Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 57 of 78
Found at i:11363604 original size:125 final size:128
Alignment explanation
Indices: 11363381--11363701 Score: 447
Period size: 125 Copynumber: 2.5 Consensus size: 128
11363371 CGTAAATGTC
* *
11363381 TAAGTATCGATACTTATAATTTCGAAACATATTACTTTAAAGTAATAGGTAAATTCATAATGTAC
1 TAAGTATCGATACTTATAATTTCGAAACATATTACTTTAAAGTAATAGGTAAATTAACAATGTAC
*
11363446 ACTGTAAACGTTTCTACCAGTATAATGAAAATA-G-AC-A-TA-AATGTATCGATACTTAT-ATA
66 ACGGTAAACGTTTCTACCAGTATAATGAAAATAGGCACAAGTACAA-GTATCGATA-TTATCATA
* *
11363505 TAAAGTATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTA
1 T-AAGTATCGATACTTATAATTTCGAAACATATTACTTTAAAGTAATAGGTAAATTAACAATGTA
* * *
11363570 CACGGTAAGCGTTTCTACCGGTATAATGAAAATAGGCACAAATGTACAAGTATCGATATTGTCAT
65 CACGGTAAACGTTTCTACCAGTATAATGAAAATAGGCAC-AA-GTACAAGTATCGATATTATCAT
11363635 A
128 A
* * * *
11363636 TAAGTATCGATACTTATAATTTTGAAACTTATTACTTTAAAGTAAGAGGTAAATTAACAATATAC
1 TAAGTATCGATACTTATAATTTCGAAACATATTACTTTAAAGTAATAGGTAAATTAACAATGTAC
11363701 A
66 A
11363702 ATGCAAATAT
Statistics
Matches: 175, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
124 1 0.01
125 90 0.51
126 1 0.01
127 2 0.01
129 1 0.01
130 63 0.36
131 15 0.09
132 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (128 bp):
TAAGTATCGATACTTATAATTTCGAAACATATTACTTTAAAGTAATAGGTAAATTAACAATGTAC
ACGGTAAACGTTTCTACCAGTATAATGAAAATAGGCACAAGTACAAGTATCGATATTATCATA
Found at i:11363811 original size:23 final size:23
Alignment explanation
Indices: 11363785--11363833 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
11363775 CCCATCAGTT
*
11363785 TTAAACAGGCGTTACTTATTACA
1 TTAAACAAGCGTTACTTATTACA
* * *
11363808 TTAAATAAGCGTTACTTGTTATA
1 TTAAACAAGCGTTACTTATTACA
11363831 TTA
1 TTA
11363834 TTATGGTCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (23 bp):
TTAAACAAGCGTTACTTATTACA
Found at i:11369420 original size:11 final size:11
Alignment explanation
Indices: 11369404--11369429 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11369394 TCCCCAAGTG
11369404 ACCAGTAAAAC
1 ACCAGTAAAAC
11369415 ACCAGTAAAAC
1 ACCAGTAAAAC
11369426 ACCA
1 ACCA
11369430 CATCAGACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.31, G:0.08, T:0.08
Consensus pattern (11 bp):
ACCAGTAAAAC
Found at i:11385026 original size:22 final size:22
Alignment explanation
Indices: 11384973--11385026 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
11384963 CAATGTTCCC
11384973 TGGTATCGATACCCTCCACATA
1 TGGTATCGATACCCTCCACATA
* *
11384995 -GGTATTGATACCTCTTCA-ATA
1 TGGTATCGATACC-CTCCACATA
11385016 TGGTATCGATA
1 TGGTATCGATA
11385027 TTGTTCATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (22 bp):
TGGTATCGATACCCTCCACATA
Found at i:11387834 original size:24 final size:25
Alignment explanation
Indices: 11387807--11387874 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
11387797 TCAAGGGGAC
*
11387807 TCATCTGTTGCAAAAGA-ACAAGTT
1 TCATCTGCTGCAAAAGACACAAGTT
*
11387831 TCATCTACTGCAAAA-ACACAAGTT
1 TCATCTGCTGCAAAAGACACAAGTT
*
11387855 TCGTCTGCTGCAAAAG-CACA
1 TCATCTGCTGCAAAAGACACA
11387875 TACCTCTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.25
Consensus pattern (25 bp):
TCATCTGCTGCAAAAGACACAAGTT
Found at i:11401517 original size:25 final size:24
Alignment explanation
Indices: 11401472--11401524 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
11401462 AAGAAGTTAT
*
11401472 ATTAAAAATTTTAGAAAATATTAA
1 ATTAAAAATTTTAGAAAATATAAA
*
11401496 ATTATAAAATTTTA-AGAGATATAAA
1 ATTA-AAAATTTTAGA-AAATATAAA
11401521 ATTA
1 ATTA
11401525 GATAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
ATTAAAAATTTTAGAAAATATAAA
Found at i:11401563 original size:15 final size:17
Alignment explanation
Indices: 11401528--11401573 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
11401518 AAAATTAGAT
*
11401528 AATTAATAAAAAATTATA
1 AATTAA-AAAAATTTATA
11401546 AA-TAAAAAAATTTA-A
1 AATTAAAAAAATTTATA
*
11401561 AATTTAAAAAATT
1 AATTAAAAAAATT
11401574 AAATTTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 3 0.12
16 17 0.68
17 3 0.12
18 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTAAAAAAATTTATA
Found at i:11401575 original size:15 final size:14
Alignment explanation
Indices: 11401534--11401576 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
11401524 AGATAATTAA
11401534 TAAAAAATTATAAAT
1 TAAAAAATTA-AAAT
*
11401549 AAAAAAATTTAAAATT
1 TAAAAAA-TTAAAA-T
11401565 TAAAAAATTAAA
1 TAAAAAATTAAA
11401577 TTTTCTAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAAAATTAAAAT
Found at i:11402899 original size:23 final size:23
Alignment explanation
Indices: 11402855--11402899 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11402845 AACATATTAC
* **
11402855 GTAGCGCTTATATAATGTAATAG
1 GTAGCACTTATATAATAAAATAG
11402878 GTAGCACTTATATAATAAAATA
1 GTAGCACTTATATAATAAAATA
11402900 AGCATTTAAC
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:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
GTAGCACTTATATAATAAAATAG
Found at i:11402956 original size:23 final size:23
Alignment explanation
Indices: 11402930--11402977 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
11402920 ATCAAGTACA
*
11402930 ATAACAAATTAGGTAGCGCTTAT
1 ATAACAAACTAGGTAGCGCTTAT
***
11402953 ATAATGTACTAGGTAGCGCTTAT
1 ATAACAAACTAGGTAGCGCTTAT
11402976 AT
1 AT
11402978 TGACATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACAAACTAGGTAGCGCTTAT
Found at i:11402966 original size:87 final size:87
Alignment explanation
Indices: 11402815--11402977 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
11402805 TATGTTATAT
* *
11402815 CATTTAACCGGAAATATTATTAAGCACAATAACATATTACGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGCACAATAACAAATTACGTAGCGCTTATATAATGTAATAGGT
11402880 AGCACTTATATAATAAAATAAG
66 AGCACTTATATAATAAAATAAG
* * *
11402902 CATTTAACCGGAAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTACTAGGT
1 CATTTAACCGGAAATATTATCAAGCACAATAACAAATTACGTAGCGCTTATATAATGTAATAGGT
*
11402967 AGCGCTTATAT
66 AGCACTTATAT
11402978 TGACATATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGCACAATAACAAATTACGTAGCGCTTATATAATGTAATAGGT
AGCACTTATATAATAAAATAAG
Found at i:11403210 original size:14 final size:15
Alignment explanation
Indices: 11403191--11403219 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11403181 TATTTGCTAA
11403191 TTAACTGG-TATATT
1 TTAACTGGTTATATT
11403205 TTAACTGGTTATATT
1 TTAACTGGTTATATT
11403220 GTAAATTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (15 bp):
TTAACTGGTTATATT
Found at i:11403381 original size:198 final size:197
Alignment explanation
Indices: 11402998--11403494 Score: 529
Period size: 198 Copynumber: 2.5 Consensus size: 197
11402988 TCTCATAAAA
* * * * * *
11402998 CCGGTAAATTTAAACTGGTTACATTATAAATTGACCTATTACATTATAAATATTGGA-TTCGATA
1 CCGGTATATTTTAACTGGTTACATTGTAAATTTACCTATTACATTATAATTA-TCGATTTCGAT-
* * * * *
11403062 TTTTCGGGATCGATACAATTTT-AAATGTATCGACACTTTATGCGTGCAACTCGTTTGTGCTTTA
64 GTTTCGGGATCGATAC-TTTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCA
* * * *
11403126 TTTTGGAAAAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATT-TGCTA
128 TTTTGGAAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATAATGTAGACCTATTCT-CTA
*
11403190 ATTAA-
192 ATGAAC
* * * * *
11403195 CTGGTATATTTTAACTGGTTATATTGTAAATTTACCTGTTACATAATAATTATCAATTTCGATGT
1 CCGGTATATTTTAACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGT
*
11403260 TTCGAGGATCGATACTTTTTACAAATGTATCGACACTTTATGCGTACACCTCGTTTG-CCATTCA
66 TTCG-GGATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTACAACTCGTTTGTCC-TTCA
* * * * * *
11403324 TTTTGGAAAAATGTATCGACACAAAATAAAAAAGTGTTGATACTTTATGTTGACCTATTCTCTTA
128 TTTTGGAAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAA
11403389 TGAAC
193 TGAAC
* * * * * **
11403394 CCGATATATTTCT-ACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTCTCTTTG
1 CCGGTATATTT-TAACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATG
* *
11403458 ATTTTGGGATCGATACTTGTTATAAATGTATCGACAC
65 -TTTCGGGATCGATACTTTTTA-AAATGTATCGACAC
11403495 AAAATCTAGC
Statistics
Matches: 248, Mismatches: 43, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
196 11 0.04
197 60 0.24
198 92 0.37
199 80 0.32
200 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (197 bp):
CCGGTATATTTTAACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGT
TTCGGGATCGATACTTTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTT
TGGAAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATGA
AC
Found at i:11404356 original size:51 final size:51
Alignment explanation
Indices: 11404301--11404411 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 51
11404291 CCTGAACCAT
* * *
11404301 GCTATATGCTGATTTGGCGACACGTGGAGTATAGCGTGCCCCATG-TACCGC
1 GCTATACGCTGACTGGGCGACACGTGGAGTATAGCGTGCCCCATGCT-CCGC
** * * *
11404352 GCTATACGCTGACTGGGTTACATGTGGGGTATAGCGTGCCCCCTGCTCCGC
1 GCTATACGCTGACTGGGCGACACGTGGAGTATAGCGTGCCCCATGCTCCGC
11404403 GCTATACGC
1 GCTATACGC
11404412 CACGTAGGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 50 0.98
52 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (51 bp):
GCTATACGCTGACTGGGCGACACGTGGAGTATAGCGTGCCCCATGCTCCGC
Found at i:11404680 original size:14 final size:15
Alignment explanation
Indices: 11404658--11404704 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
11404648 TATAAGGTAA
*
11404658 TTTTGTTATAATT-T
1 TTTTATTATAATTAT
*
11404672 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
11404687 TGTTTATTATCATTAT
1 T-TTTATTATAATTAT
11404703 TT
1 TT
11404705 GAAAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 13 0.48
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:11408042 original size:35 final size:34
Alignment explanation
Indices: 11407957--11408043 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
11407947 ATTTGGTATT
*
11407957 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
11407991 TAAATGATAACCAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
11408029 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
11408044 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:11408674 original size:18 final size:18
Alignment explanation
Indices: 11408651--11408685 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11408641 GCGATGACGG
*
11408651 CATCATATATGGTTGCGA
1 CATCATATATGGCTGCGA
11408669 CATCATATATGGCTGCG
1 CATCATATATGGCTGCG
11408686 GTGGCTGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (18 bp):
CATCATATATGGCTGCGA
Found at i:11410397 original size:111 final size:111
Alignment explanation
Indices: 11410194--11410526 Score: 612
Period size: 111 Copynumber: 3.0 Consensus size: 111
11410184 ATTACAAAAA
*
11410194 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
11410259 AATTAAAACGTTAAAATGTTACTGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
11410305 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
11410370 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
11410416 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
11410481 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
11410527 ATGATTTCCA
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:11411381 original size:182 final size:177
Alignment explanation
Indices: 11411063--11411632 Score: 673
Period size: 182 Copynumber: 3.1 Consensus size: 177
11411053 GTGGACATAA
* * *
11411063 ATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGTGCTATAACTTCTTCTCT
1 ATTGCTATGGATCGATACATTTT-ATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* * * * *
11411128 TTTAAATT-ACGAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGATAGCT
65 TTTAAATTCA-AAAAATGTCGATACTTATATTAA-CTATCGACACTTTTAATATATCCGGTAGCT
* **
11411192 TTTTACCGGTTTTATCATTTCGAGACTTGTTTTGTCATATTCTTACCTGTTAT
128 ATTTACCGGTTTTATCATTT-GA-ACCGGTTTTGTCATATT-TTACCTGTTAT
*
11411245 ATTGCTATGGATCGATAAATTTGTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
1 ATTGCTATGGATCGATACATTT-TATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* *
11411310 TTTAAATTCAAAAAATGTCGATACTTATATTAACGTATCGACACTTTTAATATATCTGGTAGCTC
65 TTTAAATTCAAAAAATGTCGATACTTATATTAAC-TATCGACACTTTTAATATATCCGGTAGCTA
*
11411375 TTTACCGGTTTTATCATTTTGTAACCGGTTTTGTCATACTTATACCTGTTAT
129 TTTACCGGTTTTATCA-TTTG-AACCGGTTTTGTCATA-TTTTACCTGTTAT
* * * *
11411427 ATTGTTATGGATCGATACGTTTTTATAAAGTATCGACACTTTATATGCGCTATTACTTCTTCTCT
1 ATTGCTATGGATCGATAC-ATTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* * * * *
11411492 TTTAAATTCCAAAACTGTCTATACTTAT-TTAAATCTAATCGATACTTTCT-ATATATCCAGTAG
65 TTTAAATTCAAAAAATGTCGATACTTATATT-AA-CT-ATCGACACTTT-TAATATATCCGGTAG
* *
11411555 CGGTATTT--CGGTTTTATCATAATGAAACCGGTTTTATCATATTTTTACCTGTTAT
126 C--TATTTACCGGTTTTATCAT-TTG-AACCGGTTTTGTCATA-TTTTACCTGTTAT
*
11411610 ATTGCTATGGAGCGATACATTTT
1 ATTGCTATGGATCGATACATTTT
11411633 TCATTTGTAT
Statistics
Matches: 340, Mismatches: 34, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
181 2 0.01
182 243 0.71
183 90 0.26
184 1 0.00
185 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (177 bp):
ATTGCTATGGATCGATACATTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTT
TTAAATTCAAAAAATGTCGATACTTATATTAACTATCGACACTTTTAATATATCCGGTAGCTATT
TACCGGTTTTATCATTTGAACCGGTTTTGTCATATTTTACCTGTTAT
Found at i:11412412 original size:20 final size:20
Alignment explanation
Indices: 11412387--11412517 Score: 147
Period size: 20 Copynumber: 6.5 Consensus size: 20
11412377 TGGGAAAATT
11412387 GCAATGCGATACTGACTATC
1 GCAATGCGATACTGACTATC
11412407 GCAATGCGATACTGACTATC
1 GCAATGCGATACTGACTATC
*
11412427 GCAATGCGATACTTACTATC
1 GCAATGCGATACTGACTATC
* *
11412447 GCAATGCGATAAT-ACAAAATC
1 GCAATGCGATACTGAC--TATC
* * *
11412468 GCAACGAGATACTGACTTTC
1 GCAATGCGATACTGACTATC
* * *
11412488 GCAACGCGATTCTGACTTTC
1 GCAATGCGATACTGACTATC
*
11412508 GCAACGCGAT
1 GCAATGCGAT
11412518 TTACATAGCG
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.83
21 13 0.13
22 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
GCAATGCGATACTGACTATC
Found at i:11412497 original size:41 final size:40
Alignment explanation
Indices: 11412394--11412497 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 40
11412384 ATTGCAATGC
* * * *
11412394 GATACTGACTATCGCAATGCGATACTGACTATCGCAATGC
1 GATACTGACTATCGCAATGCGATAATGACAATCGCAACGA
*
11412434 GATACTTACTATCGCAATGCGATAAT-ACAAAATCGCAACGA
1 GATACTGACTATCGCAATGCGATAATGAC--AATCGCAACGA
* *
11412475 GATACTGACTTTCGCAACGCGAT
1 GATACTGACTATCGCAATGCGAT
11412498 TCTGACTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.04
40 24 0.44
41 28 0.52
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (40 bp):
GATACTGACTATCGCAATGCGATAATGACAATCGCAACGA
Found at i:11412784 original size:27 final size:27
Alignment explanation
Indices: 11412728--11412787 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
11412718 ATCGCCGGCG
* *
11412728 AAATCCCTCACAACCATTCACAGTCAA
1 AAATCCCTCACAACCATTCAAAATCAA
* *
11412755 AAATCCCTCACAATCATTCAGAAATGAA
1 AAATCCCTCACAACCATTCA-AAATCAA
11412783 AAATC
1 AAATC
11412788 AACCTCCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (27 bp):
AAATCCCTCACAACCATTCAAAATCAA
Found at i:11413112 original size:19 final size:19
Alignment explanation
Indices: 11413076--11413117 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11413066 ACGAGAGAAT
*
11413076 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
* *
11413095 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAA
11413114 CGCA
1 CGCA
11413118 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:11413167 original size:19 final size:19
Alignment explanation
Indices: 11413118--11413258 Score: 131
Period size: 19 Copynumber: 7.8 Consensus size: 19
11413108 CAAAATCGCA
*
11413118 TTGCGATTTTTCATTTCGCG
1 TTGCGA-TTTTCATTTCTCG
11413138 TTGCGATTTTC---TCT--
1 TTGCGATTTTCATTTCTCG
*
11413152 TTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTCTCG
*
11413171 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
11413190 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
** *
11413204 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
*
11413223 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCTCG
11413243 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
11413259 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 10, Indels: 23
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.21
16 4 0.04
17 5 0.05
19 47 0.47
20 23 0.23
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:11413167 original size:33 final size:34
Alignment explanation
Indices: 11413118--11413181 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
11413108 CAAAATCGCA
*
11413118 TTGCGATTTTTCATTTCGCGTTGCGATTTTCTCT
1 TTGCGATTTTTCATTTCACGTTGCGATTTTCTCT
11413152 TTGCGA-TTTTCATTTCACGTTGCGATTTTC
1 TTGCGATTTTTCATTTCACGTTGCGATTTTC
11413182 ATTTCGCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 23 0.79
34 6 0.21
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.52
Consensus pattern (34 bp):
TTGCGATTTTTCATTTCACGTTGCGATTTTCTCT
Found at i:11413197 original size:52 final size:52
Alignment explanation
Indices: 11413118--11413253 Score: 191
Period size: 52 Copynumber: 2.6 Consensus size: 52
11413108 CAAAATCGCA
* **
11413118 TTGCGATTTTTCATTTCGCGTTGCGATTTTCTCTTTGCGATTTTCATTTCACG
1 TTGCGA-TTTTCATTTCGCGTTGCGATTTTCTCGTTGCGATAGTCATTTCACG
* *
11413171 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCTCGTTGCGATAGTCATTTCACG
* *
11413223 TTGCGATTCTCATTATCTCGTTGCGATTTTC
1 TTGCGATTTTCATT-TCGCGTTGCGATTTTC
11413254 ATTTCAACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 54 0.73
53 20 0.27
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCTCGTTGCGATAGTCATTTCACG
Found at i:11413206 original size:33 final size:33
Alignment explanation
Indices: 11413169--11413233 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
11413159 TTTCATTTCA
**
11413169 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
11413202 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
11413234 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:11414809 original size:63 final size:63
Alignment explanation
Indices: 11414710--11414840 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
11414700 GTTACGTGAT
11414710 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
11414773 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
11414836 GAGGT
1 GAGGT
11414841 GTCTACTTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (63 bp):
GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:11415489 original size:42 final size:42
Alignment explanation
Indices: 11415413--11415615 Score: 185
Period size: 42 Copynumber: 4.8 Consensus size: 42
11415403 GACTCGCCTG
* * * * * * *
11415413 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCTACCATTCAAGAGGCCACTA
* *
11415455 TCATTCCTCGAGAGTCCCCTCCTACCATTCAAGAGGCCATTG
1 TCATTCCTCGAGAGTCCCCTCCTACCATTCAAGAGGCCACTA
* * * * * *
11415497 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCTACCATTCAAGAGGCCACTA
* * *
11415539 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCTACCATTCAAGAGGCCACTA
* * *
11415581 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCTACCATTCAAGAG
11415616 CCCGATTCAC
Statistics
Matches: 130, Mismatches: 29, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
41 4 0.03
42 124 0.95
43 2 0.02
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCTACCATTCAAGAGGCCACTA
Found at i:11415573 original size:21 final size:21
Alignment explanation
Indices: 11415549--11415615 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
11415539 TCATTCCTCG
11415549 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
11415570 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
11415591 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
11415612 AGAG
1 AGAG
11415616 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:11415594 original size:84 final size:84
Alignment explanation
Indices: 11415410--11415585 Score: 316
Period size: 84 Copynumber: 2.1 Consensus size: 84
11415400 CCCGACTCGC
*
11415410 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
11415475 CCTACCATTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
*
11415494 TTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
11415559 CCCACCGTTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
11415578 CTGTCATC
1 CTGTCATC
11415586 GTTGAAGAGG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCATTCAAGAGGCCA
Found at i:11415615 original size:84 final size:84
Alignment explanation
Indices: 11415410--11415615 Score: 279
Period size: 84 Copynumber: 2.5 Consensus size: 84
11415400 CCCGACTCGC
* * * *
11415410 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
11415475 CCTACCATTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
* * * *
11415494 TTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
11415559 CCCACCGTTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
** *
11415578 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
11415616 CCCGATTCAC
Statistics
Matches: 110, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 106 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCATTCAAGAGGCCA
Found at i:11416991 original size:14 final size:14
Alignment explanation
Indices: 11416972--11417007 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11416962 ATTGTTTAAT
11416972 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
11416986 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
11417000 TGATTTGT
1 TGATTTGT
11417008 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:11417164 original size:33 final size:33
Alignment explanation
Indices: 11417122--11417203 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
11417112 CTATCGCAAT
11417122 GCGAAATGAAAATCGCAACGAGAGAATCACAAC
1 GCGAAATGAAAATCGCAACGAGAGAATCACAAC
*
11417155 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
1 GCGAAATGAAAATCGCAACGAGAGAATCACAAC
* *
11417188 GCGAAATTAAATTCGC
1 GCGAAATGAAAATCGC
11417204 GTTGCGATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGAGAGAATCACAAC
Found at i:11417173 original size:19 final size:19
Alignment explanation
Indices: 11417114--11417174 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
11417104 AAAAAGTACT
*
11417114 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
11417133 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
11417147 ATCACAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
11417166 ATCGCAACG
1 ATCGCAACG
11417175 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:11417184 original size:14 final size:14
Alignment explanation
Indices: 11417132--11417188 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
11417122 GCGAAATGAA
11417132 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
11417146 AATCACAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
11417165 AATCGCAACGAGAG
1 AATCGCAACGAGAG
11417179 AATCGCAACG
1 AATCGCAACG
11417189 CGAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:11417245 original size:33 final size:32
Alignment explanation
Indices: 11417203--11417329 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
11417193 ATTAAATTCG
*
11417203 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
11417236 CGTTGCGATTTTCATTTTGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
11417269 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
11417302 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
11417330 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:11417262 original size:19 final size:19
Alignment explanation
Indices: 11417199--11417329 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
11417189 CGAAATTAAA
*
11417199 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
11417218 TTCGCATTGTGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
11417234 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
11417251 TTTGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
11417265 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
11417284 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
11417300 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
11417317 TTCGCATTGCGAT
1 TTCGCATTGCGAT
11417330 AGTAATTTCC
Statistics
Matches: 81, Mismatches: 16, Indels: 30
0.64 0.13 0.24
Matches are distributed among these distances:
14 22 0.27
16 13 0.16
17 12 0.15
19 34 0.42
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:11417304 original size:66 final size:66
Alignment explanation
Indices: 11417196--11417328 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
11417186 ACGCGAAATT
* * *
11417196 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTCATTTTGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
11417261 G
66 G
*
11417262 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
11417327 G
66 G
11417328 A
1 A
11417329 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:11419629 original size:12 final size:12
Alignment explanation
Indices: 11419612--11419636 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11419602 TCTTCGGGGA
11419612 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11419624 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11419636 C
1 C
11419637 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:11419845 original size:24 final size:24
Alignment explanation
Indices: 11419811--11419864 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
11419801 CTGAAACATC
*
11419811 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
11419835 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
11419859 ATCAAA
1 ATCAAA
11419865 TTTAGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:11420877 original size:20 final size:20
Alignment explanation
Indices: 11420852--11420941 Score: 128
Period size: 20 Copynumber: 4.5 Consensus size: 20
11420842 ATTCATTTGA
*
11420852 CTATCGCAACGCGACAATGG
1 CTATCGCAACGCGAAAATGG
*
11420872 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGCGAAAATGG
*
11420892 CGATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
**
11420912 CTATCGCAACGCG-AAATTC
1 CTATCGCAACGCGAAAATGG
11420931 CTATCGCAACG
1 CTATCGCAACG
11420942 ACAAAATCGC
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
19 15 0.24
20 48 0.76
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:11421008 original size:19 final size:19
Alignment explanation
Indices: 11420967--11421031 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
11420957 GGAATGAAAA
11420967 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
11420983 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
11421000 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
11421019 TCGCATTGCGATT
1 TCGCATTGCGATT
11421032 CTCTCGTTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:11421178 original size:14 final size:14
Alignment explanation
Indices: 11421159--11421195 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11421149 CATCAATTAA
11421159 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
11421173 ACAAATCATCTTTT
1 ACAAATCAACATTT
11421187 ACAAATCAA
1 ACAAATCAA
11421196 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:11423091 original size:20 final size:20
Alignment explanation
Indices: 11423068--11423108 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11423058 ACTTAAAATT
11423068 GCAACACGAAAATGACTATC
1 GCAACACGAAAATGACTATC
* * *
11423088 GCAACGCGGAAATGGCTATC
1 GCAACACGAAAATGACTATC
11423108 G
1 G
11423109 TAATGCGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
GCAACACGAAAATGACTATC
Found at i:11423120 original size:19 final size:20
Alignment explanation
Indices: 11423077--11423121 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
11423067 TGCAACACGA
11423077 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* * *
11423097 AAATGGCTATCGTAATGC-G
1 AAATGACTATCGCAACGCGG
11423116 AAATGA
1 AAATGA
11423122 AAGTCGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:11423159 original size:18 final size:18
Alignment explanation
Indices: 11423105--11423169 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
11423095 GGAAATGGCT
*
11423105 ATCGTAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
11423123 AGTCGCAA--CGACA--AA
1 A-TCGCAATGCGAAATGAA
11423138 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
11423156 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
11423170 CACAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 16 0.42
19 5 0.13
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:11423186 original size:19 final size:18
Alignment explanation
Indices: 11423136--11423186 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
11423126 CGCAACGACA
**
11423136 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAAAC
*
11423154 AAATCGCAACGCGAAACAC
1 AAATCGCAATGCGAAA-AC
*
11423173 AAATCGCATTGCGA
1 AAATCGCAATGCGA
11423187 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAAAC
Found at i:11423217 original size:14 final size:14
Alignment explanation
Indices: 11423198--11423255 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
11423188 TTTCATTTCG
11423198 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
11423212 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
11423228 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
11423244 CGTTGCGATTTT
1 CGTTGCGATTTT
11423256 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:11423228 original size:32 final size:33
Alignment explanation
Indices: 11423181--11423271 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
11423171 ACAAATCGCA
*
11423181 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
11423214 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
11423246 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
11423272 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:11423277 original size:19 final size:20
Alignment explanation
Indices: 11423255--11423299 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
11423245 GTTGCGATTT
*
11423255 TCATTT-CGCATTGCGATAG
1 TCATTTCCGCACTGCGATAG
*
11423274 TCATTTCCGCGCTGCGATAG
1 TCATTTCCGCACTGCGATAG
11423294 TCATTT
1 TCATTT
11423300 TCGTGTTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (20 bp):
TCATTTCCGCACTGCGATAG
Found at i:11423818 original size:18 final size:18
Alignment explanation
Indices: 11423792--11423836 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
11423782 GTCGATTAGA
*
11423792 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
11423810 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
11423828 TGATGGCTC
1 TGATGGCTC
11423837 CCGAAATGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:11425180 original size:20 final size:20
Alignment explanation
Indices: 11425155--11425192 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11425145 AATAGTTACT
11425155 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
11425175 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
11425193 GTGAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:11425501 original size:22 final size:22
Alignment explanation
Indices: 11425474--11425517 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
11425464 GATGGAGATA
*
11425474 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
11425496 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
11425518 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:11425788 original size:20 final size:20
Alignment explanation
Indices: 11425702--11425836 Score: 144
Period size: 20 Copynumber: 6.7 Consensus size: 20
11425692 GATTATGTAT
* *
11425702 TATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGATAGTCAG
* * *
11425722 AATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGATAGTCAG
* * ** * *
11425742 TATCTCGTTGCGATTTTATAT
1 TATCGCATTGCGATAGT-CAG
*
11425763 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTCAG
11425783 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
*
11425803 TATCACATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
11425823 TATCGCATTGCGAT
1 TATCGCATTGCGAT
11425837 TTTCCCAATT
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
20 83 0.86
21 14 0.14
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAG
Found at i:11425788 original size:61 final size:61
Alignment explanation
Indices: 11425682--11425816 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 61
11425672 CGCTTTGAAA
* * * *
11425682 ATCACATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCACATTGCGATTATATATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
11425743 ATCTCGTTGCGATTTTATATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCACATTGCGATTATATATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
11425804 ATCACATTGCGAT
1 ATCACATTGCGAT
11425817 AGTCAGTATC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (61 bp):
ATCACATTGCGATTATATATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:11425855 original size:81 final size:81
Alignment explanation
Indices: 11425682--11425857 Score: 185
Period size: 81 Copynumber: 2.2 Consensus size: 81
11425672 CGCTTTGAAA
* * * *
11425682 ATCACATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATC
1 ATCACATTGCGA-TA-GTAAGTATCGCATTGCGAAAGTCAGAATCACATTGCGAAAGTCAGTATC
* * * *
11425746 TCGTTGCGATTTTATATT
64 GCATTGCGATTTTACAAT
* * * *
11425764 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCACATTGCGATAGTCAGTATCGC
1 ATCACATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGAATCACATTGCGAAAGTCAGTATCGC
*
11425829 ATTGCGATTTTCCCAAT
66 ATTGCGATTTT-ACAAT
*
11425846 -TCACGTTGCGAT
1 ATCACATTGCGAT
11425858 TTACTTATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
80 2 0.03
81 62 0.81
82 13 0.17
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (81 bp):
ATCACATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGAATCACATTGCGAAAGTCAGTATCGC
ATTGCGATTTTACAAT
Found at i:11429395 original size:21 final size:20
Alignment explanation
Indices: 11429369--11429419 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
11429359 ATTTTTTTTA
11429369 AAAATTAAATTTTGATGATTT
1 AAAATTAAATTTTGAT-ATTT
**
11429390 AAAATTATCTTTTGATATTT
1 AAAATTAAATTTTGATATTT
*
11429410 -GAATTAAATT
1 AAAATTAAATT
11429420 CTCAAATCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 7 0.28
20 4 0.16
21 14 0.56
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (20 bp):
AAAATTAAATTTTGATATTT
Found at i:11430118 original size:2 final size:2
Alignment explanation
Indices: 11430108--11430140 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
11430098 ATATAATTTG
11430108 TA TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11430141 CATTACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:11431552 original size:10 final size:10
Alignment explanation
Indices: 11431537--11431564 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
11431527 TTCCTTCGAT
11431537 TTTTTTTTTA
1 TTTTTTTTTA
11431547 TTTTTTTTTA
1 TTTTTTTTTA
11431557 TTTTTTTT
1 TTTTTTTT
11431565 CTTTTCGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:11431687 original size:8 final size:8
Alignment explanation
Indices: 11431674--11431698 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11431664 TTAATTGAAA
11431674 TTAAATTT
1 TTAAATTT
11431682 TTAAATTT
1 TTAAATTT
11431690 TTAAATTT
1 TTAAATTT
11431698 T
1 T
11431699 AATTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTAAATTT
Found at i:11433440 original size:20 final size:20
Alignment explanation
Indices: 11433415--11433457 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11433405 AGTCTCCAGG
*
11433415 CTTCTGGAAAAGTTTTTAAA
1 CTTCTGGAAAAGTTTCTAAA
* *
11433435 CTTCTGGGAATGTTTCTAAA
1 CTTCTGGAAAAGTTTCTAAA
11433455 CTT
1 CTT
11433458 TGCATTGCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (20 bp):
CTTCTGGAAAAGTTTCTAAA
Found at i:11433850 original size:18 final size:18
Alignment explanation
Indices: 11433827--11433866 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
11433817 GGTTAAGAAT
11433827 AGTTTATAAGATGATTTG
1 AGTTTATAAGATGATTTG
11433845 AGTTTATAAGATGATTTG
1 AGTTTATAAGATGATTTG
11433863 AGTT
1 AGTT
11433867 AAGAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (18 bp):
AGTTTATAAGATGATTTG
Found at i:11436962 original size:23 final size:22
Alignment explanation
Indices: 11436931--11436978 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
11436921 TTAAAATAAG
*
11436931 AATATTATATTTTGAAA-ATTATT
1 AATAATATATTTT-AAATATT-TT
11436954 AATAATATATTTTAAATATTTT
1 AATAATATATTTTAAATATTTT
11436976 AAT
1 AAT
11436979 TAAAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATAATATATTTTAAATATTTT
Found at i:11437289 original size:22 final size:22
Alignment explanation
Indices: 11437251--11437297 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
11437241 TAAATATATA
11437251 AAATAATATTATCTATATTAAT
1 AAATAATATTATCTATATTAAT
* *
11437273 AAAT-ATATTATATTATATTATT
1 AAATAATATTAT-CTATATTAAT
11437295 AAA
1 AAA
11437298 ATTATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATAATATTATCTATATTAAT
Found at i:11437561 original size:25 final size:24
Alignment explanation
Indices: 11437515--11437569 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
11437505 TAAAACTGAT
* *
11437515 TATATTATTATAATATTAAAAATA
1 TATATTATTAAAATATTAAAAAAA
11437539 TAATATTATTAAAATTATT-AAAAAA
1 T-ATATTATTAAAA-TATTAAAAAAA
11437564 TATATT
1 TATATT
11437570 TTGCATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 17 0.63
26 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATATTATTAAAATATTAAAAAAA
Found at i:11437618 original size:19 final size:20
Alignment explanation
Indices: 11437596--11437633 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11437586 TTAAGAATTA
*
11437596 ATATTTATATTAAA-ATATT
1 ATATTAATATTAAATATATT
11437615 ATATTAATATTAAATATAT
1 ATATTAATATTAAATATAT
11437634 AAAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTAATATTAAATATATT
Found at i:11437643 original size:25 final size:24
Alignment explanation
Indices: 11437592--11437645 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
11437582 AGAATTAAGA
*
11437592 ATTAATATTTATATTAAAATATTAT
1 ATTAATATTAATATTAAAATA-TAT
11437617 ATTAATATTAAATATATAAAATA-AT
1 ATTAATATT-AATAT-TAAAATATAT
11437642 ATTA
1 ATTA
11437646 TTTTATGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 15 0.58
26 4 0.15
27 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTAATATTAATATTAAAATATAT
Found at i:11440856 original size:21 final size:21
Alignment explanation
Indices: 11440823--11440863 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11440813 AGCGATTGAT
*
11440823 CCTTTAGGGGAAGTGATCGAC
1 CCTTTAGGGGAAGGGATCGAC
* *
11440844 CCTTTTGGTGAAGGGATCGA
1 CCTTTAGGGGAAGGGATCGA
11440864 TCCAAAACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.27
Consensus pattern (21 bp):
CCTTTAGGGGAAGGGATCGAC
Found at i:11440980 original size:21 final size:21
Alignment explanation
Indices: 11440953--11441009 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
11440943 TTGGAAGTCC
*
11440953 AAGGGATCGATCCTTTTTATT
1 AAGGGATCGATCCTTTTTACT
* *
11440974 TAGGGATTGATCC-TTTTACT
1 AAGGGATCGATCCTTTTTACT
11440994 AAGGGATCGATCCTTT
1 AAGGGATCGATCCTTT
11441010 GAGCAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTTACT
Found at i:11451370 original size:20 final size:19
Alignment explanation
Indices: 11451302--11451376 Score: 60
Period size: 21 Copynumber: 3.7 Consensus size: 19
11451292 CATTGTAAGA
*
11451302 AAGGGATCGATACTTTAAGGG
1 AAGGGATCGATCCTTT--GGG
* *
11451323 AAGAGATCGATCCATTTGGCA
1 AAGGGATCGATCC-TTTGG-G
*
11451344 AAAGGATCGATCCTTTGGTG
1 AAGGGATCGATCCTTTGG-G
*
11451364 AAGGGATCAATCC
1 AAGGGATCGATCC
11451377 AAAAGTTTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 18 0.42
21 22 0.51
22 3 0.07
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (19 bp):
AAGGGATCGATCCTTTGGG
Found at i:11454054 original size:19 final size:20
Alignment explanation
Indices: 11454030--11454073 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
11454020 ATTATCTTTT
* *
11454030 GAAAACTAAATTG-GATTTC
1 GAAAACAAAAATGAGATTTC
*
11454049 GAAAACAAAAATGAGATTTT
1 GAAAACAAAAATGAGATTTC
11454069 GAAAA
1 GAAAA
11454074 AGGATTTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (20 bp):
GAAAACAAAAATGAGATTTC
Found at i:11454591 original size:10 final size:10
Alignment explanation
Indices: 11454576--11454600 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11454566 AATTGTAATT
11454576 AGTTAGGGGG
1 AGTTAGGGGG
11454586 AGTTAGGGGG
1 AGTTAGGGGG
11454596 AGTTA
1 AGTTA
11454601 TTATTTCATG
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:0.24, C:0.00, G:0.52, T:0.24
Consensus pattern (10 bp):
AGTTAGGGGG
Found at i:11458872 original size:13 final size:15
Alignment explanation
Indices: 11458844--11458875 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
11458834 GGTACAATAA
11458844 ATGCACTCACCTAAT
1 ATGCACTCACCTAAT
11458859 ATGC-CTCA-CTAAT
1 ATGCACTCACCTAAT
11458872 ATGC
1 ATGC
11458876 TTTAAGGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.28
Consensus pattern (15 bp):
ATGCACTCACCTAAT
Found at i:11459899 original size:8 final size:8
Alignment explanation
Indices: 11459888--11459916 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
11459878 CTAAATTGTC
11459888 CTTCCATT
1 CTTCCATT
11459896 CTTCCATT
1 CTTCCATT
11459904 CTTCCATT
1 CTTCCATT
11459912 CTTCC
1 CTTCC
11459917 TAATTAGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.41, G:0.00, T:0.48
Consensus pattern (8 bp):
CTTCCATT
Found at i:11462941 original size:9 final size:10
Alignment explanation
Indices: 11462917--11462946 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
11462907 AAAACAAAAA
11462917 TCCCGGTTTT
1 TCCCGGTTTT
11462927 TCCCGGTTTT
1 TCCCGGTTTT
11462937 T-CCGGTTTT
1 TCCCGGTTTT
11462946 T
1 T
11462947 AGCCGGTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.00, C:0.27, G:0.20, T:0.53
Consensus pattern (10 bp):
TCCCGGTTTT
Found at i:11462984 original size:32 final size:33
Alignment explanation
Indices: 11462948--11463009 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
11462938 CCGGTTTTTA
* *
11462948 GCCGGTCCAGTACGAACGGTTCAA-CGGTTCTG
1 GCCGGTCCACTAAGAACGGTTCAACCGGTTCTG
* *
11462980 GCCGGTTCACTAATAACGGTTCAACCGGTT
1 GCCGGTCCACTAAGAACGGTTCAACCGGTT
11463010 TAGATTGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 20 0.80
33 5 0.20
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (33 bp):
GCCGGTCCACTAAGAACGGTTCAACCGGTTCTG
Found at i:11475636 original size:25 final size:25
Alignment explanation
Indices: 11475546--11475636 Score: 80
Period size: 25 Copynumber: 3.6 Consensus size: 25
11475536 GTTGGAGAGA
*
11475546 TTTT-AGGTTAAAGTGGTATAGGGT
1 TTTTAAGGTGAAAGTGGTATAGGGT
* *
11475570 TCATTAAGGTGAAAGTGGTGA-AGGAT
1 T-TTTAAGGTGAAAGTGGT-ATAGGGT
* *
11475596 TTTGTAA-GTTAAAGTGGTTTAGGGT
1 TTT-TAAGGTGAAAGTGGTATAGGGT
*
11475621 TTTTAAGGTGAGAGTG
1 TTTTAAGGTGAAAGTG
11475637 ATCAAGGGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
24 4 0.08
25 27 0.52
26 20 0.38
27 1 0.02
ACGTcount: A:0.27, C:0.01, G:0.34, T:0.37
Consensus pattern (25 bp):
TTTTAAGGTGAAAGTGGTATAGGGT
Found at i:11475664 original size:50 final size:51
Alignment explanation
Indices: 11475549--11475670 Score: 147
Period size: 50 Copynumber: 2.4 Consensus size: 51
11475539 GGAGAGATTT
* * * *
11475549 TAGGTTAAAGTGGTATAGGGTTCATTAAGGTGAAAGTGGTGAAGGATTTTG
1 TAGGTTAAAGTGGTTTAGGGTTCATTAAGGTGAAAGTGATCAAGGATTGTG
* * * *
11475600 TAAGTTAAAGTGGTTTAGGGTT-TTTAAGGTGAGAGTGATCAAGGGTTGTG
1 TAGGTTAAAGTGGTTTAGGGTTCATTAAGGTGAAAGTGATCAAGGATTGTG
* *
11475650 TAGGTCAAATTGGTTTAGGGT
1 TAGGTTAAAGTGGTTTAGGGT
11475671 AAGGTTTGAT
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
50 40 0.67
51 20 0.33
ACGTcount: A:0.27, C:0.02, G:0.35, T:0.35
Consensus pattern (51 bp):
TAGGTTAAAGTGGTTTAGGGTTCATTAAGGTGAAAGTGATCAAGGATTGTG
Found at i:11481911 original size:24 final size:24
Alignment explanation
Indices: 11481866--11481915 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
11481856 TGATGGTTGG
11481866 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
11481890 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
11481914 TT
1 TT
11481916 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:11485155 original size:15 final size:15
Alignment explanation
Indices: 11485131--11485173 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
11485121 TGAGTGTTTG
11485131 TTTG-TTTATTTTTA
1 TTTGTTTTATTTTTA
11485145 TTTGTTTTATTTTT-
1 TTTGTTTTATTTTTA
* *
11485159 TTAGTTTTAATTTTA
1 TTTGTTTTATTTTTA
11485174 ATATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTGTTTTATTTTTA
Found at i:11487546 original size:24 final size:24
Alignment explanation
Indices: 11487501--11487550 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
11487491 TGGTGGTTGG
11487501 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
11487525 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
11487549 TT
1 TT
11487551 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:11501339 original size:18 final size:18
Alignment explanation
Indices: 11501318--11501352 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
11501308 TCCATTATCA
11501318 ATGAGCAAGGCATTACCC
1 ATGAGCAAGGCATTACCC
11501336 ATGAGCAAGGCATTACC
1 ATGAGCAAGGCATTACC
11501353 ACCTGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (18 bp):
ATGAGCAAGGCATTACCC
Found at i:11502599 original size:20 final size:20
Alignment explanation
Indices: 11502571--11502616 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
11502561 TTCTTTTAAT
* *
11502571 ATTTTATTTTAAAAATAAAA
1 ATTTAATTTCAAAAATAAAA
* *
11502591 ATTTAATTTCATAGATAAAA
1 ATTTAATTTCAAAAATAAAA
11502611 ATTTAA
1 ATTTAA
11502617 GTGCTATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTAATTTCAAAAATAAAA
Found at i:11504493 original size:2 final size:2
Alignment explanation
Indices: 11504486--11504513 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11504476 TAATACTAAC
11504486 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
11504514 GCTTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11518077 original size:59 final size:60
Alignment explanation
Indices: 11518014--11518126 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 60
11518004 GTCGTGTGAC
11518014 CATTTTGTAACTTTTAATAATCAA-GAGACTCAA-AAAGCAACATCC-TATAGTCGAATAAT
1 CATTTTGTAACTTTTAATAATCAAGGA-ACTCAACAAAGCAACA-CCTTATAGTCGAATAAT
* * *
11518073 CATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAGCATCACCTTATAGTCG
1 CATTTTGTAACTTTTAATAATCAAGGAACTCAACAAAGCAACACCTTATAGTCG
11518127 GGACCATTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
59 30 0.62
60 18 0.38
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAATCAAGGAACTCAACAAAGCAACACCTTATAGTCGAATAAT
Found at i:11523671 original size:21 final size:21
Alignment explanation
Indices: 11523645--11523693 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
11523635 TTGTAGCATT
11523645 GATACTCGGTCTATCAGTATC
1 GATACTCGGTCTATCAGTATC
11523666 GATACTCGGTCTATCAGTATC
1 GATACTCGGTCTATCAGTATC
11523687 GATACTC
1 GATACTC
11523694 ACTGCATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (21 bp):
GATACTCGGTCTATCAGTATC
Found at i:11526096 original size:2 final size:2
Alignment explanation
Indices: 11526089--11526136 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
11526079 ACATAAACAA
11526089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11526131 AT AT AT
1 AT AT AT
11526137 GTGTGTGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11526141 original size:2 final size:2
Alignment explanation
Indices: 11526136--11526196 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
11526126 TATATATATA
* *
11526136 TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
11526178 TA TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG T
11526197 ACGTAGATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.05, C:0.00, G:0.44, T:0.51
Consensus pattern (2 bp):
TG
Found at i:11533124 original size:21 final size:20
Alignment explanation
Indices: 11533095--11533133 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
11533085 TAATGCATTA
*
11533095 AACATCATAAACAAAACAAAT
1 AACAACATAAA-AAAACAAAT
*
11533116 AACAACATACAAAAACAA
1 AACAACATAAAAAAACAA
11533134 CCATACATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (20 bp):
AACAACATAAAAAAACAAAT
Found at i:11544357 original size:13 final size:13
Alignment explanation
Indices: 11544339--11544363 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11544329 AATGAATTTT
11544339 AAGATTTTCTAAA
1 AAGATTTTCTAAA
11544352 AAGATTTTCTAA
1 AAGATTTTCTAA
11544364 GTATATTCGA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:11556400 original size:40 final size:40
Alignment explanation
Indices: 11556356--11556475 Score: 186
Period size: 40 Copynumber: 3.0 Consensus size: 40
11556346 TGTAGTGCTG
* *
11556356 CACATAAGGTCGTGCCTACAATATACACCGAAGTGTATTA
1 CACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
* * *
11556396 CACATAAGGTCGTGCCCACCACATACACCGAAATGTTTTA
1 CACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
*
11556436 CACATAAGGTCGTGCCCACCATATATACCGAAGTGTATTA
1 CACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
11556476 TAAACCTGCA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
CACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
Found at i:11566787 original size:23 final size:23
Alignment explanation
Indices: 11566761--11566814 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
11566751 ATGGTAGCAA
11566761 ATGGAAATATCATGGCAAAATGG
1 ATGGAAATATCATGGCAAAATGG
* * * *
11566784 ATGGAAATGTCGTGGGAAAGTGG
1 ATGGAAATATCATGGCAAAATGG
*
11566807 ATTGAAAT
1 ATGGAAAT
11566815 GTCTTGGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.06, G:0.31, T:0.24
Consensus pattern (23 bp):
ATGGAAATATCATGGCAAAATGG
Found at i:11570922 original size:2 final size:2
Alignment explanation
Indices: 11570915--11570949 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11570905 AGTTTTCTAT
11570915 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11570950 TAATAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11573017 original size:16 final size:16
Alignment explanation
Indices: 11572993--11573027 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11572983 GTTATGAAAA
11572993 AAATCAATTTAAATTT
1 AAATCAATTTAAATTT
* *
11573009 AAATTAATTTAATTTT
1 AAATCAATTTAAATTT
11573025 AAA
1 AAA
11573028 ATAACATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATCAATTTAAATTT
Found at i:11586474 original size:10 final size:9
Alignment explanation
Indices: 11586457--11586512 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
11586447 ACTATGCTTG
11586457 AAGAAAAAA
1 AAGAAAAAA
11586466 AATG--AAAA
1 AA-GAAAAAA
* *
11586474 AATAAAAAG
1 AAGAAAAAA
11586483 AAGAAAAAA
1 AAGAAAAAA
*
11586492 GAGAAAAAA
1 AAGAAAAAA
11586501 AAGAAAGAAA
1 AAGAAA-AAA
11586511 AA
1 AA
11586513 TGAAGAAGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
8 6 0.16
9 25 0.68
10 6 0.16
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:11586497 original size:25 final size:26
Alignment explanation
Indices: 11586456--11586509 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
11586446 TACTATGCTT
11586456 GAAGAAAAAAAATGAAAAAATAA-AAA
1 GAAGAAAAAAAATGAAAAAA-AAGAAA
*
11586482 GAAGAAAAAAGA-GAAAAAAAAGAAA
1 GAAGAAAAAAAATGAAAAAAAAGAAA
11586507 GAA
1 GAA
11586510 AAATGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 2 0.08
25 13 0.50
26 11 0.42
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.04
Consensus pattern (26 bp):
GAAGAAAAAAAATGAAAAAAAAGAAA
Found at i:11586518 original size:10 final size:10
Alignment explanation
Indices: 11586477--11586519 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
11586467 ATGAAAAAAT
11586477 AAAAAGAAGA
1 AAAAAGAAGA
*
11586487 AAAAAGAGAAA
1 AAAAAGA-AGA
11586498 AAAAAGAAAGA
1 AAAAAG-AAGA
*
11586509 AAAATGAAGA
1 AAAAAGAAGA
11586519 A
1 A
11586520 GGAGGGTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 12 0.43
11 15 0.54
12 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:11586518 original size:25 final size:25
Alignment explanation
Indices: 11586457--11586519 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 25
11586447 ACTATGCTTG
11586457 AAGAAA-AAAAATGAA-AAAATAAA
1 AAGAAAGAAAAATGAAGAAAATAAA
*
11586480 AAG-AAGAAAAAAG-AG-AAA-AAA
1 AAGAAAGAAAAATGAAGAAAATAAA
11586501 AAGAAAGAAAAATGAAGAA
1 AAGAAAGAAAAATGAAGAA
11586520 GGAGGGTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 6 0.18
22 15 0.45
23 11 0.33
24 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (25 bp):
AAGAAAGAAAAATGAAGAAAATAAA
Found at i:11587882 original size:271 final size:270
Alignment explanation
Indices: 11587480--11587970 Score: 788
Period size: 271 Copynumber: 1.8 Consensus size: 270
11587470 AAAAAGAGGT
* *
11587480 GGATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAAAAGTT
* *
11587545 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
** * * *
11587610 CTTGAGGAATTGACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGAAAAAGGGAGAA
131 CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCC--AAAAGAGAGAA
*
11587675 GAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
194 GAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
11587740 ACCTCGCTTGAG
259 ACCTCGCTTGAG
*
11587752 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAC-GAGGGAGAAAAAGTT
1 GGATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAAAAGTT
* *
11587816 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAG-CATTTCGAGTCAGGGACGCCTC
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-AGACATTTCGAATCAGGGACACCTC
* * *
11587880 GCTTGAGGGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAG
130 GCTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAG
*
11587945 AAGTTCATAATGCGAAGAACTTGTTC
195 AAGTTCATAATGAGAAGAACTTGTTC
11587971 AATCTAATAA
Statistics
Matches: 201, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
269 35 0.17
271 118 0.59
272 48 0.24
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (270 bp):
GGATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAAAAGTT
CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAGA
AGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACAC
CTCGCTTGAG
Found at i:11587888 original size:135 final size:135
Alignment explanation
Indices: 11587480--11587970 Score: 761
Period size: 136 Copynumber: 3.6 Consensus size: 135
11587470 AAAAAGAGGT
* *
11587480 GGATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACA-AGGGAGAAGAAGTT
11587545 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
11587610 CTTGAG
130 CTTGAG
* ** * * *
11587616 GAATTGACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGAAAAAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AACAAGGGAGAAGAAGTT
11587681 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
11587746 CTTGAG
130 CTTGAG
* *
11587752 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* * * *
11587817 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-CAGCATTTCGAGTCAGGGACGCCTCG
66 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGA-CATTTCGAATCAGTGACACCTCG
11587881 CTTGAG
130 CTTGAG
* * * *
11587887 GGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAA-AAGAGAGAAGAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* *
11587951 ATAATGCGAAGAACTTGTTC
66 ATAATGAGAAGAGCTTGTTC
11587971 AATCTAATAA
Statistics
Matches: 325, Mismatches: 28, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
134 32 0.10
135 125 0.38
136 166 0.51
137 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (135 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGC
TTGAG
Found at i:11593602 original size:14 final size:14
Alignment explanation
Indices: 11593585--11593620 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11593575 AAAACTCATA
11593585 AAATTAAAGGAATG
1 AAATTAAAGGAATG
*
11593599 AAATTAAAGGACTG
1 AAATTAAAGGAATG
*
11593613 AAGTTAAA
1 AAATTAAA
11593621 TAAATAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:11595541 original size:139 final size:137
Alignment explanation
Indices: 11595233--11595579 Score: 460
Period size: 139 Copynumber: 2.5 Consensus size: 137
11595223 GCAAACAAGC
*
11595233 TAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTTATTA
1 TAAGG-TGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTA
* * * *
11595298 TGAACTCTCCACAAGAAATTTTGATCCTTGAGTGAGGTGTTGTTGATTAAATTCCATATGTGATG
65 TGAACTCTCCACAAGAAATGTTGATCATTGAGTGAGGTGTTGTTGATTAAACTCCATATATGATG
*
11595363 AATCGAGC
130 AATCGAGA
* * *
11595371 TAAGGCTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCGTTA
1 TAAGG-TGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTA
** * * * *
11595436 TGAACTCTCCACTGGAGATGTTGATCATTCGAGTGAGGTGTTGTTTATTCAACTCCTTATATGAT
65 TGAACTCTCCACAAGAAATGTTGATCATT-GAGTGAGGTGTTGTTGATTAAACTCCATATATGAT
11595501 GAATCGAGA
129 GAATCGAGA
* * * * * * *
11595510 TAAGGTGGAACAGGTTCTTCTCATTATGAACTTTTTTTCCTTCTTTGGATGAGTTATTCTCATTA
1 TAAGGT-GAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTA
11595575 TGAAC
65 TGAAC
11595580 CCTTCTATTG
Statistics
Matches: 183, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
138 85 0.46
139 98 0.54
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (137 bp):
TAAGGTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTAT
GAACTCTCCACAAGAAATGTTGATCATTGAGTGAGGTGTTGTTGATTAAACTCCATATATGATGA
ATCGAGA
Found at i:11596505 original size:55 final size:55
Alignment explanation
Indices: 11596426--11597220 Score: 771
Period size: 55 Copynumber: 14.6 Consensus size: 55
11596416 ATTCATCATG
* * * *
11596426 TCAAGAAACCTT-TGGAAATTAGACTTAGTTTCTTTGAAAGCTCATTAAAAAATCA
1 TCAAGAAA-CTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * * *
11596481 TCAAGAAACTTTTGAAAAGCAGACTTAGTTTCTTTAAAAACTAATTT-GAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * * * *
11596535 TCATGAAACTTTTGAAAATAAGACTTAGTTTCTTTGAAAGCTCATTGAAAAATAA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* ** * * *
11596590 TCAAGGAACTTCCAAAAATCATATTTAG-TTCTTTAAAAGCTCATTTAAAAATAA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * *
11596644 TCAAGAAACTTCTGAAAATTAGACTTAGTTTATTTAAAAACTCATTT-CAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * * * *
11596698 TCAGGAAACTTCTAAAAATCACACTTAGTTTATTTGAAAGCTCATTTAAAAATAA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * * * **
11596753 TCAATAAACCTCCGAAAATCAGACTTA-TTT-TTT-AAA-CTCATGTGAAAATTG
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
*
11596804 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTT-AAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * * *
11596858 TCAGGAAACTTATGAAAATCAGACTTAGTTTTTTTGAAAGCTCATTTAAAAATAA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * *
11596913 TCAAGAAACTT-TCGAAAATCGGACCTAGTTTCTTTAAAAGCTCATTTAAAAATAA
1 TCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
** ** * *
11596968 TCAAGAAACTTCCAAAAAATCAGACTTAGTTTCTTTAAAAAAATCATTTGAAAATCG
1 TCAAGAAACTT-CTGAAAATCAGACTTAGTTTCTTT-AAAAGCTCATTTAAAAATCA
* * *
11597025 TTAAGAAACTTATGAAAATCAGACTTAGTTTATTTGAAAA-CTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAGCTCATTTAAAAATCA
* * * * *
11597080 TCAAGAAAGTTCTGAAAACCAGACTTAGTTTCTTTTAAAGGT-AGTTTGAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCA-TTTAAAAATCA
* * *
11597135 TCTAGAAACTTCTG-AAATC--A--TATTTTCTTTGAAAA-CTCATTAAAAATATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAGCTCATTTAAAA-ATCA
* * *
11597186 TGGCAAGAAACCTCTGAAAAACAGACTTAATTTCT
1 T--CAAGAAACTTCTGAAAATCAGACTTAGTTTCT
11597221 AAAAACAAAT
Statistics
Matches: 605, Mismatches: 110, Indels: 47
0.79 0.14 0.06
Matches are distributed among these distances:
50 15 0.02
51 44 0.07
52 7 0.01
53 17 0.03
54 207 0.34
55 239 0.40
56 44 0.07
57 25 0.04
58 7 0.01
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (55 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
Found at i:11596565 original size:109 final size:110
Alignment explanation
Indices: 11596426--11597220 Score: 778
Period size: 109 Copynumber: 7.3 Consensus size: 110
11596416 ATTCATCATG
* * *
11596426 TCAAGAAACCTT-TGGAAATTAGACTTAGTTTCTTTGAAAGCTCATTAAAAAATCATCAAGAAAC
1 TCAAGAAA-CTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAAC
* * * * *
11596490 TTTTGAAAAGCAGACTTAGTTTCTTTAAAAACTAATTT-GAAATCA
65 TTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAA
* * * * * *
11596535 TCATGAAACTTTTGAAAATAAGACTTAGTTTCTTTGAAAGCTCATTGAAAAATAATCAAGGAACT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACT
** * * *
11596600 TCCAAAAATCATATTTAG-TTCTTTAAAAGCTCATTTAAAAATAA
66 TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAA
* * * * * *
11596644 TCAAGAAACTTCTGAAAATTAGACTTAGTTTATTTAAAAACTCATTT-CAAATCATCAGGAAACT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACT
* * * * *
11596708 TCTAAAAATCACACTTAGTTTATTTGAAAGCTCATTTAAAAATAA
66 TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAA
* * * * * **
11596753 TCAATAAACCTCCGAAAATCAGACTTA-TTT-TTT-AAA-CTCATGTGAAAATTGTCAAGAAACT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACT
*
11596814 TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTT-AAAATCA
66 TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAA
* * * *
11596858 TCAGGAAACTTATGAAAATCAGACTTAGTTTTTTTGAAAGCTCATTTAAAAATAATCAAGAAACT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACT
* * *
11596923 T-TCGAAAATCGGACCTAGTTTCTTTAAAAGCTCATTTAAAAATAA
66 TCT-GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAA
** * ** * * *
11596968 TCAAGAAACTTCCAAAAAATCAGACTTAGTTTCTTTAAAAAAATCATTTGAAAATCGTTAAGAAA
1 TCAAGAAACTT-CTGAAAATCAGACTTAGTTTCTTT-GAAAGCTCATTTAAAAATCATCAAGAAA
* * * *
11597033 CTTATGAAAATCAGACTTAGTTTATTTGAAAACTCATTTAAAAATCA
64 CTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAA
* * * * * *
11597080 TCAAGAAAGTTCTGAAAACCAGACTTAGTTTCTTTTAAAGGT-AGTTTGAAAATCATCTAGAAAC
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCA-TTTAAAAATCATCAAGAAAC
* *
11597144 TTCTG-AAATC--A--TATTTTCTTTGAAAACTCA-TTAAAAATATCA
65 TTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATA--A
* * *
11597186 TGGCAAGAAACCTCTGAAAAACAGACTTAATTTCT
1 T--CAAGAAACTTCTGAAAATCAGACTTAGTTTCT
11597221 AAAAACAAAT
Statistics
Matches: 572, Mismatches: 96, Indels: 37
0.81 0.14 0.05
Matches are distributed among these distances:
104 8 0.01
105 51 0.09
106 53 0.09
107 7 0.01
108 82 0.14
109 218 0.38
110 41 0.07
111 41 0.07
112 70 0.12
113 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (110 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACT
TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAA
Found at i:11602277 original size:103 final size:103
Alignment explanation
Indices: 11602098--11602303 Score: 340
Period size: 103 Copynumber: 2.0 Consensus size: 103
11602088 TCACGGGATG
* * * *
11602098 ACTCTACTTGACTAGCTCGTGGGTGGAATGTAAGCTCCCTTTCACTTAGAGTGTGGGATAGTAGT
1 ACTCTACCTGACTAGCTCGGGGGCGGAAGGTAAGCTCCCTTTCACTTAGAGTGTGGGATAGTAGT
**
11602163 GTGATGAGATGACTCCCCTTAAAGTATGTTTAAAAAAA
66 GTGATGAGATGACTCCCCTTAAAGTATACTTAAAAAAA
* *
11602201 ACTCTACCTGACTAGCTCGGGGGCGGAAGGTATGCTCTCTTTCACTTAGAGTGTGGGATAGTAGT
1 ACTCTACCTGACTAGCTCGGGGGCGGAAGGTAAGCTCCCTTTCACTTAGAGTGTGGGATAGTAGT
11602266 GTGATGAGATGACTCCCCTTAAAGTATACTTAAAAAAA
66 GTGATGAGATGACTCCCCTTAAAGTATACTTAAAAAAA
11602304 TGAGTTGAAG
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (103 bp):
ACTCTACCTGACTAGCTCGGGGGCGGAAGGTAAGCTCCCTTTCACTTAGAGTGTGGGATAGTAGT
GTGATGAGATGACTCCCCTTAAAGTATACTTAAAAAAA
Found at i:11611098 original size:14 final size:14
Alignment explanation
Indices: 11611081--11611116 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11611071 TGAAGGGAAA
*
11611081 AAATTAAAGTCAGG
1 AAATTAAAGTAAGG
*
11611095 AAATTAAAGTAATG
1 AAATTAAAGTAAGG
11611109 AAATTAAA
1 AAATTAAA
11611117 TAATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGTAAGG
Found at i:11611125 original size:13 final size:13
Alignment explanation
Indices: 11611094--11611132 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
11611084 TTAAAGTCAG
11611094 GAAATTAAAGTAAT
1 GAAATTAAA-TAAT
11611108 GAAATTAAATAAT
1 GAAATTAAATAAT
* *
11611121 TAAATAAAATAA
1 GAAATTAAATAA
11611133 AGGACATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (13 bp):
GAAATTAAATAAT
Found at i:11624785 original size:54 final size:54
Alignment explanation
Indices: 11624701--11624993 Score: 444
Period size: 54 Copynumber: 5.4 Consensus size: 54
11624691 TAGTAATTAC
* * *
11624701 TGTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGATTTTAAGAATTTT
1 TGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
* * *
11624755 TATATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTAAGAATTTC
1 TGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
* *
11624809 TGTATTGGCACTATGTATGCAACTTAAGAAATTCATAATGAGTTTGTGAATTTT
1 TGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
11624863 TGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
1 TGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
** *
11624917 CATATTGGCAC-AGTGTGTGCAGCTTAAGAAATTCATAATGAGTTTATGAATTTT
1 TGTATTGGCACTA-TGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
* * *
11624971 CGTATTGGCAATAAGTGTGCAAC
1 TGTATTGGCACTATGTGTGCAAC
11624994 CCCACATAAT
Statistics
Matches: 219, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
53 1 0.00
54 217 0.99
55 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (54 bp):
TGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
Found at i:11630207 original size:54 final size:54
Alignment explanation
Indices: 11630120--11630237 Score: 191
Period size: 54 Copynumber: 2.2 Consensus size: 54
11630110 GAATTTCTCA
* *
11630120 TTATTAATTTCCGTATTAGCATTATGTGTGCAACATAAGAAATTCATAATGAGT
1 TTATAAATTTCCGTATTAGCATGATGTGTGCAACATAAGAAATTCATAATGAGT
* *
11630174 TTATAAATTTCCGTATTAGCATGGTGTGTGCAACTTAAGAAATTCATAATGAGT
1 TTATAAATTTCCGTATTAGCATGATGTGTGCAACATAAGAAATTCATAATGAGT
*
11630228 TTATGAATTT
1 TTATAAATTT
11630238 ATGTATTGTC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (54 bp):
TTATAAATTTCCGTATTAGCATGATGTGTGCAACATAAGAAATTCATAATGAGT
Found at i:11630396 original size:11 final size:11
Alignment explanation
Indices: 11630380--11630405 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11630370 TATACTCTTG
11630380 TTTAGAATTTA
1 TTTAGAATTTA
11630391 TTTAGAATTTA
1 TTTAGAATTTA
11630402 TTTA
1 TTTA
11630406 TGATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TTTAGAATTTA
Found at i:11631948 original size:43 final size:43
Alignment explanation
Indices: 11631882--11632148 Score: 204
Period size: 43 Copynumber: 6.3 Consensus size: 43
11631872 TGGCAACAAA
* *** * *
11631882 AAACACTGCAATAGGTAACGATATATAGCGACGTTTGT-CCAAC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTT-TACCAAC
* *
11631925 TAACACTGCAATAGGTGTTGATATTTAGCGGCGTTTTACCAAC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTACCAAC
* * * * *
11631968 AAACGCCGTAATAGGTGTGGAGATTTAGCGGCGTTTTTCCCAA-
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCG-TTTTACCAAC
* * * * *
11632011 AAACGCCGCAATAGGTGTTGAGATTTAGTGGAGTTTT-CCCAC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTACCAAC
* * *
11632053 AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTGA-C-AC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTT-ACCAAC
* * * * * *
11632095 AAACACCGAAATATGTCTTGAGATTTTA-CGGCGTTTTTCCCAC
1 AAACACCGCAATAGGTGTTGATA-TTTAGCGGCGTTTTACCAAC
*
11632138 AAACGCCGCAA
1 AAACACCGCAA
11632149 AAGATCTGGT
Statistics
Matches: 188, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.02
42 70 0.37
43 107 0.57
44 8 0.04
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTACCAAC
Found at i:11631997 original size:86 final size:85
Alignment explanation
Indices: 11631889--11632148 Score: 247
Period size: 85 Copynumber: 3.0 Consensus size: 85
11631879 AAAAAACACT
** * * * * * *
11631889 GCAATAGGTAACGATATATAGCGACGTTTGT-CCAACTAACACTGCAATAGGTGTTGATATTTAG
1 GCAATAGGTATGGAGATTTAGCGGCGTTTGTCCCAA-AAACACCGCAATAGGTGTTGAGATTTAG
*
11631953 CGGCGTTTTACCAACAAACGCC
65 CGGAGTTTT-CCAACAAACGCC
* * * * *
11631975 GTAATAGGTGTGGAGATTTAGCGGCGTTTTTCCCAAAAACGCCGCAATAGGTGTTGAGATTTAGT
1 GCAATAGGTATGGAGATTTAGCGGCGTTTGTCCCAAAAACACCGCAATAGGTGTTGAGATTTAGC
*
11632040 GGAGTTTTCCCACAAACGCC
66 GGAGTTTTCCAACAAACGCC
* ** * * * *
11632060 GCAATAGGTATTGAGATTTAGCGGCGTTT-TGACACAAACACCGAAATATGTCTTGAGATTTTA-
1 GCAATAGGTATGGAGATTTAGCGGCGTTTGTCCCAAAAACACCGCAATAGGTGTTGAGA-TTTAG
* *
11632123 CGGCGTTTTTCCCACAAACGCC
65 CGGAG-TTTTCCAACAAACGCC
11632145 GCAA
1 GCAA
11632149 AAGATCTGGT
Statistics
Matches: 144, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
84 25 0.17
85 61 0.42
86 54 0.38
87 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (85 bp):
GCAATAGGTATGGAGATTTAGCGGCGTTTGTCCCAAAAACACCGCAATAGGTGTTGAGATTTAGC
GGAGTTTTCCAACAAACGCC
Found at i:11632061 original size:42 final size:42
Alignment explanation
Indices: 11631932--11632148 Score: 265
Period size: 43 Copynumber: 5.1 Consensus size: 42
11631922 AACTAACACT
* *
11631932 GCAATAGGTGTTGATATTTAGCGGCGTTTTACCAACAAACGCC
1 GCAATAGGTGTTGAGATTTAGCGGCGTTTT-CCCACAAACGCC
* * *
11631975 GTAATAGGTGTGGAGATTTAGCGGCGTTTTTCCCAAAAACGCC
1 GCAATAGGTGTTGAGATTTAGCGGCG-TTTTCCCACAAACGCC
* *
11632018 GCAATAGGTGTTGAGATTTAGTGGAGTTTTCCCACAAACGCC
1 GCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCACAAACGCC
* ** *
11632060 GCAATAGGTATTGAGATTTAGCGGCGTTTTGACACAAACACC
1 GCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCACAAACGCC
* * *
11632102 GAAATATGTCTTGAGATTTTA-CGGCGTTTTTCCCACAAACGCC
1 GCAATAGGTGTTGAGA-TTTAGCGGCG-TTTTCCCACAAACGCC
11632145 GCAA
1 GCAA
11632149 AAGATCTGGT
Statistics
Matches: 148, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 69 0.47
43 75 0.51
44 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (42 bp):
GCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCACAAACGCC
Found at i:11632084 original size:85 final size:84
Alignment explanation
Indices: 11631926--11632148 Score: 268
Period size: 85 Copynumber: 2.6 Consensus size: 84
11631916 TTGTCCAACT
* * * * *
11631926 AACACTGCAATAGGTGTTGATATTTAGCGGCGTTTTACCAACAAACGCCGTAATAGGTGTGGAGA
1 AACACCGCAATAGGTGTTGAGATTTAGCGGCGTTTT-CCCACAAACGCCGCAATAGGTATGGAGA
*
11631991 TTTAGCGGCGTTTTTCCCAAA
65 TTTAGCGGCG-TTTTCACAAA
* * * *
11632012 AACGCCGCAATAGGTGTTGAGATTTAGTGGAGTTTTCCCACAAACGCCGCAATAGGTATTGAGAT
1 AACACCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCACAAACGCCGCAATAGGTATGGAGAT
* *
11632077 TTAGCGGCGTTTTGACACA
66 TTAGCGGCGTTTTCACAAA
* * *
11632096 AACACCGAAATATGTCTTGAGATTTTA-CGGCGTTTTTCCCACAAACGCCGCAA
1 AACACCGCAATAGGTGTTGAGA-TTTAGCGGCG-TTTTCCCACAAACGCCGCAA
11632149 AAGATCTGGT
Statistics
Matches: 117, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
84 28 0.24
85 58 0.50
86 31 0.26
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (84 bp):
AACACCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCACAAACGCCGCAATAGGTATGGAGAT
TTAGCGGCGTTTTCACAAA
Found at i:11635422 original size:42 final size:42
Alignment explanation
Indices: 11635337--11635423 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
11635327 TACGGATTAA
* ** *
11635337 AAAGTACGAGTATTTAGTGGCGTTTGTGCTTAAAATGCCACT
1 AAAGTACGAGTATTTAGCGGCGTTTGTGCTTAAAAAACAACT
* *
11635379 AAAGTACGAGTATTTGGCGGTGTTTGTGCTTAAAAAACAACT
1 AAAGTACGAGTATTTAGCGGCGTTTGTGCTTAAAAAACAACT
11635421 AAA
1 AAA
11635424 ATATATTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (42 bp):
AAAGTACGAGTATTTAGCGGCGTTTGTGCTTAAAAAACAACT
Found at i:11635603 original size:40 final size:40
Alignment explanation
Indices: 11635473--11635620 Score: 118
Period size: 40 Copynumber: 3.6 Consensus size: 40
11635463 AGTACGAGTC
* * **
11635473 TTTAGCGGCGTTTGTATAAAAAACGCCGCTAAAG-ACTCGTA
1 TTTAGCGGCGCTTGTAT-AAAAACGCCACTAAAGTA-AAGTA
* * * * * *
11635514 CTATAGCGGTGTTTGTATAAAAACGCCACTAAATTATAGTC
1 -TTTAGCGGCGCTTGTATAAAAACGCCACTAAAGTAAAGTA
* * *
11635555 TTTCGCGGCGCTTGTATAAAAATGCCACTAAAGTAAATTA
1 TTTAGCGGCGCTTGTATAAAAACGCCACTAAAGTAAAGTA
* * *
11635595 TTTAGCGGCGTTTTTATACAAACGCC
1 TTTAGCGGCGCTTGTATAAAAACGCC
11635621 GCTATAGAAC
Statistics
Matches: 85, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
40 52 0.61
41 17 0.20
42 16 0.19
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (40 bp):
TTTAGCGGCGCTTGTATAAAAACGCCACTAAAGTAAAGTA
Found at i:11641352 original size:3 final size:3
Alignment explanation
Indices: 11641344--11641450 Score: 159
Period size: 3 Copynumber: 36.3 Consensus size: 3
11641334 AGATGTTAAC
11641344 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
11641392 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA GATA A-A AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
11641436 A-A ATAA ATA A-A ATA A
1 ATA AT-A ATA ATA ATA A
11641451 AAAGACACGG
Statistics
Matches: 96, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
2 8 0.08
3 82 0.85
4 6 0.06
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:11641898 original size:130 final size:131
Alignment explanation
Indices: 11641634--11642102 Score: 482
Period size: 131 Copynumber: 3.6 Consensus size: 131
11641624 GGTCTGGATG
* * * ** *
11641634 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCAGGTCAGTGGATGACACGGCTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGATTCCTACGT
* * * * * *
11641699 GATGAAGA-GTTATGGCCATCTTTAGGAAGGGTGATAAC-CCGGTTCCTACGTTATTAGGAC-AG
66 GATGAGGACG-GAAGGCCATCCTTAGGAA---TGATAACACC-GTTCCTACGTGATGAGGACGA-
11641761 CTGGTTA
125 CTGGTTA
* * * * *
11641768 TCTAAGGGTGACACGACTCCAACGTGATGAGGAGGTCTGGTC-GGGGATGACACGGTTGCTATGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGATTCCTACGT
* * * *
11641832 GATGAGGACGGCAGGCTATCCTTAAGAATGATAACACCGTTCCTACGTGATGAGGACGACAGGTT
66 GATGAGGACGGAAGGCCATCCTTAGGAATGATAACACCGTTCCTACGTGATGAGGACGACTGGTT
11641897 A
131 A
* * * * * *
11641898 TCTAAGGTTGACGCGGCTCCTACTTGATGAGGAGGTCTGGTCGGGGGATGGCACGATTCCTACCT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGATTCCTACGT
* * * * * * *
11641963 GATGAGGATGGAAGACCAT-CTATAGGGATGATAACACAGTTTCTATGTGATGAGGACGACTGAT
66 GATGAGGACGGAAGGCCATCCT-TAGGAATGATAACACCGTTCCTACGTGATGAGGACGACTGGT
11642027 TA
130 TA
*** * *
11642029 TCTAAGGGTGGTTCAGCTCCTATGTGATGAGGAGGTCTGGT-AGGGGATGACACGATTCCTACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGATTCCTACGT
11642093 GATGAGGACG
66 GATGAGGACG
11642103 ACATACCATC
Statistics
Matches: 279, Mismatches: 51, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
130 98 0.35
131 106 0.38
133 36 0.13
134 39 0.14
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (131 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGATTCCTACGT
GATGAGGACGGAAGGCCATCCTTAGGAATGATAACACCGTTCCTACGTGATGAGGACGACTGGTT
A
Found at i:11642418 original size:38 final size:38
Alignment explanation
Indices: 11642376--11642475 Score: 157
Period size: 38 Copynumber: 2.6 Consensus size: 38
11642366 TGTTACCAAA
* *
11642376 GAAACAGACTCAAAG-TTTTTTTTCATTTTGTTTCAAGT
1 GAAACATACTCAAAGATTTTTTTT-ATTTCGTTTCAAGT
*
11642414 GAAACATACTCAAAGATTTTTTTTGTTTCGTTTCAAGT
1 GAAACATACTCAAAGATTTTTTTTATTTCGTTTCAAGT
11642452 GAAACATACTCAAAGATTTTTTTT
1 GAAACATACTCAAAGATTTTTTTT
11642476 TCAAAAGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 50 0.86
39 8 0.14
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (38 bp):
GAAACATACTCAAAGATTTTTTTTATTTCGTTTCAAGT
Done.