Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 43 of 226
Found at i:18259839 original size:15 final size:16
Alignment explanation
Indices: 18259819--18259848 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18259809 AAACTAAAAA
18259819 GAATCA-AATAAAGTC
1 GAATCAGAATAAAGTC
18259834 GAATCAGAATAAAGT
1 GAATCAGAATAAAGT
18259849 TAATATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (16 bp):
GAATCAGAATAAAGTC
Found at i:18262183 original size:31 final size:31
Alignment explanation
Indices: 18262163--18262246 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 31
18262153 AACGTTTTCA
* *
18262163 ATCATTTTTATTTTGATCACTCATGTTTTAG
1 ATCATTTTTATTTTGGTCACTCATGTTTTAC
*
18262194 ATTATTTTTATTTTGGTCACTCATGTTTTAC
1 ATCATTTTTATTTTGGTCACTCATGTTTTAC
* *
18262225 ATCGTTTCTATTTTGGTCACTC
1 ATCATTTTTATTTTGGTCACTC
18262247 TCCATTAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (31 bp):
ATCATTTTTATTTTGGTCACTCATGTTTTAC
Found at i:18271010 original size:5 final size:5
Alignment explanation
Indices: 18270995--18271032 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
18270985 TTCAAAGAGC
18270995 TTTGAG TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TT
1 TTTG-G TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TT
18271033 GGATGGATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.03, C:0.00, G:0.37, T:0.61
Consensus pattern (5 bp):
TTTGG
Found at i:18272064 original size:22 final size:23
Alignment explanation
Indices: 18272013--18272075 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
18272003 TTTAAATGTA
*
18272013 TATT-AAATAATAAAATATACAT
1 TATTAAAATAATAAAATAAACAT
*
18272035 TACTTTAAAATAAT-AATTAAACAT
1 TA--TTAAAATAATAAAATAAACAT
*
18272059 TATTAAAATATTAAAAT
1 TATTAAAATAATAAAAT
18272076 TATTTTCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 11 0.33
23 3 0.09
24 12 0.36
25 7 0.21
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (23 bp):
TATTAAAATAATAAAATAAACAT
Found at i:18275156 original size:11 final size:11
Alignment explanation
Indices: 18275133--18275163 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
18275123 GGTGACACAG
18275133 AAATAAT-AAT
1 AAATAATAAAT
18275143 AAATAATAAAT
1 AAATAATAAAT
18275154 AAATAATAAA
1 AAATAATAAA
18275164 ACGAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:18276401 original size:7 final size:7
Alignment explanation
Indices: 18276357--18276381 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18276347 TGTATATGTC
18276357 TATAAAA
1 TATAAAA
18276364 TATAAAA
1 TATAAAA
18276371 TATAAAA
1 TATAAAA
18276378 TATA
1 TATA
18276382 TAAAAGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TATAAAA
Found at i:18301493 original size:26 final size:25
Alignment explanation
Indices: 18301466--18301562 Score: 72
Period size: 25 Copynumber: 3.8 Consensus size: 25
18301456 ATATAAATAT
18301466 AAATATAAATTTTAAAAATTCAAAA
1 AAATATAAATTTTAAAAATTCAAAA
* *
18301491 TAATAAAAATATTATAAAAA-T-AAAA
1 AAATATAAAT-TT-TAAAAATTCAAAA
* * *
18301516 AAGTATTTAAATTTAAAAAATGCAAAA
1 AA--ATATAAATTTTAAAAATTCAAAA
* *
18301543 AAATTTTAATTTTCAAAAAT
1 AAATATAAATTTT-AAAAAT
18301563 ATGTATTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
25 27 0.48
26 11 0.20
27 18 0.32
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATATAAATTTTAAAAATTCAAAA
Found at i:18301517 original size:19 final size:19
Alignment explanation
Indices: 18301487--18301526 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
18301477 TTAAAAATTC
18301487 AAAATAATAAAAATATTATA
1 AAAATAATAAAAATATT-TA
*
18301507 AAAATAA-AAAAGTATTTA
1 AAAATAATAAAAATATTTA
18301525 AA
1 AA
18301527 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 8 0.42
20 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAATAATAAAAATATTTA
Found at i:18301517 original size:27 final size:26
Alignment explanation
Indices: 18301452--18301517 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
18301442 TAGGAATCTA
* *
18301452 AAAAATATAAATATAAATATAAATTTT
1 AAAAATA-AAAAATAAATAAAAATTTT
**
18301479 AAAAATTCAAAAT-AATAAAAATATTAT
1 AAAAATAAAAAATAAATAAAAAT-TT-T
18301506 AAAAATAAAAAA
1 AAAAATAAAAAA
18301518 GTATTTAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
25 8 0.26
26 6 0.19
27 17 0.55
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAATAAAAAATAAATAAAAATTTT
Found at i:18301534 original size:25 final size:24
Alignment explanation
Indices: 18301497--18301563 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 24
18301487 AAAATAATAA
*
18301497 AAATATTATAAAAATAAAAAAGTATTT
1 AAAT-TTA-AAAAATAAAAAAAT-TTT
18301524 AAATTTAAAAAATGCAAAAAAATTTT
1 AAATTTAAAAAAT--AAAAAAATTTT
* *
18301550 AATTTTCAAAAATA
1 AAATTTAAAAAATA
18301564 TGTATTTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 1 0.03
25 6 0.17
26 17 0.49
27 11 0.31
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (24 bp):
AAATTTAAAAAATAAAAAAATTTT
Found at i:18309772 original size:36 final size:36
Alignment explanation
Indices: 18309706--18309775 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
18309696 ATAATTTTAG
* ** *
18309706 ATTATTAAGAATACAATTATATGTGGAAGTGTATTT
1 ATTATTAAGAATAAAATTATATCCGAAAGTGTATTT
18309742 ATTATTAAGAATAAAATTATATCCGAAAGTGTAT
1 ATTATTAAGAATAAAATTATATCCGAAAGTGTAT
18309776 ATATATTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTATTAAGAATAAAATTATATCCGAAAGTGTATTT
Found at i:18319619 original size:39 final size:39
Alignment explanation
Indices: 18319532--18319670 Score: 170
Period size: 39 Copynumber: 3.5 Consensus size: 39
18319522 TACAGTATCG
*
18319532 GTGGCATGCTTTACATGCAATCAATATGTACGTTAATATTCA
1 GTGGCATGC-TTACATGCAATCAATA--TACGGTAATATTCA
*
18319574 GTGGCATGCTTACATGCAATCAATATACGGTAATATTTA
1 GTGGCATGCTTACATGCAATCAATATACGGTAATATTCA
* * * *
18319613 TTGGCATGCTTACATGCAATCAATATACGATAACAGTCA
1 GTGGCATGCTTACATGCAATCAATATACGGTAATATTCA
* *
18319652 ATGACATGCTTTACATGCA
1 GTGGCATGC-TTACATGCA
18319671 GATTATTTGC
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
39 53 0.61
40 9 0.10
41 16 0.18
42 9 0.10
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (39 bp):
GTGGCATGCTTACATGCAATCAATATACGGTAATATTCA
Found at i:18320829 original size:21 final size:19
Alignment explanation
Indices: 18320796--18320847 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
18320786 CCATAACATG
18320796 AAATTTGGATTAAATTGA-TT
1 AAATTT-GATTAAA-TGAGTT
18320816 AGAATATTGATTAAATGAGTT
1 A-AAT-TTGATTAAATGAGTT
18320837 AAATTTGATTA
1 AAATTTGATTA
18320848 TATAGATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.24
20 7 0.24
21 13 0.45
22 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (19 bp):
AAATTTGATTAAATGAGTT
Found at i:18321190 original size:25 final size:24
Alignment explanation
Indices: 18321156--18321293 Score: 95
Period size: 25 Copynumber: 5.6 Consensus size: 24
18321146 CTCACCACAA
*
18321156 CTCGTATGAGCTTATCGGTTTGCAG
1 CTCGTATGAGCTTA-CGATTTGCAG
*
18321181 CTCGTATGAGCTTACTGATATT-CAA
1 CTCGTATGAGCTTAC-GAT-TTGCAG
* * **
18321206 CTCGGAGGAGCTTACCG-TTTATA-
1 CTCGTATGAGCTTA-CGATTTGCAG
*
18321229 CTCGTATGAGCTTACCAATTTGCAG
1 CTCGTATGAGCTTA-CGATTTGCAG
*
18321254 CTCATATGAGCTTACTGATATT-CAG
1 CTCGTATGAGCTTAC-GAT-TTGCAG
* *
18321279 CTCGGAGGAGCTTAC
1 CTCGTATGAGCTTAC
18321294 CGTTTATCGC
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
23 16 0.18
24 8 0.09
25 61 0.68
26 5 0.06
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (24 bp):
CTCGTATGAGCTTACGATTTGCAG
Found at i:18321274 original size:73 final size:73
Alignment explanation
Indices: 18321155--18321300 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 73
18321145 ACTCACCACA
* ** *
18321155 ACTCGTATGAGCTTATCGGTTTGCAGCTCGTATGAGCTTACTGATATTCAACTCGGAGGAGCTTA
1 ACTCGTATGAGCTTACCAATTTGCAGCTCATATGAGCTTACTGATATTCAACTCGGAGGAGCTTA
18321220 CCGTTTAT
66 CCGTTTAT
*
18321228 ACTCGTATGAGCTTACCAATTTGCAGCTCATATGAGCTTACTGATATTCAGCTCGGAGGAGCTTA
1 ACTCGTATGAGCTTACCAATTTGCAGCTCATATGAGCTTACTGATATTCAACTCGGAGGAGCTTA
18321293 CCGTTTAT
66 CCGTTTAT
18321301 CGCTAGTATG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (73 bp):
ACTCGTATGAGCTTACCAATTTGCAGCTCATATGAGCTTACTGATATTCAACTCGGAGGAGCTTA
CCGTTTAT
Found at i:18327771 original size:29 final size:29
Alignment explanation
Indices: 18327721--18327779 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
18327711 TGTTTTCCTA
* *
18327721 ACAACAATGGTACTAGGGAGTGATCGAAG
1 ACAACAATGGTACTAAGAAGTGATCGAAG
* *
18327750 ACAACAATGGTATTAATAAGTGATCGAAG
1 ACAACAATGGTACTAAGAAGTGATCGAAG
18327779 A
1 A
18327780 TTAACTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.20
Consensus pattern (29 bp):
ACAACAATGGTACTAAGAAGTGATCGAAG
Found at i:18330413 original size:39 final size:39
Alignment explanation
Indices: 18330333--18330419 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
18330323 ATAAATTTAA
* * * *
18330333 TTTTAATGATTTGGGAATTTAGGTTTTTGTTTTTGTTTT
1 TTTTAATGATTTGAGAATTTAGGTTTTTCTTTTAGTCTT
* *
18330372 TTTTTATGATTTTAGAATTTAGGTTTTTACTTTTAG-CTT
1 TTTTAATGATTTGAGAATTTAGGTTTTT-CTTTTAGTCTT
18330411 TTTTGAATG
1 TTTT-AATG
18330420 TTTTTATTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.18, C:0.02, G:0.17, T:0.62
Consensus pattern (39 bp):
TTTTAATGATTTGAGAATTTAGGTTTTTCTTTTAGTCTT
Found at i:18330435 original size:6 final size:6
Alignment explanation
Indices: 18330424--18330471 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
18330414 TGAATGTTTT
* * * *
18330424 TATTAA TATTAA TATTAA TATTAA TAATAT TATT-A TCTTTA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
18330471 T
1 T
18330472 TTTTATTTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
5 3 0.09
6 31 0.91
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (6 bp):
TATTAA
Found at i:18344821 original size:24 final size:24
Alignment explanation
Indices: 18344715--18344870 Score: 228
Period size: 24 Copynumber: 6.5 Consensus size: 24
18344705 ATACGGAACA
* *
18344715 AATA-CAGAGAGCACAAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
***
18344738 AA-A-CAGAGAGCACTGGCGTGCT
1 AATATCAGAGAGCACCAACGTGCT
18344760 AAATATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCT
18344785 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
18344810 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
18344834 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
18344858 AATATCAGAGAGC
1 AATATCAGAGAGC
18344871 GCGCTAAAGT
Statistics
Matches: 122, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.13
23 4 0.03
24 62 0.51
25 40 0.33
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:18352560 original size:41 final size:41
Alignment explanation
Indices: 18352514--18352605 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
18352504 ACCGACTTTT
* * *
18352514 AGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACCTAAAGTCCGAAATATATCACCGGCATCA
* * * * *
18352555 AGCCTGCTAGACGTAAAGTCTGAATTATTTCATCGGCATCA
1 AGCCTGCTAGACCTAAAGTCCGAAATATATCACCGGCATCA
18352596 AGCCTGCTAG
1 AGCCTGCTAG
18352606 GCACATAGCC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACCTAAAGTCCGAAATATATCACCGGCATCA
Found at i:18352886 original size:2 final size:2
Alignment explanation
Indices: 18352879--18352905 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18352869 TCTAACCTCT
18352879 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
18352906 TTCATATCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18353340 original size:21 final size:21
Alignment explanation
Indices: 18353310--18353351 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
18353300 TCATAAAATC
*
18353310 AAATTTAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
18353331 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
18353352 TATATATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATTCAGCTTATAGAACATA
Found at i:18360598 original size:2 final size:2
Alignment explanation
Indices: 18360591--18360623 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18360581 TCTAACCTCT
18360591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18360624 TTCATATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18360978 original size:21 final size:21
Alignment explanation
Indices: 18360948--18360989 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
18360938 TCATAAAATC
*
18360948 AAATTTAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
18360969 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
18360990 TATATATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATTCAGCTTATAGAACATA
Found at i:18363858 original size:64 final size:64
Alignment explanation
Indices: 18363779--18363906 Score: 168
Period size: 64 Copynumber: 2.0 Consensus size: 64
18363769 AAGCATCCTA
* * * * *
18363779 ATCGGTATTAATCCTGCATATGTTGCAGACATACCATAGCTCTTTGTGAA-CGTCCTGTTATATG
1 ATCGGTATTAATCCTGCATATATTACAGACATACCACAGCTCTTTAT-AAGCGTCCTGATATATG
* * *
18363843 ATCGGTATTGATCCTGCATATATTACGGACATACCGCAGCTCTTTATAAGCGTCCTGATATATG
1 ATCGGTATTAATCCTGCATATATTACAGACATACCACAGCTCTTTATAAGCGTCCTGATATATG
18363907 GCTACCCGGA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 2 0.04
64 53 0.96
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (64 bp):
ATCGGTATTAATCCTGCATATATTACAGACATACCACAGCTCTTTATAAGCGTCCTGATATATG
Found at i:18372368 original size:2 final size:2
Alignment explanation
Indices: 18372361--18372387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18372351 TATTACATAC
18372361 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
18372388 AATTGTAAAG
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:18373954 original size:66 final size:66
Alignment explanation
Indices: 18373872--18374000 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 66
18373862 AAAACTTTTA
**
18373872 AGTAATTGAAGTATGCGTAAAACGCGTGATATGCGCGGAACAATAAAGGAATGAGGTTGTAGTTT
1 AGTAATTGAAAAATGCGTAAAACGCGTGATATGCGCGGAACAATAAAGGAATGAGGTTGTAGTTT
18373937 G
66 G
* * *
18373938 AGTAATTGAAAAATGCGTGAAACGCGTGATATGTGTGGAACAATAAAGGAATGAGGTTGTAGT
1 AGTAATTGAAAAATGCGTAAAACGCGTGATATGCGCGGAACAATAAAGGAATGAGGTTGTAGT
18374001 CACAGACACG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.36, C:0.08, G:0.30, T:0.26
Consensus pattern (66 bp):
AGTAATTGAAAAATGCGTAAAACGCGTGATATGCGCGGAACAATAAAGGAATGAGGTTGTAGTTT
G
Found at i:18380656 original size:158 final size:159
Alignment explanation
Indices: 18380359--18380675 Score: 496
Period size: 158 Copynumber: 2.0 Consensus size: 159
18380349 AGGAACTACT
* * *
18380359 TGGAGCTACAACAGAGCAAAAGTCTCAGTGGAAAATCCTGCTTGGATCGCCTCCGCTTTTCGATG
1 TGGAGCTACAACAGAGCAAAAGTCTCAGTGGAAAATCCAGCTTGGATCGCCTCCGCCTTTCGATA
* * * *
18380424 TGATCTCGTTCTAGTCACTGTGTTCATCATTTCGTCACTTAATATCAGGTGTGCCATATTTTAAT
66 TGATCTCGGTCTAGTCACCGTGTTCATCAATTCGTCACTTAATATCACGTGTGCCATATTTTAAT
*
18380489 CATAGAAAAA-GGAAAAAGTTGATTGGTG
131 CATAGAAAAAGGGAAAAAGTTAATTGGTG
* *
18380517 TGGAGCTACAACAGAGTAAAAGTCTCAGTGGAAAATCCAGCTTGGATCGCCTCTGCCTTT-GAAT
1 TGGAGCTACAACAGAGCAAAAGTCTCAGTGGAAAATCCAGCTTGGATCGCCTCCGCCTTTCG-AT
*
18380581 ATGATCTCGGTCTAGTCACCGTGTTCATCAATTCGTCACTTAATATCACGTGTGCCTTATTTTAA
65 ATGATCTCGGTCTAGTCACCGTGTTCATCAATTCGTCACTTAATATCACGTGTGCCATATTTTAA
18380646 TTCATA-AAAAAGGGAAAAAGTTAATTGGTG
130 -TCATAGAAAAAGGGAAAAAGTTAATTGGTG
18380676 CTATGTTGCT
Statistics
Matches: 145, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
157 1 0.01
158 122 0.84
159 22 0.15
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (159 bp):
TGGAGCTACAACAGAGCAAAAGTCTCAGTGGAAAATCCAGCTTGGATCGCCTCCGCCTTTCGATA
TGATCTCGGTCTAGTCACCGTGTTCATCAATTCGTCACTTAATATCACGTGTGCCATATTTTAAT
CATAGAAAAAGGGAAAAAGTTAATTGGTG
Found at i:18381543 original size:22 final size:23
Alignment explanation
Indices: 18381518--18381570 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
18381508 AAAAATATTC
18381518 TTATTTTACA-AAATA-AATTATA
1 TTATTTTA-AGAAATATAATTATA
* *
18381540 TTATTTTAAGAAATATAATTTTT
1 TTATTTTAAGAAATATAATTATA
18381563 TTATTTTA
1 TTATTTTA
18381571 TATCACGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 13 0.48
23 13 0.48
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTTTAAGAAATATAATTATA
Found at i:18386764 original size:22 final size:21
Alignment explanation
Indices: 18386734--18386774 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
18386724 AAATACAATT
*
18386734 CAAAATTATTAAATATTATTA
1 CAAAATTATAAAATATTATTA
18386755 CAAACATTATAAAATATTAT
1 CAAA-ATTATAAAATATTAT
18386775 GGATTATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (21 bp):
CAAAATTATAAAATATTATTA
Found at i:18391729 original size:2 final size:2
Alignment explanation
Indices: 18391724--18391771 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
18391714 AGAATAGGAG
18391724 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
18391766 AT AT AT
1 AT AT AT
18391772 TAAGTAACCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18409666 original size:19 final size:19
Alignment explanation
Indices: 18409642--18409687 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
18409632 TTATATATTT
*
18409642 AAAATTTAGT-TTTTTTTC
1 AAAATTTAGTCTATTTTTC
18409660 AAAAATTTAGTCTATTTTTC
1 -AAAATTTAGTCTATTTTTC
18409680 AAAATTTA
1 AAAATTTA
18409688 AAATTTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (19 bp):
AAAATTTAGTCTATTTTTC
Found at i:18414709 original size:31 final size:31
Alignment explanation
Indices: 18414671--18414742 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
18414661 AATTTGGGTC
18414671 AGGACTAAA-AT-ATCAAATTTAAAAAAGTAAA
1 AGGACTAAATATGATC-AA-TTAAAAAAGTAAA
* * *
18414702 AGGACTAAATTTGATCAATTGAAAAAGTACA
1 AGGACTAAATATGATCAATTAAAAAAGTAAA
18414733 AGGACTAAAT
1 AGGACTAAAT
18414743 CAAAAACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 30 0.83
32 3 0.08
33 3 0.08
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (31 bp):
AGGACTAAATATGATCAATTAAAAAAGTAAA
Found at i:18433593 original size:53 final size:53
Alignment explanation
Indices: 18433522--18433694 Score: 287
Period size: 53 Copynumber: 3.3 Consensus size: 53
18433512 AGCTTCTTTG
* *
18433522 GATTCAAATATGACAAATTAGA-TCCTAGTTGTCAAGAA-ATTTTTTTAAATGTT
1 GATTCAAATATGATAAATTA-ATTCATAGTTGTCAAGAACA-TTTTTTAAATGTT
*
18433575 GAATCAAATATGATAAATTAATTCATAGTTGTCAAGAACATTTTTTAAATGTT
1 GATTCAAATATGATAAATTAATTCATAGTTGTCAAGAACATTTTTTAAATGTT
18433628 GATTCAAATATGATAAATTAATTCATAGTTGTCAAGAACATTTTTTAAATGTT
1 GATTCAAATATGATAAATTAATTCATAGTTGTCAAGAACATTTTTTAAATGTT
18433681 GATTCAAATATGAT
1 GATTCAAATATGAT
18433695 TATTGTTTGT
Statistics
Matches: 114, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
52 1 0.01
53 112 0.98
54 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (53 bp):
GATTCAAATATGATAAATTAATTCATAGTTGTCAAGAACATTTTTTAAATGTT
Found at i:18434035 original size:45 final size:44
Alignment explanation
Indices: 18433942--18434070 Score: 188
Period size: 45 Copynumber: 2.9 Consensus size: 44
18433932 TATTTTCTAT
* * *
18433942 CATGTGCATGATAAAAATGGATTTGTTTGTATTAAAGTGAATGA
1 CATGTGCATGATAGAAATGGATTTTTTTGTATTAAAGTGTATGA
*
18433986 CATGTGCATGATAGAAAT-GATTTTTTTTTGTATTAAAGTGTATGG
1 CATGTGCATGATAGAAATGGA--TTTTTTTGTATTAAAGTGTATGA
*
18434031 CATGTGCATGATAGAAATGGATTTTTTTGTAATAAAGTGT
1 CATGTGCATGATAGAAATGGATTTTTTTGTATTAAAGTGT
18434071 TTGGTTATTG
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
43 2 0.03
44 35 0.45
45 38 0.49
46 2 0.03
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (44 bp):
CATGTGCATGATAGAAATGGATTTTTTTGTATTAAAGTGTATGA
Found at i:18435986 original size:33 final size:33
Alignment explanation
Indices: 18435904--18435987 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 33
18435894 TGGTCCAACC
* * ** * *
18435904 ATGGTCTTACGTTCAAGGTGTCATAACCTAGTT
1 ATGGTCTTACATTTAAAATGTCATAACCCAGCT
* *
18435937 ATGGTCTTTTCA-TTAAAATGTCATAGCCCAGCT
1 ATGGTC-TTACATTTAAAATGTCATAACCCAGCT
18435970 ATGGTCTTACATTTAAAA
1 ATGGTCTTACATTTAAAA
18435988 ATTTTCATGA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
32 4 0.10
33 33 0.82
34 3 0.08
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGTCATAACCCAGCT
Found at i:18436489 original size:27 final size:27
Alignment explanation
Indices: 18436468--18436522 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
18436458 AAATATTATA
18436468 AGCTATTACACAGCCTTTAATAAATAT
1 AGCTATTACACAGCCTTTAATAAATAT
18436495 AGCTATTACACAGCCTTTAATAAATAT
1 AGCTATTACACAGCCTTTAATAAATAT
18436522 A
1 A
18436523 CTTTAATACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (27 bp):
AGCTATTACACAGCCTTTAATAAATAT
Found at i:18436492 original size:31 final size:30
Alignment explanation
Indices: 18436457--18436521 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 30
18436447 ACACTTTATC
18436457 TAAATATTATAAGCTATTACACAGCCTTTAA
1 TAAATATTAT-AGCTATTACACAGCCTTTAA
18436488 T-AA-A-TATAGCTATTACACAGCCTTTAA
1 TAAATATTATAGCTATTACACAGCCTTTAA
18436515 TAAATAT
1 TAAATAT
18436522 ACTTTAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
27 21 0.68
28 5 0.16
29 2 0.06
30 2 0.06
31 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.35
Consensus pattern (30 bp):
TAAATATTATAGCTATTACACAGCCTTTAA
Found at i:18441358 original size:9 final size:8
Alignment explanation
Indices: 18441325--18441357 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
18441315 AATTTCATTA
18441325 TTAAT-TT
1 TTAATATT
18441332 TTAATATT
1 TTAATATT
18441340 TTAATATT
1 TTAATATT
18441348 TTAATATT
1 TTAATATT
18441356 TT
1 TT
18441358 TTGGATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTAATATT
Found at i:18452519 original size:27 final size:26
Alignment explanation
Indices: 18452489--18452540 Score: 61
Period size: 27 Copynumber: 1.9 Consensus size: 26
18452479 CATGTGGTAG
18452489 AAGC-TAATATAGAAATTGTAGTTTCAA
1 AAGCATAAT-TAGAAATTG-AGTTTCAA
*
18452516 AAGCATTAATTAGGAATTGAGTTTC
1 AAGCA-TAATTAGAAATTGAGTTTC
18452541 CAAGGCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 10 0.45
28 8 0.36
29 4 0.18
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (26 bp):
AAGCATAATTAGAAATTGAGTTTCAA
Found at i:18463571 original size:8 final size:8
Alignment explanation
Indices: 18463558--18463595 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
18463548 TAAGTAAATA
18463558 TATTATAT
1 TATTATAT
18463566 TATTATAT
1 TATTATAT
* *
18463574 AATAATA-
1 TATTATAT
18463581 TATTATAT
1 TATTATAT
18463589 TATTATA
1 TATTATA
18463596 ATAAAACAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TATTATAT
Found at i:18463627 original size:13 final size:13
Alignment explanation
Indices: 18463611--18463635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18463601 ACAAATAAAT
18463611 AAATAGAAAAAGG
1 AAATAGAAAAAGG
18463624 AAATAGAAAAAG
1 AAATAGAAAAAG
18463636 AAAGAAAGAA
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:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (13 bp):
AAATAGAAAAAGG
Found at i:18464175 original size:30 final size:31
Alignment explanation
Indices: 18464103--18464163 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
18464093 AAATTTAGGC
18464103 AAATATTTTTAAAATACTTTTTTTAATTTTA
1 AAATATTTTTAAAATACTTTTTTTAATTTTA
18464134 AAATATTTTTAAAATACTTTTTTTAATTTT
1 AAATATTTTTAAAATACTTTTTTTAATTTT
18464164 TAATTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (31 bp):
AAATATTTTTAAAATACTTTTTTTAATTTTA
Found at i:18464178 original size:47 final size:48
Alignment explanation
Indices: 18464120--18464212 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 48
18464110 TTTAAAATAC
18464120 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT-AATTTTTAA
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAATTTTTAA
*
18464167 TTTTTTTAATTTTAAAGTATTTTTAAAATACTTTTTTTAAATTTTT
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAATTTTT
18464213 TTATTTTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 37 0.84
48 7 0.16
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (48 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAATTTTTAA
Found at i:18468999 original size:219 final size:219
Alignment explanation
Indices: 18468620--18469058 Score: 878
Period size: 219 Copynumber: 2.0 Consensus size: 219
18468610 AAATGGAAAT
18468620 GAAAAGGTAATGCTTTTGAAAATCTTAAAGTTTGAAATTATATGTTCGTGTAATGTTAAATAGTA
1 GAAAAGGTAATGCTTTTGAAAATCTTAAAGTTTGAAATTATATGTTCGTGTAATGTTAAATAGTA
18468685 AAGCTAAATGAAAGGAAAGAGAAAGTGTAACGAAACTGTATAATCGTGAAATAAACCATTTGTGA
66 AAGCTAAATGAAAGGAAAGAGAAAGTGTAACGAAACTGTATAATCGTGAAATAAACCATTTGTGA
18468750 TTGATTATGGTAAATCTGGTATCGTGAAACACCCATGTCGACTAGTGTTGAACTTTTGTGGGTAT
131 TTGATTATGGTAAATCTGGTATCGTGAAACACCCATGTCGACTAGTGTTGAACTTTTGTGGGTAT
18468815 GGTTGGCTTGCTATAGGAACCTGA
196 GGTTGGCTTGCTATAGGAACCTGA
18468839 GAAAAGGTAATGCTTTTGAAAATCTTAAAGTTTGAAATTATATGTTCGTGTAATGTTAAATAGTA
1 GAAAAGGTAATGCTTTTGAAAATCTTAAAGTTTGAAATTATATGTTCGTGTAATGTTAAATAGTA
18468904 AAGCTAAATGAAAGGAAAGAGAAAGTGTAACGAAACTGTATAATCGTGAAATAAACCATTTGTGA
66 AAGCTAAATGAAAGGAAAGAGAAAGTGTAACGAAACTGTATAATCGTGAAATAAACCATTTGTGA
18468969 TTGATTATGGTAAATCTGGTATCGTGAAACACCCATGTCGACTAGTGTTGAACTTTTGTGGGTAT
131 TTGATTATGGTAAATCTGGTATCGTGAAACACCCATGTCGACTAGTGTTGAACTTTTGTGGGTAT
18469034 GGTTGGCTTGCTATAGGAACCTGA
196 GGTTGGCTTGCTATAGGAACCTGA
18469058 G
1 G
18469059 CGTTCCCATA
Statistics
Matches: 220, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 220 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (219 bp):
GAAAAGGTAATGCTTTTGAAAATCTTAAAGTTTGAAATTATATGTTCGTGTAATGTTAAATAGTA
AAGCTAAATGAAAGGAAAGAGAAAGTGTAACGAAACTGTATAATCGTGAAATAAACCATTTGTGA
TTGATTATGGTAAATCTGGTATCGTGAAACACCCATGTCGACTAGTGTTGAACTTTTGTGGGTAT
GGTTGGCTTGCTATAGGAACCTGA
Found at i:18470360 original size:22 final size:22
Alignment explanation
Indices: 18470335--18470377 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18470325 TGCTTTCTCC
*
18470335 TTATTTTGCTACCATTTTATTA
1 TTATGTTGCTACCATTTTATTA
*
18470357 TTATGTTGCTACTATTTTATT
1 TTATGTTGCTACCATTTTATT
18470378 TGCTATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (22 bp):
TTATGTTGCTACCATTTTATTA
Found at i:18470447 original size:30 final size:30
Alignment explanation
Indices: 18470413--18470471 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
18470403 ACTTATTTTA
*
18470413 TTGTTAATTTTGTTATTATTTTAAAGGCAG
1 TTGTTAATTTTATTATTATTTTAAAGGCAG
*
18470443 TTGTTAATTTTATTATTATTTTAGAGGCA
1 TTGTTAATTTTATTATTATTTTAAAGGCA
18470472 TTTGCTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.54
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAG
Found at i:18471934 original size:19 final size:19
Alignment explanation
Indices: 18471892--18471934 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
18471882 TCATGCTTTC
* * *
18471892 TATTCGCATTTTCATATTC
1 TATTCACATTTTCAAATTA
*
18471911 GATTCACATTTTCAAATTA
1 TATTCACATTTTCAAATTA
18471930 TATTC
1 TATTC
18471935 CACAATCACG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.49
Consensus pattern (19 bp):
TATTCACATTTTCAAATTA
Found at i:18472333 original size:18 final size:17
Alignment explanation
Indices: 18472287--18472340 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
18472277 TTTCCAATTC
18472287 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
* *
18472304 TCATTTCAAAATTTACTT
1 TCAATTC-AAATTCACTT
18472322 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
18472340 T
1 T
18472341 TTCATTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 23 0.74
19 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:18473065 original size:25 final size:27
Alignment explanation
Indices: 18473035--18473088 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
18473025 TTATTTCTCC
*
18473035 TTTCTTTCTT-TCCCTTTTTC-TTT-TA
1 TTTCTTT-TTCTCCCTGTTTCGTTTCTA
18473060 TTTCTTTTTCTCCCTGTTTCGTTTCTA
1 TTTCTTTTTCTCCCTGTTTCGTTTCTA
18473087 TT
1 TT
18473089 CTGTTTCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 2 0.08
25 16 0.64
26 3 0.12
27 4 0.16
ACGTcount: A:0.04, C:0.24, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTCTTTTTCTCCCTGTTTCGTTTCTA
Found at i:18473336 original size:18 final size:19
Alignment explanation
Indices: 18473295--18473336 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
18473285 CAACAACAAT
* *
18473295 AATAATTATTATAATAATA
1 AATATTTATTATAATAACA
18473314 AATATTTATT-TAATAACA
1 AATATTTATTATAATAACA
18473332 AATAT
1 AATAT
18473337 AAATATTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTTATTATAATAACA
Found at i:18473575 original size:3 final size:3
Alignment explanation
Indices: 18473562--18473605 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
18473552 AATTTATTTC
*
18473562 ATA AT- ATA ATA AT- ATA ATA AT- ATA ATA AT- ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18473606 TATTTTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
2 8 0.23
3 27 0.77
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:18473575 original size:8 final size:8
Alignment explanation
Indices: 18473562--18473597 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
18473552 AATTTATTTC
18473562 ATAATATA
1 ATAATATA
18473570 ATAATATA
1 ATAATATA
18473578 ATAATATA
1 ATAATATA
18473586 ATAATATA
1 ATAATATA
18473594 ATAA
1 ATAA
18473598 CAATAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAATATA
Found at i:18473608 original size:16 final size:16
Alignment explanation
Indices: 18473562--18473605 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
18473552 AATTTATTTC
*
18473562 ATAATATAATAATATA
1 ATAAAATAATAATATA
*
18473578 ATAATATAATAATATA
1 ATAAAATAATAATATA
18473594 ATAACAATAATA
1 ATAA-AATAATA
18473606 TATTTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAAATAATAATATA
Found at i:18474072 original size:24 final size:23
Alignment explanation
Indices: 18474045--18474089 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
18474035 AATCTAATAT
*
18474045 TAATCTAACATTAATCTCTAATGG
1 TAATATAACATTAATC-CTAATGG
* *
18474069 TAATATAATATTTATCCTAAT
1 TAATATAACATTAATCCTAAT
18474090 TTTGTTGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (23 bp):
TAATATAACATTAATCCTAATGG
Found at i:18493685 original size:23 final size:23
Alignment explanation
Indices: 18493659--18493705 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
18493649 ATAATTATAA
18493659 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
18493682 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
18493705 A
1 A
18493706 CATACTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:18493855 original size:26 final size:27
Alignment explanation
Indices: 18493804--18493860 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
18493794 ACAGAATAGC
* *
18493804 AAAACGAAAACAGGGGAGAAAGGAAAG
1 AAAAAGAAAACAGGGAAGAAAGGAAAG
18493831 AAAAAGAAAA-AGGGAAGGAAA-GAAAG
1 AAAAAGAAAACAGGGAA-GAAAGGAAAG
18493857 AAAA
1 AAAA
18493861 TTTGAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.67, C:0.04, G:0.30, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAACAGGGAAGAAAGGAAAG
Found at i:18495029 original size:37 final size:38
Alignment explanation
Indices: 18494929--18495029 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 38
18494919 NNNNNNNAGT
* *
18494929 CGATGAGACACTGGTTGTCATACTGTTACTTCGGATAGAGT
1 CGATGAGACACTGGGTGTCA-AC--TTACTTCGGATAGAGC
** ** * *
18494970 CGATGAGGTACTGGGTACCAACTTACTTCGGCTTG-GC
1 CGATGAGACACTGGGTGTCAACTTACTTCGGATAGAGC
18495007 CGATGAGACACTGGGTGTCAACT
1 CGATGAGACACTGGGTGTCAACT
18495030 ATTGCTTTGA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
37 20 0.42
38 11 0.23
40 2 0.04
41 15 0.31
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTACTTCGGATAGAGC
Found at i:18497712 original size:2 final size:2
Alignment explanation
Indices: 18497705--18497735 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18497695 CTATAAAAGC
*
18497705 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18497736 ATGTATTAAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:18498679 original size:41 final size:41
Alignment explanation
Indices: 18498632--18498905 Score: 442
Period size: 41 Copynumber: 6.7 Consensus size: 41
18498622 GGTTTTAAAA
* *
18498632 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
18498673 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
18498714 CCTAGCAGGCTAAGTGCCGGTGAAT-TGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTG-ATCTGAATCAGGCTATAAG
*
18498755 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
18498796 CCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* * *
18498837 CCTAGCAGGCTAAGTGCCGGTGAACTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
18498878 CCTAGCAGGCTAAGTGCCAGTGAATCTG
1 CCTAGCAGGCTAAGTGCCGGTG-ATCTG
18498906 TTTAAATTAA
Statistics
Matches: 218, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
40 2 0.01
41 211 0.97
42 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
Found at i:18504084 original size:3 final size:3
Alignment explanation
Indices: 18504076--18504104 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18504066 ATGGAGCTGA
18504076 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
18504105 AGAGGGCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18511315 original size:64 final size:64
Alignment explanation
Indices: 18511187--18511316 Score: 154
Period size: 64 Copynumber: 2.0 Consensus size: 64
18511177 GCGAGTATCC
* * * * * *
18511187 TGATCGATATTGATTCTGCATGTGTTACGGACATACCGCAGCTCTTTGTGAGCGTCCTGTTATA
1 TGATCGATATTGATCCTGCATATATTACGGACATACCGCAACTCTTTATGAGCGTCCTGATATA
* ** *
18511251 TGATCGGTATTGATCCTGCATATATTGTGGATATACCGCAACTCTTTATGAGCGTTCC-GATATA
1 TGATCGATATTGATCCTGCATATATTACGGACATACCGCAACTCTTTATGAGCG-TCCTGATATA
18511315 TG
1 TG
18511317 GCTCTTCATG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 52 0.95
65 3 0.05
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (64 bp):
TGATCGATATTGATCCTGCATATATTACGGACATACCGCAACTCTTTATGAGCGTCCTGATATA
Found at i:18511751 original size:42 final size:41
Alignment explanation
Indices: 18511677--18511793 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 41
18511667 GATCTTTCGA
*
18511677 GGCTTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATGCTCAG
1 GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAG
** * *
18511718 GGCTTTAGCAACGTTTTTTGAAAAAGCGTCGCTAATGCTTAG
1 GGCTTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAATGCTCAG
* * *
18511760 GGTTTTAGTGGCATTTTTGAAAAAGCGCCGCTAA
1 GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
18511794 AAACATTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 31 0.48
42 33 0.52
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAG
Found at i:18512181 original size:15 final size:14
Alignment explanation
Indices: 18512143--18512177 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
18512133 ACTATTTTAA
18512143 GGTTTAGGGAGTAT
1 GGTTTAGGGAGTAT
*
18512157 GGATTTAGGGATTAT
1 GG-TTTAGGGAGTAT
18512172 GGTTTA
1 GGTTTA
18512178 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGAGTAT
Found at i:18512190 original size:28 final size:28
Alignment explanation
Indices: 18512157--18512211 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
18512147 TAGGGAGTAT
* *
18512157 GGATTTAGGGATTATGGTTTAAGGGTTG
1 GGATTTAAGGATTATGGGTTAAGGGTTG
*
18512185 GGATTTAAGGTTTATGGGTTAAGGGTT
1 GGATTTAAGGATTATGGGTTAAGGGTT
18512212 AGACGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (28 bp):
GGATTTAAGGATTATGGGTTAAGGGTTG
Found at i:18512198 original size:21 final size:20
Alignment explanation
Indices: 18512164--18512204 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
18512154 TATGGATTTA
*
18512164 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
18512184 GGGATTTAAGGTTTATGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
18512205 AAGGGTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:18512430 original size:7 final size:7
Alignment explanation
Indices: 18512377--18512428 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
18512367 TTAATTATGA
*
18512377 TTATAGT
1 TTATGGT
18512384 TTATGGT
1 TTATGGT
18512391 TTATGGT
1 TTATGGT
18512398 TTATGGT
1 TTATGGT
*
18512405 ATATGGT
1 TTATGGT
* *
18512412 GTAGGGT
1 TTATGGT
*
18512419 TTAAGGT
1 TTATGGT
18512426 TTA
1 TTA
18512429 AGAGTTACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (7 bp):
TTATGGT
Found at i:18512831 original size:16 final size:16
Alignment explanation
Indices: 18512805--18512837 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18512795 CTTAGTTTTT
18512805 TTTATAAAAATA-TAA
1 TTTATAAAAATAGTAA
18512820 TTTATAAAAAATAGTAA
1 TTTAT-AAAAATAGTAA
18512837 T
1 T
18512838 AATAAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTATAAAAATAGTAA
Found at i:18514936 original size:36 final size:36
Alignment explanation
Indices: 18514895--18514974 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
18514885 ATAAGTGCTA
*
18514895 GATAAGTGTTATACTTATCTGATCAAGTGAAAAAGT
1 GATAAGTGTTATACTTATCTGATAAAGTGAAAAAGT
*
18514931 GATAAGTGTTATACTTATCTGATAAAGTGATAAAGT
1 GATAAGTGTTATACTTATCTGATAAAGTGAAAAAGT
18514967 GATAAGTG
1 GATAAGTG
18514975 GTAGCTTAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (36 bp):
GATAAGTGTTATACTTATCTGATAAAGTGAAAAAGT
Found at i:18520328 original size:8 final size:8
Alignment explanation
Indices: 18520315--18520344 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
18520305 TAAGATATTA
18520315 TATTATAT
1 TATTATAT
18520323 TATTATAT
1 TATTATAT
18520331 TATTATAT
1 TATTATAT
18520339 TATTAT
1 TATTAT
18520345 TACATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTATAT
Found at i:18520423 original size:11 final size:11
Alignment explanation
Indices: 18520407--18520441 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
18520397 TTCAAAACGG
18520407 AACAGGGGAGA
1 AACAGGGGAGA
18520418 AACAGGGGAGA
1 AACAGGGGAGA
18520429 AACAGGGGAGA
1 AACAGGGGAGA
18520440 AA
1 AA
18520442 GAAAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.43, T:0.00
Consensus pattern (11 bp):
AACAGGGGAGA
Found at i:18521678 original size:22 final size:22
Alignment explanation
Indices: 18521653--18521720 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
18521643 NNNCTCTGAT
*
18521653 TTTAGCACGTCAGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
*
18521675 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
* * *
18521697 TATAGCACTTTAGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
18521719 TT
1 TT
18521721 CATTAGTGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (22 bp):
TTTAGCACATCAGTGCTCTCTG
Found at i:18522491 original size:43 final size:43
Alignment explanation
Indices: 18522430--18522515 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
18522420 TGAGTTCATT
* * *
18522430 ACAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTTATTA
1 ACAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTA
* *
18522473 ACAAGATTTACTTGATTAAGAAAATGCATTGTATTTTTTATTA
1 ACAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTA
18522516 CCTTGCAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45
Consensus pattern (43 bp):
ACAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTA
Found at i:18522982 original size:65 final size:66
Alignment explanation
Indices: 18522894--18523022 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 66
18522884 CGGCGTTTTT
* *
18522894 ACAAGAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAAAAAAGCGGCGCTAAAGGTT
1 ACAAGAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGAAAAAAGCGGCGCTAAAGGTT
18522959 G
66 G
* * *
18522960 ACAA-AAGCGCCGTTAAAGGTCATGATCTTTAGCGGCGTTTGTGATAAAAGCGTCGCTAAAGGT
1 ACAAGAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGAAAAAAGCGGCGCTAAAGGT
18523023 CATGGTCTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
65 54 0.93
66 4 0.07
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (66 bp):
ACAAGAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGAAAAAAGCGGCGCTAAAGGTT
G
Found at i:18523060 original size:43 final size:43
Alignment explanation
Indices: 18522962--18523060 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 43
18522952 AAAGGTTGAC
* * *
18522962 AAAAGCGCCGTTAAAGGTCATGATCTTTAGCGGCGTTTGTGAT
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCGTTTGTCAT
* * *
18523005 AAAAGCGTCGCTAAAGGTCATGGTCTTTAGCAGCGTTTTTCAT
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCGTTTGTCAT
18523048 ATAAA-CGCCGCTA
1 A-AAAGCGCCGCTA
18523061 TAGCGGCACT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 45 0.94
44 3 0.06
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCGTTTGTCAT
Found at i:18523090 original size:18 final size:18
Alignment explanation
Indices: 18523067--18523101 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18523057 GCTATAGCGG
*
18523067 CACTTTTTGCGGCGCTTT
1 CACTTTTAGCGGCGCTTT
*
18523085 CACTTTTAGTGGCGCTT
1 CACTTTTAGCGGCGCTT
18523102 AACAACGCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.43
Consensus pattern (18 bp):
CACTTTTAGCGGCGCTTT
Found at i:18526907 original size:16 final size:16
Alignment explanation
Indices: 18526882--18526915 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18526872 TTATCTTTTG
* *
18526882 ATATATATAGATAGAT
1 ATATAAATAGAAAGAT
18526898 ATATAAATAGAAAGAT
1 ATATAAATAGAAAGAT
18526914 AT
1 AT
18526916 GTTGGAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (16 bp):
ATATAAATAGAAAGAT
Found at i:18529443 original size:23 final size:25
Alignment explanation
Indices: 18529403--18529463 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
18529393 TTTATATATC
* *
18529403 TATATTTATTCCTTTTATTCACATACA
1 TATATTT-TT-CTTATATGCACATACA
* *
18529430 TATATTTTTCTTATATGTACATATA
1 TATATTTTTCTTATATGCACATACA
18529455 TATATTTTT
1 TATATTTTT
18529464 ATATTTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 21 0.70
26 2 0.07
27 7 0.23
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (25 bp):
TATATTTTTCTTATATGCACATACA
Found at i:18532111 original size:31 final size:30
Alignment explanation
Indices: 18532065--18532124 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
18532055 TTAATTCAAT
*
18532065 TTTATTTTAATATTATATTATCCTATAAAC
1 TTTATTTTAACATTATATTATCCTATAAAC
*
18532095 TTTATATTTAACATTATATTATCTTATAAA
1 TTTAT-TTTAACATTATATTATCCTATAAA
18532125 AGTTTTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTATTTTAACATTATATTATCCTATAAAC
Found at i:18539851 original size:42 final size:42
Alignment explanation
Indices: 18539792--18539880 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
18539782 TGAAAACCAA
18539792 CCTTTCAAAACTTGAAGAGAAAACCAAAAAATGGGTTAATTT
1 CCTTTCAAAACTTGAAGAGAAAACCAAAAAATGGGTTAATTT
18539834 CCTTTCAAAACTTGAAGAGAAAACCAAAAAATGGGTTAATTT
1 CCTTTCAAAACTTGAAGAGAAAACCAAAAAATGGGTTAATTT
18539876 CCTTT
1 CCTTT
18539881 TCCTGTAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (42 bp):
CCTTTCAAAACTTGAAGAGAAAACCAAAAAATGGGTTAATTT
Found at i:18546603 original size:10 final size:10
Alignment explanation
Indices: 18546585--18546706 Score: 82
Period size: 10 Copynumber: 12.6 Consensus size: 10
18546575 AAAATTAGAA
18546585 AAAAATTATT
1 AAAAATTATT
18546595 AAAAATTA-T
1 AAAAATTATT
18546604 ATAAAA-TA-T
1 A-AAAATTATT
18546613 AAAATATTA-T
1 AAAA-ATTATT
*
18546623 AAAAA-TATA
1 AAAAATTATT
18546632 AAAAATTTATT
1 AAAAA-TTATT
*
18546643 TAAAATTATT
1 AAAAATTATT
*
18546653 TAAAATTA--
1 AAAAATTATT
18546661 AAAAATATATT
1 AAAAAT-TATT
* *
18546672 -AGAATTCTT
1 AAAAATTATT
*
18546681 AAAAAATATTT
1 AAAAATTA-TT
18546692 AAAAATTA-T
1 AAAAATTATT
18546701 AAAAAT
1 AAAAAT
18546707 ACATTTAAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
8 10 0.11
9 25 0.27
10 40 0.44
11 16 0.18
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (10 bp):
AAAAATTATT
Found at i:18546623 original size:19 final size:18
Alignment explanation
Indices: 18546594--18546635 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
18546584 AAAAAATTAT
18546594 TAAAAATTATATAAAATA
1 TAAAAATTATATAAAATA
18546612 TAAAATATTATA-AAAATA
1 TAAAA-ATTATATAAAATA
18546630 TAAAAA
1 TAAAAA
18546636 ATTTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATTATATAAAATA
Found at i:18546626 original size:27 final size:27
Alignment explanation
Indices: 18546586--18546704 Score: 82
Period size: 27 Copynumber: 4.1 Consensus size: 27
18546576 AAATTAGAAA
* *
18546586 AAAATTATTAAAAATTATATAAAATAT
1 AAAATTATTAAAAAATATAAAAAATAT
18546613 AAAA-TATTATAAAAATATAAAAAATTTATTT
1 AAAATTATTA-AAAAATATAAAAAA--TA--T
*
18546644 AAAATTATT-TAAAAT-TAAAAAATAT
1 AAAATTATTAAAAAATATAAAAAATAT
* *
18546669 ATTAGAATTCTTAAAAAATATTTAAAAATTAT
1 A--A-AATTATTAAAAAATA--TAAAAAATAT
18546701 AAAA
1 AAAA
18546705 ATACATTTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
25 2 0.03
26 5 0.07
27 19 0.26
28 6 0.08
29 16 0.22
30 6 0.08
31 5 0.07
32 14 0.19
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
AAAATTATTAAAAAATATAAAAAATAT
Found at i:18546627 original size:38 final size:38
Alignment explanation
Indices: 18546585--18546706 Score: 108
Period size: 38 Copynumber: 3.2 Consensus size: 38
18546575 AAAATTAGAA
18546585 AAAAATTATTAAAAATTATATAAAATA-TAAAATATTAT
1 AAAAATTATTAAAAATTATATAAAATATTAAAA-ATTAT
* * *
18546623 AAAAA-TATAAAAAATTTATTTAAAATTATTTAAAATTA-
1 AAAAATTATTAAAAA-TTATATAAAA-TATTAAAAATTAT
* * *
18546661 AAAAATATATT-AGAATTCTTAAAAAATATTTAAAAATTAT
1 AAAAAT-TATTAAAAATT-ATATAAAATA-TTAAAAATTAT
18546701 AAAAAT
1 AAAAAT
18546707 ACATTTAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
37 8 0.12
38 23 0.34
39 23 0.34
40 13 0.19
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (38 bp):
AAAAATTATTAAAAATTATATAAAATATTAAAAATTAT
Found at i:18546635 original size:48 final size:48
Alignment explanation
Indices: 18546564--18546707 Score: 141
Period size: 48 Copynumber: 3.0 Consensus size: 48
18546554 AAAATATTTA
* *
18546564 AAAAAATTAGAAAAATTAGAAAAAAATTATTAAAAATTATATAAAATAT
1 AAAAAATTATAAAAA-TATAAAAAAATTATTAAAAATTATATAAAATAT
* * * *
18546613 AAAATATTATAAAAATATAAAAAATTTATTTAAAATTATTTAAAAT-T
1 AAAAAATTATAAAAATATAAAAAAATTATTAAAAATTATATAAAATAT
* * * *
18546660 AAAAAATATATTAGAATTCTTAAAAAA-TATTTAAAAATTATA-AAAATA
1 AAAAAAT-TA-TAAAAATATAAAAAAATTA-TTAAAAATTATATAAAATA
18546708 CATTTAAAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
47 7 0.09
48 36 0.47
49 34 0.44
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (48 bp):
AAAAAATTATAAAAATATAAAAAAATTATTAAAAATTATATAAAATAT
Found at i:18546687 original size:29 final size:30
Alignment explanation
Indices: 18546586--18546685 Score: 95
Period size: 28 Copynumber: 3.5 Consensus size: 30
18546576 AAATTAGAAA
*
18546586 AAAATTATTAAAAATTATATAAAATATA---
1 AAAATTATTAAAAA-TATAAAAAATATATTT
*
18546614 AAATATTA-TAAAAATATAAAAAATTTATTT
1 AAA-ATTATTAAAAATATAAAAAATATATTT
*
18546644 AAAATTATTTAAAAT-TAAAAAATATA-TT
1 AAAATTATTAAAAATATAAAAAATATATTT
* *
18546672 AGAATTCTTAAAAA
1 AAAATTATTAAAAA
18546686 ATATTTAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
27 11 0.18
28 22 0.37
29 18 0.30
30 9 0.15
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (30 bp):
AAAATTATTAAAAATATAAAAAATATATTT
Found at i:18546703 original size:9 final size:9
Alignment explanation
Indices: 18546565--18546754 Score: 75
Period size: 10 Copynumber: 19.7 Consensus size: 9
18546555 AAATATTTAA
*
18546565 AAAAATTAG
1 AAAAATTAT
*
18546574 AAAAATTAGAA
1 AAAAATT--AT
18546585 AAAAATTATT
1 AAAAATTA-T
18546595 AAAAATTAT
1 AAAAATTAT
18546604 ATAAAA-TAT
1 A-AAAATTAT
18546613 AAAATATTAT
1 AAAA-ATTAT
18546623 AAAAA-TAT
1 AAAAATTAT
18546631 AAAAAATTTATT
1 -AAAAA-TTA-T
*
18546643 TAAAATTATT
1 AAAAATTA-T
*
18546653 TAAAATTA-
1 AAAAATTAT
18546661 AAAAATATAT
1 AAAAAT-TAT
* * *
18546671 TAGAATTCTT
1 AAAAATT-AT
*
18546681 AAAAAATATTT
1 -AAAAAT-TAT
18546692 AAAAATTAT
1 AAAAATTAT
*
18546701 AAAAATACATT
1 AAAAAT-TA-T
*
18546712 TAAAA-TAT
1 AAAAATTAT
**
18546720 TTAAATTGA-
1 AAAAATT-AT
18546729 AATAAATTTAT
1 AA-AAA-TTAT
18546740 AAAAATTAT
1 AAAAATTAT
18546749 AAAAAT
1 AAAAAT
18546755 AAAAATTTGA
Statistics
Matches: 143, Mismatches: 16, Indels: 44
0.70 0.08 0.22
Matches are distributed among these distances:
8 16 0.11
9 44 0.31
10 52 0.36
11 29 0.20
12 2 0.01
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:18546712 original size:21 final size:20
Alignment explanation
Indices: 18546679--18546724 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
18546669 ATTAGAATTC
*
18546679 TTAAAAAATATTTAAAA-AT
1 TTAAAAAACATTTAAAATAT
18546698 TATAAAAATACATTTAAAATAT
1 T-TAAAAA-ACATTTAAAATAT
18546720 TTAAA
1 TTAAA
18546725 TTGAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 6 0.26
21 13 0.57
22 3 0.13
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAAAACATTTAAAATAT
Found at i:18546716 original size:20 final size:20
Alignment explanation
Indices: 18546575--18546717 Score: 88
Period size: 20 Copynumber: 7.2 Consensus size: 20
18546565 AAAAATTAGA
* * *
18546575 AAAATTAGAAAAAAATTATTA
1 AAAATTATAAAAATA-TATTT
18546596 AAAATTATATAAAATATA---
1 AAAATTATA-AAAATATATTT
*
18546614 AAATATTATAAAAATATA--A
1 AAA-ATTATAAAAATATATTT
*
18546633 AAAATTTATTTAAAAT-TATTT
1 AAAA-TTA-TAAAAATATATTT
18546654 AAAATTA-AAAAATATA-TT
1 AAAATTATAAAAATATATTT
* *
18546672 AGAATTCTTAAAAA-ATATTT
1 AAAATT-ATAAAAATATATTT
*
18546692 AAAAATTATAAAAATACATTT
1 -AAAATTATAAAAATATATTT
18546713 AAAAT
1 AAAAT
18546718 ATTTAAATTG
Statistics
Matches: 99, Mismatches: 10, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
18 24 0.24
19 19 0.19
20 27 0.27
21 24 0.24
22 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (20 bp):
AAAATTATAAAAATATATTT
Found at i:18546898 original size:19 final size:19
Alignment explanation
Indices: 18546876--18546924 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
18546866 TAATATTTTT
18546876 TTATCAAACTAAAATTTCA
1 TTATCAAACTAAAATTTCA
*
18546895 TTATCCAAA-AAAAATTTCA
1 TTAT-CAAACTAAAATTTCA
*
18546914 TTATCCAACTA
1 TTATCAAACTA
18546925 TTAGCACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
19 18 0.72
20 4 0.16
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (19 bp):
TTATCAAACTAAAATTTCA
Found at i:18547414 original size:10 final size:9
Alignment explanation
Indices: 18547229--18547414 Score: 51
Period size: 9 Copynumber: 19.6 Consensus size: 9
18547219 CTTTAAATTT
18547229 TTTTTATAA
1 TTTTTATAA
*
18547238 TTTTTTTATAG
1 --TTTTTATAA
**
18547249 TTTTTATGT
1 TTTTTATAA
*
18547258 TTTTTACAAAA
1 TTTTT--ATAA
*
18547269 TTTTAATACA
1 TTTTTATA-A
18547279 TTTTTATAAA
1 TTTTTAT-AA
*
18547289 ATTTTA-AA
1 TTTTTATAA
18547297 TATTTTA-AA
1 T-TTTTATAA
*
18547306 TATGGTTTACAA
1 T-T--TTTATAA
18547318 TTTTTATAAA
1 TTTTTAT-AA
***
18547328 AAATTATAA
1 TTTTTATAA
18547337 TTTATTAT-A
1 TTT-TTATAA
18547346 TTTATTATAA
1 TTT-TTATAA
*
18547356 TATTTATAA
1 TTTTTATAA
*
18547365 GTTTATATTAA
1 -TTTTTA-TAA
*
18547376 TTTTCAT-A
1 TTTTTATAA
18547384 -TTTT-TAA
1 TTTTTATAA
**
18547391 TATTCAATAA
1 T-TTTTATAA
18547401 TTTTTATAA
1 TTTTTATAA
18547410 TTTTT
1 TTTTT
18547415 CTTTTTTTAA
Statistics
Matches: 130, Mismatches: 28, Indels: 36
0.67 0.14 0.19
Matches are distributed among these distances:
6 1 0.01
7 4 0.03
8 3 0.02
9 59 0.45
10 38 0.29
11 22 0.17
12 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:18554176 original size:24 final size:24
Alignment explanation
Indices: 18554132--18554185 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
18554122 TTTATTTTGC
*
18554132 AAATA-AAAAAAAGGTTTTATAAAT
1 AAATATAAAAAAAGGTTGTAT-AAT
*
18554156 AAATATAAAAAAATG-TGTATAAT
1 AAATATAAAAAAAGGTTGTATAAT
18554179 AAATATA
1 AAATATA
18554186 TTTAGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 10 0.37
24 9 0.33
25 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (24 bp):
AAATATAAAAAAAGGTTGTATAAT
Found at i:18554837 original size:18 final size:19
Alignment explanation
Indices: 18554814--18554849 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18554804 AATAAAAATA
*
18554814 AAAATT-TAATGATTTTTT
1 AAAATTGTAATAATTTTTT
18554832 AAAATTGTAATAATTTTT
1 AAAATTGTAATAATTTTT
18554850 ATTTAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
AAAATTGTAATAATTTTTT
Found at i:18562052 original size:6 final size:6
Alignment explanation
Indices: 18562041--18562185 Score: 80
Period size: 6 Copynumber: 22.2 Consensus size: 6
18562031 TATTGTTGAT
18562041 AATGGG AATGGG AATGGG AAATGGG AATGGG AATGGG AATGGG AGGA-GGG
1 AATGGG AATGGG AATGGG -AATGGG AATGGG AATGGG AATGGG A--ATGGG
* **
18562091 AATGGTGG AAGAGGGG AGATGGG AATGGG AAATGGG AGGA-GGG CACGGTGG
1 AAT-G-GG -A-ATGGG A-ATGGG AATGGG -AATGGG A--ATGGG -AATG-GG
* * *
18562142 AATGGG AAATGGG AATGGG TAT-TG CATGGG AATGGG AAATGGG A
1 AATGGG -AATGGG AATGGG AATGGG AATGGG AATGGG -AATGGG A
18562186 GAAGGATACG
Statistics
Matches: 112, Mismatches: 10, Indels: 34
0.72 0.06 0.22
Matches are distributed among these distances:
5 4 0.04
6 54 0.48
7 42 0.38
8 9 0.08
9 2 0.02
10 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.50, T:0.15
Consensus pattern (6 bp):
AATGGG
Found at i:18562065 original size:13 final size:13
Alignment explanation
Indices: 18562041--18562185 Score: 81
Period size: 13 Copynumber: 11.1 Consensus size: 13
18562031 TATTGTTGAT
18562041 AATGGG-AATGGG
1 AATGGGAAATGGG
18562053 AATGGGAAATGGG
1 AATGGGAAATGGG
18562066 AATGGG-AATGGG
1 AATGGGAAATGGG
*
18562078 AATGGGAGGA-GGG
1 AATGGGA-AATGGG
*
18562091 AAT-GG---TGGA
1 AATGGGAAATGGG
* *
18562100 AGAGGGGAGATGGG
1 A-ATGGGAAATGGG
18562114 AATGGGAAATGGG
1 AATGGGAAATGGG
* **
18562127 AGGA-GGGCACGGTGG
1 A--ATGGGAAATG-GG
18562142 AATGGGAAATGGG
1 AATGGGAAATGGG
*
18562155 AATGGGTATTGCATGGG
1 AATGGG-A---AATGGG
18562172 AATGGGAAATGGG
1 AATGGGAAATGGG
18562185 A
1 A
18562186 GAAGGATACG
Statistics
Matches: 102, Mismatches: 14, Indels: 33
0.68 0.09 0.22
Matches are distributed among these distances:
9 3 0.03
10 1 0.01
11 2 0.02
12 20 0.20
13 44 0.43
14 16 0.16
15 4 0.04
16 1 0.01
17 11 0.11
ACGTcount: A:0.32, C:0.02, G:0.50, T:0.15
Consensus pattern (13 bp):
AATGGGAAATGGG
Found at i:18562316 original size:31 final size:30
Alignment explanation
Indices: 18562232--18562376 Score: 152
Period size: 25 Copynumber: 5.2 Consensus size: 30
18562222 TGTATTTAAA
* *
18562232 ATTTTAAAAATAAAAAAATATATGTAATGG
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
*
18562262 ATTTT-AAAAT-AAAAAATACATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
18562290 ATTTTAAAAATAAAGAAAATATATGTAGTGT
1 ATTTTAAAAATAAA-AAAATATATGTAGTGT
*
18562321 ATTTT-AAAAT----ATATATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
*
18562346 ATTTT-AAAAT----ATATATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
18562371 ATTTTA
1 ATTTTA
18562377 TTAAATGAAT
Statistics
Matches: 106, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
25 44 0.42
28 20 0.19
29 10 0.09
30 12 0.11
31 20 0.19
ACGTcount: A:0.48, C:0.01, G:0.11, T:0.41
Consensus pattern (30 bp):
ATTTTAAAAATAAAAAAATATATGTAGTGT
Found at i:18562325 original size:59 final size:55
Alignment explanation
Indices: 18562232--18562354 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 55
18562222 TGTATTTAAA
18562232 ATTTTAAAAATAAAAAAATATATGTAATGGATTTTAAAATAAAAAATACATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAATGGATTTTAAAAT---AAATACATGTAGTGT
* * * *
18562290 ATTTTAAAAATAAAGAAAATATATGTAGTGTATTTTAAAATATATATATGTAGTGT
1 ATTTTAAAAATAAA-AAAATATATGTAATGGATTTTAAAATAAATACATGTAGTGT
18562346 ATTTTAAAA
1 ATTTTAAAA
18562355 TATATATATG
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
56 22 0.37
58 14 0.23
59 24 0.40
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.38
Consensus pattern (55 bp):
ATTTTAAAAATAAAAAAATATATGTAATGGATTTTAAAATAAATACATGTAGTGT
Found at i:18562572 original size:21 final size:21
Alignment explanation
Indices: 18562548--18562600 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
18562538 CATTATTTCT
*
18562548 AATCTCACCGTTACAGTATCC
1 AATCTCACCGTTACAGTAACC
* *
18562569 AATCTCACCGCTACAGTAACT
1 AATCTCACCGTTACAGTAACC
18562590 AATCTCACCGT
1 AATCTCACCGT
18562601 CACCGCTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGTTACAGTAACC
Found at i:18564002 original size:42 final size:42
Alignment explanation
Indices: 18563943--18564027 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
18563933 TGGAATCTTA
18563943 TCATACAAGAACATCAAAGCACGTATAATCTTATCATACACT
1 TCATACAAGAACATCAAAGCACGTATAATCTTATCATACACT
*
18563985 TCATACAAGAACATCAAAGCATGTATAATCTTATCATACACT
1 TCATACAAGAACATCAAAGCACGTATAATCTTATCATACACT
18564027 T
1 T
18564028 ACTTCTCAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.28
Consensus pattern (42 bp):
TCATACAAGAACATCAAAGCACGTATAATCTTATCATACACT
Found at i:18568690 original size:2 final size:2
Alignment explanation
Indices: 18568683--18568714 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18568673 TAATAGTAGA
18568683 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
18568715 TCATAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18571068 original size:2 final size:2
Alignment explanation
Indices: 18571061--18571153 Score: 91
Period size: 2 Copynumber: 47.5 Consensus size: 2
18571051 TTCAAATCTG
* * * * *
18571061 TA TA TA TA TA TA TA TA TA TA TT TA GA T- TT TA TA TA AA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
18571102 TA -A AA AA GA TA AA 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
18571143 TA TA TA TA TA T
1 TA TA TA TA TA T
18571154 TTCCTTACTT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:18572489 original size:20 final size:19
Alignment explanation
Indices: 18572453--18572491 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
18572443 ATTTGCCGGT
18572453 TTTAAAAATATATATTTTA
1 TTTAAAAATATATATTTTA
18572472 TTTATAAAAT-TATCATTTTA
1 TTTA-AAAATATAT-ATTTTA
18572492 ATAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAAAAATATATATTTTA
Found at i:18605374 original size:112 final size:112
Alignment explanation
Indices: 18605038--18605409 Score: 523
Period size: 114 Copynumber: 3.3 Consensus size: 112
18605028 AAAATAAGCA
* * * *
18605038 TTAGCGGCATTTTTGAGAAAGCGCCACAAAAAACCTAAGCCCAACGACGTTGTTTCCCGAGCTTT
1 TTAGCGGCGTTTTTG-GAAAGCGCCACAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTT
* * *
18605103 CGGGGATTTAGCGGCGTTTCTAAGAAAGCGTCGCTAATGCTCCGGGCT
65 CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * *
18605151 TTAGCGGCGTTTTTGCAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTATGAGCTT
1 TTAGCGGCGTTTTTG-GAAAGCGCCAC-AAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTT
* *
18605216 TCGGGGATTTAGCGGC-TTTTAAAAGGAAGCGCCGCTAATGCTCAGGGCT
64 TCGGGGATTTAGCGGCGTTTT-TAAGAAAGCGCCGCTAATGCTCAGGGCT
* * *
18605265 TTAGCGGTGTTTTTAGGAAAGCGCCACAAAAAACCTAAGCCCCACGACGCCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTT-GGAAAGCGCCACAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTT
*
18605330 -AGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
65 CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
*
18605377 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAA
1 TTAGCGGCGTTTTTGG-AAAGCGCCACAAAAAA
18605410 AACCTTGAGC
Statistics
Matches: 230, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
111 2 0.01
112 67 0.29
113 65 0.28
114 95 0.41
115 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (112 bp):
TTAGCGGCGTTTTTGGAAAGCGCCACAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTC
GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:18608664 original size:147 final size:147
Alignment explanation
Indices: 18608314--18608856 Score: 928
Period size: 147 Copynumber: 3.7 Consensus size: 147
18608304 NNNNTTTATT
* *
18608314 AAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTTAAAATGAAAAAAATTTGCGG
1 AAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTTAAAATGAAAAAAATTTGCGG
18608379 CATTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCATAAAAACGCCGCAAAGA
66 CATTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCATAAAAACGCCGCAAAGA
18608444 ATAAATCAATTTATTAA
131 ATAAATCAATTTATTAA
* *
18608461 AAAAATAAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCG
1 AAAAAT-AAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTTAAAATGAAAAAAATTTGCG
* *
18608526 GCGTTTTGTAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCATAAAAACGCCGCAAAG
65 GCATTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCATAAAAACGCCGCAAAG
18608591 AATAAATCAATTTATTAA
130 AATAAATCAATTTATTAA
* * *
18608609 AAAAATAAAAAAAATTTAGAATAGCAAAACGGCATCGTTTTGTTTAAAATGAAAAAATTTTACGG
1 AAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTTAAAATGAAAAAAATTTGCGG
*
18608674 CATTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAGA
66 CATTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCATAAAAACGCCGCAAAGA
*
18608739 ATAAATCAATTTATAAA
131 ATAAATCAATTTATTAA
* *
18608756 AAAAATAAAAAAAA-TTAGAATAGCAAAAAGGCGTCGTTTTGTTGAAAATGAAAAAAATTTGCGG
1 AAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTTAAAATGAAAAAAATTTGCGG
*
18608820 CGTTTT-TAAAGAAGCGCCGCTAAAGGTAAGCAATAGC
66 CATTTTAT-AAGAAGCGCCGCTAAAGGTAAGCAATAGC
18608857 AGAATAAATC
Statistics
Matches: 375, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
145 1 0.00
146 79 0.21
147 154 0.41
148 141 0.38
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (147 bp):
AAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTTAAAATGAAAAAAATTTGCGG
CATTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCCATAAAAACGCCGCAAAGA
ATAAATCAATTTATTAA
Found at i:18610473 original size:43 final size:43
Alignment explanation
Indices: 18610398--18610647 Score: 270
Period size: 43 Copynumber: 5.8 Consensus size: 43
18610388 TTTTCGTGAC
* ** * * * *
18610398 CTTTAGTGGCGTTTTTGGAGAAAGTGTCGCTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTGAGGAAAAAGCGCCGCTAAAGGTCTTGGT
* * * *
18610441 TTTTAGCAGCGCTTCAGGAAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGAGGAAAAAGCGCCGCTAAAGGTCTTGGT
* * *
18610484 TTTTAGCGGCGTTTGAGGGAAAAGCGCCGCTAGAGGTCTTGGT
1 CTTTAGCGGCGTTTGAGGAAAAAGCGCCGCTAAAGGTCTTGGT
* * *
18610527 CTTTAGCGGCGTTTGTGAAAAAAACGCCGCTAAAGGTCATT-GT
1 CTTTAGCGGCGTTTGAGGAAAAAGCGCCGCTAAAGGTC-TTGGT
* *
18610570 CTTTAGCGGCGTTTGTAGG-AAATGCGCCGCTAAAGATCTTGGT
1 CTTTAGCGGCGTTTG-AGGAAAAAGCGCCGCTAAAGGTCTTGGT
* * *
18610613 CTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAG
1 CTTTAGCGGCGTTTGAGGAAAAAGCGCCGCTAAAG
18610648 TTAGGGACGA
Statistics
Matches: 174, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
42 4 0.02
43 167 0.96
44 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGAGGAAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:18613376 original size:53 final size:54
Alignment explanation
Indices: 18613312--18613423 Score: 140
Period size: 53 Copynumber: 2.1 Consensus size: 54
18613302 TTATAAAACT
* *
18613312 TATATATATAAAATACA-TAATGCATTTATGAAAACAAGGAAA-ATATAAATATA
1 TATATATATAAAATACATTAATGCATTTA-CAAAAAAAGGAAATATATAAATATA
* * * *
18613365 TATATATATAAAATATATTCATGCATTTACAAAAAAATGAAATATATAAGTATA
1 TATATATATAAAATACATTAATGCATTTACAAAAAAAGGAAATATATAAATATA
18613419 -ATATA
1 TATATA
18613424 AAAACGTGGA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
53 31 0.61
54 20 0.39
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.33
Consensus pattern (54 bp):
TATATATATAAAATACATTAATGCATTTACAAAAAAAGGAAATATATAAATATA
Found at i:18613692 original size:3 final size:3
Alignment explanation
Indices: 18613684--18613723 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
18613674 ATATGTAGGT
*
18613684 ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18613724 CAAAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18613707 original size:15 final size:12
Alignment explanation
Indices: 18613686--18613737 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
18613676 ATGTAGGTAT
18613686 AATAATAATATATA
1 AATAATAATA-A-A
18613700 ATATAATAATAAA
1 A-ATAATAATAAA
18613713 AATAATAATAACA
1 AATAATAATAA-A
*
18613726 AA-ATTAATAAA
1 AATAATAATAAA
18613737 A
1 A
18613738 TAGACTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 2 0.06
12 17 0.49
13 5 0.14
14 2 0.06
15 9 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:18614184 original size:23 final size:22
Alignment explanation
Indices: 18614141--18614198 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
18614131 AAAGGGTATC
* *
18614141 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
18614162 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
18614185 TACATATCATATCT
1 TACAAATCATATCT
18614199 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:18614201 original size:19 final size:19
Alignment explanation
Indices: 18614154--18614232 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 19
18614144 AAATTAAATC
*
18614154 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
18614174 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
18614196 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
18614217 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
18614233 CTCGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.28
21 18 0.36
22 7 0.14
23 11 0.22
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:18614214 original size:21 final size:21
Alignment explanation
Indices: 18614188--18614231 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
18614178 CTAAGATTAC
18614188 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
18614209 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
18614230 AT
1 AT
18614232 CCTCGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:18616774 original size:51 final size:51
Alignment explanation
Indices: 18616717--18616827 Score: 179
Period size: 51 Copynumber: 2.2 Consensus size: 51
18616707 CTCTAATCCT
*
18616717 CTCAATTTCCTTCCAAAATTCTCTGAAA-CGCATATTTAATTTCAATTGCCC
1 CTCAATTTCCTTCCAAAATTCTCTCAAATC-CATATTTAATTTCAATTGCCC
* *
18616768 CTCAATTTCCTTCGAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCC
1 CTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTGCCC
18616819 CTCAATTTC
1 CTCAATTTC
18616828 ATTTTTAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.04, T:0.40
Consensus pattern (51 bp):
CTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTGCCC
Found at i:18617764 original size:21 final size:19
Alignment explanation
Indices: 18617734--18617773 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
18617724 GTAACGAGGT
18617734 GAATTTTATATTACATTTTG
1 GAATTTTATA-TACATTTTG
*
18617754 GAATTATTATATAGATTTTG
1 GAATT-TTATATACATTTTG
18617774 TAAGAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (19 bp):
GAATTTTATATACATTTTG
Found at i:18618934 original size:21 final size:21
Alignment explanation
Indices: 18618910--18618958 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
18618900 CAGATACCGA
*
18618910 ACCGGAAGAACCACAATCACC
1 ACCGGAAGAACAACAATCACC
* * *
18618931 ACCGGAGGAAGAACAATCGCC
1 ACCGGAAGAACAACAATCACC
18618952 -CCGGAAG
1 ACCGGAAG
18618959 CTAGAGGAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.39, C:0.33, G:0.24, T:0.04
Consensus pattern (21 bp):
ACCGGAAGAACAACAATCACC
Found at i:18619185 original size:29 final size:29
Alignment explanation
Indices: 18619148--18619227 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
18619138 ACACAATTAA
*
18619148 CTAACTTAATTAAAAACCCTAACCCTAAC
1 CTAATTTAATTAAAAACCCTAACCCTAAC
18619177 CTAATTTAATTAAAAACCCTAACCCTAAC
1 CTAATTTAATTAAAAACCCTAACCCTAAC
18619206 CTAATTTAATTAAAAACCCTAA
1 CTAATTTAATTAAAAACCCTAA
18619228 TTTAATTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (29 bp):
CTAATTTAATTAAAAACCCTAACCCTAAC
Found at i:18619290 original size:101 final size:101
Alignment explanation
Indices: 18619113--18619509 Score: 643
Period size: 101 Copynumber: 3.9 Consensus size: 101
18619103 TTTGAGGTCA
* *
18619113 TAAAAACCCTAATTTAATTTTACTAACACAATTAACTAACTTAATTAAAAACCCTAACCCTAACC
1 TAAAAACCCTAATTTAATTTTACT-A-ACAATTAACTAACTTAATTAAAAACCCAAACCCAAACC
*
18619178 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAAT
64 TAATTTAATTAAAAACCCTAACCCTAAACTAATTTAAT
*
18619216 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAATTTAATTAAAAACCCAAACCCAAACCTA
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCAAACCCAAACCTA
18619281 ATTTAATTAAAAACCCTAACCCTAAACTAATTTAAT
66 ATTTAATTAAAAACCCTAACCCTAAACTAATTTAAT
* *
18619317 TAAAAACCCTAATTTTATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCCT
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCC--A----AACCCA
18619382 AACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAAT
60 AACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAAT
*
18619424 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAAA-CT
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCAAACCC-AAACCT
18619488 AATTTAATTAAAAACCCTAACC
65 AATTTAATTAAAAACCCTAACC
18619510 ATTAACACAA
Statistics
Matches: 277, Mismatches: 10, Indels: 16
0.91 0.03 0.05
Matches are distributed among these distances:
101 151 0.55
102 3 0.01
103 25 0.09
107 98 0.35
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (101 bp):
TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCAAACCCAAACCTA
ATTTAATTAAAAACCCTAACCCTAAACTAATTTAAT
Found at i:18619326 original size:29 final size:28
Alignment explanation
Indices: 18619247--18619328 Score: 137
Period size: 29 Copynumber: 2.9 Consensus size: 28
18619237 ACTAACAATT
*
18619247 AACTAATTTAATTAAAAACCCAAACCCA
1 AACTAATTTAATTAAAAACCCTAACCCA
18619275 AACCTAATTTAATTAAAAACCCTAACCCTA
1 AA-CTAATTTAATTAAAAACCCTAACCC-A
18619305 AACTAATTTAATTAAAAACCCTAA
1 AACTAATTTAATTAAAAACCCTAA
18619329 TTTTATTTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
28 2 0.04
29 46 0.90
30 3 0.06
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (28 bp):
AACTAATTTAATTAAAAACCCTAACCCA
Found at i:18619408 original size:29 final size:29
Alignment explanation
Indices: 18619370--18619435 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
18619360 TAAAAACCCT
*
18619370 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAAACTAATTTAATTAAA
18619399 AACCCTAACCCTAAACTAATTTAATTAAA
1 AACCCTAACCCTAAACTAATTTAATTAAA
18619428 AACCCTAA
1 AACCCTAA
18619436 TTTAATTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (29 bp):
AACCCTAACCCTAAACTAATTTAATTAAA
Found at i:18619468 original size:208 final size:204
Alignment explanation
Indices: 18619113--18619509 Score: 674
Period size: 208 Copynumber: 1.9 Consensus size: 204
18619103 TTTGAGGTCA
18619113 TAAAAACCCTAATTTAATTTTACTAACACAATTAACTAACTTAATTAAAAACCCTAACCCTAACC
1 TAAAAACCCTAATTTAATTTTACTAACACAATTAACTAACTTAATTAAAAACCCTAACCCTAACC
*
18619178 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAATTTAATTTTACTAAC
66 TAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAATTTAATTTTACTAAC
*
18619243 AATTAACTAATTTAATTAAAAACCCAAACCC-AAACCTAATTTAATTAAAAACCCTAACCCTAAA
131 AATTAACTAACTTAATTAAAAACCCAAACCCTAAA-CTAATTTAATTAAAAACCCTAACCCTAAA
18619307 CTAATTTAAT
195 CTAATTTAAT
*
18619317 TAAAAACCCTAATTTTATTTTACT-A-ACAATTAACTAACTTAATTAAAAACCCTAACCCTAACC
1 TAAAAACCCTAATTTAATTTTACTAACACAATTAACTAACTTAATT--AAA----AACCCTAACC
18619380 CTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAATTTAATTTT
60 CTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAATTTAATTTT
*
18619445 ACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACC
125 ACTAACAATTAACTAACTTAATTAAAAACCCAAACCCTAAACTAATTTAATTAAAAACCCTAACC
18619510 ATTAACACAA
Statistics
Matches: 182, Mismatches: 4, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
202 19 0.10
203 1 0.01
204 26 0.14
208 133 0.73
209 3 0.02
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (204 bp):
TAAAAACCCTAATTTAATTTTACTAACACAATTAACTAACTTAATTAAAAACCCTAACCCTAACC
TAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAATTTAATTTTACTAAC
AATTAACTAACTTAATTAAAAACCCAAACCCTAAACTAATTTAATTAAAAACCCTAACCCTAAAC
TAATTTAAT
Found at i:18619479 original size:29 final size:29
Alignment explanation
Indices: 18619446--18619515 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
18619436 TTTAATTTTA
*
18619446 CTAACAATTAACTAACTTAATTAAAAACC
1 CTAACCATTAACTAACTTAATTAAAAACC
* * *
18619475 CTAACCCTAAACTAATTTAATTAAAAACC
1 CTAACCATTAACTAACTTAATTAAAAACC
18619504 CTAACCATTAAC
1 CTAACCATTAAC
18619516 ACAAATTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (29 bp):
CTAACCATTAACTAACTTAATTAAAAACC
Done.