Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008361.1 Hibiscus syriacus cultivar Beakdansim tig00111100_pilon, whole genome shotgun sequence
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: 1124086
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:828666 original size:19 final size:19
Alignment explanation
Indices: 828549--828752 Score: 176
Period size: 19 Copynumber: 11.1 Consensus size: 19
828539 TCTTTTGGTT
*
828549 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
828568 GATAATGAGAATCGCAATGC
1 GA-AATGAAAATCGCAACGC
**
828588 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
828606 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
828622 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
828640 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
828655 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
828675 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
828694 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
828713 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
828732 GAAACGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
828751 GA
1 GA
828753 TTTTGGTTTC
Statistics
Matches: 155, Mismatches: 17, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
14 19 0.12
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 80 0.52
20 44 0.28
21 2 0.01
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:828770 original size:19 final size:19
Alignment explanation
Indices: 828748--828792 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
828738 AAAATCGCAA
* *
828748 TGCGATTTTGGTTTCGTGT
1 TGCGATTTTGATTTCGCGT
*
828767 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
828786 TGCGATT
1 TGCGATT
828793 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.13, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:829438 original size:21 final size:21
Alignment explanation
Indices: 829409--829501 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
829399 ATAGTAAGTA
829409 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
829430 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
829450 TCGCATTGCAATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
829471 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
829491 TCGCATTGCGA
1 TCGCATTGCGA
829502 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:829440 original size:41 final size:41
Alignment explanation
Indices: 829395--829504 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
829385 ATTATCGCAA
*
829395 TGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAATTCGCGT
1 TGCGAT-GTAAGTATTCGCATTGCAATTTTCCCAATTCGCGT
* **
829436 TGCGATTTACTTATTCGCATTGCAATTTTCCCAATTCGCGT
1 TGCGATGTAAGTATTCGCATTGCAATTTTCCCAATTCGCGT
* **
829477 TGCGATTTACTTATTCGCATTGCGAATT
1 TGCGATGTAAGTATTCGCATTGC-AATT
829505 GGGAAAATCG
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 4 0.06
41 55 0.87
42 4 0.06
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (41 bp):
TGCGATGTAAGTATTCGCATTGCAATTTTCCCAATTCGCGT
Found at i:830041 original size:2 final size:2
Alignment explanation
Indices: 830034--830066 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
830024 GTTTAATTTA
830034 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
830067 ATGTTTCATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:830185 original size:21 final size:23
Alignment explanation
Indices: 830160--830201 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
830150 TTTGAAAATT
830160 TTAATTT-T-TTTAATAAAATAA
1 TTAATTTCTATTTAATAAAATAA
*
830181 TTAATTTCTATTTTATAAAAT
1 TTAATTTCTATTTAATAAAAT
830202 GATAACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATTTCTATTTAATAAAATAA
Found at i:835872 original size:43 final size:43
Alignment explanation
Indices: 835815--835900 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
835805 CTGAGATTTA
* *
835815 TGGGTAATAGTCAATTCTAAATGTTATATCATTTCAATCTCTT
1 TGGGTAATAATCAATTCTAAATGCTATATCATTTCAATCTCTT
* *
835858 TGGGTTATAATCAATTCTAAATGCTATATCATTTCAGTCTCTT
1 TGGGTAATAATCAATTCTAAATGCTATATCATTTCAATCTCTT
835901 ACATGGAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (43 bp):
TGGGTAATAATCAATTCTAAATGCTATATCATTTCAATCTCTT
Found at i:842358 original size:17 final size:17
Alignment explanation
Indices: 842312--842363 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 17
842302 ACCTCAAAGA
*
842312 ATAACAATAATTTATTT
1 ATAACAATATTTTATTT
842329 ATAACTGTAAATATTTTATTT
1 ATAAC----AATATTTTATTT
842350 ATAACAATATTTTA
1 ATAACAATATTTTA
842364 ATTAAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 14 0.47
21 16 0.53
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (17 bp):
ATAACAATATTTTATTT
Found at i:843063 original size:53 final size:51
Alignment explanation
Indices: 842988--843087 Score: 164
Period size: 53 Copynumber: 1.9 Consensus size: 51
842978 TGTAATATGA
* *
842988 ATAAAATAAAAAAGTGTAGCACTTAACACATACTTATACCGGTGTAAGTGG
1 ATAAAATAAAAAAATATAGCACTTAACACATACTTATACCGGTGTAAGTGG
843039 ATAAAATAAAAAAAAATATAGCACTTAACACATACTTATACCGGTGTAA
1 ATAAAAT--AAAAAAATATAGCACTTAACACATACTTATACCGGTGTAA
843088 ATATGTACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 7 0.16
53 38 0.84
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (51 bp):
ATAAAATAAAAAAATATAGCACTTAACACATACTTATACCGGTGTAAGTGG
Found at i:845857 original size:17 final size:17
Alignment explanation
Indices: 845837--845879 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
845827 TTTTTTAATT
*
845837 ATTAATTAATATTAAAA
1 ATTAAATAATATTAAAA
* *
845854 ATTAAATATTTTTAAAA
1 ATTAAATAATATTAAAA
845871 ATTAAATAA
1 ATTAAATAA
845880 AGAAAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAAATAATATTAAAA
Found at i:855878 original size:17 final size:17
Alignment explanation
Indices: 855856--855895 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
855846 TTAACCCTAA
855856 AATATTACAAATAAA-AT
1 AATATTACAAA-AAAGAT
*
855873 AATATTATAAAAAAGAT
1 AATATTACAAAAAAGAT
855890 AATATT
1 AATATT
855896 TTTGATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AATATTACAAAAAAGAT
Found at i:855968 original size:36 final size:36
Alignment explanation
Indices: 855873--855968 Score: 140
Period size: 35 Copynumber: 2.7 Consensus size: 36
855863 CAAATAAAAT
* *
855873 AATATTATAAAAAAGATAATATTTTTGATTCAATAAA
1 AATATT-TAAAAAATATAATATTTTCGATTCAATAAA
*
855910 AATA-TTAAAAAATATAAAATTTTCGATTCAATAAA
1 AATATTTAAAAAATATAATATTTTCGATTCAATAAA
*
855945 AATATTTTAAAAATATAATATTTT
1 AATATTTAAAAAATATAATATTTT
855969 AAGTTACATC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 31 0.58
36 18 0.34
37 4 0.08
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (36 bp):
AATATTTAAAAAATATAATATTTTCGATTCAATAAA
Found at i:861662 original size:27 final size:27
Alignment explanation
Indices: 861632--861718 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
861622 CCAACACAAC
*
861632 ACAAAATACACCCTTACTAATTACGCT
1 ACAAAATACACCCTTACTAATTACACT
* * *
861659 ACAAAATTA-AGCACATA-TCA-TACAAC-
1 ACAAAA-TACA-CCCTTACTAATTAC-ACT
861685 ACAAAATACACCCTTACTAATTACACT
1 ACAAAATACACCCTTACTAATTACACT
861712 ACAAAAT
1 ACAAAAT
861719 TAAGCACATA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
25 6 0.13
26 14 0.30
27 20 0.43
28 6 0.13
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.23
Consensus pattern (27 bp):
ACAAAATACACCCTTACTAATTACACT
Found at i:861693 original size:53 final size:53
Alignment explanation
Indices: 861627--861733 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
861617 AAGTTCCAAC
*
861627 ACAACACAAAATACACCCTTACTAATTACGCTACAAAATTAAGCACATATCAT
1 ACAACACAAAATACACCCTTACTAATTACACTACAAAATTAAGCACATATCAT
861680 ACAACACAAAATACACCCTTACTAATTACACTACAAAATTAAGCACATATCAT
1 ACAACACAAAATACACCCTTACTAATTACACTACAAAATTAAGCACATATCAT
861733 A
1 A
861734 TAAACCATCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.22
Consensus pattern (53 bp):
ACAACACAAAATACACCCTTACTAATTACACTACAAAATTAAGCACATATCAT
Found at i:862363 original size:25 final size:26
Alignment explanation
Indices: 862335--862395 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
862325 TAAATTGATT
862335 TTTTTAATAATTTAAT-T-TTGTAATA
1 TTTTTAATAATTTAATGTATTG-AATA
*
862360 TTTTTTAT-ATTTAATGTATTGAATA
1 TTTTTAATAATTTAATGTATTGAATA
*
862385 -TCTTAATAATT
1 TTTTTAATAATT
862396 GTTTATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 12 0.40
25 15 0.50
26 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (26 bp):
TTTTTAATAATTTAATGTATTGAATA
Found at i:863858 original size:26 final size:26
Alignment explanation
Indices: 863852--863916 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
863842 ATATATATAT
863852 AATAAAAAAATAAACAGAAATAATAA
1 AATAAAAAAATAAACAGAAATAATAA
* *
863878 AAT--AAAAATAATCAGTAAAGAATAA
1 AATAAAAAAATAAACAG-AAATAATAA
*
863903 AATTAAAAGAATAA
1 AA-TAAAAAAATAA
863917 TAAAAAGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 11 0.34
25 10 0.31
26 4 0.12
28 7 0.22
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.18
Consensus pattern (26 bp):
AATAAAAAAATAAACAGAAATAATAA
Found at i:863877 original size:24 final size:25
Alignment explanation
Indices: 863857--863910 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
863847 TATATAATAA
*
863857 AAAAATAAACAG-AAATAATAAAAT
1 AAAAATAAACAGTAAAGAATAAAAT
*
863881 AAAAATAATCAGTAAAGAATAAAAT
1 AAAAATAAACAGTAAAGAATAAAAT
*
863906 TAAAA
1 AAAAA
863911 GAATAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (25 bp):
AAAAATAAACAGTAAAGAATAAAAT
Found at i:865958 original size:105 final size:105
Alignment explanation
Indices: 865655--867230 Score: 2237
Period size: 105 Copynumber: 15.1 Consensus size: 105
865645 CATTGTTCCA
* * **
865655 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGGTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-GTTGTTGACAA
* * * *
865719 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * ** * **
865761 AGTCCAACATCCTTCGTTGTGAAGTTGAAATTGATTCTG-AA-T--GAAATT-TTGTTGAGAAGA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
*
865821 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
865861 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
865926 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
865966 ATTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAAT-TTGTTGACAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
* *
866030 AGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
866070 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAAC
*
866135 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
866176 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----GAAGTT--G----T-TTATTGAAAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
866230 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
866270 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTTTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATTGTTGTTGACAAC
*
866335 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
866376 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAAC
866440 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
866481 AGTCCAATATCCTTCGCTGTGAAGTTGAAA-TGGCTCTGAAATTGGGAATTTTTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATTGTTGTTGACAAC
* *
866545 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCAGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
866586 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTATGAAATTATTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
*
866651 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
866691 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAAC
866755 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
866796 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTTTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATTGTTGTTGACAAC
* *
866861 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCAGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
866902 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTATGAAATTATTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
866967 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
867007 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAAAT-TTGTTGACAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
* *
867071 AGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
867111 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAGTGTTTGTTGACAAT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAAC
* * ** * *
867175 CAGCCGCCCCTTCGTCAAGAAGTTGAGCTTGTGTTGTCTTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGG
* *
867217 A-TTCAAGATCCTTC
1 AGTCCAATATCCTTC
867231 ATTGAGAAGT
Statistics
Matches: 1336, Mismatches: 104, Indels: 61
0.89 0.07 0.04
Matches are distributed among these distances:
94 83 0.06
96 1 0.00
98 5 0.00
100 82 0.06
101 1 0.00
102 12 0.01
103 3 0.00
104 215 0.16
105 603 0.45
106 329 0.25
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:866204 original size:43 final size:43
Alignment explanation
Indices: 866143--866298 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 43
866133 ACCAGTGGTC
866143 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
866186 CCTTCGTTGTGAAGTTGAAATTGGGAAGTTGTTTATTGAAAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTT--G-CGTTG--T-CTGGAGTCCA-ATAT
866236 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
866280 CCTTCG-CTGTGAAGTTGAA
1 CCTTCGTC-GTGAAGTTGAA
866299 ATTGGCTCTG
Statistics
Matches: 84, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
42 1 0.01
43 37 0.44
44 1 0.01
45 7 0.08
46 5 0.06
48 5 0.06
49 7 0.08
50 1 0.01
51 20 0.24
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:871047 original size:25 final size:26
Alignment explanation
Indices: 871011--871073 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
871001 TAATATATAT
*
871011 ATAATAAA-AAAAATAAACAG-AAATA
1 ATAA-AAATAAAAATAAACAGTAAAGA
*
871036 ATAAAAATAAAAATAATCAGTAAAGA
1 ATAAAAATAAAAATAAACAGTAAAGA
*
871062 ATAAAATTAAAA
1 ATAAAAATAAAA
871074 GAATAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.09
25 15 0.45
26 15 0.45
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (26 bp):
ATAAAAATAAAAATAAACAGTAAAGA
Found at i:882935 original size:23 final size:23
Alignment explanation
Indices: 882908--882954 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
882898 ATTATAAAAG
882908 ATAAACTAAATACATAAAGTACT
1 ATAAACTAAATACATAAAGTACT
882931 ATAAACTAAATACATAAAGTACT
1 ATAAACTAAATACATAAAGTACT
882954 A
1 A
882955 ATACCTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (23 bp):
ATAAACTAAATACATAAAGTACT
Found at i:889941 original size:14 final size:14
Alignment explanation
Indices: 889922--889955 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
889912 CACATATATA
889922 ATATATGACA-AAAT
1 ATATATGA-AGAAAT
889936 ATATATGAAGAAAT
1 ATATATGAAGAAAT
889950 ATATAT
1 ATATAT
889956 ATATAATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.05
14 18 0.95
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (14 bp):
ATATATGAAGAAAT
Found at i:891427 original size:26 final size:25
Alignment explanation
Indices: 891376--891428 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
891366 TGGATACACG
* * **
891376 TATATTAATAAAATAAATAATTTTT
1 TATATGAATAAAAAAAATAAAATTT
891401 TATATGAATAAACAAAAATAAAATTT
1 TATATGAATAAA-AAAAATAAAATTT
891427 TA
1 TA
891429 AAGTAGATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
TATATGAATAAAAAAAATAAAATTT
Found at i:897699 original size:18 final size:18
Alignment explanation
Indices: 897660--897702 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
897650 TTATAGAATA
*
897660 ATTTTAT-TTTTTTGATT
1 ATTTTATATTTTTTAATT
897677 ATTTTATATTTTTTAACTT
1 ATTTTATATTTTTTAA-TT
897696 -TTTTATA
1 ATTTTATA
897703 AATATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 14 0.61
19 2 0.09
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTATATTTTTTAATT
Found at i:901521 original size:23 final size:22
Alignment explanation
Indices: 901490--901545 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
901480 GGTGACCTTT
*
901490 TGCCATTTTTGTTTCGTTGTCC
1 TGCCATTTTTGTTTCGTCGTCC
901512 TGCCATTTTTGTTTCGTCGTCC
1 TGCCATTTTTGTTTCGTCGTCC
*
901534 TGCCAATTTTGT
1 TGCCATTTTTGT
901546 CCATGCCCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.07, C:0.23, G:0.18, T:0.52
Consensus pattern (22 bp):
TGCCATTTTTGTTTCGTCGTCC
Found at i:908121 original size:249 final size:263
Alignment explanation
Indices: 907558--908141 Score: 623
Period size: 267 Copynumber: 2.2 Consensus size: 263
907548 ATTTTTATTT
* *
907558 AATATATGAATTAGAAACCCGACCTGACACGACACAA-AATAAAAAATATATTTTTTTATTCAAT
1 AATATATGAATTAGAAACCCGACCCGAC-C--CAAAATAATAAAAAA-ATA--TTTTTATTCAAT
* * * *
907622 AAAAATATTAACATAATTGGGAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAAT
60 AAAAACAGTAACATAATTGCGAAAAAATTATATAGAGAGGGGTATTATTGTAATTATTCCTAAAT
* * *
907687 ATATAAGGTAAAATTATATATTTTTTTTCGGTTCGGTCCGGTTTTTTTACCCTAAACTCGAACCC
125 ATATAAGGTAAAATTATATA-TTATTTTCGGTTC-G--CGGTTTTTTCACCCTAAACCCGAACCC
* * *
907752 GACCCGATCCGAATATCACACTTTAAAAAACCTGACTCGGCTCGACCCGAATATCACACTTAAAA
186 GACCCGACCCGAATATCACACTTTAAAAAACCTGACTCGACCCGACCC-AATA-CACAC-TAAAA
*
907817 AATCCGACCCGGCCCG
248 AATCCGACCCGACCCG
* * * ** *
907833 AACAAAATAAAGTT--TCACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAA
1 AA-TATATGAA-TTAGAAACCCGACCCGACCCAAAATAATAAAAAAATATTTTTATTCAATAAAA
* * *
907896 ACAGTGACTTAA-T-CGAAAAAA-TATATAGAGAGGTGTATTATTGTAATTATTCCTAAATATAT
64 ACAGTAACATAATTGCGAAAAAATTATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATAT
* *
907958 AAGGTAAAATTATATA-TATTTTCGGGTT-G-GGTATTTTTCACCCTAAACCCGAACTCTACCCG
129 AAGGTAAAATTATATATTATTTTC-GGTTCGCGGT-TTTTTCACCCTAAACCCGAACCCGACCCG
** *
908020 ACCCGAATATCACAC-TTAAAAAATCC-GAC-CGACCCGA-CC-A-A-A-A-T-AAAGTTTC-AC
192 ACCCGAATATCACACTTTAAAAAA-CCTGACTCGACCCGACCCAATACACACTAAAAAATCCGAC
908074 CCGACCCG
256 CCGACCCG
908082 AATATATGAATTAGAAACCCGACCCGACCCAAAATAATAAAAAAATATTTTTATTCAATA
1 AATATATGAATTAGAAACCCGACCCGACCCAAAATAATAAAAAAATATTTTTATTCAATA
908142 TATGAATAAG
Statistics
Matches: 268, Mismatches: 33, Indels: 42
0.78 0.10 0.12
Matches are distributed among these distances:
247 2 0.01
248 5 0.02
249 54 0.20
250 5 0.02
251 1 0.00
253 1 0.00
254 1 0.00
256 1 0.00
257 1 0.00
259 2 0.01
260 6 0.02
261 14 0.05
262 41 0.15
264 1 0.00
265 6 0.02
266 4 0.01
267 55 0.21
268 7 0.03
269 1 0.00
270 24 0.09
272 6 0.02
273 9 0.03
274 1 0.00
275 13 0.05
276 5 0.02
277 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (263 bp):
AATATATGAATTAGAAACCCGACCCGACCCAAAATAATAAAAAAATATTTTTATTCAATAAAAAC
AGTAACATAATTGCGAAAAAATTATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAA
GGTAAAATTATATATTATTTTCGGTTCGCGGTTTTTTCACCCTAAACCCGAACCCGACCCGACCC
GAATATCACACTTTAAAAAACCTGACTCGACCCGACCCAATACACACTAAAAAATCCGACCCGAC
CCG
Found at i:908331 original size:36 final size:36
Alignment explanation
Indices: 908284--908360 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
908274 ATCGAATTAA
908284 ACGGGGACGGGGAAAAACTGTTTATGCTAAACGGGG
1 ACGGGGACGGGGAAAAACTGTTTATGCTAAACGGGG
* *
908320 ACGGGGACGGGGAAAACCTGTTTATGTTAAACGGGG
1 ACGGGGACGGGGAAAAACTGTTTATGCTAAACGGGG
908356 ACGGG
1 ACGGG
908361 TTTAGTAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.40, T:0.17
Consensus pattern (36 bp):
ACGGGGACGGGGAAAAACTGTTTATGCTAAACGGGG
Found at i:908419 original size:12 final size:12
Alignment explanation
Indices: 908376--908419 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
908366 TAATCCCCAC
908376 CCCGATTACCTGA
1 CCCGA-TACCTGA
* *
908389 CCCGATACCCGG
1 CCCGATACCTGA
*
908401 CCTGATACCTGA
1 CCCGATACCTGA
908413 CCCGATA
1 CCCGATA
908420 AATATTAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.23, C:0.41, G:0.18, T:0.18
Consensus pattern (12 bp):
CCCGATACCTGA
Found at i:909159 original size:14 final size:15
Alignment explanation
Indices: 909112--909162 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
909102 TACTATAATT
* *
909112 TGAATTATTGGAAAA
1 TGAATTACTGAAAAA
**
909127 TGAATTACTGAAATT
1 TGAATTACTGAAAAA
909142 TGAATT-CTGAAAAA
1 TGAATTACTGAAAAA
909156 TGAATTA
1 TGAATTA
909163 TATGAAAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (15 bp):
TGAATTACTGAAAAA
Found at i:909169 original size:30 final size:31
Alignment explanation
Indices: 909091--909169 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 31
909081 TTGATTTTTC
* *
909091 GAAAAATAAATTACTAT--AATTTGAATTATT
1 GAAAAATGAATTA-TATGAAATTTGAATTACT
* *
909121 GGAAAATGAATTA-CTGAAATTTGAATT-CT
1 GAAAAATGAATTATATGAAATTTGAATTACT
909150 GAAAAATGAATTATATGAAA
1 GAAAAATGAATTATATGAAA
909170 AACGTTTTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 13 0.32
30 26 0.65
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (31 bp):
GAAAAATGAATTATATGAAATTTGAATTACT
Found at i:909191 original size:14 final size:14
Alignment explanation
Indices: 909174--909200 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
909164 ATGAAAAACG
909174 TTTTCCGGAAAATA
1 TTTTCCGGAAAATA
909188 TTTTCCGGAAAAT
1 TTTTCCGGAAAAT
909201 GAATTATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
TTTTCCGGAAAATA
Found at i:909577 original size:30 final size:29
Alignment explanation
Indices: 909537--909605 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
909527 TTATTAAAAA
*
909537 ATTATTAAAATATATAAATAA-TATTAT-T
1 ATTATTAAAA-ATATAAAAAATTATTATAT
909565 CATTATTAAAAATATAAAAAATTTATTATAT
1 -ATTATTAAAAATATAAAAAA-TTATTATAT
909596 ATTATTAAAA
1 ATTATTAAAA
909606 TAAAAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 9 0.25
29 10 0.28
30 16 0.44
31 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTATTAAAAATATAAAAAATTATTATAT
Found at i:909578 original size:19 final size:20
Alignment explanation
Indices: 909527--909579 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
909517 TTAAATATCT
909527 TTATTAAAAA-ATTATTAAA
1 TTATTAAAAATATTATTAAA
* *
909546 ATATATAAATAATATTATT-CA
1 TTAT-TAAA-AATATTATTAAA
909567 TTATTAAAAATAT
1 TTATTAAAAATAT
909580 AAAAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 8 0.29
20 8 0.29
21 6 0.21
22 6 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TTATTAAAAATATTATTAAA
Found at i:909640 original size:23 final size:24
Alignment explanation
Indices: 909609--909665 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
909599 ATTAAAATAA
*
909609 AAATATAATAT-CTTATATTATTAT
1 AAATATAATATGATTAT-TTATTAT
909633 -AATATAAT-TGATTATTTATTAT
1 AAATATAATATGATTATTTATTAT
909655 AAATATTAATA
1 AAATA-TAATA
909666 AATATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 8 0.29
23 16 0.57
24 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATATAATATGATTATTTATTAT
Found at i:909673 original size:25 final size:23
Alignment explanation
Indices: 909622--909674 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
909612 TATAATATCT
**
909622 TATA-TTATTATAATATAATTGA
1 TATATTTATTATAATATAATAAA
909644 T-TATTTATTATAAATATTAATAAA
1 TATATTTATTAT-AATA-TAATAAA
909668 TATATTT
1 TATATTT
909675 TAAATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.08
22 8 0.32
23 4 0.16
24 6 0.24
25 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTATTATAATATAATAAA
Found at i:909962 original size:41 final size:41
Alignment explanation
Indices: 909871--909987 Score: 119
Period size: 41 Copynumber: 2.8 Consensus size: 41
909861 ATGAATTACA
* *
909871 TTCCGGAAAACGAATTACGTGAAATAAAAAAG-GAAAACATT
1 TTCC-GAAAACGAATTACGTGAAATAAACACGAGAAAACATT
** * *
909912 TTATGGAAAACAAATTACGTGAAATAAACACGAGAAAATATT
1 TT-CCGAAAACGAATTACGTGAAATAAACACGAGAAAACATT
* *
909954 TTCCGAAAAAACGAATTACATGAAACAAACACGA
1 TTCCG--AAAACGAATTACGTGAAATAAACACGA
909988 ATTAATTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 27 0.44
42 10 0.16
43 24 0.39
ACGTcount: A:0.52, C:0.14, G:0.15, T:0.20
Consensus pattern (41 bp):
TTCCGAAAACGAATTACGTGAAATAAACACGAGAAAACATT
Found at i:913589 original size:17 final size:17
Alignment explanation
Indices: 913558--913590 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
913548 AACATAACGT
913558 TAATATAATTAATATAG
1 TAATATAATTAATATAG
913575 TAAT-TAATTATATATA
1 TAATATAATTA-ATATA
913591 TATATGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TAATATAATTAATATAG
Found at i:924339 original size:18 final size:18
Alignment explanation
Indices: 924316--924354 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
924306 CTTATAATAA
924316 AAAATAAATAAAAAATTT
1 AAAATAAATAAAAAATTT
* * *
924334 AAAATATATAATAATTTT
1 AAAATAAATAAAAAATTT
924352 AAA
1 AAA
924355 TTTTTAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATAAATAAAAAATTT
Found at i:925683 original size:20 final size:20
Alignment explanation
Indices: 925639--925899 Score: 150
Period size: 20 Copynumber: 12.9 Consensus size: 20
925629 AATGACCAAC
*
925639 AAAATTGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
*
925658 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
925678 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
925698 AAAATCGCAACGGTCGA--AAG
1 AAAATCGCAAC-G-CGATTCAG
925718 AAAATCGCAACGCGATCTTCA-
1 AAAATCGCAACGCGA--TTCAG
* *
925739 AAGAATCGCAATGCGATCCA-
1 AA-AATCGCAACGCGATTCAG
* **
925759 AAGAATCGCAATGCGAGCCA-
1 AA-AATCGCAACGCGATTCAG
*
925779 AAGAATCGCAATGCGATTCCA-
1 AA-AATCGCAACGCGATT-CAG
* *
925800 AGAATCGCAATGCGATCTTC-G
1 AAAATCGCAACGCGA--TTCAG
925821 AAGAATCGCAACGCGA-TCGAG
1 AA-AATCGCAACGCGATTC-AG
925842 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
925862 ATAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTCAG
*
925882 AAAATCGCAATGCGATTC
1 AAAATCGCAACGCGATTC
925900 CAAGAATCGC
Statistics
Matches: 203, Mismatches: 20, Indels: 37
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.02
19 19 0.09
20 134 0.66
21 18 0.09
22 28 0.14
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:925769 original size:62 final size:63
Alignment explanation
Indices: 925700--925877 Score: 176
Period size: 62 Copynumber: 2.9 Consensus size: 63
925690 TTGAAAAGAA
925700 AATCGCAACG-GTCGAAAGAAAATCGCAACGCGATCTTCAAAGAATCGCAATGCGATC-CAAAG
1 AATCGCAACGAGTCGAAAGAAAATCGCAACGCGAT-TTCAAAGAATCGCAATGCGATCTCAAAG
* * * *
925762 AATCGCAATGCGAG-CCAAAG--AATCGCAATGCGA-TTCCAAGAATCGCAATGCGATCTTCGAA
1 AATCGCAA--CGAGTCGAAAGAAAATCGCAACGCGATTTCAAAGAATCGCAATGCGATC-TCAAA
925823 G
63 G
* * * *
925824 AATCGCAACGCGATCG--AGAAAATCGCAACGCGA-TTCCAATAATCGCAACGCGAT
1 AATCGCAACGAG-TCGAAAGAAAATCGCAACGCGATTTCAAAGAATCGCAATGCGAT
925878 TGAGAAAATC
Statistics
Matches: 98, Mismatches: 9, Indels: 18
0.78 0.07 0.14
Matches are distributed among these distances:
60 26 0.27
62 64 0.65
64 7 0.07
65 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (63 bp):
AATCGCAACGAGTCGAAAGAAAATCGCAACGCGATTTCAAAGAATCGCAATGCGATCTCAAAG
Found at i:925786 original size:82 final size:82
Alignment explanation
Indices: 925660--925911 Score: 202
Period size: 82 Copynumber: 3.1 Consensus size: 82
925650 GCGATATCAA
** * **
925660 AATCGCAACGCGATTTAGAAAATCGCAA--CGTTGAAAAGAAAATCGCAACGGTCGAAAGAAAAT
1 AATCGCAACGCGATCCAGAAAATCGCAACGCGATGCCAAG--AATCGCAACGGTCGAAAGAAAAT
*
925723 CGCAACGCGATCTTCAAAG
64 CGCAATGCGATCTTCAAAG
* * * *
925742 AATCGCAATGCGATCCA-AAGAATCGCAATGCGA-GCCAAAGAATCGCAATGCGATTC-CAAG--
1 AATCGCAACGCGATCCAGAA-AATCGCAACGCGATGCC-AAGAATCGCAA--CG-GTCGAAAGAA
*
925802 AATCGCAATGCGATCTTCGAAG
61 AATCGCAATGCGATCTTCAAAG
* * * *
925824 AATCGCAACGCGATCGAGAAAATCGCAACGCGATTCCAATAATCGCAAC-G-CGATTGAGAAAAT
1 AATCGCAACGCGATCCAGAAAATCGCAACGCGATGCCAAGAATCGCAACGGTCGA--AAGAAAAT
*
925887 CGCAATGCGA--TTCCAAG
64 CGCAATGCGATCTTCAAAG
925904 AATCGCAA
1 AATCGCAA
925912 AACGGCAAAA
Statistics
Matches: 137, Mismatches: 19, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
77 1 0.01
80 17 0.12
81 2 0.01
82 100 0.73
83 5 0.04
84 10 0.07
85 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.16
Consensus pattern (82 bp):
AATCGCAACGCGATCCAGAAAATCGCAACGCGATGCCAAGAATCGCAACGGTCGAAAGAAAATCG
CAATGCGATCTTCAAAG
Found at i:925791 original size:40 final size:40
Alignment explanation
Indices: 925716--925911 Score: 200
Period size: 40 Copynumber: 4.8 Consensus size: 40
925706 AACGGTCGAA
* * *
925716 AGAAAATCGCAACGCGATCTTCAAAGAATCGCAATGCGATCC
1 AGAAAATCGCAATGCGA--TTCCAAGAATCGCAACGCGATCC
* *
925758 A-AAGAATCGCAATGCGA-GCCAAAGAATCGCAATGCGATTCC
1 AGAA-AATCGCAATGCGATTCC-AAGAATCGCAACGCGA-TCC
* * *
925799 A-AGAATCGCAATGCGATCTTCGAAGAATCGCAACGCGATCG
1 AGAAAATCGCAATGCGA--TTCCAAGAATCGCAACGCGATCC
* * **
925840 AGAAAATCGCAACGCGATTCCAATAATCGCAACGCGATTG
1 AGAAAATCGCAATGCGATTCCAAGAATCGCAACGCGATCC
925880 AGAAAATCGCAATGCGATTCCAAGAATCGCAA
1 AGAAAATCGCAATGCGATTCCAAGAATCGCAA
925912 AACGGCAAAA
Statistics
Matches: 132, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
39 1 0.01
40 79 0.60
41 10 0.08
42 41 0.31
43 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.16
Consensus pattern (40 bp):
AGAAAATCGCAATGCGATTCCAAGAATCGCAACGCGATCC
Found at i:925907 original size:20 final size:20
Alignment explanation
Indices: 925720--925911 Score: 176
Period size: 20 Copynumber: 9.4 Consensus size: 20
925710 GTCGAAAGAA
* *
925720 AATCGCAACGCGATCTTCAAAG
1 AATCGCAATGCGA--TTCCAAG
925742 AATCGCAATGCGA-TCCAAAG
1 AATCGCAATGCGATTCC-AAG
*
925762 AATCGCAATGCGA-GCCAAAG
1 AATCGCAATGCGATTCC-AAG
925782 AATCGCAATGCGATTCCAAG
1 AATCGCAATGCGATTCCAAG
*
925802 AATCGCAATGCGATCTTCGAAG
1 AATCGCAATGCGA--TTCCAAG
* * *
925824 AATCGCAACGCGA-TCGAGAA
1 AATCGCAATGCGATTCCA-AG
* *
925844 AATCGCAACGCGATTCCAAT
1 AATCGCAATGCGATTCCAAG
* * *
925864 AATCGCAACGCGATT-GAGAA
1 AATCGCAATGCGATTCCA-AG
925884 AATCGCAATGCGATTCCAAG
1 AATCGCAATGCGATTCCAAG
925904 AATCGCAA
1 AATCGCAA
925912 AACGGCAAAA
Statistics
Matches: 148, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
19 7 0.05
20 105 0.71
21 6 0.04
22 30 0.20
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
AATCGCAATGCGATTCCAAG
Found at i:926033 original size:6 final size:6
Alignment explanation
Indices: 926022--926054 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
926012 GACACGTATT
926022 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
926055 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:931184 original size:19 final size:20
Alignment explanation
Indices: 931145--931195 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
931135 TTGGTTCATG
931145 TAAAAATA-AAT-ATTTAAAT
1 TAAAAATATAATAATTT-AAT
931164 TAAAAATATAATAATTT-AT
1 TAAAAATATAATAATTTAAT
*
931183 TAAATATATAATA
1 TAAAAATATAATA
931196 GGGTAGGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 22 0.76
20 3 0.10
21 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAATATAATAATTTAAT
Found at i:963462 original size:14 final size:14
Alignment explanation
Indices: 963445--963472 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
963435 AGCATAACAA
963445 AATTATATAACTAT
1 AATTATATAACTAT
963459 AATTATATAACTAT
1 AATTATATAACTAT
963473 TCTTTCACTT
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:964231 original size:11 final size:11
Alignment explanation
Indices: 964215--964239 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
964205 AAAATATTAA
964215 ATATATTATTT
1 ATATATTATTT
964226 ATATATTATTT
1 ATATATTATTT
964237 ATA
1 ATA
964240 AATTTCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATATTATTT
Found at i:965997 original size:30 final size:30
Alignment explanation
Indices: 965961--966019 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
965951 CACAATGTCT
965961 CAACACAGCCTCAACATTTCTCTTAGCAAC
1 CAACACAGCCTCAACATTTCTCTTAGCAAC
965991 CAACACAGCCTCAACATTTCTCTTAGCAA
1 CAACACAGCCTCAACATTTCTCTTAGCAA
966020 ACACTACGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.36, G:0.07, T:0.24
Consensus pattern (30 bp):
CAACACAGCCTCAACATTTCTCTTAGCAAC
Found at i:971850 original size:12 final size:12
Alignment explanation
Indices: 971833--971859 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
971823 AAAGGACAAA
971833 ACAATACAAAAG
1 ACAATACAAAAG
971845 ACAATACAAAAG
1 ACAATACAAAAG
971857 ACA
1 ACA
971860 TACTCATCGC
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:0.67, C:0.19, G:0.07, T:0.07
Consensus pattern (12 bp):
ACAATACAAAAG
Found at i:972102 original size:2 final size:2
Alignment explanation
Indices: 972097--972137 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
972087 ATATTAAATT
972097 TA TA TA TA TA TA TA TA TA TA T- 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
972138 AACATTCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:973046 original size:179 final size:184
Alignment explanation
Indices: 972746--973110 Score: 677
Period size: 179 Copynumber: 2.0 Consensus size: 184
972736 TTCATCTGAT
972746 AAAAAATGACACATATCATCATTTATTAAAGGAGAAAAATAAAAAAACAAAGATACAAACTAACA
1 AAAAAATGACACATATCATCATTTATTAAAGGAGAAAAATAAAAAAACAAAGATACAAACTAACA
972811 GATTTAAAACTAGATCTTTTAGGGGAGTAACTCAACACCCTTAACCAATATAGTAATCCTTAAAC
66 GATTTAAAACTAGATCTTTTAGGGGAGTAACTCAACACCCTTAACCAATATAGTAATCCTTAAAC
972876 -TTATA-TA-GGATAGAATTAAAATTGAAATCGGTATTAA-A-ATTATTAAGGG
131 TTTATATTAGGGATAGAATTAAAATTGAAATCGGTATTAATATATTATTAAGGG
972925 AAAAAATGACACATATCATCATTTATTAAAGGAGAAAAATAAAAAAACAAAGATACAAACTAACA
1 AAAAAATGACACATATCATCATTTATTAAAGGAGAAAAATAAAAAAACAAAGATACAAACTAACA
972990 GATTTAAAACTAGATCTTTTAGGGGAGTAACTCAACACCCTTAACCAATATAGTAATCCTTAAAC
66 GATTTAAAACTAGATCTTTTAGGGGAGTAACTCAACACCCTTAACCAATATAGTAATCCTTAAAC
973055 TTATTATATTAGGGATAGAATTAAAATTGAAATCGGTATTAATATATTATTAAGGG
131 -T-TTATATTAGGGATAGAATTAAAATTGAAATCGGTATTAATATATTATTAAGGG
973111 TAAACTACAA
Statistics
Matches: 179, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
179 130 0.73
182 5 0.03
183 2 0.01
184 30 0.17
185 1 0.01
186 11 0.06
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (184 bp):
AAAAAATGACACATATCATCATTTATTAAAGGAGAAAAATAAAAAAACAAAGATACAAACTAACA
GATTTAAAACTAGATCTTTTAGGGGAGTAACTCAACACCCTTAACCAATATAGTAATCCTTAAAC
TTTATATTAGGGATAGAATTAAAATTGAAATCGGTATTAATATATTATTAAGGG
Found at i:974071 original size:36 final size:36
Alignment explanation
Indices: 974019--974088 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
974009 TTAATCCAAT
*
974019 TCTTCTTTTTCTCTCCCTCGGATGTGGTTATTTAAG
1 TCTTCTTTTTCACTCCCTCGGATGTGGTTATTTAAG
*
974055 TCTTCTTTTTCACTCCCTCGGATGTGGTTGTTTA
1 TCTTCTTTTTCACTCCCTCGGATGTGGTTATTTA
974089 GGGTTTTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.10, C:0.23, G:0.17, T:0.50
Consensus pattern (36 bp):
TCTTCTTTTTCACTCCCTCGGATGTGGTTATTTAAG
Found at i:975701 original size:20 final size:20
Alignment explanation
Indices: 975676--975718 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
975666 ACTAAGAGCC
*
975676 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
975696 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
975716 CAT
1 CAT
975719 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:977673 original size:68 final size:66
Alignment explanation
Indices: 977569--977722 Score: 154
Period size: 68 Copynumber: 2.3 Consensus size: 66
977559 TTAATATGTA
* * **
977569 GTGTTCAAATAAATTTTTTGT-CGTATTAAATCATTTTGTATGCTA-AT-GTATTGGTATATATG
1 GTGTTCAAAT-AATTTTTTATACATATTAAATCATTTT-TATG-TATATAGTATTAATATATATG
977631 TGTCT
63 TGT-T
* * *
977636 GTGTTCAAATAATTTTTTATACCATATTATATTATTTTTGTGTATATAGTATTAATATATATGTG
1 GTGTTCAAATAATTTTTTATA-CATATTAAATCATTTTTATGTATATAGTATTAATATATATGTG
977701 TT
65 TT
* *
977703 GTG-TCAAATCATTTTGTATA
1 GTGTTCAAATAATTTTTTATA
977723 TTAACTTATT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
66 26 0.35
67 19 0.26
68 29 0.39
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (66 bp):
GTGTTCAAATAATTTTTTATACATATTAAATCATTTTTATGTATATAGTATTAATATATATGTGT
T
Found at i:986255 original size:35 final size:35
Alignment explanation
Indices: 986216--986282 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
986206 AATAACACTA
*
986216 TTGAAGCAACTTATTCTTCGAGACATAATTTGTTG
1 TTGAAGCAACTTATTCTTCGACACATAATTTGTTG
986251 TTGAAGCAACTTATTCTTCGACACATAATTTG
1 TTGAAGCAACTTATTCTTCGACACATAATTTG
986283 GCCCCAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (35 bp):
TTGAAGCAACTTATTCTTCGACACATAATTTGTTG
Found at i:993825 original size:260 final size:256
Alignment explanation
Indices: 993231--993850 Score: 861
Period size: 260 Copynumber: 2.4 Consensus size: 256
993221 CCGAGATCTG
* * *
993231 ACCCGACCAAAATAAAGTTTTA-CCGACCCGACCCGAATGTATGAATTAGAAACCCGACCCGACC
1 ACCCGACCAAAATAAAGTTTCACCCGACCCGAACCGAATATATGAATTAGAAA-CCGA-CCGACC
* * * *
993295 CAAAATAATAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTAAAATATATATATATAG
64 CGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTAAAAAAAATATATATAG
*
993360 AGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGAGACGGGTCG
129 AGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATATTTT-------GTCG
* * *
993425 GGTCGGGTATTTTTCACCCTAAACCCAAACCCGACTCGACCCGAATATCACACTTAAAAAAACTG
187 GATCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCGAATATCACACTTAAAAAAACCG
*
993490 ACTCA
252 ACCCA
*
993495 ACCCGACCAAAATAAAGTTTCACCCGACCC-AACCTGAATATATGAATTAGAAATCCGACACGAG
1 ACCCGACCAAAATAAAGTTTCACCCGACCCGAACC-GAATATATGAATTAGAAA-CCGAC-CGAC
*
993559 CCGAAATAATAATAAAAATATATTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAAATTATA
63 CCGAAATAATAA-AAAAATATTTTTATTCAATAAAAACAGTGACTTAATT--AAAAAAAA-TATA
*
993624 TATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTT-TCGGA
124 TATAGAGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTGTCGGA
* *
993688 TCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTT-AAAAAACCGAC
189 TCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCGAATATCACACTTAAAAAAACCGAC
*
993752 CCG
254 CCA
** *
993755 ATGCGACCAAAATAAAATTTCACCCGACCCGAACCGAATATATGAATTAGAAACCTGACCTGACC
1 ACCCGACCAAAATAAAGTTTCACCCGACCCGAACCGAATATATGAATTAGAAACC-GACC-GACC
993820 CGAAATAATAAAAAAATATTTTTATTCAATA
64 CGAAATAATAAAAAAATATTTTTATTCAATA
993851 TATAAATAAG
Statistics
Matches: 322, Mismatches: 24, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
259 22 0.07
260 73 0.23
261 58 0.18
264 25 0.08
265 42 0.13
266 35 0.11
268 6 0.02
269 61 0.19
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (256 bp):
ACCCGACCAAAATAAAGTTTCACCCGACCCGAACCGAATATATGAATTAGAAACCGACCGACCCG
AAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTAAAAAAAATATATATAGAG
GGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTGTCGGATCGGGTA
TTTTTCACCCTAAACCCAAACCCGACCCGACCCGAATATCACACTTAAAAAAACCGACCCA
Found at i:1008173 original size:124 final size:129
Alignment explanation
Indices: 1007942--1008197 Score: 477
Period size: 125 Copynumber: 2.0 Consensus size: 129
1007932 TTTTTTCCTT
1007942 TTGCATATTAATTTTTTATCTTGTTTATAATTATACATGCATTTCTAATAAAAAAAAGTTTTAAT
1 TTGCATATTAATTTTTTATCTTGTTTATAATTATACATGCATTTCTAATAAAAAAAAGTTTTAAT
1008007 CTTTTTTTAAAGATTCAAGATAATATTTTGATTAAGATGATTAAT-AAATAATCTTCGAAATAG
66 CTTTTTTTAAAGATTCAAGATAATATTTTGATTAAGATGATTAATAAAATAATCTTCGAAATAG
1008070 TTGCATATTAATTTTTTATCTTGTTTATAA-T-TACATGCATTTCTAAT-AAAAAAAGTTTTAAT
1 TTGCATATTAATTTTTTATCTTGTTTATAATTATACATGCATTTCTAATAAAAAAAAGTTTTAAT
1008132 CTTTTTTTAAAGATTC-AGATAATATTTTGATTAAGATGATTAATAAAATAATCTTCGAAATAG
66 CTTTTTTTAAAGATTCAAGATAATATTTTGATTAAGATGATTAATAAAATAATCTTCGAAATAG
1008195 TTG
1 TTG
1008198 AAATGCGATA
Statistics
Matches: 127, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
124 28 0.22
125 52 0.41
126 16 0.13
127 1 0.01
128 30 0.24
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (129 bp):
TTGCATATTAATTTTTTATCTTGTTTATAATTATACATGCATTTCTAATAAAAAAAAGTTTTAAT
CTTTTTTTAAAGATTCAAGATAATATTTTGATTAAGATGATTAATAAAATAATCTTCGAAATAG
Found at i:1013326 original size:17 final size:17
Alignment explanation
Indices: 1013306--1013342 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1013296 GTGATATTAC
1013306 AATTATACCCATAATTT
1 AATTATACCCATAATTT
*
1013323 AATTATATCCATAATTT
1 AATTATACCCATAATTT
1013340 AAT
1 AAT
1013343 AATATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTATACCCATAATTT
Found at i:1013347 original size:17 final size:17
Alignment explanation
Indices: 1013314--1013347 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1013304 ACAATTATAC
*
1013314 CCATAATTTAATTATAT
1 CCATAATTTAATAATAT
1013331 CCATAATTTAATAATAT
1 CCATAATTTAATAATAT
1013348 ATTAACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
CCATAATTTAATAATAT
Found at i:1014841 original size:15 final size:16
Alignment explanation
Indices: 1014821--1014860 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1014811 TTTACTTCAT
*
1014821 AATGATT-AAGCGCTG
1 AATGATTCAAACGCTG
*
1014836 AATGATTCAAATGCTG
1 AATGATTCAAACGCTG
1014852 AATGATTCA
1 AATGATTCA
1014861 GAGGCTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (16 bp):
AATGATTCAAACGCTG
Found at i:1022307 original size:89 final size:89
Alignment explanation
Indices: 1022156--1022336 Score: 353
Period size: 89 Copynumber: 2.0 Consensus size: 89
1022146 ATGGTTGATG
1022156 TCCATGAGTTAAATAGCCAGGAGAGGGACTCTGCAATCTCACGTTACAAGGAGAAAAAGAAAACA
1 TCCATGAGTTAAATAGCCAGGAGAGGGACTCTGCAATCTCACGTTACAAGGAGAAAAAGAAAACA
1022221 ACGAGGTATTTGCTTTCACTTTGT
66 ACGAGGTATTTGCTTTCACTTTGT
1022245 TCCATGAGTTAAATAGCCAGGAGAGGGACTCTGCAATCTCACGTTACAAGGAGAAAAAGAAAACA
1 TCCATGAGTTAAATAGCCAGGAGAGGGACTCTGCAATCTCACGTTACAAGGAGAAAAAGAAAACA
*
1022310 AGGAGGTATTTGCTTTCACTTTGT
66 ACGAGGTATTTGCTTTCACTTTGT
1022334 TCC
1 TCC
1022337 TTACTATCCA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (89 bp):
TCCATGAGTTAAATAGCCAGGAGAGGGACTCTGCAATCTCACGTTACAAGGAGAAAAAGAAAACA
ACGAGGTATTTGCTTTCACTTTGT
Found at i:1023171 original size:16 final size:16
Alignment explanation
Indices: 1023150--1023187 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1023140 AGGTGGCGAA
1023150 AGGCGCATCCCCGGGG
1 AGGCGCATCCCCGGGG
1023166 AGGCGCATCCCCGGGG
1 AGGCGCATCCCCGGGG
*
1023182 ACGCGC
1 AGGCGC
1023188 TTTACCCGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.13, C:0.39, G:0.42, T:0.05
Consensus pattern (16 bp):
AGGCGCATCCCCGGGG
Found at i:1023865 original size:24 final size:26
Alignment explanation
Indices: 1023803--1023865 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
1023793 GTTATTTTAA
1023803 TAAAAAATAATATTTATATAATTATAT
1 TAAAAAATAATA-TTATATAATTATAT
* *
1023830 TAATATAA-AATA-TA-ATAATTATTT
1 TAA-AAAATAATATTATATAATTATAT
1023854 TAAAAAATAATA
1 TAAAAAATAATA
1023866 ACTTAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 3 0.10
24 16 0.52
25 2 0.06
27 7 0.23
28 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAAAAATAATATTATATAATTATAT
Found at i:1024158 original size:60 final size:61
Alignment explanation
Indices: 1024050--1024192 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 61
1024040 CATTTAATGA
* * * * *
1024050 AAGGCGCGTCCCCGGGGATGCGCCTTTCACACGTGGTAACCGAATCAGCAATATCCCGTG-
1 AAGGCGCGTCCCCGGGGATGCGCCTTCCACACGGGGCAACCGAATCAGCAATAACCCGGGT
* * *
1024110 AAGGCGCGTCCCTGGGGATGCGCCTTCCACACGGGGCAGCC-AACTCAGCATTAACCCGGGT
1 AAGGCGCGTCCCCGGGGATGCGCCTTCCACACGGGGCAACCGAA-TCAGCAATAACCCGGGT
* *
1024171 AAAGCGCGTCCCCAGGGATGCG
1 AAGGCGCGTCCCCGGGGATGCG
1024193 TCTTTCGCAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 2 0.03
60 49 0.70
61 19 0.27
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (61 bp):
AAGGCGCGTCCCCGGGGATGCGCCTTCCACACGGGGCAACCGAATCAGCAATAACCCGGGT
Found at i:1030199 original size:25 final size:27
Alignment explanation
Indices: 1030157--1030215 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
1030147 ATCTAACAAT
* *
1030157 ATATTTTAAAAAT-TTTAATA-ATAAA
1 ATATTATAAAAATATTAAATATATAAA
* *
1030182 ATATTATAATAATATTAAATATGTAAA
1 ATATTATAAAAATATTAAATATATAAA
1030209 ATATTAT
1 ATATTAT
1030216 TATTATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 11 0.39
26 6 0.21
27 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
ATATTATAAAAATATTAAATATATAAA
Found at i:1035911 original size:21 final size:21
Alignment explanation
Indices: 1035885--1035927 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1035875 AATAGCTAGC
1035885 GAGGAAGATCACGTCTTCCTT
1 GAGGAAGATCACGTCTTCCTT
1035906 GAGGAAGATCACGTCTTCCTT
1 GAGGAAGATCACGTCTTCCTT
1035927 G
1 G
1035928 TAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (21 bp):
GAGGAAGATCACGTCTTCCTT
Found at i:1040974 original size:3 final size:3
Alignment explanation
Indices: 1040966--1040999 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1040956 TGTAATCACC
1040966 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1041000 CAAATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1047740 original size:2 final size:2
Alignment explanation
Indices: 1047733--1047761 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1047723 TCCACTAATC
1047733 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1047762 TTCTCAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1053593 original size:2 final size:2
Alignment explanation
Indices: 1053586--1053617 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1053576 TTATAAACTA
1053586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1053618 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1054224 original size:20 final size:18
Alignment explanation
Indices: 1054186--1054224 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1054176 TGTATATTAT
*
1054186 ATCCAAAGAACAAATAAA
1 ATCCAAAGAACAAACAAA
1054204 ATCCAAGAGAATCAAACAAA
1 ATCCAA-AGAA-CAAACAAA
1054224 A
1 A
1054225 CCCCAGATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.64, C:0.18, G:0.08, T:0.10
Consensus pattern (18 bp):
ATCCAAAGAACAAACAAA
Found at i:1055951 original size:191 final size:190
Alignment explanation
Indices: 1055627--1056007 Score: 708
Period size: 191 Copynumber: 2.0 Consensus size: 190
1055617 ACGATGAACT
*
1055627 TGCAGTCTCTTCACGTTTCCGCAGTGTTTTCACGATCAAGGTCTGGAGTAAGTTCATAACTTGAA
1 TGCAGTCTCTTCACGTTCCCGCAGTGTTTTCACGATCAAGGTCTGGAGTAAGTTCATAACTTGAA
1055692 CAGCATGCACAAGAGCCGTCAATGGATCGGACATATGTTACCAGAGAACAACAATCAACATAAGC
66 CAGCATGCACAAGAGCCGTCAATGGATCGGACATATGTTACCAGAGAACAACAATCAACATAAGC
1055757 TGCTTCATTTTACGAATATTTTAAGTACATCTTTGATCTAACAATCTCCCGGATATTTACC
131 TGCTTCATTTTACGAATATTTTAAGTACATCTTTGATCTAACAATCTCCCGG-TATTTACC
*
1055818 TGCAGTCTCTTCACGTTCCCGCAGTGTTTTCACGATCAAGGTCTGGAGTAAGTTCATTACTTGAA
1 TGCAGTCTCTTCACGTTCCCGCAGTGTTTTCACGATCAAGGTCTGGAGTAAGTTCATAACTTGAA
* * *
1055883 CAGCATGCACAAGAGCCGTCAATGGATCGGACATCTTTTACCAGAGAACAATAATCAACATAAGC
66 CAGCATGCACAAGAGCCGTCAATGGATCGGACATATGTTACCAGAGAACAACAATCAACATAAGC
1055948 TGCTTCATTTTACGAATATTTTAAGTACATCTTTGATCTAACAATCTCCCGGTATTTACC
131 TGCTTCATTTTACGAATATTTTAAGTACATCTTTGATCTAACAATCTCCCGGTATTTACC
1056008 CGAGTCATAT
Statistics
Matches: 185, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
190 8 0.04
191 177 0.96
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (190 bp):
TGCAGTCTCTTCACGTTCCCGCAGTGTTTTCACGATCAAGGTCTGGAGTAAGTTCATAACTTGAA
CAGCATGCACAAGAGCCGTCAATGGATCGGACATATGTTACCAGAGAACAACAATCAACATAAGC
TGCTTCATTTTACGAATATTTTAAGTACATCTTTGATCTAACAATCTCCCGGTATTTACC
Found at i:1057479 original size:28 final size:28
Alignment explanation
Indices: 1057425--1057481 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1057415 TTAAATAAGG
* *
1057425 TGATTTATTTATTTATTAAAAATATATA
1 TGATTTATTTATTTATAAAAAAAATATA
1057453 TGATTTATTTATTT-TAAAAAGAAATATA
1 TGATTTATTTATTTATAAAAA-AAATATA
1057481 T
1 T
1057482 AAAGATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (28 bp):
TGATTTATTTATTTATAAAAAAAATATA
Found at i:1059069 original size:174 final size:176
Alignment explanation
Indices: 1058779--1059128 Score: 659
Period size: 174 Copynumber: 2.0 Consensus size: 176
1058769 TTATTGGTGA
*
1058779 CTTTGTTCCATTTTTAAACAACTTTAGGATTAAATTAAAAAGGAGTTACAAGTACAATGATTAGA
1 CTTTGTTCCATTTTTAAACAACTTTAGGATTAAATTAAAAAGAAGTTACAAGTACAATGATTAGA
* *
1058844 ATGAAAAAAAATAGAAATTGGGATAAACCGTGTGTTTACTGTGATGTTTCAAATATACTTATATT
66 ATGAAAAAAAATAGAAATTGGGATAAACCGTGTGTTTAATGTGATGTTTCAAATATAATTATATT
1058909 GTAAAACTTTGAAA-GTCGTACC-TTGTGTTTGTGTGTTTAATTTG
131 GTAAAACTTTGAAATGTCGTACCTTTGTGTTTGTGTGTTTAATTTG
1058953 CTTTGTTCCATTTTTAAACAACTTTAGGATTAAATTAAAAAGAAGTTACAAGTACAATGATTAGA
1 CTTTGTTCCATTTTTAAACAACTTTAGGATTAAATTAAAAAGAAGTTACAAGTACAATGATTAGA
1059018 ATGAAAAAAAATAGAAATTGGGATAAACCGTGTGTTTAATGTGATGTTTCAAATATAATTATATT
66 ATGAAAAAAAATAGAAATTGGGATAAACCGTGTGTTTAATGTGATGTTTCAAATATAATTATATT
1059083 GTAAAACTTTGAAATGTCGTACCTTTGTGTTTGTGTGTTTAATTTG
131 GTAAAACTTTGAAATGTCGTACCTTTGTGTTTGTGTGTTTAATTTG
1059129 AGATGATTTT
Statistics
Matches: 171, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
174 141 0.82
175 8 0.05
176 22 0.13
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (176 bp):
CTTTGTTCCATTTTTAAACAACTTTAGGATTAAATTAAAAAGAAGTTACAAGTACAATGATTAGA
ATGAAAAAAAATAGAAATTGGGATAAACCGTGTGTTTAATGTGATGTTTCAAATATAATTATATT
GTAAAACTTTGAAATGTCGTACCTTTGTGTTTGTGTGTTTAATTTG
Found at i:1060521 original size:12 final size:12
Alignment explanation
Indices: 1060504--1060528 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1060494 TAGGTAAAAA
1060504 AAATAATTTTTT
1 AAATAATTTTTT
1060516 AAATAATTTTTT
1 AAATAATTTTTT
1060528 A
1 A
1060529 CTAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATAATTTTTT
Found at i:1060812 original size:15 final size:14
Alignment explanation
Indices: 1060792--1060846 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
1060782 TGTTTGTTAC
1060792 AATTTGAATTACTAG
1 AATTTGAATTACT-G
1060807 AATTTGAATTACTG
1 AATTTGAATTACTG
** *
1060821 AAAAATAAATTACTGG
1 -AATTTGAATTACT-G
1060837 AATTTGAATT
1 AATTTGAATT
1060847 CTGTAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 1 0.03
15 30 0.94
16 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (14 bp):
AATTTGAATTACTG
Found at i:1060832 original size:30 final size:29
Alignment explanation
Indices: 1060798--1060861 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
1060788 TTACAATTTG
1060798 AATTACTAGAATTTGAATTACTGAAAAATA
1 AATTACTAGAATTTGAATT-CTGAAAAATA
* *
1060828 AATTACTGGAATTTGAATTCTGTAAAATA
1 AATTACTAGAATTTGAATTCTGAAAAATA
1060857 AATTA
1 AATTA
1060862 TACATTTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (29 bp):
AATTACTAGAATTTGAATTCTGAAAAATA
Found at i:1061243 original size:28 final size:29
Alignment explanation
Indices: 1061203--1061279 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 29
1061193 CTTTACTAAA
1061203 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTA-TTAAATATATAAATAATTATTAT
1061232 -TCATTATTAAATATATAAA-AATTATTAT
1 AT-ATTATTAAATATATAAATAATTATTAT
*
1061260 ATATTATTAAA-ATAGAAATA
1 ATATTATTAAATATATAAATA
1061280 TAATATCTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
27 8 0.19
28 30 0.70
29 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATTATTAAATATATAAATAATTATTAT
Found at i:1061327 original size:21 final size:23
Alignment explanation
Indices: 1061298--1061348 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
1061288 TATATTATAT
*
1061298 TATTATAAATA-TTAATAAAT-A
1 TATTTTAAATATTTAATAAATAA
1061319 TATTTTAAATATTTTAATAAATAA
1 TATTTTAAATA-TTTAATAAATAA
1061343 TATTTT
1 TATTTT
1061349 GATGAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 10 0.38
23 9 0.35
24 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTAAATATTTAATAAATAA
Found at i:1061578 original size:42 final size:42
Alignment explanation
Indices: 1061532--1061638 Score: 169
Period size: 42 Copynumber: 2.5 Consensus size: 42
1061522 CTGGAAAATG
* *
1061532 AATTACGTGAAACAAACACGGGAAAACATTTTCCGAAAAACA
1 AATTACGTGAAACAAACACGAGAAAACATTTTCCAAAAAACA
* *
1061574 AATTACGTGAAACAAACAAGAGAAAACATTTTCCAAAAAACG
1 AATTACGTGAAACAAACACGAGAAAACATTTTCCAAAAAACA
*
1061616 AATTACATGAAACAAACACGAGA
1 AATTACGTGAAACAAACACGAGA
1061639 TTTCGGGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16
Consensus pattern (42 bp):
AATTACGTGAAACAAACACGAGAAAACATTTTCCAAAAAACA
Found at i:1062092 original size:9 final size:9
Alignment explanation
Indices: 1062030--1062099 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 9
1062020 TTAATTTATC
*
1062030 TAAAAATTG
1 TAAAAATTA
*
1062039 TAGAAA-TA
1 TAAAAATTA
1062047 TTAAAAATGTA
1 -TAAAAAT-TA
*
1062058 TTAAAAATTC
1 -TAAAAATTA
1062068 T-AAAA-TA
1 TAAAAATTA
1062075 TCAAAAATTA
1 T-AAAAATTA
1062085 TAAAAATTA
1 TAAAAATTA
1062094 TAAAAA
1 TAAAAA
1062100 GTTTACGTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 29 0.58
10 4 0.08
11 10 0.20
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1070808 original size:10 final size:11
Alignment explanation
Indices: 1070795--1070831 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
1070785 GTTTGATGAT
1070795 TTCTCT-TTGA
1 TTCTCTCTTGA
1070805 TTCTCTCTTGA
1 TTCTCTCTTGA
*
1070816 TTCT-TGTTGA
1 TTCTCTCTTGA
1070826 TTCTCT
1 TTCTCT
1070832 TGTTTCTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.08, C:0.22, G:0.11, T:0.59
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:1078002 original size:2 final size:2
Alignment explanation
Indices: 1077995--1078026 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1077985 GAAATTATCG
1077995 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
1078027 TATGCATGAT
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:1083904 original size:2 final size:2
Alignment explanation
Indices: 1083897--1083923 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1083887 ACTGACCATG
1083897 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
1083924 TTATCTTAAT
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:1097956 original size:36 final size:40
Alignment explanation
Indices: 1097916--1097993 Score: 92
Period size: 38 Copynumber: 2.0 Consensus size: 40
1097906 CGAGTTGGGT
*
1097916 TCGGA-TCGGGTGAAAT-CTTGTT-TCATGT-GGGTCGGG
1 TCGGATTCGGGTGAAATCCTTGTTCTCAGGTCGGGTCGGG
* *
1097952 TCGGATTTCGGGTGGAGTCCTTGTTCTCAGGTCGGGTCGGG
1 TCGGA-TTCGGGTGAAATCCTTGTTCTCAGGTCGGGTCGGG
1097993 T
1 T
1097994 TGACCAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 5 0.15
38 9 0.26
39 6 0.18
40 5 0.15
41 9 0.26
ACGTcount: A:0.10, C:0.17, G:0.40, T:0.33
Consensus pattern (40 bp):
TCGGATTCGGGTGAAATCCTTGTTCTCAGGTCGGGTCGGG
Found at i:1108521 original size:22 final size:22
Alignment explanation
Indices: 1108496--1108550 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1108486 TATTTATTTT
**
1108496 TAGAAATTTTAGGTTCAATTAC
1 TAGAAATTTTAGGTTCAAGCAC
* *
1108518 TAGAAATCTTATGTTCAAGCAC
1 TAGAAATTTTAGGTTCAAGCAC
1108540 TAGAAATTTTA
1 TAGAAATTTTA
1108551 AAGTATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
TAGAAATTTTAGGTTCAAGCAC
Found at i:1109746 original size:60 final size:61
Alignment explanation
Indices: 1109652--1109780 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 61
1109642 CTAAATGTTC
* * *
1109652 CAATTT-ATTCATAAACTATGACTATCATTCTAAATTTATCCTCAAAC-TTTTGAACATTT
1 CAATTTCATCCATAAACTATGACTATCATTCTAAATTGATCCTCAAACTTTTTCAACATTT
* * *
1109711 CAATTTCATCCATAAACTAT-A-TCATTCATTCTAAATTGGTCTTCAAACTTTTTTCAGCATTT
1 CAATTTCATCCATAAACTATGACT-A-TCATTCTAAATTGATCCTCAAAC-TTTTTCAACATTT
1109773 CAATTTCA
1 CAATTTCA
1109781 ACCCAAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
58 1 0.02
59 8 0.14
60 32 0.54
62 18 0.31
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (61 bp):
CAATTTCATCCATAAACTATGACTATCATTCTAAATTGATCCTCAAACTTTTTCAACATTT
Found at i:1114153 original size:10 final size:10
Alignment explanation
Indices: 1114127--1114160 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1114117 TAATTTCCAA
*
1114127 TGTGTGTGGTC
1 TGTGTGTGG-G
1114138 TGTGTGTGGG
1 TGTGTGTGGG
1114148 TGTGTGTGGG
1 TGTGTGTGGG
1114158 TGT
1 TGT
1114161 TTTCGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.00, C:0.03, G:0.53, T:0.44
Consensus pattern (10 bp):
TGTGTGTGGG
Found at i:1117089 original size:18 final size:18
Alignment explanation
Indices: 1117068--1117106 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1117058 GATGAAAAGG
1117068 GAAAAATGAGA-AAAAAAT
1 GAAAAATGA-ATAAAAAAT
1117086 GAAAAATGAATAAAAAAT
1 GAAAAATGAATAAAAAAT
1117104 GAA
1 GAA
1117107 TAAAAGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (18 bp):
GAAAAATGAATAAAAAAT
Found at i:1117167 original size:45 final size:44
Alignment explanation
Indices: 1117109--1117193 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 44
1117099 AAAATGAATA
* * *
1117109 AAAGGGGGTTCAAGATGAAAACTCAAAAAAGGCGTCTTGAAACC
1 AAAGGAGGTTCAAGATGAAAACCCAAAAAAGGCGGCTTGAAACC
* * *
1117153 AAAGGAGGTCTCAAGTTGAAAACCCACAAAGGGCGGCTTGA
1 AAAGGAGGT-TCAAGATGAAAACCCAAAAAAGGCGGCTTGA
1117194 GTTTTAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 8 0.24
45 26 0.76
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (44 bp):
AAAGGAGGTTCAAGATGAAAACCCAAAAAAGGCGGCTTGAAACC
Found at i:1118871 original size:212 final size:214
Alignment explanation
Indices: 1118310--1119192 Score: 1147
Period size: 212 Copynumber: 4.1 Consensus size: 214
1118300 TGAAGCAAAC
* ** * *
1118310 CATCCATAAAACCTTCAGGTAGGATAATTTCAAATGAATTTGAAAATGAAAAAAATTATGTTTTA
1 CATCCATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAAT-AAAAAAATGATGTTTTA
*
1118375 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATATCACAATTTATAACTCCTTCG
65 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAA-TCCTTCG
* * *
1118440 GGCCATTAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTAAGCGTTTAGAGC
129 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* * *
1118505 AAGATG--AACTCCTTCGGGC
194 AAGATGATAAGTCATTCGGGT
* * *
1118524 CATCCATAAGACTTTC-GGT-GGATGTTTTCACATTAATTTGGAAATAAAAAAATGATGTTTTAA
1 CATCCATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATAAAAAAATGATGTTTTAA
* *
1118587 GAAGATGAAATTTTTTAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAA-CCTTCGGG
66 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAATCCTTCGGG
* ** * * *
1118651 CCATCAGTAAGTTTTTTTAGCATGATGCTTAAATCATTCGGGTCACCTATAAGCCTTTAGAGCAA
131 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1118716 GATGATAAGTCATTCGGGT
196 GATGATAAGTCATTCGGGT
* * * * *
1118735 CATCCATAAGACCTTCGGGTGGGATGTTTTTACATGAATTTGAAAAT-GAAAAATGATGATTTAA
1 CATCCATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATAAAAAAATGATGTTTTAA
* * *
1118799 GAAGATGGAATTTTTGAAAACGAAAAATGC-ATTTTCAAAATTGT-A-TATTTATAAGTCTTTCG
66 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATT-TCACAATTTATAA-TCCTTCG
* *
1118861 GACCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
129 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
1118926 AAGATGATACGTCATTCGGGT
194 AAGATGATAAGTCATTCGGGT
* *
1118947 CATCCATAAAACCTTCAGGTATGATGTTTTCACATGAATTTGAAAATAAAAAAAATGATGTTTTA
1 CATCCATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAAT-AAAAAAATGATGTTTTA
* * * *
1119012 AAAAGATGTAATTTTTGAAAACGAATAATGCGATTTTCAAAATTTCACAATTTATAAAACCTTCG
65 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTAT-AATCCTTCG
* * * * * * * * *
1119077 GGTCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCTTTTGTGAGTCTCTCGAGT
129 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* * *
1119142 AAGA-GAATAAATCCTTCAGGT
194 AAGATG-ATAAGTCATTCGGGT
* *
1119163 CATCCATAAGACCTTCGGGCAGGATGTTTT
1 CATCCATAAGACCTTCAGGTAGGATGTTTT
1119193 TCACCAAAAT
Statistics
Matches: 581, Mismatches: 74, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
209 69 0.12
210 8 0.01
211 108 0.19
212 191 0.33
213 26 0.04
214 57 0.10
215 14 0.02
216 106 0.18
217 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (214 bp):
CATCCATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATAAAAAAATGATGTTTTAA
GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAATCCTTCGGG
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCATTCGGGT
Found at i:1119651 original size:55 final size:55
Alignment explanation
Indices: 1119562--1120132 Score: 585
Period size: 55 Copynumber: 10.6 Consensus size: 55
1119552 GTGAAGCAAA
* **
1119562 TGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAAAGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * *
1119617 TGAAGATTGTTCGAGTCTCATACTATCTGAAGAAATA-GGAGCATACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
1119671 TGAA-AATGTTCGAGTCTAATACTCTCTGAAGAAATA-GG-GCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * *
1119723 TGAAAATTGTTCGAGTCTTATACTCTTTGAAGAAATAAGGAGCATACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
1119778 TGAAGATTGTTCGAGTCTCATACTCTCTTAAGAAATAGGGAGCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * **
1119833 TGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACATTATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * ** *
1119888 TGAAGATTGCTCGAGTCTTATACTCTCAGAAGGAATAGAGAATAGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * *
1119943 TGAAGGTTGTTCAAGTCATATACTCTCTGAATAAATAGGGAGC-GAACACGTTTGAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTG-T
* * * *
1119999 TGAAGA---TT-GAGTCATATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * * *
1120050 TGAAGA-T-TT--AATCTTATACTCTCTGAAGGAATAGAGAACATACATG-TTTT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * *
1120100 ATAAAGATTGTTTGAGTTTTATACTCCCTGAAG
1 -TGAAGATTGTTCGAGTCTTATACTCTCTGAAG
1120133 CAAGAGAGAG
Statistics
Matches: 438, Mismatches: 66, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
50 3 0.01
51 42 0.10
52 57 0.13
53 65 0.15
54 21 0.05
55 244 0.56
56 6 0.01
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
Found at i:1120351 original size:3 final size:3
Alignment explanation
Indices: 1120334--1120368 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1120324 ATATTATAAA
1120334 TAT TAAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1120369 ATACAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1121179 original size:14 final size:14
Alignment explanation
Indices: 1121160--1121186 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1121150 GTGTGTGGTC
1121160 TGTGTGTGGGTGTG
1 TGTGTGTGGGTGTG
1121174 TGTGTGTGGGTGT
1 TGTGTGTGGGTGT
1121187 TTTCGAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.56, T:0.44
Consensus pattern (14 bp):
TGTGTGTGGGTGTG
Found at i:1121887 original size:12 final size:12
Alignment explanation
Indices: 1121870--1121908 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1121860 TGTATGTTTG
1121870 TATTATATTTAA
1 TATTATATTTAA
1121882 TATTATATTTAA
1 TATTATATTTAA
* *
1121894 TATTAGATTTTA
1 TATTATATTTAA
1121906 TAT
1 TAT
1121909 CTTATATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
TATTATATTTAA
Done.