Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008953.1 Hibiscus syriacus cultivar Beakdansim tig00112281_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: 2822058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 15
Found at i:1960013 original size:21 final size:22
Alignment explanation
Indices: 1959987--1960027 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1959977 TCAGGATAGG
1959987 GAGTATC-GATAC-TCCTTTAAT
1 GAGTATCAG-TACTTCCTTTAAT
1960008 GAGTATCAGTACTTCCTTTA
1 GAGTATCAGTACTTCCTTTA
1960028 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (22 bp):
GAGTATCAGTACTTCCTTTAAT
Found at i:1961839 original size:103 final size:103
Alignment explanation
Indices: 1961653--1961841 Score: 254
Period size: 103 Copynumber: 1.8 Consensus size: 103
1961643 CATATTAGCC
* * * * *
1961653 CACACAGTGCTATCATATCATAATCATAATATGGACACAAAGTGCAATCACATCTAAAATATACT
1 CACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCGAAAATATACT
* *
1961718 AGTGTACCTATAGATAACACCATAGTATATCATAAGCA
66 AGTGTACCCACAGATAACACCATAGTATATCATAAGCA
* * *
1961756 CACACAATGCTATCACATCAGAATCATAATATGCCCACAAAGTGCAATCATATCGAAAATATAGT
1 CACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCGAAAATATACT
* *
1961821 TGTTTACCCACCAG-TAACACC
66 AGTGTACCCA-CAGATAACACC
1961842 GCATTATATT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
103 71 0.97
104 2 0.03
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (103 bp):
CACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCGAAAATATACT
AGTGTACCCACAGATAACACCATAGTATATCATAAGCA
Found at i:1970270 original size:48 final size:48
Alignment explanation
Indices: 1969961--1970254 Score: 426
Period size: 48 Copynumber: 6.1 Consensus size: 48
1969951 CCACTGTTAT
* * *** * *
1969961 ACAGACGTTAAACGTGCTAATTATCATCAATAGTAGTGTCGCCATCAC
1 ACAGACGTCAGACGTGCTAATTATCATCAATAGTAGCACCACCGTCAC
*
1970009 ACAGACGTCAGACGTGCTAATTATCATCAATAGTAACACCACCGTCAC
1 ACAGACGTCAGACGTGCTAATTATCATCAATAGTAGCACCACCGTCAC
* *
1970057 ACAGACATCAGACGTGCTAATTATCATCAATAGTAGCACCACCGACAC
1 ACAGACGTCAGACGTGCTAATTATCATCAATAGTAGCACCACCGTCAC
* * * *
1970105 ACAAACGTCAGGCGTGCTAACTATCATCAATAGTAGCACTACCGTCAC
1 ACAGACGTCAGACGTGCTAATTATCATCAATAGTAGCACCACCGTCAC
* * *
1970153 ACAAATGTCAGACGTGCTAATTATCATCAATAGTAGTACCACCGTCAC
1 ACAGACGTCAGACGTGCTAATTATCATCAATAGTAGCACCACCGTCAC
*
1970201 ACAGACGTCAGACATGCTAATTATCATCAATAGTAGCACCACCGTCAC
1 ACAGACGTCAGACGTGCTAATTATCATCAATAGTAGCACCACCGTCAC
1970249 ACAGAC
1 ACAGAC
1970255 ATAAGATGTG
Statistics
Matches: 220, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 220 1.00
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (48 bp):
ACAGACGTCAGACGTGCTAATTATCATCAATAGTAGCACCACCGTCAC
Found at i:1973550 original size:3 final size:3
Alignment explanation
Indices: 1973542--1973582 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
1973532 TTAATTGTTA
* *
1973542 ATT ATT ATT ATT ATT ATT ATT A-T ATT A-A ATA ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1973583 CATTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 31 0.91
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1980127 original size:25 final size:25
Alignment explanation
Indices: 1980087--1980147 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
1980077 ACGACAATTT
*
1980087 TTTTTCAAAA-TGTTTT-ATTAAATA
1 TTTTTCAAAATTATTTTAATT-AATA
* *
1980111 TTTTTCAAAATTATTTTAATTGATC
1 TTTTTCAAAATTATTTTAATTAATA
1980136 TTTTTCAAAATT
1 TTTTTCAAAATT
1980148 TGAAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.31
25 19 0.59
26 3 0.09
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTTTCAAAATTATTTTAATTAATA
Found at i:1982395 original size:102 final size:101
Alignment explanation
Indices: 1982200--1982424 Score: 263
Period size: 102 Copynumber: 2.2 Consensus size: 101
1982190 AATTTTTTCT
* * *
1982200 TGAAACAAAATTAATCTCACTTAAGATTGTTTTCCTAAAAATAAATTTCGTGTCACTTGAGATAG
1 TGAAACAAAATTAATCTCACTTAAGATTATTTTCCTAAAAATAAATTTCGTCTCACTTGAGACAG
* * *
1982265 TTTTCCCTCGAAACACACATTTTGAAATTATTTCACC
66 TTTTCCCTCGAAACACAAATTGTAAAATTATTTC-CC
* * * *
1982302 TGAAACAAAATTGATCTCACTTGAGATTATTTTTCTAAAAATAAATATT-GTCTCGCTTGAGACA
1 TGAAACAAAATTAATCTCACTTAAGATTATTTTCCTAAAAATAAAT-TTCGTCTCACTTGAGACA
* ** *
1982366 GTTTTCCCTTGAAATGCAAATTGTAAAATTGTTTCCC
65 GTTTTCCCTCGAAACACAAATTGTAAAATTATTTCCC
* *
1982403 TCAAAACAAAATTTTATCTCAC
1 T-GAAACAAAA-TTAATCTCAC
1982425 CTGAAATAGC
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
101 3 0.03
102 90 0.87
103 11 0.11
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (101 bp):
TGAAACAAAATTAATCTCACTTAAGATTATTTTCCTAAAAATAAATTTCGTCTCACTTGAGACAG
TTTTCCCTCGAAACACAAATTGTAAAATTATTTCCC
Found at i:1983162 original size:104 final size:102
Alignment explanation
Indices: 1982936--1983179 Score: 267
Period size: 104 Copynumber: 2.4 Consensus size: 102
1982926 AAATTATCCC
* *
1982936 TATTGACCCGACTTCCTCAACGAGAAGGAACAACATCATATGAAATCGGCCAAGACTTCAACATG
1 TATTGACCCGACTTCCTCAACGAGAAGGAACAACATCATAAGAAATCGGCCAAAACTTCAACATG
** * * * *
1983001 GATGAACAGTGTGGTCTTCAACACCAGATTATCTTTA
66 GATGAACAAAGTCGTCTTCAACACCAGACTATATTCA
* * * * * * * *
1983038 GATTGACTCAACTGCCTCAACAAGAAGGAACAATATCATAAGAAATTGGCCAAAACTCTTTAACA
1 TATTGACCCGACTTCCTCAACGAGAAGGAACAACATCATAAGAAATCGGCCAAAA--CTTCAACA
1983103 TGGAT-AAGCAAAGTCGTCTTCAACACCATG-CTATATTCA
64 TGGATGAA-CAAAGTCGTCTTCAACACCA-GACTATATTCA
* * *
1983142 TATTGACCCGATTTCATCAACGAGAAGAAACAACATCA
1 TATTGACCCGACTTCCTCAACGAGAAGGAACAACATCA
1983180 ACTTCAATGA
Statistics
Matches: 113, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
102 46 0.41
103 2 0.02
104 64 0.57
105 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.24
Consensus pattern (102 bp):
TATTGACCCGACTTCCTCAACGAGAAGGAACAACATCATAAGAAATCGGCCAAAACTTCAACATG
GATGAACAAAGTCGTCTTCAACACCAGACTATATTCA
Found at i:1986401 original size:23 final size:23
Alignment explanation
Indices: 1986366--1986425 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1986356 ATCAAGCACA
* **
1986366 ATAATATATTAGGTAGTGCTTAT
1 ATAATATAATAGGTAGCACTTAT
*
1986389 ATAATGTAATAGGTAGCACTTAT
1 ATAATATAATAGGTAGCACTTAT
*
1986412 ATAATAAAATAGGT
1 ATAATATAATAGGT
1986426 TAATTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGGTAGCACTTAT
Found at i:1986545 original size:15 final size:15
Alignment explanation
Indices: 1986525--1986570 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
1986515 TGGCCGACCG
1986525 AACCGAATTAACCAA
1 AACCGAATTAACCAA
*
1986540 AACCGAATTAACCAT
1 AACCGAATTAACCAA
1986555 AACCGAATTAACCAA
1 AACCGAATTAACCAA
1986570 A
1 A
1986571 CTTTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (15 bp):
AACCGAATTAACCAA
Found at i:1986922 original size:181 final size:183
Alignment explanation
Indices: 1986694--1987077 Score: 627
Period size: 183 Copynumber: 2.1 Consensus size: 183
1986684 TTTTCTAATT
* * *
1986694 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATACATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATACATAAT
1986758 TAT-AAA-AAAAAATTAGATA-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATT-GATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
1986820 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATTTTA
130 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
* *
1986874 TATATAATATATTTTATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATACATAA
*
1986938 TTATAAAATAAAAAATTTATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
65 TTATAAAATAAAAAATTGATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
1987003 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
130 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
1987057 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1987078 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 9, Indels: 9
0.91 0.04 0.04
Matches are distributed among these distances:
180 13 0.07
181 48 0.25
182 8 0.04
183 120 0.63
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATACATAAT
TATAAAATAAAAAATTGATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
GATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:1987749 original size:2 final size:2
Alignment explanation
Indices: 1987742--1987777 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1987732 AAGTATGGAC
1987742 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1987778 ATGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1988010 original size:22 final size:22
Alignment explanation
Indices: 1987983--1988027 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1987973 TTGTGGAATT
1987983 AAAGTATCGAGACAGATATAAA
1 AAAGTATCGAGACAGATATAAA
* * *
1988005 AAAGTATTGATACATATATAAA
1 AAAGTATCGAGACAGATATAAA
1988027 A
1 A
1988028 GTTTATGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (22 bp):
AAAGTATCGAGACAGATATAAA
Found at i:1991974 original size:13 final size:13
Alignment explanation
Indices: 1991939--1991976 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
1991929 TTCTAATGGG
1991939 CAATGTTTGAAAA
1 CAATGTTTGAAAA
*
1991952 TAAT-TTTGAAAA
1 CAATGTTTGAAAA
1991964 CAATGTTTGAAAA
1 CAATGTTTGAAAA
1991977 ATTATTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:1992535 original size:44 final size:44
Alignment explanation
Indices: 1992472--1992565 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
1992462 TACAAAATAG
* * *
1992472 AGTGTATCGATGCACATTCAAAGAATGCATCGGTGCACCTTCAT
1 AGTGTACCGATGCACATTCAAAGAATACATCGGTACACCTTCAT
* * * *
1992516 AGTGTACCGATGCATATTCAAGGGATACATCGGTACACTTTCAT
1 AGTGTACCGATGCACATTCAAAGAATACATCGGTACACCTTCAT
*
1992560 AATGTA
1 AGTGTA
1992566 TCTATGAACA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (44 bp):
AGTGTACCGATGCACATTCAAAGAATACATCGGTACACCTTCAT
Found at i:1996419 original size:22 final size:21
Alignment explanation
Indices: 1996377--1996416 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1996367 GAAATTATTT
1996377 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
1996398 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
1996417 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1999997 original size:199 final size:199
Alignment explanation
Indices: 1999656--2000259 Score: 908
Period size: 199 Copynumber: 3.0 Consensus size: 199
1999646 TCATTATGTT
** * * *
1999656 TCGATACTTTTAATAAATGTATCGACACTTTATGAGTGCACTTCGTTGGGCATTC-ATTATGGAC
1 TCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGG-AATCAATTATGGA-
* * * * *
1999720 CAAAAGTATCGACACAAATTTAAAAAGTGTTGATACATTATGTTGACCTATTCTCTTTTAAAACC
64 CACAAGTATCGATACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTCTCTTATAAAACC
*
1999785 GGTATATTTTTATCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCTGTTTCGATGTTT
129 GGTATATTTTTATCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCAGTTTCGATGTTT
1999850 TTGGGA
194 TTGGGA
* * *
1999856 TCGATACTTACAATAAATGCATCGACACTTTATGCGTGCACCTCGTTGGGAATCAATTCTAGACA
1 TCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGAATCAATTATGGACA
* *
1999921 TCAAGTAT-GATACAAATTTTAAAAGTATCGATACATTATGTTGACCTATTCTCTTATAAAACTG
66 -CAAGTATCGATACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTCTCTTATAAAACCG
* * * *
1999985 GTATATTTTTATCGGTTATACTGTAAATTTACCTATTACTTTATAATTATCGGTTTCGATATTTT
130 GTATATTTTTATCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCAGTTTCGATGTTTT
2000050 TGGGA
195 TGGGA
* * *
2000055 ACGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATCAATTTTGGACA
1 TCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGAATCAATTATGGAC-
* *
2000120 ACAAGTATCAATACAAATTTAAAAAGTATGGATACATTATGTTGACCTATTCTCTTATAAAACCG
65 ACAAGTATCGATACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTCTCTTATAAAACCG
* *
2000185 GTATA-TTTTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTT
130 GTATATTTTTATCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCAGTTTCGATGTTTT
2000249 TGGGA
195 TGGGA
2000254 TCGATA
1 TCGATA
2000260 TAATTTTAAA
Statistics
Matches: 365, Mismatches: 35, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
199 250 0.68
200 115 0.32
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (199 bp):
TCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGAATCAATTATGGACA
CAAGTATCGATACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTCTCTTATAAAACCGG
TATATTTTTATCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCAGTTTCGATGTTTTT
GGGA
Found at i:2000675 original size:179 final size:178
Alignment explanation
Indices: 2000253--2000676 Score: 593
Period size: 179 Copynumber: 2.4 Consensus size: 178
2000243 TGTTTTTGGG
* * * * *
2000253 ATCGATA-TAATTTTAAAATTATCGATACATTATGTTTATCTATTCTCTCATTAAACCGGTATAT
1 ATCGATACAAATTTAAAAAGTATCGATACATTATGTTAACCTATTCTCTCATTAAACCGGTATAT
* * * *
2000317 TTTACCTATTACTTTATAATTATCAGTTTCGATGTTTTTGGATCGATACTTACAATAAATGTATT
66 TTTACCAATTACTTTATAATAATCAGTTTCGATGTTTTAGGATCGATACTTACAATAAATGTATC
2000382 GACACTTTATGCGTACACTTCGTTGGGCATCTATTCTAGACAAAAAGT
131 GACACTTTATGCGTACACTTCGTTGGGCATCTATTCTAGACAAAAAGT
* * * **
2000430 ATCGATACAAATTTAAAATGTATCGATACATTATGTTGACATATTCTCTCATTAAACCAATATAT
1 ATCGATACAAATTTAAAAAGTATCGATACATTATGTTAACCTATTCTCTCATTAAACCGGTATAT
* *
2000495 TTTACCAATTAGTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTACAATAAATGTAT
66 TTTACCAATTACTTTATAATAATCAGTTTCGATGTTTT-AGGATCGATACTTACAATAAATGTAT
** *
2000560 CGACACTTTATGCGTGTA-TCTCGTTTGGCAGTC-ATTCTAGACAAAAAGT
130 CGACACTTTATGCGTACACT-TCGTTGGGCA-TCTATTCTAGACAAAAAGT
* * * *
2000609 ATCGATACAAATTTAAAAAGTATCGATACATTATATTAACCTATTCTGTCATAAAATCGGTATAT
1 ATCGATACAAATTTAAAAAGTATCGATACATTATGTTAACCTATTCTCTCATTAAACCGGTATAT
2000674 TTT
66 TTT
2000677 TTCAGTTACA
Statistics
Matches: 216, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
177 7 0.03
178 83 0.38
179 124 0.57
180 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (178 bp):
ATCGATACAAATTTAAAAAGTATCGATACATTATGTTAACCTATTCTCTCATTAAACCGGTATAT
TTTACCAATTACTTTATAATAATCAGTTTCGATGTTTTAGGATCGATACTTACAATAAATGTATC
GACACTTTATGCGTACACTTCGTTGGGCATCTATTCTAGACAAAAAGT
Found at i:2000851 original size:190 final size:192
Alignment explanation
Indices: 2000495--2000952 Score: 593
Period size: 190 Copynumber: 2.4 Consensus size: 192
2000485 ACCAATATAT
* * *
2000495 TTTACCAATTAGTTTATAATAATCGGTTTCGATG-TTTTGAGGATCGATACTTACAATAAATGTA
1 TTTACCTATTACTTTATAATTATCGGTTTCGATGTTTTTGA-GATCGATACTTACAATAAATGTA
* * * * *
2000559 TCGACACTTTATGCGTGTATCTCGTTTGGCAGTCATTCTAGACAAAAAGTATCGATACAAATTTA
65 TCG-------A-GCGTGCACCTCGTTGGGCAGTCATTATAGACAAAAAGTATCGACACAAATTTA
* *
2000624 AAAAGTATCGATACATTATATTAACCTATTCTGTCATAAAA-TCGGTATATTTTT-TCAGTTACA
122 AAAAGTATCGATACATTATATTAACCTATTCTGTCATAAAACT-GATATATTTTTACCAGTTACA
2000687 TTGTAAA
186 TTGTAAA
*
2000694 TTTACCTATTACTTTATAATTATCGGTTTTGATGTTTTTGAGATCGATACTTACAATAAATGTAT
1 TTTACCTATTACTTTATAATTATCGGTTTCGATGTTTTTGAGATCGATACTTACAATAAATGTAT
* *
2000759 CGA-CGTGCACCTCGTTGGGCA-TCAATTATTGACCAAAAGTATCGACACAAATTTAAAAAGTAT
66 CGAGCGTGCACCTCGTTGGGCAGTC-ATTATAGACAAAAAGTATCGACACAAATTTAAAAAGTAT
** * * *
2000822 TTATACATTATGTTGACCTATTCTGTCATAAAACTGATATATTTTTACCGGTTACATTGTAAA
130 CGATACATTATATTAACCTATTCTGTCATAAAACTGATATATTTTTACCAGTTACATTGTAAA
* * *
2000885 TTTATCTATTACTTTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTACAATAAATGTGT
1 TTTACCTATTACTTTATAATTATCGGTTTCGATGTTTTTGAGATCGATACTTACAATAAATGTAT
2000950 CGA
66 CGA
2000953 TATATGTTTG
Statistics
Matches: 233, Mismatches: 22, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
189 2 0.01
190 89 0.38
191 79 0.34
192 1 0.00
199 56 0.24
200 6 0.03
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (192 bp):
TTTACCTATTACTTTATAATTATCGGTTTCGATGTTTTTGAGATCGATACTTACAATAAATGTAT
CGAGCGTGCACCTCGTTGGGCAGTCATTATAGACAAAAAGTATCGACACAAATTTAAAAAGTATC
GATACATTATATTAACCTATTCTGTCATAAAACTGATATATTTTTACCAGTTACATTGTAAA
Found at i:2003785 original size:3 final size:3
Alignment explanation
Indices: 2003777--2003824 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
2003767 ACTTGTTTGG
* * * * *
2003777 ATC ATC ATC ATT ATC ATC TTC ATC TTC ATC TTC ATC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2003825 GAGTGCTTGG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (3 bp):
ATC
Found at i:2003805 original size:18 final size:18
Alignment explanation
Indices: 2003777--2003824 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
2003767 ACTTGTTTGG
*
2003777 ATCATCATCAT-TATCATC
1 ATCATCTTCATCT-TCATC
*
2003795 TTCATCTTCATCTTCATC
1 ATCATCTTCATCTTCATC
2003813 ATCATCTTCATC
1 ATCATCTTCATC
2003825 GAGTGCTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (18 bp):
ATCATCTTCATCTTCATC
Found at i:2003824 original size:12 final size:12
Alignment explanation
Indices: 2003777--2003824 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
2003767 ACTTGTTTGG
* *
2003777 ATCATCATCATT
1 ATCATCTTCATC
2003789 ATCATCTTCATC
1 ATCATCTTCATC
*
2003801 TTCATCTTCATC
1 ATCATCTTCATC
2003813 ATCATCTTCATC
1 ATCATCTTCATC
2003825 GAGTGCTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (12 bp):
ATCATCTTCATC
Found at i:2004179 original size:36 final size:36
Alignment explanation
Indices: 2004128--2004197 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
2004118 ATGGCCAGTA
* * *
2004128 GGGTCCATTTTCTCATTTTATTGTTTTAATCCAATG
1 GGGTCCATTTGCTCATTCTATTGTTCTAATCCAATG
*
2004164 GGGTCCATTTGCTCATTCTCTTGTTCTAATCCAA
1 GGGTCCATTTGCTCATTCTATTGTTCTAATCCAA
2004198 CGACATCCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (36 bp):
GGGTCCATTTGCTCATTCTATTGTTCTAATCCAATG
Found at i:2005669 original size:200 final size:199
Alignment explanation
Indices: 2005249--2006538 Score: 1675
Period size: 200 Copynumber: 6.5 Consensus size: 199
2005239 ATATCGATAC
* * *
2005249 AATTTAAAAAGTGTTGATACATTATGCTGACCTATTTTCTAATTAAA-CGGTATATTCTGACCGG
1 AATTAAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATATTCTGACCGG
* * * * *
2005313 TTACATTGTAAATCTACCTATTATATTATAATTATCGGTTTCGATGTTTTTGGGATAGATA-TAA
66 TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATG-TTTTGGGATCGATACTTA
*
2005377 CTT-TAAATGTATCGACACTTTAT-CGTGCACCTCGTTGGGCATTCATTCTGGACCAAAAGTATT
130 -TTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATT
2005440 GACACA
194 GACACA
* * *
2005446 AATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTTTAATTAAGCCGGTATATTCTGACCGG
1 AATTAAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATATTCTGACCGG
*
2005511 TTACATTATAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACTTA
66 TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATG-TTTTGGGATCGATACTTA
2005576 TTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATTG
130 TTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATTG
2005641 ACAC-
195 ACACA
* * * * ** *
2005645 AATGTAAAAAAGTATCGATACATTATGTTGACATATTCTCTCACAAAACCAGTATATTTCT-ACC
1 AAT-TAAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATA-TTCTGACC
* * * *
2005709 GGTTACATTGTAAATTTATCTATTACTTTATAATAATTGGTTTCGATGTTTTGAGGATTGATACT
64 GGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTG-GGATCGATACT
* * ** *
2005774 TATAATAAATGTATCGACACTTTAT-CGTGCACCTCGTTGGGCAATCATTCAAGACCAAAAGTAT
128 TATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTAT
2005838 TGACACA
193 TGACACA
* * * *
2005845 AATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCAGTATATTATGACCCG
1 AATTAAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATATTCTGACCGG
* *
2005910 TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTAGGATTGATACTTAT
66 TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTGGGATCGATACTTAT
* * * *
2005975 TATAAATGTATCAACACTTTATGTGTGCACCTCGTTGGGCATTCATTCTGGACAAAACGTATCGA
131 TATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATTGA
2006040 CAC-
196 CACA
* * * * * *
2006043 AATGTAAAAAAGTATCGATACATTATGTTGACATATTCTCTCATAAAACTGGTATATTTCT-ACC
1 AAT-TAAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATA-TTCTGACC
* * *
2006107 GGTTACATTGTAAATTTACCTATTACTTTATAATAATTAGTTTCGATGTTTTGAGGATCGATACT
64 GGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTG-GGATCGATACT
** * *
2006172 TACAATATATATATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGA-ACAAAAGTA
128 TATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACA-AAAAGTA
*
2006236 TGGACACA
192 TTGACACA
* ** *
2006244 AATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAATTGGTATATTCTGATCGG
1 AATTAAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATATTCTGACCGG
* * * * *
2006309 TTACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTTGTATCGATACTTA
66 TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGAT-GTTTTGGGATCGATACTTA
* ** * * *
2006374 TTATAAATGTATCGACACTTTATGCATGGTCCTCGTTGGACATTCATTCTGGACCAAAAGTATCG
130 TTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATTG
*
2006439 ATACA
195 ACACA
* * * * * * * *
2006444 ATTTATAAAAA-TATCGATACATTATGTTGACCTATTTTCTCATAAAACTGATATATTTTTACCG
1 AATTA-AAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATATTCTGACCG
* * *
2006508 TTTACATTGTAAATTTACCTTTTACTTTATA
65 GTTACATTGTAAATTTACCTATTACATTATA
2006539 GTGTATCGAT
Statistics
Matches: 957, Mismatches: 117, Indels: 35
0.86 0.11 0.03
Matches are distributed among these distances:
197 43 0.04
198 115 0.12
199 305 0.32
200 478 0.50
201 16 0.02
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (199 bp):
AATTAAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGGTATATTCTGACCGG
TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTGGGATCGATACTTAT
TATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATTGA
CACA
Found at i:2006204 original size:399 final size:397
Alignment explanation
Indices: 2005235--2006538 Score: 1911
Period size: 399 Copynumber: 3.3 Consensus size: 397
2005225 GTAATTTAAA
* * * * * * * * * *
2005235 AAAAATATCGATACAAT-TTAAAAAGTGTTGATACATTATGCTGACCTATTTTCTAATTAAAC-G
1 AAAAGTATCGACACAATGTAAAAAAGTATCGATACATTATGTTGACATATTCTCTCATAAAACTG
* * *
2005298 GTATA-TTCTGACCGGTTACATTGTAAATCTACCTATTA-TATTATAATTATCGGTTTCGATGTT
66 GTATATTTCT-ACCGGTTACATTGTAAATTTACCTATTACT-TTATAATAATTGGTTTCGATG-T
* **
2005361 TTTG-GGATAGATA-TAACTTTAAATGTATCGACACTTTATCGTGCACCTCGTTGGGCATTCATT
128 TTTGAGGATAGATACTTACAATAAATGTATCGACACTTTATCGTGCACCTCGTTGGGCATTCATT
*
2005424 CTGGACCAAAAGTATTGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTTTAAT
193 CTGGACCAAAAGTATTGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAAT
* *
2005489 TAAGCCGGTATATTCTGACCGGTTACATTATAAATTTACCTATTACATTATAATTATTGGTTTCG
258 TAAACCGGTATATTCTGACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCG
*
2005554 ATGTTTTTGGGATCGATACTTATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCAT
323 ATG-TTTTAGGATCGATACTTATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCAT
2005619 TCATTCTGGAC
387 TCATTCTGGAC
* * *
2005630 AAAAAGTATTGACACAATGTAAAAAAGTATCGATACATTATGTTGACATATTCTCTCACAAAACC
1 -AAAAGTATCGACACAATGTAAAAAAGTATCGATACATTATGTTGACATATTCTCTCATAAAACT
* *
2005695 AGTATATTTCTACCGGTTACATTGTAAATTTATCTATTACTTTATAATAATTGGTTTCGATGTTT
65 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATTGGTTTCGATGTTT
* * * *
2005760 TGAGGATTGATACTTATAATAAATGTATCGACACTTTATCGTGCACCTCGTTGGGCAATCATTCA
130 TGAGGATAGATACTTACAATAAATGTATCGACACTTTATCGTGCACCTCGTTGGGCATTCATTCT
*
2005825 AGACCAAAAGTATTGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTA
195 GGACCAAAAGTATTGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTA
* * *
2005890 AACCAGTATATTATGACCCGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGAT
260 AACCGGTATATTCTGACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGAT
* * *
2005955 GTTTTAGGATTGATACTTATTATAAATGTATCAACACTTTATGTGTGCACCTCGTTGGGCATTCA
325 GTTTTAGGATCGATACTTATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCA
2006020 TTCTGGAC
390 TTCTGGAC
2006028 AAAACGTATCGACACAATGTAAAAAAGTATCGATACATTATGTTGACATATTCTCTCATAAAACT
1 AAAA-GTATCGACACAATGTAAAAAAGTATCGATACATTATGTTGACATATTCTCTCATAAAACT
*
2006093 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATTAGTTTCGATGTTT
65 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATTGGTTTCGATGTTT
* * *
2006158 TGAGGATCGATACTTACAATATATATATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
130 TGAGGATAGATACTTACAATAAATGTATCGACACTTTAT-CGTGCACCTCGTTGGGCATTCATTC
* *
2006223 TGGAACAAAAGTATGGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATT
194 TGGACCAAAAGTATTGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATT
** * * *
2006288 AAATTGGTATATTCTGATCGGTTACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGA
259 AAACCGGTATATTCTGACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGA
* * * * ** *
2006353 TATTTTTTGTATCGATACTTATTATAAATGTATCGACACTTTATGCATGGTCCTCGTTGGACATT
324 T-GTTTTAGGATCGATACTTATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATT
2006418 CATTCTGGACC
388 CATTCTGGA-C
* * * *
2006429 AAAAGTATCGATACAATTTATAAAAA-TATCGATACATTATGTTGACCTATTTTCTCATAAAACT
1 AAAAGTATCGACACAATGTA-AAAAAGTATCGATACATTATGTTGACATATTCTCTCATAAAACT
* * * *
2006493 GATATATTTTTACCGTTTACATTGTAAATTTACCTTTTACTTTATA
65 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACTTTATA
2006539 GTGTATCGAT
Statistics
Matches: 821, Mismatches: 76, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
396 14 0.02
397 45 0.05
398 280 0.34
399 318 0.39
400 154 0.19
401 10 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (397 bp):
AAAAGTATCGACACAATGTAAAAAAGTATCGATACATTATGTTGACATATTCTCTCATAAAACTG
GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATTGGTTTCGATGTTTT
GAGGATAGATACTTACAATAAATGTATCGACACTTTATCGTGCACCTCGTTGGGCATTCATTCTG
GACCAAAAGTATTGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAA
ACCGGTATATTCTGACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATG
TTTTAGGATCGATACTTATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCAT
TCTGGAC
Found at i:2013745 original size:183 final size:182
Alignment explanation
Indices: 2013162--2013756 Score: 755
Period size: 183 Copynumber: 3.2 Consensus size: 182
2013152 TTATAAAAGT
* * * * * *
2013162 ATCGATACATTCAACATATCCGGCAGCGCTTTACCGGTTTTGTCATT-TCAAGACCGGTTTTGTC
1 ATCGATACTTTCAACATATCCTGTAGCGTTTTACC-GTTTTGTCATTATGAA-ACCGGTTTTATC
* ** * *
2013226 ATATTTTTACCTGTTATAATGTTACAGT-TCGATACATTTTTATAAAGTATCGACACTTTATAGG
64 ATATTTTTACCTGTTATATTGTT-GTGTATCGATACATGTTTATAAAGTATCGACACTTTTTAGG
* *
2013290 CGCTATTACTGCTTTTCTTTTAAATTCTAAAAGTGTCGATACTTATTTCAATGGG
128 CGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGA
* * * * *
2013345 ATCGATACTTTCAACATATCTTGTA-TGTCTTTATCAGTTTTGTCATAATGAAACCGGTTTTTTC
1 ATCGATACTTTCAACATATCCTGTAGCGT-TTTA-CCGTTTTGTCATTATGAAACCGGTTTTATC
* * *
2013409 ATATTTTTACCTGTTATATTGATGTGTATCGATACATGTTTATAAAGTATCAATACTTTTTAGGC
64 ATATTTTTACCTGTTATATTGTTGTGTATCGATACATGTTTATAAAGTATCGACACTTTTTAGGC
* * * *
2013474 GCTATTATTGCTTTTCTTTTAAATTTCAAAAGTGTCGATACTTATTTAAATGAA
129 GCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGA
* ** * * *
2013528 ATCGATACTTTCAACATATACAATAACATTTTACCGTTTTTATCATTATGAAACCGGTTTTATCA
1 ATCGATACTTTCAACATATCCTGTAGCGTTTTACCG-TTTTGTCATTATGAAACCGGTTTTATCA
* *
2013593 TATTTTTACCTATTATATTGTTGTGTATCGATACATGTTTATAAATTATCGACACTTTTTAGGCG
65 TATTTTTACCTGTTATATTGTTGTGTATCGATACATGTTTATAAAGTATCGACACTTTTTAGGCG
* ** *
2013658 CTATTACTACTTTTCTTTTAAACCCCAAAAGTGTCGATACTTTTTTCAATGGA
130 CTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGA
* *
2013711 ATTGATACTTTCAACATATCCTGTAGCGTTTTACCGATTTTCTCAT
1 ATCGATACTTTCAACATATCCTGTAGCGTTTTACCG-TTTTGTCAT
2013757 ATTTTTACCT
Statistics
Matches: 351, Mismatches: 55, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
182 5 0.01
183 341 0.97
184 5 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
ATCGATACTTTCAACATATCCTGTAGCGTTTTACCGTTTTGTCATTATGAAACCGGTTTTATCAT
ATTTTTACCTGTTATATTGTTGTGTATCGATACATGTTTATAAAGTATCGACACTTTTTAGGCGC
TATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGA
Found at i:2015321 original size:5 final size:6
Alignment explanation
Indices: 2015260--2015318 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
2015250 GACACGTATT
2015260 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2015306 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
2015319 CGAGACGAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.38
6 33 0.62
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2015845 original size:5 final size:5
Alignment explanation
Indices: 2015808--2015844 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
2015798 CCGCCGCCGC
*
2015808 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTGT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
2015845 GGTCGTGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.00, C:0.38, G:0.24, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:2016025 original size:20 final size:20
Alignment explanation
Indices: 2016000--2016073 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
2015990 ACTGCAGTGG
2016000 AATCGCAACGCGAAATGGAA
1 AATCGCAACGCGAAATGGAA
* **
2016020 AATCGCAACGCGAATTTCAA
1 AATCGCAACGCGAAATGGAA
* * *
2016040 CTATCTCAACGCAAAATGGAA
1 -AATCGCAACGCGAAATGGAA
2016061 AATCGCAACGCGA
1 AATCGCAACGCGA
2016074 TTTTCAACTA
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAAATGGAA
Found at i:2016051 original size:21 final size:21
Alignment explanation
Indices: 2016025--2016095 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
2016015 TGGAAAATCG
*
2016025 CAACGCGAATTTCAACTATCT
1 CAACGCGAATTTCAACTATCA
* * ** * *
2016046 CAACGCAAAATGGAA-AATCG
1 CAACGCGAATTTCAACTATCA
*
2016066 CAACGCGATTTTCAACTATCA
1 CAACGCGAATTTCAACTATCA
2016087 CAACGCGAA
1 CAACGCGAA
2016096 ATGCAACGCG
Statistics
Matches: 35, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (21 bp):
CAACGCGAATTTCAACTATCA
Found at i:2016061 original size:41 final size:41
Alignment explanation
Indices: 2016005--2016098 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
2015995 AGTGGAATCG
*
2016005 CAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCT
1 CAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCA
* *
2016046 CAACGCAAAATGGAAAATCGCAACGCGATTTTCAACTATCA
1 CAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCA
2016087 CAACGCGAAATG
1 CAACGCGAAATG
2016099 CAACGCGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.18
Consensus pattern (41 bp):
CAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCA
Found at i:2016102 original size:21 final size:21
Alignment explanation
Indices: 2016000--2016102 Score: 84
Period size: 20 Copynumber: 5.0 Consensus size: 21
2015990 ACTGCAGTGG
*
2016000 AATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAAATGCAAC
* *
2016020 AATCGCAACGCGAATTTCAAC
1 AATCGCAACGCGAAATGCAAC
* * * *
2016041 TATCTCAACGCAAAATGGAA-
1 AATCGCAACGCGAAATGCAAC
** *
2016061 AATCGCAACGCGATTTTCAAC
1 AATCGCAACGCGAAATGCAAC
* *
2016082 TATCACAACGCGAAATGCAAC
1 AATCGCAACGCGAAATGCAAC
2016103 GCGAATTTGC
Statistics
Matches: 60, Mismatches: 21, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
20 30 0.50
21 30 0.50
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (21 bp):
AATCGCAACGCGAAATGCAAC
Found at i:2016154 original size:20 final size:20
Alignment explanation
Indices: 2016131--2016195 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2016121 AGATCGCGTT
2016131 GCGATTTCAACTATCGCAAC
1 GCGATTTCAACTATCGCAAC
* ** *
2016151 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTTCAACTATCGCAAC
2016171 GCGATTTTCAACTATCGCAAC
1 GCGA-TTTCAACTATCGCAAC
2016192 GCGA
1 GCGA
2016196 AATGGAAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.50
21 16 0.47
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
GCGATTTCAACTATCGCAAC
Found at i:2016169 original size:142 final size:139
Alignment explanation
Indices: 2016001--2016266 Score: 451
Period size: 142 Copynumber: 1.9 Consensus size: 139
2015991 CTGCAGTGGA
*
2016001 ATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCTCAACGCAAAATGGAAAATCG
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCAAAATGGAAAA-CG
2016066 CAACGCGATTTTCAACTATCACAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGCGTT
65 C-ACGCGATTTTCAACTATCACAACGCGAAATGCAACGCGAA-TTGCGATAGTGGAGATCGCGTT
2016131 GCGATTTCAACT
128 GCGATTTCAACT
* *
2016143 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAACGC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCAAAATGGAAAACGC
* * *
2016208 ACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTGCGATAGTGGAGATCGC
66 ACGCGATTTTCAACTATCACAACGCGAAATGCAACGCGAATTGCGATAGTGGAGATCGC
2016267 AATGCGAATT
Statistics
Matches: 118, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
139 19 0.16
140 37 0.31
141 3 0.03
142 59 0.50
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (139 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCAAAATGGAAAACGC
ACGCGATTTTCAACTATCACAACGCGAAATGCAACGCGAATTGCGATAGTGGAGATCGCGTTGCG
ATTTCAACT
Found at i:2016223 original size:39 final size:41
Alignment explanation
Indices: 2016131--2016238 Score: 186
Period size: 39 Copynumber: 2.7 Consensus size: 41
2016121 AGATCGCGTT
2016131 GCGA-TTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
2016171 GCGATTTTCAACTATCGCAACGCGAAATGGAAAA-CGC-AC
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
*
2016210 GCGATTTTCAACTATCGCAATGCGAAATG
1 GCGATTTTCAACTATCGCAACGCGAAATG
2016239 CAACGTGAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
39 30 0.45
40 7 0.11
41 29 0.44
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (41 bp):
GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
Found at i:2025582 original size:35 final size:35
Alignment explanation
Indices: 2025536--2025612 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
2025526 AGGTGAAAAC
2025536 ATAATGAAAGATATTAGAATAACAAAAAAGAAATG
1 ATAATGAAAGATATTAGAATAACAAAAAAGAAATG
*
2025571 ATAATGAAAGATATTAGAATAAGAAAAAAGAAATG
1 ATAATGAAAGATATTAGAATAACAAAAAAGAAATG
*
2025606 AAAATGA
1 ATAATGA
2025613 TTCTCCTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.64, C:0.01, G:0.16, T:0.19
Consensus pattern (35 bp):
ATAATGAAAGATATTAGAATAACAAAAAAGAAATG
Found at i:2026390 original size:34 final size:34
Alignment explanation
Indices: 2026310--2026440 Score: 199
Period size: 34 Copynumber: 3.8 Consensus size: 34
2026300 CAAAATGGTC
* * * *
2026310 ATTTCCAATACTAGTGGAATAACCTAATTTAAGTAT
1 ATTTCAAATACTAGTGGGATAACCTAA-CT-AGCAT
2026346 ATTTCAAATACTAGTGGGATAACCTAACTAGCAT
1 ATTTCAAATACTAGTGGGATAACCTAACTAGCAT
*
2026380 ATTTCTAATACTAGTGGGATAACCTAACTAGCAT
1 ATTTCAAATACTAGTGGGATAACCTAACTAGCAT
2026414 ATTTCAAATACTAGTGGGATAACCTAA
1 ATTTCAAATACTAGTGGGATAACCTAA
2026441 TTTTGAGCAT
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
34 63 0.71
35 1 0.01
36 25 0.28
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (34 bp):
ATTTCAAATACTAGTGGGATAACCTAACTAGCAT
Found at i:2030866 original size:22 final size:23
Alignment explanation
Indices: 2030841--2030884 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
2030831 CATACATTAT
2030841 TATGCATTATTAT-AATAAAATG
1 TATGCATTATTATCAATAAAATG
2030863 TATGCATTATTATGCAATAAAA
1 TATGCATTATTAT-CAATAAAA
2030885 ACCCCACGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (23 bp):
TATGCATTATTATCAATAAAATG
Found at i:2031595 original size:34 final size:36
Alignment explanation
Indices: 2031509--2031596 Score: 108
Period size: 37 Copynumber: 2.5 Consensus size: 36
2031499 TAAAATGGTC
* * *
2031509 ATTTCCAATACTAGTGGAATAACCTAATTTGAGTAT
1 ATTTCAAATACTAGTGGAATAACCTAATCTGAGCAT
*
2031545 ATTTTCAAATACTAGTGGGATAACCTAA-CT-AGCAT
1 A-TTTCAAATACTAGTGGAATAACCTAATCTGAGCAT
*
2031580 ATTTCTAATACTAGTGG
1 ATTTCAAATACTAGTGG
2031597 TATGGCTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 15 0.33
35 5 0.11
36 2 0.04
37 24 0.52
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (36 bp):
ATTTCAAATACTAGTGGAATAACCTAATCTGAGCAT
Found at i:2034404 original size:12 final size:12
Alignment explanation
Indices: 2034387--2034414 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2034377 TTGCACTGAT
2034387 ACGGATACGGGG
1 ACGGATACGGGG
2034399 ACGGATACGGGG
1 ACGGATACGGGG
2034411 ACGG
1 ACGG
2034415 GGACAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.50, T:0.07
Consensus pattern (12 bp):
ACGGATACGGGG
Found at i:2034407 original size:18 final size:18
Alignment explanation
Indices: 2034384--2034418 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2034374 ATGTTGCACT
*
2034384 GATACGGATACGGGGACG
1 GATACGGAGACGGGGACG
*
2034402 GATACGGGGACGGGGAC
1 GATACGGAGACGGGGAC
2034419 AGAAAACGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.49, T:0.09
Consensus pattern (18 bp):
GATACGGAGACGGGGACG
Found at i:2036859 original size:23 final size:23
Alignment explanation
Indices: 2036824--2036871 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2036814 ATCAAGTATG
*
2036824 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
2036847 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
2036870 AT
1 AT
2036872 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:2037686 original size:182 final size:182
Alignment explanation
Indices: 2037369--2037821 Score: 726
Period size: 182 Copynumber: 2.5 Consensus size: 182
2037359 TGATCACACA
* *
2037369 ACCGATTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGAT
1 ACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
* * *
2037434 ACATTTTTATAAAGTATCGACACCTTATTGGCGCTATAACTTCTTTTATTTTAAATTCCAAAAAT
66 ACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTATTTTAAATTCCAAAAAT
* *
2037499 GTCGATACTTATAATAAAGTATCGATACTATCAACATATCCAGTAGCTCTTT
131 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCAGTAGCGCTTT
* *
2037551 ACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
1 ACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
* * *
2037616 ACATTTTTATAAAATATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
66 ACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTATTTTAAATTCCAAAAAT
*
2037681 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTT
131 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCAGTAGCGCTTT
* ** * * *
2037733 ACCTGTTTTGTCATTTATAGATCGGTTTTGTCATTTTTTTACATGTTTTATTGTTATGGATCGAT
1 ACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
*
2037798 ACATTTTTATAAAGTATTGACACT
66 ACATTTTTATAAAGTATCGACACT
2037822 ATCAACATAT
Statistics
Matches: 249, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 249 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
ACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTATTTTAAATTCCAAAAAT
GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCAGTAGCGCTTT
Found at i:2038055 original size:113 final size:112
Alignment explanation
Indices: 2037694--2038269 Score: 931
Period size: 112 Copynumber: 5.1 Consensus size: 112
2037684 GATACTTATA
* * *
2037694 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2037759 TTTGTCATTTTTTTACATGTTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
2037806 ATAAAGTATTGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2037871 TTTGTCATTTTTTTACCTGTTATAGTATTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
2037918 ATAAAGTATTGACACTTTCCATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
2037983 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
2038031 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
2038096 TTTGTCA-TTTTTTACTTTTTATATTGTTATGGATAGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
2038142 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGT-ATTTATAGACCAGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
2038206 TTTGTCATTTTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCA--TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
2038255 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
2038270 AAACCGACAA
Statistics
Matches: 437, Mismatches: 23, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
110 20 0.05
111 86 0.20
112 173 0.40
113 158 0.36
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:2040317 original size:14 final size:14
Alignment explanation
Indices: 2040300--2040337 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2040290 GAGAAAAGAA
2040300 TAATAAAAAAATAT
1 TAATAAAAAAATAT
* *
2040314 TAATATAATAATAT
1 TAATAAAAAAATAT
2040328 TAATAAAAAA
1 TAATAAAAAA
2040338 TGAAAATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAATAAAAAAATAT
Found at i:2040348 original size:2 final size:2
Alignment explanation
Indices: 2040343--2040373 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2040333 AAAAATGAAA
2040343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2040374 ACAATGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2040791 original size:33 final size:33
Alignment explanation
Indices: 2040734--2040819 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
2040724 GTTTTACTTG
*
2040734 GACTTAAA-ATGTTTCGATTTTAGTGTTTCAATAA
1 GACTTAAATATG-TT-GGTTTTAGTGTTTCAATAA
*
2040768 GACTTAAATATGTTGGTTTTAGTGTTTCAATAG
1 GACTTAAATATGTTGGTTTTAGTGTTTCAATAA
*
2040801 GACTTAAATACGTTGGTTT
1 GACTTAAATATGTTGGTTT
2040820 ATTTTTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
33 35 0.73
34 10 0.21
35 3 0.06
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (33 bp):
GACTTAAATATGTTGGTTTTAGTGTTTCAATAA
Found at i:2040915 original size:20 final size:22
Alignment explanation
Indices: 2040869--2040927 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 22
2040859 GGCCTACAAA
2040869 AATAATAAAATAAGAATATATT
1 AATAATAAAATAAGAATATATT
*
2040891 AATAATAATAATAATAA-ATATAT
1 AATAATAA-AATAAGAATATAT-T
2040914 AATGTAATAAAATA
1 AA--TAATAAAATA
2040928 TTTTTATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 12 0.38
23 10 0.31
24 4 0.12
25 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (22 bp):
AATAATAAAATAAGAATATATT
Found at i:2040921 original size:28 final size:25
Alignment explanation
Indices: 2040869--2040927 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
2040859 GGCCTACAAA
2040869 AATAATAAAATAAGAATATATTAAT
1 AATAATAAAATAAGAATATATTAAT
2040894 AATAATAATAAT-A-AATATA-TAAT
1 AATAATAA-AATAAGAATATATTAAT
*
2040917 -GTAATAAAATA
1 AATAATAAAATA
2040928 TTTTTATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.10
22 6 0.19
23 4 0.13
24 6 0.19
25 9 0.29
26 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (25 bp):
AATAATAAAATAAGAATATATTAAT
Found at i:2042565 original size:3 final size:3
Alignment explanation
Indices: 2042551--2042599 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
2042541 ACTTTAAATA
* *
2042551 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2042599 T
1 T
2042600 TATTTACATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2042666 original size:20 final size:19
Alignment explanation
Indices: 2042638--2042723 Score: 52
Period size: 18 Copynumber: 4.5 Consensus size: 19
2042628 GAAGCCCAAT
* *
2042638 CCAGTTACAAAACACGGAAC
1 CCAGATACAAAAC-CGAAAC
* *
2042658 CCAGATACAAGACC-CAAC
1 CCAGATACAAAACCGAAAC
*
2042676 CCA-ACAACAAAACCCGAAAC
1 CCAGA-TACAAAA-CCGAAAC
* *
2042696 CCAGATACAAGACC-CAAC
1 CCAGATACAAAACCGAAAC
*
2042714 CCAGTTACAA
1 CCAGATACAA
2042724 GACCCGTAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
17 1 0.02
18 23 0.44
19 5 0.10
20 22 0.42
21 1 0.02
ACGTcount: A:0.47, C:0.36, G:0.10, T:0.07
Consensus pattern (19 bp):
CCAGATACAAAACCGAAAC
Found at i:2042678 original size:18 final size:18
Alignment explanation
Indices: 2042655--2042728 Score: 87
Period size: 18 Copynumber: 4.0 Consensus size: 18
2042645 CAAAACACGG
2042655 AACCCAGATACAAGACCC
1 AACCCAGATACAAGACCC
* *
2042673 AACCCA-ACAACAAAACCC
1 AACCCAGA-TACAAGACCC
2042691 GAAACCCAGATACAAGACCC
1 --AACCCAGATACAAGACCC
*
2042711 AACCCAGTTACAAGACCC
1 AACCCAGATACAAGACCC
2042729 GTAGCACAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
17 1 0.02
18 31 0.66
20 14 0.30
21 1 0.02
ACGTcount: A:0.46, C:0.39, G:0.09, T:0.05
Consensus pattern (18 bp):
AACCCAGATACAAGACCC
Found at i:2042729 original size:38 final size:38
Alignment explanation
Indices: 2042632--2042729 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
2042622 TAACCTGAAG
* * *
2042632 CCCAATCCAGTTACAAAACACGGAACCCAGATACAAGA
1 CCCAACCCAGTTACAAAACCCGAAACCCAGATACAAGA
***
2042670 CCCAACCCAACAACAAAACCCGAAACCCAGATACAAGA
1 CCCAACCCAGTTACAAAACCCGAAACCCAGATACAAGA
*
2042708 CCCAACCCAGTTACAAGACCCG
1 CCCAACCCAGTTACAAAACCCG
2042730 TAGCACAATG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.44, C:0.38, G:0.11, T:0.07
Consensus pattern (38 bp):
CCCAACCCAGTTACAAAACCCGAAACCCAGATACAAGA
Found at i:2043640 original size:10 final size:10
Alignment explanation
Indices: 2043625--2043658 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2043615 TTAAGAGAGA
*
2043625 GAGAGTGAAT
1 GAGAGTAAAT
2043635 GAGAGTAAAT
1 GAGAGTAAAT
2043645 GAGAGTAAAT
1 GAGAGTAAAT
2043655 GAGA
1 GAGA
2043659 AGTTTGGCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.18
Consensus pattern (10 bp):
GAGAGTAAAT
Found at i:2044246 original size:2 final size:2
Alignment explanation
Indices: 2044239--2044274 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2044229 TTATTATGTC
2044239 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
2044275 TACTTAATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2057190 original size:138 final size:137
Alignment explanation
Indices: 2056942--2057582 Score: 725
Period size: 138 Copynumber: 4.6 Consensus size: 137
2056932 GCAGTCATCA
* * *
2056942 TCCACCGACCAGATCTACTCAACATGTAGGAGCAGCGTCATCCTTAGATAGCCAGACTTCCTCAT
1 TCCACTGACCAGATCTCCTCAACGTGTAGGAGCAGCGTCATCCTTAGATAGCCAGACTTCCTCAT
* * * *
2057007 CACGTAGGAACTGTGTTATCTCCATTTATCCCTATAGACGGTTAGATGTCCTCATCACGTAGGAA
66 CACGTAGGAACCGTGTTATCTCCATTTATCCCTAAAAATGGTTAGATGTCCTCATCA-GTAGGAA
*
2057072 TAATACT-G
130 CAAT-CTCG
* * * *
2057080 TCCACTGACCAGATCTCCTCAATGTGTAGGAGCATCATCATCCTTAGATAGCTAGACTTCCTCAT
1 TCCACTGACCAGATCTCCTCAACGTGTAGGAGCAGCGTCATCCTTAGATAGCCAGACTTCCTCAT
*
2057145 CACGTAGGAACCGTGTTATCTCCATTTATCCCTAAAAATGATTAGATGTCCTCATCAGTTAGGAA
66 CACGTAGGAACCGTGTTATCTCCATTTATCCCTAAAAATGGTTAGATGTCCTCATCAG-TAGGAA
*
2057210 CAATGTCG
130 CAATCTCG
* * * *
2057218 TCTA-TCGACCAGATCTCCTCAACGTGTAGGAGCAGCGTTATCCTTTGATAGCCAGACTTCCTTA
1 TCCACT-GACCAGATCTCCTCAACGTGTAGGAGCAGCGTCATCCTTAGATAGCCAGACTTCCTCA
* * *
2057282 TCACGTAAGAACCGTGTTATCTCCATTTAT-CC-AAAAATACGGTTAGACGTCCTCATCATGTAA
65 TCACGTAGGAACCGTGTTATCTCCATTTATCCCTAAAAAT--GGTTAGATGTCCTCATCA-GTAG
*
2057345 GAACAATTTCG
127 GAACAATCTCG
* * * *
2057356 TCCACTGACCAGATGTCCTCAACGCGTAGGAGTAGCGTCATCCTTAGATAGCCAGACTTCTTCAT
1 TCCACTGACCAGATCTCCTCAACGTGTAGGAGCAGCGTCATCCTTAGATAGCCAGACTTCCTCAT
* * * * * * *
2057421 CACGTAGGAACCGTATTATCTCCATTTATCCCTAAAGACGGCTAGACGCCCTCATCACATAGGAA
66 CACGTAGGAACCGTGTTATCTCCATTTATCCCTAAAAATGGTTAGATGTCCTCATCA-GTAGGAA
* *
2057486 CAATGTCA
130 CAATCTCG
* ** * * * * * ** * *
2057494 TCCA-TCGACCAGACCTCCTCATTGCGTAGGAGTAGTGTTATCCTTAGACAATCTGACTTTCTCA
1 TCCACT-GACCAGATCTCCTCAACGTGTAGGAGCAGCGTCATCCTTAGATAGCCAGACTTCCTCA
* *
2057558 TCACGTAGGAATCGTGTTGTCTCCA
65 TCACGTAGGAACCGTGTTATCTCCA
2057583 AAATCATCCC
Statistics
Matches: 432, Mismatches: 61, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
136 6 0.01
137 6 0.01
138 412 0.95
139 4 0.01
140 4 0.01
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (137 bp):
TCCACTGACCAGATCTCCTCAACGTGTAGGAGCAGCGTCATCCTTAGATAGCCAGACTTCCTCAT
CACGTAGGAACCGTGTTATCTCCATTTATCCCTAAAAATGGTTAGATGTCCTCATCAGTAGGAAC
AATCTCG
Found at i:2057442 original size:276 final size:276
Alignment explanation
Indices: 2056939--2057582 Score: 822
Period size: 276 Copynumber: 2.3 Consensus size: 276
2056929 GAAGCAGTCA
* * * *
2056939 TCATCCACCGACCAGATCTACTCAACATGTAGGAGCAGCGTCATCCTTAGATAGCCAGACTTCCT
1 TCATCCATCGACCAGATCTCCTCAACGTGTAGGAGCAGCGTTATCCTTAGATAGCCAGACTTCCT
* * ** * * *
2057004 CATCACGTAGGAACTGTGTTATCTCCATTTATCCCTATAGACGGTTAGATGTCCTCATCACGTAG
66 CATCACGTAAGAACCGTGTTATCTCCATTTATCCAAAAAGACGGTTAGACGTCCTCATCACGTAA
* * * * *
2057069 GAATAATACTGTCCACTGACCAGATCTCCTCAATGTGTAGGAGCATCATCATCCTTAGATAGCTA
131 GAACAATACTGTCCACTGACCAGATCTCCTCAACGCGTAGGAGCAGCATCATCCTTAGATAGCCA
* * * * *
2057134 GACTTCCTCATCACGTAGGAACCGTGTTATCTCCATTTATCCCTAAAAATGATTAGATGTCCTCA
196 GACTTCCTCATCACGTAGGAACCGTATTATCTCCATTTATCCCTAAAAACGACTAGACGCCCTCA
**
2057199 TCAGTTAGGAACAATG
261 TCACATAGGAACAATG
* * *
2057215 TCGTCTATCGACCAGATCTCCTCAACGTGTAGGAGCAGCGTTATCCTTTGATAGCCAGACTTCCT
1 TCATCCATCGACCAGATCTCCTCAACGTGTAGGAGCAGCGTTATCCTTAGATAGCCAGACTTCCT
* * *
2057280 TATCACGTAAGAACCGTGTTATCTCCATTTATCCAAAAATACGGTTAGACGTCCTCATCATGTAA
66 CATCACGTAAGAACCGTGTTATCTCCATTTATCCAAAAAGACGGTTAGACGTCCTCATCACGTAA
* * * *
2057345 GAACAAT-TTCGTCCACTGACCAGATGTCCTCAACGCGTAGGAGTAGCGTCATCCTTAGATAGCC
131 GAACAATACT-GTCCACTGACCAGATCTCCTCAACGCGTAGGAGCAGCATCATCCTTAGATAGCC
* * *
2057409 AGACTTCTTCATCACGTAGGAACCGTATTATCTCCATTTATCCCTAAAGACGGCTAGACGCCCTC
195 AGACTTCCTCATCACGTAGGAACCGTATTATCTCCATTTATCCCTAAAAACGACTAGACGCCCTC
2057474 ATCACATAGGAACAATG
260 ATCACATAGGAACAATG
* ** * * * * ** * *
2057491 TCATCCATCGACCAGACCTCCTCATTGCGTAGGAGTAGTGTTATCCTTAGACAATCTGACTTTCT
1 TCATCCATCGACCAGATCTCCTCAACGTGTAGGAGCAGCGTTATCCTTAGATAGCCAGACTTCCT
* * *
2057556 CATCACGTAGGAATCGTGTTGTCTCCA
66 CATCACGTAAGAACCGTGTTATCTCCA
2057583 AAATCATCCC
Statistics
Matches: 313, Mismatches: 54, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
275 1 0.00
276 312 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (276 bp):
TCATCCATCGACCAGATCTCCTCAACGTGTAGGAGCAGCGTTATCCTTAGATAGCCAGACTTCCT
CATCACGTAAGAACCGTGTTATCTCCATTTATCCAAAAAGACGGTTAGACGTCCTCATCACGTAA
GAACAATACTGTCCACTGACCAGATCTCCTCAACGCGTAGGAGCAGCATCATCCTTAGATAGCCA
GACTTCCTCATCACGTAGGAACCGTATTATCTCCATTTATCCCTAAAAACGACTAGACGCCCTCA
TCACATAGGAACAATG
Found at i:2057868 original size:3 final size:3
Alignment explanation
Indices: 2057839--2057913 Score: 107
Period size: 3 Copynumber: 25.3 Consensus size: 3
2057829 ACTTTAAATA
* * * *
2057839 TAT TAT TAA TAT TAA TGT TAA 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
2057887 TAT TAT TAT TAT TAT TAT TA- TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2057914 TACTTTTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2057978 original size:20 final size:20
Alignment explanation
Indices: 2057953--2058008 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 20
2057943 CCAATCTAAT
2057953 TACAAGACCCGGAACCCAGA
1 TACAAGACCCGGAACCCAGA
* *
2057973 TACAAGACCC--AATCCAGT
1 TACAAGACCCGGAACCCAGA
*
2057991 TACAAGACCCGGAGCCCA
1 TACAAGACCCGGAACCCA
2058009 ATGGTAGGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 16 0.53
20 14 0.47
ACGTcount: A:0.38, C:0.36, G:0.18, T:0.09
Consensus pattern (20 bp):
TACAAGACCCGGAACCCAGA
Found at i:2057994 original size:18 final size:18
Alignment explanation
Indices: 2057942--2058000 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
2057932 CAACCTGAAG
* *
2057942 CCCAATCTAATTACAAGA
1 CCCAATCCAGTTACAAGA
* *
2057960 CCCGGAACCCAGATACAAGA
1 CCC--AATCCAGTTACAAGA
2057980 CCCAATCCAGTTACAAGA
1 CCCAATCCAGTTACAAGA
2057998 CCC
1 CCC
2058001 GGAGCCCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 19 0.58
20 14 0.42
ACGTcount: A:0.39, C:0.36, G:0.12, T:0.14
Consensus pattern (18 bp):
CCCAATCCAGTTACAAGA
Found at i:2058287 original size:6 final size:6
Alignment explanation
Indices: 2058273--2058315 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
2058263 ACCACCGCTT
* * * *
2058273 AGAACA AGAAAA AGAAAA AGAAAA AGTAAG AGAGAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
2058316 AAACTAAACC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:2059248 original size:2 final size:2
Alignment explanation
Indices: 2059241--2059278 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2059231 TTATTATGTC
2059241 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
2059279 TACTTAATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2062714 original size:6 final size:6
Alignment explanation
Indices: 2062679--2062713 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
2062669 ATTTATTGCT
2062679 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA -TAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
2062714 AACAAAGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TTAAAA
Found at i:2063811 original size:45 final size:45
Alignment explanation
Indices: 2063717--2063813 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
2063707 AAAATGGTTT
* * * *
2063717 AAAAATAATATTTTAAGTAACGACTAATATTAATATTTCTGATAG
1 AAAAATAATATTTTAAGTAACGACCAATATTAACATTTCTAATAA
* * **
2063762 AAAAATAATATTTTAGGTACCTCCCAATATTAACATTT-TCAATAA
1 AAAAATAATATTTTAAGTAACGACCAATATTAACATTTCT-AATAA
2063807 AAAAATA
1 AAAAATA
2063814 TTAATATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.02
45 42 0.98
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (45 bp):
AAAAATAATATTTTAAGTAACGACCAATATTAACATTTCTAATAA
Found at i:2064234 original size:24 final size:23
Alignment explanation
Indices: 2064207--2064261 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
2064197 ATATTTTTTT
2064207 ATTTAAATGAAAAATTATAAATGA
1 ATTTAAATG-AAAATTATAAATGA
***
2064231 ATTTTCTTTGAAAATTATAAATGA
1 A-TTTAAATGAAAATTATAAATGA
*
2064255 TTTTAAA
1 ATTTAAA
2064262 CTAACTACAA
Statistics
Matches: 23, Mismatches: 7, Indels: 3
0.70 0.21 0.09
Matches are distributed among these distances:
23 3 0.13
24 15 0.65
25 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (23 bp):
ATTTAAATGAAAATTATAAATGA
Found at i:2066096 original size:15 final size:15
Alignment explanation
Indices: 2066076--2066106 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2066066 TATCTAACCT
2066076 AAATTGGAGGCTCTA
1 AAATTGGAGGCTCTA
2066091 AAATTGGAGGCTCTA
1 AAATTGGAGGCTCTA
2066106 A
1 A
2066107 TTAATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
AAATTGGAGGCTCTA
Found at i:2068803 original size:2 final size:2
Alignment explanation
Indices: 2068796--2068840 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2068786 AGTTTAGGGG
2068796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2068838 TA T
1 TA T
2068841 CACATTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2070422 original size:22 final size:22
Alignment explanation
Indices: 2070394--2070498 Score: 120
Period size: 22 Copynumber: 4.8 Consensus size: 22
2070384 GGCATGTGAA
* *
2070394 ATTTATCCCGAATGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
* * * *
2070416 ATTTATCCCAAAAGACCTCTGT
1 ATTTGTCCCGAAGGACCTATGT
*
2070438 ATATGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
* *
2070460 ATTTGTCCCAAAGGACCTCTGT
1 ATTTGTCCCGAAGGACCTATGT
*
2070482 ATATGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
2070499 GCATAGACCC
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:2070449 original size:44 final size:44
Alignment explanation
Indices: 2070399--2070498 Score: 173
Period size: 44 Copynumber: 2.3 Consensus size: 44
2070389 GTGAAATTTA
*
2070399 TCCCGAATGACCTATGTATTTATCCCAAAAGACCTCTGTATATG
1 TCCCGAAGGACCTATGTATTTATCCCAAAAGACCTCTGTATATG
* *
2070443 TCCCGAAGGACCTATGTATTTGTCCCAAAGGACCTCTGTATATG
1 TCCCGAAGGACCTATGTATTTATCCCAAAAGACCTCTGTATATG
2070487 TCCCGAAGGACC
1 TCCCGAAGGACC
2070499 GCATAGACCC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (44 bp):
TCCCGAAGGACCTATGTATTTATCCCAAAAGACCTCTGTATATG
Found at i:2075052 original size:36 final size:36
Alignment explanation
Indices: 2075014--2075262 Score: 294
Period size: 36 Copynumber: 7.0 Consensus size: 36
2075004 TGTAAGATTT
* * * *
2075014 TGTTTAAAGAGAAACACTTTCAAGTGAGATAAAATT
1 TGTTTTAAGAGAAACAATCTCAAGTGAGATAAAATA
*
2075050 TGTTTTAAG-GAAAATAATCTCAAGTGAGATAAAATA
1 TGTTTTAAGAG-AAACAATCTCAAGTGAGATAAAATA
* * * *
2075086 TGTTTTATGAAAAATAATCTCAAGTGAGATAAAATT
1 TGTTTTAAGAGAAACAATCTCAAGTGAGATAAAATA
*
2075122 TGTTTTAAGGGAAACAATCTCAAGTGAGATAAAATA
1 TGTTTTAAGAGAAACAATCTCAAGTGAGATAAAATA
2075158 TGTTTTAAG-GAAAACAA--T-AAGTGAGATAAAATA
1 TGTTTTAAGAG-AAACAATCTCAAGTGAGATAAAATA
*
2075191 TGTTTTAAGA-AAAGCAATCTCAAGTGAGATAAAATC
1 TGTTTTAAGAGAAA-CAATCTCAAGTGAGATAAAATA
** *
2075227 CATTTTAAGAAAAAACAATCTCAAGTGAGATAAAAT
1 TGTTTTAAG-AGAAACAATCTCAAGTGAGATAAAAT
2075263 CTTGAGTAAA
Statistics
Matches: 187, Mismatches: 16, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
32 3 0.02
33 27 0.14
34 1 0.01
35 3 0.02
36 128 0.68
37 22 0.12
38 3 0.02
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (36 bp):
TGTTTTAAGAGAAACAATCTCAAGTGAGATAAAATA
Found at i:2075113 original size:72 final size:72
Alignment explanation
Indices: 2075014--2075262 Score: 335
Period size: 72 Copynumber: 3.5 Consensus size: 72
2075004 TGTAAGATTT
* * * * *
2075014 TGTTTAAAGAGAAACACTTTCAAGTGAGATAAAATTTGTTTTAAGGAAAATAATCTCAAGTGAGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTGTTTTAAGGAAAACAATCTCAAGTGAGA
2075079 TAAAATA
66 TAAAATA
* * *
2075086 TGTTTTATGAAAAATAATCTCAAGTGAGATAAAATTTGTTTTAAGGGAAACAATCTCAAGTGAGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTGTTTTAAGGAAAACAATCTCAAGTGAGA
2075151 TAAAATA
66 TAAAATA
* *
2075158 TGTTTTAAGGAAAACAA--T-AAGTGAGATAAAATATGTTTTAA-GAAAAGCAATCTCAAGTGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTGTTTTAAGGAAAA-CAATCTCAAGTGAG
*
2075219 ATAAAATC
65 ATAAAATA
**
2075227 CATTTTAAGAAAAAACAATCTCAAGTGAGATAAAAT
1 TGTTTTAAG-AAAAACAATCTCAAGTGAGATAAAAT
2075263 CTTGAGTAAA
Statistics
Matches: 155, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
68 4 0.03
69 50 0.32
70 8 0.05
72 79 0.51
73 14 0.09
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (72 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTGTTTTAAGGAAAACAATCTCAAGTGAGA
TAAAATA
Found at i:2078714 original size:16 final size:17
Alignment explanation
Indices: 2078671--2078714 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2078661 AATTTCTATT
2078671 TTATTTTATTTTAGTCA
1 TTATTTTATTTTAGTCA
* * *
2078688 TTAGTTAATTTT-GTTA
1 TTATTTTATTTTAGTCA
2078704 TTATTTTATTT
1 TTATTTTATTT
2078715 ATGAATATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (17 bp):
TTATTTTATTTTAGTCA
Found at i:2079308 original size:16 final size:18
Alignment explanation
Indices: 2079289--2079323 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2079279 TTTATAAAAA
2079289 TATAAAAA-T-ATATATT
1 TATAAAAATTAATATATT
2079305 TATAAAAATTAATATATT
1 TATAAAAATTAATATATT
2079323 T
1 T
2079324 TTCTTGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAAAAATTAATATATT
Found at i:2079315 original size:148 final size:148
Alignment explanation
Indices: 2079043--2079315 Score: 356
Period size: 148 Copynumber: 1.8 Consensus size: 148
2079033 ATCATGTTTT
* * * *
2079043 TATTTATTTATTTTTAATATTAAGAAAGGGGTTGTCTTAAAGCAACTAAAAGTCTTTTTCTGATA
1 TATTTATTAATTTTTAATATTAAGAAAGAGGCTGTCTTAAAGCAACTAAAAGTCATTTTCTGATA
* * * ***
2079108 TTTTCAAATAAATAAATATCATATTTTTTATAAATTATATATAATTTATTTTTTTAATTATTTTT
66 TTTTCAAATAAATAAATATCATATTTTATATAAAATATATAAAATTTATTTTAAAAATTATTTTT
2079173 AGAAAAAGGTTTTATTAA
131 AGAAAAAGGTTTTATTAA
* *
2079191 TATTTATTAATTTTTTATATTAAGAAAGAGGCTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
1 TATTTATTAATTTTTAATATTAAGAAAGAGGCTGTCTTAAAGCAACTAAAAGTCATTTTCTGATA
* *
2079256 -TTTCTAAGTAAATAAATATCTTA-TTTATA-AAAATATA-AAAATATATATTTATAAAAATTA
66 TTTTC-AAATAAATAAATATCATATTTTATATAAAATATATAAAAT-T-TATTT-TAAAAATTA
2079316 ATATATTTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
145 4 0.04
146 8 0.07
147 14 0.13
148 81 0.76
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (148 bp):
TATTTATTAATTTTTAATATTAAGAAAGAGGCTGTCTTAAAGCAACTAAAAGTCATTTTCTGATA
TTTTCAAATAAATAAATATCATATTTTATATAAAATATATAAAATTTATTTTAAAAATTATTTTT
AGAAAAAGGTTTTATTAA
Found at i:2080714 original size:36 final size:36
Alignment explanation
Indices: 2080667--2080738 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
2080657 GAGCAATGCA
* *
2080667 CACAAAGATCCTGTTATATTAATACCAAAAGTATTC
1 CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
* *
2080703 CACAAATATCCTGTTAGATTGATACCAAAAGCATTC
1 CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
2080739 TATGGTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (36 bp):
CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
Found at i:2081528 original size:20 final size:20
Alignment explanation
Indices: 2081495--2081533 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2081485 TGCATCTTTG
* *
2081495 CATTTTTATGTTTGTATTTA
1 CATTTTCATGTTTGCATTTA
*
2081515 CATTTTCATTTTTGCATTT
1 CATTTTCATGTTTGCATTT
2081534 GCATCTTTGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.64
Consensus pattern (20 bp):
CATTTTCATGTTTGCATTTA
Found at i:2092543 original size:21 final size:22
Alignment explanation
Indices: 2092517--2092578 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
2092507 TTTATTGTAG
*
2092517 AGGGAATAGATACCCCC-TTGA
1 AGGGAACAGATACCCCCTTTGA
* *
2092538 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACAGATACCCCCTTTGA
* *
2092560 AGGGGAACCGATTCCCCCT
1 A-GGGAACAGATACCCCCT
2092579 CACATGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 14 0.39
22 5 0.14
23 17 0.47
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (22 bp):
AGGGAACAGATACCCCCTTTGA
Found at i:2092559 original size:22 final size:23
Alignment explanation
Indices: 2092529--2092578 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
2092519 GGAATAGATA
2092529 CCCCC-TTGAA-GGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
2092550 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
2092573 CCCCCT
1 CCCCCT
2092579 CACATGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 5 0.19
22 5 0.19
23 17 0.63
ACGTcount: A:0.20, C:0.38, G:0.22, T:0.20
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACCGATT
Found at i:2096976 original size:53 final size:54
Alignment explanation
Indices: 2096906--2097012 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 54
2096896 CTGACCAGAA
2096906 ATCTGTACAGAAACCATAGAAAAGGATGAATGT-TTGTCAAATGTTTTACGAAC
1 ATCTGTACAGAAACCATAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* *
2096959 ATCTGTGCA-AAAGCCATAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGTACAGAAA-CCATAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
2097013 CAGTGATTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
52 3 0.06
53 27 0.54
54 20 0.40
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (54 bp):
ATCTGTACAGAAACCATAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:2097405 original size:22 final size:22
Alignment explanation
Indices: 2097377--2097521 Score: 245
Period size: 22 Copynumber: 6.6 Consensus size: 22
2097367 ACATCTACAT
2097377 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
2097399 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
2097421 TCTTCAAAGATGATATATTCTT
1 TCTTCAAAGATGATAGATTCTC
*
2097443 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
2097465 TTTTCAAAGATGATAGATTTTC
1 TCTTCAAAGATGATAGATTCTC
2097487 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
2097509 TCTTCAAAGATGA
1 TCTTCAAAGATGA
2097522 AAGCTTTATT
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 114 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:2098583 original size:122 final size:122
Alignment explanation
Indices: 2098347--2098923 Score: 883
Period size: 122 Copynumber: 4.7 Consensus size: 122
2098337 CACTCGATGG
2098347 ATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
2098412 ATGAGAAGAACTTGTTCAACATTTTGC-TCGATTCTATC-CTAAAATGAGATAGATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTGCAT-GACTCTATCAC-AAAAGGAGATAGATCAAC
* *
2098470 A-CTAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGTGGAAGAAAAAGTTCATA
1 ATC-AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
2098534 ATGAGAAGAGCTTGTTCAATCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
65 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAAAAGGAGATAGATCAAC
*
2098592 ATCAACATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
2098657 TAAGAAGAATTTGTTCAACCTTTTGCATGACTCTATCACAAAAGGAGATATATCAGC
66 TGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAAAAGGAGATAGATCAAC
* *
2098714 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTAAAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * * *
2098779 TAAGAAGAACTTGTTTAACCTTTTGCGTGATTCTATCATAGAAA-GAGATAGATCAAC
66 TGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACA-AAAGGAGATAGATCAAC
2098836 ATCAACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAG-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
2098901 ATGAGAAGAACTTGTTCAACCTT
65 ATGAGAAGAACTTGTTCAACCTT
2098924 GCCTTAATTC
Statistics
Matches: 415, Mismatches: 33, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
122 325 0.78
123 90 0.22
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAAAAGGAGATAGATCAAC
Found at i:2100903 original size:142 final size:142
Alignment explanation
Indices: 2100705--2101089 Score: 345
Period size: 143 Copynumber: 2.7 Consensus size: 142
2100695 TTAAATAATA
* * * ** ** * *
2100705 ATATTGATTTATTTTTAAATACTCAGAAAGGACA-GTCTTAAAATAACTAGATGTCATATTCTGG
1 ATATTTATTTA-TTTTAAATATTAAGAAAGGGGATGTCTTAAAGCAACTAGAAGTCAT-TTCTGA
* * **
2100769 TATTTT-AA-AAAT-AATATCATGCTTATA-AAATATATATTTTCTTTAATTTTATATAAATTAT
64 TATTTTAAATAAATAAATATCATACTTATATAAAT-TATATATAATTTAATTTTA-AT-AATT-T
* ** *
2100830 TT-TAATCATGTTTTTATT
125 TTAGAAAAAT-ATTTTATT
2100848 -TATTTATTTATTTTAAATATTAAGAAAGGGGATGTCTTAAAGCAACTAGAAGTCATTTTCTGAT
1 ATATTTATTTATTTTAAATATTAAGAAAGGGGATGTCTTAAAGCAACTAGAAGTCA-TTTCTGAT
* * * *
2100912 ATTTTTAAATAAATAAATATCCTACTTTTATAAATTATATATAATTTATTTTTAATTATTTTTAG
65 A-TTTTAAATAAATAAATATCATACTTATATAAATTATATATAATTTAATTTTAATAATTTTTAG
2100977 AAAAATATTTTATT
129 AAAAATATTTTATT
* ** * *
2100991 AATATTTATTAATTTTTTATATTAAGAAATGGGTTGTCTT-AAGCAACTAGAAGTCATTTCTGAT
1 -ATATTTATTTATTTTAAATATTAAGAAAGGGGATGTCTTAAAGCAACTAGAAGTCATTTCTGAT
* * * *
2101055 ATTTCTAAGTAAATAAATATCTTATTTATAAAAAT
65 ATTT-TAAATAAATAAATATCATACTTATATAAAT
2101090 ATAAAAAATA
Statistics
Matches: 200, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
141 18 0.09
142 38 0.19
143 49 0.25
144 25 0.12
145 39 0.19
146 27 0.14
147 4 0.02
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (142 bp):
ATATTTATTTATTTTAAATATTAAGAAAGGGGATGTCTTAAAGCAACTAGAAGTCATTTCTGATA
TTTTAAATAAATAAATATCATACTTATATAAATTATATATAATTTAATTTTAATAATTTTTAGAA
AAATATTTTATT
Found at i:2101109 original size:17 final size:18
Alignment explanation
Indices: 2101089--2101124 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2101079 TTTATAAAAA
2101089 TATAAAAAAT-ATATATT
1 TATAAAAAATAATATATT
*
2101106 TATAAAAATTAATATATT
1 TATAAAAAATAATATATT
2101124 T
1 T
2101125 TCTTGGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAAAATAATATATT
Found at i:2104083 original size:39 final size:39
Alignment explanation
Indices: 2104039--2104132 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 39
2104029 GGCGGTTTTG
* * * *
2104039 CCTTTATTGCACTCATCAACTTCACTTTAGGCATTACCGA
1 CCTTTATTACACTCATCAACCTCACCTTAGGAATTACC-A
*
2104079 -CTTTATTACACTCATCATCCTCACCTTAGGAATTACCA
1 CCTTTATTACACTCATCAACCTCACCTTAGGAATTACCA
2104117 CCTTTTATTACACTCA
1 CC-TTTATTACACTCA
2104133 CCTAATAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 1 0.02
39 33 0.70
40 13 0.28
ACGTcount: A:0.27, C:0.31, G:0.06, T:0.36
Consensus pattern (39 bp):
CCTTTATTACACTCATCAACCTCACCTTAGGAATTACCA
Found at i:2106533 original size:48 final size:47
Alignment explanation
Indices: 2106355--2106785 Score: 601
Period size: 47 Copynumber: 9.1 Consensus size: 47
2106345 TAAACTGAAT
* * *
2106355 CCATAACTAAAAATGCATGAACGGATGCATTAAGGAATGGAATGATG
1 CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* *
2106402 CCATAACTAAAAATGCATTAACGGATGGATTAAGGCATGAAAGGATG
1 CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* *
2106449 CCATAACTAAAATTGAATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* * * *
2106496 ACATAACTAAAAAATGAATGAACAGATGCATTAAGGCATAAAAGGATG
1 CCATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* *
2106544 CCATAACTAAAAAATGCATGAATGGATGCATTAAGGCATGAAAAGATG
1 CCATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* * *
2106592 TCATAACTAAAAAATGCATGAACGAATGCATTAAGGCATAAAAGGATG
1 CCATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
*
2106640 CCATAACTAAAAATGCATGAAGGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* ** *
2106687 CCATAACTAAAAAAATACATGAATAGATGCATTAAGGCATAAAAGGATG
1 CCATAACT--AAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* * *
2106736 CCATAACTAAAAATGCATGAACGGATACATTAAAGCATGAAAAGATG
1 CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
2106783 CCA
1 CCA
2106786 AAAATGAAAT
Statistics
Matches: 342, Mismatches: 39, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
47 171 0.50
48 128 0.37
49 43 0.13
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (47 bp):
CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
Found at i:2106606 original size:96 final size:95
Alignment explanation
Indices: 2106355--2106785 Score: 625
Period size: 96 Copynumber: 4.5 Consensus size: 95
2106345 TAAACTGAAT
* * * *
2106355 CCATAACTAAAAATGCATGAACGGATGCATTAAGGAATGGAATGATGCCATAACT-AAAAATGCA
1 CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAAGATGCCATAACTAAAAAATGAA
* * * *
2106419 TTAACGGATGGATTAAGGCATGAAAGGATG
66 TGAACAGATGCATTAAGGCATAAAAGGATG
* * * *
2106449 CCATAACTAAAATTGAATGAACGGATGCATTAAGGCATGAAAGGATGACATAACTAAAAAATGAA
1 CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAAGATGCCATAACTAAAAAATGAA
2106514 TGAACAGATGCATTAAGGCATAAAAGGATG
66 TGAACAGATGCATTAAGGCATAAAAGGATG
* * *
2106544 CCATAACTAAAAAATGCATGAATGGATGCATTAAGGCATGAAAAGATGTCATAACTAAAAAATGC
1 CCATAACT-AAAAATGCATGAACGGATGCATTAAGGCATGAAAAGATGCCATAACTAAAAAATGA
2106609 ATGAAC-GAATGCATTAAGGCATAAAAGGATG
65 ATGAACAG-ATGCATTAAGGCATAAAAGGATG
* *
2106640 CCATAACTAAAAATGCATGAAGGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAAAT-A
1 CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAAGATGCCATAACT-AAAAAATGA
*
2106704 CATGAATAGATGCATTAAGGCATAAAAGGATG
65 -ATGAACAGATGCATTAAGGCATAAAAGGATG
* *
2106736 CCATAACTAAAAATGCATGAACGGATACATTAAAGCATGAAAAGATGCCA
1 CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAAGATGCCA
2106786 AAAATGAAAT
Statistics
Matches: 305, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
94 49 0.16
95 87 0.29
96 168 0.55
97 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (95 bp):
CCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAAGATGCCATAACTAAAAAATGAA
TGAACAGATGCATTAAGGCATAAAAGGATG
Found at i:2113733 original size:96 final size:96
Alignment explanation
Indices: 2113567--2113946 Score: 575
Period size: 96 Copynumber: 3.9 Consensus size: 96
2113557 TAAACCAAAT
* *
2113567 CCATAACTAAAAAATGTATGAACGGATGCCTTAAGGCATGAAAGGATGCCATAACTAAAAAAATG
1 CCATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACT-AAAAAATG
2113632 CATGAACGGATGCATTAAGGCATGAAAGGATG
65 CATGAACGGATGCATTAAGGCATGAAAGGATG
* * * * * *
2113664 TCATAACT-AAAAATGCATGAACGAATGCATTAAGGAATGAAAGTATACTATAACTAAAAAAATG
1 CCATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACT-AAAAAATG
*
2113728 CATGAACGAATGCATTAAGGCATGAAAGGATG
65 CATGAACGGATGCATTAAGGCATGAAAGGATG
* *
2113760 CCATAACTAAAAAATGCATGAATGGATGCATTAAGGCATAAAAGGATGCCATAACTAAAAAATGC
1 CCATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAATGC
* * *
2113825 ATGAACGGATGCGTTAAGACATGAAAGGTTG
66 ATGAACGGATGCATTAAGGCATGAAAGGATG
*
2113856 CCATAACTAAACAAATACATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACT-AAAAATG
1 CCATAACTAAA-AAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAATG
*
2113920 CATGAACGGATGCATTAAGGAATGAAA
65 CATGAACGGATGCATTAAGGCATGAAA
2113947 AGAGATCATA
Statistics
Matches: 254, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
96 165 0.65
97 89 0.35
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (96 bp):
CCATAACTAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAATGC
ATGAACGGATGCATTAAGGCATGAAAGGATG
Found at i:2113831 original size:145 final size:144
Alignment explanation
Indices: 2113567--2113948 Score: 574
Period size: 145 Copynumber: 2.6 Consensus size: 144
2113557 TAAACCAAAT
* *
2113567 CCATAACT-AAAAAATGTATGAACGGATGCCTTAAGGCATGAAAGGATGCCATAACTAAAAAAAT
1 CCATAACTAAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACT-AAAAAAT
* *
2113631 GCATGAACGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAATGCATGAACGAATGCATTA
65 GCATGAACGGATGCATTAAGGCATAAAAGGATGCCATAACTAAAAATGCATGAACGAATGCATTA
2113696 AGGA-ATGAAA-GTATA
130 A-GACATGAAAGGT-TA
* *
2113711 CTATAACTAAAAAAATGCATGAACGAATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAATG
1 CCATAACTAAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAATG
* * *
2113776 CATGAATGGATGCATTAAGGCATAAAAGGATGCCATAACTAAAAAATGCATGAACGGATGCGTTA
66 CATGAACGGATGCATTAAGGCATAAAAGGATGCCATAACT-AAAAATGCATGAACGAATGCATTA
*
2113841 AGACATGAAAGGTTG
130 AGACATGAAAGGTTA
* *
2113856 CCATAACTAAACAAATACATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACT-AAAAATG
1 CCATAACTAAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAATG
*
2113920 CATGAACGGATGCATTAAGGAATGAAAAG
66 CATGAACGGATGCATTAAGGCAT-AAAAG
2113949 AGATCATAAA
Statistics
Matches: 217, Mismatches: 16, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
144 82 0.38
145 133 0.61
146 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (144 bp):
CCATAACTAAAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAATG
CATGAACGGATGCATTAAGGCATAAAAGGATGCCATAACTAAAAATGCATGAACGAATGCATTAA
GACATGAAAGGTTA
Found at i:2119721 original size:29 final size:28
Alignment explanation
Indices: 2119648--2119722 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
2119638 CCCGTCCCCA
*
2119648 TCCCCGTTCCCATGTAACATAAACAATTT
1 TCCCCG-TCCCATTTAACATAAACAATTT
* * *
2119677 TCCCCGTCTCCGTTTAGCATAAACGATTT
1 TCCCCGTC-CCATTTAACATAAACAATTT
2119706 TCCCCGTCCCTATTTAA
1 TCCCCGTCCC-ATTTAA
2119723 TTCAGTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 4 0.11
29 34 0.89
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (28 bp):
TCCCCGTCCCATTTAACATAAACAATTT
Found at i:2127293 original size:2 final size:2
Alignment explanation
Indices: 2127286--2127321 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2127276 ATCATTGAGT
2127286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2127322 GTCTACAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2129033 original size:25 final size:24
Alignment explanation
Indices: 2128995--2129044 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
2128985 CTTTCTGTTA
* *
2128995 TATTTTTAAGATGCTTTTTTTGGT
1 TATTTTTAAGATGCATATTTTGGT
2129019 TATTTTGTAAGATGCATATTTTGGT
1 TATTTT-TAAGATGCATATTTTGGT
2129044 T
1 T
2129045 TTAAAAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.20, C:0.04, G:0.18, T:0.58
Consensus pattern (24 bp):
TATTTTTAAGATGCATATTTTGGT
Found at i:2137236 original size:20 final size:20
Alignment explanation
Indices: 2137211--2137261 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2137201 CACTTAGGGA
*
2137211 ACCGATTCCTCATAGGGGGT
1 ACCGATTCCCCATAGGGGGT
2137231 ACCGATTCCCCATAGGGGGT
1 ACCGATTCCCCATAGGGGGT
2137251 ACCGATTCCCC
1 ACCGATTCCCC
2137262 CACGCTCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.22
Consensus pattern (20 bp):
ACCGATTCCCCATAGGGGGT
Found at i:2142265 original size:21 final size:23
Alignment explanation
Indices: 2142241--2142290 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2142231 AGGGAATCGA
2142241 TCCCCCCTTG-A-GAGAACCGAT
1 TCCCCCCTTGAAGGAGAACCGAT
* *
2142262 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTGAAGGAGAACCGAT
2142285 TCCCCC
1 TCCCCC
2142291 ACAGGGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
22 1 0.04
23 15 0.60
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (23 bp):
TCCCCCCTTGAAGGAGAACCGAT
Found at i:2142315 original size:19 final size:20
Alignment explanation
Indices: 2142273--2142310 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2142263 CCCCCTTTGA
*
2142273 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
2142293 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
2142311 TAGGGTTCTG
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:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:2147526 original size:21 final size:21
Alignment explanation
Indices: 2147500--2147540 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2147490 GCTTAAAAAA
*
2147500 TATTATAAATATTAATTATAT
1 TATTATAAATATTAAATATAT
* *
2147521 TATTATTATTATTAAATATA
1 TATTATAAATATTAAATATA
2147541 CAAATTACAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATAAATATTAAATATAT
Found at i:2154540 original size:37 final size:35
Alignment explanation
Indices: 2154466--2154540 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
2154456 CTTTTTATAT
*
2154466 TTTAATTTTGTAAAAAATATTATAAATATTATGAA
1 TTTAATTTTGTAAAAAATATTATAAATATTATCAA
* *
2154501 TTTAATTTTTTAAAGAAA-ATATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAATAT-TATAAATATTAT-CAA
2154538 TTT
1 TTT
2154541 GTAATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 15 0.44
36 14 0.41
37 5 0.15
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (35 bp):
TTTAATTTTGTAAAAAATATTATAAATATTATCAA
Found at i:2158223 original size:18 final size:18
Alignment explanation
Indices: 2158200--2158246 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
2158190 GACACAAAAC
2158200 AGCATGCAACACTTACCT
1 AGCATGCAACACTTACCT
2158218 AGCATGCAACACTTACCT
1 AGCATGCAACACTTACCT
2158236 AGCATGCAACA
1 AGCATGCAACA
2158247 TACATCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.19
Consensus pattern (18 bp):
AGCATGCAACACTTACCT
Found at i:2160615 original size:20 final size:20
Alignment explanation
Indices: 2160579--2160616 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2160569 ATATTTGAAT
*
2160579 CTAGAAAATATTTCATCAAA
1 CTAGAAAATATTACATCAAA
2160599 CTAGAAGAA-ATTACATCA
1 CTAGAA-AATATTACATCA
2160617 GTAGTATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (20 bp):
CTAGAAAATATTACATCAAA
Found at i:2165912 original size:85 final size:84
Alignment explanation
Indices: 2165765--2165934 Score: 209
Period size: 85 Copynumber: 2.0 Consensus size: 84
2165755 ACAATCACGC
* * *
2165765 CACACGAATGTGTGTCATCTTTTTAATGAAGTGTGCTTCAATGACACGCAATGTAAGTCATAAAT
1 CACACGAATGTGTGTCATCTTTTTAATGAAGGGGGCTTCAATGACACACAATGTAAGTCATAAAT
*
2165830 GCGTGTCATAAATTTATGA
66 GCGCGTCATAAATTTATGA
* * ** *
2165849 CACATGAATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATGATGCACAATG-AGCGTCATA
1 CACACGAATGTGTGTCATCTT--TTTAATGAAGGGGGCTTCAATGACACACAATGTA-AGTCATA
*
2165912 AATGTGCGTCATAAATTTATGA
63 AATGCGCGTCATAAATTTATGA
2165934 C
1 C
2165935 GCACAGTTAC
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 21 0.29
85 49 0.67
86 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (84 bp):
CACACGAATGTGTGTCATCTTTTTAATGAAGGGGGCTTCAATGACACACAATGTAAGTCATAAAT
GCGCGTCATAAATTTATGA
Found at i:2168172 original size:16 final size:16
Alignment explanation
Indices: 2168151--2168181 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2168141 AAATGAAGGG
2168151 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
*
2168167 TAAAAATAAATTAAA
1 TAAAAATAAAATAAA
2168182 GGACTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:2168557 original size:13 final size:13
Alignment explanation
Indices: 2168539--2168564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2168529 AAAGGGAAAA
2168539 TTTCAACTTTAAG
1 TTTCAACTTTAAG
2168552 TTTCAACTTTAAG
1 TTTCAACTTTAAG
2168565 CCCTACATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTCAACTTTAAG
Found at i:2169009 original size:20 final size:20
Alignment explanation
Indices: 2168981--2169025 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2168971 CTTGAGCTTA
*
2168981 AAACCACCT-AAAACAAACCT
1 AAACTACCTGAAAAC-AACCT
*
2169001 AAACTACCTGAAAACCACCT
1 AAACTACCTGAAAACAACCT
2169021 AAACT
1 AAACT
2169026 CTTCGGCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.51, C:0.33, G:0.02, T:0.13
Consensus pattern (20 bp):
AAACTACCTGAAAACAACCT
Found at i:2169557 original size:17 final size:17
Alignment explanation
Indices: 2169535--2169573 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2169525 TACAAGAGTT
2169535 GCGTGGAGTGGAGCTTG
1 GCGTGGAGTGGAGCTTG
2169552 GCGTGGAGTGGAGCTTG
1 GCGTGGAGTGGAGCTTG
2169569 GCGTG
1 GCGTG
2169574 CATGGAGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.13, G:0.54, T:0.23
Consensus pattern (17 bp):
GCGTGGAGTGGAGCTTG
Found at i:2169726 original size:17 final size:17
Alignment explanation
Indices: 2169682--2169729 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2169672 TTCTGGCTTC
*
2169682 CTGGTTGGGTTTTAGGT
1 CTGGTTGGGTTTTGGGT
* ** *
2169699 TTAATTAGGTTTTGGGT
1 CTGGTTGGGTTTTGGGT
2169716 CTGGTTGGGTTTTG
1 CTGGTTGGGTTTTG
2169730 TTTTATTTTG
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.08, C:0.04, G:0.38, T:0.50
Consensus pattern (17 bp):
CTGGTTGGGTTTTGGGT
Found at i:2169768 original size:22 final size:22
Alignment explanation
Indices: 2169720--2169761 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2169710 TTGGGTCTGG
**
2169720 TTGGGTTTTGTTTTATTTTGTA
1 TTGGGTTGAGTTTTATTTTGTA
*
2169742 ATGGGTTGAGTTTTATTTTG
1 TTGGGTTGAGTTTTATTTTG
2169762 GTTTGGGCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.62
Consensus pattern (22 bp):
TTGGGTTGAGTTTTATTTTGTA
Found at i:2183641 original size:10 final size:10
Alignment explanation
Indices: 2183626--2183656 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
2183616 TTCCTCACAC
2183626 TCTTCTTTTT
1 TCTTCTTTTT
2183636 TCTTCTTTTT
1 TCTTCTTTTT
2183646 TCTTCTTTTT
1 TCTTCTTTTT
2183656 T
1 T
2183657 ATTTGGGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TCTTCTTTTT
Found at i:2184250 original size:23 final size:23
Alignment explanation
Indices: 2184217--2184261 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2184207 CCCAAGCTTG
2184217 GTATCGATACCATAGC-TAGGGAA
1 GTATCGATACCATA-CATAGGGAA
*
2184240 GTATCGGTACCATACATAGGGA
1 GTATCGATACCATACATAGGGA
2184262 TACCGATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (23 bp):
GTATCGATACCATACATAGGGAA
Found at i:2184973 original size:31 final size:31
Alignment explanation
Indices: 2184927--2184991 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
2184917 AAGAGTAGAG
*
2184927 GGTTACTTATATCCTTCGAGACATATGGACA
1 GGTTACCTATATCCTTCGAGACATATGGACA
* * *
2184958 GGTTACCTATTTCCTTCGGGACATATGGATA
1 GGTTACCTATATCCTTCGAGACATATGGACA
2184989 GGT
1 GGT
2184992 CCTTCGGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
GGTTACCTATATCCTTCGAGACATATGGACA
Found at i:2191700 original size:17 final size:17
Alignment explanation
Indices: 2191680--2191751 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
2191670 AATTAAGAGT
*
2191680 TAGTTTAATAAAAGAAC
1 TAGTTTAATAAATGAAC
* *
2191697 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
2191714 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
2191731 TAAGTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
2191749 TAG
1 TAG
2191752 AACTTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
17 32 0.68
18 15 0.32
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2191719 original size:34 final size:35
Alignment explanation
Indices: 2191680--2191751 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
2191670 AATTAAGAGT
*
2191680 TAGTTTAATAAAAGAACT-AGTTTGA-TGAATGAAC
1 TAGTTTAATAAAAGAACTAAGTTT-ATTCAATGAAC
* *
2191714 TAGTTTAATTAATGAACTAAGTTTATTCAATGAAC
1 TAGTTTAATAAAAGAACTAAGTTTATTCAATGAAC
2191749 TAG
1 TAG
2191752 AACTTTATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (35 bp):
TAGTTTAATAAAAGAACTAAGTTTATTCAATGAAC
Found at i:2191760 original size:20 final size:20
Alignment explanation
Indices: 2191735--2191772 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2191725 ATGAACTAAG
2191735 TTTATTCAATGAACTAGAAC
1 TTTATTCAATGAACTAGAAC
2191755 TTTATTCAATGAACTAGA
1 TTTATTCAATGAACTAGA
2191773 TGTATGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
TTTATTCAATGAACTAGAAC
Found at i:2192190 original size:26 final size:26
Alignment explanation
Indices: 2192155--2192206 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2192145 ATCAACATTC
2192155 TCTACGAACGGGAACAATTTTGATTT
1 TCTACGAACGGGAACAATTTTGATTT
*
2192181 TCTACGAACGGGAACACTTTTGATTT
1 TCTACGAACGGGAACAATTTTGATTT
2192207 ACACAAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (26 bp):
TCTACGAACGGGAACAATTTTGATTT
Found at i:2193718 original size:9 final size:9
Alignment explanation
Indices: 2193704--2193749 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
2193694 AAAAATAAAG
2193704 TTCGGTTAA
1 TTCGGTTAA
2193713 TTCGGTT-A
1 TTCGGTTAA
2193721 -T-GGTTAA
1 TTCGGTTAA
2193728 TTCGGTT-A
1 TTCGGTTAA
2193736 -T-GGTTAA
1 TTCGGTTAA
2193743 TTCGGTT
1 TTCGGTT
2193750 TGGTTCAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
6 8 0.26
7 4 0.13
8 4 0.13
9 15 0.48
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.48
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:2193727 original size:15 final size:15
Alignment explanation
Indices: 2193707--2193754 Score: 89
Period size: 15 Copynumber: 3.3 Consensus size: 15
2193697 AATAAAGTTC
2193707 GGTTAATTCGGTTAT
1 GGTTAATTCGGTTAT
2193722 GGTTAATTCGGTTAT
1 GGTTAATTCGGTTAT
2193737 GGTTAATTCGGTT-T
1 GGTTAATTCGGTTAT
2193751 GGTT
1 GGTT
2193755 CAGTTTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 5 0.15
15 28 0.85
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.48
Consensus pattern (15 bp):
GGTTAATTCGGTTAT
Found at i:2193973 original size:21 final size:21
Alignment explanation
Indices: 2193949--2193988 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2193939 CTCATTTTCA
2193949 CTCTCAAT-TCTCTTTTCAATG
1 CTCTCAATGTC-CTTTTCAATG
2193970 CTCTCAATGTCCTTTTCAA
1 CTCTCAATGTCCTTTTCAA
2193989 CTCTCGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.20, C:0.30, G:0.05, T:0.45
Consensus pattern (21 bp):
CTCTCAATGTCCTTTTCAATG
Found at i:2194841 original size:5 final size:5
Alignment explanation
Indices: 2194831--2194887 Score: 66
Period size: 5 Copynumber: 11.8 Consensus size: 5
2194821 CTCTTTAAAT
* *
2194831 TTTTC TTTTC TTTTC TTTTC -TTT- TTTTC TTTTT TTCTTT TTTTC TTTT-
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC
2194879 TTTTC TTTT
1 TTTTC TTTT
2194888 TTTCCATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
4 10 0.22
5 31 0.67
6 5 0.11
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (5 bp):
TTTTC
Found at i:2194856 original size:17 final size:16
Alignment explanation
Indices: 2194836--2194908 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 16
2194826 TAAATTTTTC
2194836 TTTTCTTTTCTTTTCTT
1 TTTTCTTTT-TTTTCTT
2194853 TTTT-TCTTTTTTTCTTT
1 TTTTCT-TTTTTTTC-TT
2194870 TTTTCTTTTTTTTCTTT
1 TTTTCTTTTTTTTC-TT
*
2194887 TTTTCCATTTTTTTTATT
1 TTTT-C-TTTTTTTTCTT
2194905 TTTT
1 TTTT
2194909 ACTAACACGA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
16 6 0.12
17 28 0.56
18 8 0.16
19 8 0.16
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTCTTTTTTTTCTT
Found at i:2194865 original size:9 final size:9
Alignment explanation
Indices: 2194831--2194908 Score: 90
Period size: 9 Copynumber: 8.7 Consensus size: 9
2194821 CTCTTTAAAT
2194831 TTTTCTTTTC
1 TTTT-TTTTC
2194841 TTTTCTTTTC
1 TTTT-TTTTC
2194851 -TTTTTTTC
1 TTTTTTTTC
2194859 -TTTTTTTC
1 TTTTTTTTC
2194867 -TTTTTTTC
1 TTTTTTTTC
2194875 TTTTTTTTC
1 TTTTTTTTC
*
2194884 TTTTTTTCC
1 TTTTTTTTC
*
2194893 ATTTTTTTTA
1 -TTTTTTTTC
2194903 TTTTTT
1 TTTTTT
2194909 ACTAACACGA
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
8 21 0.33
9 25 0.40
10 17 0.27
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:2194908 original size:1 final size:1
Alignment explanation
Indices: 2194830--2194890 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
2194820 GCTCTTTAAA
* * * * * * * *
2194830 TTTTTCTTTTCTTTTCTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2194891 CCATTTTTTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:2194908 original size:8 final size:8
Alignment explanation
Indices: 2194830--2194891 Score: 90
Period size: 8 Copynumber: 7.8 Consensus size: 8
2194820 GCTCTTTAAA
2194830 TTTTTCTT
1 TTTTTCTT
*
2194838 TTCTT-TT
1 TTTTTCTT
*
2194845 CTTTTCTT
1 TTTTTCTT
2194853 TTTTTCTT
1 TTTTTCTT
2194861 TTTTTCTT
1 TTTTTCTT
2194869 TTTTTCTTT
1 TTTTTC-TT
2194878 TTTTTCTT
1 TTTTTCTT
2194886 TTTTTC
1 TTTTTC
2194892 CATTTTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
7 5 0.10
8 35 0.73
9 8 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:2206553 original size:17 final size:17
Alignment explanation
Indices: 2206502--2206573 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
2206492 AATTAAGAGT
* *
2206502 TAGTTTAATAAAAGAAC
1 TAGTTTAATTAATGAAC
* *
2206519 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
*
2206536 TAGTTTAATTAATTAAC
1 TAGTTTAATTAATGAAC
2206553 TAAGTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
2206571 TAG
1 TAG
2206574 AACTTTATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
17 34 0.74
18 12 0.26
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Done.