Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009628.1 Hibiscus syriacus cultivar Beakdansim tig00117021_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: 2284295
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1561462 original size:17 final size:16
Alignment explanation
Indices: 1561438--1561469 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1561428 ATTTTTAGTA
1561438 TTTATTTATTTGTTTG
1 TTTATTTATTTGTTTG
1561454 TTTAGTTTATTTGTTT
1 TTTA-TTTATTTGTTT
1561470 TGGTATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.75
Consensus pattern (16 bp):
TTTATTTATTTGTTTG
Found at i:1565315 original size:23 final size:23
Alignment explanation
Indices: 1565281--1565343 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1565271 CATCTTATAT
1565281 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1565304 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
1565327 GGCACTTCGATGCATTT
1 GGCACTTCGGTGCATTT
1565344 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1568356 original size:16 final size:16
Alignment explanation
Indices: 1568335--1568420 Score: 57
Period size: 16 Copynumber: 5.0 Consensus size: 16
1568325 TTTTAAATAC
1568335 TATATTTATTTATTAT
1 TATATTTATTTATTAT
1568351 TATATTT-TCATTATTTAT
1 TATATTTAT--TTA-TTAT
* *
1568369 TATATTTAACAATTAATAT
1 TATATTT---ATTTATTAT
* * *
1568388 TATTAATTATTAATTTT
1 TA-TATTTATTTATTAT
1568405 TATATTTATTTATTAT
1 TATATTTATTTATTAT
1568421 ATTTGTCGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 16
0.67 0.13 0.21
Matches are distributed among these distances:
15 1 0.02
16 18 0.35
17 10 0.19
18 11 0.21
19 5 0.10
20 7 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTATTTATTAT
Found at i:1571290 original size:53 final size:53
Alignment explanation
Indices: 1571200--1571455 Score: 370
Period size: 53 Copynumber: 4.8 Consensus size: 53
1571190 ATGATGTGTC
* * ****
1571200 CGCTCTCTCTTG-TTCAGGGATTAAGGAACTCGAACAATCTTCTAAAAACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGTTTACGGGTT
* *
1571254 CGCTCCCTATTGCTTCAGGGAGTATAACTCGAACAATCTTCTGTTTACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTTTACGGGTT
1571307 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTTTACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTTTACGGGTT
* * * **
1571360 TGATCCCTCTTGCTTTAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTTTACGGGTT
1571413 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1571456 ATGTGATTCT
Statistics
Matches: 183, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
53 163 0.89
54 11 0.06
55 9 0.05
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.31
Consensus pattern (53 bp):
CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTTTACGGGTT
Found at i:1571904 original size:42 final size:41
Alignment explanation
Indices: 1571826--1572076 Score: 210
Period size: 42 Copynumber: 6.1 Consensus size: 41
1571816 TCCGAGAAGG
* * *
1571826 CTTA-AAATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACAAATGACCCGAAGGATTTATCATCATGCTCGAAAGA
1571866 CTTACAAATGACCCGAAGGATTTCATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGATTT-ATCATCATGCTCGAAAGA
** ** * * * * *
1571908 CTTAC---TGA-TGGATTTGCTTTATTACTCTTCGGT-G-AAGG
1 CTTACAAATGACCCGA-AGGATTTATCA-TCAT-GCTCGAAAGA
*
1571946 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGATTT-ATCATCATGCTCGAAAGA
** * *
1571988 CTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGA-TTTATCATCATGCTCGAAAGA
** *
1572030 CTTACTGATGACCCGAAGGATTTAATCATCGTGCTCGAAAGA
1 CTTACAAATGACCCGAAGGATTT-ATCATCATGCTCGAAAGA
1572072 CTTAC
1 CTTAC
1572077 TGATGACACT
Statistics
Matches: 167, Mismatches: 30, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
38 13 0.08
39 11 0.07
40 8 0.05
41 28 0.17
42 105 0.63
43 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (41 bp):
CTTACAAATGACCCGAAGGATTTATCATCATGCTCGAAAGA
Found at i:1572015 original size:122 final size:120
Alignment explanation
Indices: 1571821--1572039 Score: 348
Period size: 122 Copynumber: 1.8 Consensus size: 120
1571811 ACTTTTCCGA
* *
1571821 GAAGGCTTAAAATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGACCCGAAGGA
1 GAAGGCTTAAAATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACAAATGACCCGAAGGA
*
1571886 TTTCATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTTATTACTCTTCGGT
66 CTTCATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTTATTACTCTTCGGT
* * ** *
1571941 GAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
1 GAAGGCTTA-AAATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACAAATGACCCGAAG
1572006 GACTTCATCATCATGCTCGAAAGACTTACTGATG
64 GACTTCATCATCATGCTCGAAAGACTTACTGATG
1572040 ACCCGAAGGA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
120 9 0.10
121 15 0.17
122 65 0.73
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (120 bp):
GAAGGCTTAAAATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACAAATGACCCGAAGGA
CTTCATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTTATTACTCTTCGGT
Found at i:1572077 original size:42 final size:42
Alignment explanation
Indices: 1571956--1572083 Score: 220
Period size: 42 Copynumber: 3.0 Consensus size: 42
1571946 CTTACAAATT
1571956 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* * *
1571998 GCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
*
1572040 ACCCGAAGGATTTAATCATCGTGCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
1572082 AC
1 AC
1572084 ACTTACTGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (42 bp):
ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
Found at i:1572158 original size:93 final size:93
Alignment explanation
Indices: 1572040--1572366 Score: 557
Period size: 93 Copynumber: 3.5 Consensus size: 93
1572030 CTTACTGATG
* * *
1572040 ACCCGAAGGATTTAATCATCGTGCTCGAAAGACTTACTGATGACACTTACTGATGGATTTGCTTC
1 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTC
*
1572105 ACTACTCTTCGGTTAAGGCTTACAAATT
66 ACTACTCTTCGGTGAAGGCTTACAAATT
* * *
1572133 ACCTGAAAGACTTAATCATCATGCTCGAAAGCCTTACTGATGGCACTTACTGATGGATTTGCTTC
1 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTC
1572198 ACTACTCTTCGGTGAAGGCTTACAAATT
66 ACTACTCTTCGGTGAAGGCTTACAAATT
* *
1572226 ACCCGAAGGATTTAATCATCATGCTCGAAAGCCTTACTGATGGCACTTACTGATGGATTTGCTTC
1 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTC
1572291 ACTACTCTTCGGTGAAGGCTTACAAATT
66 ACTACTCTTCGGTGAAGGCTTACAAATT
*
1572319 ACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC-CTTA
1 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTA
1572367 AGGATTTAAG
Statistics
Matches: 222, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
92 4 0.02
93 218 0.98
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (93 bp):
ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTC
ACTACTCTTCGGTGAAGGCTTACAAATT
Found at i:1572288 original size:186 final size:180
Alignment explanation
Indices: 1571907--1572396 Score: 654
Period size: 186 Copynumber: 2.7 Consensus size: 180
1571897 TGCTCGAAAG
* * *
1571907 ACTTACTGATGGATTTGCTTTATTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAAGATTTAAT
1571972 CATCATGCTCGAAAGACTTACTGATGGCC---CGAAGGACTTCATCATCATGCTCGAAAGACTTA
66 CATCATGCTCGAAAGACTTACTGATGGCCTTACGAAGGACTTCATCATCATGCTCGAAAGACTTA
** *
1572034 CTGATGACCCGAAGGATTTAATCATCGTGCTCGAAAGACTTACTGATGAC
131 CAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAC
* * *
1572084 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTTAAGGCTTACAAATTACCTGAAAGACTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAAGATTTAAT
* * * * *
1572149 CATCATGCTCGAAAGCCTTACTGATGGCACTTACTGATGGATTTGCTTCA-CTACT-CTTCGGTG
66 CATCATGCTCGAAAGACTTACTGATGGC-CTTAC-GAAGGACTT-CATCATC-A-TGC-TC-G-A
* * * *
1572212 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGCCTTACTGATGGC
123 AAGACTTACAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAC
*
1572270 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAATGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAAGATTTAAT
* * *
1572335 CATCATGCTCGAAAGACTTACTGATGGCCTT---AAGGATTTAAGCATCATGCTCGAAAGACTTA
66 CATCATGCTCGAAAGACTTACTGATGGCCTTACGAAGGACTTCATCATCATGCTCGAAAGACTTA
1572397 TTGATGGCCC
Statistics
Matches: 271, Mismatches: 29, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
177 93 0.34
178 2 0.01
179 3 0.01
180 4 0.01
181 9 0.03
182 8 0.03
183 6 0.02
184 3 0.01
185 4 0.01
186 139 0.51
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (180 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAAGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCTTACGAAGGACTTCATCATCATGCTCGAAAGACTTA
CAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAC
Found at i:1573034 original size:69 final size:69
Alignment explanation
Indices: 1572923--1573063 Score: 255
Period size: 69 Copynumber: 2.0 Consensus size: 69
1572913 TCATGTGCTT
* * *
1572923 ATGCATGAAACACGAATGCAATTAATTGTATCAGTGTAATGCATTTTCTTTTATGCAAATGATGT
1 ATGCATGAAACACGAATGCAATTAAATATATCAGTGTAATGCATTTTATTTTATGCAAATGATGT
1572988 TCTC
66 TCTC
1572992 ATGCATGAAACACGAATGCAATTAAATATATCAGTGTAATGCATTTTATTTTATGCAAATGATGT
1 ATGCATGAAACACGAATGCAATTAAATATATCAGTGTAATGCATTTTATTTTATGCAAATGATGT
1573057 TCTC
66 TCTC
1573061 ATG
1 ATG
1573064 AATGTATAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (69 bp):
ATGCATGAAACACGAATGCAATTAAATATATCAGTGTAATGCATTTTATTTTATGCAAATGATGT
TCTC
Found at i:1575462 original size:21 final size:21
Alignment explanation
Indices: 1575436--1575480 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1575426 GATTTCTGGG
* *
1575436 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1575457 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1575478 CAA
1 CAA
1575481 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1577347 original size:103 final size:103
Alignment explanation
Indices: 1577019--1577336 Score: 582
Period size: 103 Copynumber: 3.1 Consensus size: 103
1577009 GTCGAGGGTC
*
1577019 TATGTGGTCATTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1577084 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1577122 TATGAGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1577187 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1577225 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1577290 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1577328 TATGTGGTC
1 TATGTGGTC
1577337 CTTATGGACA
Statistics
Matches: 208, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1577386 original size:23 final size:23
Alignment explanation
Indices: 1577356--1577415 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1577346 ATTATTATAT
*
1577356 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1577379 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
1577402 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
1577416 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1577423 original size:23 final size:23
Alignment explanation
Indices: 1577346--1577423 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1577336 CCTTATGGAC
* *
1577346 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
1577370 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
1577393 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
1577416 TTTATATG
1 ATTATATG
1577424 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:1584422 original size:14 final size:15
Alignment explanation
Indices: 1584363--1584428 Score: 116
Period size: 15 Copynumber: 4.5 Consensus size: 15
1584353 TAATAAGGTT
*
1584363 ATTTATTTAAAAATA
1 ATTTATTTTAAAATA
1584378 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1584393 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1584408 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1584422 ATTTATT
1 ATTTATT
1584429 AGTATGGATT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
14 12 0.24
15 38 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1584540 original size:54 final size:54
Alignment explanation
Indices: 1584408--1585191 Score: 332
Period size: 54 Copynumber: 14.4 Consensus size: 54
1584398 TTTTAAAATA
* *** * *
1584408 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGTAGTTGTATAGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTG
* * *
1584463 ATTTATTATAAATAAGTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1584517 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1584571 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTA-TTT---TAA---A--A-TATGGATTG
* * * *
1584629 ATTTATTTTAAAATAATTTATT--T-T-AAATAATTTA--TT--AGTATGGATTG
1 ATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * *
1584676 ATTTATTGT-AGT--TGTA-TA-TATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTG
** ** * ** * * *
1584731 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
* *
1584785 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * *
1584829 A-TTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-TTT---TAA---A--A-TATGG
1584893 ATTG
51 ATTG
1584897 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1584951 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
1585005 ATTTA--TT--AT--TGTACTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * *
1585049 A-TTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-TTT---TAA---A--A-TATGG
1585113 ATTG
51 ATTG
*
1585117 ATTTATTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAAATATGGATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1585170 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
1585192 TTGTAGTTGT
Statistics
Matches: 568, Mismatches: 66, Indels: 191
0.69 0.08 0.23
Matches are distributed among these distances:
42 1 0.00
43 10 0.02
44 9 0.02
45 7 0.01
46 3 0.01
47 25 0.04
48 46 0.08
49 18 0.03
50 15 0.03
51 4 0.01
52 11 0.02
53 23 0.04
54 188 0.33
55 66 0.12
56 3 0.01
57 2 0.00
58 25 0.04
59 10 0.02
60 5 0.01
61 7 0.01
62 6 0.01
63 21 0.04
64 19 0.03
65 9 0.02
66 2 0.00
67 3 0.01
68 18 0.03
69 12 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1584554 original size:18 final size:18
Alignment explanation
Indices: 1584531--1584578 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1584521 ATTTTAAATA
*
1584531 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1584549 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1584571 ATTTATTA
1 ATTTATTA
1584579 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1584628 original size:32 final size:32
Alignment explanation
Indices: 1584587--1585159 Score: 371
Period size: 32 Copynumber: 18.7 Consensus size: 32
1584577 TATTGTAGTT
1584587 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1584619 GTATGGATTGATTTATTTTAAAATAATTTATTTTA
1 GTATGGATTGATTTATTTT-AAATAATTTA--TTA
* * * * * * *
1584654 -AAT-AATTTATTAGTATGGATTGATTTATTGTAGTT-
1 GTATGGATTGATT--TAT--TTTAAATAATT-TA-TTA
**
1584689 GTATATATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1584721 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1584744 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1584775 GTATGGATTGATTTA--TT--AT--TGTAGTT-
1 GTATGGATTGATTTATTTTAAATAATTTA-TTA
1584801 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1584833 GTATAGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1584856 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1584887 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1584919 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1584942 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
**
1584973 GTATGGATTGATTTATTTTAAA-ATATGGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * * *
1585004 G-ATTTATT-ATTGTACTTGTATGGATTGATTTATT-
1 GTATGGATTGATT-TA-TT-T-T-AAATAATTTATTA
* * * * *
1585038 -T-T-AAATAATTTATTAGTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-TA-AATAATTTA--TT--A
*
1585075 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1585107 GTATGGATTGATTTATTTTAAATAA-TTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1585138 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
1585160 ATATGGATTT
Statistics
Matches: 434, Mismatches: 39, Indels: 137
0.71 0.06 0.22
Matches are distributed among these distances:
22 41 0.09
23 12 0.03
25 3 0.01
26 27 0.06
27 2 0.00
28 13 0.03
29 6 0.01
30 11 0.03
31 50 0.12
32 180 0.41
33 28 0.06
34 12 0.03
35 9 0.02
36 16 0.04
37 12 0.03
38 2 0.00
39 1 0.00
40 9 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1584658 original size:14 final size:15
Alignment explanation
Indices: 1584629--1584664 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
1584619 GTATGGATTG
1584629 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1584644 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1584658 ATTTATT
1 ATTTATT
1584665 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1584738 original size:22 final size:22
Alignment explanation
Indices: 1584722--1584764 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1584712 AATTTATTAG
1584722 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1584744 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1584765 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1584742 original size:134 final size:131
Alignment explanation
Indices: 1584431--1584682 Score: 374
Period size: 134 Copynumber: 2.0 Consensus size: 131
1584421 AATTTATTAG
* * *
1584431 TATGGATTGA-TT-T-ATTGTAGTTGTATAGATTAATTTATTATAAATAAGTTATTAGTATAGAT
1 TATGGATTGATTTATAATTGTAGTTGTATGGATTGATTTATTTTAAATAAGTTATTAGTATAGAT
1584493 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
66 TGATTTATTTTAAAATAT-GA-T-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
1584558 AAAA
128 AAAA
* * *
1584562 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTATAATTGTAGTTGTATGGATTGATTTATTTTAAATAAGTTATTAGTATAGAT
1584627 TGATTTATTTT-AAA-AT-A-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
66 TGATTTATTTTAAAATATGATATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
1584683 GTAGTTGTAT
Statistics
Matches: 113, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
127 39 0.35
130 1 0.01
131 10 0.09
132 4 0.04
133 4 0.04
134 55 0.49
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (131 bp):
TATGGATTGATTTATAATTGTAGTTGTATGGATTGATTTATTTTAAATAAGTTATTAGTATAGAT
TGATTTATTTTAAAATATGATATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
A
Found at i:1584842 original size:112 final size:112
Alignment explanation
Indices: 1584562--1585123 Score: 726
Period size: 112 Copynumber: 5.1 Consensus size: 112
1584552 TATTTTAAAA
*
1584562 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGAT
1584627 TGATTTATTTT-AAA-AT--A---ATTTATTTTAAATAATTTATTAG
66 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
** *
1584667 TATGGATTGA--T-TTATTGTAGTTGTATATATTGATTTATTTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGAT
1584729 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
66 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1584776 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGAT
1 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGAT
1584841 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
66 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
1584888 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTTA
* * * * *
1584952 TTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-TTT---TAA---A--A-
55 -TTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
*
1584996 TATGGATTGATTTATTATTGTACTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGAT
1 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGAT
1585061 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
66 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1585108 TATGGATTGATTTATT
1 TATGGATTGATTTATT
1585124 TTAAATAATT
Statistics
Matches: 400, Mismatches: 19, Indels: 69
0.82 0.04 0.14
Matches are distributed among these distances:
97 6 0.01
98 11 0.03
100 2 0.00
101 5 0.01
102 97 0.24
103 9 0.02
104 4 0.01
105 10 0.03
106 6 0.01
108 14 0.04
109 35 0.09
111 3 0.01
112 125 0.31
114 5 0.01
116 2 0.00
117 5 0.01
118 37 0.09
119 5 0.01
120 2 0.00
122 11 0.03
123 6 0.01
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (112 bp):
TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGAT
TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:1584862 original size:236 final size:234
Alignment explanation
Indices: 1584393--1585011 Score: 766
Period size: 236 Copynumber: 2.6 Consensus size: 234
1584383 TTTTAAAATA
1584393 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGTAGTTGTATA
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGTAGTTGTATA
* * * *
1584458 GATTAATTTATTATAAATAAGTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTAT
66 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
* *
1584523 TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
131 TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTATAATTG
* * * *
1584588 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
196 TATGGATAGATTGATTTT-AAT-ATTTATAAATATGGATTG
1584629 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGTAGTTGTATA
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGTAGTTGTATA
*
1584694 TATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
66 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
***
1584759 TTTAAATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT-TTAAA
131 TTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTATT--A
*
1584823 TAATT-TATTAGTATAGATTGA-TTT-AT-TTTA-AAATATGGATTG
190 TAATTGTA-T-GGATAGATTGATTTTAATATTTATAAATATGGATTG
1584865 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
1 ATTTA-TTT---T-A---A--A--AT--A---ATTTATTTTAAATAATTTATTAGTATGGATTGA
* *** *
1584930 TTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
49 TTTATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
1584994 AATATGGATTGATTTATT
114 AATATGGATTGATTTATT
1585012 ATTGTACTTG
Statistics
Matches: 337, Mismatches: 21, Indels: 34
0.86 0.05 0.09
Matches are distributed among these distances:
236 171 0.51
237 8 0.02
238 2 0.01
239 6 0.02
240 19 0.06
241 9 0.03
242 8 0.02
244 1 0.00
246 1 0.00
248 2 0.01
250 1 0.00
252 68 0.20
253 41 0.12
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (234 bp):
ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGTAGTTGTATA
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTATAATTG
TATGGATAGATTGATTTTAATATTTATAAATATGGATTG
Found at i:1584945 original size:22 final size:22
Alignment explanation
Indices: 1584920--1584962 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1584910 AATTTATTAG
1584920 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1584942 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1584963 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1585162 original size:32 final size:32
Alignment explanation
Indices: 1585076--1585159 Score: 161
Period size: 31 Copynumber: 2.7 Consensus size: 32
1585066 TATTTTAAAA
1585076 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
1585108 TATGGATTGATTTATTTTAAATAA-TTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
1585139 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1585160 ATATGGATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 28 0.54
32 24 0.46
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:1585167 original size:22 final size:22
Alignment explanation
Indices: 1585139--1585181 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1585129 TAATTATTAG
1585139 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1585161 TATGGATTTATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1585182 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1585241 original size:31 final size:31
Alignment explanation
Indices: 1585206--1585264 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1585196 AGTTGTATGG
* *
1585206 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
1585237 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
1585265 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:1586784 original size:31 final size:31
Alignment explanation
Indices: 1586705--1586784 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
1586695 CAGTTACGTT
* * *
1586705 GGGGACCATATTGCAAACGGACTAAATGTTA
1 GGGGACCATATTGCAAATGAACTAAATATTA
*
1586736 GGGGACCATATTACAAATGAACTAAATATTA
1 GGGGACCATATTGCAAATGAACTAAATATTA
**
1586767 GGGGACTGTATTGCAAAT
1 GGGGACCATATTGCAAAT
1586785 TTTAAAAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (31 bp):
GGGGACCATATTGCAAATGAACTAAATATTA
Found at i:1588306 original size:38 final size:38
Alignment explanation
Indices: 1588255--1588399 Score: 206
Period size: 38 Copynumber: 3.9 Consensus size: 38
1588245 AAATGTACAG
* *
1588255 TCCATATTTGTAAACCATAATTCATACCCAAAAAAAGC
1 TCCATATGTGTAAACCATAATTCACACCCAAAAAAAGC
* *
1588293 TCCATATGTGTAAACCATAGTTCACACCCGAAAAAAGC
1 TCCATATGTGTAAACCATAATTCACACCCAAAAAAAGC
1588331 TCCATATGTGTAAACCATAATTCACACCCAAAATAAAG-
1 TCCATATGTGTAAACCATAATTCACACCCAAAA-AAAGC
* *
1588369 TCC--ATGTGTAAACCATATTTAACACCCAAAA
1 TCCATATGTGTAAACCATAATTCACACCCAAAA
1588400 CAAAAACTCG
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
36 26 0.27
38 68 0.69
39 4 0.04
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.24
Consensus pattern (38 bp):
TCCATATGTGTAAACCATAATTCACACCCAAAAAAAGC
Found at i:1591286 original size:23 final size:23
Alignment explanation
Indices: 1591252--1591320 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
1591242 TATTATTATA
1591252 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
1591275 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1591298 TGGCACTTCGGTGCAATTTTACG
1 TGGCACTACGGTGCAATTCTACG
1591321 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1612354 original size:23 final size:23
Alignment explanation
Indices: 1612328--1612374 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1612318 TAATGCCGAT
*
1612328 ACTACGAAAGAAATTGCACATAC
1 ACTACGAAAGAAATTACACATAC
1612351 ACTACGAAAGAAATTACACATAC
1 ACTACGAAAGAAATTACACATAC
1612374 A
1 A
1612375 TACTACTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.21, G:0.11, T:0.17
Consensus pattern (23 bp):
ACTACGAAAGAAATTACACATAC
Found at i:1621972 original size:45 final size:44
Alignment explanation
Indices: 1621914--1621999 Score: 102
Period size: 44 Copynumber: 1.9 Consensus size: 44
1621904 AAAGAAACAA
* * *
1621914 ATAAAATTAATTTTTTTATTTAGA-CCAAAACTATGTCGTTTTTGT
1 ATAAAATTAA-TTTTTTA-TAAGATCCAAAACTACGTCATTTTTGT
* *
1621959 ATAAATTTGATTTTTTATAAGATCCAAAACTACGTCATTTT
1 ATAAAATTAATTTTTTATAAGATCCAAAACTACGTCATTTT
1622000 AATGTTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 4 0.11
44 23 0.66
45 8 0.23
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (44 bp):
ATAAAATTAATTTTTTATAAGATCCAAAACTACGTCATTTTTGT
Found at i:1625825 original size:3 final size:3
Alignment explanation
Indices: 1625817--1625860 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1625807 ATTATCACAA
1625817 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1625861 AATAACTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1627198 original size:23 final size:23
Alignment explanation
Indices: 1627180--1627240 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1627170 CTCGTATAAA
1627180 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1627203 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1627226 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1627241 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1628248 original size:21 final size:21
Alignment explanation
Indices: 1628216--1628258 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1628206 TGTTTGTTTA
1628216 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
1628237 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
1628258 A
1 A
1628259 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:1632880 original size:23 final size:23
Alignment explanation
Indices: 1632864--1632968 Score: 183
Period size: 23 Copynumber: 4.6 Consensus size: 23
1632854 CGTATAAATA
1632864 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
1632887 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
1632910 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
* *
1632933 CACCGTAGTGCCGCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
1632956 CACCGTAGTGCCA
1 CACCGAAGTGCCA
1632969 TATAATAATG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.18
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:1633974 original size:21 final size:21
Alignment explanation
Indices: 1633942--1633984 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1633932 TGTTTGTTTA
1633942 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
1633963 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
1633984 A
1 A
1633985 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:1650032 original size:23 final size:23
Alignment explanation
Indices: 1650006--1650074 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1649996 CACCACAGCT
*
1650006 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
1650029 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
1650052 CATAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1650075 TATAAAGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1650216 original size:103 final size:103
Alignment explanation
Indices: 1650083--1650307 Score: 423
Period size: 103 Copynumber: 2.2 Consensus size: 103
1650073 CATATAAAGT
* *
1650083 TGTCCCTAAGGACCACATATCATTCTTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
1650148 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
*
1650186 TGTCCCGAAGGACCACATATCATTCCTTAAGAATTATATACATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
1650251 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
1650289 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
1650308 GACCCTCTAC
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 119 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
Found at i:1652203 original size:3 final size:3
Alignment explanation
Indices: 1652195--1652252 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
1652185 TACCTTAATA
1652195 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1652243 TAT TAT TAT T
1 TAT TAT TAT T
1652253 TTGATAGGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1667312 original size:22 final size:22
Alignment explanation
Indices: 1667271--1667351 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
1667261 CTCGTATAAA
1667271 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1667294 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1667316 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1667338 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
1667352 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1667347 original size:13 final size:13
Alignment explanation
Indices: 1667285--1667347 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
1667275 CCGAAGTGCC
1667285 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
1667298 CC---GAAGTGC-
1 CCGTAGAATTGCA
1667307 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
1667320 CC---GAAGTGC-
1 CCGTAGAATTGCA
1667329 CCGTAGAATTGCA
1 CCGTAGAATTGCA
1667342 CCGTAG
1 CCGTAG
1667348 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:1668999 original size:21 final size:21
Alignment explanation
Indices: 1668975--1669019 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1668965 TCTTGTTCGT
* *
1668975 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1668996 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1669017 TTG
1 TTG
1669020 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1669965 original size:16 final size:17
Alignment explanation
Indices: 1669927--1669968 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1669917 GCATCAGTTA
*
1669927 TTATCACTCAAAATCCT
1 TTATCAATCAAAATCCT
* *
1669944 TAATCAATC-AAATTCT
1 TTATCAATCAAAATCCT
1669960 TTATCAATC
1 TTATCAATC
1669969 TTTAATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATCAATCAAAATCCT
Found at i:1672226 original size:22 final size:22
Alignment explanation
Indices: 1672185--1672265 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
1672175 CTCGTATAAA
1672185 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1672208 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1672230 TGCACCGAAGTGCCCATAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1672252 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
1672266 ATATAATGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
22 44 0.79
23 12 0.21
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1673880 original size:21 final size:21
Alignment explanation
Indices: 1673856--1673900 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1673846 TCTTGTTCGT
* *
1673856 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1673877 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1673898 TTG
1 TTG
1673901 CCTAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1674761 original size:3 final size:3
Alignment explanation
Indices: 1674753--1674814 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
1674743 GGCATGTTTG
*
1674753 TAA TAA TAA TAA TAC TAAA TAA -AA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
1674799 -AA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1674815 GAAAATGGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 44 0.83
4 5 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1674785 original size:24 final size:24
Alignment explanation
Indices: 1674753--1674814 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1674743 GGCATGTTTG
*
1674753 TAATAATAATAATACTAAATAAAA
1 TAATAATAATAATAATAAATAAAA
*
1674777 TAATAATAATAATAATATATAAAA
1 TAATAATAATAATAATAAATAAAA
1674801 TAATAATAATAATA
1 TAATAATAATAATA
1674815 GAAAATGGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
TAATAATAATAATAATAAATAAAA
Found at i:1681010 original size:35 final size:35
Alignment explanation
Indices: 1680926--1681106 Score: 209
Period size: 35 Copynumber: 5.0 Consensus size: 35
1680916 ATAAGGAGAG
*
1680926 GGTTCCTAGTTTAGCCTTTAGAAAAAACTAGAGGAAGAA
1 GGTT-CTAGTTTAGCC-TTAG-AAAAACTAGAGG-AGGA
* *
1680965 GGTTCTAGTTTAGCCTTAGGAAAACTAAAGGAGGA
1 GGTTCTAGTTTAGCCTTAGAAAAACTAGAGGAGGA
* * *
1681000 GGTTCTAGTTTAGCCTTAAAAAAACCAGAGGAAGA
1 GGTTCTAGTTTAGCCTTAGAAAAACTAGAGGAGGA
*
1681035 GGGTTCTAGTTTAGCCTTACAAAAACTAGAGGAGGA
1 -GGTTCTAGTTTAGCCTTAGAAAAACTAGAGGAGGA
* * *
1681071 GGTTCTAGTTAAGCCTGAAAAAAACACTAGAGGAGG
1 GGTTCTAGTTTAGCCT-TAGAAAA-ACTAGAGGAGG
1681107 TTCTATCTAA
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
35 48 0.38
36 47 0.38
37 15 0.12
38 11 0.09
39 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (35 bp):
GGTTCTAGTTTAGCCTTAGAAAAACTAGAGGAGGA
Found at i:1681040 original size:71 final size:71
Alignment explanation
Indices: 1680918--1681104 Score: 250
Period size: 71 Copynumber: 2.6 Consensus size: 71
1680908 AATCTTGGAT
*
1680918 AAGGA-GAGGGTTCCTAGTTTAGCCTTTAGAAAAAACTAGAGGAAGAAGGTTCTAGTTTAGCCTT
1 AAGGAGGA-GGTT-CTAGTTTAGCC-TTA-AAAAAACCAGAGGAAGAAGGTTCTAGTTTAGCCTT
**
1680982 AGGAAAACTA
62 ACAAAAACTA
*
1680992 AAGGAGGAGGTTCTAGTTTAGCCTTAAAAAAACCAGAGGAAGAGGGTTCTAGTTTAGCCTTACAA
1 AAGGAGGAGGTTCTAGTTTAGCCTTAAAAAAACCAGAGGAAGAAGGTTCTAGTTTAGCCTTACAA
1681057 AAACTA
66 AAACTA
* * *
1681063 GAGGAGGAGGTTCTAGTTAAGCCTGAAAAAAACACTAGAGGA
1 AAGGAGGAGGTTCTAGTTTAGCCTTAAAAAAAC-C-AGAGGA
1681105 GGTTCTATCT
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
71 71 0.69
72 4 0.04
73 17 0.17
74 9 0.09
75 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (71 bp):
AAGGAGGAGGTTCTAGTTTAGCCTTAAAAAAACCAGAGGAAGAAGGTTCTAGTTTAGCCTTACAA
AAACTA
Found at i:1681047 original size:36 final size:35
Alignment explanation
Indices: 1680926--1681104 Score: 214
Period size: 36 Copynumber: 4.9 Consensus size: 35
1680916 ATAAGGAGAG
1680926 GGTTCCTAGTTTAGCCTTTAGAAAAAACTAGAGGAAGAA
1 GGTT-CTAGTTTAGCC-TTA-AAAAAACTAGAGGAAG-A
** * *
1680965 GGTTCTAGTTTAGCCTTAGGAAAACTAAAGGAGGA
1 GGTTCTAGTTTAGCCTTAAAAAAACTAGAGGAAGA
*
1681000 GGTTCTAGTTTAGCCTTAAAAAAACCAGAGGAAGA
1 GGTTCTAGTTTAGCCTTAAAAAAACTAGAGGAAGA
* *
1681035 GGGTTCTAGTTTAGCCTTACAAAAACTAGAGGAGGA
1 -GGTTCTAGTTTAGCCTTAAAAAAACTAGAGGAAGA
* *
1681071 GGTTCTAGTTAAGCCTGAAAAAAACACTAGAGGA
1 GGTTCTAGTTTAGCCT-TAAAAAA-ACTAGAGGA
1681105 GGTTCTATCT
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
35 46 0.38
36 49 0.40
37 12 0.10
38 11 0.09
39 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.24
Consensus pattern (35 bp):
GGTTCTAGTTTAGCCTTAAAAAAACTAGAGGAAGA
Found at i:1691232 original size:20 final size:20
Alignment explanation
Indices: 1691207--1691254 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1691197 TTCGTCTGTT
*
1691207 GCCCGCTGGCCGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
* *
1691227 GCCCGCCGTCTGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
*
1691247 GTCCGCCG
1 GCCCGCCG
1691255 CCACACTCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.00, C:0.54, G:0.33, T:0.12
Consensus pattern (20 bp):
GCCCGCCGGCCGCTGCCGCC
Found at i:1702165 original size:26 final size:29
Alignment explanation
Indices: 1702119--1702174 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 29
1702109 ACACATCCTT
1702119 AAAATATATATATAAAGAATTCAAAAATA
1 AAAATATATATATAAAGAATTCAAAAATA
*
1702148 AAAATAT-TATAT-AA-AATTTAAAAATA
1 AAAATATATATATAAAGAATTCAAAAATA
1702174 A
1 A
1702175 TTAAAAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 12 0.46
27 2 0.08
28 5 0.19
29 7 0.27
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAATATATATATAAAGAATTCAAAAATA
Found at i:1702180 original size:29 final size:31
Alignment explanation
Indices: 1702117--1702180 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
1702107 TGACACATCC
1702117 TTAAAATATATATATAAAGAATTCAAAAATA
1 TTAAAATATATATATAAAGAATTCAAAAATA
*
1702148 --AAAATAT-TATAT-AA-AATTTAAAAATAA
1 TTAAAATATATATATAAAGAATTCAAAAAT-A
1702175 TTAAAA
1 TTAAAA
1702181 AACTCGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
26 10 0.34
27 3 0.10
28 5 0.17
29 11 0.38
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (31 bp):
TTAAAATATATATATAAAGAATTCAAAAATA
Found at i:1709558 original size:17 final size:17
Alignment explanation
Indices: 1709533--1709566 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1709523 GGCTGTTGGA
*
1709533 AATGCTGCCATACTTTT
1 AATGATGCCATACTTTT
1709550 AATGATGCCATACTTTT
1 AATGATGCCATACTTTT
1709567 GATGGTATAC
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:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (17 bp):
AATGATGCCATACTTTT
Found at i:1710468 original size:33 final size:33
Alignment explanation
Indices: 1710426--1710490 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1710416 TAAGTAAGTT
*
1710426 TCTTCTTGATGGCAACAATTATCATCCGATTCA
1 TCTTCTTGATGGCAACAAATATCATCCGATTCA
* *
1710459 TCTTCTTGATGGTAACAAATATCATCTGATTC
1 TCTTCTTGATGGCAACAAATATCATCCGATTC
1710491 TTGGACTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (33 bp):
TCTTCTTGATGGCAACAAATATCATCCGATTCA
Found at i:1711368 original size:21 final size:21
Alignment explanation
Indices: 1711343--1711410 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
1711333 AGTCGCTTGT
*
1711343 CGTCCGCCGTCCTCCGACCAT
1 CGTCCGCCGTCCTCCGACCAC
*
1711364 CGTCCGCCGTCCTCCAACCAC
1 CGTCCGCCGTCCTCCGACCAC
* *
1711385 CGTTCGCCGTCTTCCGACCAC
1 CGTCCGCCGTCCTCCGACCAC
1711406 CGTCC
1 CGTCC
1711411 ACCGCCGCAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.10, C:0.53, G:0.18, T:0.19
Consensus pattern (21 bp):
CGTCCGCCGTCCTCCGACCAC
Found at i:1715311 original size:12 final size:12
Alignment explanation
Indices: 1715294--1715334 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1715284 GTGTATCAGT
1715294 ACACTGTTCACG
1 ACACTGTTCACG
1715306 ACACTG-T-ACGG
1 ACACTGTTCAC-G
1715317 TACACTGTTCACG
1 -ACACTGTTCACG
1715330 ACACT
1 ACACT
1715335 ATAGCAGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 2 0.08
11 2 0.08
12 17 0.68
13 2 0.08
14 2 0.08
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (12 bp):
ACACTGTTCACG
Found at i:1718554 original size:29 final size:29
Alignment explanation
Indices: 1718512--1718568 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1718502 TTGATTTTTT
*
1718512 TGGAAATTGAATTCT-AGAAAATGAATTAG
1 TGGAAATTAAATTCTGA-AAAATGAATTAG
*
1718541 TGGAATTTAAATTCTGAAAAATGAATTA
1 TGGAAATTAAATTCTGAAAAATGAATTA
1718569 TATTTCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.33
Consensus pattern (29 bp):
TGGAAATTAAATTCTGAAAAATGAATTAG
Found at i:1718661 original size:17 final size:17
Alignment explanation
Indices: 1718635--1718673 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1718625 TGTTGATGAA
1718635 TTTT-TTAAAAT-TTAT
1 TTTTATTAAAATATTAT
1718650 TTATTATTAAAATATTAT
1 TT-TTATTAAAATATTAT
1718668 TTTTAT
1 TTTTAT
1718674 AATTTTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 2 0.10
17 11 0.52
18 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATTAAAATATTAT
Found at i:1718819 original size:23 final size:23
Alignment explanation
Indices: 1718770--1718820 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1718760 GTGTTATATT
**
1718770 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1718793 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1718816 ATATT
1 ATATT
1718821 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1718873 original size:30 final size:29
Alignment explanation
Indices: 1718839--1718915 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 29
1718829 ATTATATTAA
1718839 TATTAAATATATATAAATAATATTA-TTC
1 TATTAAATATATATAAATAATATTATTTC
*
1718867 -ATTATTAATA-AT-TTAATAATATTATTTC
1 TATTA--AATATATATAAATAATATTATTTC
*
1718895 TATGAAAT-TA-ATAAATAATAT
1 TATTAAATATATATAAATAATAT
1718916 AAATTTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
27 28 0.70
28 5 0.12
29 7 0.17
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (29 bp):
TATTAAATATATATAAATAATATTATTTC
Found at i:1718878 original size:19 final size:18
Alignment explanation
Indices: 1718808--1718878 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 18
1718798 TTAAATATCT
1718808 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATT--A
*
1718827 TTATTATATTAATATTAAATA
1 TTATTA-A-TAATATT-ATTA
*
1718848 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATT-A
1718868 TTATTAATAAT
1 TTATTAATAAT
1718879 TTAATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 17 0.40
20 10 0.24
21 3 0.07
22 10 0.24
23 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
TTATTAATAATATTATTA
Found at i:1719015 original size:32 final size:32
Alignment explanation
Indices: 1718968--1719047 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
1718958 ATAATATCTT
*
1718968 ATATTATTATAATATAAT-TGATTATT-TTAATATA
1 ATATTAATA-AATATAATATGA-TATTATTAA-A-A
*
1719002 ATATTAA-AAATATAATATTATATTATTAAAA
1 ATATTAATAAATATAATATGATATTATTAAAA
1719033 ATATTAATAAATATA
1 ATATTAATAAATATA
1719048 TATTTTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 8 0.20
32 20 0.49
33 7 0.17
34 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
ATATTAATAAATATAATATGATATTATTAAAA
Found at i:1719028 original size:22 final size:23
Alignment explanation
Indices: 1718998--1719041 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1718988 ATTATTTTAA
1718998 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
*
1719020 TATATTATTAAAAATATTAATA
1 TATAATATTAAAAATATTAATA
1719042 AATATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:1719046 original size:22 final size:24
Alignment explanation
Indices: 1718995--1719060 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
1718985 TTGATTATTT
1718995 TAATATAATATTAAAAATA-TAATA
1 TAATAT-ATATTAAAAATATTAATA
*
1719019 TTATAT-TATTAAAAATATTAATA
1 TAATATATATTAAAAATATTAATA
**
1719042 -AATATATATTTTAAATATT
1 TAATATATATTAAAAATATT
1719061 TTAATAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 15 0.42
23 16 0.44
24 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATATATATTAAAAATATTAATA
Found at i:1719051 original size:23 final size:22
Alignment explanation
Indices: 1718995--1719060 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
1718985 TTGATTATTT
1718995 TAATATAATATTAAAAATA-TAA
1 TAATAT-ATATTAAAAATATTAA
*
1719017 TATTATATTATTAAAAATATTAA
1 TAATATA-TATTAAAAATATTAA
**
1719040 TAAATATATATTTTAAATATT
1 T-AATATATATTAAAAATATT
1719061 TTAATAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.03
22 16 0.43
23 15 0.41
24 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATATATTAAAAATATTAA
Found at i:1719064 original size:25 final size:25
Alignment explanation
Indices: 1718996--1719077 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
1718986 TGATTATTTT
*
1718996 AATATA-ATATTAAAAATA-TAAT-
1 AATATATATTTTAAAAATATTAATA
1719018 -AT-TATATTATTAAAAATATTAATA
1 AATATATATT-TTAAAAATATTAATA
* *
1719042 AATATATATTTTAAATATTTTAATA
1 AATATATATTTTAAAAATATTAATA
*
1719067 ATTA-ATATTTT
1 AATATATATTTT
1719078 GATTAAAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 2 0.04
21 4 0.08
22 9 0.18
23 4 0.08
24 7 0.14
25 18 0.36
26 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATATATATTTTAAAAATATTAATA
Found at i:1719755 original size:20 final size:20
Alignment explanation
Indices: 1719730--1719768 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1719720 TGCGAATACG
1719730 TGCGATTTACGT-AATCGCAT
1 TGCGATTTA-GTAAATCGCAT
1719750 TGCGATTTAGTAAATCGCA
1 TGCGATTTAGTAAATCGCA
1719769 ACGAAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (20 bp):
TGCGATTTAGTAAATCGCAT
Found at i:1720657 original size:24 final size:24
Alignment explanation
Indices: 1720630--1720683 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1720620 GTATTCGAAA
1720630 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
1720654 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
1720678 TTTGAT
1 TTTGAT
1720684 GATTTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:1723221 original size:20 final size:19
Alignment explanation
Indices: 1723193--1723236 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1723183 CAATCATCTT
*
1723193 AATGTCTATCACAACGCGGA
1 AATGACTATCACAACGC-GA
* *
1723213 AATGACTATCGCAATGCGA
1 AATGACTATCACAACGCGA
1723232 AATGA
1 AATGA
1723237 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
AATGACTATCACAACGCGA
Found at i:1723235 original size:19 final size:17
Alignment explanation
Indices: 1723220--1723317 Score: 55
Period size: 19 Copynumber: 5.8 Consensus size: 17
1723210 GGAAATGACT
1723220 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1723239 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
1723253 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
**
1723272 ATCGCAA--CG-AGGGA
1 ATCGCAATGCGAAATGA
*
1723286 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1723305 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1723318 TTTAGTTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 16 0.26
16 9 0.15
17 9 0.15
19 28 0.45
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:1723262 original size:33 final size:33
Alignment explanation
Indices: 1723220--1723313 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1723210 GGAAATGACT
1723220 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1723253 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1723286 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1723314 CGAATTTAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1723350 original size:19 final size:19
Alignment explanation
Indices: 1723313--1723358 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1723303 AAATCGCAAC
* *
1723313 GCGAATTTAGTTTTACGTT
1 GCGATTTTAGTTTCACGTT
*
1723332 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCACGTT
*
1723351 GTGATTTT
1 GCGATTTT
1723359 GTCGTTGCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.15, C:0.11, G:0.24, T:0.50
Consensus pattern (19 bp):
GCGATTTTAGTTTCACGTT
Found at i:1723370 original size:33 final size:33
Alignment explanation
Indices: 1723328--1723413 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
1723318 TTTAGTTTTA
* * *
1723328 CGTTGCGATTTT-AGTTTCGCGTTGTGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCGTTATGATTCTCT
1723361 CGTTGCGATTTTCATTTCGCGTTATGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTATGATTCTCT
1723394 CGTTGCGATTTTCATTTCGC
1 CGTTGCGATTTTCATTTCGC
1723414 ATTGCGATAG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
33 48 0.98
34 1 0.02
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.49
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTATGATTCTCT
Found at i:1723547 original size:14 final size:14
Alignment explanation
Indices: 1723527--1723576 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
1723517 ACATCAATTA
1723527 AACAAATCAACTTT
1 AACAAATCAACTTT
* *
1723541 TACAAATCATCTTT
1 AACAAATCAACTTT
*
1723555 AACAAATCAA-TTA
1 AACAAATCAACTTT
1723568 AAC-AATCAA
1 AACAAATCAA
1723577 AAAATAAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 6 0.19
13 5 0.16
14 20 0.65
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (14 bp):
AACAAATCAACTTT
Found at i:1723571 original size:13 final size:13
Alignment explanation
Indices: 1723519--1723576 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
1723509 TTATGTTCAC
1723519 ATCAATTAAACAA
1 ATCAATTAAACAA
**
1723532 ATCAACTTTTACAA
1 ATCAA-TTAAACAA
* *
1723546 ATCATCTTTAACAA
1 ATCA-ATTAAACAA
1723560 ATCAATTAAAC-A
1 ATCAATTAAACAA
1723572 ATCAA
1 ATCAA
1723577 AAAATAAGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 6 0.16
13 10 0.27
14 21 0.57
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (13 bp):
ATCAATTAAACAA
Found at i:1725527 original size:33 final size:33
Alignment explanation
Indices: 1725452--1725584 Score: 149
Period size: 33 Copynumber: 3.8 Consensus size: 33
1725442 AAAAATGACT
* *
1725452 ATCGCAACGCGAAATCAAAATCGCAATGAGAGAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAA--CGAG-A-G--A
* * *
1725491 ATCGCAACACGAAACGAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1725524 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
1725557 ATCGCAATGCGAAATAAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
1725585 CGATTATAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
33 57 0.67
35 1 0.01
36 1 0.01
37 3 0.04
39 23 0.27
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1725547 original size:19 final size:19
Alignment explanation
Indices: 1725428--1725587 Score: 106
Period size: 19 Copynumber: 8.8 Consensus size: 19
1725418 TCTGGAACTT
*
1725428 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
1725449 ACTATCGCAACGCGAAATC
1 AAAATCGCAACGCGAAATG
* *
1725468 AAAATCGCAATGAGAGAATG
1 AAAATCGCAACGCGA-AATG
* *
1725488 AAAATCGCAACACGAAACG
1 AAAATCGCAACGCGAAATG
*
1725507 AAAATCGCAA--TG--A-G
1 AAAATCGCAACGCGAAATG
*
1725521 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
1725540 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* * *
1725554 AGAATCGCAATGCGAAATA
1 AAAATCGCAACGCGAAATG
1725573 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1725588 TTATAGTTTC
Statistics
Matches: 107, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
14 20 0.19
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 51 0.48
20 15 0.14
21 11 0.10
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1725637 original size:19 final size:19
Alignment explanation
Indices: 1725613--1725649 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1725603 GCGATTTTGT
*
1725613 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTAATTTCG
1725632 CGTTGCGATTTTAATTTC
1 CGTTGCGATTTTAATTTC
1725650 AACCAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (19 bp):
CGTTGCGATTTTAATTTCG
Found at i:1725884 original size:94 final size:92
Alignment explanation
Indices: 1725740--1726019 Score: 410
Period size: 94 Copynumber: 3.1 Consensus size: 92
1725730 ATGGATTGTA
* * *
1725740 TTAC-TTCAACCAAAAG-ACAACAAAGACAAATA-TCAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGAAAAACAAAGACAAATACT-AACTTCACAGTGTTAAA-AATACACAGT
*
1725802 TTAGCAGAATTGGCAGCAAACGAACAAAT
64 TTAGCAGAATTGGCAGCAACCGAACAAAT
1725831 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAAATACACAGT
1 TTACTTTCAACCAAAAGA-AAAACAAAGACAAATACTAACTTCACAGTGTT-AAAAATACACAGT
1725896 TTAGCAGAATTGGCAGCAACCGAACAAAT
64 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1725925 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT---AATAAACAGTT
1 TTACTTTCAACCAAAAGA-AAAACAAAGACAAATACTAACTTCACAGTGTTAAAAATACACAGTT
* *
1725987 TAGCAGTATTGGCAGCAACCGAATAAAT
65 TAGCAGAATTGGCAGCAACCGAACAAAT
1726015 TTACT
1 TTACT
1726020 AAACAATCTA
Statistics
Matches: 176, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
90 41 0.23
91 4 0.02
92 12 0.07
94 115 0.65
95 4 0.02
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (92 bp):
TTACTTTCAACCAAAAGAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAATACACAGTTT
AGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1727733 original size:20 final size:20
Alignment explanation
Indices: 1727708--1727803 Score: 75
Period size: 20 Copynumber: 5.2 Consensus size: 20
1727698 TTTTGGTTGA
1727708 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
1727728 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
1727747 AAATGACTATCGC--C-ATGAG
1 -AATGAAAATCGCAACGA-GAG
*
1727766 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1727781 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1727801 AAT
1 AAT
1727804 CGCAACGCGA
Statistics
Matches: 58, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
14 5 0.09
16 5 0.09
17 2 0.03
18 2 0.03
19 14 0.24
20 30 0.52
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1727792 original size:19 final size:19
Alignment explanation
Indices: 1727768--1727832 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1727758 GCCATGAGAG
1727768 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1727787 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1727801 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1727820 AATCGCAATGCGA
1 AATCGCAACGCGA
1727833 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1727792 original size:33 final size:33
Alignment explanation
Indices: 1727706--1727827 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
1727696 TCTTTTGGTT
1727706 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
** * *
1727745 GGAAATGACTATCGCCATGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1727779 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1727812 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1727828 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
33 45 0.61
34 11 0.15
36 1 0.01
37 1 0.01
38 3 0.04
40 13 0.18
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1727876 original size:33 final size:33
Alignment explanation
Indices: 1727828--1727920 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
1727818 AAAATCGCAA
**
1727828 TGCGATTTTGGTTTCGCGTTGCGATTATCTCAT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCAT
* *
1727861 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCAT
** *
1727894 TGCGATAGTCATTTTCGTGTTGCGATT
1 TGCGATTTTCA-TTTCGCGTTGCGATT
1727921 TTCATTTTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 38 0.73
34 14 0.27
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCAT
Found at i:1727940 original size:20 final size:20
Alignment explanation
Indices: 1727892--1727942 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1727882 CGATTCTCTC
** *
1727892 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
1727912 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
1727932 GTTGCGATTTT
1 GTTGCGATTTT
1727943 AAGTTTAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:1728517 original size:20 final size:20
Alignment explanation
Indices: 1728494--1728669 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
1728484 CGATAGTCAG
1728494 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1728514 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* *
1728534 AATTCGCATTGCGATTTTCCT
1 -ATTCGCATTGCGATTTACGT
*
1728555 AATTCGCATTGCGATTTATGT
1 -ATTCGCATTGCGATTTACGT
*
1728576 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1728596 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
* * **
1728616 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
1728637 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1728657 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1728670 ATTAGGAAAA
Statistics
Matches: 134, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
20 82 0.61
21 52 0.39
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1728546 original size:41 final size:41
Alignment explanation
Indices: 1728494--1728669 Score: 225
Period size: 41 Copynumber: 4.3 Consensus size: 41
1728484 CGATAGTCAG
*
1728494 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTT-TCCTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTAT-GTA
* *
1728535 ATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTATGTA
1 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTATGTA
1728577 A-TCGCATTGCGATTTACGTATTCGCATTGCGATTTATGTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTATGTA
* ** * *
1728617 A-TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGA-TTTACGTATTCGCATTGCGATTTATGTA
1728657 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1728670 ATTAGGAAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
40 34 0.28
41 67 0.55
42 19 0.16
43 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTATGTA
Found at i:1728650 original size:102 final size:102
Alignment explanation
Indices: 1728468--1728684 Score: 296
Period size: 102 Copynumber: 2.1 Consensus size: 102
1728458 CGAATGGCGC
*
1728468 TATGTAAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCC
1 TATGTAAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCC
* *
1728533 TAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATT
66 AAATTCGCATTGCGATTTACCT-ATTCGCATTGCGATT
* *
1728571 TATGT-AATCGCATTGCGAT--TTACGTATTCGCATTGCGATTTATGTAATCGCATTGCGATTTT
1 TATGTAAATCGCATTGCGATAGTCA-G-ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTT
* * *
1728633 CCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGAAT
64 CCAAATTCGCATTGCGATTTACCTATTCGCATTGCGATT
* *
1728672 TAGGAAAATCGCA
1 TATGTAAATCGCA
1728685 ACGCGAATTT
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
100 2 0.02
101 18 0.18
102 76 0.75
103 5 0.05
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (102 bp):
TATGTAAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCC
AAATTCGCATTGCGATTTACCTATTCGCATTGCGATT
Found at i:1728690 original size:21 final size:21
Alignment explanation
Indices: 1728666--1728711 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1728656 TATTCGCATT
1728666 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1728687 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1728708 GCGA
1 GCGA
1728712 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1729168 original size:22 final size:22
Alignment explanation
Indices: 1729120--1729168 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1729110 AATTATTATA
*
1729120 CTTTTATAGCACTTTTTTTTAT
1 CTTTTATAGCACTTTTTTCTAT
* *
1729142 GTTTTATAGCA-TATTTTTCTGT
1 CTTTTATAGCACT-TTTTTCTAT
1729164 CTTTT
1 CTTTT
1729169 GGTACGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.63
Consensus pattern (22 bp):
CTTTTATAGCACTTTTTTCTAT
Found at i:1729691 original size:21 final size:20
Alignment explanation
Indices: 1729644--1729692 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1729634 TGAATTTTAG
*
1729644 AAAATGTTTTTATAAAATAA
1 AAAATATTTTTATAAAATAA
** *
1729664 ATTATATTTTTTTAAAATGAA
1 AAAATATTTTTATAAAAT-AA
1729685 AAAATATT
1 AAAATATT
1729693 GTATTTATAC
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
AAAATATTTTTATAAAATAA
Found at i:1729824 original size:16 final size:17
Alignment explanation
Indices: 1729795--1729835 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
1729785 ATTAGAAATT
1729795 AATATTTT-AATTTTTA
1 AATATTTTAAATTTTTA
1729811 AAT-TTTTAAATTTTTA
1 AATATTTTAAATTTTTA
1729827 AATATTTTA
1 AATATTTTA
1729836 TTTAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.17
16 14 0.61
17 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATATTTTAAATTTTTA
Found at i:1729825 original size:9 final size:8
Alignment explanation
Indices: 1729799--1729835 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
1729789 GAAATTAATA
1729799 TTTT-AAT
1 TTTTAAAT
1729806 TTTTAAAT
1 TTTTAAAT
1729814 TTTTAAAT
1 TTTTAAAT
1729822 TTTTAAAT
1 TTTTAAAT
1729830 ATTTTA
1 -TTTTA
1729836 TTTAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 4 0.14
8 19 0.68
9 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTAAAT
Found at i:1729871 original size:14 final size:14
Alignment explanation
Indices: 1729854--1729921 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
1729844 TATTTATGCT
1729854 AATATTATTATTAA
1 AATATTATTATTAA
1729868 AATATTATT-TATACA
1 AATATTATTAT-TA-A
* *
1729883 AAT-TTATAAATAAA
1 AATATTAT-TATTAA
1729897 AATATTAAAATTATTAA
1 AATATT---ATTATTAA
1729914 AATATTAT
1 AATATTAT
1729922 AAAATTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 16
0.68 0.06 0.26
Matches are distributed among these distances:
13 1 0.02
14 21 0.50
15 7 0.17
16 1 0.02
17 10 0.24
18 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:1729898 original size:29 final size:29
Alignment explanation
Indices: 1729839--1729903 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1729829 TATTTTATTT
* * * *
1729839 AATATTATTTATGCTAATATTATTATTAA
1 AATATTATTTATACAAATATTATAATAAA
1729868 AATATTATTTATACAAAT-TTATAAATAAA
1 AATATTATTTATACAAATATTAT-AATAAA
1729897 AATATTA
1 AATATTA
1729904 AAATTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (29 bp):
AATATTATTTATACAAATATTATAATAAA
Found at i:1729934 original size:21 final size:21
Alignment explanation
Indices: 1729908--1729962 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
1729898 ATATTAAAAT
1729908 TATTAAAATATTATAAAATTA
1 TATTAAAATATTATAAAATTA
* *
1729929 TATT-AATTATTATAGAATTA
1 TATTAAAATATTATAAAATTA
*
1729949 -ATAAATAATATTAT
1 TATTAA-AATATTAT
1729963 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATTAAAATATTATAAAATTA
Found at i:1729941 original size:20 final size:19
Alignment explanation
Indices: 1729902--1729953 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
1729892 ATAAAAATAT
1729902 TAAAATTATTAAAATATTA
1 TAAAATTATTAAAATATTA
* *
1729921 TAAAATTATATTAATTATTA
1 TAAAATTAT-TAAAATATTA
* *
1729941 TAGAATTAATAAA
1 TAAAATTATTAAA
1729954 TAATATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAATTATTAAAATATTA
Found at i:1731631 original size:24 final size:24
Alignment explanation
Indices: 1731579--1731643 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
1731569 ATAATTATTT
*
1731579 TTATTAAAATAAAT-TTAAAATAA
1 TTATTAAATTAAATATTAAAATAA
1731602 TATATTAAATTAAATATATAAAAT-A
1 T-TATTAAATTAAATAT-TAAAATAA
**
1731627 TTATTATTTTAAATATT
1 TTATTAAATTAAATATT
1731644 TATACTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 2 0.06
24 25 0.69
25 3 0.08
26 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTATTAAATTAAATATTAAAATAA
Found at i:1732659 original size:36 final size:36
Alignment explanation
Indices: 1732612--1732695 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
1732602 ACTGCCACCG
* *
1732612 CCTCCTCCTCCA-CAGCAGCAGTATTCATATCCGCCT
1 CCTCCACCTCCACCACCAG-AGTATTCATATCCGCCT
* * * *
1732648 CCTCCACCTCCACCTCCAGATTCTTCCTATCCGCCT
1 CCTCCACCTCCACCACCAGAGTATTCATATCCGCCT
1732684 CCTCCACCTCCA
1 CCTCCACCTCCA
1732696 GATTCTTCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 37 0.90
37 4 0.10
ACGTcount: A:0.17, C:0.51, G:0.07, T:0.25
Consensus pattern (36 bp):
CCTCCACCTCCACCACCAGAGTATTCATATCCGCCT
Found at i:1732688 original size:30 final size:30
Alignment explanation
Indices: 1732654--1732724 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1732644 GCCTCCTCCA
*
1732654 CCTCCACCTCCAGATTCTTCCTATCCGCCT
1 CCTCCACCTCCAGATTCTTCCTATCCACCT
1732684 CCTCCACCTCCAGATTCTTCCTATCCACCT
1 CCTCCACCTCCAGATTCTTCCTATCCACCT
*
1732714 CCCCCACCTCC
1 CCTCCACCTCC
1732725 TTCTTTGCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.14, C:0.55, G:0.04, T:0.27
Consensus pattern (30 bp):
CCTCCACCTCCAGATTCTTCCTATCCACCT
Found at i:1732724 original size:36 final size:35
Alignment explanation
Indices: 1732639--1732724 Score: 110
Period size: 30 Copynumber: 2.5 Consensus size: 35
1732629 GCAGTATTCA
1732639 TATCCGCCTCCTCCACCTCCACCTCCAGATTCTTCC
1 TATCCGCCTCC-CCACCTCCACCTCCAGATTCTTCC
1732675 TATCCGCCT-----CCTCCACCTCCAGATTCTTCC
1 TATCCGCCTCCCCACCTCCACCTCCAGATTCTTCC
*
1732705 TATCCACCTCCCCCACCTCC
1 TATCCGCCT-CCCCACCTCC
1732725 TTCTTTGCCT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
30 29 0.67
36 14 0.33
ACGTcount: A:0.14, C:0.55, G:0.05, T:0.27
Consensus pattern (35 bp):
TATCCGCCTCCCCACCTCCACCTCCAGATTCTTCC
Found at i:1742715 original size:6 final size:6
Alignment explanation
Indices: 1742704--1742741 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1742694 TGGAGGGATT
* *
1742704 GAACAA GAACAA AAACAA GAACAA GGACAA GAACAA GA
1 GAACAA GAACAA GAACAA GAACAA GAACAA GAACAA GA
1742742 GAGATTGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.66, C:0.16, G:0.18, T:0.00
Consensus pattern (6 bp):
GAACAA
Found at i:1746163 original size:13 final size:13
Alignment explanation
Indices: 1746143--1746202 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
1746133 ACAATACAAA
*
1746143 ACTTTCATATCTC
1 ACTTTCATATTTC
* *
1746156 ATTTTCATCTTTC
1 ACTTTCATATTTC
1746169 ACTTTCATA-TTC
1 ACTTTCATATTTC
*
1746181 ACTTTCACATTTC
1 ACTTTCATATTTC
*
1746194 ATTTTCATA
1 ACTTTCATA
1746203 ATCCGTACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (13 bp):
ACTTTCATATTTC
Found at i:1746193 original size:25 final size:25
Alignment explanation
Indices: 1746143--1746222 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 25
1746133 ACAATACAAA
*
1746143 ACTTTCATATCTCATTTTCATC-TTTC
1 ACTTTCATAT-TCACTTTCA-CATTTC
1746169 ACTTTCATATTCACTTTCACATTTC
1 ACTTTCATATTCACTTTCACATTTC
* *
1746194 ATTTTCATAATCCGTACTTTCACATTTC
1 ACTTTCAT-ATTC--ACTTTCACATTTC
1746222 A
1 A
1746223 GAACTCATTC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 1 0.02
25 19 0.40
26 13 0.28
28 14 0.30
ACGTcount: A:0.24, C:0.26, G:0.01, T:0.49
Consensus pattern (25 bp):
ACTTTCATATTCACTTTCACATTTC
Found at i:1746246 original size:19 final size:19
Alignment explanation
Indices: 1746219--1746278 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
1746209 ACTTTCACAT
* *
1746219 TTCAGAACTCATTCTCAGA
1 TTCAAAACTTATTCTCAGA
* * *
1746238 TTCAAAACTTGTTCCCAAA
1 TTCAAAACTTATTCTCAGA
*
1746257 CTCAAAACTTATT-TCAGA
1 TTCAAAACTTATTCTCAGA
1746275 TTCA
1 TTCA
1746279 TATCTTAATT
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (19 bp):
TTCAAAACTTATTCTCAGA
Found at i:1746318 original size:19 final size:19
Alignment explanation
Indices: 1746267--1746310 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1746257 CTCAAAACTT
* *
1746267 ATTTCAGATTCATATCTTA
1 ATTTCATATTCATAGCTTA
1746286 ATTTCATATTCATAGCTTA
1 ATTTCATATTCATAGCTTA
*
1746305 TTTTCA
1 ATTTCA
1746311 AGTTCATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTTCATATTCATAGCTTA
Found at i:1747644 original size:14 final size:14
Alignment explanation
Indices: 1747622--1747673 Score: 86
Period size: 14 Copynumber: 3.7 Consensus size: 14
1747612 TCGATTATAT
*
1747622 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
1747636 GTTCATTTATGTTC
1 GTTCATTTATGTTC
1747650 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
1747664 ATTCATTTAT
1 GTTCATTTAT
1747674 TTTCTAACAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:1747663 original size:24 final size:26
Alignment explanation
Indices: 1747608--1747666 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 26
1747598 ACGTTCGTGA
*
1747608 ATGTTCGATTATATGTTCGTTTATGTT
1 ATGTTC-ATTATATGTTCGTTCATGTT
*
1747635 -CGTTCATT-TATGTTCGTTCAT-TT
1 ATGTTCATTATATGTTCGTTCATGTT
1747658 ATGTTCATT
1 ATGTTCATT
1747667 CATTTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 2 0.07
24 19 0.68
25 3 0.11
26 4 0.14
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.56
Consensus pattern (26 bp):
ATGTTCATTATATGTTCGTTCATGTT
Found at i:1747961 original size:10 final size:10
Alignment explanation
Indices: 1747946--1748028 Score: 60
Period size: 10 Copynumber: 7.6 Consensus size: 10
1747936 TGTGTTGTAT
1747946 GTTTATGTTC
1 GTTTATGTTC
*
1747956 GTTTATGTTA
1 GTTTATGTTC
1747966 GTTTATTATGTTC
1 G--T-TTATGTTC
1747979 GTTTATGTTCGTTC
1 GTTTA---T-GTTC
*
1747993 GTTTGTGTTC
1 GTTTATGTTC
1748003 GTTTACT-TTC
1 GTTTA-TGTTC
*
1748013 TTTTATGTTC
1 GTTTATGTTC
1748023 GTTTAT
1 GTTTAT
1748029 CATTTAAATG
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
9 1 0.02
10 36 0.62
11 3 0.05
12 1 0.02
13 9 0.16
14 8 0.14
ACGTcount: A:0.11, C:0.10, G:0.18, T:0.61
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:1747964 original size:23 final size:22
Alignment explanation
Indices: 1747947--1748028 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 22
1747937 GTGTTGTATG
1747947 TTTATGTTCGTTTATGTTAGTT
1 TTTATGTTCGTTTATGTTAGTT
*
1747969 TATTATGTTCGTTTATGTTCGTT
1 T-TTATGTTCGTTTATGTTAGTT
* *
1747992 CGTTTGTGTTCGTTTACT-TT--CT
1 --TTTATGTTCGTTTA-TGTTAGTT
1748014 TTTATGTTCGTTTAT
1 TTTATGTTCGTTTAT
1748029 CATTTAAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.02
20 13 0.25
22 2 0.04
23 20 0.38
24 14 0.27
25 2 0.04
ACGTcount: A:0.11, C:0.10, G:0.17, T:0.62
Consensus pattern (22 bp):
TTTATGTTCGTTTATGTTAGTT
Found at i:1747994 original size:14 final size:14
Alignment explanation
Indices: 1747975--1748005 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1747965 AGTTTATTAT
1747975 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
1747989 GTTCGTTTGTGTTC
1 GTTCGTTTATGTTC
1748003 GTT
1 GTT
1748006 TACTTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:1748149 original size:81 final size:81
Alignment explanation
Indices: 1748014--1748214 Score: 377
Period size: 81 Copynumber: 2.5 Consensus size: 81
1748004 TTTACTTTCT
*
1748014 TTTATGTTCGTTTA-TCATTTAAATGAACGAACATGAACAAGCTCTATTCCTTAATGAATGAACA
1 TTTATGTTCGTTTATTTA-TTAAATGAACGAACATGAACAAGCTCTATTCCTTAATGAATGAACA
1748078 TGAAAAAAAATTATTCG
65 TGAAAAAAAATTATTCG
1748095 TTTATGTTCGTTTATTTATTAAATGAACGAACATGAACAAGCTCTATTCCTTAATGAATGAACAT
1 TTTATGTTCGTTTATTTATTAAATGAACGAACATGAACAAGCTCTATTCCTTAATGAATGAACAT
1748160 GAAAAAAAATTATTCG
66 GAAAAAAAATTATTCG
1748176 TTTATGTTCGTTTATTTATTAAATGAACGAACATGAACA
1 TTTATGTTCGTTTATTTATTAAATGAACGAACATGAACA
1748215 TACATTCGTT
Statistics
Matches: 118, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
81 116 0.98
82 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (81 bp):
TTTATGTTCGTTTATTTATTAAATGAACGAACATGAACAAGCTCTATTCCTTAATGAATGAACAT
GAAAAAAAATTATTCG
Found at i:1750017 original size:30 final size:30
Alignment explanation
Indices: 1749983--1750088 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
1749973 CAAAACACCT
1749983 AACTTTTAAAAATTACACTTTTGTTCCCTA
1 AACTTTTAAAAATTACACTTTTGTTCCCTA
* * *
1750013 AACTTTTTAAAATTATC-TTTTTATTCCCTA
1 AACTTTTAAAAATTA-CACTTTTGTTCCCTA
* * *
1750043 AACTTTTCAAAACTTTACACTTTAG--CCAATA
1 AACTTTT-AAAA-ATTACACTTTTGTTCC-CTA
1750074 AACTTTTAAAAATTA
1 AACTTTTAAAAATTA
1750089 TATTTTGGTC
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
29 3 0.05
30 38 0.62
31 14 0.23
32 6 0.10
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (30 bp):
AACTTTTAAAAATTACACTTTTGTTCCCTA
Found at i:1751113 original size:23 final size:23
Alignment explanation
Indices: 1751087--1751176 Score: 117
Period size: 23 Copynumber: 3.9 Consensus size: 23
1751077 ACAACGGATG
*
1751087 TAAACGAATATAAACGAACACAA
1 TAAACGAACATAAACGAACACAA
1751110 TAAACGAACATAAACGAACACAAA
1 TAAACGAACATAAACGAACAC-AA
* ** *
1751134 CAAACGAATGTAAACAAACACAA
1 TAAACGAACATAAACGAACACAA
*
1751157 TAAATGAACATAAACGAACA
1 TAAACGAACATAAACGAACA
1751177 TAATCGAACA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 37 0.66
24 19 0.34
ACGTcount: A:0.61, C:0.19, G:0.09, T:0.11
Consensus pattern (23 bp):
TAAACGAACATAAACGAACACAA
Found at i:1751114 original size:13 final size:13
Alignment explanation
Indices: 1751096--1751132 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1751086 GTAAACGAAT
1751096 ATAAACGAACACA
1 ATAAACGAACACA
1751109 ATAAACG-A-AC-
1 ATAAACGAACACA
1751119 ATAAACGAACACA
1 ATAAACGAACACA
1751132 A
1 A
1751133 ACAAACGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
10 7 0.33
11 3 0.14
12 3 0.14
13 8 0.38
ACGTcount: A:0.62, C:0.22, G:0.08, T:0.08
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:1751128 original size:10 final size:10
Alignment explanation
Indices: 1751087--1751190 Score: 64
Period size: 10 Copynumber: 9.4 Consensus size: 10
1751077 ACAACGGATG
*
1751087 TAAACGAATA
1 TAAACGAACA
1751097 TAAACGAACACAA
1 TAAACG-A-AC-A
1751110 TAAACGAACA
1 TAAACGAACA
1751120 TAAACGAACA
1 TAAACGAACA
* *
1751130 CAAACAAACGAA
1 TAAACGAAC--A
*
1751142 TGTAAACAAACACAA
1 --TAAAC-GA-AC-A
*
1751157 TAAATGAACA
1 TAAACGAACA
1751167 TAAACGAACA
1 TAAACGAACA
*
1751177 TAATCGAACA
1 TAAACGAACA
1751187 TAAA
1 TAAA
1751191 TGAAAATAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
10 46 0.61
11 5 0.07
12 4 0.05
13 11 0.14
14 4 0.05
15 4 0.05
16 2 0.03
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.12
Consensus pattern (10 bp):
TAAACGAACA
Found at i:1756920 original size:12 final size:11
Alignment explanation
Indices: 1756897--1756930 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1756887 TCGTTAAGAA
1756897 CTCGAGTCGAG
1 CTCGAGTCGAG
1756908 CTCGAGCTCGAG
1 CTCGAG-TCGAG
*
1756920 CTCGTGTCGAG
1 CTCGAGTCGAG
1756931 TCTATTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.15, C:0.29, G:0.35, T:0.21
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:1760126 original size:8 final size:8
Alignment explanation
Indices: 1760109--1760141 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
1760099 TTTAATTGTA
1760109 AATATGTAT
1 AATAT-TAT
1760118 AATATTAT
1 AATATTAT
1760126 AATATTAT
1 AATATTAT
1760134 AATATTAT
1 AATATTAT
1760142 TTGATTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.79
9 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (8 bp):
AATATTAT
Found at i:1760794 original size:22 final size:22
Alignment explanation
Indices: 1760769--1760815 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1760759 GCAATTTTTA
*
1760769 TTAAGGGTCTCTTTATAAGAAT
1 TTAAGGATCTCTTTATAAGAAT
* *
1760791 TTAAGGATTTCTTTTTAAGAAT
1 TTAAGGATCTCTTTATAAGAAT
1760813 TTA
1 TTA
1760816 CACAGAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (22 bp):
TTAAGGATCTCTTTATAAGAAT
Done.