Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold324
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: 2336777
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 13 of 16
Found at i:1783521 original size:17 final size:18
Alignment explanation
Indices: 1783482--1783522 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1783472 CAGGTGATAT
*
1783482 TAAATTAAAATTTGTTTA
1 TAAATTTAAATTTGTTTA
*
1783500 -CAATTTAAA-TTGTTTA
1 TAAATTTAAATTTGTTTA
1783516 TAAATTT
1 TAAATTT
1783523 TAATCTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (18 bp):
TAAATTTAAATTTGTTTA
Found at i:1783708 original size:21 final size:21
Alignment explanation
Indices: 1783675--1783738 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
1783665 AACATATTTT
1783675 ATTATTAAT-TTTAATTTTATC
1 ATTA-TAATATTTAATTTTATC
*
1783696 ATTATAATATTTAATTTTATT
1 ATTATAATATTTAATTTTATC
* *
1783717 ATTATAATAATTAATCTTATC
1 ATTATAATATTTAATTTTATC
1783738 A
1 A
1783739 CCATTATTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.11
21 34 0.89
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATAATATTTAATTTTATC
Found at i:1784706 original size:50 final size:50
Alignment explanation
Indices: 1784646--1784905 Score: 396
Period size: 50 Copynumber: 5.2 Consensus size: 50
1784636 AGTTACTTAG
** * * * * *
1784646 AGTCAACAATTACAGCCACTTCTCTCGATTGTCAAAAGTTGGTAAAAAAT
1 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1784696 AGTCAACAATTAT-GTCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGT-CACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
1784746 AGTCAATAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* *
1784796 AGTCAATAATTATGGTCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
1784846 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAATGTTGGTGAAGAAT
1 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
1784896 AGTCCACAAT
1 AGTCAACAAT
1784906 GGCAACACCT
Statistics
Matches: 196, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
49 1 0.01
50 193 0.98
51 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:1789330 original size:50 final size:49
Alignment explanation
Indices: 1789264--1789417 Score: 193
Period size: 50 Copynumber: 3.1 Consensus size: 49
1789254 GTCACTTCTT
**
1789264 TTCTCTCGATTATCAAAGATTGGTGAAAAATAGTAAATAATTATAATCAC
1 TTCTCTCGATTATCAAAGATTGGTGAAAAATA-TAAATAATTACGATCAC
* * *
1789314 TTCTCTCAATTATCAAAGGTTGGT-AAAGAATCATCAATAATTACGATCAC
1 TTCTCTCGATTATCAAAGATTGGTGAAA-AAT-ATAAATAATTACGATCAC
* * *
1789364 CTCTCTCGATTATCAAAAATTGATGAAAAATAATAAATAATTACGATCAC
1 TTCTCTCGATTATCAAAGATTGGTGAAAAAT-ATAAATAATTACGATCAC
1789414 TTCT
1 TTCT
1789418 TTTGATTGTT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
49 3 0.03
50 81 0.92
51 4 0.05
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (49 bp):
TTCTCTCGATTATCAAAGATTGGTGAAAAATATAAATAATTACGATCAC
Found at i:1789432 original size:50 final size:50
Alignment explanation
Indices: 1789265--1789453 Score: 148
Period size: 50 Copynumber: 3.8 Consensus size: 50
1789255 TCACTTCTTT
* ** * ** *
1789265 TCTCTCGATTATCAAAGATTGGTGAAA-AATAGTAAATAATTATAATCACT
1 TCTCTCGATTATCAAAAATTAAT-AAATAATAATAAATAATTACGATCACC
* ** ** * * *
1789315 TCTCTCAATTATCAAAGGTTGGTAAAGAATCATCAATAATTACGATCACC
1 TCTCTCGATTATCAAAAATTAATAAATAATAATAAATAATTACGATCACC
* *
1789365 TCTCTCGATTATCAAAAATTGATGAAA-AATAATAAATAATTACGATCACT
1 TCTCTCGATTATCAAAAATTAAT-AAATAATAATAAATAATTACGATCACC
* * * * *
1789415 TCTTTTGATTGTTAAAAATTAATAAATAATAATTAATAA
1 TCTCTCGATTATCAAAAATTAATAAATAATAATAAATAA
1789454 AGATAATATC
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
49 6 0.05
50 106 0.92
51 3 0.03
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (50 bp):
TCTCTCGATTATCAAAAATTAATAAATAATAATAAATAATTACGATCACC
Found at i:1789453 original size:100 final size:100
Alignment explanation
Indices: 1789265--1789453 Score: 225
Period size: 100 Copynumber: 1.9 Consensus size: 100
1789255 TCACTTCTTT
* * * *
1789265 TCTCTCGATTATCAAAGATTGGTGAAAAATAGTAAATAATTATAATCACTTCTCTCAATTATCAA
1 TCTCTCGATTATCAAAAATTGATGAAAAATAATAAATAATTACAATCACTTCTCTCAATTATCAA
** ** *
1789330 AGGTTGGTAAAGAATCATCAATAATTACGATCACC
66 AAATTAATAAAGAATAATCAATAATTACGATCACC
* * ** * *
1789365 TCTCTCGATTATCAAAAATTGATGAAAAATAATAAATAATTACGATCACTTCTTTTGATTGTTAA
1 TCTCTCGATTATCAAAAATTGATGAAAAATAATAAATAATTACAATCACTTCTCTCAATTATCAA
* *
1789430 AAATTAATAAATAATAATTAATAA
66 AAATTAATAAAGAATAATCAATAA
1789454 AGATAATATC
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
100 72 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (100 bp):
TCTCTCGATTATCAAAAATTGATGAAAAATAATAAATAATTACAATCACTTCTCTCAATTATCAA
AAATTAATAAAGAATAATCAATAATTACGATCACC
Found at i:1789859 original size:36 final size:36
Alignment explanation
Indices: 1789804--1789881 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
1789794 TGGATTTTTT
* *
1789804 TATAAAA-TTTTAATTATATTAAATTATAGTTATTTA
1 TATAAAATTTTTAATAATATTAAA-TATAGTTATGTA
* *
1789840 TATAAAATTTTTAA-AATATTTAATATATTTATGTA
1 TATAAAATTTTTAATAATATTAAATATAGTTATGTA
1789875 -ATAAAAT
1 TATAAAAT
1789882 AAATATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 7 0.19
35 10 0.27
36 14 0.38
37 6 0.16
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (36 bp):
TATAAAATTTTTAATAATATTAAATATAGTTATGTA
Found at i:1789904 original size:24 final size:22
Alignment explanation
Indices: 1789861--1789905 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1789851 TAAAATATTT
*
1789861 AATATATTTATGTAATAAAATA
1 AATATATTTATGTAAAAAAATA
*
1789883 AATATATTTTTGATATAAAAAAT
1 AATATATTTATG-TA-AAAAAAT
1789906 TTTATATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
AATATATTTATGTAAAAAAATA
Found at i:1793351 original size:12 final size:12
Alignment explanation
Indices: 1793334--1793373 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1793324 TTGCAATTGA
1793334 ATATATATACAT
1 ATATATATACAT
*
1793346 ATATATATATAT
1 ATATATATACAT
* *
1793358 ATATATGTTCAT
1 ATATATATACAT
1793370 ATAT
1 ATAT
1793374 GAATAGAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (12 bp):
ATATATATACAT
Found at i:1793373 original size:2 final size:2
Alignment explanation
Indices: 1793334--1793363 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1793324 TTGCAATTGA
*
1793334 AT AT AT AT AC 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
1793364 GTTCATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1794981 original size:26 final size:26
Alignment explanation
Indices: 1794951--1795006 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1794941 AATTTTTATA
*
1794951 TTATAATAAAAAAAATATTTTAATTT
1 TTATAATAAAAAAAATATTTTAAGTT
***
1794977 TTAT-ATAAATTCAATATTTTAAGTT
1 TTATAATAAAAAAAATATTTTAAGTT
1795002 TTATA
1 TTATA
1795007 CTTTTGAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
TTATAATAAAAAAAATATTTTAAGTT
Found at i:1795521 original size:13 final size:14
Alignment explanation
Indices: 1795488--1795542 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
1795478 AATAATATAA
*
1795488 AAATAAATAATTAT
1 AAATATATAATTAT
1795502 AAATATATAA-TAT
1 AAATATATAATTAT
* *
1795515 GAATATA-AGAATA-
1 AAATATATA-ATTAT
1795528 AAATATATAATTAT
1 AAATATATAATTAT
1795542 A
1 A
1795543 TAAATAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 1 0.03
13 19 0.58
14 13 0.39
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (14 bp):
AAATATATAATTAT
Found at i:1797557 original size:2 final size:2
Alignment explanation
Indices: 1797550--1797580 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1797540 GTGTTAGTCT
*
1797550 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1797581 TCAAAAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1800828 original size:16 final size:17
Alignment explanation
Indices: 1800802--1800833 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1800792 ATTAATTATT
1800802 CAAGAATTAATATTAAA
1 CAAGAATTAATATTAAA
1800819 CAAG-ATTAATATTAA
1 CAAGAATTAATATTAA
1800834 GTTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
CAAGAATTAATATTAAA
Found at i:1800975 original size:18 final size:19
Alignment explanation
Indices: 1800952--1800988 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1800942 TAGATAACAA
1800952 TATTTAAT-AGATAAATAT
1 TATTTAATAAGATAAATAT
*
1800970 TATTTATTAAGATAAATAT
1 TATTTAATAAGATAAATAT
1800989 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TATTTAATAAGATAAATAT
Found at i:1803588 original size:12 final size:12
Alignment explanation
Indices: 1803571--1803604 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1803561 TTTGGAGAGC
1803571 TAATTCAAGATA
1 TAATTCAAGATA
1803583 TAATTCAAGATA
1 TAATTCAAGATA
1803595 TAATTCAAGA
1 TAATTCAAGA
1803605 AAATTTAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (12 bp):
TAATTCAAGATA
Found at i:1805195 original size:29 final size:32
Alignment explanation
Indices: 1805125--1805198 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
1805115 TTTAAAGTAT
1805125 TTTATATTTATATAAATTTTGATAAATTAATAA
1 TTTATA-TTATATAAATTTTGATAAATTAATAA
**
1805158 TTCGTATTATATAAATTTT-A-AAA-T-ATATA
1 TTTATATTATATAAATTTTGATAAATTAATA-A
1805187 TTTATATTATAT
1 TTTATATTATAT
1805199 TATATTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 3 0.08
29 12 0.33
30 3 0.08
31 1 0.03
32 13 0.36
33 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (32 bp):
TTTATATTATATAAATTTTGATAAATTAATAA
Found at i:1805225 original size:14 final size:16
Alignment explanation
Indices: 1805183--1805229 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1805173 TTTTAAAATA
1805183 TATATTTATATTATAT
1 TATATTTATATTATAT
1805199 TATATTTGA-ATTAT-T
1 TATATTT-ATATTATAT
*
1805214 T-TATTTTTATTATAT
1 TATATTTATATTATAT
1805229 T
1 T
1805230 CATGTAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 10 0.37
15 4 0.15
16 12 0.44
17 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATATTTATATTATAT
Found at i:1805860 original size:17 final size:20
Alignment explanation
Indices: 1805814--1805853 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1805804 ATCATTCATC
*
1805814 TAATATAAATTTTTAAATAA
1 TAATACAAATTTTTAAATAA
1805834 TAATACAAATTTTTAAATAA
1 TAATACAAATTTTTAAATAA
1805854 ATAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATACAAATTTTTAAATAA
Found at i:1810391 original size:21 final size:21
Alignment explanation
Indices: 1810373--1810457 Score: 76
Period size: 21 Copynumber: 4.4 Consensus size: 21
1810363 TTATAAAAGT
1810373 TATATT-TTTCATCCAAAAAA
1 TATATTATTTCATCCAAAAAA
**
1810393 TATATTATTTCATCCAATCAA
1 TATATTATTTCATCCAAAAAA
* * *
1810414 TGTATCATTTTATCC-AAAAA
1 TATATTATTTCATCCAAAAAA
1810434 TATA-T-TTTCAT--AAAAAA
1 TATATTATTTCATCCAAAAAA
1810451 TA-ATTAT
1 TATATTAT
1810458 ATATACCTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
16 1 0.02
17 8 0.16
18 6 0.12
20 12 0.24
21 24 0.47
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (21 bp):
TATATTATTTCATCCAAAAAA
Found at i:1811241 original size:28 final size:27
Alignment explanation
Indices: 1811202--1811256 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1811192 TAAAACTAAT
* *
1811202 TTATAAATATATATAA-TATTTAAATAA
1 TTATAAAAATAT-TAATTAATTAAATAA
1811229 TTATGAAAAATATTAATTAATTAAATAA
1 TTAT-AAAAATATTAATTAATTAAATAA
1811257 ATTAATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
TTATAAAAATATTAATTAATTAAATAA
Found at i:1814262 original size:2 final size:2
Alignment explanation
Indices: 1814249--1814278 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1814239 CATGAAGGGA
*
1814249 AT AT AT AC 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
1814279 GTTTTACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1814997 original size:13 final size:13
Alignment explanation
Indices: 1814964--1815002 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1814954 GAGGAAAGAG
*
1814964 AAAAAGAGAAAGA
1 AAAAAGAGAAAAA
* *
1814977 GAACAGAGAAAAA
1 AAAAAGAGAAAAA
1814990 AAAAAGAGAAAAA
1 AAAAAGAGAAAAA
1815003 TATGTGGGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:1815077 original size:32 final size:31
Alignment explanation
Indices: 1815035--1815098 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
1815025 TATGTTTATA
*
1815035 TTATTTTTTATATATTA-AAAATATTATTATTT
1 TTATTATTTAT-TATTATAAAATATT-TTATTT
*
1815067 TTATTATTTATTGTTATAAAATATTTTATTT
1 TTATTATTTATTATTATAAAATATTTTATTT
1815098 T
1 T
1815099 AAAATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (31 bp):
TTATTATTTATTATTATAAAATATTTTATTT
Found at i:1815109 original size:25 final size:26
Alignment explanation
Indices: 1815081--1815144 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
1815071 TATTTATTGT
*
1815081 TATAAAATATTTTATTTTAA-AATTA
1 TATAAAATATTTTATATTAATAATTA
1815106 TATAAAAT-TTTATATATTAATAATTA
1 TATAAAATATTT-TATATTAATAATTA
*
1815132 -ATTAATATATTTT
1 TA-TAAAATATTTT
1815145 TTATGTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
24 3 0.09
25 16 0.48
26 11 0.33
27 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TATAAAATATTTTATATTAATAATTA
Found at i:1815184 original size:23 final size:23
Alignment explanation
Indices: 1815158--1815219 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1815148 TGTTCTTGTG
1815158 TTTATATATTATATTT-ATATAAT
1 TTTATATATTATATTTAAT-TAAT
* *
1815181 TTTACATATTATGTTTAATTAAT
1 TTTATATATTATATTTAATTAAT
* *
1815204 TTTTTATATTTTATTT
1 TTTATATATTATATTT
1815220 GTGTCATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 30 0.94
24 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTATATATTATATTTAATTAAT
Found at i:1818759 original size:2 final size:2
Alignment explanation
Indices: 1818754--1818790 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1818744 AGGTATTATT
* *
1818754 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1818791 CGAGATGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1820775 original size:26 final size:26
Alignment explanation
Indices: 1820738--1820787 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1820728 TATAATATAA
* *
1820738 AAAAATATAAATATA-AAATTTTTAC
1 AAAAATAAAAATAAATAAATTTTTAC
1820763 AAAAATAAAAAATAAATAAATTTTT
1 AAAAAT-AAAAATAAATAAATTTTT
1820788 GATACTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 7 0.33
27 8 0.38
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAATAAAAATAAATAAATTTTTAC
Found at i:1820919 original size:21 final size:21
Alignment explanation
Indices: 1820893--1820937 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1820883 TCCTCCTTCA
1820893 TTTTTTTTATTCTTTCACTCT
1 TTTTTTTTATTCTTTCACTCT
* **
1820914 TTTTTTTTTTTCTTTTTCTCT
1 TTTTTTTTATTCTTTCACTCT
1820935 TTT
1 TTT
1820938 CCTCTTCCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTTATTCTTTCACTCT
Found at i:1821300 original size:28 final size:27
Alignment explanation
Indices: 1821256--1821322 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 27
1821246 TTTATAGTCA
* * *
1821256 TAATT-TTTTCATGTTATATTATATTT
1 TAATTATTTTTATATTATATCATATTT
*
1821282 TAATTAATTTTTATATTATATCGTATTT
1 TAATT-ATTTTTATATTATATCATATTT
1821310 TAATTATTTTTAT
1 TAATTATTTTTAT
1821323 GTGTATTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.14
27 8 0.23
28 22 0.63
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (27 bp):
TAATTATTTTTATATTATATCATATTT
Found at i:1825716 original size:18 final size:17
Alignment explanation
Indices: 1825693--1825727 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1825683 CTATGTAACA
*
1825693 AATTATTTTATTTTCTTT
1 AATTATGTT-TTTTCTTT
1825711 AATTATGTTTTTTCTTT
1 AATTATGTTTTTTCTTT
1825728 TTTTTTGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (17 bp):
AATTATGTTTTTTCTTT
Found at i:1827383 original size:97 final size:97
Alignment explanation
Indices: 1827182--1827383 Score: 237
Period size: 97 Copynumber: 2.1 Consensus size: 97
1827172 AATGGGATAG
* * * *
1827182 GAGTATCCCCGACAATGAAAATTTAAGTAAAAATAAGATTTAAATCTTGACGAATTTAAAAATGA
1 GAGTATCCCCAACAATGAAAATTTAAGCAAAAATAAAATTTAAATCTTGACGAATTTAAAAAAGA
* * * *
1827247 GGTTGGAGTATCCTTTCGAAAGAATGAGGTTG
66 GGTTGGAGTATCCCTTCGAAAGAACGAGATTA
* * * *
1827279 GACTATCCCCAATAATGAAAATTTAAGCAAAAATAAAATTTAAATTTTGACGAGTTTAAAAAAAG
1 GAGTATCCCCAACAATGAAAATTTAAGCAAAAATAAAATTTAAATCTTGACGAATTT-AAAAAAG
* * *
1827344 GGGTTGGAGTATCTCCTT-GGAGGAACG-GATTA
65 AGGTTGGAGTATC-CCTTCGAAAGAACGAGATTA
1827376 GAGTATCC
1 GAGTATCC
1827384 TTGATAAATA
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
97 60 0.69
98 24 0.28
99 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.28
Consensus pattern (97 bp):
GAGTATCCCCAACAATGAAAATTTAAGCAAAAATAAAATTTAAATCTTGACGAATTTAAAAAAGA
GGTTGGAGTATCCCTTCGAAAGAACGAGATTA
Found at i:1829925 original size:20 final size:20
Alignment explanation
Indices: 1829885--1829938 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1829875 TATTTCAAGC
*
1829885 ATGTATCGATATATTCACTT
1 ATGTATCGATACATTCACTT
1829905 ATGTATCGATACATT-ATCTT
1 ATGTATCGATACATTCA-CTT
*
1829925 ATTATATCGATACA
1 A-TGTATCGATACA
1829939 AATTGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 18 0.60
21 11 0.37
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:1831511 original size:12 final size:12
Alignment explanation
Indices: 1831496--1831545 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 12
1831486 ATTATAATTT
1831496 TTAAAATATAAA
1 TTAAAATATAAA
1831508 TTAAAATATTAAA
1 TTAAAATA-TAAA
1831521 TTCAATAATATAAAAA
1 TT-AA-AATAT--AAA
1831537 TTAAAATAT
1 TTAAAATAT
1831546 TTTTTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 8 0.24
13 6 0.18
14 8 0.24
15 6 0.18
16 5 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAAATATAAA
Found at i:1831756 original size:20 final size:21
Alignment explanation
Indices: 1831731--1831769 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1831721 CTCTAGACTA
*
1831731 TATTAAAAGAA-TAAAATTAT
1 TATTAAAAAAATTAAAATTAT
1831751 TATTAAAAAAATTAAAATT
1 TATTAAAAAAATTAAAATT
1831770 TAAAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
TATTAAAAAAATTAAAATTAT
Found at i:1832853 original size:14 final size:14
Alignment explanation
Indices: 1832836--1832886 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
1832826 ATATTTATTT
1832836 TTATATAATATAAA
1 TTATATAATATAAA
1832850 TTATATAATATATAA
1 TTATATAATATA-AA
* *
1832865 ATATAAAATAATAAA
1 TTATATAAT-ATAAA
*
1832880 TTTTATA
1 TTATATA
1832887 TAATTAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 12 0.40
15 15 0.50
16 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:1836123 original size:14 final size:14
Alignment explanation
Indices: 1836104--1836139 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1836094 TGAAAGGAAT
1836104 TAAAAAAAGAAAAA
1 TAAAAAAAGAAAAA
1836118 TAAAAAAAGAAAAA
1 TAAAAAAAGAAAAA
*
1836132 GAAAAAAA
1 TAAAAAAA
1836140 TTTATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.08, T:0.06
Consensus pattern (14 bp):
TAAAAAAAGAAAAA
Found at i:1837863 original size:23 final size:22
Alignment explanation
Indices: 1837819--1837864 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
1837809 TAGAAACAAA
1837819 AGAAAGTTAAATTATAAATTTTT
1 AGAAAGTTAAA-TATAAATTTTT
1837842 AGAAAGATTAAA-ATAAATTTTT
1 AGAAAG-TTAAATATAAATTTTT
1837864 A
1 A
1837865 TTACTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.50
23 6 0.27
24 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (22 bp):
AGAAAGTTAAATATAAATTTTT
Found at i:1838741 original size:13 final size:15
Alignment explanation
Indices: 1838711--1838752 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
1838701 ATAATAAAAG
1838711 AATTATAAATATTAA
1 AATTATAAATATTAA
*
1838726 AATTA-AAATTTTAA
1 AATTATAAATATTAA
*
1838740 ATTTATTAAATAT
1 AATTA-TAAATAT
1838753 CATTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.55
15 5 0.23
16 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATAAATATTAA
Found at i:1838757 original size:14 final size:14
Alignment explanation
Indices: 1838738--1838784 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
1838728 TTAAAATTTT
1838738 AAATTTATTAAATA
1 AAATTTATTAAATA
** *
1838752 TCATTTTTTAAATA
1 AAATTTATTAAATA
*
1838766 AAATTTAATAAATA
1 AAATTTATTAAATA
1838780 AAATT
1 AAATT
1838785 GAGAGTTTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATTTATTAAATA
Found at i:1839581 original size:39 final size:39
Alignment explanation
Indices: 1839434--1839624 Score: 129
Period size: 39 Copynumber: 4.9 Consensus size: 39
1839424 GTGAAAGTTG
* * * *
1839434 TGGAGCCTTTGATTAATGGAATATTTTTAAATTTAAAAGTTG
1 TGGAGCCTTTGATTAAAGGAACA---TTAAATTTAAAAATTA
* * ** *
1839476 TGGAGTCTTTG-TT-TA-GAACATCGAATTTTAAAATTA
1 TGGAGCCTTTGATTAAAGGAACATTAAATTTAAAAATTA
* * * * *
1839512 TGGAGCCTCTAATTAGAGGAGCATTTAATTTAAAAATTA
1 TGGAGCCTTTGATTAAAGGAACATTAAATTTAAAAATTA
* * * * *
1839551 TGGAGTCTTTGATTAAAGGAATATTAAATTTTAAAGTTG
1 TGGAGCCTTTGATTAAAGGAACATTAAATTTAAAAATTA
* *
1839590 TGGAGCCTTTGATTAGAA-AAACATTAGATTTAAAA
1 TGGAGCCTTTGATTA-AAGGAACATTAAATTTAAAA
1839625 GCTTCAGATT
Statistics
Matches: 113, Mismatches: 32, Indels: 11
0.72 0.21 0.07
Matches are distributed among these distances:
36 19 0.17
37 2 0.02
38 1 0.01
39 77 0.68
40 2 0.02
41 2 0.02
42 10 0.09
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (39 bp):
TGGAGCCTTTGATTAAAGGAACATTAAATTTAAAAATTA
Found at i:1841778 original size:30 final size:30
Alignment explanation
Indices: 1841743--1841838 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
1841733 TGTTACACTA
*
1841743 AAATAAACCCTTAACTTTTATTTTATGCTT
1 AAATAAACCTTTAACTTTTATTTTATGCTT
** *
1841773 AAATAAATTTTTAAATTTTAGCTTTTA--CTT
1 AAATAAACCTTTAACTTTTA--TTTTATGCTT
* * * *
1841803 AAATAAGCCTTTAACTTTTAATGTATGCCT
1 AAATAAACCTTTAACTTTTATTTTATGCTT
1841833 AAATAA
1 AAATAA
1841839 GTCTCTAAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 3 0.06
30 43 0.84
32 5 0.10
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (30 bp):
AAATAAACCTTTAACTTTTATTTTATGCTT
Found at i:1841778 original size:59 final size:60
Alignment explanation
Indices: 1841715--1841849 Score: 146
Period size: 60 Copynumber: 2.3 Consensus size: 60
1841705 ACTTTATCTC
* * * * *
1841715 AATAAATCTCTATATTTTTG-TTACACTAAAATAAACCCTTAACTTTTATTTTATGCTTA
1 AATAAATCTCTAAATTTTAGCTTACACTAAAATAAACCCTTAACTTTTAATGTATGCCTA
* * ** * * *
1841774 AATAAATTTTTAAATTTTAGCTTTTACTTAAATAAGCCTTTAACTTTTAATGTATGCCTA
1 AATAAATCTCTAAATTTTAGCTTACACTAAAATAAACCCTTAACTTTTAATGTATGCCTA
*
1841834 AATAAGTCTCTAAATT
1 AATAAATCTCTAAATT
1841850 AAATTATATA
Statistics
Matches: 60, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
59 16 0.27
60 44 0.73
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (60 bp):
AATAAATCTCTAAATTTTAGCTTACACTAAAATAAACCCTTAACTTTTAATGTATGCCTA
Found at i:1842966 original size:23 final size:23
Alignment explanation
Indices: 1842940--1842985 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1842930 GTAGCATTAA
*
1842940 GGGTTGTAGTCTGTTTCTTGATT
1 GGGTTGTAGTCTGATTCTTGATT
1842963 GGGTTGTAGTCTGATTCTTGATT
1 GGGTTGTAGTCTGATTCTTGATT
1842986 TCTAGATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.09, G:0.30, T:0.50
Consensus pattern (23 bp):
GGGTTGTAGTCTGATTCTTGATT
Found at i:1844884 original size:5 final size:5
Alignment explanation
Indices: 1844870--1844899 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1844860 AACATAATTT
*
1844870 TTTAA TTTAA ATTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
1844900 ATTATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTTAA
Found at i:1844886 original size:10 final size:10
Alignment explanation
Indices: 1844871--1844903 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1844861 ACATAATTTT
1844871 TTAATTTAAA
1 TTAATTTAAA
*
1844881 TTAATTTAAT
1 TTAATTTAAA
1844891 TTAATTTAAA
1 TTAATTTAAA
1844901 TTA
1 TTA
1844904 TTATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTAATTTAAA
Found at i:1847533 original size:35 final size:35
Alignment explanation
Indices: 1847487--1847566 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
1847477 TTTAATCTAT
*
1847487 AAAGTTTTAAAAAGATAAAATCACATCAAATTTTA
1 AAAGTTTTAAAAAAATAAAATCACATCAAATTTTA
* *
1847522 AAAGTTTTAAAAAAATAAAATCATATTAAATTTTA
1 AAAGTTTTAAAAAAATAAAATCACATCAAATTTTA
1847557 AAA--TTTAAAA
1 AAAGTTTTAAAA
1847567 TTTAAATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
33 7 0.17
35 35 0.83
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (35 bp):
AAAGTTTTAAAAAAATAAAATCACATCAAATTTTA
Found at i:1847557 original size:7 final size:7
Alignment explanation
Indices: 1847547--1847623 Score: 61
Period size: 7 Copynumber: 10.7 Consensus size: 7
1847537 TAAAATCATA
*
1847547 TTAAATT
1 TTAAAAT
1847554 TTAAAAT
1 TTAAAAT
1847561 TTAAAAT
1 TTAAAAT
1847568 TT-AAAT
1 TTAAAAT
* *
1847574 TTAGATT
1 TTAAAAT
1847581 TTAAAAAT
1 TT-AAAAT
1847589 CTAGATAAAAT
1 -T---TAAAAT
1847600 TT-AAAT
1 TTAAAAT
1847606 TT-AAAT
1 TTAAAAT
1847612 TTAAAAT
1 TTAAAAT
1847619 TTAAA
1 TTAAA
1847624 TTTCTAATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
6 18 0.31
7 29 0.50
8 3 0.05
9 1 0.02
10 1 0.02
11 5 0.09
12 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (7 bp):
TTAAAAT
Found at i:1847575 original size:6 final size:6
Alignment explanation
Indices: 1847547--1847626 Score: 54
Period size: 6 Copynumber: 12.3 Consensus size: 6
1847537 TAAAATCATA
* * *
1847547 TTAAATT TTAAAAT TTAAAAT TTAAAT TTAGATT TTAAAAAT CTAGA-
1 TTAAA-T TT-AAAT TT-AAAT TTAAAT TTA-AAT TT--AAAT TTAAAT
*
1847594 TAAAAT TTAAAT TTAAAT TTAAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TT
1847627 CTAATAATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
5 2 0.03
6 28 0.47
7 22 0.37
8 6 0.10
9 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (6 bp):
TTAAAT
Found at i:1847575 original size:13 final size:13
Alignment explanation
Indices: 1847547--1847626 Score: 58
Period size: 13 Copynumber: 6.2 Consensus size: 13
1847537 TAAAATCATA
*
1847547 TTAAATTTTAAAAT
1 TTAAAATTT-AAAT
1847561 TTAAAATTTAAAT
1 TTAAAATTTAAAT
* *
1847574 TTAGATTTTAAAAAT
1 TTAAAATTT--AAAT
* * *
1847589 CT-AGA-TAAAAT
1 TTAAAATTTAAAT
1847600 TT-AAATTTAAAT
1 TTAAAATTTAAAT
1847612 TTAAAATTTAAAT
1 TTAAAATTTAAAT
1847625 TT
1 TT
1847627 CTAATAATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
11 7 0.14
12 7 0.14
13 24 0.47
14 8 0.16
15 5 0.10
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (13 bp):
TTAAAATTTAAAT
Found at i:1849281 original size:21 final size:22
Alignment explanation
Indices: 1849238--1849282 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1849228 AAGTTAATTC
*
1849238 AAGTTTAAATCATTTCAGATTT
1 AAGTTTAAATCATATCAGATTT
* *
1849260 AAGTTTAAGTCA-ATCAGGTTT
1 AAGTTTAAATCATATCAGATTT
1849281 AA
1 AA
1849283 TAGTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (22 bp):
AAGTTTAAATCATATCAGATTT
Found at i:1849982 original size:16 final size:16
Alignment explanation
Indices: 1849961--1850002 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1849951 TAATTGTTTC
*
1849961 AATCATTTTAAATTTG
1 AATCATTTTAAATTTA
1849977 AATCATTTTAAATTTA
1 AATCATTTTAAATTTA
*
1849993 AATTATTTTA
1 AATCATTTTA
1850003 GGTACAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (16 bp):
AATCATTTTAAATTTA
Found at i:1850111 original size:22 final size:21
Alignment explanation
Indices: 1850067--1850124 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
1850057 TATTAACTCA
*
1850067 AAATAAATTAAATTAAATTTT
1 AAATTAATTAAATTAAATTTT
1850088 AAATTAATT-AATTAAATATTTT
1 AAATTAATTAAATT-AA-ATTTT
*
1850110 AAATTTAAATAAATT
1 AAA-TTAATTAAATT
1850125 TATATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 4 0.13
21 10 0.32
22 8 0.26
23 5 0.16
24 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTAATTAAATTAAATTTT
Found at i:1850427 original size:24 final size:24
Alignment explanation
Indices: 1850400--1850467 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
1850390 TATGTGAAAA
1850400 AATTTTATT-TTTAATGTTTGTATT
1 AATTTTATTATTTAATGTTT-TATT
* *
1850424 AATTTTATATATTTAAAGTATTATT
1 AATTTTAT-TATTTAATGTTTTATT
* *
1850449 ATTTTTATTATTTATTGTT
1 AATTTTATTATTTAATGTT
1850468 ATAAAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 16 0.44
25 12 0.33
26 8 0.22
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
AATTTTATTATTTAATGTTTTATT
Found at i:1852122 original size:15 final size:15
Alignment explanation
Indices: 1852102--1852132 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1852092 TATGAAACGG
*
1852102 TGTTTAATTGTGCTA
1 TGTTTAACTGTGCTA
1852117 TGTTTAACTGTGCTA
1 TGTTTAACTGTGCTA
1852132 T
1 T
1852133 TATTGCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (15 bp):
TGTTTAACTGTGCTA
Found at i:1854095 original size:17 final size:18
Alignment explanation
Indices: 1854073--1854106 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1854063 TATGCAGGCT
1854073 TTGCATT-GTCAAATGTC
1 TTGCATTCGTCAAATGTC
*
1854090 TTGCATTCGTCAGATGT
1 TTGCATTCGTCAAATGT
1854107 TTGGCTGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (18 bp):
TTGCATTCGTCAAATGTC
Found at i:1862642 original size:15 final size:15
Alignment explanation
Indices: 1862622--1862652 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1862612 TAAAAATATC
*
1862622 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1862637 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1862652 C
1 C
1862653 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1864740 original size:13 final size:13
Alignment explanation
Indices: 1864722--1864747 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1864712 ACATTTTTCT
1864722 TTGTATCGATACA
1 TTGTATCGATACA
1864735 TTGTATCGATACA
1 TTGTATCGATACA
1864748 GGGTGATTAT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1864911 original size:20 final size:19
Alignment explanation
Indices: 1864870--1864912 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1864860 ATCTTTTACA
1864870 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1864890 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1864910 AAA
1 AAA
1864913 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1867335 original size:21 final size:20
Alignment explanation
Indices: 1867289--1867341 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
1867279 GTAGCCAAAC
**
1867289 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
1867309 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACAC-AAAAAA
1867329 TTGTATCGATACA
1 TTGTATCGATACA
1867342 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:1871179 original size:2 final size:2
Alignment explanation
Indices: 1871172--1871198 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1871162 AATTTCTTCA
1871172 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
1871199 AAAGTATCTT
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:1872793 original size:2 final size:2
Alignment explanation
Indices: 1872786--1872828 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1872776 AAGGGGGTAT
*
1872786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1872828 T
1 T
1872829 CGAGATGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1873308 original size:21 final size:20
Alignment explanation
Indices: 1873279--1873322 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1873269 TTCATTCCAA
1873279 TTTTTTTTTAAATTTTTATT
1 TTTTTTTTTAAATTTTTATT
***
1873299 TTTTTATTTTGTGTTTTTATT
1 TTTTT-TTTTAAATTTTTATT
1873320 TTT
1 TTT
1873323 ATTTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTAAATTTTTATT
Found at i:1877531 original size:64 final size:63
Alignment explanation
Indices: 1877406--1877537 Score: 158
Period size: 64 Copynumber: 2.1 Consensus size: 63
1877396 TGTTTGTACA
* * ** **
1877406 CTGTTTTGGTAATTTTACAAAGTTGTAGCGTTTATGTGTGGTAACCTAGTTGCTCATTTGTATG
1 CTGTTTTGGTAATTTTACAAACTTGTAGCATTTATGCATGGTAACCTAGTACCTCA-TTGTATG
* *
1877470 CTGTTTTGGTAGTTTTACAAACTTGTAGCATTTATGCATGGTAACTTAGATACCTGC-TTGTATG
1 CTGTTTTGGTAATTTTACAAACTTGTAGCATTTATGCATGGTAACCTAG-TACCT-CATTGTATG
1877534 CTGT
1 CTGT
1877538 AAGTAATATG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 54 0.93
65 3 0.05
66 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.22, T:0.44
Consensus pattern (63 bp):
CTGTTTTGGTAATTTTACAAACTTGTAGCATTTATGCATGGTAACCTAGTACCTCATTGTATG
Found at i:1878795 original size:79 final size:79
Alignment explanation
Indices: 1878645--1878812 Score: 212
Period size: 79 Copynumber: 2.1 Consensus size: 79
1878635 ACAACGGGGC
* * * * * * *
1878645 TGGAGGATCCCTGATTATGGAAAATTTATGTTCTGGAAATAAAATCGGGGTTGGAGTATCCCCTT
1 TGGAGTATCCCTAATTATAGAAAATTGATGTTCTGAAAATAAAATCGGGATTGGAGTATCCCCTC
**
1878710 GGAAATAACAGG-GT
66 AAAAATAAC-GGAGT
* *
1878724 TGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGGATTGGAGTATCCCCTC
1 TGGAGTATCCCTAATTATAGAAAATTGATGTTCTGAAAATAAAATCGGGATTGGAGTATCCCCTC
1878789 AAAAATAACGGAGT
66 AAAAATAACGGAGT
*
1878803 TAGAGTATCC
1 TGGAGTATCC
1878813 TCGCGAAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
78 2 0.03
79 74 0.97
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (79 bp):
TGGAGTATCCCTAATTATAGAAAATTGATGTTCTGAAAATAAAATCGGGATTGGAGTATCCCCTC
AAAAATAACGGAGT
Found at i:1878811 original size:28 final size:28
Alignment explanation
Indices: 1878777--1878843 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
1878767 ATCGGGATTG
*
1878777 GAGTATCCCCTCAAAAATAACGGAGTTA
1 GAGTATCCCCGCAAAAATAACGGAGTTA
* * * * *
1878805 GAGTATCCTCGCGAAAATAGCGGGGTTG
1 GAGTATCCCCGCAAAAATAACGGAGTTA
1878833 GAGTATCCCCG
1 GAGTATCCCCG
1878844 ATTGTGAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (28 bp):
GAGTATCCCCGCAAAAATAACGGAGTTA
Found at i:1878923 original size:79 final size:79
Alignment explanation
Indices: 1878819--1878969 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 79
1878809 ATCCTCGCGA
* * * * *
1878819 AAATAGCGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTT-AGGAATAAAATTGGGGTT
1 AAATAACGAGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTGA-AAATAAAATCGGAGTT
*
1878883 GGGGTATCTCCTCAG
65 GGAGTATCTCCTCAG
* *
1878898 AAATAACGAGGTTGGAGTATCCCCGATTGTGAGAAATTAGTATTTTGAAAATAAAATCGGAGTTG
1 AAATAACGAGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTGAAAATAAAATCGGAGTTG
1878963 GAGTATC
66 GAGTATC
1878970 CCCGATTGTG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
79 62 0.98
80 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.29
Consensus pattern (79 bp):
AAATAACGAGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTGAAAATAAAATCGGAGTTG
GAGTATCTCCTCAG
Found at i:1878971 original size:51 final size:50
Alignment explanation
Indices: 1878908--1879088 Score: 247
Period size: 51 Copynumber: 3.6 Consensus size: 50
1878898 AAATAACGAG
* * *
1878908 GTTGGAGTATCCCCGATTGTGAGAAATTAGTATTTT-GAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAG-AAATAAAA-CGGA
* * *
1878959 GTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACGGA
*
1879009 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGGG
1 -GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAA-CGGA
*
1879061 GTTGGAGTATCCTCGATTATGAAAAATT
1 GTTGGAGTATCCCCGATTATGAAAAATT
1879089 GAGAAACTTA
Statistics
Matches: 118, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
50 3 0.03
51 112 0.95
52 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACGGA
Found at i:1879027 original size:102 final size:102
Alignment explanation
Indices: 1878904--1879088 Score: 282
Period size: 102 Copynumber: 1.8 Consensus size: 102
1878894 TCAGAAATAA
* * *
1878904 CGAGGTTGGAGTATCCCCGATTGTGAGAAATTAGTATTTT-GAAAATAAAATCGGAGTTGGAGTA
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAG-AAATAAAACCGGAGTTGGAGTA
* *
1878968 TCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAC
65 TCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAAC
* *
1879006 CGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAACCGGAGTTGGAGTAT
*
1879071 CCTCGATTATGAAAAATT
66 CCCCGATTATGAAAAATT
1879089 GAGAAACTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 73 0.99
103 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (102 bp):
CGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAACCGGAGTTGGAGTAT
CCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAAC
Found at i:1881493 original size:19 final size:21
Alignment explanation
Indices: 1881469--1881520 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1881459 AGCGATACAC
* *
1881469 TGTATCAATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
1881488 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
1881509 TGTATCGATACA
1 TGTATCGATACA
1881521 AATTATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 5 0.17
21 13 0.45
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:1882549 original size:55 final size:55
Alignment explanation
Indices: 1882348--1883561 Score: 1204
Period size: 55 Copynumber: 21.3 Consensus size: 55
1882338 ATAAAGTGCA
** *
1882348 TCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAAAAAGACG
1 TCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTG------AAAGGCG
* ** * *
1882409 TCCTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGTGTGGGCTTTGGAAAGAGAAAGCA
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-G-AA-AG---GCG
*
1882470 TCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1882525 TCCTGCTCTTTGAGGACTAGAAAATGCCCCCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * * *
1882580 TTCTGCTTTTTAAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * * *
1882635 TCCTGCTCATTGAGGACTGGAAAATGCCACCAACTCGTATGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * * *
1882690 TCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
1882745 TCATGCTCTTTGAGGACTGGAAAATGCCACCAATTTGTGTGGGCTTT-AAGAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* **
1882800 TCCTACTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAGGTA
1 TCCTGCTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGC-TTT-----G-AAAGGCG
* * *
1882862 TCCTGCTCTTTGAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGACG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * * *
1882917 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1882972 TCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGC-TTT-----G-AAAGGCG
* * * * *
1883034 TCCTGCTTTTTGAGGACTAGAAAATGCCACCGACTCGTGTAGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1883089 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGCCTTTAAAAGAAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT----G--AAAGGCG
** * * *
1883150 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGAGCTTTAAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
* * **
1883210 TCCTGCTTTTTGAGGACTAGAAAATGCCACCGACTCATGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
1883265 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT----G--AAAGGCG
** * * * * *
1883326 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTATGTGGGCTTTAAAAAGCA
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
1883380 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* ** * *
1883435 TCCTGTTCTTTGAGGACTA-AATGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* ** *
1883489 TCTTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1883543 TCCTGCTCTTTGAGGACTA
1 TCCTGCTCTTTGAGGACTA
1883562 AAAGGTGAAA
Statistics
Matches: 989, Mismatches: 121, Indels: 93
0.82 0.10 0.08
Matches are distributed among these distances:
54 127 0.13
55 515 0.52
56 10 0.01
57 3 0.00
58 4 0.00
59 4 0.00
60 73 0.07
61 161 0.16
62 86 0.09
63 6 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:1882947 original size:172 final size:172
Alignment explanation
Indices: 1882347--1883538 Score: 1375
Period size: 172 Copynumber: 6.9 Consensus size: 172
1882337 AATAAAGTGC
* *
1882347 ATCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAAAAAGACGTC
1 ATCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTCGTGTGGGCTTTG------AAAGGCGTC
* * *
1882411 CTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGTGTGGGCTTTGGAAAGAGAAAGCATCCTGC
59 CTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT--AAAGAG---GCGTCCTGC
* *
1882476 TCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGC
119 TCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGT
* * *
1882524 ATCCTGCTCTTTGAGGACTAGAAAATGCCCCCAACTCGTGTGGGCTTTGAAAGGCGTTCTGCTTT
1 ATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
* * * * *
1882589 TTAAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAA-AGGCGTCCTGCTCATTGAGGACT
66 TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTTTGAGGACT
* *
1882653 GGAAAA-TGCCACCAACTCGTATGGGCTTT-----G-AAAGGT
131 -GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGT
* * * * * * * *
1882689 GTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCATGCTCT
1 ATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
* * *
1882754 TTGAGGACTGGAAAATGCCACCAATTTGTGTGGGCTTT-AAGAGGCGTCCTACTCTTTGAGGACT
66 TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTTTGAGGACT
*
1882818 GAAAAATGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAGGT
131 GAAAAGTGCCACCAACTTGTGTGGGC-TTTAAAAAGAAAAGGT
* *
1882861 ATCCTGCTCTTTGAGGACTAGAAAATGCCACCGACTCGTGTGGGCTTTGAAAGACGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
* *
1882926 TTGAGGACTGGGAAGTGCCACCAACTTGTGTAGGCTTTAAA-AGGCGTCCTGCTCTTTGAGGACT
66 TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTTTGAGGACT
1882990 -AAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAGGT
131 GAAAA-GTGCCACCAACTTGTGTGGGC-TTTAAAAAGAAAAGGT
* * * * *
1883033 GTCCTGCTTTTTGAGGACTAGAAAATGCCACCGACTCGTGTAGGCTTTGAAAGGCATCCTGCTCT
1 ATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
* *
1883098 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGCCTTTAAAAGAAAAAGGCGTCCTGCTCTTTGA
66 TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAG----AGGCGTCCTGCTCTTTGA
* * *
1883163 GGACTG-AAGGTGCCACCAGCTTGTGTGAGCTTTAAAAAGAAAAGGT
126 GGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGT
* * * *
1883209 GTCCTGCTTTTTGAGGACTAGAAAATGCCACCGACTCATGTGGGCTTTGAAAGGCGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
*
1883274 TTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGTGTCCTGCTCTTTG
66 TTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAG----AGGCGTCCTGCTCTTTG
* * * *
1883338 AGGACTG-AAGGTGCCACCAGCTTATGTGGGCTTT----A-AAAA-GC
125 AGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGT
* * * * *
1883379 ATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGTTCT
1 ATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
* *
1883444 TTGAGGACT--AAATGTGCCACCAACTTGTGTGGGCTTTAAA-AGGCATCTTGCTCTTTGAGGAC
66 TTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTTTGAGGAC
*
1883506 T-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
130 TGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
1883539 GGCGTCCTGC
Statistics
Matches: 902, Mismatches: 85, Indels: 66
0.86 0.08 0.06
Matches are distributed among these distances:
163 45 0.05
164 7 0.01
165 174 0.19
166 8 0.01
168 7 0.01
169 26 0.03
170 66 0.07
171 55 0.06
172 249 0.28
173 5 0.01
176 168 0.19
177 63 0.07
178 29 0.03
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (172 bp):
ATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTTTGAGGACT
GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGT
Found at i:1885529 original size:47 final size:46
Alignment explanation
Indices: 1885460--1885557 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 46
1885450 CTGAAAGAGT
1885460 GTGAAAATGAACCAAATAGACAAAATGTGATAGGCAAAGAATAAAGG
1 GTGAAAATGAACCAAATAGACAAAATGTGATAGGCAAAGAATAAA-G
*
1885507 GTGAAAATGAACCAAATAGACAAAATGTGATAGGCAAAGAATGAAG
1 GTGAAAATGAACCAAATAGACAAAATGTGATAGGCAAAGAATAAAG
1885553 GTGAA
1 GTGAA
1885558 GATAGAAACG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 6 0.12
47 44 0.88
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.15
Consensus pattern (46 bp):
GTGAAAATGAACCAAATAGACAAAATGTGATAGGCAAAGAATAAAG
Found at i:1891752 original size:19 final size:19
Alignment explanation
Indices: 1891727--1891776 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
1891717 AGTTCAACGA
*
1891727 TTTGTATCGATAGATAA-T
1 TTTGTATCGATACATAAGT
1891745 TGTTGTATCGATACATAAGT
1 T-TTGTATCGATACATAAGT
1891765 TTTGTATCGATA
1 TTTGTATCGATA
1891777 TAATGTACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 26 0.90
20 2 0.07
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1891849 original size:13 final size:13
Alignment explanation
Indices: 1891831--1891855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1891821 ATTACTCAAA
1891831 TGTATCGATACAT
1 TGTATCGATACAT
1891844 TGTATCGATACA
1 TGTATCGATACA
1891856 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1891908 original size:52 final size:52
Alignment explanation
Indices: 1891864--1891989 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
1891854 CACTGATCTT
1891864 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
1891916 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
1891968 TGTATCGATACATGCAAGCAAA
1 TGTATCGATACATGCAGGCAAA
1891990 ATTTCATATT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:1894212 original size:24 final size:24
Alignment explanation
Indices: 1894156--1894202 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1894146 GACACTCCAA
1894156 CCCGTTTTCAATCAAAAATTAAAC
1 CCCGTTTTCAATCAAAAATTAAAC
1894180 CCCGTTTTCAATCAAAAATTAAA
1 CCCGTTTTCAATCAAAAATTAAA
1894203 TTCCTCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (24 bp):
CCCGTTTTCAATCAAAAATTAAAC
Found at i:1897525 original size:2 final size:2
Alignment explanation
Indices: 1897518--1897572 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1897508 ATCCGTTCAT
1897518 TA TA 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 TA TA
1897560 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1897573 GAGAGAGCTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1897882 original size:28 final size:28
Alignment explanation
Indices: 1897846--1897928 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
1897836 GTTGTACTCA
1897846 TAATT-TTTTTCATGACATGTTATATTT
1 TAATTATTTTTCATGACATGTTATATTT
* * * * *
1897873 TAATTATTTTTTAT-ATTATATCATAGTT
1 TAATTATTTTTCATGA-CATGTTATATTT
*
1897901 TAATTATTTTTTCATGTCATGTTCATAT
1 TAATTA-TTTTTCATGACATGTT-ATAT
1897929 ATGATATTAT
Statistics
Matches: 40, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
27 6 0.15
28 21 0.52
29 10 0.25
30 3 0.08
ACGTcount: A:0.28, C:0.07, G:0.06, T:0.59
Consensus pattern (28 bp):
TAATTATTTTTCATGACATGTTATATTT
Found at i:1899451 original size:15 final size:15
Alignment explanation
Indices: 1899431--1899464 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1899421 ACTTGTTGCT
1899431 GAATCATTTTCTAGA
1 GAATCATTTTCTAGA
1899446 GAATCATTTTCTAGA
1 GAATCATTTTCTAGA
1899461 GAAT
1 GAAT
1899465 TCTGTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (15 bp):
GAATCATTTTCTAGA
Found at i:1903685 original size:2 final size:2
Alignment explanation
Indices: 1903678--1903722 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
1903668 ATGGAAAGCT
1903678 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
1903721 TA
1 TA
1903723 ACACACAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1904486 original size:75 final size:75
Alignment explanation
Indices: 1904362--1904586 Score: 405
Period size: 75 Copynumber: 3.0 Consensus size: 75
1904352 GTGGGCAAAG
* * * *
1904362 AGCAACGCTCAAAAGCAATTATTGAAGGACAAAGACCAAGACTAGGGTAAGTCATCATCGCCATA
1 AGCAACACCCAAAAGCAATTGTTGAAGGACAAAGACCAAGACTAAGGTAAGTCATCATCGCCATA
1904427 CTCTTCTATT
66 CTCTTCTATT
1904437 AGCAACACCCAAAAGCAATTGTTGAAGGACAAAGACCAAGACTAAGGTAAGTCATCATCGCCATA
1 AGCAACACCCAAAAGCAATTGTTGAAGGACAAAGACCAAGACTAAGGTAAGTCATCATCGCCATA
1904502 CTCTTCTATT
66 CTCTTCTATT
1904512 AGCAACACCCAAAAGCAATTGTTGAAGGACAAAGACCAAGACTAAGGTAAGTCATCATCGCCATA
1 AGCAACACCCAAAAGCAATTGTTGAAGGACAAAGACCAAGACTAAGGTAAGTCATCATCGCCATA
*
1904577 CTCTTTTATT
66 CTCTTCTATT
1904587 TTTCGTACTT
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 145 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (75 bp):
AGCAACACCCAAAAGCAATTGTTGAAGGACAAAGACCAAGACTAAGGTAAGTCATCATCGCCATA
CTCTTCTATT
Found at i:1904980 original size:28 final size:28
Alignment explanation
Indices: 1904926--1904987 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1904916 TTTTTGCGGG
*
1904926 ATATAAAATAATTTTAATTATTGAATAT
1 ATATAAAATAATTTTAATAATTGAATAT
**
1904954 ATATAAAATTTTTTTAATAATAT-AATAT
1 ATATAAAATAATTTTAATAAT-TGAATAT
*
1904982 AAATAA
1 ATATAA
1904988 TAAATGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
ATATAAAATAATTTTAATAATTGAATAT
Found at i:1906053 original size:12 final size:12
Alignment explanation
Indices: 1906035--1906092 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
1906025 TATTTCTATA
*
1906035 ATTTTTAAT-TT
1 ATTTTTTATGTT
1906046 ATTTTTTATGTT
1 ATTTTTTATGTT
*
1906058 ATGTCATTTT-TATT
1 AT-T--TTTTATGTT
1906072 ATTTTTTATGTT
1 ATTTTTTATGTT
1906084 ATTTTTTAT
1 ATTTTTTAT
1906093 TTTCATCATG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 12 0.31
12 16 0.41
13 2 0.05
14 5 0.13
15 4 0.10
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (12 bp):
ATTTTTTATGTT
Found at i:1907481 original size:21 final size:21
Alignment explanation
Indices: 1907455--1907505 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1907445 AACATGATAT
*
1907455 AACTTAAACTTGAAATAATTA
1 AACTTAAACTTAAAATAATTA
*
1907476 AACTTAAACTTAAAATGATTA
1 AACTTAAACTTAAAATAATTA
*
1907497 AACTGAAAC
1 AACTTAAAC
1907506 GAATTGAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (21 bp):
AACTTAAACTTAAAATAATTA
Found at i:1908834 original size:34 final size:34
Alignment explanation
Indices: 1908788--1909005 Score: 264
Period size: 34 Copynumber: 6.5 Consensus size: 34
1908778 GTAAAAACCA
*
1908788 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1908822 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
1908856 CCATTTAATCAATAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1908890 CCATTTAATCAACAATGATAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1908923 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1908957 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1908990 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1909006 TCTCCCACTT
Statistics
Matches: 158, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
33 46 0.29
34 108 0.68
35 4 0.03
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1908953 original size:101 final size:101
Alignment explanation
Indices: 1908786--1909005 Score: 345
Period size: 101 Copynumber: 2.2 Consensus size: 101
1908776 TGGTAAAAAC
* *
1908786 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
* *
1908851 ATCACCCATTTAATCAATAATGGTAAGCTACCAAATTT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAA--T
* *
1908889 C-CCATTTAATCAACAATGATAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
*
1908952 ATCACCCATTTAATCAACAATGGTAAACTACTAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1908988 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1909006 TCTCCCACTT
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
99 2 0.02
100 16 0.15
101 60 0.55
102 30 0.28
103 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1908962 original size:67 final size:67
Alignment explanation
Indices: 1908786--1909005 Score: 298
Period size: 67 Copynumber: 3.3 Consensus size: 67
1908776 TGGTAAAAAC
* *
1908786 CACCATTTAATCAACAATGGC-AACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCA
1 CACCATTTAATCAACAATGGCAAACC-ACCAAATCTCCCATTTAATCAACAATGGTAAACTACCA
1908850 AAT
65 AAT
* * * * * * *
1908853 CACCCATTTAATCAATAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGATAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAACTACCA
1908918 AAT
65 AAT
* * * *
1908921 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAACTACCAA
1908986 AT
66 AT
1908988 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1909006 TCTCCCACTT
Statistics
Matches: 129, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
67 73 0.57
68 54 0.42
69 2 0.02
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAACTACCAA
AT
Found at i:1913098 original size:19 final size:19
Alignment explanation
Indices: 1913071--1913133 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1913061 TCACGTGTAC
* *
1913071 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1913090 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1913109 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1913128 AGTACC
1 AGTACC
1913134 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1913484 original size:34 final size:34
Alignment explanation
Indices: 1913438--1913653 Score: 260
Period size: 34 Copynumber: 6.4 Consensus size: 34
1913428 GTAAAAACCA
*
1913438 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1913472 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
1913506 CCATTTAATCAATAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1913540 CCATTTAATCAACAATGATAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1913573 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1913607 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1913640 CCATTTAATCAACA
1 CCATTTAATCAACA
1913654 CGTATGGCGT
Statistics
Matches: 156, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
33 44 0.28
34 108 0.69
35 4 0.03
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1913603 original size:101 final size:101
Alignment explanation
Indices: 1913436--1913653 Score: 341
Period size: 101 Copynumber: 2.2 Consensus size: 101
1913426 TGGTAAAAAC
* *
1913436 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
* *
1913501 ATCACCCATTTAATCAATAATGGTAAGCTACCAAATTT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAA--T
* *
1913539 C-CCATTTAATCAACAATGATAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
*
1913602 ATCACCCATTTAATCAACAATGGTAAACTACTAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1913638 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1913654 CGTATGGCGT
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
99 2 0.02
100 14 0.13
101 60 0.56
102 30 0.28
103 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1913612 original size:67 final size:67
Alignment explanation
Indices: 1913436--1913653 Score: 294
Period size: 67 Copynumber: 3.2 Consensus size: 67
1913426 TGGTAAAAAC
* *
1913436 CACCATTTAATCAACAATGGC-AACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCA
1 CACCATTTAATCAACAATGGCAAACC-ACCAAATCTCCCATTTAATCAACAATGGTAAACTACCA
1913500 AAT
65 AAT
* * * * * * *
1913503 CACCCATTTAATCAATAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGATAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAACTACCA
1913568 AAT
65 AAT
* * * *
1913571 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAACTACCAA
1913636 AT
66 AT
1913638 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1913654 CGTATGGCGT
Statistics
Matches: 127, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
67 71 0.56
68 54 0.43
69 2 0.02
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAACTACCAA
AT
Found at i:1914577 original size:35 final size:38
Alignment explanation
Indices: 1914523--1914635 Score: 169
Period size: 38 Copynumber: 3.1 Consensus size: 38
1914513 ACTTTTTTTT
* *
1914523 ATACTAATATTTATATATTTTTACAATAATTTTAAATA
1 ATACTAATATTTATATATTTTTATAATAAATTTAAATA
*
1914561 ATACT-A-A-TTATATATTTTTATAATAAATCTAAATA
1 ATACTAATATTTATATATTTTTATAATAAATTTAAATA
*
1914596 ATATTAATATTTATATATTTTTATAATAAATTTAAATA
1 ATACTAATATTTATATATTTTTATAATAAATTTAAATA
1914634 AT
1 AT
1914636 TTTTAATATA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
35 29 0.43
36 2 0.03
37 2 0.03
38 34 0.51
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.50
Consensus pattern (38 bp):
ATACTAATATTTATATATTTTTATAATAAATTTAAATA
Found at i:1914592 original size:25 final size:23
Alignment explanation
Indices: 1914547--1914600 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
1914537 ATATTTTTAC
* *
1914547 AATAATTTTAAATAATACTAATT
1 AATATTTTTAAATAATACTAAAT
1914570 ATATATTTTTATAATAA-ATCTAAAT
1 A-ATATTTTTA-AATAATA-CTAAAT
1914595 AATATT
1 AATATT
1914601 AATATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 14 0.54
25 11 0.42
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
AATATTTTTAAATAATACTAAAT
Found at i:1914619 original size:38 final size:38
Alignment explanation
Indices: 1914527--1914644 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 38
1914517 TTTTTTATAC
* * *
1914527 TAATATTTATATATTTTTACAATAATTTTAAATAATAC
1 TAATATTTATATATTTTTATAATAAATTTAAATAATAT
*
1914565 T-A-A-TTATATATTTTTATAATAAATCTAAATAATAT
1 TAATATTTATATATTTTTATAATAAATTTAAATAATAT
*
1914600 TAATATTTATATATTTTTATAATAAATTTAAATAATTTT
1 TAATATTTATATATTTTTATAATAAATTTAAATAA-TAT
1914639 TAATAT
1 TAATAT
1914645 ATAAATAGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
35 29 0.41
36 2 0.03
37 2 0.03
38 29 0.41
39 8 0.11
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.52
Consensus pattern (38 bp):
TAATATTTATATATTTTTATAATAAATTTAAATAATAT
Found at i:1915234 original size:16 final size:16
Alignment explanation
Indices: 1915199--1915235 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1915189 CTCTCTCCTT
1915199 TGTTTT-TTTTTTTTA
1 TGTTTTATTTTTTTTA
*
1915214 -ATTTTATTTTTTTTA
1 TGTTTTATTTTTTTTA
1915229 TGTTTTA
1 TGTTTTA
1915236 GCTTTCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
14 4 0.22
15 9 0.50
16 5 0.28
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (16 bp):
TGTTTTATTTTTTTTA
Found at i:1915356 original size:2 final size:2
Alignment explanation
Indices: 1915349--1915385 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1915339 GAGTTTGACA
1915349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1915386 ATCATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1915508 original size:17 final size:17
Alignment explanation
Indices: 1915488--1915547 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1915478 TTATTGTTTT
1915488 ACTATTTTTAAGTATTA
1 ACTATTTTTAAGTATTA
* *
1915505 ACTAGTATTAAGTATTAAA
1 ACTATTTTTAAGTATT--A
* *
1915524 TAATATTTTTCAGTATTA
1 -ACTATTTTTAAGTATTA
1915542 ACTATT
1 ACTATT
1915548 AAAATTGTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 19 0.58
18 1 0.03
19 1 0.03
20 12 0.36
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (17 bp):
ACTATTTTTAAGTATTA
Found at i:1916108 original size:2 final size:2
Alignment explanation
Indices: 1916095--1916128 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1916085 AAAGATTGAA
*
1916095 AT AT AC 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
1916129 GAAAAGAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1918535 original size:50 final size:50
Alignment explanation
Indices: 1918460--1918623 Score: 285
Period size: 50 Copynumber: 3.3 Consensus size: 50
1918450 AATAGAAAAT
1918460 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGGAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGGAGAG
* *
1918510 GCATGCATGGGAAAACACAAAAATTGCAATTGGAGACAAAACATGCG-GAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATG-GAGAG
*
1918560 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGGAGAG
1918610 GCATGCATGGGAAA
1 GCATGCATGGGAAA
1918624 TGAAAAAAGC
Statistics
Matches: 107, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
50 106 0.99
51 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.15
Consensus pattern (50 bp):
GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGGAGAG
Found at i:1920295 original size:53 final size:50
Alignment explanation
Indices: 1920187--1920313 Score: 150
Period size: 53 Copynumber: 2.5 Consensus size: 50
1920177 CAATTGCTCG
1920187 TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCCTT
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-CTT
* **
1920238 TAATCGAGGGGATACTCCAACCCCGGTTTTA-TTTCTAAAATATTAATTT-TT
1 TAATC--GGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTCTT
*
1920289 CATAATCGGGGATACTCCAATCCCG
1 --TAATCGGGGATACTCCAACCCCG
1920314 TTATTTTCGA
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
51 24 0.36
52 4 0.06
53 39 0.58
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (50 bp):
TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTT
Found at i:1920380 original size:79 final size:79
Alignment explanation
Indices: 1920242--1920550 Score: 519
Period size: 79 Copynumber: 3.9 Consensus size: 79
1920232 TTCCTTTAAT
* *
1920242 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCC
* *
1920307 AATCCCGTTATTTT
66 AACCCCGTTATTTC
* * * *
1920321 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCAGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCC
1920386 AACCCCGTTATTTC
66 AACCCCGTTATTTC
*
1920400 CGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATCAATTTTTCATAATCGGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCC
1920465 AACCCCGTTATTTC
66 AACCCCGTTATTTC
* *
1920479 CAAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCT
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCC
1920544 AACCCCG
66 AACCCCG
1920551 ATTTTATTTT
Statistics
Matches: 218, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 218 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (79 bp):
CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCC
AACCCCGTTATTTC
Found at i:1920630 original size:53 final size:50
Alignment explanation
Indices: 1920482--1920629 Score: 163
Period size: 53 Copynumber: 2.9 Consensus size: 50
1920472 TTATTTCCAA
* *
1920482 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATC
1 GGGGATACTCTAACCCC-GTTTTATTTCTAAAACACCAATTTTTCATAATC
* * *
1920533 GGGGATACTCTAACCCCGATTTTATTTTTTTAGAACACC-GTTTTTCCATAATC
1 GGGGATACTCTAACCCCG-TTTTA--TTTCTAAAACACCAATTTTT-CATAATC
* * *
1920586 GGGGATACTCTAGCCCCGTTGTTATCTCTAAAATACCAATTTTT
1 GGGGATACTCTAACCCCGTT-TTATTTCTAAAACACCAATTTTT
1920630 TTCTCGTCAG
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
50 1 0.01
51 30 0.38
52 12 0.15
53 37 0.46
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (50 bp):
GGGGATACTCTAACCCCGTTTTATTTCTAAAACACCAATTTTTCATAATC
Found at i:1927529 original size:15 final size:15
Alignment explanation
Indices: 1927509--1927537 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1927499 GCTTGCTACA
1927509 AATTAATTTTTTTTC
1 AATTAATTTTTTTTC
1927524 AATTAATTTTTTTT
1 AATTAATTTTTTTT
1927538 TAAGAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
AATTAATTTTTTTTC
Found at i:1927572 original size:27 final size:28
Alignment explanation
Indices: 1927542--1927597 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1927532 TTTTTTTAAG
*
1927542 AATTTT-ACATGAT-TAAATTTTTAATTA
1 AATTTTGACAT-ATATAAAATTTTAATTA
*
1927569 AATTTTGTCATATATAAAATTTTAATTA
1 AATTTTGACATATATAAAATTTTAATTA
1927597 A
1 A
1927598 CCCTTTTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (28 bp):
AATTTTGACATATATAAAATTTTAATTA
Found at i:1930115 original size:30 final size:31
Alignment explanation
Indices: 1930079--1930154 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
1930069 TGAACAGTAC
*
1930079 ATGTATCGATGCATTCT-GTTTTTTACCCAG
1 ATGTATCGATACATTCTAGTTTTTTACCCAG
*
1930109 ATGTATCGATACATTCTATTTTTTTACCCAG
1 ATGTATCGATACATTCTAGTTTTTTACCCAG
*
1930140 ATATATCGATACATT
1 ATGTATCGATACATT
1930155 ATTCAATGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 16 0.38
31 26 0.62
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.43
Consensus pattern (31 bp):
ATGTATCGATACATTCTAGTTTTTTACCCAG
Found at i:1933109 original size:2 final size:2
Alignment explanation
Indices: 1933102--1933140 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1933092 TCCAAATACA
1933102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1933141 AAGAAACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1933357 original size:23 final size:21
Alignment explanation
Indices: 1933331--1933373 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1933321 GGAAAGTGTA
1933331 TTGAAAAAATAATTTAAGAATTT
1 TTGAAAAAAT-ATTTAA-AATTT
*
1933354 TTGATAAAATATTTAAAATT
1 TTGAAAAAATATTTAAAATT
1933374 ATTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (21 bp):
TTGAAAAAATATTTAAAATTT
Found at i:1934831 original size:24 final size:23
Alignment explanation
Indices: 1934802--1934851 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
1934792 TCTACGGAAG
1934802 AATGAATAATGGATTTTGATGAGA
1 AATGAATAATGGATTTTGATGA-A
*
1934826 AATGAATAATGGATTTTGGTGAA
1 AATGAATAATGGATTTTGATGAA
1934849 AAT
1 AAT
1934852 TTTTCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.34
Consensus pattern (23 bp):
AATGAATAATGGATTTTGATGAA
Found at i:1935548 original size:9 final size:10
Alignment explanation
Indices: 1935527--1935551 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1935517 AAGAAAAAAG
1935527 AAAAAGATAA
1 AAAAAGATAA
1935537 AAAAAGATAA
1 AAAAAGATAA
1935547 AAAAA
1 AAAAA
1935552 TTGTCTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAGATAA
Found at i:1941870 original size:20 final size:19
Alignment explanation
Indices: 1941845--1941918 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 19
1941835 GGAAAAAGAC
1941845 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATT-A
1941865 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATT-A
1941885 TA-AATGTATCGATACATT-
1 -AGAATGTATCGATACATTA
1941903 -GAATGTATCGATACAT
1 AGAATGTATCGATACAT
1941919 CTGGGTAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
17 15 0.29
20 35 0.69
21 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (19 bp):
AGAATGTATCGATACATTA
Found at i:1942842 original size:28 final size:28
Alignment explanation
Indices: 1942769--1943682 Score: 875
Period size: 28 Copynumber: 32.8 Consensus size: 28
1942759 TACTAACTTG
* *
1942769 TGTGGGCTTTGAAAAGAGTCGCCACCGACTT
1 TGTGGGCTTTGAAAGGA-T-GCCACTGAC-T
* *
1942800 GTGTGGGCTTTGAAATGATGCCACTAACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
1942829 TGTGGGCTTCGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
1942857 TGTGGGCTTTG-AA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
** * * * *
1942884 TGTGGATTTTGAAAGGGTGCCATTAATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1942912 TATGGGCTTTGAAAGGATACTACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1942940 TGTGGGCTTTAAAAGGATGCTATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1942968 TGTGGACTTTGAAAGGATGCCACTGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1942996 TGTGGGCTTTGAAAGGATACTACTGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1943024 TGTGGGCTTTGAAAGGATGCTACTGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1943052 TGTGGGCTTTG-AA--ATGCTATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1943077 TGTGAGCTTTAAAAGGATG----T--CA
1 TGTGGGCTTTGAAAGGATGCCACTGACT
1943099 TGTGGGCTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
* * * *
1943127 TATAGGCTTTG-AAGAGTTGCCACTAACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
* *
1943155 TGTGGACTTTGAAA-GATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1943182 TGTGGGCTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1943210 TATGGGCTTTG-AAGAGTTGCCACTAACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
1943238 TGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1943265 TGTGGGCTTTGAAAAGG-TGCCACTAATT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
1943293 TGTGGGCTTTCAAAGCATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1943321 TGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1943349 TGTGGGCTTTG-AAGAGATGTCACTGA-T
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
*
1943376 TGTGGGCTTTG-AAGAGTTGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
1943404 TGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1943431 TGTGGGCTTTGAAGGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1943459 TGTGGGCTTTGAAAAAGATGCCACTCACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * * *
1943488 TATTGGCTTTTGAAAAAAGATGTCACTGACT
1 TGTGGGC-TTTG--AAAGGATGCCACTGACT
* *
1943519 TGTGGGCTTTGAAAAGGATGCTACTGATT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
1943548 TGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
1943576 TGTGGGCTTTGAAAAGGATGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
** * *
1943605 TGTGAACTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1943633 TGTGGGCTTTGAAAGGGTGCCACTGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1943661 TGTGGAC-TTAAAAGGGTGCCAC
1 TGTGGGCTTTGAAAGGATGCCAC
1943683 GGGGTTATAG
Statistics
Matches: 741, Mismatches: 112, Indels: 63
0.81 0.12 0.07
Matches are distributed among these distances:
21 3 0.00
22 14 0.02
24 1 0.00
25 20 0.03
26 5 0.01
27 140 0.19
28 424 0.57
29 81 0.11
30 15 0.02
31 22 0.03
32 16 0.02
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:1942918 original size:83 final size:83
Alignment explanation
Indices: 1942769--1943682 Score: 886
Period size: 83 Copynumber: 10.9 Consensus size: 83
1942759 TACTAACTTG
* * *
1942769 TGTGGGCTTTGAAAAGAGTCGCCACCGACTTGTGTGGGCTTTGAAATGATGCCACTAACTTGTGG
1 TGTGGGCTTTGAAAAGA-T-GCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACTGACTTGTGG
*
1942834 GCTTCGAAAAGGTGCCACTGACT
62 GCTTTG-AAAGGTGCCACTGACT
* ** * * * * *
1942857 TGTGGGCTTTGAAGAG-TGCCACTGACTTGTGGATTTTGAAAGGGTGCCATTAATTTATGGGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
* *
1942921 TGAAAGGATACTACTGACT
66 TGAAAGG-TGCCACTGACT
* * * *
1942940 TGTGGGCTTT-AAAAGGATGCTATTGACTTGTGGACTTTGAAAGGATGCCACTGGCTTGTGGGCT
1 TGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
* * *
1943004 TTGAAAGGATACTACTGGCT
65 TTGAAAGG-TGCCACTGACT
* * * * * *
1943024 TGTGGGCTTTGAAAGGATGCTACTGGCTTGTGGGCTTTG-AA--ATGCTATTGACTTGTGAGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
* * *
1943086 T-AAAAG-G--A-TGTCA
66 TGAAAGGTGCCACTGACT
* * * * * *
1943099 TGTGGGCTTTGAAGAGATGCCACTGACTTATAGGCTTTG-AAGAGTTGCCACTAACTTGTGGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCT
* *
1943163 TTGAAAGATGCCACTGATT
65 TTGAAAGGTGCCACTGACT
* * * *
1943182 TGTGGGCTTTGAAAAGATGCCATTGACTTATGGGCTTTG-AAGAGTTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCT
1943246 TTGAAAGGTGCCACTGACT
65 TTGAAAGGTGCCACTGACT
* * * * *
1943265 TGTGGGCTTTGAAAAGGTGCCACTAATTTGTGGGCTTTCAAAGCATGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
* *
1943330 TAAAAGGGTGCCACTAACT
66 TGAAA-GGTGCCACTGACT
* * *
1943349 TGTGGGCTTTGAAGAGATGTCACTGA-TTGTGGGCTTTG-AAGAGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCT
1943412 TTGAAAGGTGCCACTGACT
65 TTGAAAGGTGCCACTGACT
** * * * * * *
1943431 TGTGGGCTTTGAAGGGGTGCCATTGACTTGTGGGCTTTGAAAAAGATGCCACTCACTTATTGGCT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGC-
* *
1943496 TTTGAAAAAAGATGTCACTGACT
64 TTTG---AAAGGTGCCACTGACT
* * *
1943519 TGTGGGCTTTGAAAAGGATGCTACTGATTTGTGGACTTTGAAAGGATGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
1943584 TTGAAAAGGATGCCACTGACT
65 TTG-AAAGG-TGCCACTGACT
** * * * *
1943605 TGTGAACTTTGAAAAGATGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGAGTTGTGGAC-T
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
*
1943669 TAAAAGGGTGCCAC
66 TGAAA-GGTGCCAC
1943683 GGGGTTATAG
Statistics
Matches: 689, Mismatches: 112, Indels: 55
0.80 0.13 0.06
Matches are distributed among these distances:
75 38 0.06
76 1 0.00
78 16 0.02
79 3 0.00
80 5 0.01
81 18 0.03
82 46 0.07
83 244 0.35
84 146 0.21
85 63 0.09
86 24 0.03
87 4 0.01
88 62 0.09
89 19 0.03
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (83 bp):
TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
TGAAAGGTGCCACTGACT
Found at i:1942978 original size:56 final size:56
Alignment explanation
Indices: 1942769--1944064 Score: 819
Period size: 55 Copynumber: 23.3 Consensus size: 56
1942759 TACTAACTTG
* * *
1942769 TGTGGGCTTTGAAAA-GAGTCGCCACCGACTTGTGTGGGCTTTGAAATGATGCCACTAACT
1 TGTGGGCTTT-AAAAGGA-T-GCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACTGACT
*
1942829 TGTGGGCTTCGAAAAGG-TGCCACTGACTTGTGGGCTTTG-AA-GAGTGCCACTGACT
1 TGTGGGCTT-TAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
** * * * * * * * *
1942884 TGTGGATTTTGAAAGGGTGCCATTAATTTATGGGCTTTGAAAGGATACTACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
1942940 TGTGGGCTTTAAAAGGATGCTATTGACTTGTGGACTTTGAAAGGATGCCACTGGCT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
1942996 TGTGGGCTTTGAAAGGATACTACTGGCTTGTGGGCTTTGAAAGGATGCTACTGGCT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
1943052 TGTGGGCTTT-GAA--ATGCTATTGACTTGTGAGCTTTAAAAGGATG----T--CA
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
1943099 TGTGGGCTTT-GAAGAGATGCCACTGACTTATAGGCTTTG-AAGAGTTGCCACTAACT
1 TGTGGGCTTTAAAAG-GATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACT
* * * * *
1943155 TGTGGACTTTGAAA-GATGCCACTGATTTGTGGGCTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
1943210 TATGGGCTTT-GAAGAGTTGCCACTAACTTGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTAAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
1943265 TGTGGGCTTTGAAAAGG-TGCCACTAATTTGTGGGCTTTCAAAGCATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1943321 TGTGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTG-AAGAGATGTCACTGA-T
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACT
* *
1943376 TGTGGGCTTT-GAAGAGTTGCCACTGACTTGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTAAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
1943431 TGTGGGCTTTGAAGGGGTGCCATTGACTTGTGGGCTTTGAAAAAGATGCCACTCACT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACT
* * * * * *
1943488 TATTGGCTTTTGAAAAAAGATGTCACTGACTTGTGGGCTTTGAAAAGGATGCTACTGATT
1 TGTGGGC-TTT--AAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACT
* *
1943548 TGTGGACTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACT
** * * *
1943605 TGTGAACTTTGAAAA-GATGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGAGT
1 TGTGGGCTTT-AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * ** * * * * * * *
1943661 TGTGGAC-TTAAAAGGGTGCCACGGGGTTATAGACTTTAAAAGGATGTCACAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
** * * * * * * * * *
1943716 TGTGAAC-TTAAAAGGGTGTCACAGAGTTGTAGAC-TTAAAAGGGTGCCAC-GAAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTG-ACT
* * * * * * ** *
1943770 TGTGGACTTTAAAAGTATGCCAC-GACGGAGTTATGGACTTT-AAAGGGTACCACCAAGT
1 TGTGGGCTTTAAAAGGATGCCACTGAC----TTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * * * * *
1943828 TGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTACCACAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * ** * * * *
1943883 TATGGAC-TTAAAAGGATGCCACGGAGTTATGGATTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * * *
1943938 TGTGGACTTTAAAATGG-TACCACGGAGTTGTGGAC-TTAAAAGGATGCCA-TGGAGT
1 TGTGGGCTTTAAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACT-GACT
* * * ** * * * *
1943993 TGTGGACTTTAAAAGGGTACCACAAAGTTGTGGGCTTTAAAAGGGTGCCA-TAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACT-GACT
*
1944049 TGTGGACTTTAAAAGG
1 TGTGGGCTTTAAAAGG
1944065 GTACCATAGA
Statistics
Matches: 1028, Mismatches: 157, Indels: 106
0.80 0.12 0.08
Matches are distributed among these distances:
47 14 0.01
49 4 0.00
50 20 0.02
53 27 0.03
54 61 0.06
55 386 0.38
56 299 0.29
57 113 0.11
58 43 0.04
59 6 0.01
60 54 0.05
61 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (56 bp):
TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:1943682 original size:27 final size:28
Alignment explanation
Indices: 1942840--1944364 Score: 781
Period size: 28 Copynumber: 55.2 Consensus size: 28
1942830 GTGGGCTTCG
* *
1942840 AAAA-GGTGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1942867 -GAAGAGTGCCACTGACTTGTGGATTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * * * *
1942894 GAAAGGGTGCCATTAATTTATGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * * * *
1942922 GAAAGGATACTACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1942950 AAAAGGATGCTATTGACTTGTGGACTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1942978 GAAAGGATGCCACTG-GCTTGTGGGCTTT
1 AAAAGGGTGCCACTGAG-TTGTGGACTTT
* * * * *
1943006 GAAAGGATACTACTG-GCTTGTGGGCTTT
1 AAAAGGGTGCCACTGAG-TTGTGGACTTT
* * * *
1943034 GAAAGGATGCTACTG-GCTTGTGGGCTTT
1 AAAAGGGTGCCACTGAG-TTGTGGACTTT
* * * *
1943062 GAAA---TGCTATTGACTTGT-GAGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGA-CTTT
* *
1943087 AAAAGGATGTCA-T--G-TG-GG-CTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1943109 -GAAGAGATGCCACTGACTTATAGG-CTTT
1 AAAAG-GGTGCCACTGAGTTGT-GGACTTT
* * * *
1943137 -GAAGAGTTGCCACTAACTTGTGGACTTT
1 AAAAG-GGTGCCACTGAGTTGTGGACTTT
* * * *
1943165 GAAA-GATGCCACTGATTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * * *
1943192 GAAAA-GATGCCATTGACTTATGGGCTTT
1 -AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * * *
1943220 -GAAGAGTTGCCACTAACTTGTGGGCTTT
1 AAAAG-GGTGCCACTGAGTTGTGGACTTT
* * *
1943248 GAAA-GGTGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1943275 GAAAA-GGTGCCACTAATTTGTGGGCTTT
1 -AAAAGGGTGCCACTGAGTTGTGGACTTT
* ** * *
1943303 CAAAGCATGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1943331 AAAAGGGTGCCACTAACTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1943359 -GAAGAGATGTCACTGA-TTGTGGGCTTT
1 AAAAG-GGTGCCACTGAGTTGTGGACTTT
* * * *
1943386 -GAAGAGTTGCCACTGACTTGTGGGCTTT
1 AAAAG-GGTGCCACTGAGTTGTGGACTTT
* * *
1943414 GAAA-GGTGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * * *
1943441 GAAGGGGTGCCATTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * * *
1943469 GAAAAAGATGCCACTCACTTATTGG-CTTTT
1 -AAAAGGGTGCCACTGAGTT-GTGGAC-TTT
* * * * *
1943499 GAAAAAAGATGTCACTGACTTGTGGGCTTT
1 --AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1943529 GAAAAGGATGCTACTGATTTGTGGACTTT
1 -AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1943558 GAAAGGATGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1943586 GAAAAGGATGCCACTGACTTGTGAACTTT
1 -AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1943615 GAAAA-GATGCCATTGACTTGTGGGCTTT
1 -AAAAGGGTGCCACTGAGTTGTGGACTTT
*
1943643 GAAAGGGTGCCACTGAGTTGTGGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1943670 AAAAGGGTGCCACGGGGTTATAGACTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1943698 AAAAGGATGTCACAGAGTTGTGAAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1943725 AAAAGGGTGTCACAGAGTTGTAGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
1943752 AAAAGGGTGCCAC-GAAGTTGTGGACTTT
1 AAAAGGGTGCCACTG-AGTTGTGGACTTT
** * *
1943780 AAAAGTATGCCACGACGGAGTTATGGACTTT
1 AAAAGGGTG-C-C-ACTGAGTTGTGGACTTT
* **
1943811 -AAAGGGTACCACCAAGTTGTGGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* *
1943837 AAAAGGATGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1943865 AAAAGGGTACCACAGAGTTATGGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1943892 AAAAGGATGCCACGGAGTTATGGATTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
*
1943920 AAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1943948 AAAATGGTACCACGGAGTTGTGGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
*
1943975 AAAAGGATGCCA-TGGAGTTGTGGACTTT
1 AAAAGGGTGCCACT-GAGTTGTGGACTTT
* ** *
1944003 AAAAGGGTACCACAAAGTTGTGGGCTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
1944031 AAAAGGGTGCCA-TAGAGTTGTGGACTTT
1 AAAAGGGTGCCACT-GAGTTGTGGACTTT
* *
1944059 AAAAGGGTACCA-TAGAGTTATGGAC-TT
1 AAAAGGGTGCCACT-GAGTTGTGGACTTT
** * *
1944086 AAAAGAATGCCACAGAGTTGTGGAC-TG
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * * *
1944113 CATAGGATGCCACAGAGTTATGGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* *
1944140 AAAAGGTTGCCACAGAGTTGTGGACTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* *
1944168 -AAAGGGTGCCACGGAGTTGTAGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1944194 AAAAAGATGCGAC-GAAGTTGTGGACTTT
1 AAAAGGGTGCCACTG-AGTTGTGGACTTT
* * *
1944222 AAAAGGGTGGCACAGAGTTATGGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* *
1944249 AAAAGGATGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
** *
1944277 AAAATAGTGCCACAGAGTTGTGGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * *
1944304 AAAAGGATGCCACAGAGTTATGGAC-TT
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
* * * *
1944331 AAAAGGTTGCCACGGAGTTTTGGACTTA
1 AAAAGGGTGCCACTGAGTTGTGGACTTT
1944359 AAAAGG
1 AAAAGG
1944365 AATACCACTA
Statistics
Matches: 1224, Mismatches: 217, Indels: 113
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.00
22 10 0.01
23 1 0.00
24 4 0.00
25 18 0.01
26 11 0.01
27 441 0.36
28 609 0.50
29 76 0.06
30 18 0.01
31 32 0.03
32 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (28 bp):
AAAAGGGTGCCACTGAGTTGTGGACTTT
Found at i:1944365 original size:55 final size:54
Alignment explanation
Indices: 1943644--1944361 Score: 713
Period size: 55 Copynumber: 13.1 Consensus size: 54
1943634 GTGGGCTTTG
* * * *
1943644 AAAGGGTGCCACTGAGTTGTGGACTTAAAAGGGTGCCACGGGGTTATAGACTTTA
1 AAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGAC-TTA
* * * * * *
1943699 AAAGGATGTCACAGAGTTGTGAACTTAAAAGGGTGTCACAGAGTTGTAGACTTA
1 AAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTA
* ** *
1943753 AAAGGGTGCCAC-GAAGTTGTGGACTTTAAAAGTATGCCACGACGGAGTTATGGACTTT
1 AAAGGATGCCACAG-AGTTGTGGAC-TTAAAAGGGTG-C-C-ACGGAGTTATGGACTTA
* * * *
1943811 AAAGGGTACCACCA-AGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTA
1 AAAGGATGCCA-CAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGAC-TTA
* * * * *
1943866 AAAGGGTACCACAGAGTTATGGACTTAAAAGGATGCCACGGAGTTATGGATTTTA
1 AAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGA-CTTA
* * * * *
1943921 AAAGGGTGCCACGGAGTTGTGGACTTTAAAATGGTACCACGGAGTTGTGGACTTA
1 AAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTATGGACTTA
** * ** * *
1943976 AAAGGATGCCATGGAGTTGTGGACTTTAAAAGGGTACCACAAAGTTGTGGGCTTTA
1 AAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTATGGAC-TTA
* * * **
1944032 AAAGGGTGCCATAGAGTTGTGGACTTTAAAAGGGTACCATAGAGTTATGGACTTA
1 AAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTATGGACTTA
* ** * * *
1944087 AAAGAATGCCACAGAGTTGTGGACTGCATAGGATGCCACAGAGTTATGGACTTA
1 AAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTA
* * * *
1944141 AAAGGTTGCCACAGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTAGACTTA
1 AAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTA
* * * *
1944195 AAAAGATGCGAC-GAAGTTGTGGACTTTAAAAGGGTGGCACAGAGTTATGGACTTA
1 AAAGGATGCCACAG-AGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTATGGACTTA
* ** * *
1944250 AAAGGATGCCACGGAGTTGTGGACTTTAAAATAGTGCCACAGAGTTGTGGACTTA
1 AAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTATGGACTTA
* * *
1944305 AAAGGATGCCACAGAGTTATGGACTTAAAAGGTTGCCACGGAGTTTTGGACTTA
1 AAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTA
1944359 AAA
1 AAA
1944362 AGGAATACCA
Statistics
Matches: 564, Mismatches: 84, Indels: 31
0.83 0.12 0.05
Matches are distributed among these distances:
53 2 0.00
54 153 0.27
55 291 0.52
56 73 0.13
57 11 0.02
58 33 0.06
59 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (54 bp):
AAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTA
Found at i:1952773 original size:20 final size:19
Alignment explanation
Indices: 1952746--1952822 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 19
1952736 GTAAAAAGAC
1952746 AAAATGTATCGATACATTG
1 AAAATGTATCGATACATTG
*
1952765 AAGAATGTATCGATACATTC
1 AA-AATGTATCGATACATTG
*
1952785 ATACATGTATCGATACATTG
1 A-AAATGTATCGATACATTG
1952805 AAAGATGTATCGATACAT
1 AAA-ATGTATCGATACAT
1952823 CTGGGTAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
19 3 0.06
20 47 0.92
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:1954944 original size:17 final size:17
Alignment explanation
Indices: 1954922--1954955 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1954912 ATAATGTATT
1954922 AAATAAAAATATTTTTA
1 AAATAAAAATATTTTTA
*
1954939 AAATAAAATTATTTTTA
1 AAATAAAAATATTTTTA
1954956 TTTTGAACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAAAAATATTTTTA
Found at i:1959514 original size:35 final size:35
Alignment explanation
Indices: 1959473--1959539 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1959463 TGAAGAGACA
* *
1959473 AGTAAATTTTTGTTTATTTTTTTCTATACTTCAAC
1 AGTAAATCTTTGTTTATTATTTTCTATACTTCAAC
*
1959508 AGTAAATCTTTGTTTATTATTTTCTGTACTTC
1 AGTAAATCTTTGTTTATTATTTTCTATACTTC
1959540 GACTGTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.57
Consensus pattern (35 bp):
AGTAAATCTTTGTTTATTATTTTCTATACTTCAAC
Found at i:1960636 original size:2 final size:2
Alignment explanation
Indices: 1960629--1960677 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1960619 GGGAATCAAA
1960629 AT AT AT 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
1960671 AT AT AT A
1 AT AT AT A
1960678 CCCAAAGTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.