Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 65 of 208
Found at i:18779801 original size:19 final size:21
Alignment explanation
Indices: 18779747--18779805 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
18779737 TGAAAATTTT
* *
18779747 AATTTTAATTTAATATTTTTATA
1 AATTTTAA--TAATGTTTTTACA
18779770 AATTTTAATAATGTTTTTACA
1 AATTTTAATAATGTTTTTACA
18779791 AA-TTT-ATAATGTTTT
1 AATTTTAATAATGTTTT
18779806 AATTTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.29
20 3 0.09
21 13 0.38
23 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (21 bp):
AATTTTAATAATGTTTTTACA
Found at i:18781235 original size:15 final size:16
Alignment explanation
Indices: 18781195--18781236 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
18781185 TGATTGCGCT
* *
18781195 GGACTTTACAATTTGA
1 GGACTTTACAATATAA
18781211 GGACTTTACAATATAA
1 GGACTTTACAATATAA
18781227 GGA-TTTACAA
1 GGACTTTACAA
18781237 GCAAATATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (16 bp):
GGACTTTACAATATAA
Found at i:18781680 original size:18 final size:17
Alignment explanation
Indices: 18781657--18781690 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
18781647 TCCTTCACCC
18781657 TACCCATTCCTGATTTCT
1 TACCCATTCCT-ATTTCT
18781675 TACCCATTCCTATTTC
1 TACCCATTCCTATTTC
18781691 GAAAAACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.18, C:0.35, G:0.03, T:0.44
Consensus pattern (17 bp):
TACCCATTCCTATTTCT
Found at i:18782231 original size:26 final size:26
Alignment explanation
Indices: 18782080--18782232 Score: 121
Period size: 26 Copynumber: 5.8 Consensus size: 26
18782070 GTTATTATTA
* * * *
18782080 GCCACAAAGGCATCCCTTTCCATAGAC
1 GCCACAAAGGCTTCCATTT-CAGATAC
* *
18782107 TGCCACAGAGGCTTCCATTTCAGATAT
1 -GCCACAAAGGCTTCCATTTCAGATAC
* ** * *
18782134 ACCACAAAGAG-TTTAATTTTAGATAT
1 GCCACAAAG-GCTTCCATTTCAGATAC
* *
18782160 GGCACAAAGGCTTTCACTTT-AGATAC
1 GCCACAAAGGCTTCCA-TTTCAGATAC
* *
18782186 GCCACAAAGGCTTTCATTTCAAATAC
1 GCCACAAAGGCTTCCATTTCAGATAC
18782212 GCCACAAAGGCTTCCATTTCA
1 GCCACAAAGGCTTCCATTTCA
18782233 TAGATTACCA
Statistics
Matches: 103, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
25 4 0.04
26 75 0.73
27 8 0.08
28 16 0.16
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (26 bp):
GCCACAAAGGCTTCCATTTCAGATAC
Found at i:18813137 original size:26 final size:26
Alignment explanation
Indices: 18813108--18813159 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
18813098 ACACACAAGT
18813108 ATGATTCAGGTAAATGAGTGTTCGAA
1 ATGATTCAGGTAAATGAGTGTTCGAA
18813134 ATGATTCAGGTAAATGAGTGTTCGAA
1 ATGATTCAGGTAAATGAGTGTTCGAA
18813160 CTAGTCAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (26 bp):
ATGATTCAGGTAAATGAGTGTTCGAA
Found at i:18820520 original size:23 final size:23
Alignment explanation
Indices: 18820494--18820539 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
18820484 ATGCGTTAGA
18820494 GTTTGTGCACCTTAGTCAGTATG
1 GTTTGTGCACCTTAGTCAGTATG
*
18820517 GTTTGTGCGCCTTAGTCAGTATG
1 GTTTGTGCACCTTAGTCAGTATG
18820540 CGCCTGAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.17, G:0.28, T:0.39
Consensus pattern (23 bp):
GTTTGTGCACCTTAGTCAGTATG
Found at i:18824124 original size:31 final size:31
Alignment explanation
Indices: 18824089--18824150 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
18824079 ATGGAGGCCA
18824089 TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
1 TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
18824120 TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
1 TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
18824151 GACTTCTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.16, C:0.10, G:0.29, T:0.45
Consensus pattern (31 bp):
TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
Found at i:18824526 original size:22 final size:20
Alignment explanation
Indices: 18824470--18824526 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
18824460 TCAAATATAT
18824470 ATAAACATTAAATATATAAAA
1 ATAAA-ATTAAATATATAAAA
18824491 ATAGAAA-TAAATATATAAAA
1 ATA-AAATTAAATATATAAAA
*
18824511 ATTTAAAATTATATAT
1 A--TAAAATTAAATAT
18824527 TCTAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 14 0.45
21 7 0.23
22 10 0.32
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAATTAAATATATAAAA
Found at i:18825655 original size:32 final size:32
Alignment explanation
Indices: 18825614--18825706 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 32
18825604 CTCTTATCTT
*
18825614 TATAAATTCACTAACCTTGTGAGGTTTTTCTG
1 TATAAATTCACTAACCTTGTGAGGTTTGTCTG
*
18825646 TATAAATTCACTAACCTTGTGAGGTTTGTCTT
1 TATAAATTCACTAACCTTGTGAGGTTTGTCTG
*
18825678 TATAAATTCACTAACCTTGTGAGGCTTGT
1 TATAAATTCACTAACCTTGTGAGGTTTGT
18825707 GGTGTGTATA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (32 bp):
TATAAATTCACTAACCTTGTGAGGTTTGTCTG
Found at i:18826122 original size:57 final size:57
Alignment explanation
Indices: 18826030--18826143 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
18826020 TGTAAAGGTG
*
18826030 AATAAGTATTTATTTGTCACTTTTGGCATATGTATGTCTATATATATGTGCTTATAA
1 AATAAGTATTTATTTGTCACTTTTGGCATAAGTATGTCTATATATATGTGCTTATAA
18826087 AATAAGTATTTATTTGTCACTTTTGGCATAAGTATGTCTATATATATGTGCTTATAA
1 AATAAGTATTTATTTGTCACTTTTGGCATAAGTATGTCTATATATATGTGCTTATAA
18826144 TCCTTTGTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (57 bp):
AATAAGTATTTATTTGTCACTTTTGGCATAAGTATGTCTATATATATGTGCTTATAA
Found at i:18830889 original size:28 final size:28
Alignment explanation
Indices: 18830849--18830905 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
18830839 CTATCTTGAG
18830849 AAGTTATGAGTCCTTTAGGGACCCATAC
1 AAGTTATGAGTCCTTTAGGGACCCATAC
18830877 AAGTTATGAGTCCTTTAGGGACCCATAC
1 AAGTTATGAGTCCTTTAGGGACCCATAC
18830905 A
1 A
18830906 CTTTTAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (28 bp):
AAGTTATGAGTCCTTTAGGGACCCATAC
Found at i:18833275 original size:20 final size:22
Alignment explanation
Indices: 18833233--18833276 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
18833223 CAATTTTGTT
*
18833233 ATTATTTTTAAGAAAGATATCG
1 ATTATTTTCAAGAAAGATATCG
18833255 ATTATTTTCAA-AAAG-TATCG
1 ATTATTTTCAAGAAAGATATCG
18833275 AT
1 AT
18833277 ACCAAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 4 0.19
22 10 0.48
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (22 bp):
ATTATTTTCAAGAAAGATATCG
Found at i:18837048 original size:31 final size:29
Alignment explanation
Indices: 18837010--18837086 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
18837000 CTAACGGCTT
* *
18837010 AGTGACTAAAATGTTACAATGTGATAACATA
1 AGTGACTAAAATGTAAC-ATGTCA-AACATA
* *
18837041 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACATGTCAAACATA
*
18837070 AGTGACTAAAATATAAC
1 AGTGACTAAAATGTAAC
18837087 CTGAGCAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 21 0.52
30 4 0.10
31 15 0.38
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTAACATGTCAAACATA
Found at i:18837420 original size:24 final size:23
Alignment explanation
Indices: 18837372--18837421 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
18837362 AAAATTCATA
18837372 ATATTAAATATTAAAAATAGCTTT
1 ATATTAAATATTAAAAATA-CTTT
*
18837396 ATATTAATATATATTAAAATA-TTT
1 ATATTAA-ATAT-TAAAAATACTTT
18837420 AT
1 AT
18837422 TTTTATTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 12 0.52
25 4 0.17
26 7 0.30
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATTAAATATTAAAAATACTTT
Found at i:18840528 original size:30 final size:31
Alignment explanation
Indices: 18840484--18840543 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
18840474 GCTAGGGTAA
* *
18840484 TTTGGGTAACGAAGTATAGTTTTGGTACCAC
1 TTTGGGTAACGAAGTATAATTTAGGTACCAC
*
18840515 TTTGGGT-ACGAAGTTTAATTTAGGTACCA
1 TTTGGGTAACGAAGTATAATTTAGGTACCA
18840544 TTTATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (31 bp):
TTTGGGTAACGAAGTATAATTTAGGTACCAC
Found at i:18841128 original size:16 final size:15
Alignment explanation
Indices: 18841086--18841129 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
18841076 AAAAAAGTTA
18841086 AAGGATGGAAAATTG
1 AAGGATGGAAAATTG
* *
18841101 AAGGGGTAGAAAATTAG
1 AA-GGATGGAAAATT-G
18841118 AAGGATGGAAAA
1 AAGGATGGAAAA
18841130 CATAATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 2 0.09
16 18 0.78
17 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (15 bp):
AAGGATGGAAAATTG
Found at i:18860078 original size:21 final size:21
Alignment explanation
Indices: 18860054--18860094 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
18860044 ATTGCTCAAC
18860054 ACATATTTACCAAATCATTAA
1 ACATATTTACCAAATCATTAA
18860075 ACATATTTACCAAATCATTA
1 ACATATTTACCAAATCATTA
18860095 CACGACAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (21 bp):
ACATATTTACCAAATCATTAA
Found at i:18876267 original size:12 final size:12
Alignment explanation
Indices: 18876247--18876280 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18876237 TCACGAACAA
*
18876247 GCTCATTTATTG
1 GCTCGTTTATTG
18876259 GCTCGTTTATTG
1 GCTCGTTTATTG
*
18876271 ACTCGTTTAT
1 GCTCGTTTAT
18876281 GACTTGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.50
Consensus pattern (12 bp):
GCTCGTTTATTG
Found at i:18880703 original size:70 final size:70
Alignment explanation
Indices: 18880617--18880758 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
18880607 GACTAAGGAC
18880617 ATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTCGGTGTTACGATCCGACCACGTAATATCAT
1 ATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTCGGTGTTACGATCCGACCACGTAATATCAT
18880682 TTAGT
66 TTAGT
18880687 ATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTCGGTGTTACGATCCGACCACGTAATATCAT
1 ATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTCGGTGTTACGATCCGACCACGTAATATCAT
18880752 TTAGT
66 TTAGT
18880757 AT
1 AT
18880759 CAATTTAAAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (70 bp):
ATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTCGGTGTTACGATCCGACCACGTAATATCAT
TTAGT
Found at i:18882338 original size:20 final size:20
Alignment explanation
Indices: 18882313--18882354 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
18882303 TGTTAATCAT
*
18882313 ATTTTATTAAATAAAATTAC
1 ATTTTAATAAATAAAATTAC
**
18882333 ATTTTAATAAATGGAATTAC
1 ATTTTAATAAATAAAATTAC
18882353 AT
1 AT
18882355 CTGCAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (20 bp):
ATTTTAATAAATAAAATTAC
Found at i:18884128 original size:3 final size:3
Alignment explanation
Indices: 18884120--18884149 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
18884110 CATTGAAAAT
18884120 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18884150 GTTGCTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18889117 original size:25 final size:25
Alignment explanation
Indices: 18889089--18889162 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 25
18889079 TCCAAGTTGA
* *
18889089 ATAACGATAAGCTCCTTCGAGCTAT
1 ATAACGATAAGCTCATACGAGCTAT
* *
18889114 ATAATGGTAAGCTCATACGAGCTGAGT
1 ATAACGATAAGCTCATACGAGCT-A-T
* *
18889141 ATCA-G-TAAGCTCATAAGAGCTA
1 ATAACGATAAGCTCATACGAGCTA
18889163 AAATTCGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
24 1 0.02
25 34 0.83
26 2 0.05
27 4 0.10
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (25 bp):
ATAACGATAAGCTCATACGAGCTAT
Found at i:18892186 original size:50 final size:50
Alignment explanation
Indices: 18892075--18892270 Score: 230
Period size: 50 Copynumber: 3.8 Consensus size: 50
18892065 TTTTGGGTAA
* *
18892075 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
18892131 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
18892181 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
18892231 GGAAGTCCCATGTAAGACCATATCTAGGATATGGCATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
18892271 TAGTACATAA
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 80 0.65
53 3 0.02
55 1 0.01
56 40 0.32
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:18892537 original size:12 final size:12
Alignment explanation
Indices: 18892520--18892558 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
18892510 ATGAGTTTTT
18892520 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
18892532 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
18892544 TAAGTGAGTAAG
1 TAAGTAAGCAAG
18892556 TAA
1 TAA
18892559 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:18894222 original size:25 final size:25
Alignment explanation
Indices: 18894185--18894239 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
18894175 GTGTTGCGAT
*
18894185 AGCTCATATGAGCTTACTGAT-TTAC
1 AGCTCATACGAGCTTACTGATATT-C
*
18894210 AGCTCCTACGAGCTTACTGATATTC
1 AGCTCATACGAGCTTACTGATATTC
18894235 AGCTC
1 AGCTC
18894240 GAAGAAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (25 bp):
AGCTCATACGAGCTTACTGATATTC
Found at i:18894248 original size:25 final size:25
Alignment explanation
Indices: 18894194--18894251 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
18894184 TAGCTCATAT
* *
18894194 GAGCTTACTGATTTACAGCTCCTAC
1 GAGCTTACTGATTTACAGCTCCGAA
18894219 GAGCTTACTGATATT-CAGCT-CGAA
1 GAGCTTACTGAT-TTACAGCTCCGAA
18894243 GAAGCTTAC
1 G-AGCTTAC
18894252 CGTTTATCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 3 0.10
25 24 0.83
26 2 0.07
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (25 bp):
GAGCTTACTGATTTACAGCTCCGAA
Found at i:18900444 original size:16 final size:17
Alignment explanation
Indices: 18900423--18900455 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18900413 CACATTGAAG
18900423 TGTTTTC-TGAAAACCA
1 TGTTTTCATGAAAACCA
18900439 TGTTTTCATTGAAAACC
1 TGTTTTCA-TGAAAACC
18900456 CTTCTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (17 bp):
TGTTTTCATGAAAACCA
Found at i:18901024 original size:28 final size:28
Alignment explanation
Indices: 18900959--18901024 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
18900949 TTTAACAGTA
* *
18900959 ACAGTATC-GTGTGGGCCTTAGCCCAAT
1 ACAGTATCAGTGGGGGCCTAAGCCCAAT
* * *
18900986 ACAGAAACAGTGGGGGCCTAAGCCTAAT
1 ACAGTATCAGTGGGGGCCTAAGCCCAAT
18901014 ACAGTATCAGT
1 ACAGTATCAGT
18901025 ATGGTGCAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (28 bp):
ACAGTATCAGTGGGGGCCTAAGCCCAAT
Found at i:18901271 original size:32 final size:32
Alignment explanation
Indices: 18901186--18901451 Score: 264
Period size: 32 Copynumber: 8.3 Consensus size: 32
18901176 GAATGGCTTC
* * * *
18901186 AAGCCATAAGT-ACAGTAATATGATTGGCAAA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * * * *
18901217 AAGCCATTACTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
18901249 CATCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * * * * *
18901281 AAGCCATTAGCAACAGTAATATGATCAGTAAA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
18901313 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * * *
18901345 AAGCCATCAGTAATGGTATTATGATCGGTATA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * * *
18901377 AAGCCATTAGTAATGGTATTATGGTCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
18901409 AAGCCATCAATAACGGTAATATAACCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
18901441 AAGCCATCAGT
1 AAGCCATCAGT
18901452 TGCATCGCAG
Statistics
Matches: 189, Mismatches: 45, Indels: 1
0.80 0.19 0.00
Matches are distributed among these distances:
31 9 0.05
32 180 0.95
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:18901368 original size:96 final size:96
Alignment explanation
Indices: 18901197--18901451 Score: 294
Period size: 96 Copynumber: 2.7 Consensus size: 96
18901187 AGCCATAAGT
* * * * * * * *
18901197 ACAGTAATATGATTGGCAAAAAGCCATTACTAGCAGTGATATGATCGGCACACATCCATCAGTAA
1 ACAGTAATATGATCGGCAAAAAGCCATCAATAACGGTAATATGATCGGCACAAAGCCATCAGTAA
18901262 CGGTAATATGATCGACACAAAGCCATTAGCA
66 CGGTAATATGATCGACACAAAGCCATTAGCA
* * *
18901293 ACAGTAATATGATCAGTAAAAAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAA
1 ACAGTAATATGATCGGCAAAAAGCCATCAATAACGGTAATATGATCGGCACAAAGCCATCAGTAA
* * ** * *
18901358 TGGTATTATGATCGGTATAAAGCCATTAGTA
66 CGGTAATATGATCGACACAAAGCCATTAGCA
** * * * * *
18901389 ATGGTATTATGGTCGGCACAAAGCCATCAATAACGGTAATATAACCGGCACAAAGCCATCAGT
1 ACAGTAATATGATCGGCAAAAAGCCATCAATAACGGTAATATGATCGGCACAAAGCCATCAGT
18901452 TGCATCGCAG
Statistics
Matches: 133, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 133 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (96 bp):
ACAGTAATATGATCGGCAAAAAGCCATCAATAACGGTAATATGATCGGCACAAAGCCATCAGTAA
CGGTAATATGATCGACACAAAGCCATTAGCA
Found at i:18901484 original size:26 final size:26
Alignment explanation
Indices: 18901455--18901508 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
18901445 CATCAGTTGC
*
18901455 ATCGCAGCAAAGCTGCCAGCAGCAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
* *
18901481 ATCGTAGCAAAGCTGCCAGTAACAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
18901507 AT
1 AT
18901509 ATGTGGCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGCAACAGT
Found at i:18901551 original size:27 final size:27
Alignment explanation
Indices: 18901496--18901557 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
18901486 AGCAAAGCTG
*
18901496 CCAGTAACAGTATATGTGGCCAAGCCA
1 CCAGTAACAGTATATGTGGCCAAGACA
18901523 CCAGTAACAGTGAT-TGTGG-CAGAGACA
1 CCAGTAACAGT-ATATGTGGCCA-AGACA
18901550 CCAG-AACA
1 CCAGTAACA
18901558 ATATTTCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 6 0.19
27 24 0.75
28 2 0.06
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGCCAAGACA
Found at i:18901654 original size:24 final size:23
Alignment explanation
Indices: 18901627--18901682 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
18901617 TGCTCAGAAT
18901627 CAGTCATTCAAATTACAGACAAAC
1 CAGTCATTCAAA-TACAGACAAAC
* * *
18901651 CAGTCATACCAAATATAGACAAAT
1 CAGTCAT-TCAAATACAGACAAAC
18901675 CAGTCATT
1 CAGTCATT
18901683 TAACCACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (23 bp):
CAGTCATTCAAATACAGACAAAC
Found at i:18901781 original size:26 final size:27
Alignment explanation
Indices: 18901726--18901893 Score: 184
Period size: 27 Copynumber: 6.4 Consensus size: 27
18901716 GGGAAAAATA
18901726 GTCA-TTTACCC-ACCA-GGGCATTACG
1 GTCATTTTACCCTA-CAGGGGCATTACG
* *
18901751 GTCA-TTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
18901777 GTCATTTTATCCTACAGGGGCATTAAG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
18901804 GTCA-TTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
18901830 GTCATTTTACCCTACAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * *
18901857 GTCATTTTACCTTAAAGGGGTATCACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
18901884 ATCATTTTAC
1 GTCATTTTAC
18901894 AACCTTTCTG
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.11
26 35 0.29
27 73 0.60
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:18901793 original size:27 final size:27
Alignment explanation
Indices: 18901745--18901893 Score: 185
Period size: 27 Copynumber: 5.6 Consensus size: 27
18901735 CCACCAGGGC
18901745 ATTACGGTCA-TTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
18901771 ATTATGGTCATTTTATCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
18901798 ATTAAGGTCA-TTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
18901824 ATTACGGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
18901851 ATTATGGTCATTTTACCTTAAAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
18901878 ATCACGATCATTTTAC
1 ATTACGGTCATTTTAC
18901894 AACCTTTCTG
Statistics
Matches: 104, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
26 31 0.30
27 73 0.70
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:18901808 original size:53 final size:53
Alignment explanation
Indices: 18901726--18901893 Score: 216
Period size: 53 Copynumber: 3.2 Consensus size: 53
18901716 GGGAAAAATA
* *
18901726 GTCA-TTTACCC-ACCA-GGGCATTACGGTCATTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTA-CAGGGGCATTAAGGTCATTTACCCTACAGGGGTATTACG
* *
18901777 GTCATTTTATCCTACAGGGGCATTAAGGTCATTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTAAGGTCATTTACCCTACAGGGGTATTACG
* * * *
18901830 GTCATTTTACCCTACAGGGGCATTATGGTCATTTTACCTTAAAGGGGTATCACG
1 GTCATTTTACCCTACAGGGGCATTAAGGTCA-TTTACCCTACAGGGGTATTACG
*
18901884 ATCATTTTAC
1 GTCATTTTAC
18901894 AACCTTTCTG
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
51 4 0.04
52 8 0.08
53 63 0.62
54 27 0.26
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (53 bp):
GTCATTTTACCCTACAGGGGCATTAAGGTCATTTACCCTACAGGGGTATTACG
Found at i:18903158 original size:12 final size:12
Alignment explanation
Indices: 18903126--18903165 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
18903116 TTCCTCCCTT
18903126 AATCTCTCC-CA
1 AATCTCTCCACA
*
18903137 ACATCCCTCCACA
1 A-ATCTCTCCACA
18903150 AATCTCTCCACA
1 AATCTCTCCACA
18903162 AATC
1 AATC
18903166 ACTTAACCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 1 0.04
12 21 0.84
13 3 0.12
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.23
Consensus pattern (12 bp):
AATCTCTCCACA
Found at i:18907883 original size:56 final size:56
Alignment explanation
Indices: 18907793--18907949 Score: 242
Period size: 56 Copynumber: 2.8 Consensus size: 56
18907783 AGTAGTTACG
*
18907793 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATCTCCTATAATATCCCAT
1 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATCCTATAATATCCCAT
* * *
18907849 TAGGAATCAAATTGCTAAGAGATAATATCCCATAATAATATCCTATAATATCCTAT
1 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATCCTATAATATCCCAT
** * *
18907905 TACAAATCAAATTGCTAAAAGATAATGTCTCATGATAATATCCTA
1 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATCCTA
18907950 ATAGTGCACA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 91 1.00
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (56 bp):
TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATCCTATAATATCCCAT
Found at i:18909353 original size:14 final size:15
Alignment explanation
Indices: 18909329--18909367 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
18909319 AAAAATGGGT
18909329 AAGAGGGATTTTTAC
1 AAGAGGGATTTTTAC
*
18909344 AAGA-GGATTTTTAG
1 AAGAGGGATTTTTAC
18909358 AA-AGGGATTT
1 AAGAGGGATTT
18909368 GGGAAAGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 17 0.77
15 4 0.18
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (15 bp):
AAGAGGGATTTTTAC
Found at i:18919889 original size:88 final size:88
Alignment explanation
Indices: 18919759--18919935 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
18919749 TATATGGTTA
18919759 TTTGATACTAGTTATAGAATGGCATTTTGGTAAAAAAATGGTTTGTCTTTTTGTTAAGTAAATTT
1 TTTGATACTAGTTATAGAATGGCATTTTGGTAAAAAAATGGTTTGTCTTTTTGTTAAGTAAATTT
18919824 TATGGTATGTATTGATGCAAACT
66 TATGGTATGTATTGATGCAAACT
18919847 TTTGATACTAGTTATAGAATGGCATTTTGGTAAAAAAATGGTTTGTCTTTTTGTTAAGTAAATTT
1 TTTGATACTAGTTATAGAATGGCATTTTGGTAAAAAAATGGTTTGTCTTTTTGTTAAGTAAATTT
18919912 TATGGTATGTATTGATGCAAACT
66 TATGGTATGTATTGATGCAAACT
18919935 T
1 T
18919936 AGTTGGAAGT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.45
Consensus pattern (88 bp):
TTTGATACTAGTTATAGAATGGCATTTTGGTAAAAAAATGGTTTGTCTTTTTGTTAAGTAAATTT
TATGGTATGTATTGATGCAAACT
Found at i:18927686 original size:14 final size:14
Alignment explanation
Indices: 18927652--18927678 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18927642 AACATAAATT
18927652 AAAGAAAATTAAAG
1 AAAGAAAATTAAAG
18927666 AAAGAAAATTAAA
1 AAAGAAAATTAAA
18927679 AATTGAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (14 bp):
AAAGAAAATTAAAG
Found at i:18931976 original size:9 final size:9
Alignment explanation
Indices: 18931962--18931998 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
18931952 TATCGTTTGA
*
18931962 TATTCGAGT
1 TATTCGAAT
18931971 TATTCGAAT
1 TATTCGAAT
18931980 TATTCGAAT
1 TATTCGAAT
18931989 TATTCGAAT
1 TATTCGAAT
18931998 T
1 T
18931999 CAAAAACTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:18932463 original size:21 final size:21
Alignment explanation
Indices: 18932438--18932477 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18932428 AAAACCTTGC
18932438 TGTTTTGCTGCTATTTTTCTA
1 TGTTTTGCTGCTATTTTTCTA
* *
18932459 TGTTTTGCTGTTGTTTTTC
1 TGTTTTGCTGCTATTTTTC
18932478 CAACTTTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.12, G:0.17, T:0.65
Consensus pattern (21 bp):
TGTTTTGCTGCTATTTTTCTA
Found at i:18934994 original size:27 final size:27
Alignment explanation
Indices: 18934955--18935008 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
18934945 ACGGAGAAGA
*
18934955 AAGTTAGAAATTTTTTTGAT-TAAGATT
1 AAGTTAGAAATTTATTT-ATATAAGATT
* *
18934982 AAGTTATATATTTATTTATATAAGATT
1 AAGTTAGAAATTTATTTATATAAGATT
18935009 TAAATGCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (27 bp):
AAGTTAGAAATTTATTTATATAAGATT
Found at i:18936030 original size:3 final size:3
Alignment explanation
Indices: 18936022--18936068 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
18936012 TGATTTAGAA
*
18936022 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18936069 AAGGATTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18943992 original size:131 final size:131
Alignment explanation
Indices: 18943758--18943994 Score: 359
Period size: 131 Copynumber: 1.8 Consensus size: 131
18943748 GGCCATGCGA
* *
18943758 CATGGCCGTTTGTCCCCTGTAGGTTTGAAAGGTTGCATTTCAAGGGTTACACGACCTAGCACATG
1 CATGGCCGTGTGTCCCCTGTAGGTTTGAAAGGTTGCATTTCAAGGGTTACACGACCTAGCACACG
* * *
18943823 GGCGTCTGGCTTGGCTGTGTGACCTAAGTAAGAGAGTTACACGAAAACGGGCTAGGACACATGAC
66 AGCGTCTGGCTTGGCTGTGTAACCCAAGTAAGAGAGTTACACGAAAACGGGCTAGGACACATGAC
18943888 G
131 G
* * * *
18943889 CATGGCCGTGTGTCCCCTGTAGGTTTTAAAGGTTGCATTTCAAGTGTTATACGGCCTAGCACACG
1 CATGGCCGTGTGTCCCCTGTAGGTTTGAAAGGTTGCATTTCAAGGGTTACACGACCTAGCACACG
* *
18943954 AGCGTCTGGCTTGGTTGTGTAACCCATGTCAA-AGAGTTACA
66 AGCGTCTGGCTTGGCTGTGTAACCCAAGT-AAGAGAGTTACA
18943995 AGGGCACGGA
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
131 92 0.98
132 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (131 bp):
CATGGCCGTGTGTCCCCTGTAGGTTTGAAAGGTTGCATTTCAAGGGTTACACGACCTAGCACACG
AGCGTCTGGCTTGGCTGTGTAACCCAAGTAAGAGAGTTACACGAAAACGGGCTAGGACACATGAC
G
Found at i:18952333 original size:20 final size:19
Alignment explanation
Indices: 18952308--18952365 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
18952298 TTGTACGGGA
18952308 TTGCACTTCGGTGCCTCTGT
1 TTGCACTT-GGTGCCTCTGT
* * *
18952328 TTGCACATTTGTGTCTTTGT
1 TTGCAC-TTGGTGCCTCTGT
18952348 TTGCACTTTGGTGCCTCT
1 TTGCAC-TTGGTGCCTCT
18952366 ATTACACATC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.07, C:0.24, G:0.22, T:0.47
Consensus pattern (19 bp):
TTGCACTTGGTGCCTCTGT
Found at i:18975788 original size:5 final size:5
Alignment explanation
Indices: 18975778--18975807 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
18975768 GACTATAATC
*
18975778 ATACA ATACA ATACA ATGCA ATACA ATACA
1 ATACA ATACA ATACA ATACA ATACA ATACA
18975808 TAAAAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (5 bp):
ATACA
Found at i:18980013 original size:148 final size:147
Alignment explanation
Indices: 18979830--18980108 Score: 362
Period size: 148 Copynumber: 1.9 Consensus size: 147
18979820 AGGAGCAGAC
* *
18979830 TCATTATCTTTACCTTCCCTAAGCCTCCCCCCATACGACTAGGAGCAAGGTCACTATTCTTACCT
1 TCATTATCTTTACCTTCCCTAAGCCTCCCCCCATACGACTAAGAGCAAGGTAACTATTCTTACCT
* * * * *
18979895 TTCGTAAGCTTCCC-CAATGTGTTTGGGAGCAAGGCCAAATTTATTACATTTCATAAGTCGTCCC
66 TTCATAAGCTTCCCTC-ATATGTATAGGAGCAAGGCCAAATTTATTACATTTCATAAG-CCTCCC
18979959 CATTCGTTTGGGAGTAAGG
129 CATTCGTTTGGGAGTAAGG
* ** ** * * * * *
18979978 TCATTATTTTTACCTTCTGTAAGCCTCCTTCCATACGTCTAAGAGTAGGGTAACTGTTTTTACCT
1 TCATTATCTTTACCTTCCCTAAGCCTCCCCCCATACGACTAAGAGCAAGGTAACTATTCTTACCT
* *
18980043 TTCATAAGCTTCCCTCATATGTATAGGAGCAAGGCCAAATTTATTACCTTTCGTAAGCCTCCCCA
66 TTCATAAGCTTCCCTCATATGTATAGGAGCAAGGCCAAATTTATTACATTTCATAAGCCTCCCCA
18980108 T
131 T
18980109 ACATCTAGGA
Statistics
Matches: 111, Mismatches: 19, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
147 8 0.07
148 102 0.92
149 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (147 bp):
TCATTATCTTTACCTTCCCTAAGCCTCCCCCCATACGACTAAGAGCAAGGTAACTATTCTTACCT
TTCATAAGCTTCCCTCATATGTATAGGAGCAAGGCCAAATTTATTACATTTCATAAGCCTCCCCA
TTCGTTTGGGAGTAAGG
Found at i:18987430 original size:14 final size:14
Alignment explanation
Indices: 18987413--18987451 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
18987403 TAAATACCAA
18987413 GTATGAAATGAGAT
1 GTATGAAATGAGAT
18987427 GTATGAAATGAGAT
1 GTATGAAATGAGAT
*
18987441 GTAAGAAATGA
1 GTATGAAATGA
18987452 ATTTAGTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (14 bp):
GTATGAAATGAGAT
Found at i:18995356 original size:13 final size:13
Alignment explanation
Indices: 18995338--18995363 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18995328 TATGTTTTTG
18995338 GAATCCCAGTGTT
1 GAATCCCAGTGTT
18995351 GAATCCCAGTGTT
1 GAATCCCAGTGTT
18995364 AATTACTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
GAATCCCAGTGTT
Found at i:18995683 original size:19 final size:20
Alignment explanation
Indices: 18995659--18995699 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
18995649 GAATTTAGGC
*
18995659 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
18995678 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
18995698 AA
1 AA
18995700 TTGTGTAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:18996021 original size:16 final size:16
Alignment explanation
Indices: 18995996--18996029 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18995986 ATGAATATAT
* *
18995996 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
18996012 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
18996028 AT
1 AT
18996030 TGGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:19005994 original size:21 final size:21
Alignment explanation
Indices: 19005970--19006012 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
19005960 AATTGCTCTC
19005970 TGTTTCTTT-TCTTCTTTGTTT
1 TGTTTCTTTCT-TTCTTTGTTT
19005991 TGTTTCTTTCTTTCTTTGTTT
1 TGTTTCTTTCTTTCTTTGTTT
19006012 T
1 T
19006013 TTTACTTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (21 bp):
TGTTTCTTTCTTTCTTTGTTT
Found at i:19011086 original size:21 final size:20
Alignment explanation
Indices: 19011061--19011104 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
19011051 AATATATTTC
19011061 TTTGTATATA-ATTGAGATATA
1 TTTGTATATATATT-A-ATATA
19011082 TTTGTATATATATTAATATA
1 TTTGTATATATATTAATATA
19011102 TTT
1 TTT
19011105 TTAAAATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 11 0.50
22 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTGTATATATATTAATATA
Found at i:19013476 original size:22 final size:22
Alignment explanation
Indices: 19013451--19013494 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19013441 GAGGTGAATT
19013451 TTTAAAATACTTTA-ATTACATC
1 TTTAAAAT-CTTTATATTACATC
*
19013473 TTTAAAATTTTTATATTACATC
1 TTTAAAATCTTTATATTACATC
19013495 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAAAATCTTTATATTACATC
Found at i:19013500 original size:22 final size:21
Alignment explanation
Indices: 19013461--19013501 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
19013451 TTTAAAATAC
**
19013461 TTTAATTACATCTTTAAAATT
1 TTTAATTACATCAATAAAATT
19013482 TTTATATTACATCAATAAAA
1 TTTA-ATTACATCAATAAAA
19013502 AAACTTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAATTACATCAATAAAATT
Found at i:19013911 original size:9 final size:9
Alignment explanation
Indices: 19013897--19013927 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19013887 GTTAAACGAA
19013897 TCGAGTTAT
1 TCGAGTTAT
*
19013906 TCGAGTTAA
1 TCGAGTTAT
19013915 TCGAGTTAT
1 TCGAGTTAT
19013924 TCGA
1 TCGA
19013928 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:19018108 original size:23 final size:23
Alignment explanation
Indices: 19018082--19018147 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
19018072 TACCTTGTGG
19018082 AAAATTTAAAATAATTAATTTTA
1 AAAATTTAAAATAATTAATTTTA
* *
19018105 AAAAATTAAAATTAA-AATATTTTA
1 AAAATTTAAAA-TAATTA-ATTTTA
* *
19018129 AATATTAACAAATAATTAA
1 AAAATTTA-AAATAATTAA
19018148 AATGATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
23 11 0.33
24 18 0.55
25 4 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATTTAAAATAATTAATTTTA
Found at i:19018111 original size:14 final size:15
Alignment explanation
Indices: 19018086--19018123 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
19018076 TTGTGGAAAA
19018086 TTTAAAATAATTAAT
1 TTTAAAATAATTAAT
*
19018101 TTTAAAA-AATTAAA
1 TTTAAAATAATTAAT
*
19018115 ATTAAAATA
1 TTTAAAATA
19018124 TTTTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTAAAATAATTAAT
Found at i:19020162 original size:20 final size:20
Alignment explanation
Indices: 19020137--19020176 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
19020127 ACACACATGT
19020137 TAGAAAACAATACTAGCTAG
1 TAGAAAACAATACTAGCTAG
19020157 TAGAAAACAATACTAGCTAG
1 TAGAAAACAATACTAGCTAG
19020177 AAACAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (20 bp):
TAGAAAACAATACTAGCTAG
Found at i:19022926 original size:27 final size:26
Alignment explanation
Indices: 19022853--19022926 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
19022843 TTATGAAAAT
* *
19022853 TTATTATAAAATTAATTA-AAATTAA
1 TTATTTTATAATTAATTATAAATTAA
* * *
19022878 ATATTTTAATAATATAAGTATAATTTAA
1 TTATTTT-ATAAT-TAATTATAAATTAA
19022906 TTATTTTATAATTACATTATA
1 TTATTTTATAATTA-ATTATA
19022927 TTTTTCTACA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
25 5 0.13
26 6 0.16
27 15 0.39
28 12 0.32
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
TTATTTTATAATTAATTATAAATTAA
Found at i:19028291 original size:40 final size:40
Alignment explanation
Indices: 19028242--19028343 Score: 168
Period size: 40 Copynumber: 2.5 Consensus size: 40
19028232 TCTACCCCAA
* * * *
19028242 TCCAACCCTACACTCCAAAATAAGAGTTCCCTAGAACTAG
1 TCCATCCCTACACACCAAAATAAGAGTTCCCCAAAACTAG
19028282 TCCATCCCTACACACCAAAATAAGAGTTCCCCAAAACTAG
1 TCCATCCCTACACACCAAAATAAGAGTTCCCCAAAACTAG
19028322 TCCATCCCTACACACCAAAATA
1 TCCATCCCTACACACCAAAATA
19028344 GTATTTTGCG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.39, C:0.35, G:0.07, T:0.19
Consensus pattern (40 bp):
TCCATCCCTACACACCAAAATAAGAGTTCCCCAAAACTAG
Found at i:19034965 original size:48 final size:48
Alignment explanation
Indices: 19034890--19034981 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
19034880 TTAGGAGGTA
* * *
19034890 GCTGATTATTTTGGTTATCACCTATCTCTACAATAATATCCTTTTCTT
1 GCTGATTATTTTGATTATCACCCATCTCCACAATAATATCCTTTTCTT
19034938 GCTGATTATTTTGATTATCACCCATCTCCACAATAATATCCTTT
1 GCTGATTATTTTGATTATCACCCATCTCCACAATAATATCCTTT
19034982 CTTCTTGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.45
Consensus pattern (48 bp):
GCTGATTATTTTGATTATCACCCATCTCCACAATAATATCCTTTTCTT
Found at i:19035174 original size:26 final size:26
Alignment explanation
Indices: 19035145--19035207 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
19035135 CAAACAAACG
* * * *
19035145 AAAAATTAGAATATAAAAATTAAATT
1 AAAAATAAAAATATAAAAATAAAAAT
* *
19035171 AAAAACAAAAATATTAAAATAAAAAT
1 AAAAATAAAAATATAAAAATAAAAAT
19035197 AAAAATAAAAA
1 AAAAATAAAAA
19035208 ATGGCTAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (26 bp):
AAAAATAAAAATATAAAAATAAAAAT
Found at i:19035188 original size:20 final size:20
Alignment explanation
Indices: 19035159--19035203 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
19035149 ATTAGAATAT
*
19035159 AAAA-ATTAAATTAAAAACA
1 AAAATATTAAAATAAAAACA
*
19035178 AAAATATTAAAATAAAAATA
1 AAAATATTAAAATAAAAACA
19035198 AAAATA
1 AAAATA
19035204 AAAAATGGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAATATTAAAATAAAAACA
Found at i:19035193 original size:32 final size:33
Alignment explanation
Indices: 19035140--19035207 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
19035130 AGAAGCAAAC
* * *
19035140 AAACGAAAAATTAGAATATAAAAATTAAATTAA
1 AAACAAAAAATTAGAATATAAAAATAAAAATAA
19035173 AAACAAAAATATTA-AA-ATAAAAATAAAAATAA
1 AAACAAAAA-ATTAGAATATAAAAATAAAAATAA
19035205 AAA
1 AAA
19035208 ATGGCTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 17 0.55
33 10 0.32
34 4 0.13
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (33 bp):
AAACAAAAAATTAGAATATAAAAATAAAAATAA
Found at i:19035209 original size:7 final size:6
Alignment explanation
Indices: 19035157--19035207 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
19035147 AAATTAGAAT
* * *
19035157 ATAAAA ATTAAA TTAAAA ACAAAA ATATTAAA ATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATA--AAA ATAAAA ATAAAA ATAAAA
19035207 A
1 A
19035208 ATGGCTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
6 31 0.84
8 6 0.16
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (6 bp):
ATAAAA
Found at i:19037952 original size:27 final size:27
Alignment explanation
Indices: 19037896--19037954 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
19037886 ATCCTGTCAG
* *
19037896 CCTTTGTGGCATACCCTGAATGAATCA
1 CCTTTGTAGCATACCCTGAATGAATAA
* *
19037923 CCTTTGTAGCATACTCTGTAT-ATATAA
1 CCTTTGTAGCATACCCTGAATGA-ATAA
19037950 CCTTT
1 CCTTT
19037955 ATGGCGTACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (27 bp):
CCTTTGTAGCATACCCTGAATGAATAA
Found at i:19039841 original size:33 final size:33
Alignment explanation
Indices: 19039799--19039867 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
19039789 AATCAAAATC
*
19039799 TTAGTGAGTCGATTGCTGAAGAAACCTTTTCGA
1 TTAGTGAGTCAATTGCTGAAGAAACCTTTTCGA
*
19039832 TTAGTGAGTCAATTGCTGAAGAAACCTTTTTGA
1 TTAGTGAGTCAATTGCTGAAGAAACCTTTTCGA
19039865 TTA
1 TTA
19039868 CCAGACGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (33 bp):
TTAGTGAGTCAATTGCTGAAGAAACCTTTTCGA
Found at i:19040618 original size:25 final size:25
Alignment explanation
Indices: 19040586--19040770 Score: 104
Period size: 25 Copynumber: 6.9 Consensus size: 25
19040576 GTATGTTTTT
19040586 TATG-TATGTATATTACTATTTATG
1 TATGTTATGTATATTACTATTTATG
*
19040610 TATGTTATGTATTATATTTCTATTTATG
1 TATGTTATG---TATATTACTATTTATG
* * * *
19040638 TATTTTATGCATACTACTGTTTATG
1 TATGTTATGTATATTACTATTTATG
* * * *
19040663 TATGTTTTATATATCACTGTTTATATCATG
1 TATGTTATGTATATTAC----TAT-TTATG
* *
19040693 TATGTTACGTATATTACTATTTATA
1 TATGTTATGTATATTACTATTTATG
*
19040718 T-TGTGTATGTATATTAATGTTGATATTATG
1 TATGT-TATGTATATT-A--CT-AT-TTATG
* *
19040748 TATGTTATGTATACTACTGTTTA
1 TATGTTATGTATATTACTATTTA
19040771 CATTATTTAT
Statistics
Matches: 119, Mismatches: 26, Indels: 31
0.68 0.15 0.18
Matches are distributed among these distances:
24 7 0.06
25 43 0.36
26 5 0.04
27 1 0.01
28 24 0.20
29 5 0.04
30 31 0.26
31 3 0.03
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.54
Consensus pattern (25 bp):
TATGTTATGTATATTACTATTTATG
Found at i:19040634 original size:28 final size:29
Alignment explanation
Indices: 19040585--19040759 Score: 106
Period size: 30 Copynumber: 6.3 Consensus size: 29
19040575 AGTATGTTTT
19040585 TTATGTATGTATATTACTATTTATGTATG
1 TTATGTATGTATATTACTATTTATGTATG
*
19040614 TTATGTAT-TATATTTCTATTTATGTA--
1 TTATGTATGTATATTACTATTTATGTATG
* * *
19040640 TT-T-TATGCATACTACTGTTTATGTATG
1 TTATGTATGTATATTACTATTTATGTATG
* * *
19040667 TT-T-TA--TATATCACTGTTTATATCATG
1 TTATGTATGTATATTACTATTTATGT-ATG
* *
19040693 -TATGTTACGTATATTACTATTTATAT-TG
1 TTATG-TATGTATATTACTATTTATGTATG
* *
19040721 TGTATGTATATTAATGTTGA-TA-TTATGTATG
1 T-TATGTAT-GT-ATATT-ACTATTTATGTATG
19040752 TTATGTAT
1 TTATGTAT
19040760 ACTACTGTTT
Statistics
Matches: 116, Mismatches: 15, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
24 3 0.03
25 29 0.25
26 6 0.05
27 5 0.04
28 21 0.18
29 10 0.09
30 32 0.28
31 9 0.08
32 1 0.01
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.55
Consensus pattern (29 bp):
TTATGTATGTATATTACTATTTATGTATG
Found at i:19040706 original size:30 final size:30
Alignment explanation
Indices: 19040605--19040808 Score: 166
Period size: 30 Copynumber: 7.2 Consensus size: 30
19040595 ATATTACTAT
19040605 TTATGTATGTTATGTAT-TATA-T-TTCTAT-
1 TTATGTATGTTATGTATAT-TACTGTT-TATA
* * *
19040633 TTATGTATTTTATGCATACTACTGTTTAT-
1 TTATGTATGTTATGTATATTACTGTTTATA
* *
19040662 GTATGT-T-TTA--TATATCACTGTTTATA
1 TTATGTATGTTATGTATATTACTGTTTATA
* * *
19040688 TCATGTATGTTACGTATATTACTATTTATA
1 TTATGTATGTTATGTATATTACTGTTTATA
* *
19040718 -T-TG--TG-TATGTATATTAATGTTGATA
1 TTATGTATGTTATGTATATTACTGTTTATA
* *
19040743 TTATGTATGTTATGTATACTACTGTTTACA
1 TTATGTATGTTATGTATATTACTGTTTATA
* *
19040773 TTATTTATGTTATGTATATTAATGTTTATA
1 TTATGTATGTTATGTATATTACTGTTTATA
19040803 TTATGT
1 TTATGT
19040809 CACTCACTTT
Statistics
Matches: 138, Mismatches: 25, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
25 28 0.20
26 7 0.05
27 6 0.04
28 23 0.17
29 11 0.08
30 63 0.46
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (30 bp):
TTATGTATGTTATGTATATTACTGTTTATA
Found at i:19040747 original size:21 final size:19
Alignment explanation
Indices: 19040723--19040808 Score: 59
Period size: 21 Copynumber: 4.3 Consensus size: 19
19040713 TTATATTGTG
19040723 TATGTATATTAATGTTGATAT
1 TATGTATATT-ATGTT-ATAT
* *
19040744 TATGTATGTTATG-TATAC
1 TATGTATATTATGTTATAT
* *
19040762 TACTGTTTACATTAT-TTATGT
1 TA-TG--TATATTATGTTATAT
19040783 TATGTATATTAATGTTTATAT
1 TATGTATATT-ATG-TTATAT
19040804 TATGT
1 TATGT
19040809 CACTCACTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
18 10 0.20
19 5 0.10
20 5 0.10
21 30 0.60
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (19 bp):
TATGTATATTATGTTATAT
Found at i:19040782 original size:55 final size:54
Alignment explanation
Indices: 19040633--19040782 Score: 140
Period size: 55 Copynumber: 2.7 Consensus size: 54
19040623 ATATTTCTAT
* * * * * *
19040633 TTATGTATTTTATGCATACTACTGTTT-ATGTATGTTTTATATATCACTGTTTATA
1 TTATGTATGTTATGTATACTACTGTTTAAT-TAT-TTATGTATATCAATGTTGATA
* * * * * * *
19040688 TCATGTATGTTACGTATATTACTATTTATATTGTGTATGTATATTAATGTTGATA
1 TTATGTATGTTATGTATACTACTGTTTA-ATTATTTATGTATATCAATGTTGATA
19040743 TTATGTATGTTATGTATACTACTGTTTACATTATTTATGT
1 TTATGTATGTTATGTATACTACTGTTTA-ATTATTTATGT
19040783 TATGTATATT
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
55 69 0.95
56 2 0.03
57 2 0.03
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (54 bp):
TTATGTATGTTATGTATACTACTGTTTAATTATTTATGTATATCAATGTTGATA
Found at i:19054794 original size:20 final size:21
Alignment explanation
Indices: 19054761--19054800 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
19054751 CAAACCATAC
*
19054761 AAAACCCTAGAAAACCTAATG
1 AAAACCCTAGAAAAACTAATG
*
19054782 AAAACCTTA-AAAAACTAAT
1 AAAACCCTAGAAAAACTAAT
19054801 AAGCAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.57, C:0.20, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAACCCTAGAAAAACTAATG
Found at i:19055104 original size:31 final size:31
Alignment explanation
Indices: 19055046--19055105 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
19055036 TAATCCTTAT
* * *
19055046 TTAATTAAAATAATAAATTAACTCTATTTAA
1 TTAAGTAAAATAATAAACTAACCCTATTTAA
19055077 TTAAGTAAAAT-ATCAAACTAACCCTATTT
1 TTAAGTAAAATAAT-AAACTAACCCTATTT
19055106 TCATCCCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (31 bp):
TTAAGTAAAATAATAAACTAACCCTATTTAA
Found at i:19064207 original size:26 final size:27
Alignment explanation
Indices: 19064145--19064207 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
19064135 GCCCAATTTA
*
19064145 AACCCAGCGCAATTTACCCAGCACCGAAT
1 AACCCAGCCCAATTTA--CAGCACCGAAT
**
19064174 AAGACAGCCCAATTTA-AGCACCGAAT
1 AACCCAGCCCAATTTACAGCACCGAAT
19064200 AACCCAGC
1 AACCCAGC
19064208 ACCGAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 16 0.55
29 13 0.45
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.13
Consensus pattern (27 bp):
AACCCAGCCCAATTTACAGCACCGAAT
Found at i:19068728 original size:17 final size:17
Alignment explanation
Indices: 19068706--19068803 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
19068696 AATTCAAGAC
19068706 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
19068723 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
19068742 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
* **
19068760 TTATGTAGTGATTTAAAGA
1 TTATGTAATG-TTTTTA-A
*
19068779 TTTATGTAATGCTTTTAA
1 -TTATGTAATGTTTTTAA
19068797 TTATGTA
1 TTATGTA
19068804 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 24 0.41
18 9 0.16
19 8 0.14
20 17 0.29
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:19068785 original size:20 final size:18
Alignment explanation
Indices: 19068721--19068812 Score: 71
Period size: 17 Copynumber: 5.0 Consensus size: 18
19068711 TAATGTTTTT
*
19068721 AATTATGTAGTGATTCAA
1 AATTATGTAGTGATTTAA
* **
19068739 AGACTTATGTAAT-ATTTTT
1 A-A-TTATGTAGTGATTTAA
19068758 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
* * *
19068776 AGATTTATGTAATGCTTT-T
1 A-A-TTATGTAGTGATTTAA
19068795 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
19068813 TTCGGGTAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
17 20 0.36
18 8 0.15
19 7 0.13
20 20 0.36
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (18 bp):
AATTATGTAGTGATTTAA
Found at i:19068810 original size:37 final size:37
Alignment explanation
Indices: 19068701--19068812 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
19068691 GTGTTAATTC
*
19068701 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
*
19068738 AAGACTTATGTAATATTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
19068775 AAGATTTATGTAATGCTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
19068812 A
1 A
19068813 TTCGGGTAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
Found at i:19068828 original size:9 final size:9
Alignment explanation
Indices: 19068810--19068890 Score: 99
Period size: 9 Copynumber: 8.6 Consensus size: 9
19068800 TGTAGTGATT
19068810 TAATTCGGG
1 TAATTCGGG
*
19068819 TAATTTGGG
1 TAATTCGGG
19068828 TAATTTTCGGG
1 TAA--TTCGGG
*
19068839 TAACTCGGG
1 TAATTCGGG
19068848 TAATTTTCGGG
1 TAA--TTCGGG
19068859 TAATTCGGG
1 TAATTCGGG
19068868 TAATTCGGG
1 TAATTCGGG
*
19068877 TAATTCAGG
1 TAATTCGGG
19068886 TAATT
1 TAATT
19068891 TTTAACCAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
9 47 0.75
11 16 0.25
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.38
Consensus pattern (9 bp):
TAATTCGGG
Found at i:19068838 original size:20 final size:20
Alignment explanation
Indices: 19068813--19068892 Score: 119
Period size: 20 Copynumber: 4.1 Consensus size: 20
19068803 AGTGATTTAA
*
19068813 TTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTCGGGTAATT
*
19068833 TTCGGGTAACTCGGGTAATT
1 TTCGGGTAATTCGGGTAATT
19068853 TTCGGGTAATTCGGGTAA--
1 TTCGGGTAATTCGGGTAATT
*
19068871 TTCGGGTAATTCAGGTAATT
1 TTCGGGTAATTCGGGTAATT
19068891 TT
1 TT
19068893 TAACCAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
18 17 0.31
20 37 0.69
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (20 bp):
TTCGGGTAATTCGGGTAATT
Found at i:19068865 original size:29 final size:29
Alignment explanation
Indices: 19068814--19068881 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
19068804 GTGATTTAAT
19068814 TCGGGTAA-TTTGGGTAATTTTCGGGTAAC
1 TCGGGTAATTTTGGGTAA-TTTCGGGTAAC
*
19068843 TCGGGTAATTTTCGGGTAA-TTCGGGTAAT
1 TCGGGTAATTTT-GGGTAATTTCGGGTAAC
19068872 TCGGGTAATT
1 TCGGGTAATT
19068882 CAGGTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 27 0.75
30 3 0.08
31 6 0.17
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (29 bp):
TCGGGTAATTTTGGGTAATTTCGGGTAAC
Found at i:19075091 original size:30 final size:30
Alignment explanation
Indices: 19075057--19075119 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
19075047 ACTTATTTTA
19075057 TTGTTAATTTTGTTATTATTTTA-AAGTCAT
1 TTGTTAATTTTGTTATTATTTTAGAAG-CAT
19075087 TTGTTAATTTTGTTATTATTTTAGAAGCAT
1 TTGTTAATTTTGTTATTATTTTAGAAGCAT
19075117 TTG
1 TTG
19075120 CTTGTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAAGCAT
Found at i:19078350 original size:5 final size:5
Alignment explanation
Indices: 19078342--19078366 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19078332 AGGTTAGGGT
19078342 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
19078367 ACTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:19081723 original size:35 final size:35
Alignment explanation
Indices: 19081684--19081754 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
19081674 GTTGAATACT
* *
19081684 TGATAAAATTTGTGTTAATTTGTTAGATTTTAAGC
1 TGATAAAATTGGTGTTAATTTGTTAAATTTTAAGC
19081719 TGATAAAATTGGTGTTAATTTGTTAAATTTTAAGC
1 TGATAAAATTGGTGTTAATTTGTTAAATTTTAAGC
19081754 T
1 T
19081755 TAGAAGTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (35 bp):
TGATAAAATTGGTGTTAATTTGTTAAATTTTAAGC
Found at i:19083703 original size:21 final size:21
Alignment explanation
Indices: 19083640--19083704 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
19083630 TCAAAATTTC
19083640 TTCTTTCTTTCTTCTGTCAAA
1 TTCTTTCTTTCTTCTGTCAAA
* * * *
19083661 TTC-TACACTTCATCTTTC---
1 TTCTTTC-TTTCTTCTGTCAAA
19083679 TTCTTTCTTTCTTCTGTCAAA
1 TTCTTTCTTTCTTCTGTCAAA
19083700 TTCTT
1 TTCTT
19083705 GCAAGTTCAC
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 11 0.35
19 2 0.06
20 2 0.06
21 16 0.52
ACGTcount: A:0.14, C:0.26, G:0.03, T:0.57
Consensus pattern (21 bp):
TTCTTTCTTTCTTCTGTCAAA
Found at i:19091796 original size:37 final size:37
Alignment explanation
Indices: 19091723--19091797 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
19091713 ATATAGTTGG
* * *
19091723 TTCCCATTTTTTAGGGAAACACTATAGTTGGTTATTT
1 TTCCCATTTTTTAGGGAAACACTATAGCTAGATATTT
*
19091760 TTCCCTTTTTTTAGAGG-AACACTATAGCTAGATATTT
1 TTCCCATTTTTTAG-GGAAACACTATAGCTAGATATTT
19091797 T
1 T
19091798 GGAAACCCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (37 bp):
TTCCCATTTTTTAGGGAAACACTATAGCTAGATATTT
Found at i:19107703 original size:28 final size:28
Alignment explanation
Indices: 19107671--19107725 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
19107661 CATTTGTTAA
* *
19107671 TCCTTGACTAACATTCCACTTAAGATAG
1 TCCTTGACGAACATCCCACTTAAGATAG
*
19107699 TCCTTGGCGAACATCCCACTTAAGATA
1 TCCTTGACGAACATCCCACTTAAGATA
19107726 ATCCCTGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (28 bp):
TCCTTGACGAACATCCCACTTAAGATAG
Found at i:19107734 original size:28 final size:28
Alignment explanation
Indices: 19107680--19107734 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
19107670 ATCCTTGACT
* * *
19107680 AACATTCCACTTAAGATAGTCCTTGGCG
1 AACATCCCACTTAAGATAATCCCTGGCG
19107708 AACATCCCACTTAAGATAATCCCTGGC
1 AACATCCCACTTAAGATAATCCCTGGC
19107735 TTACTTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (28 bp):
AACATCCCACTTAAGATAATCCCTGGCG
Found at i:19119869 original size:43 final size:42
Alignment explanation
Indices: 19119802--19119966 Score: 149
Period size: 43 Copynumber: 3.9 Consensus size: 42
19119792 AGCTCGTACA
* * * * *
19119802 ATGCCAACGTCCCAGAC-GTGGTCTTGCATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACAG-AGTCTTACACGAAATCAAAT-ACG
* *
19119845 ATGCCACTGTCCCAGACAGAGTCTTACACGAAATCATATACG
1 ATGCCAATGTCCCAGACAGAGTCTTACACGAAATCAAATACG
19119887 ATGCCAATGTCCCAGACATG-GTCTTACACGTAAATCTCAAAT-CG
1 ATGCCAATGTCCCAGACA-GAGTCTTACACG-AAA--TCAAATACG
* * *
19119931 ATGCCAACGTCCCAGAC-GTGGTCTTACACGATATCA
1 ATGCCAATGTCCCAGACAG-AGTCTTACACGAAATCA
19119967 CATATCGAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
41 3 0.03
42 31 0.30
43 36 0.35
44 29 0.28
45 5 0.05
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGAGTCTTACACGAAATCAAATACG
Found at i:19119956 original size:86 final size:84
Alignment explanation
Indices: 19119802--19119966 Score: 201
Period size: 86 Copynumber: 1.9 Consensus size: 84
19119792 AGCTCGTACA
* * *
19119802 ATGCCAACGTCCCAGACGTGGTCTTGCATGTAATCAAATAACGATGCCACTGTCCCAGACAGAGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAAT-ACGATGCCACTGTCCCAGACAGAGT
19119867 CTTACACGAAATCATATACG
65 CTTACACGAAATCATATACG
*
19119887 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CGATGCCAAC-GTCCCAGAC-G
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AA--TCAAATACGATGCC-ACTGTCCCAGACAG
* *
19119949 TGGTCTTACACGATATCA
62 -AGTCTTACACGAAATCA
19119967 CATATCGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
85 28 0.41
86 33 0.48
87 2 0.03
88 6 0.09
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATACGATGCCACTGTCCCAGACAGAGTC
TTACACGAAATCATATACG
Found at i:19126086 original size:16 final size:17
Alignment explanation
Indices: 19126056--19126090 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
19126046 AGAGAGCTGA
*
19126056 GAGAGAGGATGAGAGAT
1 GAGAGAGGATAAGAGAT
19126073 GAGAG-GGATAAGAGAT
1 GAGAGAGGATAAGAGAT
19126089 GA
1 GA
19126091 TTATAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.43, C:0.00, G:0.46, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATAAGAGAT
Found at i:19131016 original size:20 final size:20
Alignment explanation
Indices: 19130991--19131028 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19130981 ACCCCCTTTA
19130991 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
19131011 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
19131029 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:19140348 original size:36 final size:36
Alignment explanation
Indices: 19140308--19140379 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
19140298 ATTCCCCCAT
19140308 GACTTAGTAGACAAAATAATATAAGCATAATAATTC
1 GACTTAGTAGACAAAATAATATAAGCATAATAATTC
19140344 GACTTAGTAGACAAAATAATATAAGCATAATAATTC
1 GACTTAGTAGACAAAATAATATAAGCATAATAATTC
19140380 ATTACCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (36 bp):
GACTTAGTAGACAAAATAATATAAGCATAATAATTC
Found at i:19142306 original size:50 final size:50
Alignment explanation
Indices: 19142234--19142358 Score: 124
Period size: 50 Copynumber: 2.5 Consensus size: 50
19142224 TATCTCAGAT
** ** * * * * **
19142234 ATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTCTCAGGC
1 ATGGTCTTACGGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAAC
* * *
19142284 ATGGTCTTATGGGGGACCTCTCATCTCGGTGCTAACGCCATGTCCCAAAC
1 ATGGTCTTACGGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAAC
*
19142334 ATGGTCTTACGTGGGACCTCTCATA
1 ATGGTCTTACGGGGGACCTCTCATA
19142359 ACCTCAATAA
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (50 bp):
ATGGTCTTACGGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAAC
Found at i:19147213 original size:18 final size:18
Alignment explanation
Indices: 19147190--19147225 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19147180 TATCTCATAA
19147190 TATATAATTCTTTTTCCT
1 TATATAATTCTTTTTCCT
19147208 TATATAATTCTTTTTCCT
1 TATATAATTCTTTTTCCT
19147226 ACACTATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATAATTCTTTTTCCT
Found at i:19147236 original size:18 final size:18
Alignment explanation
Indices: 19147193--19147238 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
19147183 CTCATAATAT
*
19147193 ATAATTCTTTTTCCTTAT
1 ATAATTCTTTTTCCTTAC
19147211 ATAATTCTTTTTCC-TAC
1 ATAATTCTTTTTCCTTAC
*
19147228 ACTATTTCTTT
1 A-TAATTCTTT
19147239 CAAGTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAATTCTTTTTCCTTAC
Found at i:19148751 original size:42 final size:44
Alignment explanation
Indices: 19148686--19148800 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 44
19148676 TCAAATAACA
* * * * *
19148686 ATGCCACTGTCTCAGACAGGGTCTTACGCA-AAA--TCATATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCTCAAAT-CG
*
19148728 ATGCCAATGTCCCAAACATGGTCTTACACATAAATCTCAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCTCAAATCG
* * *
19148772 ATGCCAACGTCCCAGACGTGGTCGTACAC
1 ATGCCAATGTCCCAGACATGGTCTTACAC
19148801 GATATCACAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 25 0.42
43 3 0.05
44 27 0.45
45 5 0.08
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACATGGTCTTACACATAAATCTCAAATCG
Found at i:19150943 original size:24 final size:24
Alignment explanation
Indices: 19150912--19150957 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
19150902 TTTCATCCTA
*
19150912 AAAATTAAATATTA-TTGTAAAAAT
1 AAAATTAAA-ATTACATGTAAAAAT
19150936 AAAATTAAAATTACATGTAAAA
1 AAAATTAAAATTACATGTAAAA
19150958 GAGAAAATAT
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:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAATTAAAATTACATGTAAAAAT
Found at i:19150964 original size:25 final size:24
Alignment explanation
Indices: 19150912--19150965 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
19150902 TTTCATCCTA
* *
19150912 AAAATTAAATATTATTGTAAAAAT
1 AAAATTAAATATTAATGTAAAAAG
19150936 AAAATTAAA-ATTACATGTAAAAGAG
1 AAAATTAAATATTA-ATGTAAAA-AG
19150961 AAAAT
1 AAAAT
19150966 ATAAGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.15
24 16 0.62
25 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (24 bp):
AAAATTAAATATTAATGTAAAAAG
Found at i:19160838 original size:22 final size:22
Alignment explanation
Indices: 19160810--19160874 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 22
19160800 TCTGTCATAG
*
19160810 TCACACGGCCGTGTGCCTCCTT
1 TCACACGGGCGTGTGCCTCCTT
** *
19160832 TCACACGGGCGTACG-CT-TTT
1 TCACACGGGCGTGTGCCTCCTT
19160852 TCACACGGGCGTGTGCCTCCTT
1 TCACACGGGCGTGTGCCTCCTT
19160874 T
1 T
19160875 ACATAGGAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 15 0.44
21 4 0.12
22 15 0.44
ACGTcount: A:0.11, C:0.35, G:0.25, T:0.29
Consensus pattern (22 bp):
TCACACGGGCGTGTGCCTCCTT
Found at i:19161213 original size:21 final size:21
Alignment explanation
Indices: 19161189--19161228 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19161179 ATTTGATTCC
19161189 GTATTCTATTTCTATATGCAT
1 GTATTCTATTTCTATATGCAT
19161210 GTATTCTATTTCTATATGC
1 GTATTCTATTTCTATATGC
19161229 CTGTCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (21 bp):
GTATTCTATTTCTATATGCAT
Found at i:19166530 original size:31 final size:31
Alignment explanation
Indices: 19166492--19166554 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
19166482 ATATTCTAGC
19166492 TCCCCATAGTCTCCTTGTTATCTTTCTCTCT
1 TCCCCATAGTCTCCTTGTTATCTTTCTCTCT
19166523 TCCCCATAGTCTCCTTGTTATCTTTCTCTCT
1 TCCCCATAGTCTCCTTGTTATCTTTCTCTCT
19166554 T
1 T
19166555 GATGGATCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.10, C:0.35, G:0.06, T:0.49
Consensus pattern (31 bp):
TCCCCATAGTCTCCTTGTTATCTTTCTCTCT
Found at i:19171075 original size:20 final size:19
Alignment explanation
Indices: 19171038--19171076 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
19171028 AATTTTAAAA
*
19171038 TATTTTTAAAATACTTTTT
1 TATTTTTAAAATAATTTTT
19171057 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAAT-AATTTTT
19171077 GGCGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTAAAATAATTTTT
Found at i:19177525 original size:4 final size:4
Alignment explanation
Indices: 19177516--19177540 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19177506 TTTGCAACTT
19177516 TTAG TTAG TTAG TTAG TTAG TTAG T
1 TTAG TTAG TTAG TTAG TTAG TTAG T
19177541 ATAATCCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TTAG
Found at i:19180224 original size:17 final size:17
Alignment explanation
Indices: 19180204--19180239 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
19180194 AACCACATAT
*
19180204 AATTTAGTCATTATCAC
1 AATTTACTCATTATCAC
19180221 AATTTACTCATTATCAC
1 AATTTACTCATTATCAC
19180238 AA
1 AA
19180240 ACATCCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTTACTCATTATCAC
Found at i:19180970 original size:20 final size:20
Alignment explanation
Indices: 19180945--19180985 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
19180935 CTTAGAAGAA
19180945 TAGAGAAGACAATGTCTTTC
1 TAGAGAAGACAATGTCTTTC
19180965 TAGAGAAGACAATGTCTTTC
1 TAGAGAAGACAATGTCTTTC
19180985 T
1 T
19180986 CTTTCTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (20 bp):
TAGAGAAGACAATGTCTTTC
Found at i:19183656 original size:19 final size:20
Alignment explanation
Indices: 19183614--19183657 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
19183604 ATTATTATAC
*
19183614 AATA-ATATTTTAATTTTAG
1 AATATATATTTTAATTTTAA
*
19183633 GATATATATTTT-ATTTTAA
1 AATATATATTTTAATTTTAA
19183652 AATATA
1 AATATA
19183658 ATTATATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
AATATATATTTTAATTTTAA
Found at i:19184172 original size:40 final size:40
Alignment explanation
Indices: 19184128--19184227 Score: 98
Period size: 40 Copynumber: 2.5 Consensus size: 40
19184118 AAAGAATACA
* *
19184128 AAAATTTCTAAGAGCATATTCTTA-AATATTTTGATATTTC
1 AAAATTTCTAAGAGCATATACATAGAA-ATTTTGATATTTC
* *
19184168 AAAATATCT-A-AGCATACGTACATAGAAATTTTGGTATTTC
1 AAAATTTCTAAGAGCATA--TACATAGAAATTTTGATATTTC
*
19184208 AAAATTTGTAAAGAGCATAT
1 AAAATTTCT-AAGAGCATAT
19184228 CATTAGCTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
38 6 0.12
39 1 0.02
40 31 0.65
41 3 0.06
42 1 0.02
43 6 0.12
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (40 bp):
AAAATTTCTAAGAGCATATACATAGAAATTTTGATATTTC
Found at i:19187208 original size:19 final size:19
Alignment explanation
Indices: 19187184--19187225 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
19187174 AAAAAGTTGG
19187184 AAATATAAACCCTTTAAGC
1 AAATATAAACCCTTTAAGC
19187203 AAATATAAACCCTTTAAGC
1 AAATATAAACCCTTTAAGC
19187222 AAAT
1 AAAT
19187226 TGAAAGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.19, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATATAAACCCTTTAAGC
Found at i:19188325 original size:6 final size:6
Alignment explanation
Indices: 19188316--19188353 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
19188306 GCTTTTCATT
19188316 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
19188354 ACTATTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:19188359 original size:6 final size:6
Alignment explanation
Indices: 19188350--19188396 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
19188340 TTTTTATTTT
*
19188350 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAT TATTA
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTA
19188397 TGTTTATTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAC
Found at i:19188397 original size:6 final size:6
Alignment explanation
Indices: 19188319--19188415 Score: 63
Period size: 6 Copynumber: 16.2 Consensus size: 6
19188309 TTTCATTTTT
* * * * * * *
19188319 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTA CTATTA CTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* * * *
19188367 CTATTA CTATTA CTATTA CTATTA TTATTA TGT-TTA TTATGT- TTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA T-TATTA TTAT-TA TTATTA
19188415 T
1 T
19188416 GTTTATGTAT
Statistics
Matches: 84, Mismatches: 3, Indels: 8
0.88 0.03 0.08
Matches are distributed among these distances:
5 2 0.02
6 80 0.95
7 2 0.02
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (6 bp):
TTATTA
Found at i:19188403 original size:9 final size:9
Alignment explanation
Indices: 19188391--19188421 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
19188381 ATTACTATTA
19188391 TTATTATGT
1 TTATTATGT
19188400 TTATTATGT
1 TTATTATGT
19188409 TTATTATGT
1 TTATTATGT
19188418 TTAT
1 TTAT
19188422 GTATACTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (9 bp):
TTATTATGT
Found at i:19194445 original size:17 final size:17
Alignment explanation
Indices: 19194420--19194460 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
19194410 GCGGCACCAC
*
19194420 TATTTTTTTAATAAATTT
1 TATTTTTTTAA-AAATAT
19194438 TATTTTTTTAAAAATAT
1 TATTTTTTTAAAAATAT
19194455 TATTTT
1 TATTTT
19194461 ATTAGTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTTTAAAAATAT
Found at i:19196159 original size:28 final size:29
Alignment explanation
Indices: 19196105--19196163 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
19196095 GCATTTCGTT
*
19196105 AAAAAAAATATCAACAGAGAATTTAAACAA
1 AAAAAAAATATAAACAGAGAA-TTAAACAA
19196135 AAAAAAAATA-AAACAGATGAA-TAAACAA
1 AAAAAAAATATAAACAGA-GAATTAAACAA
19196163 A
1 A
19196164 GTGAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 6 0.22
30 13 0.48
ACGTcount: A:0.71, C:0.08, G:0.07, T:0.14
Consensus pattern (29 bp):
AAAAAAAATATAAACAGAGAATTAAACAA
Found at i:19196981 original size:30 final size:29
Alignment explanation
Indices: 19196937--19196996 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
19196927 TAATTTTTAA
*
19196937 ATGTAGTGTTTTTTAAAAATAAAAAAATAT
1 ATGTAGTGTATTTTAAAAAT-AAAAAATAT
*
19196967 ATGTGGTGTATTTTAAAAATAAAAAATAT
1 ATGTAGTGTATTTTAAAAATAAAAAATAT
19196996 A
1 A
19196997 GTTTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (29 bp):
ATGTAGTGTATTTTAAAAATAAAAAATAT
Found at i:19197285 original size:23 final size:23
Alignment explanation
Indices: 19197240--19197290 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
19197230 AAAGAATAGG
* *
19197240 GAAAGAAAGGAGAGGAAGGAGAA
1 GAAAGAAAGAAGAGGAAGAAGAA
* *
19197263 GAAAGAAAGAAGATGTAGAAGAA
1 GAAAGAAAGAAGAGGAAGAAGAA
*
19197286 AAAAG
1 GAAAG
19197291 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (23 bp):
GAAAGAAAGAAGAGGAAGAAGAA
Done.