Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 107 of 163
Found at i:30249828 original size:21 final size:21
Alignment explanation
Indices: 30249783--30249836 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
30249773 CCAATTACAT
* *
30249783 TTCTACCGATACATGTGACAG
1 TTCTACCGATACATGTCACAC
**
30249804 TTCTACCGATACATGTCTTAC
1 TTCTACCGATACATGTCACAC
*
30249825 TTCTACCTATAC
1 TTCTACCGATAC
30249837 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (21 bp):
TTCTACCGATACATGTCACAC
Found at i:30249929 original size:24 final size:21
Alignment explanation
Indices: 30249877--30249932 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 21
30249867 CCTGCAACCT
*
30249877 CTACCGATACAAGCATCCTAA
1 CTACCGATACAAGCATCCAAA
30249898 CTACCGATACAAGCATACACCAAA
1 CTACCGATACAAGCAT---CCAAA
*
30249922 CTATCGATACA
1 CTACCGATACA
30249933 TATTATGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 16 0.53
24 14 0.47
ACGTcount: A:0.41, C:0.32, G:0.09, T:0.18
Consensus pattern (21 bp):
CTACCGATACAAGCATCCAAA
Found at i:30261732 original size:11 final size:11
Alignment explanation
Indices: 30261716--30261740 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30261706 ATATTTACAT
30261716 ACTCTTGAACA
1 ACTCTTGAACA
30261727 ACTCTTGAACA
1 ACTCTTGAACA
30261738 ACT
1 ACT
30261741 GGTACTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (11 bp):
ACTCTTGAACA
Found at i:30263308 original size:30 final size:29
Alignment explanation
Indices: 30263267--30263348 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
30263257 CTTTGGACAC
*
30263267 TCGAGGGCAAAATGGTAATTTTTGATAAAT
1 TCGAGGTCAAAATGGTAATTTTTGA-AAAT
* * *
30263297 TCGAGGTCAAAAT-GAAATTTTAGAAAGT
1 TCGAGGTCAAAATGGTAATTTTTGAAAAT
* *
30263325 TTG-GGTGTAAAATGGTAATTTTTG
1 TCGAGGT-CAAAATGGTAATTTTTG
30263349 GTGAAATCGG
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 3 0.07
28 10 0.24
29 17 0.40
30 12 0.29
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35
Consensus pattern (29 bp):
TCGAGGTCAAAATGGTAATTTTTGAAAAT
Found at i:30263409 original size:30 final size:29
Alignment explanation
Indices: 30263331--30263409 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
30263321 AAGTTTGGGT
*
30263331 GTAAAATGGTAATTTTTGGTGAAATCGGG
1 GTAAAATGGTAATTTTTGGAGAAATCGGG
* ***
30263360 GTTAAAAATGG-GA-TTTTGGAGGGTTCGAGG
1 G-T-AAAATGGTAATTTTTGGAGAAATCG-GG
30263390 GTAAAATGGTAATTTTTGGA
1 GTAAAATGGTAATTTTTGGA
30263410 AGTTTTGGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
28 7 0.18
29 13 0.33
30 12 0.31
31 7 0.18
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTGGAGAAATCGGG
Found at i:30263435 original size:29 final size:30
Alignment explanation
Indices: 30263402--30263478 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
30263392 AAAATGGTAA
* *
30263402 TTTTTGGAAGTTTTGGGGTT-AAAATATAT
1 TTTTTGAAAGTTTTAGGGTTAAAAATATAT
*
30263431 TTTTTTAAAGTTTTAGGGTTAAAAATATAGT
1 TTTTTGAAAGTTTTAGGGTTAAAAATATA-T
* *
30263462 TTCTTGACAG-TTTAGGG
1 TTTTTGAAAGTTTTAGGG
30263479 ACCTACAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 17 0.43
30 15 0.38
31 8 0.20
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.47
Consensus pattern (30 bp):
TTTTTGAAAGTTTTAGGGTTAAAAATATAT
Found at i:30265385 original size:19 final size:19
Alignment explanation
Indices: 30265341--30265386 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
30265331 AACTTTGGAC
*
30265341 TTGTAATTGGACTTTAATT
1 TTGTATTTGGACTTTAATT
30265360 TTGTATTTGGACATTTAATT
1 TTGTATTTGGAC-TTTAATT
30265380 TT-TATTT
1 TTGTATTT
30265387 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.24, C:0.04, G:0.13, T:0.59
Consensus pattern (19 bp):
TTGTATTTGGACTTTAATT
Found at i:30265406 original size:17 final size:17
Alignment explanation
Indices: 30265380--30265416 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
30265370 ACATTTAATT
*
30265380 TTTATTTTAAATTTAAA
1 TTTATATTAAATTTAAA
30265397 TTTATATTAAATTTAAA
1 TTTATATTAAATTTAAA
30265414 TTT
1 TTT
30265417 TAGGAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATATTAAATTTAAA
Found at i:30266173 original size:200 final size:200
Alignment explanation
Indices: 30265808--30266479 Score: 1026
Period size: 200 Copynumber: 3.4 Consensus size: 200
30265798 TCTTAGTATT
30265808 TCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTAT
1 TCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTAT
* * * * *
30265873 CTCATCAGAAAGATAACCGCCTTGCTTGTTTTAATTCGCTTCTCTGGATCTCCTTAGGAAGACGA
66 CTCATCAGGAAGATGACCGCCTTGCTTGTTTTAACTCGCTTCTTTGGATCTCCTCAGGAAGACGA
30265938 ATTTGGTCCACTTCTCTGTATCTCATTAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCA
131 ATTTGGTCCACTTCTCTGTATCTCATTAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCA
30266003 GTGTC
196 GTGTC
* *
30266008 TCATCAAGAAGCTGGGTTCGAAGATTGGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTAT
1 TCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTAT
* *
30266073 CTCATCAGGAATATGACCGCCTTGCTTGTTTTAACTCGCTTCTTTGAATCTCCTCAGGAAGACGA
66 CTCATCAGGAAGATGACCGCCTTGCTTGTTTTAACTCGCTTCTTTGGATCTCCTCAGGAAGACGA
* * * *
30266138 ATTTGGTCCACTTCTCTGTGTCTCATCAAGAAGCTAACCGTTTTATTGCTTT-GACCTGCTTCTC
131 ATTTGGTCCACTTCTCTGTATCTCATTAGGAAGCTAACCATTTTATTG-TTTCGACCTGCTTCTC
*
30266202 AGTGCC
195 AGTGTC
* ** * *
30266208 TCATCAGGAAGCTAGGTTCGAAGATTTACTCGCATTGAGCATTGGGTTGGTATTCTTCTCTGTAT
1 TCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTAT
**
30266273 CTCATCAGGAAGATGACCGCCTCACTTGTTTTAACTCGCTTCTTTGGA--T-CTCAGGAAGACGA
66 CTCATCAGGAAGATGACCGCCTTGCTTGTTTTAACTCGCTTCTTTGGATCTCCTCAGGAAGACGA
* * * *
30266335 ATTTGGTCCACTTCTTTGTATCTCATTAGGGAGCTAACCA-TTTATTGCTTCGGCCTGCTTCTCA
131 ATTTGGTCCACTTCTCTGTATCTCATTAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCA
30266399 GTGTC
196 GTGTC
30266404 TCATCAGGAAGCTGGGTTCGAAGATTGGCT--C-----GCGTTGAGTTGGTATTCTTCTCTGTAT
1 TCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTAT
30266462 CTCATCAGGAAGATGACC
66 CTCATCAGGAAGATGACC
30266480 ATTTATTGCT
Statistics
Matches: 431, Mismatches: 39, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
189 43 0.10
194 1 0.00
195 2 0.00
196 50 0.12
197 47 0.11
198 1 0.00
200 284 0.66
201 3 0.01
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (200 bp):
TCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCGTTGAGTTGGTATTCTTCTCTGTAT
CTCATCAGGAAGATGACCGCCTTGCTTGTTTTAACTCGCTTCTTTGGATCTCCTCAGGAAGACGA
ATTTGGTCCACTTCTCTGTATCTCATTAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCA
GTGTC
Found at i:30266522 original size:106 final size:108
Alignment explanation
Indices: 30266345--30266592 Score: 365
Period size: 106 Copynumber: 2.3 Consensus size: 108
30266335 ATTTGGTCCA
* * * * * *
30266345 CTTCTTTGTATCTCATTAGGGAGCTAACCATTTATTGCTTCGGCCTGCTTCTCAGTGTCTCATCA
1 CTTCTCTGTATCTCATCAGGAAGATGACCATTTATTGCTTCAGCCTGCTTCTCAGTGTCTCATCA
*
30266410 GGAAGCTGGGTTCGAAGATTGGCTCGCGTT-G-AGTTGGTATT
66 AGAAGCTGGGTTCGAAGATTGGCTCGCGTTGGTAGTTGGTATT
30266451 CTTCTCTGTATCTCATCAGGAAGATGACCATTTATTGCTTCAGCCTGCTTCTCAGTGTCTCATCA
1 CTTCTCTGTATCTCATCAGGAAGATGACCATTTATTGCTTCAGCCTGCTTCTCAGTGTCTCATCA
30266516 AGAAGCTGGGTTCGAAGATTGGCTCGCGTTGAGCGTTAAGTTGGTATT
66 AGAAGCTGGGTTCGAAGATTGGCTCGCGTT--G-G-T-AGTTGGTATT
*
30266564 CTTCTCTGTATCTCATCACGAAGATGACC
1 CTTCTCTGTATCTCATCAGGAAGATGACC
30266593 GCCTTGCTTG
Statistics
Matches: 127, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
106 88 0.69
110 1 0.01
113 38 0.30
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.35
Consensus pattern (108 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCATTTATTGCTTCAGCCTGCTTCTCAGTGTCTCATCA
AGAAGCTGGGTTCGAAGATTGGCTCGCGTTGGTAGTTGGTATT
Found at i:30267159 original size:100 final size:99
Alignment explanation
Indices: 30266996--30267220 Score: 236
Period size: 100 Copynumber: 2.2 Consensus size: 99
30266986 GCCATTTCGG
* *
30266996 CTTAAATCTTTCCTTTCTGTCTTCTGAGGTACACGGTTCACCGTTACGGCTCAAACCTTTCCCTT
1 CTTAAATCTTTCCTTTCTGTCTTCTGAGGTACACGGTCCACCGTTACGACTCAAACCTTTCCCTT
** * *
30267061 TCGTATCTTTGTGGTACTGGATTCGCCACTGCGT
66 TCACATCTTTGTGGTACTAGATCCGCCACTGCGT
* * * ** * *
30267095 CTTAAGTC-TTCCTTTCTTGTCTTTTTGAGGTACACGGTCCGCCGTTGTGACTTAGACCTTTCCC
1 CTTAAATCTTTCCTTTC-TGTC-TTCTGAGGTACACGGTCCACCGTTACGACTCAAACCTTTCCC
* ** *
30267159 TTTTACATCTTTGTGGTACTAGATCCGCCGTTACGAT
64 TTTCACATCTTTGTGGTACTAGATCCGCCACTGCG-T
* *
30267196 CTTAGATCTTTCCCTTTATGTCTTC
1 CTTAAATCTTT-CCTTTCTGTCTTC
30267221 ATGATATTGA
Statistics
Matches: 100, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
98 8 0.08
99 11 0.11
100 61 0.61
101 9 0.09
102 6 0.06
103 5 0.05
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.41
Consensus pattern (99 bp):
CTTAAATCTTTCCTTTCTGTCTTCTGAGGTACACGGTCCACCGTTACGACTCAAACCTTTCCCTT
TCACATCTTTGTGGTACTAGATCCGCCACTGCGT
Found at i:30268216 original size:7 final size:7
Alignment explanation
Indices: 30268200--30268297 Score: 80
Period size: 7 Copynumber: 14.3 Consensus size: 7
30268190 CGACCTCTCC
30268200 TTTTCTT
1 TTTTCTT
*
30268207 TTTCCTT
1 TTTTCTT
30268214 TTTT-TT
1 TTTTCTT
30268220 CCTTTTCTT
1 --TTTTCTT
30268229 TTTTC-T
1 TTTTCTT
30268235 TTTTCTTT
1 TTTTC-TT
30268243 TTTTCTT
1 TTTTCTT
30268250 TTTTCTT
1 TTTTCTT
*
30268257 TTTT-TG
1 TTTTCTT
*
30268263 TTTTGTT
1 TTTTCTT
*
30268270 TTTTC-C
1 TTTTCTT
*
30268276 TCTTCTT
1 TTTTCTT
*
30268283 TTTT-TC
1 TTTTCTT
30268289 TTTTCTT
1 TTTTCTT
30268296 TT
1 TT
30268298 ATTCATTGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
6 22 0.31
7 38 0.53
8 10 0.14
9 2 0.03
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:30268223 original size:22 final size:22
Alignment explanation
Indices: 30268197--30268261 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
30268187 CCTCGACCTC
*
30268197 TCCTTTTCTTTTTCCTTTTTTT
1 TCCTTTTCTTTTTTCTTTTTTT
30268219 TCCTTTTCTTTTTTCTTTTTCTT
1 TCCTTTTCTTTTTTCTTTTT-TT
30268242 T--TTTTCTTTTTTCTTTTTTT
1 TCCTTTTCTTTTTTCTTTTTTT
30268262 GTTTTGTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 2 0.05
21 17 0.41
22 19 0.46
23 3 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TCCTTTTCTTTTTTCTTTTTTT
Found at i:30268230 original size:13 final size:13
Alignment explanation
Indices: 30268197--30268297 Score: 93
Period size: 13 Copynumber: 7.9 Consensus size: 13
30268187 CCTCGACCTC
30268197 TCCTTTTC-TTTT
1 TCCTTTTCTTTTT
30268209 TCC--TT-TTTTT
1 TCCTTTTCTTTTT
30268219 TCCTTTTCTTTTT
1 TCCTTTTCTTTTT
*
30268232 TCTTTTTCTTTTTT
1 TCCTTTTC-TTTTT
*
30268246 TCTTTTTTCTTTTT
1 TC-CTTTTCTTTTT
** *
30268260 TTGTTTTGTTTTT
1 TCCTTTTCTTTTT
*
30268273 TCCTCTTCTTTTT
1 TCCTTTTCTTTTT
*
30268286 TTCTTTTCTTTT
1 TCCTTTTCTTTT
30268298 ATTCATTGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
10 9 0.12
12 5 0.07
13 40 0.55
14 13 0.18
15 6 0.08
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (13 bp):
TCCTTTTCTTTTT
Found at i:30268259 original size:41 final size:42
Alignment explanation
Indices: 30268200--30268292 Score: 116
Period size: 41 Copynumber: 2.2 Consensus size: 42
30268190 CGACCTCTCC
* * *
30268200 TTTTCTTTTTCCTTTTTTTTCCTTTTCTTTTTTCTTTTTCTTT
1 TTTTCTTTTT-CTCTTTTTTCCTTTTCTTTTTTCCTCTTCTTT
** *
30268243 TTTTCTTTTT-TCTTTTTTTGTTTTGTTTTTTCCTCTTCTTT
1 TTTTCTTTTTCTCTTTTTTCCTTTTCTTTTTTCCTCTTCTTT
30268284 TTTTCTTTT
1 TTTTCTTTT
30268293 CTTTTATTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 34 0.77
43 10 0.23
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (42 bp):
TTTTCTTTTTCTCTTTTTTCCTTTTCTTTTTTCCTCTTCTTT
Found at i:30273597 original size:29 final size:28
Alignment explanation
Indices: 30273553--30273654 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 28
30273543 ACACCCGGGG
*
30273553 CAAAATGGTAATTTTTGATAAAATCGAGGT
1 CAAAAT-GAAATTTTTG-TAAAATCGAGGT
**
30273583 CAAAATGAAATTTTTG-AAAATTTAGGTT
1 CAAAATGAAATTTTTGTAAAATCGAGG-T
* * *
30273611 TAAAATGATAATTTTTGGTGAAATCGGGGT
1 CAAAATGA-AATTTTT-GTAAAATCGAGGT
* *
30273641 TAAAATGAGATTTT
1 CAAAATGAAATTTT
30273655 GGAGGGTTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
27 8 0.14
28 8 0.14
29 21 0.36
30 16 0.27
31 6 0.10
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (28 bp):
CAAAATGAAATTTTTGTAAAATCGAGGT
Found at i:30273648 original size:30 final size:30
Alignment explanation
Indices: 30273554--30273648 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
30273544 CACCCGGGGC
* * * *
30273554 AAAATGGTAATTTTTGATAAAATCGAGGTC
1 AAAATGATAATTTTTGGTAAAATCGGGGTT
** *
30273584 AAAATGA-AATTTTT-G-AAAATTTAGGTTT
1 AAAATGATAATTTTTGGTAAAA-TCGGGGTT
*
30273612 AAAATGATAATTTTTGGTGAAATCGGGGTT
1 AAAATGATAATTTTTGGTAAAATCGGGGTT
30273642 AAAATGA
1 AAAATGA
30273649 GATTTTGGAG
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
27 4 0.08
28 10 0.20
29 14 0.28
30 19 0.38
31 3 0.06
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (30 bp):
AAAATGATAATTTTTGGTAAAATCGGGGTT
Found at i:30273734 original size:30 final size:29
Alignment explanation
Indices: 30273665--30273732 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
30273655 GGAGGGTTCA
30273665 AGGGT-AAAATGGTAATTTTTAGAAGTTTT
1 AGGGTCAAAAT-GTAATTTTTAGAAGTTTT
* * *
30273694 GGGGTCAAAATGTATTTTTTTGAAGTTTT
1 AGGGTCAAAATGTAATTTTTAGAAGTTTT
30273723 AGGGTCAAAA
1 AGGGTCAAAA
30273733 ATATAGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 29 0.85
30 5 0.15
ACGTcount: A:0.32, C:0.03, G:0.25, T:0.40
Consensus pattern (29 bp):
AGGGTCAAAATGTAATTTTTAGAAGTTTT
Found at i:30273743 original size:30 final size:29
Alignment explanation
Indices: 30273680--30273743 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
30273670 AAAATGGTAA
* * *
30273680 TTTTTAGAAGTTTTGGGGTCAAAATGTAT
1 TTTTTAGAAGTTTTAGGGTCAAAATATAG
*
30273709 TTTTTTGAAGTTTTAGGGTCAAAAATATAG
1 TTTTTAGAAGTTTTAGGGTC-AAAATATAG
30273739 TTTTT
1 TTTTT
30273744 GGACAGTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.48
Consensus pattern (29 bp):
TTTTTAGAAGTTTTAGGGTCAAAATATAG
Found at i:30275616 original size:19 final size:20
Alignment explanation
Indices: 30275588--30275633 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
30275578 CCAATTGGGC
*
30275588 TTGTAATTGGAC-TTTAATT
1 TTGTATTTGGACATTTAATT
30275607 TTGTATTTGGACATTTAATT
1 TTGTATTTGGACATTTAATT
30275627 TT-TATTT
1 TTGTATTT
30275634 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.24, C:0.04, G:0.13, T:0.59
Consensus pattern (20 bp):
TTGTATTTGGACATTTAATT
Found at i:30275653 original size:17 final size:17
Alignment explanation
Indices: 30275627--30275663 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
30275617 ACATTTAATT
*
30275627 TTTATTTTAAATTTAAA
1 TTTATATTAAATTTAAA
*
30275644 TTTATATTAAGTTTAAA
1 TTTATATTAAATTTAAA
30275661 TTT
1 TTT
30275664 TAGGAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATATTAAATTTAAA
Found at i:30287516 original size:16 final size:16
Alignment explanation
Indices: 30287495--30287529 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30287485 AAGCATCAGC
30287495 TTGGAA-CTGGAACAAG
1 TTGGAACCT-GAACAAG
30287511 TTGGAACCTGAACAAG
1 TTGGAACCTGAACAAG
30287527 TTG
1 TTG
30287530 TTGATAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (16 bp):
TTGGAACCTGAACAAG
Found at i:30292440 original size:21 final size:21
Alignment explanation
Indices: 30292416--30292466 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
30292406 ATAATAGCAT
30292416 AATCCAAATATAAAATTTAGA
1 AATCCAAATATAAAATTTAGA
* *
30292437 AATCCAAACATAAAATTTATA
1 AATCCAAATATAAAATTTAGA
*
30292458 AATCTAAAT
1 AATCCAAAT
30292467 TACATAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (21 bp):
AATCCAAATATAAAATTTAGA
Found at i:30293794 original size:13 final size:15
Alignment explanation
Indices: 30293766--30293797 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
30293756 AGTAAAATTC
30293766 AATTCGATTCAAAAA
1 AATTCGATTCAAAAA
30293781 AATTCGA-T-AAAAA
1 AATTCGATTCAAAAA
30293794 AATT
1 AATT
30293798 TAAATTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 1 0.06
15 7 0.41
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (15 bp):
AATTCGATTCAAAAA
Found at i:30294285 original size:15 final size:16
Alignment explanation
Indices: 30294265--30294295 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
30294255 AATTTCCAAT
30294265 AATATTAA-AAAAATG
1 AATATTAAGAAAAATG
30294280 AATATTAAGAAAAATG
1 AATATTAAGAAAAATG
30294296 TTTATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
AATATTAAGAAAAATG
Found at i:30296642 original size:24 final size:24
Alignment explanation
Indices: 30296614--30296676 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
30296604 AGAAATAATC
*
30296614 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTA
*
30296638 TTTCAATTAAACTCTGTTTATTTA
1 TTTCAGTTAAACTCTGTTTATTTA
* *
30296662 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
30296677 TATTACTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTA
Found at i:30297555 original size:16 final size:16
Alignment explanation
Indices: 30297536--30297566 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30297526 ATATTAATGT
*
30297536 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
30297552 TATTTAATATTAAAA
1 TATTTAATATTAAAA
30297567 TAATATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:30308940 original size:6 final size:6
Alignment explanation
Indices: 30308929--30308962 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
30308919 CTGTTTCTAT
*
30308929 TATGTA TATGTA TATGTA TATGTA TGTGTA TATG
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATG
30308963 GCATGAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:30310664 original size:30 final size:31
Alignment explanation
Indices: 30310595--30310673 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
30310585 GTTTAAAGTG
*
30310595 CAATTATATACATAAAACTATTATTATAATT
1 CAATTGTATACATAAAACTATTATTATAATT
* * * * *
30310626 TAAATGTATACATGAAACT-TTATTTTTATT
1 CAATTGTATACATAAAACTATTATTATAATT
30310656 CAATTGTATACATTAAAA
1 CAATTGTATACA-TAAAA
30310674 AAAGAAATAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 19 0.50
31 19 0.50
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (31 bp):
CAATTGTATACATAAAACTATTATTATAATT
Found at i:30318999 original size:31 final size:31
Alignment explanation
Indices: 30318958--30319075 Score: 147
Period size: 31 Copynumber: 3.9 Consensus size: 31
30318948 TTAATATAAT
*
30318958 ATTTGATATCTAAACTTGACACTTTTTCCTA
1 ATTTGATATCTAAACTTGACACTTTTTTCTA
* *
30318989 ATTTGGTATCTAAACTT----TTTTTTGTCTA
1 ATTTGATATCTAAACTTGACACTTTTT-TCTA
30319017 ATTTGATA-CTCAAACTTGACACTTTTTTCTA
1 ATTTGATATCT-AAACTTGACACTTTTTTCTA
*
30319048 ATTTGGTATCTAAACTTGACACTTTTTT
1 ATTTGATATCTAAACTTGACACTTTTTT
30319076 TAAAAGTTGG
Statistics
Matches: 74, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
27 7 0.09
28 16 0.22
31 44 0.59
32 7 0.09
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.49
Consensus pattern (31 bp):
ATTTGATATCTAAACTTGACACTTTTTTCTA
Found at i:30319086 original size:32 final size:31
Alignment explanation
Indices: 30318968--30319096 Score: 101
Period size: 31 Copynumber: 4.2 Consensus size: 31
30318958 ATTTGATATC
* *
30318968 TAAACTTGACACTTTTTCCTAATTTGGTA-T
1 TAAACTTGACACTTTTTTCTAAGTTGGTACT
* * *
30318998 CTAAACTT----TTTTTTGTCTAATTTGATACT
1 -TAAACTTGACACTTTTT-TCTAAGTTGGTACT
* *
30319027 CAAACTTGACACTTTTTTCTAATTTGGTA-T
1 TAAACTTGACACTTTTTTCTAAGTTGGTACT
30319057 CTAAACTTGACACTTTTTT-TAAAAGTTGGTACT
1 -TAAACTTGACACTTTTTTCT--AAGTTGGTACT
30319090 TAAACTT
1 TAAACTT
30319097 TTTGGGGTCC
Statistics
Matches: 80, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
27 5 0.06
28 16 0.20
29 1 0.01
30 2 0.03
31 35 0.44
32 20 0.25
33 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (31 bp):
TAAACTTGACACTTTTTTCTAAGTTGGTACT
Found at i:30319116 original size:91 final size:90
Alignment explanation
Indices: 30318958--30319151 Score: 232
Period size: 91 Copynumber: 2.1 Consensus size: 90
30318948 TTAATATAAT
* * *** *
30318958 ATTTGATATCTAAACTTGACACTTTTTCCTAATTTGGTATCTAAACTTTTTTTTGTCTAATTTGA
1 ATTTGGTATCTAAACTTGACACTTTTTCCTAAGTTGGTATCTAAACTTTTTGGGGTCCAATTTGA
*
30319023 TA-CTCAAACTTGACACTTTTTTCTA
66 TACCT-AAACTTGACACTTTTTCCTA
*
30319048 ATTTGGTATCTAAACTTGACACTTTTT-TTAAAAGTTGGTA-CTTAAACTTTTTGGGGTCCAATT
1 ATTTGGTATCTAAACTTGACACTTTTTCCT--AAGTTGGTATC-TAAACTTTTTGGGGTCCAATT
* *
30319111 TGATACCTGAACTTGACTCTTTTTCCTA
63 TGATACCTAAACTTGACACTTTTTCCTA
*
30319139 ATTTGGTACCTAA
1 ATTTGGTATCTAA
30319152 TCTTTTTTTA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
89 1 0.01
90 27 0.30
91 59 0.66
92 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (90 bp):
ATTTGGTATCTAAACTTGACACTTTTTCCTAAGTTGGTATCTAAACTTTTTGGGGTCCAATTTGA
TACCTAAACTTGACACTTTTTCCTA
Found at i:30319398 original size:60 final size:60
Alignment explanation
Indices: 30319300--30319430 Score: 174
Period size: 60 Copynumber: 2.2 Consensus size: 60
30319290 CAATAAATTT
* *
30319300 AGGTACCAAATTGAATCTAAAAAAAGCTTAGGAACCAAATTAGGAAAAAATGCCAAGTTC
1 AGGTACCAAATTGAATCCAAAAAAAGCTTAGGAACCAAATTAAGAAAAAATGCCAAGTTC
* ** * * *
30319360 AGGTGCCAAATTGGGTCCAAAAAAAGTTTA-GATACCAAATTAAGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTGAATCCAAAAAAAGCTTAGGA-ACCAAATTAAGAAAAAATGCCAAGTTC
30319420 AGGTACCAAAT
1 AGGTACCAAAT
30319431 ATTATATTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.03
60 59 0.97
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (60 bp):
AGGTACCAAATTGAATCCAAAAAAAGCTTAGGAACCAAATTAAGAAAAAATGCCAAGTTC
Found at i:30322005 original size:21 final size:21
Alignment explanation
Indices: 30321979--30322036 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
30321969 TAATACAAAT
*
30321979 TTCTACCGATACAAGTGATGG
1 TTCTACCGATACAAGTGATAG
*
30322000 TTCTACCGGTACAAGTGATAG
1 TTCTACCGATACAAGTGATAG
30322021 TTCTACCGATACAAGT
1 TTCTACCGATACAAGT
30322037 TTCGTCTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACAAGTGATAG
Found at i:30325806 original size:52 final size:52
Alignment explanation
Indices: 30325728--30325976 Score: 291
Period size: 52 Copynumber: 4.8 Consensus size: 52
30325718 AGCCATAGAC
*
30325728 TAAAAGGTCCGATGACTAAGTGTCATTGTGAGTATATGAATCCTTTAAAGAT
1 TAAAAGGTCCGATGACTAAGTGTCATTGTGAGTATATGAATCCTTTAAGGAT
* * *
30325780 TAAAAGGTCCGATGACTAAGTGTCATTGTGAGTATATGAATCTTTTACGAAT
1 TAAAAGGTCCGATGACTAAGTGTCATTGTGAGTATATGAATCCTTTAAGGAT
* * * * * *
30325832 TAAAAGGTCCGATGACTAATTTTCATCGTGAGTATATGGATCATTTACGGAT
1 TAAAAGGTCCGATGACTAAGTGTCATTGTGAGTATATGAATCCTTTAAGGAT
* ** * ** * *
30325884 TAAGAGGTCCGATGACTCTGTGTCATCGTGAGTATACAAATCCCTTATGGAT
1 TAAAAGGTCCGATGACTAAGTGTCATTGTGAGTATATGAATCCTTTAAGGAT
* * * * *
30325936 TATAAGGTCCGGTGGCTATGTGTCATTGTGAGTAAATGAAT
1 TAAAAGGTCCGATGACTAAGTGTCATTGTGAGTATATGAAT
30325977 GAAGTGCAAT
Statistics
Matches: 167, Mismatches: 30, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 167 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (52 bp):
TAAAAGGTCCGATGACTAAGTGTCATTGTGAGTATATGAATCCTTTAAGGAT
Found at i:30330014 original size:196 final size:196
Alignment explanation
Indices: 30329677--30330047 Score: 661
Period size: 196 Copynumber: 1.9 Consensus size: 196
30329667 ATTTCATCTA
30329677 GTAAGTTTGTATTGTTAAATTCCATTTTAAATTGCATATTTTATACTTGTATACAATTTCTGTAA
1 GTAAGTTTGTATTGTTAAATTCCATTTTAAATTGCATATTTTATACTTGTATACAATTTCTGTAA
*
30329742 ATTTGGAATGATGAACGTAAGTGAGGAAAACAGGAACAAAGGAGAGGAAAAGATAACGGGCTTTG
66 ATTTGGAATGATGAACGTAAGTGAGGAAAACAGGAACAAAGGAGAGGAAAAGATAACGAGCTTTG
***
30329807 AGTTGTAAATGCAAAAGGTCCGATGACTCTATATCATCATGAGTTTTGTACTTGTATACAATTTC
131 AGCCATAAATGCAAAAGGTCCGATGACTCTATATCATCATGAGTTTTGTACTTGTATACAATTTC
30329872 T
196 T
*
30329873 GTAAGTTTGTATTGTTAAATTCCATTTTAAATTGCATATTTTGTACTTGTATACAATTTCTGTAA
1 GTAAGTTTGTATTGTTAAATTCCATTTTAAATTGCATATTTTATACTTGTATACAATTTCTGTAA
* * * *
30329938 ATTTGGAATGATGAGCGTAAGTGAGGAAGACGGGAACAAATGAGAGGAAAAGATAACGAGCTTTG
66 ATTTGGAATGATGAACGTAAGTGAGGAAAACAGGAACAAAGGAGAGGAAAAGATAACGAGCTTTG
30330003 AGCCATAAATGCAAAAGGTCCGATGACTCTATATCATCATGAGTT
131 AGCCATAAATGCAAAAGGTCCGATGACTCTATATCATCATGAGTT
30330048 ATATGAATCC
Statistics
Matches: 166, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
196 166 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (196 bp):
GTAAGTTTGTATTGTTAAATTCCATTTTAAATTGCATATTTTATACTTGTATACAATTTCTGTAA
ATTTGGAATGATGAACGTAAGTGAGGAAAACAGGAACAAAGGAGAGGAAAAGATAACGAGCTTTG
AGCCATAAATGCAAAAGGTCCGATGACTCTATATCATCATGAGTTTTGTACTTGTATACAATTTC
T
Found at i:30330134 original size:52 final size:52
Alignment explanation
Indices: 30330018--30330306 Score: 375
Period size: 52 Copynumber: 5.5 Consensus size: 52
30330008 TAAATGCAAA
* * * *
30330018 AGGTCCGATGACTCTATATCATCATGAGTTATATGAATCCTATTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGA-TTATATGAATCCT-TTATGGATTATG
* * *
30330072 AGGTCTGATGACTATGTGTCATCGTGAATATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGATTATATGAATCCTTTATGGATTATG
* *
30330124 AGGTCCGATGA-T-TGTGTCATAGTGAGTTATATGAATCCTATTATGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGA-TTATATGAATCCT-TTATGGATTATG
*
30330176 AGGTCCGATGACTATGTGTCATTGTGATTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGATTATATGAATCCTTTATGGATTATG
** * * *
30330228 AGGTTTGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGATTATATGAATCCTTTATGGATTATG
* *
30330280 AGGTACAATGACTATGTGTCATCGTGA
1 AGGTCCGATGACTATGTGTCATCGTGA
30330307 GTATTAAATG
Statistics
Matches: 208, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
50 12 0.06
51 13 0.06
52 123 0.59
53 26 0.12
54 34 0.16
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGATTATATGAATCCTTTATGGATTATG
Found at i:30331038 original size:21 final size:22
Alignment explanation
Indices: 30331012--30331062 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
30331002 TTTTTAGTGC
*
30331012 CGGTAGAAGCT-TCACT-TGTAT
1 CGGTAGAAGCTGTCA-TAGGTAT
30331033 CGGTAGAA-CTGTCATAGGTAT
1 CGGTAGAAGCTGTCATAGGTAT
30331054 CGGTAGAAG
1 CGGTAGAAG
30331063 TCTGCATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (22 bp):
CGGTAGAAGCTGTCATAGGTAT
Found at i:30333026 original size:24 final size:24
Alignment explanation
Indices: 30332989--30333034 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
30332979 CCAATTAAGG
30332989 AATTATTGTTTAGA-TTTAATTCT
1 AATTATTGTTTAGATTTTAATTCT
*
30333012 AATTATCTTTTTAGATTTTAATT
1 AATTAT-TGTTTAGATTTTAATT
30333035 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (24 bp):
AATTATTGTTTAGATTTTAATTCT
Found at i:30336710 original size:10 final size:10
Alignment explanation
Indices: 30336679--30336725 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
30336669 CGAAAAAATT
30336679 GAAAAAAAGA
1 GAAAAAAAGA
*
30336689 -AAAAAATTGA
1 GAAAAAA-AGA
30336699 GAAAAAAAGA
1 GAAAAAAAGA
30336709 GAAGAAAAAGA
1 GAA-AAAAAGA
*
30336720 CAAAAA
1 GAAAAA
30336726 TATGTCTGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 6 0.19
10 10 0.32
11 15 0.48
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (10 bp):
GAAAAAAAGA
Found at i:30359789 original size:27 final size:27
Alignment explanation
Indices: 30359728--30359793 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
30359718 CAGAACATCT
*
30359728 ACATAAAATAGTCCTGACAGACTTTCC
1 ACATAAGATAGTCCTGACAGACTTTCC
* *
30359755 ACAAAAGATAGTCCTTACAGAC-TTCTC
1 ACATAAGATAGTCCTGACAGACTTTC-C
*
30359782 GCATAAGATAGT
1 ACATAAGATAGT
30359794 GTCCTAGCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 3 0.09
27 30 0.91
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (27 bp):
ACATAAGATAGTCCTGACAGACTTTCC
Found at i:30359953 original size:23 final size:23
Alignment explanation
Indices: 30359927--30359982 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
30359917 TCATCCCGCG
30359927 AGGGGCTCTCAAACGTCC-CATA
1 AGGGGCTCTCAAACGTCCACATA
* * * *
30359949 AAGGGTTCTTATACGTCCACATA
1 AGGGGCTCTCAAACGTCCACATA
30359972 AGGGGCTCTCA
1 AGGGGCTCTCA
30359983 TATATGGGTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
AGGGGCTCTCAAACGTCCACATA
Found at i:30361474 original size:27 final size:26
Alignment explanation
Indices: 30361436--30361492 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
30361426 AGGTTACTAG
*
30361436 TTTATCGATAAATGAATATTTTATTAA
1 TTTATCGATAAATGAATA-ATTATTAA
*
30361463 TTTATCGATAAATTAATAATTATTAA
1 TTTATCGATAAATGAATAATTATTAA
30361489 TTTA
1 TTTA
30361493 GAGAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (26 bp):
TTTATCGATAAATGAATAATTATTAA
Found at i:30363477 original size:30 final size:30
Alignment explanation
Indices: 30363441--30363535 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
30363431 CAACTTAATA
* *
30363441 AACAAATGTCTCTAAAATAGTAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
30363471 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
30363501 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
30363531 AACAA
1 AACAA
30363536 TAAAATAAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:30364250 original size:15 final size:16
Alignment explanation
Indices: 30364212--30364254 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
30364202 GAAAAATTTA
30364212 TTATTTAATCGAAATTAT
1 TTATTT-ATC-AAATTAT
*
30364230 TAATTTATCAAA-TAT
1 TTATTTATCAAATTAT
30364245 TTATTTATCA
1 TTATTTATCA
30364255 TGGTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
16 3 0.13
17 3 0.13
18 5 0.22
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (16 bp):
TTATTTATCAAATTAT
Found at i:30364498 original size:105 final size:103
Alignment explanation
Indices: 30364381--30364896 Score: 519
Period size: 105 Copynumber: 5.0 Consensus size: 103
30364371 TTTTTTGTAG
* * * *
30364381 ATTAAGGTAATTAGGAGTTTAAAATATATTACGATAATTAGAGATTTGATTTAGTTAAGATAATT
1 ATTAAGATAATTAGGAGTTTAAATTA-ATTAGGATAATTAGAG-TTTAATTTAGTTAAGATAATT
*
30364446 AGGAATTTAAATTAATAGGTTAGATAATAATTTAGATATA
64 AGGAATTTAAATTAATAGATTAGATAATAATTTAGATATA
* * * **
30364486 ATTAAGATAATTA-GAGTTTAAATTAAATTAGGATAATTAAAATTTCAATTGAAATAAGATAATT
1 ATTAAGATAATTAGGAGTTTAAATT-AATTAGGATAATTAGAGTTT-AATTTAGTTAAGATAATT
* *
30364550 AGGAATTT-AATTAATAGGTTAGATAATAATTTAGATTTTA
64 AGGAATTTAAATTAATAGATTAGATAATAATTTAGA-TATA
* * * *
30364590 GTTAACG-TAATTAGGAGTTTAAATTAAATTAGAATAATTAGAGTTCTAATTTATTTAAGATGAT
1 ATTAA-GATAATTAGGAGTTTAAATT-AATTAGGATAATTAGAGTT-TAATTTAGTTAAGATAAT
** * *
30364654 TAATAATTTAAATTAATATATTAGGTAATAATTTAG--AT-
63 TAGGAATTTAAATTAATAGATTAGATAATAATTTAGATATA
* * * * *
30364692 -TT-AGATAATTAGGAGTTTAAATTGAATTAGGATAATTAAATTTTTAATTTAGATAATAAAATT
1 ATTAAGATAATTAGGAGTTTAAATT-AATTAGGATAATTAGA-GTTTAATTTAGTTAAGATAATT
*
30364755 AGGAATTT-AATTAATAGATTAGATAATAATTTAGATTTTA
64 AGGAATTTAAATTAATAGATTAGATAATAATTTAGA-TATA
* * * * * * *
30364795 GTTAAGATAATTAGAATTTTAAATTAAGTTAAGATAATTAGAGTTCTAATTAATTTAAAATAATT
1 ATTAAGATAATTAGGAGTTTAAATTAA-TTAGGATAATTAGAGTT-TAATTTAGTTAAGATAATT
** * *
30364860 AATAATTTAAGTTAATAGATTAGATAACAATTTAGAT
64 AGGAATTTAAATTAATAGATTAGATAATAATTTAGAT
30364897 TTTTGTTAAG
Statistics
Matches: 341, Mismatches: 52, Indels: 36
0.79 0.12 0.08
Matches are distributed among these distances:
99 25 0.07
100 53 0.16
101 4 0.01
102 1 0.00
103 31 0.09
104 64 0.19
105 114 0.33
106 49 0.14
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (103 bp):
ATTAAGATAATTAGGAGTTTAAATTAATTAGGATAATTAGAGTTTAATTTAGTTAAGATAATTAG
GAATTTAAATTAATAGATTAGATAATAATTTAGATATA
Found at i:30364505 original size:26 final size:25
Alignment explanation
Indices: 30364381--30364860 Score: 120
Period size: 26 Copynumber: 18.5 Consensus size: 25
30364371 TTTTTTGTAG
* *
30364381 ATTAAGGTAATTAGGAGTTTAAAATA
1 ATTAAGATAATTA-GAGTTTAAATTA
* * *
30364407 TATTACGATAATTAGAGATTTGATTTA
1 -ATTAAGATAATTAGAG-TTTAAATTA
* *
30364434 GTTAAGATAATTAGGAATTTAAATTA
1 ATTAAGATAATTA-GAGTTTAAATTA
* *
30364460 ATAGGTTAGATAA-TA-A-TTTAGATATA
1 AT---TAAGATAATTAGAGTTTAAAT-TA
30364486 ATTAAGATAATTAGAGTTTAAATTAA
1 ATTAAGATAATTAGAGTTTAAATT-A
* * * *
30364512 ATTAGGATAATTAAAATTTCAATTGA
1 ATTAAGATAATTAGAGTTTAAATT-A
* *
30364538 AATAAGATAATTAGGAATTT-AATTA
1 ATTAAGATAATTA-GAGTTTAAATTA
* *
30364563 ATAGGTTAGATAA-TA-A-TTTAGATTTTA
1 AT---TAAGATAATTAGAGTTTA-A-ATTA
*
30364590 GTTAACG-TAATTAGGAGTTTAAATTAA
1 ATTAA-GATAATTA-GAGTTTAAATT-A
*
30364617 ATT-AGAATAATTAGAGTTCTAATTTA
1 ATTAAG-ATAATTAGAGTT-TAAATTA
* * *
30364643 TTTAAGATGATTA-A---TAATTTAA
1 ATTAAGATAATTAGAGTTTAAATT-A
* * *
30364665 ATTAATAT-ATTAG-GTAATAATTTA
1 ATTAAGATAATTAGAGT-TTAAATTA
* *
30364689 GATTTAGATAATTAGGAGTTTAAATTGA
1 -ATTAAGATAATT-AGAGTTTAAATT-A
* * * *
30364717 ATTAGGATAATTAAATTTTTAATTTA
1 ATTAAGATAATTAGA-GTTTAAATTA
* * *
30364743 GA-TAATAAAATTAGGAATTT-AATTA
1 -ATTAAGATAATTA-GAGTTTAAATTA
* *
30364768 ATAGATTAGATAA-TA-A-TTTAGATTTTA
1 AT---TAAGATAATTAGAGTTTA-A-ATTA
* *
30364795 GTTAAGATAATTAGAATTTTAAATTA
1 ATTAAGATAATTAG-AGTTTAAATTA
30364821 AGTTAAGATAATTAGAGTTCT-AATTA
1 A-TTAAGATAATTAGAGTT-TAAATTA
*
30364847 ATTTAAAATAATTA
1 A-TTAAGATAATTA
30364861 ATAATTTAAG
Statistics
Matches: 336, Mismatches: 63, Indels: 109
0.66 0.12 0.21
Matches are distributed among these distances:
21 10 0.03
22 7 0.02
23 7 0.02
24 22 0.07
25 35 0.10
26 128 0.38
27 95 0.28
28 25 0.07
29 7 0.02
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (25 bp):
ATTAAGATAATTAGAGTTTAAATTA
Found at i:30364530 original size:52 final size:53
Alignment explanation
Indices: 30364381--30364834 Score: 262
Period size: 52 Copynumber: 8.8 Consensus size: 53
30364371 TTTTTTGTAG
* * * * *
30364381 ATTAAGGTAATTAGGAGTTTAAAATATATTACGATAATTAGAGATTT-GATTTA
1 ATTAAGATAATTAGGAGTTTAAATTAAATTAGGATAATTA-AAATTTAGATTTA
* * * *
30364434 GTTAAGATAATTAGGAATTTAAATT-AA-TAGGTTAGA-TAATAATTTAGATATA
1 ATTAAGATAATTAGGAGTTTAAATTAAATTAGGATA-ATTAA-AATTTAGATTTA
*
30364486 ATTAAGATAATTA-GAGTTTAAATTAAATTAGGATAATTAAAATTTCA-ATTGA
1 ATTAAGATAATTAGGAGTTTAAATTAAATTAGGATAATTAAAATTT-AGATTTA
* * *
30364538 AATAAGATAATTAGGAATTT-AATT-AA-TAGGTTAGA-TAATAATTTAGATTTTA
1 ATTAAGATAATTAGGAGTTTAAATTAAATTAGGATA-ATTAA-AATTTAGA-TTTA
* * * *
30364590 GTTAACG-TAATTAGGAGTTTAAATTAAATTAGAATAATTAGAGTTCTA-ATTTA
1 ATTAA-GATAATTAGGAGTTTAAATTAAATTAGGATAATTAAAATT-TAGATTTA
* * ** *
30364643 TTTAAGATGATTAATAATTTAAATTAATATATTAGG-TAA-T--AATTTAGA--T-
1 ATTAAGATAATTAGGAGTTTAAATT-A-A-ATTAGGATAATTAAAATTTAGATTTA
* *
30364692 -TT-AGATAATTAGGAGTTTAAATTGAATTAGGATAATTAAATTTTTA-ATTTA
1 ATTAAGATAATTAGGAGTTTAAATTAAATTAGGATAATTAAA-ATTTAGATTTA
* * *
30364743 GA-TAATAAAATTAGGAATTT-AATT-AA-TA-GATTAGA-TAATAATTTAGATTTTA
1 -ATTAAGATAATTAGGAGTTTAAATTAAATTAGGA-TA-ATTAA-AATTTAGA-TTTA
* * * * *
30364795 GTTAAGATAATTAGAATTTTAAATTAAGTTAAGATAATTA
1 ATTAAGATAATTAGGAGTTTAAATTAAATTAGGATAATTA
30364835 GAGTTCTAAT
Statistics
Matches: 308, Mismatches: 48, Indels: 88
0.69 0.11 0.20
Matches are distributed among these distances:
44 6 0.02
45 4 0.01
46 1 0.00
47 17 0.06
48 4 0.01
49 6 0.02
50 24 0.08
51 37 0.12
52 92 0.30
53 80 0.26
54 11 0.04
55 19 0.06
56 7 0.02
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (53 bp):
ATTAAGATAATTAGGAGTTTAAATTAAATTAGGATAATTAAAATTTAGATTTA
Found at i:30364785 original size:205 final size:204
Alignment explanation
Indices: 30364382--30364898 Score: 682
Period size: 205 Copynumber: 2.5 Consensus size: 204
30364372 TTTTTGTAGA
* * * *
30364382 TTAAGGTAATTAGGAGTTTAAAATATATTACG-ATAATTAGAGATT-TGATTTAGTTAAGATAAT
1 TTAA-GTAATTAGGAGTTTAAATTAAATTA-GAATAATTAGAG-TTCTAATTTATTTAAGATAAT
** *
30364445 TAGGAATTTAAATTAATAGGTTAGATAATAATTTAGATATAATTAAGATAATTAGAGTTTAAATT
63 TAATAATTTAAATTAATAGATTAGATAATAATTTAG--AT--TTAAGATAATTAGAGTTTAAATT
* *
30364510 AAATTAGGATAATTAAAATTTCAATTGAAATAAGATAATTAGGAATTTAATTAATAGGTTAGATA
124 AAATTAGGATAATTAAAATTTCAATTGAAATAAGAAAATTAGGAATTTAATTAATAGATTAGATA
30364575 ATAATTTAGATTTTAG
189 ATAATTTAGATTTTAG
*
30364591 TTAACGTAATTAGGAGTTTAAATTAAATTAGAATAATTAGAGTTCTAATTTATTTAAGATGATTA
1 TTAA-GTAATTAGGAGTTTAAATTAAATTAGAATAATTAGAGTTCTAATTTATTTAAGATAATTA
* * *
30364656 ATAATTTAAATTAATATATTAGGTAATAATTTAGATTT-AGATAATTAGGAGTTTAAATTGAATT
65 ATAATTTAAATTAATAGATTAGATAATAATTTAGATTTAAGATAATTA-GAGTTTAAATTAAATT
* * * * *
30364720 AGGATAATTAAATTTTTAATTTAGATAATAAAATTAGGAATTTAATTAATAGATTAGATAATAAT
129 AGGATAATTAAAATTTCAATTGAAATAAGAAAATTAGGAATTTAATTAATAGATTAGATAATAAT
30364785 TTAGATTTTAG
194 TTAGATTTTAG
* * * * *
30364796 TTAAGATAATTAGAATTTTAAATTAAGTTA-AGATAATTAGAGTTCTAATTAATTTAAAATAATT
1 TTAAG-TAATTAGGAGTTTAAATTAAATTAGA-ATAATTAGAGTTCTAATTTATTTAAGATAATT
* *
30364860 AATAATTTAAGTTAATAGATTAGATAACAATTTAGATTT
64 AATAATTTAAATTAATAGATTAGATAATAATTTAGATTT
30364899 TTGTTAAGAT
Statistics
Matches: 274, Mismatches: 29, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
204 11 0.04
205 175 0.64
207 2 0.01
208 3 0.01
209 83 0.30
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (204 bp):
TTAAGTAATTAGGAGTTTAAATTAAATTAGAATAATTAGAGTTCTAATTTATTTAAGATAATTAA
TAATTTAAATTAATAGATTAGATAATAATTTAGATTTAAGATAATTAGAGTTTAAATTAAATTAG
GATAATTAAAATTTCAATTGAAATAAGAAAATTAGGAATTTAATTAATAGATTAGATAATAATTT
AGATTTTAG
Found at i:30364824 original size:27 final size:26
Alignment explanation
Indices: 30364794--30364860 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
30364784 TTTAGATTTT
*
30364794 AGTTAAGATAATTAGAATTTTAAATTA
1 AGTTAAGATAATTAGAATTCT-AATTA
*
30364821 AGTTAAGATAATTAGAGTTCTAATTA
1 AGTTAAGATAATTAGAATTCTAATTA
* *
30364847 ATTTAAAATAATTA
1 AGTTAAGATAATTA
30364861 ATAATTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 17 0.47
27 19 0.53
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.40
Consensus pattern (26 bp):
AGTTAAGATAATTAGAATTCTAATTA
Found at i:30364911 original size:53 final size:52
Alignment explanation
Indices: 30364434--30364921 Score: 179
Period size: 52 Copynumber: 9.4 Consensus size: 52
30364424 ATTTGATTTA
* * * *
30364434 GTTAAGATAATTAGGAATTTAAATTAATAGGTTAGATAATAATTTAGA-TATA
1 GTTAAGATAATTAGAAATTT-AATTAATAGATTAGATAATAATTTAGATTTTT
* * **
30364486 ATTAAGATAATTAG-AGTTTAAATT-A-A-ATTAGGATAATTAAAATTTCA-A-TTGA
1 GTTAAGATAATTAGAAATTT-AATTAATAGATTA-GATAA-T--AATTT-AGATTTTT
** * * *
30364538 AATAAGATAATTAGGAATTTAATTAATAGGTTAGATAATAATTTAGATTTTA
1 GTTAAGATAATTAGAAATTTAATTAATAGATTAGATAATAATTTAGATTTTT
* * *
30364590 GTTAACG-TAATTAGGAGTTTAAATT-A-A-ATTAGAATAATTAGAGTTCTA-ATTTAT
1 GTTAA-GATAATTAGAAATTT-AATTAATAGATTAG-ATAA-TA-A-TT-TAGATTTTT
* * *
30364644 -TTAAGATGATTA-ATAATTTAAATTAATATATTAGGTAATAATTTAGA----T
1 GTTAAGATAATTAGA-AATTT-AATTAATAGATTAGATAATAATTTAGATTTTT
* * * ** * *
30364692 -TT-AGATAATTAGGAGTTT-A--AATTGAATTAGGATAATTAAATTTTTAATTTA
1 GTTAAGATAATTAGAAATTTAATTAATAG-ATTA-GATAA-T-AATTTAGATTTTT
* * * * *
30364743 GATAATAAAATTAGGAATTTAATTAATAGATTAGATAATAATTTAGATTTTA
1 GTTAAGATAATTAGAAATTTAATTAATAGATTAGATAATAATTTAGATTTTT
* **
30364795 GTTAAGATAATTAGAATTTTAAATT-A-AG-TTAAGATAATTAGAGTTCTA-ATTAAT
1 GTTAAGATAATTAGAAATTT-AATTAATAGATT-AGATAA-TA-A-TT-TAGATTTTT
* *
30364849 -TTAAAATAATTA-ATAATTTAAGTTAATAGATTAGATAACAATTTAGATTTTT
1 GTTAAGATAATTAGA-AATTTAA-TTAATAGATTAGATAATAATTTAGATTTTT
* *
30364901 GTTAAGATAATTTGAAGTTTA
1 GTTAAGATAATTAGAAATTTA
30364922 GTGTTTCTCG
Statistics
Matches: 332, Mismatches: 52, Indels: 103
0.68 0.11 0.21
Matches are distributed among these distances:
43 3 0.01
44 4 0.01
45 5 0.02
46 1 0.00
47 18 0.05
48 6 0.02
49 6 0.02
50 9 0.03
51 32 0.10
52 101 0.30
53 84 0.25
54 29 0.09
55 23 0.07
56 11 0.03
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (52 bp):
GTTAAGATAATTAGAAATTTAATTAATAGATTAGATAATAATTTAGATTTTT
Found at i:30367844 original size:52 final size:51
Alignment explanation
Indices: 30367708--30367911 Score: 238
Period size: 52 Copynumber: 4.1 Consensus size: 51
30367698 TTCATTGCGT
* * *** *
30367708 TTTACGCTCGCCAGCTT-TCATAT--GTTTACGCTCATTAGATTGCACACG
1 TTTACGCTCGTCAGCTTATTATATGCGTTTACGCTCGCCAGCTTGCACACG
*
30367756 TTTACGCTCGTTAGC-TA-TATATGCGTTTACGCTCGCCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATTATATGCGTTTACGCTCGCCAGCTTGCACACG
* *
30367805 TTTACACTCGTCAGCTTATTTATATACGTTTACGCTCGCCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTA-TTATATGCGTTTACGCTCGCCAGCTTGCACACG
* * * *
30367857 TTTATGCTCGTCAGCTTATACATATGTGTTTACGCTCGCTAGCTTGCACACG
1 TTTACGCTCGTCAGCTTAT-TATATGCGTTTACGCTCGCCAGCTTGCACACG
30367909 TTT
1 TTT
30367912 GCGTTTACTT
Statistics
Matches: 133, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
47 5 0.04
48 13 0.10
49 34 0.26
50 2 0.02
51 1 0.01
52 78 0.59
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (51 bp):
TTTACGCTCGTCAGCTTATTATATGCGTTTACGCTCGCCAGCTTGCACACG
Found at i:30367975 original size:26 final size:26
Alignment explanation
Indices: 30367944--30368101 Score: 153
Period size: 26 Copynumber: 6.2 Consensus size: 26
30367934 CACACATTTG
*
30367944 CGCTCGTCAGCTTATATATGTGTTTA
1 CGCTCGTCAGCTTATATATGCGTTTA
* ** *
30367970 CGCTCGCCAGCTTGCACA--CGTTTA
1 CGCTCGTCAGCTTATATATGCGTTTA
* * * *
30367994 TGCTCATTAGCTTATTTATGCGTTTA
1 CGCTCGTCAGCTTATATATGCGTTTA
30368020 CGCTCGTCAGCTTATATATGCGTTTA
1 CGCTCGTCAGCTTATATATGCGTTTA
* * *
30368046 TGCTCGTCAGCTTACAGA--CGTTTA
1 CGCTCGTCAGCTTATATATGCGTTTA
* * *
30368070 TGCTCGTCATCTTATATATGTGTTTA
1 CGCTCGTCAGCTTATATATGCGTTTA
30368096 CGCTCG
1 CGCTCG
30368102 CCAAGTTGCA
Statistics
Matches: 103, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
24 36 0.35
26 67 0.65
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.39
Consensus pattern (26 bp):
CGCTCGTCAGCTTATATATGCGTTTA
Found at i:30367991 original size:81 final size:81
Alignment explanation
Indices: 30367831--30367992 Score: 254
Period size: 83 Copynumber: 2.0 Consensus size: 81
30367821 TATTTATATA
* *
30367831 CGTTTACGCTCGCCAGCTTGCACACGTTTATGCTCGTCAGCTTATACATATGTGTTTACGCTCGC
1 CGTTTACGCTCGCCAGCTTGCACACATTTACGCTCGTCAGCTTATA-ATATGTGTTTACGCTCGC
*
30367896 TAGCTTGCACACGTTTG
65 CAGCTTGCACACGTTTG
* *
30367913 CGTTTACTTCTCGCCAGCTTGCACACATTTGCGCTCGTCAGCTTAT-ATATGTGTTTACGCTCGC
1 CGTTTAC-GCTCGCCAGCTTGCACACATTTACGCTCGTCAGCTTATAATATGTGTTTACGCTCGC
30367977 CAGCTTGCACACGTTT
65 CAGCTTGCACACGTTT
30367993 ATGCTCATTA
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
81 33 0.45
82 7 0.09
83 34 0.46
ACGTcount: A:0.17, C:0.29, G:0.20, T:0.35
Consensus pattern (81 bp):
CGTTTACGCTCGCCAGCTTGCACACATTTACGCTCGTCAGCTTATAATATGTGTTTACGCTCGCC
AGCTTGCACACGTTTG
Found at i:30367998 original size:24 final size:24
Alignment explanation
Indices: 30367708--30367998 Score: 123
Period size: 24 Copynumber: 11.4 Consensus size: 24
30367698 TTCATTGCGT
* * *
30367708 TTTACGCTCGCCAGCTTTCATATG
1 TTTACGCTCGCCAGCTTGCACACG
*** *
30367732 TTTACGCTCATTAGATTGCACACG
1 TTTACGCTCGCCAGCTTGCACACG
** ** **
30367756 TTTACGCTCGTTAGCTATATATGCG
1 TTTACGCTCGCCAGCT-TGCACACG
30367781 TTTACGCTCGCCAGCTTGCACACG
1 TTTACGCTCGCCAGCTTGCACACG
* * ** *
30367805 TTTACACTCGTCAGCTTATTTATATACG
1 TTTACGCTCGCCAGC----TTGCACACG
30367833 TTTACGCTCGCCAGCTTGCACACG
1 TTTACGCTCGCCAGCTTGCACACG
* * * * *
30367857 TTTATGCTCGTCAGCTTATACATATGTG
1 TTTACGCTCGCCAGC-T-TGCACA--CG
*
30367885 TTTACGCTCGCTAGCTTGCACACGTTTGCG
1 TTTACGCTCGCCAGCTTGCACA------CG
* *
30367915 TTTACTTCTCGCCAGCTTGCACACA
1 TTTAC-GCTCGCCAGCTTGCACACG
* * ** * *
30367940 TTTGCGCTCGTCAGCTTATATATGTG
1 TTTACGCTCGCCAGCTTGCACA--CG
30367966 TTTACGCTCGCCAGCTTGCACACG
1 TTTACGCTCGCCAGCTTGCACACG
*
30367990 TTTATGCTC
1 TTTACGCTC
30367999 ATTAGCTTAT
Statistics
Matches: 193, Mismatches: 58, Indels: 32
0.68 0.20 0.11
Matches are distributed among these distances:
24 88 0.46
25 24 0.12
26 25 0.13
27 1 0.01
28 32 0.17
30 8 0.04
31 15 0.08
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (24 bp):
TTTACGCTCGCCAGCTTGCACACG
Found at i:30368057 original size:76 final size:76
Alignment explanation
Indices: 30367944--30368101 Score: 226
Period size: 76 Copynumber: 2.1 Consensus size: 76
30367934 CACACATTTG
* * *
30367944 CGCTCGTCAGCTTATATATGTGTTTACGCTCGCCAGCTTGCACACGTTTATGCTCATTAGCTTAT
1 CGCTCGTCAGCTTATATATGCGTTTACGCTCGCCAGCTTACACACGTTTATGCTCATCAGCTTAT
*
30368009 TTATGCGTTTA
66 ATATGCGTTTA
* * * * *
30368020 CGCTCGTCAGCTTATATATGCGTTTATGCTCGTCAGCTTACAGACGTTTATGCTCGTCATCTTAT
1 CGCTCGTCAGCTTATATATGCGTTTACGCTCGCCAGCTTACACACGTTTATGCTCATCAGCTTAT
*
30368085 ATATGTGTTTA
66 ATATGCGTTTA
30368096 CGCTCG
1 CGCTCG
30368102 CCAAGTTGCA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.39
Consensus pattern (76 bp):
CGCTCGTCAGCTTATATATGCGTTTACGCTCGCCAGCTTACACACGTTTATGCTCATCAGCTTAT
ATATGCGTTTA
Found at i:30368068 original size:50 final size:50
Alignment explanation
Indices: 30367708--30368101 Score: 196
Period size: 50 Copynumber: 7.7 Consensus size: 50
30367698 TTCATTGCGT
* * * * * *
30367708 TTTACGCTCGCCAGCTT-TCATAT--GTTTACGCTCATTAGATTGCACACG
1 TTTACGCTCGTCAGCTTAT-ATATGCGTTTACGCTCGTCAGCTTACAGACG
* * * *
30367756 TTTACGCTCGTTAGC-TATATATGCGTTTACGCTCGCCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATATGCGTTTACGCTCGTCAGCTTACAGACG
* * * * *
30367805 TTTACACTCGTCAGCTTATTTATATACGTTTACGCTCGCCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTA--TATATGCGTTTACGCTCGTCAGCTTACAGACG
* * *
30367857 TTTATGCTCGTCAGCTTATACATATGTGTTTACGCTCG-CTAGCTTGCACACGTTTGCG
1 TTTACGCTCGTCAGCTTAT--ATATGCGTTTACGCTCGTC-AGCTT--ACA-G---ACG
* * ** * * * * * *
30367915 TTTACTTCTCGCCAGCTTGCACA--CATTTGCGCTCGTCAGCTTATATATGTG
1 TTTAC-GCTCGTCAGCTTATATATGCGTTTACGCTCGTCAGCTTACAGA--CG
* ** * * * * *
30367966 TTTACGCTCGCCAGCTTGCACA--CGTTTATGCTCATTAGCTTATTTATG-CG
1 TTTACGCTCGTCAGCTTATATATGCGTTTACGCTCGTCAGCTTA--CA-GACG
*
30368016 TTTACGCTCGTCAGCTTATATATGCGTTTATGCTCGTCAGCTTACAGACG
1 TTTACGCTCGTCAGCTTATATATGCGTTTACGCTCGTCAGCTTACAGACG
* * *
30368066 TTTATGCTCGTCATCTTATATATGTGTTTACGCTCG
1 TTTACGCTCGTCAGCTTATATATGCGTTTACGCTCG
30368102 CCAAGTTGCA
Statistics
Matches: 273, Mismatches: 48, Indels: 48
0.74 0.13 0.13
Matches are distributed among these distances:
47 5 0.02
48 14 0.05
49 35 0.13
50 88 0.32
51 7 0.03
52 87 0.32
53 2 0.01
54 2 0.01
55 14 0.05
56 1 0.00
57 2 0.01
58 6 0.02
59 10 0.04
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (50 bp):
TTTACGCTCGTCAGCTTATATATGCGTTTACGCTCGTCAGCTTACAGACG
Found at i:30370455 original size:15 final size:16
Alignment explanation
Indices: 30370428--30370457 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30370418 TTCGTTTCTT
30370428 TTATTTTTGCTTTGTA
1 TTATTTTTGCTTTGTA
30370444 TTATTTTT-CTTTGT
1 TTATTTTTGCTTTGT
30370458 GAGTTCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (16 bp):
TTATTTTTGCTTTGTA
Found at i:30371776 original size:16 final size:16
Alignment explanation
Indices: 30371754--30371794 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
30371744 GTATCCACAT
30371754 CTGTATCT-GATCTGTC
1 CTGTATCTAGAT-TGTC
*
30371770 GTGTATCTAGATTGTC
1 CTGTATCTAGATTGTC
30371786 CTGTATCTA
1 CTGTATCTA
30371795 AAATTGTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.44
Consensus pattern (16 bp):
CTGTATCTAGATTGTC
Found at i:30374031 original size:52 final size:52
Alignment explanation
Indices: 30373957--30374098 Score: 171
Period size: 52 Copynumber: 2.7 Consensus size: 52
30373947 CTTATTGAAT
* *
30373957 AGCGTAAAACGCATAAGTATAAGCTGACGAGCGTAAACATGTGCAAGCT-GACA
1 AGCGT-AAACGCATAAGTATAAGTTGACGAGCGTAAACATGTGCAACCTGGA-A
* * ** *
30374010 AGCGTAAATGCAT-ATTAATAAGTTGACGAGCGTAAATGTGTGCAACCTGGAG
1 AGCGTAAACGCATAAGT-ATAAGTTGACGAGCGTAAACATGTGCAACCTGGAA
*
30374062 AGCGTAAACGCATAAGTATAAGTTGGCGAGCGTAAAC
1 AGCGTAAACGCATAAGTATAAGTTGACGAGCGTAAAC
30374099 GTATATGAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
51 2 0.03
52 64 0.85
53 9 0.12
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.20
Consensus pattern (52 bp):
AGCGTAAACGCATAAGTATAAGTTGACGAGCGTAAACATGTGCAACCTGGAA
Found at i:30374867 original size:39 final size:39
Alignment explanation
Indices: 30374800--30374882 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
30374790 TTTTATCTTG
* * *
30374800 CACGGGCGTGGGAATTGAGGGTGCTTGCTATAGGGCACA
1 CACGGGCGTGAGAATTGAGGGTGCTTGCTACAGGACACA
* * *
30374839 CACGGGCGTGAGACTT-AGGCGTGTTTGCTGCAGGACACA
1 CACGGGCGTGAGAATTGAGG-GTGCTTGCTACAGGACACA
30374878 CACGG
1 CACGG
30374883 CCCAGCCTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 3 0.08
39 34 0.92
ACGTcount: A:0.20, C:0.22, G:0.39, T:0.19
Consensus pattern (39 bp):
CACGGGCGTGAGAATTGAGGGTGCTTGCTACAGGACACA
Found at i:30377340 original size:24 final size:24
Alignment explanation
Indices: 30377313--30377358 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
30377303 TCTACCAACA
*
30377313 CAAGTACAC-AAACTACTGATACAT
1 CAAG-ACACAAAACTACCGATACAT
30377337 CAAGACACAAAACTACCGATAC
1 CAAGACACAAAACTACCGATAC
30377359 TCGCAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.48, C:0.28, G:0.09, T:0.15
Consensus pattern (24 bp):
CAAGACACAAAACTACCGATACAT
Found at i:30379107 original size:22 final size:21
Alignment explanation
Indices: 30379060--30379107 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
30379050 GACTTTCATA
* *
30379060 ATTAACTTAATTAATTATCTT
1 ATTAACTTAATTAATCATATT
*
30379081 TTTAACCTTAATTAATCATATT
1 ATTAA-CTTAATTAATCATATT
30379103 ATTAA
1 ATTAA
30379108 TCAATATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:30384877 original size:21 final size:21
Alignment explanation
Indices: 30384853--30384906 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
30384843 CTTATGCTAG
*
30384853 TTCTATCGATACAAGT-ATAAC
1 TTCTATCGATACAACTCAT-AC
30384874 TTCTA-CTGATACAACTCATAC
1 TTCTATC-GATACAACTCATAC
*
30384895 ATCTATCGATAC
1 TTCTATCGATAC
30384907 TAAAAACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.33
Consensus pattern (21 bp):
TTCTATCGATACAACTCATAC
Found at i:30386729 original size:22 final size:21
Alignment explanation
Indices: 30386682--30386729 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
30386672 GACTTTCATA
* *
30386682 ATTAACTTAATTAATTATCTT
1 ATTAACTTAATTAATCATATT
* *
30386703 TTTAACCTTAATTAATCCTATT
1 ATTAA-CTTAATTAATCATATT
30386725 ATTAA
1 ATTAA
30386730 TCAATATTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:30389293 original size:27 final size:28
Alignment explanation
Indices: 30389227--30389298 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
30389217 TCATTGAAGG
* *
30389227 ATAGGTCAGTTAGAGCTTTAACTCACTT
1 ATAGCTCAGGTAGAGCTTTAACTCACTT
* * * *
30389255 ACAGCTCGGGTAGAGCTTTGATTCA-TT
1 ATAGCTCAGGTAGAGCTTTAACTCACTT
30389282 ATAGCTCAGGTAGAGCT
1 ATAGCTCAGGTAGAGCT
30389299 CCGATATGCT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 17 0.47
28 19 0.53
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (28 bp):
ATAGCTCAGGTAGAGCTTTAACTCACTT
Found at i:30389338 original size:55 final size:54
Alignment explanation
Indices: 30389279--30389463 Score: 201
Period size: 55 Copynumber: 3.4 Consensus size: 54
30389269 GCTTTGATTC
* * * * *
30389279 ATTATAGCTCAGGTAGAGCTCCGATATGCTTACGTCTTATTTAGAGTGTAATGCT
1 ATTATAGCTCGGGTAGAGCTTCGACATGCTTACGTCTCA-TTAGAGAGTAATGCT
* * * *
30389334 ATTATAGCTCGGGCAGAGCTTGGACATGCTTACATCTCAATTAGAGCGTAATGCT
1 ATTATAGCTCGGGTAGAGCTTCGACATGCTTACGTCTC-ATTAGAGAGTAATGCT
* ** *
30389389 ATTATAGCT-TGGTAGAGCTTTTAACATGCTTACGTCTCGATTAGAGAGTAATGTT
1 ATTATAGCTCGGGTAGAGC-TTCGACATGCTTACGTCTC-ATTAGAGAGTAATGCT
*
30389444 ATTATAGCTCGGGTAAAGCT
1 ATTATAGCTCGGGTAGAGCT
30389464 ATGGTTTGCC
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
54 7 0.06
55 94 0.86
56 8 0.07
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (54 bp):
ATTATAGCTCGGGTAGAGCTTCGACATGCTTACGTCTCATTAGAGAGTAATGCT
Found at i:30392202 original size:73 final size:74
Alignment explanation
Indices: 30392050--30392300 Score: 339
Period size: 73 Copynumber: 3.4 Consensus size: 74
30392040 ATTTAGGTTA
* * ** * *
30392050 TGTGCCTAGTAGGCTTTGTACCGGTGTA-TCTTGTTGTGTGCCTAGTAGGCTTCATGCC-AGTGT
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAAGCTGTGTGCCTAGTAGGCTTCGTGCCGA-TGT
* *
30392113 ATTCAGGTTG
65 ATTCGGGCTG
30392123 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAAGCTGTGTGCCTAGTAGGCTTCGTGCCGATGTA
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAAGCTGTGTGCCTAGTAGGCTTCGTGCCGATGTA
30392188 TTCGGGCTG
66 TTCGGGCTG
* ** * *
30392197 T-TGCCTAGTAGGCTTTGTGCCGGTGTATTCGGGCTGTGTGCCTAGTAAGCTTCGTACCGATGTA
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAAGCTGTGTGCCTAGTAGGCTTCGTGCCGATGTA
30392261 TTCGGGCTG
66 TTCGGGCTG
30392270 TGTGACC-AGTAGGCTTCGTGCCGGTGTATTC
1 TGTG-CCTAGTAGGCTTCGTGCCGGTGTATTC
30392301 GGACCATGTG
Statistics
Matches: 160, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
73 94 0.59
74 63 0.39
75 3 0.02
ACGTcount: A:0.13, C:0.20, G:0.32, T:0.35
Consensus pattern (74 bp):
TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAAGCTGTGTGCCTAGTAGGCTTCGTGCCGATGTA
TTCGGGCTG
Found at i:30392243 original size:110 final size:111
Alignment explanation
Indices: 30392050--30392302 Score: 332
Period size: 110 Copynumber: 2.3 Consensus size: 111
30392040 ATTTAGGTTA
* * ** *
30392050 TGTGCCTAGTAGGCTTTGTACCGGTGTA-TCTTGTTGTGTGCCTAGTAGGCTTCATGCCAGTGTA
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTGTGTGCCTAGTAGGCTTCATGCCAGTGTA
* * * *
30392114 TTCAGGTTGTGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAAGCTG
66 TTCAGGCTGTGTGCCTAGTAAGCTTCGTACCGATGTATTCAAGCTG
* ** *
30392160 TGTGCCTAGTAGGCTTCGTGCCGATGTATTCGGGCTGT-TGCCTAGTAGGCTTTGTGCCGGTGTA
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTGTGTGCCTAGTAGGCTTCATGCCAGTGTA
* **
30392224 TTCGGGCTGTGTGCCTAGTAAGCTTCGTACCGATGTATTCGGGCTG
66 TTCAGGCTGTGTGCCTAGTAAGCTTCGTACCGATGTATTCAAGCTG
30392270 TGTGACC-AGTAGGCTTCGTGCCGGTGTATTCGG
1 TGTG-CCTAGTAGGCTTCGTGCCGGTGTATTCGG
30392303 ACCATGTGTC
Statistics
Matches: 124, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
110 116 0.94
111 8 0.06
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.34
Consensus pattern (111 bp):
TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTGTGTGCCTAGTAGGCTTCATGCCAGTGTA
TTCAGGCTGTGTGCCTAGTAAGCTTCGTACCGATGTATTCAAGCTG
Found at i:30392301 original size:37 final size:37
Alignment explanation
Indices: 30392050--30392302 Score: 332
Period size: 37 Copynumber: 6.9 Consensus size: 37
30392040 ATTTAGGTTA
* * ** *
30392050 TGTGCCTAGTAGGCTTTGTACCGGTGTA-TCTTGTTG
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTG
* * * *
30392086 TGTGCCTAGTAGGCTTCATGCCAGTGTATTCAGGTTG
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTG
**
30392123 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAAGCTG
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTG
*
30392160 TGTGCCTAGTAGGCTTCGTGCCGATGTATTCGGGCTG
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTG
*
30392197 T-TGCCTAGTAGGCTTTGTGCCGGTGTATTCGGGCTG
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTG
* * *
30392233 TGTGCCTAGTAAGCTTCGTACCGATGTATTCGGGCTG
1 TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTG
30392270 TGTGACC-AGTAGGCTTCGTGCCGGTGTATTCGG
1 TGTG-CCTAGTAGGCTTCGTGCCGGTGTATTCGG
30392303 ACCATGTGTC
Statistics
Matches: 192, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
36 58 0.30
37 132 0.69
38 2 0.01
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.34
Consensus pattern (37 bp):
TGTGCCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTG
Found at i:30394791 original size:15 final size:16
Alignment explanation
Indices: 30394771--30394800 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30394761 ATTGACTATA
30394771 ATAAATAT-AAAATAT
1 ATAAATATCAAAATAT
30394786 ATAAATATCAAAATA
1 ATAAATATCAAAATA
30394801 AACCCAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAATATCAAAATAT
Found at i:30397473 original size:13 final size:13
Alignment explanation
Indices: 30397455--30397485 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30397445 TTGCAAATTT
30397455 TATTTTGGCGGAA
1 TATTTTGGCGGAA
*
30397468 TATTTTGGGGGAA
1 TATTTTGGCGGAA
30397481 TATTT
1 TATTT
30397486 GAGAATTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.45
Consensus pattern (13 bp):
TATTTTGGCGGAA
Found at i:30402475 original size:21 final size:21
Alignment explanation
Indices: 30402451--30402491 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30402441 CCACCCTCTC
* *
30402451 CATCCCCACCCCCACCTCCAA
1 CATCACCACCACCACCTCCAA
*
30402472 CATCACCATCACCACCTCCA
1 CATCACCACCACCACCTCCA
30402492 CCTCCTCCGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.61, G:0.00, T:0.12
Consensus pattern (21 bp):
CATCACCACCACCACCTCCAA
Found at i:30403782 original size:79 final size:80
Alignment explanation
Indices: 30403638--30403794 Score: 178
Period size: 79 Copynumber: 2.0 Consensus size: 80
30403628 GGTATGTATC
* * * *
30403638 TGTTTTAAAAGTTAAAAGAGTCTGGATGATAACCCTTATATTTGTTCTTTTGTTGAACGATTGAG
1 TGTTTTAAAAGTTAAAAGAGTCTGGATGATAACCCTTATATCTGTTCCTTTATTGAACAATTGAG
*
30403703 CTATGTGATCCTCTT
66 CTATATGATCCTCTT
* * *
30403718 TGTTTTAAAAG-TCAAAGAGTGTGGATAGA-AACCCTTGTCATCT-TTCCTTTATTGAA-AATCT
1 TGTTTTAAAAGTTAAAAGAGTCTGGAT-GATAACCCTTAT-ATCTGTTCCTTTATTGAACAAT-T
*
30403779 GAGCTATATTATCCTC
63 GAGCTATATGATCCTC
30403795 CTTTCGATGA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
78 2 0.03
79 47 0.72
80 16 0.25
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (80 bp):
TGTTTTAAAAGTTAAAAGAGTCTGGATGATAACCCTTATATCTGTTCCTTTATTGAACAATTGAG
CTATATGATCCTCTT
Found at i:30416042 original size:15 final size:16
Alignment explanation
Indices: 30416014--30416044 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
30416004 TTGCGTCTTG
30416014 AGAAGCTCAGGAAAGA
1 AGAAGCTCAGGAAAGA
30416030 AGAAGCT-AGGAAAGA
1 AGAAGCTCAGGAAAGA
30416045 GGCTATACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.52, C:0.10, G:0.32, T:0.06
Consensus pattern (16 bp):
AGAAGCTCAGGAAAGA
Found at i:30422189 original size:15 final size:16
Alignment explanation
Indices: 30422169--30422198 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30422159 TGCCCCAAAA
30422169 TATAAAAATT-TAAAT
1 TATAAAAATTATAAAT
30422184 TATAAAAATTATAAA
1 TATAAAAATTATAAA
30422199 GAGAATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TATAAAAATTATAAAT
Found at i:30426090 original size:12 final size:13
Alignment explanation
Indices: 30426075--30426103 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
30426065 CTTTGCCATT
30426075 TTCTTCTTTT-TC
1 TTCTTCTTTTCTC
30426087 TTCTTCTTTTCTC
1 TTCTTCTTTTCTC
30426100 TTCT
1 TTCT
30426104 CTTCCTCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTCTTTTCTC
Found at i:30432136 original size:11 final size:11
Alignment explanation
Indices: 30432105--30432146 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
30432095 CCCAACTTGG
30432105 ATTTTAAATTA
1 ATTTTAAATTA
* *
30432116 AGTTTGAATTA
1 ATTTTAAATTA
*
30432127 ATTTTAAATTT
1 ATTTTAAATTA
30432138 A-TTTAAATT
1 ATTTTAAATT
30432147 TAAATTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:30432146 original size:17 final size:17
Alignment explanation
Indices: 30432107--30432168 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
30432097 CAACTTGGAT
*
30432107 TTTAAA-TTAAGTTTGA
1 TTTAAATTTAAATTTGA
* *
30432123 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
30432139 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
30432156 TTTAAATTTAAAT
1 TTTAAATTTAAAT
30432169 ACATTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:30432149 original size:22 final size:22
Alignment explanation
Indices: 30432105--30432146 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30432095 CCCAACTTGG
*
30432105 ATTTTAAATTAAGTTTGAATTA
1 ATTTTAAATTAAGTTTAAATTA
*
30432127 ATTTTAAATTTA-TTTAAATT
1 ATTTTAAATTAAGTTTAAATT
30432147 TAAATTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAAATTAAGTTTAAATTA
Found at i:30432152 original size:27 final size:27
Alignment explanation
Indices: 30432111--30432202 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
30432101 TTGGATTTTA
* *
30432111 AATTAAGTTTGAATTAATTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* **
30432138 ATTTAAATTTAAATTTGTTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* * * * *
30432165 AAATACATTTAAAATAATTTGAAACTTAA
1 AATTAAATTTAAATTAATTTTAAA-TT-T
30432194 AATTAAATT
1 AATTAAATT
30432203 AATAATGTCC
Statistics
Matches: 48, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
27 39 0.81
28 2 0.04
29 7 0.15
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (27 bp):
AATTAAATTTAAATTAATTTTAAATTT
Found at i:30432177 original size:16 final size:16
Alignment explanation
Indices: 30432124--30432177 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
30432114 TAAGTTTGAA
* *
30432124 TTAATTTTAAATTTAT
1 TTAAATTTAAATTCAT
**
30432140 TTAAATTTAAATTTGTT
1 TTAAATTTAAA-TTCAT
*
30432157 TTAAATTTAAATACAT
1 TTAAATTTAAATTCAT
30432173 TTAAA
1 TTAAA
30432178 ATAATTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAAATTTAAATTCAT
Found at i:30434250 original size:29 final size:30
Alignment explanation
Indices: 30434191--30434276 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 30
30434181 AGTCCCCAAG
*
30434191 CTTTCCAAAATTCCATTTTTGACCTCAAAA
1 CTTTCCAAAATTCCATTTTTGACCCCAAAA
*
30434221 C-TTCCAACAATTACCA-TTTT-ACCCCTAAA
1 CTTTCCAA-AATT-CCATTTTTGACCCCAAAA
* *
30434250 CTTTCCAAAAATCTCATTTTTAACCCC
1 CTTTCCAAAATTC-CATTTTTGACCCC
30434277 GATTTCACCA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
28 1 0.02
29 19 0.40
30 19 0.40
31 8 0.17
ACGTcount: A:0.33, C:0.31, G:0.01, T:0.35
Consensus pattern (30 bp):
CTTTCCAAAATTCCATTTTTGACCCCAAAA
Found at i:30434289 original size:29 final size:29
Alignment explanation
Indices: 30434257--30434408 Score: 113
Period size: 29 Copynumber: 5.2 Consensus size: 29
30434247 AAACTTTCCA
*
30434257 AAAATCTCATTTTTAACCCCGATTTCACC
1 AAAATCCCATTTTTAACCCCGATTTCACC
*
30434286 AAAAATAACCA-TTTT-ACCCTCGAACTTT--CC
1 -AAAAT-CCCATTTTTAACCC-CG-A-TTTCACC
*
30434316 AAAATCCCATTTTTAACCCCAATTTCACC
1 AAAATCCCATTTTTAACCCCGATTTCACC
*
30434345 AAAAATTACCA-TTTT-ACCCCTGAACTTT--CC
1 -AAAA-TCCCATTTTTAACCCC-G-A-TTTCACC
*
30434375 AAAATCCCATTTTTAACCCCGAGTTCACC
1 AAAATCCCATTTTTAACCCCGATTTCACC
30434404 AAAAT
1 AAAAT
30434409 TACCACTTTA
Statistics
Matches: 97, Mismatches: 8, Indels: 35
0.69 0.06 0.25
Matches are distributed among these distances:
27 5 0.05
28 9 0.09
29 37 0.38
30 32 0.33
31 8 0.08
32 6 0.06
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATCCCATTTTTAACCCCGATTTCACC
Found at i:30434341 original size:59 final size:59
Alignment explanation
Indices: 30434224--30434711 Score: 442
Period size: 59 Copynumber: 8.3 Consensus size: 59
30434214 CTCAAAACTT
* * * *
30434224 CCAACAATTACCATTTTACCCCTAAACTTTCCAAAAATCTCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCC-AAAATCCCATTTTTAACCCCAATTTCA
*
30434284 CCAAAAATAACCATTTTA-CCCTCGAACTTTCCAAAATCCCATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCT-GAACTTTCCAAAATCCCATTTTTAACCCCAATTTCA
* *
30434343 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTTAACCCCGAGTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTTAACCCCAATTTCA
* * * * * * * *** *
30434402 CC-AAAATTACCACTTTACCCCCGAACCTTCTAAAATTCTATTTTTGACTATAAAACTT--
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTTAAC--CCCAATTTCA
* *
30434460 CCAAAAATTACCATTTTACCCC-GAA-TCTTCCAAAATCTCATTTTTAA-CCCAATTTTA
1 CCAAAAATTACCATTTTACCCCTGAACT-TTCCAAAATCCCATTTTTAACCCCAATTTCA
** ** *
30434517 CCAAAAATTACCATTTTTACCCCTGAACCTTT-CAAAATTTCATGTTTT-ACTCTTAAACTT--
1 CCAAAAATTACCA-TTTTACCCCTGAA-CTTTCCAAAATCCCAT-TTTTAAC-C-CCAATTTCA
* * * * * * **
30434577 CTAAAAATTACCATTTTACCCCTAAATTTTCTAAAATCCTATTTTTAACCACGGTTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTTAACCCCAATTTCA
* * * * * *
30434636 CCAAAAATTATCATTTTACCTCTGAACTTTCTAAAATTCCATTTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCA-TTTTTAACCCCAATTTCA
30434696 CCAAAAATTA-CATTTT
1 CCAAAAATTACCATTTT
30434712 TATCCCCAAA
Statistics
Matches: 351, Mismatches: 56, Indels: 43
0.78 0.12 0.10
Matches are distributed among these distances:
55 4 0.01
57 15 0.04
58 76 0.22
59 175 0.50
60 75 0.21
61 2 0.01
62 4 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATCCCATTTTTAACCCCAATTTCA
Found at i:30434464 original size:117 final size:117
Alignment explanation
Indices: 30434197--30434681 Score: 525
Period size: 117 Copynumber: 4.1 Consensus size: 117
30434187 CAAGCTTTCC
*
30434197 AAAATTCCATTTTTGACCTCAAAACTTCCAACAATTACCATTTTACCCCTAAACTTTCCAAAAAT
1 AAAATTCCATTTTTGA-CTCAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTTCC-AAAAT
* * * * * *
30434262 CTCATTTTTAACCCCGATTTCACCAAAAATAACCATTTTACCCTCGAACTTTCC
64 CCCATTTTTAACCCCGAGTTCACCAAAAATTACCATTTTACCCCCGAACCTTCT
* * ** * *
30434316 AAAATCCCATTTTTAAC-CCCAATTTCACCAAAAATTACCATTTTACCCCTGAACTTTCCAAAAT
1 AAAATTCCATTTTTGACTCAAAACTT--CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAAT
*
30434380 CCCATTTTTAACCCCGAGTTCACC-AAAATTACCACTTTACCCCCGAACCTTCT
64 CCCATTTTTAACCCCGAGTTCACCAAAAATTACCATTTTACCCCCGAACCTTCT
* * * *
30434433 AAAATTCTATTTTTGACTATAAAACTTCCAAAAATTACCATTTTACCCCGAATC-TTCCAAAATC
1 AAAATTCCATTTTTGACT-CAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATC
* * * * *
30434497 TCATTTTTAA-CCCAATTTTACCAAAAATTACCATTTTTACCCCTGAACCTT-T
65 CCATTTTTAACCCCGAGTTCACCAAAAATTACCA-TTTTACCCCCGAACCTTCT
* * * * *
30434549 CAAAATTTCATGTTTT-ACTCTTAAACTTCTAAAAATTACCATTTTACCCCTAAATTTTCTAAAA
1 -AAAATTCCAT-TTTTGACTC-AAAACTTCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAA
* * * * * *
30434613 TCCTATTTTTAACCACG-GTTTCACCAAAAATTATCATTTTACCTCTGAACTTTCT
63 TCCCATTTTTAACCCCGAG-TTCACCAAAAATTACCATTTTACCCCCGAACCTTCT
30434668 AAAATTCCATTTTT
1 AAAATTCCATTTTT
30434682 TAACCTCGAT
Statistics
Matches: 304, Mismatches: 49, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
115 9 0.03
116 30 0.10
117 126 0.41
118 73 0.24
119 66 0.22
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (117 bp):
AAAATTCCATTTTTGACTCAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCC
CATTTTTAACCCCGAGTTCACCAAAAATTACCATTTTACCCCCGAACCTTCT
Found at i:30434489 original size:29 final size:30
Alignment explanation
Indices: 30434193--30434598 Score: 143
Period size: 30 Copynumber: 13.8 Consensus size: 30
30434183 TCCCCAAGCT
* * *
30434193 TTCC-AAAATT-CCATTTTTGACCTCAAAAC
1 TTCCAAAAATTACCATTTTT-ACCCCGAATC
* * *
30434222 TTCCAACAATTACCA-TTTTACCCCTAAAC
1 TTCCAAAAATTACCATTTTTACCCCGAATC
30434251 TTTCCAAAAA-T-CTCATTTTTAACCCCG-AT-
1 -TTCCAAAAATTAC-CATTTTT-ACCCCGAATC
*
30434280 TTCACCAAAAATAACCA-TTTTACCCTCGAA-C
1 TT--CCAAAAATTACCATTTTTACCC-CGAATC
*
30434311 TTTCC-AAAA-TCCCATTTTTAACCCC-AAT-
1 -TTCCAAAAATTACCATTTTT-ACCCCGAATC
30434339 TTCACCAAAAATTACCA-TTTTACCCCTGAA-C
1 TT--CCAAAAATTACCATTTTTACCCC-GAATC
* *
30434370 TTTCC-AAAA-TCCCATTTTTAACCCCG-A-G
1 -TTCCAAAAATTACCATTTTT-ACCCCGAATC
* * *
30434398 TTCACCAAAATTACCA-CTTTACCCCCGAACC
1 TTC-CAAAAATTACCATTTTTA-CCCCGAATC
* * **** *
30434429 TT-CTAAAATT-CTATTTTTGACTATAAAAC
1 TTCCAAAAATTACCATTTTT-ACCCCGAATC
30434458 TTCCAAAAATTACCA-TTTTACCCCGAATC
1 TTCCAAAAATTACCATTTTTACCCCGAATC
* *
30434487 TTCC-AAAA-T-CTCATTTTTAACCC-AATT
1 TTCCAAAAATTAC-CATTTTTACCCCGAATC
*
30434514 TTACCAAAAATTACCATTTTTACCCCTGAACC
1 TT-CCAAAAATTACCATTTTTACCCC-GAATC
* * * ** *
30434546 TTTC-AAAATT-TCATGTTTTACTCTTAAAC
1 TTCCAAAAATTACCAT-TTTTACCCCGAATC
*
30434575 TTCTAAAAATTACCA-TTTTACCCC
1 TTCCAAAAATTACCATTTTTACCCC
30434599 TAAATTTTCT
Statistics
Matches: 283, Mismatches: 46, Indels: 96
0.67 0.11 0.23
Matches are distributed among these distances:
26 1 0.00
27 13 0.05
28 31 0.11
29 100 0.35
30 104 0.37
31 25 0.09
32 9 0.03
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (30 bp):
TTCCAAAAATTACCATTTTTACCCCGAATC
Found at i:30440172 original size:24 final size:25
Alignment explanation
Indices: 30440126--30440175 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
30440116 CATACATTTA
*
30440126 AAATTTAATTTTTTATTATTTAATT
1 AAATTTAATTTTATATTATTTAATT
*
30440151 AAATTT-ATTTTATATCTATTAAATT
1 AAATTTAATTTTATAT-TATTTAATT
30440176 TATATTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
AAATTTAATTTTATATTATTTAATT
Found at i:30443387 original size:70 final size:70
Alignment explanation
Indices: 30443178--30443532 Score: 308
Period size: 70 Copynumber: 5.1 Consensus size: 70
30443168 GAGACCTTAG
* * * * * * * *
30443178 TATCAACTGGGAGCGTAGGTTCGTTAACTGTGTTGGAGG-TTACAATCATAAACCAACAAACCTT
1 TATCAGCTGGGAACGTAGGTCCGTTAACTGTGTTGGAGGCTGACGATCATAAATCGACAAGCCTT
**
30443242 TAAAA
66 TGTAA
* * * * * *
30443247 TATTA-CTTGGGAACATAGGTTCGATAGA-TGTGTTGGAGGC-GACGATTATAAA-CCAGCAAGC
1 TATCAGC-TGGGAACGTAGGTCCGTTA-ACTGTGTTGGAGGCTGACGATCATAAATCGA-CAAGC
30443308 CTTTGTAA
63 CTTTGTAA
* * *
30443316 TATCAGCTGGGAACGTAGGTCCATTAACTATGTTGGAGGTTGACGATCATAAATCGACAAGCCTT
1 TATCAGCTGGGAACGTAGGTCCGTTAACTGTGTTGGAGGCTGACGATCATAAATCGACAAGCCTT
30443381 TGTAA
66 TGTAA
* * * * ** * * *
30443386 TATTAGCTAGGAGCGTAGGTCCGCTAGTTGTGTTGGAGACT-AGCGATCATAAATTGACGAGCCT
1 TATCAGCTGGGAACGTAGGTCCGTTAACTGTGTTGGAGGCTGA-CGATCATAAATCGACAAGCCT
30443450 TTGTAA
65 TTGTAA
* * ** * * *
30443456 TATCAGTTGGGAACATAGGTTTGTTACCTGTGTTGGAGGCTGACAATCATAAATCGACGAGCCTT
1 TATCAGCTGGGAACGTAGGTCCGTTAACTGTGTTGGAGGCTGACGATCATAAATCGACAAGCCTT
*
30443521 TGCAA
66 TGTAA
30443526 TATCAGC
1 TATCAGC
30443533 CAAGAGCATA
Statistics
Matches: 229, Mismatches: 47, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
68 4 0.02
69 80 0.35
70 142 0.62
71 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (70 bp):
TATCAGCTGGGAACGTAGGTCCGTTAACTGTGTTGGAGGCTGACGATCATAAATCGACAAGCCTT
TGTAA
Found at i:30443543 original size:70 final size:70
Alignment explanation
Indices: 30443275--30443564 Score: 271
Period size: 70 Copynumber: 4.2 Consensus size: 70
30443265 GTTCGATAGA
* * * * * *
30443275 TGTGTTGGAGGC-GACGATTATAAA-CCAGCAAGCCTTTGTAATATCAGCTGGGAACGTAGGTCC
1 TGTGTTGGAGGCTGACGATCATAAATCGA-CGAGCCTTTGTAATATCAGCTAGGAGCATAGGTCC
** *
30443338 ATTAAC
65 GCTACC
* * * * *
30443344 TATGTTGGAGGTTGACGATCATAAATCGACAAGCCTTTGTAATATTAGCTAGGAGCGTAGGTCCG
1 TGTGTTGGAGGCTGACGATCATAAATCGACGAGCCTTTGTAATATCAGCTAGGAGCATAGGTCCG
**
30443409 CTAGT
66 CTACC
* * * * * **
30443414 TGTGTTGGAGACT-AGCGATCATAAATTGACGAGCCTTTGTAATATCAGTTGGGAACATAGGTTT
1 TGTGTTGGAGGCTGA-CGATCATAAATCGACGAGCCTTTGTAATATCAGCTAGGAGCATAGGTCC
*
30443478 GTTACC
65 GCTACC
* * * * *
30443484 TGTGTTGGAGGCTGACAATCATAAATCGACGAGCCTTTGCAATATCAGCCAAGAGCATAGGTCCA
1 TGTGTTGGAGGCTGACGATCATAAATCGACGAGCCTTTGTAATATCAGCTAGGAGCATAGGTCCG
*
30443549 CTAGC
66 CTACC
30443554 TGTGTTGGAGG
1 TGTGTTGGAGG
30443565 TTAGCGGTCA
Statistics
Matches: 177, Mismatches: 40, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
69 11 0.06
70 163 0.92
71 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (70 bp):
TGTGTTGGAGGCTGACGATCATAAATCGACGAGCCTTTGTAATATCAGCTAGGAGCATAGGTCCG
CTACC
Found at i:30443570 original size:140 final size:140
Alignment explanation
Indices: 30443305--30443563 Score: 365
Period size: 140 Copynumber: 1.9 Consensus size: 140
30443295 TAAACCAGCA
* * *
30443305 AGCCTTTGTAATATCAGCTGGGAACGTAGGTCCATTAACTATGTTGGAGGTTGACGATCATAAAT
1 AGCCTTTGTAATATCAGCTGGGAACATAGGTCCATTAACTATGTTGGAGGCTGACAATCATAAAT
* * * * * * *
30443370 CGACAAGCCTTTGTAATATTAGCTAGGAGCGTAGGTCCGCTAGTTGTGTTGGAGACTAGCGATCA
66 CGACAAGCCTTTGCAATATCAGCCAAGAGCATAGGTCCACTAGCTGTGTTGGAGACTAGCGATCA
30443435 TAAATTGACG
131 TAAATTGACG
* *** * *
30443445 AGCCTTTGTAATATCAGTTGGGAACATAGGTTTGTTACCTGTGTTGGAGGCTGACAATCATAAAT
1 AGCCTTTGTAATATCAGCTGGGAACATAGGTCCATTAACTATGTTGGAGGCTGACAATCATAAAT
*
30443510 CGACGAGCCTTTGCAATATCAGCCAAGAGCATAGGTCCACTAGCTGTGTTGGAG
66 CGACAAGCCTTTGCAATATCAGCCAAGAGCATAGGTCCACTAGCTGTGTTGGAG
30443564 GTTAGCGGTC
Statistics
Matches: 102, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
140 102 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (140 bp):
AGCCTTTGTAATATCAGCTGGGAACATAGGTCCATTAACTATGTTGGAGGCTGACAATCATAAAT
CGACAAGCCTTTGCAATATCAGCCAAGAGCATAGGTCCACTAGCTGTGTTGGAGACTAGCGATCA
TAAATTGACG
Found at i:30447260 original size:13 final size:13
Alignment explanation
Indices: 30447241--30447296 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
30447231 TTAATTGTCA
30447241 AGTCAACGGGTCG
1 AGTCAACGGGTCG
* * *
30447254 GGTCAACTGGTCAA
1 AGTCAACGGGTC-G
*
30447268 AGTCAACGGATCG
1 AGTCAACGGGTCG
*
30447281 AGTCAATGGGTCG
1 AGTCAACGGGTCG
30447294 AGT
1 AGT
30447297 TAATGAATCA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
13 24 0.73
14 9 0.27
ACGTcount: A:0.27, C:0.20, G:0.34, T:0.20
Consensus pattern (13 bp):
AGTCAACGGGTCG
Found at i:30447285 original size:40 final size:40
Alignment explanation
Indices: 30447240--30447332 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 40
30447230 ATTAATTGTC
* * *
30447240 AAGTCAACGGGTCGGGTCAACTG-GTCAAAGTCAAC-GGAT
1 AAGTCAATGGGTCGAGTCAA-TGAATCAAAGTCAACAGGAT
* *
30447279 CGAGTCAATGGGTCGAGTTAATGAATCAAAGTCAACAGGAT
1 -AAGTCAATGGGTCGAGTCAATGAATCAAAGTCAACAGGAT
30447320 AAGTCAATGGGTC
1 AAGTCAATGGGTC
30447333 AAACATCAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.04
40 39 0.87
41 4 0.09
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.20
Consensus pattern (40 bp):
AAGTCAATGGGTCGAGTCAATGAATCAAAGTCAACAGGAT
Found at i:30452710 original size:27 final size:27
Alignment explanation
Indices: 30452672--30452725 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
30452662 AATTATTAAA
*
30452672 GGGTAACTCACCAGAAGAGGAAGATTC
1 GGGTAACTCACCAAAAGAGGAAGATTC
30452699 GGGTAACTCACCAAAAGAGGAAGATTC
1 GGGTAACTCACCAAAAGAGGAAGATTC
30452726 TTGGCACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.15
Consensus pattern (27 bp):
GGGTAACTCACCAAAAGAGGAAGATTC
Found at i:30452906 original size:54 final size:54
Alignment explanation
Indices: 30452824--30452934 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
30452814 ATCTCCTTTT
* * **
30452824 GAACAGTAGTCTCCCCCTGAGCAATAGCTTCCTTTTGAACAATGGTGTTTTCTG
1 GAACAATAGTCTCCCCCTGAACAATAGCTTCCCCTTGAACAATGGTGTTTTCTG
* *
30452878 GAACAATAGTCTCCCTCTGAACAGTAGCTTCCCCTTGAACAATGGTGTTTTCTG
1 GAACAATAGTCTCCCCCTGAACAATAGCTTCCCCTTGAACAATGGTGTTTTCTG
30452932 GAA
1 GAA
30452935 TAAGGTTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (54 bp):
GAACAATAGTCTCCCCCTGAACAATAGCTTCCCCTTGAACAATGGTGTTTTCTG
Found at i:30462811 original size:17 final size:17
Alignment explanation
Indices: 30462769--30462810 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
30462759 AATGAATGAA
* *
30462769 TTTTGTTTTCTTTTCTT
1 TTTTCTTTTCTTCTCTT
*
30462786 TTCTCTTTTCTTCTCTT
1 TTTTCTTTTCTTCTCTT
30462803 TTTT-TTTT
1 TTTTCTTTT
30462811 TTTTTGCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (17 bp):
TTTTCTTTTCTTCTCTT
Found at i:30469549 original size:70 final size:70
Alignment explanation
Indices: 30469436--30469577 Score: 266
Period size: 70 Copynumber: 2.0 Consensus size: 70
30469426 TGATTTATAA
30469436 ATATGTTGGTGTGATATTGAGGCAATCGGTTTGAAGACACTTGAGTAGTACAAGAGTGTGCCTAA
1 ATATGTTGGTGTGATATTGAGGCAATCGGTTTGAAGACACTTGAGTAGTACAAGAGTGTGCCTAA
30469501 GTAGC
66 GTAGC
* *
30469506 ATATGTTGGTGTGGTATTGAGGCAATCGGTTTGAAGGCACTTGAGTAGTACAAGAGTGTGCCTAA
1 ATATGTTGGTGTGATATTGAGGCAATCGGTTTGAAGACACTTGAGTAGTACAAGAGTGTGCCTAA
30469571 GTAGC
66 GTAGC
30469576 AT
1 AT
30469578 TGGAGTGATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.30
Consensus pattern (70 bp):
ATATGTTGGTGTGATATTGAGGCAATCGGTTTGAAGACACTTGAGTAGTACAAGAGTGTGCCTAA
GTAGC
Found at i:30479036 original size:19 final size:19
Alignment explanation
Indices: 30478994--30479036 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
30478984 CTATATCATT
30478994 ATTATTAAATTATTAATAA
1 ATTATTAAATTATTAATAA
*
30479013 TTTATTAAATTATTCAA-AA
1 ATTATTAAATTATT-AATAA
30479032 ATTAT
1 ATTAT
30479037 AAGTTAGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATTAAATTATTAATAA
Found at i:30483382 original size:17 final size:17
Alignment explanation
Indices: 30483360--30483404 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
30483350 ACGCGGTCGT
30483360 TTGAGCATACTAGCTCG
1 TTGAGCATACTAGCTCG
*
30483377 TTGAGCATAGTAGCTCG
1 TTGAGCATACTAGCTCG
30483394 TTGAGCATACT
1 TTGAGCATACT
30483405 GACTCATTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (17 bp):
TTGAGCATACTAGCTCG
Found at i:30484138 original size:21 final size:21
Alignment explanation
Indices: 30484114--30484169 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
30484104 TAGAGTTTTT
30484114 AGTATCGATAGAAGCATGTCG
1 AGTATCGATAGAAGCATGTCG
*
30484135 AGTATCGATAGAAGCTTGTCG
1 AGTATCGATAGAAGCATGTCG
30484156 AGTATC-AGTAGAAG
1 AGTATCGA-TAGAAG
30484170 GTACACTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (21 bp):
AGTATCGATAGAAGCATGTCG
Found at i:30488869 original size:21 final size:21
Alignment explanation
Indices: 30488845--30488898 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
30488835 TAGAGTTTTT
*
30488845 AGTATTGGTAGAAGCATGTCG
1 AGTATCGGTAGAAGCATGTCG
* *
30488866 AGTATCGGTAGAAGCTTGTTG
1 AGTATCGGTAGAAGCATGTCG
*
30488887 AGTATCGATAGA
1 AGTATCGGTAGA
30488899 GGGTACACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (21 bp):
AGTATCGGTAGAAGCATGTCG
Found at i:30495455 original size:21 final size:21
Alignment explanation
Indices: 30495431--30495479 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
30495421 GAAGTAGGAC
30495431 TTGTTTCAGTAGAAGT-TACA
1 TTGTTTCAGTAGAAGTCTACA
*
30495451 TTTGTATT-GGTAGAAGTCTACA
1 -TTGT-TTCAGTAGAAGTCTACA
30495473 TTGTTTC
1 TTGTTTC
30495480 TACATTGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 6 0.25
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.45
Consensus pattern (21 bp):
TTGTTTCAGTAGAAGTCTACA
Found at i:30502408 original size:21 final size:21
Alignment explanation
Indices: 30502365--30502418 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
30502355 AGAGTTTTTA
*
30502365 GTATCGATAGAAGTAAGACTT
1 GTATCGATAGAAGTAACACTT
* * *
30502386 GTTTCGATAGAAGTTACATTT
1 GTATCGATAGAAGTAACACTT
*
30502407 GTATCGGTAGAA
1 GTATCGATAGAA
30502419 CTTTCCAAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (21 bp):
GTATCGATAGAAGTAACACTT
Found at i:30510582 original size:17 final size:17
Alignment explanation
Indices: 30510560--30510598 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
30510550 TTAAGAACAA
*
30510560 ATCCTTTTAAATCAATT
1 ATCCTTTCAAATCAATT
30510577 ATCC-TTCAAATCAATT
1 ATCCTTTCAAATCAATT
30510593 ATCCTT
1 ATCCTT
30510599 CAAGATTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (17 bp):
ATCCTTTCAAATCAATT
Found at i:30510587 original size:16 final size:16
Alignment explanation
Indices: 30510568--30510601 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
30510558 AAATCCTTTT
30510568 AAATCAATTATCCTTC
1 AAATCAATTATCCTTC
30510584 AAATCAATTATCCTTC
1 AAATCAATTATCCTTC
30510600 AA
1 AA
30510602 GATTGGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATCAATTATCCTTC
Found at i:30519360 original size:23 final size:24
Alignment explanation
Indices: 30519316--30519373 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
30519306 TTTTTTGGGC
* *
30519316 ATTTTGTTTACTTTTGTTTATTT-G
1 ATTTTG-TTGCTTTTGTGTATTTGG
30519340 ATTTTGTTGCTTTTGTGTATTTGG
1 ATTTTGTTGCTTTTGTGTATTTGG
30519364 ATTTCTGTTG
1 ATTT-TGTTG
30519374 GACTTTTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 14 0.47
24 11 0.37
25 5 0.17
ACGTcount: A:0.10, C:0.05, G:0.19, T:0.66
Consensus pattern (24 bp):
ATTTTGTTGCTTTTGTGTATTTGG
Found at i:30520221 original size:24 final size:22
Alignment explanation
Indices: 30520194--30520239 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
30520184 AATAAATGCT
30520194 TTTTGTAATTTTTATATATTTTTA
1 TTTT-TAATTTTT-TATATTTTTA
*
30520218 TTTTTTATTTTTTATATTTTTA
1 TTTTTAATTTTTTATATTTTTA
30520240 AAAATTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 7 0.33
24 4 0.19
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTTAATTTTTTATATTTTTA
Found at i:30520239 original size:8 final size:7
Alignment explanation
Indices: 30520201--30520239 Score: 51
Period size: 7 Copynumber: 5.1 Consensus size: 7
30520191 GCTTTTTGTA
30520201 ATTTTTAT
1 ATTTTT-T
30520209 ATATTTTT
1 AT-TTTTT
30520217 ATTTTTT
1 ATTTTTT
30520224 ATTTTTT
1 ATTTTTT
30520231 ATATTTTT
1 AT-TTTTT
30520239 A
1 A
30520240 AAAATTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 14 0.48
8 11 0.38
9 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
ATTTTTT
Found at i:30521973 original size:7 final size:7
Alignment explanation
Indices: 30521963--30521989 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30521953 AACGATCAAA
30521963 GTCAACG
1 GTCAACG
30521970 GTCAACG
1 GTCAACG
30521977 GTCAACG
1 GTCAACG
30521984 GTCAAC
1 GTCAAC
30521990 AATCAACGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:30521995 original size:14 final size:14
Alignment explanation
Indices: 30521951--30521998 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
30521941 CCGAAAAAAT
*
30521951 TCAACGATCAA-AG
1 TCAACGGTCAACAG
*
30521964 TCAACGGTCAACGG
1 TCAACGGTCAACAG
*
30521978 TCAACGGTCAACAA
1 TCAACGGTCAACAG
30521992 TCAACGG
1 TCAACGG
30521999 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (14 bp):
TCAACGGTCAACAG
Found at i:30547571 original size:22 final size:21
Alignment explanation
Indices: 30547541--30547581 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
30547531 CCAGGGATCG
*
30547541 ATGTCGTGACACATTAGGTCCT
1 ATGTCGTGACA-ATAAGGTCCT
*
30547563 ATGTTGTGACAATAAGGTC
1 ATGTCGTGACAATAAGGTC
30547582 AGTCTACTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (21 bp):
ATGTCGTGACAATAAGGTCCT
Found at i:30552573 original size:406 final size:406
Alignment explanation
Indices: 30551821--30552632 Score: 1552
Period size: 406 Copynumber: 2.0 Consensus size: 406
30551811 TAAAACAATT
*
30551821 TATGGAGAAATATAAAAATATATATATATTCTCTATTGCATACGCAAAGACTCAAACACAAGATC
1 TATGGAGAAATATAAAAATATATATATATTCCCTATTGCATACGCAAAGACTCAAACACAAGATC
30551886 AGAGAGTATACAAATGCTTAATCACTGAACCTAGGCTCATCATTGACATAAAATTACACAAAAAT
66 AGAGAGTATACAAATGCTTAATCACTGAACCTAGGCTCATCATTGACATAAAATTACACAAAAAT
30551951 AAACTTAAGCTGAACATTCCCAGATAAAGGTTGAACCAAAGAATAACAAAACTTTTCAAAATTGG
131 AAACTTAAGCTGAACATTCCCAGATAAAGGTTGAACCAAAGAATAACAAAACTTTTCAAAATTGG
*
30552016 GTCTTGAGCCCCTGATCTCAACCACGCAAGCAAAGCACATAACCACTGAAGCAAATACAAAATTA
196 GTCTTGAGCCCCTGATCTCAACCACGCAAGCAAAGCACATAACCACTGAAGCAAATACAAAATAA
* *
30552081 GTGATAGATATTAACTAACAAGAGCTCAAAATCGAGGCGTTACAAAATTAAACTAAAATATTTTA
261 GTGATAGACATTAACTAACAAGAGCTCAAAATCAAGGCGTTACAAAATTAAACTAAAATATTTTA
*
30552146 TTAAATAAATAGTCTAATTAAAATAGGTGTAAAAGTAAAGTTTGTTTATAGAAAAGAAAGGAGCA
326 TTAAATAAATAGTCTAATTAAAATAGGTGTAAAAGTAAAGTTTGTTTATAGAAAAGAAAGGAACA
*
30552211 AAAGAATGAAGAAGAA
391 AAAGAATAAAGAAGAA
*
30552227 TATGGAGAAATATAAAAATATATATATATTCCCTATTGCATACGCAAAGACTCAAACATAAGATC
1 TATGGAGAAATATAAAAATATATATATATTCCCTATTGCATACGCAAAGACTCAAACACAAGATC
30552292 AGAGAGTATACAAATGCTTAATCACTGAACCTAGGCTCATCATTGACATAAAATTACACAAAAAT
66 AGAGAGTATACAAATGCTTAATCACTGAACCTAGGCTCATCATTGACATAAAATTACACAAAAAT
30552357 AAACTTAAGCTGAACATTCCCAGATAAAGGTTGAACCAAAGAATAACAAAACTTTTCAAAATTGG
131 AAACTTAAGCTGAACATTCCCAGATAAAGGTTGAACCAAAGAATAACAAAACTTTTCAAAATTGG
30552422 GTCTTGAGCCCCTGATCTCAACCACGCAAGCAAAGCACATAACCACTGAAGCAAATACAAAATAA
196 GTCTTGAGCCCCTGATCTCAACCACGCAAGCAAAGCACATAACCACTGAAGCAAATACAAAATAA
*
30552487 GTGATAGGCATTAACTAACAAGAGCTCAAAATCAAGGCGTTACAAAATTAAACTAAAATATTTTA
261 GTGATAGACATTAACTAACAAGAGCTCAAAATCAAGGCGTTACAAAATTAAACTAAAATATTTTA
30552552 TTAAATAAATAGTCTAATTAAAATAGGTGTAAAAGTAAAGTTTGTTTATAGAAAAGAAAGGAACA
326 TTAAATAAATAGTCTAATTAAAATAGGTGTAAAAGTAAAGTTTGTTTATAGAAAAGAAAGGAACA
30552617 AAAGAATAAAGAAGAA
391 AAAGAATAAAGAAGAA
30552633 AAAAATGGTG
Statistics
Matches: 398, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
406 398 1.00
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (406 bp):
TATGGAGAAATATAAAAATATATATATATTCCCTATTGCATACGCAAAGACTCAAACACAAGATC
AGAGAGTATACAAATGCTTAATCACTGAACCTAGGCTCATCATTGACATAAAATTACACAAAAAT
AAACTTAAGCTGAACATTCCCAGATAAAGGTTGAACCAAAGAATAACAAAACTTTTCAAAATTGG
GTCTTGAGCCCCTGATCTCAACCACGCAAGCAAAGCACATAACCACTGAAGCAAATACAAAATAA
GTGATAGACATTAACTAACAAGAGCTCAAAATCAAGGCGTTACAAAATTAAACTAAAATATTTTA
TTAAATAAATAGTCTAATTAAAATAGGTGTAAAAGTAAAGTTTGTTTATAGAAAAGAAAGGAACA
AAAGAATAAAGAAGAA
Found at i:30554430 original size:18 final size:18
Alignment explanation
Indices: 30554407--30554448 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
30554397 TTCTACAGGT
30554407 GCAGATTCTCAAGGGGTC
1 GCAGATTCTCAAGGGGTC
*
30554425 GCAGATTCTCAAGGGGTT
1 GCAGATTCTCAAGGGGTC
30554443 GCAGAT
1 GCAGAT
30554449 GAGCATTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (18 bp):
GCAGATTCTCAAGGGGTC
Found at i:30559131 original size:17 final size:17
Alignment explanation
Indices: 30559097--30559138 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
30559087 ATATGGGACA
*
30559097 AAAATGAGAATGATGTG
1 AAAATGAGAATGAAGTG
30559114 AAAAT-AGAATTGAAGTG
1 AAAATGAGAA-TGAAGTG
30559131 AAATATGA
1 AAA-ATGA
30559139 TTTTTACCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 2 0.10
19 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAATGAGAATGAAGTG
Found at i:30561417 original size:18 final size:18
Alignment explanation
Indices: 30561383--30561417 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30561373 ACTTCTGCAG
*
30561383 CTCGAGGTCGTGGTAGTA
1 CTCGAGGTCGTGCTAGTA
*
30561401 CTCGAGGTGGTGCTAGT
1 CTCGAGGTCGTGCTAGT
30561418 GGCAGAGGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.17, G:0.40, T:0.29
Consensus pattern (18 bp):
CTCGAGGTCGTGCTAGTA
Found at i:30566316 original size:17 final size:17
Alignment explanation
Indices: 30566282--30566323 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
30566272 ATATGGGACA
*
30566282 AAAATGAGAATGATGTG
1 AAAATGAGAATGAAGTG
30566299 AAAAT-AGAATTGAAGTG
1 AAAATGAGAA-TGAAGTG
30566316 AAATATGA
1 AAA-ATGA
30566324 TTTTTACCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 2 0.10
19 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAATGAGAATGAAGTG
Found at i:30568675 original size:21 final size:24
Alignment explanation
Indices: 30568646--30568689 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
30568636 TTATTTTATA
30568646 TTTATGTTG-ACAAAT-TAACTCT
1 TTTATGTTGTACAAATCTAACTCT
*
30568668 TTTA-GTTGTACAGATCTAACTC
1 TTTATGTTGTACAAATCTAACTC
30568690 AGTTGCGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (24 bp):
TTTATGTTGTACAAATCTAACTCT
Found at i:30588278 original size:18 final size:18
Alignment explanation
Indices: 30588251--30588285 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30588241 AACTGAAGAA
30588251 AAGAAGGAAGAAAAGGAG
1 AAGAAGGAAGAAAAGGAG
* *
30588269 AAGAATGAAGAGAAGGA
1 AAGAAGGAAGAAAAGGA
30588286 AGATGCCCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (18 bp):
AAGAAGGAAGAAAAGGAG
Found at i:30591779 original size:25 final size:23
Alignment explanation
Indices: 30591751--30591798 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
30591741 TATTCTCCTC
30591751 CTTTATGTCTCACTCCATCTCACCT
1 CTTTATGTCTC-CTCC-TCTCACCT
* *
30591776 CTTTATTTCTCCTTCTCTCACCT
1 CTTTATGTCTCCTCCTCTCACCT
30591799 TCCTTATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 10 0.48
ACGTcount: A:0.12, C:0.40, G:0.02, T:0.46
Consensus pattern (23 bp):
CTTTATGTCTCCTCCTCTCACCT
Found at i:30591787 original size:21 final size:23
Alignment explanation
Indices: 30591763--30591811 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
30591753 TTATGTCTCA
*
30591763 CTCC-ATCTCACC-TCTTTATTT
1 CTCCTATCTCACCTTCCTTATTT
*
30591784 CTCCTTCTCTCACCTTCCTTATTT
1 CTCC-TATCTCACCTTCCTTATTT
30591808 CTCC
1 CTCC
30591812 CTTTTAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
23 7 0.30
24 12 0.52
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.47
Consensus pattern (23 bp):
CTCCTATCTCACCTTCCTTATTT
Done.