Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 402 of 427
Found at i:116632961 original size:3 final size:3
Alignment explanation
Indices: 116632948--116633035 Score: 62
Period size: 3 Copynumber: 29.3 Consensus size: 3
116632938 GACGGTATAT
116632948 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
116632992 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA A-A ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
116633035 A
1 A
116633036 AAAATAAAAC
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
2 11 0.16
3 47 0.68
4 9 0.13
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:116632970 original size:9 final size:9
Alignment explanation
Indices: 116632943--116633041 Score: 58
Period size: 9 Copynumber: 10.2 Consensus size: 9
116632933 ATGGAGACGG
*
116632943 TATATATAA
1 TATAAATAA
116632952 TATAATAATAA
1 TAT-A-AATAA
116632963 TATAAATAA
1 TATAAATAA
*
116632972 TAATATATACA
1 T-ATAAATA-A
*
116632983 TGAGAAATAA
1 T-ATAAATAA
116632993 TA-ATAATAA
1 TATA-AATAA
116633002 TATAAATAA
1 TATAAATAA
116633011 TAGTAAA-AA
1 TA-TAAATAA
116633020 TAATAAAATAA
1 T-AT-AAATAA
* *
116633031 AATAAAAAA
1 TATAAATAA
116633040 TA
1 TA
116633042 AAACAAAGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
8 1 0.01
9 34 0.47
10 21 0.29
11 16 0.22
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (9 bp):
TATAAATAA
Found at i:116632972 original size:12 final size:12
Alignment explanation
Indices: 116632948--116633031 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 12
116632938 GACGGTATAT
116632948 ATAATAT-AATA
1 ATAATATAAATA
116632959 ATAATATAAATA
1 ATAATATAAATA
116632971 ATAATATATACATGA
1 ATAATATA-A-AT-A
116632986 GA-AATA-ATAATA
1 -ATAATATA-AATA
116632998 ATAATATAAATA
1 ATAATATAAATA
* *
116633010 ATAGTAAAAATA
1 ATAATATAAATA
*
116633022 ATAAAATAAA
1 ATAATATAAA
116633032 ATAAAAAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
11 8 0.13
12 38 0.62
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:116632978 original size:30 final size:30
Alignment explanation
Indices: 116632944--116633035 Score: 82
Period size: 33 Copynumber: 2.9 Consensus size: 30
116632934 TGGAGACGGT
116632944 ATATATAATATAATAATAATATAAATAATA
1 ATATATAATATAATAATAATATAAATAATA
*
116632974 ATATATACATGAGAAATAATAATAATAATATAAATA
1 ATATATA-AT-A-TAATAATAAT-ATAA-AT-AATA
*
116633010 ATAGTA-AAAATAATAA-AATA-AAATAA
1 ATA-TATAATATAATAATAATATAAATAA
116633036 AAAATAAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
30 9 0.17
31 3 0.06
32 4 0.08
33 14 0.27
34 5 0.10
35 3 0.06
36 8 0.15
37 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (30 bp):
ATATATAATATAATAATAATATAAATAATA
Found at i:116632992 original size:21 final size:18
Alignment explanation
Indices: 116632953--116633012 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
116632943 TATATATAAT
*
116632953 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
116632971 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
116632992 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
116633010 ATA
1 ATA
116633013 GTAAAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 15 0.41
19 5 0.14
20 5 0.14
21 12 0.32
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:116633039 original size:12 final size:13
Alignment explanation
Indices: 116632987--116633044 Score: 59
Period size: 12 Copynumber: 4.6 Consensus size: 13
116632977 TATACATGAG
116632987 AAATAATAATAATA
1 AAATAA-AATAATA
*
116633001 ATAT-AAATAATA
1 AAATAAAATAATA
**
116633013 GTA-AAAATAATA
1 AAATAAAATAATA
116633025 AAATAAAATAA-A
1 AAATAAAATAATA
116633037 AAATAAAA
1 AAATAAAA
116633045 CAAAGCTCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 27 0.71
13 8 0.21
14 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:116633718 original size:14 final size:13
Alignment explanation
Indices: 116633677--116633722 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
116633667 TTTTTTGGGG
116633677 TTGGGTT-AGTGTT
1 TTGGGTTAAG-GTT
*
116633690 TTGGGCTAA-GTT
1 TTGGGTTAAGGTT
116633702 TTGGGTTAAGGGTT
1 TTGGGTTAA-GGTT
116633716 TTGGGTT
1 TTGGGTT
116633723 TGTATTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 11 0.39
13 6 0.21
14 11 0.39
ACGTcount: A:0.11, C:0.02, G:0.39, T:0.48
Consensus pattern (13 bp):
TTGGGTTAAGGTT
Found at i:116638687 original size:46 final size:46
Alignment explanation
Indices: 116638635--116638810 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
116638625 TGGTTGAGCA
*
116638635 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
116638681 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
116638726 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
116638774 CCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
116638811 GCGGGATACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:116638791 original size:93 final size:93
Alignment explanation
Indices: 116638632--116638802 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
116638622 GGATGGTTGA
* **
116638632 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
116638697 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
116638725 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
116638790 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
116638803 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:116643021 original size:3 final size:3
Alignment explanation
Indices: 116643013--116643073 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
116643003 AAATAGATAT
116643013 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
116643061 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
116643074 CATCAAATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:116643292 original size:3 final size:3
Alignment explanation
Indices: 116643280--116643328 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
116643270 AATAAAAAGA
* * *
116643280 TAT T-T TAT TAT TAT TAT TAT TAT TTT TAT TTT TAT TTT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
116643327 TA
1 TA
116643329 GTGTATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:116645650 original size:21 final size:21
Alignment explanation
Indices: 116645621--116645669 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
116645611 AAGCTCATTT
*
116645621 TATTATTAA-AATATTTTATAA
1 TATTTTTAATAATATTTTAT-A
*
116645642 TATTTTTAATTGATATTTTATA
1 TATTTTTAA-TAATATTTTATA
116645664 TATTTT
1 TATTTT
116645670 ATTAGGGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 7 0.29
23 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TATTTTTAATAATATTTTATA
Found at i:116645971 original size:21 final size:20
Alignment explanation
Indices: 116645911--116645965 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
116645901 AAACTATAAT
*
116645911 TTTTGTAATTTTTCATAAA-TA
1 TTTTG-AATTTTTTA-AAATTA
116645932 TTTTGAATTTTTTAAAATTA
1 TTTTGAATTTTTTAAAATTA
116645952 TTTTGAATGTTTTT
1 TTTTGAAT-TTTTT
116645966 GTAATTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 3 0.10
20 18 0.58
21 10 0.32
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (20 bp):
TTTTGAATTTTTTAAAATTA
Found at i:116646868 original size:21 final size:21
Alignment explanation
Indices: 116646808--116646862 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
116646798 ATAAACTTAA
*
116646808 AATTTAAA-ATTAAATGATA-
1 AATTTAAATTTTAAATGATAT
* *
116646827 CA-TTAAATTTTATATGATAT
1 AATTTAAATTTTAAATGATAT
116646847 AATTTAAATTTTAAAT
1 AATTTAAATTTTAAAT
116646863 TTTATATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 5 0.18
19 10 0.36
20 1 0.04
21 12 0.43
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
AATTTAAATTTTAAATGATAT
Found at i:116650383 original size:60 final size:61
Alignment explanation
Indices: 116650263--116650383 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 61
116650253 GGTCCCTAAA
* *
116650263 CTTCAAATCGTTCTAATTGCATCCCTAAACTATCAAGCTTATATTAATTAGGTCTTTTTGT
1 CTTCAAATCGTTCTAATTGCATCCCTAAACTATCAAGCTTATATTAATCAGGTCCTTTTGT
*
116650324 CTTCAAATCGTTCTAATTGCATCCCT-AACTATCAAGCTTATCTTAATCAGGTCCTTTTGT
1 CTTCAAATCGTTCTAATTGCATCCCTAAACTATCAAGCTTATATTAATCAGGTCCTTTTGT
116650384 TACTAAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 31 0.54
61 26 0.46
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (61 bp):
CTTCAAATCGTTCTAATTGCATCCCTAAACTATCAAGCTTATATTAATCAGGTCCTTTTGT
Found at i:116651265 original size:7 final size:7
Alignment explanation
Indices: 116651250--116651280 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
116651240 TCAATTCAAA
116651250 CTCAATT
1 CTCAATT
*
116651257 CTCAGTT
1 CTCAATT
116651264 CTCAATT
1 CTCAATT
116651271 CTCAATT
1 CTCAATT
116651278 CTC
1 CTC
116651281 TAGATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.03, T:0.42
Consensus pattern (7 bp):
CTCAATT
Found at i:116663395 original size:46 final size:46
Alignment explanation
Indices: 116663328--116663542 Score: 215
Period size: 46 Copynumber: 4.6 Consensus size: 46
116663318 GTGTGAGCTG
*
116663328 GTGTAAGACATGTCTGGGACATGCATCGGCCACATTATAAGAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCACATGATAAGAGCCA
* * *
116663374 GTGTAAGACATGTCTGGGACATGGCATCGG-CA-TTGAGACGAGAGCTA
1 GTGTAAGACATGTCTGGGACAT-GCATCGGCCACATGATA--AGAGCCA
* *
116663421 GTGTAAGACATGTCTGGGACATGCATTGGCCTCGA-GACGT-A-AGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGA--TAAGAGCCA
* ** * * *
116663467 GTGTAAGACATGTCTGGGACATGCATCGGCTACGGGATGATAGTCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCACATGATAAGAGCCA
116663513 GTGTAAGACCATGTCTGGGACATGGCATCG
1 GTGTAAGA-CATGTCTGGGACAT-GCATCG
116663543 ACTTGAGATT
Statistics
Matches: 142, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
44 1 0.01
45 4 0.03
46 78 0.55
47 51 0.36
48 8 0.06
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (46 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCCACATGATAAGAGCCA
Found at i:116663424 original size:47 final size:45
Alignment explanation
Indices: 116663328--116663588 Score: 236
Period size: 47 Copynumber: 5.6 Consensus size: 45
116663318 GTGTGAGCTG
*** * **
116663328 GTGTAAGACATGTCTGGGACATGCATCGGCCACATTATAAGAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCTTGA-GACGAGAGCCA
*
116663374 GTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGACGAGAGCTA
1 GTGTAAGACATGTCTGGGACAT-GCATCGGC-TTGAGACGAGAGCCA
* *
116663421 GTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGACGTA-AGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGG-CTTGAGACG-AGAGCCA
* * * * *
116663467 GTGTAAGACATGTCTGGGACATGCATCGGCTACGGGATGATAGTCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCT-TGAGACGAGAGCCA
* ****
116663513 GTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATTTCAGCCA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCTTGAGACGAGAGCCA
* *
116663560 GTGTAAGACCATATCTAGGACATGGCATC
1 GTGTAAGA-CATGTCTGGGACAT-GCATC
116663589 AGCACATTAC
Statistics
Matches: 184, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
45 3 0.02
46 84 0.46
47 88 0.48
48 9 0.05
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (45 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCTTGAGACGAGAGCCA
Found at i:116663481 original size:93 final size:91
Alignment explanation
Indices: 116663322--116663588 Score: 265
Period size: 93 Copynumber: 2.9 Consensus size: 91
116663312 ATTTGTGTGT
* * * *
116663322 GAGCTGGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATAAGAGCCAGTGTAAGACATG
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGA-GAT-A-AGCCAGTGTAAGACATG
*
116663386 TCTGGGACATGGCATCGGC-ATTGAGACGA
63 TCTGGGACATGGCATCGGCTA-CGAGACGA
116663415 GAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGACGTAAGCCAGTGTAAGACATGT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGA--TAAGCCAGTGTAAGACATGT
* *
116663480 CTGGGACAT-GCATCGGCTACGGGATGA
64 CTGGGACATGGCATCGGCTACGAGACGA
* * * * *
116663507 TAG-TCAGTGTAAGACCATGTCTGGGACATGGCA-TCGACTTGAGATTTCAGCCAGTGTAAGACC
1 GAGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATTGGCCTCGAGA--TAAGCCAGTGTAAGA-C
* *
116663570 ATATCTAGGACATGGCATC
60 ATGTCTGGGACATGGCATC
116663589 AGCACATTAC
Statistics
Matches: 149, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
91 1 0.01
92 24 0.16
93 101 0.68
94 17 0.11
95 6 0.04
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (91 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGATAAGCCAGTGTAAGACATGTCT
GGGACATGGCATCGGCTACGAGACGA
Found at i:116666156 original size:23 final size:23
Alignment explanation
Indices: 116666088--116666174 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 23
116666078 ACCTGATCAG
* *
116666088 AATACAACACATAA-GTGCCTGA
1 AATACGACACACAAGGTGCCTGA
*
116666110 AA-A-GACACACGAGGTGCCTG-
1 AATACGACACACAAGGTGCCTGA
116666130 -ATACGACACACAAGGTGCCTGA
1 AATACGACACACAAGGTGCCTGA
* *
116666152 AATACGACACATAAAGTGCCTGA
1 AATACGACACACAAGGTGCCTGA
116666175 TCAGTATAGC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
19 1 0.02
20 7 0.13
21 24 0.44
22 2 0.04
23 20 0.37
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (23 bp):
AATACGACACACAAGGTGCCTGA
Found at i:116666171 original size:44 final size:41
Alignment explanation
Indices: 116666089--116666175 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 41
116666079 CCTGATCAGA
* * *
116666089 ATACAACACATAAGTGCCTGAAAAGACACACGAGGTGCCTG
1 ATACAACACACAAGTGCCTGAAAAGACACACAAAGTGCCTG
* *
116666130 ATACGACACACAAGGTGCCTGAAATACGACACATAAAGTGCCTG
1 ATACAACACACAA-GTGCCTGAAA-A-GACACACAAAGTGCCTG
116666174 AT
1 AT
116666176 CAGTATAGCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 11 0.29
42 10 0.26
43 1 0.03
44 16 0.42
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (41 bp):
ATACAACACACAAGTGCCTGAAAAGACACACAAAGTGCCTG
Found at i:116666446 original size:51 final size:53
Alignment explanation
Indices: 116666379--116666511 Score: 171
Period size: 57 Copynumber: 2.5 Consensus size: 53
116666369 AACATACCAG
* *
116666379 TATAATCCTCCAAAACACACCAG-TATAATCC-TCAAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGATATAATCCATCAAAAACACACCAGAATAA
* *
116666430 TATAATCCTCCCAAACACACCAGAATAATATAATCCATCCAAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAG----ATATAATCCATCAAAAACACACCAGAATAA
116666487 TATAATCCATCCAAAACACACCAGA
1 TATAATCC-TCCAAAACACACCAGA
116666512 ATAGCACAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
51 22 0.31
54 1 0.01
56 8 0.11
57 25 0.36
58 14 0.20
ACGTcount: A:0.47, C:0.31, G:0.04, T:0.18
Consensus pattern (53 bp):
TATAATCCTCCAAAACACACCAGATATAATCCATCAAAAACACACCAGAATAA
Found at i:116666484 original size:29 final size:28
Alignment explanation
Indices: 116666379--116666514 Score: 183
Period size: 29 Copynumber: 5.0 Consensus size: 28
116666369 AACATACCAG
116666379 TATAATCCTCCAAAACACACCAG-----
1 TATAATCCTCCAAAACACACCAGAATAA
* * *
116666402 TATAATCCTCAAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
116666430 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
116666458 TATAATCCATCCAAAACACACCAGAATAA
1 TATAATCC-TCCAAAACACACCAGAATAA
116666487 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
116666515 GCACAAAGTG
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
23 22 0.22
28 32 0.32
29 47 0.47
ACGTcount: A:0.48, C:0.30, G:0.04, T:0.18
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:116671033 original size:40 final size:41
Alignment explanation
Indices: 116670961--116671093 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 41
116670951 TTAAAACATG
*
116670961 TTAAATTATAATACAATAACATGCATATTTAATTTAAAGCACA
1 TTAAATTATAATAC-A-AACATACATATTTAATTTAAAGCACA
* * *
116671004 TTAAATTATAATGC-AACATACATATTTAATTTAAAGCTCG
1 TTAAATTATAATACAAACATACATATTTAATTTAAAGCACA
*
116671044 TTAAATTATAATACAATATACATACATATTTAATTTAAAACACA
1 TTAAATTATAATAC-A-A-ACATACATATTTAATTTAAAGCACA
116671088 TTAAAT
1 TTAAAT
116671094 GAAATAAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
40 36 0.46
43 14 0.18
44 28 0.36
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (41 bp):
TTAAATTATAATACAAACATACATATTTAATTTAAAGCACA
Found at i:116671148 original size:21 final size:20
Alignment explanation
Indices: 116671118--116671220 Score: 64
Period size: 21 Copynumber: 4.7 Consensus size: 20
116671108 TGACAGAAGC
*
116671118 ATTAATATGAAAAAAATGTAA
1 ATTAAAATGAAAAAAA-GTAA
116671139 ATTAAAATGAAAAGAAAGATAA
1 ATTAAAATGAAAA-AAAG-TAA
* *
116671161 TTTAAATGAAATGAGAAAAAATTAA
1 ATT--A--AAATGA-AAAAAAGTAA
*
116671186 ATTTAAATGAATAAAAAG-ATA
1 ATTAAAATGAA-AAAAAGTA-A
*
116671207 ATTTAAATGAAAAA
1 ATTAAAATGAAAAA
116671221 GAAAAAATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
20 5 0.07
21 36 0.54
22 8 0.12
24 1 0.01
25 5 0.07
26 9 0.13
27 3 0.04
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (20 bp):
ATTAAAATGAAAAAAAGTAA
Found at i:116671172 original size:26 final size:26
Alignment explanation
Indices: 116671143--116671218 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
116671133 ATGTAAATTA
116671143 AAATGAAAAGAAAGATAATTTAAATG
1 AAATGAAAAGAAAGATAATTTAAATG
*
116671169 AAATG---AGAAA-A-AA-TTAAATTT
1 AAATGAAAAGAAAGATAATTTAAA-TG
116671190 AAATGAATAA-AAAGATAATTTAAATG
1 AAATGAA-AAGAAAGATAATTTAAATG
116671216 AAA
1 AAA
116671219 AAGAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
20 5 0.12
21 8 0.20
22 1 0.03
23 5 0.12
24 3 0.08
25 2 0.05
26 11 0.28
27 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (26 bp):
AAATGAAAAGAAAGATAATTTAAATG
Found at i:116671180 original size:47 final size:46
Alignment explanation
Indices: 116671124--116671261 Score: 155
Period size: 47 Copynumber: 3.1 Consensus size: 46
116671114 AAGCATTAAT
*
116671124 ATGAAAAAAATGTAAATTAAAATGAA-AAGAAAGATAATTTAAATGAA
1 ATGAGAAAAAT-TAAATTAAAATGAATAA-AAAGATAATTTAAATGAA
*
116671171 ATGAGAAAAAATTAAATTTAAATGAATAAAAAGATAATTTAAATGAA
1 ATGAG-AAAAATTAAATTAAAATGAATAAAAAGATAATTTAAATGAA
* * *
116671218 A--A-AGAAA--AAATT-AAATGGATAAAAAGATATTTTAAATGAA
1 ATGAGAAAAATTAAATTAAAATGAATAAAAAGATAATTTAAATGAA
116671258 ATGA
1 ATGA
116671262 AATTGGAACT
Statistics
Matches: 82, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
40 27 0.33
41 5 0.06
42 1 0.01
43 4 0.05
45 1 0.01
47 36 0.44
48 8 0.10
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (46 bp):
ATGAGAAAAATTAAATTAAAATGAATAAAAAGATAATTTAAATGAA
Found at i:116671227 original size:26 final size:26
Alignment explanation
Indices: 116671136--116671227 Score: 70
Period size: 26 Copynumber: 3.7 Consensus size: 26
116671126 GAAAAAAATG
* *
116671136 TAAATTAAAATGAAAAGAAAGATAATT
1 TAAATGAAAAAGAAAA-AAAGATAATT
* **
116671163 TAAATGAAATGAGAAAAAATTA-AATT
1 TAAATGAAA-AAGAAAAAAAGATAATT
*
116671189 TAAATG----A-ATAAAAAGATAATT
1 TAAATGAAAAAGAAAAAAAGATAATT
116671210 TAAATGAAAAAGAAAAAA
1 TAAATGAAAAAGAAAAAA
116671228 TTAAATGGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 15
0.67 0.12 0.21
Matches are distributed among these distances:
20 6 0.12
21 11 0.22
25 1 0.02
26 15 0.31
27 11 0.22
28 5 0.10
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (26 bp):
TAAATGAAAAAGAAAAAAAGATAATT
Found at i:116671232 original size:40 final size:42
Alignment explanation
Indices: 116671119--116671263 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 42
116671109 GACAGAAGCA
**
116671119 TTAATATGAAA-AAAATGTAAATTAAAATGAA-AAGAAAGATAAT
1 TTAA-ATGAAAGAAAAAATAAATT-AAATGAATAA-AAAGATAAT
116671162 TTAAATGAAATGAGAAAAAATTAAATTTAAATGAATAAAAAGATAAT
1 TTAAATG-AA--AGAAAAAA-TAAA-TTAAATGAATAAAAAGATAAT
* * *
116671209 TTAAATGAAA-AAGAAA-AAATTAAATGGATAAAAAGATATT
1 TTAAATGAAAGAAAAAATAAATTAAATGAATAAAAAGATAAT
116671249 TTAAATGAAATGAAA
1 TTAAATGAAA-GAAA
116671264 TTGGAACTGG
Statistics
Matches: 87, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
40 29 0.33
41 3 0.03
42 5 0.06
43 11 0.13
44 1 0.01
45 1 0.01
46 6 0.07
47 27 0.31
48 4 0.05
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (42 bp):
TTAAATGAAAGAAAAAATAAATTAAATGAATAAAAAGATAAT
Found at i:116671252 original size:21 final size:21
Alignment explanation
Indices: 116671153--116671255 Score: 77
Period size: 21 Copynumber: 4.8 Consensus size: 21
116671143 AAATGAAAAG
*
116671153 AAAGATAATTTAAATGAAATGAGA
1 AAAGATAATTTAAATG-GAT-A-A
* *
116671177 AAAAATTAAATTTAAATGAATAA
1 AAAGA-T-AATTTAAATGGATAA
116671200 AAAGATAATTTAAAT-G--AA
1 AAAGATAATTTAAATGGATAA
* *
116671218 AAAGAAAAAATTAAATGGATAA
1 AAAG-ATAATTTAAATGGATAA
*
116671240 AAAGATATTTTAAATG
1 AAAGATAATTTAAATG
116671256 AAATGAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
18 6 0.09
19 9 0.14
20 1 0.02
21 18 0.28
22 7 0.11
23 5 0.08
24 5 0.08
25 4 0.06
26 10 0.15
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (21 bp):
AAAGATAATTTAAATGGATAA
Found at i:116671594 original size:18 final size:18
Alignment explanation
Indices: 116671559--116671599 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
116671549 CTAATTAATA
116671559 TGAAAAATATGAAATGAAT
1 TGAAAAATA-GAAATGAAT
116671578 TGAAAAATA-AAATTGAAT
1 TGAAAAATAGAAA-TGAAT
116671596 TGAA
1 TGAA
116671600 CAAAGATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 9 0.43
19 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.27
Consensus pattern (18 bp):
TGAAAAATAGAAATGAAT
Found at i:116671688 original size:21 final size:21
Alignment explanation
Indices: 116671663--116671790 Score: 86
Period size: 21 Copynumber: 6.2 Consensus size: 21
116671653 TATTAAAAAA
116671663 AAATAAATTTAAAAGGAAATG
1 AAATAAATTTAAAAGGAAATG
116671684 AAATAAATTTAAATA--AAA--
1 AAATAAATTTAAA-AGGAAATG
* *
116671702 AATTAAA-TTAAAATGGAAATA
1 AAATAAATTTAAAA-GGAAATG
* **
116671723 AAATAAATTTAAATGGAAAAA
1 AAATAAATTTAAAAGGAAATG
* * *
116671744 AAATTAAATCTACATGGAAATG
1 AAA-TAAATTTAAAAGGAAATG
* ** *
116671766 AAATAAAATGGAAATGAAATG
1 AAATAAATTTAAAAGGAAATG
116671787 AAAT
1 AAAT
116671791 GACAAAAAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
16 1 0.01
17 5 0.06
18 6 0.07
19 3 0.04
20 3 0.04
21 43 0.51
22 23 0.27
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (21 bp):
AAATAAATTTAAAAGGAAATG
Found at i:116671725 original size:22 final size:21
Alignment explanation
Indices: 116671700--116671774 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 21
116671690 ATTTAAATAA
116671700 AAAATTAAATTAAAATGGAAAT
1 AAAATTAAATT-AAATGGAAAT
*
116671722 AAAA-TAAATTTAAATGGAAAA
1 AAAATTAAA-TTAAATGGAAAT
*
116671743 AAAATTAAATCTACATGGAAAT
1 AAAATTAAAT-TAAATGGAAAT
* *
116671765 GAAATAAAAT
1 AAAATTAAAT
116671775 GGAAATGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.40
22 27 0.60
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.25
Consensus pattern (21 bp):
AAAATTAAATTAAATGGAAAT
Found at i:116671761 original size:43 final size:40
Alignment explanation
Indices: 116671656--116671772 Score: 139
Period size: 39 Copynumber: 2.9 Consensus size: 40
116671646 AATTGTATAT
* *
116671656 TAAAAAAAAATAAATTTAAAAGGAAATGAAATAAATTTAAA
1 TAAAAAAAATTAAA-TTAAATGGAAATGAAATAAATTTAAA
*
116671697 T--AAAAAATTAAATTAAAATGGAAATAAAATAAATTTAAA
1 TAAAAAAAATTAAATT-AAATGGAAATGAAATAAATTTAAA
*
116671736 TGGAAAAAAAATTAAATCTACATGGAAATGAAATAAA
1 T--AAAAAAAATTAAAT-TAAATGGAAATGAAATAAA
116671773 ATGGAAATGA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
38 2 0.03
39 33 0.51
41 1 0.02
43 28 0.43
44 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.25
Consensus pattern (40 bp):
TAAAAAAAATTAAATTAAATGGAAATGAAATAAATTTAAA
Found at i:116671775 original size:38 final size:37
Alignment explanation
Indices: 116671657--116671779 Score: 102
Period size: 43 Copynumber: 3.1 Consensus size: 37
116671647 ATTGTATATT
* * * **
116671657 AAAAAAAAATAAATTTAAAAGGAAATGAAATAAATTTA
1 AAAAAAAATTAAA-TTAAATGGAAATGAAATAAAATGG
*
116671695 AATAAAAAATTAAATTAAAATGGAAATAAAATAAATTTAAATGG
1 AA-AAAAAATTAAATT-AAATGGAAATGAAAT--A---AAATGG
*
116671739 AAAAAAAATTAAATCTACATGGAAATGAAATAAAATGG
1 AAAAAAAATTAAAT-TAAATGGAAATGAAATAAAATGG
116671777 AAA
1 AAA
116671780 TGAAATGAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
38 13 0.19
39 23 0.33
41 2 0.03
43 25 0.36
44 6 0.09
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.24
Consensus pattern (37 bp):
AAAAAAAATTAAATTAAATGGAAATGAAATAAAATGG
Found at i:116671778 original size:16 final size:16
Alignment explanation
Indices: 116671757--116671791 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
116671747 TTAAATCTAC
116671757 ATGGAAATGAAATAAA
1 ATGGAAATGAAATAAA
*
116671773 ATGGAAATGAAATGAA
1 ATGGAAATGAAATAAA
116671789 ATG
1 ATG
116671792 ACAAAAAAAA
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:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (16 bp):
ATGGAAATGAAATAAA
Found at i:116674784 original size:93 final size:93
Alignment explanation
Indices: 116674625--116674796 Score: 238
Period size: 93 Copynumber: 1.8 Consensus size: 93
116674615 CGCCCATAAG
* * ** * **
116674625 CGAACTCGGACTCAACTCAACTAGCTCGAGCGTTCTCATCCATAGGTGAACTCGGGCTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAGCATTAGCATCCATAAGTGAACTCGAACTCAACTCA
* *
116674690 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGCTCGAATGCCTAGTTACATTTCA
*
116674718 CGAACTCGGACTCAACTCAACGAGTTCG-GACATTAGCATCCATAAGTGAACTCGAACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTCGAG-CATTAGCATCCATAAGTGAACTCGAACTCAACTC
116674782 AACGAGCTCGAATGC
65 AACGAGCTCGAATGC
116674797 TCAACCATCC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
92 1 0.01
93 67 0.99
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAGCATTAGCATCCATAAGTGAACTCGAACTCAACTCA
ACGAGCTCGAATGCCTAGTTACATTTCA
Found at i:116677300 original size:90 final size:89
Alignment explanation
Indices: 116677153--116677480 Score: 390
Period size: 90 Copynumber: 3.7 Consensus size: 89
116677143 ATTCTAGAAT
* * * * * *
116677153 ATTAATACACAAAAATATAAAATTCAAAC-AAAAATAATAC-GCACTAAATTAAATTTAAACTCC
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACAG-ACTAAATTAAATTTAAACACC
*
116677216 TAACAAACTACAAACAGATGGGTATA
65 -AACAAACTACAAACAGATGGGTAAA
* * *
116677242 ATTAATACACGAAAATTTTATATTCAAACTACATATAATACAAACTAAATTAAATTTAACCACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACAGACTAAATTAAATTTAAACA-CC
* * *
116677307 AACAAACTAAAAACATATGGATAAA
65 AACAAACTACAAACAGATGGGTAAA
* * * * *
116677332 ATTAGTGCACGAAAATTTTAAATCCAAACTATATATAACACAGACTAAATTAAATTTAAACAACC
1 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACAGACTAAATTAAATTTAAAC-ACC
** *
116677397 AACAAACTACAAATGGATAGGTAAA
65 AACAAACTACAAACAGATGGGTAAA
* *
116677422 ATTAATAGCACGAAAATTTTAATTTCAAACTACATATAATACGGACTAAATTAAATTTA
1 ATTAATA-CACGAAAATTTTAAATTCAAACTACATATAATACAGACTAAATTAAATTTA
116677481 CAGATACAAA
Statistics
Matches: 200, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
89 25 0.12
90 126 0.63
91 49 0.25
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (89 bp):
ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACAGACTAAATTAAATTTAAACACCA
ACAAACTACAAACAGATGGGTAAA
Found at i:116677567 original size:180 final size:177
Alignment explanation
Indices: 116677114--116677569 Score: 478
Period size: 180 Copynumber: 2.5 Consensus size: 177
116677104 CACAACAAAA
* *
116677114 TAAATTTACAGATACAATAAAATACAAACATTCT-AGAATATTAATACACAAAAATATAAAATTC
1 TAAATTTACAGATACAACAAAATACAAACATTCTAAGAA-ATTAATACACAAAAATATAAAAATC
* * * * *
116677178 AAAC-AAAAATAATACGCACTAAATTAAATTTAAACTCCTAACAAACTACAAACAGATGGGTATA
65 AAACTAAATATAA-AC-AACTAAATTAAATTTAAACACCTAACAAACTACAAACAGATAGGTAAA
116677242 ATTAATACACGAAAATTTTATATTCAAACTACATATAATACAAACTAAAT
128 ATTAATACACGAAAATTTTATATTCAAACTACATATAATACAAACTAAAT
* ** * * ** * * * **
116677292 TAAATTTA-ACCACCCAACAAACTAAAAACATATGGATA-AAATTAGTGCACGAAAAT-TTTAAA
1 TAAATTTACA-GATACAACAAAATACAAACAT-TCTA-AGAAATTAATACACAAAAATATAAAAA
* **
116677354 TCCAAACTATATATAACACAGACTAAATTAAATTTAAACAACC-AACAAACTACAAATGGATAGG
63 T-CAAACTAAATATAA-ACA-ACTAAATTAAATTTAAAC-ACCTAACAAACTACAAACAGATAGG
**
116677418 TAAAATTAATAGCACGAAAATTTTA-ATTTCAAACTACATATAATACGGACTAAAT
124 TAAAATTAATA-CACGAAAATTTTATA-TTCAAACTACATATAATACAAACTAAAT
*
116677473 TAAATTTACAGATACAA-AAAATACAAACATTCTAAGAAATTAATACACAAAAATATAAAAATAA
1 TAAATTTACAGATACAACAAAATACAAACATTCTAAGAAATTAATACACAAAAATATAAAAATCA
* *
116677537 AACCTTAAATCCTAAACAACTATATTAAATTTA
66 AA-C-TAAAT-ATAAACAACTAAATTAAATTTA
116677570 CAGATATAAA
Statistics
Matches: 221, Mismatches: 41, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
177 1 0.00
178 28 0.13
179 39 0.18
180 88 0.40
181 61 0.28
182 4 0.02
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (177 bp):
TAAATTTACAGATACAACAAAATACAAACATTCTAAGAAATTAATACACAAAAATATAAAAATCA
AACTAAATATAAACAACTAAATTAAATTTAAACACCTAACAAACTACAAACAGATAGGTAAAATT
AATACACGAAAATTTTATATTCAAACTACATATAATACAAACTAAAT
Found at i:116678493 original size:39 final size:39
Alignment explanation
Indices: 116678469--116678588 Score: 213
Period size: 39 Copynumber: 3.1 Consensus size: 39
116678459 AATCTAGCTA
* *
116678469 AAGCACATAAGTGCTAAACCGAAGCCTGAAGGCTAACTG
1 AAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
*
116678508 AAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAACTG
1 AAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
116678547 AAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
1 AAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
116678586 AAG
1 AAG
116678589 TTCATCAGAG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (39 bp):
AAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
Found at i:116680849 original size:26 final size:27
Alignment explanation
Indices: 116680791--116680855 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
116680781 AATTCGGTTG
*
116680791 TACACTACAAAAAACTCTTATCTATAA
1 TACACTACAAAAAACTCTTATCGATAA
* *
116680818 TCCACTACAAAAAACTCATT-T-GATGA
1 TACACTACAAAAAACTC-TTATCGATAA
116680844 TACACTACAAAA
1 TACACTACAAAA
116680856 CACTTTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 14 0.42
27 17 0.52
28 2 0.06
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (27 bp):
TACACTACAAAAAACTCTTATCGATAA
Found at i:116681249 original size:109 final size:109
Alignment explanation
Indices: 116681135--116681466 Score: 370
Period size: 108 Copynumber: 3.1 Consensus size: 109
116681125 AAGTAAAAAA
* ** *
116681135 AAAAAAAAGTGCATTGGAAGTTAAAAAATATACTTGGTGCCGACTATCTACTTGCCAACACCCAA
1 AAAAAAAAGTGCATTGGGAGTCGAAAAATATACTTGGTGCCGACTATCTACTTGCCAGCACCCAA
** **
116681200 ATTTTTTTTAAATGACGTTGGCACCAGCCATCAGTGTCCCCCCC
66 ATTTTTTTTAAATGACACTGGTGCCAGCCATCAGTGTCCCCCCC
* * * * *
116681244 -AAAAAAAGTACTTTGGGAGTCGAAAAATGTACTTGGTGCCGGCCATCTACTTGCCAGCACCCAA
1 AAAAAAAAGTGCATTGGGAGTCGAAAAATATACTTGGTGCCGACTATCTACTTGCCAGCACCCAA
* * *
116681308 AGTTTTTTTTTTAATGACACTGGTGGCAGCCA-CTAGTGT---CCCA
66 A--TTTTTTTTAAATGACACTGGTGCCAGCCATC-AGTGTCCCCCCC
* * * *
116681351 AAAAAAAATGTGCCTTGGGAGCCGAAAAATATACTTGGTGCCGA-TCATCTACTAGCCAGTACCC
1 AAAAAAAA-GTGCATTGGGAGTCGAAAAATATACTTGGTGCCGACT-ATCTACTTGCCAGCACCC
* * *
116681415 AAATTTTTTTTAAGTGATACTGGTGCCTGCCATCAGTGTCCCCCCC
64 AAATTTTTTTTAAATGACACTGGTGCCAGCCATCAGTGTCCCCCCC
116681461 AAAAAA
1 AAAAAA
116681467 TGTATTGGAG
Statistics
Matches: 183, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
107 32 0.17
108 64 0.35
109 50 0.27
110 37 0.20
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (109 bp):
AAAAAAAAGTGCATTGGGAGTCGAAAAATATACTTGGTGCCGACTATCTACTTGCCAGCACCCAA
ATTTTTTTTAAATGACACTGGTGCCAGCCATCAGTGTCCCCCCC
Found at i:116681270 original size:108 final size:108
Alignment explanation
Indices: 116681158--116681545 Score: 389
Period size: 109 Copynumber: 3.6 Consensus size: 108
116681148 TTGGAAGTTA
* ** *
116681158 AAAAATATACTTGGTGCCGACTATCTACTTGCCAACACCCAAA-TTTTTTTTAAATGACGTTGGC
1 AAAAATATACTTGGTGCCGACCATCTACTTGCCAACACCCAAATTTTTTTTTAAATGACACTGGT
* *
116681222 ACCAGCCATCAGTGTCCCCCCCAAAAAAAGTACTTTGGGAGTCG
66 GCCAGCCATCAGTGTCCCCCCCAAAAAAAGTAC-TTGGGAGCCG
* * * *
116681266 AAAAATGTACTTGGTGCCGGCCATCTACTTGCCAGCACCCAAAGTTTTTTTTTTAATGACACTGG
1 AAAAATATACTTGGTGCCGACCATCTACTTGCCAACACCCAAA-TTTTTTTTTAAATGACACTGG
* ** *
116681331 TGGCAGCCA-CTAGTGT--CCCAAAAAAAAATGTGCCTTGGGAGCCG
65 TGCCAGCCATC-AGTGTCCCCCCCAAAAAAA-GT-ACTTGGGAGCCG
* * ** * *
116681375 AAAAATATACTTGGTGCCGATCATCTACTAGCCAGTACCCAAA-TTTTTTTTAAGTGATACTGGT
1 AAAAATATACTTGGTGCCGACCATCTACTTGCCAACACCCAAATTTTTTTTTAAATGACACTGGT
* * *
116681439 GCCTGCCATCAGTGTCCCCCCCAAAAAATGTA-TT-GGAGCCCT
66 GCCAGCCATCAGTGTCCCCCCCAAAAAAAGTACTTGGGAG-CCG
* * * * * * *
116681481 AAAAATGTACTTGGTGCCAACCATTTACTGGCTAACA--CAAATTTTTTTTTAAATGTCTCTGGT
1 AAAAATATACTTGGTGCCGACCATCTACTTGCCAACACCCAAATTTTTTTTTAAATGACACTGGT
116681544 GC
66 GC
116681546 TGGCCATTAC
Statistics
Matches: 229, Mismatches: 41, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
104 4 0.02
105 23 0.10
106 33 0.14
107 29 0.13
108 52 0.23
109 59 0.26
110 29 0.13
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (108 bp):
AAAAATATACTTGGTGCCGACCATCTACTTGCCAACACCCAAATTTTTTTTTAAATGACACTGGT
GCCAGCCATCAGTGTCCCCCCCAAAAAAAGTACTTGGGAGCCG
Found at i:116685825 original size:36 final size:35
Alignment explanation
Indices: 116685785--116685896 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 35
116685775 AGTTTCATTT
* *
116685785 AGTAACATTCAATTATTCAATAGCAATTAGTTATTC
1 AGTAACA-TCAATTATTCAGTAGCAATCAGTTATTC
* **
116685821 AGTAACAATCATTTGGTCAGTAGCAATCAGTTATTC
1 AGTAAC-ATCAATTATTCAGTAGCAATCAGTTATTC
* *
116685857 AGTAACGATCAATTATTCAGTAACAGTCAGTTATTC
1 AGTAAC-ATCAATTATTCAGTAGCAATCAGTTATTC
116685893 AGTA
1 AGTA
116685897 CTTTTATTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 63 0.98
37 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (35 bp):
AGTAACATCAATTATTCAGTAGCAATCAGTTATTC
Found at i:116685829 original size:18 final size:18
Alignment explanation
Indices: 116685785--116685896 Score: 116
Period size: 18 Copynumber: 6.2 Consensus size: 18
116685775 AGTTTCATTT
* *
116685785 AGTAACATTCAATTATTC
1 AGTAACAATCAGTTATTC
* * *
116685803 AATAGCAATTAGTTATTC
1 AGTAACAATCAGTTATTC
* **
116685821 AGTAACAATCATTTGGTC
1 AGTAACAATCAGTTATTC
*
116685839 AGTAGCAATCAGTTATTC
1 AGTAACAATCAGTTATTC
* *
116685857 AGTAACGATCAATTATTC
1 AGTAACAATCAGTTATTC
*
116685875 AGTAACAGTCAGTTATTC
1 AGTAACAATCAGTTATTC
116685893 AGTA
1 AGTA
116685897 CTTTTATTTA
Statistics
Matches: 73, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 73 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
AGTAACAATCAGTTATTC
Found at i:116686118 original size:44 final size:44
Alignment explanation
Indices: 116686045--116686139 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 44
116686035 CAAAATAATC
* * *
116686045 CGAAGTAACAGTACAACACACAAGCTGCCTTATCGACTTAAAGT
1 CGAAGTAACAGTACAACACACAAGCTGCCTCATCAACTCAAAGT
** * *
116686089 CGAAGTAACAGTACAACACTTATA-TTGCCTCATCAACTCAAGGT
1 CGAAGTAACAGTACAACACACA-AGCTGCCTCATCAACTCAAAGT
116686133 CGAAGTA
1 CGAAGTA
116686140 TCCCTGAACA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (44 bp):
CGAAGTAACAGTACAACACACAAGCTGCCTCATCAACTCAAAGT
Found at i:116690314 original size:13 final size:15
Alignment explanation
Indices: 116690288--116690320 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
116690278 CATTTACTTT
116690288 ATATATATTATAATA
1 ATATATATTATAATA
116690303 ATATA-ATT-TAATA
1 ATATATATTATAATA
116690316 ATATA
1 ATATA
116690321 CTTATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 3 0.17
15 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATATTATAATA
Found at i:116693397 original size:25 final size:25
Alignment explanation
Indices: 116693380--116693429 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
116693370 TTTTACGGTC
116693380 TTTGTCACTGTCTTTTTTGTAACAT
1 TTTGTCACTGTCTTTTTTGTAACAT
116693405 TTTGTCACTGTCTTTTTTGTAACAT
1 TTTGTCACTGTCTTTTTTGTAACAT
116693430 CCCCTACCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.56
Consensus pattern (25 bp):
TTTGTCACTGTCTTTTTTGTAACAT
Found at i:116694197 original size:25 final size:25
Alignment explanation
Indices: 116694169--116694220 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
116694159 TTTGGCTTGA
**
116694169 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
116694194 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
116694219 CA
1 CA
116694221 AATTATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:116703279 original size:3 final size:3
Alignment explanation
Indices: 116703271--116703308 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
116703261 TTGCACATGA
*
116703271 TAC TAC TAC TAG TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
116703309 GTGTGTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:116703585 original size:16 final size:16
Alignment explanation
Indices: 116703566--116703596 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
116703556 TTTTTTTCCA
116703566 TTTTTGTTTTTCATTC
1 TTTTTGTTTTTCATTC
*
116703582 TTTTTTTTTTTCATT
1 TTTTTGTTTTTCATT
116703597 TACTACACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTGTTTTTCATTC
Found at i:116703590 original size:14 final size:14
Alignment explanation
Indices: 116703552--116703590 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
116703542 GATGAGGTTT
116703552 TTTTTTTTTTTCCA
1 TTTTTTTTTTTCCA
*
116703566 TTTTTGTTTTT-CA
1 TTTTTTTTTTTCCA
116703579 TTCTTTTTTTTT
1 TT-TTTTTTTTT
116703591 TTCATTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTTTCCA
Found at i:116711399 original size:14 final size:15
Alignment explanation
Indices: 116711380--116711409 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
116711370 TTGATTACAA
116711380 TTATAATT-TTTTAG
1 TTATAATTCTTTTAG
116711394 TTATAATTCTTTTAG
1 TTATAATTCTTTTAG
116711409 T
1 T
116711410 CCTACTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (15 bp):
TTATAATTCTTTTAG
Found at i:116719476 original size:28 final size:27
Alignment explanation
Indices: 116719444--116719498 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 27
116719434 AATATAAATA
116719444 TGTACACTTGTTATATAATTATTAATTT
1 TGTACACTTGTTATAT-ATTATTAATTT
116719472 TGTACACTTGTTATATATTATTAATTT
1 TGTACACTTGTTATATATTATTAATTT
116719499 ACTTAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (27 bp):
TGTACACTTGTTATATATTATTAATTT
Found at i:116719549 original size:16 final size:16
Alignment explanation
Indices: 116719528--116719558 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
116719518 GATATTTTAA
116719528 TATATTATATTAATAT
1 TATATTATATTAATAT
*
116719544 TATATTATGTTAATA
1 TATATTATATTAATA
116719559 AAATAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:116719654 original size:12 final size:12
Alignment explanation
Indices: 116719637--116719667 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
116719627 GAAGCAGGGG
116719637 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
116719649 AGAAAAAGGGAA
1 AGAAAAAGAGAA
116719661 AGAAAAA
1 AGAAAAA
116719668 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:116722544 original size:2 final size:2
Alignment explanation
Indices: 116722504--116722536 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
116722494 ATTCATCTAC
116722504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
116722537 TCATATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:116723876 original size:23 final size:23
Alignment explanation
Indices: 116723844--116723887 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
116723834 ACTACCATTT
116723844 TCTAAATAAAACAATAATAAATA
1 TCTAAATAAAACAATAATAAATA
* * *
116723867 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAACAATAATAAA
116723888 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
TCTAAATAAAACAATAATAAATA
Found at i:116737460 original size:26 final size:26
Alignment explanation
Indices: 116737431--116737509 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
116737421 CGAGCTTTCC
*
116737431 AATGTGCAAGCTGCAAGCTCAGCAAG
1 AATGTGCAAGCTGCAAGCTTAGCAAG
116737457 AATGTGCAAGCTGCAAGCTTAGCAAG
1 AATGTGCAAGCTGCAAGCTTAGCAAG
*
116737483 -ATGT-CAAAGCTGCAAGCTTAGTAAG
1 AATGTGC-AAGCTGCAAGCTTAGCAAG
116737508 AA
1 AA
116737510 GTGATAGTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
24 1 0.02
25 22 0.45
26 26 0.53
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (26 bp):
AATGTGCAAGCTGCAAGCTTAGCAAG
Found at i:116737542 original size:13 final size:13
Alignment explanation
Indices: 116737524--116737549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
116737514 TAGTTGCGAG
116737524 CCTGTTGAAGACA
1 CCTGTTGAAGACA
116737537 CCTGTTGAAGACA
1 CCTGTTGAAGACA
116737550 GTATGCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CCTGTTGAAGACA
Found at i:116740233 original size:51 final size:51
Alignment explanation
Indices: 116740162--116740329 Score: 228
Period size: 51 Copynumber: 3.2 Consensus size: 51
116740152 CTGATCACAT
116740162 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
116740213 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
* * * *
116740264 TTGTCACTTGTCACTTATCACTGGTCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 -T-T-A----TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
116740322 TTGTCACT
1 TTATCACT
116740330 GATCAGAAGT
Statistics
Matches: 105, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
51 56 0.53
52 1 0.01
53 1 0.01
54 1 0.01
56 1 0.01
57 1 0.01
58 44 0.42
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:116740265 original size:58 final size:58
Alignment explanation
Indices: 116740203--116740334 Score: 201
Period size: 58 Copynumber: 2.3 Consensus size: 58
116740193 CTAAAGCTAC
* *
116740203 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTGTCACTTATCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
* * * *
116740261 CACTTGTCACTTGTCACTTATCACTGGTCAGATAAGTGTAGCTGAGGCTACCACTTAT
1 CACTTGTCACTTATCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
*
116740319 CACTTGTCACTGATCA
1 CACTTGTCACTTATCA
116740335 GAAGTACTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 66 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (58 bp):
CACTTGTCACTTATCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
Found at i:116742625 original size:19 final size:20
Alignment explanation
Indices: 116742584--116742625 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
116742574 AATTTAACAT
116742584 GCCCGTGCAACATGGGACAC
1 GCCCGTGCAACATGGGACAC
116742604 GCCCGTGCAACATGGG-CAC
1 GCCCGTGCAACATGGGACAC
116742623 GCC
1 GCC
116742626 TGTGTCCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.21, C:0.38, G:0.31, T:0.10
Consensus pattern (20 bp):
GCCCGTGCAACATGGGACAC
Found at i:116743673 original size:6 final size:6
Alignment explanation
Indices: 116743664--116743696 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
116743654 CACTGTAAGG
116743664 GTAACA GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTA
116743697 GCGGTATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:116744108 original size:3 final size:3
Alignment explanation
Indices: 116744100--116744126 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
116744090 ATTCAATACC
116744100 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
116744127 CTTACCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:116744773 original size:22 final size:21
Alignment explanation
Indices: 116744743--116744784 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
116744733 ATTTACCCTT
*
116744743 TTTCCTTTTTTCCTTTCTTTCC
1 TTTCCTTTTCTCC-TTCTTTCC
*
116744765 TTTCTTTTTCTCCTTCTTTC
1 TTTCCTTTTCTCCTTCTTTC
116744785 TCCCCTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTCCTTTTCTCCTTCTTTCC
Found at i:116749709 original size:16 final size:17
Alignment explanation
Indices: 116749685--116749718 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
116749675 AAAAAAAATG
*
116749685 TTTTGTTTTGT-TTTTA
1 TTTTATTTTGTCTTTTA
116749701 TTTTATTTTGTCTTTTA
1 TTTTATTTTGTCTTTTA
116749718 T
1 T
116749719 ACTTGTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTTATTTTGTCTTTTA
Found at i:116757006 original size:23 final size:23
Alignment explanation
Indices: 116756954--116757006 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
116756944 TTTAGCAATA
*
116756954 AATATTTTATAGTATAAAATATG
1 AATATTTTATAATATAAAATATG
*
116756977 AAAATTTTAATAATAT-AAATATG
1 AATATTTT-ATAATATAAAATATG
*
116757000 AGTATTT
1 AATATTT
116757007 ATTTAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (23 bp):
AATATTTTATAATATAAAATATG
Found at i:116757653 original size:20 final size:21
Alignment explanation
Indices: 116757618--116757656 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
116757608 ATAATTTTCC
116757618 ATTTTAATTTTCAAAAAATAA
1 ATTTTAATTTTCAAAAAATAA
*
116757639 ATTTT-ATTTTTAAAAAAT
1 ATTTTAATTTTCAAAAAAT
116757657 TGAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTTAATTTTCAAAAAATAA
Found at i:116761079 original size:151 final size:151
Alignment explanation
Indices: 116760796--116761068 Score: 438
Period size: 151 Copynumber: 1.8 Consensus size: 151
116760786 CACGGGTAGA
* * *
116760796 GACACAGTCGTGTGTCTCAACCGTGTGGAGGGTACGGCCTAGCACACAGGTGTGTGTCTTGGCCG
1 GACACAGTCGTGTGTCTCAACCGTGTGGAGGGCACGGCCTAGCACACAGGCGTGTGTCTTGACCG
* * *
116760861 TGTGCCCCTAAATGCATACTGACGTTATAAACAGAATGTCCAAGTTCTTGGACACGGCCGAGCAC
66 TGTGCCCCTAAATGCATACTGACATCATAAACAAAATGTCCAAGTTCTTGGACACGGCCGAGCAC
116760926 ATGCCCGTGTCCCTAGCCCGT
131 ATGCCCGTGTCCCTAGCCCGT
* * * *
116760947 GACACGGTCGTGTGTCTCAACCGTGTGGAGGGCATGGCCTAGCACACGGGCGTGTGTCTTGACGG
1 GACACAGTCGTGTGTCTCAACCGTGTGGAGGGCACGGCCTAGCACACAGGCGTGTGTCTTGACCG
* *
116761012 TGTGCCCTTAAATGCATGCTGACATCATAAACAAAATGTCCAAGTTCTTGGACACGG
66 TGTGCCCCTAAATGCATACTGACATCATAAACAAAATGTCCAAGTTCTTGGACACGG
116761069 GTGATCACAT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
151 110 1.00
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (151 bp):
GACACAGTCGTGTGTCTCAACCGTGTGGAGGGCACGGCCTAGCACACAGGCGTGTGTCTTGACCG
TGTGCCCCTAAATGCATACTGACATCATAAACAAAATGTCCAAGTTCTTGGACACGGCCGAGCAC
ATGCCCGTGTCCCTAGCCCGT
Found at i:116783362 original size:8 final size:8
Alignment explanation
Indices: 116783349--116783384 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
116783339 TTTAGTATCT
116783349 ATATAAAA
1 ATATAAAA
116783357 ATATAAAA
1 ATATAAAA
116783365 ATATAAAA
1 ATATAAAA
116783373 ATA-AAATA
1 ATATAAA-A
116783381 ATAT
1 ATAT
116783385 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 3 0.12
8 23 0.88
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
ATATAAAA
Found at i:116784810 original size:2 final size:2
Alignment explanation
Indices: 116784803--116784830 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
116784793 CCAAAAGGAG
116784803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116784831 GAGTGCGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116789247 original size:16 final size:16
Alignment explanation
Indices: 116789215--116789256 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
116789205 TGAATCATTT
* *
116789215 TATTTTATATTTTTAA
1 TATTTTATAATTATAA
116789231 TATTTTATAATTATAA
1 TATTTTATAATTATAA
*
116789247 T-TTTTTTAAT
1 TATTTTATAAT
116789257 ATTTAGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTATAATTATAA
Found at i:116789261 original size:24 final size:25
Alignment explanation
Indices: 116789224--116789270 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
116789214 TTATTTTATA
* *
116789224 TTTTTAATATTTTATAATTATAATT
1 TTTTTAATATTTTAGAATAATAATT
116789249 TTTTTAATA-TTTAGAATAATAA
1 TTTTTAATATTTTAGAATAATAA
116789271 CTGAGTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTTAATATTTTAGAATAATAATT
Found at i:116789419 original size:17 final size:17
Alignment explanation
Indices: 116789397--116789430 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
116789387 AAAAGGCCAC
116789397 ATTGGCATTTTATTTAG
1 ATTGGCATTTTATTTAG
116789414 ATTGGCATTTTATTTAG
1 ATTGGCATTTTATTTAG
116789431 TGATCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (17 bp):
ATTGGCATTTTATTTAG
Found at i:116790245 original size:2 final size:2
Alignment explanation
Indices: 116790238--116790267 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
116790228 AGGAACAAAA
116790238 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
116790268 CCGTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:116791932 original size:31 final size:31
Alignment explanation
Indices: 116791896--116791958 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
116791886 TTTTTCCTTC
116791896 AATCTTTGTTCGATGATAACAAGTTTTATGT
1 AATCTTTGTTCGATGATAACAAGTTTTATGT
116791927 AATCTTTGTTCGATGATAACAAGTTTTATGT
1 AATCTTTGTTCGATGATAACAAGTTTTATGT
116791958 A
1 A
116791959 TTATTTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (31 bp):
AATCTTTGTTCGATGATAACAAGTTTTATGT
Found at i:116791966 original size:31 final size:31
Alignment explanation
Indices: 116791900--116791966 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
116791890 TCCTTCAATC
*
116791900 TTTGTTCGATGATAACAAGTTTTATGTAATC
1 TTTGTTCGATGATAACAAGTTTTATGTAATA
*
116791931 TTTGTTCGATGATAACAAGTTTTATGTATTA
1 TTTGTTCGATGATAACAAGTTTTATGTAATA
116791962 TTTGT
1 TTTGT
116791967 ATGGTCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.49
Consensus pattern (31 bp):
TTTGTTCGATGATAACAAGTTTTATGTAATA
Found at i:116805256 original size:46 final size:46
Alignment explanation
Indices: 116805189--116805277 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
116805179 CTTCATATTC
116805189 ATCAGCTGAAAAACAGCCATGGAGGAGGGTTCAAGCTGGTTTTTAT
1 ATCAGCTGAAAAACAGCCATGGAGGAGGGTTCAAGCTGGTTTTTAT
116805235 ATCAGCTGAAAAACAGCCATGGAGGAGGGTTCAAGCTGGTTTT
1 ATCAGCTGAAAAACAGCCATGGAGGAGGGTTCAAGCTGGTTTT
116805278 CATACTCTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (46 bp):
ATCAGCTGAAAAACAGCCATGGAGGAGGGTTCAAGCTGGTTTTTAT
Found at i:116807443 original size:25 final size:24
Alignment explanation
Indices: 116807413--116807612 Score: 214
Period size: 25 Copynumber: 8.4 Consensus size: 24
116807403 GACTTCAGCA
116807413 TGCTCTCTGAATATTAGCACGTCAG
1 TGCTCTCTG-ATATTAGCACGTCAG
* **
116807438 TGCTCTCTG--ATTAGCACATTTG
1 TGCTCTCTGATATTAGCACGTCAG
*
116807460 TGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTGATA-TTAGCACGTCAG
*
116807485 TGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTGATA-TTAGCACGTCAG
* *
116807510 TGCTCTCTGATTACTAGCACGCCAG
1 TGCTCTCTGA-TATTAGCACGTCAG
116807535 TGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTGATA-TTAGCACGTCAG
* **
116807560 TGCTCTCTG--ATTAGCACATTTG
1 TGCTCTCTGATATTAGCACGTCAG
*
116807582 TGCTCTCTG-TA-TAGCACTTCAG
1 TGCTCTCTGATATTAGCACGTCAG
116807604 TGCTCTCTG
1 TGCTCTCTG
116807613 TTCATTAGTG
Statistics
Matches: 153, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
22 54 0.35
23 2 0.01
24 3 0.02
25 92 0.60
26 2 0.01
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.35
Consensus pattern (24 bp):
TGCTCTCTGATATTAGCACGTCAG
Found at i:116821466 original size:26 final size:26
Alignment explanation
Indices: 116821428--116821509 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
116821418 TGATACAAAT
116821428 TGATAATGAGTTAGGTAAATGTTTCA
1 TGATAATGAGTTAGGTAAATGTTTCA
*
116821454 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGAGTTAGGTAAATGTTTCA
* *
116821480 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATGAGTTAGGTAAATGTTTCA
116821506 TGAT
1 TGAT
116821510 TGGAATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (26 bp):
TGATAATGAGTTAGGTAAATGTTTCA
Found at i:116823024 original size:26 final size:26
Alignment explanation
Indices: 116822956--116823031 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 26
116822946 AAAAACAGCT
* *
116822956 AAATTACT-ATAATACCCCTATGCATGGA
1 AAATTACTGA-AATACCCCTA-G-GTGCA
**
116822984 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGAAATACCCCTAGGTGCA
116823010 AAATTACTGAAATACCCCTAGG
1 AAATTACTGAAATACCCCTAGG
116823032 GTTAAATTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 23 0.56
27 1 0.02
28 17 0.41
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (26 bp):
AAATTACTGAAATACCCCTAGGTGCA
Found at i:116826587 original size:3 final size:3
Alignment explanation
Indices: 116826581--116826644 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
116826571 CCACTGTTGT
116826581 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
116826629 TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC T
116826645 CTTATTATTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:116833607 original size:119 final size:123
Alignment explanation
Indices: 116833477--116833794 Score: 328
Period size: 131 Copynumber: 2.6 Consensus size: 123
116833467 TCCTAATGAA
* * *
116833477 AAATCGAAACCCAGCAC-AGTAGGGCGCGATTCCTCGAATTTCCAAACATTGAATATTGCCTTGT
1 AAATCGCAACCCAGCACGA-TAGGGCACGATTCCTCGAATTGCCAAACATTGAATATTGCCTTGT
*
116833541 TTTAG-G-AAACAC-GAGTGAAATTCCAAAGG-ATATTCAATTATTTTGAACAAACAGG
65 TTTAGAGTAAACACGGAGTAAAATTCCAAAGGAATATTCAATTATTTTGAACAAACAGG
* * * *
116833596 AAATCGCAACCCAGCACGATAGGGCACGATT-CTCCTAATTGCCAAACATCGAGTATTACCTTTG
1 AAATCGCAACCCAGCACGATAGGGCACGATTCCT-CGAATTGCCAAACATTGAATATTGCC-TTG
* * ** * *
116833660 TTTTGAAGAGTTTTTAAAGACGTGAGTAAAATTTCAAAGGAATATTTGATTGTTTTGAACAAACG
64 TTTT--AGAG----TAAACACG-GAGTAAAATTCCAAAGGAATATTCAATTATTTTGAACAAACA
116833725 GG
122 GG
* *
116833727 AAATTGCAACCCAGCACGATAGGGCACGATTCC-CGAATTGCCAAACA-TCAAGTATTGCCTTCG
1 AAATCGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATTGAA-TATTGCCTT-G
116833790 TTTTA
64 TTTTA
116833795 AAGAATTTTT
Statistics
Matches: 162, Mismatches: 20, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
118 2 0.01
119 48 0.30
120 8 0.05
122 2 0.01
123 1 0.01
128 6 0.04
129 3 0.02
130 39 0.24
131 52 0.32
132 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (123 bp):
AAATCGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATTGAATATTGCCTTGTT
TTAGAGTAAACACGGAGTAAAATTCCAAAGGAATATTCAATTATTTTGAACAAACAGG
Found at i:116834322 original size:10 final size:10
Alignment explanation
Indices: 116834283--116834336 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 10
116834273 GACTGTGAGA
*
116834283 AAGAAAGGAG
1 AAGAAAGAAG
*
116834293 -AGAAAGGAG
1 AAGAAAGAAG
*
116834302 AAG-GAGAAG
1 AAGAAAGAAG
*
116834311 AAGAAGGAAG
1 AAGAAAGAAG
116834321 AAGAAAGAAG
1 AAGAAAGAAG
116834331 AAGAAA
1 AAGAAA
116834337 AAAAAAAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.43
10 21 0.57
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAG
Found at i:116834630 original size:93 final size:94
Alignment explanation
Indices: 116834532--116834711 Score: 253
Period size: 93 Copynumber: 1.9 Consensus size: 94
116834522 ATTAGGTTAC
116834532 AAATTGTTAGTGTTTAGT-GTATTAGTGTATT-GTG-ATT-T-TTTTAGTAATAATATATTTTTA
1 AAATTGTTAGTGTTTAGTAGT-TTAGTGTATTAGTGTATTGTATTTTAGTAATAATATA-TTTT-
116834592 AAAAAAATAATTTTATAGTTGATTTGGTTATAT
63 AAAAAAATAATTTTATAGTT-ATTTGGTTATAT
** *
116834625 AAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATATATTTTAA
1 AAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGT-ATTTTAGTAATAATATATTTTAA
116834690 AAAAATAATTTTATAGTTATTT
65 AAAAATAATTTTATAGTTATTT
116834712 TATTAGTAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
93 28 0.36
94 5 0.06
95 7 0.09
96 21 0.27
97 4 0.05
98 13 0.17
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (94 bp):
AAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGTATTTTAGTAATAATATATTTTAAA
AAAATAATTTTATAGTTATTTGGTTATAT
Found at i:116834738 original size:114 final size:114
Alignment explanation
Indices: 116834612--116835052 Score: 721
Period size: 114 Copynumber: 3.9 Consensus size: 114
116834602 TTTTATAGTT
* *
116834612 GATTTGGTTATATAAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
*
116834677 TAATATATTTTAAAAAAATAATTTTATAGTTATTTTATTAGTAATTTAA
66 TAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
* * *
116834726 TATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTA--GTATTAGCGTATTGTAATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
*
116834789 TAATATATTTTAAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
116834838 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
*
116834903 TAATATATTTTAAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
*
116834952 GATTAGGTTATAT--ATTGTTAGTGTTTAGTGGTTTAGTGTGTATTAATGTATTGTGATTTTTTT
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTA--GTGTATTAGTGTATTGTGA-TTTTTT
* *
116835015 TAGTAATGTA-TTTAAAAAAATAATTTTATAGTTATTTT
63 TAGTAATATATTTTAAAAAAATAATTTTATAGCTATTTT
116835053 GTGTTAGTAT
Statistics
Matches: 308, Mismatches: 14, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
112 129 0.42
114 164 0.53
115 15 0.05
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (114 bp):
GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
TAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
Found at i:116835131 original size:16 final size:15
Alignment explanation
Indices: 116835100--116835141 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
116835090 TTTAGTGTTT
116835100 TGTAATTTT-T-TAA
1 TGTAATTTTATATAA
116835113 TGTAATTTTTATATAA
1 TGTAA-TTTTATATAA
116835129 TGTAATTTTATAT
1 TGTAATTTTATAT
116835142 TATTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 4 0.15
15 9 0.35
16 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TGTAATTTTATATAA
Found at i:116837234 original size:33 final size:33
Alignment explanation
Indices: 116837197--116837282 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 33
116837187 ATTTATCTCA
* * *
116837197 GTACTCTACTCCTTCCGGCCCGTATCCACCTAT
1 GTACTCTACTCCTTCCGGCCCGTATCAACCGAC
* *
116837230 GTACTCAACTCC-TCCAGAG-CCGTATCAACCGCC
1 GTACTCTACTCCTTCC-G-GCCCGTATCAACCGAC
*
116837263 GTACTCTACTCCTCCCGGCC
1 GTACTCTACTCCTTCCGGCC
116837283 TATATTCACC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
32 4 0.10
33 35 0.83
34 3 0.07
ACGTcount: A:0.17, C:0.44, G:0.14, T:0.24
Consensus pattern (33 bp):
GTACTCTACTCCTTCCGGCCCGTATCAACCGAC
Found at i:116839868 original size:15 final size:14
Alignment explanation
Indices: 116839850--116839880 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
116839840 TTAATTTATT
116839850 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
116839865 TAATAATAATCTAA
1 TAATAATAATCTAA
116839879 TA
1 TA
116839881 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:116839891 original size:21 final size:20
Alignment explanation
Indices: 116839867--116839935 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
116839857 AATGCTAATA
116839867 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
116839888 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
116839907 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
116839928 ATAATAAT
1 ATAATAAT
116839936 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:116846537 original size:2 final size:2
Alignment explanation
Indices: 116846530--116846567 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
116846520 AGAACATGTT
116846530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
116846568 AAGAAGACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:116847903 original size:15 final size:14
Alignment explanation
Indices: 116847877--116847912 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
116847867 CTTTATAGCC
116847877 GAAAACAGAGAAAAA
1 GAAAA-AGAGAAAAA
116847892 TGAAAAAGAGAAAAA
1 -GAAAAAGAGAAAAA
116847907 GAAAAA
1 GAAAAA
116847913 AATACAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 9 0.45
16 5 0.25
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (14 bp):
GAAAAAGAGAAAAA
Found at i:116863039 original size:12 final size:12
Alignment explanation
Indices: 116863019--116863051 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
116863009 AACTCTGCTT
*
116863019 CGGCGGCGGTGG
1 CGGCTGCGGTGG
116863031 CGGCTGCGGTGG
1 CGGCTGCGGTGG
116863043 CGGCTGCGG
1 CGGCTGCGG
116863052 CGACGGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.27, G:0.61, T:0.12
Consensus pattern (12 bp):
CGGCTGCGGTGG
Found at i:116870868 original size:33 final size:32
Alignment explanation
Indices: 116870831--116870904 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
116870821 ATAAGACTAT
*
116870831 AACAACAAAACA-ACATTAACAATATGGTAGCAA
1 AACAACAAAACATA-A-TAACAATATGATAGCAA
* *
116870864 AACAACAGTAATATAATAACAATATGATAGCAA
1 AACAACA-AAACATAATAACAATATGATAGCAA
116870897 AACAACAA
1 AACAACAA
116870905 GAAAATAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 30 0.86
34 4 0.11
35 1 0.03
ACGTcount: A:0.59, C:0.16, G:0.08, T:0.16
Consensus pattern (32 bp):
AACAACAAAACATAATAACAATATGATAGCAA
Found at i:116880168 original size:12 final size:12
Alignment explanation
Indices: 116880151--116880175 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
116880141 AATGAGTTAT
116880151 ATACATAAATGC
1 ATACATAAATGC
116880163 ATACATAAATGC
1 ATACATAAATGC
116880175 A
1 A
116880176 CTAACTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
ATACATAAATGC
Found at i:116881706 original size:3 final size:3
Alignment explanation
Indices: 116881692--116881749 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
116881682 TATTTATGTT
*
116881692 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
116881740 TTA TTA TTA T
1 TTA TTA TTA T
116881750 ATATGTATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:116881785 original size:13 final size:13
Alignment explanation
Indices: 116881769--116881793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
116881759 TAAAGTAACG
116881769 AAAGAAAGAAAAA
1 AAAGAAAGAAAAA
116881782 AAAGAAAGAAAA
1 AAAGAAAGAAAA
116881794 TAGAAACAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAA
Found at i:116882729 original size:44 final size:44
Alignment explanation
Indices: 116882649--116882740 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
116882639 TGTTCAGGGA
* *
116882649 TACTTCGACCTTGAGTCGATGAAGCACTATAAGTGTCGTATTGT
1 TACTTCGACCTTGAGTCGATGAAGCACTATAAGTGTCATACTGT
* **
116882693 TACTTCGA-CTTCGAGTCGATGAGGCACCT-TGTGTGTCATACTGT
1 TACTTCGACCTT-GAGTCGATGAAGCA-CTATAAGTGTCATACTGT
116882737 TACT
1 TACT
116882741 ATTACTTCGG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 3 0.07
44 36 0.88
45 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (44 bp):
TACTTCGACCTTGAGTCGATGAAGCACTATAAGTGTCATACTGT
Found at i:116882827 original size:47 final size:47
Alignment explanation
Indices: 116882709--116882828 Score: 116
Period size: 47 Copynumber: 2.5 Consensus size: 47
116882699 GACTTCGAGT
* * ** * *
116882709 CGATGAGGCACCTTGTGTGTCATACTGTTACTATTACTTCGGTTTAATC
1 CGATGAGGCA-C-TGAGTGTCGTACTACTACTATTACTTCGGTTAAAGC
* * **
116882758 CGATGAGGTACTAAGTACCGTACTACTACTACTTACTTCGG-TAAAGC
1 CGATGAGGCACTGAGTGTCGTACTACTACTA-TTACTTCGGTTAAAGC
116882805 CGATGAGGCACTGAGTGTCGTACT
1 CGATGAGGCACTGAGTGTCGTACT
116882829 GGTGTGTTGG
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
47 37 0.66
48 10 0.18
49 9 0.16
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (47 bp):
CGATGAGGCACTGAGTGTCGTACTACTACTATTACTTCGGTTAAAGC
Found at i:116884663 original size:75 final size:75
Alignment explanation
Indices: 116884540--116884689 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 75
116884530 AGGAGATGTA
116884540 CACAATATGGTGACGGGTATATTTTTATTGTACTCAGAACCCGTTTATGCTTTAATAGATCCAGG
1 CACAATATGGTGACGGGTATATTTTTATTGTACTCAGAACCCGTTTATGCTTTAATAGATCCAGG
116884605 ATCATCACAT
66 ATCATCACAT
* * * *
116884615 CACAATATGGTGACTGGTATATTTTTATTGTACTCAGAACTCGTTTATGTTTTAATAGATCTAGG
1 CACAATATGGTGACGGGTATATTTTTATTGTACTCAGAACCCGTTTATGCTTTAATAGATCCAGG
*
116884680 ATCGTCACAT
66 ATCATCACAT
116884690 TCTTATGTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (75 bp):
CACAATATGGTGACGGGTATATTTTTATTGTACTCAGAACCCGTTTATGCTTTAATAGATCCAGG
ATCATCACAT
Found at i:116888226 original size:427 final size:427
Alignment explanation
Indices: 116887431--116888656 Score: 2098
Period size: 427 Copynumber: 2.9 Consensus size: 427
116887421 AAATGATTGG
* *
116887431 GCCAGAATTAATTCAAGAAACAGAAGATACTGTTAAA-AAGATTCGAGAAAGATTGAAAGCAGCT
1 GCCAGAATTAATTCAAGAAACAGAAGACACT-ATAAAGAAGATTCGAGAAAGATTGAAAGCAGCT
*
116887495 TTTGACAGGCAGAAGTCATATGCAGATCTGAAACGTAGAGACATTGAGTACGCGATTGGTGATAA
65 TTTGACAGGCAGAAGTCATATGCAGATCTGAAACGTAGAGACATTGAGTACGCGGTTGGTGATAA
*
116887560 GGTATTTCTAAAAGTTTCACCTTGGAAGAAAATTATGAGATTCGGTCGAAAAGGAAAACT-AAGT
130 GGTATTTCTAAAAGTTTCACCTTGGAAGAAAATTATGAGATTCGGTCGAAAAGGAAAACTAAATT
* *
116887624 CTTCGTTTTATTGGGCCATATGAGATTATTGAGAAAGTTGAACCAGTTGCATATCGTCTGGCTTT
195 C-TCGTTTTATTGGGCCATATGAGATTATTGAGAGAGTTGGACCAGTTGCATATCGTCTGGCTTT
* * *
116887689 ACTTCCAGAATTGCAAAAAATTCATGATATTTTTCATGTTTCTATGCTCAGAAGATATCGATCAG
259 GCTTCCAGAATTGCAAAAGATTCATGATGTTTTTCATGTTTCTATGCTCAGAAGATATCGATCAG
* *
116887754 ATCCTTTTTTTATTATTTCTACAGAGGAATTGAAATTAGACCTGATCTTGAATCGGTTGGGAACG
324 ATCCTTTTCTTATTATTTCTACAGAGGAATTGAAATTCGACCTGATCTTGAATCGGTTGGGAACG
116887819 TTATCTACCGTTAGCTGAATTTGTATGCAATAATAGTGA
389 TTATCTACCGTTAGCTGAATTTGTATGCAATAATAGTGA
116887858 GCCAGAATTAATTCAAGAAACAGAAGACACTATAAAGAAGATTCGAGAAAGATTGAAAGCAGCTT
1 GCCAGAATTAATTCAAGAAACAGAAGACACTATAAAGAAGATTCGAGAAAGATTGAAAGCAGCTT
*
116887923 TTAACAGGCAGAAGTCATATGCAGATCTGAAACGTAGAGACATTGAGTACGCGGTTGGTGATAAG
66 TTGACAGGCAGAAGTCATATGCAGATCTGAAACGTAGAGACATTGAGTACGCGGTTGGTGATAAG
116887988 GTATTTCTAAAAGTTTCACCTTGGAAGAAAATTATGAGATTCGGTCGAAAAGGAAAACTAAATTC
131 GTATTTCTAAAAGTTTCACCTTGGAAGAAAATTATGAGATTCGGTCGAAAAGGAAAACTAAATTC
* * * *
116888053 TCGTTTTATTAGGCCATATGAGATTATTGATAGAGTTGGACCAATTGCATATCATCTGGCTTTGC
196 TCGTTTTATTGGGCCATATGAGATTATTGAGAGAGTTGGACCAGTTGCATATCGTCTGGCTTTGC
* *
116888118 TTCCAGAATTACAAAAGATTCATGATGTTTTTCATGTTTCTATGCTCAGAAGATATCAATCAGAT
261 TTCCAGAATTGCAAAAGATTCATGATGTTTTTCATGTTTCTATGCTCAGAAGATATCGATCAGAT
116888183 CCTTTTCTTATTATTTCTACAGAGGAATTGAAATTCGACCTGATCTTGAATCGGTTGGGAACGTT
326 CCTTTTCTTATTATTTCTACAGAGGAATTGAAATTCGACCTGATCTTGAATCGGTTGGGAACGTT
*
116888248 ATCTACCGTTAGCTGAATTTGTATGCAATAATAGTGG
391 ATCTACCGTTAGCTGAATTTGTATGCAATAATAGTGA
* * * *
116888285 GCCAAAATTAATTCAAGAAACAGAAGACACTGTTAAGAAGATTCGAGAAAGATTGAAAGCAACTT
1 GCCAGAATTAATTCAAGAAACAGAAGACACTATAAAGAAGATTCGAGAAAGATTGAAAGCAGCTT
116888350 TTGAC-GGACAGAAGTCATATGCAGATCTGAAACGTAGAGACATTGAGTACGCGGTTGGTGATAA
66 TTGACAGG-CAGAAGTCATATGCAGATCTGAAACGTAGAGACATTGAGTACGCGGTTGGTGATAA
* * *
116888414 GGTATTTTTAAAAGTTTCACCTCGGAAGAAAATTATGAGATTCGGTCGAAAAGGAAAACTAAGTT
130 GGTATTTCTAAAAGTTTCACCTTGGAAGAAAATTATGAGATTCGGTCGAAAAGGAAAACTAAATT
* * *
116888479 CTCATTTTATTGGGCCATATGAGATTATTGAGAGAGTTGGACCAGTTACATATTGTCTGGCTTTG
195 CTCGTTTTATTGGGCCATATGAGATTATTGAGAGAGTTGGACCAGTTGCATATCGTCTGGCTTTG
*
116888544 CTTCCAGAATTGTAAAAGATTCATGATGTTTTTCATGTTTCTATGCTCAGAAGATATCGATCAGA
260 CTTCCAGAATTGCAAAAGATTCATGATGTTTTTCATGTTTCTATGCTCAGAAGATATCGATCAGA
* * *
116888609 TCCTTTTCTTATTATTTCTACAGTGGATACTGAAATTCAACCTGATCT
325 TCCTTTTCTTATTATTTCTACAGAGGA-ATTGAAATTCGACCTGATCT
116888657 GTCATATGAA
Statistics
Matches: 755, Mismatches: 40, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
426 6 0.01
427 727 0.96
428 22 0.03
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (427 bp):
GCCAGAATTAATTCAAGAAACAGAAGACACTATAAAGAAGATTCGAGAAAGATTGAAAGCAGCTT
TTGACAGGCAGAAGTCATATGCAGATCTGAAACGTAGAGACATTGAGTACGCGGTTGGTGATAAG
GTATTTCTAAAAGTTTCACCTTGGAAGAAAATTATGAGATTCGGTCGAAAAGGAAAACTAAATTC
TCGTTTTATTGGGCCATATGAGATTATTGAGAGAGTTGGACCAGTTGCATATCGTCTGGCTTTGC
TTCCAGAATTGCAAAAGATTCATGATGTTTTTCATGTTTCTATGCTCAGAAGATATCGATCAGAT
CCTTTTCTTATTATTTCTACAGAGGAATTGAAATTCGACCTGATCTTGAATCGGTTGGGAACGTT
ATCTACCGTTAGCTGAATTTGTATGCAATAATAGTGA
Found at i:116889204 original size:3 final size:3
Alignment explanation
Indices: 116889192--116889226 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
116889182 AAGATATTTA
116889192 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
116889227 ATATGTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:116901573 original size:30 final size:29
Alignment explanation
Indices: 116901533--116901590 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
116901523 ATGAAAGAAA
*
116901533 TAAAAAATTTAATTACT-TTTAATTATAAT
1 TAAAAAATTT-ATTAATATTTAATTATAAT
*
116901562 TAAATAAATTTATTAATATTTATTTATAA
1 TAAA-AAATTTATTAATATTTAATTATAA
116901591 GTACTCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
TAAAAAATTTATTAATATTTAATTATAAT
Found at i:116903673 original size:21 final size:22
Alignment explanation
Indices: 116903626--116903673 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
116903616 ATTAATAATT
*
116903626 AATAT-TTTTTAAAAAATTTTA
1 AATATATTTTTAAAAAATTTAA
116903647 AA-ATATTTTTAAAAAA-TTAA
1 AATATATTTTTAAAAAATTTAA
116903667 AATATAT
1 AATATAT
116903674 GAAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATATATTTTTAAAAAATTTAA
Found at i:116918249 original size:21 final size:21
Alignment explanation
Indices: 116918224--116918268 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
116918214 TTAAGATAAA
**
116918224 TATTTATATTTATGATAATTT
1 TATTTATATTTAAAATAATTT
116918245 TATTTATATTTAAAATAATTT
1 TATTTATATTTAAAATAATTT
116918266 TAT
1 TAT
116918269 ACATAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTATATTTAAAATAATTT
Found at i:116926161 original size:2 final size:2
Alignment explanation
Indices: 116926154--116926179 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
116926144 GATTTTTCAA
116926154 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
116926180 TCCACTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116929616 original size:22 final size:22
Alignment explanation
Indices: 116929583--116929645 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
116929573 GTTGTATTAT
* **
116929583 TTTTA-AAATATTAAATTGTAA
1 TTTTATAATTATTAAATTAAAA
*
116929604 TTTTACT-ATTATTAATTTAAAA
1 TTTTA-TAATTATTAAATTAAAA
116929626 TTTTATAAATTATTAAATTA
1 TTTTAT-AATTATTAAATTA
116929646 TAAAATGATG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
21 6 0.18
22 16 0.48
23 11 0.33
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTATAATTATTAAATTAAAA
Found at i:116930469 original size:24 final size:23
Alignment explanation
Indices: 116930421--116930469 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
116930411 ATGTAAATAG
* *
116930421 ATAAAAATTAAAAATATATATAC
1 ATAAAAATTAAAAATATAAAGAC
116930444 ATAAAATATT-AAAATATAAAAGAC
1 ATAAAA-ATTAAAAATAT-AAAGAC
116930468 AT
1 AT
116930470 GAATGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (23 bp):
ATAAAAATTAAAAATATAAAGAC
Found at i:116931679 original size:2 final size:2
Alignment explanation
Indices: 116931672--116931698 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
116931662 TTACCACAGA
116931672 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 A
116931699 ACCAAAGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:116938695 original size:113 final size:113
Alignment explanation
Indices: 116938464--116938802 Score: 592
Period size: 113 Copynumber: 3.0 Consensus size: 113
116938454 GAGAGAGAAA
* * *
116938464 ACACATAGTGTGAATGAGATAAAGAAATGACGAAAGAGAGGGTTTATGGGAGGGAG-AAAATG-A
1 ACACATAGAGTGAATGAGATAAAGAAATGAAGAAAGAGAGAGTTTATGGGAGGGAGAAAAATGCA
* * *
116938527 GGGTGATAGTCAGCTTGAAGACTAACATCGCCGCCAAACAAAACAAAAG
66 -GGTGATAGTCAGCTCGAAAAGTAACATCGCCGCCAAACAAAACAAAAG
116938576 ACACATAGAGTGAATGAGATAAAGAAATGAAGAAAGAGAGAGTTTATGGGAGGGAGAAAAATGCA
1 ACACATAGAGTGAATGAGATAAAGAAATGAAGAAAGAGAGAGTTTATGGGAGGGAGAAAAATGCA
116938641 GGTGATAGTCAGCTCGAAAAGTAACATCGCCGCCAAACAAAACAAAAG
66 GGTGATAGTCAGCTCGAAAAGTAACATCGCCGCCAAACAAAACAAAAG
116938689 ACACATAGAGTGAATGAGATAAAGAAATGAAGAAAGAGAGAGTTTATGGGAGGGAGAAAAATGCA
1 ACACATAGAGTGAATGAGATAAAGAAATGAAGAAAGAGAGAGTTTATGGGAGGGAGAAAAATGCA
*
116938754 GGTGATAGTCAGCTCAAAAAGTAACATCGCCGCCAAACAAAACAAAAG
66 GGTGATAGTCAGCTCGAAAAGTAACATCGCCGCCAAACAAAACAAAAG
116938802 A
1 A
116938803 AAAGAAATAA
Statistics
Matches: 218, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
112 53 0.24
113 164 0.75
114 1 0.00
ACGTcount: A:0.46, C:0.12, G:0.27, T:0.15
Consensus pattern (113 bp):
ACACATAGAGTGAATGAGATAAAGAAATGAAGAAAGAGAGAGTTTATGGGAGGGAGAAAAATGCA
GGTGATAGTCAGCTCGAAAAGTAACATCGCCGCCAAACAAAACAAAAG
Found at i:116955907 original size:18 final size:18
Alignment explanation
Indices: 116955881--116955922 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
116955871 GAAAATGAAA
116955881 TTTGGAAGAATTATTTTT
1 TTTGGAAGAATTATTTTT
*
116955899 TTTGTAAGAATTATTTTT
1 TTTGGAAGAATTATTTTT
*
116955917 ATTGGA
1 TTTGGA
116955923 TGAAACTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.55
Consensus pattern (18 bp):
TTTGGAAGAATTATTTTT
Found at i:116955978 original size:14 final size:14
Alignment explanation
Indices: 116955959--116955988 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
116955949 ATGTTAGTGA
*
116955959 ATAAATATATAAAT
1 ATAAATAAATAAAT
116955973 ATAAATAAATAAAT
1 ATAAATAAATAAAT
116955987 AT
1 AT
116955989 TTCTATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAATAAATAAAT
Found at i:116956023 original size:28 final size:30
Alignment explanation
Indices: 116955963--116956029 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
116955953 TAGTGAATAA
*
116955963 ATATATAAATATAAATAAATAAATATTTCT
1 ATATATAAATATAAATAAATAAATAATTCT
*
116955993 ATATA-AAATA-AAATAAATTGAATAATT-T
1 ATATATAAATATAAATAAA-TAAATAATTCT
*
116956021 ATATTTAAA
1 ATATATAAA
116956030 CTATGAGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 12 0.38
29 15 0.47
30 5 0.16
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (30 bp):
ATATATAAATATAAATAAATAAATAATTCT
Found at i:116956477 original size:20 final size:20
Alignment explanation
Indices: 116956452--116956500 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
116956442 AGGAGCGATT
*
116956452 AAATCAATTTGATTAAAATC
1 AAATCAAATTGATTAAAATC
*
116956472 AAATCAAATTGATTGAAATC
1 AAATCAAATTGATTAAAATC
*
116956492 AAATAAAAT
1 AAATCAAAT
116956501 CAGGATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATC
Found at i:116957290 original size:46 final size:47
Alignment explanation
Indices: 116957230--116957456 Score: 313
Period size: 46 Copynumber: 5.0 Consensus size: 47
116957220 TTTGACATGA
* * * * * *
116957230 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*** **
116957276 TGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
116957322 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
116957368 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTT-ATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
116957414 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTT-ATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAG
116957457 AGAGCACACT
Statistics
Matches: 166, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
45 14 0.08
46 149 0.90
47 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
Found at i:116959606 original size:11 final size:11
Alignment explanation
Indices: 116959590--116959641 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
116959580 TATACTAAAT
116959590 AAATAATAATA
1 AAATAATAATA
*
116959601 AAATAAT-ATT
1 AAATAATAATA
* *
116959611 AAATATCTCATA
1 AAATA-ATAATA
*
116959623 AAATATTAATA
1 AAATAATAATA
116959634 AAATAATA
1 AAATAATA
116959642 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:116965339 original size:14 final size:15
Alignment explanation
Indices: 116965310--116965339 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
116965300 GAGTCTCCTT
116965310 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
116965325 TTCTATTTT-TTTTA
1 TTCTATTTTCTTTTA
116965339 T
1 T
116965340 CTTATGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTATTTTCTTTTA
Found at i:116967133 original size:135 final size:133
Alignment explanation
Indices: 116966796--116967278 Score: 614
Period size: 132 Copynumber: 3.6 Consensus size: 133
116966786 TTATTCATTT
* * *
116966796 AAAAATTCTTTAAAACGAAGACGA-GATTTGATATTTGGCAATTCGCAGAATCGTGCCCTAACGT
1 AAAAATTCTTTAAAACGAAGGCGATG-TTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * **
116966860 GCTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATACCCCTTCAAAATTTCACCCATGTCT
65 GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCATGTCT
*
116966925 T-TT
130 TCTA
* * *
116966928 AAAAATTCTTTAAAACGAATGCGATGTTTGATATTTGGCAATTCGCGGAATCGTGCCTTAACGTG
1 AAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTG
* * *
116966993 TTGGGTTGCAATTTCTCGTTTGCTCAAAATGATCGAATATCTCTTCAAAATTTCATTCATGTCTT
66 CTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCATGTCTT
116967058 CTAAA
131 CT--A
* *
116967063 AAAAATCCTTTAAAACGAAGGCGATGTTCGATATTTGACAATTCGCGGAATCGTGCCCTAACGTG
1 AAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTG
* * * ** *
116967128 CTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGATTATCCCTTTAGAATTTTGTTCATGTTTT
66 CTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCATGTCTT
116967193 CT-
131 CTA
* ** ** * * * *
116967195 AAAAACTCTTTAAAACGAAGGTAATACTCAATGTTTGGCAATTCG-GGAGTCGTGCCCTATCGTG
1 AAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTG
* *
116967259 CTGGGTTGCGATTTCCCGTT
66 CTGGGTTGCAATTTCTCGTT
116967279 CGTTCAAGGA
Statistics
Matches: 308, Mismatches: 39, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
131 35 0.11
132 153 0.50
133 2 0.01
135 118 0.38
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (133 bp):
AAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTG
CTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCATGTCTT
CTA
Found at i:116967234 original size:267 final size:266
Alignment explanation
Indices: 116966796--116967278 Score: 664
Period size: 267 Copynumber: 1.8 Consensus size: 266
116966786 TTATTCATTT
* * *
116966796 AAAAATTCTTTAAAACGAAGACGAGATTTGATATTTGGCAATTCGCAGAATCGTGCCCTAACGTG
1 AAAAATCCTTTAAAACGAAGACGAGATTCGATATTTGACAATTCGCAGAATCGTGCCCTAACGTG
116966861 CTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATACCCCTTCAAAATTTCACCCATGTCTT
66 CTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATACCCCTTCAAAATTTCACCCATGTCTT
* * * ** ** *
116966926 TTAAAAATTCTTTAAAACGAATGCGATGTTTGATATTTGGCAATTCGCGGAATCGTGCCTTAACG
131 TTAAAAACTCTTTAAAACGAAGGCAATACTCAATATTTGGCAATTCG-GGAATCGTGCCCTAACG
* *
116966991 TGTTGGGTTGCAATTTCTCGTTTGCTCAAAATGATCGAATATCTCTTCAAAATTTCATTCATGTC
195 TGCTGGGTTGCAATTTCCCGTTTGCTCAAAATGATCGAATATCTCTTCAAAATTTCATTCATGTC
116967056 TTCTAAA
260 TTCTAAA
* *
116967063 AAAAATCCTTTAAAACGAAGGCGATG-TTCGATATTTGACAATTCGCGGAATCGTGCCCTAACGT
1 AAAAATCCTTTAAAACGAAGACGA-GATTCGATATTTGACAATTCGCAGAATCGTGCCCTAACGT
* * * * * ****
116967127 GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGATTATCCCTTTAGAATTTTGTTCATGT-T
65 GCTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATACCCCTTCAAAATTTCACCCATGTCT
* * * *
116967191 TTCTAAAAACTCTTTAAAACGAAGGTAATACTCAATGTTTGGCAATTCGGGAGTCGTGCCCTATC
130 TT-TAAAAACTCTTTAAAACGAAGGCAATACTCAATATTTGGCAATTCGGGAATCGTGCCCTAAC
*
116967256 GTGCTGGGTTGCGATTTCCCGTT
194 GTGCTGGGTTGCAATTTCCCGTT
116967279 CGTTCAAGGA
Statistics
Matches: 185, Mismatches: 29, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
266 36 0.19
267 148 0.80
268 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (266 bp):
AAAAATCCTTTAAAACGAAGACGAGATTCGATATTTGACAATTCGCAGAATCGTGCCCTAACGTG
CTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATACCCCTTCAAAATTTCACCCATGTCTT
TTAAAAACTCTTTAAAACGAAGGCAATACTCAATATTTGGCAATTCGGGAATCGTGCCCTAACGT
GCTGGGTTGCAATTTCCCGTTTGCTCAAAATGATCGAATATCTCTTCAAAATTTCATTCATGTCT
TCTAAA
Done.