
Indices: 322660--322709 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
322650 TAAAAATTAG
322660 AAATATAATTCAATTAAAAT
1 AAATATAATTCAATTAAAAT
322680 AAATATAATTCAATTAAAAT
1 AAATATAATTCAATTAAAAT
322700 AAATATAATT
1 AAATATAATT
322710 ATTTAACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATATAATTCAATTAAAAT
Found at i:323123 original size:27 final size:27
Alignment explanation
Indices: 323068--323124 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
323058 CAATTATCTC
*
323068 ATTAAATATATTTATAAAAATTAACAA
1 ATTAAATATATTTATAAAAAATAACAA
*
323095 ATTAAATTTA-TTATGAATAAAATAA-AA
1 ATTAAATATATTTAT-AA-AAAATAACAA
323122 ATT
1 ATT
323125 TTGAAGATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 16 0.62
28 6 0.23
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
ATTAAATATATTTATAAAAAATAACAA
Found at i:324894 original size:23 final size:23
Alignment explanation
Indices: 324862--324907 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
324852 TAGTGATAAC
* *
324862 TCTACGCAATAGAGTTATTTTAT
1 TCTACACAATAAAGTTATTTTAT
324885 TCTACACAATAAAGTTATTTTAT
1 TCTACACAATAAAGTTATTTTAT
324908 CACATTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (23 bp):
TCTACACAATAAAGTTATTTTAT
Found at i:328005 original size:33 final size:34
Alignment explanation
Indices: 327968--328049 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 34
327958 AGTGTGTTAA
* *
327968 ATATTTATATAAATTTTTATATGTTAATA-ATTT
1 ATATTTATATAAATTTTAATATATTAATATATTT
* *
328001 ATA-TTAAATAAATTTTAATATATTTATATATTT
1 ATATTTATATAAATTTTAATATATTAATATATTT
*
328034 ATATTATATTTAAATT
1 ATATT-TATATAAATT
328050 ATATTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 21 0.52
33 10 0.25
34 1 0.03
35 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (34 bp):
ATATTTATATAAATTTTAATATATTAATATATTT
Found at i:328075 original size:11 final size:11
Alignment explanation
Indices: 328027--328067 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
328017 AATATATTTA
*
328027 TATATTTATAT
1 TATATTTAAAT
328038 TATATTTAAAT
1 TATATTTAAAT
328049 TATATTTAAAT
1 TATATTTAAAT
328060 TATATTTA
1 TATATTTA
328068 TATCATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATTTAAAT
Found at i:328075 original size:22 final size:22
Alignment explanation
Indices: 328028--328075 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
328018 ATATATTTAT
* *
328028 ATATTTATATTATATTTAAATT
1 ATATTTAAATTATATTTAAATC
*
328050 ATATTTAAATTATATTTATATC
1 ATATTTAAATTATATTTAAATC
328072 ATAT
1 ATAT
328076 AATTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTAAATTATATTTAAATC
Found at i:328398 original size:21 final size:22
Alignment explanation
Indices: 328359--328408 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
328349 ATGAAAAATG
*
328359 AATTT-AATTTGAAACAATT-A
1 AATTTAAATTTAAAACAATTAA
*
328379 AATTTAAATTTAAAATAATTAA
1 AATTTAAATTTAAAACAATTAA
328401 AATTTAAA
1 AATTTAAA
328409 ATAATCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 5 0.19
21 12 0.46
22 9 0.35
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTTAAATTTAAAACAATTAA
Found at i:328403 original size:16 final size:16
Alignment explanation
Indices: 328379--328421 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
328369 GAAACAATTA
*
328379 AATTTAAATTTAAAAT
1 AATTAAAATTTAAAAT
328395 AATTAAAATTTAAAAT
1 AATTAAAATTTAAAAT
*
328411 AATCAAAATTT
1 AATTAAAATTT
328422 GATACAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTAAAATTTAAAAT
Found at i:332021 original size:2 final size:2
Alignment explanation
Indices: 332014--332039 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
332004 TGGTTCACGA
332014 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
332040 TTTAATTTCT
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):
AT
Found at i:332443 original size:14 final size:15
Alignment explanation
Indices: 332417--332445 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
332407 ATATATTTGA
332417 TTTAATGATATAATT
1 TTTAATGATATAATT
332432 TTTAAT-ATATAATT
1 TTTAATGATATAATT
332446 AATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTAATGATATAATT
Found at i:334143 original size:13 final size:13
Alignment explanation
Indices: 334108--334158 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
334098 TATATTCTAT
334108 ATAATATA-AATAA
1 ATAATATATAA-AA
*
334121 CATAATATATAAAT
1 -ATAATATATAAAA
*
334135 ATAAAATATAAAA
1 ATAATATATAAAA
334148 ATAATATATAA
1 ATAATATATAA
334159 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 21 0.66
14 9 0.28
15 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATATATAAAA
Found at i:335329 original size:22 final size:20
Alignment explanation
Indices: 335274--335330 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
335264 TATGATAGCG
*
335274 ATTATTATTACGATTGTGTTA
1 ATTATTATTA-TATTGTGTTA
* *
335295 ATGATTATGATATTGTGTTGTA
1 ATTATTATTATATTGTG-T-TA
335317 ATTATTATTATATT
1 ATTATTATTATATT
335331 TATTCTTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 9 0.31
22 14 0.48
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (20 bp):
ATTATTATTATATTGTGTTA
Found at i:343946 original size:53 final size:54
Alignment explanation
Indices: 343883--343993 Score: 215
Period size: 53 Copynumber: 2.1 Consensus size: 54
343873 CTTCTTTTAT
343883 TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTT-CCCTTGTTGCATTGGTA
1 TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTTGCCCTTGTTGCATTGGTA
343936 TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTTGCCCTTGTTGCATTGGTA
1 TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTTGCCCTTGTTGCATTGGTA
343990 TCTT
1 TCTT
343994 TTCCTTTCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 36 0.63
54 21 0.37
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (54 bp):
TCTTAGGATAGCATATTGTTTCTCAACTAACCTTTTGCCCTTGTTGCATTGGTA
Found at i:346923 original size:18 final size:18
Alignment explanation
Indices: 346900--346936 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
346890 ATGAAAATAA
* *
346900 TAAAATTTAATATTAAAT
1 TAAAATATAATAATAAAT
346918 TAAAATATAATAATAAAT
1 TAAAATATAATAATAAAT
346936 T
1 T
346937 TATTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATATAATAATAAAT
Found at i:346930 original size:31 final size:32
Alignment explanation
Indices: 346895--346973 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
346885 ATTCAATGAA
346895 AATAATAAAATTTAATATTAA-ATTAAAATAT
1 AATAATAAAATTTAATATTAATATTAAAATAT
* * * *
346926 AATAAT-AAATTTATTTTTAATCTTAAAGTAT
1 AATAATAAAATTTAATATTAATATTAAAATAT
346957 AATAA-AAAATATTAATA
1 AATAATAAAAT-TTAATA
346974 AAATAAAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
30 12 0.31
31 23 0.59
32 4 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
AATAATAAAATTTAATATTAATATTAAAATAT
Found at i:346994 original size:28 final size:31
Alignment explanation
Indices: 346948--347023 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 31
346938 ATTTTTAATC
* * * *
346948 TTAAAGTATAATAAAAAATATTAATA-A-AA
1 TTAAAGTATAGTGATAAATAGTAATATATAA
346977 -TAAAGTATAGTGATAAATAGTAATATATAA
1 TTAAAGTATAGTGATAAATAGTAATATATAA
347007 TTATAA-TATAGTGATAA
1 TTA-AAGTATAGTGATAA
347024 TTTATCTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 21 0.54
29 1 0.03
30 2 0.05
31 13 0.33
32 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (31 bp):
TTAAAGTATAGTGATAAATAGTAATATATAA
Found at i:352794 original size:2 final size:2
Alignment explanation
Indices: 352787--352812 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
352777 TTATAACCAA
352787 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
352813 CTAAGAGAAC
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):
AT
Found at i:353209 original size:28 final size:27
Alignment explanation
Indices: 353178--353243 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
353168 GTTCCCTTGA
* *
353178 TTTTAAAATTTAAAAATTAGATAATATT
1 TTTTAAAATTTAAAAATTAAATAACA-T
353206 TTTTAAAATTT-AAAATTAAATAACAT
1 TTTTAAAATTTAAAAATTAAATAACAT
*
353232 TTTCAAAATTTA
1 TTTTAAAATTTA
353244 GAACTGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.32
27 12 0.35
28 11 0.32
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTTAAAATTTAAAAATTAAATAACAT
Found at i:353220 original size:27 final size:26
Alignment explanation
Indices: 353178--353243 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
353168 GTTCCCTTGA
* *
353178 TTTTAAAATTTAAAAATTAGATAATATT
1 TTTTAAAATTT-AAAATTAAATAACA-T
353206 TTTTAAAATTTAAAATTAAATAACAT
1 TTTTAAAATTTAAAATTAAATAACAT
*
353232 TTTCAAAATTTA
1 TTTTAAAATTTA
353244 GAACTGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 12 0.34
27 12 0.34
28 11 0.31
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (26 bp):
TTTTAAAATTTAAAATTAAATAACAT
Found at i:354365 original size:16 final size:17
Alignment explanation
Indices: 354334--354367 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
354324 TTTCAAACTT
354334 ATTTACAATTTAAAATA
1 ATTTACAATTTAAAATA
*
354351 ATTTA-AATTTTAAATA
1 ATTTACAATTTAAAATA
354367 A
1 A
354368 GTTTGAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTACAATTTAAAATA
Found at i:363164 original size:18 final size:18
Alignment explanation
Indices: 363141--363175 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
363131 GATAAGTTCT
363141 TTACTATATCTTACCGTC
1 TTACTATATCTTACCGTC
363159 TTACTATATCTTACCGT
1 TTACTATATCTTACCGT
363176 AAGTGGATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.46
Consensus pattern (18 bp):
TTACTATATCTTACCGTC
Found at i:364901 original size:25 final size:26
Alignment explanation
Indices: 364873--364922 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
364863 TGTTTAAACG
*
364873 GGGAGAAA-TAGAGAAGTTTTATAAT
1 GGGAGAAATTAGAGAAGTTGTATAAT
364898 GGGAGAAATTAGAGAAGTTGTATAA
1 GGGAGAAATTAGAGAAGTTGTATAA
364923 GTTTGAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (26 bp):
GGGAGAAATTAGAGAAGTTGTATAAT
Found at i:365656 original size:33 final size:33
Alignment explanation
Indices: 365619--365685 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
365609 CACATCCAGA
*
365619 TGTATTGATATAAATTGCCAAGTATCGATACAT
1 TGTATCGATATAAATTGCCAAGTATCGATACAT
***
365652 TGTATCGATATAAATTGCTTTGTATCGATACAT
1 TGTATCGATATAAATTGCCAAGTATCGATACAT
365685 T
1 T
365686 ATGAATTATA
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:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATATAAATTGCCAAGTATCGATACAT
Found at i:369120 original size:16 final size:16
Alignment explanation
Indices: 369101--369148 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
369091 CATATCAATA
369101 TTTTTTGTTTTGATTT
1 TTTTTTGTTTTGATTT
*
369117 TTTTTTGTTTTGGTAGTT
1 TTTTTTGTTTT-G-ATTT
*
369135 TTTTTGGTTTTGAT
1 TTTTTTGTTTTGAT
369149 GGGACGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.44
17 2 0.07
18 13 0.48
ACGTcount: A:0.06, C:0.00, G:0.19, T:0.75
Consensus pattern (16 bp):
TTTTTTGTTTTGATTT
Found at i:369582 original size:25 final size:24
Alignment explanation
Indices: 369544--369590 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
369534 AATCTTAACA
**
369544 TATAATTAGCTTTATAATTTATTAT
1 TATAATTAAATTTA-AATTTATTAT
*
369569 TATAATTAAATTTAATTTTATT
1 TATAATTAAATTTAAATTTATT
369591 GTAACTAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TATAATTAAATTTAAATTTATTAT
Found at i:371636 original size:79 final size:79
Alignment explanation
Indices: 371540--371910 Score: 460
Period size: 79 Copynumber: 4.7 Consensus size: 79
371530 TTTGGAGATA
*** *
371540 AAAAT-GGGGTTGGAGTATCATTTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATC
1 AAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATC
*
371604 GGTGTTTT-GAAAAT
66 GATGTTTTAG-AAAT
* * * * *
371618 AAAATCGAGGTTGGAGTATCCCTTCGAAAATAACAGAGTTGGAGTATCCCCGATTGTGAAAAATC
1 AAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATC
*
371683 AATGTTTTTAGAAAT
66 GATG-TTTTAGAAAT
** * * * *
371698 AAAATCGGGGTTAAAGTATCCCCTCAAAAATAACGGGGTTCGAGTATCCCTGATTGTGAAAAATC
1 AAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATC
*
371763 GGTGTTTTAGAAAT
66 GATGTTTTAGAAAT
* * * *
371777 AAAA-CTGGGATTGGAGTATCCCCTCGGAAATAATGGGATTGGAGTATCCCCGATGGTGAAAAAT
1 AAAATC-GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAAT
371841 CGATGTTTTAGAAAT
65 CGATGTTTTAGAAAT
* ** *
371856 AAAATCGGGGTTGGAGTATCCTCTAAAAAATAATGGGGTTGGAGTATCCCCGATG
1 AAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG
371911 CTGGAAATTC
Statistics
Matches: 251, Mismatches: 37, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
78 6 0.02
79 177 0.71
80 67 0.27
81 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (79 bp):
AAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATC
GATGTTTTAGAAAT
Found at i:371791 original size:159 final size:159
Alignment explanation
Indices: 371565--372019 Score: 484
Period size: 159 Copynumber: 3.0 Consensus size: 159
371555 TATCATTTCG
371565 AAAATAACGGGGTTGGAGTAT-CCTCGATGGTGAAAAATCGGTGTTTTGAAAATAAAATCGAGGT
1 AAAATAACGGGGTTGGAGTATCCCTCGATGGTGAAAAATCGGTGTTTTGAAAATAAAATCGAGGT
* *
371629 TGGAGTATCCCTTCGAAAATAACAGAG-TTGGAGTATCCCCGATTGTGAAAAATCAATGTTTTTA
66 TGGAGTATCCCCTCGAAAATAA-AGAGATTGGAGTATCCCCGATGGTGAAAAATCAATG-TTTTA
*
371693 GAAATAAAATCGGGGTTAAAGTATCCCCTCA
129 GAAATAAAATCGGGGTTAAAGTATCCCCTAA
* *
371724 AAAATAACGGGGTTCGAGTATCCCT-GATTGTGAAAAATCGGTGTTTT-AGAAATAAAA-CTG-G
1 AAAATAACGGGGTTGGAGTATCCCTCGATGGTGAAAAATCGGTGTTTTGA-AAATAAAATC-GAG
* * * *
371785 GATTGGAGTATCCCCTCGGAAATAATGGGATTGGAGTATCCCCGATGGTGAAAAATCGATGTTTT
64 G-TTGGAGTATCCCCTCGAAAATAAAGAGATTGGAGTATCCCCGATGGTGAAAAATCAATGTTTT
** *
371850 AGAAATAAAATCGGGGTTGGAGTATCCTCTAA
128 AGAAATAAAATCGGGGTTAAAGTATCCCCTAA
* * * * *
371882 AAAATAATGGGGTTGGAGTATCCC-CGATGCTG-GAAA------TTCT--AAA-ACAA--G-GGT
1 AAAATAACGGGGTTGGAGTATCCCTCGATGGTGAAAAATCGGTGTTTTGAAAATAAAATCGAGGT
* * * ** *
371933 TAGAGTATCCCCTCGAAAATAACG-GAGTTGGAGTATCCCTGATGGTGAAAAATCGGTGTTTTAA
66 TGGAGTATCCCCTCGAAAATAAAGAGA-TTGGAGTATCCCCGATGGTGAAAAATCAATGTTTTAG
* *
371997 AAATAAAATCGGAGTTAGAGTAT
130 AAATAAAATCGGGGTTAAAGTAT
372020 TCCTAATTAT
Statistics
Matches: 262, Mismatches: 27, Indels: 28
0.83 0.09 0.09
Matches are distributed among these distances:
144 2 0.01
145 77 0.29
146 3 0.01
148 3 0.01
149 3 0.01
151 3 0.01
157 3 0.01
158 65 0.25
159 100 0.38
160 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (159 bp):
AAAATAACGGGGTTGGAGTATCCCTCGATGGTGAAAAATCGGTGTTTTGAAAATAAAATCGAGGT
TGGAGTATCCCCTCGAAAATAAAGAGATTGGAGTATCCCCGATGGTGAAAAATCAATGTTTTAGA
AATAAAATCGGGGTTAAAGTATCCCCTAA
Found at i:372033 original size:51 final size:51
Alignment explanation
Indices: 371955--372073 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
371945 TCGAAAATAA
* * * * *
371955 CGGAGTTGGAGTATCCCTGATGGTGAAAAATCGGTGTTTTAAAAATAAAAT
1 CGGAGTTAGAGTATCCCTAATGATGAAAAATCAGTATTTTAAAAATAAAAT
* * *
372006 CGGAGTTAGAGTATTCCTAATTATGAAAAATCAGTATTTTAGAAATAAAAT
1 CGGAGTTAGAGTATCCCTAATGATGAAAAATCAGTATTTTAAAAATAAAAT
*
372057 C-GAGGTTGGAGTATCCC
1 CGGA-GTTAGAGTATCCC
372074 CTCAAAAATA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 2 0.04
51 55 0.96
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (51 bp):
CGGAGTTAGAGTATCCCTAATGATGAAAAATCAGTATTTTAAAAATAAAAT
Found at i:375383 original size:61 final size:60
Alignment explanation
Indices: 375237--375983 Score: 721
Period size: 61 Copynumber: 12.3 Consensus size: 60
375227 TGAGAGAGGT
* * * *
375237 GTCCTGCTCTTTGAGGACGT-AAAGGTGCAACCAGCTTGTGTGGGCTTTTAAA--AAAGAAGT
1 GTCCTGCTCTTTGAGGAC-TAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAG-A-C
* * * * *
375297 GTCCTGCTCTTTGGGGACTAGAAGGTGCCACCAACTTATATGGGCTTTAAGATGGAAAGAC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AAGGAAAGAC
* * * * *
375358 GTCTTGCTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-GAAAAAT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGAC
* * * *
375417 GTCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGA-C
* * * * ** ** * *
375478 GCCCTACTTTTTGAGGACTGAAAGGCACCAGGTAACTCGTGTGGGCTTTAAAAGGAGAAGCC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCA-CCAACTTGTGTGGGCTTTAAAAGGA-AAGAC
* * * **
375540 ATCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAGAC
* * * * *
375601 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTATGAGCTTTAAAAAGAAAAAAC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAGAC
* * * * * * *
375662 ATCCTGCTTTTTGAGGATTGAAAAAGTGCCACCAACTTGTATGGGCTTTAAAAAGAGAAGGC
1 GTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAGAC
* * * * *
375724 GTCCTGCTCTTTGAGGACTGAAAGATGCCACAAACTTGTGTGGGCTTTAAAAAGAGAAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAGAC
* * * *
375785 GTCCTGCTCTTTGAGGACTAAAAGGTACCACCAACTTGTGTGGGTTTTGAAAGGAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGAC
* * * * * * * *
375845 ATCTTGCTCTTTGAGGACTGAAAGGTACTACCAACTTATGTGGGCTTTCAAAGGAAAAAGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGA-C
* * * *
375906 ATCCTACTCTTTGAGGACTGAAAA-GTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAAAC
1 GTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGAC
*
375967 GTCATGCTCTTTGAGGA
1 GTCCTGCTCTTTGAGGA
375984 TTGAAAGGAT
Statistics
Matches: 568, Mismatches: 105, Indels: 27
0.81 0.15 0.04
Matches are distributed among these distances:
59 53 0.09
60 102 0.18
61 304 0.54
62 103 0.18
63 6 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (60 bp):
GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGAC
Found at i:375573 original size:123 final size:121
Alignment explanation
Indices: 375237--375991 Score: 727
Period size: 123 Copynumber: 6.2 Consensus size: 121
375227 TGAGAGAGGT
* * * * **
375237 GTCCTGCTCTTTGAGGAC-GTAAAGGTGCAACCAGCTTGTGTGGGCTTTTAAAAA-AGAAGTGTC
1 GTCCTGCTCTTTGAGGACTG-AAAGGTACCACCAACTTGTGTGGGC-TTTAAAAAGAAAAGCATC
* * * * * * *
375300 CTGCTCTTTGGGGACTAGAAGGTGCCACCAACTTATATGGGCTTTAAGATG-GAAAGAC
64 CTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AAGAAAAAGGC
* * * * * ***
375358 GTCTTGCTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-GAAAGAAAAATGTCCT
1 GTCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAAGAAAAGCATCCT
* * *
375422 GCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGC
66 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGC
* * * * ** * * *
375478 GCCCTACTTTTTGAGGACTGAAAGGCACCAGGTAACTCGTGTGGGCTTTAAAAGGAGAAGCCATC
1 GTCCTGCTCTTTGAGGACTGAAAGGTACCA-CCAACTTGTGTGGGCTTTAAAAAGAAAAG-CATC
* * *
375543 CTGCTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AGAGAAGGT
64 CTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA-AAAAGGC
* * * * * *
375601 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTATGAGCTTTAAAAAGAAAAAACATCC
1 GTCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAAG-AAAAGCATCC
* * * * *
375666 TGCTTTTTGAGGATTGAAAAAGTGCCACCAACTTGTATGGGCTTTAAAA-AGAGAAGGC
65 TGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA-AAAAGGC
* * * * *
375724 GTCCTGCTCTTTGAGGACTGAAAGATGCCACAAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCC
1 GTCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAAGA-AAAGCATCC
* * * *
375789 TGCTCTTTGAGGACTAAAAGGTACCACCAACTTGTGTGGGTTTTGAAAG-GAAAGGC
65 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGC
* * * * * *
375845 ATCTTGCTCTTTGAGGACTGAAAGGTACTACCAACTTATGTGGGCTTTCAAAGGAAAAAGCATCC
1 GTCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAAG-AAAAGCATCC
* * *
375910 TACTCTTTGAGGACTGAAAA-GTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAA-AC
65 TGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGGC
* *
375967 GTCATGCTCTTTGAGGATTGAAAGG
1 GTCCTGCTCTTTGAGGACTGAAAGG
375992 ATAAAATGTT
Statistics
Matches: 518, Mismatches: 101, Indels: 29
0.80 0.16 0.04
Matches are distributed among these distances:
119 5 0.01
120 77 0.15
121 149 0.29
122 99 0.19
123 188 0.36
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (121 bp):
GTCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAAGAAAAGCATCCT
GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGC
Found at i:375710 original size:184 final size:182
Alignment explanation
Indices: 375223--375957 Score: 779
Period size: 184 Copynumber: 4.0 Consensus size: 182
375213 TTTAAAATGG
* * * *
375223 AAAATGAGAGAGGTGTCCTGCTCTTTGAGGACGT-AAAGGTGCAACCAGCTTGTGTGGGCTTTTA
1 AAAAAGAGA-AGGTGTCCTGCTCTTTGAGGAC-TAAAAGGTACCACCAACTTGTGTGGGCTTTTA
* *** * * *
375287 AAA-AAGAAGTGTCCTGCTCTTTGGGGACT-AGAAGGTGCCACCAACTTATATGGGCTTTAAGAT
64 AAAGAAAAAACATCCTGCTCTTTGAGGACTGA-AAGGTACCACCAACTTATATGGGCTTTAA-AA
* *
375350 GGA-AAGACGTCTTGCTCTTTGAA-GACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
127 GGAGAAG-CATCCTGCTCTTT-AAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* ** *
375406 -GAAAGA-AAAATGTCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGC-TTTAAA
1 AAAAAGAGAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTACCACCAACTTGTGTGGGCTTTTAAA
** * * * ** ** *
375468 AGAAAAAAGCGCCCTACTTTTTGAGGACTGAAAGGCACCAGGTAACTCGTGTGGGCTTTAAAAGG
66 AGAAAAAA-CATCCTGCTCTTTGAGGACTGAAAGGTACCA-CCAACTTATATGGGCTTTAAAAGG
375533 AGAAGCCATCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
129 AGAAG-CATCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* * * * *
375588 AAAAAGAGAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTATGAGCTTTAAAA
1 AAAAAGAGAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTACCACCAACTTGTGTGGGCTTTTAAA
* * * * * *
375653 AGAAAAAACATCCTGCTTTTTGAGGATTGAAAAAGTGCCACCAACTTGTATGGGCTTTAAAAAGA
66 AGAAAAAACATCCTGCTCTTTGAGGACTG-AAAGGTACCACCAACTTATATGGGCTTTAAAAGGA
* * * * *
375718 GAAGGCGTCCTGCTCTTTGAGGACTGAAAGATGCCACAAACTTGTGTGGGCTTT
130 GAA-GCATCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* *
375772 AAAAAGAGAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTACCACCAACTTGTGTGGG-TTTTGAA
1 AAAAAGAGAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTACCACCAACTTGTGTGGGCTTTTAAA
* ** * * * *
375836 AGGAAAGGCATCTTGCTCTTTGAGGACTGAAAGGTACTACCAACTTATGTGGGCTTTCAAAGGAA
66 AGAAAAAACATCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTATATGGGCTTTAAAAGG-A
* * * *
375901 AAAGCATCCTACTCTTTGAGGACTGAAAA-GTGCCACCAACTTGTGTAGGCTTT
130 GAAGCATCCTGCTCTTTAAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTT
375954 AAAA
1 AAAA
375958 GGAAAAAACG
Statistics
Matches: 460, Mismatches: 78, Indels: 29
0.81 0.14 0.05
Matches are distributed among these distances:
179 8 0.02
180 46 0.10
181 29 0.06
182 138 0.30
183 39 0.08
184 179 0.39
185 21 0.05
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (182 bp):
AAAAAGAGAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTACCACCAACTTGTGTGGGCTTTTAAA
AGAAAAAACATCCTGCTCTTTGAGGACTGAAAGGTACCACCAACTTATATGGGCTTTAAAAGGAG
AAGCATCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:379103 original size:269 final size:267
Alignment explanation
Indices: 378449--380722 Score: 1825
Period size: 269 Copynumber: 8.5 Consensus size: 267
378439 AAATGTATGA
* * * * * * *
378449 GGTATTAGATTCCTTCTGGCATGATAGAAAATATTTGACTGATGCCTAATAAATCTCTTAGAACC
1 GGTATTAGATT-CTTTTGACACGATAAAAAATATTTGACTAATGCATAATAAATTTCTTAGAACC
* * *
378514 CGAAAGATGTGACAGATGCAT-GAGTATCAGATTCCTTCTGACACGATAGAAAAAATTTGACTAA
65 CGAAAGATGTGACAGATGCATGGGGTATCAAATT-CTTCTGACACGATAGAAAATATTTGACTAA
* * * *
378578 TGCCTAATAAATTTATTCTT-AGAACCCAAAAGATGTGATTGATGTATAGGGTATCAGATTCCTT
129 TGCCTAATAAAATTATTCTTGA-AACCCAAAAGATGTGATAGATGCATGGGGTATCAGATTCCTT
* * * * *
378642 CTAACATGA-A-AAAATATTTGATTAAAGCATAATAAA--TTTCTTGGAACCGC-AAAGATGTGA
193 CTAACACGATAGAAAATATTTGACTAATGCCTAATAAATTTTTCTTGAAACC-CAAAAGATGTGA
*
378702 CAGATGTATAG
257 CAGATGCATAG
* * * ** *
378713 GGTATTAGATTCTTTTTTACACGAT-AAAAATATTTAATTAATGCCCAATAAAATTAATCTTGGA
1 GGTATTAGATTC-TTTTGACACGATAAAAAATATTTGACTAATGCATAAT-AAATT--TCTTAGA
** * * * *
378777 ACTTGAAAGATGTGACAGATACATAGGGTATCAGATTCCTTCTGACGCGATAGAAAATATTTGAC
62 ACCCGAAAGATGTGACAGATGCATGGGGTATCAAATT-CTTCTGACACGATAGAAAATATTTGAC
* * * * * *
378842 AAATGCTTAATAAATTTCTTCTTGAAATCCAAAAGATGTGATAGATGCATGGGGTATTAGATTCC
126 TAATGCCTAATAAAATTATTCTTGAAACCCAAAAGATGTGATAGATGCATGGGGTATCAGATTCC
* * * * * * *
378907 TTTTAACATGACAAAAAATATTTGACTAATGCTTAATAAATTTTTTCTTGAAACCCAAATGATAT
191 TTCTAACACGATAGAAAATATTTGACTAATGCCTAATAAA-TTTTTCTTGAAACCCAAAAGATGT
*
378972 GATAGATGCATAG
255 GACAGATGCATAG
* *
378985 GGTATTAGATTCTTTCTAACACGA-AAAAAATATTTGATTAATGCATAATAAATTTCTTAGAACC
1 GGTATTAGATTCTTT-TGACACGATAAAAAATATTTGACTAATGCATAATAAATTTCTTAGAACC
* * * ** * *
379049 CCAAAGATGTGACAGATGTATGGGGTATTAAATTGCTTCTGACATAACAGAAAATATTTAACTAA
65 CGAAAGATGTGACAGATGCATGGGGTATCAAATT-CTTCTGACACGATAGAAAATATTTGACTAA
* * ** * *
379114 TGCCTAATAAAATTAATCTTGGAACCTGAAAGATGTGATAGTTGCATGGAGTATCAGATTCCTTC
129 TGCCTAATAAAATTATTCTTGAAACCCAAAAGATGTGATAGATGCATGGGGTATCAGATTCCTTC
* * * *
379179 TAACACGATAGAAAATATTTGACTAATGCCTAAAAAAATTTTCTTGAAACCCAAAAGATATGATA
194 TAACACGATAGAAAATATTTGACTAATGCCTAATAAATTTTTCTTGAAACCCAAAAGATGTGACA
*
379244 GATGCATAA
259 GATGCATAG
* * * * * *
379253 GGTATCAAATTTCTTTTGATATGACATAAAATATTTGACTAATGCATAATAAATTTCTTAGAACC
1 GGTATTAGA-TTCTTTTGACACGATAAAAAATATTTGACTAATGCATAATAAATTTCTTAGAACC
* * * * * * * * * *
379318 CCAAAAATATGATAAATGCATGGGGTATCAAATTCTTTCTCATATGACAAAAAATATTTGACTAA
65 CGAAAGATGTGACAGATGCATGGGGTATCAAATTC-TTCTGACACGATAGAAAATATTTGACTAA
* *** * * *
379383 TGCCTAAT-AAATT-TT-TTGGAACTTGAAAGCTGTAATAGATGTATGGGGTATCAGATTCCTTC
129 TGCCTAATAAAATTATTCTTGAAACCCAAAAGATGTGATAGATGCATGGGGTATCAGATTCCTTC
* * ** *
379445 TGACATGATAGAAAATATTTGACTAATGCCTAATAAAATTAATCTT-AGAACTCAAAAGATGTGA
194 TAACACGATAGAAAATATTTGACTAATGCCTAAT-AAATTTTTCTTGA-AACCCAAAAGATGTGA
*
379509 CAGATGCATAT
257 CAGATGCATAG
* * * * **
379520 GGTATCATATTCATTTTGACACGACAGAAAATATGAGACTAATGTC-TAATAAATTTCTTTATGG
1 GGTATTAGATTC-TTTTGACACGATAAAAAATATTTGACTAATG-CATAATAAATTTC-TTA--G
* * * * *
379584 AACCCAAAAGATGTGACAGATACATGGGGTATTAGATTCTTTCTGACACGACA-ACAAATATTTG
61 AACCCGAAAGATGTGACAGATGCATGGGGTATCAAATTC-TTCTGACACGATAGA-AAATATTTG
* * * * * * *
379648 ACTAATGCATAAT-AAATT-TT-TTGGAACCCAAAAGATATGATAGATGAATGGAGTATTAAATT
124 ACTAATGCCTAATAAAATTATTCTTGAAACCCAAAAGATGTGATAGATGCATGGGGTATCAGATT
* ** * ** * * * *
379710 CCTTTTGGCACGATAGAAAATATTTGACTATTGTTTAAT-AA-CTTTCTTGGAGCCTTAAAAG-T
189 CCTTCTAACACGATAGAAAATATTTGACTAATGCCTAATAAATTTTTCTTGAAACC-CAAAAGAT
* *
379772 GTGATAAATGCATAG
253 GTGACAGATGCATAG
* * * * * *
379787 GGTATTAAATTCCTTTTGATACGATAAAAAATATTTGACTAATACCTAACAAATTTATT-GAAAC
1 GGTATTAGATT-CTTTTGACACGATAAAAAATATTTGACTAATGCATAATAAATTTCTTAG-AAC
** * * * *** * * * * *
379851 AAGTAAGACGTGACATATGCATATTGTATCAAATTCTTTTTAATACGATAAAAAATATTTAACTA
64 CCGAAAGATGTGACAGATGCATGGGGTATCAAATTC-TTCTGACACGATAGAAAATATTTGACTA
* * * * * * *
379916 ATACATAATAAAATTAATCTTGAAACTCAAAAGATGTGACAGATGCAT-GGGTATCAAATTCTTT
128 ATGCCTAATAAAATTATTCTTGAAACCCAAAAGATGTGATAGATGCATGGGGTATCAGATTCCTT
* * * * * * *
379980 CTAACACAATAGAAAATATTTTACTAATGCCTAATATATTTCTCCTCGGAACCCAAAAGATGTTA
193 CTAACACGATAGAAAATATTTGACTAATGCCTAATAAATTT-TTCTTGAAACCCAAAAGATGTGA
*
380045 CAGATGCATAA
257 CAGATGCATAG
* * *
380056 GGTATTAGATTCCTTTTGATATGATAAAAAATATTTGACTAATGCATAATTAATTTCTT-GAAAC
1 GGTATTAGATT-CTTTTGACACGATAAAAAATATTTGACTAATGCATAATAAATTTCTTAG-AAC
* * * * *
380120 CCTAAAGATGTGACATATGTATGAGGTATCAAATTTTTTCTGACACGATAGAAAA-ATTTGACTA
64 CCGAAAGATGTGACAGATGCATGGGGTATCAAA-TTCTTCTGACACGATAGAAAATATTTGACTA
* ** * * *
380184 ATGCCTAATAAAATTAATCTTGAAACTTGGAAAA-ATGTGGTAGATGCTTGGGGTATCAGACTCC
128 ATGCCTAATAAAATTATTCTTGAAAC--CCAAAAGATGTGATAGATGCATGGGGTATCAGATTCC
* * * * * * *
380248 TTCTAACGCGACATAAAATTTTTGATTAATGCCTAATAAAATTAATT-TTGAAACCTAAAAGATG
191 TTCTAACACGATAGAAAATATTTGACTAATGCCTAAT-AAATT-TTTCTTGAAACCCAAAAGATG
* *
380312 CGACAAATGCATA-
254 TGACAGATGCATAG
* * * * * * *
380325 GGTATCAGATTCCTTCTT-ACACAATAGAAAATATTTTATTAATGCATAATAAATTTTTTGGAAC
1 GGTATTAGATT-CTT-TTGACACGATAAAAAATATTTGACTAATGCATAATAAATTTCTTAGAAC
* * * * * * *
380389 TCGAAAGATGTAACAGGTGTAAGGGGTATCAGATTTCTTCTGACATGATAGAAAATATTTGACTA
64 CCGAAAGATGTGACAGATGCATGGGGTATCA-AATTCTTCTGACACGATAGAAAATATTTGACTA
*** * * * *
380454 ATATATAAT-AAA-T-TTCTTGAAACCCGAAAGATGTGACAGATGCATTGGGTATCAAATTCCTA
128 ATGCCTAATAAAATTATTCTTGAAACCCAAAAGATGTGATAGATGCATGGGGTATCAGATTCCT-
* * * * * *
380516 T-TGACATGACAGAAAATATTTGACTAATACCTAATAAA--TTTCTTAAAACCTAAAAGATGTGA
192 TCTAACACGATAGAAAATATTTGACTAATGCCTAATAAATTTTTCTTGAAACCCAAAAGATGTGA
*
380578 TAGATGCAT-G
257 CAGATGCATAG
* ** * * * *
380588 AGGTATTAGATTCCTTCTGA-ATTAATAGAAAATATTTGGCCAATGCATAATAAATTTCTTTTTG
1 -GGTATTAGATT-CTTTTGACA-CGATAAAAAATATTTGACTAATGCATAATAAATTTC---TTA
** * * * * * * *
380652 GAACTTGAAGGATGTGACAAATGCATAGGGTATCAGATTCCTACCGACACAATA-AATAATATTT
60 GAACCCGAAAGATGTGACAGATGCATGGGGTATCAAATT-CTTCTGACACGATAGAA-AATATTT
380716 GACTAAT
123 GACTAAT
380723 AATACGACAA
Statistics
Matches: 1628, Mismatches: 322, Indels: 117
0.79 0.16 0.06
Matches are distributed among these distances:
262 2 0.00
263 48 0.03
264 125 0.08
265 12 0.01
266 203 0.12
267 330 0.20
268 105 0.06
269 495 0.30
270 226 0.14
271 14 0.01
272 68 0.04
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (267 bp):
GGTATTAGATTCTTTTGACACGATAAAAAATATTTGACTAATGCATAATAAATTTCTTAGAACCC
GAAAGATGTGACAGATGCATGGGGTATCAAATTCTTCTGACACGATAGAAAATATTTGACTAATG
CCTAATAAAATTATTCTTGAAACCCAAAAGATGTGATAGATGCATGGGGTATCAGATTCCTTCTA
ACACGATAGAAAATATTTGACTAATGCCTAATAAATTTTTCTTGAAACCCAAAAGATGTGACAGA
TGCATAG
Found at i:379122 original size:88 final size:88
Alignment explanation
Indices: 378449--380722 Score: 1704
Period size: 88 Copynumber: 25.5 Consensus size: 88
378439 AAATGTATGA
* * * * * *
378449 GGTATTAGATTCCTTCTGGCATGATAGAAAATATTTGACTGATGCCTAATAAATCTCTTAGAACC
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
*
378514 CGAAAGATGTGACAGATGCAT-G
66 CAAAAGATGTGACAGATGCATGG
* * *
378536 AGTATCAGATTCCTTCTGACACGATAGAAAAAATTTGACTAATGCCTAATAAATTTATTCTTAGA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAA--T-TTCTTGGA
** * *
378601 ACCCAAAAGATGTGATTGATGTATAG
63 ACCCAAAAGATGTGACAGATGCATGG
* * * * *
378627 GGTATCAGATTCCTTCTAACATGA-A-AAAATATTTGATTAAAGCATAATAAATTTCTTGGAACC
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
* *
378690 GC-AAAGATGTGACAGATGTATAG
66 -CAAAAGATGTGACAGATGCATGG
* * * * * * *
378713 GGTATTAGATTCTTTTTTACACGATA-AAAATATTTAATTAATGCCCAATAAAATTAATCTTGGA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAAT-AAATT--TCTTGGA
*** * *
378777 ACTTGAAAGATGTGACAGATACATAG
63 ACCCAAAAGATGTGACAGATGCATGG
* * * *
378803 GGTATCAGATTCCTTCTGACGCGATAGAAAATATTTGACAAATGCTTAATAAATTTCTTCTTGAA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAA--T-TTCTTGGA
* *
378868 ATCCAAAAGATGTGATAGATGCATGG
63 ACCCAAAAGATGTGACAGATGCATGG
* * * * * * * *
378894 GGTATTAGATTCCTTTTAACATGACAAAAAATATTTGACTAATGCTTAATAAATTTTTTCTTGAA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAA---TTTCTTGGA
* * * *
378959 ACCCAAATGATATGATAGATGCATAG
63 ACCCAAAAGATGTGACAGATGCATGG
* * * * * * *
378985 GGTATTAGATTCTTTCTAACACGA-AAAAAATATTTGATTAATGCATAATAAATTTCTTAGAACC
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
* *
379049 CCAAAGATGTGACAGATGTATGG
66 CAAAAGATGTGACAGATGCATGG
* * * ** * *
379072 GGTATTAAATTGCTTCTGACATAACAGAAAATATTTAACTAATGCCTAATAAAATTAATCTTGGA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAAT-AAATT--TCTTGGA
** * *
379137 ACCTGAAAGATGTGATAGTTGCATGG
63 ACCCAAAAGATGTGACAGATGCATGG
* * * *
379163 AGTATCAGATTCCTTCTAACACGATAGAAAATATTTGACTAATGCCTAAAAAAATTTTCTTGAAA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCT-AATAAA-TTTCTTGGAA
* * **
379228 CCCAAAAGATATGATAGATGCATAA
64 CCCAAAAGATGTGACAGATGCATGG
* * * * * * * * *
379253 GGTATCAAATTTCTTTTGATATGACATAAAATATTTGACTAATGCATAATAAATTTCTTAGAACC
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAA-C
* * *
379318 CCAAAA-ATATGATAAATGCATGG
65 CCAAAAGATGTGACAGATGCATGG
* * * * * * * * *
379341 GGTATCAAATTCTTTCTCATATGACAAAAAATATTTGACTAATGCCTAATAAATTTTTTGGAACT
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
** * * * *
379406 TGAAAGCTGTAATAGATGTATGG
66 CAAAAGATGTGACAGATGCATGG
* *
379429 GGTATCAGATTCCTTCTGACATGATAGAAAATATTTGACTAATGCCTAATAAAATTAATCTTAGA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAAT-AAATT--TCTTGGA
* **
379494 ACTCAAAAGATGTGACAGATGCATAT
63 ACCCAAAAGATGTGACAGATGCATGG
* * * * ** *
379520 GGTATCATATTCATTTTGACACGACAGAAAATATGAGACTAATGTCTAATAAATTTCTTTATGGA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTC--T-TGGA
*
379585 ACCCAAAAGATGTGACAGATACATGG
63 ACCCAAAAGATGTGACAGATGCATGG
* * * * *
379611 GGTATTAGATTCTTTCTGACACGACA-ACAAATATTTGACTAATGCATAATAAATTTTTTGGAAC
1 GGTATCAGATTCCTTCTGACACGATAGA-AAATATTTGACTAATGCCTAATAAATTTCTTGGAAC
* * *
379675 CCAAAAGATATGATAGATGAATGG
65 CCAAAAGATGTGACAGATGCATGG
* * * * * * ** * *
379699 AGTATTAAATTCCTTTTGGCACGATAGAAAATATTTGACTATTGTTTAATAACTTTCTTGGAGCC
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
* * * *
379764 TTAAAAG-TGTGATAAATGCATAG
66 -CAAAAGATGTGACAGATGCATGG
* * * * * * * * *
379787 GGTATTAAATTCCTTTTGATACGATAAAAAATATTTGACTAATACCTAACAAATTTATT-GAA-A
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
* * **
379850 CAAGTAAGACGTGACATATGCATAT
66 CAA--AAGATGTGACAGATGCATGG
* * * * * * * * * * *
379875 TGTATCAAATTCTTTTTAATACGATAAAAAATATTTAACTAATACATAATAAAATTAATCTTGAA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAAT-AAATT--TCTTGGA
*
379940 ACTCAAAAGATGTGACAGATGCAT-G
63 ACCCAAAAGATGTGACAGATGCATGG
* * * * * *
379965 GGTATCAAATTCTTTCTAACACAATAGAAAATATTTTACTAATGCCTAATATATTTCTCCTCGGA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCT--T-GGA
* **
380030 ACCCAAAAGATGTTACAGATGCATAA
63 ACCCAAAAGATGTGACAGATGCATGG
* * * * * * * *
380056 GGTATTAGATTCCTTTTGATATGATAAAAAATATTTGACTAATGCATAATTAATTTCTTGAAACC
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
* * * *
380121 CTAAAGATGTGACATATGTATGA
66 CAAAAGATGTGACAGATGCATGG
* ** *
380144 GGTATCAAATTTTTTCTGACACGATAGAAAA-ATTTGACTAATGCCTAATAAAATTAATCTTGAA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAAT-AAATT--TCTTGGA
** ** *
380208 ACTTGGAAAA-ATGTGGTAGATGCTTGG
63 AC--CCAAAAGATGTGACAGATGCATGG
* * * * * * * * *
380235 GGTATCAGACTCCTTCTAACGCGACATAAAATTTTTGATTAATGCCTAATAAAATTAATTTTGAA
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAAT-AAATT--TCTTGGA
* * * *
380300 ACCTAAAAGATGCGACAAATGCAT-A
63 ACCCAAAAGATGTGACAGATGCATGG
* * * * * * *
380325 GGTATCAGATTCCTTCTTACACAATAGAAAATATTTTATTAATGCATAATAAATTTTTTGGAACT
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
* * * * *
380390 CGAAAGATGTAACAGGTGTAAGG
66 CAAAAGATGTGACAGATGCATGG
* * *** *
380413 GGTATCAGATTTCTTCTGACATGATAGAAAATATTTGACTAATATATAATAAATTTCTTGAAACC
1 GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
* *
380478 CGAAAGATGTGACAGATGCATTG
66 CAAAAGATGTGACAGATGCATGG
* * * * **
380501 GGTATCAAATTCCTAT-TGACATGACAGAAAATATTTGACTAATACCTAATAAATTTCTTAAAAC
1 GGTATCAGATTCCT-TCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAAC
* * *
380565 CTAAAAGATGTGATAGATGCATGA
65 CCAAAAGATGTGACAGATGCATGG
* ** * * *
380589 GGTATTAGATTCCTTCTGA-ATTAATAGAAAATATTTGGCCAATGCATAATAAATTTCTTTTTGG
1 GGTATCAGATTCCTTCTGACA-CGATAGAAAATATTTGACTAATGCCTAATAAATTTC---TTGG
*** * * *
380653 AACTTGAAGGATGTGACAAATGCATAG
62 AACCCAAAAGATGTGACAGATGCATGG
* * *
380680 GGTATCAGATTCCTACCGACACAATA-AATAATATTTGACTAAT
1 GGTATCAGATTCCTTCTGACACGATAGAA-AATATTTGACTAAT
380723 AATACGACAA
Statistics
Matches: 1755, Mismatches: 372, Indels: 116
0.78 0.17 0.05
Matches are distributed among these distances:
85 2 0.00
86 48 0.03
87 166 0.09
88 595 0.34
89 69 0.04
90 298 0.17
91 527 0.30
92 46 0.03
93 4 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (88 bp):
GGTATCAGATTCCTTCTGACACGATAGAAAATATTTGACTAATGCCTAATAAATTTCTTGGAACC
CAAAAGATGTGACAGATGCATGG
Found at i:384153 original size:18 final size:19
Alignment explanation
Indices: 384108--384154 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
384098 AGAACAACTT
384108 AACGAAAAAAATAACGCAA
1 AACGAAAAAAATAACGCAA
*
384127 AACTTAAAAAAA-AA-GCAA
1 AAC-GAAAAAAATAACGCAA
384145 AATCGAAAAA
1 AA-CGAAAAA
384155 CAATGTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 11 0.46
19 6 0.25
20 7 0.29
ACGTcount: A:0.70, C:0.13, G:0.09, T:0.09
Consensus pattern (19 bp):
AACGAAAAAAATAACGCAA
Found at i:384212 original size:17 final size:16
Alignment explanation
Indices: 384172--384231 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
384162 GGGAACTCAT
*
384172 AAAAAAAATCCCAAAA
1 AAAAAAAATACCAAAA
*
384188 AAATAAAAATGCCAAAA
1 AAA-AAAAATACCAAAA
* *
384205 CAAAAAAACTATCAAAA
1 -AAAAAAAATACCAAAA
384222 TAAAAAAAAT
1 -AAAAAAAAT
384232 TAATACTTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 3 0.08
17 30 0.83
18 3 0.08
ACGTcount: A:0.73, C:0.13, G:0.02, T:0.12
Consensus pattern (16 bp):
AAAAAAAATACCAAAA
Found at i:385055 original size:2 final size:2
Alignment explanation
Indices: 385048--385084 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
385038 GGTTTTGCCT
385048 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
385085 TTCAAATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:391681 original size:89 final size:89
Alignment explanation
Indices: 391530--391698 Score: 320
Period size: 89 Copynumber: 1.9 Consensus size: 89
391520 GTATGTTGAA
391530 AAATGTCTTTTCCTACTTGTGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTCCACCAGTAA
1 AAATGTCTTTTCCTACTTGTGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTCCACCAGTAA
*
391595 AGCCATATAATATTCCTACTTGTG
66 AGCCACATAATATTCCTACTTGTG
*
391619 AAATGTCTTTTCCTACTTGTGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTTCACCAGTAA
1 AAATGTCTTTTCCTACTTGTGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTCCACCAGTAA
391684 AGCCACATAATATTC
66 AGCCACATAATATTC
391699 TATCACTATC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
89 78 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (89 bp):
AAATGTCTTTTCCTACTTGTGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTCCACCAGTAA
AGCCACATAATATTCCTACTTGTG
Found at i:391737 original size:89 final size:87
Alignment explanation
Indices: 391549--391729 Score: 211
Period size: 89 Copynumber: 2.0 Consensus size: 87
391539 TTCCTACTTG
* *
391549 TGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTCCACCAGTAAAGCCATATAATATTCCTAC
1 TGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTCCACCAGTAAAGCCACATAATATTCATAC
* * * * *
391614 TTGTGAAATGTCTTTTCCTACTT
66 TTCTAAAATATCTTCTCATAC-T
*
391637 GTGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTTCACCAGTAAAGCCACATAATATTCTAT
1 -TGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTCCACCAGTAAAGCCACATAATATTC-AT
391702 CACTATCTACAAAATATC-TCTCGATACT
64 -ACT-TCT--AAAATATCTTCTC-ATACT
391730 ATTAATTACT
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
89 59 0.76
90 1 0.01
91 3 0.04
92 2 0.03
93 4 0.05
94 9 0.12
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (87 bp):
TGATTGAATTAGTAGCCTTTAACCAGACTTGTTTTTCCACCAGTAAAGCCACATAATATTCATAC
TTCTAAAATATCTTCTCATACT
Found at i:398203 original size:28 final size:29
Alignment explanation
Indices: 398140--398210 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
398130 TTTGATAAAA
* *
398140 AATTTATATAAAAATAATAATATTTTAAT
1 AATTTATTTTAAAATAATAATATTTTAAT
* *
398169 AAATTATTTTAAAATAATACTA-TTTAAT
1 AATTTATTTTAAAATAATAATATTTTAAT
398197 AATTTATTTATAAA
1 AATTTATTT-TAAA
398211 TTAACAGTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTTATTTTAAAATAATAATATTTTAAT
Found at i:398211 original size:28 final size:29
Alignment explanation
Indices: 398140--398211 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
398130 TTTGATAAAA
* *
398140 AATTTATATAAAAATAATAATATTTTAAT
1 AATTTATTTATAAATAATAATATTTTAAT
* *
398169 AAATTATTT-TAAAATAATACTA-TTTAAT
1 AATTTATTTAT-AAATAATAATATTTTAAT
398197 AATTTATTTATAAAT
1 AATTTATTTATAAAT
398212 TAACAGTAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 18 0.50
29 18 0.50
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTTATTTATAAATAATAATATTTTAAT
Found at i:398860 original size:6 final size:6
Alignment explanation
Indices: 398844--398884 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
398834 GAAAGTTGAG
* * *
398844 AAGAAA GAGAAA AAGAAA AAGAGA AAGCAA AAGAAA AAGAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAA
398885 GAAGGATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:399979 original size:5 final size:5
Alignment explanation
Indices: 399969--400001 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
399959 GCTAATATTG
399969 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
400002 CTGGTTCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCTC
Found at i:402690 original size:15 final size:14
Alignment explanation
Indices: 402652--402715 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
402642 AACTCTATAT
*
402652 TATTTAAATATTAA
1 TATTTAAATAGTAA
*
402666 TATTTTAATA-TAGA
1 TATTTAAATAGTA-A
402680 TATTTCAAATAGTAA
1 TATTT-AAATAGTAA
* *
402695 TATTTTAATAATAA
1 TATTTAAATAGTAA
402709 TATTTAA
1 TATTTAA
402716 TAATAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
13 2 0.05
14 28 0.67
15 10 0.24
16 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (14 bp):
TATTTAAATAGTAA
Found at i:402697 original size:29 final size:28
Alignment explanation
Indices: 402652--402715 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
402642 AACTCTATAT
*
402652 TATTTAAATATTAATATTTTAAT-ATAGA
1 TATTTAAATAGTAATATTTTAATAATA-A
402680 TATTTCAAATAGTAATATTTTAATAATAA
1 TATTT-AAATAGTAATATTTTAATAATAA
402709 TATTTAA
1 TATTTAA
402716 TAATAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 7 0.21
29 23 0.70
30 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (28 bp):
TATTTAAATAGTAATATTTTAATAATAA
Found at i:402725 original size:29 final size:29
Alignment explanation
Indices: 402664--402727 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
402654 TTTAAATATT
* *
402664 AATATTTTAATATAGATATTTCAAATAGT
1 AATATTTTAATATAGATATTTAAAATAGA
402693 AATATTTTAATAATA-ATATTTAATAATA-A
1 AATATTTTAAT-ATAGATATTTAA-AATAGA
402722 AATATT
1 AATATT
402728 ATATTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
AATATTTTAATATAGATATTTAAAATAGA
Found at i:403382 original size:15 final size:15
Alignment explanation
Indices: 403345--403392 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
403335 TTTGTATATT
*
403345 TAATAATATTCAAAA
1 TAATAATATTAAAAA
*
403360 TAAAAATATTAAAAA
1 TAATAATATTAAAAA
*
403375 TTATAATA-TAAAAA
1 TAATAATATTAAAAA
403389 TAAT
1 TAAT
403393 TTATATTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAATATTAAAAA
Found at i:403610 original size:22 final size:22
Alignment explanation
Indices: 403585--403626 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
403575 GTTGAGTAGC
*
403585 AAGTCATTTTTCATTAACCACT
1 AAGTAATTTTTCATTAACCACT
*
403607 AAGTAATTTTTCATTGACCA
1 AAGTAATTTTTCATTAACCA
403627 AACAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (22 bp):
AAGTAATTTTTCATTAACCACT
Found at i:405315 original size:14 final size:14
Alignment explanation
Indices: 405285--405392 Score: 81
Period size: 14 Copynumber: 7.5 Consensus size: 14
405275 ATTGCTGGCA
* *
405285 AAAGTACTTACGTC
1 AAAGTACTTATGCC
405299 AAAGTACTTATGCC
1 AAAGTACTTATGCC
* * *
405313 AAAAATACTTATACT
1 -AAAGTACTTATGCC
*
405328 AAAATACTTATGCC
1 AAAGTACTTATGCC
* * *
405342 AAAAGTATTTGTGCT
1 -AAAGTACTTATGCC
*
405357 AAAGTACCTATGCC
1 AAAGTACTTATGCC
* *
405371 AATAGTATTTGTGCC
1 AA-AGTACTTATGCC
405386 AAAGTAC
1 AAAGTAC
405393 CTCTACCAAA
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
14 40 0.56
15 32 0.44
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.31
Consensus pattern (14 bp):
AAAGTACTTATGCC
Found at i:405377 original size:29 final size:29
Alignment explanation
Indices: 405299--405403 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 29
405289 TACTTACGTC
* * * * *
405299 AAAGTACTTATGCCAAAAATACTTATACT
1 AAAGTACCTATGCCAAAAGTATTTGTGCT
* *
405328 AAAATACTTATGCCAAAAGTATTTGTGCT
1 AAAGTACCTATGCCAAAAGTATTTGTGCT
* *
405357 AAAGTACCTATGCCAATAGTATTTGTGCC
1 AAAGTACCTATGCCAAAAGTATTTGTGCT
* *
405386 AAAGTACCTCTACCAAAA
1 AAAGTACCTATGCCAAAA
405404 AATGCTATGG
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (29 bp):
AAAGTACCTATGCCAAAAGTATTTGTGCT
Found at i:405594 original size:3 final size:3
Alignment explanation
Indices: 405586--405647 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
405576 GATTAAACAA
405586 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
405634 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
405648 ATGATGAATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:405815 original size:3 final size:3
Alignment explanation
Indices: 405807--405841 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
405797 GAAAATTTTA
405807 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
405842 AGCATCAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:406449 original size:2 final size:2
Alignment explanation
Indices: 406442--406467 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
406432 AATATCTAAA
406442 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
406468 GAAATAAACT
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):
AT
Found at i:409154 original size:21 final size:20
Alignment explanation
Indices: 409130--409201 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 20
409120 CTATGATTTA
409130 TATCGATACAATTAGTAAATG
1 TATCGATAC-ATTAGTAAATG
* *
409151 TATCGATACATAAGTGAATG
1 TATCGATACATTAGTAAATG
409171 TATCGATACATGTA-TCAAATG
1 TATCGATACAT-TAGT-AAATG
409192 TATCGATACA
1 TATCGATACA
409202 AGACTATCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.47
21 24 0.53
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (20 bp):
TATCGATACATTAGTAAATG
Found at i:411480 original size:2 final size:2
Alignment explanation
Indices: 411475--411507 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
411465 TTTTTTTAGA
411475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
411508 ATGCCTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:418714 original size:167 final size:166
Alignment explanation
Indices: 418299--418777 Score: 614
Period size: 167 Copynumber: 2.9 Consensus size: 166
418289 TGAAATACAA
* ** * *
418299 AGTTTTTTACTGT-GTAAATTTTTTTCGGAGGGATTTTTC-AAGATTTTAATTTTTAAAATTCAT
1 AGTTTTCTACT-TCGTAAA-TTTTTTCGGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATACAT
* * * * *
418362 AAAATATTATTATTTATTTGATATTAAATTATTTTTTAAAAATT-ATTTCATTTTCATGAG-TTT
64 CAAATATTATTA-TTATTTCATATTAAATCAGTTTTTAAAAATTCA-TTCATCTTCATGAGTTTT
* * *** * **
418425 TGAATTTTTTCCTTGTAATTCTTTTATTTCGAAAATATGG
127 TGATTTTTTTCCTTGAAATTCCCCTATATAAAAAATATGG
*
418465 AGTTTTCTACTTCGTAAATTTTTTC-GA-GGATTTTTTCTTGGTTTTTTATTTTTAAAATACATC
1 AGTTTTCTACTTCGTAAATTTTTTCGGAGGGA-TTTTTCTTGGTTTTTAATTTTTAAAATACATC
*
418528 AAATATTATTATATATTTCATGTTAAATCCA-TTTTTAAAAATTCATTCATCTTCATGAGTTTTT
65 AAATATTATTAT-TATTTCATATTAAAT-CAGTTTTTAAAAATTCATTCATCTTCATGAGTTTTT
* *
418592 TATTTTTTTCCTTGAAATTCCCCTGTATAAAAAATATGG
128 GATTTTTTTCCTTGAAATTCCCCTATATAAAAAATATGG
*
418631 AGTTTTCTACTTCGTAAATTTTTTCGGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATCCATCA
1 AGTTTTCTACTTCGTAAATTTTTTCGGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATACATCA
*
418696 AATATTATTACTTATTTCATATTAAATCAGTTTTTAAAAATTCATTCATCTACATGAGTTTTTGA
66 AATATTATTA-TTATTTCATATTAAATCAGTTTTTAAAAATTCATTCATCTTCATGAGTTTTTGA
418761 TTTTTTT-CTTGAAATTC
130 TTTTTTTCCTTGAAATTC
418778 TCTTTTTCCC
Statistics
Matches: 276, Mismatches: 26, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
163 3 0.01
164 9 0.03
165 76 0.28
166 87 0.32
167 97 0.35
168 4 0.01
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (166 bp):
AGTTTTCTACTTCGTAAATTTTTTCGGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATACATCA
AATATTATTATTATTTCATATTAAATCAGTTTTTAAAAATTCATTCATCTTCATGAGTTTTTGAT
TTTTTTCCTTGAAATTCCCCTATATAAAAAATATGG
Found at i:418805 original size:166 final size:162
Alignment explanation
Indices: 418299--418851 Score: 591
Period size: 166 Copynumber: 3.3 Consensus size: 162
418289 TGAAATACAA
* ** * *
418299 AGTTTTTTACTGT-GTAAATTTTTTTCGGAGGGATTTTTC-AAGATTTTAATTTTTAAAATTCAT
1 AGTTTTCTACT-TCGTAAA-TTTTTTC-GAGGGATTTTTCTTGGTTTTTAATTTTTAAAATACAT
* * * *
418362 AAAATATTATTATTTATTTGATATTAAATTATTTTTTAAAAATT-ATTTCATTTTCATGAG-TTT
63 CAAATATTATTA-TTATTTCATATTAAATCA-TTTTTAAAAATTCA-TTCATCTTCATGAGTTTT
* * * * *
418425 TGAATTTTTTCCTTGTAATTCTTTTATTTCGAAAATATGG
125 TG-ATTTTTTTCTTGAAATTCTCTT-TTTCAAAAAAATGG
*
418465 AGTTTTCTACTTCGTAAATTTTTTCGA-GGATTTTTTCTTGGTTTTTTATTTTTAAAATACATCA
1 AGTTTTCTACTTCGTAAATTTTTTCGAGGGA-TTTTTCTTGGTTTTTAATTTTTAAAATACATCA
* *
418529 AATATTATTATATATTTCATGTTAAATCCATTTTTAAAAATTCATTCATCTTCATGAGTTTTTTA
65 AATATTATTAT-TATTTCATATTAAAT-CATTTTTAAAAATTCATTCATCTTCATGAGTTTTTGA
* * *
418594 TTTTTTTCCTTGAAATTCCCCTGTAT-AAAAAATATGG
128 TTTTTTT-CTTGAAATT-CTCTTTTTCAAAAAA-ATGG
*
418631 AGTTTTCTACTTCGTAAATTTTTTCGGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATCCATCA
1 AGTTTTCTACTTCGTAAATTTTTTC-GAGGGATTTTTCTTGGTTTTTAATTTTTAAAATACATCA
*
418696 AATATTATTACTTATTTCATATTAAATCAGTTTTTAAAAATTCATTCATCTACATGAGTTTTTGA
65 AATATTATTA-TTATTTCATATTAAATCA-TTTTTAAAAATTCATTCATCTTCATGAGTTTTTGA
* **
418761 TTTTTTTCTTGAAATTCTCTTTTTCCCAAAAAATCA
128 TTTTTTTCTTGAAATTCTCTTTTT-CAAAAAAATGG
* * * **
418797 AATTTTCTA-TTCCATAAATATTTTCGAGGGCA-TTTTCTTTGGTTTAAAATTTTTA
1 AGTTTTCTACTT-CGTAAATTTTTTCGAGGG-ATTTTTC-TTGGTTTTTAATTTTTA
418852 TATTGCACCT
Statistics
Matches: 332, Mismatches: 36, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
163 3 0.01
164 9 0.03
165 104 0.31
166 108 0.33
167 104 0.31
168 4 0.01
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.51
Consensus pattern (162 bp):
AGTTTTCTACTTCGTAAATTTTTTCGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATACATCAA
ATATTATTATTATTTCATATTAAATCATTTTTAAAAATTCATTCATCTTCATGAGTTTTTGATTT
TTTTCTTGAAATTCTCTTTTTCAAAAAAATGG
Found at i:419287 original size:14 final size:14
Alignment explanation
Indices: 419270--419296 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
419260 AAAATGGTTT
419270 TGGAAAATAAAAAA
1 TGGAAAATAAAAAA
419284 TGGAAAATAAAAA
1 TGGAAAATAAAAA
419297 CAAAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
TGGAAAATAAAAAA
Found at i:419456 original size:14 final size:13
Alignment explanation
Indices: 419419--419471 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
419409 AAAACTCAGC
419419 AAAAAAAA-AAAGG
1 AAAAAAAAGAAA-G
*
419432 AAAAAAGAGAAAG
1 AAAAAAAAGAAAG
*
419445 AAAATAAAAGAAAA
1 AAAA-AAAAGAAAG
419459 AAAAAACAAGAAA
1 AAAAAA-AAGAAA
419472 AACATCAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 14 0.41
14 20 0.59
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:420360 original size:16 final size:15
Alignment explanation
Indices: 420324--420358 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
420314 GAAAATTTCA
420324 AAAATTAAAAATAAT
1 AAAATTAAAAATAAT
420339 AAAATTAAATAATAAAT
1 AAAATTAAA-AAT-AAT
420356 AAA
1 AAA
420359 TTCTTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 3 0.17
17 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTAAAAATAAT
Found at i:420660 original size:148 final size:147
Alignment explanation
Indices: 420390--420664 Score: 329
Period size: 148 Copynumber: 1.9 Consensus size: 147
420380 TTATCACCTG
* ** *
420390 AATTTTTCAAAATTTCTAATATTTTCATGGGTATCCGTGGGGGTATGAAAATTTTTAAAACATTT
1 AATTTTTCAAAATTTCTAATATTTTCATGGGCATCCGTAAGGGTATGAAAATTTTCAAAACATTT
* * * * ** * * *
420455 CGTATCTTTTTGGTTCTCCATTAAGATACAAAATGAATTTTTTGGGAAATAAAAAAATTAAATTA
66 CATATCTTTTCGGTCCTCCATTAAGACACAAAATGAAACTGTTGCGAAA-AAAAAAAATAAATTA
420520 AATACAAATTATGAACCC
130 AATACAAATTATGAACCC
* * *
420538 AATTTTTCAGAATTTCTAATA-TTTCTATTGGCATCCGTAAGGGTATGAAAATTTTCAAAACTTT
1 AATTTTTCAAAATTTCTAATATTTTC-ATGGGCATCCGTAAGGGTATGAAAATTTTCAAAACATT
* * **
420602 TCATGTCTTTTCGGTCCTCCATTAAGGCATGAAATGAAACTGTT-CGAAAAAAACAAAATAAAT
65 TCATATCTTTTCGGTCCTCCATTAAGACACAAAATGAAACTGTTGCGAAAAAAA-AAAATAAAT
420665 ATTTTAATTA
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
146 4 0.04
147 16 0.15
148 85 0.81
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (147 bp):
AATTTTTCAAAATTTCTAATATTTTCATGGGCATCCGTAAGGGTATGAAAATTTTCAAAACATTT
CATATCTTTTCGGTCCTCCATTAAGACACAAAATGAAACTGTTGCGAAAAAAAAAAATAAATTAA
ATACAAATTATGAACCC
Found at i:421196 original size:155 final size:156
Alignment explanation
Indices: 420899--421197 Score: 403
Period size: 155 Copynumber: 1.9 Consensus size: 156
420889 CTATAAATAT
* *
420899 TTTTTAAGTCCTTTAGGGGTATTAGGCATTTCTAAGTCGAAAGTATCCCCTAGGGATATTTTGAT
1 TTTTTAAGTCCTTTAGAGGTATTAGGCATTTCTAAGTCGAAAGTATCCCCTAGGGATATTTCGAT
* * * *
420964 AATTTTTTTAGAATCAAGTCTTAAGTTATCATCGGATCTGCTTTTATGCTGAAGGTAGATATTTA
66 AATTTTTCTAGAACCAAGTCTTAAGTTATCATCAGATCCGCTTTTATGCTGAAGGTAGATATTTA
421029 AGATAGGTTCATCCCTTTGAAAGTCC
131 AGATAGGTTCATCCCTTTGAAAGTCC
* * *
421055 TTTTTAAGTCCTTTAGAGGTATTAGGTACTTT-TACGTCGAAGGTATCCCCTAGAGGCAT-TTTC
1 TTTTTAAGTCCTTTAGAGGTATTAGGCA-TTTCTAAGTCGAAAGTATCCCCTAG-GG-ATATTTC
* *
421118 G-TAA-TTTTCTAGAACCAAGTCTTAGGTTATCA-CAAGATCCGTTTTTATGCTGCAA-GTAGAT
63 GATAATTTTTCTAGAACCAAGTCTTAAGTTATCATC-AGATCCGCTTTTATGCTG-AAGGTAGAT
*
421179 ATTTAGGATAGGTTCATCC
126 ATTTAAGATAGGTTCATCC
421198 ATTCATGATT
Statistics
Matches: 126, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
154 1 0.01
155 64 0.51
156 50 0.40
157 9 0.07
158 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (156 bp):
TTTTTAAGTCCTTTAGAGGTATTAGGCATTTCTAAGTCGAAAGTATCCCCTAGGGATATTTCGAT
AATTTTTCTAGAACCAAGTCTTAAGTTATCATCAGATCCGCTTTTATGCTGAAGGTAGATATTTA
AGATAGGTTCATCCCTTTGAAAGTCC
Found at i:424769 original size:9 final size:9
Alignment explanation
Indices: 424746--424788 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
424736 TCCTCTAAAT
*
424746 AAGAAAAAC
1 AAGAAAAAA
424755 AA-AAAAAA
1 AAGAAAAAA
424763 AAGAAAAAA
1 AAGAAAAAA
*
424772 AAGGAAAAA
1 AAGAAAAAA
424781 AAGAAAAA
1 AAGAAAAA
424789 GTATGAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:425819 original size:32 final size:32
Alignment explanation
Indices: 425783--425853 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
425773 TTCAACGATT
*
425783 TGTATCGATATATAAGTGTTATATCGATACAA
1 TGTATCGATACATAAGTGTTATATCGATACAA
* * *
425815 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTATATCGATACAA
425847 TGTATCG
1 TGTATCG
425854 CTACGAAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTATATCGATACAA
Found at i:425916 original size:13 final size:13
Alignment explanation
Indices: 425898--425922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
425888 ATTACTCAAA
425898 TGTATCGATACAT
1 TGTATCGATACAT
425911 TGTATCGATACA
1 TGTATCGATACA
425923 CTGATCTTTG
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:425975 original size:52 final size:52
Alignment explanation
Indices: 425931--426059 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
425921 CACTGATCTT
*
425931 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
** *
425983 TGTATCGATACATATAGGCAAATTTGTCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
426035 TGTATCGATATATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
426060 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:427552 original size:15 final size:16
Alignment explanation
Indices: 427524--427556 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
427514 ATGAAAAGTC
*
427524 AAAAGTAAACACAAAA
1 AAAAATAAACACAAAA
427540 AAAAATAAA-ACAAAA
1 AAAAATAAACACAAAA
427555 AA
1 AA
427557 CACATACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAATAAACACAAAA
Found at i:427845 original size:21 final size:20
Alignment explanation
Indices: 427810--427860 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
427800 GTTCTTTTCC
* * *
427810 AAACACAAAAAAAAAGAAGA
1 AAACAGAAAAAAAAAAAACA
*
427830 AAAGAGAAAAAGAAAAAAACA
1 AAACAGAAAAA-AAAAAAACA
427851 AAACAGAAAA
1 AAACAGAAAA
427861 TCTCGGTGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (20 bp):
AAACAGAAAAAAAAAAAACA
Found at i:430691 original size:10 final size:10
Alignment explanation
Indices: 430673--430730 Score: 73
Period size: 10 Copynumber: 5.5 Consensus size: 10
430663 CCATTTCATA
430673 TTTTT-TTTC
1 TTTTTCTTTC
430682 TTTTTCTTTC
1 TTTTTCTTTC
430692 TTTTTCTTTC
1 TTTTTCTTTC
430702 TTTCTTCTTCATC
1 TTT-TTCTT--TC
430715 TTCTTTCTTTC
1 TT-TTTCTTTC
430726 TTTTT
1 TTTTT
430731 TACCTAACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.11
10 20 0.45
11 9 0.20
13 9 0.20
14 1 0.02
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:430701 original size:20 final size:21
Alignment explanation
Indices: 430673--430730 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 21
430663 CCATTTCATA
430673 TTTTT-TTTCTTTTTCTT-TC
1 TTTTTCTTTCTTTTTCTTATC
430692 TTTTTCTTTCTTTCTTCTTCATC
1 TTTTTCTTTCTTT-TTCTT-ATC
430715 TTCTTTCTTTCTTTTT
1 TT-TTTCTTTCTTTTT
430731 TACCTAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 5 0.15
23 6 0.18
24 11 0.32
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTCTTTCTTTTTCTTATC
Found at i:431650 original size:32 final size:32
Alignment explanation
Indices: 431587--432316 Score: 1192
Period size: 32 Copynumber: 22.8 Consensus size: 32
431577 AAAATGGTGA
* * * **
431587 TTTGAAAAGGGGTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
431619 TTTTAAATGGATTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
431651 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
431683 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
431715 TTTGGAATAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
431747 TTTGAAATGGGTTGCCACCGACTTGTGTAGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
431779 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
431811 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
431843 TTTGGAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
431875 TTTGGAATGGGTTGCCACGGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
431907 TTTGAAATGGGTTGCCACGGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
431939 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
431971 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
432003 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
432035 TTTGAAATGGGTTGCCACCGACTTTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
432067 TTTGGAATGGGTTGCCACCGACTTTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
432099 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
432131 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
432163 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
432195 TTTGAAATGGGTTGCCACTAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
432227 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
432259 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
432291 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
432317 GATTTAAAAG
Statistics
Matches: 655, Mismatches: 43, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
31 13 0.02
32 642 0.98
ACGTcount: A:0.17, C:0.18, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:432333 original size:27 final size:27
Alignment explanation
Indices: 432299--433335 Score: 1543
Period size: 27 Copynumber: 38.0 Consensus size: 27
432289 GCTTTGAAAT
* *
432299 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
432326 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
432353 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
432380 GGGTGCCACGGAGTTATGGACTTGAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
432407 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
432434 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
432462 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
432489 GAGATGCCACGGAGTTATGGATTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
432517 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
432544 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
432571 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
432598 GGGTGCCATAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
432625 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
432652 GAGATGCCAAGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
432680 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
432707 GGGTGCCACGAAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
432734 GGAATGCCACGGAGTTGTGGACTTAAAA
1 GG-GTGCCACGGAGTTGTGGACTTAAAA
432762 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
432789 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
432816 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
432843 GGGTACCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
432871 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
432898 GGGTACCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
432925 GGGTGCCACGGAATTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
432952 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
432979 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
433007 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
433034 GAGATGCCACAGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
433062 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
433089 AGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
433116 GGAATGCCACGGAGTTGTGGACTTAAAA
1 GG-GTGCCACGGAGTTGTGGACTTAAAA
* * *
433144 GGGTGCCACAGATTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
433171 GGGTACCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
433199 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
433226 GGGTACCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
433253 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
433280 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
433307 GGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
433335 G
1 G
433336 AAAATGCCAC
Statistics
Matches: 914, Mismatches: 86, Indels: 19
0.90 0.08 0.02
Matches are distributed among these distances:
27 689 0.75
28 225 0.25
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:432641 original size:191 final size:189
Alignment explanation
Indices: 432299--433335 Score: 1563
Period size: 191 Copynumber: 5.4 Consensus size: 189
432289 GCTTTGAAAT
* * * *
432299 GGGTGCCACAGAGTTGTGGATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGG
* * *
432364 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTGAAAGGGTGCCACAGAGTTGTGGACT
66 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
* *
432429 AAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
131 TAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* * * *
432489 GAGATGCCACGGAGTTATGGATTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACG
* **
432554 GAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATAGAGTTGTGGAC
65 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
432619 TAAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCA-AGGAGTTATGGACTTAAAA
130 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GGTGCCACA-GAGTTGTGGACTTAAAA
* *
432680 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTTGTGGTCTTAAAAGGAATGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG-ATGCCACG
432745 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
65 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
432810 TTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTACCACGGAGTTGTGGACTTTAAAA
130 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAA
* * * * *
432871 GGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCACAGAGTTGTGGTCTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGG
* * *
432936 AATTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACT
66 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-
* *
433001 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACAGAGTTATGGACTTAAAA
130 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GGTGCCACAGAGTTGTGGACTTAAAA
* *
433062 GGGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGTCTTAAAAGGAATGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG-ATGCCACG
* * * *
433127 GAGTTGTGGACTTAAAAGGGTGCCACAGATTTGTGGACTAAAAAGGGTACCACGGAGTTGTGGAC
65 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
433192 TTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGGAGTTGTGGTCTTAAAA
130 -TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
433253 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACAG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGG
433318 AGTTGTGGACTTTAAAAG
66 AGTTGTGGAC-TTAAAAG
433336 AAAATGCCAC
Statistics
Matches: 781, Mismatches: 56, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
190 161 0.21
191 500 0.64
192 120 0.15
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (189 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGG
AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
TAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
Found at i:434393 original size:1 final size:1
Alignment explanation
Indices: 434387--434417 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
434377 GGTGAAAAGG
*
434387 TTTTTTTTGTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
434418 AGGATTAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:442915 original size:31 final size:31
Alignment explanation
Indices: 442835--443143 Score: 346
Period size: 31 Copynumber: 10.0 Consensus size: 31
442825 TTTTCAAATC
*
442835 TCTTTTCTTTAAAGTCCACGACTCAGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
*
442866 TCTCTTTC--CAAAGTCCACGACTTAGTGGCA
1 TCT-TTTCTTCAAAGTCCACGACTCAGTGGCA
*
442896 TCTTTTCTTCAAAGCCCACGACTCAGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* * *
442927 TCTTTCCTTCAAAGTCCACAATTCAGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
442958 TCTCTTTTCTTCAAAGTCCACGACTCAGTGGCA
1 --TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* *
442991 TCTTTTCCTTCTTAAAATCCACGACTTAGTGGCA
1 TCTTTT-CTTC--AAAGTCCACGACTCAGTGGCA
* * * *
443025 TCTTGTC-TCAAAGTCTACAATTCAGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
*
443055 TCTCTTTC--CAAAGTCCATGACTCAGTGGCA
1 TCT-TTTCTTCAAAGTCCACGACTCAGTGGCA
*
443085 TCTTTTCTTCAAAGTCCACGACTCCGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* * *
443116 -CCTTT-TT-AAAGTCCACAACTCTGTGGCA
1 TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
443144 CCTTGTTCCT
Statistics
Matches: 238, Mismatches: 29, Indels: 25
0.82 0.10 0.09
Matches are distributed among these distances:
28 19 0.08
29 10 0.04
30 67 0.28
31 79 0.33
32 10 0.04
33 29 0.12
34 24 0.10
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (31 bp):
TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
Found at i:443089 original size:125 final size:122
Alignment explanation
Indices: 442834--443121 Score: 357
Period size: 125 Copynumber: 2.3 Consensus size: 122
442824 TTTTTCAAAT
* *
442834 CTCTTTTCTTTAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTTAGTGGCATCT
1 CTCTTTTCTTCAAAGTCCACGACTCAGTGGCATCT-TTTCCAAAATCCACGACTTAGTGGCATCT
* * * *
442899 TTTCTTCAAAGCCCACGACTCAGTGGCATCTTTCCTTCAAAGTCCACAATTCAGTGGCA
65 TGTCTTCAAAGCCCACAACTCAGTGGCATCTTT-CTCCAAAGTCCACAACTCAGTGGCA
442958 TCTCTTTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCCTTCTTAAAATCCACGACTTAGTGG
1 -CTCTTTTCTTCAAAGTCCACGACTCAGTGGCATCTTTT-C--C--AAAATCCACGACTTAGTGG
* * * **
443023 CATCTTGTC-TCAAAGTCTACAATTCAGTGGCATCTCTT-TCCAAAGTCCATGACTCAGTGGCA
60 CATCTTGTCTTCAAAGCCCACAACTCAGTGGCATCT-TTCTCCAAAGTCCACAACTCAGTGGCA
* *
443085 -TCTTTTCTTCAAAGTCCACGACTCCGTGGCACCTTTT
1 CTCTTTTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
443122 TAAAGTCCAC
Statistics
Matches: 144, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
124 3 0.02
125 70 0.49
127 21 0.15
128 22 0.15
129 28 0.19
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (122 bp):
CTCTTTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCCAAAATCCACGACTTAGTGGCATCTT
GTCTTCAAAGCCCACAACTCAGTGGCATCTTTCTCCAAAGTCCACAACTCAGTGGCA
Found at i:443182 original size:158 final size:158
Alignment explanation
Indices: 442850--443154 Score: 383
Period size: 158 Copynumber: 1.9 Consensus size: 158
442840 TCTTTAAAGT
* * * *
442850 CCACGACTCAGTGGCATCTCTTTC-CAAAGTCCACGACTT-AGTGGCATCTTTTCTTCAAAGCCC
1 CCACGACTTAGTGGCATCT-TGTCTCAAAGTCTAC-AATTCAGTGGCATCTTTTC-TCAAAGCCC
*
442913 ACGACTCAGTGGCATCTTTCCTTCAAAGTCCACAATTCAGTGGCATCTCTTTTCTTCAAAGTCCA
63 ACGACTCAGTGGCATCTTTCCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTTCAAAGTCCA
* * *
442978 CGACTCAGTGGCATCTTTTCCTTCTTAAAAT
128 CAACTCAGTGGCACCTTTTCCTTCTTAAAAC
* *
443009 CCACGACTTAGTGGCATCTTGTCTCAAAGTCTACAATTCAGTGGCATCTCTTTC-CAAAGTCCAT
1 CCACGACTTAGTGGCATCTTGTCTCAAAGTCTACAATTCAGTGGCATCT-TTTCTCAAAGCCCAC
* * *
443073 GACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCCGTGGCA-C-C-TTT-TT-AAAGTCCACA
65 GACTCAGTGGCATCTTTCCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTTCAAAGTCCACA
*
443133 ACTCTGTGGCACCTTGTTCCTT
130 ACTCAGTGGCACCTT-TTCCTT
443155 TTTCTAAAGC
Statistics
Matches: 129, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
153 22 0.17
154 8 0.06
155 3 0.02
156 1 0.01
157 1 0.01
158 53 0.41
159 37 0.29
160 4 0.03
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (158 bp):
CCACGACTTAGTGGCATCTTGTCTCAAAGTCTACAATTCAGTGGCATCTTTTCTCAAAGCCCACG
ACTCAGTGGCATCTTTCCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTTCAAAGTCCACAA
CTCAGTGGCACCTTTTCCTTCTTAAAAC
Found at i:443247 original size:33 final size:33
Alignment explanation
Indices: 443151--443247 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 33
443141 GCACCTTGTT
*
443151 CCTTTTTCTAAAGCCCACACAAGTTGGTGGCAA
1 CCTTCTTCTAAAGCCCACACAAGTTGGTGGCAA
* * * * *
443184 CC-CCCTCTAATGCCCACACAAGTCGATGGCAA
1 CCTTCTTCTAAAGCCCACACAAGTTGGTGGCAA
* *
443216 CCTTCTTCAAAAGTCCACACAAGTTGGTGGCA
1 CCTTCTTCTAAAGCCCACACAAGTTGGTGGCA
443248 TCTACCTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
32 26 0.52
33 24 0.48
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.23
Consensus pattern (33 bp):
CCTTCTTCTAAAGCCCACACAAGTTGGTGGCAA
Found at i:443408 original size:92 final size:92
Alignment explanation
Indices: 443251--444082 Score: 1345
Period size: 92 Copynumber: 9.0 Consensus size: 92
443241 GGTGGCATCT
443251 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
443316 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
* * *
443343 ACCTTTAAGTCCAATATCGCTGACCTTGAATCTGCATATTGTCACCTTTATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
443408 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
443435 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
443500 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
443527 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
443592 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
* *
443619 ACCTTTTAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
*
443684 TAGCTGGCCTTGAATTAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
* *
443711 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAATCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
443776 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
* *
443803 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGTCCAATA
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
*
443868 TCGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
* * *
443895 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCA-C-----CTTTAAGTCCAATA
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
* *
443954 TCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTC
66 TAGCTGGCCTTGAATCAGCACATT---G-----G-C
* *
443990 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCATCTTTAAGTCCAAT
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-ATCTTTAAGTCCAAT
* *
444054 ATCGCTGGCCTTGAATCAGCACATTGGC
65 GTAGCTGGCCTTGAATCAGCACATTGGC
444082 A
1 A
444083 TTCTTCTCTT
Statistics
Matches: 701, Mismatches: 24, Indels: 30
0.93 0.03 0.04
Matches are distributed among these distances:
86 37 0.05
89 1 0.00
91 1 0.00
92 578 0.82
93 1 0.00
94 1 0.00
95 44 0.06
98 1 0.00
101 37 0.05
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGGC
Done.