Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 2 of 172
Found at i:315808 original size:56 final size:56
Alignment explanation
Indices: 315722--315832 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 56
315712 AAAAATGATG
* *
315722 AAATGGAGAAATAGGAAACATTTGGAAATGATTATGGTTTTCT-CCTAAATGAAAAAA
1 AAATGGAGAAATA-GAAACATTTGGAAATGAATATGGTTTT-TGCCAAAATGAAAAAA
315779 AAATGGAGAAATA-AAATCATTTGGAAATGAATATGGTTTTTGCCAAAATGAAAA
1 AAATGGAGAAATAGAAA-CATTTGGAAATGAATATGGTTTTTGCCAAAATGAAAA
315833 TGACCTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
55 4 0.08
56 33 0.66
57 13 0.26
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (56 bp):
AAATGGAGAAATAGAAACATTTGGAAATGAATATGGTTTTTGCCAAAATGAAAAAA
Found at i:324276 original size:21 final size:21
Alignment explanation
Indices: 324250--324305 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
324240 AACAGCGGTG
*
324250 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
324271 GCGGTGAGATTGGATATTGTA
1 GCGGTGAGATTAGATACTGTA
324292 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
324306 AACAGCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:327706 original size:12 final size:13
Alignment explanation
Indices: 327687--327712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
327677 GATTGAGTAC
327687 CAAAAAAATTAAG
1 CAAAAAAATTAAG
327700 CAAAAAAATTAAG
1 CAAAAAAATTAAG
327713 GGTTCATTGA
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:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
CAAAAAAATTAAG
Found at i:328052 original size:12 final size:12
Alignment explanation
Indices: 328035--328066 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
328025 CTTGGAACCG
328035 CCGATTTTTTTA
1 CCGATTTTTTTA
328047 CCGATTTTTTTA
1 CCGATTTTTTTA
*
328059 CCAATTTT
1 CCGATTTT
328067 AGTGAGAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (12 bp):
CCGATTTTTTTA
Found at i:328344 original size:12 final size:12
Alignment explanation
Indices: 328327--328353 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
328317 GCAACCCAAG
328327 GGGAAGGGGAAA
1 GGGAAGGGGAAA
328339 GGGAAGGGGAAA
1 GGGAAGGGGAAA
328351 GGG
1 GGG
328354 GAGAAGAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (12 bp):
GGGAAGGGGAAA
Found at i:329158 original size:38 final size:38
Alignment explanation
Indices: 329116--329192 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
329106 AAAAAATACA
* * *
329116 TAAATCACCGGTATATCTAATGTTTTTCTGTGTCATTT
1 TAAATCACCAGTAAATCTAATATTTTTCTGTGTCATTT
*
329154 TAAATCACCAGTAAATCTAATATTTTTTTGTGTCATTT
1 TAAATCACCAGTAAATCTAATATTTTTCTGTGTCATTT
329192 T
1 T
329193 TTTAATTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.48
Consensus pattern (38 bp):
TAAATCACCAGTAAATCTAATATTTTTCTGTGTCATTT
Found at i:330017 original size:18 final size:16
Alignment explanation
Indices: 329985--330019 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
329975 TAATAAATAG
329985 AACAAAGAACAAAAGA
1 AACAAAGAACAAAAGA
330001 AACAGAAGAAGCAAAAGA
1 AACA-AAGAA-CAAAAGA
330019 A
1 A
330020 CTATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.71, C:0.11, G:0.17, T:0.00
Consensus pattern (16 bp):
AACAAAGAACAAAAGA
Found at i:331614 original size:3 final size:3
Alignment explanation
Indices: 331606--331634 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
331596 ATAATGGGAA
331606 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
331635 AGCCACTAAA
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:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:331852 original size:24 final size:24
Alignment explanation
Indices: 331824--331875 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
331814 TTCCTAGAAG
* *
331824 ATTTAATATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
331848 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
331872 ATTT
1 ATTT
331876 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:336261 original size:24 final size:24
Alignment explanation
Indices: 336227--336278 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
336217 TTTCTAGAAG
* *
336227 ATTTAGTATTTATGAGTAAAATAT
1 ATTTAGCATTTATGAGCAAAATAT
* *
336251 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCAAAATAT
336275 ATTT
1 ATTT
336279 GACCTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCAAAATAT
Found at i:337696 original size:13 final size:13
Alignment explanation
Indices: 337678--337702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
337668 GAATTGTTCA
337678 ATTAAAGAATTTG
1 ATTAAAGAATTTG
337691 ATTAAAGAATTT
1 ATTAAAGAATTT
337703 TCTTGAAAAA
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:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
ATTAAAGAATTTG
Found at i:341572 original size:45 final size:45
Alignment explanation
Indices: 341503--341588 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
341493 AGATACTCGG
* *
341503 TGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCGT
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGT
341548 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
341589 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGT
Found at i:341653 original size:51 final size:50
Alignment explanation
Indices: 341590--341785 Score: 214
Period size: 51 Copynumber: 3.9 Consensus size: 50
341580 CAATGATGTT
* *
341590 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * *
341641 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* ** * * * *
341692 TGGTATGCATAGTAGCCTGCACATAGTACAACACATGCGACC-TATCATTC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
* * *
341742 CGGTACACGTATTAGCCTGCACATAGTACTACACACATGACCAT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
341786 CACTTTCACT
Statistics
Matches: 116, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 36 0.31
51 76 0.66
52 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (50 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:341805 original size:101 final size:101
Alignment explanation
Indices: 341596--341781 Score: 248
Period size: 101 Copynumber: 1.8 Consensus size: 101
341586 TGTTCGGTTC
* *
341596 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACATAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACAACACATGCGACCA-TACCATCCGATACACATAGTAGCCTGC
* * **
341661 ACATAGTACTACACACGTGATCGAAACTATCTGGTAT
65 ACATAGTACTACACACATGATCCAAACTATCACGTAT
* * * * *
341698 GCATAGTAGCCTGCACATAGTACAACACATGCGACC-TATCATTCCGGTACACGTATTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACAACACATGCGACCATACCA-TCCGATACACATAGTAGCCTGC
341762 ACATAGTACTACACACATGA
65 ACATAGTACTACACACATGA
341782 CCATCACTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
100 4 0.05
101 38 0.51
102 33 0.44
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (101 bp):
ACATAGTAGCCTGCACATAGTACAACACATGCGACCATACCATCCGATACACATAGTAGCCTGCA
CATAGTACTACACACATGATCCAAACTATCACGTAT
Found at i:348919 original size:26 final size:26
Alignment explanation
Indices: 348889--348940 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
348879 GGAAATCAAG
348889 TAAGCAGTATTGTTCTTGATATTTCC
1 TAAGCAGTATTGTTCTTGATATTTCC
348915 TAAGCAGTATTGTTCTTGATATTTCC
1 TAAGCAGTATTGTTCTTGATATTTCC
348941 ACATTCCTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (26 bp):
TAAGCAGTATTGTTCTTGATATTTCC
Found at i:354331 original size:18 final size:19
Alignment explanation
Indices: 354294--354332 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
354284 TTATTTTGAG
*
354294 TTTGGGTTTAGTATAATATA
1 TTTGGGTTTA-TAAAATATA
354314 TTTGGGTTT-TAAAATATA
1 TTTGGGTTTATAAAATATA
354332 T
1 T
354333 ATTTTAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTTGGGTTTATAAAATATA
Found at i:359009 original size:5 final size:5
Alignment explanation
Indices: 358995--359040 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
358985 TTTACTTTAT
358995 TAATA T-ATA TAATA TAATA TAATA TATTATA TAATA -AA-A TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA--ATA TAATA TAATA TAATA TA
359041 CATAACATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
3 1 0.03
4 8 0.22
5 22 0.61
7 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:359021 original size:17 final size:17
Alignment explanation
Indices: 358999--359040 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
358989 CTTTATTAAT
*
358999 ATATATAATATAATATA
1 ATATATAATATAATAAA
*
359016 ATATATTATATAATAAA
1 ATATATAATATAATAAA
359033 ATAATATA
1 AT-ATATA
359041 CATAACATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATAATATAATAAA
Found at i:362471 original size:22 final size:22
Alignment explanation
Indices: 362445--362795 Score: 196
Period size: 24 Copynumber: 15.0 Consensus size: 22
362435 ATTTTCACAC
*
362445 CAAAATTTGGACAGCATATATA-
1 CAAAATTT-GACAGCATATACAT
**
362467 CAAAATTTAGATTGCATTTATACAT
1 CAAAATTT-GACAGCA--TATACAT
362492 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
* * *
362514 -ATATAATTGGACTGCATTTGTACAT
1 CA-A-AATTTGACAGCA--TATACAT
362539 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
* * *
362561 -ATATAATTGGACTGCATTTGTACAT
1 CA-A-AATTTGACAGCA--TATACAT
* *
362586 GAAAATTTGATAGCATATACAT
1 CAAAATTTGACAGCATATACAT
* * *
362608 -ATATAATTGGACTGCATTTGTACAT
1 CA-A-AATTTGACAGCA--TATACAT
362633 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
* *
362655 -ATATAATTGGACTA-CATTTGTACAT
1 CA-A-AATTTGAC-AGCA--TATACAT
362680 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
* *
362702 -ATATAATTGGACTGCATTTATACAT
1 CA-A-AATTTGACAGCA--TATACAT
362727 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
* * *
362749 -ATATAATTGGACTGCATTTGTACAT
1 CA-A-AATTTGACAGCA--TATACAT
362774 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
362796 TCATTTACTC
Statistics
Matches: 254, Mismatches: 40, Indels: 70
0.70 0.11 0.19
Matches are distributed among these distances:
21 6 0.02
22 63 0.25
23 59 0.23
24 69 0.27
25 51 0.20
26 6 0.02
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
CAAAATTTGACAGCATATACAT
Found at i:362793 original size:47 final size:47
Alignment explanation
Indices: 362445--362795 Score: 589
Period size: 47 Copynumber: 7.5 Consensus size: 47
362435 ATTTTCACAC
* * * * *
362445 CAAAATTTGGACAGCATAT--ATACAAAATTTAGATTGCATTTATACAT
1 CAAAATTT-GACAGCATATACATATATAA-TTGGACTGCATTTGTACAT
362492 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
362539 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
* *
362586 GAAAATTTGATAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
*
362633 CAAAATTTGACAGCATATACATATATAATTGGACTACATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
*
362680 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
362727 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
362774 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
362796 TCATTTACTC
Statistics
Matches: 289, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
46 10 0.03
47 273 0.94
48 6 0.02
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (47 bp):
CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
Found at i:363071 original size:14 final size:15
Alignment explanation
Indices: 363033--363081 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
363023 ACCATGCACA
* *
363033 CATATATATACATTAC
1 CATATAAATAC-TAAC
363049 CATATAAATACTAAC
1 CATATAAATACTAAC
363064 CATA-AAATACTAATC
1 CATATAAATACTAA-C
363079 CAT
1 CAT
363082 GATTAAAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 9 0.30
15 11 0.37
16 10 0.33
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (15 bp):
CATATAAATACTAAC
Found at i:373494 original size:22 final size:22
Alignment explanation
Indices: 373466--373511 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
373456 GGCGAATACA
373466 TCAATGCAACTAAACTTGGTTT
1 TCAATGCAACTAAACTTGGTTT
373488 TCAATGCAACTAAACTTGGTTT
1 TCAATGCAACTAAACTTGGTTT
373510 TC
1 TC
373512 TCCCCCCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (22 bp):
TCAATGCAACTAAACTTGGTTT
Found at i:385694 original size:62 final size:60
Alignment explanation
Indices: 385576--385691 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 60
385566 GTGATTATCG
* * * *
385576 TAATATTAAATTTAATTTAATGTTTATCTACAAGATAAGCATTCTATTATTTTAATATGATT
1 TAATATTAAATTTAATCTAATATTTATCT--AAGATAAACATTATATTATTTTAATATGATT
* * *
385638 TAATATTAAATTTAATCTAATATTTATCT-GGATAAATATTATATTAATTTAATA
1 TAATATTAAATTTAATCTAATATTTATCTAAGATAAACATTATATTATTTTAATA
385692 ATAAAGTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
59 20 0.43
62 27 0.57
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (60 bp):
TAATATTAAATTTAATCTAATATTTATCTAAGATAAACATTATATTATTTTAATATGATT
Found at i:387819 original size:19 final size:18
Alignment explanation
Indices: 387790--387834 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
387780 GAATAAATTA
387790 AATGAGAATAACTTTCAAG
1 AATG-GAATAACTTTCAAG
387809 AATAGGAATAACTTTCAAG
1 AAT-GGAATAACTTTCAAG
387828 AATGGAA
1 AATGGAA
387835 ATGGAACTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.16
19 20 0.80
20 1 0.04
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (18 bp):
AATGGAATAACTTTCAAG
Found at i:391954 original size:22 final size:20
Alignment explanation
Indices: 391923--392159 Score: 130
Period size: 19 Copynumber: 11.2 Consensus size: 20
391913 TAGATTAGAA
*
391923 TTTTGTATGAATATTTTAAAT
1 TTTTGTATGAATATTAT-AAT
391944 TTTTCGTATGAATATTATAAT
1 TTTT-GTATGAATATTATAAT
* *
391965 TTTTTTATGAATATTGTAA-
1 TTTTGTATGAATATTATAAT
* *
391984 TGTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTATAAT
392004 TATTT-TAT--A-ATTA-AAT
1 T-TTTGTATGAATATTATAAT
* **
392020 TTGTATTTATAGTTTTGGATTAGTAATT
1 TT-T-TGTAT-G-AAT--ATTA-TAA-T
*
392048 TTTTGTATGAATATTGTAA-
1 TTTTGTATGAATATTATAAT
392067 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTAT-AA-T
392089 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATA-T-T-ATA--AT
392114 AGTTTTGTATGAATATT-TCAATT
1 --TTTTGTATGAATATTAT-AA-T
*
392137 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTATAAT
392157 TTT
1 TTT
392160 GTAATTTTGT
Statistics
Matches: 174, Mismatches: 13, Indels: 59
0.71 0.05 0.24
Matches are distributed among these distances:
15 1 0.01
16 5 0.03
17 4 0.02
18 4 0.02
19 33 0.19
20 23 0.13
21 33 0.19
22 30 0.17
23 3 0.02
24 4 0.02
25 9 0.05
26 6 0.03
27 16 0.09
28 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (20 bp):
TTTTGTATGAATATTATAAT
Found at i:392057 original size:83 final size:84
Alignment explanation
Indices: 391957--392162 Score: 244
Period size: 83 Copynumber: 2.4 Consensus size: 84
391947 TCGTATGAAT
* *
391957 ATTATAATTTTTT-TATGAATATTGTAATGTTGTATGAATATTGT-AATTATTTTATAATTAAAT
1 ATTATAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATT-TTTTAT-A-TAAAT
392020 -TTGT-AT-TTATAGTTTTG-G
63 ATTGTAATATTATAGTTTTGTG
* *
392038 ATTAGTAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATAT
1 ATTA-TAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATTTTTTATATAAATAT
392103 TGTAATATTATAGTTTTGTATG
65 TGTAATATTATAGTTTTG--TG
*
392125 AATATTTCAATTTTTTGTATGAATATTGTAATTTTGTA
1 -AT-TAT-AATTTTTTGTATGAATATTGTAATTTTGTA
392163 ATTTTGTATG
Statistics
Matches: 108, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
81 8 0.07
82 14 0.13
83 36 0.33
84 15 0.14
87 1 0.01
88 3 0.03
89 31 0.29
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (84 bp):
ATTATAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATTTTTTATATAAATATT
GTAATATTATAGTTTTGTG
Found at i:392125 original size:27 final size:24
Alignment explanation
Indices: 392067--392207 Score: 145
Period size: 21 Copynumber: 6.0 Consensus size: 24
392057 AATATTGTAA
*
392067 TTTTGTATGAATATTATAA-A-TT
1 TTTTGTATGAATATTGTAATATTT
392089 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATATT-T
*
392114 AGTTTTGTATGAATATT-TCA-A-TT
1 --TTTTGTATGAATATTGTAATATTT
*
392137 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTGTAATATT-T
392162 AATTTTGTATGAATA-T-T-ATATTT
1 --TTTTGTATGAATATTGTAATATTT
392185 TTTTGTATGAATATTGTAATATT
1 TTTTGTATGAATATTGTAATATT
392208 CTAATATGGC
Statistics
Matches: 100, Mismatches: 5, Indels: 26
0.76 0.04 0.20
Matches are distributed among these distances:
21 28 0.28
22 21 0.21
23 4 0.04
24 12 0.12
25 4 0.04
26 3 0.03
27 28 0.28
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (24 bp):
TTTTGTATGAATATTGTAATATTT
Found at i:392156 original size:48 final size:48
Alignment explanation
Indices: 392057--392212 Score: 242
Period size: 48 Copynumber: 3.2 Consensus size: 48
392047 TTTTTGTATG
392057 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTAT-AATTTTTTGTATGAATATTGT
* *
392106 AATATTATAGTTTTGTATGAATATT-TCAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTAT-AATTTTTTGTATGAATATTGT
* *
392154 AATTTTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTGTATGAATATTGT
*
392202 AATATTCTAAT
1 AATATTGTAAT
392213 ATGGCACCAC
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
48 73 0.75
49 24 0.25
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (48 bp):
AATATTGTAATTTTGTATGAATATTATAATTTTTTGTATGAATATTGT
Found at i:392262 original size:27 final size:27
Alignment explanation
Indices: 392222--392291 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
392212 TATGGCACCA
*
392222 CGCCTCCTAGATAGGCACCACCATTGG
1 CGCCTCCCAGATAGGCACCACCATTGG
*
392249 CGCCTCCCAAATAGGCACCACCATTGG
1 CGCCTCCCAGATAGGCACCACCATTGG
*
392276 CGCCTTCCAGATAGGC
1 CGCCTCCCAGATAGGC
392292 GCCAATGCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.23, C:0.39, G:0.21, T:0.17
Consensus pattern (27 bp):
CGCCTCCCAGATAGGCACCACCATTGG
Found at i:404950 original size:26 final size:25
Alignment explanation
Indices: 404897--404956 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
404887 ACTTAACATC
*
404897 ATGCGAGCTCAATTGTAAACTCGAT
1 ATGCGAGCTCAATTGCAAACTCGAT
* * *
404922 ATGCAAGCTCAATCTGCAAACTTGGT
1 ATGCGAGCTCAAT-TGCAAACTCGAT
404948 ATGCGAGCT
1 ATGCGAGCT
404957 TAACATACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (25 bp):
ATGCGAGCTCAATTGCAAACTCGAT
Found at i:409572 original size:37 final size:37
Alignment explanation
Indices: 409513--409601 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 37
409503 TAAATATCAG
*
409513 TCAGTATATCAGTAAAACTTGCTC-AGTTAAGCTCCAA
1 TCAGTATAACAGTAAAACTTGCTCGA-TTAAGCTCCAA
* * * * * *
409550 TCAGTATAACGGTACAATTTGCTCGATTGAGCTTCAT
1 TCAGTATAACAGTAAAACTTGCTCGATTAAGCTCCAA
*
409587 TCAGTATAATAGTAA
1 TCAGTATAACAGTAA
409602 GTTTGGATTG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
37 40 0.98
38 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (37 bp):
TCAGTATAACAGTAAAACTTGCTCGATTAAGCTCCAA
Found at i:412179 original size:33 final size:33
Alignment explanation
Indices: 412136--412228 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 33
412126 TATCAGTCTA
* *
412136 GGCCTGAGCCCTATATAGTAACAGTACAGTGTG
1 GGCCTTAGCCCAATATAGTAACAGTACAGTGTG
*
412169 GGCCTTAGCCCAATACAGT-A-A-T--AGTGTG
1 GGCCTTAGCCCAATATAGTAACAGTACAGTGTG
*
412197 GGCCTTAGCCCAATATAGTAGCCAGTACAGTG
1 GGCCTTAGCCCAATATAGTA-ACAGTACAGTG
412229 CAATAATGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
28 24 0.49
30 1 0.02
31 2 0.04
32 2 0.04
33 16 0.33
34 4 0.08
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (33 bp):
GGCCTTAGCCCAATATAGTAACAGTACAGTGTG
Found at i:412620 original size:27 final size:27
Alignment explanation
Indices: 412590--412846 Score: 327
Period size: 27 Copynumber: 9.5 Consensus size: 27
412580 CATATGGAGC
* *
412590 TATTTCGATCATTTTACCCTTCGGGGG
1 TATTTCGGTCATTTTACCCTTCGAGGG
*
412617 TATTTCGGTCATTTTACCCTTCAAGGG
1 TATTTCGGTCATTTTACCCTTCGAGGG
*
412644 TATCTT-GGTCATTTTACCCTCCGAGGG
1 TAT-TTCGGTCATTTTACCCTTCGAGGG
** * *
412671 TATTTCAATCATTTTACCCTCCGAAGG
1 TATTTCGGTCATTTTACCCTTCGAGGG
* *
412698 TATTTCGATCATTTTACCCTTTGAGGG
1 TATTTCGGTCATTTTACCCTTCGAGGG
* *
412725 TATTTTGGTCATTTTACCCTTTGAGGG
1 TATTTCGGTCATTTTACCCTTCGAGGG
* *
412752 TATTTCGGTCATTTTACCTTTAGAGGG
1 TATTTCGGTCATTTTACCCTTCGAGGG
* * *
412779 TATTTTGGTCATTTTACCCTTTGGGGG
1 TATTTCGGTCATTTTACCCTTCGAGGG
* *
412806 TATTTCGGTCATTTTACCCATGGAGGG
1 TATTTCGGTCATTTTACCCTTCGAGGG
412833 TATTTCGGTCATTT
1 TATTTCGGTCATTT
412847 GCCCACAAAT
Statistics
Matches: 203, Mismatches: 25, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
26 2 0.01
27 199 0.98
28 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (27 bp):
TATTTCGGTCATTTTACCCTTCGAGGG
Found at i:418865 original size:17 final size:18
Alignment explanation
Indices: 418829--418866 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
418819 TTCGAGAGTC
*
418829 TTCCTACAGTTTTCAGTT
1 TTCCTACAGTCTTCAGTT
418847 TTCCTACAGTCTT-AGTT
1 TTCCTACAGTCTTCAGTT
418864 TTC
1 TTC
418867 TCTAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.16, C:0.24, G:0.11, T:0.50
Consensus pattern (18 bp):
TTCCTACAGTCTTCAGTT
Found at i:419778 original size:28 final size:28
Alignment explanation
Indices: 419676--419780 Score: 129
Period size: 28 Copynumber: 3.8 Consensus size: 28
419666 GTACAGCGTA
* * * * *
419676 GGCCTTAGCCCAAAATAGAAACAATGTG
1 GGCCTTAGCCCAATACAGTAATAGTGTG
*
419704 GGCCTTAGCCCAACACAGTAATAGTGTG
1 GGCCTTAGCCCAATACAGTAATAGTGTG
* *
419732 GGCCTTAACCCAGTACAGTAATAGTGTG
1 GGCCTTAGCCCAATACAGTAATAGTGTG
*
419760 GGCCGTAGCCCAATACAGTAA
1 GGCCTTAGCCCAATACAGTAA
419781 CCAGTACAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (28 bp):
GGCCTTAGCCCAATACAGTAATAGTGTG
Found at i:420181 original size:27 final size:27
Alignment explanation
Indices: 420135--420465 Score: 388
Period size: 27 Copynumber: 12.4 Consensus size: 27
420125 GGTATAACAA
* *
420135 TCATTTTA-CCTT-AAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* * **
420160 TTATTTTACCCTTCAAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCGG
* *
420187 TCATTTTACCC-TCTGGGGGTATTTCGA
1 TCATTTTACCCTTC-GAGGGTATTTCGG
*
420214 TCATTTTACCC-TCTAGGAGTATTTCGG
1 TCATTTTACCCTTCGAGG-GTATTTCGG
*
420241 -CTATTTTACTCTTCGAGGGTATTTCGG
1 TC-ATTTTACCCTTCGAGGGTATTTCGG
* *
420268 TCATTTTA-CCTTTGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGG
*
420294 TCATTTTACCCTTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* * *
420321 TCATTTTACCCTTTGAAGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* * *
420348 TCATTTTACCCATCGAGGATATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCGG
420375 TCATTTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
*
420402 TCATTTTACCCTTCGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
* *
420429 TCATTTTTCCCATCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGG
420456 TCA-TTTACCC
1 TCATTTTACCC
420466 ATAAATCACA
Statistics
Matches: 265, Mismatches: 33, Indels: 15
0.85 0.11 0.05
Matches are distributed among these distances:
25 7 0.03
26 38 0.14
27 214 0.81
28 6 0.02
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGG
Found at i:424068 original size:12 final size:12
Alignment explanation
Indices: 424047--424103 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
424037 AATTTTTTTC
424047 CTTC-TTCTTCT
1 CTTCTTTCTTCT
424058 CTTCTTTCTTCT
1 CTTCTTTCTTCT
424070 CTTCTTTTCTT-T
1 CTTC-TTTCTTCT
*
424082 CTTTCGTTCTTCT
1 C-TTCTTTCTTCT
424095 -TCTCTTTCT
1 CT-TCTTTCT
424104 CCTTAGCTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 5 0.13
12 24 0.62
13 10 0.26
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (12 bp):
CTTCTTTCTTCT
Found at i:424101 original size:20 final size:20
Alignment explanation
Indices: 424043--424103 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
424033 CATGAATTTT
424043 TTTCCTTCTTCTTCTC-TTC
1 TTTCCTTCTTCTTCTCTTTC
* *
424062 TTTCTTCTCTTCTTTTCTTTC
1 TTTCCT-TCTTCTTCTCTTTC
*
424083 TTTCGTTCTTCTTCTCTTTC
1 TTTCCTTCTTCTTCTCTTTC
424103 T
1 T
424104 CCTTAGCTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 5 0.14
20 23 0.64
21 8 0.22
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTCCTTCTTCTTCTCTTTC
Found at i:429825 original size:201 final size:201
Alignment explanation
Indices: 429480--429849 Score: 740
Period size: 201 Copynumber: 1.8 Consensus size: 201
429470 TCGCTGTAAC
429480 AGCAGTGGAACCACCTCTTGAACCCGCAACATCTTCCAATATCTCATCATCCATTTCTTTATACG
1 AGCAGTGGAACCACCTCTTGAACCCGCAACATCTTCCAATATCTCATCATCCATTTCTTTATACG
429545 CTCTTTTGATCGCTCCTTCCGGGTTTCTCCAGAAATCAGACTATCAATGACACATCATCATAATT
66 CTCTTTTGATCGCTCCTTCCGGGTTTCTCCAGAAATCAGACTATCAATGACACATCATCATAATT
429610 AATCAGGGAAAGAAAAAGGGTCGATTACCCAACAACATACCAACATTACCTGCTCAACATCTTTA
131 AATCAGGGAAAGAAAAAGGGTCGATTACCCAACAACATACCAACATTACCTGCTCAACATCTTTA
429675 ATATCG
196 ATATCG
429681 AGCAGTGGAACCACCTCTTGAACCCGCAACATCTTCCAATATCTCATCATCCATTTCTTTATACG
1 AGCAGTGGAACCACCTCTTGAACCCGCAACATCTTCCAATATCTCATCATCCATTTCTTTATACG
429746 CTCTTTTGATCGCTCCTTCCGGGTTTCTCCAGAAATCAGACTATCAATGACACATCATCATAATT
66 CTCTTTTGATCGCTCCTTCCGGGTTTCTCCAGAAATCAGACTATCAATGACACATCATCATAATT
429811 AATCAGGGAAAGAAAAAGGGTCGATTACCCAACAACATA
131 AATCAGGGAAAGAAAAAGGGTCGATTACCCAACAACATA
429850 ATTACCTGGC
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 169 1.00
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.28
Consensus pattern (201 bp):
AGCAGTGGAACCACCTCTTGAACCCGCAACATCTTCCAATATCTCATCATCCATTTCTTTATACG
CTCTTTTGATCGCTCCTTCCGGGTTTCTCCAGAAATCAGACTATCAATGACACATCATCATAATT
AATCAGGGAAAGAAAAAGGGTCGATTACCCAACAACATACCAACATTACCTGCTCAACATCTTTA
ATATCG
Found at i:444715 original size:3 final size:3
Alignment explanation
Indices: 444707--444732 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
444697 AGAAAATTGG
444707 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
444733 GCAAAACCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:445300 original size:13 final size:13
Alignment explanation
Indices: 445282--445308 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
445272 TTTTTAAAAT
445282 TAAAAAATATAAA
1 TAAAAAATATAAA
445295 TAAAAAATATAAA
1 TAAAAAATATAAA
445308 T
1 T
445309 TTATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAAATATAAA
Found at i:447199 original size:20 final size:20
Alignment explanation
Indices: 447155--447224 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
447145 TTCGTATACG
*
447155 TATATATATACCTTATATCTATA
1 TATATATATATC-T-TAT-TATA
*
447178 TATATTTATATCTTATTATA
1 TATATATATATCTTATTATA
* *
447198 TATCTATATGTCTTATTATA
1 TATATATATATCTTATTATA
447218 TATATAT
1 TATATAT
447225 CTCTTTTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 27 0.66
21 3 0.07
22 1 0.02
23 10 0.24
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (20 bp):
TATATATATATCTTATTATA
Found at i:451312 original size:19 final size:19
Alignment explanation
Indices: 451288--451352 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
451278 AAAAAAACAA
451288 AAAAAATCAAAATCAAAAT
1 AAAAAATCAAAATCAAAAT
* ** *
451307 AAAAAATAAAAAGAAAAAAG
1 AAAAAATCAAAA-TCAAAAT
*
451327 AAAAAATCAAAGTCAAAAGT
1 AAAAAATCAAAATCAAAA-T
451347 AAAAAA
1 AAAAAA
451353 AAGAAATCAA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (19 bp):
AAAAAATCAAAATCAAAAT
Found at i:451378 original size:29 final size:29
Alignment explanation
Indices: 451320--451389 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
451310 AAATAAAAAG
451320 AAAAAAGAAAAAATCAAAGTCAAAAGTAA
1 AAAAAAGAAAAAATCAAAGTCAAAAGTAA
* *
451349 AAAAAAGAAATCAATTAAAGTCAAAA-TAA
1 AAAAAAGAAA-AAATCAAAGTCAAAAGTAA
* *
451378 AAATATGAAAAA
1 AAAAAAGAAAAA
451390 GAGAAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 1 0.03
29 21 0.60
30 13 0.37
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (29 bp):
AAAAAAGAAAAAATCAAAGTCAAAAGTAA
Found at i:451784 original size:21 final size:20
Alignment explanation
Indices: 451760--451799 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
451750 AAGGGAGATG
451760 AAAAATGAAAATGGAAAATGA
1 AAAAATGAAAA-GGAAAATGA
*
451781 AAAAATGAAAAGTAAAATG
1 AAAAATGAAAAGGAAAATG
451800 GAGAGGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAAATGAAAAGGAAAATGA
Found at i:453266 original size:131 final size:131
Alignment explanation
Indices: 453062--453360 Score: 351
Period size: 131 Copynumber: 2.3 Consensus size: 131
453052 AAAGTTGCGG
* * * *
453062 ATCTTATCTTCCCC-AGAAGTAGGGAAATAGATTTAAGCCACAAGTCCTATGTCCCTGATCAGCA
1 ATCTTATCTTCCCCAAG-AGTAGGGAAACAGATTTAAGCCACAAGTCCGATGTCACTGACCAGCA
* * * * *
453126 GTGGGATAGGTT-GAAGATTGCGGATCTTATCT-TCCCTAGGAGTAG-GGAAACAGATCGAAGAC
65 GTGGAATAGGTTAGAA-ATTACAGATCTTATCTCT-CCAAGCAGTAGTGG-AACAGATCGAAGAC
453188 GGCGA
127 GGCGA
*
453193 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAAGCCACAAGTTCGATGTCACTGACCAGCAG
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAAGCCACAAGTCCGATGTCACTGACCAGCAG
* * * * *
453258 TGGAATAGGTTAGAAATTATAGATCTTGTCTCTCGAAGCAGTAGTGGGACAGATCGAGGACGGCG
66 TGGAATAGGTTAGAAATTACAGATCTTATCTCTCCAAGCAGTAGTGGAACAGATCGAAGACGGCG
453323 A
131 A
* * *
453324 ATCTTATCTT---CAAGTGTAAGGAAGCAGATTTAAGCCA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAAGCCA
453361 TGAGTCCTTT
Statistics
Matches: 146, Mismatches: 18, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
128 24 0.16
131 114 0.78
132 8 0.05
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (131 bp):
ATCTTATCTTCCCCAAGAGTAGGGAAACAGATTTAAGCCACAAGTCCGATGTCACTGACCAGCAG
TGGAATAGGTTAGAAATTACAGATCTTATCTCTCCAAGCAGTAGTGGAACAGATCGAAGACGGCG
A
Found at i:453450 original size:130 final size:130
Alignment explanation
Indices: 453300--453951 Score: 941
Period size: 130 Copynumber: 5.0 Consensus size: 130
453290 TCGAAGCAGT
* *
453300 AGTGGGACAGATCGAGGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCATGAG
1 AGTGGGACAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAG
* *
453365 TCCTTTCTCCCTGAGGTTGTAGTGAAGCAGACTAAGTAAGCAGGTCTTATCCCAACTGAAGTTGC
66 TCCTTTCTCCCTGAGGTTGTAGTGGAGCAGACTAAGTAAGCAGGTCTTATCCCGACTGAAGTTGC
453430 AGTGGGACAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAG
1 AGTGGGACAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAG
* * * *
453495 TTCTTTCTCCCTGAGGTTGCAGTGGAGCAGACTATGTAAACAGGTCTTATCCCGACTGAAGTTGC
66 TCCTTTCTCCCTGAGGTTGTAGTGGAGCAGACTAAGTAAGCAGGTCTTATCCCGACTGAAGTTGC
* *
453560 AGTGGGACAGATCGAAGATGGCGAATCTTATCTTCAAGTGTAAGGAAGAAGATTTAAGCCACGAG
1 AGTGGGACAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAG
* * * *
453625 TCCTTTCTCTCTGAGGTTGTAGTGGAACAGGCTAAGTAAGCAGGTCTTATCCCGACTGAAGTTAC
66 TCCTTTCTCCCTGAGGTTGTAGTGGAGCAGACTAAGTAAGCAGGTCTTATCCCGACTGAAGTTGC
* * * * * *
453690 AGTGGGACAAATCGAAGACGGCGACTCTTATCTTCAAGTGTAAGAAAGTAGATTTAAGCCCCGAT
1 AGTGGGACAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAG
* ** *
453755 TCCTTTCTCTCTGAGGTTACAGTGGAGAAGACTAAGTAAGCAGGTCTTATCCCGACTGAAGTTGC
66 TCCTTTCTCCCTGAGGTTGTAGTGGAGCAGACTAAGTAAGCAGGTCTTATCCCGACTGAAGTTGC
* *
453820 AGTGGGACAGATCGAAGACGGCGAATCTTACCTTCAAGTGTAAGGAAGCAGATTTAAGCCTA-TA
1 AGTGGGACAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC-ACGA
* * * * * * * * * *
453884 ATCGTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAA-TAGATCTTATCTC-TCTGAAGTT
65 GTCCTTTCTCCCTGAGGTTGTAGTGGAGCAGACT-AAGTAAGCAGGTCTTATCCCGACTGAAGTT
453947 GC
129 GC
453949 AGT
1 AGT
453952 AGAGTGGATC
Statistics
Matches: 468, Mismatches: 52, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
129 13 0.03
130 449 0.96
131 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (130 bp):
AGTGGGACAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAG
TCCTTTCTCCCTGAGGTTGTAGTGGAGCAGACTAAGTAAGCAGGTCTTATCCCGACTGAAGTTGC
Found at i:454037 original size:45 final size:44
Alignment explanation
Indices: 453970--454086 Score: 117
Period size: 45 Copynumber: 2.6 Consensus size: 44
453960 TCGCATCGAG
* * * * *
453970 TCTTATCCCCCTGAGGTCACAGTGGGGCAGACTGAAGATGACAAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGACGA-AAA
* * * *
454015 TCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGCCGATAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGACGAAAA
* **
454059 TCCTATCTCCCTGAAGTTGTAGTGGAGC
1 TCTTATCTCCCTGAAGTTACAGTGGAGC
454087 GGATTAAAGT
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
44 26 0.44
45 33 0.56
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGACGAAAA
Found at i:454110 original size:44 final size:44
Alignment explanation
Indices: 453888--454130 Score: 154
Period size: 44 Copynumber: 5.6 Consensus size: 44
453878 CCTATAATCG
*
453888 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
* * * * * *
453932 TATCTCTCTGAAGTTGCAGTAGAGTGGA-T--CG-CATCGAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGA-TCT
* * ** * * * * * * *
453973 TATCCCCCTGAGGTCACAGTGGGGCAGACTGAAGATGACAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAG-TAATAGATCT
* ** * ** *
454018 TATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAG-TAATAGATCT
*
454062 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
** * *
454106 TATCTCTTTGAAGCTGCAGTAGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
454131 AGATCGCATC
Statistics
Matches: 148, Mismatches: 44, Indels: 14
0.72 0.21 0.07
Matches are distributed among these distances:
40 4 0.03
41 23 0.16
42 1 0.01
43 4 0.03
44 80 0.54
45 34 0.23
46 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
Found at i:456078 original size:20 final size:20
Alignment explanation
Indices: 456053--456099 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
456043 ACCTTATATC
* *
456053 TATATATCTTTGTATCTTAT
1 TATATATCTATATATCTTAT
*
456073 TATATATCTATATGTCTTAT
1 TATATATCTATATATCTTAT
456093 TATATAT
1 TATATAT
456100 ATATCTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (20 bp):
TATATATCTATATATCTTAT
Found at i:481437 original size:41 final size:41
Alignment explanation
Indices: 481380--481606 Score: 348
Period size: 41 Copynumber: 5.5 Consensus size: 41
481370 TTTAACATAT
* *
481380 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGA
481421 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* *
481462 TCATCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGT
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* *
481503 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGGTTCAAA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* *
481544 TCACCGGCTCTTAGCTTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* *
481585 TCGCCGGCTCTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
481607 ACTTAAAGTC
Statistics
Matches: 171, Mismatches: 14, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
40 2 0.01
41 169 0.99
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:489127 original size:41 final size:41
Alignment explanation
Indices: 489070--489296 Score: 357
Period size: 41 Copynumber: 5.5 Consensus size: 41
489060 TTTAACATAT
* *
489070 TCACCGGCACTTAGCCTGCTAGGTTTATAGCCCGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGA
489111 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* * *
489152 TCACCGACACTTAGCCTGCTAGGTTTATAACCTTATTCAGT
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
489193 TCACTGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* *
489234 TCACCCGCTCTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
489275 TCACCGGCTCTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
489297 ACTTAAAGTC
Statistics
Matches: 172, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 2 0.01
41 170 0.99
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:489319 original size:123 final size:123
Alignment explanation
Indices: 489069--489341 Score: 374
Period size: 123 Copynumber: 2.2 Consensus size: 123
489059 ATTTAACATA
* *
489069 TTCACCGGCACTTAGCCTGCTAGGTTTATAGCCCGATTCCAATCACCGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCCGATTCCAATCACCCGCACTTAGCCTGCTAGG
** *
489134 TTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAGGTTTATAACCTTATTCAG
66 TTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAACCTAATTCAG
* * *
489192 TTCACTGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGATCACCCGCTCTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCCGATTCCA-ATCACCCGCACTTAGCCTGCTAG
* * * *
489256 GTTTATAACCTGATTCAGATCACCGGCTCTTAGCCTGCTAGACTTA-AAGTCTGAATT-AT
65 GTTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAA-CCT-AATTCAG
489315 TTCACCGGC-CTTAAGCCTGCTAGGTTT
1 TTCACCGGCACTT-AGCCTGCTAGGTTT
489342 TAAACCAGAA
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
122 7 0.05
123 123 0.92
124 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (123 bp):
TTCACCGGCACTTAGCCTGCTAGGTTTATAACCCGATTCCAATCACCCGCACTTAGCCTGCTAGG
TTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAACCTAATTCAG
Found at i:492424 original size:25 final size:25
Alignment explanation
Indices: 492391--492452 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
492381 ACGAGCTGTA
492391 AACGGTAAGCTCCTTCCAGCTGAAT
1 AACGGTAAGCTCCTTCCAGCTGAAT
* **
492416 AACGGTAAGCTCTTTTGAGCTGAAT
1 AACGGTAAGCTCCTTCCAGCTGAAT
*
492441 AGCGGTAAGCTC
1 AACGGTAAGCTC
492453 GTACGAGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (25 bp):
AACGGTAAGCTCCTTCCAGCTGAAT
Found at i:492460 original size:25 final size:24
Alignment explanation
Indices: 492375--492464 Score: 83
Period size: 25 Copynumber: 3.7 Consensus size: 24
492365 GTACATGTAT
492375 GCTCATACGAGCTGTAA-ACGGTAA
1 GCTCATACGAGCTG-AATACGGTAA
* * *
492399 GCTCCTTCCAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAAT-ACGGTAA
* **
492424 GCTCTTTTGAGCTGAATAGCGGTAA
1 GCTCATACGAGCTGAATA-CGGTAA
*
492449 GCTCGTACGAGCTGAA
1 GCTCATACGAGCTGAA
492465 ATCCGTAATC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
23 2 0.04
24 12 0.22
25 40 0.74
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (24 bp):
GCTCATACGAGCTGAATACGGTAA
Found at i:493805 original size:11 final size:11
Alignment explanation
Indices: 493791--493839 Score: 89
Period size: 11 Copynumber: 4.5 Consensus size: 11
493781 TAAACACTTG
493791 ATAAATAAATC
1 ATAAATAAATC
493802 ATAAATAAATC
1 ATAAATAAATC
*
493813 ACAAATAAATC
1 ATAAATAAATC
493824 ATAAATAAATC
1 ATAAATAAATC
493835 ATAAA
1 ATAAA
493840 GAATAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (11 bp):
ATAAATAAATC
Found at i:503894 original size:51 final size:49
Alignment explanation
Indices: 503759--503896 Score: 197
Period size: 50 Copynumber: 2.8 Consensus size: 49
503749 AAAGTGAAAG
* *
503759 TGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA
* *
503808 TGATGGGTCGCATGTGTAGTACTATGTGCAGGCTACTACGTGTATCAG-A
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA
503857 TGAGAATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 T--G-ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
503897 TGTGAACTGA
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
49 6 0.08
50 39 0.49
51 33 0.41
52 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (49 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA
Found at i:503900 original size:26 final size:26
Alignment explanation
Indices: 503819--503900 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
503809 GATGGGTCGC
503819 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTAGTACTATGTGCAGGCTACT
* * * *
503845 ACGTGTA-T-CAGATGAGAATGG-TCAC-
1 ATGTGTAGTAC-TATGTGCA-GGCT-ACT
503870 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTAGTACTATGTGCAGGCTACT
503896 ATGTG
1 ATGTG
503901 AACTGAACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.32
Consensus pattern (26 bp):
ATGTGTAGTACTATGTGCAGGCTACT
Found at i:508438 original size:56 final size:55
Alignment explanation
Indices: 508248--508438 Score: 190
Period size: 56 Copynumber: 3.4 Consensus size: 55
508238 ACTCGAGTCT
* * * *
508248 AGGTTTGCCTTAGGTCGCGAAG-TCA-TCTCGCACATACTTTTTAGAAAAC-TCAAAA
1 AGGTTTGCCTTAGGT--CGAAGACCAGT-TCGCACATACTTATTAGAAAACATGAACA
** * ** * *
508303 AGGTCCGCCTTAGGTCACAAGACTGGTTTGCACATACTTATCAGAAAACATGAACA
1 AGGTTTGCCTTAGGTC-GAAGACCAGTTCGCACATACTTATTAGAAAACATGAACA
* *
508359 GGGTTTGCCTTAGGTCGAGAGACCAGTTCGCACATACTTGTTAGAAAACATGAACA
1 AGGTTTGCCTTAGGTCGA-AGACCAGTTCGCACATACTTATTAGAAAACATGAACA
508415 AGGTTTGCCTTAGGTCGTAAGACC
1 AGGTTTGCCTTAGGTCG-AAGACC
508439 GGTTTGCTTA
Statistics
Matches: 109, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
53 1 0.01
54 3 0.03
55 33 0.30
56 71 0.65
57 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (55 bp):
AGGTTTGCCTTAGGTCGAAGACCAGTTCGCACATACTTATTAGAAAACATGAACA
Found at i:512188 original size:21 final size:21
Alignment explanation
Indices: 512126--512212 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
512116 CCTGATCTAT
*
512126 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAATGCCTG
* ** **
512146 AAACGACACACGAGGTGCCTG
1 ATACGACACATAAAATGCCTG
*
512167 ATACGACACATAAAATGTCTG
1 ATACGACACATAAAATGCCTG
*
512188 ATGTACGACACATAAAGTGCCTG
1 A--TACGACACATAAAATGCCTG
512211 AT
1 AT
512213 CATCAAAGCC
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
20 9 0.17
21 25 0.47
23 19 0.36
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (21 bp):
ATACGACACATAAAATGCCTG
Found at i:512197 original size:23 final size:23
Alignment explanation
Indices: 512161--512212 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
512151 ACACACGAGG
512161 TGCCTGA--TACGACACATAAAA
1 TGCCTGATGTACGACACATAAAA
* *
512182 TGTCTGATGTACGACACATAAAG
1 TGCCTGATGTACGACACATAAAA
512205 TGCCTGAT
1 TGCCTGAT
512213 CATCAAAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 6 0.23
23 20 0.77
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (23 bp):
TGCCTGATGTACGACACATAAAA
Found at i:513518 original size:5 final size:5
Alignment explanation
Indices: 513498--513564 Score: 64
Period size: 5 Copynumber: 13.6 Consensus size: 5
513488 TTAGTTTTTT
* * * * * *
513498 TAATA TATTT TAATA TAATA TAATA TGATA TAAAA GAATA TAATA TAAAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
*
513548 TAATA T-ATA AAATA TAA
1 TAATA TAATA TAATA TAA
513565 AAATCTAATA
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
4 3 0.06
5 44 0.94
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
TAATA
Found at i:517097 original size:8 final size:7
Alignment explanation
Indices: 517080--517113 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
517070 GGTATTCTAC
517080 TTTTTCT
1 TTTTTCT
517087 TTTTTCT
1 TTTTTCT
517094 TTTTTCTT
1 TTTTTC-T
517102 TTTTTCT
1 TTTTTCT
517109 TTTTT
1 TTTTT
517114 AGAATCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:517104 original size:15 final size:14
Alignment explanation
Indices: 517080--517113 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
517070 GGTATTCTAC
517080 TTTTTCTTTTTTCT
1 TTTTTCTTTTTTCT
517094 TTTTTCTTTTTTTCT
1 TTTTTC-TTTTTTCT
517109 TTTTT
1 TTTTT
517114 AGAATCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTCTTTTTTCT
Found at i:519748 original size:37 final size:39
Alignment explanation
Indices: 519578--519868 Score: 138
Period size: 38 Copynumber: 7.4 Consensus size: 39
519568 TGCTTAATTG
*
519578 TTTTATTAAATTATATAAGAATAT-TAAT-TATTAACAA
1 TTTTATTAAATTATATAAGAATATATAATATATTAAGAA
** *
519615 TTTTATTAAATTATATATTTTAAT-TATAATATATTTAATAA
1 TTTTATTAAATTATATA--AGAATATATAATATA-TTAAGAA
* * *** * *
519656 TTATGTTAAATTATAT-TTTATAGTATCATATATTATG-A
1 TTTTATTAAATTATATAAGAATA-TATAATATATTAAGAA
* * *
519694 TTTGAGTAAATTCATATAAGAATAT-TGAT-TATTAAGAA
1 TTTTATTAAATT-ATATAAGAATATATAATATATTAAGAA
** *
519732 TTTTATTAAATTATATATTTTAAT-TATAATATATTTAATAA
1 TTTTATTAAATTATATA--AGAATATATAATATA-TTAAGAA
* * *** * *
519773 TAATTATGTTAAATTATCT-TTTATAGTATCATATATTATG-A
1 T--TT-TATTAAATTATATAAGAATA-TATAATATATTAAGAA
* *
519814 TTTGAGTAAATTCATATAAGAATAT-TAAT-TATTAAGAA
1 TTTTATTAAATT-ATATAAGAATATATAATATATTAAGAA
*
519852 TTTTTTTAAATTATATA
1 TTTTATTAAATTATATA
519869 TTTTAATTAT
Statistics
Matches: 189, Mismatches: 42, Indels: 46
0.68 0.15 0.17
Matches are distributed among these distances:
37 39 0.21
38 48 0.25
39 27 0.14
40 18 0.10
41 33 0.17
42 3 0.02
43 10 0.05
44 11 0.06
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (39 bp):
TTTTATTAAATTATATAAGAATATATAATATATTAAGAA
Found at i:519765 original size:16 final size:16
Alignment explanation
Indices: 519744--519789 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
519734 TTATTAAATT
519744 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
519760 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
519775 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
519790 CTTTTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:519835 original size:120 final size:120
Alignment explanation
Indices: 519584--519899 Score: 568
Period size: 120 Copynumber: 2.7 Consensus size: 120
519574 ATTGTTTTAT
*
519584 TAAATT-ATATAAGAATATTAATTATTAACAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
519648 -TT--TAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAG
66 TTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAG
*
519700 TAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
*
519765 TTTAATAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAG
66 TTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAG
*
519820 TAAATTCATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
519885 TTTAATAATAATTAT
66 TTTAATAATAATTAT
519900 ATTTAAATAT
Statistics
Matches: 191, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
116 6 0.03
117 56 0.29
118 2 0.01
120 127 0.66
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
TTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAG
Found at i:519883 original size:16 final size:16
Alignment explanation
Indices: 519864--519908 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
519854 TTTTTAAATT
*
519864 ATATATTTTAATTATA
1 ATATATTTTAATAATA
519880 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
*
519895 ATTATATTTAAATA
1 A-TATATTTTAATA
519909 TGATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 9 0.36
17 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:519914 original size:16 final size:16
Alignment explanation
Indices: 519865--519905 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
519855 TTTTAAATTA
*
519865 TATATTTTAATTATAA-
1 TATA-TTTAATAATAAT
519881 TATATTTAATAATAAT
1 TATATTTAATAATAAT
519897 TATATTTAA
1 TATATTTAA
519906 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTTAATAATAAT
Found at i:520101 original size:44 final size:45
Alignment explanation
Indices: 520051--520140 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
520041 CCTCTATTCT
520051 ATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACA-ATAGATTTACTATTACGCCTCTATTCCATTAC
* *
520095 ATTCAACCAAACAATTGATTTGCTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACAATAGATTTACTATTACGCCTCTATTCCATTAC
520140 A
1 A
520141 CCTCTATTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 15 0.36
45 26 0.62
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (45 bp):
ATTCAACCAAACAATAGATTTACTATTACGCCTCTATTCCATTAC
Found at i:520144 original size:16 final size:16
Alignment explanation
Indices: 520119--520172 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
520109 TTGATTTGCT
*
520119 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
520135 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
520151 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
520167 AATACA
1 ATTACA
520173 GCGAACCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:520960 original size:23 final size:26
Alignment explanation
Indices: 520905--520964 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 26
520895 TAACGTTAAG
* *
520905 TTTTATAATATTTTATTACATTTTCA
1 TTTTATAATATTTAATTACATTATCA
520931 TTTTATAAT-TTTAATTAC-TTAT-A
1 TTTTATAATATTTAATTACATTATCA
520954 TTTTATAATAT
1 TTTTATAATAT
520965 AAGAACATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.32
24 4 0.13
25 8 0.26
26 9 0.29
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTATAATATTTAATTACATTATCA
Found at i:527123 original size:36 final size:36
Alignment explanation
Indices: 527078--527173 Score: 131
Period size: 36 Copynumber: 2.7 Consensus size: 36
527068 AATTATCACT
*
527078 CTTA-AATATCACAACTATATCATTAGGCCAAATCA
1 CTTATAATATCACAACTATATCAATAGGCCAAATCA
* * *
527113 CTTATAATATCACAAGTATATCAATAGGCCGAATTA
1 CTTATAATATCACAACTATATCAATAGGCCAAATCA
* *
527149 CTTATAATATCACAAGTACATCAAT
1 CTTATAATATCACAACTATATCAAT
527174 TCAAATATAC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 4 0.07
36 51 0.93
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (36 bp):
CTTATAATATCACAACTATATCAATAGGCCAAATCA
Found at i:535164 original size:252 final size:252
Alignment explanation
Indices: 534707--535213 Score: 924
Period size: 252 Copynumber: 2.0 Consensus size: 252
534697 TTGATCTTTC
* *
534707 AAACTTCAATCGTTGGAAGGACAAGATGTTGTTCCTTCTTACTACCTTACATATGGTGTACATTC
1 AAACTACAATCATTGGAAGGACAAGATGTTGTTCCTTCTTACTACCTTACATATGGTGTACATTC
534772 TGGATCCAAAACTACAACCTGTAGAGGATCCCGCCCCCAATGCAAGCCACAAGGAAATTACGAAA
66 TGGATCCAAAACTACAACCTGTAGAGGATCCCGCCCCCAATGCAAGCCACAAGGAAATTACGAAA
* *
534837 GTGGCCAAACTCAAGAAGAAGCATGAAGAAGACAATTTCACATGTTGAAGACACATTATCAACCC
131 GTGGCCAAACTCAAGAAGAAGCATGAAGAAGAAAATTTCACATGTTGAAAACACATTATCAACCC
534902 TTGTCTAATCAATTGTATGATCTCTACATGTTAATGTAATCCACGGTGGAAATATGA
196 TTGTCTAATCAATTGTATGATCTCTACATGTTAATGTAATCCACGGTGGAAATATGA
* * *
534959 AAACTACAATCATTGGAAGGACAAGATGTTGTTCCTTTTTACTATCTTACATGTGGTGTACATTC
1 AAACTACAATCATTGGAAGGACAAGATGTTGTTCCTTCTTACTACCTTACATATGGTGTACATTC
* *
535024 TGGATCCAAAACTACAACCTGTGGAGGATCCCGCCCCCAATGCAAGCCACGAGGAAATTACGAAA
66 TGGATCCAAAACTACAACCTGTAGAGGATCCCGCCCCCAATGCAAGCCACAAGGAAATTACGAAA
535089 GTGGCCAAACTCAAGAAGAAGCATGAAGAAGAAAATTTCACATGTTGAAAACACATTATCAACCC
131 GTGGCCAAACTCAAGAAGAAGCATGAAGAAGAAAATTTCACATGTTGAAAACACATTATCAACCC
*
535154 TTGTCTAATCAATTGTATGATCTCTACATGTTAATGTAATCCCCGGTGGAAATATGA
196 TTGTCTAATCAATTGTATGATCTCTACATGTTAATGTAATCCACGGTGGAAATATGA
535211 AAA
1 AAA
535214 GCTCTTGAAG
Statistics
Matches: 245, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
252 245 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (252 bp):
AAACTACAATCATTGGAAGGACAAGATGTTGTTCCTTCTTACTACCTTACATATGGTGTACATTC
TGGATCCAAAACTACAACCTGTAGAGGATCCCGCCCCCAATGCAAGCCACAAGGAAATTACGAAA
GTGGCCAAACTCAAGAAGAAGCATGAAGAAGAAAATTTCACATGTTGAAAACACATTATCAACCC
TTGTCTAATCAATTGTATGATCTCTACATGTTAATGTAATCCACGGTGGAAATATGA
Found at i:541195 original size:48 final size:48
Alignment explanation
Indices: 541037--541236 Score: 125
Period size: 48 Copynumber: 4.2 Consensus size: 48
541027 TACTATGCGT
* * * * *
541037 ACCGATAATCTGTTATGACACAAGGGTGGCAGGGACTGTGTGCAGGCC
1 ACCGAGAATCTGTTAAGACACAAAGGTGGCACGGACTATGTGCAGGCC
* * * * ** * * * * *
541085 ACTGATATTCTATTGTGACACAAGGGTGGCACAG-CCAGTGTGTAGGTC
1 ACCGAGAATCTGTTAAGACACAAAGGTGGCACGGACTA-TGTGCAGGCC
** * ** * *
541133 ACTAATAA-CTTGTTAAGGTACAAGGGTGGCACGGACTATGTGTAGGCC
1 ACCGAGAATC-TGTTAAGACACAAAGGTGGCACGGACTATGTGCAGGCC
** * *
541181 ACCGAGAATCTGTTATTACACAAAGGTGGTACGGACTGTGTGCAGGCC
1 ACCGAGAATCTGTTAAGACACAAAGGTGGCACGGACTATGTGCAGGCC
541229 ACCGAGAA
1 ACCGAGAA
541237 ATCTATTTTT
Statistics
Matches: 117, Mismatches: 31, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
47 2 0.02
48 112 0.96
49 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (48 bp):
ACCGAGAATCTGTTAAGACACAAAGGTGGCACGGACTATGTGCAGGCC
Found at i:550774 original size:18 final size:18
Alignment explanation
Indices: 550751--550787 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
550741 ATAAAAAAAA
550751 AGAGAGAGAGTAG-AGAGT
1 AGAGAG-GAGTAGTAGAGT
550769 AGAGAGGAGTAGTAGAGT
1 AGAGAGGAGTAGTAGAGT
550787 A
1 A
550788 AGCAATGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (18 bp):
AGAGAGGAGTAGTAGAGT
Found at i:553554 original size:65 final size:66
Alignment explanation
Indices: 553447--553593 Score: 206
Period size: 66 Copynumber: 2.2 Consensus size: 66
553437 GATACACGGA
* * * *
553447 TCTCCATCACACCAGATAGACTCATAGAGTCAAACATGTCCC-ATAAGTGAAGCATAAAACTAAC
1 TCTCCAACACACCA-ATAGACTCATAAAGTCAAACATATCCCAAAAAGTGAAGCATAAAACTAAC
553511 AC
65 AC
* * * *
553513 TCTCCAACACACCAATTGAGTCATAAAGTCGAACATATCCCAAAAAGTGAAGCATAAAGCTAACA
1 TCTCCAACACACCAATAGACTCATAAAGTCAAACATATCCCAAAAAGTGAAGCATAAAACTAACA
553578 C
66 C
553579 TCTCCAACACACCAA
1 TCTCCAACACACCAA
553594 ATATGTTTCG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 22 0.31
66 50 0.69
ACGTcount: A:0.42, C:0.29, G:0.11, T:0.18
Consensus pattern (66 bp):
TCTCCAACACACCAATAGACTCATAAAGTCAAACATATCCCAAAAAGTGAAGCATAAAACTAACA
C
Found at i:555956 original size:18 final size:18
Alignment explanation
Indices: 555933--555977 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
555923 CATGCAACAT
555933 TTGGCGAACCCTCC-AAGA
1 TTGGCGAACCC-CCTAAGA
555951 TTGGCGAACCCCCTAAGA
1 TTGGCGAACCCCCTAAGA
555969 TTGGCGAAC
1 TTGGCGAAC
555978 TCACAGTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (18 bp):
TTGGCGAACCCCCTAAGA
Found at i:556028 original size:28 final size:28
Alignment explanation
Indices: 555982--556052 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
555972 GCGAACTCAC
*
555982 AGTAAGTGGTGAGCAACCTCAAATGAAT
1 AGTAAGTGGTGAGCTACCTCAAATGAAT
* *
556010 AGTGAGTGGTGAGCTACCTCAAATGAGT
1 AGTAAGTGGTGAGCTACCTCAAATGAAT
556038 AGTAAGTGGTGAGCT
1 AGTAAGTGGTGAGCT
556053 CATTACTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (28 bp):
AGTAAGTGGTGAGCTACCTCAAATGAAT
Found at i:569823 original size:37 final size:37
Alignment explanation
Indices: 569730--569824 Score: 102
Period size: 37 Copynumber: 2.6 Consensus size: 37
569720 GCTATCGAGC
* * * *
569730 CAAATCTTATTGTTATACTAAATGAAACTCAATTGAG
1 CAAATCTTACTGTTATACTGAATGAAACTCAACTAAG
** * *
569767 CAAATCAAACTGTTATACTGAAT-AGAGCTTAACTAAG
1 CAAATCTTACTGTTATACTGAATGA-AACTCAACTAAG
569804 CAAATCTTACTGTTATACTGA
1 CAAATCTTACTGTTATACTGA
569825 CTAATATTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
36 1 0.02
37 46 0.98
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (37 bp):
CAAATCTTACTGTTATACTGAATGAAACTCAACTAAG
Found at i:573438 original size:15 final size:14
Alignment explanation
Indices: 573417--573452 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
573407 ATAATCATTA
573417 ATAATTATCTTAAT
1 ATAATTATCTTAAT
573431 ATTAATTATCTTAAT
1 A-TAATTATCTTAAT
573446 ATAATTA
1 ATAATTA
573453 AAATAGAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATTATCTTAAT
Found at i:575074 original size:49 final size:49
Alignment explanation
Indices: 575032--575144 Score: 131
Period size: 49 Copynumber: 2.3 Consensus size: 49
575022 ATCCCGGATG
* * *
575032 GCTCGACAACGATGGCAT-TCAATATCTA-ATTATTCTACCATCCTGAATA
1 GCTCGACAACGATGGC-TCTCAATATATATA-CATTCTACCATCCAGAATA
* * * *
575081 GCTCAACAACAATGGCTCTCACTATATATACATTCTATCATCCAGAATA
1 GCTCGACAACGATGGCTCTCAATATATATACATTCTACCATCCAGAATA
575130 GCTCGACAACGATGG
1 GCTCGACAACGATGG
575145 TTTTCTACCT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
48 1 0.02
49 51 0.96
50 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (49 bp):
GCTCGACAACGATGGCTCTCAATATATATACATTCTACCATCCAGAATA
Found at i:576498 original size:16 final size:17
Alignment explanation
Indices: 576477--576510 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
576467 ACATAATTAT
*
576477 TAGTAA-AAGGTTAATA
1 TAGTAATAAGGTAAATA
576493 TAGTAATAAGGTAAATA
1 TAGTAATAAGGTAAATA
576510 T
1 T
576511 TAACTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
TAGTAATAAGGTAAATA
Found at i:577434 original size:42 final size:42
Alignment explanation
Indices: 577378--577477 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
577368 CTATATGAAC
* *
577378 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
*
577420 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
*
577462 GGCACTCAGTGTGCGA
1 GGCACTAAGTGTGCGA
577478 TACCGAGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
Found at i:581594 original size:27 final size:26
Alignment explanation
Indices: 581546--581596 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
581536 TCATTTTTAT
581546 AACATATAAATATATAATTAATTAAA
1 AACATATAAATATATAATTAATTAAA
*
581572 AACA-ATAAATTTATATATCTAATTA
1 AACATATAAATATATA-AT-TAATTA
581597 TCTTGAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (26 bp):
AACATATAAATATATAATTAATTAAA
Found at i:586016 original size:3 final size:3
Alignment explanation
Indices: 586008--586034 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
585998 AAAAGGTTAT
586008 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
586035 GATGAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:587850 original size:21 final size:22
Alignment explanation
Indices: 587824--587870 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
587814 CTCTGCTCAA
*
587824 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
587845 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
587867 ACTC
1 ACTC
587871 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:590775 original size:39 final size:38
Alignment explanation
Indices: 590732--590854 Score: 112
Period size: 39 Copynumber: 3.3 Consensus size: 38
590722 TCATTGGTAA
590732 ATCCAACTAGAGCTGGGCTCACTATTTATTCGTTGGTTT
1 ATCCAACTAGAGCTGGGCTCACTA-TTATTCGTTGGTTT
* * * *
590771 ATCCAACTAGCGCTGGGCGT-A--A--ATACCTTCGGTAT
1 ATCCAACTAGAGCTGGGC-TCACTATTATTCGTT-GGTTT
* *
590806 ATCCAACTAGAGCTGCGCTCACTAATTATTCGTCGGTTT
1 ATCCAACTAGAGCTGGGCTCACT-ATTATTCGTTGGTTT
*
590845 ATCCGACTAG
1 ATCCAACTAG
590855 CGCAGGGCGC
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
34 6 0.09
35 21 0.32
37 1 0.02
38 1 0.02
39 31 0.48
40 5 0.08
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (38 bp):
ATCCAACTAGAGCTGGGCTCACTATTATTCGTTGGTTT
Found at i:590810 original size:74 final size:74
Alignment explanation
Indices: 590682--590866 Score: 264
Period size: 74 Copynumber: 2.5 Consensus size: 74
590672 TAAATAATTG
* *
590682 TTTATTCGTCGGTTTATCCGACTACCGCTGGGCACAAATATCATTGGTAAATCCAACTAGAGCTG
1 TTTATTCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATCATTGGTAAATCCAACTAGAGCTG
*
590747 GGCTCACTA
66 CGCTCACTA
* * * * *
590756 TTTATTCGTTGGTTTATCCAACTAGCGCTGGGCGTAAATA-CCTTCGGTATATCCAACTAGAGCT
1 TTTATTCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATCATT-GGTAAATCCAACTAGAGCT
590820 GCGCTCACTA
65 GCGCTCACTA
* *
590830 ATTATTCGTCGGTTTATCCGACTAGCGCAGGGCGCAA
1 TTTATTCGTCGGTTTATCCGACTAGCGCTGGGCGCAA
590867 CTTTCGTCAG
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
73 3 0.03
74 94 0.97
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (74 bp):
TTTATTCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATCATTGGTAAATCCAACTAGAGCTG
CGCTCACTA
Found at i:593743 original size:14 final size:14
Alignment explanation
Indices: 593726--593753 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
593716 CTCACATTTC
593726 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
593740 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
593754 GATTTCTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:593744 original size:19 final size:18
Alignment explanation
Indices: 593706--593750 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
593696 TACAGTACGC
593706 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
593723 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
593742 TTCTTTTCT
1 TTCTTTTCT
593751 CCAGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:597561 original size:35 final size:37
Alignment explanation
Indices: 597522--597598 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 37
597512 TTATTAAATT
597522 ATATTTAATAATA-ATTATGTTAA-AATATGATTAAA
1 ATATTTAATAATATATTATGTTAATAATATGATTAAA
* * * *
597557 ATATTT-ATATTATATTATTTTAATAATCTTATTAAA
1 ATATTTAATAATATATTATGTTAATAATATGATTAAA
597593 AT-TTTA
1 ATATTTA
597599 TAACAAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 5 0.14
35 18 0.51
36 12 0.34
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (37 bp):
ATATTTAATAATATATTATGTTAATAATATGATTAAA
Found at i:597772 original size:45 final size:44
Alignment explanation
Indices: 597692--597780 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
597682 ACCTCCGTTC
597692 CATTCAACCAAACACAAGAATACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGAATACTATTACGCCTCTATTCCATTA
* * *
597736 CATTCAACCAAACA-ATTGAATTGCTATTACGCCTCTATTCTATTA
1 CATTCAACCAAACACA-AGAA-TACTATTACGCCTCTATTCCATTA
597781 TACTTCTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 1 0.03
44 17 0.43
45 22 0.55
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (44 bp):
CATTCAACCAAACACAAGAATACTATTACGCCTCTATTCCATTA
Found at i:610882 original size:30 final size:30
Alignment explanation
Indices: 610811--610882 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
610801 TTAAAAAAAC
* *
610811 AATTTAACTCTTTTTTAAAGGTTAATGGTCA
1 AATTTAACT-TTTTTTAAAGGTTAAGGGCCA
* * *
610842 ATTTTGACTTTTTTTAAAGGTTGAGGGCCA
1 AATTTAACTTTTTTTAAAGGTTAAGGGCCA
610872 AATTTAACTTT
1 AATTTAACTTT
610883 AAAAAAAGGC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 27 0.79
31 7 0.21
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (30 bp):
AATTTAACTTTTTTTAAAGGTTAAGGGCCA
Found at i:615325 original size:26 final size:26
Alignment explanation
Indices: 615295--615346 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
615285 AATATTTAAA
*
615295 TAAATAATATTTATTTTTATGATAAT
1 TAAATAATATTTATATTTATGATAAT
615321 TAAATAATATTTATATTTATGATAAT
1 TAAATAATATTTATATTTATGATAAT
615347 ATTATTTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
TAAATAATATTTATATTTATGATAAT
Found at i:615352 original size:21 final size:21
Alignment explanation
Indices: 615323--615382 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
615313 ATGATAATTA
*
615323 AATAATATTTATATTTATGAT
1 AATATTATTTATATTTATGAT
** *
615344 AATATTATTTACCTTTGTGAT
1 AATATTATTTATATTTATGAT
* * *
615365 AATTTTATATATTTTTAT
1 AATATTATTTATATTTAT
615383 TTTCTTACAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (21 bp):
AATATTATTTATATTTATGAT
Found at i:617234 original size:21 final size:23
Alignment explanation
Indices: 617210--617257 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
617200 AAAATATAAA
617210 AATAAAATATT-AAAT-TAATTT
1 AATAAAATATTAAAATATAATTT
*
617231 AATAAAATTTTAAAATATAATTT
1 AATAAAATATTAAAATATAATTT
617254 AATA
1 AATA
617258 TAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 10 0.42
22 4 0.17
23 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAAAATATTAAAATATAATTT
Found at i:617338 original size:24 final size:24
Alignment explanation
Indices: 617217--617335 Score: 67
Period size: 24 Copynumber: 5.3 Consensus size: 24
617207 AAAAATAAAA
*
617217 TATTAAATTA-AT-TTAATAAAAT
1 TATTAAATTATATATTAATAATAT
*
617239 T-TTAAAATATA-ATT--TAATA-
1 TATTAAATTATATATTAATAATAT
* * ** *
617258 TA-AAAATAATTATATTACGAATGT
1 TATTAAATTA-TATATTAATAATAT
* * * *
617282 TATCAAATTATATATTATTATTTT
1 TATTAAATTATATATTAATAATAT
617306 TATTAAATTATAT-TTAATAATAT
1 TATTAAATTATATATTAATAATAT
617329 TATTAAA
1 TATTAAA
617336 ATTTAATAAT
Statistics
Matches: 71, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
19 5 0.07
20 6 0.08
21 10 0.14
22 4 0.06
23 17 0.24
24 24 0.34
25 5 0.07
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TATTAAATTATATATTAATAATAT
Found at i:621837 original size:138 final size:138
Alignment explanation
Indices: 621662--622216 Score: 897
Period size: 138 Copynumber: 4.1 Consensus size: 138
621652 AAACATATAT
621662 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* *
621727 AATATAAAAAATTATATAAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
621792 TGGAAAGA
131 TGGAAAGA
* * *
621800 ATATAATTAATATATGAATTTGACTCATACAATATATTAATTGTATATATTTTATCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* *
621865 AATATAAACAGTTATATTAATTTATTTCGGTCAAAATATAAAAGACAT-AGAAATTAATATTCTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGA-AAATTAATATTCTT
621929 TTGGAAAGA
130 TTGGAAAGA
* *
621938 ATATAACTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* *
622003 AA-AT----AATTATATTAATTAATTTCGGTCAAAATATTAAAGACATGAAAGTTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
622063 TGGAAAGA
131 TGGAAAGA
* * *
622071 ATATAATTAATATATGAATTTGATTCATACAAAATAATAATTGTATACATTTTATCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * *
622136 AATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTATTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
*
622201 TAGAAAGA
131 TGGAAAGA
622209 ATATAATT
1 ATATAATT
622217 CTTTTTTCTA
Statistics
Matches: 383, Mismatches: 27, Indels: 14
0.90 0.06 0.03
Matches are distributed among these distances:
133 120 0.31
134 3 0.01
137 3 0.01
138 257 0.67
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
TGGAAAGA
Found at i:622157 original size:271 final size:273
Alignment explanation
Indices: 621662--622214 Score: 930
Period size: 271 Copynumber: 2.0 Consensus size: 273
621652 AAACATATAT
* *
621662 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAACTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
621727 AATATAAAAAATTATATAAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
66 AATAT---AAATTATATAAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
* * *
621792 TGGAAAGAATATAATTAATATATGAATTTGACTCATACAATATATTAATTGTATATATTTTATCG
128 TGGAAAGAATATAATTAATATATGAATTTGACTCATACAAAATAATAATTGTATACATTTTATCG
* * *
621857 AATTTATTAATATAAACAGTTATATTAATTTATTTCGGTCAAAATATAAAAGACATAGAAATTAA
193 AATTTATTAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATAGAAATTAA
* *
621922 TATTCTTTTGGAAAGA
258 TATTATTTTAGAAAGA
621938 ATATAACTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
1 ATATAACTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
* * *
622003 AA-AT-AATTATATTAATTAATTTCGGTCAAAATATTAAAGACATGAAAGTTAATATTCTTTTGG
66 AATATAAATTATATAAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGG
*
622066 AAAGAATATAATTAATATATGAATTTGATTCATACAAAATAATAATTGTATACATTTTATCGAAT
131 AAAGAATATAATTAATATATGAATTTGACTCATACAAAATAATAATTGTATACATTTTATCGAAT
*
622131 TTATTAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATAT
196 TTATTAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATAGAAATTAATAT
622196 TATTTTAGAAAGA
261 TATTTTAGAAAGA
622209 ATATAA
1 ATATAA
622215 TTCTTTTTTC
Statistics
Matches: 262, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
271 195 0.74
275 2 0.01
276 65 0.25
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (273 bp):
ATATAACTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
AATATAAATTATATAAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGG
AAAGAATATAATTAATATATGAATTTGACTCATACAAAATAATAATTGTATACATTTTATCGAAT
TTATTAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATAGAAATTAATAT
TATTTTAGAAAGA
Found at i:623094 original size:24 final size:24
Alignment explanation
Indices: 623067--623126 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
623057 GAATGTTTTG
*
623067 TATTTTATATAATATTAATATAAA
1 TATTTTATTTAATATTAATATAAA
623091 TATTTTTATTTAA-ATTAATATAAA
1 TA-TTTTATTTAATATTAATATAAA
623115 T-TTTTATTTAAT
1 TATTTTATTTAAT
623127 TAAATTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 10 0.30
24 14 0.42
25 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTTATTTAATATTAATATAAA
Found at i:623120 original size:22 final size:24
Alignment explanation
Indices: 623069--623129 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 24
623059 ATGTTTTGTA
*
623069 TTTTATATAATATTAATATAAATAT
1 TTTTATTTAA-ATTAATATAAATAT
623094 TTTTATTTAAATTAATAT-AA-AT
1 TTTTATTTAAATTAATATAAATAT
623116 TTTTATTT-AATTAA
1 TTTTATTTAAATTAA
623130 ATTTTAAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 6 0.17
22 10 0.29
23 2 0.06
24 8 0.23
25 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTATTTAAATTAATATAAATAT
Found at i:623347 original size:31 final size:31
Alignment explanation
Indices: 623319--623379 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
623309 GAAAGTGATT
623319 AAAATAGAAATGATCTAAAACGTGAGTGACC
1 AAAATAGAAATGATCTAAAACGTGAGTGACC
** * * *
623350 GGAATAGAAATTATCTAAAACATTAGTGAC
1 AAAATAGAAATGATCTAAAACGTGAGTGAC
623380 TAAATTGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (31 bp):
AAAATAGAAATGATCTAAAACGTGAGTGACC
Found at i:627515 original size:10 final size:10
Alignment explanation
Indices: 627502--627526 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
627492 AAAAAGTACA
627502 AAAATATTTT
1 AAAATATTTT
627512 AAAATATTTT
1 AAAATATTTT
627522 AAAAT
1 AAAAT
627527 TAATTAAATG
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAAATATTTT
Found at i:634692 original size:56 final size:56
Alignment explanation
Indices: 634583--634693 Score: 124
Period size: 57 Copynumber: 2.0 Consensus size: 56
634573 TTTAAAATAC
* *
634583 TTTATTTTAACTTTTATAAATAAAATTTTTATTTATATTTAATATTATGTTAATTA
1 TTTATTTTAACTTTTATAAATAAAATTTTTATTTAAATTTAATATAATGTTAATTA
634639 TTTATTTTTAA-TTATT-TAAATAAAATATTTT-TATTAAATTTAACT-TAAT-TTAATT
1 TTTA-TTTTAACTT-TTATAAATAAAAT-TTTTAT-TTAAATTTAA-TATAATGTTAATT
634694 TAATTTAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
56 23 0.48
57 24 0.50
58 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.59
Consensus pattern (56 bp):
TTTATTTTAACTTTTATAAATAAAATTTTTATTTAAATTTAATATAATGTTAATTA
Found at i:639627 original size:23 final size:23
Alignment explanation
Indices: 639601--639645 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
639591 TTGTTAGAAA
* *
639601 TAAAAATTCAAAAGTACAAAAAT
1 TAAAAATTAAAAAGTAAAAAAAT
*
639624 TAAAAATTAAAAATTAAAAAAA
1 TAAAAATTAAAAAGTAAAAAAA
639646 ATGTTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
TAAAAATTAAAAAGTAAAAAAAT
Found at i:639635 original size:6 final size:7
Alignment explanation
Indices: 639618--639643 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
639608 TCAAAAGTAC
639618 AAAAATT
1 AAAAATT
639625 AAAAATT
1 AAAAATT
639632 AAAAATT
1 AAAAATT
639639 AAAAA
1 AAAAA
639644 AAATGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:650483 original size:21 final size:20
Alignment explanation
Indices: 650458--650506 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
650448 AATTTCAAGA
* *
650458 AAAATTATTTATAAATTTTT
1 AAAATTATTAATAAATTATT
650478 GAAAATTTATTAATAAATTATT
1 -AAAA-TTATTAATAAATTATT
650500 AAAATTA
1 AAAATTA
650507 AAAGTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 8 0.32
22 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAAATTATTAATAAATTATT
Found at i:656731 original size:9 final size:9
Alignment explanation
Indices: 656719--656743 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
656709 AGTGTTTGAA
656719 GTTAGAATT
1 GTTAGAATT
656728 GTTAGAATT
1 GTTAGAATT
656737 GTTAGAA
1 GTTAGAA
656744 GTTGGTAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (9 bp):
GTTAGAATT
Found at i:663019 original size:20 final size:20
Alignment explanation
Indices: 662978--663025 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
662968 GTAATTGGGT
662978 CACACGGGCGTGTGTCACCTC
1 CACACGGGCGTGTG-CACCTC
662999 CACACGGGCGTGTAG-ACCTC
1 CACACGGGCGTGT-GCACCTC
663019 CACACGG
1 CACACGG
663026 CCTAGGCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.46
21 13 0.50
22 1 0.04
ACGTcount: A:0.19, C:0.38, G:0.29, T:0.15
Consensus pattern (20 bp):
CACACGGGCGTGTGCACCTC
Found at i:663628 original size:38 final size:37
Alignment explanation
Indices: 663544--663636 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
663534 GGTTCTACAA
* * *
663544 ATGTGGTGTGTAGGGTGGATGGACCTATCATGGTCCT
1 ATGTGGTGTGCAGGGTGGATGGACCTATCATGCTCAT
* *
663581 ATGTGGTGTGCAGGGTGGATGGGCTTGAT-ATAGCTCAT
1 ATGTGGTGTGCAGGGTGGATGGACCT-ATCAT-GCTCAT
*
663619 ATGTGGTGTGCATGGTGG
1 ATGTGGTGTGCAGGGTGG
663637 TCGAAGTAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 25 0.52
38 23 0.48
ACGTcount: A:0.16, C:0.11, G:0.41, T:0.32
Consensus pattern (37 bp):
ATGTGGTGTGCAGGGTGGATGGACCTATCATGCTCAT
Found at i:666382 original size:19 final size:19
Alignment explanation
Indices: 666358--666411 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
666348 AATCTTCAAA
*
666358 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
*
666377 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
666396 GATATGCAATCATAGA
1 GATATGCAATCTTAGA
666412 AGATATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:666437 original size:22 final size:21
Alignment explanation
Indices: 666358--666437 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 21
666348 AATCTTCAAA
* *
666358 GATATGCAATCTT--AGATGT
1 GATATGTAATCTTAGAGATAT
666377 GATATGTAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
666396 GATATGCAATCATAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
666418 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
666438 TTAATTTGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
19 28 0.56
22 12 0.24
23 10 0.20
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:667045 original size:37 final size:37
Alignment explanation
Indices: 666969--667045 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
666959 CATACATACG
*
666969 TTTTATAATATATACATATACGTACACATTTTTTAATT
1 TTTTATAATATATACATATACG-ACACATTTTATAATT
* *
667007 TTTTATAA-ATATATATATAC-ACATACTTTTATATATT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATT
667044 TT
1 TT
667046 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.12
36 6 0.18
37 16 0.47
38 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAATATATACATATACGACACATTTTATAATT
Found at i:667470 original size:13 final size:14
Alignment explanation
Indices: 667436--667473 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
667426 TTTTCTTATG
667436 TATATTAGTTTCGTT
1 TATATTA-TTTCGTT
667451 TAT-TTATTT-GTT
1 TATATTATTTCGTT
667463 TATATTATTTC
1 TATATTATTTC
667474 TATGCCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:667500 original size:15 final size:15
Alignment explanation
Indices: 667480--667513 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
667470 TTTCTATGCC
667480 ATTGTTGTATTTATT
1 ATTGTTGTATTTATT
*
667495 ATTGTTGTATTTGTT
1 ATTGTTGTATTTATT
667510 ATTG
1 ATTG
667514 CGACATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (15 bp):
ATTGTTGTATTTATT
Found at i:673048 original size:61 final size:61
Alignment explanation
Indices: 672972--673090 Score: 193
Period size: 61 Copynumber: 2.0 Consensus size: 61
672962 TTCTTATTAA
* *
672972 ATTTTAATAGGATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATAGAATTATTACTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATCAT
* * *
673033 ATTTTAATATAATTATTACTAAATATAATTTAATAAAAATTAAAATATATAATTTAAT
1 ATTTTAATAGAATTATTACTAAATATAATTTAATAAAAATAAAAATAAATAATTTAAT
673091 ATCATTCTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (61 bp):
ATTTTAATAGAATTATTACTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATCAT
Found at i:679597 original size:13 final size:14
Alignment explanation
Indices: 679569--679597 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
679559 TTTAAAAAAG
679569 TTTTAAATTTTATT
1 TTTTAAATTTTATT
679583 TTTTAAATTTT-TT
1 TTTTAAATTTTATT
679596 TT
1 TT
679598 AAATCGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTAAATTTTATT
Found at i:680716 original size:7 final size:7
Alignment explanation
Indices: 680704--680736 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
680694 TAGTCGATTG
680704 GTATTTA
1 GTATTTA
680711 GTATTTA
1 GTATTTA
680718 GTATTTA
1 GTATTTA
*
680725 ATATTTA
1 GTATTTA
680732 GTATT
1 GTATT
680737 ATGTATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:681414 original size:18 final size:18
Alignment explanation
Indices: 681391--681428 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
681381 TGCCAAATGC
* *
681391 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
681409 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
681427 GT
1 GT
681429 TTTCTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Done.