Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 13 of 26
Found at i:2180044 original size:27 final size:27
Alignment explanation
Indices: 2179976--2180054 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
2179966 ATATAAAAAT
* *
2179976 AATATAA-TATAAATAAATAATATATTAA
1 AATATAATTAT-AATATATAATAT-TTTA
* *
2180004 AATTTATTTA-AATATATAATATTTTA
1 AATATAATTATAATATATAATATTTTA
2180030 AATATAATTATAATATATAA-ATTTT
1 AATATAATTATAATATATAATATTTT
2180055 CATAAAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 16 0.37
27 20 0.47
28 5 0.12
29 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATATAATTATAATATATAATATTTTA
Found at i:2182746 original size:22 final size:22
Alignment explanation
Indices: 2182703--2182746 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2182693 ATTTTTTATT
* **
2182703 TATTAAAAATATTATATTTTAA
1 TATTAAAAATATTAAAAATTAA
*
2182725 TATTAAAACTATTAAAAATTAA
1 TATTAAAAATATTAAAAATTAA
2182747 CTTCACTTTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATTAAAAATTAA
Found at i:2183264 original size:74 final size:75
Alignment explanation
Indices: 2183111--2183267 Score: 178
Period size: 74 Copynumber: 2.1 Consensus size: 75
2183101 CAGTTGACGG
* * *
2183111 AAAACACATGCTTGAAACTCAAGTAGATTGGCTACTGCCGTCCATTAAATGGAAACTCGTAAGCA
1 AAAA-ACATGCTTGAAACACAAGTAGATCGG--ACTGCCGTCCATCAAATGGAAACTCGTAAGCA
2183176 GTTGTTCCCTTGC
63 GTTGTTCCCTTGC
* * *
2183189 AAAAACATGCTTGGAACACAAGTAGATCGG-CTGCCGTCCA-CAGAATGATAAACTCGTAAGCTG
1 AAAAACATGCTTGAAACACAAGTAGATCGGACTGCCGTCCATCA-AATG-GAAACTCGTAAGCAG
2183252 TAT-TT-CCTTGC
64 T-TGTTCCCTTGC
2183263 AAAAA
1 AAAAA
2183268 GAAAAAGGCA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
73 1 0.01
74 25 0.36
75 16 0.23
76 1 0.01
77 23 0.33
78 4 0.06
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (75 bp):
AAAAACATGCTTGAAACACAAGTAGATCGGACTGCCGTCCATCAAATGGAAACTCGTAAGCAGTT
GTTCCCTTGC
Found at i:2189447 original size:2 final size:2
Alignment explanation
Indices: 2189440--2189465 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2189430 AAAAGTTAGG
2189440 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
2189466 CATAGCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2189560 original size:27 final size:27
Alignment explanation
Indices: 2189517--2189591 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
2189507 AATTATATTA
2189517 TATATATATTATAATAATATTTAAAATAT
1 TATATAT-TTAT-ATAATATTTAAAATAT
*
2189546 TATATATTTATATAA-ATTTTAATATAT
1 TATATATTTATATAATA-TTTAAAATAT
* *
2189573 TA-ATAATTAATATTATATT
1 TATAT-ATTTATATAATATT
2189592 AATATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 3 0.08
27 25 0.62
28 5 0.12
29 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TATATATTTATATAATATTTAAAATAT
Found at i:2190279 original size:26 final size:26
Alignment explanation
Indices: 2190182--2190279 Score: 60
Period size: 26 Copynumber: 3.7 Consensus size: 26
2190172 TTAAATTTGT
* * *
2190182 ATAAATTGATATAAT-TAATTTTTTAT
1 ATAAATT-TTATAATATAATTTATTAA
*
2190208 ATAAATTTAAATAATATAATTATATTTAA
1 ATAAATTT-TATAATATAATT-TA-TTAA
* *
2190237 TGTTTAATTTT-T-A-ATAATTTATTAA
1 --ATAAATTTTATAATATAATTTATTAA
2190262 ATAAATTTTATAATATAA
1 ATAAATTTTATAATATAA
2190280 AATTAATACT
Statistics
Matches: 54, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
23 7 0.13
24 1 0.02
25 5 0.09
26 18 0.33
27 11 0.20
28 2 0.04
29 4 0.07
31 6 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
ATAAATTTTATAATATAATTTATTAA
Found at i:2195776 original size:20 final size:18
Alignment explanation
Indices: 2195748--2195793 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
2195738 AAAATTATTT
*
2195748 TTATATTAAATAAAAATATA
1 TTATTTTAAAT-AAAA-ATA
2195768 TTATTTT-AATAAAAATA
1 TTATTTTAAATAAAAATA
2195785 TTATTTTAA
1 TTATTTTAA
2195794 TTAGATCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 10 0.42
18 5 0.21
19 3 0.12
20 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATTTTAAATAAAAATA
Found at i:2195780 original size:23 final size:22
Alignment explanation
Indices: 2195737--2195780 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2195727 TATATTTATA
*
2195737 AAAAATTATTTTTATATTAAAT
1 AAAAATTATTTTTATAATAAAT
2195759 AAAAATATATTATTT-TAATAAA
1 AAAAAT-TATT-TTTATAATAAA
2195781 AATATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 10 0.53
24 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAATTATTTTTATAATAAAT
Found at i:2195787 original size:17 final size:18
Alignment explanation
Indices: 2195760--2195794 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2195750 ATATTAAATA
2195760 AAAATATATTATTTTAAT
1 AAAATATATTATTTTAAT
2195778 AAAA-ATATTATTTTAAT
1 AAAATATATTATTTTAAT
2195795 TAGATCAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATATATTATTTTAAT
Found at i:2195920 original size:13 final size:14
Alignment explanation
Indices: 2195892--2195924 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2195882 AATTTTTTAA
2195892 TTTTTAAAATAAAT
1 TTTTTAAAATAAAT
*
2195906 TTTTTAAAA-ATAT
1 TTTTTAAAATAAAT
2195919 TTTTTA
1 TTTTTA
2195925 GAATGTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTTAAAATAAAT
Found at i:2196072 original size:18 final size:18
Alignment explanation
Indices: 2196009--2196061 Score: 62
Period size: 14 Copynumber: 3.2 Consensus size: 18
2195999 ATATCAGTTA
2196009 TAAAAATTTAA--AAAA-
1 TAAAAATTTAATTAAAAT
2196024 T-AAAATTTAATT-AAAT
1 TAAAAATTTAATTAAAAT
2196040 TAAAAATTTATATTAAAAT
1 TAAAAATTTA-ATTAAAAT
2196059 TAA
1 TAA
2196062 TATATTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 9 0.28
15 4 0.12
16 1 0.03
17 8 0.25
18 3 0.09
19 7 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATTTAATTAAAAT
Found at i:2196106 original size:17 final size:17
Alignment explanation
Indices: 2196086--2196141 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
2196076 AATTTTAATA
2196086 AAATAAAAATAAAAATT
1 AAATAAAAATAAAAATT
*
2196103 AAAT-AAATTAAAAAATT
1 AAATAAAAAT-AAAAATT
*
2196120 ATATTAAAAATTAAAATATT
1 A-AATAAAAA-TAAAA-ATT
2196140 AA
1 AA
2196142 TTATTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 2 0.06
19 8 0.26
20 5 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAAAATAAAAATT
Found at i:2196110 original size:71 final size:72
Alignment explanation
Indices: 2196019--2196160 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 72
2196009 TAAAAATTTA
* * * *
2196019 AAAAATAAAATTTAATTAAATTAAAAATTTATATT-AAAATTAATATATTAATTATTAAATTTTA
1 AAAAATAAAAATTAAATAAATTAAAAAATTATATTAAAAATTAAAATATTAATTATTAAATTTTA
2196083 ATAAAAT
66 ATAAAAT
**
2196090 AAAAATAAAAATTAAATAAATTAAAAAATTATATTAAAAATTAAAATATTAATTATTATTTTTTA
1 AAAAATAAAAATTAAATAAATTAAAAAATTATATTAAAAATTAAAATATTAATTATTAAATTTTA
2196155 ATAAAA
66 ATAAAA
2196161 AAATTTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 32 0.50
72 32 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (72 bp):
AAAAATAAAAATTAAATAAATTAAAAAATTATATTAAAAATTAAAATATTAATTATTAAATTTTA
ATAAAAT
Found at i:2196132 original size:20 final size:19
Alignment explanation
Indices: 2196107--2196144 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2196097 AAAATTAAAT
2196107 AAATTAAAAAATTATATTAA
1 AAATTAAAAAATTA-ATTAA
*
2196127 AAATTAAAATATTAATTA
1 AAATTAAAAAATTAATTA
2196145 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTAAAAAATTAATTAA
Found at i:2196803 original size:16 final size:17
Alignment explanation
Indices: 2196768--2196810 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
2196758 ATCATATATT
* *
2196768 TAAATTATTATTAATTA
1 TAAATTATTATAAATAA
2196785 TAAATT-TTATAAATAA
1 TAAATTATTATAAATAA
2196801 TAAATTATTA
1 TAAATTATTA
2196811 ACTTTTGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATTATTATAAATAA
Found at i:2197890 original size:72 final size:73
Alignment explanation
Indices: 2197813--2198148 Score: 362
Period size: 72 Copynumber: 4.6 Consensus size: 73
2197803 CTTTACATAA
* * * *
2197813 AAATTTAAACTTCTACAAATAAAGATAAATAATACCCTAAAAATTTAAACTCATATAATCA-ACT
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACCATAAAAATTTAAACTCATATAATCATACC
*
2197877 TAAAAAAT
66 CAAAAAAT
* * * * * *
2197885 AAATTTAAATTTTTACAAATAAAAATGAATTATACGATAAAAAATATAAACTCATATAATAATAC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACCAT-AAAAATTTAAACTCATATAATCATAC
* *
2197950 CCCAAAAAC
65 CCAAAAAAT
* * *
2197959 ACAA-TTAAAC-T-TA-AAATAAAAATAAATTATACCATAAAAAATTTAAATTCATATTAGCATA
1 A-AATTTAAACTTCTACAAATAAAAATAAATTATACCAT-AAAAATTTAAACTCATATAATCATA
2198020 CCCAAAAAA-
64 CCCAAAAAAT
* * * *
2198029 ACACATTTAAACTTCTACAAATAAAAATAAATTATACCCTAAAAATTTCAACTCGTATAGTCATA
1 A-A-ATTTAAACTTCTACAAATAAAAATAAATTATACCATAAAAATTTAAACTCATATAATCATA
2198094 CCC-AAAAAT
64 CCCAAAAAAT
* * * *
2198103 AAATTTAAACTTATACAAATAAAGATAAATAATACCTTAAAAATTT
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACCATAAAAATTT
2198149 TATTAATACA
Statistics
Matches: 222, Mismatches: 33, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
70 3 0.01
71 50 0.23
72 79 0.36
73 29 0.13
74 38 0.17
75 23 0.10
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (73 bp):
AAATTTAAACTTCTACAAATAAAAATAAATTATACCATAAAAATTTAAACTCATATAATCATACC
CAAAAAAT
Found at i:2198343 original size:3 final size:3
Alignment explanation
Indices: 2198337--2198377 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
2198327 AATTAAAAAA
* *
2198337 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT AGT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2198378 AAAAAACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2198796 original size:3 final size:3
Alignment explanation
Indices: 2198788--2198828 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2198778 AATTACTACA
2198788 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2198829 AAATAGCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2200441 original size:2 final size:2
Alignment explanation
Indices: 2200436--2200462 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2200426 CTCTAACTCC
2200436 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 A
2200463 ATCAATAATT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2202361 original size:2 final size:2
Alignment explanation
Indices: 2202354--2202382 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2202344 CCCTTTTACT
2202354 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 T
2202383 CCCATCTATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2204652 original size:2 final size:2
Alignment explanation
Indices: 2204645--2204671 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2204635 GTATACTTTA
2204645 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 A
2204672 GTTATAGTTG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2205145 original size:21 final size:20
Alignment explanation
Indices: 2205106--2205145 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2205096 TATAATTTTA
**
2205106 TTATCTATTTACTTTTATTT
1 TTATCTATTTACTCATATTT
2205126 TTATCATATTTACTCATATT
1 TTATC-TATTTACTCATATT
2205146 CAATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATCTATTTACTCATATTT
Found at i:2205155 original size:2 final size:2
Alignment explanation
Indices: 2205148--2205184 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2205138 CTCATATTCA
*
2205148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2205185 AAATCTATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2205665 original size:23 final size:21
Alignment explanation
Indices: 2205629--2205689 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2205619 ATAATTATAT
* *
2205629 TTAATATATATTTAAATATAAA
1 TTAAAATATTTTTAAA-ATAAA
* *
2205651 TATAAAATATTTTTAAAAGATA
1 T-TAAAATATTTTTAAAATAAA
*
2205673 TTAAAACATTTTTAAAA
1 TTAAAATATTTTTAAAA
2205690 ATAAGAATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 15 0.45
22 5 0.15
23 13 0.39
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAAATATTTTTAAAATAAA
Found at i:2205980 original size:20 final size:20
Alignment explanation
Indices: 2205955--2205994 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2205945 ATAATTAAAT
*
2205955 TTAAATAAAAATTTTTATTA
1 TTAAATAAAAATTTTAATTA
*
2205975 TTAAATAATAATTTTAATTA
1 TTAAATAAAAATTTTAATTA
2205995 AAAAATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAATAAAAATTTTAATTA
Found at i:2206000 original size:20 final size:20
Alignment explanation
Indices: 2205957--2206000 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2205947 AATTAAATTT
* **
2205957 AAATAAAAATTTTTATTATT
1 AAATAAAAATTTTAATTAAA
*
2205977 AAATAATAATTTTAATTAAA
1 AAATAAAAATTTTAATTAAA
2205997 AAAT
1 AAAT
2206001 TATATTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATAAAAATTTTAATTAAA
Found at i:2215498 original size:2 final size:2
Alignment explanation
Indices: 2215485--2215519 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2215475 CAAGGTTTCG
*
2215485 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2215520 GACAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2215933 original size:25 final size:25
Alignment explanation
Indices: 2215904--2215951 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2215894 CGGTGGTGAG
*
2215904 AGAAATCCCGACGCGTGAGAGAGAA
1 AGAAATCCCGACGAGTGAGAGAGAA
* *
2215929 AGAAATCTCGATGAGTGAGAGAG
1 AGAAATCCCGACGAGTGAGAGAG
2215952 GGATGTGACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.33, T:0.12
Consensus pattern (25 bp):
AGAAATCCCGACGAGTGAGAGAGAA
Found at i:2221206 original size:2 final size:2
Alignment explanation
Indices: 2221199--2221227 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2221189 TAATTAGCAA
2221199 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
2221228 ACCTCATTGA
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:2231822 original size:21 final size:20
Alignment explanation
Indices: 2231791--2231839 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
2231781 TACTTTTGAC
2231791 ATAATAAAATACATATAAAAT
1 ATAA-AAAATACATATAAAAT
** *
2231812 ATATAAAAATATTTTTAAAAT
1 ATA-AAAAATACATATAAAAT
2231833 ATAAAAA
1 ATAAAAA
2231840 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAAAATACATATAAAAT
Found at i:2231871 original size:22 final size:21
Alignment explanation
Indices: 2231836--2231881 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2231826 TTAAAATATA
2231836 AAAATAAAAATAAACATAAATT
1 AAAATAAAAATAAACAT-AATT
* * *
2231858 AAAATATAATTAAATATAATT
1 AAAATAAAAATAAACATAATT
2231879 AAA
1 AAA
2231882 TACGTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATAAAAATAAACATAATT
Found at i:2231872 original size:10 final size:10
Alignment explanation
Indices: 2231854--2231915 Score: 70
Period size: 10 Copynumber: 6.1 Consensus size: 10
2231844 AATAAACATA
2231854 AATTAAAATAT
1 AATT-AAATAT
2231865 AATTAAATAT
1 AATTAAATAT
*
2231875 AATTAAATAC
1 AATTAAATAT
**
2231885 GTTTAAATAT
1 AATTAAATAT
2231895 AATTAAATAT
1 AATTAAATAT
* *
2231905 ACTTGAATAT
1 AATTAAATAT
2231915 A
1 A
2231916 TTATAAAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
10 39 0.91
11 4 0.09
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (10 bp):
AATTAAATAT
Found at i:2234300 original size:3 final size:3
Alignment explanation
Indices: 2234292--2234331 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2234282 CTTCTCAACT
2234292 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2234332 ATTTCGTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2235046 original size:24 final size:27
Alignment explanation
Indices: 2234973--2235043 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
2234963 AAACAAGCCT
* *
2234973 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
2235001 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
2235028 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2235044 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:2248416 original size:20 final size:20
Alignment explanation
Indices: 2248393--2248433 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2248383 TTAATTTTAT
* *
2248393 TAATATAATATTTAATCTCA
1 TAATATAATAATTAATATCA
2248413 TAATATAATAATTAATATCA
1 TAATATAATAATTAATATCA
2248433 T
1 T
2248434 CATTACTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATAATAATTAATATCA
Found at i:2248635 original size:11 final size:11
Alignment explanation
Indices: 2248619--2248670 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
2248609 ATTTACATTG
2248619 ATATTTAAAAT
1 ATATTTAAAAT
2248630 ATATTTAAACAT
1 ATATTTAAA-AT
* *
2248642 AAATGTTAATTAT
1 ATAT-TTAA-AAT
2248655 AATATTTAAAAT
1 -ATATTTAAAAT
2248667 ATAT
1 ATAT
2248671 AAAAAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 13 0.39
12 7 0.21
13 10 0.30
14 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
ATATTTAAAAT
Found at i:2248866 original size:20 final size:20
Alignment explanation
Indices: 2248841--2248900 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
2248831 GCTTGGCATT
2248841 TAAGATGATTATGCTAATTA
1 TAAGATGATTATGCTAATTA
2248861 TAAGATGATTATGCTAATTA
1 TAAGATGATTATGCTAATTA
2248881 TAAGATGATTATGCTAATTA
1 TAAGATGATTATGCTAATTA
2248901 ATCAATAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (20 bp):
TAAGATGATTATGCTAATTA
Found at i:2249725 original size:2 final size:2
Alignment explanation
Indices: 2249713--2249750 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2249703 TAAGCCCAAA
*
2249713 AT AT GT AT AT 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 AT AT AT AT AT
2249751 GTTTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2249822 original size:22 final size:22
Alignment explanation
Indices: 2249779--2249826 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2249769 GAGTGTGGTT
*
2249779 TATTAATAATATATAATTTATA
1 TATTAATAATATATAATATATA
*
2249801 TATTGATAATATATCAA-ATATA
1 TATTAATAATATAT-AATATATA
2249823 TATT
1 TATT
2249827 TATATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTAATAATATATAATATATA
Found at i:2251784 original size:24 final size:25
Alignment explanation
Indices: 2251757--2251826 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 25
2251747 TAACTATTTG
2251757 TATTTAATATTTATATATA-ATATA
1 TATTTAATATTTATATATAGATATA
* *
2251781 TATTTAATCATTAATATGTAGATATA
1 TATTTAAT-ATTTATATATAGATATA
* *
2251807 TATATTATTATTTAAATATA
1 TAT-TTAATATTTATATATA
2251827 TAAAAATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
24 8 0.22
25 9 0.24
26 16 0.43
27 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (25 bp):
TATTTAATATTTATATATAGATATA
Found at i:2252466 original size:2 final size:2
Alignment explanation
Indices: 2252459--2252488 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2252449 CTTTGCGATA
2252459 AT 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 AT
2252489 TAAGCCCCTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2253775 original size:20 final size:20
Alignment explanation
Indices: 2253750--2253816 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
2253740 AGGTAAAAAT
2253750 ATTTAATTTTATAAACCCTA
1 ATTTAATTTTATAAACCCTA
* * **
2253770 ATTTAAATATAAGGTAAA-AAT-
1 ATTT-AATTTTA--TAAACCCTA
2253791 ATTTAATTTTATAAACCCTA
1 ATTTAATTTTATAAACCCTA
2253811 ATTTAA
1 ATTTAA
2253817 AAAAATTGGA
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 15 0.44
21 9 0.26
22 1 0.03
23 4 0.12
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTAATTTTATAAACCCTA
Found at i:2253779 original size:41 final size:41
Alignment explanation
Indices: 2253733--2253817 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
2253723 AAGAATATCC
2253733 AAATATAAGGTAAAAATATTTAATTTTATAAACCCTAATTT
1 AAATATAAGGTAAAAATATTTAATTTTATAAACCCTAATTT
2253774 AAATATAAGGTAAAAATATTTAATTTTATAAACCCTAATTT
1 AAATATAAGGTAAAAATATTTAATTTTATAAACCCTAATTT
2253815 AAA
1 AAA
2253818 AAAATTGGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.38
Consensus pattern (41 bp):
AAATATAAGGTAAAAATATTTAATTTTATAAACCCTAATTT
Found at i:2255757 original size:11 final size:11
Alignment explanation
Indices: 2255741--2255765 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2255731 GATAAATTAA
2255741 ATAATATAAAT
1 ATAATATAAAT
2255752 ATAATATAAAT
1 ATAATATAAAT
2255763 ATA
1 ATA
2255766 TAAATTATGG
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:2258272 original size:21 final size:21
Alignment explanation
Indices: 2258242--2258291 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2258232 AAAATATATA
2258242 TAAT-TAATTTTTTATCAATT
1 TAATATAATTTTTTATCAATT
*
2258262 TAATATAATTTTTTATTAATT
1 TAATATAATTTTTTATCAATT
*
2258283 AAATA-AATT
1 TAATATAATT
2258292 CTTGATTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATATAATTTTTTATCAATT
Found at i:2261294 original size:19 final size:19
Alignment explanation
Indices: 2261231--2261295 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
2261221 ATTTTTTATT
*
2261231 TAAA-TTTAAATATAAAAAA
1 TAAATTTTAAATA-ATAAAA
** *
2261250 TAAATTTTAAAATTTTAACA
1 TAAATTTT-AAATAATAAAA
*
2261270 T-TATTTTAAATAATAAAA
1 TAAATTTTAAATAATAAAA
2261288 TAAATTTT
1 TAAATTTT
2261296 GAATTGACTT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
18 9 0.26
19 14 0.41
20 7 0.21
21 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATTTTAAATAATAAAA
Found at i:2262779 original size:18 final size:19
Alignment explanation
Indices: 2262747--2262801 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
2262737 TTATAACTAG
*
2262747 TATTATAA-AATATATAAT
1 TATTATAATAAAATATAAT
* *
2262765 TATT-TTATAAAATATAAA
1 TATTATAATAAAATATAAT
2262783 TATTATAATAAAA-ATAAT
1 TATTATAATAAAATATAAT
2262801 T
1 T
2262802 TGGGTTAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.07
18 21 0.70
19 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTATAATAAAATATAAT
Found at i:2263355 original size:22 final size:24
Alignment explanation
Indices: 2263330--2263378 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2263320 CACATTGCAT
* * *
2263330 AAAA-TATATACATACATATTAAA
1 AAAATTATAAACATAAATAATAAA
2263353 AAAATTATAAACATAAATAATAAA
1 AAAATTATAAACATAAATAATAAA
2263377 AA
1 AA
2263379 TATTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAATTATAAACATAAATAATAAA
Found at i:2266433 original size:2 final size:2
Alignment explanation
Indices: 2266426--2266452 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2266416 GGAATAACAC
2266426 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 A
2266453 AAATATCCAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2266866 original size:17 final size:16
Alignment explanation
Indices: 2266816--2266872 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
2266806 TTATATGTAT
*
2266816 ATTATATATATTAAAAA
1 ATTATATTTATT-AAAA
2266833 ATTATATTTATT-AAA
1 ATTATATTTATTAAAA
*
2266848 ATTATGTTTATTAATAA
1 ATTATATTTATTAA-AA
*
2266865 ATTTTATT
1 ATTATATT
2266873 ATAATTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 14 0.41
16 1 0.03
17 19 0.56
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTATATTTATTAAAA
Found at i:2268507 original size:13 final size:14
Alignment explanation
Indices: 2268471--2268504 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
2268461 TATCCTAATT
2268471 AAAAAATTAAAAAAG
1 AAAAAATT-AAAAAG
2268486 AAAAAATTAAAAAG
1 AAAAAATTAAAAAG
2268500 CAAAA
1 -AAAA
2268505 TTATATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (14 bp):
AAAAAATTAAAAAG
Found at i:2269457 original size:21 final size:19
Alignment explanation
Indices: 2269418--2269457 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
2269408 TTTTTATTTT
*
2269418 TATTTTATTAAATAAATAA
1 TATTTTATCAAATAAATAA
2269437 TATTTTGATCAAATCAAATAA
1 TATTTT-ATCAAAT-AAATAA
2269458 AAAACTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (19 bp):
TATTTTATCAAATAAATAA
Found at i:2269816 original size:2 final size:2
Alignment explanation
Indices: 2269804--2269844 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2269794 GTCTTTTGCC
2269804 AT AT A- AT AT AT AT 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 AT AT AT AT AT AT AT
2269845 TATTTTGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2272155 original size:2 final size:2
Alignment explanation
Indices: 2272148--2272181 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2272138 ATCCGTATTA
2272148 AT AT AT 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 AT AT AT
2272182 TTGATTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2273017 original size:19 final size:19
Alignment explanation
Indices: 2272975--2273018 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2272965 GGTCCAAATA
*
2272975 ATATTTTTTATTATAATTT
1 ATATTTTTTAATATAATTT
*
2272994 TTATTTTTATAATATAA-TT
1 ATATTTTT-TAATATAATTT
2273013 ATATTT
1 ATATTT
2273019 ATTTTATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATATTTTTTAATATAATTT
Found at i:2273022 original size:23 final size:20
Alignment explanation
Indices: 2272992--2273043 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
2272982 TTATTATAAT
2272992 TTTTATTTTTATAATATAATTA
1 TTTTATTTTTATAA-A-AATTA
2273014 TATTTA-TTTTATAAAAATTA
1 T-TTTATTTTTATAAAAATTA
2273034 TTATTATTTT
1 TT-TTATTTT
2273044 ATTTTATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 1 0.04
20 9 0.33
21 4 0.15
22 9 0.33
23 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTATTTTTATAAAAATTA
Found at i:2273143 original size:14 final size:14
Alignment explanation
Indices: 2273105--2273143 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
2273095 ATGTATTTTC
2273105 AAATAATGTTAATAA
1 AAATAAT-TTAATAA
*
2273120 AAA-AACTTAATAA
1 AAATAATTTAATAA
2273133 AAATAATTTAA
1 AAATAATTTAA
2273144 CTATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 10 0.48
14 8 0.38
15 3 0.14
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (14 bp):
AAATAATTTAATAA
Found at i:2273194 original size:19 final size:19
Alignment explanation
Indices: 2273158--2273195 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2273148 TAAAATTAAA
*
2273158 TTAAAAATATATTAAAATT
1 TTAAAAATATAATAAAATT
2273177 TTAAAAA-ATAATATAAATT
1 TTAAAAATATAATA-AAATT
2273196 AATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAATATAATAAAATT
Found at i:2273544 original size:17 final size:16
Alignment explanation
Indices: 2273487--2273572 Score: 68
Period size: 17 Copynumber: 5.1 Consensus size: 16
2273477 GATGTATTAC
*
2273487 ATTTATATATTTTAAAAA
1 ATTT-TATA-TTTAATAA
*
2273505 ATTATTATATTTAATAT
1 ATT-TTATATTTAATAA
2273522 ATTTTATATTTATATAA
1 ATTTTATATTTA-ATAA
*
2273539 ATTTTAATAAATTAAT-A
1 ATTTT-AT-ATTTAATAA
*
2273556 A-TTTATATTAAATAA
1 ATTTTATATTTAATAA
2273571 AT
1 AT
2273573 ATTAAAATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 5 0.09
15 4 0.07
16 12 0.21
17 19 0.34
18 11 0.20
19 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTATATTTAATAA
Found at i:2273593 original size:33 final size:33
Alignment explanation
Indices: 2273515--2273598 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 33
2273505 ATTATTATAT
* *
2273515 TTAATATATTTTATATTTATATAAATTTTAATAAA
1 TTAATATA-TTTATA-TTAAATAAATATTAATAAA
2273550 TTAATA-ATTTATATTAAATAAATATTAA-AATA
1 TTAATATATTTATATTAAATAAATATTAATAA-A
*
2273582 TTAAAATATTTATATTA
1 TTAATATATTTATATTA
2273599 TATTACATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 2 0.05
32 19 0.43
33 16 0.36
34 1 0.02
35 6 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
TTAATATATTTATATTAAATAAATATTAATAAA
Found at i:2275860 original size:23 final size:24
Alignment explanation
Indices: 2275830--2275878 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
2275820 TTTTTTTAAT
*
2275830 ATAAAAAAGTTAT-AATTTAAGAA
1 ATAAAAAAATTATAAATTTAAGAA
*
2275853 ATAAAAAAATTATAAATTTAATAA
1 ATAAAAAAATTATAAATTTAAGAA
2275877 AT
1 AT
2275879 TTTAATTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAAAAAAATTATAAATTTAAGAA
Found at i:2277376 original size:20 final size:22
Alignment explanation
Indices: 2277353--2277397 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
2277343 AATAATTTTT
2277353 AATAAAAAATTAT-AATA-TAA
1 AATAAAAAATTATAAATATTAA
2277373 AATAAAAAATTATAAATATTAA
1 AATAAAAAATTATAAATATTAA
2277395 AAT
1 AAT
2277398 TTAAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.57
21 4 0.17
22 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAAAAAATTATAAATATTAA
Found at i:2281276 original size:10 final size:11
Alignment explanation
Indices: 2281253--2281284 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
2281243 AGGCAATAAC
2281253 AATTCTTAAAAA
1 AATT-TTAAAAA
2281265 AATTTTAAAAA
1 AATTTTAAAAA
2281276 AATTTTAAA
1 AATTTTAAA
2281285 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTTTAAAAA
Found at i:2281314 original size:26 final size:22
Alignment explanation
Indices: 2281283--2281336 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
2281273 AAAAATTTTA
2281283 AATTTTAAATTTCATTTTATTATTAT
1 AATTTT-AATTT-ATTTT-TTA-TAT
*
2281309 AATTTTAATTTATTTTTTATGT
1 AATTTTAATTTATTTTTTATAT
2281331 AATTTT
1 AATTTT
2281337 TTAGTCAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 8 0.30
23 3 0.11
24 5 0.19
25 5 0.19
26 6 0.22
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
AATTTTAATTTATTTTTTATAT
Found at i:2283332 original size:23 final size:23
Alignment explanation
Indices: 2283274--2283332 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
2283264 AATAAATATG
* * *
2283274 ATATATAT-TAAATTTGTTATGT
1 ATATATATATATATTTATTAAGT
*
2283296 -TAGATATATCATATTTATTAAGT
1 ATATATATAT-ATATTTATTAAGT
2283319 ATATATATATATAT
1 ATATATATATATAT
2283333 ATATATTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 6 0.21
22 1 0.03
23 14 0.48
24 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (23 bp):
ATATATATATATATTTATTAAGT
Found at i:2284019 original size:22 final size:20
Alignment explanation
Indices: 2283991--2284030 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2283981 TTCTTTTTCT
2283991 TTTTTTTTTCCCACTTATATAA
1 TTTTTTTTT--CACTTATATAA
2284013 TTTTTTTTTCACTTATAT
1 TTTTTTTTTCACTTATAT
2284031 GACTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTTTTCACTTATATAA
Found at i:2285934 original size:2 final size:2
Alignment explanation
Indices: 2285929--2285959 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2285919 AAAAACCCAT
2285929 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 T
2285960 TTTCTAAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2286294 original size:23 final size:24
Alignment explanation
Indices: 2286268--2286322 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
2286258 ATAAATATTT
2286268 TATATTTAAAT-TTAAT-TATAAAA
1 TATATTTAAATATTAATATA-AAAA
*
2286291 TATATATAAATATTAATATAAAAA
1 TATATTTAAATATTAATATAAAAA
2286315 TAATATTT
1 T-ATATTT
2286323 TTATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 10 0.37
24 10 0.37
25 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATATTTAAATATTAATATAAAAA
Found at i:2289180 original size:5 final size:5
Alignment explanation
Indices: 2289170--2289194 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2289160 TGTTAAGAGA
2289170 GCCTG GCCTG GCCTG GCCTG GCCTG
1 GCCTG GCCTG GCCTG GCCTG GCCTG
2289195 TTTCCCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.40, T:0.20
Consensus pattern (5 bp):
GCCTG
Found at i:2289733 original size:35 final size:34
Alignment explanation
Indices: 2289664--2289743 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 34
2289654 TATTTTGATA
* *
2289664 ATATAAATTTTGATTAATTAATAATTTAAATTAT
1 ATATAAATTTTAATTAATCAATAATTTAAATTAT
*
2289698 ATATAAATTTTAATATAATCACAT-ATTTATATTAT
1 ATATAAATTTTAAT-TAATCA-ATAATTTAAATTAT
* *
2289733 ATTTATATTTT
1 ATATAAATTTT
2289744 TTTATTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
34 13 0.33
35 24 0.62
36 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (34 bp):
ATATAAATTTTAATTAATCAATAATTTAAATTAT
Found at i:2289736 original size:11 final size:11
Alignment explanation
Indices: 2289720--2289759 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
2289710 ATATAATCAC
2289720 ATATTTATATT
1 ATATTTATATT
2289731 ATATTTATATT
1 ATATTTATATT
2289742 -T-TTT-TATT
1 ATATTTATATT
2289750 ATA-TTATATT
1 ATATTTATATT
2289760 CTTATCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.15
9 6 0.23
10 5 0.19
11 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATATTTATATT
Found at i:2290838 original size:3 final size:3
Alignment explanation
Indices: 2290830--2290863 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2290820 TTCCATGGAC
2290830 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2290864 ATACATGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2292128 original size:14 final size:14
Alignment explanation
Indices: 2292109--2292136 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2292099 GTGTAAACTG
2292109 ATGTTATTAACAGC
1 ATGTTATTAACAGC
2292123 ATGTTATTAACAGC
1 ATGTTATTAACAGC
2292137 TTTGAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ATGTTATTAACAGC
Found at i:2292261 original size:2 final size:2
Alignment explanation
Indices: 2292254--2292283 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2292244 CAGTCATTGC
2292254 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2292284 ACGTTATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2294931 original size:53 final size:53
Alignment explanation
Indices: 2294874--2294977 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 53
2294864 ATCTCTAATA
*
2294874 TATGTTTTTAATAAATATTTACAATATTTAATATTTAGTAATATTAAAAAAAG
1 TATGTTTTTAATAAATAATTACAATATTTAATATTTAGTAATATTAAAAAAAG
* * * *
2294927 TATGTTTTTTATAAATAATTACTATATTTAATATTTATTAATATTTAAAAA
1 TATGTTTTTAATAAATAATTACAATATTTAATATTTAGTAATATTAAAAAA
2294978 GAATGTGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (53 bp):
TATGTTTTTAATAAATAATTACAATATTTAATATTTAGTAATATTAAAAAAAG
Found at i:2295253 original size:18 final size:18
Alignment explanation
Indices: 2295227--2295262 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2295217 AGAAGTTACA
*
2295227 CTCCAATGTGTGGAGTTT
1 CTCCAATGTGCGGAGTTT
*
2295245 CTCCTATGTGCGGAGTTT
1 CTCCAATGTGCGGAGTTT
2295263 TCTTAGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.19, G:0.28, T:0.39
Consensus pattern (18 bp):
CTCCAATGTGCGGAGTTT
Found at i:2295340 original size:19 final size:19
Alignment explanation
Indices: 2295316--2295352 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2295306 ATGAATTTAA
2295316 TAGAAGTTACATATATATG
1 TAGAAGTTACATATATATG
2295335 TAGAAGTTACATATATAT
1 TAGAAGTTACATATATAT
2295353 AATACAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
TAGAAGTTACATATATATG
Found at i:2296624 original size:109 final size:109
Alignment explanation
Indices: 2296433--2296652 Score: 440
Period size: 109 Copynumber: 2.0 Consensus size: 109
2296423 GATCTTTAAC
2296433 CTGTTTGAATCAAACTATTGCACGTCAAATACAACAAGAATCCTATACTTACACATAAAAAGAAG
1 CTGTTTGAATCAAACTATTGCACGTCAAATACAACAAGAATCCTATACTTACACATAAAAAGAAG
2296498 AAAGAAAGAATAACAAAAAAGTTTATGTAACCTTTTGCTGGTAA
66 AAAGAAAGAATAACAAAAAAGTTTATGTAACCTTTTGCTGGTAA
2296542 CTGTTTGAATCAAACTATTGCACGTCAAATACAACAAGAATCCTATACTTACACATAAAAAGAAG
1 CTGTTTGAATCAAACTATTGCACGTCAAATACAACAAGAATCCTATACTTACACATAAAAAGAAG
2296607 AAAGAAAGAATAACAAAAAAGTTTATGTAACCTTTTGCTGGTAA
66 AAAGAAAGAATAACAAAAAAGTTTATGTAACCTTTTGCTGGTAA
2296651 CT
1 CT
2296653 AGCTGATTCC
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 111 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (109 bp):
CTGTTTGAATCAAACTATTGCACGTCAAATACAACAAGAATCCTATACTTACACATAAAAAGAAG
AAAGAAAGAATAACAAAAAAGTTTATGTAACCTTTTGCTGGTAA
Found at i:2303580 original size:21 final size:21
Alignment explanation
Indices: 2303539--2303594 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
2303529 AGTATTTTTG
**
2303539 AATAATT-AAATCGATAAAAA
1 AATAATTAAAATTAATAAAAA
*
2303559 AA-AGTTAAAATTAATAAAAA
1 AATAATTAAAATTAATAAAAA
*
2303579 AATTATTAAAATTAAT
1 AATAATTAAAATTAAT
2303595 TTTAAACTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.10
20 15 0.52
21 11 0.38
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
AATAATTAAAATTAATAAAAA
Found at i:2303729 original size:16 final size:15
Alignment explanation
Indices: 2303704--2303740 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
2303694 AGACTTATTC
2303704 TTATTAAATATTTAT
1 TTATTAAATATTTAT
*
2303719 TATATTTAATATTTAT
1 T-TATTAAATATTTAT
2303735 TTATTA
1 TTATTA
2303741 TTAAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTAAATATTTAT
Found at i:2306848 original size:2 final size:2
Alignment explanation
Indices: 2306843--2306867 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2306833 CCCTTGAACA
2306843 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
2306868 ATGATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2308996 original size:20 final size:20
Alignment explanation
Indices: 2308967--2309030 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 20
2308957 ATTATATAAT
2308967 AAAA-ATAATATAAAAAATA
1 AAAATATAATATAAAAAATA
* *
2308986 AAAATATAATATAATATA-A
1 AAAATATAATATAAAAAATA
*
2309005 AAAATATAA-ATATAAAATA
1 AAAATATAATATAAAAAATA
*
2309024 AATATAT
1 AAAATAT
2309031 GAATTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
18 5 0.14
19 21 0.57
20 11 0.30
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATATAATATAAAAAATA
Found at i:2308998 original size:34 final size:31
Alignment explanation
Indices: 2308960--2309029 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 31
2308950 TAATGTGATT
2308960 ATATAATA-AAAATAATATAAAAAATAAAAATATA
1 ATATAATATAAAA-AATAT-AAAAAT-AAAATA-A
*
2308994 ATATAATATAAAAAATATAAATATAAAATAA
1 ATATAATATAAAAAATATAAAAATAAAATAA
2309025 ATATA
1 ATATA
2309030 TGAATTATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
31 6 0.18
32 6 0.18
33 5 0.15
34 13 0.38
35 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (31 bp):
ATATAATATAAAAAATATAAAAATAAAATAA
Found at i:2309001 original size:25 final size:25
Alignment explanation
Indices: 2308964--2309029 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
2308954 GTGATTATAT
2308964 AATA-AAAATAATATAAAAAATAAA
1 AATATAAAATAATATAAAAAATAAA
* *
2308988 AATATAATATAATATAAAAAATATA
1 AATATAAAATAATATAAAAAATAAA
2309013 AATATAAAATAAATATA
1 AATATAAAAT-AATATA
2309030 TGAATTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 4 0.11
25 27 0.73
26 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AATATAAAATAATATAAAAAATAAA
Found at i:2309072 original size:32 final size:32
Alignment explanation
Indices: 2309032--2309092 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
2309022 TAAATATATG
* *
2309032 AATTATTAATTTATCAAAATTTATGTAAAATA
1 AATTATTAATATATCAAAATTTATATAAAATA
2309064 AATTATTAATATATCAAAATTTATATAAA
1 AATTATTAATATATCAAAATTTATATAAA
2309093 TATATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (32 bp):
AATTATTAATATATCAAAATTTATATAAAATA
Found at i:2309095 original size:18 final size:17
Alignment explanation
Indices: 2309043--2309095 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
2309033 ATTATTAATT
2309043 TATCAAAATTTATGTAAA
1 TATCAAAATTTAT-TAAA
2309061 -AT--AAA-TTATTAATA
1 TATCAAAATTTATTAA-A
2309075 TATCAAAATTTATATAAA
1 TATCAAAATTTAT-TAAA
2309093 TAT
1 TAT
2309096 ATAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 5 0.17
17 5 0.17
18 8 0.28
19 3 0.10
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (17 bp):
TATCAAAATTTATTAAA
Found at i:2309103 original size:19 final size:19
Alignment explanation
Indices: 2309071--2309153 Score: 67
Period size: 19 Copynumber: 4.0 Consensus size: 19
2309061 ATAAATTATT
2309071 AATATATCAAAATTTATATA
1 AATATAT-AAAATTTATATA
*
2309091 AATATATAAAATTTTCTATGTA
1 AATATATAAAA--TT-TATATA
* *
2309113 ATTATGATATAAAAATAATATA
1 A--AT-ATATAAAATTTATATA
*
2309135 AATATATAAAATTTTTATA
1 AATATATAAAATTTATATA
2309154 TTTAAATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
19 17 0.34
20 9 0.18
21 2 0.04
22 11 0.22
23 1 0.02
24 2 0.04
25 8 0.16
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATATAAAATTTATATA
Found at i:2309826 original size:22 final size:23
Alignment explanation
Indices: 2309770--2309827 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
2309760 AAAAAATTAA
* *
2309770 ATTATTTATATAATTTTAGTAAT
1 ATTATTTTTTTAATTTTAGTAAT
* *
2309793 A-TATTATCTTAATTTTA-TAAT
1 ATTATTTTTTTAATTTTAGTAAT
2309814 ATTATTTTTTTAAT
1 ATTATTTTTTTAAT
2309828 AATTTTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 5 0.18
22 22 0.79
23 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTATTTTTTTAATTTTAGTAAT
Found at i:2311474 original size:22 final size:22
Alignment explanation
Indices: 2311446--2311505 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
2311436 AAAAAAGTAA
2311446 AAATATTTTTAT-ATTAATATTT
1 AAATATTTTTATAATTAA-ATTT
*
2311468 ATATA-TTTTATAATTAAATTT
1 AAATATTTTTATAATTAAATTT
*
2311489 AAATATTTTTTTAATTA
1 AAATATTTTTATAATTA
2311506 TTAAATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATATTTTTATAATTAAATTT
Found at i:2311478 original size:21 final size:21
Alignment explanation
Indices: 2311448--2311497 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
2311438 AAAAGTAAAA
2311448 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
2311468 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
*
2311489 AAATATTTT
1 ATATATTTT
2311498 TTTAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 18 0.67
22 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:2312366 original size:11 final size:11
Alignment explanation
Indices: 2312322--2312408 Score: 71
Period size: 11 Copynumber: 8.1 Consensus size: 11
2312312 TAATAATTTG
2312322 AAATATAATA-
1 AAATATAATAT
2312332 AAAT-TAATA-
1 AAATATAATAT
2312341 AAA-ATAAT-T
1 AAATATAATAT
2312350 ATAATATAATAT
1 A-AATATAATAT
*
2312362 AAATATAATAA
1 AAATATAATAT
2312373 AAAGTAT-ATATT
1 AAA-TATAATA-T
2312385 AAATAT-ATAT
1 AAATATAATAT
2312395 AAATTATTAATAT
1 AAA-TA-TAATAT
2312408 A
1 A
2312409 TTAAAATTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 17
0.77 0.02 0.20
Matches are distributed among these distances:
9 13 0.20
10 10 0.15
11 28 0.43
12 9 0.14
13 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (11 bp):
AAATATAATAT
Found at i:2312400 original size:15 final size:16
Alignment explanation
Indices: 2312346--2312413 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 16
2312336 TAATAAAAAT
2312346 AATTATAATATAATATA
1 AATTATAATAT-ATATA
*
2312363 AA-TATAATAAAAAGTATA
1 AATTATAAT--ATA-TATA
*
2312381 TATTA-AATATATATA
1 AATTATAATATATATA
2312396 AATTATTAATATAT-TA
1 AATTA-TAATATATATA
2312412 AA
1 AA
2312414 ATTTATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
15 8 0.20
16 12 0.29
17 10 0.24
18 9 0.22
19 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (16 bp):
AATTATAATATATATA
Found at i:2312415 original size:17 final size:18
Alignment explanation
Indices: 2312381--2312444 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 18
2312371 AAAAAGTATA
2312381 TATTAAATATATATAAAT
1 TATTAAATATATATAAAT
2312399 TATT-AATATAT-TAAAATT
1 TATTAAATATATAT-AAA-T
2312417 TATATAAATA-A-ATAATAT
1 TAT-TAAATATATATAA-AT
2312435 T-TTAAATATA
1 TATTAAATATA
2312445 ATTATAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
16 7 0.18
17 12 0.31
18 12 0.31
19 4 0.10
20 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTAAATATATATAAAT
Found at i:2312415 original size:27 final size:26
Alignment explanation
Indices: 2312350--2312444 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 26
2312340 AAAAATAATT
*
2312350 ATAATATAATATAAATATA-ATAAA-A
1 ATAATATATTA-AAATATATATAAATA
2312375 AGT-ATATATT-AAATATATATAAATTA
1 A-TAATATATTAAAATATATATAAA-TA
* *
2312401 TTAATATATTAAAATTTATATAAATAA
1 ATAATATATTAAAATATATATAAAT-A
*
2312428 ATAATAT-TTTAAATATA
1 ATAATATATTAAAATATA
2312445 ATTATAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
23 7 0.12
24 5 0.09
25 8 0.14
26 18 0.32
27 19 0.33
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
ATAATATATTAAAATATATATAAATA
Found at i:2316637 original size:32 final size:32
Alignment explanation
Indices: 2316594--2316657 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2316584 ACCTGTTATC
*
2316594 CAAGACCCGCAAAAAGAATTTGAAATATAATT
1 CAAGACCCGCAAAAAGAATTTAAAATATAATT
*
2316626 CAAGACGCGCAAAAAGAATTTAAAATATAATT
1 CAAGACCCGCAAAAAGAATTTAAAATATAATT
2316658 TAATCGGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (32 bp):
CAAGACCCGCAAAAAGAATTTAAAATATAATT
Found at i:2318512 original size:30 final size:30
Alignment explanation
Indices: 2318476--2318532 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2318466 CTAATGTCAC
* *
2318476 CTGCAATTAACTATGCTACAGTCTTACCAT
1 CTGCAATTAACTATACTACAATCTTACCAT
2318506 CTGCAATTAACTATACTACAATCTTAC
1 CTGCAATTAACTATACTACAATCTTAC
2318533 GATTCGCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (30 bp):
CTGCAATTAACTATACTACAATCTTACCAT
Found at i:2325247 original size:12 final size:11
Alignment explanation
Indices: 2325209--2325249 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
2325199 AAACTCAATA
*
2325209 AAATTTAAGTT
1 AAATTTAAATT
2325220 AAATTTTAAATT
1 AAA-TTTAAATT
2325232 AAATTTAAACTT
1 AAATTTAAA-TT
2325244 AAATTT
1 AAATTT
2325250 TTTATTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:2327238 original size:21 final size:20
Alignment explanation
Indices: 2327214--2327252 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2327204 TATTTTTATT
2327214 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TA-AAAATATA
2327235 TAAATATTAATAAAAATA
1 TAAATATTAATAAAAATA
2327253 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATTAATAAAAATATA
Found at i:2327523 original size:24 final size:23
Alignment explanation
Indices: 2327499--2327547 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2327489 AAATATATTA
*
2327499 AAATAA-TATTTTTATTTAAATTT
1 AAATAATTATTTAT-TTTAAATTT
2327522 AAATAATTATTTATTTTAAA-TT
1 AAATAATTATTTATTTTAAATTT
2327544 AAAT
1 AAAT
2327548 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 12 0.50
24 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AAATAATTATTTATTTTAAATTT
Found at i:2327576 original size:28 final size:28
Alignment explanation
Indices: 2327505--2327570 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
2327495 ATTAAAATAA
* * **
2327505 TATTTTTATTTAAATTTAAATAATTATT
1 TATTTTAAATTAAATTTAAATAAAAATT
2327533 TATTTTAAATTAAATTTAAATAAAAAATAT
1 TATTTTAAATTAAATTTAAAT-AAAAAT-T
2327563 TATTTTAA
1 TATTTTAA
2327571 TAAATTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 19 0.59
29 4 0.12
30 9 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TATTTTAAATTAAATTTAAATAAAAATT
Found at i:2328925 original size:14 final size:15
Alignment explanation
Indices: 2328899--2328930 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
2328889 ATCATATAAA
2328899 ATAATTGTATAATAT
1 ATAATTGTATAATAT
2328914 ATAATT-TATAATAT
1 ATAATTGTATAATAT
2328928 ATA
1 ATA
2328931 TTATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATAATTGTATAATAT
Found at i:2341841 original size:5 final size:5
Alignment explanation
Indices: 2341833--2341866 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
2341823 TATTTATTTG
* *
2341833 AATTA AATTA AATTT ATTTA AATTA AATTA AATT
1 AATTA AATTA AATTA AATTA AATTA AATTA AATT
2341867 CATTCGAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
AATTA
Found at i:2341849 original size:20 final size:20
Alignment explanation
Indices: 2341824--2341880 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
2341814 CAAATATTTT
2341824 ATTTATTTGAATTAAATTAA
1 ATTTATTTGAATTAAATTAA
*
2341844 ATTTATTTAAATTAAATTAA
1 ATTTATTTGAATTAAATTAA
* *
2341864 ATTCATTCGAATTAAAT
1 ATTTATTTGAATTAAAT
2341881 CGAATTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
ATTTATTTGAATTAAATTAA
Found at i:2342729 original size:19 final size:19
Alignment explanation
Indices: 2342682--2342730 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2342672 TATAATTAAA
*
2342682 TTTAAATAAAATATATTAT
1 TTTAAATAAAATATAATAT
*
2342701 TTTTAATAAAA-ATAATAT
1 TTTAAATAAAATATAATAT
*
2342719 TTTAAATTAAAT
1 TTTAAATAAAAT
2342731 TTTTAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAAATAAAATATAATAT
Found at i:2343824 original size:23 final size:22
Alignment explanation
Indices: 2343789--2343855 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
2343779 TAAAATATGT
* * *
2343789 TTTAATATTAAAATTTATAATTTT
1 TTTAATA-AAAAATTTATAA-ATA
*
2343813 TTTATTAAAAAATTTATAAATA
1 TTTAATAAAAAATTTATAAATA
2343835 TTTAATAAAAAATTTTATAAA
1 TTTAATAAAAAA-TTTATAAA
2343856 AAATATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.32
23 19 0.51
24 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAATAAAAAATTTATAAATA
Found at i:2343854 original size:12 final size:12
Alignment explanation
Indices: 2343812--2343859 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
2343802 TTTATAATTT
2343812 TTTTATTAAAAAA
1 TTTTA-TAAAAAA
*
2343825 -TTTAT-AAATA
1 TTTTATAAAAAA
*
2343835 TTTAATAAAAAA
1 TTTTATAAAAAA
2343847 TTTTATAAAAAA
1 TTTTATAAAAAA
2343859 T
1 T
2343860 ATAATTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
10 4 0.14
11 5 0.17
12 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTTATAAAAAA
Found at i:2344015 original size:15 final size:15
Alignment explanation
Indices: 2343987--2344019 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2343977 CCGATTAAAA
2343987 AAAAGTCAATAATTC
1 AAAAGTCAATAATTC
2344002 AAAA-TCAATCAATTC
1 AAAAGTCAAT-AATTC
2344017 AAA
1 AAA
2344020 CTTTACATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAAGTCAATAATTC
Found at i:2344879 original size:11 final size:11
Alignment explanation
Indices: 2344865--2344903 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
2344855 TTTACGTTAC
2344865 ATTTAAAATTT
1 ATTTAAAATTT
*
2344876 ATTTATTAATTT
1 ATTTA-AAATTT
2344888 ATTTAAAATTT
1 ATTTAAAATTT
2344899 ATTTA
1 ATTTA
2344904 TTATTCGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTAAAATTT
Found at i:2344888 original size:12 final size:12
Alignment explanation
Indices: 2344871--2344906 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2344861 TTACATTTAA
2344871 AATTTATTTATT
1 AATTTATTTATT
*
2344883 AATTTATTTA-A
1 AATTTATTTATT
2344894 AATTTATTTATT
1 AATTTATTTATT
2344906 A
1 A
2344907 TTCGATCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
AATTTATTTATT
Found at i:2344982 original size:39 final size:38
Alignment explanation
Indices: 2344917--2344990 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 38
2344907 TTCGATCATA
2344917 ATTTAATAATAATATTATTTTATATTTTAT-TTTATTT
1 ATTTAATAATAATATTATTTTATATTTTATATTTATTT
*
2344954 ATTT-ATAATAATATTTTGCTTTATTATTTTATATTTA
1 ATTTAATAATAATATTAT--TTTA-TATTTTATATTTA
2344991 AATTTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 12 0.38
37 4 0.12
38 4 0.12
39 8 0.25
40 4 0.12
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (38 bp):
ATTTAATAATAATATTATTTTATATTTTATATTTATTT
Found at i:2345236 original size:16 final size:16
Alignment explanation
Indices: 2345178--2345240 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
2345168 TAAATTCTTA
*
2345178 ATAAATACAAACTAAAC
1 ATAAATAAAAAC-AAAC
*** *
2345195 ATAAATAAATTTAAAA
1 ATAAATAAAAACAAAC
2345211 ATAAAT-AAAACAAAC
1 ATAAATAAAAACAAAC
2345226 ATAAATAAAAACAAA
1 ATAAATAAAAACAAA
2345241 TTCATTCAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.31
16 17 0.47
17 8 0.22
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (16 bp):
ATAAATAAAAACAAAC
Found at i:2345866 original size:19 final size:19
Alignment explanation
Indices: 2345830--2345871 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2345820 TCATATTTTA
*
2345830 ATTATTTTTTATATATTAT
1 ATTATTTTGTATATATTAT
2345849 ATTATATTTGTATA-ATTAT
1 ATTAT-TTTGTATATATTAT
2345868 -TTAT
1 ATTAT
2345872 GAAGTTTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 10 0.48
20 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTTTGTATATATTAT
Found at i:2345871 original size:30 final size:31
Alignment explanation
Indices: 2345809--2345871 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
2345799 ATTTTTTAAA
* *
2345809 ATATATTTATATCATATTTTAATTATTTTTT
1 ATATATTTATATCATATTTTAATAATTATTT
*
2345840 ATATA-TTATATTATATTTGT-ATAATTATTT
1 ATATATTTATATCATATTT-TAATAATTATTT
2345870 AT
1 AT
2345872 GAAGTTTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (31 bp):
ATATATTTATATCATATTTTAATAATTATTT
Found at i:2346215 original size:16 final size:16
Alignment explanation
Indices: 2346194--2346245 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
2346184 ATTTATAAAT
2346194 TTATTTTATATTTATA
1 TTATTTTATATTTATA
*
2346210 TTATTTT-TTTATTATA
1 TTATTTTATAT-TTATA
2346226 TTATATTTATATTATATA
1 TTAT-TTTATATT-TATA
2346244 TT
1 TT
2346246 CGTATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 2 0.07
16 16 0.53
17 4 0.13
18 8 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTTATATTTATA
Found at i:2346219 original size:19 final size:20
Alignment explanation
Indices: 2346182--2346245 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
2346172 AATTTTAAAA
*
2346182 ATATTTATA-AATTTATTTT
1 ATATTTATATTATTTATTTT
2346201 ATATTTATATTATTT-TTTT
1 ATATTTATATTATTTATTTT
* *
2346220 ATTATATTATATT-TATATTAT
1 A-TAT-TTATATTATTTATTTT
2346241 ATATT
1 ATATT
2346246 CGTATTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 15 0.39
20 12 0.32
21 11 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATTTATATTATTTATTTT
Found at i:2346239 original size:11 final size:11
Alignment explanation
Indices: 2346192--2346281 Score: 59
Period size: 11 Copynumber: 8.5 Consensus size: 11
2346182 ATATTTATAA
*
2346192 ATTTATTTTAT
1 ATTTATATTAT
2346203 ATTTATA-T-T
1 ATTTATATTAT
2346212 ATTT-T-TT-T
1 ATTTATATTAT
2346220 A-TTATATTAT
1 ATTTATATTAT
2346230 ATTTATATTAT
1 ATTTATATTAT
*
2346241 ATATTCGTATTAT
1 AT-TT-ATATTAT
*
2346254 ATCTAATATTAT
1 AT-TTATATTAT
*
2346266 GTTTA-ATTAT
1 ATTTATATTAT
*
2346276 TTTTAT
1 ATTTAT
2346282 TTTAAGCAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 7 0.11
10 12 0.19
11 19 0.30
12 9 0.14
13 9 0.14
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:2346245 original size:7 final size:6
Alignment explanation
Indices: 2346182--2346245 Score: 55
Period size: 5 Copynumber: 10.8 Consensus size: 6
2346172 AATTTTAAAA
* *
2346182 ATATTT ATAAATTT AT-TTT ATATTT ATA-TT ATTTTT TTA-TT ATA-TT
1 ATATTT AT--ATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
2346228 ATATTT ATATTAT ATATT
1 ATATTT ATATT-T ATATT
2346246 CGTATTATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
5 18 0.38
6 18 0.38
7 6 0.12
8 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:2352209 original size:2 final size:2
Alignment explanation
Indices: 2352204--2352235 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2352194 ACTCGACTTC
2352204 AT AT 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 AT AT
2352236 GCTAATTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2355027 original size:96 final size:96
Alignment explanation
Indices: 2354856--2355340 Score: 566
Period size: 96 Copynumber: 5.1 Consensus size: 96
2354846 TTCTGCAGAC
* * * * *
2354856 TCTTTTTGGGATTTTG-CTTCTGCAGAAGATTTCTCTGATGCATCAGCAACTTCAAGCTCCTTGC
1 TCTTTTTGGGA-TTTGACTTCTGCTGGAGAGTTGTCTGATGCATCAGCAACCTCAAGCTCCTTGC
2354920 CTGTCTT-CACCTTCTTCAGCATCTTGTCACTA
65 CTGT-TTCCACCTTCTTCAGCATCTTGTCACTA
* * * * *
2354952 TATTTTTGGGATTTGGCTTCTACTGG-GTTGTTGTCTGCTGCATCAGCAACCTCAAGCTCCTTGC
1 TCTTTTTGGGATTTGACTTCTGCTGGAG-AGTTGTCTGATGCATCAGCAACCTCAAGCTCCTTGC
* *
2355016 CTGTTTCCACCTTCTTTAGCATCTTGTTACTA
65 CTGTTTCCACCTTCTTCAGCATCTTGTCACTA
* * * * * *
2355048 TCTTTTTGGGAGTCGGCATCTGCTGGAGAGTTGTCTAATGCATCAGTAACCTCAAGCTCCTTGCC
1 TCTTTTTGGGATTTGACTTCTGCTGGAGAGTTGTCTGATGCATCAGCAACCTCAAGCTCCTTGCC
* **
2355113 TGTTTTCACCTTCTTTGGCATCTTGTCACTA
66 TGTTTCCACCTTCTTCAGCATCTTGTCACTA
* * * * * * *
2355144 TCTTTCTGTGATTTGATTTCTGCTGGAGAGTTCTCTGATGCGTCAGCACCCTCAAGCTCCTTCCC
1 TCTTTTTGGGATTTGACTTCTGCTGGAGAGTTGTCTGATGCATCAGCAACCTCAAGCTCCTTGCC
**
2355209 TGTTTTTACCTTCGTT-AGCATCTTGTCACTA
66 TGTTTCCACCTTC-TTCAGCATCTTGTCACTA
* * * *
2355240 TCTATTTGGGATTTGACTTCTGCTGGGGAGTTGTCTAATTCATCAGCAACCTCAAGCTCCTTGCC
1 TCTTTTTGGGATTTGACTTCTGCTGGAGAGTTGTCTGATGCATCAGCAACCTCAAGCTCCTTGCC
* *
2355305 TG-TTCTCACCTTCTTCAGCATATTGTCACTT
66 TGTTTC-CACCTTCTTCAGCATCTTGTCACTA
2355336 TCTTT
1 TCTTT
2355341 GATCTCCATC
Statistics
Matches: 328, Mismatches: 54, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
95 11 0.03
96 314 0.96
97 3 0.01
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (96 bp):
TCTTTTTGGGATTTGACTTCTGCTGGAGAGTTGTCTGATGCATCAGCAACCTCAAGCTCCTTGCC
TGTTTCCACCTTCTTCAGCATCTTGTCACTA
Found at i:2358277 original size:14 final size:15
Alignment explanation
Indices: 2358243--2358275 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2358233 AAAATTATTA
*
2358243 AAAAATAAAAAAATT
1 AAAATTAAAAAAATT
2358258 AAAATTAAAAAAATT
1 AAAATTAAAAAAATT
2358273 AAA
1 AAA
2358276 TTTTTTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATTAAAAAAATT
Done.