Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold257
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1615106
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 208026 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:929038 original size:29 final size:29
Alignment explanation
Indices: 929006--929258 Score: 326
Period size: 29 Copynumber: 8.6 Consensus size: 29
928996 GTATTTATTT
* **
929006 AAGGAAATACGTGTAGGTTTTTAACACCA
1 AAGGAAATACATGTAGGTAATTAACACCA
* * **
929035 AAGGAAATACGTATAGGTTTTTAACACCA
1 AAGGAAATACATGTAGGTAATTAACACCA
**
929064 AAGGAAATACATGTAGGTTTTTAACACCA
1 AAGGAAATACATGTAGGTAATTAACACCA
** *
929093 AAGGAAATACATGTAGGTTTTTTAACAACA
1 AAGGAAATACATGTAGG-TAATTAACACCA
929123 AAGGAAATACATGTAGGTAATTAACACCA
1 AAGGAAATACATGTAGGTAATTAACACCA
929152 AAGGAAATACAGTCATGTAGGTAATTAACACCA
1 AAGGAAAT--A--CATGTAGGTAATTAACACCA
929185 AAGGAAATACATGTAGGTAATTAACACCA
1 AAGGAAATACATGTAGGTAATTAACACCA
* *
929214 AAGGAAATAAATGTAAGTAATTAACACCA
1 AAGGAAATACATGTAGGTAATTAACACCA
*
929243 AGGGAAATACATGTAG
1 AAGGAAATACATGTAG
929259 TTACTTCACT
Statistics
Matches: 207, Mismatches: 12, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
29 149 0.72
30 28 0.14
31 2 0.01
33 28 0.14
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (29 bp):
AAGGAAATACATGTAGGTAATTAACACCA
Found at i:932088 original size:2 final size:2
Alignment explanation
Indices: 932081--932110 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
932071 AAATTAGGTT
*
932081 AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
932111 CTTTCATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:935834 original size:17 final size:17
Alignment explanation
Indices: 935812--935848 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
935802 ACGAGAGGTT
935812 TTTTTTCTTGGTTATGA
1 TTTTTTCTTGGTTATGA
*
935829 TTTTTTTTTGGTTATGA
1 TTTTTTCTTGGTTATGA
935846 TTT
1 TTT
935849 GAACACAGAC
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:0.11, C:0.03, G:0.16, T:0.70
Consensus pattern (17 bp):
TTTTTTCTTGGTTATGA
Found at i:936159 original size:2 final size:2
Alignment explanation
Indices: 936152--936188 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
936142 GGATAAAAAT
936152 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
936189 TGCTGATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:936374 original size:2 final size:2
Alignment explanation
Indices: 936367--936420 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
936357 GAGGTAACAC
936367 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
936409 AG AG AG AG AG AG
1 AG AG AG AG AG AG
936421 TATTAAAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:937281 original size:13 final size:13
Alignment explanation
Indices: 937263--937292 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
937253 AACGGTCTTT
937263 CAAAAAACAAAAA
1 CAAAAAACAAAAA
937276 CAAAAAACAAAAA
1 CAAAAAACAAAAA
937289 CAAA
1 CAAA
937293 CCCCCCCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAACAAAAA
Found at i:937410 original size:11 final size:11
Alignment explanation
Indices: 937390--937431 Score: 59
Period size: 10 Copynumber: 3.8 Consensus size: 11
937380 AGTTCGTTAT
*
937390 ATGTATAGACA
1 ATGTAAAGACA
937401 ATGTAAAGACAA
1 ATGTAAAGAC-A
937413 ATGTAAAGA-A
1 ATGTAAAGACA
937423 ATGTAAAGA
1 ATGTAAAGA
937432 ATGTATAGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
12 10 0.34
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.21
Consensus pattern (11 bp):
ATGTAAAGACA
Found at i:937426 original size:10 final size:10
Alignment explanation
Indices: 937390--937450 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
937380 AGTTCGTTAT
*
937390 ATGTATAGACA
1 ATGTAAAGA-A
937401 ATGTAAAGACAA
1 ATGTAAAG--AA
937413 ATGTAAAGAA
1 ATGTAAAGAA
937423 ATGTAAAG-A
1 ATGTAAAGAA
* *
937432 ATGTATAGAC
1 ATGTAAAGAA
*
937442 ATGTTAAGA
1 ATGTAAAGA
937451 GTTGTGTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 8 0.19
10 17 0.40
11 7 0.17
12 9 0.21
13 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.25
Consensus pattern (10 bp):
ATGTAAAGAA
Found at i:937436 original size:19 final size:19
Alignment explanation
Indices: 937412--937450 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
937402 TGTAAAGACA
937412 AATGTAAAGAAATGTAAAG
1 AATGTAAAGAAATGTAAAG
* * *
937431 AATGTATAGACATGTTAAG
1 AATGTAAAGAAATGTAAAG
937450 A
1 A
937451 GTTGTGTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.21, T:0.26
Consensus pattern (19 bp):
AATGTAAAGAAATGTAAAG
Found at i:938839 original size:21 final size:20
Alignment explanation
Indices: 938815--938855 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
938805 ACATACATAT
938815 TTCATTATAGACCTATATAA
1 TTCATTATAGACCTATATAA
* *
938835 NTTCATTATAGGCCTTTATAA
1 -TTCATTATAGACCTATATAA
938856 GTGAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.41
Consensus pattern (20 bp):
TTCATTATAGACCTATATAA
Found at i:946272 original size:2 final size:2
Alignment explanation
Indices: 946265--946313 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
946255 NNNNNNNNNN
*
946265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
946307 TA TA TA T
1 TA TA TA T
946314 GTGTGTGTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:952128 original size:2 final size:2
Alignment explanation
Indices: 952121--952173 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
952111 GGGATAGCTG
952121 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
952163 CT CT CT CT CT C
1 CT CT CT CT CT C
952174 CATAAAAACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:952670 original size:2 final size:2
Alignment explanation
Indices: 952663--952709 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
952653 ATGAACAACT
952663 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
952705 GA GA G
1 GA GA G
952710 CAGCTATCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:954213 original size:24 final size:24
Alignment explanation
Indices: 954167--954215 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
954157 ATTTTAAAAT
* **
954167 ATAAAAAGACATTCATGTTGGGCA
1 ATAAAAAAACATTCATGCAGGGCA
*
954191 ATAAAAAAACATTTATGCAGGGCA
1 ATAAAAAAACATTCATGCAGGGCA
954215 A
1 A
954216 AGTTAAGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.22
Consensus pattern (24 bp):
ATAAAAAAACATTCATGCAGGGCA
Found at i:963861 original size:20 final size:20
Alignment explanation
Indices: 963828--963866 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
963818 AAAAGATTAT
*
963828 ATTTTTATAACAATTTATTG
1 ATTTTTATAACAATATATTG
**
963848 ATTTTTATTTCAATATATT
1 ATTTTTATAACAATATATT
963867 TTTCAAACTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTTTTATAACAATATATTG
Found at i:970305 original size:89 final size:89
Alignment explanation
Indices: 970165--970330 Score: 289
Period size: 89 Copynumber: 1.9 Consensus size: 89
970155 GATTCATTAG
* *
970165 TTTTCCTGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGGATTTGATCCGTGAATGTGTG
1 TTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGGAGTTGATCCGTGAATGTGTG
*
970230 ACTTGGGCATTAACGATTATTTGA
66 ACTGGGGCATTAACGATTATTTGA
970254 TTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCGT-GGAGTTGATCCGTGAATGTGT
1 TTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACC-TAGGAGTTGATCCGTGAATGTGT
970318 GACTGGGGCATTA
65 GACTGGGGCATTA
970331 GATTAGTTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
89 72 0.99
90 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (89 bp):
TTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGGAGTTGATCCGTGAATGTGTG
ACTGGGGCATTAACGATTATTTGA
Found at i:983835 original size:2 final size:2
Alignment explanation
Indices: 983830--983875 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
983820 TCGCTAAATC
* * *
983830 TG TG TG TG TG TA TG TG TA TG TG TG TG TG TC TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
983872 TG TG
1 TG TG
983876 ATTCGTTCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.04, C:0.02, G:0.43, T:0.50
Consensus pattern (2 bp):
TG
Found at i:987106 original size:1 final size:1
Alignment explanation
Indices: 987100--987125 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
987090 AAGGGAGGAC
987100 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
987126 TTTGAGGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:994465 original size:2 final size:2
Alignment explanation
Indices: 994460--994505 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
994450 GCCCCCCCCT
994460 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
994502 TC TC
1 TC TC
994506 ACAAAATACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:998590 original size:126 final size:126
Alignment explanation
Indices: 998365--998612 Score: 496
Period size: 126 Copynumber: 2.0 Consensus size: 126
998355 NNNNNNNNNN
998365 CGACGCCTATGTATATATATATATTAGGTTTAAAACATCTGATAATCTTGGGACTTCTTTTGTGA
1 CGACGCCTATGTATATATATATATTAGGTTTAAAACATCTGATAATCTTGGGACTTCTTTTGTGA
998430 TGCGTTAAATTCATCATGTTATTATGAACGACCAGTTTCACGGTTTGCAGCTTTGCTGCTT
66 TGCGTTAAATTCATCATGTTATTATGAACGACCAGTTTCACGGTTTGCAGCTTTGCTGCTT
998491 CGACGCCTATGTATATATATATATTAGGTTTAAAACATCTGATAATCTTGGGACTTCTTTTGTGA
1 CGACGCCTATGTATATATATATATTAGGTTTAAAACATCTGATAATCTTGGGACTTCTTTTGTGA
998556 TGCGTTAAATTCATCATGTTATTATGAACGACCAGTTTCACGGTTTGCAGCTTTGCT
66 TGCGTTAAATTCATCATGTTATTATGAACGACCAGTTTCACGGTTTGCAGCTTTGCT
998613 TGTAAAAATC
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (126 bp):
CGACGCCTATGTATATATATATATTAGGTTTAAAACATCTGATAATCTTGGGACTTCTTTTGTGA
TGCGTTAAATTCATCATGTTATTATGAACGACCAGTTTCACGGTTTGCAGCTTTGCTGCTT
Found at i:1004791 original size:2 final size:2
Alignment explanation
Indices: 1004784--1004829 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1004774 GAAGAATCCA
*
1004784 TC TC TC TC TC TC TC TC TC TC TC TC TC -C CC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1004825 TC TC T
1 TC TC T
1004830 GTTATATTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:1015909 original size:18 final size:18
Alignment explanation
Indices: 1015888--1015927 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1015878 TGATGTTGAA
* *
1015888 GATGTTGAGGGTGTTGTT
1 GATGTTGAGGATGCTGTT
1015906 GATGTTGAGGATGCTGTT
1 GATGTTGAGGATGCTGTT
1015924 GATG
1 GATG
1015928 GTGGACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.03, G:0.42, T:0.40
Consensus pattern (18 bp):
GATGTTGAGGATGCTGTT
Found at i:1018013 original size:21 final size:21
Alignment explanation
Indices: 1017987--1018056 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
1017977 GTGCAAGAAA
*
1017987 CGTTTCGTGTAAACCATTTAG
1 CGTTTCGTGTAAACCGTTTAG
* * **
1018008 CGTTTCGTGTGAATCGTAGAG
1 CGTTTCGTGTAAACCGTTTAG
*
1018029 CGTTTCTTGTAAACCGTTTAG
1 CGTTTCGTGTAAACCGTTTAG
1018050 CGTTTCG
1 CGTTTCG
1018057 GGCAAAGCGT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (21 bp):
CGTTTCGTGTAAACCGTTTAG
Found at i:1018072 original size:21 final size:21
Alignment explanation
Indices: 1018048--1018112 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1018038 TAAACCGTTT
1018048 AGCGTTTCGGGCAAAGCGTGC
1 AGCGTTTCGGGCAAAGCGTGC
** *
1018069 AGCGTTTCGAACAAAGCGTGTAA
1 AGCGTTTCGGGCAAAGCGTG--C
* *
1018092 ATCGTTTTGGGCAAAGCGTGC
1 AGCGTTTCGGGCAAAGCGTGC
1018113 GAGAACCGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.53
23 16 0.47
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (21 bp):
AGCGTTTCGGGCAAAGCGTGC
Found at i:1018073 original size:42 final size:42
Alignment explanation
Indices: 1017987--1018077 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
1017977 GTGCAAGAAA
* ** *
1017987 CGTTTCGTGTAAACCATTTAGCGTTTCGTGTGAATCGTAGAG
1 CGTTTCGTGTAAACCATTTAGCGTTTCGGGCAAAGCGTAGAG
* *
1018029 CGTTTCTTGTAAACCGTTTAGCGTTTCGGGCAAAGCGT-GCAG
1 CGTTTCGTGTAAACCATTTAGCGTTTCGGGCAAAGCGTAG-AG
1018071 CGTTTCG
1 CGTTTCG
1018078 AACAAAGCGT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.02
42 40 0.98
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (42 bp):
CGTTTCGTGTAAACCATTTAGCGTTTCGGGCAAAGCGTAGAG
Found at i:1019313 original size:130 final size:130
Alignment explanation
Indices: 1019080--1019325 Score: 456
Period size: 130 Copynumber: 1.9 Consensus size: 130
1019070 TCAAAATTAT
*
1019080 CAATGTAAATAATAACAGGTTTATTTACAGTTAGTATTTTTACATCGTATTCTCTGAAACCAATA
1 CAATGTAAATAATAACAGGTTTATTTACAGATAGTATTTTTACATCGTATTCTCTGAAACCAATA
1019145 AAAATATTAATGTGAGAAGAAAAAACAAATCCCGCCGAATACTGAAAAACCAAATTACAATGTAC
66 AAAATATTAATGTGAGAAGAAAAAACAAATCCCGCCGAATACTGAAAAACCAAATTACAATGTAC
* *
1019210 CAATGTAAATAATTACAGGTTTATTTACAGATAGTATTTTTACATCGTATTCTCTGAAACTAATA
1 CAATGTAAATAATAACAGGTTTATTTACAGATAGTATTTTTACATCGTATTCTCTGAAACCAATA
*
1019275 AAAATATTAATGTGAGAAGAAAAAACAAATCCTGCCGAATACTGAAAAACC
66 AAAATATTAATGTGAGAAGAAAAAACAAATCCCGCCGAATACTGAAAAACC
1019326 GATTTCAGTT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 112 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (130 bp):
CAATGTAAATAATAACAGGTTTATTTACAGATAGTATTTTTACATCGTATTCTCTGAAACCAATA
AAAATATTAATGTGAGAAGAAAAAACAAATCCCGCCGAATACTGAAAAACCAAATTACAATGTAC
Found at i:1019745 original size:21 final size:21
Alignment explanation
Indices: 1019721--1019810 Score: 108
Period size: 21 Copynumber: 4.3 Consensus size: 21
1019711 GTGCGAGAAT
1019721 CGTTTCGTGTAAACCGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
* *
1019742 CGTTTCGTGTAAATCGTTTAG
1 CGTTTCGTGTAAACCGTTCAG
* * * * *
1019763 TGTTTCGGGCAAAGCGTGCAG
1 CGTTTCGTGTAAACCGTTCAG
*
1019784 CCTTTCGTGTAAACCGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
1019805 CGTTTC
1 CGTTTC
1019811 TGACAAGCTG
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (21 bp):
CGTTTCGTGTAAACCGTTCAG
Found at i:1026041 original size:21 final size:21
Alignment explanation
Indices: 1026017--1026068 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1026007 ACGGACGCTA
*
1026017 AACTATAGTTAACGATTCGTT
1 AACTATAGTTAACGATCCGTT
*
1026038 AACTATAATTAACGATCCGTT
1 AACTATAGTTAACGATCCGTT
*
1026059 TACTATAGTT
1 AACTATAGTT
1026069 TTCATCTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
AACTATAGTTAACGATCCGTT
Found at i:1026432 original size:21 final size:22
Alignment explanation
Indices: 1026408--1026457 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1026398 TTTCTGTCCG
1026408 TAAACTATAGTTTA-CAACTGT
1 TAAACTATAGTTTATCAACTGT
* *
1026429 TAAAC-CTAGTTTATCGACTGT
1 TAAACTATAGTTTATCAACTGT
*
1026450 GAAACTAT
1 TAAACTAT
1026458 GATTAGCTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.30
21 15 0.65
22 1 0.04
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (22 bp):
TAAACTATAGTTTATCAACTGT
Found at i:1036251 original size:31 final size:31
Alignment explanation
Indices: 1036216--1036294 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
1036206 ATTATTCCTG
*
1036216 GTACGACTTAACAAAACCTGAA-TT-ATTTTAA
1 GTACGACTTAACAAAACC--AATTTGATTTCAA
*
1036247 GTACGAATTAACAAAAACCAATTTGATTTCAA
1 GTACGACTTAAC-AAAACCAATTTGATTTCAA
*
1036279 GAACGACTTAACAAAA
1 GTACGACTTAACAAAA
1036295 AAAATCCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.05
31 17 0.41
32 22 0.54
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (31 bp):
GTACGACTTAACAAAACCAATTTGATTTCAA
Found at i:1037032 original size:53 final size:53
Alignment explanation
Indices: 1036878--1037098 Score: 316
Period size: 53 Copynumber: 4.1 Consensus size: 53
1036868 AAAATAATAA
1036878 TAAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCC
1 TAAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCC
* * * ***
1036931 TAATTAAAAAAAACAATAGAATAACAAGAGGGTCTTCCGTTTTCAACGGAAGACCC
1 TAA--AAAGAAACCGA-AGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCC
1036987 TAAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCC
1 TAAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCC
* * * * *
1037040 TAAAAAGAATCCGAAGAAAAACAATAGGGTCCTCCGTTAGAAACGGAAGACCC
1 TAAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCC
1037093 TAAAAA
1 TAAAAA
1037099 CGGTCTTCCG
Statistics
Matches: 148, Mismatches: 17, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
53 93 0.63
54 8 0.05
55 8 0.05
56 39 0.26
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (53 bp):
TAAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCC
Found at i:1037109 original size:33 final size:33
Alignment explanation
Indices: 1037067--1037131 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1037057 AAAACAATAG
1037067 GGTCCTCCGTTAGAAACGGAAGACCCTAAAAAC
1 GGTCCTCCGTTAGAAACGGAAGACCCTAAAAAC
* * *
1037100 GGTCTTCCGTTGGAAACGTAAGACCCTAAAAA
1 GGTCCTCCGTTAGAAACGGAAGACCCTAAAAA
1037132 GTCAAGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (33 bp):
GGTCCTCCGTTAGAAACGGAAGACCCTAAAAAC
Found at i:1044955 original size:169 final size:166
Alignment explanation
Indices: 1044368--1045174 Score: 1125
Period size: 166 Copynumber: 4.8 Consensus size: 166
1044358 ATCTGCCAAT
*
1044368 TAAAACATGATCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
1 TAAAACTTGATCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
* * *
1044433 ATCTACATTATCTGAGGATGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAA
66 ATCTACACTACCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAA
*
1044498 GAAGACTTTTAAAGATTTTCTCTATATATTCCTATG
131 GAAGATTTTTAAAGATTTTCTCTATATATTCCTATG
* * * *
1044534 TATAACTTGATCCCCCTCTTGTGGCCCCACCCTATCCCTGGGGACCATGATTTGAACAAACTTGA
1 TAAAACTTGATCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
* * ** *
1044599 ATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGATTTTCTGGCCTAATAGTTTTTGAGAA
66 ATCTACACTACCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAA
* *
1044664 GAAGATTTTTACAGATTTTCTCTTTATATTCCTATG
131 GAAGATTTTTAAAGATTTTCTCTATATATTCCTATG
* *
1044700 TAAAACTTGAT-CCCATAATTGTGGCCCAACCCTACCCCCGGGGACCATGATTTGAACAAACTTG
1 TAAAACTTGATCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTG
* * *
1044764 AATCTACATTATCT-ATGGATGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
65 AATCTACACTACCTGA-GGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAG
* * * *
1044828 AAGTAGATTTTTTTTAAAGATTTTATCTATTTATTCTTATG
129 AAGAAGA---TTTTTAAAGATTTTCTCTATATATTCCTATG
*
1044869 TAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
1 TAAAACTTGATCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
* * ** *
1044934 AT-TGACACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTTCTGGCCTGATAGTTTTTGAGA
66 ATCT-ACACTACCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGA
* *
1044998 AGAAGATTTTTAAAGATGTTCTTTATATATTCCTATG
130 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATG
* * * *
1045035 TAAAACTTGATCCCCCTCTAGTGGCCCCTCCCTACCCCCGGGGAGCATGATTTGAACAAACTTGA
1 TAAAACTTGATCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
* * * * * * ** *
1045100 ATCTACACTACCTGATGATGCCTCCACACAAGTTTAAGCTTTTCAGAACTGATAGTTTTTGAGAA
66 ATCTACACTACCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAA
1045165 GAAGATTTTT
131 GAAGATTTTT
1045175 GAAAAATACC
Statistics
Matches: 562, Mismatches: 70, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
165 5 0.01
166 410 0.73
167 1 0.00
168 1 0.00
169 141 0.25
170 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (166 bp):
TAAAACTTGATCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
ATCTACACTACCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAA
GAAGATTTTTAAAGATTTTCTCTATATATTCCTATG
Found at i:1044991 original size:335 final size:336
Alignment explanation
Indices: 1044368--1045174 Score: 1227
Period size: 335 Copynumber: 2.4 Consensus size: 336
1044358 ATCTGCCAAT
* *
1044368 TAAAACATGATCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
1 TAAAACTTGATCCCCATATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
1044433 ATCTACATTATCTGA-GGATGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGA
66 ATCTACATTATCTGATGGATGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGA
* * * **
1044497 AGAAGA---CTTTTAAAGATTTTCTCTATATATTCCTATGTATAACTTGATCCCCCTCTTGTGGC
131 AGAAGATTTTTTTTAAAGATTTTATCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGC
* *
1044559 CCCACCCTATCCCTGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTCCC
196 CCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTCCC
* *
1044624 ATTTTAATTTGAGATTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTACAGATTTTCTCTT-
261 ATTTTAATTTGAGATTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATGTTCT-TTA
1044688 TATATTCCTATG
325 TATATTCCTATG
*
1044700 TAAAACTTGAT-CCCATAATTGTGGCCCAACCCTACCCCCGGGGACCATGATTTGAACAAACTTG
1 TAAAACTTGATCCCCAT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTG
1044764 AATCTACATTATCT-ATGGATGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
65 AATCTACATTATCTGATGGATGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
* * *
1044828 AAGTAGATTTTTTTTAAAGATTTTATCTATTTATTCTTATGTAAAACTTGATCCCCCAATTGTGG
130 AAGAAGATTTTTTTTAAAGATTTTATCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGG
1044893 CCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAAT-TGACACTACCTGAGGATGCTC
195 CCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCT-ACACTACCTGAGGATGCTC
* *
1044957 CCATTTTAATTTGAGCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATGTTCTTT
259 CCATTTTAATTTGAGATTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATGTTCTTT
1045022 ATATATTCCTATG
324 ATATATTCCTATG
* * * * *
1045035 TAAAACTTGATCCCCCTCTAGTGGCCCCTCCCTACCCCCGGGGAGCATGATTTGAACAAACTTGA
1 TAAAACTTGATCCCCATATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
* * * * * * * * ** *
1045100 ATCTACACTACCTGAT-GATGCCTCCACACAAGTTTAAGCTTTTCAGAACTGATAGTTTTTGAGA
66 ATCTACATTATCTGATGGATGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGA
1045164 AGAAGATTTTT
131 AGAAGATTTTT
1045175 GAAAAATACC
Statistics
Matches: 431, Mismatches: 35, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
331 5 0.01
332 124 0.29
334 3 0.01
335 293 0.68
336 6 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (336 bp):
TAAAACTTGATCCCCATATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
ATCTACATTATCTGATGGATGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGA
AGAAGATTTTTTTTAAAGATTTTATCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGC
CCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTCCC
ATTTTAATTTGAGATTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATGTTCTTTAT
ATATTCCTATG
Found at i:1056417 original size:51 final size:51
Alignment explanation
Indices: 1056346--1056448 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
1056336 GACAAGTCTT
1056346 TGGTCGTCATTTGTCAGACAATACATGTAGTTTTCAACAGTGTTTGACTTGA
1 TGGTCGTCA-TTGTCAGACAATACATGTAGTTTTCAACAGTGTTTGACTTGA
1056398 NTGGTCGTCA-TGTCAGACAATACATGTAGTTTTCAACAGTGTTTGACTTGA
1 -TGGTCGTCATTGTCAGACAATACATGTAGTTTTCAACAGTGTTTGACTTGA
1056449 AAAAAAAGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 41 0.82
53 9 0.18
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (51 bp):
TGGTCGTCATTGTCAGACAATACATGTAGTTTTCAACAGTGTTTGACTTGA
Found at i:1069972 original size:18 final size:18
Alignment explanation
Indices: 1069949--1070001 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
1069939 AATGCAGCTT
1069949 TGATTGAACTTTGAACTC
1 TGATTGAACTTTGAACTC
*
1069967 TGATTGAACTTTGACCTC
1 TGATTGAACTTTGAACTC
1069985 TGATTGAACTTTGAACT
1 TGATTGAACTTTGAACT
1070002 TTGACCAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (18 bp):
TGATTGAACTTTGAACTC
Found at i:1077968 original size:3 final size:3
Alignment explanation
Indices: 1077960--1077996 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1077950 ACAAGAGACG
1077960 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1077997 NGATTGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:1078193 original size:13 final size:13
Alignment explanation
Indices: 1078163--1078199 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1078153 AAAAGTGAAT
*
1078163 TAATG-ATAATAA
1 TAATGAATAAAAA
1078175 -AATGAATAAAAA
1 TAATGAATAAAAA
1078187 TAATGAATAAAAA
1 TAATGAATAAAAA
1078200 AATACGCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 4 0.18
12 6 0.27
13 12 0.55
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
TAATGAATAAAAA
Found at i:1089071 original size:2 final size:2
Alignment explanation
Indices: 1089064--1089121 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1089054 TTAGCAATTT
1089064 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1089106 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
1089122 AGTACATGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1092484 original size:4 final size:4
Alignment explanation
Indices: 1092475--1092501 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1092465 TCGATTTACT
1092475 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1092502 TTGTTATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1103478 original size:2 final size:2
Alignment explanation
Indices: 1103471--1103501 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1103461 GATGGCAAAG
1103471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1103502 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1123375 original size:7 final size:7
Alignment explanation
Indices: 1123363--1123429 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
1123353 GAGAAGGATC
1123363 ATTCGAG
1 ATTCGAG
1123370 ATTCGAG
1 ATTCGAG
*
1123377 ATTCGAA
1 ATTCGAG
*
1123384 ATACGAG
1 ATTCGAG
*
1123391 ATTCGAA
1 ATTCGAG
*
1123398 ATACGAG
1 ATTCGAG
1123405 ATTCGAG
1 ATTCGAG
*
1123412 ATTCGAA
1 ATTCGAG
1123419 ATTCGAG
1 ATTCGAG
1123426 ATTC
1 ATTC
1123430 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:1123931 original size:2 final size:2
Alignment explanation
Indices: 1123924--1123963 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1123914 TTGTCGATAT
1123924 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1123964 CAGACAGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1123968 original size:4 final size:4
Alignment explanation
Indices: 1123961--1123989 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1123951 AGAGAGAGAG
1123961 AGAC AGAC AGAC AGAC AGAC AGAC AGAC A
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC A
1123990 CAGAGAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:1124184 original size:2 final size:2
Alignment explanation
Indices: 1124177--1124223 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1124167 TTTACATCGA
1124177 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1124219 CT CT C
1 CT CT C
1124224 ATCACCTAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1126637 original size:7 final size:7
Alignment explanation
Indices: 1126622--1126688 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
1126612 TTTAGATATT
1126622 GAATCTC
1 GAATCTC
*
1126629 GAATTTC
1 GAATCTC
1126636 GAATCTC
1 GAATCTC
1126643 GAATCTC
1 GAATCTC
* *
1126650 GTATTTC
1 GAATCTC
1126657 GAATCTC
1 GAATCTC
* *
1126664 GTATTTC
1 GAATCTC
1126671 GAATCTC
1 GAATCTC
1126678 GAATCTC
1 GAATCTC
1126685 GAAT
1 GAAT
1126689 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:1126647 original size:21 final size:21
Alignment explanation
Indices: 1126622--1126688 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
1126612 TTTAGATATT
1126622 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
1126643 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
1126664 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
1126685 GAAT
1 GAAT
1126689 GATCCTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:1152672 original size:2 final size:2
Alignment explanation
Indices: 1152665--1152731 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1152655 GTTTCCATGC
1152665 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1152707 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1152732 AATTAAAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1155949 original size:71 final size:72
Alignment explanation
Indices: 1155832--1155975 Score: 263
Period size: 71 Copynumber: 2.0 Consensus size: 72
1155822 CGTTTTTTTT
**
1155832 TGTTTTTGGTTTTTTTCTTTATAGAAGACTGTACGATAGTTGATTATGCATATGCTTTTATCTGA
1 TGTTTTTGGGGTTTTTCTTTATAGAAGACTGTACGATAGTTGATTATGCATATGCTTTTATCTGA
1155897 ATATGAA
66 ATATGAA
1155904 TGTTTTTGGGGTTTTT-TTTATAGAAGACTGTACGATAGTTGATTATGCATATGCTTTTATCTGA
1 TGTTTTTGGGGTTTTTCTTTATAGAAGACTGTACGATAGTTGATTATGCATATGCTTTTATCTGA
1155968 ATATGAA
66 ATATGAA
1155975 T
1 T
1155976 ATTTCGAACA
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 56 0.80
72 14 0.20
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (72 bp):
TGTTTTTGGGGTTTTTCTTTATAGAAGACTGTACGATAGTTGATTATGCATATGCTTTTATCTGA
ATATGAA
Found at i:1164825 original size:2 final size:2
Alignment explanation
Indices: 1164818--1164846 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1164808 AGAATCGACC
1164818 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1164847 ATGTAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1170185 original size:161 final size:161
Alignment explanation
Indices: 1169477--1170223 Score: 770
Period size: 161 Copynumber: 4.6 Consensus size: 161
1169467 AAATGAATGT
* * * ** * **
1169477 AACTGCAAATAACTGGAATTTTTCTAAGTCCAAGGGGTATAACTC--TGCTGAAAATTGCTTTAT
1 AACTGCAAAAAACTGGAATTTTTCTACGCCCAAGGGCCATAACTCAAT-C-AAAAATTGCTCGAT
* * *
1169540 CATACCCAAAATC-AATCTTGACCTAGATATTAT-TTAGATAAACGTGTATACCAAATTTCATTC
64 CATACCCAATATCGAA-CTTGACCTAGATATTATCAT-GATAAACCTGTATACCAAATTTCATTC
* **
1169603 CAATATGTTTATCCTCTGCAAAGAAAATGAGGGGA
127 CAATATGTTCATCCTCTGTGAAGAAAATGAGGGGA
* * ** * *
1169638 AACTGCAAAAAACTGGAATTTTTCTATG-TCATAGGGCCATAACTCTGTCGAAAACTGCTC-ACT
1 AACTGCAAAAAACTGGAATTTTTCTACGCCCA-AGGGCCATAACTCAATCAAAAATTGCTCGA-T
* * * * * * *
1169701 CGTACCAAATACCAAACTTGA-ATAGATATTATCATGATAAACATGTATACCAAATTTCATTTCA
64 CATACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTCCA
* * * *
1169765 TTATGTTCATCCTTTATGAAGAAAATGAGCGGA
129 ATATGTTCATCCTCTGTGAAGAAAATGAGGGGA
* * * * * *** * * *
1169798 AACTGCAAAAAAATGGAATTTTTTTATGTCCAAGGGCCAAAACTTTGTCGAAAATTGATCGGTCA
1 AACTGCAAAAAACTGGAATTTTTCTACGCCCAAGGGCCATAACTCAATCAAAAATTGCTCGATCA
* *
1169863 CACCCAATATTGAACTTGACCTAGATATTATCATGATAAACCTGTATACATGTACACACCAAATT
66 TACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTG--T--A--T----ACCAAATT
1169928 TCATTCCAATATGTTCATCCTCTGTGAAGAAAATGAGGGGA
121 TCATTCCAATATGTTCATCCTCTGTGAAGAAAATGAGGGGA
* * * **
1169969 AACTGTAAATAACTGGAATTTTTCTACGCCCAAGGGCCATTACTCAATCAAAAATTGCTCGATTG
1 AACTGCAAAAAACTGGAATTTTTCTACGCCCAAGGGCCATAACTCAATCAAAAATTGCTCGATCA
* * *
1170034 TACCCAATATCGAAGTTGACCTAGATATTATCATGATTAACCTGTATACCAAATTTCATTTCAAT
66 TACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTCCAAT
*
1170099 ATGTTCATCCTCTGGGAAGAAAATGAGGGGA
131 ATGTTCATCCTCTGTGAAGAAAATGAGGGGA
* * * * *
1170130 AACTGTAAATAACTGGAATTTTTCTACACCCAAGGGCCATACCTCAATCAAAAATTGCTTGATCA
1 AACTGCAAAAAACTGGAATTTTTCTACGCCCAAGGGCCATAACTCAATCAAAAATTGCTCGATCA
*
1170195 TACCCAATATTGAACTTGACCTAGATATT
66 TACCCAATATCGAACTTGACCTAGATATT
1170224 TTTTAGATAA
Statistics
Matches: 494, Mismatches: 73, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
160 132 0.27
161 219 0.44
162 3 0.01
163 2 0.00
165 2 0.00
167 2 0.00
169 1 0.00
171 133 0.27
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (161 bp):
AACTGCAAAAAACTGGAATTTTTCTACGCCCAAGGGCCATAACTCAATCAAAAATTGCTCGATCA
TACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTCCAAT
ATGTTCATCCTCTGTGAAGAAAATGAGGGGA
Found at i:1170235 original size:332 final size:331
Alignment explanation
Indices: 1169589--1170223 Score: 851
Period size: 332 Copynumber: 1.9 Consensus size: 331
1169579 AAACGTGTAT
*
1169589 ACCAAATTTCATTCCAATATGTTTATCCTCTGCAAAGAAAATGAGGGGAAACTGCAAAAAACTGG
1 ACCAAATTTCATTCCAATATGTTCATCCTCTGCAAAGAAAATGAGGGGAAACTGCAAAAAACTGG
* * ** *
1169654 AATTTTTCTATGTCATAGGGCCATAACTCTGTCGAAAACTGCTCACTCGTACCAAATACCAAACT
66 AATTTTTCTACGCCATAGGGCCATAACTCAATCAAAAACTGCTCACTCGTACCAAATACCAAACT
* * *
1169719 TGAATAGATATTATCATGATAAACATGTATACCAAATTTCATTTCATTATGTTCATCCTTTATGA
131 TGAATAGATATTATCATGATAAACATGTATACCAAATTTCATTTCAATATGTTCATCCTCTAGGA
* *** *** *
1169784 AGAAAATGAGCGGAAACTGCAAAAAAATGGAATTTTTTTATGTCCAAGGGCCAAAACTTTGTCGA
196 AGAAAATGAGCGGAAACTGCAAAAAAATGGAATTTTTCTACACCCAAGGGCCAAAACTCAATCAA
*
1169849 AAATTGATCGGTCACACCCAATATTGAACTTGACCTAGATATTATCATGATAAACCTGTATACAT
261 AAATTGATCGATCACACCCAATATTGAACTTGACCTAGATATTATCATGATAAACCTGTATACAT
1169914 GTACAC
326 GTACAC
** * *
1169920 ACCAAATTTCATTCCAATATGTTCATCCTCTGTGAAGAAAATGAGGGGAAACTGTAAATAACTGG
1 ACCAAATTTCATTCCAATATGTTCATCCTCTGCAAAGAAAATGAGGGGAAACTGCAAAAAACTGG
* * * * * *
1169985 AATTTTTCTACGCCCA-AGGGCCATTACTCAATCAAAAATTGCTCGA-TTGTACCCAATATCGAA
66 AATTTTTCTACG-CCATAGGGCCATAACTCAATCAAAAACTGCTC-ACTCGTACCAAATACCAAA
* * * * *
1170048 GTTGACCTAGATATTATCATGATTAACCTGTATACCAAATTTCATTTCAATATGTTCATCCTCTG
129 CTTGA-ATAGATATTATCATGATAAACATGTATACCAAATTTCATTTCAATATGTTCATCCTCTA
* * * * * *
1170113 GGAAGAAAATGAGGGGAAACTGTAAATAACTGGAATTTTTCTACACCCAAGGGCCATACCTCAAT
193 GGAAGAAAATGAGCGGAAACTGCAAAAAAATGGAATTTTTCTACACCCAAGGGCCAAAACTCAAT
* * *
1170178 CAAAAATTGCTTGATCATACCCAATATTGAACTTGACCTAGATATT
258 CAAAAATTGATCGATCACACCCAATATTGAACTTGACCTAGATATT
1170224 TTTTAGATAA
Statistics
Matches: 259, Mismatches: 42, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
331 111 0.43
332 148 0.57
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (331 bp):
ACCAAATTTCATTCCAATATGTTCATCCTCTGCAAAGAAAATGAGGGGAAACTGCAAAAAACTGG
AATTTTTCTACGCCATAGGGCCATAACTCAATCAAAAACTGCTCACTCGTACCAAATACCAAACT
TGAATAGATATTATCATGATAAACATGTATACCAAATTTCATTTCAATATGTTCATCCTCTAGGA
AGAAAATGAGCGGAAACTGCAAAAAAATGGAATTTTTCTACACCCAAGGGCCAAAACTCAATCAA
AAATTGATCGATCACACCCAATATTGAACTTGACCTAGATATTATCATGATAAACCTGTATACAT
GTACAC
Found at i:1170739 original size:146 final size:145
Alignment explanation
Indices: 1170542--1171344 Score: 1024
Period size: 146 Copynumber: 5.5 Consensus size: 145
1170532 TTTTGCTGTT
* * * *
1170542 GGTCATTAGCAATATTTGTGTGAAGTAAGAACATTCAATGCTTCTCCATAAGAAAGACAAT-GAC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCAATGATTCTCCATAAGAAAGA-TATGGAC
* * *
1170606 TGGACATAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCATGCCCAAATGACCTTGGGTCAAG
64 CGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
** *
1170671 GTCATGATGCACCCTTT
129 GTCATGACACACCCTTA
* * * * * *
1170688 GGTCCTAAGCAATATTTGTGTGCAGTTAGAACATTCAAAGCTTCTCCATAAGAAAGATAAT-GAC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCAATGATTCTCCATAAGAAAGAT-ATGGAC
** * ** *
1170752 CGGACAGGAATTTTGCACTATTTT-TCCCAACGACCTTGACCTTGCCCAAATGACTTTGGGTCAA
64 CGGACACAAATTTTGCACT-TTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
* * *
1170816 GGACATGACATACCATTA
128 GGTCATGACACACCCTTA
* * * * * *
1170834 GGTCAAAAGCAGTCTTTGTGTGAATTAAGAACTTCCAATGTTTCTCCATAACAAAGATATGGACA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTT-CAATGATTCTCCATAAGAAAGATATGGACC
*
1170899 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTACCCAAATGACCTTGGGTCAAGG
65 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
1170964 TCATGACACACCCTTA
130 TCATGACACACCCTTA
* * * * *
1170980 GGTCATAAACAATCTATATGTGAAGTAAGAACTTCCAATAATTCCCCATAAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTT-CAATGATTCTCCATAAGAAAGATATGGACC
* *
1171045 GGACACAAATTTTGTA-TGTTTTCTGCCAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAG
65 GGACACAAATTTTGCACT-TTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
*
1171109 GTCATGACAAACCCTTA
129 GTCATGACACACCCTTA
* * * *
1171126 GGTCATAAGCAATTTTTGTGT-AGAGTAAGAACCTCCAATTATTCTCAATAAGAAAGATATGGAC
1 GGTCATAAGCAATCTTTGTGTGA-AGTAAGAA-CTTCAATGATTCTCCATAAGAAAGATATGGAC
* * *
1171190 CGGACACAAATTTTGTATTTTTTCTGCCAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAG
64 CGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
1171255 GTCATGACACACCCTTA
129 GTCATGACACACCCTTA
*
1171272 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTTCAATGTTTCT-CAGTAAGAAAGATATGGAC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCAATGATTCTCCA-TAAGAAAGATATGGAC
1171336 CGGACACAA
64 CGGACACAA
1171345 TTGGATAGAC
Statistics
Matches: 575, Mismatches: 70, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
145 12 0.02
146 555 0.97
147 8 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (145 bp):
GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCAATGATTCTCCATAAGAAAGATATGGACCG
GACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGT
CATGACACACCCTTA
Found at i:1171369 original size:12 final size:12
Alignment explanation
Indices: 1171352--1171391 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1171342 CAATTGGATA
*
1171352 GACAGACGGACG
1 GACAGACAGACG
1171364 GACAGACAGACG
1 GACAGACAGACG
* *
1171376 GACCGACAGATG
1 GACAGACAGACG
1171388 GACA
1 GACA
1171392 AGGTGATTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.38, C:0.25, G:0.35, T:0.03
Consensus pattern (12 bp):
GACAGACAGACG
Found at i:1171372 original size:16 final size:16
Alignment explanation
Indices: 1171351--1171385 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1171341 ACAATTGGAT
*
1171351 AGACAGACGGACGGAC
1 AGACAGACGGACCGAC
1171367 AGACAGACGGACCGAC
1 AGACAGACGGACCGAC
1171383 AGA
1 AGA
1171386 TGGACAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (16 bp):
AGACAGACGGACCGAC
Found at i:1171874 original size:12 final size:12
Alignment explanation
Indices: 1171857--1171882 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1171847 ATGAAAAACG
1171857 CTTATTAAATAT
1 CTTATTAAATAT
1171869 CTTATTAAATAT
1 CTTATTAAATAT
1171881 CT
1 CT
1171883 CCAAGTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (12 bp):
CTTATTAAATAT
Found at i:1172370 original size:21 final size:21
Alignment explanation
Indices: 1172329--1172379 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1172319 GTGTTAAATA
* *
1172329 GTTCGTGTAACATGGGTGATC
1 GTTCGTGTAACATGCGAGATC
*
1172350 GTTCGTGTAACGTGCGAGATC
1 GTTCGTGTAACATGCGAGATC
1172371 -TTGCGTGTA
1 GTT-CGTGTA
1172380 TCAGGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.33
Consensus pattern (21 bp):
GTTCGTGTAACATGCGAGATC
Found at i:1172853 original size:100 final size:100
Alignment explanation
Indices: 1172680--1172877 Score: 351
Period size: 100 Copynumber: 2.0 Consensus size: 100
1172670 TCCATTGTGT
* *
1172680 CTTGACTCATATTTTTAATCATATTAGCAAGAGCGACACGTTGAATGAAAGCGGCCAAGCTTAAC
1 CTTGACTCATACTTTTAATCATATAAGCAAGAGCGACACGTTGAATGAAAGCGGCCAAGCTTAAC
* *
1172745 CATTCCCCGTTTTAAACTAAACGATTATTCTCATA
66 CATTCCCCGTTTTAAACGAAACCATTATTCTCATA
*
1172780 CTTGACTCATGCTTTTAATCATATAAGCAAGAGCGACACGTTGAATGAAAGCGGCCAAGCTTAAC
1 CTTGACTCATACTTTTAATCATATAAGCAAGAGCGACACGTTGAATGAAAGCGGCCAAGCTTAAC
1172845 CATTCCCCGTTTTAAACGAAACCATTATTCTCA
66 CATTCCCCGTTTTAAACGAAACCATTATTCTCA
1172878 ACGTTTTCTT
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (100 bp):
CTTGACTCATACTTTTAATCATATAAGCAAGAGCGACACGTTGAATGAAAGCGGCCAAGCTTAAC
CATTCCCCGTTTTAAACGAAACCATTATTCTCATA
Found at i:1174166 original size:177 final size:175
Alignment explanation
Indices: 1173681--1174166 Score: 563
Period size: 177 Copynumber: 2.8 Consensus size: 175
1173671 CTGTTCCAAG
* * *
1173681 AAAA-CTTAACCTCCTCCAGCATCTGAAATCTAGGACCCAGATTTAGCATCCAAGCCTGTCAGGA
1 AAAACCTTAACCTCCTCCAGCATCTGAAATTTAGGACCCAGATTTAGCATCCAAGCCTGTCAAGT
* * *
1173745 TCATCAGTATCATAAGATGCACCACCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAG
66 TCATCAGTATCA-AAGATGCAACATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTAG
* * * *
1173810 ATATAGTCATCAGATGGCTCTTGCAACAAAAACTTTAACAATCTCTT
130 ATATAGTCATCAGAGGGCACCTGCAACAAAAACTTT-ACAACCTCTT
* * *
1173857 AAAACCTTAACTTCCTCCAGCATCTGAAATCTT-GGACCCAGATTTAGCATCCATGCCTGTCTAG
1 AAAACCTTAACCTCCTCCAGCATCTGAAAT-TTAGGACCCAGATTTAGCATCCAAGCCTGTCAAG
* * * *
1173921 TGCATCAGTATCATAAGAGGCAACATCCATGCAAGTTTGGTGAAGTTAGGACCAGCAGTAAGTTA
65 TTCATCAGTATCA-AAGATGCAACATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTA
*
1173986 GATATTG-CTATCA-AGGAGCACCTGCAACAAAAACTTT-C-ACCTGCTT
129 GATATAGTC-ATCAGAGG-GCACCTGCAACAAAAACTTTACAACCT-CTT
* * * *
1174032 CAAAAACCTTAACCTCCTCCAGCATCTAAAATTTAGGACCCAGATTCAGCATCCAAGTCTTTCAA
1 --AAAACCTTAACCTCCTCCAGCATCTGAAATTTAGGACCCAGATTTAGCATCCAAGCCTGTCAA
* * * * * * *
1174097 GTTCATAAGTAGGTC-CAGATGCATCATCCATGCAAGTTTGGTGAAGATAAGACAAGTAATAACT
64 GTTCATCAGTA--TCAAAGATGCAACATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACT
1174161 TAGATA
127 TAGATA
1174167 CAGGAACTGT
Statistics
Matches: 264, Mismatches: 36, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
174 3 0.01
175 4 0.02
176 9 0.03
177 245 0.93
178 1 0.00
179 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (175 bp):
AAAACCTTAACCTCCTCCAGCATCTGAAATTTAGGACCCAGATTTAGCATCCAAGCCTGTCAAGT
TCATCAGTATCAAAGATGCAACATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTAGA
TATAGTCATCAGAGGGCACCTGCAACAAAAACTTTACAACCTCTT
Found at i:1177548 original size:11 final size:11
Alignment explanation
Indices: 1177532--1177556 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1177522 TGCTGCATTC
1177532 AAGACTAATGA
1 AAGACTAATGA
1177543 AAGACTAATGA
1 AAGACTAATGA
1177554 AAG
1 AAG
1177557 TGTGCGTCAT
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:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (11 bp):
AAGACTAATGA
Found at i:1178335 original size:4 final size:4
Alignment explanation
Indices: 1178311--1178346 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1178301 CTTTCCTCTG
* *
1178311 CGTC CGTC AGTC CGTC TGTC CGTC CGTC CGTC CGTC
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
1178347 TGTCTGTCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.03, C:0.44, G:0.25, T:0.28
Consensus pattern (4 bp):
CGTC
Found at i:1178335 original size:12 final size:12
Alignment explanation
Indices: 1178320--1178354 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1178310 GCGTCCGTCA
1178320 GTCCGTCTGTCC
1 GTCCGTCTGTCC
*
1178332 GTCCGTCCGTCC
1 GTCCGTCTGTCC
*
1178344 GTCTGTCTGTC
1 GTCCGTCTGTC
1178355 TGTCTGTCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:1178355 original size:8 final size:8
Alignment explanation
Indices: 1178312--1178363 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1178302 TTTCCTCTGC
*
1178312 GTCCGTCA
1 GTCCGTCT
1178320 GTCCGTCT
1 GTCCGTCT
*
1178328 GTCCGTCC
1 GTCCGTCT
*
1178336 GTCCGTCC
1 GTCCGTCT
*
1178344 GTCTGTCT
1 GTCCGTCT
*
1178352 GTCTGTCT
1 GTCCGTCT
1178360 GTCC
1 GTCC
1178364 CACTTCAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.02, C:0.38, G:0.25, T:0.35
Consensus pattern (8 bp):
GTCCGTCT
Found at i:1178359 original size:12 final size:12
Alignment explanation
Indices: 1178324--1178362 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1178314 CCGTCAGTCC
*
1178324 GTCTGTCCGTCC
1 GTCTGTCCGTCT
*
1178336 GTCCGTCCGTCT
1 GTCTGTCCGTCT
*
1178348 GTCTGTCTGTCT
1 GTCTGTCCGTCT
1178360 GTC
1 GTC
1178363 CCACTTCAGT
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:0.00, C:0.36, G:0.26, T:0.38
Consensus pattern (12 bp):
GTCTGTCCGTCT
Found at i:1178789 original size:14 final size:14
Alignment explanation
Indices: 1178772--1178802 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1178762 GTATATATGT
1178772 ATAATGATATAATG
1 ATAATGATATAATG
1178786 ATAATGATATAATG
1 ATAATGATATAATG
1178800 ATA
1 ATA
1178803 TAATGATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (14 bp):
ATAATGATATAATG
Found at i:1178798 original size:22 final size:21
Alignment explanation
Indices: 1178771--1178827 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 21
1178761 AGTATATATG
1178771 TATAATGATATAATGATAATGA
1 TATAATGATATAATGATAAT-A
*
1178793 TATAATGATATAATGATAGTA
1 TATAATGATATAATGATAATA
1178814 TAT-ATG-TATAATGA
1 TATAATGATATAATGA
1178828 CGAAAAGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 8 0.24
20 3 0.09
21 4 0.12
22 19 0.56
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (21 bp):
TATAATGATATAATGATAATA
Found at i:1180342 original size:31 final size:32
Alignment explanation
Indices: 1180304--1180381 Score: 131
Period size: 31 Copynumber: 2.4 Consensus size: 32
1180294 CCTAGCCATC
*
1180304 TTTCCCCCCGGAAAAATGGCTATGTAGCAG-T
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1180335 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1180367 TTTCCCCCACGGAAA
1 TTTCCCCC-CGGAAA
1180382 GCTGACTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 29 0.66
32 9 0.20
33 6 0.14
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
Found at i:1180403 original size:33 final size:32
Alignment explanation
Indices: 1180304--1180407 Score: 120
Period size: 31 Copynumber: 3.2 Consensus size: 32
1180294 CCTAGCCATC
* *
1180304 TTTCCCCCCGGAAAAATGGCTATGTAGCA-GT
1 TTTCCCCCCGGAAAAATGACTATATAGCAGGT
* *
1180335 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGACTATATAGCAGGT
** **
1180367 TTTCCCCCACGGAAAGCTGACTATATAGTGGGT
1 TTTCCCCC-CGGAAAAATGACTATATAGCAGGT
1180400 TTTCCCCC
1 TTTCCCCC
1180408 TTTTTATAGC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 28 0.44
32 9 0.14
33 26 0.41
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGACTATATAGCAGGT
Found at i:1186839 original size:17 final size:17
Alignment explanation
Indices: 1186819--1186851 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1186809 AACCCTCAGT
1186819 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
1186836 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
1186852 ACAGAACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:1190758 original size:15 final size:15
Alignment explanation
Indices: 1190740--1190779 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1190730 GCACCTATTC
*
1190740 TGTTTCGC-CCTGAGA
1 TGTTTCGCACCTCA-A
1190755 TGTTTCGCACCTCAA
1 TGTTTCGCACCTCAA
1190770 TGTTTCGCAC
1 TGTTTCGCAC
1190780 TCTGATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.15, C:0.30, G:0.20, T:0.35
Consensus pattern (15 bp):
TGTTTCGCACCTCAA
Found at i:1193881 original size:15 final size:15
Alignment explanation
Indices: 1193861--1193891 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1193851 GTGTGTGGTC
1193861 ATCCCTGCTTGCGTT
1 ATCCCTGCTTGCGTT
*
1193876 ATCCCTGTTTGCGTT
1 ATCCCTGCTTGCGTT
1193891 A
1 A
1193892 ACGTTGGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.29, G:0.19, T:0.42
Consensus pattern (15 bp):
ATCCCTGCTTGCGTT
Found at i:1194821 original size:4 final size:4
Alignment explanation
Indices: 1194812--1194845 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1194802 AAACGTGACA
*
1194812 GACG GACG GACG GACG GACG GACA GACG GACG GA
1 GACG GACG GACG GACG GACG GACG GACG GACG GA
1194846 TGGAACAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.47, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:1194829 original size:12 final size:12
Alignment explanation
Indices: 1194808--1194845 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
1194798 AGTAAAACGT
1194808 GACAGACGGACG
1 GACAGACGGACG
*
1194820 GACGGACGGACG
1 GACAGACGGACG
1194832 GACAGACGGACG
1 GACAGACGGACG
1194844 GA
1 GA
1194846 TGGAACAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.32, C:0.24, G:0.45, T:0.00
Consensus pattern (12 bp):
GACAGACGGACG
Found at i:1198996 original size:166 final size:164
Alignment explanation
Indices: 1198715--1199449 Score: 709
Period size: 166 Copynumber: 4.5 Consensus size: 164
1198705 CACTATTCCC
* * ** * *
1198715 AAAAACCTTCTTCTCAAAAACTATTCGGCCAGGAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCACCCTCA-G
* * *
1198780 A-AGTGTGGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGAAGGGTGGGGCCACAATTGGGGG
65 ATAGTGTAGATTCAAGTTTGTTCAAATCATGGT-CCCAGGGGTAGGGTGGGGCCACAATTAGGGG
* *
1198844 ATCAAGTTTTACATAGGAATATATAGAAAAAATCTTT
129 AT-AATTTTTACATAGGAATATATAGAGAAAATCTTT
* * *
1198881 AAAAATGTTCTTCTCAAAAACTATTAGGCCCGGAAAGCTCAAATTTGAGTGGAAGCACCCTTAGA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCACCCTCAGA
* *
1198946 TAGTGTAGATTCAAGTTT-TTACAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAGTTAGGGG
66 TAGTGTAGATTCAAGTTTGTT-CAAATCATGGT-CCCAGGGGTAGGGTGGGGCCACAATTAGGGG
*
1199010 ATAAATTTTTATATAGGAATATATAGAGAAAATCTTT
129 AT-AATTTTTACATAGGAATATATAGAGAAAATCTTT
*** * * * * * * * *
1199047 AAAAAAAAATCTT-TTAAAAAC-ATTTTGGCCAAGAAAGCTCAAATTGGCGTGTAACCATCCTCA
1 -AAAAATCTTCTTCTCAAAAACTA-TTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCACCCTCA
*
1199110 GATTA-TGTAGATTCAAGTTTGTTCAAATCATGATCCCTA-GGGTAGGGTGGGGCCACAATT-GG
64 GA-TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCC-AGGGGTAGGGTGGGGCCACAATTAGG
* *
1199172 GGATAAATTTT---T----ATATAGAGAGAAAATCTTT
127 GGATAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * *
1199203 AAAAGTCTTCTTCTC-AAAACTATTAGGCAAGGAAAGCCCAAATTTGAGTGGAAGCATCCC-CAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCA-CCCTCAG
* * * * *
1199266 ATCA-TATAGATTCAAGTTTGTTTAAATAATAGT-CCAGGGGTAGGGTGAGGCCACAA-TAGGGG
65 AT-AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCAGGGGTAGGGTGGGGCCACAATTAGGGG
*
1199328 ATGAATTTTTACTTAGGAATATATAGAGAAAATCTTTT
129 AT-AATTTTTACATAGGAATATATAGAGAAAATC-TTT
* * * * * * * * * * **
1199366 AAAAATCTTCTTTTTAAAGAA-TATTTGGCCAGGTAAGCTTAAACTTGTGTAGAGGCAGCCTTGG
1 AAAAATCTTCTTCTCAAA-AACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCACCCTCAG
* *
1199430 GTAGTGTAAATTCAAGTTTG
65 ATAGTGTAGATTCAAGTTTG
1199450 CAAATTGGTA
Statistics
Matches: 467, Mismatches: 76, Indels: 54
0.78 0.13 0.09
Matches are distributed among these distances:
153 2 0.00
154 27 0.06
155 74 0.16
156 22 0.05
158 1 0.00
160 1 0.00
162 15 0.03
163 24 0.05
164 51 0.11
165 30 0.06
166 207 0.44
167 13 0.03
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (164 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCACCCTCAGA
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCAGGGGTAGGGTGGGGCCACAATTAGGGGAT
AATTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:1199057 original size:14 final size:15
Alignment explanation
Indices: 1199038--1199066 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1199028 ATATATAGAG
1199038 AAAATC-TTTAAAAA
1 AAAATCTTTTAAAAA
1199052 AAAATCTTTTAAAAA
1 AAAATCTTTTAAAAA
1199067 CATTTTGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATCTTTTAAAAA
Found at i:1201270 original size:15 final size:15
Alignment explanation
Indices: 1201250--1201279 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1201240 GTAAACTGAA
*
1201250 GCGTCCGGTTATCTG
1 GCGTCCGGATATCTG
1201265 GCGTCCGGATATCTG
1 GCGTCCGGATATCTG
1201280 AGGCCCCACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.27, G:0.33, T:0.30
Consensus pattern (15 bp):
GCGTCCGGATATCTG
Found at i:1201930 original size:15 final size:15
Alignment explanation
Indices: 1201910--1201940 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1201900 TATTTTCATA
1201910 TATTAAATCAATCTT
1 TATTAAATCAATCTT
1201925 TATTAAATCAATCTT
1 TATTAAATCAATCTT
1201940 T
1 T
1201941 TAAAATCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTAAATCAATCTT
Found at i:1203859 original size:168 final size:164
Alignment explanation
Indices: 1203488--1204026 Score: 751
Period size: 166 Copynumber: 3.2 Consensus size: 164
1203478 TGACCTTAAN
* * *
1203488 CACTACCTGAGGATG-TTTCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGA
1 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTAGCTGATTAGTTTCTGAGAAGAATA
* * * * *
1203552 TTTTTAAAGATTTACTCTATATATTACTTTGTGAATTTTCGA-CCTCCAATTGTGGCCCCACCCT
66 -TTTTAAAGATTTACTCTATATATTCCTTTGTAAACTTT-GACCCCCCCATTGTGGCCCCACCCT
1203616 ACACCCAGGGGTCATGATTTTCCCAACTTTGAATCTA
129 AC-CCCAGGGGTCATGATTTTCCCAACTTTGAATCTA
* * * *
1203653 CATTACCTGATGATGCTTCCACATAAGTTTCAGCTTTCCTTGCTGATTAGTTTCTGAGAAGAATA
1 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTAGCTGATTAGTTTCTGAGAAGAATA
* *
1203718 GTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCCCCA-TGTGGCCCAACC
66 -TTTTAAAGATTTACTCTATATATTCCTTTGT-AAACTTTGA--CCCCCCCATTGTGGCCCCACC
* *
1203782 CTACCCCAGGGGATCATGACTTTCACAACTTTGAATCTA
127 CTACCCCAGGGG-TCATGATTTTCCCAACTTTGAATCTA
* * * * *
1203821 CACTACCTAAGGATGTTTCCACACAAGTTTTAGCTTTCCCAGCTGATCAGTTTCTGAGAAGAATA
1 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTAGCTGATTAGTTTCTGAGAAGAATA
* *
1203886 TTTTAAAAGATTTACTCTATATATCCCTTTGTTAAACTATGACCCCCCCATTGTGGCCCCACCCT
66 TTTT-AAAGATTTACTCTATATATTCCTTTG-TAAACTTTGACCCCCCCATTGTGGCCCCACCCT
*
1203951 ACCCCTGGGGTCATGATTTTCCCAACTTTGAATCTA
129 ACCCCAGGGGTCATGATTTTCCCAACTTTGAATCTA
1203987 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCT
1 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCT
1204027 GGCTTAATGG
Statistics
Matches: 329, Mismatches: 36, Indels: 17
0.86 0.09 0.04
Matches are distributed among these distances:
165 13 0.04
166 144 0.44
167 39 0.12
168 127 0.39
169 6 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (164 bp):
CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTAGCTGATTAGTTTCTGAGAAGAATA
TTTTAAAGATTTACTCTATATATTCCTTTGTAAACTTTGACCCCCCCATTGTGGCCCCACCCTAC
CCCAGGGGTCATGATTTTCCCAACTTTGAATCTA
Found at i:1205848 original size:11 final size:11
Alignment explanation
Indices: 1205832--1205857 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1205822 AAAAATGAGA
1205832 TCAAATTTCGG
1 TCAAATTTCGG
1205843 TCAAATTTCGG
1 TCAAATTTCGG
1205854 TCAA
1 TCAA
1205858 TAATCATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (11 bp):
TCAAATTTCGG
Found at i:1234794 original size:13 final size:13
Alignment explanation
Indices: 1234772--1234808 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1234762 TTAGAGGATG
*
1234772 ATTTTCTATTTTT
1 ATTTTTTATTTTT
1234785 ATTTTTTATTTTT
1 ATTTTTTATTTTT
*
1234798 ATTATTTATTT
1 ATTTTTTATTT
1234809 GATTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:1264833 original size:11 final size:11
Alignment explanation
Indices: 1264817--1264856 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1264807 TAAGCAAGTC
1264817 CTTAAAGGTGG
1 CTTAAAGGTGG
*
1264828 CTTAAAGGTGA
1 CTTAAAGGTGG
*
1264839 CTTAAAGG-AG
1 CTTAAAGGTGG
1264849 CTTAAAGG
1 CTTAAAGG
1264857 CTATACAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:1264961 original size:10 final size:11
Alignment explanation
Indices: 1264926--1264965 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
1264916 TGTCCAAACT
1264926 TCTTTAAGCCA
1 TCTTTAAGCCA
*
1264937 CCTTTAAGCCA
1 TCTTTAAGCCA
1264948 TCTTTAAG-CA
1 TCTTTAAGCCA
1264958 TCTTTAAG
1 TCTTTAAG
1264966 TGGCATTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (11 bp):
TCTTTAAGCCA
Found at i:1265015 original size:22 final size:22
Alignment explanation
Indices: 1264958--1265018 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1264948 TCTTTAAGCA
* *
1264958 TCTTTAAGTGGCATTTACGCTC
1 TCTTTAAGTGGCCTTTACACTC
* *
1264980 TCTTTACACT-GCCTTTACACTG
1 TCTTTA-AGTGGCCTTTACACTC
1265002 TCTTTAAGTGGCCTTTA
1 TCTTTAAGTGGCCTTTA
1265019 AGTCAATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43
Consensus pattern (22 bp):
TCTTTAAGTGGCCTTTACACTC
Found at i:1265352 original size:2 final size:2
Alignment explanation
Indices: 1265347--1265388 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1265337 GTGTAAAAAA
1265347 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1265389 AGTTCATCCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1265800 original size:112 final size:112
Alignment explanation
Indices: 1265603--1265825 Score: 428
Period size: 112 Copynumber: 2.0 Consensus size: 112
1265593 AGTTTTGTTC
*
1265603 GTTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
*
1265668 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCAT
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
1265715 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1265780 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
1265826 CGTCAGGGTT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (112 bp):
GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
Found at i:1266853 original size:11 final size:11
Alignment explanation
Indices: 1266837--1266978 Score: 150
Period size: 11 Copynumber: 12.9 Consensus size: 11
1266827 TTTTTTTTAA
1266837 TGGCTTAAAGG
1 TGGCTTAAAGG
1266848 TGGCTTAAAGG
1 TGGCTTAAAGG
*
1266859 TAGCTTAAAGG
1 TGGCTTAAAGG
1266870 TGGCTTAAAGG
1 TGGCTTAAAGG
1266881 TGGCTTAAAGG
1 TGGCTTAAAGG
1266892 TGGCTTAAAGG
1 TGGCTTAAAGG
* *
1266903 TGGCGACCTATAAGT
1 T-G-G-CTTA-AAGG
*
1266918 TGTCCTTAAAGG
1 TG-GCTTAAAGG
1266930 TGGCTTAAAGG
1 TGGCTTAAAGG
*
1266941 T-G----NAGG
1 TGGCTTAAAGG
*
1266947 TAGCTTAAAGG
1 TGGCTTAAAGG
1266958 TGGCTTAAAGG
1 TGGCTTAAAGG
1266969 TGGCTTAAAG
1 TGGCTTAAAG
1266979 AAGTTTGGAC
Statistics
Matches: 110, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
6 4 0.04
7 1 0.01
10 1 0.01
11 86 0.78
12 6 0.05
13 4 0.04
14 4 0.04
15 4 0.04
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.27
Consensus pattern (11 bp):
TGGCTTAAAGG
Found at i:1266963 original size:88 final size:85
Alignment explanation
Indices: 1266856--1267027 Score: 235
Period size: 88 Copynumber: 2.0 Consensus size: 85
1266846 GGTGGCTTAA
1266856 AGGTAGCTTAAAGGTGGCTTAAAGGTGGCTTAAAG-G-TGG-C-TTAAAGGTGGCGACCTATAAG
1 AGGTAGCTTAAAGGTGGCTTAAAGGTGGCTTAAAGAGTTGGACATT-AA----G-GACCTATAAG
1266917 TTGTCCTTAAAGGTGGCTTAAAGGTG
60 TTGTCCTTAAAGGTGGCTTAAAGGTG
1266943 NAGGTAGCTTAAAGGTGGCTTAAAGGTGGCTTAAAGAAGTTTGGACATTAAGGACCTATAAGTTG
1 -AGGTAGCTTAAAGGTGGCTTAAAGGTGGCTTAAAG-AG-TTGGACATTAAGGACCTATAAGTTG
1267008 TCCTTAAAGGTGGCTTAAAG
63 TCCTTAAAGGTGGCTTAAAG
1267028 ATTGCCTTTA
Statistics
Matches: 78, Mismatches: 0, Indels: 12
0.87 0.00 0.13
Matches are distributed among these distances:
88 68 0.87
89 1 0.01
90 1 0.01
92 3 0.04
93 3 0.04
94 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (85 bp):
AGGTAGCTTAAAGGTGGCTTAAAGGTGGCTTAAAGAGTTGGACATTAAGGACCTATAAGTTGTCC
TTAAAGGTGGCTTAAAGGTG
Found at i:1267068 original size:11 final size:11
Alignment explanation
Indices: 1267033--1267073 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1267023 TAAAGATTGC
1267033 CTTTAAGCCAT
1 CTTTAAGCCAT
* **
1267044 CTTTACGCTTT
1 CTTTAAGCCAT
1267055 CTTTAAGCCAT
1 CTTTAAGCCAT
1267066 CTTTAAGC
1 CTTTAAGC
1267074 AACACATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (11 bp):
CTTTAAGCCAT
Found at i:1267098 original size:11 final size:11
Alignment explanation
Indices: 1267082--1267113 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1267072 GCAACACATA
1267082 TAGCTTAAAGG
1 TAGCTTAAAGG
1267093 TAGCTTAAAGG
1 TAGCTTAAAGG
*
1267104 TGGCTTAAAG
1 TAGCTTAAAG
1267114 ATCGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCTTAAAGG
Found at i:1267144 original size:21 final size:21
Alignment explanation
Indices: 1267118--1267157 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1267108 TTAAAGATCG
1267118 TCTTTAAGCTACCTTTAAGCA
1 TCTTTAAGCTACCTTTAAGCA
*
1267139 TCTTTAAGCTATCTTTAAG
1 TCTTTAAGCTACCTTTAAG
1267158 GAGAACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (21 bp):
TCTTTAAGCTACCTTTAAGCA
Found at i:1267145 original size:10 final size:11
Alignment explanation
Indices: 1267118--1267157 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
1267108 TTAAAGATCG
1267118 TCTTTAAGCTA
1 TCTTTAAGCTA
*
1267129 CCTTTAAGC-A
1 TCTTTAAGCTA
1267139 TCTTTAAGCTA
1 TCTTTAAGCTA
1267150 TCTTTAAG
1 TCTTTAAG
1267158 GAGAACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (11 bp):
TCTTTAAGCTA
Found at i:1272084 original size:27 final size:27
Alignment explanation
Indices: 1272054--1272310 Score: 113
Period size: 27 Copynumber: 9.4 Consensus size: 27
1272044 ACTTCTAAAG
*
1272054 CACACAGTCAACTGAGCACATCTGGCA
1 CACACAGTCAACTGAGCACGTCTGGCA
** * * * ***
1272081 CACACAGTCATTTCAACACGTATAATA
1 CACACAGTCAACTGAGCACGTCTGGCA
* * * * *
1272108 CACACAGCCAACTAAGCACATTTTGCA
1 CACACAGTCAACTGAGCACGTCTGGCA
* * **
1272135 CACACAGCATCAACTGAACACTTCT-AAA
1 CACACAG--TCAACTGAGCACGTCTGGCA
1272163 GCACACAGTCAACTGAGCACGTCTGGCA
1 -CACACAGTCAACTGAGCACGTCTGGCA
* ** * * * ***
1272191 CACACAATCATTTCAACACGTATAATA
1 CACACAGTCAACTGAGCACGTCTGGCA
* * * * *
1272218 CACACAGCCAACTAAGCACATTTTGCA
1 CACACAGTCAACTGAGCACGTCTGGCA
* * **
1272245 CACACAGCATCAACTGAACACTTCT-AAA
1 CACACAG--TCAACTGAGCACGTCTGGCA
*
1272273 GCACACAGTCAACTCAGCACGTCTGGCA
1 -CACACAGTCAACTGAGCACGTCTGGCA
1272301 CACACAGTCA
1 CACACAGTCA
1272311 TTTCAACACG
Statistics
Matches: 160, Mismatches: 62, Indels: 16
0.67 0.26 0.07
Matches are distributed among these distances:
27 120 0.75
28 4 0.03
29 36 0.22
ACGTcount: A:0.37, C:0.32, G:0.12, T:0.18
Consensus pattern (27 bp):
CACACAGTCAACTGAGCACGTCTGGCA
Found at i:1272112 original size:54 final size:53
Alignment explanation
Indices: 1272049--1272362 Score: 288
Period size: 54 Copynumber: 5.7 Consensus size: 53
1272039 TGAACACTTC
*
1272049 TAAAGCACACAGTCAACTGAGCACATCTGGCACACACAGTCATTTCAACACGTA
1 TAAA-CACACAGTCAACTAAGCACATCTGGCACACACAGTCATTTCAACACGTA
* * * ** * * *
1272103 TAATACACACAGCCAACTAAGCACATTTTGCACACACAGCATCAACTGAACACTTC
1 TAA-ACACACAGTCAACTAAGCACATCTGGCACACACAG--TCATTTCAACACGTA
* * *
1272159 TAAAGCACACAGTCAACTGAGCACGTCTGGCACACACAATCATTTCAACACGTA
1 TAAA-CACACAGTCAACTAAGCACATCTGGCACACACAGTCATTTCAACACGTA
* * * ** * * *
1272213 TAATACACACAGCCAACTAAGCACATTTTGCACACACAGCATCAACTGAACACTTC
1 TAA-ACACACAGTCAACTAAGCACATCTGGCACACACAG--TCATTTCAACACGTA
* *
1272269 TAAAGCACACAGTCAACTCAGCACGTCTGGCACACACAGTCATTTCAACACGTA
1 TAAA-CACACAGTCAACTAAGCACATCTGGCACACACAGTCATTTCAACACGTA
* * * *
1272323 CAACACACACAG-CAAACTAAACACATTTAGCACACACAGT
1 TAA-ACACACAGTC-AACTAAGCACATCTGGCACACACAGT
1272363 ATCAACTGAA
Statistics
Matches: 203, Mismatches: 47, Indels: 20
0.75 0.17 0.07
Matches are distributed among these distances:
53 1 0.00
54 114 0.56
55 5 0.02
56 83 0.41
ACGTcount: A:0.39, C:0.31, G:0.12, T:0.18
Consensus pattern (53 bp):
TAAACACACAGTCAACTAAGCACATCTGGCACACACAGTCATTTCAACACGTA
Found at i:1272219 original size:110 final size:110
Alignment explanation
Indices: 1272039--1272415 Score: 637
Period size: 110 Copynumber: 3.4 Consensus size: 110
1272029 CACTATCCAT
*
1272039 TGAACACTTCTAAAGCACACAGTCAACTGAGCACATCTGGCACACACAGTCATTTCAACACGTAT
1 TGAACACTTCTAAAGCACACAGTCAACTGAGCACGTCTGGCACACACAGTCATTTCAACACGTAT
1272104 AATACACACAGCCAACTAAGCACATTTTGCACACACAGCATCAAC
66 AATACACACAGCCAACTAAGCACATTTTGCACACACAGCATCAAC
*
1272149 TGAACACTTCTAAAGCACACAGTCAACTGAGCACGTCTGGCACACACAATCATTTCAACACGTAT
1 TGAACACTTCTAAAGCACACAGTCAACTGAGCACGTCTGGCACACACAGTCATTTCAACACGTAT
1272214 AATACACACAGCCAACTAAGCACATTTTGCACACACAGCATCAAC
66 AATACACACAGCCAACTAAGCACATTTTGCACACACAGCATCAAC
* *
1272259 TGAACACTTCTAAAGCACACAGTCAACTCAGCACGTCTGGCACACACAGTCATTTCAACACGTAC
1 TGAACACTTCTAAAGCACACAGTCAACTGAGCACGTCTGGCACACACAGTCATTTCAACACGTAT
* * * * *
1272324 AACACACACAGCAAACTAAACACATTTAGCACACACAGTATCAAC
66 AATACACACAGCCAACTAAGCACATTTTGCACACACAGCATCAAC
* * * *
1272369 TGAACCCTTCTAAAGCACACAGTCAACTAAGCACGCCTGACACACAC
1 TGAACACTTCTAAAGCACACAGTCAACTGAGCACGTCTGGCACACAC
1272416 TGACATATGA
Statistics
Matches: 253, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 253 1.00
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (110 bp):
TGAACACTTCTAAAGCACACAGTCAACTGAGCACGTCTGGCACACACAGTCATTTCAACACGTAT
AATACACACAGCCAACTAAGCACATTTTGCACACACAGCATCAAC
Found at i:1275062 original size:2 final size:2
Alignment explanation
Indices: 1275055--1275093 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1275045 AGAGAAGTCA
1275055 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1275094 GGAACATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1275477 original size:18 final size:18
Alignment explanation
Indices: 1275454--1275488 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1275444 CCCACAATCA
*
1275454 ATATACTAGTATTCAAAT
1 ATATACTAGTACTCAAAT
*
1275472 ATATACTGGTACTCAAA
1 ATATACTAGTACTCAAA
1275489 AGTGAATATG
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:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (18 bp):
ATATACTAGTACTCAAAT
Found at i:1276866 original size:13 final size:13
Alignment explanation
Indices: 1276848--1276882 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1276838 GGGATGAAAA
*
1276848 TAAATTTGAAATG
1 TAAATTTAAAATG
1276861 TAAATTTAAAATG
1 TAAATTTAAAATG
1276874 TAAATTTAA
1 TAAATTTAA
1276883 TAAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (13 bp):
TAAATTTAAAATG
Found at i:1277837 original size:22 final size:22
Alignment explanation
Indices: 1277811--1277856 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1277801 AAATGAACAG
1277811 TTTGCACATATAAATATCATTT
1 TTTGCACATATAAATATCATTT
1277833 TTTGCACATATAAATATCATTT
1 TTTGCACATATAAATATCATTT
1277855 TT
1 TT
1277857 AAAAAGCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.48
Consensus pattern (22 bp):
TTTGCACATATAAATATCATTT
Found at i:1283889 original size:13 final size:13
Alignment explanation
Indices: 1283873--1283898 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1283863 TAGAGGGAAA
1283873 ATGTTGAAAAATC
1 ATGTTGAAAAATC
1283886 ATGTTGAAAAATC
1 ATGTTGAAAAATC
1283899 TTTTTCTAGG
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTTGAAAAATC
Found at i:1283949 original size:17 final size:17
Alignment explanation
Indices: 1283927--1283959 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1283917 CTGGTACTGT
1283927 ACCAGTTATCGGCTAAG
1 ACCAGTTATCGGCTAAG
1283944 ACCAGTTATCGGCTAA
1 ACCAGTTATCGGCTAA
1283960 AATGAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (17 bp):
ACCAGTTATCGGCTAAG
Found at i:1285850 original size:1 final size:1
Alignment explanation
Indices: 1285844--1285869 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1285834 TATCCCGTTT
1285844 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
1285870 TAGCGTGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1286404 original size:105 final size:100
Alignment explanation
Indices: 1286223--1286431 Score: 346
Period size: 105 Copynumber: 2.0 Consensus size: 100
1286213 TGTGTTTTTC
1286223 TAATCTAATAAATTGATGTACATGTAAGATACCATGCTCGGTTTTATAAAAAAAATATTTAATGT
1 TAATCTAATAAATTGATGTACATGTAAGATACCATGCTCGGTTTTATAAAAAAAATATTTAATGT
1286288 ATTTGATTTAATGCCTTGCCGGTTAAGTTTTGTAA
66 ATTTGATTTAATGCCTTGCCGGTTAAGTTTTGTAA
* *
1286323 TAATCTAATAAATTGATTTTCATGTAAGATACCATGCATACTCGGTTTTATAAAAAAAATATTTA
1 TAATCTAATAAATTGATGTACATGTAAGATACCATG----CTCGGTTTTATAAAAAAAATATTTA
*
1286388 ATTGTATTTGATTTAATGCCTTGCTGGTTAAGTTTTGTAA
62 A-TGTATTTGATTTAATGCCTTGCCGGTTAAGTTTTGTAA
1286428 TAAT
1 TAAT
1286432 GACATTTAGT
Statistics
Matches: 101, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
100 34 0.34
104 26 0.26
105 41 0.41
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.42
Consensus pattern (100 bp):
TAATCTAATAAATTGATGTACATGTAAGATACCATGCTCGGTTTTATAAAAAAAATATTTAATGT
ATTTGATTTAATGCCTTGCCGGTTAAGTTTTGTAA
Found at i:1286682 original size:2 final size:2
Alignment explanation
Indices: 1286677--1286719 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1286667 GGCATATATA
*
1286677 CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1286719 C
1 C
1286720 CTCATAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1287259 original size:42 final size:42
Alignment explanation
Indices: 1287200--1287419 Score: 359
Period size: 42 Copynumber: 5.2 Consensus size: 42
1287190 ATTAAGTGAC
*
1287200 CTCAGGGTTTACTCAGTACCCCCAGTGCCGACCTCAGGGTCT
1 CTCAGGGTTTACTCAGTACCCTCAGTGCCGACCTCAGGGTCT
*
1287242 CTCAGGGTTTACTCAGTACCCTCAGTGTCGACCTCAGGGTCT
1 CTCAGGGTTTACTCAGTACCCTCAGTGCCGACCTCAGGGTCT
* *
1287284 CTCAGGGTTAACTCAGTACCCTCAGTGCCGACCTCAGAGTCT
1 CTCAGGGTTTACTCAGTACCCTCAGTGCCGACCTCAGGGTCT
* **
1287326 CTCAGGGTTTCCTCAGTACCCTCAGTGCAAACCTCAGGGTCT
1 CTCAGGGTTTACTCAGTACCCTCAGTGCCGACCTCAGGGTCT
**
1287368 CTCAGGGTTTACTCAGTACCCTCAGTGCAAACCTCAGGGTCT
1 CTCAGGGTTTACTCAGTACCCTCAGTGCCGACCTCAGGGTCT
1287410 CTCAGGGTTT
1 CTCAGGGTTT
1287420 TTCTCAGTGC
Statistics
Matches: 167, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 167 1.00
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (42 bp):
CTCAGGGTTTACTCAGTACCCTCAGTGCCGACCTCAGGGTCT
Found at i:1287414 original size:22 final size:22
Alignment explanation
Indices: 1287346--1287414 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
1287336 CCTCAGTACC
1287346 CTCAGTGCAAACCTCAGGGTCT
1 CTCAGTGCAAACCTCAGGGTCT
* *** *
1287368 CTCAGGGTTTA-CTCA--GTACC
1 CTCAGTGCAAACCTCAGGGT-CT
1287388 CTCAGTGCAAACCTCAGGGTCT
1 CTCAGTGCAAACCTCAGGGTCT
1287410 CTCAG
1 CTCAG
1287415 GGTTTTTCTC
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 2 0.06
20 8 0.24
21 8 0.24
22 13 0.39
23 2 0.06
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.25
Consensus pattern (22 bp):
CTCAGTGCAAACCTCAGGGTCT
Found at i:1287425 original size:22 final size:21
Alignment explanation
Indices: 1287399--1287450 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
1287389 TCAGTGCAAA
1287399 CCTCAGGGTCTCTCAGGGTTTT
1 CCTCAGGGTCTCTCAGGG-TTT
* * *
1287421 TCTCAGTGCCTCTCAGGGTTT
1 CCTCAGGGTCTCTCAGGGTTT
1287442 CCTCAGGGT
1 CCTCAGGGT
1287451 TTTTTTGATA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.10, C:0.29, G:0.27, T:0.35
Consensus pattern (21 bp):
CCTCAGGGTCTCTCAGGGTTT
Found at i:1303716 original size:13 final size:12
Alignment explanation
Indices: 1303698--1303744 Score: 62
Period size: 11 Copynumber: 4.0 Consensus size: 12
1303688 CACGTAGACC
1303698 CTGGGTTTACTTT
1 CTGGGTTTAC-TT
1303711 CTGGGTTTACTT
1 CTGGGTTTACTT
*
1303723 -TGGGTTTACTC
1 CTGGGTTTACTT
1303734 CT-GGTTTACTT
1 CTGGGTTTACTT
1303745 TTTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 18 0.58
12 3 0.10
13 10 0.32
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (12 bp):
CTGGGTTTACTT
Found at i:1303742 original size:22 final size:24
Alignment explanation
Indices: 1303699--1303745 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
1303689 ACGTAGACCC
*
1303699 TGGGTTTACTTTCTGGGTTTACTT
1 TGGGTTTACTTCCTGGGTTTACTT
1303723 TGGGTTTAC-TCCT-GGTTTACTT
1 TGGGTTTACTTCCTGGGTTTACTT
1303745 T
1 T
1303746 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.45
23 3 0.14
24 9 0.41
ACGTcount: A:0.09, C:0.15, G:0.23, T:0.53
Consensus pattern (24 bp):
TGGGTTTACTTCCTGGGTTTACTT
Found at i:1303781 original size:22 final size:22
Alignment explanation
Indices: 1303756--1303806 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1303746 TTAAAAAAAA
*
1303756 TTGGGTTCACTCAAGGTTTACT
1 TTGGGTTCACCCAAGGTTTACT
* **
1303778 TTGGGTTTACCCGGGGTTTACT
1 TTGGGTTCACCCAAGGTTTACT
1303800 TTGGGTT
1 TTGGGTT
1303807 TTGCTCGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.12, C:0.16, G:0.29, T:0.43
Consensus pattern (22 bp):
TTGGGTTCACCCAAGGTTTACT
Found at i:1304047 original size:11 final size:11
Alignment explanation
Indices: 1304029--1304062 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1304019 GGTCCACTCT
*
1304029 AGTAAACCCGG
1 AGTAAACCCAG
*
1304040 ATTAAACCCAG
1 AGTAAACCCAG
1304051 AGTAAACCCAG
1 AGTAAACCCAG
1304062 A
1 A
1304063 AAATAAACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.12
Consensus pattern (11 bp):
AGTAAACCCAG
Found at i:1306938 original size:4 final size:4
Alignment explanation
Indices: 1306931--1306965 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1306921 TTTTGTTTGT
*
1306931 CGTC CGTC CGTC CGTC TG-C CGTC CGTC CGTC CGTC
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
1306966 AACTTTTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 26 0.93
ACGTcount: A:0.00, C:0.49, G:0.26, T:0.26
Consensus pattern (4 bp):
CGTC
Found at i:1307426 original size:175 final size:163
Alignment explanation
Indices: 1307269--1307796 Score: 470
Period size: 163 Copynumber: 3.3 Consensus size: 163
1307259 GGGGGGGGGA
*
1307269 GGTCGAATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTT-CTAATCAAGAACCATTT
1 GGTCGAATTTTAAATAGGAATATATAGAG-AAATCTTTAAAAATCTTCCT-ATCAAGAACCATTT
* * * *
1307333 AGCCAGGAAAACTGAAACTTGTGTGGAAGAATCCTCAGATAGTGTAGATTTAAAGTTGGGAAAAT
64 AGCCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGCGAAAAT
* * *
1307398 TATTACCCCCGGGGGTATGGTTGGGCCACAATGGG
129 TATGACCCCAGGGGGTATGGTGGGGCCACAATGGG
* * *
1307433 GGTCGAATTTTAAATAGGTATATATTGAGAAATCTTTAAAAATCTTCCTCTCAAGAACCATTTAG
1 GGTCGAATTTTAAATAGGAATATATAGAGAAATCTTTAAAAATCTTCCTATCAAGAACCATTTAG
* * * * * ** *
1307498 CCAGGAAAGCTGAAATTTGTGTGGACGCATTCTCGGGTAGTGTAGATTCAAAACTGTGAAAATTA
66 CCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGCGAAAATTA
* *
1307563 TGACCACTGGGGGT-TGGTGGGG------T---
131 TGACCCCAGGGGGTATGGTGGGGCCACAATGGG
* * ** * * * *
1307586 -GTCGAATTTCACATAGGAATATATAGAGTACTTGTTTAAAAATCTTCTTCTCAAGAACCATTTG
1 GGTCGAATTTTAAATAGGAATATATAGAG-AAATCTTTAAAAATCTTCCTATCAAGAACCATTTA
** * * * * *
1307650 GTTAGGAAAGAAT-AAACTTATGTTGAAGCATCCTCAGGTAGTGTAGAATCAAAGTTGTGAAAAT
65 GCCAGGAAA-ACTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGCGAAAAT
* * * * * *
1307714 CATGACTCCTGGGGGTATGATGGAGCAACAATTGGG
129 TATGACCCCAGGGGGTATGGTGGGGCCACAA-TGGG
* * * * *
1307750 GGTCAAATTTTTACATAGGAGTATATAGTGAACAGTCTTTTAAAATC
1 GGTCGAA-TTTTAAATAGGAATATATAGAGAA-A-TCTTTAAAAATC
1307797 GTCTTCTCAG
Statistics
Matches: 292, Mismatches: 54, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
152 24 0.08
153 92 0.32
154 7 0.02
156 1 0.00
161 1 0.00
162 7 0.02
163 97 0.33
164 28 0.10
165 6 0.02
166 19 0.07
167 10 0.03
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (163 bp):
GGTCGAATTTTAAATAGGAATATATAGAGAAATCTTTAAAAATCTTCCTATCAAGAACCATTTAG
CCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGCGAAAATTA
TGACCCCAGGGGGTATGGTGGGGCCACAATGGG
Found at i:1309085 original size:5 final size:5
Alignment explanation
Indices: 1309075--1309125 Score: 70
Period size: 5 Copynumber: 10.4 Consensus size: 5
1309065 ATGAAAATTG
*
1309075 TATAA TATAA TATAA TATAA TGA-AA TATAA TATAA GATAA TA-AA TATAA
1 TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA TATAA TATAA
1309124 TA
1 TA
1309126 ATTGTACTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 5 0.12
5 35 0.85
6 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (5 bp):
TATAA
Found at i:1309103 original size:20 final size:19
Alignment explanation
Indices: 1309078--1309125 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
1309068 AAAATTGTAT
*
1309078 AATATAATATAATATAATGA
1 AATATAATATAAGATAAT-A
1309098 AATATAATATAAGATAATA
1 AATATAATATAAGATAATA
1309117 AATATAATA
1 AATATAATA
1309126 ATTGTACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AATATAATATAAGATAATA
Found at i:1309476 original size:5 final size:5
Alignment explanation
Indices: 1309466--1309512 Score: 78
Period size: 5 Copynumber: 9.4 Consensus size: 5
1309456 TCAATATTTG
1309466 TATAA TATAA TGA-AA TATAA TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA T-ATAA TATAA TATAA TATAA TATAA TATAA TATAA TA
1309513 GTTGTACTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 1 0.03
5 38 0.95
6 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:1310542 original size:165 final size:164
Alignment explanation
Indices: 1310161--1311175 Score: 969
Period size: 165 Copynumber: 6.1 Consensus size: 164
1310151 ATTTTTAAAG
1310161 AAATC-TTAAAACAT-TTCCTTCTCAAGAACCATTTGGCCAGAAAAGCTGAAACTTGTGTGGGAG
1 AAATCTTTAAAA-ATCTT-CTTCTCAAGAACCATTTGGCCAGAAAA-CTGAAACTTGTGT-GGAG
** * * * * * *
1310224 CATCCTCAGGTAAAGTAAATTCAAGGCTGTGAAAACCATGACCCCTGGGGGTGGGGTGGGGCAAC
62 CATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCAC
*
1310289 AATGGGAGGGGGAGGTCGAATTTTACATAGGAATATATAGAGT
127 AAT----GGGGG-TGTCGAATTTTACATAGGAATATATAGAGT
*
1310332 AAATCTTTAAAAATCTTCTTATCAAGAACCATTTGGCCAGGAAAACTGAAACTTGTGTGCGAGCA
1 AAATCTTTAAAAATCTTCTTCTCAAGAACCATTTGGCCA-GAAAACTGAAACTTGTGTG-GAGCA
* * *
1310397 TCCTCAGATAGTGTAAATTTATAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAA
64 TCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAA
*
1310462 T-GGGGTGTCGAATTTTACATAGGTATATATAGAGT
129 TGGGGGTGTCGAATTTTACATAGGAATATATAGAGT
*
1310497 AAATCTTTAAAAATCTTCTTATCAAGAACCATTTGGCCAGGAAAACTGAAACTTGTGTGCGAGCA
1 AAATCTTTAAAAATCTTCTTCTCAAGAACCATTTGGCCA-GAAAACTGAAACTTGTGTG-GAGCA
* * *
1310562 TCCTCAGATAGTGTAAATTTATAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAA
64 TCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAA
*
1310627 T-GGGGTGTCGAATTTTACATAGGTATATATAGAGT
129 TGGGGGTGTCGAATTTTACATAGGAATATATAGAGT
*
1310662 AAATCTTTAAAAATCTTCCTCTCAAG-A--A-----CCAG----CTGAAACTTGTGTGGAAGCAT
1 AAATCTTTAAAAATCTTCTTCTCAAGAACCATTTGGCCAGAAAACTGAAACTTGTGTGG-AGCAT
* * ** * * * *
1310715 TCTCGGGTAGTGTTGATTCAAAATTGTGTAAATCATGACCCCCTGTGGTAGGGTGGGGCCACAAT
65 CCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAT
* *
1310780 GGGGGTGGCGAATTTCACATAGGAATATATAGAGT
130 GGGGGTGTCGAATTTTACATAGGAATATATAGAGT
* * * *
1310815 -AAT-TTTAAAAAAATCGTCTTCTCAAGAACCATTTGGTCAAAAAAGCTGAAACTTATGTGGAAG
1 AAATCTTT--AAAAATCTTCTTCTCAAGAACCATTTGGCCAGAAAA-CTGAAACTTGTGTGG-AG
* * * * * * * *
1310878 CATCCTCAGGTAGGGTAAATTCAAAATTGTGTAAATCATGACCCCCGGGAGTATGTTGCGGCAAC
62 CATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCAC
* * * *
1310943 AAAGGGGTGGGGGGGGGTCGGATTTTACATAAGAATATATAGAGA
127 -AA----T--GGGGGTGTCGAATTTTACATAGGAATATATAGAGT
* * * *** * *
1310988 AAATATTTGAAAA-C--CTTCTC-AGAAACCAATCAACCACGAAAGCTGAAACTTATGTGGAAGC
1 AAATCTTTAAAAATCTTCTTCTCAAG-AACCATTTGGCCA-GAAAACTGAAACTTGTGTGG-AGC
* * * * * * * * *
1311049 ATTCTCAGTTATTGTAGATTCAAAGTTGTGAAAATTATGACCCCTGGGGGTATGATGAGGCCACA
63 ATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACA
* * * * *
1311114 ATAGGGG-GTCAAATTTTTACATAGGAGTATATAGTGA
128 ATGGGGGTGTCGAA-TTTTACATAGGAATATATAGAGT
* *
1311151 ACAATTTTTTAAAATCTTCTTCTCA
1 A-AATCTTTAAAAATCTTCTTCTCA
1311176 GAAACTAATT
Statistics
Matches: 724, Mismatches: 82, Indels: 79
0.82 0.09 0.09
Matches are distributed among these distances:
151 4 0.01
152 76 0.10
153 47 0.06
154 1 0.00
156 2 0.00
157 3 0.00
161 2 0.00
162 5 0.01
163 25 0.03
164 11 0.02
165 219 0.30
166 74 0.10
167 8 0.01
169 4 0.01
170 85 0.12
171 105 0.15
172 14 0.02
173 33 0.05
174 3 0.00
175 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (164 bp):
AAATCTTTAAAAATCTTCTTCTCAAGAACCATTTGGCCAGAAAACTGAAACTTGTGTGGAGCATC
CTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATG
GGGGTGTCGAATTTTACATAGGAATATATAGAGT
Found at i:1310898 original size:318 final size:322
Alignment explanation
Indices: 1310178--1311175 Score: 908
Period size: 336 Copynumber: 3.0 Consensus size: 322
1310168 AAAACATTTC
*
1310178 CTTCTCAAGAACCATTTGGCCAGAAAAGCTGAAACTTGTGTGGGAGCATCCTCAGGTAAAGTAAA
1 CTTCTCAAGAACCATTTGGCCAGAAAAGCTGAAACTTGTGT-GGAGCATCCTCAGGTAGAGTAAA
* * * *
1310243 TTCAAGGCTGTGAAAACCATGACCCCTGGGGGTGGGGTGGGGCAACAATGGGAGGGGGAGGTCGA
65 TTCAA-GTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCAACAAT----GGGGGAGGTCGA
*
1310308 ATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTATCAAGAACCATTTGGCCAGG
125 ATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCCTATCAAGAA-CA--T--CCAGG
* * *
1310373 AAAACTGAAACTTGTGTGCGAGCATCCTCAGATAGTGTAAATTTATAGTTGTGAAAATCATGACC
185 ---ACTGAAACTTGTGTGCGAGCATCCTCAGATAGTGTAAATTCAAAATTGTGAAAATCATGACC
* * *
1310438 CCCGGGGGTAGGGTGGGGCCACAATGGGGTGTCGAATTTTACATAGGTATATATAGAGTAAATCT
247 CCCGGGGGTAGGGTGGGGCCACAATGGGGTGGCGAATTTCACATAGGAATATATAGAGTAAATCT
*
1310503 TTAAAAATCTT
312 TTAAAAATCGT
* * *
1310514 CTTATCAAGAACCATTTGGCCAGGAAAA-CTGAAACTTGTGTGCGAGCATCCTCAGATAGTGTAA
1 CTTCTCAAGAACCATTTGGCCA-GAAAAGCTGAAACTTGTGTG-GAGCATCCTCAGGTAGAGTAA
* * *
1310578 ATTTATAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAT-GGGG-TGTCGAATT
64 ATTCA-AGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCAACAATGGGGGAGGTCGAATT
* *
1310641 TTACATAGGTATATATAGAGTAAATCTTTAAAAATCTTCCTCTCAAG-A-A-CCA-G-CTGAAAC
128 TTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCCTATCAAGAACATCCAGGACTGAAAC
* * * ** * * *
1310701 TTGTGTG-GAAGCATTCTCGGGTAGTGTTGATTCAAAATTGTGTAAATCATGACCCCCTGTGGTA
193 TTGTGTGCG-AGCATCCTCAGATAGTGTAAATTCAAAATTGTGAAAATCATGACCCCCGGGGGTA
1310765 GGGTGGGGCCACAATGGGGGTGGCGAATTTCACATAGGAATATATAGAGT-AAT-TTTAAAAAAA
257 GGGTGGGGCCACAAT-GGGGTGGCGAATTTCACATAGGAATATATAGAGTAAATCTTT--AAAAA
1310828 TCGT
319 TCGT
* * * *
1310832 CTTCTCAAGAACCATTTGGTCAAAAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGGGTAAA
1 CTTCTCAAGAACCATTTGGCCAGAAAAGCTGAAACTTGTGTGG-AGCATCCTCAGGTAGAGTAAA
* * * * * * *
1310897 TTCAAAATTGTGTAAATCATGACCCCCGGGAGTATGTTGCGGCAACAAAGGGGTGGGGGGGGGTC
65 TTC-AAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCAAC-AA----T-GGGGGAGGTC
* * * * * * ** * *
1310962 GGATTTTACATAAGAATATATAGAGAAAATATTTGAAAACCTT-CTCAGAAACCAATCAACCACG
123 GAATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCCT-ATCAA-GAA-CATCCA-G
* * * * * * * *
1311026 AAAGCTGAAACTTATGTG-GAAGCATTCTCAGTTATTGTAGATTCAAAGTTGTGAAAATTATGAC
184 -GA-CTGAAACTTGTGTGCG-AGCATCCTCAGATAGTGTAAATTCAAAATTGTGAAAATCATGAC
* * * * * * * * * *
1311090 CCCTGGGGGTATGATGAGGCCACAATAGGGG-GTCAAATTTTTACATAGGAGTATATAGTGAACA
246 CCCCGGGGGTAGGGTGGGGCCACAAT-GGGGTGGCGAA-TTTCACATAGGAATATATAGAGTA-A
* * *
1311154 ATTTTTTAAAATCTT
308 ATCTTTAAAAATCGT
1311169 CTTCTCA
1 CTTCTCA
1311176 GAAACTAATT
Statistics
Matches: 550, Mismatches: 79, Indels: 65
0.79 0.11 0.09
Matches are distributed among these distances:
316 4 0.01
317 81 0.15
318 127 0.23
319 3 0.01
321 1 0.00
322 3 0.01
323 1 0.00
325 6 0.01
326 41 0.07
327 1 0.00
328 1 0.00
329 1 0.00
330 53 0.10
331 7 0.01
335 5 0.01
336 189 0.34
337 20 0.04
338 3 0.01
339 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (322 bp):
CTTCTCAAGAACCATTTGGCCAGAAAAGCTGAAACTTGTGTGGAGCATCCTCAGGTAGAGTAAAT
TCAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCAACAATGGGGGAGGTCGAATTTTA
CATAGGAATATATAGAGTAAATCTTTAAAAATCTTCCTATCAAGAACATCCAGGACTGAAACTTG
TGTGCGAGCATCCTCAGATAGTGTAAATTCAAAATTGTGAAAATCATGACCCCCGGGGGTAGGGT
GGGGCCACAATGGGGTGGCGAATTTCACATAGGAATATATAGAGTAAATCTTTAAAAATCGT
Found at i:1317497 original size:4 final size:4
Alignment explanation
Indices: 1317490--1317521 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1317480 CTTGTAGTAA
1317490 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT
1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT
1317522 GTGTGTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.25, T:0.50
Consensus pattern (4 bp):
CTGT
Found at i:1317617 original size:4 final size:4
Alignment explanation
Indices: 1317610--1317649 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
1317600 CTTGCACTAA
*
1317610 CTGT CTGT CTGT CTGT CTCACT CTGT CTGT CTGT CTGT CT
1 CTGT CTGT CTGT CTGT CT--GT CTGT CTGT CTGT CTGT CT
1317650 CTCTCTTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 29 0.91
6 3 0.09
ACGTcount: A:0.03, C:0.30, G:0.20, T:0.47
Consensus pattern (4 bp):
CTGT
Found at i:1317635 original size:22 final size:22
Alignment explanation
Indices: 1317610--1317655 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1317600 CTTGCACTAA
1317610 CTGTCTGTCTGTCTGTCTCACT
1 CTGTCTGTCTGTCTGTCTCACT
*
1317632 CTGTCTGTCTGTCTGTCTCTCT
1 CTGTCTGTCTGTCTGTCTCACT
1317654 CT
1 CT
1317656 TCTCTCTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.02, C:0.33, G:0.17, T:0.48
Consensus pattern (22 bp):
CTGTCTGTCTGTCTGTCTCACT
Done.