Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 62
Found at i:1952807 original size:33 final size:33
Alignment explanation
Indices: 1952761--1952831 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
1952751 ACAAGGTTTA
* *
1952761 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
* *
1952793 TGATAAATTCAAATACTTAAAAACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1952826 CGATAA
1 CGATAA
1952832 TTGAAACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:1952851 original size:21 final size:21
Alignment explanation
Indices: 1952826--1952867 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1952816 CTTTCAAGTT
*
1952826 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAATTTA
*
1952847 CGATAATTGAAATAAAATTTA
1 CGATAATTGAAACAAAATTTA
1952868 AAAATAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAATTTA
Found at i:1955547 original size:7 final size:7
Alignment explanation
Indices: 1955537--1955562 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1955527 ATAAAATAAA
1955537 AAATTCT
1 AAATTCT
1955544 AAATTCT
1 AAATTCT
1955551 AAATTCT
1 AAATTCT
1955558 AAATT
1 AAATT
1955563 ATATCCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTCT
Found at i:1959934 original size:37 final size:37
Alignment explanation
Indices: 1959861--1959934 Score: 87
Period size: 38 Copynumber: 2.0 Consensus size: 37
1959851 GTTGAAAAAT
** *
1959861 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATAAAAAATCATAAA
* *
1959898 ATTTATATATTTTTTTTTACAAAATAAAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTAAAAAATAAAAAATCATAAA
1959935 CAGGTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.45
38 17 0.55
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATAAAAAATCATAAA
Found at i:1965663 original size:25 final size:24
Alignment explanation
Indices: 1965618--1965667 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
1965608 ACATATAATT
* *
1965618 CTTACTAATGCATTCATAATCTATA
1 CTTACTAATGCATACACAATC-ATA
1965643 CTTACTATAT-CATACACAATCATA
1 CTTACTA-ATGCATACACAATCATA
1965667 C
1 C
1965668 ATTCTGTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 16 0.73
26 2 0.09
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (24 bp):
CTTACTAATGCATACACAATCATA
Found at i:1965762 original size:23 final size:23
Alignment explanation
Indices: 1965732--1965795 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1965722 ATCTTATATA
*
1965732 AATTGCACCAAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1965755 AATTGCACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1965778 AAATACACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
1965796 TATAAGATTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1967514 original size:21 final size:21
Alignment explanation
Indices: 1967484--1967566 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
1967474 TCTGGTTCGG
* * *
1967484 TTGAAGGGGTATCGATTCCCC
1 TTGAATGGGTACCGATTCCCA
*
1967505 TTGAATGGGTACCAATTCCCA
1 TTGAATGGGTACCGATTCCCA
*
1967526 TTGAATGGGTACCGACTCCCA
1 TTGAATGGGTACCGATTCCCA
1967547 TTGAATGGGTACCGATTCCC
1 TTGAATGGGTACCGATTCCC
1967567 CTAGCCCAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCA
Found at i:1973473 original size:11 final size:12
Alignment explanation
Indices: 1973454--1973484 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1973444 ATAATTATTT
1973454 GGTTTTTTTTGA
1 GGTTTTTTTTGA
1973466 GGTTTTTTTTGA
1 GGTTTTTTTTGA
1973478 GGTTTTT
1 GGTTTTT
1973485 CTCTCCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.00, G:0.26, T:0.68
Consensus pattern (12 bp):
GGTTTTTTTTGA
Found at i:1976342 original size:7 final size:7
Alignment explanation
Indices: 1976330--1976358 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1976320 ATGAATGTCA
1976330 AGAATGT
1 AGAATGT
1976337 AGAATGT
1 AGAATGT
1976344 AGAATGT
1 AGAATGT
1976351 AGAATGT
1 AGAATGT
1976358 A
1 A
1976359 AAGAATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (7 bp):
AGAATGT
Found at i:1976369 original size:9 final size:8
Alignment explanation
Indices: 1976322--1976368 Score: 55
Period size: 7 Copynumber: 6.0 Consensus size: 8
1976312 TAAAATGAAT
1976322 GAATGTCAA
1 GAATGT-AA
1976331 GAATGT-A
1 GAATGTAA
1976338 GAATGT-A
1 GAATGTAA
1976345 GAATGT-A
1 GAATGTAA
1976352 GAATGTAAA
1 GAATGT-AA
1976361 GAATGTAA
1 GAATGTAA
1976369 ATAATGCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 21 0.58
8 2 0.06
9 13 0.36
ACGTcount: A:0.47, C:0.02, G:0.26, T:0.26
Consensus pattern (8 bp):
GAATGTAA
Found at i:1976374 original size:9 final size:9
Alignment explanation
Indices: 1976322--1976381 Score: 51
Period size: 9 Copynumber: 7.3 Consensus size: 9
1976312 TAAAATGAAT
*
1976322 GAATGTCAA
1 GAATGTAAA
1976331 GAATGT--A
1 GAATGTAAA
1976338 GAATGT--A
1 GAATGTAAA
1976345 GAATGT--A
1 GAATGTAAA
1976352 GAATGTAAA
1 GAATGTAAA
1976361 GAATGTAAA
1 GAATGTAAA
* *
1976370 TAATGCAAA
1 GAATGTAAA
1976379 GAA
1 GAA
1976382 ATTATTTCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
7 21 0.46
9 25 0.54
ACGTcount: A:0.50, C:0.03, G:0.23, T:0.23
Consensus pattern (9 bp):
GAATGTAAA
Found at i:1985737 original size:23 final size:21
Alignment explanation
Indices: 1985706--1985760 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
1985696 AATGACATGC
*
1985706 AAAACTAAAACAAGTATATAAAT
1 AAAAATAAAACAAG-ATA-AAAT
* *
1985729 AAAAATAAAATAAGATAAGAT
1 AAAAATAAAACAAGATAAAAT
1985750 AAGAAATAAAA
1 AA-AAATAAAA
1985761 AGTAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.18
22 11 0.39
23 12 0.43
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (21 bp):
AAAAATAAAACAAGATAAAAT
Found at i:1985943 original size:2 final size:2
Alignment explanation
Indices: 1985929--1985971 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1985919 TTTTCAAAAC
1985929 TA TA TA -A TA -A 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
1985969 TA T
1 TA T
1985972 TTAAAATGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1986050 original size:2 final size:2
Alignment explanation
Indices: 1986043--1986070 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1986033 TTTACCTTTA
1986043 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
1986071 TAAAACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1991473 original size:30 final size:29
Alignment explanation
Indices: 1991438--1991504 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
1991428 AATTTATTAA
* *
1991438 ATATTTT-TCTTTTTATTTCAACTTCAAAAT
1 ATATTTTATCTTATT-TTT-AACTTAAAAAT
1991468 ATATTTTAGTCTTATTTTTAACTTAAAAAT
1 ATATTTTA-TCTTATTTTTAACTTAAAAAT
1991498 A-ATTTTA
1 ATATTTTA
1991505 CTATTATCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 6 0.18
30 18 0.55
31 3 0.09
32 6 0.18
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.55
Consensus pattern (29 bp):
ATATTTTATCTTATTTTTAACTTAAAAAT
Found at i:1991630 original size:28 final size:29
Alignment explanation
Indices: 1991579--1991646 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
1991569 CTTAATTATC
* **
1991579 AAATATGTTTTATTCTTATTTTTATTTTAA
1 AAATAT-TTTTAGTCTTATTTTTAGCTTAA
1991609 AAATATTTTTAGTCTTA-TTTTAGCTTAA
1 AAATATTTTTAGTCTTATTTTTAGCTTAA
1991637 AAATATTTTT
1 AAATATTTTT
1991647 TATCTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 19 0.54
29 10 0.29
30 6 0.17
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (29 bp):
AAATATTTTTAGTCTTATTTTTAGCTTAA
Found at i:1991778 original size:27 final size:27
Alignment explanation
Indices: 1991728--1991808 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
1991718 TAAGATGTAT
* * *
1991728 TTTTTAAGTTAAAATAAGATTAAAAAA
1 TTTTAAAGTTAAAATAAAAATAAAAAA
*
1991755 TTTTAAAGTTCAAATAAAAATAAAATATA
1 TTTTAAAGTTAAAATAAAAATAAAA-A-A
* *
1991784 TTTAATAAGTTAATATAAAATATAA
1 TTTTA-AAGTTAAAATAAAA-ATAA
1991809 TATAAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 21 0.49
28 1 0.02
29 5 0.12
30 12 0.28
31 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (27 bp):
TTTTAAAGTTAAAATAAAAATAAAAAA
Found at i:1991802 original size:30 final size:28
Alignment explanation
Indices: 1991687--1991812 Score: 69
Period size: 30 Copynumber: 4.3 Consensus size: 28
1991677 TTATTTAAAT
* *
1991687 TAAAATATATTTTTAAAAGCTAAGATAAGAA
1 TAAAATATA--TTTAAAAGTTAA-ATAAAAA
* * ** * *
1991718 TAAGATGTATTTTTTAAGTTAAAATAAGAT
1 TAAAATATA-TTTAAAAGTT-AAATAAAAA
*
1991748 TAAAA-A-ATTTTAAAGTTCAAATAAAAA
1 TAAAATATATTTAAAAGTT-AAATAAAAA
1991775 TAAAATATATTTAATAAGTT-AATATAAAA
1 TAAAATATATTTAA-AAGTTAAATA-AAAA
*
1991804 TATAATATA
1 TAAAATATA
1991813 AAAATTATTT
Statistics
Matches: 76, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
27 21 0.28
28 6 0.08
29 17 0.22
30 23 0.30
31 9 0.12
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.37
Consensus pattern (28 bp):
TAAAATATATTTAAAAGTTAAATAAAAA
Found at i:1993958 original size:77 final size:77
Alignment explanation
Indices: 1993831--1993985 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
1993821 CGTGGCTTGT
1993831 AATTTACTTACTGTTGAATCCGTACTGTTTGGATTTTAGATACAAGGGCTACAGACCAAATCATA
1 AATTTACTTACTGTTGAATCCGTACTGTTTGGATTTTAGATACAAGGGCTACAGACCAAATCATA
1993896 TTTGATTTCAAG
66 TTTGATTTCAAG
1993908 AATTTACTTACTGTTGAATCCGTACTGTTTGGATTTTAGATACAAGGGCTACAGACCAAATCATA
1 AATTTACTTACTGTTGAATCCGTACTGTTTGGATTTTAGATACAAGGGCTACAGACCAAATCATA
1993973 TTTGATTTCAAG
66 TTTGATTTCAAG
1993985 A
1 A
1993986 GCTTGGTATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (77 bp):
AATTTACTTACTGTTGAATCCGTACTGTTTGGATTTTAGATACAAGGGCTACAGACCAAATCATA
TTTGATTTCAAG
Found at i:1995110 original size:26 final size:23
Alignment explanation
Indices: 1995062--1995126 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 23
1995052 ATAATTAAAG
1995062 TATTAAAAGTAATAATAAAATAA
1 TATTAAAAGTAATAATAAAATAA
1995085 TATTACAAA-TAATAATGAATATATAA
1 TATTA-AAAGTAATAAT-AA-A-ATAA
* *
1995111 AATTAAAACT-ATAATA
1 TATTAAAAGTAATAATA
1995127 TAACACACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
23 12 0.33
24 6 0.17
25 9 0.25
26 9 0.25
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (23 bp):
TATTAAAAGTAATAATAAAATAA
Found at i:1997794 original size:16 final size:15
Alignment explanation
Indices: 1997768--1997797 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1997758 TTTTGGCCTG
1997768 TAAATATAATATTAA
1 TAAATATAATATTAA
1997783 TAAATAATAATATTA
1 TAAAT-ATAATATTA
1997798 TTATTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATATAATATTAA
Found at i:1998539 original size:54 final size:55
Alignment explanation
Indices: 1998446--1998549 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 55
1998436 AATAACTAGT
* * *
1998446 TCGTAAAACATTTTGACAACACATTCATTATTTCTTGTGGCTTCTGCTCAAATGC
1 TCGTAAAACATTTTGACAACACATTCATCATCTCATGTGGCTTCTGCTCAAATGC
* *
1998501 TCGTAAAACA-TTTGACAACACATTCATCATCTCATGTGGTTTCTTCTCA
1 TCGTAAAACATTTTGACAACACATTCATCATCTCATGTGGCTTCTGCTCA
1998550 GATGTTTGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 34 0.77
55 10 0.23
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (55 bp):
TCGTAAAACATTTTGACAACACATTCATCATCTCATGTGGCTTCTGCTCAAATGC
Found at i:2000181 original size:46 final size:46
Alignment explanation
Indices: 2000088--2000351 Score: 444
Period size: 46 Copynumber: 5.8 Consensus size: 46
2000078 GATAAACTTG
* * *
2000088 AAAATAAGTTTACGAGCTTAT-GGAAT-AATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGT
*
2000132 AAAATAAGCTTACGAGCTTATGGGATTAAATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGT
*
2000178 AAAATAAGCTTACGAGTTTATGGGATTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGT
2000224 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGT
*
2000270 AAAATAAGCTTATGAGCTTATGGGATTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGT
*
2000316 AAAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAG
1 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAG
2000352 AGATTTTATC
Statistics
Matches: 210, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
44 20 0.10
45 18 0.09
46 172 0.82
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (46 bp):
AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGT
Found at i:2001093 original size:15 final size:15
Alignment explanation
Indices: 2001073--2001102 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2001063 TGTTTTTGTT
*
2001073 TTCATTCATCTTTTC
1 TTCATTCATCATTTC
2001088 TTCATTCATCATTTC
1 TTCATTCATCATTTC
2001103 ATCTTTACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (15 bp):
TTCATTCATCATTTC
Found at i:2003509 original size:20 final size:21
Alignment explanation
Indices: 2003472--2003514 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
2003462 TTAAGAAAAT
*
2003472 AAATTTTAAATCACTTTT-GA
1 AAATATTAAATCACTTTTAGA
* *
2003492 AAATATTAAATGATTTTTAGA
1 AAATATTAAATCACTTTTAGA
2003513 AA
1 AA
2003515 TTCGGGTGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
AAATATTAAATCACTTTTAGA
Found at i:2021004 original size:22 final size:21
Alignment explanation
Indices: 2020978--2021021 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2020968 AAGGTAATTG
*
2020978 TTTAACTTCATTATTTAATTTA
1 TTTAACTTCATAATTT-ATTTA
*
2021000 TTTAATTTCATAATTTATTTA
1 TTTAACTTCATAATTTATTTA
2021021 T
1 T
2021022 GTTTTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAACTTCATAATTTATTTA
Found at i:2022375 original size:13 final size:11
Alignment explanation
Indices: 2022347--2022371 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2022337 TTTTATTTTC
2022347 TTTAAAAAATA
1 TTTAAAAAATA
2022358 TTTAAAAAATA
1 TTTAAAAAATA
2022369 TTT
1 TTT
2022372 TTAATGGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:2024858 original size:19 final size:19
Alignment explanation
Indices: 2024815--2024866 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2024805 TGTAAATTCT
*
2024815 TGTTGCGAATTCAAAAATTA
1 TGTTGCGAATTC-GAAATTA
2024835 TGTTGCGAATTCGAAATTGA
1 TGTTGCGAATTCGAAATT-A
2024855 -GTTGCGAATTCG
1 TGTTGCGAATTCG
2024867 TTGGCTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (19 bp):
TGTTGCGAATTCGAAATTA
Found at i:2026204 original size:45 final size:45
Alignment explanation
Indices: 2026140--2026234 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
2026130 CCCCCGCTGC
* * *
2026140 ATTCTAGTGCAGTTGGATTAGGGGAATCTGAAGTCTGGTAAGAAG
1 ATTCTAGTGCAGTTGGATTAGGAGAATCTGAACTCTGATAAGAAG
2026185 ATTCTAGTGCAGTTGGATTAGGAGAATCTGAACTCTGATAAGAAG
1 ATTCTAGTGCAGTTGGATTAGGAGAATCTGAACTCTGATAAGAAG
2026230 ATTCT
1 ATTCT
2026235 TCGTTCTTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (45 bp):
ATTCTAGTGCAGTTGGATTAGGAGAATCTGAACTCTGATAAGAAG
Found at i:2030114 original size:6 final size:6
Alignment explanation
Indices: 2030103--2030176 Score: 71
Period size: 6 Copynumber: 12.7 Consensus size: 6
2030093 TTTGAATGCT
* * *
2030103 TATACA TATACA TATACA TATACA TATAC- -ATACA TACATA TATAAA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * * *
2030149 TATATA CATACA TATATA TATATA TATA
1 TATACA TATACA TATACA TATACA TATA
2030177 TATAAATAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
4 4 0.07
6 53 0.93
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:2030167 original size:4 final size:4
Alignment explanation
Indices: 2030103--2030180 Score: 66
Period size: 4 Copynumber: 19.5 Consensus size: 4
2030093 TTTGAATGCT
* * * * * * * *
2030103 TATA CATA TACA TATA CATA TACA TATA CATA CATA CATA TATA AATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
2030151 TATA CATA CATA TATA TATA TATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TA
2030181 AATAAATAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (4 bp):
TATA
Found at i:2030171 original size:20 final size:20
Alignment explanation
Indices: 2030116--2030174 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
2030106 ACATATACAT
* *
2030116 ATACATATACATATACATAC
1 ATACATATATATATATATAC
*
2030136 ATACATATATAAATATATAC
1 ATACATATATATATATATAC
2030156 ATACATATATATATATATA
1 ATACATATATATATATATA
2030175 TATATAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.36
Consensus pattern (20 bp):
ATACATATATATATATATAC
Found at i:2030180 original size:12 final size:12
Alignment explanation
Indices: 2030103--2030178 Score: 80
Period size: 12 Copynumber: 6.3 Consensus size: 12
2030093 TTTGAATGCT
*
2030103 TATACATATACA
1 TATACATATATA
*
2030115 TATACATATACA
1 TATACATATATA
*
2030127 TATACATACATA
1 TATACATATATA
* * *
2030139 CATATATAAATA
1 TATACATATATA
*
2030151 TATACATACATA
1 TATACATATATA
*
2030163 TATATATATATA
1 TATACATATATA
2030175 TATA
1 TATA
2030179 TAAATAAATA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 54 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (12 bp):
TATACATATATA
Found at i:2031006 original size:24 final size:26
Alignment explanation
Indices: 2030966--2031024 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 26
2030956 CGATTGTTGT
2030966 AGGAGGGAAGATCCGACGGCG-G-CG
1 AGGAGGGAAGATCCGACGGCGCGTCG
*
2030990 AGGAGGG-TGATCACGACGGCGCGTCG
1 AGGAGGGAAGATC-CGACGGCGCGTCG
2031016 AGGAGGGAA
1 AGGAGGGAA
2031025 TACTCGGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 15 0.52
25 1 0.03
26 9 0.31
ACGTcount: A:0.25, C:0.19, G:0.49, T:0.07
Consensus pattern (26 bp):
AGGAGGGAAGATCCGACGGCGCGTCG
Found at i:2031018 original size:23 final size:23
Alignment explanation
Indices: 2030975--2031018 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2030965 TAGGAGGGAA
*
2030975 GATCCGACGGCGGCGAGGAGGGT
1 GATCCGACGGCGGCGACGAGGGT
*
2030998 GATCACGACGGC-GCGTCGAGG
1 GATC-CGACGGCGGCGACGAGG
2031019 AGGGAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.18, C:0.25, G:0.48, T:0.09
Consensus pattern (23 bp):
GATCCGACGGCGGCGACGAGGGT
Found at i:2034494 original size:24 final size:24
Alignment explanation
Indices: 2034462--2034510 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2034452 AGTCTTCCTG
2034462 ATGATGTATAAAACATATATGTAC
1 ATGATGTATAAAACATATATGTAC
*
2034486 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATATATGTAC
2034510 A
1 A
2034511 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATATATGTAC
Found at i:2038994 original size:21 final size:18
Alignment explanation
Indices: 2038970--2039026 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
2038960 ATGTTTAATG
2038970 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
**
2038988 AACAAAATGATATAAATTGTT
1 -A-AAAA-GATACCAATTGTT
2039009 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
2039027 TGTTAACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.34
19 5 0.16
20 5 0.16
21 11 0.34
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:2045778 original size:18 final size:18
Alignment explanation
Indices: 2045755--2045792 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2045745 ACCGGTTATA
*
2045755 ACCCGACCCGACCTGTTG
1 ACCCGACCCAACCTGTTG
*
2045773 ACCCGACCCAATCTGTTG
1 ACCCGACCCAACCTGTTG
2045791 AC
1 AC
2045793 TTGACCCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.42, G:0.18, T:0.18
Consensus pattern (18 bp):
ACCCGACCCAACCTGTTG
Found at i:2045805 original size:13 final size:13
Alignment explanation
Indices: 2045795--2045820 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2045785 CTGTTGACTT
2045795 GACCCGTTGACCC
1 GACCCGTTGACCC
2045808 GACCCGTTGACCC
1 GACCCGTTGACCC
2045821 ATTGACCGTT
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:0.15, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
GACCCGTTGACCC
Found at i:2045806 original size:8 final size:8
Alignment explanation
Indices: 2045793--2045854 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
2045783 ATCTGTTGAC
2045793 TTGACCCG
1 TTGACCCG
2045801 TTGACCC-
1 TTGACCCG
2045808 --GACCCG
1 TTGACCCG
*
2045814 TTGACCCA
1 TTGACCCG
2045822 TTGA-CCG
1 TTGACCCG
2045829 TTGACCGGCG
1 TTGACC--CG
2045839 TTGACCACTG
1 TTGACC-C-G
2045849 TTGACC
1 TTGACC
2045855 AAAACTTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
5 5 0.11
7 6 0.14
8 17 0.39
9 1 0.02
10 15 0.34
ACGTcount: A:0.16, C:0.35, G:0.24, T:0.24
Consensus pattern (8 bp):
TTGACCCG
Found at i:2048268 original size:24 final size:24
Alignment explanation
Indices: 2048239--2048326 Score: 133
Period size: 24 Copynumber: 3.7 Consensus size: 24
2048229 ATTTGAATTT
2048239 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
2048263 TAATCTGATA-TCTGACATAGATTC
1 TGATCTGATACT-TGACATGGATTC
*
2048287 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
2048311 TGATCTGATACTTGAC
1 TGATCTGATACTTGAC
2048327 CTGATTTATG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.02
24 55 0.96
25 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:2051523 original size:30 final size:29
Alignment explanation
Indices: 2051489--2051550 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2051479 ATTTTGGTCT
* * *
2051489 CTAAACTTTTAAAAGTTTATACTTTAGCCA
1 CTAAACTTTCAAAA-CTTACACTTTAGCCA
*
2051519 CTAAACTTTCAAAACTTACACTTTAGTCA
1 CTAAACTTTCAAAACTTACACTTTAGCCA
2051548 CTA
1 CTA
2051551 GACAAACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (29 bp):
CTAAACTTTCAAAACTTACACTTTAGCCA
Found at i:2051549 original size:29 final size:29
Alignment explanation
Indices: 2051462--2051550 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 29
2051452 CTAAATATAT
* * *
2051462 AACTTTTAAAAATTACAATTTTGGTCTCTA
1 AACTTTTAAAAATTAC-ACTTTAGTCACTA
* * *
2051492 AACTTTTAAAAGTTTATACTTTAGCCACTA
1 AACTTTTAAAA-ATTACACTTTAGTCACTA
* *
2051522 AACTTTCAAAACTTACACTTTAGTCACTA
1 AACTTTTAAAAATTACACTTTAGTCACTA
2051551 GACAAACTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 15 0.31
30 30 0.62
31 3 0.06
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (29 bp):
AACTTTTAAAAATTACACTTTAGTCACTA
Found at i:2054429 original size:54 final size:54
Alignment explanation
Indices: 2054356--2054777 Score: 546
Period size: 54 Copynumber: 7.8 Consensus size: 54
2054346 TGTGTACTAT
* * *
2054356 AGGCACTAAGTGTGCAACCCATGTAATTCATCATAAGTTGATGAACAACCATTC
1 AGGCACTAAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTC
* * * *
2054410 AGGAAATAAGTGTGTAACCCACGGAATTCATCATAAGTTGATGAACAACCATTC
1 AGGCACTAAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTC
* *
2054464 AGGCACTAAGTATGCAACCCACGGAATTAATCATAAGTTGATGAACAACCGTTC
1 AGGCACTAAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTC
*
2054518 AGGCACTAAGTGTGCAACCCACGGAATTCATCTTAAGTTGATGAACAACCGTTC
1 AGGCACTAAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTC
* *
2054572 AGGCACTAAGTGTGCAACCCACGAAATTCATCATAAGTTGATGAACAATCGTTC
1 AGGCACTAAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTC
* * * *
2054626 AAGCACTAAGTGTGCAACCCACAGAATTCATCATACGTTGATG-ACGACCGTAT-
1 AGGCACTAAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGT-TC
* * * * *
2054679 AAGCACTAAGTGTGTAACCCACAGAATTCATCATATGTTGATGAACAACTGTAT-
1 AGGCACTAAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGT-TC
* * * * * *
2054733 AGGCACTCTA-TGTGCAAACCAAGAAATTCATAATAAGTTTATGAA
1 AGGCACT-AAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAA
2054778 TTTTCGTATG
Statistics
Matches: 328, Mismatches: 37, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
53 47 0.14
54 280 0.85
55 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (54 bp):
AGGCACTAAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTC
Found at i:2054527 original size:27 final size:27
Alignment explanation
Indices: 2054497--2054582 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
2054487 GAATTAATCA
2054497 TAAGTTGATGAACAACCGTTCAGGCAC
1 TAAGTTGATGAACAACCGTTCAGGCAC
* * * *
2054524 TAAG-TG-TGCAACCCACGGAATTCA-TC-T
1 TAAGTTGATG-AA-CAACCG--TTCAGGCAC
2054551 TAAGTTGATGAACAACCGTTCAGGCAC
1 TAAGTTGATGAACAACCGTTCAGGCAC
2054578 TAAGT
1 TAAGT
2054583 GTGCAACCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
25 6 0.14
26 5 0.12
27 21 0.49
28 5 0.12
29 6 0.14
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (27 bp):
TAAGTTGATGAACAACCGTTCAGGCAC
Found at i:2054945 original size:45 final size:46
Alignment explanation
Indices: 2054896--2054984 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 46
2054886 CTAAATGCAC
2054896 AACGGTGCATTAAAGGCATGAAAGGATGCCATAAAT-AAAATGAAT
1 AACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAAATGAAT
* * *
2054941 AACGGTGCATTAAAGGCATGAAATGATTCCCTAAATGAAAATGA
1 AACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAAATGA
2054985 TGAACAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 33 0.82
46 7 0.17
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (46 bp):
AACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAAATGAAT
Found at i:2054977 original size:40 final size:41
Alignment explanation
Indices: 2054885--2054979 Score: 102
Period size: 45 Copynumber: 2.2 Consensus size: 41
2054875 AAAATAAATT
*
2054885 ACTAAATGCACAACGGTGCATTAAAGGCATGAAAGGATGCC
1 ACTAAATGAACAACGGTGCATTAAAGGCATGAAAGGATGCC
* * * *
2054926 ATAAATAAAATGAATAACGGTGCATTAAAGGCATGAAATGATTCC
1 ---ACT-AAATGAACAACGGTGCATTAAAGGCATGAAAGGATGCC
2054971 -CTAAATGAA
1 ACTAAATGAA
2054980 AATGATGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
40 7 0.16
41 1 0.02
44 2 0.05
45 34 0.77
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (41 bp):
ACTAAATGAACAACGGTGCATTAAAGGCATGAAAGGATGCC
Found at i:2056715 original size:2 final size:2
Alignment explanation
Indices: 2056708--2056738 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2056698 ATGATGTCAA
2056708 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
2056739 GCTTTTCTGG
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:2059427 original size:17 final size:17
Alignment explanation
Indices: 2059393--2059427 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2059383 GATGCAAGTA
* *
2059393 GTATCGATACTGATAGG
1 GTATCGATACTAAAAGG
2059410 GTATCGATACTAAAAGG
1 GTATCGATACTAAAAGG
2059427 G
1 G
2059428 CAAGTATCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (17 bp):
GTATCGATACTAAAAGG
Found at i:2059996 original size:54 final size:53
Alignment explanation
Indices: 2059908--2060127 Score: 251
Period size: 54 Copynumber: 3.9 Consensus size: 53
2059898 ATGTGTATTA
**
2059908 TAGGCACTAAGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTT
1 TAGGCACTAAGTGTGCAACCCACAAAATTCATCATAAGTTGATGAACAACC-TT
* * * * *
2059962 CAGGTACTAAGTGTGCAACCCACAAAATTTATCATAAATTGATGAACAACATT
1 TAGGCACTAAGTGTGCAACCCACAAAATTCATCATAAGTTGATGAACAACCTT
2060015 TAGGCACTAAGTGTGCAACCCACGGAATTCACAGAATTCATCATAAGTTGATGAACAACCTT
1 TAGGCACTAAGTGTGCAA-CC-C---A--CA-A-AATTCATCATAAGTTGATGAACAACCTT
* * *
2060077 ATAGACACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAAC
1 -TAGGCACTAAGTGTGCAACCCACAAAATTCATCATAAGTTGATGAACAAC
2060128 TGCATAGGCA
Statistics
Matches: 141, Mismatches: 15, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
53 18 0.13
54 70 0.50
55 1 0.01
56 2 0.01
58 2 0.01
60 2 0.01
61 2 0.01
62 27 0.19
63 17 0.12
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.25
Consensus pattern (53 bp):
TAGGCACTAAGTGTGCAACCCACAAAATTCATCATAAGTTGATGAACAACCTT
Found at i:2060100 original size:63 final size:62
Alignment explanation
Indices: 2059982--2060100 Score: 184
Period size: 62 Copynumber: 1.9 Consensus size: 62
2059972 GTGTGCAACC
* *
2059982 CACAAAATTTATCATAAATTGATGAACAACATTTAGGCACTAAGTGTGCAACCCACGGAATT
1 CACAAAATTCATCATAAATTGATGAACAACATTTAGACACTAAGTGTGCAACCCACGGAATT
* * *
2060044 CACAGAATTCATCATAAGTTGATGAACAACCTTATAGACACTAAGTGTGCAACCCAC
1 CACAAAATTCATCATAAATTGATGAACAACATT-TAGACACTAAGTGTGCAACCCAC
2060101 ATAATTCATC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 29 0.57
63 22 0.43
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.24
Consensus pattern (62 bp):
CACAAAATTCATCATAAATTGATGAACAACATTTAGACACTAAGTGTGCAACCCACGGAATT
Found at i:2060147 original size:54 final size:55
Alignment explanation
Indices: 2060044--2060177 Score: 143
Period size: 54 Copynumber: 2.5 Consensus size: 55
2060034 CCACGGAATT
*
2060044 CACAGAATTCATCATAAGTTGATGAACAACCTTATAGACACTAAGTGTGC-AACC
1 CACAGAATTCATCATAAGTTGATGAACAACCTCATAGACACTAAGTGTGCGAACC
* * * *
2060098 CACATAATTCATCATATGTTGATGAACAA-CTGCATAGGCACTCTA-TGTGCGAA-C
1 CACAGAATTCATCATAAGTTGATGAACAACCT-CATAGACACT-AAGTGTGCGAACC
* *
2060152 CA-AGAAATTCATAATAAGTTTATGAA
1 CACAG-AATTCATCATAAGTTGATGAA
2060178 TTTCCGTATG
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
53 3 0.04
54 61 0.91
55 3 0.04
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (55 bp):
CACAGAATTCATCATAAGTTGATGAACAACCTCATAGACACTAAGTGTGCGAACC
Found at i:2060257 original size:56 final size:56
Alignment explanation
Indices: 2060153--2060260 Score: 164
Period size: 56 Copynumber: 1.9 Consensus size: 56
2060143 TGTGCGAACC
***
2060153 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTGTGTGTGCAAAAAAT
1 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTACATGTGCAAAAAAT
*
2060209 AAGAAATTCATAATAAGTTTATGAATTTCTGTAT-GAGCACTACATGTGCAAA
1 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGA-CACTACATGTGCAAA
2060261 CTATAGAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
55 2 0.04
56 45 0.96
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (56 bp):
AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTACATGTGCAAAAAAT
Found at i:2060370 original size:19 final size:19
Alignment explanation
Indices: 2060343--2060415 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
2060333 AATAAATTAC
*
2060343 TAAATGCATAACGGTGCAT
1 TAAAGGCATAACGGTGCAT
*
2060362 TAAAGGCATGAAAGGATGACAT
1 TAAAGGCAT-AACGG-TG-CAT
*
2060384 AAATGAAATGCATAACGGTGCAT
1 ---T-AAAGGCATAACGGTGCAT
2060407 TAAAGGCAT
1 TAAAGGCAT
2060416 GAAATAATGC
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
19 15 0.36
20 5 0.12
21 2 0.05
22 3 0.07
23 3 0.07
24 2 0.05
25 5 0.12
26 7 0.17
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (19 bp):
TAAAGGCATAACGGTGCAT
Found at i:2060432 original size:45 final size:45
Alignment explanation
Indices: 2060344--2060436 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
2060334 ATAAATTACT
*
2060344 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGACATAAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGAATGACATAAATG
* * *
2060389 AAATGCATAACGGTGCATTAAAGGCATGAAATAATGCCCTAAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGAATGACATAAATG
2060434 AAA
1 AAA
2060437 ATAATGAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (45 bp):
AAATGCATAACGGTGCATTAAAGGCATGAAAGAATGACATAAATG
Found at i:2060883 original size:20 final size:20
Alignment explanation
Indices: 2060847--2060884 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2060837 TTGTTGTATT
*
2060847 AAAATGTTTTTGGTTTTAAA
1 AAAATGTTTATGGTTTTAAA
2060867 AAAAT-TTTATGGATTTTA
1 AAAATGTTTATGG-TTTTA
2060885 CAAATAGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (20 bp):
AAAATGTTTATGGTTTTAAA
Found at i:2063811 original size:41 final size:42
Alignment explanation
Indices: 2063736--2063855 Score: 197
Period size: 41 Copynumber: 2.9 Consensus size: 42
2063726 CAATCAAATC
**
2063736 ATTAGGTGAATCATTGGAATTTCCAATATTATTATTAAAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAAAAGT
*
2063778 ATTAGGTGAATCATT-GAATTTCCAATAGGATTATTAGAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAAAAGT
*
2063819 ATTAGGTGAATCATTGGAATTTCCAATCGGATTATTA
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTA
2063856 GAAGGTTTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 38 0.52
42 35 0.48
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.38
Consensus pattern (42 bp):
ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAAAAGT
Found at i:2063852 original size:42 final size:42
Alignment explanation
Indices: 2063736--2063859 Score: 205
Period size: 42 Copynumber: 3.0 Consensus size: 42
2063726 CAATCAAATC
** *
2063736 ATTAGGTGAATCATTGGAATTTCCAATATTATTATTAAAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
2063778 ATTAGGTGAATCATT-GAATTTCCAATAGGATTATTAGAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
*
2063819 ATTAGGTGAATCATTGGAATTTCCAATCGGATTATTAGAAG
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAG
2063860 GTTTAACTGT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
41 38 0.49
42 39 0.51
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (42 bp):
ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
Found at i:2064017 original size:28 final size:28
Alignment explanation
Indices: 2063984--2064042 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
2063974 AAATATTTAA
*
2063984 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
*
2064012 AAGTAAACAATAAAACAAATATATTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
2064040 AAG
1 AAG
2064043 GAAAGATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTAGC
Found at i:2064429 original size:28 final size:28
Alignment explanation
Indices: 2064397--2064451 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2064387 ATACTAAGTT
2064397 TGCCGACTAAACATG-AAAGAAATGAGTG
1 TGCCGACTAAACATGCAAA-AAATGAGTG
2064425 TGCCGACTAAACATGCAAAAAATGAGT
1 TGCCGACTAAACATGCAAAAAATGAGT
2064452 AAGTTGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (28 bp):
TGCCGACTAAACATGCAAAAAATGAGTG
Found at i:2069147 original size:21 final size:21
Alignment explanation
Indices: 2069121--2069160 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2069111 GCATAGAATT
2069121 TGTCCCGAAAGACCACATAGA
1 TGTCCCGAAAGACCACATAGA
*
2069142 TGTCCCGAAGGACCACATA
1 TGTCCCGAAAGACCACATA
2069161 TAACACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (21 bp):
TGTCCCGAAAGACCACATAGA
Found at i:2084276 original size:5 final size:5
Alignment explanation
Indices: 2084266--2084301 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
2084256 TACTCTTAAG
2084266 AAAGA AAAGA AAAGA AAAGA AAAG- AAAG- AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
2084302 TGAGAGGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:2085747 original size:238 final size:237
Alignment explanation
Indices: 2085321--2086119 Score: 1043
Period size: 238 Copynumber: 3.4 Consensus size: 237
2085311 ATTCGACCTG
* * * * *
2085321 TTGCTTGACTCACAACACTTCGAATCAACAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTT
1 TTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTC
* * * * * * * *
2085386 GATTCTCAACGCTTCAAATCAGTAACT-CCCCACCATAGGGGTTAACATTTCCTTTGTTTGGTTC
66 GATTCACAACACTTCGAATCAGCAA-TGCCCCACCAGAGGGGTTAACATTTCCTTTGATCGATTC
* * ** * * * *
2085450 ACAACACTTCGAATTAGCAATACCCCACTAGAGAGGTTAACATTTCCTTTACTCGATTCACAACA
130 AAAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTTCTTTGCTCGATTCACAACA
*
2085515 CTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTA
195 CTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTA
* *
2085558 TTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTGACATTTCCTATTTCT
1 TTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT-TTGCT
* * **
2085623 CGATTCACAACACTTCGAATCAGCAATGCCTCACCAGAGCGGTTAACATTTCGATTGATCGATTC
65 CGATTCACAACACTTCGAATCAGCAATGCCCCACCAGAGGGGTTAACATTTCCTTTGATCGATTC
2085688 AAAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTTCTTTGCTCGATTCACAACA
130 AAAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTTCTTTGCTCGATTCACAACA
* * * * * *
2085753 CTTCAAATCAGTAGCACCCCACCAGAAGGGTTAAAATTTCCTA
195 CTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTA
* *
2085796 TTGCTCGATTCACAACACTTGGAATCAGCAACGCCCCACC-GAAGGGGTTGACATTTCCTATTGC
1 TTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAG-AGGGGTTAACATTTCCT-TTGC
* * * *
2085860 TCGATTCACAATACTTTGAATCAGCAATGCCCCACCAGAGGGGTTAACATGTCCTTTGCTCGATT
64 TCGATTCACAACACTTCGAATCAGCAATGCCCCACCAGAGGGGTTAACATTTCCTTTGATCGATT
* *
2085925 CATAAC-CTTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACA-TTTCATTTGCTTGATTCACA
129 CAAAACAC-TTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTTC-TTTGCTCGATTCACA
*
2085988 ACCCTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT-
192 ACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTA
* * * * *
2086033 TTGCTCGATTCACAACA-TTTCGAATCAGTAAAGCCCCACCAGAGGGGTAAATATTTTCTTTGCT
1 TTGCTCGATTCACAACACTTT-GAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCT
* *
2086097 CGATTCATAACGCTTCGAATCAG
65 CGATTCACAACACTTCGAATCAG
2086120 TGACATCTCA
Statistics
Matches: 491, Mismatches: 64, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
236 26 0.05
237 108 0.22
238 357 0.73
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (237 bp):
TTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTC
GATTCACAACACTTCGAATCAGCAATGCCCCACCAGAGGGGTTAACATTTCCTTTGATCGATTCA
AAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTTCTTTGCTCGATTCACAACAC
TTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTA
Found at i:2085925 original size:297 final size:294
Alignment explanation
Indices: 2085321--2086119 Score: 1091
Period size: 297 Copynumber: 2.7 Consensus size: 294
2085311 ATTCGACCTG
* * * *
2085321 TTGCTTGACTCACAACACTTCGAATCAACAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTT
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTT-CATTGCTT
* * * * * * * * *
2085386 GATTCTCAACGCTTCAAATCAGTAACTCCCCACCATAGGGGTTAACATTTCCTTTGTTTGGTTCA
65 GATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCA
* * * * *
2085451 CAACACTTCGAATTAGCAATACCCCACTAGAGAGGTTAACATTTCCTTTACTCGATTCACAACAC
130 CAACACTTCGAATCAGTAA-ACCCCACCAGAG-GGTTAAAATTTCCTTTGCTCGATTCACAACAC
*
2085516 TTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAACACTTTGA
193 TTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAACACTTTGA
* *
2085581 ATCAGCAACGCCCCACCAGAGGGGTTGACATTTCCTA
258 ATCAGCAACGCCCCACCAGAGGGGTTAACATGTCCTA
* * * * * *
2085618 TTTCTCGATTCACAACACTTCGAATCAGCAATGCCTCACCAGAGCGGTTAACATTTCGATTGATC
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTC-ATTGCTT
* *
2085683 GATTCAAAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTTCTTTGCTCGATTCA
65 GATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCA
* *
2085748 CAACACTTCAAATCAGTAGCACCCCACCAGAAGGGTTAAAATTTCCTATTGCTCGATTCACAACA
130 CAACACTTCGAATCAGTA-AACCCCACCAG-AGGGTTAAAATTTCCT-TTGCTCGATTCACAACA
* * *
2085813 CTTGGAATCAGCAACGCCCCACC-GAAGGGGTTGACATTTCCTATTGCTCGATTCACAATACTTT
192 CTTCGAATCAGCAACGCCCCACCAG-AGGGGTTAACATTTCCTATTGCTCGATTCACAACACTTT
*
2085877 GAATCAGCAATGCCCCACCAGAGGGGTTAACATGTCCT-
256 GAATCAGCAACGCCCCACCAGAGGGGTTAACATGTCCTA
*
2085915 TTGCTCGATTCATAAC-CTTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATTTGCT
1 TTGCTCGATTCACAACAC-TTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCA-TTGCT
*
2085979 TGATTCACAACCCTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTC
64 TGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTC
* * * * *
2086044 ACAACATTTCGAATCAGTAAAGCCCCACCAGAGGGGTAAATATTTTCTTTGCTCGATTCATAACG
129 ACAACACTTCGAATCAGTAAA-CCCCACCAGAGGGTTAAA-ATTTCCTTTGCTCGATTCACAACA
2086109 CTTCGAATCAG
192 CTTCGAATCAG
2086120 TGACATCTCA
Statistics
Matches: 441, Mismatches: 52, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
296 37 0.08
297 292 0.66
298 112 0.25
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (294 bp):
TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATTGCTTG
ATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCAC
AACACTTCGAATCAGTAAACCCCACCAGAGGGTTAAAATTTCCTTTGCTCGATTCACAACACTTC
GAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAACACTTTGAATC
AGCAACGCCCCACCAGAGGGGTTAACATGTCCTA
Found at i:2086120 original size:59 final size:59
Alignment explanation
Indices: 2085321--2086119 Score: 1035
Period size: 59 Copynumber: 13.5 Consensus size: 59
2085311 ATTCGACCTG
* * *
2085321 TTGCTTGACTCACAACACTTCGAATCAACAACGCCCCACCAGAGGGGTTAACATTTCCT
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* * * * * * *
2085380 TTGCTTGATTCTCAACGCTTCAAATCAGTAACTCCCCACCATAGGGGTTAACATTTCCT
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* * * * ** * *
2085439 TTGTTTGGTTCACAACACTTCGAATTAGCAATACCCCACTAGAGAGGTTAACATTTCCT
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* *
2085498 TTACTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* *
2085557 ATTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTGACATTTCCT
1 -TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* * * * **
2085617 ATTTCTCGATTCACAACACTTCGAATCAGCAATGCCTCACCAGAGCGGTTAACATTTCGA
1 -TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* * *
2085677 TTGATCGATTCAAAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTTCT
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* * * * * *
2085736 TTGCTCGATTCACAACACTTCAAATCAGTAGCACCCCACCAGAAGGGTTAAAATTTCCT
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* *
2085795 ATTGCTCGATTCACAACACTTGGAATCAGCAACGCCCCACC-GAAGGGGTTGACATTTCCT
1 -TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAG-AGGGGTTAACATTTCCT
* * * *
2085855 ATTGCTCGATTCACAATACTTTGAATCAGCAATGCCCCACCAGAGGGGTTAACATGTCCT
1 -TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* *
2085915 TTGCTCGATTCATAAC-CTTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCAT
1 TTGCTCGATTCACAACAC-TTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* *
2085974 TTGCTTGATTCACAACCCTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* * * * * *
2086033 TTGCTCGATTCACAACATTTCGAATCAGTAAAGCCCCACCAGAGGGGTAAATATTTTCT
1 TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
* *
2086092 TTGCTCGATTCATAACGCTTCGAATCAG
1 TTGCTCGATTCACAACACTTCGAATCAG
2086120 TGACATCTCA
Statistics
Matches: 643, Mismatches: 91, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
58 1 0.00
59 429 0.67
60 212 0.33
61 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (59 bp):
TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT
Found at i:2086949 original size:36 final size:36
Alignment explanation
Indices: 2086870--2087008 Score: 174
Period size: 36 Copynumber: 3.9 Consensus size: 36
2086860 ATGAACAATC
** *
2086870 GAATCGAAAGTGTTGACGCTTCCTTCCGTTC-ACTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCTACTT
* *
2086905 GAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTCTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCTACTT
*
2086941 GAATCGAAAGTGCCGATGCTTCCTTCCG-TCCACTTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCTAC-TT
** *
2086977 GAATCGAAAGTGCTAATGCTTCCTTTCGTTCT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCT
2087009 TCTTATTCAC
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
35 30 0.34
36 57 0.64
37 2 0.02
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.35
Consensus pattern (36 bp):
GAATCGAAAGTGCCGATGCTTCCTTCCGTTCTACTT
Found at i:2086962 original size:71 final size:72
Alignment explanation
Indices: 2086870--2087012 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 72
2086860 ATGAACAATC
** * *
2086870 GAATCGAAAGTGTTGACGCTTCCTTCCGTTCAC-TTGAATCGAAAGTGCCGATGCTTCCTTTCGT
1 GAATCGAAAGTGCCGACGCTTCCTTCCGTCCACTTTGAATCGAAAGTGCCAATGCTTCCTTTCGT
2086934 TCTTCTT
66 TCTTCTT
* *
2086941 GAATCGAAAGTGCCGATGCTTCCTTCCGTCCACTTTGAATCGAAAGTGCTAATGCTTCCTTTCGT
1 GAATCGAAAGTGCCGACGCTTCCTTCCGTCCACTTTGAATCGAAAGTGCCAATGCTTCCTTTCGT
2087006 TCTTCTT
66 TCTTCTT
2087013 ATTCACCTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 29 0.45
72 36 0.55
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (72 bp):
GAATCGAAAGTGCCGACGCTTCCTTCCGTCCACTTTGAATCGAAAGTGCCAATGCTTCCTTTCGT
TCTTCTT
Found at i:2096860 original size:26 final size:26
Alignment explanation
Indices: 2096824--2096895 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 26
2096814 AAGTGTCCAA
* *
2096824 TCTATGTTTATTTTTTTAGTTTAGTG
1 TCTAAGTTTATTTTTATAGTTTAGTG
2096850 TCTAAGTTTATTTCGTTATAGTTTAGTG
1 TCTAAGTTTATTT--TTATAGTTTAGTG
*
2096878 CCTAACGTTTTATTTTTA
1 TCTAA-G-TTTATTTTTA
2096896 CTCAAAATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 12 0.31
28 19 0.49
29 1 0.03
30 7 0.18
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.58
Consensus pattern (26 bp):
TCTAAGTTTATTTTTATAGTTTAGTG
Found at i:2098030 original size:2 final size:2
Alignment explanation
Indices: 2098023--2098055 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2098013 AATTATCTTT
2098023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2098056 TAAGCTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2099582 original size:24 final size:20
Alignment explanation
Indices: 2099533--2099577 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
2099523 TCAATCTCAT
2099533 TTTTGAGCTCTAAACCTTCC
1 TTTTGAGCTCTAAACCTTCC
2099553 TTTTGAGCTCTAAACCTTCC
1 TTTTGAGCTCTAAACCTTCC
2099573 TTTTG
1 TTTTG
2099578 GTTGAAACGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.44
Consensus pattern (20 bp):
TTTTGAGCTCTAAACCTTCC
Found at i:2103829 original size:29 final size:29
Alignment explanation
Indices: 2103797--2103855 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
2103787 ATTACCTATA
2103797 TAATTATTCAATAAATT-AAAA-TATTTTTT
1 TAATTATT-AA-AAATTAAAAATTATTTTTT
*
2103826 TAATTATTAAAATTTAAAAATTATTTTTT
1 TAATTATTAAAAATTAAAAATTATTTTTT
2103855 T
1 T
2103856 TTAAAAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 6 0.22
29 17 0.63
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
TAATTATTAAAAATTAAAAATTATTTTTT
Found at i:2103852 original size:26 final size:29
Alignment explanation
Indices: 2103797--2103852 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
2103787 ATTACCTATA
*
2103797 TAATTATTCAATAAATTAAAATATTTTTT
1 TAATTATTCAATAAATTAAAATATTATTT
*
2103826 TAATTATT-AA-AATTTAAAA-ATTATTT
1 TAATTATTCAATAAATTAAAATATTATTT
2103852 T
1 T
2103853 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 8 0.32
28 2 0.08
29 8 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATTATTCAATAAATTAAAATATTATTT
Found at i:2104704 original size:2 final size:2
Alignment explanation
Indices: 2104697--2104721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2104687 ACATAAACGG
2104697 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 A
2104722 GTTTACTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2105603 original size:40 final size:40
Alignment explanation
Indices: 2105556--2105651 Score: 192
Period size: 40 Copynumber: 2.4 Consensus size: 40
2105546 ACGCGAAATA
2105556 AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC
1 AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC
2105596 AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC
1 AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC
2105636 AAAATCGCAACGCGAT
1 AAAATCGCAACGCGAT
2105652 TCTTGAAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.36, C:0.31, G:0.16, T:0.17
Consensus pattern (40 bp):
AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC
Found at i:2105662 original size:21 final size:20
Alignment explanation
Indices: 2105536--2105733 Score: 87
Period size: 20 Copynumber: 9.8 Consensus size: 20
2105526 AAATGACCAA
**
2105536 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2105555 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2105575 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
***
2105595 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2105615 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2105635 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2105656 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2105677 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2105697 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2105718 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2105734 ACACATAAAT
Statistics
Matches: 132, Mismatches: 39, Indels: 15
0.71 0.21 0.08
Matches are distributed among these distances:
19 17 0.13
20 67 0.51
21 48 0.36
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2105762 original size:20 final size:20
Alignment explanation
Indices: 2105700--2105969 Score: 269
Period size: 20 Copynumber: 13.5 Consensus size: 20
2105690 CGATTTTCCA
* ** *
2105700 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2105720 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2105740 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2105760 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2105780 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2105800 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2105820 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2105840 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2105860 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2105880 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2105900 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2105920 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2105940 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2105960 AAATCACAAC
1 AAATCGCAAC
2105970 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 206 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2106690 original size:24 final size:24
Alignment explanation
Indices: 2106651--2106697 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2106641 AAATTTGGTC
2106651 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2106675 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2106698 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2109206 original size:19 final size:19
Alignment explanation
Indices: 2109184--2109445 Score: 305
Period size: 19 Copynumber: 14.7 Consensus size: 19
2109174 TCGCAACGAG
2109184 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
*
2109203 AAATCCCAA--C--AA-GA
1 AAATCGCAATGCGAAATGA
2109217 AAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGA
2109237 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
2109256 AAATCGCAATGCGAAATG-
1 AAATCGCAATGCGAAATGA
2109274 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
2109288 GAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGA
2109308 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
2109327 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
2109341 GAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
2109360 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
2109379 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
2109393 GAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGA
2109413 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
*
2109432 AAATCGCATTGCGA
1 AAATCGCAATGCGA
2109446 TTCTCTCGTT
Statistics
Matches: 210, Mismatches: 9, Indels: 48
0.79 0.03 0.18
Matches are distributed among these distances:
13 1 0.00
14 39 0.19
15 4 0.02
16 7 0.03
17 7 0.03
18 10 0.05
19 102 0.49
20 40 0.19
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:2109433 original size:53 final size:52
Alignment explanation
Indices: 2109172--2109439 Score: 397
Period size: 53 Copynumber: 5.1 Consensus size: 52
2109162 CGGAAATTAC
*
2109172 AATCGCAACGAGA-AATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2109218 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-A
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2109275 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
2109328 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2109380 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
2109433 AATCGCA
1 AATCGCA
2109440 TTGCGATTCT
Statistics
Matches: 205, Mismatches: 2, Indels: 23
0.89 0.01 0.10
Matches are distributed among these distances:
46 8 0.04
48 1 0.00
49 1 0.00
51 14 0.07
52 80 0.39
53 86 0.42
54 1 0.00
55 2 0.01
57 11 0.05
58 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2109479 original size:53 final size:52
Alignment explanation
Indices: 2109416--2109531 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
2109406 GAAATGAAAA
*
2109416 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
2109468 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
2109521 TCGCATTGCGA
1 TCGCATTGCGA
2109532 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2109494 original size:19 final size:19
Alignment explanation
Indices: 2109454--2109541 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
2109444 GATTCTCTCG
2109454 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2109474 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2109493 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2109507 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2109526 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2109542 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2109651 original size:14 final size:14
Alignment explanation
Indices: 2109632--2109668 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2109622 CATCAATTAC
2109632 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2109646 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2109660 ACAAATCAA
1 ACAAATCAA
2109669 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2111656 original size:14 final size:14
Alignment explanation
Indices: 2111637--2111693 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2111627 GCGAAATGAA
*
2111637 AATCGCAACGACAG
1 AATCGCAACGAAAG
2111651 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2111668 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2111684 AATCGCAACG
1 AATCGCAACG
2111694 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2111664 original size:33 final size:33
Alignment explanation
Indices: 2111618--2111710 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2111608 GCGAAACCAA
*
2111618 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2111651 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2111684 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2111711 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2111675 original size:19 final size:19
Alignment explanation
Indices: 2111581--2111715 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2111571 TAGTTTACTT
* *
2111581 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2111601 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2111620 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2111639 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2111653 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2111672 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2111686 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2111705 TCGCAATGCGA
1 TCGCAACGCGA
2111716 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2111733 original size:19 final size:19
Alignment explanation
Indices: 2111711--2111838 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
2111701 AAAATCGCAA
2111711 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2111730 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2111744 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2111762 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2111776 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2111795 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2111814 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2111834 TGCGA
1 TGCGA
2111839 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 2 0.02
14 20 0.23
16 3 0.03
17 1 0.01
18 10 0.11
19 39 0.44
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2111796 original size:33 final size:34
Alignment explanation
Indices: 2111711--2111801 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 34
2111701 AAAATCGCAA
2111711 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
2111744 TGCGA-TTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
2111776 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2111802 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:2112002 original size:93 final size:93
Alignment explanation
Indices: 2111886--2112168 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
2111876 ATGGATTGCA
2111886 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2111950 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2111978 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2112043 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2112071 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2112136 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2112164 TTACT
1 TTACT
2112169 AAGCAATCTA
Statistics
Matches: 189, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 4 0.02
93 185 0.98
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2113914 original size:19 final size:19
Alignment explanation
Indices: 2113864--2113987 Score: 99
Period size: 19 Copynumber: 7.1 Consensus size: 19
2113854 TCTTTTGGTT
*
2113864 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
***
2113883 G-AATGACTGTCGCAACGC
1 GAAATGAAAATCGCAACGC
2113901 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
2113918 --TA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2113934 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2113951 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2113967 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2113986 GA
1 GA
2113988 TTTTTGGTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
14 20 0.25
15 2 0.03
16 3 0.04
17 3 0.04
18 16 0.20
19 36 0.45
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2113934 original size:33 final size:33
Alignment explanation
Indices: 2113864--2113982 Score: 184
Period size: 33 Copynumber: 3.5 Consensus size: 33
2113854 TCTTTTGGTT
*
2113864 GAAATGAAAATCGCAACGAGAATGACTGTCGCAACGC
1 GAAATGAAAATCGCAACGAG-A-GA--ATCGCAACGC
*
2113901 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2113934 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2113967 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2113983 TGCGATTTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
33 57 0.72
35 2 0.03
36 1 0.01
37 19 0.24
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2113961 original size:14 final size:14
Alignment explanation
Indices: 2113909--2113965 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2113899 GCGAAATGAA
*
2113909 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
2113923 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2113942 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2113956 AATCGCAACG
1 AATCGCAACG
2113966 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2114036 original size:33 final size:33
Alignment explanation
Indices: 2113995--2114100 Score: 149
Period size: 33 Copynumber: 3.1 Consensus size: 33
2113985 CGATTTTTGG
2113995 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
* *
2114028 TTTCGCGTTGCAATTCTCTAGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
2114061 TTTCGCGTTGCGACAGTCATTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCG--ATTC--TCTCGTTGCGATTTTCA
2114098 TTT
1 TTT
2114101 ATCTCGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
33 42 0.66
35 3 0.05
37 19 0.30
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:2114038 original size:19 final size:19
Alignment explanation
Indices: 2114014--2114100 Score: 69
Period size: 19 Copynumber: 4.9 Consensus size: 19
2114004 GCGATTCTCT
2114014 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
2114033 CGTTGC-A-ATTC---TCT
1 CGTTGCGATTTTCATTTCG
*
2114047 AGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
2114066 CGTTGCGACAGTCA-TTCT
1 CGTTGCGATTTTCATTTCG
2114084 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
2114101 ATCTCGTTGC
Statistics
Matches: 49, Mismatches: 13, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
14 7 0.14
15 1 0.02
16 3 0.06
17 3 0.06
18 15 0.31
19 20 0.41
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2114258 original size:33 final size:33
Alignment explanation
Indices: 2114192--2114262 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
2114182 AATACTAACT
* * *
2114192 TGAAAATCGCAACGAGAGAATAGCATCGTGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2114225 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2114258 TGAAA
1 TGAAA
2114263 TCTAAGTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2114495 original size:22 final size:22
Alignment explanation
Indices: 2114443--2114497 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2114433 TGGTTGTGAG
**
2114443 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2114465 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2114487 GGATTTCTTCG
1 GGATTTCTTCG
2114498 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2114669 original size:20 final size:20
Alignment explanation
Indices: 2114644--2114758 Score: 160
Period size: 20 Copynumber: 5.7 Consensus size: 20
2114634 CTTTAAATAT
2114644 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2114664 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2114686 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2114705 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
2114725 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
2114745 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
2114759 TGTGTTCACG
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2114742 original size:40 final size:40
Alignment explanation
Indices: 2114646--2114801 Score: 183
Period size: 40 Copynumber: 3.9 Consensus size: 40
2114636 TTAAATATCG
* *
2114646 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTA-T
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGGA-TACA
* *
2114687 CGTTGCGATTTACGGATACGCGTTGCGATATACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGGATACA
*
2114727 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATG-GATACA
* ** *
2114767 CGTTGCGATTTTCATATTCGCGTTGCGATTT-TGGA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGGA
2114802 AAATCGCAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 67 0.66
41 29 0.29
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGGATACA
Found at i:2114770 original size:20 final size:20
Alignment explanation
Indices: 2114646--2114777 Score: 142
Period size: 20 Copynumber: 6.5 Consensus size: 20
2114636 TTAAATATCG
*
2114646 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
* * *
2114666 CGTTGCGATTTTATGTATTA-T
1 CGTTGCGA-TTTACGGA-TACA
*
2114687 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
*
2114707 CGTTGCGATATACGGATACA
1 CGTTGCGATTTACGGATACA
*
2114727 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
* *
2114747 CGTTGCGATTTATGTG-TTCA
1 CGTTGCGATTTACG-GATACA
2114767 CGTTGCGATTT
1 CGTTGCGATTT
2114778 TCATATTCGC
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.02
20 76 0.80
21 15 0.16
22 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACA
Found at i:2114790 original size:20 final size:19
Alignment explanation
Indices: 2114745--2114798 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2114735 TTTACGGATA
* *
2114745 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TATATT
*
2114765 CACGTTGCGATTTTCATATT
1 CGCGTTGCGATTTT-ATATT
2114785 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
2114799 GGAAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (19 bp):
CGCGTTGCGATTTTATATT
Found at i:2114814 original size:21 final size:21
Alignment explanation
Indices: 2114784--2114865 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
2114774 ATTTTCATAT
*
2114784 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2114805 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2114826 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2114847 TCGCGTTGCGA-TTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2114866 CTGATTTGCG
Statistics
Matches: 46, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
20 5 0.11
21 41 0.89
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2117404 original size:21 final size:22
Alignment explanation
Indices: 2117390--2117434 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 22
2117380 AAATGTGTCA
2117390 AAAGACAAATGAAATATATCAT
1 AAAGACAAATGAAATATATCAT
2117412 AAAGAC-AA--AAA-ATATCAT
1 AAAGACAAATGAAATATATCAT
2117430 AAAGA
1 AAAGA
2117435 TGAGTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.52
19 3 0.13
21 2 0.09
22 6 0.26
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (22 bp):
AAAGACAAATGAAATATATCAT
Found at i:2117483 original size:27 final size:28
Alignment explanation
Indices: 2117453--2117516 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 28
2117443 AACGTATCAT
*
2117453 AAATATAAAATTAT-TAA-AAAATTTAAA
1 AAATATAAAATAATATAATAAAA-TTAAA
2117480 AAATA-AAAATAATATAATAAAATTAAA
1 AAATATAAAATAATATAATAAAATTAAA
2117507 AAATAATAAA
1 AAAT-ATAAA
2117517 TACCAAGGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.22
27 17 0.53
28 5 0.16
29 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (28 bp):
AAATATAAAATAATATAATAAAATTAAA
Found at i:2117501 original size:20 final size:20
Alignment explanation
Indices: 2117478--2117518 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2117468 AAAAAATTTA
2117478 AAAAAT-AAAAATAATATAAT
1 AAAAATAAAAAATAATA-AAT
*
2117498 AAAATTAAAAAATAATAAAT
1 AAAAATAAAAAATAATAAAT
2117518 A
1 A
2117519 CCAAGGACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATAAAAAATAATAAAT
Found at i:2118161 original size:23 final size:24
Alignment explanation
Indices: 2118134--2118186 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
2118124 TAATATATAT
* *
2118134 ATACCCG-CCCGATTCCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
*
2118157 ATA-CCGACCCAATACCCGGCCTA
1 ATACCCGACCCAATACCCGGCCCA
2118180 ATACCCG
1 ATACCCG
2118187 TTTAAATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 3 0.12
23 19 0.76
24 3 0.12
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:2118184 original size:12 final size:12
Alignment explanation
Indices: 2118134--2118186 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
2118124 TAATATATAT
*
2118134 ATACCC-GCCCG
1 ATACCCGGCCCA
*
2118145 ATTCCCGGCCCA
1 ATACCCGGCCCA
*
2118157 ATA-CCGACCCA
1 ATACCCGGCCCA
*
2118168 ATACCCGGCCTA
1 ATACCCGGCCCA
2118180 ATACCCG
1 ATACCCG
2118187 TTTAAATAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 15 0.44
12 19 0.56
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:2129751 original size:22 final size:21
Alignment explanation
Indices: 2129725--2129786 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
2129715 ACTCCATCAG
2129725 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* * *
2129746 TGAAGTCCTTCGGGCCATCA--A
1 T-AAGTCTTTCGAG-CATGATGA
2129767 TAAGTCTTTCGAGCATGATG
1 TAAGTCTTTCGAGCATGATG
2129787 CTTAAATCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
19 4 0.13
20 10 0.32
21 3 0.10
22 10 0.32
23 4 0.13
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGA
Found at i:2129765 original size:42 final size:42
Alignment explanation
Indices: 2129718--2130128 Score: 316
Period size: 42 Copynumber: 10.0 Consensus size: 42
2129708 TGAAGCAACT
*
2129718 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * * *
2129760 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * * * *
2129802 TCATCAGTAAGTCTTTAGAGCATGATGATTAAATTCTTAGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
** * * * * * ***
2129844 TAATTTA-TAAG-CCTTC-ACCGAAGA-GTAGTG-AAGCAAAC---
1 CCA-TCAGTAAGTCTTTCGAGC-ATGATG-A-TGAAATCCTTCGGG
* * *
2129882 CCGTAAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGTG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
2129924 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* *
2129966 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
** ** * * *
2130008 TAATTTGTAAGCCTTTACCGAAG-A-GTAGTGAAGCAA--C-T----
1 CCATCAGTAAGTCTTT--CG-AGCATG-A-TGATGAAATCCTTCGGG
2130046 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* *
2130088 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCGTTCGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
2130129 TAATTTGTAA
Statistics
Matches: 286, Mismatches: 57, Indels: 52
0.72 0.14 0.13
Matches are distributed among these distances:
35 8 0.03
36 4 0.01
37 4 0.01
38 18 0.06
39 12 0.04
40 6 0.02
41 9 0.03
42 211 0.74
43 4 0.01
44 3 0.01
45 7 0.02
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (42 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
Found at i:2129921 original size:22 final size:21
Alignment explanation
Indices: 2129896--2130005 Score: 66
Period size: 22 Copynumber: 5.2 Consensus size: 21
2129886 AAGTAAGTCT
2129896 TTCGAGCATGATGATGAAATCC
1 TTCGAGCATGATGAT-AAATCC
* * * *
2129918 TTCGTGCCATCA-G-TAAGTCT
1 TTCGAG-CATGATGATAAATCC
2129938 TTCGAGCATGATGATGAAATCC
1 TTCGAGCATGATGAT-AAATCC
* * * *
2129960 TTCGGGCCATCA-G-TAAGTCT
1 TTCGAG-CATGATGATAAATCC
*
2129980 TTCAAGCATGATGATTAAATCC
1 TTCGAGCATGATGA-TAAATCC
2130002 TTCG
1 TTCG
2130006 GGTAATTTGT
Statistics
Matches: 62, Mismatches: 18, Indels: 16
0.65 0.19 0.17
Matches are distributed among these distances:
19 8 0.13
20 19 0.31
21 3 0.05
22 24 0.39
23 8 0.13
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (21 bp):
TTCGAGCATGATGATAAATCC
Found at i:2129948 original size:164 final size:164
Alignment explanation
Indices: 2129666--2130122 Score: 756
Period size: 164 Copynumber: 2.8 Consensus size: 164
2129656 AGTAATCAAT
*
2129666 TTAAATCCTTCGGGTAATTTTTAAGCCTTCACCGAAGAGTAGTGAAGCAACTCCATCAGTAAGTC
1 TTAAATCCTTCGGGTAATTTATAAGCCTTCACCGAAGAGTAGTGAAGCAACTCCATCAGTAAGTC
* * *
2129731 TTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCC
66 TTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCC
*
2129796 TTAGGGTCATCAGTAAGTCTTT-AGAGCATGATGA
131 TTAGGGCCATCAGTAAGTCTTTCA-AGCATGATGA
* * * *
2129830 TTAAATTCTTAGGGTAATTTATAAGCCTTCACCGAAGAGTAGTGAAGCAAAC-CCGTAAGTAAGT
1 TTAAATCCTTCGGGTAATTTATAAGCCTTCACCGAAGAGTAGTGAAGC-AACTCCATCAGTAAGT
* *
2129894 CTTTCGAGCATGATGATGAAATCCTTCGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAATC
65 CTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATC
*
2129959 CTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGA
130 CTTAGGGCCATCAGTAAGTCTTTCAAGCATGATGA
* *
2129994 TTAAATCCTTCGGGTAATTTGTAAGCCTTTACCGAAGAGTAGTGAAGCAACTCCATCAGTAAGTC
1 TTAAATCCTTCGGGTAATTTATAAGCCTTCACCGAAGAGTAGTGAAGCAACTCCATCAGTAAGTC
2130059 TTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATC
66 TTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATC
2130123 GTTCGGTAAT
Statistics
Matches: 270, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
163 3 0.01
164 263 0.97
165 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (164 bp):
TTAAATCCTTCGGGTAATTTATAAGCCTTCACCGAAGAGTAGTGAAGCAACTCCATCAGTAAGTC
TTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCC
TTAGGGCCATCAGTAAGTCTTTCAAGCATGATGA
Found at i:2130051 original size:122 final size:121
Alignment explanation
Indices: 2129924--2130208 Score: 500
Period size: 122 Copynumber: 2.3 Consensus size: 121
2129914 ATCCTTCGTG
2129924 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCAT
*
2129989 GATGATTAAATCCTTCGGGTAATTTGTAAGCCTTTACCGAAGAGTAGTGAAGC-AAC
66 GATGATTAAATCCTTC-GGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAAC
*
2130045 TCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
1 -CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCA
*
2130110 TGATGATTAAATCGTTCGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAAC
65 TGATGATTAAATCCTTCGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAAC
* *
2130167 CCGTCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
2130209 TAATTTGTAA
Statistics
Matches: 157, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
121 75 0.48
122 82 0.52
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (121 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCAT
GATGATTAAATCCTTCGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAAC
Found at i:2130085 original size:22 final size:21
Alignment explanation
Indices: 2130060--2130127 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
2130050 CAGTAAGTCT
2130060 TTCGAGCATGATGATGAAATCC
1 TTCGAGCATGATGAT-AAATCC
* * * *
2130082 TTCGGGCCATCA-G-TAAGTCT
1 TTCGAG-CATGATGATAAATCC
*
2130102 TTCGAGCATGATGATTAAATCG
1 TTCGAGCATGATGA-TAAATCC
2130124 TTCG
1 TTCG
2130128 GTAATTTGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 4 0.12
20 10 0.29
21 1 0.03
22 15 0.44
23 4 0.12
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGAGCATGATGATAAATCC
Found at i:2130244 original size:80 final size:79
Alignment explanation
Indices: 2130088--2130258 Score: 290
Period size: 80 Copynumber: 2.2 Consensus size: 79
2130078 ATCCTTCGGG
*
2130088 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCGTTCGGTAATTTGTAAGCCTTCACCGAAGA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGTAATTTGTAAGCCTTCACCGAAGA
2130153 GTAGTGAAGCAAAC-
66 GTAGTGAAGC-AACT
* *
2130167 CCGTCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCTTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC-GGTAATTTGTAAGCCTTCACCGAAG
2130232 AGTAGTGAAGCAACT
65 AGTAGTGAAGCAACT
2130247 CCATCAGTAAGT
1 CCATCAGTAAGT
2130259 GCCATCAGTA
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
79 40 0.47
80 46 0.53
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (79 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGTAATTTGTAAGCCTTCACCGAAGA
GTAGTGAAGCAACT
Found at i:2130265 original size:13 final size:13
Alignment explanation
Indices: 2130247--2130271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2130237 TGAAGCAACT
2130247 CCATCAGTAAGTG
1 CCATCAGTAAGTG
2130260 CCATCAGTAAGT
1 CCATCAGTAAGT
2130272 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:2130318 original size:42 final size:42
Alignment explanation
Indices: 2130259--2130343 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
2130249 ATCAGTAAGT
*
2130259 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCCTCGG
*
2130301 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCCTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCCTCGG
2130343 G
1 G
2130344 TAATTTGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCCTCGG
Found at i:2130431 original size:215 final size:215
Alignment explanation
Indices: 2130046--2130569 Score: 860
Period size: 215 Copynumber: 2.4 Consensus size: 215
2130036 TGAAGCAACT
2130046 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * *
2130111 GATGATTAAATCGTTC-GGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACCCGTCAGT
66 GATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCCATCAGT
* * *
2130175 AAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCTTTCACCGAAGAGTAGTGA
131 AAGTCTTTAGAGCATGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGA
2130240 AGC-AACTCCATCAGTAAGTG
196 AGCAAAC-CCATCAGTAAGTG
2130260 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
*
2130325 GATGATTAAATCCCTCGGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGC-AACTCCATCAG
66 GATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAAC-CCATCAG
*
2130389 TAAGTCTTTAGAGCATGATGATTAAAAT-CTTAGGGTAATTTGTAAGCCTTCACGGAAGAGTAGT
130 TAAGTCTTTAGAGCATGATGATT-AAATCCTTAGGGTAATTTGTAAGCCTTCACCGAAGAGTAGT
*
2130453 GAAGCAAACCCATTAGTAAGTG
194 GAAGCAAACCCATCAGTAAGTG
* *
2130475 CCATCAGTAAGTCTTTC-AGGCATGATGATGAAATCCTTCGAGCCATCAGTAAGTCTTTCAAGCA
1 CCATCAGTAAGTCTTTCGA-GCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* *
2130539 TGATGATGAAATCCTTCGGGTCATTTGTAAG
65 TGATGATTAAATCCTTCGGGTAATTTGTAAG
2130570 TCTTTCGAGC
Statistics
Matches: 291, Mismatches: 14, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
214 83 0.29
215 201 0.69
216 7 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (215 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCCATCAGT
AAGTCTTTAGAGCATGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGA
AGCAAACCCATCAGTAAGTG
Found at i:2130435 original size:80 final size:80
Alignment explanation
Indices: 2130302--2130473 Score: 258
Period size: 80 Copynumber: 2.1 Consensus size: 80
2130292 ATCCTTCGGG
* *
2130302 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCCTCGGGTAATTTGTAAGCCTTCACCAAAG
1 CCATCAGTAAGTCTTTAGAGCATGATGATTAAATCCCTAGGGTAATTTGTAAGCCTTCACCAAAG
2130367 AGTAGTGAAGC-AAC
66 AGTAGTGAAGCAAAC
* **
2130381 TCCATCAGTAAGTCTTTAGAGCATGATGATTAAAAT-CTTAGGGTAATTTGTAAGCCTTCACGGA
1 -CCATCAGTAAGTCTTTAGAGCATGATGATT-AAATCCCTAGGGTAATTTGTAAGCCTTCACCAA
2130445 AGAGTAGTGAAGCAAAC
64 AGAGTAGTGAAGCAAAC
*
2130462 CCATTAGTAAGT
1 CCATCAGTAAGT
2130474 GCCATCAGTA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
80 77 0.92
81 7 0.08
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTAGAGCATGATGATTAAATCCCTAGGGTAATTTGTAAGCCTTCACCAAAG
AGTAGTGAAGCAAAC
Found at i:2130533 original size:42 final size:42
Alignment explanation
Indices: 2130474--2130575 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
2130464 ATTAGTAAGT
*
2130474 GCCATCAGTAAGTCTTTCAGGCATGATGATGAAATCCTTCGA
1 GCCATCAGTAAGTCTTTCAAGCATGATGATGAAATCCTTCGA
*
2130516 GCCATCAGTAAGTCTTTCAAGCATGATGATGAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCAAGCATGATGATGAAATCCTTCGA
* **
2130558 GTCATTTGTAAGTCTTTC
1 GCCATCAGTAAGTCTTTC
2130576 GAGCGAGATG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCAAGCATGATGATGAAATCCTTCGA
Found at i:2130586 original size:42 final size:42
Alignment explanation
Indices: 2130474--2130587 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 42
2130464 ATTAGTAAGT
2130474 GCCATCAGTAAGTCTTTCAG-GCATGATGATGAAATCCTTCGA
1 GCCATCAGTAAGTCTTTCAGCG-ATGATGATGAAATCCTTCGA
*
2130516 GCCATCAGTAAGTCTTTCAAGC-ATGATGATGAAATCCTTCGG
1 GCCATCAGTAAGTCTTTC-AGCGATGATGATGAAATCCTTCGA
* **
2130558 GTCATTTGTAAGTCTTTCGAGCGA-GATGAT
1 GCCATCAGTAAGTCTTTC-AGCGATGATGAT
2130588 AAGTCTTCTG
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
42 61 0.95
43 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCAGCGATGATGATGAAATCCTTCGA
Found at i:2131287 original size:53 final size:53
Alignment explanation
Indices: 2130980--2131286 Score: 412
Period size: 53 Copynumber: 5.9 Consensus size: 53
2130970 AGAATCACAC
* * *
2130980 CAGAAGATTGTTCAAGTTTTACTCCCTGAAGCAAGAGGGAG-G-A-CTGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
2131030 CAGAAGATTGTTTGAGTTTTACTCCCTGAAGTAAGAGGGAG-G-A-CTGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
2131080 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
2131133 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCTTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * * *
2131186 AAGAAGATAT-TTTGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCATAAG
1 CAGAAGAT-TGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* *
2131239 CAGAAGATTGTTCGAGTTCTATTCCTTGAAGCAAGAGGGAGCGAACCC
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
2131287 ACTGGTTGAA
Statistics
Matches: 234, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
50 85 0.36
51 1 0.00
52 2 0.01
53 145 0.62
54 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.23
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:2145029 original size:38 final size:38
Alignment explanation
Indices: 2144967--2145047 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
2144957 TAACGAAGTT
* * *
2144967 ATAATCCTAGCCCTGGTTTTAAACCCTAAAGATAACTA
1 ATAATCCTAGCCCTAGATTGAAACCCTAAAGATAACTA
* *
2145005 ATAATCCTAGTCCTAGATTGAAACCCTAAAGATATCTA
1 ATAATCCTAGCCCTAGATTGAAACCCTAAAGATAACTA
*
2145043 GTAAT
1 ATAAT
2145048 GTTAGCCGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (38 bp):
ATAATCCTAGCCCTAGATTGAAACCCTAAAGATAACTA
Done.